#outDir<-"C:/Users/Elizabeth A Babcock/Box/Shrimp trawl bycatch/bycatchEstimatorRuns/Output SawfishSetNoPool" setupObj<-readRDS(file=paste0(outDir,"/",Sys.Date(),"_BycatchModelSpecification.rds")) library(tidyverse) library(kableExtra) theme_set(theme_bw()) #Unpack setupObj modelTry<-obsdat<-logdat<-yearVar<-obsEffort<-logEffort<-logUnsampledEffort<- includeObsCatch<-matchColumn<-factorNames<-randomEffects<-randomEffects2<- EstimateIndex<-EstimateBycatch<-logNum<-sampleUnit<-complexModel<-simpleModel<-indexModel<- designMethods<-designVars<-designPooling<-poolTypes<-pooledVar<-adjacentNum<- minStrataUnit<- baseDir<-runName<-runDescription<- common<-sp<-obsCatch<-catchUnit<-catchType<-NULL numSp<-modelTable<-modelSelectTable<-modFits<-modPredVals<-modIndexVals<-residualTab<-bestmod<-predbestmod<-indexbestmod<-allmods<-allindex<- modelFail<-rmsetab<-metab<-dat<-yearSum<-requiredVarNames<-allVarNames<-indexDat<-strataSum<-NumCores<-NULL for(r in 1:NROW(setupObj$bycatchInputs)) assign(names(setupObj$bycatchInputs)[r], setupObj$bycatchInputs[[r]]) for(r in 1:NROW(setupObj$bycatchOutputs)) assign(names(setupObj$bycatchOutputs)[r],setupObj$bycatchOutputs[[r]]) numericalVars<-c("Effort",allVarNames[!allVarNames %in% factorNames]) obsdat<-mutate(obsdat,SampleUnits=1) ##Function to plot by species makeObserverPlots<-function(spNum,figurenum) { ## Show where species was caught in observer data obsdatTemp <-obsdat %>% rename(Catch=!!obsCatch[spNum]) %>% mutate(Present=factor(ifelse(Catch>0,1,0)), CPUE=Catch/Effort) # Presence/absence across years cat("\n Figure ", figurenum,". Presence and absence of",common[spNum], "in each year. \n",sep="") print(ggplot(obsdatTemp,aes(x=Year,fill=Present))+ geom_bar()+ scale_fill_manual(values=c("grey","red"))+ ylab(paste0("Count of observed ",sampleUnit))) figurenum<-figurenum+1 # Presence/absence across all factors cat("\n") cat("\n Figure ", figurenum,". Presence and absence of ",common[spNum], " across factor variables. \n",sep="") temp<-obsdatTemp %>% pivot_longer(cols=all_of(factorNames),names_to="Variable",values_to = "Level") print(ggplot(temp,aes(x=Level,fill=Present))+ geom_bar()+ facet_wrap(Variable~.,scales="free")+ scale_fill_manual(values=c("grey","red"))+ ylab(paste0("Count of observed ",sampleUnit))) figurenum<-figurenum+1 # Presence/absence across numerical variables and effort cat("\n") cat("\n Figure ", figurenum,". Presence and absence of ",common[spNum], " across numerical variables. \n",sep="") temp<-obsdatTemp %>% pivot_longer(cols=all_of(c("Effort",numericalVars)),names_to="Variable",values_to = "Value") print(ggplot(temp,aes(x=Value,fill=Present))+ geom_histogram()+ facet_wrap(Variable~.,scales="free")+ scale_fill_manual(values=c("grey","red"))+ ylab(paste0("Count of observed ",sampleUnit))) figurenum<-figurenum+1 #CPUE cat("\n") cat("\n Figure ",figurenum,". Observed CPUE of ",common[spNum], " by factor levels.\n",sep="") temp<-obsdatTemp %>% pivot_longer(cols=all_of(factorNames),names_to="Variable",values_to = "Level") print(ggplot(temp,aes(x=Level,y=CPUE))+ geom_violin(fill="grey")+ facet_wrap(Variable~.,scales="free")+ stat_summary()) figurenum<-figurenum+1 cat("\n") cat("\n Figure ",figurenum,". Observed CPUE of",common[spNum], " across numerical variables. \n",sep="") temp<-obsdatTemp %>% pivot_longer(cols=all_of(numericalVars),names_to="Variable",values_to = "Value") print(ggplot(temp,aes(x=Value,y=CPUE))+ geom_point(alpha=0.3)+ stat_smooth()+ facet_wrap(Variable~.,scales="free")) figurenum } #Compare observed and logbook makeEffortPlots<-function(figurenum) { allData<-bind_rows(list(observer=select(obsdat,all_of(c(allVarNames,"Effort","SampleUnits"))), effort=select(logdat,all_of(c(allVarNames,"Effort","SampleUnits")))), .id = "Source")%>% pivot_longer(cols=all_of(factorNames),names_to="Variable",values_to = "Level") cat("\n") cat("\n Figure ",figurenum,". Total Effort by factor levels, observed and total. \n",sep="") print(ggplot(allData,aes(x=Level,weight=Effort,fill=Source))+ geom_bar(position=position_dodge())+ facet_wrap(Variable~.,ncol=2,scales="free")+ scale_fill_manual(values=c("grey","black"))+ ylab(paste0("Sum of effort"))) figurenum<-figurenum+1 cat("\n") cat("\n Figure ",figurenum,". Count of ",sampleUnit," by factor levels, observed and total. \n",sep="") print(ggplot(allData,aes(x=Level,weight=SampleUnits,fill=Source))+ geom_bar(position=position_dodge())+ facet_wrap(Variable~.,ncol=2,scales="free")+ scale_fill_manual(values=c("grey","black"))+ ylab(paste0("Count of ",sampleUnit))) figurenum<-figurenum+1 logdatTemp<-logdat %>% mutate(Effort=Effort/SampleUnits) %>% uncount(SampleUnits) allData<-bind_rows(list(observer=select(obsdat,all_of(c(allVarNames,"Effort"))), effort=select(logdatTemp,all_of(c(allVarNames,"Effort")))), .id = "Source")%>% pivot_longer(cols=all_of(numericalVars),names_to="Variable",values_to = "Value") cat("\n") cat("\n Figure ",figurenum,". Effort across numerical variables. \n",sep="") print(ggplot(allData,aes(x=Value,fill=Source))+ geom_histogram(position=position_dodge())+ facet_wrap(Variable~.,ncol=2,scales="free")+ scale_fill_manual(values=c("grey","black"))+ ylab(paste0("Count of ",sampleUnit))) figurenum<-figurenum+1 figurenum }
Summary of data for r runDescription
, r Sys.Date()
if(!"Year" %in% factorNames) { obsdat$Year<-obsdat$Year+startYear logdat$Year<-logdat$Year+startYear } fignum<-makeEffortPlots(1)
Table 1. Observed and unobserved effort by r sampleUnit
.
temp<-bind_rows(list(observer=select(obsdat,Effort), effort=select(logdat,Effort)), .id = "Source") %>% group_by(Source) %>% summarize(`Sample units` = n(), `Total effort`=sum(Effort))%>% mutate(`Proportion units`=round(`Sample units`/sum(`Sample units`),3), `Proportion effort`=round(`Total effort`/sum(`Total effort`),3)) kbl(temp,format="simple")
for(i in 1:numSp) { fignum<-makeObserverPlots(i,fignum) }
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.