plot_biomass_index: Plot index of abundance

Description Usage Arguments Value

View source: R/plot_biomass_index.R

Description

plots an index proportion to population abundance

Usage

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plot_biomass_index(TmbData, Sdreport, DirName = paste0(getwd(), "/"),
  PlotName = "Index", interval_width = 1, strata_names = NULL,
  category_names = NULL, use_biascorr = TRUE, plot_legend = TRUE,
  total_area_km2 = NULL, plot_log = FALSE, width = 4, height = 4,
  create_covariance_table = FALSE, ...)

Arguments

TmbData

Formatted data inputs, from 'VAST::make_data(...)'

Sdreport

output from fit$parameter_estimates$SD

DirName

Directory for saving plot and table

PlotName

Name for plot

interval_width

width for confidence intervals

strata_names

names for spatial strata

category_names

names for categories or a label if no categories are used

use_biascorr

Boolean, whether to use bias-corrected estimates if available

plot_legend

Add legend for labelling colors

total_area_km2

Total area for calculating a design-based estimator using one design-stratum (only recommended for model exploration)

plot_log

Boolean, whether to plot y-axis in log-scale

width

plot width in inches

height

plot height in inches

...

Other inputs to 'par()'

Value

Return Tagged list of output

Table

table of index estimates by stratum and year, e.g., for including in an assessment model


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