Title: Unifying Estimation Results with Binary Dependent Variables
Description: Calculate unified measures
that quantify the effect of a covariate on a binary dependent variable
(e.g., for meta-analyses).
This can be particularly important
if the estimation results are obtained
with different models/estimators
(e.g., linear probability model, logit, probit, ...)
and/or with different transformations of the explanatory variable of interest
(e.g., linear, quadratic, interval-coded, ...).
The calculated unified measures are:
(a) semi-elasticities of linear, quadratic, or interval-coded covariates and
(b) effects of linear, quadratic, interval-coded, or categorical covariates
when a linear or quadratic covariate changes between distinct intervals,
the reference category of a categorical variable
or the reference interval of an interval-coded variable needs to be changed,
or some categories of a categorical covariate
or some intervals of an interval-coded covariate need to be grouped together.
Approximate standard errors of the unified measures are also calculated.
All methods that are implemented in this package
are described in the 'vignette'
"Extracting and Unifying Semi-Elasticities and Effect Sizes
from Studies with Binary Dependent Variables"
that is included in this package.
Author: Arne Henningsen, Geraldine Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between urbin versions 0.1-6 dated 2018-11-03 and 0.1-8 dated 2019-02-21
DESCRIPTION | 17 ++++++++++++----- MD5 | 12 ++++++++++-- NEWS |only build |only inst |only tests/mlogit.Rout.save | 20 ++++++++++++++------ vignettes |only 7 files changed, 36 insertions(+), 13 deletions(-)
Title: Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [aut],
Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>
Diff between morse versions 3.2.0 dated 2018-11-12 and 3.2.2 dated 2019-02-21
DESCRIPTION | 8 MD5 | 148 ++-- NAMESPACE | 2 NEWS | 19 R/modelData.R | 4 R/modelData.survDataCstExp.R | 4 R/modelData.survDataVarExp.R | 8 R/morse-internal.R | 2 R/morse.R | 77 +- R/plot.survFitPredict.R | 12 R/plot.survFitPredict_Nsurv.R | 14 R/plot.survFitVarExp.R | 7 R/plot_prior_post.R | 15 R/ppc.survFitPredict_Nsurv.R | 7 R/predict_Nsurv.R | 28 R/predict_Nsurv_check.R | 57 + R/predict_Nsurv_ode.R |only R/predict_ode.survFit.R | 33 - R/print.survFitCstExp.R | 2 R/print.survFitVarExp.R | 2 R/priors_distribution.R | 11 R/reproDataCheck.R | 6 R/summary.reproData.R | 4 R/summary.survDataCstExp.R | 4 R/summary.survDataVarExp.R | 4 R/summary.survFit.R | 9 R/survData.R | 20 R/survFit.R | 109 +++ R/survFit.survDataCstExp.R | 17 R/survFit.survDataVarExp.R | 30 inst/doc/modelling.pdf |binary inst/doc/tutorial.R | 9 inst/doc/tutorial.Rmd | 70 +- inst/doc/tutorial.html | 792 ++++++++++++------------ man/cadmium1.Rd | 7 man/cadmium2.Rd | 7 man/chlordan.Rd | 7 man/copper.Rd | 7 man/dichromate.Rd | 7 man/is_exposure_constant.Rd | 4 man/modelData.Rd | 6 man/modelData.survDataCstExp.Rd | 6 man/modelData.survDataVarExp.Rd | 6 man/morse-package.Rd | 29 man/plot.survFitPredict.Rd | 12 man/plot.survFitPredict_Nsurv.Rd | 14 man/plot.survFitVarExp.Rd | 7 man/plot_prior_post.Rd | 4 man/plot_prior_post.survFit.Rd | 11 man/ppc.survFitPredict_Nsurv.Rd | 7 man/predict_Nsurv.Rd | 2 man/predict_Nsurv.survFit.Rd | 26 man/predict_Nsurv_check.Rd | 4 man/predict_Nsurv_check.survFitPredict_Nsurv.Rd | 20 man/predict_Nsurv_ode.Rd |only man/predict_ode.Rd | 6 man/predict_ode.survFit.Rd | 10 man/print.survFitCstExp.Rd | 2 man/print.survFitVarExp.Rd | 2 man/priors_distribution.Rd | 2 man/priors_distribution.survFit.Rd | 9 man/priors_survData.Rd | 6 man/propiconazole.Rd | 7 man/propiconazole_pulse_exposure.Rd | 7 man/reproDataCheck.Rd | 4 man/summary.reproData.Rd | 4 man/summary.survDataCstExp.Rd | 4 man/summary.survDataVarExp.Rd | 4 man/summary.survFit.Rd | 9 man/survData.Rd | 8 man/survData_join.Rd | 6 man/survFit.Rd | 103 +++ man/survFit.survDataCstExp.Rd | 8 man/survFit.survDataVarExp.Rd | 24 man/zinc.Rd | 7 vignettes/tutorial.Rmd | 70 +- 76 files changed, 1191 insertions(+), 838 deletions(-)
Title: Tidying Methods for Mixed Models
Description: Convert fitted objects from various R mixed-model packages
into tidy data frames along the lines of the 'broom' package.
The package provides three
S3 generics for each model: tidy(), which summarizes a model's statistical findings such as
coefficients of a regression; augment(), which adds columns to the original
data such as predictions, residuals and cluster assignments; and glance(), which
provides a one-row summary of model-level statistics.
Author: Ben Bolker [aut, cre] (<https://orcid.org/0000-0002-2127-0443>),
David Robinson [aut],
Dieter Menne [ctb],
Jonah Gabry [ctb],
Paul Buerkner [ctb],
Christopher Hua [ctb],
William Petry [ctb] (<https://orcid.org/0000-0002-5230-5987>),
Joshua Wiley [ctb] (<https://orcid.org/0000-0002-0271-6702>),
Patrick Kennedy [ctb]
Maintainer: Ben Bolker <bolker@mcmaster.ca>
Diff between broom.mixed versions 0.2.3 dated 2018-10-21 and 0.2.4 dated 2019-02-21
DESCRIPTION | 25 +++++----- MD5 | 62 +++++++++++++------------ NAMESPACE | 5 +- R/TMB_tidiers.R | 4 - R/gamlss_tidiers.R | 60 ++++++++++++++++-------- R/glmmTMB_tidiers.R | 62 ++++++------------------- R/lme4_tidiers.R | 92 +++++++++++++++++++++++++------------- R/mcmc_tidiers.R | 64 ++++++++++++++++++++++---- R/nlme_tidiers.R | 29 +++++++---- R/pscl_tidiers.R |only R/utilities.R | 6 +- inst/NEWS.Rd | 24 +++++++++ inst/doc/broom_mixed_intro.html | 30 ++++++++++-- inst/extdata/MCMCglmm_example.rda |binary inst/extdata/R2jags_example.rds |only inst/extdata/brms_example.rda |binary inst/extdata/efc.rds |binary inst/extdata/example_helpers.R | 7 ++ inst/extdata/gamlss_example.rds |only inst/extdata/glmmADMB_example.rda |binary inst/extdata/glmmTMB_example.rda |binary inst/extdata/lme4_example.rda |binary inst/extdata/nlme_example.rda |binary inst/extdata/rstan_example.rds |binary inst/extdata/rstanarm_example.rds |binary inst/extdata/test.R |only man/augment.ranef.mer.Rd | 12 ++-- man/gamlss_tidiers.Rd | 42 +++++++++++------ man/lme4_tidiers.Rd | 6 ++ man/mcmc_tidiers.Rd | 21 +++++++- tests/testthat/test-glmmTMB.R | 23 +++++++++ tests/testthat/test-lme4.R | 32 +++++++++++-- tests/testthat/test-mcmc.R | 23 +++++++++ tests/testthat/test-nlme.R | 19 +++++-- 34 files changed, 442 insertions(+), 206 deletions(-)
Title: Who are You? Bayesian Prediction of Racial Category Using
Surname and Geolocation
Description: Predicts individual race/ethnicity using surname, geolocation,
and other attributes, such as gender and age. The method utilizes the Bayes'
Rule to compute the posterior probability of each racial category for any given
individual. The package implements methods described in Imai and Khanna (2015)
"Improving Ecological Inference by Predicting Individual Ethnicity from Voter
Registration Records" <DOI:10.1093/pan/mpw001>.
Author: Kabir Khanna [aut, cre],
Kosuke Imai [aut]
Maintainer: Kabir Khanna <kabirkhanna@gmail.com>
Diff between wru versions 0.1-8 dated 2019-02-13 and 0.1-9 dated 2019-02-21
ChangeLog | 2 ++ DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/census_helper.R | 24 ++++++++++++------------ 4 files changed, 21 insertions(+), 19 deletions(-)
Title: Pathwise Calibrated Sparse Shooting Algorithm
Description: Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.
Author: Jason Ge, Xingguo Li, Haoming Jiang, Mengdi Wang, Tong Zhang, Han Liu and Tuo Zhao
Maintainer: Jason Ge <jiange@princeton.edu>
Diff between picasso versions 1.3.0 dated 2018-10-03 and 1.3.1 dated 2019-02-21
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/picasso.gaussian.R | 2 +- R/picasso.logit.R | 2 +- R/picasso.poisson.R | 2 +- R/picasso.sqrtlasso.R | 2 +- inst/doc/PICASSO.pdf |binary inst/doc/vignette.pdf |binary src/include/picasso/actgd.hpp | 2 +- src/include/picasso/actnewton.hpp | 2 +- src/include/picasso/solver_params.hpp | 2 +- vignettes/PICASSO.pdf |binary 12 files changed, 22 insertions(+), 22 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (<https://orcid.org/0000-0001-5052-066X>)
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.3.9 dated 2018-11-09 and 1.3.11 dated 2019-02-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/stanmodels.R | 24 +++++++++++++----------- 4 files changed, 24 insertions(+), 18 deletions(-)
Title: Simulation of Fossil and Taxonomy Data
Description: Simulating taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.1.0 dated 2018-11-16 and 2.1.1 dated 2019-02-21
DESCRIPTION | 6 +-- MD5 | 28 +++++++-------- NEWS.md | 4 ++ R/sim.fbd.R | 30 ++++++++-------- build/vignette.rds |binary inst/doc/SAtree.html | 77 ++++++++++++++++++++++++++++++++++++++---- inst/doc/fossils.html | 28 +++++++++++++-- inst/doc/intro.html | 28 +++++++++++++-- inst/doc/paleotree.html | 69 ++++++++++++++++++++++++++++++++++++- inst/doc/simfbd.R | 2 - inst/doc/simfbd.Rmd | 4 +- inst/doc/simfbd.html | 75 +++++++++++++++++++++++++++++++++++++--- inst/doc/taxonomy.html | 28 +++++++++++++-- man/sim.fbd.rateshift.taxa.Rd | 10 ++--- vignettes/simfbd.Rmd | 4 +- 15 files changed, 326 insertions(+), 67 deletions(-)
Title: Connecting to Various Database Platforms
Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server',
'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', and 'SQLite'). Also includes support for
fetching data as 'ffdf' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut],
Observational Health Data Science and Informatics [cph],
Microsoft Inc. [cph] (SQL Server JDBC driver),
PostgreSQL Global Development Group [cph] (PostgreSQL JDBC driver),
Oracle Inc. [cph] (Oracle JDBC driver),
Amazon Inc. [cph] (RedShift JDBC driver)
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between DatabaseConnector versions 2.2.1 dated 2018-11-25 and 2.3.0 dated 2019-02-21
DatabaseConnector-2.2.1/DatabaseConnector/man/dbIsValid-DatabaseConnectorConnection-method.Rd |only DatabaseConnector-2.2.1/DatabaseConnector/man/dbSendQuery-DatabaseConnectorConnection-character-method.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/DESCRIPTION | 17 DatabaseConnector-2.3.0/DatabaseConnector/MD5 | 73 DatabaseConnector-2.3.0/DatabaseConnector/NAMESPACE | 13 DatabaseConnector-2.3.0/DatabaseConnector/NEWS.md | 22 DatabaseConnector-2.3.0/DatabaseConnector/R/Compression.R | 4 DatabaseConnector-2.3.0/DatabaseConnector/R/Connect.R | 53 DatabaseConnector-2.3.0/DatabaseConnector/R/DBI.R | 65 DatabaseConnector-2.3.0/DatabaseConnector/R/DatabaseConnector.R | 36 DatabaseConnector-2.3.0/DatabaseConnector/R/InsertTable.R | 226 DatabaseConnector-2.3.0/DatabaseConnector/R/ListTables.R | 7 DatabaseConnector-2.3.0/DatabaseConnector/R/RStudio.R | 64 DatabaseConnector-2.3.0/DatabaseConnector/R/Sql.R | 288 DatabaseConnector-2.3.0/DatabaseConnector/README.md | 5 DatabaseConnector-2.3.0/DatabaseConnector/build/DatabaseConnector.pdf |13766 +++++----- DatabaseConnector-2.3.0/DatabaseConnector/build/vignette.rds |binary DatabaseConnector-2.3.0/DatabaseConnector/inst/COPYRIGHTS | 11 DatabaseConnector-2.3.0/DatabaseConnector/inst/doc/UsingDatabaseConnector.R | 15 DatabaseConnector-2.3.0/DatabaseConnector/inst/doc/UsingDatabaseConnector.Rmd | 40 DatabaseConnector-2.3.0/DatabaseConnector/inst/doc/UsingDatabaseConnector.pdf |binary DatabaseConnector-2.3.0/DatabaseConnector/inst/java/DatabaseConnector.jar |binary DatabaseConnector-2.3.0/DatabaseConnector/java/org/ohdsi/databaseConnector/BatchedInsert.java | 21 DatabaseConnector-2.3.0/DatabaseConnector/man/DatabaseConnectorDbiConnection-class.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/DatabaseConnectorJdbcConnection-class.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/connect.Rd | 13 DatabaseConnector-2.3.0/DatabaseConnector/man/createConnectionDetails.Rd | 13 DatabaseConnector-2.3.0/DatabaseConnector/man/dbIsValid-DatabaseConnectorDbiConnection-method.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/dbIsValid-DatabaseConnectorJdbcConnection-method.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/dbSendQuery-DatabaseConnectorDbiConnection-character-method.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/dbSendQuery-DatabaseConnectorJdbcConnection-character-method.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/executeSql.Rd | 2 DatabaseConnector-2.3.0/DatabaseConnector/man/insertTable.Rd | 6 DatabaseConnector-2.3.0/DatabaseConnector/man/jdbcDrivers.Rd | 6 DatabaseConnector-2.3.0/DatabaseConnector/man/querySql.Rd | 6 DatabaseConnector-2.3.0/DatabaseConnector/man/querySql.ffdf.Rd | 6 DatabaseConnector-2.3.0/DatabaseConnector/man/renderTranslateExecuteSql.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/renderTranslateQuerySql.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/man/renderTranslateQuerySql.ffdf.Rd |only DatabaseConnector-2.3.0/DatabaseConnector/tests/testthat/test-fetchResults.R | 16 DatabaseConnector-2.3.0/DatabaseConnector/tests/testthat/test-getTableNames.R | 11 DatabaseConnector-2.3.0/DatabaseConnector/tests/testthat/test-sendUpdates.R | 64 DatabaseConnector-2.3.0/DatabaseConnector/vignettes/UsingDatabaseConnector.Rmd | 40 43 files changed, 8696 insertions(+), 6213 deletions(-)
More information about DatabaseConnector at CRAN
Permanent link
Title: Automatic Codebooks from Metadata Encoded in Dataset Attributes
Description: Easily automate the following tasks to describe data frames:
Summarise the distributions, and labelled missings of variables graphically
and using descriptive statistics.
For surveys, compute and summarise reliabilities (internal consistencies,
retest, multilevel) for psychological scales.
Combine this information with metadata (such as item labels and labelled
values) that is derived from R attributes.
To do so, the package relies on 'rmarkdown' partials, so you can generate
HTML, PDF, and Word documents.
Codebooks are also available as tables (CSV, Excel, etc.) and in JSON-LD, so
that search engines can find your data and index the metadata.
The metadata are also available at your fingertips via RStudio Addins.
Author: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <ruben.arslan@gmail.com>
Diff between codebook versions 0.7.6 dated 2019-01-08 and 0.8.0 dated 2019-02-21
codebook-0.7.6/codebook/inst/doc/codebook_labelled_manual.R |only codebook-0.7.6/codebook/inst/doc/codebook_labelled_manual.Rmd |only codebook-0.7.6/codebook/inst/doc/codebook_labelled_manual.html |only codebook-0.7.6/codebook/inst/doc/codebook_nested_scale.R |only codebook-0.7.6/codebook/inst/doc/codebook_nested_scale.Rmd |only codebook-0.7.6/codebook/inst/doc/codebook_nested_scale.html |only codebook-0.7.6/codebook/vignettes/codebook_labelled_manual.Rmd |only codebook-0.7.6/codebook/vignettes/codebook_nested_scale.Rmd |only codebook-0.8.0/codebook/DESCRIPTION | 34 codebook-0.8.0/codebook/MD5 | 81 codebook-0.8.0/codebook/NAMESPACE | 5 codebook-0.8.0/codebook/NEWS.md | 13 codebook-0.8.0/codebook/R/codebook.R | 118 codebook-0.8.0/codebook/R/correct_attributes.R | 7 codebook-0.8.0/codebook/R/create_metadata.R | 21 codebook-0.8.0/codebook/R/misc.R | 35 codebook-0.8.0/codebook/R/plot_helpers.R | 27 codebook-0.8.0/codebook/R/psych_print.R | 19 codebook-0.8.0/codebook/R/reliability.R | 102 codebook-0.8.0/codebook/build/vignette.rds |binary codebook-0.8.0/codebook/inst/_codebook.Rmd | 6 codebook-0.8.0/codebook/inst/_codebook_data_info.Rmd | 4 codebook-0.8.0/codebook/inst/_codebook_item.Rmd | 23 codebook-0.8.0/codebook/inst/_codebook_missingness.Rmd | 7 codebook-0.8.0/codebook/inst/_codebook_scale.Rmd | 12 codebook-0.8.0/codebook/inst/_knit_print_scaleDiagnosis.Rmd |only codebook-0.8.0/codebook/inst/_metadata_jsonld.Rmd | 13 codebook-0.8.0/codebook/inst/_template_codebook.Rmd | 7 codebook-0.8.0/codebook/inst/doc/codebook.R | 447 - codebook-0.8.0/codebook/inst/doc/codebook.Rmd | 8 codebook-0.8.0/codebook/inst/doc/codebook.html | 2522 +-------- codebook-0.8.0/codebook/inst/doc/codebook_qualtrics.R | 80 codebook-0.8.0/codebook/inst/doc/codebook_qualtrics.html | 10 codebook-0.8.0/codebook/inst/doc/codebook_sav.R | 126 codebook-0.8.0/codebook/inst/doc/codebook_sav.html | 14 codebook-0.8.0/codebook/inst/doc/codebook_tutorial.R | 476 + codebook-0.8.0/codebook/inst/doc/codebook_tutorial.Rmd | 10 codebook-0.8.0/codebook/inst/doc/codebook_tutorial.html | 2527 ++-------- codebook-0.8.0/codebook/inst/www/index.html | 13 codebook-0.8.0/codebook/man/codebook.Rd | 7 codebook-0.8.0/codebook/man/codebook_survey_overview.Rd | 3 codebook-0.8.0/codebook/man/compact_codebook.Rd |only codebook-0.8.0/codebook/man/compute_reliabilities.Rd | 1 codebook-0.8.0/codebook/man/knit_print.scaleDiagnosis.Rd |only codebook-0.8.0/codebook/man/plot_labelled.Rd | 6 codebook-0.8.0/codebook/vignettes/codebook.Rmd | 8 codebook-0.8.0/codebook/vignettes/codebook_tutorial.Rmd | 10 47 files changed, 1889 insertions(+), 4913 deletions(-)
Title: Statistics Netherlands (CBS) Open Data API Client
Description: The data and meta data from Statistics
Netherlands (www.cbs.nl) can be browsed and downloaded. The client uses
the open data API of Statistics Netherlands.
Author: Edwin de Jonge [aut, cre]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between cbsodataR versions 0.3 dated 2018-04-30 and 0.3.2 dated 2019-02-21
DESCRIPTION | 10 MD5 | 87 ++++--- NAMESPACE | 2 NEWS.md | 10 R/cbs_download_data.R | 25 +- R/cbs_download_meta.R | 4 R/cbs_download_table.R | 2 R/cbs_get_data.R | 9 R/cbs_get_data_from_link.R |only R/cbs_get_meta.R | 3 R/cbs_get_themes.R | 6 R/cbs_get_toc.R | 5 R/cbsopendata.R | 3 R/deeplink.R |only R/download-data.R | 2 R/download-meta.R | 4 R/download-table.R | 2 R/get-data.R | 3 R/get-meta.R | 2 R/get-table-list.R | 4 R/get-themes.R | 6 R/resolve.R | 18 + build/vignette.rds |binary inst/doc/cbsodataR.R | 7 inst/doc/cbsodataR.Rmd | 20 + inst/doc/cbsodataR.html | 447 +++++++++++++++++++++++++++++++--------- inst/issues |only inst/iv3.R | 15 - man/cbs_download_data.Rd | 5 man/cbs_download_meta.Rd | 2 man/cbs_download_table.Rd | 2 man/cbs_get_data.Rd | 3 man/cbs_get_data_from_link.Rd |only man/cbs_get_meta.Rd | 3 man/cbs_get_tables_themes.Rd | 4 man/cbs_get_themes.Rd | 2 man/cbs_get_toc.Rd | 6 man/download_data-deprecated.Rd | 3 man/download_meta-deprecated.Rd | 2 man/download_table.Rd | 2 man/get_data.Rd | 3 man/get_meta.Rd | 3 man/get_table_list.Rd | 3 man/get_tables_themes.Rd | 3 man/get_themes.Rd | 2 man/resolve_deeplink.Rd |only vignettes/cbsodataR.Rmd | 20 + 47 files changed, 548 insertions(+), 216 deletions(-)
Title: Analysis of Simulation Studies Including Monte Carlo Error
Description: Summarise results from simulation studies and compute Monte Carlo
standard errors of commonly used summary statistics. This package is modelled
on the 'simsum' user-written command in 'Stata' (See White I.R., 2010
<http://www.stata-journal.com/article.html?article=st0200>).
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Ian R. White [aut]
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between rsimsum versions 0.3.3 dated 2018-06-20 and 0.5.0 dated 2019-02-21
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Title: Simultaneous Enrichment Analysis
Description: SEA performs simultaneous feature-set testing for (gen)omics data. It tests the unified null hypothesis and controls the family-wise error rate for all possible pathways. The unified null hypothesis is defined as: "The proportion of true features in the set is less than or equal to a threshold." Family-wise error rate control is provided through use of closed testing with Simes test. There are some practical functions to make use of three databases for genomics, GO, Reactome and Wikipathways.
Author: Mitra Ebrahimpoor
Maintainer: Mitra Ebrahimpoor<m.ebrahimpoor@lumc.nl>
Diff between rSEA versions 1.0 dated 2018-11-30 and 1.0.1 dated 2019-02-21
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/set.test-function.R | 4 ++-- man/set.test-function.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to
encode spatial vector data. Binds to 'GDAL' for reading and writing
data, to 'GEOS' for geometrical operations, and to 'PROJ' for
projection conversions and datum transformations.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb],
Thomas Lin Pedersen [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.7-2 dated 2018-12-20 and 0.7-3 dated 2019-02-21
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Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/
Licenses/GPL-3>). The 'CWB' relies on 'pcre' (BSD license, see <https://www.pcre.org/
licence.txt>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.
html>). See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.2.7 dated 2019-01-09 and 0.2.8 dated 2019-02-21
RcppCWB-0.2.7/RcppCWB/man/use_tmp_registry.Rd |only RcppCWB-0.2.8/RcppCWB/DESCRIPTION | 36 +-- RcppCWB-0.2.8/RcppCWB/MD5 | 94 +++++----- RcppCWB-0.2.8/RcppCWB/NAMESPACE | 1 RcppCWB-0.2.8/RcppCWB/NEWS.md | 11 + RcppCWB-0.2.8/RcppCWB/R/count.R | 2 RcppCWB-0.2.8/RcppCWB/R/cwb.R | 2 RcppCWB-0.2.8/RcppCWB/R/misc.R | 13 + RcppCWB-0.2.8/RcppCWB/R/zzz.R | 17 + RcppCWB-0.2.8/RcppCWB/README.md | 10 - RcppCWB-0.2.8/RcppCWB/cleanup | 4 RcppCWB-0.2.8/RcppCWB/configure | 28 +- RcppCWB-0.2.8/RcppCWB/man/cwb_utils.Rd | 2 RcppCWB-0.2.8/RcppCWB/man/get_count_vector.Rd | 2 RcppCWB-0.2.8/RcppCWB/man/tmp_registry.Rd |only RcppCWB-0.2.8/RcppCWB/src/cwb/Makefile | 18 - RcppCWB-0.2.8/RcppCWB/src/cwb/cl/Makefile | 4 RcppCWB-0.2.8/RcppCWB/src/cwb/cl/depend.mk |only RcppCWB-0.2.8/RcppCWB/src/cwb/cl/fileutils.c | 3 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/darwin-64 | 4 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/darwin-brew | 2 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/darwin-port-core2 | 2 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/darwin-universal | 2 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/linux-opteron | 2 RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/solaris_spark |only RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/solaris_x86 |only RcppCWB-0.2.8/RcppCWB/src/cwb/config/platform/unix | 3 RcppCWB-0.2.8/RcppCWB/src/cwb/cqp/Makefile | 4 RcppCWB-0.2.8/RcppCWB/src/cwb/cqp/depend.mk |only RcppCWB-0.2.8/RcppCWB/src/cwb/utils/Makefile | 4 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_attribute_size.R | 4 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_charset_name.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_cpos2id.R | 3 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_cpos2lbound.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_cpos2rbound.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_cpos2str.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_cpos2struc.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_get_cbow_matrix.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_get_count_vector.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_get_region_matrix.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_id2cpos.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_id2freq.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_id2str.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_lexicon_size.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_regex2id.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_region_matrix_to_count_matrix.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_region_matrix_to_ids.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_s_attribute_decode.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_str2id.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_struc2cpos.R | 2 RcppCWB-0.2.8/RcppCWB/tests/testthat/test_struc2str.R | 2 51 files changed, 183 insertions(+), 132 deletions(-)
Title: R Interface to 'Bloomberg'
Description: An R Interface to 'Bloomberg' is provided via the 'Blp API'.
Author: Whit Armstrong, Dirk Eddelbuettel and John Laing
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rblpapi versions 0.3.8 dated 2018-01-21 and 0.3.9 dated 2019-02-21
ChangeLog | 16 +- DESCRIPTION | 9 - MD5 | 14 - build/vignette.rds |binary inst/NEWS.Rd | 16 +- inst/doc/rblpapi-intro.Rmd | 4 inst/doc/rblpapi-intro.html | 332 +++++++++++++++++++++++++++++++++++++------- vignettes/rblpapi-intro.Rmd | 4 8 files changed, 325 insertions(+), 70 deletions(-)
Title: Estimation of the Generalised Beta Distribution of the Second
Kind from Grouped Data
Description: Estimation of the generalized beta distribution of the second
kind (GB2) and related models using grouped data in form of income shares.
The GB2 family is a general class of distributions that provides an accurate
fit to income data. 'GB2group' includes functions to estimate the GB2, the
Singh-Maddala, the Dagum, the Beta 2, the Lognormal and the Fisk distributions.
'GB2group' deploys two different econometric strategies to estimate these
parametric distributions, non-linear least squares (NLS) and the generalised
method of moments (GMM). Asymptotic standard errors are reported for the
GMM estimates. Standard errors of the NLS estimates are obtained by Monte
Carlo simulation. See Jorda et al. (2018) <arXiv:1808.09831> for a detailed
description of the estimation procedure.
Author: Vanesa Jorda <jordav@unican.es>, Jose Maria Sarabia
<jose.sarabia@unican.es>, Markus Jäntti <markus.jantti@sofi.su.se>.
Maintainer: Vanesa Jorda <jordav@unican.es>
Diff between GB2group versions 0.1.0 dated 2018-11-14 and 0.2.0 dated 2019-02-21
DESCRIPTION | 6 ++--- MD5 | 20 +++++++++--------- NAMESPACE | 6 +++++ R/fit.plot.R |only R/fitgroup_b2.R | 11 ++++++--- R/fitgroup_da.R | 9 +++++--- R/fitgroup_f.R | 9 +++++--- R/fitgroup_gb2.R | 9 +++++--- R/fitgroup_ln.R | 9 +++++--- R/fitgroup_sm.R | 9 +++++--- R/opt_func.R | 61 +++++++++++++++++++++++++++---------------------------- man/fit.plot.Rd |only 12 files changed, 88 insertions(+), 61 deletions(-)
Title: Framework for the Visualization of Distributional Regression
Models
Description: Functions for visualizing distributional regression models fitted using the 'gamlss' or 'bamlss' R package. The core of the package consists of a 'shiny' application, where the model results can be interactively explored and visualized.
Author: Stanislaus Stadlmann [cre, aut]
(<https://orcid.org/0000-0001-6542-6342>)
Maintainer: Stanislaus Stadlmann <stadlmann@uni-goettingen.de>
Diff between distreg.vis versions 1.0.1 dated 2018-10-30 and 1.1.0 dated 2019-02-21
DESCRIPTION | 8 - MD5 | 32 ++-- NAMESPACE | 1 R/external_function.R | 13 + R/moments.R | 200 ++++++++++++++++++++++++++--- R/plot_moments.R | 166 +++++++++++++++++++----- R/preds.R | 93 +++++++++++-- R/vis.R | 40 +++++ data/dists.rda |binary inst/extdata/dist_df.csv | 248 ++++++++++++++++++------------------- man/ex_f.Rd | 2 man/moments.Rd | 21 ++- man/plot_moments.Rd | 27 +++- man/preds.Rd | 25 ++- man/preds_transformer.Rd |only man/reshape_into_long.Rd |only tests/testthat/test_01_all_dists.R | 52 +++++-- tests/testthat/test_02_misc.R | 42 ++++++ 18 files changed, 712 insertions(+), 258 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. The 'GDAL' and 'PROJ.4' libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both 'GDAL' raster and 'OGR' vector map data can be imported into R, and 'GDAL' raster data and 'OGR' vector data exported. Use is made of classes defined in the 'sp' package. Windows and Mac Intel OS X binaries (including 'GDAL', 'PROJ.4' and 'Expat') are provided on 'CRAN'.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.3-6 dated 2018-10-16 and 1.3-9 dated 2019-02-21
ChangeLog | 88 ++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 22 +++++----- MD5 | 54 ++++++++++++------------ NAMESPACE | 2 R/AAA.R | 19 +++++--- R/Class-CRSx.R | 7 ++- R/ogr.R | 6 +- R/ogr_write.R | 4 - R/project.R | 57 ++++++++++++++++--------- R/wrappers.R | 10 ++++ build/vignette.rds |binary configure | 62 ++++++++++++++++++++++++---- configure.ac | 32 ++++++++++++++ data/GridsDatums.rda |binary inst/ChangeLog | 88 ++++++++++++++++++++++++++++++++++++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary man/CRS-class.Rd | 2 man/GridsDatums.Rd | 4 - man/RGB2PCT.Rd | 4 + man/displayDataset.Rd | 6 +- man/project.Rd | 17 ++++++- man/readGDAL.Rd | 5 +- src/RGDAL.def | 10 ++-- src/init.c | 16 +++---- src/ogrsource.cpp | 10 ++-- src/projectit.cpp | 6 +- src/rgdal.h | 16 +++---- 28 files changed, 430 insertions(+), 119 deletions(-)
Title: Nonlinear Time Series Analysis
Description: Functions for nonlinear time series analysis. This package permits
the computation of the most-used nonlinear statistics/algorithms
including generalized correlation dimension, information dimension,
largest Lyapunov exponent, sample entropy and Recurrence
Quantification Analysis (RQA), among others. Basic routines
for surrogate data testing are also included. Part of this work
was based on the book "Nonlinear time series analysis" by
Holger Kantz and Thomas Schreiber (ISBN: 9780521529020).
Author: Constantino A. Garcia [aut, cre],
Gunther Sawitzki [ctb]
Maintainer: Constantino A. Garcia <constantino.garciama@ceu.es>
Diff between nonlinearTseries versions 0.2.5 dated 2018-09-23 and 0.2.6 dated 2019-02-21
DESCRIPTION | 16 - MD5 | 10 R/RcppExports.R | 16 - build/vignette.rds |binary inst/doc/nonlinearTseries_quickstart.html | 436 ++++++++---------------------- src/RcppExports.cpp | 72 ++-- 6 files changed, 180 insertions(+), 370 deletions(-)
More information about nonlinearTseries at CRAN
Permanent link
Title: Model Based Clustering, Classification and Discriminant Analysis
Using the Mixture of Generalized Hyperbolic Distributions
Description: Carries out model-based clustering, classification and discriminant analysis using five different models. The models are all based on the generalized hyperbolic distribution. The first model 'MGHD' (Browne and McNicholas (2015)<doi:10.1002/cjs.11246>) is the classical mixture of generalized hyperbolic distributions. The 'MGHFA' (Tortora et al. (2016)<doi:10.1007/s11634-015-0204-z>) is the mixture of generalized hyperbolic factor analyzers for high dimensional data sets. The 'MSGHD'(Tortora et al. (2016)<arXiv:1403.2332v7>), mixture of multiple scaled generalized hyperbolic distributions. The 'cMSGHD' (Tortora et al. (2016)<arXiv:1403.2332v7>) is a 'MSGHD' with convex contour plots. The 'MCGHD' (Tortora et al. (2016)<arXiv:1403.2332v7>), mixture of coalesced generalized hyperbolic distributions is a new more flexible model.
Author: Cristina Tortora [aut, cre, cph], Aisha ElSherbiny [com], Ryan P. Browne [aut, cph], Brian C. Franczak [aut, cph], and Paul D. McNicholas [aut, cph], and Amos Donald D. [ctb].
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between MixGHD versions 2.2 dated 2018-01-31 and 2.3 dated 2019-02-21
MixGHD-2.2/MixGHD/R/MixGHD-internal.R |only MixGHD-2.3/MixGHD/DESCRIPTION | 8 ++++---- MixGHD-2.3/MixGHD/MD5 | 31 ++++++++++++++++++++----------- MixGHD-2.3/MixGHD/NAMESPACE | 2 +- MixGHD-2.3/MixGHD/R/GHD.R | 26 +++++++++++++++++++------- MixGHD-2.3/MixGHD/R/MCGHD.R | 27 +++++++++++++++++---------- MixGHD-2.3/MixGHD/R/MGHD.R | 19 ++++++++++++++++--- MixGHD-2.3/MixGHD/R/MGHFA.R | 19 +++++++++++-------- MixGHD-2.3/MixGHD/R/MSGHD.R | 19 ++++++++++++------- MixGHD-2.3/MixGHD/R/cMSGHD.R | 19 ++++++++++++------- MixGHD-2.3/MixGHD/R/dfunctions.R |only MixGHD-2.3/MixGHD/R/rfunctions.R |only MixGHD-2.3/MixGHD/man/coef.Rd |only MixGHD-2.3/MixGHD/man/dCGHD.Rd |only MixGHD-2.3/MixGHD/man/dGHD.Rd |only MixGHD-2.3/MixGHD/man/dMSGHD.Rd |only MixGHD-2.3/MixGHD/man/plot.MixGHD.Rd | 2 +- MixGHD-2.3/MixGHD/man/predict.Rd |only MixGHD-2.3/MixGHD/man/rCGHD.Rd |only MixGHD-2.3/MixGHD/man/rGHD.Rd |only MixGHD-2.3/MixGHD/man/rMSGHD.Rd |only MixGHD-2.3/MixGHD/src/GHD.c | 20 +++++++++++++------- 22 files changed, 126 insertions(+), 66 deletions(-)
Title: Differential Item Functioning in Generalized Partial Credit
Models
Description: Provides a function to detect Differential Item Functioning (DIF) in Generalized Partial Credit Models (GPCM) and special cases of the GPCM. A joint model is set up where DIF is explicitly parametrized and penalized likelihood estimation is used for parameter selection. The big advantage of the method called GPCMlasso is that several variables can be treated simultaneously and that both continuous and categorical variables can be used to detect DIF.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between GPCMlasso versions 0.1-2 dated 2018-08-02 and 0.1-3 dated 2019-02-21
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- R/GPCMlasso-package.R | 4 +++- R/GPCMlasso.R | 4 +++- R/ctrl_GPCMlasso.R | 6 ++++-- R/person.posterior.R | 5 +++-- R/plot.GPCMlasso.R | 4 +++- R/print.GPCMlasso.R | 8 ++++++-- man/GPCMlasso-package.Rd | 6 +++++- man/GPCMlasso.Rd | 6 +++++- man/ctrl_GPCMlasso.Rd | 8 ++++++-- man/plot.GPCMlasso.Rd | 6 +++++- man/print.GPCMlasso.Rd | 6 +++++- man/trait.posterior.Rd | 6 +++++- 14 files changed, 71 insertions(+), 34 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' (Schauberger and Tutz, 2017: Subject-Specific Modelling of Paired Comparison Data - a Lasso-Type Penalty Approach), a method to include different types of variables in paired
comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and
can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used
to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between BTLLasso versions 0.1-7 dated 2017-10-26 and 0.1-8 dated 2019-02-21
DESCRIPTION | 10 +- MD5 | 76 ++++++++++---------- R/BTLLasso-package.R | 169 ++++++++++++++++++++++++++++++++++++--------- R/BTLLasso.R | 26 ++++-- R/RcppExports.R | 4 - R/bin.fit.Cpp.R | 10 +- R/boot.BTLLasso.R | 13 ++- R/cum.fit.Cpp.R | 7 + R/cv.BTLLasso.R | 13 ++- R/fit.cv.BTLLasso.R | 4 - R/paths.R | 13 ++- R/plot.BTLLasso.R | 13 ++- R/plot.boot.BTLLasso.R | 13 ++- R/predict.BTLLasso.R | 13 ++- R/print.BTLLasso.R | 13 ++- R/print.boot.BTLLasso.R | 13 ++- R/print.cv.BTLLasso.R | 13 ++- R/response.BTLLasso.R | 13 ++- data/Buli1718.RData |only man/BTLLasso-package.Rd | 11 +- man/BTLLasso.Rd | 11 +- man/Buli1415.Rd | 10 +- man/Buli1516.Rd | 24 +++--- man/Buli1617.Rd | 24 +++--- man/Buli1718.Rd |only man/BuliResponse.Rd | 18 +++- man/GLES.Rd | 13 +-- man/GLESsmall.Rd | 13 +-- man/boot.BTLLasso.Rd | 11 +- man/ctrl.BTLLasso.Rd | 11 +- man/cv.BTLLasso.Rd | 11 +- man/paths.Rd | 11 +- man/plot.BTLLasso.Rd | 11 +- man/plot.boot.BTLLasso.Rd | 11 +- man/predict.BTLLasso.Rd | 11 +- man/print.BTLLasso.Rd | 11 +- man/print.boot.BTLLasso.Rd | 11 +- man/print.cv.BTLLasso.Rd | 11 +- man/response.BTLLasso.Rd | 11 +- src/RcppExports.cpp | 15 +++ 40 files changed, 450 insertions(+), 246 deletions(-)
Title: Install, Update, Load Packages from CRAN, 'GitHub', and
'Bioconductor' in One Step
Description: Automatically install, update, and load 'CRAN', 'GitHub', and 'Bioconductor'
packages in a single function call. By accepting bare unquoted names for packages,
it's easy to add or remove packages from the list.
Author: Desi Quintans [aut, cre]
Maintainer: Desi Quintans <science@desiquintans.com>
Diff between librarian versions 1.3.0 dated 2018-07-07 and 1.6.0 dated 2019-02-21
DESCRIPTION | 27 ++-- MD5 | 32 +++- NAMESPACE | 2 NEWS.md | 54 ++++++++ R/package_tools.R | 283 ++++++++++++++++++++++++++++++++++++++++---- R/private_funs.R | 175 +++++++++++++++++++++++++-- README.md | 224 ++++++++++++++++++++++++++-------- build |only inst |only man/browse_cran.Rd |only man/check_attached.Rd | 4 man/check_installed.Rd | 4 man/collapse_vec.Rd |only man/fuzzy_needle.Rd |only man/is_dots_empty.Rd |only man/is_valid_url.Rd |only man/lib_startup.Rd |only man/shelf.Rd | 10 + man/suppress_lib_message.Rd | 6 man/wrap_long.Rd |only vignettes |only 21 files changed, 705 insertions(+), 116 deletions(-)
Title: Best Subset Selection in Linear, Logistic and CoxPH Models
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2017) <arXiv:1709.06254>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen, Aijun Zhang, Shijie Quan, Xueqin Wang
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between BeSS versions 1.0.5 dated 2018-01-30 and 1.0.6 dated 2019-02-21
BeSS-1.0.5/BeSS/README |only BeSS-1.0.5/BeSS/inst |only BeSS-1.0.5/BeSS/src/bess.cpp |only BeSS-1.0.5/BeSS/src/group.cpp |only BeSS-1.0.6/BeSS/DESCRIPTION | 12 BeSS-1.0.6/BeSS/MD5 | 79 +-- BeSS-1.0.6/BeSS/NAMESPACE | 2 BeSS-1.0.6/BeSS/R/RcppExports.R | 60 +- BeSS-1.0.6/BeSS/R/aic.R | 14 BeSS-1.0.6/BeSS/R/bess.R | 750 ++++++++++----------------------- BeSS-1.0.6/BeSS/R/bess.cox.R | 115 +---- BeSS-1.0.6/BeSS/R/bess.glm.R | 103 ---- BeSS-1.0.6/BeSS/R/bess.lm.R | 70 --- BeSS-1.0.6/BeSS/R/bess.one.R | 77 +-- BeSS-1.0.6/BeSS/R/coef.bess.R | 28 - BeSS-1.0.6/BeSS/R/deviance.bess.R | 40 - BeSS-1.0.6/BeSS/R/gbess.cox.R | 56 +- BeSS-1.0.6/BeSS/R/gbess.glm.R | 55 +- BeSS-1.0.6/BeSS/R/gbess.lm.R | 79 --- BeSS-1.0.6/BeSS/R/gen.data.R | 52 +- BeSS-1.0.6/BeSS/R/logLik.bess.R | 40 - BeSS-1.0.6/BeSS/R/plot.bess.R | 96 ++-- BeSS-1.0.6/BeSS/R/predict.bess.R | 24 - BeSS-1.0.6/BeSS/R/print.bess.R | 6 BeSS-1.0.6/BeSS/R/print.bess.one.R | 6 BeSS-1.0.6/BeSS/R/summary.bess.R | 52 +- BeSS-1.0.6/BeSS/R/summary.bess.one.R | 28 - BeSS-1.0.6/BeSS/man/aic.Rd | 6 BeSS-1.0.6/BeSS/man/bess-internal.Rd | 39 + BeSS-1.0.6/BeSS/man/bess.Rd | 24 - BeSS-1.0.6/BeSS/man/bess.one.Rd | 17 BeSS-1.0.6/BeSS/man/coef.bess.Rd | 4 BeSS-1.0.6/BeSS/man/predict.bess.Rd | 6 BeSS-1.0.6/BeSS/src/Makevars |only BeSS-1.0.6/BeSS/src/Makevars.win |only BeSS-1.0.6/BeSS/src/RcppExports.cpp | 488 +++++++++++---------- BeSS-1.0.6/BeSS/src/bess_cox.cpp |only BeSS-1.0.6/BeSS/src/bess_cox_group.cpp |only BeSS-1.0.6/BeSS/src/bess_glm.cpp |only BeSS-1.0.6/BeSS/src/bess_glm_group.cpp |only BeSS-1.0.6/BeSS/src/bess_lm.cpp |only BeSS-1.0.6/BeSS/src/bess_lm_group.cpp |only BeSS-1.0.6/BeSS/src/coxph.cpp |only BeSS-1.0.6/BeSS/src/coxph.h |only BeSS-1.0.6/BeSS/src/logistic.cpp |only BeSS-1.0.6/BeSS/src/logistic.h |only BeSS-1.0.6/BeSS/src/normalize.cpp |only BeSS-1.0.6/BeSS/src/normalize.h |only BeSS-1.0.6/BeSS/src/tmp.cpp |only BeSS-1.0.6/BeSS/src/tmp.h |only 50 files changed, 1024 insertions(+), 1404 deletions(-)
Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", 'Zumel', 'Mount', 2016, DOI:10.5281/zenodo.1173314.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.3.6 dated 2019-02-09 and 1.3.7 dated 2019-02-21
DESCRIPTION | 10 +++--- MD5 | 35 +++++++++++---------- NEWS.md | 5 +++ R/design_missing_Z.R | 5 ++- R/run_vtreat_tests.R | 62 ++++++-------------------------------- R/test_simple_col_replace.R |only inst/doc/MultiClassVtreat.html | 4 +- inst/doc/SavingTreamentPlans.html | 4 +- inst/doc/VariableImportance.html | 10 +++--- inst/doc/vtreat.html | 32 +++++++++---------- inst/doc/vtreatCrossFrames.html | 38 +++++++++++------------ inst/doc/vtreatGrouping.html | 4 +- inst/doc/vtreatOverfit.html | 38 +++++++++++------------ inst/doc/vtreatRareLevels.html | 4 +- inst/doc/vtreatScaleMode.html | 16 ++++----- inst/doc/vtreatSignificance.html | 18 +++++------ inst/doc/vtreatSplitting.html | 4 +- inst/doc/vtreatVariableTypes.html | 42 ++++++++++++------------- tests/run_RUnit_tests.R | 12 ++++--- 19 files changed, 158 insertions(+), 185 deletions(-)
Title: Supporting Graphs for Analysing Time Series
Description: Provides 'ggplot2' graphics for analysing time
series data. It aims to fit into the 'tidyverse' and grammar of
graphics framework for handling temporal data.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>),
Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>),
Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>)
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between sugrrants versions 0.2.2 dated 2019-02-02 and 0.2.3 dated 2019-02-21
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + NEWS.md | 4 ++++ R/frame-calendar.R | 3 +++ 5 files changed, 15 insertions(+), 7 deletions(-)
Title: Penalized Ordinal Regression
Description: Fits ordinal regression models with elastic net penalty.
Supported model families include cumulative probability, stopping ratio,
continuation ratio, and adjacent category. These families are a subset of
vector glm's which belong to a model class we call the elementwise link
multinomial-ordinal (ELMO) class. Each family in this class links a vector
of covariates to a vector of class probabilities. Each of these families
has a parallel form, which is appropriate for ordinal response data, as
well as a nonparallel form that is appropriate for an unordered categorical
response, or as a more flexible model for ordinal data. The parallel model
has a single set of coefficients, whereas the nonparallel model has a set of
coefficients for each response category except the baseline category. It is
also possible to fit a model with both parallel and nonparallel terms, which
we call the semi-parallel model. The semi-parallel model has the flexibility
of the nonparallel model, but the elastic net penalty shrinks it toward the
parallel model. For details, refer to Wurm, Hanlon, and Rathouz (2017)
<arXiv:1706.05003>.
Author: Michael Wurm [aut, cre],
Paul Rathouz [aut],
Bret Hanlon [aut]
Maintainer: Michael Wurm <wurm@uwalumni.com>
Diff between ordinalNet versions 2.5 dated 2018-09-10 and 2.6 dated 2019-02-21
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 12 ++++++------ man/ordinalNet.Rd | 16 +++++++++------- man/predict.ordinalNet.Rd | 3 ++- tests/testthat/test-links.R | 3 ++- tests/testthat/test-ordinalNet.R | 10 +++++----- 7 files changed, 29 insertions(+), 25 deletions(-)
Title: Calculate the RR for the GAM
Description: To calculate the relative risk (RR) for the generalized additive model.
Author: Zhicheng Du,Wangjian Zhang, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between gamRR versions 0.4.0 dated 2018-03-19 and 0.5.0 dated 2019-02-21
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/gamRR.R | 39 +++++++++++++++------------------------ R/gamRR.boot.R | 9 +++------ man/gamRR.Rd | 12 ++---------- man/gamRR.boot.Rd | 27 ++++++++++----------------- 6 files changed, 38 insertions(+), 65 deletions(-)