couple small changes for multiple Ecov

R/prepare_wham_input.R

@@ -677,7 +677,7 @@ without changing ASAP file, specify M$initial_means.")
     data$Ecov_model <- sapply(ecov$process_model, match, c("rw", "ar1"))
 
   #  data$n_Ecov_pars <- c(1,3)[data$Ecov_model] # rw: 1 par (sig), ar1: 3 par (phi, sig)
-    if(!ecov$where %in% c('recruit','M')){
+    if(!any(ecov$where %in% c('recruit','M'))){
       stop("Sorry, only ecov effects on recruitment and M currently implemented.
       Set ecov$where = 'recruit' or 'M'.")
     }
@@ -735,14 +735,14 @@ Ecov years: ", data$year1_Ecov, " to ", end_Ecov,"
 
       if(data$Ecov_where[i] == 1){ # recruitment
         cat(paste0("Ecov ",i,": ",ecov$label[i],"
-",c('*NO*','Controlling','Limiting','Lethal','Masking','Directive')[data$Ecov_how+1]," (",ecov_str[[i]],") effect on: ", c('recruitment','M')[data$Ecov_where[i]],"
+",c('*NO*','Controlling','Limiting','Lethal','Masking','Directive')[data$Ecov_how[i]+1]," (",ecov_str[[i]],") effect on: ", c('recruitment','M')[data$Ecov_where[i]],"
 
 In model years:
 "))
       }
       if(data$Ecov_where[i] == 2){ # M
         cat(paste0("Ecov ",i,": ",ecov$label[i],"
-",ecov_str[[i]]," effect on: ", c('recruitment','M')[data$Ecov_where[i]],"
+",c('*NO*',ecov_str[[i]])[data$Ecov_how[i]+1]," effect on: ", c('recruitment','M')[data$Ecov_where[i]],"
 
 In model years:
 "))
@@ -753,8 +753,10 @@ lastyr <- tail(years,1)
 cat(paste0("Lag: ",data$Ecov_lag[i],"
 Ex: ",ecov$label[i]," in ",years[1]," affects ", c('recruitment','M')[data$Ecov_where[i]]," in ",years[1+data$Ecov_lag[i]],"
     ",ecov$label[i]," in ",lastyr," affects ", c('recruitment','M')[data$Ecov_where[i]]," in ",lastyr+data$Ecov_lag[i],"
+
 "))
     }
+    data$Ecov_label <- list(data$Ecov_label)
   } # end load Ecov
 
   # add vector of all observations for one step ahead residuals ==========================
@@ -1003,7 +1005,7 @@ Ex: ",ecov$label[i]," in ",years[1]," affects ", c('recruitment','M')[data$Ecov_
   for(j in 1:data$n_Ecov){
     tmp[,j] <- ifelse(data$Ecov_how[j]==0, NA, 0)
     for(i in 1:max.poly){
-      if(i > data$Ecov_poly) tmp[i,j] = NA
+      if(i > data$Ecov_poly[j]) tmp[i,j] = NA
     }
   }
   ind.notNA <- which(!is.na(tmp))

R/wham_plots_tables.R

@@ -202,7 +202,7 @@ plot.osa.residuals <- function(mod, do.tex=FALSE, do.png=FALSE, fontfam="", res=
       abline(h=0, col=plot.colors[f], lwd=2)
 
       # 2. trend vs. fitted val
-      plot(tmp$pred, tmp$residual, type='p', col=plot.colors[f], pch=19, xlab=paste0("Predicted ", mod$env$data$Ecov_label[f]), ylab="OSA Residuals",
+      plot(tmp$pred, tmp$residual, type='p', col=plot.colors[f], pch=19, xlab=paste0("Predicted ", mod$env$data$Ecov_label[[1]][f]), ylab="OSA Residuals",
            ylim=ylims)
       abline(h=0, col=plot.colors[f], lwd=2)
 
@@ -231,7 +231,7 @@ plot.osa.residuals <- function(mod, do.tex=FALSE, do.png=FALSE, fontfam="", res=
       lines(z, upper, lty=2, col=plot.colors[f])
       lines(z, lower, lty=2, col=plot.colors[f])
 
-      title (paste0("OSA residual diagnostics: Ecov ",f," (",mod$env$data$Ecov_label[f],")"), outer=T, line=-1)
+      title (paste0("OSA residual diagnostics: Ecov ",f," (",mod$env$data$Ecov_label[[1]][f],")"), outer=T, line=-1)
       if(do.tex | do.png) dev.off() else par(origpar)
     }
   }
@@ -264,7 +264,7 @@ fit.summary.text.plot.fn <- function(mod){
   text(5,nl <- nl-0.5, paste0("Index Age Comp Models: ", paste(acm[mod$env$data$age_comp_model_indices], collapse = ", ")))
   text(5,nl <- nl-0.5,paste0("Recruitment model: ", recs[mod$env$data$recruit_model]))
   if(!all(mod$env$data$Ecov_model == 0)){
-    for(ec in 1:mod$env$data$n_Ecov) text(5,nl <- nl-0.5, paste0("Environmental effect ", ec,": ", mod$env$data$Ecov_label[ec]," (",env.mod[mod$env$data$Ecov_model[ec]],") on ",env.where[mod$env$data$Ecov_where[ec]], " (", env.how[mod$env$data$Ecov_how[ec]],")"))
+    for(ec in 1:mod$env$data$n_Ecov) text(5,nl <- nl-0.5, paste0("Environmental effect ", ec,": ", mod$env$data$Ecov_label[[1]][ec]," (",env.mod[mod$env$data$Ecov_model[ec]],") on ",env.where[mod$env$data$Ecov_where[ec]], " (", env.how[mod$env$data$Ecov_how[ec]],")"))
   } else {
     text(5,nl <- nl-0.5, "Environmental effects: none")
   }
@@ -612,7 +612,7 @@ plot.all.stdresids.fn = function(mod, do.tex = FALSE, do.png = FALSE, fontfam=""
     }
     xe$row = xe$Label
     xe$Label = factor(xe$Label)
-    levels(xe$Label) = mod$env$data$Ecov_label
+    levels(xe$Label) = mod$env$data$Ecov_label[[1]]
     xe$type = "Ecov"
   }
 
@@ -723,7 +723,7 @@ plot.ecov.stdresids.fn = function(mod, years, do.tex = FALSE, do.png = FALSE, fo
     x <- rbind(x, td)
   }
   x$Ecov = factor(x$Ecov)
-  levels(x$Ecov) = mod$env$data$Ecov_label
+  levels(x$Ecov) = mod$env$data$Ecov_label[[1]]
   names(plot.colors) = levels(x$Ecov)
   ggp = ggplot2::ggplot(x, ggplot2::aes(x=Year, y = Stdres, color=Ecov)) +
     ggplot2::geom_line(size=1.1) +