getSigmaI: Extract Abundance Index Sigma

In arnima-github/scape: Statistical Catch-at-Age Plotting Environment

Extract Abundance Index Sigma

Description

Extract the sigma (magnitude of observation noise) that was used in a model, from survey or commercial abundance index data.

Usage

getSigmaI(model, what="s", series=NULL, digits=NULL)

Arguments

model	fitted scape model containing element CPUE and/or Survey.
what	which sigma to extract: "c"[ommercial] or "s"[urvey] abundance index.
series	vector of strings indicating which gears or surveys to analyze (all by default).
digits	number of decimal places to use when rounding, or NULL to suppress rounding.

Value

Numeric vector of year-specific sigmas, or a list of such vectors when analyzing multiple series.

Note

Thin wrapper to access model$element$CV, providing a uniform interface with other get* and est* functions.

See discussion in the estSigmaI documentation.

See Also

getN, getSigmaI, getSigmaR, estN, estSigmaI, and estSigmaR extract and estimate sample sizes and sigmas.

scape-package gives an overview of the package.

Examples

## Exploring candidate sigmas:

getSigmaI(x.cod)  # sigma used in assessment 0.20
estSigmaI(x.cod)  # model fit implies 0.17

## Multiple series:

getSigmaI(x.oreo, "c")                 # sigma used in assessment
getSigmaI(x.oreo, "c", digits=2)       # rounded
estSigmaI(x.oreo, "c")                 # model fit implies smaller sigma

getSigmaI(x.oreo, "c", series="Series 2-1")  # get one series
estSigmaI(x.oreo, "c", series="Series 2-1")  # estimate one series

arnima-github/scape documentation built on Jan. 17, 2024, 2:39 p.m.