runAll: Function for running all combinations of parameters of a...

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

Description

Function for running all combinations of parameters of a survey stored in the spec, which is a data frame with one row per run.

Usage

runAll(
  spec,
  run,
  dir,
  surveyPar,
  seed = 1,
  nboot = 100,
  radius = 10,
  subset = "all",
  ...
)

Arguments

spec	A data frame of the specifications of res and year (these are linked in the current PELFOSS framework), dateshift and reversed.
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).
surveyPar	A list of survey parameters as returned from setSurveyParametersPaper1.
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).
nboot	Number of bootstrap replicates.
radius	A vector of one or two elements giving the radius inside which to sample trawl stations, and the radius inside which to estimate the parameters a, b and L in the length-weight relationship. If only one element is given, the length-weight relationship is estimated from all adult super individuals.
subset	Either "all" (the default) or an integer vector giving the subset of the simulations to run.
...	Additional inputs overriding the defaults returned by pelfossDefaults().

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