Merge pull request #39 from nmfs-fish-tools/36-create-a-website-using…

…-pkgdown

36 create a website using pkgdown

.Rbuildignore

@@ -0,0 +1,5 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.github/workflows/call-update-pkgdown.yml

@@ -0,0 +1,13 @@
+# updates exiting pkgdown site for a repository
+# deploys to a branch gh-pages
+name: call-update-pkgdown
+# 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 pushes to main or master or any time a new tag is pushed
+  # workflow_dispatch:
+  push:
+    # branches: [main, master]
+    # tags: ['*']
+jobs:
+  call-workflow:
+    uses: nmfs-fish-tools/ghactions4r/.github/workflows/update-pkgdown.yml@main

.gitignore

@@ -2,4 +2,5 @@
 .Rhistory
 .RData
 .Ruserdata
-StockAssessment/*/
+StockAssessment/*/
+docs

R/FishingMortalityAtMaximumSustainableYield.R

@@ -1,4 +1,5 @@
 #' Fishing mortality at maximum sustainable yield (FMSY)
+#'
 #' A biological reference point for fisheries management
 #' based on the fishing mortality rate (F) that achieves the maximum
 #' sustainable yield (MSY).
@@ -11,8 +12,8 @@
 #' where the subscript can be in either all capital letters or all
 #' lower-case letters, some use lower-case letters for the type of reference
 #' point, and some use all capital letters.}
-#' \item{Alternatives: Fproxy, F_msy, Fmsy}{}
-#' \item{Range of possible values: 0--Inf}{}
+#' \item{Alternatives}{Fproxy, F_msy, Fmsy}
+#' \item{Range of possible values}{0--Inf}
 #' \item{Units}{\code{time^{-1}}}
 #' }
-FishingMortalityAtMaximumSustainableYield <- NULL
+FishingMortalityAtMaximumSustainableYield <- NULL

_pkgdown.yml

@@ -1,32 +1,65 @@
+development:
+  mode: auto
+
+reference:
+- title: Dictionary Terms
+  contents:
+  - AgeComposition
+  - Biomass
+  - Catch
+  - CatchPerUnitEffort
+  - Cohort
+  - FishingMortalityAtMaximumSustainableYield
+  - Forecast
+  - InstantaneousFishingMortalityRate
+  - InstaneousMortalityRate
+  - Landings
+  - LengthComposition
+  - MaximumSustainableYield
+  - NaturalLogOfUnfishedRecruitment
+  - NumbersAtAge
+  - PlusGroup
+  - Projection
+  - Recruits
+  - Sex
+  - SpawnerPerRecruit
+  - SpawningBiomass
+  - Unfished
+  - Weight
+
+- title: R Functions
+  contents:
+  - add_object
+  - read_in
+  - shiny_dd
+
 navbar:
   structure:
     left:
     - home
     - reference
+    - articles
+    right:
     - github
     - issue
-    - article
 
   components:
     home:
       icon: fas fa-home fa-lg
       href: index.html
 
     reference:
-      text: Functions
+      text: Reference
       icon: far fa-file-code fa-lg
       href: reference/index.html
-
+    
     github:
       text: Source Code
       icon: fab fa-github fa-lg
-      href: https://github.com/nmfs-fish-tools/data_dictionary/
-
+      href: https://github.com/nmfs-fish-tools/fishdictionary
+    
     issue:
       text: Issues
       icon: fas fa-question-circle fa-lg
-      href: https://github.com/nmfs-fish-tools/data_dictionary/issues/
-
-    articles:
-      text: Vignettes
-      icon: fas fa-file-contract fa-lg
+      href: https://github.com/nmfs-fish-tools/fishdictionary/issues
+