Title: Spatial Modeling on Stream Networks
Description: Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance (Ver Hoef, J.M. and Peterson, E.E., 2010. <DOI:10.1198/jasa.2009.ap08248>.) Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.
Author: Jay Ver Hoef [aut, cre],
Erin Peterson [aut]
Maintainer: Jay Ver Hoef <ver.hoef@SpatialStreamNetworks.com>
Diff between SSN versions 1.1.13 dated 2018-05-12 and 1.1.14 dated 2020-02-23
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/BlockPredict.R | 2 +- R/SimulateOnSSN.R | 2 +- R/dataXY.R | 5 ++--- R/getPreds.R | 9 +-------- R/glmssn1.R | 6 ++---- R/m2LL.stream.R | 6 ++---- R/predict.glmssn.R | 2 +- data/mf04.rda |binary data/mf04p.rda |binary data/modelFits.rda |binary man/SpatialStreamNetwork-class.Rd | 2 -- src/RdbfwriteSSN.c | 4 +++- src/dbfopenSSN.c | 37 +++++++++++++++++++++++++++---------- 15 files changed, 58 insertions(+), 53 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.4.2 dated 2019-10-21 and 1.4.3 dated 2020-02-23
DESCRIPTION | 10 MD5 | 132 +++---- R/NPMTest.R | 2 R/adAllPairsTest.R | 2 R/adKSampleTest.R | 10 R/bwsAllPairsTest.R | 4 R/sysdata.rda |binary build/vignette.rds |binary data/Pentosan.rda |binary data/algae.rda |binary data/qPCR.rda |binary data/reviewers.rda |binary data/trout.rda |binary inst/NEWS.Rd | 8 inst/doc/QuickReferenceGuide.html | 700 ++++++++++++++++++++++---------------- man/GSTTest.Rd | 13 man/NPMTest.Rd | 15 man/adAllPairsTest.Rd | 13 man/adKSampleTest.Rd | 8 man/adManyOneTest.Rd | 13 man/bwsAllPairsTest.Rd | 21 - man/bwsKSampleTest.Rd | 3 man/bwsManyOneTest.Rd | 24 - man/bwsTrendTest.Rd | 3 man/chaAllPairsNashimotoTest.Rd | 18 man/cochranTest.Rd | 13 man/cuzickTest.Rd | 23 - man/doubleGrubbsTest.Rd | 3 man/dunnettTest.Rd | 13 man/durbinAllPairsTest.Rd | 3 man/frdAllPairsConoverTest.Rd | 9 man/frdAllPairsExactTest.Rd | 9 man/frdAllPairsNemenyiTest.Rd | 3 man/frdAllPairsSiegelTest.Rd | 9 man/frdManyOneDemsarTest.Rd | 9 man/frdManyOneExactTest.Rd | 3 man/frdManyOneNemenyiTest.Rd | 9 man/friedmanTest.Rd | 3 man/johnsonTest.Rd | 13 man/jonckheereTest.Rd | 21 - man/kruskalTest.Rd | 13 man/kwAllPairsConoverTest.Rd | 18 man/kwAllPairsDunnTest.Rd | 13 man/kwAllPairsNemenyiTest.Rd | 13 man/kwManyOneConoverTest.Rd | 20 - man/kwManyOneDunnTest.Rd | 20 - man/kwManyOneNdwTest.Rd | 20 - man/leTest.Rd | 13 man/mackWolfeTest.Rd | 3 man/manyOneUTest.Rd | 20 - man/normalScoresAllPairsTest.Rd | 18 man/normalScoresManyOneTest.Rd | 18 man/pageTest.Rd | 9 man/powerMCTests.Rd | 34 + man/powerOneWayTests.Rd | 26 - man/quadeAllPairsTest.Rd | 10 man/shirleyWilliamsTest.Rd | 22 - man/siegelTukeyTest.Rd | 9 man/spearmanTest.Rd | 13 man/steelTest.Rd | 13 man/tamhaneDunnettTest.Rd | 13 man/tamhaneT2Test.Rd | 3 man/uryWigginsHochbergTest.Rd | 13 man/vanWaerdenAllPairsTest.Rd | 18 man/vanWaerdenManyOneTest.Rd | 18 man/welchManyOneTTest.Rd | 19 - man/williamsTest.Rd | 13 67 files changed, 987 insertions(+), 577 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>),
Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [aut]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.1.6 dated 2019-12-19 and 0.1.7 dated 2020-02-23
DESCRIPTION | 18 MD5 | 388 ++++++------ NAMESPACE | 12 NEWS.md | 55 + R/BenchmarkResult.R | 302 +++++---- R/DataBackend.R | 114 +-- R/DataBackendCbind.R | 6 R/DataBackendDataTable.R | 123 ++- R/DataBackendMatrix.R | 263 +++++--- R/DataBackendRbind.R | 6 R/DataBackendRename.R | 1 R/Learner.R | 376 +++++------ R/LearnerClassif.R | 52 - R/LearnerClassifDebug.R | 54 - R/LearnerClassifFeatureless.R | 51 - R/LearnerClassifRpart.R | 61 + R/LearnerRegr.R | 44 - R/LearnerRegrFeatureless.R | 53 - R/LearnerRegrRpart.R | 57 + R/Measure.R | 196 +++--- R/MeasureClassif.R | 35 - R/MeasureClassifCosts.R | 72 -- R/MeasureDebug.R | 33 - R/MeasureElapsedTime.R | 39 - R/MeasureOOBError.R | 21 R/MeasureRegr.R | 35 - R/MeasureSelectedFeatures.R | 25 R/MeasureSimple.R | 33 - R/Prediction.R | 98 +-- R/PredictionClassif.R | 111 +-- R/PredictionRegr.R | 75 +- R/ResampleResult.R | 183 +++-- R/Resampling.R | 137 ++-- R/ResamplingBootstrap.R | 29 R/ResamplingCV.R | 26 R/ResamplingCustom.R | 39 - R/ResamplingHoldout.R | 24 R/ResamplingRepeatedCV.R | 52 - R/ResamplingSubsampling.R | 29 R/Task.R | 516 ++++++++-------- R/TaskClassif.R | 72 -- R/TaskClassif_zoo.R | 5 R/TaskGenerator.R | 64 -- R/TaskGenerator2DNormals.R | 14 R/TaskGeneratorFriedman1.R | 14 R/TaskGeneratorSmiley.R | 14 R/TaskGeneratorXor.R | 14 R/TaskRegr.R | 40 - R/TaskRegr_mtcars.R | 8 R/TaskSupervised.R | 43 - R/Task_mutators.R | 117 --- R/as_data_backend.R | 14 R/assertions.R | 60 - R/benchmark.R | 26 R/benchmark_grid.R | 6 R/default_measures.R | 4 R/deprecated.R | 114 +-- R/helper.R | 22 R/mlr_coercions.R | 8 R/mlr_learners.R | 10 R/mlr_measures.R | 7 R/mlr_reflections.R | 26 R/mlr_resamplings.R | 6 R/mlr_sugar.R | 10 R/mlr_task_generators.R | 6 R/mlr_tasks.R | 9 R/predict.R | 8 R/resample.R | 29 R/worker.R | 105 ++- R/zzz.R | 16 README.md | 14 build/partial.rdb |binary inst/references.bib | 29 inst/testthat/helper_expectations.R | 57 + man/BenchmarkResult.Rd | 422 ++++++++++--- man/DataBackend.Rd | 160 ++--- man/DataBackendDataTable.Rd | 193 +++++- man/DataBackendMatrix.Rd | 190 +++++- man/Learner.Rd | 465 ++++++++++---- man/LearnerClassif.Rd | 140 +++- man/LearnerRegr.Rd | 137 +++- man/Measure.Rd | 279 +++++++- man/MeasureClassif.Rd | 139 +++- man/MeasureRegr.Rd | 139 +++- man/Prediction.Rd | 167 ++++- man/PredictionClassif.Rd | 154 +++- man/PredictionRegr.Rd | 104 ++- man/ResampleResult.Rd | 295 +++++++-- man/Resampling.Rd | 277 ++++++-- man/Task.Rd | 728 +++++++++++++++++------ man/TaskClassif.Rd | 166 +++-- man/TaskGenerator.Rd | 139 +++- man/TaskRegr.Rd | 135 +++- man/TaskSupervised.Rd | 132 +++- man/as_benchmark_result.Rd | 4 man/as_data_backend.Rd | 37 - man/benchmark.Rd | 24 man/benchmark_grid.Rd | 6 man/default_measures.Rd | 2 man/figures/block.svg |only man/figures/logo.svg | 187 ++++- man/mlr3-package.Rd | 31 man/mlr_assertions.Rd | 40 - man/mlr_coercions.Rd | 36 - man/mlr_learners.Rd | 17 man/mlr_learners_classif.debug.Rd | 89 ++ man/mlr_learners_classif.featureless.Rd | 93 ++ man/mlr_learners_classif.rpart.Rd | 95 ++- man/mlr_learners_regr.featureless.Rd | 95 ++- man/mlr_learners_regr.rpart.Rd | 95 ++- man/mlr_measures.Rd | 14 man/mlr_measures_classif.acc.Rd | 7 man/mlr_measures_classif.auc.Rd | 7 man/mlr_measures_classif.bacc.Rd | 7 man/mlr_measures_classif.ce.Rd | 7 man/mlr_measures_classif.costs.Rd | 87 ++ man/mlr_measures_classif.dor.Rd | 7 man/mlr_measures_classif.fbeta.Rd | 7 man/mlr_measures_classif.fdr.Rd | 7 man/mlr_measures_classif.fn.Rd | 7 man/mlr_measures_classif.fnr.Rd | 7 man/mlr_measures_classif.fomr.Rd | 7 man/mlr_measures_classif.fp.Rd | 7 man/mlr_measures_classif.fpr.Rd | 7 man/mlr_measures_classif.logloss.Rd | 7 man/mlr_measures_classif.mcc.Rd | 7 man/mlr_measures_classif.npv.Rd | 7 man/mlr_measures_classif.ppv.Rd | 7 man/mlr_measures_classif.precision.Rd | 7 man/mlr_measures_classif.recall.Rd | 7 man/mlr_measures_classif.sensitivity.Rd | 7 man/mlr_measures_classif.specificity.Rd | 7 man/mlr_measures_classif.tn.Rd | 7 man/mlr_measures_classif.tnr.Rd | 7 man/mlr_measures_classif.tp.Rd | 7 man/mlr_measures_classif.tpr.Rd | 7 man/mlr_measures_debug.Rd | 86 ++ man/mlr_measures_elapsed_time.Rd | 98 ++- man/mlr_measures_oob_error.Rd | 65 +- man/mlr_measures_regr.bias.Rd | 7 man/mlr_measures_regr.ktau.Rd | 7 man/mlr_measures_regr.mae.Rd | 7 man/mlr_measures_regr.mape.Rd | 7 man/mlr_measures_regr.maxae.Rd | 7 man/mlr_measures_regr.medae.Rd | 7 man/mlr_measures_regr.medse.Rd | 7 man/mlr_measures_regr.mse.Rd | 7 man/mlr_measures_regr.msle.Rd | 7 man/mlr_measures_regr.pbias.Rd | 7 man/mlr_measures_regr.rae.Rd | 7 man/mlr_measures_regr.rmse.Rd | 7 man/mlr_measures_regr.rmsle.Rd | 7 man/mlr_measures_regr.rrse.Rd | 7 man/mlr_measures_regr.rse.Rd | 7 man/mlr_measures_regr.rsq.Rd | 7 man/mlr_measures_regr.sae.Rd | 7 man/mlr_measures_regr.smape.Rd | 7 man/mlr_measures_regr.srho.Rd | 7 man/mlr_measures_regr.sse.Rd | 7 man/mlr_measures_selected_features.Rd | 85 ++ man/mlr_reflections.Rd | 26 man/mlr_resamplings.Rd | 14 man/mlr_resamplings_bootstrap.Rd | 90 ++ man/mlr_resamplings_custom.Rd | 111 +++ man/mlr_resamplings_cv.Rd | 88 ++ man/mlr_resamplings_holdout.Rd | 88 ++ man/mlr_resamplings_repeated_cv.Rd | 141 +++- man/mlr_resamplings_subsampling.Rd | 90 ++ man/mlr_sugar.Rd | 10 man/mlr_task_generators.Rd | 12 man/mlr_task_generators_2dnormals.Rd | 58 + man/mlr_task_generators_friedman1.Rd | 58 + man/mlr_task_generators_smiley.Rd | 58 + man/mlr_task_generators_xor.Rd | 58 + man/mlr_tasks.Rd | 20 man/mlr_tasks_boston_housing.Rd | 16 man/mlr_tasks_german_credit.Rd | 16 man/mlr_tasks_iris.Rd | 16 man/mlr_tasks_mtcars.Rd | 17 man/mlr_tasks_pima.Rd | 16 man/mlr_tasks_sonar.Rd | 16 man/mlr_tasks_spam.Rd | 16 man/mlr_tasks_wine.Rd | 16 man/mlr_tasks_zoo.Rd | 17 man/predict.Learner.Rd | 8 man/resample.Rd | 27 tests/testthat/test_DataBackendDataTable.R | 18 tests/testthat/test_DataBackendMatrix.R | 16 tests/testthat/test_Learner.R | 13 tests/testthat/test_Resampling.R | 2 tests/testthat/test_Task.R | 43 + tests/testthat/test_lgr.R |only tests/testthat/test_mlr_measures_classif.costs.R | 9 tests/testthat/test_mlr_task_generators.R | 5 tests/testthat/test_parallel.R | 28 tests/testthat/test_resample.R | 4 196 files changed, 8292 insertions(+), 3939 deletions(-)
Title: Population Genetic Data Analysis Using Genepop
Description: Makes the Genepop software available in R. This software implements a mixture of traditional population genetic methods and some more focused developments: it computes exact tests for Hardy-Weinberg equilibrium, for population differentiation and for genotypic disequilibrium among pairs of loci; it computes estimates of F-statistics, null allele frequencies, allele size-based statistics for microsatellites, etc.; and it performs analyses of isolation by distance from pairwise comparisons of individuals or population samples.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jimmy Lopez [ctb],
Khalid Belkhir [ctb]
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between genepop versions 1.1.4 dated 2019-12-06 and 1.1.7 dated 2020-02-23
DESCRIPTION | 14 MD5 | 46 +-- inst/NEWS.Rd | 7 inst/doc/GenepopS.Rmd | 2 inst/doc/GenepopS.pdf |binary inst/doc/GenepopS.tex | 8 inst/doc/all-menu-options.html | 10 inst/doc/bibliography.html | 10 inst/doc/code-maintenance-credits-contact-etc-.html | 10 inst/doc/copyright.html | 10 inst/doc/evaluating-the-performance-of-inferences-for-isolation-by-distance.html | 10 inst/doc/installing-genepop-and-session-examples.html | 10 inst/doc/introduction.html | 16 - inst/doc/methods.html | 12 inst/doc/sec-settings.html | 10 inst/doc/the-input-file.html | 10 src/F_est.cpp | 2 src/GenepopS.cpp | 11 src/GenepopS.h | 2 src/HW_tests.cpp | 153 +--------- src/genepop.cpp | 10 src/proba.cpp | 102 +++++- tests/testthat/tests_HW.R | 5 tests/testthat/tests_diff.R | 6 24 files changed, 230 insertions(+), 246 deletions(-)
Title: D-Score for Child Development
Description: The D-score is a quantitative measure of child development.
The D-score follows the Rasch model. See Jacobusse, van Buuren and
Verkerk (2006) <doi:10.1002/sim.2351>. The user can convert
milestone scores from 19 assessment instruments into the D-score
and the DAZ (D-score adjusted for age). Several tools assist in
mapping milestone names into the 9-position Global Scale of Early
Development (GSED) convention. Supports calculation of the D-score
using 'dutch' <doi:10.1177/0962280212473300>,
'gcdg' <doi:10.1136/bmjgh-2019-001724> and 'gsed' conversion keys.
The user can calculate DAZ using 'dutch' and 'gcdg' age-conditional
references.
Author: Stef van Buuren [cre, aut],
Iris Eekhout [aut],
Arjan Huizing [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between dscore versions 1.0.0 dated 2020-01-18 and 1.1.0 dated 2020-02-23
DESCRIPTION | 6 ++--- MD5 | 24 +++++++++++------------ NEWS.md | 13 ++++++++++++ R/count_mu.R | 22 +++++++++++---------- R/dscore.R | 40 +++++++++++++++++++-------------------- R/get_age_equivalent.R | 5 +--- README.md | 10 +++++---- inst/doc/start.html | 44 +++++++++++++++++++++---------------------- man/count_mu_dutch.Rd | 9 ++++---- man/count_mu_gcdg.Rd | 9 ++++---- man/dscore.Rd | 19 +++++++++--------- man/get_age_equivalent.Rd | 7 ------ tests/testthat/test-dscore.R | 29 ++++++++++++++++++++-------- 13 files changed, 132 insertions(+), 105 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws.common versions 0.2.5 dated 2020-01-11 and 0.2.6 dated 2020-02-23
DESCRIPTION | 6 - MD5 | 43 ++++----- NAMESPACE | 3 NEWS.md | 6 + R/custom_s3.R | 9 + R/handlers_rest.R | 11 +- R/jsonutil.R | 15 +++ R/populate.R | 12 ++ R/tags.R | 26 +++++ R/xmlutil.R | 11 +- man/new_handlers.Rd | 60 ++++++------ man/new_operation.Rd | 96 ++++++++++---------- man/new_request.Rd | 82 ++++++++--------- man/new_service.Rd | 152 ++++++++++++++++---------------- man/send_request.Rd | 56 +++++------ man/tags.Rd | 119 ++++++++++++------------- tests/testthat/test_custom_s3.R |only tests/testthat/test_handlers_jsonrpc.R | 135 ++++++++++++++++++++++++++++ tests/testthat/test_handlers_query.R | 8 - tests/testthat/test_handlers_restjson.R | 68 +++++++------- tests/testthat/test_handlers_restxml.R | 20 ++++ tests/testthat/test_struct.R | 2 tests/testthat/test_tags.R | 19 +++- 23 files changed, 604 insertions(+), 355 deletions(-)
Title: Palettes Inspired in the TV Show "Game of Thrones"
Description: Implementation of the characteristic palettes from the TV show 'Game of Thrones'.
Author: Alejandro Jimenez Rico [aut, cre]
Maintainer: Alejandro Jimenez Rico <aljrico@gmail.com>
Diff between gameofthrones versions 1.0.0 dated 2018-12-30 and 1.0.2 dated 2020-02-23
DESCRIPTION | 10 LICENSE | 4 MD5 | 20 + NAMESPACE | 24 +- R/colors.R |only R/got_palette.R | 562 +++++++++++++++++++++++++------------------------- R/sysdata.rda |binary data/got.map.rda |binary data/got_palettes.rda |only man/figures/logo.png |only man/got.Rd | 26 +- man/got_palettes.Rd |only man/scale_got.Rd | 66 ++++- 13 files changed, 384 insertions(+), 328 deletions(-)
Title: Response Probability Functions
Description: The purpose of this package is to factor out logic
and math common to Item Factor Analysis fitting, diagnostics, and
analysis. It is envisioned as core support code suitable for more
specialized IRT packages to build upon. Complete access to optimized C
functions are made available with R_RegisterCCallable().
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb],
Michael D. Hunter [ctb],
Carl F. Falk [ctb]
Maintainer: Joshua Pritikin <jpritikin@pobox.com>
Diff between rpf versions 1.0.2 dated 2020-02-19 and 1.0.3 dated 2020-02-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/rpf.pdf |binary inst/doc/diagnostics.html | 44 ++++++++++++++++++++++---------------------- src/Makevars | 4 ++-- src/ba81quad.cpp | 8 +++++--- src/diagnose.cpp | 11 +++-------- tools/rox | 2 +- 8 files changed, 44 insertions(+), 47 deletions(-)
Title: Estimate Permutation p-Values for Random Forest Importance
Metrics
Description: Estimate significance of importance metrics
for a Random Forest model by permuting the response
variable. Produces null distribution of importance
metrics for each predictor variable and p-value of
observed. Provides summary and visualization functions for 'randomForest'
results.
Author: Eric Archer [aut, cre]
Maintainer: Eric Archer <eric.archer@noaa.gov>
Diff between rfPermute versions 2.1.7 dated 2019-04-22 and 2.1.81 dated 2020-02-23
DESCRIPTION | 12 ++++++------ MD5 | 34 ++++++++++++++++++---------------- NAMESPACE | 6 +----- R/casePredictions.R |only R/impHeatmap.R | 12 +++++++----- R/internals.R | 7 ++++++- R/pctCorrect.R | 19 +++++++++++-------- R/plotNull.R | 23 ++++++++--------------- R/plotVotes.R | 16 ++++++++++++---- R/rfPermute.default.R | 28 +++++++++++----------------- R/rfPermute.formula.R | 2 +- README.md | 11 +++++++++-- man/casePredictions.Rd |only man/impHeatmap.Rd | 12 ++++++++++-- man/plot.rp.importance.Rd | 11 +++++++++-- man/plotNull.Rd | 10 ++++++++-- man/plotVotes.Rd | 8 ++++++-- man/proximityPlot.Rd | 14 +++++++++++--- man/rfPermute.Rd | 5 ++--- 19 files changed, 136 insertions(+), 94 deletions(-)
Title: Easy Calculation and Visualisation of Confidence Intervals
Description: Functions to speed up the exploratory analysis of simple
datasets using 'dplyr'. Functions are provided to do the
common tasks of calculating confidence intervals.
Author: Conor Neilson [aut, cre]
Maintainer: Conor Neilson <condwanaland@gmail.com>
Diff between summariser versions 0.1.0 dated 2017-03-23 and 2.0.0 dated 2020-02-23
summariser-0.1.0/summariser/R/summariser.R |only summariser-0.1.0/summariser/R/summary_plot.R |only summariser-0.1.0/summariser/R/summary_stats.t.R |only summariser-0.1.0/summariser/inst/CITATION |only summariser-0.1.0/summariser/man/summariser.Rd |only summariser-0.1.0/summariser/man/summary_plot.Rd |only summariser-0.1.0/summariser/man/summary_stats.t.Rd |only summariser-2.0.0/summariser/DESCRIPTION | 17 +++----- summariser-2.0.0/summariser/MD5 | 27 +++++++----- summariser-2.0.0/summariser/NAMESPACE | 8 --- summariser-2.0.0/summariser/NEWS.md |only summariser-2.0.0/summariser/R/stderr.R |only summariser-2.0.0/summariser/R/summary-impl.R |only summariser-2.0.0/summariser/R/summary_stats.R | 44 +++++++++++---------- summariser-2.0.0/summariser/inst/extdata |only summariser-2.0.0/summariser/man/summary_stats.Rd | 14 +++--- summariser-2.0.0/summariser/tests |only 17 files changed, 58 insertions(+), 52 deletions(-)
Title: Unconstrained Optimization using the Subplex Algorithm
Description: The subplex algorithm for unconstrained optimization, developed by Tom Rowan <http://www.netlib.org/opt/subplex.tgz>.
Author: Aaron A. King [aut, trl, cre],
Tom Rowan [aut]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between subplex versions 1.5-4 dated 2018-04-05 and 1.6 dated 2020-02-23
DESCRIPTION | 11 ++-- MD5 | 17 +++---- NAMESPACE | 4 + R/subplex-package.R |only R/subplex.R | 88 ++++++++++++++++++++++++++++++++++-- man/subplex-package.Rd | 46 +++++++++++------- man/subplex.Rd | 119 +++++++++++++++++++++---------------------------- src/subplx.f | 6 +- tests/ripple.Rout.save | 4 - tests/rosen.Rout.save | 4 - 10 files changed, 188 insertions(+), 111 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Tilman Davies;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Brown;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
L. Cobo Sanchez;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
H. Heydarian;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
N. Luambua;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
A. Mollie;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
T. Pollington;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
J. Sulavik;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
L. Yates;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.63-0 dated 2020-01-23 and 1.63-2 dated 2020-02-23
DESCRIPTION | 12 +-- MD5 | 165 ++++++++++++++++++++++---------------------- NAMESPACE | 4 + NEWS | 98 +++++++++++++++++++++++++- R/GJfox.R | 12 +-- R/Hest.R | 13 ++- R/Kest.R | 6 - R/anova.mppm.R | 9 +- R/anova.ppm.R | 9 +- R/blur.R | 102 ++++++++++++++++++++------- R/bugtable.R | 12 ++- R/close3Dpairs.R | 12 ++- R/evalcovar.R | 67 ++++++++++------- R/intensity.R | 19 ----- R/interact.R | 6 - R/leverage.R | 15 +++- R/linim.R | 27 ++++++- R/lixellate.R | 11 ++ R/lppm.R | 2 R/markcorr.R | 95 ++++++++++++++----------- R/model.depends.R | 32 ++++++++ R/nndistlpp.R | 125 ++++++++++++++++++--------------- R/options.R | 2 R/ord.R | 3 R/parres.R | 124 +++++++++++++-------------------- R/plot.im.R | 31 ++++++-- R/plot.owin.R | 5 - R/pointweights.R |only R/randomlpp.R | 11 ++ R/rhohat.R | 80 ++++++++++++--------- R/sdr.R | 11 +- R/smooth.ppp.R | 66 +++++++++-------- R/uniquemap.R | 5 - R/util.R | 9 +- R/vcov.ppm.R | 8 +- R/wingeom.R | 6 - inst/doc/Nickname.txt | 3 inst/doc/bugfixes.R | 22 ++++- inst/doc/bugfixes.Rnw | 67 ++++++++++------- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 24 +++++- inst/doc/updates.pdf |binary man/Gfox.Rd | 10 ++ man/Smooth.ppp.Rd | 5 - man/as.owin.Rd | 11 +- man/blur.Rd | 1 man/bugfixes.Rd | 13 ++- man/is.linim.Rd |only man/linearKcross.Rd | 2 man/linearKcross.inhom.Rd | 2 man/linearKdot.Rd | 2 man/linearKdot.inhom.Rd | 2 man/linearmarkconnect.Rd | 4 - man/linearmarkequal.Rd | 14 +-- man/linearpcfcross.Rd | 2 man/linearpcfcross.inhom.Rd | 2 man/linearpcfdot.Rd | 2 man/linearpcfdot.inhom.Rd | 2 man/markconnect.Rd | 13 ++- man/markcorr.Rd | 9 +- man/markvario.Rd | 3 man/nearestValue.Rd |only man/plot.im.Rd | 10 +- man/plot.linim.Rd | 28 ++++++- man/plot.owin.Rd | 28 +++++-- man/requireversion.Rd | 10 ++ man/rmh.default.Rd | 11 ++ man/spatstat-internal.Rd | 6 + src/lookup.c | 6 + tests/testsAtoC.R | 8 +- tests/testsD.R | 16 ++++ tests/testsGtoJ.R | 17 +++- tests/testsL.R | 44 +++++++++++ tests/testsNtoO.R | 3 tests/testsP2.R | 14 ++- tests/testsS.R | 16 +++- tests/testsT.R | 24 +++++- tests/testsUtoZ.R | 34 ++++++++- vignettes/bugfixes.Rnw | 67 ++++++++++------- vignettes/updates.Rnw | 24 +++++- 85 files changed, 1200 insertions(+), 597 deletions(-)
Title: Sliding Window Functions
Description: Provides type-stable rolling window functions over
any R data type. Cumulative and expanding windows are also supported.
For more advanced usage, an index can be used as a secondary vector
that defines how sliding windows are to be created.
Author: Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between slider versions 0.1.0 dated 2020-02-06 and 0.1.1 dated 2020-02-23
DESCRIPTION | 6 +++--- MD5 | 7 ++++--- NEWS.md |only inst/doc/rowwise.html | 10 ++-------- src/slider-vctrs.h | 12 ++++++------ 5 files changed, 15 insertions(+), 20 deletions(-)
Title: Estimators of Non-Linear Cross-Validated Risks Optimized for
Small Samples
Description: Methods for obtaining improved estimates of non-linear cross-validated risks are obtained using targeted minimum loss-based estimation, estimating equations, and one-step estimation (Benkeser, Petersen, van der Laan (2019), <doi:10.1080/01621459.2019.1668794>). Cross-validated area under the receiver operating characteristics curve (LeDell, Petersen, van der Laan (2015), <doi:10.1214/15-EJS1035>) and other metrics are included.
Author: David Benkeser [aut, cre]
Maintainer: David Benkeser <benkeser@emory.edu>
Diff between nlpred versions 1.0.0 dated 2019-09-27 and 1.0.1 dated 2020-02-23
DESCRIPTION | 10 - MD5 | 56 +++---- NEWS.md | 4 R/wrapper_functions.R | 8 - README.md | 56 +++++-- build/vignette.rds |binary inst/doc/using_nlpred.html | 213 ++++++++++++++---------------- man/F_nBn_star_nested_cv.Rd | 9 - man/adult.Rd | 34 ++-- man/bank.Rd | 12 - man/boot_auc.Rd | 3 man/boot_scrnp.Rd | 11 + man/cardio.Rd | 44 +++--- man/ci.cvAUC_withIC.Rd | 9 - man/cv_auc.Rd | 18 +- man/cv_scrnp.Rd | 19 ++ man/dot-get_density.Rd | 15 +- man/dot-get_predictions.Rd | 12 + man/dot-get_psi_distribution_nested_cv.Rd | 3 man/dot-make_long_data.Rd | 10 + man/dot-make_long_data_nested_cv.Rd | 12 + man/dot-make_targeting_data.Rd | 11 + man/dot-process_input.Rd | 10 + man/glmnet_wrapper.Rd | 14 + man/lpo_auc.Rd | 3 man/randomforest_wrapper.Rd | 13 + man/ranger_wrapper.Rd | 19 +- man/wine.Rd | 32 ++-- man/xgboost_wrapper.Rd | 15 +- 29 files changed, 400 insertions(+), 275 deletions(-)
Title: Multigroup Data Analysis
Description: Multivariate analysis methods including principal component analysis,
partial least square regression, and multiblock analysis to describe,
summarize, and visualize data with a group structure.
Author: Aida Eslami, El Mostafa Qannari, Stephanie Bougeard, Gaston Sanchez
Questions and comments go to Aida Eslami <aida.eslami@yahoo.fr> and
Stephanie Bougeard <stephanie.bougeard@anses.fr>
Maintainer: Aida Eslami <aida.eslami@yahoo.fr>
Diff between multigroup versions 0.4.4 dated 2015-03-11 and 0.4.5 dated 2020-02-23
DESCRIPTION | 16 MD5 | 86 ++-- NAMESPACE | 25 - R/BGC.R | 347 +++++++++-------- R/DCCSWA.R | 462 +++++++++++------------ R/DGPA.R | 420 ++++++++++----------- R/DSTATIS.R | 326 ++++++++-------- R/FCPCA.R | 366 +++++++++--------- R/TBWvariance.R | 187 ++++----- R/loadingsplot.R | 137 +++---- R/mbmgPCA.R | 830 +++++++++++++++++++++--------------------- R/mgPCA.R | 608 +++++++++++++++---------------- R/mgPLS.R | 871 +++++++++++++++++++++------------------------ R/normM.R | 36 - R/plot.mg.R | 119 +++--- R/scoreplot.R | 111 ++--- R/summarize.R | 198 +++++----- R/transfer_Group.R | 97 ++--- man/BGC.Rd | 131 +++--- man/DCCSWA.Rd | 119 +++--- man/DGPA.Rd | 121 +++--- man/DSTATIS.Rd | 127 +++--- man/FCPCA.Rd | 111 ++--- man/TBWvariance.Rd | 85 ++-- man/Trace.Rd | 29 - man/deflation.Rd | 39 -- man/iteraite_fun_Iter.Rd | 35 - man/loadingsplot.Rd | 64 +-- man/loadingsplotXY.Rd | 81 ++-- man/mbmgPCA.Rd | 192 +++++---- man/mgPCA.Rd | 191 ++++----- man/mgPLS.Rd | 206 +++++----- man/multigroup.Rd | 57 +- man/normM.Rd | 35 - man/normv.Rd | 35 - man/plot.mg.Rd | 51 +- man/prepare_data.Rd | 47 +- man/project.Rd | 29 - man/scoreplot.Rd | 59 +-- man/select_initial_Iter.Rd | 51 +- man/similarity_function.Rd | 29 - man/similarity_noncum.Rd | 29 - man/summarize.Rd | 73 +-- man/transfer_Group.Rd | 51 +- 44 files changed, 3662 insertions(+), 3657 deletions(-)
Title: Path Algorithm for the General Fused Lasso Signal Approximator
Description: Implements a path algorithm for the Fused Lasso Signal Approximator.
For more details see the help files or the article by Hoefling (2009) <arXiv:0910.0526>.
Author: Holger Hoefling
Maintainer: Holger Hoefling <hhoeflin@gmail.com>
Diff between flsa versions 1.5.1 dated 2019-03-13 and 1.5.2 dated 2020-02-23
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS | 7 +++---- src/FLSA.cc | 10 +++++----- src/FLSAGeneral.cc | 12 ++++++------ src/FLSAGeneralMain.cc | 4 ++-- src/GeneralFunctions.h | 2 +- src/MaxFlowGraph.cc | 2 +- src/MaxFlowGraph.h | 2 +- src/PenaltyGraph.cc | 6 +++--- src/flsaBackwards.cc | 4 ++-- src/flsa_init.cc | 2 +- src/helperFuncsSEXP.cc | 2 +- src/helperFuncsSEXP.h | 2 +- 14 files changed, 44 insertions(+), 45 deletions(-)
Title: Global Optimization by Differential Evolution
Description: Implements the differential evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector.
Author: David Ardia [aut],
Katharine Mullen [aut, cre],
Brian Peterson [aut],
Joshua Ulrich [aut],
Kris Boudt [ctb]
Maintainer: Katharine Mullen <mullenkate@gmail.com>
Diff between DEoptim versions 2.2-4 dated 2016-12-19 and 2.2-5 dated 2020-02-23
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NAMESPACE | 2 +- NEWS | 10 ++++++++++ build/vignette.rds |binary inst/doc/DEoptim.pdf |binary inst/doc/DEoptimPortfolioOptimization.pdf |binary src/DEoptim_init.c |only src/de4_0.c | 20 +++++--------------- src/evaluate.c | 2 +- 10 files changed, 29 insertions(+), 28 deletions(-)
Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models
using 'Stan' for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, count data, survival, response times, ordinal,
zero-inflated, hurdle, and even self-defined mixture models all in a
multilevel context. Further modeling options include non-linear and
smooth terms, auto-correlation structures, censored data, meta-analytic
standard errors, and quite a few more. In addition, all parameters of the
response distribution can be predicted in order to perform distributional
regression. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
Model fit can easily be assessed and compared with posterior predictive
checks and leave-one-out cross-validation. References: Bürkner (2017)
<doi:10.18637/jss.v080.i01>; Bürkner (2018) <doi:10.32614/RJ-2018-017>;
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 2.11.1 dated 2020-01-19 and 2.12.0 dated 2020-02-23
brms-2.11.1/brms/inst/chunks/fun_normal_cov.stan |only brms-2.11.1/brms/inst/chunks/fun_scale_cov_err.stan |only brms-2.11.1/brms/inst/chunks/fun_student_t_cov.stan |only brms-2.12.0/brms/DESCRIPTION | 8 brms-2.12.0/brms/MD5 | 211 brms-2.12.0/brms/NAMESPACE | 38 brms-2.12.0/brms/NEWS.md | 3786 ++++++------ brms-2.12.0/brms/R/autocor.R | 326 - brms-2.12.0/brms/R/brm.R | 984 +-- brms-2.12.0/brms/R/brm_multiple.R | 4 brms-2.12.0/brms/R/brmsfit-class.R | 15 brms-2.12.0/brms/R/brmsfit-helpers.R | 1400 ++-- brms-2.12.0/brms/R/brmsfit-methods.R | 33 brms-2.12.0/brms/R/brmsformula.R | 3208 +++++----- brms-2.12.0/brms/R/brmsterms.R | 297 - brms-2.12.0/brms/R/conditional_effects.R | 2390 ++++---- brms-2.12.0/brms/R/conditional_smooths.R | 6 brms-2.12.0/brms/R/data-helpers.R | 209 brms-2.12.0/brms/R/data-predictor.R | 1860 +++--- brms-2.12.0/brms/R/data-response.R | 1164 ++- brms-2.12.0/brms/R/distributions.R | 4150 +++++++------- brms-2.12.0/brms/R/exclude_pars.R | 228 brms-2.12.0/brms/R/exclude_terms.R |only brms-2.12.0/brms/R/extract_draws.R | 2362 +++---- brms-2.12.0/brms/R/families.R | 3331 +++++------ brms-2.12.0/brms/R/formula-ac.R |only brms-2.12.0/brms/R/formula-ad.R | 3 brms-2.12.0/brms/R/formula-gp.R | 4 brms-2.12.0/brms/R/formula-re.R | 1454 ++-- brms-2.12.0/brms/R/formula-sp.R | 1029 +-- brms-2.12.0/brms/R/hypothesis.R | 1101 +-- brms-2.12.0/brms/R/kfold.R | 6 brms-2.12.0/brms/R/log_lik.R | 1830 +++--- brms-2.12.0/brms/R/loo.R | 10 brms-2.12.0/brms/R/make_stancode.R | 476 - brms-2.12.0/brms/R/make_standata.R | 36 brms-2.12.0/brms/R/misc.R | 35 brms-2.12.0/brms/R/posterior_predict.R | 1914 +++--- brms-2.12.0/brms/R/pp_check.R | 2 brms-2.12.0/brms/R/pp_expect.R | 1554 ++--- brms-2.12.0/brms/R/predictive_error.R | 314 - brms-2.12.0/brms/R/predictor.R | 1008 +-- brms-2.12.0/brms/R/priors.R | 3809 ++++++------ brms-2.12.0/brms/R/rename_pars.R | 2 brms-2.12.0/brms/R/restructure.R | 1290 ++-- brms-2.12.0/brms/R/stan-helpers.R | 36 brms-2.12.0/brms/R/stan-likelihood.R | 42 brms-2.12.0/brms/R/stan-predictor.R | 4005 ++++++------- brms-2.12.0/brms/R/stan-prior.R | 955 +-- brms-2.12.0/brms/R/stan-response.R | 1071 +-- brms-2.12.0/brms/R/stanvars.R | 12 brms-2.12.0/brms/R/summary.R | 1087 +-- brms-2.12.0/brms/R/sysdata.rda |binary brms-2.12.0/brms/R/update.R | 13 brms-2.12.0/brms/build/vignette.rds |binary brms-2.12.0/brms/inst/chunks/fun_normal_fcor.stan |only brms-2.12.0/brms/inst/chunks/fun_normal_time.stan |only brms-2.12.0/brms/inst/chunks/fun_scale_time_err.stan |only brms-2.12.0/brms/inst/chunks/fun_student_t_fcor.stan |only brms-2.12.0/brms/inst/chunks/fun_student_t_time.stan |only brms-2.12.0/brms/inst/doc/brms_customfamilies.html | 68 brms-2.12.0/brms/inst/doc/brms_distreg.html | 98 brms-2.12.0/brms/inst/doc/brms_families.html | 12 brms-2.12.0/brms/inst/doc/brms_missings.html | 56 brms-2.12.0/brms/inst/doc/brms_monotonic.html | 134 brms-2.12.0/brms/inst/doc/brms_multilevel.pdf |binary brms-2.12.0/brms/inst/doc/brms_multivariate.html | 182 brms-2.12.0/brms/inst/doc/brms_nonlinear.Rmd | 650 +- brms-2.12.0/brms/inst/doc/brms_nonlinear.html | 98 brms-2.12.0/brms/inst/doc/brms_overview.pdf |binary brms-2.12.0/brms/inst/doc/brms_phylogenetics.html | 106 brms-2.12.0/brms/man/addition-terms.Rd | 5 brms-2.12.0/brms/man/ar.Rd |only brms-2.12.0/brms/man/arma.Rd |only brms-2.12.0/brms/man/autocor-terms.Rd |only brms-2.12.0/brms/man/autocor.brmsfit.Rd | 52 brms-2.12.0/brms/man/brm.Rd | 823 +- brms-2.12.0/brms/man/brm_multiple.Rd | 349 - brms-2.12.0/brms/man/brmsfit-class.Rd | 133 brms-2.12.0/brms/man/brmsformula-helpers.Rd | 47 brms-2.12.0/brms/man/brmsformula.Rd | 97 brms-2.12.0/brms/man/car.Rd |only brms-2.12.0/brms/man/cor_ar.Rd | 103 brms-2.12.0/brms/man/cor_arma.Rd | 105 brms-2.12.0/brms/man/cor_brms.Rd | 58 brms-2.12.0/brms/man/cor_car.Rd | 147 brms-2.12.0/brms/man/cor_cosy.Rd | 65 brms-2.12.0/brms/man/cor_fixed.Rd | 59 brms-2.12.0/brms/man/cor_ma.Rd | 93 brms-2.12.0/brms/man/cor_sar.Rd | 119 brms-2.12.0/brms/man/cosy.Rd |only brms-2.12.0/brms/man/extract_draws.Rd | 220 brms-2.12.0/brms/man/fcor.Rd |only brms-2.12.0/brms/man/get_prior.Rd | 12 brms-2.12.0/brms/man/gp.Rd | 280 brms-2.12.0/brms/man/ma.Rd |only brms-2.12.0/brms/man/make_stancode.Rd | 12 brms-2.12.0/brms/man/make_standata.Rd | 227 brms-2.12.0/brms/man/parse_bf.Rd | 12 brms-2.12.0/brms/man/posterior_linpred.brmsfit.Rd | 13 brms-2.12.0/brms/man/sar.Rd |only brms-2.12.0/brms/man/set_prior.Rd | 72 brms-2.12.0/brms/man/standata.brmsfit.Rd | 112 brms-2.12.0/brms/tests/testthat/tests.brm.R | 12 brms-2.12.0/brms/tests/testthat/tests.brmsfit-methods.R | 1795 +++--- brms-2.12.0/brms/tests/testthat/tests.brmsterms.R | 43 brms-2.12.0/brms/tests/testthat/tests.data-helpers.R | 6 brms-2.12.0/brms/tests/testthat/tests.exclude_pars.R |only brms-2.12.0/brms/tests/testthat/tests.families.R | 2 brms-2.12.0/brms/tests/testthat/tests.log_lik.R | 969 +-- brms-2.12.0/brms/tests/testthat/tests.make_stancode.R | 3973 ++++++------- brms-2.12.0/brms/tests/testthat/tests.make_standata.R | 1793 +++--- brms-2.12.0/brms/tests/testthat/tests.posterior_predict.R | 29 brms-2.12.0/brms/tests/testthat/tests.pp_expect.R | 366 - brms-2.12.0/brms/tests/testthat/tests.priors.R | 6 brms-2.12.0/brms/vignettes/brms_nonlinear.Rmd | 650 +- 116 files changed, 32097 insertions(+), 31274 deletions(-)
Title: Syllable Counting and Readability Measurements
Description: An English language syllable counter, plus readability score
measure-er. For readability, we support 'Flesch' Reading Ease and
'Flesch-Kincaid' Grade Level ('Kincaid' 'et al'. 1975)
<https://stars.library.ucf.edu/cgi/viewcontent.cgi?article=1055&context=istlibrary>,
Automated Readability Index ('Senter' and Smith 1967)
<http://www.dtic.mil/cgi-bin/GetTRDoc?AD=AD0667273>,
Simple Measure of Gobbledygook (McLaughlin 1969)
<https://www.semanticscholar.org/paper/SMOG-Grading-A-New-Readability-Formula.-Laughlin/5fccb74c14769762b3de010c5e8a1a7ce700d17a>,
and 'Coleman-Liau' (Coleman and 'Liau' 1975) <doi:10.1037/h0076540>. The
package has been carefully optimized and should be very efficient, both in
terms of run time performance and memory consumption. The main methods are
'vectorized' by document, and scores for multiple documents are computed in
parallel via 'OpenMP'.
Author: Drew Schmidt [aut, cre]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between sylcount versions 0.2-1 dated 2019-03-12 and 0.2-2 dated 2020-02-23
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/readability.r | 2 +- R/sylcount-package.r | 13 ++++++++----- README.md | 7 +++---- man/readability.Rd | 2 +- man/sylcount-package.Rd | 13 ++++++++----- src/sylcount_native.c | 2 +- 9 files changed, 37 insertions(+), 29 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.6.0 dated 2019-11-28 and 1.7.0 dated 2020-02-23
fakemake-1.6.0/fakemake/man/makelist_targets.Rd |only fakemake-1.7.0/fakemake/DESCRIPTION | 35 +- fakemake-1.7.0/fakemake/LICENSE | 2 fakemake-1.7.0/fakemake/MD5 | 62 ++--- fakemake-1.7.0/fakemake/NEWS.md | 15 + fakemake-1.7.0/fakemake/R/internals.R | 10 fakemake-1.7.0/fakemake/R/main.R | 50 ++-- fakemake-1.7.0/fakemake/R/makelists.R | 65 +++-- fakemake-1.7.0/fakemake/R/package_makelist.R | 1 fakemake-1.7.0/fakemake/R/sink_all.R | 1 fakemake-1.7.0/fakemake/R/tools.R | 9 fakemake-1.7.0/fakemake/build/vignette.rds |binary fakemake-1.7.0/fakemake/inst/doc/An_Introduction_to_fakemake.R | 54 ++-- fakemake-1.7.0/fakemake/inst/doc/An_Introduction_to_fakemake.Rmd | 77 ++++-- fakemake-1.7.0/fakemake/inst/doc/An_Introduction_to_fakemake.html | 122 ++++------ fakemake-1.7.0/fakemake/inst/doc/Building_Packages.R | 34 +- fakemake-1.7.0/fakemake/inst/doc/Building_Packages.Rmd | 15 - fakemake-1.7.0/fakemake/inst/doc/Building_Packages.html | 87 ++++--- fakemake-1.7.0/fakemake/man/add_target.Rd |only fakemake-1.7.0/fakemake/man/check_archive.Rd | 1 fakemake-1.7.0/fakemake/man/check_archive_as_cran.Rd | 1 fakemake-1.7.0/fakemake/man/get_pkg_archive_path.Rd | 3 fakemake-1.7.0/fakemake/man/get_target.Rd |only fakemake-1.7.0/fakemake/man/make.Rd | 19 + fakemake-1.7.0/fakemake/man/provide_make_list.Rd | 4 fakemake-1.7.0/fakemake/man/read_makefile.Rd | 3 fakemake-1.7.0/fakemake/man/remove_target.Rd |only fakemake-1.7.0/fakemake/man/sink_all.Rd | 1 fakemake-1.7.0/fakemake/man/touch.Rd | 1 fakemake-1.7.0/fakemake/man/visualize.Rd | 8 fakemake-1.7.0/fakemake/man/write_makefile.Rd | 3 fakemake-1.7.0/fakemake/tests/runit.R | 84 ++---- fakemake-1.7.0/fakemake/vignettes/An_Introduction_to_fakemake.Rmd | 77 ++++-- fakemake-1.7.0/fakemake/vignettes/Building_Packages.Rmd | 15 - 34 files changed, 514 insertions(+), 345 deletions(-)
Title: Extremely Fast Implementation of a Naive Bayes Classifier
Description: This is an extremely fast implementation of a Naive Bayes classifier. This
package is currently the only package that supports a Bernoulli distribution, a Multinomial
distribution, and a Gaussian distribution, making it suitable for both binary features,
frequency counts, and numerical features. Another feature is the support of a mix of
different event models. Only numerical variables are allowed, however, categorical variables
can be transformed into dummies and used with the Bernoulli distribution.
The implementation is largely based on the paper
"A comparison of event models for Naive Bayes anti-spam e-mail filtering"
written by K.M. Schneider (2003) <doi:10.3115/1067807.1067848>. Any issues can be
submitted to: <https://github.com/mskogholt/fastNaiveBayes/issues>.
Author: Martin Skogholt
Maintainer: Martin Skogholt <m.skogholt@gmail.com>
Diff between fastNaiveBayes versions 2.1.1 dated 2020-02-09 and 2.2.0 dated 2020-02-23
DESCRIPTION | 6 MD5 | 39 ++-- NAMESPACE | 10 + NEWS.md | 11 + R/fnb.bernoulli.R | 183 +++-------------------- R/fnb.check.args.R | 95 +++++++++++ R/fnb.gaussian.R | 144 +++--------------- R/fnb.multinomial.R | 173 +++------------------ R/fnb.poisson.R |only R/fnb.train.R | 172 +++++---------------- R/fnb.update.R |only R/fnb.utils.R |only inst/doc/fastnaivebayes.html | 4 man/fastNaiveBayesF.Rd | 9 + man/predict.fastNaiveBayes.Rd | 7 man/updateFNB.Rd |only tests/testthat/test-fastnaivebayes_bernoulli.R | 7 tests/testthat/test-fastnaivebayes_checkargs.R | 153 +++++++++---------- tests/testthat/test-fastnaivebayes_gaussian.R | 8 - tests/testthat/test-fastnaivebayes_multinomial.R | 26 +-- tests/testthat/test-fastnaivebayes_poisson.R |only tests/testthat/test-fastnaivebayes_train.R | 21 ++ tests/testthat/test-fastnaivebayes_utils.R |only tests/testthat/test-fnb.update.R |only 24 files changed, 401 insertions(+), 667 deletions(-)
More information about fastNaiveBayes at CRAN
Permanent link
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods, like those defined by Leclercq et al. (2013)
<doi:10.1111/j.1469-0691.2011.03703.x> and the Clinical and Laboratory
Standards Institute (2014) <isbn: 1-56238-899-1>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>),
Alexander W. Friedrich [aut, ths]
(<https://orcid.org/0000-0003-4881-038X>),
Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>),
Casper J. Albers [aut, ths] (<https://orcid.org/0000-0002-9213-6743>),
Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>),
Judith M. Fonville [ctb],
Erwin E. A. Hassing [ctb],
Eric H. L. C. M. Hazenberg [ctb],
Annick Lenglet [ctb],
Bart C. Meijer [ctb],
Sofia Ny [ctb],
Dennis Souverein [ctb]
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 1.0.0 dated 2020-02-17 and 1.0.1 dated 2020-02-23
DESCRIPTION | 8 MD5 | 64 ++-- NEWS.md | 16 + R/data.R | 12 R/disk.R | 5 R/eucast_rules.R | 2 R/filter_ab_class.R | 2 R/first_isolate.R | 3 R/mdro.R | 2 R/mic.R | 10 R/misc.R | 18 + R/resistance_predict.R | 2 R/rsi.R | 389 +++++++++++++++++++--------- data/antibiotics.rda |binary data/datalist | 1 data/example_isolates_unclean.rda |only data/rsi_translation.rda |binary inst/doc/AMR.html | 496 +++++++++++++++--------------------- inst/doc/EUCAST.html | 4 inst/doc/MDR.html | 83 ++---- inst/doc/WHONET.html | 4 inst/doc/resistance_predict.html | 31 -- man/as.rsi.Rd | 68 +++- man/eucast_rules.Rd | 2 man/example_isolates_unclean.Rd |only man/filter_ab_class.Rd | 2 man/first_isolate.Rd | 10 man/mdro.Rd | 2 man/resistance_predict.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/test-disk.R | 4 tests/testthat/test-eucast_rules.R | 4 tests/testthat/test-first_isolate.R | 6 tests/testthat/test-rsi.R | 23 + 34 files changed, 725 insertions(+), 552 deletions(-)
Title: Bayesian Modeling and Analysis of Spatially Correlated Survival
Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: proportional hazards (PH), accelerated failure time (AFT), proportional odds (PO), and accelerated hazards (AH), a super model that includes PH, AFT, PO and AH as special cases, Bayesian nonparametric nonproportional hazards (LDDPM), generalized accelerated failure time (GAFT), and spatially smoothed Polya tree density estimation. The spatial dependence is modeled via frailties under PH, AFT, PO, AH and GAFT, and via copulas under LDDPM and PH. Model choice is carried out via the logarithm of the pseudo marginal likelihood (LPML), the deviance information criterion (DIC), and the Watanabe-Akaike information criterion (WAIC). See Zhou, Hanson and Zhang (2020) <doi:10.18637/jss.v092.i09>.
Author: Haiming Zhou <zhouh@niu.edu> and Timothy Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>
Diff between spBayesSurv versions 1.1.3 dated 2018-04-23 and 1.1.4 dated 2020-02-23
spBayesSurv-1.1.3/spBayesSurv/build |only spBayesSurv-1.1.3/spBayesSurv/inst/doc |only spBayesSurv-1.1.3/spBayesSurv/vignettes |only spBayesSurv-1.1.4/spBayesSurv/DESCRIPTION | 12 spBayesSurv-1.1.4/spBayesSurv/MD5 | 64 spBayesSurv-1.1.4/spBayesSurv/R/SpatDensReg.R | 2 spBayesSurv-1.1.4/spBayesSurv/R/SuperSurvRegBayes.R | 4 spBayesSurv-1.1.4/spBayesSurv/R/indeptCoxph.R | 6 spBayesSurv-1.1.4/spBayesSurv/R/spCopulaCoxph.R | 6 spBayesSurv-1.1.4/spBayesSurv/R/spCopulaDDP.R | 2 spBayesSurv-1.1.4/spBayesSurv/R/survregbayes.R | 17 spBayesSurv-1.1.4/spBayesSurv/R/survregbayes2.R | 12 spBayesSurv-1.1.4/spBayesSurv/inst/CITATION | 33 spBayesSurv-1.1.4/spBayesSurv/man/SpatDensReg.Rd | 358 ++--- spBayesSurv-1.1.4/spBayesSurv/man/SuperSurvRegBayes.Rd | 454 +++--- spBayesSurv-1.1.4/spBayesSurv/man/anovaDDP.Rd | 2 spBayesSurv-1.1.4/spBayesSurv/man/baseline.Rd | 56 spBayesSurv-1.1.4/spBayesSurv/man/cox.snell.survregbayes.Rd | 108 - spBayesSurv-1.1.4/spBayesSurv/man/frailtyGAFT.Rd | 2 spBayesSurv-1.1.4/spBayesSurv/man/indeptCoxph.Rd | 2 spBayesSurv-1.1.4/spBayesSurv/man/spCopulaCoxph.Rd | 2 spBayesSurv-1.1.4/spBayesSurv/man/spCopulaDDP.Rd | 2 spBayesSurv-1.1.4/spBayesSurv/man/survregbayes.Rd | 682 +++++----- spBayesSurv-1.1.4/spBayesSurv/src/spSurv_AFT_BP.cpp | 80 - spBayesSurv-1.1.4/spBayesSurv/src/spSurv_AH_BP.cpp | 58 spBayesSurv-1.1.4/spBayesSurv/src/spSurv_PH_BP.cpp | 58 spBayesSurv-1.1.4/spBayesSurv/src/spSurv_PO_BP.cpp | 58 spBayesSurv-1.1.4/spBayesSurv/src/spSurv_frailty_GRF_LDTFP.cpp | 49 28 files changed, 1080 insertions(+), 1049 deletions(-)
Title: Standard and Nonstandard Statistical Models and Methods for Test
Equating
Description: Contains functions to perform various models and
methods for test equating. It currently implements the traditional
mean, linear and equipercentile equating methods. Both IRT observed-score
and true-score equating are also supported, as well as the mean-mean,
mean-sigma, Haebara and Stocking-Lord IRT linking methods.
It also supports newest methods such that local equating, kernel
equating (using Gaussian, logistic, Epanechnikov, uniform and adaptive
kernels) with presmoothing, and IRT parameter linking methods based on
asymmetric item characteristic functions. Functions to obtain both
standard error of equating (SEE) and standard error of equating differences
between two equating functions (SEED) are also implemented for the kernel method of
equating.
Author: Jorge Gonzalez [cre, aut],
Daniel Leon Acuna [ctb]
Maintainer: Jorge Gonzalez <jorge.gonzalez@mat.uc.cl>
Diff between SNSequate versions 1.3.2 dated 2020-01-23 and 1.3.3 dated 2020-02-23
DESCRIPTION | 10 +++++----- MD5 | 32 +++++++++++++++++--------------- R/SEED.R | 4 ++-- R/bandwidth.R | 4 ++-- R/irt.eq.R | 4 ++-- R/irt.link.R | 4 ++-- build/partial.rdb |binary data/SEPA.rda |only man/BNP.eq.Rd | 1 + man/BNP.eq.predict.Rd | 1 - man/SEED.Rd | 3 +-- man/SEPA.Rd |only man/SNSequate-package.Rd | 4 ++-- man/bandwidth.Rd | 4 +--- man/irt.eq.Rd | 4 +--- man/irt.link.Rd | 4 +--- man/ker.eq.Rd | 2 -- man/loglin.smooth.Rd | 5 +++-- 18 files changed, 40 insertions(+), 46 deletions(-)
Title: Multivariate Methods Based on the Oja Median and Related
Concepts
Description: Functions to calculate the Oja median, Oja signs and ranks and methods based upon them. For details, see the the corresponding publication in the Journal of Statistical Software <doi:10.18637/jss.v092.i08>.
Author: Daniel Fischer, Karl Mosler, Jyrki Möttönen, Klaus Nordhausen, Oleksii Pokotylo, Daniel Vogel
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between OjaNP versions 0.9-13 dated 2020-02-09 and 1.0-0 dated 2020-02-23
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++----------- inst/CITATION |only inst/ChangeLog | 3 +++ man/OjaNP-package.Rd | 4 ++-- man/oja1sampleTest.Rd | 3 +++ man/ojaCsampleTest.Rd | 3 +++ man/ojaMedian.Rd | 3 +++ man/ojaRCM.Rd | 3 +++ man/ojaRank.Rd | 3 +++ man/ojaSCM.Rd | 3 +++ man/ojaSign.Rd | 3 +++ man/ojaSignedRank.Rd | 3 +++ 13 files changed, 46 insertions(+), 18 deletions(-)
Title: Generalized Dynamic Principal Components
Description: Functions to compute the Generalized Dynamic Principal Components
introduced in Peña and Yohai (2016) <DOI:10.1080/01621459.2015.1072542>. The implementation
includes an automatic procedure proposed in Peña, Smucler and Yohai (2020) <DOI:10.18637/jss.v092.c02>
for the identification of both the number of lags to be used
in the generalized dynamic principal components as well as the number of components required
for a given reconstruction accuracy.
Author: Daniel Peña <daniel.pena@uc3m.es>,
Ezequiel Smucler <ezequiels.90@gmail.com>,
Victor Yohai <vyohai@dm.uba.ar>
Maintainer: Ezequiel Smucler <ezequiels.90@gmail.com>
Diff between gdpc versions 1.1.0 dated 2018-05-08 and 1.1.1 dated 2020-02-23
DESCRIPTION | 14 +++++++++----- MD5 | 9 +++++---- NEWS | 6 ++++++ inst |only man/auto.gdpc.Rd | 4 +++- man/gdpc-package.Rd | 2 ++ 6 files changed, 25 insertions(+), 10 deletions(-)
Title: A General Algorithm to Enhance the Performance of Variable
Selection Methods in Correlated Datasets
Description: An implementation of the selectboost algorithm (Bertrand et al. 2020, <arXiv:1810.01670>), which is a general algorithm that improves the precision of any existing variable selection method. This algorithm is based on highly intensive simulations and takes into account the correlation structure of the data. It can either produce a confidence index for variable selection or it can be used in an experimental design planning perspective.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>),
Ismail Aouadi [ctb],
Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between SelectBoost versions 1.4.0 dated 2019-05-27 and 2.0.0 dated 2020-02-23
SelectBoost-1.4.0/SelectBoost/data/net_confidences.RData |only SelectBoost-1.4.0/SelectBoost/demo/autoboost_huntington.R |only SelectBoost-1.4.0/SelectBoost/demo/bysteps_diabetes_quadratic_lasso_and_adaptative_parallel_bootstrap.R |only SelectBoost-1.4.0/SelectBoost/demo/bysteps_huntington.R |only SelectBoost-1.4.0/SelectBoost/demo/bysteps_huntington_community.R |only SelectBoost-1.4.0/SelectBoost/demo/diabetes_first_order_adaptative_lasso.R |only SelectBoost-1.4.0/SelectBoost/demo/diabetes_first_order_lasso.R |only SelectBoost-1.4.0/SelectBoost/demo/diabetes_first_order_lasso_multicores.R |only SelectBoost-1.4.0/SelectBoost/demo/diabetes_quadratic_lasso.R |only SelectBoost-2.0.0/SelectBoost/DESCRIPTION | 16 SelectBoost-2.0.0/SelectBoost/MD5 | 115 SelectBoost-2.0.0/SelectBoost/NAMESPACE | 16 SelectBoost-2.0.0/SelectBoost/NEWS.md | 12 SelectBoost-2.0.0/SelectBoost/R/SelectBoost-package.R | 5 SelectBoost-2.0.0/SelectBoost/R/autoboost.R | 1505 ++++++---- SelectBoost-2.0.0/SelectBoost/R/boost.R | 12 SelectBoost-2.0.0/SelectBoost/R/datasets.R | 14 SelectBoost-2.0.0/SelectBoost/R/group_func_1.R | 2 SelectBoost-2.0.0/SelectBoost/R/group_func_2.R | 2 SelectBoost-2.0.0/SelectBoost/R/lasso_cv.R | 456 ++- SelectBoost-2.0.0/SelectBoost/R/miscplots.R | 4 SelectBoost-2.0.0/SelectBoost/R/plot_selectboost_microarray.R | 2 SelectBoost-2.0.0/SelectBoost/R/selectboost_microarray.R | 2 SelectBoost-2.0.0/SelectBoost/R/simulation.R | 22 SelectBoost-2.0.0/SelectBoost/build/vignette.rds |binary SelectBoost-2.0.0/SelectBoost/data/Cascade_confidence.RData |only SelectBoost-2.0.0/SelectBoost/data/datalist |only SelectBoost-2.0.0/SelectBoost/demo/00Index | 8 SelectBoost-2.0.0/SelectBoost/demo/autoboost_diabetes_first_order.R | 442 +- SelectBoost-2.0.0/SelectBoost/demo/bysteps_diabetes_first_order_lasso_and_adaptative.R | 3 SelectBoost-2.0.0/SelectBoost/demo/bysteps_diabetes_first_order_lasso_and_adaptative_parallel.R | 7 SelectBoost-2.0.0/SelectBoost/demo/bysteps_diabetes_quadratic_lasso_and_adaptative_parallel.R | 7 SelectBoost-2.0.0/SelectBoost/inst/doc/benchmarking-selectboost-networks.R | 763 ----- SelectBoost-2.0.0/SelectBoost/inst/doc/benchmarking-selectboost-networks.Rmd | 2 SelectBoost-2.0.0/SelectBoost/inst/doc/benchmarking-selectboost-networks.html | 15 SelectBoost-2.0.0/SelectBoost/inst/doc/confidence-indices-Cascade-networks.R | 105 SelectBoost-2.0.0/SelectBoost/inst/doc/confidence-indices-Cascade-networks.Rmd | 4 SelectBoost-2.0.0/SelectBoost/inst/doc/confidence-indices-Cascade-networks.html | 61 SelectBoost-2.0.0/SelectBoost/inst/doc/sim-with-sb.R | 421 -- SelectBoost-2.0.0/SelectBoost/inst/doc/sim-with-sb.Rmd | 2 SelectBoost-2.0.0/SelectBoost/inst/doc/sim-with-sb.html | 543 --- SelectBoost-2.0.0/SelectBoost/man/Cascade_confidence.Rd | 3 SelectBoost-2.0.0/SelectBoost/man/Cascade_example.Rd | 3 SelectBoost-2.0.0/SelectBoost/man/SelectBoost.Rd | 3 SelectBoost-2.0.0/SelectBoost/man/auto.analyze.Rd | 7 SelectBoost-2.0.0/SelectBoost/man/autoboost.Rd | 34 SelectBoost-2.0.0/SelectBoost/man/boost.Rd | 60 SelectBoost-2.0.0/SelectBoost/man/fastboost.Rd | 44 SelectBoost-2.0.0/SelectBoost/man/force.non.inc.Rd |only SelectBoost-2.0.0/SelectBoost/man/group_func_1.Rd | 2 SelectBoost-2.0.0/SelectBoost/man/group_func_2.Rd | 2 SelectBoost-2.0.0/SelectBoost/man/miscplot.Rd | 2 SelectBoost-2.0.0/SelectBoost/man/network.confidence-class.Rd | 8 SelectBoost-2.0.0/SelectBoost/man/plot.selectboost.Rd | 16 SelectBoost-2.0.0/SelectBoost/man/plot.summary.selectboost.Rd | 7 SelectBoost-2.0.0/SelectBoost/man/plot_selectboost_cascade.Rd | 13 SelectBoost-2.0.0/SelectBoost/man/selectboost_cascade.Rd | 25 SelectBoost-2.0.0/SelectBoost/man/simulation.Rd | 4 SelectBoost-2.0.0/SelectBoost/man/summary.selectboost.Rd | 19 SelectBoost-2.0.0/SelectBoost/man/trajC0.Rd | 19 SelectBoost-2.0.0/SelectBoost/man/var_select.Rd | 5 SelectBoost-2.0.0/SelectBoost/man/var_select_all.Rd |only SelectBoost-2.0.0/SelectBoost/vignettes/benchmarking-selectboost-networks.Rmd | 2 SelectBoost-2.0.0/SelectBoost/vignettes/confidence-indices-Cascade-networks.Rmd | 4 SelectBoost-2.0.0/SelectBoost/vignettes/sim-with-sb.Rmd | 2 65 files changed, 2043 insertions(+), 2809 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for: 1. multivariate (and univariate) regression, with nonparametric models for the means, the variances and the correlation matrix, with variable selection, and 2. Dirichlet process mixtures.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.1.2 dated 2019-12-05 and 2.1.3 dated 2020-02-23
DESCRIPTION | 12 +-- MD5 | 30 ++++---- NAMESPACE | 3 R/bnpMulti.R | 39 ++++++----- R/plot.R | 175 ++++++++++++++++++++++++++++++++++++++-------------- man/BNSP-package.Rd | 8 +- man/chol.Rd | 8 +- man/clustering.Rd | 2 man/histCorr.Rd | 2 man/mvrm.Rd | 12 +-- man/mvrm2mcmc.Rd | 2 man/plot.mvrm.Rd | 11 +-- man/plotCorr.Rd | 2 man/sm.Rd | 2 man/summary.mvrm.Rd | 2 src/spec.BCM.h | 3 16 files changed, 203 insertions(+), 110 deletions(-)
Title: Non-Invasive Pretty Printing of R Code
Description: Pretty-prints R code without changing the user's
formatting intent.
Author: Kirill Müller [aut],
Lorenz Walthert [cre, aut]
Maintainer: Lorenz Walthert <lorenz.walthert@icloud.com>
Diff between styler versions 1.3.1 dated 2020-02-13 and 1.3.2 dated 2020-02-23
styler-1.3.1/styler/man/ensure_last_is_empty.Rd |only styler-1.3.2/styler/DESCRIPTION | 12 styler-1.3.2/styler/MD5 | 162 ++++---- styler-1.3.2/styler/NEWS.md | 12 styler-1.3.2/styler/R/addins.R | 2 styler-1.3.2/styler/R/io.R | 2 styler-1.3.2/styler/R/nest.R | 71 ++- styler-1.3.2/styler/R/parse.R | 5 styler-1.3.2/styler/R/relevel.R | 2 styler-1.3.2/styler/R/roxygen-examples.R | 18 styler-1.3.2/styler/R/rules-other.R | 5 styler-1.3.2/styler/R/stylerignore.R | 71 ++- styler-1.3.2/styler/R/testing.R | 58 ++ styler-1.3.2/styler/R/token-create.R | 6 styler-1.3.2/styler/R/transform-block.R | 1 styler-1.3.2/styler/R/ui-caching.R | 6 styler-1.3.2/styler/R/utils-cache.R | 19 styler-1.3.2/styler/R/utils-files.R | 2 styler-1.3.2/styler/R/utils.R | 12 styler-1.3.2/styler/README.md | 2 styler-1.3.2/styler/inst/WORDLIST |only styler-1.3.2/styler/inst/doc/customizing_styler.html | 6 styler-1.3.2/styler/inst/doc/introducing_styler.html | 4 styler-1.3.2/styler/man/add_stylerignore.Rd | 5 styler-1.3.2/styler/man/add_token_terminal.Rd | 9 styler-1.3.2/styler/man/apply_stylerignore.Rd | 5 styler-1.3.2/styler/man/cache_by_expression.Rd | 8 styler-1.3.2/styler/man/caching.Rd | 6 styler-1.3.2/styler/man/dir_without_..Rd | 2 styler-1.3.2/styler/man/drop_cached_children.Rd | 4 styler-1.3.2/styler/man/ensure_correct_str_txt.Rd | 4 styler-1.3.2/styler/man/ensure_last_n_empty.Rd |only styler-1.3.2/styler/man/env_add_stylerignore.Rd | 8 styler-1.3.2/styler/man/find_blank_lines_to_next_block.Rd | 1 styler-1.3.2/styler/man/find_block_id.Rd | 2 styler-1.3.2/styler/man/find_pos_id_to_keep.Rd | 24 - styler-1.3.2/styler/man/n_times_faster_with_cache.Rd |only styler-1.3.2/styler/man/read_utf8.Rd | 2 styler-1.3.2/styler/man/style_roxygen_code_example.Rd | 2 styler-1.3.2/styler/man/stylerignore_consolidate_col.Rd | 10 styler-1.3.2/styler/man/text_to_flat_pd.Rd |only styler-1.3.2/styler/man/tokenize.Rd | 2 styler-1.3.2/styler/tests/testthat/cache-with-r-cache/roxygen-cache-1.R |only styler-1.3.2/styler/tests/testthat/helpers-devel-options.R | 2 styler-1.3.2/styler/tests/testthat/stylerignore/adding-removing-in.R |only styler-1.3.2/styler/tests/testthat/stylerignore/adding-removing-in_tree |only styler-1.3.2/styler/tests/testthat/stylerignore/adding-removing-out.R |only styler-1.3.2/styler/tests/testthat/stylerignore/braces-in.R |only styler-1.3.2/styler/tests/testthat/stylerignore/braces-in_tree |only styler-1.3.2/styler/tests/testthat/stylerignore/braces-out.R |only styler-1.3.2/styler/tests/testthat/stylerignore/crossing-with-expressions-in.R |only styler-1.3.2/styler/tests/testthat/stylerignore/crossing-with-expressions-in_tree |only styler-1.3.2/styler/tests/testthat/stylerignore/crossing-with-expressions-out.R |only styler-1.3.2/styler/tests/testthat/test-cache-high-level-api.R | 195 +++++----- styler-1.3.2/styler/tests/testthat/test-cache-interaction-roxygen-code-examples.R |only styler-1.3.2/styler/tests/testthat/test-cache-low-level-api.R | 25 - styler-1.3.2/styler/tests/testthat/test-cache-with-r-cache.R | 54 +- styler-1.3.2/styler/tests/testthat/test-create_token.R | 3 styler-1.3.2/styler/tests/testthat/test-create_tree.R | 4 styler-1.3.2/styler/tests/testthat/test-fun_dec.R | 6 styler-1.3.2/styler/tests/testthat/test-identify-roxygen-examples.R | 2 styler-1.3.2/styler/tests/testthat/test-indention_curly.R | 35 - styler-1.3.2/styler/tests/testthat/test-indention_fun_calls.R | 3 styler-1.3.2/styler/tests/testthat/test-indention_multiple.R | 48 +- styler-1.3.2/styler/tests/testthat/test-indention_operators.R | 136 ++++-- styler-1.3.2/styler/tests/testthat/test-indention_round_brackets.R | 22 - styler-1.3.2/styler/tests/testthat/test-insertion_comment_interaction.R | 20 - styler-1.3.2/styler/tests/testthat/test-interaction-caching-comments.R |only styler-1.3.2/styler/tests/testthat/test-interaction-caching-stylerignore.R |only styler-1.3.2/styler/tests/testthat/test-line_breaks_and_other.R | 24 - styler-1.3.2/styler/tests/testthat/test-line_breaks_fun_call.R | 37 + styler-1.3.2/styler/tests/testthat/test-math_token_spacing.R | 11 styler-1.3.2/styler/tests/testthat/test-multiple_expressions.R | 10 styler-1.3.2/styler/tests/testthat/test-parse_comments.R | 64 +-- styler-1.3.2/styler/tests/testthat/test-parsing.R | 13 styler-1.3.2/styler/tests/testthat/test-public_api.R | 20 - styler-1.3.2/styler/tests/testthat/test-relocate_eq_assign.R | 17 styler-1.3.2/styler/tests/testthat/test-roxygen-examples-complete.R | 2 styler-1.3.2/styler/tests/testthat/test-scope_argument.R | 17 styler-1.3.2/styler/tests/testthat/test-serialize_tests.R | 23 - styler-1.3.2/styler/tests/testthat/test-spacing.R | 35 + styler-1.3.2/styler/tests/testthat/test-square_brackets.R | 4 styler-1.3.2/styler/tests/testthat/test-start_line.R | 3 styler-1.3.2/styler/tests/testthat/test-strict.R | 12 styler-1.3.2/styler/tests/testthat/test-stylerignore.R | 20 - styler-1.3.2/styler/tests/testthat/test-tidyeval.R | 9 styler-1.3.2/styler/tests/testthat/test-token_adding_removing.R | 22 - styler-1.3.2/styler/tests/testthat/test-unary.R | 15 styler-1.3.2/styler/tests/testthat/test-unindention.R | 28 - styler-1.3.2/styler/tests/testthat/test-unindention_regex.R | 25 - styler-1.3.2/styler/tests/testthat/test-varia.R | 10 91 files changed, 963 insertions(+), 585 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install packages
as they existed on CRAN on a specific snapshot date as if you had a CRAN time
machine. To achieve reproducibility, the checkpoint() function installs the
packages required or called by your project and scripts to a local library
exactly as they existed at the specified point in time. Only those packages
are available to your project, thereby avoiding any package updates that came
later and may have altered your results. In this way, anyone using checkpoint's
checkpoint() can ensure the reproducibility of your scripts or projects at any
time. To create the snapshot archives, once a day (at midnight UTC) Microsoft
refreshes the Austria CRAN mirror on the "Microsoft R Archived Network"
server (<https://mran.microsoft.com/>). Immediately after completion
of the rsync mirror process, the process takes a snapshot, thus creating the
archive. Snapshot archives exist starting from 2014-09-17.
Author: Hong Ooi [aut, cre],
Andrie de Vries [aut],
Microsoft [aut, cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between checkpoint versions 0.4.8 dated 2020-01-13 and 0.4.9 dated 2020-02-23
checkpoint-0.4.8/checkpoint/inst/doc/checkpoint.R |only checkpoint-0.4.8/checkpoint/inst/doc/managing-checkpoint-archives.R |only checkpoint-0.4.9/checkpoint/DESCRIPTION | 6 checkpoint-0.4.9/checkpoint/MD5 | 20 -- checkpoint-0.4.9/checkpoint/NEWS.md | 4 checkpoint-0.4.9/checkpoint/build/vignette.rds |binary checkpoint-0.4.9/checkpoint/inst/doc/checkpoint.Rmd | 86 +++------ checkpoint-0.4.9/checkpoint/inst/doc/checkpoint.html | 56 ++--- checkpoint-0.4.9/checkpoint/inst/doc/managing-checkpoint-archives.Rmd | 94 +++++----- checkpoint-0.4.9/checkpoint/inst/doc/managing-checkpoint-archives.html | 40 +--- checkpoint-0.4.9/checkpoint/vignettes/checkpoint.Rmd | 86 +++------ checkpoint-0.4.9/checkpoint/vignettes/managing-checkpoint-archives.Rmd | 94 +++++----- 12 files changed, 204 insertions(+), 282 deletions(-)