Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 1.4.2 dated 2025-01-07 and 1.4.3 dated 2025-09-28
DESCRIPTION | 12 +++++------ MD5 | 31 +++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 8 ++++++- R/lda.R | 6 +++-- R/seededlda.R | 22 ++++++++++++--------- R/utils.R | 23 ++++++++++++++++++++++ inst/WORDLIST | 3 -- man/as.dictionary.textmodel_lda.Rd |only man/print.textmodel_lda.Rd | 4 +-- man/terms.Rd | 10 ++++----- man/textmodel_lda.Rd | 5 ++-- src/Makevars.in | 2 - src/Makevars.win | 2 - tests/testthat/test-textmodel_lda.R | 3 +- tests/testthat/test-textmodel_seededlda.R | 2 - tests/testthat/test-utils.R | 11 ++++++++++ 17 files changed, 97 insertions(+), 48 deletions(-)
Title: Structures for Preference Data
Description: Convenient structures for creating, sourcing, reading, writing
and manipulating ordinal preference data. Methods for writing to/from PrefLib
formats. See Nicholas Mattei and Toby Walsh "PrefLib: A Library of Preference
Data" (2013) <doi:10.1007/978-3-642-41575-3_20>.
Author: Floyd Everest [aut, cre] ,
Heather Turner [aut] ,
Damjan Vukcevic [aut]
Maintainer: Floyd Everest <me@floydeverest.com>
This is a re-admission after prior archival of version 0.1.1 dated 2023-09-07
Diff between prefio versions 0.1.1 dated 2023-09-07 and 0.2.0 dated 2025-09-28
prefio-0.1.1/prefio/R/aggregate.preferences.R |only prefio-0.1.1/prefio/R/choices.R |only prefio-0.1.1/prefio/R/group.preferences.R |only prefio-0.1.1/prefio/R/utils-pipe.R |only prefio-0.1.1/prefio/man/aggregate.preferences.Rd |only prefio-0.1.1/prefio/man/choices.Rd |only prefio-0.1.1/prefio/man/group.Rd |only prefio-0.1.1/prefio/man/pipe.Rd |only prefio-0.1.1/prefio/man/reexports.Rd |only prefio-0.1.1/prefio/tests/testthat/test-aggregated_preferences.R |only prefio-0.1.1/prefio/tests/testthat/test-choices.R |only prefio-0.1.1/prefio/tests/testthat/test-group.R |only prefio-0.2.0/prefio/DESCRIPTION | 21 prefio-0.2.0/prefio/MD5 | 67 prefio-0.2.0/prefio/NAMESPACE | 65 prefio-0.2.0/prefio/NEWS.md | 12 prefio-0.2.0/prefio/R/adjacency.R | 110 prefio-0.2.0/prefio/R/pref_summaries.R |only prefio-0.2.0/prefio/R/pref_tools.R |only prefio-0.2.0/prefio/R/preferences.R | 1573 ++++------ prefio-0.2.0/prefio/R/prefio-package.R | 3 prefio-0.2.0/prefio/R/preflib.R | 152 prefio-0.2.0/prefio/R/ranking_matrix.R |only prefio-0.2.0/prefio/build/partial.rdb |binary prefio-0.2.0/prefio/inst/WORDLIST | 60 prefio-0.2.0/prefio/man/adjacency.Rd | 45 prefio-0.2.0/prefio/man/figures |only prefio-0.2.0/prefio/man/pref_add_unranked.Rd |only prefio-0.2.0/prefio/man/pref_blank.Rd |only prefio-0.2.0/prefio/man/pref_cov.Rd |only prefio-0.2.0/prefio/man/pref_get_items.Rd |only prefio-0.2.0/prefio/man/pref_get_rank.Rd |only prefio-0.2.0/prefio/man/pref_irv.Rd |only prefio-0.2.0/prefio/man/pref_keep.Rd |only prefio-0.2.0/prefio/man/pref_length.Rd |only prefio-0.2.0/prefio/man/pref_omit.Rd |only prefio-0.2.0/prefio/man/pref_pop.Rd |only prefio-0.2.0/prefio/man/pref_rev.Rd |only prefio-0.2.0/prefio/man/pref_trunc.Rd |only prefio-0.2.0/prefio/man/pref_type.Rd |only prefio-0.2.0/prefio/man/preferences.Rd | 319 -- prefio-0.2.0/prefio/man/ranking_matrix.Rd |only prefio-0.2.0/prefio/man/read_preflib.Rd | 24 prefio-0.2.0/prefio/man/write_preflib.Rd | 17 prefio-0.2.0/prefio/tests/data/sydney_2023.tsv |only prefio-0.2.0/prefio/tests/testthat/_snaps |only prefio-0.2.0/prefio/tests/testthat/test-adjacency.R | 49 prefio-0.2.0/prefio/tests/testthat/test-preferences.R | 1046 +++++- prefio-0.2.0/prefio/tests/testthat/test-preflib.R | 48 prefio-0.2.0/prefio/tests/testthat/test-rankingmatrix.R |only prefio-0.2.0/prefio/tests/testthat/test-summaries.R |only prefio-0.2.0/prefio/tests/testthat/test-tools.R |only 52 files changed, 2058 insertions(+), 1553 deletions(-)
Title: Holding the Database for the 'extrafont' Package
Description: It is meant to be used with the 'extrafont' package. The 'extrafont' package contains the code to install and use fonts, while the 'extrafontdb' package contains the font database.
Author: Winston Chang [aut],
Frederic Bertrand [cre]
Maintainer: Frederic Bertrand <frederic.bertrand@lecnam.net>
Diff between extrafontdb versions 1.0 dated 2012-06-11 and 1.1 dated 2025-09-28
extrafontdb-1.0/extrafontdb/man/extrafontdb.Rd |only extrafontdb-1.1/extrafontdb/DESCRIPTION | 31 ++++++++++++----- extrafontdb-1.1/extrafontdb/MD5 | 17 ++++++--- extrafontdb-1.1/extrafontdb/NAMESPACE | 2 + extrafontdb-1.1/extrafontdb/NEWS |only extrafontdb-1.1/extrafontdb/R/extrafontdb.r | 15 +------- extrafontdb-1.1/extrafontdb/README.md | 24 +++++++++++++ extrafontdb-1.1/extrafontdb/inst/CITATION |only extrafontdb-1.1/extrafontdb/man/extrafontdb-package.Rd |only extrafontdb-1.1/extrafontdb/tests |only 10 files changed, 64 insertions(+), 25 deletions(-)
Title: 'systemPipeShiny' Utility Functions
Description: The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>
Diff between spsUtil versions 0.2.2 dated 2021-10-30 and 0.2.2.1 dated 2025-09-28
DESCRIPTION | 8 ++-- MD5 | 26 ++++++------- R/spsUtil.R | 2 - man/checkNameSpace.Rd | 8 ++-- man/checkUrl.Rd | 2 - man/historyStack.Rd | 94 ++++++++++++++++++++++++-------------------------- man/inc.Rd | 16 ++++---- man/msg.Rd | 43 ++++++++++------------ man/notFalsy.Rd | 23 +++++------- man/quiet.Rd | 8 ++-- man/simepleStack.Rd | 48 ++++++++++++------------- man/spsOption.Rd | 14 +++---- man/strUniquefy.Rd | 2 - man/timeout.Rd | 15 ++++--- 14 files changed, 153 insertions(+), 156 deletions(-)
Title: Sparse Latent Class Model for Cognitive Diagnosis
Description: Perform a Bayesian estimation of the exploratory
Sparse Latent Class Model for Binary Data
described by Chen, Y., Culpepper, S. A., and Liang, F. (2020)
<doi:10.1007/s11336-019-09693-2>.
Author: James Joseph Balamuta [aut, cre, cph] ,
Steven Andrew Culpepper [aut, cph]
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between slcm versions 0.1.0 dated 2023-08-12 and 0.1.1 dated 2025-09-28
DESCRIPTION | 27 ++++++++++++------------ MD5 | 20 +++++++++-------- NAMESPACE | 1 R/slcm-wrapper.R | 38 +++++++++++++++++++++++++++------- R/utils.R |only README.md | 1 build/partial.rdb |binary man/attribute_pattern_table_header.Rd |only man/slcm-package.Rd | 3 -- man/slcm.Rd | 17 ++++++++------- src/Makevars | 3 ++ src/Makevars.win | 3 ++ 12 files changed, 74 insertions(+), 39 deletions(-)
Title: GSL Multi-Start Nonlinear Least-Squares Fitting
Description: An R interface to weighted nonlinear least-squares optimization with the GNU Scientific Library (GSL), see M. Galassi et al. (2009, ISBN:0954612078). The available trust region methods include the Levenberg-Marquardt algorithm with and without geodesic acceleration, the Steihaug-Toint conjugate gradient algorithm for large systems and several variants of Powell's dogleg algorithm. Multi-start optimization based on quasi-random samples is implemented using a modified version of the algorithm in Hickernell and Yuan (1997, OR Transactions). Robust nonlinear regression can be performed using various robust loss functions, in which case the optimization problem is solved by iterative reweighted least squares (IRLS). Bindings are provided to tune a number of parameters affecting the low-level aspects of the trust region algorithms. The interface mimics R's nls() function and returns model objects inheriting from the same class.
Author: Joris Chau [aut, cre]
Maintainer: Joris Chau <joris.chau@openanalytics.eu>
Diff between gslnls versions 1.4.1 dated 2025-01-17 and 1.4.2 dated 2025-09-28
DESCRIPTION | 10 MD5 | 14 NEWS.md | 8 R/nls.R | 4 R/nls_methods.R | 669 ++++++++++++++++++------------------ configure | 18 configure.ac | 2 inst/unit_tests/unit_tests_gslnls.R | 195 +++++----- 8 files changed, 489 insertions(+), 431 deletions(-)
Title: Camera Trap Data Management and Analysis Framework
Description: Management and analysis of camera trap wildlife data through an integrated workflow. Provides functions for image/video organization and metadata extraction, species/individual identification. Creates detection histories for occupancy and spatial capture-recapture analyses, with support for multi-season studies. Includes tools for fitting community occupancy models in JAGS and NIMBLE, and an interactive dashboard for survey data visualization and analysis. Features visualization of species distributions and activity patterns, plus export capabilities for GIS and reports. Emphasizes automation and reproducibility while maintaining flexibility for different study designs.
Author: Juergen Niedballa [aut, cre] ,
Alexandre Courtiol [aut] ,
Rahel Sollmann [aut] ,
John Mathai [ctb],
Seth Timothy Wong [ctb] ,
An The Truong Nguyen [ctb] ,
Azlan bin Mohamed [ctb] ,
Andrew Tilker [ctb] ,
Roshan Guharajan [ctb] ,
Ioannis Alexiou [ctb] [...truncated...]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 2.3.1 dated 2025-09-02 and 3.0.0 dated 2025-09-28
DESCRIPTION | 31 MD5 | 75 NAMESPACE | 141 NEWS.md | 156 R/PPC.residuals.R |only R/aggregateStations.R |only R/cameraOperation.R | 30 R/camtrapR-package.R | 4 R/communityModel.R | 326 R/createCovariates.R |only R/detectionHistory.R | 256 R/detectionMaps.R | 2 R/imageRename.R | 151 R/plot.R | 71 R/predict.R | 738 +- R/readWildlifeInsights.R |only R/readcamtrapDP.R |only R/recordTable.R | 15 R/recordTableIndividual.R | 16 R/speciesAccum.R |only R/surveyDashboard.R |11743 ++++++++++++++++++++++++++++++--- R/variousOtherHelperFunctions.R | 80 R/zzz.R |only README.md | 12 inst/dashboard_help |only inst/doc/camtrapr5.html | 3468 ++++++--- man/PPC.community.Rd |only man/PPC.residuals.Rd |only man/aggregateStations.Rd |only man/camtrapR-package.Rd | 3 man/communityModel.Rd | 24 man/createCovariates.Rd |only man/detectionHistory.Rd | 180 man/imageRename.Rd | 28 man/plot_coef-commOccu-method.Rd | 3 man/plot_effects-commOccu-method.Rd | 3 man/predict-commOccu-method.Rd | 10 man/readWildlifeInsights.Rd |only man/readcamtrapDP.Rd |only man/speciesAccum.Rd |only man/surveyDashboard.Rd | 123 tests/testthat/test_cameraOperation.R | 23 tests/testthat/test_detectionHistory.R | 15 43 files changed, 14859 insertions(+), 2868 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-26 1.0.5
2013-12-11 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-08-16 0.3.11
2021-12-08 0.3.10
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-02-21 1.1.1
2020-09-30 1.1.0
2020-05-06 1.0.1
2019-10-11 1.0.0
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Christophe Dervieux [aut] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dun [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.29 dated 2024-11-04 and 2.30 dated 2025-09-28
DESCRIPTION | 28 - MD5 | 47 +- NEWS.md | 14 R/html_document.R | 592 ++++++++++++++++++--------------- R/html_document_base.R | 22 - R/jupyter.R | 4 R/pandoc.R | 23 - R/render.R | 3 R/slidy_presentation.R | 2 R/util.R | 4 build/vignette.rds |binary inst/doc/lua-filters.html | 5 inst/doc/rmarkdown.R | 22 - inst/doc/rmarkdown.Rmd | 2 inst/doc/rmarkdown.html | 4 man/html_document.Rd | 86 ++-- man/html_document_base.Rd | 4 man/html_fragment.Rd | 4 man/html_notebook.Rd | 5 man/html_vignette.Rd | 10 man/ioslides_presentation.Rd | 4 man/slidy_presentation.Rd | 4 tests/testthat/resources/template.html |only tests/testthat/test-pandoc.R | 2 vignettes/rmarkdown.Rmd | 2 25 files changed, 476 insertions(+), 417 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.23 dated 2025-08-18 and 1.1.24 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS | 7 +++++-- R/lang.aff.R | 9 ++++++++- inst/doc/lingtypology_creating_maps.html | 9 +++++---- inst/doc/lingtypology_db_API.html | 9 +++++---- inst/doc/lingtypology_dplyr.html | 11 ++++++----- inst/doc/lingtypology_glottolog_functions.Rmd | 4 ++-- inst/doc/lingtypology_glottolog_functions.html | 11 ++++++----- inst/doc/lingtypology_intro.html | 9 +++++---- tests/testthat/test-lang-aff.R | 4 ++-- vignettes/lingtypology_glottolog_functions.Rmd | 4 ++-- 12 files changed, 62 insertions(+), 47 deletions(-)
Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
the Hierarchical Mutual Information (Perotti et al. 2015)
<doi:10.1103/PhysRevE.92.062825>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for identifying islands o [...truncated...]
Author: Martin R. Smith [aut, cre, cph, prg] ,
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.10.1 dated 2025-08-25 and 2.11.0 dated 2025-09-28
DESCRIPTION | 10 MD5 | 104 NAMESPACE | 25 NEWS.md | 12 R/HPart.R |only R/RcppExports.R | 32 R/VisualizeMatching.R | 10 R/hierarchical_mutual_information.R |only R/spectral_clustering.R | 2 R/tree_distance.R | 15 R/zzz.R | 56 build/partial.rdb |binary build/vignette.rds |binary inst/REFERENCES.bib | 22 inst/WORDLIST | 31 inst/doc/Generalized-RF.html | 5 inst/doc/Robinson-Foulds.html | 5 inst/doc/Using-TreeDist.html | 13 inst/doc/compare-treesets.html | 5 inst/doc/different-leaves.html | 5 inst/doc/information.html | 5 inst/doc/landscapes.html | 1954 ---------- inst/doc/treespace.html | 7 inst/doc/using-distances.html | 162 man/GeneralizedRF.Rd | 7 man/HH.Rd |only man/HPart.Rd |only man/HierarchicalMutualInfo.Rd |only man/HierarchicalMutualInformation.Rd |only man/JaccardRobinsonFoulds.Rd | 1 man/KendallColijn.Rd | 1 man/MASTSize.Rd | 161 man/MatchingSplitDistance.Rd | 1 man/NNIDist.Rd | 239 - man/NyeSimilarity.Rd | 1 man/PathDist.Rd | 1 man/Robinson-Foulds.Rd | 1 man/SPRDist.Rd | 1 man/TreeDistance.Rd | 1 man/VisualizeMatching.Rd | 3 man/clone.Rd |only src/RcppExports.cpp | 109 src/day_1985.cpp | 3 src/hmi.cpp |only src/hpart.cpp |only src/hpart.h |only src/hpart_relabel.cpp |only src/ints.h | 8 src/li_diameters.h |only src/nni_distance.cpp | 531 +- src/tree_distances.cpp | 58 src/tree_distances.h | 6 tests/testthat/_snaps/HPart |only tests/testthat/_snaps/VisualizeMatching/visualize-mci-matching.svg | 20 tests/testthat/test-HPart.R |only tests/testthat/test-hierarchical_mutual_information.R |only tests/testthat/test-hmi.cpp.R |only tests/testthat/test-information.R | 8 tests/testthat/test-spectral_clustering.R | 3 tests/testthat/test-tree_distance.R | 53 tests/testthat/test-tree_distance_nni.R | 73 61 files changed, 1081 insertions(+), 2689 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 3000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 3.4-0 dated 2025-07-25 and 3.4-1 dated 2025-09-28
DESCRIPTION | 18 ++--- MD5 | 38 ++++++----- NEWS | 7 ++ build/vignette.rds |binary inst/doc/NAobjects.R |only inst/doc/NAobjects.Rnw |only inst/doc/NAobjects.pdf |only inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 148 ++++++++++++++++++++++----------------------- inst/doc/datasets.Rnw | 32 ++++----- inst/doc/datasets.pdf |binary inst/doc/fv.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 106 ++++++++++++++++++++++++++++---- inst/doc/updates.pdf |binary inst/info/packagesizes.txt | 2 vignettes/NAobjects.Rnw |only vignettes/datasets.Rnw | 32 ++++----- vignettes/updates.Rnw | 106 ++++++++++++++++++++++++++++---- 22 files changed, 335 insertions(+), 156 deletions(-)
Title: Regularized Principal Component Analysis for Spatial Data
Description: Provide regularized principal component analysis incorporating smoothness, sparseness and orthogonality of eigen-functions
by using the alternating direction method of multipliers algorithm (Wang and Huang, 2017, <DOI:10.1080/10618600.2016.1157483>). The
method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D.
Author: Wen-Ting Wang [aut, cre] ,
Hsin-Cheng Huang [aut]
Maintainer: Wen-Ting Wang <egpivo@gmail.com>
Diff between SpatPCA versions 1.3.5 dated 2023-11-13 and 1.3.8 dated 2025-09-28
DESCRIPTION | 26 +-- MD5 | 59 ++++---- NAMESPACE | 3 NEWS.md | 13 + R/SpatPCA.R | 86 ++++++----- R/helper.R | 21 +- R/zzz.R | 4 README.md | 102 ++++++++++--- build/vignette.rds |binary inst/doc/demo-one-dim-location.R | 78 ++++++---- inst/doc/demo-one-dim-location.Rmd | 80 ++++++---- inst/doc/demo-one-dim-location.html | 82 ++++++----- inst/doc/demo-two-dim-location.R | 78 +++++----- inst/doc/demo-two-dim-location.Rmd | 81 ++++++----- inst/doc/demo-two-dim-location.html | 145 +++++++++---------- man/plot.spatpca.Rd | 2 man/predict.Rd | 2 man/predictEigenfunction.Rd | 2 man/setCores.Rd | 8 - man/spatpca.Rd | 80 +++++----- src/Makevars | 3 src/Makevars.win | 5 src/RcppExports.cpp | 36 ++-- src/RcppSpatPCA.cpp | 263 ++++++++++++++++++------------------ tests/testthat.R | 1 tests/testthat/test-SpatPCA.R | 8 - tests/testthat/test-helper.R | 12 - tests/testthat/test-zzz.R | 54 +------ tools |only vignettes/demo-one-dim-location.Rmd | 80 ++++++---- vignettes/demo-two-dim-location.Rmd | 81 ++++++----- 31 files changed, 804 insertions(+), 691 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 1.0.1 dated 2025-07-04 and 1.0.2 dated 2025-09-28
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ inst/doc/litteR-installation.html | 10 +++++----- inst/doc/litteR-manual.html | 36 ++++++++++++++++++------------------ tests/testthat/test-stats.R | 18 +++++++++--------- 6 files changed, 49 insertions(+), 42 deletions(-)
Title: Inference for High-Dimensional Mixture Transition Distribution
Models
Description: Estimates parameters in Mixture Transition Distribution (MTD) models, a class of high-order Markov chains. The set of relevant pasts (lags) is selected using either the Bayesian Information Criterion or the Forward Stepwise and Cut algorithms. Other model parameters (e.g. transition probabilities and oscillations) can be estimated via maximum likelihood estimation or the Expectation-Maximization algorithm. Additionally, 'hdMTD' includes a perfect sampling algorithm that generates samples of an MTD model from its invariant distribution. For theory, see Ost & Takahashi (2023) <http://jmlr.org/papers/v24/22-0266.html>.
Author: Maiara Gripp [aut, cre],
Guilherme Ost [ths],
Giulio Iacobelli [ths]
Maintainer: Maiara Gripp <maiara@dme.ufrj.br>
Diff between hdMTD versions 0.1.1 dated 2025-08-27 and 0.1.2 dated 2025-09-28
hdMTD-0.1.1/hdMTD/R/raindata.R |only hdMTD-0.1.1/hdMTD/R/sleepscoring.R |only hdMTD-0.1.1/hdMTD/R/testChains.R |only hdMTD-0.1.1/hdMTD/build |only hdMTD-0.1.1/hdMTD/data/raindata.rda |only hdMTD-0.1.1/hdMTD/data/sleepscoring.rda |only hdMTD-0.1.1/hdMTD/data/testChains.rda |only hdMTD-0.1.1/hdMTD/man/checkSample.Rd |only hdMTD-0.1.1/hdMTD/man/raindata.Rd |only hdMTD-0.1.1/hdMTD/man/sleepscoring.Rd |only hdMTD-0.1.1/hdMTD/man/testChains.Rd |only hdMTD-0.1.2/hdMTD/DESCRIPTION | 6 hdMTD-0.1.2/hdMTD/MD5 | 97 ++--- hdMTD-0.1.2/hdMTD/NAMESPACE | 41 ++ hdMTD-0.1.2/hdMTD/NEWS.md | 31 + hdMTD-0.1.2/hdMTD/R/MTDest-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDest.R | 392 ++++++++++++---------- hdMTD-0.1.2/hdMTD/R/MTDmodel-methods.R |only hdMTD-0.1.2/hdMTD/R/MTDmodel.R | 32 + hdMTD-0.1.2/hdMTD/R/accessors.R |only hdMTD-0.1.2/hdMTD/R/as-MTD.R |only hdMTD-0.1.2/hdMTD/R/checkSample.R | 4 hdMTD-0.1.2/hdMTD/R/countsTab.R | 9 hdMTD-0.1.2/hdMTD/R/dTV_sample.R | 53 ++ hdMTD-0.1.2/hdMTD/R/empirical_probs.R |only hdMTD-0.1.2/hdMTD/R/freqTab.R | 26 + hdMTD-0.1.2/hdMTD/R/hdMTD-methods.R |only hdMTD-0.1.2/hdMTD/R/hdMTD.R | 175 ++++++++- hdMTD-0.1.2/hdMTD/R/hdMTD_BIC.R | 68 +++ hdMTD-0.1.2/hdMTD/R/hdMTD_CUT.R | 23 - hdMTD-0.1.2/hdMTD/R/hdMTD_FS.R | 21 - hdMTD-0.1.2/hdMTD/R/hdMTD_FSC.R | 11 hdMTD-0.1.2/hdMTD/R/oscillation.R | 78 ++-- hdMTD-0.1.2/hdMTD/R/probs.R | 290 ++++++++++++---- hdMTD-0.1.2/hdMTD/R/utils.R | 50 +- hdMTD-0.1.2/hdMTD/R/validation.R | 75 ++-- hdMTD-0.1.2/hdMTD/man/MTD-accessors.Rd |only hdMTD-0.1.2/hdMTD/man/MTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest-methods.Rd |only hdMTD-0.1.2/hdMTD/man/MTDest.Rd | 105 +++-- hdMTD-0.1.2/hdMTD/man/MTDmodel.Rd | 11 hdMTD-0.1.2/hdMTD/man/as.MTD.Rd |only hdMTD-0.1.2/hdMTD/man/countsTab.Rd | 9 hdMTD-0.1.2/hdMTD/man/dTV_sample.Rd | 55 ++- hdMTD-0.1.2/hdMTD/man/empirical_probs.Rd |only hdMTD-0.1.2/hdMTD/man/freqTab.Rd | 18 - hdMTD-0.1.2/hdMTD/man/hdMTD-methods.Rd |only hdMTD-0.1.2/hdMTD/man/hdMTD.Rd | 50 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_BIC.Rd | 44 ++ hdMTD-0.1.2/hdMTD/man/hdMTD_CUT.Rd | 19 - hdMTD-0.1.2/hdMTD/man/hdMTD_FS.Rd | 17 hdMTD-0.1.2/hdMTD/man/hdMTD_FSC.Rd | 11 hdMTD-0.1.2/hdMTD/man/oscillation.Rd | 64 ++- hdMTD-0.1.2/hdMTD/man/probs.Rd | 95 +++-- hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDest.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-MTDmodel.R | 17 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD.R | 46 +- hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_BIC.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_CUT.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-hdMTD_FS.R | 4 hdMTD-0.1.2/hdMTD/tests/testthat/test-probs.R | 4 61 files changed, 1397 insertions(+), 679 deletions(-)
Title: Changepoint Detection via Modified Genetic Algorithm
Description: The Genetic Algorithm (GA) is used to perform changepoint analysis in time series data. The package also includes an extended island version of GA, as described in Lu, Lund, and Lee (2010, <doi:10.1214/09-AOAS289>). By mimicking the principles of natural selection and evolution, GA provides a powerful stochastic search technique for solving combinatorial optimization problems. In 'changepointGA', each chromosome represents a changepoint configuration, including the number and locations of changepoints, hyperparameters, and model parameters. The package employs genetic operators—selection, crossover, and mutation—to iteratively improve solutions based on the given fitness (objective) function. Key features of 'changepointGA' include encoding changepoint configurations in an integer format, enabling dynamic and simultaneous estimation of model hyperparameters, changepoint configurations, and associated parameters. The detailed algorithmic implementation can be found in the package [...truncated...]
Author: Mo Li [aut, cre],
QiQi Lu [aut]
Maintainer: Mo Li <mo.li@louisiana.edu>
Diff between changepointGA versions 0.1.1 dated 2025-05-22 and 0.1.3 dated 2025-09-28
changepointGA-0.1.1/changepointGA/R/GA.R |only changepointGA-0.1.1/changepointGA/R/IslandGA.R |only changepointGA-0.1.1/changepointGA/R/datasimulation.R |only changepointGA-0.1.1/changepointGA/R/defaultsetting.R |only changepointGA-0.1.1/changepointGA/man/GA.Rd |only changepointGA-0.1.1/changepointGA/man/GA_param.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA.Rd |only changepointGA-0.1.1/changepointGA/man/IslandGA_param.Rd |only changepointGA-0.1.1/changepointGA/man/TsPlotCheck.Rd |only changepointGA-0.1.1/changepointGA/man/operators.Rd |only changepointGA-0.1.3/changepointGA/DESCRIPTION | 11 changepointGA-0.1.3/changepointGA/MD5 | 84 changepointGA-0.1.3/changepointGA/NAMESPACE | 18 changepointGA-0.1.3/changepointGA/R/AMOCfunc.R | 57 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.Order.R | 82 changepointGA-0.1.3/changepointGA/R/ARIMA.BIC.R | 73 changepointGA-0.1.3/changepointGA/R/GAfunc.R | 164 changepointGA-0.1.3/changepointGA/R/RcppExports.R | 56 changepointGA-0.1.3/changepointGA/R/cptDist.R | 60 changepointGA-0.1.3/changepointGA/R/cptga-class.R |only changepointGA-0.1.3/changepointGA/R/cptga.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl-class.R |only changepointGA-0.1.3/changepointGA/R/cptgaisl.R |only changepointGA-0.1.3/changepointGA/R/ts.sim.R |only changepointGA-0.1.3/changepointGA/R/utils.R |only changepointGA-0.1.3/changepointGA/README.md | 209 changepointGA-0.1.3/changepointGA/build/vignette.rds |binary changepointGA-0.1.3/changepointGA/inst/doc/vignette.R | 223 changepointGA-0.1.3/changepointGA/inst/doc/vignette.Rmd | 271 changepointGA-0.1.3/changepointGA/inst/doc/vignette.html | 6808 +++++++++- changepointGA-0.1.3/changepointGA/man/AMOCcrossover.Rd | 4 changepointGA-0.1.3/changepointGA/man/AMOCmutation.Rd | 8 changepointGA-0.1.3/changepointGA/man/AMOCpopulation.Rd | 12 changepointGA-0.1.3/changepointGA/man/AMOCselection.Rd | 2 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Order.Rd | 23 changepointGA-0.1.3/changepointGA/man/ARIMA.BIC.Rd | 30 changepointGA-0.1.3/changepointGA/man/changepointGA-package.Rd |only changepointGA-0.1.3/changepointGA/man/cptDist.Rd | 14 changepointGA-0.1.3/changepointGA/man/cptga-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptga.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl-class.Rd |only changepointGA-0.1.3/changepointGA/man/cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/mutation.Rd | 18 changepointGA-0.1.3/changepointGA/man/plot.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/plot.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptga.Rd |only changepointGA-0.1.3/changepointGA/man/print.summary.cptgaisl.Rd |only changepointGA-0.1.3/changepointGA/man/random_population.Rd | 36 changepointGA-0.1.3/changepointGA/man/selectTau.Rd | 4 changepointGA-0.1.3/changepointGA/man/selection_linearrank.Rd | 2 changepointGA-0.1.3/changepointGA/man/ts.sim.Rd | 118 changepointGA-0.1.3/changepointGA/src/ARIMA_BIC.cpp |only changepointGA-0.1.3/changepointGA/src/Makevars |only changepointGA-0.1.3/changepointGA/src/Makevars.win |only changepointGA-0.1.3/changepointGA/src/PopInitia.cpp | 60 changepointGA-0.1.3/changepointGA/src/RcppExports.cpp | 32 changepointGA-0.1.3/changepointGA/vignettes/vignette.Rmd | 271 57 files changed, 7544 insertions(+), 1206 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.9 dated 2025-06-07 and 1.4.10 dated 2025-09-28
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md |only R/grid.hexagontile.R | 2 +- R/hexDensity.R | 4 ++-- R/hexbinFull.R | 3 ++- R/plotHexDensity.R | 25 +++++++++++++++++++------ R/xy2hcell.R | 2 +- man/hexbinFull.Rd | 2 +- src/hbin.f | 4 ++-- src/hbin_frac.f | 6 ++++-- 11 files changed, 45 insertions(+), 28 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 3.4-0 dated 2025-07-23 and 3.4-2 dated 2025-09-28
DESCRIPTION | 14 - MD5 | 52 ++--- NEWS | 45 ++++ R/intensity.ppm.R | 383 +++++++++++++++++++++++++---------------- R/kppm.R | 9 R/mppm.R | 50 +++-- R/ppm.R | 4 R/predictmppm.R | 105 ++++++----- R/rmh.ppm.R | 9 R/rmhmodel.ppm.R | 60 +++++- R/simulatekppm.R | 10 - R/slrm.R | 5 R/subfits.R | 28 ++ R/sysdata.rda |binary inst/doc/packagesizes.txt | 2 inst/info/packagesizes.txt | 2 man/intensity.ppm.Rd | 17 + man/rmh.ppm.Rd | 28 ++ man/rmhmodel.ppm.Rd | 21 ++ man/simulate.kppm.Rd | 20 +- man/simulate.ppm.Rd | 28 ++ man/spatstat.model-internal.Rd | 14 - tests/testsD.R | 9 tests/testsK.R | 16 + tests/testsM.R | 10 - tests/testsP2.R | 14 + tests/testsR2.R | 20 +- 27 files changed, 684 insertions(+), 291 deletions(-)
More information about spatstat.model at CRAN
Permanent link
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 0.6-1 dated 2024-11-16 and 0.6-2 dated 2025-09-28
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ NEWS.md | 4 +++ R/hgwr.R | 59 ++++++++++++++++++++++------------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/hgwrr.html | 7 +++--- src/hetero_test.cpp | 6 ++++- 8 files changed, 50 insertions(+), 48 deletions(-)