Title: Bayesian Estimation Supersedes the t-Test
Description: An alternative to t-tests, producing posterior estimates
for group means and standard deviations and their differences and
effect sizes.
Author: John K. Kruschke and Mike Meredith
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between BEST versions 0.4.0 dated 2015-12-28 and 0.5.0 dated 2017-05-27
BEST-0.4.0/BEST/R/hdi.R |only BEST-0.4.0/BEST/inst/tests/testthat/test-hdi.R |only BEST-0.4.0/BEST/man/hdi.Rd |only BEST-0.5.0/BEST/DESCRIPTION | 11 - BEST-0.5.0/BEST/MD5 | 29 +-- BEST-0.5.0/BEST/NAMESPACE | 18 -- BEST-0.5.0/BEST/NEWS | 32 ++- BEST-0.5.0/BEST/R/BESTmcmc.R | 61 +++---- BEST-0.5.0/BEST/R/BESTpower.R | 4 BEST-0.5.0/BEST/R/justRunJags.R |only BEST-0.5.0/BEST/build/vignette.rds |binary BEST-0.5.0/BEST/inst/doc/BEST.pdf |binary BEST-0.5.0/BEST/inst/tests/testthat/test-BESTmcmc.R | 113 ++++++------- BEST-0.5.0/BEST/inst/tests/testthat/test-BESTmcmc_issues.R |only BEST-0.5.0/BEST/inst/tests/testthat/test-BESTmcmc_priors.R | 106 +++--------- BEST-0.5.0/BEST/inst/tests/testthat/test-BESTpower.R | 46 ++--- BEST-0.5.0/BEST/man/BESTmcmc.Rd | 20 +- BEST-0.5.0/BEST/man/BESTpower.Rd | 5 18 files changed, 202 insertions(+), 243 deletions(-)
Title: Detection of Outliers in Time Series
Description: Detection of outliers in time series following the
Chen and Liu (1993) <DOI:10.2307/2290724> procedure.
Innovational outliers, additive outliers, level shifts,
temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>
Diff between tsoutliers versions 0.6-5 dated 2016-12-08 and 0.6-6 dated 2017-05-27
tsoutliers-0.6-5/tsoutliers/R/remove-outliers.R |only tsoutliers-0.6-5/tsoutliers/man/remove-outliers.Rd |only tsoutliers-0.6-6/tsoutliers/DESCRIPTION | 10 - tsoutliers-0.6-6/tsoutliers/MD5 | 38 +++-- tsoutliers-0.6-6/tsoutliers/NAMESPACE | 1 tsoutliers-0.6-6/tsoutliers/NEWS | 42 ++++++ tsoutliers-0.6-6/tsoutliers/R/calendar-effects.R | 3 tsoutliers-0.6-6/tsoutliers/R/discard-outliers.R |only tsoutliers-0.6-6/tsoutliers/R/locate-outliers.R | 23 +-- tsoutliers-0.6-6/tsoutliers/R/outliers-tstatistics.R | 6 tsoutliers-0.6-6/tsoutliers/R/remove-outliers-deprecated.R |only tsoutliers-0.6-6/tsoutliers/R/tso.R | 66 ++++++---- tsoutliers-0.6-6/tsoutliers/build/partial.rdb |binary tsoutliers-0.6-6/tsoutliers/build/vignette.rds |binary tsoutliers-0.6-6/tsoutliers/inst/doc/index.html | 6 tsoutliers-0.6-6/tsoutliers/inst/doc/tsoutliers-intro.R | 2 tsoutliers-0.6-6/tsoutliers/inst/doc/tsoutliers-intro.Rnw | 18 +- tsoutliers-0.6-6/tsoutliers/inst/doc/tsoutliers-intro.pdf |binary tsoutliers-0.6-6/tsoutliers/man/discard-outliers.Rd |only tsoutliers-0.6-6/tsoutliers/man/locate-outliers-loops.Rd | 5 tsoutliers-0.6-6/tsoutliers/man/remove-outliers-deprecated.Rd |only tsoutliers-0.6-6/tsoutliers/man/tsoutliers.Rd | 37 +++-- tsoutliers-0.6-6/tsoutliers/vignettes/tsoutliers-intro.Rnw | 18 +- 23 files changed, 174 insertions(+), 101 deletions(-)
Title: Time Delay Estimation for Stochastic Time Series of
Gravitationally Lensed Quasars
Description: We provide a toolbox to estimate the time delay between the brightness time series of gravitationally lensed quasar images via Bayesian and profile likelihood approaches. The model is based on a state-space representation for irregularly observed time series data generated from a latent continuous-time Ornstein-Uhlenbeck process. Our Bayesian method adopts scientifically motivated hyper-prior distributions and a Metropolis-Hastings within Gibbs sampler, producing posterior samples of the model parameters that include the time delay. A profile likelihood of the time delay is a simple approximation to the marginal posterior distribution of the time delay. Both Bayesian and profile likelihood approaches complement each other, producing almost identical results; the Bayesian way is more principled but the profile likelihood is easier to implement.
Author: Hyungsuk Tak, Kaisey Mandel, David A. van Dyk, Vinay L. Kashyap, Xiao-Li Meng, and Aneta Siemiginowska
Maintainer: Hyungsuk Tak <hyungsuk.tak@gmail.com>
Diff between timedelay versions 1.0.6 dated 2017-03-23 and 1.0.7 dated 2017-05-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/bayesian.R | 22 +++++++++++----------- man/bayesian.Rd | 4 ++-- 4 files changed, 20 insertions(+), 20 deletions(-)
Title: Tools for Conducting Respirometry Experiments
Description: Provides tools to enable the researcher to more precisely conduct
respirometry experiments. Strong emphasis is on aquatic respirometry. Tools
focus on helping the researcher setup and conduct experiments. Analysis of the
resulting data is not a focus since analyses are often specific to a particular
setup, and thus are better created by the researcher individually. This
package provides tools for intermittent, flow-through, and closed respirometry
techniques.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between respirometry versions 0.3.1 dated 2016-12-31 and 0.4.0 dated 2017-05-27
respirometry-0.3.1/respirometry/R/conv_NH4.R |only respirometry-0.3.1/respirometry/R/predict_NH4.R |only respirometry-0.3.1/respirometry/man/conv_NH4.Rd |only respirometry-0.3.1/respirometry/man/predict_NH4.Rd |only respirometry-0.4.0/respirometry/DESCRIPTION | 10 - respirometry-0.4.0/respirometry/MD5 | 78 +++++++------- respirometry-0.4.0/respirometry/NAMESPACE | 4 respirometry-0.4.0/respirometry/NEWS | 11 ++ respirometry-0.4.0/respirometry/R/Q10.R | 62 +++++++---- respirometry-0.4.0/respirometry/R/calc_MO2.R | 86 +++++++++++----- respirometry-0.4.0/respirometry/R/conv_nh4.R |only respirometry-0.4.0/respirometry/R/conv_o2.R | 14 ++ respirometry-0.4.0/respirometry/R/guess_when.R | 2 respirometry-0.4.0/respirometry/R/import_witrox.R | 2 respirometry-0.4.0/respirometry/R/predict_nh3.R |only respirometry-0.4.0/respirometry/man/Q10.Rd | 20 ++- respirometry-0.4.0/respirometry/man/RQ.Rd | 7 - respirometry-0.4.0/respirometry/man/calc_MO2.Rd | 28 +++-- respirometry-0.4.0/respirometry/man/calc_b.Rd | 7 - respirometry-0.4.0/respirometry/man/closed.Rd | 7 - respirometry-0.4.0/respirometry/man/co2_add.Rd | 7 - respirometry-0.4.0/respirometry/man/co2_flush.Rd | 7 - respirometry-0.4.0/respirometry/man/co2_rate.Rd | 7 - respirometry-0.4.0/respirometry/man/conv_nh4.Rd |only respirometry-0.4.0/respirometry/man/conv_o2.Rd | 7 - respirometry-0.4.0/respirometry/man/conv_resp_unit.Rd | 7 - respirometry-0.4.0/respirometry/man/correct_bubble.Rd | 7 - respirometry-0.4.0/respirometry/man/flush_carb.Rd | 7 - respirometry-0.4.0/respirometry/man/flush_o2.Rd | 7 - respirometry-0.4.0/respirometry/man/flush_water.Rd | 7 - respirometry-0.4.0/respirometry/man/goal_flush_pH.Rd | 7 - respirometry-0.4.0/respirometry/man/guess_TA.Rd | 7 - respirometry-0.4.0/respirometry/man/guess_when.Rd | 7 - respirometry-0.4.0/respirometry/man/import_firesting.Rd | 7 - respirometry-0.4.0/respirometry/man/import_presens.Rd | 7 - respirometry-0.4.0/respirometry/man/import_witrox.Rd | 7 - respirometry-0.4.0/respirometry/man/max_MO2.Rd | 7 - respirometry-0.4.0/respirometry/man/mean_pH.Rd | 7 - respirometry-0.4.0/respirometry/man/min_flow.Rd | 7 - respirometry-0.4.0/respirometry/man/peri_pump.Rd | 7 - respirometry-0.4.0/respirometry/man/predict_nh3.Rd |only respirometry-0.4.0/respirometry/man/predict_pH.Rd | 7 - respirometry-0.4.0/respirometry/man/respirometry.Rd | 1 respirometry-0.4.0/respirometry/man/scale_MO2.Rd | 7 - 44 files changed, 277 insertions(+), 209 deletions(-)
Title: Write Formatted Tables in Excel Workbooks
Description: Some functions are included in this package for writing tables in Excel format suitable for distribution.
Author: Jesus Maria Rodriguez Rodriguez
Maintainer: Jesus Maria Rodriguez Rodriguez <jesusmro@ono.com>
Diff between tablaxlsx versions 1.2.0 dated 2016-06-13 and 1.2.2 dated 2017-05-27
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++++------ NAMESPACE | 2 +- R/escribirTabla.R | 16 +++++++++------- R/reducir.R | 9 +++++---- R/verXL.r |only data/estilosDGE.rda |binary data/estilosDGPYE.rda |only inst/img/Thumbs.db |only man/escribirTabla.Rd | 2 +- man/estilosDGEPYE.Rd |only man/verXL.Rd |only 12 files changed, 31 insertions(+), 23 deletions(-)
Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalised ratio-of-uniforms (RU) method to simulate
from univariate and (low-dimensional) multivariate continuous distributions.
The user specifies the log-density, up to an additive constant. The RU
algorithm is applied after relocation of mode of the density to zero, and
the user can choose a tuning parameter r. For details see Wakefield, Gelfand
and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random
variates via the ratio-of-uniforms method, Statistics and Computing (1991)
1, 129-133. A Box-Cox variable transformation can be used to make the input
density suitable for the RU method and to improve efficiency. In the
multivariate case rotation of axes can also be used to improve efficiency.
From version 1.2.0 the 'Rcpp' package
<https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.
See the rust website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between rust versions 1.1.0 dated 2016-11-18 and 1.2.0 dated 2017-05-27
DESCRIPTION | 20 ++++--- MD5 | 73 ++++++++++++++++++---------- NAMESPACE | 12 ++++ NEWS.md | 61 ++++++++++++++--------- R/RcppExports.R |only R/box_cox_functions.R | 39 +++++++++------ R/box_cox_functions_rcpp.R |only R/gp_example.R | 4 + R/ru_sampling.R | 85 +++++++++++++++------------------ R/ru_sampling_rcpp.R |only R/rust.R | 28 ++++++++-- R/sample_diagnostics.R | 70 +++++++++++++++++---------- R/zzz.R |only README.md | 22 ++++++-- build/vignette.rds |binary inst/doc/rust-using-rcpp-vignette.R |only inst/doc/rust-using-rcpp-vignette.Rmd |only inst/doc/rust-using-rcpp-vignette.html |only inst/doc/rust-vignette.R | 6 +- inst/doc/rust-vignette.Rmd | 14 ++++- inst/doc/rust-vignette.html | 27 ++++++---- inst/include |only man/create_log_j_xptr.Rd |only man/create_phi_to_theta_xptr.Rd |only man/create_xptr.Rd |only man/find_lambda.Rd | 17 ++++-- man/find_lambda_one_d.Rd | 20 +++++-- man/find_lambda_one_d_rcpp.Rd |only man/find_lambda_rcpp.Rd |only man/gpd_init.Rd | 1 man/gpd_logpost.Rd | 1 man/gpd_sum_stats.Rd | 1 man/plot.ru.Rd | 19 +++---- man/rgpd.Rd | 1 man/ru.Rd | 46 +++++++++-------- man/ru_rcpp.Rd |only man/rust.Rd | 29 ++++++++--- man/summary.ru.Rd | 4 - src |only tools |only vignettes/example_user_fns.cpp |only vignettes/rust-using-rcpp-vignette.Rmd |only vignettes/rust-vignette.Rmd | 14 ++++- vignettes/rust.bib | 52 +++++++++++++++++++- 44 files changed, 440 insertions(+), 226 deletions(-)
Title: Estimates of Coefficient of Overlapping for Animal Activity
Patterns
Description: Provides functions to fit kernel density functions to
data on temporal activity patterns of animals; estimate coefficients
of overlapping of densities for two species; and calculate bootstrap
estimates of confidence intervals.
Author: Mike Meredith and Martin Ridout
Maintainer: Mike Meredith <mmeredith@wcs.org>
Diff between overlap versions 0.2.7 dated 2017-03-01 and 0.3.0 dated 2017-05-27
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++---------- NAMESPACE | 2 + NEWS | 23 +++++++---- R/bootEst.R | 79 +++++++++++++++++++++++++++++++++-------- R/checkInput.R |only R/densityPlot.R | 1 R/miscPlottingUtils.R | 4 +- R/overlapEst.R | 47 +++++++++++++++--------- R/overlapPlot.R | 2 + inst/doc/overlap.R | 14 ++----- inst/doc/overlap.Rnw | 20 ++++------ inst/doc/overlap.pdf |binary inst/tests/testthat/test-all.R | 46 +++++++++++++++++++++++ man/bootEst.Rd | 19 ++++++++- man/densityPlot.Rd | 2 - man/example_data.Rd | 11 ++--- man/overlap-package.Rd | 13 +++--- man/overlapEst.Rd | 21 +++++++--- man/overlapPlot.Rd | 2 - vignettes/overlap.Rnw | 20 ++++------ 21 files changed, 250 insertions(+), 123 deletions(-)
Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression
with interval censored data or proportional sub-distribution hazards
regression for interval censored competing risks data. The main functions
allow to estimate survival function, cumulative incidence function, Cox
and Fine & Gray regression coefficients and associated variance-covariance
matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the
'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from
the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
Diff between MIICD versions 2.3 dated 2016-11-28 and 2.4 dated 2017-05-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/get.est.cr.cox.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Interactive Cluster Heat Maps Using 'plotly'
Description: Create interactive cluster 'heatmaps' that can be saved as a stand-
alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and
available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to
show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical
method for visualizing high-dimensional data, in which a table of numbers
are encoded as a grid of colored cells. The rows and columns of the matrix
are ordered to highlight patterns and are often accompanied by 'dendrograms'.
'Heatmaps' are used in many fields for visualizing observations, correlations,
missing values patterns, and more. Interactive 'heatmaps' allow the inspection
of specific value by hovering the mouse over a cell, as well as zooming into
a region of the 'heatmap' by dragging a rectangle around the relevant area.
This work is based on the 'ggplot2' and 'plotly.js' engine. It produces
similar 'heatmaps' as 'heatmap.2' or 'd3heatmap', with the advantage of speed
('plotly.js' is able to handle larger size matrix), the ability to zoom from
the 'dendrogram' panes, and the placing of factor variables in the sides of the
'heatmap'.
Author: Tal Galili [aut, cre, cph] (https://www.r-statistics.com),
Jonathan Sidi [ctb] (https://github.com/yonicd),
Alan O'Callaghan [ctb] (https://github.com/Alanocallaghan),
Yoav Benjamini [ths]
Maintainer: Tal Galili <tal.galili@gmail.com>
Diff between heatmaply versions 0.9.1 dated 2017-04-14 and 0.10.1 dated 2017-05-27
ChangeLog | 1649 ++++++++++++++++++++++++++++++++++----------- DESCRIPTION | 15 MD5 | 34 NAMESPACE | 3 NEWS | 33 NEWS.md | 33 R/RColorBrewer.R | 152 ++++ R/heatmaply.R | 229 +++++- R/heatmapr.R | 10 R/plots.R | 4 R/zzz.R | 16 README.md | 14 inst/doc/heatmaply.R | 15 inst/doc/heatmaply.Rmd | 41 - inst/doc/heatmaply.html | 182 ++-- man/RColorBrewer_colors.Rd | 32 man/heatmaply.Rd | 74 +- vignettes/heatmaply.Rmd | 41 - 18 files changed, 1986 insertions(+), 591 deletions(-)
Title: R Interface with Google Cloud Storage
Description: Interact with Google Cloud Storage API in R. Part of the 'cloudyr' project.
Author: Mark Edmondson [aut, cre]
Maintainer: Mark Edmondson <r@sunholo.com>
Diff between googleCloudStorageR versions 0.2.0 dated 2016-09-11 and 0.3.0 dated 2017-05-27
DESCRIPTION | 14 - MD5 | 114 ++++++------ NAMESPACE | 2 NEWS.md | 15 + R/acl.R | 15 + R/auth.R | 2 R/buckets.R | 96 +++++++--- R/download.R | 138 ++++++++++++++- R/objects.R | 341 +++++++++++++++++++++++++++----------- R/options.R | 9 - R/print-method.R | 31 +-- R/rsession.R | 34 ++- R/upload.R | 42 ++++ R/utilities.R | 10 + build/vignette.rds |binary inst/doc/googleCloudStorageR.Rmd | 2 inst/doc/googleCloudStorageR.html | 10 - man/Object.Rd | 1 man/cat0.Rd | 1 man/error.message.Rd | 1 man/format_object_size.Rd | 1 man/gcs_auth.Rd | 20 +- man/gcs_create_bucket.Rd | 9 - man/gcs_create_bucket_acl.Rd | 1 man/gcs_create_lifecycle.Rd | 3 man/gcs_delete_bucket.Rd | 1 man/gcs_delete_object.Rd | 1 man/gcs_download_url.Rd | 22 +- man/gcs_get_bucket.Rd | 13 + man/gcs_get_bucket_acl.Rd | 1 man/gcs_get_global_bucket.Rd | 1 man/gcs_get_object.Rd | 55 +++++- man/gcs_get_object_acl.Rd | 1 man/gcs_global_bucket.Rd | 1 man/gcs_list_buckets.Rd | 17 + man/gcs_list_objects.Rd | 15 + man/gcs_load.Rd | 7 man/gcs_metadata_object.Rd | 3 man/gcs_parse_download.Rd | 6 man/gcs_retry_upload.Rd | 1 man/gcs_save.Rd | 12 - man/gcs_save_image.Rd | 3 man/gcs_signed_url.Rd |only man/gcs_source.Rd | 3 man/gcs_update_object_acl.Rd | 1 man/gcs_upload.Rd | 37 +++- man/idempotency.Rd | 1 man/is.NullOb.Rd | 1 man/is.error.Rd | 1 man/js_to_posix.Rd |only man/myMessage.Rd | 1 man/postwalk.Rd | 1 man/replace.kv.Rd | 1 man/rmNullObs.Rd | 1 man/substitute.list.Rd | 1 man/timestamp_to_r.Rd | 1 tests/testthat/auth.json |only tests/testthat/auth.json.enc |only tests/testthat/test.R | 168 +++++++++++++++--- vignettes/googleCloudStorageR.Rmd | 2 60 files changed, 940 insertions(+), 352 deletions(-)
More information about googleCloudStorageR at CRAN
Permanent link
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 a Python back end with 'spaCy' <https://spacy.io>
or the Java back end 'CoreNLP' <http://stanfordnlp.github.io/CoreNLP/>. A minimal back
end with no external dependencies is also provided. 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 1.5.2 dated 2017-04-12 and 1.9.0 dated 2017-05-27
cleanNLP-1.5.2/cleanNLP/README.md |only cleanNLP-1.5.2/cleanNLP/inst/doc/introduction.R |only cleanNLP-1.5.2/cleanNLP/inst/doc/introduction.Rmd |only cleanNLP-1.5.2/cleanNLP/inst/doc/introduction.html |only cleanNLP-1.5.2/cleanNLP/man/annotate.Rd |only cleanNLP-1.5.2/cleanNLP/man/from_CoNLLU.Rd |only cleanNLP-1.5.2/cleanNLP/vignettes/introduction.Rmd |only cleanNLP-1.9.0/cleanNLP/DESCRIPTION | 29 cleanNLP-1.9.0/cleanNLP/MD5 | 134 +- cleanNLP-1.9.0/cleanNLP/NAMESPACE | 7 cleanNLP-1.9.0/cleanNLP/NEWS.md |only cleanNLP-1.9.0/cleanNLP/R/accessors.R | 310 +++-- cleanNLP-1.9.0/cleanNLP/R/annotate.R | 590 +--------- cleanNLP-1.9.0/cleanNLP/R/annotate_tools.R |only cleanNLP-1.9.0/cleanNLP/R/backend_coreNLP.R | 301 +++-- cleanNLP-1.9.0/cleanNLP/R/backend_spaCy.R | 29 cleanNLP-1.9.0/cleanNLP/R/backend_tokenizers.R | 5 cleanNLP-1.9.0/cleanNLP/R/data.R | 8 cleanNLP-1.9.0/cleanNLP/R/download.R | 125 +- cleanNLP-1.9.0/cleanNLP/R/onLoad.R | 5 cleanNLP-1.9.0/cleanNLP/R/pkg.R | 38 cleanNLP-1.9.0/cleanNLP/R/tools.R | 142 +- cleanNLP-1.9.0/cleanNLP/build/vignette.rds |binary cleanNLP-1.9.0/cleanNLP/data/obama.rda |binary cleanNLP-1.9.0/cleanNLP/inst/doc/case_study.Rmd | 2 cleanNLP-1.9.0/cleanNLP/inst/doc/case_study.html | 112 - cleanNLP-1.9.0/cleanNLP/inst/doc/schema.html | 2 cleanNLP-1.9.0/cleanNLP/inst/extdata/StanfordCoreNLP-german.properties | 2 cleanNLP-1.9.0/cleanNLP/inst/extdata/cleanNLP-0.1.jar |binary cleanNLP-1.9.0/cleanNLP/inst/py/load_spacy.py | 47 cleanNLP-1.9.0/cleanNLP/java/pom.xml | 4 cleanNLP-1.9.0/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVDependencyDocumentWriter.java | 5 cleanNLP-1.9.0/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVNamedEntityDocumentWriter.java | 2 cleanNLP-1.9.0/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVSentenceDocumentWriter.java | 2 cleanNLP-1.9.0/cleanNLP/java/src/main/java/edu/richmond/nlp/Writer/CSVTokenDocumentWriter.java | 196 +++ cleanNLP-1.9.0/cleanNLP/java/target |only cleanNLP-1.9.0/cleanNLP/man/cleanNLP-package.Rd | 33 cleanNLP-1.9.0/cleanNLP/man/combine_documents.Rd | 10 cleanNLP-1.9.0/cleanNLP/man/doc_id_reset.Rd | 9 cleanNLP-1.9.0/cleanNLP/man/download_core_nlp.Rd | 43 cleanNLP-1.9.0/cleanNLP/man/extract_documents.Rd | 6 cleanNLP-1.9.0/cleanNLP/man/from_CoNLL.Rd |only cleanNLP-1.9.0/cleanNLP/man/get_coreference.Rd | 57 cleanNLP-1.9.0/cleanNLP/man/get_dependency.Rd | 68 - cleanNLP-1.9.0/cleanNLP/man/get_document.Rd | 26 cleanNLP-1.9.0/cleanNLP/man/get_entity.Rd | 28 cleanNLP-1.9.0/cleanNLP/man/get_sentence.Rd | 25 cleanNLP-1.9.0/cleanNLP/man/get_tfidf.Rd | 87 - cleanNLP-1.9.0/cleanNLP/man/get_token.Rd | 59 - cleanNLP-1.9.0/cleanNLP/man/init_coreNLP.Rd | 93 - cleanNLP-1.9.0/cleanNLP/man/init_spaCy.Rd | 4 cleanNLP-1.9.0/cleanNLP/man/obama.Rd | 3 cleanNLP-1.9.0/cleanNLP/man/print.annotation.Rd | 2 cleanNLP-1.9.0/cleanNLP/man/read_annotation.Rd | 10 cleanNLP-1.9.0/cleanNLP/man/run_annotators.Rd |only cleanNLP-1.9.0/cleanNLP/man/tidy_pca.Rd | 13 cleanNLP-1.9.0/cleanNLP/man/to_CoNNL.Rd |only cleanNLP-1.9.0/cleanNLP/man/word_frequency.Rd | 5 cleanNLP-1.9.0/cleanNLP/man/write_annotation.Rd | 9 cleanNLP-1.9.0/cleanNLP/tests/testthat.R | 2 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-annotation_utils.R | 17 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-java.R | 57 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-python.R | 34 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-tokenizers.R | 30 cleanNLP-1.9.0/cleanNLP/tests/testthat/test-tools.R | 6 cleanNLP-1.9.0/cleanNLP/vignettes/case_study.Rmd | 2 66 files changed, 1540 insertions(+), 1295 deletions(-)
Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and
diagnostic functions for Bayesian statistics, with a particular focus on
calibrating complex system models. Implemented samplers include various
Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the
T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential
Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre],
Francesco Minunno [aut],
Stefan Paul [aut],
David Cameron [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between BayesianTools versions 0.1.1 dated 2017-04-05 and 0.1.2 dated 2017-05-27
BayesianTools-0.1.1/BayesianTools/inst/examples/createUniformPrior.R |only BayesianTools-0.1.2/BayesianTools/DESCRIPTION | 8 BayesianTools-0.1.2/BayesianTools/MD5 | 181 +++++----- BayesianTools-0.1.2/BayesianTools/NEWS | 16 BayesianTools-0.1.2/BayesianTools/R/BayesianTools.R | 6 BayesianTools-0.1.2/BayesianTools/R/DIC.R | 1 BayesianTools-0.1.2/BayesianTools/R/GOF.R | 3 BayesianTools-0.1.2/BayesianTools/R/MAP.R | 1 BayesianTools-0.1.2/BayesianTools/R/SMC.R | 1 BayesianTools-0.1.2/BayesianTools/R/VSEM.R | 1 BayesianTools-0.1.2/BayesianTools/R/WAIC.R | 1 BayesianTools-0.1.2/BayesianTools/R/blockUpdate.R | 2 BayesianTools-0.1.2/BayesianTools/R/classBayesianOutput.R | 2 BayesianTools-0.1.2/BayesianTools/R/classBayesianSetup.R | 8 BayesianTools-0.1.2/BayesianTools/R/classLikelihood.R | 3 BayesianTools-0.1.2/BayesianTools/R/classMcmcSampler.R | 9 BayesianTools-0.1.2/BayesianTools/R/classMcmcSamplerList.R | 14 BayesianTools-0.1.2/BayesianTools/R/classPosterior.R | 1 BayesianTools-0.1.2/BayesianTools/R/classPrior.R | 15 BayesianTools-0.1.2/BayesianTools/R/classSMCSamplerList.R | 3 BayesianTools-0.1.2/BayesianTools/R/classSmcSampler.R | 4 BayesianTools-0.1.2/BayesianTools/R/diagnosticsGelman.R | 2 BayesianTools-0.1.2/BayesianTools/R/getVolume.R | 2 BayesianTools-0.1.2/BayesianTools/R/marginalLikelihood.R | 1 BayesianTools-0.1.2/BayesianTools/R/mcmcDE.R | 82 ++-- BayesianTools-0.1.2/BayesianTools/R/mcmcDEzs.R | 4 BayesianTools-0.1.2/BayesianTools/R/mcmcDREAM.R | 2 BayesianTools-0.1.2/BayesianTools/R/mcmcDREAMzs.R | 2 BayesianTools-0.1.2/BayesianTools/R/mcmcFrancesco.R | 4 BayesianTools-0.1.2/BayesianTools/R/mcmcMetropolis.R | 4 BayesianTools-0.1.2/BayesianTools/R/mcmcRun.R | 24 - BayesianTools-0.1.2/BayesianTools/R/mcmcTwalk.R | 1 BayesianTools-0.1.2/BayesianTools/R/plotMarginals.R | 4 BayesianTools-0.1.2/BayesianTools/R/plotSensitivityOAT.R | 1 BayesianTools-0.1.2/BayesianTools/R/plotTimeSeries.R | 29 + BayesianTools-0.1.2/BayesianTools/R/plotTrace.R | 1 BayesianTools-0.1.2/BayesianTools/R/utils-Numerics.R | 3 BayesianTools-0.1.2/BayesianTools/R/utils.R | 2 BayesianTools-0.1.2/BayesianTools/inst/doc/BayesianTools.Rmd | 1 BayesianTools-0.1.2/BayesianTools/inst/doc/BayesianTools.html | 14 BayesianTools-0.1.2/BayesianTools/inst/examples/VSEM.R | 39 +- BayesianTools-0.1.2/BayesianTools/inst/examples/WAICHelp.R | 2 BayesianTools-0.1.2/BayesianTools/inst/examples/classBayesianSetup.R | 8 BayesianTools-0.1.2/BayesianTools/inst/examples/createPrior.R | 2 BayesianTools-0.1.2/BayesianTools/inst/examples/createUniformPriorHelp.R |only BayesianTools-0.1.2/BayesianTools/inst/examples/getSampleHelp.R |only BayesianTools-0.1.2/BayesianTools/inst/examples/plotTimeSeriesHelp.R |only BayesianTools-0.1.2/BayesianTools/inst/examples/plotTimeSeriesResultsHelp.R |only BayesianTools-0.1.2/BayesianTools/inst/examples/tracePlotHelp.R |only BayesianTools-0.1.2/BayesianTools/man/AM.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/BayesianTools.Rd | 4 BayesianTools-0.1.2/BayesianTools/man/DE.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DEzs.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DIC.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DR.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DRAM.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DREAM.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/DREAMzs.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/GOF.Rd | 7 BayesianTools-0.1.2/BayesianTools/man/M.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/MAP.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/Metropolis.Rd | 4 BayesianTools-0.1.2/BayesianTools/man/Twalk.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/VSEM.Rd | 39 +- BayesianTools-0.1.2/BayesianTools/man/WAIC.Rd | 5 BayesianTools-0.1.2/BayesianTools/man/applySettingsDefault.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/checkBayesianSetup.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createBayesianSetup.Rd | 17 BayesianTools-0.1.2/BayesianTools/man/createBetaPrior.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createLikelihood.Rd | 7 BayesianTools-0.1.2/BayesianTools/man/createMcmcSamplerList.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createPosterior.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createPrior.Rd | 5 BayesianTools-0.1.2/BayesianTools/man/createPriorDensity.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createSmcSamplerList.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createTruncatedNormalPrior.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/createUniformPrior.Rd | 30 + BayesianTools-0.1.2/BayesianTools/man/gelmanDiagnostics.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/getPanels.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/getPossibleSamplerTypes.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/getSample.Rd | 20 + BayesianTools-0.1.2/BayesianTools/man/getVolume.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/logSumExp.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/marginalLikelihood.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/metropolisRatio.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/plotSensitivity.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/plotTimeSeries.Rd | 15 BayesianTools-0.1.2/BayesianTools/man/plotTimeSeriesResults.Rd | 6 BayesianTools-0.1.2/BayesianTools/man/runMCMC.Rd | 9 BayesianTools-0.1.2/BayesianTools/man/setupStartProposal.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/smcSampler.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/stopParallel.Rd | 3 BayesianTools-0.1.2/BayesianTools/man/tracePlot.Rd | 11 BayesianTools-0.1.2/BayesianTools/tests/testthat/test-settingsDefault.R |only BayesianTools-0.1.2/BayesianTools/vignettes/BayesianTools.Rmd | 1 95 files changed, 561 insertions(+), 223 deletions(-)
Title: Simple Phrase Extraction
Description: Simple noun phrase extraction using part-of-speech information.
Takes a collection of un-processed documents as input and returns a set of noun
phrases associated with those documents.
Author: Matthew J. Denny, Abram Handler, Brendan O'Connor
Maintainer: Matthew J. Denny <mdenny@psu.edu>
Diff between phrasemachine versions 1.0.0 dated 2016-10-24 and 1.1.1 dated 2017-05-27
DESCRIPTION | 10 +-- MD5 | 37 +++++++------- R/POS_tag_documents.R | 17 ++++-- R/check_for_named_regexes.R |only R/coarsen_POS_tags.R | 12 +++- R/extract_ngram_filter.R | 59 ++++++++++++++-------- R/extract_phrases.R | 10 ++- R/phrasemachine.R | 15 ++++- R/zzz.R | 2 build/vignette.rds |binary inst/doc/getting_started_with_phrasemachine.R | 7 +- inst/doc/getting_started_with_phrasemachine.Rmd | 7 +- inst/doc/getting_started_with_phrasemachine.html | 60 +++++++++++++++-------- man/POS_tag_documents.Rd | 14 +++-- man/coarsen_POS_tags.Rd | 7 +- man/extract_ngram_filter.Rd | 4 - man/extract_phrases.Rd | 11 ++-- man/phrasemachine.Rd | 14 ++++- tests/testthat/test_extract_ngram_filter.R | 31 +++++++++++ vignettes/getting_started_with_phrasemachine.Rmd | 7 +- 20 files changed, 220 insertions(+), 104 deletions(-)
Title: Regression with NA Values in Unordered Factors
Description: Fits regressions where unordered factors can be set to NA in
subsets of the data where they are not applicable or otherwise not
contrastive by using sum contrasts and setting NA values to zero.
Author: Christopher D. Eager [aut, cre]
Maintainer: Christopher D. Eager <eagerstats@gmail.com>
Diff between nauf versions 1.0.0 dated 2017-05-09 and 1.0.1 dated 2017-05-27
DESCRIPTION | 10 +-- MD5 | 16 ++--- NEWS.md | 7 ++ README.md | 30 +++++----- inst/CITATION | 4 - inst/doc/using-nauf.Rmd | 2 inst/doc/using-nauf.html | 109 +++++++++++++++++-------------------- tests/testthat/test-nauf_pmmeans.R | 17 +++-- vignettes/using-nauf.Rmd | 2 9 files changed, 103 insertions(+), 94 deletions(-)