Title: Sensitivity Analysis for Comparative Methods
Description: An implementation of sensitivity analysis for phylogenetic comparative
methods. The package is an umbrella of statistical and graphical methods that
estimate and report different types of uncertainty in PCM:
(i) Species Sampling uncertainty (sample size; influential species and clades).
(ii) Phylogenetic uncertainty (different topologies and/or branch lengths).
(iii) Data uncertainty (intraspecific variation and measurement error).
Author: Gustavo Paterno [cre, aut],
Gijsbert Werner [aut],
Caterina Penone [aut],
Pablo Martinez [ctb]
Maintainer: Gustavo Paterno <paternogbc@gmail.com>
Diff between sensiPhy versions 0.8.0 dated 2017-12-15 and 0.8.1 dated 2018-01-22
DESCRIPTION | 8 - MD5 | 32 ++--- NEWS.md | 13 ++ R/clade_physig.R | 6 R/influ_physig.R | 5 R/intra_physig.R | 27 +--- R/samp_physig.R | 5 R/tree_physig.R | 6 inst/doc/sensiPhy_vignette.R | 100 +++++++++++++++ inst/doc/sensiPhy_vignette.Rmd | 166 +++++++++++++++++++++++++ inst/doc/sensiPhy_vignette.html | 256 ++++++++++++++++++++++++++++++++++++++-- man/clade_physig.Rd | 5 man/influ_physig.Rd | 5 man/intra_physig.Rd | 26 +--- man/samp_physig.Rd | 5 man/tree_physig.Rd | 5 vignettes/sensiPhy_vignette.Rmd | 166 +++++++++++++++++++++++++ 17 files changed, 764 insertions(+), 72 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on two testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package.
Author: Mauricio Olivares-Gonzalez [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares-Gonzalez <maurice.olivares@gmail.com>
Diff between RATest versions 0.1.1 dated 2017-10-11 and 0.1.2 dated 2018-01-22
DESCRIPTION | 12 ++++++------ MD5 | 23 ++++++++++++++--------- NAMESPACE | 4 ++++ R/RDperm.R | 10 +++++----- R/RPT.R |only R/summary.RDperm.R | 17 +++++++++++++++-- R/summary.RPT.R |only README.md | 5 +++-- inst/doc/RDperm.Rnw | 8 ++++---- inst/doc/RDperm.pdf |binary man/RDperm.Rd | 6 +++--- man/RPT.Rd |only man/summary.RDperm.Rd |only man/summary.RPT.Rd |only vignettes/RDperm.Rnw | 8 ++++---- 15 files changed, 58 insertions(+), 35 deletions(-)
Title: Simple and Scalable Statistical Modelling in R
Description: Write statistical models in R and fit them by MCMC on CPUs and GPUs, using Google TensorFlow (see <https://goldingn.github.io/greta> for more information).
Author: Nick Golding [aut, cre]
Maintainer: Nick Golding <nick.golding.research@gmail.com>
Diff between greta versions 0.2.0 dated 2017-06-26 and 0.2.3 dated 2018-01-22
greta-0.2.0/greta/R/dynamics_module.R |only greta-0.2.0/greta/man/dynamics-module.Rd |only greta-0.2.0/greta/tests/testthat/test_dynamics_module.R |only greta-0.2.3/greta/DESCRIPTION | 25 greta-0.2.3/greta/MD5 | 109 +- greta-0.2.3/greta/NAMESPACE | 23 greta-0.2.3/greta/NEWS |only greta-0.2.3/greta/R/as_data.R | 3 greta-0.2.3/greta/R/distribution.R | 7 greta-0.2.3/greta/R/extract_replace_combine.R | 259 +++-- greta-0.2.3/greta/R/functions.R | 310 +++++- greta-0.2.3/greta/R/greta_array_class.R | 88 - greta-0.2.3/greta/R/greta_model_class.R | 6 greta-0.2.3/greta/R/inference.R | 8 greta-0.2.3/greta/R/internals.R |only greta-0.2.3/greta/R/node_class.R | 10 greta-0.2.3/greta/R/node_types.R | 98 +- greta-0.2.3/greta/R/operators.R | 105 -- greta-0.2.3/greta/R/overloaded.R | 4 greta-0.2.3/greta/R/package.R | 9 greta-0.2.3/greta/R/probability_distributions.R | 53 - greta-0.2.3/greta/R/progress_bar.R | 3 greta-0.2.3/greta/R/samplers.R | 2 greta-0.2.3/greta/R/structures.R | 30 greta-0.2.3/greta/R/tf_functions.R |only greta-0.2.3/greta/R/transforms.R | 35 greta-0.2.3/greta/R/unknowns_class.R | 5 greta-0.2.3/greta/R/utils.R | 478 ++++------ greta-0.2.3/greta/R/variable.R | 6 greta-0.2.3/greta/build/vignette.rds |binary greta-0.2.3/greta/inst/doc/example_models.html | 14 greta-0.2.3/greta/inst/doc/get_started.R | 197 ---- greta-0.2.3/greta/inst/doc/get_started.Rmd | 10 greta-0.2.3/greta/inst/doc/get_started.html | 24 greta-0.2.3/greta/inst/doc/technical_details.html | 14 greta-0.2.3/greta/man/as_data.Rd | 3 greta-0.2.3/greta/man/distribution.Rd | 3 greta-0.2.3/greta/man/distributions.Rd | 6 greta-0.2.3/greta/man/extract-replace-combine.Rd | 20 greta-0.2.3/greta/man/functions.Rd | 16 greta-0.2.3/greta/man/greta.Rd | 6 greta-0.2.3/greta/man/internals.Rd |only greta-0.2.3/greta/man/model.Rd | 8 greta-0.2.3/greta/man/operators.Rd | 35 greta-0.2.3/greta/man/overloaded.Rd | 20 greta-0.2.3/greta/man/structures.Rd | 3 greta-0.2.3/greta/man/transforms.Rd | 3 greta-0.2.3/greta/man/variable.Rd | 4 greta-0.2.3/greta/tests/testthat/helpers.R | 18 greta-0.2.3/greta/tests/testthat/test_as_data.R | 25 greta-0.2.3/greta/tests/testthat/test_distributions.R | 122 +- greta-0.2.3/greta/tests/testthat/test_extract_replace_combine.R | 109 ++ greta-0.2.3/greta/tests/testthat/test_functions.R | 106 ++ greta-0.2.3/greta/tests/testthat/test_greta_array_class.R | 42 greta-0.2.3/greta/tests/testthat/test_inference.R | 2 greta-0.2.3/greta/tests/testthat/test_misc.R | 46 greta-0.2.3/greta/tests/testthat/test_operators.R | 1 greta-0.2.3/greta/tests/testthat/test_syntax.R | 1 greta-0.2.3/greta/vignettes/get_started.Rmd | 10 59 files changed, 1393 insertions(+), 1151 deletions(-)
Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>
Diff between survey versions 3.32-1 dated 2017-06-22 and 3.33 dated 2018-01-22
DESCRIPTION | 10 ++++---- MD5 | 59 ++++++++++++++++++++++++++-------------------------- NAMESPACE | 12 ++++++++-- R/grake.R | 57 +++++++++++++++++++++++++++++++++++--------------- R/greg.R | 44 +++++++++++++++++++++++++------------- R/regtest.R | 40 +++++++++++++++++++++++++++++------ R/survey.R | 26 ++++++++++++++++++++-- R/surveyrep.R | 2 - R/sysdata.rda |binary build/vignette.rds |binary data/api.rda |binary data/crowd.rda |binary data/election.rda |binary data/fpc.rda |binary data/hospital.rda |binary data/mu284.rda |binary data/nhanes.rda |binary data/scd.rda |binary data/yrbs.rda |binary inst/NEWS | 13 +++++++++++ inst/doc/domain.pdf |binary inst/doc/epi.pdf |binary inst/doc/phase1.pdf |binary inst/doc/pps.pdf |binary inst/doc/survey.pdf |binary man/calibrate.Rd | 10 +++++++- man/mu284.Rd | 5 +--- man/regTermTest.Rd | 37 +++++++++++++++++++++++++------- man/svycoxph.Rd | 12 ++++++++-- man/svyglm.Rd | 9 ++----- tests/glm-scoping.R |only 31 files changed, 237 insertions(+), 99 deletions(-)
Title: Design of Experiments Suite: Generate and Evaluate Optimal
Designs
Description: Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible.
Author: Tyler Morgan-Wall [aut, cre],
George Khoury [aut]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between skpr versions 0.40.1 dated 2017-10-20 and 0.45.2 dated 2018-01-22
DESCRIPTION | 11 MD5 | 72 - NAMESPACE | 2 NEWS | 55 + R/RcppExports.R | 102 +- R/aliasmodel.R | 4 R/eval_design.R | 39 R/eval_design_custom_mc.R | 12 R/eval_design_mc.R | 79 + R/eval_design_survival_mc.R | 15 R/gen_anticoef.R | 4 R/gen_design.R | 166 +++ R/plot_correlations.R | 9 R/reduceRunMatrix.R | 1 R/skprGUI.R | 1549 ++++++++++++++++++++----------------- README.md | 4 inst/shiny/skprGUI/server.R | 65 + inst/shiny/skprGUI/ui.R | 187 +++- inst/shiny/skprGUI/www/waves.css |only inst/shiny/skprGUI/www/waves.js |only man/figures/skprGUIcomp.png |binary man/figures/vidguigif.gif |only man/gen_design.Rd | 71 + src/AOptimality.cpp | 1 src/DOptimality.cpp | 1 src/DOptimalityBlocked.cpp | 1 src/IOptimality.cpp | 1 src/RcppExports.cpp | 29 src/calcAliasTrace.cpp | 1 src/calculateAOptimalityPseudo.cpp | 1 src/calculateDEfficiency.cpp | 1 src/covarianceMatrix.cpp | 1 src/covarianceMatrixPseudo.cpp | 1 src/genOptimalDesign.cpp | 533 ++++++++++-- src/genPseudoInverse.cpp | 1 src/init.c |only tests/testthat.R | 2 tests/testthat/Rplots.pdf |binary tests/testthat/testExampleCode.R | 121 ++ 39 files changed, 2125 insertions(+), 1017 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989) <DOI:10.2307/1912557>.
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is partially based on
work supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle [aut, cre],
Dongjun You [aut],
Lennart Schneider [ctb],
Seongho Bae [ctb]
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.5 dated 2017-12-15 and 0.5-1 dated 2018-01-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/llcont.R | 45 ++++++++++++++++++++++++++++++++++++++++++++- R/vuongtest.R | 10 ++-------- inst/doc/nonnest2.pdf |binary 6 files changed, 58 insertions(+), 18 deletions(-)
Title: Color Palettes, Colormaps, and Tools to Evaluate Them
Description: A comprehensive collection of color palettes, colormaps, and tools to evaluate them.
Author: Kevin Wright [aut, cre]
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between pals versions 1.4 dated 2017-06-12 and 1.5 dated 2018-01-22
pals-1.4/pals/LICENSE.note |only pals-1.4/pals/tests/testthat/Rplots.pdf |only pals-1.5/pals/DESCRIPTION | 9 pals-1.5/pals/MD5 | 45 ++-- pals-1.5/pals/NAMESPACE | 2 pals-1.5/pals/R/colormaps.R | 16 + pals-1.5/pals/R/discrete.R | 216 ++++++++++++---------- pals-1.5/pals/R/penobscot.R |only pals-1.5/pals/R/sysdata.rda |binary pals-1.5/pals/R/tools.R | 7 pals-1.5/pals/build/vignette.rds |binary pals-1.5/pals/data |only pals-1.5/pals/inst/doc/bivariate_choropleths.R | 14 - pals-1.5/pals/inst/doc/bivariate_choropleths.Rmd | 14 - pals-1.5/pals/inst/doc/bivariate_choropleths.html | 20 +- pals-1.5/pals/inst/doc/illusion.html | 4 pals-1.5/pals/inst/doc/pals_examples.R | 2 pals-1.5/pals/inst/doc/pals_examples.Rmd | 2 pals-1.5/pals/inst/doc/pals_examples.html | 12 - pals-1.5/pals/man/continuous.Rd | 16 + pals-1.5/pals/man/discrete.Rd | 14 + pals-1.5/pals/man/penobscot.Rd |only pals-1.5/pals/tests/testthat/test_discrete.R | 9 pals-1.5/pals/vignettes/bivariate_choropleths.Rmd | 14 - pals-1.5/pals/vignettes/pals.bib | 47 +++- pals-1.5/pals/vignettes/pals_examples.Rmd | 2 26 files changed, 288 insertions(+), 177 deletions(-)
Title: A Tidy Data Model for Natural Language Processing
Description: Provides a set of fast tools for converting a textual corpus into a set of normalized
tables. Users may make use of the 'udpipe' back end with no external dependencies, a Python back
end with 'spaCy' <https://spacy.io> or the Java back end 'CoreNLP'
<http://stanfordnlp.github.io/CoreNLP/>. Exposed annotation tasks include
tokenization, part of speech tagging, named entity recognition, entity linking, sentiment
analysis, dependency parsing, coreference resolution, and word embeddings. Summary
statistics regarding token unigram, part of speech tag, and dependency type frequencies
are also included to assist with analyses.
Author: Taylor B. Arnold [aut, cre]
Maintainer: Taylor B. Arnold <taylor.arnold@acm.org>
Diff between cleanNLP versions 1.10.0 dated 2017-07-01 and 2.0.3 dated 2018-01-22
cleanNLP-1.10.0/cleanNLP/R/backend_coreNLP.R |only cleanNLP-1.10.0/cleanNLP/R/backend_spaCy.R |only cleanNLP-1.10.0/cleanNLP/inst/doc/schema.R |only cleanNLP-1.10.0/cleanNLP/inst/doc/schema.Rmd |only cleanNLP-1.10.0/cleanNLP/inst/doc/schema.html |only cleanNLP-1.10.0/cleanNLP/man/combine_documents.Rd |only cleanNLP-1.10.0/cleanNLP/man/doc_id_reset.Rd |only cleanNLP-1.10.0/cleanNLP/man/download_core_nlp.Rd |only cleanNLP-1.10.0/cleanNLP/man/extract_documents.Rd |only cleanNLP-1.10.0/cleanNLP/man/from_CoNLL.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_combine.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_coreference.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_dependency.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_document.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_entity.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_sentence.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_tfidf.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_token.Rd |only cleanNLP-1.10.0/cleanNLP/man/get_vector.Rd |only cleanNLP-1.10.0/cleanNLP/man/init_coreNLP.Rd |only cleanNLP-1.10.0/cleanNLP/man/init_spaCy.Rd |only cleanNLP-1.10.0/cleanNLP/man/init_tokenizers.Rd |only cleanNLP-1.10.0/cleanNLP/man/read_annotation.Rd |only cleanNLP-1.10.0/cleanNLP/man/run_annotators.Rd |only cleanNLP-1.10.0/cleanNLP/man/tidy_pca.Rd |only cleanNLP-1.10.0/cleanNLP/man/to_CoNNL.Rd |only cleanNLP-1.10.0/cleanNLP/man/write_annotation.Rd |only cleanNLP-1.10.0/cleanNLP/vignettes/schema.Rmd |only cleanNLP-2.0.3/cleanNLP/DESCRIPTION | 24 cleanNLP-2.0.3/cleanNLP/MD5 | 146 +- cleanNLP-2.0.3/cleanNLP/NAMESPACE | 26 cleanNLP-2.0.3/cleanNLP/NEWS.md | 26 cleanNLP-2.0.3/cleanNLP/R/accessors.R | 87 - cleanNLP-2.0.3/cleanNLP/R/annotate.R | 235 +-- cleanNLP-2.0.3/cleanNLP/R/annotate_tools.R | 643 +--------- cleanNLP-2.0.3/cleanNLP/R/backend_corenlp.R |only cleanNLP-2.0.3/cleanNLP/R/backend_spacy.R |only cleanNLP-2.0.3/cleanNLP/R/backend_tokenizers.R | 102 + cleanNLP-2.0.3/cleanNLP/R/backend_udpipe.R |only cleanNLP-2.0.3/cleanNLP/R/data.R | 12 cleanNLP-2.0.3/cleanNLP/R/download.R | 100 + cleanNLP-2.0.3/cleanNLP/R/io.R |only cleanNLP-2.0.3/cleanNLP/R/onLoad.R | 5 cleanNLP-2.0.3/cleanNLP/R/pkg.R | 30 cleanNLP-2.0.3/cleanNLP/R/renamed.R |only cleanNLP-2.0.3/cleanNLP/R/tif.R |only cleanNLP-2.0.3/cleanNLP/R/tools.R | 46 cleanNLP-2.0.3/cleanNLP/build/vignette.rds |binary cleanNLP-2.0.3/cleanNLP/data/datalist | 1 cleanNLP-2.0.3/cleanNLP/data/obama.rda |binary cleanNLP-2.0.3/cleanNLP/data/un.rda |only cleanNLP-2.0.3/cleanNLP/inst/doc/case_study.R | 36 cleanNLP-2.0.3/cleanNLP/inst/doc/case_study.Rmd | 36 cleanNLP-2.0.3/cleanNLP/inst/doc/case_study.html | 38 cleanNLP-2.0.3/cleanNLP/inst/extdata/cleanNLP-0.1.jar |binary cleanNLP-2.0.3/cleanNLP/inst/py/load_spacy.py | 24 cleanNLP-2.0.3/cleanNLP/inst/txt_files/bush-short.txt |only cleanNLP-2.0.3/cleanNLP/inst/txt_files/clinton-short.txt |only cleanNLP-2.0.3/cleanNLP/inst/txt_files/obama-short.txt |only cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/AnnotationProcessor.java | 7 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVCoreferenceDocumentWriter.java | 4 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVDependencyDocumentWriter.java | 4 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVDocumentDocumentWriter.java | 2 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVNamedEntityDocumentWriter.java | 4 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVSentenceDocumentWriter.java | 2 cleanNLP-2.0.3/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVTokenDocumentWriter.java | 4 cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/AnnotationProcessor.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVCoreferenceDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVDependencyDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVDocumentDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVNamedEntityDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVSentenceDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/java/target/classes/edu/richmond/nlp/CSVTokenDocumentWriter.class |binary cleanNLP-2.0.3/cleanNLP/man/cleanNLP-package.Rd | 30 cleanNLP-2.0.3/cleanNLP/man/cnlp_annotate.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_combine_documents.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_download_corenlp.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_download_udpipe.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_extract_documents.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_coreference.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_dependency.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_document.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_entity.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_sentence.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_tfidf.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_tif.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_token.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_get_vector.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_init_corenlp.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_init_spacy.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_init_tokenizers.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_init_udpipe.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_pca.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_read_conll.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_read_csv.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_write_conll.Rd |only cleanNLP-2.0.3/cleanNLP/man/cnlp_write_csv.Rd |only cleanNLP-2.0.3/cleanNLP/man/renamed.Rd |only cleanNLP-2.0.3/cleanNLP/man/un.Rd |only cleanNLP-2.0.3/cleanNLP/tests/testthat/test-annotation_utils.R | 51 cleanNLP-2.0.3/cleanNLP/tests/testthat/test-java.R | 146 +- cleanNLP-2.0.3/cleanNLP/tests/testthat/test-python.R | 117 - cleanNLP-2.0.3/cleanNLP/tests/testthat/test-tokenizers.R | 60 cleanNLP-2.0.3/cleanNLP/tests/testthat/test-tools.R | 35 cleanNLP-2.0.3/cleanNLP/tests/testthat/test-udpipe.R |only cleanNLP-2.0.3/cleanNLP/vignettes/case_study.Rmd | 36 106 files changed, 867 insertions(+), 1252 deletions(-)
Title: HTTP Client
Description: A simple HTTP client, with tools for making HTTP requests,
and mocking HTTP requests. The package is built on R6, and takes
inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>).
The package name is a play on curl, the widely used command line tool
for HTTP, and this package is built on top of the R package 'curl', an
interface to 'libcurl' (<https://curl.haxx.se/libcurl>).
Author: Scott Chamberlain [aut, cre] (0000-0003-1444-9135)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between crul versions 0.4.0 dated 2017-10-02 and 0.5.0 dated 2018-01-22
DESCRIPTION | 17 +- LICENSE | 2 MD5 | 69 +++++---- NAMESPACE | 1 NEWS.md | 18 ++ R/async.R | 88 ++++++++---- R/asyncvaried.R | 31 +++- R/auth.R | 19 ++ R/client.R | 8 - R/crul-package.r | 1 R/curl-options.R | 3 R/make_url.R | 6 R/paginator.R |only R/writing-options.R | 53 +++++++ README.md | 50 ++---- build/vignette.rds |binary inst/doc/async.Rmd | 54 +++---- inst/doc/async.html | 271 +++++++++++++++++++++++++++++++------ inst/doc/crul_vignette.Rmd | 36 ++--- inst/doc/crul_vignette.html | 273 ++++++++++++++++++++++++++++++++------ inst/doc/how-to-use-crul.Rmd | 8 - inst/doc/how-to-use-crul.html | 237 +++++++++++++++++++++++++++++--- man/Async.Rd | 10 - man/HttpClient.Rd | 4 man/Paginator.Rd |only man/auth.Rd | 17 +- man/crul-package.Rd | 1 man/curl-options.Rd | 3 man/writing-options.Rd | 53 +++++++ tests/testthat/test-async.R | 50 ++++++ tests/testthat/test-asyncvaried.R | 60 ++++++++ tests/testthat/test-head.R | 21 ++ tests/testthat/test-mocking.R | 2 tests/testthat/test-paginator.R |only vignettes/async.Rmd | 54 +++---- vignettes/crul_vignette.Rmd | 36 ++--- vignettes/how-to-use-crul.Rmd | 8 - 37 files changed, 1233 insertions(+), 331 deletions(-)
Title: Downloads and Organizes Financial Data for Multiple Tickers
Description: Makes it easy to download a large number of trade data from Yahoo or Google Finance.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between BatchGetSymbols versions 1.2 dated 2017-06-26 and 2.0 dated 2018-01-22
BatchGetSymbols-1.2/BatchGetSymbols/R/OnAttach.R |only BatchGetSymbols-1.2/BatchGetSymbols/inst/CITATION |only BatchGetSymbols-2.0/BatchGetSymbols/DESCRIPTION | 12 BatchGetSymbols-2.0/BatchGetSymbols/MD5 | 35 - BatchGetSymbols-2.0/BatchGetSymbols/NAMESPACE | 5 BatchGetSymbols-2.0/BatchGetSymbols/NEWS.md | 40 + BatchGetSymbols-2.0/BatchGetSymbols/R/BatchGetSymbols.R | 106 +++- BatchGetSymbols-2.0/BatchGetSymbols/R/Get_Ibov_Stocks.R |only BatchGetSymbols-2.0/BatchGetSymbols/R/Utils.R |only BatchGetSymbols-2.0/BatchGetSymbols/R/myGetSymbols.R | 240 ++++++---- BatchGetSymbols-2.0/BatchGetSymbols/README.md |only BatchGetSymbols-2.0/BatchGetSymbols/build/vignette.rds |binary BatchGetSymbols-2.0/BatchGetSymbols/inst/doc/BatchGetSymbols-vignette.R | 14 BatchGetSymbols-2.0/BatchGetSymbols/inst/doc/BatchGetSymbols-vignette.Rmd | 38 + BatchGetSymbols-2.0/BatchGetSymbols/inst/doc/BatchGetSymbols-vignette.html | 76 +-- BatchGetSymbols-2.0/BatchGetSymbols/inst/extdata |only BatchGetSymbols-2.0/BatchGetSymbols/man/BatchGetSymbols.Rd | 31 - BatchGetSymbols-2.0/BatchGetSymbols/man/GetIbovStocks.Rd |only BatchGetSymbols-2.0/BatchGetSymbols/man/calc.ret.Rd |only BatchGetSymbols-2.0/BatchGetSymbols/man/fix.ticker.name.Rd |only BatchGetSymbols-2.0/BatchGetSymbols/man/get.clean.data.Rd |only BatchGetSymbols-2.0/BatchGetSymbols/man/myGetSymbols.Rd | 14 BatchGetSymbols-2.0/BatchGetSymbols/man/reshape.wide.Rd |only BatchGetSymbols-2.0/BatchGetSymbols/vignettes/BatchGetSymbols-vignette.Rmd | 38 + 24 files changed, 438 insertions(+), 211 deletions(-)
More information about BatchGetSymbols at CRAN
Permanent link
Title: Nonlinear Time Series Models with Regime Switching
Description: Implements nonlinear autoregressive (AR) time series models. For univariate series, a non-parametric approach is available through additive nonlinear AR. Parametric modeling and testing for regime switching dynamics is available when the transition is either direct (TAR: threshold AR) or smooth (STAR: smooth transition AR, LSTAR). For multivariate series, one can estimate a range of TVAR or threshold cointegration TVECM models with two or three regimes. Tests can be conducted for TVAR as well as for TVECM (Hansen and Seo 2002 and Seo 2006).
Author: Antonio Fabio Di Narzo [aut],
Jose Luis Aznarte [ctb],
Matthieu Stigler [aut, cre]
Maintainer: Matthieu Stigler <Matthieu.Stigler@gmail.com>
Diff between tsDyn versions 0.9-44 dated 2016-05-22 and 0.9-46 dated 2018-01-22
tsDyn-0.9-44/tsDyn/R/TVAR.sim.R |only tsDyn-0.9-44/tsDyn/man/TVAR.boot.Rd |only tsDyn-0.9-46/tsDyn/DESCRIPTION | 12 tsDyn-0.9-46/tsDyn/MD5 | 159 +-- tsDyn-0.9-46/tsDyn/NAMESPACE | 3 tsDyn-0.9-46/tsDyn/R/TVAR.gen.R |only tsDyn-0.9-46/tsDyn/R/TVARestim.R | 829 +++++++++---------- tsDyn-0.9-46/tsDyn/R/TVECM.R | 7 tsDyn-0.9-46/tsDyn/R/TVECM.sim.R | 8 tsDyn-0.9-46/tsDyn/R/TVECMSeoTest.R | 2 tsDyn-0.9-46/tsDyn/R/VAR.sim.R | 61 + tsDyn-0.9-46/tsDyn/R/accuracy.R | 2 tsDyn-0.9-46/tsDyn/R/delta.R | 4 tsDyn-0.9-46/tsDyn/R/lineVar.R | 18 tsDyn-0.9-46/tsDyn/R/llar.R | 2 tsDyn-0.9-46/tsDyn/R/misc.R | 92 +- tsDyn-0.9-46/tsDyn/R/nlar-methods.R | 6 tsDyn-0.9-46/tsDyn/R/predict.R | 6 tsDyn-0.9-46/tsDyn/R/predict.TVAR.R |only tsDyn-0.9-46/tsDyn/R/predict.VAR.R | 58 - tsDyn-0.9-46/tsDyn/R/predict_rolling.R | 2 tsDyn-0.9-46/tsDyn/R/rank.select.R | 2 tsDyn-0.9-46/tsDyn/R/rank.test.R | 2 tsDyn-0.9-46/tsDyn/R/vec2var.tsDyn.R | 82 - tsDyn-0.9-46/tsDyn/build/vignette.rds |binary tsDyn-0.9-46/tsDyn/data/barry.rda |binary tsDyn-0.9-46/tsDyn/data/m.unrate.rda |only tsDyn-0.9-46/tsDyn/data/zeroyld.rda |binary tsDyn-0.9-46/tsDyn/inst/CITATION | 10 tsDyn-0.9-46/tsDyn/inst/ChangeLog | 11 tsDyn-0.9-46/tsDyn/inst/doc/ThCointOverview.pdf |binary tsDyn-0.9-46/tsDyn/inst/doc/tsDyn.pdf |binary tsDyn-0.9-46/tsDyn/man/BBCTest.Rd | 11 tsDyn-0.9-46/tsDyn/man/MAPE.Rd | 3 tsDyn-0.9-46/tsDyn/man/MakeThSpec.Rd | 14 tsDyn-0.9-46/tsDyn/man/TVAR.LRtest.Rd | 11 tsDyn-0.9-46/tsDyn/man/TVAR.Rd | 21 tsDyn-0.9-46/tsDyn/man/TVAR.sim.Rd | 75 - tsDyn-0.9-46/tsDyn/man/TVECM.HStest.Rd | 9 tsDyn-0.9-46/tsDyn/man/TVECM.Rd | 17 tsDyn-0.9-46/tsDyn/man/TVECM.SeoTest.Rd | 15 tsDyn-0.9-46/tsDyn/man/TVECM.sim.Rd | 31 tsDyn-0.9-46/tsDyn/man/VAR.boot.Rd | 74 + tsDyn-0.9-46/tsDyn/man/VARrep.Rd | 15 tsDyn-0.9-46/tsDyn/man/VECM.Rd | 47 - tsDyn-0.9-46/tsDyn/man/VECM_symbolic.Rd | 9 tsDyn-0.9-46/tsDyn/man/accuracy_stat.Rd | 11 tsDyn-0.9-46/tsDyn/man/addRegime.Rd | 11 tsDyn-0.9-46/tsDyn/man/autopairs.Rd | 11 tsDyn-0.9-46/tsDyn/man/autotriples.Rd | 11 tsDyn-0.9-46/tsDyn/man/autotriples.rgl.Rd | 11 tsDyn-0.9-46/tsDyn/man/availableModels.Rd | 5 tsDyn-0.9-46/tsDyn/man/coefB.Rd | 47 - tsDyn-0.9-46/tsDyn/man/computeGradient.Rd | 11 tsDyn-0.9-46/tsDyn/man/delta.Rd | 12 tsDyn-0.9-46/tsDyn/man/delta.lin.Rd | 11 tsDyn-0.9-46/tsDyn/man/fitted.nlVar.Rd | 9 tsDyn-0.9-46/tsDyn/man/getTh.Rd | 5 tsDyn-0.9-46/tsDyn/man/isLinear.Rd | 3 tsDyn-0.9-46/tsDyn/man/lags.select.Rd | 15 tsDyn-0.9-46/tsDyn/man/lineVar.Rd | 42 tsDyn-0.9-46/tsDyn/man/logLik.VECM.Rd | 11 tsDyn-0.9-46/tsDyn/man/logLik.nlVar.Rd | 11 tsDyn-0.9-46/tsDyn/man/m.unrate.Rd |only tsDyn-0.9-46/tsDyn/man/mse.Rd | 3 tsDyn-0.9-46/tsDyn/man/nlar.Rd | 11 tsDyn-0.9-46/tsDyn/man/oneStep.Rd | 3 tsDyn-0.9-46/tsDyn/man/predict.VAR.Rd | 79 + tsDyn-0.9-46/tsDyn/man/predict.nlar.Rd | 19 tsDyn-0.9-46/tsDyn/man/predict_rolling.Rd | 17 tsDyn-0.9-46/tsDyn/man/rank.select.Rd | 18 tsDyn-0.9-46/tsDyn/man/rank.test.Rd | 18 tsDyn-0.9-46/tsDyn/man/regime.Rd | 5 tsDyn-0.9-46/tsDyn/man/setar.Rd | 7 tsDyn-0.9-46/tsDyn/man/setar.sim.Rd | 11 tsDyn-0.9-46/tsDyn/man/sigmoid.Rd | 5 tsDyn-0.9-46/tsDyn/man/toLatex.setar.Rd | 11 tsDyn-0.9-46/tsDyn/src/llar.c | 2 tsDyn-0.9-46/tsDyn/src/tsDyn_init.c |only tsDyn-0.9-46/tsDyn/tests/00SetarAndFriends.R | 50 - tsDyn-0.9-46/tsDyn/tests/00SetarAndFriends.Rout.save | 556 ------------ tsDyn-0.9-46/tsDyn/tests/TVAR.R |only tsDyn-0.9-46/tsDyn/tests/TVAR.Rout.save |only tsDyn-0.9-46/tsDyn/tests/VAR.R | 2 tsDyn-0.9-46/tsDyn/tests/VAR.Rout.save | 10 85 files changed, 1203 insertions(+), 1591 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that provides
stricter checking and better formatting than the traditional data frame.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 1.4.1 dated 2017-12-25 and 1.4.2 dated 2018-01-22
tibble-1.4.1/tibble/R/tibble-pkg.R |only tibble-1.4.1/tibble/man/is.tibble.Rd |only tibble-1.4.2/tibble/DESCRIPTION | 24 +- tibble-1.4.2/tibble/MD5 | 98 +++++----- tibble-1.4.2/tibble/NEWS.md | 38 +++ tibble-1.4.2/tibble/R/add.R | 6 tibble-1.4.2/tibble/R/as_tibble.R | 4 tibble-1.4.2/tibble/R/check-names.R | 2 tibble-1.4.2/tibble/R/compat-purrr.R | 5 tibble-1.4.2/tibble/R/enframe.R | 7 tibble-1.4.2/tibble/R/glimpse.R | 10 - tibble-1.4.2/tibble/R/lst.R | 10 - tibble-1.4.2/tibble/R/new.R | 19 + tibble-1.4.2/tibble/R/repair-names.R | 4 tibble-1.4.2/tibble/R/rownames.R | 2 tibble-1.4.2/tibble/R/tbl-df.r | 31 +-- tibble-1.4.2/tibble/R/tibble-package.R |only tibble-1.4.2/tibble/R/tibble.R | 32 +-- tibble-1.4.2/tibble/R/tribble.R | 10 - tibble-1.4.2/tibble/R/type-sum.r | 1 tibble-1.4.2/tibble/R/utils-format.r | 38 ++- tibble-1.4.2/tibble/R/wrap.R | 29 -- tibble-1.4.2/tibble/README.md | 6 tibble-1.4.2/tibble/inst/doc/extending.html | 34 +-- tibble-1.4.2/tibble/inst/doc/tibble.R | 1 tibble-1.4.2/tibble/inst/doc/tibble.Rmd | 3 tibble-1.4.2/tibble/inst/doc/tibble.html | 6 tibble-1.4.2/tibble/man/add_column.Rd | 4 tibble-1.4.2/tibble/man/add_row.Rd | 4 tibble-1.4.2/tibble/man/as_tibble.Rd | 2 tibble-1.4.2/tibble/man/glimpse.Rd | 4 tibble-1.4.2/tibble/man/is_tibble.Rd |only tibble-1.4.2/tibble/man/tibble-options.Rd |only tibble-1.4.2/tibble/man/tibble-package.Rd | 22 -- tibble-1.4.2/tibble/man/tibble.Rd | 18 + tibble-1.4.2/tibble/man/tidy_names.Rd | 4 tibble-1.4.2/tibble/tests/testthat/output/glimpse/all-35.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/glimpse/all-50.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/glimpse/all-70.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/glimpse/iris-70-na-nrow.txt |only tibble-1.4.2/tibble/tests/testthat/output/glimpse/iris-70.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/glimpse/iris-empty-70.txt | 1 tibble-1.4.2/tibble/tests/testthat/output/trunc_mat/all--30.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/trunc_mat/all-1-30-2.txt | 4 tibble-1.4.2/tibble/tests/testthat/output/trunc_mat/iris-3-5.txt | 2 tibble-1.4.2/tibble/tests/testthat/output/trunc_mat/iris-5-30.txt | 6 tibble-1.4.2/tibble/tests/testthat/output/trunc_mat/zero-rows_unk-5-30.txt | 2 tibble-1.4.2/tibble/tests/testthat/test-enframe.R | 7 tibble-1.4.2/tibble/tests/testthat/test-glimpse.R | 9 tibble-1.4.2/tibble/tests/testthat/test-matrix.R | 6 tibble-1.4.2/tibble/tests/testthat/test-tbl-df.R | 5 tibble-1.4.2/tibble/tests/testthat/test-tribble.R | 22 +- tibble-1.4.2/tibble/vignettes/tibble.Rmd | 3 53 files changed, 318 insertions(+), 237 deletions(-)
Title: Client for the 'Alteryx Promote' API
Description: Deploy, maintain, and invoke predictive models using the 'Alteryx
Promote' REST API. 'Alteryx Promote' is available at the URL:
<https://www.alteryx.com/products/alteryx-promote>.
Author: Paul E. Promote <promotedev@alteryx.com>
Maintainer: Paul E. Promote <promotedev@alteryx.com>
Diff between promote versions 1.0.0 dated 2017-11-15 and 1.0.1 dated 2018-01-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 2 +- R/promote.R | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Objective Bayesian Model Discrimination in Follow-Up Designs
Description: Implements the objective Bayesian methodology proposed in Consonni and Deldossi in order to choose the optimal experiment that better discriminate between competing models. G.Consonni, L. Deldossi (2014) Objective Bayesian Model Discrimination in Follow-up Experimental Designs, Test. <DOI:10.1007/s11749-015-0461-3>.
Author: Laura Deldossi and Marta Nai Ruscone based on Daniel Meyer's code (2016)
Maintainer: Marta Nai Ruscone <mnairuscone@liuc.it>
Diff between OBsMD versions 0.2-0.00 dated 2017-04-12 and 2.1 dated 2018-01-22
DESCRIPTION | 15 +++++---------- MD5 | 8 ++++---- NAMESPACE | 43 ++++++++++++++++++++++--------------------- man/OBsMD-package.Rd | 4 ++-- src/obsmd.f | 6 +++--- 5 files changed, 36 insertions(+), 40 deletions(-)
Title: Accompaniment Package to ModernDive: An Introduction to
Statistical and Data Sciences via R
Description: An accompaniment R package to ModernDive: An Introduction to
Statistical and Data Sciences via R available at <http://moderndive.com/>,
in particular wrapper functions targeted at novices to easily generate tidy
linear regression output.
Author: Albert Y. Kim [cre],
Chester Ismay [aut],
Andrew Bray [ctb]
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.1.0 dated 2018-01-22 and 0.1.1 dated 2018-01-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/bowl_samples.R | 2 +- data/pennies.rda |binary man/bowl_samples.Rd | 2 +- 6 files changed, 14 insertions(+), 10 deletions(-)
Title: Genome-Wide Association and Linkage Analysis under Heterogeneity
Description: Likelihood ratio tests for genome-wide association and genome-wide linkage analysis under heterogeneity.
Author: Xiaoxia Han [aut, cre],
Yongzhao Shao [aut]
Maintainer: Xiaoxia Han <xh414@nyu.edu>
Diff between gLRTH versions 0.1.0 dated 2017-01-05 and 0.2.0 dated 2018-01-22
gLRTH-0.1.0/gLRTH/R/gLRTH.R |only gLRTH-0.1.0/gLRTH/R/gLRTH2.R |only gLRTH-0.1.0/gLRTH/README.md |only gLRTH-0.1.0/gLRTH/man/gLRTH-package.Rd |only gLRTH-0.1.0/gLRTH/man/gLRTH.Rd |only gLRTH-0.1.0/gLRTH/man/gLRTH2.Rd |only gLRTH-0.2.0/gLRTH/DESCRIPTION | 16 +++++++--------- gLRTH-0.2.0/gLRTH/MD5 | 14 ++++++-------- gLRTH-0.2.0/gLRTH/NAMESPACE | 5 ++--- gLRTH-0.2.0/gLRTH/R/gLRTH_A.R |only gLRTH-0.2.0/gLRTH/R/gLRTH_L.R |only gLRTH-0.2.0/gLRTH/man/gLRTH_A.Rd |only gLRTH-0.2.0/gLRTH/man/gLRTH_L.Rd |only 13 files changed, 15 insertions(+), 20 deletions(-)
Title: Access 'Upwave' API
Description: 'Upwave' <https://www.upwave.io/> is a task management app
organising tasks on boards and cards. 'upwaver' is a wrapper
around the 'Upwave' API <https://upwavehq.github.io/api/> that
allows listing and updating those boards and cards.
Author: Adrian Staempfli, Christoph Strauss, Fabian Leuthold, Michael
Schmid
Maintainer: Adrian Staempfli <adrian.staempfli@fhsg.ch>
Diff between upwaver versions 1.0.0 dated 2018-01-16 and 1.0.1 dated 2018-01-22
DESCRIPTION | 15 +++---- MD5 | 38 +++++++++--------- NEWS.md | 8 ++- R/burndown.R | 6 +- R/create_card.R | 4 - R/upwaver.R | 10 ++-- README.md | 12 ++--- inst/doc/upwaver.R | 8 +-- inst/doc/upwaver.Rmd | 46 +++++++++++----------- inst/doc/upwaver.html | 87 +++++++++++++++++++++--------------------- man/aufwand.Rd | 2 man/board_details.Rd | 2 man/content_as_list.Rd | 2 man/create_card_from_excel.Rd | 4 - man/list_boards.Rd | 2 man/list_cards.Rd | 2 man/request.Rd | 2 man/storypoints_and_status.Rd | 4 - tests/testthat/test-upwaver.R | 2 vignettes/upwaver.Rmd | 46 +++++++++++----------- 20 files changed, 155 insertions(+), 147 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a 'shiny' interface which can be started from R using
treespaceServer().
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treespace versions 1.0.1 dated 2017-12-14 and 1.1.0 dated 2018-01-22
DESCRIPTION | 19 MD5 | 48 NAMESPACE | 8 R/makeCollapsedTree.R |only R/relatedTreeDist.R |only R/simulateIndTree.R |only R/tipsMRCAdepths.R |only R/treeConcordance.R |only R/treespace.R | 20 README.md | 13 build/vignette.rds |binary inst/doc/DengueVignette.html | 1766 ++++++++++++++++++++----- inst/doc/TransmissionTreesVignette.html | 4 inst/doc/introduction.html | 6 inst/doc/tipCategories.R |only inst/doc/tipCategories.Rmd |only inst/doc/tipCategories.html |only inst/shiny/server.R | 22 inst/shiny/ui.R | 15 man/makeCollapsedTree.Rd |only man/relatedTreeDist.Rd |only man/simulateIndTree.Rd |only man/tipsMRCAdepths.Rd |only man/treeConcordance.Rd |only man/treespace.Rd | 6 tests/testthat.R | 1 tests/testthat/testbasics.R | 31 vignettes/figs/concordance_basic-1.png |only vignettes/figs/concordance_basic-2.png |only vignettes/figs/concordance_permuations-1.png |only vignettes/figs/plot_collapsed_trees-1.png |only vignettes/figs/plot_patient_trees-1.png |only vignettes/figs/relatedTreeDist_six_trees-1.png |only vignettes/figs/six_comparable_trees-1.png |only vignettes/figs/six_heatmap-1.png |only vignettes/tipCategories.Rmd |only 36 files changed, 1567 insertions(+), 392 deletions(-)
Title: Perform Two-Way Orthogonal Partial Least Squares
Description: Performs the O2PLS data integration method for two datasets yielding joint and data-specific parts for each dataset.
The algorithm automatically switches to a memory-efficient approach to fit O2PLS to high dimensional data.
It provides a rigorous and a faster alternative cross-validation method to select the number of components,
as well as functions to report proportions of explained variation and to construct plots of the results.
See Trygg and Wold (2003) <doi:10.1002/cem.775> and el Bouhaddani et al (2016) <doi:10.1186/s12859-015-0854-z>.
Author: Said el Bouhaddani, Jeanine Houwing-Duistermaat, Geurt Jongbloed, Szymon Kielbasa and
Hae-Won Uh
Maintainer: Said el Bouhaddani <s.el_bouhaddani@lumc.nl>
Diff between OmicsPLS versions 1.0.3 dated 2017-08-07 and 1.1.0 dated 2018-01-22
DESCRIPTION | 8 +- MD5 | 41 +++++++------- NAMESPACE | 2 R/Crossval_OmicsPLS.R | 5 + R/OmicsPLS.R | 99 ++++++++++++++++++++++++++++------- R/OmicsPLS_o2m.R | 76 ++++++++++++++------------ README.md | 34 +++++++++--- build/vignette.rds |binary inst/doc/OmicsPLS_vignette.pdf |binary man/loadings.Rd | 4 + man/o2m.Rd | 25 ++++---- man/plot.o2m.Rd | 3 + man/predict.o2m.Rd | 3 + man/scores.Rd |only man/summary.o2m.Rd | 4 + tests/testthat.R | 1 tests/testthat/Rplots.pdf |binary tests/testthat/test_error.R | 35 +++++++++++- vignettes/Figs/unnamed-chunk-2-1.pdf |binary vignettes/Figs/unnamed-chunk-5-1.pdf |binary vignettes/Figs/unnamed-chunk-5-2.pdf |binary vignettes/Figs/unnamed-chunk-6-1.pdf |binary 22 files changed, 242 insertions(+), 98 deletions(-)
Title: Biological Image Analysis
Description: Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.
Author: Zachary Colburn
Maintainer: Zachary Colburn <zcolburn@gmail.com>
Diff between Bioi versions 0.2.8 dated 2018-01-19 and 0.2.9 dated 2018-01-22
DESCRIPTION | 12 - MD5 | 16 +- NEWS.md | 9 - R/euclidean_linker.R | 6 inst/doc/Bioi.html | 4 man/euclidean_linker.Rd | 6 src/euclidean_linker_cpp.cpp | 248 +++++++++++++++------------------ src/find_min_dists_cpp.cpp | 6 tests/testthat/test.euclidean_linker.R | 17 -- 9 files changed, 151 insertions(+), 173 deletions(-)
Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial (Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses 'Stan' and 'JAGS' as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>
Diff between BANOVA versions 1.1.0 dated 2018-01-09 and 1.1.1 dated 2018-01-22
DESCRIPTION | 18 +++++++++++------- MD5 | 13 +++++++++---- NEWS | 4 ++++ build |only inst/doc |only man/BANOVA-package.Rd | 4 ++-- src/Makevars.win | 1 + vignettes |only 8 files changed, 27 insertions(+), 13 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression models
with missing values in covariates or the dependent variable
using maximum likelihood or Bayesian estimation. The regression
model can be nonlinear (e.g., including interaction or quadratic
effects). Multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between mdmb versions 0.4-15 dated 2017-08-20 and 0.5-27 dated 2018-01-22
mdmb-0.4-15/mdmb/R/coef.bct_regression.R |only mdmb-0.4-15/mdmb/R/coef.fit_bct_scaled.R |only mdmb-0.4-15/mdmb/R/coef.fit_t_scaled.R |only mdmb-0.4-15/mdmb/R/coef.fit_yjt_scaled.R |only mdmb-0.4-15/mdmb/R/coef.frm_em.R |only mdmb-0.4-15/mdmb/R/coef.frm_fb.R |only mdmb-0.4-15/mdmb/R/coef.logistic_regression.R |only mdmb-0.4-15/mdmb/R/coef.yjt_regression.R |only mdmb-0.4-15/mdmb/R/logLik.bct_regression.R |only mdmb-0.4-15/mdmb/R/logLik.fit_bct_scaled.R |only mdmb-0.4-15/mdmb/R/logLik.fit_t_scaled.R |only mdmb-0.4-15/mdmb/R/logLik.fit_yjt_scaled.R |only mdmb-0.4-15/mdmb/R/logLik.frm_em.R |only mdmb-0.4-15/mdmb/R/logLik.logistic_regression.R |only mdmb-0.4-15/mdmb/R/logLik.yjt_regression.R |only mdmb-0.4-15/mdmb/R/vcov.bct_regression.R |only mdmb-0.4-15/mdmb/R/vcov.fit_bct_scaled.R |only mdmb-0.4-15/mdmb/R/vcov.fit_t_scaled.R |only mdmb-0.4-15/mdmb/R/vcov.fit_yjt_scaled.R |only mdmb-0.4-15/mdmb/R/vcov.frm_em.R |only mdmb-0.4-15/mdmb/R/vcov.frm_fb.R |only mdmb-0.4-15/mdmb/R/vcov.logistic_regression.R |only mdmb-0.4-15/mdmb/R/vcov.yjt_regression.R |only mdmb-0.5-27/mdmb/DESCRIPTION | 10 mdmb-0.5-27/mdmb/MD5 | 277 ++++------ mdmb-0.5-27/mdmb/NAMESPACE | 14 mdmb-0.5-27/mdmb/R/bc_antitrafo.R | 2 mdmb-0.5-27/mdmb/R/bc_trafo.R | 2 mdmb-0.5-27/mdmb/R/bct_regression.R | 2 mdmb-0.5-27/mdmb/R/coef.mdmb.R |only mdmb-0.5-27/mdmb/R/dbct_scaled.R | 2 mdmb-0.5-27/mdmb/R/doprobit.R |only mdmb-0.5-27/mdmb/R/dt_scaled.R | 2 mdmb-0.5-27/mdmb/R/dyjt_scaled.R | 2 mdmb-0.5-27/mdmb/R/dyjt_scaled_log_multiplication.R | 4 mdmb-0.5-27/mdmb/R/eval_prior_list.R | 2 mdmb-0.5-27/mdmb/R/eval_prior_list_gradient_log.R | 4 mdmb-0.5-27/mdmb/R/eval_prior_list_sumlog.R | 2 mdmb-0.5-27/mdmb/R/fit_bct_scaled.R | 2 mdmb-0.5-27/mdmb/R/fit_mdmb_distribution.R | 29 - mdmb-0.5-27/mdmb/R/fit_mdmb_distribution_extract_results.R | 2 mdmb-0.5-27/mdmb/R/fit_mdmb_distribution_logLik_extract.R | 8 mdmb-0.5-27/mdmb/R/fit_mdmb_distribution_remove_NA.R | 2 mdmb-0.5-27/mdmb/R/fit_mdmb_distribution_summary.R | 6 mdmb-0.5-27/mdmb/R/fit_mdmb_distribution_summary_table.R | 2 mdmb-0.5-27/mdmb/R/fit_oprobit.R |only mdmb-0.5-27/mdmb/R/fit_t_scaled.R | 2 mdmb-0.5-27/mdmb/R/fit_yjt_scaled.R | 2 mdmb-0.5-27/mdmb/R/frm2datlist.R | 2 mdmb-0.5-27/mdmb/R/frm_append_list.R | 2 mdmb-0.5-27/mdmb/R/frm_define_model_R_function.R | 9 mdmb-0.5-27/mdmb/R/frm_descriptives_variables.R | 2 mdmb-0.5-27/mdmb/R/frm_em.R | 10 mdmb-0.5-27/mdmb/R/frm_em_avcov.R | 11 mdmb-0.5-27/mdmb/R/frm_em_calc_likelihood.R | 10 mdmb-0.5-27/mdmb/R/frm_em_calc_likelihood_estimate_model.R | 4 mdmb-0.5-27/mdmb/R/frm_em_calc_total_likelihood.R | 2 mdmb-0.5-27/mdmb/R/frm_em_calc_update_observed_likelihood.R | 2 mdmb-0.5-27/mdmb/R/frm_em_ic.R | 2 mdmb-0.5-27/mdmb/R/frm_em_include_coef_inits.R | 2 mdmb-0.5-27/mdmb/R/frm_em_linreg_density_extend_args.R | 2 mdmb-0.5-27/mdmb/R/frm_em_score_function_prepare_model.R | 2 mdmb-0.5-27/mdmb/R/frm_em_summary_print_nodes.R | 2 mdmb-0.5-27/mdmb/R/frm_fb.R | 21 mdmb-0.5-27/mdmb/R/frm_fb_descriptives_variables.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_init_imputations.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_init_matrices_saved_parameters.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_initial_parameters.R | 4 mdmb-0.5-27/mdmb/R/frm_fb_mh_refresh_imputed_values.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_mh_refresh_parameters.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_partable.R | 11 mdmb-0.5-27/mdmb/R/frm_fb_refresh_parameters_step.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_sample_imputed_values.R | 14 mdmb-0.5-27/mdmb/R/frm_fb_sample_imputed_values_eval_likelihood.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_sample_imputed_values_proposal.R | 8 mdmb-0.5-27/mdmb/R/frm_fb_sample_parameter_step.R | 8 mdmb-0.5-27/mdmb/R/frm_fb_sample_parameters.R | 8 mdmb-0.5-27/mdmb/R/frm_fb_verbose_iterations.R | 2 mdmb-0.5-27/mdmb/R/frm_fb_verbose_mh_refresh.R | 2 mdmb-0.5-27/mdmb/R/frm_formula_character.R | 2 mdmb-0.5-27/mdmb/R/frm_formula_extract_terms.R | 2 mdmb-0.5-27/mdmb/R/frm_linreg_density.R | 9 mdmb-0.5-27/mdmb/R/frm_logistic_density.R | 2 mdmb-0.5-27/mdmb/R/frm_mdmb_regression_density.R | 6 mdmb-0.5-27/mdmb/R/frm_normalize_matrix_row.R | 2 mdmb-0.5-27/mdmb/R/frm_normalize_posterior.R | 2 mdmb-0.5-27/mdmb/R/frm_normalize_vector.R | 2 mdmb-0.5-27/mdmb/R/frm_oprobit_density.R |only mdmb-0.5-27/mdmb/R/frm_partable_thresholds.R |only mdmb-0.5-27/mdmb/R/frm_prepare_data_em.R | 2 mdmb-0.5-27/mdmb/R/frm_prepare_data_fb.R | 2 mdmb-0.5-27/mdmb/R/frm_prepare_data_include_latent_data.R | 2 mdmb-0.5-27/mdmb/R/frm_prepare_model_nodes_weights.R | 18 mdmb-0.5-27/mdmb/R/frm_prepare_models.R | 2 mdmb-0.5-27/mdmb/R/frm_prepare_models_design_matrices.R | 2 mdmb-0.5-27/mdmb/R/frm_prepare_models_sigma_fixed.R | 2 mdmb-0.5-27/mdmb/R/frm_proposal_refresh_helper.R | 2 mdmb-0.5-27/mdmb/R/logLik_extract_ic.R | 8 mdmb-0.5-27/mdmb/R/logLik_mdmb.R |only mdmb-0.5-27/mdmb/R/logistic_regression.R | 2 mdmb-0.5-27/mdmb/R/logthresh_2_thresh.R |only mdmb-0.5-27/mdmb/R/mdmb_diff_quotient.R | 4 mdmb-0.5-27/mdmb/R/mdmb_regression.R | 136 ++++ mdmb-0.5-27/mdmb/R/mdmb_regression_R2.R | 12 mdmb-0.5-27/mdmb/R/mdmb_regression_adjustment_differentiation_parameter.R | 4 mdmb-0.5-27/mdmb/R/mdmb_regression_extract_parameters.R | 2 mdmb-0.5-27/mdmb/R/mdmb_regression_ic.R | 7 mdmb-0.5-27/mdmb/R/mdmb_regression_logistic_density.R | 2 mdmb-0.5-27/mdmb/R/mdmb_regression_loglike_case.R | 12 mdmb-0.5-27/mdmb/R/mdmb_regression_loglike_logpost.R | 4 mdmb-0.5-27/mdmb/R/mdmb_regression_oprobit_density.R |only mdmb-0.5-27/mdmb/R/mdmb_regression_predict.R | 11 mdmb-0.5-27/mdmb/R/mdmb_regression_predict_yjt_bct.R | 2 mdmb-0.5-27/mdmb/R/mdmb_regression_summary.R | 21 mdmb-0.5-27/mdmb/R/mdmb_regression_summary_table.R | 2 mdmb-0.5-27/mdmb/R/mdmb_sample_probabilities.R | 2 mdmb-0.5-27/mdmb/R/mdmd_regression_optim_yjt_extract.R | 2 mdmb-0.5-27/mdmb/R/offset_values_extract.R | 2 mdmb-0.5-27/mdmb/R/oprobit_regression.R |only mdmb-0.5-27/mdmb/R/plot.frm_fb.R | 2 mdmb-0.5-27/mdmb/R/predict.bct_regression.R | 2 mdmb-0.5-27/mdmb/R/predict.logistic_regression.R | 2 mdmb-0.5-27/mdmb/R/predict.oprobit_regression.R |only mdmb-0.5-27/mdmb/R/predict.yjt_regression.R | 2 mdmb-0.5-27/mdmb/R/rbct_scaled.R | 2 mdmb-0.5-27/mdmb/R/remove_NA_data_frame.R | 2 mdmb-0.5-27/mdmb/R/rt_scaled.R | 2 mdmb-0.5-27/mdmb/R/ryjt_scaled.R | 2 mdmb-0.5-27/mdmb/R/summary.bct_regression.R | 2 mdmb-0.5-27/mdmb/R/summary.fit_bct_scaled.R | 2 mdmb-0.5-27/mdmb/R/summary.fit_oprobit.R |only mdmb-0.5-27/mdmb/R/summary.fit_t_scaled.R | 2 mdmb-0.5-27/mdmb/R/summary.fit_yjt_scaled.R | 2 mdmb-0.5-27/mdmb/R/summary.frm_em.R | 2 mdmb-0.5-27/mdmb/R/summary.frm_fb.R | 2 mdmb-0.5-27/mdmb/R/summary.logistic_regression.R | 2 mdmb-0.5-27/mdmb/R/summary.oprobit_regression.R |only mdmb-0.5-27/mdmb/R/summary.yjt_regression.R | 2 mdmb-0.5-27/mdmb/R/vcov.mdmb.R |only mdmb-0.5-27/mdmb/R/yj_adjust_lambda.R | 2 mdmb-0.5-27/mdmb/R/yj_antitrafo.R | 2 mdmb-0.5-27/mdmb/R/yj_trafo.R | 2 mdmb-0.5-27/mdmb/R/yjt_regression.R | 2 mdmb-0.5-27/mdmb/R/zzz.R | 2 mdmb-0.5-27/mdmb/README.md | 6 mdmb-0.5-27/mdmb/data/data.mb01.rda |binary mdmb-0.5-27/mdmb/data/data.mb02.rda |binary mdmb-0.5-27/mdmb/inst/CITATION | 2 mdmb-0.5-27/mdmb/inst/NEWS | 36 - mdmb-0.5-27/mdmb/man/data.mb.Rd | 3 mdmb-0.5-27/mdmb/man/eval_prior_list.Rd | 3 mdmb-0.5-27/mdmb/man/frm.Rd | 103 +++ mdmb-0.5-27/mdmb/man/mdmb-package.Rd | 3 mdmb-0.5-27/mdmb/man/mdmb_regression.Rd | 45 + mdmb-0.5-27/mdmb/man/offset_values_extract.Rd | 3 mdmb-0.5-27/mdmb/man/oprobit_dist.Rd |only mdmb-0.5-27/mdmb/man/remove_NA_data_frame.Rd | 3 mdmb-0.5-27/mdmb/man/yjt_dist.Rd | 3 158 files changed, 810 insertions(+), 272 deletions(-)
More information about TimeSeries.OBeu at CRAN
Permanent link
Title: Tidy Statistical Inference
Description: The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.
Author: Andrew Bray [aut, cre],
Chester Ismay [aut],
Ben Baumer [aut],
Mine Cetinkaya-Rundel [aut],
Ted Laderas [ctb],
Nick Solomon [ctb],
Johanna Hardin [ctb],
Albert Kim [ctb]
Maintainer: Andrew Bray <abray@reed.edu>
Diff between infer versions 0.1.0 dated 2018-01-08 and 0.1.1 dated 2018-01-22
DESCRIPTION | 23 +- MD5 | 56 ++--- NAMESPACE | 1 R/calculate.R | 156 ++++++++------- R/generate.R | 55 +---- R/hypothesize.R | 98 ++++----- R/infer.R | 2 R/pipe.R | 2 R/rep_sample_n.R |only R/specify.R | 42 ++-- R/visualize.R | 6 build/vignette.rds |binary inst/doc/flights_examples.R | 73 +++---- inst/doc/flights_examples.Rmd | 88 ++++---- inst/doc/flights_examples.html | 113 +++++------ inst/doc/mtcars_examples.R | 7 inst/doc/mtcars_examples.Rmd | 11 - inst/doc/mtcars_examples.html | 379 ++++++++++++++++++------------------- man/calculate.Rd | 1 man/generate.Rd | 9 man/hypothesize.Rd | 10 man/rep_sample_n.Rd |only man/specify.Rd | 10 tests/testthat/test-calculate.R | 117 +++++++++-- tests/testthat/test-generate.R | 16 + tests/testthat/test-hypothesize.R | 8 tests/testthat/test-rep_sample_n.R |only tests/testthat/test-specify.R | 9 tests/testthat/test-visualize.R |only vignettes/flights_examples.Rmd | 88 ++++---- vignettes/mtcars_examples.Rmd | 11 - 31 files changed, 757 insertions(+), 634 deletions(-)
Title: 'R' 'Markdown' Themes for 'UIUC' Documents and Presentations
Description: A set of custom 'R' 'Markdown' templates for documents and
presentations with the University of Illinois at Urbana-Champaign (UIUC)
color scheme and identity standards.
Author: James Balamuta [aut, cre],
Steven Andrew Culpepper [ctb],
David Dalpiaz [ctb]
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between uiucthemes versions 0.1.1 dated 2016-10-27 and 0.2.0 dated 2018-01-22
uiucthemes-0.1.1/uiucthemes/R/uiuc_beamer.R |only uiucthemes-0.1.1/uiucthemes/inst/rmarkdown/templates/uiuc_beamer |only uiucthemes-0.1.1/uiucthemes/man/uiuc_beamer.Rd |only uiucthemes-0.2.0/uiucthemes/DESCRIPTION | 20 uiucthemes-0.2.0/uiucthemes/LICENSE | 4 uiucthemes-0.2.0/uiucthemes/MD5 | 48 + uiucthemes-0.2.0/uiucthemes/NAMESPACE | 10 uiucthemes-0.2.0/uiucthemes/NEWS.md | 43 + uiucthemes-0.2.0/uiucthemes/R/beamer_templates.R |only uiucthemes-0.2.0/uiucthemes/R/defunct.R |only uiucthemes-0.2.0/uiucthemes/R/latex_templates.R |only uiucthemes-0.2.0/uiucthemes/R/uiucthemes.R | 6 uiucthemes-0.2.0/uiucthemes/R/utils.R | 47 + uiucthemes-0.2.0/uiucthemes/README.md | 267 +++++----- uiucthemes-0.2.0/uiucthemes/inst/rmarkdown/templates/beamer_illinois |only uiucthemes-0.2.0/uiucthemes/inst/rmarkdown/templates/beamer_orange |only uiucthemes-0.2.0/uiucthemes/inst/rmarkdown/templates/latex_journal_format |only uiucthemes-0.2.0/uiucthemes/man/beamer_illinois.Rd |only uiucthemes-0.2.0/uiucthemes/man/beamer_orange.Rd |only uiucthemes-0.2.0/uiucthemes/man/latex_journal_format.Rd |only uiucthemes-0.2.0/uiucthemes/man/uiucthemes-defunct.Rd |only uiucthemes-0.2.0/uiucthemes/man/uiucthemes-package.Rd | 50 + uiucthemes-0.2.0/uiucthemes/tools |only 23 files changed, 309 insertions(+), 186 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (0000-0003-0645-5666),
RStudio, Inc. [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.2 dated 2017-12-19 and 0.3 dated 2018-01-22
DESCRIPTION | 6 +- LICENSE | 2 MD5 | 21 ++++----- NAMESPACE | 1 R/install.R | 48 ++++++++++++++++---- R/latex.R | 114 ++++++++++++++++++++++++++++++++----------------- R/package.R | 2 R/tlmgr.R | 48 +++++++++++++++++++- man/install_tinytex.Rd | 7 ++- man/latexmk.Rd | 33 +++++++++----- man/parse_packages.Rd | 11 +++- man/tl_sizes.Rd |only 12 files changed, 215 insertions(+), 78 deletions(-)