update run_SSMSE_iter to account for naming convention of sample_stru…

…ct SS3 input files

R/runSSMSE.R

@@ -522,6 +522,19 @@ run_SSMSE_iter <- function(out_dir = NULL,
   assertive.types::assert_is_any_of(nscen, c("integer", "numeric"))
   if (!is.null(sample_struct)) {
     assertive.types::assert_is_list(sample_struct)
+    ## Added lines below to account for different naming conventions  
+    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(!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(!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 {
     if (MS == "EM") {