Merge pull request #47 from James-Thorson-NOAA/development

Development

DESCRIPTION

@@ -1,10 +1,15 @@
 Package: FishStatsUtils
 Type: Package
 Title: Utilities (shared code and data) for FishStats spatio-temporal modeling toolbox
-Version: 2.5.0
-Date: 2019-12-01
-Authors@R: person("James","Thorson", email="[email protected]", role=c("aut","cre"))
-Maintainer: James Thorson <[email protected]>
+Version: 2.6.0
+Date: 2020-04-11
+Authors@R: 
+    c(person(given = "James",
+             family = "Thorson",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0001-7415-1010"))
+    )
 Description: FishStatsUtils contains utilities (shared code and data) used by multiple 
   packages (VAST, SpatialDeltaGLMM, MIST, Spatial_FA, SpatialDFA, surplus_production, EOFR) that are designed
   for spatio-temporal analysis of ecological data.  
@@ -29,17 +34,21 @@ Imports:
     MatrixModels,
     rgdal,
     ThorsonUtilities,
+    TMBhelper,
     abind,
     corpcor,
     pander,
     rnaturalearth,
-    formatR
+    rnaturalearthdata,
+    formatR,
+    splancs
 Depends:
     R (>= 3.1.0)
 Suggests:
     testthat
 Remotes: 
-    james-thorson/utilities
+    james-thorson/utilities,
+    kaskr/TMB_contrib_R/TMBhelper
 License: GPL-3
 LazyData: yes
 BuildVignettes: yes

NAMESPACE

@@ -36,6 +36,7 @@ export(calc_cov)
 export(calculate_proportion)
 export(combine_extrapolation_info)
 export(combine_lists)
+export(convert_shapefile)
 export(convert_version_name)
 export(fit_model)
 export(format_covariates)
@@ -70,4 +71,5 @@ export(plot_variable)
 export(project_coordinates)
 export(rotate_factors)
 export(sample_variable)
+export(simulate_data)
 export(summarize_covariance)

R/Prepare_XXXX_Extrapolation_Data_Fn.R

@@ -355,7 +355,7 @@ function( strata.limits=NULL, epu_to_use = c('All', 'Georges_Bank','Mid_Atlantic
   }
   message("Using strata ", strata.limits)
 
-  if(tolower(epu_to_use) == "all") {
+  if(any(tolower(epu_to_use) %in% "all")) {
     epu_to_use <- c('Georges_Bank','Mid_Atlantic_Bight','Scotian_Shelf','Gulf_of_Maine','Other')
   }
 
@@ -368,10 +368,12 @@ function( strata.limits=NULL, epu_to_use = c('All', 'Georges_Bank','Mid_Atlantic
   if( length(strata.limits)==1 && strata.limits[1]=="EPU" ){
     # Specify epu by 'epu_to_use'
     Data_Extrap <- Data_Extrap[Data_Extrap$EPU %in% epu_to_use, ]
-    a_el = matrix(NA, nrow=nrow(Data_Extrap), ncol=length(unique(northwest_atlantic_grid[,'EPU'])), dimnames=list(NULL,unique(northwest_atlantic_grid[,'EPU'])) )
+    Data_Extrap$EPU <- droplevels(Data_Extrap$EPU)
+
+    a_el = matrix(NA, nrow=nrow(Data_Extrap), ncol=length(epu_to_use), dimnames=list(NULL, epu_to_use) )
     Area_km2_x = Data_Extrap[, "Area_in_survey_km2"]
     for(l in 1:ncol(a_el)){
-      a_el[,l] = ifelse( Data_Extrap[,'EPU']==unique(northwest_atlantic_grid[,'EPU'])[l], Area_km2_x, 0 )
+      a_el[,l] = ifelse( Data_Extrap[,'EPU'] %in% epu_to_use[[l]], Area_km2_x, 0 )
     }
   }else{
     # Specify strata by 'stratum_number'

R/calculate_proportion.R

@@ -21,7 +21,7 @@ calculate_proportion = function( TmbData, Index, Expansion_cz=NULL, Year_Set=NUL
   interval_width=1, width=6, height=6, xlab="Category", ylab="Proportion", ... ){
 
   # Warnings and errors
-  if( !all(TmbData[['FieldConfig']] %in% c(-2,-1)) ){
+  if( !all(TmbData[['FieldConfig']] %in% c(-3,-2,-1)) ){
     message("Derivation only included for independent categories")
     return( invisible("Not run") )
   }
@@ -39,7 +39,6 @@ calculate_proportion = function( TmbData, Index, Expansion_cz=NULL, Year_Set=NUL
   Index_tl = apply(Index_ctl,MARGIN=2:3,FUN=sum)
   SE_Index_tl = sqrt(apply(SE_Index_ctl^2,MARGIN=2:3,FUN=sum,na.rm=TRUE))
 
-
   # Approximate variance for proportions, and effective sample size
   Neff_ctl = var_Prop_ctl = array(NA,dim=dim(Prop_ctl))
   for( cI in 1:dim(var_Prop_ctl)[1]){