Title: Run Code 'With' Temporarily Modified Global State
Description: A set of functions to run code 'with' safely and
temporarily modified global state. Many of these functions were
originally a part of the 'devtools' package, this provides a simple
package with limited dependencies to provide access to these
functions.
Author: Jim Hester [aut, cre],
Kirill Müller [aut],
Kevin Ushey [aut],
Hadley Wickham [aut],
Winston Chang [aut],
Richard Cotton [ctb],
RStudio [cph]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between withr versions 2.1.2 dated 2018-03-15 and 2.2.0 dated 2020-04-20
DESCRIPTION | 68 +++++++---- MD5 | 123 +++++++++++---------- NAMESPACE | 9 + NEWS.md | 28 ++++ R/collate.R | 7 + R/connection.R | 7 - R/defer.R | 67 +++++++++-- R/devices.R | 7 + R/dir.R | 20 +++ R/env.R | 7 + R/libpaths.R | 6 + R/local_.R | 2 R/locale.R | 25 ++++ R/makevars.R | 13 +- R/namespace.R | 20 ++- R/options.R | 35 +++++- R/par.R | 12 ++ R/path.R | 6 + R/rng.R |only R/seed.R | 33 +++-- R/tempfile.R | 8 + R/timezone.R |only R/utils.R | 35 ++++++ R/with.R | 2 R/with_.R | 2 README.md | 130 ++++++++++++++++------ build/vignette.rds |binary inst/doc/withr.R | 12 +- inst/doc/withr.Rmd | 2 inst/doc/withr.html | 210 +++++++++++++++++++++---------------- man/defer.Rd | 34 ++++- man/devices.Rd | 199 ++++++++++++++++++++++++++++------- man/figures |only man/makevars_user.Rd |only man/set_makevars.Rd | 16 +- man/with_.Rd | 12 +- man/with_collate.Rd | 14 +- man/with_connection.Rd | 6 - man/with_db_connection.Rd | 4 man/with_dir.Rd | 17 ++ man/with_envvar.Rd | 14 +- man/with_file.Rd | 6 - man/with_gctorture2.Rd | 4 man/with_libpaths.Rd | 19 ++- man/with_locale.Rd | 32 +++++ man/with_makevars.Rd | 22 ++- man/with_options.Rd | 33 +++++ man/with_package.Rd | 74 ++++++++----- man/with_par.Rd | 21 ++- man/with_path.Rd | 14 +- man/with_rng_version.Rd |only man/with_seed.Rd | 4 man/with_sink.Rd | 14 +- man/with_temp_libpaths.Rd | 10 + man/with_tempfile.Rd | 32 ++++- man/with_timezone.Rd |only man/withr.Rd | 31 +++++ tests/testthat/test-connection.R | 26 ++++ tests/testthat/test-defer.R | 27 ++++ tests/testthat/test-local.R | 12 ++ tests/testthat/test-rng.R |only tests/testthat/test-seed.R |only tests/testthat/test-tempdir.R |only tests/testthat/test-timezone.R |only tests/testthat/test-with.R | 17 -- vignettes/releases/withr-2.1.0.Rmd | 2 vignettes/withr.Rmd | 2 67 files changed, 1187 insertions(+), 427 deletions(-)
Title: Computation of Risk-Based Portfolios
Description: Collection of functions designed to compute risk-based portfolios as described
in Ardia et al. (2017) <doi:10.1007/s10479-017-2474-7> and Ardia et al. (2017) <doi:10.21105/joss.00171>.
Author: David Ardia [aut, cre, cph] (<https://orcid.org/0000-0003-2823-782X>),
Kris Boudt [aut],
Jean-Philippe Gagnon-Fleury [aut]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between RiskPortfolios versions 2.1.3 dated 2020-04-19 and 2.1.4 dated 2020-04-20
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 3 +++ README.md |only build/partial.rdb |binary 5 files changed, 11 insertions(+), 7 deletions(-)
More information about RiskPortfolios at CRAN
Permanent link
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: Provides the bayesGARCH() function which performs the
Bayesian estimation of the GARCH(1,1) model with Student's t innovations as described in Ardia (2008) <doi:10.1007/978-3-540-78657-3>.
Author: David Ardia [aut, cre, cph] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between bayesGARCH versions 2.1.4 dated 2020-04-19 and 2.1.5 dated 2020-04-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ README.md | 4 ++-- build/partial.rdb |binary man/bayesGARCH.Rd | 10 ++++++++-- 6 files changed, 22 insertions(+), 13 deletions(-)
Title: Adaptive Mixture of Student-t Distributions
Description: Provides functions to perform the fitting of an adaptive mixture
of Student-t distributions to a target density through its kernel function as described in
Ardia et al. (2009) <doi:10.18637/jss.v029.i03>. The
mixture approximation can then be used as the importance density in importance
sampling or as the candidate density in the Metropolis-Hastings algorithm to
obtain quantities of interest for the target density itself.
Author: David Ardia [aut, cre, cph] (<https://orcid.org/0000-0003-2823-782X>),
Lennart Hoogerheide [ctb],
Herman van Dijk [ctb]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between AdMit versions 2.1.4 dated 2020-04-19 and 2.1.5 dated 2020-04-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 3 +++ README.md | 2 +- build/partial.rdb |binary inst/doc/AdMit.pdf |binary man/AdMit.Rd | 8 +++++++- 7 files changed, 21 insertions(+), 12 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. <https://martin3141.github.io/spant/>.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 1.3.0 dated 2020-04-03 and 1.4.0 dated 2020-04-20
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++------- NAMESPACE | 1 NEWS.md | 4 ++ R/mrs_data_display.R | 23 +++++++++++++-- R/mrs_data_io.R | 21 +++++++++++-- inst/WORDLIST | 2 + inst/doc/spant-intro.html | 58 +++++++++++++++++++------------------- inst/doc/spant-preprocessing.html | 4 +- man/figures |only man/read_mrs.Rd | 2 - man/stackplot.mrs_data.Rd | 4 ++ man/write_mrs_rda.Rd |only tests/testthat/test_fitting.R | 2 - 14 files changed, 98 insertions(+), 55 deletions(-)
Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One
Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in the console or in txt, html or pdf files. Download the whole documentation of packages (html index, pdf manual, vignettes, source code, etc) with a single instruction. Visualize the package dependencies and CRAN checks. Explore CRAN archive. Use the above functions for task view maintenance. Use quick links and 70 web search engines to explore the web. A lazy evaluation of non-standard content is available throughout the package and eases the use of many functions.
Author: Patrice Kiener [aut, cre] (<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between RWsearch versions 4.7.0 dated 2020-02-15 and 4.8.0 dated 2020-04-20
RWsearch-4.7.0/RWsearch/R/n_graph.R |only RWsearch-4.7.0/RWsearch/man/n_graph.Rd |only RWsearch-4.8.0/RWsearch/DESCRIPTION | 12 RWsearch-4.8.0/RWsearch/MD5 | 137 +- RWsearch-4.8.0/RWsearch/NAMESPACE | 417 +++---- RWsearch-4.8.0/RWsearch/NEWS | 101 + RWsearch-4.8.0/RWsearch/R/a_intro.R | 25 RWsearch-4.8.0/RWsearch/R/archivedb.R | 60 - RWsearch-4.8.0/RWsearch/R/checkdb.R |only RWsearch-4.8.0/RWsearch/R/cnsc.R | 2 RWsearch-4.8.0/RWsearch/R/crandb.R | 28 RWsearch-4.8.0/RWsearch/R/e_check.R | 2 RWsearch-4.8.0/RWsearch/R/f_args.R | 3 RWsearch-4.8.0/RWsearch/R/f_pdf.R | 12 RWsearch-4.8.0/RWsearch/R/h_R.R | 16 RWsearch-4.8.0/RWsearch/R/h_engine.R | 32 RWsearch-4.8.0/RWsearch/R/p_archive.R |only RWsearch-4.8.0/RWsearch/R/p_check.R |only RWsearch-4.8.0/RWsearch/R/p_deps.R | 156 -- RWsearch-4.8.0/RWsearch/R/p_display.R | 2 RWsearch-4.8.0/RWsearch/R/p_down.R | 80 + RWsearch-4.8.0/RWsearch/R/p_graph.R |only RWsearch-4.8.0/RWsearch/R/p_html.R | 128 -- RWsearch-4.8.0/RWsearch/R/p_inun.R | 24 RWsearch-4.8.0/RWsearch/R/p_table2pdf.R | 9 RWsearch-4.8.0/RWsearch/R/p_text2pdf.R | 19 RWsearch-4.8.0/RWsearch/R/p_vers.R |only RWsearch-4.8.0/RWsearch/R/s_crandb_tvdb.R | 5 RWsearch-4.8.0/RWsearch/R/s_hs.R | 4 RWsearch-4.8.0/RWsearch/R/s_sos.R | 10 RWsearch-4.8.0/RWsearch/R/s_tvdb.R | 3 RWsearch-4.8.0/RWsearch/R/tvdb.R | 15 RWsearch-4.8.0/RWsearch/build/vignette.rds |binary RWsearch-4.8.0/RWsearch/data/zcrandb.rda |binary RWsearch-4.8.0/RWsearch/data/ztvdb.rda |binary RWsearch-4.8.0/RWsearch/inst/aabb/zCRAN-archive.html | 174 ++- RWsearch-4.8.0/RWsearch/inst/aabb/zcheck_results.rds |only RWsearch-4.8.0/RWsearch/inst/doc/RWsearch-1-Introduction.html | 48 RWsearch-4.8.0/RWsearch/inst/doc/RWsearch-2-Print-Download-Doc.html | 48 RWsearch-4.8.0/RWsearch/inst/doc/RWsearch-3-TaskViews.html | 48 RWsearch-4.8.0/RWsearch/inst/doc/RWsearch-4-Web-search-engines.Rmd | 2 RWsearch-4.8.0/RWsearch/inst/doc/RWsearch-4-Web-search-engines.html | 56 - RWsearch-4.8.0/RWsearch/man/RWsearch-package.Rd | 231 ++-- RWsearch-4.8.0/RWsearch/man/archivedb.Rd | 233 ++-- RWsearch-4.8.0/RWsearch/man/checkdb.Rd |only RWsearch-4.8.0/RWsearch/man/cnsc.Rd | 116 +- RWsearch-4.8.0/RWsearch/man/crandb.Rd | 189 +-- RWsearch-4.8.0/RWsearch/man/cranmirrors.Rd | 78 - RWsearch-4.8.0/RWsearch/man/e_check.Rd | 62 - RWsearch-4.8.0/RWsearch/man/f_args.Rd | 85 - RWsearch-4.8.0/RWsearch/man/f_pdf.Rd | 54 RWsearch-4.8.0/RWsearch/man/funmaintext.Rd | 133 +- RWsearch-4.8.0/RWsearch/man/h_R.Rd | 212 +-- RWsearch-4.8.0/RWsearch/man/h_direct.Rd | 152 +- RWsearch-4.8.0/RWsearch/man/h_engine.Rd | 548 +++++----- RWsearch-4.8.0/RWsearch/man/h_ttp.Rd | 54 RWsearch-4.8.0/RWsearch/man/p_archive.Rd |only RWsearch-4.8.0/RWsearch/man/p_check.Rd |only RWsearch-4.8.0/RWsearch/man/p_deps.Rd | 211 +-- RWsearch-4.8.0/RWsearch/man/p_display.Rd | 120 +- RWsearch-4.8.0/RWsearch/man/p_down.Rd | 235 ++-- RWsearch-4.8.0/RWsearch/man/p_graph.Rd |only RWsearch-4.8.0/RWsearch/man/p_html.Rd | 195 +-- RWsearch-4.8.0/RWsearch/man/p_inun.Rd | 102 - RWsearch-4.8.0/RWsearch/man/p_table2pdf.Rd | 241 ++-- RWsearch-4.8.0/RWsearch/man/p_text2pdf.Rd | 249 ++-- RWsearch-4.8.0/RWsearch/man/p_vers.Rd |only RWsearch-4.8.0/RWsearch/man/s_crandb.Rd | 236 ++-- RWsearch-4.8.0/RWsearch/man/s_crandb_tvdb.Rd | 197 +-- RWsearch-4.8.0/RWsearch/man/s_hs.Rd | 83 - RWsearch-4.8.0/RWsearch/man/s_sos.Rd | 82 - RWsearch-4.8.0/RWsearch/man/s_tvdb.Rd | 61 - RWsearch-4.8.0/RWsearch/man/tvdb.Rd | 173 +-- RWsearch-4.8.0/RWsearch/man/zcrandb.Rd | 40 RWsearch-4.8.0/RWsearch/man/ztvdb.Rd | 32 RWsearch-4.8.0/RWsearch/vignettes/RWsearch-4-Web-search-engines.Rmd | 2 76 files changed, 3031 insertions(+), 3053 deletions(-)
Title: Multivariate Normal Distribution Characterization Test
Description: Provides a test of multivariate normality of a sample which does
not require estimation of the nuisance parameters, the mean and covariance
matrix. Rather, a sequence of transformations removes these nuisance
parameters and results in a set of sample matrices that are positive
definite. These matrices are uniformly distributed on the space of positive
definite matrices in the unit hyperrectangle if and only if the original
data is multivariate normal. The package performs a goodness of fit test of
this hypothesis. Four sample datasets are included: a bivariate and a
trivariate normal set and a bivariate and trivariate Bernoulli set. In
addition to the test, functions in the package give rotatable visualizations
of the support region of positive definite matrices for bivariate samples.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between MVNtestchar versions 1.0.1 dated 2020-04-18 and 1.0.2 dated 2020-04-20
MVNtestchar-1.0.1/MVNtestchar/README.md |only MVNtestchar-1.0.2/MVNtestchar/DESCRIPTION | 7 ++++--- MVNtestchar-1.0.2/MVNtestchar/MD5 | 23 +++++++++++------------ MVNtestchar-1.0.2/MVNtestchar/NAMESPACE | 8 +++++++- MVNtestchar-1.0.2/MVNtestchar/NEWS.md | 4 ++++ MVNtestchar-1.0.2/MVNtestchar/R/maxv12.R | 3 ++- MVNtestchar-1.0.2/MVNtestchar/R/slice.v1.R | 1 + MVNtestchar-1.0.2/MVNtestchar/R/slice.v12.R | 1 + MVNtestchar-1.0.2/MVNtestchar/R/support.p2.R | 1 + MVNtestchar-1.0.2/MVNtestchar/R/testunknown.R | 1 + MVNtestchar-1.0.2/MVNtestchar/build/partial.rdb |binary MVNtestchar-1.0.2/MVNtestchar/inst/doc/vig1.pdf |binary MVNtestchar-1.0.2/MVNtestchar/man/maxv12.Rd | 3 ++- 13 files changed, 34 insertions(+), 18 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut, cre],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparklyr versions 1.1.0 dated 2020-01-10 and 1.2.0 dated 2020-04-20
sparklyr-1.1.0/sparklyr/java/spark-2.0.0/backend.scala |only sparklyr-1.1.0/sparklyr/java/spark-2.0.0/channel.scala |only sparklyr-1.1.0/sparklyr/tests |only sparklyr-1.2.0/sparklyr/DESCRIPTION | 135 ++ sparklyr-1.2.0/sparklyr/MD5 | 551 +++------- sparklyr-1.2.0/sparklyr/NAMESPACE | 2 sparklyr-1.2.0/sparklyr/NEWS.md | 211 ++- sparklyr-1.2.0/sparklyr/R/arrow_data.R | 6 sparklyr-1.2.0/sparklyr/R/connection_spark.R | 23 sparklyr-1.2.0/sparklyr/R/core_deserialize.R | 13 sparklyr-1.2.0/sparklyr/R/core_invoke.R | 95 - sparklyr-1.2.0/sparklyr/R/data_copy.R | 31 sparklyr-1.2.0/sparklyr/R/do_spark.R |only sparklyr-1.2.0/sparklyr/R/dplyr_spark_table.R | 6 sparklyr-1.2.0/sparklyr/R/java.R | 23 sparklyr-1.2.0/sparklyr/R/livy_connection.R | 16 sparklyr-1.2.0/sparklyr/R/ml_classification_gbt_classifier.R | 35 sparklyr-1.2.0/sparklyr/R/ml_classification_linear_svc.R | 26 sparklyr-1.2.0/sparklyr/R/ml_classification_random_forest_classifier.R | 33 sparklyr-1.2.0/sparklyr/R/ml_clustering_lda.R | 35 sparklyr-1.2.0/sparklyr/R/ml_feature_chisq_selector.R | 23 sparklyr-1.2.0/sparklyr/R/ml_feature_count_vectorizer.R | 17 sparklyr-1.2.0/sparklyr/R/ml_feature_one_hot_encoder.R | 5 sparklyr-1.2.0/sparklyr/R/ml_feature_standard_scaler.R | 5 sparklyr-1.2.0/sparklyr/R/ml_fpm_fpgrowth.R | 9 sparklyr-1.2.0/sparklyr/R/ml_model_linear_regression.R | 5 sparklyr-1.2.0/sparklyr/R/ml_model_naive_bayes.R | 6 sparklyr-1.2.0/sparklyr/R/ml_pipeline_utils.R | 65 - sparklyr-1.2.0/sparklyr/R/ml_recommendation_als.R | 52 sparklyr-1.2.0/sparklyr/R/ml_regression_aft_survival_regression.R | 23 sparklyr-1.2.0/sparklyr/R/ml_regression_decision_tree_regressor.R | 28 sparklyr-1.2.0/sparklyr/R/ml_regression_random_forest_regressor.R | 31 sparklyr-1.2.0/sparklyr/R/ml_tuning_train_validation_split.R | 18 sparklyr-1.2.0/sparklyr/R/sdf_interface.R | 54 sparklyr-1.2.0/sparklyr/R/sdf_stat.R | 3 sparklyr-1.2.0/sparklyr/R/sdf_utils.R | 3 sparklyr-1.2.0/sparklyr/R/sdf_wrapper.R | 5 sparklyr-1.2.0/sparklyr/R/shell_connection.R | 116 +- sparklyr-1.2.0/sparklyr/R/spark_apply.R | 12 sparklyr-1.2.0/sparklyr/R/spark_apply_bundle.R | 9 sparklyr-1.2.0/sparklyr/R/spark_context_config.R | 7 sparklyr-1.2.0/sparklyr/R/spark_gateway.R | 2 sparklyr-1.2.0/sparklyr/R/spark_version.R | 2 sparklyr-1.2.0/sparklyr/R/utils.R | 4 sparklyr-1.2.0/sparklyr/README.md | 235 ++-- sparklyr-1.2.0/sparklyr/inst/extdata/versions-next.json | 12 sparklyr-1.2.0/sparklyr/inst/extdata/versions.json | 12 sparklyr-1.2.0/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-2.3-2.11.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-2.4-2.11.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-3.0.0-preview-2.12.jar |binary sparklyr-1.2.0/sparklyr/inst/java/sparklyr-master-2.12.jar |binary sparklyr-1.2.0/sparklyr/java/spark-1.5.2/backend.scala | 19 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/channel.scala | 16 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/dfcollectionutils.scala |only sparklyr-1.2.0/sparklyr/java/spark-1.5.2/handler.scala | 46 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/invoke.scala | 2 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/serializer.scala | 31 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/stream.scala | 36 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/structtypeasjson.scala |only sparklyr-1.2.0/sparklyr/java/spark-1.5.2/test.scala | 4 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/tracker.scala | 28 sparklyr-1.2.0/sparklyr/java/spark-1.5.2/utils.scala | 187 +++ sparklyr-1.2.0/sparklyr/java/spark-1.6.0/sources.scala | 148 +- sparklyr-1.2.0/sparklyr/java/spark-1.6.0/workerapply.scala | 7 sparklyr-1.2.0/sparklyr/java/spark-2.3.0/dfcollectionutils.scala |only sparklyr-1.2.0/sparklyr/java/spark-2.4.0/structcolumnutils.scala |only sparklyr-1.2.0/sparklyr/man/copy_to.spark_connection.Rd | 12 sparklyr-1.2.0/sparklyr/man/ft_binarizer.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_bucketizer.Rd | 74 - sparklyr-1.2.0/sparklyr/man/ft_chisq_selector.Rd | 77 - sparklyr-1.2.0/sparklyr/man/ft_count_vectorizer.Rd | 73 - sparklyr-1.2.0/sparklyr/man/ft_dct.Rd | 82 - sparklyr-1.2.0/sparklyr/man/ft_elementwise_product.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_feature_hasher.Rd | 71 - sparklyr-1.2.0/sparklyr/man/ft_hashing_tf.Rd | 70 - sparklyr-1.2.0/sparklyr/man/ft_idf.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_imputer.Rd | 71 - sparklyr-1.2.0/sparklyr/man/ft_index_to_string.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_interaction.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_lsh.Rd | 88 - sparklyr-1.2.0/sparklyr/man/ft_lsh_utils.Rd | 18 sparklyr-1.2.0/sparklyr/man/ft_max_abs_scaler.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_min_max_scaler.Rd | 70 - sparklyr-1.2.0/sparklyr/man/ft_ngram.Rd | 70 - sparklyr-1.2.0/sparklyr/man/ft_normalizer.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_one_hot_encoder.Rd | 72 - sparklyr-1.2.0/sparklyr/man/ft_one_hot_encoder_estimator.Rd | 71 - sparklyr-1.2.0/sparklyr/man/ft_pca.Rd | 73 - sparklyr-1.2.0/sparklyr/man/ft_polynomial_expansion.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_quantile_discretizer.Rd | 81 - sparklyr-1.2.0/sparklyr/man/ft_r_formula.Rd | 73 - sparklyr-1.2.0/sparklyr/man/ft_regex_tokenizer.Rd | 73 - sparklyr-1.2.0/sparklyr/man/ft_standard_scaler.Rd | 71 - sparklyr-1.2.0/sparklyr/man/ft_stop_words_remover.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_string_indexer.Rd | 81 - sparklyr-1.2.0/sparklyr/man/ft_tokenizer.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_vector_assembler.Rd | 68 - sparklyr-1.2.0/sparklyr/man/ft_vector_indexer.Rd | 69 - sparklyr-1.2.0/sparklyr/man/ft_vector_slicer.Rd | 70 - sparklyr-1.2.0/sparklyr/man/ft_word2vec.Rd | 78 - sparklyr-1.2.0/sparklyr/man/livy_config.Rd | 11 sparklyr-1.2.0/sparklyr/man/livy_install.Rd | 7 sparklyr-1.2.0/sparklyr/man/livy_service.Rd | 9 sparklyr-1.2.0/sparklyr/man/ml-model-constructors.Rd | 74 + sparklyr-1.2.0/sparklyr/man/ml-persistence.Rd | 9 sparklyr-1.2.0/sparklyr/man/ml-transform-methods.Rd | 3 sparklyr-1.2.0/sparklyr/man/ml-tuning.Rd | 32 sparklyr-1.2.0/sparklyr/man/ml_aft_survival_regression.Rd | 70 - sparklyr-1.2.0/sparklyr/man/ml_als.Rd | 27 sparklyr-1.2.0/sparklyr/man/ml_bisecting_kmeans.Rd | 22 sparklyr-1.2.0/sparklyr/man/ml_clustering_evaluator.Rd | 11 sparklyr-1.2.0/sparklyr/man/ml_decision_tree.Rd | 112 +- sparklyr-1.2.0/sparklyr/man/ml_default_stop_words.Rd | 10 sparklyr-1.2.0/sparklyr/man/ml_evaluator.Rd | 49 sparklyr-1.2.0/sparklyr/man/ml_fpgrowth.Rd | 12 sparklyr-1.2.0/sparklyr/man/ml_gaussian_mixture.Rd | 23 sparklyr-1.2.0/sparklyr/man/ml_generalized_linear_regression.Rd | 51 sparklyr-1.2.0/sparklyr/man/ml_glm_tidiers.Rd | 20 sparklyr-1.2.0/sparklyr/man/ml_gradient_boosted_trees.Rd | 126 +- sparklyr-1.2.0/sparklyr/man/ml_isotonic_regression.Rd | 39 sparklyr-1.2.0/sparklyr/man/ml_kmeans.Rd | 24 sparklyr-1.2.0/sparklyr/man/ml_lda.Rd | 32 sparklyr-1.2.0/sparklyr/man/ml_linear_regression.Rd | 47 sparklyr-1.2.0/sparklyr/man/ml_linear_svc.Rd | 47 sparklyr-1.2.0/sparklyr/man/ml_logistic_regression.Rd | 52 sparklyr-1.2.0/sparklyr/man/ml_multilayer_perceptron_classifier.Rd | 74 - sparklyr-1.2.0/sparklyr/man/ml_multilayer_perceptron_tidiers.Rd | 3 sparklyr-1.2.0/sparklyr/man/ml_naive_bayes.Rd | 42 sparklyr-1.2.0/sparklyr/man/ml_one_vs_rest.Rd | 37 sparklyr-1.2.0/sparklyr/man/ml_random_forest.Rd | 122 +- sparklyr-1.2.0/sparklyr/man/ml_standardize_formula.Rd | 3 sparklyr-1.2.0/sparklyr/man/ml_survival_regression_tidiers.Rd | 3 sparklyr-1.2.0/sparklyr/man/ml_tree_tidiers.Rd | 12 sparklyr-1.2.0/sparklyr/man/reexports.Rd | 2 sparklyr-1.2.0/sparklyr/man/registerDoSpark.Rd |only sparklyr-1.2.0/sparklyr/man/sdf_along.Rd | 3 sparklyr-1.2.0/sparklyr/man/sdf_copy_to.Rd | 21 sparklyr-1.2.0/sparklyr/man/sdf_drop_duplicates.Rd |only sparklyr-1.2.0/sparklyr/man/sdf_len.Rd | 3 sparklyr-1.2.0/sparklyr/man/sdf_project.Rd | 9 sparklyr-1.2.0/sparklyr/man/sdf_quantile.Rd | 8 sparklyr-1.2.0/sparklyr/man/sdf_random_split.Rd | 19 sparklyr-1.2.0/sparklyr/man/sdf_register.Rd | 8 sparklyr-1.2.0/sparklyr/man/sdf_residuals.Rd | 7 sparklyr-1.2.0/sparklyr/man/sdf_sample.Rd | 8 sparklyr-1.2.0/sparklyr/man/sdf_seq.Rd | 10 sparklyr-1.2.0/sparklyr/man/sdf_sort.Rd | 8 sparklyr-1.2.0/sparklyr/man/spark-connections.Rd | 26 sparklyr-1.2.0/sparklyr/man/spark_apply.Rd | 15 sparklyr-1.2.0/sparklyr/man/spark_apply_bundle.Rd | 4 sparklyr-1.2.0/sparklyr/man/spark_compilation_spec.Rd | 12 sparklyr-1.2.0/sparklyr/man/spark_compile.Rd | 10 sparklyr-1.2.0/sparklyr/man/spark_config_kubernetes.Rd | 20 sparklyr-1.2.0/sparklyr/man/spark_default_compilation_spec.Rd | 6 sparklyr-1.2.0/sparklyr/man/spark_dependency.Rd | 10 sparklyr-1.2.0/sparklyr/man/spark_install.Rd | 27 sparklyr-1.2.0/sparklyr/man/spark_load_table.Rd | 52 sparklyr-1.2.0/sparklyr/man/spark_pipeline_stage.Rd | 28 sparklyr-1.2.0/sparklyr/man/spark_read_csv.Rd | 64 - sparklyr-1.2.0/sparklyr/man/spark_read_delta.Rd | 56 - sparklyr-1.2.0/sparklyr/man/spark_read_jdbc.Rd | 53 sparklyr-1.2.0/sparklyr/man/spark_read_json.Rd | 55 sparklyr-1.2.0/sparklyr/man/spark_read_libsvm.Rd | 52 sparklyr-1.2.0/sparklyr/man/spark_read_orc.Rd | 56 - sparklyr-1.2.0/sparklyr/man/spark_read_parquet.Rd | 56 - sparklyr-1.2.0/sparklyr/man/spark_read_source.Rd | 56 - sparklyr-1.2.0/sparklyr/man/spark_read_table.Rd | 52 sparklyr-1.2.0/sparklyr/man/spark_read_text.Rd | 55 sparklyr-1.2.0/sparklyr/man/spark_save_table.Rd | 41 sparklyr-1.2.0/sparklyr/man/spark_write_csv.Rd | 59 - sparklyr-1.2.0/sparklyr/man/spark_write_delta.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_jdbc.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_json.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_orc.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_parquet.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_source.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_table.Rd | 51 sparklyr-1.2.0/sparklyr/man/spark_write_text.Rd | 51 sparklyr-1.2.0/sparklyr/man/sql-transformer.Rd | 70 - sparklyr-1.2.0/sparklyr/man/stream_generate_test.Rd | 8 sparklyr-1.2.0/sparklyr/man/stream_read_csv.Rd | 50 sparklyr-1.2.0/sparklyr/man/stream_read_delta.Rd | 33 sparklyr-1.2.0/sparklyr/man/stream_read_json.Rd | 36 sparklyr-1.2.0/sparklyr/man/stream_read_kafka.Rd | 33 sparklyr-1.2.0/sparklyr/man/stream_read_orc.Rd | 36 sparklyr-1.2.0/sparklyr/man/stream_read_parquet.Rd | 43 sparklyr-1.2.0/sparklyr/man/stream_read_socket.Rd | 36 sparklyr-1.2.0/sparklyr/man/stream_read_text.Rd | 33 sparklyr-1.2.0/sparklyr/man/stream_write_console.Rd | 42 sparklyr-1.2.0/sparklyr/man/stream_write_csv.Rd | 53 sparklyr-1.2.0/sparklyr/man/stream_write_delta.Rd | 42 sparklyr-1.2.0/sparklyr/man/stream_write_json.Rd | 45 sparklyr-1.2.0/sparklyr/man/stream_write_kafka.Rd | 41 sparklyr-1.2.0/sparklyr/man/stream_write_memory.Rd | 41 sparklyr-1.2.0/sparklyr/man/stream_write_orc.Rd | 45 sparklyr-1.2.0/sparklyr/man/stream_write_parquet.Rd | 45 sparklyr-1.2.0/sparklyr/man/stream_write_text.Rd | 45 sparklyr-1.2.0/sparklyr/tools/readme/databricks-connect.png |only sparklyr-1.2.0/sparklyr/tools/readme/dplyr-ggplot2-1.png |binary 202 files changed, 5033 insertions(+), 3207 deletions(-)
Title: GEE Solver for Correlated Nominal or Ordinal Multinomial
Responses
Description: GEE solver for correlated nominal or ordinal multinomial responses
using a local odds ratios parameterization.
Author: Anestis Touloumis [aut, cre] (<https://orcid.org/0000-0002-5965-1639>)
Maintainer: Anestis Touloumis <A.Touloumis@brighton.ac.uk>
Diff between multgee versions 1.6.0 dated 2017-07-11 and 1.7.0 dated 2020-04-20
multgee-1.6.0/multgee/R/LORgee.default.R |only multgee-1.6.0/multgee/R/RCconstrains.R |only multgee-1.6.0/multgee/R/RRCheter.R |only multgee-1.6.0/multgee/R/RRChomog.R |only multgee-1.6.0/multgee/R/combns.R |only multgee-1.6.0/multgee/R/datacounts.R |only multgee-1.6.0/multgee/R/derivacl.R |only multgee-1.6.0/multgee/R/derivbcl.R |only multgee-1.6.0/multgee/R/derivmclm.R |only multgee-1.6.0/multgee/R/diagmod.R |only multgee-1.6.0/multgee/R/fitmm.R |only multgee-1.6.0/multgee/R/inversemat.R |only multgee-1.6.0/multgee/R/ipfp.R |only multgee-1.6.0/multgee/R/mmpar.R |only multgee-1.6.0/multgee/R/muprob.R |only multgee-1.6.0/multgee/R/normscores.R |only multgee-1.6.0/multgee/R/odds.ratio.R |only multgee-1.6.0/multgee/inst/NEWS |only multgee-1.6.0/multgee/inst/doc/multgee.R |only multgee-1.6.0/multgee/inst/doc/multgee.Rnw |only multgee-1.6.0/multgee/inst/doc/multgee.pdf |only multgee-1.6.0/multgee/vignettes/multgee.Rnw |only multgee-1.7.0/multgee/DESCRIPTION | 30 multgee-1.7.0/multgee/MD5 | 95 +- multgee-1.7.0/multgee/NAMESPACE | 40 multgee-1.7.0/multgee/R/LORgee.R | 38 multgee-1.7.0/multgee/R/LORgee.control.R | 53 - multgee-1.7.0/multgee/R/confint.LORgee.R |only multgee-1.7.0/multgee/R/fitLORgee.R | 591 +++++++------ multgee-1.7.0/multgee/R/intrinsic.pars.R | 196 +++- multgee-1.7.0/multgee/R/ipfp.control.R | 30 multgee-1.7.0/multgee/R/matrixLOR.R | 72 + multgee-1.7.0/multgee/R/multgee-package.R |only multgee-1.7.0/multgee/R/multgee_data.R |only multgee-1.7.0/multgee/R/multgee_internals_association.R |only multgee-1.7.0/multgee/R/multgee_internals_derivs.R |only multgee-1.7.0/multgee/R/multgee_internals_utils.R |only multgee-1.7.0/multgee/R/nomLORgee.R | 594 ++++++++----- multgee-1.7.0/multgee/R/ordLORgee.R | 685 +++++++++------- multgee-1.7.0/multgee/R/print.LORgee.R | 44 - multgee-1.7.0/multgee/R/print.summary.LORgee.R | 55 - multgee-1.7.0/multgee/R/print.waldts.R | 17 multgee-1.7.0/multgee/R/summary.LORgee.R | 45 - multgee-1.7.0/multgee/R/vcov.LORgee.R |only multgee-1.7.0/multgee/R/waldts.R | 101 +- multgee-1.7.0/multgee/build/vignette.rds |binary multgee-1.7.0/multgee/data/arthritis.rda |binary multgee-1.7.0/multgee/data/housing.rda |binary multgee-1.7.0/multgee/inst/NEWS.Rd |only multgee-1.7.0/multgee/inst/doc/multgee_vignette.R |only multgee-1.7.0/multgee/inst/doc/multgee_vignette.Rmd |only multgee-1.7.0/multgee/inst/doc/multgee_vignette.pdf |only multgee-1.7.0/multgee/man/LORgee.control.Rd | 83 + multgee-1.7.0/multgee/man/arthritis.Rd | 64 - multgee-1.7.0/multgee/man/confint.LORgee.Rd |only multgee-1.7.0/multgee/man/housing.Rd | 59 - multgee-1.7.0/multgee/man/intrinsic.pars.Rd | 138 +-- multgee-1.7.0/multgee/man/ipfp.control.Rd | 58 - multgee-1.7.0/multgee/man/matrixLOR.Rd | 104 +- multgee-1.7.0/multgee/man/multgee-package.Rd | 135 +-- multgee-1.7.0/multgee/man/nomLORgee.Rd | 303 ++++--- multgee-1.7.0/multgee/man/ordLORgee.Rd | 326 ++++--- multgee-1.7.0/multgee/man/vcov.LORgee.Rd |only multgee-1.7.0/multgee/man/waldts.Rd | 66 - multgee-1.7.0/multgee/vignettes/References.bib | 6 multgee-1.7.0/multgee/vignettes/jsslogo.jpg |only multgee-1.7.0/multgee/vignettes/multgee_vignette.Rmd |only 67 files changed, 2389 insertions(+), 1639 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.49.10 dated 2020-04-18 and 0.9.49.11 dated 2020-04-20
DESCRIPTION | 8 ++--- MD5 | 16 +++++----- NEWS.md | 4 ++ inst/doc/FOCUS_D.html | 12 ++++---- inst/doc/FOCUS_L.html | 60 ++++++++++++++++++++-------------------- inst/doc/mkin.html | 4 +- inst/doc/twa.html | 4 +- tests/testthat/FOCUS_2006_D.csf | 2 - tests/testthat/test_residuals.R | 4 +- 9 files changed, 59 insertions(+), 55 deletions(-)
Title: Effects and Importances of Model Ingredients
Description: Collection of tools for assessment of feature importance and feature effects.
Key functions are:
feature_importance() for assessment of global level feature importance,
ceteris_paribus() for calculation of the what-if plots,
partial_dependence() for partial dependence plots,
conditional_dependence() for conditional dependence plots,
accumulated_dependence() for accumulated local effects plots,
aggregate_profiles() and cluster_profiles() for aggregation of ceteris paribus profiles,
generic print() and plot() for better usability of selected explainers,
generic plotD3() for interactive, D3 based explanations, and
generic describe() for explanations in natural language.
The package 'ingredients' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between ingredients versions 1.1 dated 2020-03-11 and 1.2.0 dated 2020-04-20
DESCRIPTION | 14 ++-- MD5 | 50 ++++++++------- NAMESPACE | 4 - NEWS.md | 12 +++ R/bind_plots.R | 11 ++- R/describe_feature_importance.R | 2 R/feature_importance.R | 21 +----- R/plotD3_feature_importance.R | 4 - R/plot_aggregated_profiles.R | 6 - R/plot_ceteris_paribus.R | 89 ++++++++++++++++++++++++--- R/plot_ceteris_paribus_oscillations.R | 6 - R/plot_feature_importance.R | 26 -------- R/print_feature_importance.R | 1 inst/doc/vignette_describe.html | 96 ++++++++++++++++-------------- inst/doc/vignette_simulated.html | 44 +++++++++---- inst/doc/vignette_titanic.html | 46 +++++++++----- man/bind_plots.Rd | 9 +- man/describe.Rd | 2 man/feature_importance.Rd | 21 +----- man/figures/demo.gif |only man/figures/plotD3.png |only man/plot.ceteris_paribus_explainer.Rd | 6 + man/plot.ceteris_paribus_oscillations.Rd | 2 man/plot.feature_importance_explainer.Rd | 17 ----- man/plotD3_feature_importance.Rd | 4 - man/print.feature_importance_explainer.Rd | 1 tests/testthat/helper-objects.R | 15 ++-- 27 files changed, 285 insertions(+), 224 deletions(-)
Title: Model Agnostic Instance Level Variable Attributions
Description: Model agnostic tool for decomposition of predictions from black boxes.
Supports additive attributions and attributions with interactions.
The Break Down Table shows contributions of every variable to a final prediction.
The Break Down Plot presents variable contributions in a concise graphical way.
This package works for classification and regression models.
It is an extension of the 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>,
with new and faster strategies for orderings.
It supports interactions in explanations and has interactive visuals (implemented with 'D3.js' library).
The methodology behind is described in the 'iBreakDown' article (Gosiewska and Biecek 2019) <arXiv:1903.11420>
This package is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>),
Alicja Gosiewska [aut] (<https://orcid.org/0000-0001-6563-5742>),
Hubert Baniecki [aut] (<https://orcid.org/0000-0001-6661-5364>),
Adam Izdebski [aut],
Dariusz Komosinski [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between iBreakDown versions 1.1.1 dated 2020-04-15 and 1.2.0 dated 2020-04-20
DESCRIPTION | 10 MD5 | 38 NAMESPACE | 3 NEWS.md | 12 R/break_down.R | 21 R/break_down_uncertainty.R | 23 R/plot_break_down.R | 3 R/plot_break_down_uncertainty.R | 2 inst/doc/vignette_iBreakDown_classification.R | 21 inst/doc/vignette_iBreakDown_classification.Rmd | 24 inst/doc/vignette_iBreakDown_classification.html | 95 - inst/doc/vignette_iBreakDown_description.html | 100 - inst/doc/vignette_iBreakDown_regression.R | 20 inst/doc/vignette_iBreakDown_regression.Rmd | 23 inst/doc/vignette_iBreakDown_regression.html | 1890 ----------------------- inst/doc/vignette_iBreakDown_titanic.html | 70 man/break_down.Rd | 21 man/break_down_uncertainty.Rd | 22 vignettes/vignette_iBreakDown_classification.Rmd | 24 vignettes/vignette_iBreakDown_regression.Rmd | 23 20 files changed, 237 insertions(+), 2208 deletions(-)
Title: Color Palettes Based on Fish Species
Description: Implementation of color palettes based on fish species.
Author: Nina M. D. Schiettekatte [cre, aut],
Simon J. Brandl [aut],
Jordan M. Casey [aut]
Maintainer: Nina M. D. Schiettekatte <nina.schiettekatte@gmail.com>
Diff between fishualize versions 0.1.0 dated 2019-10-24 and 0.2.0 dated 2020-04-20
DESCRIPTION | 27 +++++++------ MD5 | 32 +++++++++------ NAMESPACE | 17 ++++++++ NEWS.md |only R/fish_shapes.R |only build/vignette.rds |binary data/fishcolors.csv | 85 ++++++++++++++++++++++++++++++++++++++++++ data/fishcolors.rda |binary inst/doc/contribute.R | 2 inst/doc/contribute.html | 19 ++++----- inst/doc/overview_colors.R | 6 +- inst/doc/overview_colors.html | 21 +++++----- inst/doc/overview_shapes.R |only inst/doc/overview_shapes.Rmd |only inst/doc/overview_shapes.html |only man/add_fishape.Rd |only man/fish.Rd | 19 +++++++-- man/fishapes.Rd |only man/fishcolors.Rd | 6 +- man/scale_fish.Rd | 63 +++++++++++++++++++++++++------ vignettes/overview_shapes.Rmd |only 21 files changed, 232 insertions(+), 65 deletions(-)
Title: Data Analysis using Bootstrap-Coupled Estimation
Description: Data Analysis using Bootstrap-Coupled ESTimation.
Estimation statistics is a simple framework that avoids the pitfalls of
significance testing. It uses familiar statistical concepts: means,
mean differences, and error bars. More importantly, it focuses on the
effect size of one's experiment/intervention, as opposed to a false
dichotomy engendered by P values.
An estimation plot has two key features:
1. It presents all datapoints as a swarmplot, which orders each point to
display the underlying distribution.
2. It presents the effect size as a bootstrap 95% confidence interval on a
separate but aligned axes.
Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
<doi:10.1038/s41592-019-0470-3>.
The free-to-view PDF is located at <https://rdcu.be/bHhJ4>.
Author: Joses W. Ho [cre, aut],
Tayfun Tumkaya [aut]
Maintainer: Joses W. Ho <joseshowh@gmail.com>
Diff between dabestr versions 0.2.4 dated 2020-03-21 and 0.2.5 dated 2020-04-20
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Title: Functions Supporting Packages ChemoSpec and ChemoSpec2D
Description: Functions supporting the common needs of packages 'ChemoSpec' and 'ChemoSpec2D'.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between ChemoSpecUtils versions 0.4.38 dated 2020-01-22 and 0.4.51 dated 2020-04-20
ChemoSpecUtils-0.4.38/ChemoSpecUtils/inst/tinytest/test_cosine_distance.R |only ChemoSpecUtils-0.4.51/ChemoSpecUtils/DESCRIPTION | 10 ChemoSpecUtils-0.4.51/ChemoSpecUtils/MD5 | 24 - ChemoSpecUtils-0.4.51/ChemoSpecUtils/NEWS.md | 7 ChemoSpecUtils-0.4.51/ChemoSpecUtils/R/distPlot.R | 35 +- ChemoSpecUtils-0.4.51/ChemoSpecUtils/R/removeFreq.R | 14 + ChemoSpecUtils-0.4.51/ChemoSpecUtils/R/rowDist.R | 137 +++++++--- ChemoSpecUtils-0.4.51/ChemoSpecUtils/R/sampleDist.R | 14 - ChemoSpecUtils-0.4.51/ChemoSpecUtils/R/shrinkLeaf.R | 5 ChemoSpecUtils-0.4.51/ChemoSpecUtils/inst/tinytest/test_rowDist.R |only ChemoSpecUtils-0.4.51/ChemoSpecUtils/man/colorSymbol.Rd | 4 ChemoSpecUtils-0.4.51/ChemoSpecUtils/man/removeFreq.Rd | 14 + ChemoSpecUtils-0.4.51/ChemoSpecUtils/man/rowDist.Rd | 111 ++++++-- ChemoSpecUtils-0.4.51/ChemoSpecUtils/man/sampleDist.Rd | 14 - 14 files changed, 300 insertions(+), 89 deletions(-)
More information about ChemoSpecUtils at CRAN
Permanent link
Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, posterior predictive p-values, etc.
Author: Christian Roever [aut, cre] (<https://orcid.org/0000-0002-6911-698X>),
Tim Friede [ctb] (<https://orcid.org/0000-0001-5347-7441>)
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 2.4 dated 2019-08-06 and 2.5 dated 2020-04-20
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Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-based data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre],
Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>
Diff between bnma versions 1.0.0 dated 2019-12-10 and 1.1.0 dated 2020-04-20
DESCRIPTION | 8 MD5 | 28 NEWS.md | 5 R/contrast.network.R | 3 R/network.data.R | 9 R/network.rjags.R | 11 R/network.run.R | 11 R/network.summary.R | 3 R/preprocess.data.R | 6 build/vignette.rds |binary inst/doc/my-vignette.R | 11 inst/doc/my-vignette.Rmd | 16 inst/doc/my-vignette.html | 1319 +++++++++++++++++++++------------------------- man/network.data.Rd | 8 vignettes/my-vignette.Rmd | 16 15 files changed, 710 insertions(+), 744 deletions(-)
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer and in
Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009).
Functional Data Analysis with R and Matlab (Springer).
The package includes data sets and script files working many examples
including all but one of the 76 figures in this latter book. Matlab versions
are available by ftp from
<http://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre],
Spencer Graves <spencer.graves@effectivedefense.org> [ctb],
Giles Hooker <gjh27@cornell.edu> [ctb]
Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>
Diff between fda versions 2.4.8.1 dated 2020-02-19 and 5.1.4 dated 2020-04-20
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fda-5.1.4/fda/R/quadset.R | 150 - fda-5.1.4/fda/R/rangechk.R | 28 fda-5.1.4/fda/R/reconsCurves.R |only fda-5.1.4/fda/R/register.fd.R | 1836 +++++++-------- fda-5.1.4/fda/R/register.newfd.R | 180 - fda-5.1.4/fda/R/scoresPACE.R |only fda-5.1.4/fda/R/smooth.basis.R | 828 +++--- fda-5.1.4/fda/R/smooth.basis.glm.R |only fda-5.1.4/fda/R/smooth.basis.sparse.R |only fda-5.1.4/fda/R/smooth.basisPar.R | 107 fda-5.1.4/fda/R/smooth.bibasis.R | 494 ++-- fda-5.1.4/fda/R/smooth.fd.R | 150 - fda-5.1.4/fda/R/smooth.fdPar.R | 24 fda-5.1.4/fda/R/smooth.monotone.R | 1178 ++++----- fda-5.1.4/fda/R/smooth.morph.R | 721 ++--- fda-5.1.4/fda/R/smooth.pos.R | 806 +++--- fda-5.1.4/fda/R/smooth.sparse.mean.R |only fda-5.1.4/fda/R/sparse.list.R |only fda-5.1.4/fda/R/sparse.mat.R |only fda-5.1.4/fda/R/std.fd.R | 115 fda-5.1.4/fda/R/stddev.fd.R | 103 fda-5.1.4/fda/R/stepchk.R | 95 fda-5.1.4/fda/R/stepit.R | 289 +- fda-5.1.4/fda/R/subscript.R | 69 fda-5.1.4/fda/R/svd2.R | 94 fda-5.1.4/fda/R/symsolve.R | 32 fda-5.1.4/fda/R/tperm.fd.R | 180 - 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fda-5.1.4/fda/demo/growthsmooth.R | 600 ++-- fda-5.1.4/fda/demo/handwrit.R | 1432 +++++------ fda-5.1.4/fda/demo/handwrit.pda.R | 243 - fda-5.1.4/fda/demo/lip.R | 568 ++-- fda-5.1.4/fda/demo/pinch.R | 3 fda-5.1.4/fda/demo/weatherANOVA.R | 636 ++--- fda-5.1.4/fda/man/AmpPhaseDecomp.Rd | 150 - fda-5.1.4/fda/man/CSTR.Rd | 936 +++---- fda-5.1.4/fda/man/CanadianWeather.Rd | 155 - fda-5.1.4/fda/man/Data2fd.Rd | 733 +++--- fda-5.1.4/fda/man/Eigen.Rd | 5 fda-5.1.4/fda/man/Fperm.fd.Rd | 446 +-- fda-5.1.4/fda/man/Fstat.fd.Rd | 104 fda-5.1.4/fda/man/MontrealTemp.Rd | 64 fda-5.1.4/fda/man/ReginaPrecip.Rd | 62 fda-5.1.4/fda/man/StatSciChinese.Rd | 104 fda-5.1.4/fda/man/arithmetic.fd.Rd | 18 fda-5.1.4/fda/man/as.POSIXct1970.Rd | 102 fda-5.1.4/fda/man/as.array3.Rd | 148 - fda-5.1.4/fda/man/as.fd.Rd | 332 +- fda-5.1.4/fda/man/axisIntervals.Rd | 232 - fda-5.1.4/fda/man/basisfd.Rd | 391 +-- fda-5.1.4/fda/man/bifdPar.Rd | 246 +- fda-5.1.4/fda/man/cca.fd.Rd | 3 fda-5.1.4/fda/man/center.fd.Rd | 24 fda-5.1.4/fda/man/checkDims3.Rd | 418 +-- fda-5.1.4/fda/man/checkLogicalInteger.Rd | 274 +- fda-5.1.4/fda/man/coef.Rd | 11 fda-5.1.4/fda/man/cor.fd.Rd | 7 fda-5.1.4/fda/man/covPACE.Rd |only fda-5.1.4/fda/man/create.basis.Rd | 404 +-- fda-5.1.4/fda/man/create.bspline.basis.Rd | 52 fda-5.1.4/fda/man/create.constant.basis.Rd | 106 fda-5.1.4/fda/man/create.exponential.basis.Rd | 248 +- fda-5.1.4/fda/man/create.fourier.basis.Rd | 308 +- fda-5.1.4/fda/man/create.monomial.basis.Rd | 287 +- fda-5.1.4/fda/man/create.polygonal.basis.Rd | 255 +- fda-5.1.4/fda/man/create.power.basis.Rd | 265 +- fda-5.1.4/fda/man/cycleplot.fd.Rd | 1 fda-5.1.4/fda/man/density.fd.Rd | 256 +- fda-5.1.4/fda/man/deriv.fd.Rd | 156 - fda-5.1.4/fda/man/df.residual.fRegress.Rd | 82 fda-5.1.4/fda/man/dirs.Rd | 33 fda-5.1.4/fda/man/eigen.pda.rd | 186 - fda-5.1.4/fda/man/eval.bifd.Rd | 131 - fda-5.1.4/fda/man/eval.posfd.Rd | 167 - fda-5.1.4/fda/man/evaldiag.bifd.Rd | 91 fda-5.1.4/fda/man/exponentiate.fd.Rd | 72 fda-5.1.4/fda/man/fRegress.Rd | 1189 ++++----- fda-5.1.4/fda/man/fbplot.Rd | 421 +-- fda-5.1.4/fda/man/fd.Rd | 10 fda-5.1.4/fda/man/fd2list.Rd | 2 fda-5.1.4/fda/man/fdPar.Rd | 1 fda-5.1.4/fda/man/fda-package.Rd | 158 - fda-5.1.4/fda/man/fdlabels.Rd | 82 fda-5.1.4/fda/man/getbasismatrix.Rd | 160 - fda-5.1.4/fda/man/infantGrowth.Rd | 86 fda-5.1.4/fda/man/inprod.Rd | 203 - fda-5.1.4/fda/man/is.eqbasis.Rd |only fda-5.1.4/fda/man/is.fdSmooth.Rd | 54 fda-5.1.4/fda/man/knots.fd.Rd | 63 fda-5.1.4/fda/man/lambda2df.Rd | 93 fda-5.1.4/fda/man/lambda2gcv.Rd | 94 fda-5.1.4/fda/man/landmark.reg.expData.Rd | 68 fda-5.1.4/fda/man/landmarkreg.Rd | 292 +- fda-5.1.4/fda/man/linmod.Rd | 150 - fda-5.1.4/fda/man/monomial.Rd | 6 fda-5.1.4/fda/man/nondurables.Rd | 1 fda-5.1.4/fda/man/norder.Rd | 160 - fda-5.1.4/fda/man/odesolv.Rd | 136 - fda-5.1.4/fda/man/pca.fd.Rd | 1 fda-5.1.4/fda/man/pcaPACE.Rd |only fda-5.1.4/fda/man/pda.fd.Rd | 789 +++--- fda-5.1.4/fda/man/pda.overlay.Rd | 138 - fda-5.1.4/fda/man/phaseplanePlot.Rd | 198 - fda-5.1.4/fda/man/plot.Lfd.Rd | 4 fda-5.1.4/fda/man/plot.basisfd.Rd | 4 fda-5.1.4/fda/man/plot.cca.fd.rd | 4 fda-5.1.4/fda/man/plot.fd.Rd | 84 fda-5.1.4/fda/man/plot.pda.fd.rd | 204 - fda-5.1.4/fda/man/plotfit.fd.Rd | 42 fda-5.1.4/fda/man/plotreg.fd.rd | 174 - fda-5.1.4/fda/man/ppBspline.Rd | 82 fda-5.1.4/fda/man/predict.fRegress.Rd | 150 - fda-5.1.4/fda/man/project.basis.Rd | 94 fda-5.1.4/fda/man/quadset.Rd | 178 - fda-5.1.4/fda/man/reconsCurves.Rd |only fda-5.1.4/fda/man/register.fd.Rd | 550 ++-- fda-5.1.4/fda/man/register.newfd.Rd | 2 fda-5.1.4/fda/man/scoresPACE.Rd |only fda-5.1.4/fda/man/seabird.Rd | 122 - fda-5.1.4/fda/man/smooth.basis.Rd | 1744 +++++++------- fda-5.1.4/fda/man/smooth.basis.sparse.Rd |only fda-5.1.4/fda/man/smooth.basisPar.Rd | 81 fda-5.1.4/fda/man/smooth.fd.Rd | 3 fda-5.1.4/fda/man/smooth.fdPar.Rd | 49 fda-5.1.4/fda/man/smooth.monotone.Rd | 463 +-- fda-5.1.4/fda/man/smooth.pos.Rd | 200 - fda-5.1.4/fda/man/smooth.sparse.mean.Rd |only fda-5.1.4/fda/man/sparse.list.Rd |only fda-5.1.4/fda/man/sparse.mat.Rd |only fda-5.1.4/fda/man/tperm.fd.Rd | 212 - fda-5.1.4/fda/man/trapzmat.Rd |only fda-5.1.4/fda/man/var.fd.Rd | 29 fda-5.1.4/fda/man/varmx.Rd | 90 fda-5.1.4/fda/man/zerofind.Rd | 9 324 files changed, 31398 insertions(+), 32086 deletions(-)
Title: Convert Statistical Analysis Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>),
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb],
Matthew Lincoln [ctb],
Alessandro Gasparini [ctb],
Lukasz Komsta [ctb],
Frederick Novometsky [ctb],
Wilson Freitas [ctb],
Michelle Evans [ctb],
Jason Cory Brunson [ctb],
Simon Jackson [ctb],
Ben Whalley [ctb],
Michael Kuehn [ctb],
Jorge Cimentada [ctb],
Erle Holgersen [ctb],
Karl Dunkle Werner [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between broom versions 0.5.5 dated 2020-02-29 and 0.5.6 dated 2020-04-20
broom-0.5.5/broom/inst/doc/glossary.R |only broom-0.5.5/broom/inst/doc/glossary.Rmd |only broom-0.5.5/broom/inst/doc/glossary.html |only broom-0.5.5/broom/vignettes/glossary.Rmd |only broom-0.5.6/broom/DESCRIPTION | 12 +-- broom-0.5.6/broom/MD5 | 52 +++++++--------- broom-0.5.6/broom/NAMESPACE | 2 broom-0.5.6/broom/NEWS.md | 4 + broom-0.5.6/broom/R/btergm-tidiers.R | 58 +++++++++-------- broom-0.5.6/broom/build/vignette.rds |binary broom-0.5.6/broom/inst/doc/adding-tidiers.html | 4 - broom-0.5.6/broom/inst/doc/available-methods.html | 5 - broom-0.5.6/broom/inst/doc/bootstrapping.R | 3 broom-0.5.6/broom/inst/doc/bootstrapping.Rmd | 3 broom-0.5.6/broom/inst/doc/bootstrapping.html | 71 ++++++++++++---------- broom-0.5.6/broom/inst/doc/broom.html | 53 ++++++++-------- broom-0.5.6/broom/inst/doc/broom_and_dplyr.R | 4 - broom-0.5.6/broom/inst/doc/broom_and_dplyr.Rmd | 4 - broom-0.5.6/broom/inst/doc/broom_and_dplyr.html | 14 ++-- broom-0.5.6/broom/inst/doc/kmeans.R | 6 + broom-0.5.6/broom/inst/doc/kmeans.Rmd | 6 + broom-0.5.6/broom/inst/doc/kmeans.html | 52 ++++++++-------- broom-0.5.6/broom/man/argument_glossary.Rd | 6 + broom-0.5.6/broom/man/column_glossary.Rd | 6 + broom-0.5.6/broom/man/insert_NAs.Rd | 30 ++++----- broom-0.5.6/broom/man/tidy.btergm.Rd | 56 +++++++++-------- broom-0.5.6/broom/vignettes/bootstrapping.Rmd | 3 broom-0.5.6/broom/vignettes/broom_and_dplyr.Rmd | 4 - broom-0.5.6/broom/vignettes/kmeans.Rmd | 6 + 29 files changed, 255 insertions(+), 209 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-12-21 0.1.4
2013-03-12 0.1.2
2013-03-11 0.1.1
Title: Regression with a Large Number of Potential Explanatory
Variables
Description: Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
Author: H. H. Hoeltgebaum
Maintainer: H. H. Hoeltgebaum <hh3015@ic.ac.uk>
Diff between HCmodelSets versions 1.1 dated 2019-12-16 and 1.1.1 dated 2020-04-20
HCmodelSets-1.1.1/HCmodelSets/DESCRIPTION | 14 ++++++---- HCmodelSets-1.1.1/HCmodelSets/MD5 | 18 +++++++------- HCmodelSets-1.1.1/HCmodelSets/build |only HCmodelSets-1.1.1/HCmodelSets/data/LymphomaData.rda |binary HCmodelSets-1.1.1/HCmodelSets/inst |only HCmodelSets-1.1.1/HCmodelSets/man/DGP.Rd | 2 - HCmodelSets-1.1.1/HCmodelSets/man/Exploratory.Phase.Rd | 2 - HCmodelSets-1.1.1/HCmodelSets/man/ModelSelection.Phase.Rd | 2 - HCmodelSets-1.1.1/HCmodelSets/man/Reduction.Phase.Rd | 2 - HCmodelSets-1.1.1/HCmodelSets/vignettes |only HCmodelSets-1.1/HCmodelSets/LICENSE |only HCmodelSets-1.1/HCmodelSets/README.md |only 12 files changed, 22 insertions(+), 18 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>),
Pierre Denelle [aut] (<https://orcid.org/0000-0001-5037-2281>),
Caroline Tucker [aut] (<https://orcid.org/0000-0002-4871-2010>),
François Munoz [ths] (<https://orcid.org/0000-0001-8776-4705>),
Cyrille Violle [ths] (<https://orcid.org/0000-0002-2471-9226>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between funrar versions 1.4.0 dated 2020-03-05 and 1.4.1 dated 2020-04-20
DESCRIPTION | 10 MD5 | 90 - NAMESPACE | 60 - NEWS.md | 159 +- R/check_functions.R | 498 ++++---- R/compute_dist_matrix.R | 198 +-- R/distinctiveness.R | 675 +++++------ R/distinctiveness_alt.R | 230 +-- R/distinctiveness_global.R | 120 +- R/distinctiveness_range.R | 365 +++--- R/funrar.R | 226 +-- R/make_relative.R | 180 +-- R/rarity_dimensions.R | 272 ++-- R/restrictedness.R | 366 +++--- R/scarcity.R | 351 ++--- R/stack_matrix.R | 372 +++--- R/uniqueness.R | 301 ++--- README.md | 110 - build/vignette.rds |binary inst/CITATION | 46 inst/doc/new_distinctiveness.R | 344 ++--- inst/doc/new_distinctiveness.Rmd | 828 +++++++------ inst/doc/new_distinctiveness.pdf |binary inst/doc/rarity_indices.R | 323 ++--- inst/doc/rarity_indices.Rmd | 703 +++++------ inst/doc/rarity_indices.html | 1604 +++++++++++++-------------- inst/doc/sparse_matrices.R | 186 +-- inst/doc/sparse_matrices.Rmd | 320 ++--- inst/doc/sparse_matrices.html | 932 +++++++-------- tests/testthat.R | 8 tests/testthat/test-check_functions.R | 350 ++--- tests/testthat/test-dist_matrix.R | 306 ++--- tests/testthat/test-distinctiveness.R | 674 +++++------ tests/testthat/test-distinctiveness_alt.R | 319 ++--- tests/testthat/test-distinctiveness_global.R | 158 +- tests/testthat/test-distinctiveness_range.R | 469 +++---- tests/testthat/test-funrar.R | 302 ++--- tests/testthat/test-rarity_dimensions.R | 300 ++--- tests/testthat/test-rel_abund.R | 166 +- tests/testthat/test-restrictedness.R | 105 - tests/testthat/test-scarcity.R | 306 ++--- tests/testthat/test-tidy_matrix.R | 355 ++--- tests/testthat/test-uniqueness.R | 160 +- vignettes/new_distinctiveness.Rmd | 828 +++++++------ vignettes/rarity_indices.Rmd | 703 +++++------ vignettes/sparse_matrices.Rmd | 320 ++--- 46 files changed, 7857 insertions(+), 7841 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.2.7 dated 2020-02-06 and 0.3.0 dated 2020-04-20
DHARMa-0.2.7/DHARMa/R/plotResiduals.R |only DHARMa-0.2.7/DHARMa/R/zzz.R |only DHARMa-0.2.7/DHARMa/inst/examples/helpRefit.R |only DHARMa-0.2.7/DHARMa/inst/examples/testModelHelp.R |only DHARMa-0.2.7/DHARMa/inst/examples/transformQuantilesHelp.R |only DHARMa-0.2.7/DHARMa/man/fitted.gam.Rd |only DHARMa-0.2.7/DHARMa/man/getResponse.Rd |only DHARMa-0.2.7/DHARMa/man/refit.glmmTMB.Rd |only DHARMa-0.2.7/DHARMa/man/refit.lm.Rd |only DHARMa-0.2.7/DHARMa/man/testModel.Rd |only DHARMa-0.3.0/DHARMa/DESCRIPTION | 28 DHARMa-0.3.0/DHARMa/MD5 | 121 + DHARMa-0.3.0/DHARMa/NAMESPACE | 26 DHARMa-0.3.0/DHARMa/NEWS | 21 DHARMa-0.3.0/DHARMa/R/DHARMa.R | 109 + DHARMa-0.3.0/DHARMa/R/compatibility.R | 352 ++++- DHARMa-0.3.0/DHARMa/R/helper.R | 18 DHARMa-0.3.0/DHARMa/R/plots.R |only DHARMa-0.3.0/DHARMa/R/simulateResiduals.R | 152 +- DHARMa-0.3.0/DHARMa/R/startup.R |only DHARMa-0.3.0/DHARMa/R/tests.R | 213 ++- DHARMa-0.3.0/DHARMa/R/transformQuantiles.R | 18 DHARMa-0.3.0/DHARMa/README.md | 3 DHARMa-0.3.0/DHARMa/inst/doc/DHARMa.R | 104 - DHARMa-0.3.0/DHARMa/inst/doc/DHARMa.Rmd | 305 ++-- DHARMa-0.3.0/DHARMa/inst/doc/DHARMa.html | 630 +++++----- DHARMa-0.3.0/DHARMa/inst/examples/getRandomStateHelp.R | 9 DHARMa-0.3.0/DHARMa/inst/examples/plotsHelp.R | 6 DHARMa-0.3.0/DHARMa/inst/examples/runBenchmarksHelp.R | 2 DHARMa-0.3.0/DHARMa/inst/examples/simulateResidualsHelp.R | 22 DHARMa-0.3.0/DHARMa/inst/examples/testQuantilesHelp.R |only DHARMa-0.3.0/DHARMa/inst/examples/testSpatialAutocorrelationHelp.R | 24 DHARMa-0.3.0/DHARMa/inst/examples/testsHelp.R | 40 DHARMa-0.3.0/DHARMa/inst/examples/wrappersHelp.R |only DHARMa-0.3.0/DHARMa/man/DHARMa.Rd | 1 DHARMa-0.3.0/DHARMa/man/checkModel.Rd |only DHARMa-0.3.0/DHARMa/man/checkSimulations.Rd |only DHARMa-0.3.0/DHARMa/man/createDHARMa.Rd | 8 DHARMa-0.3.0/DHARMa/man/createData.Rd | 7 DHARMa-0.3.0/DHARMa/man/ensureDHARMa.Rd |only DHARMa-0.3.0/DHARMa/man/ensurePredictor.Rd |only DHARMa-0.3.0/DHARMa/man/getFitted.Rd |only DHARMa-0.3.0/DHARMa/man/getFixedEffects.Rd |only DHARMa-0.3.0/DHARMa/man/getObservedResponse.Rd |only DHARMa-0.3.0/DHARMa/man/getQuantile.Rd | 2 DHARMa-0.3.0/DHARMa/man/getRandomState.Rd | 9 DHARMa-0.3.0/DHARMa/man/getRefit.Rd |only DHARMa-0.3.0/DHARMa/man/getSimulations.Rd | 42 DHARMa-0.3.0/DHARMa/man/hasWeigths.Rd |only DHARMa-0.3.0/DHARMa/man/hist.DHARMa.Rd | 24 DHARMa-0.3.0/DHARMa/man/plot.DHARMa.Rd | 8 DHARMa-0.3.0/DHARMa/man/plotConventionalResiduals.Rd | 2 DHARMa-0.3.0/DHARMa/man/plotQQunif.Rd | 13 DHARMa-0.3.0/DHARMa/man/plotResiduals.Rd | 39 DHARMa-0.3.0/DHARMa/man/plotSimulatedResiduals.Rd | 2 DHARMa-0.3.0/DHARMa/man/recalculateResiduals.Rd | 27 DHARMa-0.3.0/DHARMa/man/residuals.DHARMa.Rd | 33 DHARMa-0.3.0/DHARMa/man/simulateResiduals.Rd | 42 DHARMa-0.3.0/DHARMa/man/testDispersion.Rd | 49 DHARMa-0.3.0/DHARMa/man/testGeneric.Rd | 47 DHARMa-0.3.0/DHARMa/man/testOutliers.Rd | 53 DHARMa-0.3.0/DHARMa/man/testQuantiles.Rd |only DHARMa-0.3.0/DHARMa/man/testResiduals.Rd | 59 DHARMa-0.3.0/DHARMa/man/testSpatialAutocorrelation.Rd | 24 DHARMa-0.3.0/DHARMa/man/testTemporalAutocorrelation.Rd | 2 DHARMa-0.3.0/DHARMa/man/testUniformity.Rd | 53 DHARMa-0.3.0/DHARMa/man/testZeroInflation.Rd | 53 DHARMa-0.3.0/DHARMa/man/transformQuantiles.Rd | 23 DHARMa-0.3.0/DHARMa/tests/testthat/Rplots.pdf |binary DHARMa-0.3.0/DHARMa/tests/testthat/testHelper.R |only DHARMa-0.3.0/DHARMa/tests/testthat/testModelTypes.R | 196 ++- DHARMa-0.3.0/DHARMa/tests/testthat/testPlots.R | 25 DHARMa-0.3.0/DHARMa/tests/testthat/testTests.R | 8 DHARMa-0.3.0/DHARMa/vignettes/DHARMa.Rmd | 305 ++-- 74 files changed, 2129 insertions(+), 1230 deletions(-)
Title: Black Box Optimization and Exploration of Parameter Space
Description: Performs prediction of a response function from simulated response values, allowing black-box optimization of functions estimated with some error. Includes a simple user interface for such applications, as well as more specialized functions designed to be called by the Migraine software (Rousset and Leblois, 2012 <doi:10.1093/molbev/MSR262>; Leblois et al., 2014 <doi:10.1093/molbev/msu212>; and see URL). The latter functions are used for prediction of likelihood surfaces and implied likelihood ratio confidence intervals, and for exploration of predictor space of the surface. Prediction of the response is based on ordinary Kriging (with residual error) of the input. Estimation of smoothing parameters is performed by generalized cross-validation.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Raphaël Leblois [ctb] (<https://orcid.org/0000-0002-3051-4497>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between blackbox versions 1.1.27 dated 2019-08-20 and 1.1.32 dated 2020-04-20
blackbox-1.1.27/blackbox/R/toDgmuFromCanonical.R |only blackbox-1.1.27/blackbox/R/toNMratioFromCanonical.R |only blackbox-1.1.27/blackbox/R/toNactNfounderratioFromCanonical.R |only blackbox-1.1.27/blackbox/R/toNfounderNancratioFromCanonical.R |only blackbox-1.1.27/blackbox/R/toNratioFromCanonical.R |only blackbox-1.1.27/blackbox/R/toTgmuFromCanonical.R |only blackbox-1.1.27/blackbox/R/tolatt2Ns2.R |only blackbox-1.1.27/blackbox/R/tom1overmuFromCanonical.R |only blackbox-1.1.27/blackbox/R/tom2overmuFromCanonical.R |only blackbox-1.1.27/blackbox/R/tomratioFromCanonical.R |only blackbox-1.1.27/blackbox/tests/tests_private |only blackbox-1.1.32/blackbox/DESCRIPTION | 12 - blackbox-1.1.32/blackbox/MD5 | 65 +++------- blackbox-1.1.32/blackbox/NAMESPACE | 2 blackbox-1.1.32/blackbox/R/CKrigcoefs.R | 12 - blackbox-1.1.32/blackbox/R/Hreprrational.R | 2 blackbox-1.1.32/blackbox/R/blackbox.R | 14 +- blackbox-1.1.32/blackbox/R/blackbox_internals.R | 5 blackbox-1.1.32/blackbox/R/canonize.R | 2 blackbox-1.1.32/blackbox/R/conversionsFromCanon.R |only blackbox-1.1.32/blackbox/R/findReplicates.R | 12 + blackbox-1.1.32/blackbox/R/formatName.R | 2 blackbox-1.1.32/blackbox/R/generateNextpointsfromCI.R | 3 blackbox-1.1.32/blackbox/R/predict.OKrig.R | 2 blackbox-1.1.32/blackbox/R/profile.R | 4 blackbox-1.1.32/blackbox/R/provideDevice.R | 2 blackbox-1.1.32/blackbox/R/purefn.R | 2 blackbox-1.1.32/blackbox/R/resetCHull.R | 6 blackbox-1.1.32/blackbox/R/scdd.addHline.R | 8 - blackbox-1.1.32/blackbox/R/selectFn.R | 2 blackbox-1.1.32/blackbox/inst/NEWS.Rd | 15 ++ blackbox-1.1.32/blackbox/man/blackbox-internal.Rd | 2 blackbox-1.1.32/blackbox/tests/test-all.R | 2 33 files changed, 91 insertions(+), 85 deletions(-)
Title: IMAP Toolkit
Description: IMAP4rev1 (Internet Message Access Protocol, Version 4rev1)
functionalities based on the RFC 3501 manual (Crispin, 2003,
<doi:10.17487/RFC3501>), its updates, and other related documents.
'mRpostman' makes extensive use of 'curl' and 'libcurl' capabilities,
providing functions for mailboxes and electronic messages manipulation.
Author: Allan Quadros [aut, cre]
Maintainer: Allan Quadros <allanvcq@gmail.com>
Diff between mRpostman versions 0.3.0 dated 2019-10-17 and 0.3.1 dated 2020-04-20
mRpostman-0.3.0/mRpostman/R/environments-tests.R |only mRpostman-0.3.1/mRpostman/DESCRIPTION | 13 mRpostman-0.3.1/mRpostman/MD5 | 79 +-- mRpostman-0.3.1/mRpostman/R/check-args-get-attachments.R | 19 mRpostman-0.3.1/mRpostman/R/check-args-list-attachments.R |only mRpostman-0.3.1/mRpostman/R/get-attachments.R | 203 ++++++---- mRpostman-0.3.1/mRpostman/R/has-attachment.R | 2 mRpostman-0.3.1/mRpostman/R/list-attachments.R | 47 +- mRpostman-0.3.1/mRpostman/R/loop-fetch-full-msg.R | 11 mRpostman-0.3.1/mRpostman/R/loop-fetch-msg-header.R | 11 mRpostman-0.3.1/mRpostman/R/loop-fetch-msg-metadata.R | 11 mRpostman-0.3.1/mRpostman/R/loop-fetch-msg-text.R | 11 mRpostman-0.3.1/mRpostman/README.md | 32 + mRpostman-0.3.1/mRpostman/build/partial.rdb |binary mRpostman-0.3.1/mRpostman/build/vignette.rds |binary mRpostman-0.3.1/mRpostman/inst/doc/basics.R | 26 - mRpostman-0.3.1/mRpostman/inst/doc/basics.Rmd | 32 - mRpostman-0.3.1/mRpostman/inst/doc/basics.html | 30 - mRpostman-0.3.1/mRpostman/man/check_args_add_replace_flags.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_copy_msg.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_custom_search.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_delete_msg.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_expunge.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_fetch_full_msg.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_fetch_msg_header.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_fetch_msg_metadata.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_fetch_msg_text.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_get_attachments.Rd | 12 mRpostman-0.3.1/mRpostman/man/check_args_get_max_min_id.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_list_attachments.Rd |only mRpostman-0.3.1/mRpostman/man/check_args_move_msg.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_remove_flags.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_date.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_flag.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_period.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_size.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_string.Rd | 1 mRpostman-0.3.1/mRpostman/man/check_args_search_within.Rd | 1 mRpostman-0.3.1/mRpostman/man/get_attachments.Rd | 32 + mRpostman-0.3.1/mRpostman/man/has_attachment.Rd | 3 mRpostman-0.3.1/mRpostman/man/list_attachments.Rd | 7 mRpostman-0.3.1/mRpostman/vignettes/basics.Rmd | 32 - 42 files changed, 398 insertions(+), 233 deletions(-)
Title: Simulation of High-Dimensional Data and Parallelized Repeated
Penalized Regression
Description: Simulation of continuous, correlated high-dimensional data with
time to event or binary response, and parallelized functions for Lasso,
Ridge, and Elastic Net penalized regression with repeated starts and
two-dimensional tuning of the Elastic Net.
Author: Levi Waldron <lwaldron.research@gmail.com>
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between pensim versions 1.3.1 dated 2020-03-28 and 1.3.2 dated 2020-04-20
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS.md |only R/opt2D.R | 4 ++-- README.md | 4 ++++ build/vignette.rds |binary inst/doc/pensim.html | 16 ++++++++-------- tests/opt.nested.crossval.checks.R | 16 ++++++++++++++++ 8 files changed, 40 insertions(+), 19 deletions(-)
Title: Estimating Time-Varying k-Order Mixed Graphical Models
Description: Estimation of k-Order time-varying Mixed Graphical Models and mixed VAR(p) models via elastic-net regularized neighborhood regression. For details see Haslbeck & Waldorp (2020) <doi:10.18637/jss.v093.i08>.
Author: Jonas Haslbeck
Maintainer: Jonas Haslbeck <jonashaslbeck@gmail.com>
Diff between mgm versions 1.2-7 dated 2019-09-05 and 1.2-9 dated 2020-04-20
DESCRIPTION | 10 +-- MD5 | 66 ++++++++++---------- NEWS | 11 +++ R/ModelMatrix.R | 2 R/ModelMatrix_standard.R | 5 - R/Reg2Graph.R | 14 +++- R/applyTauAND.R | 64 ++++++++++++------- R/bwSelPredict.R | 8 -- R/bwSelect.R | 11 +-- R/condition.R | 10 ++- R/condition_core.R | 13 +++ R/glmnetRequirements.R | 56 ++++++++++++---- R/mgm.R | 21 +++--- R/mvarsampler.R | 1 R/plotRes.R | 11 ++- R/predictCore_stat.R | 5 + R/print.mgm.R | 5 + R/resample.R | 75 ++++++++++++++++++---- R/tvmvarsampler.R | 155 ++++++++++++++++++++++------------------------- README.md | 10 ++- inst/CITATION | 29 ++++---- man/bwSelect.Rd | 5 - man/mgm-package.Rd | 8 -- man/mgm.Rd | 14 ++-- man/mgmsampler.Rd | 2 man/mvar.Rd | 8 -- man/mvarsampler.Rd | 2 man/predict.mgm.Rd | 2 man/resample.Rd | 14 ++-- man/showInteraction.Rd | 2 man/tvmgm.Rd | 6 - man/tvmgmsampler.Rd | 2 man/tvmvar.Rd | 4 - man/tvmvarsampler.Rd | 2 34 files changed, 388 insertions(+), 265 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair>),
Polish Institute of Meterology and Water Management - National Research Institute (<https://dane.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for adding geographical coordinates for each observation.
Author: Bartosz Czernecki [aut, cre] (<https://orcid.org/0000-0001-6496-1386>),
Arkadiusz Głogowski [aut] (<https://orcid.org/0000-0002-7587-8892>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
IMGW-PIB [ctb] (source of the data)
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 0.9.3 dated 2020-03-30 and 0.9.4 dated 2020-04-20
DESCRIPTION | 9 MD5 | 42 +- NAMESPACE | 1 NEWS.md | 5 R/meteo_imgw_daily.R | 2 R/meteo_imgw_hourly.R | 2 R/meteo_imgw_monthly.R | 2 R/meteo_noaa_hourly.R |only README.md | 53 ++- inst/doc/getstarted.R | 44 +- inst/doc/getstarted.Rmd | 35 +- inst/doc/getstarted.html | 738 +++++++++++++++++++------------------------ man/climate-package.Rd | 3 man/get_coord_from_string.Rd | 6 man/imgw_hydro_abbrev.Rd | 6 man/imgw_hydro_stations.Rd | 6 man/imgw_meteo_abbrev.Rd | 6 man/imgw_meteo_stations.Rd | 6 man/meteo_imgw_daily.Rd | 2 man/meteo_imgw_hourly.Rd | 2 man/meteo_imgw_monthly.Rd | 2 man/meteo_noaa_hourly.Rd |only vignettes/getstarted.Rmd | 35 +- 23 files changed, 513 insertions(+), 494 deletions(-)
Title: Classification Based on Association Rules
Description: Provides the infrastructure for association rule-based classification including algorithms like Classification Based on Associations (CBA).
Author: Michael Hahsler [aut, cre, cph],
Ian Johnson [aut, cph],
Tyler Giallanza [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesCBA versions 1.1.6 dated 2020-01-08 and 1.2.0 dated 2020-04-20
arulesCBA-1.1.6/arulesCBA/build/vignette.rds |only arulesCBA-1.1.6/arulesCBA/inst/doc |only arulesCBA-1.1.6/arulesCBA/vignettes |only arulesCBA-1.2.0/arulesCBA/DESCRIPTION | 35 +-- arulesCBA-1.2.0/arulesCBA/MD5 | 67 +++--- arulesCBA-1.2.0/arulesCBA/NAMESPACE | 49 +++- arulesCBA-1.2.0/arulesCBA/NEWS.md | 15 + arulesCBA-1.2.0/arulesCBA/R/AAAinstalled.R |only arulesCBA-1.2.0/arulesCBA/R/CBA.R | 126 ++++++------ arulesCBA-1.2.0/arulesCBA/R/CBA.internal.R | 72 +++--- arulesCBA-1.2.0/arulesCBA/R/CBA.object.R | 115 ---------- arulesCBA-1.2.0/arulesCBA/R/FOIL.R |only arulesCBA-1.2.0/arulesCBA/R/LUCS_KDD_CBA.R |only arulesCBA-1.2.0/arulesCBA/R/RCAR.R | 87 ++++---- arulesCBA-1.2.0/arulesCBA/R/RWeka_CBA.R |only arulesCBA-1.2.0/arulesCBA/R/bCBA.R | 11 - arulesCBA-1.2.0/arulesCBA/R/classFrequency.R | 21 +- arulesCBA-1.2.0/arulesCBA/R/discretizeDF.supervised.R | 16 - arulesCBA-1.2.0/arulesCBA/R/mineCARs.R | 85 +++++--- arulesCBA-1.2.0/arulesCBA/R/predict.R |only arulesCBA-1.2.0/arulesCBA/R/prepareTransactions.R |only arulesCBA-1.2.0/arulesCBA/R/wCBA.R | 11 - arulesCBA-1.2.0/arulesCBA/README.md | 62 ++++- arulesCBA-1.2.0/arulesCBA/build/partial.rdb |only arulesCBA-1.2.0/arulesCBA/data |only arulesCBA-1.2.0/arulesCBA/inst/CITATION |only arulesCBA-1.2.0/arulesCBA/man/CBA.Rd | 59 ++--- arulesCBA-1.2.0/arulesCBA/man/CBA.object.Rd | 20 - arulesCBA-1.2.0/arulesCBA/man/FOIL.Rd |only arulesCBA-1.2.0/arulesCBA/man/LUCS_KDD_CBA.Rd |only arulesCBA-1.2.0/arulesCBA/man/Lymphography.Rd |only arulesCBA-1.2.0/arulesCBA/man/Mushroom.Rd |only arulesCBA-1.2.0/arulesCBA/man/RCAR.Rd | 52 +++- arulesCBA-1.2.0/arulesCBA/man/RWeka_CBA.Rd |only arulesCBA-1.2.0/arulesCBA/man/bCBA.Rd | 18 - arulesCBA-1.2.0/arulesCBA/man/classFrequency.Rd | 32 ++- arulesCBA-1.2.0/arulesCBA/man/mineCARs.Rd | 83 ++++++- arulesCBA-1.2.0/arulesCBA/man/prepareTransactions.Rd |only arulesCBA-1.2.0/arulesCBA/man/wCBA.Rd | 16 - arulesCBA-1.2.0/arulesCBA/tests/testthat.R | 2 arulesCBA-1.2.0/arulesCBA/tests/testthat/test-CBA.R | 8 arulesCBA-1.2.0/arulesCBA/tests/testthat/test-LUCS_KDD.R |only arulesCBA-1.2.0/arulesCBA/tests/testthat/test-classifiers.R |only 43 files changed, 597 insertions(+), 465 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps
to design cartographic representations such as proportional symbols,
choropleth, typology, flows or discontinuities maps. It also offers several
features that improve the graphic presentation of maps, for instance, map
palettes, layout elements (scale, north arrow, title...), labels or legends.
See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Nicolas Lambert [aut],
Diego Hernangómez [ctb] (<https://orcid.org/0000-0001-8457-4658>),
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.4.0 dated 2020-04-02 and 2.4.1 dated 2020-04-20
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 12 ++++++++++++ R/dotDensityLayer.R | 2 ++ R/getTiles.R | 4 ++-- R/legendHatched.R | 29 ++++++++++------------------- R/propTrianglesLayer.R | 2 +- R/waffleLayer.R | 4 ++-- inst/doc/cartography.html | 18 +++++++++--------- man/dotDensityLayer.Rd | 2 ++ man/legendHatched.Rd | 29 ++++++++++------------------- 11 files changed, 66 insertions(+), 68 deletions(-)
Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: David Blodgett [cre],
Tim Kern [aut],
Luke Winslow [aut],
Scott Chamberlain [aut],
Alison Appling [aut],
Jordan Read [aut]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between sbtools versions 1.1.10 dated 2020-03-20 and 1.1.11 dated 2020-04-20
DESCRIPTION | 8 +++--- MD5 | 50 +++++++++++++++++++++--------------------- R/REST_helpers.R | 7 +++++ R/item_get_fields.R | 4 +-- R/item_list_children.R | 8 ++++-- R/item_list_files.R | 6 +++-- R/set_endpoint.R | 6 ++--- man/folder_create.Rd | 3 -- man/item_create.Rd | 9 +++++-- man/item_file_download.Rd | 11 +++++++-- man/item_get_fields.Rd | 7 ++--- man/item_list_children.Rd | 15 +++++++++--- man/item_list_files.Rd | 8 +++--- man/item_rename_files.Rd | 3 -- man/item_replace_files.Rd | 3 -- man/item_rm.Rd | 9 +++++-- man/item_update_identifier.Rd | 10 ++++++-- man/item_upsert.Rd | 9 +++++-- man/items_create.Rd | 9 +++++-- man/items_upsert.Rd | 9 +++++-- man/query_item_identifier.Rd | 10 ++++++-- man/query_item_in_folder.Rd | 9 +++++-- man/query_sb_datatype.Rd | 3 -- man/query_sb_date.Rd | 11 ++++++--- man/query_sb_spatial.Rd | 11 +++++++-- man/set_endpoint.Rd | 6 ++--- 26 files changed, 158 insertions(+), 86 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-08 0.8.5
2016-07-21 0.8.0
Title: Empirical Transition Matrix
Description: The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Author: Arthur Allignol
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>
Diff between etm versions 1.0.5.1 dated 2020-01-29 and 1.1 dated 2020-04-20
DESCRIPTION | 11 +--- MD5 | 18 +++---- R/etm_intern.R | 12 ++--- R/print.etm.R | 38 +++++++-------- R/summary.etm.R | 2 build/vignette.rds |binary inst/doc/etmCIF_tutorial.pdf |binary src/gen_msm.cpp | 103 +++++-------------------------------------- tests/tests.etm.R | 2 tests/tests.etm.Rout.save | 28 ++++++----- 10 files changed, 68 insertions(+), 146 deletions(-)
Title: Toolkit for Credit Modeling, Analysis and Visualization
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.1.8 dated 2020-03-18 and 1.1.9 dated 2020-04-20
DESCRIPTION | 10 MD5 | 60 - NAMESPACE | 9 NEWS.md | 10 R/creditmodel.r |only R/data_anaylsis.R | 522 +++++++--- R/data_cleansing.R | 20 R/data_process_tools.R | 129 +- R/data_transformation.R | 440 +++++---- R/data_visualization.R | 1729 +++++++++++++++++++++--------------- R/essential_algorithms.R | 67 - R/example_data.r | 1 R/model_training.R | 4 R/variable_binning.R | 24 inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 312 ++---- man/char_to_num.Rd | 5 man/check_rules.Rd | 19 man/cohort_analysis.Rd | 7 man/creditmodel-package.Rd |only man/cross_table.Rd | 10 man/data_cleansing.Rd | 2 man/gather_data.Rd |only man/get_ctree_rules.Rd | 8 man/merge_category.Rd | 7 man/p_ij.Rd | 2 man/plot_bar.Rd |only man/plot_box.Rd |only man/plot_density.Rd |only man/plot_distribution.Rd |only man/plot_relative_freq_histogram.Rd |only man/read_data.Rd | 11 man/rules_filter.Rd |only man/swap_analysis.Rd |only vignettes/introduction.Rmd | 2 36 files changed, 1991 insertions(+), 1423 deletions(-)
Title: Coronavirus COVID-19 (2019-nCoV) Epidemic Datasets
Description: Unified tidy format datasets of the 2019 Novel Coronavirus COVID-19 (2019-nCoV) epidemic across several sources. The data are downloaded in real-time, cleaned and matched with exogenous variables. Vintage databases are also supported.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>),
David Ardia [ctb] (<https://orcid.org/0000-0003-2823-782X>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between COVID19 versions 0.3.0 dated 2020-04-11 and 1.0.0 dated 2020-04-20
COVID19-0.3.0/COVID19/R/diamond.R |only COVID19-0.3.0/COVID19/R/italy.R |only COVID19-0.3.0/COVID19/R/liechtenstein.R |only COVID19-0.3.0/COVID19/R/switzerland.R |only COVID19-0.3.0/COVID19/R/us.R |only COVID19-0.3.0/COVID19/inst/extdata/db/ch.csv |only COVID19-0.3.0/COVID19/inst/extdata/db/dp.csv |only COVID19-0.3.0/COVID19/inst/extdata/db/it.csv |only COVID19-0.3.0/COVID19/inst/extdata/db/wb.csv |only COVID19-0.3.0/COVID19/man/diamond.Rd |only COVID19-0.3.0/COVID19/man/italy.Rd |only COVID19-0.3.0/COVID19/man/liechtenstein.Rd |only COVID19-0.3.0/COVID19/man/switzerland.Rd |only COVID19-0.3.0/COVID19/man/us.Rd |only COVID19-0.3.0/COVID19/man/world.Rd |only COVID19-1.0.0/COVID19/DESCRIPTION | 25 +- COVID19-1.0.0/COVID19/MD5 | 75 ++++-- COVID19-1.0.0/COVID19/NAMESPACE | 7 COVID19-1.0.0/COVID19/R/ASM.R |only COVID19-1.0.0/COVID19/R/CHE.R |only COVID19-1.0.0/COVID19/R/CZE.R |only COVID19-1.0.0/COVID19/R/DPC.R |only COVID19-1.0.0/COVID19/R/GPC.R |only COVID19-1.0.0/COVID19/R/GUM.R |only COVID19-1.0.0/COVID19/R/ISO.R |only COVID19-1.0.0/COVID19/R/ITA.R |only COVID19-1.0.0/COVID19/R/LIE.R |only COVID19-1.0.0/COVID19/R/MNP.R |only COVID19-1.0.0/COVID19/R/MSZ.R |only COVID19-1.0.0/COVID19/R/PRI.R |only COVID19-1.0.0/COVID19/R/SWE.R |only COVID19-1.0.0/COVID19/R/USA.R |only COVID19-1.0.0/COVID19/R/VIR.R |only COVID19-1.0.0/COVID19/R/apple.R |only COVID19-1.0.0/COVID19/R/covid19.R |only COVID19-1.0.0/COVID19/R/datasource.R |only COVID19-1.0.0/COVID19/R/jhuCSSE.R | 109 +++++---- COVID19-1.0.0/COVID19/R/mzcr.R |only COVID19-1.0.0/COVID19/R/openZH.R | 53 ++-- COVID19-1.0.0/COVID19/R/oppnadata.R |only COVID19-1.0.0/COVID19/R/pcmdpc.R | 46 ++-- COVID19-1.0.0/COVID19/R/sysdata.rda |only COVID19-1.0.0/COVID19/R/utils.R | 212 ++++++++++++++----- COVID19-1.0.0/COVID19/R/world.R | 90 +++----- COVID19-1.0.0/COVID19/README.md | 284 ++++++++++++++++---------- COVID19-1.0.0/COVID19/build |only COVID19-1.0.0/COVID19/inst/CITATION |only COVID19-1.0.0/COVID19/inst/doc |only COVID19-1.0.0/COVID19/inst/extdata/db/AUS.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/CAN.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/CHE.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/CHN.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/CZE.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/DNK.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/FRA.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/GBR.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/ISO.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/ITA.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/NLD.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/SWE.csv |only COVID19-1.0.0/COVID19/inst/extdata/db/USA.csv |only COVID19-1.0.0/COVID19/inst/extdata/fix |only COVID19-1.0.0/COVID19/man/covid19.Rd |only COVID19-1.0.0/COVID19/vignettes |only 64 files changed, 560 insertions(+), 341 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-18 0.8.3
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a development/production release paradigm. Introduces a
generalized package installation process which supports multiple repository
and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <gabembecker@gmail.com>
Diff between switchr versions 0.14.2 dated 2020-01-25 and 0.14.3 dated 2020-04-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/biocversion.R | 4 ++++ build/vignette.rds |binary inst/doc/switchrvign.pdf |binary 5 files changed, 11 insertions(+), 7 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent access to
information contained in various R models, like model formulas, model terms,
information about random effects, data that was used to fit the model or
data from response variables. 'insight' mainly revolves around two types
of functions: Functions that find (the names of) information, starting with
'find_', and functions that get the underlying data, starting with 'get_'.
The package has a consistent syntax and works with many different model
objects, where otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.8.2 dated 2020-03-06 and 0.8.3 dated 2020-04-20
DESCRIPTION | 8 MD5 | 96 +++++----- NAMESPACE | 21 ++ NEWS.md | 24 ++ R/clean_parameters.R | 24 ++ R/compute_variances.R | 55 ------ R/find_algorithm.R | 6 R/find_formula.R | 7 R/find_parameters.R | 49 +++++ R/find_statistic.R | 19 +- R/format_ci.R | 12 + R/get_data.R | 76 ++++++++ R/get_parameters.R | 73 ++++++-- R/get_priors.R | 3 R/get_statistic.R | 110 +++++++++++- R/get_varcov.R | 10 + R/helper_functions.R | 24 +- R/is_model.R | 1 R/is_model_supported.R | 2 R/link_function.R | 20 ++ R/link_inverse.R | 16 + R/model_info.R | 27 ++- R/n_obs.R | 7 R/null_model.R |only R/print.easystats_check.R | 1 R/utils_get_data.R | 4 R/utils_model_info.R | 3 README.md | 77 ++++---- build/partial.rdb |binary inst/WORDLIST | 5 inst/doc/insight.html | 320 ++++++++++++++++++------------------ man/dot-colour_detect.Rd | 22 +- man/find_parameters.Rd | 19 +- man/get_data.Rd | 2 man/get_parameters.Rd | 5 man/get_predictors.Rd | 40 ++-- man/get_varcov.Rd | 2 man/model_info.Rd | 165 +++++++++--------- man/null_model.Rd |only tests/testthat/test-BayesFactorBF.R | 21 +- tests/testthat/test-MCMCglmm.R | 5 tests/testthat/test-blmer.R | 48 ++--- tests/testthat/test-brms.R | 73 +++----- tests/testthat/test-gbm.R | 1 tests/testthat/test-lmer.R | 85 ++++----- tests/testthat/test-mixed.R | 85 ++++----- tests/testthat/test-mlogit.R | 52 +++-- tests/testthat/test-rstanarm.R | 8 tests/testthat/test-spatial.R | 1 tests/testthat/test-zeroinfl.R | 2 50 files changed, 1082 insertions(+), 654 deletions(-)
Title: Access and Import Data from the French Open Data Portal
Description: Allows the user to access and import data from the rich French open data portal through the provided free API <https://doc.data.gouv.fr/api/reference/>.
The portal is free, and no credential is required for extracting datasets.
Author: Mohamed El Fodil Ihaddaden
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between BARIS versions 1.0.0 dated 2020-02-24 and 1.1.0 dated 2020-04-20
DESCRIPTION | 14 +-- MD5 | 23 +++-- NEWS.md |only R/BARIS_extract.R | 4 R/BARIS_ui.R |only R/memoise.R | 1 README.md | 195 +++++++++++++++++++++++++++------------------ build/vignette.rds |binary inst/doc/Introduction.R | 29 ++++++ inst/doc/Introduction.Rmd | 81 ++++++++++++++++++ inst/doc/Introduction.html | 102 +++++++++++++++++++---- inst/rstudio |only man/figures/Thumbs.db |binary vignettes/Introduction.Rmd | 81 ++++++++++++++++++ 14 files changed, 409 insertions(+), 121 deletions(-)
Title: 'SciViews' - Unit, Integration and System Testing
Description: A complete unit test system and functions to implement its GUI part.
Author: Philippe Grosjean [aut, cre] (<https://orcid.org/0000-0002-2694-9471>)
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svUnit versions 0.7-12 dated 2014-03-02 and 1.0.3 dated 2020-04-20
svUnit-0.7-12/svUnit/NEWS |only svUnit-0.7-12/svUnit/TODO |only svUnit-0.7-12/svUnit/inst/doc/svUnit.Rnw |only svUnit-0.7-12/svUnit/inst/doc/svUnit.pdf |only svUnit-0.7-12/svUnit/vignettes/svUnit.Rnw |only svUnit-0.7-12/svUnit/vignettes/svUnit.lyx |only svUnit-1.0.3/svUnit/DESCRIPTION | 30 svUnit-1.0.3/svUnit/MD5 | 75 svUnit-1.0.3/svUnit/NAMESPACE | 132 - svUnit-1.0.3/svUnit/NEWS.md |only svUnit-1.0.3/svUnit/R/Log.R | 195 +- svUnit-1.0.3/svUnit/R/check.R | 463 +++-- svUnit-1.0.3/svUnit/R/guiTestReport.R | 302 ++- svUnit-1.0.3/svUnit/R/koUnit.R | 128 + svUnit-1.0.3/svUnit/R/runExamples.R | 64 svUnit-1.0.3/svUnit/R/svSuite.R | 771 +++++---- svUnit-1.0.3/svUnit/R/svSuiteData.R | 420 +++- svUnit-1.0.3/svUnit/R/svTest.R | 352 ++-- svUnit-1.0.3/svUnit/R/svTestData.R | 284 ++- svUnit-1.0.3/svUnit/R/svUnit-internal.R | 845 +++++----- svUnit-1.0.3/svUnit/R/svUnit-package.R |only svUnit-1.0.3/svUnit/R/unitTests.svUnit.R |only svUnit-1.0.3/svUnit/build/vignette.rds |binary svUnit-1.0.3/svUnit/inst/CITATION | 10 svUnit-1.0.3/svUnit/inst/TestsvUnit.R | 59 svUnit-1.0.3/svUnit/inst/WORDLIST |only svUnit-1.0.3/svUnit/inst/doc/svUnit.R | 226 -- svUnit-1.0.3/svUnit/inst/doc/svUnit.Rmd |only svUnit-1.0.3/svUnit/inst/doc/svUnit.html |only svUnit-1.0.3/svUnit/inst/unitTests/BadTests |only svUnit-1.0.3/svUnit/inst/unitTests/VirtualClass/runitVirtualClass.R | 168 - svUnit-1.0.3/svUnit/inst/unitTests/runitsvSuite.R | 115 - svUnit-1.0.3/svUnit/inst/unitTests/runitsvTest.R | 173 +- svUnit-1.0.3/svUnit/man/Log.Rd | 115 - svUnit-1.0.3/svUnit/man/check.Rd | 168 + svUnit-1.0.3/svUnit/man/guiTestReport.Rd | 76 svUnit-1.0.3/svUnit/man/koUnit.Rd | 101 - svUnit-1.0.3/svUnit/man/svSuite.Rd | 328 ++- svUnit-1.0.3/svUnit/man/svSuiteData.Rd | 198 +- svUnit-1.0.3/svUnit/man/svTest.Rd | 257 +-- svUnit-1.0.3/svUnit/man/svTestData.Rd | 97 - svUnit-1.0.3/svUnit/man/svUnit-package.Rd | 272 +-- svUnit-1.0.3/svUnit/man/unitTests.svUnit.Rd | 42 svUnit-1.0.3/svUnit/tests |only svUnit-1.0.3/svUnit/vignettes/svUnit.Rmd |only 45 files changed, 3672 insertions(+), 2794 deletions(-)
Title: Create Japanese Administration Area and Office Maps
Description: Utilizing the data that Japanese administration area provided
by the National Land Numerical Information download service (<http://nlftp.mlit.go.jp/ksj/index.html>).
This package provide map data is based on the Digital Map 25000 (Map Image) published
by Geospatial Information Authority of Japan (Approval No.603FY2017 information usage <http://www.gsi.go.jp>).
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>),
Geospatial Information Authority of Japan [dtc] (This package data
sets, National Land numerical information by the Geographical
Survey Institute with the approval of Geographical Survey Institute
Head (Approval No.603FY2017 information usage))
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between jpndistrict versions 0.3.5 dated 2020-04-02 and 0.3.6 dated 2020-04-20
DESCRIPTION | 17 ++++++++--------- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/util.R | 8 +++----- tests/testthat/test-find_city.R | 3 ++- tests/testthat/test-util.R | 1 + 6 files changed, 24 insertions(+), 21 deletions(-)
Title: Interaction Analysis of Repeated Measure Data
Description: Extensive penalized variable selection methods have been developed in the past two decades for analyzing high dimensional omics data, such as gene expressions, single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and others. However, lipidomics data have been rarely investigated by using high dimensional variable selection methods. This package incorporates our recently developed penalization procedures to conduct interaction analysis for high dimensional lipidomics data with repeated measurements. The core module of this package is developed in C++. The development of this software package and the associated statistical methods have been partially supported by an Innovative Research Award from Johnson Cancer Research Center, Kansas State University.
Author: Fei Zhou, Jie Ren, Xiaoxi Li, Cen Wu, Yu Jiang
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between interep versions 0.3.0 dated 2019-10-14 and 0.3.1 dated 2020-04-20
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/cv.interep.R | 24 ++++++++++++++++++++++-- R/interep.R | 36 ++++-------------------------------- man/cv.interep.Rd | 24 ++++++++++++++++++++++-- man/interep.Rd | 36 ++++-------------------------------- 7 files changed, 65 insertions(+), 77 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that
provides stricter checking and better formatting than the traditional
data frame.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
Jennifer Bryan [ctb],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 3.0.0 dated 2020-03-30 and 3.0.1 dated 2020-04-20
DESCRIPTION | 6 MD5 | 48 +-- NAMESPACE | 2 NEWS.md | 29 + R/as_tibble.R | 24 - R/compat-lifecycle.R | 12 R/glimpse.R | 12 R/names.R | 2 R/print.R | 8 R/subsetting.R | 105 ++++-- R/tibble-package.R | 1 R/utils-msg-format.R | 2 build/tibble.pdf |binary build/vignette.rds |binary inst/doc/invariants.R | 20 + inst/doc/invariants.Rmd | 24 + inst/doc/invariants.html | 555 ++++++++++++++++++++--------------- inst/doc/types.html | 6 tests/testthat/helper-output.R | 2 tests/testthat/msg.txt | 4 tests/testthat/subsetting.txt | 35 +- tests/testthat/test-as_tibble.R | 59 +-- tests/testthat/test-subsetting.R | 48 ++- tests/testthat/test-zzz-data-frame.R | 4 vignettes/invariants.Rmd | 24 + 25 files changed, 654 insertions(+), 378 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta). Both classical geostatistical models, and Markov random field models on irregular grids, can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a generalized linear mixed model. Various approximations of likelihood or restricted likelihood are implemented, in particular h-likelihood (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) and Laplace approximation.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 3.1.27 dated 2020-03-10 and 3.2.0 dated 2020-04-20
DESCRIPTION | 17 +- MD5 | 102 +++++++-------- NAMESPACE | 4 R/COMPoisson.R | 15 +- R/GLM.fit.R | 16 +- R/HLCor.R | 2 R/HLFactorList.R | 25 ++- R/HLfit.R | 4 R/HLfit_Internals.R | 24 --- R/HLfit_body.R | 6 R/HLframes.R | 12 + R/LR.R | 7 - R/corrHLfit-internals.R | 26 --- R/corrHLfit.R | 6 R/cov_new_fix.R | 5 R/determine_spprec.R | 106 ++++++++------- R/extractors.R | 40 ++++- R/fit_as_ZX.R | 11 + R/fit_as_sparsePrecision.R | 1 R/fitme.R | 71 +++++++--- R/fitme_body.R | 2 R/fitmecorrHLfit_body_internals.R | 11 + R/get_cPredVar.R | 4 R/locoptim.R | 7 - R/newPLS.R | 104 +++++++++------ R/predict.R | 21 +-- R/preprocess.R | 116 +++++++++++------ R/preprocess_internals.R | 24 +++ R/sXaug_sparsePrecisions.R | 29 +++- R/safe_opt.R | 1 R/separator.R | 257 +++++++++++--------------------------- R/simulate.HL.R | 109 ++++++++++------ R/source_MV.R |only R/spaMM.data.R | 6 R/spaMM_boot.R | 26 +-- R/summary.HL.R | 11 + R/utils.R | 5 build/partial.rdb |binary inst/NEWS.Rd | 26 +++ man/dopar.Rd |only man/how.Rd | 3 man/is_separated.Rd | 30 +++- man/predict.Rd | 5 man/simulate.Rd | 8 - man/spaMM-internal.Rd | 2 man/spaMM.Rd | 2 man/update.Rd | 12 + tests/test-all.R | 4 tests/testthat/test-CAR.R | 14 +- tests/testthat/test-COMPoisson.R | 6 tests/testthat/test-poly.R | 4 tests/testthat/test-ranCoefs.R | 4 tests/testthat/test-spaMM.R | 51 ++++++- 53 files changed, 814 insertions(+), 590 deletions(-)
Title: Bridging the Gap Between Qualitative Data and Quantitative
Analysis
Description: Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse
including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted
analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user
to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R
packages that undertake higher level analysis and visualization of text. This affords the user a more efficient
and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other
areas of Text Mining/ Natural Language Processing.
Author: Tyler Rinker [aut, cre],
Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdap versions 2.3.6 dated 2020-01-09 and 2.4.1 dated 2020-04-20
qdap-2.3.6/qdap/build |only qdap-2.3.6/qdap/inst/doc |only qdap-2.3.6/qdap/man/t.DocumentTermMatrix.Rd |only qdap-2.3.6/qdap/man/t.TermDocumentMatrix.Rd |only qdap-2.3.6/qdap/vignettes |only qdap-2.4.1/qdap/DESCRIPTION | 15 qdap-2.4.1/qdap/MD5 | 529 +--- qdap-2.4.1/qdap/NAMESPACE | 1291 ++++------ qdap-2.4.1/qdap/NEWS | 15 qdap-2.4.1/qdap/R/as.tdm.R | 127 qdap-2.4.1/qdap/R/cm_code.blank.R | 4 qdap-2.4.1/qdap/R/cm_combine.dummy.R | 8 qdap-2.4.1/qdap/R/cm_d2l.R | 2 qdap-2.4.1/qdap/R/cm_df.transcript.R | 3 qdap-2.4.1/qdap/R/cm_df2long.R | 4 qdap-2.4.1/qdap/R/cm_dummy2long.R | 4 qdap-2.4.1/qdap/R/cm_r2l.R | 8 qdap-2.4.1/qdap/R/cm_range.temp.R | 2 qdap-2.4.1/qdap/R/cm_range2long.R | 4 qdap-2.4.1/qdap/R/cm_t2l.R | 8 qdap-2.4.1/qdap/R/cm_time.temp.R | 2 qdap-2.4.1/qdap/R/cm_time2long.R | 4 qdap-2.4.1/qdap/R/colSplit.R | 2 qdap-2.4.1/qdap/R/discourse_map.R | 4 qdap-2.4.1/qdap/R/formality.R | 23 qdap-2.4.1/qdap/R/gantt.R | 2 qdap-2.4.1/qdap/R/gantt_plot.R | 2 qdap-2.4.1/qdap/R/gantt_wrap.R | 3 qdap-2.4.1/qdap/R/lexical_classification.R | 5 qdap-2.4.1/qdap/R/mcsv_r.R | 3 qdap-2.4.1/qdap/R/new_project.R | 137 - qdap-2.4.1/qdap/R/polarity.R | 4 qdap-2.4.1/qdap/R/pos.R | 32 qdap-2.4.1/qdap/R/syllable_sum.R | 4 qdap-2.4.1/qdap/R/wfm.R | 2 qdap-2.4.1/qdap/R/word_position.R | 2 qdap-2.4.1/qdap/data/DATA.SPLIT.rda |binary qdap-2.4.1/qdap/data/DATA.rda |binary qdap-2.4.1/qdap/data/DATA2.rda |binary qdap-2.4.1/qdap/data/env.syl.rda |binary qdap-2.4.1/qdap/data/hamlet.rda |binary qdap-2.4.1/qdap/data/mraja1.rda |binary qdap-2.4.1/qdap/data/mraja1spl.rda |binary qdap-2.4.1/qdap/data/pres_debate_raw2012.rda |binary qdap-2.4.1/qdap/data/pres_debates2012.rda |binary qdap-2.4.1/qdap/data/raj.act.1.rda |binary qdap-2.4.1/qdap/data/raj.act.1POS.rda |binary qdap-2.4.1/qdap/data/raj.act.2.rda |binary qdap-2.4.1/qdap/data/raj.act.3.rda |binary qdap-2.4.1/qdap/data/raj.act.4.rda |binary qdap-2.4.1/qdap/data/raj.act.5.rda |binary qdap-2.4.1/qdap/data/raj.demographics.rda |binary qdap-2.4.1/qdap/data/raj.rda |binary qdap-2.4.1/qdap/data/rajPOS.rda |binary qdap-2.4.1/qdap/data/rajSPLIT.rda |binary qdap-2.4.1/qdap/data/raw.time.span.rda |binary qdap-2.4.1/qdap/data/sample.time.span.rda |binary qdap-2.4.1/qdap/inst/CITATION | 4 qdap-2.4.1/qdap/man/DATA.Rd | 4 qdap-2.4.1/qdap/man/DATA.SPLIT.Rd | 4 qdap-2.4.1/qdap/man/DATA2.Rd | 4 qdap-2.4.1/qdap/man/Network.Rd | 36 qdap-2.4.1/qdap/man/Title.Rd | 38 qdap-2.4.1/qdap/man/Trim.Rd | 44 qdap-2.4.1/qdap/man/Word_Frequency_Matrix.Rd | 2 qdap-2.4.1/qdap/man/addNetwork.Rd | 30 qdap-2.4.1/qdap/man/clean.Rd | 52 qdap-2.4.1/qdap/man/cm_df.transcript.Rd | 2 qdap-2.4.1/qdap/man/cm_range.temp.Rd | 2 qdap-2.4.1/qdap/man/cm_time.temp.Rd | 2 qdap-2.4.1/qdap/man/counts.SMOG.Rd | 36 qdap-2.4.1/qdap/man/counts.character_table.Rd | 36 qdap-2.4.1/qdap/man/counts.coleman_liau.Rd | 36 qdap-2.4.1/qdap/man/counts.end_mark_by.Rd | 36 qdap-2.4.1/qdap/man/counts.flesch_kincaid.Rd | 36 qdap-2.4.1/qdap/man/counts.formality.Rd | 36 qdap-2.4.1/qdap/man/counts.fry.Rd | 36 qdap-2.4.1/qdap/man/counts.linsear_write.Rd | 36 qdap-2.4.1/qdap/man/counts.object_pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/counts.polarity.Rd | 36 qdap-2.4.1/qdap/man/counts.pos.Rd | 36 qdap-2.4.1/qdap/man/counts.pos_by.Rd | 36 qdap-2.4.1/qdap/man/counts.pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/counts.question_type.Rd | 36 qdap-2.4.1/qdap/man/counts.subject_pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/counts.termco.Rd | 36 qdap-2.4.1/qdap/man/counts.word_length.Rd | 36 qdap-2.4.1/qdap/man/counts.word_position.Rd | 36 qdap-2.4.1/qdap/man/counts.word_stats.Rd | 36 qdap-2.4.1/qdap/man/discourse_map.Rd | 4 qdap-2.4.1/qdap/man/env.syl.Rd | 4 qdap-2.4.1/qdap/man/file_handling.Rd |only qdap-2.4.1/qdap/man/formality.Rd | 3 qdap-2.4.1/qdap/man/gantt.Rd | 2 qdap-2.4.1/qdap/man/gantt_plot.Rd | 2 qdap-2.4.1/qdap/man/gantt_wrap.Rd | 3 qdap-2.4.1/qdap/man/hamlet.Rd | 4 qdap-2.4.1/qdap/man/lexical_classification.Rd | 5 qdap-2.4.1/qdap/man/mraja1.Rd | 4 qdap-2.4.1/qdap/man/mraja1spl.Rd | 4 qdap-2.4.1/qdap/man/multicsv.Rd | 2 qdap-2.4.1/qdap/man/new_project.Rd | 14 qdap-2.4.1/qdap/man/plot.Network.Rd | 30 qdap-2.4.1/qdap/man/plot.SMOG.Rd | 30 qdap-2.4.1/qdap/man/plot.animated_character.Rd | 30 qdap-2.4.1/qdap/man/plot.animated_discourse_map.Rd | 30 qdap-2.4.1/qdap/man/plot.animated_formality.Rd | 30 qdap-2.4.1/qdap/man/plot.animated_polarity.Rd | 30 qdap-2.4.1/qdap/man/plot.automated_readability_index.Rd | 30 qdap-2.4.1/qdap/man/plot.coleman_liau.Rd | 30 qdap-2.4.1/qdap/man/plot.combo_syllable_sum.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_animated_formality.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_animated_polarity.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_combo_syllable_sum.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_end_mark.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_formality.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_lexical_classification.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_polarity.Rd | 30 qdap-2.4.1/qdap/man/plot.cumulative_syllable_freq.Rd | 30 qdap-2.4.1/qdap/man/plot.discourse_map.Rd | 30 qdap-2.4.1/qdap/man/plot.diversity.Rd | 30 qdap-2.4.1/qdap/man/plot.end_mark.Rd | 30 qdap-2.4.1/qdap/man/plot.end_mark_by.Rd | 36 qdap-2.4.1/qdap/man/plot.flesch_kincaid.Rd | 30 qdap-2.4.1/qdap/man/plot.formality_scores.Rd | 30 qdap-2.4.1/qdap/man/plot.kullback_leibler.Rd | 34 qdap-2.4.1/qdap/man/plot.linsear_write_count.Rd | 30 qdap-2.4.1/qdap/man/plot.pos.Rd | 30 qdap-2.4.1/qdap/man/plot.pos_preprocessed.Rd | 30 qdap-2.4.1/qdap/man/plot.question_type_preprocessed.Rd | 30 qdap-2.4.1/qdap/man/plot.readability_count.Rd | 34 qdap-2.4.1/qdap/man/plot.syllable_freq.Rd | 30 qdap-2.4.1/qdap/man/plot.type_token_ratio.Rd | 30 qdap-2.4.1/qdap/man/plot.wfdf.Rd | 30 qdap-2.4.1/qdap/man/plot.word_stats_counts.Rd | 34 qdap-2.4.1/qdap/man/polarity.Rd | 4 qdap-2.4.1/qdap/man/preprocessed.end_mark_by.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.formality.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.object_pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.pos.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.pos_by.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.question_type.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.subject_pronoun_type.Rd | 36 qdap-2.4.1/qdap/man/preprocessed.word_position.Rd | 36 qdap-2.4.1/qdap/man/pres_debate_raw2012.Rd | 40 qdap-2.4.1/qdap/man/pres_debates2012.Rd | 4 qdap-2.4.1/qdap/man/print.Dissimilarity.Rd | 34 qdap-2.4.1/qdap/man/print.SMOG.Rd | 34 qdap-2.4.1/qdap/man/print.adjacency_matrix.Rd | 30 qdap-2.4.1/qdap/man/print.all_words.Rd | 30 qdap-2.4.1/qdap/man/print.animated_character.Rd | 34 qdap-2.4.1/qdap/man/print.boolean_qdap.Rd | 30 qdap-2.4.1/qdap/man/print.check_spelling.Rd | 30 qdap-2.4.1/qdap/man/print.check_spelling_interactive.Rd | 30 qdap-2.4.1/qdap/man/print.coleman_liau.Rd | 34 qdap-2.4.1/qdap/man/print.colsplit2df.Rd | 30 qdap-2.4.1/qdap/man/print.combo_syllable_sum.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_animated_formality.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_animated_polarity.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_combo_syllable_sum.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_end_mark.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_formality.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_lexical_classification.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_polarity.Rd | 30 qdap-2.4.1/qdap/man/print.cumulative_syllable_freq.Rd | 30 qdap-2.4.1/qdap/man/print.diversity.Rd | 34 qdap-2.4.1/qdap/man/print.end_mark.Rd | 30 qdap-2.4.1/qdap/man/print.end_mark_by.Rd | 30 qdap-2.4.1/qdap/man/print.end_mark_by_preprocessed.Rd | 30 qdap-2.4.1/qdap/man/print.flesch_kincaid.Rd | 34 qdap-2.4.1/qdap/man/print.formality.Rd | 34 qdap-2.4.1/qdap/man/print.formality_scores.Rd | 30 qdap-2.4.1/qdap/man/print.kullback_leibler.Rd | 34 qdap-2.4.1/qdap/man/print.lexical_classification.Rd | 32 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qdap-2.4.1/qdap/tests/testthat/test-cm_2long.R | 95 qdap-2.4.1/qdap/tests/testthat/test-cm_code.blank.R | 59 qdap-2.4.1/qdap/tests/testthat/test-colSplit.R | 25 qdap-2.4.1/qdap/tests/testthat/test-formality.R | 75 qdap-2.4.1/qdap/tests/testthat/test-pos.R | 75 qdap-2.4.1/qdap/tests/testthat/test-syllable_sum.R | 28 264 files changed, 4154 insertions(+), 4093 deletions(-)
Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) <doi:10.1002/9780470747278> and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between nnTensor versions 1.0.2 dated 2019-10-25 and 1.0.4 dated 2020-04-20
DESCRIPTION | 8 MD5 | 32 +- NAMESPACE | 18 - R/NMF.R | 224 +++++++++++++- R/NTD.R | 70 ++-- R/NTF.R | 115 +++---- R/nnTensor-internal.R | 495 +++++++++++++++++++++++++++---- R/recTensor.R | 12 R/toyModel.R | 208 ++++++------- build/partial.rdb |binary inst/NEWS | 28 + man/NMF.Rd | 58 ++- man/nnTensor-package.Rd | 18 + man/plot.NMF.Rd |only tests/testthat.R | 1 tests/testthat/test_NMF_rankestimation.R |only tests/testthat/test_NTD.R | 112 ++++++- tests/testthat/test_NTF.R | 42 ++ 18 files changed, 1131 insertions(+), 310 deletions(-)
Title: Tools for Identifying Important Nodes in Networks
Description: Includes assorted tools for network analysis. Bridge centrality; goldbricker; MDS, PCA, & eigenmodel network plotting.
Author: Payton Jones [aut, cre]
Maintainer: Payton Jones <payton_jones@g.harvard.edu>
Diff between networktools versions 1.2.2 dated 2020-02-13 and 1.2.3 dated 2020-04-20
DESCRIPTION | 8 +++---- MD5 | 44 +++++++++++++++++++++---------------------- NEWS.md | 4 +++ R/bridge.R | 10 ++------- R/data_documentation.R | 37 ------------------------------------ R/expectedInf.R | 3 -- R/impact.R | 27 -------------------------- R/impact_NCT.R | 15 -------------- R/impact_boot.R | 8 ------- R/summary_print_plot.R | 32 +------------------------------ man/bridge.Rd | 10 ++------- man/depression.Rd | 15 -------------- man/expectedInf.Rd | 3 -- man/impact.NCT.Rd | 16 --------------- man/impact.Rd | 28 --------------------------- man/impact.boot.Rd | 9 -------- man/plot.all.impact.Rd | 9 -------- man/plot.bridge.Rd | 3 -- man/plot.edge.impact.Rd | 4 --- man/plot.expectedInf.Rd | 12 ----------- man/plot.global.impact.Rd | 4 --- man/plot.structure.impact.Rd | 4 --- man/social.Rd | 22 --------------------- 23 files changed, 40 insertions(+), 287 deletions(-)
Title: Non-Parametric Tests of Independence Between Random Vectors
Description: Functions for non-parametric tests of independence (mutual or serial) between some quantitative random vectors.
Author: Pierre Lafaye De Micheaux [aut, cre],
Martin Bilodeau [aut],
Yanan Fan [aut],
Spiridon Penev [aut],
Donna Salopek [aut]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
Diff between IndependenceTests versions 0.2 dated 2012-12-11 and 0.3 dated 2020-04-20
IndependenceTests-0.2/IndependenceTests/inst/doc |only IndependenceTests-0.3/IndependenceTests/DESCRIPTION | 40 +- IndependenceTests-0.3/IndependenceTests/INDEX | 1 IndependenceTests-0.3/IndependenceTests/MD5 | 83 +++- IndependenceTests-0.3/IndependenceTests/NAMESPACE | 17 IndependenceTests-0.3/IndependenceTests/R/A-dep-tests.R | 2 IndependenceTests-0.3/IndependenceTests/R/dependogram.R | 119 ++---- IndependenceTests-0.3/IndependenceTests/R/mdcov-lambdas.R |only IndependenceTests-0.3/IndependenceTests/R/mdcov-pval.R |only IndependenceTests-0.3/IndependenceTests/R/mdcov.R |only IndependenceTests-0.3/IndependenceTests/R/others |only IndependenceTests-0.3/IndependenceTests/R/zzz.R |only IndependenceTests-0.3/IndependenceTests/TODO | 13 IndependenceTests-0.3/IndependenceTests/inst/CITATION | 9 IndependenceTests-0.3/IndependenceTests/inst/HISTORY | 14 IndependenceTests-0.3/IndependenceTests/man/A-dep-tests.Rd | 86 ++-- IndependenceTests-0.3/IndependenceTests/man/dependogram.Rd | 187 ++++++---- IndependenceTests-0.3/IndependenceTests/man/dna.Rd | 10 IndependenceTests-0.3/IndependenceTests/man/mdcov.Rd |only IndependenceTests-0.3/IndependenceTests/src/Cnhat.cpp |only IndependenceTests-0.3/IndependenceTests/src/IndependenceTests_init.c |only IndependenceTests-0.3/IndependenceTests/src/Makevars |only IndependenceTests-0.3/IndependenceTests/src/cubature1.cpp |only IndependenceTests-0.3/IndependenceTests/src/dependogram.cpp | 30 - IndependenceTests-0.3/IndependenceTests/src/mdcov.cpp |only IndependenceTests-0.3/IndependenceTests/src/myzhpevx.cpp |only IndependenceTests-0.3/IndependenceTests/src/others/binarycode.c |only IndependenceTests-0.3/IndependenceTests/src/others/gauher.c |only IndependenceTests-0.3/IndependenceTests/src/others/normeRnAwR.cpp | 46 +- IndependenceTests-0.3/IndependenceTests/src/othersfortran |only IndependenceTests-0.3/IndependenceTests/src/phinhat.cpp |only IndependenceTests-0.3/IndependenceTests/src/zhpevx.f |only 32 files changed, 393 insertions(+), 264 deletions(-)
More information about IndependenceTests at CRAN
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Title: Create Tidy Data Frames of Marginal Effects for 'ggplot' from
Model Outputs
Description: Compute marginal effects from statistical models and returns the
result as tidy data frames. These data frames are ready to use with the
'ggplot2'-package. Marginal effects can be calculated for many different
models. Interaction terms, splines and polynomial terms are also supported.
The main functions are ggpredict(), ggemmeans() and ggeffect(). There is a
generic plot()-method to plot the results using 'ggplot2'.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between ggeffects versions 0.14.2 dated 2020-03-14 and 0.14.3 dated 2020-04-20
DESCRIPTION | 6 MD5 | 52 - NEWS.md | 6 R/emmeans_prediction_data.R | 8 R/get_predictions_zeroinfl.R | 2 R/ggeffect.R | 2 R/ggemmeans.R | 4 R/plot.R | 4 R/post_processing_predictions.R | 2 R/predict_zero_inflation.R | 24 R/print.R | 2 R/simulate_predictions.R | 10 R/standard_error_predictions.R | 12 R/themes.R | 4 R/utils.R | 4 R/vcov.R | 8 build/partial.rdb |binary inst/doc/ggeffects.html | 814 +++++++++++------------ inst/doc/introduction_effectsatvalues.html | 466 ++++++------- inst/doc/introduction_plotcustomize.html | 116 +-- inst/doc/introduction_plotmethod.html | 192 ++--- inst/doc/introduction_randomeffects.html | 446 ++++++------ inst/doc/practical_logisticmixedmodel.html | 234 +++--- inst/doc/practical_robustestimation.html | 214 +++--- inst/doc/technical_differencepredictemmeans.html | 294 ++++---- inst/doc/technical_stata.html | 86 +- tests/testthat/test-coxph.R | 10 27 files changed, 1579 insertions(+), 1443 deletions(-)
Title: Understand and Describe Bayesian Models and Posterior
Distributions
Description: Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Michael D. Wilson [aut] (<https://orcid.org/0000-0003-4143-7308>),
Paul-Christian Bürkner [rev],
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>),
Quentin F. Gronau [ctb] (<https://orcid.org/0000-0001-5510-6943>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between bayestestR versions 0.5.3 dated 2020-03-26 and 0.6.0 dated 2020-04-20
DESCRIPTION | 6 MD5 | 97 +++---- NAMESPACE | 15 + NEWS.md | 16 + R/bayesfactor_inclusion.R | 43 --- R/bayesfactor_parameters.R | 1 R/bayesfactor_restricted.R | 1 R/describe_posterior.R | 52 +++ R/diagnostic_posterior.R | 15 - R/equivalence_test.R | 2 R/estimate_density.R | 27 +- R/map_estimate.R | 12 R/p_direction.R | 3 R/p_significance.R | 30 ++ R/print.ci.R | 8 R/print.describe_posterior.R | 2 R/print.equivalence_test.R | 2 R/print.map_estimate.R |only R/print.mhdior.R | 2 R/print.p_direction.R | 2 R/print.p_map.R | 2 R/print.p_rope.R | 2 R/print.p_significance.R | 2 R/print.point_estimate.R | 4 R/print.rope.R | 2 R/rope_range.R | 53 +++- R/utils_bayesfactor.R | 54 ++++ R/utils_print_data_frame.R | 2 R/weighted_posteriors.R | 42 +-- README.md | 34 +- build/partial.rdb |binary man/bayesfactor_parameters.Rd | 1 man/bayesfactor_restricted.Rd | 353 +++++++++++++-------------- man/diagnostic_posterior.Rd | 15 - man/rope_range.Rd | 125 ++++----- man/weighted_posteriors.Rd | 10 tests/testthat/test-bayesfactor_restricted.R | 2 tests/testthat/test-brms.R | 7 tests/testthat/test-ci.R | 4 tests/testthat/test-density_at.R | 2 tests/testthat/test-emmGrid.R | 3 tests/testthat/test-estimate_density.R | 6 tests/testthat/test-hdi.R | 2 tests/testthat/test-map_estimate.R | 16 - tests/testthat/test-p_direction.R | 2 tests/testthat/test-p_significance.R | 4 tests/testthat/test-point_estimate.R | 4 tests/testthat/test-rope.R | 4 tests/testthat/test-simulate_data.R | 2 tests/testthat/test-weighted_posteriors.R | 49 ++- 50 files changed, 686 insertions(+), 458 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-21 2015-2.13.1
2015-02-18 2015-2.13
Title: Markov-Switching GARCH Models
Description: Fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various Markov-Switching GARCH models as described in Ardia et al. (2019) <doi:10.18637/jss.v091.i04>.
Author: David Ardia [aut] (<https://orcid.org/0000-0003-2823-782X>),
Keven Bluteau [aut, cre] (<https://orcid.org/0000-0003-2990-4807>),
Kris Boudt [ctb] (<https://orcid.org/0000-0002-1000-5142>),
Leopoldo Catania [aut] (<https://orcid.org/0000-0002-0981-1921>),
Alexios Ghalanos [ctb],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@hec.ca>
Diff between MSGARCH versions 2.31 dated 2019-10-24 and 2.42 dated 2020-04-20
DESCRIPTION | 38 +++++++++-------- MD5 | 44 +++++++++---------- NEWS | 7 ++- R/FitML.R | 11 ++-- R/Inference.R | 2 R/Kernel.R | 2 R/MSGARCH.R | 11 ++++ R/ParameterTransformation.R | 4 - R/Posterior.R | 3 - R/StartingValues.R | 9 ++++ R/zzz.R | 12 ++--- inst/CITATION | 2 man/CreateSpec.Rd | 6 +- man/MSGARCH-package.Rd | 18 ++++++-- man/PIT.Rd | 43 +++++++++++++++---- man/PredPdf.Rd | 43 +++++++++++++++---- man/Risk.Rd | 43 +++++++++++++++---- man/SMI.Rd | 4 + man/TransMat.Rd | 98 ++++++++++++++++++++++---------------------- man/dem2gbp.Rd | 4 + man/predict.Rd | 35 ++++++++++++--- man/simulate.Rd | 17 ++++--- tests/testthat/test_State.R | 98 ++++++++++++++++++++++---------------------- 23 files changed, 349 insertions(+), 205 deletions(-)
Title: Data Manipulation Extensions of 'Dplyr' and 'Tidyr'
Description: If 'dplyr' is a grammar for data manipulation, 'extdplyr' is like
a short paragraph written in 'dplyr'. 'extdplyr' extends 'dplyr' and
'tidyr' verbs to some common "routines" that manipulate data sets. It uses
the same interface and preserves all the features from 'dplyr', has good
performance, and supports various data sources.
Author: Yuchen Wang [aut, cre]
Maintainer: Yuchen Wang <ycwang0712@gmail.com>
Diff between extdplyr versions 0.1.4 dated 2017-02-27 and 0.1.5 dated 2020-04-20
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 1 + NEWS.md | 9 +++++++++ R/check_missing.R | 3 ++- R/grp_routine.R | 21 ++++++++++++--------- R/pct_routine.R | 2 +- R/utilities.R | 25 +++++++++++++++++++------ README.md | 4 ++-- man/check_missing.Rd | 4 +--- man/ind_to_char.Rd | 28 +++++++++++++++++++++------- man/pct_routine.Rd | 20 ++++++++++++++++---- tests/testthat/test_grp_routine.R | 4 ++-- 13 files changed, 102 insertions(+), 51 deletions(-)
Title: Computes and Plots Compatibility (Confidence) Intervals,
P-Values, S-Values, & Likelihood Intervals to Form Consonance,
Surprisal, & Likelihood Functions
Description: Allows one to compute compatibility (confidence)
intervals for various statistical tests along with their corresponding
P-values, S-values, and likelihoods. The intervals can be plotted to
create consonance, surprisal, and likelihood functions allowing one to
see what effect sizes are compatible with the test model at various
compatibility levels rather than being limited to one interval estimate
such as 95\%. Functions can also be compared to one another to see how much
they overlap with one another and differ. Results can also be exported for
Word, Powerpoint, and TeX documents. The package currently supports bootstrapping,
linear models, generalized linear models, linear mixed-effects models,
survival analysis, and meta-analysis. These methods are discussed by
Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002)
<doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007)
<arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008,
ISBN:9781451190052), Greenland S. (2019)
<doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019)
<arXiv:1909.08579>, and Greenland S, Chow ZR. (2019)
<arXiv:1909.08583>.
Author: Zad Rafi [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew D. Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>)
Maintainer: Zad Rafi <zad@lesslikely.com>
Diff between concurve versions 2.3.0 dated 2019-12-04 and 2.5.0 dated 2020-04-20
concurve-2.3.0/concurve/R/utils-tidy-eval.R |only concurve-2.3.0/concurve/inst/assets |only concurve-2.3.0/concurve/inst/doc/stata.R |only concurve-2.3.0/concurve/inst/doc/stata.Rmd |only concurve-2.3.0/concurve/inst/doc/stata.html |only concurve-2.3.0/concurve/inst/templates |only concurve-2.3.0/concurve/man/figures/logo.png |only concurve-2.3.0/concurve/man/tidyeval.Rd |only concurve-2.3.0/concurve/vignettes/figures |only concurve-2.3.0/concurve/vignettes/stata.Rmd |only concurve-2.5.0/concurve/DESCRIPTION | 50 + concurve-2.5.0/concurve/MD5 | 136 ++--- concurve-2.5.0/concurve/NAMESPACE | 4 concurve-2.5.0/concurve/NEWS.md | 33 + concurve-2.5.0/concurve/R/curve_boot.R | 171 +++++- concurve-2.5.0/concurve/R/curve_compare.R | 16 concurve-2.5.0/concurve/R/curve_corr.R | 7 concurve-2.5.0/concurve/R/curve_gen.R | 29 - concurve-2.5.0/concurve/R/curve_lik.R | 6 concurve-2.5.0/concurve/R/curve_lmer.R |only concurve-2.5.0/concurve/R/curve_mean.R | 7 concurve-2.5.0/concurve/R/curve_meta.R | 134 ++++- concurve-2.5.0/concurve/R/curve_rev.R | 19 concurve-2.5.0/concurve/R/curve_surv.R | 20 concurve-2.5.0/concurve/R/curve_table.R | 11 concurve-2.5.0/concurve/R/ggcurve.R | 124 +--- concurve-2.5.0/concurve/R/plot_compare.R | 119 +--- concurve-2.5.0/concurve/README.md | 182 ------ concurve-2.5.0/concurve/build/vignette.rds |binary concurve-2.5.0/concurve/inst/CITATION | 16 concurve-2.5.0/concurve/inst/WORDLIST | 62 +- concurve-2.5.0/concurve/inst/doc/bootstrap.R |only concurve-2.5.0/concurve/inst/doc/bootstrap.Rmd |only concurve-2.5.0/concurve/inst/doc/bootstrap.html |only concurve-2.5.0/concurve/inst/doc/customizing.R |only concurve-2.5.0/concurve/inst/doc/customizing.Rmd |only concurve-2.5.0/concurve/inst/doc/customizing.html |only concurve-2.5.0/concurve/inst/doc/examples.R | 78 -- concurve-2.5.0/concurve/inst/doc/examples.Rmd | 162 +----- concurve-2.5.0/concurve/inst/doc/examples.html | 395 ++++++--------- concurve-2.5.0/concurve/inst/doc/likelihood.R |only concurve-2.5.0/concurve/inst/doc/likelihood.Rmd |only concurve-2.5.0/concurve/inst/doc/likelihood.html |only concurve-2.5.0/concurve/inst/doc/meta-analysis.R |only concurve-2.5.0/concurve/inst/doc/meta-analysis.Rmd |only concurve-2.5.0/concurve/inst/doc/meta-analysis.html |only concurve-2.5.0/concurve/inst/doc/survival.R |only concurve-2.5.0/concurve/inst/doc/survival.Rmd |only concurve-2.5.0/concurve/inst/doc/survival.html |only concurve-2.5.0/concurve/inst/doc/troubleshooting.R |only concurve-2.5.0/concurve/inst/doc/troubleshooting.Rmd |only concurve-2.5.0/concurve/inst/doc/troubleshooting.html |only concurve-2.5.0/concurve/man/concurve-package.Rd | 23 concurve-2.5.0/concurve/man/curve_boot.Rd | 52 - concurve-2.5.0/concurve/man/curve_compare.Rd | 16 concurve-2.5.0/concurve/man/curve_corr.Rd | 8 concurve-2.5.0/concurve/man/curve_gen.Rd | 24 concurve-2.5.0/concurve/man/curve_lik.Rd | 9 concurve-2.5.0/concurve/man/curve_lmer.Rd |only concurve-2.5.0/concurve/man/curve_mean.Rd | 20 concurve-2.5.0/concurve/man/curve_meta.Rd | 26 concurve-2.5.0/concurve/man/curve_rev.Rd | 30 - concurve-2.5.0/concurve/man/curve_surv.Rd | 21 concurve-2.5.0/concurve/man/curve_table.Rd | 11 concurve-2.5.0/concurve/man/defunct.Rd | 22 concurve-2.5.0/concurve/man/ggcurve.Rd | 26 concurve-2.5.0/concurve/man/plot_compare.Rd | 26 concurve-2.5.0/concurve/tests/testthat/testdfstructure.R | 7 concurve-2.5.0/concurve/tests/testthat/tests3class.R |only concurve-2.5.0/concurve/vignettes/bootstrap.Rmd |only concurve-2.5.0/concurve/vignettes/customizing.Rmd |only concurve-2.5.0/concurve/vignettes/densityfunction.png |only concurve-2.5.0/concurve/vignettes/examples.Rmd | 162 +----- concurve-2.5.0/concurve/vignettes/likelihood.Rmd |only concurve-2.5.0/concurve/vignettes/meta-analysis.Rmd |only concurve-2.5.0/concurve/vignettes/references.bib | 38 - concurve-2.5.0/concurve/vignettes/survival.Rmd |only concurve-2.5.0/concurve/vignettes/troubleshooting.Rmd |only 78 files changed, 1064 insertions(+), 1238 deletions(-)