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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.