Title: Causal Mediation Analysis Using Weighting Approach
Description: We implement causal mediation analysis using the methods proposed by Hong (2010) and Hong, Deutsch & Hill (2015) <doi:10.3102/1076998615583902>. It allows the estimation and hypothesis testing of causal mediation effects through ratio of mediator probability weights (RMPW). This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. We also implement a sensitivity analysis by extending the RMPW method to assess potential bias in the presence of omitted pretreatment or posttreatment covariates. The sensitivity analysis strategy was proposed by Hong, Qin, and Yang (2018) <doi:10.3102/1076998617749561>.
Author: Xu Qin, Guanglei Hong, and Fan Yang
Maintainer: Xu Qin <xuqin@uchicago.edu>
Diff between rmpw versions 0.0.4 dated 2018-07-18 and 0.0.5 dated 2024-03-05
DESCRIPTION | 10 +-- MD5 | 12 ++-- R/rmpw.R | 134 ++++++++++++++++++++++++++++++------------------ build/partial.rdb |binary man/rmpw.Rd | 33 +++++------ man/sensitivity.Rd | 13 ++-- man/sensitivity.plot.Rd | 21 +++---- 7 files changed, 126 insertions(+), 97 deletions(-)
Title: R Commander Plug-in for Dichotomous Choice Contingent Valuation
Description: Adds menu items to the R Commander for parametric analysis of dichotomous choice contingent valuation (DCCV) data. CV is a question-based survey method to elicit individuals' preferences for goods and services. This package depends on functions regarding parametric DCCV analysis in the package DCchoice. See Carson and Hanemann (2005) <doi:10.1016/S1574-0099(05)02017-6> for DCCV.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.DCCV versions 0.1-3 dated 2023-12-06 and 0.1-4 dated 2024-03-05
DESCRIPTION | 12 ++++---- MD5 | 13 +++++---- NEWS | 5 +++ R/RcmdrPlugin.DCCV.R | 56 ++++++++++++++++++++-------------------- inst/etc/menus.txt | 6 ++-- man/RcmdrPlugin.DCCV-package.Rd | 28 ++++++++------------ man/dccvModel.Rd |only man/dccvPlot.Rd |only man/dccvWtp.Rd |only 9 files changed, 62 insertions(+), 58 deletions(-)
More information about RcmdrPlugin.DCCV at CRAN
Permanent link
Title: Simulation-Based Sensitivity Analysis for Causal Mediation
Studies
Description: Simulation-based sensitivity analysis for causal mediation studies. It numerically and graphically evaluates the sensitivity of causal mediation analysis results
to the presence of unmeasured pretreatment confounding. The proposed method has primary advantages over existing methods.
First, using an unmeasured pretreatment confounder conditional associations with the treatment, mediator, and outcome as
sensitivity parameters, the method enables users to intuitively assess sensitivity in reference to prior knowledge about the
strength of a potential unmeasured pretreatment confounder. Second, the method accurately reflects the influence of unmeasured
pretreatment confounding on the efficiency of estimation of the causal effects. Third, the method can be implemented in
different causal mediation analysis approaches, including regression-based, simulation-based, and propensity score-based
methods. It is applicable to both randomized experiments and observational studies.
Author: Xu Qin and Fan Yang
Maintainer: Xu Qin <xuqin@pitt.edu>
Diff between mediationsens versions 0.0.2 dated 2020-06-14 and 0.0.3 dated 2024-03-05
DESCRIPTION | 10 +-- MD5 | 6 +- R/mediationsens.R | 158 ++++++++++++++++++++++++++++++++++-------------------- man/sens.Rd | 14 ++-- 4 files changed, 116 insertions(+), 72 deletions(-)
Title: Simulation of Diffusion Processes
Description: It provides users with a wide range of tools to simulate, estimate, analyze, and visualize the dynamics of stochastic differential systems in both forms Ito and Stratonovich. Statistical analysis with parallel Monte Carlo and moment equations methods of SDEs <doi:10.18637/jss.v096.i02>. Enabled many searchers in different domains to use these equations to modeling practical problems in financial and actuarial modeling and other areas of application, e.g., modeling and simulate of first passage time problem in shallow water using the attractive center (Boukhetala K, 1996) ISBN:1-56252-342-2.
Author: Arsalane Chouaib Guidoum [cre, aut]
,
Kamal Boukhetala [aut]
Maintainer: Arsalane Chouaib Guidoum <acguidoum@univ-tam.dz>
Diff between Sim.DiffProc versions 4.8 dated 2020-11-08 and 4.9 dated 2024-03-05
DESCRIPTION | 18 MD5 | 120 ++--- R/ABM.R | 8 R/BB.R | 8 R/BM.R | 8 R/Euler.R | 8 R/GBM.R | 8 R/HWV.R | 8 R/Heun.R | 8 R/MCM.sde.R | 18 R/MEM.sde.r | 8 R/Milstein.R | 8 R/OU.R | 8 R/PredCorr.R | 8 R/RK.R | 8 R/SMilstein.R | 8 R/STS.R | 8 R/Tex.sde.r | 36 - R/bridgesde.R | 8 R/dsde.r | 36 - R/fitsde.R | 15 R/ftpsde.R | 8 R/rsde.R | 20 R/snssde.R | 8 R/st.int.R | 9 R/utils.R | 8 R/zzz.r | 10 README.md | 160 ++----- build/vignette.rds |binary inst/CITATION | 2 inst/NEWS.Rd | 7 inst/doc/bridgesde.Rmd | 4 inst/doc/bridgesde.html | 555 +++++++++++++++----------- inst/doc/fitsde.R | 12 inst/doc/fitsde.Rmd | 6 inst/doc/fitsde.html | 738 ++++++++++++++++++++--------------- inst/doc/fptsde.Rmd | 4 inst/doc/fptsde.html | 671 +++++++++++++++++-------------- inst/doc/mcmsde.Rmd | 7 inst/doc/mcmsde.html | 507 ++++++++++++------------ inst/doc/sdetotex.Rmd | 6 inst/doc/sdetotex.html | 370 +++++++++-------- inst/doc/snssde.Rmd | 6 inst/doc/snssde.html | 924 +++++++++++++++++++++++++++----------------- man/Sim.DiffProc-package.Rd | 10 man/fptsde1d.Rd | 4 man/fptsde2d.Rd | 4 man/fptsde3d.Rd | 4 man/rsde1d.Rd | 4 man/rsde2d.Rd | 4 man/rsde3d.Rd | 4 tests/bridgesde.R | 2 tests/fptsde.R | 2 tests/rsde.R | 2 tests/snssde.R | 4 vignettes/bridgesde.Rmd | 4 vignettes/fitsde.Rmd | 6 vignettes/fptsde.Rmd | 4 vignettes/mcmsde.Rmd | 7 vignettes/sdetotex.Rmd | 6 vignettes/snssde.Rmd | 6 61 files changed, 2511 insertions(+), 1971 deletions(-)
Title: Designing and Weighting Survey Samples
Description: Functions and datasets to support Valliant, Dever, and Kreuter (2018), <doi:10.1007/978-3-319-93632-1>, "Practical Tools for Designing and Weighting Survey Samples". Contains functions for sample size calculation for survey samples using stratified or clustered one-, two-, and three-stage sample designs, and single-stage audit sample designs. Functions are included that will group geographic units accounting for distances apart and measures of size. Other functions compute variance components for multistage designs and sample sizes in two-phase designs. A number of example data sets are included.
Author: Richard Valliant [aut, cre],
Jill A. Dever [ctb],
Frauke Kreuter [ctb],
George Zipf [aut]
Maintainer: Richard Valliant <valliant@umich.edu>
Diff between PracTools versions 1.4.2 dated 2023-12-05 and 1.4.3 dated 2024-03-05
DESCRIPTION | 8 +-- MD5 | 80 ++++++++++++++++++------------------ NAMESPACE | 12 +++-- NEWS.md | 6 ++ R/nPPS.R |only R/unitVar.R |only build/vignette.rds |binary data/Domainy1y2.RData |binary data/MDarea.popA.RData |binary data/TPV.RData |binary data/Test_Data_US.RData |binary data/ThirdGrade.RData |binary data/hospital.RData |binary data/labor.RData |binary data/mibrfss.RData |binary data/nhis.RData |binary data/nhis.large.RData |binary data/nhispart.RData |binary data/smho.N874.RData |binary data/smho98.RData |binary inst/doc/Design-effects.html | 4 - inst/doc/Distance-and-MOS-PSUs.html | 4 - inst/doc/Singlestage-samsize.html | 4 - inst/doc/Varcomps-multistage.html | 4 - man/BW2stagePPSe.Rd | 1 man/BW2stageSRS.Rd | 1 man/BW3stagePPS.Rd | 1 man/NRFUopt.Rd | 1 man/clusOpt2.Rd | 1 man/clusOpt2fixedPSU.Rd | 1 man/gamEst.Rd | 3 - man/gammaFit.Rd | 3 - man/nCont.Rd | 6 -- man/nDep2sam.Rd | 5 -- man/nDomain.Rd | 5 -- man/nPPS.Rd |only man/nProp.Rd | 4 - man/nProp2sam.Rd | 1 man/nPropMoe.Rd | 4 - man/nhispart.Rd | 1 man/smho.N874.Rd | 2 man/unitVar.Rd |only man/wtdvar.Rd | 2 43 files changed, 68 insertions(+), 96 deletions(-)
Title: 'NoSQL' Database Connector
Description: Simplified document database access and manipulation,
providing a common API across supported 'NoSQL' databases
'Elasticsearch', 'CouchDB', 'MongoDB' as well as
'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Author: Ralf Herold [aut, cre] ,
Scott Chamberlain [aut] ,
Rich FitzJohn [aut],
Jeroen Ooms [aut]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between nodbi versions 0.10.3 dated 2024-03-03 and 0.10.4 dated 2024-03-05
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS.md | 5 ++ R/query.R | 12 +++--- inst/doc/nodbi-overview.html | 76 ++++++++++++++++--------------------------- 5 files changed, 49 insertions(+), 58 deletions(-)
Title: Large Scale Single Mediator Hypothesis Testing
Description: A collection of methods for large scale single mediator hypothesis
testing. The six included methods for testing the mediation effect are Sobel's
test, Max P test, joint significance test under the composite null hypothesis,
high dimensional mediation testing, divide-aggregate composite null test,
and Sobel's test under the composite null hypothesis. Du et al (2023)
<doi:10.1002/gepi.22510>.
Author: Jiacong Du [aut],
Michael Kleinsasser [cre]
Maintainer: Michael Kleinsasser <mkleinsa@umich.edu>
Diff between medScan versions 1.0.1 dated 2022-10-05 and 1.0.2 dated 2024-03-05
DESCRIPTION | 14 ++++++-------- MD5 | 8 ++++---- R/MedScan.R | 21 +++++++++++++-------- README.md | 5 +---- man/medScan.Rd | 17 +++++++++++------ 5 files changed, 35 insertions(+), 30 deletions(-)
Title: Two-Dimensional FPCA, Marginal FPCA, and Product FPCA for
Repeated Functional Data
Description: Provides an implementation of two-dimensional functional principal component analysis (FPCA), Marginal FPCA, and Product FPCA for repeated functional data. Marginal and Product FPCA implementations are done for both dense and sparsely observed functional data.
References: Chen, K., Delicado, P., & Müller, H. G. (2017) <doi:10.1111/rssb.12160>.
Chen, K., & Müller, H. G. (2012) <doi:10.1080/01621459.2012.734196>.
Hall, P., Müller, H.G. and Wang, J.L. (2006) <doi:10.1214/009053606000000272>.
Yao, F., Müller, H. G., & Wang, J. L. (2005) <doi:10.1198/016214504000001745>.
Author: Poorbita Kundu [aut, cre],
Changbo Zhu [aut],
Kehui Chen [aut],
Pedro Delicado [aut],
Su I Iao [aut],
Hang Zhou [aut],
Han Chen [aut],
Muqing Cui [aut],
Hans-Georg Mueller [cph, ths, aut]
Maintainer: Poorbita Kundu <pkundu@ucdavis.edu>
Diff between fdarep versions 0.1.0 dated 2024-02-28 and 0.1.1 dated 2024-03-05
DESCRIPTION | 16 ++++++++-------- MD5 | 6 +++--- R/pkgname.R | 2 +- man/fdarep.Rd | 2 +- 4 files changed, 13 insertions(+), 13 deletions(-)
Title: Summarise Patient-Level Drug Utilisation in Data Mapped to the
OMOP Common Data Model
Description: Summarise patient-level drug utilisation cohorts using data mapped
to the Observational Medical Outcomes Partnership (OMOP) common data model.
New users and prevalent users cohorts can be generated and their
characteristics, indication and drug use summarised.
Author: Marti Catala [aut, cre] ,
Mike Du [aut] ,
Yuchen Guo [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [ctb] ,
Xintong Li [ctb] ,
Marta Alcalde-Herraiz [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between DrugUtilisation versions 0.5.1 dated 2024-02-28 and 0.5.2 dated 2024-03-05
DESCRIPTION | 6 - MD5 | 32 +++---- R/addDrugUse.R | 1 R/cohortUtilities.R | 7 + R/readConceptList.R | 1 inst/doc/a01_introCreateCohort.html | 4 inst/doc/a02_scalingOfInstantiateCohorts.html | 4 inst/doc/a03_addIndications-example.html | 8 - inst/doc/a04_addDrugInfo.html | 117 +++++++++++++------------- inst/doc/a05_treatmentDiscontinuation.html | 4 inst/doc/a06_treatmentSummary.html | 72 ++++++++-------- inst/doc/a07_characteriseACohort.html | 4 inst/doc/routePatternDose.html | 79 ++++++++--------- tests/testthat/test-dailyDose.R | 1 tests/testthat/test-drugUse.R | 2 tests/testthat/test-indication.R | 6 - tests/testthat/test-summariseTreatment.R | 2 17 files changed, 174 insertions(+), 176 deletions(-)
More information about DrugUtilisation at CRAN
Permanent link
Title: Import from and Export to Amiga Disk Files
Description: Amiga Disk Files (ADF) are virtual
representations of 3.5 inch floppy disks for the
Commodore Amiga. Most disk drives from other systems
(including modern drives) are not able to read these
disks. To be able to emulate this system, the ADF
format was created. This package enables you to read
ADF files and import and export files from and to such
virtual DOS-formatted disks.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between adfExplorer versions 0.1.6 dated 2021-09-05 and 0.1.8 dated 2024-03-05
adfExplorer-0.1.6/adfExplorer/NEWS |only adfExplorer-0.1.6/adfExplorer/man/adf.file.exists.Rd |only adfExplorer-0.1.8/adfExplorer/DESCRIPTION | 16 adfExplorer-0.1.8/adfExplorer/MD5 | 58 - adfExplorer-0.1.8/adfExplorer/NAMESPACE | 73 - adfExplorer-0.1.8/adfExplorer/NEWS.md |only adfExplorer-0.1.8/adfExplorer/R/00constants.r | 2 adfExplorer-0.1.8/adfExplorer/R/01genericSupport.r | 127 +-- adfExplorer-0.1.8/adfExplorer/R/02amigaDiskBasics.r | 200 ++-- adfExplorer-0.1.8/adfExplorer/R/03amigaBlockBasics.r | 28 adfExplorer-0.1.8/adfExplorer/R/04fileOperations.r | 386 ++++++++- adfExplorer-0.1.8/adfExplorer/R/05fileRemove.r | 22 adfExplorer-0.1.8/adfExplorer/R/adfExplorer-package.r |only adfExplorer-0.1.8/adfExplorer/R/data.r | 16 adfExplorer-0.1.8/adfExplorer/README.md |only adfExplorer-0.1.8/adfExplorer/build/vignette.rds |binary adfExplorer-0.1.8/adfExplorer/inst/doc/amigaDiskFiles.R | 11 adfExplorer-0.1.8/adfExplorer/inst/doc/amigaDiskFiles.Rmd | 41 - adfExplorer-0.1.8/adfExplorer/inst/doc/amigaDiskFiles.html | 527 ++++++++----- adfExplorer-0.1.8/adfExplorer/man/adf.example.Rd | 6 adfExplorer-0.1.8/adfExplorer/man/adf.exists.Rd |only adfExplorer-0.1.8/adfExplorer/man/adf.file.remove.Rd | 4 adfExplorer-0.1.8/adfExplorer/man/adfExplorer-package.Rd |only adfExplorer-0.1.8/adfExplorer/man/amigaBlock-class.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/amigaDisk-class.Rd | 6 adfExplorer-0.1.8/adfExplorer/man/amigaIntToRaw.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/boot.block.code.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/file.info.Rd |only adfExplorer-0.1.8/adfExplorer/man/get.adf.file.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/get.blockID.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/is.bootable.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/list.adf.files.Rd | 2 adfExplorer-0.1.8/adfExplorer/man/rawToBitmap.Rd | 2 adfExplorer-0.1.8/adfExplorer/vignettes/amigaDiskFiles.Rmd | 41 - 34 files changed, 1038 insertions(+), 542 deletions(-)
Title: Analysis of Archaeological Mortality Data
Description: A collection of functions for the analysis of archaeological mortality
data (on the topic see e.g. Chamberlain 2006
<https://books.google.de/books?id=nG5FoO_becAC&lpg=PA27&ots=LG0b_xrx6O&dq=life%20table%20archaeology&pg=PA27#v=onepage&q&f=false>).
It takes demographic data in different formats and displays the result in a standard life table
as well as plots the relevant indices (percentage of deaths, survivorship, probability of death, life expectancy, percentage of population).
Author: Nils Mueller-Scheessel [aut, cre, cph],
Martin Hinz [aut],
Clemens Schmid [aut],
Christoph Rinne [aut],
Daniel Knitter [aut],
Wolfgang Hamer [aut],
Dirk Seidensticker [aut],
Franziska Faupel [aut],
Carolin Tietze [aut],
Nicole Grunert [aut]
Maintainer: Nils Mueller-Scheessel <nils.mueller-scheessel@ufg.uni-kiel.de>
Diff between mortAAR versions 1.1.5 dated 2023-08-27 and 1.1.6 dated 2024-03-05
DESCRIPTION | 10 ++++--- MD5 | 34 +++++++++++++-------------- NEWS.md | 7 +++++ R/class_functions.R | 2 - R/input_functions.R | 1 R/plot_functions.R | 4 +-- R/representativity.R | 4 +-- R/system_functions.R | 2 - build/partial.rdb |binary inst/REFERENCES.bib | 2 - inst/doc/mortAAR_vignette-1.html | 10 ++++--- inst/doc/mortAAR_vignette_extended.html | 6 ++-- inst/doc/mortAAR_vignette_lt_correction.Rmd | 4 +-- inst/doc/mortAAR_vignette_lt_correction.html | 23 +++++++++--------- man/mortAAR-package.Rd | 8 ++++++ man/mortaar_life_table.Rd | 2 - tests/testthat/_snaps/representativity.md | 4 +-- vignettes/mortAAR_vignette_lt_correction.Rmd | 4 +-- 18 files changed, 74 insertions(+), 53 deletions(-)
Title: 'Pubmed' Toolkit
Description: Provides various functions for retrieving and
interpreting information from 'Pubmed' via the API,
<https://www.ncbi.nlm.nih.gov/home/develop/api/>.
Author: Benjamin Gregory Carlisle [aut, cre]
Maintainer: Benjamin Gregory Carlisle <murph@bgcarlisle.com>
Diff between pubmedtk versions 1.0.3 dated 2024-02-27 and 1.0.4 dated 2024-03-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 13 +++++++++++++ R/get_pmids_from_searches.R | 26 ++++++++++++++++++-------- R/intersection_check.R | 35 ++++++++++++++++++++++------------- man/intersection_check.Rd | 12 +++++++++++- 6 files changed, 73 insertions(+), 31 deletions(-)
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
as well as a number of specialised functions to process presences and pseudoabsences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 0.9.3 dated 2024-01-17 and 0.9.4 dated 2024-03-05
DESCRIPTION | 6 - MD5 | 38 ++++++----- NEWS.md | 7 ++ R/add_member.R | 21 ++++-- R/boyce_cont.R | 6 - R/grid_cellsize.R | 4 - R/grid_offset.R | 4 - R/kap_max.R | 6 - R/misc.R |only R/predict_simple_ensemble.R | 52 +++++++++------ R/recipes_sf_methods.R | 10 +-- R/tss_max.R | 5 - inst/doc/a0_tidysdm_overview.R | 1 inst/doc/a0_tidysdm_overview.Rmd | 1 inst/doc/a0_tidysdm_overview.html | 85 +++++++++++++------------- inst/doc/a1_palaeodata_application.html | 16 ++-- inst/doc/a2_tidymodels_additions.html | 18 ++--- inst/doc/a3_troubleshooting.html | 34 +++++----- tests/testthat/Rplots.pdf |only tests/testthat/test_predict_simple_ensemble.R | 4 + vignettes/a0_tidysdm_overview.Rmd | 1 21 files changed, 178 insertions(+), 141 deletions(-)
Title: Plotting Tools for Anyone Working in Deep Time
Description: Extends the functionality of other plotting packages like
'ggplot2' and 'lattice' to help facilitate the plotting of data over long time
intervals, including, but not limited to, geological, evolutionary, and ecological
data. The primary goal of 'deeptime' is to enable users to add highly customizable
timescales to their visualizations. Other functions are also included to assist
with other areas of deep time visualization.
Author: William Gearty [aut, cre]
Maintainer: William Gearty <willgearty@gmail.com>
Diff between deeptime versions 1.0.1 dated 2023-02-16 and 1.1.0 dated 2024-03-05
DESCRIPTION | 14 MD5 | 229 NAMESPACE | 23 NEWS.md | 229 R/coord_geo.R | 207 R/coord_geo_polar.R | 304 R/coord_geo_radial.R |only R/coord_trans_flip.R | 7 R/coord_trans_xy.R | 342 R/facet_color.R |only R/ggarrange2.R | 2 R/gggeo_scale.R | 127 R/points_range.R |only R/scales.R | 7 R/zzz.R | 22 README.md | 1 build/vignette.rds |binary inst/doc/coord.R | 2 inst/doc/coord.html | 78 inst/doc/coord_geo.R | 11 inst/doc/coord_geo.Rmd | 12 inst/doc/coord_geo.html | 267 inst/doc/ggarrange2.R | 2 inst/doc/ggarrange2.Rmd | 2 inst/doc/ggarrange2.html | 74 inst/doc/phylogenies.R | 35 inst/doc/phylogenies.Rmd | 36 inst/doc/phylogenies.html | 115 inst/doc/time.R |only inst/doc/time.Rmd |only inst/doc/time.html |only inst/doc/traits.R | 5 inst/doc/traits.Rmd | 1 inst/doc/traits.html | 151 man/coord_geo.Rd | 62 man/coord_geo_polar.Rd | 85 man/coord_geo_radial.Rd |only man/coord_trans_xy.Rd | 22 man/facet_grid_color.Rd |only man/facet_wrap_color.Rd |only man/geom_points_range.Rd |only man/scale_geo.Rd | 191 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/coord_geo/custom-discrete-scale-new.svg | 57 tests/testthat/_snaps/coord_geo/custom-discrete-scale-old.svg | 58 tests/testthat/_snaps/coord_geo/geom-fit-text-new.svg | 38 tests/testthat/_snaps/coord_geo/geom-fit-text-old.svg | 34 tests/testthat/_snaps/coord_geo/scale-on-all-facets-new.svg | 114 tests/testthat/_snaps/coord_geo/scale-on-all-facets-old.svg | 102 tests/testthat/_snaps/coord_geo/scale-on-discrete-axis-new.svg | 53 tests/testthat/_snaps/coord_geo/scale-on-discrete-axis-old.svg | 54 tests/testthat/_snaps/coord_geo/scale-on-fossil-ggtree-new.svg | 98 tests/testthat/_snaps/coord_geo/scale-on-fossil-ggtree-old.svg | 96 tests/testthat/_snaps/coord_geo/scale-on-ggtree-new.svg | 20 tests/testthat/_snaps/coord_geo/scale-on-ggtree-old.svg | 18 tests/testthat/_snaps/coord_geo/scale-on-only-one-facet-new.svg | 42 tests/testthat/_snaps/coord_geo/scale-on-only-one-facet-old.svg | 34 tests/testthat/_snaps/coord_geo/scales-on-different-sides1-new.svg | 414 tests/testthat/_snaps/coord_geo/scales-on-different-sides1-old.svg | 580 - tests/testthat/_snaps/coord_geo/scales-on-different-sides2-new.svg | 124 tests/testthat/_snaps/coord_geo/scales-on-different-sides2-old.svg | 506 - tests/testthat/_snaps/coord_geo/stacked-scales-new.svg | 48 tests/testthat/_snaps/coord_geo/stacked-scales-old.svg | 44 tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-new.svg | 102 tests/testthat/_snaps/coord_geo_polar/coord-geo-polar-old.svg | 86 tests/testthat/_snaps/coord_geo_polar/scale-on-fossil-ggtree-new.svg | 114 tests/testthat/_snaps/coord_geo_polar/scale-on-fossil-ggtree-old.svg | 98 tests/testthat/_snaps/coord_geo_polar/scale-on-fossil-ggtree-with-labels-new.svg |only tests/testthat/_snaps/coord_geo_polar/scale-on-fossil-ggtree-with-labels-old.svg |only tests/testthat/_snaps/coord_geo_polar/stacked-scales-new.svg | 140 tests/testthat/_snaps/coord_geo_polar/stacked-scales-old.svg | 124 tests/testthat/_snaps/coord_geo_radial |only tests/testthat/_snaps/coord_trans_flip/coord-trans-flip-with-different-transforms-new.svg |only tests/testthat/_snaps/coord_trans_xy/coord-trans-xy-with-expansion-new.svg | 44 tests/testthat/_snaps/coord_trans_xy/coord-trans-xy-with-expansion-old.svg | 30 tests/testthat/_snaps/coord_trans_xy/coord-trans-xy-without-expansion-new.svg | 38 tests/testthat/_snaps/coord_trans_xy/coord-trans-xy-without-expansion-old.svg | 645 - 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tests/testthat/_snaps/ggarrange2/ggarrange2-with-layout-new.svg | 2298 ++--- tests/testthat/_snaps/gggeo_scale/gggeo-scale-left-and-right-new.svg | 908 +- tests/testthat/_snaps/gggeo_scale/gggeo-scale-left-and-right-old.svg | 132 tests/testthat/_snaps/gggeo_scale/gggeo-scale-new.svg | 478 - tests/testthat/_snaps/gggeo_scale/gggeo-scale-old.svg | 34 tests/testthat/_snaps/gggeo_scale/gggeo-scale-top-new.svg | 468 - tests/testthat/_snaps/gggeo_scale/gggeo-scale-top-old.svg | 34 tests/testthat/_snaps/phylomorpho/geom-phylomorpho-new.svg | 20 tests/testthat/_snaps/points_range |only tests/testthat/_snaps/scales/scale-color-geo-new.svg | 61 tests/testthat/_snaps/scales/scale-color-geo-old.svg | 44 tests/testthat/_snaps/scales/scale-discrete-geo-new.svg | 61 tests/testthat/_snaps/scales/scale-discrete-geo-old.svg | 44 tests/testthat/_snaps/scales/scale-fill-geo-new.svg | 22 tests/testthat/setup-data.R | 8 tests/testthat/test-coord_geo.R | 4 tests/testthat/test-coord_geo_polar.R | 44 tests/testthat/test-coord_geo_radial.R |only tests/testthat/test-coord_trans_flip.R | 11 tests/testthat/test-facet_color.R |only tests/testthat/test-ggarrange2.R | 23 tests/testthat/test-points_range.R |only tests/testthat/test-scales.R | 19 vignettes/coord_geo.Rmd | 12 vignettes/ggarrange2.Rmd | 2 vignettes/phylogenies-1.png |only vignettes/phylogenies-2.png |only vignettes/phylogenies.Rmd | 36 vignettes/time.Rmd |only vignettes/traits.Rmd | 1 122 files changed, 10283 insertions(+), 9401 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [ctb] ,
Xintong Li [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 0.6.1 dated 2024-02-21 and 0.6.2 dated 2024-03-05
DESCRIPTION | 6 +- MD5 | 36 +++++++-------- R/addConceptIntersect.R | 8 +-- R/addDemographics.R | 29 ++++++++++-- R/addTableIntersect.R | 6 +- R/formattedTables.R | 6 -- R/summariseCharacteristics.R | 2 R/summariseLargeScaleCharacteristics.R | 7 ++ R/summariseResult.R | 7 ++ inst/doc/addCohortIntersections.html | 4 - inst/doc/addPatientCharacteristics.html | 4 - tests/testthat/test-addCategories.R | 15 ++---- tests/testthat/test-addCohortIntersect.R | 2 tests/testthat/test-addDemographics.R | 36 +++++++++++++++ tests/testthat/test-addInObservation.R | 6 +- tests/testthat/test-class.R | 2 tests/testthat/test-mockPatientProfiles.R | 29 ++++-------- tests/testthat/test-summariseCharacteristics.R | 15 +----- tests/testthat/test-summariseLargeScaleCharacteristics.R | 5 -- 19 files changed, 134 insertions(+), 91 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.25 dated 2023-09-18 and 2.26 dated 2024-03-05
DESCRIPTION | 12 ++++----- MD5 | 32 ++++++++++++------------ NEWS.md | 14 ++++++++++ R/base64.R | 22 ++++++---------- R/html_document_base.R | 7 ++++- R/ioslides_presentation.R | 2 - R/pandoc.R | 2 - R/render.R | 4 +-- R/rmarkdown-package.R | 3 -- R/util.R | 15 ----------- build/vignette.rds |binary inst/doc/lua-filters.html | 6 ++-- man/ioslides_presentation.Rd | 2 - man/rmarkdown-package.Rd | 56 ++++++++++++++++++++++++++++++++++++++++++ tests/testthat/site/PageA.Rmd | 2 - tests/testthat/test-render.R | 9 ++++++ tests/testthat/test-site.R | 12 ++++----- 17 files changed, 133 insertions(+), 67 deletions(-)
Title: Propensity Score Analysis Graphics
Description: A collection of functions that primarily produce graphics to
aid in a Propensity Score Analysis (PSA). Functions include: cat.psa
and box.psa to test balance within strata of categorical and
quantitative covariates, circ.psa for a representation of the
estimated effect size by stratum, loess.psa that provides a graphic
and loess based effect size estimate, and various balance functions
that provide measures of the balance achieved via a PSA in a
categorical covariate.
Author: James Helmreich [aut],
Robert Pruzek [aut],
Jason Bryer [ctb, cre] ,
KuangNan Xiong [ctb]
Maintainer: Jason Bryer <jason@bryer.org>
Diff between PSAgraphics versions 2.1.2 dated 2023-03-21 and 2.1.3 dated 2024-03-05
PSAgraphics-2.1.2/PSAgraphics/man/granova-package.Rd |only PSAgraphics-2.1.3/PSAgraphics/DESCRIPTION | 10 +++++----- PSAgraphics-2.1.3/PSAgraphics/MD5 | 12 ++++++------ PSAgraphics-2.1.3/PSAgraphics/NEWS.md | 4 ++++ PSAgraphics-2.1.3/PSAgraphics/R/PSAgraphics-package.R | 10 +++++----- PSAgraphics-2.1.3/PSAgraphics/R/circ.psa.R | 6 ++++-- PSAgraphics-2.1.3/PSAgraphics/man/PSAgraphics-package.Rd |only PSAgraphics-2.1.3/PSAgraphics/man/circ.psa.Rd | 5 ++++- 8 files changed, 28 insertions(+), 19 deletions(-)
Title: Paws Low-Level Amazon Web Services API
Description: Functions for making low-level API requests to Amazon Web Services
<https://aws.amazon.com>. The functions handle building, signing, and
sending requests, and receiving responses. They are designed to help build
higher-level interfaces to individual services, such as Simple Storage
Service (S3).
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.common versions 0.7.0 dated 2024-01-09 and 0.7.1 dated 2024-03-05
DESCRIPTION | 34 ++++---- MD5 | 66 ++++++++-------- NAMESPACE | 6 + NEWS.md | 7 + R/RcppExports.R | 30 +++++++ R/cache.R | 12 -- R/client.R | 17 ---- R/credential_providers.R | 2 R/credentials.R | 13 +++ R/custom_s3.R | 8 - R/dateutil.R | 12 ++ R/handlers_rest.R | 50 +++++------- R/handlers_restjson.R | 24 +++++ R/idempotency.R | 5 - R/iniutil.R | 6 - R/jsonutil.R | 61 ++++---------- R/paginate.R | 17 ++-- R/populate.R | 9 -- R/queryutil.R | 18 +--- R/request.R | 2 R/signer_v4.R | 2 R/url.R | 131 ++++++++++++++++---------------- R/util.R | 81 +++++++++++-------- man/locate_credentials.Rd |only src/RcppExports.cpp | 63 +++++++++++++++ src/json_escape.cpp |only src/resolve_endpoint.cpp |only src/utils.cpp |only tests/testthat/test_credentials.R | 21 +++++ tests/testthat/test_dateutil.R | 10 +- tests/testthat/test_escape.R | 6 + tests/testthat/test_handlers_ec2query.R | 4 tests/testthat/test_handlers_jsonrpc.R | 4 tests/testthat/test_handlers_restjson.R | 4 tests/testthat/test_paginate.R | 6 - tests/testthat/test_url.R | 11 ++ 36 files changed, 457 insertions(+), 285 deletions(-)
Title: Access and Analyze eBird Status and Trends Data Products
Description: Tools for accessing and analyzing eBird Status and
Trends Data Products
(<https://science.ebird.org/en/status-and-trends>). eBird
(<https://ebird.org/home>) is a global database of bird observations
collected by member of the public. eBird Status and Trends uses these
data to model global bird distributions, abundances, and population trends
at a high spatial and temporal resolution.
Author: Matthew Strimas-Mackey [aut, cre]
,
Shawn Ligocki [aut],
Tom Auer [aut] ,
Daniel Fink [aut] ,
Cornell Lab of Ornithology [cph]
Maintainer: Matthew Strimas-Mackey <mes335@cornell.edu>
Diff between ebirdst versions 3.2022.2 dated 2024-02-23 and 3.2022.3 dated 2024-03-05
DESCRIPTION | 17 ++++++++--------- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/load.R | 6 +----- data/ebirdst_runs.rda |binary inst/doc/applications.Rmd | 10 ++++++---- inst/doc/applications.html | 24 ++++++++++++++---------- man/ebirdst-package.Rd | 1 + vignettes/applications.Rmd | 10 ++++++---- 9 files changed, 49 insertions(+), 40 deletions(-)
Title: Display Idiomatic Code to Construct Most R Objects
Description: Prints code that can be used to recreate R objects. In a
sense it is similar to 'base::dput()' or 'base::deparse()' but
'constructive' strives to use idiomatic constructors.
Author: Antoine Fabri [aut, cre],
Kirill Mueller [ctb]
Maintainer: Antoine Fabri <antoine.fabri@gmail.com>
Diff between constructive versions 0.2.0 dated 2023-11-13 and 0.3.0 dated 2024-03-05
constructive-0.2.0/constructive/tests/testthat/_snaps/s3-ggplot2-Scale.md |only constructive-0.2.0/constructive/tests/testthat/_snaps/s3-ggplot2-ggplot.md |only constructive-0.3.0/constructive/DESCRIPTION | 32 + constructive-0.3.0/constructive/MD5 | 188 +++++----- constructive-0.3.0/constructive/NAMESPACE | 9 constructive-0.3.0/constructive/NEWS.md | 30 + constructive-0.3.0/constructive/R/C_wrappers.R | 14 constructive-0.3.0/constructive/R/construct.R | 88 ++++ constructive-0.3.0/constructive/R/construct_idiomatic.R | 5 constructive-0.3.0/constructive/R/construct_reprex.R |only constructive-0.3.0/constructive/R/constructive-package.R | 4 constructive-0.3.0/constructive/R/deparse_call.R | 102 +++-- constructive-0.3.0/constructive/R/environment_utils.R | 12 constructive-0.3.0/constructive/R/global-options.R |only constructive-0.3.0/constructive/R/inst |only constructive-0.3.0/constructive/R/roxygen2-tags.R | 4 constructive-0.3.0/constructive/R/s3-AsIs.R | 2 constructive-0.3.0/constructive/R/s3-Date.R | 2 constructive-0.3.0/constructive/R/s3-POSIXct.R | 2 constructive-0.3.0/constructive/R/s3-POSIXlt.R | 2 constructive-0.3.0/constructive/R/s3-array.R | 2 constructive-0.3.0/constructive/R/s3-atomic.R | 116 +++--- constructive-0.3.0/constructive/R/s3-constructive_options.R | 2 constructive-0.3.0/constructive/R/s3-data.frame.R | 34 + constructive-0.3.0/constructive/R/s3-data.table.R | 2 constructive-0.3.0/constructive/R/s3-dm.R | 2 constructive-0.3.0/constructive/R/s3-dots.R | 7 constructive-0.3.0/constructive/R/s3-environment.R | 2 constructive-0.3.0/constructive/R/s3-externalptr.R | 4 constructive-0.3.0/constructive/R/s3-factor.R | 2 constructive-0.3.0/constructive/R/s3-formula.R | 6 constructive-0.3.0/constructive/R/s3-function.R | 58 ++- constructive-0.3.0/constructive/R/s3-ggplot2-Layer.R | 2 constructive-0.3.0/constructive/R/s3-ggplot2-Scale.R | 30 + constructive-0.3.0/constructive/R/s3-ggplot2-ggplot.R | 1 constructive-0.3.0/constructive/R/s3-ggplot2-theme.R | 4 constructive-0.3.0/constructive/R/s3-grouped_df.R | 2 constructive-0.3.0/constructive/R/s3-language.R | 2 constructive-0.3.0/constructive/R/s3-list.R | 2 constructive-0.3.0/constructive/R/s3-matrix.R | 2 constructive-0.3.0/constructive/R/s3-mts.R | 2 constructive-0.3.0/constructive/R/s3-numeric_version.R | 6 constructive-0.3.0/constructive/R/s3-ordered.R | 2 constructive-0.3.0/constructive/R/s3-pairlist.R | 2 constructive-0.3.0/constructive/R/s3-quosure.R | 2 constructive-0.3.0/constructive/R/s3-quosures.R | 2 constructive-0.3.0/constructive/R/s3-rowwise_df.R | 2 constructive-0.3.0/constructive/R/s3-tbl_df.R | 4 constructive-0.3.0/constructive/R/s3-ts.R | 2 constructive-0.3.0/constructive/R/s3-vctrs_list_of.R | 2 constructive-0.3.0/constructive/R/s3-weakref.R | 2 constructive-0.3.0/constructive/R/s3_register.R |only constructive-0.3.0/constructive/R/s4-classGeneratorFunction.R | 7 constructive-0.3.0/constructive/R/s4-classPrototypeDef.R | 2 constructive-0.3.0/constructive/R/s4-classRepresentation.R | 2 constructive-0.3.0/constructive/R/s4.R | 2 constructive-0.3.0/constructive/R/utils.R | 19 - constructive-0.3.0/constructive/R/zzz.R | 2 constructive-0.3.0/constructive/inst/doc/User-defined-methods-and-constructors.R | 2 constructive-0.3.0/constructive/inst/doc/User-defined-methods-and-constructors.Rmd | 2 constructive-0.3.0/constructive/inst/doc/User-defined-methods-and-constructors.html | 10 constructive-0.3.0/constructive/man/construct.Rd | 9 constructive-0.3.0/constructive/man/construct_reprex.Rd |only constructive-0.3.0/constructive/man/constructive-global_options.Rd |only constructive-0.3.0/constructive/man/constructive-package.Rd | 5 constructive-0.3.0/constructive/man/deparse_call.Rd | 18 constructive-0.3.0/constructive/man/opts_formula.Rd | 2 constructive-0.3.0/constructive/man/opts_function.Rd | 4 constructive-0.3.0/constructive/man/opts_tbl_df.Rd | 2 constructive-0.3.0/constructive/src/constructive.c | 29 + constructive-0.3.0/constructive/tests/testthat/_snaps/abort.md | 2 constructive-0.3.0/constructive/tests/testthat/_snaps/construct_multi.md | 21 + constructive-0.3.0/constructive/tests/testthat/_snaps/construct_reprex.md |only constructive-0.3.0/constructive/tests/testthat/_snaps/deparse_call.md | 16 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-atomic.md | 52 ++ constructive-0.3.0/constructive/tests/testthat/_snaps/s3-data.frame.md | 5 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-data.table.md | 6 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-dots.md | 8 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-externalptr.md | 11 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-formula.md | 5 constructive-0.3.0/constructive/tests/testthat/_snaps/s3-function.md | 19 - constructive-0.3.0/constructive/tests/testthat/_snaps/s3-ggplot2-Coord.md | 53 -- constructive-0.3.0/constructive/tests/testthat/_snaps/s3-list.md | 8 constructive-0.3.0/constructive/tests/testthat/_snaps/s4.md | 4 constructive-0.3.0/constructive/tests/testthat/test-abort.R | 2 constructive-0.3.0/constructive/tests/testthat/test-construct_multi.R | 10 constructive-0.3.0/constructive/tests/testthat/test-construct_reprex.R |only constructive-0.3.0/constructive/tests/testthat/test-deparse_call.R | 4 constructive-0.3.0/constructive/tests/testthat/test-s3-atomic.R | 18 constructive-0.3.0/constructive/tests/testthat/test-s3-data.frame.R | 2 constructive-0.3.0/constructive/tests/testthat/test-s3-dots.R | 4 constructive-0.3.0/constructive/tests/testthat/test-s3-environment.R | 4 constructive-0.3.0/constructive/tests/testthat/test-s3-externalptr.R | 3 constructive-0.3.0/constructive/tests/testthat/test-s3-formula.R | 1 constructive-0.3.0/constructive/tests/testthat/test-s3-function.R | 5 constructive-0.3.0/constructive/tests/testthat/test-s3-ggplot2-Coord.R | 13 constructive-0.3.0/constructive/tests/testthat/test-s3-ggplot2-Scale.R | 4 constructive-0.3.0/constructive/tests/testthat/test-s3-ggplot2-ggplot.R | 14 constructive-0.3.0/constructive/tests/testthat/test-s3-list.R | 9 constructive-0.3.0/constructive/vignettes/User-defined-methods-and-constructors.Rmd | 2 100 files changed, 869 insertions(+), 359 deletions(-)
Title: ADaM in R Asset Library
Description: A toolbox for programming Clinical Data Interchange Standards
Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R.
ADaM datasets are a mandatory part of any New Drug or Biologics
License Application submitted to the United States Food and Drug
Administration (FDA). Analysis derivations are implemented in
accordance with the "Analysis Data Model Implementation Guide" (CDISC
Analysis Data Model Team, 2021,
<https://www.cdisc.org/standards/foundational/adam>).
Author: Ben Straub [aut, cre],
Stefan Bundfuss [aut],
Jeffrey Dickinson [aut],
Ross Farrugia [aut],
Adam Forys [aut],
G Gayatri [aut],
Daphne Grasselly [aut],
Dinakar Kulkarni [aut],
Edoardo Mancini [aut],
Sadchla Mascary [aut],
Gordon Miller [aut],
Sophie S [...truncated...]
Maintainer: Ben Straub <ben.x.straub@gsk.com>
Diff between admiral versions 1.0.1 dated 2024-02-01 and 1.0.2 dated 2024-03-05
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 4 R/derive_param_tte.R | 11 +- README.md | 36 ++++---- inst/doc/generic.html | 4 inst/templates/ad_adeg.R | 2 tests/testthat/test-derive_param_tte.R | 136 ++++++++++++++++++++++++++++----- 8 files changed, 162 insertions(+), 51 deletions(-)
Title: Taxonomic Name Resolution Service
Description: Provides access to the Taxonomic Name Resolution Service <https://github.com/ojalaquellueva/tnrsapi> through R. The user supplies plant taxonomic names and the package returns resolved taxonomic names along with information on decisions. Optionally, the package can also be used to parse taxonomic names.
Author: Brian Maitner [aut, cre] ,
Brad Boyle [aut],
Paul Efren [ctb]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between TNRS versions 0.3.4 dated 2023-06-13 and 0.3.5 dated 2024-03-05
TNRS-0.3.4/TNRS/tests/fixtures/gnrs_base.yml |only TNRS-0.3.4/TNRS/tests/fixtures/gnrs_citations.yml |only TNRS-0.3.4/TNRS/tests/fixtures/gnrs_sources.yml |only TNRS-0.3.4/TNRS/tests/fixtures/gnrs_version.yml |only TNRS-0.3.4/TNRS/tests/fixtures/tnrs_tropicos.yml |only TNRS-0.3.4/TNRS/tests/fixtures/tnrs_usda.yml |only TNRS-0.3.5/TNRS/DESCRIPTION | 6 TNRS-0.3.5/TNRS/MD5 | 64 - TNRS-0.3.5/TNRS/NEWS | 17 TNRS-0.3.5/TNRS/R/TNRS.R | 26 TNRS-0.3.5/TNRS/R/TNRS_core.R | 4 TNRS-0.3.5/TNRS/inst/doc/TNRS_vignette.html | 318 ++++--- TNRS-0.3.5/TNRS/inst/doc/TNRS_vignette_spa.html | 342 ++++---- TNRS-0.3.5/TNRS/man/TNRS.Rd | 6 TNRS-0.3.5/TNRS/man/TNRS_base.Rd | 92 +- TNRS-0.3.5/TNRS/man/TNRS_core.Rd | 81 - TNRS-0.3.5/TNRS/tests/fixtures/tnrs_all.yml | 22 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_base.yml |only TNRS-0.3.5/TNRS/tests/fixtures/tnrs_best.yml | 16 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_character.yml | 16 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_character_vector.yml | 28 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_citations.yml |only TNRS-0.3.5/TNRS/tests/fixtures/tnrs_example.yml | 630 +++++++-------- TNRS-0.3.5/TNRS/tests/fixtures/tnrs_high.yml | 18 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_low.yml | 46 - TNRS-0.3.5/TNRS/tests/fixtures/tnrs_parsed.yml | 12 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_parsed_2.yml | 18 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_resolved.yml | 16 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_sources.yml |only TNRS-0.3.5/TNRS/tests/fixtures/tnrs_version.yml |only TNRS-0.3.5/TNRS/tests/fixtures/tnrs_wcvp.yml | 34 TNRS-0.3.5/TNRS/tests/fixtures/tnrs_wfo.yml | 34 TNRS-0.3.5/TNRS/tests/testthat/setup-tnrs.R | 2 TNRS-0.3.5/TNRS/tests/testthat/test-TNRS.R | 60 - TNRS-0.3.5/TNRS/tests/testthat/test-TNRS_base.R | 2 TNRS-0.3.5/TNRS/tests/testthat/test-TNRS_citations.R | 2 TNRS-0.3.5/TNRS/tests/testthat/test-TNRS_sources.R | 4 TNRS-0.3.5/TNRS/tests/testthat/test-TNRS_version.R | 2 38 files changed, 995 insertions(+), 923 deletions(-)
Title: Load US Census Boundary and Attribute Data as 'tidyverse' and
'sf'-Ready Data Frames
Description: An integrated R interface to several United States Census Bureau
APIs (<https://www.census.gov/data/developers/data-sets.html>) and the US Census Bureau's
geographic boundary files. Allows R users to return Census and ACS data as
tidyverse-ready data frames, and optionally returns a list-column with feature geometry for mapping
and spatial analysis.
Author: Kyle Walker [aut, cre],
Matt Herman [aut],
Kris Eberwein [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between tidycensus versions 1.6 dated 2024-01-25 and 1.6.2 dated 2024-03-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/load_data.R | 2 +- R/pums.R | 8 ++++++-- data/pums_variables.rda |binary man/pums_variables.Rd | 2 +- 6 files changed, 17 insertions(+), 13 deletions(-)
Title: Starter Kit for New Projects
Description: Get started with new projects by dropping a skeleton of a new
project into a new or existing directory, initialise git repositories,
and create reproducible environments with the 'renv' package. The
package allows for dynamically named files, folders, file content, as
well as the functionality to drop individual template files into
existing projects.
Author: Daniel D. Sjoberg [aut, cre] ,
Emily Vertosick [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between starter versions 0.1.14 dated 2023-06-07 and 0.1.15 dated 2024-03-05
DESCRIPTION | 12 MD5 | 72 NAMESPACE | 22 NEWS.md | 4 R/create_project.R | 780 ++++----- R/create_symlink.R | 212 +- R/data.R | 28 R/starter-package.R | 46 R/use_project_file.R | 182 +- R/utils-keepers.R | 32 R/utils-mappers.R | 468 ++--- R/utils-project_root.R | 40 R/utils-safely.R | 180 +- R/utils-walkers.R | 78 README.md | 145 - build/vignette.rds |binary inst/WORDLIST | 32 inst/doc/create_project.R | 186 +- inst/doc/create_project.Rmd | 460 ++--- inst/doc/create_project.html | 1254 ++++++++-------- inst/project_templates/analysis_template/analysis.Rmd | 90 - inst/project_templates/analysis_template/references.bib | 74 inst/project_templates/analysis_template/report.Rmd | 98 - inst/project_templates/analysis_template/setup.Rmd | 124 - inst/project_templates/default_gitignore.txt | 92 - inst/project_templates/default_readme.md | 8 inst/project_templates/default_rproj.Rproj | 34 man/create_project.Rd | 172 +- man/create_symlink.Rd | 104 - man/project_templates.Rd | 50 man/starter-package.Rd | 62 man/use_project_file.Rd | 118 - tests/spelling.R | 6 tests/testthat.R | 8 tests/testthat/test-create_project.R | 214 +- tests/testthat/test-create_symlink.R | 28 vignettes/create_project.Rmd | 460 ++--- 37 files changed, 2991 insertions(+), 2984 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need to
derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Andrew Johnson [aut],
Sebastian Weber [aut],
Hamada S. Badr [aut] ,
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Modrak Martin [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cp [...truncated...]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.32.5 dated 2024-01-10 and 2.32.6 dated 2024-03-05
DESCRIPTION | 10 - MD5 | 33 ++--- R/expose_stan_functions.R | 2 R/lookup.R | 5 R/misc.R | 8 - R/zzz.R | 5 build/vignette.rds |binary exec |only inst/doc/SBC.R | 4 inst/doc/SBC.html | 6 inst/doc/external.R | 10 - inst/doc/external.html | 36 ++--- inst/doc/rstan.R | 24 +-- inst/doc/rstan.html | 220 +++++++++++++++++------------------- inst/doc/stanfit-objects.R | 40 +++--- inst/doc/stanfit-objects.html | 164 +++++++++++++------------- inst/include/rstan/io/r_ostream.hpp | 4 src/misc.cpp | 2 18 files changed, 283 insertions(+), 290 deletions(-)
Title: Monitoring Overall Survival in Pivotal Trials in Indolent
Cancers
Description: These guidelines are meant to provide a pragmatic, yet rigorous, help to drug developers and decision makers, since they are shaped by three fundamental ingredients: the clinically determined margin of detriment on OS that is unacceptably high (delta null); the benefit on OS that is plausible given the mechanism of action of the novel intervention (delta alt); and the quantity of information (i.e. survival events) it is feasible to accrue given the clinical and drug development setting. The proposed guidelines facilitate transparent discussions between stakeholders focusing on the risks of erroneous decisions and what might be an acceptable trade-off between power and the false positive error rate.
Author: Thomas Fleming [ctb],
Lisa Hampson [aut],
Bharani Bharani-Dharan [ctb],
Frank Bretz [ctb],
Arunava Chakravartty [ctb],
Thibaud Coroller [aut, cre],
Evanthia Koukouli [aut],
Janet Wittes [ctb],
Nigel Yateman [ctb],
Emmanuel Zuber [ctb],
Novartis Pharm [...truncated...]
Maintainer: Thibaud Coroller <thibaud.coroller@novartis.com>
Diff between monitOS versions 0.1.3 dated 2023-10-31 and 0.1.4 dated 2024-03-05
DESCRIPTION | 8 - MD5 | 21 ++-- NEWS.md |only R/bounds.R | 8 - R/runApp.R | 1 R/server.R | 20 +++- R/ui.R | 49 ++++++--- README.md | 12 ++ build/vignette.rds |binary inst/doc/monitOS.html | 214 +++++++++++++++++++++---------------------- inst/shiny/deploy.R | 6 - tests/testthat/test-bounds.R | 6 - 12 files changed, 192 insertions(+), 153 deletions(-)
Title: Variable Selection for Multiply Imputed Data
Description: Penalized regression methods, such as lasso and elastic net, are used in
many biomedical applications when simultaneous regression coefficient
estimation and variable selection is desired. However, missing data
complicates the implementation of these methods, particularly when
missingness is handled using multiple imputation. Applying a variable
selection algorithm on each imputed dataset will likely lead
to different sets of selected predictors, making it difficult
to ascertain a final active set without resorting to ad hoc
combination rules. 'miselect' presents Stacked Adaptive Elastic Net (saenet)
and Grouped Adaptive LASSO (galasso) for continuous and binary outcomes,
developed by Du et al (2022) <doi:10.1080/10618600.2022.2035739>. They,
by construction, force selection of the same variables across multiply
imputed data. 'miselect' also provides cross validated variants of these
methods.
Author: Michael Kleinsasser [cre],
Alexander Rix [aut],
Jiacong Du [aut]
Maintainer: Michael Kleinsasser <biostat-cran-manager@umich.edu>
Diff between miselect versions 0.9.0 dated 2020-03-31 and 0.9.2 dated 2024-03-05
DESCRIPTION | 23 - MD5 | 50 +- NEWS.md | 13 R/coef.R | 211 ++++++------ R/cv.galasso.R | 258 ++++++++------- R/cv.saenet.R | 297 +++++++++-------- R/data.R | 2 R/galasso.R | 709 +++++++++++++++++++++--------------------- R/saenet.R | 495 ++++++++++++++--------------- R/util.R | 34 -- README.md | 46 +- build/vignette.rds |binary inst/doc/miselect.R | 4 inst/doc/miselect.html | 567 +++++++++++++++++++++++++-------- man/coef.cv.galasso.Rd | 14 man/coef.cv.saenet.Rd | 14 man/coef.galasso.Rd | 14 man/coef.saenet.Rd | 12 man/cv.galasso.Rd | 34 +- man/cv.saenet.Rd | 30 - man/galasso.Rd | 36 -- man/miselect.df.Rd | 2 man/saenet.Rd | 32 - tests/testthat.R | 8 tests/testthat/test_galasso.R | 85 ++--- tests/testthat/test_saenet.R | 7 26 files changed, 1671 insertions(+), 1326 deletions(-)
Title: Multiple Aggregation Prediction Algorithm
Description: Functions and wrappers for using the Multiple Aggregation Prediction Algorithm (MAPA) for time series forecasting. MAPA models and forecasts time series at multiple temporal aggregation levels, thus strengthening and attenuating the various time series components for better holistic estimation of its structure. For details see Kourentzes et al. (2014) <doi:10.1016/j.ijforecast.2013.09.006>.
Author: Nikolaos Kourentzes [aut, cre],
Fotios Petropoulos [aut]
Maintainer: Nikolaos Kourentzes <nikolaos@kourentzes.com>
Diff between MAPA versions 2.0.6 dated 2023-11-16 and 2.0.7 dated 2024-03-05
MAPA-2.0.6/MAPA/man/plotmapa.Rd |only MAPA-2.0.7/MAPA/DESCRIPTION | 6 +++--- MAPA-2.0.7/MAPA/MD5 | 9 ++++----- MAPA-2.0.7/MAPA/NAMESPACE | 2 +- MAPA-2.0.7/MAPA/NEWS.md | 3 +++ MAPA-2.0.7/MAPA/R/mapa.estim.R | 14 +++++++------- 6 files changed, 18 insertions(+), 16 deletions(-)
Title: A Lightweight, Modern and Flexible Logging Utility
Description: Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.
Author: Gergely Daroczi [aut, cre] ,
System1 [fnd]
Maintainer: Gergely Daroczi <daroczig@rapporter.net>
Diff between logger versions 0.2.2 dated 2021-10-19 and 0.3.0 dated 2024-03-05
DESCRIPTION | 11 MD5 | 113 ++-- NAMESPACE | 10 NEWS.md | 28 + R/appenders.R | 7 R/formatters.R | 63 ++ R/helpers.R | 50 +- R/hooks.R | 68 +- R/layouts.R | 10 R/levels.R | 64 ++ R/logger.R | 291 +++++------ R/try.R | 8 R/utils.R | 38 + R/zzz.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/Intro.R | 14 inst/doc/Intro.Rmd | 20 inst/doc/Intro.html | 433 +++++++++++++---- inst/doc/anatomy.html | 842 +++++++++++++++++++++++++++------- inst/doc/customize_logger.html | 806 +++++++++++++++++++++----------- inst/doc/migration.html | 602 ++++++++++++++++++------ inst/doc/performance.html | 527 +++++++++++++++------ inst/doc/r_packages.html | 371 +++++++++++--- inst/doc/write_custom_extensions.html | 402 ++++++++++++---- man/appender_void.Rd |only man/as.loglevel.Rd |only man/catch_base_log.Rd |only man/delete_logger_index.Rd |only man/formatter_glue.Rd | 2 man/formatter_glue_or_sprintf.Rd | 2 man/formatter_glue_safe.Rd |only man/formatter_json.Rd | 4 man/formatter_logging.Rd | 2 man/formatter_pander.Rd | 2 man/formatter_paste.Rd | 2 man/formatter_sprintf.Rd | 2 man/grapes-except-grapes.Rd | 8 man/log_appender.Rd | 4 man/log_config_setter.Rd |only man/log_errors.Rd | 5 man/log_formatter.Rd | 4 man/log_layout.Rd | 4 man/log_level.Rd | 24 man/log_levels.Rd | 12 man/log_separator.Rd | 11 man/log_shiny_input_changes.Rd | 9 man/log_threshold.Rd | 2 man/log_tictoc.Rd | 2 man/log_warnings.Rd | 5 man/log_with_separator.Rd | 5 man/logger.Rd | 4 man/skip_formatter.Rd | 4 tests/testthat/test-CRANSKIP-hooks.R | 66 ++ tests/testthat/test-formatters.R | 33 + tests/testthat/test-helpers.R | 18 tests/testthat/test-layout.R | 10 tests/testthat/test-logger.R | 42 + tests/testthat/test-return.R |only tests/testthat/test-utils.R | 20 vignettes/Intro.Rmd | 20 61 files changed, 3813 insertions(+), 1297 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] ,
Florian De Boissieu [ctb] ,
Andrew Sanchez Meador [ctb] for
segment_snags),
Bourdon Jean-Francois [ctb] for
track_sensor),
Gatziolis Demetrios [ctb] for
track_sensor),
Leon Steinmeier [c [...truncated...]
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 4.1.0 dated 2024-02-01 and 4.1.1 dated 2024-03-05
DESCRIPTION | 6 MD5 | 76 ++++++------ NEWS.md | 9 + R/Class-LAScatalog.R | 21 ++- R/catalog_intersect.R | 6 R/engine_crop.R | 4 R/generate_las.R | 2 R/locate_localmaxima.R | 2 R/rasterize_terrain.R | 12 + R/st_crs.R | 23 +-- R/utils_raster.R | 2 inst/doc/lidR-LAScatalog-class.html | 198 +++++++++++++++----------------- src/LAS.cpp | 19 ++- tests/testthat/Rplots.pdf |binary tests/testthat/test-LAS.R | 1 tests/testthat/test-LAScatalog.R | 2 tests/testthat/test-apply_automerge.R | 10 + tests/testthat/test-apply_autoread.R | 3 tests/testthat/test-apply_generic.R | 4 tests/testthat/test-apply_independent.R | 4 tests/testthat/test-apply_restart.R | 2 tests/testthat/test-catalog_intersect.R | 6 tests/testthat/test-clip.R | 14 +- tests/testthat/test-decimate_points.R | 9 - tests/testthat/test-locate_trees.R | 4 tests/testthat/test-merges_spatial.R | 38 +++--- tests/testthat/test-metrics_crowns.R | 5 tests/testthat/test-metrics_pixels.R | 25 +--- tests/testthat/test-metrics_standard.R | 48 +------ tests/testthat/test-normalize_height.R | 4 tests/testthat/test-plot.R | 4 tests/testthat/test-projection.R | 6 tests/testthat/test-rasterize_canopy.R | 2 tests/testthat/test-rasterize_density.R | 1 tests/testthat/test-rasterize_terrain.R | 4 tests/testthat/test-readLAS.R | 2 tests/testthat/test-roughness.R | 6 tests/testthat/test-segment_trees.R | 9 - tests/testthat/test-st_transform.R | 2 39 files changed, 306 insertions(+), 289 deletions(-)
Title: Geometric Morphometric Analyses of 2D and 3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams [aut, cre],
Michael Collyer [aut],
Antigoni Kaliontzopoulou [aut],
Erica Baken [aut]
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 4.0.6 dated 2023-08-31 and 4.0.7 dated 2024-03-05
geomorph-4.0.6/geomorph/inst/doc/geomorph.PCA.R |only geomorph-4.0.6/geomorph/inst/doc/geomorph.PCA.Rmd |only geomorph-4.0.6/geomorph/inst/doc/geomorph.PCA.html |only geomorph-4.0.6/geomorph/inst/doc/geomorph.assistance.R |only geomorph-4.0.6/geomorph/inst/doc/geomorph.assistance.Rmd |only geomorph-4.0.6/geomorph/inst/doc/geomorph.assistance.html |only geomorph-4.0.6/geomorph/inst/doc/geomorph.functions.R |only geomorph-4.0.6/geomorph/inst/doc/geomorph.functions.Rmd |only geomorph-4.0.6/geomorph/inst/doc/geomorph.functions.html |only geomorph-4.0.6/geomorph/vignettes/geomorph.PCA.Rmd |only geomorph-4.0.6/geomorph/vignettes/geomorph.assistance.Rmd |only geomorph-4.0.6/geomorph/vignettes/geomorph.functions.Rmd |only geomorph-4.0.7/geomorph/DESCRIPTION | 10 geomorph-4.0.7/geomorph/MD5 | 234 +++++----- geomorph-4.0.7/geomorph/NAMESPACE | 2 geomorph-4.0.7/geomorph/NEWS.md | 18 geomorph-4.0.7/geomorph/R/arrayspecs.r | 12 geomorph-4.0.7/geomorph/R/bilat.symmetry.r | 84 ++- geomorph-4.0.7/geomorph/R/build.template.r | 29 - geomorph-4.0.7/geomorph/R/combine.subsets.R | 80 +-- geomorph-4.0.7/geomorph/R/compare.CR.R | 60 +- geomorph-4.0.7/geomorph/R/compare.ZVrel.R | 6 geomorph-4.0.7/geomorph/R/compare.evol.rates.r | 15 geomorph-4.0.7/geomorph/R/compare.multi.evol.rates.r | 12 geomorph-4.0.7/geomorph/R/compare.physign.z.r | 7 geomorph-4.0.7/geomorph/R/compare.pls.r | 3 geomorph-4.0.7/geomorph/R/coords.subset.r | 3 geomorph-4.0.7/geomorph/R/digit.curves.r | 22 - geomorph-4.0.7/geomorph/R/digit.fixed.r | 6 geomorph-4.0.7/geomorph/R/digitize2d.r | 11 geomorph-4.0.7/geomorph/R/digitsurface.r | 26 - geomorph-4.0.7/geomorph/R/estimate.missing.r | 28 - geomorph-4.0.7/geomorph/R/fixed.angle.r | 16 geomorph-4.0.7/geomorph/R/geomorph.data.frame.r | 4 geomorph-4.0.7/geomorph/R/geomorph.support.code.r | 298 ++++++++++---- geomorph-4.0.7/geomorph/R/geomorph.utils.r | 19 geomorph-4.0.7/geomorph/R/globalIntegration.r | 4 geomorph-4.0.7/geomorph/R/gm.measurement.error.R |only geomorph-4.0.7/geomorph/R/gm.prcomp.R | 33 - geomorph-4.0.7/geomorph/R/gpagen.r | 42 + geomorph-4.0.7/geomorph/R/gridPar.r | 32 - geomorph-4.0.7/geomorph/R/integration.Vrel.r | 8 geomorph-4.0.7/geomorph/R/integration.test.r | 10 geomorph-4.0.7/geomorph/R/interlmkdist.r | 5 geomorph-4.0.7/geomorph/R/make_ggplot.r | 48 +- geomorph-4.0.7/geomorph/R/modularity.test.r | 15 geomorph-4.0.7/geomorph/R/morphol.disparity.r | 127 +++-- geomorph-4.0.7/geomorph/R/phylo.integration.r | 16 geomorph-4.0.7/geomorph/R/phylo.modularity.r | 24 - geomorph-4.0.7/geomorph/R/physignal.r | 10 geomorph-4.0.7/geomorph/R/physignal.z.r | 16 geomorph-4.0.7/geomorph/R/picknplot.shape.r | 92 ++-- geomorph-4.0.7/geomorph/R/plotAllSpecimens.r | 14 geomorph-4.0.7/geomorph/R/plotAllometry.r | 38 - geomorph-4.0.7/geomorph/R/plotOutliers.r | 3 geomorph-4.0.7/geomorph/R/plotRefToTarget.r | 62 +- geomorph-4.0.7/geomorph/R/plotspec.r | 27 - geomorph-4.0.7/geomorph/R/procD.lm.r | 6 geomorph-4.0.7/geomorph/R/procD.pgls.r | 15 geomorph-4.0.7/geomorph/R/read.morphologika.r | 6 geomorph-4.0.7/geomorph/R/read.ply.r | 2 geomorph-4.0.7/geomorph/R/readland.tps.r | 156 ------- geomorph-4.0.7/geomorph/R/readmulti.tps.R | 61 +- geomorph-4.0.7/geomorph/R/rotate.coords.R | 2 geomorph-4.0.7/geomorph/R/shape.predictor.r | 214 +++++----- geomorph-4.0.7/geomorph/R/shapeHulls.r | 3 geomorph-4.0.7/geomorph/R/shared.support.code.R | 12 geomorph-4.0.7/geomorph/R/two.b.pls.r | 8 geomorph-4.0.7/geomorph/R/two.d.array.r | 2 geomorph-4.0.7/geomorph/build/vignette.rds |binary geomorph-4.0.7/geomorph/inst/CITATION | 8 geomorph-4.0.7/geomorph/inst/doc/geomorph.digitize3D.R | 6 geomorph-4.0.7/geomorph/inst/doc/geomorph.digitize3D.html | 23 - geomorph-4.0.7/geomorph/man/arrayspecs.Rd | 11 geomorph-4.0.7/geomorph/man/bilat.symmetry.Rd | 78 +-- geomorph-4.0.7/geomorph/man/buildtemplate.Rd | 29 - geomorph-4.0.7/geomorph/man/combine.subsets.Rd | 80 +-- geomorph-4.0.7/geomorph/man/compare.CR.Rd | 60 +- geomorph-4.0.7/geomorph/man/compare.ZVrel.Rd | 6 geomorph-4.0.7/geomorph/man/compare.evol.rates.Rd | 15 geomorph-4.0.7/geomorph/man/compare.multi.evol.rates.Rd | 12 geomorph-4.0.7/geomorph/man/compare.physignal.z.Rd | 5 geomorph-4.0.7/geomorph/man/compare.pls.Rd | 3 geomorph-4.0.7/geomorph/man/coords.subset.Rd | 3 geomorph-4.0.7/geomorph/man/digit.curves.Rd | 22 - geomorph-4.0.7/geomorph/man/digit.fixed.Rd | 6 geomorph-4.0.7/geomorph/man/digitize2d.Rd | 11 geomorph-4.0.7/geomorph/man/digitsurface.Rd | 26 - geomorph-4.0.7/geomorph/man/estimate.missing.Rd | 18 geomorph-4.0.7/geomorph/man/fixed.angle.Rd | 16 geomorph-4.0.7/geomorph/man/geomorph-package.Rd | 1 geomorph-4.0.7/geomorph/man/geomorph.data.frame.Rd | 4 geomorph-4.0.7/geomorph/man/globalIntegration.Rd | 4 geomorph-4.0.7/geomorph/man/gm.measurement.error.Rd |only geomorph-4.0.7/geomorph/man/gm.prcomp.Rd | 32 - geomorph-4.0.7/geomorph/man/gpagen.Rd | 19 geomorph-4.0.7/geomorph/man/gridPar.Rd | 32 - geomorph-4.0.7/geomorph/man/integration.Vrel.Rd | 8 geomorph-4.0.7/geomorph/man/integration.test.Rd | 10 geomorph-4.0.7/geomorph/man/interlmkdist.Rd | 5 geomorph-4.0.7/geomorph/man/make_ggplot.Rd | 48 +- geomorph-4.0.7/geomorph/man/modularity.test.Rd | 15 geomorph-4.0.7/geomorph/man/morphol.disparity.Rd | 127 +++-- geomorph-4.0.7/geomorph/man/mshape.Rd | 5 geomorph-4.0.7/geomorph/man/phylo.integration.Rd | 16 geomorph-4.0.7/geomorph/man/phylo.modularity.Rd | 24 - geomorph-4.0.7/geomorph/man/physignal.Rd | 10 geomorph-4.0.7/geomorph/man/physignal.z.Rd | 14 geomorph-4.0.7/geomorph/man/picknplot.shape.Rd | 68 +-- geomorph-4.0.7/geomorph/man/plot.gm.prcomp.Rd | 6 geomorph-4.0.7/geomorph/man/plotAllSpecimens.Rd | 12 geomorph-4.0.7/geomorph/man/plotAllometry.Rd | 20 geomorph-4.0.7/geomorph/man/plotOutliers.Rd | 3 geomorph-4.0.7/geomorph/man/plotRefToTarget.Rd | 62 +- geomorph-4.0.7/geomorph/man/plotspec.Rd | 27 - geomorph-4.0.7/geomorph/man/procD.lm.Rd | 5 geomorph-4.0.7/geomorph/man/procD.pgls.Rd | 15 geomorph-4.0.7/geomorph/man/read.morphologika.Rd | 6 geomorph-4.0.7/geomorph/man/read.ply.Rd | 2 geomorph-4.0.7/geomorph/man/readmulti.tps.Rd | 3 geomorph-4.0.7/geomorph/man/rotate.coords.Rd | 2 geomorph-4.0.7/geomorph/man/shape.predictor.Rd | 198 ++++----- geomorph-4.0.7/geomorph/man/shapeHulls.Rd | 3 geomorph-4.0.7/geomorph/man/two.b.pls.Rd | 8 geomorph-4.0.7/geomorph/man/two.d.array.Rd | 2 125 files changed, 1808 insertions(+), 1564 deletions(-)
Title: Solutions for Common Problems in Base R
Description: Contains functions for solving commonly encountered problems while
programming in R. This package is intended to provide a lightweight
supplement to Base R, and will be useful for almost any R user.
Author: David Bosak [aut, cre],
Duong Tran [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between common versions 1.1.1 dated 2023-12-19 and 1.1.2 dated 2024-03-05
DESCRIPTION | 10 - MD5 | 42 ++--- NAMESPACE | 1 NEWS.md | 5 R/common.R | 5 R/file_functions.R | 289 +++++++++++++++++++++++++++++++++++ R/subsc.R | 4 R/supsc.R | 5 build/vignette.rds |binary inst/doc/common.R | 84 ++++++++++ inst/doc/common.Rmd | 37 +++- inst/doc/common.html | 171 +++++++++++--------- man/Sys.path.Rd | 3 man/common.Rd | 20 ++ man/dir.find.Rd | 3 man/file.find.Rd | 3 man/images/sourceall.png |only man/source.all.Rd |only tests/testthat/programs |only tests/testthat/test-file_functions.R | 205 +++++++++++++++++++++++- tests/testthat/test-supsub.R | 14 + vignettes/common.Rmd | 37 +++- 22 files changed, 814 insertions(+), 124 deletions(-)
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 2.3.0 dated 2023-08-27 and 2.4.0 dated 2024-03-05
UniprotR-2.3.0/UniprotR/R/PlotEnrichedGO.R |only UniprotR-2.3.0/UniprotR/R/PlotEnrichedPathways.R |only UniprotR-2.3.0/UniprotR/man/PlotEnrichedGO.Rd |only UniprotR-2.3.0/UniprotR/man/PlotEnrichedPathways.Rd |only UniprotR-2.4.0/UniprotR/DESCRIPTION | 6 +- UniprotR-2.4.0/UniprotR/MD5 | 26 ++++------ UniprotR-2.4.0/UniprotR/NAMESPACE | 2 UniprotR-2.4.0/UniprotR/R/ConvertID.R | 29 +++++++---- UniprotR-2.4.0/UniprotR/R/PathwayAnalysis.R | 49 ++++++++++++-------- UniprotR-2.4.0/UniprotR/man/ConvertID.Rd | 7 +- UniprotR-2.4.0/UniprotR/man/Enrichment.BP.Rd | 4 + UniprotR-2.4.0/UniprotR/man/Enrichment.CC.Rd | 4 + UniprotR-2.4.0/UniprotR/man/Enrichment.KEGG.Rd | 4 + UniprotR-2.4.0/UniprotR/man/Enrichment.MF.Rd | 4 + UniprotR-2.4.0/UniprotR/man/Enrichment.REAC.Rd | 4 + UniprotR-2.4.0/UniprotR/man/Pathway.Enr.Rd | 4 + 16 files changed, 86 insertions(+), 57 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin,
2021 <doi:10.3389/fevo.2021.588292>) can be used for
a variety of multivariate problems when count data are at play, including
principal component analysis for count data, discriminant analysis, model-based clustering and
network inference. Implements variational algorithms to fit such models accompanied with a set of
functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] ,
Mahendra Mariadassou [aut] ,
Stephane Robin [aut],
Francois Gindraud [aut],
Julie Aubert [ctb],
Bastien Batardiere [ctb],
Giovanni Poggiato [ctb],
Cole Trapnell [ctb],
Maddy Duran [ctb]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 1.1.0 dated 2024-01-08 and 1.2.0 dated 2024-03-05
PLNmodels-1.1.0/PLNmodels/man/plot.PLNnetworkfamily.Rd |only PLNmodels-1.2.0/PLNmodels/DESCRIPTION | 20 PLNmodels-1.2.0/PLNmodels/MD5 | 97 + PLNmodels-1.2.0/PLNmodels/NAMESPACE | 20 PLNmodels-1.2.0/PLNmodels/NEWS.md | 8 PLNmodels-1.2.0/PLNmodels/R/PLNfit-class.R | 14 PLNmodels-1.2.0/PLNmodels/R/PLNnetwork.R | 19 PLNmodels-1.2.0/PLNmodels/R/PLNnetworkfamily-S3methods.R | 79 - PLNmodels-1.2.0/PLNmodels/R/PLNnetworkfamily-class.R | 561 ++++++---- PLNmodels-1.2.0/PLNmodels/R/PLNnetworkfit-class.R | 106 - PLNmodels-1.2.0/PLNmodels/R/RcppExports.R | 40 PLNmodels-1.2.0/PLNmodels/R/ZIPLN.R |only PLNmodels-1.2.0/PLNmodels/R/ZIPLNfit-S3methods.R |only PLNmodels-1.2.0/PLNmodels/R/ZIPLNfit-class.R |only PLNmodels-1.2.0/PLNmodels/R/ZIPLNnetwork.R |only PLNmodels-1.2.0/PLNmodels/R/plot_utils.R | 51 PLNmodels-1.2.0/PLNmodels/R/scRNA.R |only PLNmodels-1.2.0/PLNmodels/R/utils-zipln.R |only PLNmodels-1.2.0/PLNmodels/R/utils.R | 2 PLNmodels-1.2.0/PLNmodels/data/scRNA.rda |only PLNmodels-1.2.0/PLNmodels/inst/WORDLIST | 13 PLNmodels-1.2.0/PLNmodels/inst/doc/Import_data.html | 4 PLNmodels-1.2.0/PLNmodels/inst/doc/PLN.html | 6 PLNmodels-1.2.0/PLNmodels/inst/doc/PLNLDA.html | 136 +- PLNmodels-1.2.0/PLNmodels/inst/doc/PLNPCA.html | 10 PLNmodels-1.2.0/PLNmodels/inst/doc/PLNmixture.html | 22 PLNmodels-1.2.0/PLNmodels/inst/doc/PLNnetwork.html | 76 - PLNmodels-1.2.0/PLNmodels/inst/doc/Trichoptera.html | 4 PLNmodels-1.2.0/PLNmodels/inst/simus_ZIPLN |only PLNmodels-1.2.0/PLNmodels/man/Networkfamily.Rd |only PLNmodels-1.2.0/PLNmodels/man/PLNnetwork.Rd | 6 PLNmodels-1.2.0/PLNmodels/man/PLNnetwork_param.Rd | 4 PLNmodels-1.2.0/PLNmodels/man/PLNnetworkfamily.Rd | 197 --- PLNmodels-1.2.0/PLNmodels/man/PLNnetworkfit.Rd | 88 - PLNmodels-1.2.0/PLNmodels/man/ZIPLN.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLN_param.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNfit.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNfit_diagonal.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNfit_fixed.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNfit_sparse.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNfit_spherical.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNnetwork.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNnetwork_param.Rd |only PLNmodels-1.2.0/PLNmodels/man/ZIPLNnetworkfamily.Rd |only PLNmodels-1.2.0/PLNmodels/man/coef.ZIPLNfit.Rd |only PLNmodels-1.2.0/PLNmodels/man/coefficient_path.Rd | 2 PLNmodels-1.2.0/PLNmodels/man/fitted.ZIPLNfit.Rd |only PLNmodels-1.2.0/PLNmodels/man/getBestModel.Rd | 10 PLNmodels-1.2.0/PLNmodels/man/getModel.Rd | 10 PLNmodels-1.2.0/PLNmodels/man/plot.Networkfamily.Rd |only PLNmodels-1.2.0/PLNmodels/man/plot.ZIPLNfit_sparse.Rd |only PLNmodels-1.2.0/PLNmodels/man/predict.ZIPLNfit.Rd |only PLNmodels-1.2.0/PLNmodels/man/scRNA.Rd |only PLNmodels-1.2.0/PLNmodels/man/sigma.ZIPLNfit.Rd |only PLNmodels-1.2.0/PLNmodels/man/stability_selection.Rd | 6 PLNmodels-1.2.0/PLNmodels/src/RcppExports.cpp | 167 ++ PLNmodels-1.2.0/PLNmodels/src/lambertW.cpp |only PLNmodels-1.2.0/PLNmodels/src/lambertW.h |only PLNmodels-1.2.0/PLNmodels/src/optim_zi-pln.cpp |only PLNmodels-1.2.0/PLNmodels/src/utils.h | 8 PLNmodels-1.2.0/PLNmodels/tests/testthat/Rplots.pdf |binary PLNmodels-1.2.0/PLNmodels/tests/testthat/test-plnnetworkfamily.R | 20 PLNmodels-1.2.0/PLNmodels/tests/testthat/test-plnnetworkfit.R | 2 PLNmodels-1.2.0/PLNmodels/tests/testthat/test-zipln.R |only PLNmodels-1.2.0/PLNmodels/tests/testthat/test-ziplnfit.R |only PLNmodels-1.2.0/PLNmodels/tests/testthat/test-ziplnnetworkfamily.R |only 66 files changed, 1039 insertions(+), 769 deletions(-)
Title: CFO-Type Designs in Phase I Clinical Trials
Description: In phase I clinical trials, the primary objective is to ascertain the maximum tolerated dose (MTD) corresponding to a specified target toxicity rate. The 'CFO' package facilitates the implementation of dose-finding trials by utilizing calibration-free odds type (CFO-type) designs. Specifically, it encompasses the calibration-free odds (CFO) (Jin and Yin (2022) <doi:10.1177/09622802221079353>), two-dimensional CFO (2dCFO) (Wang et al. (2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO), accumulative CFO (aCFO), TITE-aCFO, and f-aCFO designs. The ‘CFO' package accommodates diverse CFO-type designs, allowing users to tailor the approach based on factors such as dose information inclusion, handling of late-onset toxicity, and the nature of the target drug (single-drug or drug-combination). The functionalities embedded in 'CFO' package include the determination of the dose level for the ne [...truncated...]
Author: Jialu Fang [aut, cre],
Wenliang Wang [aut],
Guosheng Yin [aut]
Maintainer: Jialu Fang <u3008682@connect.hku.hk>
Diff between CFO versions 1.0.0 dated 2024-02-26 and 1.1.0 dated 2024-03-05
DESCRIPTION | 6 +++--- MD5 | 38 ++++++++++++++++++++------------------ NAMESPACE | 1 + R/CFO.next.R | 2 +- R/CFO.oc.R | 2 +- R/CFO.selectmtd.R | 5 ++--- R/CFO.simu.R | 2 +- R/CFO2d.next.R | 5 +++-- R/CFO2d.oc.R | 2 +- R/CFO2d.selectmtd.R | 4 ++-- R/CFO2d.simu.R | 8 ++++---- R/aCFO.next.R | 2 +- R/lateonset.next.R | 2 +- R/lateonset.simu.R | 2 +- R/plot.cfo.R | 37 +++++++++++++++++++++++-------------- R/print.cfo.R |only R/summury.cfo.R | 31 +++++++++++++++---------------- man/CFO2d.selectmtd.Rd | 2 +- man/plot.cfo.Rd | 20 ++++++++++---------- man/print.cfo.Rd |only man/summary.cfo.Rd | 19 +++++++++---------- 21 files changed, 100 insertions(+), 90 deletions(-)
Title: Wrapper for the 'AT' Protocol Behind 'Bluesky'
Description: Wraps the 'AT' Protocol (Authenticated Transfer Protocol) behind
'Bluesky' <https://bsky.social>. Functions can be used for, among others,
retrieving posts and followers from the network or posting content.
Author: Johannes B. Gruber [aut, cre] ,
Benjamin Guinaudeau [aut, ctb]
,
Fabio Votta [aut, ctb]
Maintainer: Johannes B. Gruber <JohannesB.Gruber@gmail.com>
Diff between atrrr versions 0.0.2 dated 2024-01-10 and 0.0.3 dated 2024-03-05
atrrr-0.0.2/atrrr/R/atr-package.R |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.actor.searchActors.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getActorFeeds.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getAuthorFeed.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getFeed.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getLikes.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getPostThread.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getRepostedBy.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getTimeline.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.feed.searchPosts.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/app.bsky.unspecced.getPopularFeedGenerators.rds |only atrrr-0.0.2/atrrr/tests/testthat/recorded_responses/com.atproto.identity.resolveHandle.rds |only atrrr-0.0.3/atrrr/DESCRIPTION | 12 atrrr-0.0.3/atrrr/MD5 | 106 ++-- atrrr-0.0.3/atrrr/NAMESPACE | 2 atrrr-0.0.3/atrrr/NEWS.md | 9 atrrr-0.0.3/atrrr/R/actors.r | 21 atrrr-0.0.3/atrrr/R/atrrr-package.R |only atrrr-0.0.3/atrrr/R/auth.r | 2 atrrr-0.0.3/atrrr/R/convert.r | 4 atrrr-0.0.3/atrrr/R/feed.r | 61 ++ atrrr-0.0.3/atrrr/R/graph.r | 16 atrrr-0.0.3/atrrr/R/parse.r | 27 - atrrr-0.0.3/atrrr/R/skeet_shot.r |only atrrr-0.0.3/atrrr/R/utils.r | 63 ++ atrrr-0.0.3/atrrr/README.md | 82 ++- atrrr-0.0.3/atrrr/build/vignette.rds |binary atrrr-0.0.3/atrrr/inst/doc/Basic_Usage.Rmd | 216 ++++----- atrrr-0.0.3/atrrr/inst/doc/Basic_Usage.html | 220 ++++------ atrrr-0.0.3/atrrr/inst/doc/Feed_Analysis.Rmd | 91 ++-- atrrr-0.0.3/atrrr/inst/doc/Feed_Analysis.html | 99 ++-- atrrr-0.0.3/atrrr/inst/doc/Networks.Rmd | 120 ++--- atrrr-0.0.3/atrrr/inst/doc/Networks.html | 124 ++--- atrrr-0.0.3/atrrr/man/atrrr-package.Rd | 2 atrrr-0.0.3/atrrr/man/get_followers.Rd | 8 atrrr-0.0.3/atrrr/man/post.Rd | 13 atrrr-0.0.3/atrrr/man/search_post.Rd | 37 + atrrr-0.0.3/atrrr/man/skeet_shot.Rd |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_23a5a.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_63d49.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_a3350.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_a7fb6.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_c1f6f.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.getProfiles_f39c7.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.searchActors_275e3.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.searchActors_5a4e3.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.actor.searchActors_87617.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getActorFeeds_76b86.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getAuthorFeed_76b86.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getFeed_0bf27.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getLikes_26bda.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getLikes_95deb.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getPostThread_72827.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getPostThread_aa665.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getRepostedBy_95deb.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getTimeline_6340d.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.getTimeline_730cb.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.searchPosts_0e3ec.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.feed.searchPosts_bb16d.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/app.bsky.unspecced.getPopularFeedGenerators_8e00b.rds |only atrrr-0.0.3/atrrr/tests/testthat/recorded_responses/com.atproto.identity.resolveHandle_c81f8.rds |only atrrr-0.0.3/atrrr/tests/testthat/setup-mock.R | 14 atrrr-0.0.3/atrrr/tests/testthat/test-actors.R | 9 atrrr-0.0.3/atrrr/tests/testthat/test-feed.R | 2 atrrr-0.0.3/atrrr/vignettes/Basic_Usage.Rmd | 216 ++++----- atrrr-0.0.3/atrrr/vignettes/Basic_Usage.Rmd.orig | 10 atrrr-0.0.3/atrrr/vignettes/Feed_Analysis.Rmd | 91 ++-- atrrr-0.0.3/atrrr/vignettes/Networks.Rmd | 120 ++--- atrrr-0.0.3/atrrr/vignettes/Networks.Rmd.orig | 12 atrrr-0.0.3/atrrr/vignettes/figures/unnamed-chunk-3-1.png |binary atrrr-0.0.3/atrrr/vignettes/figures/unnamed-chunk-4-1.png |binary atrrr-0.0.3/atrrr/vignettes/figures/unnamed-chunk-44-1.png |only atrrr-0.0.3/atrrr/vignettes/figures/unnamed-chunk-6-1.png |binary 74 files changed, 1000 insertions(+), 809 deletions(-)
Title: Network-Based Interpretation of Changes in Compositional Data
Description: Provides a set of functions to interpret changes in
compositional data based on a network representation of all pairwise ratio
comparisons: computation of all pairwise ratio, construction of a
p-value matrix of all pairwise tests of these ratios between
conditions, conversion of this matrix to a network.
Author: Emmanuel Curis [aut, cre]
Maintainer: Emmanuel Curis <emmanuel.curis@parisdescartes.fr>
Diff between SARP.compo versions 0.1.5 dated 2021-05-15 and 0.1.8 dated 2024-03-05
DESCRIPTION | 8 +++---- MD5 | 18 ++++++++--------- R/creer_graphe.R | 20 +++++++++++++++++++ R/creer_matrice.R | 53 ++++++++++++++++++++++++++++++++++++++++++++++++++- R/simuler_H0.R | 31 +++++++++++++++++++++++++---- man/choix_seuil.Rd | 14 +++++++++++-- man/creer_graphe.Rd | 5 ++-- man/creer_matrice.Rd | 11 +++++++--- man/fichiers.Rd | 7 +++--- man/generef.Rd | 2 - 10 files changed, 139 insertions(+), 30 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.2.8 dated 2023-11-28 and 1.3.1 dated 2024-03-05
DESCRIPTION | 25 MD5 | 102 NEWS.md | 21 R/enum.R | 2 R/getscene.R | 2 R/knitr.R | 126 R/r3d.rgl.R | 31 R/scene.R | 5 R/setUserCallbacks.R | 2 inst/doc/WebGL.Rmd | 5 inst/doc/WebGL.html | 1422 - inst/doc/demos.Rmd | 7 inst/doc/demos.html |10823 +------------- inst/doc/deprecation.Rmd | 5 inst/doc/deprecation.html | 897 - inst/doc/pkgdown.R | 5 inst/doc/pkgdown.Rmd | 10 inst/doc/pkgdown.html | 591 inst/doc/rgl.Rmd | 6 inst/doc/rgl.html |11859 +++++++++++++--- inst/doc/transparency.R | 6 inst/doc/transparency.Rmd | 24 inst/doc/transparency.html | 781 - inst/htmlwidgets/lib/rglClass/draw.src.js | 7 inst/htmlwidgets/lib/rglClass/init.src.js | 22 inst/htmlwidgets/lib/rglClass/rglClass.min.js | 8 inst/htmlwidgets/lib/rglClass/shaders/rgl_fragment.glsl | 20 inst/htmlwidgets/lib/rglClass/shaders/rgl_vertex.glsl | 2 inst/htmlwidgets/lib/rglClass/shadersrc.src.js | 14 man/clipMesh3d.Rd | 2 man/material.Rd | 7 man/pch3d.Rd | 6 man/postscript.Rd | 2 man/setupKnitr.Rd | 5 man/sprites.Rd | 48 src/Makevars.ucrt | 17 src/SceneNode.h | 1 src/SpriteSet.cpp | 42 src/SpriteSet.h | 7 src/api.cpp | 16 src/gl2ps.c | 183 src/gl2ps.h | 27 src/rglview.cpp | 3 src/subscene.cpp | 11 tests/testthat/testdata/r3d.rds |binary vignettes/WebGL.Rmd | 5 vignettes/demos.Rmd | 7 vignettes/deprecation.Rmd | 5 vignettes/pkgdown.Rmd | 10 vignettes/rgl.Rmd | 6 vignettes/setup.R | 11 vignettes/transparency.Rmd | 24 52 files changed, 12858 insertions(+), 14417 deletions(-)
Title: Quantile Regression Model for Residual Lifetime Using an Induced
Smoothing Approach
Description: A collection of functions is provided by this package to fit quantiles regression models for censored residual lifetimes. It provides various options for regression parameters estimation: the induced smoothing approach (smooth), and L1-minimization (non-smooth). It also implements the estimation methods for standard errors of the regression parameters estimates based on an efficient partial multiplier bootstrap method and robust sandwich estimator. Furthermore, a simultaneous procedure of estimating regression parameters and their standard errors via an iterative updating procedure is implemented (iterative). For more details, see Kim, K. H., Caplan, D. J., & Kang, S. (2022), "Smoothed quantile regression for censored residual life", Computational Statistics, 1-22 <doi:10.1007/s00180-022-01262-z>.
Author: Kyu Hyun Kim [aut, cre],
Sangwook Kang [aut],
Sy Han Chiou [aut]
Maintainer: Kyu Hyun Kim <kyuhyunkim07@gmail.com>
Diff between qris versions 1.0.0 dated 2022-08-29 and 1.1.1 dated 2024-03-05
qris-1.0.0/qris/man/ghat.Rd |only qris-1.1.1/qris/DESCRIPTION | 18 - qris-1.1.1/qris/MD5 | 45 +- qris-1.1.1/qris/NAMESPACE | 83 ++--- qris-1.1.1/qris/NEWS.md |only qris-1.1.1/qris/R/RcppExports.R | 66 ++-- qris-1.1.1/qris/R/Surv.R | 34 +- qris-1.1.1/qris/R/plot.R | 200 ++++++------ qris-1.1.1/qris/R/predict.R |only qris-1.1.1/qris/R/qris.R | 367 +++++++++++----------- qris-1.1.1/qris/R/qris_fit.R | 520 ++++++++++++++++---------------- qris-1.1.1/qris/R/qris_pkg.R | 20 - qris-1.1.1/qris/R/summary.R | 162 +++++---- qris-1.1.1/qris/inst/examples/ex_plot.R | 54 +-- qris-1.1.1/qris/inst/examples/ex_qris.R | 96 ++--- qris-1.1.1/qris/man/export_Surv.Rd | 38 +- qris-1.1.1/qris/man/plot.qris.Rd | 130 ++++---- qris-1.1.1/qris/man/predict.qris.Rd |only qris-1.1.1/qris/man/qris-package.Rd | 55 +-- qris-1.1.1/qris/man/qris.Rd | 234 +++++++------- qris-1.1.1/qris/man/qris.control.Rd | 54 +-- qris-1.1.1/qris/man/qris.extend.Rd |only qris-1.1.1/qris/man/residuals.qris.Rd |only qris-1.1.1/qris/src/ghat.cpp | 3 qris-1.1.1/qris/tests |only 25 files changed, 1136 insertions(+), 1043 deletions(-)
Title: Resolution-Optimised SNPs Searcher
Description: This is a R implementation of "Minimum SNPs" software as described in "Price E.P., Inman-Bamber, J., Thiruvenkataswamy, V., Huygens, F and Giffard, P.M." (2007) <doi:10.1186/1471-2105-8-278> "Computer-aided identification of polymorphism sets diagnostic for groups of bacterial and viral genetic variants."
Author: Ludwig Kian Soon Hoon [aut, cre]
,
Peter Shaw [aut, ctb] ,
Phil Giffard [aut, ctb]
Maintainer: Ludwig Kian Soon Hoon <ldwgkshoon@gmail.com>
Diff between minSNPs versions 0.1.0 dated 2023-08-08 and 0.2.0 dated 2024-03-05
DESCRIPTION | 6 - MD5 | 49 ++++++++--- NAMESPACE | 23 +++++ NEWS.md | 3 R/addn_search.R |only R/balk.r |only R/balk_helper.r |only R/process.R | 37 ++++---- R/search.R | 77 +++++++++++------ R/search_from_reads.R | 158 +++++++++++++++++++++++++++++++----- R/search_string_generation.R | 2 R/utility.R | 60 +++++++++++++ README.md | 15 +++ inst/doc/MinSNPs_Workflow.html | 2 man/binomial_naive_bayes.Rd |only man/calculate_mcc.Rd |only man/calculate_mcc_multi.Rd |only man/calculate_simpson_by_group.Rd |only man/calculate_state.Rd |only man/check_meta_target.Rd |only man/coef.binomial_naive_bayes.Rd |only man/generate_prioritisation.Rd |only man/get_binomial_tables.Rd |only man/map_profile_to_target.Rd |only man/mcc_calculation.Rd |only man/parse_group_mcc.Rd |only man/parse_group_mcc_multi.Rd |only man/predict.binomial_naive_bayes.Rd |only man/predict_balk.Rd |only man/print.binomial_naive_bayes.Rd |only man/profile_to_group_result.Rd |only man/scramble_sequence.Rd |only man/search_from_reads.Rd |only man/summarise_result.Rd |only man/summary.binomial_naive_bayes.Rd |only man/train_balk.Rd |only man/transform_snp.Rd |only man/translate_position.Rd |only man/view_mcc.Rd |only man/view_mcc_multi.Rd |only 40 files changed, 354 insertions(+), 78 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] ,
Bernd Bischl [aut] ,
Jakob Richter [aut] ,
Patrick Schratz [aut] ,
Giuseppe Casalicchio [ctb] ,
Stefan Coors [ctb] ,
Quay Au [ctb] ,
Martin Binder [aut],
Florian Pfisterer [aut] ,
Raphael Sonabend [aut] ,
Lennart Schneider [c [...truncated...]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.17.2 dated 2024-01-09 and 0.18.0 dated 2024-03-05
DESCRIPTION | 12 - MD5 | 232 ++++++++++++++++---------------- NEWS.md | 7 R/DataBackend.R | 2 R/DataBackendDataTable.R | 4 R/Task.R | 2 R/as_data_backend.R | 2 R/as_learner.R | 15 +- R/helper.R | 8 + R/mlr_learners.R | 2 R/resample.R | 2 build/partial.rdb |binary inst/testthat/helper_expectations.R | 4 man/BenchmarkResult.Rd | 4 man/DataBackend.Rd | 2 man/DataBackendDataTable.Rd | 26 +-- man/DataBackendMatrix.Rd | 26 +-- man/Learner.Rd | 4 man/LearnerClassif.Rd | 6 man/LearnerRegr.Rd | 6 man/Measure.Rd | 4 man/MeasureClassif.Rd | 6 man/MeasureRegr.Rd | 6 man/MeasureSimilarity.Rd | 6 man/PredictionClassif.Rd | 4 man/PredictionRegr.Rd | 4 man/Resampling.Rd | 6 man/Task.Rd | 34 ++-- man/TaskClassif.Rd | 14 - man/TaskGenerator.Rd | 4 man/TaskRegr.Rd | 10 - man/TaskSupervised.Rd | 10 - man/TaskUnsupervised.Rd | 6 man/as_data_backend.Rd | 4 man/as_learner.Rd | 5 man/mlr_learners.Rd | 2 man/mlr_learners_classif.debug.Rd | 6 man/mlr_learners_classif.featureless.Rd | 6 man/mlr_learners_classif.rpart.Rd | 6 man/mlr_learners_regr.debug.Rd | 6 man/mlr_learners_regr.featureless.Rd | 6 man/mlr_learners_regr.rpart.Rd | 6 man/mlr_measures.Rd | 2 man/mlr_measures_aic.Rd | 6 man/mlr_measures_bic.Rd | 6 man/mlr_measures_classif.acc.Rd | 10 - man/mlr_measures_classif.auc.Rd | 20 +- man/mlr_measures_classif.bacc.Rd | 10 - man/mlr_measures_classif.bbrier.Rd | 20 +- man/mlr_measures_classif.ce.Rd | 10 - man/mlr_measures_classif.costs.Rd | 16 +- man/mlr_measures_classif.dor.Rd | 20 +- man/mlr_measures_classif.fbeta.Rd | 20 +- man/mlr_measures_classif.fdr.Rd | 20 +- man/mlr_measures_classif.fn.Rd | 16 +- man/mlr_measures_classif.fnr.Rd | 16 +- man/mlr_measures_classif.fomr.Rd | 20 +- man/mlr_measures_classif.fp.Rd | 16 +- man/mlr_measures_classif.fpr.Rd | 16 +- man/mlr_measures_classif.logloss.Rd | 10 - man/mlr_measures_classif.mauc_au1p.Rd | 10 - man/mlr_measures_classif.mauc_au1u.Rd | 10 - man/mlr_measures_classif.mauc_aunp.Rd | 10 - man/mlr_measures_classif.mauc_aunu.Rd | 10 - man/mlr_measures_classif.mbrier.Rd | 10 - man/mlr_measures_classif.mcc.Rd | 20 +- man/mlr_measures_classif.npv.Rd | 20 +- man/mlr_measures_classif.ppv.Rd | 20 +- man/mlr_measures_classif.prauc.Rd | 20 +- man/mlr_measures_classif.precision.Rd | 20 +- man/mlr_measures_classif.recall.Rd | 20 +- man/mlr_measures_classif.sensitivity.Rd | 20 +- man/mlr_measures_classif.specificity.Rd | 20 +- man/mlr_measures_classif.tn.Rd | 16 +- man/mlr_measures_classif.tnr.Rd | 16 +- man/mlr_measures_classif.tp.Rd | 12 - man/mlr_measures_classif.tpr.Rd | 12 - man/mlr_measures_debug_classif.Rd | 6 man/mlr_measures_elapsed_time.Rd | 6 man/mlr_measures_oob_error.Rd | 6 man/mlr_measures_selected_features.Rd | 6 man/mlr_resamplings.Rd | 2 man/mlr_resamplings_bootstrap.Rd | 6 man/mlr_resamplings_custom.Rd | 4 man/mlr_resamplings_custom_cv.Rd | 4 man/mlr_resamplings_cv.Rd | 6 man/mlr_resamplings_holdout.Rd | 6 man/mlr_resamplings_insample.Rd | 6 man/mlr_resamplings_loo.Rd | 6 man/mlr_resamplings_repeated_cv.Rd | 6 man/mlr_resamplings_subsampling.Rd | 6 man/mlr_task_generators_2dnormals.Rd | 4 man/mlr_task_generators_cassini.Rd | 4 man/mlr_task_generators_circle.Rd | 4 man/mlr_task_generators_friedman1.Rd | 4 man/mlr_task_generators_moons.Rd | 4 man/mlr_task_generators_simplex.Rd | 4 man/mlr_task_generators_smiley.Rd | 4 man/mlr_task_generators_spirals.Rd | 4 man/mlr_task_generators_xor.Rd | 4 man/mlr_tasks.Rd | 2 man/mlr_tasks_boston_housing.Rd | 6 man/mlr_tasks_breast_cancer.Rd | 6 man/mlr_tasks_german_credit.Rd | 6 man/mlr_tasks_iris.Rd | 6 man/mlr_tasks_mtcars.Rd | 6 man/mlr_tasks_penguins.Rd | 6 man/mlr_tasks_pima.Rd | 6 man/mlr_tasks_sonar.Rd | 6 man/mlr_tasks_spam.Rd | 6 man/mlr_tasks_wine.Rd | 6 man/mlr_tasks_zoo.Rd | 6 tests/testthat/test_Dictionary.R | 17 ++ tests/testthat/test_as_learner.R | 11 + tests/testthat/test_benchmark.R | 14 + tests/testthat/test_parallel.R | 1 tests/testthat/test_resample.R | 15 ++ 117 files changed, 683 insertions(+), 602 deletions(-)
Title: Stochastic Approximation Expectation Maximization (SAEM)
Algorithm
Description: The 'saemix' package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm (i) computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, (ii) provides standard errors for the maximum likelihood estimator (iii) estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm (see Comets et al. (2017) <doi:10.18637/jss.v080.i03>). Many applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. The full PDF documentation for the package including references about the algorithm and examples can be downloaded on the github of the IAME research institute for 'saemix': <h [...truncated...]
Author: Emmanuelle Comets [aut, cre],
Audrey Lavenu [aut],
Marc Lavielle [aut],
Belhal Karimi [aut],
Maud Delattre [ctb],
Marilou Chanel [ctb],
Johannes Ranke [ctb] ,
Sofia Kaisaridi [ctb],
Lucie Fayette [ctb]
Maintainer: Emmanuelle Comets <emmanuelle.comets@inserm.fr>
Diff between saemix versions 3.2 dated 2023-06-27 and 3.3 dated 2024-03-05
CHANGES | 6 + DESCRIPTION | 8 +- MD5 | 61 ++++++++--------- NAMESPACE | 1 R/SaemixData.R | 46 ++++++++++--- R/SaemixModel.R | 129 +++++++++++++++++++++++++++++++++++-- R/SaemixObject.R | 40 ++++++----- R/func_FIM.R | 16 +++- R/func_aux.R | 89 ++++++++++++++----------- R/func_bootstrap.R | 13 +++ R/func_exploreData.R | 88 ++++++++++++++++++++++++- R/func_plots.R | 20 ++--- R/func_simulations.R | 139 ++++++++++++++++++++++++++++++++++------ R/zzz.R | 2 man/checkInitialFixedEffects.Rd |only man/coef.saemix.Rd | 6 - man/default.saemix.plots.Rd | 20 ++--- man/extract-methods.Rd | 2 man/initialize-methods.Rd | 2 man/logLik.Rd | 2 man/map.saemix.Rd | 1 man/plot-SaemixData.Rd | 8 ++ man/plotDiscreteData.Rd | 19 ++++- man/predict.SaemixModel.Rd | 3 man/replaceData.Rd | 2 man/saemixData.Rd | 6 - man/saemixModel.Rd | 6 - man/simulate.SaemixObject.Rd | 14 ++-- man/simulateDiscreteSaemix.Rd | 5 + man/sub-SaemixModel-method.Rd | 2 man/sub-SaemixObject-method.Rd | 2 man/transformCatCov.Rd | 13 +++ 32 files changed, 589 insertions(+), 182 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut]
,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 3.0.1 dated 2023-12-12 and 3.0.2 dated 2024-03-05
DESCRIPTION | 8 +- MD5 | 32 +++++----- NEWS.md | 8 ++ build/vignette.rds |binary data/crops.obic.rda |binary inst/doc/description-of-the-columns.html | 4 - inst/doc/obic_introduction.html | 93 ++++++++++++++++++------------- inst/doc/obic_score_aggregation.html | 6 +- inst/doc/obic_water_functions.html | 4 - inst/doc/obic_workability.html | 6 +- man/crops.obic.Rd | 2 tests/testthat/test-obic_farm.R | 2 tests/testthat/test-obic_field.R | 10 +-- tests/testthat/test-obic_field_dt.R | 10 +-- tests/testthat/test-waterstress.R | 2 vignettes/vignettes_references.bib | 1 vignettes/workability_references.bib | 1 17 files changed, 106 insertions(+), 83 deletions(-)
Title: Visualizations for 'mlr3'
Description: Visualization package of the 'mlr3' ecosystem. It features plots
for mlr3 objects such as tasks, learners, predictions, benchmark results,
tuning instances and filters via the 'autoplot()' generic of 'ggplot2'.
The package draws plots with the 'viridis' color palette and applies the
minimal theme. Visualizations include barplots, boxplots, histograms, ROC
curves, and Precision-Recall curves.
Author: Michel Lang [cre, aut] ,
Patrick Schratz [aut] ,
Raphael Sonabend [aut] ,
Marc Becker [aut] ,
Jakob Richter [aut] ,
Damir Pulatov [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3viz versions 0.7.0 dated 2023-12-21 and 0.8.0 dated 2024-03-05
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Title: Testing Homoscedasticity, Multivariate Normality, and Missing
Completely at Random
Description: To test whether the missing data mechanism, in a set of incompletely observed data, is one of missing completely at random (MCAR).
For detailed description see Jamshidian, M. Jalal, S., and Jansen, C. (2014). "MissMech: An R Package for Testing Homoscedasticity, Multivariate Normality, and Missing Completely at Random (MCAR)", Journal of Statistical Software, 56(6), 1-31. <https://www.jstatsoft.org/v56/i06/> <doi:10.18637/jss.v056.i06>.
Author: Mortaza Jamshidian [aut],
Siavash Jalal [aut],
Camden Jansen [aut],
Mao Kobayashi [cre]
Maintainer: Mao Kobayashi <kobamao.jp@gmail.com>
Diff between MissMech versions 1.0.3 dated 2024-01-23 and 1.0.4 dated 2024-03-05
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/Impute.R | 2 +- R/TestMCARNormality.R | 4 ++-- build/partial.rdb |binary man/Impute.Rd | 2 +- man/TestMCARNormality.Rd | 2 +- 8 files changed, 20 insertions(+), 16 deletions(-)
Title: Latent Variable Models
Description: A general implementation of Structural Equation Models
with latent variables (MLE, 2SLS, and composite likelihood
estimators) with both continuous, censored, and ordinal
outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>).
Mixture latent variable models and non-linear latent variable models
(Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>).
The package also provides methods for graph exploration (d-separation,
back-door criterion), simulation of general non-linear latent variable
models, and estimation of influence functions for a broad range of
statistical models.
Author: Klaus K. Holst [aut, cre],
Brice Ozenne [ctb],
Thomas Gerds [ctb]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between lava versions 1.7.3 dated 2023-11-04 and 1.8.0 dated 2024-03-05
DESCRIPTION | 21 MD5 | 98 NAMESPACE | 11 NEWS.md | 12 R/IC.R | 10 R/Objective.R | 4 R/compare.R | 6 R/csplit.R | 60 R/diagtest.R | 10 R/estimate.default.R | 1387 ++++---- R/gkgamma.R | 6 R/glmest.R | 58 R/iid.R | 2 R/lava-package.R | 4 R/lmers.R | 68 R/merge.R | 89 R/multipletesting.R | 92 R/operators.R | 16 R/optims.R | 4 R/score.R | 4 R/sim.default.R | 51 R/sim.lvm.R | 2 R/summary.R | 18 R/twostage.R | 14 R/utils.R | 5 build/vignette.rds |binary inst/doc/correlation.Rmd | 23 inst/doc/correlation.html | 99 inst/doc/influencefunction.R |only inst/doc/influencefunction.Rmd |only inst/doc/influencefunction.html |only inst/doc/nonlinear.R | 5 inst/doc/nonlinear.Rmd | 15 inst/doc/nonlinear.html | 5690 +----------------------------------- man/Print.Rd |only man/closed.testing.Rd | 5 man/estimate.array.Rd |only man/estimate.default.Rd | 12 man/lava-package.Rd | 2 man/op_match.Rd | 2 man/twostage.lvmfit.Rd | 2 tests/testthat/test-inference.R | 22 tests/testthat/test-influence.R | 34 tests/testthat/test-model.R | 36 tests/testthat/test-sim.R | 10 vignettes/correlation.Rmd | 23 vignettes/data/nonlinear_em0.rds |binary vignettes/data/nonlinear_fitcv.rds |binary vignettes/data/nonlinear_selmod.rds |binary vignettes/figs |only vignettes/influencefunction.Rmd |only vignettes/nonlinear.Rmd | 15 vignettes/ref.bib | 187 + 53 files changed, 1756 insertions(+), 6478 deletions(-)
Title: Semi-Supervised Algorithm for Document Scaling
Description: A word embeddings-based semi-supervised model for document scaling Watanabe (2020) <doi:10.1080/19312458.2020.1832976>.
LSS allows users to analyze large and complex corpora on arbitrary dimensions with seed words exploiting efficiency of word embeddings (SVD, Glove).
It can generate word vectors on a users-provided corpus or incorporate a pre-trained word vectors.
Author: Kohei Watanabe [aut, cre, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between LSX versions 1.3.2 dated 2023-12-20 and 1.4.0 dated 2024-03-05
DESCRIPTION | 9 +-- MD5 | 30 +++++----- NAMESPACE | 2 NEWS.md | 47 +++++++++------- R/as.textmodel.R | 2 R/bootstrap.R | 43 ++++++++++++--- R/textmodel.R | 14 ++-- R/textplot.R | 82 ++++++++++++++++++++--------- build/partial.rdb |binary man/bootstrap_lss.Rd | 26 +++++++-- man/textplot_terms.Rd | 25 +++++++- tests/data/data_dictionary_ideology.RData |only tests/data/data_dictionary_sentiment.RData |only tests/testthat/Rplots.pdf |binary tests/testthat/test-bootstrap.R | 69 +++++++++++++++++++----- tests/testthat/test-textmodel.R | 9 +-- tests/testthat/test-textplot.R | 19 ++++++ 17 files changed, 267 insertions(+), 110 deletions(-)
More information about ConsensusClustering at CRAN
Permanent link
More information about teal.modules.general at CRAN
Permanent link
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data
structures and functions that facilitate the plotting of missing values and
examination of imputations. This allows missing data dependencies to be
explored with minimal deviation from the common work patterns of 'ggplot2'
and tidy data. The work is fully discussed at Tierney & Cook (2023)
<doi:10.18637/jss.v105.i07>.
Author: Nicholas Tierney [aut, cre] ,
Di Cook [aut] ,
Miles McBain [aut] ,
Colin Fay [aut] ,
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb],
Andrew Heiss [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 1.0.0 dated 2023-02-02 and 1.1.0 dated 2024-03-05
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naniar-1.1.0/naniar/tests/testthat/test-as-shadow.R | 20 naniar-1.1.0/naniar/tests/testthat/test-as_shadow_upset.R | 35 naniar-1.1.0/naniar/tests/testthat/test-cast-shadow-shift-label.R | 5 naniar-1.1.0/naniar/tests/testthat/test-cast-shadow-shift.R | 5 naniar-1.1.0/naniar/tests/testthat/test-defunct.R | 45 - naniar-1.1.0/naniar/tests/testthat/test-gather-shadow.R | 15 naniar-1.1.0/naniar/tests/testthat/test-geom-miss-point.R | 36 naniar-1.1.0/naniar/tests/testthat/test-impute-below.R | 143 +++ naniar-1.1.0/naniar/tests/testthat/test-impute-factor.R |only naniar-1.1.0/naniar/tests/testthat/test-impute-fixed.R |only naniar-1.1.0/naniar/tests/testthat/test-impute-median.R | 31 naniar-1.1.0/naniar/tests/testthat/test-impute-mode.R |only naniar-1.1.0/naniar/tests/testthat/test-impute-zero.R |only naniar-1.1.0/naniar/tests/testthat/test-impute_mean.R | 62 + naniar-1.1.0/naniar/tests/testthat/test-label-miss-1d.R | 25 naniar-1.1.0/naniar/tests/testthat/test-label-miss-2d.R | 44 - naniar-1.1.0/naniar/tests/testthat/test-miss-case-summary.R | 89 +- naniar-1.1.0/naniar/tests/testthat/test-miss-case-table.R | 48 - naniar-1.1.0/naniar/tests/testthat/test-miss-prop-summary.R | 20 naniar-1.1.0/naniar/tests/testthat/test-miss-scan-count.R | 19 naniar-1.1.0/naniar/tests/testthat/test-miss-summary.R | 78 +- naniar-1.1.0/naniar/tests/testthat/test-miss-var-case-cumsum.R |only naniar-1.1.0/naniar/tests/testthat/test-miss-var-summary.R | 10 naniar-1.1.0/naniar/tests/testthat/test-miss-var-table.R | 23 naniar-1.1.0/naniar/tests/testthat/test-miss-var-which.R | 5 naniar-1.1.0/naniar/tests/testthat/test-miss-x-pct.R | 80 +- naniar-1.1.0/naniar/tests/testthat/test-nabular.R | 20 naniar-1.1.0/naniar/tests/testthat/test-prop_row.R | 43 - naniar-1.1.0/naniar/tests/testthat/test-replace-with-na-scoped-var.R | 5 naniar-1.1.0/naniar/tests/testthat/test-replace_na_with.R |only naniar-1.1.0/naniar/tests/testthat/test-set-n-prop-miss.R | 24 naniar-1.1.0/naniar/tests/testthat/test-shade.R | 21 naniar-1.1.0/naniar/tests/testthat/test-shadow-long.R | 78 -- naniar-1.1.0/naniar/tests/testthat/test-shadow-shift.R | 89 -- naniar-1.1.0/naniar/tests/testthat/test-special-missing-values.R | 5 naniar-1.1.0/naniar/vignettes/getting-started-w-naniar.Rmd | 4 159 files changed, 2624 insertions(+), 1512 deletions(-)
More information about DiscreteDatasets at CRAN
Permanent link
Title: Data Sets for Copula Modeling
Description: Data sets used for copula modeling in addition to those in
the R package 'copula'. These include a random subsample from the US National
Education Longitudinal Study (NELS) of 1988 and nursing home data from
Wisconsin.
Author: Marius Hofert [aut, cre],
Ivan Kojadinovic [aut],
Martin Maechler [aut],
Jun Yan [aut],
Edward W. Frees [dtc]
Maintainer: Marius Hofert <mhofert@hku.hk>
Diff between copulaData versions 0.0-1 dated 2017-10-16 and 0.0-2 dated 2024-03-05
DESCRIPTION | 29 +++++++++++++++++++---------- LICENCE | 4 ++-- MD5 | 8 ++++---- man/NELS.Rd | 22 ++++++++++++++++++---- man/nursingHomes.Rd | 3 ++- 5 files changed, 45 insertions(+), 21 deletions(-)
Title: Mixed Models for Repeated Measures
Description: Mixed models for repeated measures (MMRM) are a popular
choice for analyzing longitudinal continuous outcomes in randomized
clinical trials and beyond; see Cnaan, Laird and Slasor (1997)
<doi:10.1002/(SICI)1097-0258(19971030)16:20%3C2349::AID-SIM667%3E3.0.CO;2-E>
for a tutorial and Mallinckrodt, Lane, Schnell, Peng and Mancuso
(2008) <doi:10.1177/009286150804200402> for a review. This package
implements MMRM based on the marginal linear model without random
effects using Template Model Builder ('TMB') which enables fast and
robust model fitting. Users can specify a variety of covariance
matrices, weight observations, fit models with restricted or standard
maximum likelihood inference, perform hypothesis testing with
Satterthwaite or Kenward-Roger adjustment, and extract least square
means estimates by using 'emmeans'.
Author: Daniel Sabanes Bove [aut, cre],
Liming Li [aut],
Julia Dedic [aut],
Doug Kelkhoff [aut],
Kevin Kunzmann [aut],
Brian Matthew Lang [aut],
Christian Stock [aut],
Ya Wang [aut],
Craig Gower-Page [ctb],
Dan James [aut],
Jonathan Sidi [aut],
Daniel Leibov [...truncated...]
Maintainer: Daniel Sabanes Bove <daniel.sabanes_bove@roche.com>
Diff between mmrm versions 0.3.10 dated 2024-01-26 and 0.3.11 dated 2024-03-05
DESCRIPTION | 11 MD5 | 53 NEWS.md | 7 R/data.R | 2 R/fit.R | 6 R/interop-car.R | 6 R/tmb-methods.R | 3 R/utils.R | 7 build/partial.rdb |binary inst/doc/algorithm.html | 317 +- inst/doc/between_within.html | 415 +-- inst/doc/coef_vcov.html | 139 - inst/doc/covariance.html | 310 +- inst/doc/empirical_wls.html | 232 + inst/doc/hypothesis_testing.html | 444 ++- inst/doc/introduction.html | 4086 +++++++++++++++--------------- inst/doc/kenward.html | 379 ++ inst/doc/methodological_introduction.html | 281 +- inst/doc/mmrm_review_methods.html | 320 +- inst/doc/package_structure.html | 283 +- inst/doc/predict.html | 284 +- inst/doc/satterthwaite.html | 262 + man/fev_data.Rd | 2 man/mmrm-package.Rd | 2 src/utils.h | 2 tests/testthat/test-car.R | 18 tests/testthat/test-fit.R | 12 tests/testthat/test-residual.R |only 28 files changed, 4896 insertions(+), 2987 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-17 0.4.0
2023-01-05 0.3.3
2022-12-02 0.3.2
2022-07-06 0.3.1
2022-01-11 0.3.0
2021-04-20 0.2.3
2020-11-23 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-02-16 0.1.0
Title: Tools for Spell Checking in R
Description: Spell checking common document formats including latex, markdown, manual pages,
and description files. Includes utilities to automate checking of documentation and
vignettes as a unit test during 'R CMD check'. Both British and American English are
supported out of the box and other languages can be added. In addition, packages may
define a 'wordlist' to allow custom terminology without having to abuse punctuation.
Author: Jeroen Ooms [cre, aut] ,
Jim Hester [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between spelling versions 2.2.1 dated 2023-03-22 and 2.3.0 dated 2024-03-05
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- NEWS | 4 ++++ R/check-files.R | 2 +- R/parse-markdown.R | 10 ++++++++-- R/spell-check.R | 7 ++++--- R/wordlist.R | 13 ++++++++++--- man/spell_check_files.Rd | 7 ++++--- man/spell_check_package.Rd | 5 +++-- man/wordlist.Rd | 5 +++-- 10 files changed, 52 insertions(+), 31 deletions(-)
Title: Gene-Level Variant Association Tests for Pedigree Data
Description: Gene-level variant association tests with disease status for pedigree data: kernel and burden association statistics.
Author: Schaid Daniel [aut],
Visconti Alessia [ctb],
Jason Sinnwell [aut, cre]
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between pedgene versions 3.6 dated 2022-10-18 and 3.8 dated 2024-03-05
pedgene-3.6/pedgene/R/format.relation.R |only pedgene-3.6/pedgene/man/format.relation.Rd |only pedgene-3.8/pedgene/DESCRIPTION | 14 +++++++------- pedgene-3.8/pedgene/MD5 | 15 ++++++++------- pedgene-3.8/pedgene/R/format_relation.R |only pedgene-3.8/pedgene/README.md |only pedgene-3.8/pedgene/build/vignette.rds |binary pedgene-3.8/pedgene/inst/NEWS.Rd | 5 +++++ pedgene-3.8/pedgene/inst/doc/pedgene.pdf |binary pedgene-3.8/pedgene/man/example.geno.Rd | 8 ++++---- pedgene-3.8/pedgene/man/format_relation.Rd |only 11 files changed, 24 insertions(+), 18 deletions(-)
Title: Search Spaces for 'mlr3'
Description: Collection of search spaces for hyperparameter optimization in the
'mlr3' ecosystem. It features ready-to-use search spaces for many popular
machine learning algorithms. The search spaces are from scientific articles
and work for a wide range of data sets.
Author: Marc Becker [cre, aut] ,
Michel Lang [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuningspaces versions 0.4.0 dated 2023-04-20 and 0.5.0 dated 2024-03-05
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/TuningSpace.R | 3 ++- R/tuning_spaces_rbv1.R | 8 ++++---- README.md | 26 +++++++++++++------------- man/mlr_tuning_spaces_rbv1.Rd | 6 +++--- tests/testthat/helper.R | 13 ++++++++++++- tests/testthat/test_as_search_space.R | 2 +- 9 files changed, 53 insertions(+), 36 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: Hyperparameter Optimization for 'mlr3'
Description: Hyperparameter optimization package of the 'mlr3' ecosystem. It
features highly configurable search spaces via the 'paradox' package and
finds optimal hyperparameter configurations for any 'mlr3' learner.
'mlr3tuning' works with several optimization algorithms e.g. Random
Search, Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and
Hyperband (in 'mlr3hyperband'). Moreover, it can automatically optimize
learners and estimate the performance of optimized models with nested
resampling.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.19.2 dated 2023-11-28 and 0.20.0 dated 2024-03-05
DESCRIPTION | 8 +-- MD5 | 60 ++++++++++++------------- NAMESPACE | 6 ++ NEWS.md | 5 ++ R/Tuner.R | 7 +- R/TunerIrace.R | 34 +++++++++----- R/helper.R | 31 ++++++++++-- README.md | 24 +++++----- inst/testthat/helper_misc.R | 24 ++++------ inst/testthat/helper_tuner.R | 19 ++++--- man/Tuner.Rd | 6 -- man/mlr_tuners_cmaes.Rd | 4 - man/mlr_tuners_design_points.Rd | 4 - man/mlr_tuners_gensa.Rd | 4 - man/mlr_tuners_grid_search.Rd | 4 - man/mlr_tuners_irace.Rd | 4 - man/mlr_tuners_nloptr.Rd | 4 - man/mlr_tuners_random_search.Rd | 4 - tests/testthat/helper.R | 7 ++ tests/testthat/test_ArchiveTuning.R | 8 +-- tests/testthat/test_AutoTuner.R | 32 +++++++------ tests/testthat/test_Tuner.R | 28 +++++------ tests/testthat/test_TunerCmaes.R | 2 tests/testthat/test_TunerGenSA.R | 18 ++----- tests/testthat/test_TunerGridSearch.R | 12 ++--- tests/testthat/test_TuningInstanceMultiCrit.R | 28 +++++------ tests/testthat/test_TuningInstanceSingleCrit.R | 39 ++++++++-------- tests/testthat/test_error_handling.R | 12 ++--- tests/testthat/test_hotstart.R | 16 +++--- tests/testthat/test_trafos.R | 32 +++++-------- tests/testthat/test_tune.R | 10 +--- 31 files changed, 266 insertions(+), 230 deletions(-)
Title: Hyperband for 'mlr3'
Description: Successive Halving (Jamieson and Talwalkar (2016)
<arXiv:1502.07943>) and Hyperband (Li et al. 2018 <arXiv:1603.06560>)
optimization algorithm for the mlr3 ecosystem. The implementation in
mlr3hyperband features improved scheduling and parallelizes the evaluation
of configurations. The package includes tuners for hyperparameter
optimization in mlr3tuning and optimizers for black-box optimization in
bbotk.
Author: Marc Becker [aut, cre] ,
Sebastian Gruber [aut] ,
Jakob Richter [aut] ,
Julia Moosbauer [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3hyperband versions 0.4.5 dated 2023-03-02 and 0.5.0 dated 2024-03-05
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/OptimizerHyperband.R | 2 +- tests/testthat/test_TunerHyperband.R | 8 ++++---- tests/testthat/test_TunerSuccessiveHalving.R | 8 ++++---- 6 files changed, 22 insertions(+), 18 deletions(-)
Title: Visualizations of Distributions and Uncertainty
Description: Provides primitives for visualizing distributions using 'ggplot2' that are particularly tuned for
visualizing uncertainty in either a frequentist or Bayesian mode. Both analytical distributions (such as
frequentist confidence distributions or Bayesian priors) and distributions represented as samples (such as
bootstrap distributions or Bayesian posterior samples) are easily visualized. Visualization primitives include
but are not limited to: points with multiple uncertainty intervals,
eye plots (Spiegelhalter D., 1999) <https://ideas.repec.org/a/bla/jorssa/v162y1999i1p45-58.html>,
density plots, gradient plots, dot plots (Wilkinson L., 1999) <doi:10.1080/00031305.1999.10474474>,
quantile dot plots (Kay M., Kola T., Hullman J., Munson S., 2016) <doi:10.1145/2858036.2858558>,
complementary cumulative distribution function
barplots (Fernandes M., Walls L., Munson S., Hullman J., Kay M., 2018) <doi:10.1145/3173574.3173718>,
and fit curves with multiple uncertainty ri [...truncated...]
Author: Matthew Kay [aut, cre],
Brenton M. Wiernik [ctb]
Maintainer: Matthew Kay <mjskay@northwestern.edu>
Diff between ggdist versions 3.3.1 dated 2023-11-27 and 3.3.2 dated 2024-03-05
ggdist-3.3.1/ggdist/man/scales.Rd |only ggdist-3.3.1/ggdist/tests/testthat/_snaps/test.guide_rampbar/color-ramp-without-to.svg |only ggdist-3.3.1/ggdist/tests/testthat/_snaps/test.stat_sample_slabinterval/fill-type-gradient-with-two-groups-h.svg |only ggdist-3.3.2/ggdist/DESCRIPTION | 45 ggdist-3.3.2/ggdist/MD5 | 496 +++++---- ggdist-3.3.2/ggdist/NAMESPACE | 68 - ggdist-3.3.2/ggdist/NEWS.md | 59 + ggdist-3.3.2/ggdist/R/abstract_geom.R | 30 ggdist-3.3.2/ggdist/R/abstract_stat.R | 22 ggdist-3.3.2/ggdist/R/abstract_stat_slabinterval.R | 22 ggdist-3.3.2/ggdist/R/auto_partial.R | 109 +- ggdist-3.3.2/ggdist/R/binning_methods.R | 65 - ggdist-3.3.2/ggdist/R/bounder.R | 51 - ggdist-3.3.2/ggdist/R/compat.R |only ggdist-3.3.2/ggdist/R/curve_interval.R | 72 - ggdist-3.3.2/ggdist/R/cut_cdf_qi.R | 2 ggdist-3.3.2/ggdist/R/density.R | 110 +- ggdist-3.3.2/ggdist/R/distributions.R | 227 +++- ggdist-3.3.2/ggdist/R/draw_key_slabinterval.R | 48 ggdist-3.3.2/ggdist/R/geom.R | 43 ggdist-3.3.2/ggdist/R/geom_blur_dots.R |only ggdist-3.3.2/ggdist/R/geom_dotsinterval.R | 271 +++-- ggdist-3.3.2/ggdist/R/geom_interval.R | 3 ggdist-3.3.2/ggdist/R/geom_lineribbon.R | 118 +- ggdist-3.3.2/ggdist/R/geom_pointinterval.R | 5 ggdist-3.3.2/ggdist/R/geom_slab.R | 10 ggdist-3.3.2/ggdist/R/geom_slabinterval.R | 353 +++++-- ggdist-3.3.2/ggdist/R/geom_spike.R | 38 ggdist-3.3.2/ggdist/R/geom_swarm.R | 4 ggdist-3.3.2/ggdist/R/ggdist-package.R | 3 ggdist-3.3.2/ggdist/R/guide_rampbar.R | 56 - ggdist-3.3.2/ggdist/R/lkjcorr_marginal.R | 10 ggdist-3.3.2/ggdist/R/parse_dist.R | 89 + ggdist-3.3.2/ggdist/R/partial_colour_ramp.R |only ggdist-3.3.2/ggdist/R/point_interval.R | 153 +-- ggdist-3.3.2/ggdist/R/position_dodgejust.R | 10 ggdist-3.3.2/ggdist/R/pr.R | 13 ggdist-3.3.2/ggdist/R/rd.R | 57 - ggdist-3.3.2/ggdist/R/rd_dotsinterval.R | 82 + ggdist-3.3.2/ggdist/R/rd_lineribbon.R | 14 ggdist-3.3.2/ggdist/R/rd_slabinterval.R | 28 ggdist-3.3.2/ggdist/R/scale_.R | 131 +- ggdist-3.3.2/ggdist/R/scale_colour_ramp.R | 108 +- ggdist-3.3.2/ggdist/R/scale_side_mirrored.R | 4 ggdist-3.3.2/ggdist/R/scale_thickness.R | 96 + ggdist-3.3.2/ggdist/R/smooth.R | 14 ggdist-3.3.2/ggdist/R/stat.R | 5 ggdist-3.3.2/ggdist/R/stat_dotsinterval.R | 28 ggdist-3.3.2/ggdist/R/stat_mcse_dots.R |only ggdist-3.3.2/ggdist/R/stat_slabinterval.R | 92 + ggdist-3.3.2/ggdist/R/stat_spike.R | 130 ++ ggdist-3.3.2/ggdist/R/student_t.R | 4 ggdist-3.3.2/ggdist/R/subguide.R |only ggdist-3.3.2/ggdist/R/testthat.R | 7 ggdist-3.3.2/ggdist/R/theme_ggdist.R | 17 ggdist-3.3.2/ggdist/R/tidy_format_translators.R | 23 ggdist-3.3.2/ggdist/R/util.R | 98 + ggdist-3.3.2/ggdist/R/weighted_ecdf.R | 18 ggdist-3.3.2/ggdist/R/weighted_hist.R | 239 +++- ggdist-3.3.2/ggdist/R/weighted_quantile.R | 42 ggdist-3.3.2/ggdist/inst/CITATION | 4 ggdist-3.3.2/ggdist/inst/doc/dotsinterval.R | 297 +++-- ggdist-3.3.2/ggdist/inst/doc/dotsinterval.Rmd | 333 +++--- ggdist-3.3.2/ggdist/inst/doc/dotsinterval.html | 500 +++++----- ggdist-3.3.2/ggdist/inst/doc/freq-uncertainty-vis.R | 69 - ggdist-3.3.2/ggdist/inst/doc/freq-uncertainty-vis.Rmd | 25 ggdist-3.3.2/ggdist/inst/doc/freq-uncertainty-vis.html | 79 - ggdist-3.3.2/ggdist/inst/doc/lineribbon.R | 113 +- ggdist-3.3.2/ggdist/inst/doc/lineribbon.Rmd | 47 ggdist-3.3.2/ggdist/inst/doc/lineribbon.html | 101 -- ggdist-3.3.2/ggdist/inst/doc/slabinterval.R | 363 ++++--- ggdist-3.3.2/ggdist/inst/doc/slabinterval.Rmd | 267 +++-- ggdist-3.3.2/ggdist/inst/doc/slabinterval.html | 307 +++--- ggdist-3.3.2/ggdist/man/align.Rd | 1 ggdist-3.3.2/ggdist/man/auto_partial.Rd | 17 ggdist-3.3.2/ggdist/man/bandwidth.Rd | 1 ggdist-3.3.2/ggdist/man/bin_dots.Rd | 36 ggdist-3.3.2/ggdist/man/blur.Rd |only ggdist-3.3.2/ggdist/man/bounder_cdf.Rd | 143 +- ggdist-3.3.2/ggdist/man/bounder_cooke.Rd | 7 ggdist-3.3.2/ggdist/man/bounder_range.Rd | 1 ggdist-3.3.2/ggdist/man/breaks.Rd | 32 ggdist-3.3.2/ggdist/man/curve_interval.Rd | 4 ggdist-3.3.2/ggdist/man/density_bounded.Rd | 1 ggdist-3.3.2/ggdist/man/density_histogram.Rd | 11 ggdist-3.3.2/ggdist/man/density_unbounded.Rd | 1 ggdist-3.3.2/ggdist/man/find_dotplot_binwidth.Rd | 36 ggdist-3.3.2/ggdist/man/geom_blur_dots.Rd |only ggdist-3.3.2/ggdist/man/geom_dots.Rd | 104 +- ggdist-3.3.2/ggdist/man/geom_dotsinterval.Rd | 109 +- ggdist-3.3.2/ggdist/man/geom_interval.Rd | 29 ggdist-3.3.2/ggdist/man/geom_lineribbon.Rd | 9 ggdist-3.3.2/ggdist/man/geom_pointinterval.Rd | 27 ggdist-3.3.2/ggdist/man/geom_slab.Rd | 33 ggdist-3.3.2/ggdist/man/geom_slabinterval.Rd | 38 ggdist-3.3.2/ggdist/man/geom_spike.Rd | 25 ggdist-3.3.2/ggdist/man/geom_swarm.Rd | 101 +- ggdist-3.3.2/ggdist/man/geom_weave.Rd | 101 +- ggdist-3.3.2/ggdist/man/ggdist-ggproto.Rd | 10 ggdist-3.3.2/ggdist/man/ggdist-package.Rd | 18 ggdist-3.3.2/ggdist/man/guide_rampbar.Rd | 79 - 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Title: Utilities for Graphical Rendering and Fonts Management
Description: Tools are provided to compute metrics of
formatted strings and to check the availability of a font.
Another set of functions is provided to support the collection
of fonts from 'Google Fonts' in a cache. Their use is simple within
'R Markdown' documents and 'shiny' applications but also with graphic
productions generated with the 'ggiraph', 'ragg' and 'svglite' packages
or with tabular productions from the 'flextable' package.
Author: David Gohel [aut, cre],
Hadley Wickham [aut],
Lionel Henry [aut],
Jeroen Ooms [aut] ,
Yixuan Qiu [ctb],
R Core Team [cph] ,
ArData [cph],
RStudio [cph]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between gdtools versions 0.3.6 dated 2024-02-22 and 0.3.7 dated 2024-03-05
DESCRIPTION | 6 ++-- MD5 | 17 +++++++------ NEWS | 12 +++++++++ R/font-caching.R | 45 ------------------------------------ R/fonts.R | 22 ----------------- R/gdtools.R | 1 R/liberation-sans.R |only R/sysdata.rda |binary man/liberationsansHtmlDependency.Rd | 2 - man/register_liberationsans.Rd | 2 - 10 files changed, 26 insertions(+), 81 deletions(-)
Title: Mixed Effects Cox Models
Description: Fit Cox proportional hazards models containing both
fixed and random effects. The random effects can have a general form, of which
familial interactions (a "kinship" matrix) is a particular special case.
Note that the simplest case of a mixed effects Cox model, i.e. a single random
per-group intercept, is also called a "frailty" model. The approach is based
on Ripatti and Palmgren, Biometrics 2002.
Author: Terry M. Therneau [aut, cre]
Maintainer: Terry M. Therneau <therneau.terry@mayo.edu>
Diff between coxme versions 2.2-19 dated 2024-03-02 and 2.2-20 dated 2024-03-05
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/coxme.control.R | 3 ++- inst/NEWS.Rd | 5 +++++ inst/doc/coxme.pdf |binary inst/doc/laplace.pdf |binary inst/doc/lmekin.pdf |binary inst/doc/variance.pdf |binary 8 files changed, 17 insertions(+), 11 deletions(-)