fastDivPart
is identical to the divPart
function in regards to what it calculates. The difference with this function is the speed with which it processes pairwise calculations. By using more efficient programming techniques, fastDivPart
can execute commands up to 20X faster than divPart
.
fastDivPart(infile = NULL, outfile = NULL, gp = 3, pairwise = FALSE, fst = FALSE, bs_locus = FALSE, bs_pairwise = FALSE, boots = 0, plot = FALSE, para = FALSE)
working directory
the file path must be given. The name must be a character string (i.e. enclosed in or `').infile
. Either 3 (default) or 2..xlsx
workbook by default if the package 'xlsx'
is installed, and to a .html
file if plot=TRUE
. If 'xlsx'
is not installed, results will be written to .txt
files..xlsx
file by default if the package 'xlsx'
is installed, and to a .html
file if plot=TRUE
. If 'xlsx'
is not installed, results will be written to .txt
files.boots = 0
, this is only valid when all bootstrap options are false. There is no limit on the number of bootstrap iterations, however very large numbers of bootstrap iterations can take some time to run. If time is a limiting factor, the function diffCalc
is up to 10x faster than fastDivPart
, but does not allow users to write results to xlsx workbooks or plot results from the function. If required, these must be done manually..html
image file of the plotted bootstrap results for loci if bs_locus = TRUE
and pairwise population comparisons if bs_pairwise = TRUE
. The default option is plot = FALSE
.'xlsx'
in the users local package library. If 'xlsx'
is available, results will be written to an Excel workbook. If 'xlsx'
is not available, results will be written to .txt
files.
Multi-locus estimates of Weir and Cockerham's theta are calculated as per Weir and Cockerham, 1984.
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).
R Development Core Team (2011). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org/.
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 <- fastDivPart(infile = 'mydata', outfile = "myresults',
# gp = 3, pairwise = TRUE, bs_locus = TRUE,
# bs_pairwise = TRUE, bootstraps = 1000,
# plot = TRUE)
# ## End(Not run)
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