Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH pubkey parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.1 dated 2018-11-15 and 1.2 dated 2019-01-16
openssl-1.1/openssl/man/askpass.Rd |only openssl-1.2/openssl/DESCRIPTION | 8 - openssl-1.2/openssl/MD5 | 51 +++---- openssl-1.2/openssl/NAMESPACE | 5 openssl-1.2/openssl/NEWS | 5 openssl-1.2/openssl/R/askpass.R | 43 ------ openssl-1.2/openssl/R/base.R | 2 openssl-1.2/openssl/R/cert.R | 15 -- openssl-1.2/openssl/R/signing.R | 38 +++++ openssl-1.2/openssl/build/vignette.rds |binary openssl-1.2/openssl/inst/doc/bignum.html | 93 +++++++++++-- openssl-1.2/openssl/inst/doc/crypto_hashing.html | 73 ++++++++++ openssl-1.2/openssl/inst/doc/keys.html | 107 ++++++++++++---- openssl-1.2/openssl/inst/doc/secure_rng.html | 83 ++++++++++-- openssl-1.2/openssl/inst/mac-askpass |only openssl-1.2/openssl/man/certificates.Rd | 15 -- openssl-1.2/openssl/man/reexports.Rd |only openssl-1.2/openssl/man/signatures.Rd | 28 ++++ openssl-1.2/openssl/src/bignum.c | 2 openssl-1.2/openssl/src/compatibility.c | 11 + openssl-1.2/openssl/src/compatibility.h | 4 openssl-1.2/openssl/src/password.c | 9 - openssl-1.2/openssl/src/signing.c | 33 ++++ openssl-1.2/openssl/src/stream.c | 1 openssl-1.2/openssl/tests/testthat/test_keys_dsa.R | 5 openssl-1.2/openssl/tests/testthat/test_keys_ecdsa.R | 5 openssl-1.2/openssl/tests/testthat/test_keys_ecdsa384.R | 5 openssl-1.2/openssl/tests/testthat/test_keys_ecdsa521.R | 5 28 files changed, 501 insertions(+), 145 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and
metadata from a PDF file. Also supports high quality rendering of PDF documents into
PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between pdftools versions 2.0 dated 2018-12-11 and 2.1 dated 2019-01-16
DESCRIPTION | 8 +- MD5 | 20 +++---- NAMESPACE | 1 NEWS | 5 + R/RcppExports.R | 6 +- R/tools.R | 17 ++++++ man/pdftools.Rd | 14 +++++ src/Makevars.win | 2 src/RcppExports.cpp | 21 ++++++- src/bindings.cpp | 114 ++++++++++++++++++++++++----------------- tests/testthat/test-encoding.R | 10 +-- 11 files changed, 149 insertions(+), 69 deletions(-)
Title: Detect Heatwaves and Cold-Spells
Description: The different methods of defining and detecting extreme events, known as heatwaves or cold-spells in both air and water temperature data are encompassed within this package. These detection algorithms may be used on non-temperature data as well however, this is not catered for explicitly here as no use of this technique in the literature currently exists.
Author: Robert W. Schlegel [aut, cre, ctb]
(<https://orcid.org/0000-0002-0705-1287>),
Albertus J. Smit [aut, ctb] (<https://orcid.org/0000-0002-3799-6126>)
Maintainer: Robert W. Schlegel <robwschlegel@gmail.com>
Diff between heatwaveR versions 0.3.3 dated 2018-08-02 and 0.3.6 dated 2019-01-16
DESCRIPTION | 13 LICENSE | 2 MD5 | 145 +++--- NEWS.md | 139 +++++- R/block_average.R | 86 ++- R/category.R | 130 ++++- R/clim_calc.R | 4 R/clim_spread.R | 2 R/detect_event.R | 45 + R/exceedance.R | 67 +- R/graph_functions.R | 28 - R/make_whole.R | 8 R/make_whole_fast.R | 68 --- R/na_interp.R | 4 R/proto_event.R | 31 - R/smooth_percentile.R | 28 - R/sst_med.R | 2 R/sst_nw_atl.R | 2 R/sst_wa.R | 2 R/ts2clm.R | 99 ++-- README.md | 4 build/vignette.rds |binary inst/CITATION |only inst/doc/OISST_preparation.R | 228 ++-------- inst/doc/OISST_preparation.Rmd | 286 +++--------- inst/doc/OISST_preparation.html | 594 +++++++++++++++----------- inst/doc/complex_clims.R | 202 ++++---- inst/doc/complex_clims.Rmd | 270 +++++------ inst/doc/complex_clims.html | 680 ++++++++++++++++++++---------- inst/doc/detection_and_visualisation.R | 104 ++-- inst/doc/detection_and_visualisation.Rmd | 141 ++++-- inst/doc/detection_and_visualisation.html | 607 +++++++++++++++++++------- inst/doc/event_categories.R | 14 inst/doc/event_categories.Rmd | 45 + inst/doc/event_categories.html | 524 +++++++++++++++++------ inst/doc/exceedance.R | 6 inst/doc/exceedance.Rmd | 38 + inst/doc/exceedance.html | 455 +++++++++++++++----- inst/doc/gridded_event_detection.R | 221 +++++---- inst/doc/gridded_event_detection.Rmd | 296 +++++++------ inst/doc/gridded_event_detection.html | 600 +++++++++++++++++++------- man/block_average.Rd | 21 man/category.Rd | 68 ++- man/detect_event.Rd | 30 - man/event_line.Rd | 9 man/exceedance.Rd | 3 man/make_whole_fast.Rd | 41 - man/na_interp.Rd | 4 man/proto_event.Rd | 13 man/smooth_percentile.Rd | 5 man/sst_Med.Rd | 3 man/sst_NW_Atl.Rd | 3 man/sst_WA.Rd | 3 man/ts2clm.Rd | 40 + src/Makevars | 2 src/Makevars.win | 2 src/clim_calc.cpp | 17 tests/testthat/test-block_average.R | 13 tests/testthat/test-category.R | 34 + tests/testthat/test-clim_calc.R | 2 tests/testthat/test-detect_event.R | 27 + tests/testthat/test-exceedance.R | 15 tests/testthat/test-graph_functions.R | 7 tests/testthat/test-make_whole_fast.R | 18 tests/testthat/test-na_interp.R | 14 tests/testthat/test-proto_event.R | 27 - tests/testthat/test-smooth_percentile.R | 18 tests/testthat/test-ts2clm.R | 62 ++ vignettes/OISST_preparation.Rmd | 286 +++--------- vignettes/complex_clims.Rmd | 270 +++++------ vignettes/detection_and_visualisation.Rmd | 141 ++++-- vignettes/event_categories.Rmd | 45 + vignettes/exceedance.Rmd | 38 + vignettes/gridded_event_detection.Rmd | 296 +++++++------ 74 files changed, 4794 insertions(+), 3003 deletions(-)
Title: Fast Molecular Clock Dating of Phylogenetic Trees with Rate
Variation
Description: Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. The methods are described in Volz, E.M. and S.D.W. Frost (2017) <doi:10.1093/ve/vex025>.
Author: Erik Volz [aut, cre]
Maintainer: Erik Volz <erik.volz@gmail.com>
Diff between treedater versions 0.2.0 dated 2018-05-06 and 0.3.0 dated 2019-01-16
DESCRIPTION | 15 MD5 | 31 - NAMESPACE | 1 R/boot.R | 48 +- R/treedater0.R | 103 +++++- build/vignette.rds |binary inst/doc/h3n2.R | 3 inst/doc/h3n2.Rmd | 7 inst/doc/h3n2.html | 689 +++++++++++++++++++++++++++-------------- man/boot.Rd | 10 man/dater.Rd | 4 man/parboot.Rd | 4 man/plot.bootTreedater.Rd | 5 man/relaxedClockTest.Rd | 7 man/rootToTipRegressionPlot.Rd |only man/sampleYearsFromLabels.Rd | 4 vignettes/h3n2.Rmd | 7 17 files changed, 643 insertions(+), 295 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.0-2 dated 2018-09-17 and 1.0-3 dated 2019-01-16
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- NAMESPACE | 2 - R/bernstein.R | 78 ++++++++++++++++++++++++++++++++++++++++++------- R/legendre.R | 2 - inst/NEWS.Rd | 8 +++++ man/Bernstein_basis.Rd | 7 +++- tests/Bernstein-Ex.R | 21 +++++++++++++ 8 files changed, 115 insertions(+), 25 deletions(-)
Title: Utilities for Convenient Extraction of Medical Image Metadata
Description: A collection of utilities for navigating medical image data. The DICOM and NIfTI formats
are supported. Functions provide simple interfaces to the data and metadata contained in these formats.
A particular emphasis on metadata allows simple conversion of image metadata to familiar R data structures
such as lists and data frames. Where possible, generic functions can silently process either DICOM or
NIfTI data. Additionally, image data can be extracted and viewed.
Author: Pamela Russell [aut, cre]
Maintainer: Pamela Russell <pamela.russell@ucdenver.edu>
Diff between radtools versions 1.0.2 dated 2019-01-15 and 1.0.3 dated 2019-01-16
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 4 ++++ R/image_import.R | 5 ++++- R/metadata.R | 2 +- R/view.R | 3 +++ README.md | 11 ++++++----- inst/doc/radtools_usage.Rmd | 4 ++-- inst/doc/radtools_usage.html | 10 +++++----- man/img_dimensions.Rd | 2 +- man/read_dicom.Rd | 2 +- tests/testthat/test_image_import_dicom.R | 3 +++ tests/testthat/test_view.R | 3 +++ vignettes/radtools_usage.Rmd | 4 ++-- 14 files changed, 52 insertions(+), 35 deletions(-)
Title: Tools for Evaluating Collinearity
Description: Use the perturb() function to evaluates collinearity by adding
random noise to selected variables (Hendrickx & Pelzer 2004). The colldiag
function() calculates condition numbers and variance decomposition proportions
to test for collinearity and uncover its sources (Belsley 1980).
Author: John Hendrickx
Maintainer: John Hendrickx <John_Hendrickx@yahoo.com>
Diff between perturb versions 2.05 dated 2012-02-19 and 2.10 dated 2019-01-16
DESCRIPTION | 19 ++++++++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 15 +++++++++------ NEWS | 3 +++ R/perturb.R | 18 +++++++++++++++--- data/consumption.tab.gz |binary man/colldiag.Rd | 10 +++------- man/perturb.Rd | 2 +- man/reclassify.Rd | 2 +- 9 files changed, 50 insertions(+), 35 deletions(-)
Title: R Logging Package
Description: Pure R implementation of the ubiquitous log4j package. It offers hierarchic
loggers, multiple handlers per logger, level based filtering, space handling in messages
and custom formatting.
Author: Mario Frasca [aut],
Walerian Sokolowski [cre]
Maintainer: Walerian Sokolowski <r-logging@wlogsolutions.com>
Diff between logging versions 0.8-104 dated 2018-11-30 and 0.9-105 dated 2019-01-16
logging-0.8-104/logging/cleanup |only logging-0.8-104/logging/inst |only logging-0.8-104/logging/man/addHandler.Rd |only logging-0.8-104/logging/man/basicConfig.Rd |only logging-0.8-104/logging/man/handler-actions.Rd |only logging-0.8-104/logging/man/levels.Rd |only logging-0.8-104/logging/man/log.Rd |only logging-0.8-104/logging/man/logging-internal.Rd |only logging-0.8-104/logging/tests/doSvUnit.R |only logging-0.8-104/logging/tests/report.xml |only logging-0.9-105/logging/DESCRIPTION | 14 logging-0.9-105/logging/MD5 | 48 +- logging-0.9-105/logging/NAMESPACE | 48 +- logging-0.9-105/logging/NEWS.md |only logging-0.9-105/logging/R/logger.R | 399 ++++++++++++++---- logging-0.9-105/logging/R/namedLevels.R | 58 +- logging-0.9-105/logging/R/oo.R | 290 ++++++------- logging-0.9-105/logging/R/updateOptions.R | 60 ++ logging-0.9-105/logging/R/utils.R | 154 +++++- logging-0.9-105/logging/R/zzz.R | 73 ++- logging-0.9-105/logging/man/bootstrapping.Rd |only logging-0.9-105/logging/man/getHandler.Rd | 59 +- logging-0.9-105/logging/man/getLogger.Rd | 54 +- logging-0.9-105/logging/man/handlers-management.Rd |only logging-0.9-105/logging/man/inbuilt-actions.Rd |only logging-0.9-105/logging/man/logging-entrypoints.Rd |only logging-0.9-105/logging/man/logging-package.Rd | 129 ++--- logging-0.9-105/logging/man/loglevels.Rd |only logging-0.9-105/logging/man/setLevel.Rd | 52 +- logging-0.9-105/logging/man/updateOptions.Rd |only logging-0.9-105/logging/tests/run_tests.R |only logging-0.9-105/logging/tests/test.automatic-format.R |only logging-0.9-105/logging/tests/test.data.interaction.R |only logging-0.9-105/logging/tests/test.handlers.R |only 34 files changed, 916 insertions(+), 522 deletions(-)
Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models on the cumulative incidence function with interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 1.0.4 dated 2018-11-29 and 1.0.5 dated 2019-01-16
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/bssmle_se.R | 6 ++-- R/ciregic.R | 71 +++++++++++++++++++++++++++++++++++----------------------- 4 files changed, 54 insertions(+), 37 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-11 0.1.1
Title: Bayesian State-Space Modeling of Mouse-Tracking Experiments via
Stan
Description: Estimates previously compiled state-space modeling for mouse-tracking experiments using the 'rstan' package, which provides the R interface to the Stan C++ library for Bayesian estimation.
Author: Antonio Calcagnì, Massimiliano Pastore
Maintainer: Antonio Calcagnì <ant.calcagni@gmail.com>
Diff between ssMousetrack versions 1.1.2 dated 2019-01-02 and 1.1.5 dated 2019-01-16
ssMousetrack-1.1.2/ssMousetrack/src/stan_files/fit_model.stan |only ssMousetrack-1.1.2/ssMousetrack/src/stan_files/simulate_data.stan |only ssMousetrack-1.1.5/ssMousetrack/DESCRIPTION | 8 +- ssMousetrack-1.1.5/ssMousetrack/MD5 | 38 +++++----- ssMousetrack-1.1.5/ssMousetrack/NEWS | 8 ++ ssMousetrack-1.1.5/ssMousetrack/R/check_prior.R | 6 - ssMousetrack-1.1.5/ssMousetrack/R/compute_D.R | 2 ssMousetrack-1.1.5/ssMousetrack/R/datasets.R | 10 +- ssMousetrack-1.1.5/ssMousetrack/R/evaluate_ssm.R | 21 +++-- ssMousetrack-1.1.5/ssMousetrack/R/generate_data.R | 37 ++++++--- ssMousetrack-1.1.5/ssMousetrack/R/run_ssm.R | 27 ++++--- ssMousetrack-1.1.5/ssMousetrack/R/ssMousetrack-package.R | 22 ++++- ssMousetrack-1.1.5/ssMousetrack/R/zzz.R | 11 ++ ssMousetrack-1.1.5/ssMousetrack/man/check_prior.Rd | 4 - ssMousetrack-1.1.5/ssMousetrack/man/congruency.Rd | 3 ssMousetrack-1.1.5/ssMousetrack/man/generate_data.Rd | 18 +++- ssMousetrack-1.1.5/ssMousetrack/man/language.Rd | 5 - ssMousetrack-1.1.5/ssMousetrack/man/run_ssm.Rd | 20 +++-- ssMousetrack-1.1.5/ssMousetrack/man/ssMousetrack-package.Rd | 21 ++++- ssMousetrack-1.1.5/ssMousetrack/src/stan_files/fit_model_gomp.stan |only ssMousetrack-1.1.5/ssMousetrack/src/stan_files/fit_model_log.stan |only ssMousetrack-1.1.5/ssMousetrack/src/stan_files/simulate_data_gomp.stan |only ssMousetrack-1.1.5/ssMousetrack/src/stan_files/simulate_data_log.stan |only 23 files changed, 176 insertions(+), 85 deletions(-)
Title: Exploratory Data Analysis and Manipulation of Multi-Label Data
Sets
Description: Exploratory data analysis and manipulation functions for multi-
label data sets along with an interactive Shiny application to ease their use.
Author: David Charte [cre] (<https://orcid.org/0000-0002-4830-9512>),
Francisco Charte [aut] (<https://orcid.org/0000-0002-3083-8942>),
Antonio J. Rivera [aut]
Maintainer: David Charte <fdavidcl@ugr.es>
Diff between mldr versions 0.4.0 dated 2018-02-04 and 0.4.1 dated 2019-01-16
DESCRIPTION | 23 +++++++++++++---------- MD5 | 18 +++++++++--------- R/evmetrics_av.R | 19 ++++++++++--------- R/operators.R | 4 ++-- build/vignette.rds |binary inst/doc/mldr.pdf |binary man/evmetrics-av.Rd | 9 ++++++--- man/evmetrics-ml.Rd | 1 + man/evmetrics-rk.Rd | 7 +++++-- man/mldr.Rd | 5 +++-- 10 files changed, 49 insertions(+), 37 deletions(-)
Title: Converting an Mbox File into a Tibble
Description: Importing and converting an mbox file into a tibble object.
Author: JooYoung Seo [aut, cre],
Soyoung Choi [aut]
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Diff between mboxr versions 0.1.2 dated 2018-12-30 and 0.1.3 dated 2019-01-16
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ README.md | 5 +++++ build/vignette.rds |binary inst/NEWS | 5 +++++ inst/doc/mboxr_vignette.Rmd | 2 +- inst/doc/mboxr_vignette.html | 8 ++++---- inst/python/__pycache__/mboxR.cpython-36.pyc |binary inst/python/mboxR.py | 2 +- vignettes/mboxr_vignette.Rmd | 2 +- 11 files changed, 35 insertions(+), 20 deletions(-)
Title: Animal Activity Statistics
Description: Provides functions to fit kernel density functions
to animal activity time data; plot activity distributions;
quantify overall levels of activity; statistically compare
activity metrics through bootstrapping; and evaluate variation
in linear variables with time (or other circular variables).
Author: Marcus Rowcliffe
Maintainer: Marcus Rowcliffe <marcus.rowcliffe@ioz.ac.uk>
Diff between activity versions 1.1 dated 2016-09-26 and 1.2 dated 2019-01-16
activity-1.1/activity/R/activity_code_1_1.r |only activity-1.1/activity/man/plot-actmod-methods.Rd |only activity-1.1/activity/man/plot-lincircmod-methods.Rd |only activity-1.1/activity/man/rvmkern.Rd |only activity-1.1/activity/man/show-actmod-method.Rd |only activity-1.1/activity/man/yfromx.Rd |only activity-1.2/activity/DESCRIPTION | 16 +++--- activity-1.2/activity/MD5 | 42 +++++++-------- activity-1.2/activity/NAMESPACE | 11 +--- activity-1.2/activity/R/activity_code.r |only activity-1.2/activity/man/BCIspeed.Rd | 3 - activity-1.2/activity/man/BCItime.Rd | 3 - activity-1.2/activity/man/activity.Rd | 6 -- activity-1.2/activity/man/actmod-class.Rd | 8 +-- activity-1.2/activity/man/bwcalc.Rd | 3 - activity-1.2/activity/man/compareAct.Rd | 11 ++-- activity-1.2/activity/man/compareCkern.Rd | 24 ++++----- activity-1.2/activity/man/compareTimes.Rd | 9 +-- activity-1.2/activity/man/density2.Rd |only activity-1.2/activity/man/dvmkern.Rd | 3 - activity-1.2/activity/man/fitact.Rd | 50 +++++++++++-------- activity-1.2/activity/man/fitlincirc.Rd | 8 +-- activity-1.2/activity/man/lincircKern.Rd | 12 ++-- activity-1.2/activity/man/lincircmod-class.Rd | 6 +- activity-1.2/activity/man/ovl5.Rd |only activity-1.2/activity/man/plot.actmod.Rd |only activity-1.2/activity/man/plot.lincircmod.Rd |only activity-1.2/activity/man/redf.Rd |only 28 files changed, 106 insertions(+), 109 deletions(-)
Title: Quantitative Analysis Made Accessible
Description: This is a new version of the 'userfriendlyscience' package,
which has grown a bit unwieldy. Therefore, distinct functionalities
are being 'consciously uncoupled' into different packages. This package
contains the general-purpose tools and utilities (see the
'behaviorchange' and the 'rosetta' packages for other functionality), and
is the most direct 'successor' of the original 'userfriendlyscience' package.
For example, this package contains a number of basic functions to create
higher level plots, such as diamond plots, to easily plot sampling
distributions, to generate confidence intervals, to plan study sample sizes
for confidence intervals, and to do some basic operations such as
(dis)attenuate effect size estimates.
Author: Gjalt-Jorn Peters [aut, cre, ctb]
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between ufs versions 0.0.1 dated 2018-08-02 and 0.1.0 dated 2019-01-16
DESCRIPTION | 33 ++++++--- MD5 | 94 +++++++++++++++++++++++++-- NAMESPACE | 108 ++++++++++++++++++++++++++++++++ R/IN.R | 4 - R/areColors.R |only R/associationMatrix.R |only R/associationsDiamondPlot.R |only R/associationsToDiamondPlotDf.R |only R/attenuate.d.R |only R/biAxisDiamondPlot.R |only R/cohensdCI.R |only R/cohensdDist.R |only R/confIntOmegaSq.R |only R/confIntProp.R |only R/confIntR.R |only R/confIntV.R |only R/convert.R |only R/convert.d.to.eer.R |only R/convert.d.to.nnc.R |only R/convertToNumeric.R |only R/diamondCoordinates.R |only R/diamondPlot.R |only R/disattenuate.d.R |only R/duoComparisonDiamondPlot.R |only R/extractVarName.R |only R/faConfInt.R |only R/factorLoadingDiamondCIplot.R |only R/from_MBESS_ci.pvaf.R |only R/from_MBESS_conf.limits.ncf.R |only R/from_epiR_epi.2by2.R |only R/getData.R |only R/ggBarChart.R |only R/ggDiamondLayer.R |only R/ggEasyBar.R |only R/ggEasyRidge.R |only R/ggProportionPlot.R |only R/ggSmallSampleFreqs.R |only R/massConvertToNumeric.R |only R/meanConfInt.R |only R/meanSDtoDiamondPlot.R |only R/meansComparisonDiamondPlot.R |only R/meansDiamondPlot.R |only R/multiResponse.R |only R/multiVarFreq.R |only R/omegaSqDist.R |only R/pwr.cohensdCI.R |only R/rawDataDiamondLayer.R |only R/safeRequire.R |only R/sharedSubString.R |only R/varsToDiamondPlotDf.R |only R/visualiseOperationalisations.R | 11 +-- README.md | 2 man/IN.Rd | 1 man/areColors.Rd |only man/associationMatrix.Rd |only man/associationMatrixHelperFunctions.Rd |only man/associationsDiamondPlot.Rd |only man/attenuate.d.Rd |only man/basicDiamondplotFunctions.Rd |only man/biAxisDiamondPlot.Rd |only man/cohensDdistribution.Rd |only man/comparisonDiamondPlots.Rd |only man/confIntOmegaSq.Rd |only man/confIntProp.Rd |only man/confIntR.Rd |only man/convert.Rd |only man/convert.d.to.nnc.Rd |only man/convertToNumeric.Rd |only man/cramersV.Rd |only man/diamondPlot.Rd |only man/disattenuate.d.Rd |only man/extractVarName.Rd |only man/faConfInt.Rd |only man/factorLoadingDiamondCIplot.Rd |only man/getData.Rd |only man/ggBarChart.Rd |only man/ggEasyPlots.Rd |only man/ggProportionPlot.Rd |only man/massConvertToNumeric.Rd |only man/meanConfInt.Rd |only man/meanSDtoDiamondPlot.Rd |only man/meansDiamondPlot.Rd |only man/multiResponse.Rd |only man/multiVarFreq.Rd |only man/omegasq.Rd |only man/safeRequire.Rd |only man/sharedSubString.Rd |only man/vecTxt.Rd | 6 - 88 files changed, 230 insertions(+), 29 deletions(-)
Title: Transformation Trees and Forests
Description: Recursive partytioning of transformation models with
corresponding random forest for conditional transformation models
as described in 'Transformation Forests' (Hothorn and Zeileis, 2017, <arXiv:1701.02110>)
and 'Top-Down Transformation Choice' (Hothorn, 2018, <DOI:10.1177/1471082X17748081>).
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between trtf versions 0.3-3 dated 2018-09-18 and 0.3-4 dated 2019-01-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/trees_forests.R | 23 ++++++++++++++++------- inst/NEWS.Rd | 11 ++++++++++- 4 files changed, 33 insertions(+), 15 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 2.0.0 dated 2018-11-10 and 2.1.0 dated 2019-01-16
DESCRIPTION | 26 - MD5 | 99 ++++-- NAMESPACE | 31 ++ NEWS.md | 21 + R/data.R | 29 + R/f_checkinput_copulacorrection.R | 12 R/f_checkinput_helperfunctions.R | 48 ++- R/f_checkinput_latentIV.R | 7 R/f_checkinput_multilevel.R |only R/f_copulacorrection_LL.R | 4 R/f_copulacorrection_interface.R | 51 ++- R/f_copulacorrection_optimizeLL.R | 53 ++- R/f_formula_helpers.R | 30 + R/f_helper_demean.R | 2 R/f_highermomentsIV.R | 1 R/f_latentIV.R | 75 +++- R/f_latentIV_LL.R | 2 R/f_multilevelIV.R | 307 +++++++++++++++++++- R/f_multilevel_2levels.R |only R/f_multilevel_3levels.R |only R/f_multilevel_gmmestim.R |only R/f_multilevel_helpers.R |only R/f_multilevel_omittedvar.R |only R/f_new_multilevel.R |only R/f_new_rendoivreg.R | 19 - R/f_new_rendooptimLL.R | 42 -- R/f_s3_multilevel.R |only R/f_s3_rendooptimLL.R | 40 ++ README.md | 175 ++++++++++- build |only data/dataHetIV.rda |binary data/dataMultilevelIV.rda |only inst |only man/copulaCorrection.Rd | 47 ++- man/dataMultilevelIV.Rd |only man/latentIV.Rd | 31 +- man/multilevelIV.Rd | 157 +++++++++- man/summary.rendo.multilevel.Rd |only tests/testthat/dallas2485.csv |only tests/testthat/helper_test_confint.R |only tests/testthat/helper_test_optimxargs.R |only tests/testthat/helper_test_s3methods.R | 3 tests/testthat/helper_test_s3methods_rendooptimLL.R | 22 + tests/testthat/helper_test_singlelogical.R | 12 tests/testthat/test_correctness_copulacorrections.R |only tests/testthat/test_correctness_heterrors.R |only tests/testthat/test_correctness_highermoments.R |only tests/testthat/test_correctness_latentIV.R |only tests/testthat/test_correctness_multilevel.R |only tests/testthat/test_inputchecks_copulacorrection.R | 52 ++- tests/testthat/test_inputchecks_heterrorsIV.R | 8 tests/testthat/test_inputchecks_highermomentsiv.R | 11 tests/testthat/test_inputchecks_latentIV.R | 24 + tests/testthat/test_inputchecks_multilevel.R |only tests/testthat/test_runability_copulacorrection.R | 140 +++------ tests/testthat/test_runability_heterrorsIV.R | 67 +--- tests/testthat/test_runability_highermomentsIV.R | 19 - tests/testthat/test_runability_latentIV.R | 37 -- tests/testthat/test_runability_multilevel.R |only tests/testthat/test_s3methods_copualcorrection.R | 33 +- tests/testthat/test_s3methods_multilevel.R |only vignettes |only 62 files changed, 1275 insertions(+), 462 deletions(-)
Title: Time Series Forecasting with Neural Networks
Description: Automatic time series modelling with neural networks.
Allows fully automatic, semi-manual or fully manual specification of networks. For details of the
specification methodology see: (i) Crone and Kourentzes (2010) <doi:10.1016/j.neucom.2010.01.017>;
and (ii) Kourentzes et al. (2014) <doi:10.1016/j.eswa.2013.12.011>.
Author: Nikolaos Kourentzes [aut, cre]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between nnfor versions 0.9.2 dated 2017-12-11 and 0.9.6 dated 2019-01-16
nnfor-0.9.2/nnfor/R/cmav.R |only nnfor-0.9.2/nnfor/R/lagmatrix.R |only nnfor-0.9.2/nnfor/R/mseastest.R |only nnfor-0.9.2/nnfor/R/nnfor.R |only nnfor-0.9.2/nnfor/R/seasdummy.R |only nnfor-0.9.2/nnfor/man/lagmatrix.Rd |only nnfor-0.9.2/nnfor/man/nnfor-package.Rd |only nnfor-0.9.2/nnfor/man/seasdummy.Rd |only nnfor-0.9.6/nnfor/DESCRIPTION | 16 +++++++------- nnfor-0.9.6/nnfor/MD5 | 30 +++++++++++---------------- nnfor-0.9.6/nnfor/NAMESPACE | 7 ++++-- nnfor-0.9.6/nnfor/NEWS.md | 13 +++++++++++ nnfor-0.9.6/nnfor/R/compcheck.R | 2 - nnfor-0.9.6/nnfor/R/forecast.net.R | 18 ++++++++++------ nnfor-0.9.6/nnfor/R/mlp.R | 36 +++++++++++++++++++-------------- nnfor-0.9.6/nnfor/R/nnfor-package.R |only nnfor-0.9.6/nnfor/README.md | 29 ++++++++++++++++++++++---- nnfor-0.9.6/nnfor/man/elm.Rd | 14 ++++++------ nnfor-0.9.6/nnfor/man/elm.fast.Rd | 4 +-- nnfor-0.9.6/nnfor/man/mlp.Rd | 4 +-- nnfor-0.9.6/nnfor/man/nnfor.Rd |only 21 files changed, 107 insertions(+), 66 deletions(-)
Title: Multiple-Output Directional Quantile Regression
Description: Contains basic tools for performing
multiple-output quantile regression and computing
regression quantile contours by means of directional
regression quantiles. In the location case, one can thus
obtain halfspace depth contours in two to six dimensions.
Hallin, M., Paindaveine, D. and Siman, M. (2010)
Multivariate quantiles and multiple-output regression quantiles:
from L1 optimization to halfspace depth. Annals of Statistics 38, 635-669
For more references about the method, see Help pages.
Author: Miroslav Šiman [aut],
Pavel Boček [aut, cre]
Maintainer: Pavel Boček <bocek@utia.cas.cz>
Diff between modQR versions 0.1.1 dated 2016-03-02 and 0.1.2 dated 2019-01-16
DESCRIPTION | 32 ++++++++++++++++---------------- MD5 | 8 ++++---- man/compContour.Rd | 12 ++++++------ man/getCharSTM1u.Rd | 12 ++++++------ man/getCharSTM2u.Rd | 12 ++++++------ 5 files changed, 38 insertions(+), 38 deletions(-)
Title: Solar Radiation
Description: Functions to compute insolation on complex terrain.
Author: Javier G. Corripio
Maintainer: Javier G. Corripio <jgc@meteoexploration.com>
Diff between insol versions 1.1.1 dated 2014-03-04 and 1.2 dated 2019-01-16
DESCRIPTION | 13 ++-- MD5 | 71 +++++++++++++-------------- R/GCdistance.R | 13 ++-- R/JDymd.R | 4 - R/aspect.R | 12 ++-- R/cgrad.R | 6 +- R/daylength.R | 6 +- R/declination.R | 52 +++++++++++++------ R/doshade.R | 38 +++++++------- R/doyday.R | 22 ++++---- R/eqtime.R | 4 - R/insolation.R | 6 +- R/slope.R | 6 +- R/sunr.R | 27 ++++++---- man/GCdistance.Rd | 6 +- man/JD.Rd | 11 ---- man/JDymd.Rd | 5 - man/aspect.Rd | 28 +++++----- man/cgrad.Rd | 40 +++++++-------- man/daydoy.Rd | 4 - man/daylength.Rd | 10 +-- man/declination.Rd | 22 ++------ man/doshade.Rd | 60 +++++++++++------------ man/doyday.Rd | 6 +- man/eqtime.Rd | 28 +++++----- man/hillshading.Rd | 54 ++++++++++---------- man/insol-package.Rd | 14 +---- man/insolation.Rd | 133 +++++++++++++++++++++++++-------------------------- man/normalvector.Rd | 2 man/p2rho.Rd | 6 +- man/slope.Rd | 26 ++++----- man/sunpos.Rd | 8 +-- man/sunr.Rd | 6 +- man/sunvector.Rd | 2 man/wvapsat.Rd | 2 src/doshade.f90 | 86 ++++++++++++++++---------------- src/init.c |only 37 files changed, 425 insertions(+), 414 deletions(-)
Title: Tools to Deal with Fuzzy Numbers
Description: S4 classes and methods
to deal with fuzzy numbers. They allow for computing any arithmetic
operations (e.g., by using the Zadeh extension principle),
performing approximation of arbitrary fuzzy numbers by trapezoidal
and piecewise linear ones, preparing plots for publications, computing
possibility and necessity values for comparisons, etc.
Author: Marek Gagolewski [aut, cre],
Jan Caha [ctb]
Maintainer: Marek Gagolewski <gagolews@rexamine.com>
Diff between FuzzyNumbers versions 0.4-2 dated 2018-02-14 and 0.4-5 dated 2019-01-16
DESCRIPTION | 15 - MD5 | 128 ++++---- NEWS | 10 R/class-02-PiecewiseLinearFuzzyNumber.R | 6 R/methods-alphacut.R | 2 R/methods-as.PiecewiseLinearFuzzyNumber.R | 2 build/vignette.rds |binary inst/CITATION | 4 inst/doc/FuzzyNumbersTutorial.R | 172 +++++------ inst/doc/FuzzyNumbersTutorial.Rnw | 282 +++++++++---------- inst/doc/FuzzyNumbersTutorial.pdf |binary man/Arithmetic-methods.Rd | 33 +- man/DiscontinuousFuzzyNumber-class.Rd | 3 man/DiscontinuousFuzzyNumber.Rd | 9 man/Extract-methods.Rd | 7 man/FuzzyNumber-class.Rd | 3 man/FuzzyNumber.Rd | 2 man/FuzzyNumbers-package.Rd | 9 man/PiecewiseLinearFuzzyNumber-class.Rd | 3 man/PiecewiseLinearFuzzyNumber.Rd | 2 man/PowerFuzzyNumber-class.Rd | 3 man/PowerFuzzyNumber.Rd | 2 man/TrapezoidalFuzzyNumber-class.Rd | 3 man/TrapezoidalFuzzyNumber.Rd | 2 man/TriangularFuzzyNumber.Rd | 2 man/alphaInterval-methods.Rd | 25 - man/alphacut-methods.Rd | 3 man/ambiguity-methods.Rd | 3 man/approxInvert.Rd | 2 man/arctan2.Rd | 3 man/as.FuzzyNumber.Rd | 5 man/as.PiecewiseLinearFuzzyNumber.Rd | 55 +-- man/as.PowerFuzzyNumber.Rd | 44 +- man/as.TrapezoidalFuzzyNumber.Rd | 44 +- man/as.character-methods.Rd | 8 man/convertAlpha.Rd | 2 man/convertSide.Rd | 2 man/core-methods.Rd | 3 man/distance-methods.Rd | 15 - man/evaluate-methods.Rd | 3 man/expectedInterval-methods.Rd | 27 + man/expectedValue-methods.Rd | 10 man/fapply-methods.Rd | 3 man/integrateAlpha-methods.Rd | 13 man/integrate_discont_val.Rd | 1 man/maximum.Rd | 7 man/minimum.Rd | 7 man/necessityExceedance.Rd | 22 - man/necessityStrictExceedance.Rd | 22 - man/necessityStrictUndervaluation.Rd | 22 - man/necessityUndervaluation.Rd | 22 - man/piecewiseLinearApproximation-methods.Rd | 7 man/plot-methods.Rd | 17 - man/possibilityExceedance.Rd | 22 - man/possibilityStrictExceedance.Rd | 22 - man/possibilityStrictUndervaluation.Rd | 22 - man/possibilityUndervaluation.Rd | 22 - man/pow-PiecewiseLinearFuzzyNumber-numeric-method.Rd | 9 man/show-methods.Rd | 2 man/supp-methods.Rd | 3 man/trapezoidalApproximation-methods.Rd | 7 man/value-methods.Rd | 10 man/weightedExpectedValue-methods.Rd | 10 man/width-methods.Rd | 3 vignettes/FuzzyNumbersTutorial.Rnw | 282 +++++++++---------- 65 files changed, 783 insertions(+), 732 deletions(-)
Title: Prints a Random Quote from Marcus Aurelius' Book Meditations
Description: Prints a random quote from Marcus Aurelius' book Meditations.
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between meditations versions 1.0 dated 2018-12-30 and 1.0.1 dated 2019-01-16
meditations-1.0.1/meditations/DESCRIPTION | 11 ++- meditations-1.0.1/meditations/MD5 | 9 +-- meditations-1.0.1/meditations/build/vignette.rds |binary meditations-1.0.1/meditations/inst/WORDLIST |only meditations-1.0.1/meditations/inst/doc/using_meditations.html | 30 ++++++++-- meditations-1.0.1/meditations/tests/spelling.R |only meditations-1.0/meditations/LICENSE |only 7 files changed, 37 insertions(+), 13 deletions(-)
Title: Downloads Box Office Information for Given Dates
Description: Download daily box office information (how much each movie earned
in theaters) using data from either Box Office Mojo (<http://www.boxofficemojo.com/>) or
The Numbers (<http://www.the-numbers.com/>).
Author: Jacob Kaplan [aut, cre]
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between boxoffice versions 1.2.0 dated 2018-12-19 and 1.2.1 dated 2019-01-16
DESCRIPTION | 12 +-- MD5 | 16 ++-- build/vignette.rds |binary inst/WORDLIST |only inst/doc/get_daily_box_office_info.Rmd | 4 - inst/doc/get_daily_box_office_info.html | 32 +++++++- inst/doc/top_grossing.html | 64 +++++++++++------ tests/spelling.R |only tests/testthat/test-top_grossing.R | 118 +++++++++++++++++--------------- vignettes/get_daily_box_office_info.Rmd | 4 - 10 files changed, 153 insertions(+), 97 deletions(-)
Title: A Tool for Processing Steem Data
Description: Steem is a blockchain-based social media platform (see <https://en.wikipedia.org/wiki/Steemit>). The Steem social activity data are saved in the Steem blockchain, the SteemDB database, the SteemSQL database, and so on. 'steemr' is an R package that downloads the Steem data from the SteemDB and SteemSQL servers, re-organizes the data in a user-friendly way, and visualizes the data for further analysis.
Author: Peng Zhao <pzhao@pzhao.net>
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between steemr versions 0.1.2 dated 2019-01-11 and 0.1.3 dated 2019-01-16
DESCRIPTION | 8 +++--- MD5 | 54 +++++++++++++++++++++--------------------- R/analysis.r | 7 ++++- R/build.r | 6 +++- R/get.r | 68 ++++++++++++++++++++++++++++++++++++++++++++--------- R/plothour.r | 2 + man/avotenot.Rd | 2 + man/avotep.Rd | 2 + man/bblog.Rd | 3 +- man/gaccounts.Rd | 2 + man/gblog.Rd | 2 + man/gcner.Rd | 2 + man/gcomments.Rd | 2 + man/gdelegation.Rd | 2 + man/gfollow.Rd | 2 + man/gfollower.Rd | 2 + man/gfollowing.Rd | 2 + man/gid.Rd | 2 + man/gidpostl.Rd | 2 + man/gidposts.Rd | 2 + man/gpost.Rd | 2 + man/gposts.Rd | 2 + man/gspmv.Rd | 2 + man/gur.Rd | 2 + man/gvotep.Rd | 2 + man/gvoter.Rd | 2 + man/phour.Rd | 2 + man/ssql.Rd | 2 + 28 files changed, 144 insertions(+), 46 deletions(-)
Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>),
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stéphane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Murdoch [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 0.9.0 dated 2018-05-21 and 1.0.0 dated 2019-01-16
DESCRIPTION | 18 MD5 | 103 - NAMESPACE | 11 R/add_header_above.R | 220 ++ R/add_indent.R | 4 R/as_image.R |only R/collapse_rows.R | 15 R/column_spec.R | 3 R/footnote.R | 26 R/group_rows.R | 38 R/kableExtra-package.R | 8 R/kable_as_image.R | 29 R/kable_styling.R | 210 +- R/kable_xml.R |only R/linebreak.R | 13 R/print.R | 16 R/save_kable.R | 132 + R/scroll_box.R | 28 R/util.R | 17 R/xtable2kable.R |only R/zzz.R | 6 README.md | 2 inst/NEWS.md | 20 inst/doc/awesome_table_in_html.R | 6 inst/doc/awesome_table_in_html.Rmd | 10 inst/doc/awesome_table_in_html.html | 1419 ++++++++++++++++- inst/doc/awesome_table_in_pdf.R | 11 inst/doc/awesome_table_in_pdf.Rmd | 24 inst/doc/awesome_table_in_pdf.pdf |binary inst/doc/best_practice_for_newline_in_latex_table.R | 1 inst/doc/best_practice_for_newline_in_latex_table.Rmd | 10 inst/doc/best_practice_for_newline_in_latex_table.pdf |binary inst/doc/legacy_features.html | 299 +++ inst/doc/use_kableExtra_with_formattable.html | 287 +++ inst/doc/use_kable_in_shiny.html | 269 +++ inst/kePrint-0.0.1/kePrint.js | 8 man/add_header_above.Rd | 38 man/as_image.Rd |only man/cell_spec.Rd | 18 man/collapse_rows.Rd | 3 man/footnote.Rd | 8 man/footnote_marker_number.Rd | 2 man/group_rows.Rd | 10 man/kable_as_image.Rd | 25 man/kable_as_xml.Rd |only man/kable_styling.Rd | 61 man/linebreak.Rd | 5 man/reexports.Rd | 1 man/row_spec.Rd | 7 man/save_kable.Rd | 23 man/scroll_box.Rd | 6 man/xml_as_kable.Rd |only man/xtable2kable.Rd |only vignettes/awesome_table_in_html.Rmd | 10 vignettes/awesome_table_in_pdf.Rmd | 24 vignettes/best_practice_for_newline_in_latex_table.Rmd | 10 56 files changed, 3093 insertions(+), 421 deletions(-)
Title: Use Image in 'ggplot2'
Description: Supports image files and graphic objects to be visualized in
'ggplot2' graphic system.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggimage versions 0.2.0 dated 2018-12-10 and 0.2.1 dated 2019-01-16
DESCRIPTION | 6 +-- MD5 | 29 ++++++++------ NAMESPACE | 5 ++ NEWS.md | 12 ++++++ R/color_image.R |only R/draw_key.R | 48 ++++++++++++++++++++++-- R/geom_image.R | 96 +++++++++++++++++++++++-------------------------- R/geom_phylopic.R | 57 ++++++++++++++++++++++++++++- README.md | 33 ++++++++++------ build/vignette.rds |binary inst/doc/ggimage.R | 4 -- inst/doc/ggimage.Rmd | 8 +--- inst/doc/ggimage.html | 88 ++++++++++++++++++++++---------------------- inst/extdata/Rlogo.png |only man/geom_image.Rd | 4 -- man/phylopic_uid.Rd |only vignettes/ggimage.Rmd | 8 +--- 17 files changed, 253 insertions(+), 145 deletions(-)
Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and non-convex loss functions, for both classical and robust regression and classification problems. See Wang (2011) <doi:10.2202/1557-4679.1304>, Wang (2012) <doi:10.3414/ME11-02-0020>, Wang (2018) <doi:10.1080/10618600.2018.1424635>, Wang (2018) <doi:10.1214/18-EJS1404>.
Author: Zhu Wang [aut, cre],
Torsten Hothorn [ctb]
Maintainer: Zhu Wang <wangz1@uthscsa.edu>
Diff between bst versions 0.3-15 dated 2018-07-23 and 0.3-16 dated 2019-01-16
DESCRIPTION | 15 +++++++-------- MD5 | 40 ++++++++++++++++++++-------------------- build/vignette.rds |binary inst/CITATION | 7 +++++-- inst/doc/cancer.Rnw | 5 ++--- inst/doc/cancer.pdf |binary inst/doc/khan.R | 24 ++++++++++++------------ inst/doc/khan.Rnw | 5 ++--- inst/doc/khan.pdf |binary inst/doc/mcl.Rnw | 5 ++--- inst/doc/mcl.pdf |binary inst/doc/pros.R | 32 ++++++++++++++++---------------- inst/doc/pros.Rnw | 5 ++--- inst/doc/pros.pdf |binary man/rbst.Rd | 2 +- man/rmbst.Rd | 2 +- vignettes/bst.bib | 2 ++ vignettes/cancer.Rnw | 5 ++--- vignettes/khan.Rnw | 5 ++--- vignettes/mcl.Rnw | 5 ++--- vignettes/pros.Rnw | 5 ++--- 21 files changed, 80 insertions(+), 84 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies by easing and extending the functionality of the R packages 'twang' (Ridgeway et al., 2017) <https://CRAN.R-project.org/package=twang> for generalized boosted modeling, 'CBPS' (Fong, Ratkovic, & Imai, 2018) <https://CRAN.R-project.org/package=CBPS> for covariate balancing propensity score weighting, 'ebal' (Hainmueller, 2014) <https://CRAN.R-project.org/package=ebal> for entropy balancing, 'optweight' (Greifer, 2018) <https://CRAN.R-project.org/package=optweight> for optimization-based weights, 'ATE' (Haris & Chan, 2015) <https://CRAN.R-project.org/package=ATE> for empirical balancing calibration weighting, and SuperLearner (Polley, LeDell, Kenney, & van der Laan, 2018) <https://CRAN.R-project.org/package=SuperLearner>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt' (Greifer, 2018) <https://CRAN.R-project.org/package=cobalt>.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.5.0 dated 2018-11-22 and 0.5.1 dated 2019-01-16
DESCRIPTION | 10 MD5 | 30 +- NAMESPACE | 2 NEWS.md | 8 R/SHARED.R |only R/functions_for_processing.R | 468 ++++-------------------------------- R/ps.cont.R | 2 R/weightit.R | 29 -- R/weightit.fit.R | 108 ++++---- R/weightit2method.R | 112 ++++++-- R/weightitMSM.R | 42 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/WeightIt_A0_basic_use.html | 381 ++++++----------------------- man/make.full.rank.Rd |only man/method-user.Rd | 6 man/weightitMSM.Rd | 4 17 files changed, 352 insertions(+), 850 deletions(-)
Title: Conventional Tukey Test
Description: Perform the conventional Tukey test from formula, lm, aov, aovlist and lmer objects.
Author: Jos Cludio Faria <joseclaudio.faria@gmail.com>,
Enio G. Jelihovschi <eniojelihovs@gmail.com>,
Ivan Bezerra Allaman <ivanalaman@gmail.com>
Maintainer: Ivan Bezerra Allaman <ivanalaman@gmail.com>
Diff between TukeyC versions 1.3-0 dated 2018-01-13 and 1.3-3 dated 2019-01-16
ChangeLog | 12 ++ DESCRIPTION | 10 +- MD5 | 40 ++++---- NAMESPACE | 1 R/TukeyC.aovlist.R | 45 +++------ R/TukeyC.formula.R | 10 +- R/TukeyC.lm.R | 20 ++-- R/TukeyC.lmerMod.R | 8 + R/TukeyC.nest.aovlist.R | 1 R/TukeyC.nest.lm.R | 16 --- R/boxplot.TukeyC.R |only R/make.TukeyC.groups.R | 127 ++++++++++++------------- R/plot.TukeyC.R | 45 ++++----- demo/00Index | 14 +- demo/CRD.R | 75 +++++++++------ demo/RCBD.R | 11 +- demo/SPE.R | 5 - demo/SPET.R | 10 +- demo/SSPE.R | 13 +- man/TukeyC.Rd | 236 ++++++++++++++++++++++++------------------------ man/boxplot.TukeyC.Rd |only man/plot.TukeyC.Rd | 26 ++--- 22 files changed, 373 insertions(+), 352 deletions(-)
Title: Create Interactive Timeline Visualizations in R
Description: Create rich and fully interactive timeline visualizations.
Timelines can be included in Shiny apps and R markdown documents, or viewed
from the R console and 'RStudio' Viewer. 'timevis' includes an extensive API
to manipulate a timeline after creation, and supports getting data out of
the visualization into R. Based on the 'vis.js' Timeline module and the
'htmlwidgets' R package.
Author: Dean Attali [aut, cre] (R interface),
Almende B.V. [aut, cph] (vis.js library, http://visjs.org,
http://www.almende.com/home)
Maintainer: Dean Attali <daattali@gmail.com>
Diff between timevis versions 0.4 dated 2016-09-16 and 0.5 dated 2019-01-16
timevis-0.4/timevis/inst/doc/overview.R |only timevis-0.4/timevis/inst/doc/overview.Rmd |only timevis-0.4/timevis/inst/doc/overview.html |only timevis-0.4/timevis/vignettes/overview.Rmd |only timevis-0.5/timevis/DESCRIPTION | 14 +- timevis-0.5/timevis/MD5 | 37 +++--- timevis-0.5/timevis/NEWS.md | 11 + timevis-0.5/timevis/R/api.R | 1 timevis-0.5/timevis/R/data.R |only timevis-0.5/timevis/R/timevis.R | 27 +++- timevis-0.5/timevis/R/utils.R | 6 - timevis-0.5/timevis/README.md | 142 ++++++++++++++++-------- timevis-0.5/timevis/build/vignette.rds |binary timevis-0.5/timevis/data |only timevis-0.5/timevis/inst/doc/timevis.R |only timevis-0.5/timevis/inst/doc/timevis.Rmd |only timevis-0.5/timevis/inst/doc/timevis.html |only timevis-0.5/timevis/inst/example/sampleData.R | 7 - timevis-0.5/timevis/inst/example/server.R | 4 timevis-0.5/timevis/inst/example/utils.R | 5 timevis-0.5/timevis/inst/htmlwidgets/timevis.js | 3 timevis-0.5/timevis/man/timevis.Rd | 19 +++ timevis-0.5/timevis/man/timevisData.Rd |only timevis-0.5/timevis/man/timevisDataGroups.Rd |only timevis-0.5/timevis/vignettes/timevis.Rmd |only 25 files changed, 190 insertions(+), 86 deletions(-)
Title: Practicals for Use with Davison (2003) Statistical Models
Description: Contains the datasets and a few functions for use with
the practicals outlined in Appendix A of the book
Statistical Models (Davison, 2003, Cambridge University Press).
The practicals themselves can be found at
<http://statwww.epfl.ch/davison/SM/>.
Author: Anthony Davison <Anthony.Davison@epfl.ch>
Maintainer: Anthony Davison <Anthony.Davison@epfl.ch>
Diff between SMPracticals versions 1.4-2 dated 2013-01-15 and 1.4-3 dated 2019-01-16
DESCRIPTION | 17 +++++++++-------- MD5 | 8 ++++---- NAMESPACE | 14 +++++++++++++- man/plot.glm.diag.Rd | 3 ++- man/poi.beta.laplace.Rd | 3 ++- 5 files changed, 30 insertions(+), 15 deletions(-)
Title: Analysis of Evolutionary Diversification
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: ORPHANED
Diff between geiger versions 2.0.6 dated 2015-09-07 and 2.0.6.1 dated 2019-01-16
DESCRIPTION | 13 ++++++++----- MD5 | 7 ++++--- src/Makevars | 3 +-- src/Makevars.win | 3 +-- src/init.c |only 5 files changed, 14 insertions(+), 12 deletions(-)
Title: PCIC Implementation of Climdex Routines
Description: PCIC's implementation of Climdex routines for computation of
extreme climate indices.
Author: David Bronaugh <bronaugh@uvic.ca> for the Pacific Climate Impacts
Consortium
Maintainer: ORPHANED
Diff between climdex.pcic versions 1.1-9 dated 2018-08-01 and 1.1-9.1 dated 2019-01-16
climdex.pcic-1.1-9.1/climdex.pcic/DESCRIPTION | 12 ++++++++---- climdex.pcic-1.1-9.1/climdex.pcic/MD5 | 4 +--- climdex.pcic-1.1-9/climdex.pcic/src/Makevars |only climdex.pcic-1.1-9/climdex.pcic/src/Makevars.win |only 4 files changed, 9 insertions(+), 7 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC).
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints.
The net benefit and win ratio statistics can then be estimated
and corresponding confidence intervals and p-values can be
estimated using resampling methods or the asymptotic U-statistic
theory. The software enables the use of thresholds of minimal
importance difference, stratification, and corrections to deal
with right-censored endpoints or missing values.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [aut]
Maintainer: Brice Ozenne <brice.ozenne@orange.fr>
Diff between BuyseTest versions 1.6 dated 2018-10-17 and 1.7 dated 2019-01-16
BuyseTest-1.6/BuyseTest/inst/CR |only BuyseTest-1.6/BuyseTest/inst/M2-project |only BuyseTest-1.7/BuyseTest/DESCRIPTION | 44 BuyseTest-1.7/BuyseTest/MD5 | 198 BuyseTest-1.7/BuyseTest/NAMESPACE | 89 BuyseTest-1.7/BuyseTest/NEWS | 143 BuyseTest-1.7/BuyseTest/R/0-onLoad.R | 16 BuyseTest-1.7/BuyseTest/R/1-setGeneric.R | 81 BuyseTest-1.7/BuyseTest/R/BuyseRes-confint.R | 790 +-- BuyseTest-1.7/BuyseTest/R/BuyseRes-iid.R |only BuyseTest-1.7/BuyseTest/R/BuyseRes-object.R | 304 - BuyseTest-1.7/BuyseTest/R/BuyseRes-summary.R | 824 +-- BuyseTest-1.7/BuyseTest/R/BuyseRes_get.R | 684 +- BuyseTest-1.7/BuyseTest/R/BuyseRes_show.R | 68 BuyseTest-1.7/BuyseTest/R/BuyseSim-object.R | 115 BuyseTest-1.7/BuyseTest/R/BuyseSim-summary.R | 297 - BuyseTest-1.7/BuyseTest/R/BuyseSim_show.R | 67 BuyseTest-1.7/BuyseTest/R/BuyseTest-check.R | 760 +-- BuyseTest-1.7/BuyseTest/R/BuyseTest-inference.R | 663 +- BuyseTest-1.7/BuyseTest/R/BuyseTest-initialization.R | 1340 ++--- BuyseTest-1.7/BuyseTest/R/BuyseTest-package.R | 82 BuyseTest-1.7/BuyseTest/R/BuyseTest-print.R | 260 - BuyseTest-1.7/BuyseTest/R/BuyseTest.R | 1158 ++-- BuyseTest-1.7/BuyseTest/R/BuyseTest.options-object.R | 320 - BuyseTest-1.7/BuyseTest/R/BuyseTest.options.R | 184 BuyseTest-1.7/BuyseTest/R/PairScore.R | 96 BuyseTest-1.7/BuyseTest/R/RcppExports.R | 111 BuyseTest-1.7/BuyseTest/R/constStrata.R | 172 BuyseTest-1.7/BuyseTest/R/discreteRoot.R | 546 +- BuyseTest-1.7/BuyseTest/R/powerBuyseTest.R | 785 +-- BuyseTest-1.7/BuyseTest/R/seBuyseTest.R | 26 BuyseTest-1.7/BuyseTest/R/simBuyseTest.R | 676 +- BuyseTest-1.7/BuyseTest/R/valid.R | 952 +-- BuyseTest-1.7/BuyseTest/build/vignette.rds |binary BuyseTest-1.7/BuyseTest/inst/Article-JSS |only BuyseTest-1.7/BuyseTest/inst/CITATION | 96 BuyseTest-1.7/BuyseTest/inst/Documentation |only BuyseTest-1.7/BuyseTest/inst/Issues |only BuyseTest-1.7/BuyseTest/inst/doc/overview.ltx | 2400 +++++----- BuyseTest-1.7/BuyseTest/inst/doc/overview.pdf |binary BuyseTest-1.7/BuyseTest/inst/todo.org | 13 BuyseTest-1.7/BuyseTest/man/BuyseRes-class.Rd | 32 BuyseTest-1.7/BuyseTest/man/BuyseRes-confint.Rd | 114 BuyseTest-1.7/BuyseTest/man/BuyseRes-getCount.Rd | 52 BuyseTest-1.7/BuyseTest/man/BuyseRes-getPairScore.Rd | 218 BuyseTest-1.7/BuyseTest/man/BuyseRes-getSurvival.Rd | 92 BuyseTest-1.7/BuyseTest/man/BuyseRes-iid.Rd |only BuyseTest-1.7/BuyseTest/man/BuyseRes-show.Rd | 44 BuyseTest-1.7/BuyseTest/man/BuyseRes-summary.Rd | 138 BuyseTest-1.7/BuyseTest/man/BuyseSim-class.Rd | 32 BuyseTest-1.7/BuyseTest/man/BuyseSim-show.Rd | 44 BuyseTest-1.7/BuyseTest/man/BuyseSim-summary.Rd | 73 BuyseTest-1.7/BuyseTest/man/BuyseTest-package.Rd | 68 BuyseTest-1.7/BuyseTest/man/BuyseTest.Rd | 445 - BuyseTest-1.7/BuyseTest/man/BuyseTest.options-class.Rd | 30 BuyseTest-1.7/BuyseTest/man/BuyseTest.options-methods.Rd | 46 BuyseTest-1.7/BuyseTest/man/BuyseTest.options.Rd | 68 BuyseTest-1.7/BuyseTest/man/GPC_cpp.Rd | 132 BuyseTest-1.7/BuyseTest/man/boot2pvalue.Rd | 150 BuyseTest-1.7/BuyseTest/man/calcIntegralScore_cpp.Rd | 46 BuyseTest-1.7/BuyseTest/man/constStrata.Rd | 98 BuyseTest-1.7/BuyseTest/man/dicreteRoot.Rd | 46 BuyseTest-1.7/BuyseTest/man/internal-initialization.Rd | 108 BuyseTest-1.7/BuyseTest/man/internal-print.Rd | 37 BuyseTest-1.7/BuyseTest/man/powerBuyseTest.Rd | 142 BuyseTest-1.7/BuyseTest/man/simulation.Rd | 182 BuyseTest-1.7/BuyseTest/man/testArgs.Rd | 30 BuyseTest-1.7/BuyseTest/man/validFCTs.Rd | 200 BuyseTest-1.7/BuyseTest/src/FCT_buyseTest.cpp | 439 - BuyseTest-1.7/BuyseTest/src/FCT_calcAllPairs.h | 253 - BuyseTest-1.7/BuyseTest/src/FCT_calcOnePair.h | 153 BuyseTest-1.7/BuyseTest/src/FCT_calcStatistic.h | 4 BuyseTest-1.7/BuyseTest/src/RcppExports.cpp | 53 BuyseTest-1.7/BuyseTest/tests/testthat.R | 20 BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-CR.R | 128 BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-PairScore.R | 210 BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-Pairs.R | 1121 ++-- BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-checkValues.R | 776 +-- BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-correctionTTE.R | 446 - BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-iid.R |only BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-neutralAsUnif.R | 202 BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-operator.R | 108 BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-previousBug.R | 609 +- BuyseTest-1.7/BuyseTest/tests/testthat/test-BuyseTest-resampling.R | 651 +- BuyseTest-1.7/BuyseTest/tests/testthat/test-initSurvival.R | 430 - BuyseTest-1.7/BuyseTest/tests/testthat/test-initThreshold.R | 178 BuyseTest-1.7/BuyseTest/tests/testthat/test-otherPackages.R | 294 - BuyseTest-1.7/BuyseTest/vignettes/changes.sty | 1054 ++-- BuyseTest-1.7/BuyseTest/vignettes/overview.ltx | 2400 +++++----- BuyseTest-1.7/BuyseTest/vignettes/overview.org | 2345 ++++----- 90 files changed, 14634 insertions(+), 14267 deletions(-)
Title: Bayesian Synthetic Likelihood
Description: Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>)
is an alternative to standard, non-parametric approximate Bayesian
computation (ABC). BSL assumes a multivariate normal distribution
for the summary statistic likelihood and it is suitable when the
distribution of the model summary statistics is sufficiently regular.
This package provides a Metropolis Hastings Markov chain Monte Carlo
implementation of BSL, BSLasso and semiBSL. BSL with graphical lasso
(BSLasso, An et al. (2018) <https://eprints.qut.edu.au/102263/>) is
computationally more efficient when the dimension of the summary statistic
is high. A semi-parametric version of BSL (semiBSL, An et al. (2018)
<arXiv:1809.05800>) is more robust to non-normal summary
statistics. Extensions to this package are planned.
Author: Ziwen An [aut, cre] (<https://orcid.org/0000-0002-9947-5182>),
Leah F. South [aut] (<https://orcid.org/0000-0002-5646-2963>),
Christopher C. Drovandi [aut] (<https://orcid.org/0000-0001-9222-8763>)
Maintainer: Ziwen An <ziwen.an@hdr.qut.edu.au>
Diff between BSL versions 0.1.1 dated 2018-03-23 and 2.0.0 dated 2019-01-16
BSL-0.1.1/BSL/R/S3_class.R |only BSL-0.1.1/BSL/man/plot.Rd |only BSL-2.0.0/BSL/DESCRIPTION | 51 +-- BSL-2.0.0/BSL/MD5 | 50 ++- BSL-2.0.0/BSL/NAMESPACE | 109 ++++-- BSL-2.0.0/BSL/NEWS.md | 11 BSL-2.0.0/BSL/R/BSL_package.R | 30 + BSL-2.0.0/BSL/R/S3_penbsl.R |only BSL-2.0.0/BSL/R/S4.R |only BSL-2.0.0/BSL/R/S4Functions.R |only BSL-2.0.0/BSL/R/bsl.R | 437 +++++++++++++++++----------- BSL-2.0.0/BSL/R/cell.R | 169 ++++++---- BSL-2.0.0/BSL/R/combinePlotsBSL.R |only BSL-2.0.0/BSL/R/covWarton.R |only BSL-2.0.0/BSL/R/gaussianSynLike.R |only BSL-2.0.0/BSL/R/imports.R |only BSL-2.0.0/BSL/R/kernelCDF.R |only BSL-2.0.0/BSL/R/logitTransform.R |only BSL-2.0.0/BSL/R/ma2.R | 129 +++----- BSL-2.0.0/BSL/R/multignk.R | 189 +++++++----- BSL-2.0.0/BSL/R/selectPenalty.R | 320 ++++++++++---------- BSL-2.0.0/BSL/R/semiparaKernelEstimate.R |only BSL-2.0.0/BSL/man/BSL-package.Rd | 30 + BSL-2.0.0/BSL/man/bsl-class.Rd |only BSL-2.0.0/BSL/man/bsl.Rd | 123 +++++-- BSL-2.0.0/BSL/man/cell.Rd | 141 +++++---- BSL-2.0.0/BSL/man/combinePlotsBSL.Rd |only BSL-2.0.0/BSL/man/gaussianSynLike.Rd |only BSL-2.0.0/BSL/man/ma2.Rd | 111 +++---- BSL-2.0.0/BSL/man/mgnk.Rd | 119 ++++--- BSL-2.0.0/BSL/man/penbsl.Rd |only BSL-2.0.0/BSL/man/plot.bsl.Rd |only BSL-2.0.0/BSL/man/selectPenalty.Rd | 50 +-- BSL-2.0.0/BSL/man/semiparaKernelEstimate.Rd |only BSL-2.0.0/BSL/man/show.bsl.Rd |only BSL-2.0.0/BSL/man/summary.bsl.Rd |only 36 files changed, 1218 insertions(+), 851 deletions(-)
Title: Spectral Processing for High Resolution Flow Infusion Mass
Spectrometry
Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
Author: Jasen Finch [aut, cre]
Maintainer: Jasen Finch <jsf9@aber.ac.uk>
Diff between binneR versions 2.0.6 dated 2019-01-08 and 2.0.7 dated 2019-01-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/binCentrality.R | 2 +- R/binPurity.R | 8 ++++++-- inst/doc/binneR.Rmd | 5 +++-- inst/doc/binneR.html | 20 ++++++++++---------- vignettes/binneR.Rmd | 5 +++-- 7 files changed, 32 insertions(+), 26 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms, see
Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre],
Isaac Gravestock [aut],
Robert Davies [cph],
Stephen Moshier [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Diff between bfp versions 0.0-39 dated 2018-05-14 and 0.0-39.1 dated 2019-01-16
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary src/Makevars | 6 ++---- 4 files changed, 8 insertions(+), 10 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-12 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-30 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-19 0.1.4
2018-03-22 0.1.3
2018-02-28 0.1.2
2018-02-06 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-23 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-27 2.2.16
2017-07-03 2.2.15
2017-01-26 2.2.14
2016-10-03 2.2.13
2016-08-11 2.2.12
2015-07-29 2.2.9
2014-09-15 2.2.5
2014-06-17 2.2.4
2014-04-23 2.2.3
2013-08-20 2.1.3
2013-02-21 2.0.1
2012-11-24 2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-26 0.5.3.1
2013-05-26 0.5.3
2013-01-31 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-31 2.2-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-12 1.0
Title: Time-Course Gene Set Analysis
Description: Implementation of Time-course Gene Set Analysis (TcGSA), a method for analyzing longitudinal gene-expression data at the gene set level.
Author: Boris P. Hejblum [aut, cre],
Damien Chimits [aut],
Anthony Devaux [aut]
Maintainer: Boris P. Hejblum <boris.hejblum@u-bordeaux.fr>
Diff between TcGSA versions 0.11.1 dated 2018-06-08 and 0.12.2 dated 2019-01-16
DESCRIPTION | 15 - MD5 | 62 +++--- R/TcGSA-package.R | 6 R/TcGSA.LR.R | 34 ++- R/TcGSA.LR.parallel.R | 2 R/chisqmix.R | 5 R/clustTrend.R | 11 - R/multtest.TcGSA.R | 18 - R/plot.TcGSA.R | 2 R/plot1GS.R | 45 ++-- R/plotFit.GS.R | 2 R/plotPat.TcGSA.R | 2 R/signifLRT.TcGSA.R | 11 - build/vignette.rds |binary inst/doc/TcGSA_userguide.R | 204 +++++++++++++++++++++ inst/doc/TcGSA_userguide.Rmd | 44 ++-- inst/doc/TcGSA_userguide.html | 394 ++++++++++++++++++++++-------------------- man/TcGSA-package.Rd | 6 man/TcGSA.LR.Rd | 9 man/TcGSA.LR.parallel.Rd | 2 man/chisqmix.Rd | 7 man/clustTrend.Rd | 9 man/plot.TcGSA.Rd | 23 +- man/plot1GS.Rd | 9 man/plotFit.GS.Rd | 2 man/plotMultipleGS.Rd | 9 man/plotPat.1GS.Rd | 19 +- man/plotPat.TcGSA.Rd | 23 +- man/plotSelect.GS.Rd | 13 - man/signifLRT.TcGSA.Rd | 9 man/summary.TcGSA.Rd | 1 vignettes/TcGSA_userguide.Rmd | 44 ++-- 32 files changed, 660 insertions(+), 382 deletions(-)
Title: Univariate GARCH Models
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Ghalanos [aut, cre],
Tobias Kley [ctb]
Maintainer: Alexios Ghalanos <alexios@4dscape.com>
Diff between rugarch versions 1.4-0 dated 2018-02-04 and 1.4-1 dated 2019-01-16
.Rinstignore | 4 ChangeLog | 853 +- DESCRIPTION | 13 MD5 | 284 NAMESPACE | 98 R/arfima-classes.R | 248 R/arfima-main.R | 3210 ++++---- R/arfima-methods.R | 2198 +++--- R/arfima-multi.R | 438 - R/rugarch-aparch.R | 2734 +++---- R/rugarch-armafor.R | 246 R/rugarch-benchmarks.R | 496 - R/rugarch-bootstrap.R | 1602 ++-- R/rugarch-classes.R | 308 R/rugarch-csgarch.R | 2872 ++++---- R/rugarch-cv.R | 562 - R/rugarch-cwrappers.R | 372 - R/rugarch-distributions.R | 4308 ++++++------ R/rugarch-egarch.R | 2740 +++---- R/rugarch-fgarch.R | 2852 +++---- R/rugarch-figarch.R | 2178 +++--- R/rugarch-gjrgarch.R | 2846 +++---- R/rugarch-graphs.R | 1940 ++--- R/rugarch-helperfn.R | 1538 ++-- R/rugarch-igarch.R | 2714 +++---- R/rugarch-imports.R | 1268 +-- R/rugarch-kappa.R | 574 - R/rugarch-lossfn.R | 142 R/rugarch-mcsgarch.R | 3146 ++++---- R/rugarch-methods.R | 7880 +++++++++++----------- R/rugarch-multi.R | 1084 +-- R/rugarch-numderiv.R | 310 R/rugarch-plots.R | 4410 ++++++------ R/rugarch-realgarch.R | 3362 ++++----- R/rugarch-rolling.R | 1086 +-- R/rugarch-series.R | 538 - R/rugarch-sgarch.R | 2760 +++---- R/rugarch-solvers.R | 932 +- R/rugarch-startpars.R | 3684 +++++----- R/rugarch-tests.R | 2486 +++--- R/rugarch-uncertainty.R | 380 - R/zzz.R | 40 build/vignette.rds |binary inst/CITATION | 42 inst/COPYRIGHTS | 20 inst/doc/Introduction_to_the_rugarch_package.Rnw | 74 inst/doc/Introduction_to_the_rugarch_package.pdf |binary inst/rugarch.tests/rugarch.test1.R | 1842 ++--- inst/rugarch.tests/rugarch.test10.R | 1198 +-- inst/rugarch.tests/rugarch.test11.R | 104 inst/rugarch.tests/rugarch.test12.R | 484 - inst/rugarch.tests/rugarch.test13.R | 488 - inst/rugarch.tests/rugarch.test14.R | 198 inst/rugarch.tests/rugarch.test2.R | 894 +- inst/rugarch.tests/rugarch.test3.R | 1022 +- inst/rugarch.tests/rugarch.test4.R | 874 +- inst/rugarch.tests/rugarch.test5.R | 862 +- inst/rugarch.tests/rugarch.test6.R | 1312 +-- inst/rugarch.tests/rugarch.test7.R | 248 inst/rugarch.tests/rugarch.test8.R | 534 - inst/rugarch.tests/rugarch.test9.R | 538 - inst/rugarch.tests/runtests.R | 190 man/ARFIMA-class.Rd | 34 man/ARFIMAdistribution-class.Rd | 90 man/ARFIMAfilter-class.Rd | 106 man/ARFIMAfit-class.Rd | 146 man/ARFIMAforecast-class.Rd | 110 man/ARFIMAmultifilter-class.Rd | 74 man/ARFIMAmultifit-class.Rd | 76 man/ARFIMAmultiforecast-class.Rd | 58 man/ARFIMAmultispec-class.Rd | 50 man/ARFIMApath-class.Rd | 60 man/ARFIMAroll-class.Rd | 148 man/ARFIMAsim-class.Rd | 60 man/ARFIMAspec-class.Rd | 88 man/BerkowitzTest.Rd | 210 man/DACTest.Rd | 116 man/DateTimeUtilities.Rd | 208 man/ESTest.Rd | 152 man/GARCHboot-class.Rd | 34 man/GARCHdistribution-class.Rd | 34 man/GARCHfilter-class.Rd | 34 man/GARCHfit-class.Rd | 34 man/GARCHforecast-class.Rd | 36 man/GARCHpath-class.Rd | 36 man/GARCHroll-class.Rd | 34 man/GARCHsim-class.Rd | 36 man/GARCHspec-class.Rd | 36 man/GARCHtests-class.Rd | 34 man/GMMTest.Rd | 126 man/HLTest.Rd | 136 man/VaRDurTest.Rd | 150 man/VaRTest.Rd | 140 man/VaRloss.Rd | 56 man/VaRplot.Rd | 52 man/arfimacv.Rd | 198 man/arfimadistribution-methods.Rd | 138 man/arfimafilter-methods.Rd | 82 man/arfimafit-methods.Rd | 126 man/arfimaforecast-methods.Rd | 108 man/arfimapath-methods.Rd | 88 man/arfimaroll-methods.Rd | 222 man/arfimasim-methods.Rd | 94 man/arfimaspec-methods.Rd | 142 man/autoarfima.Rd | 124 man/dji30ret.Rd | 28 man/dmbp.Rd | 40 man/ghyptransform.Rd | 82 man/mcs.Rd | 82 man/multifilter-methods.Rd | 98 man/multifit-methods.Rd | 112 man/multiforecast-methods.Rd | 110 man/multispec-methods.Rd | 76 man/rGARCH-class.Rd | 30 man/rugarch-package.Rd | 294 man/sp500ret.Rd | 24 man/spyreal.Rd | 36 man/uGARCHboot-class.Rd | 96 man/uGARCHdistribution-class.Rd | 116 man/uGARCHfilter-class.Rd | 200 man/uGARCHfit-class.Rd | 464 - man/uGARCHforecast-class.Rd | 152 man/uGARCHmultifilter-class.Rd | 74 man/uGARCHmultifit-class.Rd | 84 man/uGARCHmultiforecast-class.Rd | 58 man/uGARCHmultispec-class.Rd | 40 man/uGARCHpath-class.Rd | 82 man/uGARCHroll-class.Rd | 206 man/uGARCHsim-class.Rd | 126 man/uGARCHspec-class.Rd | 148 man/ugarchbench.Rd | 70 man/ugarchboot-methods.Rd | 280 man/ugarchdist.Rd | 294 man/ugarchdistribution-methods.Rd | 192 man/ugarchfilter-methods.Rd | 140 man/ugarchfit-methods.Rd | 284 man/ugarchforecast-methods.Rd | 188 man/ugarchpath-methods.Rd | 185 man/ugarchroll-methods.Rd | 246 man/ugarchsim-methods.Rd | 191 man/ugarchspec-methods.Rd | 344 vignettes/Introduction_to_the_rugarch_package.Rnw | 74 vignettes/rugarch.tex | 3978 +++++------ vignettes/rugarchbib.bib | 1656 ++-- 144 files changed, 48875 insertions(+), 48881 deletions(-)
Title: Quadrangle Mesh
Description: Create surface forms from matrix or 'raster' data for flexible plotting and
conversion to other mesh types. The functions 'quadmesh' or 'triangmesh'
produce a continuous surface as a 'mesh3d' object as used by the 'rgl'
package. This is used for plotting raster data in 3D (optionally with
texture), and allows the application of a map projection without data loss.
There are discrete forms of these continuous surfaces available with
'dquadmesh' and 'dtriangmesh' functions.
Author: Michael D. Sumner [aut, cre]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between quadmesh versions 0.2.0 dated 2018-11-13 and 0.3.0 dated 2019-01-16
quadmesh-0.2.0/quadmesh/R/netcdf.R |only quadmesh-0.3.0/quadmesh/DESCRIPTION | 23 quadmesh-0.3.0/quadmesh/MD5 | 82 quadmesh-0.3.0/quadmesh/NAMESPACE | 56 quadmesh-0.3.0/quadmesh/NEWS.md | 33 quadmesh-0.3.0/quadmesh/R/discrete.R |only quadmesh-0.3.0/quadmesh/R/mesh-plot.R | 294 quadmesh-0.3.0/quadmesh/R/primitives.R | 13 quadmesh-0.3.0/quadmesh/R/qsc.R |only quadmesh-0.3.0/quadmesh/R/quadmesh.R | 126 quadmesh-0.3.0/quadmesh/R/raster.R |only quadmesh-0.3.0/quadmesh/R/reproj.R |only quadmesh-0.3.0/quadmesh/R/sysdata.rda |only quadmesh-0.3.0/quadmesh/R/textures.R | 16 quadmesh-0.3.0/quadmesh/R/tri_grid.R |only quadmesh-0.3.0/quadmesh/R/triangmesh.R |only quadmesh-0.3.0/quadmesh/README.md | 344 quadmesh-0.3.0/quadmesh/build/vignette.rds |binary quadmesh-0.3.0/quadmesh/inst/doc/quadmesh.R | 173 quadmesh-0.3.0/quadmesh/inst/doc/quadmesh.Rmd | 415 quadmesh-0.3.0/quadmesh/inst/doc/quadmesh.html |12300 +++++----- quadmesh-0.3.0/quadmesh/inst/doc/topography.R | 100 quadmesh-0.3.0/quadmesh/inst/doc/topography.Rmd | 2 quadmesh-0.3.0/quadmesh/inst/doc/topography.html |12044 ++++----- quadmesh-0.3.0/quadmesh/man/bary_index.Rd |only quadmesh-0.3.0/quadmesh/man/etopo.Rd | 22 quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-4-1.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-6-1.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-7-1.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-8-1.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-8-2.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-9-1.png |only quadmesh-0.3.0/quadmesh/man/figures/README-unnamed-chunk-9-2.png |only quadmesh-0.3.0/quadmesh/man/llh2xyz.Rd | 42 quadmesh-0.3.0/quadmesh/man/mesh_plot.Rd | 118 quadmesh-0.3.0/quadmesh/man/qm_as_raster.Rd |only quadmesh-0.3.0/quadmesh/man/qsc.Rd |only quadmesh-0.3.0/quadmesh/man/quadmesh-package.Rd | 59 quadmesh-0.3.0/quadmesh/man/quadmesh.Rd | 114 quadmesh-0.3.0/quadmesh/man/reproj.Rd |only quadmesh-0.3.0/quadmesh/man/triangmesh.Rd |only quadmesh-0.3.0/quadmesh/man/triangulate_quads.Rd | 75 quadmesh-0.3.0/quadmesh/man/worldll.Rd | 24 quadmesh-0.3.0/quadmesh/man/xymap.Rd | 24 quadmesh-0.3.0/quadmesh/tests/figs |only quadmesh-0.3.0/quadmesh/tests/testthat/test-barycentric.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-basic.R | 7 quadmesh-0.3.0/quadmesh/tests/testthat/test-image.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-qsc.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-raster.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-reproject.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-texture.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-tri-quads.R |only quadmesh-0.3.0/quadmesh/tests/testthat/test-triangle-mesh.R |only quadmesh-0.3.0/quadmesh/vignettes/quadmesh.Rmd | 415 quadmesh-0.3.0/quadmesh/vignettes/topography.Rmd | 2 56 files changed, 13797 insertions(+), 13126 deletions(-)
Title: Targeted Stable Balancing Weights Using Optimization
Description: Use optimization to estimate weights that balance covariates for binary, multinomial, continuous, and longitudinal treatments in the spirit of Zubizarreta (2015) <doi:10.1080/01621459.2015.1023805>. The degree of balance can be specified for each covariate. In addition, sampling weights can be estimated that allow a sample to generalize to a population specified with given target moments of covariates.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between optweight versions 0.2.0 dated 2018-10-17 and 0.2.1 dated 2019-01-16
DESCRIPTION | 8 MD5 | 27 +-- NEWS.md | 8 R/SHARED.R |only R/check_functions.R | 6 R/functions_for_processing.R | 351 ------------------------------------------- R/optweight.R | 6 R/optweight.fit.R | 19 -- R/optweight.svy.fit.R | 19 -- R/summary.R | 2 README.md | 4 build/partial.rdb |binary man/optweight.Rd | 39 ++-- man/optweight.fit.Rd | 10 - man/optweight.svy.fit.Rd | 4 15 files changed, 83 insertions(+), 420 deletions(-)
Title: Gaussian Processes Modeling
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld [aut],
Hugh Chipman [aut, cre],
Chris Campbell [ctb],
Pritam Ranjan [aut]
Maintainer: Hugh Chipman <hugh.chipman@acadiau.ca>
Diff between GPfit versions 1.0-0 dated 2015-04-02 and 1.0-6 dated 2019-01-16
GPfit-1.0-0/GPfit/man/predict.GP.Rd |only GPfit-1.0-6/GPfit/DESCRIPTION | 20 - GPfit-1.0-6/GPfit/MD5 | 50 +- GPfit-1.0-6/GPfit/NAMESPACE | 21 + GPfit-1.0-6/GPfit/NEWS | 71 ++-- GPfit-1.0-6/GPfit/R/GP_deviance.R | 240 +++++++++---- GPfit-1.0-6/GPfit/R/GP_fit.R | 575 ++++++++++++++++++++------------- GPfit-1.0-6/GPfit/R/GPfit-package.R |only GPfit-1.0-6/GPfit/R/corr_matrix.R | 216 +++++++++--- GPfit-1.0-6/GPfit/R/dev_wrapper.R | 16 GPfit-1.0-6/GPfit/R/is.GP.R | 13 GPfit-1.0-6/GPfit/R/plot.GP.R | 316 +++++++++++++----- GPfit-1.0-6/GPfit/R/predict.GP.R | 420 +++++++++++++++--------- GPfit-1.0-6/GPfit/R/print.GP.R | 116 ++++-- GPfit-1.0-6/GPfit/R/summary.GP.R | 60 +++ GPfit-1.0-6/GPfit/inst/CITATION | 42 +- GPfit-1.0-6/GPfit/man/GP_deviance.Rd | 137 ++++--- GPfit-1.0-6/GPfit/man/GP_fit.Rd | 225 +++++++----- GPfit-1.0-6/GPfit/man/GPfit-package.Rd | 52 +- GPfit-1.0-6/GPfit/man/corr_matrix.Rd | 159 ++++----- GPfit-1.0-6/GPfit/man/plot.GP.Rd | 185 +++++----- GPfit-1.0-6/GPfit/man/predict.Rd |only GPfit-1.0-6/GPfit/man/print.GP.Rd | 87 ++-- GPfit-1.0-6/GPfit/man/scale_norm.Rd |only GPfit-1.0-6/GPfit/man/sig_invb.Rd |only GPfit-1.0-6/GPfit/man/summary.GP.Rd | 85 ++-- GPfit-1.0-6/GPfit/tests |only 27 files changed, 1980 insertions(+), 1126 deletions(-)
Title: Covariate Balance Tables and Plots
Description: Generate balance tables and plots for covariates of groups preprocessed through matching, weighting or subclassification, for example, using propensity scores. Includes integration with 'MatchIt', 'twang', 'Matching', 'optmatch', 'CBPS', 'ebal', 'WeightIt', and 'designmatch' for assessing balance on the output of their preprocessing functions. Users can also specify data for balance assessment not generated through the above packages. Also included are methods for assessing balance in clustered or multiply imputed data sets or data sets with longitudinal treatments.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between cobalt versions 3.6.0 dated 2018-11-25 and 3.6.1 dated 2019-01-16
DESCRIPTION | 13 - MD5 | 33 +-- NAMESPACE | 1 NEWS.md | 4 R/SHARED.R |only R/bal.tab.R | 6 R/functions_for_processing.R | 251 +---------------------------- R/internal_utilities.R | 164 ------------------ R/print.bal.tab.R | 14 - R/x2base.R | 128 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/cobalt_A0_basic_use.Rmd | 10 - inst/doc/cobalt_A0_basic_use.html | 59 ++++-- inst/doc/cobalt_A1_other_packages.html | 30 +++ inst/doc/cobalt_A2_cluster_imp.html | 176 +++++++++++--------- inst/doc/cobalt_A3_longitudinal_treat.html | 28 ++- vignettes/cobalt_A0_basic_use.Rmd | 10 - 18 files changed, 322 insertions(+), 605 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of one or more categorical
variables; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on one or more endpoints
for many variables (univariate or adjusted for covariates);
freqlist(), a powerful frequency table across many categorical variables;
compare.data.frame(), the S3 method for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb],
Maddie McCullough [art]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 1.5.0 dated 2018-11-09 and 2.0.0 dated 2019-01-16
arsenal-1.5.0/arsenal/tests/testthat/write2.char.html.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.freqlist.doc.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.freqlist.html.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.lm.pdf.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.modelsum.html.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.multititles.pdf.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.mylist.pdf.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.mylist2.doc.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.mylists.pdf.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.tableby.html.md |only arsenal-1.5.0/arsenal/tests/testthat/write2.yaml.pdf.md |only arsenal-2.0.0/arsenal/DESCRIPTION | 26 arsenal-2.0.0/arsenal/MD5 | 177 - arsenal-2.0.0/arsenal/NAMESPACE | 51 arsenal-2.0.0/arsenal/NEWS.md | 109 arsenal-2.0.0/arsenal/R/arsenal.R | 10 arsenal-2.0.0/arsenal/R/arsenal_table.R |only arsenal-2.0.0/arsenal/R/as.data.frame.freqlist.R |only arsenal-2.0.0/arsenal/R/as.data.frame.modelsum.R | 73 arsenal-2.0.0/arsenal/R/as.data.frame.tableby.R | 61 arsenal-2.0.0/arsenal/R/compare.internal.R | 2 arsenal-2.0.0/arsenal/R/freq.control.R |only arsenal-2.0.0/arsenal/R/freqlist.R | 247 + arsenal-2.0.0/arsenal/R/freqlist.internal.R | 100 arsenal-2.0.0/arsenal/R/internal.functions.R | 82 arsenal-2.0.0/arsenal/R/modelsum.R | 456 +-- arsenal-2.0.0/arsenal/R/modelsum.internal.R | 124 arsenal-2.0.0/arsenal/R/na.operations.R | 11 arsenal-2.0.0/arsenal/R/padjust.R |only arsenal-2.0.0/arsenal/R/paired.R | 474 +-- arsenal-2.0.0/arsenal/R/paired.internal.R | 5 arsenal-2.0.0/arsenal/R/summary.freqlist.R | 91 arsenal-2.0.0/arsenal/R/summary.modelsum.R | 86 arsenal-2.0.0/arsenal/R/summary.tableby.R | 115 arsenal-2.0.0/arsenal/R/tableby.R | 465 +-- arsenal-2.0.0/arsenal/R/tableby.internal.R | 261 - arsenal-2.0.0/arsenal/R/tableby.stat.tests.R | 9 arsenal-2.0.0/arsenal/R/write2.R | 56 arsenal-2.0.0/arsenal/R/write2.default.R | 10 arsenal-2.0.0/arsenal/R/write2.internal.R | 28 arsenal-2.0.0/arsenal/README.md | 30 arsenal-2.0.0/arsenal/inst/doc/compare.html | 2 arsenal-2.0.0/arsenal/inst/doc/freqlist.R | 65 arsenal-2.0.0/arsenal/inst/doc/freqlist.Rmd | 102 arsenal-2.0.0/arsenal/inst/doc/freqlist.html | 1378 ++++++++-- arsenal-2.0.0/arsenal/inst/doc/labels.R | 6 arsenal-2.0.0/arsenal/inst/doc/labels.Rmd | 6 arsenal-2.0.0/arsenal/inst/doc/labels.html | 20 arsenal-2.0.0/arsenal/inst/doc/modelsum.R | 15 arsenal-2.0.0/arsenal/inst/doc/modelsum.Rmd | 41 arsenal-2.0.0/arsenal/inst/doc/modelsum.html | 743 +++++ arsenal-2.0.0/arsenal/inst/doc/paired.html | 2 arsenal-2.0.0/arsenal/inst/doc/tableby.R | 22 arsenal-2.0.0/arsenal/inst/doc/tableby.Rmd | 49 arsenal-2.0.0/arsenal/inst/doc/tableby.html | 1234 ++++++++ arsenal-2.0.0/arsenal/inst/doc/write2.R | 14 arsenal-2.0.0/arsenal/inst/doc/write2.Rmd | 27 arsenal-2.0.0/arsenal/inst/doc/write2.html | 30 arsenal-2.0.0/arsenal/man/NA.operations.Rd | 7 arsenal-2.0.0/arsenal/man/arsenal_table.Rd |only arsenal-2.0.0/arsenal/man/as.data.frame.freqlist.Rd | 14 arsenal-2.0.0/arsenal/man/as.data.frame.modelsum.Rd | 11 arsenal-2.0.0/arsenal/man/as.data.frame.tableby.Rd | 10 arsenal-2.0.0/arsenal/man/figures |only arsenal-2.0.0/arsenal/man/freq.control.Rd |only arsenal-2.0.0/arsenal/man/freqlist.Rd | 37 arsenal-2.0.0/arsenal/man/freqlist.internal.Rd | 15 arsenal-2.0.0/arsenal/man/internal.functions.Rd | 16 arsenal-2.0.0/arsenal/man/modelsum.Rd | 26 arsenal-2.0.0/arsenal/man/modelsum.internal.Rd | 21 arsenal-2.0.0/arsenal/man/padjust.Rd | 2 arsenal-2.0.0/arsenal/man/paired.Rd | 15 arsenal-2.0.0/arsenal/man/reexports.Rd | 8 arsenal-2.0.0/arsenal/man/summary.freqlist.Rd | 37 arsenal-2.0.0/arsenal/man/summary.modelsum.Rd | 27 arsenal-2.0.0/arsenal/man/summary.tableby.Rd | 23 arsenal-2.0.0/arsenal/man/tableby.Rd | 25 arsenal-2.0.0/arsenal/man/tableby.internal.Rd | 47 arsenal-2.0.0/arsenal/man/write2.Rd | 48 arsenal-2.0.0/arsenal/man/write2.internal.Rd | 14 arsenal-2.0.0/arsenal/tests/testthat/helper-data.R | 28 arsenal-2.0.0/arsenal/tests/testthat/helper-script.R | 2 arsenal-2.0.0/arsenal/tests/testthat/test_freqlist.R | 144 - arsenal-2.0.0/arsenal/tests/testthat/test_lhs_freqlist.R |only arsenal-2.0.0/arsenal/tests/testthat/test_lhs_modelsum.R |only arsenal-2.0.0/arsenal/tests/testthat/test_lhs_tableby.R |only arsenal-2.0.0/arsenal/tests/testthat/test_modelsum.R | 5 arsenal-2.0.0/arsenal/tests/testthat/test_tableby.R | 76 arsenal-2.0.0/arsenal/tests/testthat/test_write2.R | 69 arsenal-2.0.0/arsenal/tests/testthat/write2.char.html.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.freqlist.doc.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.freqlist.html.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.lm.pdf.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.modelsum.html.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.multititles.pdf.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.mylist.pdf.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.mylist2.doc.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.mylists.pdf.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.render.html.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.tableby.html.Rmd |only arsenal-2.0.0/arsenal/tests/testthat/write2.yaml.pdf.Rmd |only arsenal-2.0.0/arsenal/vignettes/freqlist.Rmd | 102 arsenal-2.0.0/arsenal/vignettes/labels.Rmd | 6 arsenal-2.0.0/arsenal/vignettes/modelsum.Rmd | 41 arsenal-2.0.0/arsenal/vignettes/tableby.Rmd | 49 arsenal-2.0.0/arsenal/vignettes/write2.Rmd | 27 106 files changed, 5359 insertions(+), 2508 deletions(-)