vast.frq.index: Format the estimated index for use in MFCL

In PacificCommunity/ofp-sam-vast-utils: Utility functions for applying VAST to analysis of WCPFC tuna fisheries data.

Description

Format the estimated index for use in MFCL

Usage

vast.frq.index(
  vast_output,
  agg.years = NULL,
  ts.vec = seq(from = 1952, to = 2018.75, by = 0.25),
  region.idx = 3:11,
  region.names = paste0("R", 1:length(region.idx)),
  mean.cv = 0.2,
  missing = 0.05,
  save.dir,
  save.name
)

Arguments

vast_output	Output from a call to fit.vast where slim output is FALSE
agg.years	Years used to define the average period when rescaling
ts.vec	a vector denoting the year-quarter of each ts for the fit.vast model output
region.idx	The fit.vast model can calculate the abundance trends over many regions, some of which are superfluous. Specify the column index for the regions that you care about.
region.names	What should these regions be called? A character vector of names please
mean.cv	When rescaling the CV for MFCL, set the mean cv to rescale to.
missing	If the cv is missing for some reason (a hold over from the conventional delta-glm) set the penalty weight to this value. The smaller the value, the smaller the impact of this data point on the likelihood in MFCL.
save.dir	Path to the directory where the outputs will be saved
save.name	Name stem for the output, useful when saving many model outputs in the same directory

PacificCommunity/ofp-sam-vast-utils documentation built on Nov. 2, 2020, 7:05 p.m.