Merge pull request #267 from James-Thorson-NOAA/hotfix

Hotfix for backwards compatibility typos
James-Thorson-NOAA · Dec 10, 2020 · c6c60b7 · c6c60b7
2 parents 93fb399 + 8a714b9
commit c6c60b7
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: VAST
 Type: Package
 Title: Vector-autoregressive spatio-temporal (VAST) model
-Version: 3.6.0
-Date: 2020-09-22
+Version: 3.6.1
+Date: 2020-12-10
 Authors@R: 
     c(person(given = "James",
              family = "Thorson",

diff --git a/R/make_map.R b/R/make_map.R
@@ -219,7 +219,7 @@ function( DataList, TmbParams, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Eps
   if( ("n_f_input"%in%names(DataList)) && "n_v"%in%names(DataList) && DataList[["n_f_input"]]<0 ){
     Map[["L1_z"]] = factor(rep(NA,length(TmbParams[["L1_z"]])))
     Map[["eta1_vf"]] = factor(array(NA,dim=dim(TmbParams[["eta1_vf"]])))
-    Map[["L2_z"]] = factor(rep(NA,length(TmbParams[["L1_z"]])))
+    Map[["L2_z"]] = factor(rep(NA,length(TmbParams[["L2_z"]])))
     Map[["eta2_vf"]] = factor(array(NA,dim=dim(TmbParams[["eta2_vf"]])))
   }
   if( ("OverdispersionConfig"%in%names(DataList)) && "n_v"%in%names(DataList) ){
@@ -287,7 +287,7 @@ function( DataList, TmbParams, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Eps
       }
     }
     Map[["gamma1_j"]] = factor(Map[["gamma1_j"]])
-    Map[["gamma2_j"]] = factor(Map[["gamma1_j"]])
+    Map[["gamma2_j"]] = factor(Map[["gamma2_j"]])
   }
 
   ### Catchability variables
@@ -473,7 +473,7 @@ function( DataList, TmbParams, RhoConfig=c("Beta1"=0,"Beta2"=0,"Epsilon1"=0,"Eps
       for(cI in 1:DataList$n_c){
       for(pI in seq_pos(DataList$n_p1)){
         if(DataList$X1config_cp[cI,pI] %in% c(0,1)) Map[["Xiinput1_scp"]][,cI,pI] = NA
-        if(DataList$X1config_cp[cI,pI] %in% c(0,1)) Map[["Xiinput2_scp"]][,cI,pI] = NA
+        if(DataList$X2config_cp[cI,pI] %in% c(0,1)) Map[["Xiinput2_scp"]][,cI,pI] = NA
       }}
     }
     if( all(c("X1config_cp","X2config_cp") %in% names(DataList)) ){

diff --git a/R/make_model.R b/R/make_model.R
@@ -216,7 +216,7 @@ function( TmbData,
   }
   if( ("OverdispersionConfig"%in%names(TmbData)) ){
     if( TmbData[["OverdispersionConfig"]][1]==0 ) Bounds = boundsifpresent_fn( par=Obj$par, name="L1_z", lower=c(-Inf,-0.99), upper=c(Inf,0.99), bounds=Bounds)
-    if( TmbData[["OverdispersionConfig"]][1]==0 ) Bounds = boundsifpresent_fn( par=Obj$par, name="L2_z", lower=c(-Inf,-0.99), upper=c(Inf,0.99), bounds=Bounds)
+    if( TmbData[["OverdispersionConfig"]][2]==0 ) Bounds = boundsifpresent_fn( par=Obj$par, name="L2_z", lower=c(-Inf,-0.99), upper=c(Inf,0.99), bounds=Bounds)
   }
   #for(i in 1:4){
   #  if( TmbData[["FieldConfig"]][i]==0 ){