Description Usage Arguments Value
plot_biomass_index
plots an index proportion to population abundance for stream networks
1 2 3 4 5 6 | 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, ...)
|
TmbData |
Formatted data inputs, from 'VAST::Data_Fn(...)' |
Sdreport |
Standard deviation outputs from TMB model via |
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()' |
Return Tagged list of output
table of index estimates by stratum and year, e.g., for including in an assessment model
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