Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.8-19 dated 2019-01-30 and 2.9-5 dated 2019-05-14
raster-2.8-19/raster/inst/doc/functions.R |only raster-2.9-5/raster/ChangeLog | 18 raster-2.9-5/raster/DESCRIPTION | 9 raster-2.9-5/raster/MD5 | 97 +- raster-2.9-5/raster/R/coerce.R | 4 raster-2.9-5/raster/R/extractPolygons.R | 4 raster-2.9-5/raster/R/getData.R | 2 raster-2.9-5/raster/R/getValuesBlock.R | 8 raster-2.9-5/raster/R/hdrEnvi.R | 4 raster-2.9-5/raster/R/indexReplace.R | 15 raster-2.9-5/raster/R/kernelDensity.R | 32 raster-2.9-5/raster/R/mask.R | 2 raster-2.9-5/raster/R/modalRaster.R | 3 raster-2.9-5/raster/R/netCDFwriteCD.R | 47 - raster-2.9-5/raster/R/nsidcICE.R | 114 +- raster-2.9-5/raster/R/plotRGB.R | 6 raster-2.9-5/raster/R/predict.R | 98 +- raster-2.9-5/raster/R/print.R | 19 raster-2.9-5/raster/R/rasterFromASCII.R | 2 raster-2.9-5/raster/R/rasterFromFile.R | 2 raster-2.9-5/raster/R/reclassify.R | 2 raster-2.9-5/raster/R/show.R | 116 +- raster-2.9-5/raster/R/writeRaster.R | 27 raster-2.9-5/raster/build/vignette.rds |binary raster-2.9-5/raster/inst/doc/Raster.Rnw | 1132 +++++++++++++-------------- raster-2.9-5/raster/inst/doc/Raster.pdf |binary raster-2.9-5/raster/inst/doc/functions.Rnw | 437 ---------- raster-2.9-5/raster/inst/doc/functions.pdf |binary raster-2.9-5/raster/inst/doc/rasterfile.Rnw | 160 --- raster-2.9-5/raster/inst/doc/rasterfile.pdf |binary raster-2.9-5/raster/inst/external/test.grd | 2 raster-2.9-5/raster/man/RGB.Rd | 7 raster-2.9-5/raster/man/adjacent.Rd | 2 raster-2.9-5/raster/man/as.list.Rd | 2 raster-2.9-5/raster/man/clamp.Rd | 2 raster-2.9-5/raster/man/getData.Rd | 2 raster-2.9-5/raster/man/gridDistance.Rd | 3 raster-2.9-5/raster/man/init.Rd | 2 raster-2.9-5/raster/man/plotRGB.Rd | 5 raster-2.9-5/raster/man/raster.Rd | 340 ++++---- raster-2.9-5/raster/man/rasterFromXYZ.Rd | 19 raster-2.9-5/raster/man/stackApply.Rd | 2 raster-2.9-5/raster/man/stackSelect.Rd | 3 raster-2.9-5/raster/man/unique.Rd | 8 raster-2.9-5/raster/man/update.Rd | 3 raster-2.9-5/raster/src/RcppExports.cpp | 6 raster-2.9-5/raster/src/rcpp_xyCell.cpp | 7 raster-2.9-5/raster/vignettes/Raster.Rnw | 1132 +++++++++++++-------------- raster-2.9-5/raster/vignettes/functions.Rnw | 437 ---------- raster-2.9-5/raster/vignettes/rasterfile.Rnw | 160 --- 50 files changed, 1771 insertions(+), 2733 deletions(-)
Title: A Tidy Approach to 'NetCDF' Data Exploration and Extraction
Description: Tidy tools for 'NetCDF' data sources. Explore the contents of a
'NetCDF' source (file or URL) presented as variables organized by grid with a
database-like interface. The hyper_filter() interactive function translates the
filter value or index expressions to array-slicing form. No data is read until
explicitly requested, as a data frame or list of arrays via hyper_tibble() or
hyper_array().
Author: Michael Sumner [aut, cre],
Simon Wotherspoon [ctb],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
Jakub Nowosad [ctb],
Tim Lucas [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between tidync versions 0.1.1 dated 2019-04-27 and 0.2.0 dated 2019-05-14
tidync-0.1.1/tidync/tests/testthat/test-raster-slice.R |only tidync-0.2.0/tidync/DESCRIPTION | 23 ++-- tidync-0.2.0/tidync/MD5 | 57 ++++------ tidync-0.2.0/tidync/NAMESPACE | 1 tidync-0.2.0/tidync/NEWS.md | 15 ++ tidync-0.2.0/tidync/R/activate.R | 6 - tidync-0.2.0/tidync/R/hyper_array.R | 15 +- tidync-0.2.0/tidync/R/hyper_filter.R | 1 tidync-0.2.0/tidync/R/hyper_tbl_cube.R | 2 tidync-0.2.0/tidync/R/hyper_transforms.R | 13 +- tidync-0.2.0/tidync/R/tidync.R | 18 ++- tidync-0.2.0/tidync/R/tidync_data.R | 2 tidync-0.2.0/tidync/README.md | 90 ++++++++++------ tidync-0.2.0/tidync/build/vignette.rds |binary tidync-0.2.0/tidync/inst/WORDLIST | 5 tidync-0.2.0/tidync/inst/doc/netcdf-with-tidync.R | 6 - tidync-0.2.0/tidync/inst/doc/netcdf-with-tidync.Rmd | 25 +--- tidync-0.2.0/tidync/inst/doc/netcdf-with-tidync.html | 81 ++++++++------ tidync-0.2.0/tidync/man/hyper_array.Rd | 2 tidync-0.2.0/tidync/man/hyper_tbl_cube.Rd | 2 tidync-0.2.0/tidync/man/print.tidync_data.Rd | 2 tidync-0.2.0/tidync/man/tidync.Rd | 3 tidync-0.2.0/tidync/tests/testthat/test-activate.R | 1 tidync-0.2.0/tidync/tests/testthat/test-dimensions.R | 1 tidync-0.2.0/tidync/tests/testthat/test-files-sources.R | 2 tidync-0.2.0/tidync/tests/testthat/test-files.R | 2 tidync-0.2.0/tidync/tests/testthat/test-filter.R | 1 tidync-0.2.0/tidync/tests/testthat/test-hyper-slice.R | 1 tidync-0.2.0/tidync/tests/testthat/test-lib-version.R | 3 tidync-0.2.0/tidync/vignettes/netcdf-with-tidync.Rmd | 25 +--- 30 files changed, 246 insertions(+), 159 deletions(-)
Title: 'Pipedrive API's' Functions to Improvement and Integration's
Systems
Description: R interaction with 'pipedrive.com API'.
All functions were created and documented according to <https://developers.pipedrive.com/docs/api/v1/>.
Created with the objective of offering integration and even the development of 'APIs'.
Making possible to create workflows and easily downloading databases for analysis.
Author: Ney Moresco
Maintainer: Ney Moresco <neymoresco@hotmail.com>
Diff between Rpipedrive versions 0.1.0 dated 2019-05-08 and 0.1.1 dated 2019-05-14
DESCRIPTION | 9 ++++----- MD5 | 32 ++++++++++++++++---------------- R/activities.add.R | 1 - R/activities.update.R | 1 - R/deals.add.R | 3 +-- R/deals.update.R | 3 +-- R/get_all_.R | 3 ++- R/notes.add.R | 1 - R/notes.update.R | 1 - R/organizationrelationships.add.R | 1 - R/organizationrelationships.update.R | 1 - R/organizations.add.R | 2 +- R/organizations.update.R | 2 +- R/persons.add.R | 3 +-- R/persons.update.R | 3 +-- R/products.add.R | 2 +- R/products.update.R | 2 +- 17 files changed, 30 insertions(+), 40 deletions(-)
Title: Correct Overloaded Peaks from GC-APCI-MS Data
Description: Analyzes and modifies metabolomics raw data (generated using GC-APCI-MS, Gas Chromatography-Atmospheric Pressure Chemical Ionization-Mass Spectrometry) to correct overloaded signals, i.e. ion intensities exceeding detector saturation leading to a cut-off peak. Data in xcmsRaw format are accepted as input and mzXML files can be processed alternatively. Overloaded signals are detected automatically and modified using an Gaussian or Isotopic-Ratio approach, QC plots are generated and corrected data are stored within the original xcmsRaw or mzXML respectively to allow further processing.
Author: Jan Lisec [aut, cre]
Maintainer: Jan Lisec <jan.lisec@bam.de>
Diff between CorrectOverloadedPeaks versions 1.2.15 dated 2018-07-10 and 1.2.16 dated 2019-05-14
DESCRIPTION | 14 ++--- MD5 | 14 ++--- NAMESPACE | 1 R/CorrectOverloadedPeaks.R | 2 R/FitPeakByIsotopicRatio.R | 2 build/vignette.rds |binary inst/doc/CorrectOverloadedPeaks.html | 97 +++++++++++++++++++++++++++++++---- man/FitPeakByIsotopicRatio.Rd | 2 8 files changed, 105 insertions(+), 27 deletions(-)
More information about CorrectOverloadedPeaks at CRAN
Permanent link
Title: Computes and Plots Consonance (Confidence) Intervals, P-Values,
and S-Values to Form Consonance and Surprisal Functions
Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
Author: Zad R. Chow [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew D. Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>)
Maintainer: Zad R. Chow <zad@lesslikely.com>
Diff between concurve versions 1.0.5 dated 2019-03-21 and 1.0.6 dated 2019-05-14
concurve-1.0.5/concurve/man/figures/dotplot.svg |only concurve-1.0.5/concurve/man/figures/likelihood.svg |only concurve-1.0.5/concurve/man/figures/meta-analysis.svg |only concurve-1.0.5/concurve/vignettes/figures/dotplot.svg |only concurve-1.0.5/concurve/vignettes/figures/likelihood.svg |only concurve-1.0.5/concurve/vignettes/figures/meta-analysis.svg |only concurve-1.0.6/concurve/DESCRIPTION | 27 - concurve-1.0.6/concurve/MD5 | 79 ++-- concurve-1.0.6/concurve/NEWS.md |only concurve-1.0.6/concurve/R/plotpint.R | 28 - concurve-1.0.6/concurve/R/plotsint.R | 20 - concurve-1.0.6/concurve/README.md | 75 ++-- concurve-1.0.6/concurve/build/vignette.rds |binary concurve-1.0.6/concurve/inst/CITATION |only concurve-1.0.6/concurve/inst/doc/examples.Rmd | 130 ++++--- concurve-1.0.6/concurve/inst/doc/examples.html | 221 ++++++------ concurve-1.0.6/concurve/inst/doc/stata.R |only concurve-1.0.6/concurve/inst/doc/stata.Rmd |only concurve-1.0.6/concurve/inst/doc/stata.html |only concurve-1.0.6/concurve/man/figures/function1.png |binary concurve-1.0.6/concurve/man/figures/function2.png |binary concurve-1.0.6/concurve/man/figures/function3.png |binary concurve-1.0.6/concurve/man/figures/function4.png |binary concurve-1.0.6/concurve/man/figures/function5.png |binary concurve-1.0.6/concurve/man/figures/function6.png |binary concurve-1.0.6/concurve/man/figures/logo.png |binary concurve-1.0.6/concurve/man/figures/logo.svg | 32 - concurve-1.0.6/concurve/man/genintervals.Rd | 12 concurve-1.0.6/concurve/man/meanintervals.Rd | 13 concurve-1.0.6/concurve/man/metaintervals.Rd | 10 concurve-1.0.6/concurve/man/plotpint.Rd | 4 concurve-1.0.6/concurve/man/plotsint.Rd | 4 concurve-1.0.6/concurve/vignettes/examples.Rmd | 130 ++++--- concurve-1.0.6/concurve/vignettes/figures/function1.png |binary concurve-1.0.6/concurve/vignettes/figures/function2.png |binary concurve-1.0.6/concurve/vignettes/figures/function3.png |binary concurve-1.0.6/concurve/vignettes/figures/function4.png |binary concurve-1.0.6/concurve/vignettes/figures/function5.png |binary concurve-1.0.6/concurve/vignettes/figures/function6.png |binary concurve-1.0.6/concurve/vignettes/figures/graphmenu.png |only concurve-1.0.6/concurve/vignettes/figures/logo.png |binary concurve-1.0.6/concurve/vignettes/figures/logo.svg | 32 - concurve-1.0.6/concurve/vignettes/figures/matrix.png |only concurve-1.0.6/concurve/vignettes/figures/statacon.png |only concurve-1.0.6/concurve/vignettes/figures/statacurve.png |only concurve-1.0.6/concurve/vignettes/figures/stataoutput.png |only concurve-1.0.6/concurve/vignettes/figures/statareg.png |only concurve-1.0.6/concurve/vignettes/figures/statascatter.png |only concurve-1.0.6/concurve/vignettes/figures/statasurp.png |only concurve-1.0.6/concurve/vignettes/figures/statasurplog.png |only concurve-1.0.6/concurve/vignettes/stata.Rmd |only 51 files changed, 465 insertions(+), 352 deletions(-)
Title: Fit GLM's with High-Dimensional k-Way Fixed Effects
Description: Provides a routine to concentrate out factors with many levels during the
optimization of the log-likelihood function of the corresponding generalized linear model (glm).
The package is based on the algorithm proposed by Stammann (2018) <arXiv:1707.01815> and is
restricted to glm's that are based on maximum likelihood estimation and non-linear. It also offers
an efficient algorithm to recover estimates of the fixed effects in a post-estimation routine and
includes robust and multi-way clustered standard errors. Further the package provides an
analytical bias-correction for binary choice models (logit and probit) derived by Fernandez-Val
and Weidner (2016) <doi:10.1016/j.jeconom.2015.12.014>.
Author: Amrei Stammann [aut, cre],
Daniel Czarnowske [aut] (<https://orcid.org/0000-0002-0030-929X>)
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Diff between alpaca versions 0.2 dated 2018-07-31 and 0.3 dated 2019-05-14
alpaca-0.2/alpaca/R/feglm.control.R |only alpaca-0.2/alpaca/inst/doc/empirical.R |only alpaca-0.2/alpaca/inst/doc/empirical.Rnw |only alpaca-0.2/alpaca/inst/doc/empirical.pdf |only alpaca-0.2/alpaca/inst/doc/intro.R |only alpaca-0.2/alpaca/inst/doc/intro.Rnw |only alpaca-0.2/alpaca/inst/doc/intro.pdf |only alpaca-0.2/alpaca/man/feglm.control.Rd |only alpaca-0.2/alpaca/src/get_alpha.cpp |only alpaca-0.2/alpaca/src/pseudo_demeaning.cpp |only alpaca-0.2/alpaca/vignettes/empirical.Rnw |only alpaca-0.2/alpaca/vignettes/intro.Rnw |only alpaca-0.3/alpaca/DESCRIPTION | 24 - alpaca-0.3/alpaca/MD5 | 81 ++- alpaca-0.3/alpaca/NAMESPACE | 15 alpaca-0.3/alpaca/R/RcppExports.R | 24 - alpaca-0.3/alpaca/R/alpaca.R | 14 alpaca-0.3/alpaca/R/biasCorr.R |only alpaca-0.3/alpaca/R/feglm.R | 594 ++++++++++++++++++--------- alpaca-0.3/alpaca/R/feglm.nb.R |only alpaca-0.3/alpaca/R/generics.R | 441 ++++++++++++-------- alpaca-0.3/alpaca/R/getAPEs.R |only alpaca-0.3/alpaca/R/getFEs.R | 44 +- alpaca-0.3/alpaca/R/helpers.R |only alpaca-0.3/alpaca/R/simGLM.R | 16 alpaca-0.3/alpaca/build/vignette.rds |binary alpaca-0.3/alpaca/inst/doc/howto.R |only alpaca-0.3/alpaca/inst/doc/howto.Rmd |only alpaca-0.3/alpaca/inst/doc/howto.html |only alpaca-0.3/alpaca/inst/doc/replication.R |only alpaca-0.3/alpaca/inst/doc/replication.Rmd |only alpaca-0.3/alpaca/inst/doc/replication.html |only alpaca-0.3/alpaca/man/alpaca.Rd | 4 alpaca-0.3/alpaca/man/biasCorr.Rd |only alpaca-0.3/alpaca/man/coef.APEs.Rd |only alpaca-0.3/alpaca/man/coef.feglm.Rd | 8 alpaca-0.3/alpaca/man/coef.summary.feglm.Rd | 8 alpaca-0.3/alpaca/man/feglm.Rd | 35 - alpaca-0.3/alpaca/man/feglm.nb.Rd |only alpaca-0.3/alpaca/man/feglmControl.Rd |only alpaca-0.3/alpaca/man/fitted.feglm.Rd | 8 alpaca-0.3/alpaca/man/getAPEs.Rd |only alpaca-0.3/alpaca/man/getFEs.Rd | 5 alpaca-0.3/alpaca/man/predict.feglm.Rd | 8 alpaca-0.3/alpaca/man/print.APEs.Rd |only alpaca-0.3/alpaca/man/print.feglm.Rd | 6 alpaca-0.3/alpaca/man/print.summary.APEs.Rd |only alpaca-0.3/alpaca/man/print.summary.feglm.Rd | 6 alpaca-0.3/alpaca/man/simGLM.Rd | 6 alpaca-0.3/alpaca/man/summary.APEs.Rd |only alpaca-0.3/alpaca/man/summary.feglm.Rd | 28 - alpaca-0.3/alpaca/man/vcov.feglm.Rd | 26 - alpaca-0.3/alpaca/src/CenterVariables.cpp |only alpaca-0.3/alpaca/src/GetAlpha.cpp |only alpaca-0.3/alpaca/src/GroupSums.cpp |only alpaca-0.3/alpaca/src/RcppExports.cpp | 89 +++- alpaca-0.3/alpaca/vignettes/howto.Rmd |only alpaca-0.3/alpaca/vignettes/lit.bib | 102 +++- alpaca-0.3/alpaca/vignettes/replication.Rmd |only 59 files changed, 1065 insertions(+), 527 deletions(-)
Title: Wild Binary Segmentation for Multiple Change-Point Detection
Description: Provides efficient implementation of the Wild Binary Segmentation and Binary
Segmentation algorithms for estimation of the number and locations of
multiple change-points in the piecewise constant function plus Gaussian
noise model.
Author: Rafal Baranowski and Piotr Fryzlewicz
Maintainer: Rafal Baranowski <package_maintenance@rbaranowski.com>
Diff between wbs versions 1.3 dated 2015-02-16 and 1.4 dated 2019-05-14
DESCRIPTION | 11 ++++++----- MD5 | 41 +++++++++++++++++++++-------------------- NAMESPACE | 11 +++++++++-- R/changepoints.R | 1 + R/plot.R | 2 ++ R/random.intervals.R | 1 + R/wbs.R | 2 +- man/bic.penalty.Rd | 8 ++++++-- man/changepoints.Rd | 29 +++++++++++++++-------------- man/fixed.intervals.Rd | 8 ++++---- man/mbic.penalty.Rd | 4 ++-- man/means.between.cpt.Rd | 4 ++-- man/plot.sbs.Rd | 6 +++--- man/plot.wbs.Rd | 6 +++--- man/print.sbs.Rd | 4 ++-- man/print.wbs.Rd | 4 ++-- man/random.intervals.Rd | 6 +++--- man/sbs.Rd | 14 +++++++------- man/ssic.penalty.Rd | 4 ++-- man/wbs-package.Rd | 4 ++-- man/wbs.Rd | 16 ++++++++-------- src/wbs_init.c |only 22 files changed, 102 insertions(+), 84 deletions(-)
Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on
an additive model where non-linear trends are fit with yearly, weekly, and
daily seasonality, plus holiday effects. It works best with time series
that have strong seasonal effects and several seasons of historical data.
Prophet is robust to missing data and shifts in the trend, and typically
handles outliers well.
Author: Sean Taylor [cre, aut],
Ben Letham [aut]
Maintainer: Sean Taylor <sjtz@pm.me>
Diff between prophet versions 0.4 dated 2018-12-21 and 0.5 dated 2019-05-14
prophet-0.4/prophet/man/rolling_mean.Rd |only prophet-0.5/prophet/DESCRIPTION | 14 - prophet-0.5/prophet/MD5 | 28 +- prophet-0.5/prophet/R/diagnostics.R | 173 +++++++++++++----- prophet-0.5/prophet/R/plot.R | 49 +++-- prophet-0.5/prophet/R/prophet.R | 54 ++++- prophet-0.5/prophet/build/vignette.rds |binary prophet-0.5/prophet/inst/doc/quick_start.html | 31 +-- prophet-0.5/prophet/man/add_seasonality.Rd | 8 prophet-0.5/prophet/man/performance_metrics.Rd | 22 +- prophet-0.5/prophet/man/plot_weekly.Rd | 5 prophet-0.5/prophet/man/plot_yearly.Rd | 5 prophet-0.5/prophet/man/rolling_mean_by_h.Rd |only prophet-0.5/prophet/src/Makevars | 2 prophet-0.5/prophet/tests/testthat/test_diagnostics.R | 44 ++++ prophet-0.5/prophet/tests/testthat/test_prophet.R | 69 +++++-- 16 files changed, 380 insertions(+), 124 deletions(-)
Title: Solver for Partially Observable Markov Decision Processes
(POMDP)
Description: Provides an interface to pomdp-solve, a solver for Partially Observable Markov Decision Processes (POMDP). The package enables the user to simply define all components of a POMDP model and solve the problem using several methods. The package also contains functions to analyze and visualize the POMDP solutions (e.g., the optimal policy).
Author: Hossein Kamalzadeh [aut, cph, cre],
Michael Hahsler [aut, cph],
Anthony R. Cassandra [ctb, cph]
Maintainer: Hossein Kamalzadeh <hkamalzadeh@smu.edu>
Diff between pomdp versions 0.9.1 dated 2019-01-02 and 0.9.1-1 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- inst/doc/POMDP.pdf |binary src/mdp/mdp.c | 2 +- 5 files changed, 14 insertions(+), 10 deletions(-)
Title: Simultaneous Generation of Multivariate Data with Poisson and
Normal Marginals
Description: Generates multivariate data with count and continuous variables with a pre-specified correlation matrix. The count and continuous variables are assumed to have Poisson and normal marginals, respectively. The data generation mechanism is a combination of the normal to anything principle and a connection between Poisson and normal correlations in the mixture.
Author: Anup Amatya, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between PoisNor versions 1.3 dated 2019-02-24 and 1.3.1 dated 2019-05-14
DESCRIPTION | 8 +- MD5 | 18 ++-- R/Valid.correlation.R | 2 man/Cor.PN.Limit.Rd | 64 ++++++++-------- man/Cor.PP.Limit.Rd | 54 +++++++------- man/PoisNor-package.Rd | 6 - man/Valid.correlation.Rd | 70 +++++++++--------- man/Validate.correlation.Rd | 168 ++++++++++++++++++++++---------------------- man/cmat.star.Rd | 112 ++++++++++++++--------------- man/genPoisNor.Rd | 115 +++++++++++++++--------------- 10 files changed, 309 insertions(+), 308 deletions(-)
Title: Concurrent Generation of Ordinal and Normal Data with Given
Correlation Matrix and Marginal Distributions
Description: Implementation of a procedure for generating samples from a mixed distribution of ordinal and normal random variables with pre-specified correlation matrix and marginal distributions.
Author: Anup Amatya, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between OrdNor versions 2.2 dated 2019-02-28 and 2.2.1 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ man/LimitforON.Rd | 2 +- man/LimitforOO.Rd | 2 +- man/OrdNor-package.Rd | 6 +++--- man/genOrdNor.Rd | 4 ++-- man/ordinalize.Rd | 47 +++++++++++++++++++++++++---------------------- 7 files changed, 42 insertions(+), 39 deletions(-)
Title: Read Hierarchical Fixed Width Files
Description: Read hierarchical fixed width files like those commonly used by
many census data providers. Also allows for reading of data in chunks,
and reading 'gzipped' files without storing the full file in memory.
Author: Greg Freedman Ellis [aut],
Derek Burk [aut, cre],
Joe Grover [ctb],
Mark Padgham [ctb],
Hadley Wickham [ctb] (Code adapted from readr),
Jim Hester [ctb] (Code adapted from readr),
Romain Francois [ctb] (Code adapted from readr),
R Core Team [ctb] (Code adapted from readr),
RStudio [cph, fnd] (Code adapted from readr),
Jukka Jylänki [ctb, cph] (Code adapted from readr),
Mikkel Jørgensen [ctb, cph] (Code adapted from readr),
University of Minnesota [cph]
Maintainer: Derek Burk <ipums+cran@umn.edu>
Diff between hipread versions 0.2.0 dated 2019-02-28 and 0.2.1 dated 2019-05-14
DESCRIPTION | 17 - LICENSE | 678 ++++++++++++++++++++++---------------------- MD5 | 14 NEWS.md | 3 R/utilities.R | 8 inst/extdata/test-basic.dat | 18 - man/hipread-package.Rd | 8 tests/testthat.R | 8 8 files changed, 384 insertions(+), 370 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.2.2 dated 2019-04-08 and 0.2.3 dated 2019-05-14
DESCRIPTION | 6 - MD5 | 14 +-- NEWS.md | 6 + R/enhancements.R | 1 build/vignette.rds |binary inst/doc/lifeExpectancy.html | 158 +++++++++++++++-------------------- inst/doc/selectIndicatorsRedRed.html | 2 tests/testthat/test-deprivation.R | 2 8 files changed, 88 insertions(+), 101 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.7 dated 2019-04-23 and 9.8-1 dated 2019-05-14
fields-9.7/fields/R/print.summary.spatialProcess.R |only fields-9.8-1/fields/DESCRIPTION | 8 fields-9.8-1/fields/MD5 | 34 +- fields-9.8-1/fields/NAMESPACE | 13 - fields-9.8-1/fields/R/mKrig.R | 11 fields-9.8-1/fields/R/mKrig.family.R | 214 ++++++++++-------- fields-9.8-1/fields/R/mKrigCheckXY.R | 7 fields-9.8-1/fields/R/print.spatialProcess.R | 111 --------- fields-9.8-1/fields/R/print.spatialProcessSummary.R |only fields-9.8-1/fields/R/summary.spatialProcess.R | 103 ++++++++ fields-9.8-1/fields/man/fields-internal.Rd | 2 fields-9.8-1/fields/man/mKrig.Rd | 10 fields-9.8-1/fields/man/spatialProcess.Rd | 23 + fields-9.8-1/fields/man/summary.Krig.Rd | 5 fields-9.8-1/fields/tests/SEFixedParameters.R |only fields-9.8-1/fields/tests/SEFixedParameters.Rout.save |only fields-9.8-1/fields/tests/cov.test.R | 2 fields-9.8-1/fields/tests/cov.test.Rout.save | 8 fields-9.8-1/fields/tests/mKrigMLETest.R | 63 +++-- fields-9.8-1/fields/tests/mKrigMLETest.Rout.save | 39 ++- 20 files changed, 365 insertions(+), 288 deletions(-)
Title: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample
Corrections
Description: Provides several cluster-robust variance estimators (i.e.,
sandwich estimators) for ordinary and weighted least squares linear regression
models, including the bias-reduced linearization estimator introduced by Bell
and McCaffrey (2002)
<http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf> and
developed further by Pustejovsky and Tipton (2017)
<DOI:10.1080/07350015.2016.1247004>. The package includes functions for estimating
the variance- covariance matrix and for testing single- and multiple-
contrast hypotheses based on Wald test statistics. Tests of single regression
coefficients use Satterthwaite or saddle-point corrections. Tests of multiple-
contrast hypotheses use an approximation to Hotelling's T-squared distribution.
Methods are provided for a variety of fitted models, including lm() and mlm
objects, glm(), ivreg() (from package 'AER'), plm() (from package 'plm'), gls()
and lme() (from 'nlme'), robu() (from 'robumeta'), and rma.uni() and rma.mv()
(from 'metafor').
Author: James Pustejovsky [aut, cre] (<https://orcid.org/0000-0003-0591-9465>)
Maintainer: James Pustejovsky <jepusto@gmail.com>
Diff between clubSandwich versions 0.3.4 dated 2019-05-11 and 0.3.5 dated 2019-05-14
DESCRIPTION | 6 - MD5 | 58 ++++++------- NEWS | 2 R/utilities.R | 2 build/partial.rdb |binary inst/doc/Robust-Variance-Estimation-with-clubSandwich.html | 4 inst/doc/meta-analysis-with-CRVE.html | 4 inst/doc/panel-data-CRVE.html | 4 tests/testthat.R | 1 tests/testthat/test_Wald.R | 1 tests/testthat/test_coef.R | 1 tests/testthat/test_conf_int.R | 1 tests/testthat/test_glm_logit.R | 8 - tests/testthat/test_gls.R | 1 tests/testthat/test_ignore_absorption.R | 2 tests/testthat/test_impute_covariance_matrix.R | 1 tests/testthat/test_intercept_formulas.R | 1 tests/testthat/test_ivreg.R | 2 tests/testthat/test_lm.R | 1 tests/testthat/test_lme_2level.R | 9 +- tests/testthat/test_lme_3level.R | 8 + tests/testthat/test_mlm.R | 1 tests/testthat/test_plm-ID-variables.R | 2 tests/testthat/test_plm-first-differences.R | 4 tests/testthat/test_plm-fixed-effects.R | 1 tests/testthat/test_plm-random-effects.R | 1 tests/testthat/test_plm-unbalanced-fixed-effects.R | 1 tests/testthat/test_rma-mv.R | 1 tests/testthat/test_rma-uni.R | 1 tests/testthat/test_robu.R | 1 30 files changed, 81 insertions(+), 49 deletions(-)
Title: Batch Computing with R
Description: Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Author: Bernd Bischl <bernd_bischl@gmx.net>,
Michel Lang <michellang@gmail.com>,
Henrik Bengtsson <henrikb@braju.com>
Maintainer: Bernd Bischl <bernd_bischl@gmx.net>
Diff between BatchJobs versions 1.7 dated 2017-11-28 and 1.8 dated 2019-05-14
BatchJobs-1.7/BatchJobs/tests/testthat/test_grepLogs.R |only BatchJobs-1.8/BatchJobs/DESCRIPTION | 9 BatchJobs-1.8/BatchJobs/MD5 | 99 ++++------ BatchJobs-1.8/BatchJobs/NEWS | 3 BatchJobs-1.8/BatchJobs/R/Job.R | 3 BatchJobs-1.8/BatchJobs/R/conf.R | 29 -- BatchJobs-1.8/BatchJobs/R/database.R | 21 +- BatchJobs-1.8/BatchJobs/R/filenames.R | 2 BatchJobs-1.8/BatchJobs/R/submitJobs.R | 4 BatchJobs-1.8/BatchJobs/R/syncRegistry.R | 4 BatchJobs-1.8/BatchJobs/R/zzz.R | 15 + BatchJobs-1.8/BatchJobs/man/addRegistryPackages.Rd | 1 BatchJobs-1.8/BatchJobs/man/addRegistrySourceDirs.Rd | 1 BatchJobs-1.8/BatchJobs/man/addRegistrySourceFiles.Rd | 1 BatchJobs-1.8/BatchJobs/man/batchExport.Rd | 1 BatchJobs-1.8/BatchJobs/man/batchUnexport.Rd | 1 BatchJobs-1.8/BatchJobs/man/configuration.Rd | 1 BatchJobs-1.8/BatchJobs/man/debugMulticore.Rd | 1 BatchJobs-1.8/BatchJobs/man/debugSSH.Rd | 7 BatchJobs-1.8/BatchJobs/man/findState.Rd | 39 --- BatchJobs-1.8/BatchJobs/man/getConfig.Rd | 1 BatchJobs-1.8/BatchJobs/man/getErrorMessages.Rd | 1 BatchJobs-1.8/BatchJobs/man/getJobInfo.Rd | 1 BatchJobs-1.8/BatchJobs/man/getLogFiles.Rd | 1 BatchJobs-1.8/BatchJobs/man/grepLogs.Rd | 5 BatchJobs-1.8/BatchJobs/man/killJobs.Rd | 1 BatchJobs-1.8/BatchJobs/man/loadConfig.Rd | 1 BatchJobs-1.8/BatchJobs/man/loadExports.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctions.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsInteractive.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsLSF.Rd | 5 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsLocal.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsMulticore.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsOpenLava.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsSGE.Rd | 4 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsSLURM.Rd | 5 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsSSH.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeClusterFunctionsTorque.Rd | 1 BatchJobs-1.8/BatchJobs/man/makeSSHWorker.Rd | 5 BatchJobs-1.8/BatchJobs/man/reduceResults.Rd | 4 BatchJobs-1.8/BatchJobs/man/removeRegistryPackages.Rd | 1 BatchJobs-1.8/BatchJobs/man/removeRegistrySourceDirs.Rd | 1 BatchJobs-1.8/BatchJobs/man/removeRegistrySourceFiles.Rd | 1 BatchJobs-1.8/BatchJobs/man/resetJobs.Rd | 1 BatchJobs-1.8/BatchJobs/man/setConfig.Rd | 1 BatchJobs-1.8/BatchJobs/man/setJobFunction.Rd | 1 BatchJobs-1.8/BatchJobs/man/setRegistryPackages.Rd | 1 BatchJobs-1.8/BatchJobs/man/showLog.Rd | 1 BatchJobs-1.8/BatchJobs/man/testJob.Rd | 1 BatchJobs-1.8/BatchJobs/man/waitForJobs.Rd | 4 BatchJobs-1.8/BatchJobs/tests/testthat/test_testJob.R | 6 51 files changed, 154 insertions(+), 149 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.0.0 dated 2019-05-04 and 1.0.1 dated 2019-05-14
DESCRIPTION | 8 - MD5 | 68 +++++---- NAMESPACE | 1 NEWS.md | 28 +++ R/col_types.R | 2 R/generator.R | 2 R/utils.R | 8 + R/vroom.R | 52 ++++--- R/vroom_fwf.R | 4 R/vroom_lines.R |only README.md | 42 +++-- build/vignette.rds |binary inst/bench/all_character-benchmark.R | 2 inst/bench/all_character-times.tsv | 220 +++++++++++++++---------------- inst/bench/all_numeric-times.tsv | 224 +++++++++++++++---------------- inst/bench/sessioninfo.tsv | 4 inst/bench/taxi-benchmark.R | 2 inst/bench/taxi-times.tsv | 224 +++++++++++++++---------------- inst/bench/taxi_writing-times.tsv | 40 ++--- inst/doc/benchmarks.Rmd | 2 inst/doc/benchmarks.html | 246 +++++++++++++++++------------------ inst/doc/vroom.Rmd | 6 inst/doc/vroom.html | 5 man/gen_tbl.Rd | 2 man/vroom_lines.Rd |only src/RcppExports.cpp | 12 - src/delimited_index.cc | 8 - src/mio/include/mio/detail/mmap.ipp | 2 src/multi_progress.h | 22 ++- src/parallel.h | 12 - src/vroom.cc | 4 src/vroom_fwf.cc | 4 src/vroom_vec.h | 27 ++- tests/testthat/test-col_types.R |only tests/testthat/test-vroom_lines.R |only vignettes/benchmarks.Rmd | 2 vignettes/vroom.Rmd | 6 37 files changed, 683 insertions(+), 608 deletions(-)
Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis, 'tidyRSS' parses RSS, Atom XML, JSON and geoRSS feeds and returns a tidy data frame.
Author: Robert Myles McDonnell
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between tidyRSS versions 1.2.9 dated 2019-05-09 and 1.2.10 dated 2019-05-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/rss_parse.R | 13 +++++++++---- inst/doc/tidyrss.html | 4 ++-- 5 files changed, 23 insertions(+), 13 deletions(-)
Title: Group Animal Relocation Data by Spatial and Temporal
Relationship
Description: Detects spatial and temporal groups in GPS relocations.
It can be used to convert GPS relocations to
gambit-of-the-group format to build proximity-based social networks.
In addition, the randomizations function provides data-stream
randomization methods suitable for GPS data.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>),
Quinn Webber [aut] (<https://orcid.org/0000-0002-0434-9360>),
Eric Vander Wal [aut] (<https://orcid.org/0000-0002-8534-4317>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Diff between spatsoc versions 0.1.8 dated 2019-04-05 and 0.1.9 dated 2019-05-14
DESCRIPTION | 8 +-- MD5 | 26 ++++----- NEWS.md | 7 ++ R/randomizations.R | 55 ++++++++++++++------- inst/doc/intro-spatsoc.R | 2 inst/doc/intro-spatsoc.Rmd | 2 inst/doc/intro-spatsoc.html | 95 +++++++++++++++++++++--------------- inst/doc/using-in-sna.R | 12 +++- inst/doc/using-in-sna.Rmd | 12 +++- inst/doc/using-in-sna.html | 12 +++- man/spatsoc.Rd | 2 tests/testthat/test-random.R | 112 +++++++++++++++++++++++++++++++++++++++++-- vignettes/intro-spatsoc.Rmd | 2 vignettes/using-in-sna.Rmd | 12 +++- 14 files changed, 260 insertions(+), 99 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.6 dated 2019-05-14 and 1.1.7 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NEWS.md | 4 ++++ R/patch_env.R |only R/relop_extend.R | 2 +- R/relop_order_expr.R | 2 +- R/relop_project.R | 2 +- R/relop_select_rows.R | 2 +- R/relop_theta_join.R | 2 +- inst/doc/GroupedSampling.html | 4 ++-- inst/doc/logisticexample.html | 4 ++-- 11 files changed, 27 insertions(+), 22 deletions(-)
Title: Interface to National Sleep Research Resource
Description: Allows users to access data from the National Sleep
Research Resource ('NSRR') <https://sleepdata.org/>.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between nsrr versions 0.1.0 dated 2019-02-22 and 0.1.2 dated 2019-05-14
DESCRIPTION | 6 +- MD5 | 38 +++++++-------- NAMESPACE | 2 NEWS.md | 4 + R/nsrr_all_files.R | 12 +++- R/nsrr_datasets.R | 38 ++++++++++++++- R/nsrr_download.R | 14 ++++- R/nsrr_token.R | 1 R/nsrr_version.R | 6 ++ R/nsrr_website.R | 2 README.md | 29 +++++++++++ build/vignette.rds |binary inst/doc/downloading_data_nsrr.html | 88 ++++++++++++++++++++++-------------- man/figures/README-example-1.png |binary man/nsrr_all_dataset_files.Rd | 10 +++- man/nsrr_datasets.Rd | 18 ++++++- man/nsrr_download_url.Rd | 10 +++- man/nsrr_token.Rd | 1 man/nsrr_version.Rd | 3 + tests/testthat/test-token.R | 10 ++-- 20 files changed, 220 insertions(+), 72 deletions(-)
Title: Multivariate Pseudo-Random Number Generation
Description: Pseudo-random number generation for 11 multivariate distributions: Normal, t, Uniform, Bernoulli, Hypergeometric, Beta (Dirichlet), Multinomial, Dirichlet-Multinomial, Laplace, Wishart, and Inverted Wishart. The details of the method are explained in Demirtas (2004) <DOI:10.22237/jmasm/1099268340>.
Author: Hakan Demirtas, Rawan Allozi, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between MultiRNG versions 1.2 dated 2019-02-24 and 1.2.2 dated 2019-05-14
DESCRIPTION | 10 +- MD5 | 6 - R/draw.correlated.binary.R | 177 ++++++++++++++++++++++++++++----------------- man/MultiRNG-package.Rd | 6 - 4 files changed, 125 insertions(+), 74 deletions(-)
Title: Discovery of Process Models with the Heuristics Miner
Description: Provides the heuristics miner algorithm for process discovery
as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The
algorithm builds a causal net from an event log created with the 'bupaR'
package. Event logs are a set of ordered sequences of events for which
'bupaR' provides the S3 class eventlog(). The discovered causal nets
can be visualised as 'htmlwidgets' and it is possible to annotate them with
the occurrence frequency or processing and waiting time of process
activities.
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <felix.mannhardt@sintef.no>
Diff between heuristicsmineR versions 0.2.0 dated 2019-05-02 and 0.2.1 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 18 ++++++++++-------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/utils-pipe.R |only README.md | 6 ++++++ man/pipe.Rd |only src/count_length_two_loops.cpp | 8 ++++++-- src/count_parallel_lifecycle.cpp | 5 +++++ src/count_precedence.cpp | 4 ++++ src/count_precedence_lifecycle.cpp | 5 +++++ 11 files changed, 46 insertions(+), 14 deletions(-)
More information about heuristicsmineR at CRAN
Permanent link
Title: Gower's Distance
Description: Compute Gower's distance (or similarity) coefficient between records. Compute
the top-n matches between records. Core algorithms are executed in parallel on systems
supporting OpenMP.
Author: Mark van der Loo [aut, cre],
David Turner [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between gower versions 0.2.0 dated 2019-03-07 and 0.2.1 dated 2019-05-14
gower-0.2.0/gower/tests/testthat |only gower-0.2.0/gower/tests/testthat.R |only gower-0.2.1/gower/DESCRIPTION | 9 ++++----- gower-0.2.1/gower/MD5 | 12 ++++++------ gower-0.2.1/gower/NEWS | 3 +++ gower-0.2.1/gower/build/vignette.rds |binary gower-0.2.1/gower/inst/doc/intro.pdf |binary gower-0.2.1/gower/inst/tinytest |only gower-0.2.1/gower/tests/tinytest.R |only 9 files changed, 13 insertions(+), 11 deletions(-)
Title: Simultaneous Generation of Multivariate Binary and Normal
Variates
Description: Generating multiple binary and normal variables simultaneously given marginal characteristics and association structure based on the methodology proposed by Demirtas and Doganay (2012) <DOI:10.1080/10543406.2010.521874>.
Author: Anup Amatya, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between BinNor versions 2.3 dated 2019-03-01 and 2.3.1 dated 2019-05-14
DESCRIPTION | 8 +- MD5 | 10 +-- R/simulation.R | 139 +++++++++++++++++++++---------------------- man/BinNor-package.Rd | 4 - man/compute.sigma.star.Rd | 2 man/lower.tri.to.corr.mat.Rd | 62 +++++++++---------- 6 files changed, 112 insertions(+), 113 deletions(-)
Title: Analyze Data Generated from Syntech Servosphere Trials
Description: Functions that facilitate and speed up the analysis of data
produced by a Syntech servosphere <http://www.ockenfels-syntech.com/products/locomotion-compensation/>,
which is equipment for studying the movement behavior of arthropods.
This package is designed to make working with data produced from a
servosphere easy for someone new to or unfamiliar with R. The functions
provided in this package fall into three broad-use categories: functions for
cleaning raw data produced by the servosphere software, functions for
deriving movement variables based on position data, and functions for
summarizing movement variables for easier analysis. These functions are
built with functions from the tidyverse package to work efficiently, as a
single servosphere file may consist of hundreds of thousands of rows of data
and a user may wish to analyze hundreds of files at a time. Many of the
movement variables derivable through this package are described in the
following papers:
Otálora-Luna, Fernando; Dickens, Joseph C. (2011) <doi:10.1371/journal.pone.0020990>
Party, Virginie; Hanot, Christophe; Busser, Daniela Schmidt; Rochat, Didier; Renou, Michel (2013) <doi:10.1371/journal.pone.0052897>
Bell, William J.; Kramer, Ernest (1980) <doi:10.1007/BF01402908>
Becher, Paul G; Guerin, Patrick M. (2009) <doi:10.1016/j.jinsphys.2009.01.006>.
Author: Jacob T. Wittman [aut, cre],
Brian H. Aukema [ctb]
Maintainer: Jacob T. Wittman <wittja01@gmail.com>
Diff between servosphereR versions 0.1.0 dated 2019-03-06 and 0.1.1 dated 2019-05-14
DESCRIPTION | 6 MD5 | 12 - NEWS.md | 7 R/fetch_clean_functions.R | 12 - build/vignette.rds |binary inst/doc/my-vignette.html | 494 ++++++++++++++++++++++++++++++++-------------- man/aggregateData.Rd | 12 - 7 files changed, 377 insertions(+), 166 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.3.9 dated 2019-04-15 and 0.4.0 dated 2019-05-14
DESCRIPTION | 14 MD5 | 103 ++--- NAMESPACE | 9 R/ARMA.R | 87 ++-- R/ARMA_optim.R | 221 ++++++++--- R/Boost.R |only R/Causation.R | 31 + R/Dependence.R | 160 ++------ R/Dependence_base.R |only R/Dependence_matrix.R | 5 R/FSD.R | 4 R/Multivariate_Regression.R | 160 +++++--- R/Normalization.R | 2 R/Numerical_Differentiation.R | 9 R/Partial_Moments.R | 11 R/Partition_Map.R | 33 + R/Regression.R | 251 ++++++++----- R/SD_Efficient_Set.R | 2 R/Stack.R | 215 +++++++---- R/dy_d_wrt.R | 3 R/dy_dx.R | 3 R/gvload.R | 22 - build/vignette.rds |binary inst/doc/NNSvignette_Classification.R |only inst/doc/NNSvignette_Classification.Rmd |only inst/doc/NNSvignette_Classification.html |only inst/doc/NNSvignette_Clustering_and_Regression.R | 5 inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 27 - inst/doc/NNSvignette_Clustering_and_Regression.html | 325 ++++++++++++++--- inst/doc/NNSvignette_Correlation_and_Dependence.R | 1 inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 1 inst/doc/NNSvignette_Correlation_and_Dependence.html | 333 ++++++++++++++--- inst/doc/NNSvignette_Forecasting.R | 6 inst/doc/NNSvignette_Forecasting.Rmd | 14 inst/doc/NNSvignette_Forecasting.html | 358 +++++++++++++++---- inst/doc/NNSvignette_Partial_Moments.Rmd | 22 - inst/doc/NNSvignette_Partial_Moments.html | 358 +++++++++++++++---- man/Co.LPM.Rd | 3 man/Co.UPM.Rd | 3 man/NNS.ANOVA.Rd | 4 man/NNS.ARMA.Rd | 9 man/NNS.ARMA.optim.Rd | 31 + man/NNS.PDF.Rd | 3 man/NNS.boost.Rd |only man/NNS.caus.Rd | 8 man/NNS.dep.Rd | 5 man/NNS.diff.Rd | 3 man/NNS.reg.Rd | 13 man/NNS.stack.Rd | 23 - man/dy.d_.Rd | 3 man/dy.dx.Rd | 3 vignettes/NNSvignette_Classification.Rmd |only vignettes/NNSvignette_Clustering_and_Regression.Rmd | 27 - vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 1 vignettes/NNSvignette_Forecasting.Rmd | 14 vignettes/NNSvignette_Partial_Moments.Rmd | 22 - 56 files changed, 2078 insertions(+), 892 deletions(-)
Title: The MBESS R Package
Description: Implements methods that useful in designing research studies and analyzing data, with
particular emphasis on methods that are developed for or used within the behavioral,
educational, and social sciences (broadly defined). That being said, many of the methods
implemented within MBESS are applicable to a wide variety of disciplines. MBESS has a
suite of functions for a variety of related topics, such as effect sizes, confidence intervals
for effect sizes (including standardized effect sizes and noncentral effect sizes), sample size
planning (from the accuracy in parameter estimation [AIPE], power analytic, equivalence, and
minimum-risk point estimation perspectives), mediation analysis, various properties of
distributions, and a variety of utility functions. MBESS (pronounced 'em-bes') was originally
an acronym for 'Methods for the Behavioral, Educational, and Social Sciences,' but at this
point MBESS contains methods applicable and used in a wide variety of fields and is an
orphan acronym, in the sense that what was an acronym is now literally its name. MBESS has
greatly benefited from others, see <http://nd.edu/~kkelley/site/MBESS.html> for a detailed
list of those that have contributed and other details.
Author: Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between MBESS versions 4.4.3 dated 2018-01-10 and 4.5.0 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++---- R/ci.reliability.R | 2 ++ R/ci.sc.R | 3 ++- R/mediation.R | 2 +- R/var.ete.R |only man/var.ete.Rd |only 7 files changed, 15 insertions(+), 10 deletions(-)
Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>),
Thanh Wang [ctb] (<https://orcid.org/0000-0002-5729-1908>)
Maintainer: Miao YU <yufreecas@gmail.com>
Diff between enviGCMS versions 0.5.0 dated 2018-04-25 and 0.5.5 dated 2019-05-14
enviGCMS-0.5.0/enviGCMS/R/mzrt.R |only enviGCMS-0.5.5/enviGCMS/DESCRIPTION | 33 - enviGCMS-0.5.5/enviGCMS/MD5 | 125 +++-- enviGCMS-0.5.5/enviGCMS/NAMESPACE | 21 enviGCMS-0.5.5/enviGCMS/NEWS.md | 41 + enviGCMS-0.5.5/enviGCMS/R/deprecated.R |only enviGCMS-0.5.5/enviGCMS/R/general.R | 342 --------------- enviGCMS-0.5.5/enviGCMS/R/getdata.R |only enviGCMS-0.5.5/enviGCMS/R/getmzrt.R |only enviGCMS-0.5.5/enviGCMS/R/io.R | 547 +++++------------------- enviGCMS-0.5.5/enviGCMS/R/mda.R |only enviGCMS-0.5.5/enviGCMS/R/peaks.R | 483 +++++++++++---------- enviGCMS-0.5.5/enviGCMS/R/plotmzrt.R |only enviGCMS-0.5.5/enviGCMS/R/sccp.R | 374 +++++++++------- enviGCMS-0.5.5/enviGCMS/R/shiny.R | 13 enviGCMS-0.5.5/enviGCMS/README.md | 12 enviGCMS-0.5.5/enviGCMS/build/vignette.rds |binary enviGCMS-0.5.5/enviGCMS/data/list.rda |only enviGCMS-0.5.5/enviGCMS/inst/doc/GCMSDA.Rmd | 36 - enviGCMS-0.5.5/enviGCMS/inst/doc/GCMSDA.html | 219 ++++++++- enviGCMS-0.5.5/enviGCMS/inst/shinyapps/MDPlot |only enviGCMS-0.5.5/enviGCMS/man/Getisotopologues.Rd | 4 enviGCMS-0.5.5/enviGCMS/man/findohc.Rd |only enviGCMS-0.5.5/enviGCMS/man/getareastd.Rd | 4 enviGCMS-0.5.5/enviGCMS/man/getbgremove.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getbiotechrep.Rd | 6 enviGCMS-0.5.5/enviGCMS/man/getcsv.Rd |only enviGCMS-0.5.5/enviGCMS/man/getdata.Rd | 4 enviGCMS-0.5.5/enviGCMS/man/getdata2.Rd | 14 enviGCMS-0.5.5/enviGCMS/man/getdoe.Rd | 16 enviGCMS-0.5.5/enviGCMS/man/getfeaturesanova.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getfeaturest.Rd | 18 enviGCMS-0.5.5/enviGCMS/man/getfilter.Rd |only enviGCMS-0.5.5/enviGCMS/man/getformula.Rd |only enviGCMS-0.5.5/enviGCMS/man/getgrouprep.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getimputation.Rd | 10 enviGCMS-0.5.5/enviGCMS/man/getmass.Rd |only enviGCMS-0.5.5/enviGCMS/man/getmassdefect.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getmdh.Rd |only enviGCMS-0.5.5/enviGCMS/man/getmdr.Rd |only enviGCMS-0.5.5/enviGCMS/man/getmzrt.Rd | 34 + enviGCMS-0.5.5/enviGCMS/man/getmzrt2.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getmzrtcsv.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/getoverlapmass.Rd |only enviGCMS-0.5.5/enviGCMS/man/getoverlappeak.Rd |only enviGCMS-0.5.5/enviGCMS/man/getoverlaprt.Rd |only enviGCMS-0.5.5/enviGCMS/man/getpower.Rd |only enviGCMS-0.5.5/enviGCMS/man/getrmd.Rd |only enviGCMS-0.5.5/enviGCMS/man/getsim.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/gettechrep.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/gettimegrouprep.Rd | 6 enviGCMS-0.5.5/enviGCMS/man/getupload.Rd | 21 enviGCMS-0.5.5/enviGCMS/man/getupload2.Rd | 7 enviGCMS-0.5.5/enviGCMS/man/getupload3.Rd |only enviGCMS-0.5.5/enviGCMS/man/gifmr.Rd | 16 enviGCMS-0.5.5/enviGCMS/man/list.Rd |only enviGCMS-0.5.5/enviGCMS/man/plotden.Rd |only enviGCMS-0.5.5/enviGCMS/man/plote.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/plothm.Rd | 6 enviGCMS-0.5.5/enviGCMS/man/plotkms.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/plotmr.Rd | 14 enviGCMS-0.5.5/enviGCMS/man/plotmrc.Rd | 14 enviGCMS-0.5.5/enviGCMS/man/plotpca.Rd | 28 - enviGCMS-0.5.5/enviGCMS/man/plotridges.Rd |only enviGCMS-0.5.5/enviGCMS/man/plotrla.Rd |only enviGCMS-0.5.5/enviGCMS/man/plotrsd.Rd | 12 enviGCMS-0.5.5/enviGCMS/man/runMDPlot.Rd |only enviGCMS-0.5.5/enviGCMS/man/svabatch.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/svacor.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/svadata.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/svapca.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/svaplot.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/svaupload.Rd | 2 enviGCMS-0.5.5/enviGCMS/man/writeMSP.Rd | 2 enviGCMS-0.5.5/enviGCMS/vignettes/GCMSDA.Rmd | 36 - 75 files changed, 1153 insertions(+), 1397 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.81 dated 2019-04-12 and 1.86 dated 2019-05-14
DESCRIPTION | 10 +- MD5 | 30 +++--- R/Box20.R |only R/Box26.R |only R/GenerateBoxData.R | 79 ++++++++++------ R/Omega.R | 2 R/faMain.R | 231 ++++++++++++++++++++++++++++--------------------- R/faStandardize.R | 6 - R/fareg.R | 45 ++++++++- data/Box20.rda |only data/Box26.rda |only inst/CITATION | 4 man/BiFAD.Rd | 3 man/Box20.Rd |only man/Box26.Rd |only man/GenerateBoxData.Rd | 23 ++-- man/SLi.Rd | 3 man/SchmidLeiman.Rd | 3 man/faMain.Rd | 25 +++-- 19 files changed, 286 insertions(+), 178 deletions(-)
Title: Functions for Tabular Reporting
Description: Create pretty tables for 'HTML', 'Microsoft Word' and 'Microsoft PowerPoint' documents.
Functions are provided to let users create tables, modify and format their content.
It extends package 'officer' that does not contain any feature for customized tabular reporting
and can be used within R markdown documents.
Author: David Gohel [aut, cre],
Quentin Fazilleau [ctb],
Maxim Nazarov [ctb] (rmarkdown for docx output),
Titouan Robert [ctb]
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between flextable versions 0.5.2 dated 2019-04-02 and 0.5.4 dated 2019-05-14
flextable-0.5.2/flextable/man/add_header_footer.Rd |only flextable-0.5.4/flextable/DESCRIPTION | 14 flextable-0.5.4/flextable/MD5 | 115 +++-- flextable-0.5.4/flextable/NAMESPACE | 11 flextable-0.5.4/flextable/NEWS | 9 flextable-0.5.4/flextable/R/01_fpstruct.R | 19 flextable-0.5.4/flextable/R/05_content.R | 5 flextable-0.5.4/flextable/R/body_add_flextable.R | 4 flextable-0.5.4/flextable/R/display.R | 96 ++++ flextable-0.5.4/flextable/R/flextable.R | 52 ++ flextable-0.5.4/flextable/R/flextable_sizes.R | 57 ++ flextable-0.5.4/flextable/R/formatters.R | 41 +- flextable-0.5.4/flextable/R/ph_with_flextable.R | 4 flextable-0.5.4/flextable/R/printers.R | 126 +++++- flextable-0.5.4/flextable/R/set_headers.R | 149 ++++--- flextable-0.5.4/flextable/R/tabpart_mains.R | 5 flextable-0.5.4/flextable/R/utils.R | 3 flextable-0.5.4/flextable/README.md | 8 flextable-0.5.4/flextable/build/vignette.rds |binary flextable-0.5.4/flextable/inst/doc/display.R | 14 flextable-0.5.4/flextable/inst/doc/display.Rmd | 49 ++ flextable-0.5.4/flextable/inst/doc/display.html | 198 +++++---- flextable-0.5.4/flextable/inst/doc/format.html | 11 flextable-0.5.4/flextable/inst/doc/layout.R | 18 flextable-0.5.4/flextable/inst/doc/layout.Rmd | 36 + flextable-0.5.4/flextable/inst/doc/layout.html | 55 +- flextable-0.5.4/flextable/inst/doc/overview.R | 173 ++------ flextable-0.5.4/flextable/inst/doc/overview.Rmd | 369 ++++++------------ flextable-0.5.4/flextable/inst/doc/overview.html | 309 +++++++-------- flextable-0.5.4/flextable/inst/doc/selectors.R |only flextable-0.5.4/flextable/inst/doc/selectors.Rmd |only flextable-0.5.4/flextable/inst/doc/selectors.html |only flextable-0.5.4/flextable/inst/web_1.0.0/tabwid.css | 3 flextable-0.5.4/flextable/man/add_header.Rd |only flextable-0.5.4/flextable/man/add_header_lines.Rd |only flextable-0.5.4/flextable/man/add_header_row.Rd |only flextable-0.5.4/flextable/man/as_raster.Rd |only flextable-0.5.4/flextable/man/autofit.Rd | 9 flextable-0.5.4/flextable/man/body_add_flextable.Rd | 4 flextable-0.5.4/flextable/man/colformat_char.Rd | 14 flextable-0.5.4/flextable/man/colformat_int.Rd | 14 flextable-0.5.4/flextable/man/colformat_lgl.Rd | 16 flextable-0.5.4/flextable/man/colformat_num.Rd | 14 flextable-0.5.4/flextable/man/compose.Rd | 15 flextable-0.5.4/flextable/man/dim.flextable.Rd | 14 flextable-0.5.4/flextable/man/dim_pretty.Rd | 7 flextable-0.5.4/flextable/man/display.Rd | 2 flextable-0.5.4/flextable/man/flextable.Rd | 21 - flextable-0.5.4/flextable/man/flextable_dim.Rd |only flextable-0.5.4/flextable/man/footnote.Rd |only flextable-0.5.4/flextable/man/format.flextable.Rd | 7 flextable-0.5.4/flextable/man/height.Rd | 20 flextable-0.5.4/flextable/man/htmltools_value.Rd | 7 flextable-0.5.4/flextable/man/knit_print.flextable.Rd | 7 flextable-0.5.4/flextable/man/ph_with_flextable.Rd | 4 flextable-0.5.4/flextable/man/plot.flextable.Rd |only flextable-0.5.4/flextable/man/print.flextable.Rd | 6 flextable-0.5.4/flextable/man/save_as_html.Rd | 7 flextable-0.5.4/flextable/man/save_as_image.Rd |only flextable-0.5.4/flextable/man/set_header_footer_df.Rd | 8 flextable-0.5.4/flextable/man/width.Rd | 5 flextable-0.5.4/flextable/vignettes/display.Rmd | 49 ++ flextable-0.5.4/flextable/vignettes/layout.Rmd | 36 + flextable-0.5.4/flextable/vignettes/overview.Rmd | 369 ++++++------------ flextable-0.5.4/flextable/vignettes/selectors.Rmd |only 65 files changed, 1492 insertions(+), 1116 deletions(-)
Title: Interactive Visualizations for Profiling R Code
Description: Interactive visualizations for profiling R code.
Author: Winston Chang [aut, cre],
Javier Luraschi [aut],
Timothy Mastny [aut],
RStudio [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/www/shared/jquery-AUTHORS.txt),
Mike Bostock [ctb, cph] (D3 library),
D3 contributors [ctb] (D3 library),
Ivan Sagalaev [ctb, cph] (highlight.js library)
Maintainer: Winston Chang <winston@rstudio.com>
Diff between profvis versions 0.3.5 dated 2018-02-21 and 0.3.6 dated 2019-05-14
DESCRIPTION | 14 +++++++++----- MD5 | 19 +++++++++++-------- NAMESPACE | 3 +++ NEWS.md | 9 ++++++++- R/parse.R | 1 + R/profvis.R | 2 +- R/shiny_module.R |only inst/htmlwidgets/profvis.yaml | 2 +- inst/shinymodule |only man/print.profvis.Rd | 3 ++- man/profvis.Rd | 6 +++--- man/profvis_ui.Rd |only 12 files changed, 39 insertions(+), 20 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas
Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>,
contains copies of lattice functions written by Deepayan Sarkar
<deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.27.2 dated 2018-01-15 and 1.27.3 dated 2019-05-14
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- build/vignette.rds |binary inst/doc/hexagon_binning.pdf |binary tests/hdiffplot.Rout.save | 17 ++++++++++------- 5 files changed, 17 insertions(+), 14 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 1.4.16 dated 2018-11-16 and 1.4.17 dated 2019-05-14
DESCRIPTION | 10 - MD5 | 34 +++--- R/changeTimes.R | 217 ++++++++++++++++++++-------------------- R/classifyGENEA.R | 31 +++-- R/dataImport.R | 1 R/getGENEAsegments.R | 31 ++++- R/removeShortSegments.R | 4 R/segmentation.R | 134 +++++++++++++++++------- R/stepCounter.R | 119 ++++++++++++++++----- build/vignette.rds |binary inst/doc/GENEAclassifyDemo.R | 1 inst/doc/GENEAclassifyDemo.Rmd | 1 inst/doc/GENEAclassifyDemo.html | 31 +++++ man/classifyGENEA.Rd | 19 ++- man/getGENEAsegments.Rd | 18 ++- man/segmentation.Rd | 18 ++- man/stepCounter2.Rd | 10 + vignettes/GENEAclassifyDemo.Rmd | 1 18 files changed, 435 insertions(+), 245 deletions(-)
Title: A Computer Program to Detect Markers Responding to Selection
Description: In the new era of population genomics, surveys of genetic polymorphism ("genome scans") offer the opportunity to distinguish locus-specific from genome wide effects at many loci. Identifying presumably neutral regions of the genome that are assumed to be influenced by genome-wide effects only, and excluding presumably selected regions, is therefore critical to infer population demography and phylogenetic history reliably. Conversely, detecting locus-specific effects may help identify those genes that have been, or still are, targeted by natural selection. The software package DetSel has been developed to identify markers that show deviation from neutral expectation in pairwise comparisons of diverging populations.
Author: Renaud Vitalis <renaud.vitalis@inra.fr>.
Maintainer: Renaud Vitalis <renaud.vitalis@inra.fr>
Diff between DetSel versions 1.0.2 dated 2013-04-24 and 1.0.3 dated 2019-05-14
ChangeLog | 4 ++++ DESCRIPTION | 28 +++++++++------------------- MD5 | 11 ++++++----- NAMESPACE | 6 +++++- R/DetSel.R | 4 ++-- src/DetSel_init.c |only src/GetData.c | 2 +- 7 files changed, 27 insertions(+), 28 deletions(-)
Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and model diagnostics, in the univariate
and the multivariate case.
Author: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.5-3 dated 2018-11-08 and 1.5-4 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 8 ++++++++ R/sn-funct.R | 39 +++++++++++++++++++++------------------ R/sn_S4.R | 47 ++++++++++++++++++++++++++--------------------- data/ais.rda |binary data/barolo.rda |binary data/frontier.rda |binary data/wines.rda |binary man/extractSECdistr.Rd | 2 +- man/profile.selm.Rd | 7 +++---- 11 files changed, 73 insertions(+), 58 deletions(-)
Title: Serializable Representations
Description: String and binary representations of objects for several formats /
mime types.
Author: Philipp Angerer [aut, cre] (<https://orcid.org/0000-0002-0369-2888>),
Thomas Kluyver [aut],
Jan Schulz [aut],
abielr [ctb],
Denilson Figueiredo de Sa [ctb],
Jim Hester [ctb],
karldw [ctb],
Dave Foster [ctb],
Carson Sievert [ctb]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between repr versions 1.0.0 dated 2019-04-29 and 1.0.1 dated 2019-05-14
DESCRIPTION | 12 +++++++----- MD5 | 8 ++++---- R/repr_matrix_df.r | 6 +++--- tests/testthat/helpers.r | 10 ++++------ tests/testthat/test_repr_array_df.r | 2 +- 5 files changed, 19 insertions(+), 19 deletions(-)
Title: Handy File and String Manipulation
Description: This started out as a package for file and string manipulation.
Since then, the 'fs' and 'strex' packages emerged, offering functionality
previously given by this package (but it's done better in these new ones).
Those packages have hence almost pushed 'filesstrings' into extinction.
However, it still has a small number of unique, handy file manipulation
functions which can be seen in the vignette.
One example is a function to remove spaces from all file names in a
directory.
Author: Rory Nolan [aut, cre, cph] (<https://orcid.org/0000-0002-5239-4043>),
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between filesstrings versions 3.1.0 dated 2019-05-07 and 3.1.1 dated 2019-05-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 6 ++++++ R/filesstrings-package.R | 1 + build/partial.rdb |binary inst/doc/files.html | 4 ++-- 7 files changed, 20 insertions(+), 12 deletions(-)
Title: A Grammar of Data Manipulation
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Romain François [aut] (<https://orcid.org/0000-0002-2444-4226>),
Lionel Henry [aut],
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dplyr versions 0.8.0.1 dated 2019-02-15 and 0.8.1 dated 2019-05-14
dplyr-0.8.0.1/dplyr/inst/include/dplyr/Groups.h |only dplyr-0.8.0.1/dplyr/inst/include/dplyr/registration.h |only dplyr-0.8.0.1/dplyr/inst/include/dplyr/visitors/vector/visitor.h |only dplyr-0.8.0.1/dplyr/inst/include/dplyr_RcppExports.h |only dplyr-0.8.1/dplyr/DESCRIPTION | 30 dplyr-0.8.1/dplyr/MD5 | 270 +-- dplyr-0.8.1/dplyr/NAMESPACE | 22 dplyr-0.8.1/dplyr/NEWS.md | 48 dplyr-0.8.1/dplyr/R/RcppExports.R | 4 dplyr-0.8.1/dplyr/R/colwise-filter.R | 4 dplyr-0.8.1/dplyr/R/colwise-group-by.R | 6 dplyr-0.8.1/dplyr/R/colwise-mutate.R | 28 dplyr-0.8.1/dplyr/R/colwise-select.R | 26 dplyr-0.8.1/dplyr/R/colwise.R | 38 dplyr-0.8.1/dplyr/R/count-tally.R | 8 dplyr-0.8.1/dplyr/R/dataframe.R | 4 dplyr-0.8.1/dplyr/R/funs.R | 75 dplyr-0.8.1/dplyr/R/group-by.r | 47 dplyr-0.8.1/dplyr/R/group-indices.R | 2 dplyr-0.8.1/dplyr/R/group_map.R | 128 - dplyr-0.8.1/dplyr/R/group_nest.R | 2 dplyr-0.8.1/dplyr/R/group_trim.R | 6 dplyr-0.8.1/dplyr/R/grouped-df.r | 8 dplyr-0.8.1/dplyr/R/manip.r | 18 dplyr-0.8.1/dplyr/R/rowwise.r | 6 dplyr-0.8.1/dplyr/R/src-local.r | 2 dplyr-0.8.1/dplyr/R/tbl-df.r | 6 dplyr-0.8.1/dplyr/R/utils-tidy-eval.R | 73 dplyr-0.8.1/dplyr/README.md | 19 dplyr-0.8.1/dplyr/build/dplyr.pdf |binary dplyr-0.8.1/dplyr/build/vignette.rds |binary dplyr-0.8.1/dplyr/inst/doc/compatibility.html | 223 +- dplyr-0.8.1/dplyr/inst/doc/dplyr.html | 827 +++++----- dplyr-0.8.1/dplyr/inst/doc/programming.Rmd | 2 dplyr-0.8.1/dplyr/inst/doc/programming.html | 806 ++++----- dplyr-0.8.1/dplyr/inst/doc/two-table.Rmd | 2 dplyr-0.8.1/dplyr/inst/doc/two-table.html | 437 ++--- dplyr-0.8.1/dplyr/inst/doc/window-functions.html | 235 +- dplyr-0.8.1/dplyr/inst/include/dplyr/Collecter.h | 107 - dplyr-0.8.1/dplyr/inst/include/dplyr/NamedListAccumulator.h | 13 dplyr-0.8.1/dplyr/inst/include/dplyr/checks.h | 12 dplyr-0.8.1/dplyr/inst/include/dplyr/data/DataMask.h | 99 - dplyr-0.8.1/dplyr/inst/include/dplyr/data/GroupedDataFrame.h | 78 dplyr-0.8.1/dplyr/inst/include/dplyr/data/NaturalDataFrame.h | 24 dplyr-0.8.1/dplyr/inst/include/dplyr/data/RowwiseDataFrame.h | 29 dplyr-0.8.1/dplyr/inst/include/dplyr/dplyr.h | 4 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/Expression.h | 94 - dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/HybridVectorScalarResult.h | 8 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/hybrid.h | 26 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/scalar_result/min_max.h | 22 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/scalar_result/n_distinct.h | 35 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/scalar_result/sum.h | 2 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/vector_result/ntile.h | 6 dplyr-0.8.1/dplyr/inst/include/dplyr/hybrid/vector_result/rank.h | 8 dplyr-0.8.1/dplyr/inst/include/dplyr/main.h | 2 dplyr-0.8.1/dplyr/inst/include/dplyr/standard/GroupedCallReducer.h | 80 dplyr-0.8.1/dplyr/inst/include/dplyr/symbols.h | 11 dplyr-0.8.1/dplyr/inst/include/dplyr/visitor_set/VisitorSetHash.h | 2 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/CharacterVectorOrderer.h | 6 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/join/Column.h | 10 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/join/DataFrameJoinVisitors.h | 20 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/join/JoinVisitorImpl.h | 55 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/order/Order.h | 8 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/order/OrderVisitorImpl.h | 38 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/subset/DataFrameSelect.h | 31 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/subset/DataFrameSubsetVisitors.h | 6 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/subset/column_subset.h | 30 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/DataFrameColumnVisitor.h | 4 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/DataFrameVisitors.h | 8 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/MatrixColumnVisitor.h | 12 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/MultipleVectorVisitors.h | 26 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/VectorVisitor.h | 3 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/VectorVisitorImpl.h | 8 dplyr-0.8.1/dplyr/inst/include/dplyr/visitors/vector/visitor_impl.h | 72 dplyr-0.8.1/dplyr/inst/include/dplyr_types.h | 1 dplyr-0.8.1/dplyr/inst/include/tools/BoolResult.h | 16 dplyr-0.8.1/dplyr/inst/include/tools/Quosure.h | 23 dplyr-0.8.1/dplyr/inst/include/tools/SymbolMap.h | 33 dplyr-0.8.1/dplyr/inst/include/tools/SymbolString.h | 25 dplyr-0.8.1/dplyr/inst/include/tools/SymbolVector.h | 35 dplyr-0.8.1/dplyr/inst/include/tools/all_na.h | 4 dplyr-0.8.1/dplyr/inst/include/tools/bad.h | 108 - 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dplyr-0.8.1/dplyr/src/group_indices.cpp | 247 +- dplyr-0.8.1/dplyr/src/hybrid.cpp | 100 - dplyr-0.8.1/dplyr/src/init.cpp | 55 dplyr-0.8.1/dplyr/src/join.cpp | 16 dplyr-0.8.1/dplyr/src/join_exports.cpp | 283 +-- dplyr-0.8.1/dplyr/src/mutate.cpp | 122 - dplyr-0.8.1/dplyr/src/select.cpp | 56 dplyr-0.8.1/dplyr/src/set.cpp | 170 +- dplyr-0.8.1/dplyr/src/summarise.cpp | 105 - dplyr-0.8.1/dplyr/src/test.cpp | 66 dplyr-0.8.1/dplyr/src/utils-bindings.cpp | 6 dplyr-0.8.1/dplyr/src/utils.cpp | 109 - dplyr-0.8.1/dplyr/src/window.cpp | 18 dplyr-0.8.1/dplyr/tests/testthat/helper-hybrid.R | 4 dplyr-0.8.1/dplyr/tests/testthat/test-colwise-mutate.R | 72 dplyr-0.8.1/dplyr/tests/testthat/test-colwise-select.R | 21 dplyr-0.8.1/dplyr/tests/testthat/test-colwise.R | 12 dplyr-0.8.1/dplyr/tests/testthat/test-copy_to.R | 7 dplyr-0.8.1/dplyr/tests/testthat/test-equality.r | 1 dplyr-0.8.1/dplyr/tests/testthat/test-funs.R | 36 dplyr-0.8.1/dplyr/tests/testthat/test-group-by.r | 27 dplyr-0.8.1/dplyr/tests/testthat/test-group-indices.R | 10 dplyr-0.8.1/dplyr/tests/testthat/test-group_map.R | 66 dplyr-0.8.1/dplyr/tests/testthat/test-mutate.r | 17 dplyr-0.8.1/dplyr/tests/testthat/test-rank.R | 9 dplyr-0.8.1/dplyr/tests/testthat/test-rbind.R | 13 dplyr-0.8.1/dplyr/tests/testthat/test-summarise.r | 20 dplyr-0.8.1/dplyr/vignettes/programming.Rmd | 2 dplyr-0.8.1/dplyr/vignettes/two-table.Rmd | 2 139 files changed, 4022 insertions(+), 3521 deletions(-)
Title: Methods for Detecting Safety Signals in Clinical Trials Using
Body-Systems (System Organ Classes)
Description: Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class.The package title c212 is in reference to the original Engineering and Physical Sciences Research Council (UK) funded project which was named CASE 2/12.
Author: Raymond Carragher <rcarragh@gmail.com>
Maintainer: Raymond Carragher <rcarragh@gmail.com>
Diff between c212 versions 0.94 dated 2018-10-08 and 0.95 dated 2019-05-14
c212-0.94/c212/man/RCS |only c212-0.95/c212/DESCRIPTION | 12 - c212-0.95/c212/MD5 | 86 +++--------- c212-0.95/c212/R/c212.gen.initial.values.R | 11 + c212-0.95/c212/R/c212.interim.1a.hier2.lev0.convergence.R | 11 - c212-0.95/c212/R/c212.interim.1a.hier2.lev0.summary.stats.R | 16 +- c212-0.95/c212/R/c212.interim.1a.hier2.lev1.convergence.R | 11 - c212-0.95/c212/R/c212.interim.1a.hier2.lev1.summary.stats.R | 8 - c212-0.95/c212/R/c212.interim.1a.hier3.lev0.convergence.R | 11 - c212-0.95/c212/R/c212.interim.1a.hier3.lev0.summary.stats.R | 26 +-- c212-0.95/c212/R/c212.interim.1a.hier3.lev1.convergence.R | 13 - c212-0.95/c212/R/c212.interim.1a.hier3.lev1.summary.stats.R | 8 - c212-0.95/c212/R/c212.interim.1a.hier3.lev2.convergence.R | 11 - c212-0.95/c212/R/c212.interim.1a.hier3.lev2.summary.stats.R | 16 +- c212-0.95/c212/R/c212.interim.BB.hier2.lev0.R | 10 - c212-0.95/c212/R/c212.interim.BB.hier2.lev0.convergence.R | 13 - c212-0.95/c212/R/c212.interim.BB.hier2.lev0.summary.stats.R | 6 c212-0.95/c212/R/c212.interim.BB.hier2.lev1.R | 10 - c212-0.95/c212/R/c212.interim.BB.hier2.lev1.convergence.R | 13 - c212-0.95/c212/R/c212.interim.BB.hier3.lev0.convergence.R | 11 - c212-0.95/c212/R/c212.interim.BB.hier3.lev0.summary.stats.R | 12 - c212-0.95/c212/R/c212.interim.BB.hier3.lev1.convergence.R | 11 - c212-0.95/c212/R/c212.interim.BB.hier3.lev2.convergence.R | 11 - c212-0.95/c212/R/c212.interim.BB.hier3.lev2.summary.stats.R | 6 c212-0.95/c212/R/c212.interim.ptheta.R | 6 c212-0.95/c212/R/c212.params.R | 39 +++-- c212-0.95/c212/R/global.R | 34 ++-- 27 files changed, 153 insertions(+), 269 deletions(-)
Title: Temporal Exponential Random Graph Models by Bootstrapped
Pseudolikelihood
Description: Temporal Exponential Random Graph Models (TERGM) estimated by maximum pseudolikelihood with bootstrapped confidence intervals or Markov Chain Monte Carlo maximum likelihood. Goodness of fit assessment for ERGMs, TERGMs, and SAOMs. Micro-level interpretation of ERGMs and TERGMs.
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [ctb],
Bruce A. Desmarais [ctb]
Maintainer: Philip Leifeld <philip.leifeld@essex.ac.uk>
Diff between btergm versions 1.9.3 dated 2018-08-24 and 1.9.4 dated 2019-05-14
DESCRIPTION | 25 ++++--- MD5 | 17 +++-- NAMESPACE | 6 - R/btergm.R | 166 +++++++++++++++++++++++++++++++++++----------------- R/checkdegeneracy.R | 12 ++- R/gofmethods.R | 24 +++---- inst/CITATION | 2 man/btergm.Rd | 9 +- tests |only 9 files changed, 163 insertions(+), 98 deletions(-)
Title: API for UK Gas Market Information
Description: Allows users to access live UK gas market information via National Grid's API.
Author: Timothy Wong [aut, cre]
Maintainer: Timothy Wong <timothy.wong@hotmail.co.uk>
Diff between ukgasapi versions 0.15 dated 2018-10-17 and 0.16 dated 2019-05-14
DESCRIPTION | 8 - MD5 | 16 +- R/dataItemExplorer.R | 140 +++++++++++++----- build/vignette.rds |binary inst/doc/vignette.R | 7 inst/doc/vignette.Rmd | 12 + inst/doc/vignette.html | 357 ++++++++++++++++++++++++++++++++++++++++-------- man/dataItemExplorer.Rd | 4 vignettes/vignette.Rmd | 12 + 9 files changed, 445 insertions(+), 111 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators and tests for panel data
econometrics, as described in Baltagi (2013) Econometric Analysis of Panel Data, ISBN-13:978-1-118-67232-7,
Hsiao (2014) Analysis of Panel Data <doi:10.1017/CBO9781139839327> and
Croissant and Millo (2018), Panel Data Econometrics with R, ISBN:978-1-118-94918-4.
Author: Yves Croissant [aut, cre],
Giovanni Millo [aut],
Kevin Tappe [aut],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between plm versions 1.7-0 dated 2019-01-04 and 2.0-0 dated 2019-05-14
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Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGMs). 'ergm' is a part of the Statnet suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre] (<https://orcid.org/0000-0002-9101-3362>),
Martina Morris [aut],
Li Wang [ctb],
Kirk Li [ctb],
Skye Bender-deMoll [ctb],
Chad Klumb [ctb]
Maintainer: Pavel N. Krivitsky <pavel@uow.edu.au>
Diff between ergm versions 3.9.4 dated 2018-08-16 and 3.10.1 dated 2019-05-14
ergm-3.10.1/ergm/DESCRIPTION | 62 ergm-3.10.1/ergm/LICENSE | 4 ergm-3.10.1/ergm/MD5 | 621 - ergm-3.10.1/ergm/NAMESPACE | 69 ergm-3.10.1/ergm/R/InitErgm.bipartite.R | 136 ergm-3.10.1/ergm/R/InitErgmConstraint.R | 69 ergm-3.10.1/ergm/R/InitErgmProposal.R | 24 ergm-3.10.1/ergm/R/InitErgmProposal.blockdiag.R | 16 ergm-3.10.1/ergm/R/InitErgmReference.R | 6 ergm-3.10.1/ergm/R/InitErgmTerm.R | 2527 +++++-- ergm-3.10.1/ergm/R/InitErgmTerm.bipartite.degree.R | 6 ergm-3.10.1/ergm/R/InitErgmTerm.coincidence.R | 58 ergm-3.10.1/ergm/R/InitErgmTerm.dgw_sp.R | 42 ergm-3.10.1/ergm/R/InitErgmTerm.extra.R | 37 ergm-3.10.1/ergm/R/InitErgmTerm.indices.R | 6 ergm-3.10.1/ergm/R/InitErgmTerm.test.R | 6 ergm-3.10.1/ergm/R/InitErgmTerm.transitiveties.R | 80 ergm-3.10.1/ergm/R/InitWtErgmProposal.R | 14 ergm-3.10.1/ergm/R/InitWtErgmTerm.R | 473 + ergm-3.10.1/ergm/R/anova.ergm.R | 6 ergm-3.10.1/ergm/R/anova.ergmlist.R | 6 ergm-3.10.1/ergm/R/approx.hotelling.diff.test.R | 11 ergm-3.10.1/ergm/R/as.network.numeric.R | 6 ergm-3.10.1/ergm/R/build_term_index.R | 18 ergm-3.10.1/ergm/R/check.ErgmTerm.R | 75 ergm-3.10.1/ergm/R/control.ergm.R | 70 ergm-3.10.1/ergm/R/control.ergm.bridge.R | 6 ergm-3.10.1/ergm/R/control.gof.R | 6 ergm-3.10.1/ergm/R/control.logLik.ergm.R | 13 ergm-3.10.1/ergm/R/control.san.R | 64 ergm-3.10.1/ergm/R/control.simulate.R | 6 ergm-3.10.1/ergm/R/data.R | 18 ergm-3.10.1/ergm/R/ergm-defunct.R | 140 ergm-3.10.1/ergm/R/ergm-deprecated.R | 67 ergm-3.10.1/ergm/R/ergm-disambiguation.R |only ergm-3.10.1/ergm/R/ergm.CD.fixed.R | 50 ergm-3.10.1/ergm/R/ergm.Cprepare.R | 28 ergm-3.10.1/ergm/R/ergm.MCMCse.R | 9 ergm-3.10.1/ergm/R/ergm.MCMCse.lognormal.R | 9 ergm-3.10.1/ergm/R/ergm.MCMLE.R | 80 ergm-3.10.1/ergm/R/ergm.R | 104 ergm-3.10.1/ergm/R/ergm.allstats.R | 6 ergm-3.10.1/ergm/R/ergm.bounddeg.R | 6 ergm-3.10.1/ergm/R/ergm.bridge.R | 33 ergm-3.10.1/ergm/R/ergm.check.R | 134 ergm-3.10.1/ergm/R/ergm.coefficient.degeneracy.R | 15 ergm-3.10.1/ergm/R/ergm.curved.statsmatrix.R | 6 ergm-3.10.1/ergm/R/ergm.degeneracy.R | 6 ergm-3.10.1/ergm/R/ergm.design.R | 20 ergm-3.10.1/ergm/R/ergm.errors.R | 7 ergm-3.10.1/ergm/R/ergm.estimate.R | 6 ergm-3.10.1/ergm/R/ergm.eta.R | 7 ergm-3.10.1/ergm/R/ergm.etagrad.R | 6 ergm-3.10.1/ergm/R/ergm.etagradmult.R | 6 ergm-3.10.1/ergm/R/ergm.etamap.R | 8 ergm-3.10.1/ergm/R/ergm.geodistn.R | 6 ergm-3.10.1/ergm/R/ergm.getCDsample.R | 164 ergm-3.10.1/ergm/R/ergm.getMCMCsample.R | 106 ergm-3.10.1/ergm/R/ergm.getnetwork.R | 27 ergm-3.10.1/ergm/R/ergm.initialfit.R | 6 ergm-3.10.1/ergm/R/ergm.llik.R | 8 ergm-3.10.1/ergm/R/ergm.llik.obs.R | 6 ergm-3.10.1/ergm/R/ergm.logitreg.R | 6 ergm-3.10.1/ergm/R/ergm.mapl.R | 6 ergm-3.10.1/ergm/R/ergm.maple.R | 6 ergm-3.10.1/ergm/R/ergm.mple.R | 8 ergm-3.10.1/ergm/R/ergm.pen.glm.R | 6 ergm-3.10.1/ergm/R/ergm.phase12.R | 8 ergm-3.10.1/ergm/R/ergm.pl.R | 7 ergm-3.10.1/ergm/R/ergm.reviseinit.R | 6 ergm-3.10.1/ergm/R/ergm.robmon.R | 20 ergm-3.10.1/ergm/R/ergm.san.R | 438 - ergm-3.10.1/ergm/R/ergm.stepping.R | 62 ergm-3.10.1/ergm/R/ergm.stocapprox.R | 17 ergm-3.10.1/ergm/R/ergm.sufftoprob.R | 6 ergm-3.10.1/ergm/R/ergm.utility.R | 180 ergm-3.10.1/ergm/R/ergmMPLE.R | 6 ergm-3.10.1/ergm/R/ergm_estfun.R | 7 ergm-3.10.1/ergm/R/ergm_model.R | 14 ergm-3.10.1/ergm/R/ergm_model.utils.R | 6 ergm-3.10.1/ergm/R/ergm_proposal.R | 67 ergm-3.10.1/ergm/R/formula.utils.R | 18 ergm-3.10.1/ergm/R/get.node.attr.R | 132 ergm-3.10.1/ergm/R/godfather.R | 16 ergm-3.10.1/ergm/R/gof.ergm.R | 128 ergm-3.10.1/ergm/R/is.curved.R | 12 ergm-3.10.1/ergm/R/is.durational.R | 6 ergm-3.10.1/ergm/R/is.dyad.independent.R | 14 ergm-3.10.1/ergm/R/is.inCH.R | 60 ergm-3.10.1/ergm/R/locator.R | 21 ergm-3.10.1/ergm/R/logLik.ergm.R | 55 ergm-3.10.1/ergm/R/mcmc.diagnostics.ergm.R | 35 ergm-3.10.1/ergm/R/network.list.R | 6 ergm-3.10.1/ergm/R/network.update.R | 187 ergm-3.10.1/ergm/R/nparam.R | 15 ergm-3.10.1/ergm/R/parallel.utils.R | 196 ergm-3.10.1/ergm/R/param_names.R | 6 ergm-3.10.1/ergm/R/pending_update_network.R |only ergm-3.10.1/ergm/R/print.ergm.R | 6 ergm-3.10.1/ergm/R/print.network.list.R | 6 ergm-3.10.1/ergm/R/print.summary.ergm.R | 9 ergm-3.10.1/ergm/R/rlebdm.R | 42 ergm-3.10.1/ergm/R/simulate.ergm.R | 411 - ergm-3.10.1/ergm/R/summary.ergm.R | 31 ergm-3.10.1/ergm/R/summary.ergm_model.R | 11 ergm-3.10.1/ergm/R/summary.network.list.R | 6 ergm-3.10.1/ergm/R/summary.statistics.network.R | 56 ergm-3.10.1/ergm/R/to_ergm_Cdouble.R | 6 ergm-3.10.1/ergm/R/vcov.ergm.R | 14 ergm-3.10.1/ergm/R/wtd.median.R | 6 ergm-3.10.1/ergm/R/zzz.R | 19 ergm-3.10.1/ergm/README.md | 4 ergm-3.10.1/ergm/build/partial.rdb |binary ergm-3.10.1/ergm/data/molecule.RData |binary ergm-3.10.1/ergm/data/samplk.RData |binary ergm-3.10.1/ergm/data/sampson.RData |binary ergm-3.10.1/ergm/inst/CITATION | 4 ergm-3.10.1/ergm/inst/NEWS.Rd | 427 + ergm-3.10.1/ergm/inst/doc/ergm-term-crossRef.Rmd | 2 ergm-3.10.1/ergm/inst/doc/ergm-term-crossRef.html | 474 - ergm-3.10.1/ergm/inst/doc/ergm.R | 115 ergm-3.10.1/ergm/inst/doc/ergm.Rnw | 392 - ergm-3.10.1/ergm/inst/doc/ergm.pdf |binary ergm-3.10.1/ergm/inst/include/MCMC.h | 30 ergm-3.10.1/ergm/inst/include/MHproposal.h | 117 ergm-3.10.1/ergm/inst/include/changestat.h | 151 ergm-3.10.1/ergm/inst/include/edgelist.h | 38 ergm-3.10.1/ergm/inst/include/edgetree.h | 156 ergm-3.10.1/ergm/inst/include/ergm_MHproposal.h |only ergm-3.10.1/ergm/inst/include/ergm_changestat.h |only ergm-3.10.1/ergm/inst/include/ergm_changestat_common.do_not_include_directly.h |only ergm-3.10.1/ergm/inst/include/ergm_edgelist.h |only ergm-3.10.1/ergm/inst/include/ergm_edgetree.h |only ergm-3.10.1/ergm/inst/include/ergm_edgetree_common.do_not_include_directly.h |only ergm-3.10.1/ergm/inst/include/ergm_edgetree_inline.do_not_include_directly.h |only ergm-3.10.1/ergm/inst/include/ergm_model.h |only ergm-3.10.1/ergm/inst/include/ergm_rlebdm.h | 16 ergm-3.10.1/ergm/inst/include/ergm_stubs.c | 772 +- ergm-3.10.1/ergm/inst/include/ergm_wtMHproposal.h |only ergm-3.10.1/ergm/inst/include/ergm_wtchangestat.h |only ergm-3.10.1/ergm/inst/include/ergm_wtedgetree.h |only ergm-3.10.1/ergm/inst/include/ergm_wtedgetree_inline.do_not_include_directly.h |only ergm-3.10.1/ergm/inst/include/ergm_wtmodel.h |only ergm-3.10.1/ergm/inst/include/model.h | 45 ergm-3.10.1/ergm/inst/include/wtMCMC.h | 26 ergm-3.10.1/ergm/inst/include/wtMHproposal.h | 78 ergm-3.10.1/ergm/inst/include/wtchangestat.h | 185 ergm-3.10.1/ergm/inst/include/wtedgetree.h | 123 ergm-3.10.1/ergm/inst/include/wtmodel.h | 41 ergm-3.10.1/ergm/man/Getting.Started.Rd | 20 ergm-3.10.1/ergm/man/as.edgelist.Rd | 6 ergm-3.10.1/ergm/man/as.rlebdm.ergm.Rd |only ergm-3.10.1/ergm/man/as.rlebdm.ergm_conlist.Rd | 1 ergm-3.10.1/ergm/man/check.ErgmTerm.Rd | 15 ergm-3.10.1/ergm/man/control.ergm.Rd | 79 ergm-3.10.1/ergm/man/control.logLik.ergm.Rd | 4 ergm-3.10.1/ergm/man/control.san.Rd | 58 ergm-3.10.1/ergm/man/degreedist.Rd | 8 ergm-3.10.1/ergm/man/edges.Rd |only ergm-3.10.1/ergm/man/ergm-constraints.Rd | 45 ergm-3.10.1/ergm/man/ergm-defunct.Rd | 108 ergm-3.10.1/ergm/man/ergm-deprecated.Rd | 176 ergm-3.10.1/ergm/man/ergm-errors.Rd | 1 ergm-3.10.1/ergm/man/ergm-internal.Rd | 6 ergm-3.10.1/ergm/man/ergm-package.Rd | 22 ergm-3.10.1/ergm/man/ergm-parallel.Rd | 39 ergm-3.10.1/ergm/man/ergm-proposals.Rd | 14 ergm-3.10.1/ergm/man/ergm-references.Rd | 27 ergm-3.10.1/ergm/man/ergm-terms.Rd | 3220 +++++----- ergm-3.10.1/ergm/man/ergm.Rd | 28 ergm-3.10.1/ergm/man/ergm.estfun.Rd | 1 ergm-3.10.1/ergm/man/ergm.eta.Rd | 1 ergm-3.10.1/ergm/man/ergm.godfather.Rd | 7 ergm-3.10.1/ergm/man/ergm.mple.Rd | 3 ergm-3.10.1/ergm/man/ergm_Clist.Rd | 5 ergm-3.10.1/ergm/man/ergm_MCMC_sample.Rd | 19 ergm-3.10.1/ergm/man/ergm_model.Rd | 1 ergm-3.10.1/ergm/man/ergm_proposal.Rd | 1 ergm-3.10.1/ergm/man/ergm_proposal_table.Rd | 1 ergm-3.10.1/ergm/man/eut-upgrade.Rd | 6 ergm-3.10.1/ergm/man/faux.desert.high.Rd | 4 ergm-3.10.1/ergm/man/faux.dixon.high.Rd | 4 ergm-3.10.1/ergm/man/faux.magnolia.high.Rd | 2 ergm-3.10.1/ergm/man/faux.mesa.high.Rd | 2 ergm-3.10.1/ergm/man/fix.curved.Rd | 4 ergm-3.10.1/ergm/man/get.node.attr.Rd | 2 ergm-3.10.1/ergm/man/gof.Rd | 2 ergm-3.10.1/ergm/man/hamming.Rd |only ergm-3.10.1/ergm/man/is.inCH.Rd | 2 ergm-3.10.1/ergm/man/lasttoggle.Rd | 1 ergm-3.10.1/ergm/man/mcmc.diagnostics.Rd | 2 ergm-3.10.1/ergm/man/node-attr-api.Rd | 30 ergm-3.10.1/ergm/man/node-attr.Rd | 54 ergm-3.10.1/ergm/man/nvattr.copy.network.Rd | 1 ergm-3.10.1/ergm/man/pending_update_network.Rd |only ergm-3.10.1/ergm/man/rlebdm.Rd | 14 ergm-3.10.1/ergm/man/san.Rd | 78 ergm-3.10.1/ergm/man/simulate.ergm.Rd | 139 ergm-3.10.1/ergm/man/summary.ergm.Rd | 6 ergm-3.10.1/ergm/man/summary.ergm_model.Rd | 1 ergm-3.10.1/ergm/man/summary_formula.Rd | 7 ergm-3.10.1/ergm/man/to_ergm_Cdouble.Rd | 1 ergm-3.10.1/ergm/man/update.network.Rd |only ergm-3.10.1/ergm/src/CD.c | 55 ergm-3.10.1/ergm/src/CD.h | 14 ergm-3.10.1/ergm/src/MCMC.c | 87 ergm-3.10.1/ergm/src/MHproposal.c | 111 ergm-3.10.1/ergm/src/MHproposals.c | 166 ergm-3.10.1/ergm/src/MHproposals.h | 62 ergm-3.10.1/ergm/src/MHproposals_bipartite.c | 21 ergm-3.10.1/ergm/src/MHproposals_bipartite.h | 24 ergm-3.10.1/ergm/src/MHproposals_block.c | 24 ergm-3.10.1/ergm/src/MHproposals_block.h | 16 ergm-3.10.1/ergm/src/MHproposals_degree.c | 36 ergm-3.10.1/ergm/src/MHproposals_degree.h | 30 ergm-3.10.1/ergm/src/MPLE.c | 14 ergm-3.10.1/ergm/src/MPLE.h | 12 ergm-3.10.1/ergm/src/Makevars |only ergm-3.10.1/ergm/src/SAN.c | 131 ergm-3.10.1/ergm/src/SAN.h | 35 ergm-3.10.1/ergm/src/allstatistics.c | 61 ergm-3.10.1/ergm/src/changestat.c | 8 ergm-3.10.1/ergm/src/changestats.c | 78 ergm-3.10.1/ergm/src/changestats.h | 10 ergm-3.10.1/ergm/src/changestats_coincidence.c | 6 ergm-3.10.1/ergm/src/changestats_coincidence.h | 10 ergm-3.10.1/ergm/src/changestats_concurrentties.c | 6 ergm-3.10.1/ergm/src/changestats_concurrentties.h | 10 ergm-3.10.1/ergm/src/changestats_dgw_sp.c |only ergm-3.10.1/ergm/src/changestats_dgw_sp.h |only ergm-3.10.1/ergm/src/changestats_experimental.c | 6 ergm-3.10.1/ergm/src/changestats_experimental.h | 10 ergm-3.10.1/ergm/src/changestats_homoproportion.c | 6 ergm-3.10.1/ergm/src/changestats_homoproportion.h | 8 ergm-3.10.1/ergm/src/changestats_indices.c | 10 ergm-3.10.1/ergm/src/changestats_indices.h | 10 ergm-3.10.1/ergm/src/changestats_internal.c | 6 ergm-3.10.1/ergm/src/changestats_internal.h | 10 ergm-3.10.1/ergm/src/changestats_test.c | 8 ergm-3.10.1/ergm/src/changestats_transitiveties.c | 6 ergm-3.10.1/ergm/src/changestats_transitiveties.h | 10 ergm-3.10.1/ergm/src/edgelist.c | 8 ergm-3.10.1/ergm/src/edgetree.c | 368 - ergm-3.10.1/ergm/src/ergm_rlebdm.c | 6 ergm-3.10.1/ergm/src/geodist.c | 6 ergm-3.10.1/ergm/src/geodist.h | 8 ergm-3.10.1/ergm/src/godfather.c | 28 ergm-3.10.1/ergm/src/init.c | 34 ergm-3.10.1/ergm/src/model.c | 46 ergm-3.10.1/ergm/src/netstats.c | 24 ergm-3.10.1/ergm/src/netstats.h | 12 ergm-3.10.1/ergm/src/wtCD.c | 61 ergm-3.10.1/ergm/src/wtCD.h | 14 ergm-3.10.1/ergm/src/wtMCMC.c | 51 ergm-3.10.1/ergm/src/wtMHproposal.c | 69 ergm-3.10.1/ergm/src/wtMHproposals.c | 23 ergm-3.10.1/ergm/src/wtMHproposals.h | 16 ergm-3.10.1/ergm/src/wtSAN.c | 134 ergm-3.10.1/ergm/src/wtSAN.h | 35 ergm-3.10.1/ergm/src/wtchangestats.c | 68 ergm-3.10.1/ergm/src/wtchangestats.h | 10 ergm-3.10.1/ergm/src/wtedgetree.c | 469 - ergm-3.10.1/ergm/src/wtgodfather.c | 28 ergm-3.10.1/ergm/src/wtmodel.c | 46 ergm-3.10.1/ergm/src/wtnetstats.c | 21 ergm-3.10.1/ergm/src/wtnetstats.h | 12 ergm-3.10.1/ergm/tests/constrain_degrees_edges.R | 38 ergm-3.10.1/ergm/tests/constrain_dind.R | 6 ergm-3.10.1/ergm/tests/constraint_conflict.R | 6 ergm-3.10.1/ergm/tests/constraint_generalized.R | 8 ergm-3.10.1/ergm/tests/drop_tests.R | 6 ergm-3.10.1/ergm/tests/ergmMPLEtest.R | 6 ergm-3.10.1/ergm/tests/ergm_term_doc_test.R | 6 ergm-3.10.1/ergm/tests/fix.curved.R | 6 ergm-3.10.1/ergm/tests/gw_sp_tests.R | 6 ergm-3.10.1/ergm/tests/hamming_termtests.R | 6 ergm-3.10.1/ergm/tests/miss_tests.CD.R | 6 ergm-3.10.1/ergm/tests/miss_tests.R | 6 ergm-3.10.1/ergm/tests/mle_offset.R | 6 ergm-3.10.1/ergm/tests/mple_largenetwork.R | 6 ergm-3.10.1/ergm/tests/mple_offset.R | 6 ergm-3.10.1/ergm/tests/nodemix.R | 6 ergm-3.10.1/ergm/tests/nodrop.R | 6 ergm-3.10.1/ergm/tests/parallel.R | 31 ergm-3.10.1/ergm/tests/requireNamespaceTest.R | 6 ergm-3.10.1/ergm/tests/runtime_diags.R | 6 ergm-3.10.1/ergm/tests/scoping.R | 6 ergm-3.10.1/ergm/tests/simpletests.R | 6 ergm-3.10.1/ergm/tests/steppingtest.R | 6 ergm-3.10.1/ergm/tests/stocapprox.R | 6 ergm-3.10.1/ergm/tests/target_offset.R | 10 ergm-3.10.1/ergm/tests/termTests.b12nodematch.R | 26 ergm-3.10.1/ergm/tests/termTests.bipartite.R | 110 ergm-3.10.1/ergm/tests/termTests.directed.R | 112 ergm-3.10.1/ergm/tests/termTests.flexible.R | 72 ergm-3.10.1/ergm/tests/termTests.undirected.R | 28 ergm-3.10.1/ergm/tests/termTests.valued.R | 121 ergm-3.10.1/ergm/tests/testgflomiss.R | 6 ergm-3.10.1/ergm/tests/testgmonkmiss.R | 6 ergm-3.10.1/ergm/tests/testthat.R | 6 ergm-3.10.1/ergm/tests/testthat/test-bd.R |only ergm-3.10.1/ergm/tests/testthat/test-c-ergm_model.R | 9 ergm-3.10.1/ergm/tests/testthat/test-checkpointing.R |only ergm-3.10.1/ergm/tests/testthat/test-ergm-godfather.R | 9 ergm-3.10.1/ergm/tests/testthat/test-ergm-san.R |only ergm-3.10.1/ergm/tests/testthat/test-mple-target.R |only ergm-3.10.1/ergm/tests/testthat/test-term-b12factor.R |only ergm-3.10.1/ergm/tests/testthat/test-term-mm.R | 6 ergm-3.10.1/ergm/tests/testthat/test-term-options.R | 6 ergm-3.10.1/ergm/tests/testthat/test-valued-terms.R |only ergm-3.10.1/ergm/tests/utils_tests.R | 24 ergm-3.10.1/ergm/tests/valued_sim.R | 26 ergm-3.10.1/ergm/vignettes/ergm-term-crossRef.Rmd | 2 ergm-3.10.1/ergm/vignettes/ergm.Rnw | 392 - ergm-3.9.4/ergm/R/ergm.getterms.R |only ergm-3.9.4/ergm/R/plot.ergm.R |only ergm-3.9.4/ergm/R/plot.network.ergm.R |only ergm-3.9.4/ergm/man/empty_network.Rd |only ergm-3.9.4/ergm/man/network.update.Rd |only ergm-3.9.4/ergm/man/newnw.extract.Rd |only ergm-3.9.4/ergm/man/standardize.network.Rd |only ergm-3.9.4/ergm/src/MCMC.h |only ergm-3.9.4/ergm/src/MHproposal.h |only ergm-3.9.4/ergm/src/changestat.h |only ergm-3.9.4/ergm/src/changestats.dgw_sp.c |only ergm-3.9.4/ergm/src/changestats.dgw_sp.h |only ergm-3.9.4/ergm/src/edgelist.h |only ergm-3.9.4/ergm/src/edgetree.h |only ergm-3.9.4/ergm/src/ergm_rlebdm.h |only ergm-3.9.4/ergm/src/model.h |only ergm-3.9.4/ergm/src/wtMCMC.h |only ergm-3.9.4/ergm/src/wtMHproposal.h |only ergm-3.9.4/ergm/src/wtchangestat.h |only ergm-3.9.4/ergm/src/wtedgetree.h |only ergm-3.9.4/ergm/src/wtmodel.h |only ergm-3.9.4/ergm/tests/mple_target.stats.R |only ergm-3.9.4/ergm/tests/termTests.b12factor.R |only ergm-3.9.4/ergm/tests/valued_terms.R |only 338 files changed, 9680 insertions(+), 9725 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Daijiang Li [ctb],
Xianying Tan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.6 dated 2019-04-02 and 0.7 dated 2019-05-14
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/packages.R | 4 +++- R/revcheck.R | 11 +++++++---- build/vignette.rds |binary inst/doc/xfun.html | 8 ++++---- 7 files changed, 29 insertions(+), 18 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>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Garrick Aden-Buie [ctb],
John Little [ctb],
Joseph Casillas [ctb],
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Lemmens [ctb],
Sean Lopp [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Emi Tanaka [ctb],
Yongfu Liao [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.9 dated 2019-03-06 and 0.10 dated 2019-05-14
DESCRIPTION | 10 +++-- MD5 | 14 +++---- R/render.R | 2 - R/utils.R | 18 +++++++++- build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/default.html | 5 ++ inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 1 inst/rmarkdown/templates/xaringan_zh-CN/skeleton/skeleton.Rmd | 3 + 8 files changed, 39 insertions(+), 14 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.12 dated 2019-04-11 and 0.13 dated 2019-05-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/install.R | 23 +++++++++++++++++++++-- R/tlmgr.R | 2 +- 4 files changed, 28 insertions(+), 9 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph],
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.7 dated 2019-03-16 and 0.8 dated 2019-05-14
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Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.2.0 dated 2019-05-13 and 0.2.1 dated 2019-05-14
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Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
(<https://orcid.org/0000-0003-3463-4063>)
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 2.0-0 dated 2017-06-22 and 2.1-0 dated 2019-05-14
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metafor-2.1-0/metafor/man/ranktest.Rd | 8 metafor-2.1-0/metafor/man/regtest.Rd | 18 metafor-2.1-0/metafor/man/replmiss.Rd | 4 metafor-2.1-0/metafor/man/reporter.Rd |only metafor-2.1-0/metafor/man/residuals.rma.Rd | 48 metafor-2.1-0/metafor/man/rma.glmm.Rd | 25 metafor-2.1-0/metafor/man/rma.mh.Rd | 17 metafor-2.1-0/metafor/man/rma.mv.Rd | 68 metafor-2.1-0/metafor/man/rma.peto.Rd | 19 metafor-2.1-0/metafor/man/rma.uni.Rd | 75 metafor-2.1-0/metafor/man/robust.Rd | 20 metafor-2.1-0/metafor/man/simulate.rma.Rd | 15 metafor-2.1-0/metafor/man/to.long.Rd | 4 metafor-2.1-0/metafor/man/to.table.Rd | 4 metafor-2.1-0/metafor/man/transf.Rd | 7 metafor-2.1-0/metafor/man/trimfill.Rd | 13 metafor-2.1-0/metafor/man/update.rma.Rd | 2 metafor-2.1-0/metafor/man/vcov.rma.Rd | 16 metafor-2.1-0/metafor/man/vif.Rd |only metafor-2.1-0/metafor/man/weights.rma.Rd | 4 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_berkey1995.r | 24 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_berkey1998.r | 34 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_dersimonian2007.r | 10 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_gleser2009.r | 72 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_henmi2010.r | 18 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_ishak2007.r |only metafor-2.1-0/metafor/tests/testthat/test_analysis_example_jackson2014.r | 34 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_konstantopoulos2011.r | 113 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_law2016.r | 54 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_lipsey2001.r | 53 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_miller1978.r | 20 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_morris2008.r | 30 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_normand1999.r | 60 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_raudenbush1985.r | 55 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_raudenbush2009.r | 54 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_rothman2008.r | 250 - metafor-2.1-0/metafor/tests/testthat/test_analysis_example_stijnen2010.r | 180 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_vanhouwelingen1993.r | 50 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_vanhouwelingen2002.r | 82 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_viechtbauer2005.r | 34 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_viechtbauer2007a.r | 118 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_viechtbauer2007b.r | 58 metafor-2.1-0/metafor/tests/testthat/test_analysis_example_yusuf1985.r | 12 metafor-2.1-0/metafor/tests/testthat/test_misc_anova.r | 22 metafor-2.1-0/metafor/tests/testthat/test_misc_confint.r | 14 metafor-2.1-0/metafor/tests/testthat/test_misc_diagnostics_rma.mv.r |only metafor-2.1-0/metafor/tests/testthat/test_misc_escalc.r | 258 - metafor-2.1-0/metafor/tests/testthat/test_misc_fitstats.r | 42 metafor-2.1-0/metafor/tests/testthat/test_misc_fsn.r | 2 metafor-2.1-0/metafor/tests/testthat/test_misc_funnel.r | 4 metafor-2.1-0/metafor/tests/testthat/test_misc_handling_nas.r |only metafor-2.1-0/metafor/tests/testthat/test_misc_handling_of_edge_cases_due_to_zeros.r | 2 metafor-2.1-0/metafor/tests/testthat/test_misc_influence.r | 87 metafor-2.1-0/metafor/tests/testthat/test_misc_list_rma.r | 33 metafor-2.1-0/metafor/tests/testthat/test_misc_metan_vs_rma.mh_with_dat.bcg.r | 53 metafor-2.1-0/metafor/tests/testthat/test_misc_metan_vs_rma.peto_with_dat.bcg.r | 18 metafor-2.1-0/metafor/tests/testthat/test_misc_metan_vs_rma.uni_with_dat.bcg.r | 92 metafor-2.1-0/metafor/tests/testthat/test_misc_pdfs.r |only metafor-2.1-0/metafor/tests/testthat/test_misc_permutest.r | 145 metafor-2.1-0/metafor/tests/testthat/test_misc_plot_rma.r | 8 metafor-2.1-0/metafor/tests/testthat/test_misc_predict.r | 34 metafor-2.1-0/metafor/tests/testthat/test_misc_pub_bias.r | 19 metafor-2.1-0/metafor/tests/testthat/test_misc_residuals.r | 46 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_error_handling.r | 4 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_glmm.r | 52 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_handling_nas.r | 2 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_mv.r | 60 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_uni.r | 81 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_uni_ls.r | 37 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_vs_direct_computation.r | 2 metafor-2.1-0/metafor/tests/testthat/test_misc_rma_vs_lm.r |only metafor-2.1-0/metafor/tests/testthat/test_misc_robust.r | 14 metafor-2.1-0/metafor/tests/testthat/test_misc_setlab.r | 40 metafor-2.1-0/metafor/tests/testthat/test_misc_to_long_to_table.r | 26 metafor-2.1-0/metafor/tests/testthat/test_misc_transf.r | 24 metafor-2.1-0/metafor/tests/testthat/test_misc_update.r | 2 metafor-2.1-0/metafor/tests/testthat/test_misc_vcov.r | 10 metafor-2.1-0/metafor/tests/testthat/test_misc_weights.r | 20 metafor-2.1-0/metafor/tests/testthat/test_plots_baujat_plot.r | 4 metafor-2.1-0/metafor/tests/testthat/test_plots_caterpillar_plot.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_contour-enhanced_funnel_plot.r | 4 metafor-2.1-0/metafor/tests/testthat/test_plots_cumulative_forest_plot.r | 12 metafor-2.1-0/metafor/tests/testthat/test_plots_forest_plot_with_subgroups.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_funnel_plot_variations.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_funnel_plot_with_trim_and_fill.r | 4 metafor-2.1-0/metafor/tests/testthat/test_plots_gosh.r | 17 metafor-2.1-0/metafor/tests/testthat/test_plots_labbe_plot.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_llplot.r |only metafor-2.1-0/metafor/tests/testthat/test_plots_meta-analytic_scatterplot.r | 16 metafor-2.1-0/metafor/tests/testthat/test_plots_normal_qq_plots.r | 14 metafor-2.1-0/metafor/tests/testthat/test_plots_plot_of_cumulative_results.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_plot_of_influence_diagnostics.r | 2 metafor-2.1-0/metafor/tests/testthat/test_plots_radial_plot.r | 2 metafor-2.1-0/metafor/tests/testthat/test_tips_regression_with_rma.r | 24 metafor-2.1-0/metafor/tests/testthat/test_tips_rma_vs_lm_and_lme.r | 22 metafor-2.1-0/metafor/tests/testthat/tolerances.r |only 367 files changed, 11316 insertions(+), 5965 deletions(-)
Title: Procedures for Ecological Assessment of Surface Waters
Description: Functions for evaluating and visualizing
ecological assessment procedures for surface waters
containing physical, chemical and biological assessments
in the form of value functions.
Author: Nele Schuwirth <nele.schuwirth@eawag.ch> and Peter Reichert <peter.reichert@eawag.ch>
with contributions by Simone Langhans and Christian Michel
Maintainer: Nele Schuwirth <nele.schuwirth@eawag.ch>
Diff between ecoval versions 1.2.3 dated 2019-03-26 and 1.2.4 dated 2019-05-14
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- R/msk.macrophytes.2017.doc.R | 8 +-- R/msk.macrophytes.2017.prepare.data.R | 36 +++++----------- data/ecoval_data.RData |binary inst/NEWS | 9 ++++ inst/ecoval.dictionaries.default.dat | 48 +++++++++++----------- man/ecoval-package.Rd | 4 - man/figures/lakemorphol2016.pdf |binary man/figures/lakemorphol2016French.pdf |binary man/figures/lakemorphol2016German.pdf |binary man/msk.macrophytes.2017.read.compile.evaluate.Rd | 2 12 files changed, 67 insertions(+), 72 deletions(-)
Title: Performs a BLP Demand Estimation
Description: Provides the estimation algorithm to perform the demand estimation described in Berry, Levinsohn and Pakes (1995) <DOI:10.2307/2171802> . The routine uses analytic gradients and offers a large number of implemented integration methods and optimization routines.
Author: Daniel Brunner (aut), Constantin Weiser (ctr), Andre Romahn (ctr)
Maintainer: Daniel Brunner <daniel.brunner@hhu.de>
Diff between BLPestimatoR versions 0.2.5 dated 2018-09-15 and 0.2.9 dated 2019-05-14
BLPestimatoR-0.2.5/BLPestimatoR/R/get_BLP_dataset.R |only BLPestimatoR-0.2.5/BLPestimatoR/man/getShares_wrap.Rd |only BLPestimatoR-0.2.5/BLPestimatoR/man/get_BLP_dataset.Rd |only BLPestimatoR-0.2.5/BLPestimatoR/src/Makevars.win |only BLPestimatoR-0.2.9/BLPestimatoR/DESCRIPTION | 8 BLPestimatoR-0.2.9/BLPestimatoR/MD5 | 63 BLPestimatoR-0.2.9/BLPestimatoR/NAMESPACE | 72 BLPestimatoR-0.2.9/BLPestimatoR/R/BLP_data.R | 77 BLPestimatoR-0.2.9/BLPestimatoR/R/RcppExports.R | 62 BLPestimatoR-0.2.9/BLPestimatoR/R/estimateBLP.R | 12 BLPestimatoR-0.2.9/BLPestimatoR/R/get_elasticities.R | 248 + BLPestimatoR-0.2.9/BLPestimatoR/R/simulate_BLP_dataset.R |only BLPestimatoR-0.2.9/BLPestimatoR/R/wrappers.R | 286 - BLPestimatoR-0.2.9/BLPestimatoR/build/vignette.rds |binary BLPestimatoR-0.2.9/BLPestimatoR/inst/doc/blp_intro.R | 296 - BLPestimatoR-0.2.9/BLPestimatoR/inst/doc/blp_intro.Rmd | 89 BLPestimatoR-0.2.9/BLPestimatoR/inst/doc/blp_intro.html | 2046 ++++++------ BLPestimatoR-0.2.9/BLPestimatoR/man/BLP_data.Rd | 171 - BLPestimatoR-0.2.9/BLPestimatoR/man/demographicData.Rd | 42 BLPestimatoR-0.2.9/BLPestimatoR/man/dstddelta_wrap.Rd | 137 BLPestimatoR-0.2.9/BLPestimatoR/man/dstdtheta_wrap.Rd | 138 BLPestimatoR-0.2.9/BLPestimatoR/man/estimateBLP.Rd | 164 BLPestimatoR-0.2.9/BLPestimatoR/man/getDelta_wrap.Rd | 142 BLPestimatoR-0.2.9/BLPestimatoR/man/getJacobian_wrap.Rd | 130 BLPestimatoR-0.2.9/BLPestimatoR/man/getShareInfo.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/get_elasticities.Rd | 150 BLPestimatoR-0.2.9/BLPestimatoR/man/gmm_obj_wrap.Rd | 144 BLPestimatoR-0.2.9/BLPestimatoR/man/originalDraws.Rd | 42 BLPestimatoR-0.2.9/BLPestimatoR/man/productData.Rd | 94 BLPestimatoR-0.2.9/BLPestimatoR/man/simulate_BLP_dataset.Rd |only BLPestimatoR-0.2.9/BLPestimatoR/man/theta_guesses.Rd | 34 BLPestimatoR-0.2.9/BLPestimatoR/man/update_BLP_data.Rd | 112 BLPestimatoR-0.2.9/BLPestimatoR/man/w_guesses.Rd | 34 BLPestimatoR-0.2.9/BLPestimatoR/src/Makevars | 15 BLPestimatoR-0.2.9/BLPestimatoR/src/cppFunctions.cpp | 122 BLPestimatoR-0.2.9/BLPestimatoR/vignettes/blp_intro.Rmd | 89 36 files changed, 2779 insertions(+), 2240 deletions(-)
Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows
for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between rqdatatable versions 1.1.5 dated 2019-04-25 and 1.1.6 dated 2019-05-14
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 4 R/relop_extend.R | 2 R/relop_order_expr.R | 2 R/relop_project.R | 2 R/relop_select_rows.R | 2 R/relop_theta_join.R | 2 README.md | 39 +++- build/vignette.rds |binary inst/doc/GroupedSampling.html | 374 ++++++++++++++++++++++++++++++++---------- inst/doc/logisticexample.html | 349 +++++++++++++++++++++++++++++++-------- 12 files changed, 622 insertions(+), 182 deletions(-)
Title: Sample Size and Power for Association Studies Involving
Mitochondrial DNA Haplogroups
Description: Calculate Sample Size and Power for
Association Studies Involving Mitochondrial DNA Haplogroups.
Based on formulae by Samuels et al. AJHG, 2006. 78(4):713-720. <DOI:10.1086/502682>.
Author: Aurora Baluja [aut, cre] (<https://orcid.org/0000-0002-5204-0771>)
Maintainer: Aurora Baluja <mariauror@gmail.com>
Diff between mthapower versions 0.1.0 dated 2017-07-09 and 0.1.1 dated 2019-05-14
DESCRIPTION | 22 ++++++--- MD5 | 15 ++++-- R/mthacases.R | 4 - R/mthapower.R | 12 ++--- README.md | 122 ++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/figures |only man/mthacases.Rd | 8 +-- man/mthapower.Rd | 16 +++---- 8 files changed, 163 insertions(+), 36 deletions(-)
Title: Importing Vector Graphics
Description: Functions for converting, importing, and drawing PostScript
pictures in R plots.
Author: Paul Murrell [aut, cre],
Richard Walton [aut],
Simon Potter [ctb]
Maintainer: Paul Murrell <p.murrell@auckland.ac.nz>
Diff between grImport versions 0.9-1.1 dated 2019-01-05 and 0.9-2 dated 2019-05-14
DESCRIPTION | 8 +++++--- MD5 | 16 ++++++++-------- R/PostScript2RGML.R | 47 ++++++++++++++++++++++++++++++++++++++++++----- R/util.R | 4 ++++ build/vignette.rds |binary inst/doc/changes.txt | 10 ++++++++++ inst/doc/import.pdf |binary inst/doc/importText.pdf |binary man/PostScriptTrace.Rd | 5 ++++- 9 files changed, 73 insertions(+), 17 deletions(-)
Title: Generation of Multivariate Ordinal Variates
Description: A method for multivariate ordinal data generation given marginal distributions and correlation matrix based on the methodology proposed by Demirtas (2006).
Author: Anup Amatya, Hakan Demirtas, Ran Gao
Maintainer: Ran Gao <rgao8@uic.edu>
Diff between MultiOrd versions 2.4 dated 2019-03-03 and 2.4.1 dated 2019-05-14
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- man/MultiOrd-package.Rd | 12 ++++++------ man/genOrd.Rd | 2 +- man/generate.binary.Rd | 2 +- 5 files changed, 17 insertions(+), 17 deletions(-)
Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh
(2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller
(2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al.
(2008, <doi:10.1214/07-AOS517>); Jiang et al.
(2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre] (<https://orcid.org/0000-0002-6605-7478>),
Samuel Mueller [aut] (<https://orcid.org/0000-0002-3087-8127>),
Alan H Welsh [aut] (<https://orcid.org/0000-0002-3165-9559>)
Maintainer: Garth Tarr <garth.tarr@gmail.com>
Diff between mplot versions 1.0.2 dated 2019-01-22 and 1.0.3 dated 2019-05-14
mplot-1.0.2/mplot/R/sstab.R |only mplot-1.0.3/mplot/DESCRIPTION | 16 ++++++++-------- mplot-1.0.3/mplot/MD5 | 15 +++++++-------- mplot-1.0.3/mplot/NEWS | 9 ++++++++- mplot-1.0.3/mplot/R/af.R | 2 +- mplot-1.0.3/mplot/R/mplot.R | 18 ++++++++++++------ mplot-1.0.3/mplot/R/vis.R | 12 ++++++++---- mplot-1.0.3/mplot/man/af.Rd | 2 +- mplot-1.0.3/mplot/man/mplot.Rd | 7 ++++--- 9 files changed, 49 insertions(+), 32 deletions(-)