Title: Modeling with Unmeasured Confounding
Description: Tools for fitting and assessing Bayesian multilevel regression
models that account for unmeasured confounders.
Author: Ryan Hebdon [aut],
James Stamey [aut] ,
David Kahle [aut, cre] ,
Xiang Zhang [aut]
Maintainer: David Kahle <david@kahle.io>
Diff between unmconf versions 0.1.0 dated 2023-12-12 and 1.0.0 dated 2024-09-09
DESCRIPTION | 14 MD5 | 31 - NAMESPACE | 2 R/runm.R | 5 R/unm_glm.R | 410 ++++++++++++- R/unm_summary-old-documentation.R |only R/unm_summary.R | 105 +++ R/unmconf-package.R | 4 build/vignette.rds |binary inst/doc/unmconf.R | 28 inst/doc/unmconf.Rmd | 94 +-- inst/doc/unmconf.html | 1143 ++++++++++++++++++++------------------ man/runm.Rd | 2 man/unm_glm.Rd | 357 +++++++++++ man/unm_summary.Rd | 100 +++ man/unmconf.Rd | 3 vignettes/unmconf.Rmd | 94 +-- 17 files changed, 1685 insertions(+), 707 deletions(-)
Title: Statistical Tools for Filebacked Big Matrices
Description: Easy-to-use, efficient, flexible and scalable statistical tools.
Package bigstatsr provides and uses Filebacked Big Matrices via memory-mapping.
It provides for instance matrix operations, Principal Component Analysis,
sparse linear supervised models, utility functions and more
<doi:10.1093/bioinformatics/bty185>.
Author: Florian Prive [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths]
Maintainer: Florian Prive <florian.prive.21@gmail.com>
Diff between bigstatsr versions 1.5.12 dated 2022-10-14 and 1.6.1 dated 2024-09-09
DESCRIPTION | 10 - MD5 | 84 +++++++------- NAMESPACE | 210 +++++++++++++++++------------------ NEWS.md | 16 ++ R/FBM.R | 11 + R/biglasso.R | 2 R/bigstatsr-package.R | 8 - R/crossprodSelf.R | 14 +- R/plot.R | 35 +++-- R/randomSVD.R | 27 +++- R/read-write.R | 2 R/scaling.R | 2 R/tcrossprodSelf.R | 2 R/utils-assert.R | 11 + README.md | 2 build/partial.rdb |binary inst/CITATION | 23 +-- inst/WORDLIST | 3 man/FBM-class.Rd | 10 - man/FBM.code256-class.Rd | 6 - man/big_SVD.Rd | 8 - man/big_copy.Rd | 6 - man/big_cor.Rd | 15 +- man/big_cprodMat.Rd | 8 - man/big_crossprodSelf.Rd | 15 +- man/big_prodMat.Rd | 8 - man/big_read.Rd | 2 man/big_spLinReg.Rd | 2 man/big_spLogReg.Rd | 2 man/big_tcrossprodSelf.Rd | 8 - man/big_transpose.Rd | 6 - man/bigstatsr-package.Rd | 10 - man/theme_bigstatsr.Rd | 40 +++--- src/FBM-replace.cpp | 20 +-- src/Makevars | 2 src/RcppExports.cpp | 5 tests/testthat/helper-init.R | 8 + tests/testthat/test-FBM-convert.R | 30 +++-- tests/testthat/test-bigmemory.R | 4 tests/testthat/test-cor.R | 4 tests/testthat/test-crossprodSelf.R | 17 ++ tests/testthat/test-randomSVD.R | 19 +++ tests/testthat/test-tcrossprodSelf.R | 12 ++ 43 files changed, 432 insertions(+), 297 deletions(-)
Title: Collection of Functions for Working with Age Intervals
Description: Provides a collection of efficient functions for working with
individual ages and corresponding intervals. These include functions for
conversion from an age to an interval, aggregation of ages with associated
counts in to intervals and the splitting of interval counts based on
specified age distributions.
Author: Tim Taylor [aut, cre, cph] ,
Edwin van Leeuwen [aut]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between ageutils versions 0.0.4 dated 2024-06-26 and 0.0.5 dated 2024-09-09
ageutils-0.0.4/ageutils/R/aggregate_age_counts.R |only ageutils-0.0.4/ageutils/R/reaggregate_interval_counts.R |only ageutils-0.0.4/ageutils/R/reaggregate_interval_rates.R |only ageutils-0.0.4/ageutils/R/split_interval_counts.R |only ageutils-0.0.4/ageutils/R/standalone-assertions.R |only ageutils-0.0.4/ageutils/build |only ageutils-0.0.4/ageutils/inst |only ageutils-0.0.4/ageutils/man/aggregate_age_counts.Rd |only ageutils-0.0.4/ageutils/man/reaggregate_interval_counts.Rd |only ageutils-0.0.4/ageutils/man/reaggregate_interval_rates.Rd |only ageutils-0.0.4/ageutils/man/split_interval_counts.Rd |only ageutils-0.0.4/ageutils/src/breaks_to_interval.c |only ageutils-0.0.4/ageutils/tests/tinytest.R |only ageutils-0.0.4/ageutils/vignettes |only ageutils-0.0.5/ageutils/DESCRIPTION | 19 +- ageutils-0.0.5/ageutils/MD5 | 64 ++++---- ageutils-0.0.5/ageutils/NAMESPACE | 8 + ageutils-0.0.5/ageutils/NEWS.md | 18 ++ ageutils-0.0.5/ageutils/R/ageutils-package.R | 4 ageutils-0.0.5/ageutils/R/breaks_to_interval.R | 47 +++--- ageutils-0.0.5/ageutils/R/cut_ages.R | 73 ---------- ageutils-0.0.5/ageutils/R/deprecated.R |only ageutils-0.0.5/ageutils/R/reaggregate_counts.R |only ageutils-0.0.5/ageutils/R/reaggregate_rates.R |only ageutils-0.0.5/ageutils/R/wip.R | 17 -- ageutils-0.0.5/ageutils/man/ageutils-deprecated.Rd |only ageutils-0.0.5/ageutils/man/ageutils-package.Rd | 4 ageutils-0.0.5/ageutils/man/aggregate_age_counts-deprecated.Rd |only ageutils-0.0.5/ageutils/man/breaks_to_interval.Rd | 17 +- ageutils-0.0.5/ageutils/man/reaggregate_counts.Rd |only ageutils-0.0.5/ageutils/man/reaggregate_interval_counts-deprecated.Rd |only ageutils-0.0.5/ageutils/man/reaggregate_interval_rates-deprecated.Rd |only ageutils-0.0.5/ageutils/man/reaggregate_rates.Rd |only ageutils-0.0.5/ageutils/man/split_interval_counts-deprecated.Rd |only ageutils-0.0.5/ageutils/src/aggregate_age_counts.c | 2 ageutils-0.0.5/ageutils/src/init.c | 2 ageutils-0.0.5/ageutils/tests/testthat |only ageutils-0.0.5/ageutils/tests/testthat.R |only 38 files changed, 108 insertions(+), 167 deletions(-)
Title: Parametric and Non-Parametric Copula-Based Imputation Methods
Description: Copula-based imputation methods: parametric and non-parametric algorithms for missing multivariate data through conditional copulas.
Author: Francesca Marta Lilja Di Lascio [aut, cre],
Aurora Gatto [aut],
Simone Giannerini [aut]
Maintainer: Francesca Marta Lilja Di Lascio <marta.dilascio@unibz.it>
Diff between CoImp versions 2.0.0 dated 2024-05-09 and 2.0.1 dated 2024-09-09
ChangeLog | 12 +++++++++--- DESCRIPTION | 8 ++++---- MD5 | 27 ++++++++++++++------------- R/NPCoImp.R | 8 ++++---- inst |only man/CoImp-class.Rd | 9 ++++++--- man/CoImp.Rd | 14 ++++++++++---- man/MAR-class.Rd | 4 ++-- man/MAR.Rd | 8 ++++++-- man/MCAR-class.Rd | 3 ++- man/MCAR.Rd | 8 ++++++-- man/NPCoImp-class.Rd | 9 +++++---- man/NPCoImp.Rd | 24 ++++++++++++++---------- man/PerfMeasure-class.Rd | 8 +++++--- man/PerfMeasure.Rd | 11 ++++++++--- 15 files changed, 95 insertions(+), 58 deletions(-)
Title: Single Nucleotide Polymorphisms Linkage Disequilibrium
Visualizations
Description: Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.
Author: Thomas Charlon [aut, cre] ,
Karl Forner [aut],
Alessandro Di Cara [aut],
Jerome Wojcik [aut]
Maintainer: Thomas Charlon <charlon@protonmail.com>
Diff between snplinkage versions 1.0.0 dated 2023-05-04 and 1.2.0 dated 2024-09-09
DESCRIPTION | 15 +-- MD5 | 69 ++++++++++--- NAMESPACE | 59 +++++++++++ NEWS.md |only R/0_imports.R | 16 +++ R/4_methods.R | 134 +++++++++++++++++++++++++++ R/5_methods_genotype_data_subset.R | 14 ++ R/geno_data_fetch.R | 6 + R/ggplots_ld.R | 6 - R/gtable_associations.R | 96 +++++++++++++++++-- R/gtable_ld.R | 85 +++++++++++++++-- R/snprelate_qc.R | 7 + build/partial.rdb |binary build/vignette.rds |binary data |only inst/doc/customize.R |only inst/doc/customize.Rmd |only inst/doc/customize.html |only inst/doc/snplinkage.pdf |binary man/crohn.Rd |only man/fetch_allele1.GdsGenotypeReader.Rd |only man/fetch_allele1.GenotypeData.Rd |only man/fetch_allele1.GenotypeDataSubset.Rd |only man/fetch_allele1.default.Rd |only man/fetch_allele2.GdsGenotypeReader.Rd |only man/fetch_allele2.GenotypeData.Rd |only man/fetch_allele2.GenotypeDataSubset.Rd |only man/fetch_allele2.default.Rd |only man/fetch_gds.GdsGenotypeReader.Rd |only man/fetch_gds.GenotypeData.Rd |only man/fetch_gds.GenotypeDataSubset.Rd |only man/fetch_gds.default.Rd |only man/get_scan_annot.GenotypeData.Rd |only man/get_scan_annot.GenotypeDataSubset.Rd |only man/get_snp_annot.GenotypeData.Rd |only man/get_snp_annot.GenotypeDataSubset.Rd |only man/gtable_ld.Rd | 12 ++ man/gtable_ld_associations_combine.Rd |only man/gtable_ld_associations_gdata.Rd | 19 +++ man/gtable_ld_gdata.Rd | 11 ++ man/gtable_ld_grobs.Rd |only man/is_snp_first_dim.GdsGenotypeReader.Rd |only man/is_snp_first_dim.GenotypeData.Rd |only man/is_snp_first_dim.MatrixGenotypeReader.Rd |only man/is_snp_first_dim.NcdfGenotypeReader.Rd |only man/is_snp_first_dim.default.Rd |only man/is_snp_first_dim.gds.class.Rd |only man/load_gds_as_genotype_data.Rd | 6 + man/snprelate_qc.Rd | 7 + vignettes/biblio.bib | 21 ++-- vignettes/customize.Rmd |only 51 files changed, 531 insertions(+), 52 deletions(-)
Title: Generalized Latent Markov Models
Description: Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.
Author: Francesco Bartolucci [aut, cre],
Silvia Pandolfi [aut],
Fulvia Pennoni [aut],
Alessio Farcomeni [ctb],
Alessio Serafini [ctb]
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between LMest versions 3.2.0 dated 2024-08-30 and 3.2.1 dated 2024-09-09
DESCRIPTION | 8 ++--- MD5 | 10 +++--- R/lmestMc.R | 24 +++------------ R/mccov.R | 70 ++++++++++++++++++-------------------------- inst/doc/vignetteLMest.html | 6 +-- man/data_employment_sim.Rd | 2 - 6 files changed, 48 insertions(+), 72 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.14 dated 2024-07-03 and 1.9.15 dated 2024-09-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 9 +++++++++ inst/include/TMB.hpp | 10 ++++++++++ inst/include/TMBad/TMBad.cpp | 6 +++--- inst/include/TMBad/config.hpp | 3 +++ inst/include/config.hpp | 1 + 7 files changed, 36 insertions(+), 13 deletions(-)
Title: Estimators of Prediction Accuracy for Time-to-Event Data
Description: Provides a variety of functions to estimate
time-dependent true/false positive rates and AUC curves from a
set of censored survival data.
Author: Sergej Potapov [aut],
Werner Adler [aut],
Matthias Schmid [aut],
Frederic Bertrand [cre, aut]
Maintainer: Frederic Bertrand <frederic.bertrand@utt.fr>
Diff between survAUC versions 1.2-0 dated 2023-03-21 and 1.3-0 dated 2024-09-09
DESCRIPTION | 20 ++++++++++---- MD5 | 18 ++++++------- NEWS.md | 4 ++ src/survAUC_Cham_Diao.c | 17 ++++++------ src/survAUC_HZ.c | 23 ++++++++-------- src/survAUC_Hung_Chiang.c | 31 +++++++++++----------- src/survAUC_SongZhou.c | 27 ++++++++++--------- src/survAUC_UNO.c | 25 +++++++++--------- src/surv_measures.c | 63 +++++++++++++++++++++++----------------------- src/utils.c | 19 +++++++------ 10 files changed, 133 insertions(+), 114 deletions(-)
Title: Spatially Varying and Spatio-Temporal Dynamic Linear Models
Description: Fits, spatially predicts, and temporally forecasts space-time data using Gaussian Process (GP): (1) spatially varying coefficient process models and (2) spatio-temporal dynamic linear models. Bakar et al., (2016). Bakar et al., (2015).
Author: K. Shuvo Bakar [aut, cre] ,
Philip Kokic [ctb],
Huidong Jin [ctb]
Maintainer: K. Shuvo Bakar <shuvo.bakar@gmail.com>
Diff between spTDyn versions 2.0.2 dated 2022-11-22 and 2.0.3 dated 2024-09-09
DESCRIPTION | 30 +++- MD5 | 14 +- inst/CITATION | 73 +++--------- inst/ChangeLog | 6 man/predict.spTD.Rd | 2 man/spTDyn-package.Rd | 2 src/gibbs_gp.c | 301 -------------------------------------------------- src/mathematics.c | 18 +- 8 files changed, 70 insertions(+), 376 deletions(-)
Title: Cryptographic Hash, Extendable-Output and Base64 Functions
Description: Fast and memory-efficient streaming hash functions and base64
encoding / decoding. Hashes strings and raw vectors directly. Stream hashes
files potentially larger than memory, as well as in-memory objects through
R's serialization mechanism. Implementations include the SHA-256, SHA-3 and
'Keccak' cryptographic hash functions, SHAKE256 extendable-output function
(XOF), and 'SipHash' pseudo-random function.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between secretbase versions 1.0.1 dated 2024-07-22 and 1.0.2 dated 2024-09-09
DESCRIPTION | 17 +++++++++-------- MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/secret.R | 12 ++++++------ README.md | 13 ++++++------- man/secretbase-package.Rd | 12 ++++++------ src/base.c | 6 +++--- src/secret.c | 8 ++++---- src/secret.h | 46 +++++++++++++++++++++++++--------------------- src/secret2.c | 4 ++-- src/secret3.c | 4 ++-- 11 files changed, 77 insertions(+), 69 deletions(-)
Title: Paleoecology Functions for Regime Shift Analysis
Description: Contains a variety of functions, based around
regime shift analysis of paleoecological data.
Citations:
Rodionov() from Rodionov (2004) <doi:10.1029/2004GL019448>
Lanzante() from Lanzante (1996) <doi:10.1002/(SICI)1097-0088(199611)16:11%3C1197::AID-JOC89%3E3.0.CO;2-L>
Hellinger_trans from Numerical Ecology, Legendre & Legendre (ISBN 9780444538680)
rolling_autoc from Liu, Gao & Wang (2018) <doi:10.1016/j.scitotenv.2018.06.276>
Sample data sets lake_data & lake_RSI processed from Bush, Silman & Urrego (2004) <doi:10.1126/science.1090795>
Sample data set January_PDO from NOAA: <https://www.ncei.noaa.gov/access/monitoring/pdo/>.
Author: Alex H. Room [aut, cre, cph] ,
Felipe Franco-Gaviria [ctb, fnd]
,
Dunia H. Urrego [ctb, fnd] ,
The authors of the dependency Rust crates [ctb]
Maintainer: Alex H. Room <alexhroom+cran@protonmail.com>
Diff between rshift versions 3.1.0 dated 2024-09-03 and 3.1.1 dated 2024-09-09
DESCRIPTION | 6 ++--- LICENSE.note | 52 ++++++++++------------------------------------- MD5 | 12 +++++----- inst/AUTHORS | 41 +++++++++++-------------------------- inst/doc/STARSmanual.pdf |binary src/rust/Cargo.toml | 4 +-- src/rust/vendor.tar.xz |binary 7 files changed, 36 insertions(+), 79 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Feature selection package of the 'mlr3' ecosystem. It selects
the optimal feature set for any 'mlr3' learner. The package works with
several optimization algorithms e.g. Random Search, Recursive Feature
Elimination, and Genetic Search. Moreover, it can automatically
optimize learners and estimate the performance of optimized feature
sets with nested resampling.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
John Zobolas [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 1.0.0 dated 2024-06-29 and 1.1.0 dated 2024-09-09
DESCRIPTION | 8 ++-- MD5 | 26 +++++++-------- NAMESPACE | 1 NEWS.md | 7 ++++ R/ArchiveBatchFSelect.R | 13 ++++++- R/FSelectorBatch.R | 7 +++- R/FSelectorBatchFromOptimizerBatch.R | 7 +++- R/mlr_callbacks.R | 10 +++++ R/zzz.R | 6 +-- man/ArchiveBatchFSelect.Rd | 28 ++++++++++++++++ man/AutoFSelector.Rd | 1 tests/testthat/test_ArchiveFSelect.R | 32 +++++++++---------- tests/testthat/test_FSelectInstanceSingleCrit.R | 14 ++++++++ tests/testthat/test_extract_inner_fselect_archives.R | 14 ++++---- 14 files changed, 125 insertions(+), 49 deletions(-)
Title: Disaster Victim Identification
Description: Joint DNA-based disaster victim identification (DVI), as
described in Vigeland and Egeland (2021)
<doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by
optimising the joint likelihood of all victim samples and reference
individuals. Individual identification probabilities, conditional on
all available information, are derived from the joint solution in the
form of posterior pairing probabilities. 'dvir' is part of the
'pedsuite' collection of packages for pedigree analysis.
Author: Magnus Dehli Vigeland [aut, cre]
,
Thore Egeland [aut]
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between dvir versions 3.2.1 dated 2023-10-15 and 3.3.0 dated 2024-09-09
dvir-3.2.1/dvir/man/combineSummaries.Rd |only dvir-3.3.0/dvir/DESCRIPTION | 13 - dvir-3.3.0/dvir/MD5 | 95 +++++++------ dvir-3.3.0/dvir/NAMESPACE | 8 - dvir-3.3.0/dvir/NEWS.md | 17 ++ dvir-3.3.0/dvir/R/amDrivenDVI.R | 214 +++++++++++++++++------------- dvir-3.3.0/dvir/R/data.R | 45 ++++++ dvir-3.3.0/dvir/R/dviCompare.R | 3 dvir-3.3.0/dvir/R/dviData.R | 30 ++-- dvir-3.3.0/dvir/R/dviGLR.R |only dvir-3.3.0/dvir/R/dviJoint.R |only dvir-3.3.0/dvir/R/dviSim.R | 87 ++++++++---- dvir-3.3.0/dvir/R/dviSolve.R | 93 +++++++------ dvir-3.3.0/dvir/R/dvir-package.R | 2 dvir-3.3.0/dvir/R/expand.grid.nodup.R | 2 dvir-3.3.0/dvir/R/familias2dvir.R | 65 ++++----- dvir-3.3.0/dvir/R/findExcluded.R | 2 dvir-3.3.0/dvir/R/findNonidentifiable.R | 15 -- dvir-3.3.0/dvir/R/findUndisputed.R | 51 ++----- dvir-3.3.0/dvir/R/formatSummary.R |only dvir-3.3.0/dvir/R/generatePairings.R | 3 dvir-3.3.0/dvir/R/jointDVI.R | 8 - dvir-3.3.0/dvir/R/mergePM.R | 72 +++++----- dvir-3.3.0/dvir/R/pairwiseGLR.R |only dvir-3.3.0/dvir/R/pairwiseLR.R | 5 dvir-3.3.0/dvir/R/plotDVI.R | 189 +++++++++++++++++++------- dvir-3.3.0/dvir/R/relabelDVI.R | 29 ++-- dvir-3.3.0/dvir/R/utils.R | 104 ++++++-------- dvir-3.3.0/dvir/build/partial.rdb |binary dvir-3.3.0/dvir/data/KETPex481.rda |binary dvir-3.3.0/dvir/data/KETPex497.rda |binary dvir-3.3.0/dvir/data/KETPex498.rda |binary dvir-3.3.0/dvir/data/exclusionExample.rda |binary dvir-3.3.0/dvir/data/fire.rda |only dvir-3.3.0/dvir/data/grave.rda |binary dvir-3.3.0/dvir/data/icmp.rda |binary dvir-3.3.0/dvir/data/planecrash.rda |binary dvir-3.3.0/dvir/data/symmetricSibs.rda |only dvir-3.3.0/dvir/man/amDrivenDVI.Rd | 2 dvir-3.3.0/dvir/man/directMatch.Rd | 13 + dvir-3.3.0/dvir/man/dviGLR.Rd |only dvir-3.3.0/dvir/man/dviJoint.Rd |only dvir-3.3.0/dvir/man/dviSim.Rd | 105 ++++++++------ dvir-3.3.0/dvir/man/dviSolve.Rd | 4 dvir-3.3.0/dvir/man/familias2dvir.Rd | 9 - dvir-3.3.0/dvir/man/findUndisputed.Rd | 4 dvir-3.3.0/dvir/man/fire.Rd |only dvir-3.3.0/dvir/man/formatSummary.Rd |only dvir-3.3.0/dvir/man/generatePairings.Rd | 3 dvir-3.3.0/dvir/man/getSimpleFams.Rd | 6 dvir-3.3.0/dvir/man/icmp.Rd | 2 dvir-3.3.0/dvir/man/plotDVI.Rd | 32 +++- dvir-3.3.0/dvir/man/relabelDVI.Rd | 8 + dvir-3.3.0/dvir/man/swapOrientation.Rd |only dvir-3.3.0/dvir/man/symmetricSibs.Rd |only 55 files changed, 823 insertions(+), 517 deletions(-)
Title: A Collection of Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis.
Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included.
The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000).
Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018).
"An elliptically symmetric angular Gaussian distribution". Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>.
b) Tsagris M. and Alenazi A. (2019). "Comparison of discriminant analysis methods on the sphere".
Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>.
c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020).
"Spherical regression models with general covariates and anisotropic errors".
Statistics and Computing 30(1): 153--165. <d [...truncated...]
Author: Michail Tsagris [aut, cre],
Giorgos Athineou [aut],
Christos Adam [aut],
Anamul Sajib [ctb],
Eli Amson [ctb],
Micah J. Waldstein [ctb],
Zehao Yu [aut]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 6.7 dated 2024-07-05 and 6.8 dated 2024-09-09
Directional-6.7/Directional/R/esag.da.R |only Directional-6.7/Directional/R/esagda.pred.R |only Directional-6.7/Directional/R/purka.da.R |only Directional-6.7/Directional/R/purkada.pred.R |only Directional-6.7/Directional/R/vmf.da.R |only Directional-6.7/Directional/R/vmfda.pred.R |only Directional-6.7/Directional/man/esag.da.Rd |only Directional-6.7/Directional/man/esagda.pred.Rd |only Directional-6.7/Directional/man/purka.da.Rd |only Directional-6.7/Directional/man/purkada.pred.Rd |only Directional-6.7/Directional/man/vmf.da.Rd |only Directional-6.7/Directional/man/vmfda.pred.Rd |only Directional-6.8/Directional/DESCRIPTION | 40 +++ Directional-6.8/Directional/MD5 | 86 +++---- Directional-6.8/Directional/R/ESAGd.mle.R |only Directional-6.8/Directional/R/circpurka.reg.R | 4 Directional-6.8/Directional/R/dESAGd.R |only Directional-6.8/Directional/R/dirda.R |only Directional-6.8/Directional/R/dirda.cv.R | 188 ++++++++++++----- Directional-6.8/Directional/R/dpkbd.R | 2 Directional-6.8/Directional/R/dsespc.R | 4 Directional-6.8/Directional/R/dspcauchy.R | 2 Directional-6.8/Directional/R/esag.mle.R | 62 ++--- Directional-6.8/Directional/R/esag.reg.R | 2 Directional-6.8/Directional/R/ggvm.mle.R | 3 Directional-6.8/Directional/R/iag.mle.R | 39 +++ Directional-6.8/Directional/R/iagd.R | 50 +++- Directional-6.8/Directional/R/kent.mle.R | 2 Directional-6.8/Directional/R/mmvm.mle.R | 2 Directional-6.8/Directional/R/pkbd.mle.R | 77 ++++-- Directional-6.8/Directional/R/pkbd.mle2.R |only Directional-6.8/Directional/R/pkbd.reg.R |only Directional-6.8/Directional/R/pkbd.reg2.R |only Directional-6.8/Directional/R/pkbd2test.R |only Directional-6.8/Directional/R/rESAGd.R |only Directional-6.8/Directional/R/rpkbd.R | 23 +- Directional-6.8/Directional/R/sespc.reg.R | 2 Directional-6.8/Directional/R/spcauchy.reg.R |only Directional-6.8/Directional/R/spcauchy2test.R |only Directional-6.8/Directional/R/vmfreg.R |only Directional-6.8/Directional/R/wood.mle.R | 2 Directional-6.8/Directional/man/Directional-package.Rd | 7 Directional-6.8/Directional/man/desag.Rd | 22 + Directional-6.8/Directional/man/dirda.Rd |only Directional-6.8/Directional/man/dirda.cv.Rd | 66 ++--- Directional-6.8/Directional/man/dirknn.Rd | 6 Directional-6.8/Directional/man/dirknn.tune.Rd | 2 Directional-6.8/Directional/man/dvmf.Rd | 6 Directional-6.8/Directional/man/esag.mle.Rd | 40 ++- Directional-6.8/Directional/man/esag.reg.Rd | 4 Directional-6.8/Directional/man/iag.reg.Rd | 2 Directional-6.8/Directional/man/resag.Rd | 22 + Directional-6.8/Directional/man/spcauchy2test.Rd |only Directional-6.8/Directional/man/spml.mle.Rd | 8 Directional-6.8/Directional/man/vmf.mle.Rd | 30 +- Directional-6.8/Directional/man/vmfreg.Rd |only Directional-6.8/Directional/man/wood.mle.Rd | 1 57 files changed, 517 insertions(+), 289 deletions(-)
Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js',
a re-usable easy interface JavaScript chart library, based on D3 v4+.
Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts.
All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
NAVER Corp [cph] ,
Mike Bostock [cph]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between billboarder versions 0.4.1 dated 2023-09-29 and 0.5.0 dated 2024-09-09
DESCRIPTION | 8 MD5 | 68 NAMESPACE | 1 NEWS.md | 258 - R/bb_helpers.R | 2 R/bb_labs.R | 134 R/bb_utils.R | 23 R/billboarder-package.R | 3 R/billboarder.R | 184 R/theme.R | 6 R/utils.R | 8 README.md | 4 build/vignette.rds |binary inst/doc/billboarder-intro.R | 184 inst/doc/billboarder-intro.html | 3985 ++++++++-------- inst/doc/billboarder-mapping.R | 120 inst/doc/billboarder-mapping.html | 3851 +++++++-------- inst/doc/billboarder-options.R | 330 - inst/doc/billboarder-options.html | 4119 ++++++++--------- inst/doc/billboarder.R | 737 +-- inst/doc/billboarder.Rmd | 49 inst/doc/billboarder.html | 4581 +++++++++---------- inst/htmlwidgets/billboarder.js | 891 +-- inst/htmlwidgets/lib/billboard/billboard.min.css | 18 inst/htmlwidgets/lib/billboard/billboard.pkgd.min.js | 84 inst/htmlwidgets/lib/billboard/datalab.min.css | 18 inst/htmlwidgets/lib/billboard/graph.min.css | 18 inst/htmlwidgets/lib/billboard/insight.min.css | 18 inst/htmlwidgets/lib/billboard/modern.min.css |only inst/htmlwidgets/update.R | 1 man/bb_labs.Rd | 11 man/bb_padding.Rd |only man/bb_treemapchart.Rd | 3 man/billboard-theme.Rd | 6 man/billboarder-package.Rd | 9 vignettes/billboarder.Rmd | 49 36 files changed, 9866 insertions(+), 9915 deletions(-)
Title: Black-Box Optimization Toolkit
Description: Features highly configurable search spaces via the 'paradox'
package and optimizes every user-defined objective function. The
package includes several optimization algorithms e.g. Random Search,
Iterated Racing, Bayesian Optimization (in 'mlr3mbo') and Hyperband
(in 'mlr3hyperband'). bbotk is the base package of 'mlr3tuning',
'mlr3fselect' and 'miesmuschel'.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 1.0.1 dated 2024-07-24 and 1.1.0 dated 2024-09-09
bbotk-1.0.1/bbotk/build/vignette.rds |only bbotk-1.0.1/bbotk/inst/doc |only bbotk-1.0.1/bbotk/man/evaluate_queue_default.Rd |only bbotk-1.0.1/bbotk/tests/testthat/test_Callback.R |only bbotk-1.0.1/bbotk/vignettes |only bbotk-1.1.0/bbotk/DESCRIPTION | 31 +- bbotk-1.1.0/bbotk/MD5 | 84 +++--- bbotk-1.1.0/bbotk/NAMESPACE | 3 bbotk-1.1.0/bbotk/NEWS.md | 8 bbotk-1.1.0/bbotk/R/CallbackAsync.R | 40 ++- bbotk-1.1.0/bbotk/R/CallbackBatch.R | 5 bbotk-1.1.0/bbotk/R/ContextAsync.R | 42 +++ bbotk-1.1.0/bbotk/R/OptimInstanceAsync.R | 45 +++ bbotk-1.1.0/bbotk/R/OptimizerAsync.R | 31 -- bbotk-1.1.0/bbotk/R/OptimizerAsyncDesignPoints.R | 7 bbotk-1.1.0/bbotk/R/OptimizerAsyncGridSearch.R | 5 bbotk-1.1.0/bbotk/R/OptimizerAsyncRandomSearch.R | 14 - bbotk-1.1.0/bbotk/R/OptimizerBatch.R | 1 bbotk-1.1.0/bbotk/R/OptimizerBatchLocalSearch.R |only bbotk-1.1.0/bbotk/R/TerminatorStagnationHypervolume.R |only bbotk-1.1.0/bbotk/R/mlr_callbacks.R | 3 bbotk-1.1.0/bbotk/R/zzz.R | 2 bbotk-1.1.0/bbotk/README.md | 123 +++------- bbotk-1.1.0/bbotk/man/CallbackAsync.Rd | 8 bbotk-1.1.0/bbotk/man/ContextAsync.Rd | 12 bbotk-1.1.0/bbotk/man/Terminator.Rd | 3 bbotk-1.1.0/bbotk/man/callback_async.Rd | 16 + bbotk-1.1.0/bbotk/man/callback_batch.Rd | 6 bbotk-1.1.0/bbotk/man/mlr_optimizers_local_search.Rd |only bbotk-1.1.0/bbotk/man/mlr_terminators.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_clock_time.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_combo.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_evals.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_none.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_perf_reached.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_run_time.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_stagnation.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_stagnation_batch.Rd | 3 bbotk-1.1.0/bbotk/man/mlr_terminators_stagnation_hypervolume.Rd |only bbotk-1.1.0/bbotk/tests/testthat/_snaps/Objective.md | 12 bbotk-1.1.0/bbotk/tests/testthat/_snaps/OptimizerLocalSearch.md |only bbotk-1.1.0/bbotk/tests/testthat/test_CallbackAsync.R |only bbotk-1.1.0/bbotk/tests/testthat/test_CallbackBatch.R |only bbotk-1.1.0/bbotk/tests/testthat/test_OptimInstanceAsyncSingleCrit.R | 22 + bbotk-1.1.0/bbotk/tests/testthat/test_OptimizerAsynDesignPoints.R | 3 bbotk-1.1.0/bbotk/tests/testthat/test_OptimizerAsyncRandomSearch.R | 1 bbotk-1.1.0/bbotk/tests/testthat/test_OptimizerLocalSearch.R |only bbotk-1.1.0/bbotk/tests/testthat/test_TerminatorStagnationHypervolume.R |only bbotk-1.1.0/bbotk/tests/testthat/test_mlr_callbacks.R | 2 49 files changed, 340 insertions(+), 216 deletions(-)
Title: Explore Flora e Funga do Brasil Database
Description: A collection of functions designed to retrieve, filter and spatialize data from the Flora e Funga do Brasil dataset. For more information about the dataset, please visit <https://floradobrasil.jbrj.gov.br/consulta/>.
Author: Weverton Trindade [aut, cre]
Maintainer: Weverton Trindade <wevertonf1993@gmail.com>
Diff between florabr versions 1.2.0 dated 2024-05-16 and 1.3.0 dated 2024-09-09
DESCRIPTION | 9 MD5 | 59 - NAMESPACE | 7 NEWS.md | 13 R/check_names.R | 185 ++++- R/filter_florabr.R | 813 ++++++++++------------ R/get_binomial.R | 44 - R/get_florabr.R | 22 R/get_pam.R | 5 R/get_synonym.R | 73 +- R/helpers.R | 56 + R/select_species.R | 1273 ++++++++++++++++++----------------- R/solve_discrepancies.R | 200 ++--- R/subset_species.R | 10 README.md | 3 data/bf_data.rda |binary inst/CITATION |only inst/doc/getting_started.R | 8 inst/doc/getting_started.Rmd | 8 inst/doc/getting_started.html | 8 inst/doc/selecting_species.R | 11 inst/doc/selecting_species.Rmd | 13 inst/doc/selecting_species.html | 141 +-- man/check_names.Rd | 37 - man/get_binomial.Rd | 26 man/get_florabr.Rd | 5 man/get_synonym.Rd | 13 tests/testthat/test-get_synonym.R | 2 tests/testthat/test-subset_species.R | 3 vignettes/getting_started.Rmd | 8 vignettes/selecting_species.Rmd | 13 31 files changed, 1713 insertions(+), 1355 deletions(-)
Title: A Collection of Functions for Negligible Effect/Equivalence
Testing
Description: Researchers often want to evaluate whether there is a negligible
relationship among variables. The 'negligible' package provides functions that
are useful for conducting negligible effect testing (also called
equivalence testing). For example, there are functions for evaluating the
equivalence of means or the presence of a negligible association
(correlation or regression). Beribisky, N., Mara, C., & Cribbie, R. A. (2020) <doi:10.20982/tqmp.16.4.p424>.
Beribisky, N., Davidson, H., Cribbie, R. A. (2019) <doi:10.7717/peerj.6853>.
Shiskina, T., Farmus, L., & Cribbie, R. A. (2018) <doi:10.20982/tqmp.14.3.p167>.
Mara, C. & Cribbie, R. A. (2017) <doi:10.1080/00220973.2017.1301356>.
Counsell, A. & Cribbie, R. A. (2015) <doi:10.1111/bmsp.12045>.
van Wieringen, K. & Cribbie, R. A. (2014) <doi:10.1111/bmsp.12015>.
Goertzen, J. R. & Cribbie, R. A. (2010) <doi:10.1348/000711009x475853>.
Cribbie, R. A., Gruman, J. & Arpin-Cribbi [...truncated...]
Author: Robert Cribbie [aut, cre],
Udi Alter [aut],
Nataly Beribisky [aut],
Phil Chalmers [aut],
Alyssa Counsell [aut],
Linda Farmus [aut],
Naomi Martinez Gutierrez [aut],
Victoria Ng [ctb]
Maintainer: Robert Cribbie <cribbie@yorku.ca>
Diff between negligible versions 0.1.7 dated 2024-04-30 and 0.1.9 dated 2024-09-09
DESCRIPTION | 8 - MD5 | 6 R/neg.pd.R | 398 ++++++++++++++++++++++++++++----------------------------- R/neg.semfit.R | 9 - 4 files changed, 206 insertions(+), 215 deletions(-)
Title: Simulate DNA Methylation Dynamics on Different Genomic
Structures along Genealogies
Description: DNA methylation is an epigenetic modification involved in genomic stability,
gene regulation, development and disease.
DNA methylation occurs mainly through the addition of a methyl group to cytosines,
for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine).
Tissue-specific methylation patterns lead to genomic regions with different characteristic
methylation levels.
E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of
expressed genes tend to be unmethylated.
'MethEvolSIM' is a model-based simulation software for the generation and modification
of cytosine methylation patterns along a given tree, which can be a genealogy of
cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree.
The simulations are based on an extension of the model of
Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of
the met [...truncated...]
Author: Sara Castillo Vicente [aut, cre],
Dirk Metzler [aut, ths]
Maintainer: Sara Castillo Vicente <castillo@bio.lmu.de>
Diff between MethEvolSIM versions 0.1.5 dated 2024-08-16 and 0.1.6 dated 2024-09-09
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/multiRegion_SIM.R | 15 ++++++------- inst/doc/intro-vignette.html | 49 ++++++++++++++++++++++--------------------- 4 files changed, 39 insertions(+), 37 deletions(-)
Title: Inference of Elliptical Distributions and Copulas
Description: Provides functions for the simulation and
the nonparametric estimation of elliptical distributions,
meta-elliptical copulas and trans-elliptical distributions,
following the article Derumigny and Fermanian (2022) <doi:10.1016/j.jmva.2022.104962>.
Author: Alexis Derumigny [aut, cre] ,
Jean-David Fermanian [aut] ,
Victor Ryan [aut],
Rutger van der Spek [ctb]
Maintainer: Alexis Derumigny <a.f.f.derumigny@tudelft.nl>
Diff between ElliptCopulas versions 0.1.3 dated 2022-04-25 and 0.1.4.1 dated 2024-09-09
DESCRIPTION | 15 +- MD5 | 58 ++++++---- NAMESPACE | 12 +- NEWS.md | 48 ++++++++ R/EllDistrEst-adaptive.R |only R/EllDistrEst.R | 166 ++++++++++++++++++++++------- R/EllDistrEstDeriv.R |only R/EllDistrSim.R | 11 + R/Faa_di_Bruno.R |only R/KTMatrixEst.R | 94 +++++++++++++--- R/kernelChoice.R | 115 ++++++++++++++++++-- R/numericalAnalysis.R | 15 +- R/zz_auxiliaryFunctions.R |only README.md | 167 +++++++++++++++++++++++------ build/partial.rdb |binary man/DensityGenerator.normalize.Rd | 114 ++++++++++---------- man/EllCopEst.Rd | 214 +++++++++++++++++++------------------- man/EllCopLikelihood.Rd | 114 ++++++++++---------- man/EllCopSim.Rd | 112 +++++++++---------- man/EllDistrDerivEst.Rd |only man/EllDistrEst.Rd | 81 ++++++++++++-- man/EllDistrEst.adapt.Rd |only man/EllDistrSim.Rd | 143 +++++++++++++------------ man/EllDistrSimCond.Rd | 148 +++++++++++++------------- man/KTMatrixEst.Rd | 53 +++++++-- man/TEllDistrEst.Rd | 174 +++++++++++++++--------------- man/compute_etahat.Rd |only man/compute_matrix_alpha.Rd |only man/conv_funct.Rd | 139 ++++++++++++------------ man/derivative.psi.Rd |only man/derivative.rho.Rd |only man/derivative.tau.Rd |only man/estim_tilde_AMSE.Rd |only man/vectorized_Faa_di_Bruno.Rd |only tests |only 35 files changed, 1253 insertions(+), 740 deletions(-)
Title: Causal Analysis of Observational Time-to-Event Data
Description: Implements target trial emulation methods to apply randomized
clinical trial design and analysis in an observational setting. Using
marginal structural models, it can estimate intention-to-treat and
per-protocol effects in emulated trials using electronic health
records. A description and application of the method can be found in
Danaei et al (2013) <doi:10.1177/0962280211403603>.
Author: Roonak Rezvani [aut] ,
Isaac Gravestock [aut, cre] ,
Li Su [aut],
Medical Research Council [fnd],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Isaac Gravestock <isaac.gravestock@roche.com>
Diff between TrialEmulation versions 0.0.3.8 dated 2024-01-24 and 0.0.3.9 dated 2024-09-09
DESCRIPTION | 12 +- MD5 | 18 +-- NEWS.md | 4 R/data_extension.R | 8 - R/generics.R | 2 R/predict.R | 2 R/sampling.R | 2 build/vignette.rds |binary inst/doc/Getting-Started.html | 190 +++++++++++++++++++------------------- tests/testthat/_snaps/generics.md | 34 +++--- 10 files changed, 138 insertions(+), 134 deletions(-)
More information about TrialEmulation at CRAN
Permanent link
Title: Unified Principal Sufficient Dimension Reduction Package
Description: A unified and user-friendly framework for applying the principal sufficient dimension reduction methods for both linear and nonlinear cases. The package has an extendable power by varying loss functions for the support vector machine, even for an user-defined arbitrary function, unless those are convex and differentiable everywhere over the support (Li et al. (2011) <doi:10.1214/11-AOS932>). Also, it provides a real-time sufficient dimension reduction update procedure using the principal least squares support vector machine (Artemiou et al. (2021) <doi:10.1016/j.patcog.2020.107768>).
Author: Jungmin Shin [aut, cre],
Seung Jun Shin [aut],
Andreas Artemiou [aut]
Maintainer: Jungmin Shin <jungminshin@korea.ac.kr>
Diff between psvmSDR versions 1.0.1 dated 2024-08-30 and 1.0.2 dated 2024-09-09
psvmSDR-1.0.1/psvmSDR/tests |only psvmSDR-1.0.2/psvmSDR/DESCRIPTION | 6 +++--- psvmSDR-1.0.2/psvmSDR/MD5 | 15 +++++++-------- psvmSDR-1.0.2/psvmSDR/R/fn_npsdr.R | 2 +- psvmSDR-1.0.2/psvmSDR/R/fn_npsdr_x.R | 2 +- psvmSDR-1.0.2/psvmSDR/R/fn_psdr.R | 4 ++-- psvmSDR-1.0.2/psvmSDR/R/psvmSDR-package.R | 2 +- psvmSDR-1.0.2/psvmSDR/man/npsdr.Rd | 2 +- psvmSDR-1.0.2/psvmSDR/man/psdr.Rd | 4 ++-- 9 files changed, 18 insertions(+), 19 deletions(-)
Title: Inequality Measures for Weighted Data
Description: Computes inequality measures of a given variable taking into account weights. Suitable for ratio, interval and ordered scale. Includes Gini, Theil, Leti index, Palma ratio, 20:20 ratio, Allison and Foster index, Jenkins index, Cowell and Flechaire index, Abul Naga and Yalcin index, Apouey index, Blair and Lacy index. Bootstrap provides distribution of inequality measures enabling significance tests.
Author: Sebastian Wojcik [aut, cre] ,
Agnieszka Giemza [aut],
Katarzyna Machowska [aut],
Jaroslaw Napora [aut]
Maintainer: Sebastian Wojcik <S.Wojcik@stat.gov.pl>
Diff between wINEQ versions 1.2.0 dated 2023-04-21 and 1.2.1 dated 2024-09-09
DESCRIPTION | 10 - MD5 | 48 ++++---- NAMESPACE | 2 NEWS.md | 28 ++++ R/inequalityMeasure.R | 276 ++++++++++++++++++++++++++++++---------------- R/inequalityMeasureBoot.R | 26 ++-- data/Tourism.rda |binary data/Well_being.rda |binary man/Atkinson.Rd | 4 man/CoefVar.Rd | 4 man/Entropy.Rd | 15 +- man/Gini.Rd | 10 + man/Hoover.Rd | 6 - man/Jenkins.Rd | 4 man/Leti.Rd | 4 man/LowerSum.Rd |only man/Palma.Rd | 4 man/Prop20_20.Rd | 4 man/Quantile.Rd |only man/RicciSchutz.Rd | 6 - man/Theil_L.Rd | 5 man/Theil_T.Rd | 13 +- man/Tourism.Rd | 13 +- man/Well_being.Rd | 2 man/ineq_weighted.Rd | 7 - man/ineq_weighted_boot.Rd | 7 - 26 files changed, 328 insertions(+), 170 deletions(-)
Title: Lorenz and Penalized Lorenz Regressions
Description: Inference for the Lorenz and penalized Lorenz regressions. More broadly, the package proposes functions to assess inequality and graphically represent it. The Lorenz Regression procedure is introduced in Heuchenne and Jacquemain (2022) <doi:10.1016/j.csda.2021.107347> and in Jacquemain, A., C. Heuchenne, and E. Pircalabelu (2024) <doi:10.1214/23-EJS2200>.
Author: Alexandre Jacquemain [aut, cre]
,
Xingjie Shi [ctb]
Maintainer: Alexandre Jacquemain <aljacquemain@gmail.com>
Diff between LorenzRegression versions 1.0.0 dated 2023-02-28 and 2.0.0 dated 2024-09-09
LorenzRegression-1.0.0/LorenzRegression/R/LorenzRegression.R |only LorenzRegression-1.0.0/LorenzRegression/R/PLR-wrap.R |only LorenzRegression-1.0.0/LorenzRegression/R/boot-confint.R |only LorenzRegression-1.0.0/LorenzRegression/man/LorenzRegression.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/PLR.wrap.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/boot.confint.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/confint.LR.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/confint.PLR.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/plot.LR.Rd |only LorenzRegression-1.0.0/LorenzRegression/man/plot.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/DESCRIPTION | 17 LorenzRegression-2.0.0/LorenzRegression/MD5 | 147 +- LorenzRegression-2.0.0/LorenzRegression/NAMESPACE | 96 + LorenzRegression-2.0.0/LorenzRegression/NEWS.md |only LorenzRegression-2.0.0/LorenzRegression/R/FABS-estimation.R | 406 +++--- LorenzRegression-2.0.0/LorenzRegression/R/GA-call.R |only LorenzRegression-2.0.0/LorenzRegression/R/GA-estimation.R | 333 ++--- LorenzRegression-2.0.0/LorenzRegression/R/GA-population.R | 47 LorenzRegression-2.0.0/LorenzRegression/R/Gini-coefficient.R | 168 +- LorenzRegression-2.0.0/LorenzRegression/R/LR-coef.R | 55 LorenzRegression-2.0.0/LorenzRegression/R/LR-confint.R | 125 +- LorenzRegression-2.0.0/LorenzRegression/R/LR-ineqExplained.R |only LorenzRegression-2.0.0/LorenzRegression/R/LR-plot.R | 88 + LorenzRegression-2.0.0/LorenzRegression/R/LR-predict.R |only LorenzRegression-2.0.0/LorenzRegression/R/LR-print-summary.R |only LorenzRegression-2.0.0/LorenzRegression/R/LR-print.R | 67 - LorenzRegression-2.0.0/LorenzRegression/R/LR-summary.R | 128 +- LorenzRegression-2.0.0/LorenzRegression/R/Lorenz-bootstrap-combine.R |only LorenzRegression-2.0.0/LorenzRegression/R/Lorenz-bootstrap.R | 424 +++---- LorenzRegression-2.0.0/LorenzRegression/R/Lorenz-curve.R | 211 +-- LorenzRegression-2.0.0/LorenzRegression/R/Lorenz-graphs.R | 155 +- LorenzRegression-2.0.0/LorenzRegression/R/Lorenz-regression.R | 589 +++------- LorenzRegression-2.0.0/LorenzRegression/R/LorenzRegression-package.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-BIC.R | 99 - LorenzRegression-2.0.0/LorenzRegression/R/PLR-CV.R | 336 ++--- LorenzRegression-2.0.0/LorenzRegression/R/PLR-coef.R | 130 +- LorenzRegression-2.0.0/LorenzRegression/R/PLR-confint.R | 160 +- LorenzRegression-2.0.0/LorenzRegression/R/PLR-diagnostic.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-ineqExplained.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-normalize.R | 206 +-- LorenzRegression-2.0.0/LorenzRegression/R/PLR-plot.R | 457 ++++--- LorenzRegression-2.0.0/LorenzRegression/R/PLR-predict.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-print-summary.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-print.R | 94 + LorenzRegression-2.0.0/LorenzRegression/R/PLR-scores.R |only LorenzRegression-2.0.0/LorenzRegression/R/PLR-summary.R | 143 +- LorenzRegression-2.0.0/LorenzRegression/R/RcppExports.R | 65 - LorenzRegression-2.0.0/LorenzRegression/R/Rearrangement-estimation.R | 136 +- LorenzRegression-2.0.0/LorenzRegression/R/SCADFABS-estimation.R | 470 ++++--- LorenzRegression-2.0.0/LorenzRegression/R/ineqExplained.R |only LorenzRegression-2.0.0/LorenzRegression/R/model-matrix-PLR.R |only LorenzRegression-2.0.0/LorenzRegression/R/runif_seed.R |only LorenzRegression-2.0.0/LorenzRegression/README.md | 77 - LorenzRegression-2.0.0/LorenzRegression/man/Gini.coef.Rd | 7 LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.FABS.Rd | 64 - LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.GA.Rd | 36 LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.Population.Rd | 1 LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.Reg.Rd | 244 +--- LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.SCADFABS.Rd | 60 - LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.boot.Rd | 114 + LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.boot.combine.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.curve.Rd | 5 LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.ga.call.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/Lorenz.graphs.Rd | 70 - LorenzRegression-2.0.0/LorenzRegression/man/LorenzRegression-package.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/PLR.BIC.Rd | 18 LorenzRegression-2.0.0/LorenzRegression/man/PLR.CV.Rd | 80 - LorenzRegression-2.0.0/LorenzRegression/man/PLR.normalize.Rd | 13 LorenzRegression-2.0.0/LorenzRegression/man/PLR.scores.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/Rearrangement.estimation.Rd | 100 - LorenzRegression-2.0.0/LorenzRegression/man/autoplot.LR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/autoplot.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/coef.LR.Rd | 11 LorenzRegression-2.0.0/LorenzRegression/man/coef.PLR.Rd | 29 LorenzRegression-2.0.0/LorenzRegression/man/confint.LR_boot.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/confint.PLR_boot.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/diagnostic.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/dot-Fitness_cpp.Rd | 6 LorenzRegression-2.0.0/LorenzRegression/man/ineqExplained.LR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/ineqExplained.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/ineqExplained.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/model_matrix_PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/predict.LR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/predict.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/print.LR.Rd | 17 LorenzRegression-2.0.0/LorenzRegression/man/print.PLR.Rd | 23 LorenzRegression-2.0.0/LorenzRegression/man/print.summary.LR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/print.summary.PLR.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/runif_seed.Rd |only LorenzRegression-2.0.0/LorenzRegression/man/summary.LR.Rd | 27 LorenzRegression-2.0.0/LorenzRegression/man/summary.PLR.Rd | 29 LorenzRegression-2.0.0/LorenzRegression/src/GA_fitness.cpp | 7 LorenzRegression-2.0.0/LorenzRegression/src/GA_meanrank.cpp | 37 LorenzRegression-2.0.0/LorenzRegression/src/PLR_derivative.cpp | 5 LorenzRegression-2.0.0/LorenzRegression/src/PLR_loss.cpp | 5 LorenzRegression-2.0.0/LorenzRegression/src/RcppExports.cpp | 36 96 files changed, 3445 insertions(+), 3028 deletions(-)
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Title: Aggregation Trees
Description: Nonparametric data-driven approach to discovering heterogeneous subgroups in a selection-on-observables framework.
'aggTrees' allows researchers to assess whether there exists relevant heterogeneity in treatment effects by generating a sequence of optimal groupings,
one for each level of granularity. For each grouping, we obtain point estimation and inference about the group average treatment effects.
Please reference the use as Di Francesco (2022) <doi:10.2139/ssrn.4304256>.
Author: Riccardo Di Francesco [aut, cre, cph]
Maintainer: Riccardo Di Francesco <difrancesco.riccardo96@gmail.com>
Diff between aggTrees versions 2.0.2 dated 2023-09-20 and 2.1.0 dated 2024-09-09
DESCRIPTION | 11 - MD5 | 60 ++++--- NEWS.md | 8 + R/aggregation-trees.R | 171 ++++++++++----------- R/balance-measures.R | 5 R/generic-s3.R | 98 ++++++++---- R/rpart-functions.R | 80 +++++----- R/utils.R | 18 +- README.md | 29 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/aggTrees-vignette.R | 106 +++++++------ inst/doc/aggTrees-vignette.Rmd | 97 ++++++------ inst/doc/aggTrees-vignette.html | 306 ++++++++++++++++++++++++--------------- inst/doc/inference.R |only inst/doc/inference.Rmd |only inst/doc/inference.html |only man/avg_characteristics_rpart.Rd | 6 man/build_aggtree.Rd | 89 ++++++----- man/causal_ols_rpart.Rd | 20 +- man/descriptive_arm.Rd | 3 man/dr_scores.Rd | 4 man/estimate_rpart.Rd | 18 +- man/get_leaves.Rd | 4 man/leaf_membership.Rd | 4 man/node_membership.Rd | 4 man/plot.aggTrees.Rd | 26 ++- man/print.aggTrees.Rd | 2 man/print.aggTrees.inference.Rd | 26 ++- man/subtree.Rd | 4 man/summary.aggTrees.Rd | 2 vignettes/aggTrees-vignette.Rmd | 97 ++++++------ vignettes/inference.Rmd |only 33 files changed, 723 insertions(+), 575 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses. See e.g. Halekoh and Højsgaard, (2005,
<doi:10.18637/jss.v015.i02>), for details.
Author: Soeren Hoejsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Thorn Ekstroem [ctb],
CRAN Team [ctb]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.3.11 dated 2024-06-06 and 1.3.11.1 dated 2024-09-09
DESCRIPTION | 14 ++++++++------ MD5 | 22 +++++++++++----------- inst/include/tnt/lu.h | 2 +- inst/include/tnt/region1d.h | 4 ++-- inst/include/tnt/transv.h | 4 ++-- inst/include/tnt/vec.h | 6 +++--- inst/include/tntsupp.h | 4 ++-- man/QIC.Rd | 2 +- src/famstr.cc | 2 +- src/geesubs.cc | 2 +- src/inter.cc | 2 +- src/param.cc | 2 +- 12 files changed, 34 insertions(+), 32 deletions(-)
Title: Estimates Degrees of Relatedness (Up to the Second Degree) for
Extreme Low-Coverage Data
Description: The goal of the package is to provide an easy-to-use method
for estimating degrees of relatedness (up to the second degree)
for extreme low-coverage data. The package also allows users to
quantify and visualise the level of confidence in the estimated
degrees of relatedness.
Author: Jono Tuke [aut, cre] ,
Adam B. Rohrlach [aut] ,
Wolfgang Haak [aut] ,
Divyaratan Popli [aut]
Maintainer: Jono Tuke <simon.tuke@adelaide.edu.au>
Diff between BREADR versions 1.0.1 dated 2023-04-12 and 1.0.2 dated 2024-09-09
DESCRIPTION | 13 ++++++------- MD5 | 29 ++++++++++++++++++----------- NAMESPACE | 4 ++++ NEWS.md | 6 ++++++ R/callRelatedness.R | 3 ++- R/get_column.R |only R/plotLOAF.R | 2 +- R/processEigenstrat.R | 10 ++++++++-- R/processEigenstrat_old.R |only R/sim_geno.R |only inst/CITATION |only inst/WORDLIST | 4 +++- man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/get_column_new.Rd |only man/processEigenstrat.Rd | 2 +- man/processEigenstrat_old.Rd |only man/sim_geno.Rd |only 19 files changed, 49 insertions(+), 24 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.9.1 dated 2024-04-28 and 0.9.3 dated 2024-09-09
MiscMetabar-0.9.1/MiscMetabar/man/asv2otu.Rd |only MiscMetabar-0.9.3/MiscMetabar/DESCRIPTION | 8 MiscMetabar-0.9.3/MiscMetabar/MD5 | 314 +++---- MiscMetabar-0.9.3/MiscMetabar/NAMESPACE | 2 MiscMetabar-0.9.3/MiscMetabar/NEWS.md | 50 - MiscMetabar-0.9.3/MiscMetabar/R/Deseq2_edgeR.R | 25 MiscMetabar-0.9.3/MiscMetabar/R/MiscMetabar-package.R | 4 MiscMetabar-0.9.3/MiscMetabar/R/alpha_div_test.R | 18 MiscMetabar-0.9.3/MiscMetabar/R/beta_div_test.R | 107 +- MiscMetabar-0.9.3/MiscMetabar/R/blast.R | 58 + MiscMetabar-0.9.3/MiscMetabar/R/controls.R | 32 MiscMetabar-0.9.3/MiscMetabar/R/dada_phyloseq.R | 337 +++++--- MiscMetabar-0.9.3/MiscMetabar/R/data.R | 1 MiscMetabar-0.9.3/MiscMetabar/R/funguild.R | 12 MiscMetabar-0.9.3/MiscMetabar/R/krona.R | 9 MiscMetabar-0.9.3/MiscMetabar/R/lulu.R | 6 MiscMetabar-0.9.3/MiscMetabar/R/miscellanous.R | 80 + MiscMetabar-0.9.3/MiscMetabar/R/plot_functions.R | 405 +++++++--- MiscMetabar-0.9.3/MiscMetabar/R/speedyseq_functions.R | 30 MiscMetabar-0.9.3/MiscMetabar/R/table_functions.R | 26 MiscMetabar-0.9.3/MiscMetabar/R/targets_misc.R | 30 MiscMetabar-0.9.3/MiscMetabar/R/vsearch.R | 37 MiscMetabar-0.9.3/MiscMetabar/README.md | 3 MiscMetabar-0.9.3/MiscMetabar/build/partial.rdb |binary MiscMetabar-0.9.3/MiscMetabar/build/vignette.rds |binary MiscMetabar-0.9.3/MiscMetabar/inst/doc/MiscMetabar.html | 127 +-- MiscMetabar-0.9.3/MiscMetabar/inst/extdata/ex_R1_001.fasta |only MiscMetabar-0.9.3/MiscMetabar/inst/extdata/ex_R1_002.fasta |only MiscMetabar-0.9.3/MiscMetabar/man/LCBD_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/SRS_curve_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/accu_plot.Rd | 17 MiscMetabar-0.9.3/MiscMetabar/man/accu_plot_balanced_modality.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/accu_samp_threshold.Rd | 9 MiscMetabar-0.9.3/MiscMetabar/man/add_blast_info.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/add_dna_to_phyloseq.Rd | 18 MiscMetabar-0.9.3/MiscMetabar/man/add_funguild_info.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/add_info_to_sam_data.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/add_new_taxonomy_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/adonis_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/adonis_rarperm_pq.Rd | 18 MiscMetabar-0.9.3/MiscMetabar/man/all_object_size.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/ancombc_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/are_modality_even_depth.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/as_binary_otu_table.Rd | 15 MiscMetabar-0.9.3/MiscMetabar/man/biplot_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/blast_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/blast_to_derep.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/blast_to_phyloseq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/build_phytree_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/chimera_detection_vs.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/chimera_removal_vs.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/circle_pq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/clean_pq.Rd | 30 MiscMetabar-0.9.3/MiscMetabar/man/compare_pairs_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/count_seq.Rd | 7 MiscMetabar-0.9.3/MiscMetabar/man/cutadapt_remove_primers.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/diff_fct_diff_class.Rd | 7 MiscMetabar-0.9.3/MiscMetabar/man/dist_bycol.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/dist_pos_control.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/distri_1_taxa.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/figures/README-example-1.png |binary MiscMetabar-0.9.3/MiscMetabar/man/figures/README-unnamed-chunk-7-1.png |binary MiscMetabar-0.9.3/MiscMetabar/man/filter_asv_blast.Rd | 28 MiscMetabar-0.9.3/MiscMetabar/man/filter_trim.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/formattable_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/funguild_assign.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/get_file_extension.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/get_funguild_db.Rd | 9 MiscMetabar-0.9.3/MiscMetabar/man/ggaluv_pq.Rd | 18 MiscMetabar-0.9.3/MiscMetabar/man/ggbetween_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/ggscatt_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/ggvenn_pq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/glmutli_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/graph_test_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/heat_tree_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/hill_pq.Rd | 40 MiscMetabar-0.9.3/MiscMetabar/man/hill_test_rarperm_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/hill_tuckey_pq.Rd | 9 MiscMetabar-0.9.3/MiscMetabar/man/iNEXT_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/is_cutadapt_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/is_falco_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/is_krona_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/is_mumu_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/is_swarm_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/is_vsearch_installed.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/krona.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/list_fastq_files.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/lulu.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/lulu_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/merge_krona.Rd | 7 MiscMetabar-0.9.3/MiscMetabar/man/merge_samples2.Rd | 50 + MiscMetabar-0.9.3/MiscMetabar/man/merge_taxa_vec.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/multi_biplot_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/multipatt_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/multiplot.Rd | 13 MiscMetabar-0.9.3/MiscMetabar/man/multitax_bar_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/mumu_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/normalize_prop_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/perc.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/phyloseq_to_edgeR.Rd | 2 MiscMetabar-0.9.3/MiscMetabar/man/physeq_or_string_to_dna.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/plot_LCBD_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/plot_SCBD_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/plot_ancombc_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/plot_deseq2_pq.Rd | 16 MiscMetabar-0.9.3/MiscMetabar/man/plot_edgeR_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/plot_guild_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/plot_mt.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/plot_tax_pq.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/plot_tsne_pq.Rd | 11 MiscMetabar-0.9.3/MiscMetabar/man/plot_var_part_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/postcluster_pq.Rd |only MiscMetabar-0.9.3/MiscMetabar/man/psmelt_samples_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/rarefy_sample_count_by_modality.Rd | 18 MiscMetabar-0.9.3/MiscMetabar/man/read_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/rename_samples.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/rename_samples_otu_table.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/reorder_taxa_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/ridges_pq.Rd | 25 MiscMetabar-0.9.3/MiscMetabar/man/rotl_pq.Rd | 9 MiscMetabar-0.9.3/MiscMetabar/man/sample_data_with_new_names.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/sankey_pq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/save_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/search_exact_seq_pq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/select_one_sample.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/signif_ancombc.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/simplify_taxo.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/subsample_fastq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/subset_samples_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/subset_taxa_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/subset_taxa_tax_control.Rd | 22 MiscMetabar-0.9.3/MiscMetabar/man/summary_plot_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/swarm_clustering.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/tax_bar_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/tax_datatable.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/taxa_as_columns.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/taxa_as_rows.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/taxa_only_in_one_level.Rd | 16 MiscMetabar-0.9.3/MiscMetabar/man/tbl_sum_samdata.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/track_wkflow.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/track_wkflow_samples.Rd | 6 MiscMetabar-0.9.3/MiscMetabar/man/treemap_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/tsne_pq.Rd | 2 MiscMetabar-0.9.3/MiscMetabar/man/upset_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/upset_test_pq.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/var_par_pq.Rd | 9 MiscMetabar-0.9.3/MiscMetabar/man/var_par_rarperm_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/venn_pq.Rd | 14 MiscMetabar-0.9.3/MiscMetabar/man/verify_pq.Rd | 8 MiscMetabar-0.9.3/MiscMetabar/man/vs_search_global.Rd | 10 MiscMetabar-0.9.3/MiscMetabar/man/vsearch_clustering.Rd | 12 MiscMetabar-0.9.3/MiscMetabar/man/write_pq.Rd | 22 MiscMetabar-0.9.3/MiscMetabar/tests/testthat/Rplots.pdf |binary MiscMetabar-0.9.3/MiscMetabar/tests/testthat/match_list.txt |only MiscMetabar-0.9.3/MiscMetabar/tests/testthat/temp.fasta |only MiscMetabar-0.9.3/MiscMetabar/tests/testthat/test_clean_pq.R | 8 MiscMetabar-0.9.3/MiscMetabar/tests/testthat/test_cutadapt.R | 113 +- MiscMetabar-0.9.3/MiscMetabar/tests/testthat/test_figures_taxo.R | 4 MiscMetabar-0.9.3/MiscMetabar/tests/testthat/test_phyloseq_class.R | 2 MiscMetabar-0.9.3/MiscMetabar/tests/testthat/test_vsearch.R | 15 MiscMetabar-0.9.3/MiscMetabar/vignettes/bibliography.bib | 158 ++- 161 files changed, 2283 insertions(+), 1083 deletions(-)
Title: Joint Modelling of Functional Traits
Description: Fitting and analyzing a Joint Trait Distribution Model. The Joint Trait Distribution Model is implemented in the Bayesian framework using conjugate priors and posteriors, thus guaranteeing fast inference. In particular the package computes joint probabilities and multivariate confidence intervals, and enables the investigation of how they depend on the environment through partial response curves. The method implemented by the package is described in Poggiato et al. (2023) <doi:10.1111/geb.13706>.
Author: Giovanni Poggiato [aut, cre, cph]
Maintainer: Giovanni Poggiato <giov.poggiato@gmail.com>
Diff between jtdm versions 0.1-2 dated 2023-11-12 and 0.1-3 dated 2024-09-09
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 4 ++++ R/jtdm_fit.R | 20 ++++++++++++++------ R/plot.jtdm_fit.R | 2 +- inst/doc/ORCHAMP_dataset.html | 18 +++++++++--------- vignettes/figures/unnamed-chunk-10-1.png |binary vignettes/figures/unnamed-chunk-11-1.png |binary vignettes/figures/unnamed-chunk-12-1.png |binary vignettes/figures/unnamed-chunk-15-1.png |binary vignettes/figures/unnamed-chunk-6-1.png |binary vignettes/figures/unnamed-chunk-9-1.png |binary 12 files changed, 42 insertions(+), 30 deletions(-)
Title: Calculate the Open Bodem Index (OBI) Score
Description: The Open Bodem Index (OBI) is a method to evaluate the quality of soils of agricultural fields in The Netherlands and the sustainability of the current agricultural practices.
The OBI score is based on four main criteria: chemical, physical, biological and management, which consist of more than 21 indicators.
By providing results of a soil analysis and management info the 'OBIC' package can be use to calculate he scores, indicators and derivatives that are used by the OBI.
More information about the Open Bodem Index can be found at <https://openbodemindex.nl/>.
Author: Sven Verweij [aut, cre] ,
Gerard Ros [aut] ,
Yuki Fujita [aut] ,
Wilbrand Hendrik Riechelman [aut]
,
Kees van den Dool [aut] ,
Job de Pater [ctb],
Nutrienten Managment Instituut [cph]
Maintainer: Sven Verweij <sven.verweij@nmi-agro.nl>
Diff between OBIC versions 3.0.2 dated 2024-03-05 and 3.0.3 dated 2024-09-09
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 7 +++++++ R/obic.R | 2 +- README.md | 2 +- build/vignette.rds |binary data/crops.obic.rda |binary inst/doc/description-of-the-columns.html | 6 +++--- inst/doc/obic_introduction.html | 23 ++++++++++++----------- inst/doc/obic_score_aggregation.html | 9 +++++---- inst/doc/obic_water_functions.html | 7 ++++--- inst/doc/obic_workability.html | 17 +++++++++-------- man/crops.obic.Rd | 2 +- 13 files changed, 59 insertions(+), 48 deletions(-)
More information about FuzzyImputationTest at CRAN
Permanent link
Title: A Machine-Learning Based Tool to Automate the Identification of
Biological Database IDs
Description: The number of biological databases is growing rapidly, but different databases use different IDs to refer to the same biological entity. The inconsistency in IDs impedes the integration of various types of biological data. To resolve the problem, we developed 'MantaID', a data-driven, machine-learning based approach that automates identifying IDs on a large scale. The 'MantaID' model's prediction accuracy was proven to be 99%, and it correctly and effectively predicted 100,000 ID entries within two minutes. 'MantaID' supports the discovery and exploitation of ID patterns from large quantities of databases. (e.g., up to 542 biological databases). An easy-to-use freely available open-source software R package, a user-friendly web application, and API were also developed for 'MantaID' to improve applicability. To our knowledge, 'MantaID' is the first tool that enables an automatic, quick, accurate, and comprehensive identification of large quantities of IDs, and can therefore be used as a [...truncated...]
Author: Zhengpeng Zeng [aut, cre, ctb]
,
Longfei Mao [aut, cph] ,
Feng Yu [aut] ,
Jiamin Hu [ctb] ,
Xiting Wang [ctb]
Maintainer: Zhengpeng Zeng <molaison@foxmail.com>
Diff between MantaID versions 1.0.3 dated 2024-08-27 and 1.0.4 dated 2024-09-09
MantaID-1.0.3/MantaID/inst/extdata/final_result.rds |only MantaID-1.0.3/MantaID/inst/extdata/result_BP.rds |only MantaID-1.0.4/MantaID/DESCRIPTION | 6 - MantaID-1.0.4/MantaID/MD5 | 12 +- MantaID-1.0.4/MantaID/R/mi_balance_data.R | 76 ++++++++---------- MantaID-1.0.4/MantaID/R/mi_train_rg.R | 82 ++++++++++---------- MantaID-1.0.4/MantaID/R/mi_tune_rg.R | 4 MantaID-1.0.4/MantaID/man/mi_balance_data.Rd | 5 - 8 files changed, 87 insertions(+), 98 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-12 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-25 0.1-6
2017-07-20 0.1-5
2015-11-12 0.1-4
2013-03-12 0.1-3
2011-07-04 0.1-2
2011-06-27 0.1-1
2011-06-24 0.1
Title: Direct MLE for Multivariate Normal Mixture Distributions
Description: Multivariate Normal (i.e. Gaussian) Mixture Models (S3) Classes.
Fitting models to data using 'MLE' (maximum likelihood estimation) for
multivariate normal mixtures via smart parametrization using the 'LDL'
(Cholesky) decomposition, see McLachlan and Peel (2000, ISBN:9780471006268),
Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>.
Author: Nicolas Trutmann [aut, cre],
Martin Maechler [aut, ths]
Maintainer: Nicolas Trutmann <nicolas.trutmann@gmx.ch>
Diff between norMmix versions 0.1-1 dated 2024-04-16 and 0.2-0 dated 2024-09-09
DESCRIPTION | 16 +-- MD5 | 29 +++--- NAMESPACE | 4 R/norMmix.R | 137 ++++++++++++++++++++++++++++++-- README.md | 10 ++ build/partial.rdb |only build/vignette.rds |binary inst/doc/A_Short_Intro_to_norMmix.R | 4 inst/doc/A_Short_Intro_to_norMmix.Rmd | 2 inst/doc/A_Short_Intro_to_norMmix.html | 14 +-- man/MarronWand.Rd | 9 +- man/norMmix.Rd | 2 man/norMmixMLE.Rd | 4 tests/testthat/test-norMmix.R | 36 +++++++- tests/testthat/test-norMmixMLE.R |only tests/testthat/test-sigmaAgainstModel.R |only vignettes/A_Short_Intro_to_norMmix.Rmd | 2 17 files changed, 217 insertions(+), 52 deletions(-)
Title: Interaction Between R and REDCap
Description: Encapsulates functions to streamline calls from R to the REDCap
API. REDCap (Research Electronic Data CAPture) is a web application for
building and managing online surveys and databases developed at Vanderbilt
University. The Application Programming Interface (API) offers an avenue
to access and modify data programmatically, improving the capacity for
literate and reproducible programming.
Author: Will Beasley [aut, cre] ,
David Bard [ctb] ,
Thomas Wilson [ctb],
John J Aponte [ctb],
Rollie Parrish [ctb] ,
Benjamin Nutter [ctb],
Andrew Peters [ctb] ,
Hao Zhu [ctb] ,
Janosch Linkersdoerfer [ctb] ,
Jonathan Mang [ctb] ,
Felix Torres [ctb],
Philip [...truncated...]
Maintainer: Will Beasley <wibeasley@hotmail.com>
Diff between REDCapR versions 1.1.0 dated 2022-08-10 and 1.2.0 dated 2024-09-09
REDCapR-1.1.0/REDCapR/R/redcap-download-file-oneshot.R |only REDCapR-1.1.0/REDCapR/R/redcap-download-instrument.R |only REDCapR-1.1.0/REDCapR/R/redcap-read-dag.R |only REDCapR-1.1.0/REDCapR/R/redcap-upload-file-oneshot.R |only REDCapR-1.1.0/REDCapR/inst/test-data/delete-multiple-arm/delete-multiple-arm-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/delete-single-arm/delete-single-arm-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/longitudinal-single-arm/cdisc.REDCap.xml |only REDCapR-1.1.0/REDCapR/inst/test-data/problematic-dictionary/problematic-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/problematic-values/problematic-values-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/problematic-values/problematic-values-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-clinical-trial/clinical-trial-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-clinical-trial/clinical-trial-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-color-boxes/color-boxes-data-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-color-boxes/color-boxes-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-dag/dag-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-dag/dag-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-longitudinal/longitudinal-data-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-longitudinal/longitudinal-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-russian/russian-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-simple/simple-data-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-simple/simple-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-simple/simple-metadata.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-survey/survey-data-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/project-survey/survey-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/repeating-instruments/repeating-instruments-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/repeating-instruments/repeating-instruments-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/repeating-instruments/repeating-instruments-full.xml |only REDCapR-1.1.0/REDCapR/inst/test-data/specific-redcapr/event-instruments/default.R |only REDCapR-1.1.0/REDCapR/inst/test-data/super-wide-metadata/super-wide-metadata-dictionary.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/super-wide/super-wide-data.csv |only REDCapR-1.1.0/REDCapR/inst/test-data/super-wide/super-wide-dictionary.csv |only REDCapR-1.1.0/REDCapR/man/redcap_download_file_oneshot.Rd |only REDCapR-1.1.0/REDCapR/man/redcap_download_instrument.Rd |only REDCapR-1.1.0/REDCapR/man/redcap_upload_file_oneshot.Rd |only REDCapR-1.1.0/REDCapR/tests/testthat/test-instrument.R |only REDCapR-1.2.0/REDCapR/DESCRIPTION | 53 REDCapR-1.2.0/REDCapR/MD5 | 429 +- REDCapR-1.2.0/REDCapR/NAMESPACE | 12 REDCapR-1.2.0/REDCapR/NEWS.md | 145 REDCapR-1.2.0/REDCapR/R/REDCapR-package.R | 23 REDCapR-1.2.0/REDCapR/R/constant.R | 29 REDCapR-1.2.0/REDCapR/R/create-batch-glossary.R | 55 REDCapR-1.2.0/REDCapR/R/helpers-testing.R | 11 REDCapR-1.2.0/REDCapR/R/kernel-api.R | 73 REDCapR-1.2.0/REDCapR/R/metadata-utilities.R | 82 REDCapR-1.2.0/REDCapR/R/project-dag-write.R | 83 REDCapR-1.2.0/REDCapR/R/project-delete-multiple-arm.R | 39 REDCapR-1.2.0/REDCapR/R/project-delete-single-arm.R | 46 REDCapR-1.2.0/REDCapR/R/project-simple.R | 83 REDCapR-1.2.0/REDCapR/R/redcap-arm-export.R | 58 REDCapR-1.2.0/REDCapR/R/redcap-column-sanitize.R | 15 REDCapR-1.2.0/REDCapR/R/redcap-dag-read.R |only REDCapR-1.2.0/REDCapR/R/redcap-delete.R | 70 REDCapR-1.2.0/REDCapR/R/redcap-event-instruments.R | 106 REDCapR-1.2.0/REDCapR/R/redcap-event-read.R |only REDCapR-1.2.0/REDCapR/R/redcap-file-download-oneshot.R |only REDCapR-1.2.0/REDCapR/R/redcap-file-upload-oneshot.R |only REDCapR-1.2.0/REDCapR/R/redcap-instrument-download.R |only REDCapR-1.2.0/REDCapR/R/redcap-instruments.R | 80 REDCapR-1.2.0/REDCapR/R/redcap-log-read.R |only REDCapR-1.2.0/REDCapR/R/redcap-metadata-coltypes.R |only REDCapR-1.2.0/REDCapR/R/redcap-metadata-read.R | 135 REDCapR-1.2.0/REDCapR/R/redcap-metadata-write.R | 51 REDCapR-1.2.0/REDCapR/R/redcap-next-free-record-name.R | 43 REDCapR-1.2.0/REDCapR/R/redcap-project-info-read.R |only REDCapR-1.2.0/REDCapR/R/redcap-project.R | 36 REDCapR-1.2.0/REDCapR/R/redcap-read-eav-oneshot.R |only REDCapR-1.2.0/REDCapR/R/redcap-read-oneshot-eav.R | 236 - REDCapR-1.2.0/REDCapR/R/redcap-read-oneshot.R | 260 - REDCapR-1.2.0/REDCapR/R/redcap-read.R | 389 + REDCapR-1.2.0/REDCapR/R/redcap-report.R | 87 REDCapR-1.2.0/REDCapR/R/redcap-survey-link-export-oneshot.R | 66 REDCapR-1.2.0/REDCapR/R/redcap-users-export.R | 78 REDCapR-1.2.0/REDCapR/R/redcap-variables.R | 98 REDCapR-1.2.0/REDCapR/R/redcap-version.R | 46 REDCapR-1.2.0/REDCapR/R/redcap-write-oneshot.R | 72 REDCapR-1.2.0/REDCapR/R/redcap-write.R | 108 REDCapR-1.2.0/REDCapR/R/retrieve-credential.R | 52 REDCapR-1.2.0/REDCapR/R/sanitize-token.R | 75 REDCapR-1.2.0/REDCapR/R/utilities.R | 58 REDCapR-1.2.0/REDCapR/R/validate.R | 365 + REDCapR-1.2.0/REDCapR/README.md | 12 REDCapR-1.2.0/REDCapR/build/vignette.rds |binary REDCapR-1.2.0/REDCapR/inst/WORDLIST | 54 REDCapR-1.2.0/REDCapR/inst/doc/BasicREDCapROperations.R | 70 REDCapR-1.2.0/REDCapR/inst/doc/BasicREDCapROperations.Rmd | 88 REDCapR-1.2.0/REDCapR/inst/doc/BasicREDCapROperations.html | 813 +--- REDCapR-1.2.0/REDCapR/inst/doc/SecurityDatabase.html | 682 +-- REDCapR-1.2.0/REDCapR/inst/doc/TroubleshootingApiCalls.R | 15 REDCapR-1.2.0/REDCapR/inst/doc/TroubleshootingApiCalls.Rmd | 53 REDCapR-1.2.0/REDCapR/inst/doc/TroubleshootingApiCalls.html | 515 +- REDCapR-1.2.0/REDCapR/inst/doc/advanced-redcapr-operations.R | 35 REDCapR-1.2.0/REDCapR/inst/doc/advanced-redcapr-operations.Rmd | 52 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Title: Hypothesis Testing Based on Neyman-Pearson Lemma and Likelihood
Ratio Test
Description: Error type I and Optimal critical values to test statistical hypothesis based on Neyman-Pearson Lemma and Likelihood ratio test
based on random samples from several distributions. The families of distributions are Bernoulli, Exponential, Geometric, Inverse Normal,
Normal, Gamma, Gumbel, Lognormal, Poisson, and Weibull.
This package is an ideal resource to help with the teaching of Statistics.
The main references for this package are Casella G. and Berger R. (2003,ISBN:0-534-24312-6 , "Statistical Inference. Second Edition", Duxbury Press) and
Hogg, R., McKean, J., and Craig, A. (2019,ISBN:013468699, "Introduction to Mathematical Statistic. Eighth edition", Pearson).
Author: Carlos Alberto Cardozo Delgado [aut, cre, cph]
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between hytest versions 0.1.0 dated 2024-06-04 and 0.1.1 dated 2024-09-09
DESCRIPTION | 10 ++++++---- MD5 | 28 ++++++++++++++++++++++------ NAMESPACE | 19 +++++++++++++++++++ R/gamma_c_opt.R |only R/gamma_errorI.R | 8 ++++---- R/gumbel_c_opt.R |only R/gumbel_errorI.R |only R/invnormal_errorI.R |only R/invormal_c_opt.R |only R/lognorm_c_opt.R |only R/lognorm_errorI.R | 6 +++--- R/weibull_c_opt.R |only R/weibull_errorI.R |only man/gamma_c_opt.Rd |only man/gamma_errorI.Rd | 8 ++++---- man/gumbel_c_opt.Rd |only man/gumbel_errorI.Rd |only man/invnormal_c_opt.Rd |only man/invnormal_errorI.Rd |only man/lognorm_c_opt.Rd |only man/lognorm_errorI.Rd | 6 +++--- man/weibull_c_opt.Rd |only man/weibull_errorI.Rd |only 23 files changed, 61 insertions(+), 24 deletions(-)
Title: Fast Best Subset Selection
Description: Extremely efficient toolkit for solving the best subset selection problem <https://www.jmlr.org/papers/v23/21-1060.html>. This package is its R interface. The package implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times for linear model. It also supports best subset selection for logistic regression, Poisson regression, Cox proportional hazard model, Gamma regression, multiple-response regression, multinomial logistic regression, ordinal regression, (sequential) principal component analysis, and robust principal component analysis. The other valuable features such as the best subset of group selection <doi:10.1287/ijoc.2022.1241> and sure independence screening <doi:10.1111/j.1467-9868.2008.00674.x> are also provided.
Author: Jin Zhu [aut, cre] ,
Zezhi Wang [aut],
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Borui Tang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] ,
Xueqin Wang [aut] ,
spectra contribu [...truncated...]
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between abess versions 0.4.8 dated 2023-09-19 and 0.4.9 dated 2024-09-09
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