Title: Fit Sparse Linear Regression Models via Nonconvex Optimization
Description: Efficient procedure for fitting regularization paths between L1 and L0, using the MC+ penalty of Zhang, C.H. (2010)<doi:10.1214/09-AOS729>. Implements the methodology described in Mazumder, Friedman and Hastie (2011) <DOI: 10.1198/jasa.2011.tm09738>. Sparsenet computes the regularization surface over both the family parameter and the tuning parameter by coordinate descent.
Author: Trevor Hastie [aut, cre],
Rahul Mazumder [aut],
Jerome Friedman [aut]
Maintainer: Trevor Hastie <hastie@stanford.edu>
Diff between sparsenet versions 1.6 dated 2024-02-05 and 1.7 dated 2024-11-16
DESCRIPTION | 27 +++++++++++++++++++-------- MD5 | 8 ++++---- NAMESPACE | 2 +- R/sparsenet.R | 20 ++++++++++++++------ man/sparsenet.Rd | 4 +++- 5 files changed, 41 insertions(+), 20 deletions(-)
Title: Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data. In
particular representation, manipulation, rate estimation and
simulation for multistate data - the Lexis suite of functions, which
includes interfaces to 'mstate', 'etm' and 'cmprsk' packages.
Contains functions for Age-Period-Cohort and Lee-Carter modeling and
a function for interval censored data and some useful functions for
tabulation and plotting, as well as a number of epidemiological data
sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.56 dated 2024-10-01 and 2.57 dated 2024-11-16
CHANGES | 7 DESCRIPTION | 8 MD5 | 53 +- NAMESPACE | 3 R/lexis.R | 32 - R/mod.Lexis.R | 75 +-- build/vignette.rds |binary inst/doc/addLexis.pdf |binary inst/doc/addLexis.rnw | 2 inst/doc/crisk.R | 114 +++-- inst/doc/crisk.pdf |binary inst/doc/crisk.rnw | 42 +- inst/doc/flup.R | 329 +++++++-------- inst/doc/flup.pdf |binary inst/doc/flup.rnw | 912 +++++++++++++++++++++++--------------------- inst/doc/simLexis.pdf |binary inst/doc/simLexis.rnw | 2 inst/doc/yll.pdf |binary inst/doc/yll.rnw | 2 man/Lexis.Rd | 2 man/mod.Lexis.Rd | 40 + vignettes/Wilhelm_Lexis.jpg |only vignettes/addLexis.rnw | 2 vignettes/crisk.rnw | 42 +- vignettes/flup.rnw | 912 +++++++++++++++++++++++--------------------- vignettes/simLexis.rnw | 2 vignettes/topreport.tex | 24 + vignettes/yll.rnw | 2 28 files changed, 1415 insertions(+), 1192 deletions(-)
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor [aut, cre]
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.2.8 dated 2023-06-29 and 0.3.6 dated 2024-11-16
DFA.CANCOR-0.2.8/DFA.CANCOR/R/boc.R |only DFA.CANCOR-0.2.8/DFA.CANCOR/R/steiger.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/DESCRIPTION | 17 +- DFA.CANCOR-0.3.6/DFA.CANCOR/MD5 | 21 ++- DFA.CANCOR-0.3.6/DFA.CANCOR/NAMESPACE | 25 ++-- DFA.CANCOR-0.3.6/DFA.CANCOR/R/DFA.R | 9 - DFA.CANCOR-0.3.6/DFA.CANCOR/R/GROUP.PROFILES.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/NORMALITY.R | 132 ++++++++++++---------- DFA.CANCOR-0.3.6/DFA.CANCOR/R/OUTLIERS.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/onAttach.R | 1 DFA.CANCOR-0.3.6/DFA.CANCOR/R/umvn.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/utilities_boc.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/R/utilities_steiger.R |only DFA.CANCOR-0.3.6/DFA.CANCOR/man/GROUP.PROFILES.Rd |only DFA.CANCOR-0.3.6/DFA.CANCOR/man/NORMALITY.Rd | 35 +++-- DFA.CANCOR-0.3.6/DFA.CANCOR/man/OUTLIERS.Rd |only 16 files changed, 145 insertions(+), 95 deletions(-)
Title: Bayesian Spatial Analysis
Description: For spatial data analysis; provides exploratory spatial analysis tools, spatial regression, spatial econometric, and disease mapping models, model diagnostics, and special methods for inference with small area survey data (e.g., the America Community Survey (ACS)) and censored population health monitoring data. Models are pre-specified using the Stan programming language, a platform for Bayesian inference using Markov chain Monte Carlo (MCMC). References: Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>; Donegan (2021) <doi:10.31219/osf.io/3ey65>; Donegan (2022) <doi:10.21105/joss.04716>; Donegan, Chun and Hughes (2020) <doi:10.1016/j.spasta.2020.100450>; Donegan, Chun and Griffith (2021) <doi:10.3390/ijerph18136856>; Morris et al. (2019) <doi:10.1016/j.sste.2019.100301>.
Author: Connor Donegan [aut, cre] ,
Mitzi Morris [ctb],
Amy Tims [ctb]
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between geostan versions 0.7.0 dated 2024-09-18 and 0.8.0 dated 2024-11-16
geostan-0.7.0/geostan/inst/stan/parts/trans_params_expression_car.stan |only geostan-0.7.0/geostan/tests/testthat/test-information-criteria.R |only geostan-0.8.0/geostan/DESCRIPTION | 16 geostan-0.8.0/geostan/MD5 | 135 geostan-0.8.0/geostan/NAMESPACE | 7 geostan-0.8.0/geostan/NEWS.md | 18 geostan-0.8.0/geostan/R/convenience-functions.R | 215 geostan-0.8.0/geostan/R/geostan_fit-methods.R | 256 geostan-0.8.0/geostan/R/impacts.R |only geostan-0.8.0/geostan/R/information-criteria.R | 4 geostan-0.8.0/geostan/R/internal-functions.R | 80 geostan-0.8.0/geostan/R/moran.R | 15 geostan-0.8.0/geostan/R/posterior_predict.R | 181 geostan-0.8.0/geostan/R/stan_car.R | 180 geostan-0.8.0/geostan/R/stan_esf.R | 29 geostan-0.8.0/geostan/R/stan_glm.R | 124 geostan-0.8.0/geostan/R/stan_icar.R | 19 geostan-0.8.0/geostan/R/stan_sar.R | 305 geostan-0.8.0/geostan/README.md | 236 geostan-0.8.0/geostan/build/vignette.rds |binary geostan-0.8.0/geostan/inst/doc/custom-spatial-models.R | 78 geostan-0.8.0/geostan/inst/doc/custom-spatial-models.Rmd | 236 geostan-0.8.0/geostan/inst/doc/custom-spatial-models.html | 311 geostan-0.8.0/geostan/inst/doc/measuring-sa.Rmd | 22 geostan-0.8.0/geostan/inst/doc/measuring-sa.html | 66 geostan-0.8.0/geostan/inst/doc/raster-regression.R | 48 geostan-0.8.0/geostan/inst/doc/raster-regression.Rmd | 81 geostan-0.8.0/geostan/inst/doc/raster-regression.html | 189 geostan-0.8.0/geostan/inst/doc/spatial-analysis.R |only geostan-0.8.0/geostan/inst/doc/spatial-analysis.Rmd |only geostan-0.8.0/geostan/inst/doc/spatial-analysis.html |only geostan-0.8.0/geostan/inst/doc/spatial-me-models.R | 2 geostan-0.8.0/geostan/inst/doc/spatial-me-models.Rmd | 68 geostan-0.8.0/geostan/inst/doc/spatial-me-models.html | 317 geostan-0.8.0/geostan/inst/doc/spatial-weights-matrix.html | 77 geostan-0.8.0/geostan/inst/stan/foundation.stan | 44 geostan-0.8.0/geostan/inst/stan/parts/data.stan | 5 geostan-0.8.0/geostan/inst/stan/parts/model.stan | 151 geostan-0.8.0/geostan/inst/stan/parts/params.stan | 9 geostan-0.8.0/geostan/inst/stan/parts/priors.stan | 92 geostan-0.8.0/geostan/inst/stan/parts/trans_data.stan | 26 geostan-0.8.0/geostan/inst/stan/parts/trans_params_declaration.stan | 6 geostan-0.8.0/geostan/inst/stan/parts/trans_params_expression_auto-model.stan | 69 geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-3-1.png |binary geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-5-1.png |binary geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-8-1.png |only geostan-0.8.0/geostan/man/figures/README-unnamed-chunk-9-1.png |only geostan-0.8.0/geostan/man/impacts.Rd |only geostan-0.8.0/geostan/man/posterior_predict.Rd | 52 geostan-0.8.0/geostan/man/predict.geostan_fit.Rd | 89 geostan-0.8.0/geostan/man/row_standardize.Rd | 7 geostan-0.8.0/geostan/man/shape2mat.Rd | 2 geostan-0.8.0/geostan/man/sim_sar.Rd | 78 geostan-0.8.0/geostan/man/sp_diag.Rd | 2 geostan-0.8.0/geostan/man/stan_car.Rd | 110 geostan-0.8.0/geostan/man/stan_esf.Rd | 6 geostan-0.8.0/geostan/man/stan_glm.Rd | 106 geostan-0.8.0/geostan/man/stan_icar.Rd | 4 geostan-0.8.0/geostan/man/stan_sar.Rd | 203 geostan-0.8.0/geostan/src/stanExports_foundation.h | 3791 +++++----- geostan-0.8.0/geostan/tests/check-ME-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-ME-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/check-SEM-CAR-GLM-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-SEM-CAR-GLM-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/check-SLM-estimates-monte-carlo-output.csv |only geostan-0.8.0/geostan/tests/check-SLM-estimates-monte-carlo.R |only geostan-0.8.0/geostan/tests/missing-y.R |only geostan-0.8.0/geostan/tests/model-comparison.R |only geostan-0.8.0/geostan/tests/testthat/test-stan-glm.R | 2 geostan-0.8.0/geostan/tests/testthat/test-stan-sar.R | 40 geostan-0.8.0/geostan/vignettes/autonormal.stan |only geostan-0.8.0/geostan/vignettes/car_poisson.stan |only geostan-0.8.0/geostan/vignettes/custom-spatial-models.Rmd | 236 geostan-0.8.0/geostan/vignettes/measuring-sa.Rmd | 22 geostan-0.8.0/geostan/vignettes/raster-regression.Rmd | 81 geostan-0.8.0/geostan/vignettes/spatial-analysis.Rmd |only geostan-0.8.0/geostan/vignettes/spatial-analysis.bib |only geostan-0.8.0/geostan/vignettes/spatial-me-models.Rmd | 68 geostan-0.8.0/geostan/vignettes/wcar-lpdf.stan | 30 79 files changed, 5433 insertions(+), 3213 deletions(-)
Title: Cox Model for Case-Cohort Data with Stratified
Subcohort-Selection
Description: Contains a function, also called 'cchs', that calculates Estimator III of Borgan et al (2000), <DOI:10.1023/A:1009661900674>. This estimator is for fitting a Cox proportional hazards model to data from a case-cohort study where the subcohort was selected by stratified simple random sampling.
Author: E. Jones [aut, cre]
Maintainer: E. Jones <edmundjones79@gmail.com>
Diff between cchs versions 0.4.4 dated 2024-01-31 and 0.4.5 dated 2024-11-16
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- build/partial.rdb |binary man/cchs.Rd | 18 +++++++++--------- man/cchsData.Rd | 6 +++--- 5 files changed, 22 insertions(+), 21 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Duncan Murdoch [aut, cre],
Daniel Adler [aut],
Oleg Nenadic [ctb],
Simon Urbanek [ctb],
Ming Chen [ctb],
Albrecht Gebhardt [ctb],
Ben Bolker [ctb],
Gabor Csardi [ctb],
Adam Strzelecki [ctb],
Alexander Senger [ctb],
The R Core Team [ctb, cph],
Dirk Ed [...truncated...]
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between rgl versions 1.3.12 dated 2024-10-28 and 1.3.14 dated 2024-11-16
DESCRIPTION | 6 ++-- MD5 | 45 ++++++++++++++++----------------- NAMESPACE | 3 +- NEWS.md | 19 ++++++++++++++ R/convertScene.R | 61 ++++++++++++++++++++++++++++++++++++++++++++- R/r3d.rgl.R | 15 +++++++++-- R/scene.R | 5 ++- inst/doc/WebGL.R | 8 ++--- inst/doc/WebGL.html | 34 ++++++++++++------------- inst/doc/demos.html | 60 ++++++++++++++++++++++---------------------- inst/doc/deprecation.html | 2 - inst/doc/pkgdown.R | 2 - inst/doc/pkgdown.html | 6 ++-- inst/doc/rgl.R | 30 +++++++++++----------- inst/doc/rgl.html | 38 ++++++++++++++-------------- inst/doc/transparency.html | 18 ++++++------- man/axes3d.Rd | 26 +++++++++++-------- man/persp3d.function.Rd | 4 +- man/rgl.incrementID.Rd |only man/setAxisCallbacks.Rd | 2 - src/api.cpp | 7 +++++ src/api.h | 2 + src/init.cpp | 2 + src/subscene.cpp | 8 +---- 24 files changed, 254 insertions(+), 149 deletions(-)
Title: Identify and Correct Invalid HGNC Human Gene Symbols and MGI
Mouse Gene Symbols
Description: Contains functions for
identifying and correcting HGNC human gene symbols and MGI mouse gene symbols
which have been converted to date format by Excel, withdrawn, or aliased.
Also contains functions for reversibly converting between HGNC
symbols and valid R names.
Author: Sehyun Oh [aut],
Ayush Aggarwal [aut],
Markus Riester [aut],
Levi Waldron [aut, cre]
Maintainer: Levi Waldron <lwaldron.research@gmail.com>
Diff between HGNChelper versions 0.8.14 dated 2024-05-18 and 0.8.15 dated 2024-11-16
DESCRIPTION | 10 +-- MD5 | 22 +++---- NEWS | 7 +- R/data.R | 2 R/getCurrentMaps.R | 7 +- build/vignette.rds |binary data/hgnc.table.rda |binary data/mouse.table.rda |binary inst/doc/index.html | 110 +++++++++++++++++------------------ inst/extdata/date_of_last_update.txt | 2 man/hgnc.table.Rd | 4 - man/mouse.table.Rd | 2 12 files changed, 86 insertions(+), 80 deletions(-)
Title: Easily Work with 'Font Awesome' Icons
Description: Easily and flexibly insert 'Font Awesome' icons into 'R Markdown'
documents and 'Shiny' apps. These icons can be inserted into HTML content
through inline 'SVG' tags or 'i' tags. There is also a utility function for
exporting 'Font Awesome' icons as 'PNG' images for those situations where
raster graphics are needed.
Author: Richard Iannone [aut, cre] ,
Christophe Dervieux [ctb] ,
Winston Chang [ctb],
Dave Gandy [ctb, cph] ,
Posit Software, PBC [cph, fnd]
Maintainer: Richard Iannone <rich@posit.co>
Diff between fontawesome versions 0.5.2 dated 2023-08-19 and 0.5.3 dated 2024-11-16
DESCRIPTION | 12 +-- MD5 | 38 +++++----- NEWS.md | 10 ++ R/fa_brands.R | 2 R/fa_i.R | 2 R/fa_version.R | 2 R/sysdata.rda |binary inst/fontawesome/css/all.css | 74 +++++++++++++++++++-- inst/fontawesome/css/all.min.css | 10 +- inst/fontawesome/css/v4-shims.css | 4 - inst/fontawesome/css/v4-shims.min.css | 4 - inst/fontawesome/webfonts/fa-brands-400.ttf |binary inst/fontawesome/webfonts/fa-brands-400.woff2 |binary inst/fontawesome/webfonts/fa-regular-400.ttf |binary inst/fontawesome/webfonts/fa-regular-400.woff2 |binary inst/fontawesome/webfonts/fa-solid-900.ttf |binary inst/fontawesome/webfonts/fa-solid-900.woff2 |binary inst/fontawesome/webfonts/fa-v4compatibility.ttf |binary inst/fontawesome/webfonts/fa-v4compatibility.woff2 |binary tests/testthat/test-fa_icon.R | 11 +++ 20 files changed, 125 insertions(+), 44 deletions(-)
Title: Estimation and Projection of Age-Specific Mortality Rates
Description: Age-specific mortality rates are estimated and projected using
the Kannisto, Lee-Carter and related methods as described in
Sevcikova et al. (2016) <doi:10.1007/978-3-319-26603-9_15>.
Author: Hana Sevcikova [cre, aut],
Nan Li [aut],
Patrick Gerland [aut]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between MortCast versions 2.7-0 dated 2022-03-31 and 2.8-0 dated 2024-11-16
ChangeLog | 8 ++++++++ DESCRIPTION | 30 +++++++++++++++++++++++------- MD5 | 22 +++++++++++----------- R/LC.R | 3 ++- R/MortCast-data.R | 2 +- R/other_methods.R | 29 ++++++++++++++++++++++++----- build/partial.rdb |binary man/MortCast-package.Rd | 4 +--- man/PMDrho.Rd | 2 +- man/mortcast.blend.Rd | 4 ++-- man/pmdgroup.Rd | 8 +++++--- src/functions.c | 37 ++++++++++++++++++++++++++++++++----- 12 files changed, 110 insertions(+), 39 deletions(-)
Title: Pollution-Associated Risk Geospatial Analysis Site
Description: Offers tools to estimate and visualize levels of major pollutants
(CO, NO2, SO2, Ozone, PM2.5 and PM10) across the conterminous
United States for user-defined time ranges. Provides functions to
retrieve pollutant data from the U.S. Environmental Protection
Agency’s 'Air Quality System' (AQS) API service
<https://aqs.epa.gov/aqsweb/documents/data_api.html> for
interactive visualization through a 'shiny' application, allowing
users to explore pollutant levels for a given location over time
relative to the National Ambient Air Quality Standards (NAAQS).
Author: Jaehyun Joo [aut, cre],
Rebecca Greenblatt [aut],
Avantika Diwadkar [aut],
Nisha Narayanan [aut],
Blanca Himes [aut]
Maintainer: Jaehyun Joo <jaehyunjoo@outlook.com>
Diff between pargasite versions 2.1.0 dated 2024-04-23 and 2.1.1 dated 2024-11-16
DESCRIPTION | 8 ++-- MD5 | 14 +++---- R/draw_map.R | 32 +++++++++------- R/server.R | 106 ++++++++++++++++++++++++++++++++++------------------- R/subset_data.R | 4 +- R/summarize_by.R | 4 +- R/ui_functions.R | 5 +- build/vignette.rds |binary 8 files changed, 106 insertions(+), 67 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Fangmei Liu [aut] ,
Jianwu Yan [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.2 dated 2024-11-07 and 1.3 dated 2024-11-16
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Title: Diagnostic Analysis Using Forward Search Procedure for Various
Models
Description: Identifies potential data outliers and their impact on estimates and
analyses. Tool for evaluation of study credibility. Uses the forward
search approach of Atkinson and Riani, "Robust Diagnostic Regression
Analysis", 2000,<ISBN: o-387-95017-6> to prepare descriptive statistics
of a dataset that is to be analyzed by functions lm {stats}, glm {stats},
nls {stats}, lme {nlme}, or coxph {survival}, or their equivalent in
another language. Includes graphics functions to display the
descriptive statistics.
Author: William Fairweather [aut, cre]
Maintainer: William Fairweather <wrf343@flowervalleyconsulting.com>
Diff between forsearch versions 6.2.0 dated 2024-07-13 and 6.3.0 dated 2024-11-16
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Title: Hierarchical and Geographically Weighted Regression
Description: This model divides coefficients into three types,
i.e., local fixed effects, global fixed effects, and random effects (Hu et al., 2022)<doi:10.1177/23998083211063885>.
If data have spatial hierarchical structures (especially are overlapping on some locations),
it is worth trying this model to reach better fitness.
Author: Yigong Hu [aut, cre],
Richard Harris [aut],
Richard Timmerman [aut]
Maintainer: Yigong Hu <yigong.hu@bristol.ac.uk>
Diff between hgwrr versions 0.6-0 dated 2024-11-07 and 0.6-1 dated 2024-11-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/hetero.R | 2 +- build/partial.rdb |binary 5 files changed, 13 insertions(+), 9 deletions(-)