P2C2M: Posterior Predictive Checks of Coalescent Models

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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.

Author
Michael Gruenstaeudl, Noah Reid
Date of publication
2015-06-10 15:12:55
Maintainer
Michael Gruenstaeudl <mi.gruenstaeudl@gmail.com>
License
GPL (>= 2)
Version
0.7.6

View on CRAN

Man pages

p2c2m.complete
Execute the complete P2C2M pipeline via a single command
P2C2M-package
Posterior Predictive Checks of Coalescent Models
sim.E.003.small
Output of the data set 'sim.E.003.small'
viz_example.1
Data set of visualization example 1
viz_example.2
Data set of visualization example 2

Files in this package

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