Title: Functions for Community Data and Ordinations
Description: A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, NMDS stress/scree plots, species response curves, merging of taxa as well as calculation and sorting of synoptic tables.
Author: Friedemann von Lampe [aut, cre] ,
Schellenberg Jenny [aut]
Maintainer: Friedemann von Lampe <fvonlampe@uni-goettingen.de>
Diff between goeveg versions 0.7.6 dated 2025-06-13 and 0.7.9 dated 2025-09-03
DESCRIPTION | 12 - MD5 | 63 +++--- NAMESPACE | 3 NEWS.md | 113 ++++++----- R/clean_matrix.R | 2 R/cov2per.R | 2 R/cv.r | 1 R/globals.R |only R/hcr_resampling.R |only R/merge_taxa.R | 3 R/ordiselect.r | 2 R/racurve.r | 2 R/racurves.r | 2 R/screeplot_NMDS.R | 2 R/specresponse.R | 2 R/synsort.R | 431 +++++++++++++++++++++++++++++++----------- R/syntable.R | 502 ++++++++++++++++---------------------------------- R/syntable_long.R |only R/syntable_wide.R |only R/trans_matrix.R | 2 README.md | 25 ++ build/partial.rdb |binary man/clean_matrix.Rd | 74 +++---- man/cov2per.Rd | 2 man/cv.Rd | 2 man/hcr_resampling.Rd |only man/merge_taxa.Rd | 2 man/ordiselect.Rd | 2 man/racurve.Rd | 2 man/racurves.Rd | 2 man/screeplot_NMDS.Rd | 2 man/specresponse.Rd | 2 man/synsort.Rd | 104 +++++++--- man/syntable.Rd | 167 +++++++++++----- man/trans_matrix.Rd | 78 +++---- 35 files changed, 884 insertions(+), 724 deletions(-)
Title: Catalogues of Resolution IV 128 Run 2-Level Fractional
Factorials Up to 33 Factors that Do Have 5-Letter Words
Description: Catalogues of resolution IV regular
fractional factorial designs in 128 runs are provided
for up to 33 2-level factors. The catalogues are complete,
excluding resolution IV designs without 5-letter words,
because these do not add value for a search for unblocked
clear designs. The previous package version
1.0 with complete catalogues up to 24 runs (24 runs and a
namespace added later) can be downloaded from the authors
website.
Author: Ulrike Groemping [aut, cre]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between FrF2.catlg128 versions 1.2-3 dated 2023-10-07 and 1.2-4 dated 2025-09-03
DESCRIPTION | 12 +++--- MD5 | 6 +-- inst/NEWS | 6 ++- man/Catalogues.Rd | 98 +++++++++++++++++++++++++++--------------------------- 4 files changed, 64 insertions(+), 58 deletions(-)
Title: Building and Estimating Structural Equation Models
Description: A powerful, easy to use syntax for specifying and estimating complex
Structural Equation Models. Models can be estimated using Partial
Least Squares Path Modeling or Covariance-Based Structural Equation
Modeling or covariance based Confirmatory Factor Analysis (Ray, Danks, and Valdez 2021 <doi:10.2139/ssrn.3900621>).
Author: Soumya Ray [aut, ths],
Nicholas Patrick Danks [aut, cre],
Andre Calero Valdez [aut],
Juan Manuel Velasquez Estrada [ctb],
James Uanhoro [ctb],
Johannes Nakayama [ctb],
Lilian Koyan [ctb],
Laura Burbach [ctb],
Arturo Heynar Cano Bejar [ctb],
Susanne A [...truncated...]
Maintainer: Nicholas Patrick Danks <nicholasdanks@hotmail.com>
This is a re-admission after prior archival of version 2.3.6 dated 2025-07-24
Diff between seminr versions 2.3.6 dated 2025-07-24 and 2.3.7 dated 2025-09-03
DESCRIPTION | 12 MD5 | 38 - NAMESPACE | 2 R/clean_data.R | 12 R/compute_metrics.R | 36 + R/estimate_pls.R | 4 R/estimate_simplePLS.R | 2 R/evaluate_reliability.R | 28 + R/feature_plspredict.R | 147 +++-- R/report_lavaan.R | 67 +- R/report_summary.R | 33 + R/seminr-package.R |only README.md | 4 build/partial.rdb |only inst/doc/SEMinR.html | 10 man/estimate_pls.Rd | 3 man/mean_replacement.Rd | 1 man/report_missing.Rd |only man/seminr-package.Rd |only tests/fixtures/V_3_6_0/two_stage_predict.csv | 692 +++++++++++++-------------- tests/testthat/test-plspredict.R | 27 - tests/testthat/test-summary-cbsem.R | 2 22 files changed, 645 insertions(+), 475 deletions(-)
Title: Pretest Probability for Coronary Artery Disease
Description: An application to calculate a patient's pretest probability
(PTP) for obstructive Coronary Artery Disease (CAD) from a collection
of guidelines or studies. Guidelines usually comes from the American
Heart Association (AHA), American College of Cardiology (ACC) or
European Society of Cardiology (ESC). Examples of PTP scores that
comes from studies are the 2020 Winther et al. basic, Risk
Factor-weighted Clinical Likelihood (RF-CL) and Coronary Artery
Calcium Score-weighted Clinical Likelihood (CACS-CL) models
<doi:10.1016/j.jacc.2020.09.585>, 2019 Reeh et al. basic and clinical
models <doi:10.1093/eurheartj/ehy806> and 2017 Fordyce et al. PROMISE
Minimal-Risk Tool <doi:10.1001/jamacardio.2016.5501>. As diagnosis of
CAD involves a costly and invasive coronary angiography procedure for
patients, having a reliable PTP for CAD helps doctors to make better
decisions during patient management. This ensures high risk patients
can be diagnosed and treated early for CAD while [...truncated...]
Author: Jeremy Selva [aut, cre]
Maintainer: Jeremy Selva <jeremy1189.jjs@gmail.com>
Diff between pretestcad versions 1.0.2 dated 2025-05-19 and 1.1.0 dated 2025-09-03
DESCRIPTION | 54 - MD5 | 135 +- NAMESPACE | 93 - NEWS.md | 20 R/aha_2012_conference_ptp.R | 64 - R/aha_2021_conference_ptp.R | 87 + R/cad_consortium_ptp.R | 326 +++++- R/confirm_ptp.R | 208 +++ R/dcs_ptp.R | 796 +++++++++++---- R/diamond_forrester_ptp.R | 60 - R/esc_2019_conference_ptp.R | 121 +- R/esc_2024_conference_ptp.R | 351 +++++- R/harmonise.R |only R/lah_ptp.R | 265 ++++- R/pmrs_ptp.R | 197 +++ R/precise_ptp.R | 389 ++++++- R/reeh_ptp.R | 217 +++- R/utilities.R | 845 +++++++++++++++- R/winther_ptp.R | 182 +++ inst/WORDLIST | 3 inst/hexsticker.pptx |only man/arg_match0_allow_na.Rd | 13 man/arg_match0_integer.Rd | 23 man/arg_match0_no_na_error_message.Rd |only man/arg_match0_true_or_false.Rd | 29 man/calculate_aha_2012_tbl_9_ptp.Rd | 49 man/calculate_aha_2021_ptp.Rd | 63 - man/calculate_cad1_2011_ptp.Rd | 55 - man/calculate_cad2_2012_basic_ptp.Rd | 55 - man/calculate_cad2_2012_clinical_ccs_ptp.Rd | 149 ++ man/calculate_cad2_2012_clinical_ptp.Rd | 149 ++ man/calculate_confirm_2015_num_of_rf.Rd | 125 +- man/calculate_confirm_2015_ptp.Rd | 140 +- man/calculate_dcs_1993_lm_cad_ptp.Rd | 120 +- man/calculate_dcs_1993_pain_index.Rd | 123 +- man/calculate_dcs_1993_risk_factor_index.Rd | 78 + man/calculate_dcs_1993_severe_cad_ptp.Rd | 289 +++-- man/calculate_dcs_1993_sig_cad_ptp.Rd | 194 ++- man/calculate_dcs_1993_vascular_disease_index.Rd | 78 + man/calculate_diamond_forrester_1979_ptp.Rd | 49 man/calculate_esc_2019_ptp.Rd | 74 + man/calculate_esc_2024_fig_4_ptp.Rd | 186 ++- man/calculate_esc_2024_fig_4_ptp_simplfied.Rd | 29 man/calculate_esc_2024_num_of_rf.Rd | 128 +- man/calculate_esc_2024_symptom_score.Rd | 61 - man/calculate_lah_2022_clinical_ptp.Rd | 149 ++ man/calculate_lah_2022_extended_ptp.Rd | 149 ++ man/calculate_precise_2021_clinical_ptp.Rd | 199 ++- man/calculate_precise_2021_simple_ptp.Rd | 153 ++ man/calculate_prms_2017_ptp.Rd | 200 ++- man/calculate_reeh_2019_basic_ptp.Rd | 48 man/calculate_reeh_2019_clinical_ptp.Rd | 110 +- man/calculate_winther_2020_basic_ptp.Rd | 60 - man/calculate_winther_2020_cacs_cl_ptp.Rd | 200 ++- man/calculate_winther_2020_rf_cl_ptp.Rd | 200 ++- man/check_if_four_categories_are_mutually_exclusive.Rd |only man/check_if_integer.Rd |only man/check_if_non_negative.Rd | 32 man/check_if_numeric.Rd | 22 man/check_if_positive.Rd | 17 man/check_if_three_categories_are_mutually_exclusive.Rd |only man/check_if_two_categories_are_mutually_exclusive.Rd |only man/chr_quoted.Rd |only man/harmonise_four_labels.Rd |only man/harmonise_three_labels.Rd |only man/harmonise_two_labels.Rd |only man/oxford_comma.Rd |only tests/testthat/_snaps/aha_2012_conference_ptp.md |only tests/testthat/_snaps/esc_2019_conference_ptp.md |only tests/testthat/_snaps/esc_2024_conference_ptp.md |only tests/testthat/_snaps/harmonise.md |only tests/testthat/_snaps/utilities.md | 174 ++- tests/testthat/test-aha_2012_conference_ptp.R | 176 ++- tests/testthat/test-esc_2019_conference_ptp.R | 264 ++++ tests/testthat/test-esc_2024_conference_ptp.R | 190 +++ tests/testthat/test-harmonise.R |only tests/testthat/test-utilities.R | 253 ++++ 77 files changed, 7418 insertions(+), 1850 deletions(-)
Title: Creation of Arrays by Mixed Integer Programming
Description: 'CRAN' packages 'DoE.base' and 'Rmosek' and non-'CRAN' package 'gurobi' are enhanced with functionality for the creation of optimized arrays for experimentation, where optimization is in terms of generalized minimum aberration. It is also possible to optimally extend existing arrays to larger run size. The package writes 'MPS' (Mathematical Programming System) files for use with any mixed integer optimization software that can process such files. If at least one of the commercial products 'Gurobi' or 'Mosek' (free academic licenses available for both) is available, the package also creates arrays by optimization. For installing 'Gurobi' and its R package 'gurobi', follow instructions at <https://support.gurobi.com/hc/en-us/articles/14462206790033-How-do-I-install-Gurobi-for-R>. For installing 'Mosek' and its R package 'Rmosek', follow instructions at <https://www.mosek.com/downloads/> and <https://docs.mosek.com/8.1/rmosek/install-interface.html>, or use the functiona [...truncated...]
Author: Ulrike Groemping [aut, cre]
Maintainer: Ulrike Groemping <ulrike.groemping@bht-berlin.de>
Diff between DoE.MIParray versions 1.0-1 dated 2023-08-21 and 1.0-2 dated 2025-09-03
DESCRIPTION | 16 +++++++---- MD5 | 10 +++---- inst/NEWS | 9 +++++- man/DoE.MIParray-package.Rd | 2 - man/functionsFromDoEbase.Rd | 60 ++++++++++++++++++++++---------------------- man/mosek_MIParray.Rd | 2 - 6 files changed, 54 insertions(+), 45 deletions(-)
Title: Diagnostics for Nonlinear Mixed-Effect Models
Description: A model building aid for nonlinear mixed-effects
(population) model analysis using NONMEM, facilitating data set
checkout, exploration and visualization, model diagnostics, candidate
covariate identification and model comparison. The methods are described
in Keizer et al. (2013) <doi:10.1038/psp.2013.24>, and Jonsson et al. (1999)
<doi:10.1016/s0169-2607(98)00067-4>.
Author: Andrew C. Hooker [aut, cre, cph],
Mats O. Karlsson [aut, cph],
Justin J. Wilkins [aut],
E. Niclas Jonsson [aut, trl, cph],
Ron Keizer [ctb]
Maintainer: Andrew C. Hooker <andrew.hooker@uu.se>
Diff between xpose4 versions 4.7.3 dated 2024-02-22 and 4.7.4 dated 2025-09-03
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/xpose.VPC.categorical.R | 4 ++-- README.md | 6 ------ build/partial.rdb |binary man/xpose.VPC.categorical.Rd | 4 ++-- 7 files changed, 21 insertions(+), 23 deletions(-)
Title: Worldwide or Coordinates-Based Heat Maps
Description: Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.
Author: Luigi Annicchiarico [cre, aut]
Maintainer: Luigi Annicchiarico <luigi.annic@gmail.com>
Diff between WorldMapR versions 1.2.0 dated 2025-03-21 and 1.3.0 dated 2025-09-03
WorldMapR-1.2.0/WorldMapR/tests/testthat/test_geometry_data.R |only WorldMapR-1.3.0/WorldMapR/DESCRIPTION | 10 - WorldMapR-1.3.0/WorldMapR/MD5 | 37 ++-- WorldMapR-1.3.0/WorldMapR/NAMESPACE | 13 - WorldMapR-1.3.0/WorldMapR/NEWS.md | 8 + WorldMapR-1.3.0/WorldMapR/R/WorldMapR-package.R | 14 - WorldMapR-1.3.0/WorldMapR/R/countrycoord_data.R | 27 ++- WorldMapR-1.3.0/WorldMapR/R/empty_editable_map.R |only WorldMapR-1.3.0/WorldMapR/R/geometries_data.R | 77 +++++----- WorldMapR-1.3.0/WorldMapR/R/globals.R | 7 WorldMapR-1.3.0/WorldMapR/R/regions_ITBIH.R |only WorldMapR-1.3.0/WorldMapR/R/worldplot.R | 4 WorldMapR-1.3.0/WorldMapR/R/worldplotCat.R | 3 WorldMapR-1.3.0/WorldMapR/README.md | 2 WorldMapR-1.3.0/WorldMapR/data/regions_ITBIH.RData |only WorldMapR-1.3.0/WorldMapR/inst/doc/WorldMapR_Vignette.R | 7 WorldMapR-1.3.0/WorldMapR/inst/doc/WorldMapR_Vignette.Rmd | 15 + WorldMapR-1.3.0/WorldMapR/inst/doc/WorldMapR_Vignette.html | 21 ++ WorldMapR-1.3.0/WorldMapR/man/empty_editable_map.Rd |only WorldMapR-1.3.0/WorldMapR/man/geometries_data.Rd | 5 WorldMapR-1.3.0/WorldMapR/man/regions_ITBIH.Rd |only WorldMapR-1.3.0/WorldMapR/tests/testthat/test_countrycoord_data.R |only WorldMapR-1.3.0/WorldMapR/vignettes/WorldMapR_Vignette.Rmd | 15 + 23 files changed, 164 insertions(+), 101 deletions(-)
Title: Fast Molecular Clock Dating of Phylogenetic Trees with Rate
Variation
Description: Functions for estimating times of common ancestry and molecular clock rates of evolution using a variety of evolutionary models, parametric and nonparametric bootstrap confidence intervals, methods for detecting outlier lineages, root-to-tip regression, and a statistical test for selecting molecular clock models. For more details see Volz and Frost (2017) <doi:10.1093/ve/vex025>.
Author: Erik Volz [aut, cre]
Maintainer: Erik Volz <erik.volz@gmail.com>
This is a re-admission after prior archival of version 0.5.0 dated 2020-01-26
Diff between treedater versions 0.5.0 dated 2020-01-26 and 1.0.2 dated 2025-09-03
DESCRIPTION | 13 MD5 | 45 +- NAMESPACE | 1 R/boot.R | 138 +++--- R/multiRtT.R | 10 R/outliers0.R | 34 - R/treedater0.R | 525 ++++++++++++++--------- README.md | 5 build/vignette.rds |binary inst/doc/h3n2.R | 42 - inst/doc/h3n2.Rmd | 14 inst/doc/h3n2.html | 909 +++++++++++++++++++++++------------------ man/boot.Rd | 26 - man/dater.Rd | 38 + man/gibbs_jitter.Rd |only man/goodnessOfFitPlot.Rd | 2 man/outlierLineages.Rd | 2 man/outlierTips.Rd | 2 man/parboot.Rd | 26 - man/plot.bootTreedater.Rd | 5 man/relaxedClockTest.Rd | 7 man/rootToTipRegressionPlot.Rd | 17 man/sampleYearsFromLabels.Rd | 17 vignettes/h3n2.Rmd | 14 24 files changed, 1084 insertions(+), 808 deletions(-)
Title: R Interface to 'IGN' Web Services
Description: Automatic open data acquisition from resources of IGN
('Institut National de Information Geographique et forestiere')
(<https://www.ign.fr/>). Available datasets include various types of
raster and vector data, such as digital elevation models, state
borders, spatial databases, cadastral parcels, and more. 'happign' also
provide access to API Carto (<https://apicarto.ign.fr/api/doc/>).
Author: Paul Carteron [aut, cre]
Maintainer: Paul Carteron <carteronpaul@gmail.com>
Diff between happign versions 0.3.5 dated 2025-07-29 and 0.3.6 dated 2025-09-03
happign-0.3.5/happign/R/get_apicarto_rpg.R |only happign-0.3.5/happign/R/get_apicarto_viticole.R |only happign-0.3.5/happign/R/hit_api.R |only happign-0.3.5/happign/man/get_apicarto_rpg.Rd |only happign-0.3.5/happign/man/get_apicarto_viticole.Rd |only happign-0.3.5/happign/tests/testthat/api_gpu_x_input |only happign-0.3.5/happign/tests/testthat/fetch_data |only happign-0.3.5/happign/tests/testthat/fetch_data error dtolerance |only happign-0.3.5/happign/tests/testthat/fetch_data error no data |only happign-0.3.5/happign/tests/testthat/get_api_codes_postaux |only happign-0.3.5/happign/tests/testthat/get_apicarto_cadastre |only happign-0.3.5/happign/tests/testthat/get_apicarto_rpg |only happign-0.3.5/happign/tests/testthat/hit_api_error |only happign-0.3.5/happign/tests/testthat/test-get_apicarto_rpg.R |only happign-0.3.5/happign/tests/testthat/test-hit_api.R |only happign-0.3.6/happign/DESCRIPTION | 8 happign-0.3.6/happign/MD5 | 82 +- happign-0.3.6/happign/NAMESPACE | 8 happign-0.3.6/happign/NEWS.md | 20 happign-0.3.6/happign/R/get_apicarto_cadastre.R | 256 +++--- happign-0.3.6/happign/R/get_apicarto_codes_postaux.R | 42 - happign-0.3.6/happign/R/get_apicarto_gpu.R | 388 +++++----- happign-0.3.6/happign/R/utils.R | 41 - happign-0.3.6/happign/man/get_apicarto_cadastre.Rd | 93 +- happign-0.3.6/happign/man/get_apicarto_codes_postaux.Rd | 8 happign-0.3.6/happign/man/get_apicarto_gpu.Rd | 190 ++-- happign-0.3.6/happign/man/get_gpu_layers.Rd |only happign-0.3.6/happign/tests/testthat/apicarto-cadastre |only happign-0.3.6/happign/tests/testthat/apicarto-codes-postaux |only happign-0.3.6/happign/tests/testthat/apicarto-gpu |only happign-0.3.6/happign/tests/testthat/test-get_apicarto_cadastre.R | 255 +++--- happign-0.3.6/happign/tests/testthat/test-get_apicarto_codes_postaux.R | 43 - happign-0.3.6/happign/tests/testthat/test-get_apicarto_gpu.R | 103 +- happign-0.3.6/happign/tests/testthat/test-utils.R | 44 - 34 files changed, 848 insertions(+), 733 deletions(-)
Title: Quality Control and Semantic Enrichment of Datasets
Description: A tool for the preparation and enrichment of health datasets for analysis (Toner et al. (2023) <doi:10.1093/gigascience/giad030>). Provides functionality for assessing data quality and for improving the reliability and machine interpretability of a dataset.
'eHDPrep' also enables semantic enrichment of a dataset where metavariables are discovered from the relationships between input variables determined from user-provided ontologies.
Author: Tom Toner [aut] ,
Ian Overton [aut, cre]
Maintainer: Ian Overton <I.Overton@qub.ac.uk>
Diff between eHDPrep versions 1.3.3 dated 2023-06-05 and 1.3.4 dated 2025-09-03
eHDPrep-1.3.3/eHDPrep/tests/testthat/Rplots.pdf |only eHDPrep-1.3.4/eHDPrep/DESCRIPTION | 14 +- eHDPrep-1.3.4/eHDPrep/MD5 | 18 +-- eHDPrep-1.3.4/eHDPrep/R/semantic_enrich.R | 4 eHDPrep-1.3.4/eHDPrep/README.md |only eHDPrep-1.3.4/eHDPrep/build/partial.rdb |binary eHDPrep-1.3.4/eHDPrep/build/vignette.rds |binary eHDPrep-1.3.4/eHDPrep/inst/doc/Introduction_to_eHDPrep.R | 76 ++++++------- eHDPrep-1.3.4/eHDPrep/inst/doc/Introduction_to_eHDPrep.pdf |binary eHDPrep-1.3.4/eHDPrep/man/join_vars_to_ontol.Rd | 2 eHDPrep-1.3.4/eHDPrep/man/metavariable_agg.Rd | 2 11 files changed, 58 insertions(+), 58 deletions(-)
Title: Consistent Perturbation of Statistical Frequency- And Magnitude
Tables
Description: Data from statistical agencies and other institutions often
need to be protected before they can be published. This package
can be used to perturb statistical tables in a consistent way. The
main idea is to add - at the micro data level - a record key for each
unit. Based on these keys, for any cell in a statistical table a
cell key is computed as a function on the record keys contributing to
a specific cell. Values that are added to the cell in order to perturb
it are derived from a lookup-table that maps values of cell keys to
specific perturbation values. The theoretical basis for the methods
implemented can be found in Thompson, Broadfoot and Elazar
(2013) <https://unece.org/fileadmin/DAM/stats/documents/ece/ces/ge.46/2013/Topic_1_ABS.pdf>
which was extended and enhanced by Giessing and Tent
(2019) <https://unece.org/fileadmin/DAM/stats/documents/ece/ces/ge.46/2019/mtg1/SDC2019_S2_Germany_Giessing_Tent_AD.pdf>.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <bernhard.meindl@statistik.gv.at>
Diff between cellKey versions 1.0.2 dated 2023-11-24 and 1.0.3 dated 2025-09-03
DESCRIPTION | 14 - MD5 | 14 - NEWS.md | 4 R/cellkey_pkg.R | 3 inst/doc/introduction.Rmd | 320 ++++++++++++++++++++-------------------- inst/doc/introduction.html | 315 +++++++++++++++++++-------------------- vignettes/introduction.Rmd | 320 ++++++++++++++++++++-------------------- vignettes/introduction.Rmd.orig | 20 +- 8 files changed, 506 insertions(+), 504 deletions(-)
Title: Create Ternary and Holdridge Plots
Description: Plots ternary diagrams (simplex plots / Gibbs triangles) and
Holdridge life zone plots <doi:10.1126/science.105.2727.367> using the
standard graphics functions.
Allows custom annotation, interpolating, contouring and scaling of plotting
region.
Includes a 'Shiny' user interface for point-and-click ternary plotting.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting
functions.
Author: Martin R. Smith [aut, cre, cph] ,
Lilian Sanselme [ctb]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 2.3.4 dated 2025-05-07 and 2.3.5 dated 2025-09-03
DESCRIPTION | 6 MD5 | 98 NAMESPACE | 166 NEWS.md | 5 R/Annotate.R | 17 R/Contours.R | 25 R/Coordinates.R | 13 R/Polygons.R | 73 R/TernaryPlot.R | 8 R/data.R | 14 build/partial.rdb |binary build/vignette.rds |binary inst/TernaryApp/app.R | 1208 inst/WORDLIST | 98 inst/doc/Holdridge.Rmd | 300 inst/doc/Holdridge.html | 4 inst/doc/Ternary.Rmd | 818 inst/doc/Ternary.html | 6 inst/doc/annotation.html | 4 inst/doc/interpolation.Rmd | 350 inst/doc/interpolation.html | 4 inst/doc/new-users.Rmd | 510 inst/doc/new-users.html | 4 man/AddToTernary.Rd | 290 man/Annotate.Rd | 4 man/ColourTernary.Rd | 224 man/CoordinatesToXY.Rd | 4 man/Polygon-Geometry.Rd | 98 man/TernaryContour.Rd | 298 man/TernaryDensityContour.Rd | 344 man/TernaryPointValues.Rd | 170 man/TriangleCentres.Rd | 103 man/TriangleInHull.Rd | 119 man/cbPalettes.Rd | 12 tests/testthat/Rplots.pdf |only tests/testthat/_snaps/Annotate/annotate-zoomed.svg |only tests/testthat/_snaps/Contours/contours-skiwiff.svg | 5442 - tests/testthat/_snaps/Contours/contours.svg | 5644 - tests/testthat/_snaps/Contours/density-contours.svg | 3844 - tests/testthat/_snaps/Contours/filledcontours.svg |48210 ++++++------- tests/testthat/_snaps/Contours/lo-res-density-contours.svg | 1352 tests/testthat/_snaps/Holdridge/holdridge-basic.svg | 594 tests/testthat/test-Annotate.R | 7 tests/testthat/test-Contours.R | 10 tests/testthat/test-Coordinates.R | 310 tests/testthat/test-Holdridge.R | 56 tests/testthat/test-Polygons.R | 47 vignettes/Holdridge.Rmd | 300 vignettes/Ternary.Rmd | 818 vignettes/interpolation.Rmd | 350 vignettes/new-users.Rmd | 510 51 files changed, 36423 insertions(+), 36468 deletions(-)
Title: Spatial Seemingly Unrelated Regression Models
Description: A collection of functions to test and estimate Seemingly
Unrelated Regression (usually called SUR) models, with spatial structure, by maximum
likelihood and three-stage least squares. The package estimates the
most common spatial specifications, that is, SUR with Spatial Lag of
X regressors (called SUR-SLX), SUR with Spatial Lag Model (called SUR-SLM),
SUR with Spatial Error Model (called SUR-SEM), SUR with Spatial Durbin Model (called SUR-SDM),
SUR with Spatial Durbin Error Model (called SUR-SDEM),
SUR with Spatial Autoregressive terms and Spatial Autoregressive
Disturbances (called SUR-SARAR), SUR-SARAR with Spatial Lag of X
regressors (called SUR-GNM) and SUR with Spatially Independent Model (called SUR-SIM).
The methodology of these models can be found in next references
Minguez, R., Lopez, F.A., and Mur, J. (2022) <doi:10.18637/jss.v104.i11>
Mur, J., Lopez, F.A., and Herrera, M. (2010) <doi:10.1080/17421772.2010.516443>
Lopez, F.A., Mur, J., and Angulo, A. (2014) <d [...truncated...]
Author: Ana Angulo [aut],
Fernando A Lopez [aut],
Roman Minguez [aut, cre],
Jesus Mur [aut]
Maintainer: Roman Minguez <roman.minguez@uclm.es>
Diff between spsur versions 1.0.2.5 dated 2022-10-29 and 1.0.2.6 dated 2025-09-03
spsur-1.0.2.5/spsur/R/spSUR-package.R |only spsur-1.0.2.6/spsur/DESCRIPTION | 23 spsur-1.0.2.6/spsur/MD5 | 44 spsur-1.0.2.6/spsur/R/impactspsur.R | 8 spsur-1.0.2.6/spsur/R/spsur-package.R |only spsur-1.0.2.6/spsur/R/spsur3sls.R | 2 spsur-1.0.2.6/spsur/R/spsurgs3sls.R | 2 spsur-1.0.2.6/spsur/build/vignette.rds |binary spsur-1.0.2.6/spsur/inst/doc/Vignette_User_Guide.Rmd | 16 spsur-1.0.2.6/spsur/inst/doc/Vignette_User_Guide.html | 281 - spsur-1.0.2.6/spsur/inst/doc/montecarlo_spsur_spse.Rmd | 732 +-- spsur-1.0.2.6/spsur/inst/doc/montecarlo_spsur_spse.html | 3440 +++++++++++----- spsur-1.0.2.6/spsur/inst/doc/spsur-vs-spatialreg.Rmd | 26 spsur-1.0.2.6/spsur/inst/doc/spsur-vs-spatialreg.html | 475 -- spsur-1.0.2.6/spsur/inst/doc/spsur_pysal.Rmd | 36 spsur-1.0.2.6/spsur/inst/doc/spsur_pysal.html | 2126 +++++++-- spsur-1.0.2.6/spsur/man/impactspsur.Rd | 8 spsur-1.0.2.6/spsur/man/spsur-package.Rd | 19 spsur-1.0.2.6/spsur/man/spsur3sls.Rd | 2 spsur-1.0.2.6/spsur/man/spsurgs3sls.Rd | 2 spsur-1.0.2.6/spsur/vignettes/Vignette_User_Guide.Rmd | 16 spsur-1.0.2.6/spsur/vignettes/montecarlo_spsur_spse.Rmd | 732 +-- spsur-1.0.2.6/spsur/vignettes/spsur-vs-spatialreg.Rmd | 26 spsur-1.0.2.6/spsur/vignettes/spsur_pysal.Rmd | 36 24 files changed, 5135 insertions(+), 2917 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Description: Contains functions for mapping odds ratios, hazard ratios, or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) or Cox models for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting linearly for confounding variables, using methods described by Kelsall and Diggle (1998), Webster at al. (2006), and Bai et al. (2020). Includes convenient functions for mapping point estimates and confidence intervals, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Lu Bai [aut],
Scott Bartell [aut, cre] ,
Robin Bliss [aut],
Veronica Vieira [aut]
Maintainer: Scott Bartell <sbartell@uci.edu>
Diff between MapGAM versions 1.3 dated 2023-07-15 and 1.3-1 dated 2025-09-03
ChangeLog | 10 ++ DESCRIPTION | 30 ++++-- MD5 | 20 ++-- R/MapGAM.version.R | 26 ++--- R/gamcox.R | 220 ++++++++++++++++++++++----------------------- R/gamcox.fit.R | 161 ++++++++++++++++----------------- build/partial.rdb |binary man/MapGAM-package.Rd | 14 +- man/modgam.Rd | 23 ++-- man/plot.modgam.Rd | 2 man/sampcont.Rd | 242 +++++++++++++++++++++++++------------------------- 11 files changed, 390 insertions(+), 358 deletions(-)
Title: Fuzzy String Matching
Description: Fuzzy string matching implementation of the 'fuzzywuzzy' <https://github.com/seatgeek/fuzzywuzzy> 'python' package. It uses the Levenshtein Distance <https://en.wikipedia.org/wiki/Levenshtein_distance> to calculate the differences between sequences.
Author: Lampros Mouselimis [aut, cre] ,
SeatGeek Inc [cph]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fuzzywuzzyR versions 1.0.5 dated 2021-09-11 and 1.0.6 dated 2025-09-03
DESCRIPTION | 18 MD5 | 20 NEWS.md | 10 README.md | 55 - build/vignette.rds |binary inst/doc/functionality_of_fuzzywuzzyR_package.R | 696 ++++++++-------- inst/doc/functionality_of_fuzzywuzzyR_package.html | 863 +++++++++++++-------- man/FuzzExtract.Rd | 42 - man/FuzzMatcher.Rd | 72 - man/FuzzUtils.Rd | 48 - man/SequenceMatcher.Rd | 42 - 11 files changed, 1033 insertions(+), 833 deletions(-)
Title: General Utility Functions for Analysis of Clinical Data
Description: Utility functions to facilitate the import,
the reporting and analysis of clinical data.
Example datasets in 'SDTM' and 'ADaM' format, containing a subset of patients/domains
from the 'CDISC Pilot 01 study' are also available as R datasets to demonstrate
the package functionalities.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Arne De Roeck [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinUtils versions 0.2.0 dated 2024-05-17 and 0.2.1 dated 2025-09-03
DESCRIPTION | 10 MD5 | 16 R/knitPrintListObjects.R | 2 build/vignette.rds |binary data/dataADaMCDISCP01.RData |binary data/dataSDTMCDISCP01.RData |binary inst/NEWS | 2 inst/doc/clinUtils-vignette.html | 1177 +++++++++++++++++++++------------------ man/knitPrintListObjects.Rd | 2 9 files changed, 669 insertions(+), 540 deletions(-)
Title: Tensor-Train Decomposition
Description: Tensor-train is a compact representation for higher-order tensors. Some algorithms for performing tensor-train decomposition are available such as TT-SVD, TT-WOPT, and TT-Cross. For the details of the algorithms, see I. V. Oseledets (2011) <doi:10.1137/090752286>, Yuan Longao, et al (2017) <doi:10.48550/arXiv.1709.02641>, I. V. Oseledets (2010) <doi:10.1016/j.laa.2009.07.024>.
Author: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
This is a re-admission after prior archival of version 1.0.1 dated 2021-05-18
Diff between ttTensor versions 1.0.1 dated 2021-05-18 and 1.0.2 dated 2025-09-03
ttTensor-1.0.1/ttTensor/README.md |only ttTensor-1.0.2/ttTensor/DESCRIPTION | 14 ++++---- ttTensor-1.0.2/ttTensor/LICENSE |only ttTensor-1.0.2/ttTensor/MD5 | 24 ++++++++----- ttTensor-1.0.2/ttTensor/NAMESPACE | 6 ++- ttTensor-1.0.2/ttTensor/R/TTCross.R | 2 - ttTensor-1.0.2/ttTensor/R/ttTensor-internal.R | 16 +++++---- ttTensor-1.0.2/ttTensor/R/ttTensor-sparse.R |only ttTensor-1.0.2/ttTensor/build/partial.rdb |binary ttTensor-1.0.2/ttTensor/inst/NEWS | 6 +++ ttTensor-1.0.2/ttTensor/man/TTCross.Rd | 31 +++++++++--------- ttTensor-1.0.2/ttTensor/man/as_sptensor.Rd |only ttTensor-1.0.2/ttTensor/man/dtensor.Rd |only ttTensor-1.0.2/ttTensor/man/unfold.Rd |only ttTensor-1.0.2/ttTensor/tests/testthat.R | 1 ttTensor-1.0.2/ttTensor/tests/testthat/test_TTCross.R | 1 16 files changed, 58 insertions(+), 43 deletions(-)
Title: Latent Order Logistic Graph Models
Description: Estimation of Latent Order Logistic (LOLOG) Models for Networks.
LOLOGs are a flexible and fully general class of statistical graph models.
This package provides functions for performing MOM, GMM and variational
inference. Visual diagnostics and goodness of fit metrics are provided.
See Fellows (2018) <doi:10.48550/arXiv.1804.04583> for a detailed description of the methods.
Author: Ian E. Fellows [aut, cre],
Mark S. Handcock [ctb]
Maintainer: Ian E. Fellows <ian@fellstat.com>
Diff between lolog versions 1.3.1 dated 2023-12-07 and 1.3.2 dated 2025-09-03
DESCRIPTION | 15 +++-- MD5 | 56 ++++++++++----------- R/binary-net.R | 4 - R/inline.R | 9 ++- R/lolog.R | 20 ++++--- R/roxygen.R | 6 +- R/zzz.R | 2 build/vignette.rds |binary inst/doc/lolog-ergm.R | 6 +- inst/doc/lolog-ergm.Rmd | 8 +-- inst/doc/lolog-ergm.pdf |binary inst/doc/lolog-introduction.R | 90 +++++++++++++++++------------------ inst/doc/lolog-introduction.pdf |binary inst/include/Stats.h | 22 +++++++- man/inlineLologPlugin.Rd | 6 +- man/lolog-terms.Rd | 6 +- man/plot.Rcpp_DirectedNet.Rd | 2 man/plot.Rcpp_UndirectedNet.Rd | 2 man/plot.lologGmm.Rd | 2 src/StatController.cpp | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test-BinaryNet.R | 2 tests/testthat/test-Cpp.R | 3 - tests/testthat/test-inline.R | 3 - tests/testthat/test-likelihood.R | 2 tests/testthat/test-lolog-fit.R | 1 tests/testthat/test-model-creation.R | 1 tests/testthat/test-stats.R | 9 ++- vignettes/lolog-ergm.Rmd | 8 +-- 29 files changed, 155 insertions(+), 131 deletions(-)
Title: Loading Data from 'Google Ads API'
Description: Interface for loading data from 'Google Ads API',
see <https://developers.google.com/google-ads/api/docs/start>.
Package provide function for authorization and loading reports.
Author: Alexey Seleznev [aut, cre] ,
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rgoogleads versions 0.12.0 dated 2025-01-10 and 0.13.3 dated 2025-09-03
DESCRIPTION | 11 - MD5 | 22 +-- NAMESPACE | 2 NEWS.md | 13 ++ R/gads_check_errors.R | 204 ++++++++++++++++----------------- R/gads_get_accessible_customers.R | 2 R/gads_utils.R | 8 - R/zzz.R | 2 inst/doc/migrate_from_radrowds_us.html | 12 - inst/doc/migrate_from_radwords_ru.html | 12 - man/gads_deauth.Rd | 4 man/gads_get_accessible_customers.Rd | 3 12 files changed, 151 insertions(+), 144 deletions(-)
Title: Plackett-Luce Models for Rankings
Description: Functions to prepare rankings data and fit the Plackett-Luce model
jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce
(1959, ISBN:0486441369). The standard Plackett-Luce model is generalized
to accommodate ties of any order in the ranking. Partial rankings, in which
only a subset of items are ranked in each ranking, are also accommodated in
the implementation. Disconnected/weakly connected networks implied by the
rankings may be handled by adding pseudo-rankings with a hypothetical item.
Optionally, a multivariate normal prior may be set on the log-worth
parameters and ranker reliabilities may be incorporated as proposed by
Raman and Joachims (2014) <doi:10.1145/2623330.2623654>. Maximum a
posteriori estimation is used when priors are set. Methods are provided to
estimate standard errors or quasi-standard errors for inference as well as
to fit Plackett-Luce trees. See the package website or vignette for further
details.
Author: Heather Turner [aut, cre] ,
Ioannis Kosmidis [aut] ,
David Firth [aut] ,
Jacob van Etten [ctb]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between PlackettLuce versions 0.4.3 dated 2023-06-16 and 0.4.4 dated 2025-09-03
DESCRIPTION | 19 +- MD5 | 74 ++++---- NAMESPACE | 1 NEWS.md | 5 R/PlackettLuce-package.R | 91 +++++----- R/adjacency.R | 100 +++++------ R/anova.R | 5 R/pltree.R | 2 R/preflib.R | 4 R/qvcalc.PlackettLuce.R | 176 +++++++++---------- R/rankings.R | 2 README.md | 7 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Overview.R | 310 ++++++++++++++++++----------------- inst/doc/Overview.Rmd | 27 ++- inst/doc/Overview.html | 88 +++++---- inst/doc/PLADMM.html | 13 - inst/extdata/shirt.soc |only inst/extdata/sushi.soc |only man/PlackettLuce-package.Rd | 31 +++ man/adjacency.Rd | 2 man/figures/always-loses-1.png |binary man/figures/qv-1.png |binary man/pltree.Rd | 2 man/preflib.Rd | 4 man/qvcalc.PlackettLuce.Rd | 2 man/rankings.Rd | 2 tests/testthat/helper.R | 2 tests/testthat/test-adherence.R | 2 tests/testthat/test-admm.R | 42 ++-- tests/testthat/test-algorithms.R | 2 tests/testthat/test-log-likelihood.R | 7 vignettes/Overview.Rmd | 27 ++- vignettes/nascar_timings.rds |binary vignettes/netflix_timings.rds |binary vignettes/pltree.png |binary vignettes/sushi_timings.rds |binary vignettes/tshirt_timings.rds |binary 39 files changed, 575 insertions(+), 474 deletions(-)
Title: Distributed Online Covariance Matrix Tests
Description: Distributed Online Covariance Matrix Tests 'Docovt' is a powerful tool designed to efficiently process and analyze distributed datasets. It enables users to perform covariance matrix tests in an online, distributed manner, making it highly suitable for large-scale data analysis. By leveraging advanced computational techniques, 'Docovt' ensures robust and scalable solutions for statistical analysis, particularly in scenarios where data is dispersed across multiple nodes or sources. This package is ideal for researchers and practitioners working with high-dimensional data, providing a flexible and efficient framework for covariance matrix estimation and hypothesis testing. The philosophy of 'Docovt' is described in Guo G.(2025) <doi:10.1016/j.physa.2024.130308>.
Author: Guangbao Guo [aut, cre] ,
Congfan Zhang [aut]
Maintainer: Guangbao Guo <ggb11111111@163.com>
Diff between Docovt versions 0.2 dated 2025-06-29 and 0.3 dated 2025-09-03
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++++++- R/COVID19.R |only R/corneal.R |only R/miRNA.R |only data |only man/COVID19.Rd |only man/corneal.Rd |only man/miRNA.Rd |only 9 files changed, 15 insertions(+), 5 deletions(-)
Title: Self-Controlled Case Series
Description: Execute the self-controlled case series (SCCS) design using observational
data in the OMOP Common Data Model. Extracts all necessary data from the database and
transforms it to the format required for SCCS. Age and season can be modeled
using splines assuming constant hazard within calendar months. Event-dependent
censoring of the observation period can be corrected for. Many exposures can be
included at once (MSCCS), with regularization on all coefficients except for the
exposure of interest. Includes diagnostics for all major assumptions of the SCCS.
Author: Martijn Schuemie [aut, cre],
Patrick Ryan [aut],
Trevor Shaddox [aut],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SelfControlledCaseSeries versions 6.0.1 dated 2025-07-15 and 6.1.0 dated 2025-09-03
DESCRIPTION | 10 ++++---- MD5 | 36 ++++++++++++++--------------- NEWS.md | 17 +++++++++++++ R/DataLoadingSaving.R | 1 R/Export.R | 7 ++--- R/ModelFitting.R | 47 ++++++++++++++++++++++---------------- R/SettingsObjects.R | 11 ++++++++ README.md | 5 ++-- inst/doc/MultipleAnalyses.pdf |binary inst/doc/ResultsSchema.Rmd | 2 - inst/doc/ResultsSchema.pdf |binary inst/doc/SingleStudies.pdf |binary man/createAgeCovariateSettings.Rd | 4 +-- man/createFitSccsModelArgs.Rd | 8 ++++++ man/fitSccsModel.Rd | 5 ---- man/hasCalendarTimeEffect.Rd | 4 +-- man/hasSeasonality.Rd | 4 +-- tests/testthat/test-eunomia.R | 11 ++++++++ vignettes/ResultsSchema.Rmd | 2 - 19 files changed, 111 insertions(+), 63 deletions(-)
More information about SelfControlledCaseSeries at CRAN
Permanent link
Title: SAE using HB Twofold Subarea Model under Beta Distribution
Description: Estimates area and subarea level proportions using the Small Area Estimation (SAE) Twofold Subarea Model with a hierarchical Bayesian (HB) approach under Beta distribution. A number of simulated datasets generated for illustration purposes are also included. The 'rstan' package is employed to estimate parameters via the Hamiltonian Monte Carlo and No U-Turn Sampler algorithm. The model-based estimators include the HB mean, the variation of the mean, and quantiles. For references, see Rao and Molina (2015) <doi:10.1002/9781118735855>, Torabi and Rao (2014) <doi:10.1016/j.jmva.2014.02.001>, Leyla Mohadjer et al.(2007) <http://www.asasrms.org/Proceedings/y2007/Files/JSM2007-000559.pdf>, Erciulescu et al.(2019) <doi:10.1111/rssa.12390>, and Yudasena (2024).
Author: Nasya Zahira Putri [aut, cre],
Cucu Sumarni [aut],
Rizal Fauziarochman Yudasena [aut]
Maintainer: Nasya Zahira Putri <nasyazp28@gmail.com>
Diff between saeHB.TF.beta versions 0.1.0 dated 2025-07-14 and 0.2.0 dated 2025-09-03
DESCRIPTION | 16 - MD5 | 33 +- NAMESPACE | 8 R/explore.R |only README.md | 144 +++++++++-- inst/doc/saeHB-Twofold-Beta.R | 79 +++++- inst/doc/saeHB-Twofold-Beta.Rmd | 133 ++++++++-- inst/doc/saeHB-Twofold-Beta.html | 484 +++++++++++++++---------------------- inst/stan/saeHB_TF_beta.stan | 5 inst/stan/saeHB_TF_beta_NA.stan | 7 man/explore.Rd |only man/figures |only src/stanExports_saeHB_TF_beta.h | 337 +++++++++---------------- src/stanExports_saeHB_TF_beta_NA.h | 467 ++++++++++++----------------------- tests |only vignettes/saeHB-Twofold-Beta.Rmd | 133 ++++++++-- 16 files changed, 955 insertions(+), 891 deletions(-)
Title: Assess Mating Potential in Space and Time
Description: Simulate, manage, visualize, and analyze spatially and temporally
explicit datasets of mating potential. Implements methods to calculate
synchrony, proximity, and compatibility.Synchrony calculations are based on
methods described in Augspurger (1983) <doi:10.2307/2387650>,
Kempenaers (1993) <doi:10.2307/3676415>, Ison et al. (2014)
<doi:10.3732/ajb.1300065>, and variations on these, as described.
Author: Stuart Wagenius [cre, aut],
Danny Hanson [aut],
Amy Waananen [aut]
Maintainer: Stuart Wagenius <stuart.wagenius@gmail.com>
Diff between mateable versions 0.3.2 dated 2023-02-04 and 0.3.3 dated 2025-09-03
DESCRIPTION | 10 - MD5 | 32 ++-- R/mateable.R | 6 R/plot3DScene.R | 2 R/plot3Dpotential.R | 2 R/plotPotential.R | 2 R/spatialDataFunctions.R | 4 README.md | 4 build/vignette.rds |binary inst/doc/investigateMatingScene.R | 8 - inst/doc/investigateMatingScene.html | 244 +++++++++++++++++------------------ man/kNearNeighbors.Rd | 2 man/mateable-package.Rd | 4 man/pairDist.Rd | 2 man/plot3DPotential.Rd | 2 man/plot3DScene.Rd | 2 man/plotPotential.Rd | 2 17 files changed, 166 insertions(+), 162 deletions(-)
Title: Kernel Based Gradient Matching for Parameter Inference in
Ordinary Differential Equations
Description: The kernel ridge regression and the gradient matching algorithm proposed in Niu et al. (2016) <https://proceedings.mlr.press/v48/niu16.html> and the warping algorithm proposed in Niu et al. (2017) <DOI:10.1007/s00180-017-0753-z> are implemented for parameter inference in differential equations. Four schemes are provided for improving parameter estimation in odes by using the odes regularisation and warping.
Author: Mu Niu [aut, cre]
Maintainer: Mu Niu <mu.niu@glasgow.ac.uk>
Diff between KGode versions 1.0.4 dated 2022-08-19 and 1.0.5 dated 2025-09-03
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- R/WarpSin.r | 4 ++-- R/kernel.r | 6 +++--- R/mlp.r | 4 ++-- R/ode.r | 4 ++-- R/rbf.r | 4 ++-- R/rk3g.r | 4 ++-- R/rkhs.r | 4 ++-- man/Kernel.Rd | 4 ++-- man/MLP.Rd | 4 ++-- man/RBF.Rd | 4 ++-- man/Warp.Rd | 4 ++-- man/ode.Rd | 4 ++-- man/rkg3.Rd | 4 ++-- man/rkhs.Rd | 4 ++-- 16 files changed, 48 insertions(+), 48 deletions(-)
Title: Extended Two-Way Fixed Effects
Description: Convenience functions for implementing extended two-way
fixed effect regressions a la Wooldridge (2021, 2023)
<doi:10.2139/ssrn.3906345>, <doi:10.1093/ectj/utad016>.
Author: Grant McDermott [aut, cre] ,
Frederic Kluser [ctb]
Maintainer: Grant McDermott <gmcd@amazon.com>
This is a re-admission after prior archival of version 0.5.0 dated 2024-12-16
Diff between etwfe versions 0.5.0 dated 2024-12-16 and 0.6.0 dated 2025-09-03
DESCRIPTION | 13 MD5 | 34 NEWS.md | 40 R/emfx.R | 232 ++-- R/etwfe.R | 356 ++++-- R/plot.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/etwfe.Rmd | 4 inst/doc/etwfe.html | 2403 ++++++++++++++++++++++----------------------- inst/tinytest/test_baker.R | 258 +++- inst/tinytest/test_emfx.R | 643 +++++++++--- inst/tinytest/test_etwfe.R | 562 ++++++++-- inst/tinytest/test_xvar.R | 590 ++++++++--- man/emfx.Rd | 35 man/etwfe.Rd | 34 man/plot.emfx.Rd | 14 vignettes/etwfe.Rmd | 4 18 files changed, 3254 insertions(+), 1972 deletions(-)
Title: 'a la Carte' on Text (ConText) Embedding Regression
Description: A fast, flexible and transparent framework to estimate context-specific word and short document embeddings using the 'a la carte'
embeddings approach developed by Khodak et al. (2018) <doi:10.48550/arXiv.1805.05388> and evaluate hypotheses about covariate effects on embeddings using
the regression framework developed by Rodriguez et al. (2021)<doi:10.1017/S0003055422001228>. New version of the package applies a new estimator to measure the distance between word embeddings as described in Green et al. (2025) <doi:10.1017/pan.2024.22>.
Author: Pedro L. Rodriguez [aut, cph] ,
Arthur Spirling [aut] ,
Brandon Stewart [aut] ,
Christopher Barrie [ctb] ,
Sofia Avila [cre, aut]
Maintainer: Sofia Avila <sofiaavila@princeton.edu>
Diff between conText versions 1.4.3 dated 2023-02-09 and 3.0.0 dated 2025-09-03
conText-1.4.3/conText/man/bootstrap_ols.Rd |only conText-1.4.3/conText/man/permute_ols.Rd |only conText-1.4.3/conText/vignettes/nns_ratio.png |only conText-3.0.0/conText/DESCRIPTION | 40 conText-3.0.0/conText/MD5 | 73 - conText-3.0.0/conText/NAMESPACE | 20 conText-3.0.0/conText/R/classes.R | 3 conText-3.0.0/conText/R/compute_transform.R | 7 conText-3.0.0/conText/R/conText-package.R |only conText-3.0.0/conText/R/conText.R | 375 +++++---- conText-3.0.0/conText/R/contrast_nns.R | 2 conText-3.0.0/conText/R/cos_sim.R | 2 conText-3.0.0/conText/R/dem.R | 1 conText-3.0.0/conText/R/feature_sim.R | 4 conText-3.0.0/conText/R/fem.R | 9 conText-3.0.0/conText/R/get_grouped_similarity.R |only conText-3.0.0/conText/R/get_nns.R | 10 conText-3.0.0/conText/R/get_nns_ratio.R | 6 conText-3.0.0/conText/R/get_seq_cos_sim.R | 1 conText-3.0.0/conText/R/globals.R | 3 conText-3.0.0/conText/R/nns.R | 4 conText-3.0.0/conText/R/plot_nns_ratio.R | 6 conText-3.0.0/conText/R/zzz.R |only conText-3.0.0/conText/README.md | 11 conText-3.0.0/conText/build/partial.rdb |only conText-3.0.0/conText/build/vignette.rds |binary conText-3.0.0/conText/inst/doc/quickstart.R | 115 +- conText-3.0.0/conText/inst/doc/quickstart.Rmd | 92 +- conText-3.0.0/conText/inst/doc/quickstart.html | 833 ++++++++++---------- conText-3.0.0/conText/man/compute_transform.Rd | 4 conText-3.0.0/conText/man/conText-package.Rd |only conText-3.0.0/conText/man/conText.Rd | 40 conText-3.0.0/conText/man/contrast_nns.Rd | 2 conText-3.0.0/conText/man/feature_sim.Rd | 4 conText-3.0.0/conText/man/fem.Rd | 4 conText-3.0.0/conText/man/get_grouped_similarity.Rd |only conText-3.0.0/conText/man/get_nns.Rd | 4 conText-3.0.0/conText/man/get_nns_ratio.Rd | 6 conText-3.0.0/conText/man/get_seq_cos_sim.Rd | 1 conText-3.0.0/conText/man/plot_nns_ratio.Rd | 6 conText-3.0.0/conText/man/run_ols.Rd | 4 conText-3.0.0/conText/vignettes/quickstart.Rmd | 92 +- 42 files changed, 1035 insertions(+), 749 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],
Sungho Choi [aut],
Jaewoong Heo [aut],
Mingu Jee [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jstable versions 1.3.16 dated 2025-08-20 and 1.3.17 dated 2025-09-03
DESCRIPTION | 8 MD5 | 26 NAMESPACE | 5 NEWS.md | 14 R/cox2.R | 258 +++++-- R/gee.R | 54 + R/glmshow.R | 163 +++- R/label.R | 173 ++++- R/lmer.R | 48 + build/vignette.rds |binary inst/doc/jstable.R | 4 inst/doc/jstable.html | 676 ++++++++++---------- inst/doc/jstable_competing_risk_analysis.html | 82 +- inst/doc/jstable_options.html | 848 +++++++++++++------------- 14 files changed, 1384 insertions(+), 975 deletions(-)
Title: Tools for Managing Imaging FlowCytobot (IFCB) Data
Description: A comprehensive suite of tools for managing, processing, and
analyzing data from the IFCB. I R FlowCytobot ('iRfcb') supports
quality control, geospatial analysis, and preparation of IFCB data for
publication in databases like <https://www.gbif.org>,
<https://www.obis.org>, <https://emodnet.ec.europa.eu/en>,
<https://shark.smhi.se/>, and <https://www.ecotaxa.org>. The package
integrates with the MATLAB 'ifcb-analysis' tool, which is described in
Sosik and Olson (2007) <doi:10.4319/lom.2007.5.204>, and provides
features for working with raw, manually classified, and machine
learning–classified image datasets. Key functionalities include image
extraction, particle size distribution analysis, taxonomic data
handling, and biomass concentration calculations, essential for
plankton research.
Author: Anders Torstensson [aut, cre] ,
Kendra Hayashi [ctb] ,
Jamie Enslein [ctb],
Raphael Kudela [ctb] ,
Alle Lie [ctb] ,
Jayme Smith [ctb] ,
DTO-BioFlow [fnd] ,
SBDI [fnd]
Maintainer: Anders Torstensson <anders.torstensson@smhi.se>
Diff between iRfcb versions 0.5.1 dated 2025-04-22 and 0.5.2 dated 2025-09-03
DESCRIPTION | 58 ++++++++----- MD5 | 58 ++++++------- NEWS.md | 8 + R/ifcb_download_test_data.R | 89 ++++++++++++--------- R/ifcb_extract_biovolumes.R | 46 +++++++--- R/ifcb_get_mat_variable.R | 2 R/ifcb_is_near_land.R | 2 R/ifcb_read_features.R | 4 R/ifcb_summarize_biovolumes.R | 8 + R/zzz.R | 11 ++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 4 inst/doc/a-general-tutorial.html | 4 inst/doc/qc-tutorial.html | 4 man/ifcb_download_test_data.Rd | 12 ++ man/ifcb_extract_biovolumes.Rd | 3 man/ifcb_get_mat_variable.Rd | 2 man/ifcb_is_near_land.Rd | 2 man/ifcb_summarize_biovolumes.Rd | 3 tests/testthat/helper.R | 15 +++ tests/testthat/test-ifcb_download_dashboard_data.R | 3 tests/testthat/test-ifcb_download_test_data.R | 6 + tests/testthat/test-ifcb_extract_biovolumes.R | 17 ++-- tests/testthat/test-ifcb_get_runtime.R | 3 tests/testthat/test-ifcb_is_diatom.R | 6 - tests/testthat/test-ifcb_is_near_land.R | 3 tests/testthat/test-ifcb_match_taxa_names.R | 6 - tests/testthat/test-ifcb_prepare_whoi_plankton.R | 3 tests/testthat/test-ifcb_summarize_biovolumes.R | 6 - 30 files changed, 257 insertions(+), 131 deletions(-)
Title: Utilities for Working with Google APIs
Description: Provides utilities for working with Google APIs
<https://developers.google.com/apis-explorer>. This includes
functions and classes for handling common credential types and for
preparing, executing, and processing HTTP requests.
Author: Jennifer Bryan [aut, cre] ,
Craig Citro [aut],
Hadley Wickham [aut] ,
Google Inc [cph],
Posit Software, PBC [cph, fnd]
Maintainer: Jennifer Bryan <jenny@posit.co>
Diff between gargle versions 1.5.2 dated 2023-07-20 and 1.6.0 dated 2025-09-03
DESCRIPTION | 17 MD5 | 176 ++-- NEWS.md | 54 - R/AuthState-class.R | 273 +++--- R/Gargle-class.R | 429 +++++----- R/cred_funs.R | 26 R/credentials_app_default.R | 6 R/credentials_external_account.R | 259 +++--- R/credentials_gce.R | 284 +++--- R/credentials_service_account.R | 29 R/credentials_user_oauth2.R | 12 R/gargle-package.R | 2 R/gargle_oauth_client.R | 37 R/oauth-cache.R | 26 R/oauth-init.R | 40 R/request_develop.R | 26 R/request_make.R | 31 R/request_retry.R | 118 +- R/response_process.R | 99 +- R/roxygen-templates.R | 207 ++-- R/secret.R | 18 R/utils-ui.R | 63 - R/utils.R | 30 R/zzz.R | 3 README.md | 6 build/vignette.rds |binary inst/discovery-doc-ingest/discover-discovery.R | 2 inst/discovery-doc-ingest/drive-example.R | 8 inst/discovery-doc-ingest/ingest-functions.R | 20 inst/doc/auth-from-web.R | 20 inst/doc/auth-from-web.Rmd | 14 inst/doc/auth-from-web.html | 11 inst/doc/gargle-auth-in-client-package.R | 282 +++--- inst/doc/gargle-auth-in-client-package.Rmd | 4 inst/doc/gargle-auth-in-client-package.html | 7 inst/doc/get-api-credentials.R | 44 - inst/doc/get-api-credentials.Rmd | 16 inst/doc/get-api-credentials.html | 5 inst/doc/how-gargle-gets-tokens.R | 302 +++---- inst/doc/how-gargle-gets-tokens.Rmd | 16 inst/doc/how-gargle-gets-tokens.html | 7 inst/doc/non-interactive-auth.R | 163 --- inst/doc/non-interactive-auth.Rmd | 19 inst/doc/non-interactive-auth.html | 5 inst/doc/oauth-client-not-app.R | 102 +- inst/doc/oauth-client-not-app.html | 5 inst/doc/request-helper-functions.R | 112 +- inst/doc/request-helper-functions.html | 1 inst/doc/troubleshooting.R | 48 - inst/doc/troubleshooting.html | 5 man/gargle_oauth_client_from_json.Rd | 2 man/gargle_secret.Rd | 2 man/gce_instance_service_accounts.Rd | 2 man/request_make.Rd | 2 man/request_retry.Rd | 2 man/response_process.Rd | 2 tests/spelling.R | 3 tests/testthat/_snaps/credentials_service_account.md | 10 tests/testthat/_snaps/request_retry.md | 38 tests/testthat/_snaps/response_process.md | 31 tests/testthat/fixtures/drive-files-get-nonexistent-file-id_404.R | 5 tests/testthat/fixtures/sheets-spreadsheets-get-api-key-not-enabled_403.R | 11 tests/testthat/fixtures/sheets-spreadsheets-get-bad-field-mask_400.R | 5 tests/testthat/fixtures/sheets-spreadsheets-get-nonexistent-range_400.R | 5 tests/testthat/fixtures/sheets-spreadsheets-get-nonexistent-sheet-id_404.R | 3 tests/testthat/fixtures/sheets-spreadsheets-get-quota-exceeded-readgroup_429.R | 5 tests/testthat/fixtures/sheets-spreadsheets-get-quota-exceeded-readgroup_429.rds |binary tests/testthat/fixtures/sheets-spreadsheets-get-service-disabled.R |only tests/testthat/fixtures/sheets-spreadsheets-get-service-disabled_403.rds |only tests/testthat/helper.R | 8 tests/testthat/test-AuthState-class.R | 54 + tests/testthat/test-Gargle-class.R | 12 tests/testthat/test-assets.R | 7 tests/testthat/test-cred_funs.R | 10 tests/testthat/test-credentials_app_default.R | 24 tests/testthat/test-credentials_byo_oauth2.R | 6 tests/testthat/test-credentials_service_account.R | 6 tests/testthat/test-gargle_oauth_client.R | 17 tests/testthat/test-oauth-cache.R | 12 tests/testthat/test-oauth-refresh.R | 7 tests/testthat/test-request_develop.R | 6 tests/testthat/test-request_retry.R | 65 + tests/testthat/test-response_process.R | 14 tests/testthat/test-utils-ui.R | 19 tests/testthat/test-utils.R | 8 vignettes/auth-from-web.Rmd | 14 vignettes/gargle-auth-in-client-package.Rmd | 4 vignettes/get-api-credentials.Rmd | 16 vignettes/how-gargle-gets-tokens.Rmd | 16 vignettes/non-interactive-auth.Rmd | 19 90 files changed, 2181 insertions(+), 1780 deletions(-)
Title: Pharmacometric Modeling
Description: Facilitate Pharmacokinetic (PK) and Pharmacodynamic (PD) modeling
and simulation with powerful tools for Nonlinear Mixed-Effects (NLME)
modeling. The package provides access to the same advanced Maximum Likelihood
algorithms used by the NLME-Engine in the Phoenix platform. These tools support
a range of analyses, from parametric methods to individual and pooled data, and
support integrated use within the Pirana pharmacometric workbench
<doi:10.1002/psp4.70067>. Execution is supported both locally or on
remote machines.
Author: James Craig [aut, cre],
Michael Tomashevskiy [aut],
Vitalii Nazarov [aut],
Shuhua Hu [ctb],
Soltanshahi Fred [aut],
Certara USA, Inc. [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Diff between Certara.RsNLME versions 3.1.0 dated 2025-08-22 and 3.1.0.1 dated 2025-09-03
DESCRIPTION | 6 +- MD5 | 90 ++++++++++++++++++------------------- R/SimpleNlmeJob.R | 2 R/acceptAllEffects.R | 2 R/addTablesToColumnMapping.R | 2 R/bootstrap.r | 2 R/checkHostParams.R | 2 R/copyModel.R | 2 R/covariateModel.R | 2 R/create_model_from_metamodel.R | 2 R/create_model_info.R | 2 R/extract_mmdl.R | 2 R/fitmodel.R | 2 R/getThetas.R | 2 R/job.r | 2 R/obtain_NLMELicense.R | 4 - R/profile_estimation.r | 4 - R/run_metamodel.R | 4 - R/shotgunSearch.R | 2 R/sortfit.R | 2 R/stepwiseSearch.R | 2 R/vpc.r | 6 +- man/NlmeJobStatus.Rd | 2 man/NlmeVpcParams-class.Rd | 2 man/RunProfilePertubation.Rd | 2 man/acceptAllEffects.Rd | 2 man/bootstrap.Rd | 2 man/checkHostParams.Rd | 2 man/copyModel.Rd | 2 man/covariateModel.Rd | 2 man/createModelInfo.Rd | 2 man/create_model_from_metamodel.Rd | 2 man/extract_mmdl.Rd | 2 man/fitmodel.Rd | 2 man/getThetas.Rd | 2 man/obtain_NLMELicense.Rd | 2 man/parse_NLMEHosts.Rd | 2 man/print.SimpleNlmeJob.Rd | 2 man/profilePertubate.Rd | 2 man/remove_NLMELicense.Rd | 2 man/run_metamodel.Rd | 2 man/shotgunSearch.Rd | 2 man/simmodel.Rd | 2 man/sortfit.Rd | 2 man/stepwiseSearch.Rd | 2 man/vpcmodel.Rd | 2 46 files changed, 97 insertions(+), 97 deletions(-)
More information about Certara.RsNLME at CRAN
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