Title: R Interface to 'Apache Tika'
Description: Extract text or metadata from over a thousand file types, using Apache Tika <https://tika.apache.org/>. Get either plain text or structured XHTML content.
Author: Sasha Goodman [aut, cre],
The Apache Software Foundation [aut, cph],
Julia Silge [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191),
David Gohel [rev] (Reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/191)
Maintainer: Sasha Goodman <goodmansasha@gmail.com>
Diff between rtika versions 1.20 dated 2019-02-27 and 1.21 dated 2019-06-21
DESCRIPTION | 6 MD5 | 18 +- R/install_tika.R | 8 R/tika.R | 12 + R/zzz.R | 2 README.md | 11 - inst/doc/rtika_introduction.R | 346 +++++++++++++++++++-------------------- inst/doc/rtika_introduction.html | 188 +++++++++++++++++++-- man/install_tika.Rd | 8 man/tika.Rd | 5 10 files changed, 388 insertions(+), 216 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.0-4 dated 2018-12-03 and 1.0-5 dated 2019-06-21
DESCRIPTION | 11 ++-- MD5 | 24 ++++----- NAMESPACE | 9 ++- R/R.R | 2 R/methods.R | 20 +++++++ R/mlt.R | 6 ++ build/partial.rdb |binary inst/NEWS.Rd | 14 +++++ man/R.Rd | 2 tests/Cox-Ex.R | 17 ++---- tests/Cox-Ex.Rout.save | 65 +++++++++++-------------- tests/Rplots.pdf |binary tests/dpq-Ex.Rout.save | 127 +++++++++++++++++++++++++------------------------ 13 files changed, 168 insertions(+), 129 deletions(-)
Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct simultaneous confidence intervals for the ranks of means mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
Author: Diaa Al Mohamad and Erik W. van Zwet and Jelle J. Goeman
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>
Diff between ICRanks versions 3.0 dated 2019-06-13 and 3.1 dated 2019-06-21
DESCRIPTION | 10 - MD5 | 8 - R/ic.ranks.R | 22 +- man/ic.ranks.Rd | 22 +- src/PartitionByBlock.cpp | 368 ++--------------------------------------------- 5 files changed, 51 insertions(+), 379 deletions(-)
Title: An Alternative Conflict Resolution Strategy
Description: R's default conflict management system gives the most recently
loaded package precedence. This can make it hard to detect conflicts,
particularly when they arise because a package update creates ambiguity
that did not previously exist. 'conflicted' takes a different approach,
making every conflict an error and forcing you to choose which function
to use.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between conflicted versions 1.0.3 dated 2019-05-01 and 1.0.4 dated 2019-06-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/disambiguate.R | 4 ++-- R/shim.R | 2 +- README.md | 2 +- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis
Description: Provides functions for the Bayesian analysis of extreme value
models. The 'rust' package <https://cran.r-project.org/package=rust> is
used to simulate a random sample from the required posterior distribution.
The functionality of 'revdbayes' is similar to the 'evdbayes' package
<https://cran.r-project.org/package=evdbayes>, which uses Markov Chain
Monte Carlo ('MCMC') methods for posterior simulation. Also provided
are functions for making inferences about the extremal index, using
the K-gaps model of Suveges and Davison (2010) <doi:10.1214/09-AOAS292>.
Also provided are d,p,q,r functions for the Generalised Extreme Value
('GEV') and Generalised Pareto ('GP') distributions that deal
appropriately with cases where the shape parameter is very close to zero.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between revdbayes versions 1.3.3 dated 2019-03-08 and 1.3.4 dated 2019-06-21
DESCRIPTION | 8 MD5 | 54 +-- NEWS.md | 14 R/bayesplot.R | 416 ++++++++++++-------------- R/misc.R | 2 R/predictive.R | 2 R/priors.R | 38 +- R/rposterior.R | 112 ++++++- R/rposterior_rcpp.R | 27 + inst/doc/revdbayes-a-vignette.Rmd | 4 inst/doc/revdbayes-a-vignette.html | 16 - inst/doc/revdbayes-b-using-rcpp-vignette.Rmd | 8 inst/doc/revdbayes-b-using-rcpp-vignette.html | 52 +-- inst/doc/revdbayes-c-predictive-vignette.Rmd | 4 inst/doc/revdbayes-c-predictive-vignette.html | 8 inst/doc/revdbayes-d-kgaps-vignette.Rmd | 2 inst/doc/revdbayes-d-kgaps-vignette.html | 6 man/binpost.Rd | 36 ++ man/pp_check.evpost.Rd | 4 man/predict.evpost.Rd | 2 man/rpost.Rd | 28 + man/rpost_rcpp.Rd | 21 + man/set_bin_prior.Rd | 25 + man/set_prior.Rd | 4 vignettes/revdbayes-a-vignette.Rmd | 4 vignettes/revdbayes-b-using-rcpp-vignette.Rmd | 8 vignettes/revdbayes-c-predictive-vignette.Rmd | 4 vignettes/revdbayes-d-kgaps-vignette.Rmd | 2 28 files changed, 559 insertions(+), 352 deletions(-)
Title: Phonetic Spelling Algorithms
Description: Provides a collection of phonetic algorithms including
Soundex, Metaphone, NYSIIS, Caverphone, and others.
Author: James Howard [aut, cre],
Kyle Haynes [ctb],
Amanda Hood [ctb],
Os Keyes [ctb]
Maintainer: James Howard <jh@jameshoward.us>
Diff between phonics versions 1.3.0 dated 2019-03-01 and 1.3.2 dated 2019-06-21
DESCRIPTION | 25 ++++++++++++++----------- MD5 | 10 +++++----- README.md | 21 ++++++++++++--------- build/vignette.rds |binary inst/CITATION | 4 ++-- inst/doc/phonics.html | 9 ++++++--- 6 files changed, 39 insertions(+), 30 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Description: This is the R Interface to the C API of IBM ILOG CPLEX. It necessarily depends on IBM ILOG CPLEX (>= 12.1).
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
C. Jonathan Fritzemeier [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between cplexAPI versions 1.3.3 dated 2017-01-31 and 1.3.6 dated 2019-06-21
DESCRIPTION | 19 - MD5 | 447 +++++++++++++++++----------------- NAMESPACE | 51 +++ R/cplexAPI.R | 72 +++++ R/cplexConst.R | 64 ++++ build/vignette.rds |binary configure | 54 ++-- configure.ac | 2 inst/NEWS.Rd | 33 ++ inst/c2r.map | 23 + inst/doc/cplexAPI.R | 2 inst/doc/cplexAPI.Rnw | 8 inst/doc/cplexAPI.pdf |binary man/addColsCPLEX.Rd | 4 man/addFpDestCPLEX.Rd | 11 man/addIndConstrCPLEX.Rd | 4 man/addMIPstartsCPLEX.Rd | 4 man/addQConstrCPLEX.Rd | 4 man/addRowsCPLEX.Rd | 4 man/baroptCPLEX.Rd | 4 man/baseWriteCPLEX.Rd | 4 man/basicPresolveCPLEX.Rd | 4 man/boundSaCPLEX.Rd | 4 man/cLpWriteCPLEX.Rd | 4 man/checkAddColsCPLEX.Rd | 4 man/checkAddRowsCPLEX.Rd | 4 man/checkChgCoefListCPLEX.Rd | 4 man/checkCopyColTypeCPLEX.Rd | 4 man/checkCopyLpCPLEX.Rd | 4 man/checkCopyLpwNamesCPLEX.Rd | 4 man/checkCopyQPsepCPLEX.Rd | 4 man/checkCopyQuadCPLEX.Rd | 4 man/checkValsCPLEX.Rd | 4 man/chgBndsCPLEX.Rd | 4 man/chgCoefCPLEX.Rd | 4 man/chgCoefListCPLEX.Rd | 4 man/chgColNameCPLEX.Rd | 4 man/chgColTypeCPLEX.Rd | 4 man/chgColsBndsCPLEX.Rd | 4 man/chgMIPstartsCPLEX.Rd | 4 man/chgNameCPLEX.Rd | 4 man/chgObjCPLEX.Rd | 4 man/chgProbNameCPLEX.Rd | 4 man/chgProbTypeCPLEX.Rd | 4 man/chgQPcoefCPLEX.Rd | 4 man/chgRhsCPLEX.Rd | 4 man/chgRngValCPLEX.Rd | 4 man/chgRowNameCPLEX.Rd | 4 man/chgSenseCPLEX.Rd | 4 man/chgTerminateCPLEX.Rd | 4 man/cleanupCoefCPLEX.Rd | 4 man/cloneProbCPLEX.Rd | 4 man/closeEnvCPLEX.Rd | 4 man/closeFileCPLEX.Rd | 12 man/closeProbCPLEX.Rd | 4 man/completelpCPLEX.Rd | 4 man/copyBaseCPLEX.Rd | 4 man/copyColTypeCPLEX.Rd | 4 man/copyLpCPLEX.Rd | 4 man/copyLpwNamesCPLEX.Rd | 4 man/copyObjNameCPLEX.Rd | 4 man/copyOrderCPLEX.Rd | 4 man/copyPartBaseCPLEX.Rd | 4 man/copyQPsepCPLEX.Rd | 4 man/copyQuadCPLEX.Rd | 4 man/copyStartCPLEX.Rd | 4 man/cplexAPI-package.Rd | 4 man/cplexConstants.Rd | 124 +++++++++ man/cplexError-class.Rd | 4 man/cplexPtr-class.Rd | 4 man/delColsCPLEX.Rd | 4 man/delFpDestCPLEX.Rd | 10 man/delIndConstrsCPLEX.Rd | 4 man/delMIPstartsCPLEX.Rd | 4 man/delNamesCPLEX.Rd | 4 man/delProbCPLEX.Rd | 4 man/delQConstrsCPLEX.Rd | 4 man/delRowsCPLEX.Rd | 4 man/delSetColsCPLEX.Rd | 4 man/delSetRowsCPLEX.Rd | 4 man/delTerminateCPLEX.Rd | 4 man/disconnectChannelCPLEX.Rd | 4 man/dualWriteCPLEX.Rd | 4 man/dualoptCPLEX.Rd | 4 man/feasOptCPLEX.Rd | 4 man/fileputCPLEX.Rd | 10 man/flushChannelCPLEX.Rd | 4 man/flushStdChannelsCPLEX.Rd | 4 man/freePresolveCPLEX.Rd | 4 man/getBaseCPLEX.Rd | 4 man/getBestObjValCPLEX.Rd | 4 man/getChannelsCPLEX.Rd | 4 man/getChgParmCPLEX.Rd | 4 man/getCoefCPLEX.Rd | 4 man/getColIndexCPLEX.Rd | 4 man/getColInfeasCPLEX.Rd | 4 man/getColNameCPLEX.Rd | 4 man/getColTypeCPLEX.Rd | 4 man/getColsCPLEX.Rd | 4 man/getConflictCPLEX.Rd | 4 man/getConflictExtCPLEX.Rd | 4 man/getCutoffCPLEX.Rd | 4 man/getDblParmCPLEX.Rd | 4 man/getDblQualCPLEX.Rd | 4 man/getDbsCntCPLEX.Rd | 4 man/getDjCPLEX.Rd | 4 man/getErrorStrCPLEX.Rd | 4 man/getGradCPLEX.Rd | 4 man/getIndConstrCPLEX.Rd | 4 man/getInfoDblParmCPLEX.Rd | 4 man/getInfoIntParmCPLEX.Rd | 4 man/getInfoLongParmCPLEX.Rd | 4 man/getInfoStrParmCPLEX.Rd | 4 man/getIntParmCPLEX.Rd | 4 man/getIntQualCPLEX.Rd | 4 man/getItCntCPLEX.Rd | 4 man/getLogFileCPLEX.Rd | 8 man/getLogFileNameCPLEX.Rd |only man/getLongParmCPLEX.Rd | 4 man/getLowBndsIdsCPLEX.Rd | 4 man/getLowerBndsCPLEX.Rd | 4 man/getMIPrelGapCPLEX.Rd | 4 man/getMIPstartIndexCPLEX.Rd | 4 man/getMIPstartNameCPLEX.Rd | 4 man/getMIPstartsCPLEX.Rd | 4 man/getMethodCPLEX.Rd | 4 man/getNumColsCPLEX.Rd | 4 man/getNumMIPstartsCPLEX.Rd | 4 man/getNumNnzCPLEX.Rd | 4 man/getNumQConstrsCPLEX.Rd | 4 man/getNumQPnzCPLEX.Rd | 4 man/getNumQuadCPLEX.Rd | 4 man/getNumRowsCPLEX.Rd | 4 man/getObjCPLEX.Rd | 4 man/getObjDirCPLEX.Rd | 4 man/getObjNameCPLEX.Rd | 4 man/getObjOffsetCPLEX.Rd | 4 man/getObjValCPLEX.Rd | 4 man/getOrderCPLEX.Rd | 4 man/getParmHierNameCPLEX.Rd |only man/getParmNameCPLEX.Rd | 4 man/getParmNumCPLEX.Rd | 4 man/getParmTypeCPLEX.Rd | 4 man/getParmValCPLEX.Rd | 4 man/getPhase1CntCPLEX.Rd | 4 man/getPiCPLEX.Rd | 4 man/getPreStatCPLEX.Rd | 4 man/getProbNameCPLEX.Rd | 4 man/getProbTypeCPLEX.Rd | 4 man/getProbVarCPLEX.Rd | 4 man/getQConstrCPLEX.Rd | 4 man/getQPcoefCPLEX.Rd | 4 man/getQuadCPLEX.Rd | 4 man/getRedLpCPLEX.Rd | 4 man/getRhsCPLEX.Rd | 4 man/getRngValCPLEX.Rd | 4 man/getRowIndexCPLEX.Rd | 4 man/getRowInfeasCPLEX.Rd | 4 man/getRowNameCPLEX.Rd | 4 man/getRowsCPLEX.Rd | 4 man/getSenseCPLEX.Rd | 4 man/getSiftItCntCPLEX.Rd | 4 man/getSiftPase1CntCPLEX.Rd | 4 man/getSlackCPLEX.Rd | 4 man/getStatCPLEX.Rd | 4 man/getStatStrCPLEX.Rd | 4 man/getStrParmCPLEX.Rd | 4 man/getSubMethodCPLEX.Rd | 4 man/getSubStatCPLEX.Rd | 4 man/getTimeCPLEX.Rd | 4 man/getUppBndsIdsCPLEX.Rd | 4 man/getUpperBndsCPLEX.Rd | 4 man/getVersionCPLEX.Rd | 4 man/hybbaroptCPLEX.Rd | 4 man/hybnetoptCPLEX.Rd | 4 man/initProbCPLEX.Rd | 4 man/lpoptCPLEX.Rd | 4 man/mipoptCPLEX.Rd | 4 man/newColsCPLEX.Rd | 4 man/newRowsCPLEX.Rd | 4 man/objSaCPLEX.Rd | 4 man/openEnvCPLEX.Rd | 4 man/openFileCPLEX.Rd | 12 man/openProbCPLEX.Rd | 4 man/ordWriteCPLEX.Rd | 4 man/preslvWriteCPLEX.Rd | 4 man/presolveCPLEX.Rd | 4 man/primoptCPLEX.Rd | 4 man/printTerminateCPLEX.Rd | 4 man/qpoptCPLEX.Rd | 4 man/readCopyBaseCPLEX.Rd | 4 man/readCopyMIPstartsCPLEX.Rd | 4 man/readCopyOrderCPLEX.Rd | 4 man/readCopyParmCPLEX.Rd | 4 man/readCopyProbCPLEX.Rd | 4 man/readCopySolCPLEX.Rd | 4 man/refineConflictCPLEX.Rd | 4 man/refineConflictExtCPLEX.Rd | 4 man/refineMIPstartConflictCPLEX.Rd | 4 man/refineMIPstartConflictExtCPLEX.Rd | 4 man/return_codeCPLEX.Rd | 4 man/rhsSaCPLEX.Rd | 4 man/setDblParmCPLEX.Rd | 4 man/setDefaultParmCPLEX.Rd | 4 man/setIntParmCPLEX.Rd | 4 man/setLogFileCPLEX.Rd | 10 man/setLogFileNameCPLEX.Rd |only man/setLongParmCPLEX.Rd | 4 man/setObjDirCPLEX.Rd | 4 man/setStrParmCPLEX.Rd | 4 man/setTerminateCPLEX.Rd | 4 man/siftoptCPLEX.Rd | 4 man/solWriteCPLEX.Rd | 4 man/solnInfoCPLEX.Rd | 4 man/solutionCPLEX.Rd | 4 man/status_codeCPLEX.Rd | 4 man/tightenBndsCPLEX.Rd | 4 man/tuneParmCPLEX.Rd | 4 man/unscaleProbCPLEX.Rd | 4 man/writeMIPstartsCPLEX.Rd | 4 man/writeParmCPLEX.Rd | 4 man/writeProbCPLEX.Rd | 4 src/cplexAPI.c | 179 +++++++++++++ src/cplexAPI.h | 13 src/init.c | 17 + vignettes/cplexAPI.Rnw | 8 226 files changed, 1287 insertions(+), 694 deletions(-)
Title: Exact Test and Visualization of Multi-Set Intersections
Description: Identification of sets of objects with shared features is a common operation in all disciplines. Analysis of intersections among multiple sets is fundamental for in-depth understanding of their complex relationships. This package implements a theoretical framework for efficient computation of statistical distributions of multi-set intersections based upon combinatorial theory, and provides multiple scalable techniques for visualizing the intersection statistics. The statistical algorithm behind this package was published in Wang et al. (2015) <doi:10.1038/srep16923>.
Author: Minghui Wang, Yongzhong Zhao and Bin Zhang
Maintainer: Minghui Wang <minghui.wang@mssm.edu>
Diff between SuperExactTest versions 1.0.6 dated 2019-02-26 and 1.0.7 dated 2019-06-21
DESCRIPTION | 8 MD5 | 22 +- R/psets.R | 4 R/supertest.R | 20 + R/vis.R | 165 ++++++++++++---- build/vignette.rds |binary inst/doc/set_html.html | 505 +++++++++++++++++++++++++++++++++++-------------- man/msets.Rd | 3 man/plot.Rd | 8 src/cmp.c | 5 src/mvhyper.h | 3 src/pmvhyper.c | 31 ++- 12 files changed, 554 insertions(+), 220 deletions(-)
More information about SuperExactTest at CRAN
Permanent link
Title: Generalization of the Convex Hull of a Sample of Points in the
Plane
Description: Computation of the alpha-shape and alpha-convex
hull of a given sample of points in the plane. The concepts of
alpha-shape and alpha-convex hull generalize the definition of
the convex hull of a finite set of points. The programming is
based on the duality between the Voronoi diagram and Delaunay
triangulation. The package also includes a function that
returns the Delaunay mesh of a given sample of points and its
dual Voronoi diagram in one single object.
Author: Beatriz Pateiro-Lopez [aut, cre], Alberto Rodriguez-Casal, [aut].
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>
Diff between alphahull versions 2.1 dated 2016-02-15 and 2.2 dated 2019-06-21
DESCRIPTION | 8 ++++---- MD5 | 11 ++++++----- NAMESPACE | 2 +- R/areaahull.R | 2 +- build/vignette.rds |binary inst/doc/alphahull.pdf |binary src/alphahull_init.c |only 7 files changed, 12 insertions(+), 11 deletions(-)
Title: Subgroup Discovery and Bump Hunting
Description: Developed to assist in discovering interesting subgroups in high-dimensional data. The PRIM implementation is based on the 1998 paper "Bump hunting in high-dimensional data" by Jerome H. Friedman and Nicholas I. Fisher. <doi:10.1023/A:1008894516817> PRIM involves finding a set of "rules" which combined imply unusually large (or small) values of some other target variable. Specifically one tries to find a set of sub regions in which the target variable is substantially larger than overall mean. The objective of bump hunting in general is to find regions in the input (attribute/feature) space with relatively high (low) values for the target variable. The regions are described by simple rules of the type if: condition-1 and ... and condition-n then: estimated target value. Given the data (or a subset of the data), the goal is to produce a box B within which the target mean is as large as possible. There are many problems where finding such regions is of considerable practical interest. Often these are problems where a decision maker can in a sense choose or select the values of the input variables so as to optimize the value of the target variable. In bump hunting it is customary to follow a so-called covering strategy. This means that the same box construction (rule induction) algorithm is applied sequentially to subsets of the data.
Author: Jurian Baas [aut, cre, cph],
Ad Feelders [ctb]
Maintainer: Jurian Baas <j.baas@uu.nl>
Diff between subgroup.discovery versions 0.2.0 dated 2017-08-02 and 0.2.1 dated 2019-06-21
DESCRIPTION | 16 ++++---- MD5 | 20 +++++----- R/data.R | 2 - R/prim.R | 85 ++++++++++++++++++++++++-------------------- README.md | 2 - man/ames.Rd | 3 - man/credit.Rd | 3 - man/prim.cover.Rd | 10 ++--- man/prim.diversify.Rd | 2 - man/prim.peel.Rd | 3 + man/prim.rule.operations.Rd | 3 + 11 files changed, 76 insertions(+), 73 deletions(-)
More information about subgroup.discovery at CRAN
Permanent link
Title: Collection of Information-Based Feature Selection Filters
Description: A collection of feature selection filters performing greedy optimisation of mutual information-based usefulness criteria, inspired by the overview by Brown, Pocock, Zhao and Lujan (2012) <http://www.jmlr.org/papers/v13/brown12a.html>.
Implements, among other, minimum redundancy maximal relevancy ('mRMR') method by Peng, Long and Ding (2005) <doi:10.1109/TPAMI.2005.159>; joint mutual information ('JMI') method by Yang and Moody (1999) <http://papers.nips.cc/paper/1779-data-visualization-and-feature-selection-new-algorithms-for-nongaussian-data>; double input symmetrical relevance ('DISR') method by Meyer and Bontempi (2006) <doi:10.1007/11732242_9> as well as joint mutual information maximisation ('JMIM') method by Bennasar, Hicks and Setchi (2015) <doi:10.1016/j.eswa.2015.07.007>.
Author: Miron B. Kursa [aut, cre] (<https://orcid.org/0000-0001-7672-648X>)
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>
Diff between praznik versions 5.0.0 dated 2018-05-08 and 6.0.0 dated 2019-06-21
praznik-5.0.0/praznik/man/setOmpThreads.Rd |only praznik-6.0.0/praznik/DESCRIPTION | 12 +-- praznik-6.0.0/praznik/MD5 | 57 +++++++------- praznik-6.0.0/praznik/NAMESPACE | 2 praznik-6.0.0/praznik/R/algorithms.R | 10 ++ praznik-6.0.0/praznik/R/praznik.R | 17 ---- praznik-6.0.0/praznik/R/pure.R | 46 ++++++++---- praznik-6.0.0/praznik/R/scorers.R | 18 ++++ praznik-6.0.0/praznik/inst/NEWS | 8 ++ praznik-6.0.0/praznik/man/CMIM.Rd | 4 - praznik-6.0.0/praznik/man/DISR.Rd | 2 praznik-6.0.0/praznik/man/JIM.Rd | 2 praznik-6.0.0/praznik/man/JMI.Rd | 2 praznik-6.0.0/praznik/man/JMIM.Rd | 2 praznik-6.0.0/praznik/man/MIM.Rd | 2 praznik-6.0.0/praznik/man/MRMR.Rd | 2 praznik-6.0.0/praznik/man/NJMIM.Rd | 2 praznik-6.0.0/praznik/man/cmiScores.Rd | 2 praznik-6.0.0/praznik/man/hScores.Rd |only praznik-6.0.0/praznik/man/impScores.Rd | 2 praznik-6.0.0/praznik/man/jmiScores.Rd | 2 praznik-6.0.0/praznik/man/miScores.Rd | 2 praznik-6.0.0/praznik/man/njmiScores.Rd | 2 praznik-6.0.0/praznik/man/praznik-package.Rd | 6 - praznik-6.0.0/praznik/src/cmim.h | 3 praznik-6.0.0/praznik/src/h.h |only praznik-6.0.0/praznik/src/ht.h | 33 ++++++++ praznik-6.0.0/praznik/src/praznik.c | 2 praznik-6.0.0/praznik/src/shared.h | 12 +-- praznik-6.0.0/praznik/tests/testthat/test-input.R | 4 + praznik-6.0.0/praznik/tests/testthat/test-native-pure.R | 61 ++++++++++++---- 31 files changed, 217 insertions(+), 102 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data
econometrics, as described in Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7,
Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and
Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
Author: Yves Croissant [aut, cre],
Giovanni Millo [aut],
Kevin Tappe [aut],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between plm versions 2.0-1 dated 2019-05-23 and 2.0-2 dated 2019-06-21
DESCRIPTION | 13 MD5 | 109 NAMESPACE | 5 NEWS.md | 6 R/tool_vcovG.R | 31 build/partial.rdb |binary build/vignette.rds |binary data/Cigar.rda |binary data/Crime.rda |binary data/EmplUK.rda |binary data/Gasoline.rda |binary data/Grunfeld.rda |binary data/Hedonic.rda |binary data/LaborSupply.rda |binary data/Males.rda |binary data/Parity.rda |binary data/Produc.rda |binary data/RiceFarms.rda |binary data/Snmesp.rda |binary data/SumHes.rda |binary data/Wages.rda |binary inst/doc/plm.Rmd |only inst/doc/plm.html |only inst/doc/plmFunction.Rmd | 9 inst/doc/plmFunction.html | 2075 ----- inst/doc/plmModelComponents.Rmd | 9 inst/doc/plmModelComponents.html | 1886 ----- inst/doc/plmPackage.Rmd | 9 inst/doc/plmPackage.html | 3692 +--------- inst/removed/NEWS |only man/vcovDC.Rd | 4 man/vcovG.Rd | 5 man/vcovHC.plm.Rd | 5 man/vcovNW.Rd | 5 man/vcovSCC.Rd | 5 tests/Examples/plm-Ex.Rout.save | 201 tests/test_R2_adj_R2.Rout.save |only tests/test_as.data.frame_as.matrix.Rout.save |only tests/test_as.list.pdata.frame.Rout.save |only tests/test_detect_lin_dep_alias.Rout.save |only tests/test_fitted.plm.Rout.save |only tests/test_fixef.Rout.save |only tests/test_fixef_comp_lm_plm.Rout.save |only tests/test_is.pconsecutive.Rout.save |only tests/test_make.pconsecutive_pbalanced.Rout.save |only tests/test_misc.Rout.save |only tests/test_model.frame.Rout.save |only tests/test_model.matrix_effects.Rout.save |only tests/test_model.matrix_pmodel.response.Rout.save |only tests/test_pbgtest.Rout.save |only tests/test_pcdtest.Rout.save |only tests/test_pdata.frame_const_allNA_nonfinite.Rout.save |only tests/test_pdata.frame_extract_class_est_mod.Rout.save |only tests/test_pdata.frame_id_index_more.Rout.save |only tests/test_pdata.frame_print_duplicated_rownames.Rout.save |only tests/test_pdata.frame_unused_levels.Rout.save |only tests/test_pdiff_fd.Rout.save |only tests/test_pdwtest.Rout.save |only tests/test_pggls.Rout.save |only tests/test_plm.data.Rout.save |only tests/test_plm_na.action.Rout.save |only tests/test_preserve_rownames.Rout.save |only tests/test_pseries_subsetting.Rout.save |only tests/test_punbalancedness.Rout.save |only tests/test_pvar.Rout.save |only tests/test_pwfdtest_pwartest.Rout.save |only tests/test_pwtest.Rout.save |only tests/test_residuals_overall_fitted_exp.Rout.save |only tests/test_summary.plm_vcov.Rout.save |only tests/test_summary.pseries_character_logical_factor.Rout.save |only tests/test_vcovG_lin_dep.Rout.save |only vignettes/plm.Rmd |only vignettes/plmFunction.Rmd | 9 vignettes/plmModelComponents.Rmd | 9 vignettes/plmPackage.Rmd | 9 75 files changed, 1693 insertions(+), 6403 deletions(-)
Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on
the diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent, under various
models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
<DOI:10.1098/rspb.2011.1439>,
Etienne & Haegeman 2012, Am. Nat. 180: E75-E89,
<DOI:10.1086/667574> and
Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099,
<DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent
process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 4.0 dated 2019-04-22 and 4.1 dated 2019-06-21
DESCRIPTION | 10 +- MD5 | 24 +++--- NAMESPACE | 1 R/bd_loglik.R | 3 R/dd_KI_loglik.R | 104 +++++++++++++++++++--------- R/dd_MS_loglik.R | 84 +++++++++++++--------- R/dd_utils.R | 52 +++++++++++++- man/dd_KI_loglik.Rd | 68 +++++++++++------- man/dd_MS_loglik.Rd | 67 +++++++++--------- man/rng_respecting_sample.Rd |only src/dd_loglik_rhs_FORTRAN.f95 | 2 tests/testthat.R |only tests/testthat/test-ddd_sample2.R |only tests/testthat/test-rng_respecting_sample.R |only tests/testthat/test_DDD.R | 90 ++++++++++++++++++++---- 15 files changed, 352 insertions(+), 153 deletions(-)
Title: Non-Linear Model Selection
Description: Package to select best model among several linear and nonlinear models. The main function uses the gnls() function from the 'nlme' package to fit the data to nine regression models, named: "linear", "quadratic", "cubic", "logistic", "exponential", "power", "monod", "haldane", "logit".
Author: Carme Font <carme.font.moragon@gmail.com>
Maintainer: Carme Font <carme.font.moragon@gmail.com>
Diff between nlMS versions 1.0 dated 2019-06-19 and 1.1 dated 2019-06-21
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/MS.R | 10 +++++----- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Simultaneous Inference for Multiple Linear Contrasts in GEE
Models
Description: Provides global hypothesis tests, multiple testing procedures and simultaneous confidence intervals for multiple linear contrasts of regression
coefficients in a single generalized estimating equation (GEE) model or across multiple GEE models. GEE models are fit by a modified version of the 'geeM' package.
Author: Robin Ristl [aut, cre],
Lee McDaniel [ctb] (Author of 'geeM' package),
Nick Henderson [ctb] (Author of 'geeM' package),
Melanie Prague [ctb] (Contributor to 'geeM' package)
Maintainer: Robin Ristl <robin.ristl@meduniwien.ac.at>
Diff between mmmgee versions 1.13 dated 2018-10-29 and 1.20 dated 2019-06-21
mmmgee-1.13/mmmgee/R/Hypothesentest_funktion_verbessert_2-1Okt2018.R |only mmmgee-1.13/mmmgee/R/Paket_alle_Funktionen_Basis_v01_2-0Okt2018.R |only mmmgee-1.20/mmmgee/DESCRIPTION | 8 - mmmgee-1.20/mmmgee/MD5 | 19 ++- mmmgee-1.20/mmmgee/NAMESPACE | 7 + mmmgee-1.20/mmmgee/R/Hypothesentest_funktion_verbessert_score_ohne_update_3-1_21Juni2019.R |only mmmgee-1.20/mmmgee/R/Paket_alle_Funktionen_3-26_21Juni2019.R |only mmmgee-1.20/mmmgee/R/getAlphaInvGeneral_1-6.R |only mmmgee-1.20/mmmgee/data/datasim.RData |only mmmgee-1.20/mmmgee/man/datasim.Rd |only mmmgee-1.20/mmmgee/man/geem2.Rd | 50 ++++++---- mmmgee-1.20/mmmgee/man/keratosis.Rd | 2 mmmgee-1.20/mmmgee/man/mmmgee.Rd | 2 mmmgee-1.20/mmmgee/man/mmmgee.test.Rd | 38 +++++-- 14 files changed, 79 insertions(+), 47 deletions(-)
Title: Spatial Generalised Linear Mixed Models for Areal Unit Data
Description: Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation. The response variable can be binomial, Gaussian, multinomial, Poisson or zero-inflated Poisson (ZIP), and spatial autocorrelation is modelled by a set of random effects that are assigned a conditional autoregressive (CAR) prior distribution. A number of different models are available for univariate spatial data, including models with no random effects as well as random effects modelled by different types of CAR prior, including the BYM model (Besag et al. (1991) <doi:10.1007/BF00116466>), the Leroux model (Leroux et al. (2000) <doi:10.1007/978-1-4612-1284-3_4>) and the localised model (Lee et al. (2015) <doi:10.1002/env.2348>). Additionally, a multivariate CAR (MCAR) model for multivariate spatial data is available, as is a two-level hierarchical model for modelling data relating to individuals within areas. Full details are given in the vignette accompanying this package. The initial creation of this package was supported by the Economic and Social Research Council (ESRC) grant RES-000-22-4256, and on-going development has been supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1, ESRC grant ES/K006460/1, Innovate UK / Natural Environment Research Council (NERC) grant NE/N007352/1 and the TB Alliance.
Author: Duncan Lee
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayes versions 5.1.1 dated 2018-12-06 and 5.1.2 dated 2019-06-21
DESCRIPTION | 8 MD5 | 46 - NAMESPACE | 6 R/binomial.MVlerouxCAR.R | 1013 ++++++++++++------------- R/binomial.dissimilarityCAR.R | 1062 +++++++++++++-------------- R/binomial.lerouxCAR.R | 858 ++++++++++----------- R/binomial.localisedCAR.R | 12 R/binomial.multilevelCAR.R | 1057 +++++++++++++------------- R/gaussian.MVlerouxCAR.R | 961 ++++++++++++------------ R/gaussian.dissimilarityCAR.R | 987 ++++++++++++------------- R/gaussian.lerouxCAR.R | 789 ++++++++++---------- R/gaussian.multilevelCAR.R | 1003 ++++++++++++------------- R/multinomial.MVlerouxCAR.R | 1019 +++++++++++++------------- R/poisson.MVlerouxCAR.R | 955 ++++++++++++------------ R/poisson.dissimilarityCAR.R | 1028 +++++++++++++------------- R/poisson.lerouxCAR.R | 821 ++++++++++---------- R/poisson.localisedCAR.R | 16 R/poisson.multilevelCAR.R | 1023 +++++++++++++------------- R/zip.lerouxCAR.R | 1125 ++++++++++++++-------------- build/vignette.rds |binary inst/doc/CARBayes.Rnw | 1646 +++++++++++++++++++++--------------------- inst/doc/CARBayes.pdf |binary man/CARBayes-package.Rd | 6 vignettes/CARBayes.Rnw | 1646 +++++++++++++++++++++--------------------- 24 files changed, 8554 insertions(+), 8533 deletions(-)
Title: Extract Genotypes from a PLINK .bed File
Description: A matrix-like data structure that allows for efficient,
convenient, and scalable subsetting of binary genotype/phenotype files
generated by PLINK (<https://www.cog-genomics.org/plink2>), the whole
genome association analysis toolset, without loading the entire file into
memory.
Author: Alexander Grueneberg [aut, cre],
Gustavo de los Campos [ctb]
Maintainer: Alexander Grueneberg <alexander.grueneberg@googlemail.com>
Diff between BEDMatrix versions 1.5.0 dated 2019-04-25 and 1.6.1 dated 2019-06-21
BEDMatrix-1.5.0/BEDMatrix/R/package.R |only BEDMatrix-1.5.0/BEDMatrix/man/examples |only BEDMatrix-1.5.0/BEDMatrix/man/initialize-BEDMatrix-method.Rd |only BEDMatrix-1.5.0/BEDMatrix/man/show-BEDMatrix-method.Rd |only BEDMatrix-1.6.1/BEDMatrix/DESCRIPTION | 15 BEDMatrix-1.6.1/BEDMatrix/MD5 | 34 +- BEDMatrix-1.6.1/BEDMatrix/NAMESPACE | 6 BEDMatrix-1.6.1/BEDMatrix/NEWS.md | 61 ++- BEDMatrix-1.6.1/BEDMatrix/R/BEDMatrix.R | 168 +---------- BEDMatrix-1.6.1/BEDMatrix/README.md | 18 - BEDMatrix-1.6.1/BEDMatrix/inst/CITATION |only BEDMatrix-1.6.1/BEDMatrix/inst/THANKS |only BEDMatrix-1.6.1/BEDMatrix/man/BEDMatrix-class.Rd | 127 ++++---- BEDMatrix-1.6.1/BEDMatrix/man/BEDMatrix-package.Rd | 49 +-- BEDMatrix-1.6.1/BEDMatrix/man/BEDMatrix.Rd |only BEDMatrix-1.6.1/BEDMatrix/src/Makevars | 3 BEDMatrix-1.6.1/BEDMatrix/src/Makevars.win | 3 BEDMatrix-1.6.1/BEDMatrix/tests/testthat/helper.R | 17 - BEDMatrix-1.6.1/BEDMatrix/tests/testthat/test-BEDMatrix.R | 10 BEDMatrix-1.6.1/BEDMatrix/tests/testthat/test-extract.R | 15 BEDMatrix-1.6.1/BEDMatrix/tests/testthat/test-length.R | 2 21 files changed, 212 insertions(+), 316 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.0-4 dated 2019-02-27 and 1.0-5 dated 2019-06-21
basefun-1.0-4/basefun/R/bernstein.R |only basefun-1.0-5/basefun/DESCRIPTION | 9 ++-- basefun-1.0-5/basefun/MD5 | 9 ++-- basefun-1.0-5/basefun/R/Bernstein.R |only basefun-1.0-5/basefun/inst/NEWS.Rd | 7 +++ basefun-1.0-5/basefun/tests/Bernstein-Ex.R | 47 ++++++++++++++++++++- basefun-1.0-5/basefun/tests/Bernstein-Ex.Rout.save |only 7 files changed, 62 insertions(+), 10 deletions(-)
Title: Modelling Tools for Reproduction and Survival Data in
Ecotoxicology
Description: Tools for ecotoxicologists and regulators dedicated to the
mathematical and statistical modelling of toxicity test data. They use advanced and
innovative methods for a valuable quantitative environmental risk assessment. See also
Delignette-Muller et al. (2017) <doi:10.1021/acs.est.6b05326>. and Baudrot et al. (2018) <doi:10.1021/acs.est.7b05464>.
Author: Virgile Baudrot [aut],
Sandrine Charles [aut],
Marie Laure Delignette-Muller [aut],
Wandrille Duchemin [ctb],
Benoit Goussen [ctb],
Guillaume Kon-Kam-King [ctb],
Christelle Lopes [ctb],
Philippe Ruiz [aut],
Alexander Singer [ctb],
Philippe Veber [aut]
Maintainer: Philippe Veber <philippe.veber@univ-lyon1.fr>
Diff between morse versions 3.2.2 dated 2019-02-21 and 3.2.4 dated 2019-06-21
DESCRIPTION | 10 ++++++---- MD5 | 22 +++++++++++----------- NEWS | 12 ++++++++++++ R/morse-internal.R | 2 +- R/morse.R | 3 +-- R/plot_prior_post.R | 19 ++++++++++++++----- R/predict_Nsurv_check.R | 8 ++++---- inst/doc/modelling.pdf |binary inst/doc/tutorial.Rmd | 2 +- inst/doc/tutorial.html | 41 +++++++++++++++++++++++++++++++++-------- man/morse-package.Rd | 1 + vignettes/tutorial.Rmd | 2 +- 12 files changed, 85 insertions(+), 37 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between BIGL versions 1.3.0 dated 2019-02-28 and 1.4.1 dated 2019-06-21
DESCRIPTION | 8 - MD5 | 66 ++++----- R/Blissindependence.R | 2 R/ResponseSurface-methods.R | 15 +- R/bootstrap.R | 14 + R/fitSurface.R | 2 R/harbronLoewe.R |only R/plotReponseSurface.R | 6 R/predictOffAxis.R | 17 +- R/statistics.R | 4 build/vignette.rds |binary inst/NEWS | 4 inst/doc/analysis.R | 6 inst/doc/analysis.Rmd | 20 ++ inst/doc/analysis.html | 292 ++++++++++++++++++++++------------------ inst/doc/methodology.Rmd | 20 ++ inst/doc/methodology.html | 40 +++++ man/CPBootstrap.Rd | 5 man/bootstrapData.Rd | 5 man/boxcox.transformation.Rd | 2 man/fitSurface.Rd | 5 man/generateData.Rd | 5 man/harbronLoewe.Rd |only man/maxR.Rd | 5 man/meanR.Rd | 5 man/plotResponseSurface.Rd | 18 +- man/predictOffAxis.Rd | 5 man/simulateNull.Rd | 5 tests/testthat/test_calls.R | 45 ++++++ tests/testthat/test_marginals.R | 23 +-- tests/testthat/test_maxR.R | 20 +- tests/testthat/test_meanR.R | 15 +- tests/testthat/test_wrapper.R | 17 +- vignettes/analysis.Rmd | 20 ++ vignettes/methodology.Rmd | 20 ++ 35 files changed, 478 insertions(+), 258 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>),
Nicolas Müller [aut],
Reto Bürgin [aut],
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
(<https://orcid.org/0000-0001-7776-0903>)
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.0-11.1 dated 2019-03-22 and 2.0-12 dated 2019-06-21
DESCRIPTION | 8 ++--- MD5 | 48 +++++++++++++++--------------- NEWS | 41 ++++++++++++++++++++++---- R/alphabet-set.R | 17 ++++++---- R/seqST.R | 8 ++--- R/seqdef.R | 7 +++- R/seqdist-CHI2.R | 55 ++++++++++++++++++++++++++++------- R/seqdist-OMstran.R | 2 - R/seqdist.R | 7 ++-- R/seqici.R | 5 +-- R/seqient.R | 6 +-- build/vignette.rds |binary data/ex1.rda |binary data/ex2.rda |binary data/famform.rda |binary inst/NEWS.Rd | 34 +++++++++++++++++++++ inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 - man/actcal.Rd | 2 - man/biofam.Rd | 2 - man/seqST.Rd | 34 ++++++++++++--------- man/seqdist.Rd | 43 +++++++++++++++++---------- man/seqformat.Rd | 28 ++++++++--------- man/seqici.Rd | 29 ++++++++++-------- man/seqient.Rd | 30 ++++++++++--------- 25 files changed, 268 insertions(+), 140 deletions(-)
Title: A Tool for Automating Download and Preprocessing of MODIS Land
Products Data
Description: Allows automating the creation of time series of rasters derived
from MODIS Satellite Land Products data. It performs several typical
preprocessing steps such as download, mosaicking, reprojection and resize
of data acquired on a specified time period. All processing parameters
can be set using a user-friendly GUI. Users can select which layers of
the original MODIS HDF files they want to process, which additional
Quality Indicators should be extracted from aggregated MODIS Quality
Assurance layers and, in the case of Surface Reflectance products
, which Spectral Indexes should be computed from the original reflectance
bands. For each output layer, outputs are saved as single-band raster
files corresponding to each available acquisition date. Virtual files
allowing access to the entire time series as a single file are also created.
Command-line execution exploiting a previously saved processing options
file is also possible, allowing to automatically update time series
related to a MODIS product whenever a new image is available.
Author: Lorenzo Busetto [aut, cre] (<https://orcid.org/0000-0001-9634-6038>),
Luigi Ranghetti [aut] (<https://orcid.org/0000-0001-6207-5188>),
Leah Wasser [rev] (Leah Wasser reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/184),
Jeff Hanson [rev] (Jeff Hanson reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/184)
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Diff between MODIStsp versions 1.3.8 dated 2019-03-08 and 1.3.9 dated 2019-06-21
DESCRIPTION | 8 MD5 | 97 +-- NEWS.md | 12 R/MODIStsp.R | 31 - R/MODIStsp_GUI.R | 7 R/MODIStsp_download.R | 5 R/MODIStsp_extract.R | 6 R/MODIStsp_install_launcher.R | 32 - R/MODIStsp_process.R | 2 R/MODIStsp_process_bands.R | 9 R/MODIStsp_reset_options.R | 4 R/check_proj4string.R | 6 R/gh_changeproj.R | 4 R/reproj_bbox.R | 12 README.md | 29 - build/vignette.rds |binary inst/ExtData/Launcher/Bash/MODIStsp.desktop |only inst/ExtData/MODIStsp_ProdOpts.xml | 658 ++++++++++---------------- inst/ExtData/Previous/MODIStsp_ProdOpts.RData |binary inst/WORDLIST | 2 inst/doc/MODIStsp.Rmd | 4 inst/doc/MODIStsp.pdf |binary inst/testdata/test01.json | 2 inst/testdata/test01a.json | 2 inst/testdata/test02.json | 2 inst/testdata/test03.json | 2 inst/testdata/test03a.json | 2 inst/testdata/test04.json | 2 inst/testdata/test04a.json | 2 inst/testdata/test04b.json | 2 inst/testdata/test04c.json | 2 inst/testdata/test05.json | 2 inst/testdata/test05a.json | 2 inst/testdata/test06.json | 2 inst/testdata/test07.json | 2 inst/testdata/test07b.json | 2 inst/testdata/test_MOD10A2.json | 2 inst/testdata/test_MOD13A2.json | 2 inst/testdata/test_addindex.json | 2 inst/testdata/test_extract.json | 2 inst/testdata/test_mask.json | 2 man/MODIStsp.Rd | 31 - man/MODIStsp_extract.Rd | 4 man/MODIStsp_reset_options.Rd | 5 man/install_MODIStsp_launcher.Rd | 2 tests/spelling.R | 4 tests/spelling.Rout.save | 4 tests/testthat/test_bbox_from_file.R | 9 tests/testthat/test_check_proj4string.R | 8 vignettes/MODIStsp.Rmd | 4 50 files changed, 487 insertions(+), 550 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Martin Morgan [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.2.2 dated 2019-06-06 and 1.2.3 dated 2019-06-21
DESCRIPTION | 8 - MD5 | 37 +++--- NAMESPACE | 20 ++- NEWS.md | 11 + R/XenaHub-class.R | 41 +------ R/api_higher.R | 9 - R/api_inner.R | 44 +++---- R/api_xq.R | 2 R/fetch.R | 178 ++++++++++++++++---------------- R/shiny.R | 15 -- R/simplify.R | 21 +-- R/utils-pipe.R | 8 - R/workflow.R | 41 ++++--- README.md | 193 +++++++++++++++++++++++++++++------ inst/develop.R | 55 +++++---- inst/doc/USCSXenaTools.html | 4 man/fetch.Rd | 11 - man/figures/logo.png |binary tests/testthat/test-basic-workflow.R | 62 ++++++++--- tests/testthat/test-full-tests.R |only 20 files changed, 463 insertions(+), 297 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation (ODE) models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
VODE and LSODA are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Justin Wilkins [ctb] (<https://orcid.org/0000-0002-7099-9396>),
Simon Frost [ctb],
Heng Li [ctb],
Yu Feng [ctb],
Alan Hindmarsh [ctb],
Linda Petzold [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
J Colinge [ctb],
Hadley Wickham [ctb],
G Grothendieck [ctb],
Robert Gentleman [ctb],
Ross Ihaka [ctb],
R core team [cph],
odepack authors [cph]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 0.9.0-6 dated 2019-05-30 and 0.9.0-8 dated 2019-06-21
DESCRIPTION | 16 MD5 | 74 ++-- R/RxODE.R | 2 R/dsl.R | 23 - R/progress.R | 5 R/rxSymInv.R | 2 R/rxode-options.R | 2 R/rxsolve.R | 22 - R/rxsympy.R | 40 +- build/vignette.rds |binary configure | 36 +- configure.ac | 5 configure.win | 2 inst/doc/RxODE-cmt.html | 12 inst/doc/RxODE-covariates.html | 16 inst/doc/RxODE-data-frame.html | 10 inst/doc/RxODE-events.html | 133 ++++---- inst/doc/RxODE-intro.html | 8 inst/doc/RxODE-model-types.html | 14 inst/doc/RxODE-rxUse.Rmd | 2 inst/doc/RxODE-rxUse.html | 514 ++++++++++--------------------- inst/doc/RxODE-shiny.html | 4 inst/doc/RxODE-stiff.html | 4 inst/doc/RxODE-syntax.html | 4 inst/doc/RxODE-transit-compartments.html | 8 man/rxProgress.Rd | 4 man/rxSymPySetupPred.Rd | 3 src/Makevars.in | 2 src/dlsoda.f | 214 +++++++----- src/et.cpp | 8 src/init.c | 4 src/opkda1_abbr.f | 10 src/opkda2.f | 108 ------ src/par_solve.c | 4 src/rprintf.c | 132 +++++-- src/rxData.cpp | 37 ++ src/tran.c | 39 +- vignettes/RxODE-rxUse.Rmd | 2 38 files changed, 704 insertions(+), 821 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral,
Ulrike Groemping, Bill Venables
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.7-5 dated 2019-04-07 and 3.7-6 dated 2019-06-21
DESCRIPTION | 11 ++-- MD5 | 92 ++++++++++++++++++---------------- NAMESPACE | 2 NEWS | 8 ++ R/arctext.R | 10 +-- R/axis.break.R | 4 - R/barNest.R | 14 ++--- R/barp.R | 2 R/battleship.plot.R | 6 +- R/box.heresy.R | 10 +-- R/boxed.labels.R | 14 ++--- R/brkdn.plot.R | 32 +++++------ R/brkdnNest.R | 14 ++--- R/dendrite.R | 2 R/densityGrid.R |only R/drawNestedBars.R | 2 R/multhist.R | 53 ++++++++++--------- R/placeLabels.R | 2 R/radialtext.R | 21 ++++--- R/staxlab.R | 4 - R/taylor.diagram.R | 51 ++++++++++--------- R/thigmophobe.R | 118 ++++++++++---------------------------------- R/thigmophobe.labels.R |only R/weighted.hist.R | 126 ++++++++++++++++++++++++----------------------- data/l2010.rda |only data/soils.rda |binary demo/plotrix.R | 88 +++++++++++++++++++++----------- man/arctext.Rd | 4 - man/axis.break.Rd | 2 man/barNest.Rd | 4 - man/barlabels.Rd | 8 ++ man/barp.Rd | 6 +- man/battleship.plot.Rd | 2 man/box.heresy.Rd | 6 +- man/boxed.labels.Rd | 2 man/brkdn.plot.Rd | 18 +++--- man/bumpchart.Rd | 2 man/color.scale.Rd | 39 +++++++++++++- man/densityGrid.Rd |only man/drawNestedBars.Rd | 2 man/ehplot.Rd | 7 +- man/l2010.Rd |only man/makeDensityMatrix.Rd |only man/multhist.Rd | 1 man/plotrix-package.Rd | 8 +- man/radial.plot.Rd | 2 man/staxlab.Rd | 4 - man/taylor.diagram.Rd | 8 +- man/thigmophobe.Rd | 17 +++--- man/weighted.hist.Rd | 15 +---- 50 files changed, 438 insertions(+), 405 deletions(-)
Title: Parallel Simulation Studies
Description: Perform flexible simulation studies using one or multiple computer cores.
The package is set up to be usable on high-performance clusters in addition
to being run locally, see examples on <https://github.com/SachaEpskamp/parSim>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between parSim versions 0.1 dated 2017-11-10 and 0.1.1 dated 2019-06-21
parSim-0.1.1/parSim/DESCRIPTION | 8 ++++---- parSim-0.1.1/parSim/MD5 | 7 +++---- parSim-0.1.1/parSim/NAMESPACE | 1 + parSim-0.1.1/parSim/R/parSim.R | 6 +++--- parSim-0.1/parSim/R/parSim-internal.R |only 5 files changed, 11 insertions(+), 11 deletions(-)
Title: R Interface for 'H2O'
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models, Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes, Cox
Proportional Hazards, K-Means, PCA, Word2Vec, as well as a fully automatic
machine learning algorithm (AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric Eckstrand [ctb],
Brandon Hill [ctb],
Sebastian Vidrio [ctb],
Surekha Jadhawani [ctb],
Amy Wang [ctb],
Raymond Peck [ctb],
Wendy Wong [ctb],
Jan Gorecki [ctb],
Matt Dowle [ctb],
Yuan Tang [ctb],
Lauren DiPerna [ctb],
H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.22.1.1 dated 2019-01-10 and 3.24.0.5 dated 2019-06-21
h2o-3.22.1.1/h2o/inst/java |only h2o-3.24.0.5/h2o/DESCRIPTION | 22 h2o-3.24.0.5/h2o/MD5 | 371 +++++---- h2o-3.24.0.5/h2o/NAMESPACE | 13 h2o-3.24.0.5/h2o/R/aggregator.R | 15 h2o-3.24.0.5/h2o/R/automl.R | 180 ++-- h2o-3.24.0.5/h2o/R/classes.R | 20 h2o-3.24.0.5/h2o/R/communication.R | 55 + h2o-3.24.0.5/h2o/R/connection.R | 22 h2o-3.24.0.5/h2o/R/coxph.R | 13 h2o-3.24.0.5/h2o/R/deeplearning.R | 29 h2o-3.24.0.5/h2o/R/deepwater.R | 25 h2o-3.24.0.5/h2o/R/export.R | 18 h2o-3.24.0.5/h2o/R/frame.R | 350 +++++---- h2o-3.24.0.5/h2o/R/gbm.R | 33 h2o-3.24.0.5/h2o/R/generic.R |only h2o-3.24.0.5/h2o/R/glm.R | 32 h2o-3.24.0.5/h2o/R/glrm.R | 26 h2o-3.24.0.5/h2o/R/grid.R | 4 h2o-3.24.0.5/h2o/R/import.R | 94 ++ h2o-3.24.0.5/h2o/R/isolationforest.R | 11 h2o-3.24.0.5/h2o/R/kmeans.R | 22 h2o-3.24.0.5/h2o/R/kvstore.R | 32 h2o-3.24.0.5/h2o/R/logging.R | 26 h2o-3.24.0.5/h2o/R/models.R | 384 ++++++++-- h2o-3.24.0.5/h2o/R/naivebayes.R | 24 h2o-3.24.0.5/h2o/R/parse.R | 22 h2o-3.24.0.5/h2o/R/pca.R | 22 h2o-3.24.0.5/h2o/R/predict.R | 2 h2o-3.24.0.5/h2o/R/randomforest.R | 31 h2o-3.24.0.5/h2o/R/stackedensemble.R | 43 - h2o-3.24.0.5/h2o/R/svd.R | 22 h2o-3.24.0.5/h2o/R/targetencoder.R |only h2o-3.24.0.5/h2o/R/w2vutils.R | 4 h2o-3.24.0.5/h2o/R/word2vec.R | 18 h2o-3.24.0.5/h2o/R/xgboost.R | 25 h2o-3.24.0.5/h2o/inst/branch.txt | 2 h2o-3.24.0.5/h2o/inst/buildnum.txt | 2 h2o-3.24.0.5/h2o/man/H2OClusteringModel-class.Rd | 4 h2o-3.24.0.5/h2o/man/H2OConnection-class.Rd | 10 h2o-3.24.0.5/h2o/man/H2OConnectionMutableState.Rd | 2 h2o-3.24.0.5/h2o/man/H2OModel-class.Rd | 4 h2o-3.24.0.5/h2o/man/aaa.Rd | 2 h2o-3.24.0.5/h2o/man/apply.Rd | 2 h2o-3.24.0.5/h2o/man/as.character.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/as.data.frame.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/as.factor.Rd | 2 h2o-3.24.0.5/h2o/man/as.h2o.Rd | 4 h2o-3.24.0.5/h2o/man/as.matrix.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/as.numeric.Rd | 2 h2o-3.24.0.5/h2o/man/as.vector.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/colnames.Rd | 2 h2o-3.24.0.5/h2o/man/dim.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/dimnames.H2OFrame.Rd | 2 h2o-3.24.0.5/h2o/man/get_seed.H2OModel.Rd |only h2o-3.24.0.5/h2o/man/h2o-package.Rd | 10 h2o-3.24.0.5/h2o/man/h2o.abs.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.acos.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.aggregated_frame.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.aggregator.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.aic.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.anomaly.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.anyFactor.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.auc.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.automl.Rd | 50 - h2o-3.24.0.5/h2o/man/h2o.cbind.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.clearLog.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.clusterStatus.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.columns_by_type.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.confusionMatrix.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.cor.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.createFrame.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.cut.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.dct.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.ddply.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.deepfeatures.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.deeplearning.Rd | 7 h2o-3.24.0.5/h2o/man/h2o.deepwater.Rd | 5 h2o-3.24.0.5/h2o/man/h2o.describe.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.distance.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.downloadAllLogs.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.downloadCSV.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.download_mojo.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.download_pojo.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.entropy.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.exportFile.Rd | 8 h2o-3.24.0.5/h2o/man/h2o.fillna.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.gainsLift.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.gbm.Rd | 14 h2o-3.24.0.5/h2o/man/h2o.generic.Rd |only h2o-3.24.0.5/h2o/man/h2o.genericModel.Rd |only h2o-3.24.0.5/h2o/man/h2o.getAutoML.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.getGrid.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.getModel.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.getTimezone.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.giniCoef.Rd | 8 h2o-3.24.0.5/h2o/man/h2o.glm.Rd | 21 h2o-3.24.0.5/h2o/man/h2o.glrm.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.grep.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.grid.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.gsub.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.head.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.ifelse.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.importFile.Rd | 11 h2o-3.24.0.5/h2o/man/h2o.import_hive_table.Rd |only h2o-3.24.0.5/h2o/man/h2o.import_mojo.Rd |only h2o-3.24.0.5/h2o/man/h2o.import_sql_select.Rd | 9 h2o-3.24.0.5/h2o/man/h2o.import_sql_table.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.impute.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.init.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.insertMissingValues.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.interaction.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.kmeans.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.kurtosis.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.levels.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.listTimezones.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.list_jobs.Rd |only h2o-3.24.0.5/h2o/man/h2o.loadModel.Rd | 5 h2o-3.24.0.5/h2o/man/h2o.ls.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.lstrip.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.mae.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.make_metrics.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.match.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.mean.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.mean_per_class_error.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.mean_residual_deviance.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.median.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.merge.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.metric.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.mse.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.nacnt.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.naiveBayes.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.nchar.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.parseRaw.Rd | 5 h2o-3.24.0.5/h2o/man/h2o.parseSetup.Rd | 5 h2o-3.24.0.5/h2o/man/h2o.partialPlot.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.performance.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.pr_auc.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.prcomp.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.predict_json.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.proj_archetypes.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.quantile.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.r2.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.randomForest.Rd | 11 h2o-3.24.0.5/h2o/man/h2o.rbind.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.reconstruct.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.relevel.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.removeAll.Rd | 9 h2o-3.24.0.5/h2o/man/h2o.rmse.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.rmsle.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.rstrip.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.runif.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.scale.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.sd.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.setLevels.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.setTimezone.Rd | 4 h2o-3.24.0.5/h2o/man/h2o.set_s3_credentials.Rd |only h2o-3.24.0.5/h2o/man/h2o.shutdown.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.skewness.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.splitFrame.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.stackedEnsemble.Rd | 26 h2o-3.24.0.5/h2o/man/h2o.startLogging.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.std_coef_plot.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.stopLogging.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.stringdist.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.strsplit.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.sub.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.substring.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.sum.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.summary.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.svd.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.table.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.tabulate.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.target_encode_apply.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.target_encode_create.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.target_encode_fit.Rd |only h2o-3.24.0.5/h2o/man/h2o.target_encode_transform.Rd |only h2o-3.24.0.5/h2o/man/h2o.toFrame.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.tokenize.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.tolower.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.toupper.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.transform.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.trim.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.upload_mojo.Rd |only h2o-3.24.0.5/h2o/man/h2o.var.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.varimp_plot.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.which.Rd | 2 h2o-3.24.0.5/h2o/man/h2o.xgboost.Rd | 5 h2o-3.24.0.5/h2o/man/plot.H2OModel.Rd | 2 h2o-3.24.0.5/h2o/man/plot.H2OTabulate.Rd | 2 h2o-3.24.0.5/h2o/man/predict_contributions.H2OModel.Rd |only h2o-3.24.0.5/h2o/man/predict_leaf_node_assignment.H2OModel.Rd | 2 h2o-3.24.0.5/h2o/man/staged_predict_proba.H2OModel.Rd | 2 h2o-3.24.0.5/h2o/man/zzz.Rd | 6 194 files changed, 1485 insertions(+), 1024 deletions(-)
Title: Suite of GR Hydrological Models for Precipitation-Runoff
Modelling
Description: Hydrological modelling tools developed at Irstea-Antony (HYCAR Research Unit, France). The package includes several conceptual rainfall-runoff models (GR4H, GR4J, GR5J, GR6J, GR2M, GR1A), a snow accumulation and melt model (CemaNeige) and the associated functions for their calibration and evaluation. Use help(airGR) for package description and references.
Author: Laurent Coron [aut, trl] (<https://orcid.org/0000-0002-1503-6204>),
Olivier Delaigue [aut, cre] (<https://orcid.org/0000-0002-7668-8468>),
Guillaume Thirel [aut] (<https://orcid.org/0000-0002-1444-1830>),
Charles Perrin [aut, ths] (<https://orcid.org/0000-0001-8552-1881>),
Claude Michel [aut, ths],
Vazken Andréassian [ctb, ths] (<https://orcid.org/0000-0001-7124-9303>),
François Bourgin [ctb] (<https://orcid.org/0000-0002-2820-7260>,
'Parameter estimation' vignettes),
Pierre Brigode [ctb] (<https://orcid.org/0000-0001-8257-0741>),
Nicolas Le Moine [ctb],
Thibaut Mathevet [ctb],
Safouane Mouelhi [ctb],
Ludovic Oudin [ctb] (<https://orcid.org/0000-0002-3712-0933>),
Raji Pushpalatha [ctb],
Audrey Valéry [ctb]
Maintainer: Olivier Delaigue <airGR@irstea.fr>
Diff between airGR versions 1.2.13.16 dated 2019-04-03 and 1.3.2.23 dated 2019-06-21
airGR-1.2.13.16/airGR/man/PEdaily_Oudin.Rd |only airGR-1.2.13.16/airGR/src/frun_CEMANEIGE.f |only airGR-1.2.13.16/airGR/src/frun_GR1A.f |only airGR-1.2.13.16/airGR/src/frun_GR2M.f |only airGR-1.2.13.16/airGR/src/frun_GR4H.f |only airGR-1.2.13.16/airGR/src/frun_GR4J.f |only airGR-1.2.13.16/airGR/src/frun_GR5J.f |only airGR-1.2.13.16/airGR/src/frun_GR6J.f |only airGR-1.3.2.23/airGR/DESCRIPTION | 12 airGR-1.3.2.23/airGR/MD5 | 157 - airGR-1.3.2.23/airGR/NAMESPACE | 3 airGR-1.3.2.23/airGR/NEWS | 45 airGR-1.3.2.23/airGR/R/Calibration.R | 50 airGR-1.3.2.23/airGR/R/Calibration_Michel.R | 6 airGR-1.3.2.23/airGR/R/CreateCalibOptions.R | 773 ++--- airGR-1.3.2.23/airGR/R/CreateIniStates.R | 4 airGR-1.3.2.23/airGR/R/CreateInputsCrit.R | 48 airGR-1.3.2.23/airGR/R/CreateInputsModel.R | 605 ++-- airGR-1.3.2.23/airGR/R/CreateRunOptions.R | 10 airGR-1.3.2.23/airGR/R/DataAltiExtrapolation_Valery.R | 1102 +++---- airGR-1.3.2.23/airGR/R/ErrorCrit.R | 20 airGR-1.3.2.23/airGR/R/ErrorCrit_KGE.R | 308 -- airGR-1.3.2.23/airGR/R/ErrorCrit_KGE2.R | 342 -- airGR-1.3.2.23/airGR/R/ErrorCrit_NSE.R | 198 - airGR-1.3.2.23/airGR/R/ErrorCrit_RMSE.R | 192 - airGR-1.3.2.23/airGR/R/PE_Oudin.R |only airGR-1.3.2.23/airGR/R/PEdaily_Oudin.R | 223 - airGR-1.3.2.23/airGR/R/RunModel.R | 14 airGR-1.3.2.23/airGR/R/RunModel_CemaNeige.R | 38 airGR-1.3.2.23/airGR/R/RunModel_CemaNeigeGR4H.R |only airGR-1.3.2.23/airGR/R/RunModel_CemaNeigeGR4J.R | 11 airGR-1.3.2.23/airGR/R/RunModel_CemaNeigeGR5J.R | 11 airGR-1.3.2.23/airGR/R/RunModel_CemaNeigeGR6J.R | 11 airGR-1.3.2.23/airGR/R/RunModel_GR1A.R | 182 - airGR-1.3.2.23/airGR/R/RunModel_GR2M.R | 196 - airGR-1.3.2.23/airGR/R/RunModel_GR4H.R | 204 - airGR-1.3.2.23/airGR/R/RunModel_GR4J.R | 2 airGR-1.3.2.23/airGR/R/RunModel_GR5J.R | 204 - airGR-1.3.2.23/airGR/R/RunModel_GR6J.R | 214 - airGR-1.3.2.23/airGR/R/TransfoParam_CemaNeige.R | 86 airGR-1.3.2.23/airGR/R/Utils.R | 151 + airGR-1.3.2.23/airGR/R/plot.OutputsModel.R | 1700 ++++++------ airGR-1.3.2.23/airGR/data/X0310010.rda |binary airGR-1.3.2.23/airGR/data/datalist |only airGR-1.3.2.23/airGR/data/exampleSimPlot.rda |only airGR-1.3.2.23/airGR/inst/CITATION | 4 airGR-1.3.2.23/airGR/inst/doc/V01_get_started.R | 4 airGR-1.3.2.23/airGR/inst/doc/V01_get_started.Rmd | 4 airGR-1.3.2.23/airGR/inst/doc/V01_get_started.html | 9 airGR-1.3.2.23/airGR/inst/doc/V02.2_param_mcmc.html | 6 airGR-1.3.2.23/airGR/inst/doc/V04_cemaneige_hysteresis.html | 16 airGR-1.3.2.23/airGR/man/Calibration.Rd | 220 - airGR-1.3.2.23/airGR/man/Calibration_Michel.Rd | 294 +- airGR-1.3.2.23/airGR/man/CreateCalibOptions.Rd | 292 +- airGR-1.3.2.23/airGR/man/CreateInputsCrit.Rd | 10 airGR-1.3.2.23/airGR/man/CreateInputsModel.Rd | 222 - airGR-1.3.2.23/airGR/man/CreateRunOptions.Rd | 322 +- airGR-1.3.2.23/airGR/man/DataAltiExtrapolation_Valery.Rd | 178 - airGR-1.3.2.23/airGR/man/ErrorCrit.Rd | 236 - airGR-1.3.2.23/airGR/man/ErrorCrit_KGE.Rd | 234 - airGR-1.3.2.23/airGR/man/ErrorCrit_KGE2.Rd | 242 - airGR-1.3.2.23/airGR/man/ErrorCrit_NSE.Rd | 216 - airGR-1.3.2.23/airGR/man/ErrorCrit_RMSE.Rd | 202 - airGR-1.3.2.23/airGR/man/PE_Oudin.Rd |only airGR-1.3.2.23/airGR/man/Param_Sets_GR4J.Rd | 212 - airGR-1.3.2.23/airGR/man/RunModel.Rd | 156 - airGR-1.3.2.23/airGR/man/RunModel_CemaNeige.Rd | 270 - airGR-1.3.2.23/airGR/man/RunModel_CemaNeigeGR4H.Rd |only airGR-1.3.2.23/airGR/man/RunModel_CemaNeigeGR4J.Rd | 356 +- airGR-1.3.2.23/airGR/man/RunModel_CemaNeigeGR5J.Rd | 2 airGR-1.3.2.23/airGR/man/RunModel_CemaNeigeGR6J.Rd | 364 +- airGR-1.3.2.23/airGR/man/RunModel_GR1A.Rd | 222 - airGR-1.3.2.23/airGR/man/RunModel_GR2M.Rd | 240 - airGR-1.3.2.23/airGR/man/RunModel_GR4H.Rd | 240 - airGR-1.3.2.23/airGR/man/RunModel_GR4J.Rd | 246 - airGR-1.3.2.23/airGR/man/RunModel_GR5J.Rd | 258 - airGR-1.3.2.23/airGR/man/RunModel_GR6J.Rd | 254 - airGR-1.3.2.23/airGR/man/SeriesAggreg.Rd | 142 - airGR-1.3.2.23/airGR/man/TransfoParam.Rd | 184 - airGR-1.3.2.23/airGR/man/airGR.Rd | 131 airGR-1.3.2.23/airGR/man/plot.OutputsModel.Rd | 101 airGR-1.3.2.23/airGR/src/frun_cemaneige.f |only airGR-1.3.2.23/airGR/src/frun_gr1a.f |only airGR-1.3.2.23/airGR/src/frun_gr2m.f |only airGR-1.3.2.23/airGR/src/frun_gr4h.f |only airGR-1.3.2.23/airGR/src/frun_gr4j.f |only airGR-1.3.2.23/airGR/src/frun_gr5j.f |only airGR-1.3.2.23/airGR/src/frun_gr6j.f |only airGR-1.3.2.23/airGR/vignettes/V00_airgr_ref.bib | 304 +- airGR-1.3.2.23/airGR/vignettes/V01_get_started.Rmd | 4 90 files changed, 6748 insertions(+), 6771 deletions(-)
Title: Mixed-Effect Models, Particularly Spatial Models
Description: Inference based on mixed-effect models, including generalized linear mixed models with spatial correlations and models with non-Gaussian random effects (e.g., Beta). Both classical geostatistical models, and Markov random field models on irregular grids, can be fitted. Variation in residual variance (heteroscedasticity) can itself be represented by a generalized linear mixed model. Various approximations of likelihood or restricted likelihood are implemented, in particular h-likelihood (Lee and Nelder 2001 <doi:10.1093/biomet/88.4.987>) and Laplace approximation.
Author: François Rousset [aut, cre, cph]
(<https://orcid.org/0000-0003-4670-0371>),
Jean-Baptiste Ferdy [aut, cph],
Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>),
GSL authors [ctb] (src/gsl_bessel.*)
Maintainer: François Rousset <francois.rousset@umontpellier.fr>
Diff between spaMM versions 2.7.1 dated 2019-04-14 and 3.0.0 dated 2019-06-21
DESCRIPTION | 8 MD5 | 130 ++++++------- NAMESPACE | 9 R/CanonizeRanPars.R | 5 R/GLM.fit.R | 11 - R/HLCor_body.R | 9 R/HLfit.R | 4 R/HLfit_Internals.R | 258 +++++++++++++++---------- R/HLfit_body.R | 77 +++---- R/HLfit_body_augZXy.R | 33 ++- R/HLframes.R | 24 +- R/MakeCovEst.R | 88 +++++--- R/RcppExports.R | 20 ++ R/ZAL_class.R | 4 R/calc_LRT.R | 10 - R/calc_logdisp_cov.R | 6 R/confint.R | 15 - R/corMatern.R | 9 R/corrHLfit-internals.R | 288 +++++++++++++++++++---------- R/corrMM.LRT.R | 9 R/correlationFns.R | 4 R/determine_spprec.R | 161 +++++++--------- R/dispGammaGLM.R | 3 R/extractors.R | 59 ++++- R/fitme_body.R | 10 - R/fitmecorrHLfit_body_internals.R | 107 +++++----- R/geo_info.R | 8 R/locoptim.R | 15 + R/makeLowerUpper.R | 7 R/newPLS.R | 144 +++++++++----- R/postfit_internals.R | 184 ++++++++++++++++-- R/predict.R | 7 R/preprocess.R | 60 ++++-- R/preprocess_internals.R | 103 +++++++--- R/sXaug_EigenDense_QRP_Chol_scaled.R | 40 ---- R/sXaug_Matrix_QRP_CHM.R | 40 ---- R/sXaug_sparsePrecisions.R | 21 +- R/save.R | 2 R/spaMM.data.R | 40 ++-- R/summary.HL.R | 2 build/partial.rdb |binary inst/NEWS.Rd | 22 ++ man/AIC.Rd | 2 man/HLfit.Rd | 2 man/IMRF.Rd | 11 - man/Loaloa.Rd | 3 man/PLS-internals.Rd | 2 man/anova.HLfit.Rd | 3 man/covStruct.Rd | 3 man/fixed.Rd | 30 +-- man/options.Rd | 2 man/seaMask.Rd | 2 man/sym_svd.Rd | 2 man/vcov.Rd | 24 ++ src/Makevars.win | 2 src/RcppExports.cpp | 67 ++++++ src/spaMM_linear.cpp | 247 ++++++++++++++++++++++++ tests/testthat/test-Nugget.R | 6 tests/testthat/test-adjacency-corrMatrix.R | 2 tests/testthat/test-adjacency-long.R | 8 tests/testthat/test-augZXy.R | 24 ++ tests/testthat/test-cloglog.R | 2 tests/testthat/test-negbin1.R | 2 tests/testthat/test-poly.R | 14 - tests/testthat/test-ranCoefs.R | 35 ++- tests/testthat/test-random-slope.R | 4 66 files changed, 1699 insertions(+), 856 deletions(-)
Title: Latent Variable Network Modeling
Description: Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between lvnet versions 0.3.4 dated 2018-11-18 and 0.3.5 dated 2019-06-21
lvnet-0.3.4/lvnet/README.md |only lvnet-0.3.5/lvnet/DESCRIPTION | 6 +++--- lvnet-0.3.5/lvnet/MD5 | 8 +++++--- lvnet-0.3.5/lvnet/NEWS | 3 +++ lvnet-0.3.5/lvnet/R/BayesLNM.R |only lvnet-0.3.5/lvnet/R/BayesRNM.R |only lvnet-0.3.5/lvnet/R/zzz.R |only 7 files changed, 11 insertions(+), 6 deletions(-)
Title: A Simple Logging System for R, Based on 'log4j'
Description: The log4r package is meant to provide a fast, lightweight,
object-oriented approach to logging in R based on the widely-emulated
'log4j' system and etymology.
Author: John Myles White [aut, cph],
Kenton White [ctb],
Kirill Müller [ctb],
Aaron Jacobs [aut, cre]
Maintainer: Aaron Jacobs <atheriel@gmail.com>
Diff between log4r versions 0.2 dated 2014-09-29 and 0.3.0 dated 2019-06-21
log4r-0.2/log4r/R/write.message.R |only log4r-0.2/log4r/build |only log4r-0.2/log4r/man/write.message.Rd |only log4r-0.3.0/log4r/DESCRIPTION | 41 ++++++++++++++---------- log4r-0.3.0/log4r/MD5 | 42 +++++++++++++----------- log4r-0.3.0/log4r/NAMESPACE | 8 ++++ log4r-0.3.0/log4r/R/appenders.R |only log4r-0.3.0/log4r/R/create.logger.R | 56 +++++++++++++++++++++++++++++---- log4r-0.3.0/log4r/R/layouts.R |only log4r-0.3.0/log4r/R/level.logger.R | 25 +++++--------- log4r-0.3.0/log4r/R/log4r-package.R | 1 log4r-0.3.0/log4r/R/logfile.logger.R | 19 +++++------ log4r-0.3.0/log4r/R/logfuncs.R | 53 ++++++++++++++++++++++++++----- log4r-0.3.0/log4r/R/loglevel.R | 4 +- log4r-0.3.0/log4r/README.md |only log4r-0.3.0/log4r/inst/NEWS.Rd | 8 ++++ log4r-0.3.0/log4r/man/appenders.Rd |only log4r-0.3.0/log4r/man/create.logger.Rd | 8 ++-- log4r-0.3.0/log4r/man/layouts.Rd |only log4r-0.3.0/log4r/man/level.Rd | 15 ++++---- log4r-0.3.0/log4r/man/levellog.Rd | 13 ++++--- log4r-0.3.0/log4r/man/log4r-package.Rd | 7 ++-- log4r-0.3.0/log4r/man/logfile.Rd | 7 ++-- log4r-0.3.0/log4r/man/logformat.Rd | 7 ++-- log4r-0.3.0/log4r/man/logger.Rd |only log4r-0.3.0/log4r/man/loglevel.Rd | 14 ++++---- log4r-0.3.0/log4r/src |only 27 files changed, 217 insertions(+), 111 deletions(-)
Title: Treatment Effects with Multiple Periods and Groups
Description: The standard Difference-in-Differences (DID) setup involves two periods and two groups -- a treated group and untreated group. Many applications of DID methods involve more than two periods and have individuals that are treated at different points in time. This package contains tools for computing average treatment effect parameters in Difference in Differences models with more than two periods and with variation in treatment timing using the methods developed in Callaway and Sant'Anna (2018) <https://ssrn.com/abstract=3148250>. The main parameters are group-time average treatment effects which are the average treatment effect for a particular group at a a particular time. These can be aggregated into a fewer number of treatment effect parameters, and the package deals with the cases where there is selective treatment timing, dynamic treatment effects, calendar time effects, or combinations of these. There are also functions for testing the Difference in Differences assumption, and plotting group-time average treatment effects.
Author: Brantly Callaway [aut, cre],
Pedro H.C. Sant'Anna [aut]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>
Diff between did versions 1.2.1 dated 2019-06-14 and 1.2.2 dated 2019-06-21
DESCRIPTION | 9 MD5 | 24 +- NEWS.md | 15 + R/did.R | 143 +++++++++--- R/zzz.R | 2 README.md | 66 +++++ build/vignette.rds |binary inst/doc/did-basics.html | 364 +++++++++++-------------------- man/AGGTE.Rd | 7 man/compute.aggte.Rd | 2 man/figures/README-unnamed-chunk-5-1.png |only man/figures/README-unnamed-chunk-7-1.png |only man/ggdid.Rd | 20 + man/summary.AGGTE.Rd | 7 14 files changed, 374 insertions(+), 285 deletions(-)
Title: Tools for Antitrust Practitioners
Description: A collection of tools for antitrust practitioners, including the ability to calibrate different consumer demand systems and simulate the effects of mergers under different competitive regimes.
Author: Charles Taragin and Michael Sandfort
Maintainer: Charles Taragin <ctaragin@ftc.gov>
Diff between antitrust versions 0.99.10 dated 2018-06-10 and 0.99.11 dated 2019-06-21
antitrust-0.99.10/antitrust/R/Antitrust.R |only antitrust-0.99.10/antitrust/R/Bertrand.R |only antitrust-0.99.10/antitrust/R/Cournot.R |only antitrust-0.99.10/antitrust/R/Stackelberg.R |only antitrust-0.99.10/antitrust/R/aids.R |only antitrust-0.99.10/antitrust/R/antitrust_shiny.R |only antitrust-0.99.10/antitrust/R/auction2ndcap.R |only antitrust-0.99.10/antitrust/R/auction2ndlogit.R |only antitrust-0.99.10/antitrust/R/auction2ndlogitALM.R |only antitrust-0.99.10/antitrust/R/bert.R |only antitrust-0.99.10/antitrust/R/ces.R |only antitrust-0.99.10/antitrust/R/cesALM.R |only antitrust-0.99.10/antitrust/R/cesNests.R |only antitrust-0.99.10/antitrust/R/cmcr.R |only antitrust-0.99.10/antitrust/R/hhi.R |only antitrust-0.99.10/antitrust/R/linear.R |only antitrust-0.99.10/antitrust/R/logit.R |only antitrust-0.99.10/antitrust/R/logitALM.R |only antitrust-0.99.10/antitrust/R/logitCap.R |only antitrust-0.99.10/antitrust/R/logitCapALM.R |only antitrust-0.99.10/antitrust/R/logitNests.R |only 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Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-5 dated 2018-03-25 and 0.3-6 dated 2019-06-21
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- NAMESPACE | 2 -- R/find_max.R | 17 ++++++++++------- tests |only 5 files changed, 20 insertions(+), 17 deletions(-)