Title: The Spike-and-Slab LASSO
Description: Efficient coordinate ascent algorithm for fitting regularization paths for linear models penalized by Spike-and-Slab LASSO of Rockova and George (2018) <doi:10.1080/01621459.2016.1260469>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gm2918@columbia.edu>
Diff between SSLASSO versions 1.2-1 dated 2018-08-28 and 1.2-2 dated 2019-12-13
DESCRIPTION | 11 ++++++----- MD5 | 13 +++++++------ NAMESPACE | 3 ++- NEWS.md |only R/SSLASSO.R | 24 +++++++++++++++--------- R/standard.R | 4 ++-- man/SSLASSO.Rd | 2 +- src/SSL_gaussian.c | 2 +- 8 files changed, 34 insertions(+), 25 deletions(-)
Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with cuts (a
dissected flat-mount retina) onto a curvilinear surface (the standard retinal
shape). It can estimate the position of a point on the intact adult retina
to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in
reconstructed retinae can be transformed to visuotopic coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between retistruct versions 0.6.1 dated 2019-12-09 and 0.6.2 dated 2019-12-13
DESCRIPTION | 14 MD5 | 132 +++---- NAMESPACE | 1 NEWS | 15 R/AnnotatedOutline.R | 117 +++--- R/CountSet.R | 24 - R/FeatureSet.R | 67 +-- R/FeatureSetCommon.R |only R/Fragment.R | 23 - R/LandmarkSet.R | 23 - R/Outline.R | 79 +++- R/OutlineCommon.R | 18 R/PathOutline.R | 26 + R/PointSet.R | 22 - R/ReconstructedCountSet.R | 34 + R/ReconstructedFeatureSet.R | 50 +- R/ReconstructedLandmarkSet.R | 16 R/ReconstructedOutline.R | 426 ++++++++++++----------- R/ReconstructedPointSet.R | 44 +- R/RetinalOutline.R | 22 - R/RetinalReconstructedOutline.R | 36 + R/StitchedOutline.R | 42 -- R/TriangulatedFragment.R | 57 +-- R/TriangulatedOutline.R | 32 + R/misc.R | 2 R/r6-serialize.R | 2 R/retistruct-gui.R | 2 R/retistruct.R | 4 inst/WORDLIST | 15 man/AnnotatedOutline.Rd | 319 +++++++++++++++++ man/CountSet.Rd | 100 ++++- man/E.Rd | 22 + man/FeatureSet.Rd | 87 +++- man/FeatureSetCommon.Rd |only man/Fragment.Rd | 78 +++- man/LandmarkSet.Rd | 99 ++++- man/Outline.Rd | 287 ++++++++++++++- man/OutlineCommon.Rd |only man/PathOutline.Rd | 154 ++++++++ man/PointSet.Rd | 98 ++++- man/R6_to_list.Rd | 2 man/ReconstructedCountSet.Rd | 103 ++++- man/ReconstructedFeatureSet.Rd | 82 +++- man/ReconstructedLandmarkSet.Rd | 59 ++- man/ReconstructedOutline.Rd | 470 +++++++++++++++++++++++++- man/ReconstructedPointSet.Rd | 109 +++++- man/RetinalOutline.Rd | 120 +++++- man/RetinalReconstructedOutline.Rd | 140 ++++++- man/StitchedOutline.Rd | 135 ++++++- man/TriangulatedFragment.Rd | 123 ++++-- man/TriangulatedOutline.Rd | 140 +++++++ man/dE.Rd | 22 + man/fire.Rd | 23 + man/flatplot.AnnotatedOutline.Rd | 3 man/flatplot.Outline.Rd | 17 man/flatplot.ReconstructedOutline.Rd | 11 man/flatplot.StitchedOutline.Rd | 3 man/flatplot.TriangulatedOutline.Rd | 3 man/projection.ReconstructedOutline.Rd | 30 + man/projection.RetinalReconstructedOutline.Rd | 26 + man/report.Rd | 2 man/retistruct.batch.Rd | 12 man/retistruct.cli.Rd | 9 man/retistruct.cli.figure.Rd | 10 man/retistruct.reconstruct.Rd | 11 man/sinusoidal.Rd | 9 man/sphericalplot.ReconstructedOutline.Rd | 3 tests/spelling.R |only tests/testthat/test-reconstruct.R | 18 69 files changed, 3351 insertions(+), 933 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>),
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Kris Boudt
<kris.boudt@ugent.be>
Diff between highfrequency versions 0.6.1 dated 2019-08-29 and 0.6.2 dated 2019-12-13
highfrequency-0.6.1/highfrequency/tests/testthat/Rplots.pdf |only highfrequency-0.6.2/highfrequency/DESCRIPTION | 43 +++- highfrequency-0.6.2/highfrequency/MD5 | 87 ++++------ highfrequency-0.6.2/highfrequency/NEWS.md | 33 ++- highfrequency-0.6.2/highfrequency/R/data_handling.R | 8 highfrequency-0.6.2/highfrequency/R/internal_preavering_estimators.R | 10 - highfrequency-0.6.2/highfrequency/R/realized_measures.R | 22 +- highfrequency-0.6.2/highfrequency/R/spot_vol_and_drift.R | 12 + highfrequency-0.6.2/highfrequency/inst/doc/data_handing.R | 16 - highfrequency-0.6.2/highfrequency/inst/doc/data_handing.html | 39 +--- highfrequency-0.6.2/highfrequency/man/AJjumptest.Rd | 13 + highfrequency-0.6.2/highfrequency/man/BNSjumptest.Rd | 14 + highfrequency-0.6.2/highfrequency/man/aggregatePrice.Rd | 11 + highfrequency-0.6.2/highfrequency/man/aggregateQuotes.Rd | 10 - highfrequency-0.6.2/highfrequency/man/aggregateTrades.Rd | 10 - highfrequency-0.6.2/highfrequency/man/aggregatets.Rd | 10 - highfrequency-0.6.2/highfrequency/man/harModel.Rd | 20 +- highfrequency-0.6.2/highfrequency/man/heavyModel.Rd | 13 + highfrequency-0.6.2/highfrequency/man/ivInference.Rd | 13 + highfrequency-0.6.2/highfrequency/man/medRQ.Rd | 3 highfrequency-0.6.2/highfrequency/man/medRV.Rd | 3 highfrequency-0.6.2/highfrequency/man/minRQ.Rd | 3 highfrequency-0.6.2/highfrequency/man/minRV.Rd | 3 highfrequency-0.6.2/highfrequency/man/quotesCleanup.Rd | 21 +- highfrequency-0.6.2/highfrequency/man/rAVGCov.Rd | 9 - highfrequency-0.6.2/highfrequency/man/rBPCov.Rd | 10 - highfrequency-0.6.2/highfrequency/man/rBeta.Rd | 9 - highfrequency-0.6.2/highfrequency/man/rCov.Rd | 9 - highfrequency-0.6.2/highfrequency/man/rHYCov.Rd | 11 + highfrequency-0.6.2/highfrequency/man/rKernelCov.Rd | 13 + highfrequency-0.6.2/highfrequency/man/rKurt.Rd | 3 highfrequency-0.6.2/highfrequency/man/rMPV.Rd | 10 - highfrequency-0.6.2/highfrequency/man/rOWCov.Rd | 14 + highfrequency-0.6.2/highfrequency/man/rQPVar.Rd | 5 highfrequency-0.6.2/highfrequency/man/rQuar.Rd | 3 highfrequency-0.6.2/highfrequency/man/rRTSCov.Rd | 17 + highfrequency-0.6.2/highfrequency/man/rSkew.Rd | 3 highfrequency-0.6.2/highfrequency/man/rTPVar.Rd | 7 highfrequency-0.6.2/highfrequency/man/rTSCov.Rd | 13 + highfrequency-0.6.2/highfrequency/man/rThresholdCov.Rd | 9 - highfrequency-0.6.2/highfrequency/man/spotDrift.Rd | 12 + highfrequency-0.6.2/highfrequency/man/spotvol.Rd | 12 + highfrequency-0.6.2/highfrequency/man/tradesCleanup.Rd | 16 + highfrequency-0.6.2/highfrequency/man/tradesCleanupUsingQuotes.Rd | 8 highfrequency-0.6.2/highfrequency/tests/testthat/tests_realized_measures.R | 4 45 files changed, 399 insertions(+), 215 deletions(-)
Title: The Expectation-Maximization Approach to Bayesian Variable
Selection
Description: An efficient expectation-maximization algorithm for fitting Bayesian spike-and-slab regularization paths for linear regression. Rockova and George (2014) <doi:10.1080/01621459.2013.869223>.
Author: Veronika Rockova [aut,cre], Gemma Moran [aut]
Maintainer: Gemma Moran <gm2918@columbia.edu>
Diff between EMVS versions 1.0 dated 2018-04-24 and 1.1 dated 2019-12-13
DESCRIPTION | 12 ++++++------ MD5 | 11 ++++++----- NAMESPACE | 3 ++- NEWS.md |only R/EMVS.R | 16 +++++++++------- build/vignette.rds |binary inst/doc/EMVS_vignette.pdf |binary 7 files changed, 23 insertions(+), 19 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops. 26 datasets are available for case studies in data visualization, statistical inference, modeling, linear regression, data wrangling and machine learning.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafael_irizarry@dfci.harvard.edu>
Diff between dslabs versions 0.7.2 dated 2019-12-11 and 0.7.3 dated 2019-12-13
DESCRIPTION | 6 - MD5 | 68 ++++++++-------- NAMESPACE | 16 +-- R/us_contagious_disease.R | 3 data/us_contagious_diseases.rda |binary inst/script/make-weekly_us_contagious_diseases.R | 77 +++++++----------- man/admissions.Rd | 58 +++++++------- man/brca.Rd | 94 +++++++++++------------ man/brexit_polls.Rd | 68 ++++++++-------- man/death_prob.Rd | 56 ++++++------- man/divorce_margarine.Rd | 56 ++++++------- man/ds_theme_set.Rd | 68 ++++++++-------- man/gapminder.Rd | 72 ++++++++--------- man/greenhouse_gases.Rd | 56 ++++++------- man/heights.Rd | 48 +++++------ man/historic_co2.Rd | 56 ++++++------- man/mnist_27.Rd | 70 ++++++++--------- man/movielens.Rd | 70 ++++++++--------- man/murders.Rd | 60 +++++++------- man/na_example.Rd | 36 ++++---- man/nyc_regents_scores.Rd | 64 +++++++-------- man/olive.Rd | 70 ++++++++--------- man/outlier_example.Rd | 38 ++++----- man/polls_2008.Rd | 58 +++++++------- man/polls_us_election_2016.Rd | 84 ++++++++++---------- man/read_mnist.Rd | 78 +++++++++---------- man/reported_heights.Rd | 52 ++++++------ man/research_funding_rates.Rd | 78 +++++++++---------- man/rfalling_object.Rd | 82 ++++++++++---------- man/stars.Rd | 58 +++++++------- man/take_poll.Rd | 46 +++++------ man/temp_carbon.Rd | 60 +++++++------- man/tissue_gene_expression.Rd | 68 ++++++++-------- man/trump_tweets.Rd | 68 ++++++++-------- man/us_contagious_diseases.Rd | 65 ++++++++------- 35 files changed, 999 insertions(+), 1008 deletions(-)
Title: User Friendly Bayesian Data Analysis for Psychology
Description: Contains several Bayesian models for data analysis of psychological tests. A user friendly interface for these models should enable students and researchers to perform professional level Bayesian data analysis without advanced knowledge in programming and Bayesian statistics.
Author: Jure Demšar [cre, aut],
Grega Repovš [aut],
Erik Štrumbelj [aut],
Trustees of Columbia University [cph],
John Kruschke [cph] (R/shared_functions.R - mcmc_hdi,
src/stan_files/ttest.stan),
Rasmus Baath [cph] (R/b_bootstrap.R)
Maintainer: Jure Demšar <jure.demsar@fri.uni-lj.si>
Diff between bayes4psy versions 1.1.1 dated 2019-06-28 and 1.2.0 dated 2019-12-13
bayes4psy-1.1.1/bayes4psy/man/rstanarm-datasets.Rd |only bayes4psy-1.2.0/bayes4psy/DESCRIPTION | 13 bayes4psy-1.2.0/bayes4psy/MD5 | 140 +- bayes4psy-1.2.0/bayes4psy/NAMESPACE | 2 bayes4psy-1.2.0/bayes4psy/NEWS.md | 10 bayes4psy-1.2.0/bayes4psy/R/b_color.R | 5 bayes4psy-1.2.0/bayes4psy/R/b_linear.R | 5 bayes4psy-1.2.0/bayes4psy/R/b_reaction_time.R | 5 bayes4psy-1.2.0/bayes4psy/R/b_success_rate.R | 5 bayes4psy-1.2.0/bayes4psy/R/b_ttest.R | 17 bayes4psy-1.2.0/bayes4psy/R/color_class.R | 526 +++++----- bayes4psy-1.2.0/bayes4psy/R/data.R | 139 ++ bayes4psy-1.2.0/bayes4psy/R/linear_class.R | 299 +++-- bayes4psy-1.2.0/bayes4psy/R/reaction_time_class.R | 312 +++-- bayes4psy-1.2.0/bayes4psy/R/success_rate_class.R | 272 ++--- bayes4psy-1.2.0/bayes4psy/R/ttest_class.R | 291 +++-- bayes4psy-1.2.0/bayes4psy/README.md | 2 bayes4psy-1.2.0/bayes4psy/build |only bayes4psy-1.2.0/bayes4psy/data/adaptation_level.rda |only bayes4psy-1.2.0/bayes4psy/data/after_images.rda |only bayes4psy-1.2.0/bayes4psy/data/after_images_opponent_process.rda |only bayes4psy-1.2.0/bayes4psy/data/after_images_stimuli.rda |only bayes4psy-1.2.0/bayes4psy/data/after_images_trichromatic.rda |only bayes4psy-1.2.0/bayes4psy/data/flanker.rda |only bayes4psy-1.2.0/bayes4psy/data/stroop_extended.rda |only bayes4psy-1.2.0/bayes4psy/data/stroop_simple.rda |only bayes4psy-1.2.0/bayes4psy/inst/doc |only bayes4psy-1.2.0/bayes4psy/man/b_ttest.Rd | 4 bayes4psy-1.2.0/bayes4psy/man/bayes4psy-datasets.Rd |only bayes4psy-1.2.0/bayes4psy/man/color_class-class.Rd | 33 bayes4psy-1.2.0/bayes4psy/man/color_class-compare_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/color_class-compare_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_distributions_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_hsv.Rd |only bayes4psy-1.2.0/bayes4psy/man/color_class-plot_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/color_class-plot_means_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-class.Rd | 37 bayes4psy-1.2.0/bayes4psy/man/linear_class-compare_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-compare_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_distributions_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/linear_class-plot_means_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/plot-color_class-missing-method.Rd |only bayes4psy-1.2.0/bayes4psy/man/plot-linear_class-missing-method.Rd |only bayes4psy-1.2.0/bayes4psy/man/plot-reaction_time_class-missing-method.Rd |only bayes4psy-1.2.0/bayes4psy/man/plot-success_rate_class-missing-method.Rd |only bayes4psy-1.2.0/bayes4psy/man/plot-ttest_class-missing-method.Rd |only bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-class.Rd | 38 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-compare_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-compare_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_distributions_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/reaction_time_class-plot_means_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-class.Rd | 36 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-compare_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-compare_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_distributions_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_means.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/success_rate_class-plot_means_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/ttest_class-class.Rd | 47 bayes4psy-1.2.0/bayes4psy/man/ttest_class-compare_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/ttest_class-compare_means.Rd | 4 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_distributions.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_distributions_difference.Rd | 2 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_means.Rd | 4 bayes4psy-1.2.0/bayes4psy/man/ttest_class-plot_means_difference.Rd | 4 bayes4psy-1.2.0/bayes4psy/src/stan_files/reaction_time.stan | 4 bayes4psy-1.2.0/bayes4psy/src/stan_files/ttest.stan | 34 bayes4psy-1.2.0/bayes4psy/tests/testthat/test_bootstrap.R |only bayes4psy-1.2.0/bayes4psy/vignettes |only 74 files changed, 1354 insertions(+), 988 deletions(-)
Title: Matching and Weighting Multiply Imputed Datasets
Description: Provides the necessary tools for the pre-processing techniques of matching and weighting multiply imputed datasets to control for effects of confounders and to reduce the degree of dependence on certain modeling assumptions in studying the causal associations between an exposure and an outcome. This package includes functions to perform matching within and across the multiply imputed datasets using several matching methods, to estimate weights of units in the imputed datasets using several weighting methods, to calculate the causal effect estimate in each matched or weighted dataset using parametric or non-parametric statistical models, and to pool the obtained estimates from these models according to Rubin's rules (please see <https://github.com/FarhadPishgar/MatchThem> for details).
Author: Farhad Pishgar [aut, cre],
Noah Greifer [aut],
Clémence Leyrat [ctb],
Elizabeth Stuart [ctb]
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>
Diff between MatchThem versions 0.9.0 dated 2019-11-01 and 0.9.1 dated 2019-12-13
DESCRIPTION | 14 - MD5 | 46 ++--- NAMESPACE | 18 + NEWS.md | 16 + R/class.functions.R | 437 +++++++++++++++++++++++++++++++++++++++++++++--- R/complete.R | 23 -- R/internal.functions.R | 195 +++++++-------------- R/is.R | 107 +++++++++++ R/matchthem.R | 27 +- R/mimids.R | 2 R/mimipo.R |only R/mimira.R |only R/pool.R | 65 +++++-- R/weightthem.R | 27 +- R/wimids.R | 2 R/with.R | 35 +-- README.md | 116 ++++++------ inst/doc/cheatsheet.pdf |binary man/complete.Rd | 2 man/is.mimipo.Rd |only man/is.mimira.Rd |only man/mimids.Rd | 2 man/mimipo.Rd |only man/mimira.Rd |only man/pool.Rd | 8 man/wimids.Rd | 2 man/with.Rd | 22 -- 27 files changed, 838 insertions(+), 328 deletions(-)
Title: Mixed Model ANOVA and Statistics for Education
Description: The main functions perform mixed models analysis by least squares
or REML by adding the function r() to formulas of lm() and glm(). A collection of
text-book statistics for higher education is also included, e.g. modifications
of the functions lm(), glm() and associated summaries from the package 'stats'.
Author: Kristian Hovde Liland [aut, cre],
Solve S<e6>b<f8> [ctb],
R-Core [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between mixlm versions 1.2.3 dated 2018-01-03 and 1.2.4 dated 2019-12-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 11 ++++++++++- R/mixlm.R | 6 ++++-- R/statistics.R | 35 +++++++++++++++++++++++------------ R/utilities.R | 15 ++++++++++----- man/CIgrandMean.Rd | 1 + 7 files changed, 58 insertions(+), 30 deletions(-)
Title: Styling of Graphics using Cascading Style Sheets
Description: Provides a means to style plots through cascading style sheets.
This separates the aesthetics from the data crunching in plots and charts.
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between Rcssplot versions 0.3.0 dated 2018-02-25 and 1.0.0 dated 2019-12-13
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Title: EM Algorithms for Estimating Item Response Theory Models
Description: Various Expectation-Maximization (EM) algorithms are implemented for item response theory
(IRT) models. The current implementation includes IRT models for binary and ordinal
responses, along with dynamic and hierarchical IRT models with binary responses. The
latter two models are derived and implemented using variational EM. Subsequent edits
also include variational network and text scaling models.
Author: Kosuke Imai <kimai@princeton.edu>, James Lo <lojames@usc.edu>, Jonathan Olmsted <jpolmsted@gmail.com>
Maintainer: James Lo <lojames@usc.edu>
Diff between emIRT versions 0.0.8 dated 2017-02-14 and 0.0.9 dated 2019-12-13
ChangeLog | 7 ++++++- DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NAMESPACE | 3 ++- man/dwnom.Rd | 6 +++--- man/dynIRT.Rd | 7 +++---- man/mq_data.Rd | 7 +++---- man/ordIRT.Rd | 26 +++++++++++++------------- src/calcLB.cpp | 6 +++--- src/emIRT_init.c |only 10 files changed, 46 insertions(+), 41 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, Plumber APIs, plots, and static web content.
Author: JJ Allaire
Maintainer: Jonathan McPherson <jonathan@rstudio.com>
Diff between rsconnect versions 0.8.15 dated 2019-07-22 and 0.8.16 dated 2019-12-13
DESCRIPTION | 12 +-- MD5 | 66 ++++++++++-------- NAMESPACE | 1 NEWS.md |only R/accounts.R | 124 +++++++++++++++++++++++++++++++---- R/applications.R | 102 ++++++++++++++++++++-------- R/bundle.R | 56 +++++++++++++-- R/connect.R | 13 +++ R/dependencies.R | 6 - R/deployAPI.R | 4 - R/deployApp.R | 50 +++++++++++--- R/deploySite.R | 9 +- R/deployments.R | 11 ++- R/http.R | 41 ++++++----- R/lint-framework.R | 14 +++ R/lint-utils.R | 12 +++ R/linters.R | 36 +++++++++- R/rsa.R | 40 +++++++++-- R/utils.R | 33 +++++++-- README.md | 45 ++++++++---- inst/resources/environment.py | 12 ++- man/accounts.Rd | 4 - man/applications.Rd | 16 ++-- man/connectApiUser.Rd |only man/connectUser.Rd | 1 man/deployApp.Rd | 16 +++- man/deploySite.Rd | 14 ++- man/figures |only man/setAccountInfo.Rd | 2 man/writeManifest.Rd | 4 - tests/testthat/multibyte-characters |only tests/testthat/shinyapp-with-browser |only tests/testthat/test-bundle.R | 105 +++++++++++++++++++++++++++++ tests/testthat/test-hashes.R |only tests/testthat/test-http.R | 42 +++++++++++ tests/testthat/test-lint.R | 18 ++++- 36 files changed, 732 insertions(+), 177 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 1.3.0 dated 2019-06-27 and 1.4.0 dated 2019-12-13
fulltext-1.3.0/fulltext/inst/doc/fulltext_vignette.Rmd |only fulltext-1.3.0/fulltext/inst/doc/fulltext_vignette.html |only fulltext-1.3.0/fulltext/inst/vign/fulltext_vignette.Rmd |only fulltext-1.3.0/fulltext/inst/vign/fulltext_vignette.md |only fulltext-1.3.0/fulltext/vignettes/fulltext_vignette.Rmd |only fulltext-1.4.0/fulltext/DESCRIPTION | 15 fulltext-1.4.0/fulltext/MD5 | 89 +- fulltext-1.4.0/fulltext/NEWS.md | 24 fulltext-1.4.0/fulltext/R/ft_browse.R | 15 fulltext-1.4.0/fulltext/R/ft_get.R | 428 +++++++------ fulltext-1.4.0/fulltext/R/ft_links.R | 77 +- fulltext-1.4.0/fulltext/R/ft_table.R | 16 fulltext-1.4.0/fulltext/R/fulltext-package.R | 2 fulltext-1.4.0/fulltext/R/plos_code.R | 25 fulltext-1.4.0/fulltext/R/plugins_get.R | 90 +- fulltext-1.4.0/fulltext/R/plugins_get_links.R | 2 fulltext-1.4.0/fulltext/R/plugins_links.R | 58 + fulltext-1.4.0/fulltext/README.md | 49 - fulltext-1.4.0/fulltext/build/vignette.rds |binary fulltext-1.4.0/fulltext/inst/doc/formats.Rmd | 3 fulltext-1.4.0/fulltext/inst/doc/formats.html | 2 fulltext-1.4.0/fulltext/inst/doc/fulltext.Rmd |only fulltext-1.4.0/fulltext/inst/doc/fulltext.html |only fulltext-1.4.0/fulltext/inst/doc/getting_fulltext.Rmd | 28 fulltext-1.4.0/fulltext/inst/doc/getting_fulltext.html | 28 fulltext-1.4.0/fulltext/inst/vign/fulltext.Rmd |only fulltext-1.4.0/fulltext/inst/vign/fulltext.md |only fulltext-1.4.0/fulltext/inst/vign/getting_fulltext.md | 28 fulltext-1.4.0/fulltext/man/biorxiv_search.Rd | 3 fulltext-1.4.0/fulltext/man/cache.Rd | 13 fulltext-1.4.0/fulltext/man/cache_file_info.Rd | 5 fulltext-1.4.0/fulltext/man/eupmc.Rd | 10 fulltext-1.4.0/fulltext/man/ft_abstract.Rd | 13 fulltext-1.4.0/fulltext/man/ft_browse.Rd | 7 fulltext-1.4.0/fulltext/man/ft_get.Rd | 123 ++- fulltext-1.4.0/fulltext/man/ft_links.Rd | 11 fulltext-1.4.0/fulltext/man/ft_search.Rd | 22 fulltext-1.4.0/fulltext/man/ft_table.Rd | 3 fulltext-1.4.0/fulltext/man/ftxt_cache.Rd | 5 fulltext-1.4.0/fulltext/man/fulltext-package.Rd | 2 fulltext-1.4.0/fulltext/man/microsoft-internals.Rd | 24 fulltext-1.4.0/fulltext/man/scopus_search.Rd | 37 - fulltext-1.4.0/fulltext/tests/testthat/test-ft_abstract.R | 8 fulltext-1.4.0/fulltext/tests/testthat/test-ft_browse.R | 10 fulltext-1.4.0/fulltext/tests/testthat/test-ft_get.r | 38 + fulltext-1.4.0/fulltext/tests/testthat/test-ft_get_utils.R |only fulltext-1.4.0/fulltext/tests/testthat/test-ft_links.R | 2 fulltext-1.4.0/fulltext/tests/testthat/test-ft_search.R | 18 fulltext-1.4.0/fulltext/vignettes/formats.Rmd | 3 fulltext-1.4.0/fulltext/vignettes/fulltext.Rmd |only fulltext-1.4.0/fulltext/vignettes/getting_fulltext.Rmd | 28 51 files changed, 817 insertions(+), 547 deletions(-)
Title: Visualization Methods for Raster Data
Description: Methods for enhanced visualization and interaction with raster data. It implements visualization methods for quantitative data and categorical data, both for univariate and multivariate rasters. It also provides methods to display spatiotemporal rasters, and vector fields. See the website for examples.
Author: Oscar Perpinan Lamigueiro [cre, aut]
(<https://orcid.org/0000-0002-4134-7196>),
Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro <oscar.perpinan@gmail.com>
Diff between rasterVis versions 0.46 dated 2019-07-02 and 0.47 dated 2019-12-13
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/partial.rdb |binary man/horizonplot-methods.Rd | 3 ++- man/levelplot-methods.Rd | 11 +++++++---- man/plot3d.Rd | 6 +++--- man/vectorplot.Rd | 8 ++++---- 7 files changed, 26 insertions(+), 22 deletions(-)
Title: Utilities for Quantiles
Description: Functions for unconditional and conditional quantiles. These
include methods for transformation-based quantile regression,
quantile-based measures of location, scale and shape, methods for quantiles
of discrete variables, quantile-based multiple imputation, and restricted
quantile regression. A vignette is given in Geraci (2016, The R Journal)
<doi:10.32614/RJ-2016-037> and included in the package.
Author: Marco Geraci [aut, cph, cre] (<https://orcid.org/0000-0002-6311-8685>),
Alessio Farcomeni [ctb] (Contributions to midrq code)
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between Qtools versions 1.4.1 dated 2019-07-13 and 1.5.1 dated 2019-12-13
DESCRIPTION | 8 - MD5 | 26 +++--- NEWS | 8 + R/Qtools.R | 214 +++++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/Qtools.R | 2 inst/doc/Qtools.html | 8 + man/Qtools-package.Rd | 4 man/cmidecdf.Rd | 5 - man/midrq.Rd | 6 - man/midrqControl.Rd | 3 man/summary.midrq.Rd | 8 + man/vcov.midrq.Rd | 8 + src/Qtools.cpp | 9 +- 14 files changed, 179 insertions(+), 130 deletions(-)
Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging
For R.
Author: Qin Wenfeng, Wu Yanyi
Maintainer: Qin Wenfeng <mail@qinwenfeng.com>
Diff between jiebaR versions 0.10.99 dated 2019-03-12 and 0.11 dated 2019-12-13
jiebaR-0.10.99/jiebaR/README.md |only jiebaR-0.11/jiebaR/DESCRIPTION | 8 jiebaR-0.11/jiebaR/MD5 | 13 - jiebaR-0.11/jiebaR/build/vignette.rds |binary jiebaR-0.11/jiebaR/inst/doc/Quick_Start_Guide.Rmd | 18 +- jiebaR-0.11/jiebaR/inst/doc/Quick_Start_Guide.html | 119 +++++++------- jiebaR-0.11/jiebaR/inst/include/lib/limonp/StringUtil.hpp | 37 ++-- jiebaR-0.11/jiebaR/vignettes/Quick_Start_Guide.Rmd | 18 +- 8 files changed, 112 insertions(+), 101 deletions(-)
Title: Fishery Science Methods and Models
Description: Functions for applying a wide range of fisheries stock assessment methods.
Author: Gary A. Nelson <gary.nelson@mass.gov>
Maintainer: Gary A. Nelson <gary.nelson@mass.gov>
Diff between fishmethods versions 1.11-0 dated 2018-11-20 and 1.11-1 dated 2019-12-13
fishmethods-1.11-0/fishmethods/R/astrocalc4r.R |only fishmethods-1.11-1/fishmethods/DESCRIPTION | 12 - fishmethods-1.11-1/fishmethods/MD5 | 58 ++--- fishmethods-1.11-1/fishmethods/NAMESPACE | 5 fishmethods-1.11-1/fishmethods/R/M.empirical.R | 10 - fishmethods-1.11-1/fishmethods/R/agesurv.R | 67 ++++-- fishmethods-1.11-1/fishmethods/R/alk.R | 146 ++++++++------ fishmethods-1.11-1/fishmethods/R/astrocalc4r.r |only fishmethods-1.11-1/fishmethods/R/clus.vb.fit.R | 34 +-- fishmethods-1.11-1/fishmethods/R/dbsra.R | 1 fishmethods-1.11-1/fishmethods/R/deplet.R | 12 - fishmethods-1.11-1/fishmethods/R/dlproj.R | 1 fishmethods-1.11-1/fishmethods/R/fm_telemetry.R | 9 fishmethods-1.11-1/fishmethods/R/grotag.R | 4 fishmethods-1.11-1/fishmethods/R/growth.R | 10 - fishmethods-1.11-1/fishmethods/R/growthlrt.R | 10 - fishmethods-1.11-1/fishmethods/R/growthmultifit.R | 2 fishmethods-1.11-1/fishmethods/R/irm_cr.R | 4 fishmethods-1.11-1/fishmethods/R/irm_h.R | 2 fishmethods-1.11-1/fishmethods/R/pwpop.R | 4 fishmethods-1.11-1/fishmethods/R/sr.R | 195 +++++++++----------- fishmethods-1.11-1/fishmethods/man/M.empirical.Rd | 13 - fishmethods-1.11-1/fishmethods/man/agesurv.Rd | 22 +- fishmethods-1.11-1/fishmethods/man/astrocalc4r.Rd | 2 fishmethods-1.11-1/fishmethods/man/clus.vb.fit.Rd | 15 - fishmethods-1.11-1/fishmethods/man/dbsra.Rd | 2 fishmethods-1.11-1/fishmethods/man/dlproj.Rd | 5 fishmethods-1.11-1/fishmethods/man/growth.Rd | 4 fishmethods-1.11-1/fishmethods/man/growthResid.Rd | 5 fishmethods-1.11-1/fishmethods/man/growthTraject.Rd | 5 fishmethods-1.11-1/fishmethods/man/growthlrt.Rd | 2 31 files changed, 357 insertions(+), 304 deletions(-)
Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive Q-Learning, Q-Learning, weighted learning, and value-search methods based on Augmented Inverse Probability Weighted Estimators and Inverse Probability Weighted Estimators.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between DynTxRegime versions 4.2 dated 2019-10-17 and 4.3 dated 2019-12-13
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- NAMESPACE | 1 NEWS | 7 +++++ R/C_TypedFit_fSet.R | 1 R/F_PropensityFit_fSet.R | 56 ++++++++++++++++++++-------------------- R/H_class_OptimalSeqCoarsened.R | 1 7 files changed, 47 insertions(+), 39 deletions(-)
Title: Spatial Influence of Landscape
Description: Method to estimate the spatial influence scales of landscape variables on a response variable. The method is based on Chandler and Hepinstall-Cymerman (2016) Estimating the spatial scales of landscape effects on abundance, Landscape ecology, 31: 1383-1394, <doi:10.1007/s10980-016-0380-z>.
Author: Carpentier F. and Martin O.
Maintainer: Martin Olivier <olivier.martin@inra.fr>
Diff between siland versions 1.2 dated 2019-03-20 and 1.4.5 dated 2019-12-13
siland-1.2/siland/R/AIC.siland.R |only siland-1.2/siland/R/BIC.siland.R |only siland-1.2/siland/R/data.gis.R |only siland-1.2/siland/R/fitted.siland.R |only siland-1.2/siland/R/land.gis.R |only siland-1.2/siland/R/plotsif.R |only siland-1.2/siland/R/plotsiland.R |only siland-1.2/siland/R/plotsiland.land.R |only siland-1.2/siland/R/plotsiland.sif.R |only siland-1.2/siland/R/residuals.siland.R |only siland-1.2/siland/R/siland.R |only siland-1.2/siland/R/siland.quantile.R |only siland-1.2/siland/man/AIC.siland.Rd |only siland-1.2/siland/man/BIC.siland.Rd |only siland-1.2/siland/man/data.gis.Rd |only siland-1.2/siland/man/fitted.siland.Rd |only siland-1.2/siland/man/land.gis.Rd |only siland-1.2/siland/man/plotcontri.Rd |only siland-1.2/siland/man/plotsif.Rd |only siland-1.2/siland/man/plotsiland.Rd |only siland-1.2/siland/man/plotsiland.land.Rd |only siland-1.2/siland/man/plotsiland.sif.Rd |only siland-1.2/siland/man/print.siland.Rd |only siland-1.2/siland/man/residuals.siland.Rd |only siland-1.2/siland/man/siland.Rd |only siland-1.2/siland/man/siland.quantile.Rd |only siland-1.2/siland/man/summary.siland.Rd |only siland-1.4.5/siland/DESCRIPTION | 14 siland-1.4.5/siland/MD5 | 105 +++-- siland-1.4.5/siland/NAMESPACE | 64 ++- siland-1.4.5/siland/R/AIC.Bsiland.R |only siland-1.4.5/siland/R/AIC.Fsiland.R |only siland-1.4.5/siland/R/BIC.Bsiland.R |only siland-1.4.5/siland/R/BIC.Fsiland.R |only siland-1.4.5/siland/R/Bsiland.R |only siland-1.4.5/siland/R/Bsiland.lik.R |only siland-1.4.5/siland/R/BsilandMinusLoglik.R |only siland-1.4.5/siland/R/BsilandMinusLoglikGLMM.R |only siland-1.4.5/siland/R/BsilandMinusLoglikLMM.R |only siland-1.4.5/siland/R/Fsiland.R |only siland-1.4.5/siland/R/Fsiland.lik.R |only siland-1.4.5/siland/R/Fsiland.quantile.R |only siland-1.4.5/siland/R/bufferforsiland.R |only siland-1.4.5/siland/R/fitted.Bsiland.R |only siland-1.4.5/siland/R/fitted.Fsiland.R |only siland-1.4.5/siland/R/landtoraster.R |only siland-1.4.5/siland/R/landtorasterold.R |only siland-1.4.5/siland/R/miscsiland.R | 463 +++---------------------- siland-1.4.5/siland/R/plotBsiland.land.R |only siland-1.4.5/siland/R/plotFsiland.R |only siland-1.4.5/siland/R/plotFsiland.land.R |only siland-1.4.5/siland/R/plotFsiland.sif.R |only siland-1.4.5/siland/R/print.Bsiland.R |only siland-1.4.5/siland/R/residuals.Bsiland.R |only siland-1.4.5/siland/R/residuals.Fsiland.R |only siland-1.4.5/siland/R/summary.Bsiland.R |only siland-1.4.5/siland/build/partial.rdb |binary siland-1.4.5/siland/build/vignette.rds |only siland-1.4.5/siland/data/dataCmoth.RData |binary siland-1.4.5/siland/data/dataSiland.RData |binary siland-1.4.5/siland/data/datalist |only siland-1.4.5/siland/data/landCmoth.RData |binary siland-1.4.5/siland/data/landSiland.RData |binary siland-1.4.5/siland/inst |only siland-1.4.5/siland/man/AIC.Bsiland.Rd |only siland-1.4.5/siland/man/AIC.Fsiland.Rd |only siland-1.4.5/siland/man/BIC.Bsiland.Rd |only siland-1.4.5/siland/man/BIC.Fsiland.Rd |only siland-1.4.5/siland/man/Bsiland.Rd |only siland-1.4.5/siland/man/Bsiland.lik.Rd |only siland-1.4.5/siland/man/Fsiland.Rd |only siland-1.4.5/siland/man/Fsiland.lik.Rd |only siland-1.4.5/siland/man/Fsiland.quantile.Rd |only siland-1.4.5/siland/man/bufferforsiland.Rd |only siland-1.4.5/siland/man/dataCmoth.Rd | 17 siland-1.4.5/siland/man/dataSiland.Rd | 38 -- siland-1.4.5/siland/man/fitted.Bsiland.Rd |only siland-1.4.5/siland/man/fitted.Fsiland.Rd |only siland-1.4.5/siland/man/landCmoth.Rd | 48 -- siland-1.4.5/siland/man/landSiland.Rd | 32 - siland-1.4.5/siland/man/landtoraster.Rd |only siland-1.4.5/siland/man/plotBsiland.land.Rd |only siland-1.4.5/siland/man/plotFsiland.Rd |only siland-1.4.5/siland/man/plotFsiland.land.Rd |only siland-1.4.5/siland/man/plotFsiland.sif.Rd |only siland-1.4.5/siland/man/print.Bsiland.Rd |only siland-1.4.5/siland/man/print.Fsiland.Rd |only siland-1.4.5/siland/man/residuals.Bsiland.Rd |only siland-1.4.5/siland/man/residuals.Fsiland.Rd |only siland-1.4.5/siland/man/summary.Bsiland.Rd |only siland-1.4.5/siland/man/summary.Fsiland.Rd |only siland-1.4.5/siland/vignettes |only 92 files changed, 214 insertions(+), 567 deletions(-)
Title: Enhanced Help to Enable "Docstring"-Comments in Users Functions
Description: By overloading the R help() function, this package allows users to use "docstring" style comments within their own defined functions.
Author: Marcelo Ponce [aut, cre]
Maintainer: Marcelo Ponce <mponce@scinet.utoronto.ca>
Diff between ehelp versions 1.1 dated 2019-11-12 and 1.1.1 dated 2019-12-13
DESCRIPTION | 6 MD5 | 18 +- NEWS | 1 R/ehelp-utils.R | 6 R/ehelp.R | 3 README.md | 43 +++-- build/vignette.rds |binary inst/doc/eHelp.html | 443 ++++++++++++++++++++++++++++++++++++++-------------- man/ehelp.Rd | 1 man/print.ehelp.Rd | 4 10 files changed, 381 insertions(+), 144 deletions(-)
Title: Interface to 'TensorFlow' Datasets
Description: Interface to 'TensorFlow' Datasets, a high-level library for
building complex input pipelines from simple, re-usable pieces.
See <https://www.tensorflow.org/programmers_guide/datasets> for additional
details.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Kevin Ushey [aut],
RStudio [cph, fnd],
Google Inc. [cph]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between tfdatasets versions 1.13.1 dated 2019-04-09 and 2.0.0 dated 2019-12-13
DESCRIPTION | 14 - MD5 | 163 ++++++++++----- NAMESPACE | 42 +++- NEWS.md |only R/data.R |only R/dataset_methods.R | 119 +++++++++-- R/dataset_properties.R | 24 +- R/feature_spec.R |only R/input_fn.R | 18 - R/reexports.R | 3 R/symbols.R | 14 - R/tensors_dataset.R | 20 + R/utils.R | 30 ++ README.md | 7 build/vignette.rds |binary data |only inst/doc/feature_columns.R |only inst/doc/feature_columns.Rmd |only inst/doc/feature_columns.html |only inst/doc/feature_spec.R |only inst/doc/feature_spec.Rmd |only inst/doc/feature_spec.html |only inst/doc/introduction.R | 33 --- inst/doc/introduction.Rmd | 58 ----- inst/doc/introduction.html | 209 ++++++++------------ man/all_nominal.Rd |only man/all_numeric.Rd |only man/dataset_batch.Rd | 32 +-- man/dataset_cache.Rd | 32 +-- man/dataset_collect.Rd |only man/dataset_concatenate.Rd | 32 +-- man/dataset_decode_delim.Rd | 32 +-- man/dataset_filter.Rd | 32 +-- man/dataset_interleave.Rd | 32 +-- man/dataset_map.Rd | 35 +-- man/dataset_map_and_batch.Rd | 46 ++-- man/dataset_padded_batch.Rd | 41 ++- man/dataset_prefetch.Rd | 32 +-- man/dataset_prefetch_to_device.Rd | 32 +-- man/dataset_prepare.Rd | 16 + man/dataset_repeat.Rd | 32 +-- man/dataset_shuffle.Rd | 43 ++-- man/dataset_shuffle_and_repeat.Rd | 35 +-- man/dataset_skip.Rd | 32 +-- man/dataset_take.Rd | 32 +-- man/dataset_use_spec.Rd |only man/dataset_window.Rd |only man/delim_record_spec.Rd | 38 ++- man/dense_features.Rd |only man/feature_spec.Rd |only man/file_list_dataset.Rd | 2 man/fit.FeatureSpec.Rd |only man/fixed_length_record_dataset.Rd | 9 man/has_type.Rd |only man/hearts.Rd |only man/input_fn.Rd | 2 man/iterator_get_next.Rd | 9 man/iterator_initializer.Rd | 9 man/iterator_make_initializer.Rd | 9 man/iterator_string_handle.Rd | 9 man/layer_input_from_dataset.Rd |only man/make-iterator.Rd | 25 +- man/make_csv_dataset.Rd | 29 ++ man/read_files.Rd | 11 - man/reexports.Rd | 16 + man/scaler.Rd |only man/scaler_min_max.Rd |only man/scaler_standard.Rd |only man/selectors.Rd |only man/sparse_tensor_slices_dataset.Rd | 5 man/step_bucketized_column.Rd |only man/step_categorical_column_with_hash_bucket.Rd |only man/step_categorical_column_with_identity.Rd |only man/step_categorical_column_with_vocabulary_file.Rd |only man/step_categorical_column_with_vocabulary_list.Rd |only man/step_crossed_column.Rd |only man/step_embedding_column.Rd |only man/step_indicator_column.Rd |only man/step_numeric_column.Rd |only man/step_remove_column.Rd |only man/step_shared_embeddings_column.Rd |only man/steps.Rd |only man/tensor_slices_dataset.Rd | 5 man/tensors_dataset.Rd | 5 man/text_line_dataset.Rd | 8 man/tfrecord_dataset.Rd | 8 tests/testthat.R | 9 tests/testthat/test-dataset-fitting.R | 9 tests/testthat/test-dataset-methods.R | 45 ++++ tests/testthat/test-dataset-prepare.R | 24 ++ tests/testthat/test-dataset-properties.R | 15 + tests/testthat/test-decode-csv.R | 7 tests/testthat/test-feature_spec.R |only tests/testthat/test-iterators.R | 13 - tests/testthat/test-tensor-datasets.R | 12 + tests/testthat/utils.R | 21 +- vignettes/feature_columns.Rmd |only vignettes/feature_spec.Rmd |only vignettes/images |only vignettes/introduction.Rmd | 58 ----- 100 files changed, 1038 insertions(+), 696 deletions(-)
More information about SequenceSpikeSlab at CRAN
Permanent link
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Alexander Robitzsch [ctb],
Gerko Vink [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Rianne Schouten [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.6.0 dated 2019-07-10 and 3.7.0 dated 2019-12-13
DESCRIPTION | 22 MD5 | 139 +-- NAMESPACE | 1 NEWS.md | 978 +++++++++++++------------- R/check.R | 86 +- R/edit.setup.R | 3 R/imports.R | 2 R/method.R | 6 R/mice.impute.2l.pan.R | 4 R/mice.impute.2lonly.mean.R | 83 +- R/mice.impute.2lonly.norm.R | 106 ++ R/mice.impute.2lonly.pmm.R | 184 ++-- R/mice.impute.polr.R | 194 ++--- R/mice.impute.rf.R | 158 ++-- R/mira.R | 105 +- R/predictorMatrix.R | 2 man/ampute.Rd | 37 man/appendbreak.Rd | 3 man/bwplot.mads.Rd | 11 man/bwplot.mids.Rd | 18 man/cbind.Rd | 2 man/densityplot.mids.Rd | 19 man/extend.formula.Rd | 9 man/extend.formulas.Rd | 11 man/fluxplot.Rd | 21 man/make.blocks.Rd | 7 man/make.method.Rd | 8 man/mdc.Rd | 15 man/mice.Rd | 27 man/mice.impute.2l.bin.Rd | 7 man/mice.impute.2l.lmer.Rd | 7 man/mice.impute.2l.norm.Rd | 7 man/mice.impute.2l.pan.Rd | 23 man/mice.impute.2lonly.mean.Rd | 46 - man/mice.impute.2lonly.norm.Rd | 61 + man/mice.impute.2lonly.pmm.Rd | 31 man/mice.impute.cart.Rd | 31 man/mice.impute.jomoImpute.Rd | 14 man/mice.impute.lda.Rd | 31 man/mice.impute.logreg.Rd | 31 man/mice.impute.logreg.boot.Rd | 31 man/mice.impute.mean.Rd | 31 man/mice.impute.midastouch.Rd | 46 - man/mice.impute.norm.Rd | 31 man/mice.impute.norm.boot.Rd | 31 man/mice.impute.norm.nob.Rd | 31 man/mice.impute.norm.predict.Rd | 31 man/mice.impute.panImpute.Rd | 14 man/mice.impute.pmm.Rd | 43 - man/mice.impute.polr.Rd | 60 + man/mice.impute.polyreg.Rd | 43 - man/mice.impute.quadratic.Rd | 31 man/mice.impute.rf.Rd | 41 - man/mice.impute.ri.Rd | 31 man/mids2mplus.Rd | 10 man/mids2spss.Rd | 11 man/mipo.Rd | 13 man/mira-class.Rd | 28 man/parlmice.Rd | 16 man/plot.mids.Rd | 12 man/pool.Rd | 2 man/pool.compare.Rd | 2 man/quickpred.Rd | 10 man/squeeze.Rd | 3 man/stripplot.mids.Rd | 18 man/summary.Rd | 3 man/xyplot.mads.Rd | 11 man/xyplot.mids.Rd | 15 tests/testthat/test-mice.impute.2lonly.mean.R | 34 tests/testthat/test-mice.impute.2lonly.norm.R |only tests/testthat/test-rbind.R | 4 71 files changed, 1880 insertions(+), 1357 deletions(-)
Title: Log-Binomial Regression with Constrained Optimization
Description: Maximum likelihood estimation of log-binomial regression with special functionality when the MLE is on the boundary of the parameter space.
Author: Bernardo B. Andrade
Maintainer: Bernardo Andrade <bbandrade@unb.br>
Diff between lbreg versions 1.2 dated 2018-01-19 and 1.3 dated 2019-12-13
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS |only R/lbreg.fit.R | 39 ++++++++++++++++++--------------------- R/predict.lbreg.R | 35 ++++++++++++++--------------------- build/partial.rdb |binary man/lbreg-package.Rd | 4 ++-- man/lbreg.Rd | 2 +- man/predict.lbreg.Rd | 2 +- man/relrisk.Rd | 2 +- 10 files changed, 50 insertions(+), 59 deletions(-)
Title: Marker-Based Estimation of Heritability Using Individual Plant
or Plot Data
Description: Implements marker-based estimation of heritability when observations on genetically identical replicates are available. These can be either observations on individual plants or plot-level data in a field trial. Heritability can then be estimated using a mixed model for the individual plant or plot data. For comparison, also mixed-model based estimation using genotypic means and estimation of repeatability with ANOVA are implemented. For illustration the package contains several datasets for the model species Arabidopsis thaliana.
Author: Willem Kruijer, with a contribution from Ian White (the internal function pin). Contains data collected by Padraic Flood and Rik Kooke.
Maintainer: Willem Kruijer <willem.kruijer@wur.nl>
Diff between heritability versions 1.2 dated 2016-12-22 and 1.3 dated 2019-12-13
DESCRIPTION | 8 MD5 | 6 R/AI_algorithm.R | 498 +++++++++++++++++++++++------------------------ R/AI_algorithm_weights.r | 434 ++++++++++++++++++++-------------------- 4 files changed, 473 insertions(+), 473 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>),
Martin Morgan [ctb],
Christine Stawitz [rev] (Christine reviewed the package for ropensci,
see <https://github.com/ropensci/software-review/issues/315>),
Carl Ganz [rev] (Carl reviewed the package for ropensci, see
<https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.2.9 dated 2019-11-25 and 1.2.10 dated 2019-12-13
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ data/XenaData.rda |binary inst/doc/USCSXenaTools.Rmd | 5 ++++- inst/doc/USCSXenaTools.html | 29 +++++++++++++++-------------- vignettes/USCSXenaTools.Rmd | 5 ++++- 7 files changed, 39 insertions(+), 26 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also now included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Cleve Moler [ctb] (author of several linpack routines),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.52 dated 2019-11-09 and 5.54 dated 2019-12-13
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/boot.R | 4 ++-- R/crq.R | 2 +- build/vignette.rds |binary inst/ChangeLog | 12 ++++++++++++ man/crq.Rd | 2 +- 7 files changed, 25 insertions(+), 13 deletions(-)
Title: Data Class and Tools for Handling Spatial-Temporal Data
Description: Data class for increased interoperability working with spatial-
temporal data together with corresponding functions and methods (conversions,
basic calculations and basic data manipulation). The class distinguishes
between spatial, temporal and other dimensions to facilitate the development
and interoperability of tools build for it. Additional features are name-based
addressing of data and internal consistency checks (e.g. checking for the right
data order in calculations).
Author: Jan Philipp Dietrich [aut, cre],
Benjamin Leon Bodirsky [aut],
Markus Bonsch [aut],
Florian Humpenoeder [aut],
Stephen Bi [aut],
Kristine Karstens [aut],
Lavinia Baumstark [ctb],
Christoph Bertram [ctb],
Anastasis Giannousakis [ctb],
David Klein [ctb],
Ina Neher [ctb],
Michaja Pehl [ctb],
Anselm Schultes [ctb],
Miodrag Stevanovic [ctb],
Xiaoxi Wang [ctb]
Maintainer: Jan Philipp Dietrich <dietrich@pik-potsdam.de>
Diff between magclass versions 5.5.0 dated 2019-12-06 and 5.7.0 dated 2019-12-13
magclass-5.5.0/magclass/vignettes/magclass-concept.md |only magclass-5.5.0/magclass/vignettes/magclass.md |only magclass-5.7.0/magclass/DESCRIPTION | 8 +- magclass-5.7.0/magclass/MD5 | 33 +++++----- magclass-5.7.0/magclass/NAMESPACE | 1 magclass-5.7.0/magclass/R/getDim.R | 46 +++++++++++---- magclass-5.7.0/magclass/R/getItems.R | 15 ++++ magclass-5.7.0/magclass/R/getSets.R | 13 +++- magclass-5.7.0/magclass/R/mcalc.R | 4 - magclass-5.7.0/magclass/build/vignette.rds |binary magclass-5.7.0/magclass/inst/doc/magclass-concept.html | 4 - magclass-5.7.0/magclass/inst/doc/magclass-expansion.html | 4 - magclass-5.7.0/magclass/inst/doc/magclass.html | 7 +- magclass-5.7.0/magclass/man/getDim.Rd | 17 ++++- magclass-5.7.0/magclass/man/getItems.Rd | 2 magclass-5.7.0/magclass/man/getSets.Rd | 4 - magclass-5.7.0/magclass/tests/testthat/test-getDim.R |only magclass-5.7.0/magclass/tests/testthat/test-getItems.R | 8 ++ magclass-5.7.0/magclass/tests/testthat/test-getSets.R | 6 + 19 files changed, 120 insertions(+), 52 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Provides p-values in type I, II or III anova and summary tables
for lmer model fits (cf. lme4) via Satterthwaite's degrees of freedom method. A
Kenward-Roger method is also available via the pbkrtest package. Model selection
methods include step, drop1 and anova-like tables for random effects (ranova).
Methods for Least-Square means (LS-means) and tests of linear contrasts of fixed
effects are also available.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut],
Sofie Pødenphant Jensen [ctb, cre]
Maintainer: Sofie Pødenphant Jensen <sofp@dtu.dk>
Diff between lmerTest versions 3.1-0 dated 2019-02-11 and 3.1-1 dated 2019-12-13
DESCRIPTION | 18 ++++++++++-------- MD5 | 6 +++--- NEWS.md | 6 ++++++ tests/test_lmer.R | 14 -------------- 4 files changed, 19 insertions(+), 25 deletions(-)
Title: Significance Analysis of Event-Related Potentials Data
Description: Functions for signal detection and identification designed for Event-Related Potentials (ERP) data in a linear model framework. The functional F-test proposed in Causeur, Sheu, Perthame, Rufini (2018, submitted) for analysis of variance issues in ERP designs is implemented for signal detection (tests for mean difference among groups of curves in One-way ANOVA designs for example). Once an experimental effect is declared significant, identification of significant intervals is achieved by the multiple testing procedures reviewed and compared in Sheu, Perthame, Lee and Causeur (2016, <DOI:10.1214/15-AOAS888>). Some of the methods gathered in the package are the classical FDR- and FWER-controlling procedures, also available using function p.adjust. The package also implements the Guthrie-Buchwald procedure (Guthrie and Buchwald, 1991 <DOI:10.1111/j.1469-8986.1991.tb00417.x>), which accounts for the auto-correlation among t-tests to control erroneous detection of short intervals. The Adaptive Factor-Adjustment method is an extension of the method described in Causeur, Chu, Hsieh and Sheu (2012, <DOI:10.3758/s13428-012-0230-0>). It assumes a factor model for the correlation among tests and combines adaptively the estimation of the signal and the updating of the dependence modelling (see Sheu et al., 2016, <DOI:10.1214/15-AOAS888> for further details).
Author: David Causeur, Ching-Fan Sheu, Mei-Chen Chu, Flavia Rufini
Maintainer: David Causeur <david.causeur@agrocampus-ouest.fr>
Diff between ERP versions 2.1 dated 2018-10-05 and 2.2 dated 2019-12-13
ERP-2.1/ERP/R/ERP-internal.R |only ERP-2.2/ERP/DESCRIPTION | 8 ++-- ERP-2.2/ERP/MD5 | 15 +++---- ERP-2.2/ERP/R/emfa.R | 5 +- ERP-2.2/ERP/R/erpFtest.R | 17 ++++---- ERP-2.2/ERP/R/erpfatest.R | 83 +++++++++++++++++++++--------------------- ERP-2.2/ERP/R/ifa.R | 2 - ERP-2.2/ERP/build/partial.rdb |binary ERP-2.2/ERP/inst/doc/ERP.html | 16 ++++---- 9 files changed, 71 insertions(+), 75 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.48-2 dated 2019-11-21 and 0.48-3 dated 2019-12-13
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/cluster.Gen.r | 6 +++--- R/data.Normalization2.r |only R/speccl.r | 42 +++++++++++++++++++++--------------------- data/data_binary.rda |binary data/data_interval.rda |binary data/data_mixed.rda |binary data/data_nominal.rda |binary data/data_ordinal.rda |binary data/data_ratio.rda |binary 11 files changed, 38 insertions(+), 37 deletions(-)
Title: Bayesian t-Test
Description: Provides an Markov-Chain-Monte-Carlo algorithm for Bayesian t-tests on the effect size. The underlying Gibbs sampler is based on a two-component Gaussian mixture and approximates the posterior distributions of the effect size, the difference of means and difference of standard deviations. A posterior analysis of the effect size via the region of practical equivalence is provided, too. For more details about the Gibbs sampler see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between bayest versions 1.0 dated 2019-08-02 and 1.1 dated 2019-12-13
DESCRIPTION | 8 ++--- MD5 | 8 ++--- R/bayest.R | 74 ++++++++++++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary man/bayes.t.test.Rd | 4 +- 5 files changed, 74 insertions(+), 20 deletions(-)
Title: Scale Space Multiresolution Analysis of Random Signals
Description: A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features.
mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales.
To infer which of the captured features are credible, Bayesian analysis is used.
The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction.
(2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found.
(3) Posterior credibility analysis of the differences of smooths created.
The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011>.
Matlab code is available under <http://cc.oulu.fi/~lpasanen/MRBSiZer/>.
Author: Thimo Schuster [aut],
Roman Flury [cre, aut],
Leena Pasanen [ctb],
Reinhard Furrer [ctb]
Maintainer: Roman Flury <roman.flury@math.uzh.ch>
Diff between mrbsizeR versions 1.2 dated 2019-12-06 and 1.2.1 dated 2019-12-13
DESCRIPTION | 8 ++--- MD5 | 12 +++---- NEWS.md | 10 ++++++ R/eigenQsphere.R | 76 +++++++++++++++++++++++++------------------------- inst/doc/mrbsizeR.pdf |binary man/eigenQsphere.Rd | 8 ++--- src/rcpp_helper.cpp | 2 - 7 files changed, 63 insertions(+), 53 deletions(-)
Title: In-depth Characterization and Analysis of Mutational Signatures
('ICAMS')
Description: Analysis and visualization of experimentally elucidated mutational
signatures -- the kind of analysis and visualization in Boot et al.,
"In-depth characterization of the cisplatin mutational signature in
human cell lines and in esophageal and liver tumors", Genome Research 2018,
<doi:10.1101/gr.230219.117>. 'ICAMS' stands for In-depth Characterization
and Analysis of Mutational Signatures. 'ICAMS' has functions to read in
variant call files (VCFs) and to collate the corresponding catalogs of
mutational spectra and to analyze and plot catalogs of mutational spectra
and signatures. Handles both "counts-based" and "density-based" catalogs
of mutational spectra or signatures.
Author: Steve Rozen, Nanhai Jiang, Arnoud Boot, Mo Liu
Maintainer: Steve Rozen <steverozen@gmail.com>
Diff between ICAMS versions 2.0.8 dated 2019-07-24 and 2.0.10 dated 2019-12-13
ICAMS-2.0.10/ICAMS/DESCRIPTION | 6 ICAMS-2.0.10/ICAMS/MD5 | 186 +- ICAMS-2.0.10/ICAMS/NAMESPACE | 10 ICAMS-2.0.10/ICAMS/R/COMPOSITE.R |only ICAMS-2.0.10/ICAMS/R/ICAMS.R | 21 ICAMS-2.0.10/ICAMS/R/ID_functions.R |only ICAMS-2.0.10/ICAMS/R/VCF_to_catalog_functions.R | 844 ++++++---- ICAMS-2.0.10/ICAMS/R/data.R | 75 ICAMS-2.0.10/ICAMS/R/other_catalog_formats.R | 227 ++ ICAMS-2.0.10/ICAMS/R/plot.R | 79 ICAMS-2.0.10/ICAMS/R/read_write_catalog.R | 52 ICAMS-2.0.10/ICAMS/R/strandbias_functions.R |only ICAMS-2.0.10/ICAMS/R/sysdata.rda |binary ICAMS-2.0.10/ICAMS/R/test_functions.R | 2 ICAMS-2.0.10/ICAMS/R/utility_functions.R | 321 +++ ICAMS-2.0.10/ICAMS/README.md | 27 ICAMS-2.0.10/ICAMS/data/all.abundance.rda |binary ICAMS-2.0.10/ICAMS/data/catalog.row.order.rda |binary ICAMS-2.0.10/ICAMS/data/catalog.row.order.sp.rda |only ICAMS-2.0.10/ICAMS/data/datalist |only ICAMS-2.0.10/ICAMS/data/gene.expression.data.HepG2.rda |only ICAMS-2.0.10/ICAMS/data/gene.expression.data.MCF10A.rda |only ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCh37.rda |binary ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCh38.rda |binary ICAMS-2.0.10/ICAMS/data/trans.ranges.GRCm38.rda |binary ICAMS-2.0.10/ICAMS/inst/WORDLIST | 53 ICAMS-2.0.10/ICAMS/inst/extdata/strelka.regress.cat.dbs.144.csv | 2 ICAMS-2.0.10/ICAMS/man/AnnotateDBSVCF.Rd |only ICAMS-2.0.10/ICAMS/man/AnnotateIDVCF.Rd |only ICAMS-2.0.10/ICAMS/man/AnnotateSBSVCF.Rd |only ICAMS-2.0.10/ICAMS/man/Canonicalize1Del.Rd |only ICAMS-2.0.10/ICAMS/man/Canonicalize1ID.Rd | 14 ICAMS-2.0.10/ICAMS/man/Canonicalize1INS.Rd | 8 ICAMS-2.0.10/ICAMS/man/CanonicalizeID.Rd | 9 ICAMS-2.0.10/ICAMS/man/CatalogRowOrder.Rd | 14 ICAMS-2.0.10/ICAMS/man/CheckAndFixChrNames.Rd |only ICAMS-2.0.10/ICAMS/man/CheckAndReorderRownames.Rd |only ICAMS-2.0.10/ICAMS/man/CreateOneColDBSMatrix.Rd | 29 ICAMS-2.0.10/ICAMS/man/CreateOneColIDMatrix.Rd | 18 ICAMS-2.0.10/ICAMS/man/CreateOneColSBSMatrix.Rd | 15 ICAMS-2.0.10/ICAMS/man/FindDelMH.Rd | 66 ICAMS-2.0.10/ICAMS/man/FindMaxRepeatDel.Rd | 50 ICAMS-2.0.10/ICAMS/man/FindMaxRepeatIns.Rd | 6 ICAMS-2.0.10/ICAMS/man/GeneExpressionData.Rd |only ICAMS-2.0.10/ICAMS/man/GetExomeKmerCounts.Rd | 7 ICAMS-2.0.10/ICAMS/man/GetStrandedKmerCounts.Rd | 3 ICAMS-2.0.10/ICAMS/man/GetVAF.Rd | 9 ICAMS-2.0.10/ICAMS/man/ICAMS.Rd | 21 ICAMS-2.0.10/ICAMS/man/InferRownames.Rd |only ICAMS-2.0.10/ICAMS/man/MutectVCFFilesToCatalog.Rd | 24 ICAMS-2.0.10/ICAMS/man/MutectVCFFilesToCatalogAndPlotToPdf.Rd | 31 ICAMS-2.0.10/ICAMS/man/Plot96PartOfCompositeToPDF.Rd |only ICAMS-2.0.10/ICAMS/man/PlotCatalog.Rd | 5 ICAMS-2.0.10/ICAMS/man/PlotTransBiasGeneExp.Rd |only ICAMS-2.0.10/ICAMS/man/PlotTransBiasGeneExpToPdf.Rd |only ICAMS-2.0.10/ICAMS/man/ReadAndSplitMutectVCFs.Rd | 17 ICAMS-2.0.10/ICAMS/man/ReadAndSplitStrelkaSBSVCFs.Rd | 9 ICAMS-2.0.10/ICAMS/man/ReadBedRanges.Rd | 3 ICAMS-2.0.10/ICAMS/man/ReadCatalog.Rd | 8 ICAMS-2.0.10/ICAMS/man/ReadDukeNUSCat192.Rd | 9 ICAMS-2.0.10/ICAMS/man/ReadMutectVCF.Rd | 13 ICAMS-2.0.10/ICAMS/man/ReadMutectVCFs.Rd | 16 ICAMS-2.0.10/ICAMS/man/ReadStapleGT96SBS.Rd | 2 ICAMS-2.0.10/ICAMS/man/ReadStrelkaIDVCF.Rd | 2 ICAMS-2.0.10/ICAMS/man/ReadStrelkaIDVCFs.Rd | 15 ICAMS-2.0.10/ICAMS/man/ReadStrelkaSBSVCFs.Rd | 9 ICAMS-2.0.10/ICAMS/man/RenameColumnsWithNameStrand.Rd |only ICAMS-2.0.10/ICAMS/man/RenameColumnsWithNameVAF.Rd |only ICAMS-2.0.10/ICAMS/man/Restaple96.Rd |only ICAMS-2.0.10/ICAMS/man/StrelkaIDVCFFilesToCatalog.Rd | 23 ICAMS-2.0.10/ICAMS/man/StrelkaIDVCFFilesToCatalogAndPlotToPdf.Rd | 35 ICAMS-2.0.10/ICAMS/man/StrelkaSBSVCFFilesToCatalog.Rd | 15 ICAMS-2.0.10/ICAMS/man/StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd | 23 ICAMS-2.0.10/ICAMS/man/TestPlotCatCOMPOSITE.Rd |only ICAMS-2.0.10/ICAMS/man/TransRownames.ID.PCAWG.SigPro.Rd |only ICAMS-2.0.10/ICAMS/man/TransRownames.ID.SigPro.PCAWG.Rd |only ICAMS-2.0.10/ICAMS/man/TranscriptRanges.Rd | 17 ICAMS-2.0.10/ICAMS/man/TransformCatalog.Rd | 2 ICAMS-2.0.10/ICAMS/man/Unstaple96.Rd |only ICAMS-2.0.10/ICAMS/man/VCFsToDBSCatalogs.Rd | 6 ICAMS-2.0.10/ICAMS/man/VCFsToIDCatalogs.Rd | 21 ICAMS-2.0.10/ICAMS/man/VCFsToSBSCatalogs.Rd | 6 ICAMS-2.0.10/ICAMS/man/WriteCatalog.Rd | 2 ICAMS-2.0.10/ICAMS/man/WriteCatalogIndelSigPro.Rd |only ICAMS-2.0.10/ICAMS/man/as.catalog.Rd | 25 ICAMS-2.0.10/ICAMS/tests/testthat/test_1strandbias_functions.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_AnnotateIDVCF.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_COMPOSITE.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_CheckAndFixChrNames.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_ID_fns.R | 18 ICAMS-2.0.10/ICAMS/tests/testthat/test_MakeCatalogFromMutectGRCh38VCF.R | 2 ICAMS-2.0.10/ICAMS/tests/testthat/test_MakeCatalogFromStrelkaGRCh38VCF.R | 4 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS136Catalog.R | 4 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS144Catalog.R | 8 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.DBS78Catalog.R | 8 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.IndelCatalog.R | 4 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS1536Catalog.R | 8 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS192Catalog.R | 16 ICAMS-2.0.10/ICAMS/tests/testthat/test_PlotCatalog.SBS96Catalog.R | 8 ICAMS-2.0.10/ICAMS/tests/testthat/test_PyrPenta.R | 1 ICAMS-2.0.10/ICAMS/tests/testthat/test_ReadVCF.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_SigProfiler_formats.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_TransRownames.ID.PCAWG.SigPro.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_as.catalog.R |only ICAMS-2.0.10/ICAMS/tests/testthat/test_extended_seq.context_functions.R | 3 ICAMS-2.0.10/ICAMS/tests/testthat/test_methods_for_subsetting_catalogs.R | 14 ICAMS-2.0.10/ICAMS/tests/testthat/testdata/sigProfiler_ID_signatures.csv |only ICAMS-2.0.10/ICAMS/tests/testthat/testdata/test_AddSeqContext.Rdata |binary ICAMS-2.0.10/ICAMS/tests/testthat/testdata/test_AnnotateIDVCF.Rdata |only ICAMS-2.0.8/ICAMS/R/INDELS_related_functions.R |only ICAMS-2.0.8/ICAMS/man/AddAndCheckSequenceID.Rd |only ICAMS-2.0.8/ICAMS/man/Canonicalize1DEL.Rd |only ICAMS-2.0.8/ICAMS/tests/testthat/test_AddAndCheckSequenceID.R |only ICAMS-2.0.8/ICAMS/tests/testthat/test_ReadAndSplitVCF.R |only ICAMS-2.0.8/ICAMS/tests/testthat/testdata/test_AddAndCheckSequenceID.Rdata |only 115 files changed, 1894 insertions(+), 716 deletions(-)
Title: Tools for Environmental Analyses, Ecotoxicology and Various R
Functions
Description: Contains many functions useful for managing 'NetCDF' files (see <http://en.wikipedia.org/wiki/NetCDF>), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>
Diff between HelpersMG versions 3.8 dated 2019-10-06 and 3.9 dated 2019-12-13
DESCRIPTION | 10 +- MD5 | 138 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS | 15 ++++ R/HelpersMG-package.R | 4 - R/MHalgoGen.R | 9 +- R/MovingWindow.R |only R/d.R | 14 ++-- R/dSnbinom.R | 30 +++++--- R/plot.mcmcComposite.R | 50 +++----------- man/ChangeCoordinate.Rd | 7 +- man/ExtractAIC.glm.Rd | 6 + man/HelpersMG-package.Rd | 4 - man/IC_clean_data.Rd | 22 ++++-- man/IC_correlation_simplify.Rd | 7 +- man/IC_threshold_matrix.Rd | 23 ++++-- man/LD50.Rd | 33 ++++++--- man/LD50_MHmcmc.Rd | 31 ++++++-- man/LD50_MHmcmc_p.Rd | 15 ++-- man/MHalgoGen.Rd | 37 +++++++--- man/MovingWindow.Rd |only man/ScalePreviousPlot.Rd | 6 + man/as.mcmc.mcmcComposite.Rd | 12 ++- man/as.parameters.Rd | 13 ++- man/as.quantiles.Rd | 25 ++++--- man/asc.Rd | 6 + man/barplot_errbar.Rd | 23 ++++-- man/cArrows.Rd | 25 +++++-- man/chr.Rd | 6 + man/compare.Rd | 5 - man/compare_AIC.Rd | 6 + man/compare_AICc.Rd | 6 + man/compare_BIC.Rd | 6 + man/contingencyTable.compare.Rd | 12 ++- man/d.Rd | 18 +++-- man/dSnbinom.Rd | 23 ++++-- man/ellipse.Rd | 21 ++++-- man/flexit.Rd | 17 ++++ man/ind_long_lat.Rd | 12 ++- man/index.periodic.Rd | 11 +-- man/inside.search.Rd | 12 ++- man/invlogit.Rd | 4 - man/local.search.Rd | 10 ++ man/logLik.LD50.Rd | 9 +- man/logit.Rd | 4 - man/merge.mcmcComposite.Rd | 12 ++- man/minmax.periodic.Rd | 22 ++++-- man/moon.info.Rd | 8 +- man/newcompassRose.Rd | 11 ++- man/newdbeta.Rd | 3 man/newmap.scale.Rd | 11 ++- man/pSnbinom.Rd | 18 +++-- man/plot.IconoCorel.Rd | 22 ++++-- man/plot.LD50.Rd | 26 +++++-- man/plot.mcmcComposite.Rd | 44 +++++++----- man/plot_add.Rd | 6 + man/plot_errbar.Rd | 33 ++++++--- man/predict.LD50.Rd | 20 ++++- man/qSnbinom.Rd | 18 +++-- man/qvlmer.Rd | 3 man/rSnbinom.Rd | 6 + man/read_folder.Rd | 9 ++ man/series.compare.Rd | 8 +- man/summary.mcmcComposite.Rd | 12 ++- man/sun.info.Rd | 8 +- man/symbol.Female.Rd | 3 man/symbol.Male.Rd | 3 man/symmetricize.Rd | 7 +- man/tide.info.Rd | 18 +++-- man/tnirp.Rd | 6 + man/universalmclapply.Rd | 15 +++- 71 files changed, 702 insertions(+), 398 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-13 1.4
2018-05-16 1.3
2013-02-14 1.2
2012-10-30 1.01
2011-04-09 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-13 1.1
2017-02-07 1.0
Title: Expressions with Statistical Details
Description: Statistical processing backend for 'ggstatsplot',
this package creates expressions with details from statistical tests.
Currently, it supports only the most common types of statistical
tests: parametric, nonparametric, robust, and bayesian versions of
t-test/anova, correlation analyses, contingency table analysis.
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>),
Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between statsExpressions versions 0.1.1 dated 2019-08-28 and 0.1.2 dated 2019-12-13
DESCRIPTION | 17 MD5 | 150 ++--- NAMESPACE | 11 NEWS.md | 4 R/helpers_bf_tests.R | 7 R/helpers_contingency_tabs_expressions.R | 2 R/helpers_corr_test_expressions.R | 1 R/helpers_effsize_ci.R | 4 R/helpers_t_onesample_expressions.R | 67 +- R/helpers_t_test_expressions.R | 35 - R/reexports.R | 12 README.md | 11 inst/CITATION | 3 inst/doc/stats_details.R | 2 inst/doc/stats_details.html | 34 - inst/doc/tests_and_coverage.R | 2 inst/doc/tests_and_coverage.Rmd | 214 ++++--- inst/doc/tests_and_coverage.html | 592 ++++++++++++---------- man/Titanic_full.Rd | 72 +- man/VR_dilemma.Rd | 84 +-- man/bf_contingency_tab.Rd | 268 +++++---- man/bf_corr_test.Rd | 150 ++--- man/bf_expr.Rd | 118 ++-- man/bf_extractor.Rd | 58 +- man/bf_oneway_anova.Rd | 171 +++--- man/bf_ttest.Rd | 280 +++++----- man/bugs_long.Rd | 82 +-- man/effsize_ci_message.Rd | 46 - man/effsize_t_parametric.Rd | 271 +++++----- man/effsize_type_switch.Rd | 42 - man/expr_anova_bayes.Rd | 141 ++--- man/expr_anova_nonparametric.Rd | 192 +++---- man/expr_anova_parametric.Rd | 250 ++++----- man/expr_anova_robust.Rd | 217 ++++---- man/expr_contingency_tab.Rd | 288 +++++----- man/expr_corr_test.Rd | 202 +++---- man/expr_t_bayes.Rd | 135 ++--- man/expr_t_nonparametric.Rd | 296 +++++------ man/expr_t_onesample.Rd | 257 +++++---- man/expr_t_parametric.Rd | 240 ++++---- man/expr_t_robust.Rd | 205 ++++--- man/expr_template.Rd | 192 +++---- man/figures/README-example_anova-1.png |binary man/figures/README-example_anova_parametric-1.png |binary man/figures/README-example_contingency-1.png |binary man/figures/README-example_corr-1.png |binary man/figures/README-example_t_one-1.png |binary man/figures/README-example_t_two-1.png |binary man/intent_morality.Rd | 106 +-- man/iris_long.Rd | 84 +-- man/long_to_wide_converter.Rd | 74 +- man/movies_long.Rd | 96 +-- man/movies_wide.Rd | 100 +-- man/reexports.Rd | 64 +- man/robcor_ci.Rd | 372 ++++++------- man/stats_type_switch.Rd | 42 - man/t1way_ci.Rd | 364 ++++++------- man/yuend_ci.Rd | 374 +++++++------ tests/README.md | 216 ++++---- tests/testthat/test-effsize_helpers.R | 271 +++++----- tests/testthat/test-expr_anova_bayes.R | 5 tests/testthat/test-expr_anova_nonparametric.R | 3 tests/testthat/test-expr_anova_parametric.R | 115 ++-- tests/testthat/test-expr_anova_robust.R | 19 tests/testthat/test-expr_contingency_tab.R | 20 tests/testthat/test-expr_corr_test.R | 6 tests/testthat/test-expr_t_bayes.R | 8 tests/testthat/test-expr_t_nonparametric.R | 6 tests/testthat/test-expr_t_onesample.R | 5 tests/testthat/test-expr_t_parametric.R | 118 ++-- tests/testthat/test-expr_t_robust.R | 160 +++-- tests/testthat/test-expr_templates.R | 232 ++++---- tests/testthat/test-helpers_bf_tests.R | 18 tests/testthat/test-subtitle_misc_helpers.R | 2 tests/testthat/test-switch_statements.R | 4 vignettes/tests_and_coverage.Rmd | 214 ++++--- 76 files changed, 4463 insertions(+), 4060 deletions(-)
More information about statsExpressions at CRAN
Permanent link
Title: Sparse Linear Algebra
Description: Some basic linear algebra functionality for sparse matrices is
provided: including Cholesky decomposition and backsolving as well as
standard R subsetting and Kronecker products.
Author: Roger Koenker <rkoenker@uiuc.edu> and Pin Ng <Pin.Ng@NAU.EDU>
Maintainer: Roger Koenker <rkoenker@uiuc.edu>
Diff between SparseM versions 1.77 dated 2017-04-23 and 1.78 dated 2019-12-13
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/SparseM.R | 5 ++--- build/vignette.rds |binary inst/ChangeLog | 5 +++++ inst/doc/SparseM.pdf |binary 6 files changed, 15 insertions(+), 11 deletions(-)
Title: Generalized Poisson Binomial Distribution
Description: Functions that compute the distribution functions for the Generalized Poisson Binomial distribution as described in Zhang et al. (2018)<doi: 10.1080/00949655.2018.1440294>, which provides the cdf, pmf, quantile function, and random number generation for the distribution. The C code for fast Fourier transformation (FFT) is written by Ross Ihaka from University of Auckland, which implements the FFT algorithm in Singleton (1969) <doi: 10.1109/TAU.1969.1162042>.
Author: Yili Hong [aut, cre],
Man Zhang [aut, ctb],
Ross Ihaka [aut, cph]
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between GPB versions 1.0 dated 2017-02-07 and 1.1 dated 2019-12-13
DESCRIPTION | 16 +++++++++------- MD5 | 9 +++++---- man/GPB-package.Rd | 2 +- man/pgpb.Rd | 3 ++- src/GPB_init.c |only src/dftcf.c | 28 ++++++++++++++-------------- 6 files changed, 31 insertions(+), 27 deletions(-)
Title: Censored Regression (Tobit) Models
Description: Maximum Likelihood estimation of censored regression (Tobit) models
with cross-sectional and panel data.
Author: Arne Henningsen <arne.henningsen@gmail.com>
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between censReg versions 0.5-26 dated 2017-03-21 and 0.5-30 dated 2019-12-13
DESCRIPTION | 8 MD5 | 22 NAMESPACE | 2 R/censReg.R | 20 build/vignette.rds |binary inst/NEWS.Rd | 8 inst/doc/censReg.pdf |binary tests/censRegPanelTest.R | 53 +- tests/censRegPanelTest.RData.save |binary tests/censRegPanelTest.Rout.save | 199 ++++++- tests/censRegTest.R | 147 ++--- tests/censRegTest.Rout.save | 974 ++++++++++++++++++++++++-------------- 12 files changed, 943 insertions(+), 490 deletions(-)
Title: Damped Anderson Acceleration with Epsilon Monotonicity for
Accelerating EM-Like Monotone Algorithms
Description: Implements the DAAREM method for accelerating the convergence of slow, monotone sequences from smooth, fixed-point iterations such as the EM algorithm. For further details about the DAAREM method. see Henderson, N.C. and Varadhan, R. (2018) <arXiv:1803.06673>.
Author: Nicholas Henderson [cre, aut],
Ravi Varadhan [aut]
Maintainer: Nicholas Henderson <nchender@umich.edu>
Diff between daarem versions 0.4 dated 2019-09-27 and 0.4.1 dated 2019-12-13
DESCRIPTION | 8 +- MD5 | 8 +- NEWS | 6 + R/daarem_base_noobjfn.R | 131 ++++++++++++++++-------------------- R/daarem_base_objfn.R | 171 ++++++++++++++++++++++-------------------------- 5 files changed, 151 insertions(+), 173 deletions(-)
Title: The Poisson Binomial Distribution
Description: Implementation of both the exact and approximation methods for computing the cdf of the Poisson binomial distribution. It also provides the pmf, quantile function, and random number generation for the Poisson binomial distribution. We would like to acknowledge that the C code for FFT is adopted from R distribution (fft.c, by Ross Ihaka from University of Auckland, dated February 1997).
Author: Yili Hong
Maintainer: Yili Hong <yilihong@vt.edu>
Diff between poibin versions 1.3 dated 2018-05-16 and 1.4 dated 2019-12-13
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/funs.R | 7 +++++++ build/partial.rdb |binary man/poibin-package.Rd | 1 + man/ppoibin.Rd | 3 ++- src/dftcf.c | 28 ++++++++++++++-------------- 8 files changed, 37 insertions(+), 28 deletions(-)
Title: Phylogenetic Comparative Methods for High-Dimensional Traits
Description: Tools for studying the evolution of high-dimensional traits
(morphometric, function-valued, etc.) including ancestral state reconstruction,
estimating phylogenetic signal, and assessing correlated trait evolution. Visit
<http://www.phylocurve.org> for more information.
Author: Eric W. Goolsby
Maintainer: Eric W. Goolsby <eric.goolsby.evolution@gmail.com>
Diff between phylocurve versions 2.0.9 dated 2017-08-09 and 2.0.10 dated 2019-12-13
DESCRIPTION | 8 MD5 | 12 R/RcppExports.R | 70 R/fast_geomorph_functions.R | 1696 +++++++------- R/phylocurve.R | 5094 ++++++++++++++++++++++---------------------- man/ultraFastAnc.Rd | 102 src/RcppExports.cpp | 33 7 files changed, 3514 insertions(+), 3501 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including 'BLACS', 'PBLAS', and 'ScaLAPACK' in double precision via
'pbdMPI' based on 'ScaLAPACK' version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-6 dated 2019-06-24 and 0.2-7 dated 2019-12-13
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- configure | 4 ++-- configure.ac | 4 ++-- inst/doc/pbdSLAP-guide.pdf |binary src/BLACS/dgamn2d_.c | 8 ++++++-- src/BLACS/dgamx2d_.c | 8 ++++++-- src/BLACS/igamn2d_.c | 8 ++++++-- src/BLACS/igamx2d_.c | 8 ++++++-- vignettes/pbdSLAP-include/01-introduction.tex | 6 +++--- vignettes/pbdSLAP-include/02-extra.tex | 12 ++++++------ 12 files changed, 57 insertions(+), 36 deletions(-)
Title: Linear Quantile Mixed Models
Description: Functions to fit quantile regression models for hierarchical
data (2-level nested designs) as described in Geraci and
Bottai (2014, Statistics and Computing) <doi:10.1007/s11222-013-9381-9>.
A vignette is given in Geraci (2014, Journal of Statistical Software)
<doi:10.18637/jss.v057.i13> and included in the package documents.
The packages also provides functions to fit quantile models for
independent data and for count responses.
Author: Marco Geraci
Maintainer: Marco Geraci <geraci@mailbox.sc.edu>
Diff between lqmm versions 1.5.4 dated 2018-04-13 and 1.5.5 dated 2019-12-13
lqmm-1.5.4/lqmm/inst/doc |only lqmm-1.5.5/lqmm/DESCRIPTION | 11 +- lqmm-1.5.5/lqmm/MD5 | 13 +-- lqmm-1.5.5/lqmm/NEWS | 7 + lqmm-1.5.5/lqmm/R/auxiliary.R | 2 lqmm-1.5.5/lqmm/R/lqm.R | 142 +++++++++++++++++------------------- lqmm-1.5.5/lqmm/R/lqmm.R | 13 +-- lqmm-1.5.5/lqmm/man/lqmm-package.Rd | 4 - 8 files changed, 94 insertions(+), 98 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
Author: Søren Højsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Ekstrøm [ctb]
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.3-0 dated 2019-12-12 and 1.3-1 dated 2019-12-13
ChangeLog | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- inst/doc/geepack-manual.pdf |binary src/gee2.cc | 1 + src/ordgee.cc | 3 ++- 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Kernel Density Estimation using Lifetime Distributions
Description: A collection of asymmetrical kernels belong to lifetime distributions for kernel density estimation is presented.
Mean Squared Errors (MSE) are calculated for estimated curves. For this purpose, R functions allow the distribution to be Gamma, Exponential or Weibull.
For details see Chen (2000), Jin and Kawczak (2003) and Salha et al. (2014) <doi:10.12988/pms.2014.4616>.
Author: Javaria Ahmad Khan, Atif Akbar.
Maintainer: Javaria Ahmad Khan <jakhan0@yahoo.com>
Diff between DELTD versions 1.3.1 dated 2019-09-24 and 2.6.5 dated 2019-12-13
DELTD-1.3.1/DELTD/man/denBS.Rd |only DELTD-1.3.1/DELTD/man/denEr.Rd |only DELTD-1.3.1/DELTD/man/denGamma.Rd |only DELTD-1.3.1/DELTD/man/denLN.Rd |only DELTD-1.3.1/DELTD/man/suicide.Rd |only DELTD-2.6.5/DELTD/DESCRIPTION | 15 - DELTD-2.6.5/DELTD/MD5 | 30 +-- DELTD-2.6.5/DELTD/NAMESPACE | 12 - DELTD-2.6.5/DELTD/R/DELTD.R | 326 ++++++++++++++++++++++++--------- DELTD-2.6.5/DELTD/man/BS.Rd |only DELTD-2.6.5/DELTD/man/DELTD-package.Rd |only DELTD-2.6.5/DELTD/man/Erlang.Rd |only DELTD-2.6.5/DELTD/man/Gamma.Rd |only DELTD-2.6.5/DELTD/man/LN.Rd |only DELTD-2.6.5/DELTD/man/dencomb.Rd | 29 ++ DELTD-2.6.5/DELTD/man/mseBS.Rd | 19 + DELTD-2.6.5/DELTD/man/mseEr.Rd | 19 + DELTD-2.6.5/DELTD/man/mseGamma.Rd | 20 +- DELTD-2.6.5/DELTD/man/mseLN.Rd | 19 + DELTD-2.6.5/DELTD/man/plot.BS.Rd |only DELTD-2.6.5/DELTD/man/plot.Erlang.Rd |only DELTD-2.6.5/DELTD/man/plot.Gamma.Rd |only DELTD-2.6.5/DELTD/man/plot.LN.Rd |only 23 files changed, 350 insertions(+), 139 deletions(-)
Title: Bayesian Group Sparse Multi-Task Regression
Description: Implementation of Bayesian multi-task regression models and was developed within the context of imaging genetics. The package can currently fit two models. The Bayesian group sparse multi-task regression model of Greenlaw et al. (2017)<doi:10.1093/bioinformatics/btx215> can be fit with implementation using Gibbs sampling. An extension of this model developed by Song, Ge et al. to accommodate both spatial correlation as well as correlation across brain hemispheres can also be fit using either mean-field variational Bayes or Gibbs sampling. The model can also be used more generally for multivariate (non-imaging) phenotypes with spatial correlation.
Author: Yin Song, Shufei Ge, Liangliang Wang, Jiguo Cao, Keelin Greenlaw, Mary Lesperance, Farouk S. Nathoo
Maintainer: Yin Song <yinsong@uvic.ca>
Diff between bgsmtr versions 0.6 dated 2019-12-02 and 0.7 dated 2019-12-13
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/all_functions.R | 10 +++++----- man/sp_bgsmtr.Rd | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)