Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a
wide range of frailty distributions using a consistent and
asymptotically-normal estimator. Currently supports: gamma, power variance
function, log-normal, and inverse Gaussian frailty models.
Author: John V. Monaco [aut, cre],
Malka Gorfine [aut],
Li Hsu [aut]
Maintainer: John V. Monaco <vincent@vmonaco.com>
Diff between frailtySurv versions 1.2.2.1 dated 2016-07-10 and 1.3.1 dated 2016-12-01
DESCRIPTION | 11 - MD5 | 39 ++-- NAMESPACE | 7 NEWS.md |only R/RcppExports.R | 2 R/distributions.R | 2 R/fitfrail.R | 76 +++++++-- R/fitfrail.control.R | 8 R/fitfrail.fit.R | 49 ++++- R/frailtySurv.R | 2 R/genfrail.R | 212 +++++++++++++++---------- R/genfrail.control.R |only R/misc.R | 4 R/plot.simfrail.R | 47 +++-- R/simfrail.R | 115 +++++++++++++ R/summary.simfrail.R | 8 README.md | 24 +- man/fitfrail.control.Rd | 37 ++-- man/genfrail.Rd | 13 + man/genfrail.control.Rd |only src/RcppExports.cpp | 402 ++++++++++++++++++++++++------------------------ src/distributions.cpp | 10 - 22 files changed, 668 insertions(+), 400 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 3.31-2 dated 2016-09-23 and 3.31-5 dated 2016-12-01
DESCRIPTION | 11 +--- INDEX | 2 MD5 | 24 +++++----- R/survey.R | 128 +++++++++++++++++++++++++++++++++++++++++++++++++++--- R/svykm.R | 2 R/svyttest.R | 11 +++- THANKS | 13 ++++- TODO | 7 ++ data/yrbs.rda |only inst/CITATION | 4 - inst/NEWS | 16 ++++++ man/svyciprop.Rd | 11 +++- man/svylogrank.Rd | 4 + man/yrbs.Rd |only 14 files changed, 196 insertions(+), 37 deletions(-)
Title: Super Learner Prediction
Description: Implements the super learner prediction method and contains a
library of prediction algorithms to be used in the super learner.
Author: Eric Polley [aut, cre],
Erin LeDell [aut],
Chris Kennedy [aut],
Sam Lendle [ctb],
Mark van der Laan [aut, ths]
Maintainer: Eric Polley <polley.eric@mayo.edu>
Diff between SuperLearner versions 2.0-19 dated 2016-02-04 and 2.0-21 dated 2016-12-01
DESCRIPTION | 28 ++- MD5 | 59 +++++--- NAMESPACE | 2 R/CV.SuperLearner.R | 61 ++++++-- R/SL.bartMachine.R |only R/SL.cforest.R | 43 ++++- R/SL.gbm.R | 6 R/SL.randomForest.R | 19 +- R/SL.rpart.R | 2 R/SL.xgboost.R |only R/SuperLearner.R | 267 ++++++++++++++++++++++--------------- R/create.Learner.R |only R/mcSuperLearner.R | 268 ++++++++++++++++++++++--------------- R/method.R | 199 +++++++++++++++++++++------ R/screen.randomForest.R | 6 R/snowSuperLearner.R | 281 +++++++++++++++++++++++---------------- R/summary.CV.SuperLearner.R | 26 ++- build/vignette.rds |binary inst/NEWS | 17 ++ inst/doc/SuperLearnerPresent.pdf |binary man/CV.SuperLearner.Rd | 44 ++++-- man/SL.bartMachine.Rd |only man/SL.cforest.Rd |only man/SL.xgboost.Rd |only man/SuperLearner.Rd | 38 +++-- man/create.Learner.Rd |only man/create.SL.xgboost.Rd |only man/predict.SL.bartMachine.Rd |only man/predict.SL.xgboost.Rd |only man/write.SL.template.Rd | 4 man/write.method.template.Rd | 15 +- tests |only 32 files changed, 914 insertions(+), 471 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Multivariate mixed model solver for multiple random effects allowing the specification of variance covariance structures. ML/REML estimates are obtained using the Average Information (AI), Expectation-Maximization (EM), Newton-Raphson (NR), or Efficient Mixed Model Association (EMMA) algorithms. Designed for genomic prediction and genome wide association studies (GWAS) to include additive, dominance and epistatic relationship structures or other covariance structures in R, but also functional as a regular mixed model program. Multivariate models (multiple responses) can be fitted currently with NR, AI and EMMA algorithms allowing multiple random effects as well. Covariance structures for the residual component is currently supported only for balanced univariate Newton Raphson models.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 2.3 dated 2016-11-01 and 2.4 dated 2016-12-01
CHANGELOG | 11 ++++++ DESCRIPTION | 10 ++--- MD5 | 48 ++++++++++++++------------- R/MAI.R | 53 ++++++++++++++++++++++++----- R/MAI2.R | 62 +++++++++++++++++++++++++++++----- R/MMERM.R | 14 +++++-- R/MNR.R | 87 ++++++++++++++++++++++++++++++++++++++++--------- R/mmer.R | 22 ++++++++---- R/mmer2.R | 10 ++--- R/nna.R | 2 - data/datalist | 3 + data/gryphondata.RData |only inst/doc/sommer.R | 2 - inst/doc/sommer.Rmd | 2 - man/FDdata.Rd | 2 - man/MAI.Rd | 8 +++- man/MAI2.Rd | 3 + man/MMERM.Rd | 3 + man/MNR.Rd | 3 + man/atcg1234.Rd | 4 +- man/gryphondata.Rd |only man/mmer.Rd | 3 + man/mmer2.Rd | 7 ++- man/sommer-package.Rd | 2 - vignettes/sommer.Rmd | 2 - vignettes/sommer.html | 24 +++++++------ 26 files changed, 281 insertions(+), 106 deletions(-)
Title: Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), Mahalanobis distance are some of the many fast functions.
Author: Manos Papadakis, Michail Tsagris, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis and John Burkardt
Maintainer: Manos Papadakis <papadakm95@gmail.com>
Diff between Rfast versions 1.5 dated 2016-10-10 and 1.7 dated 2016-12-01
Rfast-1.5/Rfast/R/lower_triangle.R |only Rfast-1.5/Rfast/R/transpose.R |only Rfast-1.5/Rfast/R/upper_triangle.R |only Rfast-1.5/Rfast/man/lower_tri.Rd |only Rfast-1.5/Rfast/man/transpose.Rd |only Rfast-1.5/Rfast/src/colrange.cpp |only Rfast-1.5/Rfast/src/dg_mat.cpp |only Rfast-1.5/Rfast/src/dg_vec.cpp |only Rfast-1.5/Rfast/src/l_mat.cpp |only Rfast-1.5/Rfast/src/l_vec.cpp |only Rfast-1.5/Rfast/src/lower_triangle.cpp |only Rfast-1.5/Rfast/src/tr_mat.cpp |only Rfast-1.5/Rfast/src/tr_vec.cpp |only Rfast-1.5/Rfast/src/transpose.cpp |only Rfast-1.5/Rfast/src/upper_triangle.cpp |only Rfast-1.7/Rfast/DESCRIPTION | 8 - Rfast-1.7/Rfast/MD5 | 158 ++++++++++++++++----------------- Rfast-1.7/Rfast/NAMESPACE | 5 - Rfast-1.7/Rfast/R/Digamma.R | 5 - Rfast-1.7/Rfast/R/Lgamma.R | 5 - Rfast-1.7/Rfast/R/Trigamma.R | 5 - Rfast-1.7/Rfast/R/all_equals.R | 2 Rfast-1.7/Rfast/R/allbetas.R | 10 +- Rfast-1.7/Rfast/R/anovas.R |only Rfast-1.7/Rfast/R/beta.mle.R | 47 ++++++++- Rfast-1.7/Rfast/R/colMaxs.R | 6 + Rfast-1.7/Rfast/R/colMins.R | 6 + Rfast-1.7/Rfast/R/col_Mins_Maxs.R |only Rfast-1.7/Rfast/R/colmeans.R | 3 Rfast-1.7/Rfast/R/colrange.R | 12 +- Rfast-1.7/Rfast/R/colsums.R | 3 Rfast-1.7/Rfast/R/comb_n.R | 7 + Rfast-1.7/Rfast/R/cora.R | 8 - Rfast-1.7/Rfast/R/correls.R | 5 - Rfast-1.7/Rfast/R/cova.R | 9 - Rfast-1.7/Rfast/R/design_matrix.R | 4 Rfast-1.7/Rfast/R/ftests.R | 19 +-- Rfast-1.7/Rfast/R/is_element.R | 2 Rfast-1.7/Rfast/R/mahala.R | 2 Rfast-1.7/Rfast/R/min_max.R |only Rfast-1.7/Rfast/R/poisson_only.R | 2 Rfast-1.7/Rfast/R/racg.R | 7 - Rfast-1.7/Rfast/R/rmvlaplace.R | 22 +--- Rfast-1.7/Rfast/R/rmvnorm.R | 25 +---- Rfast-1.7/Rfast/R/rmvt.R | 6 - Rfast-1.7/Rfast/R/rowMaxs.R | 2 Rfast-1.7/Rfast/R/rowMins.R | 2 Rfast-1.7/Rfast/R/rowVars.R | 2 Rfast-1.7/Rfast/R/rowmeans.R | 3 Rfast-1.7/Rfast/R/rowsums.R | 3 Rfast-1.7/Rfast/R/score.glms.R |only Rfast-1.7/Rfast/R/score.multinomregs.R |only Rfast-1.7/Rfast/R/standardise.R | 37 +++---- Rfast-1.7/Rfast/R/ttests.R | 66 +++++++------ Rfast-1.7/Rfast/R/univglms.R | 77 +++++----------- Rfast-1.7/Rfast/R/zip.mle.R | 13 +- Rfast-1.7/Rfast/R/ztp.mle.R |only Rfast-1.7/Rfast/man/Lgamma.Rd | 8 + Rfast-1.7/Rfast/man/Rfast-package.Rd | 9 + Rfast-1.7/Rfast/man/allbetas.Rd | 7 + Rfast-1.7/Rfast/man/beta.mle.Rd | 26 +++-- Rfast-1.7/Rfast/man/colMins.Rd | 8 + Rfast-1.7/Rfast/man/colVars.Rd | 1 Rfast-1.7/Rfast/man/comb_n.Rd | 5 - Rfast-1.7/Rfast/man/correls.Rd | 8 + Rfast-1.7/Rfast/man/design_matrix.Rd | 20 ++-- Rfast-1.7/Rfast/man/ftests.Rd | 30 +++--- Rfast-1.7/Rfast/man/min_max.Rd |only Rfast-1.7/Rfast/man/rmvlaplace.Rd | 20 ++-- Rfast-1.7/Rfast/man/score.glms.Rd |only Rfast-1.7/Rfast/man/standardise.Rd | 1 Rfast-1.7/Rfast/man/ttests.Rd | 39 +++++--- Rfast-1.7/Rfast/man/univglms.Rd | 2 Rfast-1.7/Rfast/man/zip.mle.Rd | 41 +++++--- Rfast-1.7/Rfast/src/Digamma.cpp |only Rfast-1.7/Rfast/src/Lgamma.cpp |only Rfast-1.7/Rfast/src/Match.cpp | 1 Rfast-1.7/Rfast/src/Trigamma.cpp |only Rfast-1.7/Rfast/src/col_min_max.cpp |only Rfast-1.7/Rfast/src/colmaxs.cpp | 58 ++++++++---- Rfast-1.7/Rfast/src/colmins.cpp | 57 ++++++++--- Rfast-1.7/Rfast/src/design_matrix.cpp | 13 +- Rfast-1.7/Rfast/src/diri_nr_type2.cpp | 1 Rfast-1.7/Rfast/src/hash_find.cpp | 2 Rfast-1.7/Rfast/src/logistic_only.cpp | 41 ++++---- Rfast-1.7/Rfast/src/med.cpp | 10 +- Rfast-1.7/Rfast/src/min_max.cpp |only Rfast-1.7/Rfast/src/mn.cpp | 102 +++++++++++++++++++-- Rfast-1.7/Rfast/src/mn.h | 16 ++- Rfast-1.7/Rfast/src/poisson_only.cpp | 29 +++--- Rfast-1.7/Rfast/src/regression.cpp | 41 ++++---- Rfast-1.7/Rfast/src/rowMaxs.cpp | 6 - Rfast-1.7/Rfast/src/rowMins.cpp | 6 - Rfast-1.7/Rfast/src/which_isFactor.cpp | 10 +- 94 files changed, 701 insertions(+), 515 deletions(-)
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests.
Author: Selcuk Korkmaz [aut, cre], Dincer Goksuluk [aut], Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 4.0.1 dated 2016-11-30 and 4.0.2 dated 2016-12-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/MVN.Rnw | 2 +- inst/doc/MVN.pdf |binary vignettes/MVN.Rnw | 2 +- 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 0.1-2 dated 2016-11-29 and 0.1-3 dated 2016-12-01
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/NEWS.Rd | 6 ++++++ inst/doc/mlt.pdf |binary tests/timedep_covar.R | 6 ++++-- tests/timedep_covar.Rout.save | 8 +++++--- 6 files changed, 24 insertions(+), 14 deletions(-)
Title: Statistics and Metrics for Seismic Data
Description: Classes and functions for metrics calculation as part of the
'IRIS DMC MUSTANG' project. The functionality in this package
builds upon the base classes of the 'IRISSeismic' package.
Metrics include basic statistics as well as higher level
'health' metrics that can help identify problematic seismometers.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Mary Templeton [aut],
Gillian Sharer [aut, cre]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISMustangMetrics versions 1.0.1 dated 2015-09-16 and 2.0.2 dated 2016-12-01
IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/MultipleValueMetric-class.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/getLatencyValuesXml.Rd |only IRISMustangMetrics-1.0.1/IRISMustangMetrics/man/seismicMetrics-package.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/DESCRIPTION | 28 IRISMustangMetrics-2.0.2/IRISMustangMetrics/MD5 | 97 - IRISMustangMetrics-2.0.2/IRISMustangMetrics/NAMESPACE | 12 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/BSSUtils.R | 397 ++++++- IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/Class-Metric.R | 545 ++++++---- IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/DCOffsetTimesMetric.R | 2 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/ISPAQUtils.R |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/PSDMetric.R | 239 +++- IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/SNRMetric.R | 10 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/STALTAMetric.R | 22 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/basicStatsMetric.R | 21 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/correlationMetric.R | 16 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/crossCorrelationMetric.R | 63 - IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/dailyDCOffsetMetric.R | 72 - IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/gapsMetric.R | 10 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/spikesMetric.R | 46 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/stateOfHealthMetric.R | 32 IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/transferFunctionMetric.R | 95 - IRISMustangMetrics-2.0.2/IRISMustangMetrics/R/upDownTimesMetric.R | 2 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/DCOffsetTimesMetric.Rd | 2 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/GeneralValueMetric-class.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/IRISMustangMetrics-package.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/MultipleTimeValueMetric-class.Rd | 8 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/PSDMetric.Rd | 43 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/SNRMetric.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/STALTAMetric.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/SingleValueMetric-class.Rd | 9 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/SpectrumMetric-class.Rd | 4 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/basicStatsMetric.Rd | 23 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/convertBssErrors.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/correlationMetric.Rd | 8 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/createBssUrl.Rd | 7 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/crossCorrelationMetric.Rd | 40 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/dailyDCOffsetMetric.Rd | 22 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/gapsMetric.Rd | 10 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getBssMetricList.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getGeneralValueMetrics.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getMetricFunctionMetadata.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getMetricsXml.Rd | 4 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getPsdMetrics.Rd | 17 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/getSingleValueMetrics.Rd | 13 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/metricList2DF.Rd |only IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/metricList2DFList.Rd | 35 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/metricList2Xml.Rd | 14 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/saveMetricList.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/spectrumMetric2Xml.Rd | 23 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/spikesMetric.Rd | 28 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/stateOfHealthMetric.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/timesMetric2Xml.Rd | 6 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/transferFunctionMetric.Rd | 24 IRISMustangMetrics-2.0.2/IRISMustangMetrics/man/upDownTimesMetric.Rd | 6 54 files changed, 1411 insertions(+), 680 deletions(-)
More information about IRISMustangMetrics at CRAN
Permanent link
Title: Categorical Scatter (Violin Point) Plots
Description: Provides two methods of plotting categorical scatter plots such
that the arrangement of points within a category reflects the density of
data at that region, and avoids over-plotting.
Author: Erik Clarke [aut, cre],
Scott Sherrill-Mix [aut]
Maintainer: Erik Clarke <erikclarke@gmail.com>
Diff between ggbeeswarm versions 0.5.2 dated 2016-11-30 and 0.5.3 dated 2016-12-01
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/geom-beeswarm.R | 3 +-- R/position-beeswarm.R | 29 +++++++++++++++++++++++++++-- build/partial.rdb |binary inst/doc/usageExamples.R | 16 ++++++++++------ inst/doc/usageExamples.Rnw | 8 +++++--- inst/doc/usageExamples.pdf |binary man/geom_beeswarm.Rd | 9 +++------ man/position_beeswarm.Rd | 2 +- vignettes/usageExamples.Rnw | 8 +++++--- 11 files changed, 66 insertions(+), 37 deletions(-)
Title: DataRobot Predictive Modeling API
Description: For working with the DataRobot predictive modeling platform's <https://app.datarobot.com> API.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut]
Maintainer: David Chudzicki <api-maintainer@datarobot.com>
Diff between datarobot versions 2.3.1 dated 2016-08-31 and 2.4.0 dated 2016-12-01
DESCRIPTION | 8 - MD5 | 128 ++++++++++------ NAMESPACE | 27 +++ NEWS | 28 +++ R/ApplySchema.R |only R/ConnectToDataRobot.R | 42 +++++ R/CreateFeaturelist.R | 2 R/CreatePrimeCode.R |only R/DataRobotRequests.R | 3 R/DownloadPrimeCode.R |only R/Enums.R | 37 ++++ R/FeatureImpact.R | 20 +- R/Features.R | 33 +++- R/GetAllModels.R | 1 R/GetFeaturelist.R | 11 + R/GetModelFromJobId.R | 6 R/GetModelJobs.R | 19 ++ R/GetModelObject.R | 25 +++ R/GetPredictJobs.R | 12 + R/GetPredictions.R | 2 R/GetPrimeEligibility.R |only R/GetProject.R | 24 ++- R/GetProjectList.R | 1 R/GetProjectStatus.R | 9 + R/GetRecommendedBlueprints.R | 11 + R/GetRulesets.R |only R/Jobs.R | 7 R/ListFeaturelists.R | 2 R/PredictionDatasets.R | 20 +- R/PrimeFiles.R |only R/PrimeModels.R |only R/RequestApproximation.R |only R/RequestPrimeModel.R |only R/SetupProject.R | 269 +++++++++++++++++++++++++++++++++- R/StartAutopilot.R | 14 + R/TransferrableModels.R |only R/WaitForJobToComplete.R |only inst/doc/ComparingSubsets.html | 4 inst/doc/IntroductionToDataRobot.Rmd | 2 inst/doc/IntroductionToDataRobot.html | 6 inst/doc/PartialDependence.html | 4 inst/doc/VariableImportance.html | 4 man/AutopilotMode.Rd | 2 man/CreatePrimeCode.Rd |only man/DeleteTransferrableModel.Rd |only man/DownloadPrimeCode.Rd |only man/DownloadTransferrableModel.Rd |only man/GetFeatureImpactForJobId.Rd | 7 man/GetFeatureInfo.Rd | 8 - man/GetModelFromJobId.Rd | 4 man/GetModelJobs.Rd | 2 man/GetModelObject.Rd | 1 man/GetPredictions.Rd | 4 man/GetPrimeEligibility.Rd |only man/GetPrimeFile.Rd |only man/GetPrimeFileFromJobId.Rd |only man/GetPrimeModel.Rd |only man/GetPrimeModelFromJobId.Rd |only man/GetRulesets.Rd |only man/GetTransferrableModel.Rd |only man/JobStatus.Rd | 2 man/JobType.Rd |only man/ListFeatureInfo.Rd | 4 man/ListJobs.Rd | 7 man/ListPrimeFiles.Rd |only man/ListPrimeModels.Rd |only man/ListTransferrableModels.Rd |only man/PostgreSQLdrivers.Rd |only man/PrimeLanguage.Rd |only man/RequestApproximation.Rd |only man/RequestPrimeModel.Rd |only man/RequestTransferrableModel.Rd |only man/SetTarget.Rd | 4 man/SetupProject.Rd | 5 man/SetupProjectFromHDFS.Rd |only man/SetupProjectFromMySQL.Rd |only man/SetupProjectFromOracle.Rd |only man/SetupProjectFromPostgreSQL.Rd |only man/UpdateTransferrableModel.Rd |only man/UploadPredictionDataset.Rd | 7 man/UploadTransferrableModel.Rd |only man/WaitForJobToComplete.Rd |only tests/testthat/test-StartAutopilot.R | 5 vignettes/IntroductionToDataRobot.Rmd | 2 84 files changed, 715 insertions(+), 130 deletions(-)
Title: Plotting D3 Hierarchical Plots in R and Shiny
Description: Plotting hierarchical plots in R such as Sunburst, Treemap, Circle
Treemap, Partition Chart, collapsible indented tree and collapsible tree.
Author: Antoine GUILLOT [cre],
Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org. The partitionChart, sunburst, the treemap, the
zoomable circlePacking, the collapsible indented tree and the
collapsible tree are all derived from his works.),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/htmlwidgets/lib/jquery/jquery-AUTHORS.txt),
HubSpot [cph] (Tether creators and contributors),
Twitter Inc [cph] (Boostrap creators),
Bootstrap contributor [cph] (Bootstrap contributors)
Maintainer: Antoine GUILLOT <antoine.guil@outlook.fr>
Diff between D3partitionR versions 0.2.0 dated 2016-10-16 and 0.3.0 dated 2016-12-01
DESCRIPTION | 27 MD5 | 26 R/AdditionalFunctions.R | 7 R/D3partitionR.R | 11 inst/htmlwidgets/D3partitionR.js | 2919 +++++++++++--------- inst/htmlwidgets/D3partitionR.yaml | 18 inst/htmlwidgets/lib/bootstrap |only inst/htmlwidgets/lib/d3/d3-bootstrap-plugins.min.js |only inst/htmlwidgets/lib/jquery |only inst/htmlwidgets/lib/style/circle.css | 21 inst/htmlwidgets/lib/tether |only man/D3partitionR-shiny.Rd | 2 man/D3partitionR.Rd | 4 13 files changed, 1747 insertions(+), 1288 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the 'cmark' reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format. The latest version of
this package also adds support for Github extensions including tables, autolinks
and strikethrough text.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between commonmark versions 0.9 dated 2016-07-23 and 1.0 dated 2016-12-01
DESCRIPTION | 16 LICENSE | 2 MD5 | 99 NAMESPACE | 2 NEWS | 5 R/extensions.R |only R/markdown.R | 38 man/commonmark.Rd | 25 man/extensions.Rd |only src/Makevars | 8 src/cmark/arena.c |only src/cmark/blocks.c | 290 + src/cmark/buffer.h | 36 src/cmark/chunk.h | 8 src/cmark/cmark.c | 12 src/cmark/cmark.h | 183 + src/cmark/cmark_ctype.h | 7 src/cmark/cmark_extension_api.h |only src/cmark/cmark_version.h | 4 src/cmark/commonmark.c | 17 src/cmark/entities.inc | 2 src/cmark/houdini.h | 18 src/cmark/houdini_html_e.c | 2 src/cmark/houdini_html_u.c | 2 src/cmark/html.c | 163 - src/cmark/html.h |only src/cmark/inlines.c | 387 ++ src/cmark/inlines.h | 12 src/cmark/iterator.c | 52 src/cmark/latex.c | 15 src/cmark/linked_list.c |only src/cmark/main.c | 119 src/cmark/man.c | 26 src/cmark/node.c | 197 + src/cmark/node.h | 23 src/cmark/parser.h | 21 src/cmark/plugin.c |only src/cmark/plugin.h |only src/cmark/references.c | 6 src/cmark/registry.c |only src/cmark/registry.h |only src/cmark/render.c | 3 src/cmark/render.h | 11 src/cmark/scanners.c | 5848 ++++++++++++---------------------------- src/cmark/scanners.h | 7 src/cmark/scanners.re |only src/cmark/syntax_extension.c |only src/cmark/syntax_extension.h |only src/cmark/xml.c | 6 src/extensions |only src/extensions.c |only src/wrapper.c | 25 52 files changed, 3290 insertions(+), 4407 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators
(i.e., sandwich estimators) for ordinary and weighted least squares linear
regression models, including the bias-reduced linearization estimator introduced
by Bell and McCaffrey (2002) <http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf>
and developed further by Pustejovsky and Tipton (2016) <DOI:10.1080/07350015.2016.1247004>.
The package includes functions for estimating the variance-
covariance matrix and for testing single- and multiple-contrast hypotheses
based on Wald test statistics. Tests of single regression coefficients use
Satterthwaite or saddle-point corrections. Tests of multiple-contrast hypotheses
use an approximation to Hotelling's T-squared distribution. Methods are
provided for a variety of fitted models, including lm(), plm() (from package 'plm'),
gls() and lme() (from 'nlme'), robu() (from 'robumeta'), and rma.uni() and rma.mv() (from
'metafor').
Author: James Pustejovsky [aut, cre]
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.2.1 dated 2016-07-23 and 0.2.2 dated 2016-12-01
clubSandwich-0.2.1/clubSandwich/tests/testthat/test_lme.R |only clubSandwich-0.2.2/clubSandwich/DESCRIPTION | 16 clubSandwich-0.2.2/clubSandwich/MD5 | 92 ++--- clubSandwich-0.2.2/clubSandwich/NAMESPACE | 3 clubSandwich-0.2.2/clubSandwich/NEWS | 10 clubSandwich-0.2.2/clubSandwich/R/CR-adjustments.R | 27 - clubSandwich-0.2.2/clubSandwich/R/S3-methods.R | 26 + clubSandwich-0.2.2/clubSandwich/R/Wald_test.R | 92 ++--- clubSandwich-0.2.2/clubSandwich/R/clubSandwich.R | 174 +++------- clubSandwich-0.2.2/clubSandwich/R/coef_test.R | 30 - clubSandwich-0.2.2/clubSandwich/R/data-documentation.R | 20 + clubSandwich-0.2.2/clubSandwich/R/get_arrays.R |only clubSandwich-0.2.2/clubSandwich/R/gls.R | 39 +- clubSandwich-0.2.2/clubSandwich/R/ivreg.R | 17 clubSandwich-0.2.2/clubSandwich/R/lm.R | 18 - clubSandwich-0.2.2/clubSandwich/R/lme.R | 92 ++++- clubSandwich-0.2.2/clubSandwich/R/matrix-functions.R |only clubSandwich-0.2.2/clubSandwich/R/plm.R | 81 +++- clubSandwich-0.2.2/clubSandwich/R/rma-mv.R | 27 + clubSandwich-0.2.2/clubSandwich/R/rma-uni.R | 32 + clubSandwich-0.2.2/clubSandwich/R/robu.R | 26 + clubSandwich-0.2.2/clubSandwich/R/utilities.R | 34 + clubSandwich-0.2.2/clubSandwich/build/vignette.rds |binary clubSandwich-0.2.2/clubSandwich/data/SATcoaching.RData |only clubSandwich-0.2.2/clubSandwich/inst/doc/Robust-Variance-Estimation-with-clubSandwich.Rmd | 2 clubSandwich-0.2.2/clubSandwich/inst/doc/Robust-Variance-Estimation-with-clubSandwich.html | 18 - clubSandwich-0.2.2/clubSandwich/inst/doc/meta-analysis-with-CRVE.html | 66 +-- clubSandwich-0.2.2/clubSandwich/inst/doc/panel-data-CRVE.html | 90 ++--- clubSandwich-0.2.2/clubSandwich/man/SATcoaching.Rd |only clubSandwich-0.2.2/clubSandwich/man/vcovCR.Rd | 28 + clubSandwich-0.2.2/clubSandwich/man/vcovCR.gls.Rd | 12 clubSandwich-0.2.2/clubSandwich/man/vcovCR.ivreg.Rd | 11 clubSandwich-0.2.2/clubSandwich/man/vcovCR.lm.Rd | 12 clubSandwich-0.2.2/clubSandwich/man/vcovCR.lme.Rd | 12 clubSandwich-0.2.2/clubSandwich/man/vcovCR.plm.Rd | 16 clubSandwich-0.2.2/clubSandwich/man/vcovCR.rma.mv.Rd | 12 clubSandwich-0.2.2/clubSandwich/man/vcovCR.rma.uni.Rd | 12 clubSandwich-0.2.2/clubSandwich/man/vcovCR.robu.Rd | 12 clubSandwich-0.2.2/clubSandwich/tests/testthat.R | 2 clubSandwich-0.2.2/clubSandwich/tests/testthat/test_gls.R | 37 +- clubSandwich-0.2.2/clubSandwich/tests/testthat/test_lm.R | 17 clubSandwich-0.2.2/clubSandwich/tests/testthat/test_lme_2level.R |only clubSandwich-0.2.2/clubSandwich/tests/testthat/test_lme_3level.R |only clubSandwich-0.2.2/clubSandwich/tests/testthat/test_plm-first-differences.R |only clubSandwich-0.2.2/clubSandwich/tests/testthat/test_plm-fixed-effects.R | 35 +- clubSandwich-0.2.2/clubSandwich/tests/testthat/test_plm-random-effects.R | 21 - clubSandwich-0.2.2/clubSandwich/tests/testthat/test_plm-unbalanced-fixed-effects.R | 64 +-- clubSandwich-0.2.2/clubSandwich/tests/testthat/test_rma-mv.R | 34 + clubSandwich-0.2.2/clubSandwich/tests/testthat/test_rma-uni.R | 13 clubSandwich-0.2.2/clubSandwich/tests/testthat/test_robu.R | 75 ++-- clubSandwich-0.2.2/clubSandwich/vignettes/Robust-Variance-Estimation-with-clubSandwich.Rmd | 2 51 files changed, 956 insertions(+), 503 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-22 0.2.0
2014-10-10 0.1.1
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph],
Simon Blomberg [aut, cph],
Ben Bolker [aut, cph],
Julien Claude [aut, cph],
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph],
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph],
Olivier Gascuel [aut, cph],
Christoph Heibl [aut, cph],
Anthony Ives [aut, cph],
Bradley Jones [aut, cph],
Daniel Lawson [aut, cph],
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph],
Jim Lemon [aut, cph],
Rosemary McCloskey [aut, cph],
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph],
Korbinian Strimmer [aut, cph],
Damien de Vienne [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 3.5 dated 2016-05-24 and 4.0 dated 2016-12-01
ape-3.5/ape/data/landplants.newick.rda |only ape-3.5/ape/data/opsin.newick.rda |only ape-3.5/ape/man/landplants.Rd |only ape-3.5/ape/man/opsin.Rd |only ape-4.0/ape/DESCRIPTION | 14 - ape-4.0/ape/MD5 | 126 +++++---- ape-4.0/ape/NAMESPACE | 39 ++- ape-4.0/ape/R/CDF.birth.death.R | 6 ape-4.0/ape/R/DNA.R | 202 +++++++++++---- ape-4.0/ape/R/MPR.R | 2 ape-4.0/ape/R/SDM.R | 2 ape-4.0/ape/R/SlowinskiGuyer.R | 27 +- ape-4.0/ape/R/ace.R | 6 ape-4.0/ape/R/as.phylo.R | 2 ape-4.0/ape/R/checkValidPhylo.R | 9 ape-4.0/ape/R/chronoMPL.R | 2 ape-4.0/ape/R/clustal.R | 35 ++ ape-4.0/ape/R/coalescent.intervals.R | 2 ape-4.0/ape/R/dist.topo.R | 124 +++++---- ape-4.0/ape/R/is.binary.tree.R | 37 +- ape-4.0/ape/R/is.ultrametric.R | 45 ++- ape-4.0/ape/R/ltt.plot.R | 6 ape-4.0/ape/R/makeLabel.R | 6 ape-4.0/ape/R/multi2di.R | 54 +++- ape-4.0/ape/R/node.dating.R |only ape-4.0/ape/R/pic.R | 2 ape-4.0/ape/R/plot.phylo.R | 29 +- ape-4.0/ape/R/plot.phyloExtra.R | 32 ++ ape-4.0/ape/R/read.GenBank.R | 80 +++--- ape-4.0/ape/R/read.dna.R | 16 - ape-4.0/ape/R/read.gff.R |only ape-4.0/ape/R/reconstruct.R | 421 ++++++++++++++++++++++++++++----- ape-4.0/ape/R/reorder.phylo.R | 37 ++ ape-4.0/ape/R/root.R | 103 ++++++-- ape-4.0/ape/R/rtt.R | 16 - ape-4.0/ape/R/summary.phylo.R | 116 ++++++--- ape-4.0/ape/R/write.dna.R | 2 ape-4.0/ape/R/yule.R | 2 ape-4.0/ape/build/vignette.rds |binary ape-4.0/ape/data/hivtree.newick.rda |binary ape-4.0/ape/inst/doc/MoranI.pdf |binary ape-4.0/ape/man/AAbin.Rd | 3 ape-4.0/ape/man/all.equal.DNAbin.Rd |only ape-4.0/ape/man/alview.Rd | 2 ape-4.0/ape/man/ape-internal.Rd | 6 ape-4.0/ape/man/ape-package.Rd | 4 ape-4.0/ape/man/boot.phylo.Rd | 9 ape-4.0/ape/man/c.phylo.Rd | 23 + ape-4.0/ape/man/checkAlignment.Rd | 2 ape-4.0/ape/man/clustal.Rd | 31 +- ape-4.0/ape/man/dist.topo.Rd | 21 + ape-4.0/ape/man/image.DNAbin.Rd | 5 ape-4.0/ape/man/is.binary.tree.Rd | 40 +-- ape-4.0/ape/man/is.ultrametric.Rd | 39 +-- ape-4.0/ape/man/mixedFontLabel.Rd | 2 ape-4.0/ape/man/multi2di.Rd | 25 + ape-4.0/ape/man/node.dating.Rd |only ape-4.0/ape/man/plot.phyloExtra.Rd | 2 ape-4.0/ape/man/plotTreeTime.Rd |only ape-4.0/ape/man/read.GenBank.Rd | 62 ++-- ape-4.0/ape/man/read.dna.Rd | 4 ape-4.0/ape/man/read.gff.Rd |only ape-4.0/ape/man/reconstruct.Rd | 85 ++++-- ape-4.0/ape/man/reorder.phylo.Rd | 8 ape-4.0/ape/man/root.Rd | 64 +++-- ape-4.0/ape/man/summary.phylo.Rd | 20 + ape-4.0/ape/src/ape.c | 8 ape-4.0/ape/src/dist_dna.c | 122 ++++++--- ape-4.0/ape/src/read_dna.c | 26 +- 69 files changed, 1559 insertions(+), 656 deletions(-)
Title: Sparse Lightweight Arrays and Matrices
Description: Data structures and algorithms for sparse arrays and matrices,
based on index arrays and simple triplet representations, respectively.
Author: Kurt Hornik [aut, cre],
David Meyer [aut],
Christian Buchta [aut]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between slam versions 0.1-39 dated 2016-11-18 and 0.1-40 dated 2016-12-01
DESCRIPTION | 6 +++--- MD5 | 8 +++++--- NAMESPACE | 1 + R/matrix.R | 39 ++++++++++++++++++++++++++++++++++++++- tests/split.R |only tests/split.Rout.save |only 6 files changed, 47 insertions(+), 7 deletions(-)
Title: Interface to Diverse Estimation Methods of Causal Networks
Description: Unified interface for the estimation of causal networks, including
the methods 'backShift' (from package 'backShift'), 'bivariateANM' (bivariate
additive noise model), 'bivariateCAM' (bivariate causal additive model),
'CAM' (causal additive model) (from package 'CAM'), 'hiddenICP' (invariant
causal prediction with hidden variables), 'ICP' (invariant causal prediction)
(from package 'InvariantCausalPrediction'), 'GES' (greedy equivalence
search), 'GIES' (greedy interventional equivalence search), 'LINGAM', 'PC' (PC
Algorithm), 'RFCI' (really fast causal inference) (all from package 'pcalg') and
regression.
Author: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>,
Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Maintainer: Christina Heinze-Deml <heinzedeml@stat.math.ethz.ch>
Diff between CompareCausalNetworks versions 0.1.4 dated 2015-10-07 and 0.1.5 dated 2016-12-01
DESCRIPTION | 36 +++++++++++++++++------------------- MD5 | 6 +++--- NAMESPACE | 7 ++++--- R/runLINGAM.R | 8 +++++--- 4 files changed, 29 insertions(+), 28 deletions(-)
More information about CompareCausalNetworks at CRAN
Permanent link
Title: Genome Interval Arithmetic in R
Description: Read and manipulate genome intervals and signals. Provides
functionality similar to command-line tool suites within R,
enabling interactive analysis and visualization of genome-scale data.
Author: Jay Hesselberth [aut, cre],
Kent Riemondy [aut],
Ryan Sheridan [ctb]
Maintainer: Jay Hesselberth <jay.hesselberth@gmail.com>
Diff between valr versions 0.1.0 dated 2016-11-21 and 0.1.1 dated 2016-12-01
DESCRIPTION | 6 MD5 | 103 +++++------ NEWS.md | 10 + R/bed12_to_exons.r | 9 - R/bed_absdist.r | 31 +-- R/bed_cluster.r | 18 +- R/bed_complement.r | 6 R/bed_fisher.r | 13 + R/bed_glyph.r | 12 - R/bed_intersect.r | 48 +++-- R/bed_jaccard.r | 2 R/bed_map.r | 14 - R/bed_merge.r | 13 - R/bed_projection.r | 31 +-- R/bed_reldist.r | 17 + R/db.r | 19 +- R/read_bed.r | 5 R/read_genome.r | 18 +- R/spacing.r | 3 README.md |only build/vignette.rds |binary inst/doc/interval-stats.R | 131 +++++++------- inst/doc/interval-stats.Rmd | 166 ++++++++++-------- inst/doc/interval-stats.html | 384 ++++++++++++++++++++++--------------------- inst/doc/valr.R | 8 inst/doc/valr.Rmd | 14 + inst/doc/valr.html | 43 ++-- man/bed12_to_exons.Rd | 9 - man/bed_absdist.Rd | 30 +-- man/bed_closest.Rd | 10 - man/bed_cluster.Rd | 18 +- man/bed_complement.Rd | 1 man/bed_coverage.Rd | 10 - man/bed_fisher.Rd | 8 man/bed_glyph.Rd | 6 man/bed_intersect.Rd | 44 ++-- man/bed_jaccard.Rd | 5 man/bed_map.Rd | 22 +- man/bed_merge.Rd | 15 - man/bed_projection.Rd | 25 +- man/bed_reldist.Rd | 23 ++ man/bed_subtract.Rd | 10 - man/bed_window.Rd | 10 - man/bound_intervals.Rd | 7 man/db.Rd | 19 +- man/read_bed.Rd | 5 man/read_genome.Rd | 5 src/absdist.cpp | 11 + tests/testthat/test-db.r | 6 tests/testthat/test-style.r | 2 tests/testthat/test_glyph.r | 5 vignettes/interval-stats.Rmd | 166 ++++++++++-------- vignettes/valr.Rmd | 14 + 53 files changed, 909 insertions(+), 701 deletions(-)
Title: Robust Linear Mixed Effects Models
Description: A method to fit linear mixed effects models robustly.
Robustness is achieved by modification of the scoring equations
combined with the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller <koller.manuel@gmail.com>
Diff between robustlmm versions 1.8 dated 2016-01-03 and 2.1 dated 2016-12-01
robustlmm-1.8/robustlmm/man/psiFuncCached.Rd |only robustlmm-1.8/robustlmm/man/psi_func_cached-class.Rd |only robustlmm-1.8/robustlmm/vignettes/efficiency-table.tex |only robustlmm-1.8/robustlmm/vignettes/figs |only robustlmm-2.1/robustlmm/DESCRIPTION | 21 robustlmm-2.1/robustlmm/MD5 | 94 robustlmm-2.1/robustlmm/NAMESPACE | 14 robustlmm-2.1/robustlmm/R/AllClass.R | 37 robustlmm-2.1/robustlmm/R/DAS-scale.R | 42 robustlmm-2.1/robustlmm/R/fromLme4.R | 5 robustlmm-2.1/robustlmm/R/helpers.R | 10 robustlmm-2.1/robustlmm/R/lmer.R | 6 robustlmm-2.1/robustlmm/R/psiFunc2.R | 410 -- robustlmm-2.1/robustlmm/R/rlmer.R | 8 robustlmm-2.1/robustlmm/README.md | 8 robustlmm-2.1/robustlmm/build/vignette.rds |binary robustlmm-2.1/robustlmm/inst/CITATION |only robustlmm-2.1/robustlmm/inst/doc/rlmer.R | 478 -- robustlmm-2.1/robustlmm/inst/doc/rlmer.Rnw | 1633 ++++------ robustlmm-2.1/robustlmm/inst/doc/rlmer.pdf |binary robustlmm-2.1/robustlmm/inst/include |only robustlmm-2.1/robustlmm/man/chgDefaults.Rd | 23 robustlmm-2.1/robustlmm/man/other.Rd |only robustlmm-2.1/robustlmm/man/plot-methods.Rd |only robustlmm-2.1/robustlmm/man/psi-functions.Rd | 21 robustlmm-2.1/robustlmm/man/psi2propII.Rd | 19 robustlmm-2.1/robustlmm/man/rlmer.Rd | 3 robustlmm-2.1/robustlmm/man/robustlmm-package.Rd | 12 robustlmm-2.1/robustlmm/src |only robustlmm-2.1/robustlmm/tests/DAS-scale.R | 16 robustlmm-2.1/robustlmm/tests/PsiFunction.R |only robustlmm-2.1/robustlmm/tests/compare-methods.Rout.save | 16 robustlmm-2.1/robustlmm/tests/expectations.R | 6 robustlmm-2.1/robustlmm/tests/getME.R | 11 robustlmm-2.1/robustlmm/tests/getME.Rout.save | 169 - robustlmm-2.1/robustlmm/tests/psi-rho-funs.R | 39 robustlmm-2.1/robustlmm/tests/tau.R | 24 robustlmm-2.1/robustlmm/tests/testMatrices.R | 6 robustlmm-2.1/robustlmm/vignettes/Figures |only robustlmm-2.1/robustlmm/vignettes/efficiency-table-B-optimal.tex | 2 robustlmm-2.1/robustlmm/vignettes/efficiency-table-lqq-locationScale.tex | 10 robustlmm-2.1/robustlmm/vignettes/efficiency-table-lqq.tex | 8 robustlmm-2.1/robustlmm/vignettes/jss.dtx |only robustlmm-2.1/robustlmm/vignettes/jsslogo.pdf |only robustlmm-2.1/robustlmm/vignettes/rlmer.Rnw | 1633 ++++------ robustlmm-2.1/robustlmm/vignettes/rlmer.bib | 678 +--- robustlmm-2.1/robustlmm/vignettes/rlmer.sty |only robustlmm-2.1/robustlmm/vignettes/tuning-constants-table.tex | 2 48 files changed, 2262 insertions(+), 3202 deletions(-)
Title: Inference in Graphical Gaussian Models with Edge and Vertex
Symmetries
Description: Estimation, model selection and other aspects of
statistical inference in Graphical Gaussian models with edge
and vertex symmetries (Graphical Gaussian models with colours).
Author: Søren Højsgaard <sorenh@math.aau.dk>, Steffen L. Lauritzen
<steffen@stats.ox.ac.uk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between gRc versions 0.4-1 dated 2012-11-25 and 0.4-2 dated 2016-12-01
gRc-0.4-1/gRc/gRc-Ex.R |only gRc-0.4-2/gRc/DESCRIPTION | 12 ++++---- gRc-0.4-2/gRc/MD5 | 17 +++++------- gRc-0.4-2/gRc/NAMESPACE | 31 +++++++++++++++++---- gRc-0.4-2/gRc/R/RCON-IPM5.R | 17 ++++++------ gRc-0.4-2/gRc/R/display4.R | 34 ++++++++++++------------ gRc-0.4-2/gRc/R/rcor-IPM4.R | 55 +++++++++++++++++++-------------------- gRc-0.4-2/gRc/man/fitInternal.Rd | 3 +- gRc-0.4-2/gRc/man/stepwise.Rd | 6 ++-- gRc-0.4-2/gRc/src/rconipm2.c | 11 ++++--- 10 files changed, 105 insertions(+), 81 deletions(-)
Title: Time Series Clustering Along with Optimizations for the Dynamic
Time Warping Distance
Description: Time series clustering along with optimized techniques related
to the Dynamic Time Warping distance and its corresponding lower bounds.
Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole
clustering are available. Functionality can be easily extended with
custom distance measures and centroid definitions.
Author: Alexis Sarda-Espinosa
Maintainer: Alexis Sarda <alexis.sarda@gmail.com>
Diff between dtwclust versions 2.3.0 dated 2016-10-03 and 3.0.0 dated 2016-12-01
dtwclust-2.3.0/dtwclust/README.md |only dtwclust-2.3.0/dtwclust/src/update-lcm.c |only dtwclust-2.3.0/dtwclust/tests/testthat/helper_all.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_all_distances.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_centroids.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_custom_distance.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_cvis.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_dtw_basic.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_fuzzy.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_hierarchical.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_lbs.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_methods.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_partitional.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_types.R |only dtwclust-2.3.0/dtwclust/tests/testthat/test_zparallel.R |only dtwclust-2.3.0/dtwclust/vignettes/dtwclust-concordance.tex |only dtwclust-3.0.0/dtwclust/DESCRIPTION | 18 dtwclust-3.0.0/dtwclust/MD5 | 171 dtwclust-3.0.0/dtwclust/NAMESPACE | 27 dtwclust-3.0.0/dtwclust/R/DBA.R | 324 - dtwclust-3.0.0/dtwclust/R/GAK.R |only dtwclust-3.0.0/dtwclust/R/NCCc.R | 35 dtwclust-3.0.0/dtwclust/R/SBD.R | 442 +- dtwclust-3.0.0/dtwclust/R/TADPole.R | 551 +-- dtwclust-3.0.0/dtwclust/R/all-cent.R | 497 +- dtwclust-3.0.0/dtwclust/R/create-dtwclust.R |only dtwclust-3.0.0/dtwclust/R/cvi.R | 250 - dtwclust-3.0.0/dtwclust/R/ddist.R | 298 - dtwclust-3.0.0/dtwclust/R/dtw-basic.R | 438 +- dtwclust-3.0.0/dtwclust/R/dtw-lb.R | 267 - dtwclust-3.0.0/dtwclust/R/dtw2.R | 76 dtwclust-3.0.0/dtwclust/R/dtwclust-classes.R | 212 - dtwclust-3.0.0/dtwclust/R/dtwclust-methods.R | 1385 ++++--- dtwclust-3.0.0/dtwclust/R/dtwclust.R | 1770 +++++----- dtwclust-3.0.0/dtwclust/R/fuzzy.R | 42 dtwclust-3.0.0/dtwclust/R/lb-improved.R | 528 +- dtwclust-3.0.0/dtwclust/R/lb-keogh.R | 510 +- dtwclust-3.0.0/dtwclust/R/partitional.R | 254 - dtwclust-3.0.0/dtwclust/R/pkg.R | 178 - dtwclust-3.0.0/dtwclust/R/reinterpolate.R | 67 dtwclust-3.0.0/dtwclust/R/shape-extraction.R | 170 dtwclust-3.0.0/dtwclust/R/uciCT.R | 26 dtwclust-3.0.0/dtwclust/R/utils.R | 545 +-- dtwclust-3.0.0/dtwclust/R/zscore.R | 115 dtwclust-3.0.0/dtwclust/build/vignette.rds |binary dtwclust-3.0.0/dtwclust/data/uciCT.rda |binary dtwclust-3.0.0/dtwclust/inst/NEWS.Rd | 27 dtwclust-3.0.0/dtwclust/inst/doc/dtwclust.Rnw | 491 ++ dtwclust-3.0.0/dtwclust/inst/doc/dtwclust.pdf |binary dtwclust-3.0.0/dtwclust/inst/dtwclust-examples.R | 186 - dtwclust-3.0.0/dtwclust/man/DBA.Rd | 75 dtwclust-3.0.0/dtwclust/man/GAK.Rd |only dtwclust-3.0.0/dtwclust/man/NCCc.Rd | 7 dtwclust-3.0.0/dtwclust/man/SBD.Rd | 35 dtwclust-3.0.0/dtwclust/man/TADPole.Rd | 59 dtwclust-3.0.0/dtwclust/man/as.matrix.Rd |only dtwclust-3.0.0/dtwclust/man/clusterSim.Rd | 5 dtwclust-3.0.0/dtwclust/man/create_dtwclust.Rd |only dtwclust-3.0.0/dtwclust/man/cvi.Rd | 140 dtwclust-3.0.0/dtwclust/man/dtw2.Rd | 36 dtwclust-3.0.0/dtwclust/man/dtw_basic.Rd | 42 dtwclust-3.0.0/dtwclust/man/dtw_lb.Rd | 37 dtwclust-3.0.0/dtwclust/man/dtwclust-class.Rd | 27 dtwclust-3.0.0/dtwclust/man/dtwclust-methods.Rd | 105 dtwclust-3.0.0/dtwclust/man/dtwclust-package.Rd | 20 dtwclust-3.0.0/dtwclust/man/dtwclust.Rd | 723 ++-- dtwclust-3.0.0/dtwclust/man/dtwclustControl-class.Rd | 94 dtwclust-3.0.0/dtwclust/man/dtwclustFamily-class.Rd | 26 dtwclust-3.0.0/dtwclust/man/lb_improved.Rd | 40 dtwclust-3.0.0/dtwclust/man/lb_keogh.Rd | 43 dtwclust-3.0.0/dtwclust/man/randIndex.Rd | 3 dtwclust-3.0.0/dtwclust/man/reinterpolate.Rd | 30 dtwclust-3.0.0/dtwclust/man/shape_extraction.Rd | 40 dtwclust-3.0.0/dtwclust/man/uciCT.Rd | 14 dtwclust-3.0.0/dtwclust/man/zscore.Rd | 16 dtwclust-3.0.0/dtwclust/src/dtw-basic.c | 358 +- dtwclust-3.0.0/dtwclust/src/envelop.cpp | 112 dtwclust-3.0.0/dtwclust/src/logGAK.c |only dtwclust-3.0.0/dtwclust/src/pairs.c | 77 dtwclust-3.0.0/dtwclust/tests/testthat.R | 6 dtwclust-3.0.0/dtwclust/tests/testthat/acceptance |only dtwclust-3.0.0/dtwclust/tests/testthat/helper-all.R |only dtwclust-3.0.0/dtwclust/tests/testthat/integration |only dtwclust-3.0.0/dtwclust/tests/testthat/regression |only dtwclust-3.0.0/dtwclust/tests/testthat/system |only dtwclust-3.0.0/dtwclust/tests/testthat/test-01-unit.R |only dtwclust-3.0.0/dtwclust/tests/testthat/test-02-integration.R |only dtwclust-3.0.0/dtwclust/tests/testthat/test-03-acceptance.R |only dtwclust-3.0.0/dtwclust/tests/testthat/test-04-system.R |only dtwclust-3.0.0/dtwclust/tests/testthat/test-05-regression.R |only dtwclust-3.0.0/dtwclust/tests/testthat/test-06-parallel.R |only dtwclust-3.0.0/dtwclust/tests/testthat/unit |only dtwclust-3.0.0/dtwclust/vignettes/REFERENCES.bib | 84 dtwclust-3.0.0/dtwclust/vignettes/dtwclust.Rnw | 491 ++ 94 files changed, 6835 insertions(+), 5810 deletions(-)
Title: Some Tools for Imaging
Description: Tools for 3D imaging, mostly for biology/microscopy.
Read and write TIFF stacks. Functions for segmentation, filtering and analysing 3D point patterns.
Author: Volker Schmid [aut, cre], Priyanka Kukreja [ctb], Fabian Scheipl [ctb]
Maintainer: Volker Schmid <stats@volkerschmid.de>
Diff between bioimagetools versions 0.3.1 dated 2016-10-17 and 1.0.0 dated 2016-12-01
bioimagetools-0.3.1/bioimagetools/INSTALL |only bioimagetools-0.3.1/bioimagetools/R/colorsinclasses.R |only bioimagetools-0.3.1/bioimagetools/R/computedistances.R |only bioimagetools-0.3.1/bioimagetools/R/diameter.R |only bioimagetools-0.3.1/bioimagetools/R/findedges.R |only bioimagetools-0.3.1/bioimagetools/R/findmaxline.R |only bioimagetools-0.3.1/bioimagetools/R/isline.R |only bioimagetools-0.3.1/bioimagetools/R/preprocess.R |only bioimagetools-0.3.1/bioimagetools/inst/doc/reference.pdf |only bioimagetools-0.3.1/bioimagetools/inst/extdata/test.tif |only bioimagetools-0.3.1/bioimagetools/man/colors.in.classes.Rd |only bioimagetools-0.3.1/bioimagetools/man/preprocess.Rd |only bioimagetools-0.3.1/bioimagetools/man/segmentoutside.Rd |only bioimagetools-1.0.0/bioimagetools/DESCRIPTION | 27 +- bioimagetools-1.0.0/bioimagetools/MD5 | 102 +++++----- bioimagetools-1.0.0/bioimagetools/NAMESPACE | 11 - bioimagetools-1.0.0/bioimagetools/NEWS |only bioimagetools-1.0.0/bioimagetools/R/Kcross3D.R |only bioimagetools-1.0.0/bioimagetools/R/L3cross3d.R |only bioimagetools-1.0.0/bioimagetools/R/bwlabel3d.R | 1 bioimagetools-1.0.0/bioimagetools/R/cNNTest.R | 1 bioimagetools-1.0.0/bioimagetools/R/cmoments3d.R | 4 bioimagetools-1.0.0/bioimagetools/R/crossNN.R | 1 bioimagetools-1.0.0/bioimagetools/R/distance2border.R | 6 bioimagetools-1.0.0/bioimagetools/R/folder_choose.R |only bioimagetools-1.0.0/bioimagetools/R/image.R | 96 ++++++++- bioimagetools-1.0.0/bioimagetools/R/nearestclassdistances.R |only bioimagetools-1.0.0/bioimagetools/R/nearestneighbourdistribution.R |only bioimagetools-1.0.0/bioimagetools/R/onattach.R | 2 bioimagetools-1.0.0/bioimagetools/R/plot_nearest_class_distances.R |only bioimagetools-1.0.0/bioimagetools/R/readClassTIF.R | 2 bioimagetools-1.0.0/bioimagetools/R/readbmp.R | 3 bioimagetools-1.0.0/bioimagetools/R/readtif.R | 16 + bioimagetools-1.0.0/bioimagetools/R/segment.R | 29 +- bioimagetools-1.0.0/bioimagetools/R/segmentoutside.R | 11 + bioimagetools-1.0.0/bioimagetools/R/spots.R |only bioimagetools-1.0.0/bioimagetools/R/status.R | 5 bioimagetools-1.0.0/bioimagetools/R/tablen.R | 13 - bioimagetools-1.0.0/bioimagetools/R/testColoc.R | 1 bioimagetools-1.0.0/bioimagetools/R/writetif.R | 2 bioimagetools-1.0.0/bioimagetools/README.md |only bioimagetools-1.0.0/bioimagetools/build |only bioimagetools-1.0.0/bioimagetools/inst/doc/bioimagetools.R |only bioimagetools-1.0.0/bioimagetools/inst/doc/bioimagetools.Rmd |only bioimagetools-1.0.0/bioimagetools/inst/doc/bioimagetools.html |only bioimagetools-1.0.0/bioimagetools/inst/extdata/V.bmp |only bioimagetools-1.0.0/bioimagetools/inst/extdata/amask.tif |binary bioimagetools-1.0.0/bioimagetools/inst/extdata/cell.csv |only bioimagetools-1.0.0/bioimagetools/inst/extdata/kringel.tif |binary bioimagetools-1.0.0/bioimagetools/man/K.cross.3D.Rd |only bioimagetools-1.0.0/bioimagetools/man/L.cross.3D.Rd |only bioimagetools-1.0.0/bioimagetools/man/bwlabel3d.Rd | 3 bioimagetools-1.0.0/bioimagetools/man/cmoments3d.Rd | 3 bioimagetools-1.0.0/bioimagetools/man/cnnTest.Rd | 3 bioimagetools-1.0.0/bioimagetools/man/crossNN.Rd | 3 bioimagetools-1.0.0/bioimagetools/man/distance2border.Rd | 6 bioimagetools-1.0.0/bioimagetools/man/folder.choose.Rd |only bioimagetools-1.0.0/bioimagetools/man/img.Rd | 16 + bioimagetools-1.0.0/bioimagetools/man/nearest.neighbour.distribution.Rd |only bioimagetools-1.0.0/bioimagetools/man/nearestClassDistance.Rd |only bioimagetools-1.0.0/bioimagetools/man/nearestClassDistances.Rd |only bioimagetools-1.0.0/bioimagetools/man/plotNearestClassDistances.Rd |only bioimagetools-1.0.0/bioimagetools/man/readTIF.Rd | 4 bioimagetools-1.0.0/bioimagetools/man/segment.Rd | 17 + bioimagetools-1.0.0/bioimagetools/man/segment.outside.Rd |only bioimagetools-1.0.0/bioimagetools/man/spots.Rd |only bioimagetools-1.0.0/bioimagetools/man/table.n.Rd | 8 bioimagetools-1.0.0/bioimagetools/man/testColoc.Rd | 3 bioimagetools-1.0.0/bioimagetools/src/getid.c |only bioimagetools-1.0.0/bioimagetools/src/nearestClassDistances.c |only bioimagetools-1.0.0/bioimagetools/src/segment.c | 16 - bioimagetools-1.0.0/bioimagetools/vignettes |only 72 files changed, 288 insertions(+), 127 deletions(-)
Title: Estimation of Transition Probabilities for the Illness-Death
Model
Description: Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <DOI:10.1111/biom.12288> are included.
Author: Vanesa Balboa-Barreiro, Jacobo de Una-Alvarez <jacobo@uvigo.es>
and Luis Meira-Machado <lmachado@math.uminho.pt>
Maintainer: Vanesa Balboa-Barreiro <vanesa.balboa@uvigo.es>
Diff between TP.idm versions 1.0 dated 2015-09-25 and 1.2 dated 2016-12-01
DESCRIPTION | 13 - MD5 | 44 ++- NAMESPACE | 4 R/TPidm.R | 549 +++++++++++++++++++++++++++++++++++-------------- R/ci.AJ.R | 192 ++++++++--------- R/ci.NM.R | 110 ++++----- R/fun.AJ.R | 176 +++++++-------- R/fun.NM.R | 418 ++++++++++++++++++------------------- R/plot.TPidm.R | 320 ++++++++++++++++++++-------- R/prep.data.AJ.R | 320 ++++++++++++++-------------- R/prep.data.event.AJ.R | 46 ++-- R/print.TPidm.R | 146 ++++++++----- R/summary.TPidm.R | 168 +++++++++----- R/test.nm.R |only R/var.AJ.R | 146 ++++++------- R/var.NM.R | 477 ++++++++++++++++++++++++------------------ build/partial.rdb |binary man/TP.idm-package.Rd | 9 man/TPidm.Rd | 39 ++- man/colonTP.Rd | 2 man/plot.TPidm.Rd | 23 +- man/print.TPidm.Rd | 2 man/summary.TPidm.Rd | 11 man/test.nm.Rd |only 24 files changed, 1901 insertions(+), 1314 deletions(-)
Title: Forecasting Using Smoothing Functions
Description: The set of smoothing functions used for time series analysis and in forecasting.
Currently the package includes exponential smoothing models and SARIMA in state-space
form + several simulation functions.
Author: Ivan Svetunkov [aut, cre] (Research Associate at Lancaster Centre for
Forecasting, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 1.5.0 dated 2016-11-15 and 1.5.1 dated 2016-12-01
DESCRIPTION | 8 - MD5 | 50 +++++------ NEWS | 16 +++ R/ces.R | 7 - R/es.R | 14 --- R/ges.R | 7 - R/graphmaker.R | 11 +- R/iss.R | 12 +- R/methods.R | 4 R/simces.R | 23 ++++- R/simes.R | 27 +++++- R/simssarima.R | 32 ++++++- R/sma.R | 12 +- R/ssarima.R | 7 - R/ssfunctions.R | 208 ++++++++++++++++++++++++++++--------------------- README.md | 1 inst/doc/ces.html | 42 ++++----- inst/doc/es.html | 63 +++++++------- inst/doc/ges.html | 34 ++++---- inst/doc/simulate.html | 92 +++++++++++---------- inst/doc/sma.html | 26 +++--- inst/doc/smooth.html | 4 inst/doc/ssarima.html | 42 ++++----- man/simces.Rd | 2 man/simes.Rd | 30 ++++--- man/simssarima.Rd | 2 26 files changed, 445 insertions(+), 331 deletions(-)
Title: A Flexible and Robust Sys.sleep() Replacement
Description: Provides a near drop-in replacement for base::Sys.sleep() that allows more types of input
to produce delays in the execution of code and can silence/prevent typical sources of error.
Author: Russell Pierce [aut, cre],
Timothy Gann [aut]
Maintainer: Russell Pierce <russell.s.pierce@gmail.com>
Diff between naptime versions 1.0.0 dated 2016-11-12 and 1.2.0 dated 2016-12-01
ChangeLog |only DESCRIPTION | 12 +-- MD5 | 25 ++++---- NEWS.md | 26 ++++++++ R/naptime-internal.R | 12 +++ R/naptime.R | 115 ++++++++++++++++++++++--------------- README.md | 123 +++++++++++++++++++++++---------------- build/vignette.rds |binary inst/doc/naptime.R | 26 ++++++-- inst/doc/naptime.Rmd | 130 ++++++++++++++++++++++++++++++------------ inst/doc/naptime.html | 112 +++++++++++++++++++++++------------- man/naptime.Rd | 38 ++++++++---- tests/testthat/test-naptime.R | 68 +++++++++++++++------ vignettes/naptime.Rmd | 130 ++++++++++++++++++++++++++++++------------ 14 files changed, 552 insertions(+), 265 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package. Suitable for applying unidimensional and multidimensional
computerized adaptive tests (CAT) using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Additionally, optimal test designs (e.g., "shadow testing") are supported
for tests which contain a large number of item selection constraints.
Finally, package contains tools useful for performing Monte Carlo simulations
for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre, cph]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 1.2 dated 2016-11-15 and 1.2.1 dated 2016-12-01
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mirtCAT_preamble.R | 2 +- tests/GUI-tests/GUI-tests.R | 5 ----- 4 files changed, 7 insertions(+), 12 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates. Finally, latent class models such as the DINA,
DINO, multidimensional latent class, and several other discrete latent
variable models are supported.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.20.1 dated 2016-10-05 and 1.21 dated 2016-12-01
DESCRIPTION | 10 +- MD5 | 54 ++++++------ NEWS.md | 33 +++++++ R/02-item_methods.R | 4 R/03-estimation.R | 7 + R/Discrete-methods.R | 3 R/EMstep.group.R | 15 +++ R/EMstep.utils.R | 36 ++++---- R/LoadPars.R | 4 R/MultipleGroup-methods.R | 64 ++++++++++++-- R/PLCI.mirt.R | 168 +++++++++++++++++++++------------------ R/SE.methods.R | 2 R/SIBTEST.R | 65 +++++++++------ R/SingleGroup-methods.R | 82 ++++++++++++++----- R/fscores.internal.R | 19 ++-- R/itemplot.internal.R | 24 ++++- R/mirt.R | 30 +++--- R/multipleGroup.R | 3 R/utils.R | 70 +++++++++------- build/vignette.rds |binary man/PLCI.mirt.Rd | 18 +++- man/SIBTEST.Rd | 16 ++- man/mirt.Rd | 29 ++---- man/multipleGroup.Rd | 3 man/plot-method.Rd | 4 tests/tests/test-08-createItem.R | 5 + tests/tests/test-10-extras.R | 2 tests/tests/test-12-gpcm_mats.R | 2 28 files changed, 501 insertions(+), 271 deletions(-)
Title: Multidimensional Iterative Proportional Fitting and Alternative
Models
Description: An implementation of the iterative proportional fitting (IPFP),
maximum likelihood, minimum chi-square and weighted least squares procedures
for updating a N-dimensional array with respect to given target marginal
distributions (which, in turn can be multidimensional). The package also
provides an application of the IPFP to simulate multivariate Bernoulli
distributions.
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy <johan@uow.edu.au>
Diff between mipfp versions 3.0-1 dated 2016-04-29 and 3.1 dated 2016-12-01
DESCRIPTION | 10 - MD5 | 23 +- NAMESPACE | 2 R/s3_mipfp.R | 302 +++++++++++++++++------------------ R/utils.R | 71 ++++++++ man/Array2Vector.Rd | 12 - man/Corr2Odds.Rd | 166 +++++++++---------- man/Ipfp.Rd | 370 ++++++++++++++++++++++---------------------- man/ObtainModelEstimates.Rd | 286 +++++++++++++++++----------------- man/expand.Rd |only man/flat.Rd | 2 man/mipfp-package.Rd | 21 +- man/spnamur.Rd | 88 +++++----- 13 files changed, 713 insertions(+), 640 deletions(-)
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.64-3 dated 2016-09-19 and 0.65-1 dated 2016-12-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/excel_fig.R | 5 +++-- data/numbers-cap.RData |binary data/numbers.RData |binary inst/README.md | 4 ++-- man/excel_fig.Rd | 4 +++- 7 files changed, 18 insertions(+), 15 deletions(-)
Title: Age-Period-Cohort Analysis
Description: Functions for age-period-cohort analysis. The data can be organised in matrices indexed by age-cohort, age-period or cohort-period. The data can include dose and response or just doses. The statistical model is a generalized linear model (GLM) allowing for 3,2,1 or 0 of the age-period-cohort factors. The canonical parametrisation of Kuang, Nielsen and Nielsen (2008) <DOI:10.1093/biomet/asn026> is used. Thus, the analysis does not rely on ad hoc identification.
Author: Bent Nielsen
Maintainer: Bent Nielsen <bent.nielsen@nuffield.ox.ac.uk>
Diff between apc versions 1.2 dated 2016-03-21 and 1.3 dated 2016-12-01
apc-1.2/apc/inst/CITATION |only apc-1.2/apc/inst/COPYING |only apc-1.2/apc/man/apc_1.2-package.Rd |only apc-1.3/apc/DESCRIPTION | 10 apc-1.3/apc/MD5 | 47 +- apc-1.3/apc/NAMESPACE | 2 apc-1.3/apc/NEWS | 20 + apc-1.3/apc/R/apc_data.R | 559 +------------------------------- apc-1.3/apc/R/apc_data_sets.R |only apc-1.3/apc/R/apc_fit.R | 133 +++++-- apc-1.3/apc/R/apc_forecast.R | 363 ++++++++++++++++++-- apc-1.3/apc/R/apc_get_index.R | 13 apc-1.3/apc/R/apc_plot_data.R | 74 ++-- apc-1.3/apc/R/apc_plot_fit.R | 13 apc-1.3/apc/build |only apc-1.3/apc/inst/doc |only apc-1.3/apc/man/apc.data.list.Rd | 54 ++- apc-1.3/apc/man/apc.data.sums.Rd | 5 apc-1.3/apc/man/apc.fit.model.Rd | 66 +++ apc-1.3/apc/man/apc.forecast.Rd | 13 apc-1.3/apc/man/apc.forecast.ac.Rd | 79 +++- apc-1.3/apc/man/apc.forecast.ap.Rd | 45 ++ apc-1.3/apc/man/apc.forecast.apc.Rd |only apc-1.3/apc/man/apc.plot.data.all.Rd | 2 apc-1.3/apc/man/apc.plot.data.within.Rd | 13 apc-1.3/apc/man/apc_1.3-package.Rd |only apc-1.3/apc/man/data.RH.mortality.Rd |only apc-1.3/apc/man/data.asbestos.Rd | 28 + apc-1.3/apc/vignettes |only 29 files changed, 787 insertions(+), 752 deletions(-)