Title: Fire-History Analysis in R
Description: Basic tools to analyze forest fire history data (e.g. FHX) in R.
Author: Steven Malevich [aut, cre],
Christopher Guiterman [ctb],
Ellis Margolis [ctb]
Maintainer: Steven Malevich <malevich@email.arizona.edu>
Diff between burnr versions 0.3.1 dated 2019-03-08 and 0.4.0 dated 2019-07-09
DESCRIPTION | 6 +-- MD5 | 22 ++++++------- NEWS.md | 17 ++++++++-- R/io.R | 42 +++++++++++++------------ R/sea.R | 49 ++++++++++++----------------- R/utils.R | 2 - build/vignette.rds |binary inst/doc/introduction.html | 74 ++++++++++++++++++++++++--------------------- man/composite.Rd | 2 - man/list_filestrings.Rd | 4 +- man/read_fhx.Rd | 2 - man/sea.Rd | 30 +++++++++++------- 12 files changed, 136 insertions(+), 114 deletions(-)
Title: 3D Animated Interactive Visualizations Using SVG
Description: Creates 3D animated, interactive visualizations that can be viewed in a web browser.
Author: Aaron Olsen, Alejandro Romero
Maintainer: Aaron Olsen <aarolsen@gmail.com>
Diff between svgViewR versions 1.3 dated 2018-01-20 and 1.4 dated 2019-07-09
DESCRIPTION | 15 MD5 | 113 +- NAMESPACE | 7 R/JSONToobj.R |only R/RM2quat.R |only R/RcppExports.R |only R/Rhttpd2.R | 11 R/applyQuat.R |only R/applyTransform_svg.R | 1 R/avec_svg.R |only R/axisAngle2Quat.R |only R/axisAngle2Tmat.R |only R/bestAlign_svg.R |only R/box_in_box_faces.R |only R/cameraParameters.R |only R/circlePoint_svg.R |only R/create_plane_mesh.R |only R/create_sphere_mesh.R | 2 R/darkenCol.R |only R/defineCircle_svg.R |only R/distPointToPlane_svg.R |only R/distancePointToLine_svg.R |only R/dppt_svg.R |only R/image2world.R |only R/lightenCol.R |only R/objToJSON.R | 4 R/pointLineProj_svg.R |only R/pointNormalOnLine_svg.R |only R/pointPlaneProj_svg.R |only R/quat2RM.R |only R/readCam.R |only R/readOBJ.R | 71 - R/svg.arrow.R |only R/svg.arrows.R | 2 R/svg.bboxLight.R | 2 R/svg.box.R | 15 R/svg.camera.R |only R/svg.carrow.R |only R/svg.ccuboid.R |only R/svg.close.R | 131 ++ R/svg.cone.R |only R/svg.coupler.R | 8 R/svg.cplanes.R |only R/svg.cuboid.R | 49 - R/svg.cylinder.R | 56 - R/svg.dcylinder.R |only R/svg.deform.R |only R/svg.farrow.R |only R/svg.hcuboid.R |only R/svg.images.R |only R/svg.lines.R | 51 - R/svg.mesh.R | 129 +- R/svg.new.R | 202 +++- R/svg.pal.R |only R/svg.plane.R |only R/svg.socket.R | 10 R/svg.sphere.R | 10 R/svg.spheres.R | 37 R/svg.text.R | 4 R/svg.transform.R | 288 ++++-- R/svg.triangle.R |only R/svg_ranges.R | 28 R/svgviewr.new.R | 39 R/viewer_save_image.R |only R/writeOBJ.R |only R/write_html.R | 339 ++++++- inst/extdata/css/server_stylesheet.css | 227 ++++- inst/extdata/html/body.html |only inst/extdata/js/TrackballControls.js | 120 ++ inst/extdata/js/render.scene.js | 1448 +++++++++++++++++++++++++++++---- inst/extdata/js/ui_functions.js | 2 man/svg.close.Rd | 6 man/svg.lines.Rd | 4 man/svg.mesh.Rd | 7 man/svg.new.Rd | 25 man/svg.pathsC.Rd | 2 man/svgViewR-package.Rd | 51 + src |only 78 files changed, 2885 insertions(+), 631 deletions(-)
Title: Functions for Common Chart Types
Description: Wrapper for the 'ggplot2' package that creates a variety of common
charts (e.g. bar, line, area, ROC, waterfall, pie) while aiming to reduce
typing.
Author: Wojtek Kostelecki
Maintainer: Wojtek Kostelecki <wojtek.kostelecki@gmail.com>
Diff between ezplot versions 0.2.2 dated 2019-01-30 and 0.3.0 dated 2019-07-09
ezplot-0.2.2/ezplot/man/figures/README-line_plot.png |only ezplot-0.2.2/ezplot/tests/testthat/test_agg_data.R |only ezplot-0.2.2/ezplot/tests/testthat/test_ez_labels.R |only ezplot-0.3.0/ezplot/DESCRIPTION | 19 - ezplot-0.3.0/ezplot/MD5 | 98 +++++---- ezplot-0.3.0/ezplot/NAMESPACE | 4 ezplot-0.3.0/ezplot/NEWS.md |only ezplot-0.3.0/ezplot/R/agg_data.R | 84 ++----- ezplot-0.3.0/ezplot/R/area_plot.R | 44 ++-- ezplot-0.3.0/ezplot/R/bar_plot.R | 4 ezplot-0.3.0/ezplot/R/calendar_plot.R |only ezplot-0.3.0/ezplot/R/distribution_plot.R |only ezplot-0.3.0/ezplot/R/ez_data.R | 66 ++++-- ezplot-0.3.0/ezplot/R/ez_labels.R | 3 ezplot-0.3.0/ezplot/R/line_plot.R | 30 +- ezplot-0.3.0/ezplot/R/model_plot.R | 36 +++ ezplot-0.3.0/ezplot/R/pie_plot.R | 7 ezplot-0.3.0/ezplot/R/reorder_levels.R | 7 ezplot-0.3.0/ezplot/R/roc_plot.R | 9 ezplot-0.3.0/ezplot/R/secondary_plot.R |only ezplot-0.3.0/ezplot/R/side_plot.R | 2 ezplot-0.3.0/ezplot/R/tile_plot.R | 21 + ezplot-0.3.0/ezplot/R/utils.R | 6 ezplot-0.3.0/ezplot/R/waterfall_plot.R | 32 +-- ezplot-0.3.0/ezplot/README.md | 127 ++++++++---- ezplot-0.3.0/ezplot/build |only ezplot-0.3.0/ezplot/inst |only ezplot-0.3.0/ezplot/man/agg_data.Rd | 11 - ezplot-0.3.0/ezplot/man/area_plot.Rd | 29 +- ezplot-0.3.0/ezplot/man/calendar_plot.Rd |only ezplot-0.3.0/ezplot/man/distribution_plot.Rd |only ezplot-0.3.0/ezplot/man/ez_data.Rd | 4 ezplot-0.3.0/ezplot/man/ez_data2.Rd |only ezplot-0.3.0/ezplot/man/figures/README-area_plot.png |binary ezplot-0.3.0/ezplot/man/figures/README-bar_plot.png |binary ezplot-0.3.0/ezplot/man/figures/README-line_plot_1.png |only ezplot-0.3.0/ezplot/man/figures/README-line_plot_2.png |only ezplot-0.3.0/ezplot/man/figures/README-secondary_plot.png |only ezplot-0.3.0/ezplot/man/figures/README-side_plot.png |binary ezplot-0.3.0/ezplot/man/figures/README-tile_plot.png |only ezplot-0.3.0/ezplot/man/figures/README-waterfall_plot.png |binary ezplot-0.3.0/ezplot/man/line_plot.Rd | 23 +- ezplot-0.3.0/ezplot/man/model_plot.Rd | 7 ezplot-0.3.0/ezplot/man/pie_plot.Rd | 2 ezplot-0.3.0/ezplot/man/reorder_levels.Rd | 7 ezplot-0.3.0/ezplot/man/secondary_plot.Rd |only ezplot-0.3.0/ezplot/man/side_plot.Rd | 2 ezplot-0.3.0/ezplot/man/tile_plot.Rd | 22 +- ezplot-0.3.0/ezplot/tests/testthat/test-agg_data.R |only ezplot-0.3.0/ezplot/tests/testthat/test-area_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-distribution_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-ez_data.R | 22 +- ezplot-0.3.0/ezplot/tests/testthat/test-ez_labels.R |only ezplot-0.3.0/ezplot/tests/testthat/test-ez_png.R |only ezplot-0.3.0/ezplot/tests/testthat/test-line_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-model_plot.R | 6 ezplot-0.3.0/ezplot/tests/testthat/test-na_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-pie_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-roc_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-secondary_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-side_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-tile_plot.R |only ezplot-0.3.0/ezplot/tests/testthat/test-waterfall_plot.R | 5 ezplot-0.3.0/ezplot/vignettes |only 64 files changed, 473 insertions(+), 266 deletions(-)
Title: A Framework for Coalescent Simulation
Description: Coalescent simulators can rapidly simulate biological sequences
evolving according to a given model of evolution.
You can use this package to specify such models, to conduct the simulations
and to calculate additional statistics from the results.
It relies on existing simulators for doing the simulation, and currently
supports the programs 'ms', 'msms' and 'scrm'. It also supports finite-sites
mutation models by combining the simulators with the program 'seq-gen'.
Author: Paul Staab [aut, cre],
Dirk Metzler [aut, ths],
Jorge E. Amaya Romero [ctb]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between coala versions 0.5.2 dated 2017-10-30 and 0.5.3 dated 2019-07-09
DESCRIPTION | 10 MD5 | 86 ++++---- NEWS.md | 9 R/feature.R | 6 R/feature_migration.R | 4 R/model_build.R | 2 R/sumstat_ihh.R | 41 ++- README.md | 4 build/vignette.rds |binary inst/doc/coala-abc.html | 343 +++++++++++++++++++++++++++----- inst/doc/coala-data-import.html | 343 +++++++++++++++++++++++++++----- inst/doc/coala-examples.html | 377 +++++++++++++++++++++++++++++------- inst/doc/coala-extend.html | 363 ++++++++++++++++++++++++++++------ inst/doc/coala-install.html | 331 ++++++++++++++++++++++++++----- inst/doc/coala-intro.html | 397 ++++++++++++++++++++++++++++++-------- man/coal_model.Rd | 3 man/feat_growth.Rd | 4 man/feat_ignore_singletons.Rd | 1 man/feat_migration.Rd | 5 man/feat_mutation.Rd | 6 man/feat_outgroup.Rd | 1 man/feat_pop_merge.Rd | 1 man/feat_recombination.Rd | 1 man/feat_selection.Rd | 1 man/feat_size_change.Rd | 1 man/feat_unphased.Rd | 1 man/simulate.coalmodel.Rd | 4 man/simulator_ms.Rd | 1 man/simulator_msms.Rd | 4 man/simulator_scrm.Rd | 1 man/simulator_seqgen.Rd | 1 man/sumstat_dna.Rd | 1 man/sumstat_file.Rd | 1 man/sumstat_four_gamete.Rd | 1 man/sumstat_ihh.Rd | 13 - man/sumstat_jsfs.Rd | 1 man/sumstat_mcmf.Rd | 5 man/sumstat_nucleotide_div.Rd | 1 man/sumstat_omega.Rd | 1 man/sumstat_seg_sites.Rd | 1 man/sumstat_sfs.Rd | 4 man/sumstat_tajimas_d.Rd | 1 man/sumstat_trees.Rd | 1 tests/testthat/test-sumstat-iHH.R | 45 ++-- 44 files changed, 1938 insertions(+), 490 deletions(-)
Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <http://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 3.2.14 dated 2019-07-02 and 3.2.15 dated 2019-07-09
DESCRIPTION | 8 +-- LICENSE | 27 ----------- MD5 | 93 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS | 11 +++- R/INTERNAL-checkConnection.R | 2 R/close.R | 2 R/ops.R | 10 ++-- R/print.R | 4 - R/scala.R | 28 ++++++------ R/scalaConfig.R | 10 ++-- R/scalaDevelDeployJARs.R |only R/scalaDevelDownloadJARs.R |only R/scalaDisconnect.R | 6 +- R/scalaFindBridge.R | 6 +- R/scalaJARs.R | 4 - R/scalaLast.R | 4 - R/scalaLazy.R | 20 ++++---- R/scalaMemory.R | 6 +- R/scalaPush.R | 2 R/scalaPushRegister.R | 2 R/scalaSBT.R | 74 +++---------------------------- R/sysdata.rda |binary README.md | 2 inst/data-raw/urls.txt | 8 +-- inst/doc/rscala.Rnw | 19 +++++--- inst/doc/rscala.pdf |binary inst/java/scala-2.11/rscala.jar |binary inst/java/scala-2.12/rscala.jar |binary inst/java/scala-2.13/rscala.jar |binary java/rscala-source.jar |binary man/close.rscalaBridge.Rd | 2 man/plus-.rscalaBridge.Rd | 2 man/pow-.rscalaBridge.Rd | 2 man/scala.Rd | 18 +++---- man/scalaConfig.Rd | 6 +- man/scalaDevelDeployJARs.Rd | 5 +- man/scalaDevelDownloadJARs.Rd |only man/scalaDisconnect.Rd | 6 +- man/scalaFindBridge.Rd | 4 - man/scalaJARs.Rd | 4 - man/scalaLast.Rd | 4 - man/scalaLazy.Rd | 18 +++---- man/scalaMemory.Rd | 6 +- man/scalaPush.Rd | 2 man/scalaPushRegister.Rd | 2 man/scalaSBT.Rd | 11 +++- man/times-.rscalaBridge.Rd | 8 +-- vignettes/rscala.Rnw | 19 +++++--- 49 files changed, 211 insertions(+), 257 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals and tests, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between MKmisc versions 1.4 dated 2019-05-21 and 1.5 dated 2019-07-09
DESCRIPTION | 8 MD5 | 35 - NAMESPACE | 8 NEWS | 12 R/CV.R |only R/SNR.R |only R/cvCI.R |only R/perfMeasures.R | 22 R/perfScores.R |only R/powerWelchttest.R | 4 build/vignette.rds |binary inst/doc/MKmisc.R | 31 + inst/doc/MKmisc.Rmd | 64 ++ inst/doc/MKmisc.html | 1235 ++++++++++++++++++++++++++----------------------- man/0MKmisc-package.Rd | 8 man/CV.Rd |only man/IQrange.Rd | 3 man/SNR.Rd |only man/cvCI.Rd |only man/optCutoff.Rd | 4 man/perfMeasures.Rd | 34 - vignettes/MKmisc.Rmd | 64 ++ 22 files changed, 881 insertions(+), 651 deletions(-)
Title: Fast Drawing and Shading of Graphs of Statistical Distributions
Description: Provides functionality to produce graphs of probability density functions and cumulative distribution functions with few keystrokes, allows shading under the curve of the probability density function to illustrate concepts such as p-values and critical values, and fits a simple linear regression line on a scatter plot with the equation as the main title.
Author: Steven T. Garren
Maintainer: Steven T. Garren <garrenst@jmu.edu>
Diff between fastGraph versions 1.3 dated 2019-06-24 and 2.0 dated 2019-07-09
DESCRIPTION | 11 ++++++----- MD5 | 16 ++++++++-------- R/fastGraph.R | 35 +++++++++++++++++------------------ man/fastGraph-package.Rd | 41 ++++++++++++++--------------------------- man/getMinMax.Rd | 1 - man/plotDist.Rd | 22 ++++++++++++++++------ man/plotLine.Rd | 7 +++++-- man/shadeDist.Rd | 35 +++++++++++++---------------------- man/shadePhat.Rd | 17 +++++++++++------ 9 files changed, 90 insertions(+), 95 deletions(-)
Title: Tools for Preprocessing Visual World Data
Description: Gaze data from the Visual World Paradigm requires significant
preprocessing prior to plotting and analyzing the data. This package
provides functions for preparing visual world eye-tracking data for
statistical analysis and plotting. It can prepare data for linear
analyses (e.g., ANOVA, Gaussian-family LMER, Gaussian-family GAMM) as
well as logistic analyses (e.g., binomial-family LMER and binomial-family GAMM).
Additionally, it contains various plotting functions for creating grand average and
conditional average plots. See the vignette for samples of the functionality.
Currently, the functions in this package are designed for handling data
collected with SR Research Eyelink eye trackers using Sample Reports created
in SR Research Data Viewer. While we would like to add functionality
for data collected with other systems in the future, the current package is
considered to be feature-complete; further updates will mainly entail maintenance
and the addition of minor functionality.
Author: Vincent Porretta [aut, cre],
Aki-Juhani Kyröläinen [aut],
Jacolien van Rij [ctb],
Juhani Järvikivi [ctb]
Maintainer: Vincent Porretta <vincentporretta@gmail.com>
Diff between VWPre versions 1.1.0 dated 2018-03-20 and 1.2.0 dated 2019-07-09
VWPre-1.1.0/VWPre/inst/doc/SR_Basic_Preprocessing.R |only VWPre-1.1.0/VWPre/inst/doc/SR_Basic_Preprocessing.Rmd |only VWPre-1.1.0/VWPre/inst/doc/SR_Basic_Preprocessing.html |only VWPre-1.1.0/VWPre/inst/doc/SR_Interest_Areas.R |only VWPre-1.1.0/VWPre/inst/doc/SR_Interest_Areas.Rmd |only VWPre-1.1.0/VWPre/inst/doc/SR_Interest_Areas.html |only VWPre-1.1.0/VWPre/inst/doc/SR_Message_Alignment.R |only VWPre-1.1.0/VWPre/inst/doc/SR_Message_Alignment.Rmd |only VWPre-1.1.0/VWPre/inst/doc/SR_Message_Alignment.html |only VWPre-1.1.0/VWPre/inst/doc/SR_Plotting.R |only VWPre-1.1.0/VWPre/inst/doc/SR_Plotting.Rmd |only VWPre-1.1.0/VWPre/inst/doc/SR_Plotting.html |only VWPre-1.1.0/VWPre/vignettes/IAreport.txt |only VWPre-1.1.0/VWPre/vignettes/SR_Basic_Preprocessing.Rmd |only VWPre-1.1.0/VWPre/vignettes/SR_Interest_Areas.Rmd |only VWPre-1.1.0/VWPre/vignettes/SR_Message_Alignment.Rmd |only VWPre-1.1.0/VWPre/vignettes/SR_Plotting.Rmd |only VWPre-1.2.0/VWPre/DESCRIPTION | 14 VWPre-1.2.0/VWPre/LICENSE |only VWPre-1.2.0/VWPre/MD5 | 106 VWPre-1.2.0/VWPre/NAMESPACE | 4 VWPre-1.2.0/VWPre/R/VWPre.R | 22 VWPre-1.2.0/VWPre/R/calculations.R | 46 VWPre-1.2.0/VWPre/R/checking.R | 1039 +++-- VWPre-1.2.0/VWPre/R/fasttrack.R | 7 VWPre-1.2.0/VWPre/R/formatting.R | 726 +-- VWPre-1.2.0/VWPre/R/ias.R | 20 VWPre-1.2.0/VWPre/R/interactive.R | 33 VWPre-1.2.0/VWPre/R/plotting.R | 2588 +++++++------- VWPre-1.2.0/VWPre/R/trackloss.R |only VWPre-1.2.0/VWPre/R/zzz.R | 64 VWPre-1.2.0/VWPre/build/vignette.rds |binary VWPre-1.2.0/VWPre/data/VWdat.rda |binary VWPre-1.2.0/VWPre/inst/CITATION | 8 VWPre-1.2.0/VWPre/inst/NEWS | 51 VWPre-1.2.0/VWPre/inst/doc/VWPre_Basic_Preprocessing.R |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Basic_Preprocessing.Rmd |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Basic_Preprocessing.html |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Interest_Areas.R |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Interest_Areas.Rmd |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Interest_Areas.html |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Message_Alignment.R |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Message_Alignment.Rmd |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Message_Alignment.html |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Plotting.R |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Plotting.Rmd |only VWPre-1.2.0/VWPre/inst/doc/VWPre_Plotting.html |only VWPre-1.2.0/VWPre/man/VWPre.Rd | 22 VWPre-1.2.0/VWPre/man/check_all_msgs.Rd |only VWPre-1.2.0/VWPre/man/check_ia.Rd | 4 VWPre-1.2.0/VWPre/man/check_msg_time.Rd | 4 VWPre-1.2.0/VWPre/man/check_time_series.Rd | 3 VWPre-1.2.0/VWPre/man/create_binomial.Rd | 4 VWPre-1.2.0/VWPre/man/dot-check_for_PupilPre.Rd |only VWPre-1.2.0/VWPre/man/fasttrack.Rd | 8 VWPre-1.2.0/VWPre/man/make_pelogit_fnc.Rd | 2 VWPre-1.2.0/VWPre/man/mark_trackloss.Rd |only VWPre-1.2.0/VWPre/man/plot_avg_cdiff.Rd |only VWPre-1.2.0/VWPre/man/plot_avg_contour.Rd | 4 VWPre-1.2.0/VWPre/man/plot_avg_diff.Rd | 2 VWPre-1.2.0/VWPre/man/plot_indiv_app.Rd | 2 VWPre-1.2.0/VWPre/man/plot_var_app.Rd | 2 VWPre-1.2.0/VWPre/man/prep_data.Rd | 6 VWPre-1.2.0/VWPre/man/rm_extra_DVcols.Rd | 2 VWPre-1.2.0/VWPre/man/rm_trackloss_events.Rd |only VWPre-1.2.0/VWPre/man/select_recorded_eye.Rd | 5 VWPre-1.2.0/VWPre/man/transform_to_elogit.Rd | 4 VWPre-1.2.0/VWPre/vignettes/IAdat.rda |binary VWPre-1.2.0/VWPre/vignettes/VWPre_Basic_Preprocessing.Rmd |only VWPre-1.2.0/VWPre/vignettes/VWPre_Interest_Areas.Rmd |only VWPre-1.2.0/VWPre/vignettes/VWPre_Message_Alignment.Rmd |only VWPre-1.2.0/VWPre/vignettes/VWPre_Plotting.Rmd |only VWPre-1.2.0/VWPre/vignettes/aligndat.rda |only VWPre-1.2.0/VWPre/vignettes/checkdat.rda |only VWPre-1.2.0/VWPre/vignettes/model.rda |only VWPre-1.2.0/VWPre/vignettes/plotdat.rda |only 76 files changed, 2755 insertions(+), 2047 deletions(-)
Title: Ace Editor Bindings for Shiny
Description: Ace editor bindings to enable a rich text editing environment
within Shiny.
Author: Vincent Nijs [aut, cre],
Forest Fang [aut],
Trestle Technology, LLC [aut],
Jeff Allen [aut],
Institut de Radioprotection et de Surete Nucleaire [cph],
Ajax.org B.V. [ctb, cph] (Ace)
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between shinyAce versions 0.3.3 dated 2019-01-03 and 0.4.0 dated 2019-07-09
shinyAce-0.3.3/shinyAce/R/js-quote.R |only shinyAce-0.3.3/shinyAce/man/jsQuote.Rd |only shinyAce-0.3.3/shinyAce/tests/testthat/test-js-quote.R |only shinyAce-0.4.0/shinyAce/DESCRIPTION | 14 shinyAce-0.4.0/shinyAce/MD5 | 82 +- shinyAce-0.4.0/shinyAce/NAMESPACE | 1 shinyAce-0.4.0/shinyAce/NEWS.md | 13 shinyAce-0.4.0/shinyAce/R/aaa.R |only shinyAce-0.4.0/shinyAce/R/ace-autocomplete.R | 2 shinyAce-0.4.0/shinyAce/R/ace-editor.R | 296 ++------- shinyAce-0.4.0/shinyAce/R/get-ace-modes.R | 3 shinyAce-0.4.0/shinyAce/R/get-ace-themes.R | 3 shinyAce-0.4.0/shinyAce/R/update-ace-editor.R | 21 shinyAce-0.4.0/shinyAce/README.md | 54 + shinyAce-0.4.0/shinyAce/inst/examples/01-basic/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/01-basic/global.R |only shinyAce-0.4.0/shinyAce/inst/examples/01-basic/rsconnect |only shinyAce-0.4.0/shinyAce/inst/examples/01-basic/server.R | 38 - shinyAce-0.4.0/shinyAce/inst/examples/01-basic/ui.R | 52 - shinyAce-0.4.0/shinyAce/inst/examples/02-eval/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/02-eval/server.R | 7 shinyAce-0.4.0/shinyAce/inst/examples/02-eval/ui.R | 44 - shinyAce-0.4.0/shinyAce/inst/examples/03-knitr/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/03-knitr/figure |only shinyAce-0.4.0/shinyAce/inst/examples/03-knitr/server.R | 8 shinyAce-0.4.0/shinyAce/inst/examples/03-knitr/ui.R | 39 - shinyAce-0.4.0/shinyAce/inst/examples/04-shinyui/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/04-shinyui/server.R | 9 shinyAce-0.4.0/shinyAce/inst/examples/04-shinyui/ui.R | 50 - shinyAce-0.4.0/shinyAce/inst/examples/05-hotkeys/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/05-hotkeys/server.R | 37 - shinyAce-0.4.0/shinyAce/inst/examples/05-hotkeys/ui.R | 43 - shinyAce-0.4.0/shinyAce/inst/examples/06-autocomplete/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/06-autocomplete/server.R | 28 shinyAce-0.4.0/shinyAce/inst/examples/07-autocomplete-combine/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/07-autocomplete-combine/server.R | 2 shinyAce-0.4.0/shinyAce/inst/examples/08-resize/DESCRIPTION |only shinyAce-0.4.0/shinyAce/inst/examples/08-resize/server.R | 29 shinyAce-0.4.0/shinyAce/inst/examples/08-resize/ui.R | 50 - shinyAce-0.4.0/shinyAce/inst/examples/09-selectionId |only shinyAce-0.4.0/shinyAce/inst/examples/10-modules |only shinyAce-0.4.0/shinyAce/inst/examples/11-code-hotkeys |only shinyAce-0.4.0/shinyAce/inst/www/code |only shinyAce-0.4.0/shinyAce/inst/www/shinyAce.js | 315 +++++++--- shinyAce-0.4.0/shinyAce/man/aceEditor.Rd | 25 shinyAce-0.4.0/shinyAce/man/is.empty.Rd |only shinyAce-0.4.0/shinyAce/man/updateAceEditor.Rd | 2 shinyAce-0.4.0/shinyAce/tests/testthat/test-shinyAce.R |only 48 files changed, 632 insertions(+), 635 deletions(-)
Title: Permutation Tests for Nonparametric Statistics
Description: Performs a permutation test on the difference between two location parameters, a permutation correlation test, a permutation F-test, the Siegel-Tukey test, a ratio mean deviance test. Also performs some graphing techniques, such as for confidence intervals, vector addition, and Fourier analysis; and includes functions related to the Laplace (double exponential) and triangular distributions. Performs power calculations for the binomial test.
Author: Steven T. Garren
Maintainer: Steven T. Garren <GARRENST@JMU.EDU>
Diff between jmuOutlier versions 1.5 dated 2019-06-24 and 2.0 dated 2019-07-09
jmuOutlier-1.5/jmuOutlier/build |only jmuOutlier-2.0/jmuOutlier/DESCRIPTION | 12 ++++----- jmuOutlier-2.0/jmuOutlier/MD5 | 25 +++++++++++--------- jmuOutlier-2.0/jmuOutlier/NAMESPACE | 2 - jmuOutlier-2.0/jmuOutlier/R/fourier.R | 7 +++-- jmuOutlier-2.0/jmuOutlier/R/read.table2.R |only jmuOutlier-2.0/jmuOutlier/R/scan2.R |only jmuOutlier-2.0/jmuOutlier/man/coin.toss.Rd | 5 +++- jmuOutlier-2.0/jmuOutlier/man/fourier.Rd | 5 ++++ jmuOutlier-2.0/jmuOutlier/man/jmuOutlier-package.Rd | 20 +++++++--------- jmuOutlier-2.0/jmuOutlier/man/lineGraph.Rd | 9 +++++-- jmuOutlier-2.0/jmuOutlier/man/plotEcdf.Rd | 8 +++++- jmuOutlier-2.0/jmuOutlier/man/plotVector.Rd | 5 ++-- jmuOutlier-2.0/jmuOutlier/man/read.table2.Rd |only jmuOutlier-2.0/jmuOutlier/man/scan2.Rd |only jmuOutlier-2.0/jmuOutlier/man/truncHist.Rd | 10 ++++++-- 16 files changed, 68 insertions(+), 40 deletions(-)
Title: Reversible-Jump MCMC Using Post-Processing
Description: Performs reversible-jump Markov chain Monte Carlo (Green, 1995)
<doi:10.2307/2337340>, specifically the restriction introduced by
Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising
a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling
problem. Previously-calculated posterior distributions are used to
quickly estimate posterior model probabilities. Jacobian matrices are
found using automatic differentiation. For a detailed description of
the package, see Gelling, Schofield & Barker (2019)
<doi:10.1111/anzs.12263>.
Author: Nick Gelling [aut, cre],
Matthew R. Schofield [aut],
Richard J. Barker [aut]
Maintainer: Nick Gelling <nickcjgelling@gmail.com>
Diff between rjmcmc versions 0.4.4 dated 2019-03-02 and 0.4.5 dated 2019-07-09
rjmcmc-0.4.4/rjmcmc/build |only rjmcmc-0.4.4/rjmcmc/inst |only rjmcmc-0.4.4/rjmcmc/vignettes |only rjmcmc-0.4.5/rjmcmc/DESCRIPTION | 15 ++++++++------- rjmcmc-0.4.5/rjmcmc/MD5 | 18 ++---------------- rjmcmc-0.4.5/rjmcmc/R/class.R | 2 +- 6 files changed, 11 insertions(+), 24 deletions(-)
Title: Reading, Extracting, and Converting an Mbox File into a Tibble
Description: Importing and converting an mbox file into a tibble object.
Author: JooYoung Seo [aut, cre] (<https://orcid.org/0000-0002-4064-6012>),
Soyoung Choi [aut] (<https://orcid.org/0000-0002-0998-3352>)
Maintainer: JooYoung Seo <jooyoung@psu.edu>
Diff between mboxr versions 0.1.5 dated 2019-04-21 and 0.1.6 dated 2019-07-09
DESCRIPTION | 6 - MD5 | 22 ++-- NEWS.md | 5 + README.md | 48 +++++----- build/vignette.rds |binary inst/NEWS | 6 + inst/NEWS.md |only inst/doc/mboxr_vignette.R | 8 - inst/doc/mboxr_vignette.Rmd | 8 - inst/doc/mboxr_vignette.html | 124 +++++++++++++++------------ inst/python/__pycache__/mboxR.cpython-37.pyc |only inst/python/mboxR.py | 6 - vignettes/mboxr_vignette.Rmd | 8 - 13 files changed, 138 insertions(+), 103 deletions(-)
Title: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices.
The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use,
3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevičius [aut, cre]
Maintainer: Karolis Koncevičius <karolis.koncevicius@gmail.com>
Diff between matrixTests versions 0.1.4 dated 2019-06-25 and 0.1.5 dated 2019-07-09
DESCRIPTION | 6 - MD5 | 46 +++++++------- NAMESPACE | 2 NEWS | 15 ++++ R/bartlett.R | 6 - R/cor.R | 15 ++-- R/fligner.R | 13 +--- R/fvar.R |only R/jarque.R | 8 +- R/kruskal.R | 9 +- R/oneway.R | 6 - R/ttest.R | 27 ++++---- R/utils.asserts.R | 6 - R/utils.general.R | 12 ++- R/utils.tests.R | 53 ++++++++++++++-- R/wilcox.R | 23 ++++--- inst/benchmarks/row_f_var.R |only man/fvar.Rd |only man/ttest.Rd | 2 tests/testthat/test-col-versions.R | 5 + tests/testthat/test-correct-bartlett.R | 17 +++++ tests/testthat/test-correct-flignerkilleen.R | 17 +++++ tests/testthat/test-correct-ftest_var.R |only tests/testthat/test-parameters-main-errors.R | 17 +++++ tests/testthat/test-parameters-optional-errors.R | 73 +++++++++++++++++++++++ tests/testthat/test-parameters-special-cases.R | 7 +- 26 files changed, 294 insertions(+), 91 deletions(-)
Title: Fast Gaussian Process Computation Using Vecchia's Approximation
Description: Functions for fitting and doing predictions with
Gaussian process models using Vecchia's (1988) approximation.
Package also includes functions for reordering input locations,
finding ordered nearest neighbors (with help from 'FNN' package),
grouping operations, and conditional simulations.
Covariance functions for spatial and spatial-temporal data
on Euclidean domains and spheres are provided. The original
approximation is due to Vecchia (1988)
<http://www.jstor.org/stable/2345768>, and the reordering and
grouping methods are from Guinness (2018)
<doi:10.1080/00401706.2018.1437476>.
Model fitting employs a Fisher scoring algorithm described
in Guinness (2019) <arXiv:1905.08374>.
Author: Joseph Guinness [aut, cre],
Matthias Katzfuss [aut]
Maintainer: Joseph Guinness <joeguinness@gmail.com>
Diff between GpGp versions 0.2.0 dated 2019-06-29 and 0.2.1 dated 2019-07-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 4 ++++ src/basis.h | 2 +- src/vecchia_loglik_grad_info.cpp | 10 +++++++--- 5 files changed, 20 insertions(+), 12 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Functions for Bayesian meta-analysis of diagnostic test data which
are based on a scale mixtures bivariate random-effects model.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.2.1 dated 2018-09-17 and 3.3.2 dated 2019-07-09
ChangeLog | 26 +++++++++--- DESCRIPTION | 10 ++-- MD5 | 32 ++++++++------- R/bamdit-package.R | 106 +++++++++++++++++++++++++++++++++++++++++++++++--- R/metadiag.R | 12 ++++- R/plot.metadiag.R | 3 - R/plotcompare.R | 75 +++++++++++++++++++---------------- R/plotdata.R | 58 ++++++++------------------- R/plotw.R | 41 +++++++++---------- data/ct.rda |binary data/diabetes.rda |only data/rapt.rda |only man/bamdit-package.Rd | 20 ++++----- man/ct.Rd | 6 +- man/diabetes.Rd |only man/plotcompare.Rd | 29 +++++-------- man/plotdata.Rd | 43 +++----------------- man/plotw.Rd | 27 ++++++------ man/rapt.Rd |only 19 files changed, 281 insertions(+), 207 deletions(-)
Title: The Matrix Normal Distribution
Description: Computes densities, probabilities, and random deviates of the Matrix Normal (Iranmanesh et al. (2010) <doi:10.7508/ijmsi.2010.02.004>). Also includes simple but useful matrix functions. See the vignette for more information.
Author: Paul Hargarten [aut, cre]
Maintainer: Paul Hargarten <hargartenp@vcu.edu>
Diff between matrixNormal versions 0.0.0 dated 2018-10-30 and 0.0.1 dated 2019-07-09
matrixNormal-0.0.0/matrixNormal/R/matrixNormal_pkg.R |only matrixNormal-0.0.0/matrixNormal/man/matrixNormal.Rd |only matrixNormal-0.0.1/matrixNormal/DESCRIPTION | 21 - matrixNormal-0.0.1/matrixNormal/MD5 | 34 +- matrixNormal-0.0.1/matrixNormal/NEWS.md | 13 matrixNormal-0.0.1/matrixNormal/R/is_symmetric_matrix.R | 160 +++++----- matrixNormal-0.0.1/matrixNormal/R/matrixNormal_Distribution.R | 138 ++++++-- matrixNormal-0.0.1/matrixNormal/R/vec.R | 8 matrixNormal-0.0.1/matrixNormal/build |only matrixNormal-0.0.1/matrixNormal/inst |only matrixNormal-0.0.1/matrixNormal/man/is.symmetric.matrix.Rd | 63 ++- matrixNormal-0.0.1/matrixNormal/man/matrixNormal_Distribution.Rd | 36 +- matrixNormal-0.0.1/matrixNormal/man/special.matrix.Rd | 2 matrixNormal-0.0.1/matrixNormal/man/tr.Rd | 3 matrixNormal-0.0.1/matrixNormal/man/vec.Rd | 11 matrixNormal-0.0.1/matrixNormal/tests/spelling.R |only matrixNormal-0.0.1/matrixNormal/tests/testthat/test_tr.R | 20 - matrixNormal-0.0.1/matrixNormal/vignettes |only 18 files changed, 317 insertions(+), 192 deletions(-)
Title: R Functions to Download and Clean Brazilian Electoral Data
Description: Offers a set of functions to easily download and clean
Brazilian electoral data from the Superior Electoral Court website.
Among others, the package retrieves data on local and
federal elections for all positions (city councilor, mayor, state deputy,
federal deputy, governor, and president) aggregated by
state, city, and electoral zones.
Author: Denisson Silva [aut, cre],
Fernando Meireles [aut],
Beatriz Costa [ctb]
Maintainer: Denisson Silva <denissoncsol@gmail.com>
Diff between electionsBR versions 0.3.0 dated 2017-06-06 and 0.3.1 dated 2019-07-09
electionsBR-0.3.0/electionsBR/R/legislative_vote.R |only electionsBR-0.3.0/electionsBR/R/presidential_vote.R |only electionsBR-0.3.0/electionsBR/man/legislative_mun_vote.Rd |only electionsBR-0.3.0/electionsBR/man/legislative_state_vote.Rd |only electionsBR-0.3.0/electionsBR/man/president_mun_vote.Rd |only electionsBR-0.3.0/electionsBR/man/president_state_vote.Rd |only electionsBR-0.3.1/electionsBR/DESCRIPTION | 14 electionsBR-0.3.1/electionsBR/MD5 | 82 - electionsBR-0.3.1/electionsBR/NAMESPACE | 10 electionsBR-0.3.1/electionsBR/NEWS.md | 12 electionsBR-0.3.1/electionsBR/R/candidate_fed.R | 72 + electionsBR-0.3.1/electionsBR/R/candidate_local.R | 40 electionsBR-0.3.1/electionsBR/R/details_mun_zone_fed.R | 41 electionsBR-0.3.1/electionsBR/R/details_mun_zone_local.R | 27 electionsBR-0.3.1/electionsBR/R/electionsbr_rda.R |only electionsBR-0.3.1/electionsBR/R/legend_fed.R | 32 electionsBR-0.3.1/electionsBR/R/legend_local.R | 57 - electionsBR-0.3.1/electionsBR/R/party_mun_zone_fed.R | 32 electionsBR-0.3.1/electionsBR/R/party_mun_zone_local.R | 17 electionsBR-0.3.1/electionsBR/R/personal_finances_fed.R |only electionsBR-0.3.1/electionsBR/R/personal_finances_local.R |only electionsBR-0.3.1/electionsBR/R/seats_fed.R | 23 electionsBR-0.3.1/electionsBR/R/seats_local.R | 13 electionsBR-0.3.1/electionsBR/R/utils.R | 83 + electionsBR-0.3.1/electionsBR/R/vote_mun_zone_fed.R | 50 - electionsBR-0.3.1/electionsBR/R/vote_mun_zone_local.R | 27 electionsBR-0.3.1/electionsBR/R/vote_section_fed.R |only electionsBR-0.3.1/electionsBR/R/vote_section_local.R |only electionsBR-0.3.1/electionsBR/R/voter_profile.R | 38 electionsBR-0.3.1/electionsBR/build/vignette.rds |binary electionsBR-0.3.1/electionsBR/inst/doc/introduction.R | 6 electionsBR-0.3.1/electionsBR/inst/doc/introduction.Rmd | 36 electionsBR-0.3.1/electionsBR/inst/doc/introduction.html | 480 ++++++++--- electionsBR-0.3.1/electionsBR/man/candidate_fed.Rd | 43 electionsBR-0.3.1/electionsBR/man/candidate_local.Rd | 6 electionsBR-0.3.1/electionsBR/man/details_mun_zone_fed.Rd | 24 electionsBR-0.3.1/electionsBR/man/details_mun_zone_local.Rd | 2 electionsBR-0.3.1/electionsBR/man/elections_rda.Rd |only electionsBR-0.3.1/electionsBR/man/legend_fed.Rd | 11 electionsBR-0.3.1/electionsBR/man/legend_local.Rd | 7 electionsBR-0.3.1/electionsBR/man/party_mun_zone_fed.Rd | 22 electionsBR-0.3.1/electionsBR/man/party_mun_zone_local.Rd | 2 electionsBR-0.3.1/electionsBR/man/personal_finances_fed.Rd |only electionsBR-0.3.1/electionsBR/man/personal_finances_local.Rd |only electionsBR-0.3.1/electionsBR/man/seats_fed.Rd | 8 electionsBR-0.3.1/electionsBR/man/seats_local.Rd | 2 electionsBR-0.3.1/electionsBR/man/vote_mun_zone_fed.Rd | 22 electionsBR-0.3.1/electionsBR/man/vote_mun_zone_local.Rd | 4 electionsBR-0.3.1/electionsBR/man/vote_section_fed.Rd |only electionsBR-0.3.1/electionsBR/man/vote_section_local.Rd |only 50 files changed, 943 insertions(+), 402 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre],
Thomas Lumley [ctb],
Tomasz Żółtak [ctb],
Ben Schneider [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.3.4 dated 2019-01-20 and 0.3.5 dated 2019-07-09
DESCRIPTION | 22 MD5 | 55 +- NAMESPACE | 4 NEWS.md | 16 R/as_survey_rep.r | 2 R/summarise.r | 16 R/survey_statistics.r | 214 +++++++- R/survey_statistics_helpers.R | 11 R/tbl-svy.r | 6 R/utils.r | 4 README.md | 95 ++- build/vignette.rds |binary inst/doc/extending-srvyr.html | 516 ++++++++++++++------ inst/doc/srvyr-database.R | 11 inst/doc/srvyr-database.Rmd | 23 inst/doc/srvyr-database.html | 646 +++++++++++++++++--------- inst/doc/srvyr-vs-survey.html | 532 +++++++++++++++------ man/survey_quantile.Rd | 11 man/survey_total.Rd | 5 man/survey_var.Rd |only tests/testthat/test_as_survey_design.r | 2 tests/testthat/test_as_survey_twophase.r | 30 - tests/testthat/test_database.R | 30 - tests/testthat/test_survey_mean_factor.r | 2 tests/testthat/test_survey_package.r | 2 tests/testthat/test_survey_proportion.R | 2 tests/testthat/test_survey_statistics.r | 533 +++++++++++++++++---- tests/testthat/test_survey_statistics_basic.r | 113 +++- vignettes/srvyr-database.Rmd | 23 29 files changed, 2135 insertions(+), 791 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need to
derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Modrak Martin [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cph] (R/cxxfunplus.R),
The R Core Team [cph] (R/pairs.R, R/dynGet.R),
Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.18.2 dated 2018-11-07 and 2.19.2 dated 2019-07-09
rstan-2.18.2/rstan/src/lang__ast_def.cpp |only rstan-2.18.2/rstan/src/lang__grammars__bare_type_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__expression07_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__expression_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__functions_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__indexes_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__program_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__semantic_actions.cpp |only rstan-2.18.2/rstan/src/lang__grammars__statement_2_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__statement_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__term_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__var_deccls_grammar_inst.cpp |only rstan-2.18.2/rstan/src/lang__grammars__whitespace_grammar_inst.cpp |only rstan-2.19.2/rstan/DESCRIPTION | 17 rstan-2.19.2/rstan/MD5 | 150 - rstan-2.19.2/rstan/NAMESPACE | 13 rstan-2.19.2/rstan/R/SBC.R |only rstan-2.19.2/rstan/R/chains.R | 16 rstan-2.19.2/rstan/R/check_hmc_diagnostics.R | 82 rstan-2.19.2/rstan/R/cxxfunplus.R | 10 rstan-2.19.2/rstan/R/doctor_cppcode.R |only rstan-2.19.2/rstan/R/exposeStanClass.R |only rstan-2.19.2/rstan/R/expose_stan_functions.R | 4 rstan-2.19.2/rstan/R/get_rng.R | 2 rstan-2.19.2/rstan/R/gqs_light.R |only rstan-2.19.2/rstan/R/makefile_op.R | 3 rstan-2.19.2/rstan/R/misc.R | 130 rstan-2.19.2/rstan/R/monitor.R | 726 ++++- rstan-2.19.2/rstan/R/pairs.R | 36 rstan-2.19.2/rstan/R/rstan.R | 6 rstan-2.19.2/rstan/R/stan_csv.R | 12 rstan-2.19.2/rstan/R/stan_plot.R | 157 - rstan-2.19.2/rstan/R/stan_plot_helpers.R | 153 - rstan-2.19.2/rstan/R/stan_plot_options.R | 128 rstan-2.19.2/rstan/R/stanfit-class.R | 77 rstan-2.19.2/rstan/R/stanmodel-class.R | 210 + rstan-2.19.2/rstan/R/sysdata.rda |binary rstan-2.19.2/rstan/R/zzz.R | 1 rstan-2.19.2/rstan/build/vignette.rds |binary rstan-2.19.2/rstan/inst/NEWS | 9 rstan-2.19.2/rstan/inst/doc/SBC.R |only rstan-2.19.2/rstan/inst/doc/SBC.Rmd |only rstan-2.19.2/rstan/inst/doc/SBC.html |only rstan-2.19.2/rstan/inst/doc/external.html | 26 rstan-2.19.2/rstan/inst/doc/fib.hpp |only rstan-2.19.2/rstan/inst/doc/rstan.bib |only rstan-2.19.2/rstan/inst/doc/rstan.html | 186 - rstan-2.19.2/rstan/inst/doc/schools.stan |only rstan-2.19.2/rstan/inst/doc/sinc.hpp |only rstan-2.19.2/rstan/inst/doc/stanfit-objects.html | 167 - rstan-2.19.2/rstan/inst/include/rstan/boost_random_R.hpp |only rstan-2.19.2/rstan/inst/include/rstan/stan_fit.hpp | 34 rstan-2.19.2/rstan/man/Rhat.Rd |only rstan-2.19.2/rstan/man/monitor.Rd | 18 rstan-2.19.2/rstan/man/read_rdump.Rd | 7 rstan-2.19.2/rstan/man/rstan.Rd | 4 rstan-2.19.2/rstan/man/sbc.Rd |only rstan-2.19.2/rstan/man/stan_model.Rd | 2 rstan-2.19.2/rstan/man/stan_plot.Rd | 8 rstan-2.19.2/rstan/man/stan_plot_options.Rd | 2 rstan-2.19.2/rstan/man/stan_rdump.Rd | 11 rstan-2.19.2/rstan/man/stanfit-method-pairs.Rd | 2 rstan-2.19.2/rstan/man/stanmodel-method-gqs.Rd |only rstan-2.19.2/rstan/man/stanmodel-method-optimizing.Rd | 6 rstan-2.19.2/rstan/man/stanmodel-method-vb.Rd | 10 rstan-2.19.2/rstan/src/Makevars | 11 rstan-2.19.2/rstan/src/Makevars.win | 9 rstan-2.19.2/rstan/src/chains.cpp | 2 rstan-2.19.2/rstan/src/stan |only rstan-2.19.2/rstan/tools/stan-functions.txt | 1435 +++++----- rstan-2.19.2/rstan/vignettes/.install_extras |only rstan-2.19.2/rstan/vignettes/SBC.Rmd |only 72 files changed, 2430 insertions(+), 1452 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation and overimputation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.5.0 dated 2018-11-21 and 1.6.0 dated 2019-07-09
micemd-1.5.0/micemd/R/micemd-internal.R |only micemd-1.6.0/micemd/DESCRIPTION | 10 ++-- micemd-1.6.0/micemd/MD5 | 21 ++++----- micemd-1.6.0/micemd/R/mice.impute.2l.2stage.norm.intern.R | 10 +++- micemd-1.6.0/micemd/R/overimpute.R | 25 +++++------ micemd-1.6.0/micemd/data/CHEM97Na.rda |binary micemd-1.6.0/micemd/data/IPDNa.rda |binary micemd-1.6.0/micemd/man/find.defaultMethod.Rd | 10 ++-- micemd-1.6.0/micemd/man/mice.par.Rd | 30 ++++++++------ micemd-1.6.0/micemd/man/micemd-package.Rd | 8 +-- micemd-1.6.0/micemd/man/overimpute.Rd | 12 ++--- micemd-1.6.0/micemd/man/plot.mira.Rd | 9 ++-- 12 files changed, 72 insertions(+), 63 deletions(-)
Title: Simple Interface to 'Microsoft Graph'
Description: A simple interface to the 'Microsoft Graph' API <https://docs.microsoft.com/en-us/graph/overview>. 'Graph' is a comprehensive framework for accessing data in various online Microsoft services. Currently, this package aims to provide an R interface only to the 'Azure Active Directory' part, with a view to supporting interoperability of R and 'Azure': users, groups, registered apps and service principals. However it can be easily extended to cover other services. Part of the 'AzureR' family of packages.
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureGraph versions 1.0.2 dated 2019-06-05 and 1.0.3 dated 2019-07-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/call_graph.R | 31 ++++++++++++++++++++----------- R/graph_login.R | 12 ++++++------ R/ms_graph.R | 2 +- man/call_graph.Rd | 11 ++++++++--- 7 files changed, 48 insertions(+), 30 deletions(-)
Title: An Implementation of the TSIR Model
Description: An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <https://doi:10.1371/0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <DOI: 10.1111/1467-9876.00187>.
Author: Alexander D. Becker [aut, cre],
Sinead E. Morris [ctb],
Ottar N. Bjornstad [ctb]
Maintainer: Alexander D. Becker <adbecker@princeton.edu>
Diff between tsiR versions 0.4.1 dated 2019-01-29 and 0.4.2 dated 2019-07-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/estpars_function.R | 6 ++++-- R/mcmcestpars_function.R | 2 +- R/mcmctsir_function.R | 13 ++++++++----- R/runtsir_function.R | 17 ++++++++++++++--- README.md | 3 +++ 7 files changed, 40 insertions(+), 21 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight, simpler and less tested than both),
tools for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.8 dated 2019-03-18 and 0.2.9 dated 2019-07-09
reproducible-0.2.8/reproducible/R/RcppExports.R |only reproducible-0.2.8/reproducible/man/cloudCache.Rd |only reproducible-0.2.8/reproducible/man/cloudCheck.Rd |only reproducible-0.2.8/reproducible/man/cloudSyncCache.Rd |only reproducible-0.2.8/reproducible/man/cloudWrite.Rd |only reproducible-0.2.8/reproducible/man/readLinesRcpp.Rd |only reproducible-0.2.8/reproducible/man/readLinesRcppInternal.Rd |only reproducible-0.2.8/reproducible/src |only reproducible-0.2.9/reproducible/DESCRIPTION | 33 reproducible-0.2.9/reproducible/MD5 | 99 reproducible-0.2.9/reproducible/NAMESPACE | 24 reproducible-0.2.9/reproducible/NEWS.md | 9 reproducible-0.2.9/reproducible/R/cache-helpers.R | 153 reproducible-0.2.9/reproducible/R/cache-internals.R | 5 reproducible-0.2.9/reproducible/R/cache-tools.R | 51 reproducible-0.2.9/reproducible/R/cache.R | 503 +- reproducible-0.2.9/reproducible/R/cloud.R | 811 ---- reproducible-0.2.9/reproducible/R/cloudOld.R |only reproducible-0.2.9/reproducible/R/convertPaths.R | 80 reproducible-0.2.9/reproducible/R/download.R | 33 reproducible-0.2.9/reproducible/R/gis.R | 48 reproducible-0.2.9/reproducible/R/helpers.R | 50 reproducible-0.2.9/reproducible/R/options.R | 6 reproducible-0.2.9/reproducible/R/packages.R | 10 reproducible-0.2.9/reproducible/R/postProcess.R | 41 reproducible-0.2.9/reproducible/R/preProcess.R | 16 reproducible-0.2.9/reproducible/R/reproducible-package.R | 2 reproducible-0.2.9/reproducible/R/robustDigest.R | 31 reproducible-0.2.9/reproducible/R/zzz.R | 3 reproducible-0.2.9/reproducible/build/vignette.rds |binary reproducible-0.2.9/reproducible/inst/doc/Intro-to-Cache.html | 1898 +++++----- reproducible-0.2.9/reproducible/man/CacheDigest.Rd | 4 reproducible-0.2.9/reproducible/man/Deprcated.Rd |only reproducible-0.2.9/reproducible/man/Filenames.Rd |only reproducible-0.2.9/reproducible/man/Path-class.Rd | 3 reproducible-0.2.9/reproducible/man/Require.Rd | 2 reproducible-0.2.9/reproducible/man/cache-helpers.Rd | 2 reproducible-0.2.9/reproducible/man/cache.Rd | 25 reproducible-0.2.9/reproducible/man/checkAndMakeCloudFolderID.Rd |only reproducible-0.2.9/reproducible/man/cloudCheckOld.Rd |only reproducible-0.2.9/reproducible/man/cloudDownload.Rd |only reproducible-0.2.9/reproducible/man/cloudExtras.Rd | 20 reproducible-0.2.9/reproducible/man/cloudSyncCacheOld.Rd |only reproducible-0.2.9/reproducible/man/cloudUpload.Rd |only reproducible-0.2.9/reproducible/man/cloudUploadFromCache.Rd |only reproducible-0.2.9/reproducible/man/cloudWriteOld.Rd |only reproducible-0.2.9/reproducible/man/dot-removeCacheAtts.Rd |only reproducible-0.2.9/reproducible/man/fastMask.Rd | 11 reproducible-0.2.9/reproducible/man/installedVersions.Rd | 3 reproducible-0.2.9/reproducible/man/projectInputs.Rd | 11 reproducible-0.2.9/reproducible/man/reproducibleOptions.Rd | 5 reproducible-0.2.9/reproducible/man/retry.Rd |only reproducible-0.2.9/reproducible/man/robustDigest.Rd | 4 reproducible-0.2.9/reproducible/man/viewCache.Rd | 48 reproducible-0.2.9/reproducible/tests/testthat/helper-allEqual.R | 128 reproducible-0.2.9/reproducible/tests/testthat/test-cache.R | 10 reproducible-0.2.9/reproducible/tests/testthat/test-cacheHelpers.R | 76 reproducible-0.2.9/reproducible/tests/testthat/test-cloud.R | 368 + reproducible-0.2.9/reproducible/tests/testthat/test-prepInputs.R | 28 reproducible-0.2.9/reproducible/tests/testthat/test-prepInputsInNestedArchives.R | 28 60 files changed, 2378 insertions(+), 2304 deletions(-)
Title: Searching for Footprints of Selection using 'Extended Haplotype
Homozygosity' Based Tests
Description: Population genetic data such as 'Single Nucleotide
Polymorphisms' (SNPs) is often used to identify genomic regions
that have been under recent natural or artificial selection
and might provide clues about the molecular mechanisms of adaptation.
One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH),
introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to
several statistics designed for whole genome scans.
The package provides functions to compute three of these,
namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for
detecting positive or 'Darwinian' selection within a single population as well as
'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and
'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted
at differential selection between two populations.
Various plotting functions are also included to facilitate
visualization and interpretation of these statistics.
Due to changes in the API, albeit mostly minor,
this version is not compatible with versions 2.0.X.
Author: Mathieu Gautier, Alexander Klassmann and Renaud Vitalis
Maintainer: Alexander Klassmann <rehh@oneoverx.eu>
Diff between rehh versions 2.0.4 dated 2019-02-13 and 3.0.0 dated 2019-07-09
rehh-2.0.4/rehh/ChangeLog |only rehh-2.0.4/rehh/R/bifurcation.diagram.R |only rehh-2.0.4/rehh/R/ies2rsb.R |only rehh-2.0.4/rehh/R/ihsplot.R |only rehh-2.0.4/rehh/R/rsbplot.R |only rehh-2.0.4/rehh/R/xpehhplot.R |only rehh-2.0.4/rehh/man/bifurcation.diagram.Rd |only rehh-2.0.4/rehh/man/ies2rsb.Rd |only rehh-2.0.4/rehh/man/ihsplot.Rd |only rehh-2.0.4/rehh/man/rsbplot.Rd |only rehh-2.0.4/rehh/man/xpehhplot.Rd |only rehh-2.0.4/rehh/src/hh_utils.c |only rehh-2.0.4/rehh/src/hh_utils.h |only rehh-2.0.4/rehh/src/rehh_init.c |only rehh-3.0.0/rehh/DESCRIPTION | 45 rehh-3.0.0/rehh/MD5 | 155 +- rehh-3.0.0/rehh/NAMESPACE | 71 - rehh-3.0.0/rehh/NEWS.md |only rehh-3.0.0/rehh/R/as.newick.R |only rehh-3.0.0/rehh/R/calc_candidate_regions.R |only rehh-3.0.0/rehh/R/calc_ehh.R | 354 +++-- rehh-3.0.0/rehh/R/calc_ehhs.R | 284 ++-- rehh-3.0.0/rehh/R/calc_furcation.R |only rehh-3.0.0/rehh/R/calc_haplen.R |only rehh-3.0.0/rehh/R/calc_region_stats.R |only rehh-3.0.0/rehh/R/data2haplohh.R | 1118 ++++++++++++---- rehh-3.0.0/rehh/R/distribplot.R | 76 - rehh-3.0.0/rehh/R/extract_regions.R |only rehh-3.0.0/rehh/R/freqbinplot.R |only rehh-3.0.0/rehh/R/furcation-class.R |only rehh-3.0.0/rehh/R/haplohh-class.R |only rehh-3.0.0/rehh/R/ies2xpehh.R | 236 ++- rehh-3.0.0/rehh/R/ihh2ihs.R | 380 ++++- rehh-3.0.0/rehh/R/ines2rsb.R |only rehh-3.0.0/rehh/R/make.example.files.R |only rehh-3.0.0/rehh/R/manhattanplot.R |only rehh-3.0.0/rehh/R/plot.ehh.R |only rehh-3.0.0/rehh/R/plot.ehhs.R |only rehh-3.0.0/rehh/R/plot.furcation.R |only rehh-3.0.0/rehh/R/plot.haplen.R |only rehh-3.0.0/rehh/R/rehh.R |only rehh-3.0.0/rehh/R/scan_hh.R | 230 ++- rehh-3.0.0/rehh/R/subset.haplohh.R |only rehh-3.0.0/rehh/R/update_haplohh.R |only rehh-3.0.0/rehh/build/vignette.rds |binary rehh-3.0.0/rehh/data/haplohh_cgu_bta12.RData |binary rehh-3.0.0/rehh/inst/CITATION | 7 rehh-3.0.0/rehh/inst/doc/examples.R |only rehh-3.0.0/rehh/inst/doc/examples.Rmd |only rehh-3.0.0/rehh/inst/doc/examples.html |only rehh-3.0.0/rehh/inst/doc/rehh.R | 462 ++++-- rehh-3.0.0/rehh/inst/doc/rehh.Rmd | 1139 +++++++++++----- rehh-3.0.0/rehh/inst/doc/rehh.html | 1812 ++++++++++++++++++-------- rehh-3.0.0/rehh/inst/extdata |only rehh-3.0.0/rehh/man/allelefurcation-class.Rd |only rehh-3.0.0/rehh/man/as.newick.Rd |only rehh-3.0.0/rehh/man/calc_candidate_regions.Rd |only rehh-3.0.0/rehh/man/calc_ehh.Rd | 126 + rehh-3.0.0/rehh/man/calc_ehhs.Rd | 119 + rehh-3.0.0/rehh/man/calc_furcation.Rd |only rehh-3.0.0/rehh/man/calc_haplen.Rd |only rehh-3.0.0/rehh/man/calc_region_stats.Rd |only rehh-3.0.0/rehh/man/data2haplohh.Rd | 177 ++ rehh-3.0.0/rehh/man/distribplot.Rd | 61 rehh-3.0.0/rehh/man/extract_regions.Rd |only rehh-3.0.0/rehh/man/freqbinplot.Rd |only rehh-3.0.0/rehh/man/ftree-class.Rd |only rehh-3.0.0/rehh/man/furcation-class.Rd |only rehh-3.0.0/rehh/man/haplen-class.Rd |only rehh-3.0.0/rehh/man/haplohh-class.Rd | 80 - rehh-3.0.0/rehh/man/haplohh_cgu_bta12.Rd | 25 rehh-3.0.0/rehh/man/ies2xpehh.Rd | 71 - rehh-3.0.0/rehh/man/ihh2ihs.Rd | 93 + rehh-3.0.0/rehh/man/ines2rsb.Rd |only rehh-3.0.0/rehh/man/make.example.files.Rd | 45 rehh-3.0.0/rehh/man/manhattanplot.Rd |only rehh-3.0.0/rehh/man/plot.ehh.Rd |only rehh-3.0.0/rehh/man/plot.ehhs.Rd |only rehh-3.0.0/rehh/man/plot.furcation.Rd |only rehh-3.0.0/rehh/man/plot.haplen.Rd |only rehh-3.0.0/rehh/man/rehh-package.Rd | 95 - rehh-3.0.0/rehh/man/remove.example.files.Rd |only rehh-3.0.0/rehh/man/scan_hh.Rd | 118 + rehh-3.0.0/rehh/man/subset.haplohh.Rd |only rehh-3.0.0/rehh/man/update_haplohh.Rd |only rehh-3.0.0/rehh/src/CALL_ASNEWICK.c |only rehh-3.0.0/rehh/src/CALL_EHH.c | 101 - rehh-3.0.0/rehh/src/CALL_EHHS.c | 103 - rehh-3.0.0/rehh/src/CALL_FURCATION.c |only rehh-3.0.0/rehh/src/CALL_INTEGRAL.c |only rehh-3.0.0/rehh/src/CALL_SCAN_HH.c | 237 ++- rehh-3.0.0/rehh/src/asnewick.c |only rehh-3.0.0/rehh/src/asnewick.h |only rehh-3.0.0/rehh/src/calc_ehh.c |only rehh-3.0.0/rehh/src/calc_ehh.h |only rehh-3.0.0/rehh/src/calc_ehhs.c |only rehh-3.0.0/rehh/src/calc_ehhs.h |only rehh-3.0.0/rehh/src/calc_furcation.c |only rehh-3.0.0/rehh/src/calc_furcation.h |only rehh-3.0.0/rehh/src/haplotypes.c |only rehh-3.0.0/rehh/src/haplotypes.h |only rehh-3.0.0/rehh/src/homozygosity.c |only rehh-3.0.0/rehh/src/homozygosity.h |only rehh-3.0.0/rehh/src/init.c |only rehh-3.0.0/rehh/src/integrate.c |only rehh-3.0.0/rehh/src/integrate.h |only rehh-3.0.0/rehh/tests |only rehh-3.0.0/rehh/vignettes/examples.Rmd |only rehh-3.0.0/rehh/vignettes/rehh.Rmd | 1139 +++++++++++----- rehh-3.0.0/rehh/vignettes/vignette.bib | 111 + 110 files changed, 6537 insertions(+), 2533 deletions(-)
Title: A Simple S3 Class for Representing Vectors of Binary Data
('BLOBS')
Description: R's raw vector is useful for storing a single
binary object. What if you want to put a vector of them in a data
frame? The 'blob' package provides the blob object, a list of raw
vectors, suitable for use as a column in data frame.
Author: Hadley Wickham [aut],
Kirill Müller [cre],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between blob versions 1.1.1 dated 2018-03-25 and 1.2.0 dated 2019-07-09
blob-1.1.1/blob/R/accessors.R |only blob-1.1.1/blob/R/missing.R |only blob-1.2.0/blob/DESCRIPTION | 35 +++++---- blob-1.2.0/blob/MD5 | 37 ++++++---- blob-1.2.0/blob/NAMESPACE | 38 +++++++--- blob-1.2.0/blob/NEWS.md | 13 +++ blob-1.2.0/blob/R/blob.R | 74 +++++++++++++-------- blob-1.2.0/blob/R/cast.R |only blob-1.2.0/blob/R/coerce.R |only blob-1.2.0/blob/R/compat-lifecycle.R |only blob-1.2.0/blob/R/format.R | 24 +++--- blob-1.2.0/blob/R/util.R | 4 - blob-1.2.0/blob/R/zzz.R | 30 -------- blob-1.2.0/blob/README.md | 58 ++++++++++++---- blob-1.2.0/blob/man/as.blob.Rd |only blob-1.2.0/blob/man/blob.Rd | 23 ++++-- blob-1.2.0/blob/man/vec_cast.blob.Rd |only blob-1.2.0/blob/man/vec_ptype2.blob.Rd |only blob-1.2.0/blob/tests/testthat/blob.txt |only blob-1.2.0/blob/tests/testthat/helper-deprecate.R |only blob-1.2.0/blob/tests/testthat/test-accessors.R | 49 ++++++++++++- blob-1.2.0/blob/tests/testthat/test-cast.R |only blob-1.2.0/blob/tests/testthat/test-construction.R | 7 + blob-1.2.0/blob/tests/testthat/test-format.R | 17 ++++ blob-1.2.0/blob/tests/testthat/test-missing.R | 12 +++ 25 files changed, 282 insertions(+), 139 deletions(-)
Title: Connectivity to 'Alfresco' Content Management Repositories
Description: Allows you to connect to an 'Alfresco' content management repository and interact
with its contents using simple and intuitive functions. You will be able to establish a connection session to the 'Alfresco' repository,
read and upload content and manage folder hierarchies. For more details on the 'Alfresco' content management repository
see <https://www.alfresco.com/ecm-software/document-management>.
Author: Roy Wetherall <rwetherall@gmail.com>
Maintainer: Roy Wetherall <rwetherall@gmail.com>
Diff between alfr versions 1.1.0 dated 2019-07-03 and 1.2.0 dated 2019-07-09
alfr-1.1.0/alfr/man/alf_GET.Rd |only alfr-1.1.0/alfr/man/alf_POST.Rd |only alfr-1.1.0/alfr/man/alf_PUT.Rd |only alfr-1.1.0/alfr/tests/api/alfresco/versions/1/nodes/-root--deeab7.json |only alfr-1.1.0/alfr/tests/api/alfresco/versions/1/nodes/b569f89f-e5a0-4ef4-8c4e-d1314bac67a4 |only alfr-1.2.0/alfr/DESCRIPTION | 14 alfr-1.2.0/alfr/MD5 | 73 ++- alfr-1.2.0/alfr/NAMESPACE | 7 alfr-1.2.0/alfr/NEWS.md | 12 alfr-1.2.0/alfr/R/alf_http.R | 54 -- alfr-1.2.0/alfr/R/alf_node.R | 53 +- alfr-1.2.0/alfr/R/alf_session.R | 73 ++- alfr-1.2.0/alfr/R/alfr.R | 15 alfr-1.2.0/alfr/R/examples |only alfr-1.2.0/alfr/R/sysdata.rda |only alfr-1.2.0/alfr/README.md | 60 ++ alfr-1.2.0/alfr/inst/WORDLIST |only alfr-1.2.0/alfr/inst/doc/working_with_content.Rmd | 8 alfr-1.2.0/alfr/inst/doc/working_with_content.html | 5 alfr-1.2.0/alfr/inst/extdata |only alfr-1.2.0/alfr/man/alf_node.Rd | 72 ++- alfr-1.2.0/alfr/man/alf_node.delete.Rd |only alfr-1.2.0/alfr/man/alf_node.new.Rd | 49 ++ alfr-1.2.0/alfr/man/alf_session.Rd | 24 - alfr-1.2.0/alfr/man/alf_session.invalidate.Rd |only alfr-1.2.0/alfr/man/alf_session.is_valid.Rd |only alfr-1.2.0/alfr/man/alfr.Rd | 14 alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/-root- |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/-root--452a0c.json |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/-root--6e8449.json |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/-root--a3259c.json |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/16d0f110-998e-4f95-b314-8a5c2d62e8a4 |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/802b2861-9e42-402a-b896-ccf5d3295f77-c4a2ae-DELETE.204 |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/802b2861-9e42-402a-b896-ccf5d3295f77.json |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/d5544997-acd2-4af5-87ba-13d7e0ffdb7a |only alfr-1.2.0/alfr/tests/api/alfresco/versions/1/nodes/d5544997-acd2-4af5-87ba-13d7e0ffdb7a-c4a2ae-DELETE.204 |only alfr-1.2.0/alfr/tests/api/authentication/versions/1/tickets |only alfr-1.2.0/alfr/tests/api/authentication/versions/1/tickets-7b9af9-POST.R | 8 alfr-1.2.0/alfr/tests/api/authentication/versions/1/tickets-acaa1c-POST.R | 12 alfr-1.2.0/alfr/tests/capture_util.R |only alfr-1.2.0/alfr/tests/spelling.R |only alfr-1.2.0/alfr/tests/testthat/helper.R | 3 alfr-1.2.0/alfr/tests/testthat/testalf_node.R | 215 +++++++--- alfr-1.2.0/alfr/tests/testthat/testalf_session.R | 50 ++ alfr-1.2.0/alfr/vignettes/working_with_content.Rmd | 8 45 files changed, 600 insertions(+), 229 deletions(-)
Title: Wilcoxon-Mann-Whitney Sample Size Planning
Description: Calculates the minimal sample size for the Wilcoxon-Mann-Whitney test
that is needed for a given power and two sided type I error rate. The method works for metric data with and without
ties, count data, ordered categorical data, and even dichotomous data.
But data is needed for the reference group to generate synthetic data for the treatment group based on a relevant effect.
For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Arne C. Bathke [aut],
Edgar Brunner [aut],
Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Frank Konietschke [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between WMWssp versions 0.3.7 dated 2019-03-11 and 0.4.0 dated 2019-07-09
DESCRIPTION | 8 +- MD5 | 11 +-- NEWS.md |only R/samplesize.R | 136 +++++++++++++++++++++++-------------------- README.md | 20 +++--- man/WMWssp.Rd | 2 tests/testthat/test_MinMax.R | 1 7 files changed, 98 insertions(+), 80 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the
location of the species is needed and about the environmental conditions. To test
for significance habitat associations, one of the two components is randomized.
Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between shar versions 0.4 dated 2019-05-27 and 0.5 dated 2019-07-09
DESCRIPTION | 9 - MD5 | 16 - NEWS.md | 4 R/reconstruct_marks.R | 19 ++ R/reconstruct_pattern.R | 19 ++ inst/doc/get_started.html | 4 man/reconstruct_marks.Rd | 6 man/reconstruct_pattern.Rd | 4 tests/testthat/test-reconstruct_marks.R | 285 +++++++++++++++----------------- 9 files changed, 197 insertions(+), 169 deletions(-)
Title: Semi-Confirmatory Structural Equation Modeling via Penalized
Likelihood or Least Squares
Description: Fits semi-confirmatory structural equation modeling (SEM) via penalized likelihood (PL) or penalized least squares (PLS).
Author: Po-Hsien Huang [cre, aut],
Wen-Hsin Hu [aut]
Maintainer: Po-Hsien Huang <psyphh@gmail.com>
Diff between lslx versions 0.6.6 dated 2019-05-02 and 0.6.7 dated 2019-07-09
lslx-0.6.6/lslx/R/lslxData.R |only lslx-0.6.6/lslx/R/lslxFitting.R |only lslx-0.6.6/lslx/R/lslxModel.R |only lslx-0.6.6/lslx/src/utilities.cpp |only lslx-0.6.7/lslx/DESCRIPTION | 21 lslx-0.6.7/lslx/MD5 | 55 lslx-0.6.7/lslx/R/RcppExports.R | 28 lslx-0.6.7/lslx/R/lslx-class.R | 107 - lslx-0.6.7/lslx/R/lslx-fit-method.R | 36 lslx-0.6.7/lslx/R/lslx-set-block-method.R | 11 lslx-0.6.7/lslx/R/lslx-set-coefficient-method.R | 105 - lslx-0.6.7/lslx/R/lslx-set-data-method.R | 14 lslx-0.6.7/lslx/R/lslx-set-heterogeneity-method.R | 23 lslx-0.6.7/lslx/R/lslx-summarize-method.R | 31 lslx-0.6.7/lslx/R/lslxData-class.R |only lslx-0.6.7/lslx/R/lslxData-initialize-method.R |only lslx-0.6.7/lslx/R/lslxFitting-class.R |only lslx-0.6.7/lslx/R/lslxFitting-initialize-method.R |only lslx-0.6.7/lslx/R/lslxModel-class.R |only lslx-0.6.7/lslx/R/lslxModel-initialize-method.R |only lslx-0.6.7/lslx/R/prelslx-initialize-method.R | 30 lslx-0.6.7/lslx/R/prelslx-prefit-method.R |only lslx-0.6.7/lslx/inst/doc/factor-analysis.html | 4 lslx-0.6.7/lslx/inst/doc/missing-data-analysis.html | 2 lslx-0.6.7/lslx/inst/doc/multi-group-analysis.html | 10 lslx-0.6.7/lslx/inst/doc/regression-analysis.html | 2 lslx-0.6.7/lslx/inst/doc/structural-equation-modeling.html | 2 lslx-0.6.7/lslx/inst/doc/vignette-lslx.pdf |binary lslx-0.6.7/lslx/man/lslx.Rd | 98 - lslx-0.6.7/lslx/src/RcppExports.cpp | 111 - lslx-0.6.7/lslx/src/compute-moment.cpp |only lslx-0.6.7/lslx/src/compute-path.cpp |only lslx-0.6.7/lslx/src/extract-quantity.cpp |only lslx-0.6.7/lslx/src/lslxOptimizer.cpp | 1209 +++++-------- lslx-0.6.7/lslx/src/lslxOptimizer.h |only lslx-0.6.7/lslx/src/utility-function.cpp |only lslx-0.6.7/lslx/src/utility-function.h |only 37 files changed, 938 insertions(+), 961 deletions(-)
Title: Working with Files from 'LexisNexis'
Description: My PhD supervisor once told me that everyone doing newspaper
analysis starts by writing code to read in files from the 'LexisNexis' newspaper
archive (retrieved e.g., from <http://www.nexis.com/> or any of the partner
sites). However, while this is a nice exercise I do recommend, not everyone has
the time. This package takes TXT files downloaded from the newspaper archive of
'LexisNexis', reads them into R and offers functions for further processing.
Author: Johannes Gruber [aut, cre]
Maintainer: Johannes Gruber <j.gruber.1@research.gla.ac.uk>
Diff between LexisNexisTools versions 0.2.2 dated 2019-01-27 and 0.2.3 dated 2019-07-09
LexisNexisTools-0.2.2/LexisNexisTools/man/lnt_checkFiles.Rd |only LexisNexisTools-0.2.3/LexisNexisTools/DESCRIPTION | 20 LexisNexisTools-0.2.3/LexisNexisTools/MD5 | 82 LexisNexisTools-0.2.3/LexisNexisTools/NAMESPACE | 12 LexisNexisTools-0.2.3/LexisNexisTools/NEWS.md | 8 LexisNexisTools-0.2.3/LexisNexisTools/R/LexisNexisTools.R | 1664 ++++++---- LexisNexisTools-0.2.3/LexisNexisTools/README.md | 486 +- LexisNexisTools-0.2.3/LexisNexisTools/build/vignette.rds |binary LexisNexisTools-0.2.3/LexisNexisTools/inst/CITATION | 2 LexisNexisTools-0.2.3/LexisNexisTools/inst/WORDLIST | 11 LexisNexisTools-0.2.3/LexisNexisTools/inst/doc/demo.R | 99 LexisNexisTools-0.2.3/LexisNexisTools/inst/doc/demo.Rmd | 124 LexisNexisTools-0.2.3/LexisNexisTools/inst/doc/demo.html | 639 ++- LexisNexisTools-0.2.3/LexisNexisTools/man/LNToutput_methods.Rd | 3 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt2bibtex.Rd |only LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_add.Rd | 4 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_asDate.Rd | 2 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_convert.Rd | 2 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_diff.Rd | 9 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_lookup.Rd | 22 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_read.Rd | 22 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_rename.Rd | 37 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_sample.Rd | 13 LexisNexisTools-0.2.3/LexisNexisTools/man/lnt_similarity.Rd | 14 LexisNexisTools-0.2.3/LexisNexisTools/tests/files/LNToutput.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/LNToutput2.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/bibtex.RDS |only LexisNexisTools-0.2.3/LexisNexisTools/tests/files/corpustools.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/quanteda.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/quanteda_1.5.RDS |only LexisNexisTools-0.2.3/LexisNexisTools/tests/files/rDNA.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/tidytext.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/files/tm.RDS |binary LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat.R | 4 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_asDate.R | 1 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_convert.R | 63 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_diff.R | 3 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_lookup.R | 32 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_read.R | 31 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_rename.R | 31 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_sample.R | 13 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-lnt_similarity.R | 6 LexisNexisTools-0.2.3/LexisNexisTools/tests/testthat/test-methods.R | 36 LexisNexisTools-0.2.3/LexisNexisTools/vignettes/demo.Rmd | 124 44 files changed, 2313 insertions(+), 1306 deletions(-)
More information about LexisNexisTools at CRAN
Permanent link
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Müller [aut, cre],
The R Consortium [fnd],
RStudio [fnd]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between hms versions 0.4.2 dated 2018-03-10 and 0.5.0 dated 2019-07-09
DESCRIPTION | 18 +-- MD5 | 70 ++++++++----- NAMESPACE | 39 ++++++- NEWS.md | 32 ++++-- R/arith.R | 47 +++++--- R/cast.R |only R/coerce.R |only R/compat-lifecycle.R |only R/format.R | 8 - R/hms.R | 157 ++++++++++++++++++++++++------ R/parse.R | 10 + R/pillar.R | 27 +++-- R/round.R | 4 R/zzz.R | 28 ----- README.md | 68 ++++++++---- build |only man/Deprecated.Rd |only man/figures |only man/hms-package.Rd |only man/hms.Rd | 67 ++++++------ man/parse_hms.Rd | 6 - man/vec_cast.hms.Rd |only man/vec_ptype2.hms.Rd |only tests/testthat/helper-compare.R | 10 - tests/testthat/helper-pillar.R | 4 tests/testthat/out/hm.txt | 14 +- tests/testthat/out/hmss.txt | 3 tests/testthat/test-arith.R | 9 - tests/testthat/test-coercion-deprecated.R |only tests/testthat/test-coercion.R | 24 ++-- tests/testthat/test-colformat.R | 4 tests/testthat/test-combine.R | 21 +++- tests/testthat/test-construct.R | 16 ++- tests/testthat/test-output.R | 21 ++++ tests/testthat/test-parse.R | 4 tests/testthat/test-round.R | 4 tests/testthat/test-subset.R | 15 ++ 37 files changed, 499 insertions(+), 231 deletions(-)
Title: Hierarchical Bayesian Vector Autoregression
Description: Toolkit for the estimation of hierarchical Bayesian vector autoregressions. Implements hierarchical prior selection for conjugate priors in the fashion of Giannone, Lenza & Primiceri (2015) <doi:10.1162/REST_a_00483>. Allows for the computation of impulse responses and forecasts and provides functionality for assessing results.
Author: Nikolas Kuschnig [aut, cre],
Lukas Vashold [aut],
Michael McCracken [dtc] (author of the FRED-QD dataset)
Maintainer: Nikolas Kuschnig <nikolas.kuschnig@wu.ac.at>
Diff between BVAR versions 0.1.3 dated 2019-05-03 and 0.1.5 dated 2019-07-09
DESCRIPTION | 10 +++---- MD5 | 38 +++++++++++++++------------- NAMESPACE | 3 ++ R/10_bvar.R | 16 +++++++----- R/11_input.R | 4 +-- R/12_aux.R | 22 ++++++++++++++++ R/20_ml.R | 71 +++++++++++++++++++++++++++++------------------------- R/22_get.R |only R/30_metropolis.R | 7 +++-- R/40_priors.R | 3 +- R/41_minnesota.R | 52 ++++++++++++++++++++++++++++----------- R/43_sur_soc.R |only R/84_plot_hyper.R | 4 ++- R/90_method.R | 7 +++-- R/data.R | 6 +++- data/fred_qd.rda |binary man/bv_dummy.Rd | 8 +++++- man/bv_mh.Rd | 7 +++-- man/bv_mn.Rd | 32 +++++++++++++++--------- man/bv_priors.Rd | 3 +- man/fred_qd.Rd | 6 +++- 21 files changed, 193 insertions(+), 106 deletions(-)
Title: Bayesian Network Structure Learning from Data with Missing
Values
Description: Bayesian Network Structure Learning from Data with Missing Values.
The package implements the Silander-Myllymaki complete search,
the Max-Min Parents-and-Children, the Hill-Climbing, the
Max-Min Hill-climbing heuristic searches, and the Structural
Expectation-Maximization algorithm. Available scoring functions are
BDeu, AIC, BIC. The package also implements methods for generating and using
bootstrap samples, imputed data, inference.
Author: Francesco Sambo [aut],
Alberto Franzin [aut, cre]
Maintainer: Alberto Franzin <afranzin@ulb.ac.be>
Diff between bnstruct versions 1.0.5 dated 2019-07-02 and 1.0.6 dated 2019-07-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 7 ++++++- R/sm.R | 2 +- R/util.R | 2 +- inst/doc/bnstruct.pdf |binary 6 files changed, 17 insertions(+), 12 deletions(-)
Title: Functions for the Analysis of Star Trek Thematic Data
Description: An implementation of 1) the hypergeometric test for over-representation of literary themes in a storyset (a list of stories) relative to a background list of stories, and 2) a recommendation system that takes a user-selected story as input and returns a ranked list of similar stories on the basis of shared themes. The package is currently implemented for the episodes of the Star Trek television franchise series The Original Series (TOS), The Animated Series (TAS), The Next Generation (TNG), and Voyager (VOY).
Author: Paul Sheridan, Mikael Onsjö
Maintainer: Paul Sheridan <paul.sheridan.stats@gmail.com>
Diff between stoRy versions 0.1.2 dated 2018-02-25 and 0.1.3 dated 2019-07-09
DESCRIPTION | 12 MD5 | 32 - NEWS.md | 4 R/get_similar_stories.r | 6 R/sysdata.rda |binary build/vignette.rds |binary data/story_ids_by_theme.rda |binary data/story_keywords.rda |binary data/story_metadata.rda |binary data/story_settings.rda |binary data/story_themes.rda |binary data/theme_dict.rda |binary inst/datasets/story_ids_by_theme.tsv | 701 ++++++++++++------------ inst/datasets/story_themes.tsv | 990 +++++++++++++++++----------------- inst/datasets/theme_dict.tsv | 999 +++++++++++++++++------------------ inst/doc/vignette.pdf |binary man/get_similar_stories.Rd | 6 17 files changed, 1376 insertions(+), 1374 deletions(-)
Title: Taking the Pain Out of Catching and Handling Conditions
Description: R has a unique way of dealing with warnings, errors, messages,
and other conditions, but it can often be troublesome to users coming
from different programming backgrounds. The purpose of this package is
to provide flexible and useful tools for handling R conditions with
less hassle. In order to lower the barrier of entry, keep code clean
and readable, and reduce the amount of typing required, `catchr` uses
a very simple domain-specific language that simplifies things on the
front-end.
This package aims to maintain a continuous learning curve that lets new
users jump straight in to condition-handling, while simultaneously
offering depth and complexity for more advanced users.
Author: Zachary Burchill [aut, cre, cph]
Maintainer: Zachary Burchill <zach.burchill.code@gmail.com>
Diff between catchr versions 0.2.0 dated 2019-02-05 and 0.2.1 dated 2019-07-09
catchr-0.2.0/catchr/man/with_ordered_handlers.Rd |only catchr-0.2.1/catchr/DESCRIPTION | 7 - catchr-0.2.1/catchr/MD5 | 23 +-- catchr-0.2.1/catchr/NAMESPACE | 1 catchr-0.2.1/catchr/NEWS.md | 16 ++ catchr-0.2.1/catchr/R/catching-n-plans.R | 62 ---------- catchr-0.2.1/catchr/R/check-n-clean.R | 16 +- catchr-0.2.1/catchr/R/printing.R | 6 catchr-0.2.1/catchr/README.md | 2 catchr-0.2.1/catchr/inst/doc/welcome-to-catchr.Rmd | 2 catchr-0.2.1/catchr/inst/doc/welcome-to-catchr.html | 6 catchr-0.2.1/catchr/tests/testthat/test-testing.R | 122 +++++++++++--------- catchr-0.2.1/catchr/vignettes/welcome-to-catchr.Rmd | 2 13 files changed, 126 insertions(+), 139 deletions(-)
Title: Lower Confidence Bounds for Binomial Series System
Description: Calculate and compare lower confidence bounds for binomial series system reliability. The R 'shiny' application, launched by the function launch_app(), weaves together a workflow of customized simulations and delta coverage calculations to output recommended lower confidence bound methods.
Author: Edward Schuberg
Maintainer: Edward Schuberg <eschu003@ucr.edu>
Diff between serieslcb versions 0.3.0 dated 2019-03-08 and 0.4.0 dated 2019-07-09
DESCRIPTION | 8 ++-- MD5 | 21 ++++++----- NAMESPACE | 4 +- R/functions.R | 93 +++++++++++++++++++++++++++++++++++++++++++++---- inst/app.R | 25 +++++++++++-- man/bayes.Rd | 2 - man/bayes_jeffreys.Rd | 2 - man/bayes_nlg.Rd |only man/bayes_uniform.Rd | 2 - man/launch_app.Rd | 9 ++++ man/nlg.post.sample.Rd |only man/pm.Rd | 2 - man/pm.random.Rd |only 13 files changed, 137 insertions(+), 31 deletions(-)