plot.vast.index: Plot index from fit.vast model fit.

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

Description

Plot index from fit.vast model fit.

Usage

plot.vast.index(
  species,
  model.name,
  vast.frq.index,
  which.idx = "idx.std",
  region.names = paste0("R", 1:9),
  smooth.span = 0.1,
  pt.alpha = 0.1,
  plot.uncertainty = FALSE,
  scale.type = "fixed",
  color.palette = c("royalblue3", "deepskyblue1", "gold", "orange1", "indianred1",
    "firebrick2", "#AC2020"),
  save.dir,
  save.name
)

Arguments

species	String denoting the species of the analysis
model.name	What is the model name? Character string.
vast.frq.index	Output of vast.frq.index.
which.idx	Which index to plot either "idx.std" or "idx.frq"
region.names	What should these regions be called? A character vector of names please
smooth.span	Degree of smoothing used. Value between 0 and 1, where closer to 1 is more smooth.
pt.alpha	alpha transparency of quarterly points or uncertainty band.
plot.uncertainty	TRUE or FALSE: Plot the uncertainty.
scale.type	Either have yaxis fixed by panel ("fixed") or free ("free_y")
color.palette	Color palette used to differentiate betweeen models. Give exact number of colors otherwise a colorRamp will be used.
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.