trim_msom: Trim trawl data for msom

In rBatt/trawlDiversity: Long-term changes in species richness along the North American coastline

Description

Performs the trawlTrim function the clean region data, then trims down to species (not genera) that have been observed at least 10 times. Does aggregating within a haul/ spp using trawlAgg. Adds an abundance column, which is actually just 0 if wtcpue == 0, and 1 if wtcpue > 0.

Usage

trim_msom(reg, gridSize = 1, grid_stratum = TRUE, depthStratum = NULL,
  tolFraction = 1/3, plot = FALSE, cull_show_up = FALSE,
  trimYears = TRUE, trimDOY = TRUE)

Arguments

reg	Character name of region or data.table to be passed to trawlTrim.
gridSize	numeric grid size to be passed to ll2strat
grid_stratum	logical, default TRUE; whether or not the strata should be defined on a grid, or used original stratum definition
depthStratum	The depth range to use to define stratum; the default does not use depth at all. If using, a reasonable value might be 100.
tolFraction	The fraction of years that a stratum can not be sampled yet still be included in output. Default is 1/3, indicating that a stratum will be included in output so long as it is sampled for at least 2/3 of years. Actual number of years tolerated is rounded up. This value determines the strat_tol argument in check_strat
plot	Logical, default FALSE; for check_strat, should the stratum tolerance be plotted?
cull_show_up	Logical, default FALSE; should spp in show_up_spp be removed when trimming?
trimYears	Default TRUE; trim data set to a pre-determined range of years?
trimDOY	Default TRUE; trim data set to hauls occurring within a certain range of day of year?

Value

A data.table

rBatt/trawlDiversity documentation built on Aug. 14, 2021, 1:01 p.m.