Title: Extracts Sentiment and Sentiment-Derived Plot Arcs from Text
Description: Extracts sentiment and sentiment-derived plot arcs
from text using three sentiment dictionaries conveniently
packaged for consumption by R users. Implemented dictionaries include
"syuzhet" (default) developed in the Nebraska Literary Lab
"afinn" developed by Finn {\AA}rup Nielsen, "bing" developed by Minqing Hu
and Bing Liu, and "nrc" developed by Mohammad, Saif M. and Turney, Peter D.
Applicable references are available in README.md and in the documentation
for the "get_sentiment" function. The package also provides a hack for
implementing Stanford's coreNLP sentiment parser. The package provides
several methods for plot arc normalization.
Author: Matthew Jockers [aut, cre]
Maintainer: Matthew Jockers <mjockers@gmail.com>
Diff between syuzhet versions 0.2.0 dated 2015-02-21 and 1.0.0 dated 2016-04-27
DESCRIPTION | 30 +- MD5 | 49 ++-- NAMESPACE | 10 R/sysdata.rda |binary R/syuzhet.R | 267 +++++++++++++++++------- README.md | 18 - build/vignette.rds |binary inst/CITATION | 2 inst/doc/syuzhet-vignette.R | 203 +++++++++++++++--- inst/doc/syuzhet-vignette.Rmd | 279 ++++++++++++++++++++----- inst/doc/syuzhet-vignette.html | 447 ++++++++++++++++++++++++++--------------- inst/extdata/bovary.txt |only man/get_dct_transform.Rd |only man/get_nrc_sentiment.Rd | 5 man/get_nrc_values.Rd | 2 man/get_percentage_values.Rd | 7 man/get_sent_values.Rd | 6 man/get_sentences.Rd | 8 man/get_sentiment.Rd | 9 man/get_stanford_sentiment.Rd | 15 - man/get_text_as_string.Rd | 2 man/get_tokens.Rd |only man/get_transformed_values.Rd | 29 +- man/rescale.Rd | 2 man/rescale_x_2.Rd |only man/simple_plot.Rd |only tests/testthat/test-reading.R | 3 vignettes/syuzhet-vignette.Rmd | 279 ++++++++++++++++++++----- 28 files changed, 1203 insertions(+), 469 deletions(-)
Title: A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler'
Permissions Checker
Description: Provides functions to download and parse 'robots.txt' files.
Ultimately the package makes it easy to check if bots
(spiders, scrapers, ...) are allowed to access specific
resources on a domain.
Author: Peter Meissner [aut, cre],
Oliver Keys [ctb],
Rich Fitz John [ctb]
Maintainer: Peter Meissner <retep.meissner@gmail.com>
Diff between robotstxt versions 0.1.2 dated 2016-02-08 and 0.3.2 dated 2016-04-27
DESCRIPTION | 35 +-- MD5 | 39 +-- NAMESPACE | 2 NEWS |only R/parse_robotstxt.R | 47 +++- R/permissions.R | 358 +++++++++++++++++------------- R/robotstxt.R | 212 +++++++++--------- README.md | 92 ++++++- build/vignette.rds |binary inst/doc/using_robotstxt.R | 77 +++--- inst/doc/using_robotstxt.Rmd | 249 +++++++++++---------- inst/doc/using_robotstxt.html | 462 +++++++++++++++++++++++++--------------- man/get_robotstxt.Rd | 5 man/guess_domain.Rd |only man/paths_allowed.Rd | 14 - man/print.robotstxt.Rd |only man/print.robotstxt_text.Rd | 2 man/remove_domain.Rd |only man/robotstxt.Rd | 60 ++--- man/rt_cache.Rd |only tests/testthat/test_parser.R | 26 +- tests/testthat/test_robotstxt.R | 25 +- vignettes/using_robotstxt.Rmd | 249 +++++++++++---------- 23 files changed, 1144 insertions(+), 810 deletions(-)
Title: Parametric Linkage Analysis in R
Description: Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.
Author: Magnus Dehli Vigeland
Maintainer: Magnus Dehli Vigeland <magnusdv@studmed.uio.no>
Diff between paramlink versions 0.9-7 dated 2015-07-03 and 0.9-8 dated 2016-04-27
DESCRIPTION | 8 - MD5 | 32 ++-- NEWS | 8 + R/examineKinships.R | 58 -------- R/likelihood.R | 259 ++++++++++++++++++++++++++------------ R/linkageSim.R | 290 +++++++++++++++++++++---------------------- R/linkres.R | 173 +++++++++++++------------ R/markerSim.R | 3 R/modify.R | 31 ++++ R/oneMarkerDistribution.R | 12 + R/plot.linkdat.R | 136 +++++++++++--------- R/relationLR.R | 57 ++++---- R/twoMarkerDistribution.R | 51 +++++-- R/utils.R | 27 ++-- R/write.linkdat.R | 124 +++++++++--------- man/modify.Rd | 21 ++- man/twoMarkerDistribution.Rd | 9 + 17 files changed, 716 insertions(+), 583 deletions(-)
Title: Multiple Comparisons Procedures Based on Studentized Midrange
and Range Distributions
Description: Apply tests of multiple comparisons based on studentized midrange
and range distributions. The tests are: Tukey Midrange test, Student-Newman-
Keuls Midrange test, Skott-Knott Midrange test and Skott-Knott Range test.
Author: Ben Deivide [aut, cre],
Daniel Furtado [aut]
Maintainer: Ben Deivide <ben.deivide@gmail.com>
Diff between midrangeMCP versions 1.1 dated 2016-02-21 and 1.2 dated 2016-04-27
DESCRIPTION | 8 MD5 | 12 R/MRtest.R | 854 +++++++++++++++++++++++++++++------------------------------ R/SKMtest.R | 147 +++++----- R/SKRtest.R | 30 +- R/SNKMtest.R | 26 + R/TMtest.R | 54 ++- 7 files changed, 615 insertions(+), 516 deletions(-)
Title: An Introduction to Statistical Modeling of Extreme Values
Description: Functions to support the computations carried out in
`An Introduction to Statistical Modeling of Extreme Values' by
Stuart Coles. The functions may be divided into the following
groups; maxima/minima, order statistics, peaks over thresholds
and point processes.
Author: Original S functions written by Janet E. Heffernan with R port and R
documentation provided by Alec G. Stephenson.
Maintainer: Eric Gilleland <ericg@ucar.edu>
Diff between ismev versions 1.40 dated 2014-12-24 and 1.41 dated 2016-04-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 7 +++++++ data/portpirie.rda |binary data/rain.rda |binary data/venice.rda |binary man/ismev.Rd | 16 ++++++++++++++++ 7 files changed, 33 insertions(+), 10 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 0.4 dated 2015-12-04 and 1.5 dated 2016-04-27
imputeTS-0.4/imputeTS/R/data.heating.R |only imputeTS-0.4/imputeTS/R/data.nh4.R |only imputeTS-0.4/imputeTS/R/vis.barMissing.R |only imputeTS-0.4/imputeTS/R/vis.imputations.R |only imputeTS-0.4/imputeTS/R/vis.missing.R |only imputeTS-0.4/imputeTS/data/heating.rda |only imputeTS-0.4/imputeTS/data/heatingComplete.rda |only imputeTS-0.4/imputeTS/data/nh4.rda |only imputeTS-0.4/imputeTS/data/nh4Complete.rda |only imputeTS-0.4/imputeTS/inst |only imputeTS-0.4/imputeTS/man/heating.Rd |only imputeTS-0.4/imputeTS/man/nh4.Rd |only imputeTS-0.4/imputeTS/man/vis.barMissing.Rd |only imputeTS-0.4/imputeTS/man/vis.imputations.Rd |only imputeTS-0.4/imputeTS/man/vis.missing.Rd |only imputeTS-1.5/imputeTS/DESCRIPTION | 12 +- imputeTS-1.5/imputeTS/MD5 | 94 +++++++++++--------- imputeTS-1.5/imputeTS/NAMESPACE | 12 +- imputeTS-1.5/imputeTS/NEWS | 44 +++++++++ imputeTS-1.5/imputeTS/R/imputeTS-package.R | 21 +++- imputeTS-1.5/imputeTS/R/int.algoInterface.R | 21 ++-- imputeTS-1.5/imputeTS/R/int.preCheck.R | 27 ++--- imputeTS-1.5/imputeTS/R/na.interpolation.R | 39 ++++---- imputeTS-1.5/imputeTS/R/na.kalman.R |only imputeTS-1.5/imputeTS/R/na.locf.R | 39 ++++---- imputeTS-1.5/imputeTS/R/na.ma.R |only imputeTS-1.5/imputeTS/R/na.mean.R | 32 +++--- imputeTS-1.5/imputeTS/R/na.random.R | 32 +++--- imputeTS-1.5/imputeTS/R/na.remove.R | 34 +++---- imputeTS-1.5/imputeTS/R/na.replace.R | 33 +++---- imputeTS-1.5/imputeTS/R/na.seadec.R | 48 ++++------ imputeTS-1.5/imputeTS/R/na.seasplit.R | 50 +++++----- imputeTS-1.5/imputeTS/R/plotNA.distribution.R |only imputeTS-1.5/imputeTS/R/plotNA.distributionBar.R |only imputeTS-1.5/imputeTS/R/plotNA.gapsize.R |only imputeTS-1.5/imputeTS/R/plotNA.imputations.R |only imputeTS-1.5/imputeTS/R/statsNA.R |only imputeTS-1.5/imputeTS/R/tsAirgap.R |only imputeTS-1.5/imputeTS/R/tsAirgapComplete.R |only imputeTS-1.5/imputeTS/R/tsHeating.R |only imputeTS-1.5/imputeTS/R/tsHeatingComplete.R |only imputeTS-1.5/imputeTS/R/tsNH4.R |only imputeTS-1.5/imputeTS/R/tsNH4Complete.R |only imputeTS-1.5/imputeTS/README.md |only imputeTS-1.5/imputeTS/data/tsAirgap.rda |only imputeTS-1.5/imputeTS/data/tsAirgapComplete.rda |only imputeTS-1.5/imputeTS/data/tsHeating.rda |only imputeTS-1.5/imputeTS/data/tsHeatingComplete.rda |only imputeTS-1.5/imputeTS/data/tsNH4.rda |only imputeTS-1.5/imputeTS/data/tsNH4Complete.rda |only imputeTS-1.5/imputeTS/man/imputeTS-package.Rd | 22 +++- imputeTS-1.5/imputeTS/man/na.interpolation.Rd | 27 ++--- imputeTS-1.5/imputeTS/man/na.kalman.Rd |only imputeTS-1.5/imputeTS/man/na.locf.Rd | 29 ++---- imputeTS-1.5/imputeTS/man/na.ma.Rd |only imputeTS-1.5/imputeTS/man/na.mean.Rd | 23 ++-- imputeTS-1.5/imputeTS/man/na.random.Rd | 25 ++--- imputeTS-1.5/imputeTS/man/na.remove.Rd | 25 ++--- imputeTS-1.5/imputeTS/man/na.replace.Rd | 24 ++--- imputeTS-1.5/imputeTS/man/na.seadec.Rd | 34 +++---- imputeTS-1.5/imputeTS/man/na.seasplit.Rd | 34 +++---- imputeTS-1.5/imputeTS/man/plotNA.distribution.Rd |only imputeTS-1.5/imputeTS/man/plotNA.distributionBar.Rd |only imputeTS-1.5/imputeTS/man/plotNA.gapsize.Rd |only imputeTS-1.5/imputeTS/man/plotNA.imputations.Rd |only imputeTS-1.5/imputeTS/man/statsNA.Rd |only imputeTS-1.5/imputeTS/man/tsAirgap.Rd |only imputeTS-1.5/imputeTS/man/tsAirgapComplete.Rd |only imputeTS-1.5/imputeTS/man/tsHeating.Rd |only imputeTS-1.5/imputeTS/man/tsHeatingComplete.Rd |only imputeTS-1.5/imputeTS/man/tsNH4.Rd |only imputeTS-1.5/imputeTS/man/tsNH4Complete.Rd |only 72 files changed, 434 insertions(+), 347 deletions(-)
Title: Generalized Competing Event Model
Description: Generalized competing event model based on Cox PH model and Fine-Gray model.
This function is designed to develop optimized risk-stratification methods for competing
risks data, such as described in:
1. Carmona R, Gulaya S, Murphy JD, Rose BS, Wu J, Noticewala S,McHale MT, Yashar CM, Vaida F,
and Mell LK.(2014) <DOI:10.1016/j.ijrobp.2014.03.047>. Validated competing event model for thestage I-II
endometrial cancer population. Int J Radiat Oncol Biol Phys.89:888-98.
2. Carmona R, Zakeri K, Green G, Hwang L, Gulaya S, Xu B, Verma R, Williamson CW, Triplett DP, Rose
BS, Shen H, Vaida F, Murphy JD, and Mell LK.(2016) <DOI:10.1200/JCO.2015.65.0739>. Improved method to stratify
elderly cancer patients at risk for competing events. J Clin Oncol.in press.
Author: Hanjie Shen <has072@ucsd.edu>, Ruben Carmona
<ruben.carmona13@gmail.com>, Loren Mell <lmell@ucsd.edu>
Maintainer: Hanjie Shen <shenhanjie0418@gmail.com>
Diff between gcerisk versions 16.1.2 dated 2016-03-04 and 16.1.3 dated 2016-04-27
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- R/gcecox.R | 4 ++-- R/gcefg.R | 4 ++-- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Functions for Time Series Analysis
Description: Includes non-parametric estimators and tests for time series analysis. The functions are to test for presence of possibly non-monotonic trends and for synchronism of trends in multiple time series, using modern bootstrap techniques and robust non-parametric difference-based estimators.
Author: Vyacheslav Lyubchich;
Yulia R. Gel;
Xingyu Wang;
Calvin Chu
Maintainer: Vyacheslav Lyubchich <lyubchic@umces.edu>
Diff between funtimes versions 2.1 dated 2016-01-16 and 2.2 dated 2016-04-27
funtimes-2.1/funtimes/R/i.tails.R |only funtimes-2.1/funtimes/R/q.tails.R |only funtimes-2.1/funtimes/man/i.tails.Rd |only funtimes-2.1/funtimes/man/q.tails.Rd |only funtimes-2.2/funtimes/DESCRIPTION | 8 ++++---- funtimes-2.2/funtimes/MD5 | 6 +----- 6 files changed, 5 insertions(+), 9 deletions(-)
Title: Multivariate Sensitivity Analysis
Description: Functions to perform sensitivity analysis on a model with multivariate output.
Author: Caroline Bidot <caroline.bidot@jouy.inra.fr>, Matieyendou Lamboni <clamboni@yahoo.fr>, Hervé Monod <herve.monod@jouy.inra.fr>
Maintainer: Caroline Bidot <caroline.bidot@jouy.inra.fr>
Diff between multisensi versions 1.0-8 dated 2015-02-17 and 2.0 dated 2016-04-27
multisensi-1.0-8/multisensi/R/acp.r |only multisensi-1.0-8/multisensi/R/anoasg.r |only multisensi-1.0-8/multisensi/R/anovadec.r |only multisensi-1.0-8/multisensi/R/asg.r |only multisensi-1.0-8/multisensi/data/plan.rda |only multisensi-1.0-8/multisensi/man/acp.Rd |only multisensi-1.0-8/multisensi/man/anoasg.Rd |only multisensi-1.0-8/multisensi/man/anovadec.Rd |only multisensi-1.0-8/multisensi/man/asg.Rd |only multisensi-1.0-8/multisensi/man/plan.Rd |only multisensi-2.0/multisensi/DESCRIPTION | 17 - multisensi-2.0/multisensi/MD5 | 123 ++++--- multisensi-2.0/multisensi/NAMESPACE | 8 multisensi-2.0/multisensi/NEWS | 20 - multisensi-2.0/multisensi/R/analysis.anoasg.r |only multisensi-2.0/multisensi/R/analysis.sensitivity.r |only multisensi-2.0/multisensi/R/basis.ACP.r |only multisensi-2.0/multisensi/R/basis.bsplines.r |only multisensi-2.0/multisensi/R/basis.mine.r |only multisensi-2.0/multisensi/R/basis.osplines.r |only multisensi-2.0/multisensi/R/basis.poly.r |only multisensi-2.0/multisensi/R/biomasse.r | 33 ++ multisensi-2.0/multisensi/R/dynsi.r | 104 +++--- multisensi-2.0/multisensi/R/fctspline.jbrf.r |only multisensi-2.0/multisensi/R/graph.bar.r | 51 ++- multisensi-2.0/multisensi/R/graph.pc.r | 119 ++++++- multisensi-2.0/multisensi/R/grpe.gsi.r | 37 ++ multisensi-2.0/multisensi/R/gsi.r | 138 +++----- multisensi-2.0/multisensi/R/multisensi.r |only multisensi-2.0/multisensi/R/multivar.r |only multisensi-2.0/multisensi/R/planfact.as.r | 37 ++ multisensi-2.0/multisensi/R/planfact.r | 37 ++ multisensi-2.0/multisensi/R/plot.dynsi.r | 206 +++++++++++-- multisensi-2.0/multisensi/R/plot.gsi.r | 73 +++- multisensi-2.0/multisensi/R/predict.gsi.r |only multisensi-2.0/multisensi/R/print.dynsi.r | 39 ++ multisensi-2.0/multisensi/R/print.gsi.r | 41 ++ multisensi-2.0/multisensi/R/quality.r | 104 ++++-- multisensi-2.0/multisensi/R/simulmodel.r | 36 ++ multisensi-2.0/multisensi/R/summary.dynsi.r | 41 ++ multisensi-2.0/multisensi/R/summary.gsi.r | 41 ++ multisensi-2.0/multisensi/R/yapprox.r | 72 +++- multisensi-2.0/multisensi/build |only multisensi-2.0/multisensi/data/biomasseX.rda |only multisensi-2.0/multisensi/inst/doc/multisensi-manual.pdf |binary multisensi-2.0/multisensi/inst/doc/multisensi-vignette.R |only multisensi-2.0/multisensi/inst/doc/multisensi-vignette.pdf |only multisensi-2.0/multisensi/inst/doc/multisensi-vignette.rnw |only multisensi-2.0/multisensi/man/analysis.anoasg.Rd |only multisensi-2.0/multisensi/man/analysis.sensitivity.Rd |only multisensi-2.0/multisensi/man/basis.ACP.Rd |only multisensi-2.0/multisensi/man/basis.bsplines.Rd |only multisensi-2.0/multisensi/man/basis.mine.Rd |only multisensi-2.0/multisensi/man/basis.osplines.Rd |only multisensi-2.0/multisensi/man/basis.poly.Rd |only multisensi-2.0/multisensi/man/biomasse.Rd | 8 multisensi-2.0/multisensi/man/biomasseX.Rd |only multisensi-2.0/multisensi/man/biomasseY.Rd | 2 multisensi-2.0/multisensi/man/bspline.Rd |only multisensi-2.0/multisensi/man/dynsi.Rd | 41 +- multisensi-2.0/multisensi/man/graph.bar.Rd | 7 multisensi-2.0/multisensi/man/graph.pc.Rd | 24 - multisensi-2.0/multisensi/man/grpe.gsi.Rd | 5 multisensi-2.0/multisensi/man/gsi.Rd | 12 multisensi-2.0/multisensi/man/multisensi-package.Rd | 39 +- multisensi-2.0/multisensi/man/multisensi.Rd |only multisensi-2.0/multisensi/man/multivar.Rd |only multisensi-2.0/multisensi/man/planfact.Rd | 5 multisensi-2.0/multisensi/man/planfact.as.Rd | 10 multisensi-2.0/multisensi/man/plot.dynsi.Rd | 22 - multisensi-2.0/multisensi/man/plot.gsi.Rd | 24 - multisensi-2.0/multisensi/man/predict.gsi.Rd |only multisensi-2.0/multisensi/man/print.dynsi.Rd | 4 multisensi-2.0/multisensi/man/print.gsi.Rd | 4 multisensi-2.0/multisensi/man/quality.Rd | 17 - multisensi-2.0/multisensi/man/sesBsplinesNORM.Rd |only multisensi-2.0/multisensi/man/sesBsplinesORTHONORM.Rd |only multisensi-2.0/multisensi/man/simulmodel.Rd | 15 multisensi-2.0/multisensi/man/summary.dynsi.Rd | 4 multisensi-2.0/multisensi/man/summary.gsi.Rd | 4 multisensi-2.0/multisensi/man/yapprox.Rd | 13 multisensi-2.0/multisensi/vignettes |only 82 files changed, 1190 insertions(+), 447 deletions(-)
Title: Computing Statistical Indices to Detect Answer Copying on
Multiple-Choice Tests
Description: Contains several IRT and non-IRT based statistical indices proposed in the literature for detecting answer copying on multiple-choice examinations. Includes the indices that have been shown as effective and reliable based on the simulation studies. Provides results for the Omega index, Generalized Binomial Test, K index, K1 and K2 indices, and S1 and S2 indices.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>
Diff between CopyDetect versions 1.1 dated 2014-06-11 and 1.2 dated 2016-04-27
DESCRIPTION | 12 ++++++------ LICENSE |only MD5 | 15 ++++++++------- NAMESPACE | 4 +++- NEWS | 4 ++++ R/CopyDetect1.r | 8 ++++---- R/CopyDetect2.r | 8 ++++---- R/print.CopyDetect.r | 2 +- R/print.CopyDetect2.r | 2 +- 9 files changed, 31 insertions(+), 24 deletions(-)
Title: Send Messages, Images, R Objects and Files to 'Slack'
Channels/Users
Description: 'Slack' <http://slack.com/> provides a service for teams to
collaborate by sharing messages, images, links, files and more. Functions are provided
that make it possible to interact with the 'Slack' platform 'API'. When
you need to share information or data from R, rather than resort to copy/
paste in e-mails or other services like 'Skype' <http://www.skype.com/>, you
can use this package to send well-formatted output from multiple R objects and
expressions to all teammates at the same time with little effort. You can also
send images from the current graphics device, R objects (as RData), and upload
files.
Author: Bob Rudis [aut, cre], Jay Jacobs [ctb], David Severski [ctb],
Quinn Weber [ctb], Konrad Karczewski [ctb], Shinya Uryu [ctb],
Gregory Jefferis [ctb], Ed Niles [ctb], Rick Saporta [ctb]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between slackr versions 1.2 dated 2014-09-08 and 1.4.1 dated 2016-04-27
slackr-1.2/slackr/man/dev.slackr.Rd |only slackr-1.2/slackr/man/save.slackr.Rd |only slackr-1.2/slackr/man/slackrBot.Rd |only slackr-1.2/slackr/man/slackrChTrans.Rd |only slackr-1.2/slackr/man/slackrChannels.Rd |only slackr-1.2/slackr/man/slackrGroups.Rd |only slackr-1.2/slackr/man/slackrSetup.Rd |only slackr-1.2/slackr/man/slackrUpload.Rd |only slackr-1.2/slackr/man/slackrUsers.Rd |only slackr-1.4.1/slackr/DESCRIPTION | 39 - slackr-1.4.1/slackr/MD5 | 47 + slackr-1.4.1/slackr/NAMESPACE | 30 - slackr-1.4.1/slackr/NEWS |only slackr-1.4.1/slackr/R/dev_slackr.R |only slackr-1.4.1/slackr/R/gg_slackr.R |only slackr-1.4.1/slackr/R/save_slackr.R |only slackr-1.4.1/slackr/R/slackr-package.R | 28 - slackr-1.4.1/slackr/R/slackr.R | 522 ++++--------------- slackr-1.4.1/slackr/R/slackr_bot.r |only slackr-1.4.1/slackr/R/slackr_setup.r |only slackr-1.4.1/slackr/R/slackr_upload.R |only slackr-1.4.1/slackr/R/slackr_utils.R |only slackr-1.4.1/slackr/R/text_slackr.r |only slackr-1.4.1/slackr/R/zcamels.r |only slackr-1.4.1/slackr/README.md |only slackr-1.4.1/slackr/man/dev_slackr.Rd |only slackr-1.4.1/slackr/man/ggslackr.Rd | 24 slackr-1.4.1/slackr/man/save_slackr.Rd |only slackr-1.4.1/slackr/man/slackr-package.Rd | 24 slackr-1.4.1/slackr/man/slackr.Rd | 20 slackr-1.4.1/slackr/man/slackr_bot.Rd |only slackr-1.4.1/slackr/man/slackr_channels.Rd |only slackr-1.4.1/slackr/man/slackr_chtrans.Rd |only slackr-1.4.1/slackr/man/slackr_groups.Rd |only slackr-1.4.1/slackr/man/slackr_ims.Rd |only slackr-1.4.1/slackr/man/slackr_msg.Rd |only slackr-1.4.1/slackr/man/slackr_setup.Rd |only slackr-1.4.1/slackr/man/slackr_upload.Rd |only slackr-1.4.1/slackr/man/slackr_users.Rd |only slackr-1.4.1/slackr/man/text_slackr.Rd |only slackr-1.4.1/slackr/tests/testthat/test-textslackr.R |only 41 files changed, 270 insertions(+), 464 deletions(-)
Title: Structure for Organizing Monte Carlo Simulation Designs
Description: Provides tools to help safely and efficiently organize Monte Carlo simulations in R.
The package controls the structure and back-end of Monte Carlo simulations
by utilizing a general generate-analyse-summarise strategy. The functions provided control
common simulation issues such as re-simulating non-convergent results, support parallel
back-end and MPI distributed computations, save and restore temporary files,
aggregate results across independent nodes, and provide native support for debugging.
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between SimDesign versions 0.8 dated 2016-03-22 and 0.9 dated 2016-04-27
DESCRIPTION | 8 - MD5 | 26 ++--- NAMESPACE | 8 + R/SimDesign.R | 2 R/SimFunctions.R | 29 +++-- R/analysis.R | 19 ++- R/runSimulation.R | 216 ++++++++++++++++++++++++++++++++++--------- R/summary_functions.R | 14 ++ R/util.R | 4 build/vignette.rds |binary man/RMSE.Rd | 8 + man/SimFunctions.Rd | 17 +-- man/runSimulation.Rd | 59 ++++++++++- tests/tests/test-SimDesign.R | 36 +++++-- 14 files changed, 339 insertions(+), 107 deletions(-)
Title: Simulation Tools for Small Area Estimation
Description: Tools for the simulation of data in the context of small area
estimation. Combine all steps of your simulation - from data generation
over drawing samples to model fitting - in one object. This enables easy
modification and combination of different scenarios. You can store your
results in a folder or start the simulation in parallel.
Author: Sebastian Warnholz [aut, cre],
Timo Schmid [aut]
Maintainer: Sebastian Warnholz <Sebastian.Warnholz@fu-berlin.de>
Diff between saeSim versions 0.7.0 dated 2015-02-16 and 0.8.0 dated 2016-04-27
saeSim-0.7.0/saeSim/man/sim_read_data.Rd |only saeSim-0.8.0/saeSim/DESCRIPTION | 18 saeSim-0.8.0/saeSim/LICENSE | 676 -------- saeSim-0.8.0/saeSim/MD5 | 154 - saeSim-0.8.0/saeSim/NAMESPACE | 131 - saeSim-0.8.0/saeSim/NEWS | 219 +- saeSim-0.8.0/saeSim/R/00-pipe.R | 18 saeSim-0.8.0/saeSim/R/00-sim-lib.R | 34 saeSim-0.8.0/saeSim/R/01-as.data.frame.R | 28 saeSim-0.8.0/saeSim/R/01-autoplot.R | 90 - saeSim-0.8.0/saeSim/R/01-helper-lib.R | 8 saeSim-0.8.0/saeSim/R/01-plot.R | 44 saeSim-0.8.0/saeSim/R/01-select_cont.R | 28 saeSim-0.8.0/saeSim/R/01-show.R | 28 saeSim-0.8.0/saeSim/R/01-sim.R | 80 - saeSim-0.8.0/saeSim/R/01-sim_setup.R | 50 saeSim-0.8.0/saeSim/R/01-summary.R | 92 - saeSim-0.8.0/saeSim/R/03-agg.R | 92 - saeSim-0.8.0/saeSim/R/03-base-lib.R | 30 saeSim-0.8.0/saeSim/R/03-comp_var.R | 32 saeSim-0.8.0/saeSim/R/03-generator.R | 117 + saeSim-0.8.0/saeSim/R/03-sample.R | 166 +- saeSim-0.8.0/saeSim/R/03-sim_agg.R | 46 saeSim-0.8.0/saeSim/R/03-sim_base.R | 134 - saeSim-0.8.0/saeSim/R/03-sim_comp.R | 96 - saeSim-0.8.0/saeSim/R/03-sim_comp_preconf.R | 12 saeSim-0.8.0/saeSim/R/03-sim_gen.R | 76 saeSim-0.8.0/saeSim/R/03-sim_gen_cont.R | 32 saeSim-0.8.0/saeSim/R/03-sim_gen_preconf.R | 90 - saeSim-0.8.0/saeSim/R/03-sim_read_data.R | 64 saeSim-0.8.0/saeSim/R/03-sim_resp.R | 58 saeSim-0.8.0/saeSim/R/03-sim_sample.R | 54 saeSim-0.8.0/saeSim/R/03-sim_simName.R | 26 saeSim-0.8.0/saeSim/R/NAMESPACE.R | 21 saeSim-0.8.0/saeSim/build/vignette.rds |binary saeSim-0.8.0/saeSim/inst/doc/Introduction.R | 264 +-- saeSim-0.8.0/saeSim/inst/doc/Introduction.Rmd | 155 +- saeSim-0.8.0/saeSim/inst/doc/Introduction.html | 772 +++++----- saeSim-0.8.0/saeSim/man/agg_all.Rd | 48 saeSim-0.8.0/saeSim/man/as.data.frame.sim_setup.Rd | 44 saeSim-0.8.0/saeSim/man/autoplot.Rd | 54 saeSim-0.8.0/saeSim/man/base_add_id.Rd | 34 saeSim-0.8.0/saeSim/man/base_id.Rd | 54 saeSim-0.8.0/saeSim/man/comp_var.Rd | 42 saeSim-0.8.0/saeSim/man/generators.Rd | 148 + saeSim-0.8.0/saeSim/man/pipe.Rd | 34 saeSim-0.8.0/saeSim/man/plot.sim_setup.Rd | 44 saeSim-0.8.0/saeSim/man/read_data.Rd |only saeSim-0.8.0/saeSim/man/sampling.Rd | 98 - saeSim-0.8.0/saeSim/man/showMethods.Rd | 44 saeSim-0.8.0/saeSim/man/sim.Rd | 128 - saeSim-0.8.0/saeSim/man/sim_agg.Rd | 66 saeSim-0.8.0/saeSim/man/sim_base.Rd | 38 saeSim-0.8.0/saeSim/man/sim_comp.Rd | 98 - saeSim-0.8.0/saeSim/man/sim_comp_preconf.Rd | 48 saeSim-0.8.0/saeSim/man/sim_gen.Rd | 90 - saeSim-0.8.0/saeSim/man/sim_gen_cont.Rd | 72 saeSim-0.8.0/saeSim/man/sim_gen_preconf.Rd | 100 - saeSim-0.8.0/saeSim/man/sim_resp.Rd | 64 saeSim-0.8.0/saeSim/man/sim_sample.Rd | 74 saeSim-0.8.0/saeSim/man/sim_setup_preconfigured.Rd | 82 - saeSim-0.8.0/saeSim/man/sim_simName.Rd | 40 saeSim-0.8.0/saeSim/man/summary-sim_setup-method.Rd | 42 saeSim-0.8.0/saeSim/tests/test-all.R | 8 saeSim-0.8.0/saeSim/tests/testthat/helper.R | 2 saeSim-0.8.0/saeSim/tests/testthat/test-base_id.R | 38 saeSim-0.8.0/saeSim/tests/testthat/test-pipe-operator.R | 16 saeSim-0.8.0/saeSim/tests/testthat/test-preserve_attributes.R | 36 saeSim-0.8.0/saeSim/tests/testthat/test-select_cont.R | 8 saeSim-0.8.0/saeSim/tests/testthat/test-sim.R | 19 saeSim-0.8.0/saeSim/tests/testthat/test-sim_agg.R | 76 saeSim-0.8.0/saeSim/tests/testthat/test-sim_base.R | 30 saeSim-0.8.0/saeSim/tests/testthat/test-sim_comp.R | 3 saeSim-0.8.0/saeSim/tests/testthat/test-sim_generate.R | 153 + saeSim-0.8.0/saeSim/tests/testthat/test-sim_resp.R | 22 saeSim-0.8.0/saeSim/tests/testthat/test-sim_sample.R | 154 - saeSim-0.8.0/saeSim/tests/testthat/test-sim_setup.R | 10 saeSim-0.8.0/saeSim/tests/testthat/test-sim_simName.R | 14 saeSim-0.8.0/saeSim/vignettes/Introduction.Rmd | 155 +- 79 files changed, 3175 insertions(+), 3190 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between rfUtilities versions 1.0-2 dated 2015-09-29 and 2.0-0 dated 2016-04-27
DESCRIPTION | 12 +- MD5 | 82 ++++++++++++----- NAMESPACE | 35 ++++++- R/accuracy.R |only R/multi.collinear.R | 12 +- R/occurrence.threshold.R |only R/plot.occurrence.threshold.R |only R/plot.rf.cv.R |only R/plot.rf.modelSel.R |only R/plot.significance.R |only R/print.accuracy.R |only R/print.occurrence.threshold.R |only R/print.rf.cv.R |only R/print.rf.fit.R |only R/print.rf.modelSel.R |only R/print.significance.R |only R/rf.class.sensitivity.R | 52 +++++----- R/rf.classBalance.R | 80 ++++++++-------- R/rf.crossValidation.R | 173 ++++++++++++++++++++---------------- R/rf.imp.freq.R | 10 +- R/rf.modelSel.R | 121 +++++++++++++------------ R/rf.partial.ci.R | 23 ++-- R/rf.partial.prob.R | 14 +- R/rf.regression.fit.R |only R/rf.significance.R | 128 +++++++++++--------------- R/rfu.news.R |only R/summary.accuracy.R |only R/summary.occurrence.threshold.R |only R/summary.rf.cv.R |only R/summary.rf.modelSel.R |only R/summary.significance.R |only R/zzz.R |only inst/CITATION | 4 inst/NEWS | 43 +++++++- man/accuracy.Rd |only man/multi.collinear.Rd | 10 +- man/occurrence.threshold.Rd |only man/plot.occurrence.threshold.Rd |only man/plot.rf.cv.Rd |only man/plot.rf.modelSel.Rd |only man/plot.significance.Rd |only man/print.accuracy.Rd |only man/print.occurrence.threshold.Rd |only man/print.rf.cv.Rd |only man/print.rf.modelSel.Rd |only man/print.significance.Rd |only man/rf.class.sensitivity.Rd | 22 ++-- man/rf.classBalance.Rd | 21 +--- man/rf.crossValidation.Rd | 59 ++++++++---- man/rf.imp.freq.Rd | 12 +- man/rf.modelSel.Rd | 43 ++++---- man/rf.partial.ci.Rd | 9 + man/rf.partial.prob.Rd | 5 - man/rf.regression.fit.Rd |only man/rf.significance.Rd | 22 ++-- man/rfu.news.Rd |only man/summary.accuracy.Rd |only man/summary.occurrence.threshold.Rd |only man/summary.rf.cv.Rd |only man/summary.rf.modelSel.Rd |only man/summary.significance.Rd |only 61 files changed, 570 insertions(+), 422 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis'. 'MsgPack' encoding is optional
if the 'RcppMsgPack' package is detected. You can install via from
the 'ghrr' drat repository listed below.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.6 dated 2015-10-05 and 0.1.7 dated 2016-04-27
ChangeLog | 83 ++++++++++ DESCRIPTION | 22 +- MD5 | 24 +- README.md | 8 configure | 80 ++++++--- configure.ac | 61 +++++-- inst/NEWS.Rd | 24 ++ inst/tests/runit.execTests.R |only inst/tests/runit.execvTests.R | 6 inst/tests/runit.existsTests.R |only inst/tests/runit.expireTests.R |only inst/tests/runit.listTests.R | 13 + inst/tests/runit.serverIssues.R |only src/Makevars.in | 4 src/Redis.cpp | 321 +++++++++++++++++++++++++++++----------- 15 files changed, 491 insertions(+), 155 deletions(-)
Title: Extensible, Parallelizable Implementation of the Random Forest
Algorithm
Description: Scalable decision tree training and prediction.
Author: Mark Seligman
Maintainer: Mark Seligman <mseligman@suiji.org>
Diff between Rborist versions 0.1-0 dated 2015-02-14 and 0.1-1 dated 2016-04-27
Rborist-0.1-0/Rborist/man/predict.rborist.Rd |only Rborist-0.1-0/Rborist/man/rborist.Rd |only Rborist-0.1-0/Rborist/src/dectree.cc |only Rborist-0.1-0/Rborist/src/dectree.h |only Rborist-0.1-0/Rborist/src/facrun.cc |only Rborist-0.1-0/Rborist/src/facrun.h |only Rborist-0.1-0/Rborist/src/predictor.cc |only Rborist-0.1-0/Rborist/src/predictor.h |only Rborist-0.1-0/Rborist/src/rcppPredict.cc |only Rborist-0.1-0/Rborist/src/rcppPredictor.cc |only Rborist-0.1-0/Rborist/src/rcppResponse.cc |only Rborist-0.1-0/Rborist/src/rcppSample.cc |only Rborist-0.1-0/Rborist/src/rcppTrain.cc |only Rborist-0.1-1/Rborist/DESCRIPTION | 11 Rborist-0.1-1/Rborist/MD5 | 102 - Rborist-0.1-1/Rborist/NAMESPACE | 8 Rborist-0.1-1/Rborist/R/ForestFloorExport.Rborist.R |only Rborist-0.1-1/Rborist/R/PreTrain.R |only Rborist-0.1-1/Rborist/R/PreTrain.default.R |only Rborist-0.1-1/Rborist/R/Rborist.R | 2 Rborist-0.1-1/Rborist/R/Rborist.default.R | 291 +-- Rborist-0.1-1/Rborist/R/RboristNews.R |only Rborist-0.1-1/Rborist/R/predict.Rborist.R | 112 - Rborist-0.1-1/Rborist/R/zzz.R |only Rborist-0.1-1/Rborist/inst |only Rborist-0.1-1/Rborist/man/ForestFloorExport.Rborist.Rd |only Rborist-0.1-1/Rborist/man/PreTrain.default.Rd |only Rborist-0.1-1/Rborist/man/Rborist.Rd |only Rborist-0.1-1/Rborist/man/RboristNews.Rd |only Rborist-0.1-1/Rborist/man/predict.Rborist.Rd |only Rborist-0.1-1/Rborist/src/Makevars | 1 Rborist-0.1-1/Rborist/src/bv.cc |only Rborist-0.1-1/Rborist/src/bv.h |only Rborist-0.1-1/Rborist/src/callback.cc | 41 Rborist-0.1-1/Rborist/src/callback.h | 9 Rborist-0.1-1/Rborist/src/forest.cc |only Rborist-0.1-1/Rborist/src/forest.h |only Rborist-0.1-1/Rborist/src/index.cc | 588 +++--- Rborist-0.1-1/Rborist/src/index.h | 330 ++- Rborist-0.1-1/Rborist/src/leaf.cc |only Rborist-0.1-1/Rborist/src/leaf.h |only Rborist-0.1-1/Rborist/src/param.h |only Rborist-0.1-1/Rborist/src/predblock.cc |only Rborist-0.1-1/Rborist/src/predblock.h |only Rborist-0.1-1/Rborist/src/predict.cc | 301 ++- Rborist-0.1-1/Rborist/src/predict.h | 92 - Rborist-0.1-1/Rborist/src/pretree.cc | 398 ++-- Rborist-0.1-1/Rborist/src/pretree.h | 189 -- Rborist-0.1-1/Rborist/src/quant.cc | 414 +--- Rborist-0.1-1/Rborist/src/quant.h | 56 Rborist-0.1-1/Rborist/src/rcppArmadilloSample.cc |only Rborist-0.1-1/Rborist/src/rcppForest.h |only Rborist-0.1-1/Rborist/src/rcppLeaf.h |only Rborist-0.1-1/Rborist/src/rcppMonolith.cc |only Rborist-0.1-1/Rborist/src/rcppPredblock.h |only Rborist-0.1-1/Rborist/src/rcppSample.h | 19 Rborist-0.1-1/Rborist/src/response.cc | 504 ----- Rborist-0.1-1/Rborist/src/response.h | 105 - Rborist-0.1-1/Rborist/src/restage.cc |only Rborist-0.1-1/Rborist/src/restage.h |only Rborist-0.1-1/Rborist/src/rowrank.cc |only Rborist-0.1-1/Rborist/src/rowrank.h |only Rborist-0.1-1/Rborist/src/run.cc |only Rborist-0.1-1/Rborist/src/run.h |only Rborist-0.1-1/Rborist/src/sample.cc | 548 ++---- Rborist-0.1-1/Rborist/src/sample.h | 229 +- Rborist-0.1-1/Rborist/src/samplepred.cc | 334 +-- Rborist-0.1-1/Rborist/src/samplepred.h | 362 ++-- Rborist-0.1-1/Rborist/src/splitpred.cc | 1464 +++++++++-------- Rborist-0.1-1/Rborist/src/splitpred.h | 293 ++- Rborist-0.1-1/Rborist/src/splitsig.cc | 225 +- Rborist-0.1-1/Rborist/src/splitsig.h | 176 -- Rborist-0.1-1/Rborist/src/train.cc | 300 ++- Rborist-0.1-1/Rborist/src/train.h | 74 74 files changed, 3688 insertions(+), 3890 deletions(-)
Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984), bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices.
Author: R. Torices, A. J. Muñoz-Pajares
Maintainer: A. J. Muñoz-Pajares <ajesusmp@cibio.up.pt>
Diff between PHENIX versions 1.2.2 dated 2016-03-03 and 1.3 dated 2016-04-27
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 8 ++++++++ R/pint.R | 2 +- R/pint.boot.R | 2 +- R/pint.jack.R | 2 +- R/pint.p.R | 2 +- R/pintsc.R | 2 +- R/pintsc.boot.R | 2 +- R/pintsc.jack.R | 2 +- R/pintsc.p.R | 2 +- 11 files changed, 30 insertions(+), 22 deletions(-)
Title: Customisable Images of OpenStreetMap Data
Description: Produces customisable images of OpenStreetMap (OSM) data and
enables data visualisation using OSM objects.
Author: Mark Padgham [aut, cre]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between osmplotr versions 0.1-3 dated 2016-03-22 and 0.2.0 dated 2016-04-27
osmplotr-0.1-3/osmplotr/R/adjust_colours.R |only osmplotr-0.1-3/osmplotr/R/click-map.R |only osmplotr-0.1-3/osmplotr/R/highways2polygon.R |only osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.R |only osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.Rmd |only osmplotr-0.1-3/osmplotr/inst/doc/downloading-data.html |only osmplotr-0.1-3/osmplotr/man/click_map.Rd |only osmplotr-0.1-3/osmplotr/man/highways2polygon.Rd |only osmplotr-0.1-3/osmplotr/vignettes/downloading-data.Rmd |only osmplotr-0.1-3/osmplotr/vignettes/downloading-data.md |only osmplotr-0.1-3/osmplotr/vignettes/making-maps.md |only osmplotr-0.2.0/osmplotr/DESCRIPTION | 18 osmplotr-0.2.0/osmplotr/MD5 | 115 - osmplotr-0.2.0/osmplotr/NAMESPACE | 14 osmplotr-0.2.0/osmplotr/NEWS | 26 osmplotr-0.2.0/osmplotr/R/add-axes.R | 159 + osmplotr-0.2.0/osmplotr/R/add-colourbar.R | 339 ++- osmplotr-0.2.0/osmplotr/R/add-osm-groups.R | 395 ++-- osmplotr-0.2.0/osmplotr/R/add-osm-objects.R | 148 + osmplotr-0.2.0/osmplotr/R/add-osm-surface.R | 384 ++-- osmplotr-0.2.0/osmplotr/R/adjust-colours.R |only osmplotr-0.2.0/osmplotr/R/colour-mat.R | 59 osmplotr-0.2.0/osmplotr/R/connect-highways.R | 578 +++--- osmplotr-0.2.0/osmplotr/R/extract-highway.R | 12 osmplotr-0.2.0/osmplotr/R/extract-highways.R | 60 osmplotr-0.2.0/osmplotr/R/extract-osm-objects.R | 79 osmplotr-0.2.0/osmplotr/R/get-bbox.R | 7 osmplotr-0.2.0/osmplotr/R/get-highway-cycle.R |only osmplotr-0.2.0/osmplotr/R/make-osm-map.R | 65 osmplotr-0.2.0/osmplotr/R/order-lines.R | 4 osmplotr-0.2.0/osmplotr/R/osm-structures.R | 14 osmplotr-0.2.0/osmplotr/R/osmplotr.R | 73 osmplotr-0.2.0/osmplotr/R/plot-osm-basemap.R | 85 osmplotr-0.2.0/osmplotr/R/test-fns.R |only osmplotr-0.2.0/osmplotr/build/vignette.rds |binary osmplotr-0.2.0/osmplotr/data/london.rda |binary osmplotr-0.2.0/osmplotr/inst/doc/making-maps-with-data.R |only osmplotr-0.2.0/osmplotr/inst/doc/making-maps-with-data.Rmd |only osmplotr-0.2.0/osmplotr/inst/doc/making-maps-with-data.html |only osmplotr-0.2.0/osmplotr/inst/doc/making-maps.R | 544 ++--- osmplotr-0.2.0/osmplotr/inst/doc/making-maps.Rmd | 1117 +++++------- osmplotr-0.2.0/osmplotr/inst/doc/making-maps.html | 621 ++---- osmplotr-0.2.0/osmplotr/man/add_axes.Rd | 41 osmplotr-0.2.0/osmplotr/man/add_colourbar.Rd | 72 osmplotr-0.2.0/osmplotr/man/add_osm_groups.Rd | 116 - osmplotr-0.2.0/osmplotr/man/add_osm_objects.Rd | 54 osmplotr-0.2.0/osmplotr/man/add_osm_surface.Rd | 114 - osmplotr-0.2.0/osmplotr/man/adjust_colours.Rd | 35 osmplotr-0.2.0/osmplotr/man/colour_mat.Rd | 36 osmplotr-0.2.0/osmplotr/man/connect_highways.Rd | 65 osmplotr-0.2.0/osmplotr/man/extract_highway.Rd | 4 osmplotr-0.2.0/osmplotr/man/extract_highways.Rd | 8 osmplotr-0.2.0/osmplotr/man/extract_osm_objects.Rd | 26 osmplotr-0.2.0/osmplotr/man/get_bbox.Rd | 2 osmplotr-0.2.0/osmplotr/man/get_highway_cycle.Rd |only osmplotr-0.2.0/osmplotr/man/haversand.Rd |only osmplotr-0.2.0/osmplotr/man/list2df.Rd |only osmplotr-0.2.0/osmplotr/man/list2df_with_data.Rd |only osmplotr-0.2.0/osmplotr/man/london.Rd | 48 osmplotr-0.2.0/osmplotr/man/make_osm_map.Rd | 37 osmplotr-0.2.0/osmplotr/man/order_lines.Rd | 2 osmplotr-0.2.0/osmplotr/man/osm_structures.Rd | 17 osmplotr-0.2.0/osmplotr/man/osmplotr.Rd | 44 osmplotr-0.2.0/osmplotr/man/plot_osm_basemap.Rd | 36 osmplotr-0.2.0/osmplotr/man/shortest_way.Rd |only osmplotr-0.2.0/osmplotr/tests |only osmplotr-0.2.0/osmplotr/vignettes/making-maps-with-data.Rmd |only osmplotr-0.2.0/osmplotr/vignettes/making-maps.Rmd | 1117 +++++------- 68 files changed, 3695 insertions(+), 3095 deletions(-)
Title: Multidimensional Item Response Theory
Description: Analysis of dichotomous and polytomous response data using
unidimensional and multidimensional latent trait models under the Item
Response Theory paradigm. Exploratory and confirmatory models can be
estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory
bi-factor and two-tier analyses are available for modeling item testlets.
Multiple group analysis and mixed effects designs also are available for
detecting differential item and test functioning as well as modelling
item and person covariates.
Author: Phil Chalmers [aut, cre, cph],
Joshua Pritikin [ctb],
Alexander Robitzsch [ctb],
Mateusz Zoltak [ctb],
KwonHyun Kim [ctb],
Carl F. Falk [ctb],
Adam Meade [ctb]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirt versions 1.16 dated 2016-03-07 and 1.17.1 dated 2016-04-27
DESCRIPTION | 14 - MD5 | 100 ++++++----- NAMESPACE | 1 NEWS.md | 40 ++++ R/03-estimation.R | 27 ++- R/DIF.R | 18 +- R/Discrete-methods.R | 2 R/EMstep.group.R | 14 + R/LoadPars.R | 11 + R/M2.R | 11 + R/MDIFF.R | 7 R/MDISC.R | 5 R/MultipleGroup-methods.R | 16 - R/SingleGroup-methods.R | 66 ++++--- R/areainfo.R | 2 R/empirical_ES.R |only R/fscores.R | 7 R/fscores.internal.R | 34 ++-- R/itemGAM.R | 32 ++- R/itemfit.R | 304 +++++++++++++++++++++++++----------- R/mirt.R | 9 - R/mirt.model.R | 10 - R/mixedmirt.R | 10 - R/mod2values.R | 4 R/personfit.R | 4 R/shinyItemplot.R | 4 R/simdata.R | 55 ++++-- R/testinfo.R | 3 R/utils.R | 88 ++++------ build/vignette.rds |binary man/DIF.Rd | 8 man/MDIFF.Rd | 3 man/MDISC.Rd | 1 man/areainfo.Rd | 2 man/empirical_ES.Rd |only man/fscores.Rd | 45 ++--- man/itemfit.Rd | 115 +++++++++---- man/mirt.Rd | 9 - man/mirt.model.Rd | 12 + man/mixedmirt.Rd | 10 - man/numerical_deriv.Rd | 8 man/personfit.Rd | 2 man/plot-method.Rd | 6 man/simdata.Rd | 21 +- man/testinfo.Rd | 2 src/dpars.cpp | 3 tests/tests/test-00-basics.R | 4 tests/tests/test-01-mirtOne.R | 14 - tests/tests/test-02-mirtTwo.R | 7 tests/tests/test-04-multipleGroup.R | 6 tests/tests/test-05-confmirtOne.R | 7 tests/tests/test-07-mixedmirt.R | 2 52 files changed, 761 insertions(+), 424 deletions(-)
Title: MINimal VALidation for Stoichiometric Reactions
Description: For a given set of stoichiometric reactions, this package evaluates the mass balance and extracts all reactants, products, orphan metabolites, metabolite names and compartments. Also are included some options to check the compound names associated to Chemical Entities of Biological Interest (ChEBI) database <https://www.ebi.ac.uk/chebi>.
Author: Daniel Osorio [aut,cre], Janneth Gonzalez [aut], Andres Pinzon-Velasco
[aut]
Maintainer: Daniel Osorio <dcosorioh@unal.edu.co>
Diff between minval versions 0.2 dated 2016-03-14 and 0.3 dated 2016-04-27
DESCRIPTION | 9 ++++----- MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/compartments.R | 4 ++-- R/metabolites.R | 6 +++--- R/minval-internal.R | 12 +++++++----- R/products.R | 18 +++++++++--------- R/reactants.R | 12 ++++++------ R/toChEBI.R | 12 ++++++------ man/minval-package.Rd | 4 ++-- 10 files changed, 52 insertions(+), 47 deletions(-)
Title: International Assessment Data Manager
Description:
Provides tools for importing, merging, and analysing data from
international assessment studies (TIMSS, PIRLS, PISA. ICILS, and PIAAC).
Author: Daniel Caro <daniel.caro@education.ox.ac.uk>, Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Maintainer: Daniel Caro <daniel.caro@education.ox.ac.uk>
Diff between intsvy versions 1.8 dated 2015-12-01 and 1.9 dated 2016-04-27
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/intsvy.log.R | 2 +- R/intsvy.log.pv.R | 2 +- R/intsvy.reg.R | 6 +++--- R/intsvy.reg.pv.R | 18 +++++++++--------- R/plot.intsvy.reg.R | 2 +- man/intsvy-package.Rd | 4 ++-- 8 files changed, 28 insertions(+), 28 deletions(-)
Title: Hierarchical Inference Testing
Description: Hierarchical inference testing (HIT) for (generalized) linear
models with correlated covariates applicable to high-dimensional settings.
Author: Jonas Klasen [aut, cre]
Maintainer: Jonas Klasen <qtcat@gmx.de>
Diff between hit versions 0.2-1 dated 2016-01-08 and 0.2-2 dated 2016-04-27
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 1 - NEWS.md | 25 ++++++++++++++++++++----- R/anova.R | 4 ++-- R/hierarchy.R | 8 ++++---- R/hit.R | 21 ++++++++++++--------- README.md | 14 ++++++-------- man/as.hierarchy.Rd | 4 ++-- man/fast.anova.Rd | 4 ++-- man/hit.Rd | 4 ++-- src/hierarchy.cpp | 43 +++++++++++++++++++------------------------ 12 files changed, 83 insertions(+), 73 deletions(-)
Title: Interface to the 'g:Profiler' Toolkit
Description: Functional enrichment analysis, gene identifier conversion and
mapping homologous genes across related organisms via the 'g:Profiler' toolkit
(http://biit.cs.ut.ee/gprofiler/).
Author: Juri Reimand <juri.reimand@ut.ee>, Raivo Kolde
<rkolde@gmail.com>, Tambet Arak <tambet.arak@gmail.com>
Maintainer: Tambet Arak <tambet.arak@gmail.com>
Diff between gProfileR versions 0.5.3 dated 2015-04-06 and 0.6.1 dated 2016-04-27
gProfileR-0.5.3/gProfileR/man/get-sub-base-sub-url.Rd |only gProfileR-0.5.3/gProfileR/man/get-sub-user-sub-agent.Rd |only gProfileR-0.5.3/gProfileR/man/set-sub-base-sub-url.Rd |only gProfileR-0.5.3/gProfileR/man/set-sub-user-sub-agent.Rd |only gProfileR-0.6.1/gProfileR/ChangeLog | 11 gProfileR-0.6.1/gProfileR/DESCRIPTION | 15 gProfileR-0.6.1/gProfileR/MD5 | 22 - gProfileR-0.6.1/gProfileR/NAMESPACE | 10 gProfileR-0.6.1/gProfileR/R/gProfileR.R | 279 ++++++++-------- gProfileR-0.6.1/gProfileR/man/gconvert.Rd | 52 ++ gProfileR-0.6.1/gProfileR/man/get_base_url.Rd |only gProfileR-0.6.1/gProfileR/man/get_user_agent.Rd |only gProfileR-0.6.1/gProfileR/man/gorth.Rd | 60 ++- gProfileR-0.6.1/gProfileR/man/gprofiler.Rd | 108 ++++-- gProfileR-0.6.1/gProfileR/man/set_base_url.Rd |only gProfileR-0.6.1/gProfileR/man/set_user_agent.Rd |only 16 files changed, 333 insertions(+), 224 deletions(-)
Title: Create Dendrograms and Tree Diagrams Using 'ggplot2'
Description: This is a set of tools for dendrograms and
tree plots using 'ggplot2'. The 'ggplot2' philosophy is to
clearly separate data from the presentation.
Unfortunately the plot method for dendrograms plots
directly to a plot device without exposing the data.
The 'ggdendro' package resolves this by making available
functions that extract the dendrogram plot data. The package
provides implementations for tree, rpart, as well as diana and agnes
cluster diagrams.
Author: Andrie de Vries [aut, cre],
Brian D. Ripley [aut] (author of package tree)
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between ggdendro versions 0.1-18 dated 2016-02-25 and 0.1-20 dated 2016-04-27
ggdendro-0.1-18/ggdendro/man/rpart.branch.Rd |only ggdendro-0.1-18/ggdendro/man/tree.depth.Rd |only ggdendro-0.1-20/ggdendro/DESCRIPTION | 10 - ggdendro-0.1-20/ggdendro/MD5 | 32 ++-- ggdendro-0.1-20/ggdendro/NEWS | 48 ++++-- ggdendro-0.1-20/ggdendro/R/dendro_rpart.R | 19 +- ggdendro-0.1-20/ggdendro/R/dendro_tree.R | 42 ++--- ggdendro-0.1-20/ggdendro/R/ggdendrogram.R | 9 - ggdendro-0.1-20/ggdendro/R/rpart.R | 111 +++++++------- ggdendro-0.1-20/ggdendro/build/vignette.rds |binary ggdendro-0.1-20/ggdendro/inst/doc/ggdendro.html | 14 - ggdendro-0.1-20/ggdendro/man/dendro_data.rpart.Rd | 4 ggdendro-0.1-20/ggdendro/man/get_data_tree_leaf_labels.Rd | 2 ggdendro-0.1-20/ggdendro/man/tree_labels.Rd | 2 ggdendro-0.1-20/ggdendro/man/tree_segments.Rd | 2 ggdendro-0.1-20/ggdendro/tests/testthat/Rplots.pdf |binary ggdendro-0.1-20/ggdendro/tests/testthat/Rplots13.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots14.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots15.pdf |only ggdendro-0.1-20/ggdendro/tests/testthat/Rplots16.pdf |only 20 files changed, 166 insertions(+), 129 deletions(-)
Title: Compute Decision Interval and Average Run Length for CUSUM
Charts
Description: Computation of decision intervals (H) and average run lengths (ARL) for CUSUM charts.
Author: Douglas M. Hawkins, David H. Olwell, and Boxiang Wang
Maintainer: Boxiang Wang <boxiang@umn.edu>
Diff between CUSUMdesign versions 1.1.1 dated 2015-10-31 and 1.1.2 dated 2016-04-27
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/getARL.R | 5 ++--- R/getH.R | 2 +- man/getH.Rd | 4 ++-- src/ANYSUBS.f | 4 ++-- 6 files changed, 17 insertions(+), 18 deletions(-)
Title: Community Dynamics Metrics
Description: A toolbox of ecological community dynamics metrics that are
explicitly temporal. Functions fall into two categories: temporal diversity
indices and community stability metrics. The diversity indices are temporal
analogs to traditional diversity indices such as richness and rank-abundance
curves. Specifically, functions are provided to calculate species turnover, mean
rank shifts, and lags in community similarity between time points. The community
stability metrics calculate overall stability and patterns of species covariance
and synchrony over time.
Author: Lauren Hallett [aut],
Sydney K. Jones [aut],
A. Andrew M. MacDonald [aut],
Dan F. B. Flynn [aut],
Peter Slaughter [aut],
Julie Ripplinger [aut],
Scott L. Collins [aut],
Corinna Gries [aut],
Matthew B. Jones [aut, cre]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between codyn versions 1.0.1 dated 2016-01-15 and 1.1.0 dated 2016-04-27
codyn-1.0.1/codyn/man/genRand.Rd |only codyn-1.0.1/codyn/man/get_lag_i.Rd |only codyn-1.0.1/codyn/man/get_lagged_distances.Rd |only codyn-1.0.1/codyn/man/get_slope.Rd |only codyn-1.0.1/codyn/man/getintersect.Rd |only codyn-1.0.1/codyn/man/getturnover.Rd |only codyn-1.0.1/codyn/man/meanrank.Rd |only codyn-1.0.1/codyn/man/temporal_torus_translation.Rd |only codyn-1.0.1/codyn/man/temporal_torus_translation_CI.Rd |only codyn-1.1.0/codyn/DESCRIPTION | 31 - codyn-1.1.0/codyn/MD5 | 108 ++-- codyn-1.1.0/codyn/NAMESPACE | 14 codyn-1.1.0/codyn/NEWS | 15 codyn-1.1.0/codyn/R/codyn-package.R | 35 - codyn-1.1.0/codyn/R/community_stability.R | 108 ++-- codyn-1.1.0/codyn/R/rank_shift.R | 159 ++++- codyn-1.1.0/codyn/R/rate_change.R | 180 ++++-- codyn-1.1.0/codyn/R/synchrony.R | 134 +++-- codyn-1.1.0/codyn/R/temporal_torus_translation.R | 258 ++++++--- codyn-1.1.0/codyn/R/turnover.R | 98 +++ codyn-1.1.0/codyn/R/utilities.R | 62 +- codyn-1.1.0/codyn/R/variance_ratio.R | 267 ++++++---- codyn-1.1.0/codyn/README.md | 2 codyn-1.1.0/codyn/build/vignette.rds |binary codyn-1.1.0/codyn/inst/CITATION | 16 codyn-1.1.0/codyn/inst/doc/Community_Stability_Metrics.R | 56 +- codyn-1.1.0/codyn/inst/doc/Community_Stability_Metrics.Rmd | 21 codyn-1.1.0/codyn/inst/doc/Community_Stability_Metrics.html | 255 +++------ codyn-1.1.0/codyn/inst/doc/Temporal_Diversity_Indices.R | 31 - codyn-1.1.0/codyn/inst/doc/Temporal_Diversity_Indices.Rmd | 39 + codyn-1.1.0/codyn/inst/doc/Temporal_Diversity_Indices.html | 183 ++++-- codyn-1.1.0/codyn/inst/doc/codyn_overview.Rmd | 2 codyn-1.1.0/codyn/inst/doc/codyn_overview.html | 37 + codyn-1.1.0/codyn/inst/tests/test_community_stability.R | 144 +++-- codyn-1.1.0/codyn/inst/tests/test_rank_shift.R | 58 +- codyn-1.1.0/codyn/inst/tests/test_rate_change.R | 8 codyn-1.1.0/codyn/inst/tests/test_synchrony.R | 89 +-- codyn-1.1.0/codyn/inst/tests/test_temporal_torus_translation.R | 255 +++++---- codyn-1.1.0/codyn/inst/tests/test_turnover.R | 36 - codyn-1.1.0/codyn/inst/tests/test_variance_ratio.R | 198 ++++--- codyn-1.1.0/codyn/man/codyn.Rd | 17 codyn-1.1.0/codyn/man/collins08.Rd | 2 codyn-1.1.0/codyn/man/community_stability.Rd | 14 codyn-1.1.0/codyn/man/confint.cyclic_shift.Rd |only codyn-1.1.0/codyn/man/cyclic_shift.Rd |only codyn-1.1.0/codyn/man/cyclic_shift_onerep.Rd |only codyn-1.1.0/codyn/man/df_intersect.Rd |only codyn-1.1.0/codyn/man/knz_001d.Rd | 4 codyn-1.1.0/codyn/man/lag_i.Rd |only codyn-1.1.0/codyn/man/lagged_distances.Rd |only codyn-1.1.0/codyn/man/lagged_slope.Rd |only codyn-1.1.0/codyn/man/mean_rank_shift.Rd | 23 codyn-1.1.0/codyn/man/rank_onerep.Rd |only codyn-1.1.0/codyn/man/rank_shift.Rd |only codyn-1.1.0/codyn/man/rate_change.Rd | 35 - codyn-1.1.0/codyn/man/rate_change_interval.Rd | 29 - codyn-1.1.0/codyn/man/shuffle_community.Rd |only codyn-1.1.0/codyn/man/synch_onerep.Rd | 5 codyn-1.1.0/codyn/man/synchrony.Rd | 27 - codyn-1.1.0/codyn/man/turnover.Rd | 24 codyn-1.1.0/codyn/man/turnover_twoyears.Rd |only codyn-1.1.0/codyn/man/variance_ratio.Rd | 92 +-- codyn-1.1.0/codyn/vignettes/Community_Stability_Metrics.Rmd | 21 codyn-1.1.0/codyn/vignettes/Temporal_Diversity_Indices.Rmd | 39 + codyn-1.1.0/codyn/vignettes/codyn_overview.Rmd | 2 65 files changed, 1970 insertions(+), 1263 deletions(-)
Title: Phylogenetically Classifies Retention Mechanisms of Duplicate
Genes from Gene Expression Data
Description: Classification is based on the recently developed phylogenetic
approach by Assis and Bachtrog (2013). The method classifies the
evolutionary mechanisms retaining pairs of duplicate genes (conservation,
neofunctionalization, subfunctionalization, or specialization) by comparing gene
expression profiles of duplicate genes in one species to those of their single-
copy ancestral genes in a sister species.
Author: Brent Perry <brp5173@psu.edu>, Raquel Assis <rassis@psu.edu>
Maintainer: Raquel Assis <rassis@psu.edu>
Diff between CDROM versions 1.0 dated 2016-03-22 and 1.1 dated 2016-04-27
DESCRIPTION | 6 ++-- MD5 | 6 ++-- R/CDROM.R | 87 ++++++++++++++++++++++++++++++++++++++++++----------------- man/CDROM.Rd | 6 ++-- 4 files changed, 72 insertions(+), 33 deletions(-)
Title: Visualizing Generalized Canonical Discriminant and Canonical
Correlation Analysis
Description: Functions for computing and visualizing
generalized canonical discriminant analyses and canonical correlation analysis
for a multivariate linear model.
Traditional canonical discriminant analysis is restricted to a one-way 'MANOVA'
design and is equivalent to canonical correlation analysis between a set of quantitative
response variables and a set of dummy variables coded from the factor variable.
The 'candisc' package generalizes this to higher-way 'MANOVA' designs
for all factors in a multivariate linear model,
computing canonical scores and vectors for each term. The graphic functions provide low-rank (1D, 2D, 3D)
visualizations of terms in an 'mlm' via the 'plot.candisc' and 'heplot.candisc' methods. Related plots are
now provided for canonical correlation analysis when all predictors are quantitative.
Author: Michael Friendly [aut, cre], John Fox [aut]
Maintainer: Michael Friendly <friendly@yorku.ca>
Diff between candisc versions 0.6-7 dated 2015-04-19 and 0.7-0 dated 2016-04-27
DESCRIPTION | 12 ++++---- MD5 | 28 ++++++++++--------- NAMESPACE | 11 ++++++- NEWS | 11 +++++++ R/heplot.candisc.R | 8 ++--- R/plot.candisc.R | 72 ++++++++++++++++++++++++++++++++++++++----------- R/varOrder.R |only data/Grass.rda |binary data/HSB.rda |binary data/Wine.RData |only data/Wolves.rda |binary man/Wine.Rd |only man/Wolves.Rd | 4 +- man/candisc-package.Rd | 5 ++- man/candisc.Rd | 33 +++++++++++++++++----- man/plot.cancor.Rd | 2 - man/varOrder.Rd |only 17 files changed, 134 insertions(+), 52 deletions(-)