Title: Get the Same, Personal, Free 'TCP' Port over and over
Description: An R implementation of the cross-platform, language-independent "port4me" algorithm (<https://github.com/HenrikBengtsson/port4me>), which (1) finds a free Transmission Control Protocol ('TCP') port in [1024,65535] that the user can open, (2) is designed to work in multi-user environments, (3), gives different users, different ports, (4) gives the user the same port over time with high probability, (5) gives different ports for different software tools, and (6) requires no configuration.
Author: Henrik Bengtsson [aut, cre, cph]
,
Jeroen Ooms [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between port4me versions 0.7.0 dated 2024-01-15 and 0.7.1 dated 2024-02-29
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 12 ++++++++++-- build/vignette.rds |binary src/test_tcp_port.c | 7 +++++++ 5 files changed, 25 insertions(+), 10 deletions(-)
Title: Semi-Parametric Joint Modeling of Longitudinal and Survival Data
Description: Maximum likelihood estimation for the semi-parametric joint modeling of competing risks and longitudinal data applying customized linear scan algorithms, proposed by Li and colleagues (2022) <doi:10.1155/2022/1362913>.
The time-to-event data is modelled using a (cause-specific) Cox proportional hazards regression model with time-fixed covariates. The longitudinal
outcome is modelled using a linear mixed effects model. The association is captured by shared random effects. The model
is estimated using an Expectation Maximization algorithm.
Author: Shanpeng Li [aut, cre],
Ning Li [ctb],
Hong Wang [ctb],
Jin Zhou [ctb],
Hua Zhou [ctb],
Gang Li [ctb]
Maintainer: Shanpeng Li <lishanpeng0913@ucla.edu>
Diff between FastJM versions 1.4.1 dated 2024-01-09 and 1.4.2 dated 2024-02-29
DESCRIPTION | 8 ++--- MD5 | 38 ++++++++++++------------ NEWS.md | 4 ++ src/RcppExports.cpp | 64 +++++++++++++++++++++--------------------- src/getBayes.cpp | 2 - src/getCov.cpp | 2 - src/getCovSF.cpp | 2 - src/getECpseudo.cpp | 2 - src/getECpseudoSF.cpp | 2 - src/getECstandard.cpp | 2 - src/getECstandardSF.cpp | 2 - src/getMC.cpp | 2 - src/getMCSF.cpp | 2 - src/getPus.cpp | 2 - src/getPusCR.cpp | 2 - src/getfitted.cpp | 2 - src/getloglikeCpseudo.cpp | 2 - src/getloglikeCpseudoSF.cpp | 2 - src/getloglikeCstandard.cpp | 2 - src/getloglikeCstandardSF.cpp | 2 - 20 files changed, 75 insertions(+), 71 deletions(-)
Title: Client for Delphi's 'Epidata' API
Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. <https://github.com/cmu-delphi/delphi-epidata>.
Author: Logan Brooks [aut],
Dmitry Shemetov [aut],
Samuel Gratzl [aut],
David Weber [ctb, cre],
Alex Reinhart [ctb],
Daniel McDonald [ctb],
Kean Ming Tan [ctb],
Will Townes [ctb],
George Haff [ctb],
Kathryn Mazaitis [ctb]
Maintainer: David Weber <davidweb@andrew.cmu.edu>
Diff between epidatr versions 1.0.0 dated 2023-09-19 and 1.1.0 dated 2024-02-29
epidatr-1.0.0/epidatr/man/get_auth_key.Rd |only epidatr-1.1.0/epidatr/DESCRIPTION | 16 epidatr-1.1.0/epidatr/LICENSE | 2 epidatr-1.1.0/epidatr/MD5 | 147 - epidatr-1.1.0/epidatr/NAMESPACE | 8 epidatr-1.1.0/epidatr/NEWS.md | 30 epidatr-1.1.0/epidatr/R/auth.R | 79 epidatr-1.1.0/epidatr/R/avail_endpoints.R | 13 epidatr-1.1.0/epidatr/R/cache.R | 49 epidatr-1.1.0/epidatr/R/constants.R | 2 epidatr-1.1.0/epidatr/R/covidcast.R | 2 epidatr-1.1.0/epidatr/R/endpoints.R | 668 +++++- epidatr-1.1.0/epidatr/R/epidatacall.R | 118 - epidatr-1.1.0/epidatr/R/epidatr-package.R | 7 epidatr-1.1.0/epidatr/R/model.R | 142 + epidatr-1.1.0/epidatr/R/request.R | 49 epidatr-1.1.0/epidatr/R/utils.R | 27 epidatr-1.1.0/epidatr/README.md | 177 + epidatr-1.1.0/epidatr/build/vignette.rds |binary epidatr-1.1.0/epidatr/inst/doc/epidatr.R | 234 -- epidatr-1.1.0/epidatr/inst/doc/epidatr.Rmd | 487 +--- epidatr-1.1.0/epidatr/inst/doc/epidatr.html | 1166 +++++++---- epidatr-1.1.0/epidatr/inst/doc/signal-discovery.R |only epidatr-1.1.0/epidatr/inst/doc/signal-discovery.Rmd |only epidatr-1.1.0/epidatr/inst/doc/signal-discovery.html |only epidatr-1.1.0/epidatr/inst/doc/versioned-data.R |only epidatr-1.1.0/epidatr/inst/doc/versioned-data.Rmd |only epidatr-1.1.0/epidatr/inst/doc/versioned-data.html |only epidatr-1.1.0/epidatr/man/avail_endpoints.Rd | 12 epidatr-1.1.0/epidatr/man/clear_cache.Rd | 16 epidatr-1.1.0/epidatr/man/covidcast_epidata.Rd | 6 epidatr-1.1.0/epidatr/man/date_to_epiweek.Rd |only epidatr-1.1.0/epidatr/man/do_request.Rd | 2 epidatr-1.1.0/epidatr/man/epidata_call.Rd | 11 epidatr-1.1.0/epidatr/man/epidatr-package.Rd | 7 epidatr-1.1.0/epidatr/man/epirange.Rd | 11 epidatr-1.1.0/epidatr/man/fetch_args_list.Rd | 54 epidatr-1.1.0/epidatr/man/figures/README-fb-cli-signal-1.png |only epidatr-1.1.0/epidatr/man/get_api_key.Rd |only epidatr-1.1.0/epidatr/man/get_wildcard_equivalent_dates.Rd |only epidatr-1.1.0/epidatr/man/pub_covid_hosp_facility.Rd | 12 epidatr-1.1.0/epidatr/man/pub_covid_hosp_facility_lookup.Rd | 2 epidatr-1.1.0/epidatr/man/pub_covid_hosp_state_timeseries.Rd | 16 epidatr-1.1.0/epidatr/man/pub_covidcast.Rd | 8 epidatr-1.1.0/epidatr/man/pub_delphi.Rd | 5 epidatr-1.1.0/epidatr/man/pub_dengue_nowcast.Rd | 6 epidatr-1.1.0/epidatr/man/pub_ecdc_ili.Rd | 6 epidatr-1.1.0/epidatr/man/pub_flusurv.Rd | 8 epidatr-1.1.0/epidatr/man/pub_fluview.Rd | 6 epidatr-1.1.0/epidatr/man/pub_fluview_clinical.Rd | 6 epidatr-1.1.0/epidatr/man/pub_fluview_meta.Rd | 6 epidatr-1.1.0/epidatr/man/pub_gft.Rd | 6 epidatr-1.1.0/epidatr/man/pub_kcdc_ili.Rd | 6 epidatr-1.1.0/epidatr/man/pub_meta.Rd | 2 epidatr-1.1.0/epidatr/man/pub_nidss_dengue.Rd | 6 epidatr-1.1.0/epidatr/man/pub_nidss_flu.Rd | 6 epidatr-1.1.0/epidatr/man/pub_nowcast.Rd | 6 epidatr-1.1.0/epidatr/man/pub_paho_dengue.Rd | 6 epidatr-1.1.0/epidatr/man/pub_wiki.Rd | 19 epidatr-1.1.0/epidatr/man/pvt_cdc.Rd | 6 epidatr-1.1.0/epidatr/man/pvt_dengue_sensors.Rd | 6 epidatr-1.1.0/epidatr/man/pvt_ght.Rd | 6 epidatr-1.1.0/epidatr/man/pvt_meta_norostat.Rd | 5 epidatr-1.1.0/epidatr/man/pvt_norostat.Rd | 12 epidatr-1.1.0/epidatr/man/pvt_quidel.Rd | 4 epidatr-1.1.0/epidatr/man/pvt_sensors.Rd | 14 epidatr-1.1.0/epidatr/man/pvt_twitter.Rd | 21 epidatr-1.1.0/epidatr/man/reformat_epirange.Rd |only epidatr-1.1.0/epidatr/man/release_bullets.Rd |only epidatr-1.1.0/epidatr/man/request_impl.Rd | 2 epidatr-1.1.0/epidatr/man/set_cache.Rd | 16 epidatr-1.1.0/epidatr/man/timeset.Rd | 28 epidatr-1.1.0/epidatr/tests/testthat/generate_test_data.R | 8 epidatr-1.1.0/epidatr/tests/testthat/test-auth.R | 14 epidatr-1.1.0/epidatr/tests/testthat/test-endpoints.R | 385 +++ epidatr-1.1.0/epidatr/tests/testthat/test-epidatacall.R | 64 epidatr-1.1.0/epidatr/tests/testthat/test-model.R | 128 + epidatr-1.1.0/epidatr/tests/testthat/test-request.R | 2 epidatr-1.1.0/epidatr/tests/testthat/test-utils.R | 68 epidatr-1.1.0/epidatr/vignettes/epidatr.Rmd | 487 +--- epidatr-1.1.0/epidatr/vignettes/signal-discovery.Rmd |only epidatr-1.1.0/epidatr/vignettes/versioned-data.Rmd |only 82 files changed, 3310 insertions(+), 1646 deletions(-)
Title: Validate, Share, and Download Data
Description: Designed to enhance data validation and management processes by employing a set of functions that read a set of rules from a 'CSV' or 'Excel' file and apply them to a dataset. Funded by the National Renewable Energy Laboratory and Possibility Lab, maintained by the Moore Institute for Plastic Pollution Research.
Author: Hannah Sherrod [cre, aut] ,
Nick Leong [aut] ,
Hannah Hapich [aut] ,
Fabian Gomez [aut],
Shelly Moore [aut],
Win Cowger [aut] ,
Scott Coffin [ctb],
Tony Hale [ctb],
Diana Lin [ctb],
Gemma Shusterman [ctb],
Rebecca Sutton [ctb],
Adam Wong [ctb],
Haig [...truncated...]
Maintainer: Hannah Sherrod <hannah@mooreplasticresearch.org>
Diff between One4All versions 0.3 dated 2024-02-04 and 0.4 dated 2024-02-29
One4All-0.3/One4All/man/query_mongodb_api.Rd |only One4All-0.4/One4All/DESCRIPTION | 13 +- One4All-0.4/One4All/MD5 | 16 +-- One4All-0.4/One4All/NAMESPACE | 2 One4All-0.4/One4All/R/global.R | 78 ++++++++--------- One4All-0.4/One4All/README.md | 4 One4All-0.4/One4All/inst/doc/app.html | 4 One4All-0.4/One4All/inst/doc/package.html | 4 One4All-0.4/One4All/man/query_document_by_object_id.Rd |only One4All-0.4/One4All/tests/testthat/tests.R | 8 - 10 files changed, 66 insertions(+), 63 deletions(-)
Title: Spatially Explicit Capture-Recapture
Description: Functions to estimate the density and size of a spatially
distributed animal population sampled with an array of passive detectors,
such as traps, or by searching polygons or transects. Models incorporating
distance-dependent detection are fitted by maximizing the likelihood.
Tools are included for data manipulation and model selection.
Author: Murray Efford [aut, cre] ,
Philipp Jund [ctb] ),
David Fletcher [ctb] )
Maintainer: Murray Efford <murray.efford@otago.ac.nz>
Diff between secr versions 4.6.5 dated 2024-02-17 and 4.6.6 dated 2024-02-29
secr-4.6.5/secr/man/par.secr.fit.Rd |only secr-4.6.6/secr/DESCRIPTION | 8 - secr-4.6.6/secr/MD5 | 57 ++++++------- secr-4.6.6/secr/NAMESPACE | 1 secr-4.6.6/secr/NEWS | 14 +++ secr-4.6.6/secr/R/DA.R | 4 secr-4.6.6/secr/R/RMarkInput.R | 12 +- secr-4.6.6/secr/R/generalsecrloglik.R | 101 +++++++++++------------ secr-4.6.6/secr/R/list.secr.fit.R |only secr-4.6.6/secr/R/par.secr.fit.R | 29 ++++-- secr-4.6.6/secr/R/sim.popn.R | 16 ++- secr-4.6.6/secr/inst/doc/secr-datainput.pdf |binary secr-4.6.6/secr/inst/doc/secr-overview.Rmd | 121 ++-------------------------- secr-4.6.6/secr/inst/doc/secr-overview.pdf |binary secr-4.6.6/secr/man/DENSITY.Rd | 6 + secr-4.6.6/secr/man/Parallel.Rd | 8 - secr-4.6.6/secr/man/RMarkInput.Rd | 10 +- secr-4.6.6/secr/man/details.Rd | 2 secr-4.6.6/secr/man/list.secr.fit.Rd |only secr-4.6.6/secr/man/predict.secr.Rd | 7 - secr-4.6.6/secr/man/secr-deprecated.Rd | 43 +++++++++ secr-4.6.6/secr/man/secr-package.Rd | 4 secr-4.6.6/secr/man/secr.fit.Rd | 4 secr-4.6.6/secr/man/secrRNG.Rd | 2 secr-4.6.6/secr/man/sim.secr.Rd | 6 + secr-4.6.6/secr/man/snip.Rd | 6 + secr-4.6.6/secr/man/speed.Rd | 3 secr-4.6.6/secr/man/subset.capthist.Rd | 14 +++ secr-4.6.6/secr/man/subset.traps.Rd | 13 ++- secr-4.6.6/secr/src/prwipolygon.cpp | 10 +- secr-4.6.6/secr/vignettes/secr-overview.Rmd | 121 ++-------------------------- 31 files changed, 266 insertions(+), 356 deletions(-)
Title: Quantile Regression Neural Network
Description: Fit quantile regression neural network models with optional
left censoring, partial monotonicity constraints, generalized additive
model constraints, and the ability to fit multiple non-crossing quantile
functions following Cannon (2011) <doi:10.1016/j.cageo.2010.07.005>
and Cannon (2018) <doi:10.1007/s00477-018-1573-6>.
Author: Alex J. Cannon [aut, cre]
Maintainer: Alex J. Cannon <alex.cannon@ec.gc.ca>
Diff between qrnn versions 2.1 dated 2023-04-27 and 2.1.1 dated 2024-02-29
DESCRIPTION | 12 ++--- MD5 | 30 +++++++------- NAMESPACE | 2 R/mcqrnn.R | 11 +++-- R/qquantile.nw.R | 2 R/qrnn.R | 17 ++++++-- R/qrnn2.R | 19 ++++++--- R/transfer.R | 8 +++ README.md | 69 ++++++++++++++++++++++++--------- man/mcqrnn.Rd | 39 +++++++++++++++++- man/qrnn-package.Rd | 108 ++++++++++++++++++++++++++++++++++++++-------------- man/qrnn.cost.Rd | 3 - man/qrnn.fit.Rd | 19 ++++----- man/qrnn2.Rd | 8 ++- man/quantile.dtn.Rd | 20 ++++++++- man/transfer.Rd | 6 ++ 16 files changed, 273 insertions(+), 100 deletions(-)
Title: The YUIMA Project Package for SDEs
Description: Simulation and Inference for SDEs and Other Stochastic Processes.
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus <siacus@iq.harvard.edu>
Diff between yuima versions 1.15.22 dated 2022-12-20 and 1.15.27 dated 2024-02-29
DESCRIPTION | 8 - MD5 | 52 +++++---- NAMESPACE | 14 ++ NEWS | 14 +- R/AuxMethodForCARMAHawkes.R |only R/AuxMethodforPPR.R | 3 R/ClassMethodsForCarmaHawkes.R |only R/ae.R | 2 R/lambdaPPR.R | 15 ++ R/setPpr.R | 6 - R/simulate.R | 17 ++- R/yuima.R | 26 ++++ R/yuima.law.r | 182 +++++++++++++++++++++++++++++++++ R/yuima_t_regression_model_new_class.R |only R/yuima_t_student_Levy.R |only build/partial.rdb |binary inst/CITATION | 6 - man/EstimCarmaHawkes.Rd |only man/FromCF2yuima_law.Rd |only man/IC.Rd | 4 man/MWK151.Rd | 4 man/carmaHawkes.info-class.Rd |only man/estimation_LRM.Rd |only man/hyavar.Rd | 2 man/llag.Rd | 14 +- man/setCarmaHawkes.Rd |only man/setLRM.Rd |only man/setLaw_th.Rd |only man/simBmllag.Rd | 4 man/wllag.Rd | 3 man/yuima.LevyRM-class.Rd |only man/yuima.carmaHawkes-class.Rd |only man/yuima.law-class.rd | 39 +++---- man/yuima.th-class.Rd |only 34 files changed, 344 insertions(+), 71 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible
outcome to evaluate the effectiveness of a new therapy (the true endpoint) is
difficult to measure. In such a situation, it can be an effective strategy to
replace the true endpoint by a (bio)marker that is easier to measure and that
allows for a prediction of the treatment effect on the true endpoint (a
surrogate endpoint). The package 'Surrogate' allows for an evaluation of the
appropriateness of a candidate surrogate endpoint based on the meta-analytic,
information-theoretic, and causal-inference frameworks. Part of this software
has been developed using funding provided from the European Union's Seventh
Framework Programme for research, technological development and demonstration
(Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt
University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland
Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.
Author: Wim Van Der Elst [cre, aut],
Florian Stijven [aut],
Fenny Ong [aut],
Paul Meyvisch [aut],
Alvaro Poveda [aut],
Ariel Alonso [aut],
Hannah Ensor [aut],
Christoper Weir [aut],
Geert Molenberghs [aut]
Maintainer: Wim Van Der Elst <wim.vanderelst@gmail.com>
Diff between Surrogate versions 3.2.2 dated 2024-02-20 and 3.2.4 dated 2024-02-29
DESCRIPTION | 6 MD5 | 50 NEWS.md | 9 R/CbC.R | 2 R/ITCI-Dvine-inference-utils.R | 86 - R/fit_model_BinCont_copula.R | 1 R/fit_model_SurvSurv.R | 2 R/goodness_of_fit_SurvSurv.R | 7 R/sensitivity_analysis_BinCont_copula.R | 674 +++++----- R/sensitivity_analysis_SurvSurv.R | 17 R/sensitivity_intervals.R | 21 man/fit_copula_model_BinCont.Rd | 1 man/fit_model_SurvSurv.Rd | 2 man/sample_copula_parameters.Rd | 6 man/sensitivity_analysis_BinCont_copula.Rd | 14 man/sensitivity_analysis_SurvSurv_copula.Rd | 15 man/sensitivity_intervals_Dvine.Rd | 9 man/summary_level_bootstrap_ICA.Rd | 7 tests/testthat/_snaps/fit_model_SurvSurv/plot-function-for-gof.svg | 9 tests/testthat/_snaps/goodness_of_fit_SurvSurv/mean-surrogate-before-dying-gof.svg | 10 tests/testthat/_snaps/goodness_of_fit_SurvSurv/prob-of-dying-wo-progression-gof.svg | 9 tests/testthat/test-ITCI-Dvine-inference-utils.R | 17 tests/testthat/test-fit_model_SurvSurv.R | 8 tests/testthat/test-sensitivity_analysis_BinCont_copula.R | 82 - tests/testthat/test-sensitivity_analysis_SurvSurv.R | 30 tests/testthat/test-sensitivity_intervals.R | 57 26 files changed, 646 insertions(+), 505 deletions(-)
Title: Helper Functions for Simulation Studies
Description: Calculates performance criteria measures and associated Monte Carlo standard errors for simulation results. Includes functions to help run simulation studies. Our derivation and explanation of formulas and our general simulation workflow is closely aligned with the approach described by Morris, White, and Crowther (2019) <DOI:10.1002/sim.8086>.
Author: Megha Joshi [aut, cre] ,
James Pustejovsky [aut]
Maintainer: Megha Joshi <megha.j456@gmail.com>
Diff between simhelpers versions 0.2.0 dated 2024-02-23 and 0.2.1 dated 2024-02-29
DESCRIPTION | 6 +- MD5 | 14 +++--- NEWS.md | 4 + build/partial.rdb |binary inst/doc/MCSE.html | 4 - inst/doc/simulation_workflow.html | 6 +- inst/doc/visualization.html | 4 - tests/testthat/test_bundle_sim.R | 81 ++++++++++++++++++++++++++++++++++++++ 8 files changed, 102 insertions(+), 17 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<https://cwb.sourceforge.io>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/Licenses/GPL-3>).
The 'CWB' relies on 'pcre2' (BSD license, see <http://www.pcre.org/licence.txt>)
and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.html>).
See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stephanie Evert [ctb],
Arne Fitschen [ctb],
Jeroen Ooms [ctb],
Marius Bertram [ctb],
Tomas Kalibera [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.6.3 dated 2023-11-30 and 0.6.4 dated 2024-02-29
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 15 + R/cwb.R | 397 ++++++++++++++++++++++++--------------- configure | 14 + inst/doc/vignette.html | 4 man/cl_attribute_size.Rd | 10 man/cwb_charsets.Rd | 6 man/cwb_utils.Rd | 138 +++++++------ man/get_region_matrix.Rd | 25 +- tests/testthat/test_cwb_encode.R | 70 ++---- 11 files changed, 420 insertions(+), 287 deletions(-)
Title: Names Your 'R Markdown' Chunks
Description: It names the 'R Markdown' chunks of files based on
the filename.
Author: Colin Gillespie [aut, cre],
Steph Locke [aut],
Maelle Salmon [aut] ,
Ellis Valentiner [ctb],
Charlie Hadley [ctb] ,
Jumping Rivers [fnd] ,
Han Oostdijk [ctb] ,
Patrick Schratz [ctb]
Maintainer: Colin Gillespie <colin@jumpingrivers.com>
Diff between namer versions 0.1.6 dated 2022-10-06 and 0.1.8 dated 2024-02-29
DESCRIPTION | 22 +++--- LICENSE |only MD5 | 15 ++-- NEWS.md | 17 ++++- R/name_chunks.R | 2 build/vignette.rds |binary inst/doc/namer.html | 147 ++++++++++++++++++++++----------------------- man/rmdfragments/intro.Rmd | 4 - man/rmdfragments/use.Rmd | 4 - 9 files changed, 111 insertions(+), 100 deletions(-)
Title: Implementation of Remez Algorithm for Polynomial and Rational
Function Approximation
Description: Implements the algorithm of Remez (1962) for polynomial minimax
approximation and of Cody et al. (1968) <doi:10.1007/BF02162506> for
rational minimax approximation.
Author: Avraham Adler [aut, cre, cph]
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between minimaxApprox versions 0.4.0 dated 2024-02-26 and 0.4.1 dated 2024-02-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/partial.rdb |binary inst/CITATION | 2 +- inst/NEWS.Rd | 11 +++++++++++ inst/tinytest/test_MiniMaxApprox.R | 4 ++-- 6 files changed, 23 insertions(+), 12 deletions(-)
Title: Data Manipulation Functions Implemented in C
Description: Basic functions, implemented in C, for large data manipulation. Fast vectorised ifelse()/nested if()/switch() functions, psum()/pprod() functions equivalent to pmin()/pmax() plus others which are missing from base R. Most of these functions are callable at C level.
Author: Morgan Jacob [aut, cre, cph],
Sebastian Krantz [ctb]
Maintainer: Morgan Jacob <morgan.emailbox@gmail.com>
Diff between kit versions 0.0.15 dated 2023-10-01 and 0.0.16 dated 2024-02-29
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/call.R | 15 +++++++++++++-- inst/NEWS.Rd | 8 ++++++++ tests/test_kit.R | 1 - tests/test_kit.Rout.save | 2 -- 6 files changed, 30 insertions(+), 14 deletions(-)
Title: Estimation in DID with Multiple Groups and Periods
Description: Estimate the effect of a treatment on an outcome in sharp Difference-in-Difference designs with multiple groups and periods.
It computes the DIDM estimator introduced in Section 4 of "Two-Way Fixed Effects Estimators with Heterogeneous
Treatment Effects" (Chaisemartin, D'Haultfoeuille (2020) <doi:10.1257/aer.20181169>), which
generalizes the standard DID estimator with two groups, two periods and a binary treatment to situations
with many groups,many periods and a potentially non-binary treatment. For each pair of consecutive time
periods t-1 and t and for each value of the treatment d, the package computes a DID estimator comparing
the outcome evolution among the switchers, the groups whose treatment changes from d to some other value
between t-1 and t, to the same evolution among control groups whose treatment is equal to d both in t-1 and t.
Then the DIDM estimator is equal to the average of those DIDs across all pairs of consecutive time periods and
across all values of the [...truncated...]
Author: Shuo Zhang [aut],
Clement de Chaisemartin [aut],
Diego Ciccia [cre]
Maintainer: Diego Ciccia <diego.ciccia@sciencespo.fr>
Diff between DIDmultiplegt versions 0.1.2 dated 2024-02-03 and 0.1.3 dated 2024-02-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/did_multiplegt.R | 4 ++++ man/did_multiplegt.Rd | 4 +++- 4 files changed, 13 insertions(+), 7 deletions(-)
More information about SemiPar.depCens at CRAN
Permanent link
More information about rnaCrosslinkOO at CRAN
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Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis. F. Husson, S. Le and J. Pages (2017).
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@institut-agro.fr>
Diff between FactoMineR versions 2.9 dated 2023-10-12 and 2.10 dated 2024-02-29
DESCRIPTION | 6 MD5 | 42 +++--- R/MFA.R | 305 ++++++++++++++++++++++++---------------------- R/catdes.r | 2 R/coord.ellipse.R | 2 R/meansComp.R | 16 +- R/plot.FAMD.R | 2 R/plot.MFA.R | 55 +++++--- R/plot.meansComp.R | 17 ++ R/textual.r | 1 build/vignette.rds |binary data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/clustering.html | 232 ++++++++++------------------------ man/LinearModel.Rd | 3 man/MFA.Rd | 4 man/meansComp.Rd | 5 man/mortality.Rd | 7 - man/plot.MFA.Rd | 1 man/plot.meansComp.Rd | 5 vignettes/FactoMineR.html | 250 +++++++++++-------------------------- 22 files changed, 415 insertions(+), 540 deletions(-)
Title: Connect to Your 'Zendesk' Data
Description: Facilitates making a connection to the
'Zendesk' API and executing various queries. You can use it to
get ticket, ticket metrics, and user data. The 'Zendesk' documentation is
available at <https://developer.zendesk.com/rest_api
/docs/support/introduction>. This package is not supported by
'Zendesk' (owner of the software).
Author: Chris Umphlett [aut, cre],
Avinash Panigrahi [aut]
Maintainer: Chris Umphlett <christopher.umphlett@gmail.com>
Diff between zdeskR versions 0.3.0 dated 2023-05-02 and 0.4.0 dated 2024-02-29
DESCRIPTION | 10 +++++----- MD5 | 6 ++++-- NAMESPACE | 4 ++++ R/get_tickets_comments.R |only man/get_tickets_comments.Rd |only 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Boundary Adaptive Local Polynomial Conditional Density Estimator
Description: Tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024).
Author: Rajita Chandak [aut, cre]
Maintainer: Rajita Chandak <rchandak@princeton.edu>
Diff between lpcde versions 0.1.1 dated 2023-09-01 and 0.1.2 dated 2024-02-29
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ R/lpbwcde.R | 30 +++++++++++++++++++++++++----- R/lpcde.R | 49 +++++++++++++++++++++++++++++++++++++++---------- man/lpbwcde.Rd | 6 ++++++ man/lpcde.Rd | 9 +++++++++ tests/test.R | 4 ++++ 8 files changed, 103 insertions(+), 26 deletions(-)
Title: Interface to the arXiv API
Description: An interface to the API for 'arXiv',
a repository of electronic preprints for
computer science, mathematics, physics, quantitative biology,
quantitative finance, and statistics.
Author: Karthik Ram [aut] ,
Karl Broman [aut, cre]
Maintainer: Karl Broman <broman@wisc.edu>
Diff between aRxiv versions 0.8 dated 2024-01-22 and 0.10 dated 2024-02-29
DESCRIPTION | 10 +++---- LICENSE | 2 - MD5 | 16 +++++------ NEWS.md | 9 ++++++ README.md | 6 ++-- inst/doc/aRxiv.R | 9 ++++-- inst/doc/aRxiv.Rmd | 19 +++++++++---- inst/doc/aRxiv.html | 71 +++++++++++++++++++++++++++++----------------------- vignettes/aRxiv.Rmd | 19 +++++++++---- 9 files changed, 98 insertions(+), 63 deletions(-)
Title: Visualize the Climate Scenario Alignment of a Financial
Portfolio
Description: Create plots to visualize the alignment of a corporate
lending financial portfolio to climate change scenarios based on
climate indicators (production and emission intensities) across key
climate relevant sectors of the 'PACTA' methodology (Paris Agreement Capital
Transition Assessment; <https://www.transitionmonitor.com/>).
Financial institutions use 'PACTA' to study how their capital
allocation decisions align with climate change mitigation goals.
Author: Monika Furdyna [aut, ctr, cre]
,
Mauro Lepore [aut, ctr] ,
Alex Axthelm [aut, ctr] ,
Rocky Mountain Institute [cph, fnd]
Maintainer: Monika Furdyna <monika.furdyna@gmail.com>
Diff between r2dii.plot versions 0.3.1 dated 2023-05-23 and 0.4.0 dated 2024-02-29
DESCRIPTION | 12 MD5 | 83 +++-- NAMESPACE | 4 NEWS.md | 15 + R/plot_emission_intensity.R | 96 +----- R/plot_techmix.R | 197 ++++---------- R/plot_trajectory.R | 321 +++++++++-------------- R/prep_emission_intensity.R |only R/prep_techmix.R |only R/prep_trajectory.R |only R/qplot_emission_intensity.R | 16 + R/qplot_techmix.R | 13 R/qplot_trajectory.R | 24 + R/r2dii.plot-package.R | 1 R/scale_colour_r2dii.R | 18 - R/utils.R | 54 +++ README.md | 21 - man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/plot_emission_intensity.Rd | 34 -- man/plot_techmix.Rd | 53 --- man/plot_trajectory.Rd | 40 -- man/prep_emission_intensity.Rd |only man/prep_techmix.Rd |only man/prep_trajectory.Rd |only man/qplot_emission_intensity.Rd | 7 man/qplot_techmix.Rd | 12 man/qplot_trajectory.Rd | 5 man/scale_colour_r2dii.Rd | 8 man/scale_colour_r2dii_sector.Rd | 4 man/scale_colour_r2dii_tech.Rd | 4 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/plot_emission_intensity.md | 19 - tests/testthat/_snaps/plot_techmix.md | 52 --- tests/testthat/_snaps/plot_trajectory.md | 10 tests/testthat/_snaps/prep_emission_intensity.md |only tests/testthat/_snaps/prep_techmix.md |only tests/testthat/_snaps/qplot_trajectory.md | 4 tests/testthat/_snaps/scale_colour_r2dii.md | 4 tests/testthat/test-market_share.R | 4 tests/testthat/test-plot_emission_intensity.R | 211 ++++++++++++--- tests/testthat/test-plot_techmix.R | 164 +---------- tests/testthat/test-plot_trajectory.R | 110 ++----- tests/testthat/test-prep_emission_intensity.R |only tests/testthat/test-prep_techmix.R |only tests/testthat/test-prep_trajectory.R |only tests/testthat/test-qplot_trajectory.R | 2 tests/testthat/test-scale_colour_r2dii.R | 80 +++++ 48 files changed, 742 insertions(+), 960 deletions(-)
Title: Estimate Gaussian and Student's t Mixture Vector Autoregressive
Models
Description: Unconstrained and constrained maximum likelihood estimation of structural and reduced form
Gaussian mixture vector autoregressive, Student's t mixture vector autoregressive, and Gaussian and Student's t
mixture vector autoregressive models, quantile residual tests, graphical diagnostics,
simulations, forecasting, and estimation of generalized impulse response function and generalized
forecast error variance decomposition.
Leena Kalliovirta, Mika Meitz, Pentti Saikkonen (2016) <doi:10.1016/j.jeconom.2016.02.012>,
Savi Virolainen (forthcoming) <doi:10.1080/07350015.2024.2322090>,
Savi Virolainen (2022) <arXiv:2109.13648>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between gmvarkit versions 2.1.1 dated 2024-01-22 and 2.1.2 dated 2024-02-29
DESCRIPTION | 8 - MD5 | 210 +++++++++++++++---------------- NEWS.md | 7 + R/GIRFandGFEVD.R | 4 R/GSMVARconstruction.R | 16 +- R/MAINest.R | 13 - R/WaldAndLR.R | 6 R/argumentChecks.R | 4 R/data.R | 10 - R/generateParams.R | 4 R/geneticAlgorithm.R | 4 R/linearIRF.R | 6 R/loglikelihood.R | 6 R/parameterReforms.R | 4 README.md | 48 ++++--- inst/doc/gmvarkit-vignette.Rnw | 46 +++--- inst/doc/gmvarkit-vignette.pdf |binary man/GAfit.Rd | 6 man/GFEVD.Rd | 4 man/GIRF.Rd | 4 man/GMVAR.Rd | 6 man/GSMVAR.Rd | 6 man/LR_test.Rd | 4 man/Pearson_residuals.Rd | 4 man/Rao_test.Rd | 10 - man/Wald_test.Rd | 10 - man/add_data.Rd | 4 man/alt_gmvar.Rd | 4 man/alt_gsmvar.Rd | 4 man/change_parametrization.Rd | 6 man/change_regime.Rd | 6 man/check_constraints.Rd | 2 man/check_parameters.Rd | 6 man/cond_moment_plot.Rd | 4 man/cond_moments.Rd | 6 man/diagnostic_plot.Rd | 4 man/estimate_sgsmvar.Rd | 4 man/fitGMVAR.Rd | 6 man/fitGSMVAR.Rd | 11 - man/form_boldA.Rd | 4 man/get_alpha_mt.Rd | 4 man/get_boldA_eigens.Rd | 4 man/get_omega_eigens.Rd | 4 man/get_regime_autocovs.Rd | 4 man/get_regime_autocovs_int.Rd | 6 man/get_regime_means.Rd | 4 man/get_regime_means_int.Rd | 6 man/get_test_Omega.Rd | 6 man/get_unconstrained_structural_pars.Rd | 2 man/gmvar_to_sgmvar.Rd | 4 man/gsmvar_to_sgsmvar.Rd | 4 man/in_paramspace.Rd | 6 man/in_paramspace_int.Rd | 4 man/is_stationary.Rd | 6 man/iterate_more.Rd | 4 man/linear_IRF.Rd | 6 man/loglikelihood.Rd | 6 man/loglikelihood_int.Rd | 6 man/n_params.Rd | 6 man/pick_Am.Rd | 6 man/pick_Ami.Rd | 6 man/pick_Omegas.Rd | 6 man/pick_W.Rd | 6 man/pick_allA.Rd | 6 man/pick_all_phi0_A.Rd | 6 man/pick_alphas.Rd | 4 man/pick_df.Rd | 4 man/pick_lambdas.Rd | 6 man/pick_phi0.Rd | 6 man/pick_regime.Rd | 6 man/plot.gsmvarpred.Rd | 4 man/predict.gmvar.Rd | 4 man/predict.gsmvar.Rd | 4 man/print_std_errors.Rd | 4 man/profile_logliks.Rd | 4 man/quantile_residual_tests.Rd | 4 man/quantile_residuals.Rd | 4 man/quantile_residuals_int.Rd | 6 man/random_covmat.Rd | 2 man/random_ind.Rd | 6 man/random_ind2.Rd | 6 man/reform_constrained_pars.Rd | 6 man/reform_structural_pars.Rd | 6 man/regime_distance.Rd | 4 man/reorder_W_columns.Rd | 4 man/simulate.gsmvar.Rd | 4 man/simulateGMVAR.Rd | 4 man/smart_covmat.Rd | 2 man/smart_ind.Rd | 6 man/sort_W_and_lambdas.Rd | 4 man/sort_and_standardize_alphas.Rd | 2 man/sort_components.Rd | 6 man/standard_errors.Rd | 6 man/stmvar_to_gstmvar.Rd | 4 man/stmvarpars_to_gstmvar.Rd | 2 man/swap_W_signs.Rd | 4 man/swap_parametrization.Rd | 4 man/unWvec.Rd | 2 man/uncond_moments.Rd | 4 man/uncond_moments_int.Rd | 6 man/update_numtols.Rd | 4 man/usamon.Rd | 6 man/usamone.Rd | 6 tests/testthat/test_MAINest.R | 2 vignettes/gmvarkit-vignette.Rnw | 46 +++--- vignettes/refs.bib | 8 + 106 files changed, 444 insertions(+), 431 deletions(-)
Title: A Group of Fun Datasets of Various Sizes and Differing Levels of
Quality
Description: Four datasets are provided here from the 'Intendo' game
'Super Jetroid'. It is data from the 2015 year of operation and it comprises
a revenue table ('all_revenue'), a daily users table ('users_daily'), a user
summary table ('user_summary'), and a table with data on all user sessions
('all_sessions'). These core datasets come in different sizes, and, each of
them has a variant that was intentionally made faulty (totally riddled with
errors and inconsistencies). This suite of tables is useful for testing with
packages that focus on data validation and data documentation.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between intendo versions 0.1 dated 2023-02-22 and 0.1.1 dated 2024-02-29
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/get_dd.R | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: High-Dimensional Aggregate Density Forecasts
Description: Provides a forecasting method that maps vast numbers of
(scalar-valued) signals of any type into an aggregate density forecast
in a time-varying and computationally fast manner. The method proceeds
in two steps: First, it transforms a predictive signal into a density
forecast. Second, it combines the generated candidate density
forecasts into an ultimate density forecast. The methods are explained
in detail in Adaemmer et al. (2023) <doi:10.2139/ssrn.4342487>.
Author: Sven Lehmann [aut, cre, cph],
Philipp Adaemmer [aut],
Rainer Schuessler [aut]
Maintainer: Sven Lehmann <sven.lehmann@uni-rostock.de>
Diff between hdflex versions 0.2.0 dated 2023-10-31 and 0.2.1 dated 2024-02-29
hdflex-0.2.0/hdflex/R/hdflex.R |only hdflex-0.2.1/hdflex/DESCRIPTION | 16 hdflex-0.2.1/hdflex/MD5 | 32 - hdflex-0.2.1/hdflex/NEWS.md | 5 hdflex-0.2.1/hdflex/R/RcppExports.R | 16 hdflex-0.2.1/hdflex/R/dsc.R | 2 hdflex-0.2.1/hdflex/R/hdflex-package.R |only hdflex-0.2.1/hdflex/R/stsc.R | 484 ++++++++++++------------- hdflex-0.2.1/hdflex/R/tvc.R | 28 - hdflex-0.2.1/hdflex/README.md | 1 hdflex-0.2.1/hdflex/man/hdflex.Rd | 5 hdflex-0.2.1/hdflex/man/stsc.Rd | 51 +- hdflex-0.2.1/hdflex/man/tvc.Rd | 8 hdflex-0.2.1/hdflex/src/RcppExports.cpp | 34 - hdflex-0.2.1/hdflex/src/init.c | 12 hdflex-0.2.1/hdflex/src/stsc.cpp | 231 ++++++----- hdflex-0.2.1/hdflex/tests/testthat/test-stsc.R | 215 ++++++++++- hdflex-0.2.1/hdflex/tests/testthat/test-tvc.R | 2 18 files changed, 681 insertions(+), 461 deletions(-)
Title: 'SciViews' - Socket Server
Description: A socket server allows to connect clients to R.
Author: Philippe Grosjean [aut, cre] ,
Matthew Dowle [ctb]
Maintainer: Philippe Grosjean <phgrosjean@sciviews.org>
Diff between svSocket versions 1.1.0 dated 2022-05-10 and 1.1.5 dated 2024-02-29
svSocket-1.1.0/svSocket/inst/CITATION |only svSocket-1.1.5/svSocket/DESCRIPTION | 10 svSocket-1.1.5/svSocket/MD5 | 21 - svSocket-1.1.5/svSocket/NEWS.md | 20 + svSocket-1.1.5/svSocket/R/start_socket_server.R | 11 svSocket-1.1.5/svSocket/R/svSocket-package.R | 13 - svSocket-1.1.5/svSocket/build/vignette.rds |binary svSocket-1.1.5/svSocket/inst/doc/svSocket.Rmd | 4 svSocket-1.1.5/svSocket/inst/doc/svSocket.html | 243 ++++++++++----------- svSocket-1.1.5/svSocket/man/start_socket_server.Rd | 5 svSocket-1.1.5/svSocket/man/svSocket-package.Rd | 13 - svSocket-1.1.5/svSocket/vignettes/svSocket.Rmd | 4 12 files changed, 195 insertions(+), 149 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between qrng versions 0.0-9 dated 2023-04-20 and 0.0-10 dated 2024-02-29
DESCRIPTION | 11 ++++------- MD5 | 10 +++++----- R/qrng.R | 23 +++++++++++++++++++---- demo/sobol_examples.R | 8 +++----- demo/test_functions.R | 2 +- man/qrng.Rd | 21 ++++++++++++--------- 6 files changed, 44 insertions(+), 31 deletions(-)
Title: Estimation of Intrinsic and Extrinsic Noise from Single-Cell
Data
Description: Functions to calculate estimates of intrinsic and extrinsic noise from the two-reporter single-cell experiment, as in Elowitz, M. B., A. J. Levine, E. D. Siggia, and P. S. Swain (2002) Stochastic gene expression in a single cell. Science, 297, 1183-1186. Functions implement multiple estimators developed for unbiasedness or min Mean Squared Error (MSE) in Fu, A. Q. and Pachter, L. (2016). Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Statistical Applications in Genetics and Molecular Biology, 15(6), 447-471.
Author: Audrey Qiuyan Fu and Lior Pachter
Maintainer: Audrey Q. Fu <audreyqyfu@gmail.com>
Diff between noise versions 1.0.1 dated 2021-01-07 and 1.0.2 dated 2024-02-29
noise-1.0.1/noise/build |only noise-1.0.1/noise/man/noise-package.Rd |only noise-1.0.2/noise/DESCRIPTION | 10 ++++++---- noise-1.0.2/noise/MD5 | 4 +--- 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Power Under Multiplicity Project
Description: Estimates power, minimum detectable effect size (MDES) and sample size requirements. The context is multilevel randomized experiments with multiple outcomes. The estimation takes into account the use of multiple testing procedures. Development of this package was supported by a grant from the Institute of Education Sciences (R305D170030). For a full package description, including a detailed technical appendix, see <doi:10.18637/jss.v108.i06>.
Author: Kristin Porter [aut],
Luke Miratrix [aut, cre] ,
Kristen Hunter [aut] ,
Zarni Htet [aut],
MDRC [cph],
Institute of Education Sciences [fnd]
Maintainer: Luke Miratrix <luke_miratrix@gse.harvard.edu>
Diff between PUMP versions 1.0.2 dated 2023-05-22 and 1.0.3 dated 2024-02-29
PUMP-1.0.2/PUMP/man/PUMP.Rd |only PUMP-1.0.2/PUMP/tests/testthat/test-sim.R |only PUMP-1.0.3/PUMP/DESCRIPTION | 8 PUMP-1.0.3/PUMP/MD5 | 211 ++- PUMP-1.0.3/PUMP/NAMESPACE | 1 PUMP-1.0.3/PUMP/R/PUMP-package.R |only PUMP-1.0.3/PUMP/R/designs_and_models.R | 391 ++---- PUMP-1.0.3/PUMP/R/pump_mdes.R | 120 - PUMP-1.0.3/PUMP/R/pump_power.R | 693 ++++++----- PUMP-1.0.3/PUMP/R/pump_sample.R | 232 +-- PUMP-1.0.3/PUMP/R/pumpgridresult.R | 22 PUMP-1.0.3/PUMP/R/pumpresult.R | 31 PUMP-1.0.3/PUMP/R/simulation.R | 25 PUMP-1.0.3/PUMP/build/partial.rdb |only PUMP-1.0.3/PUMP/build/vignette.rds |binary PUMP-1.0.3/PUMP/inst/CITATION |only PUMP-1.0.3/PUMP/inst/doc/pump_demo.R | 4 PUMP-1.0.3/PUMP/inst/doc/pump_demo.Rmd | 2 PUMP-1.0.3/PUMP/inst/doc/pump_demo.html | 24 PUMP-1.0.3/PUMP/inst/doc/pump_sample_demo.R | 44 PUMP-1.0.3/PUMP/inst/doc/pump_sample_demo.html | 692 ++++------- PUMP-1.0.3/PUMP/inst/doc/pump_simulate.R | 4 PUMP-1.0.3/PUMP/inst/doc/pump_simulate.html | 14 PUMP-1.0.3/PUMP/man/PUMP-package.Rd |only PUMP-1.0.3/PUMP/man/calc_J.Rd | 8 PUMP-1.0.3/PUMP/man/calc_K.Rd | 12 PUMP-1.0.3/PUMP/man/calc_MT.Rd |only PUMP-1.0.3/PUMP/man/calc_SE.Rd | 2 PUMP-1.0.3/PUMP/man/calc_df.Rd | 4 PUMP-1.0.3/PUMP/man/calc_nbar.Rd | 6 PUMP-1.0.3/PUMP/man/gen_sim_data.Rd | 6 PUMP-1.0.3/PUMP/man/get_power_results.Rd | 20 PUMP-1.0.3/PUMP/man/makelist_samp.Rd | 7 PUMP-1.0.3/PUMP/man/optimize_power.Rd | 8 PUMP-1.0.3/PUMP/man/parse_d_m.Rd | 2 PUMP-1.0.3/PUMP/man/plot.pumpresult.Rd | 2 PUMP-1.0.3/PUMP/man/pump_info.Rd | 6 PUMP-1.0.3/PUMP/man/pump_mdes.Rd | 20 PUMP-1.0.3/PUMP/man/pump_mdes_grid.Rd | 6 PUMP-1.0.3/PUMP/man/pump_power.Rd | 16 PUMP-1.0.3/PUMP/man/pump_power_exact.Rd |only PUMP-1.0.3/PUMP/man/pump_sample.Rd | 24 PUMP-1.0.3/PUMP/man/pump_sample_grid.Rd | 8 PUMP-1.0.3/PUMP/man/pump_sample_raw.Rd | 2 PUMP-1.0.3/PUMP/man/strip_SEs.Rd |only PUMP-1.0.3/PUMP/man/update.pumpgridresult.Rd |only PUMP-1.0.3/PUMP/man/validate_d_m.Rd | 4 PUMP-1.0.3/PUMP/tests/testthat/Rplots.pdf |binary PUMP-1.0.3/PUMP/tests/testthat/test-M1-calls.R | 57 PUMP-1.0.3/PUMP/tests/testthat/test-grid_functions.R | 2 PUMP-1.0.3/PUMP/tests/testthat/test-porter-benchmark.R |only PUMP-1.0.3/PUMP/tests/testthat/test-powerup.R | 1056 +++++++++-------- PUMP-1.0.3/PUMP/tests/testthat/test-pump_power.R | 223 +-- PUMP-1.0.3/PUMP/tests/testthat/test-pumpresult.R | 11 PUMP-1.0.3/PUMP/tests/testthat/test-simulation.R |only PUMP-1.0.3/PUMP/tests/testthat/test-update_functions.R | 55 PUMP-1.0.3/PUMP/vignettes/output/ICCgrid.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/MDEScalc.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/MDEScalcmin1.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/MDESwithNumZero.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/numzerogrid.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/othercorrections.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/powICC.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/powR2.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/powbase.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/rhogrid.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/samplesizecalc.RDS |binary PUMP-1.0.3/PUMP/vignettes/output/samplesizeverify.RDS |binary PUMP-1.0.3/PUMP/vignettes/pump_demo.Rmd | 2 PUMP-1.0.3/PUMP/vignettes/pump_demo_cache |only PUMP-1.0.3/PUMP/vignettes/pump_demo_files |only PUMP-1.0.3/PUMP/vignettes/refs.bib | 15 72 files changed, 2155 insertions(+), 1947 deletions(-)
More information about moderate.mediation at CRAN
Permanent link
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). "An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere". Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). "Spherical regression models with general covariates and anisotropic errors". Statistics and Computing 30(1): 153--165. <d [...truncated...]
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 6.4 dated 2023-12-09 and 6.5 dated 2024-02-29
Directional-6.4/Directional/man/pcircexp.Rd |only Directional-6.4/Directional/man/pcircpurka.Rd |only Directional-6.5/Directional/DESCRIPTION | 10 - Directional-6.5/Directional/MD5 | 43 ++++---- Directional-6.5/Directional/NAMESPACE | 4 Directional-6.5/Directional/R/dmmvm.R |only Directional-6.5/Directional/R/esag.reg.R | 14 +- Directional-6.5/Directional/R/mmvm.mle.R |only Directional-6.5/Directional/R/pcardio.R |only Directional-6.5/Directional/R/pcipc.R |only Directional-6.5/Directional/R/pcircbeta.R |only Directional-6.5/Directional/R/pgcpc.R |only Directional-6.5/Directional/R/pmmvm.R |only Directional-6.5/Directional/R/pspml.R |only Directional-6.5/Directional/R/pwrapcauchy.R |only Directional-6.5/Directional/man/Directional-package.Rd | 4 Directional-6.5/Directional/man/dvm.Rd | 35 ++++-- Directional-6.5/Directional/man/esag.reg.Rd | 4 Directional-6.5/Directional/man/hcf.aov.Rd | 3 Directional-6.5/Directional/man/hcf.boot.Rd | 4 Directional-6.5/Directional/man/hcf.circaov.Rd | 4 Directional-6.5/Directional/man/hcf.perm.Rd | 4 Directional-6.5/Directional/man/hcfboot.Rd | 4 Directional-6.5/Directional/man/hcfcirc.boot.Rd | 4 Directional-6.5/Directional/man/hcfcirc.perm.Rd | 4 Directional-6.5/Directional/man/hcfcircboot.Rd | 4 Directional-6.5/Directional/man/pvm.Rd | 87 ++++++++++++++--- Directional-6.5/Directional/man/spml.mle.Rd | 28 +++-- 28 files changed, 178 insertions(+), 82 deletions(-)
Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. We further include functions for percentages (or proportions).
The standard textbook for such data is John Aitchison's (1986) "The statistical analysis of compositional data". Relevant papers include:
a) Tsagris M.T., Preston S. and Wood A.T.A. (2011). "A data-based power transformation for compositional data". Fourth International International Workshop on Compositional Data Analysis.
b) Tsagris M. (2014). "The k-NN algorithm for compositional data: a revised approach with and without zero values present". Journal of Data Science, 12(3): 519--534.
c) Tsagris M. (2015). "A novel, divergence based, regression for compositional data". Proceedings of the 28th Panhellenic Statistics Conference, 15-18 April 2015, Athens, Greece, 430--444.
d) Tsagris M. (2015). "Regression analysis with compositional data containing zero values". Chilean Journa [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Abdulaziz Alenazi [ctb],
Christos Adam [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Compositional versions 6.6 dated 2023-12-09 and 6.7 dated 2024-02-29
DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 3 +-- R/alfa.reg.R | 17 ++++++++--------- R/alfa.reg3.R | 15 +++++++++------ R/frechet.R | 10 +++++----- man/Compositional-package.Rd | 4 ++-- man/alfa.rda.Rd | 12 ++++++------ man/alfa.reg.Rd | 6 +++--- man/alfa.ridge.Rd | 2 +- man/alfarda.tune.Rd | 33 +++++++++++++++++++++------------ man/comp.knn.Rd | 4 ++-- 12 files changed, 76 insertions(+), 66 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: The standard linear regression theory whether frequentist or Bayesian is based on an 'assumed (revealed?) truth' (John Tukey) attitude to models. This is reflected in the language of statistical inference which involves a concept of truth, for example confidence intervals, hypothesis testing and consistency. The motivation behind this package was to remove the word true from the theory and practice of linear regression and to replace it by approximation. The approximations considered are the least squares approximations. An approximation is called valid if it contains no irrelevant covariates. This is operationalized using the concept of a Gaussian P-value which is the probability that pure Gaussian noise is better in term of least squares than the covariate. The precise definition given in the paper, it is intuitive and requires only four simple equations. Its overwhelming advantage compared with a standard F P-value is that is is exact and valid whatever the data. In contrast F P [...truncated...]
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <pldavies44@cantab.net>
Diff between gausscov versions 1.0.3 dated 2023-10-11 and 1.1.0 dated 2024-02-29
gausscov-1.0.3/gausscov/R/fdecode.R |only gausscov-1.0.3/gausscov/R/fgr2st.R |only gausscov-1.0.3/gausscov/R/fselect.R |only gausscov-1.0.3/gausscov/R/fvauto.R |only gausscov-1.0.3/gausscov/man/fdecode.Rd |only gausscov-1.0.3/gausscov/man/fgr2st.Rd |only gausscov-1.0.3/gausscov/man/fselect.Rd |only gausscov-1.0.3/gausscov/man/fvauto.Rd |only gausscov-1.1.0/gausscov/DESCRIPTION | 10 gausscov-1.1.0/gausscov/MD5 | 72 - gausscov-1.1.0/gausscov/R/f1st.R | 259 +++--- gausscov-1.1.0/gausscov/R/f2st.R | 115 +- gausscov-1.1.0/gausscov/R/f3st.R | 86 +- gausscov-1.1.0/gausscov/R/f3sti.R | 20 gausscov-1.1.0/gausscov/R/fasb.R | 194 ++-- gausscov-1.1.0/gausscov/R/fgeninter.R | 61 - gausscov-1.1.0/gausscov/R/fgentrig.R | 20 gausscov-1.1.0/gausscov/R/fgr1st.R | 111 -- gausscov-1.1.0/gausscov/R/flag.R | 21 gausscov-1.1.0/gausscov/R/fpval.R | 88 +- gausscov-1.1.0/gausscov/R/simgpval.R | 62 - gausscov-1.1.0/gausscov/data/abcq.rda |binary gausscov-1.1.0/gausscov/data/boston.rda |binary gausscov-1.1.0/gausscov/data/leukemia.rda |binary gausscov-1.1.0/gausscov/data/mel_temp.rda |binary gausscov-1.1.0/gausscov/data/redwine.rda |binary gausscov-1.1.0/gausscov/data/snspt.rda |binary gausscov-1.1.0/gausscov/data/vardata.rda |only gausscov-1.1.0/gausscov/man/decode.Rd | 16 gausscov-1.1.0/gausscov/man/f1st.Rd | 10 gausscov-1.1.0/gausscov/man/f2st.Rd | 11 gausscov-1.1.0/gausscov/man/f3st.Rd | 18 gausscov-1.1.0/gausscov/man/f3sti.Rd | 20 gausscov-1.1.0/gausscov/man/fasb.Rd | 11 gausscov-1.1.0/gausscov/man/fgeninter.Rd | 2 gausscov-1.1.0/gausscov/man/fgr1st.Rd | 8 gausscov-1.1.0/gausscov/man/flag.Rd | 7 gausscov-1.1.0/gausscov/man/fpval.Rd | 6 gausscov-1.1.0/gausscov/man/leukemia.Rd | 13 gausscov-1.1.0/gausscov/man/simgpval.Rd | 9 gausscov-1.1.0/gausscov/man/vardata.Rd |only gausscov-1.1.0/gausscov/src/gaucov.f | 1196 ++++++++++++++++++++++++++---- 42 files changed, 1630 insertions(+), 816 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The package
includes several optimization algorithms e.g. Random Search, Iterated
Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband (in
'mlr3hyperband'). bbotk is the base package of 'mlr3tuning', 'mlr3fselect'
and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.7.3 dated 2023-11-13 and 0.8.0 dated 2024-02-29
DESCRIPTION | 8 MD5 | 74 +++--- NAMESPACE | 3 NEWS.md | 6 R/Archive.R | 67 +++-- R/Codomain.R | 63 ++--- R/Objective.R | 5 R/Optimizer.R | 7 R/OptimizerCmaes.R | 4 R/OptimizerFocusSearch.R | 114 ++++++--- R/OptimizerGenSA.R | 1 R/OptimizerIrace.R | 10 R/OptimizerRandomSearch.R | 2 R/TerminatorCombo.R | 2 R/TerminatorEvals.R | 4 R/TerminatorPerfReached.R | 2 R/TerminatorRunTime.R | 2 R/TerminatorStagnation.R | 4 R/TerminatorStagnationBatch.R | 4 R/helper.R | 1 README.md | 20 - inst/doc/bbotk.html | 353 +++++++++++++++-------------- man/Archive.Rd | 22 + man/Codomain.Rd | 18 - man/Optimizer.Rd | 6 man/Terminator.Rd | 4 man/mlr_terminators.Rd | 4 man/mlr_terminators_clock_time.Rd | 4 man/mlr_terminators_combo.Rd | 4 man/mlr_terminators_evals.Rd | 4 man/mlr_terminators_none.Rd | 4 man/mlr_terminators_perf_reached.Rd | 4 man/mlr_terminators_run_time.Rd | 4 man/mlr_terminators_stagnation.Rd | 4 man/mlr_terminators_stagnation_batch.Rd | 4 man/shrink_ps.Rd | 12 tests/testthat/test_Archive.R | 110 +++++++++ tests/testthat/test_OptimizerFocusSearch.R | 34 +- 38 files changed, 596 insertions(+), 402 deletions(-)
Title: Random Generation Functionality for the 'spatstat' Family
Description: Functionality for random generation of spatial data in the 'spatstat' family of packages.
Generates random spatial patterns of points according to many simple rules (complete spatial randomness,
Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns
(thinning, random shift, jittering), simulated realisations of random point processes including
simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes
(using direct, Brix-Kendall, or hybrid algorithms),
log-Gaussian Cox processes, product shot noise cluster processes
and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm,
alternating Gibbs sampler, or coupling-from-the-past perfect simulation).
Also generates random spatial patterns of line segments,
random tessellations, and random images (random noise, random mosaics).
Excludes random generation on a linear network,
which is covered by the separate package 'spatstat.linnet'.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb, cph],
David Bryant [ctb, cph],
Ya-Mei Chang [ctb, cph],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Dominic Sc [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.random versions 3.2-2 dated 2023-11-29 and 3.2-3 dated 2024-02-29
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 23 +++++++++++++++++++++++ R/rLGCP.R | 6 +++--- R/random.R | 4 ++-- R/randomcircembed.R | 7 +++++-- R/randomseg.R | 2 +- R/randomtess.R | 4 ++-- inst/doc/packagesizes.txt | 1 + tests/Random.R | 32 +++++++++++++++++++++++++++++++- 10 files changed, 82 insertions(+), 25 deletions(-)
More information about spatstat.random at CRAN
Permanent link
More information about multilevelmediation at CRAN
Permanent link
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables. See Gaure (2013) <doi:10.1016/j.csda.2013.03.024>
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction (Gaure 2014 <doi:10.1002/sta4.68>).
Since version 3.0, it provides dedicated functions to estimate Poisson models.
Author: Simen Gaure [aut] ,
Grant McDermott [ctb],
Mauricio Vargas Sepulveda [ctb, cre]
,
Karl Dunkle Werner [ctb],
Matthieu Stigler [ctb] ,
Daniel Luedecke [ctb]
Maintainer: Mauricio Vargas Sepulveda <m.sepulveda@mail.utoronto.ca>
Diff between lfe versions 2.9-0 dated 2023-02-13 and 3.0-0 dated 2024-02-29
lfe-2.9-0/lfe/R/felm.old.R |only lfe-2.9-0/lfe/tests |only lfe-3.0-0/lfe/DESCRIPTION | 64 +-- lfe-3.0-0/lfe/LICENSE |only lfe-3.0-0/lfe/MD5 | 89 +--- lfe-3.0-0/lfe/NAMESPACE | 6 lfe-3.0-0/lfe/R/fepois.R |only lfe-3.0-0/lfe/R/lfe-package.R | 5 lfe-3.0-0/lfe/R/oldfelm.R | 2 lfe-3.0-0/lfe/R/trace.R | 11 lfe-3.0-0/lfe/README.md | 24 - lfe-3.0-0/lfe/build/partial.rdb |binary lfe-3.0-0/lfe/build/vignette.rds |binary lfe-3.0-0/lfe/inst/CITATION | 97 ++-- lfe-3.0-0/lfe/inst/doc/biascorrection.pdf |binary lfe-3.0-0/lfe/inst/doc/identification.pdf |binary lfe-3.0-0/lfe/inst/doc/lfehow.pdf |binary lfe-3.0-0/lfe/inst/doc/speed.pdf |binary lfe-3.0-0/lfe/man/dot-.oldfelm.Rd |only lfe-3.0-0/lfe/man/fepois.Rd |only lfe-3.0-0/lfe/man/lfe-package.Rd | 25 + lfe-3.0-0/lfe/man/mctrace.Rd | 11 lfe-3.0-0/lfe/src/crowsum.c | 48 -- lfe-3.0-0/lfe/src/demean.c | 603 +++++++++++++++--------------- lfe-3.0-0/lfe/src/factor.c | 241 ++++------- lfe-3.0-0/lfe/src/kaczmarz.c | 223 ++++------- lfe-3.0-0/lfe/src/lfe.c | 18 lfe-3.0-0/lfe/src/lfe.h | 34 - lfe-3.0-0/lfe/src/utils.c | 144 ++----- 29 files changed, 747 insertions(+), 898 deletions(-)
Title: Predicted Means for Linear and Semiparametric Models
Description: Providing functions to diagnose and make inferences from various linear models,
such as those obtained from 'aov', 'lm', 'glm', 'gls', 'lme', 'lmer', 'glmmTMB' and 'semireg'.
Inferences include predicted means and standard errors, contrasts, multiple comparisons,
permutation tests, adjusted R-square and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo <dongwen.luo@agresearch.co.nz>
Diff between predictmeans versions 1.0.9 dated 2023-10-20 and 1.1.0 dated 2024-02-29
DESCRIPTION | 11 ++- MD5 | 32 ++++++---- NAMESPACE | 4 - R/R2_glmm.R |only R/covariatemeans.R | 26 +++----- R/misc.R | 134 +++++++++++++++++++++++++++++++++++++++++++- R/predictmeans.R | 109 ++++++++++++++++++++++------------- R/se_ranef.R |only R/semipred.R | 86 ++++++++++++++++------------ R/semireg.R | 89 ++++++++++++++++------------- R/semireg_tmb.R |only R/varcomp.R | 31 +++++++--- man/R2_glmm.Rd |only man/df_term.Rd | 5 + man/predictmeans-package.Rd | 6 - man/predictmeans.Rd | 16 +++-- man/se_ranef.Rd |only man/semireg.Rd | 7 +- man/semireg_tmb.Rd |only man/varcomp.Rd | 6 - 20 files changed, 384 insertions(+), 178 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <arXiv:1712.0036v1>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang and Junfang Chen
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>
Diff between BioM2 versions 1.0.3 dated 2024-01-10 and 1.0.4 dated 2024-02-29
DESCRIPTION | 9 MD5 | 12 NAMESPACE | 2 NEWS | 5 R/BioM2.R | 90 +++--- README.md | 710 ++++++++++++++++++++++++++++++----------------------- man/PlotPathNet.Rd | 14 - 7 files changed, 486 insertions(+), 356 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-13 1.2.1
2023-08-12 1.2.0
2023-06-16 1.1.0
Title: CORe Multiple Sclerosis Outcomes Toolkit
Description: Enable operationalized evaluation of disease outcomes in
multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded
clinical data structured in long format. The package is based on the
research developed at Clinical Outcomes Research unit (CORe),
University of Melbourne and Neuroimmunology Centre, Royal Melbourne
Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>.
Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al.
(2022) <doi:10.1111/ene.15406>. Dzau et al. (2023)
<doi:10.1136/jnnp-2023-331748>.
Author: Sifat Sharmin [aut],
Johannes Lorscheider [aut],
Nathaniel Lizak [aut],
Sam Harding-Forrester [aut],
Winston Dzau [aut],
Tomas Kalincik [aut, cre, cph]
Maintainer: Tomas Kalincik <tomas.kalincik@unimelb.edu.au>
Diff between MSoutcomes versions 0.1.0 dated 2023-09-13 and 0.2.0 dated 2024-02-29
DESCRIPTION | 22 +++++++------ LICENSE | 2 - MD5 | 29 +++++++++++------ NAMESPACE | 8 +++- NEWS.md |only R/CDEseq.R |only R/CDI.R |only R/CDW.R |only R/PIRA.R |only R/SampleData.R | 2 - R/spmsDx.R | 73 +++++++++++++++++++++++++------------------- R/spmsDxnoFSS.R | 83 +++++++++++++++++++++++++++++---------------------- data/SampleData.rda |binary man/CDEseq.Rd |only man/CDI.Rd |only man/CDW.Rd |only man/PIRA.Rd |only man/SampleData.Rd | 2 - man/spmsDx.Rd | 15 +++++---- man/spmsDx_no_fss.Rd | 17 ++++++---- 20 files changed, 150 insertions(+), 103 deletions(-)
Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This
package intends to handle many file formats that were native to the
antiquated Commodore Amiga machine. This package focuses on file types from
the older Amiga operating systems (<= 3.0). It will read and write specific
file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between AmigaFFH versions 0.4.3 dated 2023-08-27 and 0.4.5 dated 2024-02-29
AmigaFFH-0.4.3/AmigaFFH/NEWS |only AmigaFFH-0.4.5/AmigaFFH/DESCRIPTION | 11 AmigaFFH-0.4.5/AmigaFFH/MD5 | 164 +- AmigaFFH-0.4.5/AmigaFFH/NEWS.md |only AmigaFFH-0.4.5/AmigaFFH/R/AmigaFFH-package.r | 92 - AmigaFFH-0.4.5/AmigaFFH/R/basic.r | 272 ++-- AmigaFFH-0.4.5/AmigaFFH/R/bitmapfont.r | 402 +++--- AmigaFFH-0.4.5/AmigaFFH/R/data.r | 375 +++--- AmigaFFH-0.4.5/AmigaFFH/R/generic_support.r | 230 +-- AmigaFFH-0.4.5/AmigaFFH/R/hardwareSprites.r | 58 AmigaFFH-0.4.5/AmigaFFH/R/iff.0.r | 673 ++++------- AmigaFFH-0.4.5/AmigaFFH/R/iff.8svx.r | 64 - AmigaFFH-0.4.5/AmigaFFH/R/iff.ilbm.r | 66 - AmigaFFH-0.4.5/AmigaFFH/R/system_configuration.r | 1004 ++++++++--------- AmigaFFH-0.4.5/AmigaFFH/R/workbench_icon.r | 150 +- AmigaFFH-0.4.5/AmigaFFH/README.md |only AmigaFFH-0.4.5/AmigaFFH/man/AmigaBasic-files.Rd | 17 AmigaFFH-0.4.5/AmigaFFH/man/AmigaBasic.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/AmigaBasicBMAP-io.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/AmigaBitmapFont.Rd | 108 - AmigaFFH-0.4.5/AmigaFFH/man/AmigaFFH-package.Rd | 94 - AmigaFFH-0.4.5/AmigaFFH/man/AmigaIcon.Rd | 126 +- AmigaFFH-0.4.5/AmigaFFH/man/ExtractBasic.Rd | 11 AmigaFFH-0.4.5/AmigaFFH/man/IFFChunk-class.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/IFFChunk.Rd | 516 +++----- AmigaFFH-0.4.5/AmigaFFH/man/SysConfig.Rd | 14 AmigaFFH-0.4.5/AmigaFFH/man/WaveToIFF.Rd | 26 AmigaFFH-0.4.5/AmigaFFH/man/amiga_display_keys.Rd | 11 AmigaFFH-0.4.5/AmigaFFH/man/amiga_display_modes.Rd | 33 AmigaFFH-0.4.5/AmigaFFH/man/amiga_monitors.Rd | 11 AmigaFFH-0.4.5/AmigaFFH/man/amiga_palettes.Rd | 21 AmigaFFH-0.4.5/AmigaFFH/man/as.AmigaBasic.Rd | 6 AmigaFFH-0.4.5/AmigaFFH/man/as.AmigaBasicBMAP.Rd | 13 AmigaFFH-0.4.5/AmigaFFH/man/as.character.Rd | 6 AmigaFFH-0.4.5/AmigaFFH/man/as.raster.Rd | 32 AmigaFFH-0.4.5/AmigaFFH/man/as.raw.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/availableFontSizes.Rd | 6 AmigaFFH-0.4.5/AmigaFFH/man/bitmapToRaster.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/c.Rd | 32 AmigaFFH-0.4.5/AmigaFFH/man/check.names.AmigaBasic.Rd | 13 AmigaFFH-0.4.5/AmigaFFH/man/deltaFibonacciCompress.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/dither.Rd | 248 ++-- AmigaFFH-0.4.5/AmigaFFH/man/figures |only AmigaFFH-0.4.5/AmigaFFH/man/fontName.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/font_example.Rd | 9 AmigaFFH-0.4.5/AmigaFFH/man/getAmigaBitmapFont.Rd | 16 AmigaFFH-0.4.5/AmigaFFH/man/getIFFChunk.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/hardwareSprite-class.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/ilbm8lores.iff.Rd | 11 AmigaFFH-0.4.5/AmigaFFH/man/index.colours.Rd | 248 ++-- AmigaFFH-0.4.5/AmigaFFH/man/interpretIFFChunk.Rd | 18 AmigaFFH-0.4.5/AmigaFFH/man/names.AmigaBasic.Rd | 4 AmigaFFH-0.4.5/AmigaFFH/man/packBitmap.Rd | 4 AmigaFFH-0.4.5/AmigaFFH/man/play.Rd | 16 AmigaFFH-0.4.5/AmigaFFH/man/plot.Rd | 16 AmigaFFH-0.4.5/AmigaFFH/man/rasterToAmigaBasicShape.Rd | 18 AmigaFFH-0.4.5/AmigaFFH/man/rasterToAmigaBitmapFont.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/rasterToBitmap.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/rasterToHWSprite.Rd | 18 AmigaFFH-0.4.5/AmigaFFH/man/rasterToIFF.Rd | 14 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaBasic.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaBasicBMAP.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaBasicShape.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaBitmapFont.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaBitmapFontSet.Rd | 14 AmigaFFH-0.4.5/AmigaFFH/man/rawToAmigaIcon.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/rawToHWSprite.Rd | 8 AmigaFFH-0.4.5/AmigaFFH/man/rawToIFFChunk.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/rawToSysConfig.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/read.AmigaBasic.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/read.AmigaBasicShape.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/read.AmigaBitmapFont.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/read.AmigaBitmapFontSet.Rd | 10 AmigaFFH-0.4.5/AmigaFFH/man/read.AmigaIcon.Rd | 14 AmigaFFH-0.4.5/AmigaFFH/man/read.SysConfig.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/read.iff.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/simpleAmigaIcon.Rd | 18 AmigaFFH-0.4.5/AmigaFFH/man/simpleSysConfig.Rd | 2 AmigaFFH-0.4.5/AmigaFFH/man/write.AmigaBasic.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/write.AmigaBasicShape.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/write.AmigaBitmapFont.Rd | 24 AmigaFFH-0.4.5/AmigaFFH/man/write.AmigaIcon.Rd | 12 AmigaFFH-0.4.5/AmigaFFH/man/write.SysConfig.Rd | 4 AmigaFFH-0.4.5/AmigaFFH/man/write.iff.Rd | 12 84 files changed, 2678 insertions(+), 2947 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-24 0.5.3
2023-10-04 0.5.2
2023-06-03 0.5.1
2023-05-29 0.5.0
2022-12-04 0.4.1
2022-09-19 0.4.0
2022-07-11 0.3.0
2022-02-09 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-14 0.1.3
2023-11-03 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-01 2024.1.23
2024-01-08 2024.1.8
2023-12-21 2023.12.20
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-01 2024.1.31
2024-01-24 2024.1.24
2023-04-03 2023.3.31
2023-03-31 2023.3.30
2022-09-19 2022.9.16
2022-08-27 2022.8.25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-09-11 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-17 1.1.2
2024-02-08 1.1.1
2023-10-07 1.1.0
2023-09-18 1.0.6
2023-09-10 1.0.5
2023-09-06 1.0.4
2023-07-19 1.0.3
2023-07-15 1.0.2
2023-07-02 1.0.1
2023-06-27 1.0.0
Title: QTL Mapping and Hotspots Detection
Description: For QTL mapping, this package comprises several functions designed to execute diverse
tasks, such as simulating or analyzing data, calculating significance thresholds, and
visualizing QTL mapping results. The single-QTL or multiple-QTL method, which enables
the fitting and comparison of various statistical models, is employed to analyze the
data for estimating QTL parameters. The models encompass linear regression, permutation
tests, normal mixture models, and truncated normal mixture models. The Gaussian stochastic
process is utilized to compute significance thresholds for QTL detection on a genetic
linkage map within experimental populations. Two types of data, complete genotyping, and
selective genotyping data from various experimental populations, including backcross, F2,
recombinant inbred (RI) populations, and advanced intercrossed (AI) populations, are
considered in the QTL mapping analysis. For QTL hotspot detection, statistical methods can
be developed based on either utilizin [...truncated...]
Author: Ping-Yuan Chung [cre],
Chen-Hung Kao [aut],
Y.-T. Guo [aut],
H.-N. Ho [aut],
H.-I. Lee [aut],
P.-Y. Wu [aut],
M.-H. Yang [aut],
M.-H. Zeng [aut]
Maintainer: Ping-Yuan Chung <pychung@webmail.stat.sinica.edu.tw>
Diff between QTLEMM versions 1.5.0 dated 2024-01-22 and 1.5.1 dated 2024-02-29
DESCRIPTION | 54 +++++++++---------- MD5 | 70 ++++++++++++------------- R/D.make.R | 45 ++++++++-------- R/EM.MIM.R | 44 ++++++++-------- R/EM.MIM2.R | 131 +++++++++++++++++++++++------------------------ R/EM.MIMv.R | 109 ++++++++++++++++++--------------------- R/EQF.permu.R | 14 ++--- R/EQF.plot.R | 12 ++-- R/IM.search.R | 95 +++++++++++++++++----------------- R/IM.search2.R | 133 ++++++++++++++++++++++++------------------------ R/LOD.QTLdetect.R | 26 ++++----- R/LRTthre.R | 42 +++++++-------- R/MIM.points.R | 84 ++++++++++++++---------------- R/MIM.points2.R | 124 ++++++++++++++++++++++----------------------- R/MIM.search.R | 78 +++++++++++++--------------- R/MIM.search2.R | 118 +++++++++++++++++++++--------------------- R/Q.make.R | 56 +++++++++----------- R/Qhot.R | 33 +++++------- R/progeny.R | 53 +++++++++---------- man/D.make.Rd | 45 ++++++++-------- man/EM.MIM.Rd | 44 ++++++++-------- man/EM.MIM2.Rd | 131 +++++++++++++++++++++++------------------------ man/EM.MIMv.Rd | 110 ++++++++++++++++++++-------------------- man/EQF.permu.Rd | 14 ++--- man/EQF.plot.Rd | 12 ++-- man/IM.search.Rd | 100 ++++++++++++++++++------------------ man/IM.search2.Rd | 140 +++++++++++++++++++++++++-------------------------- man/LOD.QTLdetect.Rd | 26 ++++----- man/LRTthre.Rd | 42 +++++++-------- man/MIM.points.Rd | 84 ++++++++++++++---------------- man/MIM.points2.Rd | 124 ++++++++++++++++++++++----------------------- man/MIM.search.Rd | 78 +++++++++++++--------------- man/MIM.search2.Rd | 118 +++++++++++++++++++++--------------------- man/Q.make.Rd | 56 +++++++++----------- man/Qhot.Rd | 32 +++++------ man/progeny.Rd | 53 +++++++++---------- 36 files changed, 1253 insertions(+), 1277 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.37.0 dated 2024-02-14 and 1.37.1 dated 2024-02-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 7 +++++++ src/test_tcp_port.c | 1 + 4 files changed, 14 insertions(+), 6 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre],
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut],
Toby Hocking [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonag [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.15.0 dated 2024-01-30 and 1.15.2 dated 2024-02-29
DESCRIPTION | 6 +- MD5 | 32 ++++++------ NEWS.md | 8 +++ inst/doc/datatable-benchmarking.html | 2 inst/doc/datatable-faq.html | 2 inst/doc/datatable-importing.html | 2 inst/doc/datatable-intro.html | 2 inst/doc/datatable-keys-fast-subset.html | 8 +-- inst/doc/datatable-programming.html | 2 inst/doc/datatable-reference-semantics.html | 2 inst/doc/datatable-reshape.html | 2 inst/doc/datatable-sd-usage.html | 2 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 10 +-- inst/tests/tests.Rraw.bz2 |binary src/fwriteR.c | 3 - src/gsumm.c | 3 - src/init.c | 2 17 files changed, 49 insertions(+), 39 deletions(-)
Title: Vector Generalized Linear and Additive Models
Description: An implementation of about 6 major classes of
statistical regression models. The central algorithm is
Fisher scoring and iterative reweighted least squares.
At the heart of this package are the vector generalized linear
and additive model (VGLM/VGAM) classes. VGLMs can be loosely
thought of as multivariate GLMs. VGAMs are data-driven
VGLMs that use smoothing. The book "Vector Generalized
Linear and Additive Models: With an Implementation in R"
(Yee, 2015) <DOI:10.1007/978-1-4939-2818-7> gives details of
the statistical framework and the package. Currently only
fixed-effects models are implemented. Many (100+) models and
distributions are estimated by maximum likelihood estimation
(MLE) or penalized MLE. The other classes are RR-VGLMs
(reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained
RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs,
RCIMs (row-column interaction models)---these classes perform
constrained and unconstrained quadratic ordination (CQO/UQO)
models in ecolog [...truncated...]
Author: Thomas Yee [aut, cre] ,
Cleve Moler [ctb]
Maintainer: Thomas Yee <t.yee@auckland.ac.nz>
Diff between VGAM versions 1.1-9 dated 2023-09-19 and 1.1-10 dated 2024-02-29
VGAM-1.1-10/VGAM/DESCRIPTION | 11 VGAM-1.1-10/VGAM/MD5 | 450 +-- VGAM-1.1-10/VGAM/NAMESPACE | 26 VGAM-1.1-10/VGAM/NEWS | 2686 ---------------------- VGAM-1.1-10/VGAM/R/Links.R | 43 VGAM-1.1-10/VGAM/R/Linksold.R | 2 VGAM-1.1-10/VGAM/R/aamethods.q | 47 VGAM-1.1-10/VGAM/R/anova.vglm.q | 2 VGAM-1.1-10/VGAM/R/attrassign.R | 2 VGAM-1.1-10/VGAM/R/bAIC.q | 2 VGAM-1.1-10/VGAM/R/build.terms.vlm.q | 2 VGAM-1.1-10/VGAM/R/calibrate.R | 2 VGAM-1.1-10/VGAM/R/cao.R | 2 VGAM-1.1-10/VGAM/R/cao.fit.q | 4 VGAM-1.1-10/VGAM/R/coef.vlm.q | 2 VGAM-1.1-10/VGAM/R/confint.vlm.R | 2 VGAM-1.1-10/VGAM/R/cqo.R | 2 VGAM-1.1-10/VGAM/R/cqo.fit.q | 89 VGAM-1.1-10/VGAM/R/deviance.vlm.q | 9 VGAM-1.1-10/VGAM/R/effects.vglm.q | 7 VGAM-1.1-10/VGAM/R/family.actuary.R | 2 VGAM-1.1-10/VGAM/R/family.aunivariate.R | 104 VGAM-1.1-10/VGAM/R/family.basics.R | 38 VGAM-1.1-10/VGAM/R/family.binomial.R | 1766 ++++++++++---- VGAM-1.1-10/VGAM/R/family.bivariate.R | 83 VGAM-1.1-10/VGAM/R/family.bunivariate.R |only VGAM-1.1-10/VGAM/R/family.categorical.R | 1114 +++++---- VGAM-1.1-10/VGAM/R/family.censored.R | 2 VGAM-1.1-10/VGAM/R/family.circular.R | 46 VGAM-1.1-10/VGAM/R/family.exp.R | 2 VGAM-1.1-10/VGAM/R/family.extremes.R | 2 VGAM-1.1-10/VGAM/R/family.functions.R | 2 VGAM-1.1-10/VGAM/R/family.gait0.R | 2 VGAM-1.1-10/VGAM/R/family.gaitd.R | 107 VGAM-1.1-10/VGAM/R/family.genetic.R | 2 VGAM-1.1-10/VGAM/R/family.glmgam.R | 2 VGAM-1.1-10/VGAM/R/family.loglin.R | 2 VGAM-1.1-10/VGAM/R/family.maths.R | 2 VGAM-1.1-10/VGAM/R/family.mixture.R | 2 VGAM-1.1-10/VGAM/R/family.nbd.R | 148 - VGAM-1.1-10/VGAM/R/family.nonlinear.R | 2 VGAM-1.1-10/VGAM/R/family.normal.R | 213 + VGAM-1.1-10/VGAM/R/family.oneinf.R | 56 VGAM-1.1-10/VGAM/R/family.others.R | 2 VGAM-1.1-10/VGAM/R/family.positive.R | 2 VGAM-1.1-10/VGAM/R/family.qreg.R | 2 VGAM-1.1-10/VGAM/R/family.rcim.R | 2 VGAM-1.1-10/VGAM/R/family.rcqo.R | 2 VGAM-1.1-10/VGAM/R/family.robust.R | 2 VGAM-1.1-10/VGAM/R/family.rrr.R | 2079 +++++++++-------- VGAM-1.1-10/VGAM/R/family.sur.R | 2 VGAM-1.1-10/VGAM/R/family.survival.R | 2 VGAM-1.1-10/VGAM/R/family.ts.R | 3 VGAM-1.1-10/VGAM/R/family.univariate.R | 493 ++-- VGAM-1.1-10/VGAM/R/family.vglm.R | 2 VGAM-1.1-10/VGAM/R/family.zeroinf.R | 2 VGAM-1.1-10/VGAM/R/fittedvlm.R | 2 VGAM-1.1-10/VGAM/R/formula.vlm.q | 2 VGAM-1.1-10/VGAM/R/generic.q | 2 VGAM-1.1-10/VGAM/R/getxvlmaug.R | 2 VGAM-1.1-10/VGAM/R/hdeff.R | 2 VGAM-1.1-10/VGAM/R/links.q | 1760 +++++++------- VGAM-1.1-10/VGAM/R/logLik.vlm.q | 2 VGAM-1.1-10/VGAM/R/lrp.R | 2 VGAM-1.1-10/VGAM/R/lrwaldtest.R | 2 VGAM-1.1-10/VGAM/R/model.matrix.vglm.q | 2 VGAM-1.1-10/VGAM/R/mux.q | 2 VGAM-1.1-10/VGAM/R/nobs.R | 2 VGAM-1.1-10/VGAM/R/plot.vgam.R | 482 ++- VGAM-1.1-10/VGAM/R/plot.vglm.R | 2 VGAM-1.1-10/VGAM/R/predict.vgam.q | 2 VGAM-1.1-10/VGAM/R/predict.vglm.q | 2 VGAM-1.1-10/VGAM/R/predict.vlm.q | 2 VGAM-1.1-10/VGAM/R/print.vglm.q | 2 VGAM-1.1-10/VGAM/R/print.vlm.q | 7 VGAM-1.1-10/VGAM/R/psv2magic.R | 2 VGAM-1.1-10/VGAM/R/qrrvglm.control.q | 2 VGAM-1.1-10/VGAM/R/qtplot.q | 2 VGAM-1.1-10/VGAM/R/residuals.vlm.q | 2 VGAM-1.1-10/VGAM/R/rootogram4.vglm.R | 2 VGAM-1.1-10/VGAM/R/rrvglm.R | 53 VGAM-1.1-10/VGAM/R/rrvglm.control.q | 152 - VGAM-1.1-10/VGAM/R/rrvglm.fit.q | 302 +- VGAM-1.1-10/VGAM/R/s.q | 2 VGAM-1.1-10/VGAM/R/s.vam.q | 2 VGAM-1.1-10/VGAM/R/simulate.vglm.R | 2 VGAM-1.1-10/VGAM/R/sm.os.R | 2 VGAM-1.1-10/VGAM/R/sm.ps.R | 2 VGAM-1.1-10/VGAM/R/smart.R | 2 VGAM-1.1-10/VGAM/R/step4.vglm.R | 2 VGAM-1.1-10/VGAM/R/summary.drrvglm.R |only VGAM-1.1-10/VGAM/R/summary.vgam.q | 6 VGAM-1.1-10/VGAM/R/summary.vglm.q | 154 - VGAM-1.1-10/VGAM/R/summary.vlm.q | 24 VGAM-1.1-10/VGAM/R/vcov.pvgam.R | 3 VGAM-1.1-10/VGAM/R/vgam.R | 2 VGAM-1.1-10/VGAM/R/vgam.control.q | 2 VGAM-1.1-10/VGAM/R/vgam.fit.q | 2 VGAM-1.1-10/VGAM/R/vgam.match.q | 2 VGAM-1.1-10/VGAM/R/vglm.R | 2 VGAM-1.1-10/VGAM/R/vglm.control.q | 2 VGAM-1.1-10/VGAM/R/vglm.fit.q | 2 VGAM-1.1-10/VGAM/R/vlm.R | 2 VGAM-1.1-10/VGAM/R/vlm.wfit.q | 10 VGAM-1.1-10/VGAM/R/vsmooth.spline.q | 2 VGAM-1.1-10/VGAM/R/wald0.R | 2 VGAM-1.1-10/VGAM/demo/binom2.or.R | 30 VGAM-1.1-10/VGAM/demo/cqo.R | 71 VGAM-1.1-10/VGAM/demo/distributions.R | 8 VGAM-1.1-10/VGAM/demo/lmsqreg.R | 31 VGAM-1.1-10/VGAM/demo/vgam.R | 20 VGAM-1.1-10/VGAM/demo/zipoisson.R | 33 VGAM-1.1-10/VGAM/man/CM.equid.Rd |only VGAM-1.1-10/VGAM/man/Coef.qrrvglm-class.Rd | 1 VGAM-1.1-10/VGAM/man/Coef.qrrvglm.Rd | 1 VGAM-1.1-10/VGAM/man/CommonVGAMffArguments.Rd | 1033 +++++--- VGAM-1.1-10/VGAM/man/Links.Rd | 235 + VGAM-1.1-10/VGAM/man/QvarUC.Rd | 2 VGAM-1.1-10/VGAM/man/Trunc.Rd | 5 VGAM-1.1-10/VGAM/man/UtilitiesVGAM.Rd | 4 VGAM-1.1-10/VGAM/man/VGAM-package.Rd | 215 + VGAM-1.1-10/VGAM/man/acat.Rd | 15 VGAM-1.1-10/VGAM/man/alogitlink.Rd |only VGAM-1.1-10/VGAM/man/alteredvglm.Rd | 4 VGAM-1.1-10/VGAM/man/asinlink.Rd |only VGAM-1.1-10/VGAM/man/betabinomUC.Rd | 1 VGAM-1.1-10/VGAM/man/betabinomial.Rd | 90 VGAM-1.1-10/VGAM/man/betabinomialff.Rd | 16 VGAM-1.1-10/VGAM/man/biclaytoncopUC.Rd | 224 - VGAM-1.1-10/VGAM/man/binomialff.Rd | 8 VGAM-1.1-10/VGAM/man/biplot-methods.Rd | 7 VGAM-1.1-10/VGAM/man/bistudentt.Rd | 4 VGAM-1.1-10/VGAM/man/calibrate.qrrvglm.Rd | 1 VGAM-1.1-10/VGAM/man/calibrate.qrrvglm.control.Rd | 2 VGAM-1.1-10/VGAM/man/calibrate.rrvglm.control.Rd | 1 VGAM-1.1-10/VGAM/man/cao.Rd | 1 VGAM-1.1-10/VGAM/man/cao.control.Rd | 2 VGAM-1.1-10/VGAM/man/chisq.Rd | 36 VGAM-1.1-10/VGAM/man/clogloglink.Rd | 82 VGAM-1.1-10/VGAM/man/constraints.Rd | 2 VGAM-1.1-10/VGAM/man/cops.Rd | 33 VGAM-1.1-10/VGAM/man/cratio.Rd | 13 VGAM-1.1-10/VGAM/man/cumulative.Rd | 205 + VGAM-1.1-10/VGAM/man/deplot.lmscreg.Rd | 7 VGAM-1.1-10/VGAM/man/dgaitdplot.Rd | 162 - VGAM-1.1-10/VGAM/man/extbetabinomUC.Rd |only VGAM-1.1-10/VGAM/man/extbetabinomial.Rd |only VGAM-1.1-10/VGAM/man/foldsqrtlink.Rd | 135 - VGAM-1.1-10/VGAM/man/gaitdbinomUC.Rd | 4 VGAM-1.1-10/VGAM/man/gaitdlog.Rd | 4 VGAM-1.1-10/VGAM/man/gaitdlogUC.Rd | 5 VGAM-1.1-10/VGAM/man/gaitdnbinomUC.Rd | 4 VGAM-1.1-10/VGAM/man/gaitdnbinomial.Rd | 5 VGAM-1.1-10/VGAM/man/gaitdpoisUC.Rd | 4 VGAM-1.1-10/VGAM/man/gaitdpoisson.Rd | 5 VGAM-1.1-10/VGAM/man/gaitdzeta.Rd | 4 VGAM-1.1-10/VGAM/man/gaitdzetaUC.Rd | 5 VGAM-1.1-10/VGAM/man/gamma2.Rd | 4 VGAM-1.1-10/VGAM/man/garma.Rd | 4 VGAM-1.1-10/VGAM/man/genpoisson1.Rd | 117 VGAM-1.1-10/VGAM/man/genpoisson2.Rd | 119 VGAM-1.1-10/VGAM/man/gensh.Rd |only VGAM-1.1-10/VGAM/man/genshUC.Rd |only VGAM-1.1-10/VGAM/man/guplot.Rd | 3 VGAM-1.1-10/VGAM/man/hdeff.Rd | 10 VGAM-1.1-10/VGAM/man/hdeffsev.Rd | 1 VGAM-1.1-10/VGAM/man/hypersecant.Rd | 1 VGAM-1.1-10/VGAM/man/logistic.Rd | 1 VGAM-1.1-10/VGAM/man/logitlink.Rd | 9 VGAM-1.1-10/VGAM/man/loglaplace.Rd | 2 VGAM-1.1-10/VGAM/man/logofflink.Rd | 50 VGAM-1.1-10/VGAM/man/lvplot.Rd | 3 VGAM-1.1-10/VGAM/man/lvplot.qrrvglm.Rd | 6 VGAM-1.1-10/VGAM/man/lvplot.rrvglm.Rd | 21 VGAM-1.1-10/VGAM/man/meplot.Rd | 3 VGAM-1.1-10/VGAM/man/model.matrixqrrvglm.Rd | 2 VGAM-1.1-10/VGAM/man/multinomial.Rd | 130 - VGAM-1.1-10/VGAM/man/nakagami.Rd | 2 VGAM-1.1-10/VGAM/man/negbinomial.Rd | 39 VGAM-1.1-10/VGAM/man/notdocumentedyet.Rd | 32 VGAM-1.1-10/VGAM/man/persp.qrrvglm.Rd | 3 VGAM-1.1-10/VGAM/man/plotdeplot.lmscreg.Rd | 5 VGAM-1.1-10/VGAM/man/plotdgaitd.Rd | 14 VGAM-1.1-10/VGAM/man/plotqrrvglm.Rd | 6 VGAM-1.1-10/VGAM/man/plotqtplot.lmscreg.Rd | 8 VGAM-1.1-10/VGAM/man/plotrcim0.Rd | 6 VGAM-1.1-10/VGAM/man/plotvgam.Rd | 3 VGAM-1.1-10/VGAM/man/plotvgam.control.Rd | 24 VGAM-1.1-10/VGAM/man/plotvglm.Rd | 5 VGAM-1.1-10/VGAM/man/predictqrrvglm.Rd | 1 VGAM-1.1-10/VGAM/man/predictvglm.Rd | 44 VGAM-1.1-10/VGAM/man/profilevglm.Rd | 52 VGAM-1.1-10/VGAM/man/propodds.Rd | 18 VGAM-1.1-10/VGAM/man/prplot.Rd | 6 VGAM-1.1-10/VGAM/man/qrrvglm.control.Rd | 5 VGAM-1.1-10/VGAM/man/qtplot.gumbel.Rd | 5 VGAM-1.1-10/VGAM/man/qtplot.lmscreg.Rd | 5 VGAM-1.1-10/VGAM/man/residualsvglm.Rd | 2 VGAM-1.1-10/VGAM/man/rlplot.gevff.Rd | 5 VGAM-1.1-10/VGAM/man/rrvglm-class.Rd | 28 VGAM-1.1-10/VGAM/man/rrvglm.Rd | 129 - VGAM-1.1-10/VGAM/man/rrvglm.control.Rd | 413 ++- VGAM-1.1-10/VGAM/man/rrvglm.optim.control.Rd | 2 VGAM-1.1-10/VGAM/man/sinmad.Rd | 24 VGAM-1.1-10/VGAM/man/sloglink.Rd |only VGAM-1.1-10/VGAM/man/specialsvglm.Rd | 6 VGAM-1.1-10/VGAM/man/spikeplot.Rd | 8 VGAM-1.1-10/VGAM/man/sratio.Rd | 14 VGAM-1.1-10/VGAM/man/summarydrrvglm.Rd |only VGAM-1.1-10/VGAM/man/summaryvglm.Rd | 1 VGAM-1.1-10/VGAM/man/topple.Rd | 7 VGAM-1.1-10/VGAM/man/trplot.Rd | 3 VGAM-1.1-10/VGAM/man/trplot.qrrvglm.Rd | 6 VGAM-1.1-10/VGAM/man/ucberk.Rd | 2 VGAM-1.1-10/VGAM/man/undocumented-methods.Rd | 19 VGAM-1.1-10/VGAM/man/uninormal.Rd | 11 VGAM-1.1-10/VGAM/man/vcovvlm.Rd | 51 VGAM-1.1-10/VGAM/man/vgam-class.Rd | 1 VGAM-1.1-10/VGAM/man/vgam.Rd | 2 VGAM-1.1-10/VGAM/man/vgam.control.Rd | 18 VGAM-1.1-10/VGAM/man/vglm-class.Rd | 1 VGAM-1.1-10/VGAM/man/vglm.Rd | 2 VGAM-1.1-10/VGAM/man/vglm.control.Rd | 5 VGAM-1.1-10/VGAM/man/vglmff-class.Rd | 1 VGAM-1.1-10/VGAM/man/vplot.profile.Rd | 3 VGAM-1.1-10/VGAM/man/zeta.Rd | 2 VGAM-1.1-10/VGAM/man/zetaUC.Rd | 4 VGAM-1.1-10/VGAM/man/zipoisson.Rd | 26 VGAM-1.1-10/VGAM/src/rgam.f | 11 VGAM-1.1-10/VGAM/src/vgam.f | 8 VGAM-1.1-9/VGAM/man/gordlink.Rd |only VGAM-1.1-9/VGAM/man/nbordlink.Rd |only VGAM-1.1-9/VGAM/man/pordlink.Rd |only 233 files changed, 9013 insertions(+), 8066 deletions(-)