Title: Kernel Distance Metric Learning for Mixed-Type Data
Description: Distance metrics for mixed-type data consisting of continuous, nominal, and ordinal variables. This methodology uses additive and product kernels to calculate similarity functions and metrics, and selects variables relevant to the underlying distance through bandwidth selection via maximum similarity cross-validation. These methods can be used in any distance-based algorithm, such as distance-based clustering. For further details, we refer the reader to Ghashti and Thompson (2024) <<doi:10.48550/arXiv.2306.01890>> for dkps() methodology, and Ghashti (2024) <doi:10.14288/1.0443975> for dkss() methodology.
Author: John R. J. Thompson [aut, cre]
,
Jesse S. Ghashti [aut]
Maintainer: John R. J. Thompson <john.thompson@ubc.ca>
Diff between kdml versions 1.0.0 dated 2024-08-27 and 1.1.0 dated 2024-09-20
DESCRIPTION | 17 +++--- MD5 | 18 ++++-- NAMESPACE | 2 R/kss.R |only R/spectral.clust.R |only man/dkps.Rd | 131 +++++++++++++++++++++++++------------------------- man/dkss.Rd | 23 ++++---- man/kdml-package.Rd | 90 +++++++++++++++++----------------- man/kss.Rd |only man/mscv.dkps.Rd | 28 +++++----- man/mscv.dkss.Rd | 18 +++--- man/spectral.clust.Rd |only 12 files changed, 168 insertions(+), 159 deletions(-)
Title: Generalized Linear Models with Clustering
Description: Binomial and Poisson regression for clustered data, fixed
and random effects with bootstrapping.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb],
Henrik Holmberg [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between glmmML versions 1.1.6 dated 2023-11-28 and 1.1.7 dated 2024-09-20
ChangeLog | 5 +- DESCRIPTION | 9 ++-- MD5 | 18 ++++---- build/vignette.rds |binary inst/doc/glmmML.pdf |binary src/bfun.c | 12 ++--- src/fun.c | 114 ++++++++++++++++++++++++++-------------------------- src/glmmb0.c | 16 +++---- src/glmmboot.c | 48 ++++++++++----------- src/glmmml.c | 74 ++++++++++++++++----------------- 10 files changed, 150 insertions(+), 146 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. [...truncated...]
Maintainer: Julia Wrobel <julia.wrobel@emory.edu>
Diff between refund versions 0.1-35 dated 2024-02-14 and 0.1-37 dated 2024-09-20
refund-0.1-35/refund/man/smooth.construct.peer.smooth.spec.Rd |only refund-0.1-37/refund/DESCRIPTION | 12 refund-0.1-37/refund/MD5 | 100 ++-- refund-0.1-37/refund/NAMESPACE | 3 refund-0.1-37/refund/R/af.R | 28 - refund-0.1-37/refund/R/af_old.R | 24 - refund-0.1-37/refund/R/fgam.R | 20 refund-0.1-37/refund/R/fosr.R | 20 refund-0.1-37/refund/R/fosr.vs.R | 60 +- refund-0.1-37/refund/R/fosr2s.R | 6 refund-0.1-37/refund/R/fpc.R | 106 ++-- refund-0.1-37/refund/R/lf.R | 56 +- refund-0.1-37/refund/R/lf.vd.R | 86 +-- refund-0.1-37/refund/R/lf_old.R | 30 - refund-0.1-37/refund/R/mfpca.face.R | 27 - refund-0.1-37/refund/R/peer.R | 64 +- refund-0.1-37/refund/R/peer_old.R | 66 +- refund-0.1-37/refund/R/pffr.R | 225 +++++----- refund-0.1-37/refund/R/pfr.R | 29 - refund-0.1-37/refund/R/poridge.R | 47 +- refund-0.1-37/refund/R/predict.fgam.R | 20 refund-0.1-37/refund/R/predict.pfr.R | 46 +- refund-0.1-37/refund/R/predict.pfr_old.R | 7 refund-0.1-37/refund/R/vis.fgam.R | 22 refund-0.1-37/refund/R/vis.pfr.R | 68 +-- refund-0.1-37/refund/man/Predict.matrix.fpc.smooth.Rd | 6 refund-0.1-37/refund/man/Predict.matrix.peer.smooth.Rd | 6 refund-0.1-37/refund/man/af.Rd | 28 - refund-0.1-37/refund/man/af_old.Rd | 24 - refund-0.1-37/refund/man/cmdscale_lanczos.Rd | 12 refund-0.1-37/refund/man/dot-smooth.spec.Rd |only refund-0.1-37/refund/man/fgam.Rd | 20 refund-0.1-37/refund/man/fosr.Rd | 20 refund-0.1-37/refund/man/fosr.vs.Rd | 6 refund-0.1-37/refund/man/fosr2s.Rd | 6 refund-0.1-37/refund/man/fpc.Rd | 26 - refund-0.1-37/refund/man/lf.Rd | 26 - refund-0.1-37/refund/man/lf.vd.Rd | 38 - refund-0.1-37/refund/man/lf_old.Rd | 16 refund-0.1-37/refund/man/mfpca.face.Rd | 8 refund-0.1-37/refund/man/pco_predict_preprocess.Rd | 18 refund-0.1-37/refund/man/peer.Rd | 10 refund-0.1-37/refund/man/peer_old.Rd | 2 refund-0.1-37/refund/man/pfr.Rd | 29 - refund-0.1-37/refund/man/predict.fgam.Rd | 18 refund-0.1-37/refund/man/predict.pfr.Rd | 18 refund-0.1-37/refund/man/smooth.construct.fpc.smooth.spec.Rd | 10 refund-0.1-37/refund/man/smooth.construct.pco.smooth.spec.Rd | 17 refund-0.1-37/refund/man/sofa.Rd | 6 refund-0.1-37/refund/man/vis.fgam.Rd | 22 refund-0.1-37/refund/man/vis.pfr.Rd | 18 refund-0.1-37/refund/tests/testthat/test-peer.R | 40 - 52 files changed, 820 insertions(+), 802 deletions(-)
Title: Tools Developed by the Long Term Ecological Research Community
Description: Set of the data science tools created by various members of the Long Term
Ecological Research (LTER) community. These functions were initially written largely
as standalone operations and have later been aggregated into this package.
Author: Nicholas Lyon [aut, cre] ,
Angel Chen [aut] ,
Miguel C. Leon [ctb] ,
National Science Foundation [fnd] ,
University of California, Santa Barbara [cph]
Maintainer: Nicholas Lyon <lyon@nceas.ucsb.edu>
Diff between ltertools versions 1.0.0 dated 2024-02-23 and 1.1.0 dated 2024-09-20
DESCRIPTION | 48 ++++---- MD5 | 48 +++++--- NAMESPACE | 2 NEWS.md | 11 + R/begin_key.R | 3 R/cv.R | 2 R/harmonize.R | 66 +++++++---- R/make_json.R |only R/read.R | 12 +- R/site_subset.R | 12 +- R/site_timeline.R | 2 R/solar_day_info.R |only README.md | 12 ++ build/vignette.rds |binary inst/doc/ltertools.R | 22 +++ inst/doc/ltertools.Rmd | 39 ++++++ inst/doc/ltertools.html | 222 ++++++++++++++++++++++++--------------- man/ltertools-package.Rd | 5 man/make_json.Rd |only man/solar_day_info.Rd |only tests |only vignettes/harmonize-workflow.png |binary vignettes/ltertools.Rmd | 39 ++++++ 23 files changed, 385 insertions(+), 160 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.18 dated 2024-08-16 and 1.1.19 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS | 3 +++ R/lang.gltc.R | 2 +- build/vignette.rds |binary inst/doc/lingtypology_creating_maps.html | 4 ++-- inst/doc/lingtypology_db_API.html | 4 ++-- inst/doc/lingtypology_dplyr.html | 6 +++--- inst/doc/lingtypology_glottolog_functions.html | 8 ++++---- inst/doc/lingtypology_intro.Rmd | 2 +- inst/doc/lingtypology_intro.html | 6 +++--- vignettes/lingtypology_intro.Rmd | 2 +- 12 files changed, 34 insertions(+), 31 deletions(-)
Title: "Risk Model Regression and Analysis with Complex Non-Linear
Models"
Description: Performs survival analysis using general non-linear models. Risk models can be the sum or product of terms. Each term is the product of exponential/linear functions of covariates. Additionally sub-terms can be defined as a sum of exponential, linear threshold, and step functions. Cox Proportional hazards <https://en.wikipedia.org/wiki/Proportional_hazards_model>, Poisson <https://en.wikipedia.org/wiki/Poisson_regression>, and Fine-Grey competing risks <https://www.publichealth.columbia.edu/research/population-health-methods/competing-risk-analysis> regression are supported. This work was sponsored by NASA Grant 80NSSC19M0161 through a subcontract from the National Council on Radiation Protection and Measurements (NCRP). The computing for this project was performed on the Beocat Research Cluster at Kansas State University, which is funded in part by NSF grants CNS-1006860, EPS-1006860, EPS-0919443, ACI-1440548, CHE-1726332, and NIH P20GM113109.
Author: Eric Giunta [aut, cre] ,
Amir Bahadori [ctb] ,
Dan Andresen [ctb],
Linda Walsh [ctb] ,
Benjamin French [ctb] ,
Lawrence Dauer [ctb],
John Boice Jr [ctb] ,
Kansas State University [cph],
NASA [fnd],
NCRP [fnd],
NRC [fnd]
Maintainer: Eric Giunta <egiunta@ksu.edu>
Diff between Colossus versions 1.1.3.1 dated 2024-09-12 and 1.1.4.1 dated 2024-09-20
DESCRIPTION | 9 - MD5 | 64 ++++---- NEWS.md | 6 R/Cox_Regression.R | 50 +++--- R/PlotTypes.R | 201 +++++++++++++++---------- R/Poisson_Regression.R | 18 +- inst/doc/Plotting_And_Analysis.R | 141 +++++++++++++++-- inst/doc/Plotting_And_Analysis.Rmd | 155 ++++++++++++++++--- inst/doc/Plotting_And_Analysis.html | 244 ++++++++++++++++++++++++++----- man/Cox_Relative_Risk.Rd | 22 +- man/RunCoxNull.Rd | 8 - man/RunCoxPlots.Rd | 24 +-- man/RunCoxRegression.Rd | 24 +-- man/RunCoxRegression_Basic.Rd | 16 +- man/RunCoxRegression_CR.Rd | 26 +-- man/RunCoxRegression_Guesses_CPP.Rd | 28 +-- man/RunCoxRegression_STRATA.Rd | 26 +-- man/RunCoxRegression_Single.Rd | 22 +- man/RunCoxRegression_Tier_Guesses.Rd | 28 +-- man/RunPoissonEventAssignment.Rd | 22 +- man/RunPoissonEventAssignment_bound.Rd | 14 - man/RunPoissonRegression.Rd | 22 +- man/RunPoissonRegression_Guesses_CPP.Rd | 26 +-- man/RunPoissonRegression_STRATA.Rd | 24 +-- man/RunPoissonRegression_Single.Rd | 18 +- man/RunPoissonRegression_Tier_Guesses.Rd | 29 ++- src/Main_Functions.cpp | 50 +++--- src/Omnibus_Pieces.cpp | 54 +++--- src/Plot_Extensions.cpp | 2 tests/testthat/test-logbound.R | 75 --------- tests/testthat/test-multidose.R | 10 - tests/testthat/test-omnibus.R | 88 ++--------- vignettes/Plotting_And_Analysis.Rmd | 155 ++++++++++++++++--- 33 files changed, 1058 insertions(+), 643 deletions(-)
Title: Sensitivity Analysis Tools for LSD Simulations
Description: Tools for sensitivity analysis of LSD simulation models. Reads object-oriented data produced by LSD simulation models and performs screening and global sensitivity analysis (Sobol decomposition method, Saltelli et al. (2008) ISBN:9780470725177). A Kriging or polynomial meta-model (Kleijnen (2009) <doi:10.1016/j.ejor.2007.10.013>) is estimated using the simulation data to provide the data required by the Sobol decomposition. LSD (Laboratory for Simulation Development) is free software developed by Marco Valente and Marcelo C. Pereira (documentation and downloads available at <https://www.labsimdev.org/>).
Author: Marcelo C. Pereira [aut, cre]
Maintainer: Marcelo C. Pereira <mcper@unicamp.br>
Diff between LSDsensitivity versions 1.2.3 dated 2022-07-03 and 1.3.0 dated 2024-09-20
DESCRIPTION | 12 +- MD5 | 16 +-- R/lsd_doe.R | 183 +++++++++++++++++++++++++----------- build/partial.rdb |binary inst/extdata/Sim1.lsd | 212 +++++++++++++++++++++--------------------- inst/extdata/ee/Sim2.lsd | 212 +++++++++++++++++++++--------------------- inst/extdata/sobol/Sim3.lsd | 212 +++++++++++++++++++++--------------------- man/LSDsensitivity-package.Rd | 1 man/read.doe.lsd.Rd | 2 9 files changed, 463 insertions(+), 387 deletions(-)
More information about LSDsensitivity at CRAN
Permanent link
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 1.6.5 dated 2024-07-25 and 1.6.6 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/helpers.R | 13 +++++++++---- R/search_variables.R | 6 +++--- R/utils.R | 2 +- man/interpolate_pw.Rd | 2 +- man/load_variables.Rd | 20 ++++++++++---------- 7 files changed, 34 insertions(+), 29 deletions(-)
Title: R Interface to 'Mapbox' Web Services
Description: Includes support for 'Mapbox' Navigation APIs, including directions,
isochrones, and route optimization; the Search API for forward and reverse geocoding;
the Maps API for interacting with 'Mapbox' vector tilesets and visualizing
'Mapbox' maps in R; and 'Mapbox Tiling Service' and 'tippecanoe' for generating map tiles.
See <https://docs.mapbox.com/api/> for more information about the 'Mapbox' APIs.
Author: Kyle Walker [aut, cre],
Eli Pousson [ctb],
Anthony North [ctb, cph],
Miles McBain [ctb]
Maintainer: Kyle Walker <kyle@walker-data.com>
Diff between mapboxapi versions 0.6 dated 2024-05-10 and 0.6.2 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/navigation.R | 3 +++ R/search.R | 12 ++++++++---- README.md | 2 +- inst/www/mapboxGeocoderBinding.js | 11 +++++------ 6 files changed, 26 insertions(+), 20 deletions(-)
Title: Write Equations in a Way that You Can Read
Description: Utilities to help you write 'LaTeX' in a more readable way. Instead of using plain code or a series of 'newcommand' statements, use 'R' functions. You will be able to write what you mean and make fewer mistakes.
Author: Nicolas Escobar [aut, cre]
Maintainer: Nicolas Escobar <nescoba@iu.edu>
Diff between latexSymb versions 0.4.0 dated 2024-08-26 and 0.4.2 dated 2024-09-20
DESCRIPTION | 16 +++--- MD5 | 29 +++++++--- NAMESPACE | 9 +++ NEWS |only R/cummulative.R |only R/environments.R | 6 +- R/function_aux.R |only README.md | 101 ++++---------------------------------- build/vignette.rds |binary data |only inst/doc/vignette1.R | 18 +++--- inst/doc/vignette1.Rmd | 40 +++++++-------- inst/doc/vignette1.html | 59 +++++++++++----------- man/common.Rd |only man/commulative.Rd |only man/function_aux.Rd |only tests/testthat/test-aux.R |only tests/testthat/test-common.R | 4 - tests/testthat/test-cummulative.R |only vignettes/vignette1.Rmd | 40 +++++++-------- 20 files changed, 130 insertions(+), 192 deletions(-)
Title: Ensemble Tool for Predictions from Species Distribution Models
Description: A tool which allows users to create and evaluate ensembles
of species distribution model (SDM) predictions.
Functionality is offered through R functions or a GUI (R Shiny app).
This tool can assist users in identifying spatial uncertainties and
making informed conservation and management decisions. The package is
further described in Woodman et al (2019) <doi:10.1111/2041-210X.13283>.
Author: Sam Woodman [aut, cre]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between eSDM versions 0.4.2 dated 2024-07-11 and 0.4.3 dated 2024-09-20
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 7 +++++++ R/overlay_sdm.R | 30 +++++++++++++++++++++--------- data/preds.1.rda |binary data/preds.2.rda |binary data/preds.3.rda |binary inst/doc/example-analysis.html | 6 +++--- man/overlay_sdm.Rd | 15 +++++++++++---- tests/testthat/test-overlay_sdm.R | 15 +++++++++++++-- 10 files changed, 69 insertions(+), 32 deletions(-)
Title: Detection and Attribution Analysis of Climate Change
Description: Conduct detection and attribution of climate change using methods including optimal fingerprinting via
generalized total least squares or estimating equation approach from Ma et al. (2023) <doi:10.1175/JCLI-D-22-0681.1>.
Provide shrinkage estimators for covariance matrix from Ledoit and Wolf (2004) <doi:10.1016/S0047-259X(03)00096-4>,
and Ledoit and Wolf (2017) <doi:10.2139/ssrn.2383361>.
Author: Yan Li [aut, cre],
Kun Chen [aut],
Jun Yan [aut]
Maintainer: Yan Li <yan.4.li@uconn.edu>
Diff between dacc versions 0.0-4 dated 2024-06-27 and 0.0-5 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/fingerprint.R | 15 +++++++++++---- R/fingerprintCEE.R | 28 +++++++++++++++++++++++++++- R/fpPrep.R | 2 +- man/fingerprint.Rd | 15 +++++++++++---- 6 files changed, 59 insertions(+), 19 deletions(-)
Title: Win Time Methods for Time-to-Event Data in Clinical Trials
Description: Performs an analysis of time-to-event clinical trial data using various "win time" methods,
including 'ewt', 'ewtr', 'rmt', 'max', 'wtr', 'rwtr', and 'pwt'. These methods are used to calculate and compare
treatment effects on ordered composite endpoints. The package handles event times, event indicators, and treatment
arm indicators and supports calculations on observed and resampled data. Detailed explanations of each method and
usage examples are provided in "Use of win time for ordered composite endpoints in clinical trials," by Troendle et al.
(2024)<https://pubmed.ncbi.nlm.nih.gov/38417455/>. For more information, see the package documentation or the vignette titled "Introduction to wintime."
Author: James Troendle [aut, cre],
Samuel Lawrence [aut]
Maintainer: James Troendle <james.troendle@nih.gov>
Diff between wintime versions 0.1.0 dated 2024-09-02 and 0.2.0 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/markov.R | 11 ++++++++--- tests/testthat/test-main_wintime_function.R | 20 ++++++++++---------- 4 files changed, 24 insertions(+), 19 deletions(-)
Title: Reporting Tables
Description: Reporting tables often have structure that goes beyond simple
rectangular data. The 'rtables' package provides a framework for
declaring complex multi-level tabulations and then applying them to
data. This framework models both tabulation and the resulting tables
as hierarchical, tree-like objects which support sibling sub-tables,
arbitrary splitting or grouping of data in row and column dimensions,
cells containing multiple values, and the concept of contextual
summary computations. A convenient pipe-able interface is provided for
declaring table layouts and the corresponding computations, and then
applying them to data.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Daniel Sabanes Bove [ctb],
Maximilian Mordig [ctb],
Davide Garolini [ctb],
Emily de la Rua [ctb],
Abinaya Yogasekaram [ctb],
Joe Zhu [ctb, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rtables versions 0.6.9 dated 2024-06-27 and 0.6.10 dated 2024-09-20
rtables-0.6.10/rtables/DESCRIPTION | 27 rtables-0.6.10/rtables/MD5 | 214 rtables-0.6.10/rtables/NAMESPACE | 5 rtables-0.6.10/rtables/NEWS.md | 34 rtables-0.6.10/rtables/R/as_html.R | 7 rtables-0.6.10/rtables/R/colby_constructors.R | 10 rtables-0.6.10/rtables/R/custom_split_funs.R |only rtables-0.6.10/rtables/R/default_split_funs.R |only rtables-0.6.10/rtables/R/summary.R | 6 rtables-0.6.10/rtables/R/tree_accessors.R | 5 rtables-0.6.10/rtables/R/tt_as_df.R |only rtables-0.6.10/rtables/R/tt_as_flextable.R |only rtables-0.6.10/rtables/R/tt_export.R | 1016 -- rtables-0.6.10/rtables/R/tt_pos_and_access.R | 1 rtables-0.6.10/rtables/R/tt_toString.R | 15 rtables-0.6.10/rtables/R/utils.R | 59 rtables-0.6.10/rtables/README.md | 14 rtables-0.6.10/rtables/build/vignette.rds |binary rtables-0.6.10/rtables/inst/doc/advanced_usage.html | 14 rtables-0.6.10/rtables/inst/doc/baseline.html | 9 rtables-0.6.10/rtables/inst/doc/clinical_trials.R | 15 rtables-0.6.10/rtables/inst/doc/clinical_trials.Rmd | 16 rtables-0.6.10/rtables/inst/doc/clinical_trials.html | 3397 +++++----- rtables-0.6.10/rtables/inst/doc/col_counts.R | 17 rtables-0.6.10/rtables/inst/doc/col_counts.Rmd | 24 rtables-0.6.10/rtables/inst/doc/col_counts.html | 209 rtables-0.6.10/rtables/inst/doc/custom_appearance.R | 13 rtables-0.6.10/rtables/inst/doc/custom_appearance.Rmd | 15 rtables-0.6.10/rtables/inst/doc/custom_appearance.html | 1600 ++-- rtables-0.6.10/rtables/inst/doc/example_analysis_coxreg.R | 13 rtables-0.6.10/rtables/inst/doc/example_analysis_coxreg.Rmd | 16 rtables-0.6.10/rtables/inst/doc/example_analysis_coxreg.html | 38 rtables-0.6.10/rtables/inst/doc/exploratory_analysis.R | 13 rtables-0.6.10/rtables/inst/doc/exploratory_analysis.Rmd | 14 rtables-0.6.10/rtables/inst/doc/exploratory_analysis.html | 615 - rtables-0.6.10/rtables/inst/doc/format_precedence.html | 19 rtables-0.6.10/rtables/inst/doc/introspecting_tables.R | 13 rtables-0.6.10/rtables/inst/doc/introspecting_tables.Rmd | 38 rtables-0.6.10/rtables/inst/doc/introspecting_tables.html | 451 - rtables-0.6.10/rtables/inst/doc/manual_table_construction.html | 9 rtables-0.6.10/rtables/inst/doc/rtables.R |only rtables-0.6.10/rtables/inst/doc/rtables.Rmd |only rtables-0.6.10/rtables/inst/doc/rtables.html |only rtables-0.6.10/rtables/inst/doc/sorting_pruning.R | 13 rtables-0.6.10/rtables/inst/doc/sorting_pruning.Rmd | 22 rtables-0.6.10/rtables/inst/doc/sorting_pruning.html | 1329 +-- rtables-0.6.10/rtables/inst/doc/split_functions.R | 13 rtables-0.6.10/rtables/inst/doc/split_functions.Rmd | 25 rtables-0.6.10/rtables/inst/doc/split_functions.html | 567 - rtables-0.6.10/rtables/inst/doc/subsetting_tables.R | 13 rtables-0.6.10/rtables/inst/doc/subsetting_tables.Rmd | 21 rtables-0.6.10/rtables/inst/doc/subsetting_tables.html | 649 - rtables-0.6.10/rtables/inst/doc/tabulation_concepts.R | 13 rtables-0.6.10/rtables/inst/doc/tabulation_concepts.Rmd | 14 rtables-0.6.10/rtables/inst/doc/tabulation_concepts.html | 978 +- rtables-0.6.10/rtables/inst/doc/tabulation_dplyr.R | 13 rtables-0.6.10/rtables/inst/doc/tabulation_dplyr.Rmd | 18 rtables-0.6.10/rtables/inst/doc/tabulation_dplyr.html | 417 - rtables-0.6.10/rtables/inst/doc/title_footer.R | 13 rtables-0.6.10/rtables/inst/doc/title_footer.Rmd | 16 rtables-0.6.10/rtables/inst/doc/title_footer.html | 914 +- rtables-0.6.10/rtables/man/add_overall_level.Rd | 85 rtables-0.6.10/rtables/man/analyze_colvars.Rd | 3 rtables-0.6.10/rtables/man/append_topleft.Rd | 3 rtables-0.6.10/rtables/man/as_html.Rd | 6 rtables-0.6.10/rtables/man/cell_values.Rd | 3 rtables-0.6.10/rtables/man/custom_split_funs.Rd | 2 rtables-0.6.10/rtables/man/data.frame_export.Rd | 2 rtables-0.6.10/rtables/man/do_base_split.Rd | 2 rtables-0.6.10/rtables/man/export_as_docx.Rd | 37 rtables-0.6.10/rtables/man/gfc.Rd | 3 rtables-0.6.10/rtables/man/int_methods.Rd | 6 rtables-0.6.10/rtables/man/matrix_form-VTableTree-method.Rd | 3 rtables-0.6.10/rtables/man/row_paths_summary.Rd | 3 rtables-0.6.10/rtables/man/rtinner.Rd | 2 rtables-0.6.10/rtables/man/split_cols_by.Rd | 3 rtables-0.6.10/rtables/man/split_cols_by_multivar.Rd | 3 rtables-0.6.10/rtables/man/split_funcs.Rd | 160 rtables-0.6.10/rtables/man/split_rows_by.Rd | 3 rtables-0.6.10/rtables/man/table_shell.Rd | 3 rtables-0.6.10/rtables/man/table_structure.Rd | 3 rtables-0.6.10/rtables/man/tostring.Rd | 3 rtables-0.6.10/rtables/man/trim_levels_to_map.Rd | 4 rtables-0.6.10/rtables/man/tsv_io.Rd | 8 rtables-0.6.10/rtables/man/tt_to_flextable.Rd | 102 rtables-0.6.10/rtables/man/varcuts.Rd | 3 rtables-0.6.10/rtables/tests/testthat/Rplots.pdf |binary rtables-0.6.10/rtables/tests/testthat/setup-fakedata.R | 21 rtables-0.6.10/rtables/tests/testthat/test-as_html.R |only rtables-0.6.10/rtables/tests/testthat/test-custom_split_funs.R |only rtables-0.6.10/rtables/tests/testthat/test-default_split_funs.R |only rtables-0.6.10/rtables/tests/testthat/test-exporters.R | 209 rtables-0.6.10/rtables/tests/testthat/test-formatting.R | 6 rtables-0.6.10/rtables/tests/testthat/test-printing.R | 3 rtables-0.6.10/rtables/tests/testthat/test-regressions.R | 36 rtables-0.6.10/rtables/tests/testthat/test-tab_afun_cfun.R | 15 rtables-0.6.10/rtables/tests/testthat/test-tt_as_flextable.R |only rtables-0.6.10/rtables/vignettes/clinical_trials.Rmd | 16 rtables-0.6.10/rtables/vignettes/col_counts.Rmd | 24 rtables-0.6.10/rtables/vignettes/custom_appearance.Rmd | 15 rtables-0.6.10/rtables/vignettes/example_analysis_coxreg.Rmd | 16 rtables-0.6.10/rtables/vignettes/exploratory_analysis.Rmd | 14 rtables-0.6.10/rtables/vignettes/introspecting_tables.Rmd | 38 rtables-0.6.10/rtables/vignettes/rtables.Rmd |only rtables-0.6.10/rtables/vignettes/sorting_pruning.Rmd | 22 rtables-0.6.10/rtables/vignettes/split_functions.Rmd | 25 rtables-0.6.10/rtables/vignettes/subsetting_tables.Rmd | 21 rtables-0.6.10/rtables/vignettes/tabulation_concepts.Rmd | 14 rtables-0.6.10/rtables/vignettes/tabulation_dplyr.Rmd | 18 rtables-0.6.10/rtables/vignettes/title_footer.Rmd | 16 rtables-0.6.9/rtables/R/simple_analysis.R |only rtables-0.6.9/rtables/R/split_funs.R |only rtables-0.6.9/rtables/inst/doc/introduction.R |only rtables-0.6.9/rtables/inst/doc/introduction.Rmd |only rtables-0.6.9/rtables/inst/doc/introduction.html |only rtables-0.6.9/rtables/man/add_combo_levels.Rd |only rtables-0.6.9/rtables/tests/testthat/test-split_funs.R |only rtables-0.6.9/rtables/vignettes/introduction.Rmd |only 118 files changed, 7014 insertions(+), 6999 deletions(-)
Title: Named Capture to Data Tables
Description: User-friendly functions for extracting a data
table (row for each match, column for each group)
from non-tabular text data using regular expressions,
and for melting columns that match a regular expression.
Patterns are defined using a readable syntax
that makes it easy to build complex patterns
in terms of simpler, re-usable sub-patterns.
Named R arguments are translated to column names
in the output; capture groups without names are used
internally in order to provide a standard interface
to three regular expression 'C' libraries
('PCRE', 'RE2', 'ICU').
Output can also include numeric columns via
user-specified type conversion functions.
Author: Toby Hocking [aut, cre]
Maintainer: Toby Hocking <toby.hocking@r-project.org>
Diff between nc versions 2024.2.21 dated 2024-02-22 and 2024.9.20 dated 2024-09-20
nc-2024.2.21/nc/po |only nc-2024.9.20/nc/DESCRIPTION | 6 nc-2024.9.20/nc/MD5 | 81 nc-2024.9.20/nc/NEWS | 17 nc-2024.9.20/nc/R/alternatives.R | 29 nc-2024.9.20/nc/R/apply_type_funs.R | 5 nc-2024.9.20/nc/R/capture_all_str.R | 4 nc-2024.9.20/nc/R/capture_first_glob.R | 2 nc-2024.9.20/nc/R/capture_first_vec.R | 3 nc-2024.9.20/nc/build/vignette.rds |binary nc-2024.9.20/nc/inst/doc/v0-overview.Rmd | 25 nc-2024.9.20/nc/inst/doc/v0-overview.html | 555 ++-- nc-2024.9.20/nc/inst/doc/v1-capture-first.Rmd | 2 nc-2024.9.20/nc/inst/doc/v1-capture-first.html | 1446 ++++++---- nc-2024.9.20/nc/inst/doc/v2-capture-all.Rmd | 2 nc-2024.9.20/nc/inst/doc/v2-capture-all.html | 1062 ++++---- nc-2024.9.20/nc/inst/doc/v3-capture-melt.Rmd | 2 nc-2024.9.20/nc/inst/doc/v3-capture-melt.html | 1128 +++++--- nc-2024.9.20/nc/inst/doc/v4-comparisons.Rmd | 2 nc-2024.9.20/nc/inst/doc/v4-comparisons.html | 2114 ++++++++-------- nc-2024.9.20/nc/inst/doc/v5-helpers.R | 23 nc-2024.9.20/nc/inst/doc/v5-helpers.Rmd | 42 nc-2024.9.20/nc/inst/doc/v5-helpers.html | 580 ++-- nc-2024.9.20/nc/inst/doc/v6-engines.Rmd | 2 nc-2024.9.20/nc/inst/doc/v6-engines.html | 499 ++- nc-2024.9.20/nc/inst/doc/v7-capture-glob.R | 7 nc-2024.9.20/nc/inst/doc/v7-capture-glob.Rmd | 11 nc-2024.9.20/nc/inst/doc/v7-capture-glob.html | 1081 +++++--- nc-2024.9.20/nc/inst/extdata/pepseq.txt | 6 nc-2024.9.20/nc/man/alternatives_with_shared_groups.Rd | 21 nc-2024.9.20/nc/man/altlist.Rd | 8 nc-2024.9.20/nc/man/capture_first_glob.Rd | 2 nc-2024.9.20/nc/tests/testthat/test-CRAN-alternatives.R | 16 nc-2024.9.20/nc/tests/testthat/test-CRAN-vec.R | 18 nc-2024.9.20/nc/vignettes/v0-overview.Rmd | 25 nc-2024.9.20/nc/vignettes/v1-capture-first.Rmd | 2 nc-2024.9.20/nc/vignettes/v2-capture-all.Rmd | 2 nc-2024.9.20/nc/vignettes/v3-capture-melt.Rmd | 2 nc-2024.9.20/nc/vignettes/v4-comparisons.Rmd | 2 nc-2024.9.20/nc/vignettes/v5-helpers.Rmd | 42 nc-2024.9.20/nc/vignettes/v6-engines.Rmd | 2 nc-2024.9.20/nc/vignettes/v7-capture-glob.Rmd | 11 42 files changed, 5456 insertions(+), 3433 deletions(-)
Title: Converts 'Monolix' Models to 'rxode2'
Description: 'Monolix' is a tool for running mixed effects model using
'saem'. This tool allows you to convert 'Monolix' models to 'rxode2'
(Wang, Hallow and James (2016) <doi:10.1002/psp4.12052>) using the
form compatible with 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>).
If available, the 'rxode2' model will
read in the 'Monolix' data and compare the simulation for the
population model individual model and residual
model to immediately show how well the translation is
performing. This saves the model development time for people who are
creating an 'rxode2' model manually. Additionally, this package reads
in all the information to allow simulation with uncertainty (that is the
number of observations, the number of subjects, and the covariance
matrix) with a 'rxode2' model. This is complementary to the
'babelmixr2' package that translates 'nlmixr2' models to 'Monolix' and can
convert the objects converted from 'monolix2rx' to a full 'nlmixr2' fit. While not
required, you c [...truncated...]
Author: Matthew Fidler [aut, cre] ,
Justin Wilkins [ctb]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between monolix2rx versions 0.0.1 dated 2024-09-20 and 0.0.2 dated 2024-09-20
DESCRIPTION | 13 +++++++------ MD5 | 4 ++-- NEWS.md | 9 +++++++++ 3 files changed, 18 insertions(+), 8 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-27 2.1.1
2024-01-30 2.0.13
2023-12-11 2.0.12
2023-03-28 2.0.11
2023-03-17 2.0.10
2022-10-11 2.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-05-27 2.0.13
2024-01-30 2.0.12
2023-12-11 2.0.11
2023-03-17 2.0.10
2022-10-13 2.0.9
Title: Single Case Design Tools
Description: In some situations where researchers would like to demonstrate
causal effects, it is hard to obtain a sample size that would allow for a
well-powered randomized controlled trial. Single case designs are experimental
designs that can be used to demonstrate causal effects with only one participant
or with only a few participants. The 'scdtb' package provides a suite of tools
for analyzing data from studies that use single case designs. The nap() function
can be used to compute the nonoverlap of all pairs as outlined by the What
Works Clearinghouse (2022) <https://ies.ed.gov/ncee/wwc/Handbooks>. The
package also offers the mixed_model_analysis() and cross_lagged() functions
which implement mixed effects models and cross lagged analyses as described
in Maric & van der Werff (2020) <doi:10.4324/9780429273872-9>. The
randomization_test() function implements randomization tests based on methods
presented in Onghena (2020) <doi:10.4324/9780429273872-8>. The scdtb() 'shiny [...truncated...]
Author: Mackson Ncube [aut, cre],
mightymetrika, LLC [cph, fnd]
Maintainer: Mackson Ncube <macksonncube.stats@gmail.com>
Diff between scdtb versions 0.1.0 dated 2024-04-30 and 0.2.0 dated 2024-09-20
DESCRIPTION | 11 MD5 | 27 +- NAMESPACE | 4 R/cross_lagged.R | 362 ++++++++++++++--------------- R/data.R | 152 ++++++------ R/mixed_model_analysis.R | 356 ++++++++++++++-------------- R/randomization_test.R | 360 ++++++++++++++-------------- R/replext_gls.R |only R/replext_gls_app.R |only R/replext_gls_app_helpers.R |only R/scdtb.R | 2 man/plot.replext_gls.Rd |only man/replext_gls.Rd |only man/replext_gls_UIParams.Rd |only man/replext_pgsql.Rd |only man/scdtb.Rd | 2 man/simulate_gls_once.Rd |only tests/testthat/test-mixed_model_analysis.R | 242 +++++++++---------- tests/testthat/test-replext_gls.R |only 19 files changed, 766 insertions(+), 752 deletions(-)
Title: Addons for the 'mclust' Package
Description: Extend the functionality of the 'mclust' package for Gaussian
finite mixture modeling by including: density estimation for data with
bounded support (Scrucca, 2019 <doi:10.1002/bimj.201800174>); modal
clustering using MEM (Modal EM) algorithm for Gaussian mixtures
(Scrucca, 2021 <doi:10.1002/sam.11527>); entropy estimation via
Gaussian mixture modeling (Robin & Scrucca, 2023
<doi:10.1016/j.csda.2022.107582>).
Author: Luca Scrucca [aut, cre, cph]
Maintainer: Luca Scrucca <luca.scrucca@unipg.it>
Diff between mclustAddons versions 0.8 dated 2024-03-01 and 0.9 dated 2024-09-20
mclustAddons-0.8/mclustAddons/R/EntropyGMM.R |only mclustAddons-0.8/mclustAddons/man/cdfDensityBounded.Rd |only mclustAddons-0.9/mclustAddons/DESCRIPTION | 47 mclustAddons-0.9/mclustAddons/MD5 | 66 mclustAddons-0.9/mclustAddons/NAMESPACE | 118 - mclustAddons-0.9/mclustAddons/NEWS.md | 11 mclustAddons-0.9/mclustAddons/R/GMM_Entropy.R |only mclustAddons-0.9/mclustAddons/R/GMM_finance.R |only mclustAddons-0.9/mclustAddons/R/MclustBounded.R |only mclustAddons-0.9/mclustAddons/R/ModalEM.R | 255 ++ mclustAddons-0.9/mclustAddons/R/densityMclustBounded.R | 1028 ++++++++-- mclustAddons-0.9/mclustAddons/R/mclustAddons-package.R |only mclustAddons-0.9/mclustAddons/R/util.R | 93 mclustAddons-0.9/mclustAddons/README.md | 17 mclustAddons-0.9/mclustAddons/build/partial.rdb |only mclustAddons-0.9/mclustAddons/build/vignette.rds |binary mclustAddons-0.9/mclustAddons/inst/doc/mclustAddons.R | 2 mclustAddons-0.9/mclustAddons/inst/doc/mclustAddons.Rmd | 4 mclustAddons-0.9/mclustAddons/inst/doc/mclustAddons.html | 109 - mclustAddons-0.9/mclustAddons/man/EntropyGMM.Rd | 84 mclustAddons-0.9/mclustAddons/man/GMMlogreturn.Rd |only mclustAddons-0.9/mclustAddons/man/GaussianMixtureMEM.Rd | 111 - mclustAddons-0.9/mclustAddons/man/MclustBounded.Rd |only mclustAddons-0.9/mclustAddons/man/MclustBoundedParameters.Rd |only mclustAddons-0.9/mclustAddons/man/MclustMEM.Rd | 66 mclustAddons-0.9/mclustAddons/man/VaR.GMMlogreturn.Rd |only mclustAddons-0.9/mclustAddons/man/VaR.Rd |only mclustAddons-0.9/mclustAddons/man/densityMclustBounded.Rd | 183 + mclustAddons-0.9/mclustAddons/man/densityMclustBounded.diagnostic.Rd | 148 + mclustAddons-0.9/mclustAddons/man/mclustAddons-internal.Rd |only mclustAddons-0.9/mclustAddons/man/mclustAddons-package.Rd | 75 mclustAddons-0.9/mclustAddons/man/mclustMarginalParams.Rd |only mclustAddons-0.9/mclustAddons/man/plot.MclustBounded.Rd |only mclustAddons-0.9/mclustAddons/man/plot.MclustMEM.Rd | 98 mclustAddons-0.9/mclustAddons/man/plot.densityMclustBounded.Rd | 104 - mclustAddons-0.9/mclustAddons/man/predict.MclustBounded.Rd |only mclustAddons-0.9/mclustAddons/man/predict.densityMclustBounded.Rd | 72 mclustAddons-0.9/mclustAddons/man/racial.Rd | 25 mclustAddons-0.9/mclustAddons/man/rangepowerTransform.Rd | 132 - mclustAddons-0.9/mclustAddons/man/suicide.Rd | 25 mclustAddons-0.9/mclustAddons/src/RangePowerTransform.cpp | 58 mclustAddons-0.9/mclustAddons/vignettes/mclustAddons.Rmd | 4 42 files changed, 2054 insertions(+), 881 deletions(-)
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, with comprehensive visualisation and bandwidth selection capabilities, including for densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre] ,
Matt Wand [ctb] ,
Jose Chacon [ctb],
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.14.2 dated 2024-01-15 and 1.14.3 dated 2024-09-20
CHANGELOG | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/binning.R | 17 ++++++++--------- R/kdde.R | 28 +++++++++++++++------------- R/kde-test.R | 12 ++++++------ R/kde.R | 6 +++--- build/vignette.rds |binary inst/doc/kde.pdf |binary man/air.Rd | 2 +- man/plot.kde.loctest.Rd | 7 +++---- 11 files changed, 57 insertions(+), 50 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Provides a new class of Bayesian meta-analysis models that incorporates a model for internal and external validity bias. In this way, it is possible to combine studies of diverse quality and different types. For example, we can combine the results of randomized control trials (RCTs) with the results of observational studies (OS).
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.4.1 dated 2024-07-12 and 3.4.2 dated 2024-09-20
bamdit |only 1 file changed
Title: Fast FFT and DCT Based on the FFTW Library
Description: Provides a simple and efficient wrapper around the fastest
Fourier transform in the west (FFTW) library <http://www.fftw.org/>.
Author: Olaf Mersmann [aut],
Sebastian Krey [ctb],
Uwe Ligges [ctb, cre]
Maintainer: Uwe Ligges <ligges@statistik.tu-dortmund.de>
Diff between fftw versions 1.0-8 dated 2024-01-08 and 1.0-9 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/fftw.c | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf cla [...truncated...]
Author: Daniel Adler [aut],
Christian Glaeser [ctb],
Oleg Nenadic [ctb],
Jens Oehlschlaegel [aut, cre],
Martijn Schuemie [ctb],
Walter Zucchini [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 4.0.12 dated 2024-01-12 and 4.5.0 dated 2024-09-20
DESCRIPTION | 41 +++++++++---- MD5 | 130 +++++++++++++++++++++--------------------- NEWS | 10 +++ R/CFUN.R | 2 R/as.ff.R | 2 R/ff.R | 114 ++++++++++++++++++------------------- R/ffapply.R | 4 - R/ffbit.R | 4 - R/ffcsv.R | 2 R/ffdf.R | 28 ++++----- R/fffactor.R | 2 R/hi.R | 36 +++++------ R/ordermerge.R | 34 +++++------ R/util.R | 2 R/vt.R | 6 - R/zzz.R | 9 ++ man/CFUN.rd | 2 man/Extract.ff.rd | 4 - man/Extract.ffdf.rd | 2 man/LimWarn.rd | 8 +- man/as.ff.bit.rd | 4 - man/as.ff.rd | 2 man/as.hi.rd | 24 +++---- man/chunk.ffdf.rd | 6 - man/clone.ff.rd | 8 +- man/clone.ffdf.rd | 6 - man/close.ff.rd | 2 man/delete.rd | 2 man/dim.ff.rd | 4 - man/dimnames.ff.rd | 2 man/ff.rd | 28 ++++----- man/ffapply.rd | 4 - man/ffdf.rd | 12 +-- man/ffdfsort.rd | 8 +- man/ffindexorder.rd | 4 - man/fforder.rd | 6 - man/ffsort.rd | 10 +-- man/filename.rd | 2 man/finalizer.rd | 4 - man/getset.ff.rd | 2 man/hi.rd | 6 - man/is.open.rd | 2 man/is.readonly.rd | 4 - man/is.sorted.rd | 10 +-- man/length.ff.rd | 4 - man/length.hi.rd | 6 - man/levels.ff.rd | 4 - man/maxlength.rd | 2 man/na.count.rd | 2 man/names.ff.rd | 2 man/open.ff.rd | 4 - man/physical.ff.rd | 4 - man/physical.ffdf.rd | 2 man/ramattribs.rd | 2 man/ramorder.default.rd | 2 man/ramsort.default.rd | 2 man/read.table.ffdf.rd | 2 man/readwrite.ff.rd | 2 man/regtest.fforder.rd | 2 man/repnam.rd | 2 man/sortLevels.rd | 2 man/update.ff.rd | 2 man/vt.rd | 6 - man/vw.rd | 4 - src/ordermerge.c | 146 ++++++++++++++++++++++++------------------------ src/r_file_resize.cpp | 2 66 files changed, 424 insertions(+), 386 deletions(-)
Title: Tools for Reading, Writing, Viewing and Manipulating CIFTI Files
Description: CIFTI files contain brain imaging data in "grayordinates," which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' provides a unified environment for reading, writing,
visualizing and manipulating CIFTI-format data. It supports the "dscalar,"
"dlabel," and "dtseries" intents. Grayordinate data is read in as a "xifti"
object, which is structured for convenient access to the data and metadata,
and includes support for surface geometry files to enable
spatially-dependent functionality such as static or interactive
visualizations and smoothing.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] ,
John Muschelli [ctb]
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.15.1 dated 2024-06-25 and 0.16.1 dated 2024-09-20
DESCRIPTION | 8 ++--- MD5 | 57 ++++++++++++++++++------------------ NAMESPACE | 2 + R/fix_xifti.R | 15 ++++++++- R/make_xifti_components.R | 12 ++++--- R/move_submask.R |only R/view_xifti_surface.R | 6 +-- R/write_cifti.R | 2 + R/write_nifti.R | 9 +++++ README.md | 2 + man/add_surf.Rd | 1 man/apply_parc.Rd | 1 man/apply_xifti.Rd | 1 man/combine_xifti.Rd | 1 man/convert_xifti.Rd | 1 man/fix_xifti.Rd | 3 + man/merge_xifti.Rd | 1 man/move_from_submask.Rd |only man/move_to_mwall.Rd | 1 man/move_to_submask.Rd |only man/newdata_xifti.Rd | 1 man/remap_cifti.Rd | 1 man/remove_xifti.Rd | 1 man/resample_cifti.Rd | 1 man/resample_cifti_from_template.Rd | 1 man/scale_xifti.Rd | 1 man/select_xifti.Rd | 1 man/set_names_xifti.Rd | 1 man/smooth_cifti.Rd | 1 man/transform_xifti.Rd | 1 tests/testthat/test-misc.R | 5 +++ 31 files changed, 96 insertions(+), 42 deletions(-)
Title: Classes and Methods for Fast Memory-Efficient Boolean Selections
Description: Provided are classes for boolean and skewed boolean vectors,
fast boolean methods, fast unique and non-unique integer sorting,
fast set operations on sorted and unsorted sets of integers, and
foundations for ff (range index, compression, chunked processing).
Author: Jens Oehlschlaegel [aut, cre],
Brian Ripley [ctb]
Maintainer: Jens Oehlschlaegel <Jens.Oehlschlaegel@truecluster.com>
Diff between bit versions 4.0.5 dated 2022-11-15 and 4.5.0 dated 2024-09-20
DESCRIPTION | 24 ++++++---- MD5 | 68 ++++++++++++++-------------- NEWS | 16 ++++++ R/bit-package.R | 17 ------- R/zzz.R | 20 ++++++++ build/vignette.rds |binary inst/doc/bit-demo.R | 6 +- inst/doc/bit-demo.pdf |binary inst/doc/bit-performance.R | 102 +++++++++++++++++++++---------------------- inst/doc/bit-performance.pdf |binary inst/doc/bit-usage.R | 8 +-- inst/doc/bit-usage.pdf |binary man/as.bit.Rd | 18 +++---- man/as.bitwhich.Rd | 18 +++---- man/as.booltype.Rd | 4 - man/as.ri.Rd | 6 +- man/as.which.Rd | 18 +++---- man/bit_setops.Rd | 12 ++--- man/bit_unidup.Rd | 10 ++-- man/chunk.Rd | 4 - man/clone.Rd | 4 - man/getsetattr.Rd | 6 +- man/intrle.Rd | 6 +- man/is.booltype.Rd | 12 ++--- man/is.na.bit.Rd | 4 - man/maxindex.Rd | 29 ++++++------ man/merge_rev.Rd | 46 +++++++++---------- man/str.bit.Rd | 2 man/str.bitwhich.Rd | 2 man/xor.Rd | 43 +++++++++--------- src/bit.c | 34 +++++++------- src/integerutil.c | 28 ++++++++--- src/merge.c | 14 ++--- src/merge.h | 4 - src/rle.c | 12 ++--- 35 files changed, 321 insertions(+), 276 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices are included (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.5.2 dated 2024-05-16 and 1.5.4 dated 2024-09-20
DESCRIPTION | 22 ++--- MD5 | 37 ++++---- NAMESPACE | 3 NEWS.md | 27 ++++++ R/FormulaSums.R | 165 ++++++++++++++++++++++++++++++-------- R/GaussSuppression.R | 13 ++ R/ModelMatrix.R | 8 + R/NumSingleton.R | 11 ++ R/Reduce0exact.R | 2 R/RowGroups.R | 125 ++++++++++++++++++++++++++++ R/aggregate_by_pkg.R |only R/formula_utils.R | 14 ++- build |only man/FormulaSums.Rd | 19 ++++ man/GaussSuppression.Rd | 12 ++ man/ModelMatrix.Rd | 7 + man/NumSingleton.Rd | 10 ++ man/Reduce0exact.Rd | 2 man/RowGroups.Rd | 13 ++ man/aggregate_by_pkg.Rd |only tests/testthat/test-ModelMatrix.R | 36 ++++++++ 21 files changed, 450 insertions(+), 76 deletions(-)
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <https://vcg.isti.cnr.it/>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb],
Tim Schaefer [ctb],
Zhengjia Wang [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.23 dated 2024-06-27 and 0.24 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/Rvcg-package.R | 4 ++-- R/vcgImport.r | 2 +- R/vcgMetro.r | 2 +- man/Rvcg-package.Rd | 4 ++-- man/vcgMetro.Rd | 2 +- src/Makevars | 4 ++-- src/vcglib/vcg/complex/algorithms/update/selection.h | 2 +- 9 files changed, 22 insertions(+), 22 deletions(-)
Title: Transcriptomic Atlas of Neuroimaging Derived Phenotypes
Description: Contains functions to query and visualize the Neuroimaging features
associated with genetically regulated gene expression (GReX). The primary utility,
neuroimaGene(), relies on a list of user-defined genes and returns a table of
neuroimaging features (NIDPs) associated with each gene. This resource
is designed to assist in the interpretation of genome-wide and transcriptome-wide
association studies that evaluate brain related traits. Bledsoe (2024)
<doi:10.1016/j.ajhg.2024.06.002>. In addition there are several visualization
functions that generate summary plots and 2-dimensional visualizations of regional
brain measures. Mowinckel (2020).
Author: Xavier Bledsoe [aut, cre] ,
Eric Gamazon [aut]
Maintainer: Xavier Bledsoe <xavier.bledsoe@vanderbilt.edu>
Diff between neuroimaGene versions 0.1.0 dated 2024-07-03 and 0.1.1 dated 2024-09-20
neuroimaGene-0.1.0/neuroimaGene/data/nidp_anno.rda |only neuroimaGene-0.1.1/neuroimaGene/DESCRIPTION | 10 +-- neuroimaGene-0.1.1/neuroimaGene/MD5 | 36 ++++++------- neuroimaGene-0.1.1/neuroimaGene/R/NIDP_names.R | 3 - neuroimaGene-0.1.1/neuroimaGene/R/anno_doc.R | 5 + neuroimaGene-0.1.1/neuroimaGene/R/neuro_vis.R | 11 +-- neuroimaGene-0.1.1/neuroimaGene/R/neuroimagene_pkg.R | 26 +++++++-- neuroimaGene-0.1.1/neuroimaGene/R/plot_gn_nidp.R | 18 ++++-- neuroimaGene-0.1.1/neuroimaGene/R/plot_nidps.R | 25 +++++++-- neuroimaGene-0.1.1/neuroimaGene/build/vignette.rds |binary neuroimaGene-0.1.1/neuroimaGene/data/nidp_anno.RData |only neuroimaGene-0.1.1/neuroimaGene/inst/doc/neuroimaGene.Rmd | 6 +- neuroimaGene-0.1.1/neuroimaGene/inst/doc/neuroimaGene.html | 16 ++--- neuroimaGene-0.1.1/neuroimaGene/man/anno.Rd | 5 + neuroimaGene-0.1.1/neuroimaGene/man/listNIDPs.Rd | 3 - neuroimaGene-0.1.1/neuroimaGene/man/neuro_vis.Rd | 6 +- neuroimaGene-0.1.1/neuroimaGene/man/neuroimaGene.Rd | 32 ++++++++--- neuroimaGene-0.1.1/neuroimaGene/man/plot_gnNIDP.Rd | 11 +++ neuroimaGene-0.1.1/neuroimaGene/man/plot_nidps.Rd | 13 ++++ neuroimaGene-0.1.1/neuroimaGene/vignettes/neuroimaGene.Rmd | 6 +- 20 files changed, 152 insertions(+), 80 deletions(-)
Title: Read Cancer Records in the NAACCR Format
Description: Functions for reading cancer record files which follow a format
defined by the North American Association of Central Cancer Registries
(NAACCR).
Author: Nathan Werth [aut, cre],
Pennsylvania Department of Health [cph],
North American Association of Cancer Registries [cph],
World Health Organization [cph],
United States Centers for Disease Control and Prevention [cph],
United States Bureau of the Cens [...truncated...]
Maintainer: Nathan Werth <nwerth@pa.gov>
Diff between naaccr versions 3.1.0 dated 2024-09-20 and 3.1.1 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 1 + R/write_naaccr.R | 13 ++++--------- tests/testthat/test-item-interpreting.R | 9 +++++++++ 5 files changed, 21 insertions(+), 16 deletions(-)
Title: Multivariate Probabilities of Scale Mixtures of Multivariate
Normal Distributions via the Genz and Bretz (2002) QRSVN Method
Description: Generates multivariate subgaussian stable probabilities using the QRSVN
algorithm as detailed in Genz and Bretz (2002) <DOI:10.1198/106186002394>
but by sampling positive stable variates not chi/sqrt(nu).
Author: Alan Genz [aut] ,
Bruce Swihart [aut, cre]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between mvgb versions 0.0.4 dated 2023-09-02 and 0.0.5 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ man/mvgb.Rd | 1 + src/F77.c | 2 +- 5 files changed, 13 insertions(+), 8 deletions(-)
Title: Analysis of Massive SNP Arrays
Description: Easy-to-use, efficient, flexible and scalable tools for analyzing
massive SNP arrays. Privé et al. (2018) <doi:10.1093/bioinformatics/bty185>.
Author: Florian Prive [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths],
Bjarni Johann Vilhjalmsson [ths]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigsnpr versions 1.12.2 dated 2023-03-28 and 1.12.15 dated 2024-09-20
bigsnpr-1.12.15/bigsnpr/DESCRIPTION | 14 bigsnpr-1.12.15/bigsnpr/MD5 | 153 ++++----- bigsnpr-1.12.15/bigsnpr/NAMESPACE | 2 bigsnpr-1.12.15/bigsnpr/NEWS.md | 50 +++ bigsnpr-1.12.15/bigsnpr/R/LDpred2.R | 6 bigsnpr-1.12.15/bigsnpr/R/PRS.R | 4 bigsnpr-1.12.15/bigsnpr/R/RcppExports.R | 4 bigsnpr-1.12.15/bigsnpr/R/SCT.R | 6 bigsnpr-1.12.15/bigsnpr/R/ancestry-summary.R |only bigsnpr-1.12.15/bigsnpr/R/apply-parallelize.R | 6 bigsnpr-1.12.15/bigsnpr/R/autoSVD.R | 103 +++--- bigsnpr-1.12.15/bigsnpr/R/bed-class.R | 11 bigsnpr-1.12.15/bigsnpr/R/bed-mat-acc.R | 7 bigsnpr-1.12.15/bigsnpr/R/bigSNP-class.R | 2 bigsnpr-1.12.15/bigsnpr/R/bigsnpr-package.R | 6 bigsnpr-1.12.15/bigsnpr/R/external-software.R | 2 bigsnpr-1.12.15/bigsnpr/R/impute.R | 2 bigsnpr-1.12.15/bigsnpr/R/ldsc.R | 18 - bigsnpr-1.12.15/bigsnpr/R/man-qq-gc.R | 3 bigsnpr-1.12.15/bigsnpr/R/match-alleles.R | 203 ------------- bigsnpr-1.12.15/bigsnpr/R/modify-positions.R |only bigsnpr-1.12.15/bigsnpr/R/read-bgen.R | 37 +- bigsnpr-1.12.15/bigsnpr/R/simu-pheno.R | 3 bigsnpr-1.12.15/bigsnpr/R/subset-QC.R | 33 +- bigsnpr-1.12.15/bigsnpr/inst/CITATION | 2 bigsnpr-1.12.15/bigsnpr/inst/WORDLIST | 3 bigsnpr-1.12.15/bigsnpr/man/LDpred2.Rd | 17 - bigsnpr-1.12.15/bigsnpr/man/SCT.Rd | 10 bigsnpr-1.12.15/bigsnpr/man/bed-mat-acc.Rd |only bigsnpr-1.12.15/bigsnpr/man/bed-methods.Rd | 6 bigsnpr-1.12.15/bigsnpr/man/bed_MAF.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_counts.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_cprodVec.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_prodVec.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_projectPCA.Rd | 12 bigsnpr-1.12.15/bigsnpr/man/bed_projectSelfPCA.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_randomSVD.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_scaleBinom.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bed_tcrossprodSelf.Rd | 10 bigsnpr-1.12.15/bigsnpr/man/bigSNP-class.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/bigsnpr-package.Rd | 6 bigsnpr-1.12.15/bigsnpr/man/snp_MAF.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_MAX3.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/snp_PRS.Rd | 6 bigsnpr-1.12.15/bigsnpr/man/snp_ancestry_summary.Rd | 24 + bigsnpr-1.12.15/bigsnpr/man/snp_asGeneticPos.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_asGeneticPos2.Rd |only bigsnpr-1.12.15/bigsnpr/man/snp_autoSVD.Rd | 23 - bigsnpr-1.12.15/bigsnpr/man/snp_beagleImpute.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/snp_clumping.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_cor.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_fastImpute.Rd | 6 bigsnpr-1.12.15/bigsnpr/man/snp_fastImputeSimple.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_gc.Rd | 15 bigsnpr-1.12.15/bigsnpr/man/snp_lassosum2.Rd | 13 bigsnpr-1.12.15/bigsnpr/man/snp_ld_scores.Rd | 132 ++++---- bigsnpr-1.12.15/bigsnpr/man/snp_ldsc.Rd | 22 - bigsnpr-1.12.15/bigsnpr/man/snp_manhattan.Rd | 15 bigsnpr-1.12.15/bigsnpr/man/snp_modifyBuild.Rd | 16 - bigsnpr-1.12.15/bigsnpr/man/snp_pcadapt.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_plinkIBDQC.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/snp_plinkKINGQC.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/snp_prodBGEN.Rd | 6 bigsnpr-1.12.15/bigsnpr/man/snp_qq.Rd | 15 bigsnpr-1.12.15/bigsnpr/man/snp_readBGEN.Rd | 27 - bigsnpr-1.12.15/bigsnpr/man/snp_readBed.Rd | 2 bigsnpr-1.12.15/bigsnpr/man/snp_simuPheno.Rd | 4 bigsnpr-1.12.15/bigsnpr/man/snp_split.Rd | 8 bigsnpr-1.12.15/bigsnpr/man/snp_subset.Rd | 4 bigsnpr-1.12.15/bigsnpr/src/Makevars | 2 bigsnpr-1.12.15/bigsnpr/src/RcppExports.cpp | 9 bigsnpr-1.12.15/bigsnpr/src/ldpred2-auto.cpp | 9 bigsnpr-1.12.15/bigsnpr/tests/testthat/test-1-readBed.R | 33 +- bigsnpr-1.12.15/bigsnpr/tests/testthat/test-1-subset.R | 17 + bigsnpr-1.12.15/bigsnpr/tests/testthat/test-2-autoSVD.R | 49 ++- bigsnpr-1.12.15/bigsnpr/tests/testthat/test-4-pcadapt.R | 3 bigsnpr-1.12.15/bigsnpr/tests/testthat/test-5-match.R | 64 +++- bigsnpr-1.12.15/bigsnpr/tests/testthat/test-8-LDpred2.R | 50 +++ bigsnpr-1.12.15/bigsnpr/tests/testthat/test-8-simu-pheno.R | 3 bigsnpr-1.12.2/bigsnpr/man/sub-bed-ANY-ANY-ANY-method.Rd |only 80 files changed, 762 insertions(+), 604 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Mont [...truncated...]
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Greg McSwiggan [aut, cph],
Tilman Davies [ctb, cph],
Mehdi Moradi [ctb, cph],
Suman Rakshit [ctb, cph],
Ottmar Cronie [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 3.2-1 dated 2024-07-15 and 3.2-2 dated 2024-09-20
DESCRIPTION | 18 +++++++++--------- MD5 | 12 ++++++------ NEWS | 8 ++++++++ inst/doc/packagesizes.txt | 1 + inst/info/packagesizes.txt | 1 + man/bw.lppl.Rd | 2 +- man/spatstat.linnet-package.Rd | 2 ++ 7 files changed, 28 insertions(+), 16 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Non-Normal Repeated Measurements Models
Description: Various functions to fit models for non-normal repeated
measurements, such as Binary Random Effects Models with Two Levels of Nesting,
Bivariate Beta-binomial Regression Models, Marginal Bivariate Binomial Regression Models,
Cormack capture-recapture models, Continuous-time Hidden Markov Chain Models,
Discrete-time Hidden Markov Chain Models,
Changepoint Location Models using a Continuous-time Two-state Hidden Markov Chain,
generalized nonlinear autoregression models, multivariate Gaussian copula models,
generalized non-linear mixed models with one random effect,
generalized non-linear mixed models using h-likelihood for one random effect,
Repeated Measurements Models for Counts with Frailty or Serial Dependence,
Repeated Measurements Models for Continuous Variables with Frailty or Serial Dependence,
Ordinal Random Effects Models with Dropouts, marginal homogeneity models for square
contingency tables, correlated negative binomial models with Kalman update.
References include Lindsey's [...truncated...]
Author: Bruce Swihart [cre, aut],
Jim Lindsey [aut] ,
T.R. Ten Have [ctb, cph] .),
Richard Cook [ctb, cph] ,
Iain MacDonald [ctb, cph] ,
Walter Zucchini [ctb, cph] ,
Burton Garbow [ctb, cph] ,
Euginia Zharichenko [ctb, cph]
Maintainer: Bruce Swihart <bruce.swihart@gmail.com>
Diff between repeated versions 1.1.8 dated 2024-06-14 and 1.1.9 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ src/kserieb.c | 8 ++++---- 4 files changed, 16 insertions(+), 10 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre] ,
Hadley Wickham [aut] ,
Posit Software, PBC [cph, fnd]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 1.0.6 dated 2024-04-11 and 1.0.8 dated 2024-09-20
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Title: 'Rcpp' Tic-Toc Timer with 'OpenMP' Support
Description: Provides 'Rcpp' bindings for 'cpptimer', a simple tic-toc timer class for benchmarking 'C++' code <https://github.com/BerriJ/cpptimer>. It's not just simple, it's blazing fast! This sleek tic-toc timer class supports overlapping timers as well as 'OpenMP' parallelism <https://www.openmp.org/>. It boasts a nanosecond-level time resolution. We did not find any overhead of the timer itself at this resolution. Results (with summary statistics) are automatically passed back to 'R' as a data frame.
Author: Jonathan Berrisch [aut, cre]
Maintainer: Jonathan Berrisch <Jonathan@Berrisch.biz>
Diff between rcpptimer versions 1.1.0 dated 2024-03-20 and 1.2.0 dated 2024-09-20
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Title: "Cereal Headers for R and C++ Serialization"
Description: To facilitate using 'cereal' with R via 'cpp11' or 'Rcpp'. 'cereal'
is a header-only C++11 serialization library. 'cereal' takes arbitrary data
types and reversibly turns them into different representations, such as
compact binary encodings, 'XML', or 'JSON'. 'cereal' was designed to be
fast, light-weight, and easy to extend - it has no external dependencies and
can be easily bundled with other code or used standalone. Please see
<https://uscilab.github.io/cereal/> for more information.
Author: Wush Wu [aut, cre] ,
Randolph Voorhies [ctb],
Shane Grant [ctb],
Stephen Wade [ctb]
Maintainer: Wush Wu <wush978@gmail.com>
Diff between Rcereal versions 1.2.1.1 dated 2020-10-14 and 1.3.2 dated 2024-09-20
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Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/error/error.h | 10 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/filereadstream.h | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/filewritestream.h | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/biginteger.h | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/diyfp.h | 37 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/dtoa.h | 8 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/ieee754.h | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/itoa.h | 82 - Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/meta.h | 9 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/regex.h | 241 +-- Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/stack.h | 10 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/strfunc.h | 14 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/internal/strtod.h | 111 - Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/istreamwrapper.h | 98 - Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/memorystream.h | 15 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/msinttypes/LICENSE |only Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/pointer.h | 92 + Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/prettywriter.h | 60 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/rapidjson.h | 113 + Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/reader.h | 601 ++++++-- Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/schema.h | 717 ++++++++-- Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/stream.h | 52 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/stringbuffer.h | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidjson/writer.h | 161 +- Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidxml/rapidxml.hpp | 88 - Rcereal-1.3.2/Rcereal/inst/include/cereal/external/rapidxml/rapidxml_print.hpp | 2 Rcereal-1.3.2/Rcereal/inst/include/cereal/macros.hpp | 41 Rcereal-1.3.2/Rcereal/inst/include/cereal/specialize.hpp |only Rcereal-1.3.2/Rcereal/inst/include/cereal/types/array.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/atomic.hpp |only Rcereal-1.3.2/Rcereal/inst/include/cereal/types/base_class.hpp | 14 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/bitset.hpp | 14 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/boost_variant.hpp | 124 + Rcereal-1.3.2/Rcereal/inst/include/cereal/types/chrono.hpp | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/common.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/complex.hpp | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/concepts/pair_associative_container.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/deque.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/forward_list.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/functional.hpp | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/list.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/map.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/memory.hpp | 62 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/optional.hpp |only Rcereal-1.3.2/Rcereal/inst/include/cereal/types/polymorphic.hpp | 42 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/queue.hpp | 10 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/set.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/stack.hpp | 8 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/string.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/tuple.hpp | 14 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/unordered_map.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/unordered_set.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/utility.hpp | 6 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/valarray.hpp | 4 Rcereal-1.3.2/Rcereal/inst/include/cereal/types/variant.hpp |only Rcereal-1.3.2/Rcereal/inst/include/cereal/types/vector.hpp | 16 Rcereal-1.3.2/Rcereal/inst/include/cereal/version.hpp |only Rcereal-1.3.2/Rcereal/man/last_version.Rd | 12 Rcereal-1.3.2/Rcereal/man/list_version.Rd | 15 Rcereal-1.3.2/Rcereal/man/update_version.Rd | 22 Rcereal-1.3.2/Rcereal/tests/testthat/cpp/test_struct_Rcpp.cpp |only Rcereal-1.3.2/Rcereal/tests/testthat/cpp/test_struct_cpp11.cpp |only Rcereal-1.3.2/Rcereal/tests/testthat/test-struct.R |only Rcereal-1.3.2/Rcereal/tests/testthat/test-update_version.R |only Rcereal-1.3.2/Rcereal/vignettes/introduction.Rmd |only 105 files changed, 3534 insertions(+), 1596 deletions(-)
Title: R Bindings for the 'prqlc' Rust Library
Description: Provides a function to convert 'PRQL' strings to 'SQL' strings.
Combined with other R functions that take 'SQL' as an argument,
'PRQL' can be used on R.
Author: Tatsuya Shima [aut, cre],
Authors of the dependency Rust crates [aut]
Maintainer: Tatsuya Shima <ts1s1andn@gmail.com>
Diff between prqlr versions 0.8.1 dated 2024-05-19 and 0.9.0 dated 2024-09-20
DESCRIPTION | 10 LICENSE.note | 378 +++++++--------------- MD5 | 42 +- NEWS.md | 16 R/000-wrappers.R | 28 - README.md | 10 build/vignette.rds |binary configure | 166 ++++++---- inst/AUTHORS | 25 - inst/doc/knitr.html | 8 inst/doc/prqlr.html | 2 src/init.c | 16 src/rust/Cargo.lock | 563 +++++++++++++--------------------- src/rust/Cargo.toml | 16 src/rust/api.h | 8 src/rust/src/lib.rs | 9 src/rust/vendor-config.toml | 4 src/rust/vendor.tar.xz |binary tests/testthat/_snaps/compile.md | 8 tests/testthat/_snaps/knitr-engine.md | 4 tests/testthat/test-compile.R | 6 tools/lib-sums.tsv | 10 22 files changed, 571 insertions(+), 758 deletions(-)
Title: Computation of Graphlet Orbit Counts in Sparse Graphs
Description: Implements orbit counting using a fast combinatorial approach.
Counts orbits of nodes and edges from edge matrix or data frame, or a
graph object from the graph package.
Author: Tomaz Hocevar [aut, cre],
Janez Demsar [aut]
Maintainer: Tomaz Hocevar <tomaz.hocevar@fri.uni-lj.si>
Diff between orca versions 1.1-2 dated 2023-12-13 and 1.1-3 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/count.cpp | 10 +++++----- 3 files changed, 11 insertions(+), 11 deletions(-)
Title: Clustering High Dimensional Data with Hidden Markov Model on
Variable Blocks
Description: Clustering of high dimensional data with Hidden Markov Model on Variable Blocks (HMM-VB) fitted via Baum-Welch algorithm. Clustering is performed by the Modal Baum-Welch algorithm (MBW), which finds modes of the density function. Lin Lin and Jia Li (2017) <https://jmlr.org/papers/v18/16-342.html>.
Author: Yevhen Tupikov [aut],
Lin Lin [aut],
Lixiang Zhang [aut],
Jia Li [aut, cre]
Maintainer: Jia Li <jiali@psu.edu>
Diff between HDclust versions 1.0.3 dated 2019-04-11 and 1.0.4 dated 2024-09-20
DESCRIPTION | 17 MD5 | 71 +-- NEWS.md |only R/hmmvbBIC.R | 2 R/hmmvbTrain.R | 2 build/vignette.rds |binary inst/doc/HDclust.R | 62 +- inst/doc/HDclust.Rmd | 10 inst/doc/HDclust.html | 984 +++++++++++++++++++++++++++++++---------------- man/HDclust-package.Rd | 4 man/clustControl.Rd | 3 man/getBIC.Rd | 1 man/getBdim.Rd | 1 man/getDim.Rd | 1 man/getLoglikehd.Rd | 1 man/getNb.Rd | 1 man/getNumst.Rd | 1 man/getVarorder.Rd | 1 man/hmmvbBIC.Rd | 12 man/hmmvbClust.Rd | 10 man/hmmvbTrain.Rd | 11 man/sim2.Rd | 4 man/sim3.Rd | 4 man/trainControl.Rd | 9 man/vbSearchControl.Rd | 11 src/RcppExports.cpp | 5 src/cluster.cpp | 48 +- src/estimate.cpp | 343 +++++++++------- src/hmm.h | 7 src/matrix.cpp | 130 +++--- src/modal.cpp | 159 +++---- src/prob.cpp | 70 +-- src/rcpp_findModes.cpp | 80 ++- src/rcpp_testsync.cpp | 373 ++++++++++------- src/rcpp_trainmaster.cpp | 40 + src/utils_rcpp.cpp | 99 ++-- vignettes/HDclust.Rmd | 10 37 files changed, 1600 insertions(+), 987 deletions(-)
Title: Event History Analysis
Description: Parametric proportional hazards fitting with left truncation and
right censoring for common families of distributions, piecewise constant
hazards, and discrete models. Parametric accelerated failure time models
for left truncated and right censored data. Proportional hazards
models for tabular and register data. Sampling of risk sets in Cox
regression, selections in the Lexis diagram, bootstrapping.
Broström (2022) <doi:10.1201/9780429503764>.
Author: Goeran Brostroem [aut, cre],
Jianming Jin [ctb]
Maintainer: Goeran Brostroem <goran.brostrom@umu.se>
Diff between eha versions 2.11.4 dated 2024-03-08 and 2.11.5 dated 2024-09-20
ChangeLog | 9 DESCRIPTION | 10 MD5 | 62 ++-- R/Makeham.R | 4 R/eha.R | 2 R/plot.coxreg.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/eha.html | 674 +++++++++++++++++------------------------------ inst/doc/gompertz.html | 108 +++---- inst/doc/parametric.html | 126 ++++---- inst/doc/parametric1.pdf |binary inst/doc/tpchreg.html | 126 ++++---- man/eha-package.Rd | 2 man/makeham.Rd | 4 man/plot.coxreg.Rd | 2 man/scania.Rd | 2 src/aftexpreg.c | 8 src/aftreg.c | 8 src/aftregGomp.c | 8 src/coxfun.c | 20 - src/coxfun2.c | 32 +- src/eha_fun.c | 40 +- src/expreg.c | 4 src/frail_ml.c | 36 +- src/loglik_ph.c | 4 src/loglik_phexp.c | 4 src/phexpreg.c | 20 - src/phreg.c | 28 - src/risk.c | 4 src/sup.c | 8 src/weibreg.c | 24 - 32 files changed, 594 insertions(+), 787 deletions(-)
Title: Tropical Cyclone (Hurricane, Typhoon) Spatial Hazard Modelling
Description: Methods for generating modelled parametric Tropical Cyclone (TC) spatial hazard fields and time series output at point locations from TC tracks. R's compatibility to simply use fast 'cpp' code via the 'Rcpp' package and the wide range spatial analysis tools via the 'terra' package makes it an attractive open source environment to study 'TCs'. This package estimates TC vortex wind and pressure fields using parametric equations originally coded up in 'python' by 'TCRM' <https://github.com/GeoscienceAustralia/tcrm> and then coded up in 'Cuda' 'cpp' by 'TCwindgen' <https://github.com/CyprienBosserelle/TCwindgen>.
Author: Julian O'Grady [aut, cre]
Maintainer: Julian O'Grady <julian.ogrady@csiro.au>
Diff between TCHazaRds versions 1.1.1 dated 2024-09-06 and 1.1.2 dated 2024-09-20
DESCRIPTION | 6 +- MD5 | 9 +-- R/WindHazaRds.R | 82 ++++++++++++++++++++++++++++++-- inst/doc/Introduction_to_TCHazaRds.html | 22 ++++---- man/TCpoints2lines.Rd |only man/update_Track.Rd | 2 6 files changed, 97 insertions(+), 24 deletions(-)
Title: 'AlphaSimR' Extension for Simulating Honeybee Populations and
Breeding Programmes
Description: An extension of the 'AlphaSimR' package
(<https://cran.r-project.org/package=AlphaSimR>) for stochastic simulations of
honeybee populations and breeding programmes. 'SIMplyBee' enables simulation of
individual bees that form a colony, which includes a queen, fathers (drones
the queen mated with), virgin queens, workers, and drones. Multiple colony can
be merged into a population of colonies, such as an apiary or a whole country
of colonies. Functions enable operations on castes, colony, or colonies, to
ease 'R' scripting of whole populations. All 'AlphaSimR' functionality with
respect to genomes and genetic and phenotype values is available and further
extended for honeybees, including haplo-diploidy, complementary sex determiner
locus, colony events (swarming, supersedure, etc.), and colony phenotype values.
Author: Jana Obsteter [aut, cre] ,
Laura Strachan [aut] ,
Jernej Bubnic [aut] ,
Gregor Gorjanc [aut]
Maintainer: Jana Obsteter <obsteter.jana@gmail.com>
Diff between SIMplyBee versions 0.4.0 dated 2024-08-26 and 0.4.1 dated 2024-09-20
DESCRIPTION | 6 MD5 | 31 +- NEWS.md | 16 + R/Class-SimParamBee.R | 5 R/Functions_L0_auxilary.R | 4 inst/doc/A_Honeybee_biology.html | 60 ++--- inst/doc/B_Multiple_colonies.html | 4 inst/doc/C_Colony_events.html | 8 inst/doc/D_Crossing.R | 20 + inst/doc/D_Crossing.Rmd | 28 +- inst/doc/D_Crossing.html | 95 ++++---- inst/doc/E_Genomics.html | 202 +++++++++--------- inst/doc/F_Quantitative_Genetics.html | 376 +++++++++++++++++----------------- inst/doc/G_Sampling_functions.html | 14 - inst/doc/Z_FAQ.html | 4 vignettes/Colony_locations.csv |only vignettes/D_Crossing.Rmd | 28 +- 17 files changed, 480 insertions(+), 421 deletions(-)
Title: Tools for Joint Sentiment and Topic Analysis of Textual Data
Description: A framework that joins topic modeling and sentiment analysis of
textual data. The package implements a fast Gibbs sampling estimation of
Latent Dirichlet Allocation (Griffiths and Steyvers (2004)
<doi:10.1073/pnas.0307752101>) and Joint Sentiment/Topic Model (Lin, He,
Everson and Ruger (2012) <doi:10.1109/TKDE.2011.48>). It offers a variety of
helpers and visualizations to analyze the result of topic modeling. The
framework also allows enriching topic models with dates and externally
computed sentiment measures. A flexible aggregation scheme enables the
creation of time series of sentiment or topical proportions from the enriched
topic models. Moreover, a novel method jointly aggregates topic proportions
and sentiment measures to derive time series of topical sentiment.
Author: Olivier Delmarcelle [aut, cre]
,
Samuel Borms [ctb] ,
Chengua Lin [cph] ,
Yulan He [cph] ,
Jose Bernardo [cph] ,
David Robinson [cph] ),
Julia Silge [cph] ,
<https://orcid.org/0000-0002-3671-836X>)
Maintainer: Olivier Delmarcelle <delmarcelle.olivier@gmail.com>
Diff between sentopics versions 0.7.3 dated 2024-04-18 and 0.7.4 dated 2024-09-20
DESCRIPTION | 13 +++++++------ MD5 | 29 +++++++++++++++-------------- NEWS.md | 4 ++++ R/conversions.R | 2 +- R/methods.R | 4 ++-- R/others.R | 9 +++++---- R/sentopics.R | 32 +++++++++++++++++--------------- build/partial.rdb |only man/LoughranMcDonald.Rd | 6 ++++-- man/PicaultRenault.Rd | 7 +++++-- man/PicaultRenault_data.Rd | 5 ++++- man/as.tokens.dfm.Rd | 2 +- man/compute_PicaultRenault_scores.Rd | 7 +++++-- man/get_ECB_press_conferences.Rd | 2 +- man/melt.sentopicmodel.Rd | 4 ++-- tests/testthat/test-conversions.R | 2 +- 16 files changed, 74 insertions(+), 54 deletions(-)
Title: Typed Parameter Tags for Integration with 'roxygen2'
Description: Provides typed parameter documentation tags for integration
with 'roxygen2'. Typed parameter tags provide a consistent interface for
annotating expected types for parameters and returned values. Tools for
converting from existing styles are also provided to easily adapt projects
which implement typed documentation by convention rather than tag. Use the
default format or provide your own.
Author: Doug Kelkhoff [aut, cre]
Maintainer: Doug Kelkhoff <doug.kelkhoff@gmail.com>
Diff between roxytypes versions 0.1.0 dated 2024-02-29 and 0.1.1 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/convert_re.R | 2 +- 4 files changed, 13 insertions(+), 7 deletions(-)
Title: Detect Copy Number Variants from SNPs Data
Description: Functions in this package will import filtered variant call format (VCF) files of SNPs data and generate data sets to detect copy number variants, visualize them and do downstream analyses with copy number variants(e.g. Environmental association analyses).
Author: Piyal Karunarathne [aut, cre] ,
Qiujie Zhou [aut] ,
Klaus Schliep [aut] ,
Pascal Milesi [aut]
Maintainer: Piyal Karunarathne <piyalkarumail@yahoo.com>
Diff between rCNV versions 1.2.0 dated 2023-08-08 and 1.3.0 dated 2024-09-20
DESCRIPTION | 10 - MD5 | 55 ++++---- NAMESPACE | 10 + NEWS.md | 8 + R/TMM_normalz.R | 20 +- R/allele_tests.R | 4 R/bias.det.R | 229 +++++++++++---------------------- R/detect.R | 105 ++++++++++++--- R/post_detect.R | 140 ++++++++++++++++++-- R/raw_process.R | 338 ++++++++++++++++++++++++++++++++++---------------- R/statistics.R | 145 +++++++-------------- man/ad.correct.Rd | 10 + man/allele.freq.Rd | 4 man/allele.info.Rd | 10 + man/cnv.Rd | 13 + man/dup.validate.Rd | 52 ++++++- man/dupGet.Rd | 7 - man/get.miss.Rd | 14 +- man/gt.format.Rd | 13 + man/h.zygosity.Rd | 4 man/hetTgen.Rd | 11 + man/maf.Rd | 4 man/norm.fact.Rd | 4 man/readVCF.Rd | 4 man/relatedness.Rd | 14 +- man/sig.hets.Rd | 7 - man/vcf.stat.Rd | 4 man/vst.Rd | 2 man/vstPermutation.Rd |only 29 files changed, 764 insertions(+), 477 deletions(-)
Title: Rarefaction-Based Species Richness Estimator
Description: Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.
Author: Peng Zhao [aut, cre] ,
Yi Zou [aut]
Maintainer: Peng Zhao <pengzhao20@outlook.com>
Diff between rarestR versions 1.0.0 dated 2024-03-20 and 1.0.3 dated 2024-09-20
DESCRIPTION | 18 +++++++++++------- MD5 | 26 ++++++++++++++++++-------- R/es.R | 2 +- R/tes.R | 11 ++++++++++- R/tess.R | 10 ++++++++++ build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/es.Rd | 2 +- man/tes.Rd | 11 ++++++++++- man/tess.Rd | 12 ++++++++++++ tests |only vignettes |only 13 files changed, 73 insertions(+), 19 deletions(-)
Title: Read, Write and Edit xlsx Files
Description: Simplifies the creation of Excel .xlsx files by providing a
high level interface to writing, styling and editing worksheets.
Through the use of 'Rcpp', read/write times are comparable to the
'xlsx' and 'XLConnect' packages with the added benefit of removing the
dependency on Java.
Author: Philipp Schauberger [aut],
Alexander Walker [aut],
Luca Braglia [ctb],
Joshua Sturm [ctb],
Jan Marvin Garbuszus [ctb, cre],
Jordan Mark Barbone [ctb] ,
David Zimmermann [ctb],
Reinhold Kainhofer [ctb]
Maintainer: Jan Marvin Garbuszus <jan.garbuszus@ruhr-uni-bochum.de>
Diff between openxlsx versions 4.2.7 dated 2024-08-30 and 4.2.7.1 dated 2024-09-20
DESCRIPTION | 8 - MD5 | 25 ++-- NEWS.md | 4 R/WorkbookClass.R | 33 ++++- R/baseXML.R | 8 - R/wrappers.R | 13 +- README.md | 2 inst/WORDLIST | 1 inst/doc/Formatting.html | 4 inst/doc/Introduction.html | 180 +++++++++++++++----------------- man/insertImage.Rd | 7 + src/write_file.cpp | 16 ++ tests/testthat/test-insertImage.R |only tests/testthat/test-write-permissions.R | 4 14 files changed, 177 insertions(+), 128 deletions(-)
Title: Haplotype-Aware CNV Analysis from scRNA-Seq
Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
Author: Teng Gao [cre, aut],
Ruslan Soldatov [aut],
Hirak Sarkar [aut],
Evan Biederstedt [aut],
Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Diff between numbat versions 1.4.0 dated 2024-02-23 and 1.4.2 dated 2024-09-20
DESCRIPTION | 17 ++++++----- MD5 | 16 +++++----- NEWS.md | 16 ++++++++++ R/class.R | 3 +- R/main.R | 66 ++++++++++++++++++++++---------------------- R/utils.R | 2 - R/vis.R | 5 ++- README.md | 1 inst/bin/pileup_and_phase.R | 12 ++++---- 9 files changed, 79 insertions(+), 59 deletions(-)
Title: Read Cancer Records in the NAACCR Format
Description: Functions for reading cancer record files which follow a format
defined by the North American Association of Central Cancer Registries
(NAACCR).
Author: Nathan Werth [aut, cre],
Pennsylvania Department of Health [cph],
North American Association of Cancer Registries [cph],
World Health Organization [cph],
United States Centers for Disease Control and Prevention [cph],
United States Bureau of the Cens [...truncated...]
Maintainer: Nathan Werth <nwerth@pa.gov>
Diff between naaccr versions 3.0.1 dated 2024-09-12 and 3.1.0 dated 2024-09-20
DESCRIPTION | 6 +-- MD5 | 8 ++-- NEWS | 7 +++ R/write_naaccr.R | 63 ++++++++++++++++++++++++-------- tests/testthat/test-item-interpreting.R | 22 +++++------ 5 files changed, 73 insertions(+), 33 deletions(-)
Title: Generalized Linear Models for Categorical Responses
Description: In statistical modeling, there is a wide variety of regression models for categorical dependent variables (nominal or ordinal data); yet, there is no software embracing all these models together in a uniform and generalized format. Following the methodology proposed by Peyhardi, Trottier, and Guédon (2015) <doi:10.1093/biomet/asv042>, we introduce 'GLMcat', an R package to estimate generalized linear models implemented under the unified specification (r, F, Z). Where r represents the ratio of probabilities (reference, cumulative, adjacent, or sequential), F the cumulative cdf function for the linkage, and Z, the design matrix.
Author: Lorena Leon [aut, cre],
Jean Peyhardi [aut],
Catherine Trottier [aut]
Maintainer: Lorena Leon <ylorenaleonv@gmail.com>
Diff between GLMcat versions 0.2.6 dated 2024-01-17 and 0.2.7 dated 2024-09-20
DESCRIPTION | 10 +++++----- MD5 | 15 +++++++++------ NEWS | 3 +++ NEWS.md | 13 ++++++++----- R/accidents.R |only data/accidents.rda |only inst/doc/Discrete_CM_examples.pdf |binary inst/doc/GLMcat_tutorial.pdf |binary inst/doc/Var_sel_ex.pdf |binary man/accidents.Rd |only 10 files changed, 25 insertions(+), 16 deletions(-)
Title: 'Shiny' Modules for General Tasks
Description: 'Shiny' apps can often make use of the same key elements, this package provides modules for common tasks (data upload, wrangling data, figure generation and saving the app state), and also a framework for developing. These modules can react and interact as well as generate code to create reproducible analyses.
Author: John Harrold [aut, cre]
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between formods versions 0.1.6 dated 2024-05-24 and 0.1.7 dated 2024-09-20
DESCRIPTION | 6 MD5 | 53 +++---- NAMESPACE | 1 NEWS.md | 8 - R/ASM_Server.R | 122 +++++++++++++++-- R/FG_Server.R | 234 ++++++++++++++++++++++++--------- R/formods.R | 150 ++++++++++++--------- build/vignette.rds |binary inst/doc/included_modules.html | 2 inst/doc/making_modules.html | 225 ++++++++++++++++--------------- inst/templates/ASM.yaml | 2 inst/templates/ASM_module_components.R | 4 inst/templates/FG.yaml | 50 ++++++- inst/templates/FG_module_components.R | 9 - inst/templates/FM_compact.R | 2 inst/templates/UD.yaml | 28 +-- inst/templates/ZZ_Server.R | 43 +++--- inst/templates/formods.yaml | 17 +- inst/test_apps/FM_compact.R | 2 man/ASM_Server.Rd | 2 man/ASM_onload.Rd |only man/DW_Server.Rd | 2 man/FG_Server.Rd | 2 man/FM_fetch_mdl.Rd | 20 +- man/UD_Server.Rd | 2 man/has_changed.Rd | 4 man/has_updated.Rd | 6 tests/testthat/test-formods.R | 5 28 files changed, 666 insertions(+), 335 deletions(-)
Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range
Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>)
and Copernicus's Data Stores. Allows for easy downloads of weather
forecasts and climate reanalysis data in R. Data stores covered include the Climate Data Store (CDS;
<https://cds-beta.climate.copernicus.eu>), Atmosphere Data Store (ADS;
<https://ads-beta.atmosphere.copernicus.eu>) and Early Warning Data Store (CEMS;
<https://ewds-beta.climate.copernicus.eu>).
Author: Koen Hufkens [aut, cre, cph] ,
Reto Stauffer [ctb] ,
Elio Campitelli [ctb] ,
BlueGreen Labs [fnd]
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between ecmwfr versions 2.0.0 dated 2024-08-28 and 2.0.1 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/wf_request_batch.R | 1 - inst/doc/advanced_vignette.html | 4 ++-- 4 files changed, 8 insertions(+), 9 deletions(-)
Title: Interface with the United Nations Comtrade API
Description: Interface with and extract data from the United Nations 'Comtrade'
API <https://comtradeplus.un.org/>. 'Comtrade' provides country level shipping
data for a variety of commodities, these functions allow for easy API query
and data returned as a tidy data frame.
Author: Paul Bochtler [aut, cre, cph] ,
Harriet Goers [aut],
Chris Muir [aut],
Alicia Schep [rev] ,
Rafael Hellwig [rev] ,
Ernest Guevarra [rev] ,
Nicholas Potter [rev] ,
Juergen Amann [ctb]
Maintainer: Paul Bochtler <paulbochtler.gh@gmail.com>
Diff between comtradr versions 1.0.1 dated 2024-05-24 and 1.0.2 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ R/ct_process_response.R | 5 ++++- R/utils.R | 8 +++++--- R/zzz.R | 2 +- build/vignette.rds |binary inst/doc/bulk_files.html | 2 +- inst/doc/caching.html | 2 +- inst/doc/comtradr.html | 2 +- inst/doc/large_data.html | 2 +- inst/doc/transition.html | 2 +- 12 files changed, 35 insertions(+), 24 deletions(-)
Title: Download Data from Brazil's Population Census
Description: Easy access to data from Brazil's population censuses. The package
provides a simple and efficient way to download and read the data
sets and the documentation of all the population censuses taken in
and after 1960 in the country. The package is built on top of the
'Arrow' platform <https://arrow.apache.org/docs/r/>, which allows
users to work with larger-than-memory census data using 'dplyr'
familiar functions. <https://arrow.apache.org/docs/r/articles/arrow.html#analyzing-arrow-data-with-dplyr>.
Author: Rafael H. M. Pereira [aut, cre]
,
Rogerio J. Barbosa [aut] ,
Diego Rabatone Oliveira [ctb],
Neal Richardson [ctb],
Ipea - Institute for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between censobr versions 0.3.2 dated 2024-03-23 and 0.4.0 dated 2024-09-20
censobr-0.3.2/censobr/tests/tests_rafa/merge_household.R |only censobr-0.4.0/censobr/DESCRIPTION | 28 censobr-0.4.0/censobr/MD5 | 122 +- censobr-0.4.0/censobr/NEWS.md | 27 censobr-0.4.0/censobr/R/censobr_cache.R | 3 censobr-0.4.0/censobr/R/data_dictionary.R | 16 censobr-0.4.0/censobr/R/docs_interview_manual.R | 2 censobr-0.4.0/censobr/R/merge_household.R |only censobr-0.4.0/censobr/R/onLoad.R | 2 censobr-0.4.0/censobr/R/read_emigration.R | 17 censobr-0.4.0/censobr/R/read_families.R | 15 censobr-0.4.0/censobr/R/read_households.R | 12 censobr-0.4.0/censobr/R/read_mortality.R | 18 censobr-0.4.0/censobr/R/read_population.R | 26 censobr-0.4.0/censobr/R/read_tracts.R | 10 censobr-0.4.0/censobr/R/set_censobr_cache_dir.R | 2 censobr-0.4.0/censobr/R/utils.R | 51 - censobr-0.4.0/censobr/README.md | 24 censobr-0.4.0/censobr/build/vignette.rds |binary censobr-0.4.0/censobr/inst/CITATION | 5 censobr-0.4.0/censobr/inst/doc/censobr.R | 49 - censobr-0.4.0/censobr/inst/doc/censobr.Rmd | 170 +++- censobr-0.4.0/censobr/inst/doc/censobr.html | 417 +++++++--- censobr-0.4.0/censobr/inst/doc/census_tracts_data.Rmd | 2 censobr-0.4.0/censobr/inst/doc/census_tracts_data.html | 111 -- censobr-0.4.0/censobr/inst/doc/documentation.R | 16 censobr-0.4.0/censobr/inst/doc/documentation.Rmd | 98 ++ censobr-0.4.0/censobr/inst/doc/documentation.html | 225 ++++- censobr-0.4.0/censobr/inst/doc/larger_than_memory.R |only censobr-0.4.0/censobr/inst/doc/larger_than_memory.Rmd |only censobr-0.4.0/censobr/inst/doc/larger_than_memory.html |only censobr-0.4.0/censobr/man/cache_message.Rd | 2 censobr-0.4.0/censobr/man/data_dictionary.Rd | 12 censobr-0.4.0/censobr/man/download_file.Rd | 52 - censobr-0.4.0/censobr/man/merge_household_var.Rd |only censobr-0.4.0/censobr/man/read_emigration.Rd | 4 censobr-0.4.0/censobr/man/read_households.Rd | 28 censobr-0.4.0/censobr/man/read_mortality.Rd | 4 censobr-0.4.0/censobr/man/read_population.Rd | 28 censobr-0.4.0/censobr/man/read_tracts.Rd | 2 censobr-0.4.0/censobr/man/roxygen/templates/1960_census_section.R |only censobr-0.4.0/censobr/man/roxygen/templates/merge_households.R |only censobr-0.4.0/censobr/tests/tests_rafa/geometry.R |only censobr-0.4.0/censobr/tests/tests_rafa/merge_household_notes.R | 22 censobr-0.4.0/censobr/tests/tests_rafa/survey.R | 38 censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge2.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_duckdb_merge3.R |only censobr-0.4.0/censobr/tests/tests_rafa/test_rafa.R | 161 ++- censobr-0.4.0/censobr/tests/testthat/test_data_dictionary.R | 58 - censobr-0.4.0/censobr/tests/testthat/test_docs_interview_manual.R | 12 censobr-0.4.0/censobr/tests/testthat/test_docs_questionnaire.R | 26 censobr-0.4.0/censobr/tests/testthat/test_labels_emigration.R | 13 censobr-0.4.0/censobr/tests/testthat/test_labels_families.R | 15 censobr-0.4.0/censobr/tests/testthat/test_labels_households.R | 30 censobr-0.4.0/censobr/tests/testthat/test_labels_mortality.R | 18 censobr-0.4.0/censobr/tests/testthat/test_labels_population.R | 13 censobr-0.4.0/censobr/tests/testthat/test_read_emigration.R | 68 + censobr-0.4.0/censobr/tests/testthat/test_read_families.R | 61 + censobr-0.4.0/censobr/tests/testthat/test_read_households.R | 84 +- censobr-0.4.0/censobr/tests/testthat/test_read_mortality.R | 75 + censobr-0.4.0/censobr/tests/testthat/test_read_population.R | 110 +- censobr-0.4.0/censobr/tests/testthat/test_read_tracts.R | 60 - censobr-0.4.0/censobr/tests/testthat/test_z_censobr_cache.R | 3 censobr-0.4.0/censobr/vignettes/censobr.Rmd | 170 +++- censobr-0.4.0/censobr/vignettes/census_tracts_data.Rmd | 2 censobr-0.4.0/censobr/vignettes/documentation.Rmd | 98 ++ censobr-0.4.0/censobr/vignettes/larger_than_memory.Rmd |only 69 files changed, 1910 insertions(+), 827 deletions(-)
Title: An Implementation of Sensitivity Analysis in Bayesian Networks
Description: An implementation of sensitivity and robustness methods in Bayesian networks in R. It includes methods to perform parameter variations via a variety of co-variation schemes, to compute sensitivity functions and to quantify the dissimilarity of two Bayesian networks via distances and divergences. It further includes diagnostic methods to assess the goodness of fit of a Bayesian networks to data, including global, node and parent-child monitors. Reference: M. Leonelli, R. Ramanathan, R.L. Wilkerson (2022) <doi:10.1016/j.knosys.2023.110882>.
Author: Manuele Leonelli [aut, cre],
Ramsiya Ramanathan [aut],
Rachel Wilkerson [aut]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnmonitor versions 0.2.0 dated 2024-07-13 and 0.2.1 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 ++++-- R/zzz.R |only README.md | 13 +++++++++++-- man/dot-onAttach.Rd |only 5 files changed, 18 insertions(+), 7 deletions(-)
Title: Biologically Explainable Machine Learning Framework
Description: Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.
Author: Shunjie Zhang [aut, cre],
Junfang Chen [aut]
Maintainer: Shunjie Zhang <zhang.shunjie@qq.com>
Diff between BioM2 versions 1.0.10 dated 2024-08-20 and 1.1.0 dated 2024-09-20
DESCRIPTION | 6 - MD5 | 8 +- NEWS | 6 + R/BioM2.R | 135 +++++++++++++++++++++++++++++++++------- man/Stage2_FeartureSelection.Rd | 2 5 files changed, 126 insertions(+), 31 deletions(-)
Title: UK Flood Estimation
Description: Functions to implement the methods of the Flood Estimation Handbook (FEH), associated updates and the revitalised flood hydrograph model (ReFH). Currently the package uses NRFA peak flow dataset version 13. Aside from FEH functionality, further hydrological functions are available. Most of the methods implemented in this package are described in one or more of the following: "Flood Estimation Handbook", Centre for Ecology & Hydrology (1999, ISBN:0 948540 94 X). "Flood Estimation Handbook Supplementary Report No. 1", Kjeldsen (2007, ISBN:0 903741 15 7). "Regional Frequency Analysis - an approach based on L-moments", Hosking & Wallis (1997, ISBN: 978 0 521 01940 8). "Proposal of the extreme rank plot for extreme value analysis: with an emphasis on flood frequency studies", Hammond (2019, <doi:10.2166/nh.2019.157>). "Making better use of local data in flood frequency estimation", Environment Agency (2017, ISBN: 978 1 84911 387 8). "Sampling uncertainty of UK design flood est [...truncated...]
Author: Anthony Hammond [aut, cre]
Maintainer: Anthony Hammond <agqhammond@gmail.com>
Diff between UKFE versions 0.3.6 dated 2024-09-10 and 0.3.7 dated 2024-09-20
DESCRIPTION | 8 +- MD5 | 19 ++-- NAMESPACE | 1 R/All.R | 29 +++++-- R/GISfuncs.R |only R/RainAPI.R | 195 +++++++++++++++++++++++++++++++++++++++++-------- man/GetFlowStage_EA.Rd |only man/GetNRFA.Rd | 4 - man/GetRainEA.Rd | 33 +++----- man/GetRainSEPA.Rd | 4 - man/GridRefConvert.Rd |only man/QMED.Rd | 9 +- 12 files changed, 231 insertions(+), 71 deletions(-)
Title: Make and Apply Customized Rounding Specifications for Tables
Description: Translate double and integer valued data into
character values formatted for tabulation in manuscripts
or other types of academic reports.
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <bjaeger@wakehealth.edu>
Diff between table.glue versions 0.0.3 dated 2023-02-07 and 0.0.4 dated 2024-09-20
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 43 +- R/table_ester.R | 608 +++++++++++++++++++++--------------------- R/table_value.R | 432 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/default_rounder.R | 2 inst/doc/default_rounder.html | 40 +- inst/doc/table_guide.R | 2 inst/doc/table_guide.html | 436 +++++++++++++++--------------- man/table.glue-package.Rd | 2 man/table_ester.Rd | 4 12 files changed, 813 insertions(+), 786 deletions(-)
Title: A Framework for Enterprise Shiny Applications
Description: A framework that supports creating and extending enterprise Shiny applications using best practices.
Author: Kamil Zyla [aut, cre],
Jakub Nowicki [aut],
Leszek Sieminski [aut],
Marek Rogala [aut],
Recle Vibal [aut],
Tymoteusz Makowski [aut],
Rodrigo Basa [aut],
Eduardo Almeida [ctb],
Appsilon Sp. z o.o. [cph]
Maintainer: Kamil Zyla <opensource+kamil@appsilon.com>
Diff between rhino versions 1.10.0 dated 2024-09-10 and 1.10.1 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 14 ++++++++++---- inst/templates/renv/dot.Rprofile | 10 ++++++---- 4 files changed, 22 insertions(+), 14 deletions(-)
Title: Automated Construction of R Data Packages from REDCap Projects
Description: Export all data, including metadata, from a REDCap (Research
Electronic Data Capture) Project via the REDCap API
<https://projectredcap.org/wp-content/resources/REDCapTechnicalOverview.pdf>.
The exported (meta)data will be processed and formatted into a stand alone R
data package which can be installed and shared between researchers. Several
default reports are generated as vignettes in the resulting package.
Author: Peter DeWitt [aut, cre]
Maintainer: Peter DeWitt <peter.dewitt@cuanschutz.edu>
Diff between REDCapExporter versions 0.2.2 dated 2021-02-02 and 0.3.0 dated 2024-09-20
REDCapExporter-0.2.2/REDCapExporter/data/avs_raw_project_info.rda |only REDCapExporter-0.2.2/REDCapExporter/inst/doc/export.R |only REDCapExporter-0.2.2/REDCapExporter/inst/doc/export.Rmd |only REDCapExporter-0.2.2/REDCapExporter/inst/doc/export.html |only REDCapExporter-0.2.2/REDCapExporter/man/REDCapExporter.Rd |only REDCapExporter-0.2.2/REDCapExporter/tests/testthat.R |only REDCapExporter-0.2.2/REDCapExporter/vignettes/export.Rmd |only REDCapExporter-0.3.0/REDCapExporter/DESCRIPTION | 23 REDCapExporter-0.3.0/REDCapExporter/MD5 | 85 - REDCapExporter-0.3.0/REDCapExporter/NAMESPACE | 7 REDCapExporter-0.3.0/REDCapExporter/NEWS.md | 19 REDCapExporter-0.3.0/REDCapExporter/R/REDCapExporter-package.R | 7 REDCapExporter-0.3.0/REDCapExporter/R/as.R | 91 - REDCapExporter-0.3.0/REDCapExporter/R/build_r_data_package.R | 4 REDCapExporter-0.3.0/REDCapExporter/R/col-type.R | 167 +- REDCapExporter-0.3.0/REDCapExporter/R/datasets.R | 56 REDCapExporter-0.3.0/REDCapExporter/R/format_record.R | 76 - REDCapExporter-0.3.0/REDCapExporter/R/keyring.R | 28 REDCapExporter-0.3.0/REDCapExporter/R/write.R | 8 REDCapExporter-0.3.0/REDCapExporter/build/vignette.rds |binary REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_core.rda |binary REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_core_json.rda |only REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_metadata.rda |binary REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_metadata_json.rda |only REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_project.rda |only REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_project_json.rda |only REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_record.rda |binary REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_record_json.rda |only REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_user.rda |binary REDCapExporter-0.3.0/REDCapExporter/data/avs_raw_user_json.rda |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/api.R | 10 REDCapExporter-0.3.0/REDCapExporter/inst/doc/api.Rmd | 46 REDCapExporter-0.3.0/REDCapExporter/inst/doc/api.html | 656 +++++++--- REDCapExporter-0.3.0/REDCapExporter/inst/doc/formatting.R |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/formatting.Rmd |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/formatting.html |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/redcap2package.R |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/redcap2package.Rmd |only REDCapExporter-0.3.0/REDCapExporter/inst/doc/redcap2package.html |only REDCapExporter-0.3.0/REDCapExporter/man/REDCapExporter-package.Rd |only REDCapExporter-0.3.0/REDCapExporter/man/REDCapExporter_keyring.Rd | 6 REDCapExporter-0.3.0/REDCapExporter/man/as.Rd | 12 REDCapExporter-0.3.0/REDCapExporter/man/build_r_data_package.Rd | 2 REDCapExporter-0.3.0/REDCapExporter/man/col_type.Rd | 58 REDCapExporter-0.3.0/REDCapExporter/man/example_data.Rd | 63 REDCapExporter-0.3.0/REDCapExporter/man/format_record.Rd | 29 REDCapExporter-0.3.0/REDCapExporter/man/read_text.Rd | 4 REDCapExporter-0.3.0/REDCapExporter/man/write_description_file.Rd | 4 REDCapExporter-0.3.0/REDCapExporter/tests/test-as.data.frame.R |only REDCapExporter-0.3.0/REDCapExporter/tests/test-build_r_pkg.R |only REDCapExporter-0.3.0/REDCapExporter/tests/test-export.R |only REDCapExporter-0.3.0/REDCapExporter/tests/test-format_record.R |only REDCapExporter-0.3.0/REDCapExporter/tests/test-keyring.R |only REDCapExporter-0.3.0/REDCapExporter/tests/testthat/test-format_records.R | 11 REDCapExporter-0.3.0/REDCapExporter/vignettes/api.Rmd | 46 REDCapExporter-0.3.0/REDCapExporter/vignettes/formatting.Rmd |only REDCapExporter-0.3.0/REDCapExporter/vignettes/redcap2package.Rmd |only 57 files changed, 968 insertions(+), 550 deletions(-)
More information about REDCapExporter at CRAN
Permanent link
Title: The Q-Matrix Validation Methods Framework
Description: Provide a variety of Q-matrix validation methods for the generalized cognitive diagnosis models, including the method based on the generalized deterministic input, noisy, and gate model (G-DINA) by de la Torre (2011) <DOI:10.1007/s11336-011-9207-7> discrimination index (the GDI method) by de la Torre and Chiu (2016) <DOI:10.1007/s11336-015-9467-8>, the step-wise Wald test method (the Wald method) by Ma and de la Torre (2020) <DOI:10.1111/bmsp.12156>, the Hull method by Najera et al. (2021) <DOI:10.1111/bmsp.12228>, the multiple logistic regression‑based Q‑matrix validation method (the MLR-B method) by Tu et al. (2022) <DOI:10.3758/s13428-022-01880-x>. Different research methods during Q-matrix validating are available.
Author: Haijiang Qin [aut, cre, cph],
Lei Guo [aut, cph]
Maintainer: Haijiang Qin <haijiang133@outlook.com>
Diff between Qval versions 0.1.7 dated 2024-07-21 and 1.0.0 dated 2024-09-20
Qval-0.1.7/Qval/R/OSR.R |only Qval-0.1.7/Qval/R/QRR.R |only Qval-0.1.7/Qval/R/TNR.R |only Qval-0.1.7/Qval/R/TPR.R |only Qval-0.1.7/Qval/R/USR.R |only Qval-0.1.7/Qval/R/VRR.R |only Qval-0.1.7/Qval/man/getOSR.Rd |only Qval-0.1.7/Qval/man/getQRR.Rd |only Qval-0.1.7/Qval/man/getTNR.Rd |only Qval-0.1.7/Qval/man/getTPR.Rd |only Qval-0.1.7/Qval/man/getUSR.Rd |only Qval-0.1.7/Qval/man/getVRR.Rd |only Qval-1.0.0/Qval/DESCRIPTION | 18 +-- Qval-1.0.0/Qval/MD5 | 78 +++++++------- Qval-1.0.0/Qval/NAMESPACE | 33 ++++-- Qval-1.0.0/Qval/NEWS.md |only Qval-1.0.0/Qval/R/CDM.R | 4 Qval-1.0.0/Qval/R/GDI.R | 6 - Qval-1.0.0/Qval/R/Hull.R | 163 +++++++++++++++++++++++------- Qval-1.0.0/Qval/R/MLR-B.R | 2 Qval-1.0.0/Qval/R/MLR.R | 6 - Qval-1.0.0/Qval/R/MLRlasso.R | 14 +- Qval-1.0.0/Qval/R/PVAF.R | 1 Qval-1.0.0/Qval/R/Qvalindex.R |only Qval-1.0.0/Qval/R/Rmatrix.R |only Qval-1.0.0/Qval/R/Wald.R | 39 +++---- Qval-1.0.0/Qval/R/Wald.test.R | 127 ++++++++++++++++++----- Qval-1.0.0/Qval/R/convex.R | 82 +++++++++------ Qval-1.0.0/Qval/R/cov.R | 6 - Qval-1.0.0/Qval/R/fit.R | 1 Qval-1.0.0/Qval/R/plot.Hull.R |only Qval-1.0.0/Qval/R/priority.R | 67 ++++++++++++ Qval-1.0.0/Qval/R/sim.MQ.R | 6 - Qval-1.0.0/Qval/R/sim.Q.R | 5 Qval-1.0.0/Qval/R/sim.data.R | 14 +- Qval-1.0.0/Qval/R/validation.R | 128 ++++++++++++++++++----- Qval-1.0.0/Qval/R/zzz.R | 6 - Qval-1.0.0/Qval/man/CDM.Rd | 4 Qval-1.0.0/Qval/man/Wald.test.Rd |only Qval-1.0.0/Qval/man/get.Rmatrix.Rd |only Qval-1.0.0/Qval/man/get.priority.Rd |only Qval-1.0.0/Qval/man/plot.Hull.Rd |only Qval-1.0.0/Qval/man/sim.Q.Rd | 3 Qval-1.0.0/Qval/man/validation.Rd | 89 ++++++++++++++-- Qval-1.0.0/Qval/man/zOSR.Rd |only Qval-1.0.0/Qval/man/zQRR.Rd |only Qval-1.0.0/Qval/man/zTNR.Rd |only Qval-1.0.0/Qval/man/zTPR.Rd |only Qval-1.0.0/Qval/man/zUSR.Rd |only Qval-1.0.0/Qval/man/zVRR.Rd |only Qval-1.0.0/Qval/tests/building.R | 9 + Qval-1.0.0/Qval/tests/demo.R | 86 +++++++-------- Qval-1.0.0/Qval/tests/realdata_analysis.R |only Qval-1.0.0/Qval/tests/repeat.R |only 54 files changed, 719 insertions(+), 278 deletions(-)
Title: Interactive Visualizations for Profiling R Code
Description: Interactive visualizations for profiling R code.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
Javier Luraschi [aut],
Timothy Mastny [aut],
Posit Software, PBC [cph, fnd],
jQuery Foundation [cph] ,
jQuery contributors [ctb, cph] ,
Mike Bostock [ctb, cph] ,
D3 contributors [ctb] ,
Ivan Sagalaev [c [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between profvis versions 0.3.8 dated 2023-05-02 and 0.4.0 dated 2024-09-20
profvis-0.3.8/profvis/R/rprof.R |only profvis-0.3.8/profvis/inst/htmlwidgets/lib/highlight/default.css |only profvis-0.3.8/profvis/inst/htmlwidgets/lib/highlight/highlight.js |only profvis-0.3.8/profvis/man/renderProfvis.Rd |only profvis-0.3.8/profvis/tests/manual-test-source.R |only profvis-0.3.8/profvis/tests/manual-tests.R |only profvis-0.3.8/profvis/tests/testthat/_snaps/rprof.md |only profvis-0.3.8/profvis/tests/testthat/test-rprof.R |only profvis-0.4.0/profvis/DESCRIPTION | 58 ++-- profvis-0.4.0/profvis/LICENSE | 97 ------- profvis-0.4.0/profvis/MD5 | 76 +++-- profvis-0.4.0/profvis/NAMESPACE | 6 profvis-0.4.0/profvis/NEWS.md | 43 ++- profvis-0.4.0/profvis/R/aaa.R | 23 - profvis-0.4.0/profvis/R/file_contents.R | 2 profvis-0.4.0/profvis/R/parse.R | 44 +-- profvis-0.4.0/profvis/R/pause.R | 19 - profvis-0.4.0/profvis/R/profvis-package.R |only profvis-0.4.0/profvis/R/profvis.R | 130 ++++++---- profvis-0.4.0/profvis/R/shiny_module.R | 17 - profvis-0.4.0/profvis/R/utils.R | 26 +- profvis-0.4.0/profvis/R/version_jquery.R |only profvis-0.4.0/profvis/R/zzz.R |only profvis-0.4.0/profvis/README.md | 36 +- profvis-0.4.0/profvis/build |only profvis-0.4.0/profvis/inst/doc |only profvis-0.4.0/profvis/inst/htmlwidgets/lib/highlight/highlight.min.js |only profvis-0.4.0/profvis/inst/htmlwidgets/lib/highlight/textmate.css | 17 - profvis-0.4.0/profvis/inst/htmlwidgets/lib/jquery/AUTHORS.txt |only profvis-0.4.0/profvis/inst/htmlwidgets/lib/jquery/jquery.min.js | 7 profvis-0.4.0/profvis/inst/htmlwidgets/lib/profvis/profvis.js | 2 profvis-0.4.0/profvis/inst/htmlwidgets/profvis.yaml | 6 profvis-0.4.0/profvis/man/parse_rprof.Rd | 3 profvis-0.4.0/profvis/man/pause.Rd | 4 profvis-0.4.0/profvis/man/print.profvis.Rd | 10 profvis-0.4.0/profvis/man/profvis-package.Rd |only profvis-0.4.0/profvis/man/profvis.Rd | 61 ++-- profvis-0.4.0/profvis/man/profvisOutput.Rd | 13 - profvis-0.4.0/profvis/man/profvis_ui.Rd | 20 - profvis-0.4.0/profvis/src/pause.c | 6 profvis-0.4.0/profvis/tests/testthat/_snaps/pause.md |only profvis-0.4.0/profvis/tests/testthat/_snaps/profvis.md |only profvis-0.4.0/profvis/tests/testthat/helper-profvis.R | 40 --- profvis-0.4.0/profvis/tests/testthat/test-parse.R | 4 profvis-0.4.0/profvis/tests/testthat/test-pause.R |only profvis-0.4.0/profvis/tests/testthat/test-profvis.R | 66 ++++- profvis-0.4.0/profvis/tests/testthat/test-utils.R |only profvis-0.4.0/profvis/tools |only profvis-0.4.0/profvis/vignettes |only 49 files changed, 417 insertions(+), 419 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.1-8 dated 2024-04-29 and 1.1-9 dated 2024-09-20
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 2 +- R/checkGH.R | 17 ++++++++--------- build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/mlt.pdf |binary man/checkGH.Rd | 3 ++- tests/truncreg-Ex.R | 13 +++---------- tests/truncreg-Ex.Rout.save | 31 +++++++++---------------------- 10 files changed, 42 insertions(+), 56 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut] ,
Yoonkyoung Jeon [aut],
Jaewoong Heo [aut],
Youngsun Park [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.5.7 dated 2024-08-20 and 1.5.8 dated 2024-09-20
DESCRIPTION | 16 +++++++++------- MD5 | 10 +++++----- NAMESPACE | 2 ++ NEWS.md | 5 +++++ R/line.R | 38 +++++++++++++++++++++++++++++++++----- inst/doc/jsmodule.html | 4 ++-- 6 files changed, 56 insertions(+), 19 deletions(-)
Title: Download and Extract Data from US EPA's ECOTOX Database
Description: The US EPA ECOTOX database is a freely available database
with a treasure of aquatic and terrestrial ecotoxicological data.
As the online search interface doesn't come with an API, this
package provides the means to easily access and search the database
in R. To this end, all raw tables are downloaded from the EPA website
and stored in a local SQLite database <doi:10.1016/j.chemosphere.2024.143078>.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between ECOTOXr versions 1.0.9 dated 2024-01-08 and 1.1.1 dated 2024-09-20
DESCRIPTION | 13 +++-- MD5 | 23 +++++----- NEWS.md | 24 +++++++--- R/database_access.r | 3 - R/sysdata.rda |binary README.md | 50 +++++++++++++--------- inst |only man/ECOTOXr-package.Rd | 2 man/check_ecotox_build.Rd | 96 +++++++++++++++++++++---------------------- man/check_ecotox_version.Rd | 72 ++++++++++++++++---------------- man/cite_ecotox.Rd | 3 - tests/testthat/test_data |only tests/testthat/test_dev.r | 20 +++++--- tests/testthat/test_online.r |only 14 files changed, 170 insertions(+), 136 deletions(-)
Title: A Modern and Flexible Web Client for R
Description: The curl() and curl_download() functions provide highly
configurable drop-in replacements for base url() and download.file() with
better performance, support for encryption (https, ftps), gzip compression,
authentication, and other 'libcurl' goodies. The core of the package implements a
framework for performing fully customized requests where data can be processed
either in memory, on disk, or streaming via the callback or connection
interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly
web client see the 'httr' package which builds on this package with http
specific tools and logic.
Author: Jeroen Ooms [aut, cre] ,
Hadley Wickham [ctb],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between curl versions 5.2.2 dated 2024-08-26 and 5.2.3 dated 2024-09-20
curl-5.2.2/curl/tests/engine.R |only curl-5.2.2/curl/tests/engine.Rout.save |only curl-5.2.3/curl/DESCRIPTION | 10 +-- curl-5.2.3/curl/MD5 | 10 +-- curl-5.2.3/curl/NEWS | 4 + curl-5.2.3/curl/inst/doc/intro.html | 106 ++++++++++++++++----------------- curl-5.2.3/curl/inst/doc/windows.html | 14 ++-- 7 files changed, 73 insertions(+), 71 deletions(-)
Title: Covariance Measure Tests for Conditional Independence
Description: Covariance measure tests for conditional independence testing
against conditional covariance and nonlinear conditional mean alternatives.
Contains versions of the generalised covariance measure test
(Shah and Peters, 2020, <doi:10.1214/19-aos1857>) and projected covariance
measure test (Lundborg et al., 2023, <doi:10.48550/arXiv.2211.02039>).
Applications can be found in
Kook and Lundborg (2024, <doi:10.1093/bib/bbae475>).
Author: Lucas Kook [aut, cre],
Anton Rask Lundborg [ctb]
Maintainer: Lucas Kook <lucasheinrich.kook@gmail.com>
Diff between comets versions 0.0-2 dated 2024-07-05 and 0.0-3 dated 2024-09-20
comets-0.0-2/comets/tests |only comets-0.0-3/comets/DESCRIPTION | 8 +- comets-0.0-3/comets/MD5 | 31 +++++----- comets-0.0-3/comets/NAMESPACE | 2 comets-0.0-3/comets/R/comet.R | 5 + comets-0.0-3/comets/R/equiv.R | 14 ++-- comets-0.0-3/comets/R/gcm.R | 88 +++++++++++++++++++++--------- comets-0.0-3/comets/R/pcm.R | 82 ++++++++++++++++++--------- comets-0.0-3/comets/R/regressions.R | 22 +++++++ comets-0.0-3/comets/R/wgcm.R | 46 +++++++++------ comets-0.0-3/comets/man/comet.Rd | 3 - comets-0.0-3/comets/man/gcm.Rd | 16 ++++- comets-0.0-3/comets/man/pcm.Rd | 27 ++++++--- comets-0.0-3/comets/man/plm_equiv_test.Rd | 2 comets-0.0-3/comets/man/plot.comet.Rd |only comets-0.0-3/comets/man/regressions.Rd | 6 +- comets-0.0-3/comets/man/wgcm.Rd | 14 +++- 17 files changed, 247 insertions(+), 119 deletions(-)
Title: Render SVG Images into PDF, PNG, (Encapsulated) PostScript, or
Bitmap Arrays
Description: Renders vector-based svg images into high-quality custom-size
bitmap arrays using 'librsvg2'. The resulting bitmap can be written to
e.g. png, jpeg or webp format. In addition, the package can convert
images directly to various formats such as pdf or postscript.
Author: Jeroen Ooms [aut, cre] ,
Salim Brueggemann [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between rsvg versions 2.6.0 dated 2023-10-08 and 2.6.1 dated 2024-09-20
rsvg-2.6.0/rsvg/tests/engine.R |only rsvg-2.6.0/rsvg/tests/engine.Rout.save |only rsvg-2.6.1/rsvg/DESCRIPTION | 10 +++++----- rsvg-2.6.1/rsvg/MD5 | 16 +++++++--------- rsvg-2.6.1/rsvg/NEWS | 4 ++++ rsvg-2.6.1/rsvg/build/vignette.rds |binary rsvg-2.6.1/rsvg/inst/doc/svg-css.html | 12 ++++++------ rsvg-2.6.1/rsvg/src/Makevars.in | 2 +- rsvg-2.6.1/rsvg/src/Makevars.win | 3 ++- rsvg-2.6.1/rsvg/src/rsvg.c | 3 --- 10 files changed, 25 insertions(+), 25 deletions(-)
Title: Density, Distribution, and Sampling Functions for Evidence
Accumulation Models
Description: Calculate the probability density functions (PDFs) for two threshold evidence
accumulation models (EAMs). These are defined using the following Stochastic
Differential Equation (SDE), dx(t) = v(x(t),t)*dt+D(x(t),t)*dW, where x(t) is
the accumulated evidence at time t, v(x(t),t) is the drift rate, D(x(t),t) is
the noise scale, and W is the standard Wiener process. The boundary conditions
of this process are the upper and lower decision thresholds, represented by b_u(t)
and b_l(t), respectively. Upper threshold b_u(t) > 0, while lower threshold b_l(t) < 0.
The initial condition of this process x(0) = z where b_l(t) < z < b_u(t). We
represent this as the relative start point w = z/(b_u(0)-b_l(0)), defined as
a ratio of the initial threshold location. This package generates the PDF using
the same approach as the 'python' package it is based upon, 'PyBEAM' by Murrow and Holmes
(2023) <doi:10.3758/s13428-023-02162-w>. First, it converts the SDE model into the
forwards Fokke [...truncated...]
Author: Raphael Hartmann [aut, cre] ,
Matthew Murrow [aut]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between ream versions 1.0-3 dated 2024-09-17 and 1.0-4 dated 2024-09-20
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/guidline.html | 4 ++-- src/R_wrapper.cpp | 47 +++++++++++++++++++++++++---------------------- 4 files changed, 33 insertions(+), 30 deletions(-)
Title: Creation of Mock Observational Medical Outcomes Partnership
Common Data Model
Description: Creates mock data for testing and package development for the
Observational Medical Outcomes Partnership common data model. The
package offers functions crafted with pipeline-friendly
implementation, enabling users to effortlessly include only the
necessary tables for their testing needs.
Author: Mike Du [aut, cre] ,
Marti Catala [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xihang Chen [aut]
Maintainer: Mike Du <mike.du@ndorms.ox.ac.uk>
Diff between omock versions 0.2.0 dated 2024-05-20 and 0.3.0 dated 2024-09-20
omock-0.2.0/omock/R/Mockchecks.R |only omock-0.3.0/omock/DESCRIPTION | 15 omock-0.3.0/omock/MD5 | 125 +++--- omock-0.3.0/omock/NAMESPACE | 2 omock-0.3.0/omock/NEWS.md | 2 omock-0.3.0/omock/R/checkInputs.R | 92 ++++ omock-0.3.0/omock/R/checks.R | 129 +++--- omock-0.3.0/omock/R/mockCdmFromTables.R | 81 ++-- omock-0.3.0/omock/R/mockCdmReference.R | 36 + omock-0.3.0/omock/R/mockCohort.R | 196 ++++++---- omock-0.3.0/omock/R/mockConcept.R | 127 ++++-- omock-0.3.0/omock/R/mockConditionOccurrence.R | 96 +++- omock-0.3.0/omock/R/mockDeath.R | 93 +++- omock-0.3.0/omock/R/mockDrugExposure.R | 78 ++- omock-0.3.0/omock/R/mockMeasurement.R | 85 ++-- omock-0.3.0/omock/R/mockObservation.R | 86 ++-- omock-0.3.0/omock/R/mockObservationPeriod.R | 85 ++-- omock-0.3.0/omock/R/mockPerson.R | 107 +++-- omock-0.3.0/omock/R/mockProcedureOccurrence.R |only omock-0.3.0/omock/R/mockVisitOccurrence.R | 120 +++--- omock-0.3.0/omock/R/mockVocabulary.R | 86 ++-- omock-0.3.0/omock/R/omock-package.R | 20 - omock-0.3.0/omock/R/reexports-omopgenerics.R | 1 omock-0.3.0/omock/R/sysdata.rda |binary omock-0.3.0/omock/README.md | 49 +- omock-0.3.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.R | 27 - omock-0.3.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.Rmd | 27 - omock-0.3.0/omock/inst/doc/a01_Creating_synthetic_clinical_tables.html | 76 ++- omock-0.3.0/omock/inst/doc/a02_Creating_synthetic_cohorts.R | 2 omock-0.3.0/omock/inst/doc/a02_Creating_synthetic_cohorts.Rmd | 2 omock-0.3.0/omock/inst/doc/a02_Creating_synthetic_cohorts.html | 35 - omock-0.3.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.R | 9 omock-0.3.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.Rmd | 9 omock-0.3.0/omock/inst/doc/a04_Building_a_bespoke_mock_cdm.html | 18 omock-0.3.0/omock/man/mockCdmFromTables.Rd | 41 +- omock-0.3.0/omock/man/mockCdmReference.Rd | 27 + omock-0.3.0/omock/man/mockCohort.Rd | 54 +- omock-0.3.0/omock/man/mockConcepts.Rd | 84 ++-- omock-0.3.0/omock/man/mockConditionOccurrence.Rd | 89 ++-- omock-0.3.0/omock/man/mockDeath.Rd | 89 ++-- omock-0.3.0/omock/man/mockDrugExposure.Rd | 71 ++- omock-0.3.0/omock/man/mockMeasurement.Rd | 71 ++- omock-0.3.0/omock/man/mockObservation.Rd | 72 ++- omock-0.3.0/omock/man/mockObservationPeriod.Rd | 24 - omock-0.3.0/omock/man/mockPerson.Rd | 48 +- omock-0.3.0/omock/man/mockProcedureOccurrence.Rd |only omock-0.3.0/omock/man/mockVisitOccurrence.Rd |only omock-0.3.0/omock/man/mockVocabularyTables.Rd | 113 +++-- omock-0.3.0/omock/man/omock-package.Rd | 6 omock-0.3.0/omock/tests/testthat.R | 24 - omock-0.3.0/omock/tests/testthat/test-mockCdmFromTables.R | 37 + omock-0.3.0/omock/tests/testthat/test-mockCdmReference.R | 3 omock-0.3.0/omock/tests/testthat/test-mockCohort.R | 68 ++- omock-0.3.0/omock/tests/testthat/test-mockConcepts.R | 15 omock-0.3.0/omock/tests/testthat/test-mockCondtitionOccurrence.R | 56 ++ omock-0.3.0/omock/tests/testthat/test-mockDeath.R | 45 +- omock-0.3.0/omock/tests/testthat/test-mockDrugExposure.R | 50 ++ omock-0.3.0/omock/tests/testthat/test-mockMeasurement.R | 35 + omock-0.3.0/omock/tests/testthat/test-mockObservation.R | 37 + omock-0.3.0/omock/tests/testthat/test-mockObservationPeriod.R | 42 +- omock-0.3.0/omock/tests/testthat/test-mockPerson.R | 76 ++- omock-0.3.0/omock/tests/testthat/test-mockProcedureOccurrence.R |only omock-0.3.0/omock/tests/testthat/test-mockVocabularyTables.R | 47 +- omock-0.3.0/omock/vignettes/a01_Creating_synthetic_clinical_tables.Rmd | 27 - omock-0.3.0/omock/vignettes/a02_Creating_synthetic_cohorts.Rmd | 2 omock-0.3.0/omock/vignettes/a04_Building_a_bespoke_mock_cdm.Rmd | 9 66 files changed, 2114 insertions(+), 1164 deletions(-)
Title: Rmetrics - Importing Economic and Financial Data
Description: Provides a collection of utility functions
to download and manage data sets from the Internet or from other
sources.
Author: Diethelm Wuertz [aut] ,
Tobias Setz [aut],
Yohan Chalabi [aut],
Georgi N. Boshnakov [cre, aut]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between fImport versions 4032.87 dated 2023-12-15 and 4041.88 dated 2024-09-20
DESCRIPTION | 12 +-- MD5 | 24 +++---- NAMESPACE | 1 NEWS.md | 8 ++ R/import-fred.R | 139 ++++++++++++++++++++++++++-------------------- data/amexListing.csv.gz |binary data/h15Listing.csv.gz |binary data/nasdaqListing.csv.gz |binary data/nyseListing.csv.gz |binary data/oandaListing.csv.gz |binary data/stoxxListing.csv.gz |binary data/swxListing.csv.gz |binary man/import-fred.Rd | 87 ++++++++++------------------ 13 files changed, 139 insertions(+), 132 deletions(-)
Title: Decompose Demographic Functions
Description: Three general demographic decomposition methods: Pseudo-continuous decomposition proposed by Horiuchi, Wilmoth, and Pletcher (2008) <doi:10.1353/dem.0.0033>, stepwise replacement decomposition proposed by Andreev, Shkolnikov and Begun (2002) <doi:10.4054/DemRes.2002.7.14>, and lifetable response experiments proposed by Caswell (1989) <doi:10.1016/0304-3800(89)90019-7>.
Author: Tim Riffe [aut, cre]
Maintainer: Tim Riffe <tim.riffe@gmail.com>
Diff between DemoDecomp versions 1.0.1 dated 2018-08-14 and 1.14.1 dated 2024-09-20
DemoDecomp-1.0.1/DemoDecomp/data/Compare.rda |only DemoDecomp-1.0.1/DemoDecomp/man/Compare.Rd |only DemoDecomp-1.14.1/DemoDecomp/DESCRIPTION | 23 +++-- DemoDecomp-1.14.1/DemoDecomp/MD5 | 31 +++--- DemoDecomp-1.14.1/DemoDecomp/NAMESPACE | 3 DemoDecomp-1.14.1/DemoDecomp/NEWS.md | 14 +-- DemoDecomp-1.14.1/DemoDecomp/R/Caswell.R |only DemoDecomp-1.14.1/DemoDecomp/R/Horiuchi.R | 69 +++------------ DemoDecomp-1.14.1/DemoDecomp/R/Stepwise.R | 38 -------- DemoDecomp-1.14.1/DemoDecomp/R/data.R |only DemoDecomp-1.14.1/DemoDecomp/build/partial.rdb |binary DemoDecomp-1.14.1/DemoDecomp/inst/REFERENCES.bib | 20 ++++ DemoDecomp-1.14.1/DemoDecomp/man/Mxc1.Rd | 10 +- DemoDecomp-1.14.1/DemoDecomp/man/Mxc2.Rd | 8 + DemoDecomp-1.14.1/DemoDecomp/man/horiuchi.Rd | 2 DemoDecomp-1.14.1/DemoDecomp/man/ltre.Rd |only DemoDecomp-1.14.1/DemoDecomp/man/rates1.Rd | 17 ++- DemoDecomp-1.14.1/DemoDecomp/man/rates2.Rd | 18 ++- DemoDecomp-1.14.1/DemoDecomp/man/stepwise_replacement.Rd | 10 +- 19 files changed, 123 insertions(+), 140 deletions(-)
Title: Embedded JavaScript and WebAssembly Engine for R
Description: An R interface to V8 <https://v8.dev>: Google's open source JavaScript
and WebAssembly engine. This package can be compiled either with V8 version 6
and up or NodeJS when built as a shared library.
Author: Jeroen Ooms [aut, cre] ,
Jan Marvin Garbuszus [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between V8 versions 5.0.0 dated 2024-08-16 and 5.0.1 dated 2024-09-20
V8-5.0.0/V8/tests/engine.R |only V8-5.0.0/V8/tests/engine.Rout.save |only V8-5.0.1/V8/DESCRIPTION | 10 +++++----- V8-5.0.1/V8/MD5 | 12 +++++------- V8-5.0.1/V8/NEWS | 4 ++++ V8-5.0.1/V8/build/partial.rdb |binary V8-5.0.1/V8/inst/doc/npm.html | 4 ++-- V8-5.0.1/V8/inst/doc/v8_intro.html | 6 +++--- 8 files changed, 19 insertions(+), 17 deletions(-)
Title: Stacked Elastic Net
Description: Implements stacked elastic net regression (Rauschenberger 2021, <doi:10.1093/bioinformatics/btaa535>). The elastic net generalises ridge and lasso regularisation (Zou 2005, <doi:10.1111/j.1467-9868.2005.00503.x>). Instead of fixing or tuning the mixing parameter alpha, we combine multiple alpha by stacked generalisation (Wolpert 1992 <doi:10.1016/S0893-6080(05)80023-1>).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <armin.rauschenberger@uni.lu>
Diff between starnet versions 0.0.6 dated 2020-11-24 and 0.0.7 dated 2024-09-20
DESCRIPTION | 12 MD5 | 42 R/functions.R | 2345 ++++++++++++++++++++++++------------------------- R/pkgname.R | 168 +-- README.md | 88 - build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 28 inst/doc/article.Rmd | 42 inst/doc/article.html | 516 +++++----- inst/doc/script.R | 944 +++++++++---------- inst/doc/script.html | 1746 ++++++++++++++++++------------------ inst/doc/starnet.R | 20 inst/doc/starnet.Rmd | 66 - inst/doc/starnet.html | 702 +++++++------- man/cv.starnet.Rd | 14 man/dot-simulate.Rd | 60 - man/starnet-package.Rd | 16 man/starnet.Rd | 4 tests/testthat/test.R | 458 ++++----- vignettes/article.Rmd | 42 vignettes/starnet.Rmd | 66 - 22 files changed, 3722 insertions(+), 3657 deletions(-)
Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and
metadata from a PDF file. Also supports high quality rendering of PDF documents into
PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between pdftools versions 3.4.0 dated 2023-09-25 and 3.4.1 dated 2024-09-20
pdftools-3.4.0/pdftools/tests/poppler.R |only pdftools-3.4.0/pdftools/tests/poppler.Rout.save |only pdftools-3.4.1/pdftools/DESCRIPTION | 10 +++++----- pdftools-3.4.1/pdftools/MD5 | 14 ++++++-------- pdftools-3.4.1/pdftools/NEWS | 4 ++++ pdftools-3.4.1/pdftools/configure | 4 ---- pdftools-3.4.1/pdftools/src/Makevars.in | 2 +- pdftools-3.4.1/pdftools/src/Makevars.win | 3 ++- pdftools-3.4.1/pdftools/src/bindings.cpp | 3 --- 9 files changed, 18 insertions(+), 22 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384, P-521, and curve25519. Cryptographic
signatures can either be created and verified manually or via x509 certificates.
AES can be used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric
(public key) encryption or EC for Diffie Hellman. High-level envelope functions
combine RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure random
number generator, and 'bignum' math methods for manually performing crypto
calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] ,
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between openssl versions 2.2.1 dated 2024-08-16 and 2.2.2 dated 2024-09-20
openssl-2.2.1/openssl/tests/engine.R |only openssl-2.2.1/openssl/tests/engine.Rout.save |only openssl-2.2.2/openssl/DESCRIPTION | 10 ++-- openssl-2.2.2/openssl/MD5 | 16 +++---- openssl-2.2.2/openssl/NEWS | 4 + openssl-2.2.2/openssl/cleanup | 1 openssl-2.2.2/openssl/inst/doc/bignum.html | 32 +++++++------- openssl-2.2.2/openssl/inst/doc/crypto_hashing.html | 4 - openssl-2.2.2/openssl/inst/doc/keys.html | 48 ++++++++++----------- openssl-2.2.2/openssl/inst/doc/secure_rng.html | 18 +++---- 10 files changed, 68 insertions(+), 65 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between magick versions 2.8.4 dated 2024-07-14 and 2.8.5 dated 2024-09-20
magick-2.8.4/magick/tests/imagemagick.R |only magick-2.8.4/magick/tests/imagemagick.Rout.save |only magick-2.8.5/magick/DESCRIPTION | 10 +- magick-2.8.5/magick/MD5 | 12 +-- magick-2.8.5/magick/NEWS | 4 + magick-2.8.5/magick/R/edit.R | 7 + magick-2.8.5/magick/inst/doc/intro.R | 10 +- magick-2.8.5/magick/inst/doc/intro.html | 93 ++++++++++-------------- 8 files changed, 65 insertions(+), 71 deletions(-)
Title: A Simple and Robust JSON Parser and Generator for R
Description: A reasonably fast JSON parser and generator, optimized for statistical
data and the web. Offers simple, flexible tools for working with JSON in R, and
is particularly powerful for building pipelines and interacting with a web API.
The implementation is based on the mapping described in the vignette (Ooms, 2014).
In addition to converting JSON data from/to R objects, 'jsonlite' contains
functions to stream, validate, and prettify JSON data. The unit tests included
with the package verify that all edge cases are encoded and decoded consistently
for use with dynamic data in systems and applications.
Author: Jeroen Ooms [aut, cre] ,
Duncan Temple Lang [ctb],
Lloyd Hilaiel [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between jsonlite versions 1.8.8 dated 2023-12-04 and 1.8.9 dated 2024-09-20
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS | 4 ++++ build/vignette.rds |binary inst/doc/json-aaquickstart.html | 10 +++++----- inst/doc/json-mapping.pdf |binary src/r-base64.c | 1 + 7 files changed, 21 insertions(+), 16 deletions(-)
Title: GNU Privacy Guard for R
Description: Bindings to GnuPG for working with OpenGPG (RFC4880) cryptographic
methods. Includes utilities for public key encryption, creating and verifying
digital signatures, and managing your local keyring. Some functionality
depends on the version of GnuPG that is installed on the system. On Windows
this package can be used together with 'GPG4Win' which provides a GUI for
managing keys and entering passphrases.
Author: Jeroen Ooms [aut, cre]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gpg versions 1.2.9 dated 2023-05-18 and 1.3.0 dated 2024-09-20
gpg-1.2.9/gpg/tests |only gpg-1.3.0/gpg/DESCRIPTION | 10 +++++----- gpg-1.3.0/gpg/MD5 | 24 +++++++++++------------- gpg-1.3.0/gpg/NEWS | 4 ++++ gpg-1.3.0/gpg/build/vignette.rds |binary gpg-1.3.0/gpg/cleanup | 1 + gpg-1.3.0/gpg/configure | 2 +- gpg-1.3.0/gpg/inst/doc/intro.html | 16 +++++----------- gpg-1.3.0/gpg/src/common.h | 2 +- gpg-1.3.0/gpg/src/encrypt.c | 2 +- gpg-1.3.0/gpg/src/keys.c | 4 ++-- gpg-1.3.0/gpg/src/keysig.c | 2 +- gpg-1.3.0/gpg/src/sign.c | 2 +- 13 files changed, 33 insertions(+), 36 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' <https://libgit2.org> with
support for SSH and HTTPS remotes. All functions in 'gert' use basic R data
types (such as vectors and data-frames) for their arguments and return values.
User credentials are shared with command line 'git' through the git-credential
store and ssh keys stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] ,
Jennifer Bryan [ctb]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between gert versions 2.1.1 dated 2024-08-16 and 2.1.2 dated 2024-09-20
gert-2.1.1/gert/tests/libgit2.R |only gert-2.1.1/gert/tests/libgit2.Rout.save |only gert-2.1.2/gert/DESCRIPTION | 16 ++++++++-------- gert-2.1.2/gert/MD5 | 18 ++++++++---------- gert-2.1.2/gert/NEWS | 4 ++++ gert-2.1.2/gert/R/credentials.R | 4 +++- gert-2.1.2/gert/R/rebase.R | 6 +++--- gert-2.1.2/gert/cleanup | 1 + gert-2.1.2/gert/inst/doc/gert.html | 12 ++++++------ gert-2.1.2/gert/man/gert-package.Rd | 6 +++--- gert-2.1.2/gert/man/git_reset.Rd | 6 +++--- 11 files changed, 39 insertions(+), 34 deletions(-)