Title: Fast Multivariate Normal and Student's t Methods
Description: Provides computationally efficient tools related to
the multivariate normal and Student's t distributions. The main functionalities are:
simulating multivariate random vectors, evaluating multivariate
normal or Student's t densities and Mahalanobis distances. These tools are very efficient
thanks to the use of C++ code and of the OpenMP API.
Author: Matteo Fasiolo, using the C++ parallel RNG of Thijs van den Berg and
Ziggurat algorithm of Jens Maurer and Steven Watanabe (boost)
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between mvnfast versions 0.1.7 dated 2016-10-10 and 0.2.0 dated 2017-02-17
DESCRIPTION | 10 ++--- MD5 | 53 ++++++++++++++++++----------- NAMESPACE | 18 +++++++-- R/dmixn.R |only R/dmixt.R |only R/dmvn.R | 3 - R/dmvt.R | 7 ++- R/maha.R | 3 - R/ms.R | 3 - R/rmixn.R |only R/rmixt.R |only R/rmvn.R | 3 - R/rmvt.R | 3 - build/vignette.rds |binary inst/doc/mvnfast.R | 5 ++ inst/doc/mvnfast.Rmd | 5 ++ inst/doc/mvnfast.html | 87 ++++++++++++++++++++++++------------------------ inst/tests/test-dmixt.R |only inst/tests/test-rmixn.R |only inst/tests/test-rmixt.R |only man/dmixn.Rd |only man/dmixt.Rd |only man/dmvn.Rd | 1 man/dmvt.Rd | 3 - man/maha.Rd | 1 man/ms.Rd | 1 man/rmixn.Rd |only man/rmixt.Rd |only man/rmvn.Rd | 7 +-- man/rmvt.Rd | 7 +-- src/dmixtCpp.cpp |only src/init.c |only src/rmixnCpp.cpp |only src/rmixtCpp.cpp |only vignettes/mvnfast.Rmd | 5 ++ 35 files changed, 126 insertions(+), 99 deletions(-)
Title: Common Plots for Analysis
Description: Example 'ggplot2' plots we have found useful, under a standardized
calling interface.
Author: Nina Zumel, John Mount
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 0.2.0 dated 2017-01-17 and 0.2.2 dated 2017-02-17
WVPlots-0.2.0/WVPlots/R/DebugFn.R |only WVPlots-0.2.0/WVPlots/man/DebugFn.Rd |only WVPlots-0.2.0/WVPlots/man/DebugPrintFn.Rd |only WVPlots-0.2.0/WVPlots/man/WVPlots-package.Rd |only WVPlots-0.2.0/WVPlots/man/calcAUC.Rd |only WVPlots-0.2.2/WVPlots/DESCRIPTION | 13 WVPlots-0.2.2/WVPlots/MD5 | 52 +- WVPlots-0.2.2/WVPlots/NAMESPACE | 13 WVPlots-0.2.2/WVPlots/R/BinaryYScatterPlot.R | 12 WVPlots-0.2.2/WVPlots/R/DoubleDensity.R | 44 - WVPlots-0.2.2/WVPlots/R/DoubleHistogram.R | 60 +- WVPlots-0.2.2/WVPlots/R/GainCurve.R | 419 ++++++++++++------- WVPlots-0.2.2/WVPlots/R/PRPlot.R | 24 - WVPlots-0.2.2/WVPlots/R/ROC.R | 127 +++-- WVPlots-0.2.2/WVPlots/R/ScatterHist.R | 59 +- WVPlots-0.2.2/WVPlots/R/ScatterHistC.R | 25 - WVPlots-0.2.2/WVPlots/R/WVPlots.R |only WVPlots-0.2.2/WVPlots/R/sharedFunctions.R | 1 WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_concept.R | 7 WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_concept.Rmd | 12 WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_concept.html | 27 - WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_examples.R | 4 WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_examples.Rmd | 16 WVPlots-0.2.2/WVPlots/inst/doc/WVPlots_examples.html | 62 +- WVPlots-0.2.2/WVPlots/man/BinaryYScatterPlot.Rd | 4 WVPlots-0.2.2/WVPlots/man/ScatterHist.Rd | 2 WVPlots-0.2.2/WVPlots/man/ScatterHistC.Rd | 3 WVPlots-0.2.2/WVPlots/man/WVPlots.Rd |only WVPlots-0.2.2/WVPlots/man/reexports.Rd |only WVPlots-0.2.2/WVPlots/vignettes/WVPlots_concept.Rmd | 12 WVPlots-0.2.2/WVPlots/vignettes/WVPlots_examples.Rmd | 16 31 files changed, 634 insertions(+), 380 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the site
http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel with contributions by Bill Evans, Mike Birdgeneau,
Henrik Bengtsson, and Seth Wenchel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RPushbullet versions 0.3.0 dated 2017-02-03 and 0.3.1 dated 2017-02-17
ChangeLog | 49 ++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 10 ++++----- MD5 | 28 ++++++++++++++++----------- NAMESPACE | 10 ++++++++- R/channel.R |only R/devices.R | 4 +-- R/init.R | 10 ++++----- R/isValid.R |only R/pushes.R | 19 +++++++++--------- R/setup.R | 42 +++++++++++++++++++++++++++++++++++++++-- R/user.R |only README.md | 14 +++++++------ inst/NEWS.Rd | 21 ++++++++++++++++++-- man/pbGetChannelInfo.Rd |only man/pbGetUser.Rd |only man/pbSetup.Rd | 5 +++- man/pbValidateConf.Rd |only tests/simpleTests.R | 26 ++++++++++++++++++++++++- 18 files changed, 193 insertions(+), 45 deletions(-)
Title: Decrypt Passwords from Gnome Keyring, Windows Data Protection
API and macOS Keychain
Description: Decrypts passwords stored in the Gnome Keyring, macOS Keychain and
strings encrypted with the Windows Data Protection API.
Author: Josh Gilfillan
Maintainer: Josh Gilfillan <joshua.i.gilfillan+keyringr@gmail.com>
Diff between keyringr versions 0.3.0 dated 2016-12-26 and 0.4.0 dated 2017-02-17
DESCRIPTION | 13 LICENSE | 4 MD5 | 32 NAMESPACE | 11 R/decrypt_dpapi_pw.R | 78 +- R/decrypt_gk_pw.R | 50 - R/decrypt_kc_pw.R | 58 - R/get_kc_account.R |only README.md | 131 ++-- build/vignette.rds |binary inst/doc/Avoiding_plain_text_passwords_in_R_with_keyringr.R | 46 - inst/doc/Avoiding_plain_text_passwords_in_R_with_keyringr.Rmd | 212 +++--- inst/doc/Avoiding_plain_text_passwords_in_R_with_keyringr.html | 322 +++++----- man/decrypt_dpapi_pw.Rd | 85 +- man/decrypt_gk_pw.Rd | 67 +- man/decrypt_kc_pw.Rd | 77 +- man/get_kc_account.Rd |only vignettes/Avoiding_plain_text_passwords_in_R_with_keyringr.Rmd | 212 +++--- 18 files changed, 729 insertions(+), 669 deletions(-)
Title: Geom for Logo Sequence Plots
Description: Visualize sequences in (modified) logo plots. The design choices
used by these logo plots allow sequencing data to be more easily analyzed.
Because it is integrated into the 'ggplot2' geom framework, these logo plots
support native features such as faceting.
Author: Heike Hofmann [aut],
Eric Hare [aut, cre],
GGobi Foundation [aut]
Maintainer: Eric Hare <erichare@iastate.edu>
Diff between gglogo versions 0.1.2 dated 2016-06-28 and 0.1.3 dated 2017-02-17
gglogo-0.1.2/gglogo/inst/visual_test |only gglogo-0.1.3/gglogo/DESCRIPTION | 13 ++--- gglogo-0.1.3/gglogo/MD5 | 64 +++++++++++++------------- gglogo-0.1.3/gglogo/NEWS.md |only gglogo-0.1.3/gglogo/R/data.r | 22 ++++++++ gglogo-0.1.3/gglogo/R/logos.r | 8 ++- gglogo-0.1.3/gglogo/build |only gglogo-0.1.3/gglogo/data/alphabet_braille.rda |only gglogo-0.1.3/gglogo/data/alphabet_comic.rda |only gglogo-0.1.3/gglogo/data/alphabet_xkcd.rda |only gglogo-0.1.3/gglogo/inst/doc |only gglogo-0.1.3/gglogo/man/aacids.Rd | 1 gglogo-0.1.3/gglogo/man/alphabet.Rd | 11 ++++ gglogo-0.1.3/gglogo/man/calcInformation.Rd | 1 gglogo-0.1.3/gglogo/man/createPolygons.Rd | 1 gglogo-0.1.3/gglogo/man/determineOrder.Rd | 1 gglogo-0.1.3/gglogo/man/fortify.Rd | 1 gglogo-0.1.3/gglogo/man/geom_logo.Rd | 3 - gglogo-0.1.3/gglogo/man/getOutline.Rd | 1 gglogo-0.1.3/gglogo/man/ggfortify.Rd | 1 gglogo-0.1.3/gglogo/man/identifyParts.Rd | 1 gglogo-0.1.3/gglogo/man/letterObject.Rd | 1 gglogo-0.1.3/gglogo/man/letterToPolygon.Rd | 1 gglogo-0.1.3/gglogo/man/logo.Rd | 1 gglogo-0.1.3/gglogo/man/mainPlusIslands.Rd | 1 gglogo-0.1.3/gglogo/man/point_line_dist.Rd | 1 gglogo-0.1.3/gglogo/man/position_logo.Rd | 5 -- gglogo-0.1.3/gglogo/man/sequences.Rd | 3 - gglogo-0.1.3/gglogo/man/simplifyPolygon.Rd | 1 gglogo-0.1.3/gglogo/man/simplify_rec.Rd | 1 gglogo-0.1.3/gglogo/man/splitSequence.Rd | 1 gglogo-0.1.3/gglogo/man/stat_logo.Rd | 1 gglogo-0.1.3/gglogo/vignettes |only 33 files changed, 82 insertions(+), 64 deletions(-)
Title: Client for the 'Enigma' 'API'
Description: The company 'Enigma' (<http://enigma.io>) holds many public
'datasets' from governments, companies, universities, and organizations.
'Enigma' provides an 'API' for data, 'metadata', and statistics on each of
the 'datasets'. 'enigma' is a client to interact with the 'Enigma' 'API',
including getting the data and 'metadata' for 'datasets' in 'Enigma', as
well as collecting statistics on 'datasets'. In addition, you can download
a 'gzipped' 'csv' file of a 'dataset' if you want the whole 'dataset'. An
'API' key from 'Enigma' is required to use 'enigma'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between enigma versions 0.2.0 dated 2015-07-08 and 0.3.0 dated 2017-02-17
enigma-0.2.0/enigma/R/tbldf_utils.R |only enigma-0.2.0/enigma/man/type_sum.Rd |only enigma-0.3.0/enigma/DESCRIPTION | 27 - enigma-0.3.0/enigma/LICENSE | 2 enigma-0.3.0/enigma/MD5 | 55 +-- enigma-0.3.0/enigma/NAMESPACE | 22 - enigma-0.3.0/enigma/NEWS.md |only enigma-0.3.0/enigma/R/enigma-package.r | 40 +- enigma-0.3.0/enigma/R/enigma_data.r | 118 +++--- enigma-0.3.0/enigma/R/enigma_fetch.r | 183 +++++----- enigma-0.3.0/enigma/R/enigma_metadata.r | 88 ++-- enigma-0.3.0/enigma/R/enigma_stats.r | 139 +++---- enigma-0.3.0/enigma/R/rate_limit.R | 10 enigma-0.3.0/enigma/R/zzz.r | 25 - enigma-0.3.0/enigma/README.md | 100 +++-- enigma-0.3.0/enigma/build/vignette.rds |binary enigma-0.3.0/enigma/inst/assets/figure/unnamed-chunk-17-1.png |binary enigma-0.3.0/enigma/inst/doc/enigma_vignette.Rmd | 22 - enigma-0.3.0/enigma/inst/doc/enigma_vignette.html | 20 - enigma-0.3.0/enigma/inst/vign/enigma_vignette.Rmd | 15 enigma-0.3.0/enigma/inst/vign/enigma_vignette.md | 22 - enigma-0.3.0/enigma/man/enigma.Rd | 40 +- enigma-0.3.0/enigma/man/enigma_data.Rd | 116 +++--- enigma-0.3.0/enigma/man/enigma_fetch.Rd | 143 ++++--- enigma-0.3.0/enigma/man/enigma_metadata.Rd | 63 ++- enigma-0.3.0/enigma/man/enigma_stats.Rd | 147 ++++---- enigma-0.3.0/enigma/man/rate_limit.Rd | 15 enigma-0.3.0/enigma/tests/testthat/test-enigma_data.R | 2 enigma-0.3.0/enigma/tests/testthat/test-enigma_stats.R | 6 enigma-0.3.0/enigma/vignettes/enigma_vignette.Rmd | 22 - 30 files changed, 760 insertions(+), 682 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.2.0 dated 2017-01-03 and 0.3.0 dated 2017-02-17
DESCRIPTION | 8 +- MD5 | 64 ++++++++++++-------- NAMESPACE | 4 + NEWS.md | 49 +++++++++++---- R/async.R |only R/asyncvaried.R |only R/client.R | 58 ++++++++++++------ R/crul-package.r | 4 + R/curl-options.R | 16 +++++ R/httprequest.R |only R/post-requests.R | 2 R/proxies.R |only R/response.R | 15 +++- R/zzz.R | 9 ++ README.md | 117 ++++++++++++++++++++++++++++++++------ build/vignette.rds |binary inst/doc/async.Rmd |only inst/doc/async.html |only inst/doc/crul_vignette.Rmd | 42 +++++++------ inst/doc/crul_vignette.html | 42 +++++++------ inst/vign/async.Rmd |only inst/vign/async.md |only inst/vign/crul_vignette.md | 42 +++++++------ man/Async.Rd |only man/AsyncVaried.Rd |only man/HttpClient.Rd | 17 +++-- man/HttpRequest.Rd |only man/HttpResponse.Rd | 1 man/crul-package.Rd | 8 +- man/curl-options.Rd | 19 +++++- man/handle.Rd | 1 man/http-headers.Rd | 1 man/post-requests.Rd | 5 - man/proxies.Rd |only man/writing-options.Rd | 1 tests/testthat/test-async.R |only tests/testthat/test-asyncvaried.R |only tests/testthat/test-paths.R | 12 ++- tests/testthat/test-request.R |only vignettes/async.Rmd |only vignettes/crul_vignette.Rmd | 42 +++++++------ 41 files changed, 394 insertions(+), 185 deletions(-)
Title: Acoustic Template Detection in R
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner <sdh11@cornell.edu> and Jon Katz <jonkatz4@gmail.com>, with code for the Fourier transform from the seewave package (by Jerome Sueur, Thierry Aubin, and Caroline Simonis), and code for the readMP3 function from the tuneR package (by Uwe Ligges). Therese Donovan provided creative direction and database design support.
Maintainer: Sasha D. Hafner <sdh11@cornell.edu>
Diff between monitoR versions 1.0.4 dated 2015-09-18 and 1.0.5 dated 2017-02-17
monitoR-1.0.4/monitoR/R/cutw.R |only monitoR-1.0.4/monitoR/man/cutw.Rd |only monitoR-1.0.5/monitoR/ChangeLog | 21 +++++++++++++++++ monitoR-1.0.5/monitoR/DESCRIPTION | 8 +++--- monitoR-1.0.5/monitoR/MD5 | 22 ++++++++---------- monitoR-1.0.5/monitoR/NAMESPACE | 1 monitoR-1.0.5/monitoR/NEWS | 10 ++++++++ monitoR-1.0.5/monitoR/build/vignette.rds |binary monitoR-1.0.5/monitoR/data/btnw.rda |binary monitoR-1.0.5/monitoR/data/oven.rda |binary monitoR-1.0.5/monitoR/data/survey.rda |binary monitoR-1.0.5/monitoR/data/survey_anno.rda |binary monitoR-1.0.5/monitoR/inst/doc/monitoR_QuickStart.pdf |binary 13 files changed, 45 insertions(+), 17 deletions(-)
Title: Biomarker Prognostic Enrichment Tool
Description: Prognostic Enrichment is a clinical trial strategy of evaluating an intervention in a patient population with a higher rate of the unwanted event than the broader patient population (R. Temple (2010) <DOI:10.1038/clpt.2010.233>). A higher event rate translates to a lower sample size for the clinical trial, which can have both practical and ethical advantages. This package is a tool to help evaluate biomarkers for prognostic enrichment of clinical trials.
Author: Jeremy Roth [cre, aut],
Kathleen F. Kerr [aut],
Kehao Zhu [aut]
Maintainer: Jeremy Roth <jhroth@uw.edu>
Diff between BioPET versions 0.2.0 dated 2016-07-04 and 0.2.1 dated 2017-02-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- data/dcaData.rda |binary 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Sankey or Ribbon Plots
Description: Sankey plots are a type of diagram that is convenient to
illustrate how flow of information, resources etc. separates and joins,
much like observing how rivers split and merge. For example, they can be
used to compare different clusterings.
Author: January Weiner <january.weiner@gmail.com>
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between riverplot versions 0.5 dated 2015-06-18 and 0.6 dated 2017-02-17
ChangeLog |only DESCRIPTION | 9 MD5 | 32 +- NAMESPACE | 14 + NEWS |only R/curveseg.R | 7 R/riverplot-styles.R | 3 R/riverplot.R | 476 ++++++++++++++++++++++++------------------- R/styles.R | 22 - data/minard.rda |binary man/colorRampPaletteAlpha.Rd | 6 man/curveseg.Rd | 7 man/makeRiver.Rd | 14 - man/minard.Rd | 6 man/riverplot-package.Rd | 4 man/riverplot-styles.Rd | 9 man/riverplot.Rd | 48 +++- man/riverplot.example.Rd | 3 18 files changed, 383 insertions(+), 277 deletions(-)
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren [aut, cre]
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 1.2 dated 2017-01-20 and 1.3 dated 2017-02-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/quantileCI.R | 6 +++--- build/partial.rdb |binary 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Bayesian Regression Models using Stan
Description: Fit Bayesian generalized (non-)linear multilevel models
using Stan for full Bayesian inference. A wide range of distributions
and link functions are supported, allowing users to fit -- among others --
linear, robust linear, binomial, Poisson, survival, response times, ordinal,
zero-inflated, hurdle, and even non-linear models all in a
multilevel context. Further modeling options include auto-correlation
and smoothing terms, user defined dependence structures, censored data,
meta-analytic standard errors, and quite a few more.
In addition, all parameters of the response distribution can be predicted
in order to perform distributional regression.
Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs.
In addition, model fit can easily be assessed and compared with
posterior predictive checks and leave-one-out cross-validation.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>
Diff between brms versions 1.4.0 dated 2017-01-27 and 1.5.0 dated 2017-02-17
DESCRIPTION | 15 MD5 | 167 ++-- NAMESPACE | 22 R/brmsfit-helpers.R | 102 +- R/brmsfit-methods.R | 226 +++--- R/brmsformula.R | 115 ++- R/correlations.R | 6 R/data-helpers.R | 366 +-------- R/data-predictor.R |only R/distributions.R | 357 +++++++-- R/extract_draws.R | 431 +++++++---- R/families.R | 113 ++- R/fitted.R | 459 ++++++------ R/formula-helpers.R | 49 - R/generics.R | 57 + R/linear_predictor.R | 179 ++-- R/loglik.R | 103 +- R/make_stancode.R | 180 ++-- R/make_standata.R | 115 +-- R/misc.R | 99 ++ R/predict.R | 89 +- R/priors.R | 493 +++++++------ R/rename.R | 616 +++++++++------- R/stan-helpers.R | 650 ++++++----------- R/stan-likelihood.R |only R/stan-predictor.R | 666 ++++++++++------- R/sysdata.rda |binary R/validate.R | 940 +++++++++++++------------ build/vignette.rds |binary inst/NEWS.Rd | 36 inst/chunks/fun_gen_extreme_value.stan |only inst/chunks/fun_horseshoe.stan |only inst/chunks/fun_hurdle_gamma.stan | 8 inst/chunks/fun_hurdle_lognormal.stan | 8 inst/chunks/fun_hurdle_negbinomial.stan | 8 inst/chunks/fun_hurdle_poisson.stan | 8 inst/chunks/fun_scale_xi.stan |only inst/chunks/fun_zero_inflated_beta.stan | 8 inst/chunks/fun_zero_inflated_binomial.stan | 10 inst/chunks/fun_zero_inflated_negbinomial.stan | 10 inst/chunks/fun_zero_inflated_poisson.stan | 10 inst/doc/brms_distreg.R | 2 inst/doc/brms_distreg.html | 4 inst/doc/brms_families.Rmd | 19 inst/doc/brms_families.html | 16 inst/doc/brms_monotonic.R | 2 inst/doc/brms_monotonic.html | 4 inst/doc/brms_multilevel.ltx |only inst/doc/brms_multilevel.pdf |only inst/doc/brms_nonlinear.R | 2 inst/doc/brms_nonlinear.html | 4 inst/doc/brms_overview.pdf |binary inst/doc/brms_phylogenetics.R | 2 inst/doc/brms_phylogenetics.html | 4 man/VarCorr.brmsfit.Rd | 8 man/brmsfamily.Rd | 16 man/coef.brmsfit.Rd | 2 man/fitted.brmsfit.Rd | 8 man/horseshoe.Rd |only man/inv_logit_scaled.Rd |only man/lasso.Rd |only man/logit_scaled.Rd |only man/marginal_effects.Rd | 6 man/marginal_smooths.Rd | 8 man/plot.brmsfit.Rd | 3 man/predict.brmsfit.Rd | 2 man/print.brmsfit.Rd | 4 man/ranef.brmsfit.Rd | 4 man/set_prior.Rd | 9 man/summary.brmsfit.Rd | 3 tests/testthat/tests.brm.R | 6 tests/testthat/tests.brmsfit-helpers.R | 5 tests/testthat/tests.brmsfit-methods.R | 36 tests/testthat/tests.distributions.R | 8 tests/testthat/tests.fitted.R | 42 - tests/testthat/tests.loglik.R | 79 +- tests/testthat/tests.make_stancode.R | 236 +++--- tests/testthat/tests.make_standata.R | 11 tests/testthat/tests.misc.R | 21 tests/testthat/tests.predict.R | 52 - tests/testthat/tests.priors.R | 7 tests/testthat/tests.rename.R | 68 - tests/testthat/tests.stan_functions.R | 8 tests/testthat/tests.validate.R | 10 vignettes/brms_families.Rmd | 19 vignettes/brms_multilevel.ltx |only vignettes/children/SETTINGS-knitr.txt | 2 vignettes/citations.bib | 506 +++++++++---- vignettes/me_loss1.pdf |only vignettes/me_loss1_year.pdf |only vignettes/me_loss3_year.pdf |only vignettes/me_zinb1.pdf |only vignettes/ppc_mm1.pdf |only 93 files changed, 4460 insertions(+), 3509 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 2.1.0 dated 2016-09-26 and 2.1.1 dated 2017-02-17
DESCRIPTION | 6 - MD5 | 24 +++---- NEWS | 4 + R/as.char.R | 2 R/lib.R | 52 ++++++++------- R/palette.R | 29 ++++++-- R/prp.R | 1 R/show.prp.palettes.R | 6 - inst/doc/prp.pdf |binary inst/slowtests/make.bat | 2 inst/slowtests/test.prp.Rout.save | 126 +++++++++++++++++++------------------- man/prp.Rd | 2 man/rpart.plot.Rd | 2 13 files changed, 138 insertions(+), 118 deletions(-)
Title: Quality Report Generation for MaxQuant Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (see <http://www.maxquant.org>).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015) <doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow <chris.bielow@mdc-berlin.de>
Maintainer: Chris Bielow <chris.bielow@mdc-berlin.de>
Diff between PTXQC versions 0.80.14 dated 2016-10-13 and 0.82.2 dated 2017-02-17
DESCRIPTION | 8 - MD5 | 36 ++--- NEWS | 23 +++ R/fcn_YAML.R | 2 R/fcn_computeQC.R | 28 +++- R/fcn_plots.R | 4 R/qcMetric.R | 1 R/qcMetric_EVD.R | 6 R/qcMetric_MSMSScans.R | 180 ++++++++++++++++++++++++++ README.md | 73 +++++----- inst/doc/PTXQC-Basic_Guide_for_R_users.html | 133 +++++++++++-------- inst/doc/PTXQC-CustomizeReport.Rmd | 29 +++- inst/doc/PTXQC-CustomizeReport.html | 22 ++- inst/doc/PTXQC-DragNDrop.html | 4 inst/doc/PTXQC-FAQ.html | 4 inst/doc/PTXQC-Input_And_Output_Data.html | 4 inst/dragNdrop/README.md | 36 +++-- inst/reportTemplate/PTXQC_report_template.Rmd | 4 vignettes/PTXQC-CustomizeReport.Rmd | 29 +++- 19 files changed, 465 insertions(+), 161 deletions(-)
Title: A Shiny GUI for some Parameter Estimation Examples
Description: Allows specification and fitting of some parameter
estimation examples inspired by time-resolved spectroscopy via
a Shiny GUI.
Author: Joris Snellenburg [cre, aut],
Katharine Mullen [aut],
Ivo van Stokkum [aut]
Maintainer: Joris Snellenburg <j.snellenburg@vu.nl>
Diff between paramGUI versions 2.1.1 dated 2017-02-09 and 2.1.2 dated 2017-02-17
DESCRIPTION | 6 MD5 | 39 +- NAMESPACE | 89 ++--- R/example_dataset.R | 24 - R/paramGUI-package.R | 16 R/paramGUI.R | 716 ++++++++++++++++++++++-------------------- R/runApp.R | 56 +-- README.md |only inst/shinyApps/paramGUI/app.R | 60 ++- man/calcE.Rd | 42 +- man/example_dataset.Rd | 44 +- man/is_compressed.Rd | 40 +- man/is_rdata.Rd | 36 +- man/kroneckercol.Rd | 40 +- man/linlogtics.Rd | 44 +- man/paramGUI.Rd | 22 - man/plotterforGUI.Rd | 70 ++-- man/runGUI.Rd | 42 +- man/simndecay_gen_paramGUI.Rd | 184 +++++----- man/spectemp.Rd | 54 +-- man/startGUI.Rd | 24 - 21 files changed, 871 insertions(+), 777 deletions(-)
Title: Power Analysis Tools for Multilevel Randomized Experiments
Description:
Statistical power analysis tools for designing multilevel randomized experiments.
Includes functions to calculate statistical power (1 - type II error), minimum detectable effect size (MDES),
minimum required sample size (MRSS), functions to solve constrained optimal sample allocation (COSA) problems,
and to visualize duo or trio relationships between statistical power, MDES, MRSS, and a component of COSA.
Author:
Metin Bulus [aut,cre]
Nianbo Dong [aut,cre]
Maintainer: Metin Bulus <bulus.metin@gmail.com>
Diff between PowerUpR versions 0.1.2 dated 2016-11-01 and 0.1.3 dated 2017-02-17
DESCRIPTION | 19 +++--- MD5 | 136 +++++++++++++++++++++++++----------------------- NAMESPACE | 9 ++- NEWS.md | 9 ++- R/obj.conv.R | 26 +++++++-- R/t1t2.error.R | 10 +-- README.md | 43 +++++++++------ build |only inst |only man/PowerUpR.Rd | 2 man/mdes.bcra3f2.Rd | 6 +- man/mdes.bcra3r2.Rd | 6 +- man/mdes.bcra4f3.Rd | 8 +- man/mdes.bcra4r2.Rd | 8 +- man/mdes.bcra4r3.Rd | 8 +- man/mdes.bira2c1.Rd | 6 +- man/mdes.bira2f1.Rd | 6 +- man/mdes.bira2r1.Rd | 6 +- man/mdes.bira3r1.Rd | 6 +- man/mdes.bira4r1.Rd | 8 +- man/mdes.cra2r2.Rd | 6 +- man/mdes.cra3r3.Rd | 6 +- man/mdes.cra4r4.Rd | 8 +- man/mdes.ira1r1.Rd | 6 +- man/mdes.to.pctl.Rd |only man/mrss.bcra3f2.Rd | 5 - man/mrss.bcra3r2.Rd | 5 - man/mrss.bcra4f3.Rd | 7 +- man/mrss.bcra4r2.Rd | 7 +- man/mrss.bcra4r3.Rd | 7 +- man/mrss.bira2c1.Rd | 5 - man/mrss.bira2f1.Rd | 5 - man/mrss.bira2r1.Rd | 5 - man/mrss.bira3r1.Rd | 5 - man/mrss.bira4r1.Rd | 7 +- man/mrss.cra2r2.Rd | 5 - man/mrss.cra3r3.Rd | 5 - man/mrss.cra4r4.Rd | 7 +- man/mrss.ira1r1.Rd | 4 - man/optimal.bcra3f2.Rd | 2 man/optimal.bcra3r2.Rd | 2 man/optimal.bcra4f3.Rd | 4 - man/optimal.bcra4r2.Rd | 4 - man/optimal.bcra4r3.Rd | 4 - man/optimal.bira2c1.Rd | 2 man/optimal.bira2f1.Rd | 2 man/optimal.bira2r1.Rd | 2 man/optimal.bira3r1.Rd | 2 man/optimal.bira4r1.Rd | 4 - man/optimal.cra2r2.Rd | 2 man/optimal.cra3r3.Rd | 2 man/optimal.cra4r4.Rd | 4 - man/optimal.ira1r1.Rd | 2 man/optimal.to.power.Rd | 2 man/power.bcra3f2.Rd | 6 +- man/power.bcra3r2.Rd | 6 +- man/power.bcra4f3.Rd | 8 +- man/power.bcra4r2.Rd | 8 +- man/power.bcra4r3.Rd | 8 +- man/power.bira2c1.Rd | 6 +- man/power.bira2f1.Rd | 6 +- man/power.bira2r1.Rd | 6 +- man/power.bira3r1.Rd | 6 +- man/power.bira4r1.Rd | 8 +- man/power.cra2r2.Rd | 6 +- man/power.cra3r3.Rd | 6 +- man/power.cra4r4.Rd | 8 +- man/power.ira1r1.Rd | 6 +- man/power.to.mdes.Rd |only vignettes |only 70 files changed, 297 insertions(+), 264 deletions(-)
Title: Three Dimensional PCA Plots
Description: Functions simplifying presentation of PCA models in a 3D interactive representation using 'rgl'.
Author: January Weiner
Maintainer: January Weiner <january.weiner@gmail.com>
Diff between pca3d versions 0.8 dated 2015-07-01 and 0.10 dated 2017-02-17
pca3d-0.10/pca3d/ChangeLog | 3 +++ pca3d-0.10/pca3d/DESCRIPTION | 9 +++++---- pca3d-0.10/pca3d/MD5 | 15 +++++++-------- pca3d-0.10/pca3d/build |only pca3d-0.10/pca3d/inst |only pca3d-0.10/pca3d/vignettes/pca3d.rmd | 1 + pca3d-0.8/pca3d/vignettes/CanvasMatrix.js |only pca3d-0.8/pca3d/vignettes/ellipses.png |only pca3d-0.8/pca3d/vignettes/fancy.png |only pca3d-0.8/pca3d/vignettes/first_plot.png |only pca3d-0.8/pca3d/vignettes/pca3d.pdf |only 11 files changed, 16 insertions(+), 12 deletions(-)
Title: Simulating and Analyzing Time to Event Data in the Presence of
Population Mortality
Description: Implements two methods: a nonparametric risk adjustment and a
data imputation method that use general population mortality tables to allow a
correct analysis of time to disease recurrence. Also includes a powerful set of
object oriented survival data simulation functions.
Author: Tomaz Stupnik [aut, cre],
Maja Pohar Perme [ctb]
Maintainer: Tomaz Stupnik <tomaz.stupnik@guest.arnes.si>
Diff between missDeaths versions 2.1 dated 2017-02-12 and 2.2 dated 2017-02-17
DESCRIPTION | 8 +-- MD5 | 12 +++- R/RcppExports.R | 5 + R/init.R |only R/library.R | 3 - src/Makevars |only src/RcppExports.cpp | 128 +++++++++++++++++++++++++++++++++---------------- src/init.c |only src/missDeaths-win.def |only 9 files changed, 104 insertions(+), 52 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: 'jamovi' is a framework for creating rich interactive statistical
analyses (see <https://www.jamovi.org> for more information). This package
represents the core libraries which jamovi analyses written in R depend
upon.
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.3.3 dated 2017-02-05 and 0.4.0 dated 2017-02-17
DESCRIPTION | 12 +- MD5 | 21 ++-- NAMESPACE | 3 R/analysis.R | 1 R/column.R | 31 +++++- R/html.R | 1 R/options.R | 14 ++- R/results.R | 1 R/table-fold.R |only R/table.R | 9 + R/utils.R | 22 +++- tests/testthat/test-table.R | 205 ++++++++++++++++++++++++++++++-------------- 12 files changed, 223 insertions(+), 97 deletions(-)
Title: A Maximum Likelihood Approach to the Analysis of Modularity
Description: Fit models of modularity to morphological landmarks. Perform model
selection on results. Fit models with a single within-module correlation or
with separate within-module correlations fitted to each module.
Author: Anjali Goswami, Tim Lucas, Prabu Sivasubramaniam, John Finarelli
Maintainer: Tim Lucas <timcdlucas@gmail.com>
Diff between EMMLi versions 0.0.2 dated 2016-07-13 and 0.0.3 dated 2017-02-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/EMMLi.R | 9 +++++---- 3 files changed, 11 insertions(+), 10 deletions(-)
Title: An R Interface to Brazilian Central Bank and Sidra APIs and the
IPEA Data
Description: Creates an R interface to the Bacen <http://api.bcb.gov.br/> and Sidra <http://api.sidra.ibge.gov.br> APIs and IPEA data <http://www.ipeadata.gov.br/Default.aspx>.
Author: Fernando Teixeira [aut, cre],
Jonatha Azevedo [aut]
Maintainer: Fernando Teixeira <fernando.teixeira@fgv.br>
Diff between ecoseries versions 0.1.00 dated 2017-01-31 and 0.1.1 dated 2017-02-17
DESCRIPTION | 13 ++++----- MD5 | 16 +++++------ NAMESPACE | 4 ++ R/aux_ipeadata.R | 26 +++++++++--------- R/series_bacen.R | 71 +++++++++++++++++++++++++++++++------------------ R/series_ipeadata.R | 17 ++++++++--- R/series_sidra.R | 75 ++++++++++++++++++++++++++++++++++++++++------------ man/series_bacen.Rd | 2 - man/series_sidra.Rd | 13 ++++++--- 9 files changed, 158 insertions(+), 79 deletions(-)
Title: Estimation, Gene Selection, and Survival Prediction Based on the
Compound Covariate Method Under the Cox Proportional Hazard
Model
Description: Estimation, gene selection, and survival prediction based on the compound covariate method under the Cox model with high-dimensional gene expressions.
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627> and
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>. Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.1 dated 2017-01-09 and 3.2 dated 2017-02-17
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- man/CG.Clayton.Rd | 2 +- man/Lung.Rd | 8 ++++---- man/X.pathway.Rd | 8 +++++++- man/X.tag.Rd | 2 +- man/cindex.CV.Rd | 2 +- man/compound.Cox-package.Rd | 4 ++-- man/dependCox.reg.CV.Rd | 4 ++-- man/dependCox.reg.Rd | 4 ++-- 10 files changed, 33 insertions(+), 27 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana, Joan Vila, Héctor Sanz, Gavin Lucas, Judith Peñafiel and David Giménez
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 3.2.2 dated 2016-12-07 and 3.2.3 dated 2017-02-17
DESCRIPTION | 8 - MD5 | 12 - R/export2word.R | 4 inst/doc/changelog | 2 inst/doc/compareGroups_vignette.html | 249 ++++++++++++++++++++--------------- man/compareGroups-package.Rd | 4 man/export2pdf.Rd | 15 +- 7 files changed, 170 insertions(+), 124 deletions(-)
Title: Chronomics Analysis Toolkit (CAT): Analyze Periodicity
Description: Performs analysis of sinusoidal rhythms in time series data: actogram, smoothing, autocorrelation, crosscorrelation, several flavors of cosinor.
Author: Cathy Lee Gierke, Ruth Helget, Germaine Cornelissen-Guillaume
Maintainer: Cathy Lee Gierke <leegi001@umn.edu>
Diff between CATkit versions 3.0.0.1 dated 2017-02-11 and 3.0.0.2 dated 2017-02-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/CatCosinor.rd | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Bayesian Inference for Discrete Weibull Regression
Description: A Bayesian regression model for discrete response, where the conditional distribution is modelled via a discrete Weibull distribution. This package provides an implementation of Metropolis-Hastings and Reversible-Jumps algorithms to draw samples from the posterior. It covers a wide range of regularizations through any two parameter prior. Examples are Laplace (Lasso), Gaussian (ridge), Uniform, Cauchy and customized priors like a mixture of priors. An extensive visual toolbox is included to check the validity of the results as well as several measures of goodness-of-fit.
Author: Hamed Haselimashhadi <hamedhaseli@gmail.com>
Maintainer: Hamed Haselimashhadi <hamedhaseli@gmail.com>
Diff between BDWreg versions 1.0.0 dated 2016-01-12 and 1.2.0 dated 2017-02-17
DESCRIPTION | 10 MD5 | 12 NAMESPACE | 4 R/bayesian.dw.R | 2499 +++++++++++++++++++++++++++++--------------------------- R/main.R | 79 + R/others.R | 8 man/bdw.Rd | 373 ++++---- 7 files changed, 1561 insertions(+), 1424 deletions(-)
Title: Bayesian Random-Effects Meta-Analysis
Description: A collection of functions allowing to derive the posterior distribution of the two parameters in a random-effects meta-analysis, and providing functionality to evaluate joint and marginal posterior probability distributions, predictive distributions, shrinkage effects, etc.
Author: Christian Roever [aut, cre], Tim Friede [ctb]
Maintainer: Christian Roever <christian.roever@med.uni-goettingen.de>
Diff between bayesmeta versions 1.3 dated 2016-11-15 and 1.4 dated 2017-02-17
DESCRIPTION | 8 MD5 | 43 ++--- NAMESPACE | 16 + R/bayesmeta.R | 371 ++++++++++++++++++++++++++++++++++++-------- inst/doc/bayesmeta.html | 12 - man/Cochran1954.Rd | 2 man/CrinsEtAl2014.Rd | 12 - man/GoralczykEtAl2011.Rd | 2 man/HinksEtAl2010.Rd | 24 +- man/Peto1980.Rd | 4 man/RhodesEtAlPrior.Rd | 15 + man/RoweEtAl2000.Rd | 8 man/Rubin1981.Rd | 2 man/SidikJonkman2007.Rd | 4 man/TurnerEtAlPrior.Rd | 13 - man/bayesmeta-package.Rd | 6 man/bayesmeta.Rd | 65 +++---- man/dhalfnormal.Rd |only man/dlomax.Rd | 190 +++++++++------------- man/drayleigh.Rd |only man/forest.bayesmeta.Rd | 2 man/forestplot.bayesmeta.Rd | 6 man/normalmixture.Rd |only man/plot.bayesmeta.Rd | 6 24 files changed, 519 insertions(+), 292 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-08-23 2.0
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.10 dated 2017-01-16 and 0.11 dated 2017-02-17
DESCRIPTION | 8 - MD5 | 65 ++++++++------- NAMESPACE | 4 NEWS | 19 ++++ R/ES.R |only R/VaR.R |only R/arx.R | 214 ++++++++++++++++++++++++++++++---------------------- R/coef.arx.R | 4 R/diagnostics.R | 2 R/eviews.R | 46 +++++++---- R/fitted.isat.R | 6 - R/gets-internal.R | 5 - R/getsm.R | 129 +++---------------------------- R/getsv.R | 121 ----------------------------- R/isat.R | 8 - R/logLik.arx.R | 37 ++++++-- R/ols.R | 36 ++++++-- R/plot.arx.R | 48 +++++++---- R/predict.isat.R | 43 ++++++++++ R/print.arx.R | 113 +++++++++++++-------------- R/print.gets.R | 4 R/print.isat.R | 17 ---- R/recursive.R | 12 +- R/stata.R | 44 ++++++---- R/vcov.arx.R | 5 + data/hpdata.rda |binary data/infldata.rda |only data/so2data.rda |only data/sp500data.rda |only man/ES.Rd |only man/arx.Rd | 6 - man/coef.isat.Rd | 3 man/eviews.Rd | 6 - man/gets-package.Rd | 4 man/hpdata.Rd | 4 man/infldata.Rd |only man/so2data.Rd |only man/sp500data.Rd |only 38 files changed, 480 insertions(+), 533 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre]
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.2.9 dated 2016-12-08 and 1.2.10 dated 2017-02-17
DESCRIPTION | 10 MD5 | 44 +- NEWS.md | 13 R/data.R | 25 + R/mlm.R | 21 - R/mlm_plot.R | 78 ++-- R/utils.R | 34 + README.md | 2 data/MEC2010.rda |only inst/CITATION | 2 inst/chunks/generated_quantities.stan | 36 +- inst/chunks/model.stan | 10 inst/chunks/parameters.stan | 2 inst/chunks/transformed_parameters.stan | 2 man/BLch9.Rd | 1 man/MEC2010.Rd |only man/bmlm.Rd | 1 man/isolate.Rd | 1 man/mlm.Rd | 12 man/mlm_pars_plot.Rd | 3 man/mlm_path_plot.Rd | 17 man/mlm_summary.Rd | 32 + man/tab2doc.Rd | 1 src/include/models.hpp | 561 ++++++++++++++++++++------------ 24 files changed, 573 insertions(+), 335 deletions(-)