plot.vast.space.time: Plot vast output by spatial knots and time block.

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

Description

Plot vast output by spatial knots and time block.

Usage

plot.vast.space.time(
  vast.output,
  coast.shp,
  region.shp.list,
  species = "BET",
  plot.type = "N",
  model.start.year = 1952,
  t.block = 4,
  plot.obs.grid = FALSE,
  x.extent = c(95, 295),
  y.extent = c(-50, 60),
  scale.trans = "identity",
  virids.pal = "D",
  save.dir,
  save.name
)

Arguments

vast.output	The output from a fit.vast function call
coast.shp	supply a coast shapefile, if missing this defaults to the coast shapefile stored in the package
region.shp.list	supply a shapefile with the regional structure, if missing this defaults to the WCPO 10N shapefile stored in the package
species	String denoting the species of the analysis
plot.type	The type of metric to plot 'pred.cpue', 'bin', 'pos', 'resid', 'bin.resid', 'pos.resid', 'N', 'Omega1', 'Omega2','Epsilon1', or 'Epsilon2' 'obs.cpue' Observed nominal cpue by knot and timeblock 'pred.cpue' Predicted density cpue by knot and timeblock 'bin' Predicted encounter rate by knot and timeblock 'pos' Predicted positive catch-rate by knot and timeblock 'resid' Standardized residual by knot and timeblock 'bin.resid' Standardized residual for encounter rate cpue by knot and timeblock 'pos.resid' Standardized residual for positive catch-rate by knot and timeblock 'N' Number of observations by knot and timeblock 'Omega1' Spatial random effect for encounter rate 'Omega2' Spatial random effect for positive catch-rate 'Epsilon1' Spatiotemporal random effect for encounter rate 'Epsilon2' Spatiotemporal random effect for positive catch-rate
model.start.year	An integer denoting the first year of data used in the model
t.block	An integer denoting the number of years to aggregate together in time blocks
plot.obs.grid	TRUE or FALSE. Plot the observations. Default is FALSE as otherwise the plot looks gross
x.extent	Specify the xlim of the plot as c(xmin,xmax) in degrees 0 to 360
y.extent	Specify the ylim of the plot as c(ymin,ymax) in degrees -90 to 90
scale.trans	A character string denoting the type of ggplot2 scale transformation to use for the color scale. Built-in transformations include "asn", "atanh", "boxcox", "date", "exp", "hms", "identity", "log", "log10", "log1p", "log2", "logit", "modulus", "probability", "probit", "pseudo_log", "reciprocal", "reverse", "sqrt" and "time".
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
viridis.pal	A character string indicating the colormap option to use. Four options are available: "magma" (or "A"), "inferno" (or "B"), "plasma" (or "C"), "viridis" (or "D", the default option) and "cividis" (or "E")

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