buildmodel.list: (Calibration Performance) Automatic Creation Of argument List

In MichaelFolkes/ctctools: Analytical tools For The Pacific Salmon Commission's Chinook Technical Committee.

Description

Constructs list of arguments to be utilized by numerous functions within ctctools.

Usage

buildmodel.list(stock.names = "all", commonstocks = FALSE,
  stockmap.pathname, data.path.vec, stocks.key.pathname.vec,
  startingyear = NA, finalyear = NULL, grouping.year, age.structure,
  totalabundance, data.type = c("escapement", "terminalrun"),
  results.path = NA, groupingby = c("stock", "agegroup"),
  ranking.method = c("ordinal", "interpolated"))

Arguments

stock.names	A vector of the three letter stock name acronyms, or "all" for all stocks.
commonstocks	A Boolean. Whether to compare results based only on common stocks across calibrations. If only running one model keep as FALSE. The default is FALSE
stockmap.pathname	A string. The path to the stockmap file.
data.path.vec	A string. The path to the ccc and fcs files.
stocks.key.pathname.vec	A string. The path to the stock key file.
age.structure	A Boolean. Include analyses based on age structure.
totalabundance	A Boolean. Include analyses for stocks having only total abundance data. year totals?
data.type	A string of length one or two. The values can be "escapement" and "terminalrun".
results.path	A character vector of length one. The absolute path or path relative to the working directory where a new directory named "results" will be written (if not already present). All output files will be written here. Default is the current working directory.

Value

A list, to be used as the argument to many functions.

Examples

## Not run: 
commonstocks <- FALSE
stock.names <- 'all'
stockmap.pathname <- "../data/Old-New_Stock_Mapping_20160916.csv"
data.path.vec <- c("../data/2016_CI_test")
stocks.key.pathname.vec <- c("../data/calibration2017/CLB17bb/stocks.oldnames.csv")
# this can be "brood.year" or "return.year":
grouping.year <- "return.year"
age.structure <- TRUE
totalabundance <- TRUE
data.type <- c("escapement", "terminalrun")
samplesize.min <- 10
results.path <- "../data/calibration2017"
ranking.method <- c('ordinal', "interpolated")
doPlots <- TRUE  # TRUE OR FALSE. ALL CAPS
savepng <-  TRUE  # TRUE OR FALSE. ALL CAPS
model.list <- buildmodel.list(commonstocks = commonstocks, stockmap.pathname = stockmap.pathname, data.path.vec = data.path.vec, stocks.key.pathname.vec = stocks.key.pathname.vec, grouping.year = grouping.year, age.structure = age.structure, totalabundance =totalabundance, data.type=data.type, results.path = results.path, stock.names = stock.names, groupingby=c( "agegroup"), ranking.method = ranking.method)

## End(Not run)
## Not run: 
model.list <- buildmodel.list(commonstocks = TRUE, stockmap.pathname = stockmap.pathname, data.path.vec = data.path.vec, stocks.key.pathname.vec = stocks.key.pathname.vec, grouping.year = grouping.year, age.structure = age.structure, totalabundance =totalabundance, data.type=data.type, results.path = results.path, stock.names = stock.names, groupingby=c( 'agegroup'), ranking = ranking)

## End(Not run)

MichaelFolkes/ctctools documentation built on May 7, 2019, 4:56 p.m.