R/newCode.R

In beast-dev/RBeast: Create BEAST and BEAST2 input files and parse their output

######################################################################
#### functions for package

readInputData <- function(file, sep) {
  inputData <-
    utils::read.csv(
      file,
      header = TRUE,
      stringsAsFactors = FALSE,
      sep = sep ,
      check.names = FALSE
    )
  cat(paste(
    "Have read table with",
    nrow(inputData),
    "lines and",
    ncol(inputData),
    "columns.\n"
  ))
  return(as.data.frame(inputData))
}


addTimeScaleToData <- function(iT, fT, data) {
  time <-  seq(iT, fT, length.out = nrow(data))
  data <-  cbind(time = time, data)
  cat(paste(
    "Have added a time scale ",
    iT,
    "-",
    fT,
    "(",
    nrow(data),
    "steps )\n"
  ))
  return(data)
}



demo <- function() {
  ######################################################################
  #### user code

  #sorting out data

  filename <- "~/Desktop/Trinidad/LTT/fractionOfPopsize2.txt"
  separator <- "\t"
  itime <- 1920
  ftime <- 2008

  data <-  readInputData(file = filename, sep = separator)
  data <- addTimeScaleToData(iT = itime, fT = ftime, data = data)
  nDataCols <-
    ncol(data) - 1 #how many data columns we have, excluding time

  # source("~/Desktop/Trinidad/LTT/plotStackedAreas.R")

  #examples of plotting

  #normal plot, little options
  plotStackedAreas(data,
                   stacked100 = FALSE,
                   ylab = "variable",
                   xlab = "time")

  #stacked plot, little options
  plotStackedAreas(data,
                   stacked100 = TRUE,
                   ylab = "relative variable",
                   xlab = "time")

  ### Load the package or install if not present
  #     if (!require("RColorBrewer")) {
  #       install.packages("RColorBrewer")
  #       library(RColorBrewer)
  #     }

  #stacked plot, working with options
  #myColours= brewer.pal(8,"Set1")
  myColours = (grDevices::rainbow(nDataCols, start = 0.11))
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours #use area colours to hide borders
  )


  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = TRUE,
    #add white area around?
    main = "with axis margins"
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  myOrder = sample(1:nDataCols, nDataCols) #random selection of data columns
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    order = myOrder,
    #choose order to plot data
    main = "with data using random order"
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    main = "playing with legends",
    #add title
    addLegend = "topright" #add a legend to it by giving position to use
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    main = "playing with legends",
    #add title
    addLegend = "topright",
    #add a legend to it
    legend.cex = 0.85 #edit legend: change font size
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    main = "playing with legends",
    #add title
    boxlwd = 2,
    #add a nice border to the entire plot
    addLegend = "topright",
    #add a legend to it
    legend.cex = 0.85,
    #edit legend: change font size
    legend.bg = "white" #edit legend: bg colour
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    main = "playing with legends",
    #add title
    boxlwd = 2,
    #add a nice border to the entire plot
    addLegend = "topright",
    #add a legend to it
    legend.cex = 0.85,
    #edit legend: change font size
    legend.bg = "white",
    #edit legend: bg colour
    file = "myoutoutfilename",
    #choose to export this plot to a PDF file
    pdfW = 5.5,
    #choose width of PDF
    pdfH = 5  #choose height of PDF
  )

  #stacked plot, working with options
  myColours = grDevices::rainbow(nDataCols, start = 0.11)
  myColours[length(myColours)] = "white"
  plotStackedAreas(
    data,
    stacked100 = TRUE,
    ylab = "relative variable",
    xlab = "time",
    colours = myColours,
    #choose colours
    areaBorderCol = myColours,
    #use area colours to hide borders
    addAxisSpace = FALSE,
    #add white area around?
    main = "final example",
    #add title
    boxlwd = 2,
    #add a nice border to the entire plot
    addLegend = "topright",
    #add a legend to it
    legend.cex = 0.85,
    #edit legend: change font size
    legend.bg = "white",
    #edit legend: bg colour
    legend.pt.cex = 1.5,
    #scalling of points in legend
    file = "myoutoutfilename",
    #choose to export this plot to a PDF file
    pdfW = 5.5,
    #choose width of PDF
    pdfH = 5  #choose height of PDF
  )

}