Description Usage Arguments Value Author(s) References Examples
This function executes the complete P2C2M pipeline from beginning to end.
1 2 3 4 5 |
path |
the absolute file path to the input directory, specified
as a double-quoted string; if |
xml.file |
the name of the BEAUTi-generated and XML-formatted
input file, specified as a double-quoted string. The default is
|
descr.stats |
the name(s) of the summary statistic(s) to be
applied, specified as a double-quoted string. If multiple
statistics are specified, they must be separated by commas. A total
of four summary statistics is currently available:
|
beast.vers |
the version of *BEAST (Heled and Drummond 2010)
used to perform the species tree inference, specified as a
double-quoted string. Data parsers are located in the subdirectory
exec/. Currently, the following parsers are available: |
single.allele |
the name of a species that is represented by
only a single allele, specified as a variable of mode vector. This
setting is useful when defining an outgroup, because the species so
defined does not contribute towards the calculation of the summary
statistic 'GSI'. The default is |
num.reps |
the number of simulation replicates to be conducted,
specified as an integer. The default is |
use.sorted |
a logical specifying if the summary statistics
generated from the posterior and from the posterior predictive
distribution are to be ranked by magnitude prior to the calculation
of the differences and the formation of the test distribution.
The default is |
use.mpi |
a logical specifying if P2C2M utilizes multiple
computer CPUs (if such exist on the system) in order to speed up
the calculations. Computations are then executed as parallel
processes. The default is |
save.metadata |
a logical specifying if P2C2M saves
the metadata of the analysis to the output variable. The default
is |
verbose |
a logical specifying if P2C2M prints status
information to the screen. The default is |
dbg |
a logical specifying if P2C2M is to be run in a
debug mode. If |
The results of a P2C2M run comprise test statistics, measures of data dispersion and deviations marked at several quantile levels (analogous to P-values under different alpha-levels in a parametric simulation) for each gene under study and of the sum of all genes.
Michael Gruenstaeudl, Noah Reid
Maintainer: Michael Gruenstaeudl gruenstaeudl.1@osu.edu
Cummings, M.P., Neel, M.C. and Shaw, K.L. (2008) A genealogical approach to quantifying lineage divergence. Evolution, 62, 2411–2422.
Gruenstaeudl, M., Reid, N.M., Wheeler, G.R. and Carstens, B.C., submitted. Posterior Predictive Checks of Coalescent Models: P2C2M, an R package.
Heled, J. and Drummond, A.J. (2010) Bayesian inference of species trees from multilocus data. Molecular Biology And Evolution, 27, 570–580.
Maddison, W.P. (1997) Gene trees in species trees. Systematic Biology, 46, 523–536.
Rannala, B. and Yang, Z. (2003) Bayes Estimation of Species Divergence Times and Ancestral Population Sizes Using DNA Sequences From Multiple Loci. Genetics, 164, 1645–1656.
1 2 3 4 5 6 7 8 9 10 11 12 | ## Example of the minimal data requirements to run P2C2M
# The absolute path to the input directory is set
inPath <- system.file("extdata", "sim.E.003.small/", package="P2C2M")
# The name of the xml-file generated by BEAUTi and located in
# "inPath" is set
inFile <- "sim.E.003.small.xml"
# Posterior predictive simulations with a setting of 2 simulation
# replicates are preformed
sim.E.003.small <- p2c2m.complete(inPath, inFile, num.reps=2, save.metadata=TRUE)
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