SCOBI: SCOBI: Salmonid COmposition Boostrap Intervals (v2.0)

Description Usage Arguments Author(s) References See Also Examples

View source: R/SCOBI.r

Description

Perform compositional analyses of adults at Lower Granite Dam.

Usage

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SCOBI(adultData = NULL, windowData = NULL, Run = "output", RTYPE = "W",
  Primary = "GenStock", Secondary = NA, SizeCut = NULL, alph = 0.1,
  B = 5000, writeThetas = FALSE, writeOutput = TRUE, pbtExpand = FALSE,
  pbtRates = NULL)

Arguments

adultData

the .csv file containing the biological data for the adults to be analyzed. The file should contain data for all fish trapped in a given spawn year and for a given species. The function lgr2SCOBI() can be used to format data exported from the LGTrappingDB to make it ready for the SCOBI() function

windowData

the .csv file containing the window count data for the adults to be analyzed. windowData should contain 3 columns: Strata, Count, and Collaps

Run

synopsis of the run being conducted. Run will be used as the prefix for all of your output files. Run should generally contain the spawn year, rear, species, primary, and (if desired) secondary categories. For example, "sy2015wSthdStockSex"

RTYPE

which rear type (wild [W], hatchery [H], or hatchery unclipped [HNC]) would you like to perform the current analysis on

Primary

the primary category in the adultData to be estimated. i.e., after RTYPE what category would you like to decompose next?

Secondary

the secondary category in the adultData to be estimated. i.e. after Primary what category would you like to decompose next? Use Secondary = NA if no secondary decomposition is desired

SizeCut

if Secondary = "LGDFLmm", what FL would you like to use to separate Sm versus Lg fish. For steelhead, set SizeCut = 780 (the default) to separate A-run and B-run fish. For Chinook, set SizeCut = 570 to separate Jacks and Adults

alph

the alpha used for confidence intervals (e.g., alph = 0.10 results in 90 percent CIs)

B

the number of bootstraps to be performed

writeThetas

would you like to write the thetas to a .csv? These are the B bootstrap estimates of the Rear, Primary, and Secondary (if set) categories.

writeOutput

would you like to write output files?

pbtExpand

should only be used is RTYPE is set to "H" or "HNC". If this is an analysis of PBT assigned fish, would you like to expand the frequencies within each time strata by the PBT tag rates defines in pbtRates? H stock proportions within each strata will then be calculated using the expanded frequencies.

pbtRates

if pbtExpand = TRUE, SCOBI() expects a .csv file containing the PBT tag rates for any H stock that occurs in the adultData. the pbtRates should contain 2 columns; the first column should contain the tag rates that correspond exactly to the H stocks in the adultData, the second column should contain the PBT tag rate for each H stock

Author(s)

Kirk Steinhorst and Mike Ackerman

References

Steinhorst, K., T. Copeland, M. W. Ackerman, W. C. Schrader, E. C. Anderson (In review) Estimates and Confidence Intervals for Run Composition of Returning Salmonids. Fishery Bulletin.

See Also

SCSrank

Examples

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SCOBI(adultData = sthdScobiInput, windowData = sthdWindowCounts, Run = "sthdDemo",
RTYPE = "W", Primary = "GenStock", Secondary = "GenSex", alph = 0.1, B = 100)

SCOBI(adultData = pbtTestFish, windowData = sthdWindowCounts, Run = "sthdPbtDemo",
RTYPE = "H", Primary = "PbtStock", Secondary = NA, alph = 0.1, B = 100)

mackerman44/SCOBI documentation built on July 20, 2019, 2:48 p.m.