Title: Fast Searching for Multiple Keywords in Multiple Texts
Description: Aho-Corasick is an optimal algorithm for finding many
keywords in a text. It can locate all matches in a text in O(N+M) time; i.e.,
the time needed scales linearly with the number of keywords (N) and the size of
the text (M). Compare this to the naive approach which takes O(N*M) time to loop
through each pattern and scan for it in the text. This implementation builds the
trie (the generic name of the data structure) and runs the search in a single
function call. If you want to search multiple texts with the same trie, the
function will take a list or vector of texts and return a list of matches to
each text. By default, all 128 ASCII characters are allowed in both the keywords
and the text. A more efficient trie is possible if the alphabet size can be
reduced. For example, DNA sequences use at most 19 distinct characters and
usually only 4; protein sequences use at most 26 distinct characters and usually
only 20. UTF-8 (Unicode) matching is not currently supported.
Author: Matt Chambers [aut, cre],
Tomas Petricek [aut, cph],
Vanderbilt University [cph]
Maintainer: Matt Chambers <matt.chambers42@gmail.com>
Diff between AhoCorasickTrie versions 0.1.2 dated 2020-09-29 and 0.1.3 dated 2025-02-04
DESCRIPTION | 12 +++----- MD5 | 20 +++++++------- R/AhoCorasickTrie.R | 2 - R/RcppExports.R | 4 +- man/AhoCorasickSearch.Rd | 2 - man/AhoCorasickSearchList.Rd | 2 - man/AhoCorasickTrie.Rd | 23 ++++++++++++++++ src/AhoCorasickTrie.cpp | 60 +++++++++++++++++++++---------------------- src/RcppExports.cpp | 5 +++ tests/AhoCorasickTrieTests.R | 16 +++++------ tests/benchmark.R | 16 +++++------ 11 files changed, 94 insertions(+), 68 deletions(-)
More information about AhoCorasickTrie at CRAN
Permanent link
Title: Simulating Realistic Gene Expression and Clinical Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with links to associated outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>. Version 2.0 adds the
ability to simulate realistic mixed-typed clinical data.
Author: Kevin R. Coombes [aut, cre],
Jiexin Zhang [aut],
Caitlin E. Coombes [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 2.0.10 dated 2020-11-10 and 2.0.11 dated 2025-02-04
Umpire-2.0.10/Umpire/tests/t02-indLogNorm.R |only Umpire-2.0.10/Umpire/tests/t02-indLogNorm.Rout.save |only Umpire-2.0.11/Umpire/DESCRIPTION | 18 Umpire-2.0.11/Umpire/MD5 | 16 Umpire-2.0.11/Umpire/build/vignette.rds |binary Umpire-2.0.11/Umpire/inst/doc/Umpire.pdf |binary Umpire-2.0.11/Umpire/inst/doc/Umpire2.R | 2 Umpire-2.0.11/Umpire/inst/doc/Umpire2.html | 441 +++++++++--------- Umpire-2.0.11/Umpire/inst/doc/surv.html | 470 +++++++++----------- Umpire-2.0.11/Umpire/man/e31-setDataTypes.Rd | 2 10 files changed, 471 insertions(+), 478 deletions(-)
Title: Estimates and Plots Single-Level and Multilevel Latent Class
Models
Description: Efficiently estimates single- and multilevel latent class models with covariates, allowing for output visualization in all specifications. For more technical details, see Lyrvall et al (2023) <doi:10.48550/arXiv.2305.07276>.
Author: Roberto Di Mari [aut, cre],
Johan Lyrvall [aut],
Zsuzsa Bakk [ctb],
Jennifer Oser [ctb],
Jouni Kuha [ctb]
Maintainer: Roberto Di Mari <roberto.dimari@unict.it>
Diff between multilevLCA versions 1.5.2 dated 2024-10-12 and 2.0.0 dated 2025-02-04
DESCRIPTION | 10 MD5 | 24 NAMESPACE | 7 R/MLCAfunctions.R | 7078 ++++++++++++++++++++++++++------------------------ R/RcppExports.R | 44 build/partial.rdb |binary data/dataIEA.rda |binary data/dataTOY.rda |binary man/multiLCA.Rd | 47 src/LCAfit.cpp | 845 +++-- src/Makevars | 1 src/RcppExports.cpp | 233 + src/multilevLC_EM.cpp | 3450 +++++++++++++++++++++++- 13 files changed, 7985 insertions(+), 3754 deletions(-)
Title: Meta-Analysis Datasets
Description: A collection of meta-analysis datasets for teaching purposes, illustrating/testing meta-analytic methods, and validating published analyses.
Author: Wolfgang Viechtbauer [aut, cre]
,
Thomas White [aut] ,
Daniel Noble [aut] ,
Alistair Senior [aut] ,
W. Kyle Hamilton [aut] ,
Guido Schwarzer [dtc]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metadat versions 1.2-0 dated 2022-04-06 and 1.4-0 dated 2025-02-04
DESCRIPTION | 28 ++-- MD5 | 216 +++++++++++++++++-------------- NEWS.md | 6 R/datsearch.r | 10 + README.md | 2 build/metadat.pdf |binary build/stage23.rdb |only data/dat.assink2016.rda |binary data/dat.bartos2023.rda |only data/dat.bassler2004.rda |only data/dat.crisafulli2020.rda |only data/dat.curtin2002.rda |only data/dat.dumouchel1994.rda |only data/dat.furukawa2003.rda |only data/dat.kalaian1996.rda |binary data/dat.roever2022.rda |only data/dat.spooner2002.rda |only data/dat.ursino2021.rda |only inst/help.rdata |binary man/dat.aloe2013.Rd | 2 man/dat.anand1999.Rd | 5 man/dat.assink2016.Rd | 19 ++ man/dat.axfors2021.Rd | 5 man/dat.bakdash2021.Rd | 7 - man/dat.baker2009.Rd | 16 -- man/dat.bangertdrowns2004.Rd | 5 man/dat.bartos2023.Rd |only man/dat.baskerville2012.Rd | 5 man/dat.bassler2004.Rd |only man/dat.bcg.Rd | 9 - man/dat.begg1989.Rd | 5 man/dat.berkey1998.Rd | 9 - man/dat.besson2016.Rd | 2 man/dat.bonett2010.Rd | 8 - man/dat.bornmann2007.Rd | 5 man/dat.bourassa1996.Rd | 33 ++++ man/dat.cannon2006.Rd | 9 - man/dat.cohen1981.Rd | 7 - man/dat.colditz1994.Rd | 9 - man/dat.collins1985a.Rd | 5 man/dat.collins1985b.Rd | 5 man/dat.craft2003.Rd | 7 - man/dat.crede2010.Rd | 5 man/dat.crisafulli2020.Rd |only man/dat.curtin2002.Rd |only man/dat.curtis1998.Rd | 7 - man/dat.dagostino1998.Rd | 7 - man/dat.damico2009.Rd | 5 man/dat.debruin2009.Rd | 5 man/dat.dogliotti2014.Rd | 14 -- man/dat.dong2013.Rd | 14 -- man/dat.dorn2007.Rd | 9 - man/dat.dumouchel1994.Rd |only man/dat.egger2001.Rd | 5 man/dat.fine1993.Rd | 23 +-- man/dat.franchini2012.Rd | 11 - man/dat.frank2008.Rd | 9 - man/dat.furukawa2003.Rd |only man/dat.gibson2002.Rd | 5 man/dat.graves2010.Rd | 5 man/dat.gurusamy2011.Rd | 14 -- man/dat.hackshaw1998.Rd | 15 +- man/dat.hahn2001.Rd | 7 - man/dat.hannum2020.Rd | 5 man/dat.hart1999.Rd | 11 - man/dat.hartmannboyce2018.Rd | 5 man/dat.hasselblad1998.Rd | 15 -- man/dat.hine1989.Rd | 5 man/dat.ishak2007.Rd | 7 - man/dat.kalaian1996.Rd | 17 +- man/dat.kearon1998.Rd | 16 +- man/dat.knapp2017.Rd | 7 - man/dat.konstantopoulos2011.Rd | 21 +-- man/dat.landenberger2005.Rd | 5 man/dat.laopaiboon2015.Rd | 5 man/dat.lau1992.Rd | 17 +- man/dat.lee2004.Rd | 5 man/dat.lehmann2018.Rd | 14 -- man/dat.li2007.Rd | 5 man/dat.lim2014.Rd | 5 man/dat.linde2005.Rd | 7 - man/dat.linde2015.Rd | 16 +- man/dat.linde2016.Rd | 16 +- man/dat.lopez2019.Rd | 14 +- man/dat.maire2019.Rd | 7 - man/dat.mccurdy2020.Rd | 13 - man/dat.mcdaniel1994.Rd | 21 ++- man/dat.michael2013.Rd | 2 man/dat.molloy2014.Rd | 7 - man/dat.moura2021.Rd | 5 man/dat.nakagawa2007.Rd | 4 man/dat.nielweise2007.Rd | 5 man/dat.nielweise2008.Rd | 5 man/dat.normand1999.Rd | 5 man/dat.obrien2003.Rd | 9 - man/dat.pagliaro1992.Rd | 7 - man/dat.pignon2000.Rd | 5 man/dat.pritz1997.Rd | 28 +++- man/dat.raudenbush1985.Rd | 5 man/dat.riley2003.Rd | 5 man/dat.roever2022.Rd |only man/dat.senn2013.Rd | 21 +-- man/dat.spooner2002.Rd |only man/dat.stowe2010.Rd | 14 -- man/dat.tannersmith2016.Rd | 5 man/dat.ursino2021.Rd |only man/dat.vanhowe1999.Rd | 5 man/dat.viechtbauer2021.Rd | 22 +-- man/dat.white2020.Rd | 2 man/dat.woods2010.Rd | 11 - man/dat.yusuf1985.Rd | 5 man/datsearch.Rd | 4 tests/testthat/test_dat.assink2016.r | 2 tests/testthat/test_dat.bartos2023.r |only tests/testthat/test_dat.bassler2004.r |only tests/testthat/test_dat.crisafulli2020.r |only tests/testthat/test_dat.curtin2002.r |only tests/testthat/test_dat.dumouchel1994.r |only tests/testthat/test_dat.furukawa2003.r |only tests/testthat/test_dat.kalaian1996.r | 2 tests/testthat/test_dat.roever2022.r |only tests/testthat/test_dat.spooner2002.r |only tests/testthat/test_dat.ursino2021.r |only 123 files changed, 530 insertions(+), 513 deletions(-)
Title: Individual Dose Optimization using Population Pharmacokinetics
Description: Personalize drug regimens using individual pharmacokinetic (PK) and
pharmacokinetic-pharmacodynamic (PK-PD) profiles. By combining therapeutic
drug monitoring (TDM) data with a population model, 'posologyr' offers
accurate posterior estimates and helps compute optimal individualized dosing
regimens. The empirical Bayes estimates are computed following the method
described by Kang et al. (2012) <doi:10.4196/kjpp.2012.16.2.97>.
Author: Cyril Leven [aut, cre, cph] ,
Matthew Fidler [ctb] ,
Emmanuelle Comets [ctb],
Audrey Lavenu [ctb],
Marc Lavielle [ctb]
Maintainer: Cyril Leven <cyril.leven@chu-brest.fr>
Diff between posologyr versions 1.2.7 dated 2024-09-13 and 1.2.8 dated 2025-02-04
DESCRIPTION | 19 +++++++++---------- MD5 | 6 +++--- NEWS.md | 5 ++++- tests/testthat/test_doseoptim_tdm.R | 2 +- 4 files changed, 17 insertions(+), 15 deletions(-)
Title: High-Level Plotting Built Upon 'ggplot2' and Other Plotting
Packages
Description: Provides high-level API and a wide range of options to create stunning, publication-quality plots effortlessly.
It is built upon 'ggplot2' and other plotting packages, and is designed to be easy to use and to work seamlessly with 'ggplot2' objects.
It is particularly useful for creating complex plots with multiple layers, facets, and annotations.
It also provides a set of functions to create plots for specific types of data, such as Venn diagrams, alluvial diagrams, and phylogenetic trees.
The package is designed to be flexible and customizable, and to work well with the 'ggplot2' ecosystem.
The API can be found at <https://pwwang.github.io/plotthis/reference/index.html>.
Author: Panwen Wang [aut, cre]
Maintainer: Panwen Wang <pwwang@pwwang.com>
Diff between plotthis versions 0.5.0 dated 2025-01-09 and 0.5.1 dated 2025-02-04
DESCRIPTION | 6 - MD5 | 20 ++-- NAMESPACE | 2 R/heatmap.R | 16 +-- R/sankeyplot.R | 218 +++++++++++++++++++++++++++++++++++------------ R/volcanoplot.R | 29 ++++-- README.md | 32 +++--- man/SankeyPlotAtomic.Rd | 24 ++--- man/VolcanoPlot.Rd | 9 + man/VolcanoPlotAtomic.Rd | 9 + man/sankeyplot.Rd | 78 +++++++++------- 11 files changed, 297 insertions(+), 146 deletions(-)
Title: Robust and Flexible Model-Based Clustering for Data Sets with
Missing Values at Random
Description: Implementations of various robust and flexible model-based clustering methods for data sets with missing values at random.
Two main models are: Multivariate Contaminated Normal Mixture (MCNM, Tong and Tortora, 2022, <doi:10.1007/s11634-021-00476-1>) and
Multivariate Generalized Hyperbolic Mixture (MGHM, Wei et al., 2019, <doi:10.1016/j.csda.2018.08.016>). Mixtures via some special or limiting
cases of the multivariate generalized hyperbolic distribution are also included: Normal-Inverse Gaussian, Symmetric Normal-Inverse Gaussian,
Skew-Cauchy, Cauchy, Skew-t, Student's t, Normal, Symmetric Generalized Hyperbolic, Hyperbolic Univariate Marginals,
Hyperbolic, and Symmetric Hyperbolic.
Author: Hung Tong [aut, cre],
Cristina Tortora [aut, ths, dgs]
Maintainer: Hung Tong <hungtongmx@gmail.com>
Diff between MixtureMissing versions 3.0.3 dated 2024-10-15 and 3.0.4 dated 2025-02-04
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/dist_Norm.R | 32 -------------------------------- R/dist_Skew_t.R | 32 -------------------------------- 4 files changed, 6 insertions(+), 70 deletions(-)
More information about MixtureMissing at CRAN
Permanent link
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.4.0 dated 2025-02-04 and 1.4.1 dated 2025-02-04
DESCRIPTION | 6 ++--- MD5 | 14 ++++++------- NEWS.md | 5 ++++ R/codebook.R | 2 - inst/CITATION | 6 ++--- inst/doc/intro_to_gmoTree.html | 18 ++++++++--------- inst/pkgdown.yml | 2 - tests/testthat/tests_codebook.R | 41 +++++++++++++++++++++++++++++----------- 8 files changed, 59 insertions(+), 35 deletions(-)
Title: Constrained, Covariance-Matching Constrained and Universal Point
or Block Kriging
Description: Provides functions for efficient computation of non-linear spatial predictions with local change of support (Hofer, C. and Papritz, A. (2011) "constrainedKriging: An R-package for customary, constrained and covariance-matching constrained point or block kriging" <doi:10.1016/j.cageo.2011.02.009>). This package supplies functions for two-dimensional spatial interpolation by constrained (Cressie, N. (1993) "Aggregation in geostatistical problems" <doi:10.1007/978-94-011-1739-5_3>), covariance-matching constrained (Aldworth, J. and Cressie, N. (2003) "Prediction of nonlinear spatial functionals" <doi:10.1016/S0378-3758(02)00321-X>) and universal (external drift) Kriging for points or blocks of any shape from data with a non-stationary mean function and an isotropic weakly stationary covariance function. The linear spatial interpolation methods, constrained and covariance-matching constrained Kriging, provide approximately unbiased prediction for non-linear target value [...truncated...]
Author: Christoph Hofer [aut],
Andreas Papritz [ctb, cre]
Maintainer: Andreas Papritz <papritz@retired.ethz.ch>
Diff between constrainedKriging versions 0.2-10 dated 2025-02-01 and 0.2-11 dated 2025-02-04
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/ChangeLog.txt | 6 +++++- src/point_block_cov.c | 13 +++++++------ 4 files changed, 19 insertions(+), 14 deletions(-)
More information about constrainedKriging at CRAN
Permanent link
Title: Collection of Methods Constructed using Kernel-Based Quadratic
Distances
Description: It includes test for multivariate normality, test for uniformity on the d-dimensional
Sphere, non-parametric two- and k-sample tests, random generation of points from the Poisson
kernel-based density and clustering algorithm for spherical data. For more information see
Saraceno G., Markatou M., Mukhopadhyay R. and Golzy M. (2024)
<doi:10.48550/arXiv.2402.02290>
Markatou, M. and Saraceno, G. (2024) <doi:10.48550/arXiv.2407.16374>,
Ding, Y., Markatou, M. and Saraceno, G. (2023) <doi:10.5705/ss.202022.0347>,
and Golzy, M. and Markatou, M. (2020) <doi:10.1080/10618600.2020.1740713>.
Author: Giovanni Saraceno [aut, cre] ,
Marianthi Markatou [aut],
Raktim Mukhopadhyay [aut],
Mojgan Golzy [aut],
Hingee Kassel [rev],
Emi Tanaka [rev]
Maintainer: Giovanni Saraceno <giovanni.saraceno@unipd.it>
Diff between QuadratiK versions 1.1.2 dated 2024-10-29 and 1.1.3 dated 2025-02-04
QuadratiK-1.1.2/QuadratiK/tests/testthat/Rplots.pdf |only QuadratiK-1.1.3/QuadratiK/DESCRIPTION | 26 - QuadratiK-1.1.3/QuadratiK/MD5 | 127 +++---- QuadratiK-1.1.3/QuadratiK/NAMESPACE | 130 ++++--- QuadratiK-1.1.3/QuadratiK/NEWS.md | 41 ++ QuadratiK-1.1.3/QuadratiK/R/QuadratiK-package.R | 5 QuadratiK-1.1.3/QuadratiK/R/RcppExports.R | 20 - QuadratiK-1.1.3/QuadratiK/R/breast_cancer.R | 2 QuadratiK-1.1.3/QuadratiK/R/classes.R | 10 QuadratiK-1.1.3/QuadratiK/R/clustering_functions.R | 137 ++++---- QuadratiK-1.1.3/QuadratiK/R/critical_value.R | 12 QuadratiK-1.1.3/QuadratiK/R/h_selection.R | 16 QuadratiK-1.1.3/QuadratiK/R/kb.test.R | 29 - QuadratiK-1.1.3/QuadratiK/R/pk.test.R | 32 + QuadratiK-1.1.3/QuadratiK/R/pkbd_functions.R | 29 - QuadratiK-1.1.3/QuadratiK/R/srr-stats-standards.R | 1 QuadratiK-1.1.3/QuadratiK/R/utility.R | 19 - QuadratiK-1.1.3/QuadratiK/R/wine.R | 2 QuadratiK-1.1.3/QuadratiK/R/wireless.R | 2 QuadratiK-1.1.3/QuadratiK/README.md | 21 - QuadratiK-1.1.3/QuadratiK/inst/CITATION | 2 QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.R | 30 - QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.Rmd | 38 +- QuadratiK-1.1.3/QuadratiK/inst/doc/Introduction.html | 124 +++---- QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.R | 28 - QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.Rmd | 14 QuadratiK-1.1.3/QuadratiK/inst/doc/TwoSample_test.html | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.R | 34 -- QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.Rmd | 26 - QuadratiK-1.1.3/QuadratiK/inst/doc/generate_rpkb.html | 203 +++++++----- QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.R | 22 - QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.Rmd | 10 QuadratiK-1.1.3/QuadratiK/inst/doc/kSample_test.html | 12 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.R | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.Rmd | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/uniformity.html | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.R | 16 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.Rmd | 8 QuadratiK-1.1.3/QuadratiK/inst/doc/wireless_clustering.html | 26 - QuadratiK-1.1.3/QuadratiK/man/QuadratiK-package.Rd | 11 QuadratiK-1.1.3/QuadratiK/man/dpkb.Rd | 23 - QuadratiK-1.1.3/QuadratiK/man/kb.test-class.Rd | 10 QuadratiK-1.1.3/QuadratiK/man/kb.test.Rd | 16 QuadratiK-1.1.3/QuadratiK/man/pk.test.Rd | 22 - QuadratiK-1.1.3/QuadratiK/man/pkbc.Rd | 34 +- QuadratiK-1.1.3/QuadratiK/man/pkbc_validation.Rd | 30 - QuadratiK-1.1.3/QuadratiK/man/plot.pkbc.Rd | 132 +++---- QuadratiK-1.1.3/QuadratiK/man/predict.pkbc.Rd | 10 QuadratiK-1.1.3/QuadratiK/man/select_h.Rd | 6 QuadratiK-1.1.3/QuadratiK/man/summary.kb.test.Rd | 72 ++-- QuadratiK-1.1.3/QuadratiK/man/summary.pk.test.Rd | 72 ++-- QuadratiK-1.1.3/QuadratiK/man/summary.pkbc.Rd | 4 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-dpkb.R | 26 - QuadratiK-1.1.3/QuadratiK/tests/testthat/test-kb.test.R | 3 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-pk.test.R | 2 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-pkbc.R | 36 +- QuadratiK-1.1.3/QuadratiK/tests/testthat/test-rpkb.R | 42 +- QuadratiK-1.1.3/QuadratiK/tests/testthat/test-select_h.R | 3 QuadratiK-1.1.3/QuadratiK/tests/testthat/test-validation.R | 2 QuadratiK-1.1.3/QuadratiK/vignettes/Introduction.Rmd | 38 +- QuadratiK-1.1.3/QuadratiK/vignettes/TwoSample_test.Rmd | 14 QuadratiK-1.1.3/QuadratiK/vignettes/generate_rpkb.Rmd | 26 - QuadratiK-1.1.3/QuadratiK/vignettes/kSample_test.Rmd | 10 QuadratiK-1.1.3/QuadratiK/vignettes/uniformity.Rmd | 8 QuadratiK-1.1.3/QuadratiK/vignettes/wireless_clustering.Rmd | 8 65 files changed, 1042 insertions(+), 920 deletions(-)
Title: Meta Clustering with Similarity Network Fusion
Description: Framework to facilitate patient subtyping with similarity network fusion and meta clustering. The similarity network fusion (SNF) algorithm was introduced by Wang et al. (2014) in <doi:10.1038/nmeth.2810>. SNF is a data integration approach that can transform high-dimensional and diverse data types into a single similarity network suitable for clustering with minimal loss of information from each initial data source. The meta clustering approach was introduced by Caruana et al. (2006) in <doi:10.1109/ICDM.2006.103>. Meta clustering involves generating a wide range of cluster solutions by adjusting clustering hyperparameters, then clustering the solutions themselves into a manageable number of qualitatively similar solutions, and finally characterizing representative solutions to find ones that are best for the user's specific context. This package provides a framework to easily transform multi-modal data into a wide range of similarity network fusion-derived cluster solutio [...truncated...]
Author: Prashanth S Velayudhan [aut, cre],
Xiaoqiao Xu [aut],
Prajkta Kallurkar [aut],
Ana Patricia Balbon [aut],
Maria T Secara [aut],
Adam Taback [aut],
Denise Sabac [aut],
Nicholas Chan [aut],
Shihao Ma [aut],
Bo Wang [aut],
Daniel Felsky [aut],
Stephanie [...truncated...]
Maintainer: Prashanth S Velayudhan <psvelayu@gmail.com>
Diff between metasnf versions 1.1.1 dated 2024-11-08 and 2.0.0 dated 2025-02-04
metasnf-1.1.1/metasnf/R/clust_algs_list.R |only metasnf-1.1.1/metasnf/R/cluster_extraction.R |only metasnf-1.1.1/metasnf/R/distance_metrics_list.R |only metasnf-1.1.1/metasnf/R/meta_cluster.R |only metasnf-1.1.1/metasnf/R/settings_matrix.R |only metasnf-1.1.1/metasnf/R/solutions_matrix.R |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.R |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.Rmd |only metasnf-1.1.1/metasnf/inst/doc/settings_matrix.html |only metasnf-1.1.1/metasnf/man/add_settings_matrix_rows.Rd |only metasnf-1.1.1/metasnf/man/arrange_dl.Rd |only metasnf-1.1.1/metasnf/man/batch_nmi.Rd |only metasnf-1.1.1/metasnf/man/calculate_db_indices.Rd |only metasnf-1.1.1/metasnf/man/calculate_dunn_indices.Rd |only metasnf-1.1.1/metasnf/man/calculate_silhouettes.Rd |only metasnf-1.1.1/metasnf/man/dl_has_duplicates.Rd |only metasnf-1.1.1/metasnf/man/dl_uid_first_col.Rd |only metasnf-1.1.1/metasnf/man/domain_merge.Rd |only metasnf-1.1.1/metasnf/man/euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/generate_data_list.Rd |only metasnf-1.1.1/metasnf/man/generate_weights_matrix.Rd |only metasnf-1.1.1/metasnf/man/get_dl_subjects.Rd |only metasnf-1.1.1/metasnf/man/gower_distance.Rd |only metasnf-1.1.1/metasnf/man/hamming_distance.Rd |only metasnf-1.1.1/metasnf/man/individual.Rd |only metasnf-1.1.1/metasnf/man/list_remove.Rd |only metasnf-1.1.1/metasnf/man/lp_solutions_matrix.Rd |only metasnf-1.1.1/metasnf/man/merge_data_lists.Rd |only metasnf-1.1.1/metasnf/man/no_subs.Rd |only metasnf-1.1.1/metasnf/man/prefix_dl_sk.Rd |only metasnf-1.1.1/metasnf/man/reduce_dl_to_common.Rd |only metasnf-1.1.1/metasnf/man/remove_dl_na.Rd |only metasnf-1.1.1/metasnf/man/reorder_dl_subs.Rd |only metasnf-1.1.1/metasnf/man/settings_matrix_heatmap.Rd |only metasnf-1.1.1/metasnf/man/sew_euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/sn_euclidean_distance.Rd |only metasnf-1.1.1/metasnf/man/spectral_eigen.Rd |only metasnf-1.1.1/metasnf/man/spectral_eigen_classic.Rd |only metasnf-1.1.1/metasnf/man/spectral_eight.Rd |only metasnf-1.1.1/metasnf/man/spectral_five.Rd |only metasnf-1.1.1/metasnf/man/spectral_four.Rd |only metasnf-1.1.1/metasnf/man/spectral_nine.Rd |only metasnf-1.1.1/metasnf/man/spectral_rot.Rd |only metasnf-1.1.1/metasnf/man/spectral_rot_classic.Rd |only metasnf-1.1.1/metasnf/man/spectral_seven.Rd |only metasnf-1.1.1/metasnf/man/spectral_six.Rd |only metasnf-1.1.1/metasnf/man/spectral_ten.Rd |only metasnf-1.1.1/metasnf/man/spectral_three.Rd |only metasnf-1.1.1/metasnf/man/spectral_two.Rd |only metasnf-1.1.1/metasnf/man/subs.Rd |only metasnf-1.1.1/metasnf/man/subsample_data_list.Rd |only metasnf-1.1.1/metasnf/man/summarize_clust_algs_list.Rd |only metasnf-1.1.1/metasnf/man/summarize_dml.Rd |only metasnf-1.1.1/metasnf/man/two_step_merge.Rd |only metasnf-1.1.1/metasnf/tests/testthat/test-settings_matrix.R |only metasnf-1.1.1/metasnf/vignettes/clust_esm_manhattan_l.png |only metasnf-1.1.1/metasnf/vignettes/settings_matrix.Rmd |only metasnf-1.1.1/metasnf/vignettes/var_manhattan_l.png |only metasnf-2.0.0/metasnf/DESCRIPTION | 13 metasnf-2.0.0/metasnf/MD5 | 614 ++- metasnf-2.0.0/metasnf/NAMESPACE | 156 metasnf-2.0.0/metasnf/NEWS.md | 39 metasnf-2.0.0/metasnf/R/alluvial_plot.R | 60 metasnf-2.0.0/metasnf/R/ari_matrix.R |only metasnf-2.0.0/metasnf/R/arrange.R |only metasnf-2.0.0/metasnf/R/as_ari_matrix.R |only metasnf-2.0.0/metasnf/R/as_data_frame.R |only metasnf-2.0.0/metasnf/R/as_data_list.R |only metasnf-2.0.0/metasnf/R/as_settings_df.R |only metasnf-2.0.0/metasnf/R/as_sim_mats_list.R |only metasnf-2.0.0/metasnf/R/as_snf_config.R |only metasnf-2.0.0/metasnf/R/as_weights_matrix.R |only metasnf-2.0.0/metasnf/R/assignment.R |only metasnf-2.0.0/metasnf/R/batch_snf.R | 973 +---- metasnf-2.0.0/metasnf/R/c.R |only metasnf-2.0.0/metasnf/R/clust_fns_list.R |only metasnf-2.0.0/metasnf/R/coclustering.R | 831 ++-- metasnf-2.0.0/metasnf/R/data.R | 22 metasnf-2.0.0/metasnf/R/data_list.R | 1023 +++-- metasnf-2.0.0/metasnf/R/deprecated.R |only metasnf-2.0.0/metasnf/R/dist_fns_list.R |only metasnf-2.0.0/metasnf/R/ext_solutions_df.R |only metasnf-2.0.0/metasnf/R/extraction.R |only metasnf-2.0.0/metasnf/R/feature_plots.R | 82 metasnf-2.0.0/metasnf/R/features.R |only metasnf-2.0.0/metasnf/R/get_representative_solutions.R |only metasnf-2.0.0/metasnf/R/heatmaps.R | 774 ++-- metasnf-2.0.0/metasnf/R/label_meta_clusters.R |only metasnf-2.0.0/metasnf/R/label_propagation.R | 304 - metasnf-2.0.0/metasnf/R/linear_adjust.R | 69 metasnf-2.0.0/metasnf/R/manhattan_plot.R | 279 - metasnf-2.0.0/metasnf/R/merge.R |only metasnf-2.0.0/metasnf/R/metasnf-package.R |only metasnf-2.0.0/metasnf/R/n_features.R |only metasnf-2.0.0/metasnf/R/n_observations.R |only metasnf-2.0.0/metasnf/R/nclust_estimation.R | 32 metasnf-2.0.0/metasnf/R/nmi.R | 190 - metasnf-2.0.0/metasnf/R/parallel.R | 206 - metasnf-2.0.0/metasnf/R/print.R |only metasnf-2.0.0/metasnf/R/quality_measures.R | 190 - metasnf-2.0.0/metasnf/R/rbind.R |only metasnf-2.0.0/metasnf/R/settings_df.R |only metasnf-2.0.0/metasnf/R/signal.R |only metasnf-2.0.0/metasnf/R/sim_mats_list.R |only metasnf-2.0.0/metasnf/R/snf_config.R |only metasnf-2.0.0/metasnf/R/solutions_df.R |only metasnf-2.0.0/metasnf/R/summary.R |only metasnf-2.0.0/metasnf/R/summary_features.R |only metasnf-2.0.0/metasnf/R/t.R |only metasnf-2.0.0/metasnf/R/uids.R |only metasnf-2.0.0/metasnf/R/utils.R | 342 - metasnf-2.0.0/metasnf/R/weights_matrix.R | 128 metasnf-2.0.0/metasnf/README.md | 71 metasnf-2.0.0/metasnf/build/partial.rdb |only metasnf-2.0.0/metasnf/build/vignette.rds |binary metasnf-2.0.0/metasnf/inst/doc/a_complete_example.R | 778 ++-- metasnf-2.0.0/metasnf/inst/doc/a_complete_example.Rmd | 595 +-- metasnf-2.0.0/metasnf/inst/doc/a_complete_example.html | 1766 +++++----- metasnf-2.0.0/metasnf/inst/doc/a_simple_example.R | 121 metasnf-2.0.0/metasnf/inst/doc/a_simple_example.Rmd | 145 metasnf-2.0.0/metasnf/inst/doc/a_simple_example.html | 360 +- metasnf-2.0.0/metasnf/inst/doc/alluvial_plots.R | 30 metasnf-2.0.0/metasnf/inst/doc/alluvial_plots.Rmd | 33 metasnf-2.0.0/metasnf/inst/doc/alluvial_plots.html | 106 metasnf-2.0.0/metasnf/inst/doc/clustering_algorithms.R | 274 - metasnf-2.0.0/metasnf/inst/doc/clustering_algorithms.Rmd | 200 - metasnf-2.0.0/metasnf/inst/doc/clustering_algorithms.html | 603 +-- metasnf-2.0.0/metasnf/inst/doc/confounders.R | 42 metasnf-2.0.0/metasnf/inst/doc/confounders.Rmd | 48 metasnf-2.0.0/metasnf/inst/doc/confounders.html | 235 - metasnf-2.0.0/metasnf/inst/doc/correlation_plots.R | 149 metasnf-2.0.0/metasnf/inst/doc/correlation_plots.Rmd | 24 metasnf-2.0.0/metasnf/inst/doc/correlation_plots.html | 67 metasnf-2.0.0/metasnf/inst/doc/data_list.R | 13 metasnf-2.0.0/metasnf/inst/doc/data_list.Rmd | 26 metasnf-2.0.0/metasnf/inst/doc/data_list.html | 45 metasnf-2.0.0/metasnf/inst/doc/distance_metrics.R | 208 - metasnf-2.0.0/metasnf/inst/doc/distance_metrics.Rmd | 272 - metasnf-2.0.0/metasnf/inst/doc/distance_metrics.html | 753 ++-- metasnf-2.0.0/metasnf/inst/doc/feature_plots.R | 22 metasnf-2.0.0/metasnf/inst/doc/feature_plots.Rmd | 27 metasnf-2.0.0/metasnf/inst/doc/feature_plots.html | 135 metasnf-2.0.0/metasnf/inst/doc/feature_weights.R | 50 metasnf-2.0.0/metasnf/inst/doc/feature_weights.Rmd | 67 metasnf-2.0.0/metasnf/inst/doc/feature_weights.html | 164 metasnf-2.0.0/metasnf/inst/doc/getting_started.R | 19 metasnf-2.0.0/metasnf/inst/doc/getting_started.Rmd | 6 metasnf-2.0.0/metasnf/inst/doc/getting_started.html | 2 metasnf-2.0.0/metasnf/inst/doc/imputations.R | 208 - metasnf-2.0.0/metasnf/inst/doc/imputations.Rmd | 79 metasnf-2.0.0/metasnf/inst/doc/imputations.html | 158 metasnf-2.0.0/metasnf/inst/doc/label_propagation.R | 113 metasnf-2.0.0/metasnf/inst/doc/label_propagation.Rmd | 120 metasnf-2.0.0/metasnf/inst/doc/label_propagation.html | 282 - metasnf-2.0.0/metasnf/inst/doc/manhattan_plots.R | 255 - metasnf-2.0.0/metasnf/inst/doc/manhattan_plots.Rmd | 87 metasnf-2.0.0/metasnf/inst/doc/manhattan_plots.html | 113 metasnf-2.0.0/metasnf/inst/doc/nmi_scores.R | 15 metasnf-2.0.0/metasnf/inst/doc/nmi_scores.Rmd | 24 metasnf-2.0.0/metasnf/inst/doc/nmi_scores.html | 48 metasnf-2.0.0/metasnf/inst/doc/parallel_processing.R | 83 metasnf-2.0.0/metasnf/inst/doc/parallel_processing.Rmd | 42 metasnf-2.0.0/metasnf/inst/doc/parallel_processing.html | 36 metasnf-2.0.0/metasnf/inst/doc/quality_measures.R | 91 metasnf-2.0.0/metasnf/inst/doc/quality_measures.Rmd | 44 metasnf-2.0.0/metasnf/inst/doc/quality_measures.html | 52 metasnf-2.0.0/metasnf/inst/doc/similarity_matrix_heatmap.R | 207 - metasnf-2.0.0/metasnf/inst/doc/similarity_matrix_heatmap.Rmd | 52 metasnf-2.0.0/metasnf/inst/doc/similarity_matrix_heatmap.html | 217 - metasnf-2.0.0/metasnf/inst/doc/snf_config.R |only metasnf-2.0.0/metasnf/inst/doc/snf_config.Rmd |only metasnf-2.0.0/metasnf/inst/doc/snf_config.html |only metasnf-2.0.0/metasnf/inst/doc/snf_schemes.R | 3 metasnf-2.0.0/metasnf/inst/doc/snf_schemes.Rmd | 18 metasnf-2.0.0/metasnf/inst/doc/snf_schemes.html | 21 metasnf-2.0.0/metasnf/inst/doc/stability_measures.R | 188 - metasnf-2.0.0/metasnf/inst/doc/stability_measures.Rmd | 77 metasnf-2.0.0/metasnf/inst/doc/stability_measures.html | 112 metasnf-2.0.0/metasnf/inst/doc/troubleshooting.Rmd | 2 metasnf-2.0.0/metasnf/inst/doc/troubleshooting.html | 2 metasnf-2.0.0/metasnf/man/add_columns.Rd | 20 metasnf-2.0.0/metasnf/man/add_settings_df_rows.Rd |only metasnf-2.0.0/metasnf/man/adjusted_rand_index_heatmap.Rd | 8 metasnf-2.0.0/metasnf/man/alluvial_cluster_plot.Rd | 37 metasnf-2.0.0/metasnf/man/anxiety.Rd | 2 metasnf-2.0.0/metasnf/man/arrange.Rd |only metasnf-2.0.0/metasnf/man/arrange_dll.Rd |only metasnf-2.0.0/metasnf/man/as.data.frame.data_list.Rd |only metasnf-2.0.0/metasnf/man/as.data.frame.ext_solutions_df.Rd |only metasnf-2.0.0/metasnf/man/as.data.frame.solutions_df.Rd |only metasnf-2.0.0/metasnf/man/as_ari_matrix.Rd |only metasnf-2.0.0/metasnf/man/as_data_list.Rd |only metasnf-2.0.0/metasnf/man/as_settings_df.Rd |only metasnf-2.0.0/metasnf/man/as_sim_mats_list.Rd |only metasnf-2.0.0/metasnf/man/as_snf_config.Rd |only metasnf-2.0.0/metasnf/man/as_weights_matrix.Rd |only metasnf-2.0.0/metasnf/man/assemble_data.Rd | 10 metasnf-2.0.0/metasnf/man/assoc_pval_heatmap.Rd | 19 metasnf-2.0.0/metasnf/man/auto_plot.Rd | 19 metasnf-2.0.0/metasnf/man/batch_row_closure.Rd | 35 metasnf-2.0.0/metasnf/man/batch_snf.Rd | 98 metasnf-2.0.0/metasnf/man/batch_snf_subsamples.Rd | 87 metasnf-2.0.0/metasnf/man/calc_aris.Rd | 48 metasnf-2.0.0/metasnf/man/calc_assoc_pval.Rd | 3 metasnf-2.0.0/metasnf/man/calc_assoc_pval_matrix.Rd | 24 metasnf-2.0.0/metasnf/man/calc_nmis.Rd |only metasnf-2.0.0/metasnf/man/calculate_coclustering.Rd | 54 metasnf-2.0.0/metasnf/man/cat_colours.Rd |only metasnf-2.0.0/metasnf/man/char_to_fac.Rd | 10 metasnf-2.0.0/metasnf/man/check_cfll_fn_args.Rd |only metasnf-2.0.0/metasnf/man/check_cfll_fns.Rd |only metasnf-2.0.0/metasnf/man/check_cfll_named.Rd |only metasnf-2.0.0/metasnf/man/check_cfll_unique_names.Rd |only metasnf-2.0.0/metasnf/man/check_compatible_sdf_cfl.Rd |only metasnf-2.0.0/metasnf/man/check_compatible_sdf_dfl.Rd |only metasnf-2.0.0/metasnf/man/check_compatible_sdf_wm.Rd |only metasnf-2.0.0/metasnf/man/check_dataless_annotations.Rd | 2 metasnf-2.0.0/metasnf/man/check_dfll_fn_args.Rd |only metasnf-2.0.0/metasnf/man/check_dfll_fn_names.Rd |only metasnf-2.0.0/metasnf/man/check_dfll_item_names.Rd |only metasnf-2.0.0/metasnf/man/check_dfll_subitems_are_fns.Rd |only metasnf-2.0.0/metasnf/man/check_dfll_unique_names.Rd |only metasnf-2.0.0/metasnf/man/check_dll_duplicate_components.Rd |only metasnf-2.0.0/metasnf/man/check_dll_duplicate_features.Rd |only metasnf-2.0.0/metasnf/man/check_dll_empty_input.Rd |only metasnf-2.0.0/metasnf/man/check_dll_four_subitems.Rd |only metasnf-2.0.0/metasnf/man/check_dll_inherits_list.Rd |only metasnf-2.0.0/metasnf/man/check_dll_subitem_classes.Rd |only metasnf-2.0.0/metasnf/man/check_dll_subitem_names.Rd |only metasnf-2.0.0/metasnf/man/check_dll_types.Rd |only metasnf-2.0.0/metasnf/man/check_dll_uid.Rd |only metasnf-2.0.0/metasnf/man/check_sdfl_colnames.Rd |only metasnf-2.0.0/metasnf/man/check_sdfl_is_df.Rd |only metasnf-2.0.0/metasnf/man/check_sdfl_numeric.Rd |only metasnf-2.0.0/metasnf/man/check_valid_k.Rd |only metasnf-2.0.0/metasnf/man/check_valid_sc.Rd |only metasnf-2.0.0/metasnf/man/chi_squared_pval.Rd | 3 metasnf-2.0.0/metasnf/man/clust_fns.Rd |only metasnf-2.0.0/metasnf/man/clust_fns_list.Rd |only metasnf-2.0.0/metasnf/man/cocluster_density.Rd | 34 metasnf-2.0.0/metasnf/man/cocluster_heatmap.Rd | 59 metasnf-2.0.0/metasnf/man/coclustering_coverage_check.Rd | 5 metasnf-2.0.0/metasnf/man/collapse_dl.Rd | 8 metasnf-2.0.0/metasnf/man/config_heatmap.Rd |only metasnf-2.0.0/metasnf/man/convert_uids.Rd | 13 metasnf-2.0.0/metasnf/man/cort_sa.Rd | 2 metasnf-2.0.0/metasnf/man/cort_t.Rd | 2 metasnf-2.0.0/metasnf/man/data_list.Rd |only metasnf-2.0.0/metasnf/man/depress.Rd | 2 metasnf-2.0.0/metasnf/man/discretisation.Rd | 1 metasnf-2.0.0/metasnf/man/discretisation_evec_data.Rd | 1 metasnf-2.0.0/metasnf/man/dist_fns.Rd |only metasnf-2.0.0/metasnf/man/dist_fns_list.Rd |only metasnf-2.0.0/metasnf/man/dl_variable_summary.Rd | 16 metasnf-2.0.0/metasnf/man/dlapply.Rd |only metasnf-2.0.0/metasnf/man/dll_uid_first_col.Rd |only metasnf-2.0.0/metasnf/man/domains.Rd | 9 metasnf-2.0.0/metasnf/man/drop_cols.Rd |only metasnf-2.0.0/metasnf/man/drop_inputs.Rd | 13 metasnf-2.0.0/metasnf/man/ensure_dll_df.Rd |only metasnf-2.0.0/metasnf/man/esm_manhattan_plot.Rd | 46 metasnf-2.0.0/metasnf/man/estimate_nclust_given_graph.Rd | 12 metasnf-2.0.0/metasnf/man/expression_df.Rd | 4 metasnf-2.0.0/metasnf/man/ext_solutions_df.Rd |only metasnf-2.0.0/metasnf/man/extend_solutions.Rd | 41 metasnf-2.0.0/metasnf/man/fav_colour.Rd | 2 metasnf-2.0.0/metasnf/man/features.Rd |only metasnf-2.0.0/metasnf/man/figures |only metasnf-2.0.0/metasnf/man/fisher_exact_pval.Rd | 3 metasnf-2.0.0/metasnf/man/generate_annotations_list.Rd | 3 metasnf-2.0.0/metasnf/man/generate_clust_algs_list.Rd | 48 metasnf-2.0.0/metasnf/man/generate_distance_metrics_list.Rd | 48 metasnf-2.0.0/metasnf/man/generate_settings_matrix.Rd | 183 - metasnf-2.0.0/metasnf/man/get_cluster_df.Rd | 24 metasnf-2.0.0/metasnf/man/get_cluster_solutions.Rd | 28 metasnf-2.0.0/metasnf/man/get_clusters.Rd | 20 metasnf-2.0.0/metasnf/man/get_complete_uids.Rd | 40 metasnf-2.0.0/metasnf/man/get_dist_matrix.Rd | 15 metasnf-2.0.0/metasnf/man/get_dl_uids.Rd |only metasnf-2.0.0/metasnf/man/get_matrix_order.Rd | 44 metasnf-2.0.0/metasnf/man/get_mean_pval.Rd | 9 metasnf-2.0.0/metasnf/man/get_min_pval.Rd | 9 metasnf-2.0.0/metasnf/man/get_pvals.Rd | 18 metasnf-2.0.0/metasnf/man/get_representative_solutions.Rd | 65 metasnf-2.0.0/metasnf/man/gexclude.Rd |only metasnf-2.0.0/metasnf/man/gselect.Rd |only metasnf-2.0.0/metasnf/man/income.Rd | 4 metasnf-2.0.0/metasnf/man/is_data_list.Rd |only metasnf-2.0.0/metasnf/man/label_meta_clusters.Rd |only metasnf-2.0.0/metasnf/man/label_prop.Rd | 23 metasnf-2.0.0/metasnf/man/label_propagate.Rd |only metasnf-2.0.0/metasnf/man/label_splits.Rd | 1 metasnf-2.0.0/metasnf/man/linear_adjust.Rd | 40 metasnf-2.0.0/metasnf/man/linear_model_pval.Rd | 3 metasnf-2.0.0/metasnf/man/mc_manhattan_plot.Rd | 73 metasnf-2.0.0/metasnf/man/merge.snf_config.Rd |only metasnf-2.0.0/metasnf/man/merge_df_list.Rd | 20 metasnf-2.0.0/metasnf/man/merge_dls.Rd |only metasnf-2.0.0/metasnf/man/meta_cluster_heatmap.Rd |only metasnf-2.0.0/metasnf/man/metasnf-package.Rd |only metasnf-2.0.0/metasnf/man/metasnf_alert.Rd |only metasnf-2.0.0/metasnf/man/metasnf_defunct.Rd |only metasnf-2.0.0/metasnf/man/metasnf_deprecated.Rd |only metasnf-2.0.0/metasnf/man/metasnf_error.Rd |only metasnf-2.0.0/metasnf/man/metasnf_warning.Rd |only 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Title: Forest Inventory Estimation and Analysis
Description: A research estimation tool for analysts that work with sample-based
inventory data from the U.S. Department of Agriculture, Forest Service,
Forest Inventory and Analysis (FIA) Program.
Author: Tracey Frescino [aut],
Gretchen Moisen [aut],
Paul Patterson [aut],
Chris Toney [aut],
Grayson White [aut, cre] ,
Joshua Yamamoto [aut]
Maintainer: Grayson White <graysonwhite13@gmail.com>
Diff between FIESTA versions 3.6.4 dated 2024-06-07 and 3.7.0 dated 2025-02-04
FIESTA-3.6.4/FIESTA/R/check.pltcnt.R |only FIESTA-3.6.4/FIESTA/R/check.popdataDWM.R |only FIESTA-3.6.4/FIESTA/R/getpse.R |only FIESTA-3.6.4/FIESTA/R/modGBdwm.R |only FIESTA-3.6.4/FIESTA/R/modWFarea.R |only FIESTA-3.6.4/FIESTA/R/modWFpop.R |only FIESTA-3.6.4/FIESTA/R/modWFtree.R |only FIESTA-3.6.4/FIESTA/R/popFilters.R |only FIESTA-3.6.4/FIESTA/R/popTableIDs.R |only FIESTA-3.6.4/FIESTA/R/popTables.R |only FIESTA-3.6.4/FIESTA/man/modGBdwm.Rd |only FIESTA-3.6.4/FIESTA/man/modWFarea.Rd |only FIESTA-3.6.4/FIESTA/man/modWFpop.Rd |only FIESTA-3.6.4/FIESTA/man/modWFtree.Rd |only FIESTA-3.6.4/FIESTA/man/popFilters.Rd |only FIESTA-3.6.4/FIESTA/man/popTableIDs.Rd |only FIESTA-3.6.4/FIESTA/man/popTables.Rd |only FIESTA-3.7.0/FIESTA/DESCRIPTION | 12 FIESTA-3.7.0/FIESTA/MD5 | 336 FIESTA-3.7.0/FIESTA/NAMESPACE | 16 FIESTA-3.7.0/FIESTA/NEWS.md | 95 FIESTA-3.7.0/FIESTA/R/DBgetCSV.R | 21 FIESTA-3.7.0/FIESTA/R/DBgetEvalid.R | 796 - FIESTA-3.7.0/FIESTA/R/DBgetPlots.R | 1553 +-- FIESTA-3.7.0/FIESTA/R/DBgetXY.R | 310 FIESTA-3.7.0/FIESTA/R/FIESTA-package.R | 52 FIESTA-3.7.0/FIESTA/R/ISAinternal.R | 31 FIESTA-3.7.0/FIESTA/R/SQLite_FIADB_ENTIRE_create_indices.R |only FIESTA-3.7.0/FIESTA/R/check.PROPvars.R | 13 FIESTA-3.7.0/FIESTA/R/check.auxiliary.R | 295 FIESTA-3.7.0/FIESTA/R/check.cond.R |only FIESTA-3.7.0/FIESTA/R/check.condCHNG.R |only FIESTA-3.7.0/FIESTA/R/check.estdata.R | 527 - FIESTA-3.7.0/FIESTA/R/check.estdataP2VEG.R |only FIESTA-3.7.0/FIESTA/R/check.estdataVOL.R |only FIESTA-3.7.0/FIESTA/R/check.outparams.R | 54 FIESTA-3.7.0/FIESTA/R/check.popdataCHNG.R | 2390 +++- FIESTA-3.7.0/FIESTA/R/check.popdataP2VEG.R | 2394 +++- FIESTA-3.7.0/FIESTA/R/check.popdataPLT.R | 1995 ++-- FIESTA-3.7.0/FIESTA/R/check.popdataVOL.R | 1586 ++- FIESTA-3.7.0/FIESTA/R/check.rowcol.R | 2424 ++-- FIESTA-3.7.0/FIESTA/R/check.titles.R | 103 FIESTA-3.7.0/FIESTA/R/check.tree.R | 396 FIESTA-3.7.0/FIESTA/R/datLUTclass.R | 145 FIESTA-3.7.0/FIESTA/R/datLUTnm.R | 32 FIESTA-3.7.0/FIESTA/R/datLUTspp.R | 204 FIESTA-3.7.0/FIESTA/R/datPivot.R | 374 FIESTA-3.7.0/FIESTA/R/datSumCond.R | 79 FIESTA-3.7.0/FIESTA/R/datSumTree.R | 3068 ++++-- FIESTA-3.7.0/FIESTA/R/datSumTreeDom.R | 1817 --- FIESTA-3.7.0/FIESTA/R/dbTables.R | 12 FIESTA-3.7.0/FIESTA/R/est.outtabs.R | 320 FIESTA-3.7.0/FIESTA/R/getADJqry.R |only FIESTA-3.7.0/FIESTA/R/getADJwhereqry.R |only FIESTA-3.7.0/FIESTA/R/getGBestimates.R |only FIESTA-3.7.0/FIESTA/R/getMAestimates.R |only FIESTA-3.7.0/FIESTA/R/getSAestimates.R |only FIESTA-3.7.0/FIESTA/R/getpopFilterqry.R |only FIESTA-3.7.0/FIESTA/R/modGBarea.R | 620 - 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Title: Iteratively Reweighted Boosting for Robust Analysis
Description: Fit a predictive model using iteratively reweighted boosting (IRBoost) to minimize robust loss functions within the CC-family (concave-convex). This constitutes an application of iteratively reweighted convex optimization (IRCO), where convex optimization is performed using the functional descent boosting algorithm. IRBoost assigns weights to facilitate outlier identification. Applications include robust generalized linear models and robust accelerated failure time models. Wang (2025) <doi:10.6339/24-JDS1138>.
Author: Zhu Wang [aut, cre]
Maintainer: Zhu Wang <zhuwang@gmail.com>
Diff between irboost versions 0.1-1.5 dated 2024-04-18 and 0.2-1.0 dated 2025-02-04
irboost-0.1-1.5/irboost/vignettes/irbst_code.pdf |only irboost-0.2-1.0/irboost/DESCRIPTION | 10 +++---- irboost-0.2-1.0/irboost/MD5 | 28 +++++++++++++------- irboost-0.2-1.0/irboost/NEWS | 6 ++++ irboost-0.2-1.0/irboost/R/irb.train.R | 2 - irboost-0.2-1.0/irboost/R/irb.train_aft.R | 2 - irboost-0.2-1.0/irboost/R/irboost.R | 2 - irboost-0.2-1.0/irboost/build/vignette.rds |binary irboost-0.2-1.0/irboost/inst/doc/static_irbst.pdf |binary irboost-0.2-1.0/irboost/vignettes/irbst.bib | 29 +++++++++++++-------- irboost-0.2-1.0/irboost/vignettes/irbst_code_files |only 11 files changed, 51 insertions(+), 28 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices are included (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.
Author: Oeyvind Langsrud [aut, cre] ,
Daniel Lupp [aut] ,
Bjoern-Helge Mevik [ctb],
Vidar Norstein Klungre [rev] ,
Statistics Norway [cph]
Maintainer: Oeyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.6.0 dated 2024-12-04 and 1.7.0 dated 2025-02-04
DESCRIPTION | 11 + MD5 | 38 +++--- NAMESPACE | 5 NEWS.md | 44 +++++++ R/Extend0fromModelMatrixInput.R |only R/GaussSuppression.R | 208 +++++++++++++++++++++++++++++++++++-- R/filter_by_variable.R |only R/formula_utils.R | 25 +++- R/hierarchies_as_vars.R | 27 ++++ R/map_hierarchies_to_data.R | 40 ++++++- R/model_aggregate.R | 63 ++++++++++- R/tables_by_formulas.R |only R/total_collapse.R | 2 man/Extend0fromModelMatrixInput.Rd |only man/GaussSuppression.Rd | 24 ++++ man/combine_formulas.Rd | 7 + man/filter_by_variable.Rd |only man/hierarchies_as_vars.Rd | 15 ++ man/map_hierarchies_to_data.Rd | 25 ++++ man/model_aggregate.Rd | 29 ++++- man/tables_by_formulas.Rd |only man/total_collapse.Rd | 2 tests/testthat/test-ModelMatrix.R | 3 23 files changed, 521 insertions(+), 47 deletions(-)
Title: Get and Modify 'oTree' Data
Description: Efficiently manage and process data from 'oTree' experiments.
Import 'oTree' data and clean them by using functions that handle
messy data, dropouts, and other problematic cases. Create IDs,
calculate the time, transfer variables between app data frames, and
delete sensitive information. Review your experimental data prior to
running the experiment and automatically generate a detailed summary
of the variables used in your 'oTree' code. Information on 'oTree' is
found in Chen, D. L., Schonger, M., & Wickens, C. (2016)
<doi:10.1016/j.jbef.2015.12.001>.
Author: Patricia F. Zauchner [aut, trl, cre, cph]
Maintainer: Patricia F. Zauchner <patricia.zauchner@gmx.at>
Diff between gmoTree versions 1.3.0 dated 2024-12-06 and 1.4.0 dated 2025-02-04
gmoTree-1.3.0/gmoTree/tests/testthat/tessts.R |only gmoTree-1.3.0/gmoTree/vignettes/intro.png |only gmoTree-1.3.0/gmoTree/vignettes/title.PNG |only gmoTree-1.4.0/gmoTree/DESCRIPTION | 14 gmoTree-1.4.0/gmoTree/MD5 | 142 gmoTree-1.4.0/gmoTree/NEWS.md | 82 gmoTree-1.4.0/gmoTree/R/apptime.R | 423 +- gmoTree-1.4.0/gmoTree/R/assignv.R | 19 gmoTree-1.4.0/gmoTree/R/assignv_to_aaw.R | 23 gmoTree-1.4.0/gmoTree/R/codebook.R | 237 - gmoTree-1.4.0/gmoTree/R/constant_col.R | 11 gmoTree-1.4.0/gmoTree/R/delete_cases.R | 93 gmoTree-1.4.0/gmoTree/R/delete_dropouts.R | 27 gmoTree-1.4.0/gmoTree/R/delete_duplicate.R | 15 gmoTree-1.4.0/gmoTree/R/delete_plabels.R | 5 gmoTree-1.4.0/gmoTree/R/delete_sessions.R | 47 gmoTree-1.4.0/gmoTree/R/extime.R | 87 gmoTree-1.4.0/gmoTree/R/import_otree.R | 141 gmoTree-1.4.0/gmoTree/R/make_ids.R | 76 gmoTree-1.4.0/gmoTree/R/messy_chat.R | 3 gmoTree-1.4.0/gmoTree/R/messy_time.R | 3 gmoTree-1.4.0/gmoTree/R/pagesec.R | 7 gmoTree-1.4.0/gmoTree/R/show_constant.R | 19 gmoTree-1.4.0/gmoTree/R/show_dropouts.R | 12 gmoTree-1.4.0/gmoTree/README.md | 14 gmoTree-1.4.0/gmoTree/inst/CITATION | 4 gmoTree-1.4.0/gmoTree/inst/doc/codebook.R | 11 gmoTree-1.4.0/gmoTree/inst/doc/codebook.Rmd | 67 gmoTree-1.4.0/gmoTree/inst/doc/codebook.html | 204 - gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.R | 2 gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.Rmd | 21 gmoTree-1.4.0/gmoTree/inst/doc/intro_to_gmoTree.html | 55 gmoTree-1.4.0/gmoTree/inst/extdata/ocode_z/settings.py | 2 gmoTree-1.4.0/gmoTree/inst/pkgdown.yml |only gmoTree-1.4.0/gmoTree/inst/rmd/codebook.Rmd | 259 - gmoTree-1.4.0/gmoTree/man/apptime.Rd | 15 gmoTree-1.4.0/gmoTree/man/assignv.Rd | 10 gmoTree-1.4.0/gmoTree/man/assignv_to_aaw.Rd | 14 gmoTree-1.4.0/gmoTree/man/codebook.Rd | 87 gmoTree-1.4.0/gmoTree/man/delete_cases.Rd | 80 gmoTree-1.4.0/gmoTree/man/delete_dropouts.Rd | 42 gmoTree-1.4.0/gmoTree/man/delete_duplicate.Rd | 15 gmoTree-1.4.0/gmoTree/man/delete_plabels.Rd | 6 gmoTree-1.4.0/gmoTree/man/delete_sessions.Rd | 49 gmoTree-1.4.0/gmoTree/man/extime.Rd | 38 gmoTree-1.4.0/gmoTree/man/import_otree.Rd | 28 gmoTree-1.4.0/gmoTree/man/make_ids.Rd | 15 gmoTree-1.4.0/gmoTree/man/messy_chat.Rd | 4 gmoTree-1.4.0/gmoTree/man/messy_time.Rd | 4 gmoTree-1.4.0/gmoTree/man/pagesec.Rd | 6 gmoTree-1.4.0/gmoTree/man/show_constant.Rd | 16 gmoTree-1.4.0/gmoTree/man/show_dropouts.Rd | 30 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_cust_data_rename |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_2.1.0.w |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_5.4.0/custexp_dictator_2025-01-10.csv |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/exp_data_5.4.0subapp/custexp_dictator_2025-01-10.csv |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f1/MIG1/models.py | 10 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f2/MIG1/models.py | 10 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f3/MIG1/models.py | 6 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f4/MIG1/models.py | 14 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f5/MIG1/models.py | 6 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_f6 |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_new4 |only gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_y1/test/models.py | 5 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z2/rankaversion/models.py | 13 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z3/rankaversion/models.py | 1 gmoTree-1.4.0/gmoTree/tests/testthat/testdata/ocode_z3/settings.py | 2 gmoTree-1.4.0/gmoTree/tests/testthat/tests.R |only gmoTree-1.4.0/gmoTree/tests/testthat/tests_codebook.R | 1667 +++++----- gmoTree-1.4.0/gmoTree/vignettes/codebook.Rmd | 67 gmoTree-1.4.0/gmoTree/vignettes/intro_to_gmoTree.Rmd | 21 gmoTree-1.4.0/gmoTree/vignettes/title.png |only 72 files changed, 2421 insertions(+), 1985 deletions(-)
Title: Set Axis Break for 'ggplot2'
Description: An implementation of scale functions for setting axis breaks of a 'gg' plot (S Xu (2021) <doi:10.3389/fgene.2021.774846>).
Author: Guangchuang Yu [aut, cre, cph]
,
Shuangbin Xu [aut]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between ggbreak versions 0.1.3 dated 2025-01-08 and 0.1.4 dated 2025-02-04
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/method-ggplot-add.R | 1 + R/scales.R | 37 ++----------------------------------- R/utilities.R | 2 ++ R/zzz.R | 16 ++++++++++++++++ inst/doc/ggbreak.html | 38 +++++++++++++++++++------------------- 7 files changed, 49 insertions(+), 63 deletions(-)
Title: Perform Recursive Computations
Description: Mass rollup for a Bill of Materials is an example of a class of computations in which elements are arranged in a tree structure and some property of each element is a computed function of the corresponding values of its child elements. Leaf elements, i.e., those with no children, have values assigned. In many cases, the combining function is simple arithmetic sum; in other cases (e.g., mass properties), the combiner may involve other information such as the geometric relationship between parent and child, or statistical relations such as root-sum-of-squares (RSS). This package implements a general function for such problems. It is adapted to specific recursive computations by functional programming techniques; the caller passes a function as the update parameter to rollup() (or, at a lower level, passes functions as the get, set, combine, and override parameters to update_prop()) at runtime to specify the desired operations. The implementation relies on graph-theoretic algorithms from [...truncated...]
Author: James Steven Jenkins [aut, cre, cph]
Maintainer: James Steven Jenkins <sjenkins@studioj.us>
Diff between rollupTree versions 0.1.0 dated 2025-01-20 and 0.2.0 dated 2025-02-04
DESCRIPTION | 6 - MD5 | 58 +++++++++------ NAMESPACE | 1 NEWS.md | 11 +++ R/fault_table.R |only R/fault_tree.R |only R/rollup.R | 36 +++++++++ R/update_prop.R | 118 ++++++++++++++++---------------- R/wbs_table.R | 2 README.md | 1 data/fault_table.rda |only data/fault_tree.rda |only inst/doc/rollupTree.R | 64 ++++++++++++++++- inst/doc/rollupTree.Rmd | 96 ++++++++++++++++++++++++-- inst/doc/rollupTree.html | 157 +++++++++++++++++++++++++++++++++++-------- man/create_rollup_tree.Rd |only man/df_get_by_id.Rd | 6 - man/df_get_by_key.Rd | 10 +- man/df_get_ids.Rd | 4 - man/df_get_keys.Rd | 4 - man/df_set_by_id.Rd | 10 +- man/df_set_by_key.Rd | 10 +- man/fault_table.Rd |only man/fault_tree.Rd |only man/update_df_prop_by_id.Rd | 14 +-- man/update_df_prop_by_key.Rd | 18 ++-- man/update_prop.Rd | 18 ++-- man/validate_df_by_id.Rd | 12 +-- man/validate_df_by_key.Rd | 12 +-- man/wbs_table.Rd | 4 - tests/testthat/test-rollup.R | 20 +++++ vignettes/fta-example.jpg |only vignettes/references.bib | 8 ++ vignettes/rollupTree.Rmd | 96 ++++++++++++++++++++++++-- 34 files changed, 604 insertions(+), 192 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project was funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut] ,
Pete Philipson [aut] ,
Andrea Jorgensen [ctb] ,
Ruwanthi Kolamunnage-Dona [aut]
,
Paula Williamson [ctb] ,
Dimitris Rizopoulos [ctb, dtc] ,
Alessandro Gasparini [aut] ,
Medical Research Council [fnd]
Maintainer: Graeme L. Hickey <graemeleehickey@gmail.com>
Diff between joineRML versions 0.4.6 dated 2023-01-19 and 0.4.7 dated 2025-02-04
joineRML-0.4.6/joineRML/src/init.c |only joineRML-0.4.7/joineRML/DESCRIPTION | 10 joineRML-0.4.7/joineRML/MD5 | 77 +- joineRML-0.4.7/joineRML/NAMESPACE | 4 joineRML-0.4.7/joineRML/NEWS.md | 28 joineRML-0.4.7/joineRML/R/bootSE.R | 11 joineRML-0.4.7/joineRML/R/confint.mjoint.R | 2 joineRML-0.4.7/joineRML/R/fixef.mjoint.R | 2 joineRML-0.4.7/joineRML/R/joineRML.R | 16 joineRML-0.4.7/joineRML/R/mjoint.R | 2 joineRML-0.4.7/joineRML/R/plot.mjoint.R | 2 joineRML-0.4.7/joineRML/R/plot.ranef.mjoint.R | 8 joineRML-0.4.7/joineRML/R/tidiers.R | 18 joineRML-0.4.7/joineRML/R/vcov.mjoint.R | 8 joineRML-0.4.7/joineRML/README.md | 14 joineRML-0.4.7/joineRML/build/partial.rdb |only joineRML-0.4.7/joineRML/build/vignette.rds |binary joineRML-0.4.7/joineRML/inst/CITATION | 6 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.R | 26 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.Rmd | 33 joineRML-0.4.7/joineRML/inst/doc/joineRML-tidy.html | 259 +++---- joineRML-0.4.7/joineRML/inst/doc/joineRML.R | 43 - joineRML-0.4.7/joineRML/inst/doc/joineRML.Rmd | 46 - joineRML-0.4.7/joineRML/inst/doc/joineRML.html | 731 ++++++++++---------- joineRML-0.4.7/joineRML/inst/doc/technical.pdf |binary joineRML-0.4.7/joineRML/man/bootSE.Rd | 4 joineRML-0.4.7/joineRML/man/confint.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/fixef.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/joineRML-package.Rd |only joineRML-0.4.7/joineRML/man/joineRML.Rd | 1 joineRML-0.4.7/joineRML/man/mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/mjoint_tidiers.Rd | 7 joineRML-0.4.7/joineRML/man/plot.mjoint.Rd | 2 joineRML-0.4.7/joineRML/man/plot.ranef.mjoint.Rd | 4 joineRML-0.4.7/joineRML/man/vcov.mjoint.Rd | 8 joineRML-0.4.7/joineRML/src/Makevars | 1 joineRML-0.4.7/joineRML/src/Makevars.win | 1 joineRML-0.4.7/joineRML/src/RcppExports.cpp | 16 joineRML-0.4.7/joineRML/tests/testthat/Rplots.pdf |binary joineRML-0.4.7/joineRML/vignettes/joineRML-tidy.Rmd | 33 joineRML-0.4.7/joineRML/vignettes/joineRML.Rmd | 46 - 41 files changed, 826 insertions(+), 649 deletions(-)
Title: Spatial and Spatio-Temporal Geostatistical Modelling, Prediction
and Simulation
Description: Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.
Author: Edzer Pebesma [aut, cre] ,
Benedikt Graeler [aut]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between gstat versions 2.1-2 dated 2024-09-05 and 2.1-3 dated 2025-02-04
DESCRIPTION | 9 - MD5 | 56 ++++----- R/predict.gstat.R | 2 build/vignette.rds |binary data/DE_RB_2005.rda |binary data/coalash.rda |binary data/fulmar.rda |binary data/jura.rda |binary data/meuse.all.rda |binary data/meuse.alt.rda |binary data/ncp.grid.rda |binary data/oxford.rda |binary data/pcb.rda |binary data/sic2004.rda |binary data/sic97.rda |binary data/tull.rda |binary data/vv.rda |binary data/walker.rda |binary data/wind.rda |binary inst/doc/gstat.pdf |binary inst/doc/prs.pdf |binary inst/doc/spatio-temporal-kriging.pdf |binary inst/doc/st.pdf |binary man/sic2004.Rd | 4 man/sic97.Rd | 5 man/walker.Rd | 7 - tests/cv.Rout.save | 204 +++++++++++++++++------------------ tests/cv3d.Rout.save | 96 ++++++++-------- tests/stars.Rout.save | 84 +++++++------- 29 files changed, 229 insertions(+), 238 deletions(-)
Title: Forensic Bayesian Networks
Description: Open-source package for computing likelihood ratios in kinship testing and human identification cases. It has the core function of the software GENis, developed by Fundación Sadosky. It relies on a Bayesian Networks framework and is particularly well suited to efficiently perform large-size queries against databases of missing individuals.
Author: Franco Marsico [aut, cre],
Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between fbnet versions 1.0.3 dated 2023-07-01 and 1.0.4 dated 2025-02-04
fbnet-1.0.3/fbnet/R/FamiliasLocus.R |only fbnet-1.0.3/fbnet/R/FamiliasPedigree.R |only fbnet-1.0.3/fbnet/R/convertPedformat.R |only fbnet-1.0.3/fbnet/R/preparePed.R |only fbnet-1.0.3/fbnet/man/FamiliasLocus.Rd |only fbnet-1.0.3/fbnet/man/FamiliasPedigree.Rd |only fbnet-1.0.3/fbnet/man/convertPedformat.Rd |only fbnet-1.0.3/fbnet/man/preparePed.Rd |only fbnet-1.0.4/fbnet/DESCRIPTION | 17 ++--- fbnet-1.0.4/fbnet/MD5 | 92 ++++++++++++++-------------- fbnet-1.0.4/fbnet/NAMESPACE | 6 - fbnet-1.0.4/fbnet/R/bnet.R |only fbnet-1.0.4/fbnet/R/buildBN.R | 4 - fbnet-1.0.4/fbnet/R/buildCPTs.R | 5 - fbnet-1.0.4/fbnet/R/evidencePrunning.R | 1 fbnet-1.0.4/fbnet/R/factorHeteroFounders.R | 1 fbnet-1.0.4/fbnet/R/fbnet.R | 1 fbnet-1.0.4/fbnet/R/getGenotypeTables.R | 1 fbnet-1.0.4/fbnet/R/getLocusCPT.R | 6 - fbnet-1.0.4/fbnet/R/getMAP.R | 1 fbnet-1.0.4/fbnet/R/getQSetRMP.R | 1 fbnet-1.0.4/fbnet/R/getValuesOut.R | 1 fbnet-1.0.4/fbnet/R/imposeEvidence.R | 1 fbnet-1.0.4/fbnet/R/initBN.R | 18 ++++- fbnet-1.0.4/fbnet/R/initBN.fromPed.R | 8 -- fbnet-1.0.4/fbnet/R/initBN.fromVars.R | 13 --- fbnet-1.0.4/fbnet/R/minOrdering.R | 1 fbnet-1.0.4/fbnet/R/pbn.R |only fbnet-1.0.4/fbnet/R/prodFactor.R | 1 fbnet-1.0.4/fbnet/R/pruneNodes.R | 1 fbnet-1.0.4/fbnet/R/removeEvidenceFromPed.R | 1 fbnet-1.0.4/fbnet/R/reportLR.R | 1 fbnet-1.0.4/fbnet/R/reportPQ.R | 1 fbnet-1.0.4/fbnet/R/reverseSplit.R | 1 fbnet-1.0.4/fbnet/R/setOrdering.R | 1 fbnet-1.0.4/fbnet/R/stateRemoval.R | 1 fbnet-1.0.4/fbnet/R/stateRemoval2.R | 1 fbnet-1.0.4/fbnet/R/stateRemovalSubnucs.R | 1 fbnet-1.0.4/fbnet/R/sumFactor.R | 1 fbnet-1.0.4/fbnet/R/velim.bn.R | 6 - fbnet-1.0.4/fbnet/README.md | 13 --- fbnet-1.0.4/fbnet/build/partial.rdb |binary fbnet-1.0.4/fbnet/data/bnet.rda |only fbnet-1.0.4/fbnet/data/pbn.rda |only fbnet-1.0.4/fbnet/man/bnet.Rd |only fbnet-1.0.4/fbnet/man/buildBN.Rd | 4 - fbnet-1.0.4/fbnet/man/buildCPTs.Rd | 5 - fbnet-1.0.4/fbnet/man/fbnet.Rd | 19 +++++ fbnet-1.0.4/fbnet/man/figures |only fbnet-1.0.4/fbnet/man/getLocusCPT.Rd | 6 - fbnet-1.0.4/fbnet/man/initBN.Rd | 15 ++++ fbnet-1.0.4/fbnet/man/pbn.Rd |only fbnet-1.0.4/fbnet/man/velim.bn.Rd | 6 - 53 files changed, 109 insertions(+), 154 deletions(-)
Title: SAGA Geoprocessing and Terrain Analysis
Description: Provides access to geocomputing and terrain analysis
functions of the geographical information system (GIS) 'SAGA' (System
for Automated Geoscientific Analyses) from within R by running the
command line version of SAGA. This package furthermore provides
several R functions for handling ASCII grids, including a flexible
framework for applying local functions (including predict methods of
fitted models) and focal functions to multiple grids. SAGA GIS is
available under GPL-2 / LGPL-2 licences from
<https://sourceforge.net/projects/saga-gis/>.
Author: Alexander Brenning [aut, cre] ,
Donovan Bangs [aut],
Marc Becker [aut],
Patrick Schratz [ctb] ,
Fabian Polakowski [ctb]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between RSAGA versions 1.4.0 dated 2022-12-09 and 1.4.2 dated 2025-02-04
DESCRIPTION | 66 ++-- MD5 | 142 +++++----- R/RSAGA-core.R | 57 ++-- R/RSAGA-modules.R | 460 ++++++++++++++++++--------------- R/RSAGA-package.R | 7 R/RSAGA-utils.R | 10 R/dem.R |only R/gridtools.R | 24 + R/landslides.R | 57 +--- R/study_area.R |only build/vignette.rds |binary data/dem.rda |only data/landslides.rda |binary data/study_area.rda |only inst/doc/RSAGA.R | 194 +++++++------ inst/doc/RSAGA.Rmd | 10 inst/doc/RSAGA.html | 257 +++++++++--------- man/RSAGA-package.Rd | 134 +++++---- man/centervalue.Rd | 53 ++- man/create.variable.name.Rd | 52 ++- man/dem.Rd |only man/focal.function.Rd | 292 ++++++++++---------- man/grid.predict.Rd | 174 ++++++------ man/grid.to.xyz.Rd | 68 ++-- man/landslides.Rd | 159 +++++------ man/match.arg.ext.Rd | 138 ++++----- man/multi.focal.function.Rd | 364 +++++++++++++------------- man/pick.from.points.Rd | 447 ++++++++++++++++---------------- man/read.ascii.grid.Rd | 262 +++++++++--------- man/relative.position.Rd | 84 +++--- man/resid.median.Rd | 78 ++--- man/rsaga.add.grid.values.to.points.Rd | 87 +++--- man/rsaga.close.gaps.Rd | 110 +++---- man/rsaga.contour.Rd | 96 +++--- man/rsaga.copy.sgrd.Rd | 53 ++- man/rsaga.env.Rd | 202 +++++++------- man/rsaga.esri.to.sgrd.Rd | 84 +++--- man/rsaga.esri.wrapper.Rd | 158 +++++------ man/rsaga.fill.sinks.Rd | 132 ++++----- man/rsaga.filter.gauss.Rd | 84 +++--- man/rsaga.filter.simple.Rd | 96 +++--- man/rsaga.geoprocessor.Rd | 216 +++++++-------- man/rsaga.get.modules.Rd | 204 +++++++------- man/rsaga.get.modules.path.Rd | 43 +-- man/rsaga.get.usage.Rd | 90 +++--- man/rsaga.get.version.Rd | 80 ++--- man/rsaga.grid.calculus.Rd | 188 ++++++------- man/rsaga.grid.to.points.Rd | 129 ++++----- man/rsaga.hillshade.Rd | 112 ++++---- man/rsaga.html.help.Rd | 91 +++--- man/rsaga.import.gdal.Rd | 115 ++++---- man/rsaga.insolation.Rd | 210 +++++++-------- man/rsaga.intersect.polygons.Rd | 112 ++++---- man/rsaga.inverse.distance.Rd | 197 +++++++------- man/rsaga.lib.prefix.Rd | 70 ++--- man/rsaga.local.morphometry.Rd | 232 ++++++++-------- man/rsaga.parallel.processing.Rd | 238 ++++++++--------- man/rsaga.pisr.Rd | 295 ++++++++++----------- man/rsaga.pisr2.Rd | 268 +++++++++---------- man/rsaga.set.env.Rd | 71 ++--- man/rsaga.sgrd.to.esri.Rd | 138 ++++----- man/rsaga.sink.removal.Rd | 84 +++--- man/rsaga.sink.route.Rd | 80 ++--- man/rsaga.slope.asp.curv.Rd | 306 ++++++++++----------- man/rsaga.solar.radiation.Rd | 189 ++++++------- man/rsaga.target.Rd | 135 ++++----- man/rsaga.topdown.processing.Rd | 272 +++++++++---------- man/rsaga.union.polygons.Rd | 116 ++++---- man/rsaga.wetness.index.Rd | 164 +++++------ man/set.file.extension.Rd | 74 ++--- man/study_area.Rd |only man/wind.shelter.Rd | 140 +++++----- tests/testthat/test-core.R | 17 + tests/testthat/test-modules.R | 50 +++ vignettes/RSAGA.Rmd | 10 75 files changed, 4785 insertions(+), 4642 deletions(-)
Title: Information Theory Tools for Forensic Analysis
Description: The 'forensIT' package is a comprehensive statistical toolkit tailored for handling missing person cases. By leveraging information theory metrics, it enables accurate assessment of kinship, particularly when limited genetic evidence is available. With a focus on optimizing statistical power, 'forensIT' empowers investigators to effectively prioritize family members, enhancing the reliability and efficiency of missing person investigations.
Author: Franco Marsico [aut, cre],
Ariel Chernomoretz [aut]
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between forensIT versions 1.0.0 dated 2023-06-22 and 1.1.1 dated 2025-02-04
forensIT-1.0.0/forensIT/R/convertPed.R |only forensIT-1.0.0/forensIT/man/convertPed.Rd |only forensIT-1.1.1/forensIT/DESCRIPTION | 12 +- forensIT-1.1.1/forensIT/MD5 | 16 +-- forensIT-1.1.1/forensIT/NAMESPACE | 2 forensIT-1.1.1/forensIT/R/run-it.R | 3 forensIT-1.1.1/forensIT/R/simMinimalEnsemble.R | 4 forensIT-1.1.1/forensIT/R/simTestIDMarkers.R | 1 forensIT-1.1.1/forensIT/README.md | 104 ++++++++++--------------- forensIT-1.1.1/forensIT/man/forensIT.Rd | 10 ++ 10 files changed, 69 insertions(+), 83 deletions(-)
Title: Miscellaneous Functions for Panel Data, Quantiles, and Printing
Results
Description: These are miscellaneous functions for working with panel data, quantiles, and printing results. For panel data, the package includes functions for making a panel data balanced (that is, dropping missing individuals that have missing observations in any time period), converting id numbers to row numbers, and to treat repeated cross sections as panel data under the assumption of rank invariance. For quantiles, there are functions to make distribution functions from a set of data points (this is particularly useful when a distribution function is created in several steps), to combine distribution functions based on some external weights, and to invert distribution functions. Finally, there are several other miscellaneous functions for obtaining weighted means, weighted distribution functions, and weighted quantiles; to generate summary statistics and their differences for two groups; and to add or drop covariates from formulas.
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@uga.edu>
Diff between BMisc versions 1.4.7 dated 2025-01-10 and 1.4.8 dated 2025-02-04
BMisc-1.4.7/BMisc/man/compareSingleBinary.Rd |only BMisc-1.4.7/BMisc/man/getWeightedQuantile.Rd |only BMisc-1.4.8/BMisc/DESCRIPTION | 9 BMisc-1.4.8/BMisc/MD5 | 65 ++- BMisc-1.4.8/BMisc/NAMESPACE | 19 BMisc-1.4.8/BMisc/NEWS.md | 8 BMisc-1.4.8/BMisc/R/BMisc.R | 457 ++++++++++++++++++----- BMisc-1.4.8/BMisc/README.md | 33 - BMisc-1.4.8/BMisc/inst |only BMisc-1.4.8/BMisc/man/BMisc.Rd | 1 BMisc-1.4.8/BMisc/man/addCovToFormla.Rd | 21 - BMisc-1.4.8/BMisc/man/add_cov_to_formula.Rd |only BMisc-1.4.8/BMisc/man/blockBootSample.Rd | 28 - BMisc-1.4.8/BMisc/man/block_boot_sample.Rd |only BMisc-1.4.8/BMisc/man/combineDfs.Rd | 26 - BMisc-1.4.8/BMisc/man/combine_ecdfs.Rd |only BMisc-1.4.8/BMisc/man/compareBinary.Rd | 10 BMisc-1.4.8/BMisc/man/compare_binary.Rd |only BMisc-1.4.8/BMisc/man/compare_binary_inner.Rd |only BMisc-1.4.8/BMisc/man/dropCovFromFormla.Rd | 19 BMisc-1.4.8/BMisc/man/drop_cov_from_formula.Rd |only BMisc-1.4.8/BMisc/man/getListElement.Rd | 17 BMisc-1.4.8/BMisc/man/getWeightedDf.Rd | 10 BMisc-1.4.8/BMisc/man/getWeightedMean.Rd | 9 BMisc-1.4.8/BMisc/man/getWeightedQuantiles.Rd | 10 BMisc-1.4.8/BMisc/man/get_list_element.Rd |only BMisc-1.4.8/BMisc/man/invertEcdf.Rd | 10 BMisc-1.4.8/BMisc/man/invert_ecdf.Rd |only BMisc-1.4.8/BMisc/man/lhs.vars.Rd | 17 BMisc-1.4.8/BMisc/man/lhs_vars.Rd |only BMisc-1.4.8/BMisc/man/makeBalancedPanel.Rd | 22 - BMisc-1.4.8/BMisc/man/makeDist.Rd | 19 BMisc-1.4.8/BMisc/man/make_balanced_panel.Rd |only BMisc-1.4.8/BMisc/man/make_dist.Rd |only BMisc-1.4.8/BMisc/man/rhs.Rd | 4 BMisc-1.4.8/BMisc/man/rhs.vars.Rd | 18 BMisc-1.4.8/BMisc/man/rhs_vars.Rd |only BMisc-1.4.8/BMisc/man/weighted.checkfun.Rd | 9 BMisc-1.4.8/BMisc/man/weighted_checkfun.Rd |only BMisc-1.4.8/BMisc/man/weighted_combine_list.Rd |only BMisc-1.4.8/BMisc/man/weighted_ecdf.Rd |only BMisc-1.4.8/BMisc/man/weighted_mean.Rd |only BMisc-1.4.8/BMisc/man/weighted_quantile.Rd |only BMisc-1.4.8/BMisc/man/weighted_quantile_inner.Rd |only 44 files changed, 533 insertions(+), 308 deletions(-)
Title: Stochastic Search Inconsistency Factor Selection
Description: Evaluating the consistency assumption of Network Meta-Analysis both globally and locally in the Bayesian framework. Inconsistencies are located by applying Bayesian variable selection to the inconsistency factors. The implementation of the method is described by Seitidis et al. (2023) <doi:10.1002/sim.9891>.
Author: Georgios Seitidis [aut, cre] ,
Stavros Nikolakopoulos [aut] ,
Ioannis Ntzoufras [aut] ,
Dimitris Mavridis [aut]
Maintainer: Georgios Seitidis <g.seitidis@uoi.gr>
Diff between ssifs versions 1.0.2 dated 2023-05-12 and 1.0.4 dated 2025-02-04
DESCRIPTION | 15 ++++++++------- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 ++ NEWS.md | 2 ++ R/higgdes.R | 6 ++++-- R/smokingcessation.R | 3 ++- R/ssifs.R | 8 ++++---- README.md | 11 +++++++++-- inst/doc/An_introduction_to_ssifs.Rmd | 2 +- inst/doc/An_introduction_to_ssifs.html | 8 +++++++- man/smokingcessation.Rd | 2 +- man/ssifs.Rd | 8 ++++---- vignettes/An_introduction_to_ssifs.Rmd | 2 +- vignettes/references.bib | 11 +++++++++++ 14 files changed, 69 insertions(+), 37 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis (Balduzzi et al., 2023) <doi:10.18637/jss.v106.i02> and supporting Schwarzer et al. (2015) <doi:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <doi:10.1002/jrsm.1058>;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2020) <doi:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <doi:10.1002/sim.8158>, or penalised logistic regression (Evrenoglou et al., 2022) <doi:10.1002/sim.9562>;
- rankograms and ranking of treatments by the Surface under the cumulative ranking curve (SUCRA) (Salanti et al., 2013) <doi:10.1016/j.jclinepi.2010.03.016>;
- ranking of treatments using P-scores (frequentist analogue of SUCRAs without resampling) according to [...truncated...]
Author: Gerta Ruecker [aut] ,
Ulrike Krahn [aut],
Jochem Koenig [aut] ,
Orestis Efthimiou [aut] ,
Annabel Davies [aut] ,
Theodoros Papakonstantinou [aut]
,
Theodoros Evrenoglou [ctb] ,
Krzysztof Ciomek [ctb] ,
Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <guido.schwarzer@uniklinik-freiburg.de>
Diff between netmeta versions 3.0-2 dated 2025-01-22 and 3.1-0 dated 2025-02-04
DESCRIPTION | 26 ++++++---- LICENSE |only MD5 | 43 +++++++++-------- NAMESPACE | 48 +++++++++++++++++++ NEWS.md | 56 +++++++++++++++++++--- R/contribution.matrix.R | 59 ++++++++++------------- R/hasse-internal.R |only R/hasse.R | 63 +++++++++++------------- R/netconnection.R | 16 +++++- R/netcontrib.R | 21 +++----- R/netleague.R | 8 +-- R/netmeta-package.R | 41 ++++++++++------ R/netmeta.R | 58 +++++++++++++---------- R/netmetabin.R | 121 +++++++++++++++++++++++------------------------- R/netposet.R | 17 ++---- R/plot.netposet.R | 3 - inst/MIT_LICENSE |only inst/doc/netmeta.pdf |binary man/hasse.netposet.Rd | 30 +++++++++-- man/netcontrib.Rd | 19 +++---- man/netleague.Rd | 8 +-- man/netmetabin.Rd | 3 - man/netposet.Rd | 15 +---- man/plot.netposet.Rd | 3 - 24 files changed, 388 insertions(+), 270 deletions(-)
Title: Constructing Hierarchical Voronoi Tessellations and Overlay
Heatmaps for Data Analysis
Description: Facilitates building topology preserving maps for data analysis.
Author: Zubin Dowlaty [aut],
Mu Sigma, Inc. [cre]
Maintainer: "Mu Sigma, Inc." <ird.experiencelab@mu-sigma.com>
Diff between HVT versions 24.9.1 dated 2024-09-11 and 25.2.1 dated 2025-02-04
HVT-24.9.1/HVT/man/getCellId.Rd |only HVT-24.9.1/HVT/man/hvq.Rd |only HVT-24.9.1/HVT/man/madPlot.Rd |only HVT-24.9.1/HVT/vignettes/scoreLayeredHVT_function.png |only HVT-24.9.1/HVT/vignettes/torus2.png |only HVT-25.2.1/HVT/DESCRIPTION | 29 HVT-25.2.1/HVT/MD5 | 110 +- HVT-25.2.1/HVT/NAMESPACE | 12 HVT-25.2.1/HVT/R/clustHVT.R | 46 - HVT-25.2.1/HVT/R/clusterPlot.R | 187 ++-- HVT-25.2.1/HVT/R/diagPlot.R | 5 HVT-25.2.1/HVT/R/diagSuggestion.R | 2 HVT-25.2.1/HVT/R/displayTable.R | 127 -- HVT-25.2.1/HVT/R/edaPlots.R | 203 +++- HVT-25.2.1/HVT/R/getCellId.R | 20 HVT-25.2.1/HVT/R/getOptimalCentroids.R | 1 HVT-25.2.1/HVT/R/getTransitionProbability.R | 113 +- HVT-25.2.1/HVT/R/hvq.R | 63 - HVT-25.2.1/HVT/R/madPlot.R | 53 - HVT-25.2.1/HVT/R/msm.R |only HVT-25.2.1/HVT/R/msm_plots.R |only HVT-25.2.1/HVT/R/plotAnimatedFlowmap.R | 723 ++++++++-------- HVT-25.2.1/HVT/R/plotHVT.R | 204 ++-- HVT-25.2.1/HVT/R/plotModelDiagnostics.R | 1 HVT-25.2.1/HVT/R/plotNovelCells.R | 4 HVT-25.2.1/HVT/R/plotQuantErrorHistogram.R | 3 HVT-25.2.1/HVT/R/plotStateTransition.R | 226 ++++- HVT-25.2.1/HVT/R/plotZscore.R |only HVT-25.2.1/HVT/R/reconcileTransitionProbability.R | 20 HVT-25.2.1/HVT/R/removeNovelty.R | 2 HVT-25.2.1/HVT/R/scoreHVT.R | 48 - HVT-25.2.1/HVT/R/scoreLayeredHVT.R | 11 HVT-25.2.1/HVT/R/summary.R |only HVT-25.2.1/HVT/R/trainHVT.R | 52 - HVT-25.2.1/HVT/README.md | 118 +- HVT-25.2.1/HVT/build/vignette.rds |binary HVT-25.2.1/HVT/inst/doc/HVT.R | 42 HVT-25.2.1/HVT/inst/doc/HVT.Rmd | 90 +- HVT-25.2.1/HVT/inst/doc/HVT.html | 769 ++++++++++++++---- HVT-25.2.1/HVT/man/clustHVT.Rd | 20 HVT-25.2.1/HVT/man/displayTable.Rd | 46 - HVT-25.2.1/HVT/man/edaPlots.Rd | 28 HVT-25.2.1/HVT/man/getTransitionProbability.Rd | 31 HVT-25.2.1/HVT/man/msm.Rd |only HVT-25.2.1/HVT/man/plotAnimatedFlowmap.Rd | 13 HVT-25.2.1/HVT/man/plotHVT.Rd | 65 - HVT-25.2.1/HVT/man/plotNovelCells.Rd | 2 HVT-25.2.1/HVT/man/plotStateTransition.Rd | 16 HVT-25.2.1/HVT/man/plotZscore.Rd |only HVT-25.2.1/HVT/man/reconcileTransitionProbability.Rd | 7 HVT-25.2.1/HVT/man/scoreHVT.Rd | 3 HVT-25.2.1/HVT/man/summary.Rd |only HVT-25.2.1/HVT/man/trainHVT.Rd | 11 HVT-25.2.1/HVT/vignettes/HVT.Rmd | 90 +- HVT-25.2.1/HVT/vignettes/pngs |only 55 files changed, 2188 insertions(+), 1428 deletions(-)
Title: Robust Bayesian Meta-Analyses
Description: A framework for estimating ensembles of meta-analytic and meta-regression models
(assuming either presence or absence of the effect, heterogeneity,
publication bias, and moderators). The RoBMA framework uses Bayesian model-averaging to
combine the competing meta-analytic models into a model ensemble, weights
the posterior parameter distributions based on posterior model probabilities
and uses Bayes factors to test for the presence or absence of the
individual components (e.g., effect vs. no effect; Bartoš et al., 2022,
<doi:10.1002/jrsm.1594>; Maier, Bartoš & Wagenmakers, 2022,
<doi:10.1037/met0000405>). Users can define a wide range of prior distributions for +
the effect size, heterogeneity, publication bias (including selection models and PET-PEESE),
and moderator components. The package provides convenient functions for summary, visualizations, and
fit diagnostics.
Author: Frantisek Bartos [aut, cre] ,
Maximilian Maier [aut] ,
Eric-Jan Wagenmakers [ths] ,
Joris Goosen [ctb],
Matthew Denwood [cph] ,
Martyn Plummer [cph]
Maintainer: Frantisek Bartos <f.bartos96@gmail.com>
Diff between RoBMA versions 3.3.0 dated 2025-01-15 and 3.4.0 dated 2025-02-04
DESCRIPTION | 6 MD5 | 87 +++--- NAMESPACE | 2 NEWS.md | 12 R/BiBMA-reg.R |only R/BiBMA.R | 182 ++++++++------ R/RoBMA-reg.R | 126 ---------- R/RoBMA.R | 28 +- R/check-priors-and-models.R | 450 ++++++++++++++++++------------------ R/fit-and-marglik.R | 150 +++++++++++- R/plots.R | 2 R/priors.R | 81 ++++++ R/tools.R | 23 - R/transformations.R | 164 +++++++++++++ R/utilities.R | 1 build/partial.rdb |binary inst/REFERENCES.bib | 2 inst/doc/CustomEnsembles.html | 4 inst/doc/FastRoBMA.html | 10 inst/doc/HierarchicalBMA.html | 4 inst/doc/MedicineBMA.html | 4 inst/doc/MedicineBiBMA.html | 4 inst/doc/MetaRegression.html | 10 inst/doc/ReproducingBMA.html | 4 man/BiBMA.Rd | 28 +- man/BiBMA.reg.Rd |only man/RoBMA-package.Rd | 84 +++--- man/RoBMA_options.Rd | 54 ++-- man/effect_sizes.Rd | 186 +++++++------- man/forest.Rd | 144 +++++------ man/interpret.Rd | 42 +-- man/plot.RoBMA.Rd | 218 ++++++++--------- man/plot_models.Rd | 164 ++++++------- man/print.RoBMA.Rd | 44 +-- man/print.summary.RoBMA.Rd | 44 +-- man/prior.Rd | 170 ++++++------- man/prior_PEESE.Rd | 156 ++++++------ man/prior_PET.Rd | 156 ++++++------ man/prior_none.Rd | 80 +++--- man/prior_weightfunction.Rd | 124 ++++----- man/sample_sizes.Rd | 120 ++++----- man/set_default_binomial_priors.Rd |only man/set_default_priors.Rd | 150 ++++++------ man/standard_errors.Rd | 190 +++++++-------- man/weighted_multivariate_normal.Rd | 72 ++--- man/weighted_normal.Rd | 206 ++++++++-------- 46 files changed, 2062 insertions(+), 1726 deletions(-)
Title: Download and Display Map Tiles
Description: To create maps from tiles, 'maptiles' downloads, composes and
displays tiles from a large number of providers (e.g. 'OpenStreetMap',
'Stadia', 'Esri', 'CARTO', or 'Thunderforest').
Author: Timothee Giraud [cre, aut] ,
Diego Hernangomez [ctb] ,
Robert J. Hijmans [ctb] ,
Hugh A. Graham [ctb]
Maintainer: Timothee Giraud <timothee.giraud@cnrs.fr>
Diff between maptiles versions 0.8.0 dated 2024-10-22 and 0.9.0 dated 2025-02-04
maptiles-0.8.0/maptiles/R/sysdata.rda |only maptiles-0.9.0/maptiles/DESCRIPTION | 10 +- maptiles-0.9.0/maptiles/MD5 | 23 ++--- maptiles-0.9.0/maptiles/NEWS.md | 13 ++ maptiles-0.9.0/maptiles/R/get_tiles.R | 60 +++++++------ maptiles-0.9.0/maptiles/R/providers.R | 62 +++++++++----- maptiles-0.9.0/maptiles/R/utils.R | 42 ++++++++- maptiles-0.9.0/maptiles/README.md | 9 +- maptiles-0.9.0/maptiles/inst/tinytest/test_maptiles.R | 13 +- maptiles-0.9.0/maptiles/man/figures/README-example-1.png |binary maptiles-0.9.0/maptiles/man/figures/README-example2-1.png |binary maptiles-0.9.0/maptiles/man/figures/README-front.png |binary maptiles-0.9.0/maptiles/man/get_tiles.Rd | 55 +++++++----- 13 files changed, 189 insertions(+), 98 deletions(-)
Title: Fast Functions for Prime Numbers
Description: Fast functions for dealing with prime numbers, such as testing
whether a number is prime and generating a sequence prime numbers.
Additional functions include finding prime factors and Ruth-Aaron pairs,
finding next and previous prime numbers in the series, finding or estimating
the nth prime, estimating the number of primes less than or equal to an
arbitrary number, computing primorials, prime k-tuples (e.g., twin primes),
finding the greatest common divisor and smallest (least) common multiple,
testing whether two numbers are coprime, and computing Euler's totient
function. Most functions are vectorized for speed and convenience.
Author: Os Keyes [aut],
Paul Egeler [aut, cre]
Maintainer: Paul Egeler <paulegeler@gmail.com>
Diff between primes versions 1.6.0 dated 2024-01-08 and 1.6.1 dated 2025-02-04
primes-1.6.0/primes/tests/failures |only primes-1.6.1/primes/DESCRIPTION | 18 +++++++++--------- primes-1.6.1/primes/MD5 | 7 +++---- primes-1.6.1/primes/R/phi.R | 2 +- primes-1.6.1/primes/README.md | 2 +- 5 files changed, 14 insertions(+), 15 deletions(-)
Title: Single-Source Capture-Recapture Models
Description: Implementation of single-source capture-recapture methods for population size estimation using zero-truncated, zero-one truncated and zero-truncated one-inflated Poisson, Geometric and Negative Binomial regression as well as Zelterman's and Chao's regression. Package includes point and interval estimators for the population size with variances estimated using analytical or bootstrap method. Details can be found in: van der Heijden et all. (2003) <doi:10.1191/1471082X03st057oa>, Böhning and van der Heijden (2019) <doi:10.1214/18-AOAS1232>, Böhning et al. (2020) Capture-Recapture Methods for the Social and Medical Sciences or Böhning and Friedl (2021) <doi:10.1007/s10260-021-00556-8>.
Author: Piotr Chlebicki [aut, ctb] ,
Maciej Beresewicz [aut, cre]
Maintainer: Maciej Beresewicz <maciej.beresewicz@ue.poznan.pl>
Diff between singleRcapture versions 0.2.1.4 dated 2025-01-07 and 0.2.2 dated 2025-02-04
singleRcapture-0.2.1.4/singleRcapture/R/methodsNotWorking.R |only singleRcapture-0.2.2/singleRcapture/DESCRIPTION | 22 - singleRcapture-0.2.2/singleRcapture/MD5 | 132 +++++----- singleRcapture-0.2.2/singleRcapture/NAMESPACE | 8 singleRcapture-0.2.2/singleRcapture/NEWS.md | 10 singleRcapture-0.2.2/singleRcapture/R/Chao.R | 12 singleRcapture-0.2.2/singleRcapture/R/Hurdleztgeom.R | 79 +++-- singleRcapture-0.2.2/singleRcapture/R/Hurdleztnegbin.R | 66 ++--- singleRcapture-0.2.2/singleRcapture/R/Hurdleztpoisson.R | 31 +- singleRcapture-0.2.2/singleRcapture/R/Internals.R | 71 +---- singleRcapture-0.2.2/singleRcapture/R/control.R | 10 singleRcapture-0.2.2/singleRcapture/R/data.R | 2 singleRcapture-0.2.2/singleRcapture/R/estimatePopsize.R | 123 +-------- singleRcapture-0.2.2/singleRcapture/R/estimatePopsizeFit.R | 32 -- singleRcapture-0.2.2/singleRcapture/R/leave-one-out.R | 5 singleRcapture-0.2.2/singleRcapture/R/linkFunctions.R | 99 +++---- singleRcapture-0.2.2/singleRcapture/R/marginal.R | 8 singleRcapture-0.2.2/singleRcapture/R/miscDiagnostics.R | 5 singleRcapture-0.2.2/singleRcapture/R/nonparametricBootstrap.R | 35 -- singleRcapture-0.2.2/singleRcapture/R/oiztgeom.R | 37 +- singleRcapture-0.2.2/singleRcapture/R/oiztnegbin.R | 18 - singleRcapture-0.2.2/singleRcapture/R/oiztpoisson.R | 17 - singleRcapture-0.2.2/singleRcapture/R/parametricBootstrap.R | 8 singleRcapture-0.2.2/singleRcapture/R/plots.R | 63 +--- singleRcapture-0.2.2/singleRcapture/R/predict.R | 2 singleRcapture-0.2.2/singleRcapture/R/sandwichMethods.R | 23 + singleRcapture-0.2.2/singleRcapture/R/semiparametricBootstrap.R | 3 singleRcapture-0.2.2/singleRcapture/R/simulate.R | 1 singleRcapture-0.2.2/singleRcapture/R/smallMethods.R | 9 singleRcapture-0.2.2/singleRcapture/R/strataEstimation.R | 19 - singleRcapture-0.2.2/singleRcapture/R/summary.R | 4 singleRcapture-0.2.2/singleRcapture/R/updates.R | 3 singleRcapture-0.2.2/singleRcapture/R/zelterman.R | 10 singleRcapture-0.2.2/singleRcapture/R/zotgeom.R | 7 singleRcapture-0.2.2/singleRcapture/R/zotnegbin.R | 39 +- singleRcapture-0.2.2/singleRcapture/R/zotpoisson.R | 16 - singleRcapture-0.2.2/singleRcapture/R/ztHurdlegeom.R | 24 + singleRcapture-0.2.2/singleRcapture/R/ztHurdlenegbin.R | 29 -- singleRcapture-0.2.2/singleRcapture/R/ztHurdlepoisson.R | 32 +- singleRcapture-0.2.2/singleRcapture/R/ztgeom.R | 15 - singleRcapture-0.2.2/singleRcapture/R/ztnegbin.R | 84 +----- singleRcapture-0.2.2/singleRcapture/R/ztoigeom.R | 26 - singleRcapture-0.2.2/singleRcapture/R/ztoinegbin.R | 18 - singleRcapture-0.2.2/singleRcapture/R/ztoipoisson.R | 33 +- singleRcapture-0.2.2/singleRcapture/R/ztpoisson.R | 8 singleRcapture-0.2.2/singleRcapture/README.md | 67 ++--- singleRcapture-0.2.2/singleRcapture/build/singleRcapture.pdf |binary singleRcapture-0.2.2/singleRcapture/build/stage23.rdb |binary singleRcapture-0.2.2/singleRcapture/build/vignette.rds |only singleRcapture-0.2.2/singleRcapture/inst/doc |only singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_developer_only.R | 1 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_inflated_hurdle.R | 2 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_singleRcapture.R | 1 singleRcapture-0.2.2/singleRcapture/inst/tinytest/test_zerotruncated.R | 1 singleRcapture-0.2.2/singleRcapture/man/estimatePopsize.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/estimatePopsizeFit.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/figures/README-plot-example-1.png |only singleRcapture-0.2.2/singleRcapture/man/figures/README-plot-inflated-1.png |only singleRcapture-0.2.2/singleRcapture/man/figures/README-unnamed-chunk-5-1.png |binary singleRcapture-0.2.2/singleRcapture/man/marginalFreq.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/netherlandsimmigrant.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/plot.singleRStaticCountData.Rd | 4 singleRcapture-0.2.2/singleRcapture/man/popSizeEst.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/predict.singleRStaticCountData.Rd | 5 singleRcapture-0.2.2/singleRcapture/man/redoPopEstimation.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/summary.singleRmargin.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/vcov.singleRStaticCountData.Rd | 2 singleRcapture-0.2.2/singleRcapture/man/vcovHC.singleRStaticCountData.Rd | 2 singleRcapture-0.2.2/singleRcapture/vignettes |only 69 files changed, 563 insertions(+), 834 deletions(-)
More information about singleRcapture at CRAN
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