library(knitr) output <- opts_knit$get("rmarkdown.pandoc.to") usingLatex <- (output=="latex") fig <- local({ i <- 0 ref <- list() list( cap=function(refName, text) { i <<- i + 1 ref[[refName]] <<- i if(! usingLatex) { paste("Figure ", i, ": ", text, sep="") }else{ text } }, ref=function(refName) { ref[[refName]] }) }) tab <- local({ i <- 0 ref <- list() list( cap=function(refName, text) { i <<- i + 1 ref[[refName]] <<- i if(! usingLatex) { paste("Tableau ", i, ": ", text, sep="") }else{ text } }, ref=function(refName) { ref[[refName]] }) })
\begin{centering} \section{Fit of catch data} \end{centering}
pic = plot(object, what = "output", var = "totalCatch", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Catch in kt", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) } else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "catchResidualsByFleet", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Residuals", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "absoluteResidualCatchByFleet", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "model - obs", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1.5, 1)))) }else{ do.call(grid.arrange, pic) }
# pic = plot(object, what = "output", var = "residualsCatchAtLengthByFleet", # scales = list(x = list(cex = 2), y = list(cex = 2)), # main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "model - obs", cex = 2), # plot = FALSE) # if(length(pic) != 1){ # do.call(grid.arrange, c(pic, list(heights = c(1.5, 1)))) # }else{ # do.call(grid.arrange, pic) # }
# pic = plot(object, what = "output", var = "lengthFitsCatch", # scales = list(x = list(cex = 2), y = list(cex = 2)), # main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "model - obs", cex = 2), # plot = FALSE) # if(length(pic) != 1){ # do.call(grid.arrange, c(pic, list(heights = c(1.5, 1)))) # }else{ # do.call(grid.arrange, pic) # }
pic = plot(object, what = "output", var = "predictedObservedCatchesByFleet", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Thousands tons", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
\newpage \begin{centering} \section{Fit of survey data} \end{centering} \vspace{2cm}
pic = plot(object, what = "output", var = "predictedObservedIndices", scales = list(x = list(cex = 1), y = list(cex = 1)), main = "", xlab = list(label = "Years", cex = 1.5), ylab = list(label = "Normalized index value", cex = 1.5), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "standardizedSurveyResiduals", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Log residuals", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "sdPerInputSeries", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "SD", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
\newpage \begin{centering} \section{Fleet and Survey Sel and $F$} \end{centering} \vspace{2cm}
pic = plot(object, what = "output", var = "selectivityFisheryByPentad", scales = list(x = list(cex = 1), y = list(cex = 1)), main = "", xlab = list(label = "Age", cex = 2), ylab = list(label = "Selectivity", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "selectivitySurveyByPentad", scales = list(x = list(cex = 1), y = list(cex = 1)), main = "", xlab = list(label = "Age", cex = 2), ylab = list(label = "Selectivity", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(2, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "fAtAGe", scales = list(x = list(cex = 0.5), y = list(cex = 0.5)), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "fProportionAtAGe", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Proportion of F at age", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "nAtAGe", scales = list(x = list(cex = 0.5), y = list(cex = 0.5)), main = "", xlab = list(label = "Years", cex = 1), ylab = list(label = "N at Age", cex = 1), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "nProportionAtAGe", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Proportion of N at age", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1.5, 1)))) }else{ do.call(grid.arrange, pic) }
# pic = plot(object, what = "output", var = "fisheryMeanLength", # scales = list(x = list(cex = 2), y = list(cex = 2)), # main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "model - obs", cex = 2), # plot = FALSE) # if(length(pic) != 1){ # do.call(grid.arrange, c(pic, list(heights = c(1.5, 1)))) # }else{ # do.call(grid.arrange, pic) # }
\newpage \begin{centering} \section{Stock summary} \end{centering} \vspace{2cm}
pic = plot(object, what = "output", var = "summarySheet2", scales = list(x = list(cex = 1), y = list(cex = 1)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "data", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "uncertaintyKeyParams", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "CV", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "matureInmatureFishes", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Biomass in kt", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "stockRecruitment", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Spawning Stock Biomass", cex = 2), ylab = list(label = "Recruitment", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
pic = plot(object, what = "output", var = "fishedUnfishedBiomass", scales = list(x = list(cex = 2), y = list(cex = 2)), main = "", xlab = list(label = "Years", cex = 2), ylab = list(label = "Total Biomass", cex = 2), plot = FALSE) if(length(pic) != 1){ do.call(grid.arrange, c(pic, list(heights = c(1, 1)))) }else{ do.call(grid.arrange, pic) }
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