plotAbundance: Plot abundance results to the graphics device or to a file

In Sea2Data/Rstox: Running Stox functionality independently in R

Description

Plots boxplot of bootstrap results together with Coefficient of Variation (CV).

Usage

plotAbundance(projectName, bootstrapMethod = "AcousticTrawl",
  var = "Abundance", unit = NULL, baseunit = NULL, grp1 = "age",
  grp2 = NULL, xlab = NULL, ylab = NULL, main = "",
  format = "png", log = NULL, filetag = NULL, ...)

plotAbundance_AcousticTrawl(projectName, var = "Abundance",
  unit = NULL, baseunit = NULL, grp1 = "age", grp2 = NULL,
  xlab = NULL, ylab = NULL, main = "", format = "png", maxcv = 1,
  log = NULL, filetag = NULL, ...)

plotAbundance_SweptAreaTotal(projectName, unit = NULL, baseunit = NULL,
  xlab = NULL, ylab = NULL, main = "", format = "png",
  log = NULL, filetag = NULL, ...)

factorNAfirst(x)

Arguments

projectName	The name or full path of the project, a baseline object (as returned from getBaseline or runBaseline, og a project object (as returned from openProject).
bootstrapMethod	The bootstrap method used to generate the data.
var	A key string indicating the variable to plot (see getPlottingUnit()$defaults$Rstox_var for available values). For plotAbundance_SweptAreaTotal() var is hard coded to "Count"
unit	A unit key string indicating the unit, or alternatively a numeric value giving the scaling factor (run getPlottingUnit() to see available values).
baseunit	The unit used in the data.
grp1	Variable used to group results, e.g. "age", "LenGrp", "sex"
grp2	An optional second grouping variable
xlab	The label to user for the x axis, with default depending on data plotted,
ylab	The label to user for the y axis, with default depending on data plotted.
main	Main title for plot (text)
format	The file format of the saved plot, given as a string naming the function to use for saving the plot (such as bmp, jpeg, png, tiff), with filename as its first argument. Arguments fo the functions are given as .... Dimensions are defaulted to width=5000, height=3000, , resolution to 500 dpi. If format has length 0, the plot is shown in the graphics window, and not saved to file.
log	Character string giving the axes to apply log10() to, or TRUE to indicate log="y".
filetag	A character string to append to the file name (before file extension).
...	Parameters passed on from other functions. Includes numberscale, which is kept for compability with older versions. Please use 'unit' instead. (Scale results with e.g. 1000 or 1000000).
maxcv	The maximum cv in the plot. Use Inf to indicate the maximum cv of the data.

Value

Plot saved to file and abundance table printed

Examples

projectName <- "Test_Rstox"
plotAbundance(projectName, grp1="age")
plotAbundance(projectName, grp1="age", unit=1)

Sea2Data/Rstox documentation built on May 14, 2019, 8:58 a.m.