Title: Select and Download Climate Data from 'DWD' (German Weather
Service)
Description: Handle climate data from the 'DWD' ('Deutscher Wetterdienst', see
<https://www.dwd.de/EN/climate_environment/cdc/cdc.html> for more information).
Choose files with 'selectDWD()', download and process data sets with 'dataDWD()' and 'readDWD()'.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between rdwd versions 0.6.1 dated 2017-01-25 and 0.7.0 dated 2017-02-03
rdwd-0.6.1/rdwd/data/mapDWD.rda |only rdwd-0.6.1/rdwd/man/mapDWD.Rd |only rdwd-0.7.0/rdwd/DESCRIPTION | 14 +- rdwd-0.7.0/rdwd/MD5 | 78 ++++++------- rdwd-0.7.0/rdwd/NAMESPACE | 2 rdwd-0.7.0/rdwd/NEWS | 21 +++ rdwd-0.7.0/rdwd/R/createIndex.R | 55 +++++---- rdwd-0.7.0/rdwd/R/dataDWD.R | 6 - rdwd-0.7.0/rdwd/R/dirDWD.R | 7 - rdwd-0.7.0/rdwd/R/fileDWD.R | 14 +- rdwd-0.7.0/rdwd/R/meta.R | 179 +++++++++++++++++++------------ rdwd-0.7.0/rdwd/R/rdwd-package.R | 5 rdwd-0.7.0/rdwd/R/readDWD.R | 2 rdwd-0.7.0/rdwd/README.md | 15 +- rdwd-0.7.0/rdwd/build/vignette.rds |binary rdwd-0.7.0/rdwd/data/fileIndex.rda |binary rdwd-0.7.0/rdwd/data/geoIndex.rda |binary rdwd-0.7.0/rdwd/data/geoIndexAll.rda |only rdwd-0.7.0/rdwd/data/metaIndex.rda |binary rdwd-0.7.0/rdwd/inst/doc/mapDWD.R | 19 +++ rdwd-0.7.0/rdwd/inst/doc/mapDWD.Rmd | 50 ++++++++ rdwd-0.7.0/rdwd/inst/doc/mapDWD.html | 32 ++++- rdwd-0.7.0/rdwd/inst/doc/rdwd.R | 7 - rdwd-0.7.0/rdwd/inst/doc/rdwd.Rmd | 29 ++--- rdwd-0.7.0/rdwd/inst/doc/rdwd.html | 84 +++++--------- rdwd-0.7.0/rdwd/man/createIndex.Rd | 15 +- rdwd-0.7.0/rdwd/man/dataDWD.Rd | 11 - rdwd-0.7.0/rdwd/man/dirDWD.Rd | 7 - rdwd-0.7.0/rdwd/man/fileDWD.Rd | 7 - rdwd-0.7.0/rdwd/man/fileIndex.Rd | 7 - rdwd-0.7.0/rdwd/man/findID.Rd | 7 - rdwd-0.7.0/rdwd/man/geoIndex.Rd | 17 ++ rdwd-0.7.0/rdwd/man/indexDWD.Rd | 1 rdwd-0.7.0/rdwd/man/metaIndex.Rd | 7 - rdwd-0.7.0/rdwd/man/metaInfo.Rd | 9 - rdwd-0.7.0/rdwd/man/rdwd.Rd | 13 +- rdwd-0.7.0/rdwd/man/readDWD.Rd | 9 - rdwd-0.7.0/rdwd/man/release_questions.Rd | 1 rdwd-0.7.0/rdwd/man/rowDisplay.Rd |only rdwd-0.7.0/rdwd/man/selectDWD.Rd | 7 - rdwd-0.7.0/rdwd/vignettes/mapDWD.Rmd | 50 ++++++++ rdwd-0.7.0/rdwd/vignettes/rdwd.Rmd | 29 ++--- 42 files changed, 501 insertions(+), 315 deletions(-)
Title: Fitting 'Maxent' Species Distribution Models with 'glmnet'
Description: Procedures to fit species distributions models from occurrence records and environmental variables, using 'glmnet' for model fitting. Model structure is the same as for the 'Maxent' Java package, version 3.4.0, with the same feature types and regularization options. See the 'Maxent' website <http://biodiversityinformatics.amnh.org/open_source/maxent> for more details.
Author: Steven Phillips
Maintainer: Steven Phillips <mrmaxent@gmail.com>
Diff between maxnet versions 0.1.0 dated 2016-11-16 and 0.1.1 dated 2017-02-03
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- R/maxnet.R | 15 ++++++++------- 3 files changed, 15 insertions(+), 13 deletions(-)
Title: Joint Confidence Regions
Description: Computing and plotting joint confidence regions and intervals. Regions include classical ellipsoids, minimum-volume or minimum-length regions, and an empirical Bayes region. Intervals include the TOST procedure with ordinary or expanded intervals and a fixed-sequence procedure. Such regions and intervals are useful e.g., for the assessment of multi-parameter (bio-)equivalence. Joint confidence regions for the mean and variance of a normal distribution are available as well.
Author: Philip Pallmann [aut, cre]
Maintainer: Philip Pallmann <p.pallmann@lancaster.ac.uk>
Diff between jocre versions 0.1 dated 2016-10-05 and 0.3 dated 2017-02-03
jocre-0.1/jocre/R/confints.R |only jocre-0.1/jocre/R/confset.R |only jocre-0.1/jocre/R/plot2D.R |only jocre-0.1/jocre/R/plotMV2D.R |only jocre-0.1/jocre/man/confints.Rd |only jocre-0.1/jocre/man/confset.Rd |only jocre-0.1/jocre/man/plot2D.Rd |only jocre-0.1/jocre/man/plotMV2D.Rd |only jocre-0.3/jocre/DESCRIPTION | 10 +++++----- jocre-0.3/jocre/MD5 | 30 +++++++++++++++--------------- jocre-0.3/jocre/NAMESPACE | 11 ++++++++++- jocre-0.3/jocre/R/cset.R |only jocre-0.3/jocre/R/csetMV.R |only jocre-0.3/jocre/R/helpers.R |only jocre-0.3/jocre/R/translate.R |only jocre-0.3/jocre/inst/CITATION | 6 +++--- jocre-0.3/jocre/inst/NEWS | 12 ++++++++++++ jocre-0.3/jocre/man/cset.Rd |only jocre-0.3/jocre/man/csetMV.Rd |only jocre-0.3/jocre/man/helpers.Rd |only jocre-0.3/jocre/man/jocre-package.Rd | 16 ++++++++-------- jocre-0.3/jocre/man/marzo.Rd | 4 ++-- jocre-0.3/jocre/man/translate.Rd |only jocre-0.3/jocre/man/wires.Rd | 6 +++--- 24 files changed, 58 insertions(+), 37 deletions(-)
Title: A Test Environment for HTTP Requests
Description: Testing code and packages that communicate with remote servers can
be painful. Dealing with authentication, bootstrapping server state,
cleaning up objects that may get created during the test run, network
flakiness, and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three test
contexts that mock the network connection in different ways, and it offers
additional expectations to assert that HTTP requests were--or were
not--made. Using these tools, one can test that code is making the intended
requests and that it handles the expected responses correctly, all without
depending on a connection to a remote API.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 1.0.0 dated 2016-12-31 and 1.1.0 dated 2017-02-03
DESCRIPTION | 10 +++++----- MD5 | 35 +++++++++++++++++++---------------- NAMESPACE | 4 ++++ NEWS.md | 5 +++++ R/expect-header.R |only R/fake-http.R | 3 ++- R/mock-api.R | 13 +++++-------- README.md | 1 + man/buildMockURL.Rd | 1 - man/expect-verb.Rd | 8 ++++++-- man/expect_header.Rd |only man/expect_json_equivalent.Rd | 1 - man/fakeResponse.Rd | 1 - man/public.Rd | 1 - man/skip_if_disconnected.Rd | 1 - man/with_fake_HTTP.Rd | 1 - man/with_mock_API.Rd | 1 - man/without_internet.Rd | 1 - tests/testthat/test-expect-header.R |only tests/testthat/test-mock-api.R | 2 ++ 20 files changed, 49 insertions(+), 40 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl], Mikko Korpela [aut, trl], Franco Biondi [aut, cph], Filipe Campelo [aut, cph], Pierre Mérian [aut, cph], Fares Qeadan [aut, cph], Christian Zang [aut, cph], Allan Buras [ctb], Jacob Cecile [ctb], Manfred Mudelsee [ctb], Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.4 dated 2016-03-16 and 1.6.5 dated 2017-02-03
ChangeLog | 52 +++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 15 ++++++------ MD5 | 47 +++++++++++++++++++++----------------- NAMESPACE | 5 +++- R/combine.rwl.R | 4 ++- R/crn.plot.R | 19 +++++++++++---- R/detrend.R | 2 - R/helpers.R | 25 ++++++++++++++++++++ R/rwl.report.R |only R/sea.R | 44 ++++++++++++++++-------------------- R/zzz.R |only TODO | 2 - build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/chron-dplR.pdf |binary inst/doc/intro-dplR.R | 13 +++++----- inst/doc/intro-dplR.pdf |binary inst/doc/timeseries-dplR.pdf |binary inst/doc/xdate-dplR.pdf |binary man/combine.rwl.Rd | 3 +- man/crn.plot.Rd | 4 ++- man/detrend.Rd | 4 +-- man/detrend.series.Rd | 4 +-- man/print.rwl.report.Rd |only man/rwl.report.Rd |only tests/testthat/test-dplR.R | 10 ++++---- vignettes/intro-dplR.Rnw | 20 ++++++---------- 27 files changed, 183 insertions(+), 90 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 2.0 dated 2015-01-29 and 3.2 dated 2017-02-03
DESCRIPTION | 14 - MD5 | 39 ++ NAMESPACE | 1 NEWS | 23 + R/emf.R | 6 configure | 387 ++++++++++++---------------- configure.ac | 34 ++ configure.win |only inst |only man/emf.Rd | 59 ++-- src/devEMF.cpp | 741 +++++++++++++++++++++++++++++------------------------- src/emf+.h |only src/emf.h | 641 +++++++++++++++++++++++++++++++++++++++++----- src/fontmetrics.h | 308 ++++++++++++++++++++-- tools |only 15 files changed, 1561 insertions(+), 692 deletions(-)
Title: 'DBHYDRO' Hydrologic and Water Quality Data
Description: Client for programmatic access to the South Florida Water
Management District's 'DBHYDRO' database at
<http://sfwmd.gov/dbhydro>, with functions
for accessing hydrologic and water quality data.
Author: Joseph Stachelek [aut, cre]
Maintainer: Joseph Stachelek <stachel2@msu.edu>
Diff between dbhydroR versions 0.2-1 dated 2016-11-24 and 0.2-2 dated 2017-02-03
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/dbhydro_get.R | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: 'd3.js' Utilities for R
Description: Helper functions for using 'd3.js' in R.
Author: Mike Bostock [aut, cph] (d3.js library in htmlwidgets/lib,
http://d3js.org),
Kent Russell [aut, cre] (R interface)
Maintainer: Kent Russell <kent.russell@timelyportfolio.com>
Diff between d3r versions 0.6.0 dated 2016-12-13 and 0.6.1 dated 2017-02-03
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/dependencies.R | 2 +- inst/www/d3/v4/dist/d3.min.js | 16 ++++++++-------- tests/testthat/test_deps.R | 1 + tests/testthat/test_igraph.R | 30 ++++++++++++++++++++---------- 8 files changed, 49 insertions(+), 32 deletions(-)
Title: Companion to Applied Linear Statistical Models
Description: Functions and Data set presented in Applied Linear Statistical Models Fifth Edition (Chapters 1-9 and 16-25), Michael H. Kutner; Christopher J. Nachtsheim; John Neter; William Li, 2005. (ISBN-10: 0071122214, ISBN-13: 978-0071122214) that do not exist in R, are gathered in this package. The whole book will be covered in the next versions.
Author: Ali Ghanbari <a.ghanbari541@gmail.com>
Maintainer: Ali Ghanbari <a.ghanbari541@gmail.com>
Diff between ALSM versions 0.1.5 dated 2016-12-27 and 0.1.9 dated 2017-02-03
DESCRIPTION | 10 - MD5 | 46 +++- NAMESPACE | 9 R/19_aligned.dot.plot.R | 37 +++ R/19_towway.ci.R | 386 ++++++++++++++++++++------------------- R/25_MLS.R |only R/25_onerandom.R |only R/25_satterthwaiteeeee.R |only R/6_ci.reg.R | 4 R/normal.cor.test.R |only data/ApexEnterprises.rda |only data/AuditorTraining_10.rda |binary data/CashOffers.rda |binary data/CrackerPromotion.rda |only data/DiskDriveService.rda |only data/GrowthHormone.rda |only data/ProductivityImprovement.rda |binary data/RoadPaintWear.rda |only data/SalableFlowers.rda |only man/ApexEnterprises.Rd |only man/AuditorTraining_10.Rd | 1 man/AuditorTraining_5.Rd | 1 man/CashOffers.Rd | 1 man/CrackerPromotion.Rd |only man/DiskDriveService.Rd |only man/GrowthHormone.Rd |only man/MLS.Rd |only man/ProductivityImprovement.Rd | 5 man/RoadPaintWear.Rd |only man/SalableFlowers.Rd |only man/normal.cor.test.Rd |only man/onerandom.Rd |only man/satterthwaite.Rd |only man/towway.ci.Rd | 9 34 files changed, 294 insertions(+), 215 deletions(-)
Title: Within Outlying Mean Indexes: Refining the OMI Analysis
Description: Complementary multivariate analysis to the Outlying Mean Index
analysis to explore niche shift of a community and biological constraint within an Euclidean space, with
graphical displays.
Author: Stephane Karasiewicz
Maintainer: Stephane Karasiewicz <stephane.karasiewicz@wanadoo.fr>
Diff between subniche versions 0.9.1 dated 2016-11-19 and 0.9.2 dated 2017-02-03
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/subniche.R | 50 +++++++++++++++++++++++++++----------------------- man/subniche.Rd | 49 ++++++++++++++++++++++++++----------------------- 4 files changed, 62 insertions(+), 55 deletions(-)
Title: Regression Standardization
Description: Contains functionality for regression standardization. Three general classes of models are allowed; generalized linear models, Cox proportional hazards models and shared gamma-Weibull frailty models.
Author: Arvid Sjolander and Elisabeth Dahlqwist
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>
Diff between stdReg versions 1.1 dated 2016-04-04 and 2.1 dated 2017-02-03
DESCRIPTION | 12 MD5 | 27 - NAMESPACE | 10 R/sourcecode.R | 802 ++++++++++++++++++++++++++++++------- build/partial.rdb |binary man/parfrailty.rd |only man/plot.stdCoxph.Rd | 11 man/plot.stdGlm.Rd | 4 man/plot.stdParfrailty.rd |only man/print.summary.parfrailty.rd |only man/print.summary.stdParfrailty.rd |only man/stdCoxph.Rd | 36 - man/stdGlm.Rd | 42 - man/stdParfrailty.rd |only man/summary.parfrailty.rd |only man/summary.stdCoxph.Rd | 4 man/summary.stdGlm.Rd | 4 man/summary.stdParfrailty.rd |only 18 files changed, 748 insertions(+), 204 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.7.1 dated 2016-12-18 and 0.8.0 dated 2017-02-03
DESCRIPTION | 21 +- MD5 | 110 +++++++------- NAMESPACE | 296 +++++++++++++++++++++------------------ NEWS | 17 ++ NEWS.md | 20 ++ R/S3-methods.R | 18 ++ R/bootstrap.R | 192 ++++++++++++------------- R/check_model_assumptions.R |only R/cv.R | 2 R/helpfunctions.R | 25 +++ R/merMod_p.R | 213 +++++++++++++--------------- R/overdisp.R | 224 +++++++++++++++++------------ R/predictive_accuracy.R |only R/prop.R | 329 +++++++++++++++++++++++++------------------- R/pseudo_r2.R | 38 ++++- R/robust.R | 57 +++++++ R/se.R | 82 +++++++++- R/sjStatistics.R | 2 R/std.R | 221 +++++++++++++++-------------- build/partial.rdb |binary man/boot_ci.Rd | 247 ++++++++++++++++----------------- man/bootstrap.Rd | 161 ++++++++++----------- man/check_assumptions.Rd |only man/chisq_gof.Rd | 119 +++++++-------- man/cod.Rd | 91 ++++++------ man/converge_ok.Rd | 105 ++++++-------- man/cv.Rd | 123 ++++++++-------- man/deff.Rd | 85 +++++------ man/efc.Rd | 67 ++++---- man/eta_sq.Rd | 85 +++++------ man/get_model_pval.Rd | 116 +++++++-------- man/hoslem_gof.Rd | 87 +++++------ man/icc.Rd | 245 ++++++++++++++++---------------- man/inequ_trend.Rd | 141 +++++++++--------- man/levene_test.Rd | 43 ++--- man/mean_n.Rd | 139 +++++++++--------- man/mwu.Rd | 105 ++++++-------- man/odds_to_rr.Rd | 123 ++++++++-------- man/overdisp.Rd | 135 +++++++++--------- man/phi.Rd | 73 ++++----- man/pred_accuracy.Rd |only man/pred_vars.Rd | 77 +++++----- man/prop.Rd | 151 ++++++++++---------- man/r2.Rd | 227 +++++++++++++++--------------- man/re_var.Rd | 125 ++++++++-------- man/reliab_test.Rd | 313 ++++++++++++++++++++--------------------- man/rmse.Rd | 153 ++++++++++---------- man/robust.Rd | 136 ++++++++++-------- man/se.Rd | 205 +++++++++++++++------------ man/se_ybar.Rd | 59 +++---- man/sjstats-package.Rd | 55 ++----- man/smpsize_lmm.Rd | 129 ++++++++--------- man/std.Rd | 128 ++++++++--------- man/std_beta.Rd | 137 +++++++++--------- man/table_values.Rd | 73 ++++----- man/var_pop.Rd | 79 +++++----- man/weight.Rd | 115 +++++++-------- man/wtd_sd.Rd | 67 ++++---- 58 files changed, 3373 insertions(+), 3013 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
between compiled C and interpreted R code. Not to be confused with
'RNiftyReg', which provides tools for image registration.
Author: Jon Clayden [cre, aut],
Bob Cox [aut],
Mark Jenkinson [aut],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.3.0 dated 2016-12-08 and 0.4.0 dated 2017-02-03
RNifti-0.3.0/RNifti/src/init.cpp |only RNifti-0.4.0/RNifti/DESCRIPTION | 8 RNifti-0.4.0/RNifti/MD5 | 24 RNifti-0.4.0/RNifti/NAMESPACE | 1 RNifti-0.4.0/RNifti/NEWS | 12 RNifti-0.4.0/RNifti/R/xform.R | 12 RNifti-0.4.0/RNifti/README.md | 4 RNifti-0.4.0/RNifti/inst/doxygen/html/_nifti_image_8h_source.html | 82 +- RNifti-0.4.0/RNifti/inst/include/lib/NiftiImage.h | 311 +++++----- RNifti-0.4.0/RNifti/inst/include/lib/NiftiImage_internal.h |only RNifti-0.4.0/RNifti/man/voxelToWorld.Rd | 8 RNifti-0.4.0/RNifti/man/writeNifti.Rd | 2 RNifti-0.4.0/RNifti/src/Makevars | 2 RNifti-0.4.0/RNifti/src/main.cpp | 57 + 14 files changed, 325 insertions(+), 198 deletions(-)
Title: R Interface for H2O
Description: R scripting functionality for H2O, the open source
math engine for big data that computes parallel distributed
machine learning algorithms such as generalized linear models,
gradient boosting machines, random forests, and neural networks
(deep learning) within various cluster environments.
Author: The H2O.ai team
Maintainer: Tom Kraljevic <tomk@0xdata.com>
Diff between h2o versions 3.10.2.2 dated 2017-01-17 and 3.10.3.3 dated 2017-02-03
DESCRIPTION | 8 +- MD5 | 60 ++++++++------- NAMESPACE | 10 ++ R/classes.R | 10 ++ R/communication.R | 65 ++++++++++++---- R/connection.R | 55 +++++++++++++ R/constants.R | 7 - R/deepwater.R | 8 +- R/export.R | 36 ++++++++- R/frame.R | 124 ++++++++++++++++++++++++++----- R/import.R | 27 +++--- R/kvstore.R | 84 ++++++++++----------- R/parse.R | 25 ++---- R/stackedensemble.R |only R/w2vutils.R |only R/word2vec.R | 171 ++++++++++++++++--------------------------- inst/branch.txt | 2 inst/buildnum.txt | 2 man/H2OConnection-class.Rd | 2 man/H2OModel-class.Rd | 1 man/H2OModelMetrics-class.Rd | 1 man/h2o-package.Rd | 6 - man/h2o.connect.Rd |only man/h2o.deepwater.Rd | 10 +- man/h2o.findSynonyms.Rd |only man/h2o.grep.Rd |only man/h2o.importFile.Rd | 8 ++ man/h2o.init.Rd | 5 + man/h2o.parseRaw.Rd | 7 + man/h2o.parseSetup.Rd | 7 + man/h2o.saveModel.Rd | 6 - man/h2o.saveMojo.Rd |only man/h2o.stackedEnsemble.Rd |only man/h2o.tokenize.Rd |only man/h2o.transform.Rd |only man/h2o.word2vec.Rd |only 36 files changed, 471 insertions(+), 276 deletions(-)
Title: A GUI-Based Program to Compute Probabilities Regarding Group
Sequential Designs
Description: A graphical user interface to compute group sequential designs
based on normally distributed test statistics, particularly critical
boundaries, power, drift, and confidence intervals of such designs. All
computations are based on the alpha spending approach by Lan-DeMets with
various alpha spending functions being available to choose among.
Author: Roman Pahl
Maintainer: Roman Pahl <roman.pahl@gmail.com>
Diff between GroupSeq versions 1.3.3 dated 2015-07-08 and 1.3.4 dated 2017-02-03
DESCRIPTION | 6 MD5 | 58 - NEWS | 50 R/alphaByUseFunction.R | 124 +- R/alpha_spending_functions.R | 48 R/calculateEqualBounds.R | 316 +++--- R/calculateTask1.R | 242 ++-- R/calculateTask2.R | 242 ++-- R/calculateTask3.R | 212 ++-- R/calculateTask4.R | 196 +-- R/computeAlphaLevel.R | 270 ++--- R/computeBounds.R | 612 +++++------ R/computeConfidenceIntervall.R | 60 - R/computeCurrentProbability.R | 100 - R/computeDrift.R | 454 ++++---- R/consoleMode.R | 2110 ++++++++++++++++++++--------------------- R/console_output.R | 392 +++---- R/findDrift.R | 30 R/guiMode.R | 114 +- R/guiOutputTask1.R | 504 ++++----- R/guiOutputTask2.R | 758 +++++++------- R/guiOutputTask3.R | 2 R/guiOutputTask4.R | 612 +++++------ R/integrateByTrapez.R | 40 R/jointDensity.R | 108 +- R/searchForBound.R | 526 +++++----- R/stdDeviations.R | 70 - R/tailProbability.R | 44 R/useSpendingFunction.R | 1070 ++++++++++---------- man/groupseq.Rd | 120 +- 30 files changed, 4745 insertions(+), 4745 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut, cre],
Yuan Tang [aut, cph]
Maintainer: Masaaki Horikoshi <sinhrks@gmail.com>
Diff between ggfortify versions 0.3.0.0 dated 2016-12-02 and 0.4.0 dated 2017-02-03
DESCRIPTION | 16 - MD5 | 254 ++++++++++--------- NAMESPACE | 4 NEWS |only R/base_fortify_list.R | 8 R/base_fortify_ts.R | 2 R/fortify_MSwM.R | 2 R/fortify_basis.R | 2 R/fortify_forecast.R | 2 R/fortify_glmnet.R | 27 -- R/fortify_performance.R |only R/fortify_spatial.R | 9 R/fortify_stats.R | 31 +- R/fortify_stats_lm.R | 73 +++-- R/fortify_surv.R | 3 R/fortify_vars.R | 2 R/geom.R | 2 R/ggfortify.R | 2 R/plotlib.R | 2 R/tslib.R | 14 - R/util.R | 15 + build/vignette.rds |binary inst/doc/intro_Chinese.html | 2 inst/doc/plot_dist.html | 2 inst/doc/plot_lm.html | 2 man/apply_facets.Rd | 1 man/as_tibble.basis.Rd | 1 man/autoplot.MSM.lm.Rd | 1 man/autoplot.RasterCommon.Rd | 1 man/autoplot.SpatialCommon.Rd | 1 man/autoplot.aareg.Rd | 1 man/autoplot.acf.Rd | 1 man/autoplot.basis.Rd | 1 man/autoplot.breakpoints.Rd | 1 man/autoplot.cpt.Rd | 1 man/autoplot.cv.glmnet.Rd | 1 man/autoplot.density.Rd | 1 man/autoplot.forecast.Rd | 1 man/autoplot.ggmultiplot.Rd | 1 man/autoplot.ggplot.Rd | 1 man/autoplot.glmnet.Rd | 1 man/autoplot.kmeans.Rd | 1 man/autoplot.list.Rd | 1 man/autoplot.lm.Rd | 1 man/autoplot.map.Rd | 1 man/autoplot.matrix.Rd | 1 man/autoplot.pca_common.Rd | 10 man/autoplot.performance.Rd |only man/autoplot.spec.Rd | 1 man/autoplot.stepfun.Rd | 1 man/autoplot.survfit.Rd | 1 man/autoplot.ts.Rd | 9 man/autoplot.tsmodel.Rd | 7 man/autoplot.varprd.Rd | 1 man/cbind_wraps.Rd | 1 man/check_names.Rd | 1 man/confint.acf.Rd | 1 man/deprecate.warning.Rd | 1 man/fitted.ar.Rd | 1 man/flatten.Rd |only man/fortify.MSM.lm.Rd | 1 man/fortify.RasterCommon.Rd | 1 man/fortify.SpatialCommon.Rd | 1 man/fortify.aareg.Rd | 1 man/fortify.acf.Rd | 1 man/fortify.basis.Rd | 1 man/fortify.cpt.Rd | 5 man/fortify.cv.glmnet.Rd | 1 man/fortify.density.Rd | 1 man/fortify.dist.Rd | 1 man/fortify.ets.Rd | 1 man/fortify.factanal.Rd | 1 man/fortify.forecast.Rd | 1 man/fortify.glmnet.Rd | 1 man/fortify.kmeans.Rd | 1 man/fortify.lfda.Rd | 1 man/fortify.list.Rd | 1 man/fortify.matrix.Rd | 1 man/fortify.performance.Rd |only man/fortify.prcomp.Rd | 1 man/fortify.spec.Rd | 1 man/fortify.stepfun.Rd | 1 man/fortify.survfit.Rd | 1 man/fortify.table.Rd | 1 man/fortify.ts.Rd | 1 man/fortify.tsmodel.Rd | 9 man/fortify.varprd.Rd | 1 man/fortify_base.Rd | 1 man/fortify_map.Rd | 1 man/geom_confint.Rd | 1 man/geom_factory.Rd | 1 man/get.dtindex.Rd | 1 man/get.dtindex.continuous.Rd | 1 man/get.layout.Rd | 1 man/get_geom_function.Rd | 1 man/ggbiplot.Rd | 1 man/ggcpgram.Rd | 1 man/ggdistribution.Rd | 1 man/ggfortify.Rd | 1 man/ggfreqplot.Rd | 1 man/gglagplot.Rd | 1 man/ggmultiplot-class.Rd | 6 man/ggtsdiag.Rd | 1 man/grid.draw.ggmultiplot.Rd | 1 man/infer.Rd | 1 man/is.univariate.Rd | 1 man/is_derived_from.Rd | 1 man/plot_confint.Rd | 1 man/plot_label.Rd | 1 man/plus-ggmultiplot-ANY-method.Rd | 1 man/post_autoplot.Rd | 1 man/post_fortify.Rd | 1 man/print-ggmultiplot-method.Rd | 1 man/rbind_ts.Rd | 1 man/residuals.ar.Rd | 1 man/show-ggmultiplot-method.Rd | 1 man/support_autoplot.Rd | 1 man/unscale.Rd | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-base-infer.R | 2 tests/testthat/test-changepoint.R | 9 tests/testthat/test-cluster.R | 4 tests/testthat/test-forecast.R | 3 tests/testthat/test-glmnet.R | 3 tests/testthat/test-performance.R |only tests/testthat/test-spatial.R | 54 ++-- tests/testthat/test-stats-lm.R | 481 +++++++++++++++++++++++++++++++++++++ tests/testthat/test-stats.R | 74 +++++ tests/testthat/test-surv.R | 32 +- tests/testthat/test-util.R | 1 tests/testthat/test_lint.R | 3 131 files changed, 895 insertions(+), 377 deletions(-)
Title: Download and Use CRU CL2.0 Climatology Data in R
Description: Provides functions that automate downloading and importing
University of East Anglia Climate Research Unit (CRU) CL2.0 climatology data
into R, facilitates the calculation of minimum temperature and maximum
temperature and formats the data into a tidy data frame or a list of raster
stack objects for use in an R session. CRU CL2.0 data are a gridded
climatology of 1961-1990 monthly means released in 2002 and cover all land
areas (excluding Antarctica) at 10-minute resolution. For more
information see the description of the data provided by the University of
East Anglia Climate Research Unit,
<https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.
Author: Adam Sparks [aut, cre]
Maintainer: Adam Sparks <adamhsparks@gmail.com>
Diff between getCRUCLdata versions 0.1.3 dated 2017-02-01 and 0.1.4 dated 2017-02-03
DESCRIPTION | 6 MD5 | 16 NEWS.md | 6 R/create_CRU_df.R | 2 R/get_CRU.R | 2 R/tidy_df.R | 37 + tests/testthat/test-create_CRU_df.R | 581 ++++++++++++++++++++++++++++ tests/testthat/test-create_CRU_stack.R | 676 ++++++++++++++++++++++++++++----- tests/testthat/test-get_CRU.R | 299 +++----------- 9 files changed, 1280 insertions(+), 345 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.3.4 dated 2016-11-29 and 0.3.5 dated 2017-02-03
DESCRIPTION | 33 ++++- MD5 | 47 +++---- NEWS | 18 ++ R/ctmm.R | 13 +- R/generic.R | 22 +++ R/kde.R | 21 ++- R/krige.R | 3 R/likelihood.R | 292 ++++++++++++++++++++++++++++++++---------------- R/select.R | 45 +++++-- R/telemetry.R | 33 +++-- R/variogram.R | 42 +++++- TODO | 41 ++---- inst/doc/akde.html | 4 inst/doc/variogram.Rmd | 4 inst/doc/variogram.html | 15 +- man/akde.Rd | 2 man/bandwidth.Rd | 5 man/buffalo.Rd | 12 + man/ctmm-FAQ.Rd |only man/ctmm-package.Rd | 22 ++- man/ctmm.fit.Rd | 8 - man/summary.UD.Rd | 3 man/summary.ctmm.Rd | 5 man/uere.Rd | 3 vignettes/variogram.Rmd | 4 25 files changed, 475 insertions(+), 222 deletions(-)
Title: Smoothing Splines for Large Samples
Description: Fits smoothing spline regression models using scalable algorithms designed for large samples. Seven marginal spline types are supported: linear, cubic, different cubic, cubic periodic, cubic thin-plate, ordinal, and nominal. Random effects and parametric effects are also supported. Response can be Gaussian or non-Gaussian: Binomial, Poisson, Gamma, Inverse Gaussian, or Negative Binomial.
Author: Nathaniel E. Helwig <helwig@umn.edu>
Maintainer: Nathaniel E. Helwig <helwig@umn.edu>
Diff between bigsplines versions 1.0-9 dated 2016-08-13 and 1.1-0 dated 2017-02-03
ChangeLog | 28 +++++++++++++++++ DESCRIPTION | 11 +++--- MD5 | 72 +++++++++++++++++++++++++-------------------- NAMESPACE | 4 ++ R/MPinv.R |only R/gcvoss.R |only R/makerkm.R | 7 ++++ R/makessa.R | 10 +++--- R/makessg.R | 10 +++--- R/makessp.R | 10 +++--- R/ordspline.R |only R/plotci.R | 9 +++-- R/predict.bigssa.R | 6 +-- R/predict.bigssg.R | 6 +-- R/predict.bigssp.R | 6 +-- R/predict.ordspline.R |only R/print.ordspline.R |only R/ssBasis.R |only R/ssawork.R | 2 - R/ssgwork.R | 2 - R/sspwork.R | 2 - man/bigspline.Rd | 4 -- man/bigsplines-internal.Rd | 2 + man/bigsplines-package.Rd | 8 +---- man/bigssa.Rd | 4 +- man/bigssg.Rd | 4 +- man/bigssp.Rd | 4 +- man/bigtps.Rd | 4 -- man/binsamp.Rd | 3 - man/makessa.Rd | 4 +- man/makessg.Rd | 4 +- man/makessp.Rd | 4 +- man/ordspline.Rd |only man/predict.bigspline.Rd | 4 -- man/predict.bigssa.Rd | 4 +- man/predict.bigssg.Rd | 4 +- man/predict.bigssp.Rd | 4 +- man/predict.bigtps.Rd | 4 -- man/predict.ordspline.Rd |only man/print.Rd | 10 ++++-- man/ssBasis.Rd |only src/ordkermon.f |only 42 files changed, 152 insertions(+), 108 deletions(-)
Title: Classical Goodness-of-Fit Tests for Univariate Distributions
Description: Cramer-Von Mises and Anderson-Darling tests of goodness-of-fit
for continuous univariate distributions, using
efficient algorithms.
Author: Julian Faraway [aut],
George Marsaglia [aut],
John Marsaglia [aut],
Adrian Baddeley [aut, cre]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between goftest versions 1.0-3 dated 2015-07-03 and 1.0-4 dated 2017-02-03
DESCRIPTION | 12 ++++++------ MD5 | 2 +- 2 files changed, 7 insertions(+), 7 deletions(-)
Title: A Modular Platform for Reproducible Modeling of Species Niches
and Distributions
Description: The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface.
Author: Jamie M. Kass [aut, cre],
Bruno Vilela [aut],
Matthew E. Aiello-Lammens [aut],
Robert Muscarella [aut],
Robert P. Anderson [aut]
Maintainer: Jamie M. Kass <jkass@gradcenter.cuny.edu>
Diff between wallace versions 0.6.2 dated 2017-02-01 and 0.6.3 dated 2017-02-03
DESCRIPTION | 12 ++++++------ MD5 | 24 ++++++++++++------------ NEWS.md | 7 ++++++- R/wallace-package.R | 6 +++--- README.md | 2 +- inst/Rmd/text_intro.Rmd | 2 +- inst/Rmd/text_intro_tab.Rmd | 2 +- inst/Rmd/userReport.Rmd | 8 ++------ inst/shiny/modules/mods_comp2.R | 1 - inst/shiny/modules/mods_comp5.R | 10 ++++++++++ inst/shiny/modules/mods_comp6.R | 16 +++++++++++++++- inst/shiny/server.R | 2 -- man/wallace-package.Rd | 6 +++--- 13 files changed, 60 insertions(+), 38 deletions(-)
Title: Stochastic Process Model for Analysis of Longitudinal and
Time-to-Event Outcomes
Description: Utilities to estimate parameters of the models with survival functions
induced by stochastic covariates. Miscellaneous functions for data preparation
and simulation are also provided. For more information, see:
(i)"Stochastic model for analysis of longitudinal data on aging and mortality"
by Yashin A. et al. (2007),
Mathematical Biosciences, 208(2), 538-551, <DOI:10.1016/j.mbs.2006.11.006>;
(ii) "Health decline, aging and mortality: how are they related?"
by Yashin A. et al. (2007),
Biogerontology 8(3), 291(302), <DOI:10.1007/s10522-006-9073-3>.
Author: I. Y. Zhbannikov, Liang He, K. G. Arbeev, E. Stallard, I. Akushevich, A. I. Yashin.
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between stpm versions 1.5.0 dated 2016-12-12 and 1.6.0 dated 2017-02-03
DESCRIPTION | 14 MD5 | 33 - NAMESPACE | 2 NEWS | 6 R/hes_spm.r |only R/hes_spm_g.r |only R/lik_con_1d.r |only R/lik_con_1d_g.r |only R/spm_con_1d.r |only R/spm_con_1d_g.r |only R/spm_time-dependent.R | 2 inst/doc/stpm-vignette.R | 16 inst/doc/stpm-vignette.Rmd | 16 inst/doc/stpm-vignette.html | 1093 +++++++++++++++++--------------------------- man/spm_con_1d.Rd |only man/spm_con_1d_g.Rd |only man/spm_time_dep.Rd | 2 src/devlik.cpp |only src/devlik_g.cpp |only src/devlik_g_2.cpp |only src/hes_spm_g.cpp |only src/loglik.cpp |only src/loglik_g.cpp |only src/loglik_g_2.cpp |only vignettes/stpm-vignette.Rmd | 16 25 files changed, 503 insertions(+), 697 deletions(-)
Title: Test and Item Analysis via Shiny
Description: Interactive shiny application for analysis of educational tests and
their items.
Author: Patricia Martinkova [aut, cre], Adela Drabinova [aut, cre], Ondrej Leder [aut], Jakub Houdek [aut], Cestmir Stuka [ctb] and Martin Vejrazka [ctb]
Maintainer: Patricia Martinkova <martinkova@cs.cas.cz>
Diff between ShinyItemAnalysis versions 1.0.0 dated 2016-11-25 and 1.1.0 dated 2017-02-03
DESCRIPTION | 15 MD5 | 60 NAMESPACE | 112 NEWS | 60 R/DDplot.R | 36 R/DistractorAnalysis.R | 21 R/dataMedical.R |only R/dataMedicalkey.R |only R/dataMedicaltest.R |only R/imports.R |only R/plotDIFLogistic.R | 4 R/plotDIFirt.R | 227 R/plotDistractorAnalysis.R | 40 R/startShinyItemAnalysis.R | 33 data |only inst/shiny-examples/ShinyItemAnalysis/DDplot.R | 9 inst/shiny-examples/ShinyItemAnalysis/DistractorAnalysis.R | 21 inst/shiny-examples/ShinyItemAnalysis/Rcode_ShinyItemAnalysis.R |only inst/shiny-examples/ShinyItemAnalysis/itemClassic.R |only inst/shiny-examples/ShinyItemAnalysis/personHist.R |only inst/shiny-examples/ShinyItemAnalysis/plotDIFLogistic.R | 4 inst/shiny-examples/ShinyItemAnalysis/plotDIFirt.R | 227 inst/shiny-examples/ShinyItemAnalysis/plotDistractorAnalysis.R | 40 inst/shiny-examples/ShinyItemAnalysis/report.Rmd |only inst/shiny-examples/ShinyItemAnalysis/reporthtml.Rmd |only inst/shiny-examples/ShinyItemAnalysis/reportpdf.Rmd |only inst/shiny-examples/ShinyItemAnalysis/server.R | 2356 ++++- inst/shiny-examples/ShinyItemAnalysis/ui.R | 4443 +++++----- inst/shiny-examples/ShinyItemAnalysis/wrightMap.R |only inst/shiny-examples/ShinyItemAnalysis/www/bootstrap.css |only man/DDplot.Rd | 9 man/DistractorAnalysis.Rd | 21 man/dataMedical.Rd |only man/dataMedicalkey.Rd |only man/dataMedicaltest.Rd |only man/plotDIFirt.Rd | 61 man/plotDistractorAnalysis.Rd | 35 man/startShinyItemAnalysis.Rd | 37 38 files changed, 5411 insertions(+), 2460 deletions(-)
More information about ShinyItemAnalysis at CRAN
Permanent link
Title: R Interface to the Pushbullet Messaging Service
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the site
http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel with contributions by Bill Evans, Mike Birdgeneau,
Henrik Bengtsson, and Seth Wenchel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RPushbullet versions 0.2.0 dated 2015-02-09 and 0.3.0 dated 2017-02-03
ChangeLog | 93 +++++++++++++++++++++++++ DESCRIPTION | 27 +++---- MD5 | 26 +++---- NAMESPACE | 6 + R/devices.R | 9 +- R/init.R | 82 +++++++++++++++------- R/pushes.R | 164 ++++++++++++++++++++++++--------------------- R/setup.R |only README.md | 69 +++++++++++++----- inst/NEWS.Rd | 28 +++++++ man/pbGetDevices.Rd | 3 man/pbPost.Rd | 19 +---- man/pbSetup.Rd |only man/rpushbullet-package.Rd | 9 +- tests/simpleTests.R | 52 +++++++++----- 15 files changed, 400 insertions(+), 187 deletions(-)
Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Can be used with censored and truncated data.
Author: Paolo Frumento <paolo.frumento@ki.se>
Maintainer: Paolo Frumento <paolo.frumento@ki.se>
Diff between qrcm versions 1.0 dated 2015-12-15 and 2.0 dated 2017-02-03
DESCRIPTION | 13 MD5 | 19 NAMESPACE | 13 NEWS.md |only R/qrcm.R | 1420 +++++++++++++++++++++++++++++---------------------- man/iqr.Rd | 61 +- man/plot.iqr.Rd | 15 man/qrcm-internal.Rd | 39 - man/qrcm-package.Rd | 20 man/summary.iqr.Rd | 19 man/test.fit.Rd | 45 + 11 files changed, 986 insertions(+), 678 deletions(-)
Title: Noncompartmental Analysis of Pharmacokinetic Data for CDISC
Standardized Parameters
Description: Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' <https://www.certara.com/software/pkpd-modeling-and-simulation/phoenix-winnonlin/>.
Some features include:
1) Use CDISC SDTM PP domain terms and generate PP domains from DM, EX, and PC domains.
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Support both 'linear-up linear-down' and 'linear-up log-down' method
4) Calculate partial(interval) AUC with 'linear' or 'log' interpolation method
5) Perform a noncompartmental analysis of CDISC standardized pharmacokinetic dataset (.XPT)
For more details on noncompartmental analysis, see the reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107)
*) Acknowledgement: Author thanks for the careful review and valuable input of Dr. Jee Eun Lee.
Author: Kyun-Seop Bae [aut, cre], Sungpil Han [aut]
Maintainer: Sungpil Han <shan@acp.kr>
Diff between ncar versions 0.3 dated 2017-01-25 and 0.3.1 dated 2017-02-03
ncar-0.3.1/ncar/DESCRIPTION | 12 ++++++------ ncar-0.3.1/ncar/MD5 | 12 ++++++------ ncar-0.3.1/ncar/NAMESPACE | 1 + ncar-0.3.1/ncar/R/runCDISC.R | 23 +++++++++++++++++++++-- ncar-0.3.1/ncar/R/sysdata.rda |binary ncar-0.3.1/ncar/inst/doc/ncar-manual.pdf |binary ncar-0.3.1/ncar/man/ncar_0.3.1-package.Rd |only ncar-0.3/ncar/man/NonCompart_0.2.6-package.Rd |only 8 files changed, 34 insertions(+), 14 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@isped.u-bordeaux2.fr>
Diff between frailtypack versions 2.10.4 dated 2017-01-04 and 2.10.5 dated 2017-02-03
DESCRIPTION | 8 - MD5 | 33 ++--- NEWS | 6 R/additivePenal.R | 2 R/frailtyPenal.R | 18 +- R/plot.epoce.R | 16 +- R/prediction.R | 297 ++++++++++++++++++++++++++++++++++++++------- R/waldtest.R | 34 ++--- man/SurvIC.Rd | 2 man/epoce.Rd | 294 ++++++++++++++++++++++---------------------- man/prediction.Rd | 4 man/timedep.Rd | 4 src/Makevars | 1 src/atestWald.f90 |only src/funcpajsplines_fam.f90 | 6 src/funcpajweib_fam.f90 | 14 +- src/prediction.f90 | 2 src/prediction_tri.f90 | 6 18 files changed, 494 insertions(+), 253 deletions(-)
Title: Analysis and Visualization of Macroevolutionary Dynamics on
Phylogenetic Trees
Description: Provides functions for analyzing and visualizing complex
macroevolutionary dynamics on phylogenetic trees. It is a companion
package to the command line program BAMM (Bayesian Analysis of
Macroevolutionary Mixtures) and is entirely oriented towards the analysis,
interpretation, and visualization of evolutionary rates. Functionality
includes visualization of rate shifts on phylogenies, estimating
evolutionary rates through time, comparing posterior distributions of
evolutionary rates across clades, comparing diversification models using
Bayes factors, and more.
Author: Dan Rabosky, Mike Grundler, Pascal Title, Carlos Anderson, Jeff Shi,
Joseph Brown, Huateng Huang, Jon Mitchell
Maintainer: Pascal Title <ptitle@umich.edu>
Diff between BAMMtools versions 2.1.5 dated 2016-10-03 and 2.1.6 dated 2017-02-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/getEventData.R | 20 +++++++++++++------- 3 files changed, 19 insertions(+), 13 deletions(-)
Title: Probabilistic Suffix Trees and Variable Length Markov Chains
Description: Provides a framework for analysing state sequences with probabilistic suffix trees (PST), the construction that stores variable length Markov chains (VLMC). Besides functions for learning and optimizing VLMC models, the PST library includes many additional tools to analyse sequence data with these models: visualization tools, functions for sequence prediction and artificial sequences generation, as well as for context and pattern mining. The package is specifically adapted to the field of social sciences by allowing to learn VLMC models from sets of individual sequences possibly containing missing values, and by accounting for case weights. The library also allows to compute probabilistic divergence between two models, and to fit segmented VLMC, where sub-models fitted to distinct strata of the learning sample are stored in a single PST. This software results from research work executed within the framework of the Swiss National Centre of Competence in Research LIVES, which is financed by the Swiss National Science Foundation. The authors are grateful to the Swiss National Science Foundation for its financial support.
Author: Alexis Gabadinho [aut, cre, cph]
Maintainer: Alexis Gabadinho <alexis.gabadinho@wanadoo.fr>
Diff between PST versions 0.92 dated 2016-11-10 and 0.94 dated 2017-02-03
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NEWS | 6 ++++++ R/PSTf-functions.R | 2 +- 4 files changed, 16 insertions(+), 10 deletions(-)