plot_biomass_index: Plot index of abundance

Description Usage Arguments Value

Description

plot_biomass_index plots an index proportion to population abundance for stream networks

Usage

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plot_biomass_index(TmbData, Sdreport, Year_Set = NULL,
  Years2Include = NULL, savedir = 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,
  treat_missing_as_zero = FALSE, create_covariance_table = FALSE, ...)

Arguments

TmbData

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

Sdreport

Standard deviation outputs from TMB model via sdreport(Obj)

Year_Set

total years

Years2Include

years with data

savedir

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 (if using package 'VAST')

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

treat_missing_as_zero

Boolean whether to treat years and species with no (or only NA) data as instances where the index should be zero

...

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