Title: Calculate and Map Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Includes tools for visualizing mappings of tree space (Smith 2022)
<doi:10.1093/sysbio/syab100>,
for calculating the median of sets of trees,
and for computing the information content of trees and splits.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 2.2.0 dated 2021-09-13 and 2.3.0 dated 2022-01-03
DESCRIPTION | 28 ++++++------ MD5 | 63 +++++++++++++-------------- NEWS.md | 9 +++ R/RcppExports.R | 4 - R/tree_distance_kendall-colijn.R | 2 R/tree_information.R | 14 ++++-- R/zzz.R | 16 +----- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 21 ++++++++- inst/REFERENCES.bib | 36 +++++++++++++-- inst/WORDLIST | 4 + inst/doc/Generalized-RF.html | 26 +++++------ inst/doc/Robinson-Foulds.html | 20 ++++---- inst/doc/Using-TreeDist.html | 10 ++-- inst/doc/information.html | 2 inst/doc/treespace.R | 18 +++++++ inst/doc/treespace.Rmd | 39 +++++++++++++++- inst/doc/treespace.html | 91 ++++++++++++++++++++++++--------------- inst/doc/using-distances.R | 2 inst/doc/using-distances.Rmd | 2 inst/doc/using-distances.html | 15 +++--- inst/treespace/app.R | 74 ++++++++++++++++++++++++------- man/TreeDist-package.Rd | 2 man/TreeDistance.Rd | 2 man/TreeInfo.Rd | 8 +-- src/RcppExports.cpp | 9 ++- src/day_1985.cpp | 19 ++++++-- src/tree_distances.cpp | 3 - tests/spelling.R |only tests/testthat/test-split_info.R | 19 ++++++-- vignettes/treespace.Rmd | 39 +++++++++++++++- vignettes/using-distances.Rmd | 2 33 files changed, 416 insertions(+), 183 deletions(-)
Title: Sensitivity Analysis for Observational Studies Using Weighted
M-Statistics
Description: Sensitivity analysis for tests, confidence intervals and estimates in matched observational studies with one or more controls using weighted or unweighted Huber-Maritz M-tests (including the permutational t-test). The method is from Rosenbaum (2014) Weighted M-statistics with superior design sensitivity in matched observational studies with multiple controls JASA, 109(507), 1145-1158 <doi:10.1080/01621459.2013.879261>.
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum <rosenbaum@wharton.upenn.edu>
Diff between sensitivitymw versions 1.1 dated 2014-07-24 and 2.1 dated 2022-01-03
DESCRIPTION | 16 +- MD5 | 39 ++--- NAMESPACE | 5 R/mscorev.R | 100 +++++++------- R/multrnks.R | 25 +-- R/newurks.R | 23 +-- R/senmw.R | 217 +++++++++++++++--------------- R/senmwCI.R | 207 ++++++++++++++++------------- R/separable1k.R | 68 ++++----- build |only data/erpcp.rda |binary data/mercury.rda |binary man/erpcp.Rd | 61 ++++---- man/mercury.Rd | 61 ++++---- man/mscorev.Rd | 106 +++++++------- man/multrnks.Rd | 91 ++++++------ man/newurks.Rd | 89 ++++++------ man/senmw.Rd | 304 +++++++++++++++++++++---------------------- man/senmwCI.Rd | 195 ++++++++++++++------------- man/sensitivitymw-package.Rd | 103 +++++++------- man/separable1k.Rd | 92 ++++++------- 21 files changed, 928 insertions(+), 874 deletions(-)
Title: Network Analysis and Causal Inference Through Structural
Equation Modeling
Description: Estimate networks and causal relationships in complex systems through
Structural Equation Modeling. This package also includes functions to import,
weight, manipulate, and fit biological network models within the
Structural Equation Modeling framework described in
Palluzzi and Grassi (2021) <arXiv:2103.08332>.
Author: Mario Grassi [aut],
Fernando Palluzzi [aut],
Barbara Tarantino [aut, cre]
Maintainer: Barbara Tarantino <barbara.tarantino01@universitadipavia.it>
Diff between SEMgraph versions 1.0.4 dated 2021-11-16 and 1.0.5 dated 2022-01-03
DESCRIPTION | 26 +++---- MD5 | 14 ++-- NAMESPACE | 4 - NEWS.md | 35 +++++----- R/semPaths.R | 186 ++++++++++++++++++++++++++++-------------------------- R/semUtils.R | 32 ++------- R/semWeights.R | 1 build/partial.rdb |binary 8 files changed, 148 insertions(+), 150 deletions(-)
Title: Relative Distribution Methods
Description: Tools for the comparison of distributions. This includes nonparametric estimation of the relative distribution PDF and CDF and numerical summaries as described in "Relative Distribution Methods in the Social Sciences" by Mark S. Handcock and Martina Morris, Springer-Verlag, 1999, Springer-Verlag, ISBN 0387987789.
Author: Mark S. Handcock <handcock@stat.ucla.edu>
Maintainer: Mark S. Handcock <handcock@stat.ucla.edu>
Diff between reldist versions 1.6-6 dated 2016-10-09 and 1.7-0 dated 2022-01-03
DESCRIPTION | 12 +++++----- LICENSE | 2 - MD5 | 26 ++++++++++++++--------- NAMESPACE | 5 +++- R/ZOSull.r |only R/reldist.R | 56 ++++++++++++++++++++++++++++++++++++++++++++------- R/trapint.r |only R/zzz.R | 2 + README.md |only build |only inst/CITATION | 6 ++--- man/Figures |only man/precipitation.Rd | 2 - man/reldist.Rd | 26 +++++++++++++++++------ man/resplot.Rd | 17 ++++++++++++--- tests/FigSM.R | 27 +++++++++++++++++++----- 16 files changed, 136 insertions(+), 45 deletions(-)
Title: Random Network Model Estimation, Selection and Parameter Tuning
Description: Model selection and parameter tuning procedures for a class of random network models. The model selection can be done by a general cross-validation framework called ECV from Li et. al. (2016) <arXiv:1612.04717> . Several other model-based and task-specific methods are also included, such as NCV from Chen and Lei (2016) <arXiv:1411.1715>, likelihood ratio method from Wang and Bickel (2015) <arXiv:1502.02069>, spectral methods from Le and Levina (2015) <arXiv:1507.00827>. Many network analysis methods are also implemented, such as the regularized spectral clustering (Amini et. al. 2013 <doi:10.1214/13-AOS1138>) and its degree corrected version and graphon neighborhood smoothing (Zhang et. al. 2015 <arXiv:1509.08588>). It also includes the consensus clustering of Gao et. al. (2014) <arXiv:1410.5837>, the method of moments estimation of nomination SBM of Li et. al. (2020) <arxiv:2008.03652>, and the network mixing method of Li and Le (2021) <arxiv:2106.02803>. It also include the informative core-periphery data processing method of Miao and Lu (2021) <arXiv:2101.06388>. The work to build and improve this package is partially supported by the NSF grants DMS-2015298 and DMS-2015134.
Author: Tianxi Li, Elizaveta Levina, Ji Zhu, Can M. Le
Maintainer: Tianxi Li <tianxili@virginia.edu>
Diff between randnet versions 0.4 dated 2021-06-08 and 0.5 dated 2022-01-03
DESCRIPTION | 10 +++++----- MD5 | 9 +++++---- NAMESPACE | 4 ++-- R/RCode.R | 36 ++++++++++++++++++++++++++++++++++++ man/InformativeCore.Rd |only man/randnet-package.Rd | 6 ++++-- 6 files changed, 52 insertions(+), 13 deletions(-)
Title: Linking Patient-Reported Outcomes Measures
Description: Perform scale linking to establish relationships between instruments
that measure similar constructs according to the PROsetta Stone methodology, as in Choi, Schalet, Cook, & Cella (2014) <doi:10.1037/a0035768>.
Author: Seung W. Choi [aut, cre] (<https://orcid.org/0000-0003-4777-5420>),
Sangdon Lim [aut] (<https://orcid.org/0000-0002-2988-014X>),
Benjamin D. Schalet [ctb],
Aaron J. Kaat [ctb],
David Cella [ctb]
Maintainer: Seung W. Choi <schoi@austin.utexas.edu>
Diff between PROsetta versions 0.3.4 dated 2021-11-23 and 0.3.5 dated 2022-01-03
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PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib3_6ecb757d917c3b80a8917b0977f68f77.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib3_6ecb757d917c3b80a8917b0977f68f77.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib3_6ecb757d917c3b80a8917b0977f68f77.rdx |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib_3d324a1e5709b8867a7ea0ec11f53417.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib_3d324a1e5709b8867a7ea0ec11f53417.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/calib_3d324a1e5709b8867a7ea0ec11f53417.rdx |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_e4b761dae393122c23eaa2b6362e9ca3.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_e4b761dae393122c23eaa2b6362e9ca3.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/eqp_dir_e4b761dae393122c23eaa2b6362e9ca3.rdx |only 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PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_c77f04b41756617480bc8bf7bc70a2b2.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_c77f04b41756617480bc8bf7bc70a2b2.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/mirt_plot_c77f04b41756617480bc8bf7bc70a2b2.rdx |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/omega_922530efd4756417baffef75c3a70a97.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/omega_922530efd4756417baffef75c3a70a97.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/omega_922530efd4756417baffef75c3a70a97.rdx |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/sl_73422a0a5e56fc31e09c3b26635a49b4.RData |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/sl_73422a0a5e56fc31e09c3b26635a49b4.rdb |only PROsetta-0.3.4/PROsetta/vignettes/PROsetta_cache/html/sl_73422a0a5e56fc31e09c3b26635a49b4.rdx |only PROsetta-0.3.5/PROsetta/DESCRIPTION | 8 PROsetta-0.3.5/PROsetta/MD5 | 112 +-- PROsetta-0.3.5/PROsetta/NAMESPACE | 1 PROsetta-0.3.5/PROsetta/NEWS.md | 6 PROsetta-0.3.5/PROsetta/R/configPROsetta.R | 7 PROsetta-0.3.5/PROsetta/R/core_functions.R | 67 + PROsetta-0.3.5/PROsetta/R/import.R | 2 PROsetta-0.3.5/PROsetta/R/linking_functions.R | 146 ++- PROsetta-0.3.5/PROsetta/R/post_functions.R | 15 PROsetta-0.3.5/PROsetta/build/vignette.rds |binary PROsetta-0.3.5/PROsetta/inst/doc/PROsetta.R | 105 +- PROsetta-0.3.5/PROsetta/inst/doc/PROsetta.Rmd | 111 +-- PROsetta-0.3.5/PROsetta/inst/doc/PROsetta.html | 369 +++++----- PROsetta-0.3.5/PROsetta/man/getCompleteData.Rd | 4 PROsetta-0.3.5/PROsetta/man/runCalibration.Rd | 3 PROsetta-0.3.5/PROsetta/man/runEquateObserved.Rd | 3 PROsetta-0.3.5/PROsetta/man/runLinking.Rd | 4 PROsetta-0.3.5/PROsetta/vignettes/PROsetta.Rmd | 111 +-- PROsetta-0.3.5/PROsetta/vignettes/PROsetta_cache/html/alpha2_2799716c55768e4980817125690d2d5e.RData |only 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Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.17.4. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
awPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot <sapan.madaan@gmail.com>, Paul Brooks
<jpbrooks@vcu.edu>,
Andrea Visentin <andrea.visentin@insight-centre.org>,
Young Woong Park <ywpark@mail.smu.edu>,
and Yi-Hui Zhou <yihui_zhou@ncsu.edu>
Maintainer: Paul Brooks <jpbrooks@vcu.edu>
Diff between pcaL1 versions 1.5.5 dated 2021-10-29 and 1.5.6 dated 2022-01-03
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS | 6 ++++++ R/sharpel1pca.R | 4 +++- configure | 18 +++++++++--------- configure.ac | 2 +- man/pcaL1-package.Rd | 4 ++-- src/Makevars.ucrt |only src/sharpel1pca.c | 2 ++ src/sharpel1pca_R.c | 4 ++++ 11 files changed, 45 insertions(+), 26 deletions(-)
Title: R Interface for the 'H2O' Scalable Machine Learning Platform
Description: R interface for 'H2O', the scalable open source machine learning
platform that offers parallelized implementations of many supervised and
unsupervised machine learning algorithms such as Generalized Linear
Models (GLM), Gradient Boosting Machines (including XGBoost), Random Forests,
Deep Neural Networks (Deep Learning), Stacked Ensembles, Naive Bayes,
Generalized Additive Models (GAM), ANOVA GLM, Cox Proportional Hazards, K-Means, PCA, ModelSelection,
Word2Vec, as well as a fully automatic machine learning algorithm (H2O AutoML).
Author: Erin LeDell [aut, cre],
Navdeep Gill [aut],
Spencer Aiello [aut],
Anqi Fu [aut],
Arno Candel [aut],
Cliff Click [aut],
Tom Kraljevic [aut],
Tomas Nykodym [aut],
Patrick Aboyoun [aut],
Michal Kurka [aut],
Michal Malohlava [aut],
Ludi Rehak [ctb],
Eric Eckstrand [ctb],
Brandon Hill [ctb],
Sebastian Vidrio [ctb],
Surekha Jadhawani [ctb],
Amy Wang [ctb],
Raymond Peck [ctb],
Wendy Wong [ctb],
Jan Gorecki [ctb],
Matt Dowle [ctb],
Yuan Tang [ctb],
Lauren DiPerna [ctb],
Tomas Fryda [ctb],
Veronika Maurerova [ctb],
H2O.ai [cph, fnd]
Maintainer: Erin LeDell <erin@h2o.ai>
Diff between h2o versions 3.34.0.6 dated 2021-12-17 and 3.36.0.1 dated 2022-01-03
h2o-3.34.0.6/h2o/R/maxrglm.R |only h2o-3.34.0.6/h2o/man/h2o.maxrglm.Rd |only h2o-3.36.0.1/h2o/DESCRIPTION | 23 - h2o-3.36.0.1/h2o/MD5 | 57 ++- h2o-3.36.0.1/h2o/NAMESPACE | 14 h2o-3.36.0.1/h2o/R/automl.R | 9 h2o-3.36.0.1/h2o/R/classes.R | 137 ++++++++ h2o-3.36.0.1/h2o/R/explain.R | 6 h2o-3.36.0.1/h2o/R/infogram.R |only h2o-3.36.0.1/h2o/R/kvstore.R | 2 h2o-3.36.0.1/h2o/R/models.R | 249 +++++++++++++-- h2o-3.36.0.1/h2o/R/modelselection.R |only h2o-3.36.0.1/h2o/R/rulefit.R | 13 h2o-3.36.0.1/h2o/R/segment.R | 2 h2o-3.36.0.1/h2o/R/upliftrandomforest.R |only h2o-3.36.0.1/h2o/inst/branch.txt | 2 h2o-3.36.0.1/h2o/inst/buildnum.txt | 2 h2o-3.36.0.1/h2o/man/H2OInfogram-class.Rd |only h2o-3.36.0.1/h2o/man/H2OInfogram.Rd |only h2o-3.36.0.1/h2o/man/H2OModel-class.Rd | 1 h2o-3.36.0.1/h2o/man/H2OModelMetrics-class.Rd | 4 h2o-3.36.0.1/h2o/man/h2o-package.Rd | 6 h2o-3.36.0.1/h2o/man/h2o.automl.Rd | 2 h2o-3.36.0.1/h2o/man/h2o.auuc.Rd |only h2o-3.36.0.1/h2o/man/h2o.auuc_table.Rd |only h2o-3.36.0.1/h2o/man/h2o.centroid_stats.Rd | 10 h2o-3.36.0.1/h2o/man/h2o.get_best_model_predictors.Rd | 4 h2o-3.36.0.1/h2o/man/h2o.get_best_r2_values.Rd | 4 h2o-3.36.0.1/h2o/man/h2o.infogram.Rd |only h2o-3.36.0.1/h2o/man/h2o.make_metrics.Rd | 13 h2o-3.36.0.1/h2o/man/h2o.modelSelection.Rd |only h2o-3.36.0.1/h2o/man/h2o.rulefit.Rd | 9 h2o-3.36.0.1/h2o/man/h2o.thresholds_and_metric_scores.Rd |only h2o-3.36.0.1/h2o/man/h2o.train_segments.Rd | 2 h2o-3.36.0.1/h2o/man/h2o.upliftRandomForest.Rd |only h2o-3.36.0.1/h2o/man/initialize-H2OInfogram-method.Rd |only h2o-3.36.0.1/h2o/man/plot.H2OInfogram.Rd |only 37 files changed, 479 insertions(+), 92 deletions(-)
Title: Download Official Spatial Data Sets of Brazil
Description: Easy access to official spatial data sets of Brazil as 'sf' objects
in R. The package includes a wide range of geospatial data available
at various geographic scales and for various years with harmonized
attributes, projection and fixed topology.
Author: Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Caio Nogueira Goncalves [aut],
Paulo Henrique Fernandes de Araujo [ctb],
Guilherme Duarte Carvalho [ctb],
Rodrigo Almeida de Arruda [ctb],
Igor Nascimento [ctb],
Barbara Santiago Pedreira da Costa [ctb],
Welligtton Silva Cavedo [ctb],
Pedro R. Andrade [ctb],
Alan da Silva [ctb],
Carlos Kauê Vieira Braga [ctb],
Carl Schmertmann [ctb],
Alessandro Samuel-Rosa [ctb],
Daniel Ferreira [ctb],
Marcus Saraiva [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between geobr versions 1.6.4 dated 2021-07-22 and 1.6.5 dated 2022-01-03
DESCRIPTION | 15 +-- MD5 | 29 +++---- R/download_metadata.R | 5 - R/list_geobr.R | 18 +++- R/lookup_muni.R | 24 +++++ R/read_health_facilities.R | 2 R/utils.R | 37 ++++++--- build/partial.rdb |binary build/vignette.rds |binary data/grid_state_correspondence_table.RData |binary inst/doc/intro_to_geobr.R | 12 +- inst/doc/intro_to_geobr.Rmd | 8 - inst/doc/intro_to_geobr.html | 118 ++++++++++++++++++++++++++++- man/read_health_facilities.Rd | 2 tests/testthat/test-check_connection.R |only vignettes/intro_to_geobr.Rmd | 8 - 16 files changed, 223 insertions(+), 55 deletions(-)
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
Description: For multiscale analysis, this package carries out empirical mode decomposition and Hilbert spectral
analysis. For usage of EMD, see Kim and Oh, 2009 (Kim, D and Oh, H.-S. (2009) EMD: A Package for Empirical
Mode Decomposition and Hilbert Spectrum, The R Journal, 1, 40-46).
Author: Donghoh Kim [aut, cre],
Hee-Seok Oh [aut]
Maintainer: Donghoh Kim <donghoh.kim@gmail.com>
Diff between EMD versions 1.5.8 dated 2018-12-05 and 1.5.9 dated 2022-01-03
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/EMD2d.R | 6 +++--- data/beryllium.rda |binary data/kospi200.rda |binary data/lena.rda |binary data/lennon.rda |binary data/solar.hs.rda |binary data/solar.lean.rda |binary data/sunspot.rda |binary 10 files changed, 16 insertions(+), 16 deletions(-)
Title: Add Gate Information to Your Tibble
Description: It interactively or programmatically label points within custom gates on two dimensions <https://github.com/stemangiola/tidygate>.
The information is added to your tibble. It is based on the package 'gatepoints' from Wajid Jawaid (who is also author of this package). The code of 'gatepoints' was nto integrated in 'tidygate'.
The benefits are (i) in interactive mode you can draw your gates on extensive 'ggplot'-like scatter plots;
(ii) you can draw multiple gates; and (iii) you can save your gates and apply the programmatically.
Author: Stefano Mangiola [aut, cre],
Wajid Jawaid [ctb]
Maintainer: Stefano Mangiola <mangiolastefano@gmail.com>
Diff between tidygate versions 0.4.7 dated 2021-05-03 and 0.4.8 dated 2022-01-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/functions_chr_int.R | 4 ++-- README.md | 25 +++++++++++++++++-------- build/tidygate.pdf |binary build/vignette.rds |binary inst/doc/introdution.html | 26 +++++++++++++------------- 7 files changed, 41 insertions(+), 32 deletions(-)
Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rwhois versions 1.0.6 dated 2021-12-18 and 1.0.8 dated 2022-01-03
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/functions.R | 42 +++++++++++++++++++++++++++++++++++++++--- README.md | 12 +++++++++++- man/Rwhois.Rd | 18 ++++++++++++++++++ 6 files changed, 78 insertions(+), 13 deletions(-)
Title: Missing Person Identification Tools
Description: Open-source software for computing Likelihood ratios thresholds and error rates in DNA kinship testing. Marsico FL. et al (2021) <doi:10.1016/j.fsigen.2021.102519>.
Author: Franco Marsico [aut, cre] (<https://orcid.org/0000-0002-0740-5516>)
Maintainer: Franco Marsico <franco.lmarsico@gmail.com>
Diff between mispitools versions 0.1.3 dated 2021-12-20 and 0.1.5 dated 2022-01-03
mispitools-0.1.3/mispitools/R/makePrelim.R |only mispitools-0.1.3/mispitools/man/makePrelim.Rd |only mispitools-0.1.5/mispitools/DESCRIPTION | 10 +++++----- mispitools-0.1.5/mispitools/MD5 | 12 ++++++++---- mispitools-0.1.5/mispitools/NAMESPACE | 5 ++++- mispitools-0.1.5/mispitools/R/getfreqs.R |only mispitools-0.1.5/mispitools/R/makeMPprelim.R |only mispitools-0.1.5/mispitools/R/makePOIprelim.R |only mispitools-0.1.5/mispitools/man/getfreqs.Rd |only mispitools-0.1.5/mispitools/man/makeMPprelim.Rd |only mispitools-0.1.5/mispitools/man/makePOIprelim.Rd |only 11 files changed, 17 insertions(+), 10 deletions(-)
Title: Basic Pipe and Open Channel Hydraulics
Description: Functions for basic hydraulic calculations related to
water flow in circular pipes both flowing full (under pressure), and
partially full (gravity flow), and trapezoidal open channels. For
pressure flow this includes friction loss calculations by solving
the Darcy-Weisbach equation for head loss, flow or diameter, and
plotting a Moody diagram. The Darcy-Weisbach friction factor is
calculated using the Colebrook (or Colebrook-White equation),
the basis of the Moody diagram, the original citation being
Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity flow, the
Manning equation is used, again solving for missing parameters. The
derivation of and solutions using the Darcy-Weisbach equation and the
Manning equation are outlined in many fluid mechanics texts such as
Finnemore and Franzini (2002, ISBN:978-0072432022). For the Manning equation
solutions, this package uses modifications of original code from the 'iemisc'
package by Irucka Embry.
Author: Ed Maurer [aut, cre], Irucka Embry [aut, ctb] (iemisc code)
Maintainer: Ed Maurer <emaurer@scu.edu>
Diff between hydraulics versions 0.3.0 dated 2021-05-19 and 0.4.0 dated 2022-01-03
DESCRIPTION | 15 MD5 | 35 - NAMESPACE | 2 NEWS.md | 69 +- R/f_colebrook.R | 4 R/hardy-cross.R |only R/water_properties.R | 53 + README.md | 86 -- build/vignette.rds |binary inst/doc/hydraulics_vignette.R | 43 + inst/doc/hydraulics_vignette.Rmd | 82 ++ inst/doc/hydraulics_vignette.html | 915 ++++++++++++++++------------ man/figures/README-moody-diagram-1.png |binary man/figures/README-spec-energy-plot-1-1.png |binary man/figures/README-xc-plot-circle-1.png |binary man/figures/README-xc-plot-trap-1.png |binary man/hardycross.Rd |only man/waterprops.Rd | 12 vignettes/hardycross_system.png |only vignettes/hydraulics_vignette.Rmd | 82 ++ 20 files changed, 867 insertions(+), 531 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 2.14.0 dated 2021-11-11 and 3.0.0 dated 2022-01-03
DESCRIPTION | 8 MD5 | 43 R/generic.predict.rfsrc.R | 143 - R/impute.rfsrc.R | 117 R/partial.rfsrc.R | 106 R/predict.rfsrc.R | 2 R/print.rfsrc.R | 3 R/rfsrc.R | 79 R/subsample.rfsrc.R | 48 R/utilities.R | 40 R/utilities.sgreedy.R |only configure | 1770 ++++++++----- configure.ac | 2 inst/NEWS | 15 man/housing.Rd | 11 man/plot.survival.rfsrc.Rd | 9 man/plot.variable.rfsrc.Rd | 16 man/predict.rfsrc.Rd | 8 man/rfsrc.Rd | 5 man/subsample.rfsrc.Rd | 7 src/R_init_randomForestSRC.c | 5 src/randomForestSRC.c | 5789 +++++++++++++++++++++++-------------------- src/randomForestSRC.h | 279 -- 23 files changed, 4891 insertions(+), 3614 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Quantification of Color Pattern Variation
Description: Quantification of variation in organismal color patterns as
obtained from image data. Patternize defines homology between pattern positions
across images either through fixed landmarks or image registration. Pattern
identification is performed by categorizing the distribution of colors using RGB
thresholds or image segmentation.
Author: Steven Van Belleghem [aut, cre]
Maintainer: Steven Van Belleghem <vanbelleghemsteven@hotmail.com>
Diff between patternize versions 0.0.2 dated 2018-11-23 and 0.0.3 dated 2022-01-03
DESCRIPTION | 10 MD5 | 120 +++-- NAMESPACE | 28 + R/GMMImage.R |only R/alignLan.R |only R/alignReg.R |only R/colorChecker.R | 927 ++++++++++++++++++++++++++++++----------- R/colorChecker_customGray.R |only R/createPhenotype.R |only R/kImage.R | 173 ++++++- R/kImageHSV.R |only R/lanArray.R | 15 R/makeList.R | 55 +- R/maskOutline.R | 9 R/patArea.R | 2 R/patGMM.R |only R/patK.R |only R/patK_HSV.R |only R/patLanHSV.R |only R/patLanK.R | 53 +- R/patLanK_HSV.R |only R/patLanRGB.R | 111 +++- R/patLanW.R | 6 R/patPCA.R | 59 +- R/patRDA.R | 34 - R/patRegHSV.R |only R/patRegK.R | 38 + R/patRegK_HSV.R |only R/patRegRGB.R | 19 R/patRegW.R | 6 R/plotHeat.R | 131 ++++- R/plotRasterStackAsImage.R |only R/sampleRGB.R | 3 R/setMask.R |only man/GMMImage.Rd |only man/alignLan.Rd |only man/alignReg.Rd |only man/colorChecker.Rd | 30 + man/colorChecker_customGray.Rd |only man/createPhenotype.Rd |only man/createTarget.Rd | 11 man/extdata.Rd | 6 man/imageList.Rd | 4 man/kImage.Rd | 7 man/kImageHSV.Rd |only man/lanArray.Rd | 8 man/landmarkArray.Rd | 4 man/landmarkList.Rd | 4 man/makeList.Rd | 16 man/maskOutline.Rd | 21 man/patArea.Rd | 19 man/patGMM.Rd |only man/patK.Rd |only man/patK_HSV.Rd |only man/patLanHSV.Rd |only man/patLanK.Rd | 34 + man/patLanK_HSV.Rd |only man/patLanRGB.Rd | 37 + man/patLanW.Rd | 36 + man/patPCA.Rd | 65 ++ man/patRDA.Rd | 50 +- man/patRegHSV.Rd |only man/patRegK.Rd | 22 man/patRegK_HSV.Rd |only man/patRegRGB.Rd | 23 - man/patRegW.Rd | 30 + man/patternize.Rd | 1 man/plotHeat.Rd | 60 ++ man/plotRasterstackAsImage.Rd |only man/rasterList_lanK.Rd | 6 man/rasterList_lanRGB.Rd | 6 man/rasterList_regK.Rd | 6 man/rasterList_regRGB.Rd | 6 man/sampleLandmarks.Rd | 3 man/sampleRGB.Rd | 3 man/setMask.Rd |only 76 files changed, 1740 insertions(+), 577 deletions(-)
Title: Convert Statistical Objects into Tidy Tibbles
Description: Summarizes key information about statistical
objects in tidy tibbles. This makes it easy to report results, create
plots and consistently work with large numbers of models at once.
Broom provides three verbs that each provide different types of
information about a model. tidy() summarizes information about model
components such as coefficients of a regression. glance() reports
information about an entire model, such as goodness of fit measures
like AIC and BIC. augment() adds information about individual
observations to a dataset, such as fitted values or influence
measures.
Author: David Robinson [aut],
Alex Hayes [aut] (<https://orcid.org/0000-0002-4985-5160>),
Simon Couch [aut, cre] (<https://orcid.org/0000-0001-5676-5107>),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>),
Derek Chiu [ctb],
Matthieu Gomez [ctb],
Boris Demeshev [ctb],
Dieter Menne [ctb],
Benjamin Nutter [ctb],
Luke Johnston [ctb],
Ben Bolker [ctb],
Francois Briatte [ctb],
Jeffrey Arnold [ctb],
Jonah Gabry [ctb],
Luciano Selzer [ctb],
Gavin Simpson [ctb],
Jens Preussner [ctb],
Jay Hesselberth [ctb],
Hadley Wickham [ctb],
Matthew Lincoln [ctb],
Alessandro Gasparini [ctb],
Lukasz Komsta [ctb],
Frederick Novometsky [ctb],
Wilson Freitas [ctb],
Michelle Evans [ctb],
Jason Cory Brunson [ctb],
Simon Jackson [ctb],
Ben Whalley [ctb],
Karissa Whiting [ctb],
Yves Rosseel [ctb],
Michael Kuehn [ctb],
Jorge Cimentada [ctb],
Erle Holgersen [ctb],
Karl Dunkle Werner [ctb] (<https://orcid.org/0000-0003-0523-7309>),
Ethan Christensen [ctb],
Steven Pav [ctb],
Paul PJ [ctb],
Ben Schneider [ctb],
Patrick Kennedy [ctb],
Lily Medina [ctb],
Brian Fannin [ctb],
Jason Muhlenkamp [ctb],
Matt Lehman [ctb],
Bill Denney [ctb] (<https://orcid.org/0000-0002-5759-428X>),
Nic Crane [ctb],
Andrew Bates [ctb],
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>),
Hideaki Hayashi [ctb],
Luis Tobalina [ctb],
Annie Wang [ctb],
Wei Yang Tham [ctb],
Clara Wang [ctb],
Abby Smith [ctb] (<https://orcid.org/0000-0002-3207-0375>),
Jasper Cooper [ctb] (<https://orcid.org/0000-0002-8639-3188>),
E Auden Krauska [ctb] (<https://orcid.org/0000-0002-1466-5850>),
Alex Wang [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Charles Gray [ctb] (<https://orcid.org/0000-0002-9978-011X>),
Jared Wilber [ctb],
Vilmantas Gegzna [ctb] (<https://orcid.org/0000-0002-9500-5167>),
Eduard Szoecs [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Angus Moore [ctb],
Nick Williams [ctb],
Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>),
Bruna Wundervald [ctb] (<https://orcid.org/0000-0001-8163-220X>),
Joyce Cahoon [ctb] (<https://orcid.org/0000-0001-7217-4702>),
Grant McDermott [ctb] (<https://orcid.org/0000-0001-7883-8573>),
Kevin Zarca [ctb],
Shiro Kuriwaki [ctb] (<https://orcid.org/0000-0002-5687-2647>),
Lukas Wallrich [ctb] (<https://orcid.org/0000-0003-2121-5177>),
James Martherus [ctb] (<https://orcid.org/0000-0002-8285-3300>),
Chuliang Xiao [ctb] (<https://orcid.org/0000-0002-8466-9398>),
Joseph Larmarange [ctb],
Max Kuhn [ctb],
Michal Bojanowski [ctb],
Hakon Malmedal [ctb],
Clara Wang [ctb],
Sergio Oller [ctb],
Luke Sonnet [ctb],
Jim Hester [ctb],
Cory Brunson [ctb],
Ben Schneider [ctb],
Bernie Gray [ctb] (<https://orcid.org/0000-0001-9190-6032>),
Mara Averick [ctb],
Aaron Jacobs [ctb],
Andreas Bender [ctb],
Sven Templer [ctb],
Paul-Christian Buerkner [ctb],
Matthew Kay [ctb],
Erwan Le Pennec [ctb],
Johan Junkka [ctb],
Hao Zhu [ctb],
Benjamin Soltoff [ctb],
Zoe Wilkinson Saldana [ctb],
Tyler Littlefield [ctb],
Charles T. Gray [ctb],
Shabbh E. Banks [ctb],
Serina Robinson [ctb],
Roger Bivand [ctb],
Riinu Ots [ctb],
Nicholas Williams [ctb],
Nina Jakobsen [ctb],
Michael Weylandt [ctb],
Lisa Lendway [ctb],
Karl Hailperin [ctb],
Josue Rodriguez [ctb],
Jenny Bryan [ctb],
Chris Jarvis [ctb],
Greg Macfarlane [ctb],
Brian Mannakee [ctb],
Drew Tyre [ctb],
Shreyas Singh [ctb],
Laurens Geffert [ctb],
Hong Ooi [ctb],
Henrik Bengtsson [ctb],
Eduard Szocs [ctb],
David Hugh-Jones [ctb],
Matthieu Stigler [ctb],
Hugo Tavares [ctb] (<https://orcid.org/0000-0001-9373-2726>),
R. Willem Vervoort [ctb],
Brenton M. Wiernik [ctb],
Josh Yamamoto [ctb],
Jasme Lee [ctb],
Taren Sanders [ctb] (<https://orcid.org/0000-0002-4504-6008>),
Ilaria Prosdocimi [ctb] (<https://orcid.org/0000-0001-8565-094X>),
Daniel D. Sjoberg [ctb] (<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Simon Couch <scouch2@jhu.edu>
Diff between broom versions 0.7.10 dated 2021-10-31 and 0.7.11 dated 2022-01-03
DESCRIPTION | 23 ++++++++++++++++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 9 +++++++-- R/cmprsk-tidiers.R | 2 +- R/lavaan-tidiers.R | 2 +- R/quantreg-rqs-tidiers.R | 4 ++-- R/rma-tidiers.R | 2 +- README.md | 4 ++-- inst/doc/adding-tidiers.html | 4 ++-- inst/doc/available-methods.html | 4 ++-- inst/doc/bootstrapping.html | 4 ++-- inst/doc/broom.html | 40 ++++++++++++++++++++-------------------- inst/doc/broom_and_dplyr.html | 24 ++++++++++++------------ tests/testthat/test-cmprsk.R | 15 +++++++++++++++ 14 files changed, 98 insertions(+), 65 deletions(-)
Title: Tools to Calibrate and Work with NEON Atmospheric Isotope Data
Description: Functions for downloading,
calibrating, and analyzing atmospheric isotope data bundled
into the eddy covariance data products of the National Ecological
Observatory Network (NEON) <https://www.neonscience.org>.
In this version, calibration tools are provided for only the
carbon isotope products. Tools for calibrating water isotope
products are under development. More details are found in Fiorella et al. (2021)
<doi:10.1029/2020JG005862>, and the readme
file at <https://github.com/SPATIAL-Lab/NEONiso>.
Author: Rich Fiorella [aut, cre] (<https://orcid.org/0000-0002-0824-4777>),
Gabriel J. Bowen [rth]
Maintainer: Rich Fiorella <rich.fiorella@utah.edu>
Diff between NEONiso versions 0.5.2 dated 2021-11-17 and 0.5.3 dated 2022-01-03
DESCRIPTION | 12 - MD5 | 8 - NEWS.md | 4 R/calibrate_standards_carbon.R | 307 +++++++++++++++++++++-------------------- build/vignette.rds |binary 5 files changed, 176 insertions(+), 155 deletions(-)
Title: Handle Error and Warning Messages
Description: Elegantly handle error and warning messages.
Author: John Coene [aut, cre],
Opifex [cph]
Maintainer: John Coene <john@opifex.org>
Diff between erratum versions 2.1.0 dated 2021-02-22 and 2.2.0 dated 2022-01-03
erratum-2.1.0/erratum/R/jab.R |only erratum-2.1.0/erratum/man/jab.Rd |only erratum-2.1.0/erratum/tests/testthat/test_jab.R |only erratum-2.2.0/erratum/DESCRIPTION | 9 +++---- erratum-2.2.0/erratum/MD5 | 22 +++++++++--------- erratum-2.2.0/erratum/NAMESPACE | 6 ++--- erratum-2.2.0/erratum/NEWS.md | 8 +++++- erratum-2.2.0/erratum/R/bash.R |only erratum-2.2.0/erratum/R/issue.R | 8 ++++-- erratum-2.2.0/erratum/R/parse.R | 6 ++--- erratum-2.2.0/erratum/R/resolve.R | 27 ----------------------- erratum-2.2.0/erratum/README.md | 1 erratum-2.2.0/erratum/man/bash.Rd |only erratum-2.2.0/erratum/man/resolves.Rd | 6 ----- erratum-2.2.0/erratum/tests/testthat/test_bash.R |only 15 files changed, 33 insertions(+), 60 deletions(-)
Title: Simple Engine for Generating Reports using R
Description: Runs R-code present in a pandoc markdown file and
includes the resulting output in the resulting markdown file. This
file can then be converted into any of the output formats
supported by pandoc. The package can also be used as an engine
for writing package vignettes.
Author: Jan van der Laan [aut, cre] (<https://orcid.org/0000-0002-0693-1514>)
Maintainer: Jan van der Laan <r@eoos.dds.nl>
Diff between simplermarkdown versions 0.0.3 dated 2021-10-27 and 0.0.4 dated 2022-01-03
simplermarkdown-0.0.3/simplermarkdown/R/vignettes.R |only simplermarkdown-0.0.4/simplermarkdown/DESCRIPTION | 6 simplermarkdown-0.0.4/simplermarkdown/MD5 | 37 ++--- simplermarkdown-0.0.4/simplermarkdown/NEWS |only simplermarkdown-0.0.4/simplermarkdown/R/filter_pandoc_json_tree.R | 5 simplermarkdown-0.0.4/simplermarkdown/R/md_figure.R | 31 +++- simplermarkdown-0.0.4/simplermarkdown/R/md_weave_to_vignette.R |only simplermarkdown-0.0.4/simplermarkdown/R/mdweave.R | 33 ++++ simplermarkdown-0.0.4/simplermarkdown/R/mdweave_to.R | 12 + simplermarkdown-0.0.4/simplermarkdown/R/output_fun.R | 6 simplermarkdown-0.0.4/simplermarkdown/build/vignette.rds |binary simplermarkdown-0.0.4/simplermarkdown/inst/doc/intro.html | 40 +++-- simplermarkdown-0.0.4/simplermarkdown/inst/doc/intro.md | 71 +++++++--- simplermarkdown-0.0.4/simplermarkdown/inst/examples/iris.md | 2 simplermarkdown-0.0.4/simplermarkdown/inst/examples_output/example1.md | 4 simplermarkdown-0.0.4/simplermarkdown/inst/examples_output/figures/test.pdf |binary simplermarkdown-0.0.4/simplermarkdown/inst/examples_output/iris.md | 13 + simplermarkdown-0.0.4/simplermarkdown/man/md_figure.Rd | 18 +- simplermarkdown-0.0.4/simplermarkdown/man/output_fun.Rd | 2 simplermarkdown-0.0.4/simplermarkdown/tests/test_mdweave.R | 14 + simplermarkdown-0.0.4/simplermarkdown/vignettes/intro.md | 71 +++++++--- 21 files changed, 265 insertions(+), 100 deletions(-)
More information about simplermarkdown at CRAN
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Title: Simplified Statistics for PA 606
Description: Simplifies functions assess normality for bivariate and multivariate statistical techniques. Includes functions designed to replicate plots and tables that would result from similar calls in 'SPSS', including hst(), box(), qq(), tab(), cormat(), and residplot(). Also includes simplified formulae, such as mode(), scatter(), p.corr(), ow.anova(), and rm.anova().
Author: Burrel Vann Jr [aut, cre]
Maintainer: Burrel Vann Jr <bvannjr@sdsu.edu>
Diff between vannstats versions 1.0.12.16 dated 2021-12-18 and 1.2.1.3 dated 2022-01-03
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++++-- NAMESPACE | 1 + R/Ideology.R |only R/Ideology_ERA.R |only R/ideo.dist.R |only data/Ideology.RData |only data/Ideology_ERA.RData |only man/Ideology.Rd |only man/Ideology_ERA.Rd |only man/ideo.dist.Rd |only 11 files changed, 15 insertions(+), 6 deletions(-)
Title: Fitting Second-Order Tensor Data
Description: An implementation of fitting generalized linear models on
second-order tensor type data. The functions within this package mainly focus on
parameter estimation, including parameter coefficients and standard deviation.
Author: Mark Chen [aut, cre],
Sheng-Mao Chang [aut],
Wenbin Lu [aut],
Jung-Ying Tzeng [aut],
Ping-Yang Chen [aut]
Maintainer: Mark Chen <l501l501l@gmail.com>
Diff between TensorTest2D versions 1.1.0 dated 2021-12-18 and 1.1.1 dated 2022-01-03
DESCRIPTION | 6 +++--- MD5 | 4 +++- tests |only 3 files changed, 6 insertions(+), 4 deletions(-)
Title: Tools to Manipulate and Query Semantic Data
Description: The Resource Description Framework, or 'RDF' is a widely used
data representation model that forms the cornerstone of the
Semantic Web. 'RDF' represents data as a graph rather than
the familiar data table or rectangle of relational databases.
The 'rdflib' package provides a friendly and concise user interface
for performing common tasks on 'RDF' data, such as reading, writing
and converting between the various serializations of 'RDF' data,
including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld';
creating new 'RDF' graphs, and performing graph queries using 'SPARQL'.
This package wraps the low level 'redland' R package which
provides direct bindings to the 'redland' C library. Additionally,
the package supports the newer and more developer friendly
'JSON-LD' format through the 'jsonld' package. The package
interface takes inspiration from the Python 'rdflib' library.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Bryce Mecum [rev] (<https://orcid.org/0000-0002-0381-3766>),
Anna Krystalli [rev] (<https://orcid.org/0000-0002-2378-4915>),
Viktor Senderov [ctb] (<https://orcid.org/0000-0003-3340-5963>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rdflib versions 0.2.3 dated 2020-01-09 and 0.2.4 dated 2022-01-03
DESCRIPTION | 9 MD5 | 26 NEWS.md | 14 R/write_nquads.R | 9 README.md | 27 build/vignette.rds |binary inst/doc/rdf_intro.R | 26 inst/doc/rdf_intro.Rmd | 33 inst/doc/rdf_intro.html | 2936 ++-------------------------------- man/write_nquads.Rd | 7 vignettes/articles/data-lake.Rmd | 123 + vignettes/articles/data-lake.Rmd.orig |only vignettes/articles/storage.Rmd | 145 + vignettes/articles/storage.Rmd.orig |only vignettes/rdf_intro.Rmd | 33 15 files changed, 515 insertions(+), 2873 deletions(-)
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Mohammed Ali [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 1.0.0 dated 2021-10-28 and 1.0.1 dated 2022-01-03
DESCRIPTION | 10 - MD5 | 64 +++---- NEWS.md | 5 R/downloadFile.R | 2 R/downloadableTable.R | 2 R/fw_helpers_internal.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/downloadFile-module.html | 4 inst/doc/downloadablePlot-module.html | 4 inst/doc/downloadableTable-module.html | 4 inst/doc/new-application.html | 4 inst/fw_templ/p_example/server_local.R | 46 ++++- inst/fw_templ/p_example/server_local_no_left.R | 46 ++++- inst/fw_templ/p_example/server_local_plus.R | 46 ++++- inst/fw_templ/p_example/server_local_plus_no_left.R | 46 ++++- tests/testthat/_snaps/download_file.md | 2 tests/testthat/_snaps/ui_functions.md | 2 tests/testthat/sample_app/program/server_global.R | 4 tests/testthat/sample_app/program/server_local.R | 83 ++++++--- tests/testthat/sample_app/www/periscope_style.yaml | 8 tests/testthat/sample_app_both_sidebar/program/server_global.R | 4 tests/testthat/sample_app_both_sidebar/program/server_local.R | 84 ++++++---- tests/testthat/sample_app_both_sidebar/www/periscope_style.yaml | 8 tests/testthat/sample_app_no_sidebar/program/server_global.R | 4 tests/testthat/sample_app_no_sidebar/program/server_local.R | 83 ++++++--- tests/testthat/sample_app_no_sidebar/www/periscope_style.yaml | 8 tests/testthat/sample_app_no_sidebar_no_resetbutton/program/server_global.R | 4 tests/testthat/sample_app_no_sidebar_no_resetbutton/program/server_local.R | 83 ++++++--- tests/testthat/sample_app_no_sidebar_no_resetbutton/www/periscope_style.yaml | 8 tests/testthat/sample_app_r_sidebar/program/server_global.R | 4 tests/testthat/sample_app_r_sidebar/program/server_local.R | 82 ++++++--- tests/testthat/sample_app_r_sidebar/www/periscope_style.yaml | 8 33 files changed, 502 insertions(+), 264 deletions(-)
Title: A Systematic Data Wrangling Idiom
Description: Supports systematic scrutiny, modification, and integration of
data. The function status() counts rows that have missing values in
grouping columns (returned by na() ), have non-unique combinations of
grouping columns (returned by dup() ), and that are not locally sorted
(returned by unsorted() ). Functions enumerate() and itemize() give
sorted unique combinations of columns, with or without occurrence counts,
respectively. Function ignore() drops columns in x that are present in y,
and informative() drops columns in x that are entirely NA; constant() returns
values that are constant, given a key. Data that have defined unique
combinations of grouping values behave more predictably during merge operations.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between wrangle versions 0.5.5 dated 2021-12-20 and 0.5.7 dated 2022-01-03
wrangle-0.5.5/wrangle/man/group_by_all.Rd |only wrangle-0.5.7/wrangle/DESCRIPTION | 8 ++++---- wrangle-0.5.7/wrangle/MD5 | 7 +++---- wrangle-0.5.7/wrangle/NAMESPACE | 1 - wrangle-0.5.7/wrangle/R/wrangle.R | 22 +++++++++++----------- 5 files changed, 18 insertions(+), 20 deletions(-)
Title: Supplementary Distributions
Description: Ten distributions supplementing those built into R.
Inverse Gauss, Kruskal-Wallis, Kendall's Tau, Friedman's chi
squared, Spearman's rho, maximum F ratio, the Pearson product
moment correlation coefficient, Johnson distributions, normal
scores and generalized hypergeometric distributions.
Author: Bob Wheeler [aut],
Thorsten Pohlert [ctb, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between SuppDists versions 1.1-9.5 dated 2020-01-14 and 1.1-9.7 dated 2022-01-03
DESCRIPTION | 12 +++++------- MD5 | 9 +++++---- R/Dists.R | 1 + inst/NEWS.Rd | 12 ++++++++++++ src/Makevars |only src/dists.cpp | 46 ++++++++++++++++++++++++++++------------------ 6 files changed, 51 insertions(+), 29 deletions(-)
Title: Linear Model Forecasting
Description: Introduces in-sample, out-of-sample, pseudo out-of-sample, and
benchmark linear model forecast tests and a new class for working with
forecast data: Forecast.
Author: Nelson Rayl [aut, cre]
Maintainer: Nelson Rayl <nelsonrayl14@gmail.com>
Diff between lmForc versions 0.0.1 dated 2021-10-13 and 0.1.0 dated 2022-01-03
lmForc-0.0.1/lmForc/R/historical_mean_forc.R |only lmForc-0.0.1/lmForc/R/mse_weighted_forc.R |only lmForc-0.0.1/lmForc/man/collect.Rd |only lmForc-0.0.1/lmForc/man/historical_mean_forc.Rd |only lmForc-0.0.1/lmForc/man/mse_weighted_forc.Rd |only lmForc-0.0.1/lmForc/tests/testthat/test_historical_mean_forc.R |only lmForc-0.0.1/lmForc/tests/testthat/test_mse_weighted_forc.R |only lmForc-0.1.0/lmForc/DESCRIPTION | 6 lmForc-0.1.0/lmForc/MD5 | 115 + lmForc-0.1.0/lmForc/NAMESPACE | 19 lmForc-0.1.0/lmForc/NEWS.md | 21 lmForc-0.1.0/lmForc/R/Forecast.R | 618 +++++----- lmForc-0.1.0/lmForc/R/autoreg_forc.R | 163 +- lmForc-0.1.0/lmForc/R/historical_average_forc.R |only lmForc-0.1.0/lmForc/R/oos_lag_forc.R | 29 lmForc-0.1.0/lmForc/R/oos_realized_forc.R | 62 - lmForc-0.1.0/lmForc/R/oos_vintage_forc.R | 34 lmForc-0.1.0/lmForc/R/performance_weighted_forc.R |only lmForc-0.1.0/lmForc/R/states_weighted_forc.R |only lmForc-0.1.0/lmForc/inst/doc/lmForc.R | 66 - lmForc-0.1.0/lmForc/inst/doc/lmForc.Rmd | 305 +++- lmForc-0.1.0/lmForc/inst/doc/lmForc.html | 277 +++- lmForc-0.1.0/lmForc/man/Forecast-class.Rd | 4 lmForc-0.1.0/lmForc/man/Forecast.Rd | 4 lmForc-0.1.0/lmForc/man/R2-Forecast-method.Rd |only lmForc-0.1.0/lmForc/man/R2.Rd |only lmForc-0.1.0/lmForc/man/autoreg_forc.Rd | 59 lmForc-0.1.0/lmForc/man/forc-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/forc-set-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/forc-set.Rd | 12 lmForc-0.1.0/lmForc/man/forc.Rd | 12 lmForc-0.1.0/lmForc/man/forc2df.Rd |only lmForc-0.1.0/lmForc/man/future-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/future-set-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/future-set.Rd | 12 lmForc-0.1.0/lmForc/man/future.Rd | 12 lmForc-0.1.0/lmForc/man/h_ahead-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/h_ahead-set-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/h_ahead-set.Rd | 12 lmForc-0.1.0/lmForc/man/h_ahead.Rd | 12 lmForc-0.1.0/lmForc/man/historical_average_forc.Rd |only lmForc-0.1.0/lmForc/man/mae-Forecast-method.Rd |only lmForc-0.1.0/lmForc/man/mae.Rd |only lmForc-0.1.0/lmForc/man/mape-Forecast-method.Rd |only lmForc-0.1.0/lmForc/man/mape.Rd |only lmForc-0.1.0/lmForc/man/mse-Forecast-method.Rd | 11 lmForc-0.1.0/lmForc/man/mse.Rd | 11 lmForc-0.1.0/lmForc/man/oos_lag_forc.Rd | 16 lmForc-0.1.0/lmForc/man/oos_realized_forc.Rd | 15 lmForc-0.1.0/lmForc/man/oos_vintage_forc.Rd | 28 lmForc-0.1.0/lmForc/man/origin-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/origin-set-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/origin-set.Rd | 12 lmForc-0.1.0/lmForc/man/origin.Rd | 12 lmForc-0.1.0/lmForc/man/performance_weighted_forc.Rd |only lmForc-0.1.0/lmForc/man/realized-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/realized-set-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/realized-set.Rd | 12 lmForc-0.1.0/lmForc/man/realized.Rd | 12 lmForc-0.1.0/lmForc/man/rmse-Forecast-method.Rd | 12 lmForc-0.1.0/lmForc/man/rmse.Rd | 11 lmForc-0.1.0/lmForc/man/show-Forecast-method.Rd | 11 lmForc-0.1.0/lmForc/man/states_weighted_forc.Rd |only lmForc-0.1.0/lmForc/man/str-Forecast-method.Rd |only lmForc-0.1.0/lmForc/tests/testthat/test_Forecast.R | 39 lmForc-0.1.0/lmForc/tests/testthat/test_autoreg_forc.R | 90 - lmForc-0.1.0/lmForc/tests/testthat/test_historical_average_forc.R |only lmForc-0.1.0/lmForc/tests/testthat/test_performance_weighted_forc.R |only lmForc-0.1.0/lmForc/tests/testthat/test_states_weighted_forc.R |only lmForc-0.1.0/lmForc/vignettes/lmForc.Rmd | 305 +++- lmForc-0.1.0/lmForc/vignettes/vignette_demo.png |only 71 files changed, 1626 insertions(+), 945 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories
(also known as a Sankey diagram), flow charts by extending the grid package,
a method for variable selection based on the SVD, Bézier lines with arrows
complementing the ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 2.1.0 dated 2021-07-23 and 3.0.0 dated 2022-01-03
Gmisc-2.1.0/Gmisc/NEWS |only Gmisc-3.0.0/Gmisc/DESCRIPTION | 14 Gmisc-3.0.0/Gmisc/MD5 | 117 - Gmisc-3.0.0/Gmisc/NAMESPACE | 15 Gmisc-3.0.0/Gmisc/NEWS.md | 236 +- Gmisc-3.0.0/Gmisc/R/boxGrobs_S3_fns.R | 12 Gmisc-3.0.0/Gmisc/R/copyAllNewAttributes.R | 2 Gmisc-3.0.0/Gmisc/R/descriptionStats.R | 7 Gmisc-3.0.0/Gmisc/R/fastDoCall.R | 4 Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy.R | 659 ++----- Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_S3_fns.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prAddDescStats.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prAddDescUnitColumn.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prAddEmptyVals.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prAddTotalDescColumn.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prFactorDescs.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prFixDescRownames.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prGetDescHeader.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prNumericDescs.R |only Gmisc-3.0.0/Gmisc/R/getDescriptionStatsBy_prPropDescs.R |only Gmisc-3.0.0/Gmisc/R/getPval.R | 5 Gmisc-3.0.0/Gmisc/R/mergeDesc.R | 80 Gmisc-3.0.0/Gmisc/R/mergeDesc_S3_fns.R |only Gmisc-3.0.0/Gmisc/R/private_functions.R | 63 Gmisc-3.0.0/Gmisc/R/sefeLoadPkg.R |only Gmisc-3.0.0/Gmisc/R/set_column_labels.R |only Gmisc-3.0.0/Gmisc/R/set_column_units.R |only Gmisc-3.0.0/Gmisc/R/transitionClass.R | 388 ++-- Gmisc-3.0.0/Gmisc/R/transitionClass_helpers.R | 116 - Gmisc-3.0.0/Gmisc/R/transitionPlot_helpers.R | 36 Gmisc-3.0.0/Gmisc/R/yamlDump.R | 22 Gmisc-3.0.0/Gmisc/build/vignette.rds |binary Gmisc-3.0.0/Gmisc/inst/doc/Descriptives.R | 191 -- Gmisc-3.0.0/Gmisc/inst/doc/Descriptives.Rmd | 227 +- Gmisc-3.0.0/Gmisc/inst/doc/Descriptives.html | 941 +++++++--- Gmisc-3.0.0/Gmisc/inst/doc/Transition-class.R | 23 Gmisc-3.0.0/Gmisc/inst/doc/Transition-class.Rmd | 26 Gmisc-3.0.0/Gmisc/inst/doc/Transition-class.html | 30 Gmisc-3.0.0/Gmisc/inst/doc/transitionPlot.html | 4 Gmisc-3.0.0/Gmisc/inst/examples/getDescriptionStatsBy_example.R | 129 - Gmisc-3.0.0/Gmisc/inst/examples/transitionClass_example.R | 6 Gmisc-3.0.0/Gmisc/man/Transition-class.Rd | 15 Gmisc-3.0.0/Gmisc/man/box.Rd | 2 Gmisc-3.0.0/Gmisc/man/describeProp.Rd | 2 Gmisc-3.0.0/Gmisc/man/fastDoCall.Rd | 2 Gmisc-3.0.0/Gmisc/man/getDescriptionStatsBy.Rd | 190 +- Gmisc-3.0.0/Gmisc/man/htmlTable_latex.Rd | 2 Gmisc-3.0.0/Gmisc/man/mergeDesc.Rd | 129 - Gmisc-3.0.0/Gmisc/man/prAddDescStats.Rd |only Gmisc-3.0.0/Gmisc/man/prAddDescUnitColumn.Rd |only Gmisc-3.0.0/Gmisc/man/prAddEmptyVals.Rd |only Gmisc-3.0.0/Gmisc/man/prAddTotalDescColumn.Rd |only Gmisc-3.0.0/Gmisc/man/prFactorDescs.Rd |only Gmisc-3.0.0/Gmisc/man/prFixDescRownames.Rd |only Gmisc-3.0.0/Gmisc/man/prGetDescHeader.Rd |only Gmisc-3.0.0/Gmisc/man/prGetStatistics.Rd | 21 Gmisc-3.0.0/Gmisc/man/prNumericDescs.Rd |only Gmisc-3.0.0/Gmisc/man/prPropDescs.Rd |only Gmisc-3.0.0/Gmisc/man/prTcPlotBoxColumn.Rd | 12 Gmisc-3.0.0/Gmisc/man/prTpGetBoxSizedTextGrob.Rd | 11 Gmisc-3.0.0/Gmisc/man/prTpPlotBox.Rd | 14 Gmisc-3.0.0/Gmisc/man/prTpPlotBoxes.Rd | 3 Gmisc-3.0.0/Gmisc/man/set_column_labels.Rd |only Gmisc-3.0.0/Gmisc/man/set_column_units.Rd |only Gmisc-3.0.0/Gmisc/man/yamlDump.Rd | 4 Gmisc-3.0.0/Gmisc/tests/testthat/Rplots.pdf |binary Gmisc-3.0.0/Gmisc/tests/testthat/test-descriptionStats.R | 2 Gmisc-3.0.0/Gmisc/tests/testthat/test-getDescriptionStats.R | 910 +-------- Gmisc-3.0.0/Gmisc/tests/testthat/test-getDescriptionStats_missing_data.R |only Gmisc-3.0.0/Gmisc/tests/testthat/test-getDescriptionStats_p-values.R |only Gmisc-3.0.0/Gmisc/tests/testthat/test-getDescriptionStats_tidyselect.R |only Gmisc-3.0.0/Gmisc/tests/testthat/test-mergeLists.R | 4 Gmisc-3.0.0/Gmisc/vignettes/Descriptives.Rmd | 227 +- Gmisc-3.0.0/Gmisc/vignettes/Transition-class.Rmd | 26 74 files changed, 2352 insertions(+), 2577 deletions(-)
Title: Fast Wild Cluster Bootstrap Inference for Linear Regression
Models
Description: Implementation of the fast algorithm for wild cluster bootstrap
inference developed in Roodman et al (2019, STATA Journal) for
linear regression models
<doi:10.1177/1536867X19830877>,
which makes it feasible to quickly calculate bootstrap test
statistics based on a large number of bootstrap draws even for
large samples - as long as the number of bootstrapping clusters
is not too large. Multiway clustering, regression weights,
bootstrap weights, fixed effects and subcluster bootstrapping
are supported. Further, both restricted (WCR) and unrestricted
(WCU) bootstrap are supported. Methods are provided for a variety
of fitted models, including 'lm()', 'feols()'
(from package 'fixest') and 'felm()' (from package 'lfe').
Author: Alexander Fischer [aut, cre],
David Roodman [aut],
Achim Zeileis [ctb] (Author of included sandwich fragments),
Nathaniel Graham [ctb] (Contributor to included sandwich fragments),
Susanne Koell [ctb] (Contributor to included sandwich fragments),
Laurent Berge [ctb] (Author of included fixest fragments),
Sebastian Krantz [ctb]
Maintainer: Alexander Fischer <alexander-fischer1801@t-online.de>
Diff between fwildclusterboot versions 0.5.1 dated 2021-11-06 and 0.7 dated 2022-01-03
fwildclusterboot-0.5.1/fwildclusterboot/inst/WORDLIST |only fwildclusterboot-0.5.1/fwildclusterboot/tests/spelling.R |only fwildclusterboot-0.7/fwildclusterboot/DESCRIPTION | 12 fwildclusterboot-0.7/fwildclusterboot/MD5 | 49 +- fwildclusterboot-0.7/fwildclusterboot/NAMESPACE | 1 fwildclusterboot-0.7/fwildclusterboot/NEWS.md | 15 fwildclusterboot-0.7/fwildclusterboot/R/boot_algo2.R | 69 +- fwildclusterboot-0.7/fwildclusterboot/R/boot_ssc.R |only fwildclusterboot-0.7/fwildclusterboot/R/boottest_felm.R | 32 + fwildclusterboot-0.7/fwildclusterboot/R/boottest_fixest.R | 39 + fwildclusterboot-0.7/fwildclusterboot/R/boottest_lm.R | 58 +- fwildclusterboot-0.7/fwildclusterboot/R/p_val_null.R | 33 - fwildclusterboot-0.7/fwildclusterboot/R/preprocess2.R | 107 +++- fwildclusterboot-0.7/fwildclusterboot/README.md | 24 - fwildclusterboot-0.7/fwildclusterboot/inst/doc/fwildclusterboot.html | 32 - fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_bootcluster.R | 2 fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_deterministic_default.R | 106 ++-- fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_deterministic_weights.R | 237 +++++----- fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_fixest_cluster_weights_input.R |only fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_r_vs_julia.R |only fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_small_n_cluster.R | 40 + fwildclusterboot-0.7/fwildclusterboot/inst/tinytest/test_small_sample_correction_tstat.R | 166 +++++-- fwildclusterboot-0.7/fwildclusterboot/man/boot_algo2.Rd | 5 fwildclusterboot-0.7/fwildclusterboot/man/boot_ssc.Rd |only fwildclusterboot-0.7/fwildclusterboot/man/boottest.felm.Rd | 11 fwildclusterboot-0.7/fwildclusterboot/man/boottest.fixest.Rd | 17 fwildclusterboot-0.7/fwildclusterboot/man/boottest.lm.Rd | 17 fwildclusterboot-0.7/fwildclusterboot/man/figures/README-unnamed-chunk-4-1.png |binary fwildclusterboot-0.7/fwildclusterboot/man/get_ssc.Rd |only 29 files changed, 709 insertions(+), 363 deletions(-)
More information about fwildclusterboot at CRAN
Permanent link
Title: Differential Evolution Optimization in Pure R
Description: Differential Evolution (DE) stochastic algorithms for global
optimization of problems with and without constraints.
The aim is to curate a collection of its state-of-the-art variants that
(1) do not sacrifice simplicity of design,
(2) are essentially tuning-free, and
(3) can be efficiently implemented directly in the R language.
Currently, it only provides an implementation of the 'jDE' algorithm by
Brest et al. (2006) <doi:10.1109/TEVC.2006.872133>.
Author: Eduardo L. T. Conceicao [aut, cre],
Martin Maechler [ctb] (<https://orcid.org/0000-0002-8685-9910>)
Maintainer: Eduardo L. T. Conceicao <mail@eduardoconceicao.org>
Diff between DEoptimR versions 1.0-9 dated 2021-05-24 and 1.0-10 dated 2022-01-03
DESCRIPTION | 44 +++++++++++++++++++----------------- MD5 | 10 ++++---- R/JDEoptim.R | 5 ++-- build/partial.rdb |binary inst/xtraR/opt-test-funs.R | 47 ++++++++++++++++++++++++++------------ tests/JDEoptim-tst.R | 55 ++++++++++++++++++++++++++++----------------- 6 files changed, 99 insertions(+), 62 deletions(-)
Title: Bayesian Power Prior Design
Description: Bayesian power/type I error calculation and model fitting using
the power prior and the normalized power prior for generalized linear models.
Detailed examples of applying the package are available at <arXiv:2112.14616>.
The Bayesian clinical trial design methodology is described in Chen et al. (2011)
<doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019)
<doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006)
<doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.
Author: Yueqi Shen [aut, cre],
Matthew A. Psioda [aut],
Joseph G. Ibrahim [aut]
Maintainer: Yueqi Shen <ys137@live.unc.edu>
Diff between BayesPPD versions 1.0.3 dated 2021-09-08 and 1.0.4 dated 2022-01-03
BayesPPD-1.0.3/BayesPPD/LICENSE |only BayesPPD-1.0.3/BayesPPD/src/NI_fixed.cpp |only BayesPPD-1.0.3/BayesPPD/src/NI_fixed_glm.cpp |only BayesPPD-1.0.3/BayesPPD/src/NI_random.cpp |only BayesPPD-1.0.3/BayesPPD/src/NI_random_glm.cpp |only BayesPPD-1.0.4/BayesPPD/DESCRIPTION | 12 BayesPPD-1.0.4/BayesPPD/MD5 | 49 +- BayesPPD-1.0.4/BayesPPD/R/BayesPPD-package.R | 2 BayesPPD-1.0.4/BayesPPD/R/PWK_helper.R | 210 +++++------ BayesPPD-1.0.4/BayesPPD/R/PWK_main.R | 377 +++++++++----------- BayesPPD-1.0.4/BayesPPD/R/RcppExports.R | 8 BayesPPD-1.0.4/BayesPPD/R/data.R | 70 +-- BayesPPD-1.0.4/BayesPPD/R/main_func.R | 113 ++++- BayesPPD-1.0.4/BayesPPD/data/actg019.RData |binary BayesPPD-1.0.4/BayesPPD/data/actg036.RData |binary BayesPPD-1.0.4/BayesPPD/man/BayesPPD-package.Rd | 2 BayesPPD-1.0.4/BayesPPD/man/actg019.Rd | 8 BayesPPD-1.0.4/BayesPPD/man/actg036.Rd | 6 BayesPPD-1.0.4/BayesPPD/man/glm.fixed.a0.Rd | 2 BayesPPD-1.0.4/BayesPPD/man/glm.random.a0.Rd | 2 BayesPPD-1.0.4/BayesPPD/man/normalizing.constant.Rd | 6 BayesPPD-1.0.4/BayesPPD/man/power.glm.fixed.a0.Rd | 19 - BayesPPD-1.0.4/BayesPPD/man/power.glm.random.a0.Rd | 8 BayesPPD-1.0.4/BayesPPD/man/two.grp.fixed.a0.Rd | 59 ++- BayesPPD-1.0.4/BayesPPD/man/two.grp.random.a0.Rd | 1 BayesPPD-1.0.4/BayesPPD/src/PP_fixed.cpp |only BayesPPD-1.0.4/BayesPPD/src/PP_fixed_glm.cpp |only BayesPPD-1.0.4/BayesPPD/src/PP_random.cpp |only BayesPPD-1.0.4/BayesPPD/src/PP_random_glm.cpp |only BayesPPD-1.0.4/BayesPPD/src/RcppExports.cpp | 39 ++ 30 files changed, 559 insertions(+), 434 deletions(-)
Title: Moran Eigenvector-Based Spatial Regression Models
Description: Functions for estimating spatial varying coefficient models, mixed models, and other spatial regression models for Gaussian and non-Gaussian data. Moran eigenvectors are used to an approximate Gaussian process modeling which is interpretable in terms of the Moran coefficient. The GP is used for modeling the spatial processes in residuals and regression coefficients. For details see Murakami (2021) <arXiv:1703.04467>.
Author: Daisuke Murakami <dmuraka@ism.ac.jp>
Maintainer: Daisuke Murakami <dmuraka@ism.ac.jp>
Diff between spmoran versions 0.2.2.1 dated 2021-11-18 and 0.2.2.2 dated 2022-01-03
DESCRIPTION | 10 - MD5 | 14 - R/predict0.R | 170 +-------------------- R/predict0_vc.R | 166 -------------------- R/resf.R | 8 - R/resf_vc.R | 443 ++++++++++++++++++++++++++++---------------------------- man/resf.Rd | 5 man/resf_vc.Rd | 5 8 files changed, 262 insertions(+), 559 deletions(-)
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results), can
handle (and impute) missing values and is delivered with a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre],
Elise Maigne [aut],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SOMbrero versions 1.4 dated 2022-01-03 and 1.4-1 dated 2022-01-03
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 6 ++++++ R/SOMbrero-package.R | 2 +- R/som.R | 10 +++++----- inst/doc/a-doc-SOMbrero-package.html | 2 +- inst/doc/b-doc-grids.html | 2 +- inst/doc/c-doc-numericSOM.html | 2 +- inst/doc/d-doc-korrespSOM.html | 2 +- inst/doc/e-doc-relationalSOM.html | 6 +++--- man/SOMbrero-package.Rd | 2 +- 11 files changed, 33 insertions(+), 27 deletions(-)
Title: Time Series Analysis Tools
Description: A system contains easy-to-use tools as a support for time series analysis courses. In particular, it incorporates a technique called Generalized Method of Wavelet Moments (GMWM) as well as its robust implementation for fast and robust parameter estimation of time series models which is described, for example, in Guerrier et al. (2013) <doi: 10.1080/01621459.2013.799920>. More details can also be found in the paper linked to via the URL below.
Author: Stéphane Guerrier [aut, cre, cph],
James Balamuta [aut, cph],
Roberto Molinari [aut, cph],
Justin Lee [aut],
Lionel Voirol [aut],
Yuming Zhang [aut],
Wenchao Yang [ctb],
Nathanael Claussen [ctb],
Yunxiang Zhang [ctb],
Christian Gunning [cph],
Romain Francois [cph],
Ross Ihaka [cph],
R Core Team [cph]
Maintainer: Stéphane Guerrier <stef.guerrier@gmail.com>
Diff between simts versions 0.1.1 dated 2019-07-21 and 0.2.0 dated 2022-01-03
simts-0.1.1/simts/data/sales.rda |only simts-0.1.1/simts/man/figures/licence.png |only simts-0.1.1/simts/man/misc |only simts-0.1.1/simts/man/sales.Rd |only simts-0.2.0/simts/DESCRIPTION | 15 simts-0.2.0/simts/MD5 | 155 ++--- simts-0.2.0/simts/NAMESPACE | 6 simts-0.2.0/simts/NEWS.md | 13 simts-0.2.0/simts/R/RcppExports.R | 18 simts-0.2.0/simts/R/data.R | 15 simts-0.2.0/simts/R/gmwm.r | 336 ++++++++++-- simts-0.2.0/simts/R/gts.R | 13 simts-0.2.0/simts/R/imu.r |only simts-0.2.0/simts/R/lts.R | 3 simts-0.2.0/simts/R/prediction_plot.R | 1 simts-0.2.0/simts/R/simts_package.R | 4 simts-0.2.0/simts/R/test_support_sin.R |only simts-0.2.0/simts/R/ts.model.R | 66 ++ simts-0.2.0/simts/R/utilities.R | 2 simts-0.2.0/simts/README.md | 78 +- simts-0.2.0/simts/build/vignette.rds |binary simts-0.2.0/simts/inst/doc/vignettes.R | 46 - simts-0.2.0/simts/inst/doc/vignettes.Rmd | 57 -- simts-0.2.0/simts/inst/doc/vignettes.html | 642 ++++++++--------------- simts-0.2.0/simts/man/SARIMA.Rd | 3 simts-0.2.0/simts/man/SIN.Rd |only simts-0.2.0/simts/man/all_bootstrapper.Rd | 14 simts-0.2.0/simts/man/australia.Rd | 9 simts-0.2.0/simts/man/auto_corr.Rd | 10 simts-0.2.0/simts/man/auto_imu_cpp.Rd | 17 simts-0.2.0/simts/man/batch_modwt_wvar_cpp.Rd | 12 simts-0.2.0/simts/man/ci_wave_variance.Rd | 10 simts-0.2.0/simts/man/compare_acf.Rd | 11 simts-0.2.0/simts/man/compute_cov_cpp.Rd | 9 simts-0.2.0/simts/man/corr_analysis.Rd | 12 simts-0.2.0/simts/man/create_imu.Rd |only simts-0.2.0/simts/man/diag_boxpierce.Rd | 3 simts-0.2.0/simts/man/diag_ljungbox.Rd | 3 simts-0.2.0/simts/man/diag_portmanteau_.Rd | 10 simts-0.2.0/simts/man/evaluate.Rd | 10 simts-0.2.0/simts/man/gen_generic_sarima.Rd | 3 simts-0.2.0/simts/man/gen_gts.Rd | 13 simts-0.2.0/simts/man/gen_lts.Rd | 15 simts-0.2.0/simts/man/gen_sarima.Rd | 3 simts-0.2.0/simts/man/gen_sin.Rd |only simts-0.2.0/simts/man/get_summary.Rd | 26 simts-0.2.0/simts/man/gmwm.Rd | 93 +-- simts-0.2.0/simts/man/gmwm_engine.Rd | 12 simts-0.2.0/simts/man/gmwm_imu.Rd | 6 simts-0.2.0/simts/man/gmwm_master_cpp.Rd | 17 simts-0.2.0/simts/man/gmwm_param_bootstrapper.Rd | 14 simts-0.2.0/simts/man/gmwm_sd_bootstrapper.Rd | 14 simts-0.2.0/simts/man/gmwm_update_cpp.Rd | 21 simts-0.2.0/simts/man/gts.Rd | 16 simts-0.2.0/simts/man/guess_initial.Rd | 14 simts-0.2.0/simts/man/guess_initial_old.Rd | 13 simts-0.2.0/simts/man/hydro.Rd | 8 simts-0.2.0/simts/man/imu.Rd |only simts-0.2.0/simts/man/lts.Rd | 14 simts-0.2.0/simts/man/make_frame.Rd | 21 simts-0.2.0/simts/man/modwt_wvar_cpp.Rd | 12 simts-0.2.0/simts/man/opt_n_gof_bootstrapper.Rd | 14 simts-0.2.0/simts/man/optimism_bootstrapper.Rd | 14 simts-0.2.0/simts/man/plot.PACF.Rd | 15 simts-0.2.0/simts/man/plot.gmwm.Rd |only simts-0.2.0/simts/man/plot.gts.Rd | 11 simts-0.2.0/simts/man/plot.lts.Rd | 11 simts-0.2.0/simts/man/plot.simtsACF.Rd | 15 simts-0.2.0/simts/man/plot_pred.Rd | 12 simts-0.2.0/simts/man/predict.fitsimts.Rd | 14 simts-0.2.0/simts/man/predict.gmwm.Rd | 2 simts-0.2.0/simts/man/rank_models_cpp.Rd | 17 simts-0.2.0/simts/man/read.imu.Rd |only simts-0.2.0/simts/man/savingrt.Rd | 6 simts-0.2.0/simts/man/select.Rd | 3 simts-0.2.0/simts/man/select_arima.Rd | 29 - simts-0.2.0/simts/man/simts-package.Rd | 7 simts-0.2.0/simts/man/sub-.imu.Rd |only simts-0.2.0/simts/man/summary.gmwm.Rd | 15 simts-0.2.0/simts/man/update.gmwm.Rd | 6 simts-0.2.0/simts/src/RcppExports.cpp | 20 simts-0.2.0/simts/src/automatic_models.cpp | 25 simts-0.2.0/simts/src/gen_process.cpp | 67 ++ simts-0.2.0/simts/src/gmwm_logic.cpp | 6 simts-0.2.0/simts/vignettes/vignettes.Rmd | 57 -- 85 files changed, 1381 insertions(+), 923 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
(<https://orcid.org/0000-0003-4668-6821>)
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 2.4.6 dated 2021-11-21 and 2.4.13 dated 2022-01-03
DESCRIPTION | 8 +-- MD5 | 116 ++++++++++++++++++++++---------------------- NAMESPACE | 2 R/Data.R | 4 - R/accuracy.r | 40 +++++++-------- R/cateNelsonFixedY.r |only R/cldList.r | 10 ++- R/cliffDelta.r | 2 R/compareGLM.r | 4 - R/countRSquare.r | 4 - R/efronRSquared.r | 4 + R/epsilonSquared.r | 5 + R/groupwiseCMH.r | 2 R/groupwiseGeometric.r | 4 - R/groupwiseHuber.r | 4 - R/groupwiseMean.r | 4 - R/groupwiseMedian.r | 4 - R/groupwisePercentile.r | 4 - R/groupwiseSum.r | 4 - R/nagelkerke.r | 2 R/ordinalEtaSquared.r | 4 + R/pairwiseMedianMatrix.r | 7 +- R/pairwiseMedianTest.r | 11 ++-- R/plotDensityHistogram.r | 2 R/plotNormalDensity.r | 2 R/plotNormalHistogram.r | 2 R/vda.r | 2 R/wilcoxonOR.r | 2 R/wilcoxonPS.r | 2 R/wilcoxonR.r | 4 - R/wilcoxonRG.r | 4 - data/AndersonBias.rda |binary data/Catbus.rda |binary man/AndersonBias.Rd | 4 - man/accuracy.Rd | 25 ++++----- man/cateNelsonFixedY.Rd |only man/cliffDelta.Rd | 2 man/compareGLM.Rd | 4 - man/countRSquare.Rd | 4 - man/efronRSquared.Rd | 4 + man/epsilonSquared.Rd | 7 +- man/groupwiseCMH.Rd | 2 man/groupwiseGeometric.Rd | 4 - man/groupwiseHuber.Rd | 4 - man/groupwiseMean.Rd | 4 - man/groupwiseMedian.Rd | 4 - man/groupwisePercentile.Rd | 4 - man/groupwiseSum.Rd | 4 - man/nagelkerke.Rd | 2 man/ordinalEtaSquared.Rd | 3 - man/pairwiseMedianMatrix.Rd | 7 +- man/pairwiseMedianTest.Rd | 10 ++- man/plotDensityHistogram.Rd | 2 man/plotNormalDensity.Rd | 2 man/plotNormalHistogram.Rd | 2 man/vda.Rd | 2 man/wilcoxonOR.Rd | 2 man/wilcoxonPS.Rd | 2 man/wilcoxonR.Rd | 4 - man/wilcoxonRG.Rd | 4 - 60 files changed, 209 insertions(+), 178 deletions(-)
Title: Tools for Working with the National Hydrography Dataset
Description: Tools for working with the National Hydrography Dataset, with
functions for querying, downloading, and networking both the NHD
<https://www.usgs.gov/national-hydrography>
and NHDPlus <https://www.epa.gov/waterdata/nhdplus-national-hydrography-dataset-plus> datasets.
Author: Jemma Stachelek [aut, cre] (<https://orcid.org/0000-0002-5924-2464>)
Maintainer: Jemma Stachelek <stachel2@msu.edu>
Diff between nhdR versions 0.5.6 dated 2021-07-17 and 0.5.7 dated 2022-01-03
DESCRIPTION | 10 - MD5 | 57 ++++---- NAMESPACE | 2 NEWS.md | 5 R/load.R | 270 ++++++++++++++++++++++++++---------------- R/network.R | 146 ++++++++++++++++++---- R/query.R | 135 ++++++++++++++++----- R/utils.R | 30 +++- R/zzz.R | 10 - README.md | 5 build/vignette.rds |binary inst/CITATION | 8 - inst/doc/demo.html | 4 inst/doc/flow.html | 4 inst/doc/network.html | 4 man/extract_network.Rd | 14 +- man/find_state.Rd |only man/leaf_reaches.Rd | 26 +++- man/nhd_dl_state.Rd |only man/nhd_load.Rd | 24 +++ man/nhd_plus_load.Rd | 15 +- man/nhd_plus_query.Rd | 16 +- man/nhd_query.Rd | 39 +++++- man/select_point_overlay.Rd | 9 - man/terminal_reaches.Rd | 9 + man/tip_reaches.Rd |only tests/testthat/test-get.R | 58 +++++++++ tests/testthat/test-list.R | 15 +- tests/testthat/test-load.R | 58 ++++++--- tests/testthat/test-network.R | 4 tests/testthat/test-query.R | 22 +++ 31 files changed, 738 insertions(+), 261 deletions(-)
Title: Search Spaces for Hyperparameter Tuning
Description: Collection of search spaces for hyperparameter tuning.
Includes various search spaces that can be directly applied on an
`mlr3` learner. Additionally, meta information about the search space
can be queried.
Author: Marc Becker [cre, aut] (<https://orcid.org/0000-0002-8115-0400>),
Michel Lang [ctb] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuningspaces versions 0.0.1 dated 2021-07-16 and 0.1.0 dated 2022-01-03
DESCRIPTION | 28 +++++++++++++--------------- MD5 | 21 +++++++++++---------- NEWS.md | 6 ++++++ R/TuningSpace.R | 31 ++++++++++++++++++++++++++----- R/bibentries.R | 26 ++++++++++++++++---------- R/tuning_spaces_default.R | 25 +++++++++++++------------ R/tuning_spaces_rbv2.R | 32 +++++++++++++++++--------------- inst |only man/TuningSpace.Rd | 28 +++++++++++++++++++++++++--- man/mlr3tuningspaces-package.Rd | 14 ++++++++++---- man/tuning_spaces_default.Rd | 7 ++++--- man/tuning_spaces_rbv2.Rd | 5 ++++- 12 files changed, 145 insertions(+), 78 deletions(-)
More information about mlr3tuningspaces at CRAN
Permanent link
Title: KONP Tests: Powerful K-Sample Tests for Right-Censored Data
Description: The K-sample omnibus non-proportional hazards (KONP) tests are powerful non-parametric tests for comparing K (>=2) hazard functions based on right-censored data (Gorfine, Schlesinger and Hsu, 2020, <doi:10.1177/0962280220907355>). These tests are consistent against any differences between the hazard functions of the groups. The KONP tests are often more powerful than other existing tests, especially under non-proportional hazard functions.
Author: Matan Schlesinger [cre, aut],
Malka Gorfine [aut]
Maintainer: Matan Schlesinger <matan.schles@gmail.com>
Diff between KONPsurv versions 1.0.3 dated 2020-03-02 and 1.0.4 dated 2022-01-03
KONPsurv-1.0.3/KONPsurv/man/KONPsurv-package.Rd |only KONPsurv-1.0.4/KONPsurv/DESCRIPTION | 10 +- KONPsurv-1.0.4/KONPsurv/MD5 | 17 ++-- KONPsurv-1.0.4/KONPsurv/NAMESPACE | 4 - KONPsurv-1.0.4/KONPsurv/README.md | 36 ++++----- KONPsurv-1.0.4/KONPsurv/build |only KONPsurv-1.0.4/KONPsurv/man/KONPSURV-package.Rd |only KONPsurv-1.0.4/KONPsurv/man/carcinoma.Rd | 48 ++++++------- KONPsurv-1.0.4/KONPsurv/man/gastric.Rd | 56 +++++++-------- KONPsurv-1.0.4/KONPsurv/man/konp_test.Rd | 88 ++++++++++++------------ KONPsurv-1.0.4/KONPsurv/src/RcppExports.cpp | 5 + 11 files changed, 135 insertions(+), 129 deletions(-)
Title: Generalized Correlations, Causal Paths and Portfolio Selection
Description: Since causal paths from data are important for all sciences, the
package provides many sophisticated functions. causeSummBlk() and causeSum2Blk()
give easy-to-interpret causal paths. Let Z denote control variables and compare
two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X,Z)+e2. Our criterion Cr1
says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent"
than in Y and causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These
inequalities between many absolute values are quantified by four orders of
stochastic dominance. Our third criterion Cr3 for the causal path X to Y
requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|.
The function parcorVec() reports generalized partials between the first
variable and all others. The package provides several R functions including
get0outliers() for outlier detection, bigfp() for numerical integration by the
trapezoidal rule, stochdom2() for stochastic dominance, pillar3D() for 3D charts,
canonRho() for generalized canonical correlations, depMeas() measures nonlinear
dependence, and causeSummary(mtx) reports summary of causal paths among matrix columns
is easiest to use. Portfolio selection: decileVote(), momentVote(), dif4mtx(),
exactSdMtx() can rank several stocks. Several functions whose names begin with 'boot' provide bootstrap
statistical inference including a new bootGcRsq() test for "Granger-causality"
allowing nonlinear relations. A new tool for evaluation of out-of-sample
portfolio performance is outOFsamp(). See six vignettes of the package for theory
and usage tips. See Vinod (2019) \doi{10.1080/03610918.2015.1122048}.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.2.1 dated 2021-12-08 and 1.2.2 dated 2022-01-03
DESCRIPTION | 17 ++-- MD5 | 126 +++++++++++++++++++++---------------- NAMESPACE | 11 +++ NEWS | 6 + R/GcRsqX12.R | 30 +++++--- R/GcRsqX12c.R | 12 ++- R/bootDom12.R | 7 +- R/bootPair2.R |only R/bootSummary2.R |only R/causeSum2Blk.R |only R/causeSummBlk.R | 57 +++++++++------- R/causeSummary.R | 9 +- R/causeSummary2.R |only R/compPortfo.R |only R/decileVote.R | 56 +++++++++------- R/depMeas.R | 8 +- R/dif4mtx.R | 7 +- R/exactSdMtx.R | 38 +++++++---- R/generalCorrInfo.R | 24 +++---- R/gmcmtx0.R | 9 +- R/momentVote.R | 10 +- R/outOFsamp.R |only R/parcorHijk.R | 16 ++-- R/parcorHijk2.R | 16 ++-- R/parcorVecH.R | 18 +++-- R/parcorVecH2.R | 10 +- R/parcor_ijk.R | 1 R/rank2return.R |only R/siPair2Blk.R |only R/silentPair2.R |only R/someCPairs.R | 26 +++---- R/stdres.R | 7 +- R/stochdom2.R | 3 R/sudoCoefParcor.R | 17 ++-- R/summaryRank.R | 26 ++++--- R/symmze.R | 6 + build/partial.rdb |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary inst/doc/generalCorr-vignette5.pdf |binary man/GcRsqX12.Rd | 30 +++++--- man/GcRsqX12c.Rd | 12 ++- man/bootDom12.Rd | 7 +- man/bootPair2.Rd |only man/bootSummary2.Rd |only man/causeSum2Blk.Rd |only man/causeSummBlk.Rd | 57 +++++++++------- man/causeSummary.Rd | 6 + man/causeSummary2.Rd |only man/compPortfo.Rd |only man/decileVote.Rd | 56 +++++++++------- man/depMeas.Rd | 8 +- man/dif4mtx.Rd | 7 +- man/exactSdMtx.Rd | 31 ++++++--- man/generalCorrInfo.Rd | 24 +++---- man/gmcmtx0.Rd | 9 +- man/momentVote.Rd | 10 +- man/outOFsamp.Rd |only man/parcorHijk.Rd | 16 ++-- man/parcorHijk2.Rd | 16 ++-- man/parcorVecH.Rd | 18 +++-- man/parcorVecH2.Rd | 11 ++- man/parcor_ijk.Rd | 1 man/rank2return.Rd |only man/siPair2Blk.Rd |only man/silentPair2.Rd |only man/someCPairs.Rd | 25 +++---- man/stdres.Rd | 7 +- man/stochdom2.Rd | 3 man/sudoCoefParcor.Rd | 17 ++-- man/summaryRank.Rd | 27 +++++-- man/symmze.Rd | 7 -- 73 files changed, 585 insertions(+), 393 deletions(-)
Title: Probability Distributions as S3 Objects
Description: Tools to create and manipulate probability
distributions using S3. Generics random(), pdf(), cdf() and
quantile() provide replacements for base R's r/d/p/q style functions.
Functions and arguments have been named carefully to minimize
confusion for students in intro stats courses. The documentation for
each distribution contains detailed mathematical notes.
Author: Alex Hayes [aut, cre] (<https://orcid.org/0000-0002-4985-5160>),
Ralph Moller-Trane [aut],
Emil Hvitfeldt [ctb] (<https://orcid.org/0000-0002-0679-1945>),
Daniel Jordan [aut],
Paul Northrop [aut],
Bruna Wundervald [ctb],
Alessandro Gasparini [ctb]
Maintainer: Alex Hayes <alexpghayes@gmail.com>
Diff between distributions3 versions 0.1.1 dated 2019-09-03 and 0.1.2 dated 2022-01-03
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distributions3-0.1.2/distributions3/tests/testthat/test-LogNormal.R | 140 - distributions3-0.1.2/distributions3/tests/testthat/test-Logistic.R | 140 - distributions3-0.1.2/distributions3/tests/testthat/test-Multinomial.R | 46 distributions3-0.1.2/distributions3/tests/testthat/test-NegativeBinomial.R | 140 - distributions3-0.1.2/distributions3/tests/testthat/test-Normal.R | 153 - distributions3-0.1.2/distributions3/tests/testthat/test-PlotDistribution.R |only distributions3-0.1.2/distributions3/tests/testthat/test-Poisson.R | 174 - distributions3-0.1.2/distributions3/tests/testthat/test-RevWeibull.R |only distributions3-0.1.2/distributions3/tests/testthat/test-StudentsT.R | 144 - distributions3-0.1.2/distributions3/tests/testthat/test-Tukey.R | 10 distributions3-0.1.2/distributions3/tests/testthat/test-Uniform.R | 149 - distributions3-0.1.2/distributions3/tests/testthat/test-Weibull.R | 144 - distributions3-0.1.2/distributions3/tests/testthat/test-methods.R | 86 distributions3-0.1.2/distributions3/tests/testthat/test-utils.R | 12 distributions3-0.1.2/distributions3/vignettes/intro-to-hypothesis-testing.Rmd | 410 ++-- distributions3-0.1.2/distributions3/vignettes/one-sample-sign-tests.Rmd | 326 +-- distributions3-0.1.2/distributions3/vignettes/one-sample-t-confidence-interval.Rmd | 330 +-- distributions3-0.1.2/distributions3/vignettes/one-sample-t-test.Rmd | 434 ++-- distributions3-0.1.2/distributions3/vignettes/one-sample-z-confidence-interval.Rmd | 296 +-- distributions3-0.1.2/distributions3/vignettes/one-sample-z-test-for-proportion.Rmd | 349 +-- distributions3-0.1.2/distributions3/vignettes/one-sample-z-test.Rmd | 684 +++---- distributions3-0.1.2/distributions3/vignettes/paired-tests.Rmd | 146 - distributions3-0.1.2/distributions3/vignettes/two-sample-z-test.Rmd | 426 ++-- 289 files changed, 20468 insertions(+), 19774 deletions(-)
More information about distributions3 at CRAN
Permanent link
Title: A Shiny App to Visualize Genetic Maps and QTL Analysis in
Polyploid Species
Description: Provides a graphical user interface to integrate, visualize and explore results
from linkage and quantitative trait loci analysis, together with genomic information for autopolyploid
species. The app is meant for interactive use and allows users to optionally upload different sources
of information, including gene annotation and alignment files, enabling the exploitation and search for
candidate genes in a genome browser. In its current version, 'VIEWpoly' supports inputs from 'MAPpoly',
'polymapR', 'diaQTL', 'QTLpoly' and 'polyqtlR' packages.
Author: Cristiane Taniguti [aut, cre],
Gabriel Gesteira [aut],
Jeekin Lau [ctb],
Guilherme Pereira [ctb],
David Byrne [ctb],
Zhao-Bang Zeng [ctb],
Oscar Riera-Lizarazu [ctb],
Marcelo Mollinari [aut]
Maintainer: Cristiane Taniguti <chtaniguti@tamu.edu>
Diff between viewpoly versions 0.1.0 dated 2021-12-16 and 0.1.1 dated 2022-01-03
viewpoly-0.1.0/viewpoly/inst/app/www/viewpoly-flowchart.jpg |only viewpoly-0.1.1/viewpoly/DESCRIPTION | 12 ++- viewpoly-0.1.1/viewpoly/MD5 | 18 ++--- viewpoly-0.1.1/viewpoly/NAMESPACE | 1 viewpoly-0.1.1/viewpoly/NEWS.md | 7 ++ viewpoly-0.1.1/viewpoly/R/app_ui.R | 1 viewpoly-0.1.1/viewpoly/R/mod_genes_view.R | 26 +++++--- viewpoly-0.1.1/viewpoly/README.md | 39 +++++++++++- viewpoly-0.1.1/viewpoly/build/partial.rdb |binary viewpoly-0.1.1/viewpoly/inst/app/www/viewpoly-flowchart.png |only viewpoly-0.1.1/viewpoly/inst/ext/about.Rmd | 30 ++++++++- 11 files changed, 106 insertions(+), 28 deletions(-)
Title: Penalized Variance Components Analysis
Description: Method to perform penalized variance component analysis.
Author: Jason Sinnwell [aut, cre] (<https://orcid.org/0000-0003-1964-5522>),
Daniel Schaid [aut] (<https://orcid.org/0000-0003-1457-6433>)
Maintainer: Jason Sinnwell <sinnwell.jason@mayo.edu>
Diff between vcpen versions 1.8 dated 2020-08-25 and 1.9 dated 2022-01-03
DESCRIPTION | 12 MD5 | 14 R/vcpen.R | 13 build/vignette.rds |binary inst/doc/vcpen.html | 636 +++++++++++++++++++++++++------------------- src/RcppExports.cpp | 5 tests/testthat/test_vcpen.R | 6 tests/testthat/vcfit.rds |binary 8 files changed, 406 insertions(+), 280 deletions(-)
Title: Time Series Models for Disease Surveillance
Description: Fits time series models for routine disease surveillance tasks and returns probability distributions for a variety of quantities of interest, including measures of health inequality, period and cumulative percent change, and age-standardized rates. Calculates Theil's index to measure inequality among multiple groups, and can be extended to measure inequality across multiple groups nested within geographies. Inference is completed using Markov chain Monte Carlo via the Stan modeling language. The models are appropriate for rare disease incidence and mortality data, employing a Poisson likelihood and first-difference (random-walk) prior for unknown risk, and optional covariance matrix for multiple correlated time series models. References: Brandt and Williams (2007, ISBN:978-1-4129-0656-2); Clayton (1996, ISBN-13:978-0-412-05551-5); Stan Development Team (2021) <https://mc-stan.org>; Theil (1972, ISBN:0-444-10378-3).
Author: Connor Donegan [aut, cre] (<https://orcid.org/0000-0002-9698-5443>)
Maintainer: Connor Donegan <connor.donegan@gmail.com>
Diff between surveil versions 0.1.0 dated 2021-11-11 and 0.1.1 dated 2022-01-03
DESCRIPTION | 10 +-- MD5 | 58 ++++++++--------- NEWS.md | 14 +++- R/apc.R | 42 ++++++------ R/group-diff.R | 18 +++-- R/methods.R | 25 +++++-- R/priors.R | 5 - R/stan_rw.R | 9 +- R/surveil-package.R | 2 R/theil.R | 14 ++-- README.md | 67 ++++---------------- build/vignette.rds |binary inst/doc/demonstration.R | 6 - inst/doc/demonstration.Rmd | 30 ++++----- inst/doc/demonstration.html | 143 +++++++++++++++++++++++--------------------- man/apc.Rd | 3 man/figures/cpc-plot.png |binary man/group_diff.Rd | 3 man/plot.surveil.Rd | 6 + man/print.apc.Rd | 4 - man/priors.Rd | 5 - man/stan_rw.Rd | 9 +- man/standardize.Rd | 3 man/surveil-package.Rd | 2 man/surveil_diff.Rd | 3 man/theil.Rd | 7 +- man/theil_methods.Rd | 3 man/waic.Rd | 3 vignettes/bib.bib | 18 +++++ vignettes/demonstration.Rmd | 30 ++++----- 30 files changed, 293 insertions(+), 249 deletions(-)
Title: Meta-Analyses for Simultaneously Estimating Individual Means
Description: Implement meta-analyses for simultaneously estimating individual means with shrinkage,
isotonic regression and pretests. Include our original implementation of the isotonic regression via the pool-adjacent-violators algorithm (PAVA) algorithm.
This methodology is published in Taketomi et al.(2021) <doi:10.3390/axioms10040267>.
Author: Nanami Taketomi, Takeshi Emura
Maintainer: Nanami Taketomi <nanamitaketomitommy@gmail.com>
Diff between meta.shrinkage versions 0.1.1 dated 2021-12-07 and 0.1.2 dated 2022-01-03
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/js.R | 8 ++++---- R/rjs.R | 16 +++++++++++----- R/rml.R | 35 ++++++++++++++++++++--------------- man/rml.Rd | 6 +++++- 7 files changed, 51 insertions(+), 34 deletions(-)
More information about meta.shrinkage at CRAN
Permanent link
Title: Integrative Dimension Reduction Analysis for Multi-Source Data
Description: The implement of integrative analysis methods based on a two-part penalization, which realizes dimension reduction analysis and mining the heterogeneity and association of multiple studies with compatible designs. The software package provides the integrative analysis methods including integrative sparse principal component analysis (Fang et al., 2018), integrative sparse partial least squares (Liang et al., 2021) and integrative sparse canonical correlation analysis, as well as corresponding individual analysis and meta-analysis versions. References: (1) Fang, K., Fan, X., Zhang, Q., and Ma, S. (2018). Integrative sparse principal component analysis. Journal of Multivariate Analysis, <doi:10.1016/j.jmva.2018.02.002>. (2) Liang, W., Ma, S., Zhang, Q., and Zhu, T. (2021). Integrative sparse partial least squares. Statistics in Medicine, <doi:10.1002/sim.8900>.
Author: Kuangnan Fang [aut],
Rui Ren [aut, cre],
Qingzhao Zhang [aut],
Shuangge Ma [aut]
Maintainer: Rui Ren <xmurr@stu.xmu.edu.cn>
Diff between iSFun versions 0.1.0 dated 2021-10-04 and 1.1.0 dated 2022-01-03
DESCRIPTION | 8 +- MD5 | 68 +++++++++--------- R/iscca.R | 174 +++++++++++++++++++++-------------------------- R/iscca.cv.R | 150 ++++++++++++++++++++--------------------- R/ispca.R | 86 +++++++++++------------ R/ispca.cv.R | 98 ++++++++++++-------------- R/ispca.plot.R | 2 R/ispls.R | 190 ++++++++++++++++++++++++++++++++++------------------ R/ispls.cv.R | 193 ++++++++++++++++++++++++++++++++++++++--------------- R/ispls.plot.R | 16 +++- R/meta.scca.R | 118 +++++++++++++++----------------- R/meta.spca.R | 48 +++++++------ R/meta.spls.R | 70 ++++++++----------- R/preview.cca.R | 15 ---- R/preview.pca.R | 5 - R/preview.pls.R | 54 -------------- R/scca.R | 123 +++++++++++++++++---------------- R/spca.R | 55 ++++++++------- R/spls.R | 76 ++++++++------------ man/iscca.Rd | 30 ++++---- man/iscca.cv.Rd | 12 +-- man/ispca.Rd | 18 ++-- man/ispca.cv.Rd | 25 +++--- man/ispca.plot.Rd | 2 man/ispls.Rd | 13 ++- man/ispls.cv.Rd | 12 +-- man/meta.scca.Rd | 2 man/meta.spca.Rd | 2 man/meta.spls.Rd | 2 man/preview.cca.Rd | 4 - man/preview.pca.Rd | 2 man/preview.pls.Rd | 6 - man/scca.Rd | 12 +-- man/spca.Rd | 8 +- man/spls.Rd | 10 +- 35 files changed, 898 insertions(+), 811 deletions(-)
Title: A Wrapper for the 'Highcharts' Library
Description: A wrapper for the 'Highcharts' library including
shortcut functions to plot R objects. 'Highcharts'
<https://www.highcharts.com/> is a charting library offering
numerous chart types with a simple configuration syntax.
Author: Joshua Kunst [aut, cre],
Nuno Agostinho [ctb] (hchart.survfit, densities and
hc_add_series_scatter),
Danton Noriega [ctb] (hcaes_),
Martin John Hadley [ctb] (hc_add_event_point improvement),
Eduardo Flores [ctb] (First version hc_add_series_df_tidy),
Dean Kilfoyle [ctb] (First version hc_add_series_boxplot),
Adline Dsilva [ctb] (First version Matrix heatmap),
Kamil Slowikowski [ctb] (<https://orcid.org/0000-0002-2843-6370>),
Christian Minich [ctb] (hcaes mutate_mapping improvement),
Jonathan Armond [ctb] (mutate_mapping bugfix),
David Breuer [ctb] (download_map_data quiet parameter),
Mauricio Vargas [ctb] (tests and gh-actions),
Michael Yan [ctb] (Motivational example for treemap/sunburst data
helper),
Bart Oortwijn [ctb] (rjson option, hc_add_yAxis, and GH issues
collaborator),
Paul Campbell [ctb] (additional proxy methods)
Maintainer: Joshua Kunst <jbkunst@gmail.com>
Diff between highcharter versions 0.8.2 dated 2020-07-26 and 0.9.4 dated 2022-01-03
highcharter-0.8.2/highcharter/inst/extdata |only highcharter-0.8.2/highcharter/inst/htmlwidgets/lib/highcharts/plugins/pattern-fill-v2.js |only highcharter-0.8.2/highcharter/inst/htmlwidgets/lib/highcharts/plugins/tooltip-delay.js |only highcharter-0.9.4/highcharter/DESCRIPTION | 20 highcharter-0.9.4/highcharter/MD5 | 519 +- highcharter-0.9.4/highcharter/NAMESPACE | 21 highcharter-0.9.4/highcharter/NEWS.md | 30 highcharter-0.9.4/highcharter/R/data-helpers.R | 258 - highcharter-0.9.4/highcharter/R/data.R | 54 highcharter-0.9.4/highcharter/R/globals.R | 7 highcharter-0.9.4/highcharter/R/hchart-shorcuts.R | 63 highcharter-0.9.4/highcharter/R/hchart.R | 23 highcharter-0.9.4/highcharter/R/helpers.R | 66 highcharter-0.9.4/highcharter/R/highcharter-package.R | 2 highcharter-0.9.4/highcharter/R/highcharter.R | 93 highcharter-0.9.4/highcharter/R/highcharts-api-add.R | 269 - highcharter-0.9.4/highcharter/R/highcharts-api-helpers.R | 124 highcharter-0.9.4/highcharter/R/highcharts-api.R | 2308 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highcharter-0.9.4/highcharter/man/highcharter.Rd | 30 highcharter-0.9.4/highcharter/man/highcharts_demo.Rd | 31 highcharter-0.9.4/highcharter/man/hw_grid.Rd | 87 highcharter-0.9.4/highcharter/man/is.hexcolor.Rd | 40 highcharter-0.9.4/highcharter/man/is.highchart.Rd | 28 highcharter-0.9.4/highcharter/man/list_parse.Rd | 48 highcharter-0.9.4/highcharter/man/mountains_panorama.Rd |only highcharter-0.9.4/highcharter/man/mutate_mapping.Rd | 50 highcharter-0.9.4/highcharter/man/pokemon.Rd | 59 highcharter-0.9.4/highcharter/man/random_id.Rd | 32 highcharter-0.9.4/highcharter/man/renderHighchart.Rd | 45 highcharter-0.9.4/highcharter/man/stars.Rd | 60 highcharter-0.9.4/highcharter/man/str_to_id.Rd | 42 highcharter-0.9.4/highcharter/man/tooltip_chart.Rd | 195 highcharter-0.9.4/highcharter/man/tooltip_table.Rd | 68 highcharter-0.9.4/highcharter/man/unemployment.Rd | 56 highcharter-0.9.4/highcharter/man/uscountygeojson.Rd | 34 highcharter-0.9.4/highcharter/man/usgeojson.Rd | 34 highcharter-0.9.4/highcharter/man/vaccines.Rd | 58 highcharter-0.9.4/highcharter/man/weather.Rd | 56 highcharter-0.9.4/highcharter/man/worldgeojson.Rd | 34 272 files changed, 9915 insertions(+), 9205 deletions(-)
Title: Maximum Likelihood Difference Scaling
Description: Difference scaling is a method for scaling perceived
supra-threshold differences. The package contains functions that
allow the user to design and run a difference scaling experiment,
to fit the resulting data by maximum likelihood and test the
internal validity of the estimated scale.
Author: Kenneth Knoblauch and Laurence T. Maloney,
based in part on C code written by Laurence T. Maloney
and J. N. Yang
Maintainer: Ken Knoblauch <ken.knoblauch@inserm.fr>
Diff between MLDS versions 0.4.5 dated 2015-08-19 and 0.4.7 dated 2022-01-03
DESCRIPTION | 8 +++---- MD5 | 53 +++++++++++++++++++++++------------------------ build/partial.rdb |only build/vignette.rds |binary data/AutumnLab.rda |binary data/Transparency.rda |binary data/kk1.rda |binary data/kk2.rda |binary data/kk3.rda |binary data/kktriad.rda |binary inst/CITATION | 12 ++++++---- inst/NEWS | 8 +++++++ inst/doc/MLDS.Stex | 2 - inst/doc/MLDS.pdf |binary man/AutumnLab.Rd | 3 +- man/Get6pts.Rd | 2 - man/MLDS-package.Rd | 4 +-- man/SimMLDS.Rd | 4 +-- man/binom.diagnostics.Rd | 2 - man/boot.mlds.Rd | 4 +-- man/fitted.mlds.Rd | 2 - man/kk.Rd | 2 - man/lik6pt.Rd | 4 +-- man/mlds.Rd | 4 +-- man/pmc.Rd | 2 - man/predict.mlds.Rd | 2 - man/simu.6pt.Rd | 4 +-- vignettes/MLDS.Stex | 2 - 28 files changed, 68 insertions(+), 56 deletions(-)
Title: Hydro-Meteorology Time-Series
Description: Functions for the management and treatment of hydrology and
meteorology time-series stored in a 'Sqlite' data base.
Author: Pierre Chevallier [aut, cre]
Maintainer: Pierre Chevallier <pierre.chevallier@ird.fr>
Diff between htsr versions 1.1.2 dated 2021-10-31 and 1.1.3 dated 2022-01-03
DESCRIPTION | 8 +-- MD5 | 50 +++++++++++-------- NAMESPACE | 2 R/ds_exp_hts.R | 2 R/f_convert.R | 116 +++++---------------------------------------- R/f_convert_hdsm2hts.R |only R/f_convert_hts2hdsm.R |only R/f_properties.R | 2 R/h_gapfill.R | 17 +++--- R/h_weightedsum.R | 2 R/hs_tstep.R | 2 R/p_hypso.R | 2 R/w_atmp_alt.R |only R/w_etp.R |only R/w_temp_alt.R |only build/vignette.rds |binary inst/doc/htsr-package.Rmd | 20 +++++-- inst/doc/htsr-package.html | 17 +++++- man/ds_exp_hts.Rd | 2 man/f_convert.Rd | 52 +++----------------- man/f_convert_hdsm2hts.Rd |only man/f_convert_hts2hdsm.Rd |only man/f_properties.Rd | 2 man/h_gapfill.Rd | 8 +-- man/h_weightedsum.Rd | 2 man/hs_tstep.Rd | 2 man/p_hypso.Rd | 2 man/w_atmp_alt.Rd |only man/w_etp.Rd |only man/w_temp_alt.Rd |only vignettes/htsr-package.Rmd | 20 +++++-- 31 files changed, 126 insertions(+), 204 deletions(-)
Title: Data Visualization Tools for Statistical Analysis Results
Description: Unified plotting tools for statistics commonly used, such as GLM,
time series, PCA families, clustering and survival analysis. The package offers
a single plotting interface for these analysis results and plots in a unified
style using 'ggplot2'.
Author: Masaaki Horikoshi [aut],
Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
Austin Dickey [ctb],
Matthias Grenié [ctb],
Ryan Thompson [ctb],
Luciano Selzer [ctb],
Dario Strbenac [ctb],
Kirill Voronin [ctb],
Damir Pulatov [ctb]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between ggfortify versions 0.4.13 dated 2021-10-25 and 0.4.14 dated 2022-01-03
DESCRIPTION | 10 +++++----- LICENSE |only MD5 | 7 ++++--- NEWS.md | 5 +++++ R/fortify_stats_lm.R | 6 +++--- 5 files changed, 17 insertions(+), 11 deletions(-)
Title: Using the Theory of Belief Functions
Description: Using the Theory of Belief Functions for evidence calculus. Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values and combined. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>
Diff between dst versions 1.4.1 dated 2020-03-28 and 1.5.1 dated 2022-01-03
DESCRIPTION | 10 MD5 | 177 ++-- NAMESPACE | 3 NEWS | 32 R/addTobca.R | 65 + R/bca.R | 162 ++-- R/bcaPrint.R | 31 R/bcaRel.R | 108 +-- R/belplau.R | 57 + R/data.R | 52 - R/decode.R | 7 R/dotprod.R | 4 R/doubles.R | 23 R/dsrwon.R | 165 +++- R/dst.R | 13 R/elim.R | 103 +- R/encode.R | 3 R/extmin.R | 103 +- R/inters.R | 23 R/marrayToMatrix.R | 58 - R/matrixToMarray.R | 46 - R/nameCols.R |only R/nameCols_prod.R |only R/nameRows.R | 54 - R/nzdsr.R | 93 +- R/peeling.R |only R/plautrans.R | 47 - R/productSpace.R | 72 +- R/reduction.R | 14 R/shape.R | 4 R/tabresul.R | 75 +- README.md | 4 build/vignette.rds |binary data/dlfm.rda |binary inst/doc/Captain_Example.R | 132 +-- inst/doc/Captain_Example.Rmd | 138 +-- inst/doc/Captain_Example.html | 899 ++++++++++++------------- inst/doc/Introduction_to_Belief_Functions.R | 139 +-- inst/doc/Introduction_to_Belief_Functions.Rmd | 260 ++----- inst/doc/Introduction_to_Belief_Functions.html | 381 +++++----- inst/doc/The_Monty_Hall_Game.R | 6 inst/doc/The_Monty_Hall_Game.Rmd | 10 inst/doc/The_Monty_Hall_Game.html | 95 +- inst/doc/Zadeh_Example.R | 152 +--- inst/doc/Zadeh_Example.Rmd | 221 ++---- inst/doc/Zadeh_Example.html | 388 +++------- inst/dst.pdf |binary man/addTobca.Rd | 29 man/ads.Rd | 14 man/bca.Rd | 80 +- man/bcaPrint.Rd | 10 man/bcaRel.Rd | 56 + man/belplau.Rd | 25 man/decode.Rd | 1 man/dlfm.Rd | 18 man/doubles.Rd | 10 man/dsrwon.Rd | 30 man/dst.Rd | 13 man/elim.Rd | 35 man/extmin.Rd | 27 man/fw.Rd | 10 man/inters.Rd | 12 man/marrayToMatrix.Rd | 18 man/matrixToMarray.Rd | 27 man/mrf.Rd | 12 man/mrt.Rd | 12 man/nameCols.Rd |only man/nameCols_prod.Rd |only man/nameRows.Rd | 26 man/nzdsr.Rd | 28 man/peeling.Rd |only man/plautrans.Rd | 10 man/productSpace.Rd | 16 man/reduction.Rd | 10 man/shape.Rd | 4 man/swr.Rd | 16 man/tabresul.Rd | 20 tests/testthat/test_addTobca.R | 12 tests/testthat/test_bca.R | 37 - tests/testthat/test_bcaRel.R | 14 tests/testthat/test_belplau.R | 4 tests/testthat/test_dsrwon.R | 17 tests/testthat/test_extmin.R | 33 tests/testthat/test_marrayToMatrix.R | 12 tests/testthat/test_matrixToMarray.R | 7 tests/testthat/test_nameCols.R |only tests/testthat/test_nameCols_prod.R |only tests/testthat/test_peeling.R |only tests/testthat/test_plautrans.R | 2 tests/testthat/test_tabresul.R | 8 vignettes/Captain_Example.Rmd | 138 +-- vignettes/Introduction_to_Belief_Functions.Rmd | 260 ++----- vignettes/The_Monty_Hall_Game.Rmd | 10 vignettes/Zadeh_Example.Rmd | 221 ++---- 94 files changed, 2903 insertions(+), 2870 deletions(-)
Title: Loading Screen for 'Shiny'
Description: Full screen and partial loading screens for 'Shiny' with spinners, progress bars, and notifications.
Author: John Coene [aut, cre],
Jinhwan Kim [ctb],
Victor Granda [ctb] (<https://orcid.org/0000-0002-0469-1991>)
Maintainer: John Coene <jcoenep@gmail.com>
Diff between waiter versions 0.2.4 dated 2021-10-04 and 0.2.5 dated 2022-01-03
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- NAMESPACE | 2 + NEWS.md | 5 ++-- R/spinners.R | 66 ++++++++++++++++++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary man/spinners.Rd | 14 +++++++++++ 7 files changed, 94 insertions(+), 13 deletions(-)
Title: A 'Shiny' App to Test Regular Expressions in an R Environment
Description: A 'Shiny' app to aid in writing, explaining, and debugging regular expressions in an R environment.
Author: Adam Spannbauer [cre, aut]
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between regexTestR versions 0.1.0 dated 2020-06-29 and 0.1.3 dated 2022-01-03
DESCRIPTION | 9 +++---- MD5 | 17 ++++++++------ NAMESPACE | 2 + R/app_server.R | 32 +++++++++++++++++++++++++++ R/app_ui.R | 36 +++++++++++++++++++++---------- R/build_save_url.R |only R/golem_utils_ui.R | 7 ++++++ R/highlight_test_str.R | 15 +++++++++--- R/parse_url_params.R |only inst/app/www/ga_tag.html |only tests/testthat/test-highlight_test_str.R | 15 ++++++++++++ 11 files changed, 106 insertions(+), 27 deletions(-)
Title: The Matrix Normal Distribution
Description: Computes densities, probabilities, and random deviates of the Matrix Normal (Iranmanesh et al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes simple but useful matrix functions. See the vignette for more information.
Author: Paul M. Hargarten [aut, cre]
Maintainer: Paul M. Hargarten <hargartenp@vcu.edu>
Diff between matrixNormal versions 0.0.5 dated 2021-04-02 and 0.1.0 dated 2022-01-03
DESCRIPTION | 6 MD5 | 34 +-- NEWS.md | 35 +++ R/is_symmetric_matrix.R | 31 +-- R/matrixNormal_Distribution.R | 104 +++++++--- R/tr.R | 3 R/vec.R | 16 + R/vech.R | 8 inst/WORDLIST | 50 ++--- inst/doc/introduction-to-matrixnormal-package.Rmd | 8 inst/doc/introduction-to-matrixnormal-package.html | 201 ++++++++++----------- man/is.symmetric.matrix.Rd | 12 - man/matrixNormal_Distribution.Rd | 27 +- man/vech.Rd | 3 tests/spelling.R | 3 tests/testthat/test_tr.R | 6 vignettes/introduction-to-matrixnormal-package.Rmd | 8 vignettes/mnvignette.bib | 7 18 files changed, 330 insertions(+), 232 deletions(-)
Title: Thematic Cartography
Description: Create and integrate thematic maps in your workflow. This package
helps to design various cartographic representations such as proportional
symbols, choropleth or typology maps. It also offers several functions to
display layout elements that improve the graphic presentation of maps
(e.g. scale bar, north arrow, title, labels). 'mapsf' maps 'sf' objects on
'base' graphics.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Diego Hernangómez [ctb] (<https://orcid.org/0000-0001-8457-4658>),
Hugues Pecout [ctb],
Ronan Ysebaert [ctb],
Ian Fellows [cph] (No overlap algorithm for labels, from wordcloud
package),
Jim Lemon [cph] (Arc drawing algorithm for annotations, from plotrix
package),
Florian Zenoni [cph] (Orthographic projection visualisation)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between mapsf versions 0.3.0 dated 2021-09-24 and 0.4.0 dated 2022-01-03
mapsf-0.3.0/mapsf/man/figures/README-example1-1.png |only mapsf-0.3.0/mapsf/man/figures/README-example4-1.png |only mapsf-0.3.0/mapsf/man/figures/README-example5-1.png |only mapsf-0.4.0/mapsf/DESCRIPTION | 8 mapsf-0.4.0/mapsf/MD5 | 66 - mapsf-0.4.0/mapsf/NEWS.md | 17 mapsf-0.4.0/mapsf/R/mf_doc_utils.R | 4 mapsf-0.4.0/mapsf/R/mf_export.R | 32 mapsf-0.4.0/mapsf/R/mf_leg_s_utils.R | 8 mapsf-0.4.0/mapsf/R/mf_map.R | 27 mapsf-0.4.0/mapsf/R/mf_raster.R | 16 mapsf-0.4.0/mapsf/R/mf_scale.R | 4 mapsf-0.4.0/mapsf/R/mf_worldmap.R | 23 mapsf-0.4.0/mapsf/README.md | 97 +- mapsf-0.4.0/mapsf/build/vignette.rds |binary mapsf-0.4.0/mapsf/inst/doc/mapsf.Rmd | 2 mapsf-0.4.0/mapsf/inst/doc/mapsf.html | 685 +++++++------------- mapsf-0.4.0/mapsf/inst/tinytest/test_export.R | 29 mapsf-0.4.0/mapsf/inst/tinytest/test_map.R | 3 mapsf-0.4.0/mapsf/man/figures/example1-1.png |only mapsf-0.4.0/mapsf/man/figures/mapsf_cheatsheet.png |only mapsf-0.4.0/mapsf/man/figures/mtq.png |binary mapsf-0.4.0/mapsf/man/figures/website.png |only mapsf-0.4.0/mapsf/man/mf_choro.Rd | 2 mapsf-0.4.0/mapsf/man/mf_export.Rd | 16 mapsf-0.4.0/mapsf/man/mf_grad.Rd | 2 mapsf-0.4.0/mapsf/man/mf_map.Rd | 2 mapsf-0.4.0/mapsf/man/mf_prop.Rd | 2 mapsf-0.4.0/mapsf/man/mf_prop_choro.Rd | 2 mapsf-0.4.0/mapsf/man/mf_prop_typo.Rd | 2 mapsf-0.4.0/mapsf/man/mf_raster.Rd | 3 mapsf-0.4.0/mapsf/man/mf_scale.Rd | 4 mapsf-0.4.0/mapsf/man/mf_symb.Rd | 2 mapsf-0.4.0/mapsf/man/mf_symb_choro.Rd | 2 mapsf-0.4.0/mapsf/man/mf_typo.Rd | 2 mapsf-0.4.0/mapsf/man/mf_worldmap.Rd | 28 mapsf-0.4.0/mapsf/vignettes/mapsf.Rmd | 2 37 files changed, 521 insertions(+), 571 deletions(-)
Title: Additional Layout Algorithms for Network Visualizations
Description: Several new layout algorithms to visualize networks are provided which are not part of 'igraph'.
Most are based on the concept of stress majorization by Gansner et al. (2004) <doi:10.1007/978-3-540-31843-9_25>.
Some more specific algorithms allow to emphasize hidden group structures in networks or focus on specific nodes.
Author: David Schoch [aut, cre] (<https://orcid.org/0000-0003-2952-4812>)
Maintainer: David Schoch <david@schochastics.net>
Diff between graphlayouts versions 0.7.2 dated 2021-11-21 and 0.8.0 dated 2022-01-03
DESCRIPTION | 15 ++++++++------- MD5 | 14 ++++++++------ NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/layout_umap.R |only R/layouts.R | 12 ++++++++++++ README.md | 1 + man/figures/README-flex_cent-1.png |binary man/layout_umap.Rd |only 9 files changed, 35 insertions(+), 13 deletions(-)
Title: Integrates 'Google Firebase' Authentication Storage, and
'Analytics' with 'Shiny'
Description: Authenticate users in 'Shiny' applications using 'Google Firebase'
with any of the many methods provided; email and password, email link, or
using a third-party provider such as 'Github', 'Twitter', or 'Google'.
use 'Firebase Storage' to store files securely, and leverage 'Firebase Analytics'
to easily log events and better understand your audience.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between firebase versions 0.2.1 dated 2021-10-24 and 1.0.0 dated 2022-01-03
firebase-0.2.1/firebase/R/zzz.R |only firebase-0.2.1/firebase/inst/firebase |only firebase-0.2.1/firebase/inst/firebase-ui |only firebase-0.2.1/firebase/inst/fireblaze |only firebase-1.0.0/firebase/DESCRIPTION | 16 firebase-1.0.0/firebase/MD5 | 102 +++-- firebase-1.0.0/firebase/NAMESPACE | 18 firebase-1.0.0/firebase/NEWS.md | 42 ++ firebase-1.0.0/firebase/R/class-analytics.R |only firebase-1.0.0/firebase/R/class-auth.R |only firebase-1.0.0/firebase/R/class-core.R | 332 +++--------------- firebase-1.0.0/firebase/R/class-email-link.R | 41 +- firebase-1.0.0/firebase/R/class-email-password.R | 29 + firebase-1.0.0/firebase/R/class-oauth.R | 33 + firebase-1.0.0/firebase/R/class-phone.R | 103 +++++ firebase-1.0.0/firebase/R/class-real-time.R |only firebase-1.0.0/firebase/R/class-social.R | 29 + firebase-1.0.0/firebase/R/class-storage.R |only firebase-1.0.0/firebase/R/class-ui.R | 31 + firebase-1.0.0/firebase/R/config.R | 180 ++++++--- firebase-1.0.0/firebase/R/dependencies.R | 159 +++++--- firebase-1.0.0/firebase/R/toggle.R | 8 firebase-1.0.0/firebase/R/utils.R | 31 + firebase-1.0.0/firebase/README.md | 34 - firebase-1.0.0/firebase/inst/app/app.R | 4 firebase-1.0.0/firebase/inst/packer |only firebase-1.0.0/firebase/man/Analytics.Rd |only firebase-1.0.0/firebase/man/Firebase.Rd | 277 --------------- firebase-1.0.0/firebase/man/FirebaseAuth.Rd |only firebase-1.0.0/firebase/man/FirebaseEmailLink.Rd | 86 +++- firebase-1.0.0/firebase/man/FirebaseEmailPassword.Rd | 74 +++- firebase-1.0.0/firebase/man/FirebaseOauthProviders.Rd | 74 +++- firebase-1.0.0/firebase/man/FirebasePhone.Rd |only firebase-1.0.0/firebase/man/FirebaseSocial.Rd | 74 +++- firebase-1.0.0/firebase/man/FirebaseUI.Rd | 76 +++- firebase-1.0.0/firebase/man/RealtimeDatabase.Rd |only firebase-1.0.0/firebase/man/Storage.Rd |only firebase-1.0.0/firebase/man/check_installed.Rd |only firebase-1.0.0/firebase/man/check_urls.Rd | 1 firebase-1.0.0/firebase/man/config.Rd | 46 ++ firebase-1.0.0/firebase/man/dependencies.Rd | 9 firebase-1.0.0/firebase/man/get_config_from_env.Rd |only firebase-1.0.0/firebase/man/get_config_from_file.Rd |only firebase-1.0.0/firebase/man/read_config.Rd | 8 firebase-1.0.0/firebase/man/recaptcha.Rd | 11 45 files changed, 1058 insertions(+), 870 deletions(-)
Title: Create Interactive Graphs with 'Echarts JavaScript' Version 5
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
36 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre, cph],
Wei Su [ctb],
Helgasoft [ctb],
Xianying Tan [ctb] (<https://orcid.org/0000-0002-6072-3521>),
Robin Cura [ctb] (<https://orcid.org/0000-0001-5926-1828>),
Mathida Chuk [ctb]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between echarts4r versions 0.4.2 dated 2021-10-04 and 0.4.3 dated 2022-01-03
DESCRIPTION | 12 - MD5 | 37 ++- NAMESPACE | 2 NEWS.md | 10 + R/callbacks.R | 14 + R/facets.R | 141 +++++++++------ README.md | 4 inst/htmlwidgets/echarts4r.js | 19 +- inst/htmlwidgets/lib/echarts-4.8.0/echarts-en.min.js | 4 inst/htmlwidgets/lib/echarts-4.8.0/echarts-gl.min.js | 2 inst/htmlwidgets/lib/echarts-4.8.0/i18n/langCS-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langCS.js | 5 inst/htmlwidgets/lib/echarts-4.8.0/i18n/langDE-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langEN-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langES-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langFI-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langFR-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langJA-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langPL-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langPL.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langPT-br-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langRU-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langRU.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langSI-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langTH-obj.js |only inst/htmlwidgets/lib/echarts-4.8.0/i18n/langZH-obj.js |only man/e_facet.Rd |only man/e_get_zr.Rd |only 28 files changed, 174 insertions(+), 76 deletions(-)
Title: Discriminating Probes Selection
Description: Set of tools for molecular probes selection and design of a microarray, e.g. the assessment of physical and chemical properties, blast performance, selection according to sensitivity and selectivity. Methods used in package are described in: Lorenz R., Stephan H.B., Höner zu Siederdissen C. et al. (2011) <doi:10.1186/1748-7188-6-26>; Camacho C., Coulouris G., Avagyan V. et al. (2009) <doi:10.1186/1471-2105-10-421>.
Author: Elena Filatova [aut, cre] (<https://orcid.org/0000-0002-6683-7191>),
Oleg Utkin [ctb] (<https://orcid.org/0000-0002-7571-525X>),
Blokhina Scientific Research Institute of Epidemiology and Microbiology
of Nizhny Novgorod, Russia [fnd]
Maintainer: Elena Filatova <filatova@nniiem.ru>
Diff between disprose versions 0.1.0 dated 2021-11-19 and 0.1.2 dated 2022-01-03
DESCRIPTION | 12 ++--- MD5 | 16 +++---- NEWS.md | 9 ++++ R/blast.R | 20 +++++++++ R/common.R | 32 ++++++++++++++- R/downloads.R | 108 +++++++++++++++++++++++++++++++++++++--------------- R/probes.R | 26 ++++++++++++ man/cut_probes.Rd | 2 man/get_seq_info.Rd | 2 9 files changed, 179 insertions(+), 48 deletions(-)
Title: Lightweight Well-Known Geometry Parsing
Description: Provides a minimal R and C++ API for parsing
well-known binary and well-known text representation of
geometries to and from R-native formats.
Well-known binary is compact
and fast to parse; well-known text is human-readable
and is useful for writing tests. These formats are only
useful in R if the information they contain can be
accessed in R, for which high-performance functions
are provided here.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
Edzer Pebesma [aut] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between wk versions 0.5.0 dated 2021-07-13 and 0.6.0 dated 2022-01-03
wk-0.5.0/wk/R/compat-data-frame.R |only wk-0.5.0/wk/R/compat-sf.R |only wk-0.5.0/wk/R/compat-vctrs.R |only wk-0.5.0/wk/R/cpp11.R |only wk-0.5.0/wk/inst/include/wk-v1-filter.hpp |only wk-0.5.0/wk/inst/include/wk-v1-handler.hpp |only wk-0.5.0/wk/inst/include/wk-v1-reader.hpp |only wk-0.5.0/wk/src/cpp11.cpp |only wk-0.5.0/wk/tests/testthat/test-compat-data-frame.R |only wk-0.5.0/wk/tests/testthat/test-compat-sf.R |only wk-0.5.0/wk/tests/testthat/test-compat-vctrs.R |only wk-0.5.0/wk/tests/testthat/test-deprecated.R |only wk-0.6.0/wk/DESCRIPTION | 11 wk-0.6.0/wk/MD5 | 178 +++-- wk-0.6.0/wk/NAMESPACE | 38 + wk-0.6.0/wk/NEWS.md | 33 + wk-0.6.0/wk/R/affine.R | 4 wk-0.6.0/wk/R/bbox.R | 58 + wk-0.6.0/wk/R/chunk.R |only wk-0.6.0/wk/R/class-data-frame.R |only wk-0.6.0/wk/R/deprecated.R | 36 - wk-0.6.0/wk/R/format.R | 10 wk-0.6.0/wk/R/handle-slice.R |only wk-0.6.0/wk/R/handle-wkt.R | 12 wk-0.6.0/wk/R/handler.R | 16 wk-0.6.0/wk/R/make.R | 33 - wk-0.6.0/wk/R/pkg-readr.R |only wk-0.6.0/wk/R/pkg-sf.R |only wk-0.6.0/wk/R/pkg-vctrs.R |only wk-0.6.0/wk/R/plot.R | 20 wk-0.6.0/wk/R/rct.R | 13 wk-0.6.0/wk/R/translate.R | 2 wk-0.6.0/wk/R/utils.R | 14 wk-0.6.0/wk/R/wk-crs.R | 195 ++++++ wk-0.6.0/wk/R/wk-rcrd.R | 24 wk-0.6.0/wk/R/wk-vctr.R | 26 wk-0.6.0/wk/R/wkb.R | 61 + wk-0.6.0/wk/R/wkt-writer.R | 9 wk-0.6.0/wk/R/wkt.R | 50 + wk-0.6.0/wk/R/xyzm.R | 11 wk-0.6.0/wk/R/zzz.R | 5 wk-0.6.0/wk/README.md | 35 - wk-0.6.0/wk/inst/include/wk/experimental |only wk-0.6.0/wk/man/deprecated.Rd | 27 wk-0.6.0/wk/man/new_wk_wkb.Rd | 5 wk-0.6.0/wk/man/new_wk_wkt.Rd | 5 wk-0.6.0/wk/man/vctrs-methods.Rd | 2 wk-0.6.0/wk/man/wk-package.Rd | 10 wk-0.6.0/wk/man/wk_bbox.Rd | 18 wk-0.6.0/wk/man/wk_chunk_map_feature.Rd |only wk-0.6.0/wk/man/wk_chunk_strategy_single.Rd |only wk-0.6.0/wk/man/wk_crs.Rd | 3 wk-0.6.0/wk/man/wk_crs_inherit.Rd | 9 wk-0.6.0/wk/man/wk_crs_proj_definition.Rd |only wk-0.6.0/wk/man/wk_handle.Rd | 27 wk-0.6.0/wk/man/wk_handle.data.frame.Rd | 21 wk-0.6.0/wk/man/wk_handle_slice.Rd |only wk-0.6.0/wk/man/wk_is_geodesic.Rd |only wk-0.6.0/wk/man/wk_linestring.Rd | 7 wk-0.6.0/wk/man/wk_plot.Rd | 12 wk-0.6.0/wk/man/wk_translate.Rd | 2 wk-0.6.0/wk/man/wk_writer.Rd | 2 wk-0.6.0/wk/man/wkb.Rd | 15 wk-0.6.0/wk/man/wkt.Rd | 9 wk-0.6.0/wk/src/altrep.h |only wk-0.6.0/wk/src/bbox-handler.c | 218 +++++++ wk-0.6.0/wk/src/handle-crc.c | 29 wk-0.6.0/wk/src/handle-rct.c | 38 + wk-0.6.0/wk/src/handle-wkb.c | 76 +- wk-0.6.0/wk/src/handle-wkt.cpp | 615 +++++--------------- wk-0.6.0/wk/src/handle-xy.c | 36 + wk-0.6.0/wk/src/init.c |only wk-0.6.0/wk/src/internal |only wk-0.6.0/wk/src/make-collection-filter.c | 21 wk-0.6.0/wk/src/make-linestring-filter.c | 19 wk-0.6.0/wk/src/make-polygon-filter.c | 33 - wk-0.6.0/wk/src/port.h | 4 wk-0.6.0/wk/src/vctr.c |only wk-0.6.0/wk/src/wkt-writer.cpp | 118 +++ wk-0.6.0/wk/tests/testthat/Rplots.pdf |binary wk-0.6.0/wk/tests/testthat/test-affine.R | 6 wk-0.6.0/wk/tests/testthat/test-bbox.R | 84 ++ wk-0.6.0/wk/tests/testthat/test-chunk.R |only wk-0.6.0/wk/tests/testthat/test-class-data-frame.R |only wk-0.6.0/wk/tests/testthat/test-debug.R | 2 wk-0.6.0/wk/tests/testthat/test-format.R | 7 wk-0.6.0/wk/tests/testthat/test-handle-slice.R |only wk-0.6.0/wk/tests/testthat/test-handle-wkt.R | 21 wk-0.6.0/wk/tests/testthat/test-handler.R | 12 wk-0.6.0/wk/tests/testthat/test-make.R | 64 ++ wk-0.6.0/wk/tests/testthat/test-pkg-readr.R |only wk-0.6.0/wk/tests/testthat/test-pkg-sf.R |only wk-0.6.0/wk/tests/testthat/test-pkg-vctrs.R |only wk-0.6.0/wk/tests/testthat/test-plot.R | 4 wk-0.6.0/wk/tests/testthat/test-problems.R | 31 - wk-0.6.0/wk/tests/testthat/test-translate.R | 2 wk-0.6.0/wk/tests/testthat/test-utils.R | 6 wk-0.6.0/wk/tests/testthat/test-void.R | 19 wk-0.6.0/wk/tests/testthat/test-wk-crs.R | 99 +++ wk-0.6.0/wk/tests/testthat/test-wk-rcrd.R | 28 wk-0.6.0/wk/tests/testthat/test-wk-vctr.R | 40 - wk-0.6.0/wk/tests/testthat/test-wkb-writer.R | 44 + wk-0.6.0/wk/tests/testthat/test-wkb.R | 35 + wk-0.6.0/wk/tests/testthat/test-wkt.R | 37 + wk-0.6.0/wk/tests/testthat/test-xyzm.R | 25 105 files changed, 1973 insertions(+), 868 deletions(-)
Title: Access Databases from the Federal Statistical Office of Germany
Description: Retrieve and import data from different databases of the Federal Statistical Office of Germany (DESTATIS) using their SOAP XML web service <https://www-genesis.destatis.de/>.
Author: Moritz Marbach <moritz.marbach@tamu.edu> [aut, cre]
Maintainer: Moritz Marbach <moritz.marbach@tamu.edu>
Diff between wiesbaden versions 1.2.4 dated 2021-04-20 and 1.2.5 dated 2022-01-03
DESCRIPTION | 10 +- MD5 | 20 ++-- NAMESPACE | 2 NEWS.md | 4 R/helper.R | 17 ++-- R/read_gv100.R | 82 ++++++++++++++----- R/wiesbaden-package.R | 9 +- build/vignette.rds |binary inst/doc/wiesbaden.html | 196 ++++++++++++++++++++++++++++++++++++++++++++++- man/read_gv100.Rd | 11 +- man/wiesbaden-package.Rd | 5 - 11 files changed, 304 insertions(+), 52 deletions(-)
Title: Psychometric Meta-Analysis Toolkit
Description: Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.
Author: Jeffrey A. Dahlke [aut, cre],
Brenton M. Wiernik [aut],
Wesley Gardiner [ctb] (Unit tests),
Michael T. Brannick [ctb] (Testing),
Jack Kostal [ctb] (Code for reshape_mat2dat function),
Sean Potter [ctb] (Testing; Code for cumulative and leave1out plots),
John Sakaluk [ctb] (Code for funnel and forest plots),
Yuejia (Mandy) Teng [ctb] (Testing)
Maintainer: Jeffrey A. Dahlke <jdahlke@humrro.org>
Diff between psychmeta versions 2.6.0 dated 2021-06-01 and 2.6.1 dated 2022-01-03
psychmeta-2.6.0/psychmeta/NEWS |only psychmeta-2.6.1/psychmeta/DESCRIPTION | 10 psychmeta-2.6.1/psychmeta/MD5 | 57 ++--- psychmeta-2.6.1/psychmeta/NAMESPACE | 4 psychmeta-2.6.1/psychmeta/NEWS.md |only psychmeta-2.6.1/psychmeta/R/correct_r.R | 10 psychmeta-2.6.1/psychmeta/R/estimate_var_rho_tsa.R | 169 ++++++++-------- psychmeta-2.6.1/psychmeta/R/heterogeneity.R | 96 ++++----- psychmeta-2.6.1/psychmeta/R/output.R | 23 -- psychmeta-2.6.1/psychmeta/R/plotting.R | 80 +++++-- psychmeta-2.6.1/psychmeta/R/var_error_tsa.R | 26 +- psychmeta-2.6.1/psychmeta/R/wt_stat.R | 101 +++------ psychmeta-2.6.1/psychmeta/R/zzz.R | 12 - psychmeta-2.6.1/psychmeta/README.md | 4 psychmeta-2.6.1/psychmeta/build/partial.rdb |binary psychmeta-2.6.1/psychmeta/build/psychmeta.pdf |binary psychmeta-2.6.1/psychmeta/inst/doc/ma_r.Rmd | 2 psychmeta-2.6.1/psychmeta/inst/doc/ma_r.html | 77 +++++-- psychmeta-2.6.1/psychmeta/inst/doc/overview.html | 75 ++----- psychmeta-2.6.1/psychmeta/man/correct_r.Rd | 8 psychmeta-2.6.1/psychmeta/man/dot-heterogeneity.Rd | 4 psychmeta-2.6.1/psychmeta/man/estimate_var_rho_tsa.Rd | 183 ++++++++++-------- psychmeta-2.6.1/psychmeta/man/heterogeneity.Rd | 46 ++-- psychmeta-2.6.1/psychmeta/man/limits_tau.Rd | 2 psychmeta-2.6.1/psychmeta/man/limits_tau2.Rd | 2 psychmeta-2.6.1/psychmeta/man/plot_forest.Rd | 12 - psychmeta-2.6.1/psychmeta/man/psychmeta_news.Rd | 4 psychmeta-2.6.1/psychmeta/man/var_error_r_bvirr.Rd | 22 +- psychmeta-2.6.1/psychmeta/man/wt_cov.Rd | 5 psychmeta-2.6.1/psychmeta/vignettes/apa.csl |only psychmeta-2.6.1/psychmeta/vignettes/ma_r.Rmd | 2 31 files changed, 546 insertions(+), 490 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and data, for continuous, discrete, and multivariate characters. A broad range of plotting methods for phylogenies and comparative data include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for computing consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.7-90 dated 2021-09-25 and 1.0-1 dated 2022-01-03
DESCRIPTION | 10 ++--- MD5 | 59 ++++++++++++++++--------------- NAMESPACE | 3 + R/bd.R | 6 +-- R/brownieREML.R | 4 +- R/cophylo.R | 89 ++++++++++++++++++++++++++++++++++++++++++++---- R/cotangleplot.R |only R/fastAnc.R | 6 +-- R/locate.yeti.R | 6 +-- R/ls.consensus.R | 5 ++ R/make.simmap.R | 39 ++++++++++++++------- R/multirateBM.R | 14 ++++--- R/pgls.Ives.R | 28 ++++++++------- R/phenogram.R | 16 +++++--- R/phyl.pairedttest.R | 11 +++-- R/phylANOVA.R | 4 +- R/phylosig.R | 7 ++- R/plotTree.datamatrix.R | 17 +++++++-- R/plotTree.wBars.R | 21 ++++++++--- R/ratebystate.R | 4 +- R/rateshift.R | 20 +++++++--- R/threshBayes.R | 4 +- R/utilities.R | 50 ++++++++++++++------------ data/mammal.data.rda |binary man/cophylo.Rd | 8 ++++ man/fitMk.Rd | 2 + man/getStates.Rd | 2 - man/make.simmap.Rd | 4 +- man/pgls.Ives.Rd | 2 - man/phyl.RMA.Rd | 14 +++++++ man/plotTree.wBars.Rd | 5 +- 31 files changed, 312 insertions(+), 148 deletions(-)
Title: Probability Computations on Pedigrees
Description: An implementation of the Elston-Stewart algorithm for
calculating pedigree likelihoods given genetic marker data (Elston and
Stewart (1971) <doi:10.1159/000152448>). The standard algorithm is
extended to allow inbred founders. 'pedprobr' is part of the 'ped
suite', a collection of packages for pedigree analysis in R. In
particular, 'pedprobr' depends on 'pedtools' for pedigree
manipulations and 'pedmut' for mutation modelling. For more
information, see 'Pedigree Analysis in R' (Vigeland, 2021,
ISBN:9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedprobr versions 0.5.0 dated 2021-03-27 and 0.6.0 dated 2022-01-03
DESCRIPTION | 41 +++++++++++++---------- MD5 | 35 ++++++++++--------- NEWS.md | 27 +++++++++++++++ R/likelihood.R | 58 +++++++++++++++++++++++++-------- R/likelihood2.R | 4 +- R/merlin.R | 21 ++++++----- R/oneMarkerDistribution.R | 41 +++++++++++++++-------- R/reduceAlleles.R | 6 +-- R/setMutationModel.R | 4 +- R/thetaCorrection.R | 20 ++++++----- R/twoMarkerDistribution.R | 23 +++++++++---- build/partial.rdb |binary man/likelihood.Rd | 42 ++++++++++++++++++----- man/lumpAlleles.Rd | 3 - man/merlin.Rd | 11 ++---- man/oneMarkerDistribution.Rd | 23 ++++++------- man/setMutationModel.Rd | 4 +- man/twoMarkerDistribution.Rd | 10 ++--- tests/testthat/test-theta-correction.R |only 19 files changed, 244 insertions(+), 129 deletions(-)
Title: Native R Kernel for the 'Jupyter Notebook'
Description: The R kernel for the 'Jupyter' environment executes R code which the front-end
('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph],
Karthik Ram [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRkernel versions 1.2 dated 2021-05-11 and 1.3 dated 2022-01-03
IRkernel-1.2/IRkernel/tests/testthat/jkt/COPYING.md |only IRkernel-1.2/IRkernel/tests/testthat/jkt/jupyter_kernel_test/messagespec.py |only IRkernel-1.2/IRkernel/tests/testthat/jkt/jupyter_kernel_test/messagespec_common.py |only IRkernel-1.3/IRkernel/DESCRIPTION | 8 IRkernel-1.3/IRkernel/MD5 | 24 +- IRkernel-1.3/IRkernel/R/execution.r | 27 +- IRkernel-1.3/IRkernel/R/installspec.r | 12 - IRkernel-1.3/IRkernel/README.md | 6 IRkernel-1.3/IRkernel/man/installspec.Rd | 7 IRkernel-1.3/IRkernel/tests/testthat/__pycache__/test_ir.cpython-310.pyc |only IRkernel-1.3/IRkernel/tests/testthat/__pycache__/test_ir.cpython-39.pyc |binary IRkernel-1.3/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__init__.py | 102 ++++++---- IRkernel-1.3/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/__init__.cpython-310.pyc |only IRkernel-1.3/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/msgspec_v5.cpython-310.pyc |only IRkernel-1.3/IRkernel/tests/testthat/jkt/jupyter_kernel_test/msgspec_v5.py |only IRkernel-1.3/IRkernel/tests/testthat/jkt/pyproject.toml |only IRkernel-1.3/IRkernel/tests/testthat/test_ir.py | 4 17 files changed, 120 insertions(+), 70 deletions(-)
Title: Utilities for the Forest Research Institute of the State
Baden-Wuerttemberg
Description: Miscellaneous utilities, tools and helper
functions for finding and searching files on disk, searching for and
removing R objects from the workspace.
These are utilities for packages
<https://CRAN.R-project.org/package=cleanr>,
<https://CRAN.R-project.org/package=document>,
<https://CRAN.R-project.org/package=fakemake>,
<https://CRAN.R-project.org/package=packager> and
<https://CRAN.R-project.org/package=rasciidoc>.
Does not import or depend on any third party package, but on core R
only (i.e. it may depend on packages with priority 'base').
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fritools versions 3.0.0 dated 2021-12-14 and 3.1.0 dated 2022-01-03
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/wipe_clean.R | 15 +++++++++++++-- R/zzz.R | 1 + inst/NEWS.rd | 9 +++++++++ inst/runit_tests/runit-batch.R | 14 +++++++++----- inst/runit_tests/runit-csv.R | 4 +++- inst/runit_tests/runit-paths.R | 4 ++++ inst/source/R/wipe_clean.R | 15 +++++++++++++-- inst/source/R/zzz.R | 1 + inst/source/man/wipe_clean.Rd | 10 ++++++++-- man/wipe_clean.Rd | 10 ++++++++-- 13 files changed, 93 insertions(+), 29 deletions(-)
Title: Linear Discriminant Function and Canonical Correlation Analysis
Description: Produces SPSS- and SAS-like output for linear discriminant
function analysis and canonical correlation analysis. The methods are described in
Manly & Alberto (2017, ISBN:9781498728966),
Rencher (2002, ISBN:0-471-41889-7), and
Tabachnik & Fidell (2019, ISBN:9780134790541).
Author: Brian P. O'Connor
Maintainer: Brian P. O'Connor <brian.oconnor@ubc.ca>
Diff between DFA.CANCOR versions 0.2.2 dated 2021-10-30 and 0.2.3 dated 2022-01-03
DFA.CANCOR-0.2.2/DFA.CANCOR/R/homogeneity.R |only DFA.CANCOR-0.2.2/DFA.CANCOR/R/linearity.R |only DFA.CANCOR-0.2.2/DFA.CANCOR/R/normality.R |only DFA.CANCOR-0.2.2/DFA.CANCOR/R/plot_linearity.R |only DFA.CANCOR-0.2.2/DFA.CANCOR/man/homogeneity.Rd |only DFA.CANCOR-0.2.2/DFA.CANCOR/man/linearity.Rd |only DFA.CANCOR-0.2.2/DFA.CANCOR/man/normality.Rd |only DFA.CANCOR-0.2.2/DFA.CANCOR/man/plot_linearity.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/DESCRIPTION | 14 DFA.CANCOR-0.2.3/DFA.CANCOR/MD5 | 36 DFA.CANCOR-0.2.3/DFA.CANCOR/NAMESPACE | 16 DFA.CANCOR-0.2.3/DFA.CANCOR/R/CANCOR.R | 98 +- DFA.CANCOR-0.2.3/DFA.CANCOR/R/DFA.R | 653 +++++++++--------- DFA.CANCOR-0.2.3/DFA.CANCOR/R/GROUP.DIFFS.R |only DFA.CANCOR-0.2.3/DFA.CANCOR/R/HOMOGENEITY.R |only DFA.CANCOR-0.2.3/DFA.CANCOR/R/LINEARITY.R |only DFA.CANCOR-0.2.3/DFA.CANCOR/R/NORMALITY.R |only DFA.CANCOR-0.2.3/DFA.CANCOR/R/PLOT_LINEARITY.R |only DFA.CANCOR-0.2.3/DFA.CANCOR/R/boc.R | 459 +++++++++--- DFA.CANCOR-0.2.3/DFA.CANCOR/man/CANCOR.Rd | 3 DFA.CANCOR-0.2.3/DFA.CANCOR/man/DFA.CANCOR-package.Rd | 6 DFA.CANCOR-0.2.3/DFA.CANCOR/man/DFA.Rd | 166 +++- DFA.CANCOR-0.2.3/DFA.CANCOR/man/GROUP.DIFFS.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/HOMOGENEITY.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/LINEARITY.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/NORMALITY.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/PLOT_LINEARITY.Rd |only DFA.CANCOR-0.2.3/DFA.CANCOR/man/data_CCA_Tabachnik.Rd | 6 28 files changed, 928 insertions(+), 529 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are four core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. Similar function is daily_response_seascorr(),
which implements partial correlations in the analysis of daily response functions.
For the enthusiast of monthly data, there is monthly_response() function.
The last core function is compare_methods(), which effectively compares several
linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.2.4 dated 2021-12-05 and 1.2.6 dated 2022-01-03
DESCRIPTION | 6 +- MD5 | 26 ++++----- NEWS.md | 3 + R/daily_response.R | 55 ++++++++++++++++++- R/daily_response_seascorr.R | 51 +++++++++++++++--- R/monthly_response.R | 58 +++++++++++++++++---- R/monthly_response_seascorr.R | 52 ++++++++++++++++-- inst/doc/Compare_different_regression_methods.html | 4 - inst/doc/Examples_with_daily_climate_data.html | 4 - man/daily_response.Rd | 15 ++--- man/daily_response_seascorr.Rd | 6 +- man/monthly_response.Rd | 19 +++--- man/monthly_response_seascorr.Rd | 2 tests/testthat/test_general.R | 2 14 files changed, 238 insertions(+), 65 deletions(-)
Title: Collective Matrix Factorization for Recommender Systems
Description: Collective matrix factorization (a.k.a. multi-view or multi-way factorization,
Singh, Gordon, (2008) <doi:10.1145/1401890.1401969>) tries to approximate a matrix 'X' as the
product of two low-dimensional matrices aided with secondary information matrices about rows
and/or columns of 'X' which are also factorized using the same latent components.
The intended usage is for recommender systems, dimensionality reduction, and missing value imputation.
Implements extensions of the original model (Cortes, (2018) <arXiv:1809.00366>) and can produce
different factorizations such as the weighted 'implicit-feedback' model (Hu, Koren, Volinsky,
(2008) <doi:10.1109/ICDM.2008.22>), the 'weighted-lambda-regularization' model,
(Zhou, Wilkinson, Schreiber, Pan, (2008) <doi:10.1007/978-3-540-68880-8_32>),
or the enhanced model with 'implicit features' (Rendle, Zhang,
Koren, (2019) <arXiv:1905.01395>), with or without side information. Can use gradient-based
procedures or alternating-least squares procedures (Koren, Bell, Volinsky, (2009)
<doi:10.1109/MC.2009.263>), with either a Cholesky solver, a faster conjugate gradient solver
(Takacs, Pilaszy, Tikk, (2011) <doi:10.1145/2043932.2043987>), or a non-negative
coordinate descent solver (Franc, Hlavac, Navara, (2005) <doi:10.1007/11556121_50>),
providing efficient methods for sparse and dense data, and mixtures thereof.
Supports L1 and L2 regularization in the main models,
offers alternative most-popular and content-based models, and implements functionality
for cold-start recommendations and imputation of 2D data.
Author: David Cortes [aut, cre, cph],
Jorge Nocedal [cph] (Copyright holder of included LBFGS library),
Naoaki Okazaki [cph] (Copyright holder of included LBFGS library),
David Blackman [cph] (Copyright holder of original Xoshiro code),
Sebastiano Vigna [cph] (Copyright holder of original Xoshiro code)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between cmfrec versions 3.2.2-2 dated 2021-11-07 and 3.3.0 dated 2022-01-03
DESCRIPTION | 6 MD5 | 26 R/fit.R | 69 +- build/vignette.rds |binary man/CMF.from.model.matrices.Rd | 2 man/fit.Rd | 15 man/topN.Rd | 4 src/Makevars | 2 src/Rwrapper.c | 37 - src/cmfrec.h | 433 +++++++++++++--- src/collective.c | 904 +++++++++++++++++++++++---------- src/common.c | 1093 +++++++++++++++++++++++++++++++++-------- src/helpers.c | 36 + src/offsets.c | 36 - 14 files changed, 2046 insertions(+), 617 deletions(-)
Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-level data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre],
Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>
Diff between bnma versions 1.4.0 dated 2021-01-13 and 1.5.0 dated 2022-01-03
DESCRIPTION | 10 MD5 | 18 NEWS.md | 4 R/network.data.R | 6 R/network.rjags.R | 30 R/preprocess.data.R | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/my-vignette.html | 1539 ++++++++++++++++++++-------------------------- man/network.data.Rd | 270 ++++---- 10 files changed, 879 insertions(+), 1004 deletions(-)
Title: R Client for 'Adobe Analytics' API 2.0
Description: Connect to the 'Adobe Analytics' API v2.0 <https://github.com/AdobeDocs/analytics-2.0-apis>
which powers 'Analysis Workspace'. The package was developed
with the analyst in mind, and it will continue to be
developed with the guiding principles of iterative,
repeatable, timely analysis.
Author: Ben Woodard [aut, cre],
Tim Wilson [aut, ctb],
Charles Gallagher [ctb],
Mark Edmondson [ctb]
Maintainer: Ben Woodard <benrwoodard@gmail.com>
Diff between adobeanalyticsr versions 0.2.0 dated 2022-01-03 and 0.2.1 dated 2022-01-03
DESCRIPTION | 6 - MD5 | 32 ++++--- NAMESPACE | 3 NEWS.md | 3 R/freeform_report.R | 13 +-- R/freeform_segments.R |only R/get_req_data.R | 4 R/get_segments.R | 4 R/globals.R | 3 R/request_format.R | 172 +++++++++++++++++++++++++++-------------- R/token.R | 4 man/adobeanalyticsr-package.Rd | 1 man/aw_auth.Rd | 29 ++++-- man/aw_auth_with.Rd | 30 ++++--- man/aw_freeform_table.Rd | 18 ++-- man/aw_segment_table.Rd |only man/aw_token.Rd | 12 ++ man/retrieve_aw_token.Rd | 6 - 18 files changed, 213 insertions(+), 127 deletions(-)
More information about adobeanalyticsr at CRAN
Permanent link
Title: SOM Bound to Realize Euclidean and Relational Outputs
Description: The stochastic (also called on-line) version of the Self-Organising
Map (SOM) algorithm is provided. Different versions of the
algorithm are implemented, for numeric and relational data and for
contingency tables as described, respectively, in Kohonen (2001)
<isbn:3-540-67921-9>, Olteanu & Villa-Vialaneix (2005)
<doi:10.1016/j.neucom.2013.11.047> and Cottrell et al (2004)
<doi:10.1016/j.neunet.2004.07.010>. The package also contains many
plotting features (to help the user interpret the results), can
handle (and impute) missing values and is delivered with a
graphical user interface based on 'shiny'.
Author: Nathalie Vialaneix [aut, cre],
Elise Maigne [aut],
Jerome Mariette [aut],
Madalina Olteanu [aut],
Fabrice Rossi [aut],
Laura Bendhaiba [ctb],
Julien Boelaert [ctb]
Maintainer: Nathalie Vialaneix <nathalie.vialaneix@inrae.fr>
Diff between SOMbrero versions 1.3-1 dated 2020-08-11 and 1.4 dated 2022-01-03
SOMbrero-1.3-1/SOMbrero/vignettes/c-doc-numericSOM_cache |only SOMbrero-1.3-1/SOMbrero/vignettes/d-doc-korrespSOM_cache |only SOMbrero-1.3-1/SOMbrero/vignettes/e-doc-relationalSOM_cache |only SOMbrero-1.4/SOMbrero/DESCRIPTION | 17 SOMbrero-1.4/SOMbrero/MD5 | 105 SOMbrero-1.4/SOMbrero/NAMESPACE | 5 SOMbrero-1.4/SOMbrero/NEWS | 27 SOMbrero-1.4/SOMbrero/R/SOMbrero-package.R | 33 SOMbrero-1.4/SOMbrero/R/data.R | 8 SOMbrero-1.4/SOMbrero/R/data_preprocessing.R |only SOMbrero-1.4/SOMbrero/R/distance_helpers.R |only SOMbrero-1.4/SOMbrero/R/ggplots_subfunctions.R | 136 - SOMbrero-1.4/SOMbrero/R/graph_som.R |only SOMbrero-1.4/SOMbrero/R/grids.R | 6 SOMbrero-1.4/SOMbrero/R/missing_helpers.R |only SOMbrero-1.4/SOMbrero/R/parameters.R | 26 SOMbrero-1.4/SOMbrero/R/plots.R | 45 SOMbrero-1.4/SOMbrero/R/prediction.R |only SOMbrero-1.4/SOMbrero/R/prototype_initialization.R |only SOMbrero-1.4/SOMbrero/R/quality.R | 21 SOMbrero-1.4/SOMbrero/R/som.R | 1069 ++-------- SOMbrero-1.4/SOMbrero/R/sombreroGUI.R | 2 SOMbrero-1.4/SOMbrero/R/superclasses.R | 2 SOMbrero-1.4/SOMbrero/build/vignette.rds |binary SOMbrero-1.4/SOMbrero/inst/doc/a-doc-SOMbrero-package.html | 35 SOMbrero-1.4/SOMbrero/inst/doc/b-doc-grids.html | 38 SOMbrero-1.4/SOMbrero/inst/doc/c-doc-numericSOM.Rmd | 8 SOMbrero-1.4/SOMbrero/inst/doc/c-doc-numericSOM.html | 48 SOMbrero-1.4/SOMbrero/inst/doc/d-doc-korrespSOM.Rmd | 14 SOMbrero-1.4/SOMbrero/inst/doc/d-doc-korrespSOM.html | 54 SOMbrero-1.4/SOMbrero/inst/doc/e-doc-relationalSOM.Rmd | 20 SOMbrero-1.4/SOMbrero/inst/doc/e-doc-relationalSOM.html | 64 SOMbrero-1.4/SOMbrero/man/SOMbrero-package.Rd | 31 SOMbrero-1.4/SOMbrero/man/impute.Rd |only SOMbrero-1.4/SOMbrero/man/initGrid.Rd | 4 SOMbrero-1.4/SOMbrero/man/initSOM.Rd | 25 SOMbrero-1.4/SOMbrero/man/myGrid.Rd | 2 SOMbrero-1.4/SOMbrero/man/plot.somRes.Rd | 12 SOMbrero-1.4/SOMbrero/man/predict.somRes.Rd | 19 SOMbrero-1.4/SOMbrero/man/presidentielles2002.Rd | 8 SOMbrero-1.4/SOMbrero/man/projectIGraph.Rd | 4 SOMbrero-1.4/SOMbrero/man/protoDist.Rd | 2 SOMbrero-1.4/SOMbrero/man/quality.Rd | 8 SOMbrero-1.4/SOMbrero/man/sombreroGUI.Rd | 2 SOMbrero-1.4/SOMbrero/man/superClass.Rd | 2 SOMbrero-1.4/SOMbrero/man/trainSOM.Rd | 66 SOMbrero-1.4/SOMbrero/tests/testthat/test-euclidian-relational.R | 9 SOMbrero-1.4/SOMbrero/tests/testthat/test-missing.R |only SOMbrero-1.4/SOMbrero/tests/testthat/test-prediction.R | 125 - SOMbrero-1.4/SOMbrero/vignettes/c-doc-numericSOM.Rmd | 8 SOMbrero-1.4/SOMbrero/vignettes/d-doc-korrespSOM.Rmd | 14 SOMbrero-1.4/SOMbrero/vignettes/dependencies.png |binary SOMbrero-1.4/SOMbrero/vignettes/e-doc-relationalSOM.Rmd | 20 53 files changed, 940 insertions(+), 1204 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] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.6.2 dated 2021-09-03 and 0.6.3 dated 2022-01-03
finbif-0.6.2/finbif/inst/vign |only finbif-0.6.2/finbif/tests/api-dev-cassettes |only finbif-0.6.2/finbif/tests/cassettes |only finbif-0.6.3/finbif/DESCRIPTION | 8 finbif-0.6.3/finbif/LICENSE | 2 finbif-0.6.3/finbif/MD5 | 313 - finbif-0.6.3/finbif/NAMESPACE | 3 finbif-0.6.3/finbif/NEWS.md | 161 finbif-0.6.3/finbif/R/api_get.R | 6 finbif-0.6.3/finbif/R/dates.R | 19 finbif-0.6.3/finbif/R/filters.R | 4 finbif-0.6.3/finbif/R/finbif_collections.R | 17 finbif-0.6.3/finbif/R/finbif_occurrence.R | 277 + finbif-0.6.3/finbif/R/finbif_occurrence_load.R | 95 finbif-0.6.3/finbif/R/finbif_records.R | 57 finbif-0.6.3/finbif/R/map-utils.R | 1 finbif-0.6.3/finbif/R/sysdata.rda |binary finbif-0.6.3/finbif/R/utils.R | 13 finbif-0.6.3/finbif/R/zzz.R | 1 finbif-0.6.3/finbif/README.md | 14 finbif-0.6.3/finbif/build/vignette.rds |binary finbif-0.6.3/finbif/data/finland_map.rda |binary finbif-0.6.3/finbif/inst/NEWS.Rd | 21 finbif-0.6.3/finbif/inst/doc/finbif.Rmd | 96 finbif-0.6.3/finbif/inst/doc/finbif.html | 154 finbif-0.6.3/finbif/inst/doc/v02_occurrence_data.Rmd | 238 - finbif-0.6.3/finbif/inst/doc/v02_occurrence_data.html | 238 - finbif-0.6.3/finbif/inst/doc/v03_selecting_variables.Rmd | 136 finbif-0.6.3/finbif/inst/doc/v03_selecting_variables.html | 136 finbif-0.6.3/finbif/inst/doc/v04_metadata.Rmd | 372 - finbif-0.6.3/finbif/inst/doc/v04_metadata.html | 390 - finbif-0.6.3/finbif/inst/doc/v05_filtering.Rmd | 242 - finbif-0.6.3/finbif/inst/doc/v05_filtering.html | 244 - finbif-0.6.3/finbif/inst/doc/v06_plotting.html | 4 finbif-0.6.3/finbif/man/figures/location-filter-1.png |binary finbif-0.6.3/finbif/man/figures/plot-finland-1.png |binary finbif-0.6.3/finbif/man/figures/plot-occurrences-eval-1.png |binary finbif-0.6.3/finbif/man/figures/plot-recent-obs-1.png |binary finbif-0.6.3/finbif/man/filters.Rd | 4 finbif-0.6.3/finbif/man/finbif-package.Rd | 12 finbif-0.6.3/finbif/man/finbif_occurrence_load.Rd | 9 finbif-0.6.3/finbif/man/hist_xy.Rd | 1 finbif-0.6.3/finbif/tests/testthat/HBF.6968.zip |only finbif-0.6.3/finbif/tests/testthat/_snaps/finbif_occurrence/fungi.svg | 2194 +++++----- finbif-0.6.3/finbif/tests/testthat/_snaps/local-finbif_occurrence_load.md | 84 finbif-0.6.3/finbif/tests/testthat/_snaps/zzz-finbif/fungi.svg | 2184 ++++----- finbif-0.6.3/finbif/tests/testthat/helper-finbif.R | 5 finbif-0.6.3/finbif/tests/testthat/test-finbif_occurrence.R | 52 finbif-0.6.3/finbif/tests/testthat/test-local-finbif_occurrence_load.R | 51 finbif-0.6.3/finbif/tests/testthat/test-zzz-finbif.R | 1 finbif-0.6.3/finbif/vignettes/finbif.Rmd | 96 finbif-0.6.3/finbif/vignettes/v02_occurrence_data.Rmd | 238 - finbif-0.6.3/finbif/vignettes/v03_selecting_variables.Rmd | 136 finbif-0.6.3/finbif/vignettes/v04_metadata.Rmd | 372 - finbif-0.6.3/finbif/vignettes/v05_filtering.Rmd | 242 - 55 files changed, 4643 insertions(+), 4300 deletions(-)
Title: Functions for Analyzing Psychophysical Data in R
Description: An assortment of functions that could be useful in analyzing data from psychophysical experiments. It includes functions for calculating d' from several different experimental designs, links for m-alternative forced-choice (mafc) data to be used with the binomial family in glm (and possibly other contexts) and self-Start functions for estimating gamma values for CRT screen calibrations.
Author: Kenneth Knoblauch
Maintainer: Ken Knoblauch <ken.knoblauch@inserm.fr>
Diff between psyphy versions 0.2-2 dated 2020-11-10 and 0.2-3 dated 2022-01-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/NEWS | 4 ++++ 3 files changed, 10 insertions(+), 6 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut] (<https://orcid.org/0000-0001-7210-1132>),
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
Norbert Mercier [aut] (<https://orcid.org/0000-0002-6375-9108>),
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>),
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [aut] (<https://orcid.org/0000-0002-5331-5087>),
Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>),
Svenja Riedesel [aut] (<https://orcid.org/0000-0003-2936-8776>),
Martin Autzen [aut] (<https://orcid.org/0000-0001-6249-426X>),
Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>),
Dirk Mittelstrass [aut] (<https://orcid.org/0000-0002-9567-8791>),
Harrison J. Gray [aut] (<https://orcid.org/0000-0002-4555-7473>),
Jean-Michel Galharret [aut] (<https://orcid.org/0000-0003-2219-8727>),
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@aber.ac.uk>
Diff between Luminescence versions 0.9.16 dated 2021-11-26 and 0.9.17 dated 2022-01-03
Luminescence-0.9.16/Luminescence/src/src_EED_Calc_Overall_StatUncertainty.cpp |only Luminescence-0.9.17/Luminescence/DESCRIPTION | 24 Luminescence-0.9.17/Luminescence/MD5 | 281 ++++------ Luminescence-0.9.17/Luminescence/NEWS.md | 87 +-- Luminescence-0.9.17/Luminescence/R/RcppExports.R | 4 Luminescence-0.9.17/Luminescence/R/calc_MinDose.R | 3 Luminescence-0.9.17/Luminescence/R/fit_EmissionSpectra.R | 43 - Luminescence-0.9.17/Luminescence/R/fit_SurfaceExposure.R | 2 Luminescence-0.9.17/Luminescence/R/plot_AbanicoPlot.R | 169 ++---- Luminescence-0.9.17/Luminescence/R/plot_RLum.Analysis.R | 8 Luminescence-0.9.17/Luminescence/R/plot_RLum.Data.Spectrum.R | 37 - Luminescence-0.9.17/Luminescence/R/plot_RLum.Results.R | 4 Luminescence-0.9.17/Luminescence/R/plot_RadialPlot.R | 186 +++--- Luminescence-0.9.17/Luminescence/build/partial.rdb |binary Luminescence-0.9.17/Luminescence/man/Analyse_SAR.OSLdata.Rd | 2 Luminescence-0.9.17/Luminescence/man/CW2pHMi.Rd | 2 Luminescence-0.9.17/Luminescence/man/CW2pLM.Rd | 2 Luminescence-0.9.17/Luminescence/man/CW2pLMi.Rd | 2 Luminescence-0.9.17/Luminescence/man/CW2pPMi.Rd | 2 Luminescence-0.9.17/Luminescence/man/GitHub-API.Rd | 2 Luminescence-0.9.17/Luminescence/man/PSL2Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum.Analysis-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum.Data.Curve-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum.Data.Image-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum.Data.Spectrum-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/RLum.Results-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/Risoe.BINfileData-class.Rd | 2 Luminescence-0.9.17/Luminescence/man/Risoe.BINfileData2RLum.Analysis.Rd | 2 Luminescence-0.9.17/Luminescence/man/Second2Gray.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_Al2O3C_CrossTalk.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_Al2O3C_ITC.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_Al2O3C_Measurement.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_FadingMeasurement.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_IRSAR.RF.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_SAR.CWOSL.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_SAR.TL.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_baSAR.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_pIRIRSequence.Rd | 2 Luminescence-0.9.17/Luminescence/man/analyse_portableOSL.Rd | 2 Luminescence-0.9.17/Luminescence/man/app_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/apply_CosmicRayRemoval.Rd | 2 Luminescence-0.9.17/Luminescence/man/apply_EfficiencyCorrection.Rd | 2 Luminescence-0.9.17/Luminescence/man/bin_RLum.Data.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_AliquotSize.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_AverageDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_CentralDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_CobbleDoseRate.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_CommonDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_CosmicDoseRate.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_FadingCorr.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_FastRatio.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_FiniteMixture.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_FuchsLang2001.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_HomogeneityTest.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_Huntley2006.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_IEU.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_Kars2008.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_Lamothe2003.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_MaxDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_MinDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_OSLLxTxDecomposed.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_OSLLxTxRatio.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_SourceDoseRate.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_Statistics.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_TLLxTxRatio.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_ThermalLifetime.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_WodaFuchs2008.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_gSGC.Rd | 2 Luminescence-0.9.17/Luminescence/man/calc_gSGC_feldspar.Rd | 2 Luminescence-0.9.17/Luminescence/man/combine_De_Dr.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_Activity2Concentration.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_BIN2CSV.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_Concentration2DoseRate.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_Daybreak2CSV.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_PSL2CSV.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_RLum2Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_SG2MG.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_Wavelength2Energy.Rd | 2 Luminescence-0.9.17/Luminescence/man/convert_XSYG2CSV.Rd | 2 Luminescence-0.9.17/Luminescence/man/extract_IrradiationTimes.Rd | 2 Luminescence-0.9.17/Luminescence/man/fit_CWCurve.Rd | 2 Luminescence-0.9.17/Luminescence/man/fit_EmissionSpectra.Rd | 5 Luminescence-0.9.17/Luminescence/man/fit_LMCurve.Rd | 2 Luminescence-0.9.17/Luminescence/man/fit_OSLLifeTimes.Rd | 2 Luminescence-0.9.17/Luminescence/man/fit_SurfaceExposure.Rd | 4 Luminescence-0.9.17/Luminescence/man/fit_ThermalQuenching.Rd | 2 Luminescence-0.9.17/Luminescence/man/get_Layout.Rd | 2 Luminescence-0.9.17/Luminescence/man/get_Quote.Rd | 2 Luminescence-0.9.17/Luminescence/man/get_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/get_Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/get_rightAnswer.Rd | 2 Luminescence-0.9.17/Luminescence/man/length_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/merge_RLum.Analysis.Rd | 2 Luminescence-0.9.17/Luminescence/man/merge_RLum.Data.Curve.Rd | 2 Luminescence-0.9.17/Luminescence/man/merge_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/merge_RLum.Results.Rd | 2 Luminescence-0.9.17/Luminescence/man/merge_Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/names_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_AbanicoPlot.Rd | 4 Luminescence-0.9.17/Luminescence/man/plot_DRCSummary.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_DRTResults.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_DetPlot.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_FilterCombinations.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_GrowthCurve.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_Histogram.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_KDE.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_NRt.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_OSLAgeSummary.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_RLum.Analysis.Rd | 4 Luminescence-0.9.17/Luminescence/man/plot_RLum.Data.Curve.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_RLum.Data.Image.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_RLum.Data.Spectrum.Rd | 13 Luminescence-0.9.17/Luminescence/man/plot_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_RLum.Results.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_ROI.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_RadialPlot.Rd | 106 ++- Luminescence-0.9.17/Luminescence/man/plot_Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/plot_ViolinPlot.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_BIN2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_Daybreak2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_PSL2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_RF2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_SPE2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_TIFF2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/read_XSYG2R.Rd | 2 Luminescence-0.9.17/Luminescence/man/replicate_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/report_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/sTeve.Rd | 2 Luminescence-0.9.17/Luminescence/man/scale_GammaDose.Rd | 2 Luminescence-0.9.17/Luminescence/man/set_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/set_Risoe.BINfileData.Rd | 2 Luminescence-0.9.17/Luminescence/man/smooth_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/structure_RLum.Rd | 2 Luminescence-0.9.17/Luminescence/man/template_DRAC.Rd | 2 Luminescence-0.9.17/Luminescence/man/tune_Data.Rd | 2 Luminescence-0.9.17/Luminescence/man/use_DRAC.Rd | 2 Luminescence-0.9.17/Luminescence/man/verify_SingleGrainData.Rd | 2 Luminescence-0.9.17/Luminescence/man/write_R2BIN.Rd | 2 Luminescence-0.9.17/Luminescence/man/write_RLum2CSV.Rd | 2 Luminescence-0.9.17/Luminescence/src/RcppExports.cpp | 15 Luminescence-0.9.17/Luminescence/tests/testthat/test_plot_RLum.Data.Spectrum.R | 15 142 files changed, 626 insertions(+), 628 deletions(-)
Title: Repeated Measurement Models for Discrete Times
Description: Companion R package for the course "Statistical analysis of correlated and repeated measurements for health science researchers"
taught by the section of Biostatistics of the University of Copenhagen.
It implements linear mixed models where the model for the variance-covariance of the residuals is specified via patterns (compound symmetry, unstructured).
Statistical inference for mean, variance, and correlation parameters is performed based on the observed information and a Satterthwaite degrees of freedom.
Normalized residuals are provided to assess model misspecification.
Statistical inference can be performed for arbitrary linear combination(s) of model coefficients.
Predictions can be computed conditional to covariates only or also to outcome values.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julie Forman [aut] (<https://orcid.org/0000-0001-7368-0869>)
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between LMMstar versions 0.4.3 dated 2021-12-19 and 0.4.4 dated 2022-01-03
LMMstar-0.4.3/LMMstar/inst/doc-software/overview.blg |only LMMstar-0.4.3/LMMstar/inst/doc-software/overview.fdb_latexmk |only LMMstar-0.4.3/LMMstar/inst/doc-software/overview.fls |only LMMstar-0.4.3/LMMstar/inst/doc-software/overview.out |only LMMstar-0.4.3/LMMstar/inst/doc-software/overview.soc |only LMMstar-0.4.4/LMMstar/DESCRIPTION | 10 LMMstar-0.4.4/LMMstar/MD5 | 21 LMMstar-0.4.4/LMMstar/R/model.matrix.R | 6 LMMstar-0.4.4/LMMstar/inst/doc-software/overview.aux | 44 - LMMstar-0.4.4/LMMstar/inst/doc-software/overview.log | 18 LMMstar-0.4.4/LMMstar/inst/doc-software/overview.org | 6 LMMstar-0.4.4/LMMstar/inst/doc-software/overview.pdf |binary LMMstar-0.4.4/LMMstar/inst/doc-software/overview.tex | 317 +++++++++-- LMMstar-0.4.4/LMMstar/inst/doc/overview.pdf |binary 14 files changed, 310 insertions(+), 112 deletions(-)
Title: A Bayesian Tool for Near Real-Time Estimation of the
Reproduction Number
Description: Estimation of the instantaneous reproduction number with
Laplacian-P-splines following the methodology of Gressani et al.(2021)
<doi:10.1101/2021.12.02.21267189>. The negative Binomial
distribution is used to model the time series of case counts. Two methods are
available for inference : (1) a sampling-free approach based on a maximum a
posteriori calibration of the hyperparameter vector and (2) a fully stochastic
approach with a Metropolis-within-Gibbs algorithm and Langevin diffusions for
efficient sampling of the posterior distribution.
Author: Oswaldo Gressani [aut, cre] (<https://orcid.org/0000-0003-4152-6159>)
Maintainer: Oswaldo Gressani <oswaldo_gressani@hotmail.fr>
Diff between EpiLPS versions 1.0.1 dated 2021-12-21 and 1.0.2 dated 2022-01-03
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 ++++++ README.md | 29 +++++++++++++++-------------- src/cubicBspline.cpp | 2 +- 5 files changed, 30 insertions(+), 23 deletions(-)
Title: Fix Really Messy Dates
Description: Fixes messy dates in data frames such as those entered via text
boxes. Standardizes / - and whitespace separation, month abbreviations, and
year first or day first by converting to R's built-in Date class. Imputes
missing date or month using user-provided values.
Author: Nathan Constantine-Cooke [aut, cre]
(<https://orcid.org/0000-0002-4437-8713>)
Maintainer: Nathan Constantine-Cooke <nathan.constantine-cooke@ed.ac.uk>
Diff between datefixR versions 0.1.2 dated 2021-11-30 and 0.1.3 dated 2022-01-03
DESCRIPTION | 8 ++-- MD5 | 26 +++++++------- NEWS.md | 4 ++ R/fix_date.R | 20 ++++++---- R/fix_dates.R | 45 +++++++++++++++++------- README.md | 26 ++------------ inst/doc/datefixR.R | 3 + inst/doc/datefixR.Rmd | 10 +++++ inst/doc/datefixR.html | 73 ++++++++++++++++++++-------------------- man/fix_date.Rd | 9 +++- man/fix_dates.Rd | 18 ++++++++- tests/testthat/test_fix_date.R | 13 +++++++ tests/testthat/test_fix_dates.R | 40 +++++++++++++++++++++ vignettes/datefixR.Rmd | 10 +++++ 14 files changed, 206 insertions(+), 99 deletions(-)
Title: Generalized Pairwise Comparisons
Description: Implementation of the Generalized Pairwise Comparisons (GPC)
as defined in Buyse (2010) <doi:10.1002/sim.3923> for complete observations,
and extended in Peron (2018) <doi:10.1177/0962280216658320> to deal with right-censoring.
GPC compare two groups of observations (intervention vs. control group)
regarding several prioritized endpoints to estimate the probability that a random observation drawn from
one group performs better than a random observation drawn from the other group (Mann-Whitney parameter).
The net benefit and win ratio statistics,
i.e. the difference and ratio between the probabilities relative to the intervention and control groups,
can then also be estimated. Confidence intervals and p-values are obtained based on asymptotic results (Ozenne 2021 <doi:10.1177/09622802211037067>),
non-parametric bootstrap, or permutations.
The software enables the use of thresholds of minimal importance difference,
stratification, non-prioritized endpoints (O Brien test), and can handle right-censoring and competing-risks.
Author: Brice Ozenne [aut, cre] (<https://orcid.org/0000-0001-9694-2956>),
Julien Peron [ctb],
Eva Cantagallo [aut]
Maintainer: Brice Ozenne <brice.mh.ozenne@gmail.com>
Diff between BuyseTest versions 2.3.5 dated 2021-10-25 and 2.3.9 dated 2022-01-03
DESCRIPTION | 18 MD5 | 132 +-- NAMESPACE | 4 NEWS | 7 R/0-onLoad.R | 3 R/BuyseMultComp.R | 314 +++++--- R/BuyseTest-Peron.R | 56 + R/BuyseTest-check.R | 26 R/BuyseTest-initialization.R | 100 ++ R/BuyseTest-package.R | 2 R/BuyseTest-print.R | 23 R/BuyseTest.R | 57 + R/BuyseTest.options.R | 55 - R/PairScore.R | 11 R/RcppExports.R | 9 R/S4-BuysePower-show.R | 8 R/S4-BuysePower-summary.R | 34 R/S4-BuysePower.R | 7 R/S4-BuyseTest-coef.R | 26 R/S4-BuyseTest-confint.R | 86 +- R/S4-BuyseTest-get.R | 19 R/S4-BuyseTest-sensitivity.R | 182 ----- R/S4-BuyseTest-summary.R | 33 R/S4-BuyseTest.R | 24 R/S4-BuyseTest.options.R | 3 R/as.data.table.performance.R |only R/auc.R | 33 R/autoplot.sensitivity.R |only R/brier.R | 17 R/performance.R | 479 ++++++++++--- R/powerBuyseTest.R | 10 R/predict.logit.R | 8 build/vignette.rds |binary inst/doc-Wilcoxon/wilcoxonTest-compress.pdf |only inst/doc-Wilcoxon/wilcoxonTest.aux | 4 inst/doc-Wilcoxon/wilcoxonTest.log | 32 inst/doc-Wilcoxon/wilcoxonTest.org | 98 +- inst/doc-Wilcoxon/wilcoxonTest.pdf |binary inst/doc-Wilcoxon/wilcoxonTest.tex | 96 +- inst/doc/overview.pdf |binary inst/doc/overview.pdf.asis | 1 inst/doc/wilcoxonTest.pdf |binary inst/doc/wilcoxonTest.pdf.asis | 1 man/BuyseMultComp.Rd | 57 + man/BuyseTest-package.Rd | 2 man/BuyseTest.Rd | 6 man/GPC_cpp.Rd | 4 man/S4BuyseTest-coef.Rd | 2 man/S4BuyseTest-confint.Rd | 4 man/S4BuyseTest-sensitivity.Rd | 2 man/as.data.table.performance.Rd |only man/autoplot.sensitivity.Rd | 2 man/internal-initialization.Rd | 9 man/internal-print.Rd | 1 man/performance.Rd | 6 man/testArgs.Rd | 1 src/FCT_buyseTest.cpp | 9 src/FCT_calcAllPairs.h | 6 src/FCT_calcOnePair.h | 1006 ++++++++++++++-------------- src/RcppExports.cpp | 23 tests/testthat/test-BuysePower.R | 6 tests/testthat/test-BuyseTest-engine.R | 8 tests/testthat/test-BuyseTest-iid.R | 24 tests/testthat/test-BuyseTest-multcomp.R |only tests/testthat/test-BuyseTest-operator.R | 5 tests/testthat/test-BuyseTest-previousBug.R | 53 + tests/testthat/test-BuyseTest-resampling.R | 5 tests/testthat/test-BuyseTest-restricted.R |only vignettes/overview.pdf.asis | 1 vignettes/wilcoxonTest.pdf.asis | 1 70 files changed, 1973 insertions(+), 1288 deletions(-)
Title: R Client for 'Adobe Analytics' API 2.0
Description: Connect to the 'Adobe Analytics' API v2.0 <https://github.com/AdobeDocs/analytics-2.0-apis>
which powers 'Analysis Workspace'. The package was developed
with the analyst in mind, and it will continue to be
developed with the guiding principles of iterative,
repeatable, timely analysis.
Author: Ben Woodard [aut, cre],
Tim Wilson [aut, ctb],
Charles Gallagher [ctb],
Mark Edmondson [ctb]
Maintainer: Ben Woodard <benrwoodard@gmail.com>
Diff between adobeanalyticsr versions 0.1.5 dated 2021-03-01 and 0.2.0 dated 2022-01-03
adobeanalyticsr-0.1.5/adobeanalyticsr/R/addmetrics_function.R |only adobeanalyticsr-0.1.5/adobeanalyticsr/R/call_data_debug.R |only adobeanalyticsr-0.1.5/adobeanalyticsr/R/metricsfilter_map_function.R |only adobeanalyticsr-0.1.5/adobeanalyticsr/R/rowsdata_function.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/DESCRIPTION | 17 adobeanalyticsr-0.2.0/adobeanalyticsr/MD5 | 63 adobeanalyticsr-0.2.0/adobeanalyticsr/NAMESPACE | 11 adobeanalyticsr-0.2.0/adobeanalyticsr/NEWS.md | 23 adobeanalyticsr-0.2.0/adobeanalyticsr/R/adobeanalyticsr-package.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/R/anomaly_report.R | 4 adobeanalyticsr-0.2.0/adobeanalyticsr/R/auth.R | 479 ++++- adobeanalyticsr-0.2.0/adobeanalyticsr/R/call_api.R | 65 adobeanalyticsr-0.2.0/adobeanalyticsr/R/call_data.R | 86 adobeanalyticsr-0.2.0/adobeanalyticsr/R/freeform_report.R | 902 ++-------- adobeanalyticsr-0.2.0/adobeanalyticsr/R/get_me.R | 67 adobeanalyticsr-0.2.0/adobeanalyticsr/R/get_metrics.R | 3 adobeanalyticsr-0.2.0/adobeanalyticsr/R/get_reportsuites.R | 2 adobeanalyticsr-0.2.0/adobeanalyticsr/R/get_req_data.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/R/globals.R | 5 adobeanalyticsr-0.2.0/adobeanalyticsr/R/make_component_lookup.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/R/request_format.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/R/token.R |only adobeanalyticsr-0.2.0/adobeanalyticsr/R/top_daterange_number_function.R | 75 adobeanalyticsr-0.2.0/adobeanalyticsr/R/utilities_function.R | 82 adobeanalyticsr-0.2.0/adobeanalyticsr/R/workspace_reports.R | 18 adobeanalyticsr-0.2.0/adobeanalyticsr/README.md | 99 - adobeanalyticsr-0.2.0/adobeanalyticsr/build/vignette.rds |binary adobeanalyticsr-0.2.0/adobeanalyticsr/inst/doc/getting-started.Rmd | 2 adobeanalyticsr-0.2.0/adobeanalyticsr/inst/doc/getting-started.html | 520 +---- adobeanalyticsr-0.2.0/adobeanalyticsr/man/adobeanalyticsr-package.Rd |only adobeanalyticsr-0.2.0/adobeanalyticsr/man/aw_auth.Rd |only adobeanalyticsr-0.2.0/adobeanalyticsr/man/aw_auth_with.Rd |only adobeanalyticsr-0.2.0/adobeanalyticsr/man/aw_freeform_table.Rd | 43 adobeanalyticsr-0.2.0/adobeanalyticsr/man/aw_token.Rd | 4 adobeanalyticsr-0.2.0/adobeanalyticsr/man/aw_workspace_report.Rd | 11 adobeanalyticsr-0.2.0/adobeanalyticsr/man/get_me.Rd | 10 adobeanalyticsr-0.2.0/adobeanalyticsr/man/retrieve_aw_token.Rd |only adobeanalyticsr-0.2.0/adobeanalyticsr/vignettes/getting-started.Rmd | 2 adobeanalyticsr-0.2.0/adobeanalyticsr/vignettes/getting-started.Rmd.orig | 22 39 files changed, 1278 insertions(+), 1337 deletions(-)
More information about adobeanalyticsr at CRAN
Permanent link
Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model-based optimization and tuning of
algorithms (hyperparameter tuning respectively hyperparameter optimization). It includes surrogate models, optimizers, and design of experiment
approaches. The main interface is spot, which uses sequentially updated
surrogate models for the purpose of efficient optimization. The main goal is
to ease the burden of objective function evaluations, when a single evaluation
requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut, cre]
(<https://orcid.org/0000-0002-5938-5158>),
Martin Zaefferer [aut] (<https://orcid.org/0000-0003-2372-2092>),
Frederik Rehbach [aut] (<https://orcid.org/0000-0003-0922-8629>),
Margarita Rebolledo [ctb],
Joerg Stork [ctb] (0000-0002-7471-3498),
Christian Lasarczyk [ctb]
Maintainer: Thomas Bartz-Beielstein <tbb@bartzundbartz.de>
Diff between SPOT versions 2.5.12 dated 2021-10-22 and 2.5.18 dated 2022-01-03
SPOT-2.5.12/SPOT/vignettes/SPOTVignetteNutshell.md |only SPOT-2.5.18/SPOT/DESCRIPTION | 10 SPOT-2.5.18/SPOT/MD5 | 34 +- SPOT-2.5.18/SPOT/NEWS.md | 9 SPOT-2.5.18/SPOT/R/buildBO.R | 246 ++++++++++++++------ SPOT-2.5.18/SPOT/build/partial.rdb |binary SPOT-2.5.18/SPOT/build/vignette.rds |binary SPOT-2.5.18/SPOT/inst/doc/SPOTVignetteNutshell.R | 3 SPOT-2.5.18/SPOT/inst/doc/SPOTVignetteNutshell.Rmd | 5 SPOT-2.5.18/SPOT/inst/doc/SPOTVignetteNutshell.html | 15 - SPOT-2.5.18/SPOT/man/buildBO.Rd | 73 +++++ SPOT-2.5.18/SPOT/man/predict.spotBOModel.Rd | 7 SPOT-2.5.18/SPOT/tests/testthat/Rplots.pdf |only SPOT-2.5.18/SPOT/vignettes/SPOTBenchmark.R |only SPOT-2.5.18/SPOT/vignettes/SPOTBenchmark.html |only SPOT-2.5.18/SPOT/vignettes/SPOTKrigingVignette.R |only SPOT-2.5.18/SPOT/vignettes/SPOTKrigingVignette.html |only SPOT-2.5.18/SPOT/vignettes/SPOTVignetteNutshell.Rmd | 5 SPOT-2.5.18/SPOT/vignettes/compSpotBartz07.R |only SPOT-2.5.18/SPOT/vignettes/compSpotBartz07b.R |only SPOT-2.5.18/SPOT/vignettes/experiments.R |only SPOT-2.5.18/SPOT/vignettes/experiments.html |only SPOT-2.5.18/SPOT/vignettes/resCompBartz07.RData |only SPOT-2.5.18/SPOT/vignettes/resCompBartz07b.RData |only 24 files changed, 312 insertions(+), 95 deletions(-)
Title: Penalized Poisson Pseudo Maximum Likelihood Regression
Description: A set of tools that enables efficient estimation of penalized
Poisson Pseudo Maximum Likelihood regressions, using lasso or ridge penalties, for models
that feature one or more sets of high-dimensional fixed effects. The methodology is based on
Breinlich, Corradi, Rocha, Ruta, Santos Silva, and Zylkin (2021) <http://hdl.handle.net/10986/35451>
and takes advantage of the method of alternating projections of Gaure (2013)
<doi:10.1016/j.csda.2013.03.024> for dealing with HDFE, as well as
the coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010)
<doi:10.18637/jss.v033.i01> for fitting lasso regressions. The package is also able to carry out
cross-validation and to implement the plugin lasso of Belloni, Chernozhukov, Hansen and Kozbur (2016)
<doi:10.1080/07350015.2015.1102733>.
Author: Diego Ferreras Garrucho [aut],
Tom Zylkin [aut],
Nicolas Apfel [cre]
Maintainer: Nicolas Apfel <nicolas.apfel@gmail.com>
Diff between penppml versions 0.1.0 dated 2021-09-09 and 0.1.1 dated 2022-01-03
DESCRIPTION | 8 LICENSE | 4 MD5 | 109 +- NAMESPACE | 34 NEWS.md |only R/RcppExports.R | 196 +-- R/data.R | 110 +- R/hdfeppml_int.R | 8 R/iceberg.R | 372 +++--- R/mlfitppml_int.R | 466 ++++---- R/penhdfeppml_cluster_int.R | 430 +++---- R/penhdfeppml_int.R | 538 ++++----- R/penppml-package.R | 76 - R/utils-pipe.R | 28 R/utils.R | 6 R/wrappers.R | 452 ++++---- R/xvalidate.R | 642 +++++------ README.md | 174 +-- build/vignette.rds |binary data/trade.rda |binary inst/doc/intro-to-penppml.R | 364 +++--- inst/doc/intro-to-penppml.html | 2048 +++++++++++++++++++------------------- man/AtA.Rd | 28 man/cluster_matrix.Rd | 42 man/collinearity_check.Rd | 50 man/compute_fes.Rd | 92 - man/countries.Rd | 54 - man/eigenMatMult.Rd | 34 man/fastolsCpp.Rd | 38 man/fastridge.Rd | 52 man/fastridgeCpp.Rd | 42 man/faststddev.Rd | 38 man/fastwmean.Rd | 38 man/genfes.Rd | 38 man/genmodel.Rd | 90 - man/hdfeppml.Rd | 192 +-- man/hdfeppml_int.Rd | 224 ++-- man/iceberg.Rd | 146 +- man/manyouter.Rd | 32 man/mlfitppml.Rd | 242 ++-- man/mlfitppml_int.Rd | 290 ++--- man/penhdfeppml.Rd | 230 ++-- man/penhdfeppml_cluster.Rd | 204 +-- man/penhdfeppml_cluster_int.Rd | 252 ++-- man/penhdfeppml_int.Rd | 296 ++--- man/penppml-package.Rd | 147 +- man/pipe.Rd | 40 man/plugin_lasso_int.Rd | 100 - man/select_fes.Rd | 44 man/standardize_wt.Rd | 50 man/trade.Rd | 100 - man/xeex.Rd | 42 man/xvalidate.Rd | 262 ++-- tests/testthat.R | 8 tests/testthat/test-RcppExports.R | 5 tests/testthat/test-hdfeppml.R | 34 56 files changed, 4829 insertions(+), 4812 deletions(-)
Title: Process and Analyze Mouse-Tracking Data
Description: Mouse-tracking, the analysis of mouse movements in computerized
experiments, is a method that is becoming increasingly popular in the
cognitive sciences. The mousetrap package offers functions for importing,
preprocessing, analyzing, aggregating, and visualizing mouse-tracking data.
An introduction into mouse-tracking analyses using mousetrap can be found
in Wulff, Kieslich, Henninger, Haslbeck, & Schulte-Mecklenbeck (2021)
<doi:10.31234/osf.io/v685r> (preprint: <https://psyarxiv.com/v685r>).
Author: Pascal J. Kieslich [aut, cre] (<https://orcid.org/0000-0002-0853-9364>),
Dirk U. Wulff [aut] (<https://orcid.org/0000-0002-4008-8022>),
Felix Henninger [aut] (<https://orcid.org/0000-0002-7730-9511>),
Jonas M. B. Haslbeck [aut],
Sarah Brockhaus [ctb]
Maintainer: Pascal J. Kieslich <pascal.kieslich@gmail.com>
Diff between mousetrap versions 3.2.0 dated 2021-06-05 and 3.2.1 dated 2022-01-03
mousetrap-3.2.0/mousetrap/man/mt_space_normalize.Rd |only mousetrap-3.2.1/mousetrap/DESCRIPTION | 16 mousetrap-3.2.1/mousetrap/MD5 | 149 ++++---- mousetrap-3.2.1/mousetrap/NAMESPACE | 3 mousetrap-3.2.1/mousetrap/NEWS.md | 25 + mousetrap-3.2.1/mousetrap/R/angles.R | 8 mousetrap-3.2.1/mousetrap/R/animate.R | 4 mousetrap-3.2.1/mousetrap/R/heatmap.R | 22 + mousetrap-3.2.1/mousetrap/R/mousetrap.R | 2 mousetrap-3.2.1/mousetrap/R/preprocess.R | 146 +++---- mousetrap-3.2.1/mousetrap/R/quantileeffect.R | 3 mousetrap-3.2.1/mousetrap/R/spatialize.R | 4 mousetrap-3.2.1/mousetrap/R/startupmessage.R | 2 mousetrap-3.2.1/mousetrap/R/utils.R | 31 + mousetrap-3.2.1/mousetrap/README.md | 31 - mousetrap-3.2.1/mousetrap/build/partial.rdb |binary mousetrap-3.2.1/mousetrap/inst/CITATION | 31 - mousetrap-3.2.1/mousetrap/man/KH2017.Rd | 70 +-- mousetrap-3.2.1/mousetrap/man/KH2017_raw.Rd | 64 +-- mousetrap-3.2.1/mousetrap/man/bezier.Rd | 8 mousetrap-3.2.1/mousetrap/man/bimodality_coefficient.Rd | 6 mousetrap-3.2.1/mousetrap/man/figures |only mousetrap-3.2.1/mousetrap/man/mousetrap.Rd | 258 +++++++------- mousetrap-3.2.1/mousetrap/man/mt_add_trajectory.Rd | 8 mousetrap-3.2.1/mousetrap/man/mt_add_variables.Rd | 12 mousetrap-3.2.1/mousetrap/man/mt_aggregate.Rd | 8 mousetrap-3.2.1/mousetrap/man/mt_aggregate_per_subject.Rd | 8 mousetrap-3.2.1/mousetrap/man/mt_align.Rd | 52 +- mousetrap-3.2.1/mousetrap/man/mt_align_start.Rd | 16 mousetrap-3.2.1/mousetrap/man/mt_align_start_end.Rd | 34 - mousetrap-3.2.1/mousetrap/man/mt_angles.Rd | 50 +- mousetrap-3.2.1/mousetrap/man/mt_animate.Rd | 56 +-- mousetrap-3.2.1/mousetrap/man/mt_average.Rd | 29 - mousetrap-3.2.1/mousetrap/man/mt_bind.Rd | 4 mousetrap-3.2.1/mousetrap/man/mt_check_bimodality.Rd | 36 - mousetrap-3.2.1/mousetrap/man/mt_check_resolution.Rd | 12 mousetrap-3.2.1/mousetrap/man/mt_cluster.Rd | 76 ++-- mousetrap-3.2.1/mousetrap/man/mt_cluster_k.Rd | 72 +-- mousetrap-3.2.1/mousetrap/man/mt_count.Rd | 12 mousetrap-3.2.1/mousetrap/man/mt_derivatives.Rd | 26 - mousetrap-3.2.1/mousetrap/man/mt_deviations.Rd | 38 +- mousetrap-3.2.1/mousetrap/man/mt_diffmap.Rd | 46 +- mousetrap-3.2.1/mousetrap/man/mt_distmat.Rd | 48 +- mousetrap-3.2.1/mousetrap/man/mt_example.Rd | 52 +- mousetrap-3.2.1/mousetrap/man/mt_example_raw.Rd | 60 +-- mousetrap-3.2.1/mousetrap/man/mt_exclude_finish.Rd |only mousetrap-3.2.1/mousetrap/man/mt_exclude_initiation.Rd | 9 mousetrap-3.2.1/mousetrap/man/mt_export_long.Rd | 18 mousetrap-3.2.1/mousetrap/man/mt_heatmap.Rd | 34 - mousetrap-3.2.1/mousetrap/man/mt_heatmap_ggplot.Rd | 28 - mousetrap-3.2.1/mousetrap/man/mt_heatmap_raw.Rd | 106 ++--- mousetrap-3.2.1/mousetrap/man/mt_import_long.Rd | 2 mousetrap-3.2.1/mousetrap/man/mt_import_mousetrap.Rd | 30 - mousetrap-3.2.1/mousetrap/man/mt_import_wide.Rd | 18 mousetrap-3.2.1/mousetrap/man/mt_length_normalize.Rd | 18 mousetrap-3.2.1/mousetrap/man/mt_map.Rd | 70 +-- mousetrap-3.2.1/mousetrap/man/mt_measures.Rd | 192 +++++----- mousetrap-3.2.1/mousetrap/man/mt_plot.Rd | 18 mousetrap-3.2.1/mousetrap/man/mt_plot_riverbed.Rd | 28 - mousetrap-3.2.1/mousetrap/man/mt_prototypes.Rd | 10 mousetrap-3.2.1/mousetrap/man/mt_qeffect.Rd | 6 mousetrap-3.2.1/mousetrap/man/mt_remap_symmetric.Rd | 4 mousetrap-3.2.1/mousetrap/man/mt_resample.Rd | 24 - mousetrap-3.2.1/mousetrap/man/mt_reshape.Rd | 14 mousetrap-3.2.1/mousetrap/man/mt_sample_entropy.Rd | 46 +- mousetrap-3.2.1/mousetrap/man/mt_scale_trajectories.Rd | 14 mousetrap-3.2.1/mousetrap/man/mt_spatialize.Rd | 20 - mousetrap-3.2.1/mousetrap/man/mt_standardize.Rd | 6 mousetrap-3.2.1/mousetrap/man/mt_subset.Rd | 8 mousetrap-3.2.1/mousetrap/man/mt_time_normalize.Rd | 22 - mousetrap-3.2.1/mousetrap/man/read_mt.Rd | 28 - mousetrap-3.2.1/mousetrap/man/scale_within.Rd | 14 mousetrap-3.2.1/mousetrap/src/RcppExports.cpp | 5 73 files changed, 1263 insertions(+), 1167 deletions(-)
Title: Java GUI for R
Description: Java GUI for R - cross-platform, universal and unified Graphical User Interface for R. For full functionality on Windows and Mac OS X JGR requires a start application which depends on your OS.
Author: Markus Helbig <mhelbig81@googlemail.com>, Simon Urbanek, Ian Fellows
Maintainer: Markus Helbig <mhelbig81@googlemail.com>
Diff between JGR versions 1.8-7 dated 2020-04-07 and 1.9-0 dated 2022-01-03
DESCRIPTION | 12 +++--- MD5 | 10 ++--- NEWS | 3 + R/JGR.R | 2 - inst/java/JGR.jar |binary java/org/rosuda/JGR/JGR.java | 76 +++++++++++++++++++++++++++++-------------- 6 files changed, 67 insertions(+), 36 deletions(-)
Title: Simple Git Client for R
Description: Simple git client for R based on 'libgit2' with support for SSH and
HTTPS remotes. All functions in 'gert' use basic R data types (such as vectors
and data-frames) for their arguments and return values. User credentials are
shared with command line 'git' through the git-credential store and ssh keys
stored on disk or ssh-agent.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Jennifer Bryan [ctb] (<https://orcid.org/0000-0002-6983-2759>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between gert versions 1.4.3 dated 2021-11-10 and 1.5.0 dated 2022-01-03
DESCRIPTION | 6 - MD5 | 10 +- NEWS | 6 + inst/doc/gert.html | 206 +++++++++++++++++++++++++++++++++++++++++++++++++++-- src/commit.c | 7 - src/init.c | 13 +++ 6 files changed, 229 insertions(+), 19 deletions(-)
Title: Easy Interface to the Statistical Disclosure Control Package
'sdcTable' Extended with the 'GaussSuppression' Method
Description: The main function, ProtectTable(), performs table suppression according to a
frequency rule with a data set as the only required input. Within this function,
protectTable(), protect_linked_tables() or runArgusBatchFile() in package 'sdcTable' is called.
Lists of level-hierarchy (parameter 'dimList') and other required input to these functions
are created automatically.
The suppression method Gauss (default) is an additional method that is not available in 'sdcTable'.
The function, PTgui(), starts a graphical user interface based on the 'shiny' package.
Author: Øyvind Langsrud [aut, cre]
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between easySdcTable versions 1.0.0 dated 2021-10-11 and 1.0.1 dated 2022-01-03
DESCRIPTION | 8 ++--- MD5 | 14 ++++---- NEWS.md | 5 +++ R/ProtectTable.R | 1 inst/doc/singletonsAndZeros.R | 16 +++++----- inst/doc/singletonsAndZeros.Rmd | 22 +++++++------ inst/doc/singletonsAndZeros.html | 62 +++++++++++++++++++-------------------- vignettes/singletonsAndZeros.Rmd | 22 +++++++------ 8 files changed, 80 insertions(+), 70 deletions(-)