Title: Provides Progress Bars in 'knitr'
Description: Provides a progress bar similar to 'dplyr' that can write progress out to a
variety of locations, including stdout(), stderr(), or from file(). Useful when using 'knitr' or 'rmarkdown',
and you still want to see progress of calculations in the terminal.
Author: Robert M Flight [aut, cre],
Hadley Wickham [ctb] (Author of included dplyr fragments),
Romain Francois [ctb] (Author of included dplyr fragments),
Lionel Henry [ctb] (Author of included dplyr fragments),
Kirill Müller [ctb] (Author of included dplyr fragments),
RStudio [cph] (Copyright holder of included dplyr fragments)
Maintainer: Robert M Flight <rflight79@gmail.com>
Diff between knitrProgressBar versions 1.0.0 dated 2018-02-09 and 1.1.0 dated 2018-02-19
DESCRIPTION | 9 MD5 | 22 +- NAMESPACE | 2 NEWS.md | 5 R/progress_mp.R |only README.md | 4 build/vignette.rds |binary inst/doc/example_progress_bars.html | 388 ++++++++++++++++++++++++------------ inst/doc/multiprocessing.R |only inst/doc/multiprocessing.Rmd |only inst/doc/multiprocessing.html |only man/set_progress_mp.Rd |only man/watch_progress_mp.Rd |only tests/testthat/test-kpb.R | 2 tests/testthat/test-multiprocess.R |only vignettes/multiprocessing.Rmd |only 16 files changed, 298 insertions(+), 134 deletions(-)
More information about knitrProgressBar at CRAN
Permanent link
Title: Plackett-Luce Models for Rankings
Description: Functions to prepare rankings data and fit the Plackett-Luce model
jointly attributed to Plackett (1975) <doi:10.2307/2346567> and Luce
(1959, ISBN:0486441369). The standard Plackett-Luce model is generalized
to accommodate ties of any order in the ranking. Partial rankings, in which
only a subset of items are ranked in each ranking, are also accommodated in
the implementation. Disconnected/weakly connected networks implied by the
rankings are handled by adding pseudo-rankings with a hypothetical item.
Methods are provided to estimate standard errors or quasi-standard errors
for inference as well as to fit Plackett-Luce trees. See the package website
or vignette for full details.
Author: Heather Turner [aut, cre],
Ioannis Kosmidis [aut],
David Firth [aut],
Jacob van Etten [ctb]
Maintainer: Heather Turner <ht@heatherturner.net>
Diff between PlackettLuce versions 0.2-1 dated 2017-12-07 and 0.2-2 dated 2018-02-19
DESCRIPTION | 6 MD5 | 58 - NAMESPACE | 13 NEWS.md | 15 R/PlackettLuce.R | 70 - R/choices.R | 3 R/coef.R | 18 R/fitted.R | 9 R/itempar.R | 2 R/plfit.R | 2 R/pltree.R | 93 + R/simulate.R |only R/utility.R | 34 README.md | 11 inst/PlackettLuce0/fitted0.R | 3 inst/WORDLIST | 7 inst/doc/Overview.R | 54 - inst/doc/Overview.Rmd | 1837 +++++++++++++++++------------------ inst/doc/Overview.html | 508 ++------- man/PlackettLuce.Rd | 8 man/figures/always-loses-1.png |binary man/figures/qv-1.png |binary man/fitted.PlackettLuce.Rd | 14 man/plfit.Rd | 2 man/pltree.Rd | 15 man/simulate.PlackettLuce.Rd |only tests/testthat/test-log-likelihood.R | 1 tests/testthat/test-pseudo.R | 9 tests/testthat/test-psycho.R | 57 + tests/testthat/test-simulate.R |only tests/testthat/test-start.R |only vignettes/Overview.Rmd | 1837 +++++++++++++++++------------------ 32 files changed, 2399 insertions(+), 2287 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Claus Thorn Ekstrøm [ctb],
Dawei Lang [ctb],
Garrick Aden-Buie [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Sean Lopp [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.5 dated 2018-01-29 and 0.6 dated 2018-02-19
DESCRIPTION | 9 ++++++--- MD5 | 6 ++++-- R/render.R | 2 +- inst/examples |only inst/rmarkdown/templates/xaringan/resources/hygge.css |only 5 files changed, 11 insertions(+), 6 deletions(-)
Title: Wrapper for 'GDAX' Cryptocurrency Exchange
Description: Allow access to both public and private end points to 'GDAX' cryptocurrency exchange.
For authenticated flow, users must have valid api, secret and passphrase to be able to connect.
Read more details on getting access to 'GDAX' API at:
<https://support.gdax.com/customer/en/portal/articles/2425383-how-can-i-create-an-api-key-for-gdax->.
Author: person("Dheeraj", "Agarwal", email = "dheeeraj.agarwal@gmail.com",
role = c("aut", "cre"))
Maintainer: Dheeraj Agarwal <dheeeraj.agarwal@gmail.com>
Diff between rgdax versions 0.3.0 dated 2018-02-18 and 0.4.0 dated 2018-02-19
DESCRIPTION | 6 +-- MD5 | 78 ++++++++++++++++++++++++------------------------ NEWS.md | 6 +++ R/account.R | 2 - R/account_hist.R | 2 - R/accounts.R | 2 - R/add_order.R | 2 - R/auth.R | 2 - R/cancel_order.R | 6 +-- R/fills.R | 2 - R/holds.R | 2 - R/parse_response.R | 2 - R/profile.R | 2 - R/public_candles.R | 4 +- R/public_daystats.R | 2 - R/public_info.R | 2 - R/public_orderbook.R | 7 ---- R/public_ticker.R | 4 +- R/public_time.R | 2 - R/public_trades.R | 4 +- R/pymt_methods.R | 2 - README.md | 2 - man/account.Rd | 2 - man/account_hist.Rd | 2 - man/accounts.Rd | 2 - man/add_order.Rd | 2 - man/auth.Rd | 2 - man/cancel_order.Rd | 6 +-- man/fills.Rd | 2 - man/holds.Rd | 2 - man/parse_response.Rd | 2 - man/profile.Rd | 2 - man/public_candles.Rd | 4 +- man/public_daystats.Rd | 2 - man/public_info.Rd | 2 - man/public_orderbook.Rd | 2 - man/public_ticker.Rd | 4 +- man/public_time.Rd | 2 - man/public_trades.Rd | 4 +- man/pymt_methods.Rd | 2 - 40 files changed, 95 insertions(+), 94 deletions(-)
Title: Multivariate Synthetic Control Method Using Time Series
Description: Three generalizations of the synthetic control method (which has
already an implementation in package 'Synth') are implemented: first,
'MSCMT' allows for using multiple outcome variables, second, time series
can be supplied as economic predictors, and third, a well-defined
cross-validation approach can be used.
Much effort has been taken to make the implementation as stable as possible
(including edge cases) without losing computational efficiency.
A detailed description of the main algorithms is given in
Becker and Klößner (2018) <doi:10.1016/j.ecosta.2017.08.002>.
Author: Martin Becker [aut, cre] (<https://orcid.org/0000-0003-2336-9751>),
Stefan Klößner [aut],
Karline Soetaert [com],
LAPACK authors [cph]
Maintainer: Martin Becker <martin.becker@mx.uni-saarland.de>
Diff between MSCMT versions 1.3.1 dated 2018-01-04 and 1.3.2 dated 2018-02-19
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 13 +++++++++++++ R/mscmt.r | 21 +++++++++++++++++++-- R/prepare.r | 14 +++++++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/WorkingWithMSCMT.html | 24 ++++++++++++------------ man/MSCMTfunction.Rd | 3 +++ 9 files changed, 68 insertions(+), 31 deletions(-)
Title: Text Mining using 'dplyr', 'ggplot2', and Other Tidy Tools
Description: Text mining for word processing and sentiment analysis using
'dplyr', 'ggplot2', and other tidy tools.
Author: Gabriela De Queiroz [ctb],
Oliver Keyes [ctb],
David Robinson [aut],
Julia Silge [aut, cre]
Maintainer: Julia Silge <julia.silge@gmail.com>
Diff between tidytext versions 0.1.6 dated 2018-01-07 and 0.1.7 dated 2018-02-19
DESCRIPTION | 6 +- MD5 | 26 +++++----- NEWS.md | 4 + R/parts_of_speech.R | 4 + README.md | 9 ++- inst/doc/tf_idf.html | 14 ++--- inst/doc/tidying_casting.html | 84 +++++++++++++++++------------------ inst/doc/tidytext.html | 22 ++++----- inst/doc/topic_modeling.html | 12 ++--- man/parts_of_speech.Rd | 5 ++ tests/testthat/test-sparse-casters.R | 2 tests/testthat/test-stm-tidiers.R | 1 tools/README-unnamed-chunk-13-1.png |binary tools/README-unnamed-chunk-9-1.png |binary 14 files changed, 102 insertions(+), 87 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 0.5.3 dated 2017-08-03 and 0.5.4 dated 2018-02-19
tidyquant-0.5.3/tidyquant/R/as_tibble.R |only tidyquant-0.5.3/tidyquant/R/as_xts.R |only tidyquant-0.5.3/tidyquant/man/as_tibble.Rd |only tidyquant-0.5.3/tidyquant/man/as_xts.Rd |only tidyquant-0.5.3/tidyquant/tests/testthat/test_as_tibble.R |only tidyquant-0.5.3/tidyquant/tests/testthat/test_as_xts.R |only tidyquant-0.5.4/tidyquant/DESCRIPTION | 27 tidyquant-0.5.4/tidyquant/LICENSE | 4 tidyquant-0.5.4/tidyquant/MD5 | 174 tidyquant-0.5.4/tidyquant/NAMESPACE | 175 tidyquant-0.5.4/tidyquant/NEWS.md | 222 - tidyquant-0.5.4/tidyquant/R/alphavantager.R |only tidyquant-0.5.4/tidyquant/R/coord_date.R | 156 tidyquant-0.5.4/tidyquant/R/data.R | 38 tidyquant-0.5.4/tidyquant/R/deprecated.R | 74 tidyquant-0.5.4/tidyquant/R/geom_bbands.R | 658 +-- tidyquant-0.5.4/tidyquant/R/geom_chart.R | 466 +- tidyquant-0.5.4/tidyquant/R/geom_ma.R | 488 +- tidyquant-0.5.4/tidyquant/R/global_vars.R | 258 - tidyquant-0.5.4/tidyquant/R/quandl.R | 124 tidyquant-0.5.4/tidyquant/R/scale_manual.R | 292 - tidyquant-0.5.4/tidyquant/R/theme_tq.R | 286 - tidyquant-0.5.4/tidyquant/R/tidyquant.R | 88 tidyquant-0.5.4/tidyquant/R/tq_get.R | 1959 ++++----- tidyquant-0.5.4/tidyquant/R/tq_mutate.R | 814 +-- tidyquant-0.5.4/tidyquant/R/tq_performance.R | 632 +-- tidyquant-0.5.4/tidyquant/R/tq_portfolio.R | 888 ++-- tidyquant-0.5.4/tidyquant/R/tq_stock_list.R | 668 +-- tidyquant-0.5.4/tidyquant/R/tq_transmute.R | 786 +-- tidyquant-0.5.4/tidyquant/R/utils-dates.R | 58 tidyquant-0.5.4/tidyquant/R/utils-formatting.R | 98 tidyquant-0.5.4/tidyquant/README.md | 173 tidyquant-0.5.4/tidyquant/build/vignette.rds |binary tidyquant-0.5.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.R | 60 tidyquant-0.5.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.Rmd | 246 - tidyquant-0.5.4/tidyquant/inst/doc/TQ00-introduction-to-tidyquant.html | 270 - tidyquant-0.5.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.R | 400 - tidyquant-0.5.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 962 ++-- tidyquant-0.5.4/tidyquant/inst/doc/TQ01-core-functions-in-tidyquant.html | 1417 +++--- tidyquant-0.5.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.R | 602 +- tidyquant-0.5.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.Rmd | 1106 ++--- tidyquant-0.5.4/tidyquant/inst/doc/TQ02-quant-integrations-in-tidyquant.html | 1544 +++---- tidyquant-0.5.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.R | 280 - tidyquant-0.5.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 652 +-- tidyquant-0.5.4/tidyquant/inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 980 ++-- tidyquant-0.5.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.R | 558 +- tidyquant-0.5.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.Rmd | 960 ++-- tidyquant-0.5.4/tidyquant/inst/doc/TQ04-charting-with-tidyquant.html | 992 ++-- tidyquant-0.5.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.R | 700 +-- tidyquant-0.5.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 1388 +++--- tidyquant-0.5.4/tidyquant/inst/doc/TQ05-performance-analysis-with-tidyquant.html | 2104 ++++------ tidyquant-0.5.4/tidyquant/man/FANG.Rd | 58 tidyquant-0.5.4/tidyquant/man/av_api_key.Rd |only tidyquant-0.5.4/tidyquant/man/coord_x_date.Rd | 136 tidyquant-0.5.4/tidyquant/man/deprecated.Rd | 86 tidyquant-0.5.4/tidyquant/man/geom_bbands.Rd | 342 - tidyquant-0.5.4/tidyquant/man/geom_chart.Rd | 248 - tidyquant-0.5.4/tidyquant/man/geom_ma.Rd | 290 - tidyquant-0.5.4/tidyquant/man/palette_tq.Rd | 46 tidyquant-0.5.4/tidyquant/man/quandl_api_key.Rd | 60 tidyquant-0.5.4/tidyquant/man/quandl_search.Rd | 72 tidyquant-0.5.4/tidyquant/man/scale_manual.Rd | 117 tidyquant-0.5.4/tidyquant/man/theme_tq.Rd | 98 tidyquant-0.5.4/tidyquant/man/tidyquant.Rd | 66 tidyquant-0.5.4/tidyquant/man/tq_get.Rd | 263 - tidyquant-0.5.4/tidyquant/man/tq_mutate.Rd | 314 - tidyquant-0.5.4/tidyquant/man/tq_performance.Rd | 206 tidyquant-0.5.4/tidyquant/man/tq_portfolio.Rd | 276 - tidyquant-0.5.4/tidyquant/man/tq_stock_list.Rd | 142 tidyquant-0.5.4/tidyquant/tests/testthat.R | 8 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_exchange.R | 68 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_compound_getters.R | 152 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_dividends.R | 56 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_economic_data.R | 72 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_exchange_rates.R | 50 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_financials.R | 68 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_key_ratios.R | 68 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_key_stats.R | 62 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_metal_prices.R | 70 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_splits.R | 56 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_get_stock_prices.R | 90 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_index.R | 98 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_mutate.R | 395 - tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_performance.R | 114 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_portfolio.R | 152 tidyquant-0.5.4/tidyquant/tests/testthat/test_tq_transmute.R | 353 - tidyquant-0.5.4/tidyquant/vignettes/TQ00-introduction-to-tidyquant.Rmd | 246 - tidyquant-0.5.4/tidyquant/vignettes/TQ01-core-functions-in-tidyquant.Rmd | 962 ++-- tidyquant-0.5.4/tidyquant/vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 1106 ++--- tidyquant-0.5.4/tidyquant/vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 652 +-- tidyquant-0.5.4/tidyquant/vignettes/TQ04-charting-with-tidyquant.Rmd | 960 ++-- tidyquant-0.5.4/tidyquant/vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 1388 +++--- 92 files changed, 17570 insertions(+), 17323 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around the
fantastic 'stringi' package. All function and argument names (and positions)
are consistent, all functions deal with "NA"'s and zero length vectors
in the same way, and the output from one function is easy to feed into
the input of another.
Author: Hadley Wickham [aut, cre, cph],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between stringr versions 1.2.0 dated 2017-02-18 and 1.3.0 dated 2018-02-19
stringr-1.2.0/stringr/R/pad-trim.r |only stringr-1.2.0/stringr/man/modifier-deprecated.Rd |only stringr-1.3.0/stringr/DESCRIPTION | 26 stringr-1.3.0/stringr/MD5 | 154 +- stringr-1.3.0/stringr/NAMESPACE | 9 stringr-1.3.0/stringr/NEWS.md | 42 stringr-1.3.0/stringr/R/c.r | 28 stringr-1.3.0/stringr/R/conv.R | 2 stringr-1.3.0/stringr/R/count.r | 6 stringr-1.3.0/stringr/R/data.R | 4 stringr-1.3.0/stringr/R/detect.r | 21 stringr-1.3.0/stringr/R/dup.r | 2 stringr-1.3.0/stringr/R/extract.r | 10 stringr-1.3.0/stringr/R/flatten.R |only stringr-1.3.0/stringr/R/glue.R |only stringr-1.3.0/stringr/R/interp.R | 27 stringr-1.3.0/stringr/R/length.r | 2 stringr-1.3.0/stringr/R/locate.r | 14 stringr-1.3.0/stringr/R/match.r | 12 stringr-1.3.0/stringr/R/modifiers.r | 67 - stringr-1.3.0/stringr/R/pad.r |only stringr-1.3.0/stringr/R/remove.r |only stringr-1.3.0/stringr/R/replace.r | 45 stringr-1.3.0/stringr/R/sort.R | 14 stringr-1.3.0/stringr/R/split.r | 10 stringr-1.3.0/stringr/R/sub.r | 31 stringr-1.3.0/stringr/R/subset.R | 14 stringr-1.3.0/stringr/R/trim.R |only stringr-1.3.0/stringr/R/trunc.R |only stringr-1.3.0/stringr/R/view.R | 8 stringr-1.3.0/stringr/R/word.r | 3 stringr-1.3.0/stringr/R/wrap.r | 2 stringr-1.3.0/stringr/README.md | 10 stringr-1.3.0/stringr/build/vignette.rds |binary stringr-1.3.0/stringr/inst/doc/regular-expressions.Rmd | 18 stringr-1.3.0/stringr/inst/doc/regular-expressions.html | 596 +++++++--- stringr-1.3.0/stringr/inst/doc/stringr.R | 2 stringr-1.3.0/stringr/inst/doc/stringr.Rmd | 50 stringr-1.3.0/stringr/inst/doc/stringr.html | 708 ++++++++----- stringr-1.3.0/stringr/man/figures |only stringr-1.3.0/stringr/man/invert_match.Rd | 2 stringr-1.3.0/stringr/man/modifiers.Rd | 20 stringr-1.3.0/stringr/man/str_c.Rd | 21 stringr-1.3.0/stringr/man/str_conv.Rd | 2 stringr-1.3.0/stringr/man/str_count.Rd | 30 stringr-1.3.0/stringr/man/str_detect.Rd | 26 stringr-1.3.0/stringr/man/str_extract.Rd | 28 stringr-1.3.0/stringr/man/str_flatten.Rd |only stringr-1.3.0/stringr/man/str_glue.Rd |only stringr-1.3.0/stringr/man/str_interp.Rd | 9 stringr-1.3.0/stringr/man/str_length.Rd | 4 stringr-1.3.0/stringr/man/str_locate.Rd | 32 stringr-1.3.0/stringr/man/str_match.Rd | 12 stringr-1.3.0/stringr/man/str_order.Rd | 4 stringr-1.3.0/stringr/man/str_pad.Rd | 6 stringr-1.3.0/stringr/man/str_remove.Rd |only stringr-1.3.0/stringr/man/str_replace.Rd | 59 - stringr-1.3.0/stringr/man/str_split.Rd | 34 stringr-1.3.0/stringr/man/str_sub.Rd | 26 stringr-1.3.0/stringr/man/str_subset.Rd | 28 stringr-1.3.0/stringr/man/str_trim.Rd | 15 stringr-1.3.0/stringr/man/str_trunc.Rd | 4 stringr-1.3.0/stringr/man/str_view.Rd | 20 stringr-1.3.0/stringr/man/str_wrap.Rd | 2 stringr-1.3.0/stringr/man/stringr-package.Rd | 2 stringr-1.3.0/stringr/man/word.Rd | 2 stringr-1.3.0/stringr/tests/testthat/test-case.R |only stringr-1.3.0/stringr/tests/testthat/test-conv.R |only stringr-1.3.0/stringr/tests/testthat/test-detect.r | 1 stringr-1.3.0/stringr/tests/testthat/test-extract.r | 8 stringr-1.3.0/stringr/tests/testthat/test-flatten.R |only stringr-1.3.0/stringr/tests/testthat/test-glue.R |only stringr-1.3.0/stringr/tests/testthat/test-interp.r | 4 stringr-1.3.0/stringr/tests/testthat/test-match.r | 11 stringr-1.3.0/stringr/tests/testthat/test-modifiers.r |only stringr-1.3.0/stringr/tests/testthat/test-remove.r |only stringr-1.3.0/stringr/tests/testthat/test-replace.r | 12 stringr-1.3.0/stringr/tests/testthat/test-sort.R |only stringr-1.3.0/stringr/tests/testthat/test-sub.r | 9 stringr-1.3.0/stringr/tests/testthat/test-subset.r | 6 stringr-1.3.0/stringr/tests/testthat/test-trim.r | 6 stringr-1.3.0/stringr/tests/testthat/test-trunc.r |only stringr-1.3.0/stringr/tests/testthat/test-view.R |only stringr-1.3.0/stringr/tests/testthat/test-wrap.r | 8 stringr-1.3.0/stringr/vignettes/regular-expressions.Rmd | 18 stringr-1.3.0/stringr/vignettes/releases/stringr-1.0.0.Rmd | 1 stringr-1.3.0/stringr/vignettes/releases/stringr-1.1.0.Rmd | 1 stringr-1.3.0/stringr/vignettes/releases/stringr-1.2.0.Rmd |only stringr-1.3.0/stringr/vignettes/stringr.Rmd | 50 89 files changed, 1481 insertions(+), 979 deletions(-)
Title: Tools for Analyzing QTL Experiments
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman <kbroman@biostat.wisc.edu> and Hao Wu, with
ideas from Gary Churchill and Saunak Sen and contributions from
Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr
Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron
Wolen, and Brian Yandell
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between qtl versions 1.42-7 dated 2018-02-18 and 1.42-8 dated 2018-02-19
DESCRIPTION | 9 +++---- MD5 | 16 ++++++------ R/scantwo.R | 3 -- R/util.R | 63 ++++++++++++++++++++++++------------------------- inst/INSTALL_ME.txt | 12 ++++----- inst/STATUS.txt | 5 +++ inst/doc/bcsft.pdf |binary inst/doc/rqtltour.pdf |binary inst/doc/rqtltour2.pdf |binary 9 files changed, 55 insertions(+), 53 deletions(-)
Title: EDGE Taxonomy Assignments Visualization
Description: Implements routines for metagenome sample taxonomy assignments collection,
aggregation, and visualization. Accepts the EDGE-formatted output from GOTTCHA/GOTTCHA2,
BWA, Kraken, MetaPhlAn, DIAMOND, and Pangia. Produces SVG and PDF heatmap-like plots
comparing taxa abundances across projects.
Author: Pavel Senin [aut, cre]
Maintainer: Pavel Senin <senin@hawaii.edu>
Diff between MetaComp versions 1.0.1 dated 2017-03-02 and 1.1.1 dated 2018-02-19
MetaComp-1.0.1/MetaComp/R/load_bwa_assignment.R |only MetaComp-1.0.1/MetaComp/R/load_bwa_assignments.R |only MetaComp-1.0.1/MetaComp/R/load_gottcha2_assignment.R |only MetaComp-1.0.1/MetaComp/R/load_gottcha2_assignments.R |only MetaComp-1.0.1/MetaComp/R/load_gottcha_assignment.R |only MetaComp-1.0.1/MetaComp/R/load_gottcha_assignments.R |only MetaComp-1.0.1/MetaComp/R/load_kraken_assignment.R |only MetaComp-1.0.1/MetaComp/R/load_kraken_assignments.R |only MetaComp-1.0.1/MetaComp/R/load_metaphlan_assignment.R |only MetaComp-1.0.1/MetaComp/R/load_metaphlan_assignments.R |only MetaComp-1.0.1/MetaComp/R/merge_bwa_assignments.R |only MetaComp-1.0.1/MetaComp/R/merge_bwa_assignments_counts.R |only MetaComp-1.0.1/MetaComp/R/merge_gottcha_assignments.R |only MetaComp-1.0.1/MetaComp/R/merge_gottcha_assignments_count.R |only MetaComp-1.0.1/MetaComp/R/merge_kraken_assignments.R |only MetaComp-1.0.1/MetaComp/R/merge_metaphlan_assignments.R |only MetaComp-1.0.1/MetaComp/R/plot_bwa_assignment.R |only MetaComp-1.0.1/MetaComp/R/plot_gottcha_assignment.R |only MetaComp-1.0.1/MetaComp/R/plot_kraken_assignment.R |only MetaComp-1.0.1/MetaComp/R/plot_metaphlan_assignment.R |only MetaComp-1.0.1/MetaComp/man/load_bwa_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/load_bwa_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/load_gottcha2_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/load_gottcha2_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/load_gottcha_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/load_gottcha_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/load_kraken_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/load_kraken_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/load_metaphlan_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/load_metaphlan_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/merge_bwa_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/merge_bwa_counts.Rd |only MetaComp-1.0.1/MetaComp/man/merge_gottcha_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/merge_gottcha_counts.Rd |only MetaComp-1.0.1/MetaComp/man/merge_kraken_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/merge_metaphlan_assignments.Rd |only MetaComp-1.0.1/MetaComp/man/plot_bwa_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/plot_gottcha_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/plot_kraken_assignment.Rd |only MetaComp-1.0.1/MetaComp/man/plot_metaphlan_assignment.Rd |only MetaComp-1.1.1/MetaComp/DESCRIPTION | 14 MetaComp-1.1.1/MetaComp/MD5 | 185 ++++++---- MetaComp-1.1.1/MetaComp/NAMESPACE | 27 - MetaComp-1.1.1/MetaComp/R/load_edge_assignment.R |only MetaComp-1.1.1/MetaComp/R/load_edge_assignments.R |only MetaComp-1.1.1/MetaComp/R/merge_edge_assignments.R |only MetaComp-1.1.1/MetaComp/R/merge_edge_counts.R |only MetaComp-1.1.1/MetaComp/R/plot_edge_assignment.R |only MetaComp-1.1.1/MetaComp/R/plot_merged_assignment.R | 42 ++ MetaComp-1.1.1/MetaComp/README.md | 16 MetaComp-1.1.1/MetaComp/inst |only MetaComp-1.1.1/MetaComp/man/load_edge_assignment.Rd |only MetaComp-1.1.1/MetaComp/man/load_edge_assignments.Rd |only MetaComp-1.1.1/MetaComp/man/merge_edge_assignments.Rd |only MetaComp-1.1.1/MetaComp/man/merge_edge_counts.Rd |only MetaComp-1.1.1/MetaComp/man/plot_edge_assignment.Rd |only MetaComp-1.1.1/MetaComp/man/plot_merged_assignment.Rd | 24 + MetaComp-1.1.1/MetaComp/tests/test_data/HMP_even |only MetaComp-1.1.1/MetaComp/tests/test_data/HMP_stagger |only MetaComp-1.1.1/MetaComp/tests/test_data/bwa_emtpy_list.txt |only MetaComp-1.1.1/MetaComp/tests/test_data/test_all_taxa |only MetaComp-1.1.1/MetaComp/tests/test_data/test_table_diamond.txt |only MetaComp-1.1.1/MetaComp/tests/test_data/test_table_gottcha2.txt | 1 MetaComp-1.1.1/MetaComp/tests/test_data/test_table_pangia.txt |only MetaComp-1.1.1/MetaComp/tests/testthat/Rplots.pdf |only MetaComp-1.1.1/MetaComp/tests/testthat/test_load_bwa_assignment.R | 17 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_bwa_assignments.R | 8 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_diamond_assignment.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_load_diamond_assignments.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_load_gottcha2_assignment.R | 10 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_gottcha2_assignments.R | 10 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_gottcha_assignment.R | 10 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_gottcha_assignments.R | 5 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_kraken_assignment.R | 8 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_kraken_assignments.R | 7 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_metaphlan_assignment.R | 14 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_metaphlan_assignments.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_load_pangia_assignment.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_load_pangia_assignments.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_bwa_assignments.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_bwa_count_assignments.R | 5 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_diamond_assignments.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_gottcha2_assignments.R | 8 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_gottcha2_count_assignments.R | 8 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_gottcha_assignments.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_kraken_assignments.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_metaphlan_assignments.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_merge_pangia_assignments.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_pipeline.R | 13 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_bwa_assignment.R | 5 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_diamond_assignment.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_gottcha_assignment.R | 4 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_kraken_assignment.R | 7 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_b.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_d.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_g.R | 4 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_g2.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_k.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_m.R | 6 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_merged_assignment_p.R |only MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_metaphlan_assignment.R | 7 MetaComp-1.1.1/MetaComp/tests/testthat/test_plot_pangia_assignment.R |only 102 files changed, 304 insertions(+), 209 deletions(-)
Title: Tools for Working with Categorical Variables (Factors)
Description: Helpers for reordering factor levels (including moving
specified levels to front, ordering by first appearance, reversing, and
randomly shuffling), and tools for modifying factor levels (including
collapsing rare levels into other, 'anonymising', and manually 'recoding').
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between forcats versions 0.2.0 dated 2017-01-23 and 0.3.0 dated 2018-02-19
forcats-0.2.0/forcats/tests/testthat/test-fct_reorder.R |only forcats-0.3.0/forcats/DESCRIPTION | 18 +- forcats-0.3.0/forcats/MD5 | 111 ++++++++------- forcats-0.3.0/forcats/NAMESPACE | 1 forcats-0.3.0/forcats/NEWS.md | 42 +++++ forcats-0.3.0/forcats/R/anon.R | 2 forcats-0.3.0/forcats/R/as_factor.R | 4 forcats-0.3.0/forcats/R/c.R | 22 +- forcats-0.3.0/forcats/R/collapse.R | 8 - forcats-0.3.0/forcats/R/count.R | 6 forcats-0.3.0/forcats/R/drop.R | 6 forcats-0.3.0/forcats/R/expand.R | 6 forcats-0.3.0/forcats/R/explicit_na.R | 23 +-- forcats-0.3.0/forcats/R/lump.R | 57 ++++++- forcats-0.3.0/forcats/R/lvls.R | 30 ++-- forcats-0.3.0/forcats/R/other.R | 4 forcats-0.3.0/forcats/R/recode.R | 10 - forcats-0.3.0/forcats/R/relabel.R | 29 ++- forcats-0.3.0/forcats/R/relevel.R | 13 - forcats-0.3.0/forcats/R/reorder.R | 47 +++--- forcats-0.3.0/forcats/R/rev.R | 4 forcats-0.3.0/forcats/R/shuffle.R | 2 forcats-0.3.0/forcats/R/unique.R | 2 forcats-0.3.0/forcats/R/utils.R | 8 - forcats-0.3.0/forcats/README.md | 71 ++++++--- forcats-0.3.0/forcats/data/gss_cat.rda |binary forcats-0.3.0/forcats/man/as_factor.Rd | 4 forcats-0.3.0/forcats/man/fct_anon.Rd | 2 forcats-0.3.0/forcats/man/fct_c.Rd | 13 - forcats-0.3.0/forcats/man/fct_collapse.Rd | 4 forcats-0.3.0/forcats/man/fct_count.Rd | 6 forcats-0.3.0/forcats/man/fct_drop.Rd | 4 forcats-0.3.0/forcats/man/fct_expand.Rd | 2 forcats-0.3.0/forcats/man/fct_explicit_na.Rd | 2 forcats-0.3.0/forcats/man/fct_lump.Rd | 19 +- forcats-0.3.0/forcats/man/fct_other.Rd | 6 forcats-0.3.0/forcats/man/fct_recode.Rd | 6 forcats-0.3.0/forcats/man/fct_relabel.Rd | 19 +- forcats-0.3.0/forcats/man/fct_relevel.Rd | 7 forcats-0.3.0/forcats/man/fct_reorder.Rd | 24 +-- forcats-0.3.0/forcats/man/fct_rev.Rd | 4 forcats-0.3.0/forcats/man/fct_shuffle.Rd | 2 forcats-0.3.0/forcats/man/fct_unique.Rd | 2 forcats-0.3.0/forcats/man/figures |only forcats-0.3.0/forcats/man/lvls.Rd | 10 - forcats-0.3.0/forcats/tests/testthat/test-anon.R |only forcats-0.3.0/forcats/tests/testthat/test-as_factor.R | 12 + forcats-0.3.0/forcats/tests/testthat/test-collapse.R |only forcats-0.3.0/forcats/tests/testthat/test-count.R |only forcats-0.3.0/forcats/tests/testthat/test-explicit_na.R |only forcats-0.3.0/forcats/tests/testthat/test-fct_c.R | 9 - forcats-0.3.0/forcats/tests/testthat/test-fct_drop.R | 9 + forcats-0.3.0/forcats/tests/testthat/test-fct_lump.R | 52 +++++++ forcats-0.3.0/forcats/tests/testthat/test-fct_other.R | 7 forcats-0.3.0/forcats/tests/testthat/test-fct_relabel.R | 11 + forcats-0.3.0/forcats/tests/testthat/test-lvls.R | 13 + forcats-0.3.0/forcats/tests/testthat/test-lvls_reorder.R | 5 forcats-0.3.0/forcats/tests/testthat/test-reorder.R |only forcats-0.3.0/forcats/tests/testthat/test-rev.R |only forcats-0.3.0/forcats/tests/testthat/test-shift.R |only forcats-0.3.0/forcats/tests/testthat/test-shuffle.R |only forcats-0.3.0/forcats/tests/testthat/test-utils.R |only 62 files changed, 517 insertions(+), 263 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to work with
remote database tables as if they are in-memory data frames. Basic features
works with any database that has a 'DBI' back end; more advanced features
require 'SQL' translation to be provided by the package author.
Author: Hadley Wickham [aut, cre],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 1.2.0 dated 2018-01-03 and 1.2.1 dated 2018-02-19
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 4 R/db-odbc-mssql.R | 2 R/db-postgres.r | 46 ++-- R/translate-sql-base.r | 13 - R/utils.r | 4 inst/doc/dbplyr.html | 332 +++++++++++++++-------------- inst/doc/new-backend.html | 118 +++++----- inst/doc/sql-translation.html | 262 +++++++++++----------- tests/testthat/test-translate-postgresql.R | 2 11 files changed, 440 insertions(+), 369 deletions(-)
Title: Colorful Hierarchical Clustering Dendrograms
Description: Build dendrograms with sample groups highlighted by different colors. Visualize results of hierarchical clustering analyses as dendrograms whose leaves and labels are colored according to sample grouping. Assess whether data point grouping aligns to naturally occurring clusters.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between colorhcplot versions 1.0 dated 2015-10-01 and 1.3.1 dated 2018-02-19
DESCRIPTION | 17 +-- MD5 | 19 ++- NAMESPACE | 2 R/colorhcplot-internal.R |only R/colorhcplot.R | 246 ++++++++++++++++++++++++++++----------------- build |only data |only inst |only man/colorhcplot-package.Rd | 21 --- man/colorhcplot.Rd | 123 +++++++++------------- man/geneData.Rd |only vignettes |only 12 files changed, 233 insertions(+), 195 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut],
Witold Chodor [ctb]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 2.2 dated 2017-11-25 and 2.3 dated 2018-02-19
DESCRIPTION | 6 +-- MD5 | 54 ++++++++++++++++++----------------- NEWS.md | 7 ++++ R/ahistory.R | 2 - R/archivistOptions.R | 11 +++++++ R/cache.R | 13 +++++--- R/copyToRepo.R | 1 R/deleteRepo.R | 3 + R/extractData.R | 40 ++++++++++++------------- R/getTags.R | 4 +- R/magrittr.R | 2 - R/md5hash.R | 2 + R/restoreLibraries.R | 1 R/rmFromRepo.R | 3 + R/saveToRepo.R | 12 +++---- R/zzz.R | 2 + build/vignette.rds |binary inst/doc/jss2342.pdf |binary man/archivistOptions.Rd | 11 +++++++ man/cache.Rd | 5 ++- man/copyToRepo.Rd | 1 man/deleteLocalRepo.Rd | 3 + man/getTags.Rd | 4 +- man/magrittr.Rd | 2 - man/restoreLibs.Rd | 1 man/saveToRepo.Rd | 2 - tests/testthat/test_hash_functions.R |only tests/testthat/test_locks.R |only tests/testthat/test_splitTags.R | 2 - 29 files changed, 119 insertions(+), 75 deletions(-)
Title: Imputation Regularized Optimization Algorithm
Description: Missing data are frequently encountered in high-dimensional data analysis, but they are usually difficult to deal with using standard algorithms, such as the EM algorithm and its variants. This package provides a general algorithm, the so-called Imputation Regularized Optimization (IRO) algorithm, for high-dimensional missing data problems. You can refer to Liang, F., Jia, B., Xue, J., Li, Q. and Luo, Y. (2018) at <arXiv:1802.02251> for detail.
Author: Bochao Jia [aut, ctb, cre, cph],
Faming Liang [ctb]
Maintainer: Bochao Jia <jbc409@ufl.edu>
Diff between IROmiss versions 1.0.0 dated 2018-01-17 and 1.0.1 dated 2018-02-19
DESCRIPTION | 14 - MD5 | 38 +-- NAMESPACE | 3 R/EyeICRO.R | 16 + R/RCLM.R | 4 R/SimRCLM.R |only R/YeastIRO.R | 36 +-- data/eye_norm.rda |binary man/EyeICRO.Rd | 14 - man/GraphIRO.Rd | 7 man/IROmiss-package.Rd | 19 - man/RCDat.Rd | 4 man/RCLM.Rd | 15 - man/RegICRO.Rd | 2 man/SimGraDat.Rd | 2 man/SimRCLM.Rd |only man/SimRegDat.Rd | 2 man/YeastIRO.Rd | 14 - man/eye_norm.Rd | 2 man/yeast.Rd | 2 src/IROmiss.c | 531 ++++++++++++++++++++++++------------------------- 21 files changed, 368 insertions(+), 357 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Thomas Jones [aut, cre],
William Doane [ctb]
Maintainer: Thomas Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 2.0.6 dated 2017-08-17 and 2.1 dated 2018-02-19
DESCRIPTION | 11 ++++---- MD5 | 63 ++++++++++++++++++++++++++++++---------------- R/CalcProbCoherence.R | 19 ++++++++----- R/Cluster2TopicModel.R | 2 - R/CreateTcm.R | 14 +++++----- R/Dtm2Tcm.R | 4 +- R/FitCtmModel.R | 2 - R/FitLdaModel.R | 2 - R/FormatRawLdaOutput.R | 35 ++++++++++++++++++++----- R/GetProbableTerms.R | 2 - R/GetVocabFromDtm.R | 2 - R/RecursiveRbind.R | 2 - build |only inst |only man/CalcProbCoherence.Rd | 8 ++--- man/Cluster2TopicModel.Rd | 2 - man/CreateTcm.Rd | 14 +++++----- man/Dtm2Tcm.Rd | 4 +- man/FitCtmModel.Rd | 2 - man/FitLdaModel.Rd | 2 - man/FormatRawLdaOutput.Rd | 5 ++- man/GetProbableTerms.Rd | 2 - man/GetVocabFromDtm.Rd | 2 - man/RecursiveRbind.Rd | 2 - vignettes |only 25 files changed, 126 insertions(+), 75 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in van Hees and colleagues (2014) <doi: 10.1152/japplphysiol.00421.2014> and (2015) <doi: 10.1371/journal.pone.0142533>. The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <http://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com/product/ax3>. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Joe Heywood [ctb],
Evgeny Mirkes [ctb],
Severine Sabia [ctb],
Jairo H Migueles [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.5-16 dated 2018-01-17 and 1.5-17 dated 2018-02-19
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/g.part3.R | 6 ++++-- R/g.shell.GGIR.R | 8 ++++++-- R/g.sib.det.R | 18 ++++++++++++------ README.md | 4 +++- inst/NEWS.Rd | 9 +++++++++ man/GGIR-package.Rd | 4 ++-- man/g.part3.Rd | 6 +++++- man/g.sib.det.Rd | 8 ++++++-- 10 files changed, 60 insertions(+), 29 deletions(-)
Title: Example Datasets from Archaeological Research
Description: The archdata package provides several types of data that are typically used in archaeological research. It provides all of the data sets used in "Quantitative Methods in Archaeology Using R" by David L Carlson, one of the Cambridge Manuals in Archaeology.
Author: David L. Carlson and Georg Roth
Maintainer: David L. Carlson <dcarlson@tamu.edu>
Diff between archdata versions 1.1 dated 2016-04-04 and 1.2 dated 2018-02-19
DESCRIPTION | 12 +++++------ MD5 | 50 +++++++++++++++++++++++++----------------------- NEWS | 3 ++ data/Arnhofen.rda |only data/OxfordPots.rda |only man/Acheulean.Rd | 4 ++- man/Arnhofen.Rd |only man/BACups.Rd | 2 - man/BarmoseI.grid.Rd | 4 ++- man/BarmoseI.pp.Rd | 4 ++- man/Bornholm.Rd | 4 +-- man/DartPoints.Rd | 2 + man/ESASites.Rd | 5 +++- man/EWBurials.Rd | 2 + man/EndScrapers.Rd | 5 ++-- man/EngrBone.Rd | 4 +-- man/Fibulae.Rd | 4 ++- man/Handaxes.Rd | 4 ++- man/Mesolithic.Rd | 2 - man/Nelson.Rd | 4 ++- man/Olorgesailie.maj.Rd | 2 + man/Olorgesailie.sub.Rd | 2 + man/OxfordPots.Rd |only man/PitHouses.Rd | 4 +++ man/RBGlass1.Rd | 2 + man/RBPottery.Rd | 6 ++++- man/Snodgrass.Rd | 5 ++-- man/archdata-package.Rd | 9 +++++--- 28 files changed, 95 insertions(+), 50 deletions(-)
Title: Functional MRI Quality Assurance Routines
Description: Methods for performing fMRI quality assurance (QA) measurements of
test objects. Heavily based on the fBIRN procedures detailed by Friedman and
Glover (2006) <doi:10.1002/jmri.20583>.
Author: Martin Wilson [cre, aut]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between fmriqa versions 0.2.0 dated 2017-12-20 and 0.3.0 dated 2018-02-19
DESCRIPTION | 10 +-- MD5 | 14 ++-- NEWS.md | 8 ++ R/run_fmriqa.R | 134 ++++++++++++++++++++++++++++------------- build/vignette.rds |binary inst/doc/fmriqa-intro.html | 24 +++---- man/run_fmriqa.Rd | 19 ++++- tests/testthat/ref_results.rds |binary 8 files changed, 141 insertions(+), 68 deletions(-)
Title: Functions to Support Extension Education Program Evaluation
Description: Functions and datasets to support "Summary and Analysis of
Extension Program Evaluation in R" and "An R
Companion for the Handbook of Biological Statistics".
Vignettes are available at <http://rcompanion.org>.
Author: Salvatore Mangiafico [aut, cre]
Maintainer: Salvatore Mangiafico <mangiafico@njaes.rutgers.edu>
Diff between rcompanion versions 1.11.1 dated 2017-11-12 and 1.11.3 dated 2018-02-19
DESCRIPTION | 8 +- MD5 | 10 +- R/cateNelson.r | 146 ++++++++++++++++++++++++++++-------------- R/pairwisePercentileTest.r | 2 man/cateNelson.Rd | 16 ++++ man/pairwisePercentileTest.Rd | 2 6 files changed, 126 insertions(+), 58 deletions(-)
Title: Simulation and Analysis Tools for Clinical Dose Response
Modeling
Description: Bayesian and ML Emax model fitting, graphics and simulation for clinical dose
response. The summary data from the dose response meta-analyses in
Thomas, Sweeney, and Somayaji (2014) <doi:10.1080/19466315.2014.924876> and
Thomas and Roy (2016) <doi:10.1080/19466315.2016.1256229> are included
in the package. The prior distributions for the Bayesian analyses default to
the posterior predictive distributions derived from these references.
Author: Neal Thomas [aut, cre] (<https://orcid.org/0000-0002-1915-8487>),
Jing Wu [aut]
Maintainer: Neal Thomas <snthomas99@gmail.com>
Diff between clinDR versions 1.6 dated 2017-12-04 and 1.7 dated 2018-02-19
DESCRIPTION | 10 - MD5 | 88 +++++----- R/Brextract.R | 8 R/DRDensityPlot.R | 8 R/emaxsim.R | 15 - R/emaxsimB.R | 14 - R/fitEmaxB.R | 13 + R/plot.emaxsim.R | 10 - R/plot.emaxsimB.R | 10 - R/plot.emaxsimobj.R | 35 ++- inst/NEWS | 12 + inst/tests/extraGraphics/cmpFiles.txt |only inst/tests/extraGraphics/pdfoutput/output.densityplot_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.densityplot_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimBobj_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.emaxsimobj_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmaxB_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmax_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.fitEmax_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotB_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotB_old.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotD_new.pdf |binary inst/tests/extraGraphics/pdfoutput/output.plotD_old.pdf |binary inst/tests/extraGraphics/runGraphics.R |only inst/tests/extraGraphics/test.densityplots.R | 13 + inst/tests/extraGraphics/test.plot.emaxsimBobj.R | 9 - inst/tests/extraGraphics/test.plot.emaxsimobj.R | 11 - inst/tests/extraGraphics/test.plot.fitEmax.R | 12 - inst/tests/extraGraphics/test.plot.fitEmaxB.R | 13 - inst/tests/extraGraphics/test.plotB.R | 63 ++++--- inst/tests/extraGraphics/test.plotD.R | 10 - inst/tests/test.emaxsim.R | 77 ++++++++ inst/tests/test.fitEmaxB.R | 4 man/clinDR-package.Rd | 4 man/compileStanModels.Rd | 2 man/emaxsim.Rd | 11 - man/emaxsimB.Rd | 7 man/fitEmaxB.Rd | 8 man/plot.emaxsim.Rd | 4 man/plot.emaxsimB.Rd | 4 man/plot.emaxsimBobj.Rd | 2 man/plot.emaxsimobj.Rd | 2 man/plotB.Rd | 3 46 files changed, 320 insertions(+), 162 deletions(-)
Title: Bundle Methods for Regularized Risk Minimization Package
Description: Bundle methods for minimization of convex and non-convex risk
under L1 or L2 regularization. Implements the algorithm proposed by Teo et
al. (JMLR 2010) as well as the extension proposed by Do and Artieres (JMLR
2012). The package comes with lot of loss functions for machine learning
which make it powerful for big data analysis. The applications includes:
structured prediction, linear SVM, multi-class SVM, f-beta optimization,
ROC optimization, ordinal regression, quantile regression,
epsilon insensitive regression, least mean square, logistic regression,
least absolute deviation regression (see package examples), etc... all with
L1 and L2 regularization.
Author: Julien Prados
Maintainer: Julien Prados <julien.prados@unige.ch>
Diff between bmrm versions 3.4 dated 2017-08-16 and 3.7 dated 2018-02-19
DESCRIPTION | 10 - MD5 | 26 +-- NAMESPACE | 3 R/loss_convex.R | 24 +- R/ml_misc.R | 85 ++++++++++ R/mmc.R | 91 +++++----- R/nrbm.R | 11 - R/svmLP.R | 2 build/vignette.rds |binary inst/doc/bmrm.html | 408 +++++++++++++++++------------------------------- man/hclust.fca.Rd |only man/iterative.hclust.Rd |only man/mmc.Rd | 32 +-- man/nrbm.Rd | 9 - man/ontologyLoss.Rd | 13 - 15 files changed, 347 insertions(+), 367 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
funrar is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>),
Pierre Denelle [aut] (<https://orcid.org/0000-0001-5037-2281>),
Caroline Tucker [aut] (<https://orcid.org/0000-0002-4871-2010>),
François Munoz [ths] (<https://orcid.org/0000-0001-8776-4705>),
Cyrille Violle [ths] (<https://orcid.org/0000-0002-2471-9226>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between funrar versions 1.2.0 dated 2017-06-30 and 1.2.1 dated 2018-02-19
DESCRIPTION | 30 MD5 | 101 +- NAMESPACE | 50 - NEWS.md | 75 +- R/check_functions.R | 501 ++++++-------- R/compute_dist_matrix.R | 191 ++--- R/distinctiveness.R | 556 +++++++-------- R/funrar.R | 226 +++--- R/make_relative.R | 180 ++--- R/rarity_dimensions.R | 272 +++---- R/restrictedness.R | 274 +++---- R/scarcity.R | 336 ++++----- R/stack_matrix.R | 338 +++++---- R/uniqueness.R | 290 ++++---- README.md | 99 +- build/vignette.rds |binary inst/CITATION |only inst/doc/rarity_indices.R | 324 ++++----- inst/doc/rarity_indices.Rmd | 700 +++++++++---------- inst/doc/rarity_indices.html | 1140 ++++++++++++++++---------------- inst/doc/sparse_matrices.R | 186 ++--- inst/doc/sparse_matrices.Rmd | 320 ++++---- inst/doc/sparse_matrices.html | 464 ++++++------- man/combination_trait_dist.Rd | 44 - man/compute_dist_matrix.Rd | 147 ++-- man/distinctiveness.Rd | 160 ++-- man/distinctiveness_com.Rd | 93 +- man/distinctiveness_dimensions.Rd | 94 +- man/distinctiveness_stack.Rd | 127 +-- man/funrar.Rd | 90 +- man/funrar_stack.Rd | 98 +- man/is_relative.Rd | 76 +- man/make_relative.Rd | 54 - man/matrix_to_stack.Rd | 92 +- man/restrictedness.Rd | 110 +-- man/restrictedness_stack.Rd | 88 +- man/scarcity.Rd | 102 +- man/scarcity_com.Rd | 82 +- man/scarcity_stack.Rd | 102 +- man/stack_to_matrix.Rd | 91 +- man/uniqueness.Rd | 128 +-- man/uniqueness_dimensions.Rd | 90 +- man/uniqueness_stack.Rd | 100 +- tests/testthat.R | 8 tests/testthat/test-check_functions.R | 350 ++++----- tests/testthat/test-dist_matrix.R | 290 ++++---- tests/testthat/test-rarity_dimensions.R | 277 ++++--- tests/testthat/test-rarity_indices.R | 622 ++++++++--------- tests/testthat/test-rel_abund.R | 166 ++-- tests/testthat/test-tidy_matrix.R | 352 +++++---- vignettes/rarity_indices.Rmd | 700 +++++++++---------- vignettes/sparse_matrices.Rmd | 320 ++++---- 52 files changed, 5914 insertions(+), 5792 deletions(-)
Title: Estimates and Bounds for the False Discovery Proportion, by
Permutation
Description: For multiple testing.
Computes estimates and confidence bounds for the
False Discovery Proportion (FDP), the fraction of false positives among
all rejected hypotheses.
The methods in the package use permutations of the data. Doing so, they
take into account the dependence structure in the data.
Author: Jesse Hemerik and Jelle Goeman
Maintainer: Jesse Hemerik <j.b.a.hemerik@lumc.nl>
Diff between confSAM versions 0.1 dated 2017-01-18 and 0.2 dated 2018-02-19
DESCRIPTION | 10 +-- MD5 | 19 +++--- R/confSAM.R | 137 ++++++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/confSAM.R | 2 inst/doc/confSAM.Rmd | 18 +++--- inst/doc/confSAM.pdf |binary man/confSAM.Rd | 15 ++--- vignettes/confSAM.Rmd | 18 +++--- vignettes/confSAM.html |only vignettes/referenties.bib | 12 ++++ 11 files changed, 133 insertions(+), 98 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: ORPHANED
Diff between XML versions 3.98-1.9 dated 2017-06-19 and 3.98-1.10 dated 2018-02-19
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/xmlInternalSource.R | 4 +++- 3 files changed, 8 insertions(+), 6 deletions(-)