bigDivPart
allows for the calculation of four main diversity partition statistics and their respective estimators from large genepop files.
bigDivPart(infile = NULL, outfile = NULL, WC_Fst = FALSE, format = NULL)
working directory
the file path must be given. The name must be a character string (i.e. enclosed in or `').txt
or xlsx
are valid when outfile
is not NULL
.divPart
function without the pairwise or bootstrapping functionality.
Guile, D.P., Shepherd, L.A., Sucheston, L., Bruno, A., and Manly, K.F., ``sendplot: Tool for sending interactive plots with tool-tip content.'', R package version 3.8.10, url: http://CRAN.R-project.org/package=sendplot, (2012).
Hedrick, P., ``A standardized genetic differentiation measure,'' Evolution, vol. 59, no. 8, pp. 1633-1638, (2005).
Jost, L., ``G ST and its relatives do not measure differentiation,'' Molec- ular Ecology, vol. 17, no. 18, pp. 4015-4026, (2008).
Manly, F.J., ``Randomization, bootstrap and Monte Carlo methods in biology'', Chapman and Hall, London, 1997.
Nei, M. and Chesser, R., ``Estimation of fixation indices and gene diver- sities,'' Ann. Hum. Genet, vol. 47, no. Pt 3, pp. 253-259, (1983).
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Revolution Analytics (2012). doParallel: Foreach parallel adaptor for the parallel package. R package version 1.0.1. http://CRAN.R-project.org/package=doParallel
Revolution Analytics (2012). foreach: Foreach looping construct for R. R package version 1.4.0. http://CRAN.R-project.org/package=foreach
Rousset, F., ``genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,'' Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).
Weir, B.S. & Cockerham, C.C., Estimating F-Statistics, for the Analysis of Population Structure, Evolution, vol. 38, No. 6, pp. 1358-1370 (1984).
## Not run:
# # simply use the following format to run the function
#
# test_result <- bigDivPart(infile = 'mydata', outfile = "myresults',
# WC_Fst = TRUE, format = "txt")
# ## End(Not run)
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