plot_maps: Plot standard maps

Description Usage Arguments Value

View source: R/plot_maps.r

Description

plots a standard set of diagnostic maps

Usage

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plot_maps(plot_set = 3, Report, Sdreport = NULL, Xlim = NULL,
  Ylim = NULL, TmbData = NULL, spatial_list = NULL,
  Panel = "Category", DirName = getwd(), PlotName = NULL,
  category_names = NULL, covar_names = NULL, legend = TRUE,
  textmargin = NULL, ...)

Arguments

plot_set

integer-vector defining plots to create

plot_set=1

Probability of encounter/non-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

Individual covariate effects on encounter probability

plot_set=16

Individual covariate effects on positive catch rates

Report

tagged list of outputs from TMB model via Obj$report()

Sdreport

Standard deviation outputs from TMB model via sdreport(Obj)

Xlim

xlimits for each panel

Ylim

ylimits for each panel

TmbData

optional tagged list of outputs from fit$data_list or VAST::make_data

spatial_list

required for Method == Stream_network, optional for other spatial models, tagged list of outputs from make_spatial_info

Panel

Whether to plot years for a given category (Panel="Category") or categories for a given year ((Panel="Year") in each panel figure

DirName

Directory (absolute path)

PlotName

plot names are automatically generated but option to add a modifier

category_names

character vector specifying names for different categories (only used for R package VAST)

covar_names

character vector specifying covariate names for labeling figures

legend

Boolean whether to plot legend or not

textmargin

option to include y-axis text

...

arguments passed to par

Value

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


merrillrudd/VASTPlotUtils documentation built on March 4, 2020, 8:27 p.m.