Finalise setup

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/CODE_OF_CONDUCT.md

@@ -1,25 +1,126 @@
-# Contributor Code of Conduct
+# Contributor Covenant Code of Conduct
 
-As contributors and maintainers of this project, we pledge to respect all people who 
-contribute through reporting issues, posting feature requests, updating documentation,
-submitting pull requests or patches, and other activities.
+## Our Pledge
 
-We are committed to making participation in this project a harassment-free experience for
-everyone, regardless of level of experience, gender, gender identity and expression,
-sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, caste, color, religion, or sexual
+identity and orientation.
 
-Examples of unacceptable behaviour by participants include the use of sexual language or
-imagery, derogatory comments or personal attacks, trolling, public or private harassment,
-insults, or other unprofessional conduct.
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
 
-Project maintainers have the right and responsibility to remove, edit, or reject comments,
-commits, code, wiki edits, issues, and other contributions that are not aligned to this 
-Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
-from the project team.
+## Our Standards
 
-Instances of abusive, harassing, or otherwise unacceptable behaviour may be reported by 
-opening an issue or contacting one or more of the project maintainers.
+Examples of behavior that contributes to a positive environment for our
+community include:
 
-This Code of Conduct is adapted from the Contributor Covenant 
-(http://contributor-covenant.org), version 1.0.0, available at 
-http://contributor-covenant.org/version/1/0/0/
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+  community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or advances of
+  any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email address,
+  without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [email protected]. 
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.1, available at
+<https://www.contributor-covenant.org/version/2/1/code_of_conduct.html>.
+
+Community Impact Guidelines were inspired by
+[Mozilla's code of conduct enforcement ladder][https://github.com/mozilla/inclusion].
+
+For answers to common questions about this code of conduct, see the FAQ at
+<https://www.contributor-covenant.org/faq>. Translations are available at <https://www.contributor-covenant.org/translations>.
+
+[homepage]: https://www.contributor-covenant.org

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty",
-  "version": "0.0.0",
+  "version": "0.0.1",
   "license": "MIT",
   "upload_type": "software",
   "description": "<p>An R package to explore calculation, interpretation and visualisation of uncertainty related to indicators based on biodiversity data cubes.<\/p>",

CITATION.cff

@@ -22,11 +22,8 @@ contact:
   orcid: 0000-0002-5900-8109
 doi: ~
 license: MIT
-repository-code: /
+repository-code: https://github.com/b-cubed-eu/dubicube/
 type: software
 abstract: "An R package to explore calculation, interpretation and visualisation of
   uncertainty related to indicators based on biodiversity data cubes."
-identifiers:
-- type: url
-  value: https://b-cubed-eu.github.io/dubicube/
-version: 0.0.0
+version: 0.0.1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: dubicube
 Title: Calculation and Interpretation of Data Cube Indicator Uncertainty
-Version: 0.0.0
+Version: 0.0.1
 Authors@R: c(
     person("Ward", "Langeraert", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-5900-8109", affiliation = "Research Institute for Nature and Forest (INBO)")),
@@ -13,9 +13,10 @@ Description: An R package to explore calculation, interpretation and
     visualisation of uncertainty related to indicators based on
     biodiversity data cubes.
 License: MIT + file LICENSE
-URL: https://github.com/b-cubed-eu/dubicube,
-    https://b-cubed-eu.github.io/dubicube/
+URL: https://github.com/b-cubed-eu/dubicube
 BugReports: https://github.com/b-cubed-eu/dubicube/issues
+Suggests: 
+    testthat (>= 3.0.0)
 Config/checklist/communities: b3; inbo
 Config/checklist/keywords: uncertainty quantification; uncertainty
     visualisation; biodiversity indicators; data cubes

NEWS.md

@@ -1,3 +1,7 @@
+# dubicube 0.0.1
+
+* Set up basic package structure
+
 # dubicube 0.0.0
 
 * Added a `NEWS.md` file to track changes to the package.

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 )
 ```
 
-# dubicube
+# dubicube <a><img src="man/figures/logo.png" align="right" height="139" alt="dubicube website" /></a>
 
 <!-- badges: start -->
 

README.md

@@ -1,7 +1,7 @@
 
 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
-# dubicube
+# dubicube <a><img src="man/figures/logo.png" align="right" height="139" alt="dubicube website" /></a>
 
 <!-- badges: start -->
 

codemeta.json

@@ -4,10 +4,11 @@
   "identifier": "dubicube",
   "description": "An R package to explore calculation, interpretation and visualisation of uncertainty related to indicators based on biodiversity data cubes.",
   "name": "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty",
+  "relatedLink": "https://b-cubed-eu.github.io/dubicube/",
   "codeRepository": "https://github.com/b-cubed-eu/dubicube",
   "issueTracker": "https://github.com/b-cubed-eu/dubicube/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "0.0.0",
+  "version": "0.0.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -52,10 +53,25 @@
       "@id": "https://orcid.org/0000-0002-5900-8109"
     }
   ],
+  "softwareSuggestions": [
+    {
+      "@type": "SoftwareApplication",
+      "identifier": "testthat",
+      "name": "testthat",
+      "version": ">= 3.0.0",
+      "provider": {
+        "@id": "https://cran.r-project.org",
+        "@type": "Organization",
+        "name": "Comprehensive R Archive Network (CRAN)",
+        "url": "https://cran.r-project.org"
+      },
+      "sameAs": "https://CRAN.R-project.org/package=testthat"
+    }
+  ],
   "softwareRequirements": {
     "SystemRequirements": null
   },
-  "fileSize": "110.382KB",
+  "fileSize": "96.489KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -73,10 +89,11 @@
         }
       },
       "name": "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.0.1",
-      "url": "/"
+      "url": "https://b-cubed-eu.github.io/dubicube/"
     }
   ],
   "releaseNotes": "https://github.com/b-cubed-eu/dubicube/blob/master/NEWS.md",
+  "readme": "https://github.com/b-cubed-eu/dubicube/blob/main/README.md",
   "contIntegration": ["https://github.com/b-cubed-eu/dubicube/actions/workflows/check_on_different_r_os.yml", "https://app.codecov.io/gh/b-cubed-eu/dubicube/"],
   "developmentStatus": "https://www.repostatus.org/#concept"
 }

inst/CITATION

@@ -2,12 +2,12 @@ citHeader("To cite `dubicube` in publications please use:")
 # begin checklist entry
 bibentry(
   bibtype = "Manual",
-  title = "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.0.0",
+  title = "dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.0.1",
   author = c( author = c(person(given = "Ward", family = "Langeraert"), person(given = "Toon", family = "Van Daele"))),
   year = 2024,
-  url = "https://b-cubed-eu.github.io/dubicube/",
+  url = "https://github.com/b-cubed-eu/dubicube/",
   abstract = "An R package to explore calculation, interpretation and visualisation of uncertainty related to indicators based on biodiversity data cubes.",
-  textVersion = "Langeraert, Ward; Van Daele, Toon (2024) dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.0.0. https://b-cubed-eu.github.io/dubicube/",
+  textVersion = "Langeraert, Ward; Van Daele, Toon (2024) dubicube: Calculation and Interpretation of Data Cube Indicator Uncertainty. Version 0.0.1. https://github.com/b-cubed-eu/dubicube/",
   keywords = "uncertainty quantification; uncertainty visualisation; biodiversity indicators; data cubes",
 )
 # end checklist entry

man/figures/create_hexasticker.R

@@ -0,0 +1,9 @@
+library(hexSticker)
+sticker("man/figures/logo-raw.png", package = "dubicube",
+        p_size = 27, p_color = "#48A529",
+        p_x = 1.02, p_y = 1.42,
+        s_x = 1.05, s_y = 0.75, s_width = 0.6, s_height = 0.6,
+        h_fill = "black", h_color = "#48A529",
+        filename = "man/figures/hexa-sticker.png")
+
+usethis::use_logo("man/figures/hexa-sticker.png")

pkgdown/extra.css

@@ -0,0 +1,31 @@
+body {
+  font-size: 16px;
+  letter-spacing: 0px;
+}
+
+a,
+a:hover {
+  color: #6cddb4;
+}
+
+/* Fix for https://github.com/r-lib/pkgdown/issues/2387 */
+.navbar-dark .navbar-brand {
+  color: #ffffff;
+}
+.navbar-dark .text-muted {
+  color: #6cddb4!important;
+}
+.navbar-dark input[type="search"] {
+  background-color: #ffffff;
+  color: #444444;
+}
+
+.navbar-dark .navbar-nav .nav-link {
+  color: #ffffff;
+}
+.navbar-dark .navbar-nav .nav-link:hover,
+.navbar-dark .navbar-nav .active .nav-link,
+.navbar-dark .navbar-nav .active .nav-link:hover {
+  background-color: #ffffff!important;
+  color: #005856!important;
+}

pkgdown/favicon/site.webmanifest

@@ -0,0 +1,21 @@
+{
+  "name": "",
+  "short_name": "",
+  "icons": [
+    {
+      "src": "/web-app-manifest-192x192.png",
+      "sizes": "192x192",
+      "type": "image/png",
+      "purpose": "maskable"
+    },
+    {
+      "src": "/web-app-manifest-512x512.png",
+      "sizes": "512x512",
+      "type": "image/png",
+      "purpose": "maskable"
+    }
+  ],
+  "theme_color": "#ffffff",
+  "background_color": "#ffffff",
+  "display": "standalone"
+}

tests/testthat.R

@@ -0,0 +1,12 @@
+# This file is part of the standard setup for testthat.
+# It is recommended that you do not modify it.
+#
+# Where should you do additional test configuration?
+# Learn more about the roles of various files in:
+# * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
+# * https://testthat.r-lib.org/articles/special-files.html
+
+library(testthat)
+library(dubicube)
+
+test_check("dubicube")

tests/testthat/test-test_f.R

@@ -0,0 +1,3 @@
+test_that("multiplication works", {
+  expect_equal(2 * 2, 4)
+})