Title: 'tint' is not 'Tufte'
Description: A 'tufte'-alike style for 'rmarkdown'.
A modern take on the 'Tufte' design for pdf and html vignettes,
building on the 'tufte' package with additional contributions
from the 'knitr' and 'ggtufte' package, and also acknowledging
the key influence of 'envisioned css'.
Author: Dirk Eddelbuettel [aut, cre] ,
Jonathan Gilligan [ctb]
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between tint versions 0.1.5 dated 2025-03-27 and 0.1.6 dated 2025-09-25
ChangeLog | 9 ++ DESCRIPTION | 14 ++- MD5 | 20 ++--- README.md | 2 build/vignette.rds |binary inst/NEWS.Rd | 7 + inst/doc/tintHtmlIntro.html | 38 +++++++--- inst/doc/tintPdfIntro.pdf |binary inst/rmarkdown/templates/tintBook/resources/auto |only inst/rmarkdown/templates/tintBook/resources/tintBook-template.tex | 2 inst/rmarkdown/templates/tintPdf/resources/auto |only inst/rmarkdown/templates/tintPdf/resources/tintPdf-template.tex | 2 12 files changed, 68 insertions(+), 26 deletions(-)
Title: Seasonal to Decadal Verification
Description: An advanced version of package 's2dverification'. Intended for
seasonal to decadal (s2d) climate forecast verification, but also applicable
to other types of forecasts or general climate analysis. This package is
specifically designed for comparing experimental and observational datasets.
It provides functionality for data retrieval, post-processing, skill score
computation against observations, and visualization. Compared to
's2dverification', 's2dv' is more compatible with the package 'startR', able
to use multiple cores for computation and handle multi-dimensional arrays
with a higher flexibility. The Climate Data Operators (CDO) version used in
development is 1.9.8. Implements methods described in Wilks (2011)
<doi:10.1016/B978-0-12-385022-5.00008-7>, DelSole and Tippett
(2016) <doi:10.1175/MWR-D-15-0218.1>, Kharin et al. (2012)
<doi:10.1029/2012GL052647>, Doblas-Reyes et al. (2003)
<doi:10.1007/s00382-003-0350-4>.
Author: BSC-CNS [aut, cph],
An-Chi Ho [aut],
Nuria Perez-Zanon [aut],
Roberto Bilbao [ctb],
Josep Cos [ctb],
Carlos Delgado [ctb],
Llorenc Lledo [ctb],
Andrea Manrique [ctb],
Deborah Verfaillie [ctb],
Eva Rifa [ctb],
Victoria Agudetse [ctb],
Nadia Milders [c [...truncated...]
Maintainer: Ariadna Batalla <ariadna.batalla@bsc.es>
This is a re-admission after prior archival of version 2.1.0 dated 2024-10-13
Diff between s2dv versions 2.1.0 dated 2024-10-13 and 2.2.0 dated 2025-09-25
DESCRIPTION | 34 ++-- MD5 | 279 ++++++++++++++++++------------------ NAMESPACE | 1 NEWS.md | 16 +- R/ACC.R | 52 +++--- R/AbsBiasSS.R | 10 - R/AnimateMap.R | 48 ++---- R/Ano.R | 20 +- R/Ano_CrossValid.R | 18 +- R/Bias.R | 10 - R/BrierScore.R | 26 +-- R/CDORemap.R | 271 +++++++++++++++++------------------ R/CRPS.R | 6 R/CRPSS.R | 10 - R/Clim.R | 21 +- R/Cluster.R | 58 +++---- R/ColorBar.R | 11 - R/Composite.R | 76 ++++----- R/ConfigApplyMatchingEntries.R | 43 +++-- R/ConfigEditDefinition.R | 42 ++--- R/ConfigEditEntry.R | 58 +++---- R/ConfigFileOpen.R | 46 +++--- R/ConfigShowSimilarEntries.R | 40 ++--- R/ConfigShowTable.R | 38 ++-- R/Consist_Trend.R | 50 +++--- R/Corr.R | 46 +++--- R/EOF.R | 42 ++--- R/Eno.R | 12 - R/EuroAtlanticTC.R | 13 - R/Filter.R | 30 +-- R/GetProbs.R | 22 +- R/Histo2Hindcast.R | 43 ++--- R/InsertDim.R | 6 R/LeapYear.R | 8 - R/Load.R | 291 +++++++++++++++++--------------------- R/LoadSampleData.R |only R/MSE.R | 36 ++-- R/MSSS.R | 22 +- R/MeanDims.R | 11 - R/NAO.R | 36 ++-- R/Persistence.R | 32 ++-- R/Plot2VarsVsLTime.R | 73 +++++---- R/PlotACC.R | 58 +++---- R/PlotAno.R | 31 ++-- R/PlotBoxWhisker.R | 69 +++------ R/PlotClim.R | 17 +- R/PlotEquiMap.R | 38 +--- R/PlotLayout.R | 41 +---- R/PlotMatrix.R | 8 - R/PlotSection.R | 12 + R/PlotStereoMap.R | 15 + R/PlotVsLTime.R | 55 +++---- R/ProbBins.R | 16 -- R/ProjectField.R | 52 +++--- R/REOF.R | 41 ++--- R/RMS.R | 40 ++--- R/RMSSS.R | 99 ++++++------ R/ROCSS.R | 22 +- R/RPS.R | 86 +++++++---- R/RPSS.R | 192 ++++++++++++++++--------- R/RandomWalkTest.R | 13 + R/RatioPredictableComponents.R | 6 R/RatioRMS.R | 71 ++++----- R/RatioSDRMS.R | 24 +-- R/Regression.R | 16 +- R/Reorder.R | 21 +- R/Season.R | 21 +- R/Smoothing.R | 27 +-- R/Spectrum.R | 30 +-- R/SprErr.R | 10 - R/Spread.R | 74 ++++----- R/StatSeasAtlHurr.R | 18 +- R/ToyModel.R | 91 ++++------- R/Trend.R | 8 - R/UltimateBrier.R | 31 +--- R/Utils.R | 57 ------- R/clim.palette.R | 17 +- build |only data/sampleDepthData.RData |binary data/sampleMap.RData |binary data/sampleTimeSeries.RData |binary man/ACC.Rd | 26 +-- man/AnimateMap.Rd | 43 +---- man/Ano.Rd | 8 - man/Ano_CrossValid.Rd | 12 - man/BrierScore.Rd | 2 man/CDORemap.Rd | 60 ++++--- man/Clim.Rd | 11 - man/Cluster.Rd | 6 man/ColorBar.Rd | 3 man/Composite.Rd | 10 - man/ConfigApplyMatchingEntries.Rd | 13 - man/ConfigEditDefinition.Rd | 12 - man/ConfigEditEntry.Rd | 19 +- man/ConfigFileOpen.Rd | 12 - man/ConfigShowSimilarEntries.Rd | 12 - man/ConfigShowTable.Rd | 10 - man/Consist_Trend.Rd | 18 +- man/Corr.Rd | 12 - man/EOF.Rd | 19 +- man/Eno.Rd | 2 man/Filter.Rd | 16 +- man/GetProbs.Rd | 6 man/Histo2Hindcast.Rd | 25 +-- man/Load.Rd | 65 ++------ man/LoadSampleData.Rd |only man/MSE.Rd | 6 man/MSSS.Rd | 2 man/MeanDims.Rd | 1 man/NAO.Rd | 6 man/Persistence.Rd | 2 man/Plot2VarsVsLTime.Rd | 29 ++- man/PlotACC.Rd | 28 +-- man/PlotAno.Rd | 9 - man/PlotBoxWhisker.Rd | 34 ---- man/PlotClim.Rd | 9 - man/PlotEquiMap.Rd | 34 ---- man/PlotLayout.Rd | 35 ---- man/PlotMatrix.Rd | 3 man/PlotSection.Rd | 6 man/PlotStereoMap.Rd | 5 man/PlotVsLTime.Rd | 21 +- man/ProbBins.Rd | 8 - man/ProjectField.Rd | 39 ++--- man/REOF.Rd | 18 +- man/RMS.Rd | 6 man/RMSSS.Rd | 39 ++--- man/RPS.Rd | 17 +- man/RPSS.Rd | 36 +++- man/RatioRMS.Rd | 23 +-- man/RatioSDRMS.Rd | 10 - man/Regression.Rd | 2 man/Reorder.Rd | 21 +- man/Season.Rd | 1 man/Smoothing.Rd | 9 - man/Spectrum.Rd | 16 +- man/Spread.Rd | 44 ++--- man/ToyModel.Rd | 41 +---- man/Trend.Rd | 2 man/UltimateBrier.Rd | 15 - man/clim.palette.Rd | 5 man/s2dv-package.Rd | 4 142 files changed, 2165 insertions(+), 2277 deletions(-)
Title: Phenotypic Integration Index
Description: Provides functions to estimate the size-controlled phenotypic integration index, a novel method by Torices & Méndez (2014) <doi:10.1086/676622> to solve problems due to individual size when estimating integration (namely, larger individuals have larger components, which will drive a correlation between components only due to resource availability that might obscure the observed measures of integration). In addition, the package also provides the classical estimation by Wagner (1984) <doi:10.1007/BF00275224>, bootstrapping and jackknife methods to calculate confidence intervals and a significance test for both integration indices. Further details can be found in Torices & Muñoz-Pajares <doi:10.3732/apps.1400104>.
Author: R. Torices [aut],
A. J. Munoz-Pajares [aut, cre]
Maintainer: A. J. Munoz-Pajares <ajesusmp@ugr.es>
This is a re-admission after prior archival of version 1.3.1 dated 2017-06-02
Diff between PHENIX versions 1.3.1 dated 2017-06-02 and 1.3.2 dated 2025-09-25
PHENIX-1.3.1/PHENIX/NEWS |only PHENIX-1.3.2/PHENIX/DESCRIPTION | 22 +++++++++++++++------- PHENIX-1.3.2/PHENIX/MD5 | 7 +++---- PHENIX-1.3.2/PHENIX/inst/CITATION | 14 +++++--------- PHENIX-1.3.2/PHENIX/man/cor.par.Rd | 1 - 5 files changed, 23 insertions(+), 21 deletions(-)
Title: Computer Modern Font for Use with Extrafont Package
Description: Computer Modern font with Paul Murrell's symbol extensions. Is is to be used with the **extrafont** package. When this font package is installed, the CM fonts will be available for PDF or Postscript output files; however, this will (probably) not make the font available for screen or bitmap output files.
Author: Winston Chang [aut],
Alexej Kryukov [aut],
Paul Murrell [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between fontcm versions 1.1 dated 2014-03-19 and 1.2 dated 2025-09-25
fontcm-1.1/fontcm/man/fontcm.Rd |only fontcm-1.2/fontcm/DESCRIPTION | 37 ++++++++++++++++++++++---------- fontcm-1.2/fontcm/MD5 | 21 ++++++++++++------ fontcm-1.2/fontcm/NAMESPACE | 2 - fontcm-1.2/fontcm/NEWS | 11 +++++++++ fontcm-1.2/fontcm/R/fontcm.r | 18 ++++++--------- fontcm-1.2/fontcm/README.md | 29 +++++++++++++++++++++++-- fontcm-1.2/fontcm/inst/CITATION |only fontcm-1.2/fontcm/man/fontcm-package.Rd |only fontcm-1.2/fontcm/tests |only 10 files changed, 88 insertions(+), 30 deletions(-)
Title: Chronological Bayesian Models Integrating Optically Stimulated
Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and C-14 age
estimates. Bayesian models are based on the following publications:
Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003>
and Combes et al. (2015) <doi:10.1016/j.quageo.2015.04.001>. This
includes, amongst others, data import, export, application of age
models and palaeodose model.
Author: Claire Christophe [aut],
Anne Philippe [aut, cre] ,
Sebastian Kreutzer [aut] ,
Guillaume Guerin [aut] ,
Frederik Harly Baumgarten [aut] ,
Nicolas Frerebeau [aut] ,
Universite Bordeaux Montaigne [cph, fnd],
CNRS [fnd],
LabEx Sciences archeologiques de [...truncated...]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between BayLum versions 0.3.2 dated 2024-06-16 and 0.3.3 dated 2025-09-25
BayLum-0.3.2/BayLum/inst/doc/BayLum.html.asis |only BayLum-0.3.2/BayLum/inst/doc/ConfigFile_Specification.html.asis |only BayLum-0.3.2/BayLum/man/figures/BayLum_logo.png |only BayLum-0.3.2/BayLum/vignettes/BayLum.html.asis |only BayLum-0.3.2/BayLum/vignettes/ConfigFile_Specification.html.asis |only BayLum-0.3.3/BayLum/DESCRIPTION | 77 - BayLum-0.3.3/BayLum/MD5 | 118 - BayLum-0.3.3/BayLum/NEWS.md | 86 - BayLum-0.3.3/BayLum/R/AgeC14_Computation.R | 4 BayLum-0.3.3/BayLum/R/AgeS_Computation.R | 2 BayLum-0.3.3/BayLum/R/Age_Computation.R | 25 BayLum-0.3.3/BayLum/R/Age_OSLC14.R | 6 BayLum-0.3.3/BayLum/R/BayLum-package.R | 72 - BayLum-0.3.3/BayLum/R/Generate_DataFile.R | 8 BayLum-0.3.3/BayLum/R/Generate_DataFile_MG.R | 4 BayLum-0.3.3/BayLum/R/Palaeodose_Computation.R | 14 BayLum-0.3.3/BayLum/R/create_DataFile.R | 2 BayLum-0.3.3/BayLum/R/plot_MCMC.R | 2 BayLum-0.3.3/BayLum/R/plot_Scatterplots.R | 2 BayLum-0.3.3/BayLum/README.md | 85 - BayLum-0.3.3/BayLum/build/partial.rdb |binary BayLum-0.3.3/BayLum/build/vignette.rds |binary BayLum-0.3.3/BayLum/inst/doc/BayLum.Rmd |only BayLum-0.3.3/BayLum/inst/doc/BayLum.html | 452 +++--- BayLum-0.3.3/BayLum/inst/doc/ConfigFile_Specification.R |only BayLum-0.3.3/BayLum/inst/doc/ConfigFile_Specification.Rmd |only BayLum-0.3.3/BayLum/inst/doc/ConfigFile_Specification.html | 65 BayLum-0.3.3/BayLum/man/AgeC14_Computation.Rd | 6 BayLum-0.3.3/BayLum/man/AgeS_Computation.Rd | 4 BayLum-0.3.3/BayLum/man/Age_Computation.Rd | 24 BayLum-0.3.3/BayLum/man/Age_OSLC14.Rd | 8 BayLum-0.3.3/BayLum/man/BayLum-package.Rd | 63 BayLum-0.3.3/BayLum/man/Generate_DataFile-deprecated.Rd | 8 BayLum-0.3.3/BayLum/man/Generate_DataFile_MG-deprecated.Rd | 6 BayLum-0.3.3/BayLum/man/LT_RegenDose-deprecated.Rd | 2 BayLum-0.3.3/BayLum/man/Model_Age.Rd | 2 BayLum-0.3.3/BayLum/man/Model_AgeC14.Rd | 2 BayLum-0.3.3/BayLum/man/Model_AgeS.Rd | 2 BayLum-0.3.3/BayLum/man/Model_Palaeodose.Rd | 2 BayLum-0.3.3/BayLum/man/Palaeodose_Computation.Rd | 16 BayLum-0.3.3/BayLum/man/SCMatrix.Rd | 2 BayLum-0.3.3/BayLum/man/SC_Ordered.Rd | 2 BayLum-0.3.3/BayLum/man/combine_DataFiles.Rd | 2 BayLum-0.3.3/BayLum/man/create_DataFile.Rd | 4 BayLum-0.3.3/BayLum/man/create_FolderTemplates.Rd | 2 BayLum-0.3.3/BayLum/man/create_ThetaMatrix.Rd | 2 BayLum-0.3.3/BayLum/man/figures/logo_BayLum.png |only BayLum-0.3.3/BayLum/man/figures/logo_archeosciences.jpg |only BayLum-0.3.3/BayLum/man/figures/logo_cnrs.jpg |only BayLum-0.3.3/BayLum/man/figures/logo_idex.png |only BayLum-0.3.3/BayLum/man/figures/logo_ubm.jpg |only BayLum-0.3.3/BayLum/man/plot_Ages.Rd | 2 BayLum-0.3.3/BayLum/man/plot_MCMC.Rd | 4 BayLum-0.3.3/BayLum/man/plot_RegDosePoints.Rd | 2 BayLum-0.3.3/BayLum/man/plot_Scatterplots.Rd | 4 BayLum-0.3.3/BayLum/man/write_BayLumFiles.Rd | 2 BayLum-0.3.3/BayLum/man/write_YAMLConfigFile.Rd | 2 BayLum-0.3.3/BayLum/vignettes/BayLum.Rmd | 698 ++++++++-- BayLum-0.3.3/BayLum/vignettes/BayLum.Rmd.orig |only BayLum-0.3.3/BayLum/vignettes/ConfigFile_Specification.Rmd | 25 BayLum-0.3.3/BayLum/vignettes/figures |only BayLum-0.3.3/BayLum/vignettes/precompile.R |only 62 files changed, 1256 insertions(+), 666 deletions(-)
Title: Generate Analysis Results Programmes Using ARS Metadata
Description: Analysis Results Standard (ARS), a foundational standard by CDISC
(Clinical Data Interchange Standards Consortium), provides a logical
data model for metadata describing all components to calculate Analysis Results.
<https://www.cdisc.org/standards/foundational/analysis-results-standard>
Using 'siera' package, ARS metadata is ingested (JSON or Excel format),
producing programmes to generate Analysis Results Datasets (ARDs).
Author: Malan Bosman [aut, cre],
Clymb Clinical [cph, fnd]
Maintainer: Malan Bosman <malanbos@gmail.com>
Diff between siera versions 0.5.3 dated 2025-08-28 and 0.5.4 dated 2025-09-25
siera-0.5.3/siera/inst/extdata/ARS_V1_Common_Safety_Displays.json |only siera-0.5.4/siera/DESCRIPTION | 10 siera-0.5.4/siera/MD5 | 59 siera-0.5.4/siera/NEWS.md | 6 siera-0.5.4/siera/R/ARS_example.R | 2 siera-0.5.4/siera/R/readARS.R | 1595 ++-------- siera-0.5.4/siera/README.md | 9 siera-0.5.4/siera/build/vignette.rds |binary siera-0.5.4/siera/inst/doc/ARD_script_structure.R |only siera-0.5.4/siera/inst/doc/ARD_script_structure.Rmd |only siera-0.5.4/siera/inst/doc/ARD_script_structure.html |only siera-0.5.4/siera/inst/doc/Getting_started.R | 56 siera-0.5.4/siera/inst/doc/Getting_started.Rmd | 113 siera-0.5.4/siera/inst/doc/Getting_started.html | 274 - siera-0.5.4/siera/inst/doc/apply-ARD.R |only siera-0.5.4/siera/inst/doc/apply-ARD.Rmd |only siera-0.5.4/siera/inst/doc/apply-ARD.html |only siera-0.5.4/siera/inst/doc/using-cards.R |only siera-0.5.4/siera/inst/doc/using-cards.Rmd |only siera-0.5.4/siera/inst/doc/using-cards.html |only siera-0.5.4/siera/inst/extdata/ADSL.csv | 510 +-- siera-0.5.4/siera/inst/extdata/ADVS.csv |only siera-0.5.4/siera/inst/extdata/ADZSDER.csv |only siera-0.5.4/siera/inst/extdata/Common_Safety_Displays_cards.xlsx |binary siera-0.5.4/siera/inst/extdata/cards_constructs.xlsx |binary siera-0.5.4/siera/inst/extdata/exampleARS_1.json |only siera-0.5.4/siera/inst/extdata/exampleARS_1a.json |only siera-0.5.4/siera/inst/extdata/exampleARS_2.json |only siera-0.5.4/siera/inst/extdata/exampleARS_2.xlsx |only siera-0.5.4/siera/inst/extdata/exampleARS_2a.xlsx |only siera-0.5.4/siera/inst/extdata/exampleARS_3.json |only siera-0.5.4/siera/inst/extdata/test_cards.json |only siera-0.5.4/siera/inst/script/ARD_Out14-1-1.R | 419 +- siera-0.5.4/siera/inst/script/ARD_Out14-3-1-1.R |only siera-0.5.4/siera/man/ARS_example.Rd | 2 siera-0.5.4/siera/man/readARS.Rd | 15 siera-0.5.4/siera/tests/testthat/test-ARD_script_example.R |only siera-0.5.4/siera/tests/testthat/test-ARS_example.R |only siera-0.5.4/siera/tests/testthat/test-readARS.R | 450 ++ siera-0.5.4/siera/vignettes/ARD_script_structure.Rmd |only siera-0.5.4/siera/vignettes/Getting_started.Rmd | 113 siera-0.5.4/siera/vignettes/apply-ARD.Rmd |only siera-0.5.4/siera/vignettes/using-cards.Rmd |only 43 files changed, 1585 insertions(+), 2048 deletions(-)
Title: Null Model Analysis for Ecological Networks
Description: Null models to analyse ecological networks (e.g. food webs,
flower-visitation networks, seed-dispersal networks) and detect resource
preferences or non-random interactions among network nodes. Tools are
provided to run null models, test for and plot preferences, plot and
analyse bipartite networks, and export null model results in a form
compatible with other network analysis packages. The underlying null model
was developed by Agusti et al. (2003) Molecular Ecology
<doi:10.1046/j.1365-294X.2003.02014.x> and the full application to
ecological networks by Vaughan et al. (2018) econullnetr: an R package
using null models to analyse the structure of ecological networks and
identify resource selection. Methods in Ecology & Evolution,
<doi:10.1111/2041-210X.12907>.
Author: Ian Vaughan [aut, cre]
Maintainer: Ian Vaughan <vaughanip@cardiff.ac.uk>
Diff between econullnetr versions 0.2.1 dated 2021-06-02 and 0.2.2 dated 2025-09-25
DESCRIPTION | 35 - MD5 | 54 +- NEWS.md | 5 R/WelshStreams_order.R | 2 R/bipartite_stats.R | 2 R/econullnetr.R | 3 R/generate_edgelist.R | 2 R/plot_bipartite.R | 18 R/plot_preferences.R | 2 R/test_interactions.R | 2 README.md | 1 build/vignette.rds |binary inst/CITATION | 33 - inst/doc/econullnetr-intro.R | 14 inst/doc/econullnetr-intro.Rmd | 2 inst/doc/econullnetr-intro.html | 916 +++++++++++++++++++++++++++++----------- man/WelshStreams.order.Rd | 2 man/econullnetr.Rd | 12 man/plot_bipartite.Rd | 14 tests/testthat/_snaps |only vignettes/econullnetr-intro.Rmd | 2 21 files changed, 801 insertions(+), 320 deletions(-)
Title: Flexible Cutoffs for Model Fit Evaluation in Covariance-Based
Structural Models
Description: A toolbox to derive flexible cutoffs for fit indices in
'Covariance-based Structural Equation Modeling' based on the paper by
'Niemand & Mai (2018)' <doi:10.1007/s11747-018-0602-9>. Flexible
cutoffs are an alternative to fixed cutoffs - rules-of-thumb -
regarding an appropriate cutoff for fit indices such as 'CFI' or
'SRMR'. It has been demonstrated that these flexible cutoffs perform
better than fixed cutoffs in grey areas where misspecification is not
easy to detect. The package provides an alternative to the tool at
<https://flexiblecutoffs.org> as it allows to tailor flexible cutoffs
to a given dataset and model, which is so far not available in the
tool. The package simulates fit indices based on a given dataset and
model and then estimates the flexible cutoffs. Some useful functions,
e.g., to determine the 'GoF-' or 'BoF-nature' of a fit index, are
provided. So far, additional options for a relative use (is a model
better than another?) are provided in an explorat [...truncated...]
Author: Thomas Niemand [aut, cre] ,
Robert Mai [ctb] ,
Nadine Schroeder [ctb] ,
Andreas Falke [ctb]
Maintainer: Thomas Niemand <thomas.niemand@gmail.com>
Diff between FCO versions 0.8.0 dated 2023-03-17 and 2.0.0 dated 2025-09-25
FCO-0.8.0/FCO/man/index_guess.Rd |only FCO-2.0.0/FCO/DESCRIPTION | 65 + FCO-2.0.0/FCO/MD5 | 65 + FCO-2.0.0/FCO/NAMESPACE | 15 FCO-2.0.0/FCO/NEWS.md | 14 FCO-2.0.0/FCO/R/check_std.R | 1 FCO-2.0.0/FCO/R/checker.R |only FCO-2.0.0/FCO/R/constr_mod.R | 1 FCO-2.0.0/FCO/R/flex_co2.R |only FCO-2.0.0/FCO/R/gen_fit.R | 4 FCO-2.0.0/FCO/R/gen_fit2.R |only FCO-2.0.0/FCO/R/gen_nnd.R |only FCO-2.0.0/FCO/R/generator.R | 11 FCO-2.0.0/FCO/R/get_cos.R |only FCO-2.0.0/FCO/R/get_free.R | 1 FCO-2.0.0/FCO/R/get_free_mod.R |only FCO-2.0.0/FCO/R/get_lvo.R |only FCO-2.0.0/FCO/R/globals.R |only FCO-2.0.0/FCO/R/hb_load.R | 1 FCO-2.0.0/FCO/R/index_guess.R | 3 FCO-2.0.0/FCO/R/merge_factors.R | 1 FCO-2.0.0/FCO/R/mini.generator.R |only FCO-2.0.0/FCO/R/mm.misspec.R |only FCO-2.0.0/FCO/R/model.builder.R |only FCO-2.0.0/FCO/R/plot_fit2.R |only FCO-2.0.0/FCO/R/pop_mod.R | 224 +++-- FCO-2.0.0/FCO/R/pop_mod_dv.R | 1 FCO-2.0.0/FCO/R/pop_mod_reg.R |only FCO-2.0.0/FCO/R/power.finder.R |only FCO-2.0.0/FCO/R/recommend.R | 62 + FCO-2.0.0/FCO/R/run_parallel.R |only FCO-2.0.0/FCO/R/rv.misspec.R |only FCO-2.0.0/FCO/R/sm.misspec.R |only FCO-2.0.0/FCO/README.md | 123 +-- FCO-2.0.0/FCO/build/partial.rdb |only FCO-2.0.0/FCO/build/vignette.rds |binary FCO-2.0.0/FCO/inst/doc/FCO.R | 363 ++++----- FCO-2.0.0/FCO/inst/doc/FCO.Rmd | 430 +++++------ FCO-2.0.0/FCO/inst/doc/FCO.html | 1503 ++++++++++++++------------------------- FCO-2.0.0/FCO/man/figures |only FCO-2.0.0/FCO/man/flex_co2.Rd |only FCO-2.0.0/FCO/man/gen_fit2.Rd |only FCO-2.0.0/FCO/man/plot_fit2.Rd |only FCO-2.0.0/FCO/man/pop_mod.Rd | 15 FCO-2.0.0/FCO/vignettes/FCO.Rmd | 430 +++++------ 45 files changed, 1533 insertions(+), 1800 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.10 dated 2025-09-24 and 0.0.11 dated 2025-09-25
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/gloss_example.R | 3 ++- 4 files changed, 12 insertions(+), 7 deletions(-)
Title: R Repository Data
Description: Retrieve metadata about packages from repositories to explore
package dependencies, links between help pages, aliases, package
availability on a given date, and other repository dependent outcome.
This metadata can be used to help package maintainers and users to
navigate changes on dependencies and with reproducibility.
Author: Lluis Revilla Sancho [aut, cre, cph]
Maintainer: Lluis Revilla Sancho <lluis.revilla@gmail.com>
Diff between repo.data versions 0.1.4 dated 2025-09-15 and 0.1.5 dated 2025-09-25
DESCRIPTION | 6 - MD5 | 119 +++++++++++++++++------------------ NEWS.md | 5 + R/alias_utils.R | 9 ++ R/base_alias.R | 6 + R/base_help.R | 23 +++++- R/base_xrefs.R | 18 +++++ R/bioconductor.R | 16 ++++ R/cran_actions.R | 8 +- R/cran_alias.R | 4 + R/cran_archive.R | 30 +++++++- R/cran_comments.R | 9 ++ R/cran_doom.R | 6 + R/cran_help.R | 51 ++++++++++++--- R/cran_history.R | 12 +++ R/cran_maintainers.R | 4 + R/cran_snapshot.R | 16 ++-- R/cran_xrefs.R | 36 +++++++++- R/dependencies.R | 25 +++++-- R/package_date.R | 19 ++++- R/repos.R | 7 +- R/utils.R | 50 +++++++++----- R/versions.R |only README.md | 4 - inst/doc/repo.data.R | 36 +++++----- inst/doc/repo.data.Rmd | 37 +++++----- inst/doc/repo.data.html | 113 +++++++++++---------------------- man/base_alias.Rd | 3 man/base_help_cliques.Rd | 7 +- man/base_help_pages_not_linked.Rd | 5 + man/base_help_pages_wo_links.Rd | 2 man/base_links.Rd | 1 man/base_pages_links.Rd | 1 man/base_pkges_links.Rd | 1 man/base_targets_links.Rd | 1 man/bioc_cran_archived.Rd | 1 man/cran_actions.Rd | 1 man/cran_alias.Rd | 1 man/cran_archive.Rd | 11 ++- man/cran_comments.Rd | 1 man/cran_doom.Rd | 3 man/cran_help_cliques.Rd | 1 man/cran_help_pages_links_wo_deps.Rd | 1 man/cran_help_pages_not_linked.Rd | 11 ++- man/cran_help_pages_wo_links.Rd | 11 ++- man/cran_history.Rd | 1 man/cran_links.Rd | 1 man/cran_maintainers.Rd | 1 man/cran_pkges_links.Rd | 1 man/cran_snapshot.Rd | 1 man/duplicated_alias.Rd | 6 + man/package_date.Rd | 1 man/package_dependencies.Rd | 1 man/package_repos.Rd | 1 man/repos_dependencies.Rd | 1 man/update_dependencies.Rd | 3 tests/test-all.R | 7 +- tests/test-cran_doom.R | 3 tests/test-package_date.R | 3 tests/test-update_dependencies.R | 3 vignettes/repo.data.Rmd | 37 +++++----- 61 files changed, 525 insertions(+), 278 deletions(-)
Title: Creation of in-Text Summary Table
Description: Creation of tables of summary statistics or counts for clinical data (for 'TLFs').
These tables can be exported as in-text table (with the 'flextable' package) for a Clinical Study Report
(Word format) or a 'topline' presentation (PowerPoint format),
or as interactive table (with the 'DT' package) to an html document for clinical data review.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
This is a re-admission after prior archival of version 3.3.4 dated 2025-09-03
Diff between inTextSummaryTable versions 3.3.4 dated 2025-09-03 and 3.3.5 dated 2025-09-25
DESCRIPTION | 14 MD5 | 62 - inst/NEWS | 4 inst/doc/inTextSummaryTable-advanced.R | 14 inst/doc/inTextSummaryTable-advanced.Rmd | 14 inst/doc/inTextSummaryTable-advanced.html | 281 +------ inst/doc/inTextSummaryTable-aesthetics.R | 7 inst/doc/inTextSummaryTable-aesthetics.Rmd | 7 inst/doc/inTextSummaryTable-aesthetics.html | 104 +- inst/doc/inTextSummaryTable-createTables.R | 7 inst/doc/inTextSummaryTable-createTables.Rmd | 7 inst/doc/inTextSummaryTable-createTables.html | 236 ++---- inst/doc/inTextSummaryTable-exportTables.R | 13 inst/doc/inTextSummaryTable-exportTables.Rmd | 13 inst/doc/inTextSummaryTable-exportTables.html | 494 ++----------- inst/doc/inTextSummaryTable-introduction.R | 7 inst/doc/inTextSummaryTable-introduction.Rmd | 7 inst/doc/inTextSummaryTable-introduction.html | 88 +- inst/doc/inTextSummaryTable-standardTables.R | 7 inst/doc/inTextSummaryTable-standardTables.Rmd | 7 inst/doc/inTextSummaryTable-standardTables.html | 112 +- inst/doc/inTextSummaryTable-visualization.R | 14 inst/doc/inTextSummaryTable-visualization.Rmd | 14 inst/doc/inTextSummaryTable-visualization.html | 97 +- tests/testthat/test_computeSummaryStatisticsTable-colVar.R | 13 vignettes/inTextSummaryTable-advanced.Rmd | 14 vignettes/inTextSummaryTable-aesthetics.Rmd | 7 vignettes/inTextSummaryTable-createTables.Rmd | 7 vignettes/inTextSummaryTable-exportTables.Rmd | 13 vignettes/inTextSummaryTable-introduction.Rmd | 7 vignettes/inTextSummaryTable-standardTables.Rmd | 7 vignettes/inTextSummaryTable-visualization.Rmd | 14 32 files changed, 540 insertions(+), 1172 deletions(-)
More information about inTextSummaryTable at CRAN
Permanent link
Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
Description: Toolbox to process raw data from closed loop flux chamber (or tent)
setups into ecosystem gas fluxes usable for analysis. It goes from a
data frame of gas concentration over time (which can contain several
measurements) and a meta data file indicating which measurement was done
when, to a data frame of ecosystem gas fluxes including quality diagnostics.
Organized with one function per step, maximizing user flexibility and backwards
compatibility. Different models to estimate the fluxes from the raw data are
available: exponential as described in
Zhao et al (2018) <doi:10.1016/j.agrformet.2018.08.022>, exponential as described in
Hutchinson and Mosier (1981) <doi:10.2136/sssaj1981.03615995004500020017x>,
quadratic, and linear. Other functions include quality assessment,
plotting for visual check, calculation of fluxes based on the setup
specific parameters (chamber size, plot area, ...), gross primary production
and transpiration rate calculation, and light response curves.
Author: Joseph Gaudard [aut, cre] ,
Richard James Telford [aut]
Maintainer: Joseph Gaudard <joseph.gaudard@pm.me>
Diff between fluxible versions 1.3.2 dated 2025-09-11 and 1.3.3 dated 2025-09-25
fluxible-1.3.2/fluxible/R/flux_plot_exp.R |only fluxible-1.3.2/fluxible/R/flux_plot_lin.R |only fluxible-1.3.2/fluxible/R/flux_plot_quadratic.R |only fluxible-1.3.2/fluxible/man/flux_plot_exp.Rd |only fluxible-1.3.2/fluxible/man/flux_plot_lin.Rd |only fluxible-1.3.2/fluxible/man/flux_plot_quadratic.Rd |only fluxible-1.3.3/fluxible/DESCRIPTION | 8 fluxible-1.3.3/fluxible/MD5 | 54 fluxible-1.3.3/fluxible/NAMESPACE | 2 fluxible-1.3.3/fluxible/NEWS.md | 4 fluxible-1.3.3/fluxible/R/flux_calc.R | 8 fluxible-1.3.3/fluxible/R/flux_fortify.R |only fluxible-1.3.3/fluxible/R/flux_fortify_exp.R |only fluxible-1.3.3/fluxible/R/flux_fortify_lin.R |only fluxible-1.3.3/fluxible/R/flux_fortify_quadratic.R |only fluxible-1.3.3/fluxible/R/flux_plot.R | 224 fluxible-1.3.3/fluxible/R/flux_plot_longpdf.R | 1 fluxible-1.3.3/fluxible/R/flux_plot_pdf.R | 8 fluxible-1.3.3/fluxible/R/flux_print_plot.R | 2 fluxible-1.3.3/fluxible/inst/CITATION | 9 fluxible-1.3.3/fluxible/inst/doc/fluxible.html | 4 fluxible-1.3.3/fluxible/inst/doc/two-gases.html | 4 fluxible-1.3.3/fluxible/man/figures/README-short-example-1.png |binary fluxible-1.3.3/fluxible/man/flux_fortify.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_exp.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_lin.Rd |only fluxible-1.3.3/fluxible/man/flux_fortify_quadratic.Rd |only fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/longpdf-and-print.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-hm-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-tz-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-exp-zhao18-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-kappamax-fit.svg | 2502 ---------- fluxible-1.3.3/fluxible/tests/testthat/_snaps/flux_plot/plot-for-quadratic-fit-with-mid-missing-data.svg | 2274 --------- fluxible-1.3.3/fluxible/tests/testthat/test-flux_plot.R | 11 35 files changed, 115 insertions(+), 17054 deletions(-)
Title: Single-Cell Meta-Path Based Omic Embedding
Description: Provide a workflow to jointly embed chromatin accessibility peaks and expressed genes into a shared low-dimensional space using paired single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq) data. It integrates regulatory relationships among peak-peak interactions (via 'Cicero'), peak-gene interactions (via Lasso, random forest, and XGBoost), and gene-gene interactions (via principal component regression). With the input of paired scATAC-seq and scRNA-seq data matrices, it assigns a low-dimensional feature vector to each gene and peak. Additionally, it supports the reconstruction of gene-gene network with low-dimensional projections (via epsilon-NN) and then the comparison of the networks of two conditions through manifold alignment implemented in 'scTenifoldNet'. See <doi:10.1093/bioinformatics/btaf483> for more details.
Author: Yuntong Hou [aut, cre] ,
Yan Zhong [aut, ctb] ,
Yeran Chen [ctb],
Youshi Chang [ctb],
Yongjian Yang [ctb] ,
Xinyue Zheng [ctb],
James Cai [ctb]
Maintainer: Yuntong Hou <houyt223@gmail.com>
Diff between scPOEM versions 0.1.2 dated 2025-08-28 and 0.1.3 dated 2025-09-25
DESCRIPTION | 23 ++++++++++++----------- MD5 | 4 ++-- inst/doc/scPOEM.pdf |binary 3 files changed, 14 insertions(+), 13 deletions(-)
Title: Tabular Data Suppression using Gaussian Elimination
Description: A statistical disclosure control tool to protect tables by suppression
using the Gaussian elimination secondary suppression algorithm
(Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is
to start by working with functions SuppressSmallCounts() and
SuppressDominantCells(). These functions use primary suppression functions for
the minimum frequency rule and the dominance rule, respectively. Novel
functionality for suppression of disclosive cells is also included. General
primary suppression functions can be supplied as input to the general working
horse function, GaussSuppressionFromData(). Suppressed frequencies can be
replaced by synthetic decimal numbers as described in
Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Hege Boevelstad [ctb] ,
Vidar Norstein Klungre [rev] ,
Jonas Lindblad [ctb],
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between GaussSuppression versions 1.1.5 dated 2025-08-25 and 1.2.0 dated 2025-09-25
GaussSuppression-1.1.5/GaussSuppression/R/OutputFixRiskyIntervals.R |only GaussSuppression-1.1.5/GaussSuppression/R/OutputIntervalIteration.R |only GaussSuppression-1.1.5/GaussSuppression/R/RangeLimits.R |only GaussSuppression-1.1.5/GaussSuppression/man/RangeLimitsDefault.Rd |only GaussSuppression-1.1.5/GaussSuppression/man/RangeOutputFunction.Rd |only GaussSuppression-1.2.0/GaussSuppression/DESCRIPTION | 12 GaussSuppression-1.2.0/GaussSuppression/MD5 | 50 - GaussSuppression-1.2.0/GaussSuppression/NAMESPACE | 9 GaussSuppression-1.2.0/GaussSuppression/NEWS.md | 39 + GaussSuppression-1.2.0/GaussSuppression/R/FixRiskyIntervals.R | 76 +- GaussSuppression-1.2.0/GaussSuppression/R/GaussSuppressionFromData.R | 248 +++++-- GaussSuppression-1.2.0/GaussSuppression/R/GaussSuppression_with_intervals.R |only GaussSuppression-1.2.0/GaussSuppression/R/IntervalLimits.R |only GaussSuppression-1.2.0/GaussSuppression/R/Intervals.R | 16 GaussSuppression-1.2.0/GaussSuppression/R/MagnitudeRule.R | 68 ++ GaussSuppression-1.2.0/GaussSuppression/R/OutputFunction.R | 63 - GaussSuppression-1.2.0/GaussSuppression/R/PackageSpecs.R | 6 GaussSuppression-1.2.0/GaussSuppression/R/Primary.R | 18 GaussSuppression-1.2.0/GaussSuppression/R/SuppressLinkedTables.R | 7 GaussSuppression-1.2.0/GaussSuppression/R/gaussSuppression_linked.R | 103 +-- GaussSuppression-1.2.0/GaussSuppression/R/interval_suppression.R | 175 ++++- GaussSuppression-1.2.0/GaussSuppression/inst/doc/Linked_table_suppression.html | 338 +++++----- GaussSuppression-1.2.0/GaussSuppression/inst/doc/Small_count_frequency_table_suppression.html | 63 - GaussSuppression-1.2.0/GaussSuppression/man/FixRiskyIntervals.Rd | 4 GaussSuppression-1.2.0/GaussSuppression/man/GaussSuppressionFromData.Rd | 75 +- GaussSuppression-1.2.0/GaussSuppression/man/IntervalLimits.Rd |only GaussSuppression-1.2.0/GaussSuppression/man/MagnitudeRule.Rd | 11 GaussSuppression-1.2.0/GaussSuppression/man/PackageSpecs.Rd | 2 GaussSuppression-1.2.0/GaussSuppression/man/PrimaryDefault.Rd | 17 GaussSuppression-1.2.0/GaussSuppression/tests/testthat/test-FixRiskyIntervals.R | 44 + 30 files changed, 964 insertions(+), 480 deletions(-)
More information about GaussSuppression at CRAN
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Title: Slide Automation for Tables, Listings and Figures
Description: The normal process of creating clinical study slides is that
a statistician manually type in the numbers from outputs and a
separate statistician to double check the typed in numbers. This
process is time consuming, resource intensive, and error prone.
Automatic slide generation is a solution to address these issues. It
reduces the amount of work and the required time when creating slides,
and reduces the risk of errors from manually typing or copying numbers
from the output to slides. It also helps users to avoid unnecessary
stress when creating large amounts of slide decks in a short time
window.
Author: Joe Zhu [cre, aut] ,
Heng Wang [aut],
Yinqi Zhao [aut],
Bo Ci [aut],
Liming Li [aut],
Laura Wang [ctb],
Xiaoli Duan [aut],
Stefan Pascal Thoma [aut],
Thomas Neitmann [ctb],
Miles Almond [aut],
Mahdi About [ctb],
Kai Lim [ctb],
Nolan Steed [ctb],
Daol [...truncated...]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between autoslider.core versions 0.2.8 dated 2025-08-25 and 0.3.1 dated 2025-09-25
autoslider.core-0.2.8/autoslider.core/tests/testthat/ft_0.docx |only autoslider.core-0.2.8/autoslider.core/tests/testthat/ft_1.docx |only autoslider.core-0.3.1/autoslider.core/DESCRIPTION | 14 +- autoslider.core-0.3.1/autoslider.core/MD5 | 63 ++++------ autoslider.core-0.3.1/autoslider.core/NAMESPACE | 1 autoslider.core-0.3.1/autoslider.core/NEWS.md | 12 + autoslider.core-0.3.1/autoslider.core/R/package.R | 2 autoslider.core-0.3.1/autoslider.core/R/to_slides.R | 17 +- autoslider.core-0.3.1/autoslider.core/inst/doc/adding_templates.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/autoslideR.html | 8 - autoslider.core-0.3.1/autoslider.core/inst/doc/generate_placeholder_slides.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.R | 13 ++ autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.Rmd | 15 ++ autoslider.core-0.3.1/autoslider.core/inst/doc/tlg_templates.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/use_LLM.html | 4 autoslider.core-0.3.1/autoslider.core/inst/doc/using_formats.html | 4 autoslider.core-0.3.1/autoslider.core/man/figure_to_slide.Rd | 3 autoslider.core-0.3.1/autoslider.core/man/format_date.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_eg_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_lb_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_mean_general.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/g_vs_slide.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_output.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_outputs.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/generate_slides.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/null_report.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/save_outputs.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/slides_from_rds.Rd | 2 autoslider.core-0.3.1/autoslider.core/man/table_to_slide.Rd | 3 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-ft_format.R | 2 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-func_wrapper.R | 2 autoslider.core-0.3.1/autoslider.core/tests/testthat/test-toslide.R |only autoslider.core-0.3.1/autoslider.core/tests/testthat/test_ai.R | 2 autoslider.core-0.3.1/autoslider.core/vignettes/tlg_templates.Rmd | 15 ++ 34 files changed, 144 insertions(+), 70 deletions(-)
More information about autoslider.core at CRAN
Permanent link
Title: Mixture Hidden Markov Models for Social Sequence Data and Other
Multivariate, Multichannel Categorical Time Series
Description: Designed for estimating variants of hidden (latent) Markov models
(HMMs), mixture HMMs, and non-homogeneous HMMs (NHMMs) for social sequence
data and other categorical time series. Special cases include
feedback-augmented NHMMs, Markov models without latent layer, mixture
Markov models, and latent class models. The package supports models for one
or multiple subjects with one or multiple parallel sequences (channels).
External covariates can be added to explain cluster membership in mixture
models as well as initial, transition and emission probabilities in NHMMs.
The package provides functions for evaluating and comparing models, as well
as functions for visualizing of multichannel sequence data and HMMs. For
NHMMs, methods for computing average causal effects and marginal state and
emission probabilities are available. Models are estimated using maximum
likelihood via the EM algorithm or direct numerical maximization with
analytical gradients. Documentation is available via several v [...truncated...]
Author: Jouni Helske [aut, cre] ,
Satu Helske [aut]
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between seqHMM versions 2.0.0 dated 2025-05-16 and 2.1.0 dated 2025-09-25
DESCRIPTION | 16 +- MD5 | 191 +++++++++++++------------- NAMESPACE | 7 NEWS.md | 38 ++++- R/RcppExports.R | 20 +- R/bootstrap.R | 66 ++++++--- R/build_mnhmm.R | 5 R/build_nhmm.R | 6 R/check_build_arguments.R | 7 R/create_base_nhmm.R | 35 +++- R/em_dnm_mnhmm.R | 8 - R/em_dnm_nhmm.R | 8 - R/em_mnhmm.R | 8 - R/em_nhmm.R | 8 - R/estimate_mnhmm.R | 5 R/estimate_nhmm.R | 13 + R/fanhmm_leaves.R | 2 R/fill_time.R | 3 R/fit_mnhmm.R | 27 ++- R/fit_model.R | 8 - R/fit_nhmm.R | 29 ++- R/formulas.R | 3 R/forwardBackward.R | 4 R/get_marginals.R | 17 +- R/get_probs.R | 4 R/logLik.R | 6 R/model_matrix.R | 51 +++--- R/most_probable_cluster.R | 10 - R/mssplot-deprecated.R | 2 R/posterior_probs.R | 12 + R/predict.R | 29 ++- R/print.R | 9 - R/seqHMM-package.R | 2 R/simulate_mnhmm.R | 34 +++- R/simulate_nhmm.R | 39 +++-- R/ssp-deprecated.R | 2 R/ssplot-deprecated.R | 2 R/stacked_sequence_plot.R | 22 ++- R/summary.mhmm.R | 2 R/update.R | 36 +++- R/utilities.R | 24 +-- R/vcov.mhmm.R | 4 README.md | 2 data/leaves.rda |binary inst/doc/seqHMM.Rnw | 2 inst/doc/seqHMM.pdf |binary inst/doc/seqHMM_algorithms.Rnw | 4 inst/doc/seqHMM_algorithms.pdf |binary inst/doc/seqHMM_estimation.pdf |binary inst/doc/seqHMM_visualization.Rnw | 2 inst/doc/seqHMM_visualization.pdf |binary man/bootstrap.Rd | 13 + man/estimate_mnhmm.Rd | 8 + man/estimate_nhmm.Rd | 10 + man/fanhmm_leaves.Rd | 2 man/fit_model.Rd | 8 - man/logLik_hmm.Rd | 6 man/mssplot.Rd | 2 man/permute_states.Rd |only man/simulate_mnhmm.Rd | 16 +- man/simulate_nhmm.Rd | 16 +- man/ssp.Rd | 2 man/ssplot.Rd | 2 man/stacked_sequence_plot.Rd | 11 - man/update_nhmm.Rd | 7 man/vcov.mhmm.Rd | 4 src/EM_mnhmm.cpp | 154 +++++++++------------ src/EM_mnhmm.h | 27 +-- src/EM_nhmm.cpp | 163 +++++++++------------- src/EM_nhmm.h | 21 +- src/R_EM_fanhmm.cpp | 5 src/R_EM_mfanhmm.cpp | 5 src/R_EM_mnhmm.cpp | 5 src/R_EM_nhmm.cpp | 5 src/RcppExports.cpp | 48 ++++-- src/backward.h | 19 ++ src/cost_matrix.cpp | 37 +++-- src/fanhmm.cpp | 22 --- src/fanhmm.h | 4 src/forward.h | 41 +++++ src/mfanhmm.cpp | 24 +-- src/mfanhmm.h | 5 src/mnhmm.cpp | 242 ++++++++++++++++----------------- src/mnhmm.h | 39 ++--- src/nhmm.cpp | 203 ++++++++++++++------------- src/nhmm.h | 31 +--- src/pre2-log_EM.cpp | 4 src/softmax.cpp | 6 src/softmax.h | 1 tests/testthat/test-forward_backward.R | 9 - tests/testthat/test-get_probs.R | 6 tests/testthat/test-hidden_paths.R | 8 - tests/testthat/test-posterior_probs.R | 8 - tests/testthat/test-predict.R | 2 vignettes/seqHMM.Rnw | 2 vignettes/seqHMM_algorithms.Rnw | 4 vignettes/seqHMM_visualization.Rnw | 2 97 files changed, 1180 insertions(+), 913 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado [aut, cre] ,
Murilo Dantas Miranda [aut],
Andre Chalom [aut]
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.6.3 dated 2024-01-16 and 0.6.5 dated 2025-09-25
sads-0.6.3/sads/README.md |only sads-0.6.5/sads/DESCRIPTION | 26 sads-0.6.5/sads/MD5 | 47 - sads-0.6.5/sads/NEWS | 6 sads-0.6.5/sads/build/partial.rdb |binary sads-0.6.5/sads/build/vignette.rds |binary sads-0.6.5/sads/inst/doc/sads_intro.Rnw | 35 - sads-0.6.5/sads/inst/doc/sads_intro.pdf |binary sads-0.6.5/sads/man/ICtab.Rd | 2 sads-0.6.5/sads/man/fitrad-class.Rd | 18 sads-0.6.5/sads/man/fitsad-class.Rd | 18 sads-0.6.5/sads/man/fitsadC-class.Rd | 18 sads-0.6.5/sads/man/fitsadC.Rd | 2 sads-0.6.5/sads/vignettes/sads_intro-woven-Biomass-octave-plot.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Octaves-plot.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Plot-of-predicted-values.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Ploting-octaves.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Ploting-profiles.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-Rad-plots.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-grasslands_coverpred_plot.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven-grasslands_hist_plot.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven-radplot1.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-radplots.pdf |binary sads-0.6.5/sads/vignettes/sads_intro-woven-rsads-bias-plots.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven.pdf |only sads-0.6.5/sads/vignettes/sads_intro-woven.tex | 339 +++++++++- sads-0.6.5/sads/vignettes/sads_intro.Rnw | 35 - 27 files changed, 456 insertions(+), 90 deletions(-)
Title: Result Model Manager
Description: Database data model management utilities for R packages in the Observational Health Data Sciences and
Informatics programme. 'ResultModelManager' provides utility functions to allow package
maintainers to migrate existing SQL database models, export and import results in consistent patterns.
Author: Jamie Gilbert [aut, cre]
Maintainer: Jamie Gilbert <gilbert@ohdsi.org>
Diff between ResultModelManager versions 0.6.0 dated 2025-09-18 and 0.6.1 dated 2025-09-25
DESCRIPTION | 8 +++--- MD5 | 34 ++++++++++++++--------------- NEWS.md | 7 +++++ R/ConnectionHandler.R | 3 +- R/DataMigrationManager.R | 3 +- R/PooledConnectionHandler.R | 2 - inst/doc/CreatingMigrations.pdf |binary inst/doc/PackageDesign.pdf |binary inst/doc/UploadFunctionality.pdf |binary inst/doc/UsingAnExportManager.pdf |binary inst/doc/UsingConnectionHandlers.pdf |binary inst/doc/UsingPythonUploads.pdf |binary inst/doc/UsingQueryNamespaces.pdf |binary man/ResultModelManager-package.Rd | 1 tests/testthat/setup.R | 23 +++++++++++-------- tests/testthat/test-DataMigrationManager.R | 1 tests/testthat/test-QueryNamespace.R | 18 ++++++++++----- tests/testthat/test-ResultExportManager.R | 4 --- 18 files changed, 60 insertions(+), 44 deletions(-)
More information about ResultModelManager at CRAN
Permanent link
Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving
specified levels to front, ordering by first appearance, reversing,
and randomly shuffling), and tools for modifying factor levels
(including collapsing rare levels into other, 'anonymising', and
manually 'recoding').
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between forcats versions 1.0.0 dated 2023-01-29 and 1.0.1 dated 2025-09-25
DESCRIPTION | 19 +- LICENSE | 2 MD5 | 78 +++++----- NEWS.md | 6 R/anon.R | 10 - R/collapse.R | 7 R/compat-obj-type.R | 30 ++-- R/compat-purrr.R | 15 +- R/compat-types-check.R | 236 +++++++++++++++++--------------- R/cross.R | 5 R/expand.R | 6 R/fct.R | 2 R/lump.R | 47 ++++-- R/lvls.R | 21 ++ R/other.R | 1 R/recode.R | 17 +- R/relabel.R | 10 - R/relevel.R | 6 R/reorder.R | 41 +++-- README.md | 33 ++-- build/vignette.rds |binary inst/doc/forcats.R | 32 ++-- inst/doc/forcats.Rmd | 36 ++-- inst/doc/forcats.html | 287 +++++++++++++++++++-------------------- man/fct_anon.Rd | 10 - man/fct_lump.Rd | 20 +- man/fct_relabel.Rd | 10 - man/fct_reorder.Rd | 2 man/figures/logo.png |binary man/forcats-package.Rd | 4 tests/testthat/_snaps/relabel.md | 2 tests/testthat/_snaps/reorder.md | 2 tests/testthat/test-collapse.R | 5 tests/testthat/test-cross.R | 24 ++- tests/testthat/test-fct.R | 4 tests/testthat/test-lump.R | 46 ++++-- tests/testthat/test-lvls.R | 26 +++ tests/testthat/test-recode.R | 5 tests/testthat/test-reorder.R | 34 +++- vignettes/forcats.Rmd | 36 ++-- 40 files changed, 682 insertions(+), 495 deletions(-)
Title: Circular Statistics
Description: Circular Statistics, from "Topics in circular Statistics" (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.
Author: Ulric Lund [aut],
Claudio Agostinelli [aut] ,
Hiroyoshi Arai [ctb],
Alessando Gagliardi [ctb],
Eduardo Garcia-Portugues [ctb, cre] ,
Dimitri Giunchi [ctb],
Jean-Olivier Irisson [ctb],
Matthew Pocernich [ctb],
Federico Rotolo [ctb]
Maintainer: Eduardo Garcia-Portugues <edgarcia@est-econ.uc3m.es>
Diff between circular versions 0.5-1 dated 2024-08-29 and 0.5-2 dated 2025-09-25
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- R/cardioid.R | 2 +- inst/NEWS | 4 ++++ man/cardioid.Rd | 7 +++++++ 5 files changed, 24 insertions(+), 13 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Susanna Marquez [cre, aut],
Namita Gupta [aut],
Nima Nouri [aut],
Ruoyi Jiang [aut],
Julian Zhou [aut],
Kenneth Hoehn [aut],
Daniel Gadala-Maria [ctb],
Edel Aron [ctb],
Cole Jensen [aut],
Gisela Gabernet [ctb],
Caroline Sullivan [ctb],
Hailong Meng [ [...truncated...]
Maintainer: Susanna Marquez <susanna.marquez@yale.edu>
Diff between alakazam versions 1.3.0 dated 2023-09-29 and 1.4.0 dated 2025-09-25
alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.R |only alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.Rmd |only alakazam-1.3.0/alakazam/inst/doc/Lineage-Vignette.pdf |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.R |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.Rmd |only alakazam-1.3.0/alakazam/inst/doc/Topology-Vignette.pdf |only alakazam-1.3.0/alakazam/vignettes/Lineage-Vignette.Rmd |only alakazam-1.3.0/alakazam/vignettes/Topology-Vignette.Rmd |only alakazam-1.4.0/alakazam/DESCRIPTION | 28 alakazam-1.4.0/alakazam/MD5 | 112 alakazam-1.4.0/alakazam/NEWS.md | 37 alakazam-1.4.0/alakazam/R/Alakazam.R | 5 alakazam-1.4.0/alakazam/R/AminoAcids.R | 12 alakazam-1.4.0/alakazam/R/Classes.R | 12 alakazam-1.4.0/alakazam/R/Core.R | 4 alakazam-1.4.0/alakazam/R/Deprecated.R | 15 alakazam-1.4.0/alakazam/R/Diversity.R | 73 alakazam-1.4.0/alakazam/R/Gene.R | 1705 ++++++++------- alakazam-1.4.0/alakazam/R/Lineage.R | 30 alakazam-1.4.0/alakazam/R/Sequence.R | 14 alakazam-1.4.0/alakazam/R/Topology.R | 20 alakazam-1.4.0/alakazam/README.md | 8 alakazam-1.4.0/alakazam/build/partial.rdb |binary alakazam-1.4.0/alakazam/build/vignette.rds |binary alakazam-1.4.0/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.R | 6 alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.Rmd | 10 alakazam-1.4.0/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Fastq-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/Files-Vignette.R | 6 alakazam-1.4.0/alakazam/inst/doc/Files-Vignette.pdf |binary alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.R | 8 alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.Rmd | 8 alakazam-1.4.0/alakazam/inst/doc/GeneUsage-Vignette.pdf |binary alakazam-1.4.0/alakazam/man/AbundanceCurve-class.Rd | 2 alakazam-1.4.0/alakazam/man/ChangeoClone-class.Rd | 2 alakazam-1.4.0/alakazam/man/DiversityCurve-class.Rd | 6 alakazam-1.4.0/alakazam/man/MRCATest-class.Rd | 2 alakazam-1.4.0/alakazam/man/alakazam-package.Rd | 9 alakazam-1.4.0/alakazam/man/alakazam.Rd | 5 alakazam-1.4.0/alakazam/man/aminoAcidProperties.Rd | 2 alakazam-1.4.0/alakazam/man/buildPhylipLineage.Rd | 6 alakazam-1.4.0/alakazam/man/collapseDuplicates.Rd | 10 alakazam-1.4.0/alakazam/man/combineIgphyml.Rd | 4 alakazam-1.4.0/alakazam/man/countClones.Rd | 4 alakazam-1.4.0/alakazam/man/countGenes.Rd | 80 alakazam-1.4.0/alakazam/man/estimateAbundance.Rd | 4 alakazam-1.4.0/alakazam/man/getSegment.Rd | 72 alakazam-1.4.0/alakazam/man/gridPlot.Rd | 2 alakazam-1.4.0/alakazam/man/groupGenes.Rd | 94 alakazam-1.4.0/alakazam/man/makeChangeoClone.Rd | 6 alakazam-1.4.0/alakazam/man/nonsquareDist.Rd | 4 alakazam-1.4.0/alakazam/man/plotAbundanceCurve.Rd | 2 alakazam-1.4.0/alakazam/man/plotDiversityCurve.Rd | 2 alakazam-1.4.0/alakazam/man/plotDiversityTest.Rd | 2 alakazam-1.4.0/alakazam/man/rarefyDiversity.Rd | 3 alakazam-1.4.0/alakazam/man/readIgphyml.Rd | 4 alakazam-1.4.0/alakazam/man/sortGenes.Rd | 22 alakazam-1.4.0/alakazam/man/testDiversity.Rd | 7 alakazam-1.4.0/alakazam/vignettes/Diversity-Vignette.Rmd | 10 alakazam-1.4.0/alakazam/vignettes/GeneUsage-Vignette.Rmd | 8 61 files changed, 1417 insertions(+), 1070 deletions(-)
Title: Descriptive Statistics and Data Management Tools
Description: Extracts and summarizes metadata from data frames, including variable names, labels, types, and missing values. Computes compact descriptive statistics, frequency tables, and cross-tabulations to assist with efficient data exploration. Facilitates the identification of missing data patterns and structural issues in datasets. Designed to streamline initial data management and exploratory analysis workflows within 'R'.
Author: Amal Tawfik [aut, cre, cph]
Maintainer: Amal Tawfik <amal.tawfik@hesav.ch>
Diff between spicy versions 0.1.0 dated 2025-05-05 and 0.2.0 dated 2025-09-25
DESCRIPTION | 13 MD5 | 65 ++- NAMESPACE | 1 NEWS.md | 13 R/copy_clipboard.R | 280 +++++++-------- R/count_n.R | 585 ++++++++++++++++----------------- R/cramer_v.R | 72 ++-- R/cross_tab.R | 28 - R/freq.R | 39 -- R/label_from_names.R |only R/mean_n.R | 9 R/print_spicy.R | 129 +++---- R/spicy-package.R | 66 +-- R/sum_n.R | 9 R/varlist.R | 115 +++--- README.md | 191 +++++++++- inst |only man/count_n.Rd | 408 +++++++++++------------ man/figures/varlist_1.png |only man/figures/varlist_2.png |only man/freq.Rd | 20 - man/label_from_names.Rd |only man/mean_n.Rd | 8 man/print.spicy.Rd | 52 +- man/spicy-package.Rd | 2 man/sum_n.Rd | 8 tests/testthat/test-copy_clipboard.R | 162 ++++----- tests/testthat/test-count_n.R | 273 +++++++-------- tests/testthat/test-cramer_v.R | 54 +-- tests/testthat/test-cross_tab.R | 222 ++++++------ tests/testthat/test-freq.R | 246 ++++++------- tests/testthat/test-label_from_names.R |only tests/testthat/test-mean_n.R | 3 tests/testthat/test-print_spicy.R | 106 ++--- tests/testthat/test-sum_n.R | 3 tests/testthat/test-varlist.R | 81 ++-- 36 files changed, 1708 insertions(+), 1555 deletions(-)
Title: Tools for Supply Chain Management, Demand and Supply Planning
Description: Perform flexible and quick calculations for Demand and Supply Planning, such as projected inventories and coverages, as well as replenishment plan. For any time bucket, daily, weekly or monthly, and any granularity level, product or group of products.
Author: Nicolas Nguyen [aut, cre]
Maintainer: Nicolas Nguyen <nikonguyen@yahoo.fr>
Diff between planr versions 0.5.1 dated 2025-02-23 and 0.6.1 dated 2025-09-25
DESCRIPTION | 6 ++-- MD5 | 17 ++++++++----- NAMESPACE | 1 R/alloc_dmd.R |only R/data.R | 43 +++++++++++++++++++++++++++++++++ README.md | 7 +++-- data/alloc_data.rda |only inst/doc/get_started.html | 24 +++++++++--------- inst/doc/user_cases.html | 52 ++++++++++++++++++++-------------------- man/alloc_data.Rd |only man/alloc_dmd.Rd |only tests/testthat/test-alloc_dmd.R |only 12 files changed, 100 insertions(+), 50 deletions(-)