Title: Tools for Reading, Tokenizing and Parsing R Code
Description: Tools for the reading and tokenization of R code. The
'sourcetools' package provides both an R and C++ interface for the tokenization
of R code, and helpers for interacting with the tokenized representation of R
code.
Author: Kevin Ushey
Maintainer: Kevin Ushey <kevinushey@gmail.com>
Diff between sourcetools versions 0.1.6 dated 2017-04-05 and 0.1.7 dated 2018-04-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 12 ++++++++++++ inst/include/sourcetools/core/util.h | 4 ++-- inst/include/sourcetools/cursor/TokenCursor.h | 2 +- 5 files changed, 22 insertions(+), 10 deletions(-)
Title: Empirical Data Platform Client
Description: R client for Empirical Data Platform. More information is at <https://empirical.com>. For support, contact support@empirical.com.
Author: Empirical Engineering
Maintainer: Madeleine Thompson <madeleine@empirical.com>
Diff between edpclient versions 0.3.1 dated 2018-03-05 and 0.5.1 dated 2018-04-24
edpclient-0.3.1/edpclient/man/wait_for.Rd |only edpclient-0.5.1/edpclient/DESCRIPTION | 8 edpclient-0.5.1/edpclient/MD5 | 23 - edpclient-0.5.1/edpclient/NAMESPACE | 1 edpclient-0.5.1/edpclient/R/create_population.R | 28 +- edpclient-0.5.1/edpclient/R/dataframes.R | 2 edpclient-0.5.1/edpclient/R/popmod.R | 130 ++-------- edpclient-0.5.1/edpclient/build/partial.rdb |binary edpclient-0.5.1/edpclient/man/build_popmod.Rd | 15 - edpclient-0.5.1/edpclient/man/joint_probability.Rd | 10 edpclient-0.5.1/edpclient/tests/testthat/test_create_population.R | 5 edpclient-0.5.1/edpclient/tests/testthat/test_date_populations.R | 25 + edpclient-0.5.1/edpclient/tests/testthat/test_session.R | 58 ++-- 13 files changed, 127 insertions(+), 178 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.8 dated 2018-02-26 and 1.0.9 dated 2018-04-24
sjlabelled-1.0.8/sjlabelled/R/get_note.R |only sjlabelled-1.0.8/sjlabelled/man/get_note.Rd |only sjlabelled-1.0.9/sjlabelled/DESCRIPTION | 10 sjlabelled-1.0.9/sjlabelled/MD5 | 61 sjlabelled-1.0.9/sjlabelled/NAMESPACE | 5 sjlabelled-1.0.9/sjlabelled/NEWS.md | 16 sjlabelled-1.0.9/sjlabelled/R/deprecated.R |only sjlabelled-1.0.9/sjlabelled/R/drop_labels.R | 16 sjlabelled-1.0.9/sjlabelled/R/get_label.R | 72 - sjlabelled-1.0.9/sjlabelled/R/get_labels.R | 26 sjlabelled-1.0.9/sjlabelled/R/get_model_labels.R | 476 +++---- sjlabelled-1.0.9/sjlabelled/R/get_na.R | 8 sjlabelled-1.0.9/sjlabelled/R/get_values.R | 13 sjlabelled-1.0.9/sjlabelled/R/helpfunctions.R | 234 --- sjlabelled-1.0.9/sjlabelled/R/read_write.R | 46 sjlabelled-1.0.9/sjlabelled/R/remove_all_labels.R | 12 sjlabelled-1.0.9/sjlabelled/R/set_label.R | 26 sjlabelled-1.0.9/sjlabelled/R/set_labels.R | 52 sjlabelled-1.0.9/sjlabelled/R/set_na.R | 37 sjlabelled-1.0.9/sjlabelled/R/zap_labels.R | 53 sjlabelled-1.0.9/sjlabelled/build/vignette.rds |binary sjlabelled-1.0.9/sjlabelled/inst/doc/intro_sjlabelled.R | 24 sjlabelled-1.0.9/sjlabelled/inst/doc/intro_sjlabelled.Rmd | 822 +++++------- sjlabelled-1.0.9/sjlabelled/inst/doc/intro_sjlabelled.html | 870 ++++++------- sjlabelled-1.0.9/sjlabelled/inst/doc/labelleddata.Rmd | 210 +-- sjlabelled-1.0.9/sjlabelled/inst/doc/labelleddata.html | 46 sjlabelled-1.0.9/sjlabelled/man/get_term_labels.Rd | 13 sjlabelled-1.0.9/sjlabelled/man/set_label.Rd | 8 sjlabelled-1.0.9/sjlabelled/man/set_note.Rd | 33 sjlabelled-1.0.9/sjlabelled/man/zap_labels.Rd | 25 sjlabelled-1.0.9/sjlabelled/man/zap_na_tags.Rd | 8 sjlabelled-1.0.9/sjlabelled/vignettes/intro_sjlabelled.Rmd | 822 +++++------- sjlabelled-1.0.9/sjlabelled/vignettes/labelleddata.Rmd | 210 +-- 33 files changed, 2000 insertions(+), 2254 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre],
Peter Rousseeuw [ctb] (Qn and Sn),
Christophe Croux [ctb] (Qn and Sn),
Valentin Todorov [aut] (most robust Cov),
Andreas Ruckstuhl [aut] (nlrob, anova, glmrob),
Matias Salibian-Barrera [aut] (lmrob orig.),
Tobias Verbeke [ctb, fnd] (mc, adjbox),
Manuel Koller [aut] (lmrob, psi-func.),
Eduardo L. T. Conceicao [aut] (MM-, tau-, CM-, and MTL- nlrob),
Maria Anna di Palma [ctb] (initial version of Comedian)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.92-8 dated 2017-11-01 and 0.93-0 dated 2018-04-24
robustbase-0.92-8/robustbase/vignettes/psi-GGW.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-Hampel.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-Huber.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-LQQ.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-Welsh.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-bisquare.pdf |only robustbase-0.92-8/robustbase/vignettes/psi-optimal.pdf |only robustbase-0.93-0/robustbase/DESCRIPTION | 14 robustbase-0.93-0/robustbase/MD5 | 144 - robustbase-0.93-0/robustbase/NAMESPACE | 4 robustbase-0.93-0/robustbase/R/lmrob.M.S.R | 22 robustbase-0.93-0/robustbase/R/lmrob.MM.R | 111 robustbase-0.93-0/robustbase/R/lmrob.R | 9 robustbase-0.93-0/robustbase/R/nlregrob.R | 47 robustbase-0.93-0/robustbase/R/nlrob.R | 68 robustbase-0.93-0/robustbase/build/partial.rdb |binary robustbase-0.93-0/robustbase/build/vignette.rds |binary robustbase-0.93-0/robustbase/data/steamUse.rda |only robustbase-0.93-0/robustbase/inst/NEWS.Rd | 54 robustbase-0.93-0/robustbase/inst/doc/fastMcd-kmini.pdf |binary robustbase-0.93-0/robustbase/inst/doc/lmrob_simulation.R | 1377 ++++------ robustbase-0.93-0/robustbase/inst/doc/lmrob_simulation.Rnw | 434 +-- robustbase-0.93-0/robustbase/inst/doc/lmrob_simulation.pdf |binary robustbase-0.93-0/robustbase/inst/doc/psi_functions.pdf |binary robustbase-0.93-0/robustbase/inst/include |only robustbase-0.93-0/robustbase/inst/xtraR/m-s_fns.R | 5 robustbase-0.93-0/robustbase/man/M.psi.Rd | 38 robustbase-0.93-0/robustbase/man/lmrob..D..fit.Rd | 3 robustbase-0.93-0/robustbase/man/lmrob..M..fit.Rd | 3 robustbase-0.93-0/robustbase/man/lmrob.M.S.Rd | 7 robustbase-0.93-0/robustbase/man/lmrob.Rd | 9 robustbase-0.93-0/robustbase/man/lmrob.S.Rd | 33 robustbase-0.93-0/robustbase/man/lmrob.control.Rd | 50 robustbase-0.93-0/robustbase/man/lmrob.fit.Rd | 3 robustbase-0.93-0/robustbase/man/lmrob.lar.Rd | 12 robustbase-0.93-0/robustbase/man/nlrob-algos.Rd | 20 robustbase-0.93-0/robustbase/man/nlrob.Rd | 10 robustbase-0.93-0/robustbase/man/psiFindc.Rd | 42 robustbase-0.93-0/robustbase/man/steamUse.Rd |only robustbase-0.93-0/robustbase/src/init.c | 26 robustbase-0.93-0/robustbase/src/lmrob.c | 270 + robustbase-0.93-0/robustbase/src/robustbase.h | 12 robustbase-0.93-0/robustbase/tests/NAcoef.R | 1 robustbase-0.93-0/robustbase/tests/NAcoef.Rout.save | 335 +- robustbase-0.93-0/robustbase/tests/Rsquared.Rout.save | 40 robustbase-0.93-0/robustbase/tests/lmrob-data.R | 3 robustbase-0.93-0/robustbase/tests/lmrob-ex12.R | 22 robustbase-0.93-0/robustbase/tests/lmrob-methods.Rout.save | 53 robustbase-0.93-0/robustbase/tests/lmrob-psifns.Rout.save | 110 robustbase-0.93-0/robustbase/tests/m-s-estimator.R | 3 robustbase-0.93-0/robustbase/tests/nlregrob-tst.R | 44 robustbase-0.93-0/robustbase/tests/nlrob-tst.R | 16 robustbase-0.93-0/robustbase/tests/weights.R | 2 robustbase-0.93-0/robustbase/tests/weights.Rout.save | 37 robustbase-0.93-0/robustbase/vignettes/lmrob_simulation.Rnw | 434 +-- robustbase-0.93-0/robustbase/vignettes/plot-fig-AdB2-1.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-Mscale-all.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-Mscale.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-cpr.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-efficiency-all.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-efficiency.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-emp-level.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-example-design.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-lqq-level.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-max-asymptotic-bias.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-meanscale.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-power-1-0_2.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-power-1-0_4.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-power-1-0_6.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-power-1-0_8.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-power-1-1.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-pred-points.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-psi-functions.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-qscale-all.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-qscale.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-sdAdB2-1.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-sdscale-1.pdf |binary robustbase-0.93-0/robustbase/vignettes/plot-fig-sdscale-all.pdf |binary 78 files changed, 2036 insertions(+), 1891 deletions(-)
Title: 'Lex' and 'Yacc'
Description: R implementation of the common parsing tools 'lex' and 'yacc'.
Author: Marek Jagielski [aut, cre, cph],
David M. Beazley [aut, cph],
Yasutaka Tanaka [ctb],
Henrico Witvliet [ctb]
Maintainer: Marek Jagielski <marek.jagielski@gmail.com>
Diff between rly versions 1.5 dated 2018-03-26 and 1.6.1 dated 2018-04-24
DESCRIPTION | 13 ++++++++----- MD5 | 5 +++-- R/lex.R | 8 +++++++- tests/testthat/test.lex_variable.R |only 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting and planning
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 0.2.4 dated 2018-03-13 and 0.2.5 dated 2018-04-24
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/AUCTest.R | 6 +++--- R/ChiSqTest.R | 2 +- R/CohenD.R | 2 +- R/CorTest.R | 2 +- R/EmpiricalFns.R | 4 ++-- R/FTest.R | 8 ++++---- R/TTest.R | 2 +- R/pwr.R | 2 +- R/toPresentation.R | 2 +- build/vignette.rds |binary inst/doc/lmExample.html | 4 ++-- inst/doc/sigrFormatting.html | 4 ++-- 15 files changed, 41 insertions(+), 37 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.2.0 dated 2018-04-24 and 0.2.1 dated 2018-04-24
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/completion.R | 12 +++++++++++- R/formatting.R | 4 ++-- R/handlers-langfeatures.R | 15 ++++++++++----- R/hover.R | 12 +++++++++++- R/signature.R | 13 ++++++++++++- R/utils.R | 28 +++++++++++++++++++++++----- 8 files changed, 79 insertions(+), 25 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: Actual Evapotranspiration with Energy Balance Models
Description: Tools and functions to calculate actual Evapotranspiration
using surface energy balance models.
Author: Guillermo Federico Olmedo [aut, cre], Samuel Ortega-Farías [aut],
David Fonseca-Luengo [aut], Daniel de la Fuente-Sáiz [aut], Fernando Fuentes
Peñailillo [aut], María Victoria Munafó [ctb]
Maintainer: Guillermo Federico Olmedo <guillermo.olmedo@gmail.com>
Diff between water versions 0.7 dated 2017-10-15 and 0.8 dated 2018-04-24
DESCRIPTION | 8 MD5 | 40 +-- NAMESPACE | 1 NEWS | 9 R/water_METRIC.R | 27 ++ R/water_RSfunctions.R | 41 +++ R/water_netRadiation.G.R | 20 + R/water_sensibleHeatFlux.R | 12 - README.md | 3 build/vignette.rds |binary inst/CITATION |only inst/doc/Landsat8.html | 342 +++++++++++++++++++++++++------- inst/doc/METRIC_advanced.html | 445 ++++++++++++++++++++++++++++++------------ inst/doc/METRIC_simple.html | 375 +++++++++++++++++++++++++++-------- man/METRIC.EB.Rd | 13 - man/calcRadiance.Rd | 4 man/calcSR.Rd | 4 man/calcTOAr.Rd | 4 man/cfmask.Rd |only man/loadImage.Rd | 2 man/loadImageSR.Rd | 2 man/soilHeatFlux.Rd | 5 22 files changed, 1031 insertions(+), 326 deletions(-)
Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and model diagnostics, in the univariate
and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.5-1 dated 2017-11-22 and 1.5-2 dated 2018-04-24
DESCRIPTION | 8 +-- MD5 | 12 ++-- NEWS | 10 +++ R/sn-funct.R | 142 +++++++++++++++++++++++++++++++----------------------- man/dst.Rd | 4 - man/selm.Rd | 17 +++--- man/sn-package.Rd | 4 - 7 files changed, 112 insertions(+), 85 deletions(-)
Title: Bayesian Model to Find Changepoints Based on Rates and Count
Data
Description: This function fits a reversible jump Bayesian piecewise exponential model that also includes the intensity of each event considered along with the rate of events.
Author: Andrew G. Chapple
Maintainer: Andrew G. Chapple <agc6@rice.edu>
Diff between PieceExpIntensity versions 1.0.2 dated 2018-03-28 and 1.0.4 dated 2018-04-24
PieceExpIntensity-1.0.2/PieceExpIntensity/R/PieceExpIntensity1.R |only PieceExpIntensity-1.0.2/PieceExpIntensity/man/PieceExpIntensity1.Rd |only PieceExpIntensity-1.0.4/PieceExpIntensity/DESCRIPTION | 6 - PieceExpIntensity-1.0.4/PieceExpIntensity/MD5 | 17 +- PieceExpIntensity-1.0.4/PieceExpIntensity/NAMESPACE | 2 PieceExpIntensity-1.0.4/PieceExpIntensity/R/PieceExpIntensity.R | 8 + PieceExpIntensity-1.0.4/PieceExpIntensity/R/RcppExports.R | 22 +++ PieceExpIntensity-1.0.4/PieceExpIntensity/man/PieceExpIntensity.Rd | 2 PieceExpIntensity-1.0.4/PieceExpIntensity/man/PieceExpIntensity2.Rd |only PieceExpIntensity-1.0.4/PieceExpIntensity/src/PieceRATE13.cpp | 57 +++------- PieceExpIntensity-1.0.4/PieceExpIntensity/src/RcppExports.cpp | 10 - 11 files changed, 66 insertions(+), 58 deletions(-)
More information about PieceExpIntensity at CRAN
Permanent link
Title: Simulation, Estimation, Model Selection and Forecasting for MARX
Models
Description: Simulate, estimate (by t-MLE), select and forecast mixed causal-noncausal autoregressive models with possibly exogenous regressors, using methods proposed in Lanne and Saikkonen (2011) <doi:10.2202/1941-1928.1080> and Hecq et al. (2016) <doi:10.15609/annaeconstat2009.123-124.0307>.
Author: Sean Telg [aut, cre, cph],
Alain Hecq [ctb],
Lenard Lieb [ctb]
Maintainer: Sean Telg <j.telg@maastrichtuniversity.nl>
Diff between MARX versions 0.1 dated 2017-06-16 and 0.2 dated 2018-04-24
DESCRIPTION | 21 - MD5 | 37 +- NAMESPACE | 5 R/MARX_functions.R | 721 +++++++++++++++++++++++++++------------------- man/aic.Rd | 1 man/arx.ls.Rd | 3 man/bic.Rd | 1 man/companion.form.Rd |only man/compute.MA.Rd |only man/forecast.marx.Rd |only man/hq.Rd | 1 man/inference.Rd | 1 man/ll.max.Rd | 1 man/marx.Rd | 4 man/marx.t.Rd | 5 man/mixed.Rd | 9 man/pseudo.Rd | 6 man/regressor.matrix.Rd | 3 man/selection.lag.Rd | 1 man/selection.lag.lead.Rd | 3 man/sim.marx.Rd | 1 21 files changed, 491 insertions(+), 333 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models
with missing values in covariates or the dependent variable
using maximum likelihood or Bayesian estimation (Ibrahim et al., 2005;
<doi:10.1198/016214504000001844>). The regression model can be nonlinear
(e.g., including interaction or quadratic effects).
Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 0.6-17 dated 2018-02-16 and 0.7-19 dated 2018-04-24
DESCRIPTION | 21 ++++++---- MD5 | 46 +++++++++++++---------- NAMESPACE | 4 +- R/RcppExports.R |only R/frm2datlist.R | 8 ++-- R/frm_em.R | 19 +++++---- R/frm_em_avcov.R | 4 +- R/frm_em_calc_likelihood.R | 14 ++++--- R/frm_em_calc_likelihood_estimate_model.R | 15 +++++-- R/frm_em_calc_update_observed_likelihood.R | 6 ++- R/frm_linreg_density.R | 26 ++++++++++--- R/frm_normalize_posterior.R | 10 ++--- R/frm_prepare_data_include_latent_data.R | 4 +- R/mdmb_lm_wfit.R |only README.md | 4 ++ inst/NEWS | 13 ++++++ man/data.mb.Rd | 6 +-- man/eval_prior_list.Rd | 4 +- man/frm.Rd | 57 ++++++++++++++++++++++------- man/mdmb-package.Rd | 18 +++++---- man/mdmb_regression.Rd | 8 ++-- man/oprobit_dist.Rd | 6 +-- man/yjt_dist.Rd | 8 ++-- src |only 24 files changed, 198 insertions(+), 103 deletions(-)
Title: Additional Themes, Theme Components and Utilities for 'ggplot2'
Description: A compilation of extra 'ggplot2' themes, scales and utilities, including a
spell check function for plot label fields and an overall emphasis on typography.
A copy of the 'Google' font 'Roboto Condensed' <https://github.com/google/roboto/>
is also included along with a copy of the 'IBM' 'Plex Sans' <https://github.com/IBM/type>
and 'Titillium Web' <https://fonts.google.com/specimen/Titillium+Web> fonts
are also included to support their respective typography-oriented themes.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>),
Patrick Kennedy [ctb],
Philipp Reiner [ctb],
Dan Wilson [ctb] (Secondary axis support),
Xavier Adam [ctb],
Google [cph] (Roboto Condensed & Titillium Web Fonts),
IBM [cph] (Plex Sans Font),
Jacob Barnett [ctb],
Thomas J. Leeper [ctb] (<https://orcid.org/0000-0003-4097-6326>)
Maintainer: Bob Rudis <bob@rud.is>
Diff between hrbrthemes versions 0.1.0 dated 2017-02-26 and 0.5.0 dated 2018-04-24
hrbrthemes-0.1.0/hrbrthemes/README.md |only hrbrthemes-0.1.0/hrbrthemes/tests/testthat/Rplots.pdf |only hrbrthemes-0.5.0/hrbrthemes/DESCRIPTION | 50 +- hrbrthemes-0.5.0/hrbrthemes/MD5 | 102 +++- hrbrthemes-0.5.0/hrbrthemes/NAMESPACE | 25 - hrbrthemes-0.5.0/hrbrthemes/NEWS.md | 45 ++ hrbrthemes-0.5.0/hrbrthemes/R/aaa.r | 9 hrbrthemes-0.5.0/hrbrthemes/R/check.r | 33 + hrbrthemes-0.5.0/hrbrthemes/R/color.r | 2 hrbrthemes-0.5.0/hrbrthemes/R/flush-ticks.R |only hrbrthemes-0.5.0/hrbrthemes/R/hrbrthemes-package.R | 11 hrbrthemes-0.5.0/hrbrthemes/R/ipsum-pdf.R |only hrbrthemes-0.5.0/hrbrthemes/R/ipsum.r |only hrbrthemes-0.5.0/hrbrthemes/R/modern.r |only hrbrthemes-0.5.0/hrbrthemes/R/plexsans.R |only hrbrthemes-0.5.0/hrbrthemes/R/roboto-condensed.r | 87 ++-- hrbrthemes-0.5.0/hrbrthemes/R/scales.r | 48 ++ hrbrthemes-0.5.0/hrbrthemes/R/theme-ipsum.r | 47 +- hrbrthemes-0.5.0/hrbrthemes/R/titillium-web.R |only hrbrthemes-0.5.0/hrbrthemes/R/utils.r |only hrbrthemes-0.5.0/hrbrthemes/R/zzz.r |only hrbrthemes-0.5.0/hrbrthemes/build/vignette.rds |binary hrbrthemes-0.5.0/hrbrthemes/inst/COPYRIGHTS | 102 ++++ hrbrthemes-0.5.0/hrbrthemes/inst/doc/why_hrbrthemes.Rmd | 4 hrbrthemes-0.5.0/hrbrthemes/inst/doc/why_hrbrthemes.html | 208 +++++++++- hrbrthemes-0.5.0/hrbrthemes/inst/fonts/plex-sans |only hrbrthemes-0.5.0/hrbrthemes/inst/fonts/roboto-slab |only hrbrthemes-0.5.0/hrbrthemes/inst/fonts/titillium-web |only hrbrthemes-0.5.0/hrbrthemes/inst/rmarkdown |only hrbrthemes-0.5.0/hrbrthemes/man/PlexSans.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/RobotoCondensed.Rd | 4 hrbrthemes-0.5.0/hrbrthemes/man/TitilliumWeb.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/flush_ticks.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/gg_check.Rd | 9 hrbrthemes-0.5.0/hrbrthemes/man/hrbrthemes.Rd | 5 hrbrthemes-0.5.0/hrbrthemes/man/import_plex_sans.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/import_roboto_condensed.Rd | 12 hrbrthemes-0.5.0/hrbrthemes/man/import_titillium_web.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/ipsum.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/ipsum_pdf.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/modern_geom_defaults.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/scale_ipsum.Rd | 46 ++ hrbrthemes-0.5.0/hrbrthemes/man/scale_x_percent.Rd | 90 ++-- hrbrthemes-0.5.0/hrbrthemes/man/theme_ipsum.Rd | 21 - hrbrthemes-0.5.0/hrbrthemes/man/theme_ipsum_ps.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/theme_ipsum_rc.Rd | 51 +- hrbrthemes-0.5.0/hrbrthemes/man/theme_ipsum_tw.Rd |only hrbrthemes-0.5.0/hrbrthemes/man/update_geom_font_defaults.Rd | 4 hrbrthemes-0.5.0/hrbrthemes/tests/figs |only hrbrthemes-0.5.0/hrbrthemes/tests/testthat/fontconfig-helper.R |only hrbrthemes-0.5.0/hrbrthemes/tests/testthat/test-hrbrthemes.R | 25 - hrbrthemes-0.5.0/hrbrthemes/tests/testthat/test-themes.R |only hrbrthemes-0.5.0/hrbrthemes/vignettes/why_hrbrthemes.Rmd | 4 53 files changed, 822 insertions(+), 222 deletions(-)
Title: An Interface to Google's 'BigQuery' 'API'
Description: Easily talk to Google's 'BigQuery' database from R.
Author: Hadley Wickham [aut, cre],
Kungliga Tekniska Högskolan [ctb] (strptime implementation),
The NetBSD Foundation, Inc. [ctb] (gmtime implementation),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between bigrquery versions 0.4.1 dated 2017-06-26 and 1.0.0 dated 2018-04-24
bigrquery-0.4.1/bigrquery/R/auth.r |only bigrquery-0.4.1/bigrquery/R/bigrquery.r |only bigrquery-0.4.1/bigrquery/R/datasets.r |only bigrquery-0.4.1/bigrquery/R/dbi-connection.r |only bigrquery-0.4.1/bigrquery/R/dbi-driver.r |only bigrquery-0.4.1/bigrquery/R/dbi-result.r |only bigrquery-0.4.1/bigrquery/R/dplyr-compat.R |only bigrquery-0.4.1/bigrquery/R/dplyr.r |only bigrquery-0.4.1/bigrquery/R/id.R |only bigrquery-0.4.1/bigrquery/R/job-extract.R |only bigrquery-0.4.1/bigrquery/R/job-query.R |only bigrquery-0.4.1/bigrquery/R/job-upload.r |only bigrquery-0.4.1/bigrquery/R/jobs.r |only bigrquery-0.4.1/bigrquery/R/projects.r |only bigrquery-0.4.1/bigrquery/R/query.r |only bigrquery-0.4.1/bigrquery/R/request.r |only bigrquery-0.4.1/bigrquery/R/tabledata.r |only bigrquery-0.4.1/bigrquery/R/tables.r |only bigrquery-0.4.1/bigrquery/R/utils.r |only bigrquery-0.4.1/bigrquery/R/zzz.r |only bigrquery-0.4.1/bigrquery/man/copy_table.Rd |only bigrquery-0.4.1/bigrquery/man/dbi_driver.Rd |only 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bigrquery-0.4.1/bigrquery/tests/testthat/test-datasets.r |only bigrquery-0.4.1/bigrquery/tests/testthat/test-id.r |only bigrquery-0.4.1/bigrquery/tests/testthat/test-sql.R |only bigrquery-0.4.1/bigrquery/tests/testthat/test-tables.r |only bigrquery-1.0.0/bigrquery/DESCRIPTION | 41 + bigrquery-1.0.0/bigrquery/MD5 | 180 +++++--- bigrquery-1.0.0/bigrquery/NAMESPACE | 94 ++++ bigrquery-1.0.0/bigrquery/NEWS.md | 106 ++++ bigrquery-1.0.0/bigrquery/R/RcppExports.R |only bigrquery-1.0.0/bigrquery/R/auth.R |only bigrquery-1.0.0/bigrquery/R/bigrquery.R |only bigrquery-1.0.0/bigrquery/R/bq-dataset.R |only bigrquery-1.0.0/bigrquery/R/bq-download.R |only bigrquery-1.0.0/bigrquery/R/bq-field.R |only bigrquery-1.0.0/bigrquery/R/bq-job.R |only bigrquery-1.0.0/bigrquery/R/bq-param.R |only bigrquery-1.0.0/bigrquery/R/bq-parse.R |only bigrquery-1.0.0/bigrquery/R/bq-perform.R |only bigrquery-1.0.0/bigrquery/R/bq-project.R |only bigrquery-1.0.0/bigrquery/R/bq-projects.R |only bigrquery-1.0.0/bigrquery/R/bq-query.R |only bigrquery-1.0.0/bigrquery/R/bq-refs.R |only bigrquery-1.0.0/bigrquery/R/bq-request.R |only bigrquery-1.0.0/bigrquery/R/bq-table.R |only bigrquery-1.0.0/bigrquery/R/bq-test.R |only bigrquery-1.0.0/bigrquery/R/dbi-connection.R |only bigrquery-1.0.0/bigrquery/R/dbi-driver.R |only bigrquery-1.0.0/bigrquery/R/dbi-result.R |only bigrquery-1.0.0/bigrquery/R/dplyr.R |only bigrquery-1.0.0/bigrquery/R/gs-object.R |only bigrquery-1.0.0/bigrquery/R/old-dataset.R |only bigrquery-1.0.0/bigrquery/R/old-id.R |only bigrquery-1.0.0/bigrquery/R/old-job-extract.R |only bigrquery-1.0.0/bigrquery/R/old-job-query.R |only bigrquery-1.0.0/bigrquery/R/old-job-upload.R |only bigrquery-1.0.0/bigrquery/R/old-job.R |only bigrquery-1.0.0/bigrquery/R/old-project.R |only bigrquery-1.0.0/bigrquery/R/old-projects.R |only bigrquery-1.0.0/bigrquery/R/old-query.R |only bigrquery-1.0.0/bigrquery/R/old-table.R |only bigrquery-1.0.0/bigrquery/R/old-tabledata.R |only bigrquery-1.0.0/bigrquery/R/secret.R |only bigrquery-1.0.0/bigrquery/R/utils.R |only bigrquery-1.0.0/bigrquery/R/zzz.R |only bigrquery-1.0.0/bigrquery/README.md | 215 +++++++--- bigrquery-1.0.0/bigrquery/inst |only bigrquery-1.0.0/bigrquery/man/DBI.Rd | 58 +- bigrquery-1.0.0/bigrquery/man/api-dataset.Rd |only bigrquery-1.0.0/bigrquery/man/api-job.Rd |only bigrquery-1.0.0/bigrquery/man/api-perform.Rd |only bigrquery-1.0.0/bigrquery/man/api-project.Rd |only bigrquery-1.0.0/bigrquery/man/api-table.Rd |only bigrquery-1.0.0/bigrquery/man/bigquery.Rd |only bigrquery-1.0.0/bigrquery/man/bigrquery-package.Rd | 4 bigrquery-1.0.0/bigrquery/man/bq_field.Rd |only bigrquery-1.0.0/bigrquery/man/bq_projects.Rd |only bigrquery-1.0.0/bigrquery/man/bq_query.Rd |only bigrquery-1.0.0/bigrquery/man/bq_refs.Rd |only bigrquery-1.0.0/bigrquery/man/bq_table_download.Rd |only bigrquery-1.0.0/bigrquery/man/bq_test_project.Rd |only bigrquery-1.0.0/bigrquery/man/dataset-dep.Rd |only 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bigrquery-1.0.0/bigrquery/tests/testthat/bq-field-print.txt |only bigrquery-1.0.0/bigrquery/tests/testthat/dbi-connection-print.txt |only bigrquery-1.0.0/bigrquery/tests/testthat/dbi-result-print.txt |only bigrquery-1.0.0/bigrquery/tests/testthat/gs-object-print.txt |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-schema-array-struct.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-schema-array.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-schema-struct-array.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-schema-struct.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-values-array-struct.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-values-array.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-values-struct-array.json |only bigrquery-1.0.0/bigrquery/tests/testthat/parse-values-struct.json |only bigrquery-1.0.0/bigrquery/tests/testthat/setup-auth.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-dataset.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-download.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-field.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-job.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-param.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-parse.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-perform.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-project-api.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-projects.r |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-refs.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-request.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-table.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-bq-test.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-camelCase.R | 2 bigrquery-1.0.0/bigrquery/tests/testthat/test-dbi-connection.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-dbi-driver.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-dbi-result.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-dplyr.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-gs-object.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-query_exec.R | 23 - bigrquery-1.0.0/bigrquery/tests/testthat/test-request.r | 34 - bigrquery-1.0.0/bigrquery/tests/testthat/test-test.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-upload.r | 15 bigrquery-1.0.0/bigrquery/tests/testthat/test-zzz-DBItest.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-zzz-dep-dataset.R |only bigrquery-1.0.0/bigrquery/tests/testthat/test-zzz-dep-id.r |only bigrquery-1.0.0/bigrquery/tests/testthat/test-zzz-dep-tables.R |only 160 files changed, 652 insertions(+), 323 deletions(-)
Title: Text Cleaning Tools
Description: Tools to clean and process text. Tools are geared at checking for
substrings that are not optimal for analysis and replacing or removing
them (normalizing) with more analysis friendly substrings (see Sproat,
Black, Chen, Kumar, Ostendorf, & Richards (2001)
<doi:10.1006/csla.2001.0169>) or extracting them into new variables.
For example, emoticons are often used in text but not always easily
handled by analysis algorithms. The 'replace_emoticon()' function
replaces emoticons with word equivalents.
Author: Tyler Rinker [aut, cre],
ctwheels StackOverflow [ctb]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between textclean versions 0.7.2 dated 2018-04-19 and 0.7.3 dated 2018-04-24
DESCRIPTION | 27 ++++--- MD5 | 14 +-- NEWS | 5 + R/sysdata.rda |binary README.md | 122 ++++++++++++++++----------------- data/DATA.rda |binary inst/CITATION | 4 - tests/testthat/test-replace_emoticon.R | 2 8 files changed, 91 insertions(+), 83 deletions(-)
Title: Similarity Network Fusion
Description: Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.
Author: Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg
Maintainer: Daniel Cole <goldenberglab@gmail.com>
Diff between SNFtool versions 2.2.1 dated 2017-11-24 and 2.3.0 dated 2018-04-24
SNFtool-2.2.1/SNFtool/R/displayClusters.r |only SNFtool-2.3.0/SNFtool/DESCRIPTION | 10 SNFtool-2.3.0/SNFtool/MD5 | 56 ++-- SNFtool-2.3.0/SNFtool/NAMESPACE | 2 SNFtool-2.3.0/SNFtool/R/SNF.R | 123 +++++---- SNFtool-2.3.0/SNFtool/R/affinityMatrix.R | 50 ++- SNFtool-2.3.0/SNFtool/R/calNMI.R | 19 + SNFtool-2.3.0/SNFtool/R/chiDist2.R | 30 +- SNFtool-2.3.0/SNFtool/R/concordanceNetworkNMI.R | 50 +-- SNFtool-2.3.0/SNFtool/R/displayClusters.R |only SNFtool-2.3.0/SNFtool/R/displayClustersWithHeatmap.R | 60 ++-- SNFtool-2.3.0/SNFtool/R/dist2.R | 32 +- SNFtool-2.3.0/SNFtool/R/estimateNumberOfClustersGivenGraph.R | 128 +++++----- SNFtool-2.3.0/SNFtool/R/getColorsForGroups.R | 43 ++- SNFtool-2.3.0/SNFtool/R/groupPredict.r | 62 ++-- SNFtool-2.3.0/SNFtool/R/plotAlluvial.R |only SNFtool-2.3.0/SNFtool/R/rankFeaturesByNMI.R | 84 +++--- SNFtool-2.3.0/SNFtool/R/spectralClustering.r | 70 +++-- SNFtool-2.3.0/SNFtool/R/standardNormalization.R | 24 + SNFtool-2.3.0/SNFtool/man/SNF.Rd | 4 SNFtool-2.3.0/SNFtool/man/affinityMatrix.Rd | 8 SNFtool-2.3.0/SNFtool/man/calNMI.Rd | 2 SNFtool-2.3.0/SNFtool/man/chiDist2.Rd | 13 - SNFtool-2.3.0/SNFtool/man/concordanceNetworkNMI.Rd | 4 SNFtool-2.3.0/SNFtool/man/displayClusters.Rd | 4 SNFtool-2.3.0/SNFtool/man/displayClustersWithHeatmap.Rd | 6 SNFtool-2.3.0/SNFtool/man/dist2.Rd | 4 SNFtool-2.3.0/SNFtool/man/estimateNumberOfClustersGivenGraph.Rd | 4 SNFtool-2.3.0/SNFtool/man/plotAlluvial.Rd |only SNFtool-2.3.0/SNFtool/man/rankFeaturesByNMI.Rd | 4 SNFtool-2.3.0/SNFtool/man/spectralClustering.Rd | 4 31 files changed, 506 insertions(+), 394 deletions(-)
Title: Calculate Text Polarity Sentiment
Description: Calculate text polarity sentiment at the sentence level and
optionally aggregate by rows or grouping variable(s).
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between sentimentr versions 2.2.3 dated 2018-01-16 and 2.3.2 dated 2018-04-24
DESCRIPTION | 18 ++--- MD5 | 40 ++++++------- NAMESPACE | 1 NEWS | 18 +++++ R/highlight.R | 7 +- R/sentiment_by.R | 48 +++++++++++++++ R/sentimentr-package.R | 13 ++-- R/utils.R | 2 README.md | 110 ++++++++++++++++++------------------ data/cannon_reviews.rda |binary inst/CITATION | 4 - inst/sfp/sfp | 4 - man/cannon_reviews.Rd | 5 - man/course_evaluations.Rd | 2 man/highlight.Rd | 7 +- man/hotel_reviews.Rd | 2 man/kaggle_movie_reviews.Rd | 2 man/nyt_articles.Rd | 2 man/sentiment_by.Rd | 51 ++++++++++++++++ tools/figure/highlight.png |binary tools/figure/unnamed-chunk-11-1.png |binary 21 files changed, 230 insertions(+), 106 deletions(-)
Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymise data, and fitting discretised Gamma distributions.
Author: Thibaut Jombart [aut, cre],
Anne Cori [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between epitrix versions 0.1.2 dated 2018-03-01 and 0.2.0 dated 2018-04-24
epitrix |only 1 file changed
Title: Detrend Images
Description: Image series affected by bleaching must be corrected by
'detrending' prior to the performance of quantitative analysis.
'detrendr' is for correctly detrending images. It uses Nolan's algorithm
(Nolan et al., 2017 <doi:10.1093/bioinformatics/btx434>).
Author: Rory Nolan [aut, cre, cph],
Sergi Padilla-Parra [ths, cph]
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between detrendr versions 0.5.0 dated 2018-04-19 and 0.5.1 dated 2018-04-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 8 +++++++- inst/doc/detrendr.html | 18 +++++++++--------- tests/testthat/test-myrs.R | 15 +++++++++++---- tests/testthat/test-utils.R | 20 ++++++++++++++------ 6 files changed, 51 insertions(+), 30 deletions(-)
Title: NMF-EM Algorithm
Description: Provides a version of the Expectation-Maximization algorithm for
mix-models, reducing the numbers of parameters to estimate using
Non-negative Matrix Factorization methods.
For more explanations, see pre-print of Carel and Alquier (2017) <arXiv:1709.03346>.
Author: Lena Carel [aut, cre]
Maintainer: Lena Carel <lena.carel@gmail.com>
Diff between nmfem versions 1.0.2 dated 2018-04-23 and 1.0.3 dated 2018-04-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/nmfem_mult.R | 7 ++++--- inst/doc/NMFEM_for_travelers.html | 4 ++-- 4 files changed, 12 insertions(+), 11 deletions(-)
Title: Semi-Parametric Variance Regression
Description: Methods for fitting semi-parametric mean and variance models, with normal or censored data. Also extended to allow a regression in the location, scale and shape parameters.
Author: Kristy Robledo [aut, cre],
Ian Marschner [ths]
Maintainer: Kristy Robledo <robledo.kristy@gmail.com>
Diff between VarReg versions 1.0.1 dated 2017-05-30 and 1.0.2 dated 2018-04-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/censlinVarReg.R | 1 - 3 files changed, 5 insertions(+), 6 deletions(-)
Title: A Time Series Toolbox for Official Statistics
Description: Plot official statistics' time series conveniently: automatic legends, highlight windows, stacked bar chars with positive and negative contributions, sum-as-line option, two y-axes with automatic horizontal grids that fit both axes and other popular chart types. 'tstools' comes with a plethora of defaults to let you plot without setting an abundance of parameters first, but gives you the flexibility to tweak the defaults. In addition to charts, 'tstools' provides a super fast, 'data.table' backed time series I/O that allows the user to export / import long format, wide format and transposed wide format data to various file types.
Author: Matthias Bannert [aut, cre],
Severin Thoeni [aut]
Maintainer: Matthias Bannert <bannert@kof.ethz.ch>
Diff between tstools versions 0.3.6 dated 2018-03-13 and 0.3.6.1 dated 2018-04-24
DESCRIPTION | 8 MD5 | 32 +- NAMESPACE | 3 NEWS | 1 R/import_helpers.R | 11 R/low_level_line_plots.R | 24 + R/regularize.R |only R/themes.R | 35 +- R/tsplot.R | 144 +++++++-- R/utils.R | 2 R/write_ts.R | 9 inst/doc/tstools.html | 88 ++--- man/init_tsplot_theme.Rd | 49 +-- man/long_to_ts.Rd |only man/regularize.Rd |only man/tsplot.Rd | 13 man/wide_to_ts.Rd |only tests/testthat/faulty.csv | 26 - tests/testthat/testWriteTimeseries.R | 544 ++++++++++++++++++----------------- 19 files changed, 574 insertions(+), 415 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances, and point-counting data with the chi-square distance. Also included are tools to plot compositional and point-counting data on ternary diagrams, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.9 dated 2018-01-02 and 2.0 dated 2018-04-24
provenance-1.9/provenance/man/as.data.frame.compositional.Rd |only provenance-1.9/provenance/man/subset.compositional.Rd |only provenance-1.9/provenance/man/subset.distributional.Rd |only provenance-2.0/provenance/DESCRIPTION | 12 provenance-2.0/provenance/MD5 | 66 - provenance-2.0/provenance/NAMESPACE | 24 provenance-2.0/provenance/R/gui.R | 168 ++- provenance-2.0/provenance/R/io.R |only provenance-2.0/provenance/R/minsorting.R | 6 provenance-2.0/provenance/R/plot.R | 251 ++-- provenance-2.0/provenance/R/radialplot.R |only provenance-2.0/provenance/R/srd.R | 3 provenance-2.0/provenance/R/ternary.R |only provenance-2.0/provenance/R/toolbox.R | 610 ++++------- provenance-2.0/provenance/data/Namib.rda |binary provenance-2.0/provenance/man/ALR.Rd |only provenance-2.0/provenance/man/CA.Rd |only provenance-2.0/provenance/man/CLR.Rd | 23 provenance-2.0/provenance/man/MDS.Rd | 3 provenance-2.0/provenance/man/PCA.Rd | 9 provenance-2.0/provenance/man/amalgamate.Rd | 3 provenance-2.0/provenance/man/as.acomp.Rd | 2 provenance-2.0/provenance/man/as.compositional.Rd | 4 provenance-2.0/provenance/man/as.data.frame.Rd |only provenance-2.0/provenance/man/central.Rd |only provenance-2.0/provenance/man/combine.Rd | 12 provenance-2.0/provenance/man/diss.Rd | 3 provenance-2.0/provenance/man/lines.ternary.Rd |only provenance-2.0/provenance/man/plot.CA.Rd |only provenance-2.0/provenance/man/plot.KDEs.Rd |only provenance-2.0/provenance/man/plot.compositional.Rd | 2 provenance-2.0/provenance/man/plot.minsorting.Rd | 3 provenance-2.0/provenance/man/plot.ternary.Rd | 23 provenance-2.0/provenance/man/points.ternary.Rd | 8 provenance-2.0/provenance/man/radialplot.Rd |only provenance-2.0/provenance/man/read.compositional.Rd | 23 provenance-2.0/provenance/man/read.counts.Rd |only provenance-2.0/provenance/man/read.densities.Rd | 2 provenance-2.0/provenance/man/read.distributional.Rd | 50 provenance-2.0/provenance/man/subset.Rd |only provenance-2.0/provenance/man/ternary.Rd | 7 provenance-2.0/provenance/man/ternary.ellipse.Rd |only provenance-2.0/provenance/man/text.ternary.Rd |only 43 files changed, 652 insertions(+), 665 deletions(-)
More information about QTL.gCIMapping at CRAN
Permanent link
Title: Survival Analysis
Description: Contains the core survival analysis routines, including
definition of Surv objects,
Kaplan-Meier and Aalen-Johansen (multi-state) curves, Cox models,
and parametric accelerated failure time models.
Author: Terry M Therneau [aut, cre],
Thomas Lumley [ctb, trl] (original S->R port and R maintainer until
2009)
Maintainer: Terry M Therneau <therneau.terry@mayo.edu>
Diff between survival versions 2.42-3 dated 2018-04-16 and 2.42-3.1 dated 2018-04-24
DESCRIPTION | 6 ++--- MD5 | 56 +++++++++++++++++++++++++-------------------------- NAMESPACE | 3 ++ data/bladder.rda |binary data/cancer.rda |binary data/cgd.rda |binary data/colon.rda |binary data/flchain.rda |binary data/genfan.rda |binary data/heart.rda |binary data/kidney.rda |binary data/leukemia.rda |binary data/logan.rda |binary data/lung.rda |binary data/mgus.rda |binary data/mgus2.rda |binary data/myeloid.rda |binary data/nwtco.rda |binary data/ovarian.rda |binary data/pbc.rda |binary data/rats.rda |binary data/retinopathy.rda |binary data/rhDNase.rda |binary data/solder.rda |binary data/stanford2.rda |binary data/survexp.rda |binary data/transplant.rda |binary data/uspop2.rda |binary data/veteran.rda |binary 29 files changed, 34 insertions(+), 31 deletions(-)
Title: Access 'Upwave' API
Description: 'Upwave' <https://www.upwave.io/> is a task management app
organising tasks on boards and cards. 'upwaver' is a wrapper
around the 'Upwave' API <https://upwavehq.github.io/api/> that
allows listing and updating those boards and cards.
Author: Adrian Staempfli, Christoph Strauss, Fabian Leuthold, Michael
Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>
Diff between upwaver versions 1.0.1 dated 2018-01-22 and 1.1.0 dated 2018-04-24
DESCRIPTION | 8 MD5 | 13 NAMESPACE | 1 NEWS.md | 6 R/burndown.R | 44 +++ inst/doc/upwaver.html | 437 ++++++++------------------------- man/storypoints_and_status_released.Rd |only tests/testthat/test-upwaver.R | 2 8 files changed, 177 insertions(+), 334 deletions(-)
Title: Get Real-Time Meteorological Data in SMET Format
Description: It manages snow and weather local time series as provided by
MeteoIO (<http://models.slf.ch/docserver/meteoio/html/index.html>, <http://
www.slf.ch/ueber/organisation/schnee_permafrost/projekte/MeteoIO/index_EN>,
<https://www.openhub.net/p/MeteoIO>). MeteoIO is a C/C++ Open Source library
which has been designed to settle both the needs of carefully crafted
simulations for a specific purpose/study and for the needs of operational
simulations that run automatically and unattended". It is integrated in physical
spatially-distributed models and tackles several issues with weather input/
output data. Here a SMET S4 class object is defined and can be imported from/
exported to a SMET ini files of MeteoIO , allowing interoperability from R to
MeteoIO and other SMET-compliant software.
Author: Emanuele Cordano
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between RSMET versions 1.2.9 dated 2016-03-17 and 1.3.8 dated 2018-04-24
RSMET-1.2.9/RSMET/README.md |only RSMET-1.3.8/RSMET/DESCRIPTION | 22 ++++++-- RSMET-1.3.8/RSMET/MD5 | 33 ++++++------ RSMET-1.3.8/RSMET/NAMESPACE | 1 RSMET-1.3.8/RSMET/R/as.data.frame.R | 59 +++++++++++++++++++++-- RSMET-1.3.8/RSMET/R/as.smet.R | 20 ++++++- RSMET-1.3.8/RSMET/R/collapse.smet.R | 3 + RSMET-1.3.8/RSMET/R/meteofrance.R | 9 +++ RSMET-1.3.8/RSMET/R/meteofranceSynop.R | 6 +- RSMET-1.3.8/RSMET/R/smet-function.R | 14 +++-- RSMET-1.3.8/RSMET/R/zbracket[.replacement.smet.R | 2 RSMET-1.3.8/RSMET/data/meteofrance.rda |binary RSMET-1.3.8/RSMET/data/meteofranceSynop.rda |binary RSMET-1.3.8/RSMET/inst/examples/131.smet |only RSMET-1.3.8/RSMET/inst/examples/84.smet |only RSMET-1.3.8/RSMET/man/as.data.frame.Rd | 7 ++ RSMET-1.3.8/RSMET/man/as.smet.Rd | 9 +++ RSMET-1.3.8/RSMET/man/meteofrance.Rd | 8 ++- RSMET-1.3.8/RSMET/man/meteofranceSynop.Rd | 6 +- 19 files changed, 153 insertions(+), 46 deletions(-)
Title: Marginal Effects for Model Objects
Description: An R port of Stata's 'margins' command, which can be used to
calculate marginal (or partial) effects from model objects.
Author: Thomas J. Leeper [aut, cre] (<https://orcid.org/0000-0003-4097-6326>),
Jeffrey Arnold [ctb],
Vincent Arel-Bundock [ctb]
Maintainer: Thomas J. Leeper <thosjleeper@gmail.com>
Diff between margins versions 0.3.0 dated 2017-03-22 and 0.3.20 dated 2018-04-24
margins-0.3.0/margins/R/delta.R |only margins-0.3.0/margins/R/formulae.R |only margins-0.3.0/margins/R/marginal_effects_methods.R |only margins-0.3.0/margins/R/margins_methods.R |only margins-0.3.20/margins/DESCRIPTION | 30 - margins-0.3.20/margins/LICENSE | 2 margins-0.3.20/margins/MD5 | 94 ++-- margins-0.3.20/margins/NAMESPACE | 12 margins-0.3.20/margins/NEWS.md | 145 +++++- margins-0.3.20/margins/R/build_margins.R | 69 ++ margins-0.3.20/margins/R/cplot.R | 9 margins-0.3.20/margins/R/cplot_clm.R |only margins-0.3.20/margins/R/cplot_polr.R | 4 margins-0.3.20/margins/R/cplot_utilities.R | 30 - margins-0.3.20/margins/R/dydx.R | 140 ++++-- margins-0.3.20/margins/R/find_terms_in_model.R |only margins-0.3.20/margins/R/get_effect_variances.R | 79 ++- margins-0.3.20/margins/R/gradient_factory.R |only margins-0.3.20/margins/R/jacobian.R |only margins-0.3.20/margins/R/marginal_effects.R | 42 + margins-0.3.20/margins/R/marginal_effects_default.R |only margins-0.3.20/margins/R/marginal_effects_glm.R |only margins-0.3.20/margins/R/marginal_effects_lm.R |only margins-0.3.20/margins/R/marginal_effects_loess.R |only margins-0.3.20/margins/R/marginal_effects_merMod.R |only margins-0.3.20/margins/R/marginal_effects_nnet.R |only margins-0.3.20/margins/R/marginal_effects_polr.R |only margins-0.3.20/margins/R/margins.R | 35 + margins-0.3.20/margins/R/margins_betareg.R |only margins-0.3.20/margins/R/margins_default.R |only margins-0.3.20/margins/R/margins_glm.R |only margins-0.3.20/margins/R/margins_lm.R |only margins-0.3.20/margins/R/margins_loess.R |only margins-0.3.20/margins/R/margins_merMod.R |only margins-0.3.20/margins/R/margins_nnet.R |only margins-0.3.20/margins/R/margins_polr.R |only margins-0.3.20/margins/R/margins_svyglm.R |only margins-0.3.20/margins/R/plot.R | 2 margins-0.3.20/margins/R/print.R | 53 +- margins-0.3.20/margins/R/summary.R | 21 margins-0.3.20/margins/R/vcov.R |only margins-0.3.20/margins/README.md | 348 +++++++++------ margins-0.3.20/margins/build/vignette.rds |binary margins-0.3.20/margins/inst/doc/Introduction.R | 17 margins-0.3.20/margins/inst/doc/Introduction.html | 236 +++++++--- margins-0.3.20/margins/inst/doc/Stata.R | 4 margins-0.3.20/margins/inst/doc/Stata.html | 77 +-- margins-0.3.20/margins/inst/doc/TechnicalDetails.Rnw | 2 margins-0.3.20/margins/inst/doc/TechnicalDetails.pdf |binary margins-0.3.20/margins/man/cplot.Rd | 20 margins-0.3.20/margins/man/dydx.Rd | 11 margins-0.3.20/margins/man/marginal_effects.Rd | 71 ++- margins-0.3.20/margins/man/margins.Rd | 77 ++- margins-0.3.20/margins/tests/testthat/tests-core.R | 11 margins-0.3.20/margins/tests/testthat/tests-edge-cases.R |only margins-0.3.20/margins/tests/testthat/tests-methods.R |only margins-0.3.20/margins/tests/testthat/tests-subset.R |only margins-0.3.20/margins/vignettes/Introduction.Rmd | 67 +- margins-0.3.20/margins/vignettes/Stata.Rmd | 23 margins-0.3.20/margins/vignettes/TechnicalDetails.Rnw | 2 margins-0.3.20/margins/vignettes/framed.sty |only margins-0.3.20/margins/vignettes/multirow.sty |only margins-0.3.20/margins/vignettes/references.bib | 8 63 files changed, 1200 insertions(+), 541 deletions(-)
Title: Item Response Models for Multiple Ratings
Description: Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program. See Robitzsch and
Steinfeld (2018) for a description of the functionality
of the package.
Author: Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.8-5 dated 2017-04-27 and 1.0-138 dated 2018-04-24
immer-0.8-5/immer/R/IRT.likelihood.immer_HRM.R |only immer-0.8-5/immer/R/immer_HRM.R |only immer-0.8-5/immer/R/logLik.lc2_agreement.R |only immer-0.8-5/immer/R/loglik_HRM.R |only immer-0.8-5/immer/R/plot.immer_HRM.R |only immer-0.8-5/immer/R/sampling_hrm_mu_theta_1dim.R |only immer-0.8-5/immer/R/simulate_hrm.R |only immer-0.8-5/immer/R/summary.immer_HRM.R |only immer-0.8-5/immer/man/immer_HRM.Rd |only immer-0.8-5/immer/man/simulate_HRM.Rd |only immer-0.8-5/immer/src/HRM_fcts.cpp |only immer-0.8-5/immer/src/init.c |only immer-1.0-138/immer/DESCRIPTION | 18 immer-1.0-138/immer/MD5 | 238 +- immer-1.0-138/immer/NAMESPACE | 59 immer-1.0-138/immer/R/IRT.likelihood.immer_hrm.R |only immer-1.0-138/immer/R/IRT.likelihood_immer.R |only immer-1.0-138/immer/R/MHprop_hrm.R | 11 immer-1.0-138/immer/R/MHprop_refresh.R | 72 immer-1.0-138/immer/R/MHprop_refresh_pars.R |only immer-1.0-138/immer/R/MHprop_refresh_parstype.R |only immer-1.0-138/immer/R/RcppExports.R | 206 ++ immer-1.0-138/immer/R/agree_aicken.R | 5 immer-1.0-138/immer/R/anova_immer.R | 57 immer-1.0-138/immer/R/coef.immer.R |only immer-1.0-138/immer/R/harm_mean.R |only immer-1.0-138/immer/R/immer_FACETS.R | 2 immer-1.0-138/immer/R/immer_IRT_likelihood_gpcm_helper.R |only immer-1.0-138/immer/R/immer_agree2.R | 10 immer-1.0-138/immer/R/immer_attach_list_elements.R |only immer-1.0-138/immer/R/immer_ccml.R |only immer-1.0-138/immer/R/immer_ccml_summary_print_ic.R |only immer-1.0-138/immer/R/immer_cml.R | 270 +- immer-1.0-138/immer/R/immer_cmml.R |only immer-1.0-138/immer/R/immer_cmml_prepare.R |only immer-1.0-138/immer/R/immer_cmml_proc_basispar.R |only immer-1.0-138/immer/R/immer_cmml_proc_parameter_index.R |only immer-1.0-138/immer/R/immer_collect_traces.R | 74 immer-1.0-138/immer/R/immer_convert_factor_data_frame.R |only immer-1.0-138/immer/R/immer_create_design_matrix_A.R |only immer-1.0-138/immer/R/immer_create_design_matrix_A_PCM.R |only immer-1.0-138/immer/R/immer_create_design_matrix_A_PCM2.R |only immer-1.0-138/immer/R/immer_create_design_matrix_formula.R |only immer-1.0-138/immer/R/immer_csink.R |only immer-1.0-138/immer/R/immer_fun_FACETS.R | 2 immer-1.0-138/immer/R/immer_hrm.R |only immer-1.0-138/immer/R/immer_hrm_simulate.R |only immer-1.0-138/immer/R/immer_hrm_verbose_iterations.R |only immer-1.0-138/immer/R/immer_ic_calc.R | 31 immer-1.0-138/immer/R/immer_ic_hrm.R | 32 immer-1.0-138/immer/R/immer_identifiers_relabel.R | 72 immer-1.0-138/immer/R/immer_install.R | 2 immer-1.0-138/immer/R/immer_jml.R |only immer-1.0-138/immer/R/immer_jml_calc_item_intercepts.R |only immer-1.0-138/immer/R/immer_jml_calc_loglike.R |only immer-1.0-138/immer/R/immer_jml_center_theta.R |only immer-1.0-138/immer/R/immer_jml_ic.R |only immer-1.0-138/immer/R/immer_jml_print_progress_line_search.R |only immer-1.0-138/immer/R/immer_jml_proc_shortcut.R |only immer-1.0-138/immer/R/immer_jml_update_item_R.R |only immer-1.0-138/immer/R/immer_jml_update_item_Rcpp.R |only immer-1.0-138/immer/R/immer_jml_update_theta_R.R |only immer-1.0-138/immer/R/immer_jml_update_theta_Rcpp.R |only immer-1.0-138/immer/R/immer_latent_regression.R |only immer-1.0-138/immer/R/immer_matrix2.R |only immer-1.0-138/immer/R/immer_matrix_add_names.R |only immer-1.0-138/immer/R/immer_mcmc_draw_variance.R | 23 immer-1.0-138/immer/R/immer_opcat.R | 39 immer-1.0-138/immer/R/immer_osink.R |only immer-1.0-138/immer/R/immer_proc_data.R |only immer-1.0-138/immer/R/immer_prox.R |only immer-1.0-138/immer/R/immer_reshape_wideformat.R | 2 immer-1.0-138/immer/R/immer_rownorm.R |only immer-1.0-138/immer/R/immer_sampling_calc_ratio.R |only immer-1.0-138/immer/R/immer_score_person_adjusted.R |only immer-1.0-138/immer/R/immer_summary_print_call.R |only immer-1.0-138/immer/R/immer_summary_print_computation_time.R |only immer-1.0-138/immer/R/immer_summary_print_ic.R |only immer-1.0-138/immer/R/immer_summary_print_mcmc_output.R |only immer-1.0-138/immer/R/immer_summary_print_objects.R |only immer-1.0-138/immer/R/immer_summary_print_package_rsession.R |only immer-1.0-138/immer/R/immer_trace.R |only immer-1.0-138/immer/R/immer_trim_increment.R |only immer-1.0-138/immer/R/immer_unique_patterns.R | 2 immer-1.0-138/immer/R/immer_vector_add_names.R |only immer-1.0-138/immer/R/inits_item_parameters.R | 21 immer-1.0-138/immer/R/inits_raterpars_hrm.R | 2 immer-1.0-138/immer/R/inits_theta_1dim.R | 21 immer-1.0-138/immer/R/lc2_agreement.R | 170 - 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Title: Plot an Epidemic Curve
Description: Creates simple or stacked epidemic curves for hourly, daily, weekly or monthly outcome data.
Author: Jean Pierre Decorps [aut, cre],
Morgane Vallee [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between EpiCurve versions 2.0-1 dated 2017-08-24 and 2.1-1 dated 2018-04-24
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ R/EpiCurve..R | 22 +++++++++++++++++++++- README.md |only inst/doc/EpiCurve.R | 2 +- inst/doc/EpiCurve.Rmd | 2 +- inst/doc/EpiCurve.pdf |binary vignettes/EpiCurve.Rmd | 2 +- 8 files changed, 36 insertions(+), 15 deletions(-)
Title: R Package Distribution of the BayesX C++ Sources
Description: BayesX performs Bayesian inference in structured additive regression (STAR) models.
The R package BayesXsrc provides the BayesX command line tool for easy installation.
A convenient R interface is provided in package R2BayesX.
Author: Nikolaus Umlauf [aut, cre],
Daniel Adler [aut],
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between BayesXsrc versions 3.0-0 dated 2018-02-22 and 3.0-1 dated 2018-04-24
BayesXsrc-3.0-0/BayesXsrc/src/bayesxsrc/structadd/design_group.cpp |only BayesXsrc-3.0-0/BayesXsrc/src/bayesxsrc/structadd/design_group.h |only BayesXsrc-3.0-1/BayesXsrc/DESCRIPTION | 8 BayesXsrc-3.0-1/BayesXsrc/MD5 | 182 +- BayesXsrc-3.0-1/BayesXsrc/src/Makefile | 6 BayesXsrc-3.0-1/BayesXsrc/src/Makefile.inner.win |only BayesXsrc-3.0-1/BayesXsrc/src/Makefile.win | 172 -- BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/Random.cpp | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/adminparse_gnu.cpp | 3 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/bandmat.cpp | 34 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/bayesreg.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/bayesreg2.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/data.cpp | 24 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/envmatrix.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/option.h | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/realvar.cpp | 8 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/remlreg.cpp | 5 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/remlreg.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/sparsemat.cpp | 8 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/statmat.cpp | 48 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/stepwisereg.cpp | 5 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tarray.cpp | 26 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tarray2d.cpp | 95 - BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tlinklst.cpp | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/bib/tpremat.cpp | 74 - BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/adjacency.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_dag.h | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_dag_ia.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_rj.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/dag/fullcond_rj_ia.cpp | 264 +-- BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/main.cpp | 17 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/distribution.cpp | 122 - BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/distribution_glasgow.cpp | 84 - BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond.cpp | 10 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond_merror.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/fullcond_nonp_gaussian.cpp | 10 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/gaussian_heteroskedastic.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/hrandom.cpp | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmc_nonp.cpp | 8 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmc_nonpbasis.cpp | 7 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmcsimul2.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/mcmcsimul2_multi.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect.cpp | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect_alt.cpp | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/randomeffect_alt2.cpp | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/remlest_multi.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/remlest_multi2.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/tvariance.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/mcmc/variance_nonp.cpp | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/IWLS_pspline.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/bsplinemat.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/fullcond_pspline_surf_gaussian.cpp | 3 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/mcmc_pspline.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/mcmc_pspline_surf.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/psplines/spline_basis.cpp | 15 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/samson/multgaussian.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom.cpp | 5 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance.cpp | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance_vec.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_hrandom_variance_vec_nmig.cpp | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_linear.cpp | 12 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_mult.cpp | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_mult.h | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp.cpp | 96 + BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp.h | 9 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_nonp_variance.cpp | 5 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_predict.cpp | 3 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/FC_variance_pen_vector.cpp | 21 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design.cpp | 95 + BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_kriging.cpp | 3 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_userdefined.cpp | 6 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/design_userdefined.h | 4 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr.cpp | 703 +++++++++- BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr.h | 171 ++ BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical.cpp | 16 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical_mult.cpp | 11 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_categorical_mult.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss.cpp | 27 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss.h | 2 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss_copula.cpp | 8 BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/distr_gamlss_nadja.cpp | 180 +- BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/mcmcsim.cpp | 75 - BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/superbayesreg.cpp | 167 +- BayesXsrc-3.0-1/BayesXsrc/src/bayesxsrc/structadd/superbayesreg.h | 4 BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile | 6 BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile.inner.win |only BayesXsrc-3.0-1/BayesXsrc/src/dev-Makefile.win | 172 -- BayesXsrc-3.0-1/BayesXsrc/src/install.libs.R | 1 BayesXsrc-3.0-1/BayesXsrc/src/rel-Makefile | 7 BayesXsrc-3.0-1/BayesXsrc/src/rel-Makefile.win | 4 94 files changed, 1897 insertions(+), 1264 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut],
Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 2.3 dated 2018-02-19 and 2.3.1 dated 2018-04-24
archivist-2.3.1/archivist/DESCRIPTION | 9 ++---- archivist-2.3.1/archivist/MD5 | 41 +++++----------------------- archivist-2.3.1/archivist/NAMESPACE | 1 archivist-2.3.1/archivist/NEWS.md | 4 ++ archivist-2.3.1/archivist/R/alink.R | 3 ++ archivist-2.3.1/archivist/R/cache.R | 4 +- archivist-2.3.1/archivist/R/saveToRepo.R | 28 +++++++++++++++++-- archivist-2.3.1/archivist/man/alink.Rd | 3 ++ archivist-2.3.1/archivist/man/saveToRepo.Rd | 16 ++++++---- archivist-2.3/archivist/build |only archivist-2.3/archivist/inst/doc |only archivist-2.3/archivist/tests |only archivist-2.3/archivist/vignettes |only 13 files changed, 60 insertions(+), 49 deletions(-)
Title: A Graphical Model Approach to Identify Primary Genes in
Perturbed Biological Pathways
Description: The algorithm pursues the identification of the set of variables driving the differences in two different experimental conditions (i.e., the primary genes) within a graphical model context. It uses the idea of simultaneously looking for the differences between two multivariate normal distributions in all marginal and conditional distributions associated with a decomposable graph, which represents the pathway under exam. The implementation accommodates genomics specific issues (low sample size and multiple testing issues) and provides a number of functions offering numerical and visual summaries to help the user interpret the obtained results. In order to use the (optional) 'Cytoscape' functionalities, the suggested 'r2cytoscape' package must be installed from the 'GitHub' repository ('devtools::install_github('cytoscape/r2cytoscape')').
Author: Elisa Salviato [aut, cre],
Vera Djordjilovic [aut],
Chiara Romualdi [aut],
Monica Chiogna [aut]
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>
Diff between SourceSet versions 0.1.0 dated 2018-02-28 and 0.1.1 dated 2018-04-24
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/mainFunctions.R | 6 ++++++ inst/doc/SourceSet.R | 8 +++++++- inst/doc/SourceSet.Rmd | 8 +++++++- inst/doc/SourceSet.html | 24 ++++++++++++++++-------- vignettes/SourceSet.Rmd | 8 +++++++- 7 files changed, 53 insertions(+), 21 deletions(-)
Title: Diversity-Dependent Diversification
Description: Implements maximum likelihood and bootstrap methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent, under various models including various types of key innovations.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>, Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574> and Etienne et al. 2016. Meth. Ecol. Evol. 7: 1092-1099, <DOI:10.1111/2041-210X.12565>.
Also contains functions to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 3.6 dated 2018-02-07 and 3.7 dated 2018-04-24
DESCRIPTION | 12 - MD5 | 39 +++--- NAMESPACE | 5 R/dd_KI_loglik.R | 6 R/dd_LR.R | 16 +- R/dd_ML.R | 1 R/dd_SR_loglik.R | 24 --- R/dd_loglik.R | 102 +++++++++++++-- R/dd_loglik_M.R | 12 + R/dd_loglik_bw_rhs.R | 83 ++---------- R/dd_loglik_rhs.R | 149 +++++++++++++---------- R/dd_utils.R | 17 ++ R/td_sim.R | 328 +++++++++++++++++++++++++-------------------------- man/DDD-internal.Rd | 8 + man/DDD-package.Rd | 8 - man/dd_KI_ML.Rd | 5 man/dd_KI_loglik.Rd | 2 man/dd_ML.Rd | 2 man/dd_loglik.Rd | 10 + src |only tests |only 21 files changed, 454 insertions(+), 375 deletions(-)
Title: Core Methods and Classes Used by 'aroma.*' Packages Part of the
Aroma Framework
Description: Core methods and classes used by higher-level 'aroma.*' packages
part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Author: Henrik Bengtsson [aut, cre, cph],
Mark Robinson [ctb],
Ken Simpson [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.core versions 3.1.1 dated 2017-09-13 and 3.1.2 dated 2018-04-24
DESCRIPTION | 12 MD5 | 389 NAMESPACE | 3 NEWS | 6001 ++++++------ R/006.fixVarArgs.R | 46 R/008.BioC.R | 32 R/009.setup.R | 66 R/998.AromaPackage.R | 70 R/999.AromaCore.R | 19 R/999.DEPRECATED.R | 52 R/999.NonDocumentedObjects.R | 6 R/AbstractCNData.R | 99 R/AbstractPSCNData.R | 105 R/Arguments.EXTRAS.R | 26 R/AromaCellCpgFile.R | 101 R/AromaCellPositionFile.R | 324 R/AromaCellSequenceFile.R | 1842 +-- R/AromaCellSequenceFile.REPEATS.R | 310 R/AromaCellSequenceFile.SNPs.R | 728 - R/AromaCellTabularBinaryFile.R | 58 R/AromaGenomeTextFile.R | 115 R/AromaMicroarrayDataFile.ATTRS.R | 137 R/AromaMicroarrayDataFile.PLOT.R | 48 R/AromaMicroarrayDataFile.R | 23 R/AromaMicroarrayDataSet.ATTRS.R | 204 R/AromaMicroarrayDataSet.EXT.R | 42 R/AromaMicroarrayDataSet.R | 30 R/AromaMicroarrayDataSetTuple.R | 165 R/AromaMicroarrayTabularBinaryFile.R | 433 R/AromaNnn.getRootName.R | 21 R/AromaPlatform.R | 13 R/AromaPlatformInterface.R | 202 R/AromaRepository.R | 1202 +- R/AromaSettings.R | 163 R/AromaTabularBinaryFile.R | 2723 ++--- R/AromaTabularBinarySet.ATTRS.R | 257 R/AromaTabularBinarySet.R | 17 R/AromaTransform.R | 1602 +-- R/AromaUcscGenomeTextFile.R | 16 R/AromaUflFile.R | 534 - R/AromaUgpFile.R | 475 R/AromaUgpFile.plotCoverageMap.R | 62 R/AromaUnitCallFile.R | 283 R/AromaUnitCallSet.R | 37 R/AromaUnitChromosomeTabularBinaryFile.R | 392 R/AromaUnitFracBCnBinaryFile.R | 14 R/AromaUnitFracBCnBinarySet.R | 28 R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R | 374 R/AromaUnitGcContentFile.R | 73 R/AromaUnitGenotypeCallFile.R | 898 - R/AromaUnitGenotypeCallSet.R | 209 R/AromaUnitPscnBinaryFile.R | 203 R/AromaUnitPscnBinarySet.R | 681 - R/AromaUnitSignalBinaryFile.R | 628 - R/AromaUnitSignalBinaryFile.writeDataFrame.R | 760 - R/AromaUnitSignalBinarySet.R | 31 R/AromaUnitSignalBinarySet.writeDataFrame.R | 949 - R/AromaUnitTabularBinaryFile.R | 460 R/AromaUnitTabularBinaryFile.writeDataFrame.R | 688 - R/AromaUnitTotalCnBinaryFile.R | 168 R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R | 89 R/AromaUnitTotalCnBinaryFile.xam.R | 183 R/AromaUnitTotalCnBinaryFileList.R | 448 R/AromaUnitTotalCnBinarySet.R | 710 - R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R | 204 R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R | 524 - R/AromaUnitTotalCnBinarySetTuple.R | 19 R/AromaUnitTypesFile.R | 49 R/BasicObject.asThis.R | 23 R/BinnedScatter.R | 454 R/CacheKeyInterface.R | 13 R/CbsModel.R | 36 R/CbsSegmentationDataFile.R | 16 R/CbsSegmentationDataSet.R | 22 R/ChromosomalModel.R | 1563 +-- R/ChromosomalModel.drawCytoband.R | 177 R/ChromosomeExplorer.LAYERS.R | 250 R/ChromosomeExplorer.R | 1318 +- R/CopyNumberChromosomalModel.R | 2507 ++--- R/CopyNumberChromosomalModel.newPlot.R | 44 R/CopyNumberChromosomalModel.plotChromosomesLayers.R | 610 - R/CopyNumberChromosomalModel.plotFitLayers.R | 436 R/CopyNumberChromosomalModel.plotRawCopyNumbers.R | 223 R/CopyNumberChromosomalModel.plotSampleLayers.R | 468 R/CopyNumberDataSetTuple.R | 68 R/CopyNumberOutliers.FOREIGN.R | 47 R/CopyNumberOutliers.R | 68 R/CopyNumberRegions.EXT.R | 186 R/CopyNumberRegions.EXT2.R | 36 R/CopyNumberRegions.PLOT.R | 12 R/CopyNumberRegions.R | 197 R/CopyNumberSegmentationModel.R | 1524 +-- R/CopyNumberSegmentationModel.plot.R | 718 - R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R | 136 R/DNAcopy.EXTS.R | 64 R/Explorer.R | 1665 +-- R/FileCacheKeyInterface.R | 21 R/GLAD.EXTS.R | 315 R/GenericDataFileSet.getParentName.R | 81 R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R | 187 R/GladModel.R | 556 - R/GladModel.onFitAddGenotypeCalls.R | 178 R/HaarSeg.EXTS.R | 93 R/HaarSegModel.R | 145 R/Image.EXTS.R | 1170 +- R/MPCBS.EXTS.R | 177 R/NonPairedPSCNData.R | 179 R/PairedPSCNData.PLOT.R | 157 R/PairedPSCNData.R | 366 R/ParametersInterface.R | 67 R/ProbePositionEffects.R | 1012 -- R/RasterImage.R | 1263 +- R/RawAlleleBFractions.R | 12 R/RawCopyNumberModel.R | 13 R/RawCopyNumbers.R | 77 R/RawGenomicSignals.OPS.R | 91 R/RawGenomicSignals.PLOT.R | 105 R/RawGenomicSignals.R | 2496 ++-- R/RawGenomicSignals.SEG.R | 281 R/RawGenomicSignals.append.R | 18 R/RawGenomicSignals.segmentByCBS.R | 645 - R/RawGenomicSignals.segmentByGLAD.R | 619 - R/RawGenomicSignals.segmentByHaarSeg.R | 554 - R/RawGenomicSignals.segmentByMPCBS.R | 559 - R/RawMirroredAlleleBFractions.R | 27 R/RawSequenceReads.EXTRAS.R | 208 R/RawSequenceReads.R | 16 R/RichDataFrame.R | 1427 +- R/SampleAnnotationFile.R | 297 R/SampleAnnotationSet.R | 497 R/SegmentationDataFile.R | 57 R/SegmentationDataSet.R | 361 R/SegmentedAlleleBFracions.R | 66 R/SegmentedCopyNumbers.R | 89 R/SegmentedGenomicSignalsInterface.COLS.R | 185 R/SegmentedGenomicSignalsInterface.R | 1100 +- R/TextUnitNamesFile.R | 254 R/UnitAnnotationDataFile.R | 392 R/UnitNamesFile.R | 203 R/UnitTypesFile.R | 95 R/backtransformGenotypeCone.matrix.R | 15 R/backtransformMultiDimensionalCone.matrix.R | 15 R/colBinnedSmoothing.R | 751 - R/colGaussianSmoothing.R | 313 R/colKernelSmoothing.R | 480 R/convertTable.R | 159 R/doCBS.R | 173 R/drawCytoband2.R | 279 R/findAnnotationData.R | 768 - R/findAnnotationDataByChipType.R | 19 R/findPngDevice.R | 82 R/fitGenotypeCone.matrix.R | 166 R/fitMultiDimensionalCone.matrix.R | 101 R/fitSplineBlockPolish.matrix.R | 23 R/fitWHLAPLM.matrix.R | 53 R/fitWHRCModel.matrix.R | 103 R/fitWRMA.matrix.R | 95 R/getAromaFullNameTranslatorSet.R | 103 R/getCommonListElements.R | 39 R/getDeviceResolution.R | 11 R/getProbePositionEffectDesignMatrix.R | 320 R/kernelWeights.R | 19 R/lapplyInChunks.R | 204 R/library.patch.R | 32 R/locallyUnique.R | 14 R/matrixBlockPolish.matrix.R | 105 R/mergeBoxplotStats.list.R | 180 R/norm2d.matrix.R | 172 R/normalizeGenotypeCone.R | 16 R/private.Machine.R | 9 R/processTime.R | 31 R/profileCGH.drawExtraAnnotations.R | 36 R/profileCGH.plotProfile2.R | 127 R/profileCGH.plotRawCNs.R | 137 R/remap.R | 77 R/requireWithMemory.R | 198 R/shakyText.R | 31 R/simpleXml.R | 136 R/smoothWRMA.matrix.R | 252 R/smoothWSA.matrix.R | 260 R/stextChipType.R | 9 R/stringTree.R | 259 R/transforms.R | 75 R/utils.R |only R/yellow.colors.R | 11 R/zzz.R | 12 man/aroma.core-package.Rd | 2 man/fitGenotypeCone.matrix.Rd | 6 man/fitGenotypeConeBySfit.matrix.Rd | 6 man/segmentByCBS.RawGenomicSignals.Rd | 9 man/writeDataFrame.AromaUnitSignalBinarySet.Rd | 2 tests/RawCopyNumbers,states.R | 130 tests/RawCopyNumbers.R | 256 tests/RawGenomicSignals.SEG.R | 9 tests/RichDataFrame.R | 122 tests/SegmentedCopyNumbers.R | 196 196 files changed, 30052 insertions(+), 34623 deletions(-)
Title: Functional Regression using Signal Compression Approach
Description: Signal compression methods for function-on-function (FOF) regression with functional response and functional predictors, including linear models with both scalar and functional predictors for a small number of functional predictors, linear models with functional predictors for a large number of functional predictors, stepwise selection for FOF models with two-way interactions, and nonlinear models. References are linked to via the URL below.
Author: Ruiyan Luo, Xin Qi
Maintainer: Ruiyan Luo <rluo@gsu.edu>
Diff between FRegSigCom versions 0.1.0 dated 2017-09-06 and 0.2.1 dated 2018-04-24
DESCRIPTION | 20 +++- MD5 | 35 +++++--- NAMESPACE | 7 + R/RcppExports.R |only R/ff.interaction.R |only data/ocean.RData |only man/air.Rd | 3 man/cv.ff.interaction.Rd |only man/cv.hd.Rd | 21 ++-- man/cv.nonlinear.Rd | 12 +- man/cv.sigcom.Rd | 178 +++++++++++++++++++++--------------------- man/getcoef.ff.interaction.Rd |only man/getcoef.hd.Rd | 4 man/getcoef.nonlinear.Rd | 6 - man/getcoef.sigcom.Rd | 2 man/ocean.Rd |only man/pred.ff.interaction.Rd |only man/pred.hd.Rd | 7 + man/pred.nonlinear.Rd | 7 + man/pred.sigcom.Rd | 7 + man/step.ff.interaction.Rd |only src |only 22 files changed, 176 insertions(+), 133 deletions(-)
Title: Differential Geometric Least Angle Regression
Description: Differential geometric least angle regression method for fitting
sparse generalized linear models. In this version of the package, the user can fit
models specifying Gaussian, Poisson, Binomial, Gamma and Inverse Gaussian family.
Furthermore, several link functions can be used to model the relationship between the
conditional expected value of the response variable and the linear predictor. The
solution curve can be computed using an efficient predictor-corrector or a cyclic
coordinate descent algorithm, as described in the paper linked to via the URL below.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between dglars versions 2.0.0 dated 2017-02-28 and 2.0.1 dated 2018-04-24
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/gdf.R | 2 +- R/predict.dglars.R | 2 +- man/dglars-package.Rd | 4 ++-- 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Lexicons for Text Analysis
Description: A collection of lexical hash tables, dictionaries, and word lists.
Author: Tyler Rinker [aut, cre, cph],
University of Notre Dame [dtc, cph],
Department of Knowledge Technologies [dtc, cph],
Unicode, Inc. [dtc, cph],
John Higgins [dtc, cph],
Grady Ward [dtc],
Heiko Possel [dtc],
Michal Boleslav Mechura [dtc, cph],
Bing Liu [dtc],
Minqing Hu [dtc],
Saif M. Mohammad [dtc],
Peter Turney [dtc],
Erik Cambria [dtc],
Soujanya Poria [dtc],
Rajiv Bajpai [dtc],
Bjoern Schuller [dtc],
SentiWordNet [dtc, cph],
Liang Wu [dtc, cph],
Fred Morstatter [dtc, cph],
Huan Liu [dtc, cph],
Grammar Revolution [dtc, cph],
Vidar Holen [dtc, cph],
Alejandro U. Alvarez [dtc, cph],
Stackoverflow User user2592414 [dtc, cph],
BannedWordList.com [dtc, cph],
Apache Software Foundation [dtc, cph],
Andrew Kachites McCallum [dtc, cph],
Alireza Savand [dtc, cph]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between lexicon versions 0.7.4 dated 2018-01-13 and 1.0.0 dated 2018-04-24
lexicon-0.7.4/lexicon/LICENSE |only lexicon-0.7.4/lexicon/R/discourse_markers_alemany.R |only lexicon-0.7.4/lexicon/R/dodds_sentiment.R |only lexicon-0.7.4/lexicon/R/enable_word_list.R |only lexicon-0.7.4/lexicon/R/hash_power.R |only lexicon-0.7.4/lexicon/R/hash_sentiment_inquirer.R |only lexicon-0.7.4/lexicon/R/hash_sentiment_vadar.R |only lexicon-0.7.4/lexicon/R/hash_strength.R |only lexicon-0.7.4/lexicon/R/hash_syllable.R |only lexicon-0.7.4/lexicon/R/key_abbreviation.R |only lexicon-0.7.4/lexicon/R/key_grades.R |only lexicon-0.7.4/lexicon/R/pos_adverb.R |only lexicon-0.7.4/lexicon/R/pos_unchanging_nouns.R |only lexicon-0.7.4/lexicon/R/profanity_google.R |only lexicon-0.7.4/lexicon/R/profanity_von_ahn.R |only lexicon-0.7.4/lexicon/R/sw_buckley_salton.R |only lexicon-0.7.4/lexicon/R/sw_onix.R |only lexicon-0.7.4/lexicon/data/discourse_markers_alemany.rda |only lexicon-0.7.4/lexicon/data/dodds_sentiment.rda |only lexicon-0.7.4/lexicon/data/enable_word_list.rda |only lexicon-0.7.4/lexicon/data/hash_power.rda |only lexicon-0.7.4/lexicon/data/hash_sentiment_inquirer.rda |only lexicon-0.7.4/lexicon/data/hash_sentiment_vadar.rda |only lexicon-0.7.4/lexicon/data/hash_strength.rda |only lexicon-0.7.4/lexicon/data/hash_syllable.rda |only lexicon-0.7.4/lexicon/data/key_abbreviation.rda |only lexicon-0.7.4/lexicon/data/pos_adverb.rda |only lexicon-0.7.4/lexicon/data/pos_unchanging_nouns.rda |only lexicon-0.7.4/lexicon/data/profanity_google.rda |only lexicon-0.7.4/lexicon/data/profanity_von_ahn.rda |only lexicon-0.7.4/lexicon/data/sw_buckley_salton.rda |only lexicon-0.7.4/lexicon/data/sw_onix.rda |only lexicon-0.7.4/lexicon/man/discourse_markers_alemany.Rd |only lexicon-0.7.4/lexicon/man/dodds_sentiment.Rd |only lexicon-0.7.4/lexicon/man/enable_word_list.Rd |only lexicon-0.7.4/lexicon/man/hash_power.Rd |only lexicon-0.7.4/lexicon/man/hash_sentiment_inquirer.Rd |only lexicon-0.7.4/lexicon/man/hash_sentiment_vadar.Rd |only lexicon-0.7.4/lexicon/man/hash_strength.Rd |only lexicon-0.7.4/lexicon/man/hash_syllable.Rd |only lexicon-0.7.4/lexicon/man/key_abbreviation.Rd |only lexicon-0.7.4/lexicon/man/pos_adverb.Rd |only lexicon-0.7.4/lexicon/man/pos_unchanging_nouns.Rd |only lexicon-0.7.4/lexicon/man/profanity_google.Rd |only lexicon-0.7.4/lexicon/man/profanity_von_ahn.Rd |only lexicon-0.7.4/lexicon/man/sw_buckley_salton.Rd |only lexicon-0.7.4/lexicon/man/sw_onix.Rd |only lexicon-1.0.0/lexicon/DESCRIPTION | 105 + lexicon-1.0.0/lexicon/MD5 | 285 ++--- lexicon-1.0.0/lexicon/NEWS | 159 -- lexicon-1.0.0/lexicon/R/constraining_loughran_mcdonald.R | 7 lexicon-1.0.0/lexicon/R/freq_first_names.R | 5 lexicon-1.0.0/lexicon/R/freq_last_names.R | 5 lexicon-1.0.0/lexicon/R/function_words.R | 4 lexicon-1.0.0/lexicon/R/grady_augmented.R | 5 lexicon-1.0.0/lexicon/R/hash_emoticons.R | 12 lexicon-1.0.0/lexicon/R/hash_grady_pos.R | 3 lexicon-1.0.0/lexicon/R/hash_internet_slang.R | 4 lexicon-1.0.0/lexicon/R/hash_lemmas.R | 542 +++++++++- lexicon-1.0.0/lexicon/R/hash_sentiment_emojis.R | 78 + lexicon-1.0.0/lexicon/R/hash_sentiment_huliu.R | 9 lexicon-1.0.0/lexicon/R/hash_sentiment_jockers_rinker.R | 6 lexicon-1.0.0/lexicon/R/hash_sentiment_loughran_mcdonald.R | 6 lexicon-1.0.0/lexicon/R/hash_sentiment_nrc.R | 8 lexicon-1.0.0/lexicon/R/hash_sentiment_senticnet.R | 12 lexicon-1.0.0/lexicon/R/hash_sentiment_sentiword.R | 5 lexicon-1.0.0/lexicon/R/hash_sentiment_slangsd.R | 15 lexicon-1.0.0/lexicon/R/hash_sentiment_socal_google.R | 6 lexicon-1.0.0/lexicon/R/hash_valence_shifters.R | 2 lexicon-1.0.0/lexicon/R/key_grade.R | 8 lexicon-1.0.0/lexicon/R/lexicon-package.R | 1 lexicon-1.0.0/lexicon/R/modal_loughran_mcdonald.R | 5 lexicon-1.0.0/lexicon/R/nrc_emotions.R | 8 lexicon-1.0.0/lexicon/R/pos_action_verb.R | 8 lexicon-1.0.0/lexicon/R/pos_df_irregular_nouns.R | 15 lexicon-1.0.0/lexicon/R/pos_interjections.R | 3 lexicon-1.0.0/lexicon/R/profanity_alvarez.R | 3 lexicon-1.0.0/lexicon/R/profanity_arr_bad.R | 4 lexicon-1.0.0/lexicon/R/profanity_banned.R | 7 lexicon-1.0.0/lexicon/R/sw_loughran_mcdonald.R | 13 lexicon-1.0.0/lexicon/R/sw_mallet.R | 92 + lexicon-1.0.0/lexicon/R/sw_python.R | 28 lexicon-1.0.0/lexicon/README.md | 388 ++----- lexicon-1.0.0/lexicon/data/common_names.rda |binary lexicon-1.0.0/lexicon/data/constraining_loughran_mcdonald.rda |binary lexicon-1.0.0/lexicon/data/datalist | 15 lexicon-1.0.0/lexicon/data/emojis_sentiment.rda |binary lexicon-1.0.0/lexicon/data/freq_first_names.rda |binary lexicon-1.0.0/lexicon/data/freq_last_names.rda |binary lexicon-1.0.0/lexicon/data/function_words.rda |binary lexicon-1.0.0/lexicon/data/grady_augmented.rda |binary lexicon-1.0.0/lexicon/data/hash_emojis.rda |binary lexicon-1.0.0/lexicon/data/hash_emojis_identifier.rda |binary lexicon-1.0.0/lexicon/data/hash_emoticons.rda |binary lexicon-1.0.0/lexicon/data/hash_grady_pos.rda |binary lexicon-1.0.0/lexicon/data/hash_internet_slang.rda |binary lexicon-1.0.0/lexicon/data/hash_lemmas.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_emojis.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_huliu.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_jockers_rinker.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_loughran_mcdonald.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_nrc.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_senticnet.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_sentiword.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_slangsd.rda |binary lexicon-1.0.0/lexicon/data/hash_sentiment_socal_google.rda |binary lexicon-1.0.0/lexicon/data/hash_valence_shifters.rda |binary lexicon-1.0.0/lexicon/data/key_contractions.rda |binary lexicon-1.0.0/lexicon/data/key_grade.rda |binary lexicon-1.0.0/lexicon/data/key_rating.rda |binary lexicon-1.0.0/lexicon/data/modal_loughran_mcdonald.rda |binary lexicon-1.0.0/lexicon/data/nrc_emotions.rda |binary lexicon-1.0.0/lexicon/data/pos_action_verb.rda |binary lexicon-1.0.0/lexicon/data/pos_df_irregular_nouns.rda |binary lexicon-1.0.0/lexicon/data/pos_df_pronouns.rda |binary lexicon-1.0.0/lexicon/data/pos_interjections.rda |binary lexicon-1.0.0/lexicon/data/pos_preposition.rda |binary lexicon-1.0.0/lexicon/data/profanity_alvarez.rda |binary lexicon-1.0.0/lexicon/data/profanity_arr_bad.rda |binary lexicon-1.0.0/lexicon/data/profanity_banned.rda |binary lexicon-1.0.0/lexicon/data/sw_dolch.rda |binary lexicon-1.0.0/lexicon/data/sw_fry_100.rda |binary lexicon-1.0.0/lexicon/data/sw_fry_1000.rda |binary lexicon-1.0.0/lexicon/data/sw_fry_200.rda |binary lexicon-1.0.0/lexicon/data/sw_fry_25.rda |binary lexicon-1.0.0/lexicon/data/sw_jockers.rda |binary lexicon-1.0.0/lexicon/data/sw_loughran_mcdonald_long.rda |binary lexicon-1.0.0/lexicon/data/sw_loughran_mcdonald_short.rda |binary lexicon-1.0.0/lexicon/data/sw_lucene.rda |binary lexicon-1.0.0/lexicon/data/sw_mallet.rda |binary lexicon-1.0.0/lexicon/data/sw_python.rda |binary lexicon-1.0.0/lexicon/inst/CITATION | 4 lexicon-1.0.0/lexicon/man/constraining_loughran_mcdonald.Rd | 11 lexicon-1.0.0/lexicon/man/emojis_sentiment.Rd | 7 lexicon-1.0.0/lexicon/man/freq_first_names.Rd | 5 lexicon-1.0.0/lexicon/man/freq_last_names.Rd | 5 lexicon-1.0.0/lexicon/man/function_words.Rd | 6 lexicon-1.0.0/lexicon/man/grady_augmented.Rd | 5 lexicon-1.0.0/lexicon/man/hash_emojis.Rd | 34 lexicon-1.0.0/lexicon/man/hash_emojis_identifier.Rd | 34 lexicon-1.0.0/lexicon/man/hash_emoticons.Rd | 12 lexicon-1.0.0/lexicon/man/hash_grady_pos.Rd | 5 lexicon-1.0.0/lexicon/man/hash_internet_slang.Rd | 2 lexicon-1.0.0/lexicon/man/hash_lemmas.Rd | 541 +++++++++ lexicon-1.0.0/lexicon/man/hash_sentiment_emojis.Rd | 7 lexicon-1.0.0/lexicon/man/hash_sentiment_huliu.Rd | 6 lexicon-1.0.0/lexicon/man/hash_sentiment_jockers_rinker.Rd | 6 lexicon-1.0.0/lexicon/man/hash_sentiment_loughran_mcdonald.Rd | 11 lexicon-1.0.0/lexicon/man/hash_sentiment_nrc.Rd | 9 lexicon-1.0.0/lexicon/man/hash_sentiment_senticnet.Rd | 11 lexicon-1.0.0/lexicon/man/hash_sentiment_sentiword.Rd | 6 lexicon-1.0.0/lexicon/man/hash_sentiment_slangsd.Rd | 16 lexicon-1.0.0/lexicon/man/hash_sentiment_socal_google.Rd | 7 lexicon-1.0.0/lexicon/man/hash_valence_shifters.Rd | 2 lexicon-1.0.0/lexicon/man/key_grade.Rd | 14 lexicon-1.0.0/lexicon/man/modal_loughran_mcdonald.Rd | 11 lexicon-1.0.0/lexicon/man/nrc_emotions.Rd | 9 lexicon-1.0.0/lexicon/man/pos_action_verb.Rd | 10 lexicon-1.0.0/lexicon/man/pos_df_irregular_nouns.Rd | 14 lexicon-1.0.0/lexicon/man/pos_interjections.Rd | 3 lexicon-1.0.0/lexicon/man/profanity_alvarez.Rd | 4 lexicon-1.0.0/lexicon/man/profanity_arr_bad.Rd | 5 lexicon-1.0.0/lexicon/man/profanity_banned.Rd | 8 lexicon-1.0.0/lexicon/man/sw_loughran_mcdonald_long.Rd | 11 lexicon-1.0.0/lexicon/man/sw_loughran_mcdonald_short.Rd | 7 lexicon-1.0.0/lexicon/man/sw_mallet.Rd | 91 + lexicon-1.0.0/lexicon/man/sw_python.Rd | 29 167 files changed, 2117 insertions(+), 732 deletions(-)
Title: Language Server Protocol
Description: An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol> for details.
Author: Randy Lai
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between languageserver versions 0.1.0 dated 2018-03-01 and 0.2.0 dated 2018-04-24
languageserver-0.1.0/languageserver/R/queue.R |only languageserver-0.1.0/languageserver/src/pairlist.c |only languageserver-0.1.0/languageserver/src/pairlist.h |only languageserver-0.2.0/languageserver/DESCRIPTION | 12 languageserver-0.2.0/languageserver/MD5 | 35 +- languageserver-0.2.0/languageserver/R/capabilities.R | 6 languageserver-0.2.0/languageserver/R/collections.R |only languageserver-0.2.0/languageserver/R/diagnostics.R | 46 +++ languageserver-0.2.0/languageserver/R/formatting.R |only languageserver-0.2.0/languageserver/R/handlers-general.R | 4 languageserver-0.2.0/languageserver/R/handlers-langfeatures.R | 9 languageserver-0.2.0/languageserver/R/handlers-textsync.R | 18 - languageserver-0.2.0/languageserver/R/handlers-workspace.R | 8 languageserver-0.2.0/languageserver/R/languageserver.R | 138 +++++---- languageserver-0.2.0/languageserver/R/signature.R | 2 languageserver-0.2.0/languageserver/R/utils.R | 37 ++ languageserver-0.2.0/languageserver/R/workspace.R | 140 +++++----- languageserver-0.2.0/languageserver/README.md | 25 + languageserver-0.2.0/languageserver/man/workspace_sync.Rd | 6 languageserver-0.2.0/languageserver/src/languageserver.c | 9 languageserver-0.2.0/languageserver/tests/testthat/test_queue.R | 23 - 21 files changed, 318 insertions(+), 200 deletions(-)
More information about languageserver at CRAN
Permanent link
Title: Efficient Iterator for Permutations and Combinations
Description: Iterator for generating permutations and combinations. They
can be either drawn with or without replacement, or with distinct/ non-distinct
items (multiset). The generated sequences are in lexicographical order
(dictionary order). The algorithms to generate permutations and combinations are
memory efficient. These iterative algorithms enable users to process all sequences
without putting all results in the memory at the same time.
The algorithms are written in C/C++ for faster performance. Note: 'iterpc' is no longer
being maintained. Users are recommended to switch to 'arrangements'.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.3.4 dated 2017-12-06 and 0.4.0 dated 2018-04-24
iterpc-0.3.4/iterpc/R/RcppExports.R |only iterpc-0.3.4/iterpc/src |only iterpc-0.4.0/iterpc/DESCRIPTION | 16 - iterpc-0.4.0/iterpc/MD5 | 35 -- iterpc-0.4.0/iterpc/NAMESPACE | 4 iterpc-0.4.0/iterpc/R/combination.R | 53 --- iterpc-0.4.0/iterpc/R/iterpc.R | 84 ++---- iterpc-0.4.0/iterpc/R/permutation.R | 53 --- iterpc-0.4.0/iterpc/README.md | 4 iterpc-0.4.0/iterpc/build/vignette.rds |binary iterpc-0.4.0/iterpc/inst/doc/combinations.html | 336 +++++++++++++++++++----- iterpc-0.4.0/iterpc/inst/doc/permutations.html | 349 ++++++++++++++++++++----- 12 files changed, 618 insertions(+), 316 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Description: Extends package 'arules' with various visualization techniques for association rules and itemsets. The package also includes several interactive visualizations for rule exploration.
Author: Michael Hahsler [aut, cre, cph],
Giallanza Tyler [ctb],
Sudheer Chelluboina [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arulesViz versions 1.3-0 dated 2017-09-09 and 1.3-1 dated 2018-04-24
DESCRIPTION | 24 ++- MD5 | 38 +++-- NAMESPACE | 22 +-- NEWS.md | 16 ++ R/AAAhelpers.R | 8 - R/graph.R | 2 R/matrix.R | 25 +++ R/plot.R | 20 ++- R/plotly.R | 64 +++++++-- R/scatterplot.R | 6 R/shiny.R |only README.md | 10 - build/vignette.rds |binary inst/doc/arulesViz.R | 125 ++++++------------ inst/doc/arulesViz.Rnw | 317 ++++++++++++++++++++---------------------------- inst/doc/arulesViz.pdf |binary man/plot.Rd | 20 +-- man/plotly_arules.Rd | 2 man/shiny.Rd |only vignettes/arulesViz.Rnw | 317 ++++++++++++++++++++---------------------------- vignettes/arulesViz.bib | 24 +++ 21 files changed, 522 insertions(+), 518 deletions(-)