Title: The R Version of WebGestalt
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 324 gene identifiers and 150,937 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis. The user-friendly output interface allow interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneous analyze multiple gene lists.
Author: Jing Wang <jingwang.uestc@gmail.com>
Maintainer: Jing Wang <jingwang.uestc@gmail.com>
Diff between WebGestaltR versions 0.0.8 dated 2017-03-08 and 0.0.9 dated 2017-04-25
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 2 R/WebGestaltR.R | 148 ++++++++++++++++++++++++++++++++++++---------- R/readGMT.R | 4 - inst/doc/WebGestaltR.R | 2 inst/doc/WebGestaltR.Rnw | 7 +- inst/doc/WebGestaltR.pdf |binary man/WebGestaltR.Rd | 9 ++ vignettes/WebGestaltR.Rnw | 7 +- 10 files changed, 149 insertions(+), 56 deletions(-)
Title: Streamline Bioacoustic Analysis
Description: A tool to streamline the analysis of animal acoustic signal structure. The package offers functions for downloading avian vocalizations from the open-access online repository Xeno-Canto, displaying the geographic extent of the recordings, manipulating sound files, detecting acoustic signals or importing detected signals from other software, assessing performance of methods that measure acoustic similarity, conducting cross-correlations, dynamic time warping, measuring acoustic parameters and analysing interactive vocal signals, among others. Most functions working iteratively allow parallelization to improve computational efficiency.
Author: Marcelo Araya-Salas & Grace Smith Vidaurre
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Diff between warbleR versions 1.1.6 dated 2017-04-05 and 1.1.7 dated 2017-04-25
DESCRIPTION | 17 +- MD5 | 67 +++++----- NAMESPACE | 5 NEWS.md | 11 + R/autodetec.R | 7 + R/catalog.R | 120 ++++++++++-------- R/catalog2pdf.R | 25 ++- R/compare.methods.R | 7 + R/coor.test.R | 7 + R/dfts.R | 7 + R/ffts.R | 7 + R/lspec.R | 7 + R/lspec2pdf.R | 11 + R/mp32wav.R | 7 + R/querxc.R | 15 ++ R/seltailor.R | 265 +++++++++++++++++++++++------------------ R/snrspecs.R | 6 R/specan.R | 63 ++++++--- R/specreator.R | 7 + R/warbleR-package.R | 9 - R/zzz.R |only build/vignette.rds |binary data/Cryp.soui.rda |binary data/Phae.long1.rda |binary data/Phae.long2.rda |binary data/Phae.long3.rda |binary data/Phae.long4.rda |binary data/selec.table.rda |binary data/selection.files.rda |binary data/sim.coor.sing.rda |binary inst/doc/warbleR_workflow.html | 4 man/querxc.Rd | 8 - man/seltailor.Rd | 26 +++- man/specan.Rd | 13 +- man/warbleR.Rd | 4 35 files changed, 465 insertions(+), 260 deletions(-)
Title: Statistical Inference of Vine Copulas
Description: Provides tools for the statistical analysis of vine copula models.
The package includes tools for parameter estimation, model selection,
simulation, goodness-of-fit tests, and visualization. Tools for estimation,
selection and exploratory data analysis of bivariate copula models are also
provided.
Author: Ulf Schepsmeier [aut],
Jakob Stoeber [aut],
Eike Christian Brechmann [aut],
Benedikt Graeler [aut],
Thomas Nagler [aut, cre],
Tobias Erhardt [aut],
Carlos Almeida [ctb],
Aleksey Min [ctb, ths],
Claudia Czado [ctb, ths],
Mathias Hofmann [ctb],
Matthias Killiches [ctb],
Harry Joe [ctb],
Thibault Vatter [ctb]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between VineCopula versions 2.1.1 dated 2017-01-11 and 2.1.2 dated 2017-04-25
DESCRIPTION | 12 MD5 | 249 ++++---- NEWS.md | 23 R/0_prep_object.R | 1 R/BB1copula.R | 623 ++++++++++---------- R/BB6copula.R | 623 ++++++++++---------- R/BB7copula.R | 629 ++++++++++----------- R/BB8copula.R | 673 +++++++++++----------- R/BiCopCDF.R | 20 R/BiCopCheck.R | 33 + R/BiCopChiPlot.R | 1 R/BiCopCompare.R | 2 R/BiCopDeriv.R | 1 R/BiCopDeriv2.R | 2 R/BiCopEst.R | 2 R/BiCopHfuncDeriv.R | 1 R/BiCopHfuncDeriv2.R | 1 R/BiCopHinv.R | 1 R/BiCopIndTest.R | 1 R/BiCopName.R | 741 ++++++++++++------------ R/BiCopPDF.R | 1 R/BiCopPar2Tau.R | 1 R/BiCopTau2Par.R | 1 R/ClaytonGumbelCopula.R | 1108 ++++++++++++++++++------------------- R/RVineClarkeTest.R | 2 R/RVineCopSelect.R | 2 R/RVineMLE.R | 1 R/RVineMatrix.R | 4 R/RVineMatrixSample.R | 19 R/RVineSim.R | 1 R/RVineStructureSelect.R | 2 R/RVineVuongTest.R | 1 R/as.copuladata.R | 131 ++-- R/joeBiCopula.R | 709 +++++++++++------------ R/pairs.R | 1 R/plot.RVineMatrix.R | 2 R/preprocessors.R | 78 +- R/tawnCopula.R | 1256 ++++++++++++++++++++---------------------- R/vineCopulas.R | 345 +++++------ README.md | 5 man/BB1Copula-class.Rd | 40 - man/BB1Copula.Rd | 11 man/BB6Copula-class.Rd | 40 - man/BB6Copula.Rd | 11 man/BB7Copula-class.Rd | 40 - man/BB7Copula.Rd | 11 man/BB8Copula-class.Rd | 40 - man/BB8Copula.Rd | 11 man/BetaMatrix.Rd | 7 man/BiCop.Rd | 7 man/BiCopCDF.Rd | 7 man/BiCopCheck.Rd | 1 man/BiCopChiPlot.Rd | 7 man/BiCopCompare.Rd | 3 man/BiCopCondSim.Rd | 7 man/BiCopDeriv.Rd | 7 man/BiCopDeriv2.Rd | 8 man/BiCopEst.Rd | 7 man/BiCopEstList.Rd | 7 man/BiCopGofTest.Rd | 7 man/BiCopHfunc.Rd | 9 man/BiCopHfuncDeriv.Rd | 7 man/BiCopHfuncDeriv2.Rd | 7 man/BiCopHinv.Rd | 9 man/BiCopIndTest.Rd | 7 man/BiCopKDE.Rd | 1 man/BiCopKPlot.Rd | 7 man/BiCopLambda.Rd | 7 man/BiCopMetaContour.Rd | 7 man/BiCopName.Rd | 7 man/BiCopPDF.Rd | 7 man/BiCopPar2Beta.Rd | 7 man/BiCopPar2TailDep.Rd | 7 man/BiCopPar2Tau.Rd | 7 man/BiCopSelect.Rd | 7 man/BiCopSim.Rd | 7 man/BiCopTau2Par.Rd | 7 man/BiCopVuongClarke.Rd | 7 man/C2RVine.Rd | 7 man/D2RVine.Rd | 7 man/RVineAIC.Rd | 8 man/RVineClarkeTest.Rd | 8 man/RVineCopSelect.Rd | 9 man/RVineCor2pcor.Rd | 2 man/RVineGofTest.Rd | 7 man/RVineGrad.Rd | 7 man/RVineHessian.Rd | 7 man/RVineLogLik.Rd | 7 man/RVineMLE.Rd | 7 man/RVineMatrix.Rd | 9 man/RVineMatrixCheck.Rd | 7 man/RVineMatrixNormalize.Rd | 1 man/RVineMatrixSample.Rd | 11 man/RVinePDF.Rd | 7 man/RVinePIT.Rd | 7 man/RVinePar2Beta.Rd | 7 man/RVinePar2Tau.Rd | 7 man/RVineSeqEst.Rd | 7 man/RVineSim.Rd | 7 man/RVineStdError.Rd | 7 man/RVineStructureSelect.Rd | 9 man/RVineTreePlot.Rd | 7 man/RVineVuongTest.Rd | 7 man/TauMatrix.Rd | 7 man/VineCopula-package.Rd | 12 man/as.copuladata.Rd | 9 man/copulaFromFamilyIndex.Rd | 1 man/daxreturns.Rd | 1 man/ddCopula.Rd | 1 man/joeBiCopula-class.Rd | 42 - man/joeBiCopula.Rd | 11 man/pairs.copuladata.Rd | 13 man/plot.BiCop.Rd | 10 man/plot.RVineMatrix.Rd | 18 man/pobs.Rd | 1 man/surClaytonCopula-class.Rd | 28 man/surClaytonCopula.Rd | 5 man/surGumbelCopula-class.Rd | 28 man/surGumbelCopula.Rd | 5 man/tawnT1Copula-class.Rd | 38 - man/tawnT1Copula.Rd | 13 man/tawnT2Copula-class.Rd | 38 - man/tawnT2Copula.Rd | 13 man/vineCopula-class.Rd | 10 man/vineCopula.Rd | 7 src/init.c |only 126 files changed, 4096 insertions(+), 4103 deletions(-)
Title: Embedded JavaScript Engine for R
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between V8 versions 1.4 dated 2017-03-31 and 1.5 dated 2017-04-25
DESCRIPTION | 8 +- MD5 | 12 +-- NEWS | 3 build/vignette.rds |binary configure | 7 -- inst/doc/npm.html | 74 ++++++++++----------- inst/doc/v8_intro.html | 169 +++++++++++++++++++++++++------------------------ 7 files changed, 142 insertions(+), 131 deletions(-)
Title: Interface to 'subspaceMOA'
Description: An interface to 'subspaceMOA', a Framework for the Evaluation of subspace stream clustering algorithms. (see <http://dme.rwth-aachen.de/de/subspacemoa> for more information.)
Author: c(person("Marwan","Hassani",role=c("aut","cre"),email="rsubspace@cs.rwth-
aachen.de") person("Matthias","Hansen",role="aut"),
person("Yunsu","Kim",role="ctb"), person("Thomas","Seidl",role="ctb"),
person("University of","Waikato",role=c("ctb","cph")))
Maintainer: Marwan Hassani <rsubspace@cs.rwth-aachen.de>
Diff between subspaceMOA versions 0.5.2 dated 2016-12-28 and 0.6.0 dated 2017-04-25
subspaceMOA-0.5.2/subspaceMOA/inst/java/added.jar |only subspaceMOA-0.5.2/subspaceMOA/inst/java/trimmeddependencies.jar |only subspaceMOA-0.5.2/subspaceMOA/java/ClusteringAccessor.java |only subspaceMOA-0.5.2/subspaceMOA/java/DataStreamAccessor.java |only subspaceMOA-0.5.2/subspaceMOA/java/DataStreamBuilder.java |only subspaceMOA-0.5.2/subspaceMOA/java/MacroClustererBuilder.java |only subspaceMOA-0.5.2/subspaceMOA/java/Makefile |only subspaceMOA-0.5.2/subspaceMOA/java/MicroClustererBuilder.java |only subspaceMOA-0.5.2/subspaceMOA/java/SubspaceClustererBuilder.java |only subspaceMOA-0.6.0/subspaceMOA/DESCRIPTION | 26 - subspaceMOA-0.6.0/subspaceMOA/MD5 | 158 +++++-- subspaceMOA-0.6.0/subspaceMOA/NAMESPACE | 5 subspaceMOA-0.6.0/subspaceMOA/R/DSC_HDDStream.R | 6 subspaceMOA-0.6.0/subspaceMOA/R/DSC_PreDeConStream.R | 6 subspaceMOA-0.6.0/subspaceMOA/R/DSC_SubspaceMOA.R | 52 -- subspaceMOA-0.6.0/subspaceMOA/R/DSC_ThreeStage.R | 110 ----- subspaceMOA-0.6.0/subspaceMOA/R/DSD_RandomRBFSubspaceGeneratorEvents.R | 6 subspaceMOA-0.6.0/subspaceMOA/R/DSD_SubspaceARFFStream.R | 8 subspaceMOA-0.6.0/subspaceMOA/R/DSD_SubspaceMOA.R | 2 subspaceMOA-0.6.0/subspaceMOA/R/evaluate.R |only subspaceMOA-0.6.0/subspaceMOA/R/helper.R | 43 -- subspaceMOA-0.6.0/subspaceMOA/R/macro.R | 8 subspaceMOA-0.6.0/subspaceMOA/R/micro.R | 4 subspaceMOA-0.6.0/subspaceMOA/R/plot.R | 204 ++++++---- subspaceMOA-0.6.0/subspaceMOA/inst/java/subspacemoa-rjar.jar |only subspaceMOA-0.6.0/subspaceMOA/java/moa |only subspaceMOA-0.6.0/subspaceMOA/man/DSC_HDDStream.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_PreDeConStream.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_ThreeStage.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_clique.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_p3c.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_proclus.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_subclu.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_subspaceCluStream.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSC_subspaceDenStream.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSD_RandomRBFSubspaceGeneratorEvents.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/DSD_SubspaceARFFStream.Rd | 1 subspaceMOA-0.6.0/subspaceMOA/man/animate_stream_interactive.Rd | 17 subspaceMOA-0.6.0/subspaceMOA/man/evaluate_subspace.Rd |only subspaceMOA-0.6.0/subspaceMOA/man/plot_stream_interactive.Rd | 5 subspaceMOA-0.6.0/subspaceMOA/man/subspaceMOA.Rd | 1 41 files changed, 343 insertions(+), 329 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut],
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-30 dated 2017-04-16 and 0.6-31 dated 2017-04-25
ChangeLog | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/gwr.R | 4 ++-- build/vignette.rds |binary inst/ChangeLog | 9 +++++++++ inst/doc/GWR.pdf |binary 7 files changed, 30 insertions(+), 12 deletions(-)
Title: Semiparametric Estimating Functions
Description: Functions for fitting semiparametric regression models for
panel count survival data. See Wang and Yan (2011)
<DOI:10.1016/j.cmpb.2010.10.005> for more details.
Author: Xiaojing Wang <wangxj03@gmail.com> and Jun Yan
<jyan@stat.uconn.edu>
Maintainer: Sy Han (Steven) Chiou <schiou@hsph.harvard.edu>
Diff between spef versions 1.0-1 dated 2016-09-22 and 1.0-3 dated 2017-04-25
ChangeLog | 2 DESCRIPTION | 16 - MD5 | 20 + NAMESPACE | 12 - R/PanelSurv.R | 4 R/panelReg.R | 633 ++++++++++++++++++++++++++++++----------------------- data/skinTumor.rda |only man/blaTum.Rd | 8 man/bladTumor.Rd | 20 - man/panelReg.Rd | 13 - man/skinTumor.Rd |only src |only 12 files changed, 426 insertions(+), 302 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.6-12 dated 2017-04-06 and 0.6-13 dated 2017-04-25
ChangeLog | 18 ++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/kpgm_new.R | 4 +++- build/vignette.rds |binary inst/ChangeLog | 18 ++++++++++++++++++ inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/nb_igraph.html | 2 +- inst/doc/sids.pdf |binary man/GMerrorsar.Rd | 6 ++++++ src/dnn.c | 20 +++++++++++++++++++- 13 files changed, 81 insertions(+), 19 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut, cre],
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between sparklyr versions 0.5.3 dated 2017-03-12 and 0.5.4 dated 2017-04-25
DESCRIPTION | 8 - MD5 | 215 ++++++++++++++++---------------- NAMESPACE | 4 R/dbi_spark_connection.R | 4 R/dbi_spark_query.R | 12 - R/dbi_spark_table.R | 9 - R/dplyr_s3.R |only R/dplyr_spark.R | 7 - R/dplyr_spark_connection.R | 24 +-- R/dplyr_spark_data.R | 6 R/dplyr_spark_table.R | 7 - R/dplyr_sql.R | 8 - R/spark_compile.R | 5 R/zzz.R | 2 README.md | 45 +++--- inst/java/sparklyr-2.1-2.11.jar |only man/DBISparkResult-class.Rd | 2 man/compile_package_jars.Rd | 1 man/connection_config.Rd | 1 man/connection_is_open.Rd | 1 man/copy_to.spark_connection.Rd | 9 - man/ensure.Rd | 9 - man/find_scalac.Rd | 1 man/ft_binarizer.Rd | 1 man/ft_bucketizer.Rd | 1 man/ft_discrete_cosine_transform.Rd | 1 man/ft_elementwise_product.Rd | 1 man/ft_index_to_string.Rd | 1 man/ft_one_hot_encoder.Rd | 1 man/ft_quantile_discretizer.Rd | 1 man/ft_regex_tokenizer.Rd | 1 man/ft_sql_transformer.Rd | 1 man/ft_string_indexer.Rd | 1 man/ft_tokenizer.Rd | 1 man/ft_vector_assembler.Rd | 1 man/invoke.Rd | 6 man/invoke_method.Rd | 1 man/livy_config.Rd | 1 man/livy_install.Rd | 5 man/livy_service.Rd | 1 man/ml_als_factorization.Rd | 1 man/ml_binary_classification_eval.Rd | 1 man/ml_classification_eval.Rd | 1 man/ml_decision_tree.Rd | 1 man/ml_generalized_linear_regression.Rd | 1 man/ml_gradient_boosted_trees.Rd | 1 man/ml_kmeans.Rd | 1 man/ml_lda.Rd | 1 man/ml_linear_regression.Rd | 1 man/ml_logistic_regression.Rd | 1 man/ml_model.Rd | 1 man/ml_multilayer_perceptron.Rd | 1 man/ml_naive_bayes.Rd | 1 man/ml_one_vs_rest.Rd | 1 man/ml_options.Rd | 1 man/ml_pca.Rd | 1 man/ml_prepare_dataframe.Rd | 1 man/ml_prepare_inputs.Rd | 5 man/ml_random_forest.Rd | 1 man/ml_saveload.Rd | 3 man/ml_survival_regression.Rd | 1 man/ml_tree_feature_importance.Rd | 1 man/na.replace.Rd | 1 man/pipe.Rd | 2 man/print_jobj.Rd | 1 man/reexports.Rd | 4 man/register_extension.Rd | 1 man/sdf-saveload.Rd | 5 man/sdf_copy_to.Rd | 3 man/sdf_mutate.Rd | 3 man/sdf_partition.Rd | 2 man/sdf_persist.Rd | 1 man/sdf_predict.Rd | 1 man/sdf_quantile.Rd | 1 man/sdf_read_column.Rd | 1 man/sdf_register.Rd | 2 man/sdf_sample.Rd | 2 man/sdf_schema.Rd | 1 man/sdf_sort.Rd | 2 man/sdf_with_unique_id.Rd | 1 man/spark-api.Rd | 8 - man/spark-connections.Rd | 5 man/spark_compilation_spec.Rd | 1 man/spark_compile.Rd | 1 man/spark_config.Rd | 1 man/spark_connection.Rd | 1 man/spark_dataframe.Rd | 1 man/spark_default_compilation_spec.Rd | 1 man/spark_dependency.Rd | 1 man/spark_home_dir.Rd | 1 man/spark_install.Rd | 5 man/spark_jobj.Rd | 1 man/spark_load_table.Rd | 1 man/spark_log.Rd | 1 man/spark_read_csv.Rd | 1 man/spark_read_json.Rd | 1 man/spark_read_parquet.Rd | 1 man/spark_save_table.Rd | 1 man/spark_version.Rd | 1 man/spark_version_from_home.Rd | 1 man/spark_web.Rd | 1 man/spark_write_csv.Rd | 1 man/spark_write_json.Rd | 1 man/spark_write_parquet.Rd | 1 man/tbl_cache.Rd | 1 man/tbl_uncache.Rd | 1 tests/testthat/test-serialization.R | 3 tools |only 108 files changed, 232 insertions(+), 280 deletions(-)
Title: Constrained Single Index Model Estimation
Description: Estimation of function and index vector in single index model with and without shape constraints including different smoothness conditions.
Author: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>,
Rohit Kumar Patra <rohit@stat.columbia.edu>
Maintainer: Arun Kumar Kuchibhotla <arunku@wharton.upenn.edu>
Diff between simest versions 0.3 dated 2016-09-05 and 0.4 dated 2017-04-25
simest-0.3/simest/src/Mfun.c |only simest-0.3/simest/src/deriv.c |only simest-0.3/simest/src/derivcvxpen.c |only simest-0.3/simest/src/pred.c |only simest-0.4/simest/DESCRIPTION | 12 ++--- simest-0.4/simest/MD5 | 53 +++++++++++++------------ simest-0.4/simest/NAMESPACE | 9 ++-- simest-0.4/simest/R/CvxLipReg.r | 2 simest-0.4/simest/R/CvxLseConReg.r |only simest-0.4/simest/R/CvxLseReg.r | 2 simest-0.4/simest/R/CvxPenReg.r | 6 +- simest-0.4/simest/R/SimEst.r | 64 ++++++++++++++++++------------ simest-0.4/simest/R/SmoothPenReg.r | 4 - simest-0.4/simest/R/SolvePenta.r | 5 -- simest-0.4/simest/README | 6 +- simest-0.4/simest/inst/CITATION | 4 - simest-0.4/simest/man/cpen.rd |only simest-0.4/simest/man/cvx.lip.reg.Rd | 10 ++-- simest-0.4/simest/man/cvx.lse.con.reg.rd |only simest-0.4/simest/man/cvx.lse.reg.Rd | 10 ++-- simest-0.4/simest/man/derivcvxpec.Rd |only simest-0.4/simest/man/fastmerge.Rd | 3 - simest-0.4/simest/man/penta.Rd |only simest-0.4/simest/man/predcvxpen.Rd |only simest-0.4/simest/man/sim.est.Rd | 47 +++++++++++----------- simest-0.4/simest/man/simestgcv.Rd | 9 +--- simest-0.4/simest/man/spen_egcv.Rd |only simest-0.4/simest/src/cpen.c | 65 +++++++++++++++++++++++++++---- simest-0.4/simest/src/derivcvxpec.c | 1 simest-0.4/simest/src/init.c |only simest-0.4/simest/src/penta.c | 1 simest-0.4/simest/src/predcvxpen.c | 30 +++++--------- simest-0.4/simest/src/simest.h |only simest-0.4/simest/src/spen_egcv.c | 1 34 files changed, 205 insertions(+), 139 deletions(-)
Title: Somoclu
Description: Somoclu is a massively parallel implementation of self-organizing maps. It exploits multicore CPUs and it can be accelerated by CUDA. The topology of the map can be planar or toroid and the grid of neurons can be rectangular or hexagonal .
Author: Peter Wittek [aut], Shichao Gao [cre]
Maintainer: Shichao Gao <xgdgsc@gmail.com>
Diff between Rsomoclu versions 1.7.2 dated 2016-11-24 and 1.7.3 dated 2017-04-25
Rsomoclu-1.7.2/Rsomoclu/src/Makefile.in |only Rsomoclu-1.7.2/Rsomoclu/src/Makefile.root.in |only Rsomoclu-1.7.2/Rsomoclu/src/config.h.in |only Rsomoclu-1.7.2/Rsomoclu/src/configure |only Rsomoclu-1.7.2/Rsomoclu/src/denseGpuKernels.cu |only Rsomoclu-1.7.2/Rsomoclu/src/install-sh |only Rsomoclu-1.7.3/Rsomoclu/DESCRIPTION | 10 +- Rsomoclu-1.7.3/Rsomoclu/MD5 | 29 ++----- Rsomoclu-1.7.3/Rsomoclu/NAMESPACE | 4 Rsomoclu-1.7.3/Rsomoclu/R/Rsomoclu.R | 2 Rsomoclu-1.7.3/Rsomoclu/data/rgbs.txt.gz |binary Rsomoclu-1.7.3/Rsomoclu/man/Rsomoclu.kohonen.Rd | 6 - Rsomoclu-1.7.3/Rsomoclu/man/Rsomoclu.train.Rd | 4 Rsomoclu-1.7.3/Rsomoclu/src/Rsomoclu.cpp | 2 Rsomoclu-1.7.3/Rsomoclu/src/Rsomoclu_init.c |only Rsomoclu-1.7.3/Rsomoclu/src/somoclu.h | 24 ++++- Rsomoclu-1.7.3/Rsomoclu/src/training.cpp | 93 ++++++++++++++++------- Rsomoclu-1.7.3/Rsomoclu/src/uMatrix.cpp | 68 +++++++++------- Rsomoclu-1.7.3/Rsomoclu/tests/R_interface_test.R | 6 - 19 files changed, 150 insertions(+), 98 deletions(-)
Title: Repeatability Estimation for Gaussian and Non-Gaussian Data
Description: Estimating repeatability (intra-class
correlation) from Gaussian, binary, proportion and count data.
Author: Martin Stoffel <martin.adam.stoffel@gmail.com>,
Shinichi Nakagawa <s.nakagawa@unsw.edu.au>,
Holger Schielzeth <holger.schielzeth@uni-jena.de>
Maintainer: Martin Stoffel <martin.adam.stoffel@gmail.com>
Diff between rptR versions 0.9.1 dated 2017-02-09 and 0.9.2 dated 2017-04-25
DESCRIPTION | 18 +-- MD5 | 55 +++++----- NEWS.md | 13 ++ R/internals.R | 31 +++-- R/rpt.R | 12 +- R/rptBinary.R | 45 ++++++-- R/rptGaussian.R | 61 +++++++---- R/rptPoisson.R | 13 ++ R/rptProportion.R | 11 ++ R/rptR.R | 11 +- README.md | 4 inst/CITATION |only inst/doc/rptR.R | 38 ++++--- inst/doc/rptR.Rmd | 143 ++++++++++++++------------ inst/doc/rptR.html | 195 +++++++++++++++++++++++------------- man/rpt.Rd | 4 man/rptBinary.Rd | 9 - man/rptGaussian.Rd | 2 man/rptPoisson.Rd | 2 man/rptProportion.Rd | 2 man/rptR.Rd | 9 + tests/testthat/test-rpt.R | 5 tests/testthat/test-rptBinary.R | 142 ++++++++++++-------------- tests/testthat/test-rptGaussian.R | 13 ++ tests/testthat/test-rptPoisson.R | 18 ++- tests/testthat/test-rptProportion.R | 2 tests/testthat/test-summary.rpt.R | 2 vignettes/rptR.Rmd | 143 ++++++++++++++------------ vignettes/vignette_out.RData |binary 29 files changed, 606 insertions(+), 397 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.2-6 dated 2017-04-06 and 1.2-7 dated 2017-04-25
ChangeLog | 33 +++++++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 28 ++++++++++----------- build/vignette.rds |binary configure | 18 +++++++------- inst/ChangeLog | 33 +++++++++++++++++++++++++ inst/SVN_VERSION | 2 - inst/doc/OGR_shape_encoding.pdf |binary man/writeOGR.Rd | 5 ++- src/OGR_write.cpp | 15 +++++++++++ src/ogr_proj.cpp | 6 ++-- src/ogrsource.cpp | 34 +++++++++++++++++++++++++- tests/tests.Rout.save | 12 +++++---- tests/tripup.R | 45 +++++++++++++++++++++-------------- tests/tripup.Rout.save | 51 +++++++++++++++++++++++----------------- 15 files changed, 210 insertions(+), 80 deletions(-)
Title: General Purpose Client for 'ERDDAP' Servers
Description: General purpose R client for 'ERDDAP' servers. Includes
functions to search for 'datasets', get summary information on
'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format.
'ERDDAP' information:
<https://upwell.pfeg.noaa.gov/erddap/information.html>.
Author: Scott Chamberlain [aut, cre],
Ben Tupper [ctb],
Roy Mendelssohn [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rerddap versions 0.3.4 dated 2016-01-14 and 0.4.0 dated 2017-04-25
rerddap-0.3.4/rerddap/NEWS |only rerddap-0.3.4/rerddap/R/tbldf.r |only rerddap-0.3.4/rerddap/man/type_sum.Rd |only rerddap-0.4.0/rerddap/DESCRIPTION | 33 +- rerddap-0.4.0/rerddap/LICENSE | 2 rerddap-0.4.0/rerddap/MD5 | 114 +++---- rerddap-0.4.0/rerddap/NAMESPACE | 22 - rerddap-0.4.0/rerddap/NEWS.md |only rerddap-0.4.0/rerddap/R/browse.R |only rerddap-0.4.0/rerddap/R/cache_delete.R | 14 rerddap-0.4.0/rerddap/R/cache_details.R | 7 rerddap-0.4.0/rerddap/R/cache_list.R | 2 rerddap-0.4.0/rerddap/R/colors.R |only rerddap-0.4.0/rerddap/R/convert_time.R | 19 - rerddap-0.4.0/rerddap/R/convert_units.R | 7 rerddap-0.4.0/rerddap/R/default-url.R | 2 rerddap-0.4.0/rerddap/R/fipscounty.R | 3 rerddap-0.4.0/rerddap/R/grid.R | 37 +- rerddap-0.4.0/rerddap/R/info.R | 49 +-- rerddap-0.4.0/rerddap/R/keywords.R | 10 rerddap-0.4.0/rerddap/R/ncdf_helpers.R | 25 + rerddap-0.4.0/rerddap/R/rerddap-package.r | 17 - rerddap-0.4.0/rerddap/R/search.R | 37 +- rerddap-0.4.0/rerddap/R/search_adv.R | 96 +++--- rerddap-0.4.0/rerddap/R/servers.R | 49 ++- rerddap-0.4.0/rerddap/R/table.R | 180 +++++++---- rerddap-0.4.0/rerddap/R/utils.R | 3 rerddap-0.4.0/rerddap/R/version.R | 3 rerddap-0.4.0/rerddap/R/zzz.r | 30 + rerddap-0.4.0/rerddap/README.md | 250 +++++----------- rerddap-0.4.0/rerddap/build/vignette.rds |binary rerddap-0.4.0/rerddap/data/colors.rda |only rerddap-0.4.0/rerddap/inst/doc/Using_rerddap.R |only rerddap-0.4.0/rerddap/inst/doc/Using_rerddap.Rmd |only rerddap-0.4.0/rerddap/inst/doc/Using_rerddap.html |only rerddap-0.4.0/rerddap/inst/extdata |only rerddap-0.4.0/rerddap/inst/vign/rerddap_vignette.Rmd | 2 rerddap-0.4.0/rerddap/man/browse.Rd |only rerddap-0.4.0/rerddap/man/cache_delete.Rd | 9 rerddap-0.4.0/rerddap/man/cache_details.Rd | 11 rerddap-0.4.0/rerddap/man/cache_list.Rd | 9 rerddap-0.4.0/rerddap/man/colors.Rd |only rerddap-0.4.0/rerddap/man/convert_time.Rd | 8 rerddap-0.4.0/rerddap/man/convert_units.Rd | 4 rerddap-0.4.0/rerddap/man/disk.Rd | 4 rerddap-0.4.0/rerddap/man/ed_search.Rd | 19 - rerddap-0.4.0/rerddap/man/ed_search_adv.Rd | 68 ++-- rerddap-0.4.0/rerddap/man/eurl.Rd | 1 rerddap-0.4.0/rerddap/man/fipscounty.Rd | 4 rerddap-0.4.0/rerddap/man/griddap.Rd | 117 ++++--- rerddap-0.4.0/rerddap/man/info.Rd | 25 - rerddap-0.4.0/rerddap/man/institutions.Rd | 1 rerddap-0.4.0/rerddap/man/ioos_categories.Rd | 1 rerddap-0.4.0/rerddap/man/key_words.Rd | 11 rerddap-0.4.0/rerddap/man/keywords.Rd | 1 rerddap-0.4.0/rerddap/man/longnames.Rd | 1 rerddap-0.4.0/rerddap/man/rerddap-package.Rd | 17 - rerddap-0.4.0/rerddap/man/servers.Rd | 1 rerddap-0.4.0/rerddap/man/standardnames.Rd | 1 rerddap-0.4.0/rerddap/man/tabledap.Rd | 162 ++++++---- rerddap-0.4.0/rerddap/man/variablenames.Rd | 1 rerddap-0.4.0/rerddap/man/version.Rd | 4 rerddap-0.4.0/rerddap/tests/testthat/test-ed_datasets.R | 4 rerddap-0.4.0/rerddap/tests/testthat/test-tabledap.R | 18 - rerddap-0.4.0/rerddap/vignettes/Using_rerddap.Rmd |only 65 files changed, 827 insertions(+), 688 deletions(-)
Title: Core Functionality for the 'rebus' Package
Description: Build regular expressions piece by piece using human readable code.
This package contains core functionality, and is primarily intended to be
used by package developers.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus.base versions 0.0-2 dated 2017-01-02 and 0.0-3 dated 2017-04-25
DESCRIPTION | 10 +++---- MD5 | 51 +++++++++++++++++++------------------ NAMESPACE | 6 ++++ NEWS | 5 ++- R/class-groups.R | 45 +++++++++++++++++++++++++++------ R/constants.R | 14 +++++++++- R/mode-modifiers.R | 37 +++++++++++++++++++++++++-- man/Anchors.Rd | 3 -- man/Backreferences.Rd | 36 +++++++++++++++++++------- man/CharacterClasses.Rd | 43 +++++++++++++++++++------------ man/ClassGroups.Rd | 64 ++++++++++++++++++++++++++++++----------------- man/Concatenation.Rd | 3 -- man/ReplacementCase.Rd |only man/SpecialCharacters.Rd | 15 +++++------ man/WordBoundaries.Rd | 3 -- man/as.regex.Rd | 1 man/capture.Rd | 3 -- man/char_class.Rd | 3 -- man/escape_special.Rd | 1 man/format.regex.Rd | 1 man/literal.Rd | 1 man/lookahead.Rd | 3 -- man/modify_mode.Rd | 7 ++--- man/or.Rd | 3 -- man/recursive.Rd | 1 man/regex.Rd | 1 man/repeated.Rd | 7 ++--- 27 files changed, 240 insertions(+), 127 deletions(-)
Title: Build Regular Expressions in a Human Readable Way
Description: Build regular expressions piece by piece using human readable code.
This package is designed for interactive use. For package development, use
the rebus.* dependencies.
Author: Richard Cotton [aut, cre]
Maintainer: Richard Cotton <richierocks@gmail.com>
Diff between rebus versions 0.1-2 dated 2017-01-03 and 0.1-3 dated 2017-04-25
DESCRIPTION | 12 +++--- MD5 | 71 +++++++++++++++++++------------------- NAMESPACE | 6 +++ NEWS | 1 R/export-base.R | 17 ++++++++- man/Anchors.Rd | 3 - man/Backreferences.Rd | 19 ++++------ man/CharacterClasses.Rd | 31 ++++++++-------- man/ClassGroups.Rd | 29 ++++++++------- man/Concatenation.Rd | 1 man/DateTime.Rd | 13 +++---- man/IsoClasses.Rd | 3 - man/ReplacementCase.Rd |only man/SpecialCharacters.Rd | 15 +++----- man/Unicode.Rd | 13 +++---- man/UnicodeGeneralCategory.Rd | 77 ++++++++++++++++++++---------------------- man/UnicodeOperators.Rd | 1 man/UnicodeProperty.Rd | 73 +++++++++++++++++++-------------------- man/WordBoundaries.Rd | 3 - man/as.regex.Rd | 1 man/capture.Rd | 3 - man/char_class.Rd | 3 - man/escape_special.Rd | 1 man/exactly.Rd | 1 man/format.regex.Rd | 1 man/get_weekdays.Rd | 3 - man/literal.Rd | 1 man/lookahead.Rd | 3 - man/modify_mode.Rd | 7 +-- man/number_range.Rd | 1 man/or.Rd | 3 - man/rebus.Rd | 8 ++-- man/recursive.Rd | 1 man/regex.Rd | 1 man/repeated.Rd | 7 +-- man/roman.Rd | 3 - man/whole_word.Rd | 1 37 files changed, 216 insertions(+), 221 deletions(-)
Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format (described at
<https://github.com/toml-lang/toml>) suitable for both human editing as well
as the common uses of a machine-readable format. This package uses 'Rcpp' to
connect the 'cpptoml' parser written by Chase Geigle (in modern C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.1.2 dated 2017-03-26 and 0.1.3 dated 2017-04-25
ChangeLog | 14 ++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/parseToml.R | 2 +- inst/NEWS.Rd | 6 ++++++ src/parse.cpp | 14 ++++++++++++-- tests/arrays.Rout.save | 18 +++++++++++------- tests/tomlExamples.Rout.save | 18 +++++++++++------- 8 files changed, 66 insertions(+), 28 deletions(-)
Title: Analyzing Archival Tagging Data
Description: A set of functions to generate, access and analyze standard data products from archival tagging data.
Author: Robert Bauer
Maintainer: Robert Bauer <robert.bauer@ird.fr>
Diff between RchivalTag versions 0.0.3 dated 2017-04-10 and 0.0.4 dated 2017-04-25
ChangeLog | 3 + DESCRIPTION | 6 +- MD5 | 8 +-- R/plot_TS.r | 107 +++++++++++++++++++++++++----------------------- inst/doc/RchivalTag.pdf |binary 5 files changed, 67 insertions(+), 57 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 0.8.0 dated 2017-04-24 and 0.8.1 dated 2017-04-25
DESCRIPTION | 13 ++++++------- MD5 | 14 +++++++------- NAMESPACE | 3 --- R/aaa.R | 1 - R/pivotr.R | 10 +++++----- R/radiant.R | 4 ++-- inst/app/tools/data/manage.R | 30 ++++++++++++++++++------------ inst/app/tools/data/manage_ui.R | 5 +++++ 8 files changed, 43 insertions(+), 37 deletions(-)
Title: Text Mining of PubMed Abstracts
Description: Text mining of PubMed Abstracts (text and XML) from <http://www.ncbi.nlm.nih.gov/pubmed>.
Author: Jyoti Rani, S.Ramachandran, Ab Rauf Shah
Maintainer: S. Ramachandran <ramuigib@gmail.com>
Diff between pubmed.mineR versions 1.0.8 dated 2017-02-09 and 1.0.9 dated 2017-04-25
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 1 + R/get_MedlinePlus.R |only man/get_MedlinePlus.Rd |only 5 files changed, 10 insertions(+), 7 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut],
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.5.6 dated 2016-11-11 and 4.6.0 dated 2017-04-25
plotly-4.5.6/plotly/R/figure.R |only plotly-4.5.6/plotly/R/plotly_POST.R |only plotly-4.5.6/plotly/R/sharingButton.R |only plotly-4.5.6/plotly/inst/examples/crosstalkShinyDT |only plotly-4.5.6/plotly/man/knit_print.plotly_figure.Rd |only plotly-4.5.6/plotly/man/print.plotly_figure.Rd |only plotly-4.5.6/plotly/tests/testthat/test-ggplot-linetype.R |only plotly-4.5.6/plotly/tests/testthat/test-ggplot-trace-order.R |only plotly-4.6.0/plotly/DESCRIPTION | 32 plotly-4.6.0/plotly/LICENSE | 4 plotly-4.6.0/plotly/MD5 | 263 +- plotly-4.6.0/plotly/NAMESPACE | 55 plotly-4.6.0/plotly/NEWS.md | 41 plotly-4.6.0/plotly/R/add.R | 3 plotly-4.6.0/plotly/R/animate.R |only plotly-4.6.0/plotly/R/api.R |only plotly-4.6.0/plotly/R/api_exports.R |only plotly-4.6.0/plotly/R/deprecated.R | 59 plotly-4.6.0/plotly/R/dev.R | 5 plotly-4.6.0/plotly/R/embed.R |only plotly-4.6.0/plotly/R/export.R | 111 + plotly-4.6.0/plotly/R/ggplotly-legacy.R |only plotly-4.6.0/plotly/R/ggplotly.R | 485 +++-- plotly-4.6.0/plotly/R/helpers.R | 138 + plotly-4.6.0/plotly/R/highlight.R |only plotly-4.6.0/plotly/R/imports.R | 26 plotly-4.6.0/plotly/R/layers2layout.R |only plotly-4.6.0/plotly/R/layers2traces.R | 358 +++- plotly-4.6.0/plotly/R/layout.R | 45 plotly-4.6.0/plotly/R/modeBarButtons.R |only plotly-4.6.0/plotly/R/plotly.R | 188 ++ plotly-4.6.0/plotly/R/plotly_IMAGE.R | 19 plotly-4.6.0/plotly/R/plotly_build.R | 327 ++- plotly-4.6.0/plotly/R/plotly_data.R | 108 + plotly-4.6.0/plotly/R/print.R | 135 - plotly-4.6.0/plotly/R/process.R | 67 plotly-4.6.0/plotly/R/shiny.R | 24 plotly-4.6.0/plotly/R/signup.R | 1 plotly-4.6.0/plotly/R/subplots.R | 109 - plotly-4.6.0/plotly/R/sysdata.rda |binary plotly-4.6.0/plotly/R/toRGB.R | 40 plotly-4.6.0/plotly/R/utils.R | 409 +++- plotly-4.6.0/plotly/demo |only plotly-4.6.0/plotly/inst/examples/onRenderHover/index.Rmd | 3 plotly-4.6.0/plotly/inst/examples/plotlyEvents/app.R | 24 plotly-4.6.0/plotly/inst/examples/plotlyLinkedClick/app.R | 2 plotly-4.6.0/plotly/inst/examples/printing.Rmd |only plotly-4.6.0/plotly/inst/examples/ternary |only plotly-4.6.0/plotly/inst/htmlwidgets/lib/colourpicker |only plotly-4.6.0/plotly/inst/htmlwidgets/lib/plotlyjs/LICENSE | 2 plotly-4.6.0/plotly/inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 128 - plotly-4.6.0/plotly/inst/htmlwidgets/lib/selectize |only plotly-4.6.0/plotly/inst/htmlwidgets/lib/typedarray |only plotly-4.6.0/plotly/inst/htmlwidgets/plotly.js | 879 +++++++++- plotly-4.6.0/plotly/inst/htmlwidgets/plotly.yaml | 2 plotly-4.6.0/plotly/inst/plotlyjs.R | 9 plotly-4.6.0/plotly/inst/stars.R |only plotly-4.6.0/plotly/man/add_annotations.Rd | 4 plotly-4.6.0/plotly/man/add_data.Rd | 1 plotly-4.6.0/plotly/man/add_fun.Rd | 1 plotly-4.6.0/plotly/man/add_trace.Rd | 37 plotly-4.6.0/plotly/man/animation.Rd |only plotly-4.6.0/plotly/man/api.Rd |only plotly-4.6.0/plotly/man/as.widget.Rd | 1 plotly-4.6.0/plotly/man/as_widget.Rd | 1 plotly-4.6.0/plotly/man/attrs_selected.Rd |only plotly-4.6.0/plotly/man/bbox.Rd | 1 plotly-4.6.0/plotly/man/colorbar.Rd | 6 plotly-4.6.0/plotly/man/config.Rd | 1 plotly-4.6.0/plotly/man/embed_notebook.Rd | 16 plotly-4.6.0/plotly/man/event_data.Rd | 7 plotly-4.6.0/plotly/man/export.Rd | 49 plotly-4.6.0/plotly/man/geom2trace.Rd | 1 plotly-4.6.0/plotly/man/get_figure.Rd | 18 plotly-4.6.0/plotly/man/gg2list.Rd | 15 plotly-4.6.0/plotly/man/ggplotly.Rd | 55 plotly-4.6.0/plotly/man/hide_colorbar.Rd | 1 plotly-4.6.0/plotly/man/hide_guides.Rd | 1 plotly-4.6.0/plotly/man/hide_legend.Rd | 1 plotly-4.6.0/plotly/man/highlight.Rd |only plotly-4.6.0/plotly/man/hobbs.Rd | 1 plotly-4.6.0/plotly/man/knit_print.api_grid.Rd |only plotly-4.6.0/plotly/man/knit_print.api_grid_local.Rd |only plotly-4.6.0/plotly/man/knit_print.api_plot.Rd |only plotly-4.6.0/plotly/man/last_plot.Rd | 1 plotly-4.6.0/plotly/man/layout.Rd | 1 plotly-4.6.0/plotly/man/mic.Rd | 1 plotly-4.6.0/plotly/man/offline.Rd | 1 plotly-4.6.0/plotly/man/plot_dendro.Rd |only plotly-4.6.0/plotly/man/plot_geo.Rd | 7 plotly-4.6.0/plotly/man/plot_ly.Rd | 35 plotly-4.6.0/plotly/man/plot_mapbox.Rd | 7 plotly-4.6.0/plotly/man/plotly-shiny.Rd | 6 plotly-4.6.0/plotly/man/plotly.Rd | 13 plotly-4.6.0/plotly/man/plotly_IMAGE.Rd | 5 plotly-4.6.0/plotly/man/plotly_POST.Rd | 23 plotly-4.6.0/plotly/man/plotly_build.Rd | 5 plotly-4.6.0/plotly/man/plotly_data.Rd | 20 plotly-4.6.0/plotly/man/plotly_empty.Rd | 1 plotly-4.6.0/plotly/man/plotly_json.Rd | 1 plotly-4.6.0/plotly/man/print.api.Rd |only plotly-4.6.0/plotly/man/print.api_grid.Rd |only plotly-4.6.0/plotly/man/print.api_grid_local.Rd |only plotly-4.6.0/plotly/man/print.api_plot.Rd |only plotly-4.6.0/plotly/man/rangeslider.Rd | 17 plotly-4.6.0/plotly/man/raster2uri.Rd |only plotly-4.6.0/plotly/man/reexports.Rd | 40 plotly-4.6.0/plotly/man/remove_typedarray_polyfill.Rd |only plotly-4.6.0/plotly/man/schema.Rd | 1 plotly-4.6.0/plotly/man/showRGB.Rd |only plotly-4.6.0/plotly/man/signup.Rd | 1 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plotly-4.6.0/plotly/tests/testthat/test-plotly-pie.R |only plotly-4.6.0/plotly/tests/testthat/test-plotly-subplot.R | 55 plotly-4.6.0/plotly/tests/testthat/test-toRGB.R | 4 149 files changed, 3707 insertions(+), 1103 deletions(-)
Title: Repeated Measurement Design for Phase I Clinical Trial
Description: Implements our Bayesian phase I repeated measurement design that accounts for multidimensional toxicity endpoints from multiple treatment cycles. The package also provides a novel design to account for both multidimensional toxicity endpoints and early-stage efficacy endpoints in the phase I design. For both designs, functions are provided to recommend the next dosage selection based on the data collected in the available patient cohorts and to simulate trial characteristics given design parameters. Yin, Jun, et al. (2017) <doi:10.1002/sim.7134>.
Author: Jun Yin, Yu Du, Sumithra Mandrekar
Maintainer: Jun Yin <vivien.jyin@gmail.com>
Diff between phase1RMD versions 1.0.5 dated 2017-03-23 and 1.0.7 dated 2017-04-25
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- R/structure.R | 10 ++++++++++ data/tox_dat.RData |binary data/tox_dat_bytype.RData |only man/tox_dat_bytype.Rd |only 6 files changed, 20 insertions(+), 8 deletions(-)
Title: Penalized Generalized Estimating Equations in High-Dimension
Description: Fits penalized generalized estimating equations to longitudinal data with high-dimensional covariates.
Author: Gul Inan (Lecturer, Middle East Technical University), Jianhui Zhou (Associate Professor, University of Virginia) and Lan Wang (Professor, University of Minnesota)
Maintainer: Gul Inan <ginan@metu.edu.tr>
Diff between PGEE versions 1.4 dated 2016-08-16 and 1.5 dated 2017-04-25
DESCRIPTION | 12 ++++----- MD5 | 16 ++++++------ R/CVfit.R | 74 ++++++++++++++++++++++++++++++--------------------------- R/MGEE.R | 21 +++++++--------- R/PGEE.R | 21 +++++++--------- man/CVfit.Rd | 4 +-- man/MGEE.Rd | 13 +++++----- man/PGEE.Rd | 28 ++++++++++----------- man/yeastG1.Rd | 31 +++++++++++------------ 9 files changed, 111 insertions(+), 109 deletions(-)
Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSel versions 0.8 dated 2017-04-24 and 0.8.1 dated 2017-04-25
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/segIBD.R | 3 ++- R/segIBDandN.R | 6 ++++-- R/segN.R | 3 ++- build/partial.rdb |binary 6 files changed, 16 insertions(+), 12 deletions(-)
Title: A Collection of Nonparametric Hypothesis Tests
Description: Contains the following 5 nonparametric hypothesis tests:
The Sign Test,
The 2 Sample Median Test,
Miller's Jackknife Procedure,
Cochran's Q Test, &
The Stuart-Maxwell Test.
Author: D. Lukke Sweet
Maintainer: D. Lukke Sweet <dls229@zips.uakron.edu>
Diff between nonpar versions 1.0.0 dated 2017-02-21 and 1.0.1 dated 2017-04-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/miller.jack.R | 10 +++++----- R/stuart.maxwell.R | 8 ++++---- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Flexible BUGS-Compatible System for Hierarchical Statistical
Modeling and Algorithm Development
Description: Flexible application of algorithms to models specified in the BUGS
language. Algorithms can be written in the NIMBLE language and made available to
any model.
Author: Perry de Valpine, Christopher Paciorek, Daniel Turek, Cliff Anderson-
Bergman, Duncan Temple Lang
Maintainer: Christopher Paciorek <paciorek@stat.berkeley.edu>
Diff between nimble versions 0.6-3 dated 2016-12-14 and 0.6-4 dated 2017-04-25
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nimble-0.6-4/nimble/R/NF_utils.R | 2 nimble-0.6-4/nimble/R/RCfunction_compile.R | 16 nimble-0.6-4/nimble/R/RCfunction_core.R | 84 nimble-0.6-4/nimble/R/all_utils.R | 4 nimble-0.6-4/nimble/R/cppDefs_RCfunction.R | 428 +- nimble-0.6-4/nimble/R/cppDefs_core.R | 54 nimble-0.6-4/nimble/R/cppDefs_cppProject.R | 4 nimble-0.6-4/nimble/R/cppDefs_namedObjects.R | 29 nimble-0.6-4/nimble/R/cppDefs_nimbleFunction.R | 307 + nimble-0.6-4/nimble/R/cppDefs_nimbleList.R |only nimble-0.6-4/nimble/R/cppDefs_variables.R | 2 nimble-0.6-4/nimble/R/cppInterfaces_modelValues.R | 107 nimble-0.6-4/nimble/R/cppInterfaces_models.R | 68 nimble-0.6-4/nimble/R/cppInterfaces_nimbleFunctions.R | 701 +++- nimble-0.6-4/nimble/R/cppInterfaces_utils.R | 83 nimble-0.6-4/nimble/R/distributions_implementations.R | 233 + nimble-0.6-4/nimble/R/distributions_inputList.R | 67 nimble-0.6-4/nimble/R/distributions_processInputList.R | 55 nimble-0.6-4/nimble/R/filtering_auxiliary.R | 5 nimble-0.6-4/nimble/R/filtering_bootstrap.R | 6 nimble-0.6-4/nimble/R/filtering_enkf.R | 8 nimble-0.6-4/nimble/R/filtering_liuwest.R | 9 nimble-0.6-4/nimble/R/genCpp_RparseTree2exprClasses.R | 3 nimble-0.6-4/nimble/R/genCpp_buildIntermediates.R | 3 nimble-0.6-4/nimble/R/genCpp_eigenization.R | 335 +- nimble-0.6-4/nimble/R/genCpp_exprClass.R | 10 nimble-0.6-4/nimble/R/genCpp_generateCpp.R | 62 nimble-0.6-4/nimble/R/genCpp_initSizes.R | 13 nimble-0.6-4/nimble/R/genCpp_insertAssertions.R | 12 nimble-0.6-4/nimble/R/genCpp_maps.R | 182 - nimble-0.6-4/nimble/R/genCpp_operatorLists.R | 116 nimble-0.6-4/nimble/R/genCpp_processSpecificCalls.R | 87 nimble-0.6-4/nimble/R/genCpp_sizeProcessing.R | 1672 ++++++++-- nimble-0.6-4/nimble/R/initializeModel.R | 25 nimble-0.6-4/nimble/R/miscFunctions.R | 10 nimble-0.6-4/nimble/R/nimbleFunction_Rexecution.R | 452 +- nimble-0.6-4/nimble/R/nimbleFunction_compile.R | 570 +-- nimble-0.6-4/nimble/R/nimbleFunction_core.R | 67 nimble-0.6-4/nimble/R/nimbleFunction_keywordProcessing.R | 692 ++-- 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nimble-0.6-4/nimble/inst/tests/test-mcmc.R | 129 nimble-0.6-4/nimble/inst/tests/test-misc.R | 2 nimble-0.6-4/nimble/inst/tests/test-modelValuesInterface.R |only nimble-0.6-4/nimble/inst/tests/test-nimbleFunctionInterfaces.R |only nimble-0.6-4/nimble/inst/tests/test-nimbleList.R |only nimble-0.6-4/nimble/inst/tests/test-numericTypes.R |only nimble-0.6-4/nimble/inst/tests/test-size.R | 108 nimble-0.6-4/nimble/inst/tests/test-types.R |only nimble-0.6-4/nimble/inst/tests/test-user.R | 20 nimble-0.6-4/nimble/inst/tests/test_utils.R | 154 nimble-0.6-4/nimble/man/BUGSdeclClass-class.Rd | 2 nimble-0.6-4/nimble/man/Categorical.Rd | 2 nimble-0.6-4/nimble/man/CmodelBaseClass-class.Rd | 2 nimble-0.6-4/nimble/man/CnimbleFunctionBase-class.Rd | 2 nimble-0.6-4/nimble/man/Constraint.Rd | 2 nimble-0.6-4/nimble/man/Dirichlet.Rd | 2 nimble-0.6-4/nimble/man/Exponential.Rd | 2 nimble-0.6-4/nimble/man/Interval.Rd | 2 nimble-0.6-4/nimble/man/Inverse-Gamma.Rd |only nimble-0.6-4/nimble/man/MCMCconf-class.Rd | 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nimble-0.6-4/nimble/man/configureMCMC.Rd | 2 nimble-0.6-4/nimble/man/decide.Rd | 2 nimble-0.6-4/nimble/man/decideAndJump.Rd | 2 nimble-0.6-4/nimble/man/declare.Rd | 2 nimble-0.6-4/nimble/man/deregisterDistributions.Rd | 2 nimble-0.6-4/nimble/man/distributionInfo.Rd | 2 nimble-0.6-4/nimble/man/eigenNimbleList.Rd |only nimble-0.6-4/nimble/man/getBUGSexampleDir.Rd | 2 nimble-0.6-4/nimble/man/getBound.Rd | 2 nimble-0.6-4/nimble/man/getDefinition.Rd | 2 nimble-0.6-4/nimble/man/getLoadingNamespace.Rd | 2 nimble-0.6-4/nimble/man/getNimbleOption.Rd | 2 nimble-0.6-4/nimble/man/getParam.Rd | 2 nimble-0.6-4/nimble/man/getsize.Rd | 2 nimble-0.6-4/nimble/man/identityMatrix.Rd | 4 nimble-0.6-4/nimble/man/initializeModel.Rd | 2 nimble-0.6-4/nimble/man/is.nf.Rd | 2 nimble-0.6-4/nimble/man/is.nl.Rd |only nimble-0.6-4/nimble/man/makeBoundInfo.Rd | 2 nimble-0.6-4/nimble/man/makeParamInfo.Rd | 2 nimble-0.6-4/nimble/man/make_MCMC_comparison_pages.Rd | 2 nimble-0.6-4/nimble/man/modelBaseClass-class.Rd | 4 nimble-0.6-4/nimble/man/modelDefClass-class.Rd | 2 nimble-0.6-4/nimble/man/modelValues.Rd | 2 nimble-0.6-4/nimble/man/modelValuesBaseClass-class.Rd | 2 nimble-0.6-4/nimble/man/modelValuesConf.Rd | 2 nimble-0.6-4/nimble/man/nfMethod.Rd | 2 nimble-0.6-4/nimble/man/nfVar.Rd | 2 nimble-0.6-4/nimble/man/nimCat.Rd | 3 nimble-0.6-4/nimble/man/nimCopy.Rd | 3 nimble-0.6-4/nimble/man/nimDim.Rd | 3 nimble-0.6-4/nimble/man/nimEigen.Rd |only nimble-0.6-4/nimble/man/nimMatrix.Rd | 42 nimble-0.6-4/nimble/man/nimNumeric.Rd | 33 nimble-0.6-4/nimble/man/nimPrint.Rd | 3 nimble-0.6-4/nimble/man/nimStop.Rd | 5 nimble-0.6-4/nimble/man/nimSvd.Rd |only nimble-0.6-4/nimble/man/nimble-R-functions.Rd |only nimble-0.6-4/nimble/man/nimble-internal.Rd | 7 nimble-0.6-4/nimble/man/nimble-math.Rd | 1 nimble-0.6-4/nimble/man/nimbleCode.Rd | 2 nimble-0.6-4/nimble/man/nimbleFunction.Rd | 4 nimble-0.6-4/nimble/man/nimbleFunctionBase-class.Rd | 2 nimble-0.6-4/nimble/man/nimbleFunctionList-class.Rd | 2 nimble-0.6-4/nimble/man/nimbleFunctionVirtual.Rd | 2 nimble-0.6-4/nimble/man/nimbleList.Rd |only nimble-0.6-4/nimble/man/nimbleModel.Rd | 6 nimble-0.6-4/nimble/man/nimbleOptions.Rd | 2 nimble-0.6-4/nimble/man/nimbleType-class.Rd |only nimble-0.6-4/nimble/man/nodeFunctions.Rd | 4 nimble-0.6-4/nimble/man/rankSample.Rd | 2 nimble-0.6-4/nimble/man/readBUGSmodel.Rd | 2 nimble-0.6-4/nimble/man/registerDistributions.Rd | 6 nimble-0.6-4/nimble/man/rename_MCMC_comparison_method.Rd | 2 nimble-0.6-4/nimble/man/reshape_comparison_results.Rd | 2 nimble-0.6-4/nimble/man/resize.Rd | 2 nimble-0.6-4/nimble/man/run.time.Rd | 2 nimble-0.6-4/nimble/man/runMCMC.Rd | 2 nimble-0.6-4/nimble/man/samplers.Rd | 69 nimble-0.6-4/nimble/man/setAndCalculate.Rd | 2 nimble-0.6-4/nimble/man/setAndCalculateOne.Rd | 2 nimble-0.6-4/nimble/man/setSize.Rd | 12 nimble-0.6-4/nimble/man/setupOutputs.Rd | 2 nimble-0.6-4/nimble/man/simNodes.Rd | 2 nimble-0.6-4/nimble/man/simNodesMV.Rd | 2 nimble-0.6-4/nimble/man/singleVarAccessClass-class.Rd | 2 nimble-0.6-4/nimble/man/svdNimbleList.Rd |only nimble-0.6-4/nimble/man/t.Rd | 2 nimble-0.6-4/nimble/man/testBUGSmodel.Rd | 2 nimble-0.6-4/nimble/man/updateMCMCcomparisonWithHighOrderESS.Rd | 2 nimble-0.6-4/nimble/man/valueInCompiledNimbleFunction.Rd | 2 nimble-0.6-4/nimble/man/values.Rd | 8 nimble-0.6-4/nimble/src/Makevars.in | 4 nimble-0.6-4/nimble/src/nimble.cpp | 24 233 files changed, 8776 insertions(+), 3010 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD),
and forecasting time-series using fuzzy rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 1.3 dated 2016-04-22 and 1.4 dated 2017-04-25
lfl-1.3/lfl/R/aggregate.R |only lfl-1.3/lfl/man/aggregate.Rd |only lfl-1.3/lfl/tests/testthat/test-aggregate.R |only lfl-1.4/lfl/DESCRIPTION | 10 +- lfl-1.4/lfl/MD5 | 60 ++++++------ lfl-1.4/lfl/NAMESPACE | 83 ++++++++++++++++- lfl-1.4/lfl/R/aggregateConsequents.R |only lfl-1.4/lfl/R/algebra.R | 14 +- lfl-1.4/lfl/R/lcut.numeric.R | 2 lfl-1.4/lfl/R/mult.R | 2 lfl-1.4/lfl/R/pbld.R | 7 - lfl-1.4/lfl/R/perceive.R | 21 +--- lfl-1.4/lfl/R/plot.fsets.R | 3 lfl-1.4/lfl/R/reduce.R | 2 lfl-1.4/lfl/R/searchrules.R | 10 ++ lfl-1.4/lfl/cleanup |only lfl-1.4/lfl/configure | 4 lfl-1.4/lfl/configure.ac | 4 lfl-1.4/lfl/inst/CITATION | 5 - lfl-1.4/lfl/man/aggregateConsequents.Rd |only lfl-1.4/lfl/man/defuzz.Rd | 2 lfl-1.4/lfl/man/fire.Rd | 2 lfl-1.4/lfl/man/lfl-package.Rd | 2 lfl-1.4/lfl/man/pbld.Rd | 2 lfl-1.4/lfl/src/lfl_init.c |only lfl-1.4/lfl/src/mult.cpp | 2 lfl-1.4/lfl/src/mult.h | 2 lfl-1.4/lfl/src/reduce.cpp | 2 lfl-1.4/lfl/src/reduce.h | 2 lfl-1.4/lfl/tests/testthat/test-aggregateConsequents.R |only lfl-1.4/lfl/tests/testthat/test-lcut.data.frame.R | 5 + lfl-1.4/lfl/tests/testthat/test-lcut.matrix.R | 1 lfl-1.4/lfl/tests/testthat/test-lcut.numeric.R | 2 lfl-1.4/lfl/tests/testthat/test-pbld.R | 19 +++ lfl-1.4/lfl/tests/testthat/test-perceive.R | 70 ++++++++++++-- 35 files changed, 251 insertions(+), 89 deletions(-)
Title: Lambert-W Function
Description: Implements both real-valued branches of the Lambert-W function, also known as the product logarithm, without the need for installing the entire GSL.
Author: Avraham Adler [aut, cph, cre]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between lamW versions 1.2.0 dated 2016-10-27 and 1.3.0 dated 2017-04-25
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 +- README.md | 5 +++-- build/partial.rdb |binary inst/News.Rd | 9 ++++++++- man/lamW-internal.Rd | 3 +++ man/lamW-package.Rd | 4 ++-- src/init.c |only 9 files changed, 30 insertions(+), 17 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project is funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut],
Pete Philipson [aut],
Andrea Jorgensen [aut],
Ruwanthi Kolamunnage-Dona [aut],
Paula Williamson [ctb],
Dimitris Rizopoulos [ctb, dtc] (data/renal.rda, R/hessian.R, R/vcov.R)
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>
Diff between joineRML versions 0.2.0 dated 2017-03-27 and 0.2.1 dated 2017-04-25
joineRML-0.2.0/joineRML/src/joineRML_init.c |only joineRML-0.2.1/joineRML/DESCRIPTION | 10 +++---- joineRML-0.2.1/joineRML/MD5 | 26 +++++++++---------- joineRML-0.2.1/joineRML/NAMESPACE | 7 ----- joineRML-0.2.1/joineRML/NEWS.md | 14 ++++++++++ joineRML-0.2.1/joineRML/R/initsSurv.R | 6 ++-- joineRML-0.2.1/joineRML/R/mjoint.R | 10 ++++--- joineRML-0.2.1/joineRML/R/sigma.mjoint.R | 9 +----- joineRML-0.2.1/joineRML/README.md | 2 - joineRML-0.2.1/joineRML/build/vignette.rds |binary joineRML-0.2.1/joineRML/inst/doc/joineRML.html | 6 ++-- joineRML-0.2.1/joineRML/inst/doc/technical.pdf |binary joineRML-0.2.1/joineRML/man/sigma.mjoint.Rd | 2 - joineRML-0.2.1/joineRML/src/init.c |only joineRML-0.2.1/joineRML/tests/testthat/test-models.R | 5 ++- 15 files changed, 52 insertions(+), 45 deletions(-)
Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and
repository management web application gitlab. For many common tasks (repository
file access, issue assignment and status, commenting) convenience wrappers
are provided, and in addition the full API can be used by specifying request
locations. Gitlab is open-source software and can be self-hosted or used on
gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between gitlabr versions 0.7 dated 2017-03-06 and 0.9 dated 2017-04-25
gitlabr-0.7/gitlabr/man/gl_get_file.Rd |only gitlabr-0.7/gitlabr/man/prefix.Rd |only gitlabr-0.9/gitlabr/DESCRIPTION | 14 - gitlabr-0.9/gitlabr/MD5 | 61 +++---- gitlabr-0.9/gitlabr/NAMESPACE | 3 gitlabr-0.9/gitlabr/NEWS.md | 17 +- gitlabr-0.9/gitlabr/R/ci.R | 96 +++++++++-- gitlabr-0.9/gitlabr/R/comments.R | 121 +++++++------- gitlabr-0.9/gitlabr/R/connect.R | 113 +++++++------ gitlabr-0.9/gitlabr/R/gitlab_api.R | 91 +++++++--- gitlabr-0.9/gitlabr/R/gitlabr-package.R | 2 gitlabr-0.9/gitlabr/R/global_env.R | 6 gitlabr-0.9/gitlabr/R/issues.R | 109 ++++++++---- gitlabr-0.9/gitlabr/R/magrittr_extensions.R | 2 gitlabr-0.9/gitlabr/R/projects_and_repos.R | 151 ++++++++++-------- gitlabr-0.9/gitlabr/R/shiny_module_login.R | 34 ++-- gitlabr-0.9/gitlabr/R/update_code.R | 2 gitlabr-0.9/gitlabr/README.md |only gitlabr-0.9/gitlabr/inst/doc/quick-start-gitlabr.pdf |binary gitlabr-0.9/gitlabr/man/gitlab.Rd | 18 ++ gitlabr-0.9/gitlabr/man/gitlabci.Rd | 15 + gitlabr-0.9/gitlabr/man/gl_archive.Rd | 6 gitlabr-0.9/gitlabr/man/gl_builds.Rd | 32 +++ gitlabr-0.9/gitlabr/man/gl_comments.Rd | 15 + gitlabr-0.9/gitlabr/man/gl_connection.Rd | 25 ++ gitlabr-0.9/gitlabr/man/gl_edit_issue.Rd | 7 gitlabr-0.9/gitlabr/man/gl_list_issues.Rd | 16 + gitlabr-0.9/gitlabr/man/gl_list_projects.Rd | 6 gitlabr-0.9/gitlabr/man/gl_push_file.Rd | 8 gitlabr-0.9/gitlabr/man/gl_repository.Rd | 32 +++ gitlabr-0.9/gitlabr/man/gl_to_issue_id.Rd | 9 - gitlabr-0.9/gitlabr/man/set_gitlab_connection.Rd | 5 gitlabr-0.9/gitlabr/vignettes/quick-start-gitlabr.Rmd | 43 +---- 33 files changed, 700 insertions(+), 359 deletions(-)
Title: Generalized Additive Models
Description: Functions for fitting and working with generalized
additive models, as described in chapter 7 of "Statistical Models in
S" (Chambers and Hastie (eds), 1991), and "Generalized Additive
Models" (Hastie and Tibshirani, 1990).
Author: Trevor Hastie
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between gam versions 1.14-3 dated 2017-04-21 and 1.14-4 dated 2017-04-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/gam_init.c | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 53 insertions(+), 5 deletions(-)
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob J Hyndman and Han Lin Shang
Maintainer: Han Lin Shang <hanlin.shang@anu.edu.au>
Diff between ftsa versions 4.7 dated 2016-03-15 and 4.8 dated 2017-04-25
ftsa-4.7/ftsa/R/median.R |only ftsa-4.7/ftsa/build |only ftsa-4.7/ftsa/inst/doc/ftsa.R |only ftsa-4.7/ftsa/inst/doc/ftsa.Rnw |only ftsa-4.7/ftsa/inst/doc/ftsa_test.Rnw |only ftsa-4.7/ftsa/man/median.Rd |only ftsa-4.8/ftsa/ChangeLog | 8 ++ ftsa-4.8/ftsa/DESCRIPTION | 10 +-- ftsa-4.8/ftsa/MD5 | 38 +++++------ ftsa-4.8/ftsa/NAMESPACE | 10 +-- ftsa-4.8/ftsa/R/FlatTop.r |only ftsa-4.8/ftsa/R/Long_run_covariance_estimation.r |only ftsa-4.8/ftsa/R/kweights.r |only ftsa-4.8/ftsa/R/median.fts.R | 2 ftsa-4.8/ftsa/R/sd.fts.R | 64 +++++++++++--------- ftsa-4.8/ftsa/R/smape.R | 2 ftsa-4.8/ftsa/R/smdape.R | 2 ftsa-4.8/ftsa/R/var.fts.R | 64 +++++++++++--------- ftsa-4.8/ftsa/inst/CITATION | 4 - ftsa-4.8/ftsa/inst/doc/ftsa.pdf |binary ftsa-4.8/ftsa/inst/doc/ftsa_test.pdf |binary ftsa-4.8/ftsa/man/ftsa-package.Rd | 13 +++- ftsa-4.8/ftsa/man/long_run_covariance_estimation.Rd |only ftsa-4.8/ftsa/man/median.fts.Rd | 5 - ftsa-4.8/ftsa/vignettes/ftsa.tex |only ftsa-4.8/ftsa/vignettes/ftsa_test.tex |only 26 files changed, 128 insertions(+), 94 deletions(-)
Title: Format R Code Automatically
Description: Provides a function tidy_source() to format R source code. Spaces
and indent will be added to the code automatically, and comments will be
preserved under certain conditions, so that R code will be more
human-readable and tidy. There is also a Shiny app as a user interface in
this package (see tidy_app()).
Author: Yihui Xie [aut, cre],
Eugene Ha [ctb],
Kohske Takahashi [ctb],
Ed Lee [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between formatR versions 1.4 dated 2016-05-09 and 1.5 dated 2017-04-25
DESCRIPTION | 25 + MD5 | 35 +- NAMESPACE | 3 NEWS | 12 R/eval.R | 4 R/tidy.R | 34 +- R/usage.R | 137 +++++++++- R/utils.R | 7 build/vignette.rds |binary inst/doc/formatR.R | 59 ++-- inst/doc/formatR.Rmd | 98 ++++--- inst/doc/formatR.html | 602 ++++++++++++++++++++++++---------------------- man/tidy_app.Rd | 1 man/tidy_dir.Rd | 26 + man/tidy_eval.Rd | 5 man/tidy_source.Rd | 11 man/usage.Rd | 32 ++ tests/testit/test-usage.R |only vignettes/formatR.Rmd | 98 ++++--- 19 files changed, 744 insertions(+), 445 deletions(-)
Title: Fast Covariance Estimation for Sparse Functional Data
Description: Fast covariance estimation for sparse functional data or longitudinal data for the paper Xiao et al., Stat. Comput., <doi:10.1007/s11222-017-9744-8>.
Author: Luo Xiao [aut,cre], Cai Li [aut], William Checkley [aut], Ciprian
Crainiceanu [aut]
Maintainer: Luo Xiao <lxiao5@ncsu.edu>
Diff between face versions 0.1-2 dated 2017-01-02 and 0.1-3 dated 2017-04-25
DESCRIPTION | 8 ++++---- MD5 | 25 +++++++++++++------------ R/construct.knots.r | 7 ++++--- R/face.sparse.inner.r | 2 +- R/predict.face.sparse.r | 2 +- R/pspline.setting.R | 2 +- R/select.knots.r | 5 +++-- build |only man/cor.face.Rd | 2 +- man/face-package.Rd | 6 +++--- man/face.sparse.Rd | 4 ++-- man/predict.face.sparse.Rd | 2 +- man/predict.pspline.Rd | 2 +- man/pspline.Rd | 2 +- 14 files changed, 36 insertions(+), 33 deletions(-)
Title: Read and Write Ecological Metadata Language Files
Description: Parse and serialize Ecological Metadata Language ('EML', see
<https://en.wikipedia.org/wiki/Ecological_Metadata_Language> for
more information) files into S4 objects.
Author: Carl Boettiger [aut, cre],
Matthew B. Jones [aut],
Bryce Mecum [ctb],
Maëlle Salmon [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between EML versions 1.0.1 dated 2016-12-20 and 1.0.2 dated 2017-04-25
EML-1.0.1/EML/R/xml-s4.R |only EML-1.0.1/EML/inst/examples/eml_find.R |only EML-1.0.1/EML/inst/examples/eml_show.R |only EML-1.0.1/EML/man/message_validation_error.Rd |only EML-1.0.2/EML/DESCRIPTION | 23 EML-1.0.2/EML/MD5 | 126 EML-1.0.2/EML/NAMESPACE | 16 EML-1.0.2/EML/NEWS.md |only EML-1.0.2/EML/R/classes.R | 252 EML-1.0.2/EML/R/eml_find.R | 8 EML-1.0.2/EML/R/eml_get.R | 14 EML-1.0.2/EML/R/eml_validate.R | 90 EML-1.0.2/EML/R/eml_view.R |only EML-1.0.2/EML/R/get_TextType.R | 29 EML-1.0.2/EML/R/get_attributes.R | 6 EML-1.0.2/EML/R/get_unitList.R | 7 EML-1.0.2/EML/R/methods.R | 2745 ++++------ EML-1.0.2/EML/R/read_eml.R | 16 EML-1.0.2/EML/R/s4_to_xml.R |only EML-1.0.2/EML/R/set_TextType.R | 17 EML-1.0.2/EML/R/set_attributes.R | 44 EML-1.0.2/EML/R/set_unitList.R | 21 EML-1.0.2/EML/R/show_methods.R |only EML-1.0.2/EML/R/write_eml.R | 95 EML-1.0.2/EML/R/xml_to_s4.R |only EML-1.0.2/EML/R/zzz.R | 2 EML-1.0.2/EML/README.md | 7 EML-1.0.2/EML/build/vignette.rds |binary EML-1.0.2/EML/inst/doc/creating-EML.R | 7 EML-1.0.2/EML/inst/doc/creating-EML.Rmd | 8 EML-1.0.2/EML/inst/doc/creating-EML.html | 19 EML-1.0.2/EML/inst/doc/metadata-repositories.html | 6 EML-1.0.2/EML/inst/doc/parsing-EML.R | 10 EML-1.0.2/EML/inst/doc/parsing-EML.Rmd | 23 EML-1.0.2/EML/inst/doc/parsing-EML.html | 30 EML-1.0.2/EML/inst/doc/working-with-units.html | 18 EML-1.0.2/EML/inst/examples/create-full-eml.R |only EML-1.0.2/EML/inst/examples/example-eml-2.1.0.xml | 6 EML-1.0.2/EML/inst/examples/hf001.xml |only EML-1.0.2/EML/inst/xsd/test/eml-datasetWithAccessUnitsLiteralLayout.xml | 2 EML-1.0.2/EML/man/c-methods.Rd | 2 EML-1.0.2/EML/man/eml_find.Rd | 1 EML-1.0.2/EML/man/eml_get.Rd | 6 EML-1.0.2/EML/man/eml_locate_schema.Rd | 9 EML-1.0.2/EML/man/eml_validate.Rd | 9 EML-1.0.2/EML/man/eml_view.Rd |only EML-1.0.2/EML/man/get_TextType.Rd | 11 EML-1.0.2/EML/man/get_attributes.Rd | 1 EML-1.0.2/EML/man/get_taxonomicCoverage.Rd | 1 EML-1.0.2/EML/man/get_unitList.Rd | 6 EML-1.0.2/EML/man/is_standardUnit.Rd | 1 EML-1.0.2/EML/man/read_eml.Rd | 3 EML-1.0.2/EML/man/set_TextType.Rd | 1 EML-1.0.2/EML/man/set_attributes.Rd | 1 EML-1.0.2/EML/man/set_coverage.Rd | 1 EML-1.0.2/EML/man/set_methods.Rd | 1 EML-1.0.2/EML/man/set_physical.Rd | 1 EML-1.0.2/EML/man/set_taxonomicCoverage.Rd | 1 EML-1.0.2/EML/man/set_unitList.Rd | 1 EML-1.0.2/EML/man/write_eml.Rd | 12 EML-1.0.2/EML/tests/testthat/eml-utf8.xml |only EML-1.0.2/EML/tests/testthat/test-TextType.R | 34 EML-1.0.2/EML/tests/testthat/test-attributes.R | 108 EML-1.0.2/EML/tests/testthat/test-eml.R | 1 EML-1.0.2/EML/tests/testthat/test-eml_get.R | 6 EML-1.0.2/EML/tests/testthat/test-testfiles.R | 89 EML-1.0.2/EML/tests/testthat/test-units.R | 2 EML-1.0.2/EML/tests/testthat/test-validation.R | 64 EML-1.0.2/EML/tests/testthat/test-view.R |only EML-1.0.2/EML/vignettes/creating-EML.Rmd | 8 EML-1.0.2/EML/vignettes/parsing-EML.Rmd | 23 71 files changed, 2202 insertions(+), 1849 deletions(-)
Title: Forecasting Mortality, Fertility, Migration and Population Data
Description: Functions for demographic analysis including lifetable
calculations; Lee-Carter modelling; functional data analysis of
mortality rates, fertility rates, net migration numbers; and
stochastic population forecasting.
Author: Rob J Hyndman with contributions from Heather Booth, Leonie Tickle and John Maindonald.
Maintainer: Rob J Hyndman <Rob.Hyndman@monash.edu>
Diff between demography versions 1.19 dated 2017-02-16 and 1.20 dated 2017-04-25
ChangeLog | 341 ++++++++++++++++++++++++++++++------------------------------ DESCRIPTION | 10 - MD5 | 6 - NAMESPACE | 2 4 files changed, 184 insertions(+), 175 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous or categorical data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means.
Author: Alfonso Iodice D'Enza [aut], Angelos Markos [aut, cre], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.1.0 dated 2016-12-06 and 1.1.9 dated 2017-04-25
clustrd-1.1.0/clustrd/man/tune_clusmca.Rd |only clustrd-1.1.0/clustrd/man/tune_cluspca.Rd |only clustrd-1.1.9/clustrd/DESCRIPTION | 10 - clustrd-1.1.9/clustrd/MD5 | 53 ++++---- clustrd-1.1.9/clustrd/NAMESPACE | 13 +- clustrd-1.1.9/clustrd/R/EmptyKmeans.r | 90 ++++++------- clustrd-1.1.9/clustrd/R/MCAk.r | 55 ++++---- clustrd-1.1.9/clustrd/R/clu_means.R | 74 ++--------- clustrd-1.1.9/clustrd/R/clusCA.R | 14 +- clustrd-1.1.9/clustrd/R/clusmca.R | 15 +- clustrd-1.1.9/clustrd/R/cluspca.R | 27 +--- clustrd-1.1.9/clustrd/R/clusval.R | 2 clustrd-1.1.9/clustrd/R/iFCB.r | 15 +- clustrd-1.1.9/clustrd/R/outOfIndependence.r | 4 clustrd-1.1.9/clustrd/R/plot.clusmca.R | 161 +++++++------------------ clustrd-1.1.9/clustrd/R/plot.cluspca.R | 106 +++++++--------- clustrd-1.1.9/clustrd/R/print.clusmca.R |only clustrd-1.1.9/clustrd/R/print.cluspca.R |only clustrd-1.1.9/clustrd/R/print.clusval.R |only clustrd-1.1.9/clustrd/R/print.tune_clusmca.R |only clustrd-1.1.9/clustrd/R/print.tune_cluspca.R |only clustrd-1.1.9/clustrd/R/summary.clusmca.R |only clustrd-1.1.9/clustrd/R/summary.cluspca.R |only clustrd-1.1.9/clustrd/R/summary.tune_clusmca.R |only clustrd-1.1.9/clustrd/R/summary.tune_cluspca.R |only clustrd-1.1.9/clustrd/R/tune_clusmca.R | 112 ++++++++--------- clustrd-1.1.9/clustrd/R/tune_cluspca.R | 27 +++- clustrd-1.1.9/clustrd/R/tuneclus.R |only clustrd-1.1.9/clustrd/man/clusmca.Rd | 42 ++++-- clustrd-1.1.9/clustrd/man/cluspca.Rd | 43 ++++-- clustrd-1.1.9/clustrd/man/clusval.Rd | 19 ++ clustrd-1.1.9/clustrd/man/plot.clusmca.Rd | 46 +++++-- clustrd-1.1.9/clustrd/man/plot.cluspca.Rd | 37 ++++- clustrd-1.1.9/clustrd/man/tuneclus.Rd |only 34 files changed, 474 insertions(+), 491 deletions(-)
Title: Clinical Trial Design and Data Analysis Functions
Description: Utilities to make your clinical collaborations easier if not
fun. It contains functions for designing studies such as Simon
2-stage and group sequential designs and for data analysis such
as Jonckheere-Terpstra test and estimating survival quantiles.
Author: Venkatraman E. Seshan
Maintainer: Venkatraman E. Seshan <seshanv@mskcc.org>
Diff between clinfun versions 1.0.13 dated 2016-11-30 and 1.0.14 dated 2017-04-25
CHANGES | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 5 +++-- src/init.c |only 4 files changed, 10 insertions(+), 5 deletions(-)
Title: Lightweight Biology Software Installer
Description: Can be used to install and download massive bioinformatics analysis softwares and databases, such as NGS reads mapping tools with its required databases.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between BioInstaller versions 0.0.3 dated 2017-04-02 and 0.1.0 dated 2017-04-25
ChangeLog | 17 +++ DESCRIPTION | 8 - MD5 | 22 ++-- R/BioInstaller.R | 6 - R/install.R | 66 +++++++++---- R/install_utils.R | 21 ++-- R/utils_function.R | 25 ++++- README.md | 38 +++---- inst/extdata/github.toml | 186 +++++++++++++++++++++++++++++++++++--- inst/extdata/nongithub.toml | 210 ++++++++++++++++++++++++++++++++++++++++--- inst/extdata/parse_version.R | 81 +++++++++++++++- man/BioInstaller.Rd | 12 -- 12 files changed, 585 insertions(+), 107 deletions(-)
Title: 'Taxonomic' Specification and Parsing Methods
Description: Includes functions for working with taxonomic data,
including functions for combining, separating, and filtering
taxonomic groups by any rank or name. Allows standard ('SE')
and non-standard evaluation ('NSE').
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between binomen versions 0.1.0 dated 2015-12-07 and 0.1.2 dated 2017-04-25
DESCRIPTION | 14 +++++----- LICENSE | 2 - MD5 | 61 ++++++++++++++++++++++---------------------- NAMESPACE | 2 - NEWS.md |only R/binomen-package.R | 2 - R/gethier.R | 10 ++++--- R/make_taxon.R | 4 +- R/make_taxon_fromclass.R | 3 -- R/scatter.R | 2 - README.md | 22 +++++++++++---- build/vignette.rds |binary man/binomen-package.Rd | 3 -- man/binomial.Rd | 1 man/gethier.Rd | 9 ++---- man/grouping.Rd | 1 man/make_taxon.Rd | 4 -- man/make_taxon_fromclass.Rd | 3 -- man/parts.Rd | 9 ++---- man/pick.Rd | 1 man/pipe.Rd | 1 man/pop.Rd | 1 man/rank_table.Rd | 1 man/scatter.Rd | 3 -- man/span.Rd | 1 man/strain.Rd | 1 man/taxa.Rd | 1 man/taxon.Rd | 1 man/taxon_classes.Rd | 1 man/taxon_df.Rd | 1 man/taxonref.Rd | 1 man/taxonrefs.Rd | 1 32 files changed, 78 insertions(+), 89 deletions(-)
More information about ANOVAreplication at CRAN
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