Title: Topic Inference to Identify Tissue Architecture in Multiplexed
Images
Description: A novel spatial topic model to integrate both cell type and spatial information to identify the complex spatial tissue architecture on multiplexed tissue images without human intervention. The Package implements a collapsed Gibbs sampling algorithm for inference. The method is highly scalable to large-scale image datasets without extracting neighborhood information for every single cell. The package supports spatially resolved cell-level data analysis, topic inference, visualization, and downstream biological interpretation of tissue microenvironments.
Author: Xiyu Peng [aut, cre] ,
Nikki Xiao [aut]
Maintainer: Xiyu Peng <pansypeng124@gmail.com>
Diff between SpaTopic versions 1.2.0 dated 2025-03-03 and 1.3.1 dated 2026-05-29
DESCRIPTION | 30 ++-- MD5 | 35 +++- NAMESPACE | 46 +++--- NEWS.md | 6 R/Gibbs_sampler.R | 84 ++++++++--- R/frex_topic.R |only R/label_topics.R |only R/lift_topic.R |only R/prob_topic.R |only R/score_topic.R |only R/spatial_func.R | 254 ++++++++++++++++++++++++----------- README.md | 53 ++++++- build/partial.rdb |only inst/CITATION |only inst/WORDLIST |only inst/doc/Intro_SpaTopic.html | 2 man/SpaTopic-Package.Rd | 2 man/SpaTopic_inference.Rd | 10 + man/frex_topic.Rd |only man/label_topics.Rd |only man/lift_topic.Rd |only man/prob_topic.Rd |only man/score_topic.Rd |only man/stratified_sampling_3D_via_2D.Rd |only src/Gibbs.cpp | 1 tests |only 26 files changed, 378 insertions(+), 145 deletions(-)
Title: Latent Space Item Response Model
Description: Analysis of dichotomous, ordinal, and continuous response data using latent space item response model ('LSIRM'). Provides 1PL and 2PL 'LSIRM' for binary response data as described in Jeon et al. (2021) <doi:10.1007/s11336-021-09762-5>, graded response models ('GRM') for ordinal data (De Carolis et al., 2025, <doi:10.1080/00273171.2025.2605678>), and extensions for continuous response data. Supports Bayesian model selection with spike-and-slab priors, adaptive MCMC algorithms, and methods for handling missing data under missing at random ('MAR') and missing completely at random ('MCAR') assumptions. Provides various diagnostic plots to inspect the latent space and summaries of estimated parameters.
Author: Dongyoung Go [aut],
Gwanghee Kim [aut, cre],
Jina Park [aut],
Ickhoon Jin [ctb],
Minjeong Jeon [ctb]
Maintainer: Gwanghee Kim <musagh08@yonsei.ac.kr>
Diff between lsirm12pl versions 2.0.1 dated 2026-05-04 and 2.0.2 dated 2026-05-29
DESCRIPTION | 8 MD5 | 184 ++++++------- R/data.R | 2 R/diagnostic.lsirm.R | 66 ++++ R/lsirm1pl_fixed_gamma_mar.R | 8 R/lsirm1pl_fixed_gamma_mcar.R | 8 R/lsirm1pl_mar.R | 8 R/lsirm1pl_mar_ss.R | 6 R/lsirm1pl_mcar.R | 8 R/lsirm1pl_mcar_ss.R | 8 R/lsirm1pl_normal_fixed_gamma.R | 5 R/lsirm1pl_normal_fixed_gamma_mar.R | 11 R/lsirm1pl_normal_fixed_gamma_mcar.R | 11 R/lsirm1pl_normal_mar.R | 359 +++++++++++++------------- R/lsirm1pl_normal_mar_ss.R | 9 R/lsirm1pl_normal_mcar.R | 357 +++++++++++++------------- R/lsirm1pl_normal_mcar_ss.R | 399 ++++++++++++++--------------- R/lsirm1pl_normal_o.R | 323 ++++++++++++------------ R/lsirm1pl_normal_ss.R | 363 +++++++++++++-------------- R/lsirm2pl_fixed_gamma_mar.R | 6 R/lsirm2pl_fixed_gamma_mcar.R | 6 R/lsirm2pl_mar.R | 6 R/lsirm2pl_mar_ss.R | 6 R/lsirm2pl_mcar.R | 6 R/lsirm2pl_mcar_ss.R | 6 R/lsirm2pl_normal_fixed_gamma.R | 303 +++++++++++----------- R/lsirm2pl_normal_fixed_gamma_mar.R | 335 ++++++++++++------------ R/lsirm2pl_normal_fixed_gamma_mcar.R | 335 ++++++++++++------------ R/lsirm2pl_normal_mar.R | 381 ++++++++++++++-------------- R/lsirm2pl_normal_mar_ss.R | 429 ++++++++++++++++---------------- R/lsirm2pl_normal_mcar.R | 381 ++++++++++++++-------------- R/lsirm2pl_normal_mcar_ss.R | 415 +++++++++++++++--------------- R/lsirm2pl_normal_o.R | 337 ++++++++++++------------- R/lsirm2pl_normal_ss.R | 357 +++++++++++++------------- R/lsirmgrm.R | 41 --- R/lsirmgrm2pl.R | 25 - R/lsirmgrm2pl_fixed_gamma.R | 2 R/lsirmgrm2pl_mcar.R | 2 R/lsirmgrm2pl_ss.R | 2 R/lsirmgrm_fixed_gamma.R | 2 R/lsirmgrm_mcar.R | 2 R/lsirmgrm_ss.R | 2 R/plot.lsirm.R | 174 ++++++++---- R/print.summary.lsirm.R | 153 ++++++++++- R/summary.lsirm.R | 145 ++++++++++ R/utilities.R | 10 man/TDRI.Rd | 2 man/diagnostic.Rd | 16 + man/lsirm1pl_fixed_gamma_mar.Rd | 4 man/lsirm1pl_fixed_gamma_mcar.Rd | 4 man/lsirm1pl_mar.Rd | 4 man/lsirm1pl_mar_ss.Rd | 2 man/lsirm1pl_mcar.Rd | 4 man/lsirm1pl_mcar_ss.Rd | 4 man/lsirm1pl_normal_fixed_gamma.Rd | 5 man/lsirm1pl_normal_fixed_gamma_mar.Rd | 7 man/lsirm1pl_normal_fixed_gamma_mcar.Rd | 7 man/lsirm1pl_normal_mar.Rd | 7 man/lsirm1pl_normal_mar_ss.Rd | 5 man/lsirm1pl_normal_mcar.Rd | 7 man/lsirm1pl_normal_mcar_ss.Rd | 7 man/lsirm1pl_normal_o.Rd | 5 man/lsirm1pl_normal_ss.Rd | 5 man/lsirm2pl_fixed_gamma_mar.Rd | 2 man/lsirm2pl_fixed_gamma_mcar.Rd | 2 man/lsirm2pl_mar.Rd | 2 man/lsirm2pl_mar_ss.Rd | 2 man/lsirm2pl_mcar.Rd | 2 man/lsirm2pl_mcar_ss.Rd | 2 man/lsirm2pl_normal_fixed_gamma.Rd | 5 man/lsirm2pl_normal_fixed_gamma_mar.Rd | 5 man/lsirm2pl_normal_fixed_gamma_mcar.Rd | 5 man/lsirm2pl_normal_mar.Rd | 5 man/lsirm2pl_normal_mar_ss.Rd | 5 man/lsirm2pl_normal_mcar.Rd | 5 man/lsirm2pl_normal_mcar_ss.Rd | 5 man/lsirm2pl_normal_o.Rd | 5 man/lsirm2pl_normal_ss.Rd | 5 man/lsirmgrm.Rd | 33 -- man/lsirmgrm2pl.Rd | 17 - man/lsirmgrm2pl_fixed_gamma.Rd | 2 man/lsirmgrm2pl_mcar.Rd | 2 man/lsirmgrm2pl_o.Rd | 2 man/lsirmgrm2pl_ss.Rd | 2 man/lsirmgrm_fixed_gamma.Rd | 2 man/lsirmgrm_mcar.Rd | 2 man/lsirmgrm_o.Rd | 2 man/lsirmgrm_ss.Rd | 2 man/plot.Rd | 23 + man/print.summary.lsirm.Rd | 8 man/summary.lsirm.Rd | 17 + src/lsirm1pl.cpp | 14 - src/lsirm2pl.cpp | 12 93 files changed, 3365 insertions(+), 2939 deletions(-)
Title: Transport Modeling: Network Processing, Route Enumeration, and
Traffic Assignment
Description: High-performance tools for transport modeling - network processing, route
enumeration, and traffic assignment in R. The package implements the Path-Sized Logit
model for traffic assignment - Ben-Akiva and Bierlaire (1999) <doi:10.1007/978-1-4615-5203-1_2> -
an efficient route enumeration algorithm, and provides powerful utility functions for (multimodal)
network generation, consolidation/contraction, and/or simplification. The user is expected to provide
a transport network (either a graph or collection of linestrings) and an origin-destination (OD)
matrix of trade/traffic flows. Maintained by transport consultants at CPCS (cpcs.ca).
Author: Sebastian Krantz [aut, cre],
Kamol Roy [ctb]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between flownet versions 0.2.2 dated 2026-03-22 and 0.3.0 dated 2026-05-29
DESCRIPTION | 12 MD5 | 36 - NAMESPACE | 1 NEWS.md | 43 + R/critical_link_analysis.R |only R/utils.R | 678 +++++++++++++++++++++++---- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.html | 103 ++-- man/consolidate_graph.Rd | 8 man/create_undirected_graph.Rd | 7 man/critical_link_analysis.Rd |only man/flownet-package.Rd | 1 man/simplify_network.Rd | 33 + src/Makevars |only src/Makevars.win |only src/critical_link_analysis.c |only src/init.c | 5 src/utils.c | 176 +++++++ tests/testthat/test-consolidation.R | 424 ++++++++++++++++ tests/testthat/test-critical-link-analysis.R |only 22 files changed, 1348 insertions(+), 180 deletions(-)
Title: Missing Value Imputation with Compositional Data
Description: Functions to perform missing value imputation with compositional data using the Jensen-Shannon divergence based k--NN and a--k--NN algorithms. The functions are based on the following paper:
Tsagris M., Alenazi A. and Stewart C. (2026). "A Jensen--Shannon divergence based k--NN algorithm for missing value imputation in compositional data", <doi:10.1080/02664763.2026.2677908>.
Author: Michail Tsagris [aut, cre]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between CompositionalNAimp versions 1.0 dated 2026-03-31 and 1.1 dated 2026-05-29
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ man/CompositionalNAimp-package.Rd | 5 +++-- man/alfa.knnimp.Rd | 1 + man/alfaknnimp.tune.Rd | 1 + man/cv.knnimp.Rd | 3 ++- man/knnimp.Rd | 1 + 7 files changed, 19 insertions(+), 15 deletions(-)
More information about CompositionalNAimp at CRAN
Permanent link
Title: Toolkit for Reduced Form and Structural Smooth Transition Vector
Autoregressive Models
Description: Penalized and non-penalized maximum likelihood estimation of smooth
transition vector autoregressive models with various types of transition weight
functions, conditional distributions, and identification methods. Constrained
estimation with various types of constraints is available. Residual based
model diagnostics, forecasting, simulations, counterfactual analysis, and
computation of impulse response functions, generalized impulse response functions,
generalized forecast error variance decompositions, as well as historical
decompositions. See
Heather Anderson, Farshid Vahid (1998) <doi:10.1016/S0304-4076(97)00076-6>,
Helmut Lütkepohl, Aleksei Netšunajev (2017) <doi:10.1016/j.jedc.2017.09.001>,
Markku Lanne, Savi Virolainen (2025) <doi:10.1016/j.jedc.2025.105162>,
Savi Virolainen (in press) <doi:10.1080/07474938.2026.2673986>.
Author: Savi Virolainen [aut, cre]
Maintainer: Savi Virolainen <savi.virolainen@helsinki.fi>
Diff between sstvars versions 1.2.3 dated 2026-01-26 and 1.2.4 dated 2026-05-29
DESCRIPTION | 10 +-- MD5 | 130 +++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 12 +++ R/GIRFandGFEVD.R | 12 ++- R/LSest.R | 10 +-- R/MAINest.R | 7 +- R/RcppExports.R | 46 ++++++++++++++ R/STVARconstruction.R | 7 -- R/argumentChecks.R | 5 - R/data.R | 6 - R/distributionFuns.R | 5 - R/histDecomp.R | 2 R/jointSpectralRadius.R | 42 ++++++------- R/loglikelihood.R | 5 - R/matcal.R | 2 R/miscellaneous.R | 27 ++++++++ R/moreEst.R | 7 -- R/plotMethods.R | 68 +++++++++++++-------- README.md | 24 +++---- build/vignette.rds |binary inst/doc/sstvars-vignette.R | 2 inst/doc/sstvars-vignette.Rnw | 62 ++++++++++--------- inst/doc/sstvars-vignette.pdf |binary man/GIRF.Rd | 20 ++++-- man/GIRF_int.Rd | 8 +- man/STVAR.Rd | 7 -- man/alt_stvar.Rd | 5 - man/bound_JSR.Rd | 44 ++++--------- man/bound_jsr_G.Rd | 5 - man/bound_jsr_G_Cpp.Rd |only man/cfact_girf.Rd | 2 man/change_regime.Rd | 5 - man/check_params.Rd | 5 - man/diag_Omegas.Rd | 2 man/diagnostic_plot.Rd | 5 - man/estim_LS.Rd | 5 - man/estim_NLS.Rd | 5 - man/fitSSTVAR.Rd | 7 -- man/fitSTVAR.Rd | 8 +- man/fitbsSSTVAR.Rd | 5 - man/get_IC.Rd | 2 man/get_alpha_mt.Rd | 5 - man/get_penalized_IC.Rd |only man/get_residuals.Rd | 5 - man/hist_decomp.Rd | 5 - man/in_paramspace.Rd | 5 - man/iterate_more.Rd | 5 - man/loglikelihood.Rd | 5 - man/n_params.Rd | 5 - man/plot_struct_shocks.Rd | 5 - man/predict.stvar.Rd | 5 - man/profile_logliks.Rd | 5 - man/reform_constrained_pars.Rd | 5 - man/regime_distance.Rd | 5 - man/simulate.stvar.Rd | 5 - man/simulate_from_regime.Rd | 5 - man/simulate_stvar_int.Rd | 5 - man/spectral_radius.Rd |only man/sstvars-package.Rd | 5 + man/stand_t_dens.Rd | 5 - man/standard_errors.Rd | 5 - man/swap_parametrization.Rd | 5 - man/usacpu.Rd | 6 - src/RcppExports.cpp | 15 ++++ src/bound_jsr_G_Cpp.cpp |only vignettes/refs.bib | 9 +- vignettes/sstvars-vignette.Rnw | 62 ++++++++++--------- 68 files changed, 457 insertions(+), 362 deletions(-)
Title: Calculate (Stratified) Percentiles
Description: Calculate (stratified) percentiles on a data.frame
Stratification will split the data.frame into subgroups and calculate percentiles for each independently.
Author: Dr Peter Amin Marquardt [aut, cre]
Maintainer: Dr Peter Amin Marquardt <peter@kmarquardt.de>
Diff between percentiles versions 0.2.3 dated 2026-04-03 and 0.3.0 dated 2026-05-29
DESCRIPTION | 15 +- MD5 | 15 +- R/Stratified_percentile_calculator.R | 6 R/calculate_percentiles.R | 34 +---- man/Stratified_percentile_calculator_generator.Rd | 133 ++++++++++------------ man/calculate_percentiles.Rd | 2 man/calculate_stratified_percentiles.Rd | 2 tests |only 8 files changed, 95 insertions(+), 112 deletions(-)
Title: Multivariate Normal and t Distributions
Description: Computes multivariate normal and t probabilities, quantiles, random deviates,
and densities. Log-likelihoods for multivariate Gaussian models and Gaussian copulae
parameterised by Cholesky factors of covariance or precision matrices are implemented
for interval-censored and exact data, or a mix thereof. Score functions for these
log-likelihoods are available. A class representing multiple lower triangular matrices
and corresponding methods are part of this package.
Author: Alan Genz [aut],
Frank Bretz [aut],
Tetsuhisa Miwa [aut],
Xuefei Mi [aut],
Friedrich Leisch [ctb],
Fabian Scheipl [ctb],
Bjoern Bornkamp [ctb] ,
Martin Maechler [ctb] ,
Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mvtnorm versions 1.3-7 dated 2026-04-15 and 1.4-0 dated 2026-05-29
DESCRIPTION | 12 MD5 | 50 NAMESPACE | 8 R/interface.R | 15 R/lpmvnorm.R | 36 R/ltMatrices.R | 383 +++-- R/mvnorm.R | 2 R/mvt.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 49 inst/doc/MVT_Rnews.pdf |binary inst/doc/lmvnorm_src.R | 303 ++-- inst/doc/lmvnorm_src.Rnw | 2727 ++++++++++++++++++++-------------------- inst/doc/lmvnorm_src.pdf |binary inst/include/mvtnorm.h | 6 inst/nuweb |only man/ltMatrices.Rd | 11 src/C_FORTRAN_interface.c | 2 src/ltMatrices.c | 479 ++----- src/mvt.f | 2 src/mvtnorm-init.c | 10 src/mvtnorm.h | 6 tests/regtest-Mult-crossprod.R |only tests/regtest-aperm.R | 1 vignettes/lmvnorm_src.Rnw | 2727 ++++++++++++++++++++-------------------- vignettes/lmvnorm_src.Rout.save | 138 +- 27 files changed, 3640 insertions(+), 3329 deletions(-)
Title: 'GitHub' 'API'
Description: Minimal client to access the 'GitHub' 'API'.
Author: Gabor Csardi [cre, ctb],
Jennifer Bryan [aut],
Hadley Wickham [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between gh versions 1.5.0 dated 2025-05-26 and 1.6.0 dated 2026-05-29
gh-1.5.0/gh/tests/testthat/helper-offline.R |only gh-1.6.0/gh/DESCRIPTION | 14 gh-1.6.0/gh/MD5 | 95 ++-- gh-1.6.0/gh/NAMESPACE | 3 gh-1.6.0/gh/NEWS.md | 39 + gh-1.6.0/gh/R/fake-github-app.R |only gh-1.6.0/gh/R/gh.R | 275 +++++++++++--- gh-1.6.0/gh/R/gh_gql.R | 2 gh-1.6.0/gh/R/gh_rate_limit.R | 4 gh-1.6.0/gh/R/gh_request.R | 10 gh-1.6.0/gh/R/gh_response.R | 25 + gh-1.6.0/gh/R/gh_token.R | 86 +++- gh-1.6.0/gh/R/import-standalone-obj-type.R |only gh-1.6.0/gh/R/import-standalone-types-check.R |only gh-1.6.0/gh/R/pagination.R | 49 -- gh-1.6.0/gh/R/utils.R | 41 -- gh-1.6.0/gh/README.md | 77 ++- gh-1.6.0/gh/build/vignette.rds |binary gh-1.6.0/gh/inst/WORDLIST | 3 gh-1.6.0/gh/inst/doc/managing-personal-access-tokens.html | 3 gh-1.6.0/gh/man/fake_github_app.Rd |only gh-1.6.0/gh/man/gh.Rd | 34 + gh-1.6.0/gh/man/gh_gql.Rd | 2 gh-1.6.0/gh/man/gh_next.Rd | 2 gh-1.6.0/gh/man/gh_token.Rd | 13 gh-1.6.0/gh/man/gh_tree_remote.Rd | 2 gh-1.6.0/gh/man/gh_whoami.Rd | 4 gh-1.6.0/gh/tests/testthat/_snaps/gh.md | 22 + gh-1.6.0/gh/tests/testthat/_snaps/gh_gql.md |only gh-1.6.0/gh/tests/testthat/_snaps/gh_rate_limit.md | 2 gh-1.6.0/gh/tests/testthat/_snaps/gh_request.md | 8 gh-1.6.0/gh/tests/testthat/_snaps/gh_response.md | 8 gh-1.6.0/gh/tests/testthat/_snaps/gh_token.md | 51 ++ gh-1.6.0/gh/tests/testthat/_snaps/gh_whoami.md | 2 gh-1.6.0/gh/tests/testthat/_snaps/git.md |only gh-1.6.0/gh/tests/testthat/_snaps/pagination.md | 8 gh-1.6.0/gh/tests/testthat/_snaps/print.md | 21 - gh-1.6.0/gh/tests/testthat/_snaps/utils.md | 10 gh-1.6.0/gh/tests/testthat/helper-fake-github.R |only gh-1.6.0/gh/tests/testthat/helper.R | 47 ++ gh-1.6.0/gh/tests/testthat/setup.R | 13 gh-1.6.0/gh/tests/testthat/test-gh.R | 157 +++++++ gh-1.6.0/gh/tests/testthat/test-gh_gql.R |only gh-1.6.0/gh/tests/testthat/test-gh_rate_limit.R | 30 + gh-1.6.0/gh/tests/testthat/test-gh_request.R | 33 + gh-1.6.0/gh/tests/testthat/test-gh_response.R | 56 ++ gh-1.6.0/gh/tests/testthat/test-gh_token.R | 74 +++ gh-1.6.0/gh/tests/testthat/test-gh_whoami.R | 8 gh-1.6.0/gh/tests/testthat/test-git.R | 78 +++ gh-1.6.0/gh/tests/testthat/test-mock-repos.R | 6 gh-1.6.0/gh/tests/testthat/test-pagination.R | 95 ++++ gh-1.6.0/gh/tests/testthat/test-print.R | 2 gh-1.6.0/gh/tests/testthat/test-utils.R | 89 ++++ 53 files changed, 1293 insertions(+), 310 deletions(-)
Title: Ecological Stability Metrics
Description: Standardises and facilitates the use of eleven established stability properties that have been used to assess systems’ responses to press or pulse disturbances at different ecological levels (e.g. population, community). There are two sets of functions. The first set corresponds to functions that measure stability at any level of organisation, from individual to community and can be applied to a time series of a system’s state variables (e.g., body mass, population abundance, or species diversity). The properties included in this set are: invariability, resistance, extent and rate of recovery, persistence, and overall ecological vulnerability. The second set of functions can be applied to Jacobian matrices. The functions in this set measure the stability of a community at short and long time scales. In the short term, the community’s response is measured by maximal amplification, reactivity and initial resilience (i.e. initial rate of return to equilibrium). In the long term, stability [...truncated...]
Author: Ludmilla Figueiredo [aut, cre] ,
Viktoriia Radchuk [aut] ,
Cedric Scherer [ctb]
Maintainer: Ludmilla Figueiredo <ludmilla.figueiredo@protonmail.com>
Diff between estar versions 1.0-1 dated 2025-11-28 and 2.0-0 dated 2026-05-29
DESCRIPTION | 10 MD5 | 65 - NEWS.md |only R/asympt_resil.R | 15 R/common_params.R | 4 R/data.R | 158 +- R/extractB.R | 76 - R/init_resil.R | 76 - R/max_amp.R | 108 - R/oev.R | 244 ++-- R/reactivity.R | 94 - R/recovery_extent.R | 2 R/recovery_rate.R | 25 R/resistance.R | 508 ++++----- R/stoch_var.R | 86 - README.md | 2 inst/doc/functional_stability_properties.R | 20 inst/doc/functional_stability_properties.Rmd | 1406 +++++++++++++------------- inst/doc/functional_stability_properties.html | 165 +-- inst/doc/jacobian_stability_properties.R | 45 inst/doc/jacobian_stability_properties.Rmd | 986 +++++++++--------- inst/doc/jacobian_stability_properties.html | 622 +++++------ man/asympt_resil.Rd | 300 ++--- man/extractB.Rd | 282 ++--- man/figures/hex_sticker.png |binary man/max_amp.Rd | 328 +++--- man/oev.Rd | 290 ++--- man/recovery_rate.Rd | 24 man/resistance.Rd | 432 +++---- vignettes/MARSS_example_vignette.R |only vignettes/figures/B_matrix.png |only vignettes/functional_stability_properties.Rmd | 1406 +++++++++++++------------- vignettes/jacobian_stability_properties.Rmd | 986 +++++++++--------- vignettes/performance_analysis.R | 1006 +++++++++--------- vignettes/references.bib | 256 ++-- 35 files changed, 5058 insertions(+), 4969 deletions(-)
Title: Steve's R Markdown Templates
Description: These are my collection of 'R Markdown' templates, mostly for compilation to PDF.
These are useful for all things academic and professional, if you are using 'R Markdown'
for things like your CV or your articles and manuscripts.
Author: Steven Miller [aut, cre]
Maintainer: Steven Miller <steve@svmiller.com>
Diff between stevetemplates versions 1.1.0 dated 2025-02-07 and 1.3.0 dated 2026-05-29
DESCRIPTION | 11 MD5 | 74 ++--- NEWS.md | 11 R/article.R | 2 R/article2.R | 2 R/article3.R | 2 R/beamer.R | 2 R/cover_letter.R | 5 R/cv.R | 2 R/cv2.R | 2 R/memo.R | 2 R/resume.R | 2 R/syllabus.R | 4 README.md | 145 +++++----- inst/rmarkdown/templates/anonms/resources/template.tex | 43 ++ inst/rmarkdown/templates/article/resources/template.tex | 41 ++ inst/rmarkdown/templates/article2/resources/template.tex | 83 ++++- inst/rmarkdown/templates/article3/resources/template.tex | 88 ++++-- inst/rmarkdown/templates/beamer/resources/template.tex | 43 ++ inst/rmarkdown/templates/cover_letter/resources/template.tex | 61 +++- inst/rmarkdown/templates/cv/resources/template.tex | 44 ++- inst/rmarkdown/templates/cv2/resources/template.tex | 46 ++- inst/rmarkdown/templates/ekohist_thesis/resources/template.tex | 46 ++- inst/rmarkdown/templates/memo/resources/template.tex | 61 +++- inst/rmarkdown/templates/resume/resources/template.tex | 52 ++- inst/rmarkdown/templates/statement/resources/template.tex | 62 +++- inst/rmarkdown/templates/syllabus/resources/template.tex | 41 ++ inst/rmarkdown/templates/syllabus2/resources/template.tex | 47 ++- man/article.Rd | 2 man/article2.Rd | 2 man/article3.Rd | 2 man/beamer.Rd | 2 man/cover_letter.Rd | 5 man/cv.Rd | 2 man/cv2.Rd | 2 man/memo.Rd | 2 man/resume.Rd | 2 man/syllabus.Rd | 4 38 files changed, 752 insertions(+), 297 deletions(-)
More information about stevetemplates at CRAN
Permanent link
More information about ElicitationWizard at CRAN
Permanent link
Title: Download Administrative Boundary Data from 'geoBoundaries'
Description: Tools for downloading administrative boundary data from
'geoBoundaries' <https://www.geoboundaries.org/> across multiple
administrative levels. Boundary data are returned as 'sf' objects for
mapping and spatial analysis. See Runfola, D. et al. (2020)
"geoBoundaries: A global database of political administrative
boundaries." PLOS ONE 15(4), e0231866.
<doi:10.1371/journal.pone.0231866>.
Author: Diego Hernangomez [aut, cre, cph] ,
William and Mary geoLab [cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between geobounds versions 0.1.1 dated 2026-03-24 and 0.1.2 dated 2026-05-29
DESCRIPTION | 21 +- MD5 | 82 +++---- NAMESPACE | 36 +-- NEWS.md | 59 +++-- R/gb-cache.R | 201 +++++++++---------- R/gb-get-adm.R | 52 ++-- R/gb-get-max-lvl.R | 13 - R/gb-get-metadata.R | 164 ++++++--------- R/gb-get-world.R | 46 +--- R/gb-get.R | 154 +++++--------- R/utils.R | 145 ++++++++++--- README.md | 104 +++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 114 +++++----- inst/COPYRIGHTS | 130 ++++++------ inst/REFERENCES.bib | 38 +-- inst/WORDLIST | 63 +++--- inst/doc/geobounds.html | 129 ++++++------ inst/doc/geobounds.qmd | 163 ++++++++------- inst/schemaorg.json | 10 man/figures/README-map-coverage-1.png |binary man/gb_clear_cache.Rd | 118 +++++------ man/gb_detect_cache_dir.Rd | 59 ++--- man/gb_get.Rd | 250 +++++++++++------------ man/gb_get_adm.Rd | 325 +++++++++++++++---------------- man/gb_get_max_adm_lvl.Rd | 115 +++++----- man/gb_get_metadata.Rd | 244 +++++++++++------------ man/gb_get_world.Rd | 175 ++++++++-------- man/gb_set_cache_dir.Rd | 161 +++++++-------- man/geobounds-package.Rd | 67 +++--- tests/testthat/_snaps/gb-get-metadata.md | 6 tests/testthat/_snaps/gb-get-world.md | 2 tests/testthat/_snaps/gb-get.md | 8 tests/testthat/_snaps/utils.md | 12 - tests/testthat/test-gb-get-metadata.R | 34 --- tests/testthat/test-gb-get-world.R | 4 tests/testthat/test-utils.R | 129 +++++------- vignettes/REFERENCES.bib | 38 +-- vignettes/cgaz-1.png |binary vignettes/geobounds.qmd | 163 ++++++++------- vignettes/intersect-1.png |binary 42 files changed, 1802 insertions(+), 1832 deletions(-)
Title: Detection of Multiple Changes in Slope in Univariate Time-Series
Description: Detects multiple changes in slope using the CPOP dynamic programming approach of Fearnhead, Maidstone, and Letchford (2019) <doi:10.1080/10618600.2018.1512868>. This method finds the best continuous piecewise linear fit to data under a criterion that measures fit to data using the residual sum of squares, but penalizes complexity based on an L0 penalty on changes in slope. Further information regarding the use of this package with detailed examples can be found in Fearnhead and Grose (2024) <doi:10.18637/jss.v109.i07>.
Author: Daniel Grose [aut, cre],
Paul Fearnhead [aut]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between cpop versions 1.0.8 dated 2025-06-11 and 1.0.9 dated 2026-05-29
cpop-1.0.8/cpop/build/cpop.pdf |only cpop-1.0.9/cpop/DESCRIPTION | 10 +++++----- cpop-1.0.9/cpop/MD5 | 15 +++++++-------- cpop-1.0.9/cpop/NEWS.md | 5 +++++ cpop-1.0.9/cpop/R/cpop.R | 33 ++++++++++++++++----------------- cpop-1.0.9/cpop/R/cpop.crops.R | 11 +++++------ cpop-1.0.9/cpop/build/partial.rdb |binary cpop-1.0.9/cpop/build/stage23.rdb |binary cpop-1.0.9/cpop/man/cpop.Rd | 6 +++--- 9 files changed, 41 insertions(+), 39 deletions(-)
Title: Optimize and Compress Image Files with 'reSmush.it'
Description: Optimize and compress local image files, directories and
online images with the 'reSmush.it' API <https://resmush.it/>.
Supports 'png', 'jpg/jpeg', 'gif', 'bmp' and 'tiff' files.
Author: Diego Hernangomez [aut, cre, cph]
Maintainer: Diego Hernangomez <diego.hernangomezherrero@gmail.com>
Diff between resmush versions 1.0.0 dated 2026-03-14 and 1.0.1 dated 2026-05-29
DESCRIPTION | 14 MD5 | 78 +- NAMESPACE | 16 NEWS.md | 53 + R/resmush-package.R | 14 R/resmush_clean_dir.R | 152 ++--- R/resmush_dir.R | 211 +++---- R/resmush_file.R | 480 ++++++---------- R/resmush_url.R | 490 ++++++---------- R/show_report.R | 68 -- R/sysdata.rda |binary R/utils.R | 361 ++++++++---- README.md | 110 ++- build/vignette.rds |binary inst/CITATION | 42 - inst/REFERENCES.bib | 8 inst/WORDLIST | 4 inst/doc/resmush.html | 110 ++- inst/doc/resmush.qmd | 115 ++- inst/schemaorg.json | 6 man/resmush-package.Rd | 57 + man/resmush_clean_dir.Rd | 125 ++-- man/resmush_dir.Rd | 208 +++---- man/resmush_file.Rd | 203 +++---- man/resmush_url.Rd | 190 +++--- man/roxygen/meta.R | 12 tests/testthat.R | 24 tests/testthat/_snaps/formats.md | 8 tests/testthat/_snaps/remush_url.md | 20 tests/testthat/_snaps/resmuh_dir.md | 2 tests/testthat/_snaps/show_report.md | 62 +- tests/testthat/test-formats-local.R | 186 +++--- tests/testthat/test-formats.R | 256 ++++---- tests/testthat/test-remush_url.R | 923 +++++++++++++++----------------- tests/testthat/test-resmuh_dir.R | 454 +++++++-------- tests/testthat/test-resmush_clean_dir.R | 131 ++-- tests/testthat/test-resmush_file.R | 799 +++++++++++++-------------- tests/testthat/test-utils.R | 82 +- vignettes/REFERENCES.bib | 8 vignettes/resmush.qmd | 115 ++- 40 files changed, 3037 insertions(+), 3160 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-03 1.2.2
2019-01-06 1.2.1
2018-10-17 1.2.0
2015-12-16 1.1.2
2015-07-16 1.1.1
2015-06-08 1.1.0
2014-05-30 1.0.2
2013-04-10 1.0.1
2013-02-14 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2026-01-06 0.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-12-06 0.1.0
Title: Linear Mixed Models with Sparse Matrix Methods and Smoothing
Description: Provides tools for fitting linear mixed models using sparse matrix
methods and variance component estimation. Applications include spline-based
modeling of spatial and temporal trends using penalized splines (Boer, 2023)
<doi:10.1177/1471082X231178591>.
Author: Martin Boer [aut] ,
Bart-Jan van Rossum [aut, cre]
Maintainer: Bart-Jan van Rossum <bart-jan.vanrossum@wur.nl>
Diff between LMMsolver versions 1.0.12 dated 2025-12-05 and 1.0.13 dated 2026-05-29
DESCRIPTION | 10 - MD5 | 120 +++++++----- NAMESPACE | 5 NEWS.md | 9 R/HarvilleODE.R |only R/LMMsolve-class.R | 55 ++++- R/LMMsolve.R | 25 ++ R/chkInputLMMsolve.R | 14 - R/constructFixed.R | 101 +++++++++- R/constructRandom.R | 154 +++++++++++++--- R/fitLMM.R | 4 R/getHeritability.R |only R/ginverse.R |only R/makeGrid.R |only R/orthoBsplines.R |only R/orthoModel.R |only R/sparseMixedModels.R | 143 +++++++++++++++ R/utils.R | 132 ++++++++++---- README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Solving_Linear_Mixed_Models.R | 33 +-- inst/doc/Solving_Linear_Mixed_Models.Rmd | 41 +--- inst/doc/Solving_Linear_Mixed_Models.html | 277 ++++++++++++++---------------- inst/tinytest/GLMMFull |binary inst/tinytest/LMMsolve0 |binary inst/tinytest/LMMsolve1 |binary inst/tinytest/LMMsolve2 |binary inst/tinytest/LMMsolve3 |binary inst/tinytest/LMMsolve4 |binary inst/tinytest/LMMsolve5 |binary inst/tinytest/binomial1 |binary inst/tinytest/binomial2 |binary inst/tinytest/binomial3 |binary inst/tinytest/cfFull |binary inst/tinytest/effDim0 |binary inst/tinytest/effDims |binary inst/tinytest/gam1DFull |binary inst/tinytest/mLogLik0 |binary inst/tinytest/modCoefs |binary inst/tinytest/modCoefsSe |binary inst/tinytest/modFit |binary inst/tinytest/modResid |binary inst/tinytest/multinomial1 |binary inst/tinytest/ortho_fit1 |only inst/tinytest/ortho_fit2 |only inst/tinytest/pred10 |only inst/tinytest/spl1DFull |binary inst/tinytest/spl2DFull |binary inst/tinytest/spl2DFull2 |binary inst/tinytest/spl2DFull3 |binary inst/tinytest/spl3DFull |binary inst/tinytest/spl3DFull2 |binary inst/tinytest/spl3DFull3 |binary inst/tinytest/test_HarvilleODE.R |only inst/tinytest/test_LMMsolve.R | 30 +-- inst/tinytest/test_gam.R | 2 inst/tinytest/test_getHeritability.R |only inst/tinytest/test_orthoBsplines.R |only inst/tinytest/test_orthoModel.R |only inst/tinytest/test_predict.R | 48 ++++- inst/tinytest/test_spl1D.R | 2 inst/tinytest/test_spl2D.R | 22 +- inst/tinytest/test_spl3D.R | 6 man/LMMsolveObject.Rd | 2 man/as.ginverse.Rd |only man/getHeritability.Rd |only man/makeGrid.Rd |only vignettes/Solving_Linear_Mixed_Models.Rmd | 41 +--- 69 files changed, 858 insertions(+), 426 deletions(-)
Title: Geographically Weighted Panel Regression
Description: A modern, first implementation of Geographically Weighted Panel Regression (GWPR) for spatial panel data. The package provides a unified public API supporting Gaussian and binomial family models, within/pooling/random panel effects, three bandwidth search strategies (grid, Stochastic Gradient Descent, random), five kernel functions, and optional parallel execution via the 'future' framework. Diagnostic tools include spatial Moran's I, local F-test, Hausman test, and Lagrange Multiplier test.
Author: Chao Li [aut, cre] ,
Shunsuke Managi [aut]
Maintainer: Chao Li <chaoli0394@gmail.com>
This is a re-admission after prior archival of version 0.2.1 dated 2022-06-21
Diff between GWPR.light versions 0.2.1 dated 2022-06-21 and 1.0.0 dated 2026-05-29
GWPR.light-0.2.1/GWPR.light/R/AIC_A.R |only GWPR.light-0.2.1/GWPR.light/R/AIC_A_para.R |only GWPR.light-0.2.1/GWPR.light/R/AIC_F.R |only GWPR.light-0.2.1/GWPR.light/R/AIC_F_para.R |only GWPR.light-0.2.1/GWPR.light/R/CV_A.R |only GWPR.light-0.2.1/GWPR.light/R/CV_A_para.R |only GWPR.light-0.2.1/GWPR.light/R/CV_F.R |only GWPR.light-0.2.1/GWPR.light/R/CV_F_para.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.light-package.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.moran.test.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.pFtest.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.phtest.R |only GWPR.light-0.2.1/GWPR.light/R/GWPR.plmtest.R |only GWPR.light-0.2.1/GWPR.light/R/bw_GWPR.R |only GWPR.light-0.2.1/GWPR.light/R/drop_ID_with_single_observation.R |only GWPR.light-0.2.1/GWPR.light/R/golden_selection_function.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_A.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_A_pFtest.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_A_phtest.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_A_plmtest.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_F.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_F_pFtest.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_F_phtest.R |only GWPR.light-0.2.1/GWPR.light/R/gwpr_F_plmtest.R |only GWPR.light-0.2.1/GWPR.light/R/progress_bar.R |only GWPR.light-0.2.1/GWPR.light/R/protect_model_with_enough_freedom.R |only GWPR.light-0.2.1/GWPR.light/R/protect_model_with_least_individuals.R |only GWPR.light-0.2.1/GWPR.light/man/GWPR.Rd |only GWPR.light-0.2.1/GWPR.light/man/GWPR.light-package.Rd |only GWPR.light-0.2.1/GWPR.light/man/GWPR.moran.test.Rd |only GWPR.light-0.2.1/GWPR.light/man/GWPR.pFtest.Rd |only GWPR.light-0.2.1/GWPR.light/man/GWPR.phtest.Rd |only GWPR.light-0.2.1/GWPR.light/man/GWPR.plmtest.Rd |only GWPR.light-0.2.1/GWPR.light/man/bw.GWPR.Rd |only GWPR.light-1.0.0/GWPR.light/DESCRIPTION | 26 GWPR.light-1.0.0/GWPR.light/MD5 | 179 - GWPR.light-1.0.0/GWPR.light/NAMESPACE | 52 GWPR.light-1.0.0/GWPR.light/NEWS.md |only GWPR.light-1.0.0/GWPR.light/R/California.R | 36 GWPR.light-1.0.0/GWPR.light/R/TransAirPolCalif.R | 84 GWPR.light-1.0.0/GWPR.light/R/api.R |only GWPR.light-1.0.0/GWPR.light/R/bandwidth_grid.R |only GWPR.light-1.0.0/GWPR.light/R/bandwidth_random.R |only GWPR.light-1.0.0/GWPR.light/R/bandwidth_sgd.R |only GWPR.light-1.0.0/GWPR.light/R/context.R |only GWPR.light-1.0.0/GWPR.light/R/data_prepare.R |only GWPR.light-1.0.0/GWPR.light/R/diagnostics.R |only GWPR.light-1.0.0/GWPR.light/R/memory.R |only GWPR.light-1.0.0/GWPR.light/R/metrics.R |only GWPR.light-1.0.0/GWPR.light/R/model_linear.R |only GWPR.light-1.0.0/GWPR.light/R/model_logistic.R |only GWPR.light-1.0.0/GWPR.light/R/parallel.R |only GWPR.light-1.0.0/GWPR.light/R/result.R |only GWPR.light-1.0.0/GWPR.light/R/spatial_sf.R |only GWPR.light-1.0.0/GWPR.light/R/validation.R |only GWPR.light-1.0.0/GWPR.light/R/weights.R |only GWPR.light-1.0.0/GWPR.light/README.md | 343 -- GWPR.light-1.0.0/GWPR.light/build/vignette.rds |binary GWPR.light-1.0.0/GWPR.light/data/California.rda |binary GWPR.light-1.0.0/GWPR.light/inst/doc/gwpr-introduction.R |only GWPR.light-1.0.0/GWPR.light/inst/doc/gwpr-introduction.Rmd |only GWPR.light-1.0.0/GWPR.light/inst/doc/gwpr-introduction.html |only GWPR.light-1.0.0/GWPR.light/inst/doc/introduction_of_GWPR.R | 209 - GWPR.light-1.0.0/GWPR.light/inst/doc/introduction_of_GWPR.Rmd | 544 +-- GWPR.light-1.0.0/GWPR.light/inst/doc/introduction_of_GWPR.html | 1400 +++++----- GWPR.light-1.0.0/GWPR.light/man/California.Rd | 9 GWPR.light-1.0.0/GWPR.light/man/TransAirPolCalif.Rd | 100 GWPR.light-1.0.0/GWPR.light/man/align_spatial_to_panel.Rd |only GWPR.light-1.0.0/GWPR.light/man/api.Rd |only GWPR.light-1.0.0/GWPR.light/man/assert_sf.Rd |only GWPR.light-1.0.0/GWPR.light/man/bandwidth_grid.Rd |only GWPR.light-1.0.0/GWPR.light/man/bandwidth_random.Rd |only GWPR.light-1.0.0/GWPR.light/man/bandwidth_sgd.Rd |only GWPR.light-1.0.0/GWPR.light/man/build_distance_context.Rd |only GWPR.light-1.0.0/GWPR.light/man/build_id_map.Rd |only GWPR.light-1.0.0/GWPR.light/man/build_model_frame.Rd |only GWPR.light-1.0.0/GWPR.light/man/build_model_matrix.Rd |only GWPR.light-1.0.0/GWPR.light/man/build_neighbor_structure.Rd |only GWPR.light-1.0.0/GWPR.light/man/classify_memory_risk.Rd |only GWPR.light-1.0.0/GWPR.light/man/compute_distance.Rd |only GWPR.light-1.0.0/GWPR.light/man/compute_kernel_weights.Rd |only GWPR.light-1.0.0/GWPR.light/man/context.Rd |only GWPR.light-1.0.0/GWPR.light/man/data_prepare.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnose_gwpr.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnose_hausman.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnose_lm.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnose_local_f.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnose_moran.Rd |only GWPR.light-1.0.0/GWPR.light/man/diagnostics.Rd |only GWPR.light-1.0.0/GWPR.light/man/dot-make_na_history_row.Rd |only GWPR.light-1.0.0/GWPR.light/man/dot-make_scorer.Rd |only GWPR.light-1.0.0/GWPR.light/man/dot-rows_to_df.Rd |only GWPR.light-1.0.0/GWPR.light/man/effect_to_feglm_fml.Rd |only GWPR.light-1.0.0/GWPR.light/man/effect_to_glmmtmb_fml.Rd |only GWPR.light-1.0.0/GWPR.light/man/effect_to_plm.Rd |only GWPR.light-1.0.0/GWPR.light/man/estimate_memory.Rd |only GWPR.light-1.0.0/GWPR.light/man/extract_coordinates.Rd |only GWPR.light-1.0.0/GWPR.light/man/extract_coords_from_sf.Rd |only GWPR.light-1.0.0/GWPR.light/man/extract_geometry.Rd |only GWPR.light-1.0.0/GWPR.light/man/extract_linear_local_result.Rd |only GWPR.light-1.0.0/GWPR.light/man/extract_logistic_local_result.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_gwpr.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_linear_local_model.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_logistic_fixed.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_logistic_local_model.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_logistic_pooling.Rd |only GWPR.light-1.0.0/GWPR.light/man/fit_logistic_random.Rd |only GWPR.light-1.0.0/GWPR.light/man/format_memory_warning.Rd |only GWPR.light-1.0.0/GWPR.light/man/get_local_distances.Rd |only GWPR.light-1.0.0/GWPR.light/man/gwpr.Rd |only GWPR.light-1.0.0/GWPR.light/man/memory.Rd |only GWPR.light-1.0.0/GWPR.light/man/metrics.Rd |only GWPR.light-1.0.0/GWPR.light/man/model_linear.Rd |only GWPR.light-1.0.0/GWPR.light/man/model_logistic.Rd |only GWPR.light-1.0.0/GWPR.light/man/new_gwpr_context.Rd |only GWPR.light-1.0.0/GWPR.light/man/parallel_map.Rd |only GWPR.light-1.0.0/GWPR.light/man/parallel_module.Rd |only GWPR.light-1.0.0/GWPR.light/man/predict_linear_local_model.Rd |only GWPR.light-1.0.0/GWPR.light/man/predict_logistic_local_model.Rd |only GWPR.light-1.0.0/GWPR.light/man/prepare_data.Rd |only GWPR.light-1.0.0/GWPR.light/man/prepare_panel_data.Rd |only GWPR.light-1.0.0/GWPR.light/man/prepare_spatial_data.Rd |only GWPR.light-1.0.0/GWPR.light/man/print.gwpr_bandwidth.Rd |only GWPR.light-1.0.0/GWPR.light/man/print.gwpr_diagnostics.Rd |only GWPR.light-1.0.0/GWPR.light/man/print.gwpr_fit.Rd |only GWPR.light-1.0.0/GWPR.light/man/result.Rd |only GWPR.light-1.0.0/GWPR.light/man/score_bandwidth_candidate.Rd |only GWPR.light-1.0.0/GWPR.light/man/select_bandwidth.Rd |only GWPR.light-1.0.0/GWPR.light/man/spatial_sf.Rd |only GWPR.light-1.0.0/GWPR.light/man/standardize_binary_response.Rd |only GWPR.light-1.0.0/GWPR.light/man/standardize_logistic_response.Rd |only GWPR.light-1.0.0/GWPR.light/man/summary.gwpr_bandwidth.Rd |only GWPR.light-1.0.0/GWPR.light/man/summary.gwpr_diagnostics.Rd |only GWPR.light-1.0.0/GWPR.light/man/summary.gwpr_fit.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_bandwidth.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_bandwidth_control.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_binary_response.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_family_response.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_formula.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_gwpr_context.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_inputs.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_panel_index.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_spatial.Rd |only GWPR.light-1.0.0/GWPR.light/man/validate_workers.Rd |only GWPR.light-1.0.0/GWPR.light/man/validation.Rd |only GWPR.light-1.0.0/GWPR.light/man/weights.Rd |only GWPR.light-1.0.0/GWPR.light/man/with_reproducible_seed.Rd |only GWPR.light-1.0.0/GWPR.light/tests |only GWPR.light-1.0.0/GWPR.light/vignettes/gwpr-introduction.Rmd |only GWPR.light-1.0.0/GWPR.light/vignettes/introduction_of_GWPR.Rmd | 544 +-- 151 files changed, 1756 insertions(+), 1770 deletions(-)
Title: Polynomial Maximization Method for Non-Gaussian Regression
Description: Implements the Polynomial Maximization Method ('PMM') for parameter estimation
in linear and time series models when error distributions deviate from normality.
The 'PMM2' variant achieves lower variance parameter estimates compared to ordinary
least squares ('OLS') when errors exhibit significant skewness. The 'PMM3' variant
(S=3) targets symmetric platykurtic error distributions, reducing variance when
excess kurtosis is negative. Includes automatic method selection ('pmm_dispatch'),
linear regression, 'AR'/'MA'/'ARMA'/'ARIMA' models, and bootstrap inference.
Methodology described in Zabolotnii, Warsza, and Tkachenko (2018) <doi:10.1007/978-3-319-77179-3_75>,
Zabolotnii, Tkachenko, and Warsza (2022) <doi:10.1007/978-3-031-03502-9_37>, and
Zabolotnii, Tkachenko, and Warsza (2023) <doi:10.1007/978-3-031-25844-2_21>, and
Zabolotnii (2025) <doi:10.48550/arXiv.2511.07059>.
Author: Serhii Zabolotnii [aut, cre]
Maintainer: Serhii Zabolotnii <zabolotniua@gmail.com>
Diff between EstemPMM versions 0.3.2 dated 2026-05-15 and 0.4.0 dated 2026-05-29
EstemPMM-0.3.2/EstemPMM/man/AIC-PMM2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/AIC-PMM3fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/AIC-TS2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/AIC-TS3fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/BIC-PMM2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/BIC-PMM3fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/BIC-TS2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/BIC-TS3fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/logLik-PMM2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/logLik-PMM3fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/logLik-TS2fit-method.Rd |only EstemPMM-0.3.2/EstemPMM/man/logLik-TS3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/DESCRIPTION | 18 - EstemPMM-0.4.0/EstemPMM/MD5 | 114 ++++--- EstemPMM-0.4.0/EstemPMM/NAMESPACE | 22 + EstemPMM-0.4.0/EstemPMM/NEWS.md | 100 ++++++ EstemPMM-0.4.0/EstemPMM/R/pmm2_classes.R | 57 +-- EstemPMM-0.4.0/EstemPMM/R/pmm2_inference.R | 148 ++++++--- EstemPMM-0.4.0/EstemPMM/R/pmm2_main.R | 65 +--- EstemPMM-0.4.0/EstemPMM/R/pmm2_ts_methods.R | 62 +--- EstemPMM-0.4.0/EstemPMM/R/pmm3_classes.R | 55 ++- EstemPMM-0.4.0/EstemPMM/R/pmm3_dispatch.R | 98 +++++- EstemPMM-0.4.0/EstemPMM/R/pmm3_main.R | 99 ++++-- EstemPMM-0.4.0/EstemPMM/R/pmm3_ts_classes.R | 50 --- EstemPMM-0.4.0/EstemPMM/R/pmm3_ts_methods.R | 128 +++++--- EstemPMM-0.4.0/EstemPMM/R/pmm3_utils.R | 43 ++ EstemPMM-0.4.0/EstemPMM/R/pmm_base_classes.R |only EstemPMM-0.4.0/EstemPMM/R/pmm_show_methods.R |only EstemPMM-0.4.0/EstemPMM/R/pmm_unified_api.R |only EstemPMM-0.4.0/EstemPMM/build/partial.rdb |binary EstemPMM-0.4.0/EstemPMM/build/vignette.rds |binary EstemPMM-0.4.0/EstemPMM/inst/doc/bootstrap_inference.html | 154 +++++----- EstemPMM-0.4.0/EstemPMM/inst/doc/pmm2_introduction.html | 44 +- EstemPMM-0.4.0/EstemPMM/inst/doc/pmm2_time_series.html | 32 +- EstemPMM-0.4.0/EstemPMM/inst/doc/pmm3_symmetric_errors.html | 80 ++--- EstemPMM-0.4.0/EstemPMM/inst/doc/pmm3_time_series.html | 40 +- EstemPMM-0.4.0/EstemPMM/inst/doc/seasonal_models.html | 6 EstemPMM-0.4.0/EstemPMM/inst/notes |only EstemPMM-0.4.0/EstemPMM/man/BasePMM2-class.Rd | 19 - EstemPMM-0.4.0/EstemPMM/man/BasePMM3-class.Rd |only EstemPMM-0.4.0/EstemPMM/man/EstemPMM-package.Rd | 5 EstemPMM-0.4.0/EstemPMM/man/PMM3fit-class.Rd | 35 -- EstemPMM-0.4.0/EstemPMM/man/PMMfit-class.Rd |only EstemPMM-0.4.0/EstemPMM/man/PMMtsfit-class.Rd |only EstemPMM-0.4.0/EstemPMM/man/TS2fit-class.Rd | 39 -- EstemPMM-0.4.0/EstemPMM/man/TS3fit-class.Rd | 47 --- EstemPMM-0.4.0/EstemPMM/man/ar_pmm2.Rd | 10 EstemPMM-0.4.0/EstemPMM/man/arima_pmm2.Rd | 10 EstemPMM-0.4.0/EstemPMM/man/arma_pmm2.Rd | 10 EstemPMM-0.4.0/EstemPMM/man/confint-PMM3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/confint-TS3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/format.PMMdispatch.Rd |only EstemPMM-0.4.0/EstemPMM/man/logLik.PMM2fit.Rd |only EstemPMM-0.4.0/EstemPMM/man/logLik.PMM3fit.Rd |only EstemPMM-0.4.0/EstemPMM/man/logLik.TS2fit.Rd |only EstemPMM-0.4.0/EstemPMM/man/logLik.TS3fit.Rd |only EstemPMM-0.4.0/EstemPMM/man/ma_pmm2.Rd | 10 EstemPMM-0.4.0/EstemPMM/man/pmm2_inference.Rd | 30 + EstemPMM-0.4.0/EstemPMM/man/pmm3_variance_matrices.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_ar.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_arima.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_arma.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_dispatch.Rd | 4 EstemPMM-0.4.0/EstemPMM/man/pmm_lm.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_ma.Rd |only EstemPMM-0.4.0/EstemPMM/man/pmm_sarima.Rd |only EstemPMM-0.4.0/EstemPMM/man/print.PMMdispatch.Rd |only EstemPMM-0.4.0/EstemPMM/man/show-PMM2fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/show-PMM3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/show-TS2fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/show-TS3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/summary.PMMdispatch.Rd |only EstemPMM-0.4.0/EstemPMM/man/ts_pmm2.Rd | 10 EstemPMM-0.4.0/EstemPMM/man/ts_pmm2_inference.Rd | 23 + EstemPMM-0.4.0/EstemPMM/man/vcov-PMM3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/man/vcov-TS3fit-method.Rd |only EstemPMM-0.4.0/EstemPMM/tests/testthat/Rplots.pdf |binary EstemPMM-0.4.0/EstemPMM/tests/testthat/test-s4-generics.R | 107 ++++++ EstemPMM-0.4.0/EstemPMM/tests/testthat/test-v040-new-features.R |only 79 files changed, 1070 insertions(+), 704 deletions(-)
Title: Differential Pattern Analysis via Linear Modeling
Description: Individual gene expression patterns are encoded into a series of eigenvector patterns ('WGCNA' package). Using the framework of linear model-based differential expression comparisons ('limma' package), time-course expression patterns for genes in different conditions are compared and analyzed for significant pattern changes. For reference, see: Greenham K, Sartor RC, Zorich S, Lou P, Mockler TC and McClung CR. eLife. 2020 Sep 30;9(4). <doi:10.7554/eLife.58993>.
Author: Ryan C. Sartor [aut, cre],
Kathleen Greenham [aut],
William Gustafson [aut]
Maintainer: Ryan C. Sartor <sartorry@gmail.com>
Diff between DiPALM versions 1.2 dated 2022-06-27 and 1.3 dated 2026-05-29
DESCRIPTION | 30 ++++++++++++++++++++++-------- MD5 | 20 ++++++++++++++++---- NAMESPACE | 2 ++ R/Interface.R |only data/datalist | 1 + data/smallTestData.txt.gz |only inst/CITATION | 4 ++-- man/col_format_sub.Rd |only man/dipalm.Rd |only man/joinOutputs.Rd |only man/main.Rd |only man/make_TCs.Rd |only man/msub.Rd |only man/open_log.Rd |only man/re_esc.Rd |only man/sampleReplicates.Rd |only man/smallTestData.Rd |only 17 files changed, 43 insertions(+), 14 deletions(-)
Title: Multivariate Weather-State Approach Conditionally Skew-Normal
Generator
Description: A multivariate weather generator for daily climate variables based
on weather-states (Flecher et al. (2010) <doi:10.1029/2009WR008098>).
It uses a Markov chain for modeling the succession of weather states.
Conditionally to the weather states, the multivariate variables are modeled
using the family of Complete Skew-Normal distributions. Parameters are
estimated on measured series. Must include the variable 'Rain' and can
accept as many other variables as desired.
Author: Denis Allard [aut] ,
Ronan Trepos [aut, cre]
Maintainer: Ronan Trepos <ronan.trepos@inrae.fr>
Diff between WACS versions 1.1.0 dated 2020-06-05 and 1.2.0 dated 2026-05-29
DESCRIPTION | 32 +++++++++++++++++++++----------- MD5 | 28 ++++++++++++++-------------- R/WACScompare.R | 12 ++++++------ R/WACSdata.R | 3 ++- R/WACSestim.R | 9 +++++---- R/WACSplot.R | 24 +++++++++++++----------- R/WACSplotdensity.R | 2 +- R/WACSreadAgroclim.R | 10 ++++------ R/WACSsimul.R | 4 ++-- R/WACSvalid.R | 8 ++++---- R/wacs-package.R | 25 ++++++++++++------------- R/wacs.simul_innercall.R | 2 +- data/ClimateSeries.rda |binary man/WACS.Rd | 37 +++++++++++++++++++++++++++---------- man/WACSreadAgroclim.Rd | 10 ++++------ 15 files changed, 116 insertions(+), 90 deletions(-)
Title: Genotype-by-Environment Interaction in Polygenic Score Models
Description: A novel PRS model is introduced to enhance the prediction accuracy by utilising GxE effects. This package performs Genome Wide Association Studies (GWAS) and Genome Wide Environment Interaction Studies (GWEIS) using a discovery dataset. The package has the ability to obtain polygenic risk scores (PRSs) for a target sample. Finally it predicts the risk values of each individual in the target sample. Users have the choice of using existing models (Li et al., 2015) <doi:10.1093/annonc/mdu565>, (Pandis et al., 2013) <doi:10.1093/ejo/cjt054>, (Peyrot et al., 2018) <doi:10.1016/j.biopsych.2017.09.009> and (Song et al., 2022) <doi:10.1038/s41467-022-32407-9>, as well as newly proposed models for genomic risk prediction (refer to the URL for more details).
Author: Dovini Jayasinghe [aut, cre, cph],
Hong Lee [aut, cph],
Moksedul Momin [aut, cph]
Maintainer: Dovini Jayasinghe <dovini.jayasinghe@mymail.unisa.edu.au>
Diff between GxEprs versions 1.2 dated 2024-05-29 and 1.3 dated 2026-05-29
DESCRIPTION | 10 MD5 | 46 - data/Bcov_discovery.rda |binary data/Bcov_target.rda |binary data/Qcov_discovery.rda |binary data/Qcov_target.rda |binary data/Qphe_discovery.rda |binary data/Qphe_target.rda |binary inst/Bcov_discovery.txt | 1600 ++++++++++++++++++++++++------------------------ inst/Bcov_target.txt | 400 ++++++------ inst/Qcov_discovery.txt | 1600 ++++++++++++++++++++++++------------------------ inst/Qcov_target.txt | 400 ++++++------ inst/Qphe_discovery.txt | 1600 ++++++++++++++++++++++++------------------------ inst/Qphe_target.txt | 400 ++++++------ man/Bcov_discovery.Rd | 36 - man/Bcov_target.Rd | 36 - man/Bphe_discovery.Rd | 6 man/Bphe_target.Rd | 6 man/DummyData.bim.Rd | 12 man/DummyData.fam.Rd | 12 man/Qcov_discovery.Rd | 36 - man/Qcov_target.Rd | 36 - man/Qphe_discovery.Rd | 6 man/Qphe_target.Rd | 6 24 files changed, 3124 insertions(+), 3124 deletions(-)
Title: Earth Observation Data Cubes from Satellite Image Collections
Description: Processing collections of Earth observation images as on-demand multispectral, multitemporal raster data cubes. Users
define cubes by spatiotemporal extent, resolution, and spatial reference system and let 'gdalcubes' automatically apply cropping, reprojection, and
resampling using the 'Geospatial Data Abstraction Library' ('GDAL'). Implemented functions on data cubes include reduction over space and time,
applying arithmetic expressions on pixel band values, moving window aggregates over time, filtering by space, time, bands, and predicates on pixel values,
exporting data cubes as 'netCDF' or 'GeoTIFF' files, plotting, and extraction from spatial and or spatiotemporal features.
All computational parts are implemented in C++, linking to the 'GDAL', 'netCDF', 'CURL', and 'SQLite' libraries.
See Appel and Pebesma (2019) <doi:10.3390/data4030092> for further details.
Author: Marius Appel [aut, cre] ,
Edzer Pebesma [ctb] ,
Roger Bivand [ctb],
Jeroen Ooms [ctb] ,
Lewis Van Winkle [cph],
Ole Christian Eidheim [cph],
Howard Hinnant [cph],
Adrian Colomitchi [cph],
Florian Dang [cph],
Paul Thompson [cph],
Tomasz Kaminski [cph] [...truncated...]
Maintainer: Marius Appel <marius.appel@hs-bochum.de>
Diff between gdalcubes versions 0.7.3 dated 2026-01-18 and 0.7.4 dated 2026-05-29
gdalcubes-0.7.3/gdalcubes/src/gdalcubes/src/gdalcubes.cpp |only gdalcubes-0.7.3/gdalcubes/src/gdalcubes/src/progress.cpp |only gdalcubes-0.7.3/gdalcubes/src/gdalcubes/src/progress.h |only gdalcubes-0.7.4/gdalcubes/DESCRIPTION | 10 ++-- gdalcubes-0.7.4/gdalcubes/MD5 | 22 ++++------ gdalcubes-0.7.4/gdalcubes/NEWS.md | 5 ++ gdalcubes-0.7.4/gdalcubes/build/vignette.rds |binary gdalcubes-0.7.4/gdalcubes/configure.ac | 2 gdalcubes-0.7.4/gdalcubes/inst/doc/gc01_MODIS.html | 7 +-- gdalcubes-0.7.4/gdalcubes/man/gdalcubes.Rd | 5 ++ gdalcubes-0.7.4/gdalcubes/src/gdalcubes/src/config.h | 2 gdalcubes-0.7.4/gdalcubes/src/gdalcubes/src/gdalcubes.h | 2 gdalcubes-0.7.4/gdalcubes/src/gdalcubes/src/image_collection.cpp | 8 +-- gdalcubes-0.7.4/gdalcubes/src/gdalcubes/src/progress_virt.h |only 14 files changed, 36 insertions(+), 27 deletions(-)
Title: Nonlinear Dependence and Lead-Lag Analysis via Chatterjee's Xi
Description: Computes Chatterjee's non-parametric correlation coefficient for time series data. It extends the original metric to time series analysis by providing the univariate Xi-Autocorrelation Function (Xi-ACF), directional Xi-Cross-Correlation Function (Xi-CCF), and multivariate network evaluation matrices. The package allows users to test for non-linear dependence using Iterative Amplitude Adjusted Fourier Transform (IAAFT) and Multivariate IAAFT (MIAAFT) surrogate data with strict Family-Wise Error Rate ('FWER') control via Max-statistic approaches. Methodologies are based on Chatterjee (2021) <doi:10.1080/01621459.2020.1758115>, surrogate data testing methods by Schreiber and Schmitz (1996) <doi:10.1103/PhysRevLett.77.635>, and local structural identification by Watanabe (2026) <doi:10.2139/ssrn.6829431>.
Author: Yasunori Watanabe [aut, cre]
Maintainer: Yasunori Watanabe <watanabe.yasunori@outlook.com>
Diff between xiacf versions 0.5.0 dated 2026-05-17 and 0.6.0 dated 2026-05-29
xiacf-0.5.0/xiacf/man/figures/README-ccf-example-1.png |only xiacf-0.5.0/xiacf/man/figures/README-extract_example-1.png |only xiacf-0.5.0/xiacf/man/figures/README-plot_xi_matrix-1.png |only xiacf-0.5.0/xiacf/man/figures/README-xi-acf-test-1.png |only xiacf-0.5.0/xiacf/man/figures/README-xi-ccf-rolling-1.png |only xiacf-0.5.0/xiacf/man/figures/README-xi-ccf-test-1.png |only xiacf-0.5.0/xiacf/man/figures/README-xi_matrix_example-1.png |only xiacf-0.6.0/xiacf/DESCRIPTION | 12 xiacf-0.6.0/xiacf/MD5 | 52 - xiacf-0.6.0/xiacf/NEWS.md | 10 xiacf-0.6.0/xiacf/R/RcppExports.R | 4 xiacf-0.6.0/xiacf/R/autoplot.R | 281 ++++++---- xiacf-0.6.0/xiacf/R/extract.R | 205 +++---- xiacf-0.6.0/xiacf/R/globals.R | 7 xiacf-0.6.0/xiacf/R/xi_ccf.R | 226 +++++--- xiacf-0.6.0/xiacf/R/xi_matrix.R | 31 - xiacf-0.6.0/xiacf/R/xi_rolling_ccf.R | 27 - xiacf-0.6.0/xiacf/README.md | 289 +++++------ xiacf-0.6.0/xiacf/inst/CITATION | 56 +- xiacf-0.6.0/xiacf/man/extract_xi_acf.Rd | 17 xiacf-0.6.0/xiacf/man/extract_xi_ccf.Rd | 19 xiacf-0.6.0/xiacf/man/figures/README-xi-acf-1.png |only xiacf-0.6.0/xiacf/man/figures/README-xi-ccf-1.png |only xiacf-0.6.0/xiacf/man/figures/README-xi-matrix-1.png |only xiacf-0.6.0/xiacf/man/figures/README-xi-matrix-2.png |only xiacf-0.6.0/xiacf/man/print.xi_ccf.Rd |only xiacf-0.6.0/xiacf/man/reexports.Rd | 2 xiacf-0.6.0/xiacf/man/xi_ccf.Rd | 35 - xiacf-0.6.0/xiacf/src/RcppExports.cpp | 9 xiacf-0.6.0/xiacf/src/testing_engine.cpp | 78 +- xiacf-0.6.0/xiacf/tests/testthat/test-extractors.R | 84 +-- xiacf-0.6.0/xiacf/tests/testthat/test-xi_ccf.R | 58 +- xiacf-0.6.0/xiacf/tests/testthat/test-xi_matrix.R | 55 -- 33 files changed, 872 insertions(+), 685 deletions(-)
Title: Parametric Statistical Modelling and Inference for the
'spatstat' Family
Description: Functionality for parametric statistical modelling and inference for spatial data,
mainly spatial point patterns, in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Supports parametric modelling, formal statistical inference, and model validation.
Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope t [...truncated...]
Author: Adrian Baddeley [aut, cre, cph] ,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb, cph],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.model versions 3.7-0 dated 2026-03-29 and 3.7-1 dated 2026-05-29
DESCRIPTION | 16 ++++----- MD5 | 54 ++++++++++++++++---------------- NAMESPACE | 18 ++++++++++ NEWS | 68 +++++++++++++++++++++++++++++++++++++++++ R/Kcom.R | 10 +++--- R/detPPF-class.R | 10 ++++++ R/kppm.R | 44 ++++++++++++++++++++++---- R/makepspace.R | 52 ++++++++++++++++++++++++++++--- R/mppm.R | 19 +++++++++-- R/percy.R | 32 ++++++++++++------- R/ppmclass.R | 13 +++++++ R/predict.ppm.R | 5 ++- R/predictmppm.R | 24 +++++++++++--- R/relrisk.ppm.R | 12 ++++--- R/rppm.R | 5 ++- R/slrm.R | 11 +++++- R/sysdata.rda |binary build/partial.rdb |binary inst/doc/packagesizes.txt | 2 - inst/info/packagesizes.txt | 2 - man/intensity.kppm.Rd |only man/intensity.mppm.Rd |only man/intensity.ppm.Rd | 18 ++++++++-- man/macros/defns.Rd | 1 man/predict.mppm.Rd | 13 +++++++ man/predict.ppm.Rd | 19 +++++++++++ man/relrisk.ppm.Rd | 21 ++++++++++++ man/repul.Rd | 65 +++++++++++++++++++++++++++++++++------ man/spatstat.model-internal.Rd | 20 +++++------- 29 files changed, 449 insertions(+), 105 deletions(-)
More information about spatstat.model at CRAN
Permanent link
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating
random and regular graphs, graph visualization, centrality methods and
much more.
Author: Gabor Csardi [aut] ,
Tamas Nepusz [aut] ,
Vincent Traag [aut] ,
Szabolcs Horvat [aut] ,
Fabio Zanini [aut] ,
Daniel Noom [aut],
Kirill Mueller [aut, cre] ,
Michael Antonov [ctb],
Chan Zuckerberg Initiative [fnd] ,
David Schoch [aut] ,
Maelle Salmon [a [...truncated...]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between igraph versions 2.3.1 dated 2026-05-04 and 2.3.2 dated 2026-05-29
DESCRIPTION | 6 ++--- MD5 | 12 +++++----- NEWS.md | 7 ++++++ inst/doc/igraph.html | 52 +++++++++++++++++++++++----------------------- inst/doc/igraph_ES.html | 52 +++++++++++++++++++++++----------------------- src/vendor/arpack/dmout.f | 2 - src/vendor/arpack/dvout.f | 2 - 7 files changed, 70 insertions(+), 63 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2025-07-23 0.9.1
2023-02-10 0.9.0
Title: Recreates Some 'SAS®' Procedures in 'R'
Description: Contains functions to simulate the most commonly used
'SAS®' procedures. Specifically, the package aims to
simulate the functionality of 'proc freq', 'proc means', 'proc ttest',
'proc reg', 'proc transpose', 'proc sort', and 'proc print'.
The simulation will include recreating
all statistics with the highest fidelity possible.
Author: David Bosak [aut, cre],
Diyu Yang [aut],
Athenkosi Nkonyeni [aut],
Kevin Kramer [ctb],
Brian Varney [ctb],
Duong Tran [ctb],
Yifei Chen [ctb]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between procs versions 1.0.8 dated 2026-03-20 and 1.0.9 dated 2026-05-29
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Title: Green Index Quantification, Analysis and Visualization
Description: Quantification, analysis, and visualization of urban greenness within city networks using data from 'OpenStreetMap' <https://www.openstreetmap.org>.
Author: Sachit Mahajan [aut, cre]
Maintainer: Sachit Mahajan <sachitmahajan90@gmail.com>
Diff between greenR versions 0.0.1.6 dated 2025-11-30 and 0.0.1.7 dated 2026-05-29
DESCRIPTION | 29 MD5 | 55 - NAMESPACE | 74 + R/RcppExports.R |only R/accessibility_greenspace.R | 4 R/chm_analysis.R | 1395 ++++++++++++++++++++++++++------- R/get_osm_data.R | 330 +++++-- R/uh_decision.R |only R/uh_svf.R |only R/zzz.R | 14 inst/doc/introduction.R | 36 inst/doc/introduction.Rmd | 66 + inst/doc/introduction.html | 78 + man/assess_urban_priority_equity.Rd |only man/build_street_canyon_priority.Rd |only man/build_urban_block_priority.Rd |only man/build_urban_priority_grid.Rd |only man/chm_analysis.Rd | 138 +-- man/compute_gini_bootstrap.Rd |only man/dot-way_geom_to_matrix.Rd |only man/emulate_canyon_microclimate.Rd |only man/get_osm_data.Rd | 50 - man/plot_canyon_diamond_bivariate.Rd |only man/plot_canyon_priority_map.Rd |only man/plot_hybrid_field_map.Rd |only man/plot_multilayer_leaflet.Rd |only man/plot_priority_3d_explorer.Rd |only man/plot_priority_3d_isometric.Rd |only man/plot_priority_action_classes.Rd |only man/plot_priority_bivariate.Rd |only man/plot_priority_diamond_bivariate.Rd |only man/plot_priority_interactive.Rd |only man/save_3d_deckgl_dashboard.Rd |only man/uh_decision.Rd |only man/uh_svf.Rd |only man/uh_svf_plot_distribution.Rd |only man/uh_svf_plot_skyline.Rd |only src |only tests/testthat/test.R | 56 + vignettes/chm.jpg |binary vignettes/introduction.Rmd | 66 + 41 files changed, 1886 insertions(+), 505 deletions(-)
Title: Extra Analysis Results Data Utilities
Description: Create extra Analysis Results Data (ARD) summary objects.
The package supplements the simple ARD functions from the 'cards'
package, exporting functions to put statistical results in the ARD
format. These objects are used and re-used to construct summary
tables, visualizations, and written reports.
Author: Daniel D. Sjoberg [aut, cre] ,
Abinaya Yogasekaram [aut],
Emily de la Rua [aut],
Malcolm Barrett [ctb] ,
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between cardx versions 0.3.2 dated 2026-02-05 and 0.3.3 dated 2026-05-29
DESCRIPTION | 10 - MD5 | 128 ++++++++--------- NEWS.md | 10 + R/ard_aod_wald_test.R | 5 R/ard_car_anova.R | 2 R/ard_car_vif.R | 12 + R/ard_categorical_ci.R | 4 R/ard_categorical_ci.survey.design.R | 4 R/ard_continuous.survey.design.R | 7 R/ard_continuous_ci.R | 2 R/ard_continuous_ci.survey.design.R | 4 R/ard_effectsize_cohens_d.R | 6 R/ard_effectsize_hedges_g.R | 6 R/ard_emmeans_contrast.R | 2 R/ard_emmeans_emmeans.R | 2 R/ard_incidence_rate.R | 2 R/ard_missing.survey.design.R | 4 R/ard_regression.R | 2 R/ard_smd_smd.R | 4 R/ard_stats_anova.R | 2 R/ard_stats_aov.R | 2 R/ard_stats_chisq_test.R | 4 R/ard_stats_fisher_test.R | 4 R/ard_stats_kruskal_test.R | 4 R/ard_stats_mantelhaen_test.R | 4 R/ard_stats_mcnemar_test.R | 6 R/ard_stats_mood_test.R | 4 R/ard_stats_oneway_test.R | 2 R/ard_stats_poisson_test.R | 4 R/ard_stats_prop_test.R | 7 R/ard_stats_t_test.R | 6 R/ard_stats_t_test_onesample.R | 4 R/ard_stats_wilcox_test.R | 6 R/ard_stats_wilcox_test_onesample.R | 4 R/ard_survey_svychisq.R | 4 R/ard_survey_svyranktest.R | 4 R/ard_survey_svyttest.R | 4 R/ard_survival_survdiff.R | 2 R/ard_survival_survfit.R | 45 ++++- R/ard_survival_survfit_diff.R | 2 R/ard_tabulate.survey.design.R | 5 R/ard_tabulate_abnormal.R | 2 R/ard_tabulate_max.R | 2 R/ard_tabulate_value.survey.design.R | 2 R/deprecated.R | 4 man/ard_car_vif.Rd | 2 man/ard_effectsize_hedges_g.Rd | 2 man/ard_emmeans.Rd | 3 man/cardx-package.Rd | 1 man/deprecated.Rd | 6 man/dot-extract_wald_results.Rd | 4 man/dot-format_proptest_results.Rd | 4 man/reexports.Rd | 4 tests/testthat/_snaps/ard_car_vif.md | 29 +++ tests/testthat/_snaps/ard_stats_mood_test.md | 17 -- tests/testthat/_snaps/ard_survival_survfit.md | 4 tests/testthat/test-ard_car_vif.R | 24 +++ tests/testthat/test-ard_categorical_ci.data.frame.R | 12 + tests/testthat/test-ard_categorical_ci.survey.design.R | 2 tests/testthat/test-ard_continuous_ci.survey.design.R | 2 tests/testthat/test-ard_stats_mood_test.R | 3 tests/testthat/test-ard_stats_t_test_onesample.R | 2 tests/testthat/test-ard_stats_wilcox_test_onesample.R | 2 tests/testthat/test-ard_survival_survfit.R | 22 ++ tests/testthat/test-ard_tabulate_max.R | 3 65 files changed, 321 insertions(+), 182 deletions(-)
Title: Unified Interface for AI Model Providers
Description: A production-grade AI toolkit for R featuring a layered
architecture (Specification, Utilities, Providers, Core), request
interception support, robust error handling with exponential retry
delays, support for multiple AI model providers ('OpenAI',
'Anthropic', etc.), local small language model inference,
distributed 'MCP' ecosystem, multi-agent orchestration, progressive
knowledge loading through skills, and a global skill store for
sharing AI capabilities.
Author: Yonghe Xia [aut, cre]
Maintainer: Yonghe Xia <xiayh17@gmail.com>
Diff between aisdk versions 1.1.0 dated 2026-03-31 and 1.4.10 dated 2026-05-29
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Title: Embed 'SWI'-'Prolog'
Description: Interface to 'SWI'-'Prolog', <https://www.swi-prolog.org/>. This package is normally not loaded directly, please refer to package 'rolog' instead. The purpose of this package is to provide the 'Prolog' runtime on systems that do not have a software installation of 'SWI'-'Prolog'.
Author: Matthias Gondan [aut, com, cre] ,
Jan Wielemaker [ctb, cph] ,
European Commission [fnd]
Maintainer: Matthias Gondan <Matthias.Gondan-Rochon@uibk.ac.at>
Diff between rswipl versions 10.1.7 dated 2026-05-12 and 10.1.8 dated 2026-05-29
DESCRIPTION | 8 MD5 | 187 ++- NEWS.md | 6 inst/swipl |only src/install.libs.R | 2 src/swipl-devel/CMakeLists.txt | 10 src/swipl-devel/VERSION | 2 src/swipl-devel/boot/build_home.pl | 11 src/swipl-devel/boot/toplevel.pl | 4 src/swipl-devel/cmake/Install.cmake | 30 src/swipl-devel/cmake/InstallSource.cmake | 10 src/swipl-devel/cmake/Locations.cmake | 61 + src/swipl-devel/cmake/LocationsPostPorts.cmake | 4 src/swipl-devel/cmake/PackageSelection.cmake | 2 src/swipl-devel/cmake/macos_app_fixup |only src/swipl-devel/cmake/port/Darwin.cmake | 61 - src/swipl-devel/desktop/Framework-Info.plist.in |only src/swipl-devel/desktop/distribution.xml.in |only src/swipl-devel/desktop/installer-background.png |only src/swipl-devel/desktop/swipl.entitlements.plist |only src/swipl-devel/doc/MacOSXInstaller.md |only src/swipl-devel/library/dialect/swi/syspred_options.pl | 7 src/swipl-devel/library/writef.pl | 6 src/swipl-devel/packages/clib/bsd-crypt.c | 5 src/swipl-devel/packages/clib/process.c.rej |only src/swipl-devel/packages/cpp/SWI-cpp2.cpp | 15 src/swipl-devel/packages/cpp/SWI-cpp2.h | 93 + src/swipl-devel/packages/cpp/pl2cpp.plx | 164 ++- src/swipl-devel/packages/cpp/test_cpp.cpp | 81 + src/swipl-devel/packages/cpp/test_cpp.cpp.orig |only src/swipl-devel/packages/cpp/test_cpp.pl | 55 - 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Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020) <doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.5.1 dated 2025-09-19 and 0.6.0 dated 2026-05-29
DESCRIPTION | 15 - MD5 | 69 ++++---- NAMESPACE | 4 NEWS.md | 48 ++++- R/compute.ci.R | 19 +- R/fwb.R | 245 +++++++++++++++++++----------- R/fwb.array.R | 31 ++- R/fwb.ci.R | 64 +++---- R/plot.fwb.R | 65 ++++--- R/set_fwb_wtype.R | 32 +-- R/simultaneous.R | 28 +-- R/summary.fwb.R | 59 +++---- R/utils.R | 226 +++++++-------------------- R/vcovFWB.R | 205 +++++++++++++++---------- R/weighted-statistics.R | 39 +++- README.md | 86 ++++++---- build/stage23.rdb |binary build/vignette.rds |binary inst/doc/fwb-rep.Rmd | 22 +- inst/doc/fwb-rep.html | 58 ++++--- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/fwb-package.Rd | 5 man/fwb.Rd | 48 ++++- man/fwb.array.Rd | 9 - man/fwb.ci.Rd | 14 + man/macros/macros.Rd | 2 man/plot.fwb.Rd | 6 man/set_fwb_wtype.Rd | 12 - man/summary.fwb.Rd | 6 man/vcovFWB.Rd | 28 ++- tests/testthat/helpers.R | 4 tests/testthat/test-fwb.R | 66 +++++++- tests/testthat/test-vcovFWB.R |only vignettes/fwb-rep.Rmd | 22 +- 36 files changed, 866 insertions(+), 671 deletions(-)