Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general engine for big data
processing, see <http://spark.apache.org>. This package supports connecting to
local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end,
and provides an interface to Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut, cre],
Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between sparklyr versions 0.7.0 dated 2018-01-23 and 0.8.0 dated 2018-04-30
sparklyr-0.7.0/sparklyr/inst/livy/spark-1.5.2/livyutils.scala |only sparklyr-0.7.0/sparklyr/java/spark-1.6.0/rdd.scala |only sparklyr-0.7.0/sparklyr/java/spark-1.6.0/worker.scala |only sparklyr-0.7.0/sparklyr/man/ml_tree_feature_importance.Rd |only sparklyr-0.7.0/sparklyr/tests/testthat/log4j.spark.log |only sparklyr-0.7.0/sparklyr/tests/testthat/log4j.spark.log.2018-01-18 |only sparklyr-0.7.0/sparklyr/tests/testthat/logs |only sparklyr-0.7.0/sparklyr/tests/testthat/output/print/cross-validator-model.txt |only sparklyr-0.8.0/sparklyr/DESCRIPTION | 15 sparklyr-0.8.0/sparklyr/MD5 | 395 - sparklyr-0.8.0/sparklyr/NAMESPACE | 26 sparklyr-0.8.0/sparklyr/NEWS.md | 109 sparklyr-0.8.0/sparklyr/R/connection_shinyapp.R | 2 sparklyr-0.8.0/sparklyr/R/connection_spark.R | 22 sparklyr-0.8.0/sparklyr/R/core_jobj.R | 1 sparklyr-0.8.0/sparklyr/R/core_serialize.R | 20 sparklyr-0.8.0/sparklyr/R/core_worker_config.R | 4 sparklyr-0.8.0/sparklyr/R/data_interface.R | 2 sparklyr-0.8.0/sparklyr/R/dplyr_sql.R | 28 sparklyr-0.8.0/sparklyr/R/install_spark_versions.R | 22 sparklyr-0.8.0/sparklyr/R/install_tools.R | 1 sparklyr-0.8.0/sparklyr/R/livy_connection.R | 130 sparklyr-0.8.0/sparklyr/R/livy_install.R | 24 sparklyr-0.8.0/sparklyr/R/livy_sources.R | 23 sparklyr-0.8.0/sparklyr/R/ml_classification_decision_tree_classifier.R | 7 sparklyr-0.8.0/sparklyr/R/ml_classification_gbt_classifier.R | 17 sparklyr-0.8.0/sparklyr/R/ml_classification_linear_svc.R | 5 sparklyr-0.8.0/sparklyr/R/ml_classification_logistic_regression.R | 43 sparklyr-0.8.0/sparklyr/R/ml_classification_multilayer_perceptron_classifier.R | 3 sparklyr-0.8.0/sparklyr/R/ml_classification_naive_bayes.R | 7 sparklyr-0.8.0/sparklyr/R/ml_classification_one_vs_rest.R | 3 sparklyr-0.8.0/sparklyr/R/ml_classification_random_forest_classifier.R | 8 sparklyr-0.8.0/sparklyr/R/ml_clustering_bisecting_kmeans.R | 3 sparklyr-0.8.0/sparklyr/R/ml_clustering_gaussian_mixture.R | 3 sparklyr-0.8.0/sparklyr/R/ml_clustering_kmeans.R | 16 sparklyr-0.8.0/sparklyr/R/ml_clustering_lda.R | 28 sparklyr-0.8.0/sparklyr/R/ml_evaluation_clustering.R |only sparklyr-0.8.0/sparklyr/R/ml_evaluation_prediction.R |only sparklyr-0.8.0/sparklyr/R/ml_evaluator.R | 232 sparklyr-0.8.0/sparklyr/R/ml_feature_count_vectorizer.R | 8 sparklyr-0.8.0/sparklyr/R/ml_feature_feature_hasher.R |only sparklyr-0.8.0/sparklyr/R/ml_feature_pca.R | 12 sparklyr-0.8.0/sparklyr/R/ml_feature_quantile_discretizer_bucketizer.R | 124 sparklyr-0.8.0/sparklyr/R/ml_feature_stop_words_remover.R | 4 sparklyr-0.8.0/sparklyr/R/ml_feature_string_indexer.R | 34 sparklyr-0.8.0/sparklyr/R/ml_feature_string_indexer_model.R |only sparklyr-0.8.0/sparklyr/R/ml_helpers.R |only sparklyr-0.8.0/sparklyr/R/ml_mapping_tables.R | 15 sparklyr-0.8.0/sparklyr/R/ml_model_constructors.R | 2 sparklyr-0.8.0/sparklyr/R/ml_model_decision_tree.R | 2 sparklyr-0.8.0/sparklyr/R/ml_model_gradient_boosted_trees.R | 4 sparklyr-0.8.0/sparklyr/R/ml_model_random_forest.R | 13 sparklyr-0.8.0/sparklyr/R/ml_model_utils.R | 30 sparklyr-0.8.0/sparklyr/R/ml_persistence.R | 6 sparklyr-0.8.0/sparklyr/R/ml_print_utils.R | 41 sparklyr-0.8.0/sparklyr/R/ml_regression_aft_survival_regression.R | 5 sparklyr-0.8.0/sparklyr/R/ml_regression_decision_tree_regressor.R | 8 sparklyr-0.8.0/sparklyr/R/ml_regression_gbt_regressor.R | 17 sparklyr-0.8.0/sparklyr/R/ml_regression_generalized_linear_regression.R | 17 sparklyr-0.8.0/sparklyr/R/ml_regression_isotonic_regression.R | 3 sparklyr-0.8.0/sparklyr/R/ml_regression_linear_regression.R | 19 sparklyr-0.8.0/sparklyr/R/ml_regression_random_forest_regressor.R | 9 sparklyr-0.8.0/sparklyr/R/ml_stat.R |only sparklyr-0.8.0/sparklyr/R/ml_transformation_methods.R | 41 sparklyr-0.8.0/sparklyr/R/ml_tuning.R | 37 sparklyr-0.8.0/sparklyr/R/ml_tuning_cross_validator.R | 18 sparklyr-0.8.0/sparklyr/R/ml_tuning_train_validation_split.R | 18 sparklyr-0.8.0/sparklyr/R/ml_validator_feature.R | 10 sparklyr-0.8.0/sparklyr/R/mutation.R | 30 sparklyr-0.8.0/sparklyr/R/shell_connection.R | 8 sparklyr-0.8.0/sparklyr/R/spark_apply.R | 44 sparklyr-0.8.0/sparklyr/R/spark_compile.R | 7 sparklyr-0.8.0/sparklyr/R/spark_compile_embedded.R | 10 sparklyr-0.8.0/sparklyr/R/spark_connection.R | 17 sparklyr-0.8.0/sparklyr/R/spark_debug_backend.R | 2 sparklyr-0.8.0/sparklyr/R/spark_utils.R | 4 sparklyr-0.8.0/sparklyr/R/sysdata.rda |binary sparklyr-0.8.0/sparklyr/R/worker_apply.R | 17 sparklyr-0.8.0/sparklyr/R/worker_main.R | 14 sparklyr-0.8.0/sparklyr/R/yarn_cluster.R | 4 sparklyr-0.8.0/sparklyr/README.md | 384 - sparklyr-0.8.0/sparklyr/inst/extdata/versions.json | 12 sparklyr-0.8.0/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-0.8.0/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-0.8.0/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-0.8.0/sparklyr/inst/java/sparklyr-2.1-2.11.jar |binary sparklyr-0.8.0/sparklyr/inst/java/sparklyr-2.2-2.11.jar |binary sparklyr-0.8.0/sparklyr/inst/java/sparklyr-2.3-2.11.jar |only sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/backend.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/channel.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/handler.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/invoke.scala | 48 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/logger.scala | 3 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/mlutils.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/serializer.scala | 18 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/stream.scala | 92 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/tracker.scala | 12 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.5.2/utils.scala | 15 sparklyr-0.8.0/sparklyr/inst/livy/spark-1.6.0 |only sparklyr-0.8.0/sparklyr/inst/livy/spark-2.0.0/livyutils.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-2.0.0/mlutils2.scala |only sparklyr-0.8.0/sparklyr/inst/livy/spark-2.3.0 |only sparklyr-0.8.0/sparklyr/java/spark-1.5.2/backend.scala | 47 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/channel.scala | 38 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/handler.scala | 47 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/invoke.scala | 48 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/serializer.scala | 18 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/stream.scala | 92 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/test.scala | 4 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/tracker.scala | 12 sparklyr-0.8.0/sparklyr/java/spark-1.5.2/utils.scala | 15 sparklyr-0.8.0/sparklyr/java/spark-1.6.0/classutils.scala | 2 sparklyr-0.8.0/sparklyr/java/spark-1.6.0/fileutils.scala | 6 sparklyr-0.8.0/sparklyr/java/spark-1.6.0/rscript.scala | 94 sparklyr-0.8.0/sparklyr/java/spark-1.6.0/sources.scala | 2432 +++++----- sparklyr-0.8.0/sparklyr/java/spark-1.6.0/workercontext.scala |only sparklyr-0.8.0/sparklyr/java/spark-1.6.0/workerhelper.scala |only sparklyr-0.8.0/sparklyr/java/spark-1.6.0/workerrdd.scala |only sparklyr-0.8.0/sparklyr/java/spark-2.3.0 |only sparklyr-0.8.0/sparklyr/man/ft_binarizer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_bucketizer.Rd | 13 sparklyr-0.8.0/sparklyr/man/ft_chisq_selector.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_count_vectorizer.Rd | 8 sparklyr-0.8.0/sparklyr/man/ft_dct.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_elementwise_product.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_feature_hasher.Rd |only sparklyr-0.8.0/sparklyr/man/ft_hashing_tf.Rd | 3 sparklyr-0.8.0/sparklyr/man/ft_idf.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_imputer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_index_to_string.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_interaction.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_lsh.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_max_abs_scaler.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_min_max_scaler.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_ngram.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_normalizer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_one_hot_encoder.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_pca.Rd | 14 sparklyr-0.8.0/sparklyr/man/ft_polynomial_expansion.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_quantile_discretizer.Rd | 20 sparklyr-0.8.0/sparklyr/man/ft_r_formula.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_regex_tokenizer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_standard_scaler.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_stop_words_remover.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_string_indexer.Rd | 19 sparklyr-0.8.0/sparklyr/man/ft_tokenizer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_vector_assembler.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_vector_indexer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_vector_slicer.Rd | 1 sparklyr-0.8.0/sparklyr/man/ft_word2vec.Rd | 1 sparklyr-0.8.0/sparklyr/man/livy_config.Rd | 5 sparklyr-0.8.0/sparklyr/man/livy_install.Rd | 2 sparklyr-0.8.0/sparklyr/man/ml-transform-methods.Rd | 2 sparklyr-0.8.0/sparklyr/man/ml-tuning.Rd | 32 sparklyr-0.8.0/sparklyr/man/ml_chisquare_test.Rd |only sparklyr-0.8.0/sparklyr/man/ml_clustering_evaluator.Rd |only sparklyr-0.8.0/sparklyr/man/ml_corr.Rd |only sparklyr-0.8.0/sparklyr/man/ml_default_stop_words.Rd | 4 sparklyr-0.8.0/sparklyr/man/ml_evaluator.Rd | 4 sparklyr-0.8.0/sparklyr/man/ml_feature_importances.Rd |only sparklyr-0.8.0/sparklyr/man/ml_generalized_linear_regression.Rd | 10 sparklyr-0.8.0/sparklyr/man/ml_gradient_boosted_trees.Rd | 38 sparklyr-0.8.0/sparklyr/man/ml_kmeans.Rd | 8 sparklyr-0.8.0/sparklyr/man/ml_lda.Rd | 3 sparklyr-0.8.0/sparklyr/man/ml_linear_regression.Rd | 11 sparklyr-0.8.0/sparklyr/man/spark-connections.Rd | 2 sparklyr-0.8.0/sparklyr/man/spark_apply.Rd | 25 sparklyr-0.8.0/sparklyr/man/spark_connection-class.Rd |only sparklyr-0.8.0/sparklyr/man/spark_install.Rd | 4 sparklyr-0.8.0/sparklyr/man/spark_install_sync.Rd | 1 sparklyr-0.8.0/sparklyr/man/spark_jobj-class.Rd |only sparklyr-0.8.0/sparklyr/man/spark_write_csv.Rd | 2 sparklyr-0.8.0/sparklyr/man/sql-transformer.Rd | 1 sparklyr-0.8.0/sparklyr/tests/testthat/helper-initialize.R | 6 sparklyr-0.8.0/sparklyr/tests/testthat/output/print/aft-model.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/decision-tree.txt | 2 sparklyr-0.8.0/sparklyr/tests/testthat/output/print/decision_tree_classifier.txt | 2 sparklyr-0.8.0/sparklyr/tests/testthat/output/print/glm-summary.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/glm.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/linear-regression-summary.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/linear-regression.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/logreg.txt |only sparklyr-0.8.0/sparklyr/tests/testthat/output/print/naive_bayes.txt | 2 sparklyr-0.8.0/sparklyr/tests/testthat/test-binds.R | 8 sparklyr-0.8.0/sparklyr/tests/testthat/test-copy-to.R | 14 sparklyr-0.8.0/sparklyr/tests/testthat/test-dplyr.R | 23 sparklyr-0.8.0/sparklyr/tests/testthat/test-invoke.R | 61 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-backwards-compat.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-clustering-kmeans.R | 9 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-clustering-lda.R | 26 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-evaluation-clustering.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-bucketizer.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-estimator-transformers.R | 33 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-feature-hasher.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-sql-transformer.R | 1 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-standard-transformers.R | 39 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-stop-words-remover.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-feature-string-indexer.R | 25 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-helpers.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-persistence.R | 7 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-pipeline-utils.R | 21 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-print-methods.R | 31 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-regression-generalized-linear-regression.R | 30 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-regression-linear-regression.R | 24 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-regression-survival-regression.R | 2 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-stat-chisq.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-stat-corr.R |only sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-supervised-decision-tree.R | 10 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-supervised-gradient-boosted-trees.R | 19 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-supervised-random-forest.R | 10 sparklyr-0.8.0/sparklyr/tests/testthat/test-ml-tuning.R | 90 sparklyr-0.8.0/sparklyr/tests/testthat/test-read-write.R | 35 sparklyr-0.8.0/sparklyr/tests/testthat/test-spark-apply.R | 48 sparklyr-0.8.0/sparklyr/tests/testthat/test-zzz-livy.R | 22 sparklyr-0.8.0/sparklyr/tools/readme/ggplot2-1.png |binary sparklyr-0.8.0/sparklyr/tools/readme/sparklyr-package.png |only 216 files changed, 3561 insertions(+), 2586 deletions(-)
Title: SODA: Main and Interaction Effects Selection for Logistic
Regression, Quadratic Discriminant and General Index Models
Description: Variable and interaction selection are essential to classification in high-dimensional setting. In this package, we provide the implementation of SODA procedure, which is a forward-backward algorithm that selects both main and interaction effects under logistic regression and quadratic discriminant analysis. We also provide an extension, S-SODA, for dealing with the variable selection problem for semi-parametric models with continuous responses.
Author: Yang Li, Jun S. Liu
Maintainer: Yang Li <yangli.stat@gmail.com>
Diff between sodavis versions 1.0 dated 2017-05-29 and 1.1 dated 2018-04-30
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/pure_soda.R | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Interactive Visual and Numerical Diagnostics and Posterior
Analysis for Bayesian Models
Description: A graphical user interface for interactive Markov chain Monte
Carlo (MCMC) diagnostics and plots and tables helpful for analyzing a
posterior sample. The interface is powered by the 'Shiny' web
application framework from 'RStudio' and works with the output of MCMC
programs written in any programming language (and has extended
functionality for 'Stan' models fit using the 'rstan' and 'rstanarm'
packages).
Author: Jonah Gabry [aut, cre],
Stan Development Team [ctb],
Michael Andreae [ctb],
Michael Betancourt [ctb],
Bob Carpenter [ctb],
Yuanjun Gao [ctb],
Andrew Gelman [ctb],
Ben Goodrich [ctb],
Daniel Lee [ctb],
Dongying Song [ctb],
Rob Trangucci [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between shinystan versions 2.4.0 dated 2017-08-02 and 2.5.0 dated 2018-04-30
shinystan-2.4.0/shinystan/inst/CITATION |only shinystan-2.5.0/shinystan/DESCRIPTION | 14 +- shinystan-2.5.0/shinystan/MD5 | 35 +++---- shinystan-2.5.0/shinystan/NEWS.md | 31 ++++-- shinystan-2.5.0/shinystan/R/launch_shinystan.R | 4 shinystan-2.5.0/shinystan/R/shinystan-objects.R | 30 +++++- shinystan-2.5.0/shinystan/R/shinystan-package.R | 47 +++++---- shinystan-2.5.0/shinystan/build/vignette.rds |binary shinystan-2.5.0/shinystan/data/eight_schools.rda |binary shinystan-2.5.0/shinystan/inst/ShinyStan/ui_files/pp_about.R | 10 -- shinystan-2.5.0/shinystan/inst/doc/deploy_shinystan.html | 2 shinystan-2.5.0/shinystan/inst/doc/shinystan-package.Rmd | 23 +++- shinystan-2.5.0/shinystan/inst/doc/shinystan-package.html | 18 ++- shinystan-2.5.0/shinystan/man/figures/stanlogo.png |binary shinystan-2.5.0/shinystan/man/launch_shinystan.Rd | 11 ++ shinystan-2.5.0/shinystan/man/shinystan-class.Rd | 6 + shinystan-2.5.0/shinystan/man/shinystan-package.Rd | 53 +++++++---- shinystan-2.5.0/shinystan/tests/testthat/test_misc.R | 12 ++ shinystan-2.5.0/shinystan/vignettes/shinystan-package.Rmd | 23 +++- 19 files changed, 214 insertions(+), 105 deletions(-)
Title: Multi-Species sIZE Spectrum Modelling in R
Description: A set of classes and methods to set up and run multi-species, trait
based and community size spectrum ecological models, focused on the marine
environment.
Author: Finlay Scott [aut, cph],
Julia Blanchard [aut, cph],
Ken Andersen [aut, cph],
Gustav Delius [ctb, cre],
Richard Southwell [ctb]
Maintainer: Gustav Delius <gustav.delius@york.ac.uk>
Diff between mizer versions 0.4 dated 2017-12-14 and 1.0 dated 2018-04-30
DESCRIPTION | 17 MD5 | 125 ++- NAMESPACE | 10 NEWS | 37 + R/MizerParams-class.R | 180 ++++- R/MizerSim-class.R | 52 - R/data.R | 13 R/help.R | 5 R/plots.R | 1001 ++++++++++++++++++++++++++----- R/project.R | 88 +- R/project_methods.R | 183 +++-- R/summary_methods.R | 34 - R/wrapper_functions.R | 895 +++++++++++++++++++++++++++ README.md | 2 build/vignette.rds |binary inst/doc/mizer_vignette.R | 184 +++++ inst/doc/mizer_vignette.Rnw | 807 +++++++++++++++++++++++- inst/doc/mizer_vignette.pdf |binary inst/shiny |only man/MizerParams-class.Rd | 37 + man/MizerSim-class.Rd | 2 man/NS_species_params.Rd | 7 man/NS_species_params_gears.Rd | 6 man/addSpecies.Rd |only man/display_frames.Rd |only man/getBiomass.Rd | 2 man/getBiomassFrame.Rd |only man/getEGrowth.Rd | 8 man/getEReproAndGrowth.Rd | 2 man/getESpawning.Rd | 9 man/getFMort.Rd | 15 man/getFeedingLevel.Rd | 10 man/getM2.Rd | 6 man/getM2Background.Rd | 8 man/getMeanMaxWeight.Rd | 2 man/getMeanWeight.Rd | 2 man/getPhiPrey.Rd | 9 man/getPredRate.Rd | 2 man/getRDD.Rd | 4 man/getRDI.Rd | 2 man/getSSBFrame.Rd |only man/getZ.Rd | 8 man/get_initial_n.Rd | 2 man/log_breaks.Rd |only man/mizer.Rd | 2 man/plotBiomass.Rd | 51 + man/plotFMort.Rd | 16 man/plotFeedingLevel.Rd | 20 man/plotGrowthCurves.Rd |only man/plotM2.Rd | 26 man/plotMizerSim.Rd | 2 man/plotSpectra.Rd | 69 +- man/plotYield.Rd | 47 + man/plotYieldGear.Rd | 29 man/project.Rd | 31 man/retune_abundance.Rd |only man/setBackground.Rd |only man/set_scaling_model.Rd |only man/set_trait_model.Rd | 9 man/steady.Rd |only man/wrapper_functions.Rd |only tests/testthat/test-MizerSim.R | 26 tests/testthat/test-project.R | 143 +++- tests/testthat/test-project_methods.R | 6 tests/testthat/test-summary_methods.R | 16 tests/testthat/test-wrapper_functions.R | 31 vignettes/mizer_vignette-concordance.tex |only vignettes/mizer_vignette.Rnw | 807 +++++++++++++++++++++++- vignettes/reflib.bib | 47 + 69 files changed, 4471 insertions(+), 683 deletions(-)
Title: R to Symbolic Data Analysis
Description: Symbolic Data Analysis (SDA) was proposed by professor Edwin Diday in 1987, the main purpose of SDA is to substitute the set of rows (cases) in the data table for a concept (second order statistical unit). This package implements, to the symbolic case, certain techniques of automatic classification, as well as some linear models.
Author: Oldemar Rodriguez R. with contributions from Carlos Aguero, Olger Calderon, Roberto Zuniga and Jorge Arce
Maintainer: Oldemar Rodriguez <oldemar.rodriguez@ucr.ac.cr>
Diff between RSDA versions 2.0.3 dated 2018-02-14 and 2.0.4 dated 2018-04-30
DESCRIPTION | 11 MD5 | 68 ++-- NAMESPACE | 12 R/RSDA.R | 2 R/calculate.probs.R | 3 R/classic.to.sym.R | 552 +++++++++++++++++++++++++------------- R/data.R | 14 R/dist.interval.R | 4 R/sym.continuos.plot.R | 13 R/sym.hist.plot.R | 13 R/sym.interval.pc.2.j.r | 20 - R/sym.interval.pc.R | 67 ++-- R/sym.interval.pc.limits.2.j.r | 17 - R/sym.interval.pc.limits.R | 19 - R/sym.interval.pca.limits.new.j.r | 16 - R/sym.interval.plot.R | 13 R/sym.modal.plot.R | 4 R/sym.radar.plot.R | 28 - R/sym.set.plot.R | 7 man/USCrime.Rd | 5 man/add_concept.Rd |only man/classic.to.sym.Rd | 28 + man/create.meta.data.Rd |only man/ex1_db2so.Rd | 7 man/extract_length_starts.Rd |only man/extract_sym_types.Rd |only man/facedata.Rd | 2 man/read.sym.table.Rd | 2 man/remove_meta_info.Rd |only man/spark_bar.Rd |only man/sym.continuos.plot.Rd | 9 man/sym.dist.interval.Rd | 4 man/sym.hist.plot.Rd | 9 man/sym.interval.pc.Rd | 3 man/sym.interval.plot.Rd | 9 man/type.continuous.Rd |only man/type.histogram.Rd |only man/type.interval.Rd |only man/type.modal.Rd |only man/type.set.Rd |only man/type.symbolic.Rd |only 41 files changed, 615 insertions(+), 346 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (see 'citation("recmap")' for details). This algorithm
draws maps according to a given statistical value (e.g., election results,
population or epidemiological data). The basic idea of the RecMap algorithm is
that each map region (e.g., different countries) is represented by a
rectangle. The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about RecMap is
provided by a vignette included in this package.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 0.5.31 dated 2018-03-24 and 0.5.33 dated 2018-04-30
recmap-0.5.31/recmap/inst/shiny-examples/US.county |only recmap-0.5.31/recmap/inst/shiny-examples/state.x77 |only recmap-0.5.31/recmap/src/recmap.h |only recmap-0.5.31/recmap/tests/testthat/test-recmapGA.R |only recmap-0.5.33/recmap/DESCRIPTION | 10 recmap-0.5.33/recmap/MD5 | 54 - recmap-0.5.33/recmap/NAMESPACE | 1 recmap-0.5.33/recmap/R/recmap.R | 58 + recmap-0.5.33/recmap/README.md | 7 recmap-0.5.33/recmap/build/partial.rdb |binary recmap-0.5.33/recmap/build/vignette.rds |binary recmap-0.5.33/recmap/data/jss2711.RData |binary recmap-0.5.33/recmap/inst/NEWS.Rd | 14 recmap-0.5.33/recmap/inst/doc/recmap.R | 53 - recmap-0.5.33/recmap/inst/doc/recmap.Rmd | 62 - recmap-0.5.33/recmap/inst/doc/recmap.html | 311 +++---- recmap-0.5.33/recmap/inst/include |only recmap-0.5.33/recmap/inst/shiny-examples/server.R |only recmap-0.5.33/recmap/inst/shiny-examples/ui.R |only recmap-0.5.33/recmap/man/jss2711.Rd | 291 +++++- recmap-0.5.33/recmap/man/recmap.Rd | 1 recmap-0.5.33/recmap/src/Makevars |only recmap-0.5.33/recmap/src/Makevars.win |only recmap-0.5.33/recmap/src/Rrecmap.cpp | 2 recmap-0.5.33/recmap/tests/testthat/test-get_angle.R | 8 recmap-0.5.33/recmap/tests/testthat/test-jss2711.R |only recmap-0.5.33/recmap/tests/testthat/test-recmap.R | 2 recmap-0.5.33/recmap/tests/testthat/test-recmapGRASP.R |only recmap-0.5.33/recmap/tests/testthat/test-sp.R | 17 recmap-0.5.33/recmap/tests/testthat/test-topoloy_error.R | 2 recmap-0.5.33/recmap/vignettes/jss2711.bib | 652 ++++++--------- recmap-0.5.33/recmap/vignettes/recmap.Rmd | 62 - 32 files changed, 907 insertions(+), 700 deletions(-)
Title: Fetch Species Origin Data from the Web
Description: Get species origin data (whether species is native/invasive) from the
following sources on the web: Encyclopedia of Life (<http://eol.org>), Flora
'Europaea' (<http://rbg-web2.rbge.org.uk/FE/fe.html>), Global Invasive Species
Database (<http://www.iucngisd.org/gisd>), the Native Species Resolver
(<http://bien.nceas.ucsb.edu/bien/tools/nsr/nsr-ws/>), Integrated Taxonomic
Information Service (<http://www.itis.gov/>), and Global Register of
Introduced and Invasive Species (<http://www.griis.org/>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Ignasi Bartomeus [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between originr versions 0.2.0 dated 2016-12-07 and 0.3.0 dated 2018-04-30
DESCRIPTION | 27 ++-- LICENSE | 2 MD5 | 53 ++++---- NAMESPACE | 8 - NEWS.md | 14 ++ R/eol.R | 230 ++++++++++++++++++++++------------- R/flora_europaea.R | 54 ++++---- R/gisd.R | 26 ++- R/globals.R |only R/griis.R | 12 + R/is_native.R | 7 - R/nsr.R | 43 ++++-- R/originr-package.R | 24 +++ R/zzz.R | 16 ++ README.md | 4 data |only man/eol.Rd | 113 ++++++++++------- man/flora_europaea.Rd | 34 ++--- man/gisd.Rd | 13 + man/griis.Rd | 9 - man/is_native.Rd | 3 man/nsr.Rd | 24 ++- man/nsr_countries.Rd |only man/nsr_pol_divisions.Rd |only man/originr-package.Rd | 14 +- tests/testthat/test-eol.R | 9 - tests/testthat/test-flora_europaea.R | 6 tests/testthat/test-gisd.R | 4 tests/testthat/test-nsr.R | 4 29 files changed, 468 insertions(+), 285 deletions(-)
Title: Get Landsat 8 Data from Amazon Public Data Sets
Description: Get Landsat 8 Data from Amazon Web Services ('AWS')
public data sets (<https://registry.opendata.aws/landsat-8/>).
Includes functions for listing images and fetching them, and handles
caching to prevent unnecessary additional requests.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between getlandsat versions 0.1.0 dated 2016-08-16 and 0.2.0 dated 2018-04-30
DESCRIPTION | 25 ++++++++------- LICENSE | 2 - MD5 | 52 ++++++++++++++++----------------- NAMESPACE | 4 -- NEWS.md | 9 +++++ R/cache.R | 24 ++++++++------- R/getlandsat-package.R | 5 +-- R/lsat_image.R | 16 +++++----- R/lsat_list.R | 14 ++++---- R/lsat_scenes.R | 16 +++++----- R/lsat_scenes_files.R | 8 ++--- R/zzz.R | 18 +++++------ README.md | 52 +++++++++++++++++---------------- build/vignette.rds |binary inst/doc/getlandsat_vignette.Rmd | 2 - inst/doc/getlandsat_vignette.html | 2 - inst/img/unnamed-chunk-9-1.png |binary inst/vign/getlandsat_vignette.Rmd | 2 - inst/vign/getlandsat_vignette.md | 2 - man/getlandsat-package.Rd | 5 +-- man/lsat_cache.Rd | 22 +++++++------ man/lsat_image.Rd | 13 ++++---- man/lsat_list.Rd | 10 ++---- man/lsat_scene_files.Rd | 11 +++--- man/lsat_scenes.Rd | 15 ++++----- tests/testthat/test-lsat_scene_files.R | 4 -- vignettes/getlandsat_vignette.Rmd | 2 - 27 files changed, 172 insertions(+), 163 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Also contains two-stage binomial modelling that can do pairwise odds-ratio
dependence modelling based marginal logistic regression models. This is an
alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst and Thomas Scheike
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.2.3 dated 2018-02-09 and 1.2.3.1 dated 2018-04-30
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 3 +++ R/twinlm.R | 12 +++++++----- build/vignette.rds |binary inst/doc/basic-dutils.pdf |binary inst/doc/binomial-case-control-ascertainment.pdf |binary inst/doc/binomial-family.pdf |binary inst/doc/binomial-twin.pdf |binary inst/doc/quantitative-twin.pdf |binary 10 files changed, 23 insertions(+), 18 deletions(-)
Title: GAMLSS Data
Description: Data used as examples to demonstrate GAMLSS models.
Author: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>, Bob
Rigby, Fernanda De Bastiani
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.data versions 5.0-0 dated 2016-10-18 and 5.0-1 dated 2018-04-30
DESCRIPTION | 16 ++++---- MD5 | 86 ++++++++++++++++++++++++------------------------ data/CD4.rda |binary data/LGAclaims.rda |binary data/Leukemia.RData |binary data/Mums.rda |binary data/VictimsOfCrime.rda |binary data/acidity.rda |binary data/aep.rda |binary data/aids.rda |binary data/alveolar.rda |binary data/computer.rda |binary data/datalist | 1 data/db.rda |binary data/dbbmi.rda |binary data/dbhh.RData |only data/eu15.RData |binary data/fabric.rda |binary data/film30.rda |binary data/film90.RData |binary data/glass.rda |binary data/glasses.RData |binary data/grip.RData |binary data/hodges.rda |binary data/hodges1.rda |binary data/lice.rda |binary data/margolin.rda |binary data/meta.rda |binary data/mvi.rda |binary data/mviBig.rda |binary data/oil.RData |binary data/parzen.rda |binary data/polio.rda |binary data/rent.rda |binary data/rent99.polys.rda |binary data/rent99.rda |binary data/respInf.rda |binary data/species.rda |binary data/stylo.rda |binary data/tensile.rda |binary data/trd.RData |binary data/tse.rda |binary data/usair.rda |binary data/vas5.rda |binary man/dbhh.Rd |only 45 files changed, 53 insertions(+), 50 deletions(-)
Title: A 'Java' Platform Integration for 'R' with Programming Languages
'Groovy', 'JavaScript', 'JRuby' ('Ruby'), 'Jython' ('Python'),
and 'Kotlin'
Description: Provides a high-level integration for the 'Java' platform that makes 'Java' objects easy to use from within 'R'; provides a unified interface to integrate 'R' with several programming languages; and features extensive data exchange between 'R' and 'Java'. The 'jsr223'-supported programming languages include 'Groovy', 'JavaScript', 'JRuby' ('Ruby'), 'Jython' ('Python'), and 'Kotlin'. Any of these languages can use and extend 'Java' classes in natural syntax. Furthermore, solutions developed in any of the 'jsr223'-supported languages are also accessible to 'R' developers. The 'jsr223' package also features callbacks, script compiling, and string interpolation. In all, 'jsr223' significantly extends the computing capabilities of the 'R' software environment.
Author: Floid R. Gilbert [aut, cre],
David B. Dahl [aut]
Maintainer: Floid R. Gilbert <floid.r.gilbert@gmail.com>
Diff between jsr223 versions 0.3.1 dated 2018-04-05 and 0.3.2 dated 2018-04-30
DESCRIPTION | 8 +- MD5 | 22 +++---- NEWS | 12 +++ R/Private.R | 49 ++++++++++++--- R/Public.R | 14 +--- R/ScriptEngine.R | 9 +- inst/doc/jsr223.Rnw | 77 +++++++++++++----------- inst/doc/jsr223.pdf |binary man/getKotlinScriptEngineJars.Rd | 6 - tests/test-00-class-interfaces.R | 10 ++- tests/test-01-data-exchange.R | 122 +++++++++++++++++++++++---------------- vignettes/jsr223.Rnw | 77 +++++++++++++----------- 12 files changed, 249 insertions(+), 157 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape
Description: Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.
Author: Mikis Stasinopoulos [aut, cre, cph],
Bob Rigby [aut],
Vlasios Voudouris [ctb],
Calliope Akantziliotou [ctb],
Marco Enea [ctb],
Daniil Kiose [ctb]
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss versions 5.0-6 dated 2017-12-11 and 5.0-8 dated 2018-04-30
DESCRIPTION | 12 +- MD5 | 36 ++++--- NAMESPACE | 5 - R/HistDist-03-10-13.R | 9 + R/chooseDistParallel.R |only R/extra.R | 2 R/fitDist-17-05-13.R | 107 +++++++++++++---------- R/fitDistPred.R |only R/gamlss.R | 3 R/gamlssML.R | 118 +++++++++++++++++-------- R/gamlssVGD.R | 226 +++++++++++++++++++++++-------------------------- R/pbm.R | 2 R/predictAll.R | 27 +++-- R/pvc.R | 4 R/rqres.R | 11 +- R/wp.R | 4 inst/doc/NEWS.txt | 55 ++++++++++- man/fitDist.Rd | 112 ++++++++++++++++++++---- man/gamlssML.Rd | 64 ++++++++++++- man/gamlssVGD.Rd | 4 20 files changed, 519 insertions(+), 282 deletions(-)
Title: Depth-Based Classification and Calculation of Data Depth
Description: Contains procedures for depth-based supervised learning, which are entirely non-parametric, in particular the DDalpha-procedure (Lange, Mosler and Mozharovskyi, 2014 <doi:10.1007/s00362-012-0488-4>). The training data sample is transformed by a statistical depth function to a compact low-dimensional space, where the final classification is done. It also offers an extension to functional data and routines for calculating certain notions of statistical depth functions. 50 multivariate and 5 functional classification problems are included.
Author: Oleksii Pokotylo [aut, cre],
Pavlo Mozharovskyi [aut],
Rainer Dyckerhoff [aut],
Stanislav Nagy [aut]
Maintainer: Oleksii Pokotylo <alexey.pokotylo@gmail.com>
Diff between ddalpha versions 1.3.2 dated 2018-04-08 and 1.3.3 dated 2018-04-30
DESCRIPTION | 12 MD5 | 38 R/dataf.geneexp.r | 1026 ----- R/dataf.growth.r | 946 ---- R/dataf.medflies.r | 2014 ---------- R/dataf.population.r | 247 - R/dataf.population2010.r | 247 - R/dataf.tecator.r | 8639 -------------------------------------------- data/geneexp.rda |only data/growth.rda |only data/medflies.rda |only data/population.rda |only data/population2010.rda |only data/tecator.rda |only man/dataf..Rd | 140 man/dataf.geneexp.Rd | 123 man/dataf.growth.Rd | 131 man/dataf.medflies.Rd | 139 man/dataf.population.Rd | 135 man/dataf.population2010.Rd | 135 man/dataf.tecator.Rd | 139 man/ddalpha-package.Rd | 4 man/getdata.Rd | 394 +- 23 files changed, 715 insertions(+), 13794 deletions(-)
Title: Tools to Gather Data from Major League Baseball Advanced Media
(MLBAM)
Description: Multi-core processing of Gameday data from Major League Baseball Advanced Media <http://gd2.mlb.com/components/game/mlb/>. Additional tools to parallelize large data sets and write them to a database.
Author: Kris Eberwein [aut, cre]
Maintainer: Kris Eberwein <eberwein@knights.ucf.edu>
Diff between mlbgameday versions 0.1.1 dated 2018-03-15 and 0.1.2 dated 2018-04-30
DESCRIPTION | 6 +++--- MD5 | 29 +++++++++++++++++++---------- NAMESPACE | 1 + NEWS.md | 10 ++++++++++ R/payload_methods.R | 5 +++-- R/utils.R | 21 +++++++++++++++++++++ build/vignette.rds |binary inst/doc/data_automation.R |only inst/doc/data_automation.Rmd |only inst/doc/data_automation.html |only inst/doc/data_storage.R |only inst/doc/data_storage.Rmd |only inst/doc/data_storage.html |only inst/doc/database_connections.html | 4 ++-- inst/doc/parallel_processing.html | 4 ++-- inst/doc/pitch_plotting.html | 9 ++++----- inst/doc/search_games.html | 4 ++-- man/pitch_count.Rd |only vignettes/data_automation.Rmd |only vignettes/data_storage.Rmd |only 20 files changed, 67 insertions(+), 26 deletions(-)
Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models.
See '?umx' for help, and file.show(system.file("NEWS", package="umx")) for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 2.4.0 dated 2018-03-19 and 2.6.5 dated 2018-04-30
umx-2.4.0/umx/man/figures/front_page.graffle |only umx-2.4.0/umx/man/figures/umx_help_figures/umx_help_figures.png@1x.png |only umx-2.6.5/umx/DESCRIPTION | 10 umx-2.6.5/umx/MD5 | 309 ++-- umx-2.6.5/umx/NAMESPACE | 59 umx-2.6.5/umx/NEWS | 32 umx-2.6.5/umx/R/build_run_modify.r | 320 ++-- umx-2.6.5/umx/R/datasets.R | 63 umx-2.6.5/umx/R/fit_and_reporting.r | 764 +++++----- umx-2.6.5/umx/R/misc_and_utility.r | 266 ++- umx-2.6.5/umx/R/polychoricMatrix3.R |only umx-2.6.5/umx/R/umxACEcov_fixed.R | 4 umx-2.6.5/umx/R/umxACEv.R | 110 - umx-2.6.5/umx/R/umxGxE_biv.R | 41 umx-2.6.5/umx/R/umxSexLim.R | 47 umx-2.6.5/umx/R/umxSimplex.R |only umx-2.6.5/umx/R/uxm_stash_CIs.R |only umx-2.6.5/umx/R/xmu.r | 59 umx-2.6.5/umx/data/iqdat.rda |only umx-2.6.5/umx/man/GFF.Rd | 2 umx-2.6.5/umx/man/RMSEA.MxModel.Rd | 1 umx-2.6.5/umx/man/RMSEA.Rd | 1 umx-2.6.5/umx/man/RMSEA.summary.mxmodel.Rd | 1 umx-2.6.5/umx/man/extractAIC.MxModel.Rd | 1 umx-2.6.5/umx/man/figures/simplex.png |only umx-2.6.5/umx/man/figures/umx_help_figures.graffle |binary umx-2.6.5/umx/man/figures/umx_help_figures/ACEv@1x.png |only umx-2.6.5/umx/man/figures/umx_help_figures/simplex@1x.png |only umx-2.6.5/umx/man/install.OpenMx.Rd | 7 umx-2.6.5/umx/man/iqdat.Rd |only umx-2.6.5/umx/man/loadings.MxModel.Rd | 6 umx-2.6.5/umx/man/loadings.Rd | 1 umx-2.6.5/umx/man/plot.MxModel.Rd | 10 umx-2.6.5/umx/man/qm.Rd | 7 umx-2.6.5/umx/man/reliability.Rd | 2 umx-2.6.5/umx/man/residuals.MxModel.Rd | 1 umx-2.6.5/umx/man/tmx_is.identified.Rd | 6 umx-2.6.5/umx/man/umx.Rd | 54 umx-2.6.5/umx/man/umxACE.Rd | 13 umx-2.6.5/umx/man/umxACE_cov_fixed.Rd | 5 umx-2.6.5/umx/man/umxACEcov.Rd | 5 umx-2.6.5/umx/man/umxACEv.Rd | 45 umx-2.6.5/umx/man/umxAPA.Rd | 6 umx-2.6.5/umx/man/umxAlgebra.Rd |only umx-2.6.5/umx/man/umxBrownie.Rd | 9 umx-2.6.5/umx/man/umxCI.Rd | 1 umx-2.6.5/umx/man/umxCI_boot.Rd | 1 umx-2.6.5/umx/man/umxCP.Rd | 50 umx-2.6.5/umx/man/umxCompare.Rd | 1 umx-2.6.5/umx/man/umxConfint.Rd | 63 umx-2.6.5/umx/man/umxCovData.Rd | 19 umx-2.6.5/umx/man/umxEval.Rd | 6 umx-2.6.5/umx/man/umxExpCov.Rd | 1 umx-2.6.5/umx/man/umxExpMeans.Rd | 1 umx-2.6.5/umx/man/umxFactor.Rd | 19 umx-2.6.5/umx/man/umxFactorScores.Rd | 6 umx-2.6.5/umx/man/umxFitIndices.Rd | 1 umx-2.6.5/umx/man/umxGetParameters.Rd | 6 umx-2.6.5/umx/man/umxGxE.Rd | 20 umx-2.6.5/umx/man/umxGxE_biv.Rd | 10 umx-2.6.5/umx/man/umxGxE_window.Rd | 5 umx-2.6.5/umx/man/umxHetCor.Rd | 17 umx-2.6.5/umx/man/umxIP.Rd | 57 umx-2.6.5/umx/man/umxMatrix.Rd | 10 umx-2.6.5/umx/man/umxModel.Rd | 1 umx-2.6.5/umx/man/umxModify.Rd | 18 umx-2.6.5/umx/man/umxPadAndPruneForDefVars.Rd | 23 umx-2.6.5/umx/man/umxPath.Rd | 6 umx-2.6.5/umx/man/umxPlotACE.Rd | 6 umx-2.6.5/umx/man/umxPlotACEcov.Rd | 6 umx-2.6.5/umx/man/umxPlotACEv.Rd | 5 umx-2.6.5/umx/man/umxPlotCP.Rd | 6 umx-2.6.5/umx/man/umxPlotGxE.Rd | 19 umx-2.6.5/umx/man/umxPlotGxE_biv.Rd | 4 umx-2.6.5/umx/man/umxPlotIP.Rd | 4 umx-2.6.5/umx/man/umxPlotSimplex.Rd |only umx-2.6.5/umx/man/umxRAM.Rd | 8 umx-2.6.5/umx/man/umxReduce.Rd | 6 umx-2.6.5/umx/man/umxRun.Rd | 6 umx-2.6.5/umx/man/umxSexLim.Rd | 5 umx-2.6.5/umx/man/umxSimplex.Rd |only umx-2.6.5/umx/man/umxSummary.MxModel.Rd | 1 umx-2.6.5/umx/man/umxSummary.Rd | 14 umx-2.6.5/umx/man/umxSummaryACE.Rd | 19 umx-2.6.5/umx/man/umxSummaryACEcov.Rd | 8 umx-2.6.5/umx/man/umxSummaryACEv.Rd | 17 umx-2.6.5/umx/man/umxSummaryCP.Rd | 53 umx-2.6.5/umx/man/umxSummaryGxE.Rd | 8 umx-2.6.5/umx/man/umxSummaryGxE_biv.Rd | 10 umx-2.6.5/umx/man/umxSummaryIP.Rd | 10 umx-2.6.5/umx/man/umxSummarySexLim.Rd | 20 umx-2.6.5/umx/man/umxSummarySimplex.Rd |only umx-2.6.5/umx/man/umxSuperModel.Rd | 6 umx-2.6.5/umx/man/umxVersion.Rd | 5 umx-2.6.5/umx/man/umx_APA_model_CI.Rd | 5 umx-2.6.5/umx/man/umx_APA_pval.Rd | 1 umx-2.6.5/umx/man/umx_aggregate.Rd | 1 umx-2.6.5/umx/man/umx_array_shift.Rd | 18 umx-2.6.5/umx/man/umx_as_numeric.Rd | 23 umx-2.6.5/umx/man/umx_check_model.Rd | 4 umx-2.6.5/umx/man/umx_cont_2_quantiles.Rd | 18 umx-2.6.5/umx/man/umx_cov2raw.Rd | 14 umx-2.6.5/umx/man/umx_drop_ok.Rd | 1 umx-2.6.5/umx/man/umx_explode.Rd | 3 umx-2.6.5/umx/man/umx_explode_twin_names.Rd | 11 umx-2.6.5/umx/man/umx_find_object.Rd | 9 umx-2.6.5/umx/man/umx_grep.Rd | 2 umx-2.6.5/umx/man/umx_lower2full.Rd | 17 umx-2.6.5/umx/man/umx_make.Rd | 15 umx-2.6.5/umx/man/umx_make_MR_data.Rd | 20 umx-2.6.5/umx/man/umx_make_TwinData.Rd | 2 umx-2.6.5/umx/man/umx_make_bin_cont_pair_data.Rd | 18 umx-2.6.5/umx/man/umx_make_fake_data.Rd | 16 umx-2.6.5/umx/man/umx_merge_CIs.Rd | 4 umx-2.6.5/umx/man/umx_msg.Rd | 9 umx-2.6.5/umx/man/umx_names.Rd | 69 umx-2.6.5/umx/man/umx_object_as_str.Rd | 4 umx-2.6.5/umx/man/umx_open_CRAN_page.Rd | 9 umx-2.6.5/umx/man/umx_pad.Rd | 19 umx-2.6.5/umx/man/umx_parameters.Rd | 3 umx-2.6.5/umx/man/umx_paste_names.Rd | 8 umx-2.6.5/umx/man/umx_pb_note.Rd | 11 umx-2.6.5/umx/man/umx_polychoric.Rd |only umx-2.6.5/umx/man/umx_polypairwise.Rd |only umx-2.6.5/umx/man/umx_polytriowise.Rd |only umx-2.6.5/umx/man/umx_print.Rd | 13 umx-2.6.5/umx/man/umx_read_lower.Rd | 16 umx-2.6.5/umx/man/umx_rename.Rd | 17 umx-2.6.5/umx/man/umx_reorder.Rd | 17 umx-2.6.5/umx/man/umx_rot.Rd | 2 umx-2.6.5/umx/man/umx_round.Rd | 1 umx-2.6.5/umx/man/umx_scale.Rd | 20 umx-2.6.5/umx/man/umx_scale_wide_twin_data.Rd | 8 umx-2.6.5/umx/man/umx_show.Rd | 5 umx-2.6.5/umx/man/umx_show_fit_or_comparison.Rd |only umx-2.6.5/umx/man/umx_stack.Rd | 15 umx-2.6.5/umx/man/umx_standardize_ACE.Rd | 4 umx-2.6.5/umx/man/umx_standardize_ACEcov.Rd | 4 umx-2.6.5/umx/man/umx_standardize_ACEv.Rd | 4 umx-2.6.5/umx/man/umx_standardize_CP.Rd | 4 umx-2.6.5/umx/man/umx_standardize_IP.Rd | 4 umx-2.6.5/umx/man/umx_standardize_RAM.Rd | 4 umx-2.6.5/umx/man/umx_standardize_Simplex.Rd |only umx-2.6.5/umx/man/umx_stash_CIs.Rd |only umx-2.6.5/umx/man/umx_swap_a_block.Rd | 17 umx-2.6.5/umx/man/umx_time.Rd | 5 umx-2.6.5/umx/man/umx_trim.Rd | 2 umx-2.6.5/umx/man/umx_write_to_clipboard.Rd | 2 umx-2.6.5/umx/man/us_skinfold_data.Rd | 3 umx-2.6.5/umx/man/xmuHasSquareBrackets.Rd | 1 umx-2.6.5/umx/man/xmuLabel_MATRIX_Model.Rd | 1 umx-2.6.5/umx/man/xmuLabel_Matrix.Rd | 1 umx-2.6.5/umx/man/xmuLabel_RAM_Model.Rd | 1 umx-2.6.5/umx/man/xmuMI.Rd | 1 umx-2.6.5/umx/man/xmuMakeDeviationThresholdsMatrices.Rd | 1 umx-2.6.5/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd | 1 umx-2.6.5/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd | 1 umx-2.6.5/umx/man/xmuMaxLevels.Rd | 1 umx-2.6.5/umx/man/xmuMinLevels.Rd | 1 umx-2.6.5/umx/man/xmuPropagateLabels.Rd | 1 umx-2.6.5/umx/man/xmu_check_levels_identical.Rd | 1 umx-2.6.5/umx/man/xmu_dot_make_paths.Rd | 1 umx-2.6.5/umx/man/xmu_dot_make_residuals.Rd | 1 umx-2.6.5/umx/man/xmu_simplex_corner.Rd |only umx-2.6.5/umx/man/xmu_start_value_list.Rd | 3 umx-2.6.5/umx/man/xmu_twin_check.Rd | 10 166 files changed, 1962 insertions(+), 1421 deletions(-)
Title: Multiresolution Kriging Based on Markov Random Fields
Description: Methods for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) Moreover, the covariance model for
this method can approximate the Matern covariance family but also
allows for a multi-resolution model and supports efficient
computation of the profile likelihood for estimating covariance
parameters. This is accomplished through compactly supported basis
functions and a Markov random field model for the basis
coefficients. These features lead to sparse matrices for the
computations and this package makes of the R spam package for this.
An extension of this version over previous ones ( < 5.4 ) is the
support for different geometries besides a rectangular domain. The
Markov random field approach combined with a basis function
representation makes the implementation of different geometries
simple where only a few specific functions need to be added with
most of the computation and evaluation done by generic routines that
have been tuned to be efficient. One benefit of this package's
model/approach is the facility to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating non-stationary covariances
and also the case when the observations are a linear combination
(e.g. an integral) of the spatial process. Included are generic
methods for prediction, standard errors for prediction, plotting of
the estimated surface and conditional and unconditional simulation.
Author: Douglas Nychka [aut, cre],
Dorit Hammerling [aut],
Stephan Sain [aut],
Nathan Lenssen [aut],
Colette Smirniotis [aut]
Maintainer: Douglas Nychka <nychka@ucar.edu>
Diff between LatticeKrig versions 6.4 dated 2017-05-22 and 7.0 dated 2018-04-30
DESCRIPTION | 14 + MD5 | 132 +++++++------- NAMESPACE | 1 R/LKinfoCheck.R | 6 R/LKrig.MLE.R | 7 R/LKrig.R | 7 R/LKrig.basis.R | 50 ++++- R/LKrig.coef.R | 16 + R/LKrig.cov.R | 5 R/LKrig.lnPlike.R | 2 R/LKrig.precision.R | 16 - R/LKrig.sim.R | 11 - R/LKrig.sim.conditional.R | 15 + R/LKrig.traceA.R | 3 R/LKrigFindLambdaAwght.R | 18 +- R/LKrigSetup.R | 16 + R/LKrigSetupAlpha.R | 33 +-- R/LKrigSetupAwght.R | 6 R/LKrigSetupAwghtObject.R |only R/ModelInterval.R | 12 - R/ModelLKSphere.R | 3 R/ModelRectangle.R | 256 +++++++++++++++++++---------- R/predict.LKrig.R | 9 - R/predictLKrigFixedFunction.R | 5 R/predictSE.LKrig.R | 12 + R/predictSurface.LKrig.R | 24 ++ R/print.LKinfo.R | 27 ++- R/print.LKrig.R | 21 +- R/print.LatticeKrig.R | 3 R/summary.LKrig.R | 8 man/LKGeometry.Rd | 20 +- man/LKRectangle.Rd |only man/LKinfoCheck.Rd | 2 man/LKrig.MLE.Rd | 58 ++++-- man/LKrig.Rd | 58 +++--- man/LKrig.basis.Rd | 42 +++- man/LKrigDefaultFixedFunction.Rd | 6 man/LKrigInternal.Rd | 8 man/LKrigSetup.Rd | 89 ++++++---- man/LKrigSetupAwght.Rd | 33 +++ man/LatticeKrig.Rd | 61 +++++- man/PeriodicGeometry.Rd | 4 man/nonstationaryModels.Rd |only tests/LKrig.FindNorm.test.R | 7 tests/LKrig.FindNorm.test.Rout.save | 26 -- tests/LKrig.LKCylinder.test.R | 2 tests/LKrig.LKCylinder.test.Rout.save | 27 --- tests/LKrig.LKSphere.test.R | 2 tests/LKrig.basis.test.R | 2 tests/LKrig.basis.test.Rout.save | 26 -- tests/LKrig.lnPLike.test.R | 59 +++++- tests/LKrig.lnPlike.test.Rout.save | 38 +--- tests/LKrig.nullspace.test.R | 2 tests/LKrig.nullspace.test.Rout.save | 26 -- tests/LKrig.precision.test.R | 82 ++------- tests/LKrig.precision.test.Rout.save | 37 ---- tests/LKrig.se.test.R | 2 tests/LKrig.se.test.Rout.save | 24 -- tests/LKrig.test.3D.R | 2 tests/LKrig.test.3D.Rout.save | 26 -- tests/LKrig.test.Nonstationary.R |only tests/LKrig.test.R | 64 ------- tests/LKrig.test.Rout.save | 36 ---- tests/LKrig.test.inverse.R | 2 tests/LKrig.test.inverse.Rout.save | 26 -- tests/LKrig.testFindAwght.R | 30 ++- tests/LKrig.testFindAwght.Rout.save | 34 +-- tests/LKrigMarginalVariance.test.R | 2 tests/LKrigMarginalVariance.test.Rout.save | 26 -- 69 files changed, 938 insertions(+), 791 deletions(-)
Title: Distributions for Generalized Additive Models for Location Scale
and Shape
Description: A set of distributions which can be used for modelling the response variables in Generalized Additive Models for Location Scale and Shape, Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The distributions can be continuous, discrete or mixed distributions. Extra distributions can be created, by transforming, any continuous distribution defined on the real line, to a distribution defined on ranges 0 to infinity or 0 to 1, by using a "log" or a "logit" transformation respectively.
Author: c(person("Mikis", "Stasinopoulos", role = c("aut", "cre", "cph"),
email = "d.stasinopoulos@londonmet.ac.uk"),
person("Bob", "Rigby", role = c("aut")),
person("Calliope", "Akantziliotou", role = "ctb"),
person("Vlasios", "Voudouris", role = "ctb",
email= "vlasios.voudouris@abm-analytics.com"),
person("Gillian", "Heller", role = "ctb"),
person("Raydonal", "Ospina", role = "ctb",
email= "rospina@ime.usp.br"),
person("Nicoletta", "Motpan", role = "ctb"),
person("Fiona", "McElduff", role = "ctb"),
person("Majid", "Djennad", role = "ctb"),
person("Marco", "Enea", role = "ctb"),
person("Alexios", "Ghalanos", role = "ctb"),
person("Christos", "Argyropoulos", role = "ctb"),
person("Almond", "Stocker", role = "ctb")
)
Maintainer: Mikis Stasinopoulos <d.stasinopoulos@londonmet.ac.uk>
Diff between gamlss.dist versions 5.0-4 dated 2017-12-11 and 5.0-5 dated 2018-04-30
DESCRIPTION | 15 +++--- MD5 | 10 ++-- R/NET.R | 141 ++++++++++++++++++++++++++++++++++-------------------------- R/ZAGA.R | 56 +++++++++-------------- man/NET.Rd | 21 ++++++-- man/ZAGA.Rd | 7 -- 6 files changed, 133 insertions(+), 117 deletions(-)
Title: Client for the 'DKAN' API
Description: Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.
Author: Tony Fujs [aut, cre],
Meera Desai [aut],
Karthik Ramanathan [aut]
Maintainer: Tony Fujs <tonyfujs@gmail.com>
Diff between dkanr versions 0.1.0 dated 2018-03-16 and 0.1.1 dated 2018-04-30
DESCRIPTION | 6 ++-- MD5 | 15 ++++++------ NEWS.md | 5 ++++ R/get_resource_url.R | 5 +++- README.md | 1 build/vignette.rds |binary inst/doc/getting_started_with_dkanr.html | 4 +-- tests/testthat/test-get_resource_url.R | 17 ++++++++++++++ tests/testthat/www.statistics.digitalresources.jisc.ac.uk |only 9 files changed, 40 insertions(+), 13 deletions(-)
More information about bigIntegerAlgos at CRAN
Permanent link
Title: Interface to the Australian Statistical Geography Standard
Description: The Australian Statistical Geography Standard ('ASGS') is
a set of shapefiles by the Australian Bureau of Statistics. This package
provides an interface to those shapefiles, as well as methods for converting
coordinates to shapefiles.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between ASGS.foyer versions 0.1.0 dated 2018-03-21 and 0.2.0 dated 2018-04-30
DESCRIPTION | 6 - MD5 | 9 +- NEWS.md | 8 ++ R/install_ASGS.R | 124 +++++++++++++++++++++++++++++++++---- man/install_ASGS.Rd | 29 +++++++- tests/testthat/test-install_asgs.R |only 6 files changed, 151 insertions(+), 25 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. The code for Concorde
itself is not included in the package and has to be obtained separately.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between TSP versions 1.1-5 dated 2017-02-22 and 1.1-6 dated 2018-04-30
DESCRIPTION | 10 ++++----- MD5 | 26 ++++++++++++------------- NEWS.md | 6 +++++ R/solve_TSP.R | 8 +++---- R/tsp_insertion.R | 2 - README.md | 5 ++-- build/vignette.rds |binary data/USCA312.rda |binary data/USCA312_map.rda |binary data/USCA50.rda |binary inst/doc/TSP.pdf |binary man/Concorde.Rd | 4 +-- man/solve_TSP.Rd | 2 - src/tour_length.c | 52 ++++++++++++++++++++++++++------------------------- 14 files changed, 61 insertions(+), 54 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.8.400.0.0 dated 2018-03-01 and 0.8.500.0 dated 2018-04-30
ChangeLog | 60 + DESCRIPTION | 9 MD5 | 203 ++--- build/vignette.rds |binary configure | 134 ++- configure.ac | 101 +- inst/NEWS.Rd | 28 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/armadillo | 15 inst/include/armadillo_bits/BaseCube_bones.hpp | 8 inst/include/armadillo_bits/BaseCube_meat.hpp | 4 inst/include/armadillo_bits/Base_bones.hpp | 8 inst/include/armadillo_bits/Base_meat.hpp | 4 inst/include/armadillo_bits/Col_meat.hpp | 2 inst/include/armadillo_bits/Cube_bones.hpp | 8 inst/include/armadillo_bits/Cube_meat.hpp | 4 inst/include/armadillo_bits/MapMat_bones.hpp | 80 - inst/include/armadillo_bits/MapMat_meat.hpp | 401 +++++---- inst/include/armadillo_bits/Mat_bones.hpp | 8 inst/include/armadillo_bits/Mat_meat.hpp | 18 inst/include/armadillo_bits/Op_bones.hpp | 2 inst/include/armadillo_bits/Proxy.hpp | 171 ++++ inst/include/armadillo_bits/Row_meat.hpp | 2 inst/include/armadillo_bits/SpBase_bones.hpp | 16 inst/include/armadillo_bits/SpBase_meat.hpp | 8 inst/include/armadillo_bits/SpMat_bones.hpp | 73 + inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 373 ++++++--- inst/include/armadillo_bits/SpMat_meat.hpp | 598 ++++++++++++-- inst/include/armadillo_bits/SpSubview_bones.hpp | 138 +-- inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 605 ++++++++++----- inst/include/armadillo_bits/SpSubview_meat.hpp | 191 ++++ inst/include/armadillo_bits/arma_forward.hpp | 7 inst/include/armadillo_bits/arma_ostream_meat.hpp | 101 -- inst/include/armadillo_bits/arma_version.hpp | 4 inst/include/armadillo_bits/arrayops_meat.hpp | 20 inst/include/armadillo_bits/auxlib_meat.hpp | 91 -- inst/include/armadillo_bits/compiler_setup.hpp | 13 inst/include/armadillo_bits/config.hpp.cmake | 2 inst/include/armadillo_bits/diskio_meat.hpp | 15 inst/include/armadillo_bits/field_bones.hpp | 4 inst/include/armadillo_bits/field_meat.hpp | 2 inst/include/armadillo_bits/fn_accu.hpp | 24 inst/include/armadillo_bits/fn_as_scalar.hpp | 62 + inst/include/armadillo_bits/fn_eye.hpp | 4 inst/include/armadillo_bits/fn_flip.hpp | 26 inst/include/armadillo_bits/fn_norm.hpp | 4 inst/include/armadillo_bits/fn_normalise.hpp | 20 inst/include/armadillo_bits/fn_randn.hpp | 6 inst/include/armadillo_bits/fn_randu.hpp | 6 inst/include/armadillo_bits/fn_repelem.hpp |only inst/include/armadillo_bits/fn_reverse.hpp |only inst/include/armadillo_bits/fn_roots.hpp |only inst/include/armadillo_bits/fn_speye.hpp | 4 inst/include/armadillo_bits/fn_sprandn.hpp | 4 inst/include/armadillo_bits/fn_sprandu.hpp | 4 inst/include/armadillo_bits/fn_strans.hpp | 40 inst/include/armadillo_bits/fn_trace.hpp | 282 ++++-- inst/include/armadillo_bits/fn_trans.hpp | 76 - inst/include/armadillo_bits/memory.hpp | 2 inst/include/armadillo_bits/mp_misc.hpp | 16 inst/include/armadillo_bits/mtOp_bones.hpp | 1 inst/include/armadillo_bits/mul_gemm.hpp | 4 inst/include/armadillo_bits/op_clamp_bones.hpp | 7 inst/include/armadillo_bits/op_clamp_meat.hpp | 94 +- inst/include/armadillo_bits/op_flip_bones.hpp | 14 inst/include/armadillo_bits/op_flip_meat.hpp | 225 ++++- inst/include/armadillo_bits/op_normalise_meat.hpp | 53 - inst/include/armadillo_bits/op_repelem_bones.hpp |only inst/include/armadillo_bits/op_repelem_meat.hpp |only inst/include/armadillo_bits/op_reverse_bones.hpp |only inst/include/armadillo_bits/op_reverse_meat.hpp |only inst/include/armadillo_bits/op_roots_bones.hpp |only inst/include/armadillo_bits/op_roots_meat.hpp |only inst/include/armadillo_bits/operator_ostream.hpp | 4 inst/include/armadillo_bits/operator_times.hpp | 60 - inst/include/armadillo_bits/podarray_meat.hpp | 9 inst/include/armadillo_bits/running_stat_vec_meat.hpp | 10 inst/include/armadillo_bits/sp_auxlib_meat.hpp | 1 inst/include/armadillo_bits/spdiagview_bones.hpp | 20 inst/include/armadillo_bits/spdiagview_meat.hpp | 10 inst/include/armadillo_bits/spglue_join_bones.hpp | 2 inst/include/armadillo_bits/spglue_join_meat.hpp | 93 +- inst/include/armadillo_bits/spglue_kron_bones.hpp | 3 inst/include/armadillo_bits/spglue_kron_meat.hpp | 137 ++- inst/include/armadillo_bits/spglue_times_bones.hpp | 13 inst/include/armadillo_bits/spglue_times_meat.hpp | 194 ++++ inst/include/armadillo_bits/spop_diagmat_meat.hpp | 85 +- inst/include/armadillo_bits/spop_htrans_bones.hpp | 4 inst/include/armadillo_bits/spop_htrans_meat.hpp | 38 inst/include/armadillo_bits/spop_mean_meat.hpp | 20 inst/include/armadillo_bits/spop_misc_bones.hpp | 24 inst/include/armadillo_bits/spop_misc_meat.hpp | 72 - inst/include/armadillo_bits/spop_normalise_bones.hpp |only inst/include/armadillo_bits/spop_normalise_meat.hpp |only inst/include/armadillo_bits/spop_repmat_bones.hpp |only inst/include/armadillo_bits/spop_repmat_meat.hpp |only inst/include/armadillo_bits/spop_reverse_bones.hpp |only inst/include/armadillo_bits/spop_reverse_meat.hpp |only inst/include/armadillo_bits/spop_strans_bones.hpp | 9 inst/include/armadillo_bits/spop_strans_meat.hpp | 142 +-- inst/include/armadillo_bits/spop_sum_meat.hpp | 28 inst/include/armadillo_bits/subview_bones.hpp | 3 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 2 inst/include/armadillo_bits/subview_cube_meat.hpp | 10 inst/include/armadillo_bits/subview_elem1_meat.hpp | 2 inst/include/armadillo_bits/subview_meat.hpp | 71 - inst/include/armadillo_bits/unwrap_spmat.hpp | 21 inst/unitTests/cpp/Rlapack.cpp |only inst/unitTests/runit.Rlapack.R |only 111 files changed, 3846 insertions(+), 1750 deletions(-)
Title: Read and Write BAM (Binary Alignment) Files
Description: Provides an R interface to functions of the 'SAMtools' C-Library by Heng Li <http://www.htslib.org/>.
Author: Wolfgang Kaisers [aut, cre],
Heng Li [ctb, cph],
Jue Ruan [ctb, cph]
Maintainer: Wolfgang Kaisers <wolfgang.kaisers@gmail.com>
Diff between rbamtools versions 2.16.6 dated 2017-03-24 and 2.16.10 dated 2018-04-30
DESCRIPTION | 23 ++++++++++++++++------- MD5 | 7 ++++--- build/vignette.rds |binary inst/COPYRIGHTS |only inst/doc/rbamtools.pdf |binary 5 files changed, 20 insertions(+), 10 deletions(-)
Title: Get Network Representation of an R Package
Description: Tools from the domain of graph theory can be used to quantify the complexity
and vulnerability to failure of a software package. That is the guiding philosophy
of this package. 'pkgnet' provides tools to analyze the dependencies between functions
in an R package and between its imported packages.
Author: Brian Burns [aut, cre],
James Lamb [aut],
Patrick Boueri [ctb],
Jay Qi [ctb]
Maintainer: Brian Burns <brian.burns@uptake.com>
Diff between pkgnet versions 0.1.0 dated 2018-04-13 and 0.2.0 dated 2018-04-30
pkgnet-0.1.0/pkgnet/inst/doc/pkgnet-intro.R |only pkgnet-0.1.0/pkgnet/tests |only pkgnet-0.2.0/pkgnet/DESCRIPTION | 9 pkgnet-0.2.0/pkgnet/MD5 | 52 pkgnet-0.2.0/pkgnet/NAMESPACE | 2 pkgnet-0.2.0/pkgnet/R/AbstractGraphReporter.R | 4 pkgnet-0.2.0/pkgnet/R/AbstractPackageReporter.R | 9 pkgnet-0.2.0/pkgnet/R/CreatePackageReport.R | 10 pkgnet-0.2.0/pkgnet/R/PackageDependencyReporter.R | 4 pkgnet-0.2.0/pkgnet/R/PackageFunctionReporter.R | 11 pkgnet-0.2.0/pkgnet/README.md | 10 pkgnet-0.2.0/pkgnet/build/vignette.rds |binary pkgnet-0.2.0/pkgnet/inst/doc/pkgnet-intro.Rmd | 5577 +++++++++ pkgnet-0.2.0/pkgnet/inst/doc/pkgnet-intro.html | 5861 +++++++++- pkgnet-0.2.0/pkgnet/inst/package_report/header.html |only pkgnet-0.2.0/pkgnet/inst/package_report/lubridate_report.html |only pkgnet-0.2.0/pkgnet/inst/package_report/package_dependency_reporter.Rmd | 4 pkgnet-0.2.0/pkgnet/inst/package_report/package_report.Rmd | 13 pkgnet-0.2.0/pkgnet/inst/package_report/package_summary_reporter.Rmd | 4 pkgnet-0.2.0/pkgnet/man/AbstractGraphReporter.Rd | 4 pkgnet-0.2.0/pkgnet/man/AbstractPackageReporter.Rd | 6 pkgnet-0.2.0/pkgnet/man/CreatePackageReport.Rd | 9 pkgnet-0.2.0/pkgnet/man/FunctionReporter.Rd | 7 pkgnet-0.2.0/pkgnet/man/SummaryReporter.Rd | 6 pkgnet-0.2.0/pkgnet/vignettes/pkgnet-intro.Rmd | 5577 +++++++++ 25 files changed, 16252 insertions(+), 927 deletions(-)
Title: Statistics Netherlands (CBS) Open Data API Client
Description: The data and meta data from Statistics
Netherlands (www.cbs.nl) can be browsed and downloaded. The client uses
the open data API of Statistics Netherlands.
Author: Edwin de Jonge [aut, cre]
Maintainer: Edwin de Jonge <edwindjonge@gmail.com>
Diff between cbsodataR versions 0.2.5 dated 2018-02-01 and 0.3 dated 2018-04-30
cbsodataR-0.2.5/cbsodataR/README.md |only cbsodataR-0.2.5/cbsodataR/inst/doc/cbsodata.R |only cbsodataR-0.2.5/cbsodataR/inst/doc/cbsodata.Rmd |only cbsodataR-0.2.5/cbsodataR/inst/doc/cbsodata.html |only cbsodataR-0.2.5/cbsodataR/man/download_data.Rd |only cbsodataR-0.2.5/cbsodataR/man/download_meta.Rd |only cbsodataR-0.2.5/cbsodataR/vignettes/cbsodata.Rmd |only cbsodataR-0.3/cbsodataR/DESCRIPTION | 13 +- cbsodataR-0.3/cbsodataR/MD5 | 74 ++++++++++------ cbsodataR-0.3/cbsodataR/NAMESPACE | 11 ++ cbsodataR-0.3/cbsodataR/NEWS.md | 13 ++ cbsodataR-0.3/cbsodataR/R/add_column_labels.R |only cbsodataR-0.3/cbsodataR/R/cbs-table.R | 7 + cbsodataR-0.3/cbsodataR/R/cbs_add_date_column.R |only cbsodataR-0.3/cbsodataR/R/cbs_add_label_columns.R |only cbsodataR-0.3/cbsodataR/R/cbs_default_selection.R |only cbsodataR-0.3/cbsodataR/R/cbs_download_data.R |only cbsodataR-0.3/cbsodataR/R/cbs_download_meta.R |only cbsodataR-0.3/cbsodataR/R/cbs_download_table.R |only cbsodataR-0.3/cbsodataR/R/cbs_extract_table_id.R |only cbsodataR-0.3/cbsodataR/R/cbs_get_data.R |only cbsodataR-0.3/cbsodataR/R/cbs_get_meta.R |only cbsodataR-0.3/cbsodataR/R/cbs_get_themes.R |only cbsodataR-0.3/cbsodataR/R/cbs_get_toc.R |only cbsodataR-0.3/cbsodataR/R/download-data.R | 53 ++--------- cbsodataR-0.3/cbsodataR/R/download-meta.R | 25 +---- cbsodataR-0.3/cbsodataR/R/download-table.R | 26 ++--- cbsodataR-0.3/cbsodataR/R/get-data.R | 2 cbsodataR-0.3/cbsodataR/R/get-meta.R | 25 ++++- cbsodataR-0.3/cbsodataR/R/get-table-list.R | 7 - cbsodataR-0.3/cbsodataR/R/get-themes.R | 6 - cbsodataR-0.3/cbsodataR/R/get_datatype.R |only cbsodataR-0.3/cbsodataR/R/resolve.R | 12 +- cbsodataR-0.3/cbsodataR/R/store_labels.R |only cbsodataR-0.3/cbsodataR/build/vignette.rds |binary cbsodataR-0.3/cbsodataR/inst/doc/cbsodataR.R |only cbsodataR-0.3/cbsodataR/inst/doc/cbsodataR.Rmd |only cbsodataR-0.3/cbsodataR/inst/doc/cbsodataR.html |only cbsodataR-0.3/cbsodataR/inst/iv3.R | 24 ++--- cbsodataR-0.3/cbsodataR/man/cbs_add_date_column.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_add_label_columns.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_default_selection.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_download_data.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_download_meta.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_download_table.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_extract_table_id.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_data.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_meta.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_meta_from_dir.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_tables_themes.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_themes.Rd |only cbsodataR-0.3/cbsodataR/man/cbs_get_toc.Rd |only cbsodataR-0.3/cbsodataR/man/download_data-deprecated.Rd |only cbsodataR-0.3/cbsodataR/man/download_meta-deprecated.Rd |only cbsodataR-0.3/cbsodataR/man/download_table.Rd | 7 + cbsodataR-0.3/cbsodataR/man/get_meta.Rd | 6 - cbsodataR-0.3/cbsodataR/man/get_themes.Rd | 7 + cbsodataR-0.3/cbsodataR/vignettes/cbsodataR.Rmd |only 58 files changed, 175 insertions(+), 143 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package allows various cartographic representations such as proportional symbols, choropleth, typology, flows or discontinuities maps. It also offers several features enhancing the graphic presentation of maps like cartographic palettes, layout elements (scale, north arrow, title...), labels, legends or access to some cartographic APIs. See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut],
Nicolas Lambert [aut],
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.0.2 dated 2017-11-13 and 2.1.0 dated 2018-04-30
DESCRIPTION | 16 MD5 | 142 +++---- NAMESPACE | 29 + NEWS | 18 R/Package.R | 6 R/barscale.R | 14 R/choroLayer.R | 7 R/data.R | 4 R/discLayer.R | 14 R/dotDensityLayer.R | 8 R/getBorders.R | 23 - R/getBreaks.R | 8 R/getFigDim.R | 6 R/getGridLayer.R | 42 +- R/getLinkLayer.R | 5 R/getOuterBorders.R | 19 R/getTiles.R | 5 R/gradLinkLayer.R | 7 R/gradLinkTypoLayer.R | 7 R/labelLayer.R | 12 R/layoutLayer.R | 14 R/legends.R | 53 +- R/north.R | 2 R/palettes.R | 53 +- R/propLinkLayer.R | 4 R/propSymbolsChoroLayer.R | 18 R/propSymbolsLayer.R | 14 R/propSymbolsTypoLayer.R | 12 R/propTrianglesLayer.R | 22 - R/smoothLayer.R | 2 R/tilesLayer.R | 9 R/typoLayer.R | 5 R/utils.R | 25 - README.md | 39 - build/vignette.rds |binary inst/doc/cartography.html | 852 ++++++++++++++++++++++++++----------------- man/barscale.Rd | 2 man/carto.pal.Rd | 10 man/cartography.Rd | 6 man/choroLayer.Rd | 7 man/countries.spdf.Rd | 2 man/discLayer.Rd | 6 man/dotDensityLayer.Rd | 5 man/getBorders.Rd | 3 man/getBreaks.Rd | 3 man/getFigDim.Rd | 4 man/getGridLayer.Rd | 2 man/getLinkLayer.Rd | 1 man/getOuterBorders.Rd | 8 man/getTiles.Rd | 4 man/gradLinkLayer.Rd | 1 man/gradLinkTypoLayer.Rd | 1 man/labelLayer.Rd | 5 man/layoutLayer.Rd | 8 man/legendBarsSymbols.Rd | 10 man/legendChoro.Rd | 1 man/legendCirclesSymbols.Rd | 10 man/legendGradLines.Rd | 1 man/legendPropLines.Rd | 1 man/legendPropTriangles.Rd | 1 man/legendSquaresSymbols.Rd | 10 man/legendTypo.Rd | 1 man/north.Rd | 2 man/propLinkLayer.Rd | 1 man/propSymbolsChoroLayer.Rd | 2 man/propSymbolsLayer.Rd | 2 man/propSymbolsTypoLayer.Rd | 4 man/propTrianglesLayer.Rd | 3 man/smoothLayer.Rd | 2 man/tilesLayer.Rd | 2 man/twincities.df.Rd | 2 man/typoLayer.Rd | 4 72 files changed, 1009 insertions(+), 644 deletions(-)
Title: Quantile Treatment Effects
Description: Provides several methods for computing the Quantile Treatment Effect (QTE) and Quantile Treatment Effect on the Treated (QTT). The main cases covered are (i) Treatment is randomly assigned, (ii) Treatment is as good as randomly assigned after conditioning on some covariates (also called conditional independence or selection on observables) using the methods developed in Firpo (2007) <doi:10.1111/j.1468-0262.2007.00738.x>, (iii) Identification is based on a Difference in Differences assumption (several varieties are available in the package e.g. Athey and Imbens (2006) <doi:10.1111/j.1468-0262.2006.00668.x> Callaway and Li (2017) <https://ssrn.com/abstract=3013341>, Callaway, Li, and Oka (2017) <arXiv:1702.03618>).
Author: Brantly Callaway [aut, cre]
Maintainer: Brantly Callaway <brantly.callaway@temple.edu>
Diff between qte versions 1.2.1 dated 2018-02-26 and 1.2.2 dated 2018-04-30
DESCRIPTION | 14 +++--------- MD5 | 12 +++++----- NEWS.md | 3 ++ R/qte.R | 27 +++++++++++------------- R/spatt.R | 58 +++++++++++++++++++++++++++-------------------------- README.md | 2 - build/vignette.rds |binary 7 files changed, 57 insertions(+), 59 deletions(-)
Title: Kernel-Based Machine Learning Lab
Description: Kernel-based machine learning methods for classification,
regression, clustering, novelty detection, quantile regression
and dimensionality reduction. Among other methods 'kernlab'
includes Support Vector Machines, Spectral Clustering, Kernel
PCA, Gaussian Processes and a QP solver.
Author: Alexandros Karatzoglou [aut, cre],
Alex Smola [aut],
Kurt Hornik [aut]
Maintainer: Alexandros Karatzoglou <alexandros.karatzoglou@gmail.com>
Diff between kernlab versions 0.9-25 dated 2016-10-03 and 0.9-26 dated 2018-04-30
DESCRIPTION | 6 MD5 | 31 +-- NAMESPACE | 2 R/kernels.R | 444 +++++++++++++++++++++++++++++++++++++++++++++----- R/ksvm.R | 135 ++++++--------- build/vignette.rds |binary data/income.rda |binary data/musk.rda |binary data/promotergene.rda |binary data/reuters.rda |binary data/spam.rda |binary data/spirals.rda |binary data/ticdata.rda |binary inst/doc/kernlab.pdf |binary man/kkmeans.Rd | 2 src/init.c |only vignettes/jss.bib | 2 17 files changed, 480 insertions(+), 142 deletions(-)
Title: R Package for Designing and Analyzing Randomized Experiments
Description: Provides various statistical methods for
designing and analyzing randomized experiments. One functionality
of the package is the implementation of randomized-block and
matched-pair designs based on possibly multivariate pre-treatment
covariates. The package also provides the tools to analyze various
randomized experiments including cluster randomized experiments,
two-stage randomized experiments, randomized experiments with
noncompliance, and randomized experiments with missing data.
Author: Kosuke Imai [aut, cre],
Zhichao Jiang [aut]
Maintainer: Kosuke Imai <kimai@princeton.edu>
Diff between experiment versions 1.1-3 dated 2018-04-19 and 1.1-4 dated 2018-04-30
DESCRIPTION | 13 +++++++------ MD5 | 10 +++++----- NAMESPACE | 2 ++ R/CADErand.R | 39 ++++++++++++++++++++++++++++++--------- man/CADErand.Rd | 25 ++++++++++++++++++------- man/seguro.Rd | 2 +- 6 files changed, 63 insertions(+), 28 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-24 0.2.1
2017-09-06 0.1.0
Title: Nonparametric Maximum Likelihood Estimation for Random Effect
Models
Description: Nonparametric maximum likelihood estimation or Gaussian
quadrature for overdispersed generalized linear models and
variance component models.
Author: Jochen Einbeck, Ross Darnell and John Hinde
Maintainer: Jochen Einbeck <jochen.einbeck@durham.ac.uk>
Diff between npmlreg versions 0.46-1 dated 2014-10-20 and 0.46-3 dated 2018-04-30
DESCRIPTION | 16 MD5 | 28 R/alldist.R | 23 build/vignette.rds |binary data/hosp.rda |binary data/irlsuicide.rda |binary data/missouri.rda |binary data/rainfall.txt.gz |only inst/doc/npmlreg-v.R | 92 +- inst/doc/npmlreg-v.Rtex | 1519 +++++++++++++++++++++++------------------------ inst/doc/npmlreg-v.pdf |binary man/alldist.Rd | 718 +++++++++++----------- man/irlsuicide.Rd | 95 +- man/predict.glmmNPML.Rd | 228 +++---- man/rainfall.Rd |only vignettes/npmlreg-v.Rtex | 1519 +++++++++++++++++++++++------------------------ 16 files changed, 2122 insertions(+), 2116 deletions(-)
Title: Scale Space Multiresolution Analysis of Random Signals
Description: A method for the multiresolution analysis of spatial fields and images to capture scale-dependent features.
mrbsizeR is based on scale space smoothing and uses differences of smooths at neighbouring scales for finding features on different scales.
To infer which of the captured features are credible, Bayesian analysis is used.
The scale space multiresolution analysis has three steps: (1) Bayesian signal reconstruction.
(2) Using differences of smooths, scale-dependent features of the reconstructed signal can be found.
(3) Posterior credibility analysis of the differences of smooths created.
The method has first been proposed by Holmstrom, Pasanen, Furrer, Sain (2011) <DOI:10.1016/j.csda.2011.04.011>.
Author: Thimo Schuster [aut],
Roman Flury [cre, ctb],
Leena Pasanen [ctb],
Reinhard Furrer [ctb]
Maintainer: Roman Flury <roman.flury@math.uzh.ch>
Diff between mrbsizeR versions 1.0.1 dated 2017-04-03 and 1.1.0 dated 2018-04-30
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Title: Quantify the Relationship Between Development Rate and
Temperature in Ectotherms
Description: A set of functions to quantify the relationship between development
rate and temperature and to built phenological models. The package comprises
a set of models and estimated parameters borrowed from a literature review
in ectotherms (mostly arthropods).
Author: Francois Rebaudo [aut, cre] (2016-2018),
Tanusson Selvarajah [ctb] (L2 student; 2018),
Nicolas Bonnal [ctb] (M1 student; 2018),
Badre Rabhi [ctb] (L2 student; 2017),
Quentin Struelens [ctb] (VIA; 2016)
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>
Diff between devRate versions 0.1.6 dated 2018-01-25 and 0.1.7 dated 2018-04-30
DESCRIPTION | 29 +++++--- MD5 | 94 +++++++++++++------------ NEWS.md | 11 ++- R/devRate_plot.R | 16 ++-- build/vignette.rds |binary data/analytis_77.RData |binary data/bayoh_03.RData |binary data/beta_16.RData |binary data/beta_95.RData |binary data/bieri1_83.RData |binary data/briere1_99.RData |binary data/briere2_99.RData |binary data/campbell_74.RData |binary data/damos_08.RData |binary data/damos_11.RData |binary data/davidson_44.RData |binary data/devRateEqList.RData |binary data/harcourtYee_82.RData |binary data/hilbertLogan_83.RData |binary data/janisch_32.RData |binary data/kontodimas_04.RData |binary data/lactin1_95.RData |binary data/lactin2_95.RData |binary data/lamb_92.RData |binary data/logan10_76.RData |binary data/logan6_76.RData |binary data/perf2_11.RData |binary data/poly2.RData |binary data/poly4.RData |binary data/ratkowsky_82.RData |binary data/ratkowsky_83.RData |binary data/regniere_12.RData |binary data/rootsq_82.RData |binary data/schoolfieldHigh_81.RData |binary data/schoolfieldLow_81.RData |binary data/schoolfield_81.RData |binary data/sharpeDeMichele_77.RData |binary data/shi_11.RData |binary data/stinner_74.RData |binary data/taylor_81.RData |binary data/wagner_88.RData |binary data/wang_82.RData |binary data/wangengel_98.RData |binary inst/CITATION | 11 +-- inst/doc/guiaDelUsuario.R |only inst/doc/guiaDelUsuario.Rmd |only inst/doc/guiaDelUsuario.html |only inst/doc/modelEvaluation.html | 11 +-- inst/doc/quickUserGuide.html | 152 +++++++++++++++++++++--------------------- vignettes/guiaDelUsuario.Rmd |only 50 files changed, 170 insertions(+), 154 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-21 1.1
2014-04-02 1.0
Title: Sparsity by Worst-Case Quadratic Penalties
Description: Fits classical sparse regression models with
efficient active set algorithms by solving quadratic problems. Also
provides a few methods for model selection purpose (cross-validation,
stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inra.fr>
Diff between quadrupen versions 0.2-5 dated 2017-03-06 and 0.2-6 dated 2018-04-30
quadrupen-0.2-5/quadrupen/inst/examples/Rplots.pdf |only quadrupen-0.2-6/quadrupen/DESCRIPTION | 13 quadrupen-0.2-6/quadrupen/MD5 | 58 +-- quadrupen-0.2-6/quadrupen/NAMESPACE | 13 quadrupen-0.2-6/quadrupen/NEWS | 4 quadrupen-0.2-6/quadrupen/R/crossval-class.R | 7 quadrupen-0.2-6/quadrupen/R/crossval.R | 3 quadrupen-0.2-6/quadrupen/R/init.R | 12 quadrupen-0.2-6/quadrupen/R/quadrupen-class.R | 3 quadrupen-0.2-6/quadrupen/R/quadrupen-package.R | 2 quadrupen-0.2-6/quadrupen/R/quadrupen.R | 2 quadrupen-0.2-6/quadrupen/R/stability-class.R | 2 quadrupen-0.2-6/quadrupen/R/stability.R | 2 quadrupen-0.2-6/quadrupen/README.md |only quadrupen-0.2-6/quadrupen/inst/CITATION | 4 quadrupen-0.2-6/quadrupen/inst/tests/test-cg.R | 2 quadrupen-0.2-6/quadrupen/man/bounded.reg.Rd | 279 ++++++++--------- quadrupen-0.2-6/quadrupen/man/crossval.Rd | 114 +++---- quadrupen-0.2-6/quadrupen/man/cvpen-class.Rd | 66 ++-- quadrupen-0.2-6/quadrupen/man/elastic.net.Rd | 258 +++++++--------- quadrupen-0.2-6/quadrupen/man/plot.cvpen.Rd | 35 +- quadrupen-0.2-6/quadrupen/man/plot.quadrupen.Rd | 100 ++---- quadrupen-0.2-6/quadrupen/man/plot.stability.path.Rd | 94 ++--- quadrupen-0.2-6/quadrupen/man/quadrupen-class.Rd | 152 ++++----- quadrupen-0.2-6/quadrupen/man/quadrupen-package.Rd | 287 ++++++++---------- quadrupen-0.2-6/quadrupen/man/stability.Rd | 99 ++---- quadrupen-0.2-6/quadrupen/man/stability.path-class.Rd | 33 +- quadrupen-0.2-6/quadrupen/src/bounded_reg.cpp | 2 quadrupen-0.2-6/quadrupen/src/elastic_net.cpp | 4 quadrupen-0.2-6/quadrupen/src/quadratic.cpp | 2 quadrupen-0.2-6/quadrupen/src/utils.cpp | 10 31 files changed, 798 insertions(+), 864 deletions(-)
Title: Gaussian Copula Marginal Regression
Description: Likelihood inference in Gaussian copula marginal
regression models.
Author: Guido Masarotto and Cristiano Varin
Maintainer: Cristiano Varin <sammy@unive.it>
Diff between gcmr versions 1.0.0 dated 2017-04-28 and 1.0.1 dated 2018-04-30
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 1 - NEWS | 5 +++++ build/partial.rdb |binary man/plot.gcmr.Rd | 2 +- 6 files changed, 16 insertions(+), 12 deletions(-)
Title: Interface to the 'CDK' Libraries
Description: Allows the user to access functionality in the
'CDK', a Java framework for chemoinformatics. This allows the user to load
molecules, evaluate fingerprints, calculate molecular descriptors and so on.
In addition, the 'CDK' API allows the user to view structures in 2D.
Author: Rajarshi Guha [aut, cph],
Zachary Charlop-Powers [cre],
Emma Schymanski [ctb]
Maintainer: Zachary Charlop-Powers <zach.charlop.powers@gmail.com>
Diff between rcdk versions 3.4.5 dated 2017-10-31 and 3.4.7 dated 2018-04-30
rcdk-3.4.5/rcdk/inst/doc/rcdk.R |only rcdk-3.4.5/rcdk/inst/doc/rcdk.Rnw |only rcdk-3.4.5/rcdk/inst/doc/rcdk.pdf |only rcdk-3.4.5/rcdk/vignettes/rcdk.Rnw |only rcdk-3.4.7/rcdk/DESCRIPTION | 13 ++++++----- rcdk-3.4.7/rcdk/MD5 | 34 +++++++++++++++++++------------ rcdk-3.4.7/rcdk/NEWS | 2 + rcdk-3.4.7/rcdk/R/formula.R | 2 - rcdk-3.4.7/rcdk/R/io.R | 8 ++++--- rcdk-3.4.7/rcdk/R/rcdk.R | 6 ++--- rcdk-3.4.7/rcdk/R/stereo.R |only rcdk-3.4.7/rcdk/R/visual.R | 6 ++--- rcdk-3.4.7/rcdk/build/vignette.rds |binary rcdk-3.4.7/rcdk/inst/cont/rcdk.jar |binary rcdk-3.4.7/rcdk/inst/doc/molform.R |only rcdk-3.4.7/rcdk/inst/doc/molform.Rmd |only rcdk-3.4.7/rcdk/inst/doc/molform.html |only rcdk-3.4.7/rcdk/inst/doc/using-rcdk.R |only rcdk-3.4.7/rcdk/inst/doc/using-rcdk.Rmd |only rcdk-3.4.7/rcdk/inst/doc/using-rcdk.html |only rcdk-3.4.7/rcdk/man/get.element.types.Rd |only rcdk-3.4.7/rcdk/man/get.stereo.types.Rd |only rcdk-3.4.7/rcdk/man/get.stereocenters.Rd |only rcdk-3.4.7/rcdk/tests/doRUnit.R | 13 +++++------ rcdk-3.4.7/rcdk/vignettes/molform.Rmd |only rcdk-3.4.7/rcdk/vignettes/using-rcdk.Rmd |only 26 files changed, 48 insertions(+), 36 deletions(-)
Title: IRT Models for Polytomous and Continuous Item Responses
Description: Estimates the multidimensional polytomous Rasch model
(Rasch, 1961) and the Continuous Rating Scale model (Mueller, 1987).
Author: Christine Hohensinn [cre,aut]
Maintainer: Christine Hohensinn <research@christinehohensinn.at>
Diff between pcIRT versions 0.2.2 dated 2016-04-29 and 0.2.3 dated 2018-04-30
pcIRT-0.2.2/pcIRT/R/packmsg.R |only pcIRT-0.2.3/pcIRT/DESCRIPTION | 13 +++++---- pcIRT-0.2.3/pcIRT/MD5 | 46 +++++++++++++++++---------------- pcIRT-0.2.3/pcIRT/NAMESPACE | 4 ++ pcIRT-0.2.3/pcIRT/R/DRM.R | 28 +++++++++++--------- pcIRT-0.2.3/pcIRT/R/RcppExports.R | 2 - pcIRT-0.2.3/pcIRT/R/pcIRT-package.R | 18 +++++++----- pcIRT-0.2.3/pcIRT/R/simDRM.R |only pcIRT-0.2.3/pcIRT/inst/CITATION | 37 ++++++++++++++------------ pcIRT-0.2.3/pcIRT/man/crsm.Rd | 17 +++++++----- pcIRT-0.2.3/pcIRT/man/dLR.Rd | 20 ++++++++------ pcIRT-0.2.3/pcIRT/man/drm.Rd | 16 ++++++----- pcIRT-0.2.3/pcIRT/man/extraversion.Rd | 13 ++------- pcIRT-0.2.3/pcIRT/man/gmc.Rd | 14 ++++++---- pcIRT-0.2.3/pcIRT/man/iccplot.Rd | 22 ++++++++++----- pcIRT-0.2.3/pcIRT/man/lrt.Rd | 22 ++++++++++----- pcIRT-0.2.3/pcIRT/man/mprm.Rd | 15 +++++----- pcIRT-0.2.3/pcIRT/man/pcIRT-package.Rd | 19 ++++++++----- pcIRT-0.2.3/pcIRT/man/perspar.Rd | 23 ++++++++++------ pcIRT-0.2.3/pcIRT/man/reason.test.Rd | 4 -- pcIRT-0.2.3/pcIRT/man/simCRSM.Rd | 12 +++++--- pcIRT-0.2.3/pcIRT/man/simDRM.Rd |only pcIRT-0.2.3/pcIRT/man/simMPRM.Rd | 11 ++++--- pcIRT-0.2.3/pcIRT/man/wt.Rd | 20 ++++++++------ pcIRT-0.2.3/pcIRT/src/RcppExports.cpp | 10 +++---- pcIRT-0.2.3/pcIRT/src/init.c |only 26 files changed, 219 insertions(+), 167 deletions(-)
Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression a la McCulloch and George (1997).
Author: Steven L. Scott <steve.the.bayesian@gmail.com>
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between BoomSpikeSlab versions 0.9.0 dated 2017-05-28 and 1.0.0 dated 2018-04-30
DESCRIPTION | 18 +++++++-------- MD5 | 18 ++++++++++----- R/lm.spike.R | 7 ++---- R/poisson.spike.R | 53 ++++++++++++++++++++++++++++++---------------- inst |only man/predict.lm.spike.Rd | 10 +++++++- src/Makevars | 4 +-- src/spike_slab_wrapper.cc | 2 - tests |only 9 files changed, 71 insertions(+), 41 deletions(-)
Title: Zig-Zag Sampler
Description: Implements the Zig-Zag algorithm with subsampling and control variates (ZZ-CV) of (Bierkens, Fearnhead, Roberts, 2016) <arXiv:1607.03188> as applied to Bayesian logistic regression, as well as basic Zig-Zag for a Gaussian target distribution, and Bouncy Particle Sampler for a Gaussian target.
Author: Joris Bierkens
Maintainer: Joris Bierkens <joris.bierkens@tudelft.nl>
Diff between RZigZag versions 0.1.5 dated 2018-04-12 and 0.1.6 dated 2018-04-30
DESCRIPTION | 10 MD5 | 20 - NEWS.md | 5 R/RcppExports.R | 71 ++--- man/BPSGaussian.Rd | 19 - man/ZigZagGaussian.Rd | 18 - man/ZigZagLogistic.Rd | 44 +-- src/LogisticData.cpp |only src/LogisticData.h |only src/RZigZag.cpp | 696 ++++++++++++++++++++------------------------------ src/RZigZag.h | 58 +--- src/RcppExports.cpp | 45 +-- 12 files changed, 438 insertions(+), 548 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-10 0.3.5
2018-03-20 0.3.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-25 0.1.1
2018-04-11 0.1.0
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins <david@wilkox.org>
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.4.0 dated 2017-11-18 and 2.5.0 dated 2018-04-30
treemapify-2.4.0/treemapify/R/treemapify_fixed.R |only treemapify-2.5.0/treemapify/DESCRIPTION | 9 treemapify-2.5.0/treemapify/MD5 | 63 - treemapify-2.5.0/treemapify/NAMESPACE | 4 treemapify-2.5.0/treemapify/NEWS.md |only treemapify-2.5.0/treemapify/R/data.R | 2 treemapify-2.5.0/treemapify/R/geom_treemap.R | 41 treemapify-2.5.0/treemapify/R/geom_treemap_subgroup_border.R | 118 + treemapify-2.5.0/treemapify/R/geom_treemap_subgroup_text.R | 143 +- treemapify-2.5.0/treemapify/R/geom_treemap_text.R | 42 treemapify-2.5.0/treemapify/R/treemap_fixed.R |only treemapify-2.5.0/treemapify/R/treemap_squarified.R |only treemapify-2.5.0/treemapify/R/treemapify.R | 487 +------ treemapify-2.5.0/treemapify/README.md | 71 - treemapify-2.5.0/treemapify/build/vignette.rds |binary treemapify-2.5.0/treemapify/data/G20.rda |binary treemapify-2.5.0/treemapify/inst/doc/introduction-to-treemapify.R | 53 treemapify-2.5.0/treemapify/inst/doc/introduction-to-treemapify.Rmd | 82 - treemapify-2.5.0/treemapify/inst/doc/introduction-to-treemapify.html | 613 ++++------ treemapify-2.5.0/treemapify/man/G20.Rd | 2 treemapify-2.5.0/treemapify/man/figures/README-basic_treemap-1.png |binary treemapify-2.5.0/treemapify/man/figures/README-complex_treemap-1.png |binary treemapify-2.5.0/treemapify/man/figures/README-geom_treemap_text-1.png |binary treemapify-2.5.0/treemapify/man/figures/README-multiple_subgrouped_treemap-1.png |only treemapify-2.5.0/treemapify/man/figures/README-subgrouped_treemap-1.png |binary treemapify-2.5.0/treemapify/man/figures/animated_treemap.gif |binary treemapify-2.5.0/treemapify/man/geom_treemap.Rd | 16 treemapify-2.5.0/treemapify/man/geom_treemap_subgroup_border.Rd | 47 treemapify-2.5.0/treemapify/man/geom_treemap_subgroup_text.Rd | 57 treemapify-2.5.0/treemapify/man/geom_treemap_text.Rd | 6 treemapify-2.5.0/treemapify/man/treemapify.Rd | 83 - treemapify-2.5.0/treemapify/tests/testthat/test_G20.R | 2 treemapify-2.5.0/treemapify/tests/testthat/test_geoms.R | 18 treemapify-2.5.0/treemapify/tests/testthat/test_treemapify.R | 21 treemapify-2.5.0/treemapify/vignettes/introduction-to-treemapify.Rmd | 82 - 35 files changed, 896 insertions(+), 1166 deletions(-)
Title: Power Analysis for Generalised Linear Mixed Models by Simulation
Description: Calculate power for generalised linear mixed models, using
simulation. Designed to work with models fit using the 'lme4' package.
Described in Green and MacLeod, 2016 <doi:10.1111/2041-210X.12504>.
Author: Green Peter [aut, cre] (<https://orcid.org/0000-0002-0238-9852>),
MacLeod Catriona [aut],
Alday Phillip [ctb]
Maintainer: Green Peter <simr.peter@gmail.com>
Diff between simr versions 1.0.3 dated 2017-09-29 and 1.0.4 dated 2018-04-30
simr-1.0.3/simr/R/glm.R |only simr-1.0.3/simr/R/glmm.R |only simr-1.0.3/simr/R/lm.r |only simr-1.0.3/simr/tests/testthat/test_fixef.R |only simr-1.0.4/simr/DESCRIPTION | 15 simr-1.0.4/simr/MD5 | 66 ++-- simr-1.0.4/simr/NAMESPACE | 2 simr-1.0.4/simr/NEWS.md | 29 + simr-1.0.4/simr/R/binomial.R |only simr-1.0.4/simr/R/doFit.R | 43 ++ simr-1.0.4/simr/R/doSim.R | 30 + simr-1.0.4/simr/R/doTest.R | 2 simr-1.0.4/simr/R/extend.R | 21 + simr-1.0.4/simr/R/graphics.R | 7 simr-1.0.4/simr/R/lmerTest.R |only simr-1.0.4/simr/R/modify.R | 2 simr-1.0.4/simr/R/new.R | 4 simr-1.0.4/simr/R/options.R | 42 +- simr-1.0.4/simr/R/print.R | 6 simr-1.0.4/simr/R/testLibrary.R | 127 ++++---- simr-1.0.4/simr/README.md | 4 simr-1.0.4/simr/build/vignette.rds |binary simr-1.0.4/simr/inst/doc/examples.html | 372 ++++++++++++++++++------ simr-1.0.4/simr/inst/doc/fromscratch.R | 6 simr-1.0.4/simr/inst/doc/fromscratch.Rmd | 6 simr-1.0.4/simr/inst/doc/fromscratch.html | 316 ++++++++++++++++---- simr-1.0.4/simr/man/doSim.Rd | 2 simr-1.0.4/simr/man/doTest.Rd | 2 simr-1.0.4/simr/man/makeGlmer.Rd | 4 simr-1.0.4/simr/man/modify.Rd | 2 simr-1.0.4/simr/man/print.powerSim.Rd | 4 simr-1.0.4/simr/man/simrOptions.Rd | 2 simr-1.0.4/simr/man/tests.Rd | 8 simr-1.0.4/simr/tests/testthat/test_binomial.R | 66 +++- simr-1.0.4/simr/tests/testthat/test_contrasts.R |only simr-1.0.4/simr/tests/testthat/test_extend.r | 25 + simr-1.0.4/simr/tests/testthat/test_fixef.r |only simr-1.0.4/simr/vignettes/fromscratch.Rmd | 6 38 files changed, 900 insertions(+), 321 deletions(-)
Title: QTL Genome-Wide Composite Interval Mapping
Description: Conduct multi-Quantitative trait locus (QTL) mapping under the framework of random-QTL-effect mixed linear model. First, each position on the genome is detected in order to construct a negative logarithm P-value curve against genome position. Then, all the peaks on each effect (additive or dominant) curve are viewed as potential QTL, all the effects of the potential QTL are included in a multi-QTL model, their effects are estimated by empirical Bayes in doubled haploid or by adaptive lasso in F2, and true QTL are identified by likelihood radio test. Wang S-B, Wen Y-J, Ren W-L, Ni Y-L, Zhang J, Feng J-Y, Zhang Y-M (2016) <doi:10.1038/srep29951>.
Author: Zhang Ya-Wen, Wen Yang-Jun, Wang Shi-Bo, Zhang Yuan-Ming
Maintainer: Yuanming Zhang<soyzhang@mail.hzau.edu.cn>
Diff between QTL.gCIMapping versions 1.0 dated 2018-04-24 and 2.0 dated 2018-04-30
QTL.gCIMapping-1.0/QTL.gCIMapping/data/f2data.rda |only QTL.gCIMapping-1.0/QTL.gCIMapping/inst/doc/instruction.pdf |only QTL.gCIMapping-1.0/QTL.gCIMapping/man/f2data.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/DESCRIPTION | 16 QTL.gCIMapping-2.0/QTL.gCIMapping/MD5 | 32 QTL.gCIMapping-2.0/QTL.gCIMapping/NAMESPACE | 9 QTL.gCIMapping-2.0/QTL.gCIMapping/R/QTL.gCIMapping.R | 672 +------------ QTL.gCIMapping-2.0/QTL.gCIMapping/R/gcimFunc.R | 4 QTL.gCIMapping-2.0/QTL.gCIMapping/R/server.R |only QTL.gCIMapping-2.0/QTL.gCIMapping/R/ui.R |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/gen.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/genf2.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/map.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/mapf2.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/phe.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/data/phef2.rda |only QTL.gCIMapping-2.0/QTL.gCIMapping/inst/doc/Instruction.pdf |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/QTL.gCIMapping.Rd | 38 QTL.gCIMapping-2.0/QTL.gCIMapping/man/WangF.Rd | 7 QTL.gCIMapping-2.0/QTL.gCIMapping/man/WenF.Rd | 7 QTL.gCIMapping-2.0/QTL.gCIMapping/man/gen.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/genf2.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/map.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/mapf2.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/phe.Rd |only QTL.gCIMapping-2.0/QTL.gCIMapping/man/phef2.Rd |only 26 files changed, 115 insertions(+), 670 deletions(-)
More information about QTL.gCIMapping at CRAN
Permanent link
Title: Binary Classification via GMDH-Type Neural Network Algorithm
Description: Performs binary classification via Group Method of Data Handling (GMDH) - type neural network algorithm. There exist two main algorithms available in GMDH() and dceGMDH() functions. GMDH() performs classification via GMDH algorithm for a binary response and returns important variables. dceGMDH() performs classification via diverse classifiers ensemble based on GMDH (dce-GMDH) algorithm. Also, the package produces a well-formatted table of descriptives for a binary response. Moreover, it produces confusion matrix and related statistics and scatter plot (2D and 3D) with classification labels of binary classes to assess the prediction performance. All 'GMDH2' functions are designed for a binary response. See Dag O. and Yozgatligil C. (2016, ISSN:2073-4859) and Kondo T. and Ueno J. (2016, ISSN:1349-4198) for the details of GMDH algorithms.
Author: Osman Dag [aut, cre], Erdem Karabulut [aut], Reha Alpar [aut]
Maintainer: Osman Dag <osman.dag@hacettepe.edu.tr>
Diff between GMDH2 versions 1.1 dated 2018-04-14 and 1.2 dated 2018-04-30
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 1 + R/GMDH.R | 16 ++++------------ R/Table.R | 10 +++++----- R/dceGMDH.R | 20 +++++++------------- R/plot.GMDHplot.R |only man/GMDH.Rd | 7 +++---- man/Table.Rd | 4 ++-- man/dceGMDH.Rd | 10 +++++----- man/plot.GMDHplot.Rd |only man/predict.GMDH.Rd | 2 +- man/predict.dceGMDH.Rd | 2 +- 13 files changed, 45 insertions(+), 57 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-49 dated 2018-02-23 and 7.3-50 dated 2018-04-30
DESCRIPTION | 10 +++--- LICENCE.note | 2 - MD5 | 10 +++--- inst/po/en@quot/LC_MESSAGES/R-MASS.mo |binary po/R-MASS.pot | 4 +- tests/Examples/MASS-Ex.Rout.save | 56 +++++++++++++++++----------------- 6 files changed, 42 insertions(+), 40 deletions(-)
Title: Models for Continuous Traits Evolving in Macroevolutionary
Landscapes of any Shape
Description: Provides a set of functions to fit general macroevolutionary models for continuous traits evolving in adaptive landscapes of any shape. This package implements the Fokker-Planck-Kolmogorov model (FPK), in which the trait evolves under random diffusion but is also subject to a force that pulls it towards specific values - this force can be of any shape. FPK has a version in which hard reflective bounds exist at the extremes of the trait interval: this second model is called BBMV.
Author: Florian C. Boucher
Maintainer: Florian C. Boucher <flofloboucher@gmail.com>
Diff between BBMV versions 2.0 dated 2017-10-23 and 2.1 dated 2018-04-30
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NAMESPACE | 4 ++-- R/add.ML.landscape.FPK.R |only R/posterior_vs_prior.R |only build/partial.rdb |binary man/get.landscape.FPK.Rd | 10 ++++++++-- man/posterior_vs_prior.Rd |only 8 files changed, 21 insertions(+), 12 deletions(-)