Description Usage Arguments Details Value Examples
A single function to analyse STRUCTURE, TESS, BAPS or BASIC text runs. Converts runs to a qlist, tabulates, summarises, runs evanno method (for STRUCTURE runs), aligns clusters and plots all runs.
1 2 3 4 5 6 7 8 9 10 11 12 |
files |
A character or character vector of one or more STRUCTURE, TESS,
BAPS or BASIC run files. Use |
evannomethod |
A logical indicating if evanno method should be performed. Applies only to STRUCTURE runs. |
align |
A logical indicating if clusters must be aligned within and across K. |
plotruns |
A logical indicating if the runs should be exported as barplots. |
imgoutput |
A character indicating if files are plotted as separate image files ("sep") or joined into a single image ("join"). |
grplab |
A dataframe with one or more columns (group label sets), and rows equal to the number of individuals. |
clustercol |
A character vector of colours for colouring clusters. If
NA, colours are automatically generated. K 1 to 12 are custom unique colours
while K>12 are coloured by function |
writetable |
A logical TRUE or FALSE. Setting to TRUE writes the output table to the working directory. |
sorttable |
A logical indicating if the tabulated output table must be sorted. Sorts table by loci, ind and K when available. |
exportpath |
A path to export output files. To use current working directory, set |
The function analyseQ
is a wrapper around several other
pophelper
functions. All arguments for all sub-functions are
not available. If more arguments/options are required, consider running the functions separately.
See the vignette for more details.
A qlist (list of data.frames) is returned.
1 2 3 4 5 6 7 | ## Not run:
# structure files
sfiles <- list.files(path=system.file("files/structure",package="pophelper"),
full.names=TRUE)
analyseQ(sfiles,exportpath=getwd())
## End(Not run)
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