Title: CORe Multiple Sclerosis Outcomes Toolkit
Description: Enable operationalized evaluation of disease outcomes in
multiple sclerosis. ‘MSoutcomes’ requires longitudinally recorded
clinical data structured in long format. The package is based on the
research developed at Clinical Outcomes Research unit (CORe),
University of Melbourne and Neuroimmunology Centre, Royal Melbourne
Hospital. Kalincik et al. (2015) <doi:10.1093/brain/awv258>.
Lorscheider et al. (2016) <doi:10.1093/brain/aww173>. Sharmin et al.
(2022) <doi:10.1111/ene.15406>. Dzau et al. (2023)
<doi:10.1136/jnnp-2023-331748>.
Author: Sifat Sharmin [aut],
Johannes Lorscheider [aut],
Nathaniel Lizak [aut],
Sam Harding-Forrester [aut],
Winston Dzau [aut],
Jannis Mueller [aut],
Izanne Roos [aut],
Tomas Kalincik [aut, cre, cph]
Maintainer: Tomas Kalincik <tomas.kalincik@unimelb.edu.au>
Diff between MSoutcomes versions 0.2.0 dated 2024-02-29 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 +++++++++----- LICENSE | 2 +- MD5 | 16 ++++++++-------- NAMESPACE | 2 ++ NEWS.md | 11 +++++++++++ R/CDEseq.R | 59 ++++++++++++++++++++++++++++++++++++----------------------- R/CDI.R | 34 +++++++++++++++++++++------------- R/CDW.R | 34 +++++++++++++++++++++------------- R/PIRA.R | 34 +++++++++++++++++++++------------- 9 files changed, 130 insertions(+), 76 deletions(-)
Title: PD-Clustering and Related Methods
Description: Probabilistic distance clustering (PD-clustering) is an iterative, distribution-free, probabilistic clustering method. PD-clustering assigns units to a cluster according to their probability of membership under the constraint that the product of the probability and the distance of each point to any cluster center is a constant. PD-clustering is a flexible method that can be used with elliptical clusters, outliers, or noisy data. PDQ is an extension of the algorithm for clusters of different sizes. GPDC and TPDC use a dissimilarity measure based on densities. Factor PD-clustering (FPDC) is a factor clustering method that involves a linear transformation of variables and a cluster optimizing the PD-clustering criterion. It works on high-dimensional data sets.
Author: Cristina Tortora [aut, cre, cph],
Noe Vidales [aut],
Francesco Palumbo [aut],
Tina Kalra [aut],
Paul D. McNicholas [fnd]
Maintainer: Cristina Tortora <grikris1@gmail.com>
Diff between FPDclustering versions 2.3.4 dated 2025-02-13 and 2.3.5 dated 2025-03-05
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/PDQ.R | 5 ++--- 3 files changed, 8 insertions(+), 9 deletions(-)
Title: Free Knot-Bayesian Model Averaging
Description: Analysis of Bayesian adaptive enrichment clinical trial using Free-Knot Bayesian Model Averaging (FK-BMA) method of Maleyeff et al. (2024) for Gaussian data. Maleyeff, L., Golchi, S., Moodie, E. E. M., & Hudson, M. (2024) "An adaptive enrichment design using Bayesian model averaging for selection and threshold-identification of predictive variables" <doi:10.1093/biomtc/ujae141>.
Author: Lara Maleyeff [aut, cre],
Shirin Golchi [aut],
Erica E. M. Moodie [aut]
Maintainer: Lara Maleyeff <lara.maleyeff@mcgill.ca>
Diff between fkbma versions 0.1.0 dated 2025-01-31 and 0.2.0 dated 2025-03-05
fkbma-0.1.0/fkbma/man/fittedTrtEff.Rd |only fkbma-0.1.0/fkbma/man/predictTrtEff.Rd |only fkbma-0.2.0/fkbma/DESCRIPTION | 6 fkbma-0.2.0/fkbma/MD5 | 44 +- fkbma-0.2.0/fkbma/NAMESPACE | 5 fkbma-0.2.0/fkbma/R/data_generate.R | 4 fkbma-0.2.0/fkbma/R/rjMCMC.R | 81 ++-- fkbma-0.2.0/fkbma/R/s3-methods.R | 495 +++++++++++++------------ fkbma-0.2.0/fkbma/data/simulated_data.rda |binary fkbma-0.2.0/fkbma/man/coef.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/credint.Rd | 7 fkbma-0.2.0/fkbma/man/fitted.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/fittedExposureEff.Rd |only fkbma-0.2.0/fkbma/man/getEffectiveSubspace.Rd | 20 - fkbma-0.2.0/fkbma/man/pip.Rd | 25 - fkbma-0.2.0/fkbma/man/plot.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/plotHistTrace.Rd | 8 fkbma-0.2.0/fkbma/man/predict.rjMCMC.Rd | 24 - fkbma-0.2.0/fkbma/man/predictExposureEff.Rd |only fkbma-0.2.0/fkbma/man/print.rjMCMC.Rd | 16 fkbma-0.2.0/fkbma/man/rhats.Rd | 33 - fkbma-0.2.0/fkbma/man/rjMCMC.Rd | 27 - fkbma-0.2.0/fkbma/man/simulated_data.Rd | 2 fkbma-0.2.0/fkbma/man/summary.rjMCMC.Rd | 26 - fkbma-0.2.0/fkbma/tests/testthat/test-rjMCMC.R | 18 25 files changed, 491 insertions(+), 422 deletions(-)
Title: An Extension of the Gap Statistic for Ordinal/Categorical Data
Description: The gap statistic approach is extended to estimate the number of clusters for categorical response format data. This approach and accompanying software is designed to be used with the output of any clustering algorithm and with distances specifically designed for categorical (i.e. multiple choice) or ordinal survey response data.
Author: Jeffrey Miecznikowski [aut],
Eduardo Cortes [aut, cre]
Maintainer: Eduardo Cortes <ecortesg@buffalo.edu>
Diff between DiscreteGapStatistic versions 1.0.0 dated 2024-12-09 and 1.1.2 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 66 +++++------ R/AuxFuns.R | 11 + R/DiscreteClusGapFuns.R | 10 + R/DistanceFuns.R | 76 ++++++++---- R/SimDataFun.R | 3 R/VisualFuns.R | 35 ++++- R/data.R | 13 +- README.md | 185 +++++++++++++++++++------------ man/BhattacharyyaDist.Rd | 2 man/ChisqDist.Rd | 2 man/CramerV.Rd | 2 man/HellingerDist.Rd | 2 man/ResHeatmap.Rd | 21 ++- man/SimData.Rd | 3 man/clusGapDiscr.Rd | 4 man/clusGapDiscr0.Rd | 4 man/clusterFunSel.Rd | 5 man/concussion.Rd | 6 - man/cramersVmod.Rd | 8 - man/dissbhattacharyya.Rd | 8 - man/disschisquare.Rd | 8 - man/disscramerv.Rd | 8 - man/disshamming.Rd | 8 - man/disshellinger.Rd | 8 - man/distanceHeat.Rd | 15 +- man/distancematrix.Rd | 9 - man/figures/README-clusGapDiscrFit-1.png |binary man/figures/README-clusGapDiscrFit-2.png |binary man/figures/README-clusGapDiscrFit-3.png |binary man/findK.Rd | 2 man/kmodesD.Rd | 5 man/likert.heat.plot2.Rd | 8 - man/mass.Rd | 11 - 34 files changed, 320 insertions(+), 234 deletions(-)
More information about DiscreteGapStatistic at CRAN
Permanent link
Title: Tools and Metrics for 3D Surfaces and Objects
Description: A collection of functions for sampling and simulating 3D surfaces and objects
and estimating metrics like rugosity, fractal dimension, convexity, sphericity, circularity,
second moments of area and volume, and more.
Author: Joshua Madin [aut] ,
Nina Schiettekatte [aut, cre]
Maintainer: Nina Schiettekatte <nina.schiettekatte@gmail.com>
Diff between habtools versions 1.0.7 dated 2024-11-15 and 1.1.1 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++---------- NAMESPACE | 4 ++ NEWS.md | 6 +++ R/entropy.R |only R/fd_boxes.R | 6 +-- R/fd_cubes.R | 13 ++++--- R/fd_diagnose.R | 36 +++++++++++--------- R/planar.R | 7 ---- R/rg.R | 2 - R/smv.R | 4 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/DEM_intro.html | 6 +-- inst/doc/fractal_intro.html | 76 ++++++++++++++++++++++---------------------- inst/doc/mesh_intro.html | 38 +++++++++++----------- man/entropy.Rd |only man/entropy_1d.Rd |only man/entropy_2d.Rd |only man/entropy_3d.Rd |only man/fd_cubes.Rd | 2 - man/fd_diagnose.Rd | 6 ++- man/smv.Rd | 4 +- 23 files changed, 138 insertions(+), 119 deletions(-)
Title: Miscellaneous Functions for Processing and Sample Selection of
Spectroscopic Data
Description: Functions to preprocess spectroscopic data
and conduct (representative) sample selection/calibration sampling.
Author: Antoine Stevens [aut] ,
Leonardo Ramirez-Lopez [aut, cre]
Maintainer: Leonardo Ramirez-Lopez <ramirez.lopez.leo@gmail.com>
Diff between prospectr versions 0.2.7 dated 2024-02-16 and 0.2.8 dated 2025-03-05
prospectr-0.2.7/prospectr/build/prospectr.pdf |only prospectr-0.2.8/prospectr/DESCRIPTION | 29 +++++++---- prospectr-0.2.8/prospectr/LICENSE | 2 prospectr-0.2.8/prospectr/MD5 | 30 +++++------ prospectr-0.2.8/prospectr/NEWS.md | 15 +++++ prospectr-0.2.8/prospectr/R/gapDer.R | 10 +-- prospectr-0.2.8/prospectr/R/kenstone.R | 5 + prospectr-0.2.8/prospectr/README.md | 14 ++--- prospectr-0.2.8/prospectr/build/stage23.rdb |only prospectr-0.2.8/prospectr/build/vignette.rds |binary prospectr-0.2.8/prospectr/inst/doc/prospectr.R | 46 ++++++++--------- prospectr-0.2.8/prospectr/inst/doc/prospectr.html | 54 ++++++++++----------- prospectr-0.2.8/prospectr/man/gapDer.Rd | 6 +- prospectr-0.2.8/prospectr/man/kenStone.Rd | 5 + prospectr-0.2.8/prospectr/man/prospectr-package.Rd | 2 prospectr-0.2.8/prospectr/src/Makevars | 1 prospectr-0.2.8/prospectr/src/Makevars.win | 1 17 files changed, 122 insertions(+), 98 deletions(-)
Title: Power Analysis for PLS Classification
Description: It estimates power and sample size for Partial Least Squares-based methods described in Andreella, et al., (2024), <doi:10.48550/arXiv.2403.10289>.
Author: Angela Andreella [aut, cre]
Maintainer: Angela Andreella <angela.andreella@unitn.it>
Diff between powerPLS versions 0.2.0 dated 2024-09-30 and 0.2.1 dated 2025-03-05
DESCRIPTION | 14 ++-- MD5 | 62 +++++++++++++-------- NAMESPACE | 10 +++ NEWS.md | 4 + R/AUCTest.R |only R/F1Test.R |only R/FMTest.R |only R/IDA.R | 25 ++++---- R/PLSc.R | 91 ++++++++++++++----------------- R/R2Test.R | 75 ++++++++++++++----------- R/computePower.R | 136 ++++++++++++++++++++++------------------------- R/computeSampleSize.R | 35 +++++------- R/computeWT.R | 55 ++++++++----------- R/dQ2Test.R |only R/global.R | 2 R/mccTest.R | 113 +++++++++++++++++++++------------------ R/ptPLSc.R | 64 +++++++++++----------- R/repeatedCV_test.R |only R/scoreTest.R | 109 ++++++++++++++++++++----------------- R/sensitivityTest.R |only R/sim_Tscore.R | 25 ++++---- R/sim_XY.R | 99 ++++++++++++++++------------------ R/simulatePilotData.R | 34 ++++++----- R/specificityTest.R |only R/utils.R | 128 ++++++++++++++++++++++++++++++++------------ README.md | 2 man/AUCTest.Rd |only man/F1Test.Rd |only man/FMTest.Rd |only man/PLSc.Rd | 8 +- man/R2Test.Rd | 16 ++++- man/computePower.Rd | 14 ++-- man/computeSampleSize.Rd | 8 +- man/dQ2Test.Rd |only man/mccTest.Rd | 18 ++++-- man/repeatedCV_test.Rd |only man/scoreTest.Rd | 16 ++++- man/sensitivityTest.Rd |only man/specificityTest.Rd |only 39 files changed, 645 insertions(+), 518 deletions(-)
Title: Download Official Data on Brazil's Federal Budget
Description: Allows users to download and analyze official data on Brazil's federal budget through the 'SPARQL' endpoint
provided by the Integrated Budget and Planning System ('SIOP'). This package enables access to detailed information on budget
allocations and expenditures of the federal government, making it easier to analyze and visualize these data. Technical
information on the Brazilian federal budget is available (Portuguese only) at <https://www1.siop.planejamento.gov.br/mto/>.
The 'SIOP' endpoint is available at <https://www1.siop.planejamento.gov.br/sparql/>.
Author: Daniel Gersten Reiss [aut, cre]
,
Bernardo Borba de Andrade [ctb]
,
Gustavo Jose de Guimaraes e Souza [ctb]
,
Ministerio do Planejamento e Orcamento [cph, fnd]
Maintainer: Daniel Gersten Reiss <daniel.reiss@planejamento.gov.br>
Diff between orcamentoBR versions 1.0.2 dated 2025-02-20 and 1.0.3 dated 2025-03-05
DESCRIPTION | 13 +++++++------ MD5 | 12 ++++++------ R/orcamentoBR.R | 8 +++++--- R/quaisDimensoes.R | 4 ++-- man/despesaDetalhada.Rd | 2 ++ man/quaisMembros.Rd | 2 +- man/whichMembers.Rd | 2 +- 7 files changed, 24 insertions(+), 19 deletions(-)
Title: Diagnostic Tools for a Multivariate Negative Binomial Regression
Model
Description: Diagnostic tools as residual analysis, global,
local and total-local influence for the multivariate model
from the random intercept Poisson generalized log gamma model
are available in this package. Including also, the estimation
process by maximum likelihood method, for details see
Fabio, L. C; Villegas, C. L.; Carrasco, J.M.F and de Castro, M. (2023)
<doi:10.1080/03610926.2021.1939380> and Fábio, L. C.; Villegas, C.;
Mamun, A. S. M. A. and Carrasco, J. M. F. (2025) <doi:10.28951/bjb.v43i1.728>.
Author: Jalmar Carrasco [aut, cre],
Cristian Lobos [aut],
Lizandra Fabio [aut]
Maintainer: Jalmar Carrasco <carrascojalmar@gmail.com>
Diff between MNB versions 1.1.0 dated 2022-04-22 and 1.2.0 dated 2025-03-05
DESCRIPTION | 18 - MD5 | 38 +-- R/Local.R | 650 ++++++++++++++++++++++++++-------------------------- R/MNB.R | 217 ++++++++--------- R/enveSim.R | 277 +++++++++++----------- R/estimate.R | 219 ++++++++--------- R/global.R | 180 +++++++------- R/qMNB.R | 215 ++++++++--------- R/rMNB.R | 96 +++---- R/residual.R | 393 +++++++++++++++---------------- man/MNB.Rd | 11 man/alzheimer.Rd | 7 man/envelope.MNB.Rd | 11 man/fit.MNB.Rd | 11 man/global.MNB.Rd | 8 man/local.MNB.Rd | 8 man/qMNB.Rd | 11 man/rMNB.Rd | 4 man/re.MNB.Rd | 11 man/seizures.Rd | 11 20 files changed, 1216 insertions(+), 1180 deletions(-)
Title: Assessing Complex Heterogeneity in Surrogacy
Description: Provides functions to assess and test for complex heterogeneity in the utility of a surrogate marker with respect to multiple baseline covariates, using both a parametric model and a semiparametric two-step model. More details are available in: Knowlton, R., Tian, L., & Parast, L. (2025). "A General Framework to Assess Complex Heterogeneity in the Strength of a Surrogate Marker," Statistics in Medicine, 44(5), e70001 <doi:10.1002/sim.70001>. A tutorial for this package can be found at <https://laylaparast.com/home/cohetsurr.html>.
Author: Rebecca Knowlton [aut],
Layla Parast [aut, cre]
Maintainer: Layla Parast <parast@austin.utexas.edu>
Diff between cohetsurr versions 1.0 dated 2024-11-21 and 1.1 dated 2025-03-05
DESCRIPTION | 17 ++-- MD5 | 4 - man/complex.heterogeneity.Rd | 158 +++++++++++++++++++++---------------------- 3 files changed, 90 insertions(+), 89 deletions(-)
Title: Calculate Mass Properties and Uncertainties of Tree Structures
Description: Recursively calculates mass properties (mass, center of mass, moments and products of inertia, and optionally, their uncertainties) for arbitrary decomposition trees. R. L. Zimmerman, J. H. Nakai. (2005) <https://www.sawe.org/product/paper-3360/>).
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between massProps versions 0.2.0 dated 2025-01-30 and 0.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 57 + NAMESPACE | 6 NEWS.md | 17 R/massprops.R | 42 - R/mp_table_small.R |only R/mp_tree_small.R |only R/radii.R |only R/test_unc_table.R |only README.md | 114 +++ data/mp_table_small.rda |only data/mp_tree.rda |binary data/mp_tree_small.rda |only data/test_tree.rda |binary data/test_unc_table.rda |only inst/doc/massProps.R | 142 +++- inst/doc/massProps.Rmd | 692 +++++++++++++++-------- inst/doc/massProps.html | 719 +++++++++++++++--------- man/add_radii_of_gyration.Rd |only man/get_mass_props_and_unc_and_radii.Rd |only man/get_mass_props_and_unc_and_radii_and_unc.Rd |only man/mp_table_small.Rd |only man/mp_tree_small.Rd |only man/rollup_mass_props.Rd | 2 man/rollup_mass_props_and_unc.Rd | 2 man/rollup_mass_props_and_unc_fast.Rd | 2 man/rollup_mass_props_unc.Rd | 4 man/rollup_radii_of_gyration_unc.Rd |only man/set_mass_props_unc.Rd | 2 man/set_radii_of_gyration.Rd |only man/set_radii_of_gyration_unc.Rd |only man/test_unc_table.Rd |only man/validate_mass_props_and_unc_table.Rd | 2 man/validate_mass_props_table.Rd | 2 tests/testthat/test-massProps.R | 1 tests/testthat/test-radii.R |only vignettes/massProps.Rmd | 692 +++++++++++++++-------- vignettes/references.bib | 8 38 files changed, 1709 insertions(+), 803 deletions(-)
Title: Retrieve Data from the Census APIs
Description: A wrapper for the U.S. Census Bureau APIs that returns data frames of
Census data and metadata. Available datasets include the
Decennial Census, American Community Survey, Small Area Health Insurance Estimates,
Small Area Income and Poverty Estimates, Population Estimates and Projections, and more.
Author: Hannah Recht [aut, cre]
Maintainer: Hannah Recht <censusapi.rstats@gmail.com>
Diff between censusapi versions 0.8.0 dated 2022-08-09 and 0.9.0 dated 2025-03-05
DESCRIPTION | 13 - MD5 | 36 ++-- NAMESPACE | 3 NEWS.md | 34 +++- R/api-key.R |only R/datasets.R | 2 R/getcensus_functions.R | 371 +++++++++++++++++++++++++++++++--------------- R/makevar_functions.R | 32 ++- R/metadata_functions.R | 250 ++++++++++++++++++++++-------- README.md | 146 +++++++++++++++++- build |only inst |only man/fips.Rd | 2 man/getCensus.Rd | 104 ++++++------ man/getFunction.Rd | 7 man/get_api_key.Rd |only man/has_api_key.Rd |only man/listCensusApis.Rd | 58 ++++++- man/listCensusMetadata.Rd | 128 +++++++++------ man/makeVarlist.Rd | 33 ++-- vignettes |only 21 files changed, 868 insertions(+), 351 deletions(-)
Title: Fast and Simple 'MongoDB' Client for R
Description: High-performance MongoDB client based on 'mongo-c-driver' and 'jsonlite'.
Includes support for aggregation, indexing, map-reduce, streaming, encryption,
enterprise authentication, and GridFS. The online user manual provides an overview
of the available methods in the package: <https://jeroen.github.io/mongolite/>.
Author: Jeroen Ooms [aut, cre] ,
MongoDB, Inc [cph]
Maintainer: Jeroen Ooms <jeroenooms@gmail.com>
Diff between mongolite versions 3.1.0 dated 2025-02-25 and 3.1.1 dated 2025-03-05
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS | 3 +++ src/Makevars.in | 2 +- src/osx/Makevars | 2 +- 5 files changed, 12 insertions(+), 9 deletions(-)
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the Web Service methods provided by
the National 'Phenology' Network (<https://usanpn.org/>), which
includes data on various life history events that occur at specific
times.
Author: Jeff Switzer [aut, cre],
Scott Chamberlain [aut],
Lee Marsh [aut],
Kevin Wong [aut],
Eric R Scott [aut] ,
David LeBauer [ctb]
Maintainer: Jeff Switzer <jeff@usanpn.org>
Diff between rnpn versions 1.2.9.0 dated 2024-08-19 and 1.3.0 dated 2025-03-05
rnpn-1.2.9.0/rnpn/man/check_geo_service.Rd |only rnpn-1.2.9.0/rnpn/man/check_service.Rd |only rnpn-1.2.9.0/rnpn/tests/test-all.R |only rnpn-1.3.0/rnpn/DESCRIPTION | 47 rnpn-1.3.0/rnpn/LICENSE | 4 rnpn-1.3.0/rnpn/MD5 | 194 - rnpn-1.3.0/rnpn/NAMESPACE | 8 rnpn-1.3.0/rnpn/NEWS.md | 78 rnpn-1.3.0/rnpn/R/base-reqs.R |only rnpn-1.3.0/rnpn/R/defunct.R | 12 rnpn-1.3.0/rnpn/R/lookup_names.R | 24 rnpn-1.3.0/rnpn/R/npn_data_download.R | 1460 ++++++------ rnpn-1.3.0/rnpn/R/npn_dataset.R | 21 rnpn-1.3.0/rnpn/R/npn_geoserver.R | 897 +++---- rnpn-1.3.0/rnpn/R/npn_get_species.R | 180 - rnpn-1.3.0/rnpn/R/npn_partner_groups.R | 47 rnpn-1.3.0/rnpn/R/npn_phenophases.R | 269 +- rnpn-1.3.0/rnpn/R/npn_stations.R | 121 rnpn-1.3.0/rnpn/R/release-reminders.R |only rnpn-1.3.0/rnpn/R/rnpn-package.R | 17 rnpn-1.3.0/rnpn/R/test-helpers.R |only rnpn-1.3.0/rnpn/R/utils.R |only rnpn-1.3.0/rnpn/R/zzz.R | 180 - rnpn-1.3.0/rnpn/README.md | 20 rnpn-1.3.0/rnpn/inst/CITATION |only rnpn-1.3.0/rnpn/inst/doc/III_individual_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/II_status_intensity.html | 2 rnpn-1.3.0/rnpn/inst/doc/IV_site_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/doc/I_introduction.html | 2 rnpn-1.3.0/rnpn/inst/doc/VIII_data_cleaning.html | 2 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.R | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/inst/doc/VII_combine_raster_point.html | 47 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/inst/doc/VI_geospatial.html | 40 rnpn-1.3.0/rnpn/inst/doc/V_magnitude_phenometrics.html | 2 rnpn-1.3.0/rnpn/inst/release-tasks.R |only rnpn-1.3.0/rnpn/man/get_additional_rasters.Rd | 13 rnpn-1.3.0/rnpn/man/npn_abundance_categories.Rd | 11 rnpn-1.3.0/rnpn/man/npn_check_point_cached.Rd | 8 rnpn-1.3.0/rnpn/man/npn_datasets.Rd | 9 rnpn-1.3.0/rnpn/man/npn_download_geospatial.Rd | 35 rnpn-1.3.0/rnpn/man/npn_download_individual_phenometrics.Rd | 183 - rnpn-1.3.0/rnpn/man/npn_download_magnitude_phenometrics.Rd | 155 - rnpn-1.3.0/rnpn/man/npn_download_site_phenometrics.Rd | 207 + rnpn-1.3.0/rnpn/man/npn_download_status_data.Rd | 169 - rnpn-1.3.0/rnpn/man/npn_get_agdd_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_get_common_query_vars.Rd | 5 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_raster.Rd | 42 rnpn-1.3.0/rnpn/man/npn_get_custom_agdd_time_series.Rd | 55 rnpn-1.3.0/rnpn/man/npn_get_data.Rd | 28 rnpn-1.3.0/rnpn/man/npn_get_data_by_year.Rd | 63 rnpn-1.3.0/rnpn/man/npn_get_download_url.Rd | 10 rnpn-1.3.0/rnpn/man/npn_get_layer_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_get_phenophases_for_taxon.Rd | 57 rnpn-1.3.0/rnpn/man/npn_get_point_data.Rd | 29 rnpn-1.3.0/rnpn/man/npn_groups.Rd | 20 rnpn-1.3.0/rnpn/man/npn_lookup_names.Rd | 17 rnpn-1.3.0/rnpn/man/npn_merge_geo_data.Rd | 8 rnpn-1.3.0/rnpn/man/npn_pheno_classes.Rd | 12 rnpn-1.3.0/rnpn/man/npn_phenophase_definitions.Rd | 10 rnpn-1.3.0/rnpn/man/npn_phenophase_details.Rd | 19 rnpn-1.3.0/rnpn/man/npn_phenophases.Rd | 9 rnpn-1.3.0/rnpn/man/npn_phenophases_by_species.Rd | 21 rnpn-1.3.0/rnpn/man/npn_species.Rd | 57 rnpn-1.3.0/rnpn/man/npn_species_types.Rd | 14 rnpn-1.3.0/rnpn/man/npn_stations.Rd | 6 rnpn-1.3.0/rnpn/man/npn_stations_by_location.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_by_state.Rd | 4 rnpn-1.3.0/rnpn/man/npn_stations_with_spp.Rd | 8 rnpn-1.3.0/rnpn/man/resolve_six_raster.Rd | 31 rnpn-1.3.0/rnpn/man/rnpn-defunct.Rd | 12 rnpn-1.3.0/rnpn/man/rnpn-package.Rd | 29 rnpn-1.3.0/rnpn/tests/fixtures |only rnpn-1.3.0/rnpn/tests/testthat.R |only rnpn-1.3.0/rnpn/tests/testthat/test-npn-datasets.R | 13 rnpn-1.3.0/rnpn/tests/testthat/test-npn-defunct.R | 15 rnpn-1.3.0/rnpn/tests/testthat/test-npn-geoserver.R | 181 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-get-species.R | 96 rnpn-1.3.0/rnpn/tests/testthat/test-npn-observations.R | 506 +--- rnpn-1.3.0/rnpn/tests/testthat/test-npn-partners.R | 20 rnpn-1.3.0/rnpn/tests/testthat/test-npn-phenophases.R | 154 - rnpn-1.3.0/rnpn/tests/testthat/test-npn-stations.R | 68 rnpn-1.3.0/rnpn/vignettes/VII_combine_raster_point.Rmd | 49 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd | 84 rnpn-1.3.0/rnpn/vignettes/VI_geospatial.Rmd.orig | 44 86 files changed, 3478 insertions(+), 3020 deletions(-)
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2020) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] ,
Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MoEClust versions 1.5.2 dated 2023-12-11 and 1.6.0 dated 2025-03-05
MoEClust-1.5.2/MoEClust/R/MoEClust.R |only MoEClust-1.6.0/MoEClust/DESCRIPTION | 14 MoEClust-1.6.0/MoEClust/MD5 | 66 +- MoEClust-1.6.0/MoEClust/NAMESPACE | 7 MoEClust-1.6.0/MoEClust/R/Functions.R | 452 +++++++++++-------- MoEClust-1.6.0/MoEClust/R/MoEClust-package.R |only MoEClust-1.6.0/MoEClust/R/Plotting_Functions.R | 553 ++++++++++++++---------- MoEClust-1.6.0/MoEClust/R/data.R | 4 MoEClust-1.6.0/MoEClust/README.md | 2 MoEClust-1.6.0/MoEClust/build/partial.rdb |binary MoEClust-1.6.0/MoEClust/build/vignette.rds |binary MoEClust-1.6.0/MoEClust/inst/NEWS.md | 81 +++ MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.R | 87 +-- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.Rmd | 61 +- MoEClust-1.6.0/MoEClust/inst/doc/MoEClust.html | 75 +-- MoEClust-1.6.0/MoEClust/man/CO2data.Rd | 2 MoEClust-1.6.0/MoEClust/man/FARI.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoEClust-package.Rd | 210 ++++----- MoEClust-1.6.0/MoEClust/man/MoE_Uncertainty.Rd | 130 +++-- MoEClust-1.6.0/MoEClust/man/MoE_clust.Rd | 26 - MoEClust-1.6.0/MoEClust/man/MoE_compare.Rd | 16 MoEClust-1.6.0/MoEClust/man/MoE_control.Rd | 396 ++++++++--------- MoEClust-1.6.0/MoEClust/man/MoE_crit.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_cstep.Rd | 2 MoEClust-1.6.0/MoEClust/man/MoE_estep.Rd | 6 MoEClust-1.6.0/MoEClust/man/MoE_gpairs.Rd | 107 ++-- MoEClust-1.6.0/MoEClust/man/MoE_news.Rd | 4 MoEClust-1.6.0/MoEClust/man/MoE_plotCrit.Rd | 11 MoEClust-1.6.0/MoEClust/man/MoE_stepwise.Rd | 4 MoEClust-1.6.0/MoEClust/man/ais.Rd | 84 +-- MoEClust-1.6.0/MoEClust/man/as.Mclust.Rd | 51 +- MoEClust-1.6.0/MoEClust/man/expert_covar.Rd | 4 MoEClust-1.6.0/MoEClust/man/noise_vol.Rd | 2 MoEClust-1.6.0/MoEClust/man/plot.MoEClust.Rd | 8 MoEClust-1.6.0/MoEClust/vignettes/MoEClust.Rmd | 61 +- 35 files changed, 1423 insertions(+), 1107 deletions(-)
Title: Get Images Out of DICOM Format Quickly
Description: Provides tools to sort DICOM-format medical image files, and
convert them to NIfTI-1 format.
Author: Jon Clayden [aut, cre] ,
Chris Rorden [aut],
Martin J Fiedler [cph],
Cong Xu [cph],
Pascal Gloor [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between divest versions 1.1.1 dated 2024-10-20 and 1.2.0 dated 2025-03-05
divest-1.1.1/divest/R/attribs.R |only divest-1.1.1/divest/build |only divest-1.1.1/divest/inst/tinytest/attributes.json |only divest-1.1.1/divest/man/bidsJson.Rd |only divest-1.1.1/divest/man/imageAttributes.Rd |only divest-1.2.0/divest/DESCRIPTION | 10 +++--- divest-1.2.0/divest/MD5 | 28 ++++++++----------- divest-1.2.0/divest/NAMESPACE | 4 ++ divest-1.2.0/divest/NEWS | 16 ++++++++++ divest-1.2.0/divest/R/read.R | 21 ++++++++------ divest-1.2.0/divest/R/zzz.R | 9 ++++++ divest-1.2.0/divest/configure | 20 ++++++------- divest-1.2.0/divest/configure.ac | 4 +- divest-1.2.0/divest/inst/tinytest/test-05-read.R | 7 ---- divest-1.2.0/divest/man/readDicom.Rd | 5 ++- divest-1.2.0/divest/man/reexports.Rd |only divest-1.2.0/divest/src/dcm2niix/nii_dicom_batch.cpp | 2 - divest-1.2.0/divest/src/main.cpp | 2 - 18 files changed, 76 insertions(+), 52 deletions(-)
Title: Data Quality in Epidemiological Research
Description: Data quality assessments guided by a
'data quality framework introduced by Schmidt and colleagues, 2021'
<doi:10.1186/s12874-021-01252-7> target the
data quality dimensions integrity, completeness, consistency, and
accuracy. The scope of applicable functions rests on the
availability of extensive metadata which can be provided in
spreadsheet tables. Either standardized (e.g. as 'html5' reports) or
individually tailored reports can be generated. For an introduction
into the specification of corresponding metadata, please refer to the
'package website'
<https://dataquality.qihs.uni-greifswald.de/VIN_Annotation_of_Metadata.html>.
Author: University Medicine Greifswald [cph],
Elisa Kasbohm [aut] ,
Elena Salogni [aut] ,
Joany Marino [aut] ,
Adrian Richter [aut] ,
Carsten Oliver Schmidt [aut] ,
Stephan Struckmann [aut, cre] ,
German Research Foundation [fnd],
National Research Data Inf [...truncated...]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 2.5.0 dated 2025-02-20 and 2.5.1 dated 2025-03-05
DESCRIPTION | 18 MD5 | 280 +-- NEWS.md | 25 R/000_options.R | 24 R/acc_loess.R | 34 R/acc_margins.R | 8 R/acc_varcomp.R | 26 R/dq_report_by.R | 31 R/prep_check_for_dataquieR_updates.R | 1 R/summary.dataquieR_resultset2.R | 149 + R/util_acc_loess_bin.R | 64 R/util_acc_loess_continuous.R | 44 R/util_acc_varcomp.R | 16 R/util_compress_ggplots_in_res.R | 2 R/util_condition_constructor_factory.R | 9 R/util_eval_to_dataquieR_result.R | 3 R/util_evaluate_calls.R | 4 R/util_generate_pages_from_report.R | 2 R/util_generate_table_indicators_descriptors.R | 26 R/util_get_rule_sets.R | 13 R/util_interpret_limits.R | 2 R/util_margins_bin.R | 83 - R/util_margins_lm.R | 42 R/util_margins_nom.R | 19 R/util_margins_ord.R | 6 R/util_margins_poi.R | 39 R/util_view_file.R | 20 R/zzz_globs.R | 2 build/vignette.rds |binary inst/grading_rulesets.xlsx |binary inst/hovertext.rds |binary inst/menu/script.js | 3 inst/templates/default/grading_ruleset_text.html | 4 inst/templates/default/ruleset_formats_text.html | 4 man/acc_loess.Rd | 14 man/acc_varcomp.Rd | 3 man/dataquieR.CONDITIONS_LEVEL_TRHESHOLD.Rd | 2 man/dataquieR.CONDITIONS_WITH_STACKTRACE.Rd | 2 man/dataquieR.ELEMENT_MISSMATCH_CHECKTYPE.Rd | 2 man/dataquieR.ERRORS_WITH_CALLER.Rd | 2 man/dataquieR.GAM_for_LOESS.Rd | 2 man/dataquieR.MAX_LABEL_LEN.Rd | 2 man/dataquieR.MAX_VALUE_LABEL_LEN.Rd | 2 man/dataquieR.MESSAGES_WITH_CALLER.Rd | 2 man/dataquieR.MULTIVARIATE_OUTLIER_CHECK.Rd | 2 man/dataquieR.Rd | 6 man/dataquieR.VALUE_LABELS_htmlescaped.Rd | 2 man/dataquieR.WARNINGS_WITH_CALLER.Rd | 2 man/dataquieR.acc_loess.exclude_constant_subgroups.Rd | 2 man/dataquieR.acc_loess.mark_time_points.Rd | 2 man/dataquieR.acc_loess.min_bw.Rd |only man/dataquieR.acc_loess.min_proportion.Rd |only man/dataquieR.acc_loess.plot_format.Rd | 2 man/dataquieR.acc_loess.plot_observations.Rd | 2 man/dataquieR.acc_margins_num.Rd | 2 man/dataquieR.acc_margins_sort.Rd | 2 man/dataquieR.acc_multivariate_outlier.scale.Rd | 2 man/dataquieR.col_con_con_empirical.Rd | 2 man/dataquieR.col_con_con_logical.Rd | 2 man/dataquieR.debug.Rd | 2 man/dataquieR.des_summary_hard_lim_remove.Rd | 2 man/dataquieR.dontwrapresults.Rd | 2 man/dataquieR.fix_column_type_on_read.Rd | 2 man/dataquieR.flip_mode.Rd | 2 man/dataquieR.force_item_specific_missing_codes.Rd | 2 man/dataquieR.force_label_col.Rd | 2 man/dataquieR.grading_formats.Rd | 2 man/dataquieR.grading_rulesets.Rd | 2 man/dataquieR.guess_missing_codes.Rd | 2 man/dataquieR.lang.Rd | 2 man/dataquieR.max_group_var_levels_in_plot.Rd | 2 man/dataquieR.max_group_var_levels_with_violins.Rd | 2 man/dataquieR.min_obs_per_group_var_in_plot.Rd | 2 man/dataquieR.non_disclosure.Rd | 2 man/dataquieR.progress_fkt.Rd | 2 man/dataquieR.progress_msg_fkt.Rd | 2 man/dataquieR.scale_level_heuristics_control_binaryrecodelimit.Rd | 2 man/dataquieR.scale_level_heuristics_control_metriclevels.Rd | 2 man/dataquieR.testdebug.Rd | 2 man/util_acc_loess_bin.Rd | 14 man/util_acc_loess_continuous.Rd | 8 man/util_acc_varcomp.Rd | 4 man/util_generate_table_indicators_descriptors.Rd | 4 man/util_margins_bin.Rd | 8 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-both-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-combined-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-ok.svg | 47 tests/testthat/_snaps/R4.3/acc_loess/loess-combined-plot-for-crp-0-with-covars-ok.svg | 39 tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-both-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-facets-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-ok.svg | 175 +- tests/testthat/_snaps/R4.3/acc_loess/loess-facets-plot-for-crp-0-with-covars-ok.svg | 139 - 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Title: Extending Lasso Model Fitting to Big Data
Description: Extend lasso and elastic-net model fitting for large data sets that
cannot be loaded into memory. Designed to be more memory- and
computation-efficient than existing lasso-fitting packages like 'glmnet' and
'ncvreg', thus allowing the user to analyze big data with limited RAM
<doi:10.32614/RJ-2021-001>.
Author: Yaohui Zeng [aut],
Chuyi Wang [aut],
Tabitha Peter [aut],
Patrick Breheny [aut, cre]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between biglasso versions 1.6.0 dated 2024-04-21 and 1.6.1 dated 2025-03-05
DESCRIPTION | 37 +++++++++--------- MD5 | 39 +++++++++++-------- NAMESPACE | 3 - NEWS.md | 9 ++++ R/biglasso-package.R | 34 ++++++++++++----- R/biglasso.R | 18 ++++++--- R/cv-biglasso.R | 7 --- R/predict.R | 7 ++- R/setupX.R | 2 - README.md |only build/partial.rdb |only build/vignette.rds |binary inst/doc/biglasso.html | 24 ++++++------ inst/tinytest |only man/biglasso-package.Rd | 32 +++++++++++----- man/biglasso.Rd | 6 +++ man/setupX.Rd | 2 - src/binomial.cpp | 9 ---- src/init.c | 6 ++- src/utilities.cpp | 95 +++++++++++++----------------------------------- tests |only 21 files changed, 168 insertions(+), 162 deletions(-)
Title: Species Distribution Models with Tidymodels
Description: Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.
Author: Michela Leonardi [aut],
Margherita Colucci [aut],
Andrea Vittorio Pozzi [aut],
Eleanor M.L. Scerri [aut],
Ben Tupper [ctb],
Andrea Manica [aut, cre]
Maintainer: Andrea Manica <am315@cam.ac.uk>
Diff between tidysdm versions 0.9.5 dated 2024-06-23 and 1.0.0 dated 2025-03-05
tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_future_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_present_10m.nc |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_climate_sf.RDS |only tidysdm-0.9.5/tidysdm/inst/extdata/lacerta_land_mask.nc |only tidysdm-0.9.5/tidysdm/inst/notes |only tidysdm-1.0.0/tidysdm/DESCRIPTION | 34 tidysdm-1.0.0/tidysdm/MD5 | 349 - tidysdm-1.0.0/tidysdm/NAMESPACE | 6 tidysdm-1.0.0/tidysdm/NEWS.md | 20 tidysdm-1.0.0/tidysdm/R/add_member.R | 37 tidysdm-1.0.0/tidysdm/R/add_repeat.R | 18 tidysdm-1.0.0/tidysdm/R/autoplot_simple_ensemble.R | 11 tidysdm-1.0.0/tidysdm/R/autoplot_spatial_initial_split.R | 5 tidysdm-1.0.0/tidysdm/R/blockcv2rsample.R | 42 tidysdm-1.0.0/tidysdm/R/boyce_cont.R | 103 tidysdm-1.0.0/tidysdm/R/calib_class_thresh.R | 63 tidysdm-1.0.0/tidysdm/R/check_coords_names.R | 5 tidysdm-1.0.0/tidysdm/R/check_sdm_presence.R | 15 tidysdm-1.0.0/tidysdm/R/check_split_balance.R | 77 tidysdm-1.0.0/tidysdm/R/clamp_predictors.R | 88 tidysdm-1.0.0/tidysdm/R/collect_metrics.R | 10 tidysdm-1.0.0/tidysdm/R/confusion_matrix_df.R | 3 tidysdm-1.0.0/tidysdm/R/datasets_docs.R | 5 tidysdm-1.0.0/tidysdm/R/dist_pres_vs_bg.R | 20 tidysdm-1.0.0/tidysdm/R/explain_tidysdm.R | 74 tidysdm-1.0.0/tidysdm/R/extrapol_mess.R | 301 - tidysdm-1.0.0/tidysdm/R/filter_caret.R | 83 tidysdm-1.0.0/tidysdm/R/filter_collinear.R | 273 - tidysdm-1.0.0/tidysdm/R/filter_high_cor.R | 61 tidysdm-1.0.0/tidysdm/R/filter_vif.R | 82 tidysdm-1.0.0/tidysdm/R/gam_formula.R | 10 tidysdm-1.0.0/tidysdm/R/geom_split_violin.R | 46 tidysdm-1.0.0/tidysdm/R/grid_cellsize.R | 22 tidysdm-1.0.0/tidysdm/R/grid_offset.R | 15 tidysdm-1.0.0/tidysdm/R/kap_max.R | 86 tidysdm-1.0.0/tidysdm/R/make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/R/make_maxent.R | 17 tidysdm-1.0.0/tidysdm/R/maxent.R | 28 tidysdm-1.0.0/tidysdm/R/maxent_params.R | 15 tidysdm-1.0.0/tidysdm/R/maxnet_fit.R | 28 tidysdm-1.0.0/tidysdm/R/niche_overlap.R | 60 tidysdm-1.0.0/tidysdm/R/optim_thresh.R | 54 tidysdm-1.0.0/tidysdm/R/out_of_range_warning.R | 50 tidysdm-1.0.0/tidysdm/R/pairs.R |only tidysdm-1.0.0/tidysdm/R/plot_pres_vs_bg.R | 18 tidysdm-1.0.0/tidysdm/R/predict_raster.R | 42 tidysdm-1.0.0/tidysdm/R/predict_repeat_ensemble.R | 37 tidysdm-1.0.0/tidysdm/R/predict_simple_ensemble.R | 151 tidysdm-1.0.0/tidysdm/R/prob_metrics.R | 24 tidysdm-1.0.0/tidysdm/R/recipe_sf.R | 46 tidysdm-1.0.0/tidysdm/R/recipes_sf_methods.R | 54 tidysdm-1.0.0/tidysdm/R/repeat_ensemble.R | 8 tidysdm-1.0.0/tidysdm/R/sample_background.R | 92 tidysdm-1.0.0/tidysdm/R/sample_background_time.R | 180 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs.R | 107 tidysdm-1.0.0/tidysdm/R/sample_pseudoabs_time.R | 147 tidysdm-1.0.0/tidysdm/R/sdm_spec_boost_tree.R | 52 tidysdm-1.0.0/tidysdm/R/sdm_spec_gam.R | 26 tidysdm-1.0.0/tidysdm/R/sdm_spec_glm.R | 15 tidysdm-1.0.0/tidysdm/R/sdm_spec_maxent.R | 24 tidysdm-1.0.0/tidysdm/R/sdm_spec_rand_forest.R | 13 tidysdm-1.0.0/tidysdm/R/simple_ensemble.R | 16 tidysdm-1.0.0/tidysdm/R/spatial_initial_split.R | 29 tidysdm-1.0.0/tidysdm/R/thin_by_cell.R | 68 tidysdm-1.0.0/tidysdm/R/thin_by_cell_time.R | 75 tidysdm-1.0.0/tidysdm/R/thin_by_dist.R | 51 tidysdm-1.0.0/tidysdm/R/thin_by_dist_time.R | 68 tidysdm-1.0.0/tidysdm/R/tidysdm-package.R | 3 tidysdm-1.0.0/tidysdm/R/tss.R | 50 tidysdm-1.0.0/tidysdm/R/tss_max.R | 63 tidysdm-1.0.0/tidysdm/R/zzz.R | 10 tidysdm-1.0.0/tidysdm/README.md | 62 tidysdm-1.0.0/tidysdm/build/partial.rdb |binary tidysdm-1.0.0/tidysdm/build/vignette.rds |binary tidysdm-1.0.0/tidysdm/data/horses.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_ensemble.rda |binary tidysdm-1.0.0/tidysdm/data/lacerta_rep_ens.rda |binary tidysdm-1.0.0/tidysdm/data/lacertidae_background.rda |binary tidysdm-1.0.0/tidysdm/inst/WORDLIST | 10 tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.R | 402 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/inst/doc/a0_tidysdm_overview.html | 2337 ++-------- tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.R | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/inst/doc/a1_palaeodata_application.html | 26 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.R | 136 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/inst/doc/a2_tidymodels_additions.html | 649 +- tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.R | 19 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.Rmd | 15 tidysdm-1.0.0/tidysdm/inst/doc/a3_troubleshooting.html | 149 tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_future_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_climate_present_10m.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_land_mask.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin.rds |only tidysdm-1.0.0/tidysdm/inst/extdata/lacerta_thin_all_vars.rds |only tidysdm-1.0.0/tidysdm/man/autoplot.simple_ensemble.Rd | 2 tidysdm-1.0.0/tidysdm/man/blockcv2rsample.Rd | 8 tidysdm-1.0.0/tidysdm/man/boyce_cont.Rd | 67 tidysdm-1.0.0/tidysdm/man/calib_class_thresh.Rd | 19 tidysdm-1.0.0/tidysdm/man/check_sdm_presence.Rd | 7 tidysdm-1.0.0/tidysdm/man/check_splits_balance.Rd | 12 tidysdm-1.0.0/tidysdm/man/clamp_predictors.Rd | 25 tidysdm-1.0.0/tidysdm/man/collect_metrics.simple_ensemble.Rd | 9 tidysdm-1.0.0/tidysdm/man/conf_matrix_df.Rd | 3 tidysdm-1.0.0/tidysdm/man/dist_pres_vs_bg.Rd | 13 tidysdm-1.0.0/tidysdm/man/explain_tidysdm.Rd | 16 tidysdm-1.0.0/tidysdm/man/extrapol_mess.Rd | 30 tidysdm-1.0.0/tidysdm/man/filter_collinear.Rd | 87 tidysdm-1.0.0/tidysdm/man/filter_high_cor.Rd | 44 tidysdm-1.0.0/tidysdm/man/form_resp.Rd | 3 tidysdm-1.0.0/tidysdm/man/geom_split_violin.Rd | 31 tidysdm-1.0.0/tidysdm/man/grid_cellsize.Rd | 15 tidysdm-1.0.0/tidysdm/man/grid_offset.Rd | 15 tidysdm-1.0.0/tidysdm/man/kap_max.Rd | 73 tidysdm-1.0.0/tidysdm/man/lacertidae_background.Rd | 5 tidysdm-1.0.0/tidysdm/man/make_mask_from_presence.Rd |only tidysdm-1.0.0/tidysdm/man/maxent.Rd | 24 tidysdm-1.0.0/tidysdm/man/maxent_params.Rd | 11 tidysdm-1.0.0/tidysdm/man/maxnet_fit.Rd | 20 tidysdm-1.0.0/tidysdm/man/niche_overlap.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh.Rd | 16 tidysdm-1.0.0/tidysdm/man/optim_thresh_kap_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_sens.Rd | 4 tidysdm-1.0.0/tidysdm/man/optim_thresh_tss_max.Rd | 4 tidysdm-1.0.0/tidysdm/man/pairs-stars.Rd |only tidysdm-1.0.0/tidysdm/man/plot_pres_vs_bg.Rd | 7 tidysdm-1.0.0/tidysdm/man/predict.repeat_ensemble.Rd | 37 tidysdm-1.0.0/tidysdm/man/predict.simple_ensemble.Rd | 41 tidysdm-1.0.0/tidysdm/man/predict_raster.Rd | 14 tidysdm-1.0.0/tidysdm/man/prob_metrics_sf.Rd | 22 tidysdm-1.0.0/tidysdm/man/recipe.sf.Rd | 34 tidysdm-1.0.0/tidysdm/man/repeat_ensemble.Rd | 4 tidysdm-1.0.0/tidysdm/man/sample_background.Rd | 43 tidysdm-1.0.0/tidysdm/man/sample_background_time.Rd | 86 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs.Rd | 47 tidysdm-1.0.0/tidysdm/man/sample_pseudoabs_time.Rd | 79 tidysdm-1.0.0/tidysdm/man/sdm_spec_boost_tree.Rd | 18 tidysdm-1.0.0/tidysdm/man/sdm_spec_gam.Rd | 27 tidysdm-1.0.0/tidysdm/man/sdm_spec_glm.Rd | 13 tidysdm-1.0.0/tidysdm/man/sdm_spec_maxent.Rd | 14 tidysdm-1.0.0/tidysdm/man/simple_ensemble.Rd | 10 tidysdm-1.0.0/tidysdm/man/spatial_initial_split.Rd | 15 tidysdm-1.0.0/tidysdm/man/thin_by_cell.Rd | 38 tidysdm-1.0.0/tidysdm/man/thin_by_cell_time.Rd | 61 tidysdm-1.0.0/tidysdm/man/thin_by_dist.Rd | 35 tidysdm-1.0.0/tidysdm/man/thin_by_dist_time.Rd | 47 tidysdm-1.0.0/tidysdm/man/tidysdm-package.Rd | 8 tidysdm-1.0.0/tidysdm/man/tss.Rd | 58 tidysdm-1.0.0/tidysdm/man/tss_max.Rd | 63 tidysdm-1.0.0/tidysdm/tests/spelling.R | 9 tidysdm-1.0.0/tidysdm/tests/testthat/Rplots.pdf |only tidysdm-1.0.0/tidysdm/tests/testthat/test_blockcv2rsample.R | 104 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_sdm_presence.R | 6 tidysdm-1.0.0/tidysdm/tests/testthat/test_check_split_balance.R | 39 tidysdm-1.0.0/tidysdm/tests/testthat/test_clamp_predictors.R | 181 tidysdm-1.0.0/tidysdm/tests/testthat/test_dist_pres_vs_bg.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_explain_tidysdm.R | 105 tidysdm-1.0.0/tidysdm/tests/testthat/test_extrapol_mess.R | 117 tidysdm-1.0.0/tidysdm/tests/testthat/test_filter_collinear.R | 109 tidysdm-1.0.0/tidysdm/tests/testthat/test_initial_spatial_split.R | 56 tidysdm-1.0.0/tidysdm/tests/testthat/test_make_mask_from_presence.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_maxnet_fit.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_out_of_range_warning.R | 26 tidysdm-1.0.0/tidysdm/tests/testthat/test_overlap_niche.R | 33 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_repeat_ensemble.R | 49 tidysdm-1.0.0/tidysdm/tests/testthat/test_predict_simple_ensemble.R | 83 tidysdm-1.0.0/tidysdm/tests/testthat/test_prob_metrics_sf.R | 28 tidysdm-1.0.0/tidysdm/tests/testthat/test_recipe_sf.R | 48 tidysdm-1.0.0/tidysdm/tests/testthat/test_repeat_ensemble.R | 16 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background.R | 82 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_background_time.R | 239 - tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs.R | 85 tidysdm-1.0.0/tidysdm/tests/testthat/test_sample_pseudoabs_time.R | 245 - tidysdm-1.0.0/tidysdm/tests/testthat/test_simple_ensemble.R | 37 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell.R |only tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_cell_time.R | 21 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist.R | 35 tidysdm-1.0.0/tidysdm/tests/testthat/test_thin_by_dist_time.R | 48 tidysdm-1.0.0/tidysdm/vignettes/a0_tidysdm_overview.Rmd | 450 + tidysdm-1.0.0/tidysdm/vignettes/a1_palaeodata_application.Rmd | 5 tidysdm-1.0.0/tidysdm/vignettes/a2_tidymodels_additions.Rmd | 154 tidysdm-1.0.0/tidysdm/vignettes/a3_troubleshooting.Rmd | 15 184 files changed, 6935 insertions(+), 5019 deletions(-)
Title: Interlinear Glossed Linguistic Examples and Abbreviation Lists
Generation
Description: Helps to render interlinear glossed linguistic examples in html
'rmarkdown' documents and then semi-automatically compiles the list of
glosses at the end of the document. It also provides a database of linguistic
glosses.
Author: George Moroz [aut, cre]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingglosses versions 0.0.8 dated 2024-09-06 and 0.0.9 dated 2025-03-05
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 7 +++++++ NEWS.md | 7 +++++-- R/gloss_example.R | 44 ++++++++++++++++++++++++++++++++++++++++++-- data/glosses_df.RData |binary man/gloss_example.Rd | 1 + 7 files changed, 66 insertions(+), 15 deletions(-)
Title: Multivariate Markov Chains
Description: Provides routines to estimate the Mixture Transition Distribution Model based on Raftery (1985) <http://www.jstor.org/stable/2345788> and Nicolau (2014) <doi:10.1111/sjos.12087> specifications, for multivariate data. Additionally, provides a function for the estimation of a new model for multivariate non-homogeneous Markov chains. This new specification, Generalized Multivariate Markov Chains (GMMC) was proposed by Carolina Vasconcelos and Bruno Damasio and considers (continuous or discrete) covariates exogenous to the Markov chain.
Author: Carolina Vasconcelos [aut, cre],
Bruno Damasio [aut]
Maintainer: Carolina Vasconcelos <cvasconcelos@novaims.unl.pt>
Diff between GenMarkov versions 0.2.0 dated 2023-12-19 and 0.2.1 dated 2025-03-05
DESCRIPTION | 6 ++-- MD5 | 10 ++++---- R/CalculateInitialValues.R | 12 ++++++++- R/ProbValuesXDependent.R | 55 ++++++++++++++++++++++++++++++++++++++------- R/multi.mtd.R | 7 ++++- build/partial.rdb |binary 6 files changed, 71 insertions(+), 19 deletions(-)
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.1.1 dated 2025-02-06 and 1.1.2 dated 2025-03-05
Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.Rd |only Coxmos-1.1.1/Coxmos/man/plot_LP.multipleObservations.list.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.Rd |only Coxmos-1.1.1/Coxmos/man/plot_pseudobeta_newObservation.list.Rd |only Coxmos-1.1.2/Coxmos/DESCRIPTION | 15 Coxmos-1.1.2/Coxmos/MD5 | 144 Coxmos-1.1.2/Coxmos/NAMESPACE | 233 Coxmos-1.1.2/Coxmos/R/Coxmos_common_functions.R | 249 Coxmos-1.1.2/Coxmos/R/Coxmos_coxEN.R | 44 Coxmos-1.1.2/Coxmos/R/Coxmos_evaluation_functions.R | 28 Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdacox_dynamic.R | 1206 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox.R | 1218 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsdrcox_dynamic.R | 1284 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_isb_splsicox.R | 1220 ++-- Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_mb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_multiblock_functions.R | 1878 +++--- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions.R | 1276 +++- Coxmos-1.1.2/Coxmos/R/Coxmos_plot_functions_others.R | 16 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdacox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox.R | 1620 ++--- Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsdrcox_dynamic.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_sb_splsicox.R | 50 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdacox_dynamic.R | 52 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox.R | 48 Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_dynamic.R | 2127 +++---- Coxmos-1.1.2/Coxmos/R/Coxmos_splsdrcox_median.R | 2777 +++++----- Coxmos-1.1.2/Coxmos/R/Coxmos_splsicox.R | 64 Coxmos-1.1.2/Coxmos/README.md | 6 Coxmos-1.1.2/Coxmos/build/partial.rdb |binary Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.R | 72 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-MO-pipeline.html | 427 - Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.R | 20 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.Rmd | 30 Coxmos-1.1.2/Coxmos/inst/doc/Coxmos-pipeline.html | 253 Coxmos-1.1.2/Coxmos/man/cv.coxEN.Rd | 18 Coxmos-1.1.2/Coxmos/man/cv.isb.splsdacox.Rd | 356 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsdrcox_penalty.Rd | 390 - Coxmos-1.1.2/Coxmos/man/cv.isb.splsicox.Rd | 12 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdacox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.mb.splsdrcox.Rd | 14 Coxmos-1.1.2/Coxmos/man/cv.sb.splsdacox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox.Rd | 496 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsdrcox_penalty.Rd | 454 - Coxmos-1.1.2/Coxmos/man/cv.sb.splsicox.Rd | 16 Coxmos-1.1.2/Coxmos/man/cv.splsdacox.Rd | 448 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox.Rd | 466 - Coxmos-1.1.2/Coxmos/man/cv.splsdrcox_penalty.Rd | 636 +- Coxmos-1.1.2/Coxmos/man/cv.splsicox.Rd | 30 Coxmos-1.1.2/Coxmos/man/getAutoKM.Rd | 3 Coxmos-1.1.2/Coxmos/man/getAutoKM.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/getTestKM.Rd | 5 Coxmos-1.1.2/Coxmos/man/getTestKM.list.Rd | 3 Coxmos-1.1.2/Coxmos/man/loadingplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/man/loadingplot.fromVector.Coxmos.Rd | 5 Coxmos-1.1.2/Coxmos/man/mb.splsdacox.Rd | 4 Coxmos-1.1.2/Coxmos/man/mb.splsdrcox.Rd | 4 Coxmos-1.1.2/Coxmos/man/plot_evaluation.Rd | 19 Coxmos-1.1.2/Coxmos/man/plot_evaluation.list.Rd | 18 Coxmos-1.1.2/Coxmos/man/plot_events.Rd | 25 Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.Rd |only Coxmos-1.1.2/Coxmos/man/plot_multipleObservations.LP.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.Rd |only Coxmos-1.1.2/Coxmos/man/plot_observation.pseudobeta.list.Rd |only Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.Rd | 31 Coxmos-1.1.2/Coxmos/man/plot_pseudobeta.list.Rd | 36 Coxmos-1.1.2/Coxmos/man/plot_time.list.Rd | 6 Coxmos-1.1.2/Coxmos/man/sb.splsdacox.Rd | 426 - Coxmos-1.1.2/Coxmos/man/sb.splsdrcox.Rd | 420 - Coxmos-1.1.2/Coxmos/man/splsdacox.Rd | 406 - Coxmos-1.1.2/Coxmos/man/splsdrcox.Rd | 428 - Coxmos-1.1.2/Coxmos/man/splsdrcox_penalty.Rd | 4 Coxmos-1.1.2/Coxmos/man/w.starplot.Coxmos.Rd | 10 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-MO-pipeline.Rmd | 87 Coxmos-1.1.2/Coxmos/vignettes/Coxmos-pipeline.Rmd | 30 77 files changed, 11996 insertions(+), 10898 deletions(-)
Title: Local Regression, Likelihood and Density Estimation
Description: Local regression, likelihood and density estimation methods as described in the 1999 book by Loader.
Author: Catherine Loader [aut],
Jiayang Sun [ctb],
Lucent Technologies [cph],
Andy Liaw [cre]
Maintainer: Andy Liaw <andy_liaw@merck.com>
Diff between locfit versions 1.5-9.11 dated 2025-02-03 and 1.5-9.12 dated 2025-03-05
DESCRIPTION | 8 - MD5 | 54 ++++---- src/S_enter.c | 14 ++ src/band.c | 10 - src/cversion.h | 30 ++++ src/dbinom.c | 15 ++ src/dens_int.c | 1 src/density.c | 5 src/design.h | 2 src/ev_kdtre.c | 1 src/ev_trian.c | 14 ++ src/frend.c | 4 src/lf_nbhd.c | 1 src/lffuns.h | 346 +++++++++++++++++++++++++++++++++++++++++++++----------- src/m_eigen.c | 2 src/m_icirc.c | 4 src/m_imont.c | 2 src/m_isimp.c | 7 + src/m_isphr.c | 8 + src/m_jacob.c | 2 src/math.c | 2 src/mutil.h | 22 ++- src/prob.c | 5 src/scb.c | 1 src/scb_iface.c | 2 src/smisc.c | 4 src/tube.h | 33 ++++- src/weight.c | 1 28 files changed, 465 insertions(+), 135 deletions(-)
More information about ApplyPolygenicScore at CRAN
Permanent link
Title: REDCap Metadata Casting and Castellated Data Handling
Description: Casting metadata for REDCap database creation and handling of
castellated data using repeated instruments and longitudinal projects in
'REDCap'. Keeps a focused data export approach, by allowing to only export
required data from the database. Also for casting new REDCap databases based
on datasets from other sources.
Originally forked from the R part of 'REDCapRITS' by Paul Egeler.
See <https://github.com/pegeler/REDCapRITS>.
'REDCap' (Research Electronic Data Capture) is a secure, web-based software
platform designed to support data capture for research studies, providing
1) an intuitive interface for validated data capture; 2) audit trails for
tracking data manipulation and export procedures; 3) automated export
procedures for seamless data downloads to common statistical packages; and
4) procedures for data integration and interoperability with external
sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>;
Harris et al (2019) <doi:10.1016/j.jbi.2019.103208> [...truncated...]
Author: Andreas Gammelgaard Damsbo [aut, cre]
,
Paul Egeler [aut]
Maintainer: Andreas Gammelgaard Damsbo <agdamsbo@clin.au.dk>
Diff between REDCapCAST versions 25.1.1 dated 2025-01-29 and 25.3.1 dated 2025-03-05
DESCRIPTION | 17 +- MD5 | 40 ++-- NAMESPACE | 3 NEWS.md | 10 + R/REDCap_split.r | 5 R/as_factor.R | 21 ++ R/as_logical.R |only R/ds2dd_detailed.R | 49 +++-- R/easy_redcap.R | 39 ++++ R/read_redcap_tables.R | 69 ++++---- README.md | 3 inst/WORDLIST | 2 inst/doc/Database-creation.html | 5 inst/doc/REDCapCAST.html | 335 ++++++++++++++++++++-------------------- inst/doc/Shiny-app.html | 5 man/as_factor.Rd | 11 + man/as_logical.Rd |only man/ds2dd.Rd | 2 man/ds2dd_detailed.Rd | 7 man/easy_redcap.Rd | 16 + man/format_redcap_factor.Rd | 2 man/read_redcap_tables.Rd | 4 22 files changed, 376 insertions(+), 269 deletions(-)
Title: R6-Based ML Learners for 'mlexperiments'
Description: Enhances 'mlexperiments'
<https://CRAN.R-project.org/package=mlexperiments> with additional
machine learning ('ML') learners. The package provides R6-based
learners for the following algorithms: 'glmnet'
<https://CRAN.R-project.org/package=glmnet>, 'ranger'
<https://CRAN.R-project.org/package=ranger>, 'xgboost'
<https://CRAN.R-project.org/package=xgboost>, and 'lightgbm'
<https://CRAN.R-project.org/package=lightgbm>. These can be used
directly with the 'mlexperiments' R package.
Author: Lorenz A. Kapsner [cre, aut, cph]
Maintainer: Lorenz A. Kapsner <lorenz.kapsner@gmail.com>
Diff between mllrnrs versions 0.0.4 dated 2024-07-05 and 0.0.5 dated 2025-03-05
DESCRIPTION | 10 MD5 | 118 +++++----- NAMESPACE | 18 - R/learner_glmnet.R | 24 +- R/learner_xgboost.R | 14 - R/zzz.R | 58 ++--- build/vignette.rds |binary inst/doc/mllrnrs_glmnet_binary.html | 5 inst/doc/mllrnrs_glmnet_binary.qmd | 1 inst/doc/mllrnrs_glmnet_multiclass.R | 29 +- inst/doc/mllrnrs_glmnet_multiclass.html | 68 ++--- inst/doc/mllrnrs_glmnet_multiclass.qmd | 30 +- inst/doc/mllrnrs_glmnet_regression.html | 5 inst/doc/mllrnrs_glmnet_regression.qmd | 1 inst/doc/mllrnrs_lightgbm_binary.html | 5 inst/doc/mllrnrs_lightgbm_binary.qmd | 1 inst/doc/mllrnrs_lightgbm_multiclass.R | 39 +-- inst/doc/mllrnrs_lightgbm_multiclass.html | 78 +++--- inst/doc/mllrnrs_lightgbm_multiclass.qmd | 40 +-- inst/doc/mllrnrs_lightgbm_regression.html | 5 inst/doc/mllrnrs_lightgbm_regression.qmd | 1 inst/doc/mllrnrs_ranger_binary.html | 5 inst/doc/mllrnrs_ranger_binary.qmd | 1 inst/doc/mllrnrs_ranger_multiclass.R | 25 +- inst/doc/mllrnrs_ranger_multiclass.html | 68 ++--- inst/doc/mllrnrs_ranger_multiclass.qmd | 26 +- inst/doc/mllrnrs_ranger_regression.html | 5 inst/doc/mllrnrs_ranger_regression.qmd | 1 inst/doc/mllrnrs_xgboost_binary.html | 5 inst/doc/mllrnrs_xgboost_binary.qmd | 1 inst/doc/mllrnrs_xgboost_multiclass.R | 34 +- inst/doc/mllrnrs_xgboost_multiclass.html | 73 ++---- inst/doc/mllrnrs_xgboost_multiclass.qmd | 35 +-- inst/doc/mllrnrs_xgboost_regression.html | 5 inst/doc/mllrnrs_xgboost_regression.qmd | 1 man/LearnerGlmnet.Rd | 296 ++++++++++++------------- man/LearnerLightgbm.Rd | 342 +++++++++++++++--------------- man/LearnerRanger.Rd | 298 +++++++++++++------------- man/LearnerXgboost.Rd | 342 +++++++++++++++--------------- tests/testthat.R | 27 +- tests/testthat/test-glmnet_binary.R | 288 ++++++++++++------------- tests/testthat/test-glmnet_regression.R | 300 +++++++++++++------------- tests/testthat/test-lightgbm_regression.R | 314 +++++++++++++-------------- tests/testthat/test-lints.R | 26 +- tests/testthat/test-ranger_regression.R | 284 ++++++++++++------------ tests/testthat/test-xgboost_binary.R | 211 ++++++++---------- tests/testthat/test-xgboost_multiclass.R | 15 - tests/testthat/test-xgboost_regression.R | 295 ++++++++++++------------- vignettes/mllrnrs_glmnet_binary.qmd | 1 vignettes/mllrnrs_glmnet_multiclass.qmd | 30 +- vignettes/mllrnrs_glmnet_regression.qmd | 1 vignettes/mllrnrs_lightgbm_binary.qmd | 1 vignettes/mllrnrs_lightgbm_multiclass.qmd | 40 +-- vignettes/mllrnrs_lightgbm_regression.qmd | 1 vignettes/mllrnrs_ranger_binary.qmd | 1 vignettes/mllrnrs_ranger_multiclass.qmd | 26 +- vignettes/mllrnrs_ranger_regression.qmd | 1 vignettes/mllrnrs_xgboost_binary.qmd | 1 vignettes/mllrnrs_xgboost_multiclass.qmd | 35 +-- vignettes/mllrnrs_xgboost_regression.qmd | 1 60 files changed, 1955 insertions(+), 2057 deletions(-)
Title: Helper Functions for Creating Tutorials
Description: Helper functions for creating, editing, and testing tutorials
created with the 'learnr' package. Provides a simple method for allowing
students to download their answers to tutorial questions. For examples
of its use, see the 'r4ds.tutorials' package.
Author: David Kane [aut, cre, cph]
Maintainer: David Kane <dave.kane@gmail.com>
Diff between tutorial.helpers versions 0.3.1 dated 2024-12-07 and 0.4.2 dated 2025-03-05
tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/addins.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/books.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/cloud.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/downloads.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/instructions.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/doc/testing.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/inst/tutorials/getting-started |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_inputs/format_input_2.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_inputs/format_input_3.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_inputs/format_input_4.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_inputs/format_input_5.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_outputs/format_output_2.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_outputs/format_output_3.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_outputs/format_output_4.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/tests/testthat/fixtures/addin_test_outputs/format_output_5.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/addins.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/books.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/cloud.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/downloads.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-code-exercise.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-file.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-graphic.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-hint-1.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-hint-2.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-written-1.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/example-written-2.txt |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/instructions.Rmd |only tutorial.helpers-0.3.1/tutorial.helpers/vignettes/testing.Rmd |only tutorial.helpers-0.4.2/tutorial.helpers/DESCRIPTION | 15 tutorial.helpers-0.4.2/tutorial.helpers/MD5 | 95 - tutorial.helpers-0.4.2/tutorial.helpers/NAMESPACE | 5 tutorial.helpers-0.4.2/tutorial.helpers/NEWS.md | 12 tutorial.helpers-0.4.2/tutorial.helpers/R/check_current_tutorial.R | 2 tutorial.helpers-0.4.2/tutorial.helpers/R/format_tutorial.R | 584 +++++----- tutorial.helpers-0.4.2/tutorial.helpers/R/make_exercise.R | 3 tutorial.helpers-0.4.2/tutorial.helpers/R/set_positron_settings.R |only tutorial.helpers-0.4.2/tutorial.helpers/R/submission_functions.R | 7 tutorial.helpers-0.4.2/tutorial.helpers/R/utils.R |only tutorial.helpers-0.4.2/tutorial.helpers/README.md | 28 tutorial.helpers-0.4.2/tutorial.helpers/build/vignette.rds |binary tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/addins.html | 333 ++--- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/addins.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/books.html | 184 +-- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/books.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/cloud.html | 128 -- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/cloud.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/downloads.html | 248 +--- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/downloads.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/instructions.R | 167 +- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/instructions.html | 578 ++++----- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/instructions.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/testing.html | 122 -- tutorial.helpers-0.4.2/tutorial.helpers/inst/doc/testing.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/inst/tutorials/tutorials-in-positron |only tutorial.helpers-0.4.2/tutorial.helpers/inst/tutorials/tutorials-in-rstudio |only tutorial.helpers-0.4.2/tutorial.helpers/man/ensure_quarto.Rd |only tutorial.helpers-0.4.2/tutorial.helpers/man/format_tutorial.Rd | 37 tutorial.helpers-0.4.2/tutorial.helpers/man/set_positron_settings.Rd |only tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/fixtures/addin_test_inputs/format_input_1.Rmd | 79 + tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/fixtures/addin_test_outputs/format_output_1.Rmd | 108 + tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/test-code-chunks.R | 43 tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/test-format_tutorial.R | 61 - tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/test-knit_tutorials.R | 11 tutorial.helpers-0.4.2/tutorial.helpers/tests/testthat/test-set_positron_settings.R |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/addins.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/books.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/cloud.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/downloads.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/instructions.qmd |only tutorial.helpers-0.4.2/tutorial.helpers/vignettes/testing.qmd |only 70 files changed, 1323 insertions(+), 1527 deletions(-)
More information about tutorial.helpers at CRAN
Permanent link
Title: Expression Data Analysis and Visualization
Description: The Gene Expression Omnibus (<https://www.ncbi.nlm.nih.gov/geo/>) and The Cancer Genome Atlas (<https://portal.gdc.cancer.gov/>) are widely used medical public databases. Our platform integrates routine analysis and visualization tools for expression data to provide concise and intuitive data analysis and presentation.
Author: Xiaojie Sun [aut, cre]
Maintainer: Xiaojie Sun <18763899370@163.com>
Diff between tinyarray versions 2.4.2 dated 2024-06-13 and 2.4.3 dated 2025-03-05
DESCRIPTION | 8 ++-- MD5 | 17 +++++---- NAMESPACE | 2 + NEWS.md | 6 +++ R/2_geo_id.R | 83 +++++++++++++++++++++++++++++++++++++++++++--- R/7_quick_double_enrich.R | 7 ++- R/get_anno.R |only R/start_massage.R | 2 - R/tmp.R |only man/double_enrich.Rd | 4 +- man/geo_parser.Rd |only 11 files changed, 109 insertions(+), 20 deletions(-)
Title: Simple Framework for Simple Automation
Description: Build a project framework for users with
access to only the most basic of automation tools.
Author: Alexander Senetcky [aut, cre, cph]
Maintainer: Alexander Senetcky <asenetcky@gmail.com>
Diff between strata versions 1.4.0 dated 2025-02-03 and 1.4.3 dated 2025-03-05
DESCRIPTION | 6 LICENSE | 4 MD5 | 102 - NAMESPACE | 44 NEWS.md | 8 R/adhoc-core.R | 405 +++---- R/adhoc-utils.R | 154 +- R/build-core.R | 414 +++---- R/build-quick.R | 454 ++++---- R/log-core.R | 172 +-- R/main-core.R | 104 - R/main-utils.R | 502 ++++---- R/strata-package.R | 18 R/survey-core.R | 372 +++--- R/survey-utils.R | 236 ++-- R/toml-core.R | 272 ++-- R/toml-io.R | 274 ++-- R/toml-utils.R | 300 ++--- README.md | 1852 ++++++++++++++++----------------- man/adhoc.Rd | 86 - man/adhoc_lamina.Rd | 72 - man/adhoc_stratum.Rd | 72 - man/build_lamina.Rd | 60 - man/build_outlined_strata_project.Rd | 116 +- man/build_quick_strata_project.Rd | 66 - man/build_stratum.Rd | 54 man/edit_toml.Rd | 146 +- man/figures/lifecycle-deprecated.svg | 42 man/figures/lifecycle-experimental.svg | 42 man/figures/lifecycle-stable.svg | 58 - man/figures/lifecycle-superseded.svg | 42 man/log_error.Rd | 58 - man/log_message.Rd | 74 - man/log_total_time.Rd | 64 - man/main.Rd | 114 +- man/strata-package.Rd | 48 man/survey_log.Rd | 82 - man/survey_strata.Rd | 82 - man/survey_tomls.Rd | 58 - man/view_toml.Rd | 48 tests/testthat.R | 24 tests/testthat/test-adhoc-core.R | 440 +++---- tests/testthat/test-adhoc-utils.R | 154 +- tests/testthat/test-build-core.R | 250 ++-- tests/testthat/test-build-quick.R | 718 ++++++------ tests/testthat/test-log-core.R | 72 - tests/testthat/test-main-core.R | 148 +- tests/testthat/test-main-utils.R | 107 + tests/testthat/test-survey-core.R | 264 ++-- tests/testthat/test-survey-utils.R | 104 - tests/testthat/test-toml-core.R | 368 +++--- tests/testthat/test-toml-utils.R | 200 +-- 52 files changed, 5022 insertions(+), 5004 deletions(-)
Title: A Package for Analyzing Skew Factor Models
Description: Generates Skew Factor Models data and applies Sparse Online Principal Component (SOPC), Incremental Principal Component (IPC), Projected Principal Component (PPC), Perturbation Principal Component (PPC), Stochastic Approximation Principal Component (SAPC), Sparse Principal Component (SPC) and other PC methods to estimate model parameters. It includes capabilities for calculating mean squared error, relative error, and sparsity of the loading matrix.The philosophy of the package is described in Guo G. (2023) <doi:10.1007/s00180-022-01270-z>.
Author: Guangbao Guo [aut, cre],
Yu Jin [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between SFM versions 0.1.0 dated 2024-11-12 and 0.2.0 dated 2025-03-05
SFM-0.1.0/SFM/R/SOPC_estimation.R |only SFM-0.1.0/SFM/R/huber.reg.adaptive.skew.R |only SFM-0.1.0/SFM/man/SOPC_estimation.Rd |only SFM-0.1.0/SFM/man/huber.reg.adaptive.skew.Rd |only SFM-0.2.0/SFM/DESCRIPTION | 12 ++++----- SFM-0.2.0/SFM/MD5 | 36 ++++++++++++++++++++------- SFM-0.2.0/SFM/NAMESPACE | 26 ++++++++++++------- SFM-0.2.0/SFM/R/FanPC.SFM.R |only SFM-0.2.0/SFM/R/GulPC.SFM.R |only SFM-0.2.0/SFM/R/IPC.SFM.R |only SFM-0.2.0/SFM/R/OPC.SFM.R |only SFM-0.2.0/SFM/R/PC1.SFM.R |only SFM-0.2.0/SFM/R/PC2.SFM.R |only SFM-0.2.0/SFM/R/PPC1.SFM.R |only SFM-0.2.0/SFM/R/PPC2.SFM.R |only SFM-0.2.0/SFM/R/SAPC.SFM.R |only SFM-0.2.0/SFM/R/SFM.R | 4 ++- SFM-0.2.0/SFM/R/SOPC.SFM.R |only SFM-0.2.0/SFM/R/SPC.SFM.R |only SFM-0.2.0/SFM/R/calculate_errors.R | 4 +-- SFM-0.2.0/SFM/man/FanPC.SFM.Rd |only SFM-0.2.0/SFM/man/GulPC.SFM.Rd |only SFM-0.2.0/SFM/man/IPC.SFM.Rd |only SFM-0.2.0/SFM/man/OPC.SFM.Rd |only SFM-0.2.0/SFM/man/PC1.SFM.Rd |only SFM-0.2.0/SFM/man/PC2.SFM.Rd |only SFM-0.2.0/SFM/man/PPC1.SFM.Rd |only SFM-0.2.0/SFM/man/PPC2.SFM.Rd |only SFM-0.2.0/SFM/man/SAPC.SFM.Rd |only SFM-0.2.0/SFM/man/SFM.Rd | 1 SFM-0.2.0/SFM/man/SOPC.SFM.Rd |only SFM-0.2.0/SFM/man/SPC.SFM.Rd |only 32 files changed, 55 insertions(+), 28 deletions(-)
Title: Identify Characteristics of Patients in the OMOP Common Data
Model
Description: Identify the characteristics of patients in data mapped to the Observational Medical Outcomes Partnership (OMOP) common data model.
Author: Marti Catala [aut, cre] ,
Yuchen Guo [aut] ,
Mike Du [aut] ,
Kim Lopez-Guell [aut] ,
Edward Burn [aut] ,
Nuria Mercade-Besora [aut] ,
Xintong Li [ctb] ,
Xihang Chen [ctb]
Maintainer: Marti Catala <marti.catalasabate@ndorms.ox.ac.uk>
Diff between PatientProfiles versions 1.3.0 dated 2025-02-26 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 MD5 | 26 +-- NEWS.md | 6 R/addCategories.R | 305 +++++++++++++++++++----------------- R/checks.R | 62 ------- R/filterCohortId.R | 1 R/summariseResult.R | 4 inst/doc/cohort-intersect.html | 64 +++---- inst/doc/concept-intersect.html | 94 +++++------ inst/doc/demographics.html | 220 ++++++++++++------------- inst/doc/summarise.html | 196 +++++++++++------------ inst/doc/table-intersect.html | 86 +++++----- man/addCategories.Rd | 6 tests/testthat/test-addCategories.R | 6 14 files changed, 529 insertions(+), 553 deletions(-)
More information about PatientProfiles at CRAN
Permanent link
Title: Extra Functionality for 'leaflet' Package
Description: Several 'leaflet' plugins are integrated, which are available as extension to the 'leaflet' package.
Author: Gatscha Sebastian [aut, cre],
Ricardo Rodrigo Basa [ctb],
Jeffrey O Hanson [ctb]
Maintainer: Gatscha Sebastian <sebastian_gatscha@gmx.at>
Diff between leaflet.extras2 versions 1.3.0 dated 2025-01-12 and 1.3.1 dated 2025-03-05
DESCRIPTION | 6 - MD5 | 10 +-- NEWS.md | 115 ++++++++++++++++++------------------ R/clusterCharts.R | 3 inst/examples/sidebar_app.R | 10 ++- tests/testthat/test-clustercharts.R | 2 6 files changed, 78 insertions(+), 68 deletions(-)
More information about leaflet.extras2 at CRAN
Permanent link
Title: Easily Create and Style Tables for LaTeX, HTML and Other Formats
Description: Creates styled tables for data presentation. Export to HTML, LaTeX,
RTF, 'Word', 'Excel', and 'PowerPoint'. Simple, modern interface to manipulate
borders, size, position, captions, colours, text styles and number formatting.
Table cells can span multiple rows and/or columns.
Includes a 'huxreg' function for creation of regression tables, and 'quick_*'
one-liners to print data to a new document.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 5.5.7 dated 2024-10-01 and 5.6.0 dated 2025-03-05
huxtable-5.5.7/huxtable/tests/testthat/404.html |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.aux |only huxtable-5.5.7/huxtable/tests/testthat/quarto-test.log |only huxtable-5.6.0/huxtable/DESCRIPTION | 6 huxtable-5.6.0/huxtable/MD5 | 54 huxtable-5.6.0/huxtable/NEWS.md | 15 huxtable-5.6.0/huxtable/R/Workbook.R | 5 huxtable-5.6.0/huxtable/R/dplyr.R | 60 - huxtable-5.6.0/huxtable/R/latex-dependencies.R | 11 huxtable-5.6.0/huxtable/R/zzz.R | 10 huxtable-5.6.0/huxtable/README.md | 68 - huxtable-5.6.0/huxtable/build/vignette.rds |binary huxtable-5.6.0/huxtable/inst/doc/design-principles-html.html | 10 huxtable-5.6.0/huxtable/inst/doc/design-principles-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxreg-html.html | 19 huxtable-5.6.0/huxtable/inst/doc/huxreg-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/huxtable-html.html | 46 huxtable-5.6.0/huxtable/inst/doc/huxtable-pdf.pdf |binary huxtable-5.6.0/huxtable/inst/doc/themes-html.html | 6 huxtable-5.6.0/huxtable/man/as_Workbook.Rd | 3 huxtable-5.6.0/huxtable/man/huxtable-news.Rd | 21 huxtable-5.6.0/huxtable/tests/testthat/filecec5332acc3.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec53854bfe2.log |only huxtable-5.6.0/huxtable/tests/testthat/filecec567db13c6.log |only huxtable-5.6.0/huxtable/tests/testthat/multirow.rds |binary huxtable-5.6.0/huxtable/tests/testthat/quarto-test-tex-labels-out.pdf |binary huxtable-5.6.0/huxtable/tests/testthat/table-tester-2.log | 550 +++++----- huxtable-5.6.0/huxtable/tests/testthat/test-dplyr.R | 11 huxtable-5.6.0/huxtable/tests/testthat/test-latex-dependencies.R | 42 huxtable-5.6.0/huxtable/tests/testthat/test-openxlsx.R | 8 huxtable-5.6.0/huxtable/tests/testthat/test-print.R | 11 31 files changed, 488 insertions(+), 468 deletions(-)
Title: Bootstrap p-Values
Description: Computation of bootstrap p-values through inversion of confidence intervals, including convenience functions for regression models and tests of location.
Author: Mans Thulin [aut, cre]
Maintainer: Mans Thulin <mans@statistikkonsult.com>
Diff between boot.pval versions 0.6 dated 2025-01-14 and 0.7.0 dated 2025-03-05
boot.pval-0.6/boot.pval/man/figures/bootpval_hex.png |only boot.pval-0.7.0/boot.pval/DESCRIPTION | 12 boot.pval-0.7.0/boot.pval/MD5 | 41 +- boot.pval-0.7.0/boot.pval/NAMESPACE | 10 boot.pval-0.7.0/boot.pval/NEWS.md | 3 boot.pval-0.7.0/boot.pval/R/boot.pval.R | 28 + boot.pval-0.7.0/boot.pval/R/boot_summary.R | 4 boot.pval-0.7.0/boot.pval/R/boot_test.R |only boot.pval-0.7.0/boot.pval/R/censboot_summary.R | 6 boot.pval-0.7.0/boot.pval/README.md | 113 ++++++ boot.pval-0.7.0/boot.pval/build/partial.rdb |binary boot.pval-0.7.0/boot.pval/build/vignette.rds |binary boot.pval-0.7.0/boot.pval/inst/doc/boot_summary.R | 10 boot.pval-0.7.0/boot.pval/inst/doc/boot_summary.Rmd | 37 +- boot.pval-0.7.0/boot.pval/inst/doc/boot_summary.html | 308 ++++++++++--------- boot.pval-0.7.0/boot.pval/inst/doc/boot_t_test.R |only boot.pval-0.7.0/boot.pval/inst/doc/boot_t_test.Rmd |only boot.pval-0.7.0/boot.pval/inst/doc/boot_t_test.html |only boot.pval-0.7.0/boot.pval/man/boot.pval.Rd | 15 boot.pval-0.7.0/boot.pval/man/boot_median_test.Rd |only boot.pval-0.7.0/boot.pval/man/boot_summary.Rd | 5 boot.pval-0.7.0/boot.pval/man/boot_t_test.Rd |only boot.pval-0.7.0/boot.pval/man/censboot_summary.Rd | 2 boot.pval-0.7.0/boot.pval/man/figures/logo.png |only boot.pval-0.7.0/boot.pval/vignettes/boot_summary.Rmd | 37 +- boot.pval-0.7.0/boot.pval/vignettes/boot_t_test.Rmd |only 26 files changed, 430 insertions(+), 201 deletions(-)
Title: Create Tests According to QTI 2.1 Standard
Description: Create tests and tasks compliant with the Question & Test Interoperability (QTI) information model version 2.1. Input sources are Rmd/md description files or S4-class objects. Output formats include standalone zip or xml files. Supports the generation of basic task types (single and multiple choice, order, pair association, matching tables, filling gaps and essay) and provides a comprehensive set of attributes for customizing tests.
Author: Andrey Shevandrin [aut, cre, cph]
,
Petr Bondarenko [ctb] ,
Ivonne Ojeda [ctb],
Johannes Titz [aut, cph] ,
Brian Mottershead [cph] ,
Stiftung fuer Innovation in der Hochschullehre [fnd]
Maintainer: Andrey Shevandrin <shevandrin@gmail.com>
Diff between rqti versions 0.3.0 dated 2024-07-19 and 1.0.0 dated 2025-03-05
rqti-0.3.0/rqti/R/api_opal.R |only rqti-0.3.0/rqti/man/auth_opal.Rd |only rqti-0.3.0/rqti/man/get_course_elements.Rd |only rqti-0.3.0/rqti/man/get_course_results.Rd |only rqti-0.3.0/rqti/man/get_resource_url.Rd |only rqti-0.3.0/rqti/man/get_resources.Rd |only rqti-0.3.0/rqti/man/publish_course.Rd |only rqti-0.3.0/rqti/man/update_course_test.Rd |only rqti-0.3.0/rqti/tests/testthat/test-api_opal.R |only rqti-1.0.0/rqti/DESCRIPTION | 24 rqti-1.0.0/rqti/MD5 | 259 rqti-1.0.0/rqti/NAMESPACE | 253 rqti-1.0.0/rqti/NEWS.md | 86 rqti-1.0.0/rqti/R/AssessmentItem.R | 21 rqti-1.0.0/rqti/R/AssessmentSection.R | 49 rqti-1.0.0/rqti/R/AssessmentTest.R | 87 rqti-1.0.0/rqti/R/AssessmentTestOpal.R | 93 rqti-1.0.0/rqti/R/CorrectFeedback.R | 7 rqti-1.0.0/rqti/R/DirectedPair.R | 274 rqti-1.0.0/rqti/R/Entry.R | 7 rqti-1.0.0/rqti/R/Essay.R | 327 rqti-1.0.0/rqti/R/LMS.R |only rqti-1.0.0/rqti/R/ModalFeedback.R | 7 rqti-1.0.0/rqti/R/MultipleChoice.R | 7 rqti-1.0.0/rqti/R/MultipleChoiceTable.R | 345 rqti-1.0.0/rqti/R/OneInColTable.R | 247 rqti-1.0.0/rqti/R/OneInRowTable.R | 247 rqti-1.0.0/rqti/R/Opal.R |only rqti-1.0.0/rqti/R/Ordering.R | 345 rqti-1.0.0/rqti/R/QtiMetadata.R | 70 rqti-1.0.0/rqti/R/SingleChoice.R | 291 rqti-1.0.0/rqti/R/WrongFeedback.R | 7 rqti-1.0.0/rqti/R/character.R | 39 rqti-1.0.0/rqti/R/extract_results.R | 31 rqti-1.0.0/rqti/R/knit_functions.R | 8 rqti-1.0.0/rqti/R/object_builder.R | 25 rqti-1.0.0/rqti/R/qti_task.R | 44 rqti-1.0.0/rqti/R/qti_test.R | 479 rqti-1.0.0/rqti/R/response_processing.R | 20 rqti-1.0.0/rqti/R/rqti_project.R | 3 rqti-1.0.0/rqti/R/section_builder.R | 741 rqti-1.0.0/rqti/inst/QTIJS/index.xml | 315 rqti-1.0.0/rqti/inst/QTIJS/qti.js | 32 rqti-1.0.0/rqti/inst/QTIJS/rqti.js | 2 rqti-1.0.0/rqti/inst/QTIJS/themecc/style.css | 12 rqti-1.0.0/rqti/inst/exercises/metadata_template.Rmd | 38 rqti-1.0.0/rqti/inst/imsqti_v2p1p2.xsd |20968 +++++----- rqti-1.0.0/rqti/inst/qti_v2p1p2_extension.xsd |only rqti-1.0.0/rqti/inst/rmarkdown/templates/directedpair-complex/skeleton/skeleton.Rmd | 6 rqti-1.0.0/rqti/inst/rmarkdown/templates/directedpair-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/directedpair-simple/skeleton/skeleton.Rmd | 3 rqti-1.0.0/rqti/inst/rmarkdown/templates/directedpair-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/dropdown-complex/skeleton/skeleton.Rmd | 10 rqti-1.0.0/rqti/inst/rmarkdown/templates/dropdown-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/dropdown-simple/skeleton/skeleton.Rmd | 9 rqti-1.0.0/rqti/inst/rmarkdown/templates/dropdown-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/essay-complex/skeleton/skeleton.Rmd | 10 rqti-1.0.0/rqti/inst/rmarkdown/templates/essay-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/essay-simple/skeleton/skeleton.Rmd | 8 rqti-1.0.0/rqti/inst/rmarkdown/templates/essay-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/skeleton/skeleton.Rmd | 26 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/gap-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/skeleton/skeleton.Rmd | 3 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/skeleton/skeleton.Rmd | 4 rqti-1.0.0/rqti/inst/rmarkdown/templates/multiplechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/skeleton/skeleton.Rmd | 9 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/skeleton/skeleton.Rmd | 6 rqti-1.0.0/rqti/inst/rmarkdown/templates/order-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/skeleton/skeleton.Rmd | 61 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/singlechoice-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/skeleton/skeleton.Rmd | 14 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-complex/template.yaml | 2 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/skeleton/skeleton.Rmd | 15 rqti-1.0.0/rqti/inst/rmarkdown/templates/table-simple/template.yaml | 2 rqti-1.0.0/rqti/inst/test_results.zip |binary rqti-1.0.0/rqti/man/AssessmentItem-class.Rd | 2 rqti-1.0.0/rqti/man/AssessmentTest-class.Rd | 8 rqti-1.0.0/rqti/man/AssessmentTestOpal-class.Rd | 8 rqti-1.0.0/rqti/man/DirectedPair-class.Rd | 2 rqti-1.0.0/rqti/man/Entry-class.Rd | 2 rqti-1.0.0/rqti/man/Essay-class.Rd | 2 rqti-1.0.0/rqti/man/LMS-class.Rd |only rqti-1.0.0/rqti/man/MatchTable-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/MultipleChoiceTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInColTable-class.Rd | 2 rqti-1.0.0/rqti/man/OneInRowTable-class.Rd | 2 rqti-1.0.0/rqti/man/Opal-class.Rd |only rqti-1.0.0/rqti/man/Ordering-class.Rd | 2 rqti-1.0.0/rqti/man/QtiContributor-class.Rd | 2 rqti-1.0.0/rqti/man/SingleChoice-class.Rd | 2 rqti-1.0.0/rqti/man/assessmentSection.Rd |only rqti-1.0.0/rqti/man/assessmentTest.Rd |only rqti-1.0.0/rqti/man/assessmentTestOpal.Rd |only rqti-1.0.0/rqti/man/authLMS-methods.Rd |only rqti-1.0.0/rqti/man/correctFeedback.Rd | 6 rqti-1.0.0/rqti/man/createQtiTask-methods.Rd | 6 rqti-1.0.0/rqti/man/create_qti_task.Rd | 5 rqti-1.0.0/rqti/man/create_question_object.Rd |only rqti-1.0.0/rqti/man/directedPair.Rd | 11 rqti-1.0.0/rqti/man/essay.Rd | 29 rqti-1.0.0/rqti/man/extract_results.Rd | 11 rqti-1.0.0/rqti/man/getCourseElements-methods.Rd |only rqti-1.0.0/rqti/man/getCourseResult-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourceURL-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResources-methods.Rd |only rqti-1.0.0/rqti/man/getLMSResourcesByName-methods.Rd |only rqti-1.0.0/rqti/man/isUserLoggedIn-methods.Rd |only rqti-1.0.0/rqti/man/modalFeedback.Rd | 6 rqti-1.0.0/rqti/man/multipleChoice.Rd | 6 rqti-1.0.0/rqti/man/multipleChoiceTable.Rd | 8 rqti-1.0.0/rqti/man/oneInColTable.Rd | 8 rqti-1.0.0/rqti/man/oneInRowTable.Rd | 8 rqti-1.0.0/rqti/man/opal.Rd |only rqti-1.0.0/rqti/man/ordering.Rd | 6 rqti-1.0.0/rqti/man/publishCourse-Opal-method.Rd |only rqti-1.0.0/rqti/man/publishCourse-missing-method.Rd |only rqti-1.0.0/rqti/man/publishCourse.Rd |only rqti-1.0.0/rqti/man/qtiContributor.Rd |only rqti-1.0.0/rqti/man/qtiMetadata.Rd |only rqti-1.0.0/rqti/man/qti_contributor.Rd | 6 rqti-1.0.0/rqti/man/qti_metadata.Rd | 2 rqti-1.0.0/rqti/man/singleChoice.Rd | 6 rqti-1.0.0/rqti/man/test.Rd | 12 rqti-1.0.0/rqti/man/test4opal.Rd | 12 rqti-1.0.0/rqti/man/updateCourseElementResource-Opal-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource-missing-method.Rd |only rqti-1.0.0/rqti/man/updateCourseElementResource.Rd |only rqti-1.0.0/rqti/man/upload2LMS-methods.Rd |only rqti-1.0.0/rqti/man/upload2opal.Rd | 18 rqti-1.0.0/rqti/man/verify_qti.Rd |only rqti-1.0.0/rqti/man/wrongFeedback.Rd | 6 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/InlineChoice_sign_more_less.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/NumericGap.xml | 8 rqti-1.0.0/rqti/tests/testthat/file/xml/TextGapOpal.xml | 8 rqti-1.0.0/rqti/tests/testthat/test-api_lms.R |only rqti-1.0.0/rqti/tests/testthat/test-assessment_test.R | 98 rqti-1.0.0/rqti/tests/testthat/test-extract_results.R | 18 rqti-1.0.0/rqti/tests/testthat/test-qti_metadata.R | 8 rqti-1.0.0/rqti/tests/testthat/test-qti_task.R | 2 rqti-1.0.0/rqti/tests/testthat/test-text_gap.R | 835 rqti-1.0.0/rqti/tests/testthat/test-text_inline_choice.R | 524 149 files changed, 14224 insertions(+), 13549 deletions(-)
Title: One-Dimensional Probability Distribution Support for the
'spatstat' Family
Description: Estimation of one-dimensional probability distributions
including kernel density estimation, weighted empirical cumulative
distribution functions, Kaplan-Meier and reduced-sample estimators
for right-censored data, heat kernels, kernel properties,
quantiles and integration.
Author: Adrian Baddeley [aut, cre, cph]
,
Tilman M. Davies [aut, ctb, cph]
,
Martin L. Hazelton [aut, ctb, cph]
,
Ege Rubak [aut, cph] ,
Rolf Turner [aut, cph] ,
Greg McSwiggan [ctb, cph]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.univar versions 3.1-1 dated 2024-11-04 and 3.1-2 dated 2025-03-05
DESCRIPTION | 10 +- MD5 | 14 +-- NEWS | 8 + R/adaptive.R | 6 + inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/densityBC.Rd | 181 +++++++++++++++++++++++++++++++++++++-------- man/macros/newdefns.Rd | 4 8 files changed, 179 insertions(+), 46 deletions(-)
More information about spatstat.univar at CRAN
Permanent link
Title: Hierarchical Bayesian Aldrich-McKelvey Scaling via 'Stan'
Description: Perform hierarchical Bayesian Aldrich-McKelvey scaling using Hamiltonian Monte
Carlo via 'Stan'. Aldrich-McKelvey ('AM') scaling is a method for estimating the ideological
positions of survey respondents and political actors on a common scale using positional survey
data. The hierarchical versions of the Bayesian 'AM' model included in this package outperform
other versions both in terms of yielding meaningful posterior distributions for respondent
positions and in terms of recovering true respondent positions in simulations. The package
contains functions for preparing data, fitting models, extracting estimates, plotting key
results, and comparing models using cross-validation. The original version of the default
model is described in Bølstad (2024) <doi:10.1017/pan.2023.18>.
Author: Joergen Boelstad [aut, cre]
Maintainer: Joergen Boelstad <jorgen.bolstad@stv.uio.no>
Diff between hbamr versions 2.4.1 dated 2025-02-13 and 2.4.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 10 R/hbam.R | 8 R/inits.R | 2 R/prep_data.R | 6 inst/doc/hbamr.R | 3 inst/doc/hbamr.Rmd | 12 inst/doc/hbamr.html | 91 ++--- inst/stan/omni.stan | 27 - man/hbam.Rd | 5 src/stanExports_omni.h | 835 ++++++++++++++++++++++++------------------------- vignettes/hbamr.Rmd | 12 13 files changed, 521 insertions(+), 520 deletions(-)
Title: Two Highly Customizable 'rmarkdown' Themes for Scientific
Reports
Description: Offers 'markdown' output formats designed with various styles, allowing users to generate HTML reports tailored for scientific or machine learning showcase. The output has a contemporary appearance with vibrant visuals, providing numerous styles for effective highlighting. Created using the 'tufte' <https://rstudio.github.io/tufte/> package code as a starting point.
Author: Obinna Obianom [aut, cre]
Maintainer: Obinna Obianom <idonshayo@gmail.com>
Diff between scientific versions 2025.0 dated 2025-02-02 and 2025.1 dated 2025-03-05
DESCRIPTION | 6 +-- MD5 | 20 ++++++----- NEWS.md | 13 +++++-- R/base_func.R | 4 -- R/markdown.R | 11 +++++- README.md | 2 + inst/doc/Introduction.html | 6 +-- inst/rmarkdown/templates/html/layout/template1.tpl2 |only inst/rmarkdown/templates/html/layout/template2.tpl | 36 +------------------- inst/rmarkdown/templates/html/layout/template2.tpl2 |only inst/rmarkdown/templates/html/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/html/template.yaml | 2 - 12 files changed, 43 insertions(+), 59 deletions(-)
Title: Signal and Image Processing Toolbox for Analyzing Intracranial
Electroencephalography Data
Description: Implemented fast and memory-efficient Notch-filter,
Welch-periodogram, discrete wavelet spectrogram for minutes of
high-resolution signals, fast 3D convolution, image registration,
3D mesh manipulation; providing fundamental toolbox for intracranial
Electroencephalography (iEEG) pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://rave.wiki>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre],
John Magnotti [aut],
Michael Beauchamp [aut],
Trustees of the University of Pennsylvania [cph] ,
Karim Rahim [cph, ctb] ,
Thomas Possidente [cph, ctb] ,
Michael Prerau [cph, ctb] ,
Marcus Geelnard [ctb, cph] ,
Stefan Schlage [...truncated...]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.2.1 dated 2025-01-24 and 0.2.2 dated 2025-03-05
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 4 R/dijkstras-path.R | 1 src/vcglib/vcg/complex/algorithms/parametrization/voronoi_atlas.h | 6 src/vcglib/vcg/complex/algorithms/voronoi_processing.h | 20 +- src/vcglib/vcg/complex/allocate.h | 72 +++++----- src/vcglib/wrap/callback.h | 37 ++--- 8 files changed, 83 insertions(+), 77 deletions(-)
Title: Create Tables from Different Types of Regression
Description: Create regression tables from generalized linear model(GLM), generalized estimating equation(GEE), generalized linear mixed-effects model(GLMM), Cox proportional hazards model, survey-weighted generalized linear model(svyglm) and survey-weighted Cox model results for publication.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Yoonkyoung Jeon [aut],
Jaehun Shon [aut],
Hyojong Myung [aut],
Hyungwoo Jo [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.8 dated 2024-12-11 and 1.3.9 dated 2025-03-05
DESCRIPTION | 8 +- MD5 | 21 ++++-- NEWS.md | 3 R/cox2.R | 8 +- build/vignette.rds |binary inst/doc/jstable.html | 88 +++++++++++++------------- inst/doc/jstable_competing_risk_analysis.R |only inst/doc/jstable_competing_risk_analysis.Rmd |only inst/doc/jstable_competing_risk_analysis.html |only inst/doc/jstable_options.R |only inst/doc/jstable_options.Rmd |only inst/doc/jstable_options.html |only tests/testthat/test-forestcox.R | 1 vignettes/jstable_competing_risk_analysis.Rmd |only vignettes/jstable_options.Rmd |only vignettes/vignette-styles.css |only 16 files changed, 73 insertions(+), 56 deletions(-)
Title: Design and Analysis of Hierarchical Composite Endpoints
Description: Simulate and analyze hierarchical composite endpoints. Win odds is the main analysis method, but other win statistics (win ratio, net benefit) are also implemented, provided there is no censoring. See Gasparyan SB et al (2023) "Hierarchical Composite Endpoints in COVID-19: The DARE-19 Trial." Case Studies in Innovative Clinical Trials, 95-148. Chapman; Hall/CRC. <doi:10.1201/9781003288640-7>.
Author: Samvel B. Gasparyan [aut, cre]
Maintainer: Samvel B. Gasparyan <gasparyan.co@gmail.com>
Diff between hce versions 0.6.7 dated 2025-01-07 and 0.7.0 dated 2025-03-05
DESCRIPTION | 6 MD5 | 76 ++++---- NAMESPACE | 2 NEWS.md | 11 + R/IWP.R |only R/as_hce.data.frame.R | 13 - R/as_hce.default.R |only R/calcWINS_data_frame.R | 121 ++++++++---- R/calcWINS_formula.R | 24 +- R/calcWINS_hce.R | 22 +- R/data.R | 2 R/plot_hce.R | 37 +++ R/simHCE.R | 126 +++++++++---- README.md | 2 inst/doc/Introduction.R | 6 inst/doc/Introduction.Rmd | 18 + inst/doc/Introduction.html | 106 +++++++++-- inst/doc/Wins.R | 2 inst/doc/Wins.Rmd | 2 inst/doc/Wins.html | 6 inst/doc/hce.R | 24 +- inst/doc/hce.Rmd | 117 ++++++++++-- inst/doc/hce.html | 391 +++++++++++++++++++----------------------- inst/doc/maraca.R | 2 inst/doc/maraca.Rmd | 2 inst/doc/maraca.html | 6 man/ADLB.Rd | 2 man/IWP.Rd |only man/as_hce.data.frame.Rd | 3 man/as_hce.default.Rd |only man/calcWINS.data.frame.Rd | 57 +++++- man/calcWINS.formula.Rd | 20 +- man/calcWINS.hce.Rd | 20 +- man/plot.hce.Rd | 16 + man/simHCE.Rd | 8 tests/testthat/test-test-WO.R | 51 +++++ vignettes/Introduction.Rmd | 18 + vignettes/REFERENCES.bib | 93 +++++++++ vignettes/Wins.Rmd | 2 vignettes/hce.Rmd | 117 ++++++++++-- vignettes/maraca.Rmd | 2 41 files changed, 1045 insertions(+), 488 deletions(-)
Title: Permutation Test for Weighted Quantile Sum Regression
Description: Implements a permutation test method for the weighted quantile sum (WQS) regression, building off the 'gWQS' package (Renzetti et al. <https://CRAN.R-project.org/package=gWQS>). Weighted quantile sum regression is a statistical technique to evaluate the effect of complex exposure mixtures on an outcome (Carrico et al. 2015 <doi:10.1007/s13253-014-0180-3>). The model features a statistical power and Type I error (i.e., false positive) rate trade-off, as there is a machine learning step to determine the weights that optimize the linear model fit. This package provides an alternative method based on a permutation test that should reliably allow for both high power and low false positive rate when utilizing WQS regression (Day et al. 2022 <doi:10.1289/EHP10570>).
Author: Drew Day [aut, cre],
James Peng [aut],
Adam Szpiro [aut]
Maintainer: Drew Day <dday612@gmail.com>
Diff between wqspt versions 1.0.1 dated 2023-03-06 and 1.0.2 dated 2025-03-05
DESCRIPTION | 17 - MD5 | 36 ++- NAMESPACE | 43 ++-- NEWS.md |only R/utils.R |only R/wqs_full_perm.R | 123 ++++++++----- R/wqs_pt.R | 182 +++++++++++-------- R/wqs_sim.R | 29 +-- R/wqspt_plot.R | 90 ++++++--- README.md | 109 +++++------ build/vignette.rds |binary inst/WORDLIST | 14 - inst/doc/introduction.R | 215 +++++++++++----------- inst/doc/introduction.Rmd | 201 ++++++++++++++------- inst/doc/introduction.html | 425 +++++++++++++++++++++++++-------------------- man/wqs_full_perm.Rd | 271 ++++++++++++++++------------ man/wqs_pt.Rd | 287 ++++++++++++++++-------------- man/wqs_sim.Rd | 275 ++++++++++++++--------------- man/wqspt_plot.Rd | 185 ++++++++++++------- vignettes/introduction.Rmd | 201 ++++++++++++++------- 20 files changed, 1571 insertions(+), 1132 deletions(-)
Title: Indices and Graphics for Assess Seed Germination Process
Description: A collection of different indices and visualization techniques for evaluate the seed germination process in ecophysiological studies (Lozano-Isla et al. 2019) <doi:10.1111/1440-1703.1275>.
Author: Flavio Lozano-Isla [aut, cre] ,
Omar Benites Alfaro [aut] ,
Marcelo F. Pompelli [aut, ths]
,
Denise Garcia de Santana [aut],
Marli A. Ranal [aut],
Federal University of Pernambuco [cph] ,
Federal Rural University of Pernambuco [cph] ,
Inkaverse [ctb]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between GerminaR versions 2.1.4 dated 2022-05-18 and 2.1.5 dated 2025-03-05
DESCRIPTION | 14 MD5 | 36 NEWS.md | 11 R/utils.R | 7 build/vignette.rds |binary inst/CITATION | 39 inst/GerminaQuant/rsconnect/shinyapps.io/flavjack/germinaquant.dcf | 10 inst/GerminaQuant/ui.R | 49 inst/doc/GerminaQuant.R | 2 inst/doc/GerminaQuant.Rmd | 2 inst/doc/GerminaQuant.html | 75 - inst/doc/GerminaR.R | 14 inst/doc/GerminaR.html | 611 +++++----- inst/doc/introduction.html | 63 - inst/rstudio/addins.dcf | 4 man/figures/logo.png |binary man/gquant_analysis.Rd | 122 - vignettes/GerminaQuant.Rmd | 2 vignettes/files/pkgs.bib | 332 ----- 19 files changed, 598 insertions(+), 795 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-09-17 0.3.4
2022-05-31 0.3.3