Title: Multivariate Spatio-Temporal Models using Structural Equations
Description: Fits a wide variety of multivariate spatio-temporal models
with simultaneous and lagged interactions among variables (including
vector autoregressive spatio-temporal ('VAST') dynamics)
for areal, continuous, or network spatial domains.
It includes time-variable, space-variable, and space-time-variable
interactions using dynamic structural equation models ('DSEM')
as expressive interface, and the 'mgcv' package to specify splines
via the formula interface. See Thorson et al. (2024)
<doi:10.48550/arXiv.2401.10193> for more details.
Author: James T. Thorson [aut, cre] ,
Sean C. Anderson [aut]
Maintainer: James T. Thorson <James.Thorson@noaa.gov>
Diff between tinyVAST versions 1.1.1 dated 2025-05-07 and 1.2.0 dated 2025-07-19
DESCRIPTION | 14 - MD5 | 64 +++---- NAMESPACE | 7 NEWS.md | 20 ++ R/cAIC.R | 5 R/fit.R | 104 +++++++++-- R/internal.R | 118 ++++++++++++ R/make_dsem_ram.R | 8 R/predict.R | 32 +++ R/project.R |only R/sfnetwork.R | 5 R/utility.R | 110 +----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dsem.html | 2 inst/doc/model-description.Rmd | 49 +++-- inst/doc/model-description.html | 283 +++++++++++++++++++++++++++---- inst/doc/spatial.html | 2 inst/doc/spatial_factor_analysis.html | 6 man/cAIC.Rd | 4 man/classify_variables.Rd | 2 man/conditional_gmrf.Rd |only man/figures |only man/parse_path.Rd | 2 man/project.Rd |only man/rmvnorm_prec.Rd | 10 - man/simulate_sfnetwork.Rd | 2 man/tinyVAST.Rd | 43 +++- man/tinyVASTcontrol.Rd | 11 + src/tinyVAST.cpp | 132 ++++++++++++-- tests/testthat/Rplots.pdf |only tests/testthat/test-basic-fits.R | 62 ++++++ tests/testthat/test-deviance-residuals.R | 60 ++++++ tests/testthat/test-smooths.R | 6 vignettes/model-description.Rmd | 49 +++-- vignettes/tinyVAST_vignettes.bib |only 36 files changed, 945 insertions(+), 267 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico [aut, cre],
Matias D. Cattaneo [aut],
Max H. Farrell [aut]
Maintainer: Sebastian Calonico <scalonico@ucdavis.edu>
Diff between rdrobust versions 2.2 dated 2023-11-03 and 3.0.0 dated 2025-07-19
DESCRIPTION | 30 MD5 | 24 R/functions.R | 774 ++++++++-------- R/rdbwselect.R | 1055 +++++++++++----------- R/rdbwselect_2014.R | 932 +++++++++---------- R/rdplot.R | 1328 ++++++++++++++-------------- R/rdrobust.R | 2213 ++++++++++++++++++++++++----------------------- man/rdbwselect.Rd | 282 ++--- man/rdbwselect_2014.Rd | 172 +-- man/rdplot.Rd | 266 ++--- man/rdrobust-package.Rd | 56 - man/rdrobust.Rd | 353 +++---- man/rdrobust_RDsenate.Rd | 44 13 files changed, 3825 insertions(+), 3704 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 4.0.0 dated 2025-07-15 and 4.0.1 dated 2025-07-19
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 5 R/nlmixr2_md5.R | 2 src/inner.cpp | 1 tests/testthat/test-00-reload-ll.R | 72 +++---- tests/testthat/test-bad-print.R | 66 +++---- tests/testthat/test-manual-back-transform.R | 236 ++++++++++++------------- tests/testthat/test-saem-mu.R | 260 ++++++++++++++-------------- tests/testthat/test-saem-no-pop.R | 60 +++--- tests/testthat/test-uninformative-etas.R | 156 ++++++++-------- tests/testthat/test-warfarin.R | 152 ++++++++-------- 12 files changed, 529 insertions(+), 509 deletions(-)
Title: A 'ggplot2' Extension for Geometric Data Analysis
Description: A variety of multivariable data summary statistics and
constructions have been proposed, either to generalize univariable analogs
or to exploit multivariable properties.
Notable among these are the bivariate peelings surveyed by Green
(1981, ISBN:978-0-471-28039-2),
the bag-and-bolster plots proposed by Rousseeuw &al (1999)
<doi:10.1080/00031305.1999.10474494>, and the minimum spanning trees used by
Jolliffe (2002) <doi:10.1007/b98835> to represent high-dimensional
relationships among data in a low-dimensional plot.
Additionally, biplots of singular value--decomposed tabular data, such as
from principal components analysis, make use of vectors, calibrated axes,
and other representations of variable elements to complement point markers
for case elements; see Gabriel (1971) <doi:10.1093/biomet/58.3.453> and
Gower & Harding (1988) <doi:10.1093/biomet/75.3.445> for original proposals.
Because they treat the abscissa and ordinate as commensurate or the data
e [...truncated...]
Author: Jason Cory Brunson [aut, cre] ,
Emily Paul [ctb],
John Gracey [aut]
Maintainer: Jason Cory Brunson <cornelioid@gmail.com>
Diff between gggda versions 0.1.0 dated 2025-07-09 and 0.1.1 dated 2025-07-19
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 10 ++++++++++ NEWS.md | 6 ++++++ R/geom-rule.r | 18 ++++++++++-------- R/gggda.r | 5 +++-- R/stat-bagplot.r | 3 ++- R/stat-peel.r | 5 ++++- R/stat-rule.r | 5 +++-- inst/doc/gggda.html | 24 +++++++++++++----------- man/gggda.Rd | 5 +++-- tests/testthat/test-stat-peel.r |only tests/testthat/test-stat-scale.r |only 13 files changed, 69 insertions(+), 40 deletions(-)
Title: JAR Dependency for MCMC Using 'BEAST'
Description: Provides JAR to perform Markov chain Monte Carlo (MCMC) inference using
the popular Bayesian Evolutionary Analysis by Sampling Trees 'BEAST X' software
library of Baele et al (2025) <doi:10.1038/s41592-025-02751-x>. 'BEAST X' supports
auto-tuning Metropolis-Hastings, slice, Hamiltonian Monte Carlo and Sequential Monte
Carlo sampling for a large variety of composable standard and phylogenetic
statistical models using high performance computing. By placing the 'BEAST X' JAR in
this package, we offer an efficient distribution system for 'BEAST X' use by other R
packages using CRAN.
Author: Marc A. Suchard [aut, cre, cph],
Andrew Rambaut [cph],
Alexei J. Drummond [cph]
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between BeastJar versions 1.10.6 dated 2020-10-26 and 10.5.0 dated 2025-07-19
DESCRIPTION | 23 +++++++++++------------ MD5 | 8 ++++---- NEWS.md | 9 +++++++-- inst/java/beast.jar |binary tests/testthat/test-installation.R | 2 +- 5 files changed, 23 insertions(+), 19 deletions(-)
Title: Nonparametric Varying Coefficient Spike-and-Slab Lasso
Description: Fits Bayesian regularized varying coefficient models with the Nonparametric Varying Coefficient Spike-and-Slab Lasso (NVC-SSL) introduced by Bai et al. (2023) <https://jmlr.org/papers/volume24/20-1437/20-1437.pdf>. Functions to fit frequentist penalized varying coefficients are also provided, with the option of employing the group lasso penalty of Yuan and Lin (2006) <doi:10.1111/j.1467-9868.2005.00532.x>, the group minimax concave penalty (MCP) of Breheny and Huang <doi:10.1007/s11222-013-9424-2>, or the group smoothly clipped absolute deviation (SCAD) penalty of Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>.
Author: Ray Bai [aut, cre]
Maintainer: Ray Bai <raybaistat@gmail.com>
Diff between NVCSSL versions 2.0 dated 2023-09-17 and 3.0 dated 2025-07-19
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- man/NVC_SSL.Rd | 2 +- man/NVC_frequentist.Rd | 2 +- man/NVC_predict.Rd | 2 +- man/SimulatedData.Rd | 2 +- 6 files changed, 19 insertions(+), 16 deletions(-)
Title: Spatiotemporal Modeling of Seasonal Infectious Disease
Description: Spatiotemporal individual-level model of seasonal infectious disease transmission within the Susceptible-Exposed-Infectious-Recovered-Susceptible (SEIRS) framework are applied to model seasonal infectious disease transmission. This package employs a likelihood based Monte Carlo Expectation Conditional Maximization (MCECM) algorithm for estimating model parameters. In addition to model fitting and parameter estimation, the package offers functions for calculating AIC using real pandemic data and conducting simulation studies customized to user-specified model configurations.
Author: Amin Abed [aut, cre, cph] ,
Mahmoud Torabi [ths],
Zeinab Mashreghi [ths]
Maintainer: Amin Abed <abeda@myumanitoba.ca>
Diff between SeasEpi versions 0.0.1 dated 2025-06-06 and 0.0.2 dated 2025-07-19
SeasEpi-0.0.1/SeasEpi/R |only SeasEpi-0.0.1/SeasEpi/man/SeasEpi_Par_Est.Rd |only SeasEpi-0.0.1/SeasEpi/man/SeasEpi_Sim_Par_Est.Rd |only SeasEpi-0.0.2/SeasEpi/DESCRIPTION | 6 +++--- SeasEpi-0.0.2/SeasEpi/MD5 | 10 +++------- SeasEpi-0.0.2/SeasEpi/NAMESPACE | 6 ------ SeasEpi-0.0.2/SeasEpi/man/data.Rd | 4 ++-- 7 files changed, 8 insertions(+), 18 deletions(-)
Title: Multivariate Bayesian Model with Shrinkage Priors
Description: Gibbs sampler for fitting multivariate Bayesian linear regression with shrinkage priors (MBSP), using the three parameter beta normal family. The method is described in Bai and Ghosh (2018) <doi:10.1016/j.jmva.2018.04.010>.
Author: Ray Bai [aut, cre]
Maintainer: Ray Bai <raybaistat@gmail.com>
Diff between MBSP versions 4.0 dated 2023-05-17 and 5.0 dated 2025-07-19
DESCRIPTION | 15 +++++++++------ MD5 | 2 +- 2 files changed, 10 insertions(+), 7 deletions(-)
Title: Access 'Google Charts' Map Data
Description: Connects to the 'Google Charts' geographic data resources described in
<https://developers.google.com/chart/interactive/docs/gallery/geochart>, allowing
the user to download contents to use as a reference for related services
like 'Google Trends'.
Author: Oscar de Leon [aut, cre, cph]
Maintainer: Oscar de Leon <odeleon@emory.edu>
Diff between gchartsmap versions 0.1.3 dated 2025-06-12 and 1.0.1 dated 2025-07-19
gchartsmap-0.1.3/gchartsmap/man/gchart_process_us_areas.Rd |only gchartsmap-1.0.1/gchartsmap/DESCRIPTION | 12 gchartsmap-1.0.1/gchartsmap/MD5 | 23 - gchartsmap-1.0.1/gchartsmap/NAMESPACE | 2 gchartsmap-1.0.1/gchartsmap/NEWS.md | 8 gchartsmap-1.0.1/gchartsmap/R/gcharts_geo_process.R |only gchartsmap-1.0.1/gchartsmap/R/gcharts_global_areas.R |only gchartsmap-1.0.1/gchartsmap/R/gcharts_us_areas.R | 203 ---------- gchartsmap-1.0.1/gchartsmap/R/gchartsmap-package.R |only gchartsmap-1.0.1/gchartsmap/man/gchart_available_areas.Rd | 11 gchartsmap-1.0.1/gchartsmap/man/gchart_countries.Rd |only gchartsmap-1.0.1/gchartsmap/man/gchart_generate_countries.Rd |only gchartsmap-1.0.1/gchartsmap/man/gchart_get_countries.Rd |only gchartsmap-1.0.1/gchartsmap/man/gchart_process_areas.Rd |only gchartsmap-1.0.1/gchartsmap/man/gchartsmap-package.Rd |only gchartsmap-1.0.1/gchartsmap/tests/testthat/test-gcharts_geo_process.R |only gchartsmap-1.0.1/gchartsmap/tests/testthat/test-gcharts_global_areas.R |only gchartsmap-1.0.1/gchartsmap/tests/testthat/test-gcharts_us_areas.R | 16 18 files changed, 50 insertions(+), 225 deletions(-)
Title: Summarize CRAN Check Results in the Terminal
Description: The CRAN check results and where your package stands in the
CRAN submission queue in your R terminal.
Author: Francois Michonneau [aut, cre],
Ben Bolker [ctb]
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between foghorn versions 1.6.0 dated 2024-07-02 and 1.6.1 dated 2025-07-19
DESCRIPTION | 6 - MD5 | 44 +++++------ NAMESPACE | 1 NEWS.md | 8 ++ R/cran_check_table.R | 8 +- R/cran_details.R | 150 +++++++++++++++++++++++++-------------- R/cran_files.R | 42 ++++++----- R/cran_flavors.R | 14 ++- R/cran_queue.R | 55 ++++++++------ R/cran_results.R | 54 ++++++++++---- R/deadline.R | 73 ++++++++++++------- R/defaults.R | 5 + R/deprecated.R | 1 R/foghorn.R | 130 ++++++++++++++++++++++++---------- R/utils.R | 11 +- R/visit_cran_check.R | 3 R/winbuilder_queue.R | 18 ++-- build/vignette.rds |binary inst/doc/foghorn.Rmd | 143 +++++++++++--------------------------- inst/doc/foghorn.html | 154 ++++++++++++++--------------------------- tests/testthat/test-foghorn.R | 153 ++++++++++++++++++++++++++++++---------- tests/testthat/test-incoming.R | 24 ++++-- vignettes/foghorn.Rmd | 143 +++++++++++--------------------------- 23 files changed, 682 insertions(+), 558 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-07-06 1.3.1.1
2023-05-17 1.3.1
2023-02-01 1.3.0.1
2022-05-17 1.2.0.1
Title: One-Step to Cluster and Visualize Gene Expression Data
Description: Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.
Author: Jun Zhang [aut, cre]
Maintainer: Jun Zhang <3219030654@stu.cpu.edu.cn>
Diff between ClusterGVis versions 0.1.3 dated 2025-06-17 and 0.1.4 dated 2025-07-19
ClusterGVis-0.1.3/ClusterGVis/man/cell_data_set.Rd |only ClusterGVis-0.1.4/ClusterGVis/DESCRIPTION | 20 +-- ClusterGVis-0.1.4/ClusterGVis/MD5 | 24 ++-- ClusterGVis-0.1.4/ClusterGVis/NAMESPACE | 17 --- ClusterGVis-0.1.4/ClusterGVis/R/2.clusterData.R | 8 + ClusterGVis-0.1.4/ClusterGVis/R/3.enrichCluster.R | 4 ClusterGVis-0.1.4/ClusterGVis/R/4.visCluster.R | 38 +++++++ ClusterGVis-0.1.4/ClusterGVis/R/check-packages.R | 13 +- ClusterGVis-0.1.4/ClusterGVis/R/monocleHeatmap.R | 17 +++ ClusterGVis-0.1.4/ClusterGVis/R/utils.R | 52 +++++----- ClusterGVis-0.1.4/ClusterGVis/README.md | 4 ClusterGVis-0.1.4/ClusterGVis/build/vignette.rds |binary ClusterGVis-0.1.4/ClusterGVis/man/cell_data_set-class.Rd |only ClusterGVis-0.1.4/ClusterGVis/vignettes/clusterGVis.png |only ClusterGVis-0.1.4/ClusterGVis/vignettes/clusterGvis_graphic_abstract.jpg |only 15 files changed, 126 insertions(+), 71 deletions(-)