Title: Exploring Biological Relevance of Environmental Chemistry
Observations
Description: Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell et al. (2017) <doi:10.1021/acs.est.7b01613>.
Author: Laura DeCicco [aut, cre] (<https://orcid.org/0000-0002-3915-9487>),
Steven Corsi [aut] (<https://orcid.org/0000-0003-0583-5536>),
Daniel Villeneuve [aut] (<https://orcid.org/0000-0003-2801-0203>),
Brett Blackwell [aut],
Gerald Ankley [aut] (<https://orcid.org/0000-0002-9937-615X>),
Alison Appling [rev] (Reviewed for USGS),
Dalma Martinovic [rev] (Reviewed for USGS)
Maintainer: Laura DeCicco <ldecicco@usgs.gov>
Diff between toxEval versions 1.0.3 dated 2019-03-06 and 1.0.4 dated 2019-03-22
DESCRIPTION | 6 MD5 | 65 ++-- NAMESPACE | 4 R/explore_endpoints.R | 4 R/plot_chemical_boxplots.R | 30 +- R/plot_group_boxplots.R | 9 R/plot_tox_endpoints.R | 53 ++- R/plot_tox_stacks.R | 52 +++ R/rank_sites.R | 2 README.md | 32 +- build/vignette.rds |binary inst/doc/Introduction.R | 15 - inst/doc/Introduction.Rmd | 39 -- inst/doc/Introduction.html | 362 +++++++++++++++++++++----- inst/doc/PrepareData.html | 193 +++++++++++++- inst/doc/basicWorkflow.html | 599 +++++++++++++++++++++++++++++--------------- inst/doc/benchmarks.R |only inst/doc/benchmarks.Rmd |only inst/doc/benchmarks.html |only inst/doc/shinyApp.R | 4 inst/doc/shinyApp.Rmd | 3 inst/doc/shinyApp.html | 318 ++++++++++++++++++++--- inst/shiny/boxPlot.R | 45 +-- inst/shiny/endpointGraph.R | 61 ++-- inst/shiny/heatMap.R | 50 +-- inst/shiny/mapStuff.R | 16 - inst/shiny/server.R | 11 inst/shiny/stackPlot.R | 53 +-- inst/shiny/ui.R | 89 ++++-- man/plot_tox_boxplots.Rd | 9 man/plot_tox_endpoints.Rd | 9 man/plot_tox_stacks.Rd | 7 vignettes/Introduction.Rmd | 39 -- vignettes/benchmarks.Rmd |only vignettes/shinyApp.Rmd | 3 vignettes/wq_benchmarks.csv |only 36 files changed, 1549 insertions(+), 633 deletions(-)
Title: Multichannel Wavelet Deconvolution with Additive Long Memory
Noise
Description: Computes the Wavelet deconvolution estimate of a common signal
present in multiple channels that have possible different levels of blur
and long memory additive error.
Author: Justin Rory Wishart
Maintainer: Justin Rory Wishart <justin.wishart@mq.edu.au>
Diff between mwaved versions 1.1.5 dated 2017-07-13 and 1.1.6 dated 2019-03-22
mwaved-1.1.5/mwaved/R/RcppExports.R |only mwaved-1.1.6/mwaved/DESCRIPTION | 13 mwaved-1.1.6/mwaved/MD5 | 79 - mwaved-1.1.6/mwaved/NAMESPACE | 98 - mwaved-1.1.6/mwaved/NEWS | 163 +-- mwaved-1.1.6/mwaved/R/functions.R | 1214 +++++++++++----------- mwaved-1.1.6/mwaved/R/makeFunctions.R | 611 +++++------ mwaved-1.1.6/mwaved/R/utility-mwaved.R | 903 ++++++++--------- mwaved-1.1.6/mwaved/README.md | 42 mwaved-1.1.6/mwaved/TODO | 10 mwaved-1.1.6/mwaved/build/vignette.rds |binary mwaved-1.1.6/mwaved/cleanup | 2 mwaved-1.1.6/mwaved/configure | 1 mwaved-1.1.6/mwaved/configure.ac | 9 mwaved-1.1.6/mwaved/inst/doc/mWaveD.R | 578 +++++----- mwaved-1.1.6/mwaved/inst/doc/mWaveD.html | 1481 ++++++++++++++++------------ mwaved-1.1.6/mwaved/man/blurSignal.Rd | 68 - mwaved-1.1.6/mwaved/man/boxcarBlur.Rd | 80 - mwaved-1.1.6/mwaved/man/detectBlur.Rd | 34 mwaved-1.1.6/mwaved/man/directBlur.Rd | 38 mwaved-1.1.6/mwaved/man/gammaBlur.Rd | 92 - mwaved-1.1.6/mwaved/man/mWaveDDemo.Rd | 22 mwaved-1.1.6/mwaved/man/makeSignals.Rd | 98 - mwaved-1.1.6/mwaved/man/multiCoef.Rd | 150 +- mwaved-1.1.6/mwaved/man/multiEstimate.Rd | 168 +-- mwaved-1.1.6/mwaved/man/multiNoise.Rd | 74 - mwaved-1.1.6/mwaved/man/multiProj.Rd | 92 - mwaved-1.1.6/mwaved/man/multiSigma.Rd | 63 - mwaved-1.1.6/mwaved/man/multiThresh.Rd | 138 +- mwaved-1.1.6/mwaved/man/multiWaveD.Rd | 146 +- mwaved-1.1.6/mwaved/man/mwaved.Rd | 46 mwaved-1.1.6/mwaved/man/plot.mWaveD.Rd | 82 - mwaved-1.1.6/mwaved/man/plot.waveletCoef.Rd | 64 - mwaved-1.1.6/mwaved/man/resolutionMethod.Rd | 36 mwaved-1.1.6/mwaved/man/sigmaSNR.Rd | 76 - mwaved-1.1.6/mwaved/man/summary.mWaveD.Rd | 100 - mwaved-1.1.6/mwaved/man/theoreticalEta.Rd | 68 - mwaved-1.1.6/mwaved/man/waveletThresh.Rd | 138 +- mwaved-1.1.6/mwaved/src/Makevars.win | 2 mwaved-1.1.6/mwaved/src/RcppExports.cpp | 44 mwaved-1.1.6/mwaved/src/mwaved.cpp | 2 41 files changed, 3707 insertions(+), 3418 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular,
symmetric, and diagonal matrices, both dense and sparse and with
pattern, logical and numeric entries. Numerous methods for and
operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut],
Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Timothy A. Davis [ctb] (SuiteSparse and 'cs' C libraries, notably
CHOLMOD, AMD; collaborators listed in dir(pattern =
'^[A-Z]+[.]txt$', full.names=TRUE, system.file('doc',
'SuiteSparse', package='Matrix'))),
Jens Oehlschlägel [ctb] (initial nearPD()),
Jason Riedy [ctb] (condest() and onenormest() for octave, Copyright:
Regents of the University of California),
R Core Team [ctb] (base R matrix implementation)
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-16 dated 2019-03-08 and 1.2-17 dated 2019-03-22
DESCRIPTION | 13 ++++------ MD5 | 46 ++++++++++++++++++------------------ R/Auxiliaries.R | 2 - R/Matrix.R | 5 +--- R/zzz.R | 5 ++++ TODO | 2 + build/partial.rdb |binary inst/NEWS.Rd | 16 ++++++++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary man/nearPD.Rd | 23 +++++++++--------- src/Csparse.c | 4 +-- src/Mutils.h | 4 +-- src/Syms.h | 1 src/chm_common.c | 48 +++++++++++++++++++++----------------- src/cs_utils.c | 8 +++--- src/dense.c | 56 ++++++++++++++++++++------------------------- src/dgCMatrix.c | 13 +++++----- src/init.c | 3 ++ src/sparseQR.c | 4 +-- tests/Simple.R | 12 ++++++++- 24 files changed, 149 insertions(+), 116 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <http://cyclestreets.net/>;
calculation of route segment attributes such as bearing and aggregate flow;
and 'travel watershed' analysis.
See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Malcolm Morgan [ctb] (Co-author of angle_diff),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlin [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.2.7 dated 2019-01-07 and 0.2.8 dated 2019-03-22
stplanr-0.2.7/stplanr/R/od_coords.R |only stplanr-0.2.7/stplanr/demo |only stplanr-0.2.7/stplanr/inst/doc/introducing-stplanr.R |only stplanr-0.2.7/stplanr/inst/doc/introducing-stplanr.Rmd |only stplanr-0.2.7/stplanr/inst/doc/introducing-stplanr.html |only stplanr-0.2.7/stplanr/vignettes/README-cycle-trip-1.png |only stplanr-0.2.7/stplanr/vignettes/README-plot1-1.png |only stplanr-0.2.7/stplanr/vignettes/README-plot2-1.png |only stplanr-0.2.7/stplanr/vignettes/README-rnet-1.png |only stplanr-0.2.7/stplanr/vignettes/README-unnamed-chunk-11-1.png |only stplanr-0.2.7/stplanr/vignettes/introducing-stplanr.Rmd |only stplanr-0.2.8/stplanr/DESCRIPTION | 37 - stplanr-0.2.8/stplanr/MD5 | 272 ++++----- stplanr-0.2.8/stplanr/NAMESPACE | 4 stplanr-0.2.8/stplanr/NEWS.md | 21 stplanr-0.2.8/stplanr/R/SpatialLinesNetwork.R | 15 stplanr-0.2.8/stplanr/R/aggregate_funs.R | 22 stplanr-0.2.8/stplanr/R/catchmentArea.R | 8 stplanr-0.2.8/stplanr/R/crs-funs.R | 2 stplanr-0.2.8/stplanr/R/cyclestreets.R | 4 stplanr-0.2.8/stplanr/R/data.r | 56 -- stplanr-0.2.8/stplanr/R/depreciated.R |only stplanr-0.2.8/stplanr/R/geo-functions.R | 11 stplanr-0.2.8/stplanr/R/geo_code.R | 1 stplanr-0.2.8/stplanr/R/google-functions.R | 2 stplanr-0.2.8/stplanr/R/line_match.R | 1 stplanr-0.2.8/stplanr/R/line_sample.R | 2 stplanr-0.2.8/stplanr/R/line_via.R | 4 stplanr-0.2.8/stplanr/R/linefuns.R | 10 stplanr-0.2.8/stplanr/R/load-stats19.R | 31 + stplanr-0.2.8/stplanr/R/loadABS.R | 1 stplanr-0.2.8/stplanr/R/od-funs.R | 152 ++++- stplanr-0.2.8/stplanr/R/oneway.R | 1 stplanr-0.2.8/stplanr/R/osrmfunctions.R | 13 stplanr-0.2.8/stplanr/R/overline.R | 280 ++++++++-- stplanr-0.2.8/stplanr/R/quadrants.R | 1 stplanr-0.2.8/stplanr/R/radiate.R | 2 stplanr-0.2.8/stplanr/R/route-transport-api.R | 8 stplanr-0.2.8/stplanr/R/route.R | 72 ++ stplanr-0.2.8/stplanr/R/route_local.R | 25 stplanr-0.2.8/stplanr/R/routes.R | 14 stplanr-0.2.8/stplanr/R/stplanr-package.R | 3 stplanr-0.2.8/stplanr/R/toptail.R | 7 stplanr-0.2.8/stplanr/README.md | 162 +++-- stplanr-0.2.8/stplanr/build/vignette.rds |binary stplanr-0.2.8/stplanr/data/osm_net_example.rda |only stplanr-0.2.8/stplanr/inst/CITATION |only stplanr-0.2.8/stplanr/inst/doc/stplanr-paper.R | 6 stplanr-0.2.8/stplanr/inst/doc/stplanr-paper.Rmd | 15 stplanr-0.2.8/stplanr/inst/doc/stplanr-paper.html | 20 stplanr-0.2.8/stplanr/inst/doc/stplanr.R |only stplanr-0.2.8/stplanr/inst/doc/stplanr.Rmd |only stplanr-0.2.8/stplanr/inst/doc/stplanr.html |only stplanr-0.2.8/stplanr/man/SpatialLinesNetwork.Rd | 15 stplanr-0.2.8/stplanr/man/angle_diff.Rd | 15 stplanr-0.2.8/stplanr/man/bbox_scale.Rd | 9 stplanr-0.2.8/stplanr/man/buff_geo.Rd | 12 stplanr-0.2.8/stplanr/man/calc_catchment.Rd | 19 stplanr-0.2.8/stplanr/man/calc_catchment_sum.Rd | 15 stplanr-0.2.8/stplanr/man/calc_moving_catchment.Rd | 15 stplanr-0.2.8/stplanr/man/calc_network_catchment.Rd | 15 stplanr-0.2.8/stplanr/man/cents.Rd | 22 stplanr-0.2.8/stplanr/man/crs_select_aeq.Rd | 9 stplanr-0.2.8/stplanr/man/decode_gl.Rd | 12 stplanr-0.2.8/stplanr/man/destination_zones.Rd | 7 stplanr-0.2.8/stplanr/man/dist_google.Rd | 8 stplanr-0.2.8/stplanr/man/figures |only stplanr-0.2.8/stplanr/man/find_network_nodes.Rd | 16 stplanr-0.2.8/stplanr/man/flow.Rd | 40 - stplanr-0.2.8/stplanr/man/flow_dests.Rd | 1 stplanr-0.2.8/stplanr/man/flowlines.Rd | 7 stplanr-0.2.8/stplanr/man/gclip.Rd | 9 stplanr-0.2.8/stplanr/man/geo_bb.Rd | 8 stplanr-0.2.8/stplanr/man/geo_bb_matrix.Rd | 9 stplanr-0.2.8/stplanr/man/geo_code.Rd | 5 stplanr-0.2.8/stplanr/man/geo_toptail.Rd | 13 stplanr-0.2.8/stplanr/man/gsection.Rd | 19 stplanr-0.2.8/stplanr/man/is_linepoint.Rd | 13 stplanr-0.2.8/stplanr/man/islines.Rd | 16 stplanr-0.2.8/stplanr/man/line2df.Rd | 13 stplanr-0.2.8/stplanr/man/line2route.Rd | 16 stplanr-0.2.8/stplanr/man/line2routeRetry.Rd | 12 stplanr-0.2.8/stplanr/man/lineLabels.Rd | 16 stplanr-0.2.8/stplanr/man/line_bearing.Rd | 13 stplanr-0.2.8/stplanr/man/line_match.Rd | 13 stplanr-0.2.8/stplanr/man/line_midpoint.Rd | 13 stplanr-0.2.8/stplanr/man/line_sample.Rd | 13 stplanr-0.2.8/stplanr/man/line_segment.Rd | 13 stplanr-0.2.8/stplanr/man/line_via.Rd | 13 stplanr-0.2.8/stplanr/man/locate2spdf.Rd | 5 stplanr-0.2.8/stplanr/man/mapshape.Rd | 9 stplanr-0.2.8/stplanr/man/mapshape_available.Rd | 9 stplanr-0.2.8/stplanr/man/mats2line.Rd | 15 stplanr-0.2.8/stplanr/man/n_sample_length.Rd | 13 stplanr-0.2.8/stplanr/man/n_vertices.Rd | 13 stplanr-0.2.8/stplanr/man/nearest2spdf.Rd | 12 stplanr-0.2.8/stplanr/man/nearest_cyclestreets.Rd | 3 stplanr-0.2.8/stplanr/man/nearest_google.Rd | 5 stplanr-0.2.8/stplanr/man/nearest_osm.Rd | 5 stplanr-0.2.8/stplanr/man/od2line.Rd | 33 - stplanr-0.2.8/stplanr/man/od2odf.Rd | 17 stplanr-0.2.8/stplanr/man/od_aggregate.Rd | 15 stplanr-0.2.8/stplanr/man/od_coords.Rd | 12 stplanr-0.2.8/stplanr/man/od_coords2line.Rd |only stplanr-0.2.8/stplanr/man/od_dist.Rd | 13 stplanr-0.2.8/stplanr/man/od_radiation.Rd | 8 stplanr-0.2.8/stplanr/man/onewaygeo.Rd | 13 stplanr-0.2.8/stplanr/man/onewayid.Rd | 13 stplanr-0.2.8/stplanr/man/osm_net_example.Rd |only stplanr-0.2.8/stplanr/man/overline.Rd | 19 stplanr-0.2.8/stplanr/man/overline2.Rd |only stplanr-0.2.8/stplanr/man/plot-SpatialLinesNetwork-ANY-method.Rd | 15 stplanr-0.2.8/stplanr/man/plot-sfNetwork-ANY-method.Rd | 15 stplanr-0.2.8/stplanr/man/points2flow.Rd | 8 stplanr-0.2.8/stplanr/man/points2line.Rd | 13 stplanr-0.2.8/stplanr/man/points2odf.Rd | 8 stplanr-0.2.8/stplanr/man/quadrant.Rd | 9 stplanr-0.2.8/stplanr/man/read_table_builder.Rd | 1 stplanr-0.2.8/stplanr/man/reproject.Rd | 9 stplanr-0.2.8/stplanr/man/route.Rd | 15 stplanr-0.2.8/stplanr/man/route_cyclestreet.Rd | 14 stplanr-0.2.8/stplanr/man/route_dodgr.Rd |only stplanr-0.2.8/stplanr/man/route_graphhopper.Rd | 10 stplanr-0.2.8/stplanr/man/route_local.Rd | 26 stplanr-0.2.8/stplanr/man/route_network.Rd | 2 stplanr-0.2.8/stplanr/man/route_osrm.Rd | 12 stplanr-0.2.8/stplanr/man/route_transportapi_public.Rd | 13 stplanr-0.2.8/stplanr/man/routes_fast.Rd | 2 stplanr-0.2.8/stplanr/man/routes_slow.Rd | 2 stplanr-0.2.8/stplanr/man/sln2points.Rd | 15 stplanr-0.2.8/stplanr/man/sp_aggregate.Rd | 15 stplanr-0.2.8/stplanr/man/stplanr-deprecated.Rd |only stplanr-0.2.8/stplanr/man/sum_network_links.Rd | 15 stplanr-0.2.8/stplanr/man/sum_network_routes.Rd | 14 stplanr-0.2.8/stplanr/man/toptail_buff.Rd | 13 stplanr-0.2.8/stplanr/man/toptailgs.Rd | 13 stplanr-0.2.8/stplanr/man/update_line_geometry.Rd | 13 stplanr-0.2.8/stplanr/man/viaroute.Rd | 13 stplanr-0.2.8/stplanr/man/viaroute2sldf.Rd | 11 stplanr-0.2.8/stplanr/man/writeGeoJSON.Rd | 2 stplanr-0.2.8/stplanr/man/zones.Rd | 11 stplanr-0.2.8/stplanr/tests/testthat/test-calc_catchment.R | 4 stplanr-0.2.8/stplanr/tests/testthat/test-route_cyclestreet.R | 2 stplanr-0.2.8/stplanr/vignettes/references.bib | 14 stplanr-0.2.8/stplanr/vignettes/stplanr-citation.bib |only stplanr-0.2.8/stplanr/vignettes/stplanr-paper.Rmd | 15 stplanr-0.2.8/stplanr/vignettes/stplanr.Rmd |only 147 files changed, 1792 insertions(+), 533 deletions(-)
Title: Spatial Covariance Functions
Description: R functions for analyzing spatial (cross-)covariance: the
nonparametric (cross-)covariance function, the spline correlogram, the
nonparametric phase coherence function, local indicators of spatial
association (LISA), (Mantel) correlogram, (Partial) Mantel test.
Author: Ottar N. Bjornstad [aut, cre],
Jun Cai [ctb]
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between ncf versions 1.2-6 dated 2018-10-11 and 1.2-8 dated 2019-03-22
CHANGES | 6 ++++- DESCRIPTION | 10 ++++----- MD5 | 45 ++++++++++++++++++++++---------------------- R/Sncf.R | 20 +++++++------------ R/Sncf2D.R | 2 - R/correlog.R | 6 ++--- R/lisa.R | 26 ++++++++++++------------- R/mSynch.R | 2 - R/mantel-test.R | 4 +-- R/spline-correlog.R | 8 ++----- R/spline-correlog2D.R | 2 - README.md |only man/Sncf.Rd | 8 +++---- man/Sncf.srf.Rd | 6 ++--- man/Sncf2D.Rd | 4 +-- man/correlog.nc.Rd | 4 +-- man/lisa.Rd | 4 +-- man/lisa.nc.Rd | 2 - man/plot.Sncf.Rd | 6 +---- man/plot.Sncf.cov.Rd | 4 --- man/plot.Sncf2D.Rd | 3 +- man/plot.lisa.Rd | 7 +++--- man/plot.spline.correlog.Rd | 4 --- man/spline.correlog.Rd | 6 ++--- 24 files changed, 92 insertions(+), 97 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure.
Author: Hong Ooi [aut, cre],
httr development team [ctb] (Original OAuth listener code),
Scott Holden [ctb] (Advice on AAD authentication),
Chris Stone [ctb] (Advice on AAD authentication),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureAuth versions 1.0.0 dated 2019-02-22 and 1.0.1 dated 2019-03-22
DESCRIPTION | 12 - MD5 | 26 +- NAMESPACE | 1 NEWS.md |only R/AzureToken.R | 2 R/initfuncs.R | 2 R/utils.R | 63 ++++-- README.md | 4 build/vignette.rds |binary inst/doc/token.Rmd | 2 inst/doc/token.html | 383 ++++++++++++++++++++++++++------------- man/decode_jwt.Rd |only tests/testthat/test01_v1_token.R | 2 tests/testthat/test02_v2_token.R | 2 vignettes/token.Rmd | 2 15 files changed, 337 insertions(+), 164 deletions(-)
Title: C-Like 'getopt' Behavior
Description: Package designed to be used with Rscript to write
``#!'' shebang scripts that accept short and long flags/options.
Many users will prefer using instead the packages optparse or argparse
which add extra features like automatically generated help option and usage,
support for default values, positional argument support, etc.
Author: Trevor L Davis [aut, cre],
Allen Day [aut] (Original package author),
Roman Zenka [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between getopt versions 1.20.2 dated 2018-02-16 and 1.20.3 dated 2019-03-22
getopt-1.20.2/getopt/NEWS |only getopt-1.20.3/getopt/DESCRIPTION | 24 +++++--- getopt-1.20.3/getopt/MD5 | 13 ++-- getopt-1.20.3/getopt/NEWS.md |only getopt-1.20.3/getopt/R/getopt.R | 46 ++++++++-------- getopt-1.20.3/getopt/README.md |only getopt-1.20.3/getopt/exec/example.R | 20 +++---- getopt-1.20.3/getopt/man/getopt.Rd | 24 ++++---- getopt-1.20.3/getopt/tests/testthat/test-getopt.R | 61 +++++++++++++--------- 9 files changed, 105 insertions(+), 83 deletions(-)
Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc).
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between parsnip versions 0.0.1 dated 2018-11-12 and 0.0.2 dated 2019-03-22
parsnip-0.0.1/parsnip/man/other_predict.Rd |only parsnip-0.0.1/parsnip/man/varying_args.Rd |only parsnip-0.0.1/parsnip/tests/testthat/derby.log |only parsnip-0.0.2/parsnip/DESCRIPTION | 15 parsnip-0.0.2/parsnip/MD5 | 194 +++---- parsnip-0.0.2/parsnip/NAMESPACE | 53 + parsnip-0.0.2/parsnip/NEWS.md | 54 +- parsnip-0.0.2/parsnip/R/aaa_spark_helpers.R | 6 parsnip-0.0.2/parsnip/R/arguments.R | 10 parsnip-0.0.2/parsnip/R/boost_tree.R | 14 parsnip-0.0.2/parsnip/R/convert_data.R | 4 parsnip-0.0.2/parsnip/R/data.R | 59 ++ parsnip-0.0.2/parsnip/R/decision_tree.R | 12 parsnip-0.0.2/parsnip/R/descriptors.R | 1 parsnip-0.0.2/parsnip/R/engines.R | 2 parsnip-0.0.2/parsnip/R/fit.R | 36 - parsnip-0.0.2/parsnip/R/fit_control.R | 22 parsnip-0.0.2/parsnip/R/fit_helpers.R | 46 + parsnip-0.0.2/parsnip/R/linear_reg.R | 108 +++- parsnip-0.0.2/parsnip/R/logistic_reg.R | 131 +++- parsnip-0.0.2/parsnip/R/logistic_reg_data.R | 52 + parsnip-0.0.2/parsnip/R/mars.R | 6 parsnip-0.0.2/parsnip/R/misc.R | 4 parsnip-0.0.2/parsnip/R/mlp.R | 8 parsnip-0.0.2/parsnip/R/mlp_data.R | 2 parsnip-0.0.2/parsnip/R/multinom_reg.R | 135 ++--- parsnip-0.0.2/parsnip/R/nearest_neighbor.R | 2 parsnip-0.0.2/parsnip/R/nullmodel.R |only parsnip-0.0.2/parsnip/R/nullmodel_data.R |only parsnip-0.0.2/parsnip/R/predict.R | 83 ++- parsnip-0.0.2/parsnip/R/predict_class.R | 44 - parsnip-0.0.2/parsnip/R/predict_classprob.R | 35 - parsnip-0.0.2/parsnip/R/predict_interval.R | 78 +- parsnip-0.0.2/parsnip/R/predict_numeric.R | 33 - parsnip-0.0.2/parsnip/R/predict_quantile.R | 43 - parsnip-0.0.2/parsnip/R/predict_raw.R | 35 - parsnip-0.0.2/parsnip/R/rand_forest.R | 8 parsnip-0.0.2/parsnip/R/surv_reg.R | 8 parsnip-0.0.2/parsnip/R/svm_poly.R | 6 parsnip-0.0.2/parsnip/R/svm_rbf.R | 6 parsnip-0.0.2/parsnip/R/tidy.R |only parsnip-0.0.2/parsnip/R/translate.R | 7 parsnip-0.0.2/parsnip/R/varying.R | 267 ++++++---- parsnip-0.0.2/parsnip/README.md | 2 parsnip-0.0.2/parsnip/build/parsnip.pdf |binary parsnip-0.0.2/parsnip/build/vignette.rds |binary parsnip-0.0.2/parsnip/data/check_times.rda |only parsnip-0.0.2/parsnip/data/datalist | 1 parsnip-0.0.2/parsnip/inst/doc/parsnip_Intro.html | 24 parsnip-0.0.2/parsnip/man/boost_tree.Rd | 14 parsnip-0.0.2/parsnip/man/check_times.Rd |only parsnip-0.0.2/parsnip/man/decision_tree.Rd | 12 parsnip-0.0.2/parsnip/man/fit.Rd | 12 parsnip-0.0.2/parsnip/man/fit_control.Rd | 3 parsnip-0.0.2/parsnip/man/linear_reg.Rd | 30 - parsnip-0.0.2/parsnip/man/logistic_reg.Rd | 30 - parsnip-0.0.2/parsnip/man/mars.Rd | 8 parsnip-0.0.2/parsnip/man/mlp.Rd | 10 parsnip-0.0.2/parsnip/man/multi_predict.Rd | 1 parsnip-0.0.2/parsnip/man/multinom_reg.Rd | 30 - parsnip-0.0.2/parsnip/man/nearest_neighbor.Rd | 2 parsnip-0.0.2/parsnip/man/null_model.Rd |only parsnip-0.0.2/parsnip/man/nullmodel.Rd |only parsnip-0.0.2/parsnip/man/predict.model_fit.Rd | 50 + parsnip-0.0.2/parsnip/man/rand_forest.Rd | 10 parsnip-0.0.2/parsnip/man/reexports.Rd | 5 parsnip-0.0.2/parsnip/man/set_args.Rd | 6 parsnip-0.0.2/parsnip/man/set_engine.Rd | 2 parsnip-0.0.2/parsnip/man/surv_reg.Rd | 10 parsnip-0.0.2/parsnip/man/svm_poly.Rd | 8 parsnip-0.0.2/parsnip/man/svm_rbf.Rd | 8 parsnip-0.0.2/parsnip/man/tidy.model_fit.Rd |only parsnip-0.0.2/parsnip/man/translate.Rd | 6 parsnip-0.0.2/parsnip/man/varying_args.model_spec.Rd |only parsnip-0.0.2/parsnip/tests/testthat/test_boost_tree_C50.R | 24 parsnip-0.0.2/parsnip/tests/testthat/test_boost_tree_spark.R | 12 parsnip-0.0.2/parsnip/tests/testthat/test_boost_tree_xgboost.R | 12 parsnip-0.0.2/parsnip/tests/testthat/test_failed_models.R |only parsnip-0.0.2/parsnip/tests/testthat/test_fit_interfaces.R | 25 parsnip-0.0.2/parsnip/tests/testthat/test_linear_reg.R | 11 parsnip-0.0.2/parsnip/tests/testthat/test_linear_reg_glmnet.R | 177 ++++-- parsnip-0.0.2/parsnip/tests/testthat/test_linear_reg_spark.R | 2 parsnip-0.0.2/parsnip/tests/testthat/test_linear_reg_stan.R | 37 - parsnip-0.0.2/parsnip/tests/testthat/test_logistic_reg.R | 45 - parsnip-0.0.2/parsnip/tests/testthat/test_logistic_reg_glmnet.R | 172 ++++-- parsnip-0.0.2/parsnip/tests/testthat/test_logistic_reg_keras.R | 4 parsnip-0.0.2/parsnip/tests/testthat/test_logistic_reg_spark.R | 4 parsnip-0.0.2/parsnip/tests/testthat/test_logistic_reg_stan.R | 117 ++-- parsnip-0.0.2/parsnip/tests/testthat/test_mars.R | 16 parsnip-0.0.2/parsnip/tests/testthat/test_mlp_keras.R | 21 parsnip-0.0.2/parsnip/tests/testthat/test_mlp_nnet.R | 22 parsnip-0.0.2/parsnip/tests/testthat/test_multinom_reg_glmnet.R | 30 - parsnip-0.0.2/parsnip/tests/testthat/test_multinom_reg_keras.R | 4 parsnip-0.0.2/parsnip/tests/testthat/test_multinom_reg_spark.R | 4 parsnip-0.0.2/parsnip/tests/testthat/test_nearest_neighbor_kknn.R | 14 parsnip-0.0.2/parsnip/tests/testthat/test_nullmodel.R |only parsnip-0.0.2/parsnip/tests/testthat/test_predict_formats.R | 34 + parsnip-0.0.2/parsnip/tests/testthat/test_rand_forest_randomForest.R | 33 - parsnip-0.0.2/parsnip/tests/testthat/test_rand_forest_ranger.R | 41 + parsnip-0.0.2/parsnip/tests/testthat/test_rand_forest_spark.R | 15 parsnip-0.0.2/parsnip/tests/testthat/test_svm_poly.R | 25 parsnip-0.0.2/parsnip/tests/testthat/test_svm_rbf.R | 23 parsnip-0.0.2/parsnip/tests/testthat/test_varying.R | 208 +++++-- parsnip-0.0.2/parsnip/vignettes/articles/Classification.Rmd | 22 parsnip-0.0.2/parsnip/vignettes/articles/Regression.Rmd | 12 105 files changed, 1945 insertions(+), 1134 deletions(-)
Title: Trajectory Miner: a Toolbox for Exploring and Rendering
Sequences
Description: Toolbox for the manipulation, description and rendering of sequences, and more generally the mining of sequence data in the field of social sciences. Although the toolbox is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers, its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for converting sequences from one format to another. It offers several functions for describing and rendering sequences, for computing distances between sequences with different metrics (among which optimal matching), original dissimilarity-based analysis tools, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph] (<https://orcid.org/0000-0002-6269-1412>),
Nicolas Müller [aut],
Reto Bürgin [aut],
Pierre-Alexandre Fonta [aut],
Gilbert Ritschard [aut, cre, cph]
(<https://orcid.org/0000-0001-7776-0903>)
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineR versions 2.0-11 dated 2019-03-18 and 2.0-11.1 dated 2019-03-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 7 +++++++ inst/NEWS.Rd | 12 +++++++++++- inst/doc/TraMineR-state-sequence.pdf |binary man/TraMineR-package.Rd | 2 +- src/eventseq.cpp | 12 ++++++++---- 7 files changed, 37 insertions(+), 16 deletions(-)
Title: Minimal Working Examples for Particle Metropolis-Hastings
Description: Routines for state estimate in a linear
Gaussian state space model and a simple stochastic volatility model using
particle filtering. Parameter inference is also carried out in these models
using the particle Metropolis-Hastings algorithm that includes the particle
filter to provided an unbiased estimator of the likelihood. This package is
a collection of minimal working examples of these algorithms and is only
meant for educational use and as a start for learning to them on your own.
Author: Johan Dahlin
Maintainer: Johan Dahlin <uni@johandahlin.com>
Diff between pmhtutorial versions 1.4 dated 2019-01-11 and 1.5 dated 2019-03-22
DESCRIPTION | 6 +- MD5 | 47 ++++++++-------- R/dataGeneration.R | 9 +-- R/example1-lgss.R | 13 ++-- R/example2-lgss.R | 13 ++-- R/example3-sv.R | 13 ++-- R/example4-sv.R | 13 ++-- R/example5-sv.R | 13 ++-- R/parameterEstimation.R | 27 +++++---- R/plotting.R | 9 +-- R/stateEstimation.R | 27 +++++---- inst |only man/example1_lgss.Rd | 9 +-- man/example2_lgss.Rd | 9 +-- man/example3_sv.Rd | 9 +-- man/example4_sv.Rd | 9 +-- man/example5_sv.Rd | 9 +-- man/generateData.Rd | 9 +-- man/kalmanFilter.Rd | 9 +-- man/makePlotsParticleMetropolisHastingsSVModel.Rd | 9 +-- man/particleFilter.Rd | 9 +-- man/particleFilterSVmodel.Rd | 9 +-- man/particleMetropolisHastings.Rd | 9 +-- man/particleMetropolisHastingsSVmodel.Rd | 9 +-- man/particleMetropolisHastingsSVmodelReparameterised.Rd | 9 +-- 25 files changed, 167 insertions(+), 140 deletions(-)
Title: Utilities for Importing Data from Plain Text Accounting Files
Description: Utilities for querying plain text accounting files from 'Ledger', 'HLedger', and 'Beancount'.
Author: Trevor L Davis [aut, cre],
Jenya Sovetkin [ctb]
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between ledger versions 2.0.0 dated 2019-01-15 and 2.0.1 dated 2019-03-22
DESCRIPTION | 6 MD5 | 8 NEWS.md | 15 - R/register.r | 1 README.md | 821 +++++++++++++++++++++++++++++++++-------------------------- 5 files changed, 484 insertions(+), 367 deletions(-)
Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score
(Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser
comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>)
using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Hojjat Salmasian [ctb] (ICD-9-CM scores)
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between comorbidity versions 0.2.0 dated 2018-10-08 and 0.3.0 dated 2019-03-22
DESCRIPTION | 10 MD5 | 44 +- NEWS.md | 18 + R/comorbidity-package.R | 2 R/comorbidity.R | 32 +- R/labelled.R | 2 R/sample_diag.R | 6 README.md | 68 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/comorbidityscores.Rmd | 63 +++- inst/doc/comorbidityscores.html | 519 ++++++++++++++++++++++----------- man/comorbidity.Rd | 24 + man/figures/hex.png |binary man/sample_diag.Rd | 4 tests/testthat.R | 2 tests/testthat/test-charlson-icd10.R | 2 tests/testthat/test-comorbidity.R | 12 tests/testthat/test-data.R | 2 tests/testthat/test-elixhauser-icd10.R | 2 tests/testthat/test-elixhauser-icd9.R | 2 tests/testthat/test-sample_diag.R | 2 vignettes/comorbidityscores.Rmd | 63 +++- 23 files changed, 601 insertions(+), 278 deletions(-)
Title: Powell Miscellaneous Functions for Teaching and Learning
Statistics
Description: Miscellaneous functions useful for teaching statistics as well as actually practicing the art. They typically are not “new” methods but rather wrappers around either base R or other packages.
Author: Chuck Powell [aut, cre]
Maintainer: Chuck Powell <ibecav@gmail.com>
Diff between CGPfunctions versions 0.5.0 dated 2019-03-21 and 0.5.2 dated 2019-03-22
DESCRIPTION | 8 MD5 | 20 +- NAMESPACE | 1 NEWS.md | 9 R/CGPfunctions.R | 2 R/Plot2WayANOVA.R | 327 ++++++++++++++++++++++-------------- inst/doc/Using-Plot2WayANOVA.html | 112 ++++++------ inst/doc/Using-PlotXTabs.html | 4 inst/doc/Using-newggslopegraph.html | 18 - man/CGPfunctions.Rd | 2 man/Plot2WayANOVA.Rd | 85 +++++---- 11 files changed, 353 insertions(+), 235 deletions(-)
More information about ActiveDriverWGS at CRAN
Permanent link
Title: Numerical Calibration of Proxy-Climate Relationships
Description: Bootstrapped response and correlation functions,
seasonal correlations and evaluation of reconstruction
skills for use in dendroclimatology and dendroecology.
Author: Christian Zang [aut, cre, cph, trl],
Franco Biondi [ctb, cph]
Maintainer: Christian Zang <christian.zang@wzw.tum.de>
Diff between treeclim versions 2.0.0 dated 2016-09-02 and 2.0.3 dated 2019-03-22
DESCRIPTION | 11 +- MD5 | 108 +++++++++++++-------------- NAMESPACE | 38 ++++++--- R/RcppExports.R | 24 +++--- R/dcc.R | 4 + R/generics.R | 47 ++++++++--- R/seascorr.R | 5 - R/tc_correlation.R | 12 +-- R/tc_response.R | 8 +- README.md | 2 inst/Changelog | 162 +++++++++++++++++++++-------------------- man/abbrev_name.Rd | 1 man/apply_var_names.Rd | 1 man/as_tcclimate.Rd | 1 man/check_months.Rd | 1 man/correct_continuous.Rd | 1 man/dcc.Rd | 9 +- man/dlm.Rd | 1 man/eval_selection.Rd | 1 man/exclude_from.Rd | 1 man/format_month.Rd | 1 man/g_test.Rd | 1 man/init_boot_data.Rd | 1 man/is_continuous.Rd | 1 man/make_pmat.Rd | 1 man/make_range_list.Rd | 1 man/muc_clim.Rd | 1 man/muc_fake.Rd | 1 man/muc_spruce.Rd | 1 man/norw015.Rd | 1 man/norway_prec.Rd | 1 man/norway_temp.Rd | 1 man/ptest.Rd | 1 man/rt_prec.Rd | 1 man/rt_spruce.Rd | 1 man/rt_temp.Rd | 1 man/seascorr.Rd | 14 +-- man/shift_year.Rd | 1 man/skills.Rd | 1 man/spai020.Rd | 1 man/spain_prec.Rd | 1 man/spain_temp.Rd | 1 man/tc_correlation.Rd | 1 man/tc_design.Rd | 1 man/tc_efunc.Rd | 1 man/tc_mfunc.Rd | 1 man/tc_response.Rd | 1 man/traceplot.Rd | 1 man/treeclim-modifiers.Rd | 5 - man/treeclim-shifters.Rd | 3 man/truncate_input.Rd | 1 man/unify_selection.Rd | 1 src/RcppExports.cpp | 101 ++++++++++++++----------- tests/testthat/test_dcc.R | 5 + tests/testthat/test_seascorr.R | 3 55 files changed, 309 insertions(+), 289 deletions(-)
Title: Synchrony in Motion Energy Analysis (MEA) Time-Series
Description: A suite of tools useful to read, visualize and export bivariate motion energy time-series. Lagged synchrony between subjects can be analyzed through windowed cross-correlation. Surrogate data generation allows an estimation of pseudosynchrony that helps to estimate the effect size of the observed synchronization. Ramseyer & Tschacher (2011) <doi:10.1037/a0023419>.
Author: Johann R. Kleinbub, Fabian Ramseyer
Maintainer: Johann R. Kleinbub <johann.kleinbub@gmail.com>
Diff between rMEA versions 1.0.0 dated 2018-03-16 and 1.1.0 dated 2019-03-22
rMEA-1.0.0/rMEA/man/plot.MEAlist.Rd |only rMEA-1.1.0/rMEA/DESCRIPTION | 13 rMEA-1.1.0/rMEA/MD5 | 121 rMEA-1.1.0/rMEA/NAMESPACE | 98 rMEA-1.1.0/rMEA/NEWS.md | 38 rMEA-1.1.0/rMEA/R/rMEA_IO.R | 676 rMEA-1.1.0/rMEA/R/rMEA_ccf.R | 315 rMEA-1.1.0/rMEA/R/rMEA_class.R | 435 rMEA-1.1.0/rMEA/R/rMEA_get.R |only rMEA-1.1.0/rMEA/R/rMEA_graphics.R | 1517 - rMEA-1.1.0/rMEA/R/rMEA_rand.R | 159 rMEA-1.1.0/rMEA/R/rMEA_util.R | 379 rMEA-1.1.0/rMEA/R/rMea_filter.R | 474 rMEA-1.1.0/rMEA/README.md | 440 rMEA-1.1.0/rMEA/inst/CITATION |only rMEA-1.1.0/rMEA/inst/extdata/dropout/100_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/101_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/102_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/103_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/104_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/105_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/106_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/107_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/108_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/dropout/109_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/200_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/201_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/202_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/203_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/204_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/205_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/206_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/207_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/208_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/inst/extdata/normal/209_01.txt |30002 +++++++++++----------- rMEA-1.1.0/rMEA/man/MEA.Rd | 97 rMEA-1.1.0/rMEA/man/MEAccf.Rd | 112 rMEA-1.1.0/rMEA/man/MEAdistplot.Rd | 114 rMEA-1.1.0/rMEA/man/MEAheatmap.Rd | 47 rMEA-1.1.0/rMEA/man/MEAlagplot.Rd | 122 rMEA-1.1.0/rMEA/man/MEAlist.Rd | 50 rMEA-1.1.0/rMEA/man/MEAmap.Rd | 54 rMEA-1.1.0/rMEA/man/MEAoutlier.Rd | 76 rMEA-1.1.0/rMEA/man/MEAscale.Rd | 123 rMEA-1.1.0/rMEA/man/MEAsmooth.Rd | 86 rMEA-1.1.0/rMEA/man/ccfResNames.Rd |only rMEA-1.1.0/rMEA/man/cohens_d.Rd |only rMEA-1.1.0/rMEA/man/colTrans.Rd | 42 rMEA-1.1.0/rMEA/man/diagnosticPlot.Rd | 66 rMEA-1.1.0/rMEA/man/getCCF.Rd |only rMEA-1.1.0/rMEA/man/id.Rd |only rMEA-1.1.0/rMEA/man/lagNames.Rd |only rMEA-1.1.0/rMEA/man/lines.MEA.Rd |only rMEA-1.1.0/rMEA/man/plot.MEA.Rd | 85 rMEA-1.1.0/rMEA/man/readMEA.Rd | 153 rMEA-1.1.0/rMEA/man/setGroup.Rd | 54 rMEA-1.1.0/rMEA/man/shuffle.Rd | 80 rMEA-1.1.0/rMEA/man/timeMaster.Rd | 58 rMEA-1.1.0/rMEA/man/writeMEA.Rd | 90 rMEA-1.1.0/rMEA/tools/TODO.Rmd |only rMEA-1.1.0/rMEA/tools/TODO.md |only rMEA-1.1.0/rMEA/tools/readme/README-example-1.png |binary rMEA-1.1.0/rMEA/tools/readme/README-example-2.png |binary rMEA-1.1.0/rMEA/tools/readme/README-example-3.png |binary rMEA-1.1.0/rMEA/tools/readme/README-example-4.png |binary rMEA-1.1.0/rMEA/tools/readme/README-example-5.png |binary rMEA-1.1.0/rMEA/tools/readme/README-example-6.png |binary 67 files changed, 303256 insertions(+), 302958 deletions(-)
Title: Tools for Analysing UK Politics
Description: Provides various tools for analysing UK political data,
including creating political cartograms and retrieving data.
Author: Evan Odell [aut, cre] (<https://orcid.org/0000-0003-1845-808X>)
Maintainer: Evan Odell <evanodell91@gmail.com>
Diff between parlitools versions 0.3.0 dated 2019-01-07 and 0.3.1 dated 2019-03-22
parlitools-0.3.0/parlitools/man/bes.Rd |only parlitools-0.3.1/parlitools/DESCRIPTION | 9 parlitools-0.3.1/parlitools/LICENSE | 4 parlitools-0.3.1/parlitools/MD5 | 100 parlitools-0.3.1/parlitools/NAMESPACE | 36 parlitools-0.3.1/parlitools/NEWS.md | 7 parlitools-0.3.1/parlitools/R/council_seats.R | 350 parlitools-0.3.1/parlitools/R/current_mps.R | 2 parlitools-0.3.1/parlitools/R/data.R | 29 parlitools-0.3.1/parlitools/R/mps_on_date.R | 7 parlitools-0.3.1/parlitools/R/parlitools-package.R | 32 parlitools-0.3.1/parlitools/R/parlitools_tidy.R | 236 parlitools-0.3.1/parlitools/README.md | 228 parlitools-0.3.1/parlitools/build/vignette.rds |binary parlitools-0.3.1/parlitools/data/datalist | 16 parlitools-0.3.1/parlitools/data/leave_votes_west.rda |binary parlitools-0.3.1/parlitools/inst/CITATION | 1 parlitools-0.3.1/parlitools/inst/doc/bes-2015.Rmd | 222 parlitools-0.3.1/parlitools/inst/doc/bes-2015.html | 1433 - parlitools-0.3.1/parlitools/inst/doc/bes-2017.Rmd | 282 parlitools-0.3.1/parlitools/inst/doc/bes-2017.html | 1743 + parlitools-0.3.1/parlitools/inst/doc/census-11.Rmd | 418 parlitools-0.3.1/parlitools/inst/doc/census-11.html | 2809 +-- parlitools-0.3.1/parlitools/inst/doc/introduction.R | 215 parlitools-0.3.1/parlitools/inst/doc/introduction.Rmd | 23 parlitools-0.3.1/parlitools/inst/doc/introduction.html | 8722 +++++----- parlitools-0.3.1/parlitools/inst/doc/mapping-local-authorities.R | 100 parlitools-0.3.1/parlitools/inst/doc/mapping-local-authorities.Rmd | 132 parlitools-0.3.1/parlitools/inst/doc/mapping-local-authorities.html | 8503 ++++----- parlitools-0.3.1/parlitools/inst/doc/using-cartograms.R | 118 parlitools-0.3.1/parlitools/inst/doc/using-cartograms.Rmd | 166 parlitools-0.3.1/parlitools/inst/doc/using-cartograms.html | 8533 ++++----- parlitools-0.3.1/parlitools/man/bes_2015.Rd |only parlitools-0.3.1/parlitools/man/bes_2017.Rd |only parlitools-0.3.1/parlitools/man/census_11.Rd |only parlitools-0.3.1/parlitools/man/council_seats.Rd | 78 parlitools-0.3.1/parlitools/man/current_mps.Rd | 60 parlitools-0.3.1/parlitools/man/la_codes.Rd | 52 parlitools-0.3.1/parlitools/man/leave_votes_west.Rd | 86 parlitools-0.3.1/parlitools/man/maps.Rd | 80 parlitools-0.3.1/parlitools/man/mps_on_date.Rd | 113 parlitools-0.3.1/parlitools/man/parlitools.Rd | 22 parlitools-0.3.1/parlitools/man/party_colour.Rd | 56 parlitools-0.3.1/parlitools/tests/testthat.R | 8 parlitools-0.3.1/parlitools/tests/testthat/test-council_seats.R | 18 parlitools-0.3.1/parlitools/tests/testthat/test_current_mps.R | 22 parlitools-0.3.1/parlitools/tests/testthat/test_mps_on_date.R | 56 parlitools-0.3.1/parlitools/vignettes/bes-2015.Rmd | 222 parlitools-0.3.1/parlitools/vignettes/bes-2017.Rmd | 282 parlitools-0.3.1/parlitools/vignettes/census-11.Rmd | 418 parlitools-0.3.1/parlitools/vignettes/introduction.Rmd | 23 parlitools-0.3.1/parlitools/vignettes/mapping-local-authorities.Rmd | 132 parlitools-0.3.1/parlitools/vignettes/using-cartograms.Rmd | 166 53 files changed, 18245 insertions(+), 18125 deletions(-)
Title: Markov Chain Models for Phylogenetic Trees
Description: Allows for fitting of maximum likelihood models using Markov chains
on phylogenetic trees for analysis of discrete character data. Examples of such
discrete character data include restriction sites, gene family presence/absence,
intron presence/absence, and gene family size data. Hypothesis-driven user-
specified substitution rate matrices can be estimated. Allows for biologically
realistic models combining constrained substitution rate matrices, site rate
variation, site partitioning, branch-specific rates, allowing for non-stationary
prior root probabilities, correcting for sampling bias, etc. See Dang and Golding
(2016) <doi:10.1093/bioinformatics/btv541> for more details.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>
Diff between markophylo versions 1.0.6 dated 2018-01-30 and 1.0.7 dated 2019-03-22
DESCRIPTION | 8 +-- MD5 | 14 ++--- NAMESPACE | 2 NEWS | 6 ++ R/custom-general14.R | 2 R/estimatesrates_f.R | 2 build/vignette.rds |binary inst/doc/estimaterates.html | 117 ++++++++++++++++++++++++++------------------ 8 files changed, 91 insertions(+), 60 deletions(-)
Title: Interim Monitoring Using Adaptively Weighted Log-Rank Test in
Clinical Trials
Description: For any spending function specified by the user, this
package provides corresponding boundaries for interim testing using
the adaptively weighted log-rank test developed by Yang and Prentice
(2010 <doi:10.1111/j.1541-0420.2009.01243.x>).
The package uses a re-sampling method to obtain stopping boundaries
at the interim looks.The output consists of stopping boundaries
and observed values of the test statistics at the interim looks,
along with nominal p-values defined as the probability of the test
exceeding the specific observed test statistic value or critical
value, regardless of the test behavior at other looks.
The asymptotic validity of the stopping boundaries is established
in Yang (2018 <doi:10.1002/sim.7958>).
Author: Daewoo Pak and Song Yang
Maintainer: Daewoo Pak <heavyrain.pak@gmail.com>
Diff between YPInterimTesting versions 1.0.1 dated 2019-03-15 and 1.0.2 dated 2019-03-22
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ R/ypinterim.default.R | 3 ++- 4 files changed, 11 insertions(+), 7 deletions(-)
More information about YPInterimTesting at CRAN
Permanent link
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.1.0 dated 2018-08-25 and 2.2.0 dated 2019-03-22
strvalidator-2.1.0/strvalidator/R/calculateAllele.r |only strvalidator-2.1.0/strvalidator/R/calculateSpike.r |only strvalidator-2.1.0/strvalidator/R/calculateSpike_gui.r |only strvalidator-2.2.0/strvalidator/DESCRIPTION | 15 strvalidator-2.2.0/strvalidator/MD5 | 402 strvalidator-2.2.0/strvalidator/NAMESPACE | 3 strvalidator-2.2.0/strvalidator/NEWS | 68 strvalidator-2.2.0/strvalidator/R/addColor.r | 266 strvalidator-2.2.0/strvalidator/R/addData.r | 215 strvalidator-2.2.0/strvalidator/R/addData_gui.r | 615 - strvalidator-2.2.0/strvalidator/R/addDye_gui.r | 467 - strvalidator-2.2.0/strvalidator/R/addMarker.r | 105 strvalidator-2.2.0/strvalidator/R/addMarker_gui.r | 377 strvalidator-2.2.0/strvalidator/R/addOrder.r | 80 strvalidator-2.2.0/strvalidator/R/addSize.r | 166 strvalidator-2.2.0/strvalidator/R/addSize_gui.r | 388 strvalidator-2.2.0/strvalidator/R/auditTrail.R | 130 strvalidator-2.2.0/strvalidator/R/calculateAT.r | 438 - strvalidator-2.2.0/strvalidator/R/calculateAT6.r | 229 strvalidator-2.2.0/strvalidator/R/calculateAT6_gui.r | 621 - strvalidator-2.2.0/strvalidator/R/calculateAT_gui.r | 1208 +- strvalidator-2.2.0/strvalidator/R/calculateAllT.r | 319 strvalidator-2.2.0/strvalidator/R/calculateAllT_gui.r | 372 strvalidator-2.2.0/strvalidator/R/calculateAllele.R |only strvalidator-2.2.0/strvalidator/R/calculateAllele_gui.r | 299 strvalidator-2.2.0/strvalidator/R/calculateCapillary.r | 298 strvalidator-2.2.0/strvalidator/R/calculateCapillary_gui.r | 441 - strvalidator-2.2.0/strvalidator/R/calculateConcordance.r | 282 strvalidator-2.2.0/strvalidator/R/calculateConcordance_gui.r | 591 - strvalidator-2.2.0/strvalidator/R/calculateCopies.r | 119 strvalidator-2.2.0/strvalidator/R/calculateCopies_gui.r | 369 strvalidator-2.2.0/strvalidator/R/calculateDropout.r | 681 - strvalidator-2.2.0/strvalidator/R/calculateDropout_gui.r | 712 - strvalidator-2.2.0/strvalidator/R/calculateHb.r | 238 strvalidator-2.2.0/strvalidator/R/calculateHb_gui.r | 627 - strvalidator-2.2.0/strvalidator/R/calculateHeight.r | 349 strvalidator-2.2.0/strvalidator/R/calculateHeight_gui.r | 667 - strvalidator-2.2.0/strvalidator/R/calculateLb.r | 379 strvalidator-2.2.0/strvalidator/R/calculateLb_gui.r | 822 + strvalidator-2.2.0/strvalidator/R/calculateMixture.r | 414 strvalidator-2.2.0/strvalidator/R/calculateMixture_gui.r | 629 - strvalidator-2.2.0/strvalidator/R/calculateOL.r | 188 strvalidator-2.2.0/strvalidator/R/calculateOL_gui.r | 412 strvalidator-2.2.0/strvalidator/R/calculateOverlap.r | 332 strvalidator-2.2.0/strvalidator/R/calculateOverlap_gui.r | 606 - strvalidator-2.2.0/strvalidator/R/calculatePeaks.r | 147 strvalidator-2.2.0/strvalidator/R/calculatePeaks_gui.r | 442 - strvalidator-2.2.0/strvalidator/R/calculatePullup.r | 334 strvalidator-2.2.0/strvalidator/R/calculatePullup_gui.r | 692 - strvalidator-2.2.0/strvalidator/R/calculateRatio.r | 258 strvalidator-2.2.0/strvalidator/R/calculateRatio_gui.r | 719 - strvalidator-2.2.0/strvalidator/R/calculateResultType.r | 389 strvalidator-2.2.0/strvalidator/R/calculateResultType_gui.r | 514 - strvalidator-2.2.0/strvalidator/R/calculateSlope.r | 215 strvalidator-2.2.0/strvalidator/R/calculateSlope_gui.r | 586 - strvalidator-2.2.0/strvalidator/R/calculateSpike.R |only strvalidator-2.2.0/strvalidator/R/calculateSpike_gui.R |only strvalidator-2.2.0/strvalidator/R/calculateStutter.r | 422 strvalidator-2.2.0/strvalidator/R/calculateStutter_gui.r | 673 - strvalidator-2.2.0/strvalidator/R/calculateT.r | 148 strvalidator-2.2.0/strvalidator/R/checkDataset.r | 119 strvalidator-2.2.0/strvalidator/R/checkSubset.r | 96 strvalidator-2.2.0/strvalidator/R/checkSubset_gui.r | 446 - strvalidator-2.2.0/strvalidator/R/colConvert.r | 33 strvalidator-2.2.0/strvalidator/R/colNames.r | 94 strvalidator-2.2.0/strvalidator/R/columns.r | 131 strvalidator-2.2.0/strvalidator/R/columns_gui.r | 518 - strvalidator-2.2.0/strvalidator/R/combineBinsAndPanels.r | 86 strvalidator-2.2.0/strvalidator/R/combine_gui.r | 323 strvalidator-2.2.0/strvalidator/R/cropData_gui.r | 885 +- strvalidator-2.2.0/strvalidator/R/detectKit.r | 483 - strvalidator-2.2.0/strvalidator/R/editData_gui.r | 710 - strvalidator-2.2.0/strvalidator/R/export.r | 333 strvalidator-2.2.0/strvalidator/R/export_gui.r | 573 - strvalidator-2.2.0/strvalidator/R/filterProfile.r | 644 - strvalidator-2.2.0/strvalidator/R/filterProfile_gui.r | 747 - strvalidator-2.2.0/strvalidator/R/generateEPG.r | 442 - strvalidator-2.2.0/strvalidator/R/generateEPG_gui.r | 720 - strvalidator-2.2.0/strvalidator/R/getDb.r | 90 strvalidator-2.2.0/strvalidator/R/getKit.r | 389 strvalidator-2.2.0/strvalidator/R/ggsave_gui.r | 828 + strvalidator-2.2.0/strvalidator/R/globals.R | 44 strvalidator-2.2.0/strvalidator/R/guessProfile.r | 147 strvalidator-2.2.0/strvalidator/R/guessProfile_gui.r | 420 strvalidator-2.2.0/strvalidator/R/heightToPeak.r | 95 strvalidator-2.2.0/strvalidator/R/hooks.r | 6 strvalidator-2.2.0/strvalidator/R/import.r | 192 strvalidator-2.2.0/strvalidator/R/import_gui.r | 758 - strvalidator-2.2.0/strvalidator/R/listObjects.r | 48 strvalidator-2.2.0/strvalidator/R/makeKit_gui.r | 879 +- strvalidator-2.2.0/strvalidator/R/maskAT.r | 382 strvalidator-2.2.0/strvalidator/R/modelDropout_gui.r | 1715 ++-- strvalidator-2.2.0/strvalidator/R/plotAT_gui.r | 827 + strvalidator-2.2.0/strvalidator/R/plotBalance_gui.r | 1585 +-- strvalidator-2.2.0/strvalidator/R/plotCapillary_gui.r | 945 +- strvalidator-2.2.0/strvalidator/R/plotContamination_gui.r | 614 - strvalidator-2.2.0/strvalidator/R/plotDistribution_gui.r | 1226 +- strvalidator-2.2.0/strvalidator/R/plotDropout_gui.r | 1404 +-- strvalidator-2.2.0/strvalidator/R/plotGroups_gui.r | 743 - strvalidator-2.2.0/strvalidator/R/plotKit_gui.r | 614 - strvalidator-2.2.0/strvalidator/R/plotPeaks_gui.r | 608 - strvalidator-2.2.0/strvalidator/R/plotPrecision_gui.r | 1435 +-- strvalidator-2.2.0/strvalidator/R/plotPullup_gui.r | 1278 +- strvalidator-2.2.0/strvalidator/R/plotRatio_gui.r | 687 - strvalidator-2.2.0/strvalidator/R/plotResultType_gui.r | 637 - strvalidator-2.2.0/strvalidator/R/plotSlope_gui.r | 655 - strvalidator-2.2.0/strvalidator/R/plotStutter_gui.r | 1158 +- strvalidator-2.2.0/strvalidator/R/readBinsFile.r | 134 strvalidator-2.2.0/strvalidator/R/readPanelsFile.r | 118 strvalidator-2.2.0/strvalidator/R/removeArtefact.r | 144 strvalidator-2.2.0/strvalidator/R/removeArtefact_gui.r | 319 strvalidator-2.2.0/strvalidator/R/removeSpike.r | 167 strvalidator-2.2.0/strvalidator/R/removeSpike_gui.r | 300 strvalidator-2.2.0/strvalidator/R/saveObject.r | 166 strvalidator-2.2.0/strvalidator/R/scrambleAlleles.r | 107 strvalidator-2.2.0/strvalidator/R/slim.r | 199 strvalidator-2.2.0/strvalidator/R/slim_gui.r | 693 - strvalidator-2.2.0/strvalidator/R/sortMarker.r | 199 strvalidator-2.2.0/strvalidator/R/strvalidator-package.r | 95 strvalidator-2.2.0/strvalidator/R/strvalidator.r | 4277 +++++----- strvalidator-2.2.0/strvalidator/R/tableBalance.r | 130 strvalidator-2.2.0/strvalidator/R/tableBalance_gui.r | 396 strvalidator-2.2.0/strvalidator/R/tableCapillary.r | 342 strvalidator-2.2.0/strvalidator/R/tableCapillary_gui.r | 392 strvalidator-2.2.0/strvalidator/R/tablePrecision.r | 160 strvalidator-2.2.0/strvalidator/R/tablePrecision_gui.r | 912 +- strvalidator-2.2.0/strvalidator/R/tableStutter.r | 130 strvalidator-2.2.0/strvalidator/R/tableStutter_gui.r | 402 strvalidator-2.2.0/strvalidator/R/trim.r | 290 strvalidator-2.2.0/strvalidator/R/trim_gui.r | 861 +- strvalidator-2.2.0/strvalidator/README.md | 50 strvalidator-2.2.0/strvalidator/man/addColor.Rd | 10 strvalidator-2.2.0/strvalidator/man/addData.Rd | 6 strvalidator-2.2.0/strvalidator/man/addData_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/addMarker_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/auditTrail.Rd | 6 strvalidator-2.2.0/strvalidator/man/calculateAT.Rd | 4 strvalidator-2.2.0/strvalidator/man/calculateAllT.Rd | 10 strvalidator-2.2.0/strvalidator/man/calculateAllele.Rd | 4 strvalidator-2.2.0/strvalidator/man/calculateCapillary_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateConcordance.Rd | 4 strvalidator-2.2.0/strvalidator/man/calculateDropout.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateHb.Rd | 4 strvalidator-2.2.0/strvalidator/man/calculateHeight_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateLb.Rd | 5 strvalidator-2.2.0/strvalidator/man/calculateMixture.Rd | 8 strvalidator-2.2.0/strvalidator/man/calculateOverlap.Rd | 4 strvalidator-2.2.0/strvalidator/man/calculateOverlap_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculatePeaks.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculatePullup.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateRatio.Rd | 12 strvalidator-2.2.0/strvalidator/man/calculateResultType_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateSpike.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateSpike_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateStutter.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateStutter_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/calculateT.Rd | 2 strvalidator-2.2.0/strvalidator/man/checkSubset.Rd | 2 strvalidator-2.2.0/strvalidator/man/columns.Rd | 8 strvalidator-2.2.0/strvalidator/man/combineBinsAndPanels.Rd | 4 strvalidator-2.2.0/strvalidator/man/export.Rd | 2 strvalidator-2.2.0/strvalidator/man/export_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/filterProfile.Rd | 2 strvalidator-2.2.0/strvalidator/man/generateEPG_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/getKit.Rd | 4 strvalidator-2.2.0/strvalidator/man/guessProfile.Rd | 2 strvalidator-2.2.0/strvalidator/man/import_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/listObjects.Rd | 5 strvalidator-2.2.0/strvalidator/man/makeKit_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/maskAT.Rd | 2 strvalidator-2.2.0/strvalidator/man/modelDropout_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/plotContamination_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/plotDropout_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/plotGroups_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/plotPeaks_gui.Rd | 4 strvalidator-2.2.0/strvalidator/man/plotRatio_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/plotResultType_gui.Rd | 4 strvalidator-2.2.0/strvalidator/man/plotStutter_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/saveObject.Rd | 2 strvalidator-2.2.0/strvalidator/man/slim_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/sortMarker.Rd | 2 strvalidator-2.2.0/strvalidator/man/strvalidator-package.Rd | 4 strvalidator-2.2.0/strvalidator/man/strvalidator.Rd | 3 strvalidator-2.2.0/strvalidator/man/tableBalance_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/tableCapillary.Rd | 2 strvalidator-2.2.0/strvalidator/man/tableCapillary_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/tablePrecision_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/tableStutter_gui.Rd | 2 strvalidator-2.2.0/strvalidator/man/trim.Rd | 2 strvalidator-2.2.0/strvalidator/man/trim_gui.Rd | 2 strvalidator-2.2.0/strvalidator/tests/testthat.R | 4 strvalidator-2.2.0/strvalidator/tests/testthat/test-addSize.r | 152 strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateAllT.r | 451 - strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateConcordance.r | 779 - strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateDropout.r | 392 strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateHb.r | 662 - strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateHeight.r | 536 - strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateLb.r | 1011 +- strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateMixture.r | 1027 +- strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateOL.r | 235 strvalidator-2.2.0/strvalidator/tests/testthat/test-calculateStutter.r | 559 - strvalidator-2.2.0/strvalidator/tests/testthat/test-filterProfile.r | 965 +- strvalidator-2.2.0/strvalidator/tests/testthat/test-heightToPeak.r | 122 strvalidator-2.2.0/strvalidator/tests/testthat/test-tableBalance.r | 170 strvalidator-2.2.0/strvalidator/tests/testthat/test-trim.r | 336 205 files changed, 35364 insertions(+), 32481 deletions(-)
Title: Toolkit for Encryption, Signatures and Certificates Based on
OpenSSL
Description: Bindings to OpenSSL libssl and libcrypto, plus custom SSH key parsers.
Supports RSA, DSA and EC curves P-256, P-384 and P-521. Cryptographic signatures
can either be created and verified manually or via x509 certificates. AES can be
used in cbc, ctr or gcm mode for symmetric encryption; RSA for asymmetric (public
key) encryption or EC for Diffie Hellman. High-level envelope functions combine
RSA and AES for encrypting arbitrary sized data. Other utilities include key
generators, hash functions (md5, sha1, sha256, etc), base64 encoder, a secure
random number generator, and 'bignum' math methods for manually performing
crypto calculations on large multibyte integers.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Oliver Keyes [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between openssl versions 1.2.2 dated 2019-03-01 and 1.3 dated 2019-03-22
openssl-1.2.2/openssl/tests/keys/id_rsa.sshpem1 |only openssl-1.3/openssl/DESCRIPTION | 8 openssl-1.3/openssl/LICENSE | 2 openssl-1.3/openssl/MD5 | 66 +++-- openssl-1.3/openssl/NAMESPACE | 3 openssl-1.3/openssl/NEWS | 4 openssl-1.3/openssl/R/bcrypt.R |only openssl-1.3/openssl/R/build.R | 29 +- openssl-1.3/openssl/R/read.R | 4 openssl-1.3/openssl/R/ssh2.R | 200 ++++++++++++++-- openssl-1.3/openssl/build/vignette.rds |binary openssl-1.3/openssl/configure | 2 openssl-1.3/openssl/inst/doc/bignum.html | 41 +-- openssl-1.3/openssl/inst/doc/crypto_hashing.html | 21 + openssl-1.3/openssl/inst/doc/keys.html | 55 ++-- openssl-1.3/openssl/inst/doc/secure_rng.html | 31 +- openssl-1.3/openssl/man/pbkdf.Rd |only openssl-1.3/openssl/src/Makevars.in | 13 - openssl-1.3/openssl/src/Makevars.win | 26 +- openssl-1.3/openssl/src/bcrypt |only openssl-1.3/openssl/src/openssh.c | 16 + openssl-1.3/openssl/src/pbkdf.c |only openssl-1.3/openssl/tests/keys/id_dsa.openssh |only openssl-1.3/openssl/tests/keys/id_dsa.openssh.pw |only openssl-1.3/openssl/tests/keys/id_dsa.sshpub |only openssl-1.3/openssl/tests/keys/id_ecdsa.openssh |only openssl-1.3/openssl/tests/keys/id_ecdsa.openssh.pw |only openssl-1.3/openssl/tests/keys/id_ecdsa.sshpub |only openssl-1.3/openssl/tests/keys/id_ecdsa384.openssh |only openssl-1.3/openssl/tests/keys/id_ecdsa384.openssh.pw |only openssl-1.3/openssl/tests/keys/id_ecdsa384.sshpub |only openssl-1.3/openssl/tests/keys/id_ecdsa521.openssh |only openssl-1.3/openssl/tests/keys/id_ecdsa521.openssh.pw |only openssl-1.3/openssl/tests/keys/id_ecdsa521.sshpub |only openssl-1.3/openssl/tests/keys/id_ed25519.openssh |only openssl-1.3/openssl/tests/keys/id_ed25519.sshpub |only openssl-1.3/openssl/tests/keys/id_rsa.openssh |only openssl-1.3/openssl/tests/keys/id_rsa.openssh.pw |only openssl-1.3/openssl/tests/keys/id_rsa.sshpub |only openssl-1.3/openssl/tests/testthat/test_keys_dsa.R | 9 openssl-1.3/openssl/tests/testthat/test_keys_ecdsa.R | 9 openssl-1.3/openssl/tests/testthat/test_keys_ecdsa384.R | 8 openssl-1.3/openssl/tests/testthat/test_keys_ecdsa521.R | 8 openssl-1.3/openssl/tests/testthat/test_keys_rsa.R | 6 44 files changed, 420 insertions(+), 141 deletions(-)
Title: Mediterranean Forest Simulation
Description: Functions to simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>].
Author: Miquel De Cáceres [aut, cre],
Víctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between medfate versions 0.7.3 dated 2019-03-19 and 0.7.4 dated 2019-03-22
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS | 5 +++++ inst/doc/ComplexWaterBalance.html | 4 ++-- inst/doc/ForestGrowth.html | 4 ++-- inst/doc/PackageOverview.html | 4 ++-- inst/doc/SimpleWaterBalance.html | 12 ++++++------ man/spwbpoints.Rd | 4 +++- src/biophysicsutils.cpp | 4 ++-- src/fuelmoisture.cpp | 2 -- src/growth.cpp | 4 ++-- src/hydraulics.cpp | 1 - src/incgamma.cpp | 4 ++-- src/soil.cpp | 8 ++++---- src/spwb.cpp | 32 ++++++++++++++++++++++---------- src/transpiration.cpp | 2 +- 16 files changed, 71 insertions(+), 55 deletions(-)
Title: Insertion Deletion Analysis While Accounting for Possible
Missing Data
Description: Genome-wide gene insertion and deletion rates can be modelled in a maximum
likelihood framework with the additional flexibility of modelling potential missing
data using the models included within. These models simultaneously estimate insertion
and deletion (indel) rates of gene families and proportions of "missing" data for
(multiple) taxa of interest. The likelihood framework is utilized for parameter
estimation. A phylogenetic tree of the taxa and gene presence/absence patterns
(with data ordered by the tips of the tree) are required. See Dang et al.
(2016) <doi:10.1534/genetics.116.191973> for more details.
Author: Utkarsh J. Dang and G. Brian Golding
Maintainer: Utkarsh J. Dang <udang@binghamton.edu>
Diff between indelmiss versions 1.0.8 dated 2018-01-30 and 1.0.9 dated 2019-03-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 2 +- NEWS | 6 ++++++ R/indel-functions.R | 2 +- tests/testthat/test_main.R | 2 +- 6 files changed, 18 insertions(+), 12 deletions(-)
Title: Cognitive Models
Description: Hierarchical Bayesian models. The package provides tools to fit two popular response time models, using population-based Markov Chain Monte Carlo (pMCMC). The paper by Heathcote, Lin, Reynolds, Strickland, Gretton, and Matzke (2018, <doi:10.3758/s13428-018-1067-y>) describes the prototype of the package.
Author: Yi-Shin Lin [aut, cre], Andrew Heathcote [aut]
Maintainer: Yi-Shin Lin <yishinlin001@gmail.com>
Diff between ggdmc versions 0.2.5.2 dated 2018-09-01 and 0.2.5.6 dated 2019-03-22
ggdmc-0.2.5.2/ggdmc/NEWS |only ggdmc-0.2.5.2/ggdmc/R/likelihood.R |only ggdmc-0.2.5.2/ggdmc/inst/CITATION |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/clba.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/ddm.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/density.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/hyper.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/pda.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/prior.hpp |only ggdmc-0.2.5.2/ggdmc/inst/include/ggdmc/utils.hpp |only ggdmc-0.2.5.2/ggdmc/man/CheckDMI.Rd |only ggdmc-0.2.5.2/ggdmc/man/CheckRJ.Rd |only ggdmc-0.2.5.2/ggdmc/man/ConvertChains2.Rd |only ggdmc-0.2.5.2/ggdmc/man/GetConstIdx.Rd |only ggdmc-0.2.5.2/ggdmc/man/GetGamma.Rd |only ggdmc-0.2.5.2/ggdmc/man/GetTheta0.Rd |only ggdmc-0.2.5.2/ggdmc/man/MakeForce.Rd |only ggdmc-0.2.5.2/ggdmc/man/MakeLevelArray.Rd |only ggdmc-0.2.5.2/ggdmc/man/PickChains.Rd |only ggdmc-0.2.5.2/ggdmc/man/ac.Rd |only ggdmc-0.2.5.2/ggdmc/man/assign_pp.Rd |only ggdmc-0.2.5.2/ggdmc/man/autocor.Rd |only ggdmc-0.2.5.2/ggdmc/man/cellIdx2Mat.Rd |only ggdmc-0.2.5.2/ggdmc/man/censor.Rd |only ggdmc-0.2.5.2/ggdmc/man/checkddm2.Rd |only ggdmc-0.2.5.2/ggdmc/man/dprior.Rd |only ggdmc-0.2.5.2/ggdmc/man/fac2df.Rd |only ggdmc-0.2.5.2/ggdmc/man/g_minus.Rd |only ggdmc-0.2.5.2/ggdmc/man/hsumloglike.Rd |only ggdmc-0.2.5.2/ggdmc/man/ismanymodels.Rd |only ggdmc-0.2.5.2/ggdmc/man/likelihood_norm.Rd |only ggdmc-0.2.5.2/ggdmc/man/maker.Rd |only ggdmc-0.2.5.2/ggdmc/man/n1PDF_cnorm.Rd |only ggdmc-0.2.5.2/ggdmc/man/n1PDF_gpu.Rd |only ggdmc-0.2.5.2/ggdmc/man/n1PDF_plba0_gpu.Rd |only ggdmc-0.2.5.2/ggdmc/man/pairs.model.Rd |only ggdmc-0.2.5.2/ggdmc/man/profile.model.Rd |only ggdmc-0.2.5.2/ggdmc/man/rca.Rd |only ggdmc-0.2.5.2/ggdmc/man/removet0.Rd |only ggdmc-0.2.5.2/ggdmc/man/rlnr.Rd |only ggdmc-0.2.5.2/ggdmc/man/rplba1R.Rd |only ggdmc-0.2.5.2/ggdmc/man/run.Rd |only ggdmc-0.2.5.2/ggdmc/man/run_many.Rd |only ggdmc-0.2.5.2/ggdmc/man/run_one.Rd |only ggdmc-0.2.5.2/ggdmc/man/score.Rd |only ggdmc-0.2.5.2/ggdmc/man/spdf.Rd |only ggdmc-0.2.5.2/ggdmc/man/sumloglike.Rd |only ggdmc-0.2.5.2/ggdmc/src/clba.cpp |only ggdmc-0.2.5.2/ggdmc/src/ddm.cpp |only ggdmc-0.2.5.2/ggdmc/src/density.cpp |only ggdmc-0.2.5.2/ggdmc/src/hyper.cpp |only ggdmc-0.2.5.2/ggdmc/src/initialise.cpp |only ggdmc-0.2.5.2/ggdmc/src/lnr.cpp |only ggdmc-0.2.5.2/ggdmc/src/pda.cpp |only ggdmc-0.2.5.2/ggdmc/src/prior.cpp |only ggdmc-0.2.5.2/ggdmc/src/run.cpp |only ggdmc-0.2.5.2/ggdmc/src/utils.cpp |only ggdmc-0.2.5.6/ggdmc/DESCRIPTION | 21 ggdmc-0.2.5.6/ggdmc/MD5 | 196 - ggdmc-0.2.5.6/ggdmc/NAMESPACE | 90 ggdmc-0.2.5.6/ggdmc/R/RcppExports.R | 821 -------- ggdmc-0.2.5.6/ggdmc/R/analysis.R | 437 ++-- ggdmc-0.2.5.6/ggdmc/R/model.R | 1304 ++++-------- ggdmc-0.2.5.6/ggdmc/R/plotting.R | 529 ++--- ggdmc-0.2.5.6/ggdmc/R/prior.R | 402 +++ ggdmc-0.2.5.6/ggdmc/R/random.R | 792 ++----- ggdmc-0.2.5.6/ggdmc/R/sampling.R | 850 ++------ ggdmc-0.2.5.6/ggdmc/R/utils.R | 422 ---- ggdmc-0.2.5.6/ggdmc/README.md | 618 ++---- ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc.hpp | 17 ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Design.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/FCalculator.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/LBA.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Likelihood.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Parameters.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Phi.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Prior.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/Sampler.hpp |only ggdmc-0.2.5.6/ggdmc/inst/include/ggdmc/tnorm.hpp | 111 - ggdmc-0.2.5.6/ggdmc/man/BuildDMI.Rd | 22 ggdmc-0.2.5.6/ggdmc/man/BuildModel.Rd | 46 ggdmc-0.2.5.6/ggdmc/man/BuildPrior.Rd | 2 ggdmc-0.2.5.6/ggdmc/man/ConvertChains.Rd | 4 ggdmc-0.2.5.6/ggdmc/man/DIC.Rd |only ggdmc-0.2.5.6/ggdmc/man/GetNsim.Rd | 17 ggdmc-0.2.5.6/ggdmc/man/GetPNames.Rd | 4 ggdmc-0.2.5.6/ggdmc/man/GetParameterMatrix.Rd | 32 ggdmc-0.2.5.6/ggdmc/man/PickStuck.Rd | 2 ggdmc-0.2.5.6/ggdmc/man/StartNewsamples.Rd | 173 - ggdmc-0.2.5.6/ggdmc/man/TableParameters.Rd | 18 ggdmc-0.2.5.6/ggdmc/man/check_pvec.Rd | 9 ggdmc-0.2.5.6/ggdmc/man/dbeta_lu.Rd | 21 ggdmc-0.2.5.6/ggdmc/man/dcauchy_l.Rd | 21 ggdmc-0.2.5.6/ggdmc/man/dconstant.Rd | 19 ggdmc-0.2.5.6/ggdmc/man/deviance.model.Rd |only ggdmc-0.2.5.6/ggdmc/man/dgamma_l.Rd | 21 ggdmc-0.2.5.6/ggdmc/man/dlnorm_l.Rd | 21 ggdmc-0.2.5.6/ggdmc/man/dtnorm.Rd | 16 ggdmc-0.2.5.6/ggdmc/man/effectiveSize.Rd | 14 ggdmc-0.2.5.6/ggdmc/man/gelman.Rd | 4 ggdmc-0.2.5.6/ggdmc/man/get_os.Rd | 4 ggdmc-0.2.5.6/ggdmc/man/ggdmc.Rd | 17 ggdmc-0.2.5.6/ggdmc/man/iseffective.Rd | 9 ggdmc-0.2.5.6/ggdmc/man/isflat.Rd | 4 ggdmc-0.2.5.6/ggdmc/man/ismixed.Rd | 6 ggdmc-0.2.5.6/ggdmc/man/isstuck.Rd | 20 ggdmc-0.2.5.6/ggdmc/man/likelihood.Rd |only ggdmc-0.2.5.6/ggdmc/man/plot_prior.Rd | 45 ggdmc-0.2.5.6/ggdmc/man/random.Rd | 16 ggdmc-0.2.5.6/ggdmc/man/rlba_norm.Rd |only ggdmc-0.2.5.6/ggdmc/man/rprior.Rd | 10 ggdmc-0.2.5.6/ggdmc/man/simulate.model.Rd | 62 ggdmc-0.2.5.6/ggdmc/man/summary.model.Rd | 23 ggdmc-0.2.5.6/ggdmc/man/summary_mcmc_list.Rd | 2 ggdmc-0.2.5.6/ggdmc/man/theta2mcmclist.Rd | 33 ggdmc-0.2.5.6/ggdmc/src/Density.cpp |only ggdmc-0.2.5.6/ggdmc/src/FCalculator.cpp |only ggdmc-0.2.5.6/ggdmc/src/Initialise.cpp |only ggdmc-0.2.5.6/ggdmc/src/LBA.cpp |only ggdmc-0.2.5.6/ggdmc/src/Makevars | 11 ggdmc-0.2.5.6/ggdmc/src/Makevars.win | 12 ggdmc-0.2.5.6/ggdmc/src/Parameters.cpp |only ggdmc-0.2.5.6/ggdmc/src/Prior.cpp |only ggdmc-0.2.5.6/ggdmc/src/RcppExports.cpp | 1721 +---------------- ggdmc-0.2.5.6/ggdmc/src/tnorm.cpp | 306 +-- ggdmc-0.2.5.6/ggdmc/tests |only 126 files changed, 2889 insertions(+), 6488 deletions(-)
Title: Fast, Dependency-Free Geodesic Distance Calculations
Description: Dependency-free, ultra fast calculation of geodesic distances.
Includes the reference nanometre-accuracy geodesic distances of Karney
(2013) <doi:10.1007/s00190-012-0578-z>, as used by the 'sf' package, as well
as Haversine and Vincenty distances. Default distance measure is the "Mapbox
cheap ruler" which is generally more accurate than Haversine or Vincenty for
distances out to a few hundred kilometres, and is considerably faster. The
main function accepts one or two inputs in almost any generic rectangular
form, and returns either matrices of pairwise distances, or vectors of
sequential distances.
Author: Mark Padgham [aut, cre],
Michael D. Sumner [aut],
Charles F.F Karney [cph] (Original author of included code for geodesic
distances)
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between geodist versions 0.0.1 dated 2018-07-13 and 0.0.2 dated 2019-03-22
DESCRIPTION | 8 +-- MD5 | 31 ++++++++----- NAMESPACE | 16 ++++++ NEWS.md | 11 ++++ R/geodist.R | 35 +++++++++++++-- R/georange.R |only R/utils.R | 35 ++++++++++----- build/vignette.rds |binary inst/doc/geodist.html | 85 +++++++++++++++++++++++++++++++++---- man/geodist.Rd | 6 ++ man/georange.Rd |only src/dists_paired.c |only src/dists_seq.c | 6 +- src/geodist_init.c | 56 +++++++++++++++++++----- src/range_seq.c |only src/range_x.c |only src/range_xy.c |only tests/testthat/test-geodist.R | 23 ++++++++++ tests/testthat/test-georange.R |only tests/testthat/test-input-format.R | 19 ++++++++ 20 files changed, 276 insertions(+), 55 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
L. Cobo Sanchez;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
H. Heydarian;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
J. Sulavik;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
L. Yates;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.58-2 dated 2019-01-10 and 1.59-0 dated 2019-03-22
DESCRIPTION | 17 - MD5 | 340 +++++++++++++++++---------------- NAMESPACE | 32 ++- NEWS | 303 +++++++++++++++++++++++++++++ R/Jinhom.R | 77 +++++-- R/adaptive.density.R | 68 +----- R/affine.R | 64 +++--- R/alltypes.R | 18 + R/anova.mppm.R | 6 R/areadiff.R | 107 ++++------ R/blur.R | 16 - R/bw.abram.R |only R/circarcs.R |only R/close3Dpairs.R | 7 R/closepairs.R | 59 +++++ R/colourschemes.R | 38 ++- R/colourtables.R | 45 ++-- R/dclftest.R | 3 R/deldir.R | 5 R/densityAdaptiveKernel.R |only R/densityVoronoi.R |only R/densitylppVoronoi.R |only R/discarea.R | 4 R/distbdry.R | 111 ++++++---- R/edgeTrans.R | 4 R/effectfun.R | 18 - R/envelope.R | 436 +++++++++++++++++++++++++------------------ R/eval.fv.R | 4 R/ewcdf.R | 79 +++++-- R/fgk3.R | 7 R/funxy.R | 2 R/hierpair.family.R | 6 R/images.R | 148 +++++++++----- R/ippm.R | 20 + R/is.cadlag.R | 2 R/is.subset.owin.R | 30 +- R/kppm.R | 44 +++- R/leverage.R | 4 R/linearK.R | 70 +++++- R/linearKmulti.R | 121 +++++++---- R/lineardisc.R | 15 - R/linearpcf.R | 22 -- R/linearpcfmulti.R | 60 +---- R/linfun.R | 19 - R/linnet.R | 58 ++--- R/lintess.R | 96 ++++++++- R/logistic.R | 36 +-- R/lohboot.R | 140 +++++++------ R/lpp.R | 4 R/lurkmppm.R | 33 +-- R/measures.R | 10 R/mpl.R | 6 R/news.R | 10 R/nncorr.R | 59 ++++- R/nndist.R | 5 R/otherpackages.R | 47 ++-- R/pairorient.R | 4 R/pairwise.R | 6 R/parres.R | 12 - R/pcf.R | 47 ++++ R/plot.im.R | 40 +-- R/polartess.R |only R/pp3.R | 5 R/predict.ppm.R | 4 R/predictmppm.R | 18 + R/psp.R | 23 -- R/pspcross.R | 94 +++++---- R/quadclass.R | 7 R/quadrattest.R | 8 R/quantess.R | 174 +++++++++++------ R/random.R | 16 - R/randomNS.R | 10 R/relrisk.R | 2 R/rescale.R | 8 R/rmh.default.R | 4 R/rmhResolveTypes.R | 4 R/rmhmodel.R | 6 R/round.R | 8 R/saturated.R | 6 R/simulate.detPPF.R | 9 R/sparsecommon.R | 52 ++++- R/spatialcdf.R | 30 +- R/sysdata.rda |binary R/tess.R | 22 +- R/treebranches.R | 4 R/units.R | 4 R/window.R | 6 R/wingeom.R | 4 build/vignette.rds |binary demo/spatstat.R | 25 +- demo/sumfun.R | 29 ++ inst/doc/Nickname.txt | 3 inst/doc/bugfixes.Rnw | 67 ++++++ inst/doc/bugfixes.pdf |binary inst/doc/datasets.R | 2 inst/doc/datasets.Rnw | 2 inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/updates.Rnw | 201 ++++++++++++++++++- inst/doc/updates.pdf |binary man/Finhom.Rd | 13 + man/Ginhom.Rd | 13 + man/Jinhom.Rd | 13 + man/LennardJones.Rd | 7 man/adaptive.density.Rd | 90 ++------ man/alltypes.Rd | 9 man/anova.mppm.Rd | 10 man/bw.abram.Rd |only man/bw.stoyan.Rd | 7 man/bw.voronoi.Rd |only man/clusterfit.Rd | 6 man/coords.Rd | 5 man/cut.ppp.Rd | 5 man/densityAdaptiveKernel.Rd |only man/densityVoronoi.Rd |only man/densityVoronoi.lpp.Rd |only man/divide.linnet.Rd | 2 man/effectfun.Rd | 7 man/envelope.Rd | 22 +- man/envelope.lpp.Rd | 27 ++ man/envelope.pp3.Rd | 3 man/ewcdf.Rd | 28 +- man/funxy.Rd | 14 - man/integral.msr.Rd | 5 man/intersect.tess.Rd | 7 man/ippm.Rd | 3 man/kppm.Rd | 16 - man/laslett.Rd | 3 man/latest.news.Rd | 18 + man/lineardisc.Rd | 3 man/lineartileindex.Rd |only man/linequad.Rd | 13 + man/linfun.Rd | 40 ++- man/lohboot.Rd | 3 man/nestsplit.Rd | 9 man/nncorr.Rd | 19 + man/nndist.Rd | 19 + man/pairorient.Rd | 24 +- man/parres.Rd | 6 man/pcf.ppp.Rd | 19 + man/polartess.Rd |only man/pp3.Rd | 18 + man/quadrats.Rd | 11 - man/quantess.Rd | 34 ++- man/rmh.default.Rd | 1 man/rmhmodel.Rd | 1 man/rmhmodel.default.Rd | 4 man/scalardilate.Rd | 8 man/selfcut.psp.Rd | 8 man/shift.im.Rd | 36 ++- man/shift.owin.Rd | 33 ++- man/shift.ppp.Rd | 31 ++- man/shift.psp.Rd | 31 ++- man/simulate.kppm.Rd | 20 + man/spatialcdf.Rd | 11 - man/spatstat-internal.Rd | 41 +++- man/spatstat-package.Rd | 3 man/tess.Rd | 11 - man/venn.tess.Rd | 9 src/g3.c | 2 src/init.c | 325 ++++++++++++++++---------------- src/linalg.c | 4 src/lintileindex.c |only src/nearestpix.c |only src/proto.h | 5 src/tabnum.c |only tests/testsAtoD.R | 83 +++++++- tests/testsEtoF.R | 43 +++- tests/testsGtoK.R | 117 ++++++++++- tests/testsLtoM.R | 164 ++++++++++++++-- tests/testsNtoP.R | 55 +++++ tests/testsQtoR.R | 74 ++++++- tests/testsStoZ.R | 84 +++++++- vignettes/bugfixes.Rnw | 67 ++++++ vignettes/datasets.Rnw | 2 vignettes/updates.Rnw | 201 ++++++++++++++++++- 179 files changed, 4125 insertions(+), 1802 deletions(-)
Title: Polygonal Symbolic Data Analysis
Description: An implementation of symbolic polygonal data analysis. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation.
In addition, a method to obtain polygonal data from classical data is presented. Empirical probability distribution function based on
polygonal histogram and a regression model with its main measures are presented.
Author: Wagner Silva [aut, cre, ths],
Renata Souza [aut],
Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>
Diff between psda versions 1.3.0 dated 2019-03-19 and 1.3.1 dated 2019-03-22
DESCRIPTION | 8 +++---- MD5 | 59 +++++++++++++++++++++++++++++++++++++++++++++++++++++++--- NAMESPACE | 32 +++++++++++++++++++++++++++++++ R |only data |only inst/CITATION | 8 ++++--- man |only 7 files changed, 97 insertions(+), 10 deletions(-)
Title: Orthodromic Spatial Clustering
Description: Allows distance based spatial clustering of georeferenced data by implementing the City Clustering Algorithm - CCA. Multiple versions allow clustering for matrix, raster and single coordinates on a plain (euclidean distance) or on a sphere (great-circle or orthodromic distance).
Author: Steffen Kriewald, Till Fluschnik, Dominik Reusser, Diego Rybski
Maintainer: Steffen Kriewald <kriewald@pik-potsdam.de>
Diff between osc versions 1.0.0 dated 2016-05-10 and 1.0.4 dated 2019-03-22
DESCRIPTION | 11 +- MD5 | 41 ++++---- NAMESPACE | 2 R/code_revised_cca.R | 58 +++++++++++- README.md |only build/vignette.rds |binary data/exampledata.rda |binary data/landcover.rda |binary data/population.rda |binary inst/doc/paper.R | 50 ++++++++++ inst/doc/paper.pdf |binary inst/doc/paper.rnw | 49 +++++++++- man/cca.Rd | 47 ++++----- man/osc.buffer.Rd | 18 +++ src/ccaRevolution.c | 178 +++++++++++++++++++++++++++++++++++-- src/registerDynamicSymbol.c |only vignettes/paper.rnw | 49 +++++++++- vignettes/pics/exdat1.pdf |binary vignettes/pics/exdat2.pdf |binary vignettes/pics/fig-concordance.tex | 9 + vignettes/pics/landcover.pdf |binary vignettes/pics/point_data.pdf |only vignettes/pics/raster.pdf |binary 23 files changed, 441 insertions(+), 71 deletions(-)
Title: Optimized Kernel Regularized Least Squares
Description: Functions for Kernel-Regularized Least Squares optimized for speed and memory usage are provided along with visualization tools. For working papers, sample code, and recent presentations visit <https://sites.google.com/site/petemohanty/software/>. bigKRLS, as well its dependencies, require current versions of R and its compilers (and RStudio if used). For details, see <https://github.com/rdrr1990/bigKRLS/blob/master/INSTALL.md>.
Author: Pete Mohanty [aut, cre] (<https://orcid.org/0000-0001-8531-3345>),
Robert Shaffer [aut] (<https://orcid.org/0000-0002-2081-2407>)
Maintainer: Pete Mohanty <pete.mohanty@gmail.com>
Diff between bigKRLS versions 3.0.2 dated 2019-02-24 and 3.0.5 dated 2019-03-22
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/bigKRLS.R | 6 ++++-- inst/doc/bigKRLS_basics.html | 2 +- man/bigKRLS.Rd | 6 ++++-- 5 files changed, 18 insertions(+), 14 deletions(-)
Title: Functions for Text Mining and Topic Modeling
Description: An aid for text mining in R, with a syntax that
should be familiar to experienced R users. Provides a wrapper for several
topic models that take similarly-formatted input and give similarly-formatted
output. Has additional functionality for analyzing and diagnostics for
topic models.
Author: Tommy Jones [aut, cre],
William Doane [ctb]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between textmineR versions 3.0.2 dated 2019-01-09 and 3.0.3 dated 2019-03-22
textmineR-3.0.2/textmineR/tools |only textmineR-3.0.3/textmineR/DESCRIPTION | 20 - textmineR-3.0.3/textmineR/MD5 | 32 +- textmineR-3.0.3/textmineR/NAMESPACE | 5 textmineR-3.0.3/textmineR/NEWS.md |only textmineR-3.0.3/textmineR/R/textmineR.R | 1 textmineR-3.0.3/textmineR/R/topic_modeling_core.R | 118 +++++++++- textmineR-3.0.3/textmineR/README.md | 8 textmineR-3.0.3/textmineR/build/vignette.rds |binary textmineR-3.0.3/textmineR/inst/doc/a_start_here.html | 17 + textmineR-3.0.3/textmineR/inst/doc/b_document_clustering.html | 9 textmineR-3.0.3/textmineR/inst/doc/c_topic_modeling.html | 11 textmineR-3.0.3/textmineR/inst/doc/d_text_embeddings.html | 9 textmineR-3.0.3/textmineR/inst/doc/e_doc_summarization.html | 9 textmineR-3.0.3/textmineR/inst/doc/f_tidytext_example.html | 9 textmineR-3.0.3/textmineR/man/figures |only textmineR-3.0.3/textmineR/man/posterior.Rd |only textmineR-3.0.3/textmineR/man/posterior.lda_topic_model.Rd |only textmineR-3.0.3/textmineR/man/update.Rd |only textmineR-3.0.3/textmineR/man/update.lda_topic_model.Rd | 7 20 files changed, 202 insertions(+), 53 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.9.200.7.1 dated 2019-03-08 and 0.9.300.2.0 dated 2019-03-22
ChangeLog | 14 DESCRIPTION | 8 MD5 | 110 +++---- build/vignette.rds |binary inst/NEWS.Rd | 20 + inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/armadillo | 2 inst/include/armadillo_bits/BaseCube_bones.hpp | 2 inst/include/armadillo_bits/BaseCube_meat.hpp | 33 ++ inst/include/armadillo_bits/Base_bones.hpp | 26 + inst/include/armadillo_bits/Base_meat.hpp | 178 +++++++---- inst/include/armadillo_bits/Cube_bones.hpp | 2 inst/include/armadillo_bits/Cube_meat.hpp | 4 inst/include/armadillo_bits/Gen_bones.hpp | 2 inst/include/armadillo_bits/MapMat_meat.hpp | 160 ++++++---- inst/include/armadillo_bits/Mat_bones.hpp | 3 inst/include/armadillo_bits/Mat_meat.hpp | 187 ++++++------ inst/include/armadillo_bits/SpBase_bones.hpp | 2 inst/include/armadillo_bits/SpBase_meat.hpp | 33 ++ inst/include/armadillo_bits/SpMat_bones.hpp | 6 inst/include/armadillo_bits/SpMat_meat.hpp | 161 ++++++++-- inst/include/armadillo_bits/arma_rel_comparators.hpp |only inst/include/armadillo_bits/arma_version.hpp | 9 inst/include/armadillo_bits/auxlib_bones.hpp | 13 inst/include/armadillo_bits/auxlib_meat.hpp | 253 +++++++++++++++++ inst/include/armadillo_bits/compiler_setup.hpp | 2 inst/include/armadillo_bits/debug.hpp | 22 - inst/include/armadillo_bits/def_hdf5.hpp | 36 +- inst/include/armadillo_bits/def_lapack.hpp | 18 + inst/include/armadillo_bits/diskio_meat.hpp | 2 inst/include/armadillo_bits/eop_aux.hpp | 27 + inst/include/armadillo_bits/eop_core_bones.hpp | 2 inst/include/armadillo_bits/eop_core_meat.hpp | 6 inst/include/armadillo_bits/fn_eig_gen.hpp | 33 +- inst/include/armadillo_bits/fn_eig_sym.hpp | 18 - inst/include/armadillo_bits/fn_elem.hpp | 57 +++ inst/include/armadillo_bits/fn_interp2.hpp |only inst/include/armadillo_bits/fn_misc.hpp | 91 ------ inst/include/armadillo_bits/fn_spsolve.hpp | 68 ++-- inst/include/armadillo_bits/fn_trace.hpp | 223 +++++++++++++- inst/include/armadillo_bits/op_shift_meat.hpp | 2 inst/include/armadillo_bits/op_shuffle_meat.hpp | 2 inst/include/armadillo_bits/op_sort_bones.hpp | 56 --- inst/include/armadillo_bits/op_sort_meat.hpp | 6 inst/include/armadillo_bits/op_var_meat.hpp | 8 inst/include/armadillo_bits/op_wishrnd_meat.hpp | 134 ++++----- inst/include/armadillo_bits/podarray_bones.hpp | 4 inst/include/armadillo_bits/podarray_meat.hpp | 114 +++---- inst/include/armadillo_bits/sp_auxlib_meat.hpp | 6 inst/include/armadillo_bits/span.hpp | 14 inst/include/armadillo_bits/subview_cube_each_meat.hpp | 2 inst/include/armadillo_bits/subview_cube_meat.hpp | 8 inst/include/armadillo_bits/subview_each_meat.hpp | 2 inst/include/armadillo_bits/typedef_mat.hpp | 12 inst/include/armadillo_bits/unwrap.hpp | 88 +++++ inst/include/armadillo_bits/wrapper_lapack.hpp | 46 +++ 57 files changed, 1605 insertions(+), 732 deletions(-)
Title: Item Response Theory and Computer-Based Testing in R
Description: A suite of psychometric analysis tools for research and operation, including:
(1) computation of probability, information, and likelihood for the 3PL, GPCM, and GRM;
(2) parameter estimation using joint or marginal likelihood estimation method;
(3) simulation of computerized adaptive testing using built-in or customized algorithms;
(4) assembly and simulation of multistage testing.
The full documentation and tutorials are at <https://github.com/xluo11/xxIRT>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Diff between xxIRT versions 2.1.1 dated 2018-10-02 and 2.1.2 dated 2019-03-22
xxIRT-2.1.1/xxIRT/R/module0_helpers.R |only xxIRT-2.1.1/xxIRT/R/module0_misc.R |only xxIRT-2.1.1/xxIRT/R/module0_utils.R |only xxIRT-2.1.1/xxIRT/man/helpers.Rd |only xxIRT-2.1.1/xxIRT/man/misc.Rd |only xxIRT-2.1.1/xxIRT/man/utils.Rd |only xxIRT-2.1.2/xxIRT/DESCRIPTION | 27 xxIRT-2.1.2/xxIRT/MD5 | 55 - xxIRT-2.1.2/xxIRT/NAMESPACE | 166 +-- xxIRT-2.1.2/xxIRT/R/module0_ctt_utils.R |only xxIRT-2.1.2/xxIRT/R/module0_irt_utils.R |only xxIRT-2.1.2/xxIRT/R/module0_stat_utils.R |only xxIRT-2.1.2/xxIRT/R/module1_helpers.R |only xxIRT-2.1.2/xxIRT/R/module1_model_3pl.R | 552 +--------- xxIRT-2.1.2/xxIRT/R/module1_model_gpcm.R | 636 +++--------- xxIRT-2.1.2/xxIRT/R/module1_model_grm.R |only xxIRT-2.1.2/xxIRT/R/module2_estimate_3pl.R |only xxIRT-2.1.2/xxIRT/R/module2_estimate_gpcm.R |only xxIRT-2.1.2/xxIRT/R/module2_estimate_grm.R |only xxIRT-2.1.2/xxIRT/R/module3_ata.R | 1191 +++++++++-------------- xxIRT-2.1.2/xxIRT/R/module3_ata_helpers.R |only xxIRT-2.1.2/xxIRT/R/module4_cat.R | 751 +++++++------- xxIRT-2.1.2/xxIRT/R/module5_mst.R | 858 ++++++++-------- xxIRT-2.1.2/xxIRT/R/module5_mst_sim.R | 256 ++-- xxIRT-2.1.2/xxIRT/man/ata.Rd | 358 +++--- xxIRT-2.1.2/xxIRT/man/ata_helpers.Rd |only xxIRT-2.1.2/xxIRT/man/cat_sim.Rd | 319 +++--- xxIRT-2.1.2/xxIRT/man/cronbach_alpha.Rd |only xxIRT-2.1.2/xxIRT/man/estimate_3pl.Rd |only xxIRT-2.1.2/xxIRT/man/estimate_gpcm.Rd |only xxIRT-2.1.2/xxIRT/man/estimate_grm.Rd |only xxIRT-2.1.2/xxIRT/man/estimate_helpers.Rd |only xxIRT-2.1.2/xxIRT/man/expected_raw_score_dist.Rd |only xxIRT-2.1.2/xxIRT/man/freq.Rd |only xxIRT-2.1.2/xxIRT/man/hermite_gauss.Rd |only xxIRT-2.1.2/xxIRT/man/model_3pl.Rd | 277 +---- xxIRT-2.1.2/xxIRT/man/model_gpcm.Rd | 267 ++--- xxIRT-2.1.2/xxIRT/man/model_grm.Rd |only xxIRT-2.1.2/xxIRT/man/mst.Rd | 437 ++++---- xxIRT-2.1.2/xxIRT/man/mst_sim.Rd | 105 -- xxIRT-2.1.2/xxIRT/man/rmse.Rd |only xxIRT-2.1.2/xxIRT/man/spearman_brown.Rd |only 42 files changed, 2616 insertions(+), 3639 deletions(-)
Title: Integrated Stratigraphy
Description: Includes bases for litholog generation: graphical functions
based on R base graphics, interval management functions and svg importation
functions among others. Also include stereographic projection functions,
and other functions made to deal with large datasets while keeping options
to get into the details of the data.
The palaeomagnetism functions are based on:
Tauxe, L., 2010. Essentials of Paleomagnetism. University of California
Press. <https://earthref.org/MagIC/books/Tauxe/Essentials/>;
Allmendinger, R. W., Cardozo, N. C., and Fisher, D., 2013, Structural
Geology Algorithms: Vectors & Tensors: Cambridge, England, Cambridge
University Press, 289 pp.;
Cardozo, N., and Allmendinger, R. W., 2013, Spherical projections
with OSXStereonet: Computers & Geosciences, v. 51, no. 0, p. 193 - 205,
<doi: 10.1016/j.cageo.2012.07.021>.
Author: Sebastien Wouters [aut, cre], Adam D. Smith [ctb]
Maintainer: Sebastien Wouters <sebastien.wouters@doct.uliege.be>
Diff between StratigrapheR versions 0.0.2 dated 2019-03-11 and 0.0.3 dated 2019-03-22
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/StratigrapheR.R | 2 +- R/convertAxis.R | 10 ++++++---- R/dipfix.R | 5 +++-- R/minorAxis.R | 4 ++-- R/multilines.R | 2 +- man/minorAxis.Rd | 2 +- man/multilines.Rd | 2 +- 9 files changed, 27 insertions(+), 24 deletions(-)
Title: 'Yingyang' K-Means and K-NN using NVIDIA CUDA
Description: K-means implementation is base on "Yingyang K-Means: A Drop-In Replacement of the Classic K-Means with Consistent Speedup". While it introduces some overhead and many conditional clauses which are bad for CUDA, it still shows 1.6-2x speedup against the Lloyd algorithm. K-nearest neighbors employ the same triangle inequality idea and require precalculated centroids and cluster assignments, similar to the flattened ball tree.
Author: Vadim Markovtsev, Charles Determan
Maintainer: Charles Determan <cdetermanjr@gmail.com>
Diff between kmcudaR versions 1.0.0 dated 2017-05-03 and 1.1.0 dated 2019-03-22
kmcudaR-1.0.0/kmcudaR/README.md |only kmcudaR-1.1.0/kmcudaR/DESCRIPTION | 22 kmcudaR-1.1.0/kmcudaR/LICENSE | 196 + kmcudaR-1.1.0/kmcudaR/MD5 | 46 kmcudaR-1.1.0/kmcudaR/NAMESPACE | 12 kmcudaR-1.1.0/kmcudaR/R/RcppExports.R | 22 kmcudaR-1.1.0/kmcudaR/R/kmcudaR.R | 238 - kmcudaR-1.1.0/kmcudaR/configure | 1 kmcudaR-1.1.0/kmcudaR/configure.ac | 4 kmcudaR-1.1.0/kmcudaR/inst/include/fp_abstraction.h | 4 kmcudaR-1.1.0/kmcudaR/inst/include/kmcuda.h | 59 kmcudaR-1.1.0/kmcudaR/inst/include/private.h | 79 kmcudaR-1.1.0/kmcudaR/inst/include/tricks.cuh | 141 - kmcudaR-1.1.0/kmcudaR/inst/include/wrappers.h | 7 kmcudaR-1.1.0/kmcudaR/man/kmeans_cuda.Rd | 111 kmcudaR-1.1.0/kmcudaR/man/knn_cuda.Rd | 79 kmcudaR-1.1.0/kmcudaR/src/CMakeLists.txt |only kmcudaR-1.1.0/kmcudaR/src/Makevars.win |only kmcudaR-1.1.0/kmcudaR/src/RcppExports.cpp | 20 kmcudaR-1.1.0/kmcudaR/src/cmake |only kmcudaR-1.1.0/kmcudaR/src/kmcuda.cc | 7 kmcudaR-1.1.0/kmcudaR/src/kmeans.cu | 2624 ++++++++++---------- kmcudaR-1.1.0/kmcudaR/src/knn.cu | 1068 ++++---- kmcudaR-1.1.0/kmcudaR/src/transpose.cu | 236 - kmcudaR-1.1.0/kmcudaR/tests/testthat.R | 8 kmcudaR-1.1.0/kmcudaR/tests/testthat/test.R | 174 - 26 files changed, 2759 insertions(+), 2399 deletions(-)
Title: Platform for EDGAR Filing Management and Textual Analysis
Description: In the USA, companies file different forms with the U.S.
Securities and Exchange Commission (SEC) through EDGAR (Electronic
Data Gathering, Analysis, and Retrieval system). The EDGAR
database automated system collects all the different necessary
filings and makes it publicly available. Investors, regulators,
and researchers often require these forms for various purposes.
This package helps in bulk data gathering and textual analysis of
EDGAR filings. It downloads filings from SEC server in bulk with
a single query. Additionally, it provides various useful functions:
extracts 8-K triggering events, extract "Business (Item 1)" and
"Management's Discussion and Analysis(Item 7)" sections of annual
statements, search filings for desired words, provides sentiment
measures, parse filing header information, and provides HTML
view of SEC filings.
Author: Gunratan Lonare <lonare.gunratan@gmail.com>, Bharat Patil
<bharatspatil@gmail.com>
Maintainer: Gunratan Lonare <lonare.gunratan@gmail.com>
Diff between edgar versions 2.0.0 dated 2019-03-18 and 2.0.1 dated 2019-03-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/get8KItems.R | 2 +- R/getFilings.R | 9 +++++++-- R/getMgmtDisc.R | 3 ++- man/get8KItems.Rd | 2 +- 6 files changed, 19 insertions(+), 13 deletions(-)
Title: Data Cloning and MCMC Tools for Maximum Likelihood Methods
Description: Low level functions for implementing
maximum likelihood estimating procedures for
complex models using data cloning and Bayesian
Markov chain Monte Carlo methods
as described in Solymos 2010 (R Journal 2(2):29--37).
Sequential and parallel MCMC support
for 'JAGS', 'WinBUGS', 'OpenBUGS', and 'Stan'.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between dclone versions 2.2-0 dated 2018-02-26 and 2.3-0 dated 2019-03-22
DESCRIPTION | 14 - MD5 | 58 ++++---- NAMESPACE | 9 + R/bugs.parfit.R | 2 R/dc.fit.R | 3 R/dc.parfit.R | 40 ++++- R/dcFit.R | 15 +- R/errlines.default.R | 142 +++++++++---------- R/jags.parfit.R | 2 R/stan.fit.R |only R/stan.model.R |only R/stan.model.mcmc.list.R |only R/stan.model.mcmc.list.dc.R |only R/stan.parfit.R |only man/DcloneEnv.Rd | 206 ++++++++++++++-------------- man/bugs.fit.Rd | 318 ++++++++++++++++++++++---------------------- man/coef.mcmc.list.Rd | 230 +++++++++++++++---------------- man/dc.fit.Rd | 40 +++++ man/dc.parfit.Rd | 44 +++++- man/dcFit.Rd | 3 man/dclone-package.Rd | 12 - man/errlines.Rd | 188 +++++++++++++------------- man/evalParallelArgument.Rd | 86 +++++------ man/jags.fit.Rd | 256 +++++++++++++++++------------------ man/make.symmetric.Rd | 90 ++++++------ man/mcmcapply.Rd | 120 ++++++++-------- man/nclones.Rd | 80 +++++------ man/ovenbird.Rd | 82 +++++------ man/pairs.mcmc.list.Rd | 152 ++++++++++----------- man/parallel.inits.Rd | 136 +++++++++--------- man/regmod.Rd | 104 +++++++------- man/stan.fit.Rd |only man/update.mcmc.list.Rd | 26 +-- 33 files changed, 1291 insertions(+), 1167 deletions(-)
Title: Fast Enrichment Analysis via Circular Permutations
Description: Fast enrichment analysis for locally correlated statistics
via circular permutations.
The analysis can be performed at multiple significance thresholds
for both primary and auxiliary data sets with
efficient correction for multiple testing.
Author: Andrey A Shabalin [aut, cre] (<https://orcid.org/0000-0003-0309-6821>),
Edwin J C G van den Oord [aut]
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
Diff between shiftR versions 1.4 dated 2018-03-03 and 1.5 dated 2019-03-22
DESCRIPTION | 8 MD5 | 8 build/vignette.rds |binary inst/doc/intro.html | 440 +++++++++++++++++++++++++++++++++------------------- src/c_code.c | 40 ++-- 5 files changed, 315 insertions(+), 181 deletions(-)
Title: Seawater Carbonate Chemistry
Description: Calculates parameters of the seawater carbonate system and assists the design of ocean acidification perturbation experiments.
Author: Jean-Pierre Gattuso [aut, cre, cph],
Jean-Marie Epitalon [aut],
Heloise Lavigne [aut],
James Orr [aut],
Bernard Gentili [ctb],
Mathilde Hagens [ctb],
Andreas Hofmann [ctb],
Jens-Daniel Mueller [ctb],
Aurélien Proye [ctb],
James Rae [ctb],
Karline Soetaert [ctb]
Maintainer: Jean-Pierre Gattuso <gattuso@obs-vlfr.fr>
Diff between seacarb versions 3.2.11 dated 2019-01-19 and 3.2.12 dated 2019-03-22
ChangeLog | 6 +++++- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/errors.R | 29 ++++++++++------------------- 4 files changed, 22 insertions(+), 27 deletions(-)
Title: A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
Description: A collection of functions to implement a class for univariate
polynomial manipulations.
Author: Bill Venables [aut, cre] (S original),
Kurt Hornik [aut] (R port),
Martin Maechler [aut] (R port)
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between polynom versions 1.3-9 dated 2016-12-08 and 1.4-0 dated 2019-03-22
ChangeLog | 17 + DESCRIPTION | 20 +- MD5 | 28 +- NAMESPACE | 18 + R/polybase.R | 339 ++++++++++++++++------------------- R/polylist.R | 190 +++++++++---------- R/polyxtra.R | 458 +++++++++++++++++++++++------------------------- R/utils.R | 17 + build |only inst/CITATION | 2 inst/doc |only man/lines.polynomial.Rd | 2 man/plot.polynomial.Rd | 7 man/polylist.Rd | 2 vignettes |only 15 files changed, 538 insertions(+), 562 deletions(-)
Title: EM Algorithm for Model-Based Clustering of Finite Mixture
Gaussian Distribution
Description: EM algorithms and several efficient
initialization methods for model-based clustering of finite
mixture Gaussian distribution with unstructured dispersion
in both of unsupervised and semi-supervised learning.
Author: Wei-Chen Chen [aut, cre],
Ranjan Maitra [aut],
Volodymyr Melnykov [ctb],
Dan Nettleton [ctb],
David Faden [ctb],
Rouben Rostamian [ctb],
R Core team [ctb] (some functions are modified from the R source code)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between EMCluster versions 0.2-11 dated 2019-03-07 and 0.2-12 dated 2019-03-22
ChangeLog | 3 +++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/it_R_emptr.c | 23 ++++++++++++----------- 4 files changed, 21 insertions(+), 17 deletions(-)
Title: Helps You to Code Cleaner
Description: Check your R code for some of the most common
layout flaws. Many tried to teach us how to write code less dreadful,
be it implicitly as B. W. Kernighan and D. M. Ritchie (1988)
<ISBN:0-13-110362-8> in 'The C Programming Language' did, be it
explicitly as R.C. Martin (2008) <ISBN:0-13-235088-2> in 'Clean Code:
A Handbook of Agile Software Craftsmanship' did. So we should check
our code for files too long or wide, functions with too many lines,
too wide lines, too many arguments or too many levels of nesting.
Note: This is not a static code analyzer like pylint or the like.
Checkout <https://cran.r-project.org/package=lintr> instead.
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between cleanr versions 1.1.3 dated 2017-01-17 and 1.2.0 dated 2019-03-22
cleanr-1.1.3/cleanr/inst/tests |only cleanr-1.1.3/cleanr/tests/cleanr_R_code.html |only cleanr-1.1.3/cleanr/tests/results |only cleanr-1.1.3/cleanr/tests/runit |only cleanr-1.2.0/cleanr/DESCRIPTION | 52 +++---- cleanr-1.2.0/cleanr/LICENSE | 4 cleanr-1.2.0/cleanr/MD5 | 122 ++++++++---------- cleanr-1.2.0/cleanr/NAMESPACE | 1 cleanr-1.2.0/cleanr/NEWS.md |only cleanr-1.2.0/cleanr/R/checks.R | 37 ++--- cleanr-1.2.0/cleanr/R/cleanr-package.R | 3 cleanr-1.2.0/cleanr/R/internals.R | 3 cleanr-1.2.0/cleanr/R/options.R | 32 ++-- cleanr-1.2.0/cleanr/R/throw.R |only cleanr-1.2.0/cleanr/R/utils.R | 2 cleanr-1.2.0/cleanr/R/wrappers.R | 91 ++++++++++--- cleanr-1.2.0/cleanr/README.md | 70 +++++++--- cleanr-1.2.0/cleanr/build/cleanr.pdf |binary cleanr-1.2.0/cleanr/build/vignette.rds |binary cleanr-1.2.0/cleanr/inst/doc/cleanr_Introduction.R | 4 cleanr-1.2.0/cleanr/inst/doc/cleanr_Introduction.Rmd | 6 cleanr-1.2.0/cleanr/inst/doc/cleanr_Introduction.html | 91 +++++++------ cleanr-1.2.0/cleanr/inst/runit_tests |only cleanr-1.2.0/cleanr/inst/source/R/checks.R | 37 ++--- cleanr-1.2.0/cleanr/inst/source/R/cleanr-package.R | 3 cleanr-1.2.0/cleanr/inst/source/R/internals.R | 3 cleanr-1.2.0/cleanr/inst/source/R/options.R | 32 ++-- cleanr-1.2.0/cleanr/inst/source/R/throw.R |only cleanr-1.2.0/cleanr/inst/source/R/utils.R | 2 cleanr-1.2.0/cleanr/inst/source/R/wrappers.R | 91 ++++++++++--- cleanr-1.2.0/cleanr/man/check_directory.Rd | 17 +- cleanr-1.2.0/cleanr/man/check_file.Rd | 6 cleanr-1.2.0/cleanr/man/check_file_layout.Rd | 8 - cleanr-1.2.0/cleanr/man/check_function_layout.Rd | 13 - cleanr-1.2.0/cleanr/man/check_functions_in_file.Rd | 8 - cleanr-1.2.0/cleanr/man/check_package.Rd |only cleanr-1.2.0/cleanr/man/cleanr-package.Rd | 6 cleanr-1.2.0/cleanr/man/file_checks.Rd | 23 +-- cleanr-1.2.0/cleanr/man/function_checks.Rd | 30 ++-- cleanr-1.2.0/cleanr/man/get_cleanr_options.Rd | 18 +- cleanr-1.2.0/cleanr/man/get_function_body.Rd | 4 cleanr-1.2.0/cleanr/man/is_not_false.Rd | 4 cleanr-1.2.0/cleanr/man/load_internal_functions.Rd | 4 cleanr-1.2.0/cleanr/man/set_cleanr_options.Rd | 22 +-- cleanr-1.2.0/cleanr/man/throw.Rd | 23 ++- cleanr-1.2.0/cleanr/man/tidy_findings.Rd | 4 cleanr-1.2.0/cleanr/tests/runit.R | 107 ++++++--------- cleanr-1.2.0/cleanr/tests/testthat |only cleanr-1.2.0/cleanr/tests/testthat.R |only cleanr-1.2.0/cleanr/vignettes/cleanr_Introduction.Rmd | 6 50 files changed, 530 insertions(+), 459 deletions(-)
Title: Covariate Balancing Propensity Score
Description: Implements the covariate balancing propensity score (CBPS) proposed
by Imai and Ratkovic (2014) <DOI:10.1111/rssb.12027>. The propensity score is
estimated such that it maximizes the resulting covariate balance as well as the
prediction of treatment assignment. The method, therefore, avoids an iteration
between model fitting and balance checking. The package also implements optimal
CBPS from Fan et al. (2016) <https://imai.fas.harvard.edu/research/CBPStheory.html>,
several extensions of the CBPS beyond the cross-sectional, binary treatment setting.
They include the CBPS for longitudinal settings so that it can be used in
conjunction with marginal structural models from Imai and Ratkovic (2015)
<DOI:10.1080/01621459.2014.956872>, treatments with three- and four-valued treatment
variables, continuous-valued treatments from Fong, Hazlett, and Imai (2018)
<DOI:10.1214/17-AOAS1101>, propensity score estimation with a large number of
covariates from Ning, Peng, and Imai (2018) <arXiv:1812.08683>, and the situation
with multiple distinct binary treatments administered simultaneously. In the future
it will be extended to other settings including the generalization of experimental
and instrumental variable estimates.
Author: Christian Fong [aut, cre],
Marc Ratkovic [aut],
Kosuke Imai [aut],
Chad Hazlett [ctb],
Xiaolin Yang [ctb],
Sida Peng [ctb]
Maintainer: Christian Fong <christianfong@stanford.edu>
Diff between CBPS versions 0.19 dated 2018-06-17 and 0.20 dated 2019-03-22
ChangeLog | 5 +++-- DESCRIPTION | 35 +++++++++++++++++------------------ MD5 | 12 ++++++------ R/CBMSM.R | 7 ++++--- R/CBPSContinuous.r | 16 +++++++++------- R/hdCBPS.R | 4 ++-- tests/testthat/test-all.R | 16 ++++++++-------- 7 files changed, 49 insertions(+), 46 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-03-08 1.6.1
2015-11-21 1.4
2015-01-03 1.2
2014-09-26 1.0
2014-07-30 0.3.2
2014-04-24 0.3.1
2014-02-17 0.2
2014-02-12 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-16 0.4.3
2017-05-18 0.4.2
2017-05-09 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-07-13 0.7.1.0
Title: A Fully Featured Logging Framework
Description: A flexible, feature-rich yet light-weight logging
framework based on 'R6' classes. It supports hierarchical loggers,
custom log levels, arbitrary data fields in log events, logging to
plaintext, 'JSON', memory buffers, and databases, as well as email and
push notifications. For a full list of features with examples please
refer to the package vignette.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between lgr versions 0.1.1 dated 2019-02-22 and 0.2.0 dated 2019-03-22
DESCRIPTION | 22 - MD5 | 119 +++++---- NAMESPACE | 9 NEWS.md | 26 +- R/Appender.R | 28 +- R/Filterable.R | 18 - R/LogEvent.R | 2 R/Logger.R | 283 +++++++++++++++------- R/get_logger.R |only R/lgr-package.R | 16 - R/log_levels.R | 3 R/logger_config.R |only R/print_Logger.R | 44 ++- R/simple_logging.R | 71 +++++ R/test.R |only R/use_logger.R | 2 R/utils-logging.R | 54 ++-- R/utils-rd.R | 13 - R/utils.R | 15 + README.md | 23 - build/vignette.rds |binary inst/WORDLIST | 8 inst/doc/lgr-simple.html | 10 inst/doc/lgr.R | 74 +++-- inst/doc/lgr.Rmd | 114 ++++++-- inst/doc/lgr.html | 216 +++++++++------- man/Appender.Rd | 2 man/AppenderBuffer.Rd | 9 man/AppenderConsole.Rd | 6 man/AppenderDbi.Rd | 2 man/AppenderDt.Rd | 13 - man/AppenderFile.Rd | 4 man/AppenderGmail.Rd | 4 man/AppenderJson.Rd | 4 man/AppenderPushbullet.Rd | 4 man/AppenderRjdbc.Rd | 2 man/AppenderSendmail.Rd | 4 man/LayoutDbi.Rd | 5 man/LayoutFormat.Rd | 4 man/LayoutGlue.Rd | 2 man/LayoutJson.Rd | 2 man/LogEvent.Rd | 4 man/Logger.Rd | 129 +++++----- man/LoggerRoot.Rd |only man/basic_config.Rd |only man/get_logger.Rd |only man/lgr-package.Rd | 2 man/logger_config.Rd |only man/print.Logger.Rd | 11 man/suspend_logging.Rd | 25 + tests/testthat/manual_tests/test_AppenderDigest.R | 6 tests/testthat/test_Appender.R | 20 - tests/testthat/test_AppenderDbi.R | 8 tests/testthat/test_Filterable.R | 1 tests/testthat/test_Logger.R | 21 + tests/testthat/test_get_logger.R |only tests/testthat/test_logger_config.R |only tests/testthat/test_parallel.R | 44 ++- tests/testthat/test_print.R | 6 tests/testthat/test_print_Logger.R | 6 tests/testthat/test_read_json_log.R | 2 tests/testthat/test_utils-logging.R | 20 - tests/testthat/test_utils.R | 15 - tests/testthat/testdata |only vignettes/lgr.Rmd | 114 ++++++-- 65 files changed, 1081 insertions(+), 590 deletions(-)
Title: Partitioning of Individual Autozygosity into Multiple
Homozygous-by-Descent Classes
Description: Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to
estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes
with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct
for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the
segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the
parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity
probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017)
<doi:10.1111/mec.14324>.
Author: Tom Druet, Naveen Kumar Kadri, Amandine Bertrand and Mathieu Gautier
Maintainer: Tom Druet <tom.druet@uliege.be>
Diff between RZooRoH versions 0.2.2 dated 2018-11-19 and 0.2.3 dated 2019-03-22
DESCRIPTION | 6 - MD5 | 13 ++-- R/zooroh.R | 4 - inst/CITATION |only inst/doc/zooroh-vignette.Rmd | 129 ++++++++++++++++++++++-------------------- inst/doc/zooroh-vignette.pdf |binary tests/testthat/test2.R | 6 - vignettes/zooroh-vignette.Rmd | 129 ++++++++++++++++++++++-------------------- 8 files changed, 151 insertions(+), 136 deletions(-)
Title: An Improved Heatmap Package
Description: An improved heatmap package. Completely
compatible with the original R function 'heatmap',
and provides more powerful and convenient features.
Author: Shilin Zhao, Linlin Yin, Yan Guo, Quanhu Sheng, Yu Shyr
Maintainer: Shilin Zhao <shilin.zhao@vanderbilt.edu>
Diff between heatmap3 versions 1.1.1 dated 2015-04-08 and 1.1.6 dated 2019-03-22
heatmap3-1.1.1/heatmap3/vignettes/cache |only heatmap3-1.1.6/heatmap3/DESCRIPTION | 13 +-- heatmap3-1.1.6/heatmap3/MD5 | 32 +++---- heatmap3-1.1.6/heatmap3/NAMESPACE | 15 +++ heatmap3-1.1.6/heatmap3/NEWS | 103 ++++++++++++++----------- heatmap3-1.1.6/heatmap3/R/colByValue.R | 92 +++++++++++----------- heatmap3-1.1.6/heatmap3/R/heatmap3.R | 49 ++++++++--- heatmap3-1.1.6/heatmap3/README.md | 2 heatmap3-1.1.6/heatmap3/build/vignette.rds |binary heatmap3-1.1.6/heatmap3/inst/doc/vignette.R | 2 heatmap3-1.1.6/heatmap3/inst/doc/vignette.Rnw | 7 - heatmap3-1.1.6/heatmap3/man/colByValue.Rd | 7 - heatmap3-1.1.6/heatmap3/man/heatmap3.Rd | 44 ++++++---- heatmap3-1.1.6/heatmap3/man/showAnn.Rd | 6 - heatmap3-1.1.6/heatmap3/man/showLegend.Rd | 8 - heatmap3-1.1.6/heatmap3/vignettes/vignette.Rnw | 7 - 16 files changed, 224 insertions(+), 163 deletions(-)
Title: Basic Functions for Supporting an Implementation of Case 2
Best-Worst Scaling
Description: Provides three basic functions that support an implementation of Case 2 (profile case) best-worst scaling. The first is to convert an orthogonal main-effect design into questions, the second is to create a dataset suitable for analysis, and the third is to calculate count-based scores.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS2 versions 0.2-1 dated 2019-01-06 and 0.2-2 dated 2019-03-22
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 6 ++++++ R/bws2.dataset.R | 21 ++++++++++++++------- man/agritourism.Rd | 4 ++-- man/bws2.dataset.Rd | 28 ++++++++++++++++++---------- 6 files changed, 49 insertions(+), 28 deletions(-)
Title: Calculate Text Polarity Sentiment
Description: Calculate text polarity sentiment at the sentence level and
optionally aggregate by rows or grouping variable(s).
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between sentimentr versions 2.6.1 dated 2018-10-20 and 2.7.1 dated 2019-03-22
DESCRIPTION | 10 +- LICENSE | 4 - MD5 | 101 ++++++++++++++------------ NAMESPACE | 20 +++++ NEWS | 43 +++++++++++ R/emotion.R |only R/emotion_by.R |only R/extract_emotion_terms.R |only R/extract_profanity_terms.R | 14 +-- R/extract_sentiment_terms.R | 54 +++++++++++++ R/get_sentences.R | 17 ++++ R/highlight.R | 2 R/profanity.R | 55 +++++++++++--- R/profanity_by.R | 7 + R/sentiment.R | 20 +++-- R/sentiment_by.R | 3 R/sentimentr-package.R | 6 - R/uncombine.R | 18 +++- R/utils.R | 7 + README.md | 54 +++++++------ data/course_evaluations.rda |binary data/crowdflower_deflategate.rda |binary data/crowdflower_products.rda |binary data/crowdflower_self_driving_cars.rda |binary data/crowdflower_weather.rda |binary data/hotel_reviews.rda |binary data/hu_liu_apex_reviews.rda |binary data/hu_liu_cannon_reviews.rda |binary data/hu_liu_jukebox_reviews.rda |binary data/hu_liu_nikon_reviews.rda |binary data/hu_liu_nokia_reviews.rda |binary data/kaggle_movie_reviews.rda |binary data/kotzias_reviews_amazon_cells.rda |binary data/kotzias_reviews_imdb.rda |binary data/kotzias_reviews_yelp.rda |binary data/nyt_articles.rda |binary data/presidential_debates_2012.rda |binary data/sam_i_am.rda |binary inst/CITATION | 8 +- man/course_evaluations.Rd | 2 man/emotion.Rd |only man/emotion_by.Rd |only man/extract_emotion_terms.Rd |only man/extract_profanity_terms.Rd | 4 - man/extract_sentiment_terms.Rd | 52 +++++++++++++ man/kaggle_movie_reviews.Rd | 2 man/nyt_articles.Rd | 2 man/plot.emotion.Rd |only man/plot.emotion_by.Rd |only man/print.extract_emotion_terms.Rd |only man/profanity.Rd | 37 ++++++++- man/profanity_by.Rd | 5 + man/sentiment.Rd | 2 tests/testthat/test-extract_sentiment_terms.R | 1 tests/testthat/test-update_key.R | 8 +- tools/figure/unnamed-chunk-11-1.png |binary 56 files changed, 430 insertions(+), 128 deletions(-)
Title: Seamless Integration Between R and 'Julia'
Description: Provides an R interface to 'Julia',
which is a high-level, high-performance dynamic programming language
for numerical computing, see <https://julialang.org/> for more information.
It provides a high-level interface as well as a low-level interface.
Using the high level interface, you could call any 'Julia' function just like
any R function with automatic type conversion. Using the low level interface,
you could deal with C-level SEXP directly while enjoying the convenience of
using a high-level programming language like 'Julia'.
Author: Changcheng Li [aut, cre],
Randy Lai [ctb],
Dmitri Grominski [ctb],
Nagi Teramo [ctb]
Maintainer: Changcheng Li <cxl508@psu.edu>
Diff between JuliaCall versions 0.16.4 dated 2019-02-18 and 0.16.5 dated 2019-03-22
DESCRIPTION | 8 - LICENSE | 2 MD5 | 31 +++-- NEWS.md | 18 ++- R/interface.R | 31 +++-- R/zzz.R | 22 +++- README.md | 141 +++++++++++++++++--------- build/vignette.rds |binary inst/CITATION |only inst/doc/JuliaCall_in_Jupyter_R_Notebook.html | 9 + inst/doc/Julia_in_RMarkdown.html | 9 + inst/julia/install_dependency.jl | 24 ---- inst/julia/rebuildRCall.jl |only man/call.Rd | 8 + man/julia_command.Rd | 12 +- man/julia_eval.Rd | 13 +- man/julia_setup.Rd | 10 + tests/testthat/test_rebuild.R |only 18 files changed, 215 insertions(+), 123 deletions(-)