Title: Phylogenetic Tools for comparative biology (and other things)
Diff between phytools versions 0.1-9 dated 2012-08-08 and 0.2-0 dated 2012-09-29
Description: phytools provides various functions for phylogenetic
analysis, mostly relevant to comparative biology.
Author: Liam J. Revell
Maintainer: Liam J. Revell
DESCRIPTION | 8 ++--
MD5 | 44 +++++++++++++++-----------
NAMESPACE | 6 +--
R/bmPlot.R |only
R/estDiversity.R | 35 ++++++++++++---------
R/fancyTree.R | 44 +++++++++++++++++++++++++-
R/fitDiversityModel.R | 77 +++++++++++++++++++++++++++++++----------------
R/pbtree.R | 5 +--
R/phyl.RMA.R | 42 +------------------------
R/phyl.cca.R | 69 ++++++++++++++----------------------------
R/phyl.pca.R | 58 ++++++++---------------------------
R/phyl.resid.R | 13 -------
R/phylosig.R | 43 --------------------------
R/threshBayes.R |only
R/utilities.R |only
R/vcvPhylo.R | 23 ++++++++++++++
man/anc.trend.Rd | 3 +
man/bmPlot.Rd |only
man/fancyTree.Rd | 16 ++++++---
man/fitDiversityModel.Rd | 7 +---
man/likMlambda.Rd |only
man/pbtree.Rd | 5 +--
man/phyl.vcv.Rd | 2 -
man/phytools-package.Rd | 2 -
man/threshBayes.Rd |only
man/write.simmap.Rd | 2 -
26 files changed, 233 insertions(+), 271 deletions(-)
Title: GAMLSS Data.
Diff between gamlss.data versions 4.1-0 dated 2012-02-15 and 4.2-0 dated 2012-09-29
Description: Data for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.data-4.1-0/gamlss.data/data/abdom.tab.gz |only
gamlss.data-4.2-0/gamlss.data/DESCRIPTION | 12 +--
gamlss.data-4.2-0/gamlss.data/MD5 | 62 +++++++++---------
gamlss.data-4.2-0/gamlss.data/data/CD4.rda |binary
gamlss.data-4.2-0/gamlss.data/data/LGAclaims.rda |binary
gamlss.data-4.2-0/gamlss.data/data/Mums.rda |binary
gamlss.data-4.2-0/gamlss.data/data/VictimsOfCrime.rda |binary
gamlss.data-4.2-0/gamlss.data/data/abdom.tab.xz |only
gamlss.data-4.2-0/gamlss.data/data/acidity.rda |binary
gamlss.data-4.2-0/gamlss.data/data/aep.rda |binary
gamlss.data-4.2-0/gamlss.data/data/aids.rda |binary
gamlss.data-4.2-0/gamlss.data/data/alveolar.rda |binary
gamlss.data-4.2-0/gamlss.data/data/computer.rda |binary
gamlss.data-4.2-0/gamlss.data/data/datalist | 3
gamlss.data-4.2-0/gamlss.data/data/db.rda |binary
gamlss.data-4.2-0/gamlss.data/data/dbbmi.rda |binary
gamlss.data-4.2-0/gamlss.data/data/fabric.rda |binary
gamlss.data-4.2-0/gamlss.data/data/film30.rda |only
gamlss.data-4.2-0/gamlss.data/data/film90.rda |binary
gamlss.data-4.2-0/gamlss.data/data/glass.rda |binary
gamlss.data-4.2-0/gamlss.data/data/hodges.rda |binary
gamlss.data-4.2-0/gamlss.data/data/hodges1.rda |binary
gamlss.data-4.2-0/gamlss.data/data/lice.rda |binary
gamlss.data-4.2-0/gamlss.data/data/margolin.rda |binary
gamlss.data-4.2-0/gamlss.data/data/parzen.rda |binary
gamlss.data-4.2-0/gamlss.data/data/polio.rda |binary
gamlss.data-4.2-0/gamlss.data/data/rent.rda |binary
gamlss.data-4.2-0/gamlss.data/data/species.rda |binary
gamlss.data-4.2-0/gamlss.data/data/stylo.rda |binary
gamlss.data-4.2-0/gamlss.data/data/tensile.rda |binary
gamlss.data-4.2-0/gamlss.data/data/tse.rda |binary
gamlss.data-4.2-0/gamlss.data/data/usair.rda |binary
gamlss.data-4.2-0/gamlss.data/data/vas5.rda |binary
gamlss.data-4.2-0/gamlss.data/man/film30.Rd |only
34 files changed, 40 insertions(+), 37 deletions(-)
Title: GAMLSS Additive.
Diff between gamlss.add versions 4.1-0 dated 2012-02-21 and 4.2-0 dated 2012-09-29
Description: Extra additive terms for GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.add-4.1-0/gamlss.add/R/fk-new-gamlss.R |only
gamlss.add-4.1-0/gamlss.add/R/gam_gamlss.R |only
gamlss.add-4.2-0/gamlss.add/DESCRIPTION | 10
gamlss.add-4.2-0/gamlss.add/MD5 | 26 +
gamlss.add-4.2-0/gamlss.add/NAMESPACE | 36 ++
gamlss.add-4.2-0/gamlss.add/R/blag-3-1-12.R |only
gamlss.add-4.2-0/gamlss.add/R/fk-gamlss.R |only
gamlss.add-4.2-0/gamlss.add/R/freeKnots-14-07-10.R |only
gamlss.add-4.2-0/gamlss.add/R/gam_gamlss_21-8-12.R |only
gamlss.add-4.2-0/gamlss.add/R/la-gamlss-3-1-12.R |only
gamlss.add-4.2-0/gamlss.add/R/nnet_gamlss.R | 352 ++++++++++-----------
gamlss.add-4.2-0/gamlss.add/R/penLags-3-1-12.R |only
gamlss.add-4.2-0/gamlss.add/man/blag.Rd |only
gamlss.add-4.2-0/gamlss.add/man/fitFixBP.Rd |only
gamlss.add-4.2-0/gamlss.add/man/fk.Rd | 22 -
gamlss.add-4.2-0/gamlss.add/man/ga.Rd | 304 +++++++++++-------
gamlss.add-4.2-0/gamlss.add/man/gamlss.nn.Rd | 2
gamlss.add-4.2-0/gamlss.add/man/la.Rd |only
gamlss.add-4.2-0/gamlss.add/man/nn.Rd | 4
gamlss.add-4.2-0/gamlss.add/man/penLags.Rd |only
20 files changed, 446 insertions(+), 310 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-17 0.0.3
2011-11-09 0.0.2
Title: Distributions to be used for GAMLSS modelling.
Diff between gamlss.dist versions 4.1-6 dated 2012-08-14 and 4.2-0 dated 2012-09-29
Description: This package contains the distributions for GAMLSS
modelling.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss.dist-4.1-6/gamlss.dist/R/SICHEL.R |only
gamlss.dist-4.2-0/gamlss.dist/DESCRIPTION | 8 +++----
gamlss.dist-4.2-0/gamlss.dist/MD5 | 23 +++++++++++++---------
gamlss.dist-4.2-0/gamlss.dist/NAMESPACE | 4 +++
gamlss.dist-4.2-0/gamlss.dist/R/MN3.R |only
gamlss.dist-4.2-0/gamlss.dist/R/MN4.R |only
gamlss.dist-4.2-0/gamlss.dist/R/MN5.R |only
gamlss.dist-4.2-0/gamlss.dist/R/PIG.R | 12 +++++------
gamlss.dist-4.2-0/gamlss.dist/R/SI.R | 10 ++++-----
gamlss.dist-4.2-0/gamlss.dist/R/SICHEL-10-09-12.R |only
gamlss.dist-4.2-0/gamlss.dist/R/multin-23-09-12.R |only
gamlss.dist-4.2-0/gamlss.dist/man/Multinomial.Rd |only
gamlss.dist-4.2-0/gamlss.dist/src/cdfSICHEL.f | 4 +--
gamlss.dist-4.2-0/gamlss.dist/src/tofy.f | 2 -
gamlss.dist-4.2-0/gamlss.dist/src/tofys.f | 5 +---
gamlss.dist-4.2-0/gamlss.dist/src/tofysin.f | 2 -
16 files changed, 39 insertions(+), 31 deletions(-)
Title: Generalized Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.1-8 dated 2012-08-14 and 4.2-0 dated 2012-09-29
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.1-8/gamlss/R/PROFILE.R |only
gamlss-4.1-8/gamlss/R/gamlssML.R |only
gamlss-4.1-8/gamlss/R/profterm.R |only
gamlss-4.1-8/gamlss/R/qstats.R |only
gamlss-4.2-0/gamlss/DESCRIPTION | 8 -
gamlss-4.2-0/gamlss/MD5 | 24 ++--
gamlss-4.2-0/gamlss/R/PROFILE_new_19-08-12.R |only
gamlss-4.2-0/gamlss/R/fitDist.R | 7 -
gamlss-4.2-0/gamlss/R/gamlssML-11-9-12.R |only
gamlss-4.2-0/gamlss/R/pb_19-04-2012.R | 24 ++--
gamlss-4.2-0/gamlss/R/profterm_new_18_8_12.R |only
gamlss-4.2-0/gamlss/R/qstats-20-09-12.R |only
gamlss-4.2-0/gamlss/inst/doc/NEWS.txt | 41 +++++++-
gamlss-4.2-0/gamlss/man/Q.stats.Rd | 5
gamlss-4.2-0/gamlss/man/fitDist.Rd | 5
gamlss-4.2-0/gamlss/man/prof.dev.Rd | 20 ++-
gamlss-4.2-0/gamlss/man/prof.term.Rd | 138 +++++++++++++--------------
17 files changed, 159 insertions(+), 113 deletions(-)
Title: Astronomy: time and position functions, misc. utilities
Diff between astroFns versions 4.0-0 dated 2012-07-06 and 4.1-0 dated 2012-09-29
Description: Miscellaneous astronomy functions, utilities, and data.
Author: Andrew Harris
Maintainer: Andrew Harris
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/dmjd2ut.R | 9 ++++++---
man/astroFns-package.Rd | 4 ++--
4 files changed, 15 insertions(+), 12 deletions(-)
Title: Everyone's Statistical Software
Diff between Zelig versions 3.5.5 dated 2012-04-05 and 4.0-11 dated 2012-09-29
Description: Zelig is an easy-to-use program that can estimate, and
help interpret the results of, an enormous range of statistical
models. It literally is ``everyone's statistical software''
because Zelig's simple unified framework incorporates everyone
else's (R) code. We also hope it will become ``everyone's
statistical software'' for applications and teaching, and so
have designed Zelig so that anyone can easily use it or add
their programs to it. Zelig also comes with infrastructure
that facilitates the use of any existing method, such as by
allowing multiply imputed data for any model, and mimicking the
program Clarify (for Stata) that takes the raw output of
existing statistical procedures and translates them into
quantities of direct interest.
Author: Matt Owen
Maintainer: Matt Owen
Zelig-3.5.5/Zelig/R/Diff.R |only
Zelig-3.5.5/Zelig/R/MIsimulation.R |only
Zelig-3.5.5/Zelig/R/arima.wrap.R |only
Zelig-3.5.5/Zelig/R/callnetlm.R |only
Zelig-3.5.5/Zelig/R/callnetlogit.R |only
Zelig-3.5.5/Zelig/R/callsystemfit.R |only
Zelig-3.5.5/Zelig/R/categories.R |only
Zelig-3.5.5/Zelig/R/check.describe.R |only
Zelig-3.5.5/Zelig/R/chopitcode.R |only
Zelig-3.5.5/Zelig/R/class.ind.R |only
Zelig-3.5.5/Zelig/R/coef.BetaReg.R |only
Zelig-3.5.5/Zelig/R/current.packages.R |only
Zelig-3.5.5/Zelig/R/describe.aov.R |only
Zelig-3.5.5/Zelig/R/describe.arima.R |only
Zelig-3.5.5/Zelig/R/describe.blogit.R |only
Zelig-3.5.5/Zelig/R/describe.bprobit.R |only
Zelig-3.5.5/Zelig/R/describe.chopit.R |only
Zelig-3.5.5/Zelig/R/describe.coxph.R |only
Zelig-3.5.5/Zelig/R/describe.ei.RxC.R |only
Zelig-3.5.5/Zelig/R/describe.ei.dynamic.R |only
Zelig-3.5.5/Zelig/R/describe.ei.hier.R |only
Zelig-3.5.5/Zelig/R/describe.factor.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.factor.mix.R |only
Zelig-3.5.5/Zelig/R/describe.factor.ord.R |only
Zelig-3.5.5/Zelig/R/describe.gam.logit.R |only
Zelig-3.5.5/Zelig/R/describe.gam.normal.R |only
Zelig-3.5.5/Zelig/R/describe.gam.poisson.R |only
Zelig-3.5.5/Zelig/R/describe.gam.probit.R |only
Zelig-3.5.5/Zelig/R/describe.gamma.gee.R |only
Zelig-3.5.5/Zelig/R/describe.gamma.mixed.R |only
Zelig-3.5.5/Zelig/R/describe.gamma.survey.R |only
Zelig-3.5.5/Zelig/R/describe.irt1d.R |only
Zelig-3.5.5/Zelig/R/describe.irtkd.R |only
Zelig-3.5.5/Zelig/R/describe.lm.mixed.R |only
Zelig-3.5.5/Zelig/R/describe.logit.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.logit.gee.R |only
Zelig-3.5.5/Zelig/R/describe.logit.mixed.R |only
Zelig-3.5.5/Zelig/R/describe.logit.survey.R |only
Zelig-3.5.5/Zelig/R/describe.lognorm.R |only
Zelig-3.5.5/Zelig/R/describe.mlogit.R |only
Zelig-3.5.5/Zelig/R/describe.mlogit.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.negbin.R |only
Zelig-3.5.5/Zelig/R/describe.netcloglog.R |only
Zelig-3.5.5/Zelig/R/describe.netgamma.R |only
Zelig-3.5.5/Zelig/R/describe.netlogit.R |only
Zelig-3.5.5/Zelig/R/describe.netls.R |only
Zelig-3.5.5/Zelig/R/describe.netnormal.R |only
Zelig-3.5.5/Zelig/R/describe.netpoisson.R |only
Zelig-3.5.5/Zelig/R/describe.netprobit.R |only
Zelig-3.5.5/Zelig/R/describe.normal.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.normal.gee.R |only
Zelig-3.5.5/Zelig/R/describe.normal.survey.R |only
Zelig-3.5.5/Zelig/R/describe.ologit.R |only
Zelig-3.5.5/Zelig/R/describe.oprobit.R |only
Zelig-3.5.5/Zelig/R/describe.oprobit.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.poisson.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.poisson.gee.R |only
Zelig-3.5.5/Zelig/R/describe.poisson.mixed.R |only
Zelig-3.5.5/Zelig/R/describe.poisson.survey.R |only
Zelig-3.5.5/Zelig/R/describe.probit.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.probit.gee.R |only
Zelig-3.5.5/Zelig/R/describe.probit.mixed.R |only
Zelig-3.5.5/Zelig/R/describe.probit.survey.R |only
Zelig-3.5.5/Zelig/R/describe.quantile.R |only
Zelig-3.5.5/Zelig/R/describe.relogit.R |only
Zelig-3.5.5/Zelig/R/describe.rq.R |only
Zelig-3.5.5/Zelig/R/describe.sur.R |only
Zelig-3.5.5/Zelig/R/describe.threesls.R |only
Zelig-3.5.5/Zelig/R/describe.tobit.bayes.R |only
Zelig-3.5.5/Zelig/R/describe.twosls.R |only
Zelig-3.5.5/Zelig/R/describe.weibull.R |only
Zelig-3.5.5/Zelig/R/dims.R |only
Zelig-3.5.5/Zelig/R/eiRxC.R |only
Zelig-3.5.5/Zelig/R/formula.vglm.R |only
Zelig-3.5.5/Zelig/R/get.R |only
Zelig-3.5.5/Zelig/R/gsource.R |only
Zelig-3.5.5/Zelig/R/lag.eps.R |only
Zelig-3.5.5/Zelig/R/lag.y.R |only
Zelig-3.5.5/Zelig/R/load.first.R |only
Zelig-3.5.5/Zelig/R/mcmcei.R |only
Zelig-3.5.5/Zelig/R/model.end.R |only
Zelig-3.5.5/Zelig/R/model.frame.gamF.R |only
Zelig-3.5.5/Zelig/R/multi.R |only
Zelig-3.5.5/Zelig/R/names.ZeligS4vglm.R |only
Zelig-3.5.5/Zelig/R/names.summary.vglm.R |only
Zelig-3.5.5/Zelig/R/names.summary.zelig.R |only
Zelig-3.5.5/Zelig/R/names.summary.zelig.relogit.R |only
Zelig-3.5.5/Zelig/R/names.zelig.R |only
Zelig-3.5.5/Zelig/R/names.zelig.relogit.R |only
Zelig-3.5.5/Zelig/R/netbinom.R |only
Zelig-3.5.5/Zelig/R/netgamma.R |only
Zelig-3.5.5/Zelig/R/netlogit.zelig.R |only
Zelig-3.5.5/Zelig/R/netnormal.R |only
Zelig-3.5.5/Zelig/R/netpoisson.R |only
Zelig-3.5.5/Zelig/R/network.R |only
Zelig-3.5.5/Zelig/R/packageConflicts.R |only
Zelig-3.5.5/Zelig/R/param.MCMCZelig.R |only
Zelig-3.5.5/Zelig/R/param.default.R |only
Zelig-3.5.5/Zelig/R/param.eiRxC.R |only
Zelig-3.5.5/Zelig/R/param.gam.R |only
Zelig-3.5.5/Zelig/R/param.gee.R |only
Zelig-3.5.5/Zelig/R/param.glm.R |only
Zelig-3.5.5/Zelig/R/param.lm.R |only
Zelig-3.5.5/Zelig/R/param.mixed.R |only
Zelig-3.5.5/Zelig/R/param.multinom.R |only
Zelig-3.5.5/Zelig/R/param.multiple.R |only
Zelig-3.5.5/Zelig/R/param.netglm.R |only
Zelig-3.5.5/Zelig/R/param.netlm.R |only
Zelig-3.5.5/Zelig/R/param.polr.R |only
Zelig-3.5.5/Zelig/R/param.rq.R |only
Zelig-3.5.5/Zelig/R/param.survreg.R |only
Zelig-3.5.5/Zelig/R/param.svyglm.R |only
Zelig-3.5.5/Zelig/R/param.vglm.R |only
Zelig-3.5.5/Zelig/R/param.zaov.R |only
Zelig-3.5.5/Zelig/R/parse.par.R |only
Zelig-3.5.5/Zelig/R/plot.ci.R |only
Zelig-3.5.5/Zelig/R/plot.surv.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.arima.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.blogit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.bprobit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.coxph.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.default.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.gamma.gee.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.logit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.logit.gam.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.logit.gee.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.logit.survey.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.mlogit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.negbin.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.netcloglog.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.netlogit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.netpoisson.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.netprobit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.normal.gee.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.ologit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.oprobit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.poisson.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.poisson.gam.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.poisson.gee.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.poisson.survey.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.probit.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.probit.gam.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.probit.gee.R |only
Zelig-3.5.5/Zelig/R/plot.zelig.probit.survey.R |only
Zelig-3.5.5/Zelig/R/plot.zeliglist.R |only
Zelig-3.5.5/Zelig/R/print.BetaReg.R |only
Zelig-3.5.5/Zelig/R/print.arimaSummary.R |only
Zelig-3.5.5/Zelig/R/print.coxhazard.R |only
Zelig-3.5.5/Zelig/R/print.eiRxC.R |only
Zelig-3.5.5/Zelig/R/print.names.relogit.R |only
Zelig-3.5.5/Zelig/R/print.names.zelig.R |only
Zelig-3.5.5/Zelig/R/print.relogit.R |only
Zelig-3.5.5/Zelig/R/print.relogit2.R |only
Zelig-3.5.5/Zelig/R/print.summary.MCMCZelig.R |only
Zelig-3.5.5/Zelig/R/print.summary.MI.R |only
Zelig-3.5.5/Zelig/R/print.summary.lm.robust.R |only
Zelig-3.5.5/Zelig/R/print.summary.strata.R |only
Zelig-3.5.5/Zelig/R/print.summary.zelig.R |only
Zelig-3.5.5/Zelig/R/print.summary.zelig.strata.R |only
Zelig-3.5.5/Zelig/R/print.zaovlist.R |only
Zelig-3.5.5/Zelig/R/put.start.R |only
Zelig-3.5.5/Zelig/R/qi.BetaReg.R |only
Zelig-3.5.5/Zelig/R/qi.MCMCZelig.R |only
Zelig-3.5.5/Zelig/R/qi.aov.R |only
Zelig-3.5.5/Zelig/R/qi.coxph.R |only
Zelig-3.5.5/Zelig/R/qi.eiRxC.R |only
Zelig-3.5.5/Zelig/R/qi.gam.R |only
Zelig-3.5.5/Zelig/R/qi.gee.R |only
Zelig-3.5.5/Zelig/R/qi.glm.R |only
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Zelig-4.0-11/Zelig/R/getResponseTerms.formula.R |only
Zelig-4.0-11/Zelig/R/getResponseTerms.list.R |only
Zelig-4.0-11/Zelig/R/help.zelig.R | 7
Zelig-4.0-11/Zelig/R/ignore.R |only
Zelig-4.0-11/Zelig/R/is.formula.R |only
Zelig-4.0-11/Zelig/R/labels.mi.R |only
Zelig-4.0-11/Zelig/R/list.depth.R |only
Zelig-4.0-11/Zelig/R/make.parameters.R | 8
Zelig-4.0-11/Zelig/R/makeModelMatrix.R |only
Zelig-4.0-11/Zelig/R/mi.R | 228 ++
Zelig-4.0-11/Zelig/R/model.frame.multiple.R | 12
Zelig-4.0-11/Zelig/R/model.matrix.multiple.R | 14
Zelig-4.0-11/Zelig/R/model.matrix.parseFormula.R |only
Zelig-4.0-11/Zelig/R/model.warnings.R |only
Zelig-4.0-11/Zelig/R/multipleUtil.R | 27
Zelig-4.0-11/Zelig/R/param.R | 60
Zelig-4.0-11/Zelig/R/param.exp.R |only
Zelig-4.0-11/Zelig/R/param.gamma.R |only
Zelig-4.0-11/Zelig/R/param.logit.R |only
Zelig-4.0-11/Zelig/R/param.ls.R |only
Zelig-4.0-11/Zelig/R/param.negbinom.R |only
Zelig-4.0-11/Zelig/R/param.normal.R |only
Zelig-4.0-11/Zelig/R/param.poisson.R |only
Zelig-4.0-11/Zelig/R/param.probit.R |only
Zelig-4.0-11/Zelig/R/param.relogit.R | 106 -
Zelig-4.0-11/Zelig/R/param.tobit.R |only
Zelig-4.0-11/Zelig/R/parameters.R |only
Zelig-4.0-11/Zelig/R/parse.formula.R | 7
Zelig-4.0-11/Zelig/R/parseFormula.R |only
Zelig-4.0-11/Zelig/R/plot.MI.sim.R |only
Zelig-4.0-11/Zelig/R/plot.pooled.sim.R |only
Zelig-4.0-11/Zelig/R/plot.sim.R |only
Zelig-4.0-11/Zelig/R/print.setx.MI.R |only
Zelig-4.0-11/Zelig/R/print.setx.R |only
Zelig-4.0-11/Zelig/R/print.sim.R |only
Zelig-4.0-11/Zelig/R/print.summary.pooled.sim.R |only
Zelig-4.0-11/Zelig/R/print.summary.relogit.R | 39
Zelig-4.0-11/Zelig/R/print.summary.relogit2.R | 16
Zelig-4.0-11/Zelig/R/print.summary.sim.R |only
Zelig-4.0-11/Zelig/R/print.summarySim.MI.R |only
Zelig-4.0-11/Zelig/R/print.zelig.R | 24
Zelig-4.0-11/Zelig/R/qi.R | 38
Zelig-4.0-11/Zelig/R/qi.exp.R |only
Zelig-4.0-11/Zelig/R/qi.gamma.R |only
Zelig-4.0-11/Zelig/R/qi.logit.R |only
Zelig-4.0-11/Zelig/R/qi.ls.R |only
Zelig-4.0-11/Zelig/R/qi.negbinom.R |only
Zelig-4.0-11/Zelig/R/qi.normal.R |only
Zelig-4.0-11/Zelig/R/qi.poisson.R |only
Zelig-4.0-11/Zelig/R/qi.probit.R |only
Zelig-4.0-11/Zelig/R/qi.relogit.R | 189 +
Zelig-4.0-11/Zelig/R/qi.summarized.R |only
Zelig-4.0-11/Zelig/R/qi.tobit.R |only
Zelig-4.0-11/Zelig/R/register.R |only
Zelig-4.0-11/Zelig/R/register.default.R |only
Zelig-4.0-11/Zelig/R/relogit.R | 32
Zelig-4.0-11/Zelig/R/repl.R | 8
Zelig-4.0-11/Zelig/R/repl.default.R | 15
Zelig-4.0-11/Zelig/R/repl.sim.R |only
Zelig-4.0-11/Zelig/R/robust.glm.hook.R |only
Zelig-4.0-11/Zelig/R/setx.MI.R | 65
Zelig-4.0-11/Zelig/R/setx.R | 47
Zelig-4.0-11/Zelig/R/setx.default.R | 464 ++--
Zelig-4.0-11/Zelig/R/sim.MI.R |only
Zelig-4.0-11/Zelig/R/sim.R | 96
Zelig-4.0-11/Zelig/R/sim.default.R | 271 ++
Zelig-4.0-11/Zelig/R/sim.relogit.R |only
Zelig-4.0-11/Zelig/R/simulation.matrix.R |only
Zelig-4.0-11/Zelig/R/simulations.plot.R |only
Zelig-4.0-11/Zelig/R/summarize.R | 12
Zelig-4.0-11/Zelig/R/summarize.default.R | 141 +
Zelig-4.0-11/Zelig/R/summary.MI.R | 62
Zelig-4.0-11/Zelig/R/summary.MI.sim.R |only
Zelig-4.0-11/Zelig/R/summary.glm.robust.R | 9
Zelig-4.0-11/Zelig/R/summary.pooled.sim.R |only
Zelig-4.0-11/Zelig/R/summary.relogit.R | 29
Zelig-4.0-11/Zelig/R/summary.relogit2.R | 15
Zelig-4.0-11/Zelig/R/summary.sim.R |only
Zelig-4.0-11/Zelig/R/summary.zelig.R | 106 -
Zelig-4.0-11/Zelig/R/t.setx.R |only
Zelig-4.0-11/Zelig/R/terms.multiple.R | 10
Zelig-4.0-11/Zelig/R/terms.vglm.R | 7
Zelig-4.0-11/Zelig/R/terms.zelig.R |only
Zelig-4.0-11/Zelig/R/termsFromFormula.R |only
Zelig-4.0-11/Zelig/R/toString.call.R |only
Zelig-4.0-11/Zelig/R/user.prompt.R | 16
Zelig-4.0-11/Zelig/R/vcov.glm.robust.R | 9
Zelig-4.0-11/Zelig/R/vcov.relogit.R | 4
Zelig-4.0-11/Zelig/R/z.R |only
Zelig-4.0-11/Zelig/R/zelig.R | 299 ++
Zelig-4.0-11/Zelig/R/zelig.skeleton.R |only
Zelig-4.0-11/Zelig/R/zelig2.R |only
Zelig-4.0-11/Zelig/R/zelig2exp.R | 62
Zelig-4.0-11/Zelig/R/zelig2gamma.R | 28
Zelig-4.0-11/Zelig/R/zelig2logit.R | 31
Zelig-4.0-11/Zelig/R/zelig2ls.R | 27
Zelig-4.0-11/Zelig/R/zelig2negbinom.R |only
Zelig-4.0-11/Zelig/R/zelig2normal.R | 29
Zelig-4.0-11/Zelig/R/zelig2poisson.R | 29
Zelig-4.0-11/Zelig/R/zelig2probit.R | 29
Zelig-4.0-11/Zelig/R/zelig2relogit.R | 56
Zelig-4.0-11/Zelig/R/zelig2tobit.R | 132 -
Zelig-4.0-11/Zelig/R/zzz.R |only
Zelig-4.0-11/Zelig/R/zzz_S4_generics.R |only
Zelig-4.0-11/Zelig/R/zzz_citation.R |only
Zelig-4.0-11/Zelig/R/zzz_environment_hacks.R |only
Zelig-4.0-11/Zelig/R/zzz_generics.R |only
Zelig-4.0-11/Zelig/R/zzz_numerical.R |only
Zelig-4.0-11/Zelig/R/zzz_operators.R |only
Zelig-4.0-11/Zelig/R/zzz_plots.R |only
Zelig-4.0-11/Zelig/R/zzz_run.R |only
Zelig-4.0-11/Zelig/R/zzz_skeleton.R |only
Zelig-4.0-11/Zelig/R/zzz_stats.R |only
Zelig-4.0-11/Zelig/R/zzz_utils.R |only
Zelig-4.0-11/Zelig/README | 33
Zelig-4.0-11/Zelig/RELEASE_NOTES |only
Zelig-4.0-11/Zelig/data/friendship.RData |binary
Zelig-4.0-11/Zelig/data/sna.ex.RData |binary
Zelig-4.0-11/Zelig/demo/00Index | 79
Zelig-4.0-11/Zelig/demo/Zelig.HelloWorld.R |only
Zelig-4.0-11/Zelig/demo/gamma.R | 25
Zelig-4.0-11/Zelig/demo/logit.R | 64
Zelig-4.0-11/Zelig/demo/ls.R | 42
Zelig-4.0-11/Zelig/demo/mi.R | 53
Zelig-4.0-11/Zelig/demo/negbinom.R |only
Zelig-4.0-11/Zelig/demo/normal.R | 47
Zelig-4.0-11/Zelig/demo/poisson.R | 24
Zelig-4.0-11/Zelig/demo/probit.R | 58
Zelig-4.0-11/Zelig/inst/doc/gamma.pdf |binary
Zelig-4.0-11/Zelig/inst/doc/logit.pdf |binary
Zelig-4.0-11/Zelig/inst/doc/ls.pdf |binary
Zelig-4.0-11/Zelig/inst/doc/manual.pdf |only
Zelig-4.0-11/Zelig/inst/doc/negbinom.pdf |only
Zelig-4.0-11/Zelig/inst/doc/normal.pdf |only
Zelig-4.0-11/Zelig/inst/doc/parse.formula.pdf |only
Zelig-4.0-11/Zelig/inst/doc/poisson.pdf |binary
Zelig-4.0-11/Zelig/inst/doc/probit.pdf |binary
Zelig-4.0-11/Zelig/inst/po |only
Zelig-4.0-11/Zelig/inst/templates |only
Zelig-4.0-11/Zelig/man/GetObject.Rd |only
Zelig-4.0-11/Zelig/man/GetSlot.Rd |only
Zelig-4.0-11/Zelig/man/GetSlot.zelig.Rd |only
Zelig-4.0-11/Zelig/man/Max.Rd |only
Zelig-4.0-11/Zelig/man/Median.Rd |only
Zelig-4.0-11/Zelig/man/Min.Rd |only
Zelig-4.0-11/Zelig/man/Mode.Rd |only
Zelig-4.0-11/Zelig/man/NextFrame.Rd |only
Zelig-4.0-11/Zelig/man/NextLabel.Rd |only
Zelig-4.0-11/Zelig/man/Reset.Rd |only
Zelig-4.0-11/Zelig/man/TexCite.Rd |only
Zelig-4.0-11/Zelig/man/Zelig-package.Rd | 181 -
Zelig-4.0-11/Zelig/man/ZeligDescribeModel.Rd |only
Zelig-4.0-11/Zelig/man/ZeligListModels.Rd |only
Zelig-4.0-11/Zelig/man/ZeligListTitles.Rd |only
Zelig-4.0-11/Zelig/man/alpha.Rd |only
Zelig-4.0-11/Zelig/man/as.bootlist.Rd |only
Zelig-4.0-11/Zelig/man/as.bootvector.Rd |only
Zelig-4.0-11/Zelig/man/as.data.frame.setx.Rd |only
Zelig-4.0-11/Zelig/man/as.description.Rd |only
Zelig-4.0-11/Zelig/man/as.description.description.Rd |only
Zelig-4.0-11/Zelig/man/as.description.list.Rd |only
Zelig-4.0-11/Zelig/man/as.matrix.pooled.setx.Rd |only
Zelig-4.0-11/Zelig/man/as.matrix.setx.Rd |only
Zelig-4.0-11/Zelig/man/as.parameters.Rd |only
Zelig-4.0-11/Zelig/man/as.parameters.default.Rd |only
Zelig-4.0-11/Zelig/man/as.parameters.list.Rd |only
Zelig-4.0-11/Zelig/man/as.parameters.parameters.Rd |only
Zelig-4.0-11/Zelig/man/as.qi.Rd |only
Zelig-4.0-11/Zelig/man/as.qi.default.Rd |only
Zelig-4.0-11/Zelig/man/as.qi.list.Rd |only
Zelig-4.0-11/Zelig/man/as.qi.qi.Rd |only
Zelig-4.0-11/Zelig/man/as.summarized.Rd |only
Zelig-4.0-11/Zelig/man/as.summarized.list.Rd |only
Zelig-4.0-11/Zelig/man/as.summarized.summarized.qi.Rd |only
Zelig-4.0-11/Zelig/man/attach.env.Rd |only
Zelig-4.0-11/Zelig/man/bootfn.default.Rd |only
Zelig-4.0-11/Zelig/man/bootstrap.Rd |only
Zelig-4.0-11/Zelig/man/bootstrap.default.Rd |only
Zelig-4.0-11/Zelig/man/bootstrap.gamma.Rd |only
Zelig-4.0-11/Zelig/man/bootstrap.negbinom.Rd |only
Zelig-4.0-11/Zelig/man/bootstrap.normal.Rd |only
Zelig-4.0-11/Zelig/man/cite.Rd |only
Zelig-4.0-11/Zelig/man/cluster.formula.Rd |only
Zelig-4.0-11/Zelig/man/cmvglm.Rd |only
Zelig-4.0-11/Zelig/man/coef.parameters.Rd |only
Zelig-4.0-11/Zelig/man/combine.Rd |only
Zelig-4.0-11/Zelig/man/constructDataFrame.Rd |only
Zelig-4.0-11/Zelig/man/constructDesignMatrix.Rd |only
Zelig-4.0-11/Zelig/man/depends.on.zelig.Rd |only
Zelig-4.0-11/Zelig/man/describe.Rd |only
Zelig-4.0-11/Zelig/man/describe.default.Rd |only
Zelig-4.0-11/Zelig/man/describe.exp.Rd |only
Zelig-4.0-11/Zelig/man/describe.gamma.Rd |only
Zelig-4.0-11/Zelig/man/describe.logit.Rd |only
Zelig-4.0-11/Zelig/man/describe.ls.Rd |only
Zelig-4.0-11/Zelig/man/describe.negbinom.Rd |only
Zelig-4.0-11/Zelig/man/describe.normal.Rd |only
Zelig-4.0-11/Zelig/man/describe.poisson.Rd |only
Zelig-4.0-11/Zelig/man/describe.probit.Rd |only
Zelig-4.0-11/Zelig/man/describe.tobit.Rd |only
Zelig-4.0-11/Zelig/man/describe.zelig.Rd |only
Zelig-4.0-11/Zelig/man/description.Rd |only
Zelig-4.0-11/Zelig/man/eval.in.Rd |only
Zelig-4.0-11/Zelig/man/find.match.Rd |only
Zelig-4.0-11/Zelig/man/get.package.Rd |only
Zelig-4.0-11/Zelig/man/getPredictorTerms.Rd |only
Zelig-4.0-11/Zelig/man/getResponseTerms.Formula-not-formula.Rd |only
Zelig-4.0-11/Zelig/man/getResponseTerms.Rd |only
Zelig-4.0-11/Zelig/man/getResponseTerms.formula.Rd |only
Zelig-4.0-11/Zelig/man/getResponseTerms.list.Rd |only
Zelig-4.0-11/Zelig/man/has.zelig2.Rd |only
Zelig-4.0-11/Zelig/man/help.zelig.Rd | 42
Zelig-4.0-11/Zelig/man/ignore.Rd |only
Zelig-4.0-11/Zelig/man/is.formula.Rd |only
Zelig-4.0-11/Zelig/man/is.qi.Rd |only
Zelig-4.0-11/Zelig/man/is.valid.qi.list.Rd |only
Zelig-4.0-11/Zelig/man/is.zelig.compliant.Rd |only
Zelig-4.0-11/Zelig/man/is.zelig.package.Rd |only
Zelig-4.0-11/Zelig/man/labels.mi.Rd |only
Zelig-4.0-11/Zelig/man/length.mi.Rd |only
Zelig-4.0-11/Zelig/man/link.Rd |only
Zelig-4.0-11/Zelig/man/linkinv.Rd |only
Zelig-4.0-11/Zelig/man/list.depth.Rd |only
Zelig-4.0-11/Zelig/man/list.zelig.dependent.packages.Rd |only
Zelig-4.0-11/Zelig/man/list.zelig.models.Rd |only
Zelig-4.0-11/Zelig/man/make.mi.Rd |only
Zelig-4.0-11/Zelig/man/make.parameters.Rd |only
Zelig-4.0-11/Zelig/man/makeModelMatrix.Rd |only
Zelig-4.0-11/Zelig/man/makeZeligObject.Rd |only
Zelig-4.0-11/Zelig/man/mi.Rd | 47
Zelig-4.0-11/Zelig/man/mix.Rd |only
Zelig-4.0-11/Zelig/man/model.frame.multiple.Rd | 69
Zelig-4.0-11/Zelig/man/model.matrix.multiple.Rd | 97
Zelig-4.0-11/Zelig/man/model.matrix.parseFormula.Rd |only
Zelig-4.0-11/Zelig/man/multilevel.Rd |only
Zelig-4.0-11/Zelig/man/name.frames.Rd |only
Zelig-4.0-11/Zelig/man/name.object.Rd |only
Zelig-4.0-11/Zelig/man/names.qi.Rd |only
Zelig-4.0-11/Zelig/man/param.Rd |only
Zelig-4.0-11/Zelig/man/param.default.Rd |only
Zelig-4.0-11/Zelig/man/param.exp.Rd |only
Zelig-4.0-11/Zelig/man/param.gamma.Rd |only
Zelig-4.0-11/Zelig/man/param.logit.Rd |only
Zelig-4.0-11/Zelig/man/param.ls.Rd |only
Zelig-4.0-11/Zelig/man/param.negbinom.Rd |only
Zelig-4.0-11/Zelig/man/param.normal.Rd |only
Zelig-4.0-11/Zelig/man/param.poisson.Rd |only
Zelig-4.0-11/Zelig/man/param.probit.Rd |only
Zelig-4.0-11/Zelig/man/param.relogit.Rd |only
Zelig-4.0-11/Zelig/man/param.relogit2.Rd |only
Zelig-4.0-11/Zelig/man/param.tobit.Rd |only
Zelig-4.0-11/Zelig/man/parameters.Rd |only
Zelig-4.0-11/Zelig/man/parse.formula.Rd | 90
Zelig-4.0-11/Zelig/man/parseFormula.Rd |only
Zelig-4.0-11/Zelig/man/parseFormula.formula.Rd |only
Zelig-4.0-11/Zelig/man/parseFormula.list.Rd |only
Zelig-4.0-11/Zelig/man/plot.MI.sim.Rd |only
Zelig-4.0-11/Zelig/man/plot.ci.Rd | 100
Zelig-4.0-11/Zelig/man/plot.pooled.sim.Rd |only
Zelig-4.0-11/Zelig/man/plot.sim.Rd |only
Zelig-4.0-11/Zelig/man/plot.simulations.Rd |only
Zelig-4.0-11/Zelig/man/print.qi.Rd |only
Zelig-4.0-11/Zelig/man/print.qi.summarized.Rd |only
Zelig-4.0-11/Zelig/man/print.setx.Rd |only
Zelig-4.0-11/Zelig/man/print.setx.mi.Rd |only
Zelig-4.0-11/Zelig/man/print.sim.Rd |only
Zelig-4.0-11/Zelig/man/print.summary.pooled.sim.Rd |only
Zelig-4.0-11/Zelig/man/print.summary.relogit.Rd |only
Zelig-4.0-11/Zelig/man/print.summary.relogit2.Rd |only
Zelig-4.0-11/Zelig/man/print.summary.sim.Rd |only
Zelig-4.0-11/Zelig/man/print.summarySim.MI.Rd |only
Zelig-4.0-11/Zelig/man/print.zelig.Rd |only
Zelig-4.0-11/Zelig/man/qi.Rd |only
Zelig-4.0-11/Zelig/man/qi.exp.Rd |only
Zelig-4.0-11/Zelig/man/qi.gamma.Rd |only
Zelig-4.0-11/Zelig/man/qi.logit.Rd |only
Zelig-4.0-11/Zelig/man/qi.ls.Rd |only
Zelig-4.0-11/Zelig/man/qi.negbinom.Rd |only
Zelig-4.0-11/Zelig/man/qi.normal.Rd |only
Zelig-4.0-11/Zelig/man/qi.poisson.Rd |only
Zelig-4.0-11/Zelig/man/qi.probit.Rd |only
Zelig-4.0-11/Zelig/man/qi.relogit.Rd |only
Zelig-4.0-11/Zelig/man/qi.relogit2.Rd |only
Zelig-4.0-11/Zelig/man/qi.summarize.Rd |only
Zelig-4.0-11/Zelig/man/qi.tobit.Rd |only
Zelig-4.0-11/Zelig/man/reduceMI.Rd |only
Zelig-4.0-11/Zelig/man/register.Rd |only
Zelig-4.0-11/Zelig/man/register.default.Rd |only
Zelig-4.0-11/Zelig/man/relogit.Rd |only
Zelig-4.0-11/Zelig/man/repl.Rd | 86
Zelig-4.0-11/Zelig/man/repl.default.Rd |only
Zelig-4.0-11/Zelig/man/repl.sim.Rd |only
Zelig-4.0-11/Zelig/man/replace.call.Rd |only
Zelig-4.0-11/Zelig/man/retrieve.factors.Rd |only
Zelig-4.0-11/Zelig/man/robust.glm.hook.Rd |only
Zelig-4.0-11/Zelig/man/rocplot.Rd | 139 -
Zelig-4.0-11/Zelig/man/setx.MI.Rd |only
Zelig-4.0-11/Zelig/man/setx.Rd | 148 -
Zelig-4.0-11/Zelig/man/setx.default.Rd |only
Zelig-4.0-11/Zelig/man/sim.MI.Rd |only
Zelig-4.0-11/Zelig/man/sim.Rd | 240 +-
Zelig-4.0-11/Zelig/man/sim.default.Rd |only
Zelig-4.0-11/Zelig/man/sim.relogit.Rd |only
Zelig-4.0-11/Zelig/man/simulation.matrix.Rd |only
Zelig-4.0-11/Zelig/man/simulations.parameters.Rd |only
Zelig-4.0-11/Zelig/man/simulations.plot.Rd |only
Zelig-4.0-11/Zelig/man/special_print_LIST.Rd |only
Zelig-4.0-11/Zelig/man/special_print_MATRIX.Rd |only
Zelig-4.0-11/Zelig/man/splitUp.Rd |only
Zelig-4.0-11/Zelig/man/store.object.Rd |only
Zelig-4.0-11/Zelig/man/structuralToReduced.Rd |only
Zelig-4.0-11/Zelig/man/summarize.Rd |only
Zelig-4.0-11/Zelig/man/summarize.default.Rd |only
Zelig-4.0-11/Zelig/man/summary.MI.Rd |only
Zelig-4.0-11/Zelig/man/summary.MI.sim.Rd |only
Zelig-4.0-11/Zelig/man/summary.Relogit2.Rd |only
Zelig-4.0-11/Zelig/man/summary.glm.robust.Rd |only
Zelig-4.0-11/Zelig/man/summary.pooled.sim.Rd |only
Zelig-4.0-11/Zelig/man/summary.relogit.Rd |only
Zelig-4.0-11/Zelig/man/summary.sim.Rd |only
Zelig-4.0-11/Zelig/man/summary.zelig.Rd | 58
Zelig-4.0-11/Zelig/man/t.setx.Rd |only
Zelig-4.0-11/Zelig/man/table.levels.Rd |only
Zelig-4.0-11/Zelig/man/terms.multiple.Rd |only
Zelig-4.0-11/Zelig/man/terms.vglm.Rd |only
Zelig-4.0-11/Zelig/man/terms.zelig.Rd |only
Zelig-4.0-11/Zelig/man/termsFromFormula.Rd |only
Zelig-4.0-11/Zelig/man/toBuildFormula.Rd |only
Zelig-4.0-11/Zelig/man/toString.call.Rd |only
Zelig-4.0-11/Zelig/man/tolmerFormat.Rd |only
Zelig-4.0-11/Zelig/man/ucfirst.Rd |only
Zelig-4.0-11/Zelig/man/user.prompt.Rd | 31
Zelig-4.0-11/Zelig/man/vcov.glm.robust.Rd |only
Zelig-4.0-11/Zelig/man/z.Rd |only
Zelig-4.0-11/Zelig/man/zelig.Rd | 135 -
Zelig-4.0-11/Zelig/man/zelig.call.Rd |only
Zelig-4.0-11/Zelig/man/zelig.skeleton.Rd |only
Zelig-4.0-11/Zelig/man/zelig2.Rd |only
Zelig-4.0-11/Zelig/man/zelig2exp.Rd |only
Zelig-4.0-11/Zelig/man/zelig2gamma.Rd |only
Zelig-4.0-11/Zelig/man/zelig2logit.Rd |only
Zelig-4.0-11/Zelig/man/zelig2ls.Rd |only
Zelig-4.0-11/Zelig/man/zelig2negbinom.Rd |only
Zelig-4.0-11/Zelig/man/zelig2normal.Rd |only
Zelig-4.0-11/Zelig/man/zelig2poisson.Rd |only
Zelig-4.0-11/Zelig/man/zelig2probit.Rd |only
Zelig-4.0-11/Zelig/man/zelig2relogit.Rd |only
Zelig-4.0-11/Zelig/man/zelig2tobit.Rd |only
Zelig-4.0-11/Zelig/messages |only
Zelig-4.0-11/Zelig/po |only
Zelig-4.0-11/Zelig/tests |only
Zelig-4.0-11/Zelig/vignettes/Sweave.sty | 8
Zelig-4.0-11/Zelig/vignettes/Zelig.bib |only
Zelig-4.0-11/Zelig/vignettes/Zelig.sty |only
Zelig-4.0-11/Zelig/vignettes/gk.bib | 36
Zelig-4.0-11/Zelig/vignettes/gkpubs.bib | 39
855 files changed, 3975 insertions(+), 3341 deletions(-)
Title: Statistical Modeling
Diff between statmod versions 1.4.15 dated 2012-08-06 and 1.4.16 dated 2012-09-29
Description: Various statistical modeling functions including growth
curve comparisons, limiting dilution analysis, mixed linear
models, heteroscedastic regression, Tweedie family generalized
linear models, the inverse-Gaussian distribution and Gauss
quadrature.
Author: Gordon Smyth with contributions from Yifang Hu, Peter Dunn and
Belinda Phipson.
Maintainer: Gordon Smyth
DESCRIPTION | 9 --
MD5 | 17 ++-
NAMESPACE | 4
R/gaussquad.R | 60 ++++++-------
inst/doc/changelog.txt | 12 ++
man/gauss.quad.Rd | 18 ++--
man/gauss.quad.prob.Rd | 16 ++-
src |only
tests/statmod-Tests.R | 37 +++++++-
tests/statmod-Tests.Rout.save | 188 +++++++++++++++++++++++-------------------
10 files changed, 215 insertions(+), 146 deletions(-)
Title: A collection of handy, useful functions
Diff between useful versions 1.1.5 dated 2012-06-15 and 1.1.6 dated 2012-09-29
Description: A set of little functions that have been found useful to
do little odds and ends
Author: Jared P. Lander
Maintainer:
useful-1.1.5/useful/LISCENSE |only
useful-1.1.5/useful/test |only
useful-1.1.5/useful/useful.Rproj |only
useful-1.1.6/useful/DESCRIPTION | 12 +++++++-----
useful-1.1.6/useful/MD5 | 19 ++++++++-----------
useful-1.1.6/useful/NAMESPACE | 26 +++++++++++++-------------
useful-1.1.6/useful/NEWS | 4 ++++
useful-1.1.6/useful/R/buildFormula.r | 5 +++++
useful-1.1.6/useful/R/hartigan.r | 2 +-
useful-1.1.6/useful/R/kmeansPlotting.r | 4 ++--
useful-1.1.6/useful/R/tsPlot.r | 4 ++--
useful-1.1.6/useful/man/MapToInterval.Rd | 2 +-
12 files changed, 43 insertions(+), 35 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.7 dated 2012-08-30 and 0.9.8 dated 2012-09-29
Description: A High-performance computing toolset for relatedness and
principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8
MD5 | 34 -
NEWS | 13
R/main.r | 822 ++++++++++++++++++++++++++++++++++------
inst/doc/SNPRelateTutorial.Rnw | 49 +-
inst/doc/SNPRelateTutorial.pdf |binary
inst/extdata/hapmap.geno.gds |binary
man/SNPRelate-package.Rd | 12
man/snpgdsCutTree.Rd |only
man/snpgdsDiss.Rd |only
man/snpgdsHCluster.Rd |only
man/snpgdsIBS.Rd | 2
man/snpgdsOption.Rd |only
man/snpgdsVCF2GDS.Rd | 57 ++
src/CoreGDSLink.cpp | 2
src/CoreGDSLink.h | 11
src/genIBD.cpp | 2
src/main.cpp | 211 +++++++---
tests/runTests.R | 20
vignettes/SNPRelateTutorial.Rnw | 49 +-
20 files changed, 1024 insertions(+), 268 deletions(-)
Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.4.2 dated 2012-08-13 and 1.4.3 dated 2012-09-29
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
NCBI2R-1.4.2/NCBI2R/R/order.to.original.snplist.r |only
NCBI2R-1.4.3/NCBI2R/DESCRIPTION | 8
NCBI2R-1.4.3/NCBI2R/MD5 | 82 ++---
NCBI2R-1.4.3/NCBI2R/NAMESPACE | 2
NCBI2R-1.4.3/NCBI2R/R/AnnotateDataframe.r | 140 +++++----
NCBI2R-1.4.3/NCBI2R/R/AnnotateSNPFile.r | 2
NCBI2R-1.4.3/NCBI2R/R/AnnotateSNPList.r | 42 --
NCBI2R-1.4.3/NCBI2R/R/GetClosestGeneInfo.r | 37 +-
NCBI2R-1.4.3/NCBI2R/R/GetGeneInfo.r | 80 +++--
NCBI2R-1.4.3/NCBI2R/R/GetGeneNames.r | 45 ++
NCBI2R-1.4.3/NCBI2R/R/GetGenesInSNPs.r |only
NCBI2R-1.4.3/NCBI2R/R/GetNeighGenes.r | 34 +-
NCBI2R-1.4.3/NCBI2R/R/GetSNPInfo.r | 2
NCBI2R-1.4.3/NCBI2R/R/GetSNPsInGenes.r | 4
NCBI2R-1.4.3/NCBI2R/R/GetTax.r | 4
NCBI2R-1.4.3/NCBI2R/R/GetTaxInfo.r | 6
NCBI2R-1.4.3/NCBI2R/R/MergeSNPsGenes.r | 2
NCBI2R-1.4.3/NCBI2R/R/check.package.r | 154 +++++++++-
NCBI2R-1.4.3/NCBI2R/R/checkAllNumerics.r | 28 -
NCBI2R-1.4.3/NCBI2R/R/errorHandler.r |only
NCBI2R-1.4.3/NCBI2R/R/extract.genenames.from.genetabletxt.r | 2
NCBI2R-1.4.3/NCBI2R/R/get.file.r | 4
NCBI2R-1.4.3/NCBI2R/R/getListFromXML.r | 19 +
NCBI2R-1.4.3/NCBI2R/R/getSNPInfo.master.docset.r | 4
NCBI2R-1.4.3/NCBI2R/R/getSNPInfo.master.xml.r | 14
NCBI2R-1.4.3/NCBI2R/R/getSNPInfo.singlebatch.trimmednames.docset.r | 48 ++-
NCBI2R-1.4.3/NCBI2R/R/getSNPInfo.singlebatch.trimmednames.xml.r | 26 +
NCBI2R-1.4.3/NCBI2R/R/order.to.original.list.r | 2
NCBI2R-1.4.3/NCBI2R/R/randomExamples.r |only
NCBI2R-1.4.3/NCBI2R/R/randomGene.r |only
NCBI2R-1.4.3/NCBI2R/R/randomSNP.r | 11
NCBI2R-1.4.3/NCBI2R/R/tryScan.r | 9
NCBI2R-1.4.3/NCBI2R/man/AnnotateDataframe.Rd | 21 +
NCBI2R-1.4.3/NCBI2R/man/AnnotateSNPFile.Rd | 20 -
NCBI2R-1.4.3/NCBI2R/man/AnnotateSNPList.Rd | 16 -
NCBI2R-1.4.3/NCBI2R/man/GetClosestGeneInfo.Rd | 12
NCBI2R-1.4.3/NCBI2R/man/GetGeneInfo.Rd | 15
NCBI2R-1.4.3/NCBI2R/man/GetGeneTable.Rd | 8
NCBI2R-1.4.3/NCBI2R/man/GetGenesInSNPs.Rd |only
NCBI2R-1.4.3/NCBI2R/man/GetIDs.Rd | 32 +-
NCBI2R-1.4.3/NCBI2R/man/GetNeighGenes.Rd | 4
NCBI2R-1.4.3/NCBI2R/man/GetSNPInfo.Rd | 14
NCBI2R-1.4.3/NCBI2R/man/MakeExcel.Rd | 12
NCBI2R-1.4.3/NCBI2R/man/NatureJobs.Rd | 13
NCBI2R-1.4.3/NCBI2R/man/PrintFilters.Rd | 15
45 files changed, 683 insertions(+), 310 deletions(-)
Title: Robust Estimation of Overdispersed Multinomial Regression Models
Diff between multinomRob versions 1.8-4 dated 2010-05-09 and 1.8-6 dated 2012-09-29
Description: MNL and overdispersed multinomial regression using robust
(LQD and tanh) estimation
Author: Walter R. Mebane, Jr.
Maintainer: Jasjeet Singh Sekhon
DESCRIPTION | 8 ++++----
MD5 |only
R/multinomMLE.R | 6 +++---
R/multinomRob.R | 20 +++++++++++---------
R/multinomT.R | 2 +-
R/multinomTanh.R | 6 +++---
R/zzz.R | 11 +----------
man/multinomMLE.Rd | 26 ++++++++++++++++++++++++++
man/multinomRob.Rd | 11 +++++++++++
src/fit_lqd2.cpp | 24 +++++++++++-------------
10 files changed, 71 insertions(+), 43 deletions(-)
Title: R API to Interactive Brokers Trader Workstation
Diff between IBrokers versions 0.9-9 dated 2012-09-09 and 0.9-10 dated 2012-09-29
Description: Provides native R access to Interactive Brokers Trader
Workstation API.
Author: Jeffrey A. Ryan
Maintainer: Jeffrey A. Ryan
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/processMsg.R | 2 --
R/twsConnect.R | 2 +-
R/zzz.R | 2 +-
inst/doc/IBrokers.pdf |binary
inst/doc/IBrokersREFCARD.pdf |binary
inst/doc/RealTime.pdf |binary
8 files changed, 13 insertions(+), 15 deletions(-)
Title: Plots Coefficients from Fitted Models
Diff between coefplot versions 1.1.7 dated 2012-04-13 and 1.1.8 dated 2012-09-29
Description: Plots the coefficients from a model object
Author: Jared P. Lander
Maintainer:
coefplot-1.1.7/coefplot/.gitignore |only
coefplot-1.1.7/coefplot/LISCENSE |only
coefplot-1.1.7/coefplot/coefplot.Rproj |only
coefplot-1.1.8/coefplot/DESCRIPTION | 12 +++++++-----
coefplot-1.1.8/coefplot/MD5 | 16 +++++++---------
coefplot-1.1.8/coefplot/NAMESPACE | 12 ++++++------
coefplot-1.1.8/coefplot/NEWS | 4 ++++
coefplot-1.1.8/coefplot/R/coefplot.r | 4 ++--
coefplot-1.1.8/coefplot/R/utilities.r | 4 ++--
coefplot-1.1.8/coefplot/man/coefplot.Rd | 2 +-
coefplot-1.1.8/coefplot/man/coefplot.lm.Rd | 2 +-
11 files changed, 30 insertions(+), 26 deletions(-)
Title: R Package for Covariate Balancing Propensity Score
Diff between CBPS versions 0.1 dated 2012-07-19 and 0.2 dated 2012-09-29
Description: CBPS is an R package that implements the covariate
balancing propensity score proposed by Imai and Ratkovic
(2012). The propensity score is estimated such that it
maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore,
avoids an iteration between model fitting and balance checking.
Currently, the package can only deal with binary treatment in
the cross section setting but in the future it will be extended
to other settings including non-binary treatments and causal
inference with longitudinal data.
Author: Marc Ratkovic
Maintainer: Marc Ratkovic
CBPS-0.1/CBPS/man/CBPSlogit.Rd |only
CBPS-0.1/CBPS/man/summary.CBPSlogit.Rd |only
CBPS-0.2/CBPS/ChangeLog | 2
CBPS-0.2/CBPS/DESCRIPTION | 8 -
CBPS-0.2/CBPS/MD5 | 15 +-
CBPS-0.2/CBPS/NAMESPACE | 7 -
CBPS-0.2/CBPS/R/CovarBalFunc.R | 221 +++++++++++++++++++++++++--------
CBPS-0.2/CBPS/man/CBPS.Rd |only
CBPS-0.2/CBPS/man/DR.rd |only
CBPS-0.2/CBPS/man/IPW.Rd |only
CBPS-0.2/CBPS/man/summary.CBPS.Rd |only
CBPS-0.2/CBPS/man/vcov.CBPS.Rd |only
12 files changed, 190 insertions(+), 63 deletions(-)