extractIndivs: Extract tracks of individuals from a DisMELS model run

In wStockhausen/wtsDisMELSConn: Functions for dealing with DisMELS IBM model output, including calculating and analyzing connectivity matrices

Description

Function to extract tracks of individuals from a DisMELS model run.

Usage

extractIndivs(indivConn = NULL, results = NULL,
  lhsTypeInfo = getLifeStageInfo.ATF(), lhsTypes = NULL,
  onlySuccessful = FALSE, onlyUnsuccessful = FALSE,
  successful = "where (end_typeName=\"benthic.juvenile\")",
  nurseryZones = c("NurseryArea_000to050m", "NurseryArea_050to150m"),
  returnList = TRUE, writeOutput = TRUE, outDir = "./",
  outBaseCSV = "allIndivs", verbose = FALSE)

Arguments

indivConn	- individual connectivity file (or dataframe)
results	- DisMELS results file (or dataframe)
lhsTypeInfo	- life stage info list for IBM
lhsTypes	- vector of lhs types to process (NULL = all)
onlySuccessful	- flag (T/F) to extract only successful indivs (if TRUE)
onlyUnsuccessful	- flag (T/F) to extract only unsuccessful indivs (if TRUE)
successful	- sql "where" clause to determine final state for individuals regarded as successful
nurseryZones	- vector of names of zones used as nursery areas in the IBM
returnList	- flag (T/F) indicating whether a list should be returned (otherwise NULL–helps with memory)
writeOutput	- flag (T/F) indicating whether output files should be written
outDir	- folder for output
outBaseCSV	- base name for output csv files
verbose	- flag (T/F) to print debugging info

Details

If indivConn or results are NULL, the user will be prompted to select the corresponding file(s) using a file chooser dialog. Uses functions wtsUtilities::getCSV and sqldf::sqldf.

Value

list of dataframes with indiv results by lhs type name if returnList=TRUE, otherwise NULL.

wStockhausen/wtsDisMELSConn documentation built on May 3, 2019, 7:36 p.m.