chore: Adds call-spell-check.yml from {ghactions4r}

Performed in the FIMS GHA workflows Fixes the double space was causing roxygen2 to render the file with @Seealso rather than interpreting the @ as a tag. This caused seealso to be needed in the WORDLIST. Changes proirs to priors in c++ documentation related to #662 Co-authored-by: Jane Sullivan <[email protected]> Co-authored-by: Kathryn Doering <[email protected]>
NOAA-FIMS · Dec 5, 2024 · 3eda154 · 3eda154
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diff --git a/.github/workflows/call-spell-check.yml b/.github/workflows/call-spell-check.yml
@@ -0,0 +1,17 @@
+# run devtools::spell_check()
+name: call-spell-check
+# on specifies the build triggers. See more info at https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+# this workflow runs on pushing to main, pull requests to main, and manually.
+  push:
+    branches:
+      - main
+      - dev
+  pull_request:
+    branches:
+      - main
+      - dev
+  workflow_dispatch:
+jobs:
+  call-workflow:
+    uses: nmfs-fish-tools/ghactions4r/.github/workflows/spell-check.yml@main
diff --git a/R/distribution_formulas.R b/R/distribution_formulas.R
@@ -439,7 +439,7 @@ initialize_process_distribution <- function(
 #' \item{family}{character: the family name.}
 #' \item{link}{character: the link name.}
 #'
-#'  @seealso
+#' @seealso
 #' * [stats::family()]
 #' * [stats::gaussian()]
 #' * [stats::glm()]

diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 # Overview
 The repository for development of FIMS. 
 
-The NOAA Fisheries Integrated Modeling System is a software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. A team of experts within NOAA Fisheries is designing and developing the system, and we are advised by the FIMS Council which includes academic, industry, and international partners. The roles of internal and external collaborators are outlined in the [governance section](https://noaa-fims.github.io/collaborative_workflow/fims-governance.html) of our developer guide. We plan to have an operational software system that is released to the public in 2023. In the meantime, users and developers are welcome to submit feedback using Github issues. Please use the issues under [collaborative workflow](https://github.com/NOAA-FIMS/collaborative_workflow/issues) to make suggestions about the [developer guide](https://noaa-fims.github.io/collaborative_workflow/) and the issues under the FIMS software [repo](https://github.com/NOAA-FIMS/FIMS/issues) for software design and development feedback. You can follow the team discussion [here](https://github.com/NOAA-FIMS/FIMS/discussions).
+The NOAA Fisheries Integrated Modeling System is a software system designed to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. A team of experts within NOAA Fisheries is designing and developing the system, and we are advised by the FIMS Council which includes academic, industry, and international partners. The roles of internal and external collaborators are outlined in the [governance section](https://noaa-fims.github.io/collaborative_workflow/fims-governance.html) of our developer guide. We plan to have an operational software system that is released to the public in 2023. In the meantime, users and developers are welcome to submit feedback using Github issues. Please use the issues under [collaborative workflow](https://github.com/NOAA-FIMS/collaborative_workflow/issues) to make suggestions about the [developer guide](https://noaa-fims.github.io/collaborative_workflow/) and the issues under the FIMS software [repo](https://github.com/NOAA-FIMS/FIMS/issues) for software design and development feedback. You can follow the team discussion [here](https://github.com/NOAA-FIMS/FIMS/discussions).
 
 ## Installing from R
 
@@ -34,7 +34,7 @@ All contributors participating and contributing to the FIMS project are expected
 
 This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an 'as is' basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
 
-Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
+Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. section 105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
 
 ****************************
 

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -0,0 +1,50 @@
+Arith
+Beverton
+CMD
+Codecov
+FIMSFit
+FIMSFrame
+Github
+JSON
+Lifecycle
+LogEntry
+LogisticMaturity
+LogisticMaturityInterface
+NOAA
+ParameterVector
+Rcpp
+TMB
+agecomp
+al
+codebase
+cov
+cummax
+cumprod
+cumsum
+cyclomatic
+digamma
+doxygen
+eg
+et
+expm
+fims
+fimsframe
+functors
+github
+grey
+hpp
+lengthcomp
+lgamma
+lm
+popdy
+pre
+precompiled
+rapidjson
+rcpp
+repo
+sdreport
+stan
+tabset
+testthat
+trigamma
+trunc
diff --git a/inst/include/distributions/functors/density_components_base.hpp b/inst/include/distributions/functors/density_components_base.hpp
@@ -38,7 +38,7 @@ struct DensityComponentBase : public fims_model_object::FIMSObject<Type> {
  uint32_t observed_data_id_m = -999; /*!< id of observed data component*/
  std::shared_ptr<fims_data_object::DataObject<Type>>
       observed_values; /**< observed data*/
- fims::Vector<Type > x; /**< input value of distribution function for proirs or random effects*/
+ fims::Vector<Type > x; /**< input value of distribution function for priors or random effects*/
  fims::Vector<Type> expected_values; /**< expected value of distribution function */
  fims::Vector<Type> lpdf_vec; /**< vector to record observation level negative log-likelihood values */
  std::string  input_type; /**< string classifies the type of the negative log-likelihood; options are: "priors", "random_effects", and "data" */

diff --git a/man/lognormal.Rd b/man/lognormal.Rd
diff --git a/vignettes/fims-demo.Rmd b/vignettes/fims-demo.Rmd
@@ -14,8 +14,7 @@ knitr::opts_chunk$set(echo = TRUE)
 ```
 
 ## Fisheries Integrated Modeling System
-
-The NOAA Fisheries Integrated Modeling System (FIMS) is a new modeling framework for fisheries modeling. FIMS is a software system designed and architected to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. It's important to note that FIMS itself is not a model, but rather a framework for creating models. The framework is made up of many modules that come together to create a "the best model" that suites the needs of the end-user. What follows is a demo of creating a catch-at-age assessment model using FIMS. 
+The NOAA Fisheries Integrated Modeling System (FIMS) is a new modeling framework for fisheries modeling. FIMS is a software system designed to support next-generation fisheries stock assessment, ecosystem, and socioeconomic modeling. It's important to note that FIMS itself is not a model, but rather a framework for creating models. The framework is made up of many modules that come together to create a "the best model" that suites the needs of the end-user. What follows is a demo of creating a catch-at-age assessment model using FIMS. 
 
 ## Import Libraries and Clear Memory