Title: Identify Sites for Your Bird List
Description: A suite of tools to use the 'eBird' database
(<https://ebird.org/home/>) and APIs to compare users' species lists to
recent observations and create a report of the top sites to visit to see
new species.
Author: Jeffrey Oliver [aut, cre]
Maintainer: Jeffrey Oliver <jcoliver@arizona.edu>
Diff between lifeR versions 0.9.6 dated 2022-10-03 and 0.9.7 dated 2023-06-02
DESCRIPTION | 6 - MD5 | 18 +-- NEWS.md | 4 R/SitesReport.R | 2 README.md | 20 ++- inst/doc/lifer-intro.R | 13 ++ inst/doc/lifer-intro.Rmd | 44 ++++++-- man/SitesReport.Rd | 2 vignettes/lifer-intro.Rmd | 44 ++++++-- vignettes/lifer-intro.html | 244 +++++++++++++++++++++++---------------------- 10 files changed, 242 insertions(+), 155 deletions(-)
Title: Shoreline Dating Coastal Stone Age Sites
Description: Provides tools for shoreline dating coastal Stone Age sites. The
implemented method was developed in Roalkvam (2023)
<doi:10.1016/j.quascirev.2022.107880> for the Norwegian Skagerrak coast.
Although it can be extended to other areas, this also forms the core area for
application of the package. Shoreline dating is based on the present-day
elevation of a site, a reconstruction of past relative sea-level change, and
empirically derived estimates of the likely elevation of the sites above the
contemporaneous sea-level when they were in use. The geographical and temporal
coverage of the method thus follows from the availability of local geological
reconstructions of shoreline displacement and the degree to which the
settlements to be dated have been located on or close to the shoreline when
they were in use. Methods for numerical treatment and visualisation of the
dates are provided, along with basic tools for visualising and evaluating the
location of sites.
Author: Isak Roalkvam [aut, cre]
Maintainer: Isak Roalkvam <isakroa@protonmail.com>
Diff between shoredate versions 1.0.2 dated 2023-05-02 and 1.1.0 dated 2023-06-02
shoredate-1.0.2/shoredate/R/check_target_location.R |only shoredate-1.0.2/shoredate/man/check_target_location.Rd |only shoredate-1.0.2/shoredate/tests/testthat/test-check_target_location.R |only shoredate-1.1.0/shoredate/DESCRIPTION | 44 shoredate-1.1.0/shoredate/MD5 | 149 shoredate-1.1.0/shoredate/NAMESPACE | 18 shoredate-1.1.0/shoredate/NEWS.md | 24 shoredate-1.1.0/shoredate/R/create_isobases.R | 16 shoredate-1.1.0/shoredate/R/displacement_plot.R | 169 shoredate-1.1.0/shoredate/R/interpolate_curve.R | 70 shoredate-1.1.0/shoredate/R/print.R | 25 shoredate-1.1.0/shoredate/R/shoredate_hdr.R | 11 shoredate-1.1.0/shoredate/R/shoredate_plot.R | 162 shoredate-1.1.0/shoredate/R/shoredate_sumplot.R | 4 shoredate-1.1.0/shoredate/R/shoreline_date.R | 118 shoredate-1.1.0/shoredate/R/sum_shoredates.R | 6 shoredate-1.1.0/shoredate/R/target_plot.R | 349 shoredate-1.1.0/shoredate/R/utilities.R | 72 shoredate-1.1.0/shoredate/README.md | 228 shoredate-1.1.0/shoredate/build/vignette.rds |binary shoredate-1.1.0/shoredate/inst/CITATION | 13 shoredate-1.1.0/shoredate/inst/doc/extending-shoredate.Rmd |only shoredate-1.1.0/shoredate/inst/doc/extending-shoredate.html |only shoredate-1.1.0/shoredate/inst/doc/shoredate.Rmd | 103 shoredate-1.1.0/shoredate/inst/doc/shoredate.html | 371 shoredate-1.1.0/shoredate/inst/extdata/naturalearth_basemap.gpkg |binary shoredate-1.1.0/shoredate/inst/extdata/orland_displacement_curve.rda |only shoredate-1.1.0/shoredate/man/create_isobases.Rd | 16 shoredate-1.1.0/shoredate/man/displacement_plot.Rd | 47 shoredate-1.1.0/shoredate/man/figures/coverage.png |binary shoredate-1.1.0/shoredate/man/figures/coverage_annotated.png |binary shoredate-1.1.0/shoredate/man/figures/date-1.png |binary shoredate-1.1.0/shoredate/man/figures/interpolated_curve-1.png |binary shoredate-1.1.0/shoredate/man/interpolate_curve.Rd | 34 shoredate-1.1.0/shoredate/man/print.shoreline_date.Rd | 4 shoredate-1.1.0/shoredate/man/shoredate_hdr.Rd | 8 shoredate-1.1.0/shoredate/man/shoredate_plot.Rd | 69 shoredate-1.1.0/shoredate/man/shoredate_sumplot.Rd | 2 shoredate-1.1.0/shoredate/man/shoreline_date.Rd | 20 shoredate-1.1.0/shoredate/man/sum_shoredates.Rd | 2 shoredate-1.1.0/shoredate/man/target_plot.Rd | 121 shoredate-1.1.0/shoredate/tests/testthat/_snaps/displacement_plot/bare-displacement-plot.svg | 30 shoredate-1.1.0/shoredate/tests/testthat/_snaps/displacement_plot/greyscale-plot-no-curve.svg | 30 shoredate-1.1.0/shoredate/tests/testthat/_snaps/displacement_plot/greyscale-plot.svg | 78 shoredate-1.1.0/shoredate/tests/testthat/_snaps/displacement_plot/plot-renamed-interpolated-curve.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/displacement_plot/plot-with-interpolated-curve.svg | 78 shoredate-1.1.0/shoredate/tests/testthat/_snaps/interpolate_curve.md |12510 +++++++++- shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoredate_plot/graphical-parameters.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoredate_plot/plot-with-a-summed-directions.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoredate_plot/plot-with-no-distance-model.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoredate_plot/plot-without-hdr.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoredate_plot/plot-without-probability.svg |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/shoreline_date.md | 19 shoredate-1.1.0/shoredate/tests/testthat/_snaps/sum_shoredates.md |only shoredate-1.1.0/shoredate/tests/testthat/_snaps/target_plot |only shoredate-1.1.0/shoredate/tests/testthat/test-displacement_plot.R | 9 shoredate-1.1.0/shoredate/tests/testthat/test-interpolate_curve.R | 12 shoredate-1.1.0/shoredate/tests/testthat/test-print.R | 25 shoredate-1.1.0/shoredate/tests/testthat/test-shoredate_plot.R | 46 shoredate-1.1.0/shoredate/tests/testthat/test-shoreline_date.R | 34 shoredate-1.1.0/shoredate/tests/testthat/test-sum_shoredates.R | 18 shoredate-1.1.0/shoredate/tests/testthat/test-target_plot.R | 218 shoredate-1.1.0/shoredate/vignettes/extend-earliest-1.png |only shoredate-1.1.0/shoredate/vignettes/extend-examples-plot-1.png |only shoredate-1.1.0/shoredate/vignettes/extend-maps-1.png |only shoredate-1.1.0/shoredate/vignettes/extend-maps-2.png |only shoredate-1.1.0/shoredate/vignettes/extend-orland-dateplot-1.png |only shoredate-1.1.0/shoredate/vignettes/extend-orland-disp-1.png |only shoredate-1.1.0/shoredate/vignettes/extending-shoredate.Rmd |only shoredate-1.1.0/shoredate/vignettes/extending-shoredate.Rmd.orig |only shoredate-1.1.0/shoredate/vignettes/shore-greyscale-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-multipoint-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-plot_example-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-plot_example_isobases-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-plot_example_isobases-2.png |binary shoredate-1.1.0/shoredate/vignettes/shore-plot_intcurve-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-plot_sum_isobases-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-sparse-1.png |binary shoredate-1.1.0/shoredate/vignettes/shore-tpq_date-1.png |only shoredate-1.1.0/shoredate/vignettes/shoredate.Rmd | 103 shoredate-1.1.0/shoredate/vignettes/shoredate.Rmd.orig | 102 81 files changed, 14538 insertions(+), 1049 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to 'FishBase', re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to 'SeaLifeBase' data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] ,
Scott Chamberlain [aut] ,
Duncan Temple Lang [aut],
Peter Wainwright [aut],
Kevin Cazelles [ctb]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 4.1.1 dated 2023-02-20 and 4.1.2 dated 2023-06-02
DESCRIPTION | 6 MD5 | 15 NEWS.md | 5 R/fb_import.R |only R/parquet_db.R | 43 README.md | 115 inst/prov/fb.prov |12856 ++++++++++++++++++++++++++++++++++++++++------------- inst/prov/slb.prov |10600 ++++++++++++++++++++++++++++++++++--------- man/fb_import.Rd | 2 9 files changed, 18261 insertions(+), 5381 deletions(-)
Title: Multivariate Normal Distribution
Description: Calculates and differentiates probabilities and density of (conditional) multivariate normal distribution and Gaussian copula (with various marginal distributions) using methods described in A. Genz (2004) <doi:10.1023/B:STCO.0000035304.20635.31>, A. Genz, F. Bretz (2009) <doi:10.1007/978-3-642-01689-9> and E. Kossova, B. Potanin (2018) <https:ideas.repec.org/a/ris/apltrx/0346.html>.
Author: Bogdan Potanin [aut, cre, ctb],
Sofiia Dolgikh [ctb]
Maintainer: Bogdan Potanin <bogdanpotanin@gmail.com>
Diff between mnorm versions 1.1.1 dated 2023-05-07 and 1.2.0 dated 2023-06-02
DESCRIPTION | 15 +++-- MD5 | 28 +++++----- NAMESPACE | 2 R/RcppExports.R | 35 +++++++++++-- inst/include/mnorm_RcppExports.h | 56 ++++++++++++++++++--- man/cmnorm.Rd | 4 - man/dmnorm.Rd | 13 ++-- man/fromBase.Rd |only man/halton.Rd | 7 ++ man/pmnorm.Rd | 37 +++++++------ man/toBase.Rd |only src/RcppExports.cpp | 104 +++++++++++++++++++++++++++++++++------ src/dmnorm.cpp | 14 +++-- src/halton.cpp | 101 ++++++++++++++++++++++++++++++++++--- src/halton.h | 6 +- src/pmnorm.cpp | 76 +++++++++++++++++++++++++--- 16 files changed, 402 insertions(+), 96 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. References: H. Chan, A. Darwiche (2002) <doi:10.1613/jair.967>; C. Goergen, M. Leonelli (2020) <ArXiv:1809.10794>; M. Leonelli, R. Ramanathan, R.L. Wilkerson (2021) <ArXiv:2107.11785>.
Author: Manuele Leonelli [aut, cre],
Ramsiya Ramanathan [aut],
Rachel Wilkerson [aut]
Maintainer: Manuele Leonelli <manuele.leonelli@ie.edu>
Diff between bnmonitor versions 0.1.3 dated 2022-04-20 and 0.1.4 dated 2023-06-02
bnmonitor-0.1.3/bnmonitor/NEWS.md |only bnmonitor-0.1.4/bnmonitor/DESCRIPTION | 6 bnmonitor-0.1.4/bnmonitor/MD5 | 83 +++---- bnmonitor-0.1.4/bnmonitor/NAMESPACE | 218 ++++++++++---------- bnmonitor-0.1.4/bnmonitor/R/sensitivity.R | 5 bnmonitor-0.1.4/bnmonitor/man/CD.Rd | 114 +++++----- bnmonitor-0.1.4/bnmonitor/man/Fro.CI.Rd | 86 +++---- bnmonitor-0.1.4/bnmonitor/man/Fro.GBN.Rd | 70 +++--- bnmonitor-0.1.4/bnmonitor/man/Fro.Rd | 50 ++-- bnmonitor-0.1.4/bnmonitor/man/Jeffreys.CI.Rd | 84 +++---- bnmonitor-0.1.4/bnmonitor/man/Jeffreys.GBN.Rd | 78 +++---- bnmonitor-0.1.4/bnmonitor/man/Jeffreys.Rd | 50 ++-- bnmonitor-0.1.4/bnmonitor/man/KL.CI.Rd | 84 +++---- bnmonitor-0.1.4/bnmonitor/man/KL.GBN.Rd | 82 +++---- bnmonitor-0.1.4/bnmonitor/man/KL.Rd | 50 ++-- bnmonitor-0.1.4/bnmonitor/man/KL.bn.fit.Rd | 114 +++++----- bnmonitor-0.1.4/bnmonitor/man/KL_bounds.Rd | 78 +++---- bnmonitor-0.1.4/bnmonitor/man/bn2.Rd | 56 ++--- bnmonitor-0.1.4/bnmonitor/man/bnmonitor.Rd | 182 ++++++++-------- bnmonitor-0.1.4/bnmonitor/man/cachexia.Rd | 88 ++++---- bnmonitor-0.1.4/bnmonitor/man/chds.Rd | 82 +++---- bnmonitor-0.1.4/bnmonitor/man/covariance_var.Rd | 90 ++++---- bnmonitor-0.1.4/bnmonitor/man/covariation.Rd | 108 ++++----- bnmonitor-0.1.4/bnmonitor/man/covariation_matrix.Rd | 96 ++++---- bnmonitor-0.1.4/bnmonitor/man/diabetes.Rd | 54 ++-- bnmonitor-0.1.4/bnmonitor/man/final_node_monitor.Rd | 86 +++---- bnmonitor-0.1.4/bnmonitor/man/fire_alarm.Rd | 54 ++-- bnmonitor-0.1.4/bnmonitor/man/global_monitor.Rd | 66 +++--- bnmonitor-0.1.4/bnmonitor/man/influential_obs.Rd | 68 +++--- bnmonitor-0.1.4/bnmonitor/man/mathmarks.Rd | 52 ++-- bnmonitor-0.1.4/bnmonitor/man/mean_var.Rd | 72 +++--- bnmonitor-0.1.4/bnmonitor/man/model_pres_cov.Rd | 98 ++++---- bnmonitor-0.1.4/bnmonitor/man/node_monitor.Rd | 78 +++---- bnmonitor-0.1.4/bnmonitor/man/plot.Rd | 104 ++++----- bnmonitor-0.1.4/bnmonitor/man/print.Rd | 94 ++++---- bnmonitor-0.1.4/bnmonitor/man/psd_check.Rd | 110 +++++----- bnmonitor-0.1.4/bnmonitor/man/sensitivity.Rd | 130 +++++------ bnmonitor-0.1.4/bnmonitor/man/sensquery.Rd | 106 ++++----- bnmonitor-0.1.4/bnmonitor/man/seq_node_monitor.Rd | 102 ++++----- bnmonitor-0.1.4/bnmonitor/man/seq_pa_ch_monitor.Rd | 98 ++++---- bnmonitor-0.1.4/bnmonitor/man/synthetic_bn.Rd | 48 ++-- bnmonitor-0.1.4/bnmonitor/man/synthetic_cbn.Rd | 56 ++--- bnmonitor-0.1.4/bnmonitor/man/travel.Rd | 54 ++-- 43 files changed, 1742 insertions(+), 1742 deletions(-)
Title: Markov Chain Monte Carlo Small Area Estimation
Description: Fit multi-level models with possibly correlated
random effects using Markov Chain Monte Carlo simulation.
Such models allow smoothing over space and time and are useful in,
for example, small area estimation.
Author: Harm Jan Boonstra [aut, cre],
Grzegorz Baltissen [ctb]
Maintainer: Harm Jan Boonstra <hjboonstra@gmail.com>
Diff between mcmcsae versions 0.7.2 dated 2023-02-04 and 0.7.3 dated 2023-06-02
DESCRIPTION | 29 - MD5 | 120 +++---- NAMESPACE | 6 NEWS | 14 R/MCMCsim.R | 20 - R/MatrixUtils.R | 45 ++ R/RcppExports.R | 28 + R/TMVN_methods.R |only R/TMVN_sampler.R | 651 +++++++++++++++++++++++++++----------- R/aux_closures.R | 12 R/cholesky.R | 2 R/conjugate_gradients.R | 6 R/family.R | 2 R/formulas.R | 6 R/mc_bart.R |only R/mc_block.R | 26 + R/mc_gen.R | 169 +++++---- R/mc_mec.R | 39 +- R/mc_reg.R | 79 +++- R/mc_vfac.R | 2 R/mc_vreg.R | 2 R/model_eval.R | 8 R/modelmatrix.R | 17 R/models.R | 34 - R/opts.R | 9 R/plots.R | 2 R/prediction.R | 46 +- R/samplers.R | 152 ++++---- R/tabMatrix.R | 267 +++++++++------ R/utils.R | 9 build/vignette.rds |binary inst/doc/area_level.html | 68 +-- inst/doc/linear_weighting.R | 4 inst/doc/linear_weighting.Rmd | 6 inst/doc/linear_weighting.html | 99 ++--- inst/doc/unit_level.Rmd | 1 inst/doc/unit_level.html | 326 +++++++++---------- man/bart.Rd |only man/create_TMVN_sampler.Rd | 78 ++-- man/create_sampler.Rd | 11 man/gen.Rd | 2 man/generate_data.Rd | 22 - man/mcmcsae-TMVN-method.Rd |only man/mcmcsae-family.Rd | 2 man/mcmcsae_example.Rd | 4 man/mec.Rd | 2 man/nchains-ndraws-nvars.Rd | 2 man/reg.Rd | 2 man/set_opts.Rd | 7 man/tabMatrix-indexing.Rd | 6 man/vfac.Rd | 2 man/vreg.Rd | 2 src/RcppExports.cpp | 88 ++++- src/TN.cpp | 133 +++++++ src/mcmcsae_init.c | 285 ++++++++-------- src/speed_ups.cpp | 168 +++++++++ src/tabMatrix.cpp | 254 +++++--------- tests/testthat/test_TMVN.R | 37 +- tests/testthat/test_binreg.R | 14 tests/testthat/test_linalg.R | 82 ++++ tests/testthat/test_modelmatrix.R | 29 + vignettes/linear_weighting.Rmd | 6 vignettes/unit_level.Rmd | 1 63 files changed, 2246 insertions(+), 1299 deletions(-)
Title: Tools for Preparing Text for Tokenizers
Description: Tokenizers break text into pieces that are more usable by
machine learning models. Many tokenizers share some preparation steps.
This package provides those shared steps, along with a simple
tokenizer.
Author: Jon Harmon [aut, cre] ,
Jonathan Bratt [aut] ,
Bedford Freeman & Worth Pub Grp LLC DBA Macmillan Learning [cph]
Maintainer: Jon Harmon <jonthegeek@gmail.com>
Diff between piecemaker versions 1.0.1 dated 2022-03-03 and 1.0.2 dated 2023-06-02
piecemaker-1.0.1/piecemaker/man/dot-coerce_to_utf8.Rd |only piecemaker-1.0.2/piecemaker/DESCRIPTION | 41 ++++------ piecemaker-1.0.2/piecemaker/MD5 | 15 +-- piecemaker-1.0.2/piecemaker/NAMESPACE | 1 piecemaker-1.0.2/piecemaker/NEWS.md | 4 piecemaker-1.0.2/piecemaker/R/clean.R | 65 ++++------------ piecemaker-1.0.2/piecemaker/R/piecemaker-package.R |only piecemaker-1.0.2/piecemaker/README.md | 6 + piecemaker-1.0.2/piecemaker/man/piecemaker-package.Rd |only piecemaker-1.0.2/piecemaker/tests/testthat/test-clean.R | 8 + 10 files changed, 58 insertions(+), 82 deletions(-)
Title: Design and Evaluate Choice-Based Conjoint Survey Experiments
Description: Design and evaluate choice-based conjoint survey experiments in R. Generate survey designs, including randomized designs and Bayesian D-efficient designs as well as designs with "no choice" options and labeled designs. Conveniently inspect the design balance and overlap, and simulate choice data for a survey design either randomly or according to a multinomial or mixed logit utility model defined by user-provided prior parameters. Conduct power analyses on a survey design by estimating the same model multiple times using different subsets of the data to simulate different sample sizes. Choice simulation and model estimation are handled using the 'logitr' package, and Bayesian D-efficient designs are obtained using the 'idefix' package. For more details see Helveston (2023) <doi:10.18637/jss.v105.i10> and Traets et al (2020) <doi:10.18637/jss.v096.i03>.
Author: John Helveston [cre, aut, cph]
Maintainer: John Helveston <john.helveston@gmail.com>
Diff between cbcTools versions 0.3.2 dated 2023-05-23 and 0.3.3 dated 2023-06-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 5 +++++ R/design.R | 41 +++++++++++++++++++++++++++-------------- R/input_checks.R | 27 +++++++++++++++++++++++++-- README.md | 16 +++++++--------- 6 files changed, 72 insertions(+), 33 deletions(-)
Title: Flexible Relative Survival Analysis
Description: Package for parametric relative survival analyses. It allows to model non-linear and
non-proportional effects and both non proportional and non linear effects, using splines (B-spline and truncated power basis), Weighted Cumulative Index of Exposure effect, with correction model for
the life table. Both non proportional and non linear effects are described in
Remontet, L. et al. (2007) <doi:10.1002/sim.2656> and
Mahboubi, A. et al. (2011) <doi:10.1002/sim.4208>.
Author: Isabelle Clerc-Urmes [aut],
Michel Grzebyk [aut, cre],
Guy Hedelin [ctb],
CENSUR working survival group [ctb]
Maintainer: Michel Grzebyk <michel.grzebyk@inrs.fr>
Diff between flexrsurv versions 2.0.16 dated 2023-04-04 and 2.0.17 dated 2023-06-02
flexrsurv-2.0.16/flexrsurv/R/CalculHazardTable.R |only flexrsurv-2.0.16/flexrsurv/R/gr_ll_flexrsurv_fromto_1WCEaddBr0PeriodControlOLD.R |only flexrsurv-2.0.16/flexrsurv/R/opg_flexrsurv_fromto_GA0B0ABE0Br0PeriodControl.testfrogr.R |only flexrsurv-2.0.17/flexrsurv/DESCRIPTION | 20 - flexrsurv-2.0.17/flexrsurv/MD5 | 159 ++++------ flexrsurv-2.0.17/flexrsurv/NEWS | 7 flexrsurv-2.0.17/flexrsurv/R/Flexrsurv.R | 2 flexrsurv-2.0.17/flexrsurv/R/ReadDesignFlexrsurv.R | 4 flexrsurv-2.0.17/flexrsurv/R/ReadDesignFlexrsurvWCE.R | 4 flexrsurv-2.0.17/flexrsurv/R/SplineParam.R | 16 - flexrsurv-2.0.17/flexrsurv/R/computeCumulativeHazard.1wceadd.R | 2 flexrsurv-2.0.17/flexrsurv/R/computeCumulativeHazard.R | 22 - flexrsurv-2.0.17/flexrsurv/R/computeLinearPredictor.1wceadd.R | 2 flexrsurv-2.0.17/flexrsurv/R/computeLinearPredictor.R | 4 flexrsurv-2.0.17/flexrsurv/R/computeLinearPredictor_WCE.R | 6 flexrsurv-2.0.17/flexrsurv/R/computeStdErrorCumulativeHazard.R | 4 flexrsurv-2.0.17/flexrsurv/R/computeStdErrorLinearPredictor.R | 4 flexrsurv-2.0.17/flexrsurv/R/computeStdErrorLinearPredictor_WCE.R | 6 flexrsurv-2.0.17/flexrsurv/R/fix.flexrsurv.formula.R | 2 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.glmiterative.fit.R | 2 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.R | 2 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fit.R | 8 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.brass.1wceadd.fitCoptim.R | 8 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.brass.period.1wceadd.fitCoptim.R | 10 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.brass.period.wce.fitCoptim.R | 12 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.brass.wce.fitCoptim.R | 12 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.brass.wce.fitoptim.R | 12 flexrsurv-2.0.17/flexrsurv/R/flexrsurv.ll.fromto.fit.R | 8 flexrsurv-2.0.17/flexrsurv/R/flexrsurvclt.R | 2 flexrsurv-2.0.17/flexrsurv/R/flexrsurvclt.ll.R | 2 flexrsurv-2.0.17/flexrsurv/R/getHazardFromTable.R | 2 flexrsurv-2.0.17/flexrsurv/R/getPseudoHazardFromTable.R | 82 ++--- flexrsurv-2.0.17/flexrsurv/R/gr_cumhaz_flexrsurv_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_cumhaz_flexrsurv_GA0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_cumhaz_flexrsurv_fromto_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_cumhaz_flexrsurv_fromto_GA0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_linkrate_flexrsurv_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_linkrate_flexrsurv_fromto_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_GA0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_1WCEaddBr0Control.R | 8 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_1WCEaddBr0PeriodControl.R | 16 - flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_GA0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_GA0B0ABE0Br0Control.R | 14 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_GA0B0ABE0Br0PeriodControl.R | 14 flexrsurv-2.0.17/flexrsurv/R/gr_ll_flexrsurv_fromto_GA0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_GA0B0AB.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_GA0B0AB_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_alpha0alpha.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_alpha0alpha_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_beta0beta.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_beta0beta_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_1WCEaddBr0Control.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_1WCEaddBr0PeriodControl.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_GA0B0AB.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_GA0B0ABE0Br0.R | 6 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_GA0B0ABE0Br0Control.R | 6 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_GA0B0ABE0Br0PeriodControl.R | 6 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_GA0B0AB_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_alpha0alpha.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_alpha0alpha_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_beta0beta.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_beta0beta_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_gamma0.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_fromto_gamma0_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_gamma0.R | 4 flexrsurv-2.0.17/flexrsurv/R/ll_flexrsurv_gamma0_bh.R | 4 flexrsurv-2.0.17/flexrsurv/R/ndf.flexrsurvclt.ll.R | 2 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_G0A0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_G0A0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_1WCEaddBr0Control.R | 12 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_1WCEaddBr0PeriodControl.R | 12 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_G0A0B0AB.R | 2 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_G0A0B0AB_bh.R | 2 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_GA0B0ABE0Br0Control.R | 14 flexrsurv-2.0.17/flexrsurv/R/opg_flexrsurv_fromto_GA0B0ABE0Br0PeriodControl.R | 14 flexrsurv-2.0.17/flexrsurv/R/split_data.R | 6 flexrsurv-2.0.17/flexrsurv/build/partial.rdb |binary flexrsurv-2.0.17/flexrsurv/man/Flexrsurv.Rd | 20 - flexrsurv-2.0.17/flexrsurv/man/FlexrsurvLT.Rd | 33 +- flexrsurv-2.0.17/flexrsurv/man/Flexrsurvpackage.Rd | 2 flexrsurv-2.0.17/flexrsurv/man/getPseudoHazardFromTable.Rd | 5 82 files changed, 370 insertions(+), 346 deletions(-)
Title: Interface to 'JDemetra+' Seasonal Adjustment Software
Description: Interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>), the seasonal adjustment software officially
recommended to the members of the European Statistical System (ESS) and the European System of Central Banks.
It offers full access to all options and outputs of 'JDemetra+', including the two leading seasonal adjustment methods
TRAMO/SEATS+ and X-12ARIMA/X-13ARIMA-SEATS.
Author: Alain Quartier-la-Tente [aut, cre]
,
Anna Michalek [aut],
Jean Palate [aut],
Raf Baeyens [aut]
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between RJDemetra versions 0.2.2 dated 2023-04-27 and 0.2.3 dated 2023-06-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/regarima_rslts.R | 6 +++--- 4 files changed, 13 insertions(+), 9 deletions(-)
Title: 'REDCap' Data Management
Description: Access and manage 'REDCap' data. 'REDCap' (Research Electronic Data CAPture; <https://projectredcap.org>) is a web application for building and managing online surveys and databases developed at Vanderbilt University. The API allows users to programmatic access data and project meta data (such as the data dictionary) from the web. This package allows us to read 'REDCap' data, exported or using an API connection, identify missing or extreme values, identify missing 'REDCap' events in each observation, do a follow-up of the queries initially identified and it also facilitates the process of data management.
Author: Joao Carmezim [aut, cre],
Judith Penafiel [aut],
Pau Satorra [aut],
Esther Garcia [aut],
Natalia Pallares [aut],
Cristian Tebe [aut]
Maintainer: Joao Carmezim <jcarmezim@igtp.cat>
Diff between REDCapDM versions 0.6.0 dated 2023-03-31 and 0.7.0 dated 2023-06-02
DESCRIPTION | 13 - MD5 | 34 +-- NEWS.md | 32 +++ R/check_queries.R | 14 + R/rd_event.R | 32 ++- R/rd_export.R | 10 - R/rd_query.R | 173 +++++++++++++------ R/rd_transform.R | 128 +++++++++++--- R/redcap_data.R | 34 +++ R/utils-transform.R | 101 ++++++++++- build/vignette.rds |binary inst/doc/REDCapDM.R | 54 ++++-- inst/doc/REDCapDM.Rmd | 111 ++++++++---- inst/doc/REDCapDM.html | 425 ++++++++++++++++++++++++++++++------------------- man/check_queries.Rd | 2 man/rd_query.Rd | 23 +- man/to_factor.Rd | 4 vignettes/REDCapDM.Rmd | 111 ++++++++---- 18 files changed, 905 insertions(+), 396 deletions(-)
Title: Adaptive Gauss Hermite Quadrature for Bayesian Inference
Description: Adaptive Gauss Hermite Quadrature for Bayesian inference.
The AGHQ method for normalizing posterior distributions
and making Bayesian inferences based on them. Functions are provided for doing
quadrature and marginal Laplace approximations, and summary methods are provided
for making inferences based on the results.
See Stringer (2021). "Implementing Adaptive Quadrature for Bayesian Inference:
the aghq Package" <arXiv:2101.04468>.
Author: Alex Stringer
Maintainer: Alex Stringer <alex.stringer@uwaterloo.ca>
Diff between aghq versions 0.4.0 dated 2022-03-07 and 0.4.1 dated 2023-06-02
DESCRIPTION | 8 - MD5 | 65 +++++----- NAMESPACE | 3 NEWS.md | 8 + R/00-misc-support-functions.R | 7 + R/02-normalization.R | 129 +++++++++++++++++++-- R/03-summary-statistics.R | 16 +- R/04-aghq.R | 34 +++-- man/aghq.Rd | 1 man/get_hessian.Rd | 1 man/get_log_normconst.Rd | 1 man/get_mode.Rd | 1 man/get_nodesandweights.Rd | 1 man/get_numquadpoints.Rd | 1 man/get_opt_results.Rd | 1 man/get_param_dim.Rd | 1 man/laplace_approximation.Rd | 1 man/marginal_laplace.Rd | 1 man/marginal_laplace_tmb.Rd | 1 man/nested.Rd |only man/normalize_logpost.Rd | 5 man/optimize_theta.Rd | 1 man/plot.aghq.Rd | 2 man/print.aghq.Rd | 1 man/print.aghqsummary.Rd | 2 man/print.laplace.Rd | 1 man/print.laplacesummary.Rd | 2 man/print.marginallaplacesummary.Rd | 1 man/summary.aghq.Rd | 1 man/summary.laplace.Rd | 2 man/summary.marginallaplace.Rd | 1 tests/testthat/setup-01-optimization.R | 200 ++++++++++++++++++++++++++++++++- tests/testthat/test-02-normalization.R | 200 ++++++++++++++++++++++++++++++++- tests/testthat/test-04-aghq.R | 7 + 34 files changed, 625 insertions(+), 82 deletions(-)
Title: WISP Multiple Criteria Sorting Method
Description: Implementation of the Integrated Simple Weighted Sum Product Method (WISP), a multiple criteria sorting method create by Dragisa Stanujkic (2021) <doi:10.1109/TEM.2021.3075783>.
Author: Bernardo Silva [aut, cre]
Maintainer: Bernardo Silva <bernardo.silva@furg.br>
Diff between rwisp versions 1.0.1 dated 2023-06-01 and 1.0.3 dated 2023-06-02
DESCRIPTION | 10 +++++++--- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/rwisp.r | 20 +++++++++++++++++++- README.md | 16 +++++++++------- man/rwispfromcsv.Rd | 5 ++++- man/wispcalc.Rd | 12 ++++++++++++ 7 files changed, 59 insertions(+), 18 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic models
(assuming either presence or absence of the effect, heterogeneity, and
publication bias). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>). Users can define a wide range of non-informative
or informative prior distributions for the effect size, heterogeneity,
and publication bias components (including selection models and PET-PEESE).
The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.0.0 dated 2023-06-01 and 3.0.1 dated 2023-06-02
DESCRIPTION | 6 MD5 | 104 ++--- NEWS.md | 5 R/utilities.R | 1 build/partial.rdb |binary configure.ac | 3 inst/doc/CustomEnsembles.html | 4 inst/doc/HierarchicalBMA.html | 4 inst/doc/MedicineBMA.html | 4 inst/doc/ReproducingBMA.html | 4 man/Anderson2010.Rd | 52 +- man/Bem2011.Rd | 54 +-- man/Kroupova2021.Rd | 58 +-- man/Lui2015.Rd | 60 +-- man/Poulsen2006.Rd | 56 +-- man/RoBMA-package.Rd | 86 ++-- man/RoBMA.Rd | 628 ++++++++++++++++++------------------ man/RoBMA.reg.Rd | 550 +++++++++++++++---------------- man/RoBMA_control.Rd | 142 ++++---- man/RoBMA_options.Rd | 54 +-- man/check_RoBMA.Rd | 40 +- man/check_setup.Rd | 224 ++++++------ man/check_setup.reg.Rd | 430 ++++++++++++------------ man/combine_data.Rd | 224 ++++++------ man/contr.meandif.Rd | 68 +-- man/contr.orthonormal.Rd | 60 +-- man/diagnostics.Rd | 246 +++++++------- man/effect_sizes.Rd | 186 +++++----- man/forest.Rd | 144 ++++---- man/interpret.Rd | 42 +- man/is.RoBMA.Rd | 40 +- man/marginal_plot.Rd | 126 +++---- man/marginal_summary.Rd | 84 ++-- man/plot.RoBMA.Rd | 218 ++++++------ man/plot_models.Rd | 164 ++++----- man/print.RoBMA.Rd | 44 +- man/print.marginal_summary.RoBMA.Rd | 44 +- man/print.summary.RoBMA.Rd | 44 +- man/prior.Rd | 170 ++++----- man/prior_PEESE.Rd | 156 ++++---- man/prior_PET.Rd | 156 ++++---- man/prior_factor.Rd | 198 +++++------ man/prior_informed.Rd | 138 +++---- man/prior_none.Rd | 80 ++-- man/prior_weightfunction.Rd | 108 +++--- man/sample_sizes.Rd | 120 +++--- man/standard_errors.Rd | 190 +++++----- man/summary.RoBMA.Rd | 176 +++++----- man/update.RoBMA.Rd | 350 ++++++++++---------- man/weighted_multivariate_normal.Rd | 72 ++-- man/weighted_normal.Rd | 206 +++++------ src/Makevars.in | 5 src/source/mnorm.cc | 1 53 files changed, 3220 insertions(+), 3209 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.1-3 dated 2021-10-08 and 1.2-0 dated 2023-06-02
DESCRIPTION | 19 - MD5 | 75 +++--- NAMESPACE | 38 ++- R/lpmvnorm.R |only R/ltMatrices.R |only R/mvnorm.R | 33 +- R/mvt.R | 82 +++++- R/tvpack.R | 6 build/partial.rdb |only build/vignette.rds |binary cleanup | 13 + inst/CITATION | 36 -- inst/NEWS | 493 +--------------------------------------- inst/NEWS.old |only inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.R |only inst/doc/lmvnorm_src.Rnw |only inst/doc/lmvnorm_src.pdf |only inst/include/mvtnorm.h | 12 inst/litdb.bib |only man/Mvnorm.Rd | 31 ++ man/lpmvnorm.Rd |only man/ltMatrices.Rd |only man/margcond.Rd |only man/mvtnorm-package.Rd |only man/pmvnorm.Rd | 31 +- man/pmvt.Rd | 22 + man/qmvnorm.Rd | 13 - man/qmvt.Rd | 19 - src/Makevars |only src/lpmvnorm.c |only src/ltMatrices.c |only src/miwa.c | 2 src/mvt.f | 6 src/mvtnorm-init.c | 24 + src/mvtnorm.h | 12 tests/bugfix-tests.R | 67 +++-- tests/bugfix-tests.Rout.save | 74 +++--- tests/dmvnorm-Ex.R |only tests/plmvnorm-Ex.R |only tests/plmvnorm-Ex.Rout.save |only tests/regtest-TVPACK.R | 20 - tests/regtest-TVPACK.Rout.save | 26 +- tests/regtest-scores.R |only tests/regtest-scores.Rout.save |only tests/rmvnorm.R | 28 +- tests/slpmvnorm.R |only vignettes/litdb.bib | 31 ++ vignettes/lmvnorm_src.Rnw |only vignettes/lmvnorm_src.Rout.save |only 50 files changed, 488 insertions(+), 725 deletions(-)
Title: Assessment of Regression Models Performance
Description: Utilities for computing measures to assess model quality,
which are not directly provided by R's 'base' or 'stats' packages.
These include e.g. measures like r-squared, intraclass correlation
coefficient (Nakagawa, Johnson & Schielzeth (2017)
<doi:10.1098/rsif.2017.0213>), root mean squared error or functions to
check models for overdispersion, singularity or zero-inflation and
more. Functions apply to a large variety of regression models,
including generalized linear models, mixed effects models and Bayesian
models. References: Lüdecke et al. (2021) <doi:10.21105/joss.03139>.
Author: Daniel Luedecke [aut, cre] ,
Dominique Makowski [aut, ctb] ,
Mattan S. Ben-Shachar [aut, ctb]
,
Indrajeet Patil [aut, ctb] ,
Philip Waggoner [aut, ctb] ,
Brenton M. Wiernik [aut, ctb] ,
Vincent Arel-Bundock [ctb] ,
Remi Theriault [ctb] ,
Martin Jullum [...truncated...]
Maintainer: Daniel Luedecke <d.luedecke@uke.de>
Diff between performance versions 0.10.3 dated 2023-04-07 and 0.10.4 dated 2023-06-02
DESCRIPTION | 6 - MD5 | 49 +++++---- NEWS.md | 33 +++++- R/binned_residuals.R | 11 +- R/check_collinearity.R | 9 + R/check_model.R | 33 +++++- R/check_predictions.R | 85 ++++++++++++++-- R/icc.R | 140 +++++++++++++++++++++++---- R/performance_accuracy.R | 19 +++ R/r2_nakagawa.R | 83 ++++++++++++---- README.md | 9 + inst/WORDLIST | 16 +++ man/binned_residuals.Rd | 11 +- man/check_collinearity.Rd | 2 man/check_model.Rd | 21 +++- man/check_predictions.Rd | 40 ++++++- man/icc.Rd | 15 ++ man/model_performance.merMod.Rd | 2 man/performance_accuracy.Rd | 3 man/r2_nakagawa.Rd | 15 ++ tests/testthat/_snaps/bootstrapped_icc_ci.md |only tests/testthat/_snaps/check_collinearity.md | 8 - tests/testthat/test-bootstrapped_icc_ci.R |only tests/testthat/test-check_collinearity.R | 15 ++ tests/testthat/test-check_outliers.R | 2 tests/testthat/test-icc.R | 8 - tests/testthat/test-performance_auc.R |only 27 files changed, 516 insertions(+), 119 deletions(-)
Title: Maximum Likelihood Multiple Imputation
Description: Implements so called Maximum Likelihood Multiple Imputation as described by von Hippel and Bartlett (2021) <doi:10.1214/20-STS793>. A number of different imputations are available, by utilising the 'norm', 'cat' and 'mix' packages. Inferences can be performed either using combination rules similar to Rubin's or using a likelihood score based approach based on theory by Wang and Robins (1998) <doi:10.1093/biomet/85.4.935>.
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <jonathan.bartlett1@lshtm.ac.uk>
Diff between mlmi versions 1.1.1 dated 2021-11-20 and 1.1.2 dated 2023-06-02
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- build/partial.rdb |binary 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Distances on Directed Graphs
Description: Distances on dual-weighted directed graphs using
priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>).
Weighted directed graphs have weights from A to B which may differ
from those from B to A. Dual-weighted directed graphs have two sets
of such weights. A canonical example is a street network to be used
for routing in which routes are calculated by weighting distances
according to the type of way and mode of transport, yet lengths of
routes must be calculated from direct distances.
Author: Mark Padgham [aut, cre],
Andreas Petutschnig [aut],
David Cooley [aut],
Robin Lovelace [ctb],
Andrew Smith [ctb],
Malcolm Morgan [ctb],
Shane Saunders [cph]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between dodgr versions 0.2.19 dated 2023-01-13 and 0.2.21 dated 2023-06-02
DESCRIPTION | 10 - MD5 | 205 +++++++++++++------------ NAMESPACE | 2 NEWS.md | 36 ++++ R/RcppExports.R | 22 ++ R/cache.R | 51 +++--- R/centrality.R | 13 - R/compare-heaps.R | 8 - R/dists-categorical.R | 79 ++++++--- R/dists-nearest.R |only R/dists.R | 46 ++--- R/dodgr-package.R | 8 - R/dodgr-streetnet.R | 4 R/flowmap.R | 5 R/flows.R | 12 - R/fund-cycles.R | 7 R/graph-contraction.R | 4 R/graph-conversion.R | 34 +--- R/graph-functions-misc.R | 4 R/graph-functions.R | 17 -- R/graph-merge.R | 2 R/iso.R | 21 +- R/match-points.R | 165 +++++++++++++++----- R/paths.R | 2 R/times.R | 2 R/utils.R | 3 R/weight-streetnet-times.R | 26 ++- R/weight-streetnet.R | 256 +++++++++++++++++++------------- R/weighting_profiles.R | 2 README.md | 23 +- build/vignette.rds |binary inst/CITATION | 6 inst/doc/dists-categorical.html | 22 +- inst/doc/dodgr.html | 97 ++++++++---- inst/doc/flows.html | 4 inst/doc/parallel.html | 4 inst/doc/times.html | 4 man/add_nodes_to_graph.Rd | 29 ++- man/clear_dodgr_cache.Rd | 15 - man/compare_heaps.Rd | 4 man/dodgr.Rd | 2 man/dodgr_cache_off.Rd | 7 man/dodgr_cache_on.Rd | 6 man/dodgr_centrality.Rd | 5 man/dodgr_components.Rd | 2 man/dodgr_contract_graph.Rd | 2 man/dodgr_distances.Rd | 3 man/dodgr_dists.Rd | 3 man/dodgr_dists_categorical.Rd | 19 ++ man/dodgr_dists_nearest.Rd |only man/dodgr_flowmap.Rd | 5 man/dodgr_flows_aggregate.Rd | 5 man/dodgr_flows_disperse.Rd | 5 man/dodgr_flows_si.Rd | 11 - man/dodgr_full_cycles.Rd | 2 man/dodgr_fundamental_cycles.Rd | 2 man/dodgr_insert_vertex.Rd | 2 man/dodgr_isochrones.Rd | 8 - man/dodgr_isodists.Rd | 8 - man/dodgr_isoverts.Rd | 8 - man/dodgr_paths.Rd | 3 man/dodgr_sample.Rd | 2 man/dodgr_sflines_to_poly.Rd | 3 man/dodgr_streetnet.Rd | 2 man/dodgr_streetnet_sc.Rd | 2 man/dodgr_times.Rd | 3 man/dodgr_to_igraph.Rd | 2 man/dodgr_to_sf.Rd | 11 - man/dodgr_to_sfc.Rd | 2 man/dodgr_to_tidygraph.Rd | 2 man/dodgr_uncontract_graph.Rd | 2 man/dodgr_vertices.Rd | 4 man/estimate_centrality_threshold.Rd | 6 man/estimate_centrality_time.Rd | 2 man/hampi.Rd | 2 man/igraph_to_dodgr.Rd | 2 man/match_points_to_graph.Rd | 16 +- man/match_points_to_verts.Rd | 6 man/match_pts_to_graph.Rd | 14 + man/match_pts_to_verts.Rd | 9 - man/merge_directed_graph.Rd | 2 man/os_roads_bristol.Rd | 2 man/summary.dodgr_dists_categorical.Rd | 4 man/weight_railway.Rd | 2 man/weight_streetnet.Rd | 23 ++ man/weighting_profiles.Rd | 2 man/write_dodgr_wt_profile.Rd | 2 src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 32 ++++ src/pathfinders.cpp | 37 ++++ src/pathfinders.h | 8 - src/run_sp.cpp | 152 +++++++++++++++---- src/run_sp.h | 14 + src/run_sp_categorical.cpp | 247 +++++++++++++++++++++++------- src/turn_penalty.h | 2 tests/sc-conversion-fns.R | 86 ++++++---- tests/testthat/test-dists-categorical.R | 69 ++++++++ tests/testthat/test-dists-nearest.R |only tests/testthat/test-graph-fns.R | 10 - tests/testthat/test-match-pts-fns.R | 4 tests/testthat/test-save-load.R | 1 tests/testthat/test-sc.R | 11 - tests/testthat/test-wt-profiles.R | 8 - vignettes/dodgr.bib | 2 105 files changed, 1433 insertions(+), 743 deletions(-)
Title: Native Access Medical Record Retriever for High Yield Analytics
Description: A toolkit for medical records data analysis. The 'naryn'
package implements an efficient data structure for storing medical
records, and provides a set of functions for data extraction,
manipulation and analysis.
Author: Misha Hoichman [aut],
Aviezer Lifshitz [aut, cre],
Ben Gilat [aut],
Netta Mendelson-Cohen [ctb],
Rami Jaschek [ctb],
Weizmann Institute of Science [cph]
Maintainer: Aviezer Lifshitz <aviezer.lifshitz@weizmann.ac.il>
Diff between naryn versions 2.6.14 dated 2023-01-09 and 2.6.21 dated 2023-06-02
DESCRIPTION | 10 - MD5 | 98 +++++++----- NAMESPACE | 12 + NEWS.md | 37 ++++ R/db.R | 13 + R/entries.R |only R/filter.R | 65 +------- R/logical-track.R | 3 R/time.R | 4 R/track-vars.R | 13 + R/track.R | 85 ++++++++-- R/utils-names.R |only R/utils.R | 114 ++++++++++++++ R/vtrack.R | 167 ++++++++++++++++++++ R/zzz.R | 5 inst/WORDLIST |only inst/testdb.tar.gz |binary man/dot-create_logical_track_filter.Rd |only man/dot-emr_expr_vars.Rd |only man/dot-emr_filter.Rd |only man/dot-emr_vtrack.get.Rd |only man/dot-naryn.Rd |only man/emr_db.connect.Rd | 5 man/emr_entries.get.Rd |only man/emr_entries.get_all.Rd |only man/emr_entries.ls.Rd |only man/emr_entries.reload.Rd |only man/emr_entries.rm.Rd |only man/emr_entries.rm_all.Rd |only man/emr_entries.set.Rd |only man/emr_track.addto.Rd | 4 man/emr_track.create.Rd | 9 + man/emr_track.import.Rd | 37 ++++ man/emr_track.rm.Rd | 2 man/emr_vtrack.create.Rd | 2 man/emr_vtrack.create_from_name.Rd |only man/emr_vtrack.name.Rd |only man/string_to_var.Rd |only man/var_to_string.Rd |only src/EMRDb.cpp | 7 src/EMRDb.h | 2 src/EMRTrack.h | 2 src/EMRTrackSparse.h | 1 src/Makevars | 2 src/NRImport.cpp | 55 +++++- src/NRTrack.cpp | 20 +- src/naryn-init.cpp | 6 tests/spelling.R |only tests/testthat/helper-regression.R | 16 -- tests/testthat/test-date2time.R | 4 tests/testthat/test-entries.R |only tests/testthat/test-extract.R | 14 - tests/testthat/test-logical_tracks.R | 60 +++++++ tests/testthat/test-track.attr.R | 26 +++ tests/testthat/test-track.create.R | 20 ++ tests/testthat/test-track.import.R | 109 +++++++++++++ tests/testthat/test-track.ls.R | 12 + tests/testthat/test-track.readonly.R | 19 ++ tests/testthat/test-utils.R |only tests/testthat/test-vtrack.R | 263 +++++++++++++++++++++++++-------- tests/testthat/test-x_multiple_db.R | 1 61 files changed, 1066 insertions(+), 258 deletions(-)
Title: Functions that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. There are also optimized vector-based methods, e.g. binMeans(), madDiff() and weightedMedian().
Author: Henrik Bengtsson [aut, cre, cph],
Constantin Ahlmann-Eltze [ctb],
Hector Corrada Bravo [ctb],
Robert Gentleman [ctb],
Jan Gleixner [ctb],
Peter Hickey [ctb],
Ola Hossjer [ctb],
Harris Jaffee [ctb],
Dongcan Jiang [ctb],
Peter Langfelder [ctb],
Brian M [...truncated...]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.63.0 dated 2022-11-18 and 1.0.0 dated 2023-06-02
DESCRIPTION | 8 MD5 | 292 +++++++++++------------ NEWS.md | 59 ++++ R/000.DEPRECATION.R | 5 R/anyMissing.R | 8 R/diff2.R | 11 R/rowAlls.R | 21 + R/rowCollapse.R | 8 R/rowCounts.R | 16 - R/rowCumsums.R | 24 + R/rowDiffs.R | 6 R/rowIQRs.R | 6 R/rowLogSumExps.R | 6 R/rowMads.R | 8 R/rowMeans2.R | 14 - R/rowMedians.R | 6 R/rowOrderStats.R | 6 R/rowProds.R | 8 R/rowQuantiles.R | 68 ++++- R/rowRanges.R | 18 - R/rowRanks.R | 8 R/rowSds.R | 13 - R/rowSums2.R | 6 R/rowTabulates.R | 8 R/rowVars.R | 26 +- R/rowWeightedMeans.R | 12 R/rowWeightedMedians.R | 8 R/varDiff.R | 50 ++- R/weightedMad.R | 14 - R/weightedVar.R | 16 - build/vignette.rds |binary inst/WORDLIST | 3 inst/doc/matrixStats-methods.html | 221 +++++------------ man/anyMissing.Rd | 15 - man/diff2.Rd | 7 man/rowAlls.Rd | 15 - man/rowCollapse.Rd | 11 man/rowCounts.Rd | 11 man/rowCumsums.Rd | 23 - man/rowDiffs.Rd | 11 man/rowIQRs.Rd | 13 - man/rowLogSumExps.Rd | 11 man/rowMeans2.Rd | 19 - man/rowMedians.Rd | 11 man/rowOrderStats.Rd | 11 man/rowProds.Rd | 11 man/rowQuantiles.Rd | 22 + man/rowRanges.Rd | 19 - man/rowRanks.Rd | 11 man/rowSds.Rd | 23 + man/rowSums2.Rd | 11 man/rowTabulates.Rd | 11 man/rowVars.Rd | 21 - man/rowWeightedMeans.Rd | 11 man/rowWeightedMedians.Rd | 11 man/varDiff.Rd | 23 - man/weightedMad.Rd | 11 man/weightedVar.Rd | 15 - src/000.api.h | 6 src/000.init.c | 6 src/000.templates-types.h | 11 src/anyMissing.c | 5 src/anyMissing_lowlevel.h | 2 src/anyMissing_lowlevel_template.h | 71 +++-- src/colCounts.c | 26 +- src/colCounts_lowlevel.h | 6 src/colCounts_lowlevel_template.h | 198 ++++++++++++++- src/colOrderStats.c | 4 src/colRanges.c | 14 - src/colRanges_lowlevel.h | 4 src/colRanges_lowlevel_template.h | 198 +++++++++++---- src/diff2.c | 23 + src/diff2_lowlevel.h | 4 src/diff2_lowlevel_template.h | 41 ++- src/logSumExp.c | 5 src/logSumExp_lowlevel_template.h | 72 +++++ src/mean2.c | 7 src/mean2_lowlevel.h | 4 src/mean2_lowlevel_template.h | 23 + src/naming.c | 63 ++++ src/naming.h | 1 src/productExpSumLog.c | 7 src/productExpSumLog_lowlevel.h | 4 src/productExpSumLog_lowlevel_template.h | 8 src/rowCounts.c | 16 - src/rowCounts_lowlevel.h | 6 src/rowCounts_lowlevel_template.h | 192 +++++++++++++-- src/rowCumMinMaxs_lowlevel_template.h | 126 ++++++++- src/rowCummaxs.c | 14 - src/rowCummaxs_lowlevel.h | 4 src/rowCummins.c | 14 - src/rowCummins_lowlevel.h | 4 src/rowCumprods.c | 16 - src/rowCumprods_lowlevel.h | 4 src/rowCumprods_lowlevel_template.h | 108 +++++++- src/rowCumsums.c | 15 - src/rowCumsums_lowlevel.h | 4 src/rowCumsums_lowlevel_template.h | 102 +++++++- src/rowDiffs.c | 16 - src/rowDiffs_lowlevel.h | 4 src/rowDiffs_lowlevel_template.h | 126 ++++++++- src/rowLogSumExp.c | 12 src/rowLogSumExp_lowlevel.h | 2 src/rowLogSumExp_lowlevel_template.h | 11 src/rowMads.c | 13 - src/rowMads_lowlevel.h | 4 src/rowMads_lowlevel_template.h | 104 +++++--- src/rowMeans2.c | 24 + src/rowMeans2_lowlevel.h | 4 src/rowMeans2_lowlevel_template.h | 119 +++++++-- src/rowMedians.c | 14 - src/rowMedians_lowlevel.h | 4 src/rowMedians_lowlevel_template.h | 108 +++++--- src/rowOrderStats.c | 4 src/rowRanges.c | 14 - src/rowRanges_lowlevel.h | 4 src/rowRanges_lowlevel_template.h | 23 - src/rowRanksWithTies.c | 118 ++++----- src/rowRanksWithTies_lowlevel.h | 6 src/rowRanksWithTies_lowlevel_template.h | 40 ++- src/rowSums2.c | 13 - src/rowSums2_lowlevel.h | 4 src/rowSums2_lowlevel_template.h | 179 +++++++------- src/rowVars.c | 22 + src/rowVars_lowlevel.h | 4 src/rowVars_lowlevel_template.h | 100 +++++-- src/signTabulate.c | 7 src/signTabulate_lowlevel.h | 4 src/signTabulate_lowlevel_template.h | 8 src/sum2.c | 7 src/sum2_lowlevel.h | 4 src/sum2_lowlevel_template.h | 20 + src/validateIndices.c | 4 src/weightedMean.c | 7 src/weightedMean_lowlevel.h | 4 src/weightedMean_lowlevel_template.h | 18 - src/weightedMedian.c | 7 src/weightedMedian_lowlevel.h | 4 src/weightedMedian_lowlevel_template.h | 18 - src/x_OP_y.c | 39 +-- src/x_OP_y_lowlevel.h | 32 +- src/x_OP_y_lowlevel_template.h | 393 ++++++++++++++++++++++++++----- tests/diff2.R | 38 +- tests/diff2_subset.R | 25 + tests/rowCumMinMaxs_subset.R | 4 tests/rowQuantiles.R | 7 tests/rowQuantiles_subset.R | 7 147 files changed, 3100 insertions(+), 1432 deletions(-)
Title: Estimate Structured Additive Regression Models with 'BayesX'
Description: An R interface to estimate structured additive regression (STAR) models with 'BayesX'.
Author: Nikolaus Umlauf [aut, cre] ,
Thomas Kneib [aut],
Stefan Lang [aut],
Achim Zeileis [aut]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>
Diff between R2BayesX versions 1.1-3 dated 2022-06-13 and 1.1-4 dated 2023-06-02
DESCRIPTION | 17 +++++----- MD5 | 14 ++++---- NAMESPACE | 1 R/blow.up.resid.R | 2 - R/plotmap.R | 4 +- R/unique.id.R | 2 - inst/CITATION | 80 ++++++++++++++++++++++++++---------------------- man/bayesx.construct.Rd | 1 8 files changed, 66 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-20 0.0.3
2022-03-30 0.0.2
2022-03-23 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-19 0.9.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-10 1.0.2
2018-08-05 1.0.1
2017-06-01 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-01-20 0.1.0
2022-06-21 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-11 0.0.4