Title: Everyone's Statistical Software
Description: A framework that brings together an abundance of common
statistical models found across packages into a unified interface, and
provides a common architecture for estimation and interpretation, as well
as bridging functions to absorb increasingly more models into the
collective library. Zelig allows each individual package, for each
statistical model, to be accessed by a common uniformly structured call and
set of arguments. Moreover, Zelig automates all the surrounding building
blocks of a statistical workflow --procedures and algorithms that may be
essential to one user's application but which the original package
developer did use in their own research and might not themselves support.
These include bootstrapping, jackknifing, and reweighting of data, and in
particular, Zelig automatically generates predicted and simulated
quantities of interest (such as relative risk ratios, average treatment
effects, first differences and predicted and expected values) to interpret
and visualize complex models.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between Zelig versions 4.2-1 dated 2013-09-21 and 5.0-7 dated 2015-11-10
Zelig-4.2-1/Zelig/CHANGES |only Zelig-4.2-1/Zelig/COPYING |only Zelig-4.2-1/Zelig/NEWS |only Zelig-4.2-1/Zelig/R/GetObject.R |only Zelig-4.2-1/Zelig/R/GetSlot.R |only Zelig-4.2-1/Zelig/R/GetSlot.zelig.R |only Zelig-4.2-1/Zelig/R/MCMChook.R |only Zelig-4.2-1/Zelig/R/MLutils.R |only Zelig-4.2-1/Zelig/R/Zelig-package.R |only Zelig-4.2-1/Zelig/R/as.dataframe.setx.R |only Zelig-4.2-1/Zelig/R/as.matrix.pooled.setx.R |only Zelig-4.2-1/Zelig/R/as.matrix.setx.R |only Zelig-4.2-1/Zelig/R/as.parameters.R |only Zelig-4.2-1/Zelig/R/as.qi.R |only Zelig-4.2-1/Zelig/R/as.summarized.R |only Zelig-4.2-1/Zelig/R/as.summarized.list.R |only Zelig-4.2-1/Zelig/R/attach.env.R |only Zelig-4.2-1/Zelig/R/bootfn.default.R |only Zelig-4.2-1/Zelig/R/bootstrap.R |only Zelig-4.2-1/Zelig/R/bootstrap.gamma.R |only Zelig-4.2-1/Zelig/R/bootstrap.negbinom.R |only Zelig-4.2-1/Zelig/R/bootstrap.normal.R |only Zelig-4.2-1/Zelig/R/callToString.R |only Zelig-4.2-1/Zelig/R/cluster.formula.R |only Zelig-4.2-1/Zelig/R/cmvglm.R |only Zelig-4.2-1/Zelig/R/common-methods.R |only Zelig-4.2-1/Zelig/R/describe.R |only Zelig-4.2-1/Zelig/R/describe.default.R |only Zelig-4.2-1/Zelig/R/describe.zelig.R |only Zelig-4.2-1/Zelig/R/description.R |only Zelig-4.2-1/Zelig/R/exp.R |only Zelig-4.2-1/Zelig/R/factor.bayes.R |only Zelig-4.2-1/Zelig/R/gamma.R |only Zelig-4.2-1/Zelig/R/gamma.gee.R |only Zelig-4.2-1/Zelig/R/gamma.survey.R |only Zelig-4.2-1/Zelig/R/get.package.R |only Zelig-4.2-1/Zelig/R/getPredictorTerms.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.formula.R |only Zelig-4.2-1/Zelig/R/getResponseTerms.list.R |only Zelig-4.2-1/Zelig/R/help.zelig.R |only Zelig-4.2-1/Zelig/R/ignore.R |only Zelig-4.2-1/Zelig/R/is.formula.R |only Zelig-4.2-1/Zelig/R/list.depth.R |only Zelig-4.2-1/Zelig/R/logit.R |only Zelig-4.2-1/Zelig/R/logit.bayes.R |only Zelig-4.2-1/Zelig/R/logit.gee.R |only Zelig-4.2-1/Zelig/R/logit.survey.R |only Zelig-4.2-1/Zelig/R/lognorm.R |only Zelig-4.2-1/Zelig/R/ls.R |only Zelig-4.2-1/Zelig/R/make.parameters.R |only Zelig-4.2-1/Zelig/R/makeModelMatrix.R |only Zelig-4.2-1/Zelig/R/mi.R |only Zelig-4.2-1/Zelig/R/mlogit.bayes.R |only Zelig-4.2-1/Zelig/R/model.frame.multiple.R |only Zelig-4.2-1/Zelig/R/model.matrix.multiple.R |only Zelig-4.2-1/Zelig/R/model.matrix.parseFormula.R |only Zelig-4.2-1/Zelig/R/model.warnings.R |only Zelig-4.2-1/Zelig/R/multi.dataset.R |only Zelig-4.2-1/Zelig/R/multipleUtil.R |only Zelig-4.2-1/Zelig/R/names.relogit.R |only Zelig-4.2-1/Zelig/R/negbinom.R |only Zelig-4.2-1/Zelig/R/normal.R |only Zelig-4.2-1/Zelig/R/normal.bayes.R |only Zelig-4.2-1/Zelig/R/normal.gee.R |only Zelig-4.2-1/Zelig/R/normal.survey.R |only Zelig-4.2-1/Zelig/R/oprobit.bayes.R |only Zelig-4.2-1/Zelig/R/param.R |only Zelig-4.2-1/Zelig/R/parameters.R |only Zelig-4.2-1/Zelig/R/parse.formula.R |only Zelig-4.2-1/Zelig/R/parseFormula.R |only Zelig-4.2-1/Zelig/R/poisson.R |only Zelig-4.2-1/Zelig/R/poisson.bayes.R |only Zelig-4.2-1/Zelig/R/poisson.gee.R |only Zelig-4.2-1/Zelig/R/poisson.survey.R |only Zelig-4.2-1/Zelig/R/print.R |only Zelig-4.2-1/Zelig/R/probit.R |only Zelig-4.2-1/Zelig/R/probit.bayes.R |only Zelig-4.2-1/Zelig/R/probit.gee.R |only Zelig-4.2-1/Zelig/R/probit.survey.R |only Zelig-4.2-1/Zelig/R/qi.R |only Zelig-4.2-1/Zelig/R/qi.summarized.R |only Zelig-4.2-1/Zelig/R/relogit.R |only Zelig-4.2-1/Zelig/R/repl.R |only Zelig-4.2-1/Zelig/R/robust.glm.hook.R |only Zelig-4.2-1/Zelig/R/robust.hook.R |only Zelig-4.2-1/Zelig/R/setx.R |only Zelig-4.2-1/Zelig/R/sim.MI.R |only Zelig-4.2-1/Zelig/R/sim.R |only Zelig-4.2-1/Zelig/R/sim.default.R |only Zelig-4.2-1/Zelig/R/simulation.matrix.R |only Zelig-4.2-1/Zelig/R/simulations.plot.R |only Zelig-4.2-1/Zelig/R/summarize.R |only Zelig-4.2-1/Zelig/R/summary.R |only Zelig-4.2-1/Zelig/R/t.setx.R |only Zelig-4.2-1/Zelig/R/terms.R |only Zelig-4.2-1/Zelig/R/termsFromFormula.R |only Zelig-4.2-1/Zelig/R/tobit.R |only Zelig-4.2-1/Zelig/R/twosls.R |only Zelig-4.2-1/Zelig/R/user.prompt.R |only Zelig-4.2-1/Zelig/R/vcov.R |only Zelig-4.2-1/Zelig/R/z.R |only Zelig-4.2-1/Zelig/R/zelig.R |only Zelig-4.2-1/Zelig/R/zelig.skeleton.R |only Zelig-4.2-1/Zelig/R/zelig2.R |only Zelig-4.2-1/Zelig/R/zeligBuildWeights.R |only Zelig-4.2-1/Zelig/R/zzz.R |only Zelig-4.2-1/Zelig/README |only Zelig-4.2-1/Zelig/build |only Zelig-4.2-1/Zelig/data/PErisk.txt.bz2 |only Zelig-4.2-1/Zelig/data/approval.tab.bz2 |only Zelig-4.2-1/Zelig/data/bivariate.tab.bz2 |only Zelig-4.2-1/Zelig/data/coalition.tab.xz |only Zelig-4.2-1/Zelig/data/coalition2.txt.xz |only Zelig-4.2-1/Zelig/data/free1.tab.bz2 |only Zelig-4.2-1/Zelig/data/free2.tab.bz2 |only Zelig-4.2-1/Zelig/data/homerun.txt.xz |only Zelig-4.2-1/Zelig/data/immi1.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi2.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi3.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi4.tab.bz2 |only Zelig-4.2-1/Zelig/data/immi5.tab.bz2 |only Zelig-4.2-1/Zelig/data/immigration.tab.bz2 |only Zelig-4.2-1/Zelig/data/macro.tab.xz |only Zelig-4.2-1/Zelig/data/mexico.tab.bz2 |only Zelig-4.2-1/Zelig/data/mid.tab.bz2 |only Zelig-4.2-1/Zelig/data/newpainters.txt.bz2 |only Zelig-4.2-1/Zelig/data/sanction.tab.bz2 |only Zelig-4.2-1/Zelig/data/swiss.txt.bz2 |only Zelig-4.2-1/Zelig/data/turnout.tab.bz2 |only Zelig-4.2-1/Zelig/data/voteincome.txt.bz2 |only Zelig-4.2-1/Zelig/demo/Zelig.HelloWorld.R |only Zelig-4.2-1/Zelig/demo/exp.R |only Zelig-4.2-1/Zelig/demo/factor.bayes.R |only Zelig-4.2-1/Zelig/demo/gamma.R |only Zelig-4.2-1/Zelig/demo/gamma.gee.R |only Zelig-4.2-1/Zelig/demo/gamma.survey.R |only Zelig-4.2-1/Zelig/demo/logit.R |only Zelig-4.2-1/Zelig/demo/logit.bayes.R |only Zelig-4.2-1/Zelig/demo/logit.gee.R |only Zelig-4.2-1/Zelig/demo/logit.survey.R |only Zelig-4.2-1/Zelig/demo/lognorm.R |only Zelig-4.2-1/Zelig/demo/ls.R |only Zelig-4.2-1/Zelig/demo/mi.R |only Zelig-4.2-1/Zelig/demo/mlogit.bayes.R |only Zelig-4.2-1/Zelig/demo/negbinom.R |only Zelig-4.2-1/Zelig/demo/normal.R |only Zelig-4.2-1/Zelig/demo/normal.bayes.R |only Zelig-4.2-1/Zelig/demo/normal.gee.R |only Zelig-4.2-1/Zelig/demo/normal.survey.R |only Zelig-4.2-1/Zelig/demo/oprobit.bayes.R |only Zelig-4.2-1/Zelig/demo/poisson.R |only Zelig-4.2-1/Zelig/demo/poisson.bayes.R |only Zelig-4.2-1/Zelig/demo/poisson.gee.R |only Zelig-4.2-1/Zelig/demo/poisson.survey.R |only Zelig-4.2-1/Zelig/demo/probit.R |only Zelig-4.2-1/Zelig/demo/probit.bayes.R |only Zelig-4.2-1/Zelig/demo/probit.gee.R |only Zelig-4.2-1/Zelig/demo/probit.survey.R |only Zelig-4.2-1/Zelig/demo/relogit.R |only Zelig-4.2-1/Zelig/demo/twosls.R |only Zelig-4.2-1/Zelig/demo/vertci.R |only Zelig-4.2-1/Zelig/inst/doc |only Zelig-4.2-1/Zelig/inst/templates |only Zelig-4.2-1/Zelig/man/GetObject.Rd |only Zelig-4.2-1/Zelig/man/GetSlot.Rd |only Zelig-4.2-1/Zelig/man/GetSlot.zelig.Rd |only Zelig-4.2-1/Zelig/man/MCMChook.Rd |only Zelig-4.2-1/Zelig/man/Max.Rd |only Zelig-4.2-1/Zelig/man/McmcHookFactor.Rd |only Zelig-4.2-1/Zelig/man/Min.Rd |only Zelig-4.2-1/Zelig/man/TexCite.Rd |only Zelig-4.2-1/Zelig/man/Zelig-package.Rd |only Zelig-4.2-1/Zelig/man/ZeligDescribeModel.Rd |only Zelig-4.2-1/Zelig/man/ZeligListModels.Rd |only Zelig-4.2-1/Zelig/man/ZeligListTitles.Rd |only Zelig-4.2-1/Zelig/man/alpha.Rd |only Zelig-4.2-1/Zelig/man/as.bootlist.Rd |only Zelig-4.2-1/Zelig/man/as.bootvector.Rd |only Zelig-4.2-1/Zelig/man/as.data.frame.setx.Rd |only Zelig-4.2-1/Zelig/man/as.description.Rd |only Zelig-4.2-1/Zelig/man/as.description.description.Rd |only Zelig-4.2-1/Zelig/man/as.description.list.Rd |only Zelig-4.2-1/Zelig/man/as.matrix.pooled.setx.Rd |only Zelig-4.2-1/Zelig/man/as.matrix.setx.Rd |only Zelig-4.2-1/Zelig/man/as.parameters.Rd |only Zelig-4.2-1/Zelig/man/as.parameters.default.Rd |only Zelig-4.2-1/Zelig/man/as.parameters.list.Rd |only Zelig-4.2-1/Zelig/man/as.parameters.parameters.Rd |only Zelig-4.2-1/Zelig/man/as.qi.Rd |only Zelig-4.2-1/Zelig/man/as.qi.default.Rd |only Zelig-4.2-1/Zelig/man/as.qi.list.Rd |only Zelig-4.2-1/Zelig/man/as.qi.qi.Rd |only Zelig-4.2-1/Zelig/man/as.summarized.Rd |only Zelig-4.2-1/Zelig/man/as.summarized.list.Rd |only Zelig-4.2-1/Zelig/man/as.summarized.summarized.qi.Rd |only Zelig-4.2-1/Zelig/man/attach.env.Rd |only Zelig-4.2-1/Zelig/man/bootfn.default.Rd |only Zelig-4.2-1/Zelig/man/bootstrap.Rd |only Zelig-4.2-1/Zelig/man/bootstrap.default.Rd |only Zelig-4.2-1/Zelig/man/bootstrap.gamma.Rd |only Zelig-4.2-1/Zelig/man/bootstrap.negbinom.Rd |only Zelig-4.2-1/Zelig/man/bootstrap.normal.Rd |only Zelig-4.2-1/Zelig/man/callToString.Rd |only Zelig-4.2-1/Zelig/man/cite.Rd |only Zelig-4.2-1/Zelig/man/cmvglm.Rd |only Zelig-4.2-1/Zelig/man/coef.parameters.Rd |only Zelig-4.2-1/Zelig/man/combine.Rd |only Zelig-4.2-1/Zelig/man/constructDataFrame.Rd |only Zelig-4.2-1/Zelig/man/constructDesignMatrix.Rd |only Zelig-4.2-1/Zelig/man/depends.on.zelig.Rd |only Zelig-4.2-1/Zelig/man/describe.Rd |only Zelig-4.2-1/Zelig/man/describe.default.Rd |only Zelig-4.2-1/Zelig/man/describe.exp.Rd |only Zelig-4.2-1/Zelig/man/describe.gamma.Rd |only Zelig-4.2-1/Zelig/man/describe.logit.Rd |only Zelig-4.2-1/Zelig/man/describe.ls.Rd |only Zelig-4.2-1/Zelig/man/describe.negbinom.Rd |only Zelig-4.2-1/Zelig/man/describe.normal.Rd |only Zelig-4.2-1/Zelig/man/describe.poisson.Rd |only Zelig-4.2-1/Zelig/man/describe.probit.Rd |only Zelig-4.2-1/Zelig/man/describe.tobit.Rd |only Zelig-4.2-1/Zelig/man/describe.zelig.Rd |only Zelig-4.2-1/Zelig/man/description.Rd |only Zelig-4.2-1/Zelig/man/find.match.Rd |only Zelig-4.2-1/Zelig/man/get.package.Rd |only Zelig-4.2-1/Zelig/man/getPredictorTerms.Rd |only Zelig-4.2-1/Zelig/man/getResponseTerms.Formula-not-formula.Rd |only Zelig-4.2-1/Zelig/man/getResponseTerms.Rd |only Zelig-4.2-1/Zelig/man/getResponseTerms.formula.Rd |only Zelig-4.2-1/Zelig/man/getResponseTerms.list.Rd |only Zelig-4.2-1/Zelig/man/has.zelig2.Rd |only Zelig-4.2-1/Zelig/man/help.zelig.Rd |only Zelig-4.2-1/Zelig/man/ignore.Rd |only Zelig-4.2-1/Zelig/man/is.formula.Rd |only Zelig-4.2-1/Zelig/man/is.qi.Rd |only Zelig-4.2-1/Zelig/man/is.valid.qi.list.Rd |only Zelig-4.2-1/Zelig/man/is.zelig.compliant.Rd |only Zelig-4.2-1/Zelig/man/is.zelig.package.Rd |only Zelig-4.2-1/Zelig/man/link.Rd |only Zelig-4.2-1/Zelig/man/linkinv.Rd |only Zelig-4.2-1/Zelig/man/list.depth.Rd |only Zelig-4.2-1/Zelig/man/list.zelig.dependent.packages.Rd |only Zelig-4.2-1/Zelig/man/list.zelig.models.Rd |only Zelig-4.2-1/Zelig/man/loadDependencies.Rd |only Zelig-4.2-1/Zelig/man/make.parameters.Rd |only Zelig-4.2-1/Zelig/man/makeModelMatrix.Rd |only Zelig-4.2-1/Zelig/man/makeZeligObject.Rd |only Zelig-4.2-1/Zelig/man/mi.Rd |only Zelig-4.2-1/Zelig/man/mix.Rd |only Zelig-4.2-1/Zelig/man/model.frame.multiple.Rd |only Zelig-4.2-1/Zelig/man/model.matrix.multiple.Rd |only Zelig-4.2-1/Zelig/man/model.matrix.parseFormula.Rd |only Zelig-4.2-1/Zelig/man/multilevel.Rd |only Zelig-4.2-1/Zelig/man/name.object.Rd |only Zelig-4.2-1/Zelig/man/names.qi.Rd |only Zelig-4.2-1/Zelig/man/param.Rd |only Zelig-4.2-1/Zelig/man/param.default.Rd |only Zelig-4.2-1/Zelig/man/param.exp.Rd |only Zelig-4.2-1/Zelig/man/param.gamma.Rd |only Zelig-4.2-1/Zelig/man/param.logit.Rd |only Zelig-4.2-1/Zelig/man/param.ls.Rd |only Zelig-4.2-1/Zelig/man/param.negbinom.Rd |only Zelig-4.2-1/Zelig/man/param.normal.Rd |only Zelig-4.2-1/Zelig/man/param.poisson.Rd |only Zelig-4.2-1/Zelig/man/param.probit.Rd |only Zelig-4.2-1/Zelig/man/param.relogit.Rd |only Zelig-4.2-1/Zelig/man/param.relogit2.Rd |only Zelig-4.2-1/Zelig/man/param.tobit.Rd |only Zelig-4.2-1/Zelig/man/parameters.Rd |only Zelig-4.2-1/Zelig/man/parse.formula.Rd |only Zelig-4.2-1/Zelig/man/parseFormula.Rd |only Zelig-4.2-1/Zelig/man/parseFormula.formula.Rd |only Zelig-4.2-1/Zelig/man/parseFormula.list.Rd |only Zelig-4.2-1/Zelig/man/plot.MI.sim.Rd |only Zelig-4.2-1/Zelig/man/plot.ci.Rd |only Zelig-4.2-1/Zelig/man/plot.pooled.sim.Rd |only Zelig-4.2-1/Zelig/man/plot.sim.Rd |only Zelig-4.2-1/Zelig/man/plot.simulations.Rd |only Zelig-4.2-1/Zelig/man/print.qi.Rd |only Zelig-4.2-1/Zelig/man/print.qi.summarized.Rd |only Zelig-4.2-1/Zelig/man/print.setx.Rd |only Zelig-4.2-1/Zelig/man/print.setx.mi.Rd |only Zelig-4.2-1/Zelig/man/print.sim.Rd |only Zelig-4.2-1/Zelig/man/print.summary.MCMCZelig.Rd |only Zelig-4.2-1/Zelig/man/print.summary.pooled.sim.Rd |only Zelig-4.2-1/Zelig/man/print.summary.relogit.Rd |only Zelig-4.2-1/Zelig/man/print.summary.relogit2.Rd |only Zelig-4.2-1/Zelig/man/print.summary.sim.Rd |only Zelig-4.2-1/Zelig/man/print.summarySim.MI.Rd |only Zelig-4.2-1/Zelig/man/print.zelig.Rd |only Zelig-4.2-1/Zelig/man/qi.Rd |only Zelig-4.2-1/Zelig/man/qi.exp.Rd |only Zelig-4.2-1/Zelig/man/qi.summarize.Rd |only Zelig-4.2-1/Zelig/man/reduceMI.Rd |only Zelig-4.2-1/Zelig/man/repl.Rd |only Zelig-4.2-1/Zelig/man/repl.default.Rd |only Zelig-4.2-1/Zelig/man/repl.sim.Rd |only Zelig-4.2-1/Zelig/man/replace.call.Rd |only Zelig-4.2-1/Zelig/man/robust.gee.hook.Rd |only Zelig-4.2-1/Zelig/man/robust.glm.hook.Rd |only Zelig-4.2-1/Zelig/man/setx.MI.Rd |only Zelig-4.2-1/Zelig/man/setx.default.Rd |only Zelig-4.2-1/Zelig/man/sim.MI.Rd |only Zelig-4.2-1/Zelig/man/sim.default.Rd |only Zelig-4.2-1/Zelig/man/simulation.matrix.Rd |only Zelig-4.2-1/Zelig/man/simulations.parameters.Rd |only Zelig-4.2-1/Zelig/man/special_print_LIST.Rd |only Zelig-4.2-1/Zelig/man/special_print_MATRIX.Rd |only Zelig-4.2-1/Zelig/man/splitUp.Rd |only Zelig-4.2-1/Zelig/man/store.object.Rd |only Zelig-4.2-1/Zelig/man/structuralToReduced.Rd |only Zelig-4.2-1/Zelig/man/summarize.Rd |only Zelig-4.2-1/Zelig/man/summarize.default.Rd |only Zelig-4.2-1/Zelig/man/summary.MI.Rd |only Zelig-4.2-1/Zelig/man/summary.MI.sim.Rd |only Zelig-4.2-1/Zelig/man/summary.Relogit2.Rd |only Zelig-4.2-1/Zelig/man/summary.glm.robust.Rd |only Zelig-4.2-1/Zelig/man/summary.pooled.sim.Rd |only Zelig-4.2-1/Zelig/man/summary.relogit.Rd |only Zelig-4.2-1/Zelig/man/summary.sim.Rd |only Zelig-4.2-1/Zelig/man/summary.zelig.Rd |only Zelig-4.2-1/Zelig/man/t.setx.Rd |only Zelig-4.2-1/Zelig/man/terms.multiple.Rd |only Zelig-4.2-1/Zelig/man/terms.vglm.Rd |only Zelig-4.2-1/Zelig/man/terms.zelig.Rd |only Zelig-4.2-1/Zelig/man/termsFromFormula.Rd |only Zelig-4.2-1/Zelig/man/toBuildFormula.Rd |only Zelig-4.2-1/Zelig/man/tolmerFormat.Rd |only Zelig-4.2-1/Zelig/man/ucfirst.Rd |only Zelig-4.2-1/Zelig/man/user.prompt.Rd |only Zelig-4.2-1/Zelig/man/z.Rd |only Zelig-4.2-1/Zelig/man/zelig.call.Rd |only Zelig-4.2-1/Zelig/man/zelig.skeleton.Rd |only Zelig-4.2-1/Zelig/man/zelig2-bayes.Rd |only Zelig-4.2-1/Zelig/man/zelig2-core.Rd |only Zelig-4.2-1/Zelig/man/zelig2-gee.Rd |only Zelig-4.2-1/Zelig/man/zelig2-survey.Rd |only Zelig-4.2-1/Zelig/man/zelig2.Rd |only Zelig-4.2-1/Zelig/man/zeligBuildWeights.Rd |only Zelig-4.2-1/Zelig/po |only Zelig-4.2-1/Zelig/tests/MatchIt.R |only Zelig-4.2-1/Zelig/tests/amelia.R |only Zelig-4.2-1/Zelig/tests/by.R |only Zelig-4.2-1/Zelig/tests/lognorm.R |only Zelig-4.2-1/Zelig/tests/mi.R |only Zelig-4.2-1/Zelig/tests/mix.R |only 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Title: A Toolbox for Multivariate Meta-Analysis
Description: A toolbox for meta-analysis. This package includes a collection of functions for (1) implementing robust multivariate meta-analysis of continuous or binary outcomes; and (2) testing and correcting of publication bias in multivariate meta-analysis settings.
Author: Yong Chen, Chuan Hong, Haitao Chu
Maintainer: Yong Chen <ychen.upenn@gmail.com>
Diff between xmeta versions 1.0-1 dated 2015-10-12 and 1.0-2 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++++++++--------- NAMESPACE | 5 ++++- R/galaxy.R | 7 +++---- R/mmeta.R | 43 +++++++++++++++++++++++++------------------ R/mpbt.R | 7 +++++-- R/summary.galaxy.R |only R/summary.mmeta.R |only R/summary.mpbt.R |only data |only man/ca125.Rd |only man/galaxy.Rd | 18 +++++------------- man/mmeta.Rd | 27 +++++++++++++-------------- man/mpbt.Rd | 16 +++------------- man/nat2.Rd |only man/prostate.Rd |only man/summary.galaxy.rd |only man/summary.mmeta.rd |only man/summary.mpbt.rd |only man/xmeta-package.Rd | 4 ++-- 20 files changed, 85 insertions(+), 80 deletions(-)
Title: Simple Variable Treatment
Description: Prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: Inf, NA, too many categorical values, rare categorical values, new categorical values (levels seen during application, but not during training). 'vtreat::prepare' should be used as you would use 'model.matrix'.
Author: John Mount, Nina Zumel
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 0.5.20 dated 2015-11-05 and 0.5.21 dated 2015-11-10
DESCRIPTION | 8 - MD5 | 22 +-- R/vtreat.R | 33 ++--- README.md | 2 build/vignette.rds |binary inst/doc/vtreat.html | 272 ++++++++++++++++++++++---------------------- inst/doc/vtreatOverfit.R | 5 inst/doc/vtreatOverfit.Rmd | 7 - inst/doc/vtreatOverfit.html | 162 +++++++++++--------------- man/designTreatmentsC.Rd | 7 - man/designTreatmentsN.Rd | 7 - man/vtreat-package.Rd | 4 12 files changed, 253 insertions(+), 276 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.1 dated 2015-09-28 and 0.6.2 dated 2015-11-10
DESCRIPTION | 10 ++- MD5 | 61 ++++++++++++-------- NAMESPACE | 2 NEWS | 20 ++++++ R/classify.R | 12 +++- R/crossv.R |only R/delete.markup.R | 111 +++++++++++++++++++++++++------------- R/delete.stop.words.R | 37 ++++++++---- R/gui.classify.R | 7 +- R/gui.oppose.R | 1 R/gui.stylo.R | 4 - R/make.frequency.list.R | 2 R/make.frequency.list.optimized.R |only R/make.ngrams.R | 25 +++++++- R/make.samples.R | 1 R/make.table.of.frequencies.R | 40 ++++++++----- R/oppose.R | 38 ++++++++----- R/parse.corpus.R |only R/perform.nsc.R | 10 +-- R/perform.svm.R | 5 - R/rolling.classify.r | 4 - R/rolling.delta.R | 7 +- R/stylo.R | 86 +++++++++++++++++------------ R/stylo.default.settings.R | 16 +++-- R/txt.to.features.R | 38 +++++++++++-- R/txt.to.words.R | 38 ++++++++++++- R/txt.to.words.ext.R | 44 +++++++++++++-- data |only man/galbraith.Rd |only man/lee.Rd |only man/make.frequency.list.Rd | 2 man/novels.Rd |only man/parse.corpus.Rd |only man/perform.nsc.Rd | 10 +++ 34 files changed, 444 insertions(+), 187 deletions(-)
Title: Transmission Ratio Distortion
Description: Transmission Ratio Distortion (TRD) is a genetic phenomenon where the two alleles from either parent are not transmitted to the offspring at the expected 1:1 ratio under Mendelian inheritance, leading to spurious signals in genetic association studies. Functions in this package are developed to account for this phenomenon using loglinear model and Transmission Disequilibrium Test (TDT). Some population information can also be calculated.
Author: Lam Opal Huang
Maintainer: Lam Opal Huang <opal.huang@mail.mcgill.ca>
Diff between TRD versions 1.0 dated 2015-01-21 and 1.1 dated 2015-11-10
TRD-1.0/TRD/R/findr.R |only TRD-1.0/TRD/man/findr.Rd |only TRD-1.0/TRD/man/tdt.cnt.Rd |only TRD-1.1/TRD/DESCRIPTION | 12 +- TRD-1.1/TRD/MD5 | 46 ++++---- TRD-1.1/TRD/NAMESPACE | 7 - TRD-1.1/TRD/R/find.maf.R | 214 +++++++++++++++++++++++++++----------- TRD-1.1/TRD/R/find.t.R |only TRD-1.1/TRD/R/gcount.R | 134 ++++++++++++++++++++--- TRD-1.1/TRD/R/ll.R | 43 ++++++- TRD-1.1/TRD/R/ll.domi.R |only TRD-1.1/TRD/R/ll.gdi.R |only TRD-1.1/TRD/R/ll.grri.R |only TRD-1.1/TRD/R/out.stats.R | 229 +++++++++++++++++++++++++++++------------ TRD-1.1/TRD/R/prev.R | 48 +++++--- TRD-1.1/TRD/R/rtrios.R | 90 +++++++++++----- TRD-1.1/TRD/R/strata.cnt.R | 92 ++++++++++------ TRD-1.1/TRD/R/tdt.R | 67 ++++++++--- TRD-1.1/TRD/R/tdt.cnt.R | 49 ++++++-- TRD-1.1/TRD/man/TRD-package.Rd | 28 +++-- TRD-1.1/TRD/man/find.maf.Rd | 50 ++------ TRD-1.1/TRD/man/find.t.Rd |only TRD-1.1/TRD/man/gcount.Rd | 46 ++------ TRD-1.1/TRD/man/ll.Rd | 53 ++++----- TRD-1.1/TRD/man/prev.Rd | 43 +------ TRD-1.1/TRD/man/rtrios.Rd | 53 +++------ TRD-1.1/TRD/man/strata.cnt.Rd | 53 +++------ TRD-1.1/TRD/man/tdt.Rd | 47 ++------ 28 files changed, 857 insertions(+), 547 deletions(-)
Title: In-Source Documentation for R
Description: A 'Doxygen'-like in-source documentation system
for Rd, collation, and 'NAMESPACE' files.
Author: Hadley Wickham [aut, cre, cph],
Peter Danenberg [aut, cph],
Manuel Eugster [aut, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between roxygen2 versions 5.0.0 dated 2015-10-28 and 5.0.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/object-from-call.R | 4 ++-- R/parse-preref.R | 8 ++++++-- R/roclet-rd.R | 2 +- R/roxygenize.R | 2 +- R/tag-registry.R | 2 +- build/vignette.rds |binary inst/doc/collate.html | 4 ++-- inst/doc/formatting.html | 4 ++-- inst/doc/namespace.html | 4 ++-- inst/doc/rd.html | 4 ++-- inst/doc/rdkeywords.html | 4 ++-- inst/doc/roxygen2.html | 4 ++-- tests/testthat/test-namespace.R | 12 ++++++++++++ tests/testthat/test-package-doc.R | 2 -- 16 files changed, 54 insertions(+), 40 deletions(-)
Title: Quick Wraps 2
Description: A collection of (wrapper) functions the creator found useful for
quickly placing data summaries and formatted regression results into .Rnw or
.Rmd files. Functions for generating commonly used graphics, such as receiver
operating curves or Bland-Altman plots, are also provided by 'qwraps2'.
'qwraps2' is a updated version of a package 'qwraps'. The original version
'qwraps' was never submitted to CRAN but can be found at
https://github.com/dewittpe/qwraps. The implementation and limited scope of the
functions within 'qwraps2' (https://github.com/dewittpe/qwraps2) is fundamentally
different from 'qwraps'.
Author: Peter DeWitt [aut, cre],
Tell Bennett [ctb]
Maintainer: Peter DeWitt <dewittpe@gmail.com>
Diff between qwraps2 versions 0.1.1 dated 2015-04-20 and 0.1.2 dated 2015-11-10
DESCRIPTION | 17 +++++++---- MD5 | 42 +++++++++++++++------------ NAMESPACE | 19 +++++++++++- R/confusion_matrix.R |only R/extract.R | 2 - R/mean_sd.R | 2 - R/median_iqr.R |only R/n_perc.R | 63 ++++++++++++++++++++++++++++++++++++++++- R/qable.R |only R/qkmplot.R | 73 ++++++++++++++++++++++++++++++++++++++++++++++-- R/qroc.R | 2 - README.md | 10 +++++- man/confusion_matrix.Rd |only man/extract.Rd | 2 - man/frmt.Rd | 2 - man/frmtp.Rd | 2 - man/mean_sd.Rd | 2 - man/median_iqr.Rd |only man/n_perc.Rd | 21 +++++++++++++ man/qable.Rd |only man/qacf.Rd | 2 - man/qblandaltman.Rd | 2 - man/qkmplot.Rd | 16 +++++++++- man/qroc.Rd | 2 - man/qwraps2.Rd | 2 - 25 files changed, 237 insertions(+), 46 deletions(-)
Title: Taxonomic Monographs Tools
Description: Contains functions intended to facilitate the production of plant taxonomic monographs. The package includes functions to convert tables into taxonomic descriptions, lists of collectors, examined specimens, and can generate a monograph skeleton. Additionally, wrapper functions to batch the production of phenology charts and distributional and diversity maps are also available.
Author: Marcelo Reginato
Maintainer: Marcelo Reginato <reginatobio@yahoo.com.br>
Diff between monographaR versions 1.0 dated 2015-09-07 and 1.01 dated 2015-11-10
monographaR-1.0/monographaR/R/monographaR-package.r |only monographaR-1.01/monographaR/DESCRIPTION | 12 monographaR-1.01/monographaR/MD5 | 48 +- monographaR-1.01/monographaR/NAMESPACE | 16 monographaR-1.01/monographaR/R/buildMonograph.R |only monographaR-1.01/monographaR/R/collectorList.R | 9 monographaR-1.01/monographaR/R/collectorList2.R |only monographaR-1.01/monographaR/R/examinedSpecimens.R | 4 monographaR-1.01/monographaR/R/examinedSpecimens2.R |only monographaR-1.01/monographaR/R/mapBatch.R | 177 ++++++--- monographaR-1.01/monographaR/R/mapDiversity.R | 7 monographaR-1.01/monographaR/R/mapTable.R | 4 monographaR-1.01/monographaR/R/monographaR-internal.R | 251 ++++++------- monographaR-1.01/monographaR/R/phenoHist.R | 4 monographaR-1.01/monographaR/R/tableToDescription.R | 5 monographaR-1.01/monographaR/R/tableToDescription2.R |only monographaR-1.01/monographaR/data/monographaR_examples.rda |binary monographaR-1.01/monographaR/inst/CITATION | 4 monographaR-1.01/monographaR/inst/doc/tutorial.R | 73 ++- monographaR-1.01/monographaR/inst/doc/tutorial.Rmd | 127 ++++-- monographaR-1.01/monographaR/inst/doc/tutorial.html | 136 ++++--- monographaR-1.01/monographaR/man/buildMonograph.Rd |only monographaR-1.01/monographaR/man/collectorList.Rd | 116 +++--- monographaR-1.01/monographaR/man/mapBatch.Rd | 103 +++-- monographaR-1.01/monographaR/man/monographaR-package.Rd | 14 monographaR-1.01/monographaR/man/monographaR_examples.Rd | 3 monographaR-1.01/monographaR/man/phenoHist.Rd | 222 +++++------ monographaR-1.01/monographaR/vignettes/tutorial.Rmd | 127 ++++-- 28 files changed, 878 insertions(+), 584 deletions(-)
Title: Performing Continuous-Time Microsimulation
Description: This entry-level toolkit allows performing generic continuous-time microsimulation for a wide range of demograhic applications.
Author: Sabine Zinn
Maintainer: Sabine Zinn <sabine.zinn@lifbi.de>
Diff between MicSim versions 1.0.9 dated 2015-07-24 and 1.0.10 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/micSim.r | 22 +++++++++++++++++----- inst/NEWS.Rd | 13 ++++++++++--- man/MicSim-package.Rd | 8 ++++---- 5 files changed, 39 insertions(+), 20 deletions(-)
Title: Convert GBM Object Trees to SAS Code
Description: Writes SAS code to get predicted values from every tree of a gbm.object.
Author: John R. Dixon
Maintainer: John R. Dixon <gbm2sas@gmail.com>
Diff between gbm2sas versions 2.0 dated 2015-11-08 and 2.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/gbm2sas.Rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Planning and Analyzing Dose Finding Experiments
Description: The DoseFinding package provides functions for the design and analysis
of dose-finding experiments (with focus on pharmaceutical Phase
II clinical trials). It provides functions for: multiple contrast
tests, fitting non-linear dose-response models (using Bayesian and
non-Bayesian estimation), calculating optimal designs and an
implementation of the MCPMod methodology.
Author: Bjoern Bornkamp, Jose Pinheiro, Frank Bretz
Maintainer: Bjoern Bornkamp <bbnkmp@gmail.com>
Diff between DoseFinding versions 0.9-12 dated 2014-09-28 and 0.9-13 dated 2015-11-10
ChangeLog | 8 ++++++++ DESCRIPTION | 10 +++++----- MD5 | 15 ++++++++------- NAMESPACE | 9 ++++++++- R/MCTtest.R | 8 +++++--- R/bFitMod.R | 33 ++++++++++++++++++--------------- R/qmvtDF.R |only man/DoseFinding-package.Rd | 10 ++-------- src/Makevars | 2 +- 9 files changed, 55 insertions(+), 40 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Efficient statistical testing and scalable visualization of intersections among multiple sets.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 0.99.1 dated 2015-11-09 and 0.99.2 dated 2015-11-10
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/set_html.html | 4 ++-- src/dmvhyper.c | 3 +-- src/dmvhyperLog.c | 9 +-------- 5 files changed, 11 insertions(+), 19 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Software Tools for the Statistical Analysis of Network Data
Description: An integrated set of tools for the representation, visualization, analysis, and simulation of network data. For an introduction, type help(package='statnet').
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut],
Skye Bender-deMoll [aut],
Martina Morris [aut, cre]
Maintainer: Martina Morris <morrism@u.washington.edu>
Diff between statnet versions 2015.6.2 dated 2015-07-18 and 2015.11.0 dated 2015-11-10
DESCRIPTION | 20 +-- MD5 | 4 man/statnet-package.Rd | 302 +++++++++++++++++++------------------------------ 3 files changed, 134 insertions(+), 192 deletions(-)
Title: Nonparametric Hypothesis Tests of Isotropy and Symmetry
Description: Implements nonparametric hypothesis tests to check isotropy and
symmetry properties for two-dimensional spatial data.
Author: Zachary Weller [aut, cre]
Maintainer: Zachary Weller <wellerz@stat.colostate.edu>
Diff between spTest versions 0.2.2 dated 2015-09-24 and 0.2.3 dated 2015-11-10
DESCRIPTION | 18 MD5 | 87 NAMESPACE | 3 R/GuanTestGrid.R | 12 R/GuanTestGrid_help.R | 46 R/GuanTestUnif.R | 36 R/GuanTestUnif_help.R | 46 R/LuTest.R | 8 R/LuTest_help.R | 21 R/MaityTest.R | 10 R/MaityTest_help.R | 40 R/coords_aniso.R | 2 R/htestIso_class.R |only build/vignette.rds |binary inst/doc/spTest-vig.R | 8 inst/doc/spTest-vig.pdf |binary inst/doc/spTest-vig.rnw | 8 man/GuanTestGrid.Rd | 8 man/GuanTestUnif.Rd | 34 man/LuTest.Rd | 4 man/MaityTest.Rd | 8 man/WRFG.Rd | 8 man/coords.aniso.Rd | 12 man/htestIso-class.Rd |only man/print.htestIso.Rd |only man/spTest.Rd | 6 vignettes/figures/fig-dirsemi1-eps-converted-to.pdf |binary vignettes/figures/fig-dsvar2-eps-converted-to.pdf |binary vignettes/figures/fig-elev-eps-converted-to.pdf |binary vignettes/figures/fig-elev.eps | 735 vignettes/figures/fig-grid-eps-converted-to.pdf |binary vignettes/figures/fig-grid.eps | 686 vignettes/figures/fig-heatmap1-eps-converted-to.pdf |binary vignettes/figures/fig-heatmap1.eps | 146 vignettes/figures/fig-iso2-eps-converted-to.pdf |binary vignettes/figures/fig-iso2.eps | 125 vignettes/figures/fig-narccap-eps-converted-to.pdf |binary vignettes/figures/fig-narccap.eps |16095 +++++++++----------- vignettes/figures/fig-narccap2-eps-converted-to.pdf |binary vignettes/figures/fig-narccap2.eps | 5414 +++--- vignettes/figures/fig-precipdv-eps-converted-to.pdf |binary vignettes/figures/fig-rain-eps-converted-to.pdf |binary vignettes/figures/fig-rain.eps | 785 vignettes/figures/fig-rain1-eps-converted-to.pdf |binary vignettes/figures/fig-rain2-eps-converted-to.pdf |binary vignettes/spTest-vig.rnw | 8 46 files changed, 11525 insertions(+), 12894 deletions(-)
Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete
Variant (CEEMDAN)
Description: An R interface for C library libeemd for performing the ensemble
empirical mode decomposition (EEMD), its complete variant (CEEMDAN) or the
regular empirical mode decomposition (EMD).
Author: Jouni Helske [aut, cre] (R interface),
Perttu Luukko [aut] (Original libeemd C library)
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between Rlibeemd versions 1.3.5 dated 2015-07-07 and 1.3.6 dated 2015-11-10
Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_ceemdan.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_eemd.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_emd.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_emd_num_imfs.R |only Rlibeemd-1.3.5/Rlibeemd/tests/testthat/test_extrema.R |only Rlibeemd-1.3.6/Rlibeemd/DESCRIPTION | 9 +- Rlibeemd-1.3.6/Rlibeemd/MD5 | 30 +++---- Rlibeemd-1.3.6/Rlibeemd/R/ceemdan.R | 31 +++++-- Rlibeemd-1.3.6/Rlibeemd/R/ecg.R | 32 +++---- Rlibeemd-1.3.6/Rlibeemd/R/eemd.R | 26 ++++-- Rlibeemd-1.3.6/Rlibeemd/R/emd.R | 15 ++- Rlibeemd-1.3.6/Rlibeemd/R/emd_num_imfs.R | 2 Rlibeemd-1.3.6/Rlibeemd/configure.ac | 54 ++++++------- Rlibeemd-1.3.6/Rlibeemd/man/nIMFs.Rd | 2 Rlibeemd-1.3.6/Rlibeemd/src/eemdR.cpp | 3 Rlibeemd-1.3.6/Rlibeemd/tests/test-all.R | 4 Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-ceemdan.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-eemd.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-emd.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-emd_num_imfs.R |only Rlibeemd-1.3.6/Rlibeemd/tests/testthat/test-extrema.R |only 21 files changed, 122 insertions(+), 86 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to http://www.fishbase.org, re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to http://www.sealifebase.org data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@ropensci.org>
Diff between rfishbase versions 2.0.3 dated 2015-09-09 and 2.1.0 dated 2015-11-10
rfishbase-2.0.3/rfishbase/inst/doc/tutorial.R |only rfishbase-2.1.0/rfishbase/DESCRIPTION | 17 - rfishbase-2.1.0/rfishbase/MD5 | 134 ++++++------ rfishbase-2.1.0/rfishbase/NAMESPACE | 16 + rfishbase-2.1.0/rfishbase/NEWS | 6 rfishbase-2.1.0/rfishbase/R/00-endpoint.R | 20 + rfishbase-2.1.0/rfishbase/R/check_and_parse.R | 2 rfishbase-2.1.0/rfishbase/R/common_names.R | 17 - rfishbase-2.1.0/rfishbase/R/distribution.R | 14 - rfishbase-2.1.0/rfishbase/R/docs.R | 1 rfishbase-2.1.0/rfishbase/R/fishbase.R | 6 rfishbase-2.1.0/rfishbase/R/heartbeat.R | 6 rfishbase-2.1.0/rfishbase/R/list_fields.R | 4 rfishbase-2.1.0/rfishbase/R/species.R | 7 rfishbase-2.1.0/rfishbase/R/species_list.R | 9 rfishbase-2.1.0/rfishbase/R/species_names.R | 4 rfishbase-2.1.0/rfishbase/R/synonyms.R | 9 rfishbase-2.1.0/rfishbase/R/trophic_ecology.R | 1 rfishbase-2.1.0/rfishbase/build/vignette.rds |binary rfishbase-2.1.0/rfishbase/data/datalist |only rfishbase-2.1.0/rfishbase/data/sealifebase.rda |binary rfishbase-2.1.0/rfishbase/inst/doc/tutorial.Rmd | 128 ----------- rfishbase-2.1.0/rfishbase/inst/doc/tutorial.html | 133 ----------- rfishbase-2.1.0/rfishbase/man/common_names.Rd | 4 rfishbase-2.1.0/rfishbase/man/common_to_sci.Rd | 6 rfishbase-2.1.0/rfishbase/man/diet.Rd | 2 rfishbase-2.1.0/rfishbase/man/distribution.Rd | 2 rfishbase-2.1.0/rfishbase/man/docs.Rd | 6 rfishbase-2.1.0/rfishbase/man/ecology.Rd | 2 rfishbase-2.1.0/rfishbase/man/ecosystem.Rd | 2 rfishbase-2.1.0/rfishbase/man/faoareas.Rd | 2 rfishbase-2.1.0/rfishbase/man/fecundity.Rd | 2 rfishbase-2.1.0/rfishbase/man/fishbase.Rd | 2 rfishbase-2.1.0/rfishbase/man/fooditems.Rd | 2 rfishbase-2.1.0/rfishbase/man/heartbeat.Rd | 2 rfishbase-2.1.0/rfishbase/man/introductions.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_freq.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_length.Rd | 2 rfishbase-2.1.0/rfishbase/man/length_weight.Rd | 12 - rfishbase-2.1.0/rfishbase/man/list_fields.Rd | 2 rfishbase-2.1.0/rfishbase/man/load_taxa.Rd | 4 rfishbase-2.1.0/rfishbase/man/maturity.Rd | 2 rfishbase-2.1.0/rfishbase/man/morphology.Rd | 2 rfishbase-2.1.0/rfishbase/man/morphometrics.Rd | 2 rfishbase-2.1.0/rfishbase/man/occurrence.Rd | 2 rfishbase-2.1.0/rfishbase/man/oxygen.Rd | 2 rfishbase-2.1.0/rfishbase/man/ping.Rd | 2 rfishbase-2.1.0/rfishbase/man/popchar.Rd | 4 rfishbase-2.1.0/rfishbase/man/popgrowth.Rd | 2 rfishbase-2.1.0/rfishbase/man/popqb.Rd | 2 rfishbase-2.1.0/rfishbase/man/predators.Rd | 2 rfishbase-2.1.0/rfishbase/man/ration.Rd | 2 rfishbase-2.1.0/rfishbase/man/reproduction.Rd | 2 rfishbase-2.1.0/rfishbase/man/rfishbase-package.Rd | 9 rfishbase-2.1.0/rfishbase/man/sci_to_common.Rd | 6 rfishbase-2.1.0/rfishbase/man/sealifebase.Rd | 2 rfishbase-2.1.0/rfishbase/man/spawning.Rd | 2 rfishbase-2.1.0/rfishbase/man/species.Rd | 8 rfishbase-2.1.0/rfishbase/man/species_fields.Rd | 2 rfishbase-2.1.0/rfishbase/man/species_list.Rd | 10 rfishbase-2.1.0/rfishbase/man/species_names.Rd | 2 rfishbase-2.1.0/rfishbase/man/speed.Rd | 2 rfishbase-2.1.0/rfishbase/man/stocks.Rd | 2 rfishbase-2.1.0/rfishbase/man/swimming.Rd | 2 rfishbase-2.1.0/rfishbase/man/synonyms.Rd | 8 rfishbase-2.1.0/rfishbase/man/validate_names.Rd | 2 rfishbase-2.1.0/rfishbase/tests/testthat/helper_rfishbase.R | 12 - rfishbase-2.1.0/rfishbase/tests/testthat/test_ecology.R | 4 rfishbase-2.1.0/rfishbase/tests/testthat/test_synonyms.R | 8 69 files changed, 242 insertions(+), 457 deletions(-)
Title: A Fast Implementation of Random Forests
Description: A fast implementation of Random Forests, particularly suited for high dimensional data.
Ensembles of classification, regression, survival and probability prediction trees are
supported. Data from genome-wide association studies can be analyzed efficiently. In addition to
data frames, datasets of class 'gwaa.data' (R package GenABEL) can be directly analyzed.
Author: Marvin N. Wright
Maintainer: Marvin N. Wright <wright@imbs.uni-luebeck.de>
Diff between ranger versions 0.2.7 dated 2015-07-29 and 0.3.0 dated 2015-11-10
DESCRIPTION | 20 +--- MD5 | 36 ++++--- NEWS |only R/predict.R | 71 +++++++++++---- R/ranger.R | 15 ++- man/ranger.Rd | 8 + src/Forest.cpp | 206 ++++++++++++++++++++++++++++++++++----------- src/Forest.h | 11 +- src/Makevars | 1 src/Makevars.win | 2 src/Tree.cpp | 31 +++--- src/Tree.h | 9 - src/TreeClassification.cpp | 2 src/TreeProbability.cpp | 2 src/TreeRegression.cpp | 2 src/rangerCpp.cpp | 4 src/utility.h | 15 +++ src/version.h | 2 tests |only 19 files changed, 310 insertions(+), 127 deletions(-)
Title: High Frequency Portfolio Analytics by PortfolioEffect
Description: R interface to PortfolioEffect Quant service for backtesting
high frequency trading (HFT) strategies, intraday portfolio analysis
and optimization. Includes auto-calibrating model pipeline for market
microstructure noise, risk factors, price jumps/outliers, tail risk
(high-order moments) and price fractality (long memory). Constructed
portfolios could use client-side market data or access HF intraday price
history for all major US Equities. See https://www.portfolioeffect.com/
for more information on the PortfolioEffect high frequency portfolio
analytics platform.
Author: Aleksey Zemnitskiy [aut, cre],
Andrey Kostin [aut],
Oleg Nechaev [aut],
Craig Otis and others [ctb, cph] (OpenFAST library),
Daniel Lemire, Muraoka Taro and others [ctb, cph] (JavaFastPFOR
library),
Joe Walnes, Jorg Schaible and others [ctb, cph] (XStream library),
Dain Sundstrom [ctb, cph] (Snappy library),
Extreme! Lab, Indiana University [ctb, cph] (XPP3 library),
The Apache Software Foundation [ctb, cph] (Apache Log4j and Commons
Lang libraries),
Google, Inc. [ctb, cph] (GSON library),
Free Software Foundation [ctb, cph] (GNU Trove and GNU Crypto
libraries)
Maintainer: Aleksey Zemnitskiy <aleksey.zemnitskiy@portfolioeffect.com>
Diff between PortfolioEffectHFT versions 1.2 dated 2015-09-29 and 1.3 dated 2015-11-10
DESCRIPTION | 6 MD5 | 316 ++++++++++----------- NAMESPACE | 1 NEWS |only R/message.R | 2 R/optimization.R | 10 R/plot.R | 69 ++-- R/portfolio.R | 58 +-- R/util.R | 2 build/vignette.rds |binary demo/alpha_decay_demo.R | 18 - demo/efficient_frontier_demo.R | 10 demo/holding_period_risks_demo.R | 32 +- demo/lf_hf_strategy_demo.R | 12 demo/portfolio_metrics_demo.R | 24 - demo/portfolio_optimization_demo.R | 12 demo/txnCosts_demo.R | 24 - inst/doc/PortfolioEffectHFT.Rnw | 130 +++++--- inst/doc/PortfolioEffectHFT.pdf |binary inst/java/portfolioeffect-quant-client-1.0.jar |binary man/aapl.data.Rd | 7 man/optimization_constraint_CVaR.Rd | 5 man/optimization_constraint_VaR.Rd | 5 man/optimization_constraint_allWeights.Rd | 1 man/optimization_constraint_beta.Rd | 1 man/optimization_constraint_expectedReturn.Rd | 1 man/optimization_constraint_modifiedSharpeRatio.Rd | 5 man/optimization_constraint_portfolioValue.Rd | 1 man/optimization_constraint_return.Rd | 1 man/optimization_constraint_sharpeRatio.Rd | 1 man/optimization_constraint_starrRatio.Rd | 3 man/optimization_constraint_sumOfAbsWeights.Rd | 1 man/optimization_constraint_variance.Rd | 1 man/optimization_constraint_weight.Rd | 1 man/optimization_forecast.Rd | 5 man/optimization_goal.Rd | 3 man/optimization_info.Rd | 1 man/optimization_run.Rd | 1 man/optimizer-class.Rd | 1 man/portfolio-class.Rd | 1 man/portfolioPlot-class.Rd | 1 man/portfolio_CVaR.Rd | 7 man/portfolio_VaR.Rd | 7 man/portfolio_addPosition.Rd | 1 man/portfolio_alpha.Rd | 1 man/portfolio_availableSymbols.Rd |only man/portfolio_beta.Rd | 1 man/portfolio_calmarRatio.Rd | 1 man/portfolio_create.Rd | 1 man/portfolio_cumulant.Rd | 1 man/portfolio_downCaptureRatio.Rd | 1 man/portfolio_downNumberRatio.Rd | 1 man/portfolio_downPercentageRatio.Rd | 1 man/portfolio_downsideVariance.Rd | 1 man/portfolio_endBatch.Rd | 13 man/portfolio_expectedDownsideReturn.Rd | 1 man/portfolio_expectedReturn.Rd | 1 man/portfolio_expectedUpsideReturn.Rd | 1 man/portfolio_fractalDimension.Rd | 1 man/portfolio_gainLossVarianceRatio.Rd | 1 man/portfolio_gainVariance.Rd | 1 man/portfolio_getSettings.Rd | 3 man/portfolio_hurstExponent.Rd | 1 man/portfolio_informationRatio.Rd | 1 man/portfolio_jensensAlpha.Rd | 1 man/portfolio_kurtosis.Rd | 1 man/portfolio_lossVariance.Rd | 1 man/portfolio_maxDrawdown.Rd | 1 man/portfolio_modifiedSharpeRatio.Rd | 7 man/portfolio_moment.Rd | 1 man/portfolio_omegaRatio.Rd | 1 man/portfolio_pdf.Rd | 1 man/portfolio_profit.Rd | 1 man/portfolio_rachevRatio.Rd | 7 man/portfolio_removePosition.Rd | 1 man/portfolio_return.Rd | 1 man/portfolio_settings.Rd | 6 man/portfolio_sharpeRatio.Rd | 1 man/portfolio_skewness.Rd | 1 man/portfolio_sortinoRatio.Rd | 1 man/portfolio_starrRatio.Rd | 5 man/portfolio_startBatch.Rd | 13 man/portfolio_symbols.Rd | 1 man/portfolio_treynorRatio.Rd | 1 man/portfolio_txnCosts.Rd | 1 man/portfolio_upCaptureRatio.Rd | 1 man/portfolio_upNumberRatio.Rd | 1 man/portfolio_upPercentageRatio.Rd | 1 man/portfolio_upsideDownsideVarianceRatio.Rd | 1 man/portfolio_upsideVariance.Rd | 1 man/portfolio_value.Rd | 1 man/portfolio_variance.Rd | 1 man/position_CVaR.Rd | 7 man/position_VaR.Rd | 7 man/position_alpha.Rd | 1 man/position_beta.Rd | 1 man/position_calmarRatio.Rd | 1 man/position_correlation.Rd | 1 man/position_correlationMatrix.Rd | 1 man/position_covariance.Rd | 1 man/position_covarianceMatrix.Rd | 1 man/position_cumulant.Rd | 1 man/position_downCaptureRatio.Rd | 1 man/position_downNumberRatio.Rd | 1 man/position_downPercentageRatio.Rd | 1 man/position_downsideVariance.Rd | 1 man/position_expectedDownsideReturn.Rd | 1 man/position_expectedReturn.Rd | 1 man/position_expectedUpsideReturn.Rd | 1 man/position_fractalDimension.Rd | 1 man/position_gainLossVarianceRatio.Rd | 1 man/position_gainVariance.Rd | 1 man/position_hurstExponent.Rd | 1 man/position_informationRatio.Rd | 1 man/position_jensensAlpha.Rd | 1 man/position_kurtosis.Rd | 1 man/position_lossVariance.Rd | 1 man/position_maxDrawdown.Rd | 1 man/position_modifiedSharpeRatio.Rd | 7 man/position_moment.Rd | 1 man/position_omegaRatio.Rd | 1 man/position_pdf.Rd | 1 man/position_price.Rd | 1 man/position_profit.Rd | 1 man/position_quantity.Rd | 1 man/position_rachevRatio.Rd | 7 man/position_return.Rd | 1 man/position_returnAutocovariance.Rd | 1 man/position_returnJumpSize.Rd | 1 man/position_setQuantity.Rd | 1 man/position_sharpeRatio.Rd | 1 man/position_skewness.Rd | 1 man/position_sortinoRatio.Rd | 5 man/position_starrRatio.Rd | 7 man/position_treynorRatio.Rd | 1 man/position_txnCosts.Rd | 1 man/position_upCaptureRatio.Rd | 1 man/position_upNumberRatio.Rd | 1 man/position_upPercentageRatio.Rd | 1 man/position_upsideDownsideVarianceRatio.Rd | 1 man/position_upsideVariance.Rd | 1 man/position_value.Rd | 1 man/position_variance.Rd | 1 man/position_weight.Rd | 1 man/util_POSIXTimeToDate.Rd | 1 man/util_cleanCredentials.Rd | 1 man/util_colorScheme.Rd | 3 man/util_dateToPOSIXTime.Rd | 1 man/util_fillScheme.Rd | 1 man/util_getComputeTime.Rd | 1 man/util_ggplot.Rd | 1 man/util_line2d.Rd | 11 man/util_multiplot.Rd | 1 man/util_plot2d.Rd | 5 man/util_plot2df.Rd | 9 man/util_plotDensity.Rd | 1 man/util_plotTheme.Rd | 3 man/util_setCredentials.Rd | 1 man/util_summary.Rd | 1 vignettes/PortfolioEffectHFT.Rnw | 130 +++++--- 160 files changed, 692 insertions(+), 447 deletions(-)
More information about PortfolioEffectHFT at CRAN
Permanent link
Title: Procrustes Application to Cophylogenetic Analysis
Description: Procrustes analyses to infer co-phylogenetic
matching between pairs of (ultrametric) phylogenetic trees.
Author: Juan Antonio Balbuena <j.a.balbuena@uv.es>, Timothee Poisot
<tim@poisotlab.io>, Matthew Hutchinson <matthewhutchinson15@gmail.com>,
Fernando Cagua <fernando@cagua.co>
Maintainer: Timothee Poisot <tim@poisotlab.io>
Diff between paco versions 0.2.2 dated 2015-10-09 and 0.2.3 dated 2015-11-10
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/PACo.r | 8 +++++--- man/PACo.Rd | 9 ++++++--- man/add_pcoord.Rd | 2 +- man/coordpcoa.Rd | 2 +- man/gl_links.Rd | 2 +- man/gophertree.Rd | 2 +- man/licetree.Rd | 2 +- man/paco_links.Rd | 2 +- man/prepare_paco_data.Rd | 2 +- man/residuals.paco.Rd | 2 +- 13 files changed, 39 insertions(+), 33 deletions(-)
Title: Fitting Structural Equation Mixture Models
Description: Estimation of structural equation models with nonlinear effects
and underlying nonnormal distributions.
Author: Nora Umbach [aut, cre],
Katharina Naumann [aut],
David Hoppe [aut],
Holger Brandt [aut],
Augustin Kelava [ctb],
Bernhard Schmitz [ctb]
Maintainer: Nora Umbach <nora.umbach@web.de>
Diff between nlsem versions 0.5.1 dated 2015-09-21 and 0.6 dated 2015-11-10
nlsem-0.5.1/nlsem/R/fscores.R |only nlsem-0.5.1/nlsem/man/get_factor_scores.Rd |only nlsem-0.6/nlsem/ChangeLog | 11 + nlsem-0.6/nlsem/DESCRIPTION | 8 nlsem-0.6/nlsem/MD5 | 26 +- nlsem-0.6/nlsem/NAMESPACE | 1 nlsem-0.6/nlsem/R/em.R | 4 nlsem-0.6/nlsem/R/qml.R | 6 nlsem-0.6/nlsem/R/s3generics.R | 286 +++++++++++++---------------- nlsem-0.6/nlsem/R/semm.R | 58 +++++ nlsem-0.6/nlsem/data/australia.txt.gz |only nlsem-0.6/nlsem/man/australia.Rd |only nlsem-0.6/nlsem/man/em.Rd | 8 nlsem-0.6/nlsem/man/jordan.Rd | 47 +++- nlsem-0.6/nlsem/man/nlsem-package.Rd | 9 nlsem-0.6/nlsem/man/qml.Rd | 3 16 files changed, 272 insertions(+), 195 deletions(-)
Title: Matrix Functions for Teaching and Learning Linear Algebra and
Multivariate Statistics
Description: A collection of matrix functions for teaching and learning matrix
linear algebra as used in multivariate statistical methods. These functions are
mainly for tutorial purposes in learning matrix algebra ideas using R. In some
cases, functions are provided for concepts available elsewhere in R, but where
the function call or name is not obvious. In other cases, functions are provided
to show or demonstrate an algorithm.
Author: Michael Friendly [aut, cre], John Fox [ctb], Georges Monette [ctb]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between matlib versions 0.4.1 dated 2015-11-05 and 0.5.1 dated 2015-11-10
matlib-0.4.1/matlib/man/proj.Rd |only matlib-0.5.1/matlib/DESCRIPTION | 9 matlib-0.5.1/matlib/MD5 | 69 +-- matlib-0.5.1/matlib/NAMESPACE | 14 matlib-0.5.1/matlib/R/QR.R | 6 matlib-0.5.1/matlib/R/R.R |only matlib-0.5.1/matlib/R/eig.R | 4 matlib-0.5.1/matlib/R/gaussian-elimination.R | 4 matlib-0.5.1/matlib/R/gsorth.R | 3 matlib-0.5.1/matlib/R/len.R |only matlib-0.5.1/matlib/R/matlib.R | 58 -- matlib-0.5.1/matlib/R/plotEqn.R | 144 ++++-- matlib-0.5.1/matlib/R/proj.R |only matlib-0.5.1/matlib/R/rowops.R | 2 matlib-0.5.1/matlib/R/showEqn.R | 17 matlib-0.5.1/matlib/R/vectors.R |only matlib-0.5.1/matlib/README.md | 25 - matlib-0.5.1/matlib/build/vignette.rds |binary matlib-0.5.1/matlib/inst/doc/eigen-ex1.html | 466 +++++++++++++++----- matlib-0.5.1/matlib/inst/doc/eigen-ex2.R | 9 matlib-0.5.1/matlib/inst/doc/eigen-ex2.Rmd | 12 matlib-0.5.1/matlib/inst/doc/eigen-ex2.html | 467 ++++++++++++++++----- matlib-0.5.1/matlib/inst/doc/linear-equations.R |only matlib-0.5.1/matlib/inst/doc/linear-equations.Rmd |only matlib-0.5.1/matlib/inst/doc/linear-equations.html |only matlib-0.5.1/matlib/man/Ginv.Rd | 3 matlib-0.5.1/matlib/man/Proj.Rd |only matlib-0.5.1/matlib/man/QR.Rd | 6 matlib-0.5.1/matlib/man/R.Rd | 21 matlib-0.5.1/matlib/man/SVD.Rd | 4 matlib-0.5.1/matlib/man/cholesky.Rd | 3 matlib-0.5.1/matlib/man/echelon.Rd | 3 matlib-0.5.1/matlib/man/gsorth.Rd | 3 matlib-0.5.1/matlib/man/len.Rd |only matlib-0.5.1/matlib/man/matlib.Rd |only matlib-0.5.1/matlib/man/plotEqn.Rd | 20 matlib-0.5.1/matlib/man/plotEqn3d.Rd |only matlib-0.5.1/matlib/man/rowswap.Rd | 4 matlib-0.5.1/matlib/man/showEqn.Rd | 10 matlib-0.5.1/matlib/man/vectors.Rd |only matlib-0.5.1/matlib/vignettes/CanvasMatrix.js |only matlib-0.5.1/matlib/vignettes/eigen-ex2.Rmd | 12 matlib-0.5.1/matlib/vignettes/linear-equations.Rmd |only 43 files changed, 1020 insertions(+), 378 deletions(-)
Title: Stable Isotope Mixing Model
Description: Estimates diet contributions from isotopic sources using JAGS.
Includes estimation of concentration dependence and measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson <troutinthemilk@gmail.com>
Diff between IsotopeR versions 0.5 dated 2015-11-07 and 0.5.1 dated 2015-11-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + NEWS | 4 +++- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: An S4 Lattice-Based Package for the Representation of
Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between adegraphics versions 1.0-3 dated 2015-06-24 and 1.0-4 dated 2015-11-10
adegraphics-1.0-3/adegraphics/R/s.hist.R |only adegraphics-1.0-4/adegraphics/DESCRIPTION | 21 +- adegraphics-1.0-4/adegraphics/MD5 | 41 ++-- adegraphics-1.0-4/adegraphics/NAMESPACE | 136 ++++++++-------- adegraphics-1.0-4/adegraphics/R/ADEg.S2.R | 32 +++ adegraphics-1.0-4/adegraphics/R/ADEgS.R | 5 adegraphics-1.0-4/adegraphics/R/S2.distri.R | 2 adegraphics-1.0-4/adegraphics/R/ade4-plot.R | 2 adegraphics-1.0-4/adegraphics/R/ade4-scatter.R | 25 ++ adegraphics-1.0-4/adegraphics/R/adeGsenv.R | 2 adegraphics-1.0-4/adegraphics/R/panelfunctions.R | 65 ++++++- adegraphics-1.0-4/adegraphics/build/vignette.rds |binary adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.Rnw | 10 - adegraphics-1.0-4/adegraphics/inst/doc/adegraphics.pdf |binary adegraphics-1.0-4/adegraphics/man/adeg.panel.hist.Rd |only adegraphics-1.0-4/adegraphics/man/adeg.panel.join.Rd |only adegraphics-1.0-4/adegraphics/man/adeg.panel.label.Rd | 2 adegraphics-1.0-4/adegraphics/man/adeg.panel.nb.Rd | 23 +- adegraphics-1.0-4/adegraphics/man/adeg.panel.values.Rd | 2 adegraphics-1.0-4/adegraphics/man/changelatticetheme.Rd | 6 adegraphics-1.0-4/adegraphics/tests/panelSpatial.R | 3 adegraphics-1.0-4/adegraphics/tests/parameter.R | 9 + adegraphics-1.0-4/adegraphics/vignettes/adegraphics.Rnw | 10 - 23 files changed, 255 insertions(+), 141 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-44 dated 2015-08-30 and 7.3-45 dated 2015-11-10
DESCRIPTION | 10 ++++---- INDEX |only LICENCE.note |only MD5 | 6 ++-- R/fitdistr.R | 2 - inst/NEWS | 3 +- man/Animals.Rd |only man/Boston.Rd |only man/Cars93.Rd |only man/GAGurine.Rd |only man/Skye.Rd |only man/Traffic.Rd |only man/VA.Rd |only man/abbey.Rd |only man/addterm.Rd |only man/area.Rd |only man/bandwidth.nrd.Rd |only man/beav2.Rd |only man/birthwt.Rd |only man/caith.Rd |only man/contr.sdif.Rd |only man/cov.trob.Rd |only man/crabs.Rd |only man/deaths.Rd |only man/epil.Rd |only man/fgl.Rd |only man/gamma.dispersion.Rd |only man/gehan.Rd |only man/hills.Rd |only man/leuk.Rd |only man/mcycle.Rd |only man/menarche.Rd |only man/newcomb.Rd |only man/npr1.Rd |only man/petrol.Rd |only man/plot.lda.Rd |only man/plot.profile.Rd | 59 ++++++++++++++++++++++++++++++++++++++++++++++++ man/predict.lda.Rd |only man/predict.qda.Rd |only man/quine.Rd |only man/rational.Rd |only man/rotifer.Rd |only man/shoes.Rd |only man/snails.Rd |only man/steam.Rd |only man/stepAIC.Rd |only man/studres.Rd |only man/summary.rlm.Rd |only man/waders.Rd |only 49 files changed, 70 insertions(+), 10 deletions(-)
More information about TruncatedNormal at CRAN
Permanent link
Title: Six Sigma Tools for Quality Control and Improvement
Description: Functions and utilities to perform
Statistical Analyses in the Six Sigma way.
Through the DMAIC cycle (Define, Measure, Analyze, Improve, Control),
you can manage several Quality Management studies:
Gage R&R, Capability Analysis, Control Charts, Loss Function Analysis,
etc. Data frames used in the books "Six Sigma with R" (Springer, 2012)
and "Quality Control with R" (Springer, 2015)
are also included in the package.
Author: Emilio L. Cano, Javier M. Moguerza, Mariano Prieto and Andrés Redchuk
Maintainer: Emilio L. Cano <emilio.lopez@urjc.es>
Diff between SixSigma versions 0.8-1 dated 2014-03-07 and 0.9-0 dated 2015-11-10
DESCRIPTION | 21 MD5 | 102 +- NAMESPACE | 53 - NEWS | 145 ++-- R/SixSigma-package.R | 179 ++-- R/auxf.R | 74 -- R/data.R | 1305 ++++++++++++++++++++---------------- R/qcr.profiles.R |only R/ss.ca.R | 1167 ++++++++++++++++---------------- R/ss.rr.R | 578 ++++++++------- build/vignette.rds |binary data/ss.data.bills.RData |only data/ss.data.density.RData |only data/ss.data.thickness.RData |only data/ss.data.thickness2.RData |only data/ss.data.wbx.RData |only data/ss.data.wby.RData |only inst/CITATION | 48 - inst/doc/HelicopterInstructions.R | 19 inst/doc/HelicopterInstructions.pdf |binary inst/doc/ShewhartConstants.R |only inst/doc/ShewhartConstants.Rnw |only inst/doc/ShewhartConstants.pdf |only man/SixSigma.Rd | 174 ++-- man/climProfiles.Rd |only man/outProfiles.Rd |only man/plotControlProfiles.Rd |only man/plotProfiles.Rd |only man/smoothProfiles.Rd |only man/ss.ca.yield.Rd | 94 +- man/ss.ca.z.Rd | 117 +-- man/ss.cc.Rd | 140 +-- man/ss.cc.constants.Rd | 82 +- man/ss.ceDiag.Rd | 142 +-- man/ss.ci.Rd | 156 ++-- man/ss.data.batteries.Rd | 87 +- man/ss.data.bills.Rd |only man/ss.data.bolts.Rd | 81 +- man/ss.data.ca.Rd | 80 +- man/ss.data.density.Rd |only man/ss.data.doe1.Rd | 88 +- man/ss.data.doe2.Rd | 88 +- man/ss.data.pastries.Rd | 84 +- man/ss.data.pb1.Rd | 84 +- man/ss.data.pb2.Rd | 88 +- man/ss.data.pb3.Rd | 90 +- man/ss.data.pb4.Rd | 73 +- man/ss.data.pc.Rd | 84 +- man/ss.data.pc.big.Rd | 81 +- man/ss.data.pc.r.Rd | 80 +- man/ss.data.rr.Rd | 84 +- man/ss.data.strings.Rd | 82 +- man/ss.data.thickness.Rd |only man/ss.data.thickness2.Rd |only man/ss.data.wbx.Rd |only man/ss.data.wby.Rd |only man/ss.heli.Rd | 80 +- man/ss.lf.Rd | 99 +- man/ss.lfa.Rd | 144 +-- man/ss.pMap.Rd | 216 ++--- man/ss.rr.Rd | 178 ++-- man/ss.study.ca.Rd | 115 +-- vignettes/ShewhartConstants.Rnw |only 63 files changed, 3459 insertions(+), 3223 deletions(-)
Title: Genetic Data Manipulation (Quality Control, GRM and LD
Computations, PCA), Linear Mixed Models (AIREML Algorithm),
Association Testing
Description: Manipulation of genetic data (SNPs), computation of Genetic Relationship Matrix, Linkage Disequilibrium, etc. Efficient algorithms for Linear Mixed Model (AIREML, diagonalisation trick).
Author: Hervé Perdry & Claire Dandine-Roulland
Maintainer: Hervé Perdry <herve.perdry@u-psud.fr>
Diff between gaston versions 1.1 dated 2015-10-02 and 1.2 dated 2015-11-10
gaston-1.1/gaston/src/export-crossprod.cpp |only gaston-1.1/gaston/src/export-inverse.cpp |only gaston-1.1/gaston/src/m4_kinship2.cpp |only gaston-1.2/gaston/DESCRIPTION | 6 ++-- gaston-1.2/gaston/MD5 | 36 ++++++++++++-------------- gaston-1.2/gaston/R/bm_grm.r | 13 ++------- gaston-1.2/gaston/R/lmm_simu.r | 2 - gaston-1.2/gaston/inst/doc/gaston.R | 26 +++++++++--------- gaston-1.2/gaston/inst/doc/gaston.Rnw | 18 ++++++++++--- gaston-1.2/gaston/inst/doc/gaston.pdf |binary gaston-1.2/gaston/man/gaston-package.Rd | 6 ++-- gaston-1.2/gaston/man/lik.contour.Rd | 2 - gaston-1.2/gaston/src/ai-reml-1k-covar.h | 2 - gaston-1.2/gaston/src/ai-reml-1k.h | 2 - gaston-1.2/gaston/src/ai-reml-nk-covar.h | 2 - gaston-1.2/gaston/src/ai-reml-nk.h | 2 - gaston-1.2/gaston/src/loubar.h | 2 - gaston-1.2/gaston/src/m4_kinship.cpp | 40 +++++++++++++++-------------- gaston-1.2/gaston/src/m4_kinship_p.cpp | 35 +++++++++++++------------ gaston-1.2/gaston/src/m4_kinship_type.h |only gaston-1.2/gaston/vignettes/gaston.Rnw | 18 ++++++++++--- 21 files changed, 115 insertions(+), 97 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre], Kurt Hornik [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-1 dated 2015-05-19 and 0.0-3 dated 2015-11-10
qrmtools-0.0-1/qrmtools/R/device.R |only qrmtools-0.0-1/qrmtools/R/worst_VaR.R |only qrmtools-0.0-1/qrmtools/demo |only qrmtools-0.0-1/qrmtools/man/device.Rd |only qrmtools-0.0-1/qrmtools/man/worst_VaR.Rd |only qrmtools-0.0-1/qrmtools/src/worst_VaR.c |only qrmtools-0.0-1/qrmtools/src/worst_VaR.h |only qrmtools-0.0-3/qrmtools/DESCRIPTION | 11 ++++--- qrmtools-0.0-3/qrmtools/MD5 | 38 +++++++++++++++++---------- qrmtools-0.0-3/qrmtools/NAMESPACE | 20 +++++++++----- qrmtools-0.0-3/qrmtools/R/GPD.R | 18 ++++++++++++ qrmtools-0.0-3/qrmtools/R/VaR_bounds.R |only qrmtools-0.0-3/qrmtools/R/risk_measures.R |only qrmtools-0.0-3/qrmtools/TODO | 5 +-- qrmtools-0.0-3/qrmtools/build |only qrmtools-0.0-3/qrmtools/inst |only qrmtools-0.0-3/qrmtools/man/VaR_bounds.Rd |only qrmtools-0.0-3/qrmtools/man/risk_measures.Rd |only qrmtools-0.0-3/qrmtools/src/VaR_bounds.c |only qrmtools-0.0-3/qrmtools/src/VaR_bounds.h |only qrmtools-0.0-3/qrmtools/src/init.c | 9 +++--- qrmtools-0.0-3/qrmtools/vignettes |only 22 files changed, 68 insertions(+), 33 deletions(-)
Title: Construction and Analysis of Matrix Population Models
Description: Construct and analyze projection matrix models from a demography study of marked individuals classified by age or stage. The package covers methods described in Matrix Population Models by Caswell (2001) and Quantitative Conservation Biology by Morris and Doak (2002).
Author: Chris Stubben, Brook Milligan, Patrick Nantel
Maintainer: Chris Stubben <stubben@lanl.gov>
Diff between popbio versions 2.4 dated 2012-03-20 and 2.4.2 dated 2015-11-10
popbio-2.4.2/popbio/DESCRIPTION | 21 +++++------ popbio-2.4.2/popbio/MD5 | 52 +++++++++++++++-------------- popbio-2.4.2/popbio/NAMESPACE | 14 ++++++- popbio-2.4.2/popbio/R/QPmat.R | 19 ++++++---- popbio-2.4.2/popbio/R/logi.hist.plot.R | 2 - popbio-2.4.2/popbio/R/secder.R |only popbio-2.4.2/popbio/R/stoch.sens.R |only popbio-2.4.2/popbio/data/grizzly.rda |binary popbio-2.4.2/popbio/data/hudsonia.rda |binary popbio-2.4.2/popbio/data/hudvrs.rda |binary popbio-2.4.2/popbio/data/nematode.rda |binary popbio-2.4.2/popbio/data/teasel.rda |binary popbio-2.4.2/popbio/data/tortoise.rda |binary popbio-2.4.2/popbio/data/whale.rda |binary popbio-2.4.2/popbio/data/woodpecker.rda |binary popbio-2.4.2/popbio/inst/ChangeLog | 13 ++++++- popbio-2.4.2/popbio/man/02Caswell.Rd | 41 +++++++++++----------- popbio-2.4.2/popbio/man/LTRE.Rd | 6 ++- popbio-2.4.2/popbio/man/QPmat.Rd | 14 ++++--- popbio-2.4.2/popbio/man/betaval.Rd | 9 +---- popbio-2.4.2/popbio/man/eigen.analysis.Rd | 12 ++---- popbio-2.4.2/popbio/man/hudcorrs.Rd | 5 +- popbio-2.4.2/popbio/man/hudmxdef.Rd | 4 +- popbio-2.4.2/popbio/man/pfister.plot.Rd | 15 +++++--- popbio-2.4.2/popbio/man/secder.Rd |only popbio-2.4.2/popbio/man/stoch.quasi.ext.Rd | 6 +-- popbio-2.4.2/popbio/man/stoch.sens.Rd |only popbio-2.4.2/popbio/man/vitalsim.Rd | 18 +++++----- popbio-2.4/popbio/R/colorguide.R |only popbio-2.4/popbio/man/colorguide.Rd |only 30 files changed, 138 insertions(+), 113 deletions(-)
Title: Open Perimetry Interface
Description: Implementation of the Open Perimetry Interface (OPI) for simulating and controlling visual field machines using R. The OPI is a standard for interfacing with visual field testing machines (perimeters). It specifies basic functions that allow many visual field tests to be constructed. As of February 2015 it is fully implemented on the Octopus 600 and Octopus 900 and partially on the Heidelberg Edge Perimeter and the Kowa AP 7000. It also has a cousin: the R package visualFields, which has tools for analysing and manipulating visual field data.
Author: Andrew Turpin, David Lawson, Matthias Muller
Maintainer: Andrew Turpin <aturpin@unimelb.edu.au>
Diff between OPI versions 2.1 dated 2014-12-21 and 2.3 dated 2015-11-10
ChangeLog | 10 + DESCRIPTION | 12 - MD5 | 30 ++-- NAMESPACE | 6 R/kowaAP7000Client.r | 294 +++++++++++++++++++++++++++++---------------- R/octopus900Client.r | 198 ++++++++++++++++-------------- R/opi.r | 8 + man/chooseOpi.Rd | 6 man/opiClose.Rd | 2 man/opiInitialize.Rd | 30 +++- man/opiKineticStimulus.Rd | 21 ++- man/opiPresent.Rd | 31 +++- man/opiQueryDevice.Rd | 15 ++ man/opiSetBackground.Rd | 18 +- man/opiStaticStimulus.Rd | 17 ++ man/opiTemporalStimulus.Rd | 5 16 files changed, 459 insertions(+), 244 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to
data files written using Unidata's
netCDF library (version 4 or earlier), which are binary data files that are portable
across platforms and include metadata information in addition to the data sets.
Using this package, netCDF files (either version 4
or "classic" version 3) can be opened and data sets read in easily.
It is also easy to create new netCDF dimensions, variables, and files,
in either version 3 or 4 format, and manipulate existing netCDF files.
This package replaces the former ncdf package, which only worked with
netcdf version 3 files. For various reasons the names of the functions
have had to be changed from the names in the ncdf package. The old ncdf package is still
available at the URL given below, if you need to have backward compatibility.
It should be possible to have both the ncdf and ncdf4 packages installed
simultaneously without a problem.
However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.13 dated 2014-09-16 and 1.14 dated 2015-11-10
ncdf4-1.13/ncdf4/tools/configure.in |only ncdf4-1.14/ncdf4/DESCRIPTION | 16 ncdf4-1.14/ncdf4/MD5 | 24 ncdf4-1.14/ncdf4/R/ncdf4.R | 2 ncdf4-1.14/ncdf4/R/ncdf4_priv_var.R | 5 ncdf4-1.14/ncdf4/configure | 1044 ++++++++++++++++++++++++- ncdf4-1.14/ncdf4/tools/autom4te.cache/output.0 | 1020 ++++++++++++++++++++++++ ncdf4-1.14/ncdf4/tools/autom4te.cache/output.1 | 1020 ++++++++++++++++++++++++ ncdf4-1.14/ncdf4/tools/autom4te.cache/output.2 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/output.3 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/requests | 93 ++ ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.0 | 16 ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.1 | 48 + ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.2 |only ncdf4-1.14/ncdf4/tools/autom4te.cache/traces.3 |only ncdf4-1.14/ncdf4/tools/configure.ac |only 16 files changed, 3253 insertions(+), 35 deletions(-)
Title: Statistical Functions for the Censored and Uncensored
Epanechnikov Distribution
Description: Analyzing censored variables usually requires the use of optimization algorithms. This package provides an alternative algebraic approach to the task of determining the expected value of a random censored variable with a known censoring point. Likewise this approach allows for the determination of the censoring point if the expected value is known. These results are derived under the assumption that the variable follows an Epanechnikov kernel distribution with known mean and range prior to censoring. Statistical functions related to the uncensored Epanechnikov distribution are also provided by this package.
Author: Mathias Borritz Milfeldt [aut, cre]
Maintainer: Mathias Borritz Milfeldt <mathias@milfeldt.dk>
Diff between epandist versions 1.0.1 dated 2015-10-01 and 1.0.2 dated 2015-11-10
DESCRIPTION | 6 +++--- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- R/cepan.R | 22 ++++++++++++++-------- R/depan.R | 11 +++++++++-- R/evepan.R | 17 ++++++++++++++++- R/pepan.R | 13 ++++++++++++- R/qepan.R | 11 +++++++++-- R/repan.R | 3 ++- inst/doc/Vignette_epandist.Rmd | 2 +- inst/doc/Vignette_epandist.html | 13 ++++++------- man/cepan.Rd | 7 ++++++- man/depan.Rd | 11 +++++++++-- man/evepan.Rd | 17 ++++++++++++++++- man/pepan.Rd | 13 ++++++++++++- man/qepan.Rd | 9 ++++++++- man/repan.Rd | 3 ++- vignettes/Vignette_epandist.Rmd | 2 +- 18 files changed, 144 insertions(+), 52 deletions(-)
Title: Case-Control Analysis of Multi-Allelic Loci
Description: Data sets and functions for chi-squared Hardy-Weinberg and case-
control association tests of highly polymorphic genetic data [e.g., human
leukocyte antigen (HLA) data]. Performs association tests at multiple levels of
polymorphism (haplotype, locus and HLA amino-acids). Combines rare variants to
a common class to account for sparse cells in tables as described by Hollenbach
JA, Mack SJ, Thomson G, Gourraud PA. 'Analytical methods for disease association
studies with immunogenetic data.' Methods Mol Biol. 2012;882:245-66.
Author: Derek Pappas <dpappas@chori.org>, Steve Mack <sjmack@chori.org>, Jill
Hollenbach <Jill.Hollenbach@ucsf.edu>
Maintainer: Steve Mack <sjmack@chori.org>
Diff between BIGDAWG versions 1.1.1 dated 2015-10-29 and 1.2.1 dated 2015-11-10
DESCRIPTION | 20 +- MD5 | 87 +++++----- NEWS |only R/BIGDAWG.R | 99 ++++++----- R/HWE.R | 156 +++++++++--------- R/check_functions.R | 374 ++++++++++++++++++++++---------------------- R/general_functions.R | 327 +++++++++++++++++++------------------- R/sysdata.rda |binary build/vignette.rds |binary inst/doc/BIGDAWG.Rmd | 312 ++++++++++++++++++------------------ inst/doc/BIGDAWG.html | 382 ++++++++++++++++++++++----------------------- man/A.Rd | 64 +++---- man/AA.df.check.Rd | 36 ++-- man/AAtable.builder.Rd | 40 ++-- man/AlignObj.Create.Rd | 44 ++--- man/AlignObj.Update.Rd | 44 ++--- man/AlignmentFilter.Rd | 44 ++--- man/BIGDAWG.Rd | 108 ++++++------ man/CheckAlleles.Rd | 48 ++--- man/CheckHLA.Rd | 36 ++-- man/CheckLoci.Rd | 40 ++-- man/EVSremoval.Rd | 40 ++-- man/ExonPtnAlign.Create.Rd | 40 ++-- man/ExonPtnList.Rd | 30 +-- man/GetField.Rd | 40 ++-- man/GetFiles.Rd | 36 ++-- man/H.Rd | 40 ++-- man/HLA_data.Rd | 30 +-- man/HWEChiSq.Rd | 40 ++-- man/L.Rd | 56 +++--- man/PgrpExtract.Rd | 40 ++-- man/PgrpFormat.Rd | 40 ++-- man/PreCheck.Rd | 48 ++--- man/RunChiSq.Rd | 36 ++-- man/TableMaker.Rd | 36 ++-- man/UpdateRelease.Rd | 44 ++--- man/cci.Rd | 100 +++++------ man/cci.pval.Rd | 36 ++-- man/cci.pval.list.Rd | 36 ++-- man/getCS.Mat.Rd | 48 ++--- man/getObsFreq.Rd | 40 ++-- man/make2x2.Rd | 48 ++--- man/makeComb.Rd | 36 ++-- man/rmABstrings.Rd | 36 ++-- vignettes/BIGDAWG.Rmd | 312 ++++++++++++++++++------------------ 45 files changed, 1792 insertions(+), 1757 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex macroevolutionary dynamics on phylogenetic trees. It is a companion package to the command line program BAMM (Bayesian Analysis of Macroevolutionary Mixtures) and is entirely oriented towards the analysis, interpretation, and visualization of evolutionary rates. Functionality includes visualization of rate shifts on phylogenies, estimating evolutionary rates through time, comparing posterior distributions of evolutionary rates across clades, comparing diversification models using Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi, Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.0.6 dated 2015-09-11 and 2.1.0 dated 2015-11-10
BAMMtools-2.0.6/BAMMtools/R/BAMMtools-internal.R |only BAMMtools-2.0.6/BAMMtools/R/as.phylo.branchprior.R |only BAMMtools-2.0.6/BAMMtools/R/bayesFactorBranches.R |only BAMMtools-2.0.6/BAMMtools/R/print.branchprior.R |only BAMMtools-2.0.6/BAMMtools/R/summary.branchprior.R |only BAMMtools-2.0.6/BAMMtools/data/prior.primates.rda |only BAMMtools-2.0.6/BAMMtools/data/prior.whales.rda |only BAMMtools-2.0.6/BAMMtools/man/bayesFactorBranches.Rd |only BAMMtools-2.0.6/BAMMtools/man/summary.branchprior.Rd |only BAMMtools-2.1.0/BAMMtools/DESCRIPTION | 12 BAMMtools-2.1.0/BAMMtools/MD5 | 134 +++---- BAMMtools-2.1.0/BAMMtools/NAMESPACE | 85 ++++ BAMMtools-2.1.0/BAMMtools/R/BAMMlikelihood.R |only BAMMtools-2.1.0/BAMMtools/R/addBAMMlegend.R | 208 +++++++++-- BAMMtools-2.1.0/BAMMtools/R/assignColorBreaks.R | 2 BAMMtools-2.1.0/BAMMtools/R/computeBayesFactors.R | 67 +-- BAMMtools-2.1.0/BAMMtools/R/credibleShiftSet.R | 24 - BAMMtools-2.1.0/BAMMtools/R/distinctShiftConfigurations.R | 36 - BAMMtools-2.1.0/BAMMtools/R/generateControlFile.R |only BAMMtools-2.1.0/BAMMtools/R/getBestShiftConfiguration.R | 8 BAMMtools-2.1.0/BAMMtools/R/getBranchShiftPriors.R | 32 - BAMMtools-2.1.0/BAMMtools/R/getCladeRates.R | 16 BAMMtools-2.1.0/BAMMtools/R/getEventData.R | 4 BAMMtools-2.1.0/BAMMtools/R/getJenksBreaks.R | 5 BAMMtools-2.1.0/BAMMtools/R/marginalOddsRatioBranches.R |only BAMMtools-2.1.0/BAMMtools/R/plot.bammdata.R | 32 + BAMMtools-2.1.0/BAMMtools/R/plotPrior.R |only BAMMtools-2.1.0/BAMMtools/R/ratesHistogram.R |only BAMMtools-2.1.0/BAMMtools/R/setBAMMpriors.R | 19 - BAMMtools-2.1.0/BAMMtools/data/events.fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/events.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/events.whales.rda |binary BAMMtools-2.1.0/BAMMtools/data/fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/mass.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/mcmc.primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/mcmc.whales.rda |binary BAMMtools-2.1.0/BAMMtools/data/primates.rda |binary BAMMtools-2.1.0/BAMMtools/data/traits.fishes.rda |binary BAMMtools-2.1.0/BAMMtools/data/whales.rda |binary BAMMtools-2.1.0/BAMMtools/inst/CITATION | 2 BAMMtools-2.1.0/BAMMtools/man/BAMMlikelihood.Rd |only BAMMtools-2.1.0/BAMMtools/man/BAMMtools-data.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/BAMMtools-internal.Rd | 14 BAMMtools-2.1.0/BAMMtools/man/BAMMtools-package.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/ShiftProbsTree.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/addBAMMlegend.Rd | 78 +++- BAMMtools-2.1.0/BAMMtools/man/addBAMMshifts.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/assignColorBreaks.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/cohorts.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/computeBayesFactors.Rd | 19 - BAMMtools-2.1.0/BAMMtools/man/credibleShiftSet.Rd | 30 - BAMMtools-2.1.0/BAMMtools/man/distinctShiftConfigurations.Rd | 38 +- BAMMtools-2.1.0/BAMMtools/man/dtRates.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/generateControlFile.Rd |only BAMMtools-2.1.0/BAMMtools/man/getBestShiftConfiguration.Rd | 23 - BAMMtools-2.1.0/BAMMtools/man/getBranchShiftPriors.Rd | 52 -- BAMMtools-2.1.0/BAMMtools/man/getCladeRates.Rd | 12 BAMMtools-2.1.0/BAMMtools/man/getCohortMatrix.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/getEventData.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/getJenksBreaks.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getMeanBranchLengthTree.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getShiftNodesFromIndex.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/getTipRates.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/marginalOddsRatioBranches.Rd |only BAMMtools-2.1.0/BAMMtools/man/maximumShiftCredibility.Rd | 5 BAMMtools-2.1.0/BAMMtools/man/plot.bammdata.Rd | 15 BAMMtools-2.1.0/BAMMtools/man/plot.bammshifts.Rd | 17 BAMMtools-2.1.0/BAMMtools/man/plot.credibleshiftset.Rd | 7 BAMMtools-2.1.0/BAMMtools/man/plotPrior.Rd |only BAMMtools-2.1.0/BAMMtools/man/ratesHistogram.Rd |only BAMMtools-2.1.0/BAMMtools/man/setBAMMpriors.Rd | 19 - BAMMtools-2.1.0/BAMMtools/man/speciesByRatesMatrix.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/subsetEventData.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/subtreeBAMM.Rd | 2 BAMMtools-2.1.0/BAMMtools/man/summary.credibleshiftset.Rd | 11 BAMMtools-2.1.0/BAMMtools/man/testTimeVariableBranches.Rd | 3 BAMMtools-2.1.0/BAMMtools/man/traitDependentBAMM.Rd | 6 BAMMtools-2.1.0/BAMMtools/man/transparentColor.Rd |only 78 files changed, 642 insertions(+), 443 deletions(-)