Title: Authenticate and Create Google APIs
Description: Create R functions that interact with OAuth2 Google APIs
<https://developers.google.com/apis-explorer/> easily,
with auto-refresh and Shiny compatibility.
Author: Mark Edmondson [aut, cre] (<https://orcid.org/0000-0002-8434-3881>),
Jennifer Bryan [ctb],
Johann deBoer [ctb],
Neal Richardson [ctb],
David Kulp [ctb],
Joe Cheng [ctb]
Maintainer: Mark Edmondson <m@sunholo.com>
Diff between googleAuthR versions 0.6.3 dated 2018-06-21 and 0.7.0 dated 2018-11-16
googleAuthR-0.6.3/googleAuthR/inst/drive |only googleAuthR-0.6.3/googleAuthR/inst/embed |only googleAuthR-0.6.3/googleAuthR/inst/flexdashbord |only googleAuthR-0.6.3/googleAuthR/inst/shiny |only googleAuthR-0.6.3/googleAuthR/man/authReturnCode.Rd |only googleAuthR-0.6.3/googleAuthR/man/createCode.Rd |only googleAuthR-0.6.3/googleAuthR/man/gar_auth_js.Rd |only googleAuthR-0.6.3/googleAuthR/man/gar_auth_jsUI.Rd |only googleAuthR-0.6.3/googleAuthR/man/gar_shiny_getAuthUrl.Rd |only googleAuthR-0.6.3/googleAuthR/man/gar_shiny_getToken.Rd |only googleAuthR-0.6.3/googleAuthR/man/gar_shiny_getUrl.Rd |only googleAuthR-0.6.3/googleAuthR/man/loginOutput.Rd |only googleAuthR-0.6.3/googleAuthR/man/reactiveAccessToken.Rd |only googleAuthR-0.6.3/googleAuthR/man/renderLogin.Rd |only googleAuthR-0.6.3/googleAuthR/man/revokeEventObserver.Rd |only googleAuthR-0.6.3/googleAuthR/tests/testthat/gdrive.oauth |only googleAuthR-0.7.0/googleAuthR/DESCRIPTION | 14 googleAuthR-0.7.0/googleAuthR/MD5 | 120 + googleAuthR-0.7.0/googleAuthR/NAMESPACE | 16 googleAuthR-0.7.0/googleAuthR/NEWS.md | 8 googleAuthR-0.7.0/googleAuthR/R/auth.R | 7 googleAuthR-0.7.0/googleAuthR/R/batch.R | 23 googleAuthR-0.7.0/googleAuthR/R/deprecated.R | 415 ------ googleAuthR-0.7.0/googleAuthR/R/discovery_build.R | 2 googleAuthR-0.7.0/googleAuthR/R/discovery_utilities.R | 27 googleAuthR-0.7.0/googleAuthR/R/gce.R | 3 googleAuthR-0.7.0/googleAuthR/R/generator.R | 69 - googleAuthR-0.7.0/googleAuthR/R/options.R | 16 googleAuthR-0.7.0/googleAuthR/R/page_results.R |only googleAuthR-0.7.0/googleAuthR/R/shiny-auth.R |only googleAuthR-0.7.0/googleAuthR/R/shiny-js-auth.R |only googleAuthR-0.7.0/googleAuthR/R/shiny-js-signin.R |only googleAuthR-0.7.0/googleAuthR/R/shiny-modifyurl.R |only googleAuthR-0.7.0/googleAuthR/R/shiny.R | 358 ----- googleAuthR-0.7.0/googleAuthR/R/utility.R | 17 googleAuthR-0.7.0/googleAuthR/inst/css |only googleAuthR-0.7.0/googleAuthR/inst/doc/advanced-building.Rmd | 76 + googleAuthR-0.7.0/googleAuthR/inst/doc/advanced-building.html | 76 + googleAuthR-0.7.0/googleAuthR/inst/doc/building.Rmd | 2 googleAuthR-0.7.0/googleAuthR/inst/doc/building.html | 6 googleAuthR-0.7.0/googleAuthR/inst/doc/google-authentication-types.Rmd | 170 ++ googleAuthR-0.7.0/googleAuthR/inst/doc/google-authentication-types.html | 166 ++ googleAuthR-0.7.0/googleAuthR/inst/doc/setup.html | 4 googleAuthR-0.7.0/googleAuthR/inst/doc/troubleshooting.html | 4 googleAuthR-0.7.0/googleAuthR/inst/googledrive_shiny_demo |only googleAuthR-0.7.0/googleAuthR/inst/img |only googleAuthR-0.7.0/googleAuthR/inst/js |only googleAuthR-0.7.0/googleAuthR/inst/js_auth_demo |only googleAuthR-0.7.0/googleAuthR/inst/server_side_auth_demo |only googleAuthR-0.7.0/googleAuthR/inst/server_side_auth_function |only googleAuthR-0.7.0/googleAuthR/inst/signin_demo |only googleAuthR-0.7.0/googleAuthR/man/gar_api_page.Rd |only googleAuthR-0.7.0/googleAuthR/man/gar_gce_auth.Rd | 4 googleAuthR-0.7.0/googleAuthR/man/gar_shiny_auth.Rd |only googleAuthR-0.7.0/googleAuthR/man/gar_shiny_auth_url.Rd |only googleAuthR-0.7.0/googleAuthR/man/gar_shiny_login_ui.Rd |only googleAuthR-0.7.0/googleAuthR/man/gar_shiny_ui.Rd |only googleAuthR-0.7.0/googleAuthR/man/googleAuth.Rd | 4 googleAuthR-0.7.0/googleAuthR/man/googleAuthUI.Rd | 4 googleAuthR-0.7.0/googleAuthR/man/googleAuth_js.Rd |only googleAuthR-0.7.0/googleAuthR/man/googleAuth_jsUI.Rd |only googleAuthR-0.7.0/googleAuthR/man/googleSignIn.Rd |only googleAuthR-0.7.0/googleAuthR/man/googleSignInUI.Rd |only googleAuthR-0.7.0/googleAuthR/man/silent_auth.Rd |only googleAuthR-0.7.0/googleAuthR/man/with_shiny.Rd | 13 googleAuthR-0.7.0/googleAuthR/tests/testthat/googleAuthR_tests.httr-oauth |binary googleAuthR-0.7.0/googleAuthR/tests/testthat/googledrive.oauth |only googleAuthR-0.7.0/googleAuthR/tests/testthat/mock/50c397f6f2ca31ed |only googleAuthR-0.7.0/googleAuthR/tests/testthat/mock/8075926ac5b2e94a |only googleAuthR-0.7.0/googleAuthR/tests/testthat/test-integration.R | 3 googleAuthR-0.7.0/googleAuthR/tests/testthat/test-paging.R |only googleAuthR-0.7.0/googleAuthR/tests/www.googleapis.com/discovery/v1/apis.json | 630 ++++++---- googleAuthR-0.7.0/googleAuthR/tests/www.googleapis.com/discovery/v1/apis/acceleratedmobilepageurl/v1/rest.json | 140 +- googleAuthR-0.7.0/googleAuthR/tests/www.googleapis.com/urlshortener/v1/url-bd4cc3-POST.json | 2 googleAuthR-0.7.0/googleAuthR/vignettes/advanced-building.Rmd | 76 + googleAuthR-0.7.0/googleAuthR/vignettes/building.Rmd | 2 googleAuthR-0.7.0/googleAuthR/vignettes/google-authentication-types.Rmd | 170 ++ 77 files changed, 1456 insertions(+), 1191 deletions(-)
Title: Epimed Solutions Collection for Data Editing, Analysis, and
Benchmark of Health Units
Description: Collection of functions for data analysis and
editing of clinical and epidemiological data.
Most of them are related to benchmark with prediction models.
Author: Lunna Borges [aut, cre],
Pedro Brasil [aut],
Camila Cardoso [aut]
Maintainer: Lunna Borges <lunna.borges@epimedsolutions.com>
Diff between ems versions 1.2.0 dated 2018-07-28 and 1.2.1 dated 2018-11-16
DESCRIPTION | 19 ++++++++----------- MD5 | 6 +++--- NEWS | 6 ++++++ R/miscellaneous.R | 4 ++-- 4 files changed, 19 insertions(+), 16 deletions(-)
Title: Neyman-Pearson (NP) Classification Algorithms and NP Receiver
Operating Characteristic (NP-ROC) Curves
Description: In many binary classification applications, such as disease
diagnosis and spam detection, practitioners commonly face the need to limit
type I error (i.e., the conditional probability of misclassifying a class 0
observation as class 1) so that it remains below a desired threshold. To address
this need, the Neyman-Pearson (NP) classification paradigm is a natural choice;
it minimizes type II error (i.e., the conditional probability of misclassifying
a class 1 observation as class 0) while enforcing an upper bound, alpha, on the
type I error. Although the NP paradigm has a century-long history in hypothesis
testing, it has not been well recognized and implemented in classification
schemes. Common practices that directly limit the empirical type I error to
no more than alpha do not satisfy the type I error control objective because
the resulting classifiers are still likely to have type I errors much larger
than alpha. As a result, the NP paradigm has not been properly implemented
for many classification scenarios in practice. In this work, we develop the
first umbrella algorithm that implements the NP paradigm for all scoring-type
classification methods, including popular methods such as logistic regression,
support vector machines and random forests. Powered by this umbrella algorithm,
we propose a novel graphical tool for NP classification methods: NP receiver
operating characteristic (NP-ROC) bands, motivated by the popular receiver
operating characteristic (ROC) curves. NP-ROC bands will help choose in a data
adaptive way and compare different NP classifiers.
Author: Yang Feng, Jingyi Jessica Li, Xin Tong, and Ye Tian
Maintainer: Yang Feng <yang.feng@columbia.edu>
Diff between nproc versions 2.1.1 dated 2018-02-13 and 2.1.4 dated 2018-11-16
ChangeLog | 2 DESCRIPTION | 12 MD5 | 20 - R/npc.R | 17 - R/npfuns.R | 584 +++++++++++++++++++++++----------------------- R/nproc.R | 1 build/vignette.rds |binary man/npc.Rd | 13 - man/nproc.Rd | 6 man/rocCV.Rd | 6 vignettes/nproc-demo.html | 280 ++++++++++++++++++---- 11 files changed, 575 insertions(+), 366 deletions(-)
Title: ToxCast Data Analysis Pipeline
Description: A set of tools for processing and modeling high-throughput and
high-content chemical screening data. The package was developed for the
the chemical screening data generated by the US EPA ToxCast program, but
can be used for diverse chemical screening efforts.
Author: Richard S Judson [cre, ths],
Dayne L Filer [aut],
Jason Brown [ctb],
Parth Kothiya [ctb],
Woodrow R Setzer [ctb],
Matthew T Martin [ctb, ths]
Maintainer: Richard S Judson <Judson.Richard@epa.gov>
Diff between tcpl versions 2.0.0 dated 2018-11-10 and 2.0.1 dated 2018-11-16
DESCRIPTION | 6 +-- MD5 | 12 +++--- NEWS | 5 ++ inst/doc/Data_processing.R | 84 +++++++++++++++++++++++------------------- inst/doc/Data_processing.Rmd | 76 +++++++++++++++++++++----------------- inst/doc/Data_processing.html | 58 ++++++++++++++--------------- vignettes/Data_processing.Rmd | 76 +++++++++++++++++++++----------------- 7 files changed, 176 insertions(+), 141 deletions(-)
Title: Load Data from 'MyTarget API'
Description: Allows work with 'MyTarget API v2' <https://target.my.com/doc/apiv2/ru/detailed.html> and
load data by ads, campaigns, agency clients and statistic from
your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rmytarget versions 1.1.1 dated 2018-11-09 and 2.0.0 dated 2018-11-16
rmytarget-1.1.1/rmytarget/R/myTarGetTotalStats.R |only rmytarget-1.1.1/rmytarget/man/myTarGetTotalStats.Rd |only rmytarget-2.0.0/rmytarget/DESCRIPTION | 12 - rmytarget-2.0.0/rmytarget/MD5 | 22 +- rmytarget-2.0.0/rmytarget/NAMESPACE | 5 rmytarget-2.0.0/rmytarget/R/myTarAuth.R | 133 ++++++++------ rmytarget-2.0.0/rmytarget/R/myTarGetAdList.R | 48 +++-- rmytarget-2.0.0/rmytarget/R/myTarGetCampaignList.R | 45 ++-- rmytarget-2.0.0/rmytarget/R/myTarGetClientList.R | 56 ++++- rmytarget-2.0.0/rmytarget/R/myTarGetStats.R | 187 ++++++++++++++------ rmytarget-2.0.0/rmytarget/build/partial.rdb |binary rmytarget-2.0.0/rmytarget/man/myTarGetStats.Rd | 183 ++++++++++++++++++- rmytarget-2.0.0/rmytarget/man/rmytarget-package.Rd | 65 ++++-- 13 files changed, 545 insertions(+), 211 deletions(-)
Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing.
Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut],
Aimee Gott [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre],
Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>
Diff between GENEAclassify versions 1.4.14 dated 2018-08-13 and 1.4.16 dated 2018-11-16
DESCRIPTION | 8 +- MD5 | 31 ++++++----- NAMESPACE | 3 + R/classifyGENEA.R | 7 ++ R/dataImport.R | 14 +++- R/getGENEAsegments.R | 27 ++++++--- R/segmentation.R | 117 ++++++++++++++++++++++++++++++++++------- R/statistics.R | 48 +++++++++++++++++ R/stepCounter.R | 135 ++++++++++++++++++++++++++---------------------- man/GENEAamplitude.Rd |only man/GENEAdistance.Rd |only man/GENEAwavelength.Rd |only man/classifyGENEA.Rd | 27 +++++---- man/dataImport.Rd | 5 + man/getGENEAsegments.Rd | 25 +++++--- man/segmentation.Rd | 22 ++++--- man/stepCounter.Rd | 3 - man/stepCounter2.Rd | 9 +-- 18 files changed, 334 insertions(+), 147 deletions(-)
Title: Regional Economic Analysis Toolbox
Description: Collection of models and analysis methods used in regional and urban economics and (quantitative) economic geography, e.g. measures of inequality, regional disparities and convergence, regional specialization as well as accessibility and spatial interaction models.
Author: Thomas Wieland
Maintainer: Thomas Wieland <thomas.wieland.geo@googlemail.com>
Diff between REAT versions 2.1.0 dated 2018-10-17 and 2.1.1 dated 2018-11-16
DESCRIPTION | 9 ++++----- MD5 | 28 ++++++++++++++++++---------- NAMESPACE | 2 +- R/conc.R |only R/curvefit.R |only R/locq.R | 4 ++-- R/locq.growth.R |only R/shiftd.R | 2 +- R/shiftid.R |only data/EU28.emp.rda |binary data/G.counties.gdp.rda |binary man/conc.Rd |only man/curvefit.Rd |only man/locq.Rd | 10 +++++++--- man/locq.growth.Rd |only man/portfolio.Rd | 2 +- man/shiftd.Rd | 10 ++++++++-- man/shifti.Rd | 2 +- man/shiftid.Rd |only 19 files changed, 43 insertions(+), 26 deletions(-)
Title: Package for Reading Binary Files
Description: Functions and analytics for GENEA-compatible accelerometer data
into R objects. See topic 'GENEAread' for an introduction to the package.
Author: Zhou Fang [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre]
Maintainer: Charles Sweetland <charles@sweetland-solutions.co.uk>
Diff between GENEAread versions 2.0.5 dated 2018-07-17 and 2.0.6 dated 2018-11-16
DESCRIPTION | 20 ++++++++---------- MD5 | 24 ++++++++++++---------- NAMESPACE | 3 +- R/GENEActiv.calibrate.r |only R/Recalibrate.R | 24 ++++++++++++---------- R/header.info.R | 33 +++++++++++++++++------------- R/read.bin.R | 49 +++++++++++++++++++++++++++++++++------------ R/stftmod.R | 10 ++++----- man/GENEActiv.calibrate.Rd |only man/Recalibrate.Rd | 18 +++++++++++----- man/g.downsample.Rd |only man/plot.stft.Rd |only man/seq.log.Rd | 4 +-- man/stft.Rd | 1 man/stftcalc.Rd | 6 ++--- 15 files changed, 116 insertions(+), 76 deletions(-)
Title: Compositional Data Analysis in Practice
Description: Univariate and multivariate methods for compositional data analysis,
based on logratios.
Author: Michael Greenacre
Maintainer: Michael Greenacre <michael.greenacre@upf.edu>
Diff between easyCODA versions 0.25 dated 2018-08-03 and 0.28 dated 2018-11-16
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++++------ R/CA.r |only R/LRA.r | 4 +++- R/PLOT.CA.r |only R/PLOT.PCA.r | 7 +++++-- R/STEP.r | 54 +++++++++++++++++++++++++++--------------------------- build/partial.rdb |binary man/CA.Rd |only man/PLOT.CA.Rd |only man/STEP.Rd | 27 +++++++++++++++------------ 11 files changed, 66 insertions(+), 54 deletions(-)
Title: 'Rcpp' Interface for Querying System Configuration Variables
Description: The 'getconf' command-line tool provided by 'libc' allows
querying of a large number of system variables. This package provides
similar functionality.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppGetconf versions 0.0.2 dated 2016-08-01 and 0.0.3 dated 2018-11-16
ChangeLog | 12 ++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/RcppExports.R | 20 ++++++++++++-------- README.md | 6 ++++-- inst/NEWS.Rd | 6 ++++++ man/getAll.Rd | 11 ++++++----- man/getConfig.Rd | 13 +++++++------ src/RcppExports.cpp | 35 +++++++++++++++++++++++------------ src/getconf.cpp | 14 +++++++++----- 10 files changed, 93 insertions(+), 52 deletions(-)
Title: Evaluation of the FIM in NLMEMs using MCMC
Description: Evaluation and optimization of the Fisher Information Matrix in NonLinear Mixed Effect Models using Markov Chains Monte Carlo for continuous and discrete data.
Author: Marie-Karelle Riviere-Jourdan and France Mentre <france.mentre@inserm.fr>
Maintainer: Marie-Karelle Riviere-Jourdan <eldamjh@gmail.com>
Diff between MIXFIM versions 1.0 dated 2015-08-31 and 1.1 dated 2018-11-16
DESCRIPTION | 8 MD5 | 18 R/MIXFIM.R | 1265 ++++++++++++++++++------------------ inst/extdata/model_b_given_y.stan | 6 inst/extdata/model_derivatives.stan | 4 inst/extdata/model_y.stan | 8 man/MIXFIM-package.Rd | 48 - man/fisher_evaluation.Rd | 154 ++-- man/fisher_optimization.Rd | 156 ++-- man/template_model.Rd | 105 +- 10 files changed, 922 insertions(+), 850 deletions(-)
Title: Simulating Neutral Landscape Models
Description: Provides neutral landscape models (<doi:10.1007/BF02275262>,
<http://sci-hub.tw/10.1007/bf02275262>).
Neutral landscape models range from "hard"
neutral models (completely random distributed), to "soft" neutral models
(definable spatial characteristics) and generate landscape patterns that are
independent of ecological processes.
Thus, these patterns can be used as null models in landscape ecology. 'nlmr'
combines a large number of algorithms from other published software for
simulating neutral landscapes. The simulation results are obtained in a
geospatial data format (raster* objects from the 'raster' package) and can,
therefore, be used in any sort of raster data operation that is performed
with standard observation data.
Author: Marco Sciaini [aut, cre] (<https://orcid.org/0000-0002-3042-5435>),
Matthias Fritsch [aut],
Craig Simpkins [aut] (<https://orcid.org/0000-0003-3212-1379>),
Cédric Scherer [aut] (<https://orcid.org/0000-0003-0465-2543>),
Sebastian Hanß [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura Graham [rev] (Laura reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/188),
Jeffrey Hollister [rev] (Jeffrey reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/188)
Maintainer: Marco Sciaini <sciaini.marco@gmail.com>
Diff between NLMR versions 0.3.2 dated 2018-10-02 and 0.4 dated 2018-11-16
NLMR-0.3.2/NLMR/vignettes/getstarted_cache |only NLMR-0.3.2/NLMR/vignettes/getstarted_files |only NLMR-0.4/NLMR/DESCRIPTION | 16 - NLMR-0.4/NLMR/MD5 | 103 +++---- NLMR-0.4/NLMR/NAMESPACE | 2 NLMR-0.4/NLMR/NEWS.md | 11 NLMR-0.4/NLMR/R/NLMR.R | 45 +-- NLMR-0.4/NLMR/R/RcppExports.R |only NLMR-0.4/NLMR/R/nlm_curds.R | 238 ++++++++--------- NLMR-0.4/NLMR/R/nlm_distancegradient.R | 178 ++++++------- NLMR-0.4/NLMR/R/nlm_edgegradient.R | 176 ++++++------- NLMR-0.4/NLMR/R/nlm_fbm.R | 212 ++++++++------- NLMR-0.4/NLMR/R/nlm_gaussianfield.R | 220 ++++++++-------- NLMR-0.4/NLMR/R/nlm_mosaicfield.R | 2 NLMR-0.4/NLMR/R/nlm_mosaicgibbs.R | 232 ++++++++--------- NLMR-0.4/NLMR/R/nlm_mosaictess.R | 166 ++++++------ NLMR-0.4/NLMR/R/nlm_mpd.R | 62 ---- NLMR-0.4/NLMR/R/nlm_neigh.R | 297 ++++++++-------------- NLMR-0.4/NLMR/R/nlm_percolation.R | 166 ++++++------ NLMR-0.4/NLMR/R/nlm_planargradient.R | 182 ++++++------- NLMR-0.4/NLMR/R/nlm_random.R | 132 ++++----- NLMR-0.4/NLMR/R/nlm_randomcluster.R | 2 NLMR-0.4/NLMR/R/nlm_randomrectangularcluster.R | 200 ++++++-------- NLMR-0.4/NLMR/inst/doc/getstarted.R | 20 - NLMR-0.4/NLMR/inst/doc/getstarted.Rmd | 34 -- NLMR-0.4/NLMR/inst/doc/getstarted.html | 66 ++-- NLMR-0.4/NLMR/man/NLMR-package.Rd | 1 NLMR-0.4/NLMR/man/nlm_curds.Rd | 4 NLMR-0.4/NLMR/man/nlm_distancegradient.Rd | 2 NLMR-0.4/NLMR/man/nlm_edgegradient.Rd | 2 NLMR-0.4/NLMR/man/nlm_fbm.Rd | 6 NLMR-0.4/NLMR/man/nlm_gaussianfield.Rd | 2 NLMR-0.4/NLMR/man/nlm_mosaicfield.Rd | 2 NLMR-0.4/NLMR/man/nlm_mosaicgibbs.Rd | 2 NLMR-0.4/NLMR/man/nlm_mosaictess.Rd | 2 NLMR-0.4/NLMR/man/nlm_mpd.Rd | 5 NLMR-0.4/NLMR/man/nlm_neigh.Rd | 4 NLMR-0.4/NLMR/man/nlm_percolation.Rd | 2 NLMR-0.4/NLMR/man/nlm_planargradient.Rd | 2 NLMR-0.4/NLMR/man/nlm_random.Rd | 2 NLMR-0.4/NLMR/man/nlm_randomcluster.Rd | 2 NLMR-0.4/NLMR/man/nlm_randomrectangularcluster.Rd | 5 NLMR-0.4/NLMR/src |only NLMR-0.4/NLMR/vignettes/getstarted.Rmd | 34 -- 44 files changed, 1349 insertions(+), 1492 deletions(-)
Title: Low-Rank Interaction Contingency Tables
Description: Analysis of count data with covariates. LORI uses a log-linear model where main row and column effects are decomposed as regression terms on known covariates. A residual low-rank interaction term is also fitted.
Author: Genevieve Robin [aut, cre]
Maintainer: Genevieve Robin <genevieve.robin@polytechnique.edu>
Diff between lori versions 0.2.1 dated 2018-10-05 and 1.0.0 dated 2018-11-16
DESCRIPTION | 8 MD5 | 20 +- R/lori.R | 493 ++++++++++++++++++++++++++++---------------------- R/lori_plots.R | 4 R/lori_tools.R | 88 ++++++++ inst/doc/example.html | 213 --------------------- man/altmin.Rd | 8 man/lori.Rd | 19 - man/plot_counts.Rd | 2 man/plot_cov.Rd | 2 man/qut.Rd | 6 11 files changed, 402 insertions(+), 461 deletions(-)
Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>),
Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>), Cochrane Library (<http://www.cochranelibrary.com/>)
and PubMed (<https://www.ncbi.nlm.nih.gov/pubmed/>) databases, performing bibliometric analysis
and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 2.0.1 dated 2018-10-09 and 2.0.2 dated 2018-11-16
DESCRIPTION | 8 MD5 | 84 ++++---- NAMESPACE | 4 NEWS | 23 ++ R/biblioAnalysis.R | 14 - R/biblioNetwork.R | 10 R/bradford.R |only R/conceptualStructure.R | 71 ++++-- R/convert2df.R | 3 R/countries.R | 5 R/metaTagExtraction.R | 2 R/networkPlot.R | 27 +- R/networkStat.R | 121 ++++++----- R/plotThematicEvolution.R | 2 R/summary.bibliometrix.R | 6 R/summary.bibliometrix_netstat.R | 202 ++++++++++--------- R/termExtraction.R | 5 R/thematicEvolution.R | 36 +++ R/thematicMap.R | 20 + build/partial.rdb |binary data/biblio.rda |binary data/biblio_df.rda |binary data/countries.rda |binary data/garfield.rda |binary data/isiCollection.rda |binary data/scientometrics.rda |binary data/scientometrics_text.rda |binary data/scopusCollection.rda |binary data/stopwords.rda |binary inst/biblioshiny/server.R | 368 +++++++++++++++++++++++++++++++----- inst/biblioshiny/ui.R | 271 ++++++++++++++++++++------ inst/doc/bibliometrix-vignette.Rmd | 2 inst/doc/bibliometrix-vignette.html | 169 +--------------- man/biblioNetwork.Rd | 4 man/bradford.Rd |only man/conceptualStructure.Rd | 14 - man/countries.Rd | 5 man/networkPlot.Rd | 6 man/networkStat.Rd | 9 man/plotThematicEvolution.Rd | 2 man/summary.bibliometrix.Rd | 2 man/summary.bibliometrix_netstat.Rd | 2 man/thematicEvolution.Rd | 6 vignettes/bibliometrix-vignette.Rmd | 2 44 files changed, 978 insertions(+), 527 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 0.9.4 dated 2018-09-18 and 0.9.5 dated 2018-11-16
jmv-0.9.4/jmv/data/bugs.csv.gz |only jmv-0.9.5/jmv/DESCRIPTION | 10 +-- jmv-0.9.5/jmv/MD5 | 96 +++++++++++++++++------------------ jmv-0.9.5/jmv/R/ancova.b.R | 14 +---- jmv-0.9.5/jmv/R/ancova.h.R | 2 jmv-0.9.5/jmv/R/anova.h.R | 2 jmv-0.9.5/jmv/R/anovanp.h.R | 6 +- jmv-0.9.5/jmv/R/anovaonew.b.R | 8 -- jmv-0.9.5/jmv/R/anovaonew.h.R | 5 + jmv-0.9.5/jmv/R/anovarm.b.R | 10 +-- jmv-0.9.5/jmv/R/anovarm.h.R | 2 jmv-0.9.5/jmv/R/anovarmnp.b.R | 4 - jmv-0.9.5/jmv/R/anovarmnp.h.R | 1 jmv-0.9.5/jmv/R/cfa.h.R | 1 jmv-0.9.5/jmv/R/conttables.h.R | 4 + jmv-0.9.5/jmv/R/conttablespaired.h.R | 3 + jmv-0.9.5/jmv/R/corrmatrix.b.R | 4 - jmv-0.9.5/jmv/R/corrmatrix.h.R | 1 jmv-0.9.5/jmv/R/descriptives.b.R | 83 +++++++++++++++++------------- jmv-0.9.5/jmv/R/descriptives.h.R | 2 jmv-0.9.5/jmv/R/efa.h.R | 50 ++++++++++++++++-- jmv-0.9.5/jmv/R/linreg.b.R | 19 +----- jmv-0.9.5/jmv/R/linreg.h.R | 2 jmv-0.9.5/jmv/R/loglinear.b.R | 7 -- jmv-0.9.5/jmv/R/loglinear.h.R | 2 jmv-0.9.5/jmv/R/logregbin.b.R | 7 -- jmv-0.9.5/jmv/R/logregbin.h.R | 3 + jmv-0.9.5/jmv/R/logregmulti.b.R | 7 -- jmv-0.9.5/jmv/R/logregmulti.h.R | 3 + jmv-0.9.5/jmv/R/logregord.b.R | 1 jmv-0.9.5/jmv/R/logregord.h.R | 3 + jmv-0.9.5/jmv/R/mancova.b.R | 4 - jmv-0.9.5/jmv/R/mancova.h.R | 2 jmv-0.9.5/jmv/R/pca.b.R | 68 +++++++++++++++++++----- jmv-0.9.5/jmv/R/pca.h.R | 15 +++++ jmv-0.9.5/jmv/R/proptest2.b.R | 8 -- jmv-0.9.5/jmv/R/proptest2.h.R | 2 jmv-0.9.5/jmv/R/proptestn.h.R | 2 jmv-0.9.5/jmv/R/reliability.b.R | 4 - jmv-0.9.5/jmv/R/reliability.h.R | 5 + jmv-0.9.5/jmv/R/ttestis.b.R | 4 - jmv-0.9.5/jmv/R/ttestis.h.R | 2 jmv-0.9.5/jmv/R/ttestones.b.R | 4 - jmv-0.9.5/jmv/R/ttestones.h.R | 1 jmv-0.9.5/jmv/R/ttestps.b.R | 8 -- jmv-0.9.5/jmv/R/ttestps.h.R | 1 jmv-0.9.5/jmv/data/bugs.csv |only jmv-0.9.5/jmv/man/anovaNP.Rd | 2 jmv-0.9.5/jmv/man/efa.Rd | 23 +++++--- jmv-0.9.5/jmv/man/pca.Rd | 9 ++- 50 files changed, 320 insertions(+), 206 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight and simpler than both), tools
for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.3 dated 2018-08-07 and 0.2.5 dated 2018-11-16
DESCRIPTION | 37 MD5 | 143 +- NAMESPACE | 34 NEWS.md | 50 R/cache-helpers.R | 162 +- R/cache-tools.R | 54 R/cache.R | 61 R/checksums.R | 37 R/consistentPaths.R | 11 R/convertPaths.R | 5 R/download.R | 240 ++- R/gis.R | 59 R/git.R | 7 R/helpers.R | 25 R/objectSize.R | 3 R/packages.R | 196 +-- R/pipe.R | 27 R/postProcess.R | 631 +++++++-- R/preProcess.R | 693 +++++++++- R/prepInputs.R | 223 ++- R/reproducible-package.R | 1 R/robustDigest.R | 58 R/search.R | 15 R/zzz.R | 34 README.md | 22 build/vignette.rds |binary inst/doc/Intro-to-Cache.html | 1877 ++++++++++++++++------------- inst/examples/example_assessDataTypeGDAL.R |only man/Checksums.Rd | 3 man/Require.Rd | 86 - man/assessDataType.Rd | 6 man/assessDataTypeGDAL.Rd |only man/assessDataTypeGDALhelpers.Rd |only man/available.packagesMem.Rd | 5 man/cache.Rd | 30 man/checkCacheRepo.Rd | 4 man/checkPath.Rd | 12 man/checkoutVersion.Rd | 8 man/copyFile.Rd | 26 man/cropInputs.Rd | 8 man/determineFilename.Rd | 3 man/dlGeneric.Rd | 2 man/dot-formalsNotInCurrentDots.Rd |only man/downloadFile.Rd | 12 man/extractFromArchive.Rd | 12 man/grepSysCalls.Rd |only man/guessAtTarget.Rd | 4 man/installPackages.Rd | 4 man/installVersions.Rd | 25 man/linkOrCopy.Rd |only man/maskInputs.Rd | 4 man/newLibPaths.Rd | 8 man/pkgDep.Rd | 15 man/postProcess.Rd | 11 man/preProcess.Rd | 16 man/prefix.Rd | 2 man/prepInputs.Rd | 16 man/projectInputs.Rd | 3 man/reproducible-package.Rd | 7 man/robustDigest.Rd | 68 - man/search.Rd | 14 man/viewCache.Rd | 14 man/writeOutputs.Rd | 18 tests/testthat/helper-allEqual.R | 129 + tests/testthat/test-cache.R | 338 ++++- tests/testthat/test-cacheArguments.R | 42 tests/testthat/test-checksums.R | 5 tests/testthat/test-cluster.R | 7 tests/testthat/test-download.R | 13 tests/testthat/test-examples.R | 8 tests/testthat/test-gis.R | 39 tests/testthat/test-misc.R |only tests/testthat/test-packages.R | 39 tests/testthat/test-preProcessDoesntWork.R |only tests/testthat/test-preProcessMessages.R |only tests/testthat/test-preProcessWorks.R |only tests/testthat/test-prepInputs.R | 772 ++++++++--- tests/testthat/test-robustDigest.R |only 78 files changed, 4556 insertions(+), 1987 deletions(-)
Title: Simulation of Fossil and Taxonomy Data
Description: Simulating taxonomy and fossil data on phylogenetic trees under mechanistic
models of speciation, preservation and sampling.
Author: Rachel Warnock [aut, cph],
Joelle Barido-Sottani [aut, cre, cph],
Walker Pett [aut, cph],
O'Reilly Joseph [aut, cph]
Maintainer: Joelle Barido-Sottani <joelle.barido-sottani@m4x.org>
Diff between FossilSim versions 2.0.0 dated 2018-07-28 and 2.1.0 dated 2018-11-16
FossilSim-2.0.0/FossilSim/man/plot.SAtree.Rd |only FossilSim-2.1.0/FossilSim/DESCRIPTION | 13 FossilSim-2.1.0/FossilSim/MD5 | 174 - FossilSim-2.1.0/FossilSim/NAMESPACE | 129 - FossilSim-2.1.0/FossilSim/NEWS.md |only FossilSim-2.1.0/FossilSim/R/BEAST.output.R |only FossilSim-2.1.0/FossilSim/R/FossilSim.R |only FossilSim-2.1.0/FossilSim/R/SAtree.R | 236 +- FossilSim-2.1.0/FossilSim/R/conversions.R | 1080 ++++----- FossilSim-2.1.0/FossilSim/R/fossils.R | 160 - FossilSim-2.1.0/FossilSim/R/plot.asymmetric.tree.R | 453 ++-- FossilSim-2.1.0/FossilSim/R/plot.fossils.R | 1078 ++++----- FossilSim-2.1.0/FossilSim/R/plot.taxonomy.R | 545 ++-- FossilSim-2.1.0/FossilSim/R/reconcile.fossils.taxonomy.R | 124 - FossilSim-2.1.0/FossilSim/R/sim.fbd.R | 406 +-- FossilSim-2.1.0/FossilSim/R/sim.fossils.R | 1096 +++++----- FossilSim-2.1.0/FossilSim/R/sim.interval.ages.R | 430 +-- FossilSim-2.1.0/FossilSim/R/sim.taxonomy.R | 760 +++--- FossilSim-2.1.0/FossilSim/R/sim.tip.sampling.R | 294 +- FossilSim-2.1.0/FossilSim/R/sim.trait.values.R | 358 +-- FossilSim-2.1.0/FossilSim/R/subsampling.R |only FossilSim-2.1.0/FossilSim/R/taxonomy.R | 197 - FossilSim-2.1.0/FossilSim/R/utils.R | 563 ++--- FossilSim-2.1.0/FossilSim/README.md | 94 FossilSim-2.1.0/FossilSim/build/vignette.rds |binary FossilSim-2.1.0/FossilSim/inst/WORDLIST | 82 FossilSim-2.1.0/FossilSim/inst/doc/SAtree.R | 46 FossilSim-2.1.0/FossilSim/inst/doc/SAtree.Rmd | 119 - FossilSim-2.1.0/FossilSim/inst/doc/SAtree.html | 400 +-- FossilSim-2.1.0/FossilSim/inst/doc/fossils.R | 582 ++--- FossilSim-2.1.0/FossilSim/inst/doc/fossils.Rmd | 940 ++++---- FossilSim-2.1.0/FossilSim/inst/doc/fossils.html | 1044 ++++----- FossilSim-2.1.0/FossilSim/inst/doc/intro.R | 62 FossilSim-2.1.0/FossilSim/inst/doc/intro.Rmd | 248 +- FossilSim-2.1.0/FossilSim/inst/doc/intro.html | 322 +- FossilSim-2.1.0/FossilSim/inst/doc/paleotree.R | 44 FossilSim-2.1.0/FossilSim/inst/doc/paleotree.Rmd | 92 FossilSim-2.1.0/FossilSim/inst/doc/paleotree.html | 707 +++--- FossilSim-2.1.0/FossilSim/inst/doc/simfbd.R | 47 FossilSim-2.1.0/FossilSim/inst/doc/simfbd.Rmd | 116 - FossilSim-2.1.0/FossilSim/inst/doc/simfbd.html | 383 +-- FossilSim-2.1.0/FossilSim/inst/doc/taxonomy.R | 112 - FossilSim-2.1.0/FossilSim/inst/doc/taxonomy.Rmd | 344 +-- FossilSim-2.1.0/FossilSim/inst/doc/taxonomy.html | 470 ++-- FossilSim-2.1.0/FossilSim/man/FossilSim.Rd |only FossilSim-2.1.0/FossilSim/man/SAtree.Rd | 32 FossilSim-2.1.0/FossilSim/man/SAtree.from.fossils.Rd | 66 FossilSim-2.1.0/FossilSim/man/beast.fbd.format.Rd | 76 FossilSim-2.1.0/FossilSim/man/count.fossils.Rd | 34 FossilSim-2.1.0/FossilSim/man/count.fossils.binned.Rd | 38 FossilSim-2.1.0/FossilSim/man/fossils.Rd | 66 FossilSim-2.1.0/FossilSim/man/fossils.to.BEAST.constraints.Rd |only FossilSim-2.1.0/FossilSim/man/fossils.to.BEAST.start.tree.Rd |only FossilSim-2.1.0/FossilSim/man/fossils.to.paleotree.record.Rd | 66 FossilSim-2.1.0/FossilSim/man/fossils.to.pyrate.Rd | 132 - FossilSim-2.1.0/FossilSim/man/get.tip.descs.Rd |only FossilSim-2.1.0/FossilSim/man/paleotree.record.to.fossils.Rd | 76 FossilSim-2.1.0/FossilSim/man/place.fossils.Rd |only FossilSim-2.1.0/FossilSim/man/plot.fossils.Rd | 225 +- FossilSim-2.1.0/FossilSim/man/plot.taxonomy.Rd | 106 FossilSim-2.1.0/FossilSim/man/prune.fossil.tips.Rd |only FossilSim-2.1.0/FossilSim/man/prune.fossils.Rd | 74 FossilSim-2.1.0/FossilSim/man/rangeplot.asymmetric.Rd |only FossilSim-2.1.0/FossilSim/man/reconcile.fossils.taxonomy.Rd | 70 FossilSim-2.1.0/FossilSim/man/remove.stem.fossils.Rd |only FossilSim-2.1.0/FossilSim/man/remove.stem.lineages.Rd |only FossilSim-2.1.0/FossilSim/man/sampled.tree.from.combined.Rd | 74 FossilSim-2.1.0/FossilSim/man/sim.anagenetic.species.Rd | 60 FossilSim-2.1.0/FossilSim/man/sim.cryptic.species.Rd | 56 FossilSim-2.1.0/FossilSim/man/sim.extant.samples.Rd | 82 FossilSim-2.1.0/FossilSim/man/sim.fbd.age.Rd | 112 - FossilSim-2.1.0/FossilSim/man/sim.fbd.rateshift.taxa.Rd | 89 FossilSim-2.1.0/FossilSim/man/sim.fbd.taxa.Rd | 90 FossilSim-2.1.0/FossilSim/man/sim.fossils.environment.Rd | 200 - FossilSim-2.1.0/FossilSim/man/sim.fossils.intervals.Rd | 149 - FossilSim-2.1.0/FossilSim/man/sim.fossils.poisson.Rd | 109 FossilSim-2.1.0/FossilSim/man/sim.gradient.Rd | 70 FossilSim-2.1.0/FossilSim/man/sim.interval.ages.Rd | 120 - FossilSim-2.1.0/FossilSim/man/sim.taxonomy.Rd | 69 FossilSim-2.1.0/FossilSim/man/sim.tip.samples.Rd | 70 FossilSim-2.1.0/FossilSim/man/sim.trait.values.Rd | 149 - FossilSim-2.1.0/FossilSim/man/species.end.Rd |only FossilSim-2.1.0/FossilSim/man/species.start.Rd |only FossilSim-2.1.0/FossilSim/man/subsample.fossils.oldest.Rd |only FossilSim-2.1.0/FossilSim/man/subsample.fossils.oldest.and.youngest.Rd |only FossilSim-2.1.0/FossilSim/man/subsample.fossils.uniform.Rd |only FossilSim-2.1.0/FossilSim/man/subsample.fossils.youngest.Rd |only FossilSim-2.1.0/FossilSim/man/summary.taxonomy.Rd | 46 FossilSim-2.1.0/FossilSim/man/taxonomy.Rd | 97 FossilSim-2.1.0/FossilSim/man/tree.max.Rd | 48 FossilSim-2.1.0/FossilSim/vignettes/SAtree.Rmd | 119 - FossilSim-2.1.0/FossilSim/vignettes/bibliography.bib | 140 - FossilSim-2.1.0/FossilSim/vignettes/fossils.Rmd | 940 ++++---- FossilSim-2.1.0/FossilSim/vignettes/intro.Rmd | 248 +- FossilSim-2.1.0/FossilSim/vignettes/mee.csl | 362 +-- FossilSim-2.1.0/FossilSim/vignettes/paleotree.Rmd | 92 FossilSim-2.1.0/FossilSim/vignettes/simfbd.Rmd | 116 - FossilSim-2.1.0/FossilSim/vignettes/taxonomy.Rmd | 344 +-- 98 files changed, 9782 insertions(+), 9680 deletions(-)
Title: A Friendly Package Manager
Description: Manage project dependencies from your DESCRIPTION file. Create a reproducible virtual environment with minimal additional files in your project. Provides tools to add, remove, and update dependencies as well as install existing dependencies with a single function.
Author: Andrew Kane [aut, cre]
Maintainer: Andrew Kane <andrew@chartkick.com>
Diff between jetpack versions 0.4.0 dated 2018-10-30 and 0.4.1 dated 2018-11-16
DESCRIPTION | 10 +-- MD5 | 13 ++-- NAMESPACE | 1 NEWS.md | 11 +++ R/jetpack.R | 164 ++++++++++++++++++++++++++++++++++++++++++-------------- README.md | 47 ++++++++++++++-- man/outdated.Rd |only man/update.Rd | 4 + 8 files changed, 191 insertions(+), 59 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-13 0.4
2016-03-20 0.3
2016-01-15 0.2
2014-06-25 0.1