knitr::opts_chunk$set(echo=FALSE, error=FALSE, message=FALSE, warning=FALSE, dpi=300,fig.width=6.5,fig.height=3.9)
require(pander); require(ggplot2); require(ggthemes); require(reshape2); require(rTCSAM2013); require(wtsUtilities); panderOptions("table.caption.prefix","Table ") panderOptions("table.split.table",Inf) paths<-params$paths; obj<-params$obj; numRecent<-params$numRecent; plot1stObs<-as.logical(params$plot1stObs); figno<-1; tblno<-1; cat("Working dir = '",getwd(),"'\n\n");
if (is.null(obj)){ if (!is.character(paths)){ cat("'paths' parameter is not a character vector!\n"); stop(); } obj<-list(); for (case in names(paths)){ cat(case,": '",paths[case],"'\n",sep=''); res<-getResLst(inp.dir=paths[case]); if (is.null(res)) { #remove path from paths paths<-paths[names(paths)!=case]; } else { #add res to obj list obj[[case]]<-res; } rm(res); } } else { obj<-convertToListOfResults(obj); } cases<-names(obj); ncases<-length(cases);
if (!is.null(paths)){ t<-as.data.frame(list(case=cases, path=getSubPaths(paths,last=3))); t$path<-paste0("'",t$path,"'"); } else { t<-as.data.frame(list(case=cases)); } row.names(t)<-NULL; pander(t,caption=paste0(tblno,". Model cases for comparison.")); tblno<-tblno+1;
plots<-compareModelResults.ObjFunComponents(obj,y='objFun', showPlot=FALSE); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
if (length(cases)>1){ plots<-compareModelResults.ObjFunComponents(obj,y="diff", showPlot=FALSE); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots); } else { cat("No differences plotted: only one model case considered.\n") }
If available, parameter confidence intervals are +/- one standard deviation. Triangles indicate initial prameter values, circles represent final parameter values. Dark grey shading indicates parameter bounds (if any).
plots<-compareModelResults.Params(obj, showPlot=FALSE);
ps<-plots[["population"]][["recruitment"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["population"]][["recruitment devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["population"]][["initial recruitment devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["population"]][["natural mortality multipliers"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["population"]][["growth"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["population"]][["molt-to-maturity: females"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["population"]][["molt-to-maturity: males"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots$surveys[["surveys"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["surveys"]][["survey selectivity"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["fisheries"]][["TCF selectivity"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["fisheries"]][["TCF retention"]]; figno<-(printGGList(ps[[1]],figno=figno,cap=names(ps),show=TRUE))$figno; rm(ps);
ps<-plots[["fisheries"]][["SCF selectivity"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["fisheries"]][["RKF selectivity"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["fisheries"]][["GTF selectivity"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["fisheries"]][["mortality or capture rate"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps);
ps<-plots[["fisheries"]][["TCF mortality or capture rate devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["fisheries"]][["SCF mortality or capture rate devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["fisheries"]][["RKF mortality or capture rate devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; ps<-plots[["fisheries"]][["GTF mortality or capture rate devs"]]; figno<-(printGGList(ps,figno=figno,show=TRUE))$figno; rm(ps,plots);
plots<-compareModelResults.SurveySelFcns(obj); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
Retained mortality or retention (GMacs FMM) functions for males in the directed fishery, pre-1991 and post-1990.
plots<-compareModelResults.FisheryRetFcns(obj); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
Bycatch selectivity functions for females in the directed fishery and males and females in the snow crab, BBRKC fisheries, and groundfish fisheries. Capture and/or total fishing mortality selectivity functions for males in the directed fishery prior to 1991.
plots<-compareModelResults.FisherySelFcns(obj); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
Annual male total-catch capture and/or fishing mortality selectivity functions for the directed fishery starting in 1991/92. The directed fishery was closed during 1997/98-2004/05 and 2010/11-2012/13. During these time periods, the "mean" selectivity function that forms the basis for the annual deviations is shown.
plots<-compareModelResults.FisheryTCFMaleSelFcns(obj); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.PopProcesses(obj); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.PopQuantities(obj, numRecent=numRecent); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.SurveyQuantities(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.SurveyZCs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.SurveyPRs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.SurveyMeanZCs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.FisheryQuantities(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.FisheryZCs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.FisheryPRs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.FisheryMeanZCs(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
plots<-compareModelResults.FisheryRates(obj, numRecent=numRecent, plot1stObs=plot1stObs); figno<-(printGGList(plots,figno=figno,show=TRUE))$figno; rm(plots);
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.