Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash', 'murmurhash' and 'spookyhash' algorithms) permitting easy
comparison of R language objects, as well as functions such as'hmac()' to
create hash-based message authentication code. Please note that this package
is not meant to be deployed for cryptographic purposes for which more
comprehensive (and widely tested) libraries such as 'OpenSSL' should be
used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko, Kurt Hornik, Radford Neal, Kendon Bell,
and Matthew de Queljoe.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.20 dated 2019-07-04 and 0.6.21 dated 2019-09-20
ChangeLog | 24 +++++++++++++++ DESCRIPTION | 11 +++---- MD5 | 24 +++++++++------ NAMESPACE | 3 + R/vdigest.R |only README.md | 14 ++++----- build/vignette.rds |binary demo |only inst/doc/sha1.html | 10 ++++-- inst/tinytest/test_digest.R | 65 +++++++++++++++++++++++++++++++++++++++++-- inst/tinytest/test_num2hex.R | 6 +-- man/digest.Rd | 9 +++-- man/vdigest.Rd |only src/digest.c | 22 ++++++++++++++ 14 files changed, 152 insertions(+), 36 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 0.5.6 dated 2019-04-22 and 0.5.7 dated 2019-09-20
DESCRIPTION | 19 + MD5 | 113 ++++++----- NAMESPACE | 2 NEWS.md | 23 ++ R/coord_date.R | 6 R/geom_bbands.R | 19 + R/geom_chart.R | 56 +++-- R/geom_ma.R | 10 - R/global_vars.R | 4 R/scale_manual.R | 92 ++++----- R/theme_tq.R | 2 R/tidyquant.R | 1 R/tq_get.R | 3 R/tq_mutate.R | 16 - R/tq_performance.R | 13 - R/tq_portfolio.R | 21 +- R/tq_stock_list.R | 5 R/tq_transmute.R | 18 - R/utils-pipe.R |only R/zzz.R |only README.md | 27 ++ inst/doc/TQ00-introduction-to-tidyquant.R | 2 inst/doc/TQ00-introduction-to-tidyquant.Rmd | 2 inst/doc/TQ00-introduction-to-tidyquant.html | 10 - inst/doc/TQ01-core-functions-in-tidyquant.R | 3 inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 3 inst/doc/TQ01-core-functions-in-tidyquant.html | 111 ++++++----- inst/doc/TQ02-quant-integrations-in-tidyquant.R | 7 inst/doc/TQ02-quant-integrations-in-tidyquant.Rmd | 7 inst/doc/TQ02-quant-integrations-in-tidyquant.html | 43 ++-- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.R | 3 inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 3 inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 119 ++++++------ inst/doc/TQ04-charting-with-tidyquant.R | 7 inst/doc/TQ04-charting-with-tidyquant.Rmd | 11 - inst/doc/TQ04-charting-with-tidyquant.html | 65 +++--- inst/doc/TQ05-performance-analysis-with-tidyquant.R | 5 inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 3 inst/doc/TQ05-performance-analysis-with-tidyquant.html | 163 ++++++++--------- man/coord_x_date.Rd | 6 man/geom_bbands.Rd | 3 man/geom_chart.Rd | 12 - man/geom_ma.Rd | 2 man/pipe.Rd |only man/scale_manual.Rd | 2 man/theme_tq.Rd | 2 man/tq_get.Rd | 1 man/tq_mutate.Rd | 3 man/tq_performance.Rd | 1 man/tq_portfolio.Rd | 1 tests/testthat.R | 1 tests/testthat/test_tq_mutate.R | 6 tests/testthat/test_tq_transmute.R | 4 vignettes/TQ00-introduction-to-tidyquant.Rmd | 2 vignettes/TQ01-core-functions-in-tidyquant.Rmd | 3 vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 7 vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 3 vignettes/TQ04-charting-with-tidyquant.Rmd | 11 - vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 3 59 files changed, 611 insertions(+), 479 deletions(-)
Title: Tools for Working with ...
Description: The ellipsis is a powerful tool for extending functions. Unfortunately
this power comes at a cost: misspelled arguments will be silently ignored.
The ellipsis package provides a collection of functions to catch problems
and alert the user.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ellipsis versions 0.2.0.1 dated 2019-07-02 and 0.3.0 dated 2019-09-20
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ R/check.R | 43 +++++++++++++++++++++++++------------------ README.md | 2 +- man/check_dots_empty.Rd | 5 ++++- man/check_dots_unnamed.Rd | 5 ++++- man/check_dots_used.Rd | 5 ++++- man/ellipsis-package.Rd | 3 ++- tests/testthat/test-check.R | 22 ++++++++++++++++++++-- tests/testthat/test-safe.R | 2 +- 11 files changed, 81 insertions(+), 41 deletions(-)
Title: Regression Analysis and Forecasting Using Textual Data from a
Time-Varying Dictionary
Description: Provides functionalities based on the paper "Time Varying Dictionary and the Predictive Power of FED Minutes" (Lima, 2018) <doi:10.2139/ssrn.3312483>. It selects the most predictive terms, that we call time-varying dictionary using supervised machine learning techniques as lasso and elastic net.
Author: Luiz Renato Lima [aut],
Lucas Godeiro [aut, cre]
Maintainer: Lucas Godeiro <lucas.godeiro@hotmail.com>
Diff between TextForecast versions 0.1.1 dated 2019-03-06 and 0.1.2 dated 2019-09-20
DESCRIPTION | 13 +-- MD5 | 26 +++---- NAMESPACE | 6 - R/get_collocations.R | 31 ++++---- R/get_terms.R | 17 ++-- R/get_words.R | 165 ++++++++++++--------------------------------- R/tv_dictionary.R | 10 +- R/tv_sentiment_index.R | 1 build/vignette.rds |binary inst/doc/textforecast.html | 17 +++- man/get_collocations.Rd | 5 - man/get_terms.Rd | 9 +- man/get_words.Rd | 2 man/tv_dictionary.Rd | 2 14 files changed, 119 insertions(+), 185 deletions(-)
Title: Mean Length-Based Estimators of Mortality using TMB
Description: Estimation functions and diagnostic tools for mean length-based total mortality estimators based on Gedamke and Hoenig (2006) <doi:10.1577/T05-153.1>.
Author: Quang Huynh [aut, cre],
Todd Gedamke [ctb],
Amy Then [ctb]
Maintainer: Quang Huynh <q.huynh@oceans.ubc.ca>
Diff between MLZ versions 0.1.1 dated 2018-06-12 and 0.1.3 dated 2019-09-20
DESCRIPTION | 9 MD5 | 57 ++-- NEWS.md |only R/compare_models.R | 25 +- R/estimation.R | 104 +++++--- R/internal_misc.R | 11 R/methods.R | 132 ++++++---- R/profile.R | 2 README.md | 12 build/vignette.rds |binary inst/doc/MLZ.R | 6 inst/doc/MLZ.Rmd | 6 inst/doc/MLZ.html | 405 ++++++++++++++++++++++++++------ inst/include/ML.h | 74 +++--- inst/include/MLCR.h | 142 +++++------ inst/include/MLeffort.h | 200 ++++++++-------- inst/include/MSM1S.h | 124 +++++----- inst/include/MSM23.h | 148 ++++++------ inst/include/functions.h | 528 +++++++++++++++++++++---------------------- man/ML.Rd | 7 man/MLCR.Rd | 4 man/MLZ_model-class.Rd | 2 man/MLmulti.Rd | 12 man/compare_models.Rd | 8 man/plot-MLZ_data-method.Rd | 11 man/plot-MLZ_model-method.Rd | 1 man/profile_ML.Rd | 3 man/profile_MLCR.Rd | 4 man/profile_MLmulti.Rd | 6 vignettes/MLZ.Rmd | 6 30 files changed, 1184 insertions(+), 865 deletions(-)
Title: Analysis, Seriation and Visualization of Archaeological Count
Data
Description: An easy way to examine archaeological count data. This package
provides a convenient and reproducible toolkit for relative and absolute
dating and analysis of (chronological) patterns. It includes functions for
matrix seriation (reciprocal ranking, CA-based seriation), chronological
modeling and dating of archaeological assemblages and/or objects.
Beyond these, the package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.),
turnover and similarity (Brainerd-Robinson, etc.).
The package make it easy to visualize count data and statistical thresholds:
rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>),
Matthew Peeples [ctb] (<https://orcid.org/0000-0003-4496-623X>),
Ben Marwick [ctb] (<https://orcid.org/0000-0001-7879-4531>),
Anne Philippe [ctb],
Jean-Baptiste Fourvel [ctb] (<https://orcid.org/0000-0002-1061-4642>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 1.2.0 dated 2019-03-20 and 1.3.0 dated 2019-09-20
tabula-1.2.0/tabula/R/diversity.R |only tabula-1.2.0/tabula/R/plot.R |only tabula-1.2.0/tabula/R/rarefaction.R |only tabula-1.2.0/tabula/R/richness.R |only tabula-1.2.0/tabula/R/similarity.R |only tabula-1.2.0/tabula/R/tabula.R |only tabula-1.2.0/tabula/R/turnover.R |only tabula-1.2.0/tabula/inst/doc/tabula.R |only tabula-1.2.0/tabula/inst/doc/tabula.Rmd |only tabula-1.2.0/tabula/inst/doc/tabula.html |only tabula-1.2.0/tabula/inst/examples/ex-plotBar.R |only tabula-1.2.0/tabula/inst/examples/ex-plotMatrix.R |only tabula-1.2.0/tabula/inst/examples/ex-plotRank.R |only tabula-1.2.0/tabula/inst/examples/ex-plotSpot.R |only tabula-1.2.0/tabula/man/accessors.Rd |only tabula-1.2.0/tabula/man/diversity-method.Rd |only tabula-1.2.0/tabula/man/figures/README-plot-freq-1.png |only tabula-1.2.0/tabula/man/figures/README-seriograph-1.png |only tabula-1.2.0/tabula/man/plotBar-method.Rd |only tabula-1.2.0/tabula/man/plotDate-method.Rd |only tabula-1.2.0/tabula/man/plotMatrix-method.Rd |only tabula-1.2.0/tabula/man/plotRank-method.Rd |only tabula-1.2.0/tabula/man/plotSpot-method.Rd |only tabula-1.2.0/tabula/man/richness-method.Rd |only tabula-1.2.0/tabula/vignettes/figures |only tabula-1.2.0/tabula/vignettes/tabula.Rmd |only tabula-1.3.0/tabula/DESCRIPTION | 110 - tabula-1.3.0/tabula/MD5 | 280 +- tabula-1.3.0/tabula/NAMESPACE | 47 tabula-1.3.0/tabula/NEWS.md | 200 + tabula-1.3.0/tabula/R/AllClasses.R | 698 ++++-- tabula-1.3.0/tabula/R/AllGenerics.R | 1035 +++++++--- tabula-1.3.0/tabula/R/check.R |only tabula-1.3.0/tabula/R/coerce.R | 202 + tabula-1.3.0/tabula/R/data.R | 123 - tabula-1.3.0/tabula/R/date.R | 374 +-- tabula-1.3.0/tabula/R/deprecate.R |only tabula-1.3.0/tabula/R/extract.R | 427 +++- tabula-1.3.0/tabula/R/index-diversity.R |only tabula-1.3.0/tabula/R/index-rarefaction.R |only tabula-1.3.0/tabula/R/index-richness.R |only tabula-1.3.0/tabula/R/index-similarity.R |only tabula-1.3.0/tabula/R/index-turnover.R |only tabula-1.3.0/tabula/R/plot-bar.R |only tabula-1.3.0/tabula/R/plot-date.R |only tabula-1.3.0/tabula/R/plot-matrix.R |only tabula-1.3.0/tabula/R/plot-prepare.R |only tabula-1.3.0/tabula/R/plot-rank.R |only tabula-1.3.0/tabula/R/plot-spot.R |only tabula-1.3.0/tabula/R/plot-time.R |only tabula-1.3.0/tabula/R/predicates.R |only tabula-1.3.0/tabula/R/refine.R | 279 ++ tabula-1.3.0/tabula/R/seriate.R | 115 - tabula-1.3.0/tabula/R/seriation.R | 101 tabula-1.3.0/tabula/R/show.R | 50 tabula-1.3.0/tabula/R/statistics.R | 140 - tabula-1.3.0/tabula/R/tabula-package.R |only tabula-1.3.0/tabula/R/test.R |only tabula-1.3.0/tabula/R/utilities.R | 275 +- tabula-1.3.0/tabula/R/validate.R | 537 ++--- tabula-1.3.0/tabula/R/zzz.R | 2 tabula-1.3.0/tabula/README.md | 311 ++- tabula-1.3.0/tabula/build/vignette.rds |binary tabula-1.3.0/tabula/data/merzbach.rda |only tabula-1.3.0/tabula/inst/CITATION | 21 tabula-1.3.0/tabula/inst/doc/bibliography.R |only tabula-1.3.0/tabula/inst/doc/bibliography.Rmd |only tabula-1.3.0/tabula/inst/doc/bibliography.html |only tabula-1.3.0/tabula/inst/doc/dating.R |only tabula-1.3.0/tabula/inst/doc/dating.Rmd |only tabula-1.3.0/tabula/inst/doc/dating.html |only tabula-1.3.0/tabula/inst/doc/diversity.R | 40 tabula-1.3.0/tabula/inst/doc/diversity.Rmd | 161 + tabula-1.3.0/tabula/inst/doc/diversity.html | 600 ++++- tabula-1.3.0/tabula/inst/doc/matrix.R |only tabula-1.3.0/tabula/inst/doc/matrix.Rmd |only tabula-1.3.0/tabula/inst/doc/matrix.html |only tabula-1.3.0/tabula/inst/doc/seriation.R |only tabula-1.3.0/tabula/inst/doc/seriation.Rmd |only tabula-1.3.0/tabula/inst/doc/seriation.html |only tabula-1.3.0/tabula/inst/examples/ex-abundance-class.R | 31 tabula-1.3.0/tabula/inst/examples/ex-coerce.R |only tabula-1.3.0/tabula/inst/examples/ex-dating.R | 60 tabula-1.3.0/tabula/inst/examples/ex-geography.R |only tabula-1.3.0/tabula/inst/examples/ex-logical-class.R | 19 tabula-1.3.0/tabula/inst/examples/ex-plot_bar.R |only tabula-1.3.0/tabula/inst/examples/ex-plot_line.R |only tabula-1.3.0/tabula/inst/examples/ex-plot_matrix.R |only tabula-1.3.0/tabula/inst/examples/ex-plot_rank.R |only tabula-1.3.0/tabula/inst/examples/ex-plot_spot.R |only tabula-1.3.0/tabula/inst/examples/ex-richness.R | 4 tabula-1.3.0/tabula/inst/examples/ex-seriation.R | 31 tabula-1.3.0/tabula/inst/examples/ex-similarity.R | 2 tabula-1.3.0/tabula/inst/examples/ex-test.R |only tabula-1.3.0/tabula/inst/examples/ex-turnover.R | 13 tabula-1.3.0/tabula/man/BootCA-class.Rd | 84 tabula-1.3.0/tabula/man/CountMatrix-class.Rd | 116 - tabula-1.3.0/tabula/man/DateModel-class.Rd | 101 tabula-1.3.0/tabula/man/FrequencyMatrix-class.Rd | 115 - tabula-1.3.0/tabula/man/IncidenceMatrix-class.Rd | 93 tabula-1.3.0/tabula/man/LogicalMatrix-class.Rd |only tabula-1.3.0/tabula/man/Matrix-class.Rd |only tabula-1.3.0/tabula/man/NumericMatrix-class.Rd |only tabula-1.3.0/tabula/man/OccurrenceMatrix-class.Rd | 102 tabula-1.3.0/tabula/man/PermutationOrder-class.Rd | 38 tabula-1.3.0/tabula/man/SimilarityMatrix-class.Rd | 75 tabula-1.3.0/tabula/man/SpaceTime-class.Rd |only tabula-1.3.0/tabula/man/access.Rd |only tabula-1.3.0/tabula/man/boves.Rd | 6 tabula-1.3.0/tabula/man/coerce.Rd |only tabula-1.3.0/tabula/man/compiegne.Rd | 8 tabula-1.3.0/tabula/man/date.Rd | 302 ++ tabula-1.3.0/tabula/man/deprecated.Rd |only tabula-1.3.0/tabula/man/diversity.Rd |only tabula-1.3.0/tabula/man/figures/README-bertin-1.png |only tabula-1.3.0/tabula/man/figures/README-date-1.png |binary tabula-1.3.0/tabula/man/figures/README-date-2.png |only tabula-1.3.0/tabula/man/figures/README-ford-1.png |only tabula-1.3.0/tabula/man/figures/README-permute-incidence-1.png |binary tabula-1.3.0/tabula/man/figures/README-permute-incidence-2.png |binary tabula-1.3.0/tabula/man/figures/README-plot-occ-1.png |binary tabula-1.3.0/tabula/man/figures/README-plot-rank-1.png |binary tabula-1.3.0/tabula/man/figures/README-plot-time-1.png |only tabula-1.3.0/tabula/man/figures/README-similarity-brainerd-1.png |binary tabula-1.3.0/tabula/man/figures/logo.png |only tabula-1.3.0/tabula/man/figures/logo.svg | 179 + tabula-1.3.0/tabula/man/geography.Rd |only tabula-1.3.0/tabula/man/merzbach.Rd |only tabula-1.3.0/tabula/man/mississippi.Rd | 12 tabula-1.3.0/tabula/man/plot_bar.Rd |only tabula-1.3.0/tabula/man/plot_date.Rd |only tabula-1.3.0/tabula/man/plot_line.Rd |only tabula-1.3.0/tabula/man/plot_matrix.Rd |only tabula-1.3.0/tabula/man/plot_spot.Rd |only tabula-1.3.0/tabula/man/richness.Rd |only tabula-1.3.0/tabula/man/seriation.Rd | 177 - tabula-1.3.0/tabula/man/similarity-method.Rd | 27 tabula-1.3.0/tabula/man/subset.Rd |only tabula-1.3.0/tabula/man/tabula-package.Rd | 46 tabula-1.3.0/tabula/man/test.Rd |only tabula-1.3.0/tabula/man/turnover-method.Rd | 39 tabula-1.3.0/tabula/man/zuni.Rd | 8 tabula-1.3.0/tabula/tests/figs |only tabula-1.3.0/tabula/tests/testthat/helper.R |only tabula-1.3.0/tabula/tests/testthat/test-check.R |only tabula-1.3.0/tabula/tests/testthat/test-class-matrix.R |only tabula-1.3.0/tabula/tests/testthat/test-classes.R | 299 +- tabula-1.3.0/tabula/tests/testthat/test-coerce.R | 95 tabula-1.3.0/tabula/tests/testthat/test-date.R | 109 - tabula-1.3.0/tabula/tests/testthat/test-diversity.R | 56 tabula-1.3.0/tabula/tests/testthat/test-extract.R | 155 + tabula-1.3.0/tabula/tests/testthat/test-plots.R | 123 - tabula-1.3.0/tabula/tests/testthat/test-predicates.R |only tabula-1.3.0/tabula/tests/testthat/test-rarefaction.R | 16 tabula-1.3.0/tabula/tests/testthat/test-richness.R | 56 tabula-1.3.0/tabula/tests/testthat/test-seriation.R | 62 tabula-1.3.0/tabula/tests/testthat/test-similarity.R | 32 tabula-1.3.0/tabula/tests/testthat/test-statistics.R | 38 tabula-1.3.0/tabula/tests/testthat/test-test.R |only tabula-1.3.0/tabula/tests/testthat/test-turnover.R | 12 tabula-1.3.0/tabula/tests/testthat/test-utilities.R | 119 - tabula-1.3.0/tabula/vignettes/bibliography.Rmd |only tabula-1.3.0/tabula/vignettes/bibliography.bib | 281 +- tabula-1.3.0/tabula/vignettes/classes.svg |only tabula-1.3.0/tabula/vignettes/dating.Rmd |only tabula-1.3.0/tabula/vignettes/diversity.Rmd | 161 + tabula-1.3.0/tabula/vignettes/matrix.Rmd |only tabula-1.3.0/tabula/vignettes/seriation.Rmd |only 168 files changed, 6341 insertions(+), 3089 deletions(-)
Title: 'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest
Neighbors
Description: 'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This
package provides a minimal R interface by relying on the 'Rcpp' package. See
<https://github.com/nmslib/hnswlib> for more on 'hnswlib'. 'hnswlib' is
released under Version 2.0 of the Apache License.
Author: James Melville [aut, cre],
Aaron Lun [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between RcppHNSW versions 0.1.0 dated 2019-01-21 and 0.2.0 dated 2019-09-20
DESCRIPTION | 8 MD5 | 20 + NEWS.md | 26 ++ R/hnsw.R | 13 - inst/include/bruteforce.h | 35 ++- inst/include/hnswalg.h | 373 ++++++++++++++++++++++++++----------- man/hnsw_build.Rd | 4 man/hnsw_search.Rd | 8 src/Makevars | 2 src/hnsw.cpp | 25 ++ tests/testthat/test_resize_index.R |only tests/testthat/test_search_one.R |only 12 files changed, 368 insertions(+), 146 deletions(-)
Title: Enterprise Streamlined 'Shiny' Application Framework
Description: An enterprise-targeted scalable and UI-standardized 'shiny' framework
including a variety of developer convenience functions with the goal of both
streamlining robust application development while assisting with creating a
consistent user experience regardless of application or developer.
Author: Constance Brett [aut, cre],
Isaac Neuhaus [aut] (canvasXpress JavaScript Library Maintainer),
Ger Inberg [ctb],
Bristol-Meyers Squibb (BMS) [cph]
Maintainer: Constance Brett <connie@aggregate-genius.com>
Diff between periscope versions 0.4.4 dated 2019-08-29 and 0.4.5 dated 2019-09-20
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 5 +++-- R/downloadableTable.R | 1 - inst/doc/downloadFile-module.html | 4 ++-- inst/doc/downloadablePlot-module.html | 4 ++-- inst/doc/downloadableTable-module.html | 4 ++-- inst/doc/new-application.html | 4 ++-- tests/testthat/test_downloadable_table.R | 1 - 9 files changed, 22 insertions(+), 23 deletions(-)
Title: Symbolic Differentiation
Description: R-based solution for symbolic differentiation. It admits
user-defined function as well as function substitution
in arguments of functions to be differentiated. Some symbolic
simplification is part of the work.
Author: Andrew Clausen [aut],
Serguei Sokol [aut, cre] (<https://orcid.org/0000-0002-5674-3327>)
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between Deriv versions 3.8.5 dated 2018-06-11 and 3.9.0 dated 2019-09-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS | 9 +++++++++ R/Deriv.R | 7 +++++-- inst/CITATION | 2 +- man/Deriv-package.Rd | 6 +++--- 6 files changed, 29 insertions(+), 17 deletions(-)
Title: Secure Authentication in Shiny with Auth0
Description: Uses Auth0 API (see <https://auth0.com> for more
information) to use a simple and secure authentication system. It provides
tools to log in and out a shiny application using social networks or a list
of e-mails.
Author: Julio Trecenti [cre],
Daniel Falbel [aut],
José Jesus [ctb],
Dean Attali [ctb],
C Lente [ctb]
Maintainer: Julio Trecenti <julio.trecenti@gmail.com>
Diff between auth0 versions 0.1.1 dated 2019-02-13 and 0.2.0 dated 2019-09-20
DESCRIPTION | 19 ++- MD5 | 56 ++++++++--- NAMESPACE | 9 + R/auth0.R | 93 +++++++++--------- R/logout.R |only R/shiny.R | 189 +++++++++++++++++++++++++------------- R/utils.R |only build |only inst/bookmark |only inst/doc |only inst/logout/_auth0.yml | 3 inst/logout/app.R | 23 ---- inst/simple/_auth0.yml | 3 inst/simple/app.R | 2 inst/ui-server |only inst/ui-server-bookmark |only inst/userinfo/_auth0.yml | 2 inst/userinfo/app.R | 4 man/auth0_config.Rd |only man/auth0_find_config_file.Rd |only man/auth0_info.Rd |only man/auth0_logout_url.Rd | 31 +++--- man/figures/README-myapp-vars.png |only man/logout.Rd |only man/logoutButton.Rd |only man/logout_url.Rd |only man/shinyAppAuth0.Rd |only man/shinyAuth0App.Rd | 10 -- man/ui-server.Rd |only man/use_auth0.Rd | 3 vignettes |only 31 files changed, 271 insertions(+), 176 deletions(-)
More information about changepointsHD at CRAN
Permanent link
Title: Create Visuals for Publication
Description: A small set of functions for making visuals for publication in 'ggplot2'. Key functions include geom_stepconfint() for drawing a step confidence interval on a Kaplan-Meier curve and theme_white()/theme_black() which are minimalist 'ggplot2' themes with transparent backgrounds.
Author: Eric Finnesgard [aut, cre]
Maintainer: Eric Finnesgard <finnesgard.eric@mayo.edu>
Diff between utile.visuals versions 0.2.0 dated 2019-07-11 and 0.2.1 dated 2019-09-20
DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/append.R | 42 +++++++++++++++++++++++++++--------------- R/connect.R |only R/gg.R | 33 +++++++++++++++++++++++++++++---- R/themes.R | 2 ++ README.md | 31 ++++++++++++++++++------------- man/append_table.Rd | 13 +++++++++---- man/connect_origin.Rd |only man/ggrisktable.Rd | 12 +++++++++--- 12 files changed, 117 insertions(+), 52 deletions(-)
Title: Cluster High Dimensional Categorical Datasets
Description: Scalable Bayesian clustering of categorical datasets. The package implements a hierarchical Dirichlet
(Process) mixture of multinomial distributions. It is thus a probabilistic latent class model (LCM) and can be used
to reduce the dimensionality of hierarchical data and cluster individuals into latent classes. It can automatically
infer an appropriate number of latent classes or find k classes, as defined by the user. The model is based on a
paper by Dunson and Xing (2009) <doi:10.1198/jasa.2009.tm08439>, but implements a scalable variational inference algorithm so that it is
applicable to large datasets. It is described and tested in the accompanying paper by
Ahlmann-Eltze and Yau (2018) <doi:10.1109/DSAA.2018.00068>.
Author: Constantin Ahlmann-Eltze [aut, cre]
(<https://orcid.org/0000-0002-3762-068X>),
Christopher Yau [ths] (<https://orcid.org/0000-0001-7615-8523>)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between mixdir versions 0.2.0 dated 2019-03-11 and 0.3.0 dated 2019-09-20
DESCRIPTION | 17 ++++++++++------- MD5 | 10 +++++----- NEWS.md | 6 ++++++ R/mixdir_vi.R | 5 +++++ R/mixdir_vi_dp.R | 5 +++++ tests/testthat/test-mixdir.R | 8 ++++++++ 6 files changed, 39 insertions(+), 12 deletions(-)
Title: Fast Fixed-Effects Estimations
Description: Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial.
The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://wwwen.uni.lu/content/download/110162/1299525/file/2018_13>.
Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.
Author: Laurent Berge [aut, cre]
Maintainer: Laurent Berge <laurent.berge@uni.lu>
Diff between fixest versions 0.1.0 dated 2019-09-03 and 0.1.1 dated 2019-09-20
DESCRIPTION | 6 MD5 | 16 R/ESTIMATION_FUNS.R | 49 - R/MiscFuns.R | 86 +-- inst/NEWS.Rd | 28 inst/doc/fixest_walkthrough.Rmd | 10 inst/doc/fixest_walkthrough.html | 1102 +++++++++++++++++++-------------------- man/feNmlm.Rd | 1 vignettes/fixest_walkthrough.Rmd | 10 9 files changed, 683 insertions(+), 625 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureGraph versions 1.0.3 dated 2019-07-09 and 1.0.4 dated 2019-09-20
DESCRIPTION | 9 +++++---- MD5 | 20 +++++++++++--------- NEWS.md | 6 ++++++ R/az_object.R | 5 ++--- R/call_graph.R | 23 +++++++++++++++++++---- R/graph_login.R | 7 +++---- README.md | 8 +++++--- build/vignette.rds |binary man/figures |only tests/testthat/test01_auth.R | 2 +- tests/testthat/test03_usergrp.R | 2 +- tests/testthat/test04_aad_v2.R |only 12 files changed, 53 insertions(+), 29 deletions(-)
Title: Gradient Boosting for Survival Data
Description: Gradient boosting for optimizing loss functions of different types of survival data,
including stratified data.
Emily Morris, Kevin He, Yanming Li, Yi Li, Jian Kang (2018) <arXiv:1803.07715> see for
description of methods.
Author: Emily Morris, Kevin He, Yanming Li, Yi Li, Jian Kang
Maintainer: Emily Morris <emorrisl@umich.edu>
Diff between SurvBoost versions 0.1.1 dated 2019-03-23 and 0.1.2 dated 2019-09-20
SurvBoost-0.1.1/SurvBoost/man/modelfit.boosting.Rd |only SurvBoost-0.1.2/SurvBoost/DESCRIPTION | 6 SurvBoost-0.1.2/SurvBoost/MD5 | 21 +- SurvBoost-0.1.2/SurvBoost/NAMESPACE | 1 SurvBoost-0.1.2/SurvBoost/NEWS.md | 3 SurvBoost-0.1.2/SurvBoost/R/boosting_function.R | 190 +++++++++----------- SurvBoost-0.1.2/SurvBoost/man/boosting_core.Rd | 30 ++- SurvBoost-0.1.2/SurvBoost/man/inference.boosting.Rd | 2 SurvBoost-0.1.2/SurvBoost/man/plot.boosting.Rd | 2 SurvBoost-0.1.2/SurvBoost/man/predict.boosting.Rd | 6 SurvBoost-0.1.2/SurvBoost/man/print.boosting.Rd | 2 SurvBoost-0.1.2/SurvBoost/man/summary.boosting.Rd | 7 12 files changed, 140 insertions(+), 130 deletions(-)
Title: Computation of High-Order Sobol' Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to third-order Sobol' indices
using the estimators by Saltelli et al. 2010 <doi:10.1016/j.cpc.2009.09.018> and
Jansen 1999 <doi:10.1016/S0010-4655(98)00154-4>. The 'sensobol' package also implements
the algorithm by Khorashadi Zadeh et al. 2017 <doi:10.1016/j.envsoft.2017.02.001> to
calculate the approximation error in the computation of Sobol' first and
total indices, an approach that allows to robustly screen influential from non-influential
model inputs. Finally, it also provides functions to obtain publication-ready figures
of the model output uncertainty and sensitivity-related analysis.
Author: Arnald Puy [aut, cre] (<https://orcid.org/0000-0001-9469-2156>),
Bertrand Ioos [ctb] (Author of included 'sensitivity' fragments),
Gilles Pujol [ctb] (Author of included 'sensitivity' fragments),
RStudio [cph] (Copyright holder of included 'sensitivity' fragments)
Maintainer: Arnald Puy <arnald.puy@gmail.com>
Diff between sensobol versions 0.2.0 dated 2019-04-30 and 0.2.1 dated 2019-09-20
DESCRIPTION | 6 +-- MD5 | 26 +++++++------ NAMESPACE | 2 + NEWS.md | 9 ++++ R/group_ranking.R |only R/plot_sobol.R | 9 +++- R/sobol_boot.R | 66 ++++++++++++++++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/sensobol.R | 38 ++++++++++--------- inst/doc/sensobol.Rmd | 40 ++++++++++---------- inst/doc/sensobol.html | 92 ++++++++++++++++++++++++------------------------ man/plot_uncertainty.Rd | 6 ++- man/sobol_replicas.Rd |only vignettes/sensobol.Rmd | 40 ++++++++++---------- 15 files changed, 214 insertions(+), 120 deletions(-)
Title: Tools for Interacting with 'PostgreSQL' / 'PostGIS' Databases
Description: Functions to convert geometry and 'hstore' data types from
'PostgreSQL' into standard R objects, as well as to simplify
the import of R data frames (including spatial data frames) into 'PostgreSQL'.
Note: This package is deprecated. For new projects, we recommend
using the 'sf' package to interface with geodatabases.
Author: Philippe Marchand [aut, cre],
Richard Ellison [aut]
Maintainer: Philippe Marchand <marchand.philippe@gmail.com>
Diff between postGIStools versions 0.2.3 dated 2019-05-03 and 0.2.4 dated 2019-09-20
postGIStools-0.2.3/postGIStools/build |only postGIStools-0.2.3/postGIStools/inst |only postGIStools-0.2.3/postGIStools/tests/testthat/country_sp.rds |only postGIStools-0.2.3/postGIStools/tests/testthat/test_get_query.R |only postGIStools-0.2.3/postGIStools/tests/testthat/test_insert_update.R |only postGIStools-0.2.3/postGIStools/vignettes |only postGIStools-0.2.4/postGIStools/DESCRIPTION | 7 ++--- postGIStools-0.2.4/postGIStools/MD5 | 12 +--------- postGIStools-0.2.4/postGIStools/NEWS.md | 5 ++++ 9 files changed, 10 insertions(+), 14 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.5.4 dated 2019-09-17 and 0.5.5 dated 2019-09-20
greybox-0.5.4/greybox/man/c.ts.Rd |only greybox-0.5.5/greybox/DESCRIPTION | 8 greybox-0.5.5/greybox/MD5 | 21 - greybox-0.5.5/greybox/NAMESPACE | 1 greybox-0.5.5/greybox/NEWS | 7 greybox-0.5.5/greybox/R/methods.R | 37 -- greybox-0.5.5/greybox/README.md | 1 greybox-0.5.5/greybox/build/partial.rdb |binary greybox-0.5.5/greybox/inst/doc/alm.html | 152 ++++----- greybox-0.5.5/greybox/inst/doc/greybox.html | 322 ++++++++++----------- greybox-0.5.5/greybox/inst/doc/maUsingGreybox.html | 4 greybox-0.5.5/greybox/inst/doc/ro.html | 22 - 12 files changed, 272 insertions(+), 303 deletions(-)
Title: Data Mining and R Programming for Beginners
Description: Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Author: Alexandre Blansché [aut, cre]
Maintainer: Alexandre Blansché <alexandre.blansche@univ-lorraine.fr>
Diff between fdm2id versions 0.8.7 dated 2019-08-23 and 0.9.0 dated 2019-09-20
DESCRIPTION | 11 +- MD5 | 91 +++++++++-------- NAMESPACE | 14 ++ R/association.R | 4 R/classification.R | 245 +++++++++++++++++++++++++++++++++------------- R/clustering.R | 48 +++++---- R/dataset.R | 8 + R/feature.R | 16 ++- R/misc.R | 8 - R/text.R |only R/visualization.R | 21 ++- man/DBSCAN.Rd | 4 man/EM.Rd | 4 man/FEATURESELECTION.Rd | 4 man/HCA.Rd | 4 man/KMEANS.Rd | 10 + man/MEANSHIFT.Rd | 10 + man/MLP.Rd | 7 - man/NMF.Rd | 6 - man/SPECTRAL.Rd | 4 man/SVD.Rd | 8 + man/SVM.Rd | 5 man/SVMl.Rd | 6 - man/SVMr.Rd | 6 - man/TEXTMINING.Rd |only man/TSNE.Rd | 2 man/bootstrap.Rd | 7 - man/bootstrap.curves.Rd | 6 - man/cartinfo.Rd | 6 - man/cartleafs.Rd | 6 - man/cartnodes.Rd | 6 - man/cartplot.Rd | 6 - man/cookies.Rd | 2 man/data.parabol.Rd | 4 man/data.target1.Rd | 4 man/data.target2.Rd | 4 man/data.twomoons.Rd | 4 man/evaluate.Rd |only man/evaluation.Rd | 1 man/filter.rules.Rd | 2 man/frequentwords.Rd |only man/general.rules.Rd | 2 man/getvocab.Rd |only man/loadtext.Rd |only man/plotcloud.Rd |only man/plotzipf.Rd |only man/predict.textmining.Rd |only man/query.docs.Rd |only man/query.words.Rd |only man/textmining-class.Rd |only man/titanic.Rd | 2 man/vectorize.docs.Rd |only man/vectorize.words.Rd |only man/vectorizer-class.Rd |only 54 files changed, 409 insertions(+), 199 deletions(-)
Title: Identification of Cell Types and Inference of Lineage Trees from
Single-Cell RNA-Seq Data
Description: Application of 'RaceID' allows inference of cell types and prediction of lineage trees by he StemID2 algorithm. Herman, J.S., Sagar, Grün D. (2018) <DOI:10.1038/nmeth.4662>.
Author: Dominic Grün <dominic.gruen@gmail.com>
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Diff between RaceID versions 0.1.3 dated 2019-01-22 and 0.1.4 dated 2019-09-20
RaceID-0.1.3/RaceID/man/plotprojections.Rd |only RaceID-0.1.4/RaceID/DESCRIPTION | 18 - RaceID-0.1.4/RaceID/MD5 | 72 ++-- RaceID-0.1.4/RaceID/NAMESPACE | 47 ++ RaceID-0.1.4/RaceID/R/RaceID.R | 493 +++++++++++++++++++++------- RaceID-0.1.4/RaceID/R/RaceID_utils.R | 24 + RaceID-0.1.4/RaceID/R/RcppExports.R |only RaceID-0.1.4/RaceID/R/StemID.R | 108 +++--- RaceID-0.1.4/RaceID/R/VarID_functions.R |only RaceID-0.1.4/RaceID/inst/doc/RaceID.R | 186 ++++++++++ RaceID-0.1.4/RaceID/inst/doc/RaceID.Rmd | 403 ++++++++++++++++++++++ RaceID-0.1.4/RaceID/inst/doc/RaceID.html | 272 +++++++++++++-- RaceID-0.1.4/RaceID/man/RaceID-package.Rd |only RaceID-0.1.4/RaceID/man/SCseq.Rd | 4 RaceID-0.1.4/RaceID/man/baseLineVar.Rd |only RaceID-0.1.4/RaceID/man/compNoise.Rd |only RaceID-0.1.4/RaceID/man/compdist.Rd | 11 RaceID-0.1.4/RaceID/man/compmedoids.Rd | 3 RaceID-0.1.4/RaceID/man/comptsne.Rd | 7 RaceID-0.1.4/RaceID/man/compumap.Rd |only RaceID-0.1.4/RaceID/man/createKnnMatrix.Rd |only RaceID-0.1.4/RaceID/man/diffNoisyGenes.Rd |only RaceID-0.1.4/RaceID/man/filterdata.Rd | 2 RaceID-0.1.4/RaceID/man/fitBackVar.Rd |only RaceID-0.1.4/RaceID/man/fractDotPlot.Rd |only RaceID-0.1.4/RaceID/man/getExpData.Rd |only RaceID-0.1.4/RaceID/man/graphCluster.Rd |only RaceID-0.1.4/RaceID/man/maxNoisyGenes.Rd |only RaceID-0.1.4/RaceID/man/noiseBaseFit.Rd |only RaceID-0.1.4/RaceID/man/plotBackVar.Rd |only RaceID-0.1.4/RaceID/man/plotNoiseModel.Rd |only RaceID-0.1.4/RaceID/man/plotPearsonRes.Rd |only RaceID-0.1.4/RaceID/man/plotRegNB.Rd |only RaceID-0.1.4/RaceID/man/plotTrProbs.Rd |only RaceID-0.1.4/RaceID/man/plotexpmap.Rd | 9 RaceID-0.1.4/RaceID/man/plotgraph.Rd | 14 RaceID-0.1.4/RaceID/man/plotlabelsmap.Rd | 8 RaceID-0.1.4/RaceID/man/plotmap.Rd | 7 RaceID-0.1.4/RaceID/man/plotmarkergenes.Rd | 8 RaceID-0.1.4/RaceID/man/plotspantree.Rd | 11 RaceID-0.1.4/RaceID/man/plotsymbolsmap.Rd | 8 RaceID-0.1.4/RaceID/man/projcells.Rd | 7 RaceID-0.1.4/RaceID/man/pruneKnn.Rd |only RaceID-0.1.4/RaceID/man/rcpp_hello_world.Rd |only RaceID-0.1.4/RaceID/man/transitionProbs.Rd |only RaceID-0.1.4/RaceID/man/updateSC.Rd |only RaceID-0.1.4/RaceID/src |only RaceID-0.1.4/RaceID/vignettes/RaceID.Rmd | 403 ++++++++++++++++++++++ 48 files changed, 1840 insertions(+), 285 deletions(-)
Title: Create Pivot Tables in R
Description: Create regular pivot tables with just a few lines of R.
More complex pivot tables can also be created, e.g. pivot tables
with irregular layouts, multiple calculations and/or derived
calculations based on multiple data frames. Pivot tables are
constructed using R only and can be written to a range of
output formats (plain text, 'HTML', 'Latex' and 'Excel'),
including with styling/formatting.
Author: Christopher Bailiss [aut, cre]
Maintainer: Christopher Bailiss <cbailiss@gmail.com>
Diff between pivottabler versions 1.2.1 dated 2019-08-05 and 1.2.2 dated 2019-09-20
DESCRIPTION | 6 - MD5 | 36 ++++----- NEWS.md | 10 ++ R/PivotTable.R | 36 +++++---- inst/doc/v01-introduction.html | 100 ++++++++++++------------- inst/doc/v02-datagroups.html | 60 +++++++-------- inst/doc/v03-calculations.html | 80 ++++++++++---------- inst/doc/v04-outputs.html | 16 ++-- inst/doc/v05-latexoutput.html | 8 +- inst/doc/v06-styling.html | 52 ++++++------- inst/doc/v07-findingandformatting.html | 132 ++++++++++++++++----------------- inst/doc/v08-cellcontext.html | 24 +++--- inst/doc/v09-irregularlayout.html | 60 +++++++-------- inst/doc/v10-performance.html | 52 ++++++------- inst/doc/v11-shiny.html | 4 - inst/doc/v12-excelexport.html | 8 +- inst/doc/vA1-appendix.html | 16 ++-- inst/doc/vA2-appendix.html | 76 +++++++++---------- inst/doc/vA3-appendix.html | 8 +- 19 files changed, 399 insertions(+), 385 deletions(-)
Title: Comprehensive Luminescence Dating Data Analysis
Description: A collection of various R functions for the purpose of Luminescence
dating data analysis. This includes, amongst others, data import, export,
application of age models, curve deconvolution, sequence analysis and
plotting of equivalent dose distributions.
Author: Sebastian Kreutzer [aut, trl, cre, dtc]
(<https://orcid.org/0000-0002-0734-2199>),
Christoph Burow [aut, trl, dtc]
(<https://orcid.org/0000-0002-5023-4046>),
Michael Dietze [aut] (<https://orcid.org/0000-0001-6063-1726>),
Margret C. Fuchs [aut],
Christoph Schmidt [aut] (<https://orcid.org/0000-0002-2309-3209>),
Manfred Fischer [aut, trl],
Johannes Friedrich [aut] (<https://orcid.org/0000-0002-0805-9547>),
Norbert Mercier [ctb] (<https://orcid.org/0000-0002-6375-9108>),
Rachel K. Smedley [ctb] (<https://orcid.org/0000-0001-7773-5193>),
Claire Christophe [ctb],
Antoine Zink [ctb] (<https://orcid.org/0000-0001-7146-1101>),
Julie Durcan [ctb] (<https://orcid.org/0000-0001-8724-8022>),
Georgina E. King [ctb, dtc] (<https://orcid.org/0000-0003-1059-8192>),
Anne Philippe [ctb],
Guillaume Guerin [ctb] (<https://orcid.org/0000-0001-6298-5579>),
Svenja Riedesel [ctb] (<https://orcid.org/0000-0003-2936-8776>),
Martin Autzen [ctb],
Pierre Guibert [ctb] (<https://orcid.org/0000-0001-8969-8684>),
Markus Fuchs [ths]
Maintainer: Sebastian Kreutzer <sebastian.kreutzer@u-bordeaux-montaigne.fr>
Diff between Luminescence versions 0.9.4 dated 2019-09-19 and 0.9.5 dated 2019-09-20
DESCRIPTION | 18 +- MD5 | 238 ++++++++++++++++----------------- NEWS.md | 6 README.md | 2 build/partial.rdb |binary man/Analyse_SAR.OSLdata.Rd | 2 man/CW2pHMi.Rd | 2 man/CW2pLM.Rd | 2 man/CW2pLMi.Rd | 2 man/CW2pPMi.Rd | 2 man/GitHub-API.Rd | 2 man/PSL2Risoe.BINfileData.Rd | 2 man/RLum-class.Rd | 2 man/RLum.Analysis-class.Rd | 2 man/RLum.Data.Curve-class.Rd | 2 man/RLum.Data.Image-class.Rd | 2 man/RLum.Data.Spectrum-class.Rd | 2 man/RLum.Results-class.Rd | 2 man/Risoe.BINfileData-class.Rd | 2 man/Risoe.BINfileData2RLum.Analysis.Rd | 2 man/Second2Gray.Rd | 2 man/analyse_Al2O3C_CrossTalk.Rd | 2 man/analyse_Al2O3C_ITC.Rd | 2 man/analyse_Al2O3C_Measurement.Rd | 2 man/analyse_FadingMeasurement.Rd | 2 man/analyse_IRSAR.RF.Rd | 2 man/analyse_SAR.CWOSL.Rd | 2 man/analyse_SAR.TL.Rd | 2 man/analyse_baSAR.Rd | 2 man/analyse_pIRIRSequence.Rd | 2 man/analyse_portableOSL.Rd | 2 man/app_RLum.Rd | 2 man/apply_CosmicRayRemoval.Rd | 2 man/apply_EfficiencyCorrection.Rd | 2 man/bin_RLum.Data.Rd | 2 man/calc_AliquotSize.Rd | 2 man/calc_AverageDose.Rd | 2 man/calc_CentralDose.Rd | 2 man/calc_CommonDose.Rd | 2 man/calc_CosmicDoseRate.Rd | 2 man/calc_FadingCorr.Rd | 2 man/calc_FastRatio.Rd | 2 man/calc_FiniteMixture.Rd | 2 man/calc_FuchsLang2001.Rd | 2 man/calc_HomogeneityTest.Rd | 2 man/calc_Huntley2006.Rd | 2 man/calc_IEU.Rd | 2 man/calc_Kars2008.Rd | 2 man/calc_Lamothe2003.Rd | 2 man/calc_MaxDose.Rd | 2 man/calc_MinDose.Rd | 2 man/calc_OSLLxTxRatio.Rd | 2 man/calc_SourceDoseRate.Rd | 2 man/calc_Statistics.Rd | 2 man/calc_TLLxTxRatio.Rd | 2 man/calc_ThermalLifetime.Rd | 2 man/calc_WodaFuchs2008.Rd | 2 man/calc_gSGC.Rd | 2 man/convert_Activity2Concentration.Rd | 2 man/convert_BIN2CSV.Rd | 2 man/convert_Daybreak2CSV.Rd | 2 man/convert_PSL2CSV.Rd | 2 man/convert_RLum2Risoe.BINfileData.Rd | 2 man/convert_Wavelength2Energy.Rd | 2 man/convert_XSYG2CSV.Rd | 2 man/extract_IrradiationTimes.Rd | 2 man/fit_CWCurve.Rd | 2 man/fit_LMCurve.Rd | 2 man/fit_OSLLifeTimes.Rd | 2 man/fit_SurfaceExposure.Rd | 2 man/fit_ThermalQuenching.Rd | 2 man/get_Layout.Rd | 2 man/get_Quote.Rd | 2 man/get_RLum.Rd | 2 man/get_Risoe.BINfileData.Rd | 2 man/get_rightAnswer.Rd | 2 man/length_RLum.Rd | 2 man/merge_RLum.Analysis.Rd | 2 man/merge_RLum.Data.Curve.Rd | 2 man/merge_RLum.Rd | 2 man/merge_RLum.Results.Rd | 2 man/merge_Risoe.BINfileData.Rd | 2 man/names_RLum.Rd | 2 man/plot_AbanicoPlot.Rd | 2 man/plot_DRCSummary.Rd | 2 man/plot_DRTResults.Rd | 2 man/plot_DetPlot.Rd | 2 man/plot_FilterCombinations.Rd | 2 man/plot_GrowthCurve.Rd | 2 man/plot_Histogram.Rd | 2 man/plot_KDE.Rd | 2 man/plot_NRt.Rd | 2 man/plot_RLum.Analysis.Rd | 2 man/plot_RLum.Data.Curve.Rd | 2 man/plot_RLum.Data.Image.Rd | 2 man/plot_RLum.Data.Spectrum.Rd | 2 man/plot_RLum.Rd | 2 man/plot_RLum.Results.Rd | 2 man/plot_RadialPlot.Rd | 2 man/plot_Risoe.BINfileData.Rd | 2 man/plot_ViolinPlot.Rd | 2 man/read_BIN2R.Rd | 2 man/read_Daybreak2R.Rd | 2 man/read_PSL2R.Rd | 2 man/read_SPE2R.Rd | 2 man/read_XSYG2R.Rd | 2 man/replicate_RLum.Rd | 2 man/report_RLum.Rd | 2 man/sTeve.Rd | 2 man/scale_GammaDose.Rd | 2 man/set_RLum.Rd | 2 man/set_Risoe.BINfileData.Rd | 2 man/smooth_RLum.Rd | 2 man/structure_RLum.Rd | 2 man/template_DRAC.Rd | 2 man/tune_Data.Rd | 2 man/use_DRAC.Rd | 2 man/verify_SingleGrainData.Rd | 2 man/write_R2BIN.Rd | 2 man/write_RLum2CSV.Rd | 2 120 files changed, 249 insertions(+), 245 deletions(-)
Title: Multiple Testing Methods for Exploratory Research
Description: Provides an alternative approach to multiple testing
by calculating a simultaneous upper confidence bounds for the
number of true null hypotheses among any subset of the hypotheses of interest,
using the methods of Goeman and Solari (2011) <doi:10.1214/11-STS356>.
Author: Jelle Goeman, Aldo Solari, Rosa Meijer
Maintainer: Jelle Goeman <j.j.goeman@lumc.nl>
Diff between cherry versions 0.6-12 dated 2018-01-29 and 0.6-13 dated 2019-09-20
cherry-0.6-12/cherry/man/hommel-class.Rd |only cherry-0.6-13/cherry/ChangeLog | 3 + cherry-0.6-13/cherry/DESCRIPTION | 10 ++-- cherry-0.6-13/cherry/MD5 | 15 ++---- cherry-0.6-13/cherry/NAMESPACE | 4 + cherry-0.6-13/cherry/R/shortcuts.R | 74 ++++++++++++++++++++++++++----- cherry-0.6-13/cherry/build/vignette.rds |binary cherry-0.6-13/cherry/inst/doc/cherry.pdf |binary cherry-0.6-13/cherry/man/hommelFast.Rd | 8 +-- 9 files changed, 86 insertions(+), 28 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 2.0.2 dated 2019-07-24 and 2.0.3 dated 2019-09-20
DESCRIPTION | 11 MD5 | 136 - NEWS.md | 20 R/class_analysis_dataset.R | 659 +++++--- R/class_analysis_stage_results.R | 272 +++ R/class_core_parameter_set.R | 398 ++++ R/class_core_plot_settings.R | 20 R/class_design.R | 177 +- R/class_design_plan.R | 225 +- R/class_design_power_and_asn.R | 1 R/class_design_set.R | 42 R/class_simulation_results.R | 9 R/class_time.R | 22 R/f_analysis.R | 54 R/f_analysis_means.R | 61 R/f_analysis_means_multiarmed.R |only R/f_analysis_rates.R | 40 R/f_analysis_survival.R | 21 R/f_core_assertions.R | 180 +- R/f_core_constants.R | 60 R/f_core_output_formats.R | 4 R/f_core_plot.R | 68 R/f_core_utilities.R | 31 R/f_design_fisher_combination_test.R | 21 R/f_design_group_sequential.R | 71 R/f_design_sample_size_calculator.R | 151 + R/f_design_utilities.R | 213 ++ R/f_simulation_means.R | 2 R/f_simulation_rates.R | 2 R/f_simulation_survival.R | 2 R/pkgname.R | 2 README.md | 12 inst/tests/testthat/test-class_analysis_dataset.R | 204 -- inst/tests/testthat/test-class_time.R | 2 inst/tests/testthat/test-f_analysis_means.R | 50 inst/tests/testthat/test-f_analysis_rates.R | 2 inst/tests/testthat/test-f_analysis_survival.R | 2 inst/tests/testthat/test-f_core_assertions.R | 3 inst/tests/testthat/test-f_core_output_formats.R | 2 inst/tests/testthat/test-f_core_utilities.R | 11 inst/tests/testthat/test-f_design_fisher_combination_test.R | 2 inst/tests/testthat/test-f_design_group_sequential_design.R | 2 inst/tests/testthat/test-f_design_power_calculator.R | 92 - inst/tests/testthat/test-f_design_sample_size_calculator.R | 297 +-- inst/tests/testthat/test-f_design_utilities.R | 971 +++++++++++- inst/tests/testthat/test-f_simulation_means.R | 44 inst/tests/testthat/test-f_simulation_rates.R | 33 inst/tests/testthat/test-f_simulation_survival.R | 127 - man/ParameterSet_summary.Rd | 2 man/TrialDesignConditionalDunnett.Rd |only man/TrialDesignPlanSurvival_summary.Rd | 2 man/getPowerMeans.Rd | 2 man/getPowerSurvival.Rd | 2 man/plot.StageResults.Rd | 3 tests/testthat/test-class_analysis_dataset.R | 204 -- tests/testthat/test-class_time.R | 2 tests/testthat/test-f_analysis_means.R | 50 tests/testthat/test-f_analysis_rates.R | 2 tests/testthat/test-f_analysis_survival.R | 2 tests/testthat/test-f_core_assertions.R | 3 tests/testthat/test-f_core_output_formats.R | 2 tests/testthat/test-f_core_utilities.R | 11 tests/testthat/test-f_design_fisher_combination_test.R | 2 tests/testthat/test-f_design_group_sequential_design.R | 2 tests/testthat/test-f_design_power_calculator.R | 92 - tests/testthat/test-f_design_sample_size_calculator.R | 297 +-- tests/testthat/test-f_design_utilities.R | 971 +++++++++++- tests/testthat/test-f_simulation_means.R | 44 tests/testthat/test-f_simulation_rates.R | 33 tests/testthat/test-f_simulation_survival.R | 127 - 70 files changed, 4842 insertions(+), 1844 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward' and 'stepwise' steps. Procedure can use Akaike information criterion, corrected Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, corrected Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria. Multicollinearity detection in regression model are performed by checking tolerance value. Continuous variables nested within class effect and weighted stepwise regression are also considered in this package.
Author: Junhui Li,Xiaohuan Lu,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.2.0 dated 2019-05-31 and 1.2.1 dated 2019-09-20
StepReg-1.2.0/StepReg/man/optimization.Rd |only StepReg-1.2.1/StepReg/DESCRIPTION | 10 - StepReg-1.2.1/StepReg/MD5 | 18 +-- StepReg-1.2.1/StepReg/NAMESPACE | 2 StepReg-1.2.1/StepReg/R/RcppExports.R | 4 StepReg-1.2.1/StepReg/R/stepwise.R | 69 ++++++++++--- StepReg-1.2.1/StepReg/man/StepReg-package.Rd | 4 StepReg-1.2.1/StepReg/man/stepOne.Rd |only StepReg-1.2.1/StepReg/man/stepwise.Rd | 4 StepReg-1.2.1/StepReg/src/RcppExports.cpp | 10 - StepReg-1.2.1/StepReg/src/Rcppeigen_StepwiseRegression.cpp | 14 +- 11 files changed, 87 insertions(+), 48 deletions(-)
Title: Sample Size Calculation for the Comparison of Means or
Proportions in Phase III Clinical Trials
Description: There are four categories of Phase III clinical trials according to different research goals, including (1) Testing for equality, (2) Superiority trial, (3) Non-inferiority trial, and (4) Equivalence trial. This package aims to help researchers to calculate sample size when comparing means or proportions in Phase III clinical trials with different research goals. The ssc function can calculate the sample size with pre-specified type I error rate, statistical power and effect size.
Author: Hongchao Qi, Fang Zhu
Maintainer: Hongchao Qi <hcqi0086@gmail.com>
Diff between SampleSize4ClinicalTrials versions 0.1.0 dated 2017-09-17 and 0.1.1 dated 2019-09-20
DESCRIPTION | 19 +++++------ MD5 | 8 +++- R/SampleSize4ClinicalTrials.R | 64 +++++++++++++++++---------------------- R/manual_namespace_gen.R |only man/SampleSize4ClinicalTrials.Rd |only man/ssc.Rd | 36 ++++++++++----------- 6 files changed, 61 insertions(+), 66 deletions(-)
More information about SampleSize4ClinicalTrials at CRAN
Permanent link
Title: Network Analysis and Visualization
Description: Collection of functions for fast manipulation, handling, and analysis of large-scale
networks based on family and social data. Functions are utility functions used to manipulate data
in three "formats": sparse adjacency matrices, pedigree trio family data, and pedigree family data.
When possible, the functions should be able to handle millions of data points quickly for use in combination
with data from large public national registers and databases.
Kenneth Lange (2003, ISBN:978-8181281135).
Author: Claus Thorn Ekstrøm [aut, cre],
Bendix Carstensen [ctb]
Maintainer: Claus Thorn Ekstrøm <ekstrom@sund.ku.dk>
Diff between networkR versions 0.1.0-0 dated 2018-01-29 and 0.1.2 dated 2019-09-20
networkR-0.1.0-0/networkR/man/kinship.Rd |only networkR-0.1.0-0/networkR/src/kinship_fam.cpp |only networkR-0.1.2/networkR/DESCRIPTION | 13 ++++++------- networkR-0.1.2/networkR/MD5 | 12 +++++------- networkR-0.1.2/networkR/NAMESPACE | 1 - networkR-0.1.2/networkR/R/RcppExports.R | 21 --------------------- networkR-0.1.2/networkR/src/RcppExports.cpp | 22 ++++------------------ networkR-0.1.2/networkR/src/cluster_fam.cpp | 21 +++++++++++---------- 8 files changed, 26 insertions(+), 64 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-28 dated 2019-03-21 and 1.8-29 dated 2019-09-20
ChangeLog | 44 + DESCRIPTION | 6 MD5 | 117 ++--- NAMESPACE | 14 R/bam.r | 513 +++++++++++++--------- R/coxph.r | 50 -- R/efam.r | 25 - R/fast-REML.r | 379 ++++++++++++++-- R/gam.fit3.r | 24 - R/gam.fit4.r | 42 + R/gamlss.r | 757 +++++++++++++++++++++++++++------ R/gamm.r | 80 +-- R/mgcv.r | 98 ++-- R/misc.r | 145 +++++- R/mvam.r | 43 - R/plots.r | 2 R/smooth.r | 13 inst/po/de/LC_MESSAGES/R-mgcv.mo |binary inst/po/de/LC_MESSAGES/mgcv.mo |binary inst/po/en@quot/LC_MESSAGES/R-mgcv.mo |binary inst/po/en@quot/LC_MESSAGES/mgcv.mo |binary inst/po/fr/LC_MESSAGES/R-mgcv.mo |binary inst/po/fr/LC_MESSAGES/mgcv.mo |binary inst/po/ko/LC_MESSAGES/R-mgcv.mo |binary inst/po/ko/LC_MESSAGES/mgcv.mo |binary inst/po/pl/LC_MESSAGES/R-mgcv.mo |binary inst/po/pl/LC_MESSAGES/mgcv.mo |binary man/Sl.initial.repara.Rd | 11 man/Sl.setup.Rd | 3 man/XWXd.Rd |only man/blas.thread.test.Rd |only man/formula.gam.Rd | 2 man/gam.Rd | 4 man/gamm.Rd | 2 man/gammals.Rd |only man/ldetS.Rd | 2 man/missing.data.Rd | 2 man/predict.bam.Rd | 3 man/predict.gam.Rd | 7 man/random.effects.Rd | 12 man/smooth.construct.re.smooth.spec.Rd | 2 man/tensor.prod.model.matrix.Rd | 11 po/R-de.po | 108 +++- po/R-fr.po | 68 ++ po/R-ko.po | 72 ++- po/R-mgcv.pot | 64 ++ po/R-pl.po | 99 ++++ po/de.po | 6 po/fr.po | 6 po/ko.po | 6 po/mgcv.pot | 8 po/pl.po | 6 src/discrete.c | 577 +++++++++++++++++++++++-- src/gdi.c | 10 src/init.c | 7 src/mat.c | 146 +++--- src/mgcv.c | 2 src/mgcv.h | 50 +- src/misc.c | 8 src/mvn.c | 6 src/tprs.c | 6 61 files changed, 2815 insertions(+), 853 deletions(-)
Title: A Parallelized Algorithm for Least-Squares Curve Fitting
Description: This algorithm provides a numerical solution to the
problem of minimizing (or maximizing) a function. This is more efficient than
the Gauss-Newton-like algorithm when starting from points very
far from the final minimum (or maximum). A new convergence test is
implemented (RDM) in addition to the usual stopping criterion :
stopping rule is when the gradients are small enough in the
parameters metric (GH-1G).
Author: Melanie Prague, Viviane Philipps, Cecile Proust-Lima, Boris Hejblum, Daniel Commenges, Amadou Diakite
Maintainer: Viviane Philipps <viviane.philipps@u-bordeaux.fr>
Diff between marqLevAlg versions 1.1 dated 2013-03-18 and 2.0.1 dated 2019-09-20
marqLevAlg-1.1/marqLevAlg/R/firstlib.R |only marqLevAlg-2.0.1/marqLevAlg/DESCRIPTION | 27 - marqLevAlg-2.0.1/marqLevAlg/MD5 | 41 +- marqLevAlg-2.0.1/marqLevAlg/NAMESPACE | 22 + marqLevAlg-2.0.1/marqLevAlg/R/deriva.R | 144 ++++++-- marqLevAlg-2.0.1/marqLevAlg/R/deriva_grad.R | 75 +++- marqLevAlg-2.0.1/marqLevAlg/R/marqLevAlg-package.R |only marqLevAlg-2.0.1/marqLevAlg/R/marqLevAlg.R | 248 ++++++++++++-- marqLevAlg-2.0.1/marqLevAlg/R/print.marqLevAlg.R | 7 marqLevAlg-2.0.1/marqLevAlg/R/searpas.R | 24 - marqLevAlg-2.0.1/marqLevAlg/R/summary.marqLevAlg.R | 45 +- marqLevAlg-2.0.1/marqLevAlg/R/valfpa.R | 10 marqLevAlg-2.0.1/marqLevAlg/build |only marqLevAlg-2.0.1/marqLevAlg/man/ForInternalUse.Rd | 1 marqLevAlg-2.0.1/marqLevAlg/man/deriva.Rd | 92 ++--- marqLevAlg-2.0.1/marqLevAlg/man/deriva_grad.Rd |only marqLevAlg-2.0.1/marqLevAlg/man/marqLevAlg-package.Rd | 116 ++---- marqLevAlg-2.0.1/marqLevAlg/man/marqLevAlg.Rd | 305 ++++++++++-------- marqLevAlg-2.0.1/marqLevAlg/man/weib.Rd | 2 marqLevAlg-2.0.1/marqLevAlg/src/Makevars |only marqLevAlg-2.0.1/marqLevAlg/src/dchole.f90 | 220 ++++++------ marqLevAlg-2.0.1/marqLevAlg/src/dmfsd.f90 | 202 +++++------ marqLevAlg-2.0.1/marqLevAlg/src/dsinv.f90 | 264 +++++++-------- marqLevAlg-2.0.1/marqLevAlg/src/init.c |only marqLevAlg-2.0.1/marqLevAlg/src/marqLevAlg.h |only 25 files changed, 1090 insertions(+), 755 deletions(-)
More information about Copula.Markov.survival at CRAN
Permanent link
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.4.2 dated 2019-07-29 and 1.4.3 dated 2019-09-20
DESCRIPTION | 8 MD5 | 62 +- NAMESPACE | 5 R/RcppExports.R | 28 - R/auxiliary_routines.R | 20 R/fit_hbd_model_on_grid.R | 78 +-- R/fit_hbd_model_parametric.R | 109 ++-- R/fit_hbd_pdr_on_grid.R | 106 ++-- R/fit_hbd_pdr_parametric.R | 90 ++- R/fit_hbd_psr_on_grid.R | 64 +- R/generate_random_tree.R | 9 R/get_clade_list.R |only R/loglikelihood_hbd.R | 38 + R/read_tree.R | 17 R/simulate_deterministic_hbd.R | 40 - R/split_tree_at_height.R |only R/tree_from_branching_ages.R |only R/trim_tree_at_height.R | 8 R/write_tree.R | 13 man/fit_hbd_model_on_grid.Rd | 39 + man/fit_hbd_model_parametric.Rd | 58 +- man/fit_hbd_pdr_on_grid.Rd | 21 man/fit_hbd_pdr_parametric.Rd | 62 +- man/fit_hbd_psr_on_grid.Rd | 14 man/generate_random_tree.Rd | 4 man/get_clade_list.Rd |only man/loglikelihood_hbd.Rd | 24 man/read_tree.Rd | 27 - man/simulate_deterministic_hbd.Rd | 58 +- man/split_tree_at_height.Rd |only man/tree_from_branching_ages.Rd |only man/trim_tree_at_height.Rd | 5 man/write_tree.Rd | 28 - src/RcppExports.cpp | 98 +++ src/phylogenetics_cpp_routines.cpp | 917 ++++++++++++++++++++++++++++++++----- 35 files changed, 1571 insertions(+), 479 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tibbletime versions 0.1.2 dated 2019-02-11 and 0.1.3 dated 2019-09-20
DESCRIPTION | 14 +- MD5 | 40 +++--- NAMESPACE | 1 NEWS.md | 14 ++ R/aaa.R | 2 R/collapse_index.R | 4 R/compat-tidyr.R | 118 +++++++++++++++---- R/index-based-generics.R | 4 R/round-index.R | 4 R/seq.R | 2 R/to_posixct_numeric.R | 2 build/vignette.rds |binary inst/doc/TT-01-time-based-filtering.html | 9 - inst/doc/TT-02-changing-time-periods.html | 9 - inst/doc/TT-03-rollify-for-rolling-analysis.html | 139 ++++++++++++----------- inst/doc/TT-04-use-with-dplyr.html | 93 +++++++-------- tests/testthat/test_ceiling_index.R | 2 tests/testthat/test_coercion.R | 6 tests/testthat/test_collapse_index.R | 26 ++++ tests/testthat/test_compat-tidyr.R | 34 +++++ tests/testthat/test_floor_index.R | 2 21 files changed, 342 insertions(+), 183 deletions(-)
Title: Resampled Data Frames
Description: Create data frames with virtual groups that can be used with
'dplyr' to efficiently compute resampled statistics, generate the data for
hypothetical outcome plots, and fit multiple models on resampled variations
of the original data.
Author: Davis Vaughan [aut, cre]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between strapgod versions 0.0.3 dated 2019-07-18 and 0.0.4 dated 2019-09-20
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 13 +++++++++---- R/collect.R | 4 ++-- R/compat-tidyr.R | 5 +++-- R/samplify.R | 2 +- R/zzz.R | 7 ++++++- tests/testthat/test-bootstrapify.R | 19 ++++++++++++++++++- tests/testthat/test-collect.R | 2 ++ tests/testthat/test-compat-tidyr.R | 2 +- 11 files changed, 57 insertions(+), 26 deletions(-)
Title: Entropy-Based Segregation Indices
Description: Computes entropy-based segregation indices, as developed by
Theil (1971) <isbn:978-0471858454>, with a focus on
the Mutual Information Index (M) and Theil's Information Index (H).
The M, further described by Mora and Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x>
and Frankel and Volij (2011) <doi:10.1016/j.jet.2010.10.008>,
is a measure of segregation that is highly decomposable. The package provides
tools to decompose the index by units and groups (local segregation),
and by within and between terms.
Includes standard error estimation by bootstrapping.
Author: Benjamin Elbers [aut, cre] (<https://orcid.org/0000-0001-5392-3448>)
Maintainer: Benjamin Elbers <be2239@columbia.edu>
Diff between segregation versions 0.2.0 dated 2019-01-14 and 0.3.0 dated 2019-09-20
DESCRIPTION | 6 MD5 | 42 ++--- NEWS.md | 12 + R/ipf.R | 98 ++++++++---- R/mutual.R | 86 +++++----- R/mutual_difference.R | 103 +++++++++---- R/segregation.R | 43 +++-- README.md | 35 ++-- man/entropy.Rd | 3 man/ipf.Rd | 8 - man/mutual_difference.Rd | 29 ++- man/mutual_local.Rd | 17 +- man/mutual_total.Rd | 21 +- man/mutual_within.Rd | 15 - man/segregation.Rd | 2 tests/testthat/test_entropy.R | 2 tests/testthat/test_ipf.R | 76 ++++++--- tests/testthat/test_lintr.R | 6 tests/testthat/test_mutual_difference.R | 252 +++++++++++++++++++------------- tests/testthat/test_mutual_local.R | 48 +++--- tests/testthat/test_mutual_total.R | 75 ++++++--- tests/testthat/test_mutual_within.R | 51 ++++-- 22 files changed, 646 insertions(+), 384 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.19 dated 2019-04-26 and 0.2.20 dated 2019-09-20
DESCRIPTION | 13 ++++++------ MD5 | 42 ++++++++++++++++++++-------------------- NEWS | 11 ++++++++++ R/rglobi.R | 7 +----- build/vignette.rds |binary inst/doc/rglobi_vignette.Rmd | 4 +-- inst/doc/rglobi_vignette.html | 4 +-- man/get_child_taxa.Rd | 1 man/get_data_fields.Rd | 1 man/get_interaction_areas.Rd | 1 man/get_interaction_matrix.Rd | 1 man/get_interaction_table.Rd | 5 ++-- man/get_interaction_types.Rd | 1 man/get_interactions.Rd | 4 ++- man/get_interactions_by_taxa.Rd | 1 man/get_interactions_by_type.Rd | 1 man/get_interactions_in_area.Rd | 1 man/get_predators_of.Rd | 1 man/get_prey_of.Rd | 1 man/query.Rd | 2 - tests/testthat/test-globi.R | 4 +-- vignettes/rglobi_vignette.Rmd | 4 +-- 22 files changed, 66 insertions(+), 44 deletions(-)
Title: Quantitative Exploration of Elastic Net Families for Generalized
Linear Models
Description: Provides a quantitative toolkit to explore elastic net families and to uncover correlates contributing to prediction under a cross-validation framework. Fits linear, binomial (logistic), multinomial and Cox regression models. Candia J and Tsang JS, BMC Bioinformatics (2019) 20:189 <doi:10.1186/s12859-019-2778-5>.
Author: Julian Candia and John S. Tsang
Maintainer: Julian Candia <julian.candia@nih.gov>
Diff between eNetXplorer versions 1.0.2 dated 2019-04-17 and 1.1.0 dated 2019-09-20
ChangeLog | 9 ++ DESCRIPTION | 14 +-- MD5 | 67 +++++++++------- NAMESPACE | 4 R/eNetXplorer.R | 38 ++++++--- R/eNetXplorerBinomial.R | 33 ++++---- R/eNetXplorerCox.R |only R/eNetXplorerGaussian.R | 33 ++++---- R/eNetXplorerMultinomial.R | 38 +++++---- R/export.R | 153 ++++++++++++++++++++++++++++---------- R/plot.eNetXplorer.R | 19 ++++ R/plotContingency.R | 2 R/plotFeatureCaterpillar.R | 6 - R/plotFeatureHeatmap.R | 8 - R/plotKaplanMeier.R |only R/plotMeasuredVsOOB.R | 2 R/plotMeasuredVsOOBCateg.R | 2 R/plotSummary.R | 2 R/plotSurvROC.R |only R/summaryPDF.R | 17 +++- data/breastCancerSurv.RData |only inst/doc/eNetXplorer_vignette.pdf |binary man/H1N1_Flow.Rd | 4 man/breastCancerSurv.Rd |only man/eNetXplorer-internal.Rd | 7 + man/eNetXplorer-package.Rd | 10 +- man/eNetXplorer.Rd | 109 +++++++++++++++++++++------ man/export.Rd | 16 ++- man/plot.eNetXplorer.Rd | 22 +++-- man/plotContingency.Rd | 4 man/plotFeatureCaterpillar.Rd | 22 ++--- man/plotFeatureHeatmap.Rd | 34 ++++---- man/plotKaplanMeier.Rd |only man/plotLambdaVsQF.Rd | 5 - man/plotMeasuredVsOOB.Rd | 11 +- man/plotSummary.Rd | 6 - man/plotSurvROC.Rd |only man/summaryPDF.Rd | 9 +- 38 files changed, 472 insertions(+), 234 deletions(-)
Title: Diagnostics for Confounding of Time-Varying and Other Joint
Exposures
Description: Implements three covariate-balance diagnostics for time-varying confounding and selection-bias in complex longitudinal data, as described in Jackson (2016) <doi:10.1097/EDE.0000000000000547> and Jackson (2019) <doi:10.1093/aje/kwz136>. Diagnostic 1 assesses measured confounding/selection-bias, diagnostic 2 assesses exposure-covariate feedback, and diagnostic 3 assesses residual confounding/selection-bias after inverse probability weighting or propensity score stratification. All diagnostics appropriately account for exposure history, can be adapted to assess a particular depth of covariate history, and can be implemented in right-censored data. Balance assessments can be obtained for all times, selected-times, or averaged across person-time. The balance measures are reported as tables or plots. These diagnostics can be applied to the study of multivariate exposures including time-varying exposures, direct effects, interaction, and censoring.
Author: John W. Jackson [aut, cre],
Erin Schnellinger [ctb],
Linda Valeri [ctb]
Maintainer: John W. Jackson <john.jackson@jhu.edu>
Diff between confoundr versions 1.1 dated 2019-09-13 and 1.2 dated 2019-09-20
DESCRIPTION | 6 MD5 | 36 R/RFunctions_1_0_2.r | 61 README.md | 10 build/vignette.rds |binary data/datalist | 18 inst/doc/quickdemo.R | 252 +-- inst/doc/quickdemo.html | 697 ++++------ inst/doc/selectionbias.R | 910 +++++++------- inst/doc/selectionbias.html | 2841 ++++++++++++++++++++------------------------ man/apply.scope.Rd | 2 man/balance.Rd | 10 man/diagnose.Rd | 6 man/lengthen.Rd | 6 man/makehistory.one.Rd | 6 man/makehistory.two.Rd | 3 man/makeplot.Rd | 6 man/omit.history.Rd | 12 man/widen.Rd | 4 19 files changed, 2310 insertions(+), 2576 deletions(-)