Title: Typed JSON
Description: TSON, short for Typed JSON, is a binary-encoded serialization of
JSON like document that support JavaScript typed data (https://github.com/amaurel/TSON).
Author: Alexandre Maurel
Maintainer: Alexandre Maurel <alexandre.maurel@gmail.com>
Diff between rtson versions 1.0 dated 2015-11-25 and 1.1 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 1 + R/deserializer.R | 19 ++++++++++++++----- R/utils.R | 16 ++++++++++++++++ README.md | 8 ++++++++ man/tson.scalar.Rd |only tests/testthat/test_rtson.R | 21 ++++++++++++++++----- 8 files changed, 65 insertions(+), 19 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Description: Provides tools for transforming, time-scaling, and
modifying phylogenies containing extinct (i.e. fossil) lineages. In particular,
most users are interested in the functions timePaleoPhy, bin_timePaleoPhy,
cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which time-scale cladograms of
fossil taxa into dated phylogenies. This package also contains a large number
of likelihood functions for estimating sampling and diversification rates from
different types of data available from the fossil record (e.g. range data,
occurrence data, etc). paleotree users can also simulate diversification and
sampling in the fossil record using the function simFossilRecord, which is a
detailed simulator for branching birth-death-sampling processes composed of
discrete taxonomic units arranged in ancestor-descendant relationships. Users
can use simFossilRecord to simulate diversification in incompletely sampled
fossil records, under various models of morphological differentiation (i.e.
the various patterns by which morphotaxa originate from one another), and
with time-dependent, longevity-dependent and/or diversity-dependent rates of
diversification, extinction and sampling. Additional functions allow users to
translate simulated ancestor-descendant data from simFossilRecord into standard
time-scaled phylogenies or unscaled cladograms that reflect the relationships
among taxon units.
Author: David W. Bapst
Maintainer: David W. Bapst <dwbapst@gmail.com>
Diff between paleotree versions 2.5 dated 2015-09-21 and 2.6 dated 2015-12-02
paleotree-2.5/paleotree/R/getSampProbDisc.R |only paleotree-2.5/paleotree/R/getSampRateCont.R |only paleotree-2.5/paleotree/R/simFossilTaxa.R |only paleotree-2.5/paleotree/R/simFossilTaxa_SRCond.R |only paleotree-2.5/paleotree/R/simPaleoTrees.R |only paleotree-2.5/paleotree/man/getSampProbDisc.Rd |only paleotree-2.5/paleotree/man/getSampRateCont.Rd |only paleotree-2.5/paleotree/man/simFossilTaxa.Rd |only paleotree-2.5/paleotree/man/simFossilTaxa_SRCond.Rd |only paleotree-2.5/paleotree/man/simPaleoTrees.Rd |only paleotree-2.6/paleotree/CHANGELOG | 15 + paleotree-2.6/paleotree/DESCRIPTION | 31 +- paleotree-2.6/paleotree/MD5 | 215 +++++++--------- paleotree-2.6/paleotree/NAMESPACE | 7 paleotree-2.6/paleotree/R/DiversityCurves.R | 23 + paleotree-2.6/paleotree/R/SamplingConv.R | 4 paleotree-2.6/paleotree/R/binTimeData.R | 12 paleotree-2.6/paleotree/R/branchClasses.R | 6 paleotree-2.6/paleotree/R/cal3TimePaleoPhy.R | 80 +++-- paleotree-2.6/paleotree/R/cladogeneticTraitCont.R | 33 +- paleotree-2.6/paleotree/R/compareTimescaling.R | 12 paleotree-2.6/paleotree/R/constrainParPaleo.R | 4 paleotree-2.6/paleotree/R/dateNodes.R | 8 paleotree-2.6/paleotree/R/depthRainbow.R | 2 paleotree-2.6/paleotree/R/divCurveFossilRecordSim.R | 33 ++ paleotree-2.6/paleotree/R/durationFreq.R | 24 + paleotree-2.6/paleotree/R/freqRat.R | 66 +++- paleotree-2.6/paleotree/R/horizonSampRate.R | 5 paleotree-2.6/paleotree/R/inverseSurv.R | 9 paleotree-2.6/paleotree/R/macroperforateForam.R | 10 paleotree-2.6/paleotree/R/minBranchLength.R | 10 paleotree-2.6/paleotree/R/modelMethods.R | 4 paleotree-2.6/paleotree/R/modifyTerminalBranches.R | 30 +- paleotree-2.6/paleotree/R/multiDiv.R | 43 +-- paleotree-2.6/paleotree/R/paleotree-package.R | 6 paleotree-2.6/paleotree/R/parentChild2taxonTree.R | 6 paleotree-2.6/paleotree/R/perCapitaRates.R | 9 paleotree-2.6/paleotree/R/plotTraitgram.R | 6 paleotree-2.6/paleotree/R/sampleRanges.R | 22 + paleotree-2.6/paleotree/R/seqTimeList.R | 12 paleotree-2.6/paleotree/R/simFossilRecord.R | 23 + paleotree-2.6/paleotree/R/simFossilRecordInternal.R | 5 paleotree-2.6/paleotree/R/simFossilRecordMethods.R | 15 - paleotree-2.6/paleotree/R/taxa2cladogram.R | 32 +- paleotree-2.6/paleotree/R/taxa2phylo.R | 36 +- paleotree-2.6/paleotree/R/taxonSortPBDBocc.R | 17 - paleotree-2.6/paleotree/R/termTaxa.R | 97 ++++--- paleotree-2.6/paleotree/R/timeLadderTree.R | 4 paleotree-2.6/paleotree/R/timePaleoPhy.R | 14 - paleotree-2.6/paleotree/R/timeSliceTree.R | 26 + paleotree-2.6/paleotree/README | 6 paleotree-2.6/paleotree/man/DiversityCurves.Rd | 41 +-- paleotree-2.6/paleotree/man/SamplingConv.Rd | 9 paleotree-2.6/paleotree/man/SongZhangDicrano.Rd | 11 paleotree-2.6/paleotree/man/binTimeData.Rd | 16 - paleotree-2.6/paleotree/man/branchClasses.Rd | 22 - paleotree-2.6/paleotree/man/cal3TimePaleoPhy.Rd | 100 ++++--- paleotree-2.6/paleotree/man/cladogeneticTraitCont.Rd | 27 +- paleotree-2.6/paleotree/man/communityEcology.Rd | 7 paleotree-2.6/paleotree/man/compareTimescaling.Rd | 8 paleotree-2.6/paleotree/man/constrainParPaleo.Rd | 23 - paleotree-2.6/paleotree/man/createMrBayesConstraints.Rd | 6 paleotree-2.6/paleotree/man/dateNodes.Rd | 10 paleotree-2.6/paleotree/man/degradeTree.Rd | 14 - paleotree-2.6/paleotree/man/depthRainbow.Rd | 4 paleotree-2.6/paleotree/man/divCurveFossilRecordSim.Rd | 7 paleotree-2.6/paleotree/man/durationFreq.Rd | 35 +- paleotree-2.6/paleotree/man/equation2function.Rd | 2 paleotree-2.6/paleotree/man/expandTaxonTree.Rd | 4 paleotree-2.6/paleotree/man/footeValues.Rd | 44 +-- paleotree-2.6/paleotree/man/freqRat.Rd | 68 +++-- paleotree-2.6/paleotree/man/graptDisparity.Rd | 16 - paleotree-2.6/paleotree/man/graptPBDB.Rd | 6 paleotree-2.6/paleotree/man/horizonSampRate.Rd | 9 paleotree-2.6/paleotree/man/inverseSurv.Rd | 39 +- paleotree-2.6/paleotree/man/kanto.Rd | 7 paleotree-2.6/paleotree/man/macroperforateForam.Rd | 34 +- paleotree-2.6/paleotree/man/makePBDBtaxonTree.Rd | 15 - paleotree-2.6/paleotree/man/minBranchLength.Rd | 9 paleotree-2.6/paleotree/man/minCharChange.Rd | 29 +- paleotree-2.6/paleotree/man/modelMethods.Rd | 9 paleotree-2.6/paleotree/man/modifyTerminalBranches.Rd | 22 + paleotree-2.6/paleotree/man/multiDiv.Rd | 52 ++- paleotree-2.6/paleotree/man/nearestNeighborDist.Rd | 17 - paleotree-2.6/paleotree/man/occData2timeList.Rd | 10 paleotree-2.6/paleotree/man/optimPaleo.Rd | 5 paleotree-2.6/paleotree/man/paleotree-package.Rd | 12 paleotree-2.6/paleotree/man/parentChild2taxonTree.Rd | 14 - paleotree-2.6/paleotree/man/perCapitaRates.Rd | 31 +- paleotree-2.6/paleotree/man/perfectParsCharTree.Rd | 8 paleotree-2.6/paleotree/man/plotOccData.Rd | 9 paleotree-2.6/paleotree/man/plotTraitgram.Rd | 4 paleotree-2.6/paleotree/man/pqr2Ps.Rd | 4 paleotree-2.6/paleotree/man/probAnc.Rd | 27 +- paleotree-2.6/paleotree/man/resolveTreeChar.Rd | 20 - paleotree-2.6/paleotree/man/retiolitinae.Rd | 11 paleotree-2.6/paleotree/man/reverseList.Rd | 4 paleotree-2.6/paleotree/man/rootSplit.Rd | 4 paleotree-2.6/paleotree/man/sampleRanges.Rd | 26 + paleotree-2.6/paleotree/man/seqTimeList.Rd | 22 - paleotree-2.6/paleotree/man/simFossilRecord.Rd | 77 +++-- paleotree-2.6/paleotree/man/simFossilRecordMethods.Rd | 14 - paleotree-2.6/paleotree/man/taxa2cladogram.Rd | 29 +- paleotree-2.6/paleotree/man/taxa2phylo.Rd | 29 +- paleotree-2.6/paleotree/man/taxonSortPBDBocc.Rd | 32 +- paleotree-2.6/paleotree/man/taxonTable2taxonTree.Rd | 4 paleotree-2.6/paleotree/man/termTaxa.Rd | 63 ++-- paleotree-2.6/paleotree/man/testEdgeMat.Rd | 3 paleotree-2.6/paleotree/man/timeLadderTree.Rd | 10 paleotree-2.6/paleotree/man/timeList2fourDate.Rd | 3 paleotree-2.6/paleotree/man/timePaleoPhy.Rd | 46 +-- paleotree-2.6/paleotree/man/timeSliceTree.Rd | 20 - paleotree-2.6/paleotree/man/unitLengthTree.Rd | 4 paleotree-2.6/paleotree/tests |only 114 files changed, 1367 insertions(+), 922 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.7.0 dated 2015-10-15 and 0.8.0 dated 2015-12-02
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NAMESPACE | 5 ++++- R/ndtvAnimationWidget.R | 5 ++++- inst/doc/ndtv.pdf |binary inst/htmlwidgets/ndtvAnimationWidget.js | 19 +++++++++++++++---- man/ndtvAnimationWidget.Rd |only man/stergm.sim.1.Rd | 4 +++- 9 files changed, 43 insertions(+), 19 deletions(-)
Title: Animal Movement Modelling using Hidden Markov Models
Description: Provides tools for animal movement modelling using hidden Markov models.
These include processing of tracking data, fitting HMMs to movement data, visualization of
data and fitted model, decoding of the state process...
Author: Theo Michelot, Roland Langrock, Toby Patterson, Eric Rexstad
Maintainer: Theo Michelot <theo.michelot@insa-rouen.fr>
Diff between moveHMM versions 1.0 dated 2015-10-23 and 1.1 dated 2015-12-02
moveHMM-1.0/moveHMM/inst/doc/moveHMM-guide.pdf.asis |only moveHMM-1.0/moveHMM/vignettes/moveHMM-guide.pdf.asis |only moveHMM-1.1/moveHMM/DESCRIPTION | 19 +- moveHMM-1.1/moveHMM/MD5 | 133 +++++++++---------- moveHMM-1.1/moveHMM/NAMESPACE | 3 moveHMM-1.1/moveHMM/R/CI.R | 24 +++ moveHMM-1.1/moveHMM/R/angleCI.R | 3 moveHMM-1.1/moveHMM/R/exGen.R | 2 moveHMM-1.1/moveHMM/R/fitHMM.R | 46 +++++- moveHMM-1.1/moveHMM/R/logAlpha.R | 4 moveHMM-1.1/moveHMM/R/logBeta.R | 4 moveHMM-1.1/moveHMM/R/moveHMM.R | 11 - moveHMM-1.1/moveHMM/R/parDef.R | 19 +- moveHMM-1.1/moveHMM/R/plotPR.R | 21 ++- moveHMM-1.1/moveHMM/R/plotStates.R | 4 moveHMM-1.1/moveHMM/R/plot_moveData.R | 1 moveHMM-1.1/moveHMM/R/plot_moveHMM.R | 53 ++++--- moveHMM-1.1/moveHMM/R/prepData.R | 1 moveHMM-1.1/moveHMM/R/print_moveHMM.R | 30 ---- moveHMM-1.1/moveHMM/R/pseudoRes.R | 9 - moveHMM-1.1/moveHMM/R/simData.R | 127 ++++++++++++++---- moveHMM-1.1/moveHMM/R/summary_moveData.R | 5 moveHMM-1.1/moveHMM/R/viterbi.R | 4 moveHMM-1.1/moveHMM/README.md |only moveHMM-1.1/moveHMM/build/vignette.rds |binary moveHMM-1.1/moveHMM/data/example.RData |binary moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.R |only moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.Rnw |only moveHMM-1.1/moveHMM/inst/doc/moveHMM-guide.pdf |binary moveHMM-1.1/moveHMM/man/AIC.moveHMM.Rd | 3 moveHMM-1.1/moveHMM/man/CI.Rd | 3 moveHMM-1.1/moveHMM/man/allProbs.Rd | 2 moveHMM-1.1/moveHMM/man/angleCI.Rd | 2 moveHMM-1.1/moveHMM/man/dexp_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dgamma_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dlnorm_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dvm_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dweibull_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/dwrpcauchy_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/exGen.Rd | 2 moveHMM-1.1/moveHMM/man/example.Rd | 2 moveHMM-1.1/moveHMM/man/fitHMM.Rd | 7 - moveHMM-1.1/moveHMM/man/is.moveData.Rd | 2 moveHMM-1.1/moveHMM/man/is.moveHMM.Rd | 2 moveHMM-1.1/moveHMM/man/logAlpha.Rd | 2 moveHMM-1.1/moveHMM/man/logBeta.Rd | 2 moveHMM-1.1/moveHMM/man/moveData.Rd | 2 moveHMM-1.1/moveHMM/man/moveHMM.Rd | 10 - moveHMM-1.1/moveHMM/man/n2w.Rd | 3 moveHMM-1.1/moveHMM/man/nLogLike.Rd | 3 moveHMM-1.1/moveHMM/man/nLogLike_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/parDef.Rd | 5 moveHMM-1.1/moveHMM/man/plot.moveData.Rd | 3 moveHMM-1.1/moveHMM/man/plot.moveHMM.Rd | 9 + moveHMM-1.1/moveHMM/man/plotPR.Rd | 12 + moveHMM-1.1/moveHMM/man/plotStates.Rd | 3 moveHMM-1.1/moveHMM/man/prepData.Rd | 3 moveHMM-1.1/moveHMM/man/print.moveHMM.Rd | 3 moveHMM-1.1/moveHMM/man/pseudoRes.Rd | 5 moveHMM-1.1/moveHMM/man/simData.Rd | 49 ++++--- moveHMM-1.1/moveHMM/man/stateProbs.Rd | 3 moveHMM-1.1/moveHMM/man/summary.moveData.Rd | 3 moveHMM-1.1/moveHMM/man/trMatrix_rcpp.Rd | 2 moveHMM-1.1/moveHMM/man/turnAngle.Rd | 2 moveHMM-1.1/moveHMM/man/viterbi.Rd | 3 moveHMM-1.1/moveHMM/man/w2n.Rd | 4 moveHMM-1.1/moveHMM/tests/testthat/test_fitHMM.R | 1 moveHMM-1.1/moveHMM/tests/testthat/test_parDef.R | 4 moveHMM-1.1/moveHMM/vignettes/models.RData |only moveHMM-1.1/moveHMM/vignettes/moveHMM-guide.Rnw |only moveHMM-1.1/moveHMM/vignettes/step_angle_figure.pdf |only moveHMM-1.1/moveHMM/vignettes/struct.pdf |only 72 files changed, 433 insertions(+), 265 deletions(-)
Title: Make Dealing with Dates a Little Easier
Description: Functions to work with date-times and timespans: fast and user
friendly parsing of date-time data, extraction and updating of components of
a date-time (years, months, days, hours, minutes, and seconds), algebraic
manipulation on date-time and timespan objects. The 'lubridate' package has
a consistent and memorable syntax that makes working with dates easy and
fun.
Author: Garrett Grolemund [aut],
Vitalie Spinu [aut, cre],
Hadley Wickham [aut],
Jan Lyttle [ctb],
Imanuel Constigan [ctb],
Jason Law [ctb],
Doug Mitarotonda [ctb],
Joseph Larmarange [ctb],
Jonathan Boiser [ctb],
Chel Hee Lee [ctb]
Maintainer: Vitalie Spinu <spinuvit@gmail.com>
Diff between lubridate versions 1.3.3 dated 2013-12-31 and 1.5.0 dated 2015-12-02
lubridate-1.3.3/lubridate/NEWS |only lubridate-1.3.3/lubridate/inst/tests |only lubridate-1.3.3/lubridate/man/ceiling_date.Rd |only lubridate-1.3.3/lubridate/man/dseconds.Rd |only lubridate-1.3.3/lubridate/man/floor_date.Rd |only lubridate-1.3.3/lubridate/man/is.duration.Rd |only lubridate-1.3.3/lubridate/man/is.interval.Rd |only lubridate-1.3.3/lubridate/man/is.period.Rd |only lubridate-1.3.3/lubridate/man/lubridate.Rd |only lubridate-1.3.3/lubridate/man/lubridate_formats.Rd |only lubridate-1.3.3/lubridate/man/new_difftime.Rd |only lubridate-1.3.3/lubridate/man/new_duration.Rd |only lubridate-1.3.3/lubridate/man/new_interval.Rd |only lubridate-1.3.3/lubridate/man/new_period.Rd |only lubridate-1.3.3/lubridate/man/seconds.Rd |only lubridate-1.3.3/lubridate/man/seconds_to_period.Rd |only lubridate-1.3.3/lubridate/man/sundays.Rd |only lubridate-1.3.3/lubridate/man/wday.Rd |only lubridate-1.3.3/lubridate/man/yday.Rd |only lubridate-1.3.3/lubridate/tests/test-all.R |only lubridate-1.5.0/lubridate/DESCRIPTION | 81 +-- lubridate-1.5.0/lubridate/MD5 | 298 ++++++------- lubridate-1.5.0/lubridate/NAMESPACE | 50 +- lubridate-1.5.0/lubridate/NEWS.md |only lubridate-1.5.0/lubridate/R/POSIXt.r | 16 lubridate-1.5.0/lubridate/R/accessors-day.r | 143 +++--- lubridate-1.5.0/lubridate/R/accessors-dst.r | 6 lubridate-1.5.0/lubridate/R/accessors-hour.r | 11 lubridate-1.5.0/lubridate/R/accessors-minute.r | 9 lubridate-1.5.0/lubridate/R/accessors-month.r | 69 ++- lubridate-1.5.0/lubridate/R/accessors-second.r | 7 lubridate-1.5.0/lubridate/R/accessors-tz.r | 11 lubridate-1.5.0/lubridate/R/accessors-week.r | 30 - lubridate-1.5.0/lubridate/R/accessors-year.r | 21 lubridate-1.5.0/lubridate/R/coercion.r | 293 ++++++++----- lubridate-1.5.0/lubridate/R/constants.r |only lubridate-1.5.0/lubridate/R/decimal-dates.r | 60 +- lubridate-1.5.0/lubridate/R/deprecated.r |only lubridate-1.5.0/lubridate/R/difftimes.r | 117 +++-- lubridate-1.5.0/lubridate/R/durations.r | 389 ++++++++---------- lubridate-1.5.0/lubridate/R/epochs.r | 16 lubridate-1.5.0/lubridate/R/guess.r | 322 ++++++-------- lubridate-1.5.0/lubridate/R/help.r | 13 lubridate-1.5.0/lubridate/R/instants.r | 2 lubridate-1.5.0/lubridate/R/intervals.r | 217 +++++----- lubridate-1.5.0/lubridate/R/ops-%m+%.r | 169 ++++--- lubridate-1.5.0/lubridate/R/ops-addition.r | 22 - lubridate-1.5.0/lubridate/R/ops-division.r | 35 - lubridate-1.5.0/lubridate/R/ops-modulo.r | 27 - lubridate-1.5.0/lubridate/R/parse.r | 176 ++++---- lubridate-1.5.0/lubridate/R/periods.r | 452 +++++++++------------ lubridate-1.5.0/lubridate/R/pretty.r | 62 +- lubridate-1.5.0/lubridate/R/round.r | 208 ++++----- lubridate-1.5.0/lubridate/R/stamp.r | 13 lubridate-1.5.0/lubridate/R/timespans.r | 51 ++ lubridate-1.5.0/lubridate/R/update.r | 216 +++++----- lubridate-1.5.0/lubridate/R/util.r | 2 lubridate-1.5.0/lubridate/README.md |only lubridate-1.5.0/lubridate/build/vignette.rds |binary lubridate-1.5.0/lubridate/inst/doc/lubridate.R | 25 - lubridate-1.5.0/lubridate/inst/doc/lubridate.Rmd | 6 lubridate-1.5.0/lubridate/inst/doc/lubridate.html | 180 ++++---- lubridate-1.5.0/lubridate/man/DateCoercion.Rd | 5 lubridate-1.5.0/lubridate/man/DateUpdate.Rd | 64 -- lubridate-1.5.0/lubridate/man/Deprecated.Rd |only lubridate-1.5.0/lubridate/man/Duration-class.Rd | 37 - lubridate-1.5.0/lubridate/man/Interval-class.Rd | 50 +- lubridate-1.5.0/lubridate/man/Period-class.Rd | 130 +++--- lubridate-1.5.0/lubridate/man/Timespan-class.Rd | 10 lubridate-1.5.0/lubridate/man/add_epoch_to_date.Rd | 17 lubridate-1.5.0/lubridate/man/am.Rd | 15 lubridate-1.5.0/lubridate/man/as.duration.Rd | 50 +- lubridate-1.5.0/lubridate/man/as.interval.Rd | 46 +- lubridate-1.5.0/lubridate/man/as.period.Rd | 106 ++-- lubridate-1.5.0/lubridate/man/date_decimal.Rd | 19 lubridate-1.5.0/lubridate/man/day.Rd |only lubridate-1.5.0/lubridate/man/days_in_month.Rd | 14 lubridate-1.5.0/lubridate/man/decimal_date.Rd | 11 lubridate-1.5.0/lubridate/man/dst.Rd | 21 lubridate-1.5.0/lubridate/man/duration.Rd | 89 ++-- lubridate-1.5.0/lubridate/man/fit_to_timeline.Rd | 75 ++- lubridate-1.5.0/lubridate/man/force_tz.Rd | 34 - lubridate-1.5.0/lubridate/man/guess_formats.Rd | 34 - lubridate-1.5.0/lubridate/man/here.Rd | 10 lubridate-1.5.0/lubridate/man/hm.Rd | 32 - lubridate-1.5.0/lubridate/man/hms.Rd | 36 - lubridate-1.5.0/lubridate/man/hour.Rd | 15 lubridate-1.5.0/lubridate/man/int_aligns.Rd | 26 - lubridate-1.5.0/lubridate/man/int_diff.Rd | 19 lubridate-1.5.0/lubridate/man/int_end.Rd | 20 lubridate-1.5.0/lubridate/man/int_flip.Rd | 21 lubridate-1.5.0/lubridate/man/int_length.Rd | 17 lubridate-1.5.0/lubridate/man/int_overlaps.Rd | 19 lubridate-1.5.0/lubridate/man/int_shift.Rd | 26 - lubridate-1.5.0/lubridate/man/int_standardize.Rd | 12 lubridate-1.5.0/lubridate/man/int_start.Rd | 20 lubridate-1.5.0/lubridate/man/interval.Rd |only lubridate-1.5.0/lubridate/man/is.Date.Rd | 13 lubridate-1.5.0/lubridate/man/is.POSIXt.Rd | 14 lubridate-1.5.0/lubridate/man/is.difftime.Rd | 16 lubridate-1.5.0/lubridate/man/is.instant.Rd | 17 lubridate-1.5.0/lubridate/man/is.timespan.Rd | 15 lubridate-1.5.0/lubridate/man/lakers.Rd | 22 - lubridate-1.5.0/lubridate/man/leap_year.Rd | 15 lubridate-1.5.0/lubridate/man/lubridate-package.Rd |only lubridate-1.5.0/lubridate/man/make_difftime.Rd | 54 ++ lubridate-1.5.0/lubridate/man/minute.Rd | 15 lubridate-1.5.0/lubridate/man/month.Rd | 40 - lubridate-1.5.0/lubridate/man/mplus.Rd | 75 ++- lubridate-1.5.0/lubridate/man/ms.Rd | 33 - lubridate-1.5.0/lubridate/man/new_epoch.Rd | 17 lubridate-1.5.0/lubridate/man/now.Rd | 19 lubridate-1.5.0/lubridate/man/olson_time_zones.Rd | 22 - lubridate-1.5.0/lubridate/man/origin.Rd | 13 lubridate-1.5.0/lubridate/man/parse_date_time.Rd | 357 ++++++++-------- lubridate-1.5.0/lubridate/man/period.Rd | 92 ++-- lubridate-1.5.0/lubridate/man/period_to_seconds.Rd | 21 lubridate-1.5.0/lubridate/man/pretty_dates.Rd | 32 - lubridate-1.5.0/lubridate/man/quarter.Rd | 26 - lubridate-1.5.0/lubridate/man/quick_durations.Rd |only lubridate-1.5.0/lubridate/man/quick_epochs.Rd |only lubridate-1.5.0/lubridate/man/quick_periods.Rd |only lubridate-1.5.0/lubridate/man/reclass_date.Rd | 6 lubridate-1.5.0/lubridate/man/reclass_timespan.Rd | 11 lubridate-1.5.0/lubridate/man/rollback.Rd | 50 +- lubridate-1.5.0/lubridate/man/round_date.Rd | 90 +++- lubridate-1.5.0/lubridate/man/second.Rd | 15 lubridate-1.5.0/lubridate/man/stamp.Rd | 85 +-- lubridate-1.5.0/lubridate/man/time_length.Rd |only lubridate-1.5.0/lubridate/man/timespan.Rd | 135 ++---- lubridate-1.5.0/lubridate/man/today.Rd | 14 lubridate-1.5.0/lubridate/man/tz.Rd | 65 +-- lubridate-1.5.0/lubridate/man/week.Rd | 33 - lubridate-1.5.0/lubridate/man/with_tz.Rd | 29 - lubridate-1.5.0/lubridate/man/within-interval.Rd | 20 lubridate-1.5.0/lubridate/man/year.Rd | 26 - lubridate-1.5.0/lubridate/man/ymd.Rd | 83 +-- lubridate-1.5.0/lubridate/man/ymd_hms.Rd | 85 +-- lubridate-1.5.0/lubridate/src/tparse.c | 138 +++--- lubridate-1.5.0/lubridate/tests/testthat |only lubridate-1.5.0/lubridate/tests/testthat.R |only lubridate-1.5.0/lubridate/vignettes/lubridate.Rmd | 8 142 files changed, 3605 insertions(+), 3141 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: The georob package provides functions for efficiently fitting
linear models with spatially correlated errors by robust and
Gaussian (Restricted) Maximum Likelihood and for computing robust
and customary point and block external-drift kriging predictions,
along with utility functions for variogram modelling
in ad-hoc geostatistical analyses, model building, model evaluation
by cross-validation and for unbiased back-transformation of kriging
predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.2-1 dated 2015-09-02 and 0.2-2 dated 2015-12-02
ChangeLog | 12 + DESCRIPTION | 10 MD5 | 47 ++-- NAMESPACE | 10 NEWS | 2 R/georob.S3methods.R | 2 R/georob.cv.R | 158 +++++++++----- R/georob.exported.functions.R | 86 ++++++-- R/georob.predict.R | 136 +++++++----- R/georob.private.functions.R | 76 +++++-- R/variogram.R | 447 ++++++++++++++++++++++++++++++++++-------- man/S3methods.georob.Rd | 10 man/compress.Rd | 4 man/control.georob.Rd | 20 - man/cv.georob.Rd | 10 man/fit.variogram.model.Rd | 62 ++--- man/georob.Rd | 123 ++++++----- man/georobModelBuilding.Rd | 2 man/lgnpp.Rd | 6 man/param.defaults.Rd |only man/plot.georob.Rd | 81 +++++-- man/predict.georob.Rd | 6 man/profilelogLik.Rd | 15 - man/sample.variogram.Rd | 72 +++++- man/validate.predictions.Rd | 27 +- 25 files changed, 991 insertions(+), 433 deletions(-)
Title: Batch Effect Removal (in Phenotype Prediction using Gene Data)
Description: Various tools dealing with batch effects, in particular enabling the
removal of discrepancies between training and test sets in prediction scenarios.
The following batch effect removal methods are implemented: FAbatch, ComBat, (f)SVA,
mean-centering, standardization, Ratio-A and Ratio-G. For each of these we provide
an additional function which enables a posteriori ('addon') batch effect removal
in independent batches ('test data'). Here, the (already batch effect adjusted)
training data is not altered. For evaluating the success of batch effect adjustment
several metrics are provided. Moreover, the package implements a plot for the
visualization of batch effects using principal component analysis. The main functions
of the package are ba() and baaddon() which enable batch effect removal and addon
batch effect removal, respectively, with one of the seven methods mentioned above.
Another important function is bametric() which is a wrapper function for all implemented
methods for evaluating the success of batch effect removal.
Author: Roman Hornung, David Causeur
Maintainer: Roman Hornung <hornung@ibe.med.uni-muenchen.de>
Diff between bapred versions 0.1 dated 2015-09-04 and 0.2 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/svaba.R | 41 ++++++++++++++++++++++++++++------------- R/svabaaddon.R | 12 ++++++++---- 4 files changed, 42 insertions(+), 23 deletions(-)
Title: Parametric Network Enrichment Analysis
Description: Includes functions and examples for Parametric Network Enrichment Analysis.
Author: Mirko Signorelli, Veronica Vinciotti and Ernst C. Wit
Maintainer: Mirko Signorelli <m.signorelli@rug.nl>
Diff between pnea versions 1.2.0 dated 2015-11-23 and 1.2.1 dated 2015-12-02
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/pnea.R | 10 ++++++++-- man/pnea.Rd | 10 +++------- 4 files changed, 19 insertions(+), 17 deletions(-)
Title: 'Rcpp' Bindings for the 'CCTZ' Library
Description: 'Rcpp' Access to the 'CCTZ' timezone library is provided.
'CCTZ' is a C++ library for translating between absolute and civil times
using the rules of a time zone.
The 'CCTZ' source code, released under the Apache 2.0 License, is included in
this package. See <https://github.com/google/cctz> for more details.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppCCTZ versions 0.0.1 dated 2015-12-01 and 0.0.2 dated 2015-12-02
ChangeLog | 11 +++++++++++ DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ README.md | 6 ++++-- inst/NEWS.Rd |only inst/include/src/cctz_libc.h | 4 ++++ src/cctz_if.cc | 4 +++- src/cctz_libc.cc | 4 ++++ 8 files changed, 37 insertions(+), 13 deletions(-)
Title: Power and Sample Size Based on Two One-Sided t-Tests (TOST) for
(Bio)Equivalence Studies
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits (EMA recommended) based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
Contains further functions power.HVNTID() and sampleN.HVNTID() to calculate
power and sample size for the BE decision via the FDA procedure for
highly variable NTID's (see FDA Dabigatran / rivaroxaban guidances)
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / sample size estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [aut]
Maintainer: Detlew Labes <DetlewLabes@gmx.de>
Diff between PowerTOST versions 1.3-01 dated 2015-09-30 and 1.3-02 dated 2015-12-02
DESCRIPTION | 13 +++++++------ MD5 | 21 ++++++++++++++------- NAMESPACE | 5 ++++- NEWS | 4 ++++ R/SampleSize.R | 8 ++++---- R/power_RSABE_pure.R |only R/power_scABEL.R | 4 ++-- R/power_scABEL_pure.R |only R/power_type1_2TOST.R |only R/sampleN_2TOST.R |only man/power.2TOST.Rd |only man/power.NTIDFDA.Rd | 19 ++++++++++++++++++- man/sampleN.2TOST.Rd |only man/sampleN.NTIDFDA.Rd | 14 +++++++++++++- man/type1error.2TOST.Rd |only 15 files changed, 66 insertions(+), 22 deletions(-)
Title: General Package for Meta-Analysis
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package 'metafor' is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between meta versions 4.3-1 dated 2015-11-16 and 4.3-2 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 12 ++++++++++++ R/metacont.R | 12 ++++-------- R/metaprop.R | 2 +- 5 files changed, 25 insertions(+), 17 deletions(-)
Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see http://en.wikipedia.org/wiki/NetCDF), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 1.2.3 dated 2015-10-09 and 1.3.2 dated 2015-12-02
HelpersMG-1.2.3/HelpersMG/R/compassRose2.R |only HelpersMG-1.2.3/HelpersMG/R/map.scale2.R |only HelpersMG-1.2.3/HelpersMG/man/compassRose2.Rd |only HelpersMG-1.2.3/HelpersMG/man/map.scale2.Rd |only HelpersMG-1.3.2/HelpersMG/DESCRIPTION | 10 - HelpersMG-1.3.2/HelpersMG/MD5 | 96 ++++++++--------- HelpersMG-1.3.2/HelpersMG/NAMESPACE | 6 - HelpersMG-1.3.2/HelpersMG/NEWS | 7 + HelpersMG-1.3.2/HelpersMG/R/BinomialConfidence.R | 2 HelpersMG-1.3.2/HelpersMG/R/HelpersMG-package.R | 4 HelpersMG-1.3.2/HelpersMG/R/MHalgoGen.R | 29 ++--- HelpersMG-1.3.2/HelpersMG/R/ind_long_lat.R | 31 ++--- HelpersMG-1.3.2/HelpersMG/R/local.search.R | 2 HelpersMG-1.3.2/HelpersMG/R/newcompassRose.R |only HelpersMG-1.3.2/HelpersMG/R/newmap.scale.R |only HelpersMG-1.3.2/HelpersMG/R/plot.mcmcComposite.R | 7 - HelpersMG-1.3.2/HelpersMG/R/similar.R | 2 HelpersMG-1.3.2/HelpersMG/R/wget.R | 2 HelpersMG-1.3.2/HelpersMG/man/ChangeCoordinate.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/HelpersMG-package.Rd | 38 +++--- HelpersMG-1.3.2/HelpersMG/man/LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/MHalgoGen.Rd | 28 ++-- HelpersMG-1.3.2/HelpersMG/man/ScalePreviousPlot.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/as.mcmc.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/as.parameters.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/asc.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/barplot_errbar.Rd | 22 +-- HelpersMG-1.3.2/HelpersMG/man/chr.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/clean.knitr.Rd | 4 HelpersMG-1.3.2/HelpersMG/man/compare_AIC.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/convert.tz.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/growlnotify.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/ind_long_lat.Rd | 11 + HelpersMG-1.3.2/HelpersMG/man/index.periodic.Rd | 20 +-- HelpersMG-1.3.2/HelpersMG/man/inside.search.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/local.search.Rd | 4 HelpersMG-1.3.2/HelpersMG/man/logLik.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/merge.mcmcComposite.Rd | 28 ++-- HelpersMG-1.3.2/HelpersMG/man/minmax.periodic.Rd | 22 +-- HelpersMG-1.3.2/HelpersMG/man/moon.info.Rd | 14 +- HelpersMG-1.3.2/HelpersMG/man/newcompassRose.Rd |only HelpersMG-1.3.2/HelpersMG/man/newmap.scale.Rd |only HelpersMG-1.3.2/HelpersMG/man/plot.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/plot.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/plot_add.Rd | 8 - HelpersMG-1.3.2/HelpersMG/man/plot_errbar.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/predict.LD50.Rd | 6 - HelpersMG-1.3.2/HelpersMG/man/read_folder.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/similar.Rd | 2 HelpersMG-1.3.2/HelpersMG/man/summary.mcmcComposite.Rd | 26 ++-- HelpersMG-1.3.2/HelpersMG/man/sun.info.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/tide.info.Rd | 10 - HelpersMG-1.3.2/HelpersMG/man/wget.Rd | 4 53 files changed, 304 insertions(+), 299 deletions(-)
Title: wrapper for the Gnu Scientific Library
Description:
An R wrapper for the special functions and quasi random number
generators of the Gnu Scientific Library
(http://www.gnu.org/software/gsl/). See gsl-package.Rd for details of
overall package organization, and Misc.Rd for some functions that are
widely used in the package, and some tips on installation.
Author: Robin K. S. Hankin; qrng functions by Duncan Murdoch and
multimin by Andrew Clausen
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between gsl versions 1.9-10 dated 2013-12-10 and 1.9-10.1 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- configure | 2 +- configure.ac | 2 +- src/ellint.c | 5 +++++ src/legendre.c | 6 ++++++ 6 files changed, 22 insertions(+), 11 deletions(-)
Title: Zelig Choice Models
Description: Add-on package for Zelig 5. Enables the use of a variety of logit
and probit regressions.
Author: Christine Choirat, James Honaker, Kosuke Imai, Gary King, Olivia Lau
Maintainer: James Honaker <zelig-zee@iq.harvard.edu>
Diff between ZeligChoice versions 0.8-1 dated 2013-09-23 and 0.9-0 dated 2015-12-02
ZeligChoice-0.8-1/ZeligChoice/R/ZeligChoice-package.R |only ZeligChoice-0.8-1/ZeligChoice/R/blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/common-methods.R |only ZeligChoice-0.8-1/ZeligChoice/R/describe.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/param.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/plot.sim.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/qi.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/summarize.ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/summarize.oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2blogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2ologit.R |only ZeligChoice-0.8-1/ZeligChoice/R/zelig2oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/build |only ZeligChoice-0.8-1/ZeligChoice/demo/blogit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/bprobit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/mlogit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/ologit.R |only ZeligChoice-0.8-1/ZeligChoice/demo/oprobit.R |only ZeligChoice-0.8-1/ZeligChoice/inst/doc |only ZeligChoice-0.8-1/ZeligChoice/man/ZeligChoice-package.R.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/describe.mlogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/summarize.ologit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/summarize.oprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2blogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2bprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2mlogit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2ologit.Rd |only ZeligChoice-0.8-1/ZeligChoice/man/zelig2oprobit.Rd |only ZeligChoice-0.8-1/ZeligChoice/tests/tests.R |only ZeligChoice-0.8-1/ZeligChoice/vignettes |only ZeligChoice-0.9-0/ZeligChoice/DESCRIPTION | 30 +--- ZeligChoice-0.9-0/ZeligChoice/MD5 | 89 ++++-------- ZeligChoice-0.9-0/ZeligChoice/NAMESPACE | 54 ++----- ZeligChoice-0.9-0/ZeligChoice/R/create-json.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-bbinchoice.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-blogit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-bprobit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-mlogit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-obinchoice.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-ologit.R |only ZeligChoice-0.9-0/ZeligChoice/R/model-oprobit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/00Index | 10 - ZeligChoice-0.9-0/ZeligChoice/demo/demo-blogit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-bprobit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-mlogit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-ologit.R |only ZeligChoice-0.9-0/ZeligChoice/demo/demo-oprobit.R |only ZeligChoice-0.9-0/ZeligChoice/inst/JSON |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-bbinchoice-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-blogit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-bprobit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-mlogit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-obinchoice-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-ologit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/Zelig-oprobit-class.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/construct.v.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/createJSONzeligchoice.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/ev.mlogit.Rd |only ZeligChoice-0.9-0/ZeligChoice/man/pv.mlogit.Rd |only ZeligChoice-0.9-0/ZeligChoice/tests/testthat |only ZeligChoice-0.9-0/ZeligChoice/tests/testthat.R |only 80 files changed, 67 insertions(+), 116 deletions(-)
Title: Search 'Vertnet', a 'Database' of Vertebrate Specimen Records
Description: Retrieve, map and summarize data from the 'VertNet.org' archives.
Functions allow searching by many parameters, including 'taxonomic' names,
places, and dates. In addition, there is an interface for conducting spatially
delimited searches, and another for requesting large 'datasets' via email.
Author: Scott Chamberlain [aut, cre], Chris Ray [aut], Vijay Barve [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rvertnet versions 0.4.0 dated 2015-11-26 and 0.4.1 dated 2015-12-02
DESCRIPTION | 6 +++--- MD5 | 20 +++++++++++--------- R/bigsearch.R | 32 +++++++++++++++++--------------- R/searchbyterm.R | 14 +++++++------- R/vert_id.R | 12 +++++++----- R/vertmap.R | 3 ++- build/vignette.rds |binary man/bigsearch.Rd | 2 +- man/vert_id.Rd | 13 +++++++++---- tests/testthat/test-dump.R |only tests/testthat/test-vert_id.R |only tests/testthat/test-vertmap.R | 14 ++++++++++++++ 12 files changed, 71 insertions(+), 45 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at http://www.ncdc.noaa.gov/cdo-web/webservices/v2, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Hart Edmund [ctb],
Scott Chamberlain [aut, cre],
Karthik Ram [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.4.2 dated 2015-07-07 and 0.5.0 dated 2015-12-02
DESCRIPTION | 31 +++-- MD5 | 154 +++++++++++++++------------- NAMESPACE | 26 ++++ R/buoy.R | 78 +++++--------- R/ersst.R |only R/gefs.R |only R/ghcnd.R | 39 +++++-- R/homr_definitions.R | 1 R/isd.R | 202 ++++++++++++++++++++++++++----------- R/isd_stations.R |only R/ncdc.r | 2 R/ncdc_plot.r | 38 +++--- R/ncdc_stations.r | 1 R/rnoaa-package.r | 45 +++++--- R/seaice.r | 5 R/swdi.r | 7 - R/zzz.r | 12 ++ README.md | 191 +++++++++++++--------------------- build/vignette.rds |binary inst/isd_stations.rds |only inst/js/LICENSE-turf-buffer |only inst/js/LICENSE-turf-extent |only man/buoy.Rd | 17 ++- man/caching.Rd | 2 man/check_response.Rd | 2 man/check_response_swdi.Rd | 2 man/erddap_clear_cache-defunct.Rd | 2 man/erddap_data-defunct.Rd | 2 man/erddap_datasets-defunct.Rd | 2 man/erddap_grid-defunct.Rd | 2 man/erddap_info-defunct.Rd | 2 man/erddap_search-defunct.Rd | 2 man/erddap_table-defunct.Rd | 2 man/ersst.Rd |only man/fipscodes.Rd | 2 man/gefs.Rd |only man/ghcnd.Rd | 4 man/homr.Rd | 4 man/homr_definitions.Rd | 2 man/is.ncdc_data.Rd | 2 man/isd.Rd | 63 +++++++++-- man/isd_stations.Rd |only man/ncdc.Rd | 16 +- man/ncdc_combine.Rd | 2 man/ncdc_datacats.Rd | 2 man/ncdc_datasets.Rd | 14 +- man/ncdc_datatypes.Rd | 16 +- man/ncdc_leg_data-defunct.Rd | 2 man/ncdc_leg_site_info-defunct.Rd | 2 man/ncdc_leg_sites-defunct.Rd | 2 man/ncdc_leg_variables-defunct.Rd | 2 man/ncdc_locs.Rd | 2 man/ncdc_locs_cats.Rd | 2 man/ncdc_plot.Rd | 2 man/ncdc_stations.Rd | 26 ++-- man/ncdc_theme.Rd | 2 man/noaa-defunct.Rd | 2 man/noaa_combine-defunct.Rd | 2 man/noaa_datacats-defunct.Rd | 2 man/noaa_datasets-defunct.Rd | 2 man/noaa_datatypes-defunct.Rd | 2 man/noaa_locs-defunct.Rd | 2 man/noaa_locs_cats-defunct.Rd | 2 man/noaa_plot-defunct.Rd | 2 man/noaa_seaice-defunct.Rd | 2 man/noaa_stations-defunct.Rd | 2 man/readshpfile.Rd | 2 man/rnoaa-defunct.Rd | 4 man/rnoaa-package.Rd | 31 ++--- man/seaice.Rd | 2 man/seaiceeurls.Rd | 2 man/storm_columns.Rd | 2 man/storm_names.Rd | 2 man/storms.Rd | 2 man/swdi.Rd | 6 - man/theme_ice.Rd | 2 man/tornadoes.Rd | 2 man/type_summ.Rd | 2 tests/testthat/plot_data.Rds |only tests/testthat/test-buoy.R | 51 +++++++-- tests/testthat/test-gefs.R |only tests/testthat/test-isd.R | 12 -- tests/testthat/test-isd_stations.R |only tests/testthat/test-ncdc_plot.r | 13 +- 84 files changed, 687 insertions(+), 506 deletions(-)
Title: Multiple Mediation Analysis
Description: Used for general multiple mediation analysis.
The analysis method is described in Yu et al. 2014, "General Multiple Mediation Analysis With an Application to Explore Racial Disparity in Breast Cancer Survival", published on Journal of Biometrics & Biostatistics, 5(2):189.
Author: Qingzhao Yu
Maintainer: Qingzhao Yu <qyu@lsuhsc.edu>
Diff between mma versions 2.0-0 dated 2015-04-24 and 2.0-1 dated 2015-12-02
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 6 ++++++ R/mma.r | 37 +++++++++++++++++++++++++------------ man/boot.med.binx.Rd | 14 +++++++++----- man/boot.med.contx.Rd | 9 ++++++--- man/mma-package.Rd | 7 ++++--- man/mma.Rd | 19 ++++++++++++------- 8 files changed, 73 insertions(+), 41 deletions(-)
Title: Curve Fitting and Mixture Toxicity Assessment
Description: Curve Fitting for monotonic(sigmoidal) & non-monotonic(J-shaped)
concentration-response data. Toxicity prediction of chemical mixtures using reference
models such as 'concentration addition' and 'independent action' (Backhaus, T., Faust,
M., Environmental Science and Technology. 2012, 46, 2564-2573. doi:10.1021/es2034125).
Author: Xiangwei Zhu
Maintainer: Xiangwei Zhu <xwzhunc@gmail.com>
Diff between mixtox versions 1.1 dated 2015-10-19 and 1.2 dated 2015-12-02
DESCRIPTION | 17 ++-- MD5 | 58 +++++++------ NAMESPACE | 2 R/CEx.R | 36 +++++++- R/ECx.R | 21 ++++- R/NOEC.R | 3 R/curveFit.R | 209 ++++++++++++++++++++++++++++++++++++++++---------- R/ecaPred.R | 7 + R/eiaPred.R | 5 - R/gcaHill.R | 4 R/gcaPred.R | 7 + R/iaPred.R | 5 - R/nmECx.R |only R/showEq.R | 45 ++++++++-- data/antibiotox.rda |only data/hormesis.rda |only man/CEx.Rd | 43 +++------- man/ECx.Rd | 49 ++++++----- man/NOEC.Rd | 8 - man/antibiotox.Rd |only man/caPred.Rd | 17 +--- man/curveFit.Rd | 199 +++++++++++++++++++++++++++++++++-------------- man/cytotox.Rd | 20 ++-- man/ecaPred.Rd | 19 ++-- man/eiaPred.Rd | 33 ++++++- man/gcaHill.Rd | 25 +++-- man/gcaPred.Rd | 27 ++---- man/hormesis.Rd |only man/iaPred.Rd | 38 ++++----- man/mixtox-package.Rd | 30 ++++--- man/nmECx.Rd |only man/showEq.Rd | 49 +++++++---- man/unidTab.Rd | 2 33 files changed, 662 insertions(+), 316 deletions(-)