From 17a5371205e2ec1d212b60e029a34d066d3fb3a3 Mon Sep 17 00:00:00 2001
From: annakrystalli <annakrystalli@googlemail.com>
Date: Fri, 29 Sep 2023 07:23:34 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20Infectio?=
 =?UTF-8?q?us-Disease-Modeling-Hubs/hubValidations@4e0be464c4011356b863cf9?=
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MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 pkgdown.yml                             | 2 +-
 reference/validate_submission.html      | 2 +-
 reference/validate_submission_time.html | 2 +-
 search.json                             | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgdown.yml b/pkgdown.yml
index 53d37173..3dbb2115 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   custom-functions: custom-functions.html
-last_built: 2023-09-28T15:36Z
+last_built: 2023-09-29T07:23Z
 urls:
   reference: https://infectious-disease-modeling-hubs.github.io/hubValidations/reference
   article: https://infectious-disease-modeling-hubs.github.io/hubValidations/articles
diff --git a/reference/validate_submission.html b/reference/validate_submission.html
index 3fc3cb6d..51ecbb8b 100644
--- a/reference/validate_submission.html
+++ b/reference/validate_submission.html
@@ -132,7 +132,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">hub_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testhubs/simple"</span>, package <span class="op">=</span> <span class="st">"hubValidations"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">file_path</span> <span class="op">&lt;-</span> <span class="st">"team1-goodmodel/2022-10-08-team1-goodmodel.csv"</span></span></span>
 <span class="r-in"><span><span class="fu">validate_submission</span><span class="op">(</span><span class="va">hub_path</span>, <span class="va">file_path</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ::notice ::✔ simple: All hub config files are valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  <span style="color: #0000BB;">model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv</span>.%0A✔ 2022-10-08-team1-goodmodel.csv: File name <span style="color: #0000BB;">"2022-10-08-team1-goodmodel.csv"</span> is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  <span style="color: #0000BB;">model-metadata/team1-goodmodel.yaml</span>.%0A✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column <span style="color: #0000BB;">"origin_date"</span> contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` <span style="color: #0000BB;">"origin_date"</span> values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped.%0A! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time <span style="color: #0000BB;">2023-09-28 15:36:46.668269</span> is%0A  outside window <span style="color: #0000BB;">2022-10-02 EDT--2022-10-09 23:59:59 EDT</span>.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ::notice ::✔ simple: All hub config files are valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  <span style="color: #0000BB;">model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv</span>.%0A✔ 2022-10-08-team1-goodmodel.csv: File name <span style="color: #0000BB;">"2022-10-08-team1-goodmodel.csv"</span> is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  <span style="color: #0000BB;">model-metadata/team1-goodmodel.yaml</span>.%0A✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column <span style="color: #0000BB;">"origin_date"</span> contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` <span style="color: #0000BB;">"origin_date"</span> values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped.%0A! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time <span style="color: #0000BB;">2023-09-29 07:23:25.004255</span> is%0A  outside window <span style="color: #0000BB;">2022-10-02 EDT--2022-10-09 23:59:59 EDT</span>.</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/validate_submission_time.html b/reference/validate_submission_time.html
index cc13528d..9e382863 100644
--- a/reference/validate_submission_time.html
+++ b/reference/validate_submission_time.html
@@ -93,7 +93,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">hub_path</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span><span class="st">"testhubs/simple"</span>, package <span class="op">=</span> <span class="st">"hubValidations"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">file_path</span> <span class="op">&lt;-</span> <span class="st">"team1-goodmodel/2022-10-08-team1-goodmodel.csv"</span></span></span>
 <span class="r-in"><span><span class="fu">validate_submission_time</span><span class="op">(</span><span class="va">hub_path</span>, <span class="va">file_path</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> ::notice ::! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time <span style="color: #0000BB;">2023-09-28 15:36:47.309799</span> is%0A  outside window <span style="color: #0000BB;">2022-10-02 EDT--2022-10-09 23:59:59 EDT</span>.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> ::notice ::! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time <span style="color: #0000BB;">2023-09-29 07:23:25.614611</span> is%0A  outside window <span style="color: #0000BB;">2022-10-02 EDT--2022-10-09 23:59:59 EDT</span>.</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/search.json b/search.json
index a6f91478..be6cf455 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement TODO. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to hubValidations","title":"Contributing to hubValidations","text":"outlines propose change hubValidations. detailed info contributing , tidyverse packages, please see development contributing guide. : Develop link contributing guideines based : https://rstd.io/tidy-contrib ## Fixing typos can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to hubValidations","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to hubValidations","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"Infectious-Disease-Modeling-Hubs/hubValidations\", fork = TRUE). Install development dependencies devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to hubValidations","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to hubValidations","text":"Please note hubValidations project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 Consortium Infectious Disease Modeling Hubs Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"validations-yml-structure","dir":"Articles","previous_headings":"","what":"validations.yml structure","title":"Include custom validation functions","text":"validations.yml files follow nested structure described :","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"default-configuration","dir":"Articles","previous_headings":"validations.yml structure","what":"Default configuration","title":"Include custom validation functions","text":"top validations.yml file, required default: top level property, contain default custom validation configurations executed regardless round ID. Within default configuration, individual checks can configured 3 validation functions run part validate_submission(), using following structure validation function: fn: name check function run, character string (required). pkg: name package namespace get check function. Must supplied function distributed part package. source: Path .R script containing function code sourced. relative, relative hub’s directory root. Must supplied function part package exists script. args: yaml dictionary key/value pairs arguments passed custom function. Values can yaml lists even executable R code (optional). Note validate_*() functions contain standard objects call environment passed automatically custom check function therefore need including args configuration. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. tbl: tibble model output data validated. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. round_id_col: character string name tbl column containing round_id information. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. args configuration can used override objects caller environment well defaults. ’s example configuration single check (opt_check_tbl_horizon_timediff()) run part validate_model_data() validation function checks content model data submission files. configuration file relies default values arguments horizon_colname (\"horizon\") timediff (lubridate::weeks()). can use validations.yml args list override default values. ’s example includes executable r code value argument.","code":"default:     validate_model_data:       horizon_timediff:         fn: \"opt_check_tbl_horizon_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\" default:     validate_model_data:       horizon_timediff:         fn: \"opt_check_tbl_horizon_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"           horizon_colname: \"horizons\"           timediff: !expr lubridate::weeks(2)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"round-specific-configuration","dir":"Articles","previous_headings":"validations.yml structure","what":"Round specific configuration","title":"Include custom validation functions","text":"Additional round specific configurations can included validations.yml can add override default configurations. example, following validations.yml deploys opt_check_tbl_col_timediff() optional check, file validated submitted round round ID \"2023-08-15\", default col_timediff check configuration overridden 2023-08-15 configuration.","code":"default:     validate_model_data:       col_timediff:         fn: \"opt_check_tbl_col_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"  2023-08-15:     validate_model_data:       col_timediff:         fn: \"opt_check_tbl_col_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"           timediff: !expr lubridate::weeks(1)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"managing-dependencies-of-custom-sourced-functions","dir":"Articles","previous_headings":"","what":"Managing dependencies of custom sourced functions","title":"Include custom validation functions","text":"TODO","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anna Krystalli. Author, maintainer. Hugo Gruson. Author. Consortium Infectious Disease Modeling Hubs. Copyright holder.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Krystalli , Gruson H (2023). hubValidations: Testing framework hubverse hub validations. https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations, https://infectious-disease-modeling-hubs.github.io/hubValidations/.","code":"@Manual{,   title = {hubValidations: Testing framework for hubverse hub validations},   author = {Anna Krystalli and Hugo Gruson},   year = {2023},   note = {https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations, https://infectious-disease-modeling-hubs.github.io/hubValidations/}, }"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/index.html","id":"hubvalidations-","dir":"","previous_headings":"","what":"Testing framework for hubverse hub validations","title":"Testing framework for hubverse hub validations","text":"goal hubValidations provide testing framework performing hubverse hub validations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Testing framework for hubverse hub validations","text":"can install development version hubValidations like :","code":"remotes::install_github(\"Infectious-Disease-Modeling-Hubs/hubValidations\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture a condition of the result of validation check. — capture_check_cnd","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Capture condition result validation check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"","code":"capture_check_cnd(   check,   file_path,   msg_subject,   msg_attribute,   msg_verbs = c(\"is\", \"must be\"),   error = FALSE,   details = NULL,   ... )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"check logical, result validation check. check FALSE, validation failed. check TRUE, validation succeeded. file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg_subject character string. subject validation. msg_attribute character string. attribute subject validated. msg_verbs character vector length 2. verbs describing state attribute relation validation subject. first element describes state validation succeeds, second element, validation fails. error logical. case validation failure, whether function return object class <error/check_error> (TRUE) <warning/check_failure> (FALSE, default). details details appended output message. ... <dynamic> Named data fields stored inside condition object.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Depending whether validation succeeded value error argument, one : <message/check_success> condition class object. <warning/check_failure> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Arguments msg_subject, msg_attribute, msg_verbs details accept text can interpreted formatted cli::format_inline().","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"","code":"capture_check_cnd(   check = TRUE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = FALSE ) #> <message/check_success> #> Message: #> `round_id` is valid. capture_check_cnd(   check = FALSE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = FALSE,   details = \"Must be one of 'A' or 'B', not 'C'\" ) #> <warning/check_failure> #> Warning: #> `round_id` must be valid.  Must be one of 'A' or 'B', not 'C' capture_check_cnd(   check = FALSE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = TRUE,   details = \"Must be one of {.val {c('A', 'B')}}, not {.val C}\" ) #> <error/check_error> #> Error: #> ! `round_id` must be valid.  Must be one of \"A\" and \"B\", not \"C\""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture a simple info message condition — capture_check_info","title":"Capture a simple info message condition — capture_check_info","text":"Capture simple info message condition. Useful communicating check ignored skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture a simple info message condition — capture_check_info","text":"","code":"capture_check_info(file_path, msg)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture a simple info message condition — capture_check_info","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. Accepts text can interpreted formatted cli::format_inline().","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture a simple info message condition — capture_check_info","text":"<message/check_info> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture an execution error condition — capture_exec_error","title":"Capture an execution error condition — capture_exec_error","text":"Capture execution error condition. Useful communicating check execution failed. Usually used conjunction try.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture an execution error condition — capture_exec_error","text":"","code":"capture_exec_error(file_path, msg, call = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture an execution error condition — capture_exec_error","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. call Character string. Name parent call failed execute. NULL (default), caller's call name captured.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture an execution error condition — capture_exec_error","text":"<error/check_exec_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture an execution warning condition — capture_exec_warning","title":"Capture an execution warning condition — capture_exec_warning","text":"Capture execution warning condition. Useful communicating check execution failed. Usually used conjunction try.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture an execution warning condition — capture_exec_warning","text":"","code":"capture_exec_warning(file_path, msg, call = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture an execution warning condition — capture_exec_warning","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. call Character string. Name parent call failed execute. NULL (default), caller's call name captured.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture an execution warning condition — capture_exec_warning","text":"<warning/check_exec_warn> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"Check hub correctly configured — check_config_hub_valid","title":"Check hub correctly configured — check_config_hub_valid","text":"Checks admin tasks configuration files directory hub-config valid.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check hub correctly configured — check_config_hub_valid","text":"","code":"check_config_hub_valid(hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check hub correctly configured — check_config_hub_valid","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check hub correctly configured — check_config_hub_valid","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file exists at the file path specified — check_file_exists","title":"Check file exists at the file path specified — check_file_exists","text":"Check file exists file path specified","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file exists at the file path specified — check_file_exists","text":"","code":"check_file_exists(   file_path,   hub_path = \".\",   subdir = c(\"model-output\", \"model-metadata\", \"hub-config\") )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file exists at the file path specified — check_file_exists","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. subdir subdirectory within hub","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file exists at the file path specified — check_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file format is accepted by hub. — check_file_format","title":"Check file format is accepted by hub. — check_file_format","text":"Check file format accepted hub.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file format is accepted by hub. — check_file_format","text":"","code":"check_file_format(file_path, hub_path, round_id)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file format is accepted by hub. — check_file_format","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id character string. round identifier.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file format is accepted by hub. — check_file_format","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file is being submitted to the correct folder — check_file_location","title":"Check file is being submitted to the correct folder — check_file_location","text":"Checks model_id metadata file name matches directory name file submitted .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file is being submitted to the correct folder — check_file_location","text":"","code":"check_file_location(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file is being submitted to the correct folder — check_file_location","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file is being submitted to the correct folder — check_file_location","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Check a model output file name can be correctly parsed. — check_file_name","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"Check model output file name can correctly parsed.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"","code":"check_file_name(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file can be read successfully — check_file_read","title":"Check file can be read successfully — check_file_read","text":"Check file can read successfully","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file can be read successfully — check_file_read","text":"","code":"check_file_read(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file can be read successfully — check_file_read","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file can be read successfully — check_file_read","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":null,"dir":"Reference","previous_headings":"","what":"Raise conditions stored in a hub_validations object — check_for_errors","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"meant used CI workflows raise conditions hub_validations objects.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"","code":"check_for_errors(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"x hub_validations object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"error one elements x class check_failure, check_error, check_exec_error check_exec_warning. TRUE invisibly otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata schema file exists — check_metadata_file_exists","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"Check whether metadata schema file exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"","code":"check_metadata_file_exists(hub_path = \".\", file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-metadata directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file is being submitted to the correct folder — check_metadata_file_ext","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"Checks model_id metadata file name matches directory name file submitted .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"","code":"check_metadata_file_ext(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"Check metadata file submitted correct folder","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"","code":"check_metadata_file_location(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"file_path character string. Path file validated relative hub's model-metadata directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"Check whether file name metadata file matches model_id combination team_abbr model_abbr specified within metadata file","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"","code":"check_metadata_file_name(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"file_path character string. Path file validated relative hub's model-metadata directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"Check whether metadata file matches schema provided hub","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"","code":"check_metadata_matches_schema(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"file_path character string. Path file validated relative hub's model-metadata directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata schema file exists — check_metadata_schema_exists","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"Check whether metadata schema file exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"","code":"check_metadata_schema_exists(hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"Check whether metadata file given model exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"","code":"check_submission_metadata_file_exists(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks submission is within the valid submission window for a given round. — check_submission_time","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"Checks submission within valid submission window given round.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"","code":"check_submission_time(hub_path, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model data column data types — check_tbl_col_types","title":"Check model data column data types — check_tbl_col_types","text":"Check model output data column datatypes conform define hub config.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model data column data types — check_tbl_col_types","text":"","code":"check_tbl_col_types(tbl, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model data column data types — check_tbl_col_types","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model data column data types — check_tbl_col_types","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Check column names of model output data — check_tbl_colnames","title":"Check column names of model output data — check_tbl_colnames","text":"Checks tibble/data.frame data read file validated contains expected task ID standard column names according round configuration validated .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check column names of model output data — check_tbl_colnames","text":"","code":"check_tbl_colnames(tbl, round_id, file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check column names of model output data — check_tbl_colnames","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check column names of model output data — check_tbl_colnames","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"Check model output data tbl round ID matches submission round ID.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"","code":"check_tbl_match_round_id(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_error> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. valid round_id_col name provided can extracted config (check check_valid_round_id_col), <message/check_error> condition class object returned rest check skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model data rows are all unique — check_tbl_rows_unique","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"Checks combinations task ID, output type output type ID value combinations unique, checking duplicate rows across tbl columns excluding value column.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"","code":"check_tbl_rows_unique(tbl, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"Check model output data tbl contains single unique round ID.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"","code":"check_tbl_unique_round_id(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_error> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. valid round_id_col name provided can extracted config (check check_valid_round_id_col), <message/check_error> condition class object returned rest check skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check output type values of model output data against config — check_tbl_value_col","title":"Check output type values of model output data against config — check_tbl_value_col","text":"Checks values value column tibble/data.frame data read file validated conform configuration output type appropriate model task.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check output type values of model output data against config — check_tbl_value_col","text":"","code":"check_tbl_value_col(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check output type values of model output data against config — check_tbl_value_col","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check output type values of model output data against config — check_tbl_value_col","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"Checks values value column quantile cdf output type data unique task ID/output type combination non-descending arranged increasing output_type_id order. Check performed tbl contains quantile cdf output type data. , check skipped <message/check_info> condition class object returned.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"","code":"check_tbl_value_col_ascending(tbl, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"Checks values value column pmf output type data unique task ID combination sum 1. Check performed tbl contains pmf output type data. , check skipped <message/check_info> condition class object returned.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"","code":"check_tbl_value_col_sum1(tbl, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl contains valid value combinations — check_tbl_values","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"Check model output data tbl contains valid value combinations","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"","code":"check_tbl_values(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":null,"dir":"Reference","previous_headings":"","what":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"Check required task ID/output type/output type ID value combinations present model data.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"","code":"check_tbl_values_required(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether the round_id determined for the submission is valid — check_valid_round_id","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"Check whether round_id determined submission valid","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"","code":"check_valid_round_id(round_id, file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"Check round_id_col name provided extracted hub config valid.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"","code":"check_valid_round_id_col(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_warning> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate hub_validations S3 class objects — combine","title":"Concatenate hub_validations S3 class objects — combine","text":"Concatenate hub_validations S3 class objects","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate hub_validations S3 class objects — combine","text":"","code":"combine(...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate hub_validations S3 class objects — combine","text":"... hub_validations S3 class objects concatenated.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate hub_validations S3 class objects — combine","text":"hub_validations S3 class object.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":null,"dir":"Reference","previous_headings":"","what":"Get status of a hub check — is_success","title":"Get status of a hub check — is_success","text":"Get status hub check","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get status of a hub check — is_success","text":"","code":"is_success(x)  is_failure(x)  is_error(x)  is_info(x)  not_pass(x)  is_exec_error(x)  is_exec_warn(x)  is_any_error(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get status of a hub check — is_success","text":"x object inherits class <hub_check> test.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get status of a hub check — is_success","text":"Logical. given status check TRUE?","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get status of a hub check — is_success","text":"is_success(): check success? is_failure(): check failure? is_error(): check error? is_info(): check info? not_pass(): check pass? is_exec_error(): exec error? is_exec_warn(): exec warning? is_any_error(): error exec error?","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new or convert list to hub_validations S3 class object — new_hub_validations","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"Create new convert list hub_validations S3 class object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"","code":"new_hub_validations(...)  as_hub_validations(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"... named elements included. element must object inherits class <hub_check>. x list named elements. element must object inherits class <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"S3 object class <hub_validations>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"new_hub_validations(): Create new <hub_validations> S3 class object as_hub_validations(): Convert list <hub_validations> S3 class object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"","code":"new_hub_validations() #> ::notice ::Empty <hub_validations>  hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" new_hub_validations(   file_exists = check_file_exists(file_path, hub_path),   file_name = check_file_name(file_path) ) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid. x <- list(   file_exists = check_file_exists(file_path, hub_path),   file_name = check_file_name(file_path) ) as_hub_validations(x) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":null,"dir":"Reference","previous_headings":"","what":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"Check time difference values two date columns equal defined period.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"","code":"opt_check_tbl_col_timediff(   tbl,   file_path,   hub_path,   t0_colname,   t1_colname,   timediff = lubridate::weeks(2) )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. t0_colname Character string. name time zero date column. t1_colname Character string. name time zero + 1 time step date column. timediff object class lubridate Period length 1.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"Check predicted values per location less total location population.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"","code":"opt_check_tbl_counts_lt_popn(   tbl,   file_path,   hub_path,   targets = NULL,   popn_file_path = \"auxiliary-data/locations.csv\",   popn_col = \"population\",   location_col = \"location\" )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. targets Either single target key list list multiple target key lists. popn_file_path Character string. Path population data relative hub root. Defaults auxiliary-data/locations.csv. popn_col Character string. name population size column population data set. location_col Character string. name location column. Used join population data submission file data. Must shared files.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"applied rows containing count predictions. Use argument targets filter tbl data appropriate count target rows.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"","code":"hub_path <- system.file(\"testhubs/flusight\", package = \"hubValidations\") file_path <- \"hub-ensemble/2023-05-08-hub-ensemble.parquet\" tbl <- hubValidations::read_model_out_file(file_path, hub_path) # Single target key list targets <- list(\"target\" = \"wk ahead inc flu hosp\") opt_check_tbl_counts_lt_popn(tbl, file_path, hub_path, targets = targets) #> <message/check_success> #> Message: #> Target counts are less than location population size."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":null,"dir":"Reference","previous_headings":"","what":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"Check time difference values two date columns equal defined period.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"","code":"opt_check_tbl_horizon_timediff(   tbl,   file_path,   hub_path,   t0_colname,   t1_colname,   horizon_colname = \"horizon\",   timediff = lubridate::weeks() )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. t0_colname Character string. name time zero date column. t1_colname Character string. name time zero + 1 time step date column. horizon_colname Character string. name horizon column. Defaults \"horizon\". timediff object class lubridate Period length 1. period single horizon. Default 1 week.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Print results of validate_...() function as a bullet list — print.hub_validations","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"Print results validate_...() function bullet list","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"","code":"# S3 method for hub_validations print(x, ...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"x object class hub_validations ... Unused argument present class consistency","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"Print results validate_pr() function bullet list","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"","code":"# S3 method for pr_hub_validations print(x, ...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"x object class pr_hub_validations ... Unused argument present class consistency","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file can be read successfully — read_model_out_file","title":"Check file can be read successfully — read_model_out_file","text":"Check file can read successfully","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file can be read successfully — read_model_out_file","text":"","code":"read_model_out_file(file_path, hub_path = \".\", use_hub_schema = FALSE)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file can be read successfully — read_model_out_file","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. use_hub_schema Logical. reading csv files, whether use hub's schema specify column data types.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file can be read successfully — read_model_out_file","text":"tibble contents model output file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap check expression to capture check execution errors — try_check","title":"Wrap check expression to capture check execution errors — try_check","text":"Wrap check expression capture check execution errors","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap check expression to capture check execution errors — try_check","text":"","code":"try_check(expr, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap check expression to capture check execution errors — try_check","text":"expr check function expression run. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap check expression to capture check execution errors — try_check","text":"expr executes correctly, output expr returned. execution error message attached attribute msg.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate the contents of a submitted model data file — validate_model_data","title":"Validate the contents of a submitted model data file — validate_model_data","text":"Validate contents submitted model data file","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate the contents of a submitted model data file — validate_model_data","text":"","code":"validate_model_data(   hub_path,   file_path,   round_id_col = NULL,   validations_cfg_path = NULL )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate the contents of a submitted model data file — validate_model_data","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate the contents of a submitted model data file — validate_model_data","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate the contents of a submitted model data file — validate_model_data","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_model_data(hub_path, file_path) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column \"origin_date\" contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` \"origin_date\" values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Valid file level properties of a submitted model output file. — validate_model_file","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"Valid file level properties submitted model output file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"","code":"validate_model_file(hub_path, file_path, validations_cfg_path = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") validate_model_file(hub_path,   file_path = \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" ) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  model-metadata/team1-goodmodel.yaml. validate_model_file(hub_path,   file_path = \"team1-goodmodel/2022-10-15-team1-goodmodel.csv\" ) #> ::notice ::✖ 2022-10-15-team1-goodmodel.csv: File does not exist at path%0A  model-output/team1-goodmodel/2022-10-15-team1-goodmodel.csv."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Valid properties of a metadata file. — validate_model_metadata","title":"Valid properties of a metadata file. — validate_model_metadata","text":"Valid properties metadata file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Valid properties of a metadata file. — validate_model_metadata","text":"","code":"validate_model_metadata(   hub_path,   file_path,   round_id = \"default\",   validations_cfg_path = NULL )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Valid properties of a metadata file. — validate_model_metadata","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id character string. round identifier. Used primarily indicate whether \"default\" round specific configuration used custom validations. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Valid properties of a metadata file. — validate_model_metadata","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Valid properties of a metadata file. — validate_model_metadata","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") validate_model_file(hub_path,   file_path = \"team1-goodmodel.yml\" ) #> ::notice ::✖ team1-goodmodel.yml: File does not exist at path%0A  model-output/team1-goodmodel.yml."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate Pull Request — validate_pr","title":"Validate Pull Request — validate_pr","text":"Validate Pull Request","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate Pull Request — validate_pr","text":"","code":"validate_pr(   hub_path = \".\",   gh_repo,   pr_number,   round_id_col = NULL,   validations_cfg_path = NULL,   skip_submit_window_check = FALSE )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate Pull Request — validate_pr","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. gh_repo GitHub repository address format username/repo pr_number Number pull request validate round_id_col Character string. name column containing round_ids. required files contain column contains round_id details configured via round_id_from_variable: true round_id: hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml. skip_submit_window_check Logical. Whether skip submission window check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate Pull Request — validate_pr","text":"object class hub_validations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate Pull Request — validate_pr","text":"","code":"if (FALSE) { validate_pr(   hub_path = \".\",   gh_repo = \"Infectious-Disease-Modeling-Hubs/ci-testhub-simple\",   pr_number = 3 ) }"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"Validate submitted model data file. Checks file level properties like file name, extension, location etc well model output data, .e. contents file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"","code":"validate_submission(   hub_path,   file_path,   round_id_col = NULL,   validations_cfg_path = NULL,   skip_submit_window_check = FALSE,   skip_check_config = FALSE )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml. skip_submit_window_check Logical. Whether skip submission window check. skip_check_config Logical. Whether skip hub config validation check. check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_submission(hub_path, file_path) #> ::notice ::✔ simple: All hub config files are valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  model-metadata/team1-goodmodel.yaml.%0A✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column \"origin_date\" contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` \"origin_date\" values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped.%0A! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time 2023-09-28 15:36:46.668269 is%0A  outside window 2022-10-02 EDT--2022-10-09 23:59:59 EDT."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a submitted model data file submission time. — validate_submission_time","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"Validate submitted model data file submission time.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"","code":"validate_submission_time(hub_path, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_submission_time(hub_path, file_path) #> ::notice ::! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time 2023-09-28 15:36:47.309799 is%0A  outside window 2022-10-02 EDT--2022-10-09 23:59:59 EDT."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/news/index.html","id":"hubvalidations-0009000","dir":"Changelog","previous_headings":"","what":"hubValidations 0.0.0.9000","title":"hubValidations 0.0.0.9000","text":"Added NEWS.md file track changes package.","code":""}]
+[{"path":[]},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement TODO. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired [Mozilla’s code conduct enforcement ladder][https://github.com/mozilla/inclusion]. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to hubValidations","title":"Contributing to hubValidations","text":"outlines propose change hubValidations. detailed info contributing , tidyverse packages, please see development contributing guide. : Develop link contributing guideines based : https://rstd.io/tidy-contrib ## Fixing typos can fix typos, spelling mistakes, grammatical errors documentation directly using GitHub web interface, long changes made source file. generally means ’ll need edit roxygen2 comments .R, .Rd file. can find .R file generates .Rd reading comment first line.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"bigger-changes","dir":"","previous_headings":"","what":"Bigger changes","title":"Contributing to hubValidations","text":"want make bigger change, ’s good idea first file issue make sure someone team agrees ’s needed. ’ve found bug, please file issue illustrates bug minimal reprex (also help write unit test, needed).","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"pull-request-process","dir":"","previous_headings":"Bigger changes","what":"Pull request process","title":"Contributing to hubValidations","text":"Fork package clone onto computer. haven’t done , recommend using usethis::create_from_github(\"Infectious-Disease-Modeling-Hubs/hubValidations\", fork = TRUE). Install development dependencies devtools::install_dev_deps(), make sure package passes R CMD check running devtools::check(). R CMD check doesn’t pass cleanly, ’s good idea ask help continuing. Create Git branch pull request (PR). recommend using usethis::pr_init(\"brief-description--change\"). Make changes, commit git, create PR running usethis::pr_push(), following prompts browser. title PR briefly describe change. body PR contain Fixes #issue-number. user-facing changes, add bullet top NEWS.md (.e. just first header). Follow style described https://style.tidyverse.org/news.html.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"code-style","dir":"","previous_headings":"Bigger changes","what":"Code style","title":"Contributing to hubValidations","text":"New code follow tidyverse style guide. can use styler package apply styles, please don’t restyle code nothing PR. use roxygen2, Markdown syntax, documentation. use testthat unit tests. Contributions test cases included easier accept.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contributing to hubValidations","text":"Please note hubValidations project released Contributor Code Conduct. contributing project agree abide terms.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 Consortium Infectious Disease Modeling Hubs Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"validations-yml-structure","dir":"Articles","previous_headings":"","what":"validations.yml structure","title":"Include custom validation functions","text":"validations.yml files follow nested structure described :","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"default-configuration","dir":"Articles","previous_headings":"validations.yml structure","what":"Default configuration","title":"Include custom validation functions","text":"top validations.yml file, required default: top level property, contain default custom validation configurations executed regardless round ID. Within default configuration, individual checks can configured 3 validation functions run part validate_submission(), using following structure validation function: fn: name check function run, character string (required). pkg: name package namespace get check function. Must supplied function distributed part package. source: Path .R script containing function code sourced. relative, relative hub’s directory root. Must supplied function part package exists script. args: yaml dictionary key/value pairs arguments passed custom function. Values can yaml lists even executable R code (optional). Note validate_*() functions contain standard objects call environment passed automatically custom check function therefore need including args configuration. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. tbl: tibble model output data validated. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. round_id_col: character string name tbl column containing round_id information. file_path: character string path file validated relative model-output directory. hub_path: character string path hub. round_id: character string round_id file_meta: named list containing round_id, team_abbr, model_abbr model_id details. args configuration can used override objects caller environment well defaults. ’s example configuration single check (opt_check_tbl_horizon_timediff()) run part validate_model_data() validation function checks content model data submission files. configuration file relies default values arguments horizon_colname (\"horizon\") timediff (lubridate::weeks()). can use validations.yml args list override default values. ’s example includes executable r code value argument.","code":"default:     validate_model_data:       horizon_timediff:         fn: \"opt_check_tbl_horizon_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\" default:     validate_model_data:       horizon_timediff:         fn: \"opt_check_tbl_horizon_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"           horizon_colname: \"horizons\"           timediff: !expr lubridate::weeks(2)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"round-specific-configuration","dir":"Articles","previous_headings":"validations.yml structure","what":"Round specific configuration","title":"Include custom validation functions","text":"Additional round specific configurations can included validations.yml can add override default configurations. example, following validations.yml deploys opt_check_tbl_col_timediff() optional check, file validated submitted round round ID \"2023-08-15\", default col_timediff check configuration overridden 2023-08-15 configuration.","code":"default:     validate_model_data:       col_timediff:         fn: \"opt_check_tbl_col_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"  2023-08-15:     validate_model_data:       col_timediff:         fn: \"opt_check_tbl_col_timediff\"         pkg: \"hubValidations\"         args:           t0_colname: \"forecast_date\"           t1_colname: \"target_end_date\"           timediff: !expr lubridate::weeks(1)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/articles/custom-functions.html","id":"managing-dependencies-of-custom-sourced-functions","dir":"Articles","previous_headings":"","what":"Managing dependencies of custom sourced functions","title":"Include custom validation functions","text":"TODO","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Anna Krystalli. Author, maintainer. Hugo Gruson. Author. Consortium Infectious Disease Modeling Hubs. Copyright holder.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Krystalli , Gruson H (2023). hubValidations: Testing framework hubverse hub validations. https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations, https://infectious-disease-modeling-hubs.github.io/hubValidations/.","code":"@Manual{,   title = {hubValidations: Testing framework for hubverse hub validations},   author = {Anna Krystalli and Hugo Gruson},   year = {2023},   note = {https://github.com/Infectious-Disease-Modeling-Hubs/hubValidations, https://infectious-disease-modeling-hubs.github.io/hubValidations/}, }"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/index.html","id":"hubvalidations-","dir":"","previous_headings":"","what":"Testing framework for hubverse hub validations","title":"Testing framework for hubverse hub validations","text":"goal hubValidations provide testing framework performing hubverse hub validations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Testing framework for hubverse hub validations","text":"can install development version hubValidations like :","code":"remotes::install_github(\"Infectious-Disease-Modeling-Hubs/hubValidations\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture a condition of the result of validation check. — capture_check_cnd","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Capture condition result validation check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"","code":"capture_check_cnd(   check,   file_path,   msg_subject,   msg_attribute,   msg_verbs = c(\"is\", \"must be\"),   error = FALSE,   details = NULL,   ... )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"check logical, result validation check. check FALSE, validation failed. check TRUE, validation succeeded. file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg_subject character string. subject validation. msg_attribute character string. attribute subject validated. msg_verbs character vector length 2. verbs describing state attribute relation validation subject. first element describes state validation succeeds, second element, validation fails. error logical. case validation failure, whether function return object class <error/check_error> (TRUE) <warning/check_failure> (FALSE, default). details details appended output message. ... <dynamic> Named data fields stored inside condition object.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Depending whether validation succeeded value error argument, one : <message/check_success> condition class object. <warning/check_failure> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"Arguments msg_subject, msg_attribute, msg_verbs details accept text can interpreted formatted cli::format_inline().","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_cnd.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Capture a condition of the result of validation check. — capture_check_cnd","text":"","code":"capture_check_cnd(   check = TRUE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = FALSE ) #> <message/check_success> #> Message: #> `round_id` is valid. capture_check_cnd(   check = FALSE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = FALSE,   details = \"Must be one of 'A' or 'B', not 'C'\" ) #> <warning/check_failure> #> Warning: #> `round_id` must be valid.  Must be one of 'A' or 'B', not 'C' capture_check_cnd(   check = FALSE, file_path = \"test/file.csv\",   msg_subject = \"{.var round_id}\", msg_attribute = \"valid.\", error = TRUE,   details = \"Must be one of {.val {c('A', 'B')}}, not {.val C}\" ) #> <error/check_error> #> Error: #> ! `round_id` must be valid.  Must be one of \"A\" and \"B\", not \"C\""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture a simple info message condition — capture_check_info","title":"Capture a simple info message condition — capture_check_info","text":"Capture simple info message condition. Useful communicating check ignored skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture a simple info message condition — capture_check_info","text":"","code":"capture_check_info(file_path, msg)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture a simple info message condition — capture_check_info","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. Accepts text can interpreted formatted cli::format_inline().","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_check_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture a simple info message condition — capture_check_info","text":"<message/check_info> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture an execution error condition — capture_exec_error","title":"Capture an execution error condition — capture_exec_error","text":"Capture execution error condition. Useful communicating check execution failed. Usually used conjunction try.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture an execution error condition — capture_exec_error","text":"","code":"capture_exec_error(file_path, msg, call = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture an execution error condition — capture_exec_error","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. call Character string. Name parent call failed execute. NULL (default), caller's call name captured.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_error.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture an execution error condition — capture_exec_error","text":"<error/check_exec_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":null,"dir":"Reference","previous_headings":"","what":"Capture an execution warning condition — capture_exec_warning","title":"Capture an execution warning condition — capture_exec_warning","text":"Capture execution warning condition. Useful communicating check execution failed. Usually used conjunction try.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Capture an execution warning condition — capture_exec_warning","text":"","code":"capture_exec_warning(file_path, msg, call = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Capture an execution warning condition — capture_exec_warning","text":"file_path character string. Path file validated. Must relative path hub's model-output (equivalent) directory. msg Character string. call Character string. Name parent call failed execute. NULL (default), caller's call name captured.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/capture_exec_warning.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Capture an execution warning condition — capture_exec_warning","text":"<warning/check_exec_warn> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":null,"dir":"Reference","previous_headings":"","what":"Check hub correctly configured — check_config_hub_valid","title":"Check hub correctly configured — check_config_hub_valid","text":"Checks admin tasks configuration files directory hub-config valid.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check hub correctly configured — check_config_hub_valid","text":"","code":"check_config_hub_valid(hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check hub correctly configured — check_config_hub_valid","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_config_hub_valid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check hub correctly configured — check_config_hub_valid","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file exists at the file path specified — check_file_exists","title":"Check file exists at the file path specified — check_file_exists","text":"Check file exists file path specified","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file exists at the file path specified — check_file_exists","text":"","code":"check_file_exists(   file_path,   hub_path = \".\",   subdir = c(\"model-output\", \"model-metadata\", \"hub-config\") )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file exists at the file path specified — check_file_exists","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. subdir subdirectory within hub","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file exists at the file path specified — check_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file format is accepted by hub. — check_file_format","title":"Check file format is accepted by hub. — check_file_format","text":"Check file format accepted hub.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file format is accepted by hub. — check_file_format","text":"","code":"check_file_format(file_path, hub_path, round_id)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file format is accepted by hub. — check_file_format","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id character string. round identifier.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_format.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file format is accepted by hub. — check_file_format","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file is being submitted to the correct folder — check_file_location","title":"Check file is being submitted to the correct folder — check_file_location","text":"Checks model_id metadata file name matches directory name file submitted .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file is being submitted to the correct folder — check_file_location","text":"","code":"check_file_location(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file is being submitted to the correct folder — check_file_location","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file is being submitted to the correct folder — check_file_location","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Check a model output file name can be correctly parsed. — check_file_name","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"Check model output file name can correctly parsed.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"","code":"check_file_name(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check a model output file name can be correctly parsed. — check_file_name","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file can be read successfully — check_file_read","title":"Check file can be read successfully — check_file_read","text":"Check file can read successfully","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file can be read successfully — check_file_read","text":"","code":"check_file_read(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file can be read successfully — check_file_read","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_file_read.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file can be read successfully — check_file_read","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":null,"dir":"Reference","previous_headings":"","what":"Raise conditions stored in a hub_validations object — check_for_errors","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"meant used CI workflows raise conditions hub_validations objects.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"","code":"check_for_errors(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"x hub_validations object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_for_errors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Raise conditions stored in a hub_validations object — check_for_errors","text":"error one elements x class check_failure, check_error, check_exec_error check_exec_warning. TRUE invisibly otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata schema file exists — check_metadata_file_exists","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"Check whether metadata schema file exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"","code":"check_metadata_file_exists(hub_path = \".\", file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-metadata directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata schema file exists — check_metadata_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file is being submitted to the correct folder — check_metadata_file_ext","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"Checks model_id metadata file name matches directory name file submitted .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"","code":"check_metadata_file_ext(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_ext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file is being submitted to the correct folder — check_metadata_file_ext","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"Check metadata file submitted correct folder","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"","code":"check_metadata_file_location(file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"file_path character string. Path file validated relative hub's model-metadata directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_location.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that the metadata file is being submitted to the correct folder — check_metadata_file_location","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"Check whether file name metadata file matches model_id combination team_abbr model_abbr specified within metadata file","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"","code":"check_metadata_file_name(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"file_path character string. Path file validated relative hub's model-metadata directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_file_name.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether the file name of a metadata file matches the model_id or\ncombination of team_abbr and model_abbr specified within the metadata file — check_metadata_file_name","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"Check whether metadata file matches schema provided hub","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"","code":"check_metadata_matches_schema(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"file_path character string. Path file validated relative hub's model-metadata directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_matches_schema.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata file matches the schema provided by the hub — check_metadata_matches_schema","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata schema file exists — check_metadata_schema_exists","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"Check whether metadata schema file exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"","code":"check_metadata_schema_exists(hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_metadata_schema_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata schema file exists — check_metadata_schema_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"Check whether metadata file given model exists","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"","code":"check_submission_metadata_file_exists(file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_metadata_file_exists.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether a metadata file for the given model exists — check_submission_metadata_file_exists","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Checks submission is within the valid submission window for a given round. — check_submission_time","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"Checks submission within valid submission window given round.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"","code":"check_submission_time(hub_path, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_submission_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checks submission is within the valid submission window for a given round. — check_submission_time","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model data column data types — check_tbl_col_types","title":"Check model data column data types — check_tbl_col_types","text":"Check model output data column datatypes conform define hub config.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model data column data types — check_tbl_col_types","text":"","code":"check_tbl_col_types(tbl, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model data column data types — check_tbl_col_types","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_col_types.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model data column data types — check_tbl_col_types","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Check column names of model output data — check_tbl_colnames","title":"Check column names of model output data — check_tbl_colnames","text":"Checks tibble/data.frame data read file validated contains expected task ID standard column names according round configuration validated .","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check column names of model output data — check_tbl_colnames","text":"","code":"check_tbl_colnames(tbl, round_id, file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check column names of model output data — check_tbl_colnames","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_colnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check column names of model output data — check_tbl_colnames","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"Check model output data tbl round ID matches submission round ID.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"","code":"check_tbl_match_round_id(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_error> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. valid round_id_col name provided can extracted config (check check_valid_round_id_col), <message/check_error> condition class object returned rest check skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_match_round_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check model output data tbl round ID matches submission round ID. — check_tbl_match_round_id","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model data rows are all unique — check_tbl_rows_unique","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"Checks combinations task ID, output type output type ID value combinations unique, checking duplicate rows across tbl columns excluding value column.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"","code":"check_tbl_rows_unique(tbl, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_rows_unique.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model data rows are all unique — check_tbl_rows_unique","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"Check model output data tbl contains single unique round ID.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"","code":"check_tbl_unique_round_id(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_error> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. valid round_id_col name provided can extracted config (check check_valid_round_id_col), <message/check_error> condition class object returned rest check skipped.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_unique_round_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check model output data tbl contains a single unique round ID. — check_tbl_unique_round_id","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check output type values of model output data against config — check_tbl_value_col","title":"Check output type values of model output data against config — check_tbl_value_col","text":"Checks values value column tibble/data.frame data read file validated conform configuration output type appropriate model task.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check output type values of model output data against config — check_tbl_value_col","text":"","code":"check_tbl_value_col(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check output type values of model output data against config — check_tbl_value_col","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check output type values of model output data against config — check_tbl_value_col","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"Checks values value column quantile cdf output type data unique task ID/output type combination non-descending arranged increasing output_type_id order. Check performed tbl contains quantile cdf output type data. , check skipped <message/check_info> condition class object returned.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"","code":"check_tbl_value_col_ascending(tbl, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_ascending.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that quantile and cdf output type values of model output data\nare non-descending — check_tbl_value_col_ascending","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"Checks values value column pmf output type data unique task ID combination sum 1. Check performed tbl contains pmf output type data. , check skipped <message/check_info> condition class object returned.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"","code":"check_tbl_value_col_sum1(tbl, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_value_col_sum1.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that pmf output type values of model output data sum to 1. — check_tbl_value_col_sum1","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Check model output data tbl contains valid value combinations — check_tbl_values","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"Check model output data tbl contains valid value combinations","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"","code":"check_tbl_values(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check model output data tbl contains valid value combinations — check_tbl_values","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":null,"dir":"Reference","previous_headings":"","what":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"Check required task ID/output type/output type ID value combinations present model data.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"","code":"check_tbl_values_required(tbl, round_id, file_path, hub_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"tbl tibble/data.frame contents file validated. round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_tbl_values_required.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check all required task ID/output type/output type ID value combinations present\nin model data. — check_tbl_values_required","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Check whether the round_id determined for the submission is valid — check_valid_round_id","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"Check whether round_id determined submission valid","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"","code":"check_valid_round_id(round_id, file_path, hub_path = \".\")"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"round_id character string. round identifier. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check whether the round_id determined for the submission is valid — check_valid_round_id","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <error/check_error> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"Check round_id_col name provided extracted hub config valid.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"","code":"check_valid_round_id_col(tbl, file_path, hub_path, round_id_col = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_warning> condition class object. round_id_from_variable: false round_id_col name provided, check skipped <message/check_info> condition class object returned. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/check_valid_round_id_col.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check that any round_id_col name provided or extracted from the hub config is\nvalid. — check_valid_round_id_col","text":"check applies files submitted rounds round_id_from_variable: true round_id_col name explicitly provided. Skipped otherwise.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":null,"dir":"Reference","previous_headings":"","what":"Concatenate hub_validations S3 class objects — combine","title":"Concatenate hub_validations S3 class objects — combine","text":"Concatenate hub_validations S3 class objects","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Concatenate hub_validations S3 class objects — combine","text":"","code":"combine(...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Concatenate hub_validations S3 class objects — combine","text":"... hub_validations S3 class objects concatenated.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/combine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Concatenate hub_validations S3 class objects — combine","text":"hub_validations S3 class object.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":null,"dir":"Reference","previous_headings":"","what":"Get status of a hub check — is_success","title":"Get status of a hub check — is_success","text":"Get status hub check","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get status of a hub check — is_success","text":"","code":"is_success(x)  is_failure(x)  is_error(x)  is_info(x)  not_pass(x)  is_exec_error(x)  is_exec_warn(x)  is_any_error(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get status of a hub check — is_success","text":"x object inherits class <hub_check> test.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get status of a hub check — is_success","text":"Logical. given status check TRUE?","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/is_success.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get status of a hub check — is_success","text":"is_success(): check success? is_failure(): check failure? is_error(): check error? is_info(): check info? not_pass(): check pass? is_exec_error(): exec error? is_exec_warn(): exec warning? is_any_error(): error exec error?","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Create new or convert list to hub_validations S3 class object — new_hub_validations","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"Create new convert list hub_validations S3 class object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"","code":"new_hub_validations(...)  as_hub_validations(x)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"... named elements included. element must object inherits class <hub_check>. x list named elements. element must object inherits class <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"S3 object class <hub_validations>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"new_hub_validations(): Create new <hub_validations> S3 class object as_hub_validations(): Convert list <hub_validations> S3 class object","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/new_hub_validations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create new or convert list to hub_validations S3 class object — new_hub_validations","text":"","code":"new_hub_validations() #> ::notice ::Empty <hub_validations>  hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" new_hub_validations(   file_exists = check_file_exists(file_path, hub_path),   file_name = check_file_name(file_path) ) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid. x <- list(   file_exists = check_file_exists(file_path, hub_path),   file_name = check_file_name(file_path) ) as_hub_validations(x) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":null,"dir":"Reference","previous_headings":"","what":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"Check time difference values two date columns equal defined period.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"","code":"opt_check_tbl_col_timediff(   tbl,   file_path,   hub_path,   t0_colname,   t1_colname,   timediff = lubridate::weeks(2) )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. t0_colname Character string. name time zero date column. t1_colname Character string. name time zero + 1 time step date column. timediff object class lubridate Period length 1.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_col_timediff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_col_timediff","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":null,"dir":"Reference","previous_headings":"","what":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"Check predicted values per location less total location population.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"","code":"opt_check_tbl_counts_lt_popn(   tbl,   file_path,   hub_path,   targets = NULL,   popn_file_path = \"auxiliary-data/locations.csv\",   popn_col = \"population\",   location_col = \"location\" )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. targets Either single target key list list multiple target key lists. popn_file_path Character string. Path population data relative hub root. Defaults auxiliary-data/locations.csv. popn_col Character string. name population size column population data set. location_col Character string. name location column. Used join population data submission file data. Must shared files.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"applied rows containing count predictions. Use argument targets filter tbl data appropriate count target rows.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_counts_lt_popn.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check that predicted values per location are less than total location population. — opt_check_tbl_counts_lt_popn","text":"","code":"hub_path <- system.file(\"testhubs/flusight\", package = \"hubValidations\") file_path <- \"hub-ensemble/2023-05-08-hub-ensemble.parquet\" tbl <- hubValidations::read_model_out_file(file_path, hub_path) # Single target key list targets <- list(\"target\" = \"wk ahead inc flu hosp\") opt_check_tbl_counts_lt_popn(tbl, file_path, hub_path, targets = targets) #> <message/check_success> #> Message: #> Target counts are less than location population size."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":null,"dir":"Reference","previous_headings":"","what":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"Check time difference values two date columns equal defined period.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"","code":"opt_check_tbl_horizon_timediff(   tbl,   file_path,   hub_path,   t0_colname,   t1_colname,   horizon_colname = \"horizon\",   timediff = lubridate::weeks() )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"tbl tibble/data.frame contents file validated. file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. t0_colname Character string. name time zero date column. t1_colname Character string. name time zero + 1 time step date column. horizon_colname Character string. name horizon column. Defaults \"horizon\". timediff object class lubridate Period length 1. period single horizon. Default 1 week.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/opt_check_tbl_horizon_timediff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check time difference between values in two date columns equal a defined period. — opt_check_tbl_horizon_timediff","text":"Depending whether validation succeeded, one : <message/check_success> condition class object. <warning/check_failure> condition class object. Returned object also inherits subclass <hub_check>.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Print results of validate_...() function as a bullet list — print.hub_validations","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"Print results validate_...() function bullet list","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"","code":"# S3 method for hub_validations print(x, ...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print results of validate_...() function as a bullet list — print.hub_validations","text":"x object class hub_validations ... Unused argument present class consistency","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":null,"dir":"Reference","previous_headings":"","what":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"Print results validate_pr() function bullet list","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"","code":"# S3 method for pr_hub_validations print(x, ...)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/print.pr_hub_validations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Print results of validate_pr() function as a bullet list — print.pr_hub_validations","text":"x object class pr_hub_validations ... Unused argument present class consistency","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Check file can be read successfully — read_model_out_file","title":"Check file can be read successfully — read_model_out_file","text":"Check file can read successfully","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check file can be read successfully — read_model_out_file","text":"","code":"read_model_out_file(file_path, hub_path = \".\", use_hub_schema = FALSE)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check file can be read successfully — read_model_out_file","text":"file_path character string. Path file validated relative hub's model-output directory. hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. use_hub_schema Logical. reading csv files, whether use hub's schema specify column data types.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/read_model_out_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check file can be read successfully — read_model_out_file","text":"tibble contents model output file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap check expression to capture check execution errors — try_check","title":"Wrap check expression to capture check execution errors — try_check","text":"Wrap check expression capture check execution errors","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap check expression to capture check execution errors — try_check","text":"","code":"try_check(expr, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap check expression to capture check execution errors — try_check","text":"expr check function expression run. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/try_check.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap check expression to capture check execution errors — try_check","text":"expr executes correctly, output expr returned. execution error message attached attribute msg.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate the contents of a submitted model data file — validate_model_data","title":"Validate the contents of a submitted model data file — validate_model_data","text":"Validate contents submitted model data file","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate the contents of a submitted model data file — validate_model_data","text":"","code":"validate_model_data(   hub_path,   file_path,   round_id_col = NULL,   validations_cfg_path = NULL )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate the contents of a submitted model data file — validate_model_data","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate the contents of a submitted model data file — validate_model_data","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate the contents of a submitted model data file — validate_model_data","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_model_data(hub_path, file_path) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column \"origin_date\" contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` \"origin_date\" values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":null,"dir":"Reference","previous_headings":"","what":"Valid file level properties of a submitted model output file. — validate_model_file","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"Valid file level properties submitted model output file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"","code":"validate_model_file(hub_path, file_path, validations_cfg_path = NULL)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_file.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Valid file level properties of a submitted model output file. — validate_model_file","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") validate_model_file(hub_path,   file_path = \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" ) #> ::notice ::✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  model-metadata/team1-goodmodel.yaml. validate_model_file(hub_path,   file_path = \"team1-goodmodel/2022-10-15-team1-goodmodel.csv\" ) #> ::notice ::✖ 2022-10-15-team1-goodmodel.csv: File does not exist at path%0A  model-output/team1-goodmodel/2022-10-15-team1-goodmodel.csv."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Valid properties of a metadata file. — validate_model_metadata","title":"Valid properties of a metadata file. — validate_model_metadata","text":"Valid properties metadata file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Valid properties of a metadata file. — validate_model_metadata","text":"","code":"validate_model_metadata(   hub_path,   file_path,   round_id = \"default\",   validations_cfg_path = NULL )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Valid properties of a metadata file. — validate_model_metadata","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id character string. round identifier. Used primarily indicate whether \"default\" round specific configuration used custom validations. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Valid properties of a metadata file. — validate_model_metadata","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_model_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Valid properties of a metadata file. — validate_model_metadata","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") validate_model_file(hub_path,   file_path = \"team1-goodmodel.yml\" ) #> ::notice ::✖ team1-goodmodel.yml: File does not exist at path%0A  model-output/team1-goodmodel.yml."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate Pull Request — validate_pr","title":"Validate Pull Request — validate_pr","text":"Validate Pull Request","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate Pull Request — validate_pr","text":"","code":"validate_pr(   hub_path = \".\",   gh_repo,   pr_number,   round_id_col = NULL,   validations_cfg_path = NULL,   skip_submit_window_check = FALSE )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate Pull Request — validate_pr","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. gh_repo GitHub repository address format username/repo pr_number Number pull request validate round_id_col Character string. name column containing round_ids. required files contain column contains round_id details configured via round_id_from_variable: true round_id: hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml. skip_submit_window_check Logical. Whether skip submission window check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate Pull Request — validate_pr","text":"object class hub_validations.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_pr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate Pull Request — validate_pr","text":"","code":"if (FALSE) { validate_pr(   hub_path = \".\",   gh_repo = \"Infectious-Disease-Modeling-Hubs/ci-testhub-simple\",   pr_number = 3 ) }"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"Validate submitted model data file. Checks file level properties like file name, extension, location etc well model output data, .e. contents file.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"","code":"validate_submission(   hub_path,   file_path,   round_id_col = NULL,   validations_cfg_path = NULL,   skip_submit_window_check = FALSE,   skip_check_config = FALSE )"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory. round_id_col Character string. name column containing round_ids. Usually, value round property round_id hub tasks.json config file. validations_cfg_path Path validations.yml file. NULL defaults hub-config/validations.yml. skip_submit_window_check Logical. Whether skip submission window check. skip_check_config Logical. Whether skip hub config validation check. check.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a submitted model data file. Checks both file level properties like\nfile name, extension, location etc as well as model output data, i.e. the contents\nof the file. — validate_submission","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_submission(hub_path, file_path) #> ::notice ::✔ simple: All hub config files are valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File exists at path%0A  model-output/team1-goodmodel/2022-10-08-team1-goodmodel.csv.%0A✔ 2022-10-08-team1-goodmodel.csv: File name \"2022-10-08-team1-goodmodel.csv\" is%0A  valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File directory name matches `model_id`%0A  metadata in file name.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: File is accepted hub format.%0A✔ 2022-10-08-team1-goodmodel.csv: Metadata file exists at path%0A  model-metadata/team1-goodmodel.yaml.%0A✔ 2022-10-08-team1-goodmodel.csv: File could be read successfully.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id_col` name is valid.%0A✔ 2022-10-08-team1-goodmodel.csv: `round_id` column \"origin_date\" contains a%0A  single, unique round ID value.%0A✔ 2022-10-08-team1-goodmodel.csv: All `round_id_col` \"origin_date\" values match%0A  submission `round_id` from file name.%0A✔ 2022-10-08-team1-goodmodel.csv: Column names are consistent with expected%0A  round task IDs and std column names.%0A✔ 2022-10-08-team1-goodmodel.csv: Column data types match hub schema.%0A✔ 2022-10-08-team1-goodmodel.csv: Data rows contain valid value combinations%0A✔ 2022-10-08-team1-goodmodel.csv: All combinations of task ID%0A  column/`output_type`/`output_type_id` values are unique.%0A✔ 2022-10-08-team1-goodmodel.csv: Required task ID/output type/output type ID%0A  combinations all present.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in column `value` all valid with%0A  respect to modeling task config.%0A✔ 2022-10-08-team1-goodmodel.csv: Values in `value` column are non-decreasing%0A  as output_type_ids increase for all unique task ID value/output type%0A  combinations of quantile or cdf output types.%0Aℹ 2022-10-08-team1-goodmodel.csv: No pmf output types to check for sum of 1.%0A  Check skipped.%0A! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time 2023-09-29 07:23:25.004255 is%0A  outside window 2022-10-02 EDT--2022-10-09 23:59:59 EDT."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":null,"dir":"Reference","previous_headings":"","what":"Validate a submitted model data file submission time. — validate_submission_time","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"Validate submitted model data file submission time.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"","code":"validate_submission_time(hub_path, file_path)"},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"hub_path Either character string path local Modeling Hub directory object class <SubTreeFileSystem> created using functions s3_bucket() gs_bucket() providing string S3 GCS bucket name path Modeling Hub directory stored cloud. details consult Using cloud storage (S3, GCS) arrow package. hub must fully configured valid admin.json tasks.json files within hub-config directory. file_path character string. Path file validated relative hub's model-output directory.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"object class hub_validations. named element contains hub_check class object reflecting result given check. Function return early check returns error.","code":""},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/reference/validate_submission_time.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Validate a submitted model data file submission time. — validate_submission_time","text":"","code":"hub_path <- system.file(\"testhubs/simple\", package = \"hubValidations\") file_path <- \"team1-goodmodel/2022-10-08-team1-goodmodel.csv\" validate_submission_time(hub_path, file_path) #> ::notice ::! 2022-10-08-team1-goodmodel.csv: Submission time must be within accepted%0A  submission window for round.  Current time 2023-09-29 07:23:25.614611 is%0A  outside window 2022-10-02 EDT--2022-10-09 23:59:59 EDT."},{"path":"https://infectious-disease-modeling-hubs.github.io/hubValidations/news/index.html","id":"hubvalidations-0009000","dir":"Changelog","previous_headings":"","what":"hubValidations 0.0.0.9000","title":"hubValidations 0.0.0.9000","text":"Added NEWS.md file track changes package.","code":""}]