R/cpue-class.R

In CriscelyLP/imarpe:

# plot.fishery

print.cpue = function(x, language="spanish"){

  if(language == "english"){
    cat("Data from: ", sQuote(x$info$file), "\n", sep="")
    cat("Number of records: ", x$info$records, "\n", sep="")
    cat("Number of months of data: ", x$info$months, "\n", sep="")
    cat("Number of years of data: ", x$info$years, "\n", sep="")
    cat("Number of ports of data: ", x$info$ports, "\n", sep="")
    cat("Analyzed species: ", x$info$sp, "\n", sep="")
    cat("Effort type: ", x$info$efforType, "\n", sep="")
  } else {
    cat("Datos de : ", sQuote(x$info$file), "\n", sep="")
    cat("Numero de registros: ", x$info$records, "\n", sep="")
    cat("Numero de meses de la data: ", x$info$months, "\n", sep="")
    cat("Numero de ahnos de la data: ", x$info$years, "\n", sep="")
    cat("Numero de puertos: ", x$info$ports, "\n", sep="")
    cat("Especie analizada: ", x$info$sp, "\n", sep="")
    cat("Tipo de esfuerzo: ", x$info$efforType, "\n", sep="")
  }

  return(invisible())
}


summary.cpue = function(object, language = "spanish"){

  object2 = object
  if(language=="spanish"){
    object2$data$month = engToSpa(object2$data$month)
    colnames(object2$data) = c("anho", "mes", "dia", "cpue")

    object2$dataPortDay$month = engToSpa(object2$dataPortDay$month)
    colnames(object2$dataPortDay)[1:3] = c("anho", "mes", "dia")

  } else{
    object2$data$month = object2$data$month
    colnames(object2$data) = c("year", "month", "day", "cpue")
  }

  output = list()
  output$portDay =  object2$dataPortDay
  output$day     =  object2$data
  output$port    =  object2$dataPort
  output$months  =  .getMonth.cpue(object = object, language = language)
  output$years   =  .getYear.cpue(object = object)

  class(output) = "summary.cpue"
  return(output)
}


print.summary.cpue = function(x, language = "spanish"){

  x2 = x
  class(x2) = 'cpue'

  if(language == "english"){
    cat("\nCPUE by port and day (non-zero only):\n\n") ; print(x$portDay[x$portDay[,1]>0, ,drop=FALSE])
    cat("\nCPUE by day:\n\n") ; print(x$day)
    cat("\nCPUE by port (non-zero only):\n\n") ; print(x$port[x$port[,1]>0, ,drop=FALSE])
    cat("\nMonthly CPUE:\n\n") ; print(t(x$months))
    cat("\nAnnual CPUE:\n\n") ; print(x$years)}
  else {
    cat("\nCPUE por puerto y dia (solo positivos):\n\n") ; print(x$portDay[x$portDay[,1]>0, ,drop=FALSE])
    cat("\nCPUE por dia:\n\n") ; print(x$day)
    cat("\nCPUE por puerto (non-zero only):\n\n") ; print(x$port[x$port[,1]>0, ,drop=FALSE])
    cat("\nCPUE mensual:\n\n") ; print(t(x$months))
    cat("\nCPUE anual:\n\n") ; print(x$years)}

  return(invisible())
}


plot.cpue = function(x, language, ploType = NULL, daysToPlot = c(1,8,15,22), textAxis2 = NULL, textAxis4 = NULL, ...){

  if(is.null(ploType)) ploType = "plotDaily"
  if(ploType %in% c("plotNC", "plotS")){
    x2 = list()
    x2$data = x$dataPortDay
    x2$info$varType = x$info$varType
    x2$info$efforType = x$info$efforType

    dataRegion = .getRegionData(x = x2)}

  switch(ploType,
         plotDaily   = .plotDays.cpue(x=x, language=language, daysToPlot = daysToPlot,
                                     textAxis2 = textAxis2, textAxis4 = textAxis4, ...),
         plotMonthly = .plotMonths.cpue(x=x, language=language, ...),
         plotYearly  = .plotYears.cpue(x=x, language=language, ...),
         plotNC      = .plotRegion(x = dataRegion, region = "NC", daysToPlot = daysToPlot,
                                   textAxis2 = textAxis2, textAxis4 = textAxis4, ...),
         plotS       = .plotRegion(x = dataRegion, region = "S", daysToPlot = daysToPlot,
                                   textAxis2 = textAxis2, textAxis4 = textAxis4, ...))

  return(invisible())
}


report = function(x, ...) {
  UseMethod("report")
}


report.cpue = function(x, format = "latex", tangle=FALSE, output = NULL, daysToPlot = c(1,8,15,22),
                       textAxis2 = NULL, textAxis4 = NULL){

  if(is.null(output)) output = getwd()
  outputName = deparse(substitute(x))

  skeleton = system.file("reports", "cpue-report.Rmd", package = "imarpe")

  if(isTRUE(tangle)) {
    knit(skeleton, tangle=TRUE, encoding = "latin1")
    f1 = gsub(pattern = ".Rmd", replacement = "\\.R", skeleton)
    file.rename(from=basename(f1), to=paste0(outputName, ".R"))
  }

  outputFile = paste0(outputName, "_output.pdf")
  render(skeleton, c("pdf_document"), output_file=outputFile, output_dir=output, encoding = "latin1")

  if(isTRUE(open)) shell.exec(outputFile)

  return(invisible(file.path(output, outputFile)))

}