Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.2.1 dated 2017-04-26 and 0.2.2 dated 2017-06-22
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- NEWS.md | 3 +++ R/as_survey.r | 2 +- inst/doc/srvyr-database.html | 4 ++-- inst/doc/srvyr-vs-survey.html | 14 +++++++------- man/as_survey.Rd | 4 ++-- tests/testthat/test_survey_package.r | 2 -- 9 files changed, 29 insertions(+), 28 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 3.32 dated 2017-06-07 and 3.32-1 dated 2017-06-22
DESCRIPTION | 11 ++++++---- MD5 | 54 ++++++++++++++++++++++++++-------------------------- R/grake.R | 33 +++++++++++++++++++++++++++++++ R/multistage.R | 10 +++++++++ R/surveyrep.R | 8 ++++--- R/sysdata.rda |binary R/twophase.R | 3 ++ R/twophase2.R | 4 ++- THANKS | 1 build/vignette.rds |binary data/api.rda |binary data/crowd.rda |binary data/election.rda |binary data/fpc.rda |binary data/hospital.rda |binary data/mu284.rda |binary data/nhanes.rda |binary data/scd.rda |binary data/yrbs.rda |binary inst/NEWS | 6 +++++ inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/phase1.pdf |binary inst/doc/pps.pdf |binary inst/doc/survey.pdf |binary man/make.calfun.Rd | 5 +++- man/psrsq.Rd | 2 - man/svyglm.Rd | 2 - 28 files changed, 101 insertions(+), 38 deletions(-)
Title: Integrated Prediction using Uni-Variate and Multivariate Random
Forests
Description: An implementation of a framework for drug sensitivity prediction from various genetic characterizations using ensemble approaches. Random Forests or Multivariate Random Forest predictive models can be generated from each genetic characterization that are then combined using a Least Square Regression approach. It also provides options for the use of different error estimation approaches of Leave-one-out, Bootstrap, N-fold cross validation and 0.632+Bootstrap along with generation of prediction confidence interval using Jackknife-after-Bootstrap approach.
Author: Raziur Rahman, Ranadip Pal
Maintainer: Raziur Rahman <razeeebuet@gmail.com>
Diff between IntegratedMRF versions 1.1.5 dated 2016-08-10 and 1.1.8 dated 2017-06-22
IntegratedMRF-1.1.5/IntegratedMRF/src/Node_Cost_C.cpp |only IntegratedMRF-1.1.8/IntegratedMRF/DESCRIPTION | 15 IntegratedMRF-1.1.8/IntegratedMRF/MD5 | 37 + IntegratedMRF-1.1.8/IntegratedMRF/NAMESPACE | 6 IntegratedMRF-1.1.8/IntegratedMRF/R/CombPredict.R | 62 +-- IntegratedMRF-1.1.8/IntegratedMRF/R/CombPredictSpecific.R | 77 --- IntegratedMRF-1.1.8/IntegratedMRF/R/IntegratedMRF.R | 196 +--------- IntegratedMRF-1.1.8/IntegratedMRF/R/IntegratedPrediction.R | 86 ++-- IntegratedMRF-1.1.8/IntegratedMRF/R/RcppExports.R | 10 IntegratedMRF-1.1.8/IntegratedMRF/R/build_single_tree.R | 15 IntegratedMRF-1.1.8/IntegratedMRF/R/predicting.R |only IntegratedMRF-1.1.8/IntegratedMRF/R/single_tree_prediction.R | 2 IntegratedMRF-1.1.8/IntegratedMRF/R/split_node.R |only IntegratedMRF-1.1.8/IntegratedMRF/man/CombPredict.Rd | 34 - IntegratedMRF-1.1.8/IntegratedMRF/man/CombPredictSpecific.Rd | 34 - IntegratedMRF-1.1.8/IntegratedMRF/man/Combination.Rd | 72 +-- IntegratedMRF-1.1.8/IntegratedMRF/man/IntegratedPrediction.Rd | 40 +- IntegratedMRF-1.1.8/IntegratedMRF/man/predicting.Rd | 4 IntegratedMRF-1.1.8/IntegratedMRF/man/split_node.Rd | 6 IntegratedMRF-1.1.8/IntegratedMRF/src/RcppExports.cpp | 51 -- IntegratedMRF-1.1.8/IntegratedMRF/src/rcpp_hello.cpp |only IntegratedMRF-1.1.8/IntegratedMRF/src/registerDynamicSymbol.cpp |only 22 files changed, 262 insertions(+), 485 deletions(-)
Title: Text Corpus Analysis
Description: Text corpus data analysis, with full support for Unicode. Functions for reading data from newline-delimited JSON files, for normalizing and tokenizing text, for searching for term occurrences, and for computing term occurrence frequencies (including n-grams).
Author: Patrick O. Perry [aut, cre],
Martin Porter and Richard Boulton [ctb, cph] (Snowball),
Unicode, Inc. [ctb, cph] (Unicode Character Database)
Maintainer: Patrick O. Perry <pperry@stern.nyu.edu>
Diff between corpus versions 0.6.0 dated 2017-06-06 and 0.7.0 dated 2017-06-22
corpus-0.6.0/corpus/R/methods.R |only corpus-0.6.0/corpus/R/text-proc.R |only corpus-0.6.0/corpus/man/text.Rd |only corpus-0.6.0/corpus/man/tokens.Rd |only corpus-0.6.0/corpus/src/tokens.c |only corpus-0.6.0/corpus/tests/testthat/test-tokens.R |only corpus-0.7.0/corpus/DESCRIPTION | 10 corpus-0.7.0/corpus/MD5 | 125 corpus-0.7.0/corpus/NAMESPACE | 22 corpus-0.7.0/corpus/NEWS | 39 corpus-0.7.0/corpus/R/coerce.R |only corpus-0.7.0/corpus/R/filter.R |only corpus-0.7.0/corpus/R/json.R | 10 corpus-0.7.0/corpus/R/sentence.R |only corpus-0.7.0/corpus/R/term.R |only corpus-0.7.0/corpus/R/text.R | 24 corpus-0.7.0/corpus/R/text_locate.R |only corpus-0.7.0/corpus/R/text_split.R | 90 corpus-0.7.0/corpus/R/text_types.R |only corpus-0.7.0/corpus/R/token.R |only corpus-0.7.0/corpus/R/wordlist.R |only corpus-0.7.0/corpus/demo/chinese.R | 12 corpus-0.7.0/corpus/man/abbreviations.Rd | 17 corpus-0.7.0/corpus/man/as_text.Rd |only corpus-0.7.0/corpus/man/corpus-package.Rd | 13 corpus-0.7.0/corpus/man/stopwords.Rd | 10 corpus-0.7.0/corpus/man/term_counts.Rd | 8 corpus-0.7.0/corpus/man/term_matrix.Rd | 65 corpus-0.7.0/corpus/man/text_locate.Rd |only corpus-0.7.0/corpus/man/text_split.Rd | 102 corpus-0.7.0/corpus/man/text_tokens.Rd |only corpus-0.7.0/corpus/man/text_types.Rd |only corpus-0.7.0/corpus/src/Makevars | 11 corpus-0.7.0/corpus/src/corpus/NEWS.md | 6 corpus-0.7.0/corpus/src/corpus/corpus.xcodeproj/project.pbxproj | 22 corpus-0.7.0/corpus/src/corpus/src/array.c | 142 corpus-0.7.0/corpus/src/corpus/src/array.h | 26 corpus-0.7.0/corpus/src/corpus/src/intset.c |only corpus-0.7.0/corpus/src/corpus/src/intset.h |only corpus-0.7.0/corpus/src/corpus/src/search.c |only corpus-0.7.0/corpus/src/corpus/src/search.h |only corpus-0.7.0/corpus/src/corpus/src/termset.c | 2 corpus-0.7.0/corpus/src/corpus/src/text.c | 19 corpus-0.7.0/corpus/src/corpus/src/text.h | 18 corpus-0.7.0/corpus/src/corpus/src/typemap.c | 38 corpus-0.7.0/corpus/src/corpus/src/unicode.c | 49 corpus-0.7.0/corpus/src/corpus/src/unicode.h | 37 corpus-0.7.0/corpus/src/corpus/src/unicode/charwidth.h |only corpus-0.7.0/corpus/src/corpus/src/unicode/combining.h | 204 - corpus-0.7.0/corpus/src/corpus/src/unicode/sentbreakprop.h | 228 - corpus-0.7.0/corpus/src/corpus/src/unicode/wordbreakprop.h | 1549 +++++----- corpus-0.7.0/corpus/src/corpus/tests/check_charwidth.c |only corpus-0.7.0/corpus/src/corpus/tests/check_intset.c |only corpus-0.7.0/corpus/src/corpus/tests/check_search.c |only corpus-0.7.0/corpus/src/corpus/tests/check_termset.c | 1 corpus-0.7.0/corpus/src/corpus/tests/check_unicode.c | 54 corpus-0.7.0/corpus/src/corpus/tests/wcwidth9 |only corpus-0.7.0/corpus/src/corpus/util/gen-charwidth.py |only corpus-0.7.0/corpus/src/decode.c | 7 corpus-0.7.0/corpus/src/filter.c | 122 corpus-0.7.0/corpus/src/format_text.c |only corpus-0.7.0/corpus/src/init.c | 16 corpus-0.7.0/corpus/src/json.c | 9 corpus-0.7.0/corpus/src/mkchar.c | 44 corpus-0.7.0/corpus/src/rcorpus.h | 52 corpus-0.7.0/corpus/src/search.c |only corpus-0.7.0/corpus/src/sentfilter.c |only corpus-0.7.0/corpus/src/term_counts.c | 14 corpus-0.7.0/corpus/src/term_matrix.c | 217 - corpus-0.7.0/corpus/src/termset.c |only corpus-0.7.0/corpus/src/text.c | 2 corpus-0.7.0/corpus/src/text_locate.c |only corpus-0.7.0/corpus/src/text_nunit.c |only corpus-0.7.0/corpus/src/text_split.c | 58 corpus-0.7.0/corpus/src/text_tokens.c |only corpus-0.7.0/corpus/src/text_types.c |only corpus-0.7.0/corpus/src/util.c | 21 corpus-0.7.0/corpus/tests/testthat/test-term_counts.R | 2 corpus-0.7.0/corpus/tests/testthat/test-term_matrix.R | 57 corpus-0.7.0/corpus/tests/testthat/test-text_nunit.R |only corpus-0.7.0/corpus/tests/testthat/test-text_split_sentences.R | 41 corpus-0.7.0/corpus/tests/testthat/test-text_tokens.R |only 82 files changed, 1965 insertions(+), 1650 deletions(-)
Title: A System for Working with Templates
Description: Provides tools to work with template code and text in R. It aims to
provide a simple substitution mechanism for R-expressions inside these
templates. Templates can be written in other languages like 'SQL', can
simply be represented by characters in R, or can themselves be R-expressions
or functions.
Author: Sebastian Warnholz [aut, cre]
Maintainer: Sebastian Warnholz <wahani@gmail.com>
Diff between templates versions 0.1.0 dated 2017-01-07 and 0.2.0 dated 2017-06-22
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + NEWS |only R/NAMESPACE.R | 1 + R/helper.R | 6 ++++++ R/utils.R | 10 +++++----- build/vignette.rds |binary inst/doc/Template_Programming_in_R.html | 10 +++++----- man/tmpl.Rd | 3 +-- man/utils.Rd | 13 ++++++------- tests/testthat/test-utils.R | 17 +++++++++++++++++ 12 files changed, 58 insertions(+), 34 deletions(-)
Title: The Official SolveBio API Client for R
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 0.4.0 dated 2017-06-19 and 0.4.1 dated 2017-06-22
DESCRIPTION | 15 +++-- MD5 | 79 +++++++++++++++--------------- NAMESPACE | 2 R/annotation.R |only man/Annotator.annotate.Rd |only man/Dataset.all.Rd | 1 man/Dataset.count.Rd | 1 man/Dataset.create.Rd | 1 man/Dataset.data.Rd | 1 man/Dataset.facets.Rd | 1 man/Dataset.get_or_create_by_full_name.Rd | 1 man/Dataset.query.Rd | 1 man/Dataset.retrieve.Rd | 1 man/DatasetCommit.all.Rd | 1 man/DatasetCommit.retrieve.Rd | 1 man/DatasetExport.all.Rd | 1 man/DatasetExport.create.Rd | 1 man/DatasetExport.retrieve.Rd | 1 man/DatasetField.all.Rd | 1 man/DatasetField.create.Rd | 1 man/DatasetField.facets.Rd | 1 man/DatasetField.retrieve.Rd | 1 man/DatasetImport.all.Rd | 1 man/DatasetImport.create.Rd | 1 man/DatasetImport.retrieve.Rd | 1 man/DatasetMigration.all.Rd | 1 man/DatasetMigration.create.Rd | 1 man/DatasetMigration.retrieve.Rd | 1 man/Depository.all.Rd | 1 man/Depository.create.Rd | 1 man/Depository.latest_version.Rd | 1 man/Depository.retrieve.Rd | 1 man/Depository.versions.Rd | 1 man/DepositoryVersion.all.Rd | 1 man/DepositoryVersion.create.Rd | 1 man/DepositoryVersion.datasets.Rd | 1 man/DepositoryVersion.retrieve.Rd | 1 man/Expression.evaluate.Rd |only man/Upload.all.Rd | 1 man/Upload.create.Rd | 1 man/Upload.retrieve.Rd | 1 man/login.Rd | 1 42 files changed, 51 insertions(+), 81 deletions(-)
Title: Phylogenetic Tree Manipulation Class and Methods
Description: S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
Author: D.J. Bennett
Maintainer: D.J. Bennett <dominic.john.bennett@gmail.com>
Diff between treeman versions 1.0 dated 2016-04-17 and 1.1 dated 2017-06-22
treeman-1.0/treeman/R/get-methods.R |only treeman-1.0/treeman/man/TreeMan-method.Rd |only treeman-1.0/treeman/man/as-TreeMen.Rd |only treeman-1.0/treeman/man/getNdPrid.Rd |only treeman-1.0/treeman/man/getNdPtid.Rd |only treeman-1.0/treeman/man/getNdsPrid.Rd |only treeman-1.0/treeman/man/getNdsPtid.Rd |only treeman-1.0/treeman/man/rmTip.Rd |only treeman-1.0/treeman/man/setTol.Rd |only treeman-1.0/treeman/tests/testthat/test-get-methods.R |only treeman-1.1/treeman/DESCRIPTION | 22 treeman-1.1/treeman/MD5 | 212 +++-- treeman-1.1/treeman/NAMESPACE | 54 + treeman-1.1/treeman/R/calc-methods.R | 212 +++-- treeman-1.1/treeman/R/check_methods.R |only treeman-1.1/treeman/R/cnvrt-methods.R |only treeman-1.1/treeman/R/gen-methods.R | 226 +++-- treeman-1.1/treeman/R/get-nd-methods.R |only treeman-1.1/treeman/R/get-nds-methods.R |only treeman-1.1/treeman/R/get-spcl-methods.R |only treeman-1.1/treeman/R/manip-methods.R | 531 +++++++++---- treeman-1.1/treeman/R/ndlst-methods.R |only treeman-1.1/treeman/R/ndmtrx-methods.R |only treeman-1.1/treeman/R/node-declaration.R | 94 +- treeman-1.1/treeman/R/read-write-methods.R | 457 ++++++++--- treeman-1.1/treeman/R/server-methods.R |only treeman-1.1/treeman/R/set-methods.R | 228 ++--- treeman-1.1/treeman/R/treeman-declaration.R | 276 ++---- treeman-1.1/treeman/R/treemen-declaration.R | 69 - treeman-1.1/treeman/R/update-methods.R | 245 ++--- treeman-1.1/treeman/R/viz-methods.R |only treeman-1.1/treeman/README.md | 27 treeman-1.1/treeman/data/birds.rda |only treeman-1.1/treeman/data/mammals.rda |binary treeman-1.1/treeman/data/plants.rda |only treeman-1.1/treeman/man/Node-class.Rd | 24 treeman-1.1/treeman/man/TreeMan-class.Rd | 86 +- treeman-1.1/treeman/man/TreeMan-to-phylo.Rd |only treeman-1.1/treeman/man/TreeMen-class.Rd | 27 treeman-1.1/treeman/man/TreeMen-to-multiPhylo.Rd |only treeman-1.1/treeman/man/addClade.Rd |only treeman-1.1/treeman/man/addNdmtrx.Rd |only treeman-1.1/treeman/man/addTip.Rd | 42 - treeman-1.1/treeman/man/birds.Rd |only treeman-1.1/treeman/man/blncdTree.Rd |only treeman-1.1/treeman/man/cTrees.Rd | 3 treeman-1.1/treeman/man/calcDstBLD.Rd | 8 treeman-1.1/treeman/man/calcDstMtrx.Rd | 9 treeman-1.1/treeman/man/calcDstRF.Rd | 8 treeman-1.1/treeman/man/calcDstTrp.Rd | 8 treeman-1.1/treeman/man/calcFrPrp.Rd | 7 treeman-1.1/treeman/man/calcNdBlnc.Rd | 7 treeman-1.1/treeman/man/calcNdsBlnc.Rd | 11 treeman-1.1/treeman/man/calcOvrlp.Rd | 8 treeman-1.1/treeman/man/calcPhyDv.Rd | 10 treeman-1.1/treeman/man/calcPrtFrPrp.Rd |only treeman-1.1/treeman/man/checkNdlst.Rd |only treeman-1.1/treeman/man/checkTreeMen.Rd |only treeman-1.1/treeman/man/fastCheckTreeMan.Rd |only treeman-1.1/treeman/man/getAge.Rd |only treeman-1.1/treeman/man/getCnnctdNds.Rd |only treeman-1.1/treeman/man/getDcsd.Rd |only treeman-1.1/treeman/man/getLvng.Rd |only treeman-1.1/treeman/man/getNdAge.Rd | 14 treeman-1.1/treeman/man/getNdKids.Rd | 3 treeman-1.1/treeman/man/getNdLng.Rd | 7 treeman-1.1/treeman/man/getNdPD.Rd |only treeman-1.1/treeman/man/getNdPrdst.Rd |only treeman-1.1/treeman/man/getNdPrids.Rd |only treeman-1.1/treeman/man/getNdPtids.Rd |only treeman-1.1/treeman/man/getNdSlt.Rd | 4 treeman-1.1/treeman/man/getNdSstr.Rd | 3 treeman-1.1/treeman/man/getNdsAge.Rd | 15 treeman-1.1/treeman/man/getNdsKids.Rd | 9 treeman-1.1/treeman/man/getNdsLng.Rd | 13 treeman-1.1/treeman/man/getNdsPD.Rd |only treeman-1.1/treeman/man/getNdsPrdst.Rd |only treeman-1.1/treeman/man/getNdsPrids.Rd |only treeman-1.1/treeman/man/getNdsPtids.Rd |only treeman-1.1/treeman/man/getNdsSlt.Rd | 10 treeman-1.1/treeman/man/getNdsSstr.Rd | 9 treeman-1.1/treeman/man/getOtgrp.Rd | 3 treeman-1.1/treeman/man/getPath.Rd | 3 treeman-1.1/treeman/man/getPrnt.Rd | 3 treeman-1.1/treeman/man/getSpnAge.Rd | 12 treeman-1.1/treeman/man/getSpnsAge.Rd | 16 treeman-1.1/treeman/man/getSubtree.Rd | 8 treeman-1.1/treeman/man/getTxnyms.Rd | 23 treeman-1.1/treeman/man/getUnqNds.Rd |only treeman-1.1/treeman/man/isUltrmtrc.Rd |only treeman-1.1/treeman/man/list-to-TreeMen.Rd |only treeman-1.1/treeman/man/loadTreeMan.Rd |only treeman-1.1/treeman/man/mammals.Rd | 8 treeman-1.1/treeman/man/multiPhylo-class.Rd |only treeman-1.1/treeman/man/multiPhylo-to-TreeMen.Rd |only treeman-1.1/treeman/man/phylo-class.Rd |only treeman-1.1/treeman/man/phylo-to-TreeMan.Rd |only treeman-1.1/treeman/man/pinTips.Rd | 12 treeman-1.1/treeman/man/plants.Rd |only treeman-1.1/treeman/man/pstMnp.Rd |only treeman-1.1/treeman/man/randTree.Rd | 12 treeman-1.1/treeman/man/readTree.Rd | 18 treeman-1.1/treeman/man/readTrmn.Rd |only treeman-1.1/treeman/man/rmClade.Rd |only treeman-1.1/treeman/man/rmNdmtrx.Rd |only treeman-1.1/treeman/man/rmNodes.Rd |only treeman-1.1/treeman/man/rmTips.Rd |only treeman-1.1/treeman/man/saveTreeMan.Rd |only treeman-1.1/treeman/man/searchTxnyms.Rd |only treeman-1.1/treeman/man/setAge.Rd | 3 treeman-1.1/treeman/man/setNdID.Rd | 6 treeman-1.1/treeman/man/setNdOther.Rd | 2 treeman-1.1/treeman/man/setNdSpn.Rd | 8 treeman-1.1/treeman/man/setNdsID.Rd | 10 treeman-1.1/treeman/man/setNdsOther.Rd | 16 treeman-1.1/treeman/man/setNdsSpn.Rd | 13 treeman-1.1/treeman/man/setPD.Rd | 3 treeman-1.1/treeman/man/setTxnyms.Rd |only treeman-1.1/treeman/man/taxaResolve.Rd |only treeman-1.1/treeman/man/twoer.Rd |only treeman-1.1/treeman/man/ultrTree.Rd |only treeman-1.1/treeman/man/unblncdTree.Rd |only treeman-1.1/treeman/man/updateSlts.Rd |only treeman-1.1/treeman/man/writeTree.Rd | 17 treeman-1.1/treeman/man/writeTrmn.Rd |only treeman-1.1/treeman/src |only treeman-1.1/treeman/tests/testthat/test-calc-methods.R | 63 - treeman-1.1/treeman/tests/testthat/test-check-methods.R |only treeman-1.1/treeman/tests/testthat/test-cnvrt-methods.R |only treeman-1.1/treeman/tests/testthat/test-display-methods.R | 12 treeman-1.1/treeman/tests/testthat/test-gen-methods.R | 29 treeman-1.1/treeman/tests/testthat/test-get-nd-methods.R |only treeman-1.1/treeman/tests/testthat/test-get-nds-methods.R |only treeman-1.1/treeman/tests/testthat/test-get-spcl-methods.R |only treeman-1.1/treeman/tests/testthat/test-manip-methods.R | 144 ++- treeman-1.1/treeman/tests/testthat/test-ndlst-methods.R |only treeman-1.1/treeman/tests/testthat/test-ndmtrx-methods.R |only treeman-1.1/treeman/tests/testthat/test-node.R | 18 treeman-1.1/treeman/tests/testthat/test-rw-methods.R | 118 ++ treeman-1.1/treeman/tests/testthat/test-set-methods.R | 53 - treeman-1.1/treeman/tests/testthat/test-treeman.R | 5 treeman-1.1/treeman/tests/testthat/test-treemen.R | 5 treeman-1.1/treeman/tests/testthat/test-update-methods.R | 141 --- treeman-1.1/treeman/tests/testthat/test_server_methods.R |only 144 files changed, 2272 insertions(+), 1510 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 1.9-9 dated 2016-09-25 and 2.0-0 dated 2017-06-22
metafor-1.9-9/metafor/R/head_tail.list.rma.r |only metafor-1.9-9/metafor/R/print.escalc.r |only metafor-1.9-9/metafor/R/print.list.rma.r |only metafor-1.9-9/metafor/R/ranef.r |only metafor-1.9-9/metafor/R/summary.escalc.r |only metafor-1.9-9/metafor/inst/doc/metafor_diagram.pdf |only metafor-1.9-9/metafor/inst/doc/metafor_diagram.pdf.asis |only metafor-1.9-9/metafor/tests/testthat/test_misc_head_tail_list_rma.r |only metafor-1.9-9/metafor/vignettes/metafor_diagram.pdf.asis |only metafor-2.0-0/metafor/DESCRIPTION | 12 metafor-2.0-0/metafor/MD5 | 474 ++-- metafor-2.0-0/metafor/NAMESPACE | 9 metafor-2.0-0/metafor/NEWS | 91 metafor-2.0-0/metafor/R/AIC.rma.r | 2 metafor-2.0-0/metafor/R/BIC.rma.r | 2 metafor-2.0-0/metafor/R/addpoly.default.r | 14 metafor-2.0-0/metafor/R/addpoly.rma.r | 4 metafor-2.0-0/metafor/R/anova.rma.r | 45 metafor-2.0-0/metafor/R/baujat.rma.r | 26 metafor-2.0-0/metafor/R/blup.rma.uni.r | 15 metafor-2.0-0/metafor/R/coef.permutest.rma.uni.r | 2 metafor-2.0-0/metafor/R/coef.rma.r | 13 metafor-2.0-0/metafor/R/coef.summary.rma.r | 14 metafor-2.0-0/metafor/R/confint.rma.mh.r | 16 metafor-2.0-0/metafor/R/confint.rma.mv.r | 38 metafor-2.0-0/metafor/R/confint.rma.peto.r | 16 metafor-2.0-0/metafor/R/confint.rma.uni.r | 64 metafor-2.0-0/metafor/R/cooks.distance.rma.mv.r | 15 metafor-2.0-0/metafor/R/cooks.distance.rma.uni.r | 19 metafor-2.0-0/metafor/R/cumul.rma.mh.r | 28 metafor-2.0-0/metafor/R/cumul.rma.peto.r | 28 metafor-2.0-0/metafor/R/cumul.rma.uni.r | 34 metafor-2.0-0/metafor/R/deviance.rma.r | 2 metafor-2.0-0/metafor/R/df.residual.rma.r | 2 metafor-2.0-0/metafor/R/dfbetas.rma.uni.r | 26 metafor-2.0-0/metafor/R/escalc.default.r | 301 ++- metafor-2.0-0/metafor/R/escalc.formula.r | 17 metafor-2.0-0/metafor/R/fitstats.rma.r | 2 metafor-2.0-0/metafor/R/fitted.rma.r | 20 metafor-2.0-0/metafor/R/forest.cumul.rma.r | 17 metafor-2.0-0/metafor/R/forest.default.r | 25 metafor-2.0-0/metafor/R/forest.rma.r | 96 metafor-2.0-0/metafor/R/fsn.r | 4 metafor-2.0-0/metafor/R/funnel.default.r | 67 metafor-2.0-0/metafor/R/funnel.rma.r | 55 metafor-2.0-0/metafor/R/gosh.rma.r | 64 metafor-2.0-0/metafor/R/hatvalues.rma.mv.r | 6 metafor-2.0-0/metafor/R/hatvalues.rma.uni.r | 6 metafor-2.0-0/metafor/R/hc.rma.uni.r | 37 metafor-2.0-0/metafor/R/influence.rma.uni.r | 34 metafor-2.0-0/metafor/R/labbe.rma.r | 12 metafor-2.0-0/metafor/R/leave1out.rma.mh.r | 28 metafor-2.0-0/metafor/R/leave1out.rma.peto.r | 28 metafor-2.0-0/metafor/R/leave1out.rma.uni.r | 34 metafor-2.0-0/metafor/R/llplot.r | 26 metafor-2.0-0/metafor/R/logLik.rma.r | 2 metafor-2.0-0/metafor/R/methods.escalc.r |only metafor-2.0-0/metafor/R/methods.list.rma.r |only metafor-2.0-0/metafor/R/misc.func.exported.r | 147 - metafor-2.0-0/metafor/R/misc.func.hidden.r | 846 +++++++- metafor-2.0-0/metafor/R/model.matrix.rma.r | 15 metafor-2.0-0/metafor/R/permutest.rma.uni.r | 70 metafor-2.0-0/metafor/R/plot.cumul.rma.r | 2 metafor-2.0-0/metafor/R/plot.gosh.rma.r | 2 metafor-2.0-0/metafor/R/plot.infl.rma.uni.r | 4 metafor-2.0-0/metafor/R/plot.profile.rma.r | 24 metafor-2.0-0/metafor/R/plot.rma.uni.r | 6 metafor-2.0-0/metafor/R/predict.rma.r | 31 metafor-2.0-0/metafor/R/print.anova.rma.r | 4 metafor-2.0-0/metafor/R/print.gosh.rma.r |only metafor-2.0-0/metafor/R/print.hc.rma.uni.r | 2 metafor-2.0-0/metafor/R/print.permutest.rma.uni.r | 9 metafor-2.0-0/metafor/R/print.regtest.rma.r | 4 metafor-2.0-0/metafor/R/print.rma.glmm.r | 9 metafor-2.0-0/metafor/R/print.rma.mh.r | 21 metafor-2.0-0/metafor/R/print.rma.mv.r | 25 metafor-2.0-0/metafor/R/print.rma.peto.r | 14 metafor-2.0-0/metafor/R/print.rma.uni.r | 29 metafor-2.0-0/metafor/R/print.robust.rma.r | 13 metafor-2.0-0/metafor/R/profile.rma.mv.r | 75 metafor-2.0-0/metafor/R/profile.rma.uni.r | 28 metafor-2.0-0/metafor/R/qqnorm.rma.uni.r | 10 metafor-2.0-0/metafor/R/radial.rma.r | 33 metafor-2.0-0/metafor/R/ranef.rma.mv.r |only metafor-2.0-0/metafor/R/ranef.rma.uni.r | 15 metafor-2.0-0/metafor/R/ranktest.default.r |only metafor-2.0-0/metafor/R/ranktest.rma.r | 17 metafor-2.0-0/metafor/R/regtest.default.r |only metafor-2.0-0/metafor/R/regtest.rma.r | 14 metafor-2.0-0/metafor/R/residuals.rma.r | 89 metafor-2.0-0/metafor/R/rma.glmm.r | 172 - metafor-2.0-0/metafor/R/rma.mh.r | 214 +- metafor-2.0-0/metafor/R/rma.mv.r | 984 ++-------- metafor-2.0-0/metafor/R/rma.peto.r | 76 metafor-2.0-0/metafor/R/rma.uni.r | 806 +++++--- metafor-2.0-0/metafor/R/robust.rma.mv.r | 54 metafor-2.0-0/metafor/R/robust.rma.uni.r | 54 metafor-2.0-0/metafor/R/rstandard.rma.mh.r | 6 metafor-2.0-0/metafor/R/rstandard.rma.mv.r | 13 metafor-2.0-0/metafor/R/rstandard.rma.peto.r | 6 metafor-2.0-0/metafor/R/rstandard.rma.uni.r | 15 metafor-2.0-0/metafor/R/rstudent.rma.mh.r | 18 metafor-2.0-0/metafor/R/rstudent.rma.peto.r | 18 metafor-2.0-0/metafor/R/rstudent.rma.uni.r | 24 metafor-2.0-0/metafor/R/simulate.rma.r |only metafor-2.0-0/metafor/R/summary.rma.r | 2 metafor-2.0-0/metafor/R/to.long.r | 285 ++ metafor-2.0-0/metafor/R/to.table.r | 221 +- metafor-2.0-0/metafor/R/transf.r | 2 metafor-2.0-0/metafor/R/trimfill.rma.uni.r | 24 metafor-2.0-0/metafor/R/vcov.rma.r | 16 metafor-2.0-0/metafor/R/zzz.r | 2 metafor-2.0-0/metafor/README.md | 2 metafor-2.0-0/metafor/build/vignette.rds |binary metafor-2.0-0/metafor/data/dat.bangertdrowns2004.rda |binary metafor-2.0-0/metafor/data/dat.bcg.rda |binary metafor-2.0-0/metafor/data/dat.begg1989.rda |binary metafor-2.0-0/metafor/data/dat.berkey1998.rda |binary metafor-2.0-0/metafor/data/dat.bonett2010.rda |binary metafor-2.0-0/metafor/data/dat.bourassa1996.rda |binary metafor-2.0-0/metafor/data/dat.colditz1994.rda |binary metafor-2.0-0/metafor/data/dat.collins1985a.rda |binary metafor-2.0-0/metafor/data/dat.collins1985b.rda |binary metafor-2.0-0/metafor/data/dat.curtis1998.rda |binary metafor-2.0-0/metafor/data/dat.debruin2009.rda |binary metafor-2.0-0/metafor/data/dat.egger2001.rda |binary metafor-2.0-0/metafor/data/dat.fine1993.rda |binary metafor-2.0-0/metafor/data/dat.gibson2002.rda |binary metafor-2.0-0/metafor/data/dat.hackshaw1998.rda |binary metafor-2.0-0/metafor/data/dat.hart1999.rda |binary metafor-2.0-0/metafor/data/dat.hasselblad1998.rda |binary metafor-2.0-0/metafor/data/dat.hine1989.rda |binary metafor-2.0-0/metafor/data/dat.ishak2007.rda |binary metafor-2.0-0/metafor/data/dat.konstantopoulos2011.rda |binary metafor-2.0-0/metafor/data/dat.laopaiboon2015.rda |only metafor-2.0-0/metafor/data/dat.lee2004.rda |binary metafor-2.0-0/metafor/data/dat.li2007.rda |binary metafor-2.0-0/metafor/data/dat.linde2005.rda |binary metafor-2.0-0/metafor/data/dat.mcdaniel1994.rda |binary metafor-2.0-0/metafor/data/dat.molloy2014.rda |binary metafor-2.0-0/metafor/data/dat.nielweise2007.rda |binary metafor-2.0-0/metafor/data/dat.nielweise2008.rda |binary metafor-2.0-0/metafor/data/dat.normand1999.rda |binary metafor-2.0-0/metafor/data/dat.pagliaro1992.rda |only metafor-2.0-0/metafor/data/dat.pignon2000.rda |binary metafor-2.0-0/metafor/data/dat.pritz1997.rda |binary metafor-2.0-0/metafor/data/dat.raudenbush1985.rda |binary metafor-2.0-0/metafor/data/dat.riley2003.rda |binary metafor-2.0-0/metafor/data/dat.senn2013.rda |binary metafor-2.0-0/metafor/data/dat.yusuf1985.rda |binary metafor-2.0-0/metafor/inst/doc/diagram.pdf |only metafor-2.0-0/metafor/inst/doc/diagram.pdf.asis |only metafor-2.0-0/metafor/man/addpoly.default.Rd | 12 metafor-2.0-0/metafor/man/addpoly.rma.Rd | 10 metafor-2.0-0/metafor/man/anova.rma.Rd | 2 metafor-2.0-0/metafor/man/baujat.Rd | 3 metafor-2.0-0/metafor/man/blup.Rd | 12 metafor-2.0-0/metafor/man/coef.permutest.rma.uni.Rd | 2 metafor-2.0-0/metafor/man/coef.rma.Rd | 2 metafor-2.0-0/metafor/man/confint.rma.Rd | 2 metafor-2.0-0/metafor/man/cumul.Rd | 11 metafor-2.0-0/metafor/man/dat.colditz1994.Rd | 6 metafor-2.0-0/metafor/man/dat.curtis1998.Rd | 2 metafor-2.0-0/metafor/man/dat.fine1993.Rd | 6 metafor-2.0-0/metafor/man/dat.hasselblad1998.Rd | 2 metafor-2.0-0/metafor/man/dat.konstantopoulos2011.Rd | 4 metafor-2.0-0/metafor/man/dat.laopaiboon2015.Rd |only metafor-2.0-0/metafor/man/dat.lee2004.Rd | 2 metafor-2.0-0/metafor/man/dat.linde2005.Rd | 6 metafor-2.0-0/metafor/man/dat.pagliaro1992.Rd |only metafor-2.0-0/metafor/man/dat.pritz1997.Rd | 7 metafor-2.0-0/metafor/man/escalc.Rd | 171 + metafor-2.0-0/metafor/man/fitstats.Rd | 10 metafor-2.0-0/metafor/man/fitted.rma.Rd | 2 metafor-2.0-0/metafor/man/forest.cumul.rma.Rd | 9 metafor-2.0-0/metafor/man/forest.default.Rd | 15 metafor-2.0-0/metafor/man/forest.rma.Rd | 19 metafor-2.0-0/metafor/man/fsn.Rd | 4 metafor-2.0-0/metafor/man/funnel.Rd | 21 metafor-2.0-0/metafor/man/gosh.Rd | 3 metafor-2.0-0/metafor/man/hc.Rd | 2 metafor-2.0-0/metafor/man/influence.rma.uni.Rd | 6 metafor-2.0-0/metafor/man/labbe.Rd | 6 metafor-2.0-0/metafor/man/leave1out.Rd | 11 metafor-2.0-0/metafor/man/llplot.Rd | 3 metafor-2.0-0/metafor/man/metafor-package.Rd | 4 metafor-2.0-0/metafor/man/model.matrix.rma.Rd | 2 metafor-2.0-0/metafor/man/permutest.Rd | 2 metafor-2.0-0/metafor/man/plot.cumul.rma.Rd | 2 metafor-2.0-0/metafor/man/plot.infl.rma.uni.Rd | 2 metafor-2.0-0/metafor/man/plot.rma.Rd | 2 metafor-2.0-0/metafor/man/predict.rma.Rd | 17 metafor-2.0-0/metafor/man/print.escalc.Rd | 2 metafor-2.0-0/metafor/man/print.gosh.rma.Rd |only metafor-2.0-0/metafor/man/print.list.rma.Rd | 5 metafor-2.0-0/metafor/man/profile.rma.Rd | 5 metafor-2.0-0/metafor/man/qqnorm.rma.Rd | 2 metafor-2.0-0/metafor/man/radial.Rd | 6 metafor-2.0-0/metafor/man/ranef.Rd | 25 metafor-2.0-0/metafor/man/ranktest.Rd | 22 metafor-2.0-0/metafor/man/regtest.Rd | 48 metafor-2.0-0/metafor/man/residuals.rma.Rd | 24 metafor-2.0-0/metafor/man/rma.glmm.Rd | 6 metafor-2.0-0/metafor/man/rma.mh.Rd | 13 metafor-2.0-0/metafor/man/rma.mv.Rd | 4 metafor-2.0-0/metafor/man/rma.peto.Rd | 5 metafor-2.0-0/metafor/man/rma.uni.Rd | 13 metafor-2.0-0/metafor/man/robust.Rd | 4 metafor-2.0-0/metafor/man/simulate.rma.Rd |only metafor-2.0-0/metafor/man/transf.Rd | 10 metafor-2.0-0/metafor/man/trimfill.Rd | 4 metafor-2.0-0/metafor/man/update.rma.Rd | 2 metafor-2.0-0/metafor/man/vcov.rma.Rd | 4 metafor-2.0-0/metafor/man/weights.rma.Rd | 2 metafor-2.0-0/metafor/tests/testthat.R | 2 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_berkey1995.r | 7 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_dersimonian2007.r | 2 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_henmi2010.r | 4 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_jackson2014.r | 4 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_konstantopoulos2011.r | 29 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_law2016.r | 16 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_morris2008.r | 15 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_raudenbush2009.r | 8 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_vanhouwelingen1993.r | 21 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_vanhouwelingen2002.r | 6 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_viechtbauer2005.r | 20 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_viechtbauer2007b.r | 23 metafor-2.0-0/metafor/tests/testthat/test_analysis_example_yusuf1985.r | 1 metafor-2.0-0/metafor/tests/testthat/test_misc_anova.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_escalc.r | 59 metafor-2.0-0/metafor/tests/testthat/test_misc_fitstats.r | 2 metafor-2.0-0/metafor/tests/testthat/test_misc_fsn.r | 4 metafor-2.0-0/metafor/tests/testthat/test_misc_handling_of_edge_cases_due_to_zeros.r | 12 metafor-2.0-0/metafor/tests/testthat/test_misc_list_rma.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_metan_vs_rma.mh_with_dat.bcg.r | 6 metafor-2.0-0/metafor/tests/testthat/test_misc_metan_vs_rma.peto_with_dat.bcg.r | 2 metafor-2.0-0/metafor/tests/testthat/test_misc_metan_vs_rma.uni_with_dat.bcg.r | 66 metafor-2.0-0/metafor/tests/testthat/test_misc_predict.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_pub_bias.r | 16 metafor-2.0-0/metafor/tests/testthat/test_misc_residuals.r | 8 metafor-2.0-0/metafor/tests/testthat/test_misc_rma_glmm.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_rma_uni_ls.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_rma_vs_direct_computation.r | 6 metafor-2.0-0/metafor/tests/testthat/test_misc_setlab.r |only metafor-2.0-0/metafor/tests/testthat/test_misc_to_long_to_table.r | 8 metafor-2.0-0/metafor/tests/testthat/test_plots_caterpillar_plot.r |only metafor-2.0-0/metafor/tests/testthat/test_plots_cumulative_forest_plot.r | 14 metafor-2.0-0/metafor/tests/testthat/test_plots_forest_plot_with_subgroups.r | 32 metafor-2.0-0/metafor/tests/testthat/test_plots_gosh.r | 11 metafor-2.0-0/metafor/tests/testthat/test_plots_meta-analytic_scatterplot.r | 8 metafor-2.0-0/metafor/tests/testthat/test_plots_normal_qq_plots.r | 11 metafor-2.0-0/metafor/tests/testthat/test_plots_plot_of_cumulative_results.r | 2 metafor-2.0-0/metafor/tests/testthat/test_plots_plot_of_influence_diagnostics.r | 1 metafor-2.0-0/metafor/vignettes/diagram.pdf.asis |only 254 files changed, 4594 insertions(+), 2906 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-3 dated 2016-11-28 and 1.2-0 dated 2017-06-22
DESCRIPTION | 11 MD5 | 109 NAMESPACE | 2 R/AAA.R | 2 R/Confints.R | 18 R/ContingencyTests.R | 27 R/ContrastTest.R | 2 R/CorrelationTests.R | 16 R/ExactDistributions.R | 244 - R/IndependenceTest.R | 5 R/LocationTests.R | 24 R/MTP.R | 110 R/MarginalHomogeneityTests.R | 7 R/MaximallySelectedStatisticsTests.R | 7 R/Methods.R | 335 + R/MonteCarloDistributions.R | 13 R/ScaleTests.R | 24 R/SurvivalTests.R | 15 R/SymmetryTest.R | 3 R/SymmetryTests.R | 18 R/Transformations.R | 254 - R/helpers.R | 37 R/zAccess.R | 76 build/vignette.rds |binary inst/NEWS.Rd | 52 inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.pdf |binary inst/doc/coin_implementation.Rnw | 6 inst/doc/coin_implementation.pdf |binary man/CWD.Rd | 2 man/GTSG.Rd | 4 man/LocationTests.Rd | 61 man/NullDistribution-class.Rd | 16 man/PermutationDistribution-methods.Rd | 14 man/SurvivalTests.Rd | 113 man/SymmetryTests.Rd | 2 man/Transformations.Rd | 4 man/glioma.Rd | 4 man/hohnloser.Rd | 4 man/ocarcinoma.Rd | 4 man/photocar.Rd | 4 src/Helpers.c | 10 src/Makevars | 1 src/coin-init.c |only src/coin-win.def |only src/coin.h |only tests/Examples/coin-Ex.Rout.save | 5987 ++++++++++++++++----------------- tests/bugfixes.R | 52 tests/bugfixes.Rout.save | 77 tests/regtest_MTP.Rout.save | 8 tests/regtest_distribution.R | 348 + tests/regtest_distribution.Rout.save | 653 +++ tests/regtest_libcoin.R |only tests/regtest_libcoin.Rout.save |only tests/regtest_trafo.R | 23 tests/regtest_trafo.Rout.save | 38 vignettes/coin_implementation.Rnw | 6 58 files changed, 4805 insertions(+), 4047 deletions(-)
Title: IUCN Redlisting Tools
Description: Includes algorithms to facilitate the assessment of extinction
risk of species according to the IUCN (International Union for Conservation of
Nature, see <http://www.iucn.org> for more information) red list criteria.
Author: Pedro Cardoso
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between red versions 1.1.0 dated 2017-06-20 and 1.1.1 dated 2017-06-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 1 + R/red.R | 60 +++++++++++++++++++++++++++++++++++++++--------------------- man/aoo.Rd | 2 +- 5 files changed, 49 insertions(+), 30 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre],
Romain Francois [aut],
Lionel Henry [aut],
Kirill Müller [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.7.0 dated 2017-06-09 and 0.7.1 dated 2017-06-22
DESCRIPTION | 11 MD5 | 78 +++--- NAMESPACE | 2 NEWS.md | 20 + R/dataframe.R | 2 R/dplyr.r | 2 R/grouped-df.r | 2 R/src_dbi.R | 2 R/tbl-cube.r | 2 R/top-n.R | 11 README.md | 4 inst/doc/compatibility.html | 152 +++++++------ inst/doc/dplyr.html | 204 +++++++++-------- inst/doc/programming.R | 7 inst/doc/programming.Rmd | 15 - inst/doc/programming.html | 366 ++++++++++++++++---------------- inst/doc/two-table.html | 154 +++++++------ inst/doc/window-functions.html | 124 ++++++---- inst/include/dplyr/Result/LazySubsets.h | 6 inst/include/dplyr/Result/Rank.h | 9 inst/include/dplyr/bad.h | 18 - inst/include/dplyr_RcppExports.h | 2 inst/include/tools/utils.h | 4 src/between.cpp | 4 src/hybrid_count.cpp | 2 src/hybrid_in.cpp | 4 src/hybrid_minmax.cpp | 3 src/hybrid_nth.cpp | 2 src/hybrid_offset.cpp | 2 src/hybrid_simple.cpp | 2 src/hybrid_window.cpp | 8 src/rlang-export.c | 8 src/summarise.cpp | 2 src/utils.cpp | 16 + tests/testthat/helper-hybrid.R | 2 tests/testthat/test-equality.r | 2 tests/testthat/test-hybrid.R | 111 +++++++++ tests/testthat/test-mutate.r | 7 tests/testthat/test-select.r | 8 vignettes/programming.Rmd | 15 - 40 files changed, 841 insertions(+), 554 deletions(-)
Title: GUI for Cohen's and Fleiss' Kappa
Description: Offers a complete and interactive GUI to work out Cohen's and Fleiss' Kappa.
Author: Frederic Santos
Maintainer: Frederic Santos <frederic.santos@u-bordeaux.fr>
Diff between KappaGUI versions 1.2 dated 2015-03-26 and 1.2.1 dated 2017-06-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NAMESPACE | 2 ++ R/StartKappa.R | 4 ++-- man/KappaGUI-package.Rd | 8 +++----- 5 files changed, 16 insertions(+), 16 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 1.2.0 dated 2017-05-28 and 1.3.0 dated 2017-06-22
excerptr-1.2.0/excerptr/vignettes/excerptr_Introduction.md |only excerptr-1.3.0/excerptr/DESCRIPTION | 6 excerptr-1.3.0/excerptr/MD5 | 74 +++++----- excerptr-1.3.0/excerptr/NEWS.md | 18 +- excerptr-1.3.0/excerptr/R/excerptr-package.R | 6 excerptr-1.3.0/excerptr/R/excerptr.R | 13 - excerptr-1.3.0/excerptr/R/get_excerpts.R | 15 +- excerptr-1.3.0/excerptr/R/internals.R | 5 excerptr-1.3.0/excerptr/R/options.R | 6 excerptr-1.3.0/excerptr/R/utils.R | 7 excerptr-1.3.0/excerptr/README.md | 9 - excerptr-1.3.0/excerptr/inst/doc/excerptr_Introduction.Rmd | 2 excerptr-1.3.0/excerptr/inst/doc/excerptr_Introduction.html | 2 excerptr-1.3.0/excerptr/inst/excerpts/NEWS.rst |only excerptr-1.3.0/excerptr/inst/excerpts/codes_doxygen/main.py | 14 + excerptr-1.3.0/excerptr/inst/excerpts/codes_doxygen/op.py | 15 +- excerptr-1.3.0/excerptr/inst/excerpts/codes_doxygen/ui.py | 5 excerptr-1.3.0/excerptr/inst/excerpts/docs/doxygen/html/namespacemembers_func.html | 2 excerptr-1.3.0/excerptr/inst/excerpts/docs/excerpts.main.html | 14 + excerptr-1.3.0/excerptr/inst/excerpts/docs/excerpts.op.html | 5 excerptr-1.3.0/excerptr/inst/excerpts/docs/excerpts.ui.html | 5 excerptr-1.3.0/excerptr/inst/excerpts/excerpts.egg-info/PKG-INFO | 4 excerptr-1.3.0/excerptr/inst/excerpts/excerpts.egg-info/SOURCES.txt | 2 excerptr-1.3.0/excerptr/inst/excerpts/excerpts/main.py | 14 + excerptr-1.3.0/excerptr/inst/excerpts/excerpts/op.py | 9 - excerptr-1.3.0/excerptr/inst/excerpts/excerpts/ui.py | 5 excerptr-1.3.0/excerptr/inst/excerpts/setup.py | 4 excerptr-1.3.0/excerptr/inst/excerpts/tests/files/some_file.html |only excerptr-1.3.0/excerptr/inst/excerpts/tests/files/some_file.rst |only excerptr-1.3.0/excerptr/inst/excerpts/tests/test_basic.py | 34 ++++ excerptr-1.3.0/excerptr/inst/tests/testthat/test_basic.R | 25 +++ excerptr-1.3.0/excerptr/man/concatenate_python_codes.Rd | 3 excerptr-1.3.0/excerptr/man/construct_path.Rd | 7 excerptr-1.3.0/excerptr/man/excerptr-package.Rd | 8 - excerptr-1.3.0/excerptr/man/excerptr.Rd | 10 - excerptr-1.3.0/excerptr/man/get_excerpts.Rd | 16 +- excerptr-1.3.0/excerptr/man/get_excerpts_path.Rd | 8 - excerptr-1.3.0/excerptr/man/load_excerpts.Rd | 4 excerptr-1.3.0/excerptr/tests/testthat/test_basic.R | 25 +++ excerptr-1.3.0/excerptr/vignettes/excerptr_Introduction.Rmd | 2 40 files changed, 270 insertions(+), 133 deletions(-)
Title: An Implementation of Parsing and Writing Configuration File
(JSON/INI/YAML/TOML)
Description: Implements the JSON, INI, YAML and TOML parser for R setting and writing of configuration file. The functionality of this package is similar to that of package 'config'.
Author: Jianfeng Li [aut, cre]
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between configr versions 0.2.3 dated 2017-05-26 and 0.3.0 dated 2017-06-22
ChangeLog | 6 + DESCRIPTION | 11 +- MD5 | 39 +++++--- NAMESPACE | 1 R/configr.R | 2 R/parse.R | 72 ++++++++++++++- R/read.R | 10 +- R/utils.R | 6 - README.md | 193 ++++-------------------------------------- build |only inst/doc |only inst/extdata/config.ini | 5 + inst/extdata/config.json | 6 + inst/extdata/config.toml | 6 + inst/extdata/config.yaml | 5 + man/parse.extra.Rd | 18 +++ man/read.config.Rd | 8 + tests/testthat/test_k_parse.R | 111 +++++++++++++++--------- vignettes |only 19 files changed, 258 insertions(+), 241 deletions(-)
Title: Score Test Based on Saddlepoint Approximation
Description: Performs score test using saddlepoint approximation to estimate the null distribution.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>
Diff between SPAtest versions 1.1.0 dated 2017-03-30 and 1.1.1 dated 2017-06-22
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/ScoreTest_SPA.Rd | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Permutational Group Sequential Test for Time-to-Event Data
Description: Permutational group-sequential tests for time-to-event data based on the log-rank test statistic. Supports exact permutation test when the censoring distributions are equal in the treatment and the control group and approximate imputation-permutation methods when the censoring distributions are different.
Author: Matthias Brueckner [aut, cre],
Martin Posch [aut],
Franz Koenig [aut]
Maintainer: Matthias Brueckner <matthias.brueckner@posteo.de>
Diff between permGS versions 0.2.3 dated 2017-01-24 and 0.2.4 dated 2017-06-22
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- R/permLR.R | 4 ++-- man/createPermGS.Rd | 1 - man/exactLR.Rd | 1 - man/imputeHeinze.Rd | 1 - man/imputeIPT.Rd | 1 - man/imputeIPZ.Rd | 1 - man/nextStage.Rd | 1 - man/parseFormula.Rd | 1 - man/permGS.Rd | 7 +++---- man/permHeinze.Rd | 1 - man/permIPT.Rd | 1 - man/permIPZ.Rd | 1 - man/permLR.Rd | 1 - man/permuteHeinze.Rd | 1 - man/permuteIPT.Rd | 1 - man/permuteIPZ.Rd | 1 - man/sampleFromCondKM.Rd | 1 - man/sampleFromKM.Rd | 1 - man/shuffleBlock.Rd | 1 - man/summary.permGS.Rd | 1 - 22 files changed, 31 insertions(+), 50 deletions(-)
Title: Exploring Machine Learning Better, Together
Description: 'OpenML.org' is an online machine learning platform where
researchers can easily download and upload data sets, share machine learning
tasks and experiments and organize them online to work and collaborate more
effectively.
We provide an R interface to the OpenML REST API in order to download and
upload data sets, tasks, flows and runs, see <http://www.openml.org/guide>
for more information.
Author: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>,
Bernd Bischl <bernd_bischl@gmx.net>,
Dominik Kirchhoff <dom.kirchhoff@gmail.com>,
Michel Lang <michellang@gmail.com>,
Benjamin Hofner <benjamin.hofner@fau.de>,
Jakob Bossek <j.bossek@gmail.com>,
Pascal Kerschke <kerschke@uni-muenster.de>,
Joaquin Vanschoren <joaquin.vanschoren@gmail.com>
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between OpenML versions 1.3 dated 2017-03-30 and 1.4 dated 2017-06-22
DESCRIPTION | 10 +-- LICENSE | 3 - MD5 | 48 +++++++++--------- NAMESPACE | 7 ++ NEWS | 8 +++ R/OMLDataSet_Class.R | 10 +++ R/OMLRunParList_Class.R | 27 +++++++--- R/OMLTask_Class.R | 12 ++++ R/convertOMLMeasuresToMlr.R | 9 ++- R/convertOMLRunToBMR.R | 58 ++++++++++++---------- R/downloadOMLObject.R | 46 +++++++++-------- R/getOMLRun.R | 110 +++++++++++++++++++++---------------------- R/helpers.R | 35 +++++++------ R/listOMLRunEvaluations.R | 57 ++++++++++++---------- R/listOMLRuns.R | 12 ++-- R/zzz.R | 2 build/vignette.rds |binary inst/CITATION | 15 +++-- inst/doc/OpenML.html.asis | 4 - man/convertOMLRunToBMR.Rd | 3 - man/downloadOMLObject.Rd | 6 +- man/getOMLRun.Rd | 5 + man/listOMLRunEvaluations.Rd | 29 +++++++---- man/listOMLRuns.Rd | 14 ++--- vignettes/OpenML.html.asis | 4 - 25 files changed, 313 insertions(+), 221 deletions(-)
Title: Direct, Chain and Average Equating Coefficients with Standard
Errors Using IRT Methods
Description: Computation of direct, chain and average (bisector) equating coefficients with standard errors using Item Response Theory (IRT) methods for dichotomous items. Test scoring can be performed by true score equating and observed score equating methods.
Author: Michela Battauz
Maintainer: Michela Battauz <michela.battauz@uniud.it>
Diff between equateIRT versions 2.0-2 dated 2017-03-30 and 2.0-3 dated 2017-06-22
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/functions.r | 27 +++++++++++++++++++++------ inst/NEWS | 5 ++--- inst/doc/equateIRT_paper.pdf |binary inst/doc/equateIRT_tutorial.R | 15 +++++++-------- inst/doc/equateIRT_tutorial.Rmd | 15 +++++++-------- inst/doc/equateIRT_tutorial.html | 15 +++++++-------- man/bisectorec.Rd | 12 ++++++------ man/chainec.Rd | 13 +++++++------ man/convert.Rd | 4 ++-- man/direc.Rd | 20 ++++++++++++++------ man/eqc.Rd | 6 +++--- man/equateIRT-package.Rd | 4 ++-- man/itm.Rd | 6 +++--- man/score.Rd | 8 ++++---- vignettes/equateIRT_tutorial.Rmd | 15 +++++++-------- 17 files changed, 112 insertions(+), 93 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.8-2 dated 2017-05-09 and 2.8-3 dated 2017-06-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/multiconstrained.R | 9 +++++---- inst/ChangeLog | 10 ++++++++++ inst/etc/BiodiversityGUI.R | 44 ++++++++++++++++++++++---------------------- man/multiconstrained.Rd | 8 ++++---- 6 files changed, 50 insertions(+), 39 deletions(-)
Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up
to nanosecond granularity is provided, with easy transition to and from the
standard 'POSIXct' type.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.1.2 dated 2017-03-27 and 0.2.0 dated 2017-06-22
nanotime-0.1.2/nanotime/build |only nanotime-0.1.2/nanotime/man/nanotime-package.Rd |only nanotime-0.2.0/nanotime/ChangeLog | 97 ++++ nanotime-0.2.0/nanotime/DESCRIPTION | 14 nanotime-0.2.0/nanotime/MD5 | 24 - nanotime-0.2.0/nanotime/NAMESPACE | 52 +- nanotime-0.2.0/nanotime/R/nanotime.R | 487 +++++++++++++++++++----- nanotime-0.2.0/nanotime/README.md | 5 nanotime-0.2.0/nanotime/inst/NEWS.Rd | 18 nanotime-0.2.0/nanotime/inst/unitTests |only nanotime-0.2.0/nanotime/man/nanotime.Rd | 169 ++++++-- nanotime-0.2.0/nanotime/tests/runTests.R |only nanotime-0.2.0/nanotime/tests/simpleTests.R | 4 13 files changed, 702 insertions(+), 168 deletions(-)
Title: Interactive Interfaces for Results Exploration
Description: Shiny interfaces and graphical functions for multivariate analysis results exploration.
Author: Julien Barnier [aut, cre]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between explor versions 0.3.1 dated 2016-12-15 and 0.3.2 dated 2017-06-22
DESCRIPTION | 10 MD5 | 56 +- NEWS | 9 R/MCA_plots.R | 16 R/PCA_plots.R | 16 R/explor_multi.R | 54 ++ R/explor_multi_CA.R | 7 R/explor_multi_MCA.R | 35 + R/explor_multi_PCA.R | 39 + R/prepare_results_CA.R | 2 R/prepare_results_MCA.R | 2 R/prepare_results_PCA.R | 26 - build/vignette.rds |binary inst/doc/introduction_en.html | 689 ++++++++++++++++++------------ inst/doc/introduction_fr.html | 714 +++++++++++++++++++------------- inst/po/en@quot/LC_MESSAGES/R-explor.mo |binary inst/po/fr/LC_MESSAGES/R-explor.mo |binary man/CA_var_plot.Rd | 1 man/MCA_ind_plot.Rd | 16 man/MCA_var_plot.Rd | 1 man/PCA_ind_plot.Rd | 10 man/PCA_var_plot.Rd | 1 man/explor.Rd | 16 man/ggind.Rd | 1 man/ggvar.Rd | 7 man/prepare_results.Rd | 54 +- po/R-explor.pot | 18 po/R-fr.mo |binary po/R-fr.po | 18 29 files changed, 1117 insertions(+), 701 deletions(-)
Title: A Null Model Adapted to Abundance Class Data in Ecology
Description: A null model randomizing semi-quantitative multi-classes (or ordinal) data by swapping sub-matrices while both the row and the column marginal sums are held constant.
Author: Benjamin Borgy, Remi Perronne, Xavier Reboud
Maintainer: Benjamin Borgy <benjamin.borgy@gmail.com>
Diff between swapClass versions 1.0 dated 2017-06-20 and 1.0.1 dated 2017-06-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/code_file.R | 2 +- man/swapClass-package.Rd | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Diagnostic and Prognostic Meta-Analysis
Description: Meta-analysis of diagnostic and prognostic modeling studies. Summarize estimates of diagnostic test accuracy and prediction model performance. Validate, update and combine published prediction models.
Author: Thomas Debray
Maintainer: Thomas Debray <thomas.debray@gmail.com>
Diff between metamisc versions 0.1.4 dated 2017-03-31 and 0.1.5 dated 2017-06-22
DESCRIPTION | 16 - MD5 | 38 +-- NAMESPACE | 9 R/basics.r | 79 +++--- R/bugsmodels.r | 2 R/riley.r | 604 ++++++++++++++++++++++++------------------------ R/uvmeta.r | 205 ++++------------ R/valmeta.r | 349 +++++++++++++++------------ data/Collins.rda |binary data/DVTipd.rda |binary data/DVTmodels.rda |binary data/Daniels.rda |binary data/EuroSCORE.rda |binary data/Framingham.rda |binary data/Kertai.rda |binary data/Roberts.rda |binary data/Scheidler.rda |binary man/metamisc-package.Rd | 6 man/uvmeta.Rd | 37 +- man/valmeta.Rd | 83 +++--- 20 files changed, 702 insertions(+), 726 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre],
Blake LeBaron [ctb] (BDS test code)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-41 dated 2017-05-29 and 0.10-42 dated 2017-06-22
ChangeLog | 31 +++++++++++++++++++------------ DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/finance.R | 4 ++-- 4 files changed, 27 insertions(+), 20 deletions(-)