P2C2M: Posterior Predictive Checks of Coalescent Models
Version 0.7.6

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.

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

Getting started

Package overview

Popular 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
See all...

All man pages Function index File listing

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

Functions

Mode Source code
P2C2M Man page
P2C2M-package Man page
calc.coal Source code
calc.gsi Source code
calc.lcwt Source code
calc.ndc Source code
calc.parse Source code
calchelpers.brprob Source code
calchelpers.descend Source code
calchelpers.dmvparse Source code
calchelpers.gtreeparse Source code
calchelpers.nodetips Source code
calchelpers.probcalc Source code
corehelpers.metrics Source code
frmtMntse Source code
is.character0 Source code
is.integer0 Source code
loghelpers.prntmngr Source code
ms.exec Source code
onAttach Source code
onLoad Source code
p2c2m.analyze Source code
p2c2m.complete Man page Source code
p2c2m.readstarb Source code
readhelpers.extract_br_and_meta Source code
readhelpers.formatmeta Source code
readhelpers.makeCFtable Source code
readhelpers.parsetrees Source code
readtree.gtree Source code
readtree.phybase Source code
readtree.stree Source code
rmOutlrs Source code
rmext Source code
rowMedians Source code
rowModes Source code
rtnlc Source code
sim.E.003.small Man page
sourceDir Source code
stats.acrGenes Source code
stats.coord Source code
stats.main Source code
stats.perGene Source code
statshelpers.cv Source code
statshelpers.diffrnce Source code
statshelpers.qntls Source code
statshelpers.sigsgn Source code
str2lst Source code
viz_example_1 Man page
viz_example_2 Man page

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
P2C2M documentation built on May 19, 2017, 8:45 p.m.

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