do_steelhead: Do the steelhead stock analysis in the current working...

In eriqande/lowergranite: assessing variability of abundances of salmon in different strata

Description

Note that you have to be sure that stock_group_start_col is appropriate for the input file. The input file can be modified to do stock-sex or stock-age if desired.

Usage

do_steelhead(STOCK.DATA.XLSX, stock_group_start_col, nsim, B, DO_GSI_ON_PROP)

Arguments

STOCK.DATA.XLSX	The basename of the file with the data in it for running the simulation The function assumes that the file is in the "data_files" directory of the package.
stock_group_start_col	The column at which the stock groups start in the xlsx file (or, equivalently, in the data frame W). That data frame, (whether it was passed in as W or read from an xlsx file) must have column names that correspond to the groupings of stocks that you want to do the bootstrapping for. (For example, "UPSALM", "MFSALM", "SFSALM", ... ). The column at which those names start must be passed to this function as stock_group_start_col. You must specify a value for this. There is no default. Note: there must be no other columns in the data frame after the stock group columns.
nsim	number of simulation replicates to do. The default is 2 — much lower than it should be (should be more like 500) because it takes a long time and this is better for testing
B	number of bootstrap replicates. The default is 5 — much lower than it should be (should be more like 500) because it takes a long time and this is better for testing.
DO_GSI_ON_PROP	if set to TRUE then gsi_sim is used to create assignments that replace the assignments in the variable Prop. If FALSE then the true origins are used.

eriqande/lowergranite documentation built on May 16, 2019, 8:47 a.m.