ConcatenateResults: Concatenate PHRAPL Results from Different Runs
In bomeara/phrapl: Phylogeography using Approximate Likelihood

Description Usage Arguments Details Author(s) References See Also Examples

This function builds a table with details for each model analyzed using a grid or heuristic search, which can be spread across several phrapl result files. This table gives AICs, model weights, details of each model, and parameter estimates. 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.

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ConcatenateResults(rdaFilesPath = "./", rdaFiles = NULL, migrationArray,
rm.n0 = TRUE, longNames = FALSE, addTime.elapsed = FALSE, addAICweights=TRUE,
outFile = NULL, nonparmCols=5)

`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.
`migrationArray`	The migrationArray used in the phrapl analysis. The model numbers in the output table will be matched to those in the migrationArray, thus it is important that these match up properly.
`rm.n0`	If TRUE, will exclude all n0multiplier parameters from the table. This is a way to de-clutter parameter output if models do not vary population size.
`longNames`	If TRUE, will use long descriptive names for each parameter rather than abbreviations
`addTime.elapsed`	If elapsed time is being tracked, this adds a column for this to the table.
`addAICweights`	If true, model ranks, differences in AIC (dAIC) and AIC weights (wAIC) are calculated and printed to the table.
`outFile`	If specified, gives the file name to which an output table will be printed.
`nonparmCols`	This gives the number of columns in the phrapl output that do not contain parameters.

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.

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

Maintainer: Brian O'Meara <bomeara@utk.edu>

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

GridSearch, CalculateModelAverages.

## 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)