P2C2M: Posterior Predictive Checks of Coalescent Models

Conducts posterior predictive checks of coalescent models using gene and species trees generated by 'BEAST' or '*BEAST'. The functionality of P2C2M can be extended via two third-party R packages that are available from the author websites: 'genealogicalSorting' and 'phybase'. To use these optional packages, the installation of the Python libraries 'NumPy' (>= 1.9.0) and 'DendroPy' (= 3.12.0) is required.

Install the latest version of this package by entering the following in R:
install.packages("P2C2M")
AuthorMichael Gruenstaeudl, Noah Reid
Date of publication2015-06-10 15:12:55
MaintainerMichael Gruenstaeudl <mi.gruenstaeudl@gmail.com>
LicenseGPL (>= 2)
Version0.7.6

View on CRAN

Files

inst
inst/CITATION
inst/extdata
inst/extdata/sim.E.003.small
inst/extdata/sim.E.003.small/gene5.trees
inst/extdata/sim.E.003.small/gene8.trees
inst/extdata/sim.E.003.small/gene1.trees
inst/extdata/sim.E.003.small/gene7.trees
inst/extdata/sim.E.003.small/gene9.trees
inst/extdata/sim.E.003.small/gene2.trees
inst/extdata/sim.E.003.small/species.trees
inst/extdata/sim.E.003.small/sim.E.003.small.xml
inst/extdata/sim.E.003.small/gene3.trees
inst/extdata/sim.E.003.small/gene4.trees
inst/extdata/sim.E.003.small/gene6.trees
inst/extdata/sim.E.003.small/gene10.trees
inst/doc
inst/doc/P2C2M_CmdList.pdf
inst/doc/P2C2M_Vignette.pdf
inst/doc/P2C2M_Vignette.R
inst/doc/P2C2M_Vignette.Rnw
inst/msdir
inst/msdir/corresp_about_license.pdf
inst/msdir/stats.c
inst/msdir/sample_stats.c
inst/msdir/dist3.c
inst/msdir/rand2.c
inst/msdir/rand1t.c
inst/msdir/tajd.c
inst/msdir/rand2t.c
inst/msdir/rand1.c
inst/msdir/microsat.c
inst/msdir/ms.c
inst/msdir/ms.h
inst/msdir/streec.c
exec
exec/parseBEAUTiXML_1.8.py
exec/BEAST2phybase_1.8.py
exec/P2C2M.installRlibs.R
exec/parseBEAUTiXML_1.7.py
exec/BEAST2phybase_1.7.py
exec/P2C2M.installPylibs.py
NAMESPACE
data
data/viz_example_2.rda
data/sim.E.003.small.rda
data/viz_example_1.rda
R
R/statshelpers.qntls.R R/calc.ndc.R R/stats.perGene.R R/calc.gsi.R R/calchelpers.nodetips.R R/calc.lcwt.R R/readhelpers.formatmeta.R R/p2c2m.analyze.R R/loghelpers.prntmngr.R R/rmOutlrs.R R/calchelpers.descend.R R/str2lst.R R/stats.coord.R R/statshelpers.cv.R R/rmext.R R/frmtMntse.R R/sourceDir.R R/is.integer0.R R/statshelpers.sigsgn.R R/readhelpers.extract_br_and_meta.R R/readtree.stree.R R/calc.parse.R R/readhelpers.makeCFtable.R R/ms.exec.R R/rowModes.R R/calchelpers.dmvparse.R R/P2C2M-internal.R R/rowMedians.R R/calchelpers.brprob.R R/p2c2m.readstarb.R R/calchelpers.gtreeparse.R R/calchelpers.probcalc.R R/p2c2m.complete.R R/readhelpers.parsetrees.R R/corehelpers.metrics.R R/is.character0.R R/statshelpers.diffrnce.R R/readtree.phybase.R R/stats.main.R R/calc.coal.R R/readtree.gtree.R R/stats.acrGenes.R R/Mode.R R/rtnlc.R
vignettes
vignettes/P2C2M_Vignette.bib
vignettes/P2C2M_Vignette.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/viz_example.1.Rd man/P2C2M-package.Rd man/viz_example.2.Rd man/sim.E.003.small.Rd man/p2c2m.complete.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.