nicholsonppp: Evolution simulation and classification

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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.

Author
Toby Dylan Hocking
Date of publication
None
Maintainer
Toby Dylan Hocking <toby.hocking@etu.upmc.fr>
License
GPL-3
Version
1.0

View on R-Forge

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

Files in this package

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