Title: Causal Mediation Analysis
Description: We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010) <DOI:10.1214/10-STS321>, Imai, Keele and Tingley (2010) <DOI:10.1037/a0020761>, Imai, Tingley and Yamamoto (2013) <DOI:10.1111/j.1467-985X.2012.01032.x>, Imai and Yamamoto (2013) <DOI:10.1093/pan/mps040> and Yamamoto (2013) <http://web.mit.edu/teppei/www/research/IVmediate.pdf>. In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley <dtingley@gov.harvard.edu>,
Teppei Yamamoto <teppei@mit.edu>,
Kentaro Hirose <hirose@princeton.edu>,
Luke Keele <ljk20@psu.edu>,
Kosuke Imai <kimai@princeton.edu>,
Minh Trinh <mdtrinh@mit.edu>,
Weihuang Wong <wwong@mit.edu>
Maintainer: Teppei Yamamoto <teppei@mit.edu>
Diff between mediation versions 4.4.7 dated 2019-03-16 and 4.5.0 dated 2019-10-08
ChangeLog | 3 DESCRIPTION | 20 MD5 | 103 +- NAMESPACE | 186 ++- NEWS.md |only R/amelidiate.R | 355 ++++--- R/data.R |only R/globals.R |only R/ivmediate.R | 276 +++++ R/mediate.R | 1994 +++++++++++++++++++++++++++++------------- R/mediate.designs.R | 483 +++++++++- R/mediate_tsls.R |only R/mediation.R |only R/mediations.R | 542 +++++++---- R/medsens.R | 366 +++++++ R/medtests.R | 153 +++ R/multimed.R | 269 +++++ R/onAttach.R | 2 R/use_speed.R |only build/vignette.rds |binary inst/doc/mediation-old.pdf |binary inst/doc/mediation.pdf |binary man/CEDdata.Rd | 55 - man/amelidiate.Rd | 52 - man/boundsdata.Rd | 80 + man/framing.Rd | 63 - man/ivmediate.Rd | 221 +++- man/jobs.Rd | 93 + man/mediate.Rd | 515 +++++++--- man/mediate.ced.Rd | 143 +-- man/mediate.pd.Rd | 142 +- man/mediate.ped.Rd | 135 +- man/mediate.sed.Rd | 143 +-- man/mediate_tsls.Rd |only man/mediation.Rd |only man/mediations.Rd | 192 +++- man/medsens.Rd | 241 +++-- man/multimed.Rd | 230 +++- man/plot.ivmediate.Rd | 97 +- man/plot.mediate.Rd | 98 +- man/plot.mediate.mer.Rd | 86 + man/plot.mediations.Rd | 61 - man/plot.medsens.Rd | 193 ++-- man/plot.multimed.Rd | 115 +- man/school.Rd | 51 - man/student.Rd | 66 - man/summary.ivmediate.Rd | 59 - man/summary.mediate.Rd | 78 + man/summary.mediate.design.Rd | 70 - man/summary.mediate.mer.Rd | 81 + man/summary.mediations.Rd | 53 - man/summary.medsens.Rd | 87 + man/summary.multimed.Rd | 62 - man/test.TMint.Rd | 76 + man/test.modmed.Rd | 94 + tests |only 56 files changed, 6069 insertions(+), 2415 deletions(-)
Title: Bayesian Logistic Regression with Heavy-Tailed Priors
Description: Efficient Bayesian multinomial logistic regression based on heavy-tailed
(hyper-LASSO, non-convex) priors. The posterior of coefficients and hyper-parameters
is sampled with restricted Gibbs sampling for leveraging the high-dimensionality and
Hamiltonian Monte Carlo for handling the high-correlation among coefficients. A detailed
description of the method: Li and Yao (2018), JSCS, 88:14, 2827-2851, <arXiv:1405.3319>.
Author: Longhai Li [aut, cre] (<https://orcid.org/0000-0002-3074-8584>),
Steven Liu [aut]
Maintainer: Longhai Li <longhai@math.usask.ca>
Diff between HTLR versions 0.4 dated 2019-10-06 and 0.4-1 dated 2019-10-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++-- README.md | 6 ++++-- inst/doc/simu.html | 8 ++++---- src/ars.cpp | 2 +- 6 files changed, 19 insertions(+), 17 deletions(-)
Title: Package Directives and Collaboration Networks in CRAN
Description: Core visualizations and summaries for the CRAN package database. The package provides comprehensive methods for cleaning up and organizing the information in the CRAN package database, for building package directives networks (depends, imports, suggests, enhances, linking to) and collaboration networks, producing package dependence trees, and for computing useful summaries and producing interactive visualizations from the resulting networks and summaries. The resulting networks can be coerced to 'igraph' <https://CRAN.R-project.org/package=igraph> objects for further analyses and modelling.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between cranly versions 0.5.3 dated 2019-07-22 and 0.5.4 dated 2019-10-08
DESCRIPTION | 6 MD5 | 14 - NEWS.md | 3 R/extractors.R | 14 - inst/doc/cranly.html | 138 ++++++------ inst/doc/dependence_trees.html | 172 ++++++++-------- inst/doc/extractors.html | 437 +++++++++++++++++++++-------------------- inst/doc/glms.html | 140 ++++++------- 8 files changed, 482 insertions(+), 442 deletions(-)
Title: Quasi Variances for Factor Effects in Statistical Models
Description: Functions to compute quasi variances and associated measures of approximation error.
Author: David Firth
Maintainer: David Firth <d.firth@warwick.ac.uk>
Diff between qvcalc versions 1.0.0 dated 2019-05-09 and 1.0.1 dated 2019-10-08
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 3 ++- NEWS.md | 18 ++++++++++++++---- R/qvcalc.coxph.R |only man/qvcalc.Rd | 29 +++++++++++++++++++++++------ 6 files changed, 50 insertions(+), 21 deletions(-)
Title: Dynamic Generation and Quality Checks of Formula Objects
Description: Many statistical models and analyses in R are implemented through formula objects. The formulaic package creates a unified approach for programmatically and dynamically generating formula objects. Users may specify the outcome and inputs of a model directly, search for variables to include based upon naming patterns, incorporate interactions, and identify variables to exclude. A wide range of quality checks are implemented to identify issues such as misspecified variables, duplication, a lack of contrast in the inputs, and a large number of levels in categorical data. Variables that do not meet these quality checks can be automatically excluded from the model. These issues are documented and reported in a manner that provides greater accountability and useful information to guide an investigation of the data.
Author: David Shilane [aut],
Caffrey Lee [ctb],
Zichen Huang [ctb],
Anderson Nelson [ctb, cre]
Maintainer: Anderson Nelson <an2908@columbia.edu>
Diff between formulaic versions 0.0.3 dated 2019-08-30 and 0.0.4 dated 2019-10-08
DESCRIPTION | 8 MD5 | 12 NEWS.md | 5 R/create.formula.R | 23 - inst/doc/Introduction-to-formulaic.html | 411 ++++++++++++++++---------------- man/add.backtick.Rd | 2 man/create.formula.Rd | 2 7 files changed, 246 insertions(+), 217 deletions(-)
Title: Normalized Stochasticity Ratio
Description: To estimate ecological stochasticity in community assembly. Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. The new index, normalized stochasticity ratio (NST), is to estimate ecological stochasticity, i.e. relative importance of stochastic processes, in community assembly. With functions in this package, NST can be calculated based on different similarity metrics and/or different null model algorithms, as well as some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard Effect Size (SES), modified Raup-Crick metrics (RC). Functions for permutational test and bootstrapping analysis are also included. Previous ST is published by Zhou et al (2014) <doi:10.1073/pnas.1324044111>. NST is modified from ST by considering two alternative situations and normalizing the index to range from 0 to 1 (Ning et al 2019) <doi:10.1073/pnas.1904623116>. A modified version, MST, is a special case of NST, used in some recent or upcoming publications, e.g. Liang et al (2019) <doi:10.1101/638908>. SES is calculated as described in Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as reported by Chase et al (2011) <doi:10.1890/es10-00117.1> and Stegen et al (2013) <doi:10.1038/ismej.2013.93>.
Author: Daliang Ning
Maintainer: Daliang Ning <ningdaliang@ou.edu>
Diff between NST versions 2.0.3 dated 2019-06-15 and 2.0.4 dated 2019-10-08
DESCRIPTION | 10 +++++----- MD5 | 11 ++++++----- inst |only man/NST-package.Rd | 8 ++++---- man/nst.boot.Rd | 3 ++- man/nst.panova.Rd | 7 ++++--- man/tNST.Rd | 12 +++++++----- 7 files changed, 28 insertions(+), 23 deletions(-)
Title: Nested and Crossed Block Designs for Factorial, Fractional
Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal nested and crossed
block designs for unstructured or general factorial treatment designs.
The treatment design, if required, is found from a model
matrix design formula and can be added sequentially, if required.
The block design is found from a defined
set of block factors and is conditional on the defined treatment design.
The block factors are added in sequence and each added block factor
is optimized conditional on all previously added block factors.
The block design can have repeated nesting down to any required
depth of nesting with either simple nested blocks or a
crossed blocks design at each level of nesting. Outputs include a table
showing the allocation of treatments to blocks and tables showing
the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 3.5 dated 2019-05-28 and 3.6 dated 2019-10-08
blocksdesign-3.5/blocksdesign/R/MOLS.R |only blocksdesign-3.5/blocksdesign/man/orthogLS.Rd |only blocksdesign-3.6/blocksdesign/DESCRIPTION | 10 ++-- blocksdesign-3.6/blocksdesign/MD5 | 22 ++++++---- blocksdesign-3.6/blocksdesign/NAMESPACE | 6 +- blocksdesign-3.6/blocksdesign/R/Lattice.R |only blocksdesign-3.6/blocksdesign/R/blocks.r | 46 +++++++--------------- blocksdesign-3.6/blocksdesign/R/design.r | 12 ++--- blocksdesign-3.6/blocksdesign/R/isPrmePower.R |only blocksdesign-3.6/blocksdesign/R/ppMOLS.R |only blocksdesign-3.6/blocksdesign/build/vignette.rds |binary blocksdesign-3.6/blocksdesign/man/MOLS.Rd |only blocksdesign-3.6/blocksdesign/man/blocks.Rd | 15 +------ blocksdesign-3.6/blocksdesign/man/design.Rd | 12 ++--- blocksdesign-3.6/blocksdesign/man/isPrimePower.Rd |only blocksdesign-3.6/blocksdesign/man/lattices.Rd |only 16 files changed, 54 insertions(+), 69 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: Daniel Falbel [ctb, cph, cre],
JJ Allaire [aut, cph],
François Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>),
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid Keydana [ctb]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between keras versions 2.2.4.1 dated 2019-04-05 and 2.2.5.0 dated 2019-10-08
keras-2.2.4.1/keras/tests/testthat/test_custom_wrappers.R |only keras-2.2.5.0/keras/DESCRIPTION | 11 keras-2.2.5.0/keras/MD5 | 201 +++--- keras-2.2.5.0/keras/NAMESPACE | 8 keras-2.2.5.0/keras/NEWS.md | 35 + keras-2.2.5.0/keras/R/applications.R | 30 keras-2.2.5.0/keras/R/callbacks.R | 258 +++++++- keras-2.2.5.0/keras/R/initializers.R | 202 ++++-- keras-2.2.5.0/keras/R/install.R | 19 keras-2.2.5.0/keras/R/layers-convolutional.R | 4 keras-2.2.5.0/keras/R/layers-core.R | 11 keras-2.2.5.0/keras/R/layers-features.R |only keras-2.2.5.0/keras/R/layers-recurrent.R | 2 keras-2.2.5.0/keras/R/losses.R | 19 keras-2.2.5.0/keras/R/model-persistence.R | 308 ++++++++-- keras-2.2.5.0/keras/R/model.R | 107 ++- keras-2.2.5.0/keras/R/optimizers.R | 37 - keras-2.2.5.0/keras/R/package.R | 10 keras-2.2.5.0/keras/R/preprocessing.R | 4 keras-2.2.5.0/keras/R/utils.R | 3 keras-2.2.5.0/keras/R/wrapper_custom.R | 2 keras-2.2.5.0/keras/build/vignette.rds |binary keras-2.2.5.0/keras/inst/doc/about_keras_layers.html | 9 keras-2.2.5.0/keras/inst/doc/about_keras_models.Rmd | 2 keras-2.2.5.0/keras/inst/doc/about_keras_models.html | 11 keras-2.2.5.0/keras/inst/doc/applications.html | 9 keras-2.2.5.0/keras/inst/doc/backend.html | 9 keras-2.2.5.0/keras/inst/doc/custom_layers.html | 9 keras-2.2.5.0/keras/inst/doc/custom_models.html | 9 keras-2.2.5.0/keras/inst/doc/custom_wrappers.html | 9 keras-2.2.5.0/keras/inst/doc/eager_guide.html | 9 keras-2.2.5.0/keras/inst/doc/faq.html | 9 keras-2.2.5.0/keras/inst/doc/functional_api.html | 9 keras-2.2.5.0/keras/inst/doc/getting_started.html | 11 keras-2.2.5.0/keras/inst/doc/guide_keras.html | 9 keras-2.2.5.0/keras/inst/doc/saving_serializing.R |only keras-2.2.5.0/keras/inst/doc/saving_serializing.Rmd |only keras-2.2.5.0/keras/inst/doc/saving_serializing.html |only keras-2.2.5.0/keras/inst/doc/sequential_model.html | 9 keras-2.2.5.0/keras/inst/doc/training_callbacks.Rmd | 40 + keras-2.2.5.0/keras/inst/doc/training_callbacks.html | 39 + keras-2.2.5.0/keras/inst/doc/training_visualization.html | 9 keras-2.2.5.0/keras/inst/doc/tutorial_basic_classification.html | 9 keras-2.2.5.0/keras/inst/doc/tutorial_basic_regression.html | 9 keras-2.2.5.0/keras/inst/doc/tutorial_basic_text_classification.html | 9 keras-2.2.5.0/keras/inst/doc/tutorial_overfit_underfit.html | 9 keras-2.2.5.0/keras/inst/doc/tutorial_save_and_restore.html | 9 keras-2.2.5.0/keras/inst/doc/why_use_keras.Rmd | 2 keras-2.2.5.0/keras/inst/doc/why_use_keras.html | 9 keras-2.2.5.0/keras/inst/python/kerastools/callback.py | 74 +- keras-2.2.5.0/keras/man/callback_lambda.Rd | 42 + keras-2.2.5.0/keras/man/callback_model_checkpoint.Rd | 9 keras-2.2.5.0/keras/man/callback_tensorboard.Rd | 10 keras-2.2.5.0/keras/man/evaluate.keras.engine.training.Model.Rd | 4 keras-2.2.5.0/keras/man/evaluate_generator.Rd | 4 keras-2.2.5.0/keras/man/export_savedmodel.keras.engine.training.Model.Rd | 3 keras-2.2.5.0/keras/man/get_weights.Rd | 1 keras-2.2.5.0/keras/man/initializer_lecun_normal.Rd | 2 keras-2.2.5.0/keras/man/initializer_lecun_uniform.Rd | 1 keras-2.2.5.0/keras/man/initializer_variance_scaling.Rd | 7 keras-2.2.5.0/keras/man/install_keras.Rd | 4 keras-2.2.5.0/keras/man/layer_activation.Rd | 1 keras-2.2.5.0/keras/man/layer_activity_regularization.Rd | 1 keras-2.2.5.0/keras/man/layer_dense.Rd | 1 keras-2.2.5.0/keras/man/layer_dense_features.Rd |only keras-2.2.5.0/keras/man/layer_dropout.Rd | 1 keras-2.2.5.0/keras/man/layer_flatten.Rd | 1 keras-2.2.5.0/keras/man/layer_gru.Rd | 2 keras-2.2.5.0/keras/man/layer_input.Rd | 1 keras-2.2.5.0/keras/man/layer_lambda.Rd | 1 keras-2.2.5.0/keras/man/layer_masking.Rd | 1 keras-2.2.5.0/keras/man/layer_permute.Rd | 1 keras-2.2.5.0/keras/man/layer_repeat_vector.Rd | 1 keras-2.2.5.0/keras/man/layer_reshape.Rd | 1 keras-2.2.5.0/keras/man/loss_mean_squared_error.Rd | 3 keras-2.2.5.0/keras/man/model_from_saved_model.Rd |only keras-2.2.5.0/keras/man/model_to_json.Rd | 1 keras-2.2.5.0/keras/man/model_to_saved_model.Rd |only keras-2.2.5.0/keras/man/model_to_yaml.Rd | 1 keras-2.2.5.0/keras/man/predict.keras.engine.training.Model.Rd | 5 keras-2.2.5.0/keras/man/predict_generator.Rd | 4 keras-2.2.5.0/keras/man/save_model_hdf5.Rd | 1 keras-2.2.5.0/keras/man/save_model_tf.Rd |only keras-2.2.5.0/keras/man/save_model_weights_hdf5.Rd | 1 keras-2.2.5.0/keras/man/save_model_weights_tf.Rd |only keras-2.2.5.0/keras/man/serialize_model.Rd | 1 keras-2.2.5.0/keras/tests/testthat.R | 8 keras-2.2.5.0/keras/tests/testthat/test-applications.R | 6 keras-2.2.5.0/keras/tests/testthat/test-callbacks.R | 194 ++++++ keras-2.2.5.0/keras/tests/testthat/test-constraints.R | 2 keras-2.2.5.0/keras/tests/testthat/test-custom-models.R | 4 keras-2.2.5.0/keras/tests/testthat/test-custom_wrappers.R |only keras-2.2.5.0/keras/tests/testthat/test-generators.R | 83 ++ keras-2.2.5.0/keras/tests/testthat/test-layer-methods.R | 2 keras-2.2.5.0/keras/tests/testthat/test-layers.R | 63 ++ keras-2.2.5.0/keras/tests/testthat/test-losses.R | 4 keras-2.2.5.0/keras/tests/testthat/test-metrics.R | 59 + keras-2.2.5.0/keras/tests/testthat/test-model-persistence.R | 65 +- keras-2.2.5.0/keras/tests/testthat/test-model.R | 29 keras-2.2.5.0/keras/tests/testthat/test-preprocessing.R | 45 + keras-2.2.5.0/keras/tests/testthat/test-tfdatasets.R |only keras-2.2.5.0/keras/tests/testthat/test-utils.R | 2 keras-2.2.5.0/keras/tests/testthat/train.R | 10 keras-2.2.5.0/keras/tests/testthat/utils.R | 22 keras-2.2.5.0/keras/vignettes/about_keras_models.Rmd | 2 keras-2.2.5.0/keras/vignettes/saving_serializing.Rmd |only keras-2.2.5.0/keras/vignettes/training_callbacks.Rmd | 40 + keras-2.2.5.0/keras/vignettes/why_use_keras.Rmd | 2 108 files changed, 1963 insertions(+), 408 deletions(-)
Title: Moments of Folded and Doubly Truncated Multivariate
Distributions
Description: It computes the raw moments for the truncated and folded multivariate normal, Skew-normal (SN), Extended skew normal (ESN) and Student's t-distribution. It also offers specific functions to compute the mean and variance-covariance matrix as well as the cumulative distribution function (cdf) for the folded normal, SN, ESN, and folded t-distribution. Density and random deviates are offered for the ESN (SN as particular case) distribution. Most algorithms are extensions based on Kan, R., & Robotti, C. (2017) <doi:10.1080/10618600.2017.1322092>.
Author: Christian E. Galarza, Victor H. Lachos
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between MomTrunc versions 4.51 dated 2019-09-09 and 4.59 dated 2019-10-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/AUX_esn.R | 11 +++++++++++ R/TESN1_mv.R | 7 +++++-- R/TN_mv_Kan.R | 15 +++++++++++++++ R/TN_mv_Vaida.R | 19 ++++++++++++++++++- 6 files changed, 57 insertions(+), 11 deletions(-)
Title: Length-Based Multispecies Analysis by Numerical Simulation
Description: Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.
Author: Michael A. Spence [aut, cre] (<https://orcid.org/0000-0002-3445-7979>),
Hayley J. Bannister [aut] (<https://orcid.org/0000-0002-2546-5168>),
Johnathan E. Ball [aut],
Paul J. Dolder [aut] (<https://orcid.org/0000-0002-4179-712X>),
Robert B. Thorpe [aut] (<https://orcid.org/0000-0001-8193-6932>),
Christopher A. Griffiths [ctb]
Maintainer: Michael A. Spence <michael.spence@cefas.co.uk>
Diff between LeMaRns versions 0.1.0 dated 2019-06-03 and 0.1.1 dated 2019-10-08
LeMaRns-0.1.0/LeMaRns/man/L50.Rd |only LeMaRns-0.1.0/LeMaRns/man/eta.Rd |only LeMaRns-0.1.0/LeMaRns/man/mixed_fish.Rd |only LeMaRns-0.1.1/LeMaRns/DESCRIPTION | 10 - LeMaRns-0.1.1/LeMaRns/MD5 | 45 ++--- LeMaRns-0.1.1/LeMaRns/R/NS_par.R | 16 +- LeMaRns-0.1.1/LeMaRns/R/param_setup.R | 7 LeMaRns-0.1.1/LeMaRns/R/plot_SSB.R | 17 +- LeMaRns-0.1.1/LeMaRns/R/plot_indicators.R | 35 ++-- LeMaRns-0.1.1/LeMaRns/R/run_LeMans.R | 6 LeMaRns-0.1.1/LeMaRns/data/NS_par.rda |binary LeMaRns-0.1.1/LeMaRns/data/gear.rda |binary LeMaRns-0.1.1/LeMaRns/inst/doc/lemarns.R | 126 ++++++++-------- LeMaRns-0.1.1/LeMaRns/inst/doc/lemarns.Rmd | 160 ++++++++++---------- LeMaRns-0.1.1/LeMaRns/inst/doc/lemarns.html | 208 +++++++++++++-------------- LeMaRns-0.1.1/LeMaRns/man/LeMansParam.Rd | 7 LeMaRns-0.1.1/LeMaRns/man/NS_L50.Rd |only LeMaRns-0.1.1/LeMaRns/man/NS_eta.Rd |only LeMaRns-0.1.1/LeMaRns/man/NS_mixed_fish.Rd |only LeMaRns-0.1.1/LeMaRns/man/NS_other.Rd |only LeMaRns-0.1.1/LeMaRns/man/comb_LeMans_run.Rd | 2 LeMaRns-0.1.1/LeMaRns/man/plot_SSB.Rd | 7 LeMaRns-0.1.1/LeMaRns/man/plot_indicators.Rd | 12 - LeMaRns-0.1.1/LeMaRns/man/run_LeMans.Rd | 4 LeMaRns-0.1.1/LeMaRns/vignettes/lemarns.Rmd | 160 ++++++++++---------- LeMaRns-0.1.1/LeMaRns/vignettes/nash.rda |binary LeMaRns-0.1.1/LeMaRns/vignettes/sce.rda |binary 27 files changed, 423 insertions(+), 399 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 3.0 dated 2019-08-05 and 3.1 dated 2019-10-08
DESCRIPTION | 8 MD5 | 69 +- NAMESPACE | 4 R/PbPb.R | 33 - R/UPb.R | 22 R/age.R | 17 R/agespectrum.R | 59 +- R/cad.R | 15 R/central.R | 3 R/ci.R | 36 - R/commonPb.R | 103 +++- R/concordia.R | 36 - R/discordia.R | 111 ++-- R/diseq.R | 19 R/io.R | 6 R/isochron.R | 99 +++- R/kde.R | 18 R/ludwig.R | 1201 +++++++++++++++++++++++----------------------------- R/peakfit.R | 28 - R/radialplot.R | 17 R/toolbox.R | 10 R/weightedmean.R | 19 R/york.R | 2 inst/UPb41.csv |only man/Pb0corr.Rd | 10 man/age.Rd | 19 man/agespectrum.Rd | 20 man/cad.Rd | 17 man/concordia.Rd | 38 - man/isochron.Rd | 79 ++- man/kde.Rd | 16 man/ludwig.Rd | 35 - man/peakfit.Rd | 14 man/radialplot.Rd | 16 man/read.data.Rd | 4 man/weightedmean.Rd | 16 36 files changed, 1139 insertions(+), 1080 deletions(-)
Title: Run Dose-Response MBNMA Models
Description: Fits Bayesian dose-response model-based network meta-analysis (MBNMA)
that incorporate multiple doses within an agent by modelling different dose-response functions, as
described by Mawdsley et al. (2016) <doi:10.1002/psp4.12091>.
By modelling dose-response relationships this can connect networks of evidence that might
otherwise be disconnected, and can improve precision on treatment estimates. Several common
dose-response functions are provided; others may be added by the user. Various characteristics
and assumptions can be flexibly added to the models, such as shared class effects. The consistency
of direct and indirect evidence in the network can be assessed using unrelated mean effects models
and/or by node-splitting at the treatment level.
Author: Hugo Pedder [aut, cre],
David Mawdsley [rev],
Nicky Welton [rev],
Sofia Dias [rev],
Meg Bennetts [rev],
Martin Boucher [rev],
Adil Karim [ctb]
Maintainer: Hugo Pedder <hugopedder@gmail.com>
Diff between MBNMAdose versions 0.2.3 dated 2019-07-25 and 0.2.4 dated 2019-10-08
MBNMAdose-0.2.3/MBNMAdose/man/NMA.nodesplit.Rd |only MBNMAdose-0.2.3/MBNMAdose/man/NMA.run.Rd |only MBNMAdose-0.2.3/MBNMAdose/man/plot.MBNMA.rank.Rd |only MBNMAdose-0.2.3/MBNMAdose/man/predict.MBNMA.Rd |only MBNMAdose-0.2.3/MBNMAdose/man/rank.MBNMA.predict.Rd |only MBNMAdose-0.2.3/MBNMAdose/tests/testthat/Rplots.pdf |only MBNMAdose-0.2.4/MBNMAdose/DESCRIPTION | 9 MBNMAdose-0.2.4/MBNMAdose/MD5 | 79 - MBNMAdose-0.2.4/MBNMAdose/NEWS.md | 25 MBNMAdose-0.2.4/MBNMAdose/R/inconsistency.functions.R | 50 - MBNMAdose-0.2.4/MBNMAdose/R/plot.functions.R | 27 MBNMAdose-0.2.4/MBNMAdose/R/predict.functions.R | 18 MBNMAdose-0.2.4/MBNMAdose/R/prepare.functions.R | 10 MBNMAdose-0.2.4/MBNMAdose/R/print.functions.R | 4 MBNMAdose-0.2.4/MBNMAdose/R/rank.functions.R | 2 MBNMAdose-0.2.4/MBNMAdose/R/run.functions.R | 31 MBNMAdose-0.2.4/MBNMAdose/build/partial.rdb |binary MBNMAdose-0.2.4/MBNMAdose/inst/REFERENCES.bib | 14 MBNMAdose-0.2.4/MBNMAdose/inst/doc/mbnmadose.Rmd | 2 MBNMAdose-0.2.4/MBNMAdose/inst/doc/mbnmadose.html | 455 ++++------ MBNMAdose-0.2.4/MBNMAdose/man/MBNMAdose-package.Rd | 10 MBNMAdose-0.2.4/MBNMAdose/man/devplot.Rd | 21 MBNMAdose-0.2.4/MBNMAdose/man/drop.comp.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/figures |only MBNMAdose-0.2.4/MBNMAdose/man/fitplot.Rd | 12 MBNMAdose-0.2.4/MBNMAdose/man/inconsistency.loops.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.emax.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.emax.hill.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.exponential.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.linear.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.run.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/man/mbnma.update.Rd | 12 MBNMAdose-0.2.4/MBNMAdose/man/nma.nodesplit.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/nma.run.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/pDcalc.Rd | 2 MBNMAdose-0.2.4/MBNMAdose/man/plot.mbnma.rank.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/predict.mbnma.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/print.mbnma.predict.Rd | 2 MBNMAdose-0.2.4/MBNMAdose/man/rank.mbnma.predict.Rd |only MBNMAdose-0.2.4/MBNMAdose/man/ref.synth.Rd | 2 MBNMAdose-0.2.4/MBNMAdose/man/summary.nma.nodesplit.Rd | 4 MBNMAdose-0.2.4/MBNMAdose/tests/testthat/test_inconsistency.functions.R | 32 MBNMAdose-0.2.4/MBNMAdose/tests/testthat/test_plot.functions.R | 20 MBNMAdose-0.2.4/MBNMAdose/tests/testthat/test_predict.functions.R | 8 MBNMAdose-0.2.4/MBNMAdose/tests/testthat/test_run.functions.R | 80 - MBNMAdose-0.2.4/MBNMAdose/vignettes/REFERENCES.bib | 14 MBNMAdose-0.2.4/MBNMAdose/vignettes/mbnmadose.Rmd | 2 47 files changed, 493 insertions(+), 478 deletions(-)
Title: Reads Fixed-Width ASCII Data Files (.txt or .dat) that Have
Accompanying Setup Files (.sps or .sas)
Description: Lets you open a fixed-width ASCII file (.txt or
.dat) that has an accompanying setup file (.sps or .sas). These file
combinations are sometimes referred to as .txt+.sps, .txt+.sas,
.dat+.sps, or .dat+.sas. This will only run in a txt-sps or txt-sas
pair in which the setup file contains instructions to open that text
file. It will NOT open other text files, .sav, .sas, or .por data
files. Fixed-width ASCII files with setup files are common in older
(pre-2000) government data.
Author: Jacob Kaplan [aut, cre] (<https://orcid.org/0000-0002-0601-0387>)
Maintainer: Jacob Kaplan <jkkaplan6@gmail.com>
Diff between asciiSetupReader versions 2.1.0 dated 2019-06-28 and 2.2.0 dated 2019-10-08
DESCRIPTION | 9 +++++---- MD5 | 15 +++++++++------ NAMESPACE | 1 + NEWS.md | 5 +++++ R/read_ascii_setup_addin.R |only inst/doc/Introduction_to_asciiSetupReader.html | 4 ++-- inst/doc/making-an-sps-file.html | 4 ++-- inst/doc/parsing-an-sps-or-sas-file.html | 4 ++-- inst/rstudio |only man/read_ascii_setup_addin.Rd |only 10 files changed, 26 insertions(+), 16 deletions(-)
More information about asciiSetupReader at CRAN
Permanent link
Title: Tidy Tools for Forecasting
Description: Tidies up the forecasting modeling and prediction work flow,
extends the 'broom' package
with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions
for various forecasting models,
and enables converting 'forecast' objects to
"tidy" data frames with 'sw_sweep'.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between sweep versions 0.2.1.1 dated 2018-08-19 and 0.2.2 dated 2019-10-08
DESCRIPTION | 21 MD5 | 150 +- NAMESPACE | 98 - NEWS.md | 25 R/global_vars.R | 4 R/sales_data.R | 68 - R/sw_augment.R | 80 - R/sw_glance.R | 82 - R/sw_sweep.R | 333 ++--- R/sw_tidy.R | 97 - R/sw_tidy_decomp.R | 91 - R/sweep-package.R | 44 R/tidiers_HoltWinters.R | 371 +++--- R/tidiers_StructTS.R | 277 ++-- R/tidiers_arima.R | 305 ++-- R/tidiers_bats.R | 375 +++--- R/tidiers_decomposed_ts.R | 141 +- R/tidiers_ets.R | 413 +++--- R/tidiers_nnetar.R | 271 ++-- R/tidiers_robets.R | 413 +++--- R/tidiers_stl.R | 185 +-- R/utils-broom.R | 222 +-- R/utils-forecast.R | 304 ++-- README.md | 241 ++- build/vignette.rds |binary data/bike_sales.rda |binary inst/doc/SW00_Introduction_to_sweep.R | 314 ++--- inst/doc/SW00_Introduction_to_sweep.Rmd | 602 ++++----- inst/doc/SW00_Introduction_to_sweep.html | 1347 ++++++++++++---------- inst/doc/SW01_Forecasting_Time_Series_Groups.R | 264 ++-- inst/doc/SW01_Forecasting_Time_Series_Groups.Rmd | 506 ++++---- inst/doc/SW01_Forecasting_Time_Series_Groups.html | 1127 +++++++++++------- inst/doc/SW02_Forecasting_Multiple_Models.R | 330 ++--- inst/doc/SW02_Forecasting_Multiple_Models.Rmd | 604 ++++----- inst/doc/SW02_Forecasting_Multiple_Models.html | 1185 +++++++++++-------- man/add_index.Rd | 34 man/arima_string.Rd | 34 man/bats_string.Rd | 30 man/bike_sales.Rd | 86 - man/reexports.Rd | 32 man/sw_augment.Rd | 66 - man/sw_augment.default.Rd | 38 man/sw_augment_columns.Rd | 42 man/sw_glance.Rd | 70 - man/sw_glance.default.Rd | 38 man/sw_sweep.Rd | 135 +- man/sw_tidy.Rd | 85 - man/sw_tidy.default.Rd | 38 man/sw_tidy_decomp.Rd | 97 - man/sweep_package.Rd | 46 man/tbats_string.Rd | 30 man/tidiers_HoltWinters.Rd | 199 +-- man/tidiers_StructTS.Rd | 173 +- man/tidiers_arima.Rd | 173 +- man/tidiers_bats.Rd | 197 +-- man/tidiers_decomposed_ts.Rd | 97 - man/tidiers_ets.Rd | 205 +-- man/tidiers_nnetar.Rd | 173 +- man/tidiers_robets.Rd | 205 +-- man/tidiers_stl.Rd | 115 - man/validate_index.Rd | 34 tests/testthat.R | 15 tests/testthat/test_sw_sweep.R | 352 ++--- tests/testthat/test_tidiers_StructTS.R | 120 - tests/testthat/test_tidiers_arima.R | 220 +-- tests/testthat/test_tidiers_bats_tbats.R | 250 ++-- tests/testthat/test_tidiers_decomposed_ts.R | 70 - tests/testthat/test_tidiers_ets.R | 144 +- tests/testthat/test_tidiers_hw.R | 166 +- tests/testthat/test_tidiers_lm.R | 72 - tests/testthat/test_tidiers_nnetar.R | 146 +- tests/testthat/test_tidiers_robets.R | 145 +- tests/testthat/test_tidiers_stl.R | 92 - vignettes/SW00_Introduction_to_sweep.Rmd | 602 ++++----- vignettes/SW01_Forecasting_Time_Series_Groups.Rmd | 506 ++++---- vignettes/SW02_Forecasting_Multiple_Models.Rmd | 604 ++++----- 76 files changed, 8788 insertions(+), 8078 deletions(-)
Title: Searching for Optimal MDS Procedure for Metric and
Interval-Valued Data
Description: Selecting the optimal multidimensional scaling (MDS) procedure for metric data via metric MDS (ratio, interval, mspline) and nonmetric MDS (ordinal). Selecting the optimal multidimensional scaling (MDS) procedure for interval-valued data via metric MDS (ratio, interval, mspline).Selecting the optimal multidimensional scaling procedure for interval-valued data by varying all combinations of normalization and optimization methods.Selecting the optimal MDS procedure for statistical data referring to the evaluation of tourist attractiveness of Lower Silesian counties.
(Borg, I., Groenen, P.J.F., Mair, P. (2013) <doi:10.1007/978-3-642-31848-1>,
Groenen, P.J.F., Winsberg, S., Rodriguez, O., Diday, E. (2006) <doi:10.1016/j.csda.2006.04.003>,
Walesiak, M. (2016) <doi:10.15611/ekt.2016.2.01>,
Walesiak, M. (2017) <doi:10.15611/ekt.2017.3.01>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between mdsOpt versions 0.4-2 dated 2019-08-28 and 0.4-3 dated 2019-10-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/mdsOpt.ltx | 31 +++++++++++++++++-------------- inst/doc/mdsOpt.pdf |binary vignettes/mdsOpt.ltx | 31 +++++++++++++++++-------------- 5 files changed, 42 insertions(+), 36 deletions(-)
Title: Hierarchical Ensemble Methods for Directed Acyclic Graphs
Description: An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).
Author: Marco Notaro [aut, cre] (<https://orcid.org/0000-0003-4309-2200>),
Alessandro Petrini [ctb] (<https://orcid.org/0000-0002-0587-1484>),
Giorgio Valentini [aut] (<https://orcid.org/0000-0002-5694-3919>)
Maintainer: Marco Notaro <marco.notaro@unimi.it>
Diff between HEMDAG versions 2.4.8 dated 2019-05-02 and 2.5.9 dated 2019-10-08
HEMDAG-2.4.8/HEMDAG/R/HEMDAG-defunct.R |only HEMDAG-2.4.8/HEMDAG/R/htd.R |only HEMDAG-2.4.8/HEMDAG/inst/HEMDAG_2.4.8.pdf |only HEMDAG-2.4.8/HEMDAG/man/HEMDAG-defunct.Rd |only HEMDAG-2.5.9/HEMDAG/DESCRIPTION | 9 HEMDAG-2.5.9/HEMDAG/MD5 | 145 - HEMDAG-2.5.9/HEMDAG/NAMESPACE | 50 HEMDAG-2.5.9/HEMDAG/NEWS.md | 80 HEMDAG-2.5.9/HEMDAG/R/GPAV.R | 846 +++--- HEMDAG-2.5.9/HEMDAG/R/HTD.R |only HEMDAG-2.5.9/HEMDAG/R/IO.fun.R | 212 - HEMDAG-2.5.9/HEMDAG/R/TPR-DAG.R | 1363 +++++----- HEMDAG-2.5.9/HEMDAG/R/graph.utility.R | 1377 +++++------ HEMDAG-2.5.9/HEMDAG/R/heuristic.methods.R | 747 +++-- HEMDAG-2.5.9/HEMDAG/R/norm.fun.R | 94 HEMDAG-2.5.9/HEMDAG/R/perf.meas.R | 1290 +++++----- HEMDAG-2.5.9/HEMDAG/R/pkg.attach.R | 2 HEMDAG-2.5.9/HEMDAG/R/pkg.import.R | 18 HEMDAG-2.5.9/HEMDAG/inst/HEMDAG_2.5.9.pdf |only HEMDAG-2.5.9/HEMDAG/inst/extdata/gene2pheno.txt.gz |binary HEMDAG-2.5.9/HEMDAG/man/AUPRC.Rd | 18 HEMDAG-2.5.9/HEMDAG/man/AUROC.Rd | 16 HEMDAG-2.5.9/HEMDAG/man/Do.GPAV.Rd | 58 HEMDAG-2.5.9/HEMDAG/man/Do.GPAV.holdout.Rd | 62 HEMDAG-2.5.9/HEMDAG/man/Do.HTD.Rd | 60 HEMDAG-2.5.9/HEMDAG/man/Do.HTD.holdout.Rd | 64 HEMDAG-2.5.9/HEMDAG/man/Do.flat.scores.normalization.Rd | 16 HEMDAG-2.5.9/HEMDAG/man/Do.full.annotation.matrix.Rd | 26 HEMDAG-2.5.9/HEMDAG/man/Do.heuristic.methods.Rd | 64 HEMDAG-2.5.9/HEMDAG/man/Do.heuristic.methods.holdout.Rd | 68 HEMDAG-2.5.9/HEMDAG/man/FMM.Rd | 44 HEMDAG-2.5.9/HEMDAG/man/GPAV.Rd | 32 HEMDAG-2.5.9/HEMDAG/man/GPAV.over.examples.Rd | 10 HEMDAG-2.5.9/HEMDAG/man/GPAV.parallel.Rd | 14 HEMDAG-2.5.9/HEMDAG/man/HEMDAG-package.Rd | 21 HEMDAG-2.5.9/HEMDAG/man/HTD-DAG.Rd | 8 HEMDAG-2.5.9/HEMDAG/man/Heuristic-Methods.Rd | 36 HEMDAG-2.5.9/HEMDAG/man/Multilabel.F.measure.Rd | 36 HEMDAG-2.5.9/HEMDAG/man/PXR.Rd | 22 HEMDAG-2.5.9/HEMDAG/man/TPR-DAG-cross-validation.Rd | 56 HEMDAG-2.5.9/HEMDAG/man/TPR-DAG-holdout.Rd | 60 HEMDAG-2.5.9/HEMDAG/man/TPR-DAG-variants.Rd | 28 HEMDAG-2.5.9/HEMDAG/man/adj.upper.tri.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/ancestors.Rd | 4 HEMDAG-2.5.9/HEMDAG/man/build.consistent.graph.Rd |only HEMDAG-2.5.9/HEMDAG/man/check.DAG.integrity.Rd | 8 HEMDAG-2.5.9/HEMDAG/man/check.annotation.matrix.integrity.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/children.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/compute.flipped.graph.Rd | 4 HEMDAG-2.5.9/HEMDAG/man/constraints.matrix.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/create.stratified.fold.df.Rd | 16 HEMDAG-2.5.9/HEMDAG/man/descendants.Rd | 4 HEMDAG-2.5.9/HEMDAG/man/distances.from.leaves.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/do.edges.from.HPO.obo.Rd | 7 HEMDAG-2.5.9/HEMDAG/man/do.subgraph.Rd | 10 HEMDAG-2.5.9/HEMDAG/man/do.submatrix.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/do.unstratified.cv.data.Rd | 8 HEMDAG-2.5.9/HEMDAG/man/example.datasets.Rd | 2 HEMDAG-2.5.9/HEMDAG/man/find.best.f.Rd | 44 HEMDAG-2.5.9/HEMDAG/man/find.leaves.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/full.annotation.matrix.Rd | 8 HEMDAG-2.5.9/HEMDAG/man/graph.levels.Rd | 2 HEMDAG-2.5.9/HEMDAG/man/hierarchical.checkers.Rd | 28 HEMDAG-2.5.9/HEMDAG/man/normalize.max.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/parents.Rd | 12 HEMDAG-2.5.9/HEMDAG/man/read.graph.Rd | 4 HEMDAG-2.5.9/HEMDAG/man/read.undirected.graph.Rd | 2 HEMDAG-2.5.9/HEMDAG/man/root.node.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/scores.normalization.Rd | 10 HEMDAG-2.5.9/HEMDAG/man/specific.annotation.list.Rd | 4 HEMDAG-2.5.9/HEMDAG/man/specific.annotation.matrix.Rd | 28 HEMDAG-2.5.9/HEMDAG/man/stratified.cross.validation.Rd | 16 HEMDAG-2.5.9/HEMDAG/man/transitive.closure.annotations.Rd | 6 HEMDAG-2.5.9/HEMDAG/man/tupla.matrix.Rd | 16 HEMDAG-2.5.9/HEMDAG/man/weighted.adjacency.matrix.Rd | 20 HEMDAG-2.5.9/HEMDAG/man/write.graph.Rd | 6 HEMDAG-2.5.9/HEMDAG/src/GPAV.cpp | 180 - 77 files changed, 3841 insertions(+), 3714 deletions(-)
Title: Simplifies Exploratory Data Analysis
Description: Interactive data exploration with one line of code or use an easy to remember set of tidy functions for exploratory data analysis. Introduces three main verbs. explore() to graphically explore a variable or table, describe() to describe a variable or table and report() to create an automated report.
Author: Roland Krasser
Maintainer: Roland Krasser <roland.krasser@gmail.com>
Diff between explore versions 0.5.0 dated 2019-09-19 and 0.5.1 dated 2019-10-08
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 13 ++ R/explore.R | 195 +++++++++++++++++++++++++++++++++++-------- README.md | 18 ++- inst/doc/explore.html | 16 +-- inst/doc/explore_mtcars.html | 4 7 files changed, 205 insertions(+), 61 deletions(-)
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann+rtdists@gmail.com>
Diff between rtdists versions 0.9-0 dated 2018-08-29 and 0.10-0 dated 2019-10-08
DESCRIPTION | 9 MD5 | 22 NEWS | 6 R/lba_race.R | 2 build/vignette.rds |binary inst/doc/reanalysis_rr98.R | 4 inst/doc/reanalysis_rr98.Rmd | 4 inst/doc/reanalysis_rr98.html | 1676 ++++++++++++++++++----------------------- man/Diffusion.Rd | 17 tests/testthat/test-lba-bugs.R | 21 tests/testthat/test-rrd.R | 2 vignettes/reanalysis_rr98.Rmd | 4 12 files changed, 804 insertions(+), 963 deletions(-)
Title: Measurement Units for R Vectors
Description: Support for measurement units in R vectors, matrices
and arrays: automatic propagation, conversion, derivation
and simplification of units; raising errors in case of unit
incompatibility. Compatible with the POSIXct, Date and difftime
classes. Uses the UNIDATA udunits library and unit database for
unit compatibility checking and conversion.
Documentation about 'units' is provided in the paper by Pebesma, Mailund &
Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a
vignette; see 'citation("units")' for details.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Thomas Mailund [aut],
Tomasz Kalinowski [aut],
James Hiebert [ctb],
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between units versions 0.6-4 dated 2019-08-22 and 0.6-5 dated 2019-10-08
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 2 inst/doc/measurement_units_in_R.html | 84 +++++++++++----------- inst/doc/units.html | 131 ++++++++++++++++++----------------- tests/testthat/test_misc.R | 1 6 files changed, 123 insertions(+), 111 deletions(-)
Title: R Interface to the 'Yacas' Computer Algebra System
Description: Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Author: Mikkel Meyer Andersen [aut, cre, cph],
Rob Goedman [aut, cph],
Gabor Grothendieck [aut, cph],
Søren Højsgaard [aut, cph],
Grzegorz Mazur [aut, cph],
Ayal Pinkus [aut, cph],
Nemanja Trifunovic [cph] (UTF-8 part of yacas
(src/yacas/include/yacas/utf8*))
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between Ryacas versions 1.0.0 dated 2019-08-29 and 1.1.0 dated 2019-10-08
Ryacas-1.0.0/Ryacas/R/legacy.R |only Ryacas-1.0.0/Ryacas/man/Clear.Rd |only Ryacas-1.0.0/Ryacas/man/Conjugate.Rd |only Ryacas-1.0.0/Ryacas/man/Eval.Rd |only Ryacas-1.0.0/Ryacas/man/Expand.Rd |only Ryacas-1.0.0/Ryacas/man/Expr.Rd |only Ryacas-1.0.0/Ryacas/man/Exprq.Rd |only Ryacas-1.0.0/Ryacas/man/Factor.Rd |only Ryacas-1.0.0/Ryacas/man/Factorial.Rd |only Ryacas-1.0.0/Ryacas/man/I.Rd |only Ryacas-1.0.0/Ryacas/man/Identity.Rd |only Ryacas-1.0.0/Ryacas/man/Infinity.Rd |only Ryacas-1.0.0/Ryacas/man/Integrate.Rd |only Ryacas-1.0.0/Ryacas/man/Inverse.Rd |only Ryacas-1.0.0/Ryacas/man/InverseTaylor.Rd |only Ryacas-1.0.0/Ryacas/man/Limit.Rd |only Ryacas-1.0.0/Ryacas/man/List.Rd |only Ryacas-1.0.0/Ryacas/man/N.Rd |only Ryacas-1.0.0/Ryacas/man/Newton.Rd |only Ryacas-1.0.0/Ryacas/man/Pi.Rd |only Ryacas-1.0.0/Ryacas/man/Precision.Rd |only Ryacas-1.0.0/Ryacas/man/PrettyForm.Rd |only Ryacas-1.0.0/Ryacas/man/PrettyPrinter.Rd |only Ryacas-1.0.0/Ryacas/man/Ryacas_options.Rd |only Ryacas-1.0.0/Ryacas/man/Set.Rd |only Ryacas-1.0.0/Ryacas/man/SimplifyOld.Rd |only Ryacas-1.0.0/Ryacas/man/Solve.Rd |only Ryacas-1.0.0/Ryacas/man/Subst.Rd |only Ryacas-1.0.0/Ryacas/man/Sym.Rd |only Ryacas-1.0.0/Ryacas/man/Taylor.Rd |only Ryacas-1.0.0/Ryacas/man/TeXForm.Rd |only Ryacas-1.0.0/Ryacas/man/Transpose.Rd |only Ryacas-1.0.0/Ryacas/man/Ver.Rd |only Ryacas-1.0.0/Ryacas/man/as.Sym.Rd |only Ryacas-1.0.0/Ryacas/man/as.expression.Sym.Rd |only Ryacas-1.0.0/Ryacas/man/as.expression.yacas.Rd |only Ryacas-1.0.0/Ryacas/man/as.language.Rd |only Ryacas-1.0.0/Ryacas/man/dep_msg.Rd |only Ryacas-1.0.0/Ryacas/man/deriv.Rd |only Ryacas-1.0.0/Ryacas/man/determinant.Rd |only Ryacas-1.0.0/Ryacas/man/getSyms.Rd |only Ryacas-1.0.0/Ryacas/man/root.Rd |only Ryacas-1.0.0/Ryacas/man/stripvar.Rd |only Ryacas-1.0.0/Ryacas/man/syacas.Rd |only Ryacas-1.0.0/Ryacas/man/y_ls.Rd |only Ryacas-1.0.0/Ryacas/man/yacas.Rd |only Ryacas-1.0.0/Ryacas/man/yacas_evaluate.Rd |only Ryacas-1.0.0/Ryacas/man/yacmode.Rd |only Ryacas-1.1.0/Ryacas/DESCRIPTION | 6 Ryacas-1.1.0/Ryacas/MD5 | 98 +----- Ryacas-1.1.0/Ryacas/NAMESPACE | 56 --- Ryacas-1.1.0/Ryacas/R/internal.R |only Ryacas-1.1.0/Ryacas/R/util.R | 6 Ryacas-1.1.0/Ryacas/R/y-fn.R | 5 Ryacas-1.1.0/Ryacas/R/yac-symbol.R | 237 ++++++++++++++-- Ryacas-1.1.0/Ryacas/README.md | 40 +- Ryacas-1.1.0/Ryacas/inst/NEWS | 7 Ryacas-1.1.0/Ryacas/inst/doc/arbitrary-precision.html | 4 Ryacas-1.1.0/Ryacas/inst/doc/getting-started.html | 4 Ryacas-1.1.0/Ryacas/inst/doc/high-level.R | 47 +++ Ryacas-1.1.0/Ryacas/inst/doc/high-level.Rmd | 104 ++++++- Ryacas-1.1.0/Ryacas/inst/doc/high-level.html | 221 +++++++++++--- Ryacas-1.1.0/Ryacas/inst/doc/latent-variable-model.html | 4 Ryacas-1.1.0/Ryacas/inst/doc/low-level.R | 9 Ryacas-1.1.0/Ryacas/inst/doc/low-level.Rmd | 32 +- Ryacas-1.1.0/Ryacas/inst/doc/low-level.html | 85 +++-- Ryacas-1.1.0/Ryacas/inst/doc/ssm-matrix.html | 4 Ryacas-1.1.0/Ryacas/inst/doc/yacas-rules.html | 6 Ryacas-1.1.0/Ryacas/man/Hessian.Rd |only Ryacas-1.1.0/Ryacas/man/Jacobian.Rd |only Ryacas-1.1.0/Ryacas/man/as.character.yac_symbol.Rd |only Ryacas-1.1.0/Ryacas/man/deriv.yac_symbol.Rd |only Ryacas-1.1.0/Ryacas/man/solve.yac_symbol.Rd | 37 ++ Ryacas-1.1.0/Ryacas/man/sub-sub-.yac_symbol.Rd |only Ryacas-1.1.0/Ryacas/tests/testthat/test-symbol.R | 78 +++++ Ryacas-1.1.0/Ryacas/vignettes/high-level.Rmd | 104 ++++++- Ryacas-1.1.0/Ryacas/vignettes/low-level.Rmd | 32 +- 77 files changed, 937 insertions(+), 289 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [aut, ctb, cph],
Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 0.1-15 dated 2019-10-07 and 0.1-16 dated 2019-10-08
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/simulate_rtmpt.R | 29 ++++++++++++++++++----------- R/simulate_rtmpt_SBC.R | 31 +++++++++++++++++++------------ build/vignette.rds |binary inst/doc/rtmpt_intro.Rmd | 8 ++++---- inst/doc/rtmpt_intro.html | 12 ++++++------ vignettes/rtmpt_intro.Rmd | 8 ++++---- 8 files changed, 62 insertions(+), 48 deletions(-)
Title: Multinomial Processing Tree Models
Description: Fitting and testing multinomial processing tree (MPT) models, a
class of nonlinear models for categorical data. The parameters are the
link probabilities of a tree-like graph and represent the latent cognitive
processing steps executed to arrive at observable response categories
(Batchelder & Riefer, 1999 <doi:10.3758/bf03210812>; Erdfelder et al., 2009
<doi:10.1027/0044-3409.217.3.108>; Riefer & Batchelder, 1988
<doi:10.1037/0033-295x.95.3.318>).
Author: Florian Wickelmaier [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Florian Wickelmaier <wickelmaier@web.de>
Diff between mpt versions 0.6-0 dated 2019-04-25 and 0.6-1 dated 2019-10-08
ChangeLog | 5 +++++ DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- R/mpt.R | 36 +++++++++++++++++++++--------------- R/mptspec.R | 17 +++++++++++++---- build/partial.rdb |binary data/proact.rda |binary data/recogROC.rda |binary data/retroact.rda |binary data/selectiontask.rda |binary man/mptspec.Rd | 5 +++-- 11 files changed, 56 insertions(+), 35 deletions(-)
Title: Wizardry Code Offensive Programming R Documentation
Description: Allows to generate automatically R documentation files from offensive
programming test cases. It populates most of the section of the documentation
content from the offensive programming instrumentation. This reduces greatly the
package producer effort and time to get to a fully documented manual page for
any instrumented function. Following documentation sections are now automatically
filled from instrumentation data: title, description, usage, arguments, value,
author, examples. Sections references, notes and keyword are instrumented to
industrialize their production. Produced manual pages are ready for completion
(e.g note section if needed), language and phrasal adjustments. Main task for
the package producer is now review, no more content production. Refer to
chapter 11 of Offensive Programming Book, Fabien GELINEAU (2019,
ISBN:979-10-699-4075-8), to learn about details and get value from this
package.
Author: Fabien Gelineau <neonira@gmail.com>
Maintainer: Fabien Gelineau <neonira@gmail.com>
Diff between wyz.code.rdoc versions 1.1.6 dated 2019-08-23 and 1.1.7 dated 2019-10-08
wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/abort.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/catn.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/destroySpaces.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/ensureFilenameExtension.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getObjectClassNames.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getObjectFunctionArguments.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getObjectFunctionNames.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getObjectFunctionSignatures.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getRClassTypicalFunctionNames.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/getRObjectClassKind.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/guardExecution.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/normalizeSpaces.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/strBracket.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/strJoin.R |only wyz.code.rdoc-1.1.6/wyz.code.rdoc/R/strParenthesis.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/DESCRIPTION | 12 +- wyz.code.rdoc-1.1.7/wyz.code.rdoc/MD5 | 59 +++++----- wyz.code.rdoc-1.1.7/wyz.code.rdoc/NAMESPACE | 13 +- wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/WrapperObject.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/generateDocumentationContent.R | 50 ++++++-- wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/generateWrapperObject.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/getObjectSignature.R | 17 +- wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/manageSingleStrings.R | 12 +- wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/outOfPackage.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/R/retrievePackageFunctionNames.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/build/partial.rdb |binary wyz.code.rdoc-1.1.7/wyz.code.rdoc/build/vignette.rds |binary wyz.code.rdoc-1.1.7/wyz.code.rdoc/inst/doc/wyz.code.rdoc.Rmd | 22 +++ wyz.code.rdoc-1.1.7/wyz.code.rdoc/inst/doc/wyz.code.rdoc.html | 24 +++- wyz.code.rdoc-1.1.7/wyz.code.rdoc/inst/unit-testing/ut-env.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/inst/unit-testing/ut-generateDocumentationFiles.R | 47 +++---- wyz.code.rdoc-1.1.7/wyz.code.rdoc/inst/unit-testing/ut-generateManualPageFromFunction.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/man/WrapperObject.Rd |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/man/generateWrapperObject.Rd |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/man/getObjectSignature.Rd |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/man/retrievePackageFunctionNames.Rd |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat.R | 10 + wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_createManualPage.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_generateContent.R | 3 wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_generateDocumentationContent.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_generateDocumentationFile.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_generateWrapperObject.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_getObjectSignature.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_manageSingleStrings.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_outOfPackage.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/tests/testthat/test_retrievePackageFunctionNames.R |only wyz.code.rdoc-1.1.7/wyz.code.rdoc/vignettes/wyz.code.rdoc.Rmd | 22 +++ 47 files changed, 196 insertions(+), 95 deletions(-)
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut],
Joe Cheng [aut, cre],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between htmlwidgets versions 1.5 dated 2019-10-04 and 1.5.1 dated 2019-10-08
DESCRIPTION | 6 +-- MD5 | 16 ++++----- build/vignette.rds |binary inst/NEWS | 5 ++ inst/doc/develop_advanced.R | 2 - inst/doc/develop_advanced.html | 19 ++++++---- inst/doc/develop_intro.html | 17 ++++++--- inst/doc/develop_sizing.html | 17 ++++++--- inst/www/htmlwidgets.js | 72 +++++++++++++++++++++++------------------ 9 files changed, 93 insertions(+), 61 deletions(-)
Title: Convolution of Gamma Distributions
Description: Evaluation for density and distribution function of convolution of gamma
distributions in R. Two related exact methods and one approximate method are
implemented with efficient algorithm and C++ code. A quick guide for choosing
correct method and usage of this package is given in package vignette. For the
detail of methods used in this package, we refer the user to
Mathai(1982)<doi:10.1007/BF02481056>,
Moschopoulos(1984)<doi:10.1007/BF02481123>,
Hu et al.(2019)<doi:10.1007/s00180-019-00924-9>.
Author: Chaoran Hu [aut, cre],
Vladimir Pozdnyakov [ths],
Jun Yan [ths]
Maintainer: Chaoran Hu <chaoran.hu@uconn.edu>
Diff between coga versions 1.0.0 dated 2018-05-08 and 1.1.0 dated 2019-10-08
DESCRIPTION | 16 ++- MD5 | 32 ++++--- NEWS.md | 11 ++ R/RcppExports.R | 8 + R/coga.R | 2 R/salvo_method.R |only build/vignette.rds |binary cleanup | 2 configure | 18 ++-- configure.ac | 2 inst/CITATION | 20 +++- inst/doc/quick_guide.pdf |binary inst/include/coga_RcppExports.h | 86 ++++++++++++++++++++ inst/src_vign/quick_guide.Rmd | 7 - man/coga.Rd | 2 src/RcppExports.cpp | 167 ++++++++++++++++++++++++++++++++++++++++ src/approxcoga.cpp | 3 src/salvo_c_part.cpp |only 18 files changed, 334 insertions(+), 42 deletions(-)
Title: Interface to NetCDF Datasets
Description: An interface to the NetCDF file format designed by Unidata
for efficient storage of array-oriented scientific data and descriptions.
This R interface is closely based on the C API of the NetCDF4 library,
and it includes calendar conversions from the Unidata UDUNITS2 library.
Author: Pavel Michna [aut],
Milton Woods [aut, cre]
Maintainer: Milton Woods <miltonjwoods@gmail.com>
Diff between RNetCDF versions 1.9-1 dated 2017-10-08 and 2.0-3 dated 2019-10-08
RNetCDF-1.9-1/RNetCDF/R/load.R.in |only RNetCDF-1.9-1/RNetCDF/R/windows |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits.dat |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits2-accepted.xml |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits2-base.xml |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits2-common.xml |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits2-derived.xml |only RNetCDF-1.9-1/RNetCDF/inst/udunits/udunits2-prefixes.xml |only RNetCDF-1.9-1/RNetCDF/src/RNetCDF.c |only RNetCDF-2.0-3/RNetCDF/COPYING | 39 RNetCDF-2.0-3/RNetCDF/DESCRIPTION | 33 RNetCDF-2.0-3/RNetCDF/INSTALL | 19 RNetCDF-2.0-3/RNetCDF/LICENSE | 34 RNetCDF-2.0-3/RNetCDF/MD5 | 106 RNetCDF-2.0-3/RNetCDF/NEWS | 7 RNetCDF-2.0-3/RNetCDF/R/RNetCDF.R | 2302 ++++++--------- RNetCDF-2.0-3/RNetCDF/R/load.R |only RNetCDF-2.0-3/RNetCDF/README.md | 7 RNetCDF-2.0-3/RNetCDF/cleanup | 2 RNetCDF-2.0-3/RNetCDF/configure | 360 -- RNetCDF-2.0-3/RNetCDF/configure.ac | 87 RNetCDF-2.0-3/RNetCDF/inst/udunits/udunits2.xml | 259 + RNetCDF-2.0-3/RNetCDF/man/00RNetCDF.Rd | 68 RNetCDF-2.0-3/RNetCDF/man/att.copy.nc.Rd | 12 RNetCDF-2.0-3/RNetCDF/man/att.delete.nc.Rd | 10 RNetCDF-2.0-3/RNetCDF/man/att.get.nc.Rd | 30 RNetCDF-2.0-3/RNetCDF/man/att.inq.nc.Rd | 16 RNetCDF-2.0-3/RNetCDF/man/att.put.nc.Rd | 17 RNetCDF-2.0-3/RNetCDF/man/att.rename.nc.Rd | 10 RNetCDF-2.0-3/RNetCDF/man/close.nc.Rd | 6 RNetCDF-2.0-3/RNetCDF/man/create.nc.Rd | 35 RNetCDF-2.0-3/RNetCDF/man/dim.def.nc.Rd | 8 RNetCDF-2.0-3/RNetCDF/man/dim.inq.nc.Rd | 10 RNetCDF-2.0-3/RNetCDF/man/dim.rename.nc.Rd | 6 RNetCDF-2.0-3/RNetCDF/man/file.inq.nc.Rd | 12 RNetCDF-2.0-3/RNetCDF/man/grp.def.nc.Rd |only RNetCDF-2.0-3/RNetCDF/man/grp.inq.nc.Rd |only RNetCDF-2.0-3/RNetCDF/man/grp.rename.nc.Rd |only RNetCDF-2.0-3/RNetCDF/man/open.nc.Rd | 10 RNetCDF-2.0-3/RNetCDF/man/print.nc.Rd | 28 RNetCDF-2.0-3/RNetCDF/man/read.nc.Rd | 39 RNetCDF-2.0-3/RNetCDF/man/sync.nc.Rd | 26 RNetCDF-2.0-3/RNetCDF/man/type.def.nc.Rd |only RNetCDF-2.0-3/RNetCDF/man/type.inq.nc.Rd |only RNetCDF-2.0-3/RNetCDF/man/utcal.nc.Rd | 125 RNetCDF-2.0-3/RNetCDF/man/utinit.nc.Rd | 17 RNetCDF-2.0-3/RNetCDF/man/utinvcal.nc.Rd | 15 RNetCDF-2.0-3/RNetCDF/man/var.def.nc.Rd | 26 RNetCDF-2.0-3/RNetCDF/man/var.get.nc.Rd | 41 RNetCDF-2.0-3/RNetCDF/man/var.inq.nc.Rd | 29 RNetCDF-2.0-3/RNetCDF/man/var.put.nc.Rd | 29 RNetCDF-2.0-3/RNetCDF/man/var.rename.nc.Rd | 6 RNetCDF-2.0-3/RNetCDF/src/Makevars.win | 6 RNetCDF-2.0-3/RNetCDF/src/RNetCDF.h |only RNetCDF-2.0-3/RNetCDF/src/attribute.c |only RNetCDF-2.0-3/RNetCDF/src/common.c |only RNetCDF-2.0-3/RNetCDF/src/common.h |only RNetCDF-2.0-3/RNetCDF/src/convert.c |only RNetCDF-2.0-3/RNetCDF/src/convert.h |only RNetCDF-2.0-3/RNetCDF/src/dataset.c |only RNetCDF-2.0-3/RNetCDF/src/dimension.c |only RNetCDF-2.0-3/RNetCDF/src/group.c |only RNetCDF-2.0-3/RNetCDF/src/init.c |only RNetCDF-2.0-3/RNetCDF/src/type.c |only RNetCDF-2.0-3/RNetCDF/src/udunits.c |only RNetCDF-2.0-3/RNetCDF/src/variable.c |only RNetCDF-2.0-3/RNetCDF/tests/RNetCDF-test.R | 1031 +++++- RNetCDF-2.0-3/RNetCDF/tools/winlibs.R | 2 68 files changed, 2790 insertions(+), 2135 deletions(-)
Title: R Wrappers for EXPOKIT; Other Matrix Functions
Description: Wraps some of the matrix exponentiation
utilities from EXPOKIT (<http://www.maths.uq.edu.au/expokit/>),
a FORTRAN library that is widely recommended for matrix
exponentiation (Sidje RB, 1998. "Expokit: A Software Package
for Computing Matrix Exponentials." ACM Trans. Math. Softw.
24(1): 130-156). EXPOKIT includes functions for
exponentiating both small, dense matrices, and large, sparse
matrices (in sparse matrices, most of the cells have value 0).
Rapid matrix exponentiation is useful in phylogenetics when we
have a large number of states (as we do when we are inferring
the history of transitions between the possible geographic
ranges of a species), but is probably useful in other ways as
well.
Author: Nicholas J. Matzke [aut, cre, cph],
Roger B. Sidje [aut, cph],
Drew Schmidt [aut]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>
Diff between rexpokit versions 0.26.6.4 dated 2019-07-02 and 0.26.6.5 dated 2019-10-08
DESCRIPTION | 8 +- MD5 | 14 ++--- NEWS | 22 +++++++ R/rexpokit-package.R | 4 - inst/CITATION | 2 inst/notes/2019-07-02_submission_email.txt |only inst/notes/src_changes_notes/installation_by_hand_0.26.6.5.txt |only man/00_rexpokit-package.Rd | 4 - src/my_expokit.f | 28 ++++++++-- 9 files changed, 63 insertions(+), 19 deletions(-)
Title: Download and Tidy Time Series Data from the Australian Bureau of
Statistics
Description: Downloads, imports, and tidies time series data from the
Australian Bureau of Statistics <https://www.abs.gov.au/>.
Author: Matt Cowgill [aut, cre],
Zoe Meers [aut],
Jaron Lee [aut],
David Diviny [ctb],
Hugh Parsonage [ctb]
Maintainer: Matt Cowgill <mattcowgill@gmail.com>
Diff between readabs versions 0.4.1 dated 2019-08-20 and 0.4.2 dated 2019-10-08
DESCRIPTION | 18 - MD5 | 59 +++-- NEWS.md | 3 R/download_abs.R | 2 R/extract_abs_sheets.R | 5 R/read_abs.R | 27 +- R/read_abs_data.R | 6 R/read_abs_local.R | 5 R/read_cpi.R | 2 R/zzz.R |only README.md | 49 ++-- build/vignette.rds |binary inst/doc/readabs_vignette.R | 3 inst/doc/readabs_vignette.Rmd | 19 + inst/doc/readabs_vignette.html | 442 ++++++++++++++++++++--------------------- man/extract_abs_sheets.Rd | 5 man/read_abs.Rd | 30 ++ man/read_abs_local.Rd | 6 man/read_cpi.Rd | 4 tests/testthat/test_readabs.R | 2 vignettes/data |only vignettes/readabs_vignette.Rmd | 19 + 22 files changed, 400 insertions(+), 306 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-03 0.9.4
2018-05-06 0.9.2
2018-04-21 0.9.1
2012-10-08 0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-18 1.0.2
Title: Genomic Simulation of Purebred and Crossbred Populations
Description: Simulation of purebred and crossbred genomic data as well as pedigree and phenotypes are possible by this package. 'xbreed' can be used for the simulation of populations with flexible genome structures and trait genetic architectures. It can also be used to evaluate breeding schemes and generate genetic data to test statistical tools.
Author: Hadi Esfandyari [aut, cre],
Anders Christian Sørensen [aut]
Maintainer: Hadi Esfandyari <esfandyari.hadi@gmail.com>
Diff between xbreed versions 1.0.1 dated 2017-04-03 and 1.0.1.1 dated 2019-10-08
DESCRIPTION | 6 MD5 | 12 build/vignette.rds |binary inst/doc/xbreedvignette.R | 2126 +++++++++++++++++++++---------------------- inst/doc/xbreedvignette.Rmd | 3 inst/doc/xbreedvignette.pdf |binary vignettes/xbreedvignette.Rmd | 3 7 files changed, 1076 insertions(+), 1074 deletions(-)
Title: Fast Implementation of a Key-Value Store
Description: Fast implementation of a key-value store. Environments are commonly
used as key-value stores, but every time a new key is used, it is added to
R's global symbol table, causing a small amount of memory leakage. This can
be problematic in cases where many different keys are used. Fastmap avoids
this memory leak issue by implementing the map using data structures in C++.
Author: Winston Chang [aut, cre],
RStudio [cph, fnd],
Tessil [cph] (hopscotch_map library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between fastmap versions 1.0.0 dated 2019-07-28 and 1.0.1 dated 2019-10-08
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS.md |only README.md | 10 ++++++---- src/fastmap.cpp | 1 + 5 files changed, 15 insertions(+), 11 deletions(-)