runPelfoss: Run the PELFOSS framework.

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

Description

This function runs the entire PELFOSS framework from the NORWECOM model output files (biomass in a grid and superindividuals), through surveyPlaner() and StoX to the estimated total stock biomass compared to the corresponding theoretical values:

Usage

runPelfoss(
  dir,
  run = "Run1",
  biomass = NULL,
  superind = NULL,
  surveyPar = list(),
  year = 2010,
  res = 4,
  dateshift = 0,
  reversed = FALSE,
  seed = 0,
  projectName = "PELFOSS_Project_StoX",
  nboot = 10,
  xsd = list(acoustic = "1", biotic = "1.4"),
  format = "png",
  ...
)

Arguments

dir	The directory holding the NORWECOM files, the stratum files and the output xml files from the function (temporary stored for insertion into the StoX project).
run	The name of the run, which could be used to reflect the input parameters, such as "Run1_parallel" or "Run1_zigzag".
biomass, superind	The biomass and superind data read from readNcVarsAndAttrs (used in readNorwecomBiomass and readNorwecomSuperind).
surveyPar	A list of parameters to be used as input to biomass2tsb (see ?biomass2tsb).
year, res	The year and resolution (in km) to run. The NORWECOM files are located in the following folder structure: species / resolution / year, where the resolution folders has names such as "res_4km".
dateshift	An integer number of days to shift the survey by, negative values shifting to earlier in the year.
reversed	Logical: If TRUE run the survey in the opposite direciton.
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).
projectName	The name or full path of the StoX project of the simulated survey.
nboot	Number of bootstrap replicates.
xsd	A named list of xsd versions of the acoustic and biotic file format.
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.
...	Additional inputs overriding the defaults returned by pelfossDefaults().

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