plotPelfossReports: Function for plotting the PELFOSS report form one PELFOSS...

In Sea2Data/pelfoss: Simulate acosutic-trawl surveys and produce survey estimated using Rstox

Description

Function for plotting the PELFOSS report form one PELFOSS run.

Usage

plotPelfossReports(
  run,
  dir,
  var = c("TSB_5percentByInsideAll", "TSB_meanByInsideAll", "TSB_95percentByInsideAll"),
  seed = NULL,
  ylim = NULL,
  subdir = TRUE,
  case_adj = c(0.15, 0.95),
  add.cv = FALSE,
  width = NA,
  height = NA,
  adds = list(),
  report = NULL,
  face = NULL
)

Arguments

run	The name of the simulation run (which is three timings (-30, 0, +30 days), two directions (normal, reversed), and two resolutions (low, high), in total 12 individual runs).
dir	The directory of the PELFOSS folder structure (see getPelfossSkeleton).
seed	A single integer, or a list of seeds used in the funciton, including the following seeds: ('transect') for drawing transects using surveyPlanner(), ('trawl') for drawing trawl stations along the transects with probability as a funciton of the NASC (see probfact), and ('bootstrap') for getting the final estimate using runBootstrap() (see nboot).
ylim	The ylim of the plot, useful for setting the same ylim on several related plots.
subdir	The folder in which to put the plots in the "reports" folder of dir. If TRUE this is interpreted as "allPlots".
case_adj	A two element vector giving the adjustment of the labels of each survey (A, B, ...).
by	A string specifying which variable to plot. The options are "Inside" (only inside the strata with positive NASC), InsideAll (inside the strata used in the survey) and "Total" (all possible strata in the strata system).

Sea2Data/pelfoss documentation built on Dec. 7, 2020, 12:31 a.m.