Title: One-Way Tests in Independent Groups Designs
Description: Performs one-way tests in independent groups designs; one-way analysis of variance (ANOVA), Welch's heteroscedastic F test, Welch's heteroscedastic F test with trimmed means and Winsorized variances, Brown-Forsythe test, Alexander-Govern test, James second order test, Kruskal-Wallis test, Scott-Smith test, Box F test and Johansen F test. The package performs pairwise comparisons and graphical approaches. Also, the package includes Student's t test, Welch's t test and Mann-Whitney U test for two samples. Moreover, it assesses variance homogeneity and normality of data in each group via tests and plots (Dag et al., 2018, <https://journal.r-project.org/archive/2018/RJ-2018-022/RJ-2018-022.pdf>).
Author: Osman Dag [aut, cre], Anil Dolgun [aut], N. Meric Konar [aut]
Maintainer: Osman Dag <osman.dag@outlook.com>
Diff between onewaytests versions 2.2 dated 2019-04-26 and 2.3 dated 2019-05-17
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/mw.test.R | 2 ++ R/paircomp.R | 2 ++ R/paircomp.jt.R | 5 +++++ R/st.test.R | 2 ++ R/wt.test.R | 2 ++ man/ag.test.Rd | 10 ++++++++-- man/box.test.Rd | 2 +- man/mw.test.Rd | 5 +---- man/st.test.Rd | 5 +---- man/wt.test.Rd | 5 +---- 12 files changed, 41 insertions(+), 31 deletions(-)
Title: Gene ID Mapping for Genotype-Tissue Expression (GTEx) Data
Description: Convert 'Ensembl' gene identifiers from Genotype-Tissue
Expression (GTEx) data to identifiers in other annotation systems,
including 'Entrez', 'HGNC', and 'UniProt'.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Gao Wang [aut],
Lei Sun [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between grex versions 1.8 dated 2018-04-23 and 1.9 dated 2019-05-17
grex-1.8/grex/R/grex-package.R |only grex-1.8/grex/man/grex-package.Rd |only grex-1.8/grex/vignettes/grex.css |only grex-1.9/grex/DESCRIPTION | 14 grex-1.9/grex/MD5 | 36 - grex-1.9/grex/NEWS.md | 12 grex-1.9/grex/R/grex-datalist.R | 6 grex-1.9/grex/R/grex.R | 39 + grex-1.9/grex/R/sysdata.rda |binary grex-1.9/grex/README.md | 12 grex-1.9/grex/build/vignette.rds |binary grex-1.9/grex/data/gtexv6.rda |binary grex-1.9/grex/data/gtexv6p.rda |binary grex-1.9/grex/data/gtexv7.rda |binary grex-1.9/grex/inst/doc/grex.R | 12 grex-1.9/grex/inst/doc/grex.Rmd | 23 - grex-1.9/grex/inst/doc/grex.html | 735 +++++++++++++++++++++++++------------ grex-1.9/grex/man/cleanid.Rd | 2 grex-1.9/grex/man/grex.Rd | 10 grex-1.9/grex/vignettes/custom.css |only grex-1.9/grex/vignettes/grex.Rmd | 23 - 21 files changed, 602 insertions(+), 322 deletions(-)
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],
Samuel Macedo [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between sparklyr versions 1.0.0 dated 2019-02-25 and 1.0.1 dated 2019-05-17
sparklyr-1.0.0/sparklyr/man/sdf_partition.Rd |only sparklyr-1.0.1/sparklyr/DESCRIPTION | 8 sparklyr-1.0.1/sparklyr/MD5 | 243 +++++----- sparklyr-1.0.1/sparklyr/NAMESPACE | 15 sparklyr-1.0.1/sparklyr/NEWS.md | 54 ++ sparklyr-1.0.1/sparklyr/R/connection_spark.R | 3 sparklyr-1.0.1/sparklyr/R/dplyr_spark_table.R | 2 sparklyr-1.0.1/sparklyr/R/install_spark_versions.R | 4 sparklyr-1.0.1/sparklyr/R/java.R | 8 sparklyr-1.0.1/sparklyr/R/kubernetes_config.R | 7 sparklyr-1.0.1/sparklyr/R/livy_connection.R | 3 sparklyr-1.0.1/sparklyr/R/ml_classification_linear_svc.R | 2 sparklyr-1.0.1/sparklyr/R/ml_classification_logistic_regression.R | 99 ++-- sparklyr-1.0.1/sparklyr/R/ml_classification_multilayer_perceptron_classifier.R | 2 sparklyr-1.0.1/sparklyr/R/ml_classification_naive_bayes.R | 2 sparklyr-1.0.1/sparklyr/R/ml_clustering_bisecting_kmeans.R | 10 sparklyr-1.0.1/sparklyr/R/ml_clustering_gaussian_mixture.R | 8 sparklyr-1.0.1/sparklyr/R/ml_clustering_kmeans.R | 8 sparklyr-1.0.1/sparklyr/R/ml_clustering_lda.R | 148 +++++- sparklyr-1.0.1/sparklyr/R/ml_evaluate.R |only sparklyr-1.0.1/sparklyr/R/ml_evaluation_clustering.R | 2 sparklyr-1.0.1/sparklyr/R/ml_evaluation_prediction.R | 6 sparklyr-1.0.1/sparklyr/R/ml_evaluator.R | 9 sparklyr-1.0.1/sparklyr/R/ml_feature_one_hot_encoder_estimator.R |only sparklyr-1.0.1/sparklyr/R/ml_model_bisecting_kmeans.R | 19 sparklyr-1.0.1/sparklyr/R/ml_model_decision_tree.R | 2 sparklyr-1.0.1/sparklyr/R/ml_model_gradient_boosted_trees.R | 2 sparklyr-1.0.1/sparklyr/R/ml_model_helpers.R | 17 sparklyr-1.0.1/sparklyr/R/ml_model_kmeans.R | 22 sparklyr-1.0.1/sparklyr/R/ml_model_random_forest.R | 2 sparklyr-1.0.1/sparklyr/R/ml_regression_aft_survival_regression.R | 2 sparklyr-1.0.1/sparklyr/R/ml_regression_generalized_linear_regression.R | 68 +- sparklyr-1.0.1/sparklyr/R/ml_regression_isotonic_regression.R | 2 sparklyr-1.0.1/sparklyr/R/ml_regression_linear_regression.R | 43 + sparklyr-1.0.1/sparklyr/R/ml_summary.R | 19 sparklyr-1.0.1/sparklyr/R/mutation.R | 4 sparklyr-1.0.1/sparklyr/R/project_template.R | 11 sparklyr-1.0.1/sparklyr/R/sdf_interface.R | 2 sparklyr-1.0.1/sparklyr/R/sdf_ml.R | 18 sparklyr-1.0.1/sparklyr/R/sdf_stat.R |only sparklyr-1.0.1/sparklyr/R/shell_connection.R | 10 sparklyr-1.0.1/sparklyr/R/spark_apply.R | 3 sparklyr-1.0.1/sparklyr/R/spark_compile.R | 7 sparklyr-1.0.1/sparklyr/R/spark_extensions.R | 7 sparklyr-1.0.1/sparklyr/R/worker_apply.R | 5 sparklyr-1.0.1/sparklyr/README.md | 4 sparklyr-1.0.1/sparklyr/inst/extdata/versions.json | 52 ++ sparklyr-1.0.1/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-1.0.1/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-1.0.1/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-1.0.1/sparklyr/inst/java/sparklyr-2.3-2.11.jar |binary sparklyr-1.0.1/sparklyr/inst/livy/spark-1.5.2/backend.scala | 8 sparklyr-1.0.1/sparklyr/inst/rstudio/connections.dcf | 2 sparklyr-1.0.1/sparklyr/inst/rstudio/templates/project/skeleton.dcf | 2 sparklyr-1.0.1/sparklyr/inst/sparkml/class_mapping.json | 2 sparklyr-1.0.1/sparklyr/java/spark-1.5.2/backend.scala | 8 sparklyr-1.0.1/sparklyr/java/spark-1.5.2/shell.scala | 11 sparklyr-1.0.1/sparklyr/man/ft_binarizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_bucketizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_chisq_selector.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_count_vectorizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_dct.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_elementwise_product.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_feature_hasher.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_hashing_tf.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_idf.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_imputer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_index_to_string.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_interaction.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_lsh.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_max_abs_scaler.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_min_max_scaler.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_ngram.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_normalizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_one_hot_encoder.Rd | 4 sparklyr-1.0.1/sparklyr/man/ft_one_hot_encoder_estimator.Rd |only sparklyr-1.0.1/sparklyr/man/ft_pca.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_polynomial_expansion.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_quantile_discretizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_r_formula.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_regex_tokenizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_standard_scaler.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_stop_words_remover.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_string_indexer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_tokenizer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_vector_assembler.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_vector_indexer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_vector_slicer.Rd | 1 sparklyr-1.0.1/sparklyr/man/ft_word2vec.Rd | 1 sparklyr-1.0.1/sparklyr/man/ml_aft_survival_regression.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_bisecting_kmeans.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_clustering_evaluator.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_decision_tree.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_evaluate.Rd | 31 + sparklyr-1.0.1/sparklyr/man/ml_evaluator.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_gaussian_mixture.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_generalized_linear_regression.Rd | 11 sparklyr-1.0.1/sparklyr/man/ml_gradient_boosted_trees.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_isotonic_regression.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_kmeans.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_lda.Rd | 27 - sparklyr-1.0.1/sparklyr/man/ml_linear_regression.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_linear_svc.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_logistic_regression.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_multilayer_perceptron_classifier.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_naive_bayes.Rd | 2 sparklyr-1.0.1/sparklyr/man/ml_random_forest.Rd | 2 sparklyr-1.0.1/sparklyr/man/sdf_copy_to.Rd | 2 sparklyr-1.0.1/sparklyr/man/sdf_crosstab.Rd |only sparklyr-1.0.1/sparklyr/man/sdf_random_split.Rd |only sparklyr-1.0.1/sparklyr/man/sdf_register.Rd | 2 sparklyr-1.0.1/sparklyr/man/sdf_sample.Rd | 4 sparklyr-1.0.1/sparklyr/man/sdf_sort.Rd | 4 sparklyr-1.0.1/sparklyr/man/spark_apply.Rd | 3 sparklyr-1.0.1/sparklyr/man/spark_dependency.Rd | 4 sparklyr-1.0.1/sparklyr/man/spark_extension.Rd |only sparklyr-1.0.1/sparklyr/man/sql-transformer.Rd | 1 sparklyr-1.0.1/sparklyr/tests/testthat/helper-initialize.R | 8 sparklyr-1.0.1/sparklyr/tests/testthat/test-binds.R | 76 ++- sparklyr-1.0.1/sparklyr/tests/testthat/test-feature-one-hot-encoder-estimator.R |only sparklyr-1.0.1/sparklyr/tests/testthat/test-ml-classification-naive-bayes.R | 2 sparklyr-1.0.1/sparklyr/tests/testthat/test-ml-evaluate.R |only sparklyr-1.0.1/sparklyr/tests/testthat/test-ml-evaluation-clustering.R | 34 + sparklyr-1.0.1/sparklyr/tests/testthat/test-ml-feature-string-indexer.R | 6 sparklyr-1.0.1/sparklyr/tests/testthat/test-project-template.R | 4 sparklyr-1.0.1/sparklyr/tests/testthat/test-sdf-stat.R |only sparklyr-1.0.1/sparklyr/tests/testthat/test-serialization.R | 8 sparklyr-1.0.1/sparklyr/tests/testthat/test-stream.R | 27 - 128 files changed, 919 insertions(+), 396 deletions(-)
Title: Descriptive mAchine Learning EXplanations
Description: Machine Learning (ML) models are widely used and have various applications in classification
or regression. Models created with boosting, bagging, stacking or similar techniques are often
used due to their high performance, but such black-box models usually lack of interpretability.
DALEX package contains various explainers that help to understand the link between input variables and model output.
The single_variable() explainer extracts conditional response of a model as a function of a single selected variable.
It is a wrapper over packages 'pdp' (Greenwell 2017) <doi:10.32614/RJ-2017-016>,
'ALEPlot' (Apley 2018) <arXiv:1612.08468> and 'factorMerger' (Sitko and Biecek 2017) <arXiv:1709.04412>.
The single_prediction() explainer attributes parts of a model prediction to particular variables used in the model.
It is a wrapper over 'breakDown' package (Staniak and Biecek 2018) <doi:10.32614/RJ-2018-072>.
The variable_dropout() explainer calculates variable importance scores based on variable shuffling
(Fisher at al. 2018) <arXiv:1801.01489>.
All these explainers can be plotted with generic plot() function and compared across different models.
'DALEX' is a part of the 'DrWhy.AI' universe (Biecek 2018) <arXiv:1806.08915>.
Author: Przemyslaw Biecek [aut, cre] (<https://orcid.org/0000-0001-8423-1823>)
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between DALEX versions 0.3.0 dated 2019-03-25 and 0.4 dated 2019-05-17
DALEX-0.3.0/DALEX/R/plot_model_feature_response.R |only DALEX-0.3.0/DALEX/R/plot_single_prediction.R |only DALEX-0.3.0/DALEX/R/plot_single_variable.R |only DALEX-0.3.0/DALEX/R/plot_variable_dropout.R |only DALEX-0.3.0/DALEX/R/single_feature.R |only DALEX-0.3.0/DALEX/R/single_prediction.R |only DALEX-0.3.0/DALEX/R/single_variable.R |only DALEX-0.3.0/DALEX/R/variable_dropout.R |only DALEX-0.3.0/DALEX/man/model_feature_response.Rd |only DALEX-0.3.0/DALEX/man/plot.model_feature_response_explainer.Rd |only DALEX-0.4/DALEX/DESCRIPTION | 10 - DALEX-0.4/DALEX/MD5 | 61 +++++----- DALEX-0.4/DALEX/NAMESPACE | 11 + DALEX-0.4/DALEX/NEWS.md | 11 + DALEX-0.4/DALEX/R/explain.R | 6 DALEX-0.4/DALEX/R/feature_response.R |only DALEX-0.4/DALEX/R/install_dependencies.R | 2 DALEX-0.4/DALEX/R/misc.R |only DALEX-0.4/DALEX/R/plot_feature_response.R |only DALEX-0.4/DALEX/R/plot_model_performance.R | 18 +- DALEX-0.4/DALEX/R/plot_prediction_breakdown.R |only DALEX-0.4/DALEX/R/plot_variable_importance.R |only DALEX-0.4/DALEX/R/plot_variable_response.R |only DALEX-0.4/DALEX/R/prediction_breakdown.R |only DALEX-0.4/DALEX/R/theme_drwhy.R | 2 DALEX-0.4/DALEX/R/variable_importance.R |only DALEX-0.4/DALEX/R/variable_response.R |only DALEX-0.4/DALEX/R/yhat.R | 11 + DALEX-0.4/DALEX/R/zzz.R | 18 ++ DALEX-0.4/DALEX/man/feature_response.Rd |only DALEX-0.4/DALEX/man/install_dependencies.Rd | 4 DALEX-0.4/DALEX/man/plot.feature_response_explainer.Rd |only DALEX-0.4/DALEX/man/plot.model_performance_explainer.Rd | 5 DALEX-0.4/DALEX/man/plot.prediction_breakdown_explainer.Rd | 2 DALEX-0.4/DALEX/man/plot.variable_importance_explainer.Rd | 2 DALEX-0.4/DALEX/man/plot.variable_response_explainer.Rd | 2 DALEX-0.4/DALEX/man/prediction_breakdown.Rd | 7 - DALEX-0.4/DALEX/man/variable_importance.Rd | 7 - DALEX-0.4/DALEX/man/variable_response.Rd | 5 DALEX-0.4/DALEX/man/yhat.Rd | 6 DALEX-0.4/DALEX/tests/testthat/test_single_feature.R | 24 +-- DALEX-0.4/DALEX/tests/testthat/test_variable_response.R | 1 42 files changed, 138 insertions(+), 77 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project.
Some code in the BOOM libraries has been modified from other open source
projects. These include Cephes (obtained from Netlib, written by Stephen
L. Moshier), NEWUOA (M.J.D Powell, obtained from Powell's web site), and a
modified version of the R math libraries (R core development team). Original
copyright notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications made to the
original code. Google claims copyright for code written while Steven
L. Scott was employed at Google from 2008 - 2018, but BOOM is not an
officially supported Google project.
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.8 dated 2018-04-29 and 0.9 dated 2019-05-17
Boom-0.8/Boom/inst/include/BOOM.hpp |only Boom-0.8/Boom/inst/include/LinAlg/Kronecker.hpp |only Boom-0.8/Boom/inst/include/LinAlg/LinAlgExceptions.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/CumulativeLogitModel.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/CumulativeProbitModel.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/MvReg2.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/MvnGivenXandSigma.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.hpp |only Boom-0.8/Boom/inst/include/Models/Glm/PosteriorSamplers/MvRegSampler.hpp |only Boom-0.8/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp |only Boom-0.8/Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.hpp |only Boom-0.8/Boom/inst/include/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.hpp |only Boom-0.8/Boom/inst/include/cpputil/str2d.hpp |only Boom-0.8/Boom/inst/include/r_interface/create_state_model.hpp |only Boom-0.8/Boom/src/LinAlg/Kronecker.cpp |only Boom-0.8/Boom/src/LinAlg/LinAlgExceptions.cpp |only Boom-0.8/Boom/src/Models/Glm/CumulativeLogitModel.cpp |only Boom-0.8/Boom/src/Models/Glm/CumulativeProbitModel.cpp |only Boom-0.8/Boom/src/Models/Glm/MvReg2.cpp |only Boom-0.8/Boom/src/Models/Glm/MvnGivenXandSigma.cpp |only Boom-0.8/Boom/src/Models/Glm/PosteriorSamplers/CumulativeLogitSampler.cpp |only Boom-0.8/Boom/src/Models/Glm/PosteriorSamplers/CumulativeProbitSampler.cpp |only Boom-0.8/Boom/src/Models/Glm/PosteriorSamplers/MvRegSampler.cpp |only Boom-0.8/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.cpp |only Boom-0.8/Boom/src/Models/PointProcess/PosteriorSamplers/HomogeneousPoissonProcessPosteriorSampler.cpp |only Boom-0.8/Boom/src/Models/PointProcess/PosteriorSamplers/MarkovModulatedPoissonProcessPosteriorSampler.cpp |only Boom-0.8/Boom/src/cpputil/cat_string.cpp |only Boom-0.8/Boom/src/cpputil/str2d.cpp |only Boom-0.8/Boom/src/create_state_model.cpp |only Boom-0.9/Boom/DESCRIPTION | 11 Boom-0.9/Boom/MD5 | 1265 ++++++---- Boom-0.9/Boom/NAMESPACE | 80 Boom-0.9/Boom/R/boxplot.true.R | 13 Boom-0.9/Boom/R/check.data.R | 25 Boom-0.9/Boom/R/check.mcmc.matrix.R | 43 Boom-0.9/Boom/R/circle.R |only Boom-0.9/Boom/R/compare.den.R | 2 Boom-0.9/Boom/R/compare.many.ts.R | 2 Boom-0.9/Boom/R/compare.vector.distribution.R | 3 Boom-0.9/Boom/R/function.R |only Boom-0.9/Boom/R/log.integrated.gaussian.likelihood.R |only Boom-0.9/Boom/R/plot.dynamic.distribution.R | 6 Boom-0.9/Boom/R/plot.many.ts.R | 11 Boom-0.9/Boom/R/prior_specification.R | 42 Boom-0.9/Boom/R/sufstats.R | 12 Boom-0.9/Boom/inst/include/Bmath/Bmath.hpp | 9 Boom-0.9/Boom/inst/include/Bmath/nmath.hpp | 10 Boom-0.9/Boom/inst/include/Eigen |only Boom-0.9/Boom/inst/include/LinAlg/Array.hpp | 71 Boom-0.9/Boom/inst/include/LinAlg/Cholesky.hpp | 18 Boom-0.9/Boom/inst/include/LinAlg/DiagonalMatrix.hpp | 33 Boom-0.9/Boom/inst/include/LinAlg/LU.hpp |only Boom-0.9/Boom/inst/include/LinAlg/Matrix.hpp | 147 - Boom-0.9/Boom/inst/include/LinAlg/QR.hpp | 21 Boom-0.9/Boom/inst/include/LinAlg/SWEEP.hpp | 2 Boom-0.9/Boom/inst/include/LinAlg/Selector.hpp | 267 +- Boom-0.9/Boom/inst/include/LinAlg/SpdMatrix.hpp | 31 Boom-0.9/Boom/inst/include/LinAlg/SubMatrix.hpp | 75 Boom-0.9/Boom/inst/include/LinAlg/Vector.hpp | 70 Boom-0.9/Boom/inst/include/LinAlg/VectorView.hpp | 118 Boom-0.9/Boom/inst/include/Models/Bart/Bart.hpp | 8 Boom-0.9/Boom/inst/include/Models/BetaModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/BinomialModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/CategoricalData.hpp | 16 Boom-0.9/Boom/inst/include/Models/CompositeData.hpp | 2 Boom-0.9/Boom/inst/include/Models/DataPair.hpp | 2 Boom-0.9/Boom/inst/include/Models/DataTypes.hpp | 70 Boom-0.9/Boom/inst/include/Models/DirichletModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/ExponentialIncrementModel.hpp |only Boom-0.9/Boom/inst/include/Models/ExponentialModel.hpp | 6 Boom-0.9/Boom/inst/include/Models/GammaModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/GaussianModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/GaussianModelBase.hpp | 54 Boom-0.9/Boom/inst/include/Models/GaussianModelGivenSigma.hpp | 3 Boom-0.9/Boom/inst/include/Models/Glm/AggregatedRegressionModel.hpp | 27 Boom-0.9/Boom/inst/include/Models/Glm/BinomialLogitModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/BinomialProbitModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/BinomialRegressionData.hpp | 4 Boom-0.9/Boom/inst/include/Models/Glm/ChoiceData.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/GammaRegressionModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/Glm.hpp | 20 Boom-0.9/Boom/inst/include/Models/Glm/GlmCoefs.hpp | 62 Boom-0.9/Boom/inst/include/Models/Glm/IndependentRegressionModels.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/LogisticRegressionModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/ModelSelectionConcepts.hpp | 26 Boom-0.9/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/MultinomialProbitModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/MultivariateRegression.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/MvnGivenX.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/MvtRegModel.hpp | 13 Boom-0.9/Boom/inst/include/Models/Glm/OrdinalCutpointModel.hpp | 217 + Boom-0.9/Boom/inst/include/Models/Glm/PoissonRegressionData.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/AdaptiveSpikeSlabRegressionSampler.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.hpp | 4 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialLogitSamplerTim.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/BinomialProbitDataImputer.hpp | 6 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp | 115 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/CorrelationMap.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/IndependentRegressionModelsPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/MultivariateRegressionSpikeSlabSampler.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/MvtRegSampler.hpp | 10 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.hpp | 101 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/OrdinalLogitImputer.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/OrdinalLogitPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionConjSampler.hpp | 22 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/SpikeSlabSampler.hpp | 18 Boom-0.9/Boom/inst/include/Models/Glm/PosteriorSamplers/VsPriorSampler.hpp | 17 Boom-0.9/Boom/inst/include/Models/Glm/ProbitRegression.hpp | 2 Boom-0.9/Boom/inst/include/Models/Glm/RegressionModel.hpp | 73 Boom-0.9/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp | 181 + Boom-0.9/Boom/inst/include/Models/Glm/WeightedRegressionModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/Glm/ZeroInflatedGammaRegression.hpp | 2 Boom-0.9/Boom/inst/include/Models/HMM/Clickstream/NestedHmm.hpp | 12 Boom-0.9/Boom/inst/include/Models/HMM/Clickstream/Stream.hpp | 2 Boom-0.9/Boom/inst/include/Models/HMM/HMM2.hpp | 2 Boom-0.9/Boom/inst/include/Models/HMM/HealthStateModel.hpp | 8 Boom-0.9/Boom/inst/include/Models/HMM/HmmFilter.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/HierarchicalDirichletModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/HierarchicalGammaModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/HierarchicalPoissonModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierGaussianRegressionAsisSampler.hpp |only Boom-0.9/Boom/inst/include/Models/IRT/DafePcrRwm.hpp | 3 Boom-0.9/Boom/inst/include/Models/IRT/IRT.hpp | 2 Boom-0.9/Boom/inst/include/Models/IRT/IrtModel.hpp | 19 Boom-0.9/Boom/inst/include/Models/IRT/Item.hpp | 32 Boom-0.9/Boom/inst/include/Models/IRT/PartialCreditModel.hpp | 10 Boom-0.9/Boom/inst/include/Models/IRT/Subject.hpp | 18 Boom-0.9/Boom/inst/include/Models/IRT/multisubscale_logit_cutpoint_model.hpp | 2 Boom-0.9/Boom/inst/include/Models/IndependentMvnModel.hpp | 31 Boom-0.9/Boom/inst/include/Models/IndependentMvnModelGivenScalarSigma.hpp | 2 Boom-0.9/Boom/inst/include/Models/MarkovModel.hpp | 24 Boom-0.9/Boom/inst/include/Models/MatrixNormalModel.hpp |only Boom-0.9/Boom/inst/include/Models/Mixtures/ConditionalFiniteMixtureModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Mixtures/MvnMetaAnalysisDPMPriorModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/ModelTypes.hpp | 15 Boom-0.9/Boom/inst/include/Models/MultinomialModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/MvnBase.hpp | 6 Boom-0.9/Boom/inst/include/Models/MvnGivenScalarSigma.hpp | 3 Boom-0.9/Boom/inst/include/Models/Nnet |only Boom-0.9/Boom/inst/include/Models/ParamTypes.hpp | 43 Boom-0.9/Boom/inst/include/Models/PointProcess/HomogeneousPoissonProcess.hpp | 2 Boom-0.9/Boom/inst/include/Models/PointProcess/MarkovModulatedPoissonProcess.hpp | 8 Boom-0.9/Boom/inst/include/Models/PointProcess/PointProcess.hpp | 21 Boom-0.9/Boom/inst/include/Models/PointProcess/PoissonClusterProcess.hpp | 10 Boom-0.9/Boom/inst/include/Models/PointProcess/PosteriorSamplers/HomogPoissonProcessPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/PointProcess/PosteriorSamplers/MmppPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/PointProcess/WeeklyCyclePoissonProcess.hpp | 2 Boom-0.9/Boom/inst/include/Models/PoissonGammaModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/PoissonModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/Policies/CompositeParamPolicy.hpp | 3 Boom-0.9/Boom/inst/include/Models/Policies/IID_DataPolicy.hpp | 3 Boom-0.9/Boom/inst/include/Models/Policies/ParamPolicy_2.hpp | 69 Boom-0.9/Boom/inst/include/Models/Policies/PriorPolicy.hpp | 1 Boom-0.9/Boom/inst/include/Models/Policies/SufstatDataPolicy.hpp | 1 Boom-0.9/Boom/inst/include/Models/PosteriorSamplers/GenericGaussianVarianceSampler.hpp | 2 Boom-0.9/Boom/inst/include/Models/PosteriorSamplers/IndependentMvnVarSampler.hpp | 3 Boom-0.9/Boom/inst/include/Models/PosteriorSamplers/MvnConjSampler.hpp | 51 Boom-0.9/Boom/inst/include/Models/PosteriorSamplers/MvnVarSampler.hpp | 57 Boom-0.9/Boom/inst/include/Models/PosteriorSamplers/PosteriorSampler.hpp | 3 Boom-0.9/Boom/inst/include/Models/ProductDirichletModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/ScaledChisqModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/SpdData.hpp | 49 Boom-0.9/Boom/inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp | 45 Boom-0.9/Boom/inst/include/Models/StateSpace/DynamicInterceptRegression.hpp | 213 + Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/ConditionalIidKalmanFilter.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/KalmanFilterBase.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/MultivariateKalmanFilterBase.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/ScalarKalmanFilter.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/SparseKalmanTools.hpp | 56 Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/SparseMatrix.hpp | 592 +++- Boom-0.9/Boom/inst/include/Models/StateSpace/Filters/SparseVector.hpp | 3 Boom-0.9/Boom/inst/include/Models/StateSpace/MultivariateStateSpaceModel.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/MultivariateStateSpaceModelBase.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/MultivariateStateSpaceRegressionModel.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/PosteriorSamplers/DynamicInterceptRegressionPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/PosteriorSamplers/MultivariateStateSpaceModelSampler.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/PosteriorSamplers/MvStateSpaceRegressionPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/PosteriorSamplers/SharedLocalLevelPosteriorSampler.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.hpp | 4 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModelVector.hpp |only Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 17 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionArStateModel.hpp | 37 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp | 31 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/GeneralSeasonalStateModel.hpp | 15 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/HierarchicalRegressionHolidayStateModel.hpp | 79 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/Holiday.hpp | 4 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp | 213 + Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 29 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp | 63 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/RegressionHolidayStateModel.hpp | 90 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/RegressionStateModel.hpp | 37 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp | 20 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp | 25 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 118 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/StaticInterceptStateModel.hpp | 16 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp | 23 Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp | 200 - Boom-0.9/Boom/inst/include/Models/StateSpace/StateModels/test_utils |only Boom-0.9/Boom/inst/include/Models/StateSpace/StateSpaceLogitModel.hpp | 5 Boom-0.9/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp | 34 Boom-0.9/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 939 ++----- Boom-0.9/Boom/inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp | 4 Boom-0.9/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp | 3 Boom-0.9/Boom/inst/include/Models/StateSpace/tests |only Boom-0.9/Boom/inst/include/Models/TimeSeries/ArModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/TimeSeries/ArmaModel.hpp | 18 Boom-0.9/Boom/inst/include/Models/TimeSeries/AugmentedTimeSeries.hpp | 4 Boom-0.9/Boom/inst/include/Models/TimeSeries/NonzeroMeanAr1Model.hpp | 4 Boom-0.9/Boom/inst/include/Models/TimeSeries/TimeSeries.hpp | 18 Boom-0.9/Boom/inst/include/Models/UniformModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/WeightedData.hpp | 4 Boom-0.9/Boom/inst/include/Models/WeightedGaussianSuf.hpp | 2 Boom-0.9/Boom/inst/include/Models/WeightedMvnModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/WishartModel.hpp | 2 Boom-0.9/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 2 Boom-0.9/Boom/inst/include/Samplers/UnivariateSliceSampler.hpp | 6 Boom-0.9/Boom/inst/include/TargetFun/LogPost.hpp | 2 Boom-0.9/Boom/inst/include/cpputil/Constants.hpp | 1 Boom-0.9/Boom/inst/include/cpputil/Date.hpp | 16 Boom-0.9/Boom/inst/include/cpputil/DateTime.hpp | 27 Boom-0.9/Boom/inst/include/cpputil/DefaultVnames.hpp | 4 Boom-0.9/Boom/inst/include/cpputil/OutputTable.hpp | 4 Boom-0.9/Boom/inst/include/cpputil/ParamHolder.hpp | 35 Boom-0.9/Boom/inst/include/cpputil/ProgressTracker.hpp | 2 Boom-0.9/Boom/inst/include/cpputil/Redirector.hpp | 11 Boom-0.9/Boom/inst/include/cpputil/Split.hpp | 12 Boom-0.9/Boom/inst/include/cpputil/ThreadTools.hpp | 6 Boom-0.9/Boom/inst/include/cpputil/file_utils.hpp | 2 Boom-0.9/Boom/inst/include/cpputil/portable_math.hpp | 6 Boom-0.9/Boom/inst/include/cpputil/string_utils.hpp | 83 Boom-0.9/Boom/inst/include/cpputil/timer.hpp |only Boom-0.9/Boom/inst/include/distributions.hpp | 158 + Boom-0.9/Boom/inst/include/distributions/rng.hpp | 31 Boom-0.9/Boom/inst/include/numopt.hpp | 6 Boom-0.9/Boom/inst/include/r_interface/boom_r_tools.hpp | 73 Boom-0.9/Boom/inst/include/r_interface/create_mixture_component.hpp | 4 Boom-0.9/Boom/inst/include/r_interface/create_point_process.hpp | 2 Boom-0.9/Boom/inst/include/r_interface/create_poisson_cluster_components.hpp | 2 Boom-0.9/Boom/inst/include/r_interface/create_poisson_process.hpp | 2 Boom-0.9/Boom/inst/include/r_interface/determine_nthreads.hpp | 2 Boom-0.9/Boom/inst/include/r_interface/list_io.hpp | 944 ++++--- Boom-0.9/Boom/inst/include/r_interface/parse_model_formula.hpp | 2 Boom-0.9/Boom/inst/include/r_interface/prior_specification.hpp | 30 Boom-0.9/Boom/inst/include/r_interface/seed_rng_from_R.hpp | 12 Boom-0.9/Boom/inst/include/r_interface/sufstats.hpp | 4 Boom-0.9/Boom/inst/include/stats/AsciiDistributionCompare.hpp | 18 Boom-0.9/Boom/inst/include/stats/DataTable.hpp | 25 Boom-0.9/Boom/inst/include/stats/Design.hpp | 2 Boom-0.9/Boom/inst/include/stats/FreqDist.hpp | 8 Boom-0.9/Boom/inst/include/stats/NaturalSpline.hpp | 1 Boom-0.9/Boom/inst/include/stats/Resampler.hpp | 2 Boom-0.9/Boom/inst/include/stats/simple_random_sample.hpp | 2 Boom-0.9/Boom/inst/include/stats/summary.hpp |only Boom-0.9/Boom/inst/include/uint.hpp | 6 Boom-0.9/Boom/man/ToString.Rd | 2 Boom-0.9/Boom/man/ar1.coefficient.prior.Rd | 4 Boom-0.9/Boom/man/beta.prior.Rd | 4 Boom-0.9/Boom/man/boxplot.true.Rd | 30 Boom-0.9/Boom/man/check.Rd | 25 Boom-0.9/Boom/man/check.data.Rd | 4 Boom-0.9/Boom/man/circles.Rd |only Boom-0.9/Boom/man/compare.vector.distributions.Rd | 2 Boom-0.9/Boom/man/dirichlet-distribution.Rd | 2 Boom-0.9/Boom/man/dirichlet.prior.Rd | 4 Boom-0.9/Boom/man/discrete-uniform-prior.Rd | 2 Boom-0.9/Boom/man/dmvn.Rd | 4 Boom-0.9/Boom/man/double.model.Rd | 4 Boom-0.9/Boom/man/gamma.prior.Rd | 4 Boom-0.9/Boom/man/generate_factor_data.Rd | 2 Boom-0.9/Boom/man/inverse-wishart.Rd | 2 Boom-0.9/Boom/man/invgamma.Rd | 2 Boom-0.9/Boom/man/lmgamma.Rd | 2 Boom-0.9/Boom/man/log.integrated.gaussian.likelihood.Rd |only Boom-0.9/Boom/man/lognormal.prior.Rd | 4 Boom-0.9/Boom/man/markov.prior.Rd | 4 Boom-0.9/Boom/man/match_data_frame.Rd | 2 Boom-0.9/Boom/man/mscan.Rd | 2 Boom-0.9/Boom/man/mvn.diagonal.prior.Rd | 4 Boom-0.9/Boom/man/mvn.independent.sigma.prior.Rd | 2 Boom-0.9/Boom/man/mvn.prior.Rd | 4 Boom-0.9/Boom/man/normal.inverse.gamma.prior.Rd | 4 Boom-0.9/Boom/man/normal.inverse.wishart.prior.Rd | 4 Boom-0.9/Boom/man/normal.prior.Rd | 2 Boom-0.9/Boom/man/plot.dynamic.distribution.Rd | 2 Boom-0.9/Boom/man/regression.coefficient.conjugate.prior.Rd | 2 Boom-0.9/Boom/man/rmvn.Rd | 4 Boom-0.9/Boom/man/rvectorfunction.Rd |only Boom-0.9/Boom/man/scaled.matrix.normal.prior.Rd |only Boom-0.9/Boom/man/sd.prior.Rd | 4 Boom-0.9/Boom/man/sufstat.Rd | 9 Boom-0.9/Boom/man/suggest.burn.log.likelihood.Rd | 2 Boom-0.9/Boom/man/thin.matrix.Rd | 2 Boom-0.9/Boom/man/timeseries.boxplot.Rd | 2 Boom-0.9/Boom/man/traceproduct.Rd | 2 Boom-0.9/Boom/man/uniform.prior.Rd | 2 Boom-0.9/Boom/man/wishart.Rd | 2 Boom-0.9/Boom/src/Bmath/Bmath.hpp | 9 Boom-0.9/Boom/src/Bmath/dlogis.cpp | 16 Boom-0.9/Boom/src/Bmath/gammalims.cpp | 55 Boom-0.9/Boom/src/Bmath/mathlib_error.cpp | 12 Boom-0.9/Boom/src/Bmath/mlutils.cpp | 9 Boom-0.9/Boom/src/Bmath/nmath.hpp | 10 Boom-0.9/Boom/src/Bmath/pbeta.cpp | 2 Boom-0.9/Boom/src/Bmath/pgamma.cpp | 2 Boom-0.9/Boom/src/Bmath/plogis.cpp | 19 Boom-0.9/Boom/src/Bmath/pnchisq.cpp | 13 Boom-0.9/Boom/src/Bmath/qchisq.cpp | 8 Boom-0.9/Boom/src/Bmath/qgamma.cpp | 28 Boom-0.9/Boom/src/Bmath/rbinom.cpp | 2 Boom-0.9/Boom/src/Bmath/rpois.cpp | 6 Boom-0.9/Boom/src/LinAlg/Array.cpp | 72 Boom-0.9/Boom/src/LinAlg/Cholesky.cpp | 55 Boom-0.9/Boom/src/LinAlg/CorrelationMatrix.cpp | 1 Boom-0.9/Boom/src/LinAlg/DiagonalMatrix.cpp | 61 Boom-0.9/Boom/src/LinAlg/Eigen.cpp | 2 Boom-0.9/Boom/src/LinAlg/LU.cpp |only Boom-0.9/Boom/src/LinAlg/Matrix.cpp | 166 - Boom-0.9/Boom/src/LinAlg/QR.cpp | 79 Boom-0.9/Boom/src/LinAlg/SVD.cpp | 2 Boom-0.9/Boom/src/LinAlg/Selector.cpp | 704 +++-- Boom-0.9/Boom/src/LinAlg/SpdMatrix.cpp | 72 Boom-0.9/Boom/src/LinAlg/SubMatrix.cpp | 217 + Boom-0.9/Boom/src/LinAlg/Vector.cpp | 230 + Boom-0.9/Boom/src/LinAlg/VectorView.cpp | 14 Boom-0.9/Boom/src/Makevars | 17 Boom-0.9/Boom/src/Models/Bart/Bart.cpp | 4 Boom-0.9/Boom/src/Models/BetaModel.cpp | 2 Boom-0.9/Boom/src/Models/BinomialModel.cpp | 6 Boom-0.9/Boom/src/Models/CategoricalData.cpp | 16 Boom-0.9/Boom/src/Models/CompositeData.cpp | 2 Boom-0.9/Boom/src/Models/DataTypes.cpp | 43 Boom-0.9/Boom/src/Models/DirichletModel.cpp | 2 Boom-0.9/Boom/src/Models/ExponentialIncrementModel.cpp |only Boom-0.9/Boom/src/Models/ExponentialModel.cpp | 16 Boom-0.9/Boom/src/Models/GammaModel.cpp | 4 Boom-0.9/Boom/src/Models/GaussianModel.cpp | 21 Boom-0.9/Boom/src/Models/GaussianModelBase.cpp | 53 Boom-0.9/Boom/src/Models/Glm/AggregatedRegressionModel.cpp | 18 Boom-0.9/Boom/src/Models/Glm/BinomialRegressionData.cpp | 14 Boom-0.9/Boom/src/Models/Glm/ChoiceData.cpp | 2 Boom-0.9/Boom/src/Models/Glm/GlmCoefs.cpp | 53 Boom-0.9/Boom/src/Models/Glm/IndependentRegressionModels.cpp |only Boom-0.9/Boom/src/Models/Glm/MultinomialLogitModel.cpp | 2 Boom-0.9/Boom/src/Models/Glm/MultinomialProbitModel.cpp | 4 Boom-0.9/Boom/src/Models/Glm/MultivariateRegression.cpp |only Boom-0.9/Boom/src/Models/Glm/MvnGivenX.cpp | 3 Boom-0.9/Boom/src/Models/Glm/MvtRegModel.cpp | 16 Boom-0.9/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 494 ++- Boom-0.9/Boom/src/Models/Glm/PoissonRegressionData.cpp | 2 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/AdaptiveSpikeSlabRegressionSampler.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitCompositeSpikeSlabSampler.cpp | 4 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitDataImputer.cpp | 19 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.cpp | 2 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/BinomialProbitTimSampler.cpp | 3 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 99 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/CorrelationMap.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/MLVS_data_imputer.cpp | 9 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/MultivariateRegressionSpikeSlabSampler.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/MvtRegSampler.cpp | 8 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/NormalMixtureApproximation.cpp | 13 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/OrdinalLogitImputer.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/OrdinalLogitPosteriorSampler.cpp |only Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/RegressionCoefficientSampler.cpp | 4 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/RegressionConjSampler.cpp | 58 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/RegressionShrinkageSampler.cpp | 2 Boom-0.9/Boom/src/Models/Glm/PosteriorSamplers/VsPriorSampler.cpp | 18 Boom-0.9/Boom/src/Models/Glm/RegressionModel.cpp | 109 Boom-0.9/Boom/src/Models/Glm/VariableSelectionPrior.cpp | 253 +- Boom-0.9/Boom/src/Models/Glm/WeightedRegressionModel.cpp | 2 Boom-0.9/Boom/src/Models/HMM/Clickstream/NestedHmm.cpp | 10 Boom-0.9/Boom/src/Models/HMM/GeneralHmmStateSpaceWrapper.cpp | 2 Boom-0.9/Boom/src/Models/HMM/HealthStateModel.cpp | 2 Boom-0.9/Boom/src/Models/HMM/HmmFilter.cpp | 4 Boom-0.9/Boom/src/Models/HMM/PosteriorSamplers/LiuWestParticleFilter.cpp | 2 Boom-0.9/Boom/src/Models/Hierarchical/HierarchicalDirichletModel.cpp | 2 Boom-0.9/Boom/src/Models/Hierarchical/HierarchicalPoissonModel.cpp | 2 Boom-0.9/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedGammaModel.cpp | 2 Boom-0.9/Boom/src/Models/Hierarchical/HierarchicalZeroInflatedPoissonModel.cpp | 2 Boom-0.9/Boom/src/Models/Hierarchical/PosteriorSamplers/HierGaussianRegressionAsisSampler.cpp |only Boom-0.9/Boom/src/Models/IRT/IrtModel.cpp | 57 Boom-0.9/Boom/src/Models/IRT/Item.cpp | 34 Boom-0.9/Boom/src/Models/IRT/PartialCreditModel.cpp | 10 Boom-0.9/Boom/src/Models/IRT/Subject.cpp | 16 Boom-0.9/Boom/src/Models/IndependentMvnModel.cpp | 106 Boom-0.9/Boom/src/Models/IndependentMvnModelGivenScalarSigma.cpp | 6 Boom-0.9/Boom/src/Models/MarkovModel.cpp | 22 Boom-0.9/Boom/src/Models/MatrixNormalModel.cpp |only Boom-0.9/Boom/src/Models/Mixtures/ConditionalFiniteMixtureModel.cpp | 2 Boom-0.9/Boom/src/Models/Mixtures/MvnMetaAnalysisDPMPriorModel.cpp | 2 Boom-0.9/Boom/src/Models/ModelTypes.cpp | 22 Boom-0.9/Boom/src/Models/MultinomialModel.cpp | 10 Boom-0.9/Boom/src/Models/MvnBase.cpp | 5 Boom-0.9/Boom/src/Models/Nnet |only Boom-0.9/Boom/src/Models/ParamTypes.cpp | 6 Boom-0.9/Boom/src/Models/PointProcess/HomogeneousPoissonProcess.cpp | 2 Boom-0.9/Boom/src/Models/PointProcess/MarkovModulatedPoissonProcess.cpp | 4 Boom-0.9/Boom/src/Models/PointProcess/PointProcess.cpp | 4 Boom-0.9/Boom/src/Models/PointProcess/PoissonClusterProcess.cpp | 175 - Boom-0.9/Boom/src/Models/PointProcess/PosteriorSamplers/HomogPoissonProcessPosteriorSampler.cpp |only Boom-0.9/Boom/src/Models/PointProcess/PosteriorSamplers/MmppPosteriorSampler.cpp |only Boom-0.9/Boom/src/Models/PointProcess/WeeklyCyclePoissonProcess.cpp | 2 Boom-0.9/Boom/src/Models/PoissonGammaModel.cpp | 2 Boom-0.9/Boom/src/Models/PoissonModel.cpp | 2 Boom-0.9/Boom/src/Models/PosteriorSamplers/BetaPosteriorSampler.cpp | 7 Boom-0.9/Boom/src/Models/PosteriorSamplers/CorrelationSampler.cpp | 2 Boom-0.9/Boom/src/Models/PosteriorSamplers/DirichletPosteriorSampler.cpp | 2 Boom-0.9/Boom/src/Models/PosteriorSamplers/IndependentMvnVarSampler.cpp | 15 Boom-0.9/Boom/src/Models/PosteriorSamplers/MvnConjSampler.cpp | 39 Boom-0.9/Boom/src/Models/PosteriorSamplers/SepStratSampler.cpp | 4 Boom-0.9/Boom/src/Models/ProductDirichletModel.cpp | 4 Boom-0.9/Boom/src/Models/SpdData.cpp | 68 Boom-0.9/Boom/src/Models/StateSpace/AggregatedStateSpaceRegression.cpp | 25 Boom-0.9/Boom/src/Models/StateSpace/DynamicInterceptRegression.cpp | 258 +- Boom-0.9/Boom/src/Models/StateSpace/Filters/ConditionalIidKalmanFilter.cpp |only Boom-0.9/Boom/src/Models/StateSpace/Filters/ConditionallyIndependentKalmanFilter.cpp |only Boom-0.9/Boom/src/Models/StateSpace/Filters/KalmanFilterBase.cpp |only Boom-0.9/Boom/src/Models/StateSpace/Filters/KalmanTools.cpp | 4 Boom-0.9/Boom/src/Models/StateSpace/Filters/MultivariateKalmanFilterBase.cpp |only Boom-0.9/Boom/src/Models/StateSpace/Filters/ScalarKalmanFilter.cpp |only Boom-0.9/Boom/src/Models/StateSpace/Filters/SparseKalmanTools.cpp | 136 + Boom-0.9/Boom/src/Models/StateSpace/Filters/SparseMatrix.cpp | 502 +++ Boom-0.9/Boom/src/Models/StateSpace/Filters/SparseVector.cpp | 2 Boom-0.9/Boom/src/Models/StateSpace/MultivariateStateSpaceModel.cpp |only Boom-0.9/Boom/src/Models/StateSpace/MultivariateStateSpaceModelBase.cpp |only Boom-0.9/Boom/src/Models/StateSpace/MultivariateStateSpaceRegressionModel.cpp |only Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.cpp | 4 Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/MultivariateStateSpaceModelSampler.cpp |only Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/MvStateSpaceRegressionPosteriorSampler.cpp |only Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/SharedLocalLevelPosteriorSampler.cpp |only Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp | 23 Boom-0.9/Boom/src/Models/StateSpace/PosteriorSamplers/StudentLocalLinearTrendPosteriorSampler.cpp | 55 Boom-0.9/Boom/src/Models/StateSpace/StateModelVector.cpp |only Boom-0.9/Boom/src/Models/StateSpace/StateModels/ArStateModel.cpp | 12 Boom-0.9/Boom/src/Models/StateSpace/StateModels/DynamicRegressionArStateModel.cpp | 10 Boom-0.9/Boom/src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp | 42 Boom-0.9/Boom/src/Models/StateSpace/StateModels/HierarchicalRegressionHolidayStateModel.cpp | 78 Boom-0.9/Boom/src/Models/StateSpace/StateModels/Holiday.cpp | 3 Boom-0.9/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp | 272 ++ Boom-0.9/Boom/src/Models/StateSpace/StateModels/LocalLinearTrend.cpp | 21 Boom-0.9/Boom/src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp | 17 Boom-0.9/Boom/src/Models/StateSpace/StateModels/RegressionHolidayStateModel.cpp | 141 - Boom-0.9/Boom/src/Models/StateSpace/StateModels/RegressionStateModel.cpp | 29 Boom-0.9/Boom/src/Models/StateSpace/StateModels/SeasonalStateModel.cpp | 3 Boom-0.9/Boom/src/Models/StateSpace/StateModels/SemilocalLinearTrend.cpp | 28 Boom-0.9/Boom/src/Models/StateSpace/StateModels/StateModel.cpp | 15 Boom-0.9/Boom/src/Models/StateSpace/StateModels/StaticInterceptStateModel.cpp | 6 Boom-0.9/Boom/src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp | 9 Boom-0.9/Boom/src/Models/StateSpace/StateModels/TrigStateModel.cpp | 66 Boom-0.9/Boom/src/Models/StateSpace/StateModels/test_utils |only Boom-0.9/Boom/src/Models/StateSpace/StateSpaceLogitModel.cpp | 59 Boom-0.9/Boom/src/Models/StateSpace/StateSpaceModel.cpp | 76 Boom-0.9/Boom/src/Models/StateSpace/StateSpaceModelBase.cpp | 827 +----- Boom-0.9/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp | 16 Boom-0.9/Boom/src/Models/StateSpace/StateSpaceRegressionModel.cpp | 52 Boom-0.9/Boom/src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp | 47 Boom-0.9/Boom/src/Models/StateSpace/tests |only Boom-0.9/Boom/src/Models/TimeSeries/ArModel.cpp | 2 Boom-0.9/Boom/src/Models/TimeSeries/ArmaModel.cpp | 58 Boom-0.9/Boom/src/Models/TimeSeries/NonzeroMeanAr1Model.cpp | 2 Boom-0.9/Boom/src/Models/UniformModel.cpp | 4 Boom-0.9/Boom/src/Models/WeightedGaussianSuf.cpp | 2 Boom-0.9/Boom/src/Models/WeightedMvnModel.cpp | 2 Boom-0.9/Boom/src/Models/WishartModel.cpp | 4 Boom-0.9/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 2 Boom-0.9/Boom/src/Samplers/MH_Proposals.cpp | 6 Boom-0.9/Boom/src/Samplers/ScalarSliceSampler.cpp | 26 Boom-0.9/Boom/src/Samplers/TIM.cpp | 2 Boom-0.9/Boom/src/TargetFun/Transformation.cpp | 2 Boom-0.9/Boom/src/boom_r_tools.cpp | 137 - Boom-0.9/Boom/src/cpputil/Date.cpp | 54 Boom-0.9/Boom/src/cpputil/DateTime.cpp | 8 Boom-0.9/Boom/src/cpputil/DefaultVnames.cpp | 6 Boom-0.9/Boom/src/cpputil/OutputTable.cpp | 4 Boom-0.9/Boom/src/cpputil/ParamHolder.cpp | 13 Boom-0.9/Boom/src/cpputil/gll.cpp | 11 Boom-0.9/Boom/src/cpputil/is_all_white.cpp | 7 Boom-0.9/Boom/src/cpputil/is_numeric.cpp | 4 Boom-0.9/Boom/src/cpputil/parse_range.cpp | 31 Boom-0.9/Boom/src/cpputil/print_columns.cpp | 11 Boom-0.9/Boom/src/cpputil/read_file.cpp | 13 Boom-0.9/Boom/src/cpputil/split.cpp | 33 Boom-0.9/Boom/src/cpputil/split_delimited.cpp | 9 Boom-0.9/Boom/src/cpputil/split_string.cpp | 20 Boom-0.9/Boom/src/create_mixture_component.cpp | 6 Boom-0.9/Boom/src/create_point_process.cpp | 2 Boom-0.9/Boom/src/create_poisson_cluster_components.cpp | 4 Boom-0.9/Boom/src/create_poisson_process.cpp | 10 Boom-0.9/Boom/src/determine_nthreads.cpp | 2 Boom-0.9/Boom/src/distributions/Markov.cpp | 2 Boom-0.9/Boom/src/distributions/matrix_normal.cpp | 38 Boom-0.9/Boom/src/distributions/mvn.cpp | 54 Boom-0.9/Boom/src/distributions/rmulti.cpp | 1 Boom-0.9/Boom/src/distributions/rng.cpp | 17 Boom-0.9/Boom/src/distributions/trun_norm.cpp | 3 Boom-0.9/Boom/src/distributions/usp.cpp | 2 Boom-0.9/Boom/src/extract_mixture_data.cpp | 4 Boom-0.9/Boom/src/list_io.cpp | 916 +++---- Boom-0.9/Boom/src/numopt/NelderMead.cpp | 1 Boom-0.9/Boom/src/numopt/NumericalDerivatives.cpp | 4 Boom-0.9/Boom/src/numopt/bfgs.cpp | 5 Boom-0.9/Boom/src/numopt/max_nd.cpp | 6 Boom-0.9/Boom/src/numopt/newton.cpp | 5 Boom-0.9/Boom/src/parse_model_formula.cpp | 4 Boom-0.9/Boom/src/prior_specification.cpp | 103 Boom-0.9/Boom/src/seed_rng_from_R.cpp | 10 Boom-0.9/Boom/src/spike_slab_prior.cpp | 8 Boom-0.9/Boom/src/stats/AsciiDistributionCompare.cpp | 36 Boom-0.9/Boom/src/stats/DataTable.cpp | 65 Boom-0.9/Boom/src/stats/Design.cpp | 2 Boom-0.9/Boom/src/stats/FreqDist.cpp | 2 Boom-0.9/Boom/src/stats/NaturalSpline.cpp | 6 Boom-0.9/Boom/src/stats/Spline.cpp | 2 Boom-0.9/Boom/src/stats/summary.cpp |only Boom-0.9/Boom/src/sufstats.cpp | 4 521 files changed, 10999 insertions(+), 6306 deletions(-)
Title: Knockoffs for Hidden Markov Models and Genetic Data
Description: Generate knockoffs for genetic data and hidden Markov models.
For more information, see the website below and the accompanying papers:
"Gene hunting with hidden Markov model knockoffs", Sesia et al., Biometrika, 2019, (<doi:10.1093/biomet/asy033>).
"Multi-resolution localization of causal variants across the genome", Sesia et al., bioRxiv, 2019, (<doi:10.1101/631390>).
Author: Matteo Sesia [aut, cre]
Maintainer: Matteo Sesia <msesia@stanford.edu>
Diff between SNPknock versions 0.7.1 dated 2018-05-30 and 0.8.2 dated 2019-05-17
SNPknock-0.7.1/SNPknock/man/GenotypeModel_wrapper.Rd |only SNPknock-0.7.1/SNPknock/man/HaplotypeModel_wrapper.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.fp.loadFit.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.fp.loadFit_hmm.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.fp.runFastPhase.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.fp.writeX.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.knockoffDMC.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.knockoffGenotypes.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.knockoffHMM.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.knockoffHaplotypes.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.models.sampleDMC.Rd |only SNPknock-0.7.1/SNPknock/man/SNPknock.models.sampleHMM.Rd |only SNPknock-0.7.1/SNPknock/src/dmc_knock.cpp |only SNPknock-0.7.1/SNPknock/src/dmc_knock.h |only SNPknock-0.7.1/SNPknock/src/hmm_knock.cpp |only SNPknock-0.7.1/SNPknock/src/hmm_knock.h |only SNPknock-0.7.1/SNPknock/src/knockoffs.cpp |only SNPknock-0.7.1/SNPknock/vignettes/bibliography.bib |only SNPknock-0.8.2/SNPknock/DESCRIPTION | 37 SNPknock-0.8.2/SNPknock/MD5 | 129 SNPknock-0.8.2/SNPknock/NAMESPACE | 1 SNPknock-0.8.2/SNPknock/NEWS | 23 SNPknock-0.8.2/SNPknock/R/RcppExports.R | 24 SNPknock-0.8.2/SNPknock/R/fastphase.R | 299 SNPknock-0.8.2/SNPknock/R/knockoffs.R | 335 SNPknock-0.8.2/SNPknock/R/knockoffs_snp.R |only SNPknock-0.8.2/SNPknock/R/models.R | 64 SNPknock-0.8.2/SNPknock/README.md |only SNPknock-0.8.2/SNPknock/build/partial.rdb |only SNPknock-0.8.2/SNPknock/build/vignette.rds |binary SNPknock-0.8.2/SNPknock/inst/CITATION |only SNPknock-0.8.2/SNPknock/inst/REFERENCES.bib |only SNPknock-0.8.2/SNPknock/inst/auto |only SNPknock-0.8.2/SNPknock/inst/doc/SNPknock.R | 18 SNPknock-0.8.2/SNPknock/inst/doc/SNPknock.Rmd | 36 SNPknock-0.8.2/SNPknock/inst/doc/SNPknock.html | 429 - SNPknock-0.8.2/SNPknock/inst/doc/genotypes.R | 28 SNPknock-0.8.2/SNPknock/inst/doc/genotypes.Rmd | 80 SNPknock-0.8.2/SNPknock/inst/doc/genotypes.html | 450 - SNPknock-0.8.2/SNPknock/inst/extdata/genotypes.RData |binary SNPknock-0.8.2/SNPknock/inst/extdata/genotypes.inp | 402 - SNPknock-0.8.2/SNPknock/inst/extdata/genotypes_alphahat.txt | 3916 ++++++----- SNPknock-0.8.2/SNPknock/inst/extdata/genotypes_hmm.RData |only SNPknock-0.8.2/SNPknock/inst/extdata/genotypes_origchars | 1164 +++ SNPknock-0.8.2/SNPknock/inst/extdata/genotypes_rhat.txt | 3914 ++++++---- SNPknock-0.8.2/SNPknock/inst/extdata/genotypes_thetahat.txt | 3916 ++++++----- SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes.RData |binary SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes.inp | 402 - SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes_alphahat.txt | 3916 ++++++----- SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes_hmm.RData |only SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes_origchars | 1140 +++ SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes_rhat.txt | 3914 ++++++---- SNPknock-0.8.2/SNPknock/inst/extdata/haplotypes_thetahat.txt | 3916 ++++++----- SNPknock-0.8.2/SNPknock/inst/extdata/hmm.RData |only SNPknock-0.8.2/SNPknock/man/GroupGenotypes_wrapper.Rd |only SNPknock-0.8.2/SNPknock/man/GroupHaplotypes_wrapper.Rd |only SNPknock-0.8.2/SNPknock/man/knockoffDMC.Rd |only SNPknock-0.8.2/SNPknock/man/knockoffDMC_wrapper.Rd | 7 SNPknock-0.8.2/SNPknock/man/knockoffGenotypes.Rd |only SNPknock-0.8.2/SNPknock/man/knockoffHMM.Rd |only SNPknock-0.8.2/SNPknock/man/knockoffHMM_wrapper.Rd | 6 SNPknock-0.8.2/SNPknock/man/knockoffHaplotypes.Rd |only SNPknock-0.8.2/SNPknock/man/loadHMM.Rd |only SNPknock-0.8.2/SNPknock/man/runFastPhase.Rd |only SNPknock-0.8.2/SNPknock/man/sampleDMC.Rd |only SNPknock-0.8.2/SNPknock/man/sampleHMM.Rd |only SNPknock-0.8.2/SNPknock/man/writeXtoInp.Rd |only SNPknock-0.8.2/SNPknock/src/Makevars.win |only SNPknock-0.8.2/SNPknock/src/RcppExports.cpp | 41 SNPknock-0.8.2/SNPknock/src/dmc.cpp |only SNPknock-0.8.2/SNPknock/src/dmc.h |only SNPknock-0.8.2/SNPknock/src/genotypes.cpp | 289 SNPknock-0.8.2/SNPknock/src/genotypes.h | 70 SNPknock-0.8.2/SNPknock/src/haplotypes.cpp | 177 SNPknock-0.8.2/SNPknock/src/haplotypes.h | 54 SNPknock-0.8.2/SNPknock/src/hmm.cpp |only SNPknock-0.8.2/SNPknock/src/hmm.h |only SNPknock-0.8.2/SNPknock/src/interface.cpp | 24 SNPknock-0.8.2/SNPknock/src/interface.h | 25 SNPknock-0.8.2/SNPknock/src/utils.cpp | 2 SNPknock-0.8.2/SNPknock/src/utils.h | 2 SNPknock-0.8.2/SNPknock/src/wrapper.cpp |only SNPknock-0.8.2/SNPknock/tests/testthat/test_fastphase.R |only SNPknock-0.8.2/SNPknock/tests/testthat/test_genetic.R |only SNPknock-0.8.2/SNPknock/tests/testthat/test_group.R |only SNPknock-0.8.2/SNPknock/tests/testthat/test_knockoffs.R | 10 SNPknock-0.8.2/SNPknock/vignettes/SNPknock.Rmd | 36 SNPknock-0.8.2/SNPknock/vignettes/auto |only SNPknock-0.8.2/SNPknock/vignettes/bibliography_old.bib |only SNPknock-0.8.2/SNPknock/vignettes/genotypes.Rmd | 80 90 files changed, 18964 insertions(+), 10412 deletions(-)
Title: Relevant Component Analysis for Supervised Distance Metric
Learning
Description: Relevant Component Analysis (RCA) tries to find a linear
transformation of the feature space such that the effect of irrelevant
variability is reduced in the transformed space.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>)
Maintainer: Nan Xiao <me@nanx.me>
Diff between RECA versions 1.6 dated 2018-05-16 and 1.7 dated 2019-05-17
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/RECA-package.R | 19 ++----------------- README.md | 14 ++++---------- man/RECA-package.Rd | 27 +++++++++++++++++---------- 5 files changed, 33 insertions(+), 47 deletions(-)
Title: Statistical Functions for the Delaporte Distribution
Description: Provides probability mass, distribution, quantile, random-variate generation, and method-of-moments parameter-estimation functions for the Delaporte distribution. The Delaporte is a discrete probability distribution which can be considered the convolution of a negative binomial distribution with a Poisson distribution. Alternatively, it can be considered a counting distribution with both Poisson and negative binomial components. It has been studied in actuarial science as a frequency distribution which has more variability than the Poisson, but less than the negative binomial.
Author: Avraham Adler [aut, cph, cre] (<https://orcid.org/0000-0002-3039-0703>)
Maintainer: Avraham Adler <Avraham.Adler@gmail.com>
Diff between Delaporte versions 7.0.1 dated 2019-04-05 and 7.0.2 dated 2019-05-17
Delaporte-7.0.1/Delaporte/src/delaporte.mod |only Delaporte-7.0.1/Delaporte/src/lgam.mod |only Delaporte-7.0.1/Delaporte/src/utils.mod |only Delaporte-7.0.2/Delaporte/DESCRIPTION | 8 ++++---- Delaporte-7.0.2/Delaporte/MD5 | 15 ++++++--------- Delaporte-7.0.2/Delaporte/build/partial.rdb |binary Delaporte-7.0.2/Delaporte/inst/NEWS.Rd | 17 +++++++++++++++++ Delaporte-7.0.2/Delaporte/man/Delaporte-package.Rd | 4 ++-- Delaporte-7.0.2/Delaporte/src/Makevars | 8 +++++--- Delaporte-7.0.2/Delaporte/src/utils.f95 | 2 ++ 10 files changed, 36 insertions(+), 18 deletions(-)
Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with support for multi-step adaptive MCP-net (MSAMNet) and
multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Qing-Song Xu [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 3.0 dated 2018-12-14 and 3.1 dated 2019-05-17
msaenet-3.0/msaenet/vignettes/msaenet.css |only msaenet-3.1/msaenet/DESCRIPTION | 10 msaenet-3.1/msaenet/MD5 | 26 msaenet-3.1/msaenet/NEWS.md | 13 msaenet-3.1/msaenet/R/msaenet-package.R | 5 msaenet-3.1/msaenet/R/msaenet-sim.R | 7 msaenet-3.1/msaenet/README.md | 6 msaenet-3.1/msaenet/build/vignette.rds |binary msaenet-3.1/msaenet/inst/doc/msaenet.R | 8 msaenet-3.1/msaenet/inst/doc/msaenet.Rmd | 19 msaenet-3.1/msaenet/inst/doc/msaenet.html | 818 ++++++++++++++---------- msaenet-3.1/msaenet/man/msaenet-package.Rd | 5 msaenet-3.1/msaenet/man/msaenet.sim.gaussian.Rd | 9 msaenet-3.1/msaenet/vignettes/custom.css |only msaenet-3.1/msaenet/vignettes/msaenet.Rmd | 19 15 files changed, 581 insertions(+), 364 deletions(-)
Title: Modeling Correlational Magnitude Transformations in
Discretization Contexts
Description: Modeling the correlation transitions under specified distributional assumptions within the realm of discretization in the context of the latency and threshold concepts. The details of the method are explained in Demirtas, H. and Vardar-Acar, C. (2017) <DOI:10.1007/978-981-10-3307-0_4>.
Author: Rawan Allozi, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between CorrToolBox versions 1.6 dated 2019-03-03 and 1.6.1 dated 2019-05-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/CorrToolBox-package.Rd | 4 ++-- man/corrZ2corrY.Rd | 2 +- 4 files changed, 10 insertions(+), 10 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd
and lz4 code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.15.1 dated 2019-04-07 and 0.16.1 dated 2019-05-17
qs-0.15.1/qs/src/BLOSC/LICENSCE |only qs-0.15.1/qs/vignettes/dataframe_bench.png |only qs-0.15.1/qs/vignettes/headline_bench.png |only qs-0.15.1/qs/vignettes/qshex.png |only qs-0.16.1/qs/ChangeLog |only qs-0.16.1/qs/DESCRIPTION | 10 qs-0.16.1/qs/MD5 | 95 - qs-0.16.1/qs/R/help_files.R | 9 qs-0.16.1/qs/README.md | 129 - qs-0.16.1/qs/build/vignette.rds |binary qs-0.16.1/qs/configure | 50 qs-0.16.1/qs/configure.ac | 50 qs-0.16.1/qs/data/starnames.rda |binary qs-0.16.1/qs/inst/doc/vignette.R | 41 qs-0.16.1/qs/inst/doc/vignette.html | 201 +- qs-0.16.1/qs/inst/doc/vignette.rmd | 75 qs-0.16.1/qs/src/BLOSC/LICENSE |only qs-0.16.1/qs/src/LZ4/lz4.c | 896 +++++++--- qs-0.16.1/qs/src/LZ4/lz4.h | 375 ++-- qs-0.16.1/qs/src/LZ4/lz4hc.c | 360 ++-- qs-0.16.1/qs/src/LZ4/lz4hc.h | 248 +- qs-0.16.1/qs/src/ZSTD/common/compiler.h | 2 qs-0.16.1/qs/src/ZSTD/common/fse.h | 2 qs-0.16.1/qs/src/ZSTD/common/threading.c | 4 qs-0.16.1/qs/src/ZSTD/common/xxhash.c | 4 qs-0.16.1/qs/src/ZSTD/common/zstd_internal.h | 59 qs-0.16.1/qs/src/ZSTD/compress/fse_compress.c | 4 qs-0.16.1/qs/src/ZSTD/compress/zstd_compress.c | 719 ++++---- qs-0.16.1/qs/src/ZSTD/compress/zstd_compress_internal.h | 25 qs-0.16.1/qs/src/ZSTD/compress/zstd_fast.c | 327 ++- qs-0.16.1/qs/src/ZSTD/compress/zstd_lazy.h | 2 qs-0.16.1/qs/src/ZSTD/compress/zstd_ldm.c | 2 qs-0.16.1/qs/src/ZSTD/compress/zstd_opt.c | 38 qs-0.16.1/qs/src/ZSTD/compress/zstdmt_compress.c | 90 - qs-0.16.1/qs/src/ZSTD/compress/zstdmt_compress.h | 69 qs-0.16.1/qs/src/ZSTD/decompress/zstd_ddict.c | 8 qs-0.16.1/qs/src/ZSTD/decompress/zstd_decompress.c | 421 +++- qs-0.16.1/qs/src/ZSTD/decompress/zstd_decompress_block.c | 98 - qs-0.16.1/qs/src/ZSTD/decompress/zstd_decompress_internal.h | 7 qs-0.16.1/qs/src/ZSTD/dictBuilder/cover.c | 71 qs-0.16.1/qs/src/ZSTD/dictBuilder/cover.h | 29 qs-0.16.1/qs/src/ZSTD/dictBuilder/divsufsort.c | 12 qs-0.16.1/qs/src/ZSTD/dictBuilder/fastcover.c | 38 qs-0.16.1/qs/src/ZSTD/dictBuilder/zdict.h | 26 qs-0.16.1/qs/src/ZSTD/zstd.h | 1021 ++++++------ qs-0.16.1/qs/src/qs_common.h | 15 qs-0.16.1/qs/src/qs_deserialization_stream.h |only qs-0.16.1/qs/src/qs_functions.cpp | 125 + qs-0.16.1/qs/src/qs_inspect.h | 77 qs-0.16.1/qs/src/qs_serialization_stream.h |only qs-0.16.1/qs/vignettes/df_bench_read.png |only qs-0.16.1/qs/vignettes/df_bench_summary.csv |only qs-0.16.1/qs/vignettes/df_bench_write.png |only qs-0.16.1/qs/vignettes/vignette.rmd | 75 54 files changed, 3691 insertions(+), 2218 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector Graphics'.
'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] (Early line dashing code),
David Gohel [ctb] (Line dashing code and raster code),
Yixuan Qiu [ctb] (Improved styles; polypath implementation),
Håkon Malmedal [ctb] (Opacity code),
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between svglite versions 1.2.1 dated 2017-09-11 and 1.2.2 dated 2019-05-17
DESCRIPTION | 6 MD5 | 32 +- NEWS.md | 15 + README.md | 2 build/vignette.rds |binary inst/doc/fonts.html | 433 +++++++++++++++++++++++++++++-------- inst/doc/scaling.html | 325 ++++++++++++++++++++++++--- src/SvgStream.h | 8 src/devSVG.cpp | 25 +- src/utils.h |only tests/testthat/test-clip.svg | 14 - tests/testthat/test-lines.R | 15 - tests/testthat/test-no-clip.svg | 4 tests/testthat/test-scale-text.svg | 4 tests/testthat/test-text-fonts.R | 14 + tests/testthat/test-text.R | 1 tests/testthat/test-text.svg | 2 vignettes/releases |only 18 files changed, 720 insertions(+), 180 deletions(-)
Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of
algorithms. It includes surrogate models, optimizers and design of experiment
approaches. The main interface is spot, which uses sequentially updated
surrogate models for the purpose of efficient optimization. The main goal is
to ease the burden of objective function evaluations, when a single evaluation
requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut],
Joerg Stork [aut],
Martin Zaefferer [aut, cre],
Margarita Rebolledo [ctb],
Christian Lasarczyk [ctb],
Joerg Ziegenhirt [ctb],
Wolfgang Konen [ctb],
Oliver Flasch [ctb],
Patrick Koch [ctb],
Martina Friese [ctb],
Lorenzo Gentile [ctb],
Frederik Rehbach [ctb]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>
Diff between SPOT versions 2.0.3 dated 2018-05-14 and 2.0.4 dated 2019-05-17
DESCRIPTION | 10 MD5 | 100 +-- NAMESPACE | 1 NEWS | 8 R/buildKrigingDACE.R | 30 R/buildRSM.R | 425 ++++++------- R/initialInputCheck.R |only R/optimDE.R | 2 R/optimES.R | 4 R/optimGenoud.R | 2 R/package.R | 4 R/plotData.R | 4 R/plotFunction.R | 6 R/plotModel.R | 4 R/satter.R |only R/spot.R | 631 ++++++++++---------- data/dataGasSensor.RData |binary man/SPOT-package.Rd | 4 man/buildKrigingDACE.Rd | 2 man/checkForNAs.Rd |only man/checkFunEvalsDesignSize.Rd |only man/checkInputDimensionsionalityCorrect.Rd |only man/checkInputTypesInControl.Rd |only man/checkLowerNotEqualsUpper.Rd |only man/checkLowerSmallerThanUpper.Rd |only man/checkTypesOfInput.Rd |only man/corrcubic.Rd | 2 man/correxp.Rd | 2 man/correxpg.Rd | 2 man/corrgauss.Rd | 2 man/corrkriging.Rd | 2 man/corrlin.Rd | 2 man/corrnoisygauss.Rd | 2 man/corrnoisykriging.Rd | 2 man/corrspherical.Rd | 2 man/corrspline.Rd | 2 man/funCyclone.Rd | 12 man/initialInputCheck.Rd |only man/plotData.Rd | 4 man/plotFunction.Rd | 12 man/plotModel.Rd | 10 man/predict.dace.Rd | 2 man/print.spotLOESS.Rd | 3 man/regpoly0.Rd | 2 man/regpoly1.Rd | 2 man/regpoly2.Rd | 2 man/satter.Rd |only man/spotAlgEs.Rd | 10 man/spotAlgEsDominantReco.Rd | 3 man/spotAlgEsIndividualInitial.Rd | 4 man/spotAlgEsInitParentPop.Rd | 4 tests/testthat/test.designLHD.R | 30 tests/testthat/test.designUinformRandom.R | 30 tests/testthat/test.inequalityConstraint.R | 126 ++- tests/testthat/test.initialInputCheck.ControlList.R |only tests/testthat/test.initialInputCheck.xLowerUpper.R |only tests/testthat/test.main.R | 31 tests/testthat/test.satter.R |only 58 files changed, 803 insertions(+), 741 deletions(-)
Title: Verbal Autopsy Data Transformation for InSilicoVA and InterVA5
Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1)
or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and
InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but
this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.
Author: Peter Byass [aut],
Eungang Choi [aut],
Sam Clark [aut],
Zehang Li [aut],
Nicolas Maire [aut],
Tyler McCormick [aut],
Jason Thomas [aut, cre]
Maintainer: Jason Thomas <jarathomas@gmail.com>
Diff between CrossVA versions 0.9.7 dated 2019-04-21 and 0.9.8 dated 2019-05-17
DESCRIPTION | 14 MD5 | 12 R/odk2openVA_2014.R | 4 R/odk2openVA_v141.R | 2 R/odk2openVA_v151.R | 10 build/vignette.rds |binary inst/doc/using-crossva-and-openva.html | 1177 +++++++++++++++------------------ 7 files changed, 581 insertions(+), 638 deletions(-)
More information about AFheritability at CRAN
Permanent link
Title: Fast Pseudo Random Number Generators
Description: Several fast random number generators are provided as C++
header only libraries: The PCG family by O'Neill (2014
<https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as
Xoroshiro128+ and Xoshiro256+ by Blackman and Vigna (2018
<arXiv:1805.01407>). In addition fast functions for generating random
numbers according to a uniform, normal and exponential distribution
are included. The latter two use the Ziggurat algorithm originally
proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>).
These functions are exported to R and as a C++ interface and are
enabled for use with the default 64 bit generator from the PCG family,
Xoroshiro128+ and Xoshiro256+ as well as the 64 bit version of the 20 rounds
Threefry engine (Salmon et al., 2011 <doi:10.1145/2063384.2063405>) as
provided by the package 'sitmo'.
Author: Ralf Stubner [aut, cre],
daqana GmbH [cph],
David Blackman [ctb],
Melissa O'Neill [ctb],
Sebastiano Vigna [ctb],
Aaron Lun [ctb]
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>
Diff between dqrng versions 0.2.0 dated 2019-04-22 and 0.2.1 dated 2019-05-17
DESCRIPTION | 10 MD5 | 27 - NEWS.md | 6 README.md | 48 +- build/vignette.rds |binary inst/doc/cpp-api.html | 314 ++--------------- inst/doc/dqrng.html | 686 +++++++++++++------------------------- inst/doc/parallel.html | 490 +++++++-------------------- inst/include/convert_seed.h | 14 inst/include/dqrng_distribution.h | 4 inst/include/dqrng_generator.h | 10 inst/include/mystdint.h |only inst/include/xoshiro.h | 13 man/dqrng-package.Rd | 2 src/dqrng.cpp | 1 15 files changed, 507 insertions(+), 1118 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <http://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Heidi Seibold [ctb] (<https://orcid.org/0000-0002-8960-9642>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-3 dated 2019-01-31 and 1.2-4 dated 2019-05-17
DESCRIPTION | 10 MD5 | 99 ++-- R/plot.R | 6 build/vignette.rds |binary inst/NEWS.Rd | 9 inst/doc/constparty.R | 1 inst/doc/constparty.Rnw | 1 inst/doc/constparty.pdf |binary inst/doc/ctree.R | 1 inst/doc/ctree.Rnw | 1 inst/doc/ctree.pdf |binary inst/doc/mob.R | 7 inst/doc/mob.Rnw | 1 inst/doc/mob.pdf |binary inst/doc/partykit.R | 1 inst/doc/partykit.Rnw | 1 inst/doc/partykit.pdf |binary man/HuntingSpiders.Rd | 6 man/panelfunctions.Rd | 2 tests/Examples/partykit-Ex.Rout.save | 58 -- tests/bugfixes.R | 1 tests/bugfixes.Rout.save | 14 tests/regtest-MIA.R | 1 tests/regtest-MIA.Rout.save | 1 tests/regtest-cforest.R | 1 tests/regtest-cforest.Rout.save | 1 tests/regtest-ctree.R | 2 tests/regtest-ctree.Rout.save | 2 tests/regtest-glmtree.R | 1 tests/regtest-glmtree.Rout.save | 1 tests/regtest-lmtree.R | 2 tests/regtest-nmax.R | 1 tests/regtest-nmax.Rout.save | 1 tests/regtest-node.R | 2 tests/regtest-node.Rout.save | 2 tests/regtest-party-random.R | 2 tests/regtest-party.R | 2 tests/regtest-party.Rout.save | 703 +++++++++++++++++------------------ tests/regtest-split.R | 2 tests/regtest-split.Rout.save | 2 tests/regtest-weights.R | 2 tests/regtest-weights.Rout.save | 2 vignettes/constparty.Rnw | 1 vignettes/constparty.Rout.save | 2 vignettes/ctree.Rnw | 1 vignettes/ctree.Rout.save | 2 vignettes/mob.Rnw | 1 vignettes/mob.Rout.save |only vignettes/party.bib | 23 - vignettes/partykit.Rnw | 1 vignettes/partykit.Rout.save | 2 51 files changed, 517 insertions(+), 468 deletions(-)
Title: Data Science Labs
Description: Datasets and functions that can be used for data analysis practice, homework and projects in data science courses and workshops.
Author: Rafael A. Irizarry, Amy Gill
Maintainer: Rafael A. Irizarry <rafa@jimmy.harvard.edu>
Diff between dslabs versions 0.5.2 dated 2018-12-19 and 0.6.0 dated 2019-05-17
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++++++-- R/brexit_polls.R |only R/nyc_regents_scores.R |only data/brexit_polls.rda |only data/datalist | 2 ++ data/nyc_regents_scores.rda |only inst/extdata/2010_bigfive_regents.xls |only inst/script/make-brexit_polls.R |only inst/script/make-nyc_regents_scores.R |only man/brexit_polls.Rd |only man/nyc_regents_scores.Rd |only 12 files changed, 18 insertions(+), 7 deletions(-)
Title: The MBESS R Package
Description: Implements methods that useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but at this
point MBESS contains methods applicable and used in a wide variety of fields and is an
orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has
greatly benefited from others, see <http://nd.edu/~kkelley/site/MBESS.html> for a detailed
list of those that have contributed and other details.
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.5.0 dated 2019-05-14 and 4.5.1 dated 2019-05-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ci.reliability.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code.
Author: Amine Gassem [cre, aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Qing Xi Ooi [ctr],
Novartis Pharma AG [cph]
Maintainer: Amine Gassem <contact@ag-study.com>
Diff between ggPMX versions 0.9.1 dated 2019-05-16 and 0.9.2 dated 2019-05-17
ggPMX-0.9.1/ggPMX/inst/doc/introduction.Rmd |only ggPMX-0.9.2/ggPMX/DESCRIPTION | 6 +++--- ggPMX-0.9.2/ggPMX/MD5 | 5 ++--- ggPMX-0.9.2/ggPMX/inst/doc/ggPMX-guide.html | 4 ++-- 4 files changed, 7 insertions(+), 8 deletions(-)
Title: Estimation of Ego-Temporal Exponential Random Graph Models via
Expectation Maximization (EM)
Description: Estimation of ego-temporal exponential random graph models with two-stage estimation including initialization through k-means clustering on temporal exponential random graph model parameters and EM as per Campbell (2018) <doi:10.7910/DVN/TWHEZ9>.
Author: Benjamin W. Campbell [aut, cre],
Michael Salter-Townshend [ctb],
Thomas Brendan Murphy [ctb]
Maintainer: Benjamin W. Campbell <campbell.1721@osu.edu>
Diff between egoTERGM versions 2.1.0 dated 2019-02-05 and 2.1.1 dated 2019-05-17
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NAMESPACE | 4 ---- NEWS.md |only build/vignette.rds |binary inst/doc/KnechtVignette.html | 33 +++++++++++++++++++++++++++++---- 6 files changed, 40 insertions(+), 18 deletions(-)
Title: Adapt Numerical Records to Fit (in)Equality Restrictions
Description: Minimally adjust the values of numerical records in a data.frame, such
that each record satisfies a predefined set of equality and/or inequality
constraints. The constraints can be defined using the 'validate' package.
The core algorithms have recently been moved to the 'lintools' package,
refer to 'lintools' for a more basic interface and access to a version
of the algorithm that works with sparse matrices.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between rspa versions 0.2.3 dated 2018-07-30 and 0.2.4 dated 2019-05-17
rspa-0.2.3/rspa/tests/testthat |only rspa-0.2.3/rspa/tests/testthat.R |only rspa-0.2.4/rspa/DESCRIPTION | 11 +++++----- rspa-0.2.4/rspa/MD5 | 33 +++++++++++++++--------------- rspa-0.2.4/rspa/NEWS | 7 +++++- rspa-0.2.4/rspa/R/match_restrictions.R | 7 ++++++ rspa-0.2.4/rspa/R/rspa.R | 6 ++--- rspa-0.2.4/rspa/inst |only rspa-0.2.4/rspa/man/match_restrictions.Rd | 9 ++++++++ rspa-0.2.4/rspa/man/remove_tag.Rd | 1 rspa-0.2.4/rspa/man/rspa-package.Rd | 6 ++--- rspa-0.2.4/rspa/man/sparseConstraints.Rd | 7 +++--- rspa-0.2.4/rspa/man/tag_missing.Rd | 1 rspa-0.2.4/rspa/man/tagged_values.Rd | 1 rspa-0.2.4/rspa/tests/tinytest.R |only 15 files changed, 58 insertions(+), 31 deletions(-)
Title: Unified Interface to Parallelization Back-Ends
Description: Unified parallelization framework for multiple
back-end, designed for internal package and interactive usage. The
main operation is parallel mapping over lists. Supports 'local',
'multicore', 'mpi' and 'BatchJobs' mode. Allows tagging of the
parallel operation with a level name that can be later selected by the
user to switch on parallel execution for exactly this operation.
Author: Bernd Bischl [cre, aut],
Michel Lang [aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between parallelMap versions 1.3 dated 2015-06-09 and 1.4 dated 2019-05-17
parallelMap-1.3/parallelMap/tests/test-all.R |only parallelMap-1.4/parallelMap/DESCRIPTION | 44 ++++-- parallelMap-1.4/parallelMap/LICENSE | 2 parallelMap-1.4/parallelMap/MD5 | 61 ++++----- parallelMap-1.4/parallelMap/NAMESPACE | 7 - parallelMap-1.4/parallelMap/NEWS | 6 parallelMap-1.4/parallelMap/R/autodetectCpus.R | 2 parallelMap-1.4/parallelMap/R/batchtools.R |only parallelMap-1.4/parallelMap/R/clusterMapLB.R |only parallelMap-1.4/parallelMap/R/getExtraPackages.R | 10 - parallelMap-1.4/parallelMap/R/getOption.R | 13 + parallelMap-1.4/parallelMap/R/parallelExport.R | 10 + parallelMap-1.4/parallelMap/R/parallelMap.R | 67 ++++++++-- parallelMap-1.4/parallelMap/R/parallelSource.R | 8 + parallelMap-1.4/parallelMap/R/parallelStart.R | 62 ++++++--- parallelMap-1.4/parallelMap/R/zzz.R | 5 parallelMap-1.4/parallelMap/man/parallelExport.Rd | 3 parallelMap-1.4/parallelMap/man/parallelGetOptions.Rd | 3 parallelMap-1.4/parallelMap/man/parallelGetRegisteredLevels.Rd | 3 parallelMap-1.4/parallelMap/man/parallelLapply.Rd | 6 parallelMap-1.4/parallelMap/man/parallelLibrary.Rd | 3 parallelMap-1.4/parallelMap/man/parallelMap.Rd | 5 parallelMap-1.4/parallelMap/man/parallelRegisterLevels.Rd | 3 parallelMap-1.4/parallelMap/man/parallelSource.Rd | 3 parallelMap-1.4/parallelMap/man/parallelStart.Rd | 45 ++++-- parallelMap-1.4/parallelMap/man/parallelStop.Rd | 3 parallelMap-1.4/parallelMap/tests/run-all.R |only parallelMap-1.4/parallelMap/tests/testthat/helper_sockettest.R | 4 parallelMap-1.4/parallelMap/tests/testthat/helpers.R | 21 ++- parallelMap-1.4/parallelMap/tests/testthat/test_batchjobs.R | 10 - parallelMap-1.4/parallelMap/tests/testthat/test_batchtools.R |only parallelMap-1.4/parallelMap/tests/testthat/test_local.R | 2 parallelMap-1.4/parallelMap/tests/testthat/test_mpi.R | 6 parallelMap-1.4/parallelMap/tests/testthat/test_multicore.R | 19 -- 34 files changed, 296 insertions(+), 140 deletions(-)
Title: Colocalisation Tests of Two Genetic Traits
Description: Performs the colocalisation tests described in
Plagnol et al (2009) <doi:10.1093/biostatistics/kxn039>,
Wallace et al (2013) <doi:10.1002/gepi.21765> and
Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>.
Author: Chris Wallace [aut, cre],
Claudia Giambartolomei [aut],
Vincent Plagnol [ctb]
Maintainer: Chris Wallace <cew54@cam.ac.uk>
Diff between coloc versions 3.1 dated 2018-02-24 and 3.2-1 dated 2019-05-17
coloc-3.1/coloc/ChangeLog |only coloc-3.1/coloc/inst/doc/vignette.Rhtml |only coloc-3.1/coloc/vignettes/vignette.Rhtml |only coloc-3.2-1/coloc/DESCRIPTION | 16 coloc-3.2-1/coloc/MD5 | 32 coloc-3.2-1/coloc/NEWS.md |only coloc-3.2-1/coloc/R/claudia.R | 45 coloc-3.2-1/coloc/README.md | 25 coloc-3.2-1/coloc/build/vignette.rds |binary coloc-3.2-1/coloc/inst/doc/vignette.R | 26 coloc-3.2-1/coloc/inst/doc/vignette.Rmd |only coloc-3.2-1/coloc/inst/doc/vignette.html | 1480 ++++++++--------------- coloc-3.2-1/coloc/man/Var.data.Rd | 2 coloc-3.2-1/coloc/man/coloc.bma.Rd | 4 coloc-3.2-1/coloc/man/coloc.test.summary.Rd | 5 coloc-3.2-1/coloc/man/colocPCs-class.Rd | 1 coloc-3.2-1/coloc/man/pcs.model.Rd | 5 coloc-3.2-1/coloc/man/plot-methods.Rd | 2 coloc-3.2-1/coloc/tests/testthat/test-examples.R | 2 coloc-3.2-1/coloc/vignettes/vignette.Rmd |only 20 files changed, 618 insertions(+), 1027 deletions(-)
Title: Robust Regression with Data Driven Tuning Parameter
Description: Data driven approach for robust regression estimation in homoscedastic and heteroscedastic context. See Wang et al. (2007), <doi:10.1198/106186007X180156> regarding homoscedastic framework.
Author: You-Gan Wang
Maintainer: You-Gan Wang <you-gan.wang@qut.edu.au>
Diff between rlmDataDriven versions 0.2.1 dated 2019-03-12 and 0.3.0 dated 2019-05-17
DESCRIPTION | 9 + MD5 | 10 +- R/rlmDD_het.R | 265 ++++++++++++++++++++++++------------------------------- man/rlmDD.Rd | 11 +- man/rlmDD_het.Rd | 7 - man/whm.Rd | 4 6 files changed, 143 insertions(+), 163 deletions(-)
Title: Kaplan-Meier Plot with 'ggplot2'
Description: The function 'jskm()' creates publication quality Kaplan-Meier plot with at risk tables below. 'svyjskm()' provides plot for weighted Kaplan-Meier estimator.
Author: Jinseob Kim [aut, cre] (<https://orcid.org/0000-0002-9403-605X>),
Zarathu [cph, fnd]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jskm versions 0.3.1 dated 2019-03-12 and 0.3.5 dated 2019-05-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 8 +++++++- R/svyjskm.R | 6 +++--- build/vignette.rds |binary inst/doc/jskm.html | 9 ++++++--- 6 files changed, 25 insertions(+), 16 deletions(-)
Title: Joint Models for Longitudinal Measurements and Competing Risks
Failure Time Data
Description: Fit joint models of continuous or ordinal longitudinal data and time-to-event data with competing risks. For a detailed information, see Robert Elashoff, Gang li and Ning Li (2016, ISBN:9781439807828) ; Robert M. Elashoff,Gang Li and Ning Li (2008) <doi:10.1111/j.1541-0420.2007.00952.x> ; Ning Li, Robert Elashoff, Gang Li and Jeffrey Saver (2010) <doi:10.1002/sim.3798> .
Author: Hong Wang<wh@csu.edu.cn>, Ning Li<nli@biomath.ucla.edu> and Gang Li<vli@ucla.edu>
Maintainer: Hong Wang <wh@csu.edu.cn>
Diff between JMcmprsk versions 0.9.3 dated 2017-12-10 and 0.9.4 dated 2019-05-17
DESCRIPTION | 12 MD5 | 46 NAMESPACE | 1 R/JMcmprsk.R | 1 R/RcppExports.R | 8 R/jmc.R | 73 R/jmo.R | 87 build/vignette.rds |binary inst/doc/JMcmprsk.html | 31 inst/extdata/fvc621_y.txt | 1432 +++++++-------- inst/extdata/jmcsimy.txt | 238 +- inst/extdata/jmosimc.txt | 22 inst/extdata/jmosimm.txt | 20 inst/extdata/jmosimy.txt | 61 inst/extdata/ninds_nrank_y.txt | 3814 ++++++++++++++++++++--------------------- man/anova.JMcmprsk.Rd | 3 man/jmc.Rd | 9 man/jmo.Rd | 13 src/JMcmprsk.cpp | 9 src/RcppExports.cpp | 20 src/jmc.cpp | 31 src/jmc.h | 37 src/jmo.cpp | 28 src/jmo.h | 129 - 24 files changed, 3053 insertions(+), 3072 deletions(-)
Title: Fuzzy Clustering
Description: Algorithms for fuzzy clustering, cluster validity indices and plots for cluster validity and visualizing fuzzy clustering results.
Author: Paolo Giordani, Maria Brigida Ferraro, Alessio Serafini
Maintainer: Paolo Giordani <paolo.giordani@uniroma1.it>
Diff between fclust versions 2.0.1 dated 2018-10-22 and 2.1 dated 2019-05-17
DESCRIPTION | 8 MD5 | 128 ++++---- NAMESPACE | 2 NEWS.md | 8 R/ARI.F.R | 41 +- R/FKM.R | 18 - R/FKM.ent.R | 18 - R/FKM.ent.noise.R | 22 - R/FKM.gk.R | 16 - R/FKM.gk.ent.R | 18 - R/FKM.gk.ent.noise.R | 23 - R/FKM.gk.noise.R | 22 - R/FKM.gkb.R | 18 - R/FKM.gkb.ent.R | 18 - R/FKM.gkb.ent.noise.R | 22 - R/FKM.gkb.noise.R | 22 - R/FKM.med.R | 18 - R/FKM.med_noise.R | 22 - R/FKM.noise.R | 22 - R/FKM.pf.R | 19 - R/FKM.pf.noise.R | 23 - R/Fclust.R | 696 +++++++++++++++++------------------------------ R/Fclust.compare.R | 40 +- R/Fclust.index.R | 2 R/JACCARD.F.R | 40 +- R/NEFRC.R | 108 +++---- R/NEFRC.noise.R | 34 -- R/RI.F.R | 40 +- R/RcppExports.R | 64 ++-- man/ARI.F.Rd | 14 man/FKM.Rd | 14 man/FKM.ent.Rd | 12 man/FKM.ent.noise.Rd | 14 man/FKM.gk.Rd | 12 man/FKM.gk.ent.Rd | 12 man/FKM.gk.ent.noise.Rd | 16 - man/FKM.gk.noise.Rd | 14 man/FKM.gkb.Rd | 8 man/FKM.gkb.ent.Rd | 12 man/FKM.gkb.ent.noise.Rd | 14 man/FKM.gkb.noise.Rd | 14 man/FKM.med.Rd | 10 man/FKM.med.noise.Rd | 10 man/FKM.noise.Rd | 12 man/FKM.pf.Rd | 12 man/FKM.pf.noise.Rd | 12 man/Fclust.Rd | 34 +- man/Fclust.compare.Rd | 19 - man/Fclust.index.Rd | 6 man/JACCARD.F.Rd | 14 man/MPC.Rd | 2 man/NEFRC.Rd | 14 man/NEFRC.noise.Rd | 15 - man/PC.Rd | 2 man/PE.Rd | 2 man/RI.F.Rd | 14 man/SIL.F.Rd | 6 man/SIL.Rd | 8 man/XB.Rd | 2 man/cl.memb.H.Rd | 2 man/cl.memb.Rd | 2 man/cl.memb.t.Rd | 2 src/FKM_rcpp.cpp | 307 +++++++++++++++++--- src/RcppExports.cpp | 254 ++++++++--------- src/centroids.cpp | 2 65 files changed, 1210 insertions(+), 1241 deletions(-)
Title: Functions for Analysis of fMRI Datasets Stored in the ANALYZE or
NIFTI Format
Description: Functions for I/O, visualisation and analysis of functional Magnetic Resonance Imaging (fMRI) datasets stored in the ANALYZE or NIFTI format. Note that the latest version of XQuartz seems to be necessary under MacOS.
Author: Pierre Lafaye De Micheaux [aut, cre],
Jonathan L Marchini [aut]
Maintainer: Pierre Lafaye De Micheaux <lafaye@unsw.edu.au>
Diff between AnalyzeFMRI versions 1.1-17 dated 2018-05-14 and 1.1-18 dated 2019-05-17
DESCRIPTION | 19 ++- MD5 | 12 +- inst/HISTORY | 11 ++ src/Makevars.in | 2 src/analyzeFMRI.c | 198 +++++++++++++++++++++------------------ src/niftiFMRI.c | 109 ++++++++++----------- src/spatial.filters.non.linear.c | 3 7 files changed, 193 insertions(+), 161 deletions(-)
Title: Implementation of the Radar-Boxplot
Description: Creates the radar-boxplot, a plot that was created by the
author during his doctoring in forest resources.
The radar-boxplot is a visualization feature suited for
multivariate classification/clustering. It provides an intuitive
deep understanding of the data.
Author: Caio Hamamura [aut, cre]
Maintainer: Caio Hamamura <caiohamamura@gmail.com>
Diff between radarBoxplot versions 0.2.6 dated 2019-05-13 and 1.0.0 dated 2019-05-17
DESCRIPTION | 12 - MD5 | 14 - R/radarBoxplot.R | 515 +++++++++++++++++++++++++++++++----------------- R/utils.R | 105 +++++++++ README.md | 58 +++-- inst/NEWS | 2 man/figures/Example.png |binary man/radarBoxplot.Rd | 55 +++-- 8 files changed, 523 insertions(+), 238 deletions(-)
Title: End-Member Modelling of Grain-Size Data
Description: End-member modelling analysis of grain-size data is an approach
to unmix a data set's underyling distributions and their contribution to
the data set. EMMAgeo provides deterministic and robust protocols for
that purpose.
Author: Michael Dietze, Elisabeth Dietze
Maintainer: Michael Dietze <mdietze@gfz-potsdam.de>
Diff between EMMAgeo versions 0.9.4 dated 2016-03-19 and 0.9.6 dated 2019-05-17
EMMAgeo-0.9.4/EMMAgeo/R/Mqs.uncertainty.R |only EMMAgeo-0.9.4/EMMAgeo/R/define.limits.R |only EMMAgeo-0.9.4/EMMAgeo/R/model.em.R |only EMMAgeo-0.9.4/EMMAgeo/data/TR.rda |only EMMAgeo-0.9.4/EMMAgeo/data/X.rda |only EMMAgeo-0.9.4/EMMAgeo/data/rEM.rda |only EMMAgeo-0.9.4/EMMAgeo/man/Mqs.uncertainty.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/TR.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/define.limits.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/model.em.Rd |only EMMAgeo-0.9.4/EMMAgeo/man/rEM.Rd |only EMMAgeo-0.9.6/EMMAgeo/DESCRIPTION | 25 EMMAgeo-0.9.6/EMMAgeo/MD5 | 113 +-- EMMAgeo-0.9.6/EMMAgeo/NAMESPACE | 20 EMMAgeo-0.9.6/EMMAgeo/NEWS | 8 EMMAgeo-0.9.6/EMMAgeo/R/EMMA.R | 205 +++--- EMMAgeo-0.9.6/EMMAgeo/R/EMMAgeo-package.R | 46 - EMMAgeo-0.9.6/EMMAgeo/R/GUI.R | 14 EMMAgeo-0.9.6/EMMAgeo/R/check.data.R | 96 -- EMMAgeo-0.9.6/EMMAgeo/R/click.limits.R |only EMMAgeo-0.9.6/EMMAgeo/R/convert.units.R | 15 EMMAgeo-0.9.6/EMMAgeo/R/create.EM.R | 40 - EMMAgeo-0.9.6/EMMAgeo/R/get.l.R | 44 - EMMAgeo-0.9.6/EMMAgeo/R/get.l.opt.R | 53 - EMMAgeo-0.9.6/EMMAgeo/R/get.limits.R | 84 +- EMMAgeo-0.9.6/EMMAgeo/R/get.q.R | 59 + EMMAgeo-0.9.6/EMMAgeo/R/interpolate.classes.R | 45 - EMMAgeo-0.9.6/EMMAgeo/R/mix.EM.R | 16 EMMAgeo-0.9.6/EMMAgeo/R/model.EM.R |only EMMAgeo-0.9.6/EMMAgeo/R/residual.EM.R | 38 - EMMAgeo-0.9.6/EMMAgeo/R/robust.EM.R | 779 ++++++++++++----------- EMMAgeo-0.9.6/EMMAgeo/R/robust.loadings.R |only EMMAgeo-0.9.6/EMMAgeo/R/robust.scores.R |only EMMAgeo-0.9.6/EMMAgeo/R/test.factors.R | 150 ++-- EMMAgeo-0.9.6/EMMAgeo/R/test.l.R | 18 EMMAgeo-0.9.6/EMMAgeo/R/test.l.max.R | 23 EMMAgeo-0.9.6/EMMAgeo/R/test.parameters.R | 108 +-- EMMAgeo-0.9.6/EMMAgeo/R/test.robustness.R | 56 - EMMAgeo-0.9.6/EMMAgeo/R/zzz.R |only EMMAgeo-0.9.6/EMMAgeo/data/example_EMpot.rda |only EMMAgeo-0.9.6/EMMAgeo/data/example_EMrob.rda |only EMMAgeo-0.9.6/EMMAgeo/data/example_X.rda |only EMMAgeo-0.9.6/EMMAgeo/inst/shiny/EMMA/server.R | 4 EMMAgeo-0.9.6/EMMAgeo/inst/shiny/EMMA/ui.R | 2 EMMAgeo-0.9.6/EMMAgeo/man/EMMA.Rd | 88 +- EMMAgeo-0.9.6/EMMAgeo/man/EMMAgeo-package.Rd | 29 EMMAgeo-0.9.6/EMMAgeo/man/EMpot.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/EMrob.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/GUI.Rd | 25 EMMAgeo-0.9.6/EMMAgeo/man/X.Rd | 21 EMMAgeo-0.9.6/EMMAgeo/man/check.data.Rd | 58 - EMMAgeo-0.9.6/EMMAgeo/man/click.limits.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/convert.units.Rd | 23 EMMAgeo-0.9.6/EMMAgeo/man/create.EM.Rd | 51 - EMMAgeo-0.9.6/EMMAgeo/man/get.l.Rd | 44 - EMMAgeo-0.9.6/EMMAgeo/man/get.l.opt.Rd | 59 - EMMAgeo-0.9.6/EMMAgeo/man/get.limits.Rd | 56 - EMMAgeo-0.9.6/EMMAgeo/man/get.q.Rd | 65 + EMMAgeo-0.9.6/EMMAgeo/man/interpolate.classes.Rd | 64 - EMMAgeo-0.9.6/EMMAgeo/man/mix.EM.Rd | 24 EMMAgeo-0.9.6/EMMAgeo/man/model.EM.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/residual.EM.Rd | 43 - EMMAgeo-0.9.6/EMMAgeo/man/robust.EM.Rd | 166 ++-- EMMAgeo-0.9.6/EMMAgeo/man/robust.loadings.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/robust.scores.Rd |only EMMAgeo-0.9.6/EMMAgeo/man/test.factors.Rd | 50 - EMMAgeo-0.9.6/EMMAgeo/man/test.l.Rd | 26 EMMAgeo-0.9.6/EMMAgeo/man/test.l.max.Rd | 32 EMMAgeo-0.9.6/EMMAgeo/man/test.parameters.Rd | 94 +- EMMAgeo-0.9.6/EMMAgeo/man/test.robustness.Rd | 72 +- 70 files changed, 1730 insertions(+), 1421 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 1.4.0 dated 2019-04-23 and 1.5.0 dated 2019-05-17
DESCRIPTION | 10 MD5 | 29 - R/AM.R | 20 - R/FPR4AM.R | 2 R/OpenGUI.R | 5 R/ReadMap.R | 6 R/ReadPheno.R | 4 R/check_inputs_mlam.R | 6 R/find_qtl.R | 26 - R/form_results.R | 8 R/onAttach.R | 2 R/summary_am.R | 14 inst/shiny_app/app.R | 540 ++++++++++++++++++++++++++---- inst/shiny_app/www/images/plot_banner.jpg |only man/OpenGUI.Rd | 5 man/SummaryAM.Rd | 2 16 files changed, 566 insertions(+), 113 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-03 0.1.0