AIestimate: Estimate Index of Sea Lamprey Adults
In JVAdams/GLFC: Great Lakes Fishery Commission

AIestimate

R Documentation

Estimate Index of Sea Lamprey Adults

Description

Estimate the Adult Index of sea lampreys in a single Great Lake.

Usage

AIestimate(streamDat, minNMR = 2)

Arguments

streamDat

A data frame of old and new stream mark-recapture estimates used to estimate the lake-wide Adult Indices, typically the output from AIprep. The data frame must include these 10 columns:

year;
lake;
lscode, the lake-stream ID (see details);
PEmr, the population estimate;
CVmr, the coefficient of variation (100% * sqrt(variance(PEmr)) / PEmr);
index, a logical identifying the index streams (TRUE for index);
maintain, a logical identifying the streams that will continue to have ongoing trapping even if not part of the Adult Index;
indexContrib the stream population estimate that will be used in the Adult Index (NA for new);
indexContribCV the stream CV that will be used to generate 95% confidence intervals for the Adult Index (NA for new); and
complete a logical identifying streams and years for which the Adult Index has already been estimated (FALSE for new).

minNMR

An integer scalar greater than or equal to 2, the minimum number of mark-recapture estimates needed in a year to generate an index, default 2.

Details

The annual Adult Index is simply the sum of stream population estimates for each year. Missing stream estimates are estimated by a lake-specific ANOVA model relating the log of the stream estimates to the main effects of each stream and each year, weighted by the inverse of the CV squared.

Value

A list with 2 data frames:

streamPE - stream mark-recapture and Adult Index contributions for the incomplete rows in streamDat, with the same variables as streamDat; and
lakeIndex - annual lake-wide Adult Indices with 5 columns: lake, year, the Adult Index index, and the lower and upper 95% confidence interval ilo and ihi.

References

Adams, JV, JM Barber, GA Bravener, SA Lewandoski. 2021. Quantifying Great Lakes sea lamprey populations using an index of adults. Journal of Great Lakes Research. [link]

JVAdams/GLFC documentation built on Jan. 5, 2023, 12:59 a.m.