Title: The Generalized DINA Model Framework
Description: A set of psychometric tools for cognitive diagnosis modeling based on the generalized deterministic inputs, noisy and gate (G-DINA) model by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> and its extensions, including the sequential G-DINA model by Ma and de la Torre (2016) <DOI:10.1111/bmsp.12070> for polytomous responses, and the polytomous G-DINA model by Chen and de la Torre <DOI:10.1177/0146621613479818> for polytomous attributes. Joint attribute distribution can be independent, saturated, higher-order, loglinear smoothed or structured. Q-matrix validation, item and model fit statistics, model comparison at test and item level and differential item functioning can also be conducted. A graphical user interface is also provided.
Author: Wenchao Ma [aut, cre, cph],
Jimmy de la Torre [aut, cph],
Miguel Sorrel [ctb],
Zhehan Jiang [ctb]
Maintainer: Wenchao Ma <wenchao.ma@ua.edu>
Diff between GDINA versions 2.7.0 dated 2019-08-08 and 2.7.3 dated 2019-08-19
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++-------- NEWS.md | 6 ++++ R/GDI.R | 9 +++++- R/MultipleGroup_Estimation.R | 2 - R/SingleGroup_Estimation.R | 2 - R/print.GDINA.R | 6 ++-- R/score.R | 13 +++++++- R/summary.GDINA.R | 6 ++-- README.md | 2 - inst/doc/GDINA.html | 4 +- inst/shiny/server.R | 63 ++++++++++--------------------------------- inst/shiny/ui.R | 2 - 13 files changed, 69 insertions(+), 78 deletions(-)
Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm.
There was used quantitative models with a closed-form solution. Thus package is based on linear algebra operations.
The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used.
A single evaluation of a quantitative model for the multiple imputations is another major enhancement.
Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between miceFast versions 0.2.3 dated 2018-05-06 and 0.5.1 dated 2019-08-19
DESCRIPTION | 17 MD5 | 75 ++-- NAMESPACE | 40 ++ NEWS.md | 11 R/RcppExports.R | 213 ------------ R/VIF.R |only R/data.R |only R/fill_NA.R |only R/fill_NA_N.R |only build/vignette.rds |binary data |only inst/doc/miceFast-intro.R | 197 ++++++++++- inst/doc/miceFast-intro.Rmd | 272 +++++++++++---- inst/doc/miceFast-intro.html | 638 +++++++++++++++++++++++++++++------- inst/extdata/images/g1.png |binary inst/extdata/images/g10.png |only inst/extdata/images/g2.png |binary inst/extdata/images/g3.png |binary inst/extdata/images/g4.png |binary inst/extdata/images/g5.png |binary inst/extdata/images/g6.png |binary inst/extdata/images/g7.png |binary inst/extdata/images/g8.png |binary inst/extdata/images/g9.png |binary inst/extdata/images/g_summary.png |binary inst/extdata/performance_validity.R | 193 ++++++---- man/VIF.Rd | 52 +- man/air_miss.Rd |only man/fill_NA.Rd | 223 +++++++++--- man/fill_NA_N.Rd | 226 +++++++++--- man/miceFast-package.Rd | 8 src/Makevars | 2 src/Makevars.win | 2 src/R_funs.cpp | 314 ++++------------- src/RcppExports.cpp | 32 - src/corrData.cpp | 10 src/miceFast.h | 2 src/miceFast_class.cpp | 8 src/miceFast_quantmodels.cpp | 25 - tests/testthat.R | 3 tests/testthat/test-imputes_funcs.R | 167 ++++++++- vignettes/miceFast-intro.Rmd | 272 +++++++++++---- 42 files changed, 2005 insertions(+), 997 deletions(-)
Title: Sparse VAR/VECM Models Estimation
Description: A wrapper for sparse VAR/VECM time series models estimation
using penalties like ENET (Elastic Net), SCAD (Smoothly Clipped
Absolute Deviation) and MCP (Minimax Concave Penalty).
Based on the work of Sumanta Basu and George Michailidis
<doi:10.1214/15-AOS1315>.
Author: Simone Vazzoler [aut, cre]
Maintainer: Simone Vazzoler <svazzole@gmail.com>
Diff between sparsevar versions 0.0.10 dated 2016-11-07 and 0.0.11 dated 2019-08-19
sparsevar-0.0.10/sparsevar/inst/doc/using.pdf |only sparsevar-0.0.11/sparsevar/DESCRIPTION | 30 - sparsevar-0.0.11/sparsevar/MD5 | 107 ++- sparsevar-0.0.11/sparsevar/NAMESPACE | 4 sparsevar-0.0.11/sparsevar/NEWS.md | 4 sparsevar-0.0.11/sparsevar/R/createSparseMatrix.R | 7 sparsevar-0.0.11/sparsevar/R/fitVAR.R | 225 ++++++-- sparsevar-0.0.11/sparsevar/R/fitVARX.R |only sparsevar-0.0.11/sparsevar/R/fitVECM.R | 98 +++ sparsevar-0.0.11/sparsevar/R/impulseResponse.R | 376 ++++++++++++-- sparsevar-0.0.11/sparsevar/R/mcSimulations.R | 9 sparsevar-0.0.11/sparsevar/R/plotIRF.R | 121 +++- sparsevar-0.0.11/sparsevar/R/plotMatrix.R | 67 +- sparsevar-0.0.11/sparsevar/R/simulateVAR.R | 43 - sparsevar-0.0.11/sparsevar/R/simulateVARX.R |only sparsevar-0.0.11/sparsevar/R/timeSlice.R | 72 +- sparsevar-0.0.11/sparsevar/R/twoStepOLS.R |only sparsevar-0.0.11/sparsevar/R/utils.R | 2 sparsevar-0.0.11/sparsevar/R/utilsVAR.R | 82 ++- sparsevar-0.0.11/sparsevar/README.md | 29 - sparsevar-0.0.11/sparsevar/build/vignette.rds |binary sparsevar-0.0.11/sparsevar/inst/doc/using.R | 7 sparsevar-0.0.11/sparsevar/inst/doc/using.html |only sparsevar-0.0.11/sparsevar/man/accuracy.Rd | 1 sparsevar-0.0.11/sparsevar/man/bootstrappedVAR.Rd | 1 sparsevar-0.0.11/sparsevar/man/checkImpulseZero.Rd | 1 sparsevar-0.0.11/sparsevar/man/checkIsVar.Rd | 1 sparsevar-0.0.11/sparsevar/man/companionVAR.Rd | 1 sparsevar-0.0.11/sparsevar/man/computeForecasts.Rd | 1 sparsevar-0.0.11/sparsevar/man/createSparseMatrix.Rd | 3 sparsevar-0.0.11/sparsevar/man/decomposePi.Rd |only sparsevar-0.0.11/sparsevar/man/errorBandsIRF.Rd | 8 sparsevar-0.0.11/sparsevar/man/fitVAR.Rd | 41 - sparsevar-0.0.11/sparsevar/man/fitVARX.Rd |only sparsevar-0.0.11/sparsevar/man/fitVECM.Rd | 1 sparsevar-0.0.11/sparsevar/man/frobNorm.Rd | 1 sparsevar-0.0.11/sparsevar/man/impulseResponse.Rd | 1 sparsevar-0.0.11/sparsevar/man/informCrit.Rd | 1 sparsevar-0.0.11/sparsevar/man/l1norm.Rd | 1 sparsevar-0.0.11/sparsevar/man/l2norm.Rd | 1 sparsevar-0.0.11/sparsevar/man/lInftyNorm.Rd | 1 sparsevar-0.0.11/sparsevar/man/maxNorm.Rd | 1 sparsevar-0.0.11/sparsevar/man/mcSimulations.Rd | 6 sparsevar-0.0.11/sparsevar/man/multiplot.Rd |only sparsevar-0.0.11/sparsevar/man/plotIRF.Rd | 1 sparsevar-0.0.11/sparsevar/man/plotIRFGrid.Rd | 5 sparsevar-0.0.11/sparsevar/man/plotMatrix.Rd | 5 sparsevar-0.0.11/sparsevar/man/plotVAR.Rd | 10 sparsevar-0.0.11/sparsevar/man/plotVECM.Rd | 1 sparsevar-0.0.11/sparsevar/man/simulateVAR.Rd | 1 sparsevar-0.0.11/sparsevar/man/simulateVARX.Rd |only sparsevar-0.0.11/sparsevar/man/spectralNorm.Rd | 1 sparsevar-0.0.11/sparsevar/man/spectralRadius.Rd | 1 sparsevar-0.0.11/sparsevar/man/testGranger.Rd | 1 sparsevar-0.0.11/sparsevar/man/transformData.Rd | 1 sparsevar-0.0.11/sparsevar/man/varENET.Rd | 1 sparsevar-0.0.11/sparsevar/man/varMCP.Rd | 1 sparsevar-0.0.11/sparsevar/man/varSCAD.Rd | 5 sparsevar-0.0.11/sparsevar/tests/testthat/testIsWorking.R | 7 59 files changed, 1005 insertions(+), 391 deletions(-)
Title: Client for 'Mapzen' and Related Map APIs
Description: Provides an interface to 'Mapzen'-based APIs (including
geocode.earth, Nextzen, and NYC GeoSearch) for geographic search
and geocoding, isochrone calculation, and vector data to draw map tiles.
See <https://mapzen.com/documentation/> for more information. The original
Mapzen has gone out of business, but 'rmapzen' can be set up to work with
any provider who implements the Mapzen API.
Author: Tarak Shah [aut, cre],
Daniel Possenriede [ctb]
Maintainer: Tarak Shah <tarak.shah@gmail.com>
Diff between rmapzen versions 0.4.1 dated 2018-10-07 and 0.4.2 dated 2019-08-19
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/geocode.R | 2 +- R/mz-bbox.R | 8 ++++---- R/mz-coordinates.R | 2 +- R/tidy.R | 21 +++++++++++++++------ R/vector-tiles.R | 10 ++++++---- build/vignette.rds |binary inst/doc/rmapzen-introduction.html | 36 ++++++++++++++++++------------------ man/mz_vector_tiles.Rd | 4 +++- 11 files changed, 67 insertions(+), 50 deletions(-)
Title: A Bayesian Nonparametric Algorithm for Time Series Clustering
Description: Performs the algorithm for time series clustering described in Nieto-Barajas and Contreras-Cristan (2014).
Author: Martell-Juarez, D.A. & Nieto-Barajas, L.E.
Maintainer: David Alejandro Martell Juarez <alex91599@gmail.com>
Diff between BNPTSclust versions 1.1 dated 2015-04-19 and 2.0 dated 2019-08-19
BNPTSclust-1.1/BNPTSclust/inst/doc/BNPTSclust1.1.pdf |only BNPTSclust-1.1/BNPTSclust/vignettes |only BNPTSclust-2.0/BNPTSclust/DESCRIPTION | 10 BNPTSclust-2.0/BNPTSclust/MD5 | 57 +-- BNPTSclust-2.0/BNPTSclust/NAMESPACE | 5 BNPTSclust-2.0/BNPTSclust/R/clusterplots.R | 19 - BNPTSclust-2.0/BNPTSclust/R/designmatrices.R | 56 +-- BNPTSclust-2.0/BNPTSclust/R/scaleandperiods.R | 59 ++-- BNPTSclust-2.0/BNPTSclust/R/tseriesca.R | 178 ++++++------ BNPTSclust-2.0/BNPTSclust/R/tseriescm.R | 152 +++++----- BNPTSclust-2.0/BNPTSclust/R/tseriescq.R | 278 ++++++++++--------- BNPTSclust-2.0/BNPTSclust/data/gdp.rda |binary BNPTSclust-2.0/BNPTSclust/data/houses.rda |binary BNPTSclust-2.0/BNPTSclust/data/stocks.rda |binary BNPTSclust-2.0/BNPTSclust/data/tseriesca.out.rda |binary BNPTSclust-2.0/BNPTSclust/data/tseriescm.out.rda |binary BNPTSclust-2.0/BNPTSclust/data/tseriescq.out.rda |binary BNPTSclust-2.0/BNPTSclust/inst/doc/BNPTSclust2_0.pdf |only BNPTSclust-2.0/BNPTSclust/man/BNPTSclust-package.Rd | 10 BNPTSclust-2.0/BNPTSclust/man/clusterplots.Rd | 9 BNPTSclust-2.0/BNPTSclust/man/designmatrices.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/diagplots.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/gdp.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/houses.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/scaleandperiods.Rd | 11 BNPTSclust-2.0/BNPTSclust/man/stocks.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/tseriesca.Rd | 45 --- BNPTSclust-2.0/BNPTSclust/man/tseriesca.out.Rd | 2 BNPTSclust-2.0/BNPTSclust/man/tseriescm.Rd | 33 -- BNPTSclust-2.0/BNPTSclust/man/tseriescq.Rd | 29 - BNPTSclust-2.0/BNPTSclust/man/tseriescq.out.Rd | 2 31 files changed, 507 insertions(+), 458 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 1.1.0 dated 2019-07-23 and 1.2.0 dated 2019-08-19
DESCRIPTION | 6 +- MD5 | 36 ++++++------ NAMESPACE | 1 R/cli.R | 6 +- R/install.R | 35 +++++++++--- R/model-serve.R | 49 ++++++++++++++++- R/model.R | 4 - R/project-run.R | 4 - R/python.R | 17 +++++- R/tracking-experiments.R | 30 +++++++++- man/install_mlflow.Rd | 18 +++++- man/mlflow_get_experiment.Rd | 2 man/mlflow_load_model.Rd | 2 man/mlflow_rfunc_serve.Rd | 9 ++- man/mlflow_run.Rd | 4 - man/mlflow_set_experiment_tag.Rd |only tests/testthat.R | 2 tests/testthat/test-bypass-conda.R |only tests/testthat/test-serve.R | 82 +++++++++++++++++++++++++++++ tests/testthat/test-tracking-experiments.R | 43 +++++++++++++++ 20 files changed, 300 insertions(+), 50 deletions(-)
Title: Mosquito Gene Drive Explorer
Description: Provides a model designed to be a reliable testbed where various gene
drive interventions for mosquito-borne diseases control. It is being developed to
accommodate the use of various mosquito-specific gene drive systems within a
population dynamics framework that allows migration of individuals between patches
in landscape. Previous work developing the population dynamics can be found in Deredec et al.
(2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>,
and extensions to accommodate basic CRISPR homing dynamics in Marshall et al. (2017)
<doi:10.1038/s41598-017-02744-7>.
Author: Héctor Manuel Sánchez Castellanos [aut, cre],
Jared Bennett [aut],
Sean Wu [aut],
John M. Marshall [aut]
Maintainer: Héctor Manuel Sánchez Castellanos <sanchez.hmsc@berkeley.edu>
Diff between MGDrivE versions 1.0.0 dated 2019-07-12 and 1.1.0 dated 2019-08-19
DESCRIPTION | 11 +- MD5 | 121 ++++++++++++------------- NEWS.md |only R/Cube-CRISPR2MF.R | 2 R/Cube-KillerRescue.R | 4 R/Cube-RIDL.R | 2 R/Cube-Wolbachia.R | 2 R/MGDrivE-Auxiliary.R | 26 ++--- R/MGDrivE-Graphics.R | 50 +++++++--- R/MGDrivE.R | 6 - R/Network-Class.R | 23 ++-- R/Network-Parameters.R | 6 - R/Network-Simulation.R | 40 +------- R/Patch-Migration.R | 4 R/Patch-Simulation.R | 8 - R/RcppExports.R | 69 +++++++++++--- R/zzz.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/mgdrive_examples.R | 12 ++ inst/doc/mgdrive_examples.Rmd | 48 +++++---- inst/doc/mgdrive_examples.html | 91 +++++++++--------- inst/doc/mgdrive_math.Rmd | 8 - inst/doc/mgdrive_math.html | 8 - inst/doc/mgdrive_run.Rmd | 10 +- inst/doc/mgdrive_run.html | 14 +- man/MGDrivE-Model.Rd | 2 man/MGDrivE.Rd | 4 man/Network.Rd | 17 +-- man/calcAquaticStageSurvivalProbability.Rd | 2 man/calcAquaticStagesSurvivalProbability.Rd | 2 man/calcCos.Rd | 2 man/calcDensityDependentDeathRate.Rd | 2 man/calcExpKernel.Rd | 10 ++ man/calcGammaKernel.Rd | 11 ++ man/calcHaversine.Rd | 4 man/calcHurdleExpKernel.Rd | 29 ++++- man/calcLognormalKernel.Rd | 10 ++ man/calcQuantiles.Rd | 14 +- man/calcVinEll.Rd | 2 man/calcZeroInflation.Rd | 2 man/cubeHomingDrive.Rd | 2 man/cubeKillerRescue.Rd | 4 man/cubeRIDL.Rd | 2 man/cubeWolbachia.Rd | 2 man/get_wildType_Network.Rd | 2 man/oneDay_admSurvival_deterministic_Patch.Rd | 2 man/oneDay_admSurvival_stochastic_Patch.Rd | 2 man/oneDay_af1Survival_deterministic_Patch.Rd | 2 man/oneDay_af1Survival_stochastic_Patch.Rd | 2 man/oneDay_migrationOut_deterministic_Patch.Rd | 2 man/oneDay_migrationOut_stochastic_Patch.Rd | 2 man/plotMGDrivEMult.Rd | 6 - man/rDirichlet.Rd | 2 man/retrieveOutput.Rd | 2 src/MGDrivE-Auxilary.cpp | 4 src/MGDrivE-DistanceFunctions.cpp | 12 +- src/MGDrivE-Kernels.cpp | 63 +++++++++++-- src/RcppExports.cpp | 8 - vignettes/mgdrive_examples.Rmd | 48 +++++---- vignettes/mgdrive_math.Rmd | 8 - vignettes/mgdrive_run.Rmd | 10 +- 62 files changed, 521 insertions(+), 346 deletions(-)
Title: Access the NASS 'Quick Stats' API
Description: Interface to access data via the United States Department of
Agriculture's National Agricultural Statistical Service (NASS) 'Quick Stats'
web API <https://quickstats.nass.usda.gov/api>. Convenience functions
facilitate building queries based on available parameters and valid parameter
values.
Author: Nicholas Potter [aut, cre],
Jonathan Adams [ctb],
Joseph Stachelek [ctb],
Julia Piaskowski [ctb],
Adam Sparks [rev],
Neal Richardson [ctb, rev]
Maintainer: Nicholas Potter <potter.nicholas@gmail.com>
Diff between rnassqs versions 0.4.0 dated 2019-05-03 and 0.5.0 dated 2019-08-19
rnassqs-0.4.0/rnassqs/R/data.R |only rnassqs-0.4.0/rnassqs/man/expand_list.Rd |only rnassqs-0.4.0/rnassqs/man/nassqs_area.Rd |only rnassqs-0.4.0/rnassqs/man/nassqs_yield.Rd |only rnassqs-0.4.0/rnassqs/man/release_questions.Rd |only rnassqs-0.4.0/rnassqs/tests/testthat/test-local.R |only rnassqs-0.4.0/rnassqs/tests/testthat/test-oncran.R |only rnassqs-0.5.0/rnassqs/DESCRIPTION | 27 rnassqs-0.5.0/rnassqs/MD5 | 71 rnassqs-0.5.0/rnassqs/NAMESPACE | 6 rnassqs-0.5.0/rnassqs/NEWS.md | 21 rnassqs-0.5.0/rnassqs/R/auth.R |only rnassqs-0.5.0/rnassqs/R/helpers.R | 113 - rnassqs-0.5.0/rnassqs/R/nassqs.R | 262 --- rnassqs-0.5.0/rnassqs/R/params.R |only rnassqs-0.5.0/rnassqs/R/request.R |only rnassqs-0.5.0/rnassqs/R/wrappers.R |only rnassqs-0.5.0/rnassqs/README.md | 345 +++- rnassqs-0.5.0/rnassqs/build/vignette.rds |binary rnassqs-0.5.0/rnassqs/inst/CITATION |only rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.R | 7 rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.Rmd | 255 ++- rnassqs-0.5.0/rnassqs/inst/doc/rnassqs.html | 781 +++++----- rnassqs-0.5.0/rnassqs/inst/examples/example_parameters.R | 3 rnassqs-0.5.0/rnassqs/inst/figures |only rnassqs-0.5.0/rnassqs/man/nassqs.Rd | 40 rnassqs-0.5.0/rnassqs/man/nassqs_GET.Rd | 80 - rnassqs-0.5.0/rnassqs/man/nassqs_acres.Rd |only rnassqs-0.5.0/rnassqs/man/nassqs_auth.Rd | 39 rnassqs-0.5.0/rnassqs/man/nassqs_check.Rd | 15 rnassqs-0.5.0/rnassqs/man/nassqs_fields.Rd | 11 rnassqs-0.5.0/rnassqs/man/nassqs_param_values.Rd | 17 rnassqs-0.5.0/rnassqs/man/nassqs_params.Rd | 24 rnassqs-0.5.0/rnassqs/man/nassqs_parse.Rd | 52 rnassqs-0.5.0/rnassqs/man/nassqs_record_count.Rd | 20 rnassqs-0.5.0/rnassqs/man/nassqs_yields.Rd |only rnassqs-0.5.0/rnassqs/man/rnassqs-package.Rd | 11 rnassqs-0.5.0/rnassqs/tests/testthat/helper.R |only rnassqs-0.5.0/rnassqs/tests/testthat/quickstats.nass.usda.gov |only rnassqs-0.5.0/rnassqs/tests/testthat/test-auth.R |only rnassqs-0.5.0/rnassqs/tests/testthat/test-helpers.R |only rnassqs-0.5.0/rnassqs/tests/testthat/test-params.R |only rnassqs-0.5.0/rnassqs/tests/testthat/test-request.R |only rnassqs-0.5.0/rnassqs/tests/testthat/test-wrappers.R |only rnassqs-0.5.0/rnassqs/tests/testthat/testdata |only rnassqs-0.5.0/rnassqs/vignettes/rnassqs.Rmd | 255 ++- 46 files changed, 1419 insertions(+), 1036 deletions(-)
Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database
(<https://www.pangaea.de>), including functions for searching for data,
fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea'
'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre],
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pangaear versions 0.6.0 dated 2018-01-03 and 0.8.0 dated 2019-08-19
DESCRIPTION | 20 +- LICENSE | 2 MD5 | 78 ++++---- NAMESPACE | 5 NEWS.md | 18 + R/caching.R | 52 ++++- R/onload.R |only R/pangaear-package.R | 9 R/pg_cache.R | 26 -- R/pg_data.R | 65 +++--- R/pg_list_identifiers.R | 4 R/pg_search.R | 2 R/pg_search_es.R | 2 R/zzz.R | 62 ++++++ README.md | 225 ++++++++++++----------- build/vignette.rds |binary inst/doc/pangaear_vignette.Rmd | 339 +++++++++++++++++++----------------- inst/doc/pangaear_vignette.html | 339 +++++++++++++++++++----------------- inst/vign/pangaear_vignette.md | 339 +++++++++++++++++++----------------- man/pangaear-package.Rd | 7 man/pg_cache.Rd |only man/pg_cache_clear-defunct.Rd |only man/pg_cache_list-defunct.Rd |only man/pg_data.Rd | 42 +--- man/pg_get_record.Rd | 1 man/pg_identify.Rd | 1 man/pg_list_identifiers.Rd | 1 man/pg_list_metadata_formats.Rd | 1 man/pg_list_records.Rd | 1 man/pg_list_sets.Rd | 1 man/pg_search_es.Rd | 4 tests/fixtures |only tests/testthat/helper-pangaear.R |only tests/testthat/test-oai_functions.R | 45 ++-- tests/testthat/test-pg_data.R | 36 +++ tests/testthat/test-pg_identify.R | 6 tests/testthat/test-pg_search.r | 26 +- tests/testthat/test-pg_search_es.R | 13 - vignettes/pangaear_vignette.Rmd | 339 +++++++++++++++++++----------------- 39 files changed, 1197 insertions(+), 914 deletions(-)
Title: Probing Factor-Dependent Long-Range Contacts using Regression
with Higher-Order Interaction Terms
Description: We propose a generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.
Author: Raphael Mourad
Maintainer: Raphael Mourad <raphael.mourad@ibcg.biotoul.fr>
Diff between HiCglmi versions 1.3 dated 2018-04-18 and 1.4 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/HiCglmiMiscFun.R | 2 +- build/partial.rdb |binary data/dataExample.RData |binary 5 files changed, 9 insertions(+), 9 deletions(-)
Title: Automated R Instructor
Description: Create videos from 'R Markdown' documents, or images and audio
files. These images can come from image files or HTML slides, and the audio
files can be provided by the user or computer voice narration can be created
using 'Amazon Polly'. The purpose of this package is to allow users to create
accessible, translatable, and reproducible lecture videos. See
<https://aws.amazon.com/polly/> for more information.
Author: Sean Kross [aut, cre],
John Muschelli [ctb]
Maintainer: Sean Kross <sean@seankross.com>
Diff between ari versions 0.3.1 dated 2019-07-13 and 0.3.2 dated 2019-08-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/ari_spin.R | 8 ++++++++ R/ari_stitch.R | 51 +++++++++++++++++++++++++++++++++++++++++++-------- R/ffmpeg_codecs.R | 15 ++++++++++++++- man/ari_stitch.Rd | 23 ++++++++++++++++++++--- 7 files changed, 100 insertions(+), 21 deletions(-)
Title: Geo-Processing Helper Functions
Description: Helper tools for facilitating basic geo-processing tasks, such as reading/writing
Shapefiles, merging polygons or generating terrain contours.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between APfun versions 0.1.3 dated 2018-04-03 and 0.1.4 dated 2019-08-19
APfun-0.1.3/APfun/man/APKML2SHP.Rd |only APfun-0.1.4/APfun/DESCRIPTION | 12 +-- APfun-0.1.4/APfun/MD5 | 19 +++-- APfun-0.1.4/APfun/NAMESPACE | 2 APfun-0.1.4/APfun/NEWS.md | 4 + APfun-0.1.4/APfun/R/APSHP.R | 90 ++++++++-------------------- APfun-0.1.4/APfun/R/APcontours.R | 7 +- APfun-0.1.4/APfun/R/APpolygonize.R | 9 +- APfun-0.1.4/APfun/R/APrasterfiles.R |only APfun-0.1.4/APfun/README.md | 2 APfun-0.1.4/APfun/data/rasterExtensions.rda |only APfun-0.1.4/APfun/man/APrasterFiles.Rd |only APfun-0.1.4/APfun/man/rasterExtensions.Rd |only 13 files changed, 61 insertions(+), 84 deletions(-)
Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests.
P-values based on response surface regressions are available for both tests.
P-values based on bootstrap are available for seasonal unit root tests.
Author: Javier López-de-Lacalle [aut],
Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between uroot versions 2.0-11 dated 2019-08-19 and 2.1-0 dated 2019-08-19
uroot-2.0-11/uroot/R/hegy-test.R.in |only uroot-2.0-11/uroot/cleanup |only uroot-2.0-11/uroot/cleanup.win |only uroot-2.0-11/uroot/configure |only uroot-2.0-11/uroot/configure.ac |only uroot-2.0-11/uroot/configure.win |only uroot-2.0-11/uroot/src |only uroot-2.0-11/uroot/tools |only uroot-2.1-0/uroot/DESCRIPTION | 13 +++++-------- uroot-2.1-0/uroot/MD5 | 23 +++++------------------ uroot-2.1-0/uroot/NAMESPACE | 2 -- uroot-2.1-0/uroot/NEWS | 9 ++++++++- uroot-2.1-0/uroot/R/hegy-test.R |only uroot-2.1-0/uroot/inst/doc/uroot-intro.pdf |binary 14 files changed, 18 insertions(+), 29 deletions(-)
Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique
for dimension reduction. The algorithm was described by McInnes and
Healy (2018) in <arXiv:1802.03426>. This package provides an interface
for two implementations. One is written from scratch, including components
for nearest-neighbor search and for embedding. The second implementation
is a wrapper for 'python' package 'umap-learn' (requires separate
installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between umap versions 0.2.2.0 dated 2019-05-13 and 0.2.3 dated 2019-08-19
DESCRIPTION | 9 - MD5 | 50 +++--- NAMESPACE | 2 R/RcppExports.R | 21 ++ R/coo.R | 2 R/umap_checks.R | 89 ++++++------ R/umap_naive.R | 287 +++++++++++++++++++--------------------- R/umap_universal.R | 123 ++++++++++------- R/utils.R | 36 ++--- inst/doc/umap.R | 6 inst/doc/umap.Rmd | 67 +++++++-- inst/doc/umap.html | 87 ++++++++---- inst/doc/umap_learn.R | 1 inst/doc/umap_learn.Rmd | 16 +- inst/doc/umap_learn.html | 34 +++- man/column.seeds.Rd |only man/naive.optimize.embedding.Rd | 6 man/optimize_embedding.Rd |only man/optimize_epoch.Rd | 7 src/RcppExports.cpp | 18 ++ src/optimize.cpp | 64 ++++++++ tests/testthat/test_methods.R | 11 - tests/testthat/test_naive.R | 107 ++++++++++---- tests/testthat/test_synthetic.R | 14 - tests/testthat/test_universal.R | 26 +++ vignettes/umap.Rmd | 67 +++++++-- vignettes/umap_learn.Rmd | 16 +- 27 files changed, 747 insertions(+), 419 deletions(-)
Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source
or Commercial Software
Description: An interface to the 'mclust' package to easily
carry out latent profile analysis ("LPA"). Provides functionality to
estimate commonly-specified models. Follows a tidy approach, in that
output is in the form of a data frame that can subsequently be
computed on. Also has functions to interface to the commercial 'MPlus'
software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Caspar van Lissa [aut],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 1.0.3 dated 2019-07-30 and 1.0.4 dated 2019-08-19
DESCRIPTION | 6 +- MD5 | 24 ++++++---- NEWS.md | 4 + R/calc_functions.R | 10 ++-- R/empathy.R |only R/estimate-profiles-mclust.R | 24 +++++++--- R/estimate-profiles-mplus.R | 3 - R/id_edu.R |only R/plot-profiles.R | 1 data/empathy.csv |only data/id_edu.csv |only inst/doc/Introduction_to_tidyLPA.html | 66 ++++++++++++++-------------- inst/doc/benchmarking-mclust-and-mplus.html | 4 - inst/doc/introduction-to-major-changes.html | 6 +- man/empathy.Rd |only man/id_edu.Rd |only 16 files changed, 87 insertions(+), 61 deletions(-)
Title: Forecasting Using State Space Models
Description: Functions implementing Single Source of Error state space models for purposes of time series analysis and forecasting.
The package includes Exponential Smoothing (Hyndman et al., 2008, <doi: 10.1007/978-3-540-71918-2>),
SARIMA (Svetunkov & Boylan, 2019 <doi: 10.1080/00207543.2019.1600764>),
Complex Exponential Smoothing (Svetunkov & Kourentzes, 2018, <doi: 10.13140/RG.2.2.24986.29123>),
Simple Moving Average (Svetunkov & Petropoulos, 2018 <doi: 10.1080/00207543.2017.1380326>),
Vector Exponential Smoothing (de Silva et al., 2010, <doi: 10.1177/1471082X0901000401>) in state space forms,
several simulation functions and intermittent demand state space models. It also allows dealing with
intermittent demand based on the iETS framework (Svetunkov & Boylan, 2017, <doi: 10.13140/RG.2.2.35897.06242>).
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between smooth versions 2.5.2 dated 2019-07-25 and 2.5.3 dated 2019-08-19
DESCRIPTION | 10 +- MD5 | 44 +++++------ NAMESPACE | 1 NEWS | 20 +++++ R/cma.R | 2 R/es.R | 92 ++++++++++++++++++++++- R/methods.R | 5 + R/simes.R | 2 R/ssfunctions.R | 25 ++++-- R/vssFunctions.R | 57 ++++++++++++-- build/partial.rdb |binary inst/doc/ces.html | 34 ++++---- inst/doc/es.html | 140 ++++++++++++++++++------------------ inst/doc/gum.html | 18 ++-- inst/doc/oes.Rmd | 4 - inst/doc/oes.html | 189 +++++++++++++++++++++++++------------------------ inst/doc/simulate.html | 76 +++++++++---------- inst/doc/sma.html | 6 - inst/doc/smooth.html | 4 - inst/doc/ssarima.html | 30 +++---- inst/doc/ves.html | 6 - src/ssGeneral.cpp | 10 +- vignettes/oes.Rmd | 4 - 23 files changed, 471 insertions(+), 308 deletions(-)
Title: Data Sharpening
Description: Functions and data sets inspired by data sharpening -
data perturbation to achieve improved performance in
nonparametric estimation, as described in Choi, E., Hall, P.
and Rousson, V. (2000) <doi:10.1214/aos/1015957396>.
Capabilities for enhanced local linear regression function
and derivative estimation are included, as well as an
asymptotically correct iterated data sharpening estimator
for any degree of local polynomial regression estimation.
A cross-validation-based bandwidth selector is included which,
in concert with the iterated sharpener, will often provide
superior performance, according to a median integrated squared
error criterion. Sample data sets are provided to illustrate
function usage.
Author: W.J. Braun
Maintainer: W.J. Braun <john.braun@ubc.ca>
Diff between sharpData versions 1.1 dated 2019-08-02 and 1.2 dated 2019-08-19
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++++++++-- NAMESPACE | 6 ++++-- R/LL.fit.R |only R/LLmat.R |only R/LLmono.R |only R/NW.fit.R |only R/NWmat.R |only R/NWmono.R |only man/LL.fit.Rd |only man/LLmat.Rd |only man/LLmono.Rd |only man/NW.fit.Rd |only man/NWmat.Rd |only man/NWmono.Rd |only src |only 16 files changed, 24 insertions(+), 9 deletions(-)
Title: Lazy Search in R Packages, Task Views, CRAN, the Web. All-in-One
Download
Description: Search by keywords in R packages, task views, CRAN, the web and display the results in console, txt, html or pdf pages. Download the whole documentation (html index, pdf manual, vignettes, source code, etc) with a single instruction. Visualize the package dependencies. Several functions for task view maintenance and exploration of CRAN archive. Quick links to more than 70 web search engines. Lazy evaluation of non-standard content is available throughout the package and eases the use of many functions.
Author: Patrice Kiener [aut, cre] (<https://orcid.org/0000-0002-0505-9920>)
Maintainer: Patrice Kiener <fattailsr@inmodelia.com>
Diff between RWsearch versions 4.6 dated 2019-05-29 and 4.6.2 dated 2019-08-19
DESCRIPTION | 8 MD5 | 34 +- NAMESPACE | 3 NEWS | 15 + R/archivedb.R | 9 R/h_R.R | 8 R/h_engine.R | 27 +- build/vignette.rds |binary data/datalist | 4 inst/doc/RWsearch-1-Introduction.html | 258 ++++++++++---------- inst/doc/RWsearch-2-Print-Download-Doc.html | 212 ++++++++-------- inst/doc/RWsearch-3-TaskViews.html | 354 ++++++++++++++-------------- inst/doc/RWsearch-4-Web-search-engines.Rmd | 5 inst/doc/RWsearch-4-Web-search-engines.html | 78 +++--- man/archivedb.Rd | 3 man/h_R.Rd | 3 man/h_engine.Rd | 11 vignettes/RWsearch-4-Web-search-engines.Rmd | 5 18 files changed, 560 insertions(+), 477 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.100.26 dated 2019-07-08 and 0.100.30 dated 2019-08-19
DESCRIPTION | 6 - MD5 | 32 +++---- NAMESPACE | 2 R/ashape3d.R | 4 R/mesh3d.R | 191 ++++++++++++++++++++++++++++++++++++---------- build/vignette.rds |binary inst/NEWS | 13 +++ inst/doc/WebGL.html | 6 - inst/doc/legacyWebGL.html | 76 +++++++++--------- inst/doc/rgl.html | 10 +- man/as.mesh3d.ashape3d.Rd | 6 + man/mesh3d.Rd | 42 +++++----- src/Makevars.in | 1 src/gl2ps.c | 2 src/gl2ps.h | 10 +- src/scene.cpp | 3 src/subscene.cpp | 12 +- 17 files changed, 281 insertions(+), 135 deletions(-)
Title: Convert Among Citation Formats
Description: Converts among many citation formats, including 'BibTeX',
'Citeproc', 'Codemeta', 'RDF XML', 'RIS', and 'Schema.org'. A low
level 'R6' class is provided, as well as stand-alone functions
for each citation format for both read and write.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <sckott@protonmail.com>
Diff between handlr versions 0.1.0 dated 2019-02-27 and 0.2.0 dated 2019-08-19
DESCRIPTION | 8 +- MD5 | 39 ++++++------ NAMESPACE | 2 NEWS.md | 13 ++++ R/client.R | 4 + R/handl.R | 52 +++++++++++++++- R/handl_to_df.R |only R/zzz.R | 4 + README.md | 86 ++++++++++++++++++++-------- man/handl.Rd | 55 ++++++++++++++++- man/handl_to_df.Rd |only tests/testthat/test-bibtex_reader.R | 2 tests/testthat/test-bibtex_writer.R | 6 + tests/testthat/test-citeproc_reader.R | 2 tests/testthat/test-client.R | 2 tests/testthat/test-client_guesses_format.R | 2 tests/testthat/test-codemeta_reader.R | 4 + tests/testthat/test-codemeta_writer.R | 6 + tests/testthat/test-handl-class.R | 2 tests/testthat/test-handl_to_df.R |only tests/testthat/test-ris_reader.R | 4 + tests/testthat/test-ris_writer.R | 6 + 22 files changed, 247 insertions(+), 52 deletions(-)
Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles
of species distribution model (SDM) predictions.
Functionality is offered through R functions or a GUI (R Shiny app).
This tool can assist users in identifying spatial uncertainties and
making informed conservation and management decisions. The package is
further described in Woodman et al. (in press - contact author for paper).
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between eSDM versions 0.2.1 dated 2019-07-26 and 0.3.0 dated 2019-08-19
DESCRIPTION | 13 MD5 | 57 NEWS.md |only build/vignette.rds |binary inst/CITATION | 6 inst/doc/example-analysis.R | 48 inst/doc/example-analysis.Rmd | 74 inst/doc/example-analysis.html | 990 +++++----- inst/eSDM_vignette_helper.R | 24 inst/shiny/server.R | 4 inst/shiny/server_2_overlay/server_2_overlay_overlayModels.R | 2 inst/shiny/server_3_createEns/server_3_createEns_create.R | 12 inst/shiny/server_4_evalMetrics/server_4_evalMetrics.R | 57 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_plot.R | 13 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_prep.R | 39 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_renderUI.R | 10 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update.R | 94 inst/shiny/server_5_prettyPlot/server_5_prettyPlot_update_renderUI.R | 69 inst/shiny/server_6_export/server_6_export.R | 16 inst/shiny/server_other/server_plots.R | 4 inst/shiny/server_other/server_plots_funcs.R | 4 inst/shiny/server_other/server_render.R | 12 inst/shiny/server_other/server_roadmap_download.R | 35 inst/shiny/server_other/server_tables.R | 4 inst/shiny/server_other/server_workspace.R | 3 inst/shiny/ui_files/ui_0_roadmap.R | 52 inst/shiny/ui_files/ui_4_evalMetrics.R | 4 inst/shiny/ui_files/ui_5_prettyPlot.R | 63 inst/shiny/www/eSDM_manual.pdf |binary vignettes/example-analysis.Rmd | 74 30 files changed, 889 insertions(+), 894 deletions(-)
Title: Document the R Working Environment
Description: Prints out information about the R working environment
(system, R version,loaded and attached packages and versions) from a single
function "env_doc()". Optionally adds information on git repository,
tags, commits and remotes (if available).
Author: Donald Jackson [aut, cre]
Maintainer: Donald Jackson <donald.jackson@bms.com>
Diff between envDocument versions 2.4.0 dated 2017-09-19 and 2.4.1 dated 2019-08-19
DESCRIPTION | 12 - MD5 | 60 ++++---- NAMESPACE | 24 +-- NEWS.md | 4 R/env_doc.R | 182 ++++++++++++------------- R/fileStatus.R | 11 + R/getDominoInfo.R | 128 ++++++++--------- R/getGitInfo.R | 177 ++++++++++++++---------- R/getTag.R | 24 +++ R/infoNotFound.R | 10 - build/vignette.rds |binary inst/doc/envDocument-vignette.R | 26 +-- inst/doc/envDocument-vignette.Rmd | 92 ++++++------ inst/doc/envDocument-vignette.html | 236 ++++++++++++++++----------------- man/collapseInfo.Rd | 28 +-- man/envDocument-package.Rd | 78 +++++----- man/env_doc.Rd | 118 ++++++++-------- man/getDominoInfo.Rd | 40 ++--- man/getGitInfo.Rd | 46 +++--- man/getPackageInfo.Rd | 30 ++-- man/getRepo.Rd | 34 ++-- man/getScriptInfo.Rd | 42 ++--- man/getScriptPath.Rd | 46 +++--- man/getSysInfo.Rd | 32 ++-- man/get_Rversion.Rd | 28 +-- man/infoNotFound.Rd | 22 +-- man/prettyPrintInfo.Rd | 30 ++-- man/remoteInfo.Rd | 28 +-- tests/test_envDocument.html |only tests/testthat/test-gitinfo.R |only tests/testthat/test-return_dataframe.R | 38 ++--- vignettes/envDocument-vignette.Rmd | 92 ++++++------ 32 files changed, 890 insertions(+), 828 deletions(-)
Title: Automated Cytometry Gating and Annotation
Description: Given the hypothesis of a bi-modal distribution of cells for
each marker, the algorithm constructs a binary tree, the nodes of which are
subpopulations of cells. At each node, observed cells and markers are modeled
by both a family of normal distributions and a family of bi-modal normal mixture
distributions. Splitting is done according to a normalized difference of AIC
between the two families.
Author: Chariff Alkhassim, Boris Hejblum, Anthony Devaux, Van Hung Huynh Tran
Maintainer: Boris Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between cytometree versions 1.3.0 dated 2019-01-12 and 2.0.0 dated 2019-08-19
DESCRIPTION | 10 - MD5 | 38 +++- NAMESPACE | 2 NEWS.md | 3 R/AsinhTransformation.R |only R/BiexpTransformation.R |only R/CytofEM.R |only R/CytofTree.R |only R/Cytof_BinaryTree.R |only R/HIPC.R | 3 R/IMdata.R |only R/Log10Transformation.R |only R/cytometree-package.R | 4 build/vignette.rds |binary data/IMdata.RData |only data/datalist |only inst/doc/autogating_cytometree.html | 279 ++++++++++++++++++------------------ inst/doc/cytoftree.R |only inst/doc/cytoftree.Rmd |only inst/doc/cytoftree.html |only man/AsinhTransformation.Rd |only man/BiexpTransformation.Rd |only man/CytofEM.Rd |only man/CytofTree.Rd |only man/Cytof_BinaryTree.Rd |only man/HIPC.Rd | 3 man/IMdata.Rd |only man/Log10Transformation.Rd |only man/cytometree-package.Rd | 4 vignettes/cytoftree.Rmd |only 30 files changed, 191 insertions(+), 155 deletions(-)
Title: Busy Indicator for 'Shiny' Applications
Description: Add a global indicator (spinner, progress bar, gif) in your 'shiny' applications to show the user that the server is busy.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Silex Technologies [fnd] (https://www.silex-ip.com),
Tobias Ahlin [cph] (spin.css),
Chris Antonellis [cph] (freezeframe.js),
Jacobo Tabernero [cph] (nanobar.js)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between shinybusy versions 0.1.2 dated 2019-05-07 and 0.1.3 dated 2019-08-19
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/busy-spinner.R | 2 +- inst/assets/js/shinybusy.js | 22 ++++++++++++++++++++++ 5 files changed, 35 insertions(+), 8 deletions(-)
Title: Estimate (Generalized) Linear Mixed Models with Factor
Structures
Description: Utilizes the 'lme4' and 'optimx' packages (previously the optim()
function from 'stats') to estimate (generalized) linear mixed models (GLMM)
with factor structures using a profile likelihood approach, as outlined in
Jeon and Rabe-Hesketh (2012) <doi:10.3102/1076998611417628> and
Rockwood and Jeon (2019) <doi:10.1080/00273171.2018.1516541>.
Factor analysis and item response models can be extended to allow
for an arbitrary number of nested and crossed random effects,
making it useful for multilevel and cross-classified models.
Author: Minjeong Jeon [aut],
Nicholas Rockwood [aut, cre]
Maintainer: Nicholas Rockwood <nrockwood@llu.edu>
Diff between PLmixed versions 0.1.3 dated 2018-05-02 and 0.1.4 dated 2019-08-19
DESCRIPTION | 23 +- MD5 | 23 +- NAMESPACE | 1 R/PLmixed_add_functions.R | 58 +++--- R/PLmixed_main_function.R | 75 +++++-- build/vignette.rds |binary inst/CITATION |only inst/doc/PLmixed_intro.Rmd | 5 inst/doc/PLmixed_intro.html | 414 ++++++++++++++++++++++++++++++++++---------- man/PLmixed-package.Rd | 12 + man/PLmixed.Rd | 31 ++- vignettes/PLmixed_intro.Rmd | 5 vignettes/biblio.bib | 12 + 13 files changed, 476 insertions(+), 183 deletions(-)
Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Will try to fit decision trees that try to "predict" values for each column based on the values of each other column.
Along the way, each time a split is evaluated, it will take the observations that fall into each branch as a homogeneous
cluster in which it will search for outliers in the 1-d distribution of the column being predicted. Outliers are determined
according to confidence intervals on this 1-d distribution, and need to have a large gap with respect to the next observation
in sorted order to be flagged as outliers. Since outliers are searched for in a decision tree branch, it will know the conditions
that make it a rare observation compared to others that meet the same conditions, and the conditions will always be correlated
with the target variable (as it's being predicted from them). Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between outliertree versions 1.0 dated 2019-07-31 and 1.0.1 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/helpers.R | 6 +++--- src/clusters.cpp | 2 +- src/fit_model.cpp | 1 + src/outlier_tree.h | 1 - 6 files changed, 14 insertions(+), 14 deletions(-)
Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs; one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test, Generalized tests equivalent to Parametric Bootstrap and Fiducial tests. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut], Sam Weerahandi [ctb], Malwane Ananda [ctb]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between onewaytests versions 2.3 dated 2019-05-17 and 2.4 dated 2019-08-19
DESCRIPTION | 12 ++++++------ MD5 | 14 ++++++++------ NAMESPACE | 4 ++-- R/gp.test.R |only R/paircomp.R | 3 +++ R/paircomp.jt.R | 1 + man/box.test.Rd | 2 +- man/gp.test.Rd |only man/onewaytests.Rd | 2 +- 9 files changed, 22 insertions(+), 16 deletions(-)
Title: Multivariate Analysis and Visualization for Biological Data
Description: Code to support a systems biology research program from inception through publication. The methods focus on dimension reduction approaches to detect patterns in complex, multivariate experimental data and places an emphasis on informative visualizations. The goal for this project is to create a package that will evolve over time, thereby remaining relevant and reflective of current methods and techniques. As a result, we encourage suggested additions to the package, both methodological and graphical.
Author: Samuel V. Scarpino
Maintainer: Samuel V. Scarpino <scarpino@utexas.edu>
Diff between multiDimBio versions 1.1.1 dated 2016-12-16 and 1.2.0 dated 2019-08-19
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/h2Estimate.R | 29 +++++++++++++++++------------ man/multiDimBio-package.Rd | 11 ++++++----- 4 files changed, 32 insertions(+), 26 deletions(-)
Title: Weighted Metrics, Scoring Functions and Performance Measures for
Machine Learning
Description: Provides weighted versions of several metrics,
scoring functions and performance measures used in machine learning,
including average unit deviances of the Bernoulli, Tweedie, Poisson,
and Gamma distributions, see Jorgensen B. (1997, ISBN:
978-0412997112). The package also contains a weighted version of
generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN:
978-0805822236). Furthermore, 'dplyr' chains are supported.
Author: Michael Mayer [aut, cre, cph],
Christian Lorentzen [rev]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between MetricsWeighted versions 0.1.0 dated 2019-07-28 and 0.2.0 dated 2019-08-19
DESCRIPTION | 40 ++-- MD5 | 102 ++++++------ NAMESPACE | 5 NEWS.md | 10 - R/AUC.R | 22 +- R/accuracy.R | 12 - R/classification_error.R | 13 - R/deviance_bernoulli.R | 15 - R/deviance_gamma.R | 35 ++-- R/deviance_normal.R | 25 +-- R/deviance_poisson.R | 35 ++-- R/deviance_tweedie.R | 62 ++++--- R/f1_score.R | 11 - R/gini_coefficient.R | 15 - R/logLoss.R | 24 +- R/mae.R | 18 -- R/mape.R | 24 +- R/medae.R |only R/mse.R | 20 -- R/performance.R | 19 -- R/precision.R | 14 - R/r_squared.R | 31 +-- R/recall.R | 13 - R/rmse.R | 19 -- R/weighted_mean.R | 22 +- R/weighted_median.R |only R/weighted_quantile.R |only README.md | 4 inst/doc/MetricsWeighted.R | 28 +++ inst/doc/MetricsWeighted.Rmd | 54 ++++-- inst/doc/MetricsWeighted.html | 341 +++++++++++++++++++++++------------------- man/AUC.Rd | 11 - man/accuracy.Rd | 6 man/classification_error.Rd | 8 man/deviance_bernoulli.Rd | 12 - man/deviance_gamma.Rd | 24 +- man/deviance_normal.Rd | 19 -- man/deviance_poisson.Rd | 24 +- man/deviance_tweedie.Rd | 22 +- man/f1_score.Rd | 8 man/gini_coefficient.Rd | 12 - man/logLoss.Rd | 14 - man/mae.Rd | 13 - man/mape.Rd | 19 -- man/medae.Rd |only man/mse.Rd | 14 - man/performance.Rd | 11 - man/precision.Rd | 6 man/r_squared.Rd | 24 +- man/recall.Rd | 6 man/rmse.Rd | 14 - man/weighted_mean.Rd | 13 - man/weighted_median.Rd |only man/weighted_quantile.Rd |only vignettes/MetricsWeighted.Rmd | 54 ++++-- 55 files changed, 701 insertions(+), 666 deletions(-)
More information about MetricsWeighted at CRAN
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Title: A Homogeneity Test under the Presence of Measurement Errors
Description: Provides a function me.test() to test equality of distributions when observations are subject to measurement errors.
Author: DongHyuk Lee, Samiran Sinha
Maintainer: DongHyuk Lee <leedhyuk@gmail.com>
Diff between MEtest versions 1.0 dated 2019-04-25 and 1.1 dated 2019-08-19
DESCRIPTION | 8 - MD5 | 10 - NAMESPACE | 2 R/Sources_MEtest.R | 35 +++-- man/me.test.Rd | 8 - src/TScomp.f90 | 370 ++++++++++++++++++++++++++--------------------------- 6 files changed, 224 insertions(+), 209 deletions(-)
Title: Harmonic Mean p-Values and Model Averaging by Mean Maximum
Likelihood
Description: The harmonic mean p-value (HMP) test combines p-values and corrects for multiple testing while controlling the strong-sense family-wise error rate. It is more powerful than common alternatives including Bonferroni and Simes procedures when combining large proportions of all the p-values, at the cost of slightly lower power when combining small proportions of all the p-values. It is more stringent than controlling the false discovery rate, and possesses theoretical robustness to positive correlations between tests and unequal weights. It is a multi-level test in the sense that a superset of one or more significant tests is certain to be significant and conversely when the superset is non-significant, the constituent tests are certain to be non-significant. It is based on MAMML (model averaging by mean maximum likelihood), a frequentist analogue to Bayesian model averaging, and is theoretically grounded in generalized central limit theorem. For detailed examples type vignette("harmonicmeanp") after installation. Version 3.0 addresses errors in versions 1.0 and 2.0 that led function p.hmp to control the familywise error rate only in the weak sense, rather than the strong sense as intended.
Author: Daniel J. Wilson
Maintainer: Daniel Wilson <hmp.R.package@gmail.com>
Diff between harmonicmeanp versions 2.0 dated 2019-07-06 and 3.0 dated 2019-08-19
DESCRIPTION | 10 - MD5 | 24 ++-- R/hmp.R | 18 ++- build/vignette.rds |binary inst/doc/harmonicmeanp.R | 54 ++++++++-- inst/doc/harmonicmeanp.Rmd | 105 +++++++++++++------- inst/doc/harmonicmeanp.html | 230 +++++++++++++++++++++++++------------------- man/harmonicmeanp.Rd | 6 - man/hmp.stat.Rd | 2 man/p.hmp.Rd | 17 ++- man/p.mamml.Rd | 2 man/pharmonicmeanp.Rd | 2 vignettes/harmonicmeanp.Rmd | 105 +++++++++++++------- 13 files changed, 369 insertions(+), 206 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.8-3 dated 2019-05-28 and 9.8-6 dated 2019-08-19
DESCRIPTION | 8 ++--- MD5 | 23 ++++++++-------- R/Krig.family.R | 2 - R/color.scale.R | 10 +++++-- R/image.plot.R | 5 ++- R/snow.colors.R |only R/spatialProcess.R | 1 R/stationary.cov.R | 5 +++ R/tim.colors.R | 20 -------------- data/datalist | 3 +- man/image.plot.Rd | 73 +++++++++++++++++++++++++++++++---------------------- man/mKrigMLE.Rd | 16 ++++++----- man/tim.colors.Rd | 69 +++++++++++++++++++++++++++++++------------------- 13 files changed, 133 insertions(+), 102 deletions(-)
Title: Fast Embedding Guided by Self-Organizing Map
Description: Provides a smooth mapping of multidimensional points into
low-dimensional space defined by a self-organizing map. Designed to work
with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019)
<doi:10.1101/496869>.
Author: Mirek Kratochvil [aut, cre],
Sofie Van Gassen [cph],
Britt Callebaut [cph],
Yvan Saeys [cph],
Ron Wehrens [cph]
Maintainer: Mirek Kratochvil <exa.exa@gmail.com>
Diff between EmbedSOM versions 1.9 dated 2019-08-19 and 1.9.1 dated 2019-08-19
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/embed.R | 14 ++++++++++++-- R/som.R | 25 +++++++++++++++++++------ inst/doc/embedding.html | 34 +++++++++++++++++----------------- man/EmbedSOM.Rd | 2 +- man/MapDataToCodes.Rd | 4 ++-- src/embed.cpp | 2 ++ src/som.cpp | 2 +- 9 files changed, 65 insertions(+), 40 deletions(-)
Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data
analysis, drake rebuilds intermediate data objects when their
dependencies change, and it skips work when the results are already up
to date. Not every execution starts from scratch, there is native
support for parallel and distributed computing, and completed projects
have tangible evidence that they are reproducible. Extensive
documentation, from beginner-friendly tutorials to practical examples
and more, is available at the reference website
<https://ropensci.github.io/drake/> and the online manual
<https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>),
Tristan Mahr [ctb] (<https://orcid.org/0000-0002-8890-5116>),
Miles McBain [ctb] (<https://orcid.org/0000-0003-2865-2548>),
Noam Ross [ctb] (<https://orcid.org/0000-0002-2136-0000>),
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 7.5.2 dated 2019-07-21 and 7.6.1 dated 2019-08-19
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drake-7.6.1/drake/man/drake_quotes.Rd | 5 drake-7.6.1/drake/man/drake_session.Rd | 6 drake-7.6.1/drake/man/drake_slice.Rd | 5 drake-7.6.1/drake/man/drake_strings.Rd | 5 drake-7.6.1/drake/man/drake_tip.Rd | 5 drake-7.6.1/drake/man/drake_unquote.Rd | 5 drake-7.6.1/drake/man/eager_load_target.Rd | 5 drake-7.6.1/drake/man/evaluate.Rd | 4 drake-7.6.1/drake/man/evaluate_plan.Rd | 7 drake-7.6.1/drake/man/example_drake.Rd | 4 drake-7.6.1/drake/man/examples_drake.Rd | 4 drake-7.6.1/drake/man/expand.Rd | 4 drake-7.6.1/drake/man/expand_plan.Rd | 5 drake-7.6.1/drake/man/expose_imports.Rd | 7 drake-7.6.1/drake/man/failed.Rd | 4 drake-7.6.1/drake/man/figures/hist2-1.png |only drake-7.6.1/drake/man/figures/histhistory-1.png |only drake-7.6.1/drake/man/figures/readdhist-1.png |only drake-7.6.1/drake/man/figures/recoverhist-1.png |only drake-7.6.1/drake/man/file_in.Rd | 36 drake-7.6.1/drake/man/file_out.Rd | 24 drake-7.6.1/drake/man/file_store.Rd | 6 drake-7.6.1/drake/man/find_cache.Rd | 5 drake-7.6.1/drake/man/find_knitr_doc.Rd | 4 drake-7.6.1/drake/man/find_project.Rd | 7 drake-7.6.1/drake/man/from_plan.Rd | 4 drake-7.6.1/drake/man/future_build.Rd | 5 drake-7.6.1/drake/man/gather.Rd | 4 drake-7.6.1/drake/man/gather_by.Rd | 6 drake-7.6.1/drake/man/gather_plan.Rd | 7 drake-7.6.1/drake/man/get_cache.Rd | 5 drake-7.6.1/drake/man/ignore.Rd | 20 drake-7.6.1/drake/man/imported.Rd | 5 drake-7.6.1/drake/man/in_progress.Rd | 7 drake-7.6.1/drake/man/is_function_call.Rd | 4 drake-7.6.1/drake/man/isolate_example.Rd | 7 drake-7.6.1/drake/man/knitr_deps.Rd | 5 drake-7.6.1/drake/man/knitr_in.Rd | 20 drake-7.6.1/drake/man/legend_nodes.Rd | 5 drake-7.6.1/drake/man/load_basic_example.Rd | 4 drake-7.6.1/drake/man/load_main_example.Rd | 5 drake-7.6.1/drake/man/load_mtcars_example.Rd | 5 drake-7.6.1/drake/man/long_hash.Rd | 5 drake-7.6.1/drake/man/macros |only drake-7.6.1/drake/man/make.Rd | 42 drake-7.6.1/drake/man/make_imports.Rd | 5 drake-7.6.1/drake/man/make_targets.Rd | 5 drake-7.6.1/drake/man/make_with_config.Rd | 5 drake-7.6.1/drake/man/manage_memory.Rd | 5 drake-7.6.1/drake/man/map.Rd |only drake-7.6.1/drake/man/map_plan.Rd | 6 drake-7.6.1/drake/man/max_useful_jobs.Rd | 4 drake-7.6.1/drake/man/migrate_drake_project.Rd | 4 drake-7.6.1/drake/man/missed.Rd | 5 drake-7.6.1/drake/man/new_cache.Rd | 11 drake-7.6.1/drake/man/no_deps.Rd | 20 drake-7.6.1/drake/man/outdated.Rd | 5 drake-7.6.1/drake/man/parallel_stages.Rd | 4 drake-7.6.1/drake/man/parallelism_choices.Rd | 5 drake-7.6.1/drake/man/plan.Rd | 4 drake-7.6.1/drake/man/plan_analyses.Rd | 5 drake-7.6.1/drake/man/plan_drake.Rd | 4 drake-7.6.1/drake/man/plan_summaries.Rd | 5 drake-7.6.1/drake/man/plan_to_code.Rd | 6 drake-7.6.1/drake/man/plan_to_notebook.Rd | 6 drake-7.6.1/drake/man/plot_graph.Rd | 4 drake-7.6.1/drake/man/predict_load_balancing.Rd | 5 drake-7.6.1/drake/man/predict_runtime.Rd | 5 drake-7.6.1/drake/man/predict_workers.Rd | 5 drake-7.6.1/drake/man/process_import.Rd | 7 drake-7.6.1/drake/man/progress.Rd | 12 drake-7.6.1/drake/man/prune_drake_graph.Rd | 5 drake-7.6.1/drake/man/r_make.Rd | 16 drake-7.6.1/drake/man/r_recipe_wildcard.Rd | 5 drake-7.6.1/drake/man/rate_limiting_times.Rd | 4 drake-7.6.1/drake/man/read_config.Rd | 4 drake-7.6.1/drake/man/read_drake_config.Rd | 5 drake-7.6.1/drake/man/read_drake_graph.Rd | 5 drake-7.6.1/drake/man/read_drake_meta.Rd | 4 drake-7.6.1/drake/man/read_drake_plan.Rd | 5 drake-7.6.1/drake/man/read_drake_seed.Rd | 5 drake-7.6.1/drake/man/read_graph.Rd | 4 drake-7.6.1/drake/man/read_plan.Rd | 4 drake-7.6.1/drake/man/readd.Rd | 5 drake-7.6.1/drake/man/recover_cache.Rd | 12 drake-7.6.1/drake/man/recoverable.Rd | 8 drake-7.6.1/drake/man/reduce_by.Rd | 5 drake-7.6.1/drake/man/reduce_plan.Rd | 6 drake-7.6.1/drake/man/render_drake_ggraph.Rd | 7 drake-7.6.1/drake/man/render_drake_graph.Rd | 5 drake-7.6.1/drake/man/render_graph.Rd | 4 drake-7.6.1/drake/man/render_sankey_drake_graph.Rd | 7 drake-7.6.1/drake/man/render_static_drake_graph.Rd | 5 drake-7.6.1/drake/man/render_text_drake_graph.Rd | 7 drake-7.6.1/drake/man/rescue_cache.Rd | 5 drake-7.6.1/drake/man/rs_addin_loadd.Rd | 18 drake-7.6.1/drake/man/rs_addin_r_make.Rd | 8 drake-7.6.1/drake/man/rs_addin_r_outdated.Rd | 8 drake-7.6.1/drake/man/rs_addin_r_vis_drake_graph.Rd | 8 drake-7.6.1/drake/man/running.Rd | 5 drake-7.6.1/drake/man/sankey_drake_graph.Rd | 7 drake-7.6.1/drake/man/session.Rd | 4 drake-7.6.1/drake/man/shell_file.Rd | 5 drake-7.6.1/drake/man/short_hash.Rd | 5 drake-7.6.1/drake/man/show_source.Rd | 5 drake-7.6.1/drake/man/split.Rd |only drake-7.6.1/drake/man/static_drake_graph.Rd | 5 drake-7.6.1/drake/man/summaries.Rd | 4 drake-7.6.1/drake/man/target.Rd | 106 + drake-7.6.1/drake/man/target_namespaces.Rd | 6 drake-7.6.1/drake/man/text_drake_graph.Rd | 6 drake-7.6.1/drake/man/this_cache.Rd | 5 drake-7.6.1/drake/man/tracked.Rd | 5 drake-7.6.1/drake/man/transform_plan.Rd | 61 drake-7.6.1/drake/man/trigger.Rd | 5 drake-7.6.1/drake/man/triggers.Rd | 5 drake-7.6.1/drake/man/type_sum.expr_list.Rd | 3 drake-7.6.1/drake/man/use_drake.Rd | 5 drake-7.6.1/drake/man/vis_drake_graph.Rd | 5 drake-7.6.1/drake/man/workflow.Rd | 4 drake-7.6.1/drake/man/workplan.Rd | 4 drake-7.6.1/drake/tests/scenarios/tests-all.R | 2 drake-7.6.1/drake/tests/testthat/helper-checkers.R |only drake-7.6.1/drake/tests/testthat/helper-dbug.R |only drake-7.6.1/drake/tests/testthat/helper-operators.R |only drake-7.6.1/drake/tests/testthat/helper-scenarios.R |only drake-7.6.1/drake/tests/testthat/helper-testrun.R |only drake-7.6.1/drake/tests/testthat/helper-testthat.R |only drake-7.6.1/drake/tests/testthat/test-analysis.R |only drake-7.6.1/drake/tests/testthat/test-build.R |only drake-7.6.1/drake/tests/testthat/test-cache.R | 365 +++- drake-7.6.1/drake/tests/testthat/test-checks.R |only drake-7.6.1/drake/tests/testthat/test-commands.R |only drake-7.6.1/drake/tests/testthat/test-decorated-storr.R |only drake-7.6.1/drake/tests/testthat/test-deprecate.R | 18 drake-7.6.1/drake/tests/testthat/test-dsl.R | 354 ++++ drake-7.6.1/drake/tests/testthat/test-encoding.R |only drake-7.6.1/drake/tests/testthat/test-examples.R | 10 drake-7.6.1/drake/tests/testthat/test-files.R |only drake-7.6.1/drake/tests/testthat/test-flow.R |only drake-7.6.1/drake/tests/testthat/test-future.R | 2 drake-7.6.1/drake/tests/testthat/test-graph.R | 22 drake-7.6.1/drake/tests/testthat/test-hash-tables.R |only drake-7.6.1/drake/tests/testthat/test-history.R | 26 drake-7.6.1/drake/tests/testthat/test-hpc.R |only drake-7.6.1/drake/tests/testthat/test-imports.R |only drake-7.6.1/drake/tests/testthat/test-interactive.R |only drake-7.6.1/drake/tests/testthat/test-lazy.R |only drake-7.6.1/drake/tests/testthat/test-lock.R |only drake-7.6.1/drake/tests/testthat/test-memory.R | 10 drake-7.6.1/drake/tests/testthat/test-meta.R |only drake-7.6.1/drake/tests/testthat/test-missed.R |only drake-7.6.1/drake/tests/testthat/test-plans.R | 132 + drake-7.6.1/drake/tests/testthat/test-prework.R |only drake-7.6.1/drake/tests/testthat/test-queue.R |only drake-7.6.1/drake/tests/testthat/test-rng.R |only drake-7.6.1/drake/tests/testthat/test-rstudio.R |only drake-7.6.1/drake/tests/testthat/test-testing.R | 13 drake-7.6.1/drake/tests/testthat/test-time.R | 1 drake-7.6.1/drake/tests/testthat/test-utils.R | 317 --- drake-7.6.1/drake/tests/testthat/test-visuals.R | 33 drake-7.6.1/drake/tests/testthat/test-zzz-callr.R | 28 388 files changed, 3549 insertions(+), 1316 deletions(-)
Title: Comparison of Algorithms with Iterative Sample Size Estimation
Description: Functions for performing experimental comparisons of algorithms
using adequate sample sizes for power and accuracy. Implements the
methodology originally presented in Campelo and Takahashi (2019)
<doi:10.1007/s10732-018-9396-7>
for the comparison of two algorithms, and later generalised in
Campelo and Wanner (Submitted, 2019) <arxiv:1908.01720>.
Author: Felipe Campelo [aut, cre],
Fernanda Takahashi [ctb],
Elizabeth Wanner [ctb]
Maintainer: Felipe Campelo <f.campelo@aston.ac.uk>
Diff between CAISEr versions 1.0.14 dated 2019-08-02 and 1.0.15 dated 2019-08-19
DESCRIPTION | 19 +++-- MD5 | 18 ++-- NEWS.md | 5 + R/onAttach.R | 6 - R/plot_caiser.R | 2 inst/doc/Adapting_Algorithm_for_CAISEr.R | 3 inst/doc/Adapting_Algorithm_for_CAISEr.Rmd | 13 ++- inst/doc/Adapting_Algorithm_for_CAISEr.html | 101 ++++++++++++++-------------- man/plot.CAISEr.Rd | 2 vignettes/Adapting_Algorithm_for_CAISEr.Rmd | 13 ++- 10 files changed, 103 insertions(+), 79 deletions(-)
Title: Maximal Biclique Enumeration in Bipartite Graphs
Description: A tool for enumerating maximal complete bipartite graphs. The input should be a edge list file or a binary matrix file.
The output are maximal complete bipartite graphs. Algorithms used can be found in this paper Y Zhang et al. BMC Bioinformatics 2014 15:110 <doi:10.1186/1471-2105-15-110>.
Author: Yuping Lu [aut, cre, cph],
Charles Phillips [aut],
Michael Langston [aut],
Department of Computer Science, University of Tennessee, Knoxville
[cph]
Maintainer: Yuping Lu <yupinglu89@gmail.com>
Diff between biclique versions 1.0.2 dated 2019-04-07 and 1.0.3 dated 2019-08-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ README.md | 4 ++++ src/R_biclique_driver.c | 4 ++-- src/biclique.c | 6 +++--- 6 files changed, 21 insertions(+), 13 deletions(-)
Title: Computation of Optimal Transport Plans and Wasserstein Distances
Description: Solve optimal transport problems. Compute Wasserstein distances (a.k.a. Kantorovitch, Fortet--Mourier, Mallows, Earth Mover's, or minimal L_p distances), return the corresponding transference plans, and display them graphically. Objects that can be compared include grey-scale images, (weighted) point patterns, and mass vectors.
Author: Dominic Schuhmacher [aut, cre],
Björn Bähre [aut] (aha and power diagrams),
Nicolas Bonneel [aut] (networkflow),
Carsten Gottschlich [aut] (simplex and shortlist),
Valentin Hartmann [aut] (semidiscrete1),
Florian Heinemann [aut] (transport_track and networkflow integration),
Bernhard Schmitzer [aut] (shielding),
Jörn Schrieber [aut] (subsampling),
Timo Wilm [ctb] (wpp)
Maintainer: Dominic Schuhmacher <dominic.schuhmacher@mathematik.uni-goettingen.de>
Diff between transport versions 0.12-0 dated 2019-08-06 and 0.12-1 dated 2019-08-19
transport-0.12-0/transport/cleanup |only transport-0.12-0/transport/configure |only transport-0.12-0/transport/configure.ac |only transport-0.12-0/transport/src/Makevars.in |only transport-0.12-0/transport/src/Makevars.win |only transport-0.12-1/transport/DESCRIPTION | 8 ++++---- transport-0.12-1/transport/MD5 | 14 +++++--------- transport-0.12-1/transport/NEWS | 14 ++++++++++++++ transport-0.12-1/transport/R/fundament.R | 16 +++++++--------- transport-0.12-1/transport/man/transport-package.Rd | 4 ++-- transport-0.12-1/transport/src/Makevars |only 11 files changed, 32 insertions(+), 24 deletions(-)
Title: Stratified Medicine
Description: A toolkit for stratified medicine, subgroup identification, and precision medicine.
Current tools include (1) filtering models (reduce covariate space), (2) patient-level estimate
models (counterfactual patient-level quantities, for example the individual treatment effect),
(3) subgroup identification models (find subsets of patients with similar treatment effects),
and (4) parameter estimation and inference (for the overall population and discovered subgroups).
These tools can directly feed into stratified medicine algorithms including PRISM
(patient response identifiers for stratified medicine; Jemielita and Mehrotra 2019 (in progress)).
PRISM is a flexible and general framework which accepts user-created models/functions. This
package is in beta and will be continually updated.
Author: Thomas Jemielita [aut, cre]
Maintainer: Thomas Jemielita <thomasjemielita@gmail.com>
Diff between StratifiedMedicine versions 0.1.1 dated 2019-07-22 and 0.1.2 dated 2019-08-19
DESCRIPTION | 6 MD5 | 58 ++++--- NAMESPACE | 4 R/PRISM.R | 295 ++++++--------------------------------- R/PRISM_resamp.R |only R/PRISM_train.R |only R/filter_glmnet.R | 1 R/filter_ranger.R | 3 R/param_cox.R | 17 +- R/param_dr.R | 26 ++- R/param_lm.R | 39 +++-- R/param_ple.R | 25 ++- R/param_rmst.R | 13 + R/ple_bart.R | 1 R/ple_causal_forest.R | 5 R/ple_glmnet.R | 1 R/ple_ranger.R | 13 - R/plot.R | 37 +++- README.md | 40 ++++- inst/doc/SM_PRISM.R | 33 +--- inst/doc/SM_PRISM.Rmd | 41 +---- inst/doc/SM_PRISM.html | 140 +++++++++--------- man/PRISM.Rd | 27 +-- man/PRISM_resamp.Rd |only man/PRISM_train.Rd |only man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/figures/README-example-4.png |binary man/ple_ranger.Rd | 6 man/plot.PRISM.Rd | 7 man/predict.ple_ranger.Rd | 2 vignettes/SM_PRISM.Rmd | 41 +---- 32 files changed, 377 insertions(+), 504 deletions(-)
More information about StratifiedMedicine at CRAN
Permanent link
Title: Parse and Test Robots Exclusion Protocol Files and Rules
Description: The 'Robots Exclusion Protocol' <https://www.robotstxt.org/orig.html> documents
a set of standards for allowing or excluding robot/spider crawling of different areas of
site content. Tools are provided which wrap The 'rep-cpp' <https://github.com/seomoz/rep-cpp>
C++ library for processing these 'robots.txt' files.
Author: Bob Rudis (bob@rud.is) [aut, cre], SEOmoz, Inc [aut]
Maintainer: Bob Rudis <bob@rud.is>
Diff between spiderbar versions 0.2.1 dated 2017-11-17 and 0.2.2 dated 2019-08-19
spiderbar-0.2.1/spiderbar/README.md |only spiderbar-0.2.2/spiderbar/DESCRIPTION | 17 ++-- spiderbar-0.2.2/spiderbar/MD5 | 9 +- spiderbar-0.2.2/spiderbar/R/spiderbar-package.R | 2 spiderbar-0.2.2/spiderbar/man/spiderbar.Rd | 2 spiderbar-0.2.2/spiderbar/src/robots.cpp | 85 +++++++++++++----------- 6 files changed, 62 insertions(+), 53 deletions(-)
Title: Identify and Parse Web Security Policies Files
Description: When security risks in web services are discovered by independent
security researchers who understand the severity of the risk, they
often lack the channels to properly disclose them. As a result,
security issues may be left unreported. The 'security.txt' 'Web Security Policies'
specification defines an 'IETF' draft standard <https://tools.ietf.org/html/draft-foudil-securitytxt-00>
to help organizations define the process for security researchers to securely
disclose security vulnerabilities. Tools are provided to help identify and
parse 'security.txt' files to enable analysis of the usage and adoption of these policies.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>),
SEOmoz Inc [aut, cph] (url-cpp library,
<https://github.com/seomoz/url-cpp>)
Maintainer: Bob Rudis <bob@rud.is>
Diff between securitytxt versions 0.1.0 dated 2017-10-21 and 0.1.1 dated 2019-08-19
securitytxt-0.1.0/securitytxt/README.md |only securitytxt-0.1.1/securitytxt/DESCRIPTION | 17 +-- securitytxt-0.1.1/securitytxt/MD5 | 5 - securitytxt-0.1.1/securitytxt/src/security.cpp | 117 ++++++++++++++----------- 4 files changed, 77 insertions(+), 62 deletions(-)
Title: A Modified Sequential Probability Ratio Test (MSPRT)
Description: A modified SPRT (MSPRT) can be designed and implemented with the help of this package. In a
MSPRT design, (i) the maximum sample size of an experiment is fixed prior to the start of an
experiment; (ii) the alternative hypothesis used to define the rejection region of the test is derived
from the size of the test (Type I error), the maximum available sample size (N), and (iii) the targeted Type 2
error (equals to 1 minus the power) is also prespecified. Given these values, the MSPRT is defined in a
manner very similar to Wald's initial proposal. This test can reduce the average sample size required to
perform statistical hypothesis tests at the specified level of significance and power. This package
implements one-sample proportion tests, one-sample Z-tests, one-sample T-tests, two-sample
Z-tests and two-sample T-tests. A user guidance for this package is provided here.
One can also refer to the supplemental information for the same.
Author: Sandipan Pramanik [aut, cre],
Valen E. Johnson [aut],
Anirban Bhattacharya [aut]
Maintainer: Sandipan Pramanik <sandy@stat.tamu.edu>
Diff between MSPRT versions 2.0 dated 2019-02-17 and 2.1 dated 2019-08-19
DESCRIPTION | 10 MD5 | 12 R/MSPRT.R |13156 +++++++++++++++++++++++++------------------------ build/partial.rdb |binary man/OC.MSPRT.Rd | 389 - man/design.MSPRT.Rd | 46 man/implement.MSPRT.Rd | 60 7 files changed, 7148 insertions(+), 6525 deletions(-)
Title: Colour Schemes for Scientific Data Visualization
Description: An implementation of Paul Tol's colour schemes for
use with 'graphics' or 'ggplot2'. These schemes are ready for each
type of data (qualitative, diverging or sequential), with colours that
are distinct for all people, including colour-blind readers. This
package provides tools to simulate colour-blindness and to test how
well the colours of any palette are identifiable. Several scientific
thematic schemes (geologic timescale, land cover, FAO soils, etc.) are
also implemented.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between khroma versions 1.1.3 dated 2019-06-05 and 1.2.0 dated 2019-08-19
khroma-1.1.3/khroma/man/figures/README-tol-diverging-1.png |only khroma-1.1.3/khroma/man/figures/README-tol-qualitative-1.png |only khroma-1.1.3/khroma/man/figures/README-tol-sequential-1.png |only khroma-1.2.0/khroma/DESCRIPTION | 31 +- khroma-1.2.0/khroma/MD5 | 87 +++--- khroma-1.2.0/khroma/NAMESPACE | 3 khroma-1.2.0/khroma/R/anomalize.R |only khroma-1.2.0/khroma/R/colour.R | 45 ++- khroma-1.2.0/khroma/R/ggplot2-science.R | 14 - khroma-1.2.0/khroma/R/ggplot2-tol.R | 35 +- khroma-1.2.0/khroma/R/ggplot2.R | 8 khroma-1.2.0/khroma/R/khroma-package.R | 13 khroma-1.2.0/khroma/R/plot.R |only khroma-1.2.0/khroma/R/sysdata.rda |binary khroma-1.2.0/khroma/README.md | 140 ++++++++-- khroma-1.2.0/khroma/build |only khroma-1.2.0/khroma/inst/CITATION | 19 + khroma-1.2.0/khroma/inst/doc |only khroma-1.2.0/khroma/inst/examples/ex-anomalize.R |only khroma-1.2.0/khroma/inst/examples/ex-palettes.R | 38 +- khroma-1.2.0/khroma/inst/examples/ex-plot.R |only khroma-1.2.0/khroma/inst/examples/ex-science-land.R | 10 khroma-1.2.0/khroma/inst/examples/ex-science-soil.R | 10 khroma-1.2.0/khroma/inst/examples/ex-science-stratigraphy.R | 12 khroma-1.2.0/khroma/inst/examples/ex-tol-discrete.R | 54 +-- khroma-1.2.0/khroma/inst/examples/ex-tol-diverging.R | 19 - khroma-1.2.0/khroma/inst/examples/ex-tol-sequential.R | 17 - khroma-1.2.0/khroma/man/colour.Rd | 72 +++-- khroma-1.2.0/khroma/man/convert.Rd |only khroma-1.2.0/khroma/man/figures/README-usage-1.png |only khroma-1.2.0/khroma/man/figures/README-usage-colourblind-1.png |only khroma-1.2.0/khroma/man/figures/README-usage-colourblind-2.png |only khroma-1.2.0/khroma/man/figures/README-usage-colourblind-3.png |only khroma-1.2.0/khroma/man/figures/README-usage-colourblind-4.png |only khroma-1.2.0/khroma/man/figures/README-usage-colourblind-5.png |only khroma-1.2.0/khroma/man/figures/README-usage-ggplot2-1.png |only khroma-1.2.0/khroma/man/figures/logo.png |binary khroma-1.2.0/khroma/man/figures/logo.svg | 14 - khroma-1.2.0/khroma/man/khroma-package.Rd | 21 - khroma-1.2.0/khroma/man/plot.Rd |only khroma-1.2.0/khroma/man/scale.Rd | 10 khroma-1.2.0/khroma/man/scale_land.Rd | 20 - khroma-1.2.0/khroma/man/scale_soil.Rd | 15 - khroma-1.2.0/khroma/man/scale_stratigraphy.Rd | 17 - khroma-1.2.0/khroma/man/scale_tol_discrete.Rd | 64 ++-- khroma-1.2.0/khroma/man/scale_tol_diverging.Rd | 37 +- khroma-1.2.0/khroma/man/scale_tol_sequential.Rd | 35 +- khroma-1.2.0/khroma/tests/figs |only khroma-1.2.0/khroma/tests/testthat/test-colour.R | 46 ++- khroma-1.2.0/khroma/tests/testthat/test-plot.R |only khroma-1.2.0/khroma/vignettes |only 51 files changed, 572 insertions(+), 334 deletions(-)
Title: An Interface to Google Drive
Description: Manage Google Drive files from R.
Author: Lucy D'Agostino McGowan [aut],
Jennifer Bryan [aut, cre] (<https://orcid.org/0000-0002-6983-2759>),
RStudio [cph, fnd]
Maintainer: Jennifer Bryan <jenny@rstudio.com>
Diff between googledrive versions 0.1.3 dated 2019-01-24 and 1.0.0 dated 2019-08-19
googledrive-0.1.3/googledrive/R/generate_request.R |only googledrive-0.1.3/googledrive/R/make_request.R |only googledrive-0.1.3/googledrive/R/process_response.R |only googledrive-0.1.3/googledrive/man/drive_api_key.Rd |only googledrive-0.1.3/googledrive/man/drive_auth_config.Rd |only googledrive-0.1.3/googledrive/man/generate_request.Rd |only googledrive-0.1.3/googledrive/man/is_legit_token.Rd |only googledrive-0.1.3/googledrive/man/make_request.Rd |only googledrive-0.1.3/googledrive/man/process_response.Rd |only googledrive-0.1.3/googledrive/man/token_available.Rd |only googledrive-0.1.3/googledrive/tests/testthat/clean.html |only googledrive-0.1.3/googledrive/tests/testthat/test-drive_mkdir.R |only googledrive-0.1.3/googledrive/tests/testthat/test-files/right-content.rds |only googledrive-0.1.3/googledrive/tests/testthat/test-files/wrong-content.rds |only googledrive-0.1.3/googledrive/tests/testthat/test-process_response.R |only googledrive-0.1.3/googledrive/vignettes/articles |only googledrive-1.0.0/googledrive/DESCRIPTION | 18 googledrive-1.0.0/googledrive/LICENSE | 4 googledrive-1.0.0/googledrive/MD5 | 187 ++- googledrive-1.0.0/googledrive/NAMESPACE | 16 googledrive-1.0.0/googledrive/NEWS.md | 159 +++ googledrive-1.0.0/googledrive/R/aaa.R | 39 googledrive-1.0.0/googledrive/R/as_dribble.R | 13 googledrive-1.0.0/googledrive/R/as_id.R | 16 googledrive-1.0.0/googledrive/R/deprecated.R |only googledrive-1.0.0/googledrive/R/dribble.R | 3 googledrive-1.0.0/googledrive/R/drive_about.R | 6 googledrive-1.0.0/googledrive/R/drive_auth.R | 470 +++------- googledrive-1.0.0/googledrive/R/drive_cp.R | 51 - googledrive-1.0.0/googledrive/R/drive_create.R |only googledrive-1.0.0/googledrive/R/drive_download.R | 12 googledrive-1.0.0/googledrive/R/drive_endpoints.R | 47 - googledrive-1.0.0/googledrive/R/drive_fields.R | 6 googledrive-1.0.0/googledrive/R/drive_find.R | 63 - googledrive-1.0.0/googledrive/R/drive_get.R | 58 - googledrive-1.0.0/googledrive/R/drive_ls.R | 4 googledrive-1.0.0/googledrive/R/drive_mkdir.R | 76 - googledrive-1.0.0/googledrive/R/drive_mv.R | 60 - googledrive-1.0.0/googledrive/R/drive_publish.R | 14 googledrive-1.0.0/googledrive/R/drive_put.R |only googledrive-1.0.0/googledrive/R/drive_rename.R | 24 googledrive-1.0.0/googledrive/R/drive_reveal.R | 12 googledrive-1.0.0/googledrive/R/drive_reveal_path.R | 7 googledrive-1.0.0/googledrive/R/drive_rm.R | 13 googledrive-1.0.0/googledrive/R/drive_share.R | 14 googledrive-1.0.0/googledrive/R/drive_trash.R | 22 googledrive-1.0.0/googledrive/R/drive_update.R | 25 googledrive-1.0.0/googledrive/R/drive_upload.R | 65 - googledrive-1.0.0/googledrive/R/drive_user.R | 4 googledrive-1.0.0/googledrive/R/googledrive-package.R | 13 googledrive-1.0.0/googledrive/R/request_generate.R |only googledrive-1.0.0/googledrive/R/request_make.R |only googledrive-1.0.0/googledrive/R/sysdata.rda |binary googledrive-1.0.0/googledrive/R/team_drive_create.R | 6 googledrive-1.0.0/googledrive/R/team_drive_find.R | 4 googledrive-1.0.0/googledrive/R/team_drive_get.R | 6 googledrive-1.0.0/googledrive/R/team_drive_rm.R | 6 googledrive-1.0.0/googledrive/R/team_drive_update.R | 8 googledrive-1.0.0/googledrive/R/utils-paths.R | 93 + googledrive-1.0.0/googledrive/R/utils-pipe.R |only googledrive-1.0.0/googledrive/R/utils.R | 32 googledrive-1.0.0/googledrive/README.md | 73 - googledrive-1.0.0/googledrive/build/vignette.rds |binary googledrive-1.0.0/googledrive/inst/doc/googledrive.html | 7 googledrive-1.0.0/googledrive/inst/extdata/files_fields.csv | 44 googledrive-1.0.0/googledrive/inst/extdata/mime_tbl.csv | 7 googledrive-1.0.0/googledrive/inst/extdata/translate_mime_types.csv | 142 +-- googledrive-1.0.0/googledrive/inst/secret |only googledrive-1.0.0/googledrive/man/as_dribble.Rd | 10 googledrive-1.0.0/googledrive/man/drive_auth.Rd | 147 +-- googledrive-1.0.0/googledrive/man/drive_auth_configure.Rd |only googledrive-1.0.0/googledrive/man/drive_cp.Rd | 37 googledrive-1.0.0/googledrive/man/drive_create.Rd |only googledrive-1.0.0/googledrive/man/drive_deauth.Rd | 27 googledrive-1.0.0/googledrive/man/drive_download.Rd | 6 googledrive-1.0.0/googledrive/man/drive_endpoints.Rd | 39 googledrive-1.0.0/googledrive/man/drive_find.Rd | 55 - googledrive-1.0.0/googledrive/man/drive_get.Rd | 12 googledrive-1.0.0/googledrive/man/drive_has_token.Rd |only googledrive-1.0.0/googledrive/man/drive_mkdir.Rd | 47 - googledrive-1.0.0/googledrive/man/drive_mv.Rd | 29 googledrive-1.0.0/googledrive/man/drive_put.Rd |only googledrive-1.0.0/googledrive/man/drive_rename.Rd | 39 googledrive-1.0.0/googledrive/man/drive_reveal.Rd | 4 googledrive-1.0.0/googledrive/man/drive_token.Rd | 31 googledrive-1.0.0/googledrive/man/drive_update.Rd | 12 googledrive-1.0.0/googledrive/man/drive_upload.Rd | 51 - googledrive-1.0.0/googledrive/man/figures |only googledrive-1.0.0/googledrive/man/googledrive-deprecated.Rd |only googledrive-1.0.0/googledrive/man/pipe.Rd | 4 googledrive-1.0.0/googledrive/man/request_generate.Rd |only googledrive-1.0.0/googledrive/man/request_make.Rd |only googledrive-1.0.0/googledrive/tests/testthat/all-test-clean.R |only googledrive-1.0.0/googledrive/tests/testthat/all-test-setup.R |only googledrive-1.0.0/googledrive/tests/testthat/all-test-setup.html |only googledrive-1.0.0/googledrive/tests/testthat/driver.R | 10 googledrive-1.0.0/googledrive/tests/testthat/helper.R | 67 - googledrive-1.0.0/googledrive/tests/testthat/setup-testing.R |only googledrive-1.0.0/googledrive/tests/testthat/test-as_id.R | 10 googledrive-1.0.0/googledrive/tests/testthat/test-dplyr-compatibility.R | 10 googledrive-1.0.0/googledrive/tests/testthat/test-drive_auth.R |only googledrive-1.0.0/googledrive/tests/testthat/test-drive_create.R |only googledrive-1.0.0/googledrive/tests/testthat/test-drive_endpoints.R |only googledrive-1.0.0/googledrive/tests/testthat/test-drive_get.R | 13 googledrive-1.0.0/googledrive/tests/testthat/test-drive_link.R | 13 googledrive-1.0.0/googledrive/tests/testthat/test-drive_ls.R | 2 googledrive-1.0.0/googledrive/tests/testthat/test-drive_put.R |only googledrive-1.0.0/googledrive/tests/testthat/test-drive_update.R | 26 googledrive-1.0.0/googledrive/tests/testthat/test-drive_upload.R | 44 googledrive-1.0.0/googledrive/tests/testthat/test-files/client_secret_123.googleusercontent.com.json |only googledrive-1.0.0/googledrive/tests/testthat/test-generate_request.R | 57 - googledrive-1.0.0/googledrive/tests/testthat/test-path-utils.R | 131 ++ googledrive-1.0.0/googledrive/tests/testthat/test-utils.R | 8 113 files changed, 1672 insertions(+), 1218 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.9 dated 2019-07-04 and 1.2.0 dated 2019-08-19
DESCRIPTION | 14 +++++++------- MD5 | 18 +++++++++--------- NEWS.md | 5 +++++ R/relop_non_sql.R | 4 ++-- R/rq_ufn.R | 4 ++-- inst/doc/GroupedSampling.html | 10 +++++++--- inst/doc/R_mapping.html | 10 +++++++--- inst/doc/logisticexample.html | 10 +++++++--- man/rq_df_funciton_node.Rd | 2 +- man/rq_ufn.Rd | 2 +- 10 files changed, 48 insertions(+), 31 deletions(-)
Title: A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS'
API
Description: A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database
used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides
access to 'WISKI' databases via HTTP requests (<https://water.kisters.de/en/technology-trends/kisters-and-open-data/>).
Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL.
Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Author: Ryan Whaley [aut, cre],
Sam Albers [ctb]
Maintainer: Ryan Whaley <rdgwhaley@gmail.com>
Diff between kiwisR versions 0.1.6 dated 2019-05-28 and 0.1.7 dated 2019-08-19
DESCRIPTION | 6 MD5 | 30 ++-- NEWS.md | 9 + R/ki_group_list.R | 2 R/ki_station_list.R | 12 + R/ki_timeseries_list.R | 3 R/ki_timeseries_values.R | 2 R/utils.R | 6 README.md | 187 ++++++++++++++--------------- man/ki_group_list.Rd | 2 man/ki_station_list.Rd | 2 man/ki_timeseries_list.Rd | 5 man/ki_timeseries_values.Rd | 2 tests/testthat/test_ki_group_list.R | 2 tests/testthat/test_ki_timeseries_list.R | 13 +- tests/testthat/test_ki_timeseries_values.R | 6 16 files changed, 163 insertions(+), 126 deletions(-)
Title: Tools for Data Diagnosis, Exploration, Transformation
Description: A collection of tools that support data diagnosis, exploration, and transformation.
Data diagnostics provides information and visualization of missing values and outliers and
unique and negative values to help you understand the distribution and quality of your data.
Data exploration provides information and visualization of the descriptive statistics of
univariate variables, normality tests and outliers, correlation of two variables, and
relationship between target variable and predictor. Data transformation supports binning
for categorizing continuous variables, imputates missing values and outliers, resolving skewness.
And it creates automated reports that support these three tasks.
Author: Choonghyun Ryu [aut, cre]
Maintainer: Choonghyun Ryu <choonghyun.ryu@gmail.com>
Diff between dlookr versions 0.3.9 dated 2019-03-16 and 0.3.11 dated 2019-08-19
DESCRIPTION | 10 - MD5 | 30 ++--- NAMESPACE | 1 NEWS | 34 +++++ R/binning.R | 5 R/diagnose.R | 26 +++- R/discribe.R | 57 ++++++--- R/imputation.R | 80 +++++++++++-- R/transform.R | 4 inst/doc/EDA.html | 12 +- inst/doc/transformation.html | 184 ++++++++++--------------------- inst/report/03_Transformation.Rnw | 21 +++ inst/report/03_Transformation_KR.Rnw | 21 +++ inst/report/Transformation_Report.Rmd | 20 +++ inst/report/Transformation_Report_KR.Rmd | 21 +++ man/imputate_na.Rd | 2 16 files changed, 339 insertions(+), 189 deletions(-)
Title: Fast Inference for Large Spatial Datasets using BRISC
Description: Fits Bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using Nearest Neighbor Gaussian Processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
Author: Arkajyoti Saha [aut, cre],
Abhirup Datta [aut],
Jorge Nocedal [ctb],
Naoaki Okazaki [ctb]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between BRISC versions 0.1.0 dated 2018-07-22 and 0.2.0 dated 2019-08-19
DESCRIPTION | 10 ++--- MD5 | 22 ++++++------ NAMESPACE | 2 + R/Brisc_Variogram.CI.R |only R/bootstrap.R | 17 ++++----- R/bootstrap_brisc.R | 4 +- R/estimation.R | 9 +++- R/prediction.R | 20 +++++++++-- man/BRISC_bootstrap.Rd | 4 +- man/BRISC_estimation.Rd | 8 ++-- man/BRISC_prediction.Rd | 8 ++-- man/BRISC_variogram.ci.Rd |only src/BRISC.cpp | 83 +++++++++++++++++++++++----------------------- 13 files changed, 110 insertions(+), 77 deletions(-)
Title: Calculate TL-Moments and Convert Them to Distribution Parameters
Description: Calculates empirical TL-moments (trimmed L-moments) of arbitrary
order and trimming, and converts them to distribution parameters.
Author: Jona Lilienthal
Maintainer: Jona Lilienthal <lilienthal@statistik.tu-dortmund.de>
Diff between TLMoments versions 0.7.4.3 dated 2019-04-30 and 0.7.4.4 dated 2019-08-19
DESCRIPTION | 8 MD5 | 30 - R/summary.PWMs.R | 2 R/summary.TLMoments.R | 4 R/summary.parameters.R | 2 R/summary.quantiles.R | 2 build/vignette.rds |binary inst/doc/comparison_of_computation_time.Rmd | 28 - inst/doc/comparison_of_computation_time.html | 606 ++++++++++++++-------- inst/doc/short_introduction.R | 87 +-- inst/doc/short_introduction.Rmd | 150 +++-- inst/doc/short_introduction.html | 740 ++++++++++++++++++--------- src/PWM.cpp | 5 src/TLMoments.cpp | 10 vignettes/comparison_of_computation_time.Rmd | 28 - vignettes/short_introduction.Rmd | 150 +++-- 16 files changed, 1198 insertions(+), 654 deletions(-)
Title: Template for Clinical Trial Protocol
Description: Contains an R Markdown template for a clinical trial
protocol adhering to the SPIRIT statement. The SPIRIT (Standard Protocol
Items for Interventional Trials) statement outlines recommendations for a
minimum set of elements to be addressed in a clinical trial protocol.
Also contains functions to create a xml document from the template and
upload it to clinicaltrials.gov<https://www.clinicaltrials.gov/> for
trial registration.
Author: Aaron Conway [aut, cre] (<https://orcid.org/0000-0002-9583-8636>)
Maintainer: Aaron Conway <aaron.conway@utoronto.ca>
Diff between spiritR versions 0.1.0 dated 2019-08-10 and 0.1.1 dated 2019-08-19
DESCRIPTION | 12 +++++++----- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ README.md | 7 ++++--- inst/doc/spiritR.html | 4 ++-- man/spiritR-package.Rd | 8 ++++++++ tests/testthat/tests.R | 6 ++++++ 7 files changed, 41 insertions(+), 16 deletions(-)
Title: Measuring Information Flow Between Time Series with Shannon and
Renyi Transfer Entropy
Description: Measuring information flow between time series with Shannon and Rényi transfer entropy. See also Dimpfl and Peter (2013) <doi:10.1515/snde-2012-0044> and Dimpfl and Peter (2014) <doi:10.1016/j.intfin.2014.03.004> for theory and applications to financial time series. Additional references can be found in the theory part of the vignette.
Author: Simon Behrendt [aut, cre],
David Zimmermann [aut],
Thomas Dimpfl [aut],
Franziska Peter [aut]
Maintainer: Simon Behrendt <simon.behrendt@zu.de>
Diff between RTransferEntropy versions 0.2.8 dated 2019-03-12 and 0.2.12 dated 2019-08-19
DESCRIPTION | 6 - MD5 | 33 +++---- R/calc_ete.R | 6 - R/calc_te.R | 6 - R/te_class.R | 151 ++++++++++++++++++++++++++------- R/transfer_entropy.R | 16 ++- R/zzz.R | 31 ++++++ README.md | 47 ++++++---- build/vignette.rds |binary inst/CITATION |only inst/doc/transfer-entropy.html | 59 ++++++------ man/calc_ete.Rd | 6 + man/calc_te.Rd | 6 + man/figures/README-contemp_plot-1.png |binary man/print.transfer_entropy.Rd | 23 ++++- man/transfer_entropy.Rd | 5 - tests/testthat.R | 3 tests/testthat/test.transfer_entropy.R | 22 +++- 18 files changed, 308 insertions(+), 112 deletions(-)
More information about RTransferEntropy at CRAN
Permanent link
Title: Bayesian Graphical Models using MCMC
Description: Interface to the JAGS MCMC library.
Author: Martyn Plummer [aut, cre],
Alexey Stukalov [ctb],
Matt Denwood [ctb]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between rjags versions 4-8 dated 2018-10-19 and 4-9 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/Makevars.win | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Blind Source Separation Methods Based on Joint Diagonalization
and Some BSS Performance Criteria
Description: Cardoso's JADE algorithm as well as his functions for joint diagonalization are ported to R. Also several other blind source separation (BSS) methods, like AMUSE and SOBI, and some criteria for performance evaluation of BSS algorithms, are given. The package is described in Miettinen, Nordhausen and Taskinen (2017) <doi:10.18637/jss.v076.i02>.
Author: Klaus Nordhausen, Jean-Francois Cardoso, Jari Miettinen, Hannu Oja, Esa Ollila, Sara Taskinen
Maintainer: Klaus Nordhausen <klaus.nordhausen@tuwien.ac.at>
Diff between JADE versions 2.0-1 dated 2018-03-02 and 2.0-2 dated 2019-08-19
JADE-2.0-1/JADE/data/datalist |only JADE-2.0-2/JADE/DESCRIPTION | 8 - JADE-2.0-2/JADE/MD5 | 23 +-- JADE-2.0-2/JADE/NAMESPACE | 2 JADE-2.0-2/JADE/R/frjd.R | 108 +++++++++++------- JADE-2.0-2/JADE/build/partial.rdb |binary JADE-2.0-2/JADE/build/vignette.rds |binary JADE-2.0-2/JADE/inst/ChangeLog | 4 JADE-2.0-2/JADE/inst/doc/JADE-BSSasymp.pdf |binary JADE-2.0-2/JADE/man/CPPdata.Rd | 4 JADE-2.0-2/JADE/man/JADE-package.Rd | 4 JADE-2.0-2/JADE/man/SOBI.Rd | 4 JADE-2.0-2/JADE/man/rjd.Rd | 171 +++++++++++++++-------------- 13 files changed, 181 insertions(+), 147 deletions(-)
Title: Inference Using Simulation
Description: Implements functions for simulation-based inference. In particular, implements functions to perform likelihood inference from data summaries whose distributions are simulated (Rousset et al. 2017 <doi:10.1111/1755-0998.12627>).
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between Infusion versions 1.3.0 dated 2018-09-24 and 1.4.1 dated 2019-08-19
DESCRIPTION | 10 MD5 | 66 +++-- NAMESPACE | 2 R/MSL.R | 10 R/Rmixmod.R | 186 ++++++++++------ R/SLik.R | 10 R/SLikSQuant.R | 472 +++++++++++++++++++++++------------------ R/add_simulation.R | 57 ++-- R/calc_all_slices.R | 3 R/confintLR.SLik.R | 2 R/coresWrapper.R | 20 + R/generate_data.R | 4 R/infer_logLs.R | 18 + R/infer_surface.R | 9 R/jointDens.R | 396 ++++++++++++++++++++++++++-------- R/keras.R |only R/mclust.R | 36 +-- R/minImIze.R |only R/plot.SLik.R | 8 R/plot.SLik_j.R | 11 R/plotProfiles.R | 29 +- R/profile.R | 20 + R/project.R | 320 +++++++++++++++++++-------- inst/NEWS.Rd | 27 ++ man/Infusion.Rd | 46 --- man/MSL.Rd | 11 man/add.simulation.Rd | 19 + man/dMixmod.Rd |only man/example_raw.Rd |only man/example_reftable.Rd |only man/infer_jointDens.Rd | 19 - man/options.Rd | 10 man/project.Rd | 46 +-- man/refine.SLik.Rd | 19 + tests/test-all.R | 1 tests/testthat/test-3par.R | 2 tests/testthat/test-reftable.R |only 37 files changed, 1214 insertions(+), 675 deletions(-)
Title: Horizontal 'ggplot2' Components
Description: A 'ggplot2' extension that provides flipped components:
horizontal versions of 'Stats' and 'Geoms', and vertical versions
of 'Positions'.
Author: Lionel Henry [aut, cre],
Hadley Wickham [aut],
Winston Chang [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between ggstance versions 0.3.2 dated 2019-06-24 and 0.3.3 dated 2019-08-19
DESCRIPTION | 6 MD5 | 21 NEWS.md | 8 R/position-dodge2v.R | 4 R/position-stackv.R | 2 man/position-vertical.Rd | 2 tests/figs/geoms/geom-boxploth-facet-wrap-with-fill.svg | 402 +++++----- tests/figs/geoms/geom-boxploth-with-fill.svg | 122 +-- tests/figs/positions/boxplot-with-legend-order-aligned-to-bar-order.svg |only tests/figs/positions/position-stackv-with-hjust-argument.svg | 4 tests/testthat/test-geoms.R | 1 tests/testthat/test-positions.R | 9 12 files changed, 300 insertions(+), 281 deletions(-)
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. Additionally, 'grouped_' and
'boot_' variants of the generics provides a convenient way to execute
functions across a combination of grouping variable(s) in a dataframe
or bootstrap them.
Author: Indrajeet Patil [aut, cre, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 0.0.4 dated 2019-06-25 and 0.0.5 dated 2019-08-19
broomExtra-0.0.4/broomExtra/tests/testthat/test_boot_generics.R |only broomExtra-0.0.4/broomExtra/tests/testthat/test_generics.R |only broomExtra-0.0.4/broomExtra/tests/testthat/test_grouped_generics.R |only broomExtra-0.0.5/broomExtra/DESCRIPTION | 12 broomExtra-0.0.5/broomExtra/MD5 | 62 ++--- broomExtra-0.0.5/broomExtra/NAMESPACE | 10 broomExtra-0.0.5/broomExtra/NEWS.md | 23 + broomExtra-0.0.5/broomExtra/R/boot_generics.R | 89 +++---- broomExtra-0.0.5/broomExtra/R/generics.R | 67 +++-- broomExtra-0.0.5/broomExtra/R/global_vars.R | 3 broomExtra-0.0.5/broomExtra/R/grouped_generics.R | 30 +- broomExtra-0.0.5/broomExtra/R/reexports.R | 18 + broomExtra-0.0.5/broomExtra/README.md | 124 ++++------ broomExtra-0.0.5/broomExtra/build/broomExtra.pdf |binary broomExtra-0.0.5/broomExtra/build/vignette.rds |binary broomExtra-0.0.5/broomExtra/inst/WORDLIST | 1 broomExtra-0.0.5/broomExtra/inst/doc/available_methods.html | 98 +++++-- broomExtra-0.0.5/broomExtra/inst/doc/tests_and_coverage.Rmd | 50 ++-- broomExtra-0.0.5/broomExtra/inst/doc/tests_and_coverage.html | 70 ++--- broomExtra-0.0.5/broomExtra/man/augment.Rd | 9 broomExtra-0.0.5/broomExtra/man/boot_augment.Rd | 21 + broomExtra-0.0.5/broomExtra/man/boot_glance.Rd | 21 + broomExtra-0.0.5/broomExtra/man/boot_tidy.Rd | 21 + broomExtra-0.0.5/broomExtra/man/glance.Rd | 9 broomExtra-0.0.5/broomExtra/man/grouped_augment.Rd | 9 broomExtra-0.0.5/broomExtra/man/grouped_glance.Rd | 9 broomExtra-0.0.5/broomExtra/man/grouped_tidy.Rd | 9 broomExtra-0.0.5/broomExtra/man/reexports.Rd | 10 broomExtra-0.0.5/broomExtra/man/tidy.Rd | 15 + broomExtra-0.0.5/broomExtra/tests/README.md | 52 ++-- broomExtra-0.0.5/broomExtra/tests/spelling.R | 3 broomExtra-0.0.5/broomExtra/tests/testthat/test-boot_generics.R |only broomExtra-0.0.5/broomExtra/tests/testthat/test-generics.R |only broomExtra-0.0.5/broomExtra/tests/testthat/test-grouped_generics.R |only broomExtra-0.0.5/broomExtra/vignettes/tests_and_coverage.Rmd | 50 ++-- 35 files changed, 536 insertions(+), 359 deletions(-)
Title: Crowd Sourced System Benchmarks
Description: Benchmark your CPU and compare against other CPUs.
Also provides functions for obtaining system specifications, such as
RAM, CPU type, and R version.
Author: Colin Gillespie [aut, cre] (<https://orcid.org/0000-0003-1787-0275>)
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between benchmarkme versions 1.0.0 dated 2019-01-28 and 1.0.2 dated 2019-08-19
DESCRIPTION | 35 ++++++++++++++++++++--------------- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ R/get_byte_compiler.R | 2 +- README.md | 5 +++++ build/vignette.rds |binary inst/doc/a_introduction.R | 2 +- inst/doc/a_introduction.Rmd | 10 +++++++++- inst/doc/a_introduction.html | 14 +++++++++++--- vignettes/a_introduction.Rmd | 10 +++++++++- 10 files changed, 71 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-18 0.4
2011-02-02 0.2
2010-04-19 0.1
Title: Load Data From 'Yandex Direct'
Description: Load data from 'Yandex Direct' API V5
<https://tech.yandex.ru/direct/doc/dg/concepts/about-docpage/> into R.
Provide function for load lists of campaings, ads, keywords and other
objects from 'Yandex Direct' account. Also you can load statistic from
API 'Reports Service' <https://tech.yandex.ru/direct/doc/reports/reports-docpage/>.
And allows keyword bids management.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between ryandexdirect versions 3.2.0 dated 2019-07-01 and 3.2.1 dated 2019-08-19
DESCRIPTION | 8 +- MD5 | 22 +++---- NEWS.md | 4 + R/yadirGetKeyWordsBids.R | 8 ++ R/yadirSetAutoKeyWordsBids.R | 92 ++++++++++++++++-------------- R/yadirSetKeyWordsBids.R | 78 ++++++++++++++----------- README.md | 15 ++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/yandex-direct-auth.html | 4 - inst/doc/yandex-direct-get-statistic.html | 4 - inst/doc/yandex-direct-keyword-bids.html | 4 - 12 files changed, 143 insertions(+), 96 deletions(-)
Title: R Bindings to the 'Quantuccia' Header-Only Essentials of
'QuantLib'
Description: 'QuantLib' bindings are provided for R using 'Rcpp' and the
header-only 'Quantuccia' variant (put together by Peter Caspers) offering
an essential subset of 'QuantLib'. See the included file 'AUTHORS' for a full
list of contributors to both 'QuantLib' and 'Quantuccia'.
Author: Dirk Eddelbuettel; the authors and contributors of QuantLib
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppQuantuccia versions 0.0.2 dated 2017-11-06 and 0.0.3 dated 2019-08-19
RcppQuantuccia-0.0.2/RcppQuantuccia/inst/include/ql/math/randomnumbers/sobolrsg.hpp |only RcppQuantuccia-0.0.2/RcppQuantuccia/inst/include/ql/models |only RcppQuantuccia-0.0.3/RcppQuantuccia/ChangeLog | 45 ++ RcppQuantuccia-0.0.3/RcppQuantuccia/DESCRIPTION | 8 RcppQuantuccia-0.0.3/RcppQuantuccia/MD5 | 50 +-- RcppQuantuccia-0.0.3/RcppQuantuccia/README.md | 12 RcppQuantuccia-0.0.3/RcppQuantuccia/build/partial.rdb |binary RcppQuantuccia-0.0.3/RcppQuantuccia/inst/NEWS.Rd | 11 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/array.hpp | 38 +- RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/distributions/normaldistribution.hpp | 16 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/functional.hpp | 161 +++++++++- RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/generallinearleastsquares.hpp | 3 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/matrix.hpp | 44 +- RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/optimization/levenbergmarquardt.hpp | 14 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/randomnumbers/all.hpp | 5 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/randomnumbers/rngtraits.hpp | 8 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/math/statistics/incrementalstatistics.hpp | 16 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/quantlib.hpp | 2 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/calendars/unitedstates.hpp | 6 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/date.hpp | 18 - RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/time/imm.hpp | 14 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/timegrid.hpp | 4 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/utilities/dataparsers.hpp | 16 RcppQuantuccia-0.0.3/RcppQuantuccia/inst/include/ql/utilities/null.hpp | 14 RcppQuantuccia-0.0.3/RcppQuantuccia/src/Makevars | 2 25 files changed, 348 insertions(+), 159 deletions(-)
More information about RcppQuantuccia at CRAN
Permanent link
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise discriminante linear (LDA) e quadratica (QDA), analise de cluster hierarquico e nao hierarquico, regressao linear simples e multipla, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 2.0.7 dated 2019-07-30 and 2.0.8 dated 2019-08-19
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++-------- R/Biplot.R | 6 ++-- R/GrandTour.R | 72 ++++++++++++++++++++++++------------------------- R/MDS.R | 14 ++++----- R/Plot.CA.R | 22 +++++++------- R/Plot.CCA.R | 21 +++++++------- R/Plot.FA.R | 24 ++++++++-------- R/Plot.MFA.R | 27 +++++++++--------- R/Plot.PCA.R | 17 ++++++----- R/Plot.PP.R | 30 ++++++++++---------- R/Plot.Regr.R | 12 ++++---- man/MVar.pt-package.Rd | 4 +- 13 files changed, 142 insertions(+), 139 deletions(-)
Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), linear (LDA) and quadratic discriminant analysis (QDA), hierarchical and non-hierarchical cluster analysis, simple and multiple linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar versions 2.0.7 dated 2019-07-30 and 2.0.8 dated 2019-08-19
DESCRIPTION | 8 +++---- MD5 | 24 ++++++++++----------- R/Biplot_English.R | 6 ++--- R/GrandTour_English.R | 56 +++++++++++++++++++++++++------------------------- R/MDS_English.R | 20 ++++++++--------- R/Plot.CA_English.R | 38 ++++++++++++++++----------------- R/Plot.CCA_English.R | 39 +++++++++++++++++----------------- R/Plot.FA_English.R | 32 ++++++++++++++-------------- R/Plot.MFA_English.R | 45 ++++++++++++++++++++-------------------- R/Plot.PCA_English.R | 27 ++++++++++++------------ R/Plot.PP_English.R | 38 ++++++++++++++++----------------- R/Plot.Regr_English.R | 22 +++++++++---------- man/MVar-package.Rd | 4 +-- 13 files changed, 181 insertions(+), 178 deletions(-)
Title: Matching Multiply Imputed Datasets
Description: Simplifies the process of matching control and treatment groups of multiply imputed datasets; selects matched samples from the control and treatment groups, enables complete data analysis, and pools the obtained results on each imputed dataset according to Rubin’s rules. Please see the package repository <https://github.com/FarhadPishgar/MatchIt.mice> for details.
Author: Farhad Pishgar
Maintainer: Farhad Pishgar <Farhad.Pishgar@Gmail.com>
Diff between MatchIt.mice versions 2.0.2 dated 2019-07-02 and 2.1.5 dated 2019-08-19
DESCRIPTION | 6 +- MD5 | 77 +++++++++++++++++++------------------ NAMESPACE | 6 ++ NEWS.md | 12 +++-- R/as2.mids.R |only R/binditmice.R | 96 +++++++++++++++++++++++++++++++++++++++++------ R/handoa.R | 1 R/is.R | 6 ++ R/matchitmice.R | 10 ++-- R/matchitmice.data.R | 12 +++-- R/mergeitmice.R |only R/plot.mimids.R | 4 + R/plot.wimids.R | 4 + R/pool.R | 15 +++++-- R/print.mimids.R | 4 + R/print.wimids.R | 6 ++ R/summary.mimids.R | 4 + R/summary.wimids.R | 7 +-- R/weightitmice.R | 13 ++---- R/weightitmice.data.R | 13 ++++-- R/with.mimids.R | 4 + R/with.wimids.R | 4 + README.md | 16 +++---- man/binditmice.Rd | 11 +++-- man/handoa.Rd | 1 man/is.mimids.Rd | 1 man/is.wimids.Rd | 3 - man/matchitmice.Rd | 7 --- man/matchitmice.data.Rd | 5 +- man/mergeitmice.Rd |only man/plot.mimids.Rd | 3 - man/plot.wimids.Rd | 3 - man/pool.Rd | 5 +- man/print.mimids.Rd | 3 - man/print.wimids.Rd | 3 - man/summary.mimids.Rd | 3 - man/summary.wimids.Rd | 6 -- man/weightitmice.Rd | 10 ---- man/weightitmice.data.Rd | 5 +- man/with.mimids.Rd | 3 - man/with.wimids.Rd | 3 - 41 files changed, 258 insertions(+), 137 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 2.3 dated 2019-07-10 and 2.4 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/GSED.R | 2 +- man/GSED-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Mapping ML Scores to Calibrated Predictions
Description: Transforms your uncalibrated Machine Learning scores to well-calibrated prediction estimates that can be interpreted as probability estimates. The implemented BBQ (Bayes Binning in Quantiles) model is taken from Naeini (2015, ISBN:0-262-51129-0). Please cite this paper: Schwarz J and Heider D, Bioinformatics 2019, 35(14):2458-2465.
Author: Johanna Schwarz, Dominik Heider
Maintainer: Dominik Heider <heiderd@mathematik.uni-marburg.de>
Diff between CalibratR versions 0.1.1 dated 2018-08-27 and 0.1.2 dated 2019-08-19
DESCRIPTION | 11 +++++------ MD5 | 13 +++++++------ NAMESPACE | 8 ++++++-- R/build_GUESS.R | 3 ++- R/getECE.R | 5 +++-- R/getMCE.R | 3 ++- R/predict_GUESS.R | 3 ++- inst |only 8 files changed, 27 insertions(+), 19 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@ab.mpg.de>
Maintainer: Damien R. Farine <dfarine@ab.mpg.de>
Diff between asnipe versions 1.1.11 dated 2018-11-22 and 1.1.12 dated 2019-08-19
DESCRIPTION | 12 ++++----- MD5 | 14 +++++----- R/get_network.R | 59 +++++++++++++++++++++++++++++++-------------- R/get_sampling_periods.R | 2 - R/network_permutation.R | 34 ++++++++++++++++++++++--- man/asnipe-package.Rd | 6 ++-- man/get_network.Rd | 11 +++++++- man/network_permutation.Rd | 12 ++++++++- 8 files changed, 109 insertions(+), 41 deletions(-)
Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets
parallel processes send and receive messages,
and it can help coordinate the work
of complicated parallel tasks.
Processes can push new messages to the queue,
pop old messages, and obtain a
log of all the messages ever pushed. File locking
preserves the integrity of the data even when
multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Ian E. Fellows [ctb],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between txtq versions 0.1.4 dated 2019-07-19 and 0.1.5 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/utils.R | 2 +- tests/testthat/test-txtq.R | 7 +++++++ 5 files changed, 20 insertions(+), 9 deletions(-)
Title: Interfaces to Various State-of-Art SVD and Eigensolvers
Description: R bindings to SVD and eigensolvers (PROPACK, nuTRLan).
Author: Anton Korobeynikov [aut, cre], Rasmus Munk Larsen [ctb, cph], Lawrence Berkeley National Laboratory [ctb, cph]
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between svd versions 0.4.3 dated 2019-04-05 and 0.5 dated 2019-08-19
svd-0.4.3/svd/src/propack/printstat.f |only svd-0.5/svd/DESCRIPTION | 6 +++--- svd-0.5/svd/MD5 | 24 ++++++++++++------------ svd-0.5/svd/src/Makevars | 2 +- svd-0.5/svd/src/propack/printstat.f90 |only svd-0.5/svd/src/propack/propack_svd.c | 31 ++++++++++++------------------- svd-0.5/svd/src/propack/stat.h | 33 ++++++++++++++++----------------- svd-0.5/svd/src/trlan/dstqrb.c | 30 +++++++++++++++++------------- svd-0.5/svd/src/trlan/trlan.c | 14 +++++++++----- svd-0.5/svd/src/trlan/trlan_R.c | 10 +++++++--- svd-0.5/svd/src/trlan/trlaux.c | 9 +++++---- svd-0.5/svd/src/trlan/trlcore.c | 10 +++++++--- svd-0.5/svd/src/trlan/trlmap.c | 12 ++++++++---- svd-0.5/svd/src/trlan/ztrlan_R.c | 10 +++++++--- 14 files changed, 104 insertions(+), 87 deletions(-)
Title: 'Opal' Data Repository Client and 'DataSHIELD' Utils
Description: Data integration Web application for biobanks by 'OBiBa'. 'Opal' is
the core database application for biobanks. Participant data, once
collected from any data source, must be integrated and stored in a central
data repository under a uniform model. 'Opal' is such a central repository.
It can import, process, validate, query, analyze, report, and export data.
'Opal' is typically used in a research center to analyze the data acquired at
assessment centres. Its ultimate purpose is to achieve seamless
data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal'
web services and to perform operations on the R server side. 'DataSHIELD'
administration tools are also provided.
Author: Yannick Marcon [aut, cre] (<https://orcid.org/0000-0003-0138-2023>),
Amadou Gaye [ctb] (<https://orcid.org/0000-0002-1180-2792>),
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between opalr versions 1.1.0 dated 2019-06-26 and 1.2.0 dated 2019-08-19
opalr-1.1.0/opalr/man/dot-authToken.Rd |only opalr-1.2.0/opalr/DESCRIPTION | 6 - opalr-1.2.0/opalr/MD5 | 38 +++---- opalr-1.2.0/opalr/R/opal.admin.r | 2 opalr-1.2.0/opalr/R/opal.r | 79 +++++++++------ opalr-1.2.0/opalr/build/vignette.rds |binary opalr-1.2.0/opalr/inst/doc/opal-files.html | 10 + opalr-1.2.0/opalr/inst/doc/opal-projects.html | 10 + opalr-1.2.0/opalr/inst/doc/opal-rsession.html | 10 + opalr-1.2.0/opalr/inst/examples/opal-login-certificate.R |only opalr-1.2.0/opalr/inst/examples/opal-login-token.R |only opalr-1.2.0/opalr/inst/reports/basic/opal.Rmd | 6 - opalr-1.2.0/opalr/inst/reports/report-exec.R | 6 - opalr-1.2.0/opalr/inst/reports/table/opal-table.Rmd | 14 +- opalr-1.2.0/opalr/inst/reports/tutorial/opal-dev.Rmd | 6 - opalr-1.2.0/opalr/inst/reports/tutorial/opal-exec.R | 2 opalr-1.2.0/opalr/inst/reports/tutorial/opal-prod.Rmd | 6 - opalr-1.2.0/opalr/inst/reports/tutorial/opal-prod.html |only opalr-1.2.0/opalr/inst/reports/tutorial/opal.R | 4 opalr-1.2.0/opalr/man/dot-authorizationHeader.Rd |only opalr-1.2.0/opalr/man/dot-opal.login.Rd | 3 opalr-1.2.0/opalr/man/dot-tokenHeader.Rd |only opalr-1.2.0/opalr/man/opal.login.Rd | 20 +++ 23 files changed, 140 insertions(+), 82 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.2.0 dated 2019-05-08 and 2.3.0 dated 2019-08-19
MAINT.Data-2.2.0/MAINT.Data/R/Idtoutl_methods.R |only MAINT.Data-2.3.0/MAINT.Data/CHANGELOG | 2 MAINT.Data-2.3.0/MAINT.Data/DESCRIPTION | 10 MAINT.Data-2.3.0/MAINT.Data/MD5 | 83 ++-- MAINT.Data-2.3.0/MAINT.Data/NAMESPACE | 8 MAINT.Data-2.3.0/MAINT.Data/R/CEMGauss.R |only MAINT.Data-2.3.0/MAINT.Data/R/CPMaxLik.R | 3 MAINT.Data-2.3.0/MAINT.Data/R/ClasGenMetDef.R | 13 MAINT.Data-2.3.0/MAINT.Data/R/DACrossVal.R | 206 +++++------ MAINT.Data-2.3.0/MAINT.Data/R/IData.R | 60 +-- MAINT.Data-2.3.0/MAINT.Data/R/IdtMaxLikSN.R | 5 MAINT.Data-2.3.0/MAINT.Data/R/IdtMclust_methods.R | 155 ++++++-- MAINT.Data-2.3.0/MAINT.Data/R/IdtOutl_methods.R |only MAINT.Data-2.3.0/MAINT.Data/R/Idtmclust.R | 252 +++++++------- MAINT.Data-2.3.0/MAINT.Data/R/RepEMGauss.R |only MAINT.Data-2.3.0/MAINT.Data/R/RepLOptim.R | 18 - MAINT.Data-2.3.0/MAINT.Data/R/RestCPMaxLik.R | 2 MAINT.Data-2.3.0/MAINT.Data/R/RobMxtDEst.R | 1 MAINT.Data-2.3.0/MAINT.Data/R/Robldaqda.R | 2 MAINT.Data-2.3.0/MAINT.Data/R/fasttle.R | 1 MAINT.Data-2.3.0/MAINT.Data/R/fulltle.R | 1 MAINT.Data-2.3.0/MAINT.Data/R/lqda.R | 13 MAINT.Data-2.3.0/MAINT.Data/R/mle.R | 78 +++- MAINT.Data-2.3.0/MAINT.Data/R/mleVCOV.R | 2 MAINT.Data-2.3.0/MAINT.Data/R/q1Config.R |only MAINT.Data-2.3.0/MAINT.Data/R/sknda.R | 5 MAINT.Data-2.3.0/MAINT.Data/man/ConfTests-class.Rd | 6 MAINT.Data-2.3.0/MAINT.Data/man/IData-class.Rd | 152 ++++---- MAINT.Data-2.3.0/MAINT.Data/man/IDtOutl-class.Rd | 130 +++---- MAINT.Data-2.3.0/MAINT.Data/man/IdtMANOVA-class.Rd | 6 MAINT.Data-2.3.0/MAINT.Data/man/IdtOutl-methods.Rd | 6 MAINT.Data-2.3.0/MAINT.Data/man/LRTest-class.Rd | 6 MAINT.Data-2.3.0/MAINT.Data/man/MAINT.Data-package.Rd | 4 MAINT.Data-2.3.0/MAINT.Data/man/MANOVAPermTest.Rd |only MAINT.Data-2.3.0/MAINT.Data/man/RobEstControl-class.Rd | 4 MAINT.Data-2.3.0/MAINT.Data/man/RobEstControl.Rd | 4 MAINT.Data-2.3.0/MAINT.Data/man/fasttle-methods.Rd | 4 MAINT.Data-2.3.0/MAINT.Data/man/fulltle-methods.Rd | 4 MAINT.Data-2.3.0/MAINT.Data/man/getIdtOutl.Rd | 2 MAINT.Data-2.3.0/MAINT.Data/man/pcoordplot-methos.Rd |only MAINT.Data-2.3.0/MAINT.Data/man/plot-methods.Rd | 80 ++-- MAINT.Data-2.3.0/MAINT.Data/src/AuxTmplFoo.cpp | 32 - MAINT.Data-2.3.0/MAINT.Data/src/CEMGauss.cpp |only MAINT.Data-2.3.0/MAINT.Data/src/CEMGauss.h |only MAINT.Data-2.3.0/MAINT.Data/src/EigenTmplFoo.cpp | 88 ++++ MAINT.Data-2.3.0/MAINT.Data/src/MDataGaussLogLik.cpp |only MAINT.Data-2.3.0/MAINT.Data/src/MDataGaussLogLik.h |only MAINT.Data-2.3.0/MAINT.Data/src/registerDynamicSimbol.cpp | 4 48 files changed, 858 insertions(+), 594 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers. The package is enhanced when the 'gt' package is installed.
Use this code to install: 'remotes::install_github("rstudio/gt")'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 0.1.0 dated 2019-05-10 and 1.2.0 dated 2019-08-19
gtsummary-0.1.0/gtsummary/R/add_comparison.R |only gtsummary-0.1.0/gtsummary/R/add_global.R |only gtsummary-0.1.0/gtsummary/R/as_tibble.R |only gtsummary-0.1.0/gtsummary/R/bold_labels.R |only gtsummary-0.1.0/gtsummary/R/bold_levels.R |only gtsummary-0.1.0/gtsummary/R/fmt_beta.R |only gtsummary-0.1.0/gtsummary/R/fmt_percent.R |only gtsummary-0.1.0/gtsummary/R/fmt_pvalue.R |only gtsummary-0.1.0/gtsummary/R/fmt_regression.R |only gtsummary-0.1.0/gtsummary/R/fmt_table1.R |only gtsummary-0.1.0/gtsummary/R/fmt_uni_regression.R |only gtsummary-0.1.0/gtsummary/R/indent_key.R |only gtsummary-0.1.0/gtsummary/R/italicize_labels.R |only gtsummary-0.1.0/gtsummary/R/italicize_levels.R |only gtsummary-0.1.0/gtsummary/R/knit_print.R |only gtsummary-0.1.0/gtsummary/R/row_to_name.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_class.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_dichotomous_value.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_stat_display.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_summary_type.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_test.R |only gtsummary-0.1.0/gtsummary/R/utils-assign_var_label.R |only gtsummary-0.1.0/gtsummary/R/utils-calculate_pvalue.R |only gtsummary-0.1.0/gtsummary/R/utils-calculate_summary_stat.R |only gtsummary-0.1.0/gtsummary/R/utils-continuous_digits_guess.R |only gtsummary-0.1.0/gtsummary/R/utils-create_header.R |only gtsummary-0.1.0/gtsummary/R/utils-fill_blanks.R |only gtsummary-0.1.0/gtsummary/R/utils-get_by_info.R |only gtsummary-0.1.0/gtsummary/R/utils-null-default.R |only gtsummary-0.1.0/gtsummary/R/utils-parse_terms.R |only gtsummary-0.1.0/gtsummary/R/utils-pipe.R |only gtsummary-0.1.0/gtsummary/R/utils-summarize_categorical.R |only gtsummary-0.1.0/gtsummary/R/utils-summarize_continuous.R |only gtsummary-0.1.0/gtsummary/R/utils-table1_header.R |only gtsummary-0.1.0/gtsummary/R/utils-table1_input_checks.R |only gtsummary-0.1.0/gtsummary/R/utils-tee.R |only gtsummary-0.1.0/gtsummary/R/utils-tidy_wrap.R |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.R |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.Rmd |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_regression.html |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.R |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.Rmd |only gtsummary-0.1.0/gtsummary/inst/doc/fmt_table1.html |only gtsummary-0.1.0/gtsummary/man/add_comparison.Rd |only gtsummary-0.1.0/gtsummary/man/add_global.Rd |only gtsummary-0.1.0/gtsummary/man/add_global.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/add_global.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/add_q.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/add_q.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/as_data_frame.Rd |only gtsummary-0.1.0/gtsummary/man/as_tibble.Rd |only gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/as_tibble.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/assign_class.Rd |only gtsummary-0.1.0/gtsummary/man/assign_dichotomous_value.Rd |only gtsummary-0.1.0/gtsummary/man/assign_stat_display.Rd |only gtsummary-0.1.0/gtsummary/man/assign_summary_type.Rd |only gtsummary-0.1.0/gtsummary/man/assign_test.Rd |only gtsummary-0.1.0/gtsummary/man/bold_labels.Rd |only gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/bold_labels.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/bold_levels.Rd |only gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/bold_levels.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/bold_p.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/bold_p.fmt_table1.Rd |only 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gtsummary-0.1.0/gtsummary/man/indent_key.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/inline_text.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/inline_text.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_labels.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_labels.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_levels.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/italicize_levels.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/knit_print.Rd |only gtsummary-0.1.0/gtsummary/man/knit_print.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/knit_print.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/knit_print.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/modify_header.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/modify_header.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/modify_header.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/null-default.Rd |only gtsummary-0.1.0/gtsummary/man/parse_terms.Rd |only gtsummary-0.1.0/gtsummary/man/pipe.Rd |only gtsummary-0.1.0/gtsummary/man/print.fmt_regression.Rd |only gtsummary-0.1.0/gtsummary/man/print.fmt_table1.Rd |only gtsummary-0.1.0/gtsummary/man/print.fmt_uni_regression.Rd |only gtsummary-0.1.0/gtsummary/man/row_to_name.Rd |only gtsummary-0.1.0/gtsummary/man/summarize_categorical.Rd |only gtsummary-0.1.0/gtsummary/man/summarize_continuous.Rd |only gtsummary-0.1.0/gtsummary/man/tidy_wrap.Rd |only gtsummary-0.1.0/gtsummary/tests/testthat/test-add_global.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-as_tibble.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_percent.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_pvalue.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_regression.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-fmt_uni_regression.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-indent_key.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-inline_text.table1.R |only gtsummary-0.1.0/gtsummary/tests/testthat/test-table1.R |only gtsummary-0.1.0/gtsummary/vignettes/fmt_regression.Rmd |only gtsummary-0.1.0/gtsummary/vignettes/fmt_table1.Rmd |only gtsummary-1.2.0/gtsummary/DESCRIPTION | 81 - gtsummary-1.2.0/gtsummary/MD5 | 334 +++-- gtsummary-1.2.0/gtsummary/NAMESPACE | 196 ++- gtsummary-1.2.0/gtsummary/NEWS.md | 93 + gtsummary-1.2.0/gtsummary/R/add_global_p.R |only gtsummary-1.2.0/gtsummary/R/add_n.R | 143 +- gtsummary-1.2.0/gtsummary/R/add_nevent.R |only gtsummary-1.2.0/gtsummary/R/add_overall.R | 101 - gtsummary-1.2.0/gtsummary/R/add_p.R |only gtsummary-1.2.0/gtsummary/R/add_q.R | 251 +++- gtsummary-1.2.0/gtsummary/R/add_stat_label.R | 121 -- gtsummary-1.2.0/gtsummary/R/as_gt.R |only gtsummary-1.2.0/gtsummary/R/as_kable.R |only gtsummary-1.2.0/gtsummary/R/bold_italicise_labels_levels.R |only gtsummary-1.2.0/gtsummary/R/bold_p.R | 263 ++-- gtsummary-1.2.0/gtsummary/R/compat-lifecycle.R |only gtsummary-1.2.0/gtsummary/R/data.R | 2 gtsummary-1.2.0/gtsummary/R/deprecated.R |only gtsummary-1.2.0/gtsummary/R/gtsummary-package.R | 19 gtsummary-1.2.0/gtsummary/R/gtsummary_logo.R |only gtsummary-1.2.0/gtsummary/R/inline_text.R | 585 ++++++---- gtsummary-1.2.0/gtsummary/R/modify_header.R | 517 ++------ gtsummary-1.2.0/gtsummary/R/print.R | 180 ++- gtsummary-1.2.0/gtsummary/R/reexport.R |only gtsummary-1.2.0/gtsummary/R/select_helpers.R |only gtsummary-1.2.0/gtsummary/R/sort_p.R |only gtsummary-1.2.0/gtsummary/R/style_percent.R |only gtsummary-1.2.0/gtsummary/R/style_pvalue.R |only gtsummary-1.2.0/gtsummary/R/style_ratio.R |only gtsummary-1.2.0/gtsummary/R/style_sigfig.R |only 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gtsummary-1.2.0/gtsummary/inst/doc/tbl_summary.Rmd |only gtsummary-1.2.0/gtsummary/inst/doc/tbl_summary.html |only gtsummary-1.2.0/gtsummary/man/add_global_p.Rd |only gtsummary-1.2.0/gtsummary/man/add_global_p.tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/add_global_p.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/add_n.Rd | 42 gtsummary-1.2.0/gtsummary/man/add_nevent.Rd |only gtsummary-1.2.0/gtsummary/man/add_nevent.tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/add_nevent.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/add_overall.Rd | 41 gtsummary-1.2.0/gtsummary/man/add_p.Rd |only gtsummary-1.2.0/gtsummary/man/add_q.Rd | 15 gtsummary-1.2.0/gtsummary/man/add_q.tbl_summary.Rd |only gtsummary-1.2.0/gtsummary/man/add_q.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/add_stat_label.Rd | 43 gtsummary-1.2.0/gtsummary/man/as_gt.Rd |only gtsummary-1.2.0/gtsummary/man/as_kable.Rd |only gtsummary-1.2.0/gtsummary/man/assign_var_label.Rd | 5 gtsummary-1.2.0/gtsummary/man/bold_italicize_labels_levels.Rd |only gtsummary-1.2.0/gtsummary/man/bold_p.Rd | 17 gtsummary-1.2.0/gtsummary/man/bold_p.tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/bold_p.tbl_stack.Rd |only gtsummary-1.2.0/gtsummary/man/bold_p.tbl_summary.Rd |only gtsummary-1.2.0/gtsummary/man/bold_p.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/deprecated.Rd |only gtsummary-1.2.0/gtsummary/man/figures |only gtsummary-1.2.0/gtsummary/man/gtsummary-package.Rd | 45 gtsummary-1.2.0/gtsummary/man/gtsummary_logo.Rd |only gtsummary-1.2.0/gtsummary/man/inline_text.Rd | 17 gtsummary-1.2.0/gtsummary/man/inline_text.tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/inline_text.tbl_summary.Rd |only gtsummary-1.2.0/gtsummary/man/inline_text.tbl_survival.Rd |only gtsummary-1.2.0/gtsummary/man/inline_text.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/modify_header.Rd | 108 + gtsummary-1.2.0/gtsummary/man/print_gtsummary.Rd |only gtsummary-1.2.0/gtsummary/man/reexports.Rd |only gtsummary-1.2.0/gtsummary/man/select_helpers.Rd |only gtsummary-1.2.0/gtsummary/man/sort_p.Rd |only gtsummary-1.2.0/gtsummary/man/sort_p.tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/sort_p.tbl_summary.Rd |only gtsummary-1.2.0/gtsummary/man/sort_p.tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/style_percent.Rd |only gtsummary-1.2.0/gtsummary/man/style_pvalue.Rd |only gtsummary-1.2.0/gtsummary/man/style_ratio.Rd |only gtsummary-1.2.0/gtsummary/man/style_sigfig.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_merge.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_regression.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_stack.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_summary.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_survival.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_survival.survfit.Rd |only gtsummary-1.2.0/gtsummary/man/tbl_uvregression.Rd |only gtsummary-1.2.0/gtsummary/man/trial.Rd | 2 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_global_p.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-add_n.R | 9 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_nevent.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-add_overall.R | 18 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_p.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-add_p_test_safe.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-add_q.R | 45 gtsummary-1.2.0/gtsummary/tests/testthat/test-add_stat_label.R | 12 gtsummary-1.2.0/gtsummary/tests/testthat/test-as_gt.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-as_kable.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_dichotomous_value-.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_dichotomous_value.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-assign_summary_type.R | 2 gtsummary-1.2.0/gtsummary/tests/testthat/test-bold_italicize_labels_levels.R |only 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gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_survival.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-tbl_uvregression.R |only gtsummary-1.2.0/gtsummary/tests/testthat/test-utils-calculate_summary_stat.R |only gtsummary-1.2.0/gtsummary/vignettes/tbl_regression.Rmd |only gtsummary-1.2.0/gtsummary/vignettes/tbl_summary.Rmd |only 260 files changed, 2097 insertions(+), 1442 deletions(-)
Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape
constraints on the component functions of the linear predictor
(Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>.
Models can contain multiple shape constrained (univariate
and/or bivariate) and unconstrained terms. The routines of gam()
in package 'mgcv' are used for setting up the model matrix,
printing and plotting the results. Penalized likelihood
maximization based on Newton-Raphson method is used to fit a
model with multiple smoothing parameter selection by GCV or
UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>
Diff between scam versions 1.2-4 dated 2019-06-14 and 1.2-5 dated 2019-08-19
ChangeLog | 9 ++ DESCRIPTION | 8 +- MD5 | 20 ++--- R/bfgs.R | 133 +------------------------------------ R/estimate.scam.R | 183 ++++++++++++++++++++++++++++++++++++++++++++++++++-- R/print.scam.R | 2 R/scam.check.R | 12 ++- R/scam.r | 15 +++- build/partial.rdb |binary man/scam.Rd | 13 +++ man/scam.control.Rd | 10 ++ 11 files changed, 245 insertions(+), 160 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 0.9.9 dated 2019-07-14 and 1.0.0 dated 2019-08-19
DESCRIPTION | 11 MD5 | 42 - NAMESPACE | 2 NEWS.md | 26 R/FilePsInput.R | 277 ++++++---- R/FileRepeatedInput.R | 155 ++++- R/FileSurveyInput.R | 209 +++++-- R/coxph.R | 86 +-- R/csvFileInput.R | 166 ++++- R/gee.R | 112 ++-- R/jsBasicGadget.R | 181 ++++-- R/jsPropensityGadget.R | 257 ++++++--- R/jsRepeatedGadget.R | 189 +++++- R/jsSurveyGadget.R | 245 ++++++-- R/kaplan.R | 124 ++-- R/regress.R | 165 +++-- R/roc.R | 176 ++++-- R/tb1.R | 26 R/timeroc.R | 133 +++- inst/doc/jsmodule.html | 10 tests/testthat/shinytest/basic/app.R | 8 tests/testthat/shinytest/basic/tests/basicTest-expected/001.json | 1 22 files changed, 1808 insertions(+), 793 deletions(-)
Title: Incomplete Split-Plot Designs
Description: A collection of several functions related to construction and analysis of incomplete split-plot designs. The package contains functions to obtain and analyze incomplete split-plot designs for three kinds of situations namely (i) when blocks are complete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments, (ii) when blocks are incomplete with respect to main plot treatments and main plots are complete with respect to subplot treatments and (iii) when blocks are incomplete with respect to main plot treatments and main plots are incomplete with respect to subplot treatments.
Author: Baidya Nath Mandal [aut, cre],
Sukanta Dash [aut],
Rajender Parsad [aut]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Diff between ispd versions 0.1 dated 2019-07-18 and 0.2 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ispd.R | 30 +++++++++++++++--------------- 3 files changed, 21 insertions(+), 21 deletions(-)
Title: Methods for Closed Testing with Simes Inequality, in Particular
Hommel's Method
Description: Provides methods for closed testing using Simes local tests. In particular, calculates adjusted p-values for Hommel's multiple testing method, and provides lower confidence bounds for true discovery proportions. A robust but more conservative variant of the closed testing procedure that does not require the assumption of Simes inequality is also implemented. The methods have been described in detail in Goeman et al (2016) <arXiv:1611.06739v2>.
Author: Jelle Goeman, Rosa Meijer, Thijmen Krebs
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between hommel versions 1.2 dated 2018-11-15 and 1.3 dated 2019-08-19
ChangeLog | 5 + DESCRIPTION | 12 +- MD5 | 27 +++--- NAMESPACE | 2 R/RcppExports.R | 4 R/concentration-function.R | 3 R/discoveries-function.R | 109 ++++++------------------- R/localtest-function.R |only man/concentration-function.Rd | 2 man/fdp-function.Rd | 17 ++- man/hommel-class.Rd | 4 man/hommel-function.Rd | 4 man/localtest-function.Rd | 5 - src/RcppExports.cpp | 17 --- src/hommel.cpp | 182 +++++++++++++++++++++--------------------- 15 files changed, 172 insertions(+), 221 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Exploratory and descriptive analysis of event based data. Provides methods for describing and selecting process data, and for preparing event log data for process mining. Builds on the S3-class for event logs implemented in the package 'bupaR'.
Author: Gert Janssenswillen [aut, cre],
Marijke Swennen [ctb]
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between edeaR versions 0.8.2 dated 2019-02-22 and 0.8.3 dated 2019-08-19
DESCRIPTION | 18 - MD5 | 62 ++-- R/filter_endpoints_percentile.R | 6 R/filter_trace_frequency_percentile.R | 25 + R/resource_frequency_resource_activity.R | 3 build/vignette.rds |binary inst/doc/filters.html | 361 +++++++++++++++++++++++----- inst/doc/metrics.html | 399 ++++++++++++++++++++++++------- man/activity_frequency.Rd | 3 man/end_activities.Rd | 4 man/filter_activity.Rd | 3 man/filter_activity_presence.Rd | 7 man/filter_endpoints.Rd | 5 man/filter_lifecycle.Rd | 3 man/filter_lifecycle_presence.Rd | 7 man/filter_precedence.Rd | 7 man/filter_processing_time.Rd | 10 man/filter_throughput_time.Rd | 10 man/filter_time_period.Rd | 11 man/filter_trace_frequency.Rd | 4 man/filter_trim_lifecycle.Rd | 4 man/idle_time.Rd | 8 man/number_of_repetitions.Rd | 16 - man/number_of_selfloops.Rd | 12 man/processing_time.Rd | 16 - man/resource_involvement.Rd | 6 man/resource_specialisation.Rd | 10 man/size_of_repetitions.Rd | 11 man/start_activities.Rd | 4 man/throughput_time.Rd | 7 man/trace_coverage.Rd | 9 man/trace_length.Rd | 9 32 files changed, 785 insertions(+), 275 deletions(-)
Title: Fast Adaptive Spectral Clustering for Single and Multi-View Data
Description: A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens connections in the graph based on common nearest neighbours. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. The method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.
Author: Christopher R John, David Watson
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between Spectrum versions 0.7 dated 2019-07-29 and 0.8 dated 2019-08-19
Spectrum-0.7/Spectrum/man/CNN_kernel_mine_b.Rd |only Spectrum-0.8/Spectrum/DESCRIPTION | 8 - Spectrum-0.8/Spectrum/MD5 | 24 ++-- Spectrum-0.8/Spectrum/NAMESPACE | 2 Spectrum-0.8/Spectrum/R/data.R | 2 Spectrum-0.8/Spectrum/R/spectrum.R | 29 +++- Spectrum-0.8/Spectrum/R/spectrum_functions.R | 80 ++++++++++++- Spectrum-0.8/Spectrum/inst/doc/Spectrum_vignette.R | 11 + Spectrum-0.8/Spectrum/inst/doc/Spectrum_vignette.Rmd | 108 +++++++++++------- Spectrum-0.8/Spectrum/inst/doc/Spectrum_vignette.pdf |binary Spectrum-0.8/Spectrum/man/CNN_kernel.Rd |only Spectrum-0.8/Spectrum/man/Spectrum.Rd | 12 +- Spectrum-0.8/Spectrum/man/brain.Rd | 2 Spectrum-0.8/Spectrum/vignettes/Spectrum_vignette.Rmd | 108 +++++++++++------- 14 files changed, 265 insertions(+), 121 deletions(-)
Title: A Wrapper of the 'JavaScript' Library 'jExcel'
Description: An R interface to 'jExcel' library to create web-based interactive tables and spreadsheets compatible with 'Excel' or any other spreadsheet software.
Author: Swechhya Bista [aut, cre],
Kent Russell [ctb],
Mārcis Bratka [ctb]
Maintainer: Swechhya Bista <swechhyabista@gmail.com>
Diff between excelR versions 0.2.0 dated 2019-07-26 and 0.2.1 dated 2019-08-19
DESCRIPTION | 12 ++++--- MD5 | 12 +++---- NEWS.md | 10 ++++++ R/jexcel.R | 3 + inst/htmlwidgets/jexcel.js | 44 ++++++++++++++++++++++++--- inst/htmlwidgets/lib/jexcel/js/jexcel.min.js | 7 +++- man/excelTable.Rd | 1 7 files changed, 72 insertions(+), 17 deletions(-)
Title: 'RStudio' Add-in to Insert Markdown Citations
Description: Functions and an 'RStudio' add-in that search 'Bib(La)TeX'-files or
'Zotero' libraries (via the 'Better BibTeX' plugin) to insert formatted Markdown
citations into the current document.
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>),
Yihui Xie [ctb],
Robin Lovelace [ctb],
Garrick Aden-Buie [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between citr versions 0.3.1 dated 2019-08-06 and 0.3.2 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/insert_citation.R | 7 ++++--- 4 files changed, 15 insertions(+), 10 deletions(-)
Title: Accessing Statistics Canada Data Table and Vectors
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data
tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for
bilingual English or French language data retrieval, and bundles convenience functions
to make it easier to work with retrieved table data. Optional caching features are provided.
Author: Jens von Bergmann [cre],
Dmitry Shkolnik [aut]
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between cansim versions 0.3.0 dated 2019-07-18 and 0.3.1 dated 2019-08-19
DESCRIPTION | 6 +-- MD5 | 12 +++---- NEWS.md | 8 +++++ R/cansim_helpers.R | 79 +++++++++++++++++++++++++++++++++++++++------------ R/cansim_vectors.R | 71 +++++++++++++++++++++++++-------------------- README.md | 1 inst/doc/cansim.html | 46 ++++++++++++++++------------- 7 files changed, 143 insertions(+), 80 deletions(-)
Title: Goodness-of-Fit Test for Weibull Distribution (Weibullness)
Description: Performs a goodness-of-fit test of Weibull distribution (weibullness test) and provides the maximum likelihood estimates of the three-parameter Weibull distribution. Note that the threshold parameter is estimated based on the correlation from the Weibull plot. For more details, see Park (2018) <doi:10.1155/2018/6056975>. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (No. NRF-2017R1A2B4004169).
Author: Chanseok Park [aut, cre] (<https://orcid.org/0000-0002-2208-3498>)
Maintainer: Chanseok Park <statpnu@gmail.com>
Diff between weibullness versions 1.18.6 dated 2018-05-24 and 1.19.8 dated 2019-08-19
weibullness-1.18.6/weibullness/R/WeibullnessTest.R |only weibullness-1.18.6/weibullness/man/print.wp.test.critical.value.Rd |only weibullness-1.19.8/weibullness/DESCRIPTION | 25 +++--- weibullness-1.19.8/weibullness/MD5 | 23 +++-- weibullness-1.19.8/weibullness/NAMESPACE | 6 + weibullness-1.19.8/weibullness/R/weibull.estimate.R |only weibullness-1.19.8/weibullness/R/weibullness.R |only weibullness-1.19.8/weibullness/data/Weibull_Quantiles_from_3_to_1000-bunzip2.rda |binary weibullness-1.19.8/weibullness/inst/CITATION | 17 ++-- weibullness-1.19.8/weibullness/man/Weibull.Plot.Quantiles.Rd | 3 weibullness-1.19.8/weibullness/man/print.weibull.estimate.Rd |only weibullness-1.19.8/weibullness/man/print.wp.test.critical.Rd |only weibullness-1.19.8/weibullness/man/weibull.mle.Rd |only weibullness-1.19.8/weibullness/man/weibull.threshold.Rd |only weibullness-1.19.8/weibullness/man/weibull.wp.Rd |only weibullness-1.19.8/weibullness/man/wp.test.Rd | 39 +++------- weibullness-1.19.8/weibullness/man/wp.test.critical.Rd |only weibullness-1.19.8/weibullness/man/wp.test.pvalue.Rd |only 18 files changed, 59 insertions(+), 54 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information.
Author: Ali Mostafa [aut],
Mohamed Soudy [aut, cre]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 1.0.2 dated 2019-08-06 and 1.0.3 dated 2019-08-19
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/GetpdbStructure.R | 2 +- R/PlotProteinTaxa.R | 8 +++++--- R/PlotSummaryInfo.R | 11 +++++------ R/plot_GO.R | 16 +++++++--------- man/UniprotR.Rd | 5 +++++ 7 files changed, 32 insertions(+), 28 deletions(-)
Title: Interface to 'Tushare Pro' API
Description: Helps the R users to get data from 'Tushare Pro'<https://tushare.pro>.
'Tushare Pro' is a platform as well as a community with a lot of staffs working in financial area.
We support financial data such as stock price, financial report statements and digital coins data.
Author: Feifei ZHANG
Maintainer: Feifei ZHANG<tushare_pro@163.com>
Diff between Tushare versions 0.1.2 dated 2019-07-15 and 0.1.3 dated 2019-08-19
DESCRIPTION | 6 - MD5 | 6 - R/Tushare.R | 273 ++++++++++++++++++++++++++---------------------------- build/partial.rdb |binary 4 files changed, 142 insertions(+), 143 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: ORPHANED
Diff between lpSolve versions 5.6.13.2 dated 2019-08-04 and 5.6.13.3 dated 2019-08-19
DESCRIPTION | 6 ++--- MD5 | 6 ++--- src/hbio.c | 63 ++++++++++++++++++++++++++++++++++++++++-------------------- src/mmio.c | 2 - 4 files changed, 49 insertions(+), 28 deletions(-)
Title: Fractional Factorial Designs with 2-Level Factors
Description: Regular and non-regular Fractional Factorial 2-level designs
can be created. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias).
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between FrF2 versions 2.0 dated 2019-08-09 and 2.1 dated 2019-08-19
DESCRIPTION | 8 - MD5 | 39 +++-- NAMESPACE | 3 R/FF_from_X.R |only R/FrF2.R | 82 +++++++++--- R/colpick.R | 136 ++++++++++---------- R/colpickIV.R |only R/estimable2fis.R | 23 ++- R/godolphin.R | 4 R/mapcalc.block.R |only R/utilcat.R | 2 inst/NEWS | 37 +++++ man/FrF2-package.Rd | 8 - man/FrF2.Rd | 46 +++++- man/block.Rd | 16 +- man/estimable.2fis.Rd | 23 +++ man/godolphin.Rd | 112 ++++++++++++++-- man/utilitiesCat.Rd | 9 + tests/FrF2test.R | 19 ++ tests/FrF2test.Rout.save | 280 ++++++++++++++++++++++++++++++++++++++---- tests/godolphintest.R | 7 - tests/godolphintest.Rout.save | 24 ++- 22 files changed, 695 insertions(+), 183 deletions(-)
Title: Data Set for the 'benchmarkme' Package
Description: Crowd sourced benchmarks from running the
'benchmarkme' package.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie <csgillespie@gmail.com>
Diff between benchmarkmeData versions 1.0.1 dated 2019-03-08 and 1.0.2 dated 2019-08-19
DESCRIPTION | 28 +++++++++++++++++----------- MD5 | 8 ++++---- NEWS.md | 3 +++ data/past_results.RData |binary data/past_results_v2.RData |binary 5 files changed, 24 insertions(+), 15 deletions(-)
More information about benchmarkmeData at CRAN
Permanent link
Title: Unit Root Tests for Seasonal Time Series
Description: Seasonal unit roots and seasonal stability tests.
P-values based on response surface regressions are available for both tests.
P-values based on bootstrap are available for seasonal unit root tests.
A parallel implementation of the bootstrap method requires a CUDA capable GPU
with compute capability >= 3.0, otherwise a debugging version fully coded in R is used.
Author: Javier López-de-Lacalle [aut],
Georgi N. Boshnakov [cre]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between uroot versions 2.0-10 dated 2019-06-24 and 2.0-11 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++++++++ build/vignette.rds |binary configure | 2 +- configure.ac | 2 +- inst/doc/uroot-intro.pdf |binary 7 files changed, 20 insertions(+), 12 deletions(-)
Title: Load Data from 'MyTarget API v2'
Description: Allows work with 'MyTarget API v2'
<https://target.my.com/doc/apiv2/ru/detailed.html> and
load data by ads, campaigns, agency clients and statistic from
your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rmytarget versions 2.1.7 dated 2019-05-27 and 2.1.8 dated 2019-08-19
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NEWS.md | 4 ++++ R/myTarGetStats.R | 2 +- README.md | 8 +++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rmytarget-auth.html | 4 ++-- inst/doc/rmytarget-intro.html | 4 ++-- inst/logo |only 10 files changed, 28 insertions(+), 20 deletions(-)
Title: Mixtures of Continuous Time Markov Models
Description: Provides an expectation maximization (EM) algorithm to fit a mixture of continuous time Markov models for use with clickstream or other sequence type data. Gallaugher, M.P.B and McNicholas, P.D. (2018) <arXiv:1802.04849>.
Author: Michael P.B. Gallaugher, Paul D. McNicholas
Maintainer: Michael P.B. Gallaugher <gallaump@mcmaster.ca>
Diff between ClickClustCont versions 0.1.6 dated 2019-08-08 and 0.1.7 dated 2019-08-19
ChangeLog |only DESCRIPTION | 8 ++++---- MD5 | 9 ++++++--- data/mMSNBC.rda |only man/ClickClust_EM.Rd | 5 ++++- man/SimData.Rd | 5 ++++- man/mMSNBC.Rd |only 7 files changed, 18 insertions(+), 9 deletions(-)
More information about ClickClustCont at CRAN
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Title: Bayesian Inference for Directed Acyclic Graphs
Description: Implementation of a collection of MCMC methods for Bayesian structure learning
of directed acyclic graphs (DAGs), both from continuous and discrete data. For efficient
inference on larger DAGs, the space of DAGs is pruned according to the data. To filter
the search space, the algorithm employs a hybrid approach, combining constraint-based
learning with search and score. A reduced search space is initially defined on the basis
of a skeleton obtained by means of the PC-algorithm, and then iteratively improved with
search and score. Search and score is then performed following two approaches:
Order MCMC, or Partition MCMC.
The BGe score is implemented for continuous data and the BDe score is implemented
for binary data or categorical data. The algorithms may provide the maximum a posteriori
(MAP) graph or a sample (a collection of DAGs) from the posterior distribution given the data.
All algorithms are also applicable to structure learning of dynamic Bayesian networks.
References:
J. Kuipers, P. Suter and G. Moffa (2018) <arXiv:1803.07859v2>,
N. Friedman and D. Koller (2003) <doi:10.1023/A:1020249912095>,
D. Geiger and D. Heckerman (2002) <doi:10.1214/aos/1035844981>,
J. Kuipers and G. Moffa (2017) <doi:10.1080/01621459.2015.1133426>,
M. Kalisch et al.(2012) <doi:10.18637/jss.v047.i11>.
Author: Polina Suter [aut, cre], Jack Kuipers [aut]
Maintainer: Polina Suter <polina.minkina@bsse.ethz.ch>
Diff between BiDAG versions 1.1.2 dated 2018-05-24 and 1.2.0 dated 2019-08-19
DESCRIPTION | 24 - MD5 | 79 ++-- NAMESPACE | 6 R/RcppExports.R | 12 R/WeightedCI.R | 95 ++++ R/corescore.R | 232 +++++++---- R/genericmethods.R | 119 ++++-- R/initpar.R | 333 +++++++++++++++- R/iterativeMCMC.R | 823 +++++++++++++++++++++++++----------------- R/main.R | 32 + R/newcatscoring.R |only R/orderMCMCbase.R | 32 + R/orderMCMCbasemax.R | 30 - R/orderMCMCplus1.R | 28 - R/orderMCMCplus1max.R | 32 - R/orderposetfns.R | 61 ++- R/orderscore.R | 73 ++- R/orderscoremax.R | 24 - R/other.R | 8 R/partitionMCMC.R | 82 ++-- R/partitionMCMCmain.R | 74 ++- R/partitionfns.R | 12 R/partitionmoves.R | 361 +++++++++++++++++- R/partitionposetfns.R | 147 +++++-- R/partitionscore.R | 144 ++++--- R/performanceassess.R | 28 - R/samplefns.R | 158 +++++++- R/scoreagainstdag.R | 184 ++++++--- R/scorefns.R | 115 ++--- R/spacefns.R | 111 +++-- R/usrscorefns.R |only man/DAGscore.Rd | 8 man/edges.posterior.Rd | 6 man/iterativeMCMCsearch.Rd | 9 man/orderMCMC.Rd | 11 man/partitionMCMC.Rd | 2 man/sample.check.Rd | 4 man/scoreagainstDAG.Rd | 11 man/scoreparameters.Rd | 42 +- man/scoreparameters.tested.Rd |only src/RcppExports.cpp | 49 ++ src/cppfns.cpp | 37 + 42 files changed, 2629 insertions(+), 1009 deletions(-)