Adding feature fine_scale=TRUE

James-Thorson-NOAA · May 10, 2019 · 66f0121 · 66f0121
2 parents 5affccb + c4dcb13
commit 66f0121
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: VAST
 Type: Package
 Title: Vector-autoregressive spatio-temporal (VAST) model
-Version: 2.1.0
-Date: 2019-03-01
+Version: 3.0.0
+Date: 2019-05-09
 Authors@R: person("James","Thorson", email="James.Thorson@noaa.gov", role=c("aut","cre"))
 Maintainer: James Thorson <James.Thorson@noaa.gov>
 Description: VAST is an R package for conducting spatio-temporal analysis
@@ -35,11 +35,11 @@ Imports:
     TMBhelper
 Depends:
     R (>= 3.1.0),
-    FishStatsUtils
 Suggests:
     testthat,
     knitr,
     rmarkdown,
+    FishStatsUtils,
     R.rsp
 Remotes:
     james-thorson/FishStatsUtils,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,23 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
 export(Build_TMB_Fn)
-export(Coherence)
-export(Crossvalidate_Fn)
 export(Data_Fn)
 export(Make_Map)
 export(Param_Fn)
 export(Plot_Overdispersion)
 export(Plot_factors)
-export(Rerun_Fn)
 export(Summarize)
 export(Summarize_Covariance)
-export(calc_coherence)
-export(calc_cov)
-export(calc_synchrony)
-export(calculate_proportion)
 export(make_data)
+export(make_map)
 export(make_model)
-export(plot_eigen)
+export(make_parameters)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,png)

diff --git a/R/Coherence.R b/R/Coherence.R
diff --git a/R/Crossvalidate_Fn.R b/R/Crossvalidate_Fn.R
diff --git a/R/Make_Map.R b/R/Make_Map.R
@@ -1,5 +1,5 @@
 #' @export
-Make_Map <-
+make_map <-
 function( DataList, TmbParams, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Epsilon2"=0), Npool=0 ){
 
   # Local functions
@@ -262,9 +262,15 @@ function( DataList, TmbParams, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Eps
   Map[["lambda2_k"]] = factor(Map[["lambda2_k"]])
 
   # Dynamic covariates
-  if( "X_xtp" %in% names(DataList) ){
-    Var_p = apply( DataList[["X_xtp"]], MARGIN=3, FUN=function(array){var(as.vector(array))})
-    Var_tp = apply( DataList[["X_xtp"]], MARGIN=2:3, FUN=var )
+  if( any(c("X_xtp","X_itp") %in% names(DataList)) ){
+    if( "X_xtp" %in% names(DataList) ){
+      Var_p = apply( DataList[["X_xtp"]], MARGIN=3, FUN=function(array){var(as.vector(array))})
+      Var_tp = apply( DataList[["X_xtp"]], MARGIN=2:3, FUN=var )
+    }
+    if( "X_itp" %in% names(DataList) ){
+      Var_p = apply( DataList[["X_itp"]], MARGIN=3, FUN=function(array){var(as.vector(array))})
+      Var_tp = apply( DataList[["X_itp"]], MARGIN=2:3, FUN=var )
+    }
     if( "gamma1_tp" %in% names(TmbParams) ){
       Map[["gamma1_tp"]] = Map[["gamma2_tp"]] = matrix( 1:(DataList$n_t*DataList$n_p), nrow=DataList$n_t, ncol=DataList$n_p )
       # By default:

diff --git a/R/Plot_Overdispersion.R b/R/Plot_Overdispersion.R