nicholsonppp: Evolution simulation and classification
Version 1.0

After measuring gene frequencies of modern populations that have a common ancestor, we estimate ancestral allele frequency and selection state for each gene. A bayesian model is used and verified using the included simulator.

AuthorToby Dylan Hocking
Date of publicationNone
MaintainerToby Dylan Hocking <toby.hocking@etu.upmc.fr>
LicenseGPL-3
Version1.0
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("nicholsonppp", repos="http://R-Forge.R-project.org")

Getting started

Package overview

Popular man pages

classify.loci: classify loci
display.params: display params
loci.over.time: Allele frequency time series plots
nicholsonppp-package: Evolution simulation and classification
ppp.df: ppp df
roc.loci: roc loci
selection.colors.default: selection colors default
See all...

All man pages Function index File listing

Man pages

anc.est.naive: Naive ancestral allele frequency estimates
anc.est.nicholson: anc est nicholson
anc.est.plot: Ancestral estimate plot
cex.title: cex title
classify.loci: classify loci
cutoff.plot: cutoff plot
deduce.param.label: Deduce parameters for plot subtitles
dens.several.s: dens several s
display.params: display params
estc.df: estc df
estc.over.time: estc over time
evolution.animation: evolution animation
fixation.endpoints: Plot allele frequency by selection type
hilite.best: hilite best
interesting.loci: interesting loci
loci.over.time: Allele frequency time series plots
nicholsonppp: Enhanced Nicholson model
nicholsonppp-internal: Internal nicholsonppp objects
nicholsonppp.list: nicholsonppp list
nicholsonppp-package: Evolution simulation and classification
nppp.over.time: nppp over time
pop.colors.default: pop colors default
ppp.df: ppp df
roc.loci: roc loci
selection.colors.default: selection colors default
selection.symbols.default: selection symbols default
sim2df: Convert simulation result to data frame
sim.drift.selection: Simulate drift and selection
sim.several.s: sim several s
sim.summary.plot: Simulation summary plot

Functions

.First.lib Man page
First.lib Source code
anc.est.naive Man page Source code
anc.est.nicholson Man page Source code
anc.est.plot Man page Source code
cex.title Man page
classify.loci Man page Source code
cutoff.plot Man page Source code
deduce.param.label Man page Source code
dens.several.s Man page Source code
display.params Man page
estc.df Man page Source code
estc.over.time Man page Source code
evolution.animation Man page Source code
fixation.endpoints Man page Source code
hilite.best Man page Source code
interesting.loci Man page Source code
loci.over.time Man page Source code
nicholsonppp Man page Source code
nicholsonppp-package Man page
nicholsonppp.list Man page Source code
nppp.over.time Man page Source code
pop.colors.default Man page
ppp.df Man page Source code
roc.loci Man page Source code
selection.colors.default Man page
selection.symbols.default Man page
sim.drift.selection Man page Source code
sim.several.s Man page Source code
sim.summary.plot Man page Source code
sim2df Man page Source code

Files

NAMESPACE
R
R/sensitivity.R
R/model.R
R/c.R
R/firstlib.R
R/sim.R
R/plot.R
tests
tests/simulate.drift.selection.R
tests/interesting.loci.R
tests/fixation.endpoints.R
tests/nicholsonppp.R
tests/anc.est.plot.R
tests/evolution.animation.R
tests/sim2df.R
tests/sim.summary.plot.R
tests/loci.over.time.R
DESCRIPTION
etc
etc/sims.models.Rdata
etc/c.models.4.same.Rdata
etc/interactive.R
etc/describe.alleles.R
etc/sims.models.gp.Rdata
etc/gen-pop.R
etc/c.models.8.Rdata
etc/nicholson.run.R
etc/sensitivity.R
etc/db.R
etc/gamma.R
etc/naive.R
etc/c.models.4.diff.Rdata
etc/runsim.R
etc/c.R
etc/nicholson.analyze.R
etc/c.Rdata
etc/Makefile
etc/sims.few.models.Rdata
etc/s.models.Rdata
etc/c.est.pdf
etc/sims.neu.models.Rdata
etc/cplot.R
etc/bugs
etc/bugs/TestR2WINBUGS.R
etc/bugs/nicholson.R
etc/bugs/run.R
etc/bugs/nicholson.bugs.1
etc/bugs/nicholson.bugs.0.7
etc/bugs/2009-08-27-notbeta.pdf
etc/bugs/Test_model.txt
etc/bugs/all.models.Rdata
etc/bugs/nicholson.bugs
etc/bugs/winbugs-compare.R
etc/bugs/nicholson.Rdata
etc/bugs/schools.R
etc/bugs/schools.bugs
etc/bugs/R_file_2_Winbugs.awk
etc/compare.R
man
man/roc.loci.Rd
man/hilite.best.Rd
man/interesting.loci.Rd
man/sim.several.s.Rd
man/anc.est.naive.Rd
man/anc.est.plot.Rd
man/ppp.df.Rd
man/anc.est.nicholson.Rd
man/nicholsonppp.Rd
man/estc.df.Rd
man/dens.several.s.Rd
man/nppp.over.time.Rd
man/loci.over.time.Rd
man/sim.summary.plot.Rd
man/nicholsonppp.list.Rd
man/pop.colors.default.Rd
man/sim.drift.selection.Rd
man/evolution.animation.Rd
man/fixation.endpoints.Rd
man/selection.symbols.default.Rd
man/selection.colors.default.Rd
man/nicholsonppp-package.Rd
man/cex.title.Rd
man/sim2df.Rd
man/display.params.Rd
man/classify.loci.Rd
man/nicholsonppp-internal.Rd
man/estc.over.time.Rd
man/cutoff.plot.Rd
man/deduce.param.label.Rd
src
src/fitnicholsonppp.f90
src/2utils_stat.f90
src/test.R
src/1prob_module.f90
src/0mers_twist.f90
nicholsonppp documentation built on May 21, 2017, 3:28 a.m.

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