nicholsonppp: Evolution simulation and classification

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

View on R-Forge

Functions

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

Files

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

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.