plot.dharma.resid: Plot DHARMa style residuals for VAST model.

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

Description

Plot DHARMa style residuals for VAST model.

Usage

plot.dharma.resid(
  vast.output,
  n.samp = 999999,
  seed = 123,
  plot.type = "all",
  palette.cols = c("royalblue3", "deepskyblue1", "gold", "orange1", "indianred1",
    "firebrick2", "#AC2020"),
  smooth.span = 0.1,
  ts.start = 1952,
  ts.step = 0.25,
  factor.grouping = 5,
  save.dir,
  save.name
)

Arguments

vast.output	The output from a fit.vast function call
n.samp	Integer giving the number of records to plot the QQ relationship. Default is to use everyting.
seed	The random seed for the subsampling
plot.type	The type of metric to plot 'all', 'time', or 'knot', if you want to plot QQ by factor. 'all' Observed nominal cpue by knot and timeblock 'time' Predicted density cpue by knot and timeblock 'knot' Predicted encounter rate by knot and timeblock
palette.cols	A color palette to use for plotting
smooth.span	Value between 0 and 1. Degree of smoothing to use for the QQ plot
ts.start	Integer giving the first year of the model
ts.step	The timestep of the model 1 for year and 0.25 for quarter
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.