Title: General Purpose Optimization in R using C++
Description: Perform general purpose optimization in R using C++. A unified
wrapper interface is provided to call C functions of the five optimization
algorithms ('Nelder-Mead', 'BFGS', 'CG', 'L-BFGS-B' and 'SANN') underlying
optim().
Author: Yi Pan [aut, cre]
Maintainer: Yi Pan <ypan1988@gmail.com>
Diff between roptim versions 0.1.1 dated 2018-10-18 and 0.1.2 dated 2018-11-12
DESCRIPTION | 8 +++++--- MD5 | 6 +++++- build |only inst/doc |only vignettes |only 5 files changed, 10 insertions(+), 4 deletions(-)
Title: Interface to 'MLflow'
Description: R interface to 'MLflow', open source platform for the complete machine
learning life cycle, see <https://mlflow.org/>. This package supports installing
'MLflow', tracking experiments, creating and running projects, and saving and
serving models.
Author: Matei Zaharia [aut, cre],
Javier Luraschi [aut],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
RStudio [cph]
Maintainer: Matei Zaharia <matei@databricks.com>
Diff between mlflow versions 0.7.0 dated 2018-10-06 and 0.8.0 dated 2018-11-12
DESCRIPTION | 6 +- MD5 | 68 ++++++++++++++-------------- R/model-keras.R | 18 +++---- R/model.R | 2 R/tracking-client.R | 1 R/tracking-fluent.R | 2 R/tracking-rest.R | 2 README.md | 11 ++-- man/mlflow_client_create_experiment.Rd | 19 ------- man/mlflow_client_create_run.Rd | 19 ------- man/mlflow_client_delete_experiment.Rd | 19 ------- man/mlflow_client_delete_run.Rd | 19 ------- man/mlflow_client_download_artifacts.Rd | 19 ------- man/mlflow_client_get_experiment.Rd | 19 ------- man/mlflow_client_get_experiment_by_name.Rd | 19 ------- man/mlflow_client_get_run.Rd | 19 ------- man/mlflow_client_list_artifacts.Rd | 19 ------- man/mlflow_client_list_experiments.Rd | 19 ------- man/mlflow_client_log_artifact.Rd | 19 ------- man/mlflow_client_log_metric.Rd | 19 ------- man/mlflow_client_log_param.Rd | 19 ------- man/mlflow_client_restore_experiment.Rd | 19 ------- man/mlflow_client_restore_run.Rd | 19 ------- man/mlflow_client_set_tag.Rd | 19 ------- man/mlflow_client_set_terminated.Rd | 19 ------- man/mlflow_create_experiment.Rd | 10 ---- man/mlflow_end_run.Rd | 10 ---- man/mlflow_log_artifact.Rd | 10 ---- man/mlflow_log_metric.Rd | 10 ---- man/mlflow_log_param.Rd | 10 ---- man/mlflow_set_experiment.Rd | 10 ---- man/mlflow_set_tag.Rd | 10 ---- man/mlflow_start_run.Rd | 10 ---- tests/testthat/test-tracking.R | 11 ++++ tests/testthat/test_keras_model.R | 6 +- 35 files changed, 69 insertions(+), 461 deletions(-)
Title: R Interface to a 'PostGIS' Database
Description: Provides an interface between R and 'PostGIS'-enabled
'PostgreSQL' databases to transparently transfer spatial
data. Both vector (points, lines, polygons) and raster data are
supported in read and write modes. Also provides convenience
functions to execute common procedures in 'PostgreSQL/PostGIS'.
Author: Mathieu Basille [aut],
David Bucklin [aut, cre]
Maintainer: David Bucklin <david.bucklin@gmail.com>
Diff between rpostgis versions 1.4.1 dated 2018-08-17 and 1.4.2 dated 2018-11-12
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS.md | 12 ++++++++++++ R/pgInsertize.R | 16 +++++++++++----- R/pgWriteRast.R | 3 ++- man/dbColumn.Rd | 3 ++- man/dbDrop.Rd | 5 +++-- man/dbIndex.Rd | 5 +++-- man/pgInsert.Rd | 3 ++- man/pgInsertizeGeom.Rd | 10 +++++----- man/pgMakePts.Rd | 5 +++-- 11 files changed, 58 insertions(+), 34 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.4.0 dated 2018-08-15 and 1.4.1 dated 2018-11-12
DESCRIPTION | 8 MD5 | 28 + NAMESPACE | 4 R/GSTTest.R | 38 +- R/hartleyTest.R |only R/sysdata.rda |binary data/Pentosan.rda |binary data/algae.rda |binary data/qPCR.rda |binary data/reviewers.rda |binary data/trout.rda |binary demo/trout.R | 61 ++-- inst/NEWS.Rd | 14 inst/doc/QuickReferenceGuide.html | 556 ++++++++++++++++---------------------- man/GSTTest.Rd | 15 - man/hartleyTest.Rd |only 16 files changed, 355 insertions(+), 369 deletions(-)
Title: 'Rcpp' Implementation of 'FSelector' Entropy-Based Feature
Selection Algorithms with a Sparse Matrix Support
Description: 'Rcpp' (free of 'Java'/'Weka') implementation of 'FSelector' entropy-based feature selection
algorithms based on an MDL discretization (Fayyad U. M., Irani K. B.: Multi-Interval Discretization of Continuous-Valued Attributes for Classification Learning.
In 13'th International Joint Conference on Uncertainly in Artificial Intelligence (IJCAI93), pages 1022-1029, Chambery, France, 1993.) <https://www.ijcai.org/Proceedings/93-2/Papers/022.pdf>
with a sparse matrix support. It is also equipped with a parallel backend.
Author: Zygmunt Zawadzki [aut, cre],
Marcin Kosinski [aut],
Krzysztof Slomczynski [ctb],
Damian Skrzypiec [ctb]
Maintainer: Zygmunt Zawadzki <zygmunt@zstat.pl>
Diff between FSelectorRcpp versions 0.2.1 dated 2018-08-02 and 0.3.0 dated 2018-11-12
DESCRIPTION | 9 MD5 | 62 +- R/RcppExports.R | 8 R/discretize.R | 78 +- R/discretize_transform.R | 5 R/feature_search.R | 8 R/information_gain.R | 35 - build/vignette.rds |binary inst/dev |only inst/doc/benchmarks_discretize.R | 246 ++++---- inst/doc/benchmarks_discretize.Rmd | 32 - inst/doc/benchmarks_discretize.html | 883 +++++------------------------ inst/doc/get_started.R | 1 inst/doc/get_started.Rmd | 8 inst/doc/get_started.html | 763 +++---------------------- inst/doc/integer-variables.R |only inst/doc/integer-variables.Rmd |only inst/doc/integer-variables.html |only man/discretize.Rd | 6 man/information_gain.Rd | 6 src/Makevars | 4 src/Makevars.win | 6 src/RcppExports.cpp | 14 src/discretize.cpp | 30 src/information_gain.cpp | 64 +- src/init.c | 4 tests/testthat/test-discretize.R | 61 +- tests/testthat/test-discretize_transform.R | 2 tests/testthat/test-information_gain.R | 47 + tests/testthat/test-na.R |only tests/testthat/test-param-search.R | 4 tests/testthat/test-support.R | 23 vignettes/benchmarks_discretize.Rmd | 32 - vignettes/get_started.Rmd | 8 vignettes/integer-variables.Rmd |only 35 files changed, 798 insertions(+), 1651 deletions(-)
Title: Deployment Interface for R Markdown Documents and Shiny
Applications
Description: Programmatic deployment interface for 'RPubs', 'shinyapps.io', and
'RStudio Connect'. Supported content types include R Markdown documents,
Shiny applications, Plumber APIs, plots, and static web content.
Author: JJ Allaire
Maintainer: Jonathan McPherson <jonathan@rstudio.com>
Diff between rsconnect versions 0.8.8 dated 2018-03-08 and 0.8.11 dated 2018-11-12
rsconnect-0.8.11/rsconnect/DESCRIPTION | 11 rsconnect-0.8.11/rsconnect/MD5 | 147 ++++----- rsconnect-0.8.11/rsconnect/NAMESPACE | 2 rsconnect-0.8.11/rsconnect/R/accounts.R | 17 - rsconnect-0.8.11/rsconnect/R/applications.R | 23 - rsconnect-0.8.11/rsconnect/R/auth.R | 8 rsconnect-0.8.11/rsconnect/R/bundle.R | 253 ++++++++++------ rsconnect-0.8.11/rsconnect/R/client.R | 6 rsconnect-0.8.11/rsconnect/R/configureApp.R | 17 - rsconnect-0.8.11/rsconnect/R/connect.R | 2 rsconnect-0.8.11/rsconnect/R/dependencies.R | 25 - rsconnect-0.8.11/rsconnect/R/deployAPI.R | 20 - rsconnect-0.8.11/rsconnect/R/deployApp.R | 143 ++++++--- rsconnect-0.8.11/rsconnect/R/deployDoc.R | 21 - rsconnect-0.8.11/rsconnect/R/deploySite.R | 1 rsconnect-0.8.11/rsconnect/R/deployTFModel.R | 45 +- rsconnect-0.8.11/rsconnect/R/deployments.R | 93 +++++ rsconnect-0.8.11/rsconnect/R/http.R | 103 ++++-- rsconnect-0.8.11/rsconnect/R/ide.R | 5 rsconnect-0.8.11/rsconnect/R/json.R |only rsconnect-0.8.11/rsconnect/R/lint-framework.R | 8 rsconnect-0.8.11/rsconnect/R/lint-utils.R | 4 rsconnect-0.8.11/rsconnect/R/lucid.R | 13 rsconnect-0.8.11/rsconnect/R/onLoad.R | 10 rsconnect-0.8.11/rsconnect/R/packages.R |only rsconnect-0.8.11/rsconnect/R/proxies.R |only rsconnect-0.8.11/rsconnect/R/restartApp.R | 7 rsconnect-0.8.11/rsconnect/R/rpubs.R | 20 - rsconnect-0.8.11/rsconnect/R/rsa.R | 12 rsconnect-0.8.11/rsconnect/R/rsconnect-package.R | 106 +++--- rsconnect-0.8.11/rsconnect/R/servers.R | 18 - rsconnect-0.8.11/rsconnect/R/tasks.R | 20 - rsconnect-0.8.11/rsconnect/R/terminateApp.R | 6 rsconnect-0.8.11/rsconnect/R/title.R | 4 rsconnect-0.8.11/rsconnect/R/usage.R | 12 rsconnect-0.8.11/rsconnect/R/utils.R | 25 + rsconnect-0.8.11/rsconnect/README.md | 7 rsconnect-0.8.11/rsconnect/man/accounts.Rd | 11 rsconnect-0.8.11/rsconnect/man/addAuthorizedUser.Rd | 7 rsconnect-0.8.11/rsconnect/man/addLinter.Rd | 4 rsconnect-0.8.11/rsconnect/man/appDependencies.Rd | 38 +- rsconnect-0.8.11/rsconnect/man/applications.Rd | 9 rsconnect-0.8.11/rsconnect/man/configureApp.Rd | 20 - rsconnect-0.8.11/rsconnect/man/connectUser.Rd | 15 rsconnect-0.8.11/rsconnect/man/deployAPI.Rd | 21 - rsconnect-0.8.11/rsconnect/man/deployApp.Rd | 70 ++-- rsconnect-0.8.11/rsconnect/man/deployDoc.Rd | 32 +- rsconnect-0.8.11/rsconnect/man/deploySite.Rd | 22 - rsconnect-0.8.11/rsconnect/man/deployTFModel.Rd | 36 +- rsconnect-0.8.11/rsconnect/man/deployments.Rd | 10 rsconnect-0.8.11/rsconnect/man/forgetDeployment.Rd |only rsconnect-0.8.11/rsconnect/man/generateAppName.Rd | 3 rsconnect-0.8.11/rsconnect/man/lint.Rd | 2 rsconnect-0.8.11/rsconnect/man/linter.Rd | 2 rsconnect-0.8.11/rsconnect/man/listBundleFiles.Rd | 14 rsconnect-0.8.11/rsconnect/man/makeLinterMessage.Rd | 2 rsconnect-0.8.11/rsconnect/man/options.Rd | 9 rsconnect-0.8.11/rsconnect/man/removeAuthorizedUser.Rd | 2 rsconnect-0.8.11/rsconnect/man/restartApp.Rd | 9 rsconnect-0.8.11/rsconnect/man/rpubsUpload.Rd | 13 rsconnect-0.8.11/rsconnect/man/rsconnect-package.Rd | 57 +-- rsconnect-0.8.11/rsconnect/man/rsconnectPackages.Rd |only rsconnect-0.8.11/rsconnect/man/servers.Rd | 2 rsconnect-0.8.11/rsconnect/man/setAccountInfo.Rd | 5 rsconnect-0.8.11/rsconnect/man/setProperty.Rd | 4 rsconnect-0.8.11/rsconnect/man/showInvited.Rd | 2 rsconnect-0.8.11/rsconnect/man/showMetrics.Rd | 18 - rsconnect-0.8.11/rsconnect/man/showUsage.Rd | 2 rsconnect-0.8.11/rsconnect/man/showUsers.Rd | 2 rsconnect-0.8.11/rsconnect/man/taskLog.Rd | 4 rsconnect-0.8.11/rsconnect/man/tasks.Rd | 4 rsconnect-0.8.11/rsconnect/man/terminateApp.Rd | 6 rsconnect-0.8.11/rsconnect/man/writeManifest.Rd |only rsconnect-0.8.11/rsconnect/tests/testthat/test-bundle.R | 44 ++ rsconnect-0.8.11/rsconnect/tests/testthat/test-http.R | 6 rsconnect-0.8.11/rsconnect/tests/testthat/test-rmds |only rsconnect-0.8.8/rsconnect/man/packages.Rd |only rsconnect-0.8.8/rsconnect/man/proxies.Rd |only 78 files changed, 1071 insertions(+), 650 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>
Diff between QGglmm versions 0.7.1 dated 2018-06-15 and 0.7.2 dated 2018-11-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 5 +++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/QGglmmHowTo.Rnw | 5 +++-- inst/doc/QGglmmHowTo.pdf |binary vignettes/QGglmmHowTo.Rnw | 5 +++-- 8 files changed, 20 insertions(+), 17 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: Provides the next iteration of the EMU Speech
Database Management System (EMU-SDMS) with database management, data
extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between emuR versions 1.1.0 dated 2018-10-26 and 1.1.1 dated 2018-11-12
emuR-1.1.0/emuR/vignettes/pics/aeGraph.aux |only emuR-1.1.0/emuR/vignettes/pics/aeGraph.fdb_latexmk |only emuR-1.1.0/emuR/vignettes/pics/aeGraph.log |only emuR-1.1.0/emuR/vignettes/pics/aeGraph.synctex.gz |only emuR-1.1.0/emuR/vignettes/pics/autobuild_linkFromTimesGraph.aux |only emuR-1.1.0/emuR/vignettes/pics/fromScratchDBgraph.aux |only emuR-1.1.0/emuR/vignettes/pics/fromScratchDBgraph.fdb_latexmk |only emuR-1.1.0/emuR/vignettes/pics/fromScratchDBgraph.log |only emuR-1.1.0/emuR/vignettes/pics/fromScratchDBgraph.synctex.gz |only emuR-1.1.0/emuR/vignettes/pics/functionGraph.aux |only emuR-1.1.0/emuR/vignettes/pics/functionGraph.fls |only emuR-1.1.0/emuR/vignettes/pics/msajc003.aux |only emuR-1.1.0/emuR/vignettes/pics/positionSimple.aux |only emuR-1.1.1/emuR/DESCRIPTION | 6 emuR-1.1.1/emuR/MD5 | 27 emuR-1.1.1/emuR/NEWS.md | 9 emuR-1.1.1/emuR/R/emuR-emuRtrackdata.R | 4 emuR-1.1.1/emuR/inst/doc/EQL.html | 244 ++--- emuR-1.1.1/emuR/inst/doc/emuDB.html | 485 ++++------ emuR-1.1.1/emuR/inst/doc/emuR_intro.html | 282 ++--- emuR-1.1.1/emuR/tests/testthat/test_emuR-emuRtrackdata.R | 32 21 files changed, 552 insertions(+), 537 deletions(-)
Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in
'RStan' and R. Some designs are implemented in R for the first
time (e.g. 'EffTox' by Thall and Cook, 2004,
<https://biostatistics.mdanderson.org/softwaredownload/SingleSoftware.aspx?Software_Id=2>).
Given the emphasis on flexibility in Bayesian analysis,
the implementations in a common language and style may serve as a cookbook
to encourage the use of Bayesian methods in trials. Compiled 'RStan' models
are provided in addition to helper classes and functions to perform
simulations and inference on observed trial outcomes.
There is a preponderance of early phase trial designs because this is where
Bayesian methods are used most. If there is a published Bayesian design you
want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre],
Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between trialr versions 0.0.4 dated 2018-10-24 and 0.0.5 dated 2018-11-12
DESCRIPTION | 9 ++- MD5 | 30 ++++++------ NEWS.md | 68 +++++++++++++++-------------- build/partial.rdb |binary inst/doc/BEBOP.html | 4 - inst/doc/CRM-visualisation.html | 4 - inst/doc/CRM.html | 4 - inst/doc/EffTox.html | 6 +- inst/doc/HierarchicalBayesianResponse.html | 4 - inst/doc/trialr-overview.html | 4 - man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary src/Makevars | 2 src/Makevars.win | 2 tests/testthat/test_stan_efftox.R | 4 - vignettes/library.bib | 3 - 16 files changed, 75 insertions(+), 69 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 3.1.1 dated 2018-06-12 and 3.2.0 dated 2018-11-12
DESCRIPTION | 16 MD5 | 101 +- NAMESPACE | 13 NEWS | 25 R/JAGS_models.R | 117 ++- R/LCx.survFit.R | 5 R/modelData.R | 18 R/modelData.survDataCstExp.R | 23 R/modelData.survDataVarExp.R | 26 R/morse-internal.R | 6 R/morse.R | 31 R/plot.survFitCstExp.R | 7 R/plot.survFitPredict.R | 7 R/plot.survFitPredict_Nsurv.R |only R/plot.survFitVarExp.R | 29 R/plot_prior_post.R |only R/ppc.R | 4 R/ppc.survFitCstExp.R | 6 R/ppc.survFitPredict_Nsurv.R |only R/predict.survFit.R | 54 - R/predict_Nsurv.R |only R/predict_Nsurv_check.R |only R/predict_ode.survFit.R |only R/priors_distribution.R | 34 R/summary.survFit.R | 80 +- R/survFit.R | 40 - R/survFit.survDataCstExp.R | 46 - R/survFit.survDataVarExp.R | 49 - inst/doc/modelling.pdf |binary inst/doc/tutorial.R | 9 inst/doc/tutorial.Rmd | 152 ++++ inst/doc/tutorial.html | 844 ++++++++++++++---------- man/modelData.Rd |only man/modelData.survDataCstExp.Rd |only man/modelData.survDataVarExp.Rd |only man/morse-package.Rd | 27 man/plot.reproData.Rd | 4 man/plot.reproFitTT.Rd | 8 man/plot.survFitCstExp.Rd | 2 man/plot.survFitPredict.Rd | 4 man/plot.survFitPredict_Nsurv.Rd |only man/plot.survFitTT.Rd | 10 man/plot.survFitVarExp.Rd | 8 man/plot_prior_post.Rd |only man/plot_prior_post.survFit.Rd |only man/ppc.survFitPredict_Nsurv.Rd |only man/predict.survFit.Rd | 5 man/predict_Nsurv.Rd |only man/predict_Nsurv.survFit.Rd |only man/predict_Nsurv_check.Rd |only man/predict_Nsurv_check.survFitPredict_Nsurv.Rd |only man/predict_ode.Rd |only man/predict_ode.survFit.Rd |only man/priors_distribution.survFit.Rd | 6 man/reproFitTT.Rd | 4 man/summary.survFit.Rd | 10 man/survFit.survDataCstExp.Rd | 11 man/survFit.survDataVarExp.Rd | 12 man/survFitTT.survDataCstExp.Rd | 4 tests/testthat/test-modelData.R | 124 +-- vignettes/tutorial.Rmd | 152 ++++ 61 files changed, 1448 insertions(+), 685 deletions(-)
Title: Stratified and Personalised Models Based on Model-Based Trees
and Forests
Description: Model-based trees for subgroup analyses in clinical trials and
model-based forests for the estimation and prediction of personalised
treatment effects (personalised models). Currently partitioning of linear
models, lm(), generalised linear models, glm(), and Weibull models,
survreg(), is supported. Advanced plotting functionality is supported for
the trees and a test for parameter heterogeneity is provided for the
personalised models. For details on model-based trees for subgroup analyses
see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for
details on model-based forests for estimation of individual treatment effects
see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre],
Achim Zeileis [aut],
Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>
Diff between model4you versions 0.9-2 dated 2018-06-15 and 0.9-3 dated 2018-11-12
DESCRIPTION | 10 - MD5 | 52 +++++-- R/helpers.R | 6 R/plot-pmtree.R | 168 ++++++++++++++---------- R/pmforest.R | 56 ++++---- R/pmtree.R | 8 - inst/JORS/figure |only inst/JORS/journal_correspondence |only inst/JORS/man_model4you-concordance.tex |only inst/JORS/man_model4you.R |only inst/JORS/man_model4you.Rnw | 224 +++++++++++++++++++------------- inst/JORS/man_model4you.aux |only inst/JORS/man_model4you.bbl |only inst/JORS/man_model4you.blg |only inst/JORS/man_model4you.log |only inst/JORS/man_model4you.out |only inst/JORS/man_model4you.pdf |only inst/JORS/man_model4you.tex |only inst/JORS/ref_model4you.bib | 46 ++++++ inst/NEWS.Rd | 8 + man/dot-add_modelinfo.Rd |only man/dot-modelfit.Rd |only man/dot-prepare_args.Rd |only man/node_pmterminal.Rd | 8 - man/objfun.Rd | 3 man/objfun.pmtree.Rd | 4 man/pmforest.Rd | 96 ++++++++++++- man/pmodel.Rd | 4 man/pmtree.Rd | 4 man/survreg_plot.Rd | 3 man/varimp.pmforest.Rd | 4 31 files changed, 472 insertions(+), 232 deletions(-)
Title: R Interface to Google Charts
Description: R interface to Google's chart tools, allowing users
to create interactive charts based on data frames. Charts
are displayed locally via the R HTTP help server. A modern
browser with an Internet connection is required and for some
charts a Flash player. The data remains local and is not
uploaded to Google.
Author: Markus Gesmann [aut, cre],
Diego de Castillo [aut],
Joe Cheng [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between googleVis versions 0.6.2 dated 2017-01-01 and 0.6.3 dated 2018-11-12
DESCRIPTION | 10 MD5 | 154 +-- NAMESPACE | 1 NEWS | 22 R/gvis.R | 14 R/gvisAnnotatedTimeLine.R | 6 R/gvisAnnotationChart.R | 2 R/gvisBubbleChart.R | 2 R/gvisCalendar.R | 2 R/gvisCoreCharts.R | 2 R/gvisGeoChart.R | 18 R/gvisGeoMap.R | 8 R/gvisMap.R | 8 R/gvisMethods.R | 4 R/gvisMotionChart.R | 6 R/gvisSankey.R | 2 R/gvisTimeLine.R | 2 R/shiny.R | 6 R/zzz.R | 2 README.md | 14 build/googleVis.pdf |binary build/vignette.rds |binary demo/AnimatedGeoChart.R | 2 demo/EventListener.R | 4 demo/Roles.R | 2 demo/WorldBank.R | 6 inst/brew/Stock.html | 2 inst/doc/Using_Roles_via_googleVis.R | 2 inst/doc/Using_Roles_via_googleVis.html | 224 ++--- inst/doc/Using_Trendlines_with_googleVis.html | 80 - inst/doc/Using_googleVis_with_knitr.Rmd | 4 inst/doc/Using_googleVis_with_knitr.html | 78 - inst/doc/googleVis.R | 2 inst/doc/googleVis.Rnw | 50 - inst/doc/googleVis.pdf |binary inst/doc/googleVis_examples.Rmd | 2 inst/doc/googleVis_examples.html | 752 +++++++++--------- inst/mansections/GoogleChartToolsURL.txt | 2 inst/mansections/GoogleChartToolsURLConfigOptions.txt | 2 inst/rsp/index.rsp | 316 +++---- inst/rsp/myAnalysis/index.rsp | 2 inst/rsp/src/simpleFooter.rsp | 4 man/Andrew.Rd | 2 man/OpenClose.Rd | 2 man/Population.Rd | 2 man/createGoogleGadget.Rd | 2 man/googleVis-package.Rd | 4 man/gvisAnnotatedTimeLine.Rd | 18 man/gvisAnnotationChart.Rd | 11 man/gvisAreaChart.Rd | 11 man/gvisBarChart.Rd | 13 man/gvisBubbleChart.Rd | 15 man/gvisCalendar.Rd | 17 man/gvisCandlestickChart.Rd | 15 man/gvisColumnChart.Rd | 14 man/gvisComboChart.Rd | 11 man/gvisGauge.Rd | 14 man/gvisGeoChart.Rd | 25 man/gvisGeoMap.Rd | 16 man/gvisHistogram.Rd | 11 man/gvisIntensityMap.Rd | 16 man/gvisLineChart.Rd | 11 man/gvisMap.Rd | 22 man/gvisMethods.Rd | 4 man/gvisMotionChart.Rd | 18 man/gvisOrgChart.Rd | 11 man/gvisPieChart.Rd | 14 man/gvisSankey.Rd | 8 man/gvisScatterChart.Rd | 11 man/gvisSteppedAreaChart.Rd | 11 man/gvisTable.Rd | 11 man/gvisTimeline.Rd | 11 man/gvisTreeMap.Rd | 12 man/renderGvis.Rd | 6 vignettes/Using_googleVis_with_knitr.Rmd | 4 vignettes/googleVis.Rnw | 50 - vignettes/googleVis.bib | 52 - vignettes/googleVis_examples.Rmd | 2 78 files changed, 1148 insertions(+), 1150 deletions(-)
Title: Fast Probabilistic Record Linkage with Missing Data
Description: Implements a Fellegi-Sunter probabilistic record linkage model that allows for missing data
and the inclusion of auxiliary information. This includes functionalities to conduct a merge of two datasets under the Fellegi-Sunter model
using the Expectation-Maximization algorithm. In addition, tools for preparing, adjusting, and summarizing
data merges are included. The package implements methods described in Enamorado, Fifield,
and Imai (2017) ''Using a Probabilistic Model to Assist Merging of Large-scale Administrative
Records'', available at <http://imai.princeton.edu/research/linkage.html>.
Author: Ted Enamorado [aut, cre],
Ben Fifield [aut],
Kosuke Imai [aut]
Maintainer: Ted Enamorado <fastlinkr@gmail.com>
Diff between fastLink versions 0.4.0 dated 2018-05-15 and 0.5.0 dated 2018-11-12
DESCRIPTION | 8 ++-- MD5 | 53 +++++++++++++++------------- NAMESPACE | 4 ++ R/aggconfusion.R | 2 - R/blockData.R |only R/confusion.R | 43 ++++++++++++++++------- R/emlinkMARmov.R | 12 +++++- R/emlinklog.R | 6 ++- R/fastLink-package.R | 10 ++--- R/fastLink.R | 33 ++++++++++++++--- R/gammaCK2par.R | 42 ++++++++++++++-------- R/gammaCKpar.R | 59 +++++++++++++++++++------------ R/gammaKpar.R | 36 ++++++++++--------- R/gammaNUMCK2par.R | 43 ++++++++++++++--------- R/gammaNUMCKpar.R | 46 +++++++++++++++--------- R/getMatches.R | 89 +++++++++++++++++++++++++++++++++++++++++++----- R/matchesLink.R | 13 ++++--- R/nameReweight.R | 6 ++- R/plot.R | 4 +- R/preprocText.R | 51 ++++++++++++++++++--------- R/tableCounts.R | 15 ++++---- man/aggconfusion.Rd | 2 - man/blockData.Rd |only man/confusion.Rd | 2 - man/fastLink-package.Rd | 10 ++--- man/fastLink.Rd | 4 +- man/getMatches.Rd | 11 ++++- man/preprocText.Rd | 7 +++ man/stringSubset.Rd |only 29 files changed, 414 insertions(+), 197 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 0.5.0 dated 2018-11-02 and 0.5.2 dated 2018-11-12
DESCRIPTION | 8 - MD5 | 15 +- NEWS.md | 20 +++ inst/CITATION |only inst/doc/RcppThread-vignette.pdf |binary inst/include/RcppThread/Thread.hpp | 3 inst/include/RcppThread/ThreadPool.hpp | 7 - inst/include/RcppThread/parallelFor.hpp | 2 tests/tests.cpp | 163 ++++++++++++++------------------ 9 files changed, 112 insertions(+), 106 deletions(-)
Title: Statistical Methods and Models for Claims Reserving in General
Insurance
Description: Various statistical methods and models which are
typically used for the estimation of outstanding claims reserves
in general insurance, including those to estimate the claims
development result as required under Solvency II.
Author: Markus Gesmann [aut, cre],
Daniel Murphy [aut],
Yanwei (Wayne) Zhang [aut],
Alessandro Carrato [aut],
Giuseppe Crupi [ctb],
Christophe Dutang [ctb],
Arnaud Lacoume [ctb],
Arthur Charpentier [ctb],
Mario Wuthrich [aut],
Fabio Concina [aut],
Eric Dal Moro [aut],
Yuriy Krvavych [ctb],
Vincent Goulet [ctb]
Maintainer: Markus Gesmann <markus.gesmann@googlemail.com>
Diff between ChainLadder versions 0.2.7 dated 2018-10-16 and 0.2.8 dated 2018-11-12
DESCRIPTION | 18 - MD5 | 90 +++--- NAMESPACE | 2 R/BootstrapReserve.R | 1 R/MackChainLadderFunctions.R | 220 +++++++-------- R/MunichChainLadderFunctions.R | 1 R/QuantileIFRS17.R | 2 R/Triangles.R | 45 +-- R/ata.r | 6 R/clark.r | 4 R/glmReserve.R | 5 R/tweedieReserve.R | 2 README.md | 12 THANKS | 1 inst/doc/ChainLadder.R | 111 ++++--- inst/doc/ChainLadder.Rnw | 100 +----- inst/doc/ChainLadder.pdf |binary inst/doc/NEWS.Rmd | 7 inst/doc/NEWS.html | 64 ++-- inst/unitTests/runit.BootChainLadder.R |only inst/unitTests/runit.MackChainLadder.R | 6 inst/unitTests/runit.MunichChainLadder.R |only inst/unitTests/runit.ata.R |only inst/unitTests/runit.clark.r | 22 - inst/unitTests/runit.glmReserving.r | 5 inst/unitTests/runit.triangle.R |only inst/unitTests/runit.tweedieReserve.R | 9 man/CDR.Rd | 2 man/CLFMdelta.rd | 2 man/ChainLadder-package.Rd | 4 man/ClarkCapeCod.rd | 448 +++++++++++++++---------------- man/ClarkLDF.Rd | 412 ++++++++++++++-------------- man/Join2Fits.Rd | 2 man/MW2014.Rd | 2 man/MackChainLadder.Rd | 30 +- man/Mse-methods.Rd | 2 man/MultiChainLadder-class.Rd | 176 ++++++------ man/MultiChainLadder.Rd | 24 - man/MunichChainLadder.Rd | 8 man/Table65.rd | 2 man/UKMotor.Rd | 2 man/USAA.Rd | 2 man/chainladder.Rd | 142 ++++----- man/quantile.MackChainLadder.Rd | 2 tests/doRUnit.R | 2 vignettes/ChainLadder.Rnw | 100 +----- vignettes/ChainLadder.bib | 56 +-- vignettes/NEWS.Rmd | 7 48 files changed, 1062 insertions(+), 1098 deletions(-)
Title: Bayesian Hierarchical Regression on Clearance Rates in the
Presence of Lag and Tail Phases
Description: An implementation of the Bayesian Clearance Estimator (Fogarty et al. (2015) <doi:10.1111/biom.12307>).
It takes serial measurements of a response on an individual (e.g., parasite load
after treatment) that is decaying over time and performs Bayesian hierarchical
regression of the clearance rates on the given covariates. This package provides
tools to calculate WWARN PCE (WorldWide Antimalarial Resistance Network's
Parasite Clearance Estimator) estimates of the clearance rates as well.
Author: Colin B. Fogarty [cre] <cfogarty@mit.edu>,
Saeed Sharifi-Malvajerdi [aut] <saeedsh@wharton.upenn.edu>,
Feiyu Zhu [aut] <feiyuzhu@sas.upenn.edu>
Maintainer: Colin B. Fogarty <cfogarty@mit.edu>
Diff between bhrcr versions 1.0.1 dated 2018-08-28 and 1.0.2 dated 2018-11-12
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/clearanceEstimatorBayes.R | 8 ++++---- R/plot.R | 23 ++++++++++++++++++----- inst/CITATION | 3 +-- inst/doc/bhrcr-tutorial.Rmd | 8 ++++---- inst/doc/bhrcr-tutorial.html | 16 ++++++++-------- man/clearanceEstimatorBayes.Rd | 8 ++++---- vignettes/bhrcr-tutorial.Rmd | 8 ++++---- vignettes/figures/patient_1.pdf |binary vignettes/figures/patient_81.pdf |binary 11 files changed, 57 insertions(+), 45 deletions(-)
Title: Probability-Scale Residuals and Residual Correlations
Description: Computes probability-scale residuals and residual correlations
for continuous, ordinal, binary, count, and time-to-event data.
Author: Charles Dupont, Jeffrey Horner, Chun Li, Qi Liu, Bryan Shepherd
Maintainer: Bryan Shepherd <bryan.shepherd@VANDERBILT.EDU>
Diff between PResiduals versions 0.2-5 dated 2017-10-06 and 0.2-6 dated 2018-11-12
PResiduals-0.2-5/PResiduals/R/conditional.Spearman.R |only PResiduals-0.2-5/PResiduals/R/partial.Spearman.R |only PResiduals-0.2-5/PResiduals/R/plot.conditional.Spearman.R |only PResiduals-0.2-5/PResiduals/R/print.conditional.Spearman.R |only PResiduals-0.2-5/PResiduals/R/print.partial.Spearman.R |only PResiduals-0.2-5/PResiduals/man/conditional.partial.Spearman.Rd |only PResiduals-0.2-5/PResiduals/man/partial.Spearman.Rd |only PResiduals-0.2-5/PResiduals/man/plot.conditional.Spearman.Rd |only PResiduals-0.2-5/PResiduals/man/print.conditional.Spearman.Rd |only PResiduals-0.2-5/PResiduals/man/print.partial.Spearman.Rd |only PResiduals-0.2-6/PResiduals/DESCRIPTION | 26 PResiduals-0.2-6/PResiduals/MD5 | 37 PResiduals-0.2-6/PResiduals/NAMESPACE | 10 PResiduals-0.2-6/PResiduals/R/PResidData.R |only PResiduals-0.2-6/PResiduals/R/conditional_Spearman.R |only PResiduals-0.2-6/PResiduals/R/partial_Spearman.R |only PResiduals-0.2-6/PResiduals/R/plot.conditional_Spearman.R |only PResiduals-0.2-6/PResiduals/R/presid.R | 794 +++++----- PResiduals-0.2-6/PResiduals/R/print.conditional_Spearman.R |only PResiduals-0.2-6/PResiduals/R/print.partial_Spearman.R |only PResiduals-0.2-6/PResiduals/man/PResidData.Rd | 36 PResiduals-0.2-6/PResiduals/man/cobot.Rd | 6 PResiduals-0.2-6/PResiduals/man/conditional_Spearman.Rd |only PResiduals-0.2-6/PResiduals/man/countbot.Rd | 7 PResiduals-0.2-6/PResiduals/man/megabot.Rd | 6 PResiduals-0.2-6/PResiduals/man/partial_Spearman.Rd |only PResiduals-0.2-6/PResiduals/man/plot.conditional_Spearman.Rd |only PResiduals-0.2-6/PResiduals/man/presid.Rd | 10 PResiduals-0.2-6/PResiduals/man/print.conditional_Spearman.Rd |only PResiduals-0.2-6/PResiduals/man/print.partial_Spearman.Rd |only 30 files changed, 470 insertions(+), 462 deletions(-)
Title: Local Interpretable (Model-Agnostic) Visual Explanations
Description: Interpretability of complex machine learning models is a growing concern.
This package helps to understand key factors that drive the
decision made by complicated predictive model (so called black box model).
This is achieved through local approximations that are either based on
additive regression like model or CART like model that allows for
higher interactions. The methodology is based on Tulio Ribeiro, Singh, Guestrin (2016) <doi:10.1145/2939672.2939778>.
More details can be found in Staniak, Biecek (2018) <arXiv:1804.01955>.
Author: Mateusz Staniak [cre, aut],
Przemysław Biecek [aut]
Maintainer: Mateusz Staniak <mateusz.staniak@math.uni.wroc.pl>
Diff between live versions 1.5.8 dated 2018-09-24 and 1.5.9 dated 2018-11-12
live-1.5.8/live/R/old_interface.R |only live-1.5.8/live/man/add_predictions2.Rd |only live-1.5.8/live/man/calculate_weights.Rd |only live-1.5.8/live/man/check_conditions.Rd |only live-1.5.8/live/man/check_for_na.Rd |only live-1.5.8/live/man/create_task.Rd |only live-1.5.8/live/man/fit_explanation2.Rd |only live-1.5.8/live/man/generate_neighbourhood.Rd |only live-1.5.8/live/man/generate_neighbourhood2.Rd |only live-1.5.8/live/man/give_predictions.Rd |only live-1.5.8/live/man/give_predictions2.Rd |only live-1.5.8/live/man/normal_neighbourhood.Rd |only live-1.5.8/live/man/permutation_neighbourhood.Rd |only live-1.5.8/live/man/plot_explanation.Rd |only live-1.5.8/live/man/plot_explanation2.Rd |only live-1.5.8/live/man/plot_regression.Rd |only live-1.5.8/live/man/plot_regression2.Rd |only live-1.5.8/live/man/sample_locally2.Rd |only live-1.5.8/live/man/select_variables.Rd |only live-1.5.8/live/man/set_constant_dates.Rd |only live-1.5.8/live/man/set_constant_variables.Rd |only live-1.5.8/live/tests/testthat/test_old.R |only live-1.5.9/live/DESCRIPTION | 10 live-1.5.9/live/MD5 | 96 +--- live-1.5.9/live/NAMESPACE | 62 +- live-1.5.9/live/NEWS.md | 200 ++++---- live-1.5.9/live/R/app.R | 117 ++--- live-1.5.9/live/R/dalex_shortcut.R | 100 ++-- live-1.5.9/live/R/explain.R | 300 ++++++------- live-1.5.9/live/R/explore.R | 316 ++++++-------- live-1.5.9/live/R/helpers.R | 116 +---- live-1.5.9/live/R/live.R | 69 +-- live-1.5.9/live/R/plot.R | 113 ++--- live-1.5.9/live/R/sampling_methods.R | 156 ++---- live-1.5.9/live/README.md | 101 ++-- live-1.5.9/live/build/vignette.rds |binary live-1.5.9/live/inst/doc/wine_quality.R | 64 +- live-1.5.9/live/inst/doc/wine_quality.Rmd | 218 ++++----- live-1.5.9/live/inst/doc/wine_quality.html | 262 +++++------ live-1.5.9/live/man/add_predictions.Rd | 101 ++-- live-1.5.9/live/man/euclidean_kernel.Rd | 38 - live-1.5.9/live/man/fit_explanation.Rd | 91 ++-- live-1.5.9/live/man/gaussian_kernel.Rd | 38 - live-1.5.9/live/man/identity_kernel.Rd | 42 - live-1.5.9/live/man/live.Rd | 58 +- live-1.5.9/live/man/live_shiny.Rd | 48 +- live-1.5.9/live/man/local_approximation.Rd | 98 ++-- live-1.5.9/live/man/local_permutation_importance.Rd | 90 +-- live-1.5.9/live/man/plot.live_explainer.Rd | 68 +-- live-1.5.9/live/man/plot.local_permutation_importance.Rd | 38 - live-1.5.9/live/man/print.live_explainer.Rd | 32 - live-1.5.9/live/man/print.live_explorer.Rd | 32 - live-1.5.9/live/man/print.local_permutation_importance.Rd | 32 - live-1.5.9/live/man/sample_locally.Rd | 97 ++-- live-1.5.9/live/man/wine.Rd | 38 - live-1.5.9/live/tests/testthat.R | 111 ++-- live-1.5.9/live/tests/testthat/test_explaining.R | 127 ++--- live-1.5.9/live/tests/testthat/test_local_varimp.R | 47 +- live-1.5.9/live/tests/testthat/test_simulating.R | 196 ++++---- live-1.5.9/live/vignettes/wine_quality.Rmd | 218 ++++----- 60 files changed, 1923 insertions(+), 2017 deletions(-)
Title: Library of Research Designs
Description: A simple interface to build designs using the package 'DeclareDesign'.
In one line of code, users can specify the parameters of individual
designs and diagnose their properties. The designers can also be used
to compare performance of a given design across a range of combinations
of parameters, such as effect size, sample size, and assignment probabilities.
Author: Graeme Blair [aut],
Jasper Cooper [aut, cre],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Clara Bicalho [aut],
Neal Fultz [aut],
Lily Medina [aut]
Maintainer: Jasper Cooper <jjc2247@columbia.edu>
Diff between DesignLibrary versions 0.1.1 dated 2018-08-25 and 0.1.2 dated 2018-11-12
DesignLibrary-0.1.1/DesignLibrary/R/simple_factorial_designer.R |only DesignLibrary-0.1.1/DesignLibrary/R/simple_iv_designer.R |only DesignLibrary-0.1.1/DesignLibrary/R/simple_spillover_designer.R |only DesignLibrary-0.1.1/DesignLibrary/R/simple_two_arm_designer.R |only DesignLibrary-0.1.1/DesignLibrary/man/simple_factorial_designer.Rd |only DesignLibrary-0.1.1/DesignLibrary/man/simple_iv_designer.Rd |only DesignLibrary-0.1.1/DesignLibrary/man/simple_spillover_designer.Rd |only DesignLibrary-0.1.1/DesignLibrary/man/simple_two_arm_designer.Rd |only DesignLibrary-0.1.2/DesignLibrary/DESCRIPTION | 16 - DesignLibrary-0.1.2/DesignLibrary/MD5 | 57 +++---- DesignLibrary-0.1.2/DesignLibrary/NAMESPACE | 10 - DesignLibrary-0.1.2/DesignLibrary/NEWS.md | 30 +++ DesignLibrary-0.1.2/DesignLibrary/R/binary_iv_designer.R |only DesignLibrary-0.1.2/DesignLibrary/R/block_cluster_two_arm_designer.R | 43 +++-- DesignLibrary-0.1.2/DesignLibrary/R/cluster_sampling_designer.R | 4 DesignLibrary-0.1.2/DesignLibrary/R/factorial_designer.R | 10 - DesignLibrary-0.1.2/DesignLibrary/R/mediation_analysis_designer.R | 8 DesignLibrary-0.1.2/DesignLibrary/R/multi_arm_designer.R | 16 + DesignLibrary-0.1.2/DesignLibrary/R/pretest_posttest_designer.R | 8 DesignLibrary-0.1.2/DesignLibrary/R/process_tracing_designer.R | 9 - DesignLibrary-0.1.2/DesignLibrary/R/randomized_response_designer.R | 3 DesignLibrary-0.1.2/DesignLibrary/R/regression_discontinuity_designer.R | 2 DesignLibrary-0.1.2/DesignLibrary/R/spillover_designer.R |only DesignLibrary-0.1.2/DesignLibrary/R/two_arm_attrition_designer.R | 1 DesignLibrary-0.1.2/DesignLibrary/R/two_arm_designer.R |only DesignLibrary-0.1.2/DesignLibrary/R/two_by_two_designer.R |only DesignLibrary-0.1.2/DesignLibrary/inst/extdata/overview.csv | 14 - DesignLibrary-0.1.2/DesignLibrary/man/binary_iv_designer.Rd |only DesignLibrary-0.1.2/DesignLibrary/man/block_cluster_two_arm_designer.Rd | 15 + DesignLibrary-0.1.2/DesignLibrary/man/mediation_analysis_designer.Rd | 4 DesignLibrary-0.1.2/DesignLibrary/man/process_tracing_designer.Rd | 6 DesignLibrary-0.1.2/DesignLibrary/man/spillover_designer.Rd |only DesignLibrary-0.1.2/DesignLibrary/man/two_arm_designer.Rd |only DesignLibrary-0.1.2/DesignLibrary/man/two_by_two_designer.Rd |only DesignLibrary-0.1.2/DesignLibrary/tests/testthat/test_designers.R | 81 ++++++---- DesignLibrary-0.1.2/DesignLibrary/tests/testthat/test_diagnose_designers.R |only DesignLibrary-0.1.2/DesignLibrary/tests/testthat/test_fanout.R |only DesignLibrary-0.1.2/DesignLibrary/tests/testthat/test_overview_table.R | 5 DesignLibrary-0.1.2/DesignLibrary/tests/testthat/test_simulate_designers.R |only 39 files changed, 216 insertions(+), 126 deletions(-)
Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <imarinfr@optocom.es>
Maintainer: Ivan Marin-Franch <imarinfr@optocom.es>
Diff between visualFields versions 0.5.4 dated 2018-06-20 and 0.5.5 dated 2018-11-12
visualFields-0.5.4/visualFields/R/colormapgraph2.R |only visualFields-0.5.4/visualFields/R/vflayout2.R |only visualFields-0.5.4/visualFields/R/vflayout2_legoplot.R |only visualFields-0.5.4/visualFields/R/vflayout2_poplr.R |only visualFields-0.5.4/visualFields/R/vflayout2ghr.R |only visualFields-0.5.4/visualFields/R/vfplot2.R |only visualFields-0.5.4/visualFields/R/vfplot2_poplr.R |only visualFields-0.5.4/visualFields/R/vfplotloc2.R |only visualFields-0.5.4/visualFields/man/colormapgraph2.Rd |only visualFields-0.5.4/visualFields/man/vflayout2.Rd |only visualFields-0.5.4/visualFields/man/vflayout2_legoplot.Rd |only visualFields-0.5.4/visualFields/man/vflayout2_poplr.Rd |only visualFields-0.5.4/visualFields/man/vflayout2ghr.Rd |only visualFields-0.5.4/visualFields/man/vfplot2.Rd |only visualFields-0.5.4/visualFields/man/vfplot2_poplr.Rd |only visualFields-0.5.4/visualFields/man/vfplotloc2.Rd |only visualFields-0.5.5/visualFields/DESCRIPTION | 12 - visualFields-0.5.5/visualFields/MD5 | 36 --- visualFields-0.5.5/visualFields/NAMESPACE | 146 ++++++-------- visualFields-0.5.5/visualFields/R/vfplot.R | 4 visualFields-0.5.5/visualFields/R/vfplot_poplr.R | 4 visualFields-0.5.5/visualFields/R/vfstats.R | 37 +-- visualFields-0.5.5/visualFields/inst/news.txt | 5 visualFields-0.5.5/visualFields/man/hist_poplr.Rd | 2 visualFields-0.5.5/visualFields/man/poplr.Rd | 2 visualFields-0.5.5/visualFields/man/poplr_cstat.Rd | 2 visualFields-0.5.5/visualFields/man/poplr_pstat.Rd | 2 27 files changed, 116 insertions(+), 136 deletions(-)
Title: Basic Functions to Investigate Metabolomics Data Matrices
Description: A set of functions to investigate raw data from (metabol)omics experiments intended to be used on a raw data matrix, i.e. following peak picking and signal deconvolution. Functions can be used to normalize data, detect biomarkers and perform sample classification.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between MetabolomicsBasics versions 1.0 dated 2018-03-23 and 1.1 dated 2018-11-12
DESCRIPTION | 14 +-- MD5 | 48 +++++----- NAMESPACE | 32 +++++-- R/AdjustSymbols.R | 2 R/ClassificationCV.R | 187 +++++++++++++++++++++++------------------ R/ClassificationHistogram.R | 13 -- R/ClassificationWrapper.R | 47 +++++----- R/MBoxplot.R | 25 +++-- R/MetaboliteANOVA.R | 10 +- R/PlotMetabolitePCA.R | 4 R/RemoveFactorsByANOVA.R | 14 +-- R/met-data.R | 2 R/raw-data.R | 2 R/sam-data.R | 2 man/CheckForOutliers.Rd | 4 man/ClassificationCV.Rd | 39 +------- man/ClassificationHistogram.Rd | 14 --- man/ClassificationWrapper.Rd | 26 +++-- man/MetaboliteANOVA.Rd | 4 man/PlotMetabolitePCA.Rd | 5 - man/RemoveFactorsByANOVA.Rd | 6 - man/RestrictedPCA.Rd | 4 man/met.Rd | 4 man/raw.Rd | 4 man/sam.Rd | 4 25 files changed, 275 insertions(+), 241 deletions(-)
More information about MetabolomicsBasics at CRAN
Permanent link
Title: Delineate Region of Interests (ROI's) and Extract Time-Series
Data from Digital Repeat Photography Images
Description: Digital repeat photography and near-surface remote sensing have been used by environmental scientists to study the environmental change for nearly a decade. However, a user-friendly, reliable, and robust platform to extract color-based statistics and time-series from a large stack of images is still lacking. Here, we present an interactive open-source toolkit, called 'xROI', that facilitate the process time-series extraction and improve the quality of the final data. 'xROI' provides a responsive environment for scientists to interactively a) delineate regions of interest (ROI), b) handle field of view (FOV) shifts, and c) extract and export time series data characterizing image color (i.e. red, green and blue channel digital numbers for the defined ROI). Using 'xROI', user can detect FOV shifts without minimal difficulty. The software gives user the opportunity to readjust the mask files or redraw new ones every time an FOV shift occurs. 'xROI' helps to significantly improve data accuracy and continuity.
Author: Bijan Seyednasrollah, Thomas Milliman, Andrew D. Richardson
Maintainer: Bijan Seyednasrollah <bijan.s.nasr@gmail.com>
Diff between xROI versions 0.9.10 dated 2018-11-02 and 0.9.11 dated 2018-11-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ README.md | 37 +++++++++++++++++++++++++++++++------ inst/doc/Launch-xROI.R | 5 ----- inst/doc/Launch-xROI.Rmd | 27 +++++++++++++-------------- inst/doc/Launch-xROI.html | 32 ++++++++++++++------------------ vignettes/Launch-xROI.Rmd | 27 +++++++++++++-------------- 7 files changed, 81 insertions(+), 67 deletions(-)
Title: Star Trek Fonts Collection
Description: Provides a collection of true type and open type Star Trek-themed fonts.
Author: Matthew Leonawicz [aut, cre] (<https://orcid.org/0000-0001-9452-2771>)
Maintainer: Matthew Leonawicz <matt_leonawicz@esource.com>
Diff between trekfont versions 0.9.2 dated 2018-05-23 and 0.9.3 dated 2018-11-12
DESCRIPTION | 19 ++++++++++++------- MD5 | 6 +++--- NEWS.md | 6 +++++- README.md | 22 ++++++++++++++++++---- 4 files changed, 38 insertions(+), 15 deletions(-)
Title: Develop a 'Telegram Bot' with R
Description: Provides a pure interface for the 'Telegram Bot API' <http://core.telegram.org/bots/api>. In addition to the pure API implementation, it features a number of tools to make the development of 'Telegram' bots with R easy and straightforward, providing an easy-to-use interface that takes some work off the programmer.
Author: Ernest Benedito [aut, cre]
Maintainer: Ernest Benedito <ebeneditos@gmail.com>
Diff between telegram.bot versions 2.0.0 dated 2018-11-10 and 2.1.0 dated 2018-11-12
telegram.bot-2.0.0/telegram.bot/R/filters.R |only telegram.bot-2.0.0/telegram.bot/man/Filters.Rd |only telegram.bot-2.1.0/telegram.bot/DESCRIPTION | 6 telegram.bot-2.1.0/telegram.bot/MD5 | 78 +++++----- telegram.bot-2.1.0/telegram.bot/NAMESPACE | 2 telegram.bot-2.1.0/telegram.bot/NEWS.md | 13 + telegram.bot-2.1.0/telegram.bot/R/bot.R | 13 + telegram.bot-2.1.0/telegram.bot/R/commandhandler.R | 2 telegram.bot-2.1.0/telegram.bot/R/messagefilters.R |only telegram.bot-2.1.0/telegram.bot/R/messagehandler.R | 4 telegram.bot-2.1.0/telegram.bot/R/replymarkup.R | 26 +-- telegram.bot-2.1.0/telegram.bot/R/updater.R | 3 telegram.bot-2.1.0/telegram.bot/README.md | 16 +- telegram.bot-2.1.0/telegram.bot/build/vignette.rds |binary telegram.bot-2.1.0/telegram.bot/inst/doc/set-a-proxy.R |only telegram.bot-2.1.0/telegram.bot/inst/doc/set-a-proxy.Rmd |only telegram.bot-2.1.0/telegram.bot/inst/doc/set-a-proxy.html |only telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-basic-functionalities.R | 4 telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-basic-functionalities.Rmd | 14 - telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-basic-functionalities.html | 18 +- telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-building-a-bot.Rmd | 6 telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-building-a-bot.html | 10 - telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-custom-filters.R | 2 telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-custom-filters.Rmd | 4 telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-custom-filters.html | 8 - telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-introduction.R | 13 - telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-introduction.Rmd | 19 +- telegram.bot-2.1.0/telegram.bot/inst/doc/telegrambot-introduction.html | 25 +-- telegram.bot-2.1.0/telegram.bot/man/Bot.Rd | 3 telegram.bot-2.1.0/telegram.bot/man/CommandHandler.Rd | 2 telegram.bot-2.1.0/telegram.bot/man/ForceReply.Rd | 6 telegram.bot-2.1.0/telegram.bot/man/InlineKeyboardMarkup.Rd | 6 telegram.bot-2.1.0/telegram.bot/man/MessageFilters.Rd |only telegram.bot-2.1.0/telegram.bot/man/MessageHandler.Rd | 4 telegram.bot-2.1.0/telegram.bot/man/ReplyKeyboardMarkup.Rd | 6 telegram.bot-2.1.0/telegram.bot/man/ReplyKeyboardRemove.Rd | 8 - telegram.bot-2.1.0/telegram.bot/man/Updater.Rd | 3 telegram.bot-2.1.0/telegram.bot/man/sendMessage.Rd | 4 telegram.bot-2.1.0/telegram.bot/man/sendPhoto.Rd | 4 telegram.bot-2.1.0/telegram.bot/vignettes/set-a-proxy.Rmd |only telegram.bot-2.1.0/telegram.bot/vignettes/telegrambot-basic-functionalities.Rmd | 14 - telegram.bot-2.1.0/telegram.bot/vignettes/telegrambot-building-a-bot.Rmd | 6 telegram.bot-2.1.0/telegram.bot/vignettes/telegrambot-custom-filters.Rmd | 4 telegram.bot-2.1.0/telegram.bot/vignettes/telegrambot-introduction.Rmd | 19 +- 44 files changed, 199 insertions(+), 176 deletions(-)
Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of
Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>,
<DOI:10.1037/10409-008>. Penalized maximum likelihood
estimation and Markov Chain Monte Carlo estimation are
also provided, see Luedtke, Robitzsch and Wagner (2018)
<DOI:10.1037/met0000155>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between STARTS versions 0.4-24 dated 2018-06-08 and 0.5-28 dated 2018-11-12
DESCRIPTION | 20 +- MD5 | 86 ++++++------ NAMESPACE | 4 R/RcppExports.R |only R/coef.starts_uni.R | 4 R/digamma2.R |only R/logLik.starts_uni.R | 4 R/plot.starts_uni.R | 4 R/starts_cov.R | 8 - R/starts_deprecated.R | 8 - R/starts_estimate_description.R | 6 R/starts_estimate_model_fit.R | 14 +- R/starts_estimate_model_fit_rmsea.R | 8 - R/starts_estimate_model_fit_srmr.R | 6 R/starts_ic_add.R | 8 - R/starts_sim1dim.R | 13 - R/starts_summary_print_computation_time.R | 10 - R/starts_summary_print_ic.R | 29 ++-- R/starts_uni_cov.R | 35 +---- R/starts_uni_cov_pars.R | 8 - R/starts_uni_estimate.R | 115 ++++++++--------- R/starts_uni_estimate_prepare_fitting.R | 36 ++--- R/starts_uni_estimate_prepare_fitting_prior_model.R | 20 +- R/starts_uni_estimate_prepare_fitting_prior_variance.R | 6 R/starts_uni_estimate_proc.R | 58 +++++--- R/starts_uni_estimate_proc_modify_suff_stat.R | 8 - R/starts_uni_estimate_variance_proportions_mcmc.R | 6 R/starts_uni_estimate_variance_proportions_pml.R | 16 +- R/starts_uni_sim.R | 32 ++-- R/starts_vector_with_names.R | 4 R/summary.starts_uni.R | 105 +++++++-------- R/summary_starts_uni_print_model_fit.R | 14 +- R/vcov.starts_uni.R | 4 R/zzz.R | 16 +- README.md | 2 build |only data/data.starts01a.rda |binary data/data.starts01b.rda |binary data/data.starts02.rda |binary inst/NEWS | 17 ++ man/STARTS-package.Rd | 40 +---- man/STARTS-utilities.Rd |only man/data.starts.Rd | 30 ++-- man/starts_uni.Rd | 90 ++++++------- src |only 45 files changed, 454 insertions(+), 440 deletions(-)
Title: A Server-Side File System Viewer for Shiny
Description: Provides functionality for client-side navigation of
the server side file system in shiny apps. In case the app is running
locally this gives the user direct access to the file system without the
need to "download" files to a temporary location. Both file and folder
selection as well as file saving is available.
Author: Thomas Lin Pedersen [cre, aut],
Vincent Nijs [aut],
Thomas Schaffner [aut],
Eric Nantz [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between shinyFiles versions 0.7.1 dated 2018-09-18 and 0.7.2 dated 2018-11-12
DESCRIPTION | 12 MD5 | 18 - NAMESPACE | 2 NEWS.md | 21 + R/dirchoose.R | 41 +-- R/filechoose.R | 18 + R/filesave.R | 16 - inst/www/shinyFiles.js | 605 ++++++++++++++++++++++++++++++++++++++++++++-- inst/www/styles.css | 22 + man/shinyFiles-package.Rd | 1 10 files changed, 696 insertions(+), 60 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis functions
of the geographical information system (GIS) 'SAGA' (System for Automated
Geoscientific Analyses) from within R by running the command line version of
SAGA. This package furthermore provides several R functions for handling ASCII
grids, including a flexible framework for applying local functions (including
predict methods of fitted models) and focal functions to multiple grids. SAGA
GIS is available under GPLv2 / LGPLv2 licence from
<http://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] (<https://orcid.org/0000-0001-6640-679X>),
Donovan Bangs [aut],
Marc Becker [aut],
Patrick Schratz [ctb] (<https://orcid.org/0000-0003-0748-6624>),
Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 1.2.0 dated 2018-07-04 and 1.3.0 dated 2018-11-12
DESCRIPTION | 14 LICENSE | 678 +-- MD5 | 140 NAMESPACE | 187 - R/RSAGA-core.R | 2482 ++++++------- R/RSAGA-modules.R | 5989 ++++++++++++++++----------------- R/RSAGA-package.R | 116 R/RSAGA-utils.R | 130 R/gridtools.R | 4200 +++++++++++------------ R/landslides.R | 158 build/vignette.rds |binary inst/doc/RSAGA.R | 236 - inst/doc/RSAGA.Rmd | 545 +-- inst/doc/RSAGA.html | 974 ++--- man/RSAGA-package.Rd | 126 man/centervalue.Rd | 50 man/create.variable.name.Rd | 49 man/focal.function.Rd | 256 - man/grid.predict.Rd | 158 man/grid.to.xyz.Rd | 69 man/landslides.Rd | 176 man/match.arg.ext.Rd | 126 man/multi.focal.function.Rd | 290 - man/pick.from.points.Rd | 340 - man/read.ascii.grid.Rd | 209 - man/relative.position.Rd | 87 man/resid.median.Rd | 81 man/rsaga.add.grid.values.to.points.Rd | 76 man/rsaga.close.gaps.Rd | 110 man/rsaga.contour.Rd | 80 man/rsaga.copy.sgrd.Rd | 50 man/rsaga.env.Rd | 188 - man/rsaga.esri.to.sgrd.Rd | 76 man/rsaga.esri.wrapper.Rd | 136 man/rsaga.fill.sinks.Rd | 118 man/rsaga.filter.gauss.Rd | 72 man/rsaga.filter.simple.Rd | 83 man/rsaga.geoprocessor.Rd | 189 - man/rsaga.get.modules.Rd | 182 - man/rsaga.get.modules.path.Rd | 41 man/rsaga.get.usage.Rd | 90 man/rsaga.get.version.Rd | 80 man/rsaga.grid.calculus.Rd | 172 man/rsaga.grid.to.points.Rd | 110 man/rsaga.hillshade.Rd | 98 man/rsaga.html.help.Rd | 78 man/rsaga.import.gdal.Rd | 516 +- man/rsaga.insolation.Rd | 166 man/rsaga.intersect.polygons.Rd | 166 man/rsaga.inverse.distance.Rd | 138 man/rsaga.lib.prefix.Rd | 70 man/rsaga.local.morphometry.Rd | 164 man/rsaga.parallel.processing.Rd | 213 - man/rsaga.pisr.Rd | 242 - man/rsaga.pisr2.Rd | 217 - man/rsaga.set.env.Rd | 54 man/rsaga.sgrd.to.esri.Rd | 124 man/rsaga.sink.removal.Rd | 84 man/rsaga.sink.route.Rd | 80 man/rsaga.slope.asp.curv.Rd | 275 - man/rsaga.solar.radiation.Rd | 160 man/rsaga.target.Rd | 120 man/rsaga.topdown.processing.Rd | 237 - man/rsaga.union.polygons.Rd | 164 man/rsaga.wetness.index.Rd | 138 man/set.file.extension.Rd | 74 man/wind.shelter.Rd | 140 tests/testthat.R | 10 tests/testthat/test-core.R | 44 tests/testthat/test-modules.R | 361 - vignettes/RSAGA.Rmd | 545 +-- 71 files changed, 12221 insertions(+), 12176 deletions(-)
Title: Tools to Conduct Meteorological Normalisation on Air Quality
Data
Description: An integrated set of tools to allow data users to conduct
meteorological normalisation on air quality data. This meteorological
normalisation technique uses predictive random forest models to remove
variation of pollutant concentrations so trends and interventions can be
explored in a robust way. For examples, see Grange et al. (2018)
<doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019)
<doi:10.1016/j.scitotenv.2018.10.344>.
Author: Stuart K. Grange [cre, aut] (<https://orcid.org/0000-0003-4093-3596>)
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>
Diff between rmweather versions 0.1.2 dated 2018-07-16 and 0.1.3 dated 2018-11-12
rmweather-0.1.2/rmweather/R/no_global_variable_notes.R |only rmweather-0.1.3/rmweather/DESCRIPTION | 19 +- rmweather-0.1.3/rmweather/MD5 | 75 +++++----- rmweather-0.1.3/rmweather/NAMESPACE | 1 rmweather-0.1.3/rmweather/NEWS.md | 8 + rmweather-0.1.3/rmweather/R/data_london.R | 2 rmweather-0.1.3/rmweather/R/data_london_normalised.R | 2 rmweather-0.1.3/rmweather/R/dplyr_re_exports.R | 2 rmweather-0.1.3/rmweather/R/rmw_do_all.R | 5 rmweather-0.1.3/rmweather/R/rmw_find_breakpoints.R | 8 - rmweather-0.1.3/rmweather/R/rmw_model_statistics.R | 10 - rmweather-0.1.3/rmweather/R/rmw_normalise.R | 15 -- rmweather-0.1.3/rmweather/R/rmw_partial_dependencies.R | 5 rmweather-0.1.3/rmweather/R/rmw_predict_the_test_set.R | 2 rmweather-0.1.3/rmweather/R/rmw_prepare_data.R | 8 - rmweather-0.1.3/rmweather/R/rmw_train_model.R | 6 rmweather-0.1.3/rmweather/R/rmweather_plotting_functions.R | 6 rmweather-0.1.3/rmweather/R/zzz.R |only rmweather-0.1.3/rmweather/README.md | 17 +- rmweather-0.1.3/rmweather/data/data_london.rda |binary rmweather-0.1.3/rmweather/data/data_london_normalised.rda |binary rmweather-0.1.3/rmweather/data/model_london.rda |binary rmweather-0.1.3/rmweather/inst |only rmweather-0.1.3/rmweather/man/data_london.Rd | 2 rmweather-0.1.3/rmweather/man/data_london_normalised.Rd | 2 rmweather-0.1.3/rmweather/man/figures/normalised_no2_example.png |binary rmweather-0.1.3/rmweather/man/rmw_do_all.Rd | 6 rmweather-0.1.3/rmweather/man/rmw_find_breakpoints.Rd | 6 rmweather-0.1.3/rmweather/man/rmw_model_statistics.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_normalise.Rd | 7 rmweather-0.1.3/rmweather/man/rmw_partial_dependencies.Rd | 5 rmweather-0.1.3/rmweather/man/rmw_plot_normalised.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_plot_partial_dependencies.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_plot_test_prediction.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_predict.Rd | 3 rmweather-0.1.3/rmweather/man/rmw_predict_the_test_set.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_prepare_data.Rd | 2 rmweather-0.1.3/rmweather/man/rmw_train_model.Rd | 9 - rmweather-0.1.3/rmweather/tests/testthat/test_01_utilities.R | 4 rmweather-0.1.3/rmweather/tests/testthat/test_02_rmw_functions.R | 38 +++-- 40 files changed, 154 insertions(+), 131 deletions(-)
Title: Powerful Classes for HTTP Requests and Responses
Description: In order to facilitate parsing of http requests and creating
appropriate responses this package provides two classes to handle a lot of
the housekeeping involved in working with http exchanges. The infrastructure
builds upon the 'rook' specification and is thus well suited to be combined
with 'httpuv' based web servers.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between reqres versions 0.2.1 dated 2017-10-25 and 0.2.2 dated 2018-11-12
reqres-0.2.1/reqres/man/figures/reqres_logo.png |only reqres-0.2.2/reqres/DESCRIPTION | 11 ++++---- reqres-0.2.2/reqres/MD5 | 28 +++++++++++----------- reqres-0.2.2/reqres/NEWS.md | 4 +++ reqres-0.2.2/reqres/R/formatters.R | 6 +++- reqres-0.2.2/reqres/R/parsers.R | 6 +++- reqres-0.2.2/reqres/R/reqres-package.R |only reqres-0.2.2/reqres/R/request.R | 8 ++++-- reqres-0.2.2/reqres/R/response.R | 6 +++- reqres-0.2.2/reqres/README.md | 2 - reqres-0.2.2/reqres/man/Request.Rd | 6 +++- reqres-0.2.2/reqres/man/Response.Rd | 6 +++- reqres-0.2.2/reqres/man/figures/logo.png |only reqres-0.2.2/reqres/man/formatters.Rd | 14 +++++++---- reqres-0.2.2/reqres/man/parsers.Rd | 10 +++++-- reqres-0.2.2/reqres/man/reqres-package.Rd |only reqres-0.2.2/reqres/tests/testthat/test-request.R | 2 - 17 files changed, 74 insertions(+), 35 deletions(-)
Title: Maximum Likelihood Estimation of DNA Methylation and
Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions
of 5-mC and 5-hmC in the DNA using information from BS-conversion,
TAB-conversion, and oxBS-conversion methods. One can use information from all three methods
or any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and
Kiihl et al. (2018, to appear).
Author: Samara Kiihl [aut, cre],
Maria Jose Martinez-Garrido [aut],
Arce Domingo-Relloso [aut],
Jose Bermudez [aut],
Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>
Diff between MLML2R versions 0.3.0 dated 2018-09-30 and 0.3.1 dated 2018-11-12
MLML2R-0.3.0/MLML2R/data/MethylatedBS_sim.rda |only MLML2R-0.3.0/MLML2R/data/MethylatedOxBS_sim.rda |only MLML2R-0.3.0/MLML2R/data/MethylatedTAB_sim.rda |only MLML2R-0.3.0/MLML2R/data/UnMethylatedBS_sim.rda |only MLML2R-0.3.0/MLML2R/data/UnMethylatedOxBS_sim.rda |only MLML2R-0.3.0/MLML2R/data/UnMethylatedTAB_sim.rda |only MLML2R-0.3.0/MLML2R/man/MethylatedBS_sim.Rd |only MLML2R-0.3.0/MLML2R/man/MethylatedOxBS_sim.Rd |only MLML2R-0.3.0/MLML2R/man/MethylatedTAB_sim.Rd |only MLML2R-0.3.0/MLML2R/man/UnMethylatedBS_sim.Rd |only MLML2R-0.3.0/MLML2R/man/UnMethylatedOxBS_sim.Rd |only MLML2R-0.3.0/MLML2R/man/UnMethylatedTAB_sim.Rd |only MLML2R-0.3.1/MLML2R/DESCRIPTION | 8 MLML2R-0.3.1/MLML2R/MD5 | 51 +- MLML2R-0.3.1/MLML2R/R/MLML.R | 92 +-- MLML2R-0.3.1/MLML2R/R/data.R | 24 MLML2R-0.3.1/MLML2R/data/C_BS_sim.rda |only MLML2R-0.3.1/MLML2R/data/C_OxBS_sim.rda |only MLML2R-0.3.1/MLML2R/data/C_TAB_sim.rda |only MLML2R-0.3.1/MLML2R/data/T_BS_sim.rda |only MLML2R-0.3.1/MLML2R/data/T_OxBS_sim.rda |only MLML2R-0.3.1/MLML2R/data/T_TAB_sim.rda |only MLML2R-0.3.1/MLML2R/inst/doc/vignette.R | 437 +++++++++++------ MLML2R-0.3.1/MLML2R/inst/doc/vignette.Rmd | 510 ++++++++++++++------- MLML2R-0.3.1/MLML2R/inst/doc/vignette.pdf |binary MLML2R-0.3.1/MLML2R/man/C_BS_sim.Rd |only MLML2R-0.3.1/MLML2R/man/C_OxBS_sim.Rd |only MLML2R-0.3.1/MLML2R/man/C_TAB_sim.Rd |only MLML2R-0.3.1/MLML2R/man/MLML.Rd | 90 +-- MLML2R-0.3.1/MLML2R/man/T_BS_sim.Rd |only MLML2R-0.3.1/MLML2R/man/T_OxBS_sim.Rd |only MLML2R-0.3.1/MLML2R/man/T_TAB_sim.Rd |only MLML2R-0.3.1/MLML2R/vignettes/Data_sim2.rds |binary MLML2R-0.3.1/MLML2R/vignettes/Real1_estimates.pdf |binary MLML2R-0.3.1/MLML2R/vignettes/Real2a_estimates.pdf |binary MLML2R-0.3.1/MLML2R/vignettes/Real3a_estimates.pdf |only MLML2R-0.3.1/MLML2R/vignettes/True_parameters.pdf |binary MLML2R-0.3.1/MLML2R/vignettes/refs.bib | 171 ++++--- MLML2R-0.3.1/MLML2R/vignettes/vignette.Rmd | 510 ++++++++++++++------- 39 files changed, 1230 insertions(+), 663 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.1.9 dated 2018-08-31 and 0.2.0 dated 2018-11-12
DESCRIPTION | 15 + MD5 | 58 +++---- NEWS.md | 12 + R/area_types.R | 32 ---- R/deprivation_decile.R | 33 ++-- R/fingertipsR.R | 4 R/fingertips_data.R | 20 -- R/indicators.R | 52 ++---- R/profiles.R | 7 R/retrieve_data.R | 127 ++++++++-------- R/select_indicators.R | 3 R/utils.R |only inst/doc/lifeExpectancy.Rmd | 2 inst/doc/lifeExpectancy.html | 269 ++++++++++++++--------------------- inst/doc/selectIndicatorsRedRed.html | 2 man/area_types.Rd | 1 man/category_types.Rd | 1 man/deprivation_decile.Rd | 9 - man/fingertips_data.Rd | 5 man/fingertips_redred.Rd | 1 man/get_fingertips_api.Rd |only man/indicator_areatypes.Rd | 1 man/indicator_metadata.Rd | 5 man/indicator_order.Rd | 1 man/indicators.Rd | 1 man/indicators_unique.Rd | 1 man/nearest_neighbours.Rd | 1 man/profiles.Rd | 1 tests/testthat/test-deprivation.R | 16 +- tests/testthat/test-extract.R | 4 vignettes/lifeExpectancy.Rmd | 2 31 files changed, 322 insertions(+), 364 deletions(-)
Title: Fifty-Fifty MANOVA
Description: General linear modeling with multiple responses (MANCOVA). An
overall p-value for each model term is calculated by the 50-50 MANOVA
method, which handles collinear responses. Rotation testing is used
to compute adjusted single response p-values according to familywise
error rates and false discovery rates.
Author: Øyvind Langsrud [aut, cre],
Bjørn-Helge Mevik [aut]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between ffmanova versions 0.2-2 dated 2012-12-01 and 0.9.1 dated 2018-11-12
DESCRIPTION | 36 +++-- MD5 | 84 +++++++------ NAMESPACE | 69 ++++------- R/addNames.R |only R/adjust.R | 16 ++ R/c2df.R | 1 R/c2m.R | 1 R/ffmanova-package.R |only R/ffmanova.R | 152 ++++++++++++++++++++++++- R/ffmanova_div.R | 83 +++++++++++++ R/ffmanovatest.R | 96 +++++++++++++++ R/linregEnd.R | 1 R/linregEst.R | 44 +++++++ R/linregStart.R | 1 R/m2c.R | 32 +++++ R/manova_5050.R | 43 ++++++- R/myorth.R | 26 ++++ R/rotationtest.R | 58 +++++++++ R/stdize.R | 43 ++++++- R/summaries.R | 22 +++ R/unitest.R | 39 ++++++ R/x_Obj.R | 47 +++++++ R/xy_Obj.R | 39 ++++++ man/adjust.Rd | 52 ++++---- man/dressing.Rd | 124 ++++++++++---------- man/ffmanova.Rd | 297 +++++++++++++++++++++++++------------------------ man/ffmanovatest.Rd | 114 ++++++++++-------- man/fixModelMatrix.Rd | 121 ++++++++++--------- man/linregEst.Rd | 123 ++++++++++---------- man/m2c.Rd | 95 ++++++++------- man/manova5050.Rd | 106 +++++++++-------- man/matlabColon.Rd | 67 ++++++----- man/multiPvalues.Rd | 86 +++++++------- man/multiStatistics.Rd | 60 ++++----- man/my_pValueF.Rd | 57 ++++----- man/myorth.Rd | 83 +++++++------ man/norm.Rd | 51 ++++---- man/orth_D.Rd | 60 +++++---- man/print.ffmanova.Rd | 66 ++++++---- man/rotationtest.Rd | 132 ++++++++++++--------- man/stdize.Rd | 104 +++++++++-------- man/unitest.Rd | 112 +++++++++--------- man/x_Obj.Rd | 89 +++++++------- man/xy_Obj.Rd | 99 +++++++++------- 44 files changed, 1922 insertions(+), 1109 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>
Diff between Directional versions 3.3 dated 2018-07-11 and 3.4 dated 2018-11-12
DESCRIPTION | 10 +- MD5 | 44 +++++---- NAMESPACE | 9 + R/dirda.cv.R | 212 +++++++++++++++++++++++++++------------------ R/fishkent.R | 2 R/group.gof.R | 1 R/iagesag.R |only R/makefolds.R |only R/racg.R | 9 - R/spher.cor.R | 10 +- R/spher.reg.R | 2 R/sphereplot.R |only R/spml.reg.R | 2 man/Directional-package.Rd | 4 man/ESAGmle.Rd | 10 +- man/dirda.cv.Rd | 19 +--- man/fishkent.Rd | 3 man/iagesag.Rd |only man/kent.mle.Rd | 2 man/makefolds.Rd |only man/spher.reg.Rd | 2 man/spherconc.test.Rd | 2 man/sphereplot.Rd |only man/spml.reg.Rd | 9 + man/vmf.contour.Rd | 2 man/wood.mle.Rd | 2 26 files changed, 198 insertions(+), 158 deletions(-)
Title: Serialize R Objects to JSON, JavaScript Object Notation
Description: This is a package that allows conversion to and from
data in Javascript object notation (JSON) format.
This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code
and allows R programmers to read and convert JSON content to R objects.
This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON
and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases.
This package uses methods and is readily extensible by defining methods for different classes,
vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R.
The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional
options to allow customizing the generation and processing of JSON content.
This package uses libjson rather than implementing yet another JSON parser. The aim is to support
other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang [aut, cre] (<https://orcid.org/0000-0003-0159-1546>),
ninja9578 [aut] (Author of included libjson sources)
Maintainer: ORPHANED
Diff between RJSONIO versions 1.3-0 dated 2014-07-28 and 1.3-1 dated 2018-11-12
CRAN_changes |only Changes | 10 ++++ Changes.html | 24 ++++++++-- DESCRIPTION | 21 ++++++-- MD5 | 56 ++++++++++++----------- R/json.R | 19 ++++---- README | 3 + cleanup | 4 + cleanup.in | 4 + configure | 8 +++ configure.in | 9 +++ src/JSON_parser.c | 10 ++-- src/Makevars.in | 4 - src/Makevars.win | 6 +- src/RJSON.c | 24 +++++----- src/init.c |only src/libjson/Source/JSONChildren.cpp | 26 ++++++----- src/libjson/Source/JSONChildren.h | 75 ++++++++++++++++---------------- src/libjson/Source/JSONDefs/GNU_C.h | 4 + src/libjson/Source/JSONMemory.h | 2 src/libjson/Source/JSONNode.h | 2 src/libjson/Source/JSONSharedString.h | 10 ++-- src/libjson/Source/JSONStream.h | 17 +++---- src/libjson/Source/JSONWorker.cpp | 8 +-- src/libjson/Source/internalJSONNode.cpp | 2 src/libjson/Source/internalJSONNode.h | 4 - src/libjson/Source/libjson.cpp | 10 ++-- src/rlibjson.c | 20 +++++++- src/rparser.c | 5 -- tests/stringFun.R | 2 30 files changed, 237 insertions(+), 152 deletions(-)
Title: Tools for Quantitative Risk Management
Description: Functions and data sets for reproducing selected results from
the book "Quantitative Risk Management: Concepts, Techniques and Tools".
Furthermore, new developments and auxiliary functions for Quantitative
Risk Management practice.
Author: Marius Hofert [aut, cre],
Kurt Hornik [aut],
Alexander J. McNeil [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrmtools versions 0.0-9 dated 2018-04-28 and 0.0-10 dated 2018-11-12
qrmtools-0.0-10/qrmtools/DESCRIPTION | 6 qrmtools-0.0-10/qrmtools/MD5 | 66 qrmtools-0.0-10/qrmtools/NAMESPACE | 17 qrmtools-0.0-10/qrmtools/R/BMM.R |only qrmtools-0.0-10/qrmtools/R/GPD.R | 8 qrmtools-0.0-10/qrmtools/R/GPDtail.R |only qrmtools-0.0-10/qrmtools/R/POT.R |only qrmtools-0.0-10/qrmtools/R/VaR_ES_bounds.R | 4 qrmtools-0.0-10/qrmtools/R/fit_GEV.R | 10 qrmtools-0.0-10/qrmtools/R/graphics.R | 10 qrmtools-0.0-10/qrmtools/R/risk_measures.R | 12 qrmtools-0.0-10/qrmtools/TODO | 3 qrmtools-0.0-10/qrmtools/build/vignette.rds |binary qrmtools-0.0-10/qrmtools/inst/NEWS.Rd | 20 qrmtools-0.0-10/qrmtools/inst/doc/ARMA_GARCH_VaR.R | 156 qrmtools-0.0-10/qrmtools/inst/doc/ARMA_GARCH_VaR.Rmd | 161 - qrmtools-0.0-10/qrmtools/inst/doc/ARMA_GARCH_VaR.html | 600 ++- qrmtools-0.0-10/qrmtools/inst/doc/VaR_bounds.R | 275 + qrmtools-0.0-10/qrmtools/inst/doc/VaR_bounds.Rmd | 404 +- qrmtools-0.0-10/qrmtools/inst/doc/VaR_bounds.html | 1610 +++++----- qrmtools-0.0-10/qrmtools/inst/doc/geometric_risk_measures.html | 543 ++- qrmtools-0.0-10/qrmtools/man/GEV.Rd | 5 qrmtools-0.0-10/qrmtools/man/GEV_shape_plot.Rd |only qrmtools-0.0-10/qrmtools/man/GPD.Rd | 11 qrmtools-0.0-10/qrmtools/man/GPD_shape_plot.Rd | 30 qrmtools-0.0-10/qrmtools/man/GPDtail.Rd |only qrmtools-0.0-10/qrmtools/man/edf_plot.Rd | 4 qrmtools-0.0-10/qrmtools/man/fire.Rd | 2 qrmtools-0.0-10/qrmtools/man/matrix_plot.Rd | 21 qrmtools-0.0-10/qrmtools/man/risk_measures.Rd | 13 qrmtools-0.0-10/qrmtools/man/tail_plot.Rd | 25 qrmtools-0.0-10/qrmtools/src/VaR_bounds.c | 3 qrmtools-0.0-10/qrmtools/src/VaR_bounds.h | 3 qrmtools-0.0-10/qrmtools/src/init.c | 4 qrmtools-0.0-10/qrmtools/vignettes/ARMA_GARCH_VaR.Rmd | 161 - qrmtools-0.0-10/qrmtools/vignettes/VaR_bounds.Rmd | 404 +- qrmtools-0.0-9/qrmtools/R/POT_method.R |only 37 files changed, 2905 insertions(+), 1686 deletions(-)
Title: Free Brazilian Repository for Open Soil Data
Description: Making the access to the Free Brazilian Repository for Open Soil Data <http://www.ufsm.br/febr/> as easy
as possible.
Author: Alessandro Samuel-Rosa [aut, cre]
(<https://orcid.org/0000-0003-0877-1320>),
Universidade Federal de Santa Maria [fnd],
Universidade Tecnológica Federal do Paraná [fnd]
Maintainer: Alessandro Samuel-Rosa <alessandrosamuelrosa@gmail.com>
Diff between febr versions 1.0-0 dated 2018-03-09 and 1.0.1 dated 2018-11-12
DESCRIPTION | 21 ++--- MD5 | 46 +++++------ NEWS.md | 61 ++++++++++++++ R/febrHelper.R | 63 +++++++++++++-- R/header.R | 4 R/layer.R | 80 ++++++++++++------- R/layersHelper.R | 28 +++--- R/observation.R | 70 +++++++++++----- R/standard.R | 8 + R/unit.R | 3 build/vignette.rds |binary inst/doc/febr.R | 9 +- inst/doc/febr.Rmd | 14 +-- inst/doc/febr.html | 220 ++++++++++++++++++----------------------------------- man/dataset.Rd | 6 - man/febr.Rd | 4 man/febr2spdf.Rd | 2 man/header.Rd | 16 +-- man/layer.Rd | 32 +++---- man/metadata.Rd | 6 - man/observation.Rd | 22 ++--- man/standard.Rd | 7 - man/unit.Rd | 2 vignettes/febr.Rmd | 14 +-- 24 files changed, 416 insertions(+), 322 deletions(-)