Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <https://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Martin Lysy [aut],
Andrew Johnson [aut],
Hamada S. Badr [ctb],
Marco Colombo [ctb],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 2.3.0 dated 2023-03-09 and 2.3.1 dated 2023-03-29
DESCRIPTION | 10 ++--- MD5 | 16 ++++---- NEWS.md | 7 +++ R/init_cpp.R | 2 + R/nsamples.R | 3 - R/rstan_config.R | 28 ++++++-------- inst/doc/minimal-rstan-package.html | 72 ++++++++++++++++++------------------ man/init_cpp.Rd | 1 man/nsamples.Rd | 3 + 9 files changed, 75 insertions(+), 67 deletions(-)
Title: Propensity Score Matching for Unordered 3-Group Data
Description: You can use this program for 3 sets of categorical data for propensity score matching.
Assume that the data has 3 different categorical variables. You can use it to perform propensity matching of baseline indicator groupings.
The matching will make the differences in the baseline data smaller.
This method was described by Alvaro Fuentes (2022) <doi:10.1080/00273171.2021.1925521>.
Author: Qiang LIU [aut, cre]
Maintainer: Qiang LIU <dege857@163.com>
Diff between pm3 versions 0.1.4 dated 2023-03-14 and 0.1.5 dated 2023-03-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/pm3.R | 2 +- R/pm3datalist.R | 2 +- 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Likelihood Ratio Tests and Confidence Intervals
Description: A collection of hypothesis tests and confidence intervals based on the likelihood ratio
<https://en.wikipedia.org/wiki/Likelihood-ratio_test>.
Author: Greg McMahan
Maintainer: Greg McMahan <gmcmacran@gmail.com>
Diff between LRTesteR versions 1.0.1 dated 2022-09-17 and 1.0.2 dated 2023-03-29
LRTesteR-1.0.1/LRTesteR/R/a_function_factories.R |only LRTesteR-1.0.1/LRTesteR/tests/testthat/test_a_function_factories.R |only LRTesteR-1.0.2/LRTesteR/DESCRIPTION | 9 LRTesteR-1.0.2/LRTesteR/MD5 | 38 +- LRTesteR-1.0.2/LRTesteR/NAMESPACE | 2 LRTesteR-1.0.2/LRTesteR/NEWS.md | 3 LRTesteR-1.0.2/LRTesteR/R/a_function_factories_case_one.R |only LRTesteR-1.0.2/LRTesteR/R/a_function_factories_case_two.R |only LRTesteR-1.0.2/LRTesteR/R/empirical_tests.R |only LRTesteR-1.0.2/LRTesteR/R/print.R | 2 LRTesteR-1.0.2/LRTesteR/README.md | 157 +++++----- LRTesteR-1.0.2/LRTesteR/build/vignette.rds |binary LRTesteR-1.0.2/LRTesteR/inst/doc/Analysis_of_Deviance.R | 16 - LRTesteR-1.0.2/LRTesteR/inst/doc/Analysis_of_Deviance.Rmd | 26 - LRTesteR-1.0.2/LRTesteR/inst/doc/Analysis_of_Deviance.html | 157 ++++------ LRTesteR-1.0.2/LRTesteR/inst/doc/Nonparametric_Tests.R |only LRTesteR-1.0.2/LRTesteR/inst/doc/Nonparametric_Tests.Rmd |only LRTesteR-1.0.2/LRTesteR/inst/doc/Nonparametric_Tests.html |only LRTesteR-1.0.2/LRTesteR/man/empirical_mu_one_sample.Rd |only LRTesteR-1.0.2/LRTesteR/man/empirical_mu_one_way.Rd |only LRTesteR-1.0.2/LRTesteR/tests/testthat/test_a_function_factories_case_one.R |only LRTesteR-1.0.2/LRTesteR/tests/testthat/test_a_function_factories_case_two.R |only LRTesteR-1.0.2/LRTesteR/tests/testthat/test_binomial_tests.R | 2 LRTesteR-1.0.2/LRTesteR/tests/testthat/test_empirical_tests.R |only LRTesteR-1.0.2/LRTesteR/tests/testthat/test_print.R | 52 +++ LRTesteR-1.0.2/LRTesteR/vignettes/Analysis_of_Deviance.Rmd | 26 - LRTesteR-1.0.2/LRTesteR/vignettes/Nonparametric_Tests.Rmd |only 27 files changed, 281 insertions(+), 209 deletions(-)
Title: Global Adaptive Generative Adjustment Algorithm for Generalized
Linear Models
Description: Fits linear regression, logistic and multinomial regression models, Poisson regression, Cox model via Global Adaptive Generative Adjustment Algorithm.
For more detailed information, see Bin Wang, Xiaofei Wang and Jianhua Guo (2022) <arXiv:1911.00658>.
This paper provides the theoretical properties of Gaga linear model when the load matrix is orthogonal.
Further study is going on for the nonorthogonal cases and generalized linear models.
These works are in part supported by the National Natural Foundation of China (No.12171076).
Author: Bin Wang [aut, cre],
Xiaofei Wang [ctb],
Jianhua Guo [ths]
Maintainer: Bin Wang <eatingbeen@hotmail.com>
Diff between GAGAs versions 0.5.1 dated 2022-12-08 and 0.6.1 dated 2023-03-29
DESCRIPTION | 12 +++--- MD5 | 74 +++++++++++++++++++++-------------------- NAMESPACE | 3 + NEWS.md | 10 +++++ R/GAGAs.R | 57 ++++++++++++++++--------------- R/LM_GAGA.R | 7 ++- R/RcppExports.R | 22 +++++++----- R/cal.F1Score.R |only R/cal.acc.R | 6 +-- R/cal.cindex.R | 2 - R/cal.w.acc.R | 6 +-- R/cox_GAGA.R | 19 +++++----- R/logistic_GAGA.R | 11 +++--- R/multinomial_GAGA.R | 11 +++--- R/poisson_GAGA.R | 14 +++---- R/predict.GAGA.R | 6 +-- R/summary.GAGA.R |only man/GAGAs.Rd | 47 +++++++++++++------------- man/LM_GAGA.Rd | 6 +-- man/cal.F1Score.Rd |only man/cal.acc.Rd | 6 +-- man/cal.cindex.Rd | 2 - man/cal.w.acc.Rd | 6 +-- man/cox_GAGA.Rd | 19 ++++++---- man/cpp_COX_gaga.Rd | 7 ++- man/cpp_logistic_gaga.Rd | 5 ++ man/cpp_multinomial_gaga.Rd | 5 ++ man/cpp_poisson_gaga.Rd | 14 +++++++ man/logistic_GAGA.Rd | 11 +++--- man/multinomial_GAGA.Rd | 11 +++--- man/poisson_GAGA.Rd | 13 ++++--- man/predict.GAGA.Rd | 6 +-- man/summary.GAGA.Rd |only src/LM_GAGA.cpp | 79 +++++++++++++++++++++++--------------------- src/Makevars | 2 - src/RcppExports.cpp | 36 +++++++++++--------- src/cox_GAGA.cpp | 38 +++++++++++---------- src/logistic_GAGA.cpp | 18 ++++++---- src/multinomial_GAGA.cpp | 20 ++++++----- src/poisson_GAGA.cpp | 31 +++++++++-------- 40 files changed, 363 insertions(+), 279 deletions(-)
Title: Search, Composite, and Download 'Google Earth Engine' Imagery
with the 'Python' Module 'geedim'
Description: Search, composite, and download 'Google Earth Engine' imagery with 'reticulate' bindings for the 'Python' module 'geedim' by Dugal Harris. Read the 'geedim' documentation here: <https://geedim.readthedocs.io/>.
Wrapper functions are provided to make it more convenient to use 'geedim' to download images larger than the 'Google Earth Engine' size limit <https://developers.google.com/earth-engine/apidocs/ee-image-getdownloadurl>.
By default the "High Volume" API endpoint <https://developers.google.com/earth-engine/cloud/highvolume> is used to download data and this URL can be customized during initialization of the package.
Author: Andrew Brown [aut, cre],
Dugal Harris [cph]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between rgeedim versions 0.2.1 dated 2023-02-14 and 0.2.2 dated 2023-03-29
DESCRIPTION | 6 - MD5 | 40 ++++---- NAMESPACE | 2 NEWS.md | 12 ++ R/AAAA.R | 9 + R/composite.R | 14 +- R/install.R |only R/regions.R | 148 ++++++++++++++++++++++--------- R/search.R | 16 ++- README.md | 15 +-- inst/tinytest/test_rgeedim.R | 5 - man/figures/README-inspect-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-7-2.png |binary man/gd_bbox.Rd | 2 man/gd_composite.Rd | 14 +- man/gd_install.Rd |only man/gd_properties.Rd | 14 +- man/gd_region.Rd | 17 ++- man/gd_search.Rd | 2 22 files changed, 218 insertions(+), 98 deletions(-)
Title: Basic Robust Statistics
Description: "Essential" Robust Statistics.
Tools allowing to analyze data with robust methods. This includes
regression methodology including model selections and multivariate
statistics where we strive to cover the book "Robust Statistics,
Theory and Methods" by 'Maronna, Martin and Yohai'; Wiley 2006.
Author: Martin Maechler [aut, cre] ,
Peter Rousseeuw [ctb] ,
Christophe Croux [ctb] ,
Valentin Todorov [aut] ,
Andreas Ruckstuhl [aut] ,
Matias Salibian-Barrera [aut] ,
Tobias Verbeke [ctb, fnd] ,
Manuel Koller [aut] ,
Eduardo L. T. Conceicao [aut] ,
Maria A [...truncated...]
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between robustbase versions 0.95-0 dated 2022-04-02 and 0.95-1 dated 2023-03-29
DESCRIPTION | 10 +- MD5 | 76 +++++++++-------- NAMESPACE | 10 +- R/BYlogreg.R | 2 R/covMcd.R | 27 ++++-- R/lmrob.R | 9 +- R/mc.R | 9 -- R/nlrob.R | 27 +++--- TODO | 1 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 7 - inst/NEWS.Rd | 34 +++++++- inst/doc/fastMcd-kmini.pdf |binary inst/doc/lmrob_simulation.pdf |binary inst/doc/psi_functions.pdf |binary inst/xtraR/test-tools.R |only man/M.psi.Rd | 6 + man/aircraft.Rd | 2 man/lmc-rmc.Rd |only src/lmrob.c | 2 src/monitor.c | 2 tests/MT-tst.R | 6 - tests/NAcoef.R | 6 - tests/NAcoef.Rout.save | 13 +-- tests/comedian-tst.R | 3 tests/glmrob-1.R | 5 - tests/lmrob-data.R | 2 tests/lmrob-ex12.R | 6 - tests/lmrob-psifns.R | 2 tests/lmrob-psifns.Rout.save | 9 -- tests/m-s-estimator.R | 2 tests/mc-strict.R | 9 +- tests/nlregrob-tst.R | 2 tests/nlrob-tst.R | 178 +++++++++++++++++++++++++++++++++++++++++- tests/poisson-ex.R | 5 - tests/subsample.R | 4 tests/tmcd.R | 4 tests/weights.R | 58 ++++++++----- tests/weights.Rout.save | 137 ++++++++++++++++++++++++++------ 40 files changed, 509 insertions(+), 166 deletions(-)
Title: Tools for Matrix Algebra, Optimization and Inference
Description: Matrix is an universal and sometimes primary object/unit in applied mathematics and statistics. We provide a number of algorithms for selected problems in optimization and statistical inference. For general exposition to the topic with focus on statistical context, see the book by Banerjee and Roy (2014, ISBN:9781420095388).
Author: Kisung You [aut, cre]
Maintainer: Kisung You <kisungyou@outlook.com>
Diff between maotai versions 0.2.4 dated 2022-02-03 and 0.2.5 dated 2023-03-29
DESCRIPTION | 13 +++++++------ MD5 | 37 +++++++++++++++++++++++-------------- NAMESPACE | 3 +++ NEWS.md | 13 +++++++------ R/RcppExports.R | 4 ++++ R/aux_hidden_dist.R | 14 +++++++++++++- R/metricdepth.R |only R/package-maotai.R | 3 ++- R/rotationS2.R |only R/zzz.R | 6 +++--- README.md | 7 +++++-- build/partial.rdb |binary inst/REFERENCES.bib | 16 ++++++++++++---- man/metricdepth.Rd |only man/rotationS2.Rd |only src/Makevars | 11 ++++++++--- src/Makevars.win | 11 ++++++++--- src/RcppExports.cpp | 12 ++++++++++++ src/cpp_casket.cpp | 41 +++++++++++++++++++++++++++++++++++++++++ tests |only 20 files changed, 148 insertions(+), 43 deletions(-)
Title: Linkage Disequilibrium of Ancestry (LDA) and LDA Score (LDAS)
Description: Computation of linkage disequilibrium of ancestry (LDA) and linkage disequilibrium of ancestry score (LDAS). LDA calculates the pairwise linkage disequilibrium of ancestry between single nucleotide polymorphisms (SNPs). LDAS calculates the LDA score of SNPs. The methods are described in Barrie W, Yang Y, Attfield K E, et al (2022) <doi:10.1101/2022.09.23.509097>.
Author: Yaoling Yang [aut, cre] ,
Daniel Lawson [aut]
Maintainer: Yaoling Yang <yaoling.yang@bristol.ac.uk>
Diff between LDAandLDAS versions 1.0.2 dated 2022-10-14 and 1.1.0 dated 2023-03-29
DESCRIPTION | 8 ++-- MD5 | 12 +++---- R/LDA.R | 96 ++++++++++++++++++++++++++++++++++++++++++-------------- R/LDAS.R | 88 ++++++++++++++++++++++++++++++++------------------- man/LDA.Rd | 15 +++++++- man/LDAS.Rd | 36 +++++++++++++++++++-- src/cal_lda.cpp | 7 ++-- 7 files changed, 189 insertions(+), 73 deletions(-)
Title: Color Palettes Inspired by Video Games
Description: Palettes based on video games.
Author: Nathan Constantine-Cooke [aut, cre]
,
Hugh Warden [ctb]
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>
Diff between gameR versions 0.0.4 dated 2023-02-16 and 0.0.5 dated 2023-03-29
DESCRIPTION | 10 ++-- MD5 | 51 ++++++++++++------------ NEWS.md | 6 ++ R/palettes.R | 3 + README.md | 63 ++++++++++++++++++++---------- build/vignette.rds |binary inst/WORDLIST | 4 + man/figures/README-unnamed-chunk-10-1.png |binary man/figures/README-unnamed-chunk-11-1.png |binary man/figures/README-unnamed-chunk-12-1.png |binary man/figures/README-unnamed-chunk-13-1.png |binary man/figures/README-unnamed-chunk-14-1.png |binary man/figures/README-unnamed-chunk-15-1.png |binary man/figures/README-unnamed-chunk-16-1.png |binary man/figures/README-unnamed-chunk-17-1.png |binary man/figures/README-unnamed-chunk-18-1.png |binary man/figures/README-unnamed-chunk-19-1.png |binary man/figures/README-unnamed-chunk-20-1.png |binary man/figures/README-unnamed-chunk-21-1.png |only man/figures/README-unnamed-chunk-22-1.png |only man/figures/README-unnamed-chunk-23-1.png |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-9-1.png |binary man/gameR_cols.Rd | 2 man/gameR_cont.Rd | 2 28 files changed, 91 insertions(+), 50 deletions(-)
Title: Fast Implementation of Reading/Dump for .hic Files
Description: API for fast data extraction for .hic files that provides programmatic access to the matrices. It doesn't store the pointer data for all the matrices, only the one queried, and currently we are only supporting matrices (not vectors).
Author: Neva Cherniavsky Durand [aut, cre],
Muhammad Saad Shamim [aut],
Aiden Lab [cph]
Maintainer: Neva Cherniavsky Durand <neva@broadinstitute.org>
Diff between strawr versions 0.0.9 dated 2021-09-13 and 0.0.91 dated 2023-03-29
DESCRIPTION | 8 LICENSE | 4 MD5 | 33 NAMESPACE | 15 R/RcppExports.R | 119 +- R/strawr.R | 18 README.md | 26 man/readHicBpResolutions.Rd | 40 man/readHicChroms.Rd | 40 man/readHicNormTypes.Rd |only man/straw.Rd | 86 - man/strawr.Rd | 18 src/Makevars | 1 src/RcppExports.cpp | 27 src/straw.cpp | 126 ++ tools/symbols-in-versions | 1904 ++++++++++++++++++++++---------------------- tools/symbols.R | 102 +- tools/winlibs.R | 18 18 files changed, 1368 insertions(+), 1217 deletions(-)
Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching.
Core functionality includes automated training of emulators to data, diagnostic functions
to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
For details on the mathematical background, there are many papers available on the topic
(see references attached to function help files); for details of the functions in this package,
consult the manual or help files.
Author: Andrew Iskauskas [aut, cre] ,
TJ McKinley [aut]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>
Diff between hmer versions 1.2.0 dated 2022-11-08 and 1.4.0 dated 2023-03-29
DESCRIPTION | 20 MD5 | 178 +-- NAMESPACE | 10 NEWS.md | 22 R/Emulator.R | 18 R/EmulatorDocumentation.R | 1 R/ProtoEmulatorDocumentation.R |only R/Proto_emulator.R |only R/VarianceEmulator.R | 21 R/diagnosticplots.R | 8 R/diagnostics.R | 56 R/genpoints.R | 1367 +++++++++++++----------- R/idemc.R | 517 +++++---- R/implausibility.R | 10 R/modelbuilding.R | 80 - R/multiwaveplot.R | 43 R/plotting.R | 55 R/sysdata.rda |only R/utils.R | 54 build/vignette.rds |binary data/BirthDeath.rda |binary data/SIREmulators.rda |binary data/SIRImplausibility.rda |binary data/SIRMultiWaveData.rda |binary data/SIRMultiWaveEmulators.rda |binary data/SIRSample.rda |binary data/bimodalData.rda |binary data/problemData.rda |binary inst/doc/demonstrating-the-hmer-package.Rmd | 4 inst/doc/demonstrating-the-hmer-package.html | 6 inst/doc/emulationhandbook.Rmd | 10 inst/doc/emulationhandbook.html | 12 inst/doc/low-dimensional-examples.Rmd | 73 - inst/doc/low-dimensional-examples.html | 169 +- inst/doc/stochasticandbimodalemulation.Rmd | 16 inst/doc/stochasticandbimodalemulation.html | 56 man/Proto_emulator.Rd |only man/collect_emulators.Rd |only man/emulator_plot.Rd | 6 man/generate_new_runs.Rd | 235 ++-- man/idemc.Rd | 118 +- man/nth_implausible.Rd | 6 man/plot_lattice.Rd | 16 man/space_removal.Rd | 14 tests/testthat/Rplots.pdf |binary tests/testthat/test-cluster.R |only tests/testthat/test-custom_functionality.R |only tests/testthat/test-emulator.R | 44 tests/testthat/test-point_gen.R | 32 tests/testthat/test-proto_em.R |only tests/testthat/test-validation_diag.R | 6 tests/testthat/test-variance_ems.R | 2 vignettes/demonstrating-the-hmer-package.Rmd | 4 vignettes/emulationhandbook.Rmd | 10 vignettes/low-dimensional-examples.Rmd | 73 - vignettes/lowdim-changed-2d-validation-1.png |binary vignettes/lowdim-gen-1d-points-2-1.png |binary vignettes/lowdim-gen-2d-points-2-1.png |binary vignettes/lowdim-gen-2d-points-first-1.png |binary vignettes/lowdim-plot-1d-results-first-1.png |binary vignettes/lowdim-plot-2d-ems-1.png |binary vignettes/lowdim-plot-2d-ems-2.png |binary vignettes/lowdim-plot-2d-ems-corr-1.png |binary vignettes/lowdim-plot-2d-ems-imp-1.png |binary vignettes/lowdim-plot-2d-ems-imp-2.png |binary vignettes/lowdim-plot-2d-ems-with-augment-1.png |binary vignettes/lowdim-plot-2d-imp-2-1.png |binary vignettes/lowdim-plot-2d-waves-1.png |binary vignettes/lowdim-plot-2d-waves-2.png |binary vignettes/lowdim-plot-2d-waves-3.png |binary vignettes/lowdim-validate-2d-ems-1.png |binary vignettes/lowdim-validate-2d-ems-2-1.png |binary vignettes/lowdim-wave-2-1d-1.png |binary vignettes/stoch-bimodal-demo-1.png |binary vignettes/stoch-bimodal-imp-1.png |binary vignettes/stoch-bimodal-indiv-imp-1.png |binary vignettes/stoch-bimodal-indiv-imp-2.png |binary vignettes/stoch-plot-bimodal-1.png |binary vignettes/stoch-plot-bimodal-2.png |binary vignettes/stoch-plot-modes-1.png |binary vignettes/stoch-plot-modes-2.png |binary vignettes/stoch-plot-stoch-ems-1.png |binary vignettes/stoch-plot-stoch-ems-2.png |binary vignettes/stoch-plot-stoch-imp-1.png |binary vignettes/stoch-plot-stoch-var-1.png |binary vignettes/stoch-propose-bimodal-1.png |binary vignettes/stoch-propose-var-em-1.png |binary vignettes/stoch-validate-bimodal-1.png |binary vignettes/stoch-validate-bimodal-2.png |binary vignettes/stoch-validate-stoch-em-1.png |binary vignettes/stoch-validate-stoch-em-2.png |binary vignettes/stoch-validate-stoch-em-3.png |binary vignettes/stoch-validate-var-em-1.png |binary vignettes/stochasticandbimodalemulation.Rmd | 16 94 files changed, 1923 insertions(+), 1465 deletions(-)
Title: Dose Titration Algorithm Tuning
Description: Dose Titration Algorithm Tuning (DTAT) is a methodologic framework
allowing dose individualization to be conceived as a continuous
learning process that begins in early-phase clinical trials and
continues throughout drug development, on into clinical practice.
This package includes code that researchers may use to reproduce
or extend key results of the DTAT research programme, plus tools
for trialists to design and simulate a '3+3/PC' dose-finding study.
Please see Norris (2017a) <doi:10.12688/f1000research.10624.3> and
Norris (2017c) <doi:10.1101/240846>.
Author: David C. Norris [aut, cre]
Maintainer: David C. Norris <david@precisionmethods.guru>
Diff between DTAT versions 0.3-5 dated 2023-03-10 and 0.3-6 dated 2023-03-29
DESCRIPTION | 12 ++++++------ MD5 | 13 +++++++++---- R/titrate.R | 21 ++++++++++----------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/dtat.R |only inst/doc/dtat.Rmd |only inst/doc/dtat.pdf |only inst/doc/widget_D3-viz.html |only vignettes/dtat.Rmd |only 10 files changed, 25 insertions(+), 21 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects. This is demonstrated in Monnahan & Kristensen (2018) <DOI:10.1371/journal.pone.0197954>.
Author: Kasper Kristensen
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.0.7 dated 2023-03-24 and 1.0.9 dated 2023-03-29
DESCRIPTION | 12 ++++++------ MD5 | 10 ++++++---- R/tmbstan.R | 2 +- inst/model.hpp |only man/tmbstan.Rd | 2 +- src/Makevars | 8 ++++++-- src/include/model.hpp |only 7 files changed, 20 insertions(+), 14 deletions(-)
Title: Practical Significance Ranking of Regressors
Description: Consider a possibly nonlinear nonparametric regression
with p regressors. We provide evaluations by 13 methods to rank
regressors by their practical significance or importance using
various methods, including machine learning tools. Comprehensive
methods are as follows.
m6=Generalized partial correlation coefficient or
GPCC by Vinod (2021)<doi:10.1007/s10614-021-10190-x> and
Vinod (2022)<https://www.mdpi.com/1911-8074/15/1/32>.
m7= a generalization of psychologists' effect size incorporating
nonlinearity and many variables.
m8= local linear partial (dy/dxi) using the 'np' package for kernel
regressions.
m9= partial (dy/dxi) using the 'NNS' package.
m10= importance measure using the 'NNS' boost function.
m11= Shapley Value measure of importance (cooperative game theory).
m12 and m13= two versions of the random forest algorithm.
Author: Hrishikesh Vinod [aut, cre]
Maintainer: Hrishikesh Vinod <vinod@fordham.edu>
Diff between practicalSigni versions 0.1.0 dated 2023-02-17 and 0.1.1 dated 2023-03-29
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS |only R/pracSig13.R | 10 +++++++--- R/reportRank.R | 13 ++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/practicalSigni-vignette.pdf |binary man/reportRank.Rd | 5 ++++- 9 files changed, 31 insertions(+), 20 deletions(-)
More information about practicalSigni at CRAN
Permanent link
Title: A Model Library for 'nlmixr2'
Description: A model library for 'nlmixr2'. The models include
(and plan to include) pharmacokinetic, pharmacodynamic, and
disease models used in pharmacometrics. Where applicable,
references for each model are included in the meta-data for
each individual model. The package also includes model
composition and modification functions to make model updates
easier.
Author: Richard Hooijmaijers [aut],
Matthew Fidler [aut] ,
Bill Denney [aut, cre]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between nlmixr2lib versions 0.1.0 dated 2022-10-31 and 0.2.0 dated 2023-03-29
nlmixr2lib-0.1.0/nlmixr2lib/R/reexport.R |only nlmixr2lib-0.1.0/nlmixr2lib/man/reexports.Rd |only nlmixr2lib-0.2.0/nlmixr2lib/DESCRIPTION | 11 +- nlmixr2lib-0.2.0/nlmixr2lib/MD5 | 50 +++++----- nlmixr2lib-0.2.0/nlmixr2lib/NAMESPACE | 3 nlmixr2lib-0.2.0/nlmixr2lib/NEWS.md | 24 ++++ nlmixr2lib-0.2.0/nlmixr2lib/R/addEta.R | 30 ++++-- nlmixr2lib-0.2.0/nlmixr2lib/R/addResErr.R | 7 + nlmixr2lib-0.2.0/nlmixr2lib/R/modeldb.R | 16 +-- nlmixr2lib-0.2.0/nlmixr2lib/R/readModelDb.R | 4 nlmixr2lib-0.2.0/nlmixr2lib/R/updateOncologyXenograftSimeoni2004.R |only nlmixr2lib-0.2.0/nlmixr2lib/README.md | 1 nlmixr2lib-0.2.0/nlmixr2lib/build/vignette.rds |binary nlmixr2lib-0.2.0/nlmixr2lib/data/modeldb.rda |binary nlmixr2lib-0.2.0/nlmixr2lib/inst/WORDLIST | 16 +++ nlmixr2lib-0.2.0/nlmixr2lib/inst/doc/create-model-library.Rmd | 32 ++++++ nlmixr2lib-0.2.0/nlmixr2lib/inst/doc/create-model-library.html | 36 +++++++ nlmixr2lib-0.2.0/nlmixr2lib/inst/modeldb/PK_2cmt_tdcl_des.R |only nlmixr2lib-0.2.0/nlmixr2lib/inst/modeldb/pharmacokinetics |only nlmixr2lib-0.2.0/nlmixr2lib/inst/modeldb/specificDrugs |only nlmixr2lib-0.2.0/nlmixr2lib/inst/modeldb/therapeuticArea |only nlmixr2lib-0.2.0/nlmixr2lib/man/addEta.Rd | 1 nlmixr2lib-0.2.0/nlmixr2lib/man/addResErr.Rd | 1 nlmixr2lib-0.2.0/nlmixr2lib/man/modeldb.Rd | 2 nlmixr2lib-0.2.0/nlmixr2lib/man/updateOncologyXenograftSimeoni2004.Rd |only nlmixr2lib-0.2.0/nlmixr2lib/tests/testthat/test-addEta.R | 37 +++++++ nlmixr2lib-0.2.0/nlmixr2lib/tests/testthat/test-readModelDb.R | 4 nlmixr2lib-0.2.0/nlmixr2lib/tests/testthat/test-updateOncologyXenograftSimeoni2004.R |only nlmixr2lib-0.2.0/nlmixr2lib/vignettes/create-model-library.Rmd | 32 ++++++ 29 files changed, 257 insertions(+), 50 deletions(-)
Title: Competitive Gene Sets Test with the Mann-Whitney-Wilcoxon Test
Description: Friendly implementation of the Mann-Whitney-Wilcoxon test for competitive gene set enrichment analysis.
Author: Stefano Maria Pagnotta [aut, cre, cph]
Maintainer: Stefano Maria Pagnotta <pagnotta@unisannio.it>
Diff between massiveGST versions 1.0.1 dated 2022-06-10 and 1.2.3 dated 2023-03-29
DESCRIPTION | 8 MD5 | 36 NAMESPACE | 6 R/geneSets.sim.R | 4 R/massiveORT.R |only R/plot.mGST.R | 2 R/plot.mORT.R |only R/plot.network.R | 49 R/print.mORT.R |only R/summary.mGST.R | 5 R/summary.mORT.R |only build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 inst/doc/vignette.R | 22 inst/doc/vignette.Rmd | 42 inst/doc/vignette.html | 2071 +- inst/extdata/pre_ranked_list.txt |35628 +++++++++++++++++++-------------------- man/geneSets.sim.Rd |only man/massiveGST.Rd | 24 man/massiveORT.Rd |only vignettes/vignette.Rmd | 42 22 files changed, 19509 insertions(+), 18432 deletions(-)
Title: Estimation and Additional Tools for Alternative Shared Frailty
Models
Description: Provide estimation and data generation tools for some new multivariate frailty models.
This version includes the gamma, inverse Gaussian, weighted Lindley and Birnbaum-Saunders
as the distribution for the frailty terms.
For the basal model, it is considered a parametric approach based on the Weibull and the
piecewise exponential distributions and a semiparametric approach. For details, see
Gallardo and Bourguignon (2022) <arXiv:2206.12973>.
Author: Diego Gallardo [aut, cre],
Marcelo Bourguignon [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between extrafrail versions 1.3 dated 2023-01-29 and 1.4 dated 2023-03-29
DESCRIPTION | 16 MD5 | 18 NAMESPACE | 1 NEWS.md | 4 R/baseCH.R | 5 R/frailty.fit.R | 3170 +++++++++++++++++++++++++++++++------------------ R/print.extrafrail.R | 107 - R/summary.extrafrail.R | 231 ++- man/baseCH.Rd | 6 man/frailty.fit.Rd | 16 10 files changed, 2257 insertions(+), 1317 deletions(-)
Title: A General Framework for Combining Ecosystem Models
Description: Fit and sample from the ensemble model described in Spence et al (2018): "A general framework for combining ecosystem models"<https://onlinelibrary.wiley.com/doi/abs/10.1111/faf.12310>.
Author: Michael A. Spence [aut, cre] ,
James A. Martindale [aut] ,
Michael J. Thomson [aut]
Maintainer: Michael A. Spence <michael.spence@cefas.gov.uk>
Diff between EcoEnsemble versions 1.0.2 dated 2023-03-17 and 1.0.3 dated 2023-03-29
EcoEnsemble-1.0.2/EcoEnsemble/vignettes/data/vignette_plots.Rdata |only EcoEnsemble-1.0.3/EcoEnsemble/DESCRIPTION | 6 +-- EcoEnsemble-1.0.3/EcoEnsemble/MD5 | 16 +++++----- EcoEnsemble-1.0.3/EcoEnsemble/inst/doc/EcoEnsemble.R | 8 ++--- EcoEnsemble-1.0.3/EcoEnsemble/inst/doc/EcoEnsemble.Rmd | 11 +++--- EcoEnsemble-1.0.3/EcoEnsemble/inst/doc/EcoEnsemble.html | 12 +++---- EcoEnsemble-1.0.3/EcoEnsemble/inst/doc/ExploringPriors.html | 12 +++---- EcoEnsemble-1.0.3/EcoEnsemble/vignettes/EcoEnsemble.Rmd | 11 +++--- EcoEnsemble-1.0.3/EcoEnsemble/vignettes/data/plot_initial_customised.png |only EcoEnsemble-1.0.3/EcoEnsemble/vignettes/data/plot_initial_outputs.png |only EcoEnsemble-1.0.3/EcoEnsemble/vignettes/data/plot_priors_only.png |only 11 files changed, 38 insertions(+), 38 deletions(-)
Title: Chaotic Time Series Analysis
Description: Chaos theory has been hailed as a revolution of thoughts and attracting ever increasing
attention of many scientists from diverse disciplines. Chaotic systems are nonlinear deterministic
dynamic systems which can behave like an erratic and apparently random motion. A relevant field
inside chaos theory and nonlinear time series analysis is the detection of a chaotic behaviour
from empirical time series data. One of the main features of chaos is the well known initial value
sensitivity property. Methods and techniques related to test the hypothesis of chaos try to quantify
the initial value sensitive property estimating the Lyapunov exponents. The DChaos package
provides different useful tools and efficient algorithms which test robustly the hypothesis of chaos
based on the Lyapunov exponent in order to know if the data generating process behind time series
behave chaotically or not.
Author: Julio E. Sandubete [aut, cre],
Lorenzo Escot [aut]
Maintainer: Julio E. Sandubete <jsandube@ucm.es>
Diff between DChaos versions 0.1-6 dated 2021-02-10 and 0.1-7 dated 2023-03-29
DESCRIPTION | 15 - MD5 | 44 ++- NAMESPACE | 2 R/embedding.R | 161 ++++++------- R/gauss.sim.R | 29 +- R/henon.sim.R | 46 ++- R/jacobian.net.R | 55 ++-- R/logistic.sim.R | 31 +- R/lyapunov.R | 197 +++++++---------- R/lyapunov.max.R | 365 +++++++++++++++---------------- R/lyapunov.spec.R | 590 +++++++++++++++++++++++++-------------------------- R/netfit.R | 73 ++---- R/rossler.sim.R | 94 +++----- R/summary.lyapunov.R | 36 +-- R/w0.net.R | 39 +-- build |only inst |only man/henon.sim.Rd | 4 man/jacobian.net.Rd | 5 man/lyapunov.Rd | 7 man/netfit.Rd | 5 man/rossler.sim.Rd | 4 man/w0.net.Rd | 5 vignettes |only 24 files changed, 860 insertions(+), 947 deletions(-)
Title: Sensitivity Analysis Tools for Dependence and Asymptotic
Dependence
Description: Tools for analyzing tail dependence in any sample or in particular theoretical models. The package uses only theoretical and non parametric methods, without inference. The primary goals of the package are to provide: (a)symmetric multivariate extreme value models in any dimension; theoretical and empirical indices to order tail dependence; theoretical and empirical graphical methods to visualize tail dependence.
Author: Cecile Mercadier [aut, cre]
Maintainer: Cecile Mercadier <mercadier@math.univ-lyon1.fr>
Diff between satdad versions 1.0 dated 2023-03-03 and 1.1 dated 2023-03-29
satdad-1.0/satdad/man/supportAnalysisEmp.Rd |only satdad-1.1/satdad/DESCRIPTION | 8 - satdad-1.1/satdad/MD5 | 17 +--- satdad-1.1/satdad/R/satdad_Rfunctions.R | 119 ---------------------------- satdad-1.1/satdad/inst/doc/satdad.R | 6 - satdad-1.1/satdad/inst/doc/satdad.Rmd | 17 ---- satdad-1.1/satdad/inst/doc/satdad.html | 97 +++++++--------------- satdad-1.1/satdad/man/France.Rd | 2 satdad-1.1/satdad/man/graphsEmp.Rd | 2 satdad-1.1/satdad/vignettes/satdad.Rmd | 17 ---- 10 files changed, 57 insertions(+), 228 deletions(-)
Title: Functions for Drawing Ellipses and Ellipse-Like Confidence
Regions
Description: Contains various routines for drawing
ellipses and ellipse-like confidence regions, implementing the plots
described in Murdoch and Chow (1996, <doi:10.2307/2684435>). There are
also routines implementing the profile plots described in Bates and
Watts (1988, <doi:10.1002/9780470316757>).
Author: Duncan Murdoch and E. D. Chow
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between ellipse versions 0.4.3 dated 2022-05-31 and 0.4.4 dated 2023-03-29
ellipse-0.4.3/ellipse/README |only ellipse-0.4.4/ellipse/DESCRIPTION | 9 ++++++--- ellipse-0.4.4/ellipse/MD5 | 17 ++++++++++------- ellipse-0.4.4/ellipse/NEWS.md |only ellipse-0.4.4/ellipse/R/ellipse.default.R | 9 +++++++-- ellipse-0.4.4/ellipse/README.md |only ellipse-0.4.4/ellipse/build/partial.rdb |binary ellipse-0.4.4/ellipse/man/ellipse-package.Rd | 4 ++-- ellipse-0.4.4/ellipse/man/ellipse.Rd | 10 ++++++++-- ellipse-0.4.4/ellipse/man/ellipse.profile.glm.Rd | 2 +- ellipse-0.4.4/ellipse/man/figures |only 11 files changed, 34 insertions(+), 17 deletions(-)
Title: 'WhiteboxTools' R Frontend
Description: An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. [...truncated...]
Author: Qiusheng Wu [aut],
Andrew Brown [ctb, cre]
Maintainer: Andrew Brown <brown.andrewg@gmail.com>
Diff between whitebox versions 2.2.0 dated 2022-10-27 and 2.3.0 dated 2023-03-29
DESCRIPTION | 11 MD5 | 1202 ++++++------ NAMESPACE | 22 NEWS.md | 22 R/data_tools.R | 247 +- R/gis_analysis.R | 352 ++- R/gis_analysis_distance.R | 48 R/gis_analysis_overlay.R | 234 +- R/gis_analysis_patch_shape.R | 112 - R/hydro_analysis.R | 511 +++-- R/image_analysis.R | 160 + R/image_analysis_classification.R | 48 R/image_analysis_enhancement.R | 112 - R/image_analysis_filters.R | 280 +- R/lidar_analysis.R | 600 ++++-- R/machine_learning.R | 80 R/math_stat_analysis.R | 745 +++++-- R/precision_agriculture.R | 48 R/stream_network_analysis.R | 192 +- R/terrain_analysis.R | 914 ++++++--- R/wbt-method.R |only R/wbt.R | 211 +- R/wbt_source.R |only R/whitebox-package.R | 31 R/whitebox_utilities.R |only R/zzz.R | 8 README.md | 127 - build/partial.rdb |binary build/vignette.rds |binary data/wbttoolparameters.rda |binary data/wbttools.rda |binary inst/CITATION | 16 inst/WORDLIST | 38 inst/doc/datasets.Rmd | 20 inst/doc/datasets.html | 602 +++--- inst/doc/demo.R | 12 inst/doc/demo.Rmd | 87 inst/doc/demo.html | 1516 +++++++--------- inst/doc/wbt-method.R |only inst/doc/wbt-method.Rmd |only inst/doc/wbt-method.html |only man/check_whitebox_binary.Rd | 7 man/figures/README-unnamed-chunk-8-1.png |binary man/install_whitebox.Rd | 16 man/sample_dem_data.Rd | 2 man/wbt.Rd |only man/wbt_absolute_value.Rd | 3 man/wbt_accumulation_curvature.Rd | 3 man/wbt_activate.Rd | 5 man/wbt_adaptive_filter.Rd | 3 man/wbt_add.Rd | 3 man/wbt_add_point_coordinates_to_table.Rd | 3 man/wbt_aggregate_raster.Rd | 3 man/wbt_and.Rd | 3 man/wbt_anova.Rd | 3 man/wbt_arc_cos.Rd | 3 man/wbt_arc_sin.Rd | 3 man/wbt_arc_tan.Rd | 3 man/wbt_arcosh.Rd | 3 man/wbt_arsinh.Rd | 3 man/wbt_artanh.Rd | 3 man/wbt_ascii_to_las.Rd | 3 man/wbt_aspect.Rd | 3 man/wbt_assess_route.Rd | 3 man/wbt_atan2.Rd | 3 man/wbt_attribute_correlation.Rd | 3 man/wbt_attribute_correlation_neighbourhood_analysis.Rd | 3 man/wbt_attribute_histogram.Rd | 5 man/wbt_attribute_scattergram.Rd | 3 man/wbt_average_flowpath_slope.Rd | 3 man/wbt_average_normal_vector_angular_deviation.Rd | 3 man/wbt_average_overlay.Rd | 3 man/wbt_average_upslope_flowpath_length.Rd | 3 man/wbt_balance_contrast_enhancement.Rd | 3 man/wbt_basins.Rd | 3 man/wbt_bilateral_filter.Rd | 3 man/wbt_block_maximum_gridding.Rd | 3 man/wbt_block_minimum_gridding.Rd | 3 man/wbt_boundary_shape_complexity.Rd | 3 man/wbt_breach_depressions.Rd | 3 man/wbt_breach_depressions_least_cost.Rd | 3 man/wbt_breach_single_cell_pits.Rd | 3 man/wbt_breakline_mapping.Rd | 3 man/wbt_buffer_raster.Rd | 3 man/wbt_burn_streams_at_roads.Rd | 3 man/wbt_canny_edge_detection.Rd | 3 man/wbt_ceil.Rd | 3 man/wbt_centroid.Rd | 3 man/wbt_centroid_vector.Rd | 3 man/wbt_change_vector_analysis.Rd | 3 man/wbt_circular_variance_of_aspect.Rd | 3 man/wbt_classify_buildings_in_lidar.Rd | 3 man/wbt_classify_lidar.Rd | 3 man/wbt_classify_overlap_points.Rd | 3 man/wbt_clean_vector.Rd | 3 man/wbt_clip.Rd | 3 man/wbt_clip_lidar_to_polygon.Rd | 3 man/wbt_clip_raster_to_polygon.Rd | 5 man/wbt_closing.Rd | 3 man/wbt_clump.Rd | 3 man/wbt_colourize_based_on_class.Rd | 3 man/wbt_colourize_based_on_point_returns.Rd | 3 man/wbt_compactness_ratio.Rd | 3 man/wbt_conditional_evaluation.Rd | 5 man/wbt_conditioned_latin_hypercube.Rd | 3 man/wbt_conservative_smoothing_filter.Rd | 3 man/wbt_construct_vector_tin.Rd | 3 man/wbt_contours_from_points.Rd | 3 man/wbt_contours_from_raster.Rd | 3 man/wbt_convert_nodata_to_zero.Rd | 3 man/wbt_convert_raster_format.Rd | 3 man/wbt_corner_detection.Rd | 3 man/wbt_correct_vignetting.Rd | 3 man/wbt_cos.Rd | 3 man/wbt_cosh.Rd | 3 man/wbt_cost_allocation.Rd | 3 man/wbt_cost_distance.Rd | 3 man/wbt_cost_pathway.Rd | 3 man/wbt_count_if.Rd | 3 man/wbt_create_colour_composite.Rd | 3 man/wbt_create_hexagonal_vector_grid.Rd | 3 man/wbt_create_plane.Rd | 3 man/wbt_create_rectangular_vector_grid.Rd | 3 man/wbt_crispness_index.Rd | 3 man/wbt_cross_tabulation.Rd | 3 man/wbt_csv_points_to_vector.Rd | 3 man/wbt_cumulative_distribution.Rd | 3 man/wbt_curvedness.Rd | 3 man/wbt_d8_flow_accumulation.Rd | 3 man/wbt_d8_mass_flux.Rd | 3 man/wbt_d8_pointer.Rd | 3 man/wbt_d_inf_flow_accumulation.Rd | 3 man/wbt_d_inf_mass_flux.Rd | 3 man/wbt_d_inf_pointer.Rd | 3 man/wbt_dbscan.Rd | 3 man/wbt_decrement.Rd | 3 man/wbt_dem_void_filling.Rd |only man/wbt_depth_in_sink.Rd | 3 man/wbt_depth_to_water.Rd | 3 man/wbt_dev_from_mean_elev.Rd | 3 man/wbt_diff_from_mean_elev.Rd | 3 man/wbt_diff_of_gaussian_filter.Rd | 3 man/wbt_difference.Rd | 3 man/wbt_difference_curvature.Rd | 3 man/wbt_direct_decorrelation_stretch.Rd | 3 man/wbt_directional_relief.Rd | 3 man/wbt_dissolve.Rd | 3 man/wbt_distance_to_outlet.Rd | 3 man/wbt_diversity_filter.Rd | 3 man/wbt_divide.Rd | 3 man/wbt_downslope_distance_to_stream.Rd | 3 man/wbt_downslope_flowpath_length.Rd | 3 man/wbt_downslope_index.Rd | 3 man/wbt_edge_contamination.Rd | 5 man/wbt_edge_density.Rd | 3 man/wbt_edge_preserving_mean_filter.Rd | 3 man/wbt_edge_proportion.Rd | 3 man/wbt_elev_above_pit.Rd | 3 man/wbt_elev_percentile.Rd | 3 man/wbt_elev_relative_to_min_max.Rd | 3 man/wbt_elev_relative_to_watershed_min_max.Rd | 3 man/wbt_elevation_above_stream.Rd | 3 man/wbt_elevation_above_stream_euclidean.Rd | 3 man/wbt_eliminate_coincident_points.Rd | 3 man/wbt_elongation_ratio.Rd | 3 man/wbt_embankment_mapping.Rd | 3 man/wbt_emboss_filter.Rd | 3 man/wbt_equal_to.Rd | 3 man/wbt_erase.Rd | 3 man/wbt_erase_polygon_from_lidar.Rd | 3 man/wbt_erase_polygon_from_raster.Rd | 3 man/wbt_euclidean_allocation.Rd | 3 man/wbt_euclidean_distance.Rd | 3 man/wbt_evaluate_training_sites.Rd | 3 man/wbt_exp.Rd | 3 man/wbt_exp2.Rd | 3 man/wbt_export_table_to_csv.Rd | 3 man/wbt_exposure_towards_wind_flux.Rd | 5 man/wbt_extend_vector_lines.Rd | 3 man/wbt_extract_nodes.Rd | 3 man/wbt_extract_raster_values_at_points.Rd | 3 man/wbt_extract_streams.Rd | 3 man/wbt_extract_valleys.Rd | 3 man/wbt_farthest_channel_head.Rd | 3 man/wbt_fast_almost_gaussian_filter.Rd | 3 man/wbt_fd8_flow_accumulation.Rd | 3 man/wbt_fd8_pointer.Rd | 3 man/wbt_feature_preserving_smoothing.Rd | 3 man/wbt_fetch_analysis.Rd | 3 man/wbt_fill_burn.Rd | 3 man/wbt_fill_depressions.Rd | 3 man/wbt_fill_depressions_planchon_and_darboux.Rd | 3 man/wbt_fill_depressions_wang_and_liu.Rd | 3 man/wbt_fill_missing_data.Rd | 3 man/wbt_fill_single_cell_pits.Rd | 3 man/wbt_filter_lidar.Rd | 3 man/wbt_filter_lidar_classes.Rd | 3 man/wbt_filter_lidar_scan_angles.Rd | 3 man/wbt_filter_raster_features_by_area.Rd | 3 man/wbt_find_flightline_edge_points.Rd | 3 man/wbt_find_lowest_or_highest_points.Rd | 3 man/wbt_find_main_stem.Rd | 3 man/wbt_find_no_flow_cells.Rd | 3 man/wbt_find_parallel_flow.Rd | 3 man/wbt_find_patch_or_class_edge_cells.Rd | 3 man/wbt_find_ridges.Rd | 3 man/wbt_fix_dangling_arcs.Rd | 3 man/wbt_flatten_lakes.Rd | 3 man/wbt_flightline_overlap.Rd | 3 man/wbt_flip_image.Rd | 3 man/wbt_flood_order.Rd | 3 man/wbt_floor.Rd | 3 man/wbt_flow_accumulation_full_workflow.Rd | 3 man/wbt_flow_length_diff.Rd | 3 man/wbt_gamma_correction.Rd | 3 man/wbt_gaussian_contrast_stretch.Rd | 3 man/wbt_gaussian_curvature.Rd | 3 man/wbt_gaussian_filter.Rd | 3 man/wbt_gaussian_scale_space.Rd | 5 man/wbt_generalize_classified_raster.Rd | 3 man/wbt_generalize_with_similarity.Rd | 3 man/wbt_generating_function.Rd | 3 man/wbt_geomorphons.Rd | 3 man/wbt_greater_than.Rd | 3 man/wbt_hack_stream_order.Rd | 3 man/wbt_heat_map.Rd | 5 man/wbt_height_above_ground.Rd | 5 man/wbt_help.Rd | 7 man/wbt_high_pass_bilateral_filter.Rd | 3 man/wbt_high_pass_filter.Rd | 3 man/wbt_high_pass_median_filter.Rd | 3 man/wbt_highest_position.Rd | 3 man/wbt_hillshade.Rd | 3 man/wbt_hillslopes.Rd | 3 man/wbt_histogram_equalization.Rd | 3 man/wbt_histogram_matching.Rd | 3 man/wbt_histogram_matching_two_images.Rd | 5 man/wbt_hole_proportion.Rd | 3 man/wbt_horizon_angle.Rd | 3 man/wbt_horizontal_excess_curvature.Rd | 3 man/wbt_horton_stream_order.Rd | 3 man/wbt_hydrologic_connectivity.Rd | 3 man/wbt_hypsometric_analysis.Rd | 3 man/wbt_hypsometrically_tinted_hillshade.Rd | 3 man/wbt_idw_interpolation.Rd | 3 man/wbt_ihs_to_rgb.Rd | 3 man/wbt_image_autocorrelation.Rd | 3 man/wbt_image_correlation.Rd | 3 man/wbt_image_correlation_neighbourhood_analysis.Rd | 3 man/wbt_image_regression.Rd | 3 man/wbt_image_segmentation.Rd | 3 man/wbt_image_slider.Rd | 3 man/wbt_image_stack_profile.Rd | 3 man/wbt_impoundment_size_index.Rd | 3 man/wbt_in_place_add.Rd | 3 man/wbt_in_place_divide.Rd | 3 man/wbt_in_place_multiply.Rd | 3 man/wbt_in_place_subtract.Rd | 3 man/wbt_increment.Rd | 3 man/wbt_individual_tree_detection.Rd |only man/wbt_init.Rd | 36 man/wbt_insert_dams.Rd | 3 man/wbt_install_wb_extension.Rd |only man/wbt_integer_division.Rd | 3 man/wbt_integral_image.Rd | 3 man/wbt_intersect.Rd | 3 man/wbt_inverse_principal_component_analysis.Rd | 3 man/wbt_is_no_data.Rd | 3 man/wbt_isobasins.Rd | 3 man/wbt_jenson_snap_pour_points.Rd | 3 man/wbt_join_tables.Rd | 3 man/wbt_k_means_clustering.Rd | 3 man/wbt_k_nearest_mean_filter.Rd | 3 man/wbt_kappa_index.Rd | 3 man/wbt_knn_classification.Rd | 3 man/wbt_knn_regression.Rd | 3 man/wbt_ks_test_for_normality.Rd | 3 man/wbt_laplacian_filter.Rd | 3 man/wbt_laplacian_of_gaussian_filter.Rd | 3 man/wbt_las_to_ascii.Rd | 3 man/wbt_las_to_laz.Rd | 3 man/wbt_las_to_multipoint_shapefile.Rd | 3 man/wbt_las_to_shapefile.Rd | 3 man/wbt_las_to_zlidar.Rd | 3 man/wbt_launch_wb_runner.Rd |only man/wbt_layer_footprint.Rd | 3 man/wbt_laz_to_las.Rd | 3 man/wbt_lee_sigma_filter.Rd | 3 man/wbt_length_of_upstream_channels.Rd | 3 man/wbt_less_than.Rd | 3 man/wbt_license.Rd | 5 man/wbt_lidar_block_maximum.Rd | 3 man/wbt_lidar_block_minimum.Rd | 3 man/wbt_lidar_classify_subset.Rd | 3 man/wbt_lidar_colourize.Rd | 3 man/wbt_lidar_contour.Rd | 6 man/wbt_lidar_digital_surface_model.Rd | 3 man/wbt_lidar_eigenvalue_features.Rd | 3 man/wbt_lidar_elevation_slice.Rd | 3 man/wbt_lidar_ground_point_filter.Rd | 3 man/wbt_lidar_hex_binning.Rd | 3 man/wbt_lidar_hillshade.Rd | 3 man/wbt_lidar_histogram.Rd | 3 man/wbt_lidar_idw_interpolation.Rd | 3 man/wbt_lidar_info.Rd | 3 man/wbt_lidar_join.Rd | 3 man/wbt_lidar_kappa_index.Rd | 3 man/wbt_lidar_nearest_neighbour_gridding.Rd | 5 man/wbt_lidar_point_density.Rd | 3 man/wbt_lidar_point_return_analysis.Rd | 3 man/wbt_lidar_point_stats.Rd | 3 man/wbt_lidar_ransac_planes.Rd | 3 man/wbt_lidar_rbf_interpolation.Rd | 3 man/wbt_lidar_remove_duplicates.Rd | 3 man/wbt_lidar_remove_outliers.Rd | 3 man/wbt_lidar_rooftop_analysis.Rd | 3 man/wbt_lidar_segmentation.Rd | 3 man/wbt_lidar_segmentation_based_filter.Rd | 3 man/wbt_lidar_shift.Rd | 3 man/wbt_lidar_sibson_interpolation.Rd | 3 man/wbt_lidar_sort_by_time.Rd | 3 man/wbt_lidar_thin.Rd | 3 man/wbt_lidar_thin_high_density.Rd | 3 man/wbt_lidar_tile.Rd | 3 man/wbt_lidar_tile_footprint.Rd | 3 man/wbt_lidar_tin_gridding.Rd | 3 man/wbt_lidar_tophat_transform.Rd | 3 man/wbt_line_detection_filter.Rd | 3 man/wbt_line_intersections.Rd | 3 man/wbt_line_thinning.Rd | 3 man/wbt_linearity_index.Rd | 3 man/wbt_lines_to_polygons.Rd | 3 man/wbt_list_tools.Rd | 5 man/wbt_list_unique_values.Rd | 5 man/wbt_list_unique_values_raster.Rd |only man/wbt_ln.Rd | 3 man/wbt_local_hypsometric_analysis.Rd | 3 man/wbt_local_quadratic_regression.Rd | 5 man/wbt_log10.Rd | 3 man/wbt_log2.Rd | 3 man/wbt_logistic_regression.Rd | 3 man/wbt_long_profile.Rd | 3 man/wbt_long_profile_from_points.Rd | 3 man/wbt_longest_flowpath.Rd | 3 man/wbt_low_points_on_headwater_divides.Rd | 3 man/wbt_lowest_position.Rd | 3 man/wbt_majority_filter.Rd | 3 man/wbt_map_off_terrain_objects.Rd | 3 man/wbt_max.Rd | 3 man/wbt_max_absolute_overlay.Rd | 3 man/wbt_max_anisotropy_dev.Rd | 3 man/wbt_max_anisotropy_dev_signature.Rd | 3 man/wbt_max_branch_length.Rd | 3 man/wbt_max_difference_from_mean.Rd | 3 man/wbt_max_downslope_elev_change.Rd | 3 man/wbt_max_elev_dev_signature.Rd | 3 man/wbt_max_elevation_deviation.Rd | 3 man/wbt_max_overlay.Rd | 3 man/wbt_max_upslope_elev_change.Rd | 3 man/wbt_max_upslope_flowpath_length.Rd | 3 man/wbt_max_upslope_value.Rd | 5 man/wbt_maximal_curvature.Rd | 3 man/wbt_maximum_filter.Rd | 3 man/wbt_md_inf_flow_accumulation.Rd | 3 man/wbt_mean_curvature.Rd | 3 man/wbt_mean_filter.Rd | 3 man/wbt_median_filter.Rd | 3 man/wbt_medoid.Rd | 3 man/wbt_merge_line_segments.Rd | 3 man/wbt_merge_table_with_csv.Rd | 3 man/wbt_merge_vectors.Rd | 3 man/wbt_min.Rd | 3 man/wbt_min_absolute_overlay.Rd | 3 man/wbt_min_dist_classification.Rd | 3 man/wbt_min_downslope_elev_change.Rd | 3 man/wbt_min_max_contrast_stretch.Rd | 3 man/wbt_min_overlay.Rd | 3 man/wbt_minimal_curvature.Rd | 3 man/wbt_minimum_bounding_box.Rd | 3 man/wbt_minimum_bounding_circle.Rd | 3 man/wbt_minimum_bounding_envelope.Rd | 3 man/wbt_minimum_convex_hull.Rd | 3 man/wbt_minimum_filter.Rd | 3 man/wbt_modified_k_means_clustering.Rd | 3 man/wbt_modify_lidar.Rd | 3 man/wbt_modify_no_data_value.Rd | 5 man/wbt_modulo.Rd | 3 man/wbt_mosaic.Rd | 3 man/wbt_mosaic_with_feathering.Rd | 3 man/wbt_multi_part_to_single_part.Rd | 3 man/wbt_multidirectional_hillshade.Rd | 3 man/wbt_multiply.Rd | 3 man/wbt_multiply_overlay.Rd | 3 man/wbt_multiscale_curvatures.Rd |only man/wbt_multiscale_elevation_percentile.Rd | 3 man/wbt_multiscale_roughness.Rd | 3 man/wbt_multiscale_roughness_signature.Rd | 3 man/wbt_multiscale_std_dev_normals.Rd | 3 man/wbt_multiscale_std_dev_normals_signature.Rd | 3 man/wbt_multiscale_topographic_position_image.Rd | 6 man/wbt_narrowness_index.Rd | 3 man/wbt_natural_neighbour_interpolation.Rd | 3 man/wbt_nearest_neighbour_gridding.Rd | 3 man/wbt_negate.Rd | 3 man/wbt_new_raster_from_base.Rd | 3 man/wbt_normal_vectors.Rd | 3 man/wbt_normalize_lidar.Rd |only man/wbt_normalized_difference_index.Rd | 3 man/wbt_not.Rd | 3 man/wbt_not_equal_to.Rd | 3 man/wbt_num_downslope_neighbours.Rd | 3 man/wbt_num_inflowing_neighbours.Rd | 3 man/wbt_num_upslope_neighbours.Rd | 3 man/wbt_olympic_filter.Rd | 3 man/wbt_opening.Rd | 3 man/wbt_openness.Rd | 3 man/wbt_or.Rd | 3 man/wbt_paired_sample_t_test.Rd | 3 man/wbt_panchromatic_sharpening.Rd | 3 man/wbt_parallelepiped_classification.Rd | 3 man/wbt_patch_orientation.Rd | 3 man/wbt_pennock_landform_class.Rd | 3 man/wbt_percent_elev_range.Rd | 3 man/wbt_percent_equal_to.Rd | 3 man/wbt_percent_greater_than.Rd | 3 man/wbt_percent_less_than.Rd | 3 man/wbt_percentage_contrast_stretch.Rd | 3 man/wbt_percentile_filter.Rd | 3 man/wbt_perimeter_area_ratio.Rd | 3 man/wbt_phi_coefficient.Rd | 3 man/wbt_pick_from_list.Rd | 3 man/wbt_piecewise_contrast_stretch.Rd | 3 man/wbt_plan_curvature.Rd | 3 man/wbt_polygon_area.Rd | 3 man/wbt_polygon_long_axis.Rd | 5 man/wbt_polygon_perimeter.Rd | 3 man/wbt_polygon_short_axis.Rd | 5 man/wbt_polygonize.Rd | 3 man/wbt_polygons_to_lines.Rd | 3 man/wbt_power.Rd | 3 man/wbt_prewitt_filter.Rd | 3 man/wbt_principal_component_analysis.Rd | 3 man/wbt_print_geo_tiff_tags.Rd | 3 man/wbt_profile.Rd | 3 man/wbt_profile_curvature.Rd | 3 man/wbt_qin_flow_accumulation.Rd | 5 man/wbt_quantiles.Rd | 3 man/wbt_quinn_flow_accumulation.Rd | 5 man/wbt_radial_basis_function_interpolation.Rd | 3 man/wbt_radius_of_gyration.Rd | 3 man/wbt_raise_walls.Rd | 3 man/wbt_random_field.Rd | 3 man/wbt_random_forest_classification.Rd | 3 man/wbt_random_forest_regression.Rd | 3 man/wbt_random_sample.Rd | 3 man/wbt_range_filter.Rd | 3 man/wbt_raster_area.Rd | 3 man/wbt_raster_calculator.Rd | 5 man/wbt_raster_cell_assignment.Rd | 3 man/wbt_raster_histogram.Rd | 3 man/wbt_raster_perimeter.Rd | 3 man/wbt_raster_streams_to_vector.Rd | 3 man/wbt_raster_summary_stats.Rd | 3 man/wbt_raster_to_vector_lines.Rd | 3 man/wbt_raster_to_vector_points.Rd | 3 man/wbt_raster_to_vector_polygons.Rd | 3 man/wbt_rasterize_streams.Rd | 3 man/wbt_reciprocal.Rd | 3 man/wbt_reclass.Rd | 3 man/wbt_reclass_equal_interval.Rd | 3 man/wbt_reclass_from_file.Rd | 3 man/wbt_reconcile_multiple_headers.Rd | 3 man/wbt_recover_flightline_info.Rd | 3 man/wbt_recreate_pass_lines.Rd | 3 man/wbt_reinitialize_attribute_table.Rd | 3 man/wbt_related_circumscribing_circle.Rd | 3 man/wbt_relative_aspect.Rd | 3 man/wbt_relative_topographic_position.Rd | 3 man/wbt_remove_field_edge_points.Rd | 3 man/wbt_remove_off_terrain_objects.Rd | 3 man/wbt_remove_polygon_holes.Rd | 3 man/wbt_remove_raster_polygon_holes.Rd |only man/wbt_remove_short_streams.Rd | 3 man/wbt_remove_spurs.Rd | 3 man/wbt_repair_stream_vector_topology.Rd | 3 man/wbt_resample.Rd | 3 man/wbt_rescale_value_range.Rd | 3 man/wbt_rgb_to_ihs.Rd | 3 man/wbt_rho8_flow_accumulation.Rd | 5 man/wbt_rho8_pointer.Rd | 3 man/wbt_ring_curvature.Rd | 3 man/wbt_river_centerlines.Rd |only man/wbt_roberts_cross_filter.Rd | 3 man/wbt_root_mean_square_error.Rd | 3 man/wbt_rotor.Rd | 3 man/wbt_round.Rd | 3 man/wbt_ruggedness_index.Rd | 3 man/wbt_run_tool.Rd | 3 man/wbt_rust_backtrace.Rd | 1 man/wbt_scharr_filter.Rd | 3 man/wbt_sediment_transport_index.Rd | 3 man/wbt_select_tiles_by_polygon.Rd | 3 man/wbt_set_nodata_value.Rd | 5 man/wbt_shadow_animation.Rd | 3 man/wbt_shadow_image.Rd | 3 man/wbt_shape_complexity_index.Rd | 3 man/wbt_shape_complexity_index_raster.Rd | 3 man/wbt_shape_index.Rd | 3 man/wbt_shreve_stream_magnitude.Rd | 3 man/wbt_sigmoidal_contrast_stretch.Rd | 3 man/wbt_sin.Rd | 3 man/wbt_single_part_to_multi_part.Rd | 3 man/wbt_sinh.Rd | 3 man/wbt_sink.Rd | 3 man/wbt_slope.Rd | 3 man/wbt_slope_vs_aspect_plot.Rd | 3 man/wbt_slope_vs_elevation_plot.Rd | 3 man/wbt_smooth_vectors.Rd | 3 man/wbt_smooth_vegetation_residual.Rd | 3 man/wbt_snap_pour_points.Rd | 3 man/wbt_sobel_filter.Rd | 3 man/wbt_sort_lidar.Rd | 3 man/wbt_source.Rd |only man/wbt_spherical_std_dev_of_normals.Rd | 3 man/wbt_split_colour_composite.Rd | 5 man/wbt_split_lidar.Rd | 3 man/wbt_split_vector_lines.Rd | 5 man/wbt_split_with_lines.Rd | 3 man/wbt_square.Rd | 3 man/wbt_square_root.Rd | 3 man/wbt_standard_deviation_contrast_stretch.Rd | 3 man/wbt_standard_deviation_filter.Rd | 3 man/wbt_standard_deviation_of_slope.Rd | 3 man/wbt_stochastic_depression_analysis.Rd | 3 man/wbt_strahler_order_basins.Rd | 3 man/wbt_strahler_stream_order.Rd | 3 man/wbt_stream_link_class.Rd | 3 man/wbt_stream_link_identifier.Rd | 3 man/wbt_stream_link_length.Rd | 3 man/wbt_stream_link_slope.Rd | 3 man/wbt_stream_power_index.Rd | 3 man/wbt_stream_slope_continuous.Rd | 3 man/wbt_subbasins.Rd | 3 man/wbt_subtract.Rd | 3 man/wbt_sum_overlay.Rd | 3 man/wbt_surface_area_ratio.Rd | 3 man/wbt_svm_classification.Rd | 3 man/wbt_svm_regression.Rd | 3 man/wbt_symmetrical_difference.Rd | 3 man/wbt_tan.Rd | 3 man/wbt_tangential_curvature.Rd | 3 man/wbt_tanh.Rd | 3 man/wbt_thicken_raster_line.Rd | 3 man/wbt_time_in_daylight.Rd | 3 man/wbt_tin_gridding.Rd | 3 man/wbt_to_degrees.Rd | 3 man/wbt_to_radians.Rd | 3 man/wbt_tool_help.Rd | 3 man/wbt_tool_parameters.Rd | 3 man/wbt_toolbox.Rd | 1 man/wbt_tophat_transform.Rd | 3 man/wbt_topo_render.Rd |only man/wbt_topographic_position_animation.Rd | 3 man/wbt_topological_stream_order.Rd | 3 man/wbt_total_curvature.Rd | 3 man/wbt_total_filter.Rd | 3 man/wbt_trace_downslope_flowpaths.Rd | 3 man/wbt_travelling_salesman_problem.Rd | 5 man/wbt_trend_surface.Rd | 3 man/wbt_trend_surface_vector_points.Rd | 3 man/wbt_tributary_identifier.Rd | 3 man/wbt_truncate.Rd | 3 man/wbt_turning_bands_simulation.Rd | 3 man/wbt_two_sample_ks_test.Rd | 3 man/wbt_union.Rd | 3 man/wbt_unnest_basins.Rd | 3 man/wbt_unsharp_masking.Rd | 3 man/wbt_unsphericity.Rd | 3 man/wbt_update_nodata_cells.Rd | 3 man/wbt_upslope_depression_storage.Rd | 3 man/wbt_user_defined_weights_filter.Rd | 3 man/wbt_vector_hex_binning.Rd | 3 man/wbt_vector_lines_to_raster.Rd | 3 man/wbt_vector_points_to_raster.Rd | 3 man/wbt_vector_polygons_to_raster.Rd | 3 man/wbt_vector_stream_network_analysis.Rd | 3 man/wbt_version.Rd | 12 man/wbt_vertical_excess_curvature.Rd | 3 man/wbt_view_code.Rd | 3 man/wbt_viewshed.Rd | 3 man/wbt_visibility_index.Rd | 3 man/wbt_voronoi_diagram.Rd | 3 man/wbt_watershed.Rd | 3 man/wbt_weighted_overlay.Rd | 3 man/wbt_weighted_sum.Rd | 3 man/wbt_wetness_index.Rd | 3 man/wbt_wilcoxon_signed_rank_test.Rd | 3 man/wbt_write_function_memory_insertion.Rd | 3 man/wbt_xor.Rd | 3 man/wbt_yield_filter.Rd | 3 man/wbt_yield_map.Rd | 3 man/wbt_yield_normalization.Rd | 3 man/wbt_z_scores.Rd | 3 man/wbt_zlidar_to_las.Rd | 3 man/wbt_zonal_statistics.Rd | 3 man/wbttoolparameters.Rd | 29 man/wbttools.Rd | 29 man/whitebox-package.Rd | 6 tests/testthat/test-toolchains.R |only vignettes/datasets.Rmd | 20 vignettes/demo.Rmd | 87 vignettes/wbt-method.Rmd |only 612 files changed, 6394 insertions(+), 4156 deletions(-)
Title: Draw Ordered Oxford Grids
Description: Use standard genomics file format (BED) and a table of orthologs to
illustrate pair-wise synteny conservation at the genome-wide scale.
Significantly conserved linkage groups are identified as described in Simakov et al. (2020) <doi:10.1038/s41559-020-1156-z>
and displayed on an Oxford Grid (Edwards (1991) <doi:10.1111/j.1469-1809.1991.tb00394.x>).
The package provides a function that uses a network-based greedy algorithm to find communities (Clauset et al. (2004) <doi:10.1103/PhysRevE.70.066111>)
and so automatically order the chromosomes on the plot to improve interpretability.
Author: Sami El Hilali [aut, cre] ,
Richard Copley [aut]
Maintainer: Sami El Hilali <elhilali.sami@gmail.com>
Diff between macrosyntR versions 0.2.14 dated 2023-01-18 and 0.2.19 dated 2023-03-29
DESCRIPTION | 14 ++--- MD5 | 34 ++++++++------ NAMESPACE | 3 + NEWS.md |only R/get_syntenic_genes.R |only R/load_orthologs.R | 4 - R/plot_macrosynteny.R | 4 - R/plot_oxford_grid.R | 48 +++++++++++++++----- R/reorder_macrosynteny.R | 74 ++++++++++++++++++++---------- R/reverse_species_order.R |only README.md | 19 +++++-- inst/CITATION |only inst/doc/macrosyntR.R | 54 ++++++++++++++++++++++ inst/doc/macrosyntR.Rmd | 86 ++++++++++++++++++++++++++++++++++- inst/doc/macrosyntR.html | 103 ++++++++++++++++++++++++++++++++++++++++--- inst/img |only man/get_syntenic_genes.Rd |only man/plot_oxford_grid.Rd | 13 ++++- man/reorder_macrosynteny.Rd | 9 ++- man/reverse_species_order.Rd |only vignettes/macrosyntR.Rmd | 86 ++++++++++++++++++++++++++++++++++- 21 files changed, 466 insertions(+), 85 deletions(-)
Title: Conducting the Peak Fitting Based on the EM Algorithm
Description: The peak fitting of spectral data is performed by using the frame work of EM algorithm. We adapted the EM algorithm for the peak fitting of spectral data set by considering the weight of the intensity corresponding to the measurement energy steps (Matsumura, T., Nagamura, N., Akaho, S., Nagata, K., & Ando, Y. (2019, 2021 and 2023) <doi:10.1080/14686996.2019.1620123>, <doi:10.1080/27660400.2021.1899449> <doi:10.1080/27660400.2022.2159753>. The package efficiently estimates the parameters of Gaussian mixture model during iterative calculation between E-step and M-step, and the parameters are converged to a local optimal solution. This package can support the investigation of peak shift with two advantages: (1) a large amount of data can be processed at high speed; and (2) stable and automatic calculation can be easily performed.
Author: Tarojiro Matsumura [aut, cre]
Maintainer: Tarojiro Matsumura <matsumura-tarojiro@aist.go.jp>
Diff between EMpeaksR versions 0.3.0 dated 2023-03-07 and 0.3.1 dated 2023-03-29
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/PVMM_linearback_fittingcurve.R | 9 +-------- README.md | 3 +++ man/DSGMM.Rd | 4 ++-- man/DSGMM_fitting_graph.Rd | 4 ++-- man/GMM.Rd | 2 +- man/GMM_fitting_graph.Rd | 2 +- man/LMM.Rd | 2 +- man/LMM_fitting_graph.Rd | 2 +- man/PVMM.Rd | 4 ++-- man/PVMM_fitting_graph.Rd | 4 ++-- man/PVMM_lback.Rd | 18 +++++------------- man/PVMM_lback_fitting_graph.Rd | 10 +++++----- 15 files changed, 48 insertions(+), 56 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.1.0.2 dated 2023-02-20 and 2.1.0.3 dated 2023-03-29
DESCRIPTION | 6 - MD5 | 34 +++---- NEWS.md | 13 ++ R/check_data.R | 2 R/check_priors.R | 2 R/define_prior.R | 6 - R/helpers.R | 5 - R/inits_functions.R | 4 R/rhat.R | 18 ++-- R/set_distribution.R | 14 ++- README.md | 135 ++++++++++++++++--------------- man/check_priors.Rd | 68 ++++++++------- man/rhat.Rd | 8 - tests/testthat/test-amend.R | 1 tests/testthat/test-bayesmanec_methods.R | 6 + tests/testthat/test-ecx.R | 70 +++++++++------- tests/testthat/test-expand_classes.R | 9 ++ tests/testthat/test-nsec.R | 76 ++++++++++------- 18 files changed, 276 insertions(+), 201 deletions(-)
Title: Phylogenetic Analysis with Discrete Character Data
Description: Reconstruct phylogenetic trees from discrete data.
Inapplicable character states are handled using the algorithm of Brazeau,
Guillerme and Smith (2019) <doi:10.1093/sysbio/syy083> with the "Morphy"
library, under equal or implied step weights.
Contains a "shiny" user interface for interactive tree search and exploration
of results, including character visualization, rogue taxon detection,
tree space mapping, and cluster consensus trees (Smith 2022a, b)
<doi:10.1093/sysbio/syab099>, <doi:10.1093/sysbio/syab100>.
Profile Parsimony (Faith and Trueman, 2001) <doi:10.1080/10635150118627>,
Successive Approximations (Farris, 1969) <doi:10.2307/2412182>
and custom optimality criteria are implemented.
Author: Martin R. Smith [aut, cre, cph]
,
Martin Brazeau [cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeSearch versions 1.3.0 dated 2023-02-20 and 1.3.1 dated 2023-03-29
DESCRIPTION | 6 ++--- MD5 | 38 +++++++++++++++++----------------- NEWS.md | 10 ++++++++- R/PlotCharacter.R | 11 +++++----- R/RandomTreeScore.R | 4 +-- R/mpl_morphyex.R | 46 +++++++++++++++++++++--------------------- R/mpl_visualise.R | 2 - R/tree_length.R | 6 ++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 9 +++++--- inst/Parsimony/app.R | 44 +++++++++++++++++++++++++++------------- inst/datasets/Wills2012.nex | 5 ++-- inst/doc/custom.html | 14 ++++++------ inst/doc/getting-started.html | 4 +-- inst/doc/profile-scores.html | 4 +-- inst/doc/profile.html | 4 +-- inst/doc/tree-search.html | 4 +-- inst/doc/tree-space.html | 4 +-- man/PlotCharacter.Rd | 9 ++++---- 20 files changed, 127 insertions(+), 97 deletions(-)
Title: Permutation Tests for Randomization Model
Description: Perform permutation-based hypothesis testing for randomized
experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470>
and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al.
(2022) <doi:10.1016/j.chemosphere.2022.136736>.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between peramo versions 0.1.1 dated 2022-12-19 and 0.1.2 dated 2023-03-29
peramo-0.1.1/peramo/R/copper-data.R |only peramo-0.1.1/peramo/data/copper.RData |only peramo-0.1.1/peramo/man/copper.Rd |only peramo-0.1.2/peramo/DESCRIPTION | 16 +++++++++------- peramo-0.1.2/peramo/MD5 | 24 ++++++++++++++---------- peramo-0.1.2/peramo/NAMESPACE | 8 ++++++++ peramo-0.1.2/peramo/R/XY.R |only peramo-0.1.2/peramo/R/copper_temp-data.R |only peramo-0.1.2/peramo/R/peramo-package.R | 14 ++++++++------ peramo-0.1.2/peramo/R/tw_complex.R |only peramo-0.1.2/peramo/R/zzz.R | 8 ++++---- peramo-0.1.2/peramo/build/partial.rdb |binary peramo-0.1.2/peramo/data/copper_temp.RData |only peramo-0.1.2/peramo/inst/CITATION | 26 ++++++++++++++------------ peramo-0.1.2/peramo/man/XY.Rd |only peramo-0.1.2/peramo/man/copper_temp.Rd |only peramo-0.1.2/peramo/man/peramo-package.Rd | 11 ++++++----- peramo-0.1.2/peramo/man/tw_complex.Rd |only 18 files changed, 63 insertions(+), 44 deletions(-)
Title: Exploration of Multiple Biomarker Responses using Effect Size
Description: Summarize multiple biomarker responses of aquatic organisms to
contaminants using Cliff’s delta, as described in Pham & Sokolova (2023)
<doi:10.1002/ieam.4676>.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between mbRes versions 0.1.6 dated 2022-12-18 and 0.1.7 dated 2023-03-29
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ R/mbRes-package.R | 4 ++-- R/zzz.R | 8 ++++---- build/partial.rdb |binary inst/CITATION | 23 ++++++++++++++++------- man/mbRes-package.Rd | 4 ++-- 7 files changed, 38 insertions(+), 29 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb]
,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.9.9 dated 2023-02-27 and 1.9.10 dated 2023-03-29
DESCRIPTION | 6 +- MD5 | 10 ++-- build/vignette.rds |binary inst/doc/iq-fast.html | 118 ++++++++++++++++++++++++-------------------------- inst/doc/iq.html | 4 - src/iq.cpp | 9 +-- 6 files changed, 72 insertions(+), 75 deletions(-)
Title: Verbs and Nouns for Corpus Analysis
Description: Package for corpus analysis using the Corpus Workbench
('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing
and querying large corpora. The package offers functionality to flexibly create
subcorpora and to carry out basic statistical operations (count, co-occurrences
etc.). The original full text of documents can be reconstructed and inspected at
any time. Beyond that, the package is intended to serve as an interface to
packages implementing advanced statistical procedures. Respective data structures
(document-term matrices, term-co-occurrence matrices etc.) can be created based
on the indexed corpora.
Author: Andreas Blaette [aut, cre] ,
Christoph Leonhardt [ctb],
Marius Bertram [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between polmineR versions 0.8.7 dated 2022-08-26 and 0.8.8 dated 2023-03-29
DESCRIPTION | 19 MD5 | 167 +-- NAMESPACE | 18 NEWS.md | 56 + R/S4classes.R | 33 R/TermDocumentMatrix.R | 409 +++++---- R/as.VCorpus.R | 11 R/as.markdown.R | 37 R/as.sparseMatrix.R | 17 R/as.speeches.R | 118 ++ R/bundle.R | 29 R/context.R | 5 R/cooccurrences.R | 11 R/corpus.R | 198 ++-- R/count.R | 65 + R/cpos.R | 116 +- R/decode.R | 26 R/dispersion.R | 13 R/enrich.R | 83 + R/features.R | 14 R/hits.R | 62 - R/html.R | 65 - R/ngrams.R | 87 +- R/p_attributes.R | 4 R/partition.R | 26 R/partition_bundle.R | 43 R/polmineR-defunct.R | 12 R/polmineR.R | 42 R/read.R | 11 R/s_attributes.R | 110 +- R/split.R | 191 ++-- R/token_stream.R | 42 R/tooltips.R | 8 R/trim.R | 136 ++- R/use.R | 78 + R/utils.R | 80 + build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 11 inst/css/markdown.css |only inst/css/tooltips.css | 8 inst/doc/OpenCPU.html | 128 +- inst/doc/encodings.html | 18 inst/doc/vignette.html | 1427 ++++++++++++++++++++------------- inst/fulltext/merkel_as_html.html | 13 inst/fulltext/reading_reuters.html | 12 inst/fulltext/reuters_as_html.html | 12 man/all-cooccurrences-class.Rd | 6 man/as.DocumentTermMatrix.Rd | 39 man/as.VCorpus.Rd | 11 man/bundle.Rd | 40 man/capitalize.Rd |only man/cooccurrences.Rd | 7 man/corpus-class.Rd | 4 man/corpus_methods.Rd | 13 man/count-method.Rd | 2 man/cpos-method.Rd | 61 - man/features.Rd | 14 man/get_token_stream-method.Rd | 4 man/hits.Rd | 21 man/html-method.Rd | 38 man/is_nested.Rd |only man/ngrams.Rd | 6 man/partition.Rd | 7 man/partition_bundle-class.Rd | 14 man/partition_bundle-method.Rd | 12 man/partition_class.Rd | 14 man/polmineR-defunct.Rd | 3 man/polmineR-package.Rd | 42 man/ranges.Rd | 4 man/s_attributes-method.Rd | 51 - man/subcorpus-class.Rd | 10 man/subcorpus_bundle.Rd | 8 man/trim-method.Rd | 44 - man/use.Rd | 12 tests/testthat/test_aggregate.R | 11 tests/testthat/test_as.markdown.R | 41 tests/testthat/test_as.regions.R | 3 tests/testthat/test_as.speeches.R | 23 tests/testthat/test_capitalize.R |only tests/testthat/test_count.R | 14 tests/testthat/test_dispersion.R | 11 tests/testthat/test_enrich.R | 22 tests/testthat/test_ngrams.R | 12 tests/testthat/test_subcorpus.R | 62 + tests/testthat/test_subcorpus_bundle.R | 8 tests/testthat/test_use.R |only 87 files changed, 3104 insertions(+), 1661 deletions(-)
Title: HMM-Based Model for Genotyping and Cross-Over Identification
Description: Our method integrates information from all sequenced samples, thus avoiding loss of alleles due to low coverage. Moreover, it increases the statistical power to uncover sequencing or alignment errors <doi:10.1093/plphys/kiad191>.
Author: Rafael Campos-Martin [cre] ,
Sophia Schmickler [aut],
Manish Goel [ctb],
Korbinian Schneeberger [aut],
Achim Tresch [aut]
Maintainer: Rafael Campos-Martin <rfael.mpi@gmail.com>
Diff between RTIGER versions 1.99.0 dated 2022-03-28 and 2.1.0 dated 2023-03-29
DESCRIPTION | 14 - MD5 | 24 + NAMESPACE | 8 R/Optimization_Rvalue.R |only R/RTIGER-Class.R | 3 R/aux_Fun.R | 21 + R/mainfun.R | 39 ++- README.md | 60 ++++ build/vignette.rds |binary data/ATseqlengths.rda |binary data/fittedExample.rda |binary inst/doc/tutorial_RTIGER.html | 546 ++++++++++++++++++++++++++++++++---------- man/RTIGER.Rd | 12 man/optimize_R.Rd |only 14 files changed, 571 insertions(+), 156 deletions(-)
Title: Track Changes in Data
Description: A framework that allows for easy logging of changes in data.
Main features: start tracking changes by adding a single line of code to
an existing script. Track changes in multiple datasets, using multiple
loggers. Add custom-built loggers or use loggers offered by other
packages. <doi:10.18637/jss.v098.i01>.
Author: Mark van der Loo [aut, cre] ,
Floris Ruijter [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between lumberjack versions 1.2.1 dated 2021-05-26 and 1.3.1 dated 2023-03-29
DESCRIPTION | 19 +++++++++++-------- MD5 | 25 ++++++++++++++----------- NAMESPACE | 1 + NEWS | 8 ++++++++ R/no_logger.R |only build/vignette.rds |binary inst/doc/JSS_4008.pdf |binary inst/doc/using_lumberjack.pdf |binary inst/tinytest/test_no_log.R |only inst/tinytest/test_simple.R | 3 +++ man/cellwise.Rd | 1 + man/expression_logger.Rd | 1 + man/filedump.Rd | 1 + man/no_log.Rd |only man/simple.Rd | 3 ++- 15 files changed, 42 insertions(+), 20 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre]
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.7.2 dated 2023-02-06 and 0.8.0 dated 2023-03-29
finbif-0.7.2/finbif/R/token.R |only finbif-0.7.2/finbif/tests/testthat/_snaps/local-finbif_occurrence_load.md |only finbif-0.7.2/finbif/tests/testthat/test-finbif_token.R |only finbif-0.7.2/finbif/tests/testthat/test-local-finbif_coords.R |only finbif-0.7.2/finbif/tests/testthat/test-local-finbif_occurrence_load.R |only finbif-0.7.2/finbif/tests/testthat/test-local-finbif_request_token.R |only finbif-0.8.0/finbif/DESCRIPTION | 11 finbif-0.8.0/finbif/MD5 | 112 finbif-0.8.0/finbif/NAMESPACE | 9 finbif-0.8.0/finbif/NEWS.md | 18 finbif-0.8.0/finbif/R/api_get.R | 286 - finbif-0.8.0/finbif/R/caching.R | 10 finbif-0.8.0/finbif/R/coords.R | 42 finbif-0.8.0/finbif/R/data.R | 4 finbif-0.8.0/finbif/R/dates.R | 249 - finbif-0.8.0/finbif/R/finbif-package.R | 13 finbif-0.8.0/finbif/R/finbif_check_taxa.R | 116 finbif-0.8.0/finbif/R/finbif_clear_cache.R | 28 finbif-0.8.0/finbif/R/finbif_collections.R | 472 +- finbif-0.8.0/finbif/R/finbif_informal_groups.R | 188 finbif-0.8.0/finbif/R/finbif_metadata.R | 403 + finbif-0.8.0/finbif/R/finbif_occurrence.R | 1731 +++++-- finbif-0.8.0/finbif/R/finbif_occurrence_load.R | 1923 ++++++-- finbif-0.8.0/finbif/R/finbif_records.R | 1678 ++++++- finbif-0.8.0/finbif/R/finbif_request_token.R | 109 finbif-0.8.0/finbif/R/finbif_taxa.R | 78 finbif-0.8.0/finbif/R/map-utils.R | 80 finbif-0.8.0/finbif/R/methods.R | 1133 ++++- finbif-0.8.0/finbif/R/sysdata.R |only finbif-0.8.0/finbif/R/sysdata.rda |binary finbif-0.8.0/finbif/R/utils.R | 687 ++- finbif-0.8.0/finbif/R/zzz.R | 60 finbif-0.8.0/finbif/README.md | 4 finbif-0.8.0/finbif/build/vignette.rds |binary finbif-0.8.0/finbif/data/finland_map.rda |binary finbif-0.8.0/finbif/inst/CITATION | 4 finbif-0.8.0/finbif/inst/NEWS.Rd | 20 finbif-0.8.0/finbif/man/as.data.frame.finbif_records.Rd | 6 finbif-0.8.0/finbif/man/breaks_xy.Rd | 4 finbif-0.8.0/finbif/man/finbif-package.Rd | 7 finbif-0.8.0/finbif/man/finbif_clear_cache.Rd | 1 finbif-0.8.0/finbif/man/finbif_collections.Rd | 1 finbif-0.8.0/finbif/man/finbif_informal_groups.Rd | 18 finbif-0.8.0/finbif/man/finbif_metadata.Rd | 4 finbif-0.8.0/finbif/man/finbif_occurrence.Rd | 35 finbif-0.8.0/finbif/man/finbif_occurrence_load.Rd | 17 finbif-0.8.0/finbif/man/finbif_records.Rd | 34 finbif-0.8.0/finbif/man/finbif_request_token.Rd | 1 finbif-0.8.0/finbif/man/finbif_taxa.Rd | 8 finbif-0.8.0/finbif/man/finland_map.Rd | 4 finbif-0.8.0/finbif/man/hist_xy.Rd | 4 finbif-0.8.0/finbif/tests/testthat/_snaps/finbif_occurrence/fungi.svg | 2200 +++++----- finbif-0.8.0/finbif/tests/testthat/_snaps/finbif_occurrence_load.md |only finbif-0.8.0/finbif/tests/testthat/helper-finbif.R | 123 finbif-0.8.0/finbif/tests/testthat/test-finbif_check_taxa.R | 4 finbif-0.8.0/finbif/tests/testthat/test-finbif_clear_cache.R | 6 finbif-0.8.0/finbif/tests/testthat/test-finbif_coords.R |only finbif-0.8.0/finbif/tests/testthat/test-finbif_occurrence.R | 23 finbif-0.8.0/finbif/tests/testthat/test-finbif_occurrence_load.R |only finbif-0.8.0/finbif/tests/testthat/test-finbif_request_token.R |only finbif-0.8.0/finbif/tests/testthat/test-metadata.R | 129 finbif-0.8.0/finbif/tests/testthat/test-sysdata.R |only finbif-0.8.0/finbif/tests/testthat/test-utils.R | 20 63 files changed, 8610 insertions(+), 3507 deletions(-)
Title: Convolution-Closed Models for Count Time Series
Description: Useful tools for fitting, validating, and forecasting of practical convolution-closed time series models for low counts are provided. Marginal distributions of the data can be modeled via Poisson and Generalized Poisson innovations. Regression effects can be modelled via time varying innovation rates. The models are described in Jung and Tremayne (2011) <doi:10.1111/j.1467-9892.2010.00697.x> and the model assessment tools are presented in Czado et al. (2009) <doi:10.1111/j.1541-0420.2009.01191.x>, Gneiting and Raftery (2007) <doi:10.1198/016214506000001437> and, Tsay (1992) <doi:10.2307/2347612>.
Author: Manuel Huth [aut, cre],
Robert C. Jung [aut],
Andy Tremayne [aut]
Maintainer: Manuel Huth <manuel.huth@yahoo.com>
Diff between coconots versions 1.1 dated 2023-03-13 and 1.1.1 dated 2023-03-29
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- R/cocoReg.R | 4 ++-- R/cocoSim.R | 7 ++++--- R/cocoSim_cov.R | 33 ++++++++++++++++++++++++++------- README.md | 15 ++++++++------- man/cocoReg.Rd | 4 ++-- src/cfunctions.cpp | 3 ++- tests/testthat/test-coconots.R | 35 +++++++++++++++++++++++++++++++---- 9 files changed, 86 insertions(+), 37 deletions(-)
Title: Tools for Case 1 Best-Worst Scaling
Description: Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. See Louviere et al. (2015) <doi:10.1017/CBO9781107337855> for details on best-worst scaling, and Aizaki and Fogarty (2023) <doi:10.1016/j.jocm.2022.100394> for the package.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.4-5 dated 2023-01-09 and 0.4-6 dated 2023-03-29
DESCRIPTION | 8 ++-- MD5 | 10 ++--- NEWS | 4 ++ R/bws.count.R | 110 ++++++++++++++++++++++++++++++++++++++++++++++--------- inst/CITATION | 20 +++++----- man/bws.count.Rd | 12 ++++-- 6 files changed, 124 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-08 0.1.0
Title: Systematic Conservation Prioritization in R
Description: Systematic conservation prioritization using mixed integer linear
programming (MILP). It provides a flexible interface for building and
solving conservation planning problems. Once built, conservation planning
problems can be solved using a variety of commercial and open-source exact
algorithm solvers. By using exact algorithm solvers, solutions can be
generated that are guaranteed to be optimal (or within a pre-specified
optimality gap). Furthermore, conservation problems can be constructed to
optimize the spatial allocation of different management actions or zones,
meaning that conservation practitioners can identify solutions that benefit
multiple stakeholders. To solve large-scale or complex conservation
planning problems, users should install the Gurobi optimization software
(available from <https://www.gurobi.com/>) and the 'gurobi' R package (see
Gurobi Installation Guide vignette for details). Users can also install the
IBM CPLEX software (<https://www.ibm.com/products [...truncated...]
Author: Jeffrey O Hanson [aut] ,
Richard Schuster [aut, cre] ,
Nina Morrell [aut],
Matthew Strimas-Mackey [aut] ,
Brandon P M Edwards [aut] ,
Matthew E Watts [aut],
Peter Arcese [aut] ,
Joseph Bennett [aut] ,
Hugh P Possingham [aut]
Maintainer: Richard Schuster <richard.schuster@glel.carleton.ca>
Diff between prioritizr versions 7.2.2 dated 2022-09-17 and 8.0.0 dated 2023-03-29
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Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: A system for querying, retrieving and analyzing
protocol- and results-related information on clinical trials from
three public registers, the 'European Union Clinical Trials Register'
('EUCTR', <https://www.clinicaltrialsregister.eu/>),
'ClinicalTrials.gov' ('CTGOV', <https://clinicaltrials.gov/>),
the 'ISRCTN' (<http://www.isrctn.com/>) and the
'European Union Clinical Trials Information System'
('CTIS', <https://euclinicaltrials.eu/>).
Trial information is downloaded, converted and stored in a database
('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi').
Functions are included to identify deduplicated records,
to easily find and extract variables (fields) of interest even
from complex nesting as used by the registers, and
to update previous queries.
The package can be used for meta-analysis and trend-analysis of
the design and conduct as well as for results of clinical trials.
Author: Ralf Herold [aut, cre]
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.12.0 dated 2023-03-26 and 1.12.1 dated 2023-03-29
DESCRIPTION | 12 +++-- MD5 | 16 +++---- NAMESPACE | 1 NEWS.md | 6 ++ R/ctrdata-registers.R | 6 +- R/main.R | 105 ++++++++++++++++++++++++++++++++++++---------- README.md | 27 +++++++---- man/ctrLoadQueryIntoDb.Rd | 2 man/ctrdata-registers.Rd | 6 +- 9 files changed, 130 insertions(+), 51 deletions(-)