ConcatenateResults: ConcatenateResults

In phrapl: Phylogeography using Approximate Likelihood

Description

This function builds a table with details for each model analyzed using a grid or heuristic search. It give AICs, model weights, details of each model, and parameter estimates and indexes. The function can either import one or more R object files (with the extention .rda) located in the specified rdaFilePath, in which phrapl output is stored, or can be passed a vector of file names to be imported.This is the major output of phrapl.

Usage

ConcatenateResults(rdaFilesPath = "./", rdaFiles = NULL, outFile = NULL, 
addAICweights = TRUE, rmNaParameters = TRUE, addTime.elapsed = FALSE)

Arguments

rdaFilesPath	Path to where R object files (which must have the extention .rda) are located which contain results from GridSearch (default is the current dir).
rdaFiles	As an alternative to reading in all .rda files in the specified directory, a vector of file names (located in the directory specified above) can be given.
outFile	If specified, gives the file name to which an output table will be printed.
addAICweights	If TRUE, will add AICweights to the table.
rmNaParameters	If true, this removes all parameter columns from the table that only include NAs.
addTime.elapsed	If elapsed time is being tracked, this adds a column for this.

Details

If subsets of models from a migrationArray are run in separate analyses, one should save the results as R object files (.rda) after each analysis (e.g., save(list=ls(), FILENAME)). Once all models are run, ConcatenateResults can then cull the results from all the files into a master result table.

Author(s)

Brian O'Meara, Bryan Carstens, Nathan Jackson, Ariadna Morales-Garcia

Maintainer: Brian O'Meara <[e-mail]>

References

O'Meara, B.C., N. Jackson, A. Morales-Garcia, and B. Carstens (2014) Phrapl in prep.

See Also

GridSearch, CalculateModelAverages.

Examples

## Not run: 
totalData<-ConcatenateResults(
rdaFilesPath="/path_to_rdaFiles/",
rdaFiles=NULL,
outFile=NULL,
addAICweights=TRUE,
rmNaParameters=TRUE)

##Save results to a .txt file
write(t(totalData), file = "totalData.txt", ncolumns = 40, append = FALSE, 
sep = "\t")	

## End(Not run)	

phrapl documentation built on May 2, 2019, 4:52 p.m.