Update renaming section of run_SSMSE_iter to account for input sample…

…_struct with no SE (following failed test)
nmfs-fish-tools · Jan 31, 2024 · 93ff768 · 93ff768
1 parent 132b649
commit 93ff768
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/R/runSSMSE.R b/R/runSSMSE.R
@@ -526,14 +526,14 @@ run_SSMSE_iter <- function(out_dir = NULL,
     if(!is.null(names(sample_struct$catch)[1])){if(names(sample_struct$catch)[1]=="year"){ names(sample_struct$catch)[1]<-"Yr"}}    
     if(!is.null(names(sample_struct$catch)[2])){if(names(sample_struct$catch)[2]=="seas"){ names(sample_struct$catch)[2]<-"Seas"}}   
     if(!is.null(names(sample_struct$catch)[3])){if(names(sample_struct$catch)[3]=="fleet"){ names(sample_struct$catch)[3]<-"FltSvy"}} 
-    if(!is.null(names(sample_struct$catch)[4])){if(names(sample_struct$catch)[4]=="catch_se"){ names(sample_struct$catch)[4]<-"SE"}} 
+    if(ncol(sample_struct$catch)>3){ if(!is.null(names(sample_struct$catch)[4])){if(names(sample_struct$catch)[4]=="catch_se"){ names(sample_struct$catch)[4]<-"SE"}} }
 
     if(!is.null(names(sample_struct$CPUE)[1])){if(names(sample_struct$CPUE)[1]=="year"){ names(sample_struct$CPUE)[1]<-"Yr"}}     
     if(!is.null(names(sample_struct$CPUE)[2])){if(names(sample_struct$CPUE)[2]=="seas"){ names(sample_struct$CPUE)[2]<-"Seas"}}     
     if(!is.null(names(sample_struct$CPUE)[3])){if(names(sample_struct$CPUE)[3]=="index"){ names(sample_struct$CPUE)[3]<-"FltSvy"}}    
-    if(!is.null(names(sample_struct$CPUE)[4])){if(names(sample_struct$CPUE)[4]=="se_log"){ names(sample_struct$CPUE)[4]<-"SE"}}      
+    if(ncol(sample_struct$CPUE)>3){ if(!is.null(names(sample_struct$CPUE)[4])){if(names(sample_struct$CPUE)[4]=="se_log"){ names(sample_struct$CPUE)[4]<-"SE"}} }     
 
-    if(!is.null(names(sample_struct$lencomp)[4])){ if(names(sample_struct$lencomp)[4]=="Gender"){ names(sample_struct$lencomp)[4]<-"Sex"} } 
+    if(!is.null(names(sample_struct$lencomp)[4])){if(names(sample_struct$lencomp)[4]=="Gender"){ names(sample_struct$lencomp)[4]<-"Sex"} } 
     if(!is.null(names(sample_struct$agecomp)[4])){if(names(sample_struct$agecomp)[4]=="Gender"){ names(sample_struct$agecomp)[4]<-"Sex"}} 
     sample_struct <- check_sample_struct(sample_struct)
   } else {