updates

.github/.gitignore

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

.github/workflows/pkgdown.yaml

@@ -0,0 +1,50 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -2,3 +2,4 @@
 ^\.Rproj\.user$
 .Rproj.user
 *.pdf
+docs

DESCRIPTION

@@ -40,3 +40,4 @@ Remotes:
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
 LazyData: true
+URL: https://james-thorson-noaa.github.io/EcoState/

R/myode.R

@@ -5,8 +5,8 @@
 #' @description 
 #' Interface for \code{RTMBode::ode}, itself an interface for \code{deSolve::ode}
 #'
-#' @param f function in the differential equation y' = f(x, y);
-#'        defined as a function R \times R^m \rightarrow R^m, where m is the number of equations.
+#' @param f function in the differential equation \eqn{y' = f(x, y)};
+#'        defined as a function \eqn{R \times R^m \rightarrow R^m}, where \eqn{m} is the number of equations.
 #' @param a starting time for the interval to integrate
 #' @param b ending time for the interval to integrate.
 #' @param y0 starting values at time \code{a}

R/ode23.R

@@ -4,8 +4,8 @@
 #' @description 
 #' Runge-Kutta (2, 3)-method with variable step size, resp
 #'
-#' @param f function in the differential equation y' = f(x, y);
-#'        defined as a function R \times R^m \rightarrow R^m, where m is the number of equations.
+#' @param f function in the differential equation \eqn{y' = f(x, y)};
+#'        defined as a function \eqn{R \times R^m \rightarrow R^m}, where \eqn{m} is the number of equations.
 #' @param a starting time for the interval to integrate
 #' @param b ending time for the interval to integrate.
 #' @param y0 starting values at time \code{a}

R/rk4sys.R

@@ -4,8 +4,8 @@
 #' @description 
 #' Classical Runge-Kutta of order 4.
 #'
-#' @param f function in the differential equation y' = f(x, y);
-#'        defined as a function R \times R^m \rightarrow R^m, where m is the number of equations.
+#' @param f function in the differential equation \eqn{y' = f(x, y)};
+#'        defined as a function \eqn{R \times R^m \rightarrow R^m}, where \eqn{m} is the number of equations.
 #' @param a starting time for the interval to integrate
 #' @param b ending time for the interval to integrate.
 #' @param y0 starting values at time \code{a}

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+

inst/CITATION

@@ -0,0 +1,25 @@
+citHeader("For methodological details regarding EcoState, please see Thorson et al. (In review).")
+
+bibentry(bibtype = "Article",
+           textVersion = "Thorson, J.  Kristensen, K., Aydin, K., Gaichas, S., Kimmel, D.G., McHuron, E.A., Nielsen, J.N., Townsend, H., Whitehouse, G.A. EcoState:  Extending Ecopath with Ecosim to estimate biological parameters and process errors using RTMB and time-series data",
+           title = "EcoState:  Extending Ecopath with Ecosim to estimate biological parameters and process errors using RTMB and time-series data",
+           journal = "In review",
+           year = "2024",
+           author = c(person(given = c("J.", "T."),
+                             family = "Thorson"),
+                      person(given = c("K."),
+                             family = "Kristensen"),
+                      person(given = c("K."),
+                             family = "Aydin"),
+                      person(given = c("S."),
+                             family = "Gaichas"),
+                      person(given = c("D.", "G."),
+                             family = "Kimmel"),
+                      person(given = c("E.", "A."),
+                             family = "McHuron"),
+                      person(given = c("J.", "N."),
+                             family = "Nielsen"),
+                      person(given = c("H."),
+                             family = "Townsend"),
+                      person(given = c("G.", "A."),
+                             family = "Whitehouse")))

scratch/build_pkgdown_website.R

@@ -6,7 +6,9 @@
 
 #-----------------------------------------------------------------
 # Install locally if needed
+# devtools::document( R'(C:\Users\James.Thorson\Desktop\Git\EcoState)' )
 # devtools::install_local( R'(C:\Users\James.Thorson\Desktop\Git\EcoState)', force=TRUE )
+# remotes::install_github( "James-Thorson-NOAA/EcoState", force=TRUE, dep=TRUE )
 
 # load needed libraries
 library(pkgdown)
@@ -16,10 +18,10 @@ library(pkgdown)
 if( FALSE ){
   setwd(R'(C:\Users\James.Thorson\Desktop\Git\EcoState\vignettes)')
 
-  knitr::knit( "web_only/eastern_bering_sea.Rmd.orig", output = "web_only/eastern_bering_sea.Rmd" )
+  #knitr::knit( "web_only/eastern_bering_sea.Rmd.orig", output = "web_only/eastern_bering_sea.Rmd" )
 }
 
-setwd(R'(C:\Users\James.Thorson\Desktop\Git\tinyVAST)')
+setwd(R'(C:\Users\James.Thorson\Desktop\Git\EcoState)')
 
 # Only needed once
 if( FALSE ){