Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.3.1 dated 2017-10-16 and 0.3.2 dated 2017-11-30
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/nlr.R | 4 ++-- inst/NEWS.Rd | 8 +++++++- inst/doc/wnl-manual.pdf |binary man/nlr.Rd | 6 ++++-- man/wnl-package.Rd | 4 ++-- man/wnl5.Rd | 4 ++-- 8 files changed, 27 insertions(+), 19 deletions(-)
Title: Wrangle Phylogenetic Distance Matrices and Other Utilities
Description: Harriet was Charles Darwin's pet tortoise (possibly). 'harrietr'
implements some function to manipulate distance matrices and phylogenetic trees
to make it easier to plot with 'ggplot2' and to manipulate using 'tidyverse'
tools.
Author: Anders Gonçalves da Silva [aut, cre]
Maintainer: Anders Gonçalves da Silva <andersgs@gmail.com>
Diff between harrietr versions 0.2.2 dated 2017-02-22 and 0.2.3 dated 2017-11-30
harrietr-0.2.2/harrietr/inst |only harrietr-0.2.3/harrietr/DESCRIPTION | 15 ++++++----- harrietr-0.2.3/harrietr/MD5 | 32 +++++++++++++----------- harrietr-0.2.3/harrietr/NAMESPACE | 2 - harrietr-0.2.3/harrietr/NEWS.md | 8 +++--- harrietr-0.2.3/harrietr/R/harrietr.R |only harrietr-0.2.3/harrietr/R/join_metadata.R | 25 ++++++++++++------ harrietr-0.2.3/harrietr/R/melt_distance.R | 2 - harrietr-0.2.3/harrietr/README.md | 31 ++++++++++++++++------- harrietr-0.2.3/harrietr/man/dist_long.Rd | 1 harrietr-0.2.3/harrietr/man/figures |only harrietr-0.2.3/harrietr/man/get_node_support.Rd | 1 harrietr-0.2.3/harrietr/man/harrietr.Rd |only harrietr-0.2.3/harrietr/man/join_metadata.Rd | 3 -- harrietr-0.2.3/harrietr/man/melt_dist.Rd | 1 harrietr-0.2.3/harrietr/man/woodmouse.Rd | 1 harrietr-0.2.3/harrietr/man/woodmouse_iqtree.Rd | 1 harrietr-0.2.3/harrietr/man/woodmouse_meta.Rd | 1 18 files changed, 72 insertions(+), 52 deletions(-)
Title: Rapid Deployment of Machine Learning Algorithms
Description: Supervised machine learning has an increasingly important role in data
analysis. This package introduces a framework for rapidly building and deploying
supervised machine learning in a high-throughput manner. This package provides a
user-friendly interface that empowers investigators to execute state-of-the-art
binary and multi-class classification, as well as regression, with minimal
programming experience necessary.
Author: Thomas Quinn [aut, cre],
Daniel Tylee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between exprso versions 0.2.0 dated 2017-11-18 and 0.2.6 dated 2017-11-30
exprso-0.2.0/exprso/R/0-global.R |only exprso-0.2.0/exprso/R/0-tidy.R |only exprso-0.2.0/exprso/R/5.3-doMulti.R |only exprso-0.2.0/exprso/R/6-predict.R |only exprso-0.2.0/exprso/R/8.1-pipe.R |only exprso-0.2.0/exprso/R/8.2-ens.R |only exprso-0.2.0/exprso/R/9-import.R |only exprso-0.2.0/exprso/R/9-mod.R |only exprso-0.2.0/exprso/man/ExprsCont-class.Rd |only exprso-0.2.6/exprso/DESCRIPTION | 25 - exprso-0.2.6/exprso/MD5 | 216 +++++++------- exprso-0.2.6/exprso/NAMESPACE | 13 exprso-0.2.6/exprso/NEWS.md | 68 ++++ exprso-0.2.6/exprso/R/1.1-classes.R | 69 +++- exprso-0.2.6/exprso/R/1.2-methods.R | 121 +++++++ exprso-0.2.6/exprso/R/1.3-exprso.R | 77 ++-- exprso-0.2.6/exprso/R/2-mod.R | 78 +++++ exprso-0.2.6/exprso/R/3-split.R | 15 exprso-0.2.6/exprso/R/4-conjoin.R | 13 exprso-0.2.6/exprso/R/5.1-fs.R | 60 ++- exprso-0.2.6/exprso/R/5.2-build.R | 84 ++++- exprso-0.2.6/exprso/R/6.1-predict.R |only exprso-0.2.6/exprso/R/6.2-calc.R |only exprso-0.2.6/exprso/R/7.1-plCV.R | 35 -- exprso-0.2.6/exprso/R/7.2-plGrid.R | 114 ------- exprso-0.2.6/exprso/R/7.3-plGridMulti.R | 20 - exprso-0.2.6/exprso/R/7.4-plMonteCarlo.R | 136 +------- exprso-0.2.6/exprso/R/7.5-plNested.R | 110 +------ exprso-0.2.6/exprso/R/8-pipe.R |only exprso-0.2.6/exprso/R/9-deprecated.R |only exprso-0.2.6/exprso/R/9-global.R |only exprso-0.2.6/exprso/build/vignette.rds |binary exprso-0.2.6/exprso/inst/doc/a_introduction-vignette.Rmd | 8 exprso-0.2.6/exprso/inst/doc/a_introduction-vignette.html | 35 +- exprso-0.2.6/exprso/inst/doc/b_advanced-vignette.R | 10 exprso-0.2.6/exprso/inst/doc/b_advanced-vignette.Rmd | 12 exprso-0.2.6/exprso/inst/doc/b_advanced-vignette.html | 96 +++--- exprso-0.2.6/exprso/inst/doc/c_readme.Rmd | 2 exprso-0.2.6/exprso/inst/doc/c_readme.html | 4 exprso-0.2.6/exprso/man/ExprsArray-class.Rd | 3 exprso-0.2.6/exprso/man/ExprsEnsemble-class.Rd | 9 exprso-0.2.6/exprso/man/ExprsMachine-class.Rd | 4 exprso-0.2.6/exprso/man/ExprsModel-class.Rd | 9 exprso-0.2.6/exprso/man/ExprsModule-class.Rd | 4 exprso-0.2.6/exprso/man/ExprsPipeline-class.Rd | 9 exprso-0.2.6/exprso/man/ExprsPredict-class.Rd | 7 exprso-0.2.6/exprso/man/GSE2eSet.Rd | 2 exprso-0.2.6/exprso/man/RegrsArray-class.Rd |only exprso-0.2.6/exprso/man/RegrsModel-class.Rd |only exprso-0.2.6/exprso/man/RegrsPredict-class.Rd |only exprso-0.2.6/exprso/man/array.Rd | 2 exprso-0.2.6/exprso/man/arrayExprs.Rd | 3 exprso-0.2.6/exprso/man/arrayMulti.Rd | 2 exprso-0.2.6/exprso/man/build..Rd | 3 exprso-0.2.6/exprso/man/build.Rd | 13 exprso-0.2.6/exprso/man/buildANN.Rd | 3 exprso-0.2.6/exprso/man/buildDNN.Rd | 3 exprso-0.2.6/exprso/man/buildEnsemble.Rd | 56 +-- exprso-0.2.6/exprso/man/buildLDA.Rd | 3 exprso-0.2.6/exprso/man/buildNB.Rd | 3 exprso-0.2.6/exprso/man/buildRF.Rd | 3 exprso-0.2.6/exprso/man/buildSVM.Rd | 3 exprso-0.2.6/exprso/man/calcMonteCarlo.Rd | 4 exprso-0.2.6/exprso/man/calcNested.Rd | 4 exprso-0.2.6/exprso/man/calcStats.Rd | 50 +-- exprso-0.2.6/exprso/man/check.ctrlGS.Rd | 7 exprso-0.2.6/exprso/man/classCheck.Rd | 2 exprso-0.2.6/exprso/man/compare.Rd | 2 exprso-0.2.6/exprso/man/conjoin.Rd | 15 exprso-0.2.6/exprso/man/ctrlFeatureSelect.Rd | 2 exprso-0.2.6/exprso/man/ctrlGridSearch.Rd | 2 exprso-0.2.6/exprso/man/ctrlModSet.Rd |only exprso-0.2.6/exprso/man/ctrlSplitSet.Rd | 2 exprso-0.2.6/exprso/man/defaultArg.Rd | 2 exprso-0.2.6/exprso/man/doMulti.Rd | 61 --- exprso-0.2.6/exprso/man/exprso-predict.Rd | 85 +---- exprso-0.2.6/exprso/man/exprso.Rd | 13 exprso-0.2.6/exprso/man/forceArg.Rd | 2 exprso-0.2.6/exprso/man/fs..Rd | 2 exprso-0.2.6/exprso/man/fs.Rd | 42 +- exprso-0.2.6/exprso/man/fsANOVA.Rd | 3 exprso-0.2.6/exprso/man/fsCor.Rd |only exprso-0.2.6/exprso/man/fsEbayes.Rd | 2 exprso-0.2.6/exprso/man/fsEdger.Rd | 2 exprso-0.2.6/exprso/man/fsInclude.Rd | 3 exprso-0.2.6/exprso/man/fsMrmre.Rd | 2 exprso-0.2.6/exprso/man/fsNULL.Rd | 4 exprso-0.2.6/exprso/man/fsPathClassRFE.Rd | 2 exprso-0.2.6/exprso/man/fsPrcomp.Rd | 2 exprso-0.2.6/exprso/man/fsPropd.Rd | 6 exprso-0.2.6/exprso/man/fsSample.Rd | 2 exprso-0.2.6/exprso/man/fsStats.Rd | 2 exprso-0.2.6/exprso/man/getArgs.Rd | 2 exprso-0.2.6/exprso/man/getFeatures.Rd | 7 exprso-0.2.6/exprso/man/makeGridFromArgs.Rd | 2 exprso-0.2.6/exprso/man/mod.Rd | 6 exprso-0.2.6/exprso/man/modAcomp.Rd |only exprso-0.2.6/exprso/man/modCLR.Rd |only exprso-0.2.6/exprso/man/modCluster.Rd | 2 exprso-0.2.6/exprso/man/modHistory.Rd | 33 -- exprso-0.2.6/exprso/man/modSubset.Rd | 2 exprso-0.2.6/exprso/man/modSwap.Rd | 2 exprso-0.2.6/exprso/man/packageCheck.Rd | 2 exprso-0.2.6/exprso/man/pipeFilter.Rd | 55 --- exprso-0.2.6/exprso/man/pipeUnboot.Rd | 23 - exprso-0.2.6/exprso/man/plCV.Rd | 30 - exprso-0.2.6/exprso/man/plGrid.Rd | 53 --- exprso-0.2.6/exprso/man/plGridMulti.Rd | 15 exprso-0.2.6/exprso/man/plMonteCarlo.Rd | 18 - exprso-0.2.6/exprso/man/plNested.Rd | 18 - exprso-0.2.6/exprso/man/reRank.Rd | 13 exprso-0.2.6/exprso/man/splitSample.Rd | 3 exprso-0.2.6/exprso/man/trainingSet.Rd | 2 exprso-0.2.6/exprso/man/validationSet.Rd | 2 exprso-0.2.6/exprso/tests/testthat/test-fs-etc.R | 41 ++ exprso-0.2.6/exprso/tests/testthat/test-fs.R | 6 exprso-0.2.6/exprso/tests/testthat/test-regrs.R |only exprso-0.2.6/exprso/vignettes/a_introduction-vignette.Rmd | 8 exprso-0.2.6/exprso/vignettes/b_advanced-vignette.Rmd | 12 exprso-0.2.6/exprso/vignettes/c_readme.Rmd | 2 120 files changed, 1040 insertions(+), 1211 deletions(-)
Title: Dynamic Estimation of Group-Level Opinion
Description: Fit dynamic group-level IRT and MRP models from individual or
aggregated item response data. This package handles common preprocessing
tasks and extends functions for inspecting results, poststratification, and
quick iteration over alternative models.
Author: James Dunham [aut, cre],
Devin Caughey [aut],
Christopher Warshaw [aut]
Maintainer: James Dunham <james@jdunham.io>
Diff between dgo versions 0.2.11 dated 2017-10-29 and 0.2.12 dated 2017-11-30
DESCRIPTION | 8 +- MD5 | 22 +++--- NEWS.md | 16 ++++ R/restrict_input_data.r | 7 -- R/shape_hierarchical.r | 9 +- README.md | 129 ++++++++++++++++++++++++++------------- data/toy_dgirt_in.rda |binary data/toy_dgirtfit.rda |binary tests/testthat/dgirt_ret.Rds |binary tests/testthat/dgmrp_ret.Rds |binary tests/testthat/test-defaults.r | 16 ++++ tests/testthat/test-shape_misc.r | 31 +++++++++ 12 files changed, 170 insertions(+), 68 deletions(-)
Title: Identify Event Sequences Using Time Series Joins
Description: Examine any number of time series data frames to identify
instances in which various criteria are met within specified time
frames. In clinical medicine, these types of events are often
called "constellations of signs and symptoms", because a single
condition depends on a series of events occurring within a certain
amount of time of each other. This package was written to work with
any number of time series data frames and is optimized for speed
to work well with data frames with millions of rows.
Author: Mark Sendak [aut, cre]
Maintainer: Mark Sendak <mark.sendak@gmail.com>
Diff between constellation versions 0.0.1 dated 2017-11-02 and 0.1.0 dated 2017-11-30
DESCRIPTION | 6 MD5 | 29 + NAMESPACE | 1 R/bundle.R |only R/constellate.R | 6 R/constellate_criteria.R | 134 +++++--- README.md | 117 +++++-- inst/doc/identify_sepsis.R | 2 inst/doc/identify_sepsis.Rmd | 2 inst/doc/identify_sepsis.html | 444 ++++++++++++++++++++--------- man/bundle.Rd |only man/constellate.Rd | 1 man/constellate_criteria.Rd | 59 ++- tests/testthat/test-bundle.R |only tests/testthat/test-constellate.R | 17 - tests/testthat/test-constellate_criteria.R | 115 +++++-- vignettes/identify_sepsis.Rmd | 2 17 files changed, 648 insertions(+), 287 deletions(-)
Title: Wraps the API for the Brazilian Chamber of Deputies
Description: Provides propositions, votings, deputies and parties data from
Brazilian Chamber of Deputies <https://dadosabertos.camara.leg.br> in data frames.
Author: Paulo Vinícius Soares [aut, cre],
Nazareno Andrade [aut],
Laboratório Analytics (UFCG) [cph, fnd]
Maintainer: Paulo Vinícius Soares <paulo.soares@ccc.ufcg.edu.br>
Diff between rcongresso versions 0.2.1 dated 2017-11-03 and 0.3.0 dated 2017-11-30
DESCRIPTION | 8 +- MD5 | 31 +++++---- R/constants.R | 3 R/deputados.R | 35 ++++++----- R/proposicoes.R | 57 ++---------------- R/utils.R | 94 ++++++++++++++++++++++++++++++ inst/doc/introducao-rcongresso.R | 2 inst/doc/introducao-rcongresso.Rmd | 2 inst/doc/introducao-rcongresso.html | 16 ++--- inst/doc/purrr-e-rcongresso.html | 10 +-- man/fetch_deputado.Rd | 20 +++++- man/fetch_despesas_deputado.Rd | 2 man/fetch_proposicao.Rd | 6 - man/fetch_ultimo_status_deputado.Rd | 2 tests/testthat/test_proposicoes.R | 14 +++- vignettes/introducao-rcongresso.Rmd | 2 vignettes/utilizando-fetch-proposicao.Rmd |only 17 files changed, 196 insertions(+), 108 deletions(-)
Title: Nonparametric Estimation of Regression Models with
Factor-by-Curve Interactions
Description: A method for obtaining nonparametric estimates of regression models
with or without factor-by-curve interactions using local polynomial kernel
smoothers or splines. Additionally, a parametric model (allometric model) can be
estimated.
Author: Marta Sestelo [aut, cre] (0000-0003-4284-6509),
Nora M. Villanueva [aut],
Javier Roca-Pardinas [aut]
Maintainer: Marta Sestelo <sestelo@uvigo.es>
Diff between npregfast versions 1.5.0 dated 2017-10-30 and 1.5.1 dated 2017-11-30
npregfast-1.5.0/npregfast/man/npregfast.Rd |only npregfast-1.5.1/npregfast/DESCRIPTION | 17 ++++++----- npregfast-1.5.1/npregfast/MD5 | 36 ++++++++++++------------ npregfast-1.5.1/npregfast/NEWS | 4 ++ npregfast-1.5.1/npregfast/R/barnacle.R | 5 +++ npregfast-1.5.1/npregfast/R/critical.R | 4 ++ npregfast-1.5.1/npregfast/R/criticaldiff.R | 4 ++ npregfast-1.5.1/npregfast/R/frfast.R | 4 ++ npregfast-1.5.1/npregfast/R/globaltest.R | 5 +++ npregfast-1.5.1/npregfast/R/localtest.R | 4 ++ npregfast-1.5.1/npregfast/R/npregfast-package.R | 12 ++------ npregfast-1.5.1/npregfast/R/summary.frfast.R | 3 ++ npregfast-1.5.1/npregfast/inst/CITATION |only npregfast-1.5.1/npregfast/man/barnacle.Rd | 4 ++ npregfast-1.5.1/npregfast/man/critical.Rd | 4 ++ npregfast-1.5.1/npregfast/man/criticaldiff.Rd | 4 ++ npregfast-1.5.1/npregfast/man/frfast.Rd | 4 ++ npregfast-1.5.1/npregfast/man/globaltest.Rd | 5 +++ npregfast-1.5.1/npregfast/man/localtest.Rd | 4 ++ npregfast-1.5.1/npregfast/man/summary.frfast.Rd | 4 ++ 20 files changed, 91 insertions(+), 36 deletions(-)
Title: A Self-Describing Dataset Format and Interface
Description: Defines a compact data format that includes metadata.
The function fold() creates the format by converting
from data.frame, and unfold() converts back. The predictability
of the folded format supports reusability of data processing tools,
while the presence of embedded metadata improves portability,
interpretability, and efficiency.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between fold versions 0.2.2 dated 2017-08-14 and 0.2.4 dated 2017-11-30
DESCRIPTION | 6 - MD5 | 45 +++++++---- NAMESPACE | 11 ++ R/folded.R |only R/meta.R | 171 ++++++-------------------------------------- R/package-fold.R | 53 ++++++------- R/unfolded.R |only man/anti_join.folded.Rd | 2 man/anti_join.unfolded.Rd |only man/arrange.folded.Rd | 2 man/arrange.unfolded.Rd |only man/filter.folded.Rd | 2 man/filter.unfolded.Rd |only man/fold.data.frame.Rd | 2 man/foldpkg.Rd | 53 ++++++------- man/group_by.folded.Rd | 2 man/group_by.unfolded.Rd |only man/left_join.folded.Rd | 2 man/left_join.unfolded.Rd |only man/mutate.folded.Rd | 2 man/mutate.unfolded.Rd |only man/select.folded.Rd | 2 man/select.unfolded.Rd |only man/semi_join.folded.Rd |only man/semi_join.unfolded.Rd |only man/transmutate.folded.Rd | 2 man/transmutate.unfolded.Rd |only man/unfold.folded.Rd | 6 + man/ungroup.folded.Rd | 2 man/ungroup.unfolded.Rd |only 30 files changed, 135 insertions(+), 230 deletions(-)
Title: Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Description: This is an R interface to the
python package 'excerpts' (<https://pypi.python.org/pypi/excerpts>).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between excerptr versions 1.3.1 dated 2017-07-08 and 1.4.0 dated 2017-11-30
DESCRIPTION | 6 +-- MD5 | 14 +++---- NEWS.md | 6 +++ R/excerptr.R | 66 ++++++++++++++++++++++++++++++------ inst/doc/excerptr_Introduction.R | 4 ++ inst/doc/excerptr_Introduction.Rmd | 11 ++++-- inst/doc/excerptr_Introduction.html | 7 ++- vignettes/excerptr_Introduction.Rmd | 11 ++++-- 8 files changed, 98 insertions(+), 27 deletions(-)
Title: Represent Ordered Lists and Pairs as Strings
Description: Interconverts between ordered lists and compact string notation.
Useful for capturing code lists, and pair-wise codes and decodes, for text storage.
Analogous to factor levels and labels. Generics encode() and decode()
perform interconversion, while codes() and decodes() extract components of an encoding.
The function encoded() checks whether something is interpretable as an encoding.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between encode versions 0.3 dated 2017-04-13 and 0.3.2 dated 2017-11-30
DESCRIPTION | 7 +- MD5 | 12 ++-- R/encode.R | 119 ++++++++++++++++++++++++------------------------ man/decode.default.Rd | 4 - man/encode.Rd | 30 ++++++++---- man/encode.character.Rd | 2 man/encoded.default.Rd | 5 +- 7 files changed, 98 insertions(+), 81 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985), <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
CORMACK, R.M. (1971) <doi:10.2307/2344237>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
CARMONE, F.J., KARA, A., MAXWELL, S. (1999) <doi:10.2307/3152003>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
KRZANOWSKI, W.J., LAI, Y.T. (1988) <doi:10.2307/2531893>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.46-2 dated 2017-09-21 and 0.47-1 dated 2017-11-30
DESCRIPTION | 12 - MD5 | 10 + R/dist.Symbolic.r | 138 ++++++++++----------- R/interval_normalization.r |only data/data_symbolic_interval_polish_voivodships.rda |only man/data_symbolic_interval_polish_voivodships.rd |only man/dist.Symbolic.rd | 20 +-- man/interval_normalization.rd |only 8 files changed, 91 insertions(+), 89 deletions(-)
Title: Statistical Experiments on Batch Computing Clusters
Description: Extends the BatchJobs package to run statistical experiments on
batch computing clusters. For further details see the project web page.
Author: Bernd Bischl <bernd_bischl@gmx.net>,
Michel Lang <michellang@gmail.com>,
Olaf Mersmann <olafm@p-value.net>
Maintainer: Michel Lang <michellang@gmail.com>
Diff between BatchExperiments versions 1.4.1 dated 2015-03-18 and 1.4.2 dated 2017-11-30
DESCRIPTION | 15 ++-- MD5 | 101 ++++++++++++++++---------------- NAMESPACE | 9 ++ NEWS | 5 + R/Algorithm.R | 2 R/ExperimentRegistry.R | 19 +++--- R/Problem.R | 6 - R/addExperiments.R | 47 ++++++++++---- R/database.R | 69 ++++++++++++++------- R/findExperiments.R | 8 +- R/generateProblemInstance.R | 2 R/getAlgorithm.R | 2 R/getAlgorithmIds.R | 7 +- R/getExperimentParts.R | 7 +- R/getIndex.R | 6 - R/getJob.R | 5 + R/getJobInfo.R | 4 - R/getProblem.R | 2 R/getProblemIds.R | 7 +- R/reduceResultsExperiments.R | 24 +++---- R/reduceResultsExperimentsParallel.R | 37 +++++------ R/removeAlgorithm.R | 4 - R/removeExperiments.R | 19 +++--- R/removeProblem.R | 4 - R/summarizeExperiments.R | 8 -- R/updateExperimentRegistry.R | 2 R/zzz.R | 27 +++++++- man/BatchExperiments.Rd | 2 man/ExperimentJob.Rd | 3 man/addAlgorithm.Rd | 8 -- man/addExperiments.Rd | 8 -- man/addProblem.Rd | 8 -- man/findExperiments.Rd | 6 - man/generateProblemInstance.Rd | 5 - man/getAlgorithm.Rd | 11 +-- man/getAlgorithmIds.Rd | 13 +--- man/getExperimentParts.Rd | 13 +--- man/getIndex.Rd | 3 man/getJobs.ExperimentRegistry.Rd | 13 +--- man/getProblem.Rd | 11 +-- man/getProblemIds.Rd | 13 +--- man/getResultVars.Rd | 3 man/makeDesign.Rd | 5 - man/makeExperimentRegistry.Rd | 5 - man/reduceResultsExperiments.Rd | 7 -- man/reduceResultsExperimentsParallel.Rd | 3 man/removeAlgorithm.Rd | 5 - man/removeExperiments.Rd | 5 - man/removeProblem.Rd | 5 - man/summarizeExperiments.Rd | 7 -- tests/run-all.R | 1 tests/testthat/test_ExperimentRegisty.R |only 52 files changed, 337 insertions(+), 274 deletions(-)
More information about BatchExperiments at CRAN
Permanent link
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.7.6 dated 2017-08-01 and 0.7.9 dated 2017-11-30
DESCRIPTION | 6 MD5 | 90 ++++++++++--- NAMESPACE | 8 + R/init.R | 8 - R/likebut.R | 13 + R/model.R | 6 R/partab.R | 22 +++ R/superset.R | 257 +++++++++++++++++++++++++++++++++++---- inst/doc/parameter-table.html | 58 ++++---- inst/project/model/1001/1001.ctl | 4 inst/project/model/2001 |only inst/project/model/2002 |only inst/project/model/2003 |only inst/project/model/2004 |only inst/project/model/2005 |only inst/project/model/2006 |only inst/project/model/2007 |only man/generalize.Rd |only man/likebut.Rd | 3 man/metaplot.character.Rd | 2 man/ninput.Rd |only man/ninput.character.Rd |only man/ninput.numeric.Rd |only man/partab.character.Rd | 8 + man/runlog.Rd | 3 man/runlog.character.Rd | 11 + man/shuffle.Rd |only man/superset.character.Rd | 20 ++- man/superspec.Rd |only man/superspec.character.Rd |only man/superspec.numeric.Rd |only man/tweak.Rd | 5 man/tweak.default.Rd | 5 man/tweak.init.Rd | 5 man/tweak.inits.Rd | 5 man/tweak.model.Rd | 5 36 files changed, 445 insertions(+), 99 deletions(-)
Title: Bucky's Archive for Data Analysis in the Social Sciences
Description: Provides functions for various statistical techniques commonly used in the social sciences, including functions to compute clustered robust standard errors, combine results across multiply-imputed data sets, and simplify the addition of robust and clustered robust standard errors. The package was originally developed, in part, to assist porting of replication code from 'Stata' and attempts to replicate default options from 'Stata' where possible.
Author: Alexander Tahk [aut, cre]
Maintainer: Alexander Tahk <tahk@alum.mit.edu>
Diff between bucky versions 1.0.3 dated 2017-11-22 and 1.0.4 dated 2017-11-30
DESCRIPTION | 14 +++--- MD5 | 19 ++++----- NAMESPACE | 12 +++-- NEWS |only R/clustered-robust.R | 66 ++++++++++++++++++++++++++++++++ R/mult-imp.R | 83 +++++++++++++++++++++++++++++++--------- build/partial.rdb |binary man/bucky-package.Rd | 23 +++++++++-- man/mi.eval.Rd | 104 +++++++++++++++++++++++++++++---------------------- man/robustify.Rd | 18 +++++++- man/vcovCR.Rd | 36 ++++++++--------- 11 files changed, 271 insertions(+), 104 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-09 2.1.8
2013-08-22 2.1.7
2013-01-07 2.1.6
2012-07-23 2.1.4
2012-07-11 2.1.3
2012-07-10 2.1.1
2012-07-03 2.1.0
2012-03-26 2.0.5
2011-10-20 1.1.0
2011-03-28 1.0.0
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] (SSCC, Univ. of Wisconsin-Madison)
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between SASmarkdown versions 0.3.3 dated 2017-07-10 and 0.4.3 dated 2017-11-30
DESCRIPTION | 15 ++++++++++----- MD5 | 30 ++++++++++++++++++------------ NAMESPACE | 1 + R/misc.r | 4 ++-- R/sas_collectcode.r | 14 +++++++++++++- R/spinsas.r |only inst/NEWS.Rd |only inst/doc/collectcode.html | 30 ++++++++++++------------------ inst/doc/index.html | 5 +++++ inst/doc/spinSASmarkdown.html |only inst/doc/vigsource/DESCRIPTION | 4 ++-- inst/doc/vigsource/README.html | 13 +++++++------ inst/doc/vigsource/README.md | 10 +++++++--- inst/doc/vigsource/autoexec.txt |only inst/doc/vigsource/collectcode.rmd | 27 +++++++++++---------------- inst/doc/vigsource/spinSASmarkdown.rmd |only man/SASmarkdown-package.rd | 3 +++ man/sas_collectcode.Rd | 16 ++++++++++------ man/spinsas.Rd |only 19 files changed, 101 insertions(+), 71 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://ropensci.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and others.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.8 dated 2017-10-07 and 1.0.9 dated 2017-11-30
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS | 4 ++++ R/afbo.feature.R | 11 +++++++---- R/aff.lang.R | 2 +- R/map.feature.R | 20 +++++++++++++++++++- R/wals.R | 2 +- R/wals.feature.R | 4 ++-- inst/doc/lingtypology.R | 4 ++-- inst/doc/lingtypology.Rmd | 4 ++-- inst/doc/lingtypology.html | 8 ++++---- inst/doc/manual/lingtypology.pdf |binary man/afbo.feature.Rd | 2 +- man/map.feature.Rd | 18 ++++++++++++------ man/wals.Rd | 2 +- vignettes/lingtypology.Rmd | 4 ++-- 16 files changed, 76 insertions(+), 45 deletions(-)
Title: Total Cophenetic Index: An R Package to Quantify Tree Balance
Description: For a given phylogenetic tree, calculates the Total Cophenetic Index.
Reference - A. Mir, F. Rossello, L. A. Rotger, A new balance index for phylogenetic trees.
Math. Biosci. 241, 125-136 (2013).
Author: Martin R. Smith
Maintainer: Martin R. Smith <martins@gmail.com>
Diff between TotalCopheneticIndex versions 0.1 dated 2016-03-26 and 1.0.0 dated 2017-11-30
DESCRIPTION | 20 +++++++++++--------- MD5 | 15 +++++++++------ NAMESPACE | 2 +- NEWS.md |only R/total.cophenetic.index.R | 2 +- README.md |only inst |only man/list.ancestors.Rd | 16 +++++++++++----- man/tci.Rd | 15 ++++++++++----- man/tci.context.Rd | 18 +++++++++++++----- 10 files changed, 56 insertions(+), 32 deletions(-)
More information about TotalCopheneticIndex at CRAN
Permanent link
Title: Regression Models with Break-Points / Change-Points Estimation
Description: Given a regression model, segmented `updates' the model by adding one or more segmented (i.e., piece-wise linear) relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between segmented versions 0.5-2.2 dated 2017-09-19 and 0.5-3.0 dated 2017-11-30
DESCRIPTION | 8 ++++---- MD5 | 38 ++++++++++++++++++++------------------ NAMESPACE | 5 +++-- NEWS | 11 +++++++++-- R/aapc.r |only R/confint.segmented.R | 4 ++-- R/intercept.r | 2 +- R/plot.segmented.R | 8 ++++++-- R/seg.Ar.fit.r | 10 +++++++--- R/segmented.Arima.r | 10 +++++++--- R/slope.R | 8 ++++---- data/down.rda |binary data/plant.rda |binary data/stagnant.rda |binary man/aapc.Rd |only man/confint.segmented.Rd | 4 ++-- man/intercept.Rd | 4 ++-- man/plot.segmented.Rd | 2 +- man/segmented-package.Rd | 4 ++-- man/segmented.Rd | 11 +++-------- man/slope.Rd | 7 ++----- 21 files changed, 75 insertions(+), 61 deletions(-)
Title: Travel Smoothly Between Country Name and Code Formats
Description: Smooths the process of working with country names and codes via
powerful parsing, standardization, and conversion utilities arranged in a
simple, consistent API. Country name formats include multiple sources
including the Unicode Common Locale Data
Repository (CLDR, <http://cldr.unicode.org/>) common-sense standardized
names in hundreds of languages.
Author: Edward Visel [aut, cre]
Maintainer: Edward Visel <edward.visel@gmail.com>
Diff between passport versions 0.1.1 dated 2017-07-09 and 0.2.0 dated 2017-11-30
passport-0.1.1/passport/inst/aggregation.nb.html |only passport-0.2.0/passport/DESCRIPTION | 8 passport-0.2.0/passport/MD5 | 50 ++-- passport-0.2.0/passport/NAMESPACE | 1 passport-0.2.0/passport/NEWS.md | 11 passport-0.2.0/passport/R/as_country_code.R | 13 - passport-0.2.0/passport/R/as_country_name.R | 16 - passport-0.2.0/passport/R/convert_country.R | 31 +- passport-0.2.0/passport/R/country_format.R | 115 +++++++++- passport-0.2.0/passport/R/parse_country.R | 56 ++-- passport-0.2.0/passport/README.md | 63 +++-- passport-0.2.0/passport/build/vignette.rds |binary passport-0.2.0/passport/inst/aggregation.Rmd | 2 passport-0.2.0/passport/inst/doc/passport.R | 49 ++-- passport-0.2.0/passport/inst/doc/passport.Rmd | 54 ++-- passport-0.2.0/passport/inst/doc/passport.html | 59 ++--- passport-0.2.0/passport/man/as_country_code.Rd | 8 passport-0.2.0/passport/man/as_country_name.Rd | 7 passport-0.2.0/passport/man/country_format.Rd | 14 - passport-0.2.0/passport/man/figures/README-format-1.png |binary passport-0.2.0/passport/man/order_countries.Rd |only passport-0.2.0/passport/man/parse_country.Rd | 11 passport-0.2.0/passport/tests/testthat/test_as_country_code.R | 24 +- passport-0.2.0/passport/tests/testthat/test_as_country_name.R | 36 +-- passport-0.2.0/passport/tests/testthat/test_country_format.R | 24 +- passport-0.2.0/passport/tests/testthat/test_parse_country.R | 95 +++++--- passport-0.2.0/passport/vignettes/passport.Rmd | 54 ++-- 27 files changed, 519 insertions(+), 282 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. Reference: Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets, Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>.
Author: Michail Tsagris [aut, cre], Ioannis Tsamardinos [aut, cph], Vincenzo Lagani [aut, cph], Giorgos Athineou [aut], Giorgos Borboudakis [ctb], Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 1.3.0 dated 2017-11-16 and 1.3.1 dated 2017-11-30
DESCRIPTION | 8 - MD5 | 210 +++++++++++++++++++++++-------------------- NAMESPACE | 43 ++++---- R/MMPC.R | 12 -- R/Ness.R |only R/SES.R | 6 - R/bic.fsreg.R | 8 + R/bic.zipfsreg.R | 7 + R/bn.skel.utils.R | 9 + R/bn.skel.utils2.R |only R/bs.reg.R | 8 + R/compare_p_values.R | 6 - R/conf.edge.lower.R |only R/cor.bsreg.R |only R/cor.drop1.R |only R/corfs.network.R | 4 R/cv.ses.R | 15 --- R/ebic.fbed.zip.R | 23 ++-- R/ebic.zip.bsreg.R | 12 +- R/fbed.glmm.reg.R | 2 R/fbed.reg.R | 3 R/fbed.zip.R | 21 ++-- R/fs.reg.R | 6 - R/gammabsreg.R | 40 ++++---- R/gammafsreg.R | 50 +++++----- R/gammafsreg_2.R | 41 ++++---- R/glm.bsreg.R | 4 R/glmm.pc.skel.R | 25 ++--- R/mmhc.skel.R | 78 ++++++++-------- R/mmpc.model.R | 37 +++---- R/mmpc.or.R | 2 R/mmpc.temporal.model.R | 20 ++-- R/mmpcbackphase.R | 30 +++--- R/normlog.bsreg.R | 230 ++++++++++++++++++++++++------------------------ R/normlog.fsreg.R | 66 +++++++------ R/normlog.fsreg_2.R | 80 ++++++++-------- R/pc.skel.R | 112 ++++++++++++----------- R/pc.skel.boot.R | 2 R/perm.Internalmmpc.R | 3 R/perm.max_min_assoc.R | 2 R/perm.mmpc.R | 28 ++--- R/perm.ses.R | 6 - R/permBeta.R | 6 - R/permBinom.R | 8 - R/permCR.R | 6 - R/permDcor.R | 4 R/permFisher.R | 8 - R/permGamma.R | 14 +- R/permIGreg.R | 8 - R/permLogistic.R | 16 +-- R/permMVreg.R | 26 ++--- R/permNB.R | 14 +- R/permNormLog.R | 12 +- R/permPois.R | 16 +-- R/permRQ.R | 18 +-- R/permReg.R | 10 +- R/permWR.R | 4 R/permZIP.R | 12 +- R/pi0est.R |only R/pval.mixbeta.R |only R/reg.fit.R | 2 R/rint.regs.R | 64 ------------- R/ses.model.R | 24 ++--- R/shd.R | 12 +- R/testIndBeta.R | 8 - R/testIndBinom.R | 16 +-- R/testIndClogit.R | 4 R/testIndFisher.R | 10 +- R/testIndGLMM.R | 12 +- R/testIndGamma.R | 12 +- R/testIndIGreg.R | 12 +- R/testIndLogistic.R | 22 ++-- R/testIndMVreg.R | 34 +++---- R/testIndNB.R | 4 R/testIndNormLog.R | 6 - R/testIndPois.R | 6 - R/testIndRQ.R | 10 +- R/testIndReg.R | 14 +- R/testIndSpearman.R | 4 R/testIndSpeedglm.R | 6 - R/testIndZIP.R | 11 +- R/univregs.R | 51 ++++------ R/wald.mmpc.R | 2 R/wald.ses.R | 4 R/wald.univregs.R | 8 - R/waldGamma.R | 2 R/waldNormLog.R | 2 R/zip.bsreg.R | 21 ++-- R/zip.fsreg.R | 22 ++-- R/zip.fsreg_2.R | 27 +++-- R/zip.regs.R | 2 inst/doc/article.pdf |binary inst/doc/guide.pdf |binary man/MXM-internal.Rd | 4 man/MXM-package.Rd | 4 man/Ness.Rd |only man/auc.Rd | 2 man/bn.skel.utils.Rd | 42 ++++++-- man/bs.reg.Rd | 3 man/conf.edge.lower.Rd |only man/cor.drop1.Rd |only man/cv.ses.Rd | 20 ++-- man/fbed.reg.Rd | 1 man/local.mmhc.skel.Rd | 2 man/mmhc.skel.Rd | 21 ++-- man/mmpc.or.Rd | 14 +- man/pc.or.Rd | 13 +- man/pc.skel.Rd | 20 +++- man/pi0est.Rd |only man/pval.mixbeta.Rd |only man/testIndGamma.Rd | 19 +++ man/testIndReg.Rd | 21 ---- 112 files changed, 1047 insertions(+), 1014 deletions(-)
Title: Tests in Linear Mixed Effects Models
Description: Different kinds of tests for linear mixed effects models as implemented
in 'lme4' package are provided. The tests comprise types I - III F tests
for fixed effects, LR tests for random effects.
The package also provides the calculation of population means for fixed factors
with confidence intervals and corresponding plots. Finally the backward
elimination of non-significant effects is implemented.
Author: Alexandra Kuznetsova [aut],
Per Bruun Brockhoff [aut, ths, cre],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Per Bruun Brockhoff <perbb@dtu.dk>
Diff between lmerTest versions 2.0-33 dated 2016-12-03 and 2.0-36 dated 2017-11-30
lmerTest-2.0-33/lmerTest/tests/Examples |only lmerTest-2.0-33/lmerTest/tests/packageExamplesExtra.Rout.save |only lmerTest-2.0-33/lmerTest/tests/test-all.R |only lmerTest-2.0-33/lmerTest/tests/testExamplesFromPaper.Rout.save |only lmerTest-2.0-33/lmerTest/tests/testKeep.Rout.save |only lmerTest-2.0-33/lmerTest/tests/testRand.Rout.save |only lmerTest-2.0-33/lmerTest/tests/testTVbo.Rout.save |only lmerTest-2.0-36/lmerTest/DESCRIPTION | 25 +- lmerTest-2.0-36/lmerTest/MD5 | 22 -- lmerTest-2.0-36/lmerTest/NEWS | 3 lmerTest-2.0-36/lmerTest/R/satterth.R | 2 lmerTest-2.0-36/lmerTest/inst/CITATION |only lmerTest-2.0-36/lmerTest/man/lmerTest-package.Rd | 6 lmerTest-2.0-36/lmerTest/tests/DamonData.R | 24 +- lmerTest-2.0-36/lmerTest/tests/testRand.R | 94 +++++----- lmerTest-2.0-36/lmerTest/tests/testSlopesFactors.R | 16 - 16 files changed, 98 insertions(+), 94 deletions(-)
Title: Kernel k Nearest Neighbors
Description: Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between KernelKnn versions 1.0.6 dated 2017-10-30 and 1.0.7 dated 2017-11-30
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS.md | 7 + R/dist_kernelknn.R | 8 +- build/vignette.rds |binary inst/doc/binary_classification_using_the_ionosphere_data.html | 38 +++++----- inst/doc/image_classification_using_MNIST_CIFAR_data.html | 4 - inst/doc/regression_using_the_housing_data.html | 4 - man/distMat.KernelKnn.Rd | 2 src/distance_metrics.cpp | 4 - tests/testthat/test-distmat_kernelknn.R | 1 11 files changed, 54 insertions(+), 42 deletions(-)
Title: A GeoJson Processing Toolkit
Description: Includes functions for processing GeoJson objects <https://en.wikipedia.org/wiki/GeoJSON> relying on 'RFC 7946' <https://tools.ietf.org/pdf/rfc7946.pdf>. The geojson encoding is based on 'json11', a tiny JSON library for 'C++11' <https://github.com/dropbox/json11>. Furthermore, the source code is exported in R through the 'Rcpp' and 'RcppArmadillo' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between geojsonR versions 1.0.3 dated 2017-09-05 and 1.0.4 dated 2017-11-30
DESCRIPTION | 8 - MD5 | 20 +-- NEWS.md | 5 R/RcppExports.R | 22 +-- README.md | 1 build/vignette.rds |binary inst/doc/the_geojsonR_package.html | 222 ++++++++++++++++++------------------- src/Makevars | 6 - src/Makevars.win | 6 - src/RcppExports.cpp | 22 +-- src/init.c | 46 +++---- 11 files changed, 181 insertions(+), 177 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans and
K-Medoids Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans and k-medoids
clustering with the option to plot, validate, predict (new data) and estimate the
optimal number of clusters. The package takes advantage of 'RcppArmadillo' to
speed up the computationally intensive parts of the functions.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.0.8 dated 2017-10-28 and 1.0.9 dated 2017-11-30
DESCRIPTION | 8 - MD5 | 24 ++--- NEWS.md | 5 + R/RcppExports.R | 4 R/clustering_functions.R | 128 +++++++++++++++-------------- README.md | 2 build/vignette.rds |binary inst/doc/the_clusterR_package.html | 20 ++-- man/Optimal_Clusters_KMeans.Rd | 2 src/RcppExports.cpp | 23 +---- src/init.c | 2 src/kmeans_miniBatchKmeans_GMM_Medoids.cpp | 85 +++++++++---------- tests/testthat/test-kmeans.R | 4 13 files changed, 153 insertions(+), 154 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.8.1 dated 2017-11-27 and 0.8.2 dated 2017-11-30
clustermq-0.8.1/clustermq/R/fill_template.r |only clustermq-0.8.1/clustermq/man/fill_template.Rd |only clustermq-0.8.1/clustermq/tests/performance |only clustermq-0.8.1/clustermq/tests/testthat/test-fill_template.r |only clustermq-0.8.2/clustermq/DESCRIPTION | 6 clustermq-0.8.2/clustermq/MD5 | 78 -- clustermq-0.8.2/clustermq/R/Q_rows.r | 50 - clustermq-0.8.2/clustermq/R/qsys.r | 5 clustermq-0.8.2/clustermq/R/qsys_local.r | 7 clustermq-0.8.2/clustermq/R/qsys_lsf.r | 12 clustermq-0.8.2/clustermq/R/qsys_multicore.r | 7 clustermq-0.8.2/clustermq/R/qsys_sge.r | 18 clustermq-0.8.2/clustermq/R/qsys_slurm.r | 18 clustermq-0.8.2/clustermq/R/worker.r | 11 clustermq-0.8.2/clustermq/R/workers.r | 5 clustermq-0.8.2/clustermq/inst/doc/clustermq.html | 372 +++++++--- clustermq-0.8.2/clustermq/man/worker.Rd | 4 clustermq-0.8.2/clustermq/man/workers.Rd | 2 clustermq-0.8.2/clustermq/tests/testthat/helper-util.r | 17 clustermq-0.8.2/clustermq/tests/testthat/test-qsys.r | 20 clustermq-0.8.2/clustermq/tests/testthat/test-ssh_proxy.r | 10 clustermq-0.8.2/clustermq/tests/testthat/test-worker.r | 29 22 files changed, 443 insertions(+), 228 deletions(-)
Title: Statistical Tools for Filebacked Big Matrices
Description: Easy-to-use, efficient, flexible and scalable statistical tools.
Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping.
It provides for instance matrix operations, Principal Component Analysis,
sparse linear supervised models, utility functions and more.
Preprint: <doi:10.1101/190926>.
Author: Florian Privé [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigstatsr versions 0.2.1 dated 2017-09-02 and 0.2.3 dated 2017-11-30
DESCRIPTION | 14 MD5 | 239 +++++----- NAMESPACE | 120 ++--- NEWS.md | 18 R/AUC.R | 215 ++++----- R/CMSA.R | 236 +++++----- R/FBM-attach.R | 76 +-- R/FBM-code256.R | 306 ++++++------- R/FBM-copy.R | 138 +++--- R/FBM.R | 446 ++++++++++---------- R/RcppExports.R | 246 +++++------ R/SVD.R | 222 +++++----- R/apply-parallelize.R | 326 +++++++------- R/biglasso.R | 598 +++++++++++++-------------- R/bigstatsr.R | 98 ++-- R/colstats.R | 52 +- R/counts.R | 90 ++-- R/crochet.R | 304 ++++++------- R/crossprodSelf.R | 188 ++++---- R/plot.R | 474 ++++++++++----------- R/predict.R | 344 +++++++-------- R/randomSVD.R | 404 +++++++++--------- R/read.R | 228 +++++----- R/scaling.R | 122 ++--- R/sparseSVM.R | 378 ++++++++--------- R/tcrossprodSelf.R | 102 ++-- R/transpose.R | 82 +-- R/univLinReg.R | 144 +++--- R/univLogReg.R | 220 ++++----- R/utils-assert.R | 382 ++++++++--------- R/utils-mult.R | 362 ++++++++-------- R/utils.R | 230 +++++----- R/zzz.R | 46 +- README.md | 95 ++-- inst/CITATION |only inst/WORDLIST |only inst/extdata/example.ped | 20 inst/include/bigstatsr/BMAcc.h | 232 +++++----- inst/include/bigstatsr/BMCodeAcc.h | 126 ++--- inst/include/bigstatsr/FBM.h | 58 +- inst/include/bigstatsr/SubIntMatCovAcc.h | 104 ++-- inst/include/bigstatsr/SubMatCovAcc.h | 232 +++++----- inst/include/bigstatsr/biglasso/linear.hpp | 404 +++++++++--------- inst/include/bigstatsr/biglasso/logistic.hpp | 564 ++++++++++++------------- inst/include/bigstatsr/biglasso/utils.hpp | 354 +++++++-------- inst/include/bigstatsr/colstats.hpp | 86 +-- inst/include/bigstatsr/prodMatVec.hpp | 142 +++--- inst/include/bigstatsr/types.h | 42 - inst/include/bigstatsr/univLinReg.hpp | 134 +++--- inst/include/bigstatsr/univLogReg.hpp | 194 ++++---- inst/include/bigstatsr/utils.h | 38 - man/AUC.Rd | 134 +++--- man/COPY_biglasso.Rd | 212 ++++----- man/COPY_sparseSVM.Rd | 174 +++---- man/Extract.Rd | 70 +-- man/FBM-class.Rd | 136 +++--- man/FBM-methods.Rd | 98 ++-- man/FBM.code256-class.Rd | 148 +++--- man/FBM.code256-methods.Rd | 60 +- man/Replace.Rd | 74 +-- man/asPlotlyText.Rd | 62 +- man/big_CMSA.Rd | 138 +++--- man/big_SVD.Rd | 204 ++++----- man/big_apply.Rd | 170 +++---- man/big_attach.Rd | 60 +- man/big_colstats.Rd | 110 ++-- man/big_copy.Rd | 130 ++--- man/big_cor.Rd | 124 ++--- man/big_counts.Rd | 122 ++--- man/big_cprodMat.Rd | 108 ++-- man/big_cprodVec.Rd | 94 ++-- man/big_crossprodSelf.Rd | 140 +++--- man/big_parallelize.Rd | 182 ++++---- man/big_prodMat.Rd | 108 ++-- man/big_prodVec.Rd | 94 ++-- man/big_randomSVD.Rd | 210 ++++----- man/big_read.Rd | 116 ++--- man/big_scale.Rd | 96 ++-- man/big_spLinReg.Rd | 298 ++++++------- man/big_spLogReg.Rd | 298 ++++++------- man/big_spSVM.Rd | 250 +++++------ man/big_tcrossprodSelf.Rd | 136 +++--- man/big_transpose.Rd | 86 +-- man/big_univLinReg.Rd | 168 +++---- man/big_univLogReg.Rd | 198 ++++---- man/bigstatsr-package.Rd | 153 +++--- man/block_size.Rd | 52 +- man/nb_cores.Rd | 58 +- man/pasteLoc.Rd | 62 +- man/plot.big_SVD.Rd | 162 +++---- man/plot.mhtest.Rd | 104 ++-- man/predict.big_CMSA.Rd | 64 +- man/predict.big_SVD.Rd | 156 +++---- man/predict.big_sp.Rd | 102 ++-- man/predict.mhtest.Rd | 56 +- man/seq-dim.Rd | 50 +- src/AUC.cpp | 74 ++- src/RcppExports.cpp | 14 tests/spelling.R |only tests/testthat.R | 8 tests/testthat/helper-init.R | 96 ++-- tests/testthat/test-AUC.R | 87 ++- tests/testthat/test-CMSA.R | 104 ++-- tests/testthat/test-FBM-accessors.R | 202 ++++----- tests/testthat/test-SVD.R | 222 +++++----- tests/testthat/test-apply.R | 96 ++-- tests/testthat/test-checkArgs.R | 260 +++++------ tests/testthat/test-colstats.R | 54 +- tests/testthat/test-copy.R | 164 +++---- tests/testthat/test-cor.R | 94 ++-- tests/testthat/test-counts.R | 130 ++--- tests/testthat/test-crossprodSelf.R | 140 +++--- tests/testthat/test-prodVec.R | 84 +-- tests/testthat/test-randomSVD.R | 214 ++++----- tests/testthat/test-readBM.R | 164 +++---- tests/testthat/test-spLinReg.R | 156 +++---- tests/testthat/test-spLogReg.R | 162 +++---- tests/testthat/test-spSVM.R | 162 +++---- tests/testthat/test-tcrossprodSelf.R | 140 +++--- tests/testthat/test-transpose.R | 38 - tests/testthat/test-univLinReg.R | 128 ++--- tests/testthat/test-univLogReg.R | 152 +++--- 122 files changed, 9658 insertions(+), 9589 deletions(-)
Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of
algorithms. It includes surrogate models, optimizers and design of experiment
approaches. The main interface is spot, which uses sequentially updated
surrogate models for the purpose of efficient optimization. The main goal is
to ease the burden of objective function evaluations, when a single evaluation
requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut],
Joerg Stork [aut],
Martin Zaefferer [aut, cre],
Margarita Rebolledo [ctb],
Christian Lasarczyk [ctb],
Joerg Ziegenhirt [ctb],
Wolfgang Konen [ctb],
Oliver Flasch [ctb],
Patrick Koch [ctb],
Martina Friese [ctb]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>
Diff between SPOT versions 2.0.1 dated 2017-03-08 and 2.0.2 dated 2017-11-30
SPOT-2.0.1/SPOT/R/buildSO.R |only SPOT-2.0.1/SPOT/man/buildSO.Rd |only SPOT-2.0.1/SPOT/man/predict.spotSecondOrderModel.Rd |only SPOT-2.0.1/SPOT/man/print.spotSecondOrderModel.Rd |only SPOT-2.0.2/SPOT/DESCRIPTION | 11 SPOT-2.0.2/SPOT/MD5 | 98 ++-- SPOT-2.0.2/SPOT/NAMESPACE | 27 - SPOT-2.0.2/SPOT/NEWS | 10 SPOT-2.0.2/SPOT/R/buildEnsembleStack.R | 6 SPOT-2.0.2/SPOT/R/buildKrigingDACE.R | 7 SPOT-2.0.2/SPOT/R/buildKrigingForrester.R | 19 SPOT-2.0.2/SPOT/R/buildLM.R | 247 +++++----- SPOT-2.0.2/SPOT/R/buildLOESS.R |only SPOT-2.0.2/SPOT/R/buildRSM.R |only SPOT-2.0.2/SPOT/R/buildRandomForest.R | 8 SPOT-2.0.2/SPOT/R/cyclone.R | 316 +++++++++---- SPOT-2.0.2/SPOT/R/designLHD.R | 48 + SPOT-2.0.2/SPOT/R/optimDE.R |only SPOT-2.0.2/SPOT/R/optimES.R |only SPOT-2.0.2/SPOT/R/optimGenoud.R |only SPOT-2.0.2/SPOT/R/optimLHD.R | 4 SPOT-2.0.2/SPOT/R/optimNLOPTR.R |only SPOT-2.0.2/SPOT/R/package.R | 121 ++-- SPOT-2.0.2/SPOT/R/plotData.R |only SPOT-2.0.2/SPOT/R/plotFunction.R |only SPOT-2.0.2/SPOT/R/plotModel.R |only SPOT-2.0.2/SPOT/R/spot.R | 186 +++++-- SPOT-2.0.2/SPOT/data/dataGasSensor.RData |binary SPOT-2.0.2/SPOT/inst/CITATION | 2 SPOT-2.0.2/SPOT/man/SPOT-package.Rd | 8 SPOT-2.0.2/SPOT/man/buildKriging.Rd | 8 SPOT-2.0.2/SPOT/man/buildLOESS.Rd |only SPOT-2.0.2/SPOT/man/buildRSM.Rd |only SPOT-2.0.2/SPOT/man/buildRandomForest.Rd | 2 SPOT-2.0.2/SPOT/man/calculationBarthMuschelknautz.Rd | 20 SPOT-2.0.2/SPOT/man/calculationMothes.Rd |only SPOT-2.0.2/SPOT/man/descentSpotRSM.Rd |only SPOT-2.0.2/SPOT/man/designLHD.Rd | 13 SPOT-2.0.2/SPOT/man/designLHDNorm.Rd | 5 SPOT-2.0.2/SPOT/man/funCyclone.Rd | 24 SPOT-2.0.2/SPOT/man/optimDE.Rd |only SPOT-2.0.2/SPOT/man/optimES.Rd |only SPOT-2.0.2/SPOT/man/optimGenoud.Rd |only SPOT-2.0.2/SPOT/man/optimLHD.Rd | 4 SPOT-2.0.2/SPOT/man/optimNLOPTR.Rd |only SPOT-2.0.2/SPOT/man/plot.spotRSM.Rd |only SPOT-2.0.2/SPOT/man/plotData.Rd |only SPOT-2.0.2/SPOT/man/plotFunction.Rd |only SPOT-2.0.2/SPOT/man/plotModel.Rd |only SPOT-2.0.2/SPOT/man/predict.kriging.Rd | 2 SPOT-2.0.2/SPOT/man/predict.spotLOESS.Rd |only SPOT-2.0.2/SPOT/man/predict.spotRSM.Rd |only SPOT-2.0.2/SPOT/man/print.spotLOESS.Rd |only SPOT-2.0.2/SPOT/man/print.spotRSM.Rd |only SPOT-2.0.2/SPOT/man/spot.Rd | 46 - SPOT-2.0.2/SPOT/man/spotAlgEs.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsDominantReco.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsGetSuccessRate.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsHps.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsIndividualInitial.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsInitParentPop.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsInterReco.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsInterRecoBeSw02.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsMarriage.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsMarriageWithReplace.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsObjMutation.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsSelection.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsStratMutation.Rd |only SPOT-2.0.2/SPOT/man/spotAlgEsTermination.Rd |only SPOT-2.0.2/SPOT/man/spotControl.Rd |only SPOT-2.0.2/SPOT/man/spotLoop.Rd |only SPOT-2.0.2/SPOT/tests/testthat/test.inequalityConstraint.R |only SPOT-2.0.2/SPOT/tests/testthat/test.main.R | 2 73 files changed, 783 insertions(+), 461 deletions(-)
Title: Goodness-of-Fit for Time-to-Event Data
Description: Extension of 'gof' package to survival models.
Author: Patrick Sfumato and Jean-Marie Boher.
Maintainer: Patrick Sfumato <sfumatop@gmail.com>
Diff between goftte versions 1.0.4 dated 2017-11-06 and 1.0.5 dated 2017-11-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/CITATION | 4 ++-- src/Makevars | 5 +++-- src/cumres.cpp | 4 ++-- 5 files changed, 15 insertions(+), 14 deletions(-)
Title: Ordinal Regression Analysis for Continuous Scales
Description: A regression framework for response variables which are continuous
self-rating scales such as the Visual Analog Scale (VAS) used in pain
assessment, or the Linear Analog Self-Assessment (LASA) scales in quality
of life studies. These scales measure subjects' perception of an intangible
quantity, and cannot be handled as ratio variables because of their inherent
non-linearity. We treat them as ordinal variables, measured on a continuous
scale. A function (the g function) connects the scale with an underlying
continuous latent variable. The link function is the inverse of the CDF of the
assumed underlying distribution of the latent variable. Currently the logit
link, which corresponds to a standard logistic distribution, is implemented.
Author: Maurizio Manuguerra [aut, cre],
Gillian Heller [aut]
Maintainer: Maurizio Manuguerra <maurizio.manuguerra@mq.edu.au>
Diff between ordinalCont versions 1.2 dated 2017-06-16 and 1.2.2 dated 2017-11-30
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS | 8 ++ R/ocm.methods.R | 162 +++++++++++++++++++++++++++++++++----------------------- R/utils.R | 4 - man/plot.ocm.Rd | 8 +- 6 files changed, 122 insertions(+), 78 deletions(-)