plot_maps: Plot standard maps

In merrillrudd/StreamUtils: Additional utilities for FishStats spatio-temporal modeling toolbox focusing on stream networks

Description

plot_maps plots a standard set of diagnostic maps for stream network models

Usage

plot_maps(plot_set = 3, Report, Sdreport = NULL, TmbData = NULL,
  savedir = paste0(getwd(), "/"), category_names = NULL,
  covar_names = NULL, cex_network = 1, X_xtp, ...)

Arguments

plot_set	integer-vector defining plots to create plot_set=1 Probability of encounter/no-encounter plot_set=2 Log-expected positive catch rate plot_set=3 Log-predicted density (product of encounter probability and positive catch rates) plot_set=4 Log-positive catch rates (rescaled) plot_set=5 Log-predicted density (rescaled) plot_set=6 Spatio-temporal variation in encounter probability plot_set=7 Spatio-temporal variation in log-positive catch rates plot_set=8 Linear predictor for encounter probability plot_set=9 Linear predictor for positive catch rates plot_set=10 Coefficient of variation for predicted density (available only if Data_Fn(...,Options=c('SD_site_logdensity'=1,...)) plot_set=11 Covariates that are included in the model plot_set=12 Total biomass across all categories (only useful in a multivariate model) plot_set=13 Covariate effects on encounter probability plot_set=14 Covariate effects on positive catch rates plot_set=15 Covariate effect on encounter probability by covariate
Report	tagged list of outputs from TMB model via Obj$report()
Sdreport	Standard deviation outputs from TMB model via sdreport(Obj)
savedir	Directory (absolute path) and base for filenames of plots
category_names	character vector specifying names for different categories (only used for R package VAST)
covar_names	character vector specifying names for different covariates
cex_network	point size for network
...	arguments passed to PlotMap_Fn
Year_Set	total years
Years2Include	years with data

Value

Mat_xt a matrix (rows: modeled knots; column: modeled year) for plotted output of last element of plot_set

merrillrudd/StreamUtils documentation built on May 29, 2019, 9:31 a.m.