pelfossDefaults: Utility functions of the pelfoss package.

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

Description

pelfossDefaults Defines default values which can be overridden by the ... option in runPelfoss.

getPelfossPaths Given a root directory of a pelfoss folder structure (see ?pelfoss) and a survey name, this function returns the paths to biomass and superind NetCDF4-files, stratum polygons, fishery data files (any data format) of the species as interpreted from the survey name. .

Usage

pelfossDefaults()

getPelfossSkeleton(dir, run = "Run1")

getPelfossPaths(
  dirs,
  run = "Run1",
  survey = "Herring_IESNS",
  year = 2010,
  res = 4,
  reversed = FALSE,
  dateshift = 0,
  seed = 0
)

createPelfossSkeleton(dir, run = "Run1")

fitLengthWeightSuperind(
  superindDay,
  superind,
  count = "inumb",
  superindFilter = NULL,
  stratumPolygons = NULL,
  a = NULL,
  b = NULL,
  transectsXyOfDay = NULL,
  insideRange = NULL
)

fitLengthWeight(L, W = NULL, a = NULL, b = NULL, count = NULL, filter = NULL)

plotLengthWeight(x, cols = c(1, 2), useJitter = FALSE, ...)

Arguments

dirs	A list of paths to directories as returned from link{getPelfossSkeleton}.
survey	The survey name.
year	The year.
res	The resoludion.
reversed	Logical: If TRUE reverse the direction of the survey as generated by surveyPlanner.
dateshift	The number of days to shift the timing of the survey by.
seed	The seed used in surveyPlanner.

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