Merge branch 'dev' of github.com:NOAA-EDAB/Rpath into docs_pre_release

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, UnitTests]
+    branches: [main, master, UnitTests, dev]
   pull_request:
-    branches: [main, master]
+    branches: [main, master, dev]
 
 name: R-CMD-check
 

.gitignore

@@ -25,12 +25,19 @@ Rpath.Rcheck*
 vignettes/*.html
 src/*.o
 src/*.dll
+.github/workflows/tests.yaml
 tests/testthat/data/output/*
 tests/testthat/data/bkup/*
 tests/testthat/data/input/REcosystem_Current_*.dat
+tests/testthat/data/input/REcosystem_Current_*.rds
 tests/testthat/data/input/REcosystem_Current_*.csv
 tests/testthat/old/*
 tests/testthat/bkup/*
 tests/testthat/old dat files/*
 
-Rpath.Rproj
+docs
+doc
+Meta
+Rpath.Rproj
+
+inst/doc

DESCRIPTION

@@ -22,14 +22,15 @@ Imports:
     MASS,
     Rcpp (>= 0.11.3),
     stats,
-    utils
+    utils,
+    ggrepel,
+    ggplot2
 LinkingTo: Rcpp
 Suggests:
     here,
     knitr,
     rmarkdown,
     distillery,
-    ggplot2,
     ggpubr,
     rlist,
     stringr,

NAMESPACE

@@ -19,6 +19,7 @@ export(get.rsim.forcing)
 export(get.rsim.params)
 export(get.rsim.stanzas)
 export(get.rsim.start_state)
+export(ggwebplot)
 export(read.rpath.params)
 export(rpath)
 export(rpath.consumers)
@@ -45,11 +46,13 @@ export(rsim.state)
 export(rsim.step)
 export(set.rsim.scene)
 export(stanzaplot)
+export(summarize.for.webplot)
 export(webplot)
 export(write.Rpath)
 export(write.Rsim)
 export(write.rpath.params)
 import(data.table)
+import(ggplot2)
 import(graphics)
 import(stats)
 import(utils)

R/Adjustments.R

@@ -119,15 +119,15 @@ adjust.fishing <- function(Rsim.scenario, parameter, group = NA, sim.year = 1,
 #'@export 
 adjust.scenario <- function(Rsim.scenario, parameter, group, groupto = NA, value){
   #Lookup group numbers
-  if(group == 'all'){
+  if(group[1] == 'all'){
     groupnum <- 0:Rsim.scenario$params$NUM_GROUPS
   } else {
     groupnum <- Rsim.scenario$params$spnum[which(Rsim.scenario$params$spname 
-                                                 == group)]
+                                                 %in% group)]
   }
   if(!is.na(groupto)){
     groupnumto <- Rsim.scenario$params$spnum[which(Rsim.scenario$params$spname 
-                                                 == groupto)]
+                                                 %in% groupto)]
   }
 
   #Lookup parameter number