Title: Data for Sunlight Spectra
Description: Data for the extraterrestrial solar spectral irradiance and ground
level solar spectral irradiance and irradiance. In addition data for
shade light under vegetation and irradiance time series. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, trl, cre]
(<https://orcid.org/0000-0003-3385-972X>),
T. Matthew Robson [ctb] (<https://orcid.org/0000-0002-8631-796X>),
Saara M. Hartiakinen [ctb] (<https://orcid.org/0000-0002-8430-6861>),
Anders Lindfors [ctb],
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologySun versions 0.4.0 dated 2018-02-27 and 0.4.1 dated 2019-03-27
photobiologySun-0.4.0/photobiologySun/R/on-load.R |only photobiologySun-0.4.0/photobiologySun/inst/doc/data-catalogue.html |only photobiologySun-0.4.1/photobiologySun/DESCRIPTION | 32 photobiologySun-0.4.1/photobiologySun/MD5 | 50 - photobiologySun-0.4.1/photobiologySun/NEWS | 15 photobiologySun-0.4.1/photobiologySun/R/example.solar.irrad.data.r | 6 photobiologySun-0.4.1/photobiologySun/R/example.solar.spectra.data.r | 4 photobiologySun-0.4.1/photobiologySun/R/photobiologySun.R | 6 photobiologySun-0.4.1/photobiologySun/R/sun-reference-mspct.r | 2 photobiologySun-0.4.1/photobiologySun/README.md | 5 photobiologySun-0.4.1/photobiologySun/build/vignette.rds |binary photobiologySun-0.4.1/photobiologySun/data/broad-band.rda |binary photobiologySun-0.4.1/photobiologySun/data/gap-mspct.rda |binary photobiologySun-0.4.1/photobiologySun/data/sun-hourly-spct.rda |binary photobiologySun-0.4.1/photobiologySun/data/sun-may-morning-spct.rda |binary photobiologySun-0.4.1/photobiologySun/data/sun-reference-mspct.rda |binary photobiologySun-0.4.1/photobiologySun/inst/doc/user-guide.R | 15 photobiologySun-0.4.1/photobiologySun/inst/doc/user-guide.Rmd | 19 photobiologySun-0.4.1/photobiologySun/inst/doc/user-guide.html | 496 +++++++--- photobiologySun-0.4.1/photobiologySun/man/irrad_Kipp.data.Rd | 2 photobiologySun-0.4.1/photobiologySun/man/photobiologySun-package.Rd | 22 photobiologySun-0.4.1/photobiologySun/man/ppfd_BF.data.Rd | 2 photobiologySun-0.4.1/photobiologySun/man/ppfd_LICOR.data.Rd | 2 photobiologySun-0.4.1/photobiologySun/man/sun_hourly_august.spct.Rd | 2 photobiologySun-0.4.1/photobiologySun/man/sun_hourly_june.spct.Rd | 2 photobiologySun-0.4.1/photobiologySun/man/sun_reference.mspct.Rd | 2 photobiologySun-0.4.1/photobiologySun/vignettes/user-guide.Rmd | 19 27 files changed, 470 insertions(+), 233 deletions(-)
More information about photobiologySun at CRAN
Permanent link
Title: Time-Varying Coefficient Linear Regression for Single and
Multi-Equations
Description: Fitting time-varying coefficient models both for single and multi-equation regressions, using kernel smoothing techniques.
Author: Isabel Casas and Ruben Fernandez-Casal
Maintainer: Isabel Casas <casasis@gmail.com>
Diff between tvReg versions 0.3.0 dated 2018-06-05 and 0.4.0 dated 2019-03-27
tvReg-0.3.0/tvReg/R/deprecated_tvReg.R |only tvReg-0.3.0/tvReg/man/tvReg-deprecated.Rd |only tvReg-0.4.0/tvReg/DESCRIPTION | 15 tvReg-0.4.0/tvReg/MD5 | 113 +- tvReg-0.4.0/tvReg/NAMESPACE | 133 +- tvReg-0.4.0/tvReg/NEWS.md |only tvReg-0.4.0/tvReg/R/bw.R | 559 +++++------ tvReg-0.4.0/tvReg/R/confint_tvReg.R | 59 - tvReg-0.4.0/tvReg/R/data.R | 15 tvReg-0.4.0/tvReg/R/forecast_tvreg.R |only tvReg-0.4.0/tvReg/R/plot_tvReg.R | 43 tvReg-0.4.0/tvReg/R/predict_tvReg.R |only tvReg-0.4.0/tvReg/R/print_tvReg.R | 300 ++--- tvReg-0.4.0/tvReg/R/summary_tvReg.R | 31 tvReg-0.4.0/tvReg/R/tvA.R | 13 tvReg-0.4.0/tvReg/R/tvAR.R | 114 -- tvReg-0.4.0/tvReg/R/tvB.R | 17 tvReg-0.4.0/tvReg/R/tvBOOT.R | 55 - tvReg-0.4.0/tvReg/R/tvGLS.R | 649 +++++------- tvReg-0.4.0/tvReg/R/tvIRF.R | 19 tvReg-0.4.0/tvReg/R/tvLM.R | 273 ++--- tvReg-0.4.0/tvReg/R/tvOLS.R | 330 ++++-- tvReg-0.4.0/tvReg/R/tvPhi.R | 11 tvReg-0.4.0/tvReg/R/tvPsi.R | 16 tvReg-0.4.0/tvReg/R/tvSURE.R | 57 - tvReg-0.4.0/tvReg/R/tvVAR.R | 56 - tvReg-0.4.0/tvReg/R/update.R | 134 +- tvReg-0.4.0/tvReg/R/utils.R | 1 tvReg-0.4.0/tvReg/build/vignette.rds |binary tvReg-0.4.0/tvReg/data/RV.rdata |binary tvReg-0.4.0/tvReg/inst/CITATION | 20 tvReg-0.4.0/tvReg/inst/doc/tvReg-vignette.R | 300 +++-- tvReg-0.4.0/tvReg/inst/doc/tvReg-vignette.Rmd | 947 ++++++++++-------- tvReg-0.4.0/tvReg/inst/doc/tvReg-vignette.html | 1268 ++++++++++++++----------- tvReg-0.4.0/tvReg/man/CEES.Rd | 58 - tvReg-0.4.0/tvReg/man/FF5F.Rd | 148 +- tvReg-0.4.0/tvReg/man/RV.Rd | 81 - tvReg-0.4.0/tvReg/man/bw.Rd | 152 +- tvReg-0.4.0/tvReg/man/bwCov.Rd | 72 - tvReg-0.4.0/tvReg/man/confint.tvReg.Rd | 151 +- tvReg-0.4.0/tvReg/man/forecast.Rd |only tvReg-0.4.0/tvReg/man/methods.tvReg.Rd | 34 tvReg-0.4.0/tvReg/man/plot.tvReg.Rd | 97 - tvReg-0.4.0/tvReg/man/predict.tvReg.Rd |only tvReg-0.4.0/tvReg/man/print.tvReg.Rd | 73 - tvReg-0.4.0/tvReg/man/summary.tvReg.Rd | 84 - tvReg-0.4.0/tvReg/man/tvAR.Rd | 273 ++--- tvReg-0.4.0/tvReg/man/tvAcoef.Rd | 61 - tvReg-0.4.0/tvReg/man/tvBcoef.Rd | 64 - tvReg-0.4.0/tvReg/man/tvCov.Rd | 104 +- tvReg-0.4.0/tvReg/man/tvGLS.Rd | 172 +-- tvReg-0.4.0/tvReg/man/tvIRF.Rd | 173 +-- tvReg-0.4.0/tvReg/man/tvLM.Rd | 242 ++-- tvReg-0.4.0/tvReg/man/tvOLS.Rd | 81 - tvReg-0.4.0/tvReg/man/tvPhi.Rd | 41 tvReg-0.4.0/tvReg/man/tvPsi.Rd | 64 - tvReg-0.4.0/tvReg/man/tvReg-internals.Rd | 146 +- tvReg-0.4.0/tvReg/man/tvSURE.Rd | 333 +++--- tvReg-0.4.0/tvReg/man/tvVAR.Rd | 155 +-- tvReg-0.4.0/tvReg/man/update.tvReg.Rd | 64 - tvReg-0.4.0/tvReg/vignettes/tvReg-vignette.Rmd | 947 ++++++++++-------- 61 files changed, 4882 insertions(+), 4536 deletions(-)
Title: Extract and Tidy Canadian 'Hydrometric' Data
Description: Provides functions to access historical and real-time national 'hydrometric'
data from Water Survey of Canada data sources (<http://dd.weather.gc.ca/hydrometric/csv/> and
<http://collaboration.cmc.ec.gc.ca/cmc/hydrometrics/www/>) and then applies tidy data principles.
Author: Sam Albers [aut, cre] (<https://orcid.org/0000-0002-9270-7884>),
David Hutchinson [ctb],
Dewey Dunnington [ctb],
Ryan Whaley [ctb],
Province of British Columbia [cph],
Luke Winslow [rev] (Reviewed for rOpenSci),
Laura DeCicco [rev] (Reviewed for rOpenSci)
Maintainer: Sam Albers <sam.albers@gov.bc.ca>
Diff between tidyhydat versions 0.3.5 dated 2018-08-22 and 0.4.0 dated 2019-03-27
DESCRIPTION | 8 MD5 | 155 +++--- NAMESPACE | 4 NEWS.md | 17 R/hy-classes.R |only R/hy.R | 37 + R/hy_annual_instant_peaks.R | 6 R/hy_annual_stats.R | 8 R/hy_daily.R | 15 R/hy_daily_flows.R | 9 R/hy_daily_levels.R | 7 R/hy_monthly_flows.R | 7 R/hy_monthly_levels.R | 10 R/hy_plot.R | 147 +++++- R/hy_sed_daily_loads.R | 8 R/hy_sed_daily_suscon.R | 9 R/hy_sed_monthly_loads.R | 9 R/hy_sed_monthly_suscon.R | 7 R/hy_sed_samples.R | 9 R/hy_sed_samples_psd.R | 7 R/hy_stations.R | 15 R/hy_stn_regulation.R | 3 R/realtime-classes.R |only R/realtime.R | 33 - R/realtime_plot.R | 79 +++ R/utils-realtime.R | 10 R/utils-search.R | 2 R/utils.R | 45 + R/zzz.R | 2 README.md | 86 ++- build/vignette.rds |binary data/allstations.rda |binary inst/doc/tidyhydat_an_introduction.R | 17 inst/doc/tidyhydat_an_introduction.Rmd | 25 - inst/doc/tidyhydat_an_introduction.html | 469 ++++++------------- inst/doc/tidyhydat_example_analysis.Rmd | 2 inst/doc/tidyhydat_example_analysis.html | 524 +++++++--------------- inst/doc/tidyhydat_hydat_db.html | 425 +++++------------ inst/test_db/tinyhydat.sqlite3 |binary man/hy_annual_instant_peaks.Rd | 2 man/hy_annual_stats.Rd | 2 man/hy_daily.Rd | 8 man/hy_daily_flows.Rd | 2 man/hy_daily_levels.Rd | 2 man/hy_monthly_flows.Rd | 2 man/hy_monthly_levels.Rd | 2 man/hy_plot.Rd | 15 man/hy_sed_daily_loads.Rd | 2 man/hy_sed_daily_suscon.Rd | 2 man/hy_sed_monthly_loads.Rd | 2 man/hy_sed_monthly_suscon.Rd | 2 man/hy_sed_samples.Rd | 2 man/hy_sed_samples_psd.Rd | 2 man/hy_stations.Rd | 2 man/hy_stn_data_coll.Rd | 2 man/hy_stn_data_range.Rd | 2 man/hy_stn_datum_conv.Rd | 2 man/hy_stn_datum_unrelated.Rd | 2 man/hy_stn_op_schedule.Rd | 2 man/hy_stn_regulation.Rd | 2 man/hy_stn_remarks.Rd | 2 man/plot.Rd |only man/pull_station_number.Rd | 6 man/realtime_dd.Rd | 6 man/realtime_stations.Rd | 4 man/station_choice.Rd | 2 tests/testthat/helper-tidyhydat.R |only tests/testthat/test-hy-plot.R |only tests/testthat/test_hy_annual_instant_peaks.R | 2 tests/testthat/test_hy_daily.R | 5 tests/testthat/test_hy_sed_samples_psd.R | 4 tests/testthat/test_realtime_add_local_datetime.R | 3 tests/testthat/test_realtime_network.R | 1 tests/testthat/test_realtime_plot.R | 4 tests/testthat/test_search.R | 2 tests/testthat/test_station_choice.R | 5 tests/testthat/test_utils.R | 9 tools/readme/README-unnamed-chunk-8-1.png |binary tools/readme/README-unnamed-chunk-8-2.png |only tools/readme/README-unnamed-chunk-9-1.png |only vignettes/tidyhydat_an_introduction.Rmd | 25 - vignettes/tidyhydat_example_analysis.Rmd | 2 82 files changed, 1072 insertions(+), 1287 deletions(-)
Title: Some Nonparametric CUSUM Tests for Change-Point Detection in
Possibly Multivariate Observations
Description: Provides nonparametric CUSUM tests for detecting changes
in possibly serially dependent univariate or multivariate
observations. Tests sensitive to changes in the expectation, the
variance, the covariance, the autocovariance, the distribution
function, Spearman's rho, Kendall's tau, Gini's mean difference, and
the copula are provided, as well as a test for detecting changes in
the distribution of independent block maxima (with environmental
studies in mind). The latest additions are a test sensitive to
changes in the autocopula and a combined test of stationarity
sensitive to changes in the distribution function and the
autocopula.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between npcp versions 0.1-10 dated 2019-03-27 and 0.1-11 dated 2019-03-27
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/utilities.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Retrieve and Analyze Information on Clinical Trials from Public
Registers
Description: Provides functions for querying, retrieving and analysing protocol- and results-related information on clinical trials from two public registers, the European Union Clinical Trials Register (EUCTR, <https://www.clinicaltrialsregister.eu/>) and ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The information is transformed and then stored in a database (mongo). Functions are provided for accessing and analysing the locally stored information on the clinical trials, as well as for identifying duplicate records. The package is motivated by the need for aggregating and trend-analysing the design, conduct and outcomes across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 0.14.1 dated 2019-03-12 and 0.17.0 dated 2019-03-27
ctrdata-0.14.1/ctrdata/exec/json2split.sh |only ctrdata-0.14.1/ctrdata/man/installMongoFindBinaries.Rd |only ctrdata-0.14.1/ctrdata/man/progressOut.Rd |only ctrdata-0.17.0/ctrdata/DESCRIPTION | 7 ctrdata-0.17.0/ctrdata/MD5 | 66 ctrdata-0.17.0/ctrdata/NAMESPACE | 2 ctrdata-0.17.0/ctrdata/NEWS.md | 42 ctrdata-0.17.0/ctrdata/R/main.R | 718 +++++----- ctrdata-0.17.0/ctrdata/R/onload.R | 5 ctrdata-0.17.0/ctrdata/R/utils.R | 820 +++++------- ctrdata-0.17.0/ctrdata/README.md | 79 - ctrdata-0.17.0/ctrdata/build/vignette.rds |binary ctrdata-0.17.0/ctrdata/exec/euctr2json.sh | 35 ctrdata-0.17.0/ctrdata/exec/xml2json.php | 4 ctrdata-0.17.0/ctrdata/inst/doc/ctrdata_get_started.Rmd | 4 ctrdata-0.17.0/ctrdata/inst/doc/ctrdata_get_started.html | 9 ctrdata-0.17.0/ctrdata/inst/doc/ctrdata_usage_examples.R | 150 -- ctrdata-0.17.0/ctrdata/inst/doc/ctrdata_usage_examples.Rmd | 156 -- ctrdata-0.17.0/ctrdata/inst/doc/ctrdata_usage_examples.html | 230 --- ctrdata-0.17.0/ctrdata/man/addMetaData.Rd | 19 ctrdata-0.17.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 41 ctrdata-0.17.0/ctrdata/man/ctrLoadQueryIntoDbCtgov.Rd | 30 ctrdata-0.17.0/ctrdata/man/ctrLoadQueryIntoDbEuctr.Rd | 30 ctrdata-0.17.0/ctrdata/man/ctrMongo.Rd | 26 ctrdata-0.17.0/ctrdata/man/ctrRerunQuery.Rd | 41 ctrdata-0.17.0/ctrdata/man/dbCTRAnnotateQueryRecords.Rd | 23 ctrdata-0.17.0/ctrdata/man/dbCTRLoadJSONFiles.Rd |only ctrdata-0.17.0/ctrdata/man/dbCTRUpdateQueryHistory.Rd | 24 ctrdata-0.17.0/ctrdata/man/dbFindFields.Rd | 38 ctrdata-0.17.0/ctrdata/man/dbFindIdsUniqueTrials.Rd | 23 ctrdata-0.17.0/ctrdata/man/dbGetFieldsIntoDf.Rd | 24 ctrdata-0.17.0/ctrdata/man/dbQueryHistory.Rd | 23 ctrdata-0.17.0/ctrdata/man/dfFindUniqueEuctrRecord.Rd | 2 ctrdata-0.17.0/ctrdata/tests/testthat/testfunctions.R | 335 ++-- ctrdata-0.17.0/ctrdata/vignettes/ctrdata_get_started.Rmd | 4 ctrdata-0.17.0/ctrdata/vignettes/ctrdata_usage_examples.Rmd | 156 -- 36 files changed, 1358 insertions(+), 1808 deletions(-)
Title: Efficient Bayesian Inference for Stochastic Volatility (SV)
Models
Description: Efficient algorithms for fully Bayesian estimation of stochastic volatility (SV) models via Markov chain Monte Carlo (MCMC) methods. Methodological details are given in Kastner and Frühwirth-Schnatter (2014) <doi:10.1016/j.csda.2013.01.002>; the most common use cases are described in Kastner (2016) <doi:10.18637/jss.v069.i05>. Also incorporates SV with leverage.
Author: Gregor Kastner [aut] (<https://orcid.org/0000-0002-8237-8271>),
Darjus Hosszejni [aut, cre] (<https://orcid.org/0000-0002-3803-691X>)
Maintainer: Darjus Hosszejni <darjus.hosszejni@wu.ac.at>
Diff between stochvol versions 2.0.1 dated 2019-02-26 and 2.0.2 dated 2019-03-27
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS | 3 +++ R/utilities_svdraws.R | 10 ++++++---- R/wrappers.R | 12 +++++++++--- inst/doc/article.pdf |binary inst/doc/heavytails.pdf |binary 7 files changed, 27 insertions(+), 16 deletions(-)
Title: R Bindings to the Feather 'API'
Description: Read and write feather files, a lightweight binary columnar
data store designed for maximum speed.
Author: Hadley Wickham [aut, cre],
RStudio [cph],
Feather developers [ctb] (Bundled feather library),
Google [ctb] (Bundled flatbuffers code),
LevelDB Authors [ctb]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between feather versions 0.3.2 dated 2019-01-07 and 0.3.3 dated 2019-03-27
feather-0.3.2/feather/src/feather/CMakeFiles |only feather-0.3.2/feather/src/feather/CTestTestfile.cmake |only feather-0.3.2/feather/src/feather/Makefile |only feather-0.3.2/feather/src/feather/cmake_install.cmake |only feather-0.3.3/feather/DESCRIPTION | 8 - feather-0.3.3/feather/MD5 | 67 +--------------- feather-0.3.3/feather/NEWS.md | 8 + feather-0.3.3/feather/R/feather.R | 1 feather-0.3.3/feather/tests/testthat/helper-roundtrip.R | 2 feather-0.3.3/feather/tests/testthat/test-overwrite.R | 4 10 files changed, 21 insertions(+), 69 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-27 0.6.0
2018-11-30 0.5.0
2018-10-01 0.4.0
Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org>
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2D, 3D, 4D, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees),
C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Pavlo Mozharovskyi [cph, aut],
David C. Sterratt [cph, aut, cre]
(<https://orcid.org/0000-0001-9092-9099>)
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.4.0 dated 2019-02-18 and 0.4.1 dated 2019-03-27
DESCRIPTION | 11 +- MD5 | 70 +++++++-------- NEWS | 23 +++++ R/cart2pol.R | 3 R/cart2sph.R | 3 R/convhulln.R | 8 - R/delaunayn.R | 4 R/distmesh2d.R | 6 - R/distmeshnd.R | 2 R/entry.value.R | 20 +--- R/extprod3d.R | 2 R/halfspacen.R | 47 ++++------ R/inhulln.R | 12 +- R/intersectn.R | 54 ++++++++--- R/pol2cart.R | 3 R/sph2cart.R | 2 R/tsearch.R | 8 - build/vignette.rds |binary inst/doc/qhull-eg.pdf |binary man/bary2cart.Rd | 2 man/cart2bary.Rd | 2 man/cart2pol.Rd | 3 man/cart2sph.Rd | 3 man/distmesh2d.Rd | 6 - man/distmeshnd.Rd | 2 man/extprod3d.Rd | 2 man/halfspacen.Rd | 21 ++-- man/inhulln.Rd | 14 ++- man/intersectn.Rd | 19 +++- man/pol2cart.Rd | 3 man/sph2cart.Rd | 2 man/tsearch.Rd | 2 man/tsearchn.Rd | 2 src/Rinhulln.c | 3 tests/testthat/test-inhulln.R | 8 + tests/testthat/test-intersectn.R | 176 ++++++++++++++++++++++++++++++++++++++- 36 files changed, 394 insertions(+), 154 deletions(-)
Title: Tools for Working with 3D Surface Measurements
Description: The x3p file format is specified in ISO standard 5436:2000 to
describe 3d surface measurements. 'x3ptools' allows reading, writing and
basic modifications to the 3D surface measurements.
Author: Heike Hofmann [aut, cre],
Susan Vanderplas [aut],
Ganesh Krishnan [aut],
Eric Hare [aut]
Maintainer: Heike Hofmann <hofmann@iastate.edu>
Diff between x3ptools versions 0.0.1 dated 2018-04-05 and 0.0.2 dated 2019-03-27
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Title: Perform the Complete Processing of a Set of Proton Nuclear
Magnetic Resonance Spectra
Description: Perform the complete processing of a set of proton nuclear magnetic resonance spectra from the free induction decay (raw data) and based on a processing sequence (macro-command file). An additional file specifies all the spectra to be considered by associating their sample code as well as the levels of experimental factors to which they belong. More detail can be found in Jacob et al. (2017) <doi:10.1007/s11306-017-1178-y>.
Author: Daniel Jacob [cre, aut] (<https://orcid.org/0000-0002-6687-7169>),
Catherine Deborde [ctb],
Marie Lefebvre [ctb]
Maintainer: Daniel Jacob <daniel.jacob@inra.fr>
Diff between Rnmr1D versions 1.2.1 dated 2018-09-11 and 1.2.4 dated 2019-03-27
Rnmr1D-1.2.1/Rnmr1D/build/partial.rdb |only Rnmr1D-1.2.4/Rnmr1D/DESCRIPTION | 11 Rnmr1D-1.2.4/Rnmr1D/MD5 | 37 - Rnmr1D-1.2.4/Rnmr1D/NAMESPACE | 5 Rnmr1D-1.2.4/Rnmr1D/R/Rnmr.R | 248 +++++++- Rnmr1D-1.2.4/Rnmr1D/R/RnmrTools.R | 4 Rnmr1D-1.2.4/Rnmr1D/R/StatTools.R | 19 Rnmr1D-1.2.4/Rnmr1D/R/doProcessing.R | 64 +- Rnmr1D-1.2.4/Rnmr1D/R/generateMetadata.R | 206 +++++- Rnmr1D-1.2.4/Rnmr1D/R/ggplotTools.R |only Rnmr1D-1.2.4/Rnmr1D/README.md | 19 Rnmr1D-1.2.4/Rnmr1D/build/vignette.rds |binary Rnmr1D-1.2.4/Rnmr1D/inst/doc/Rnmr1D.R | 44 - Rnmr1D-1.2.4/Rnmr1D/inst/doc/Rnmr1D.Rmd | 64 +- Rnmr1D-1.2.4/Rnmr1D/inst/doc/Rnmr1D.html | 859 ++++++++++++++++------------- Rnmr1D-1.2.4/Rnmr1D/man/Rnmr1D-package.Rd | 9 Rnmr1D-1.2.4/Rnmr1D/man/Spec1rProcpar.Rd | 2 Rnmr1D-1.2.4/Rnmr1D/man/ggplotClusters.Rd |only Rnmr1D-1.2.4/Rnmr1D/man/ggplotCriterion.Rd |only Rnmr1D-1.2.4/Rnmr1D/man/ggplotLoadings.Rd |only Rnmr1D-1.2.4/Rnmr1D/man/ggplotPlotly.Rd |only Rnmr1D-1.2.4/Rnmr1D/man/ggplotScores.Rd |only Rnmr1D-1.2.4/Rnmr1D/vignettes/Rnmr1D.Rmd | 64 +- 23 files changed, 1072 insertions(+), 583 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.7 dated 2019-03-16 and 1.4.8 dated 2019-03-27
DESCRIPTION | 6 MD5 | 135 +++++----- NEWS.md | 4 R/demo.R | 2 R/onload.R | 3 build/vignette.rds |binary demo/unitizer.R | 14 - inst/expkg/flm0/tests/extra/inpkg.R | 2 inst/expkg/flm0/tests/unitizer/fastlm1.R | 2 inst/expkg/flm0/tests/unitizer/unitizer.fastlm.R | 2 inst/expkg/flm0/utzflm_Rcheck/00_pkg_src/utzflm/tests/extra/inpkg.R | 2 inst/expkg/flm0/utzflm_Rcheck/00_pkg_src/utzflm/tests/unitizer/fastlm1.R | 2 inst/expkg/flm0/utzflm_Rcheck/00_pkg_src/utzflm/tests/unitizer/unitizer.fastlm.R | 2 inst/expkg/flm0/utzflm_Rcheck/tests/extra/inpkg.R | 2 inst/expkg/flm0/utzflm_Rcheck/tests/unitizer/fastlm1.R | 2 inst/expkg/flm0/utzflm_Rcheck/tests/unitizer/unitizer.fastlm.R | 2 inst/expkg/flm1/tests/unitizer/fastlm1.R | 2 inst/expkg/flm1/tests/unitizer/unitizer.fastlm.R | 2 inst/expkg/flm2/tests/unitizer/fastlm1.R | 2 inst/expkg/flm2/tests/unitizer/unitizer.fastlm.R | 2 inst/expkg/flm2/tests/unitizer/unitizer.fastlm2.R | 2 tests/testpkg1.R | 12 tests/testthat/helper/refobjs/demo_res1.rds |binary tests/testthat/helper/refobjs/demo_res2.rds |binary tests/testthat/helper/refobjs/demo_res3.rds |binary tests/testthat/helper/refobjs/inpkg_txt1.rds |binary tests/testthat/helper/refobjs/inpkg_txt2.rds |binary tests/testthat/helper/refobjs/inpkg_txt2.rds.new |only tests/testthat/helper/refobjs/unitize2_del_sec.rds |binary tests/testthat/helper/refobjs/unitize2_rerun_a.rds |binary tests/testthat/helper/refobjs/unitize2_rerun_res.rds |binary tests/testthat/helper/refobjs/unitize2_unreview.rds |binary tests/testthat/helper/refobjs/unitize_errintry.rds |binary tests/testthat/helper/refobjs/unitize_faildiff.rds |binary tests/testthat/helper/refobjs/unitize_invalid_unrev.rds |binary tests/testthat/helper/refobjs/unitize_multiaccept1.rds |binary tests/testthat/helper/refobjs/unitize_multiaccept2.rds |binary tests/testthat/helper/refobjs/unitize_multiaccept3.rds |binary tests/testthat/helper/refobjs/unitize_multinput.rds |binary tests/testthat/helper/refobjs/unitize_multisect1.rds |binary tests/testthat/helper/refobjs/unitize_nav1.rds |binary tests/testthat/helper/refobjs/unitize_nsconf1.rds |binary tests/testthat/helper/refobjs/unitize_nsconf2.rds |binary tests/testthat/helper/refobjs/unitize_reeval1.rds |binary tests/testthat/helper/refobjs/unitize_reeval2.rds |binary tests/testthat/helper/refobjs/unitize_reeval2b.rds |binary tests/testthat/helper/refobjs/unitize_res1.rds |binary tests/testthat/helper/refobjs/unitize_res7a.rds |binary tests/testthat/helper/refobjs/unitize_resprint2.rds |binary tests/testthat/helper/refobjs/unitize_revdir1.rds |binary tests/testthat/helper/refobjs/unitize_revdir1a.rds |binary tests/testthat/helper/refobjs/unitize_revdir1b.rds |binary tests/testthat/helper/refobjs/unitize_revdir1c.rds |binary tests/testthat/helper/refobjs/unitize_revdir2.rds |binary tests/testthat/helper/refobjs/unitize_revdir3.rds |binary tests/testthat/helper/refobjs/unitize_revdir4.rds |binary tests/testthat/helper/refobjs/unitize_showdiff.rds |binary tests/testthat/helper/refobjs/unitize_txtcd2.rds |binary tests/testthat/helper/refobjs/unitize_txtdir.rds |binary tests/testthat/helper/refobjs/unitize_txtdir1.rds |binary tests/testthat/helper/refobjs/unitize_txtdir_quitall.rds |binary tests/testthat/helper/refobjs/unitize_usediff_no.rds |binary tests/testthat/helper/runtt.R | 18 + tests/testthat/testthat.demo.R | 12 tests/testthat/testthat.inpkg.R | 4 tests/testthat/testthat.search.R | 18 - tests/testthat/testthat.shim.R | 2 tests/testthat/testthat.utz1.R | 14 - tests/testthat/testthat.utz2.R | 8 69 files changed, 163 insertions(+), 117 deletions(-)
Title: Secure Shell (SSH) Client for R
Description: Connect to a remote server over SSH to transfer files via SCP,
setup a secure tunnel, or run a command or script on the host while
streaming stdout and stderr directly to the client.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between ssh versions 0.4 dated 2019-02-19 and 0.5 dated 2019-03-27
DESCRIPTION | 8 ++-- MD5 | 43 +++++++++++++----------- NAMESPACE | 11 ++++++ NEWS | 8 ++++ R/connect.R | 10 +++-- R/credentials.R |only R/exec.R | 3 + R/scp.R | 1 R/tunnel.R | 4 +- build/vignette.rds |binary inst/doc/intro.Rmd | 36 +++++++++++++++++--- inst/doc/intro.html | 39 ++++++++++++++++------ man/scp.Rd | 4 +- man/ssh.Rd | 6 ++- man/ssh_credentials.Rd |only man/ssh_exec.Rd | 5 +- man/ssh_tunnel.Rd | 2 - src/init.c | 2 - src/session.c | 76 +++++++++++++++++++++++-------------------- src/tunnel.c | 33 +++++++++++------- tests/testthat/test-exec.R |only tests/testthat/test-scp.R | 4 +- tests/testthat/test-tunnel.R | 28 ++++++++++----- vignettes/intro.Rmd | 36 +++++++++++++++++--- 24 files changed, 245 insertions(+), 114 deletions(-)
Title: The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Description: The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to
estimate the phylogenetic heritability of continuous traits, to test
hypotheses of neutral evolution versus stabilizing selection, to quantify
the strength of stabilizing selection, to estimate measurement error and to
make predictions about the evolution of a phenotype and phenotypic variation
in a population. The package implements combined maximum likelihood and
Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed
Model, fast parallel likelihood calculation, maximum likelihood
inference of the genotypic values at the tips, functions for summarizing and
plotting traces and posterior samples, functions for simulation of a univariate
continuous trait evolution model along a phylogenetic tree. So far, the
package has been used for estimating the heritability of quantitative traits
in macroevolutionary and epidemiological studies, see e.g.
Bertels et al. (2017) <doi:10.1093/molbev/msx246> and
Mitov and Stadler (2018) <doi:10.1093/molbev/msx328>. The algorithm for
parallel POUMM likelihood calculation has been published in
Mitov and Stadler (2019) <doi:10.1111/2041-210X.13136>.
Author: Venelin Mitov [aut, cre, cph],
Matt Dowle [ctb]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between POUMM versions 2.1.2 dated 2018-11-15 and 2.1.5 dated 2019-03-27
POUMM-2.1.2/POUMM/vignettes/UserGuideCache.RData |only POUMM-2.1.5/POUMM/DESCRIPTION | 32 +++-- POUMM-2.1.5/POUMM/MD5 | 51 +++++---- POUMM-2.1.5/POUMM/NEWS.md |only POUMM-2.1.5/POUMM/R/fitPOUMM.R | 18 +-- POUMM-2.1.5/POUMM/R/paramsPOUMM.R | 1 POUMM-2.1.5/POUMM/R/specPOUMM.R | 6 - POUMM-2.1.5/POUMM/R/summaryPOUMM.R | 73 +++++++------ POUMM-2.1.5/POUMM/R/utilities.R | 11 -- POUMM-2.1.5/POUMM/R/vignetteCachedResults.R |only POUMM-2.1.5/POUMM/README.md | 2 POUMM-2.1.5/POUMM/data |only POUMM-2.1.5/POUMM/inst/CITATION | 36 +++--- POUMM-2.1.5/POUMM/inst/REFERENCES.bib | 63 ++++++++++- POUMM-2.1.5/POUMM/inst/doc/InterpretingPOUMM.R | 13 +- POUMM-2.1.5/POUMM/inst/doc/InterpretingPOUMM.Rmd | 15 +- POUMM-2.1.5/POUMM/inst/doc/InterpretingPOUMM.html | 61 +++++++++-- POUMM-2.1.5/POUMM/inst/doc/UserGuide.R | 27 +++-- POUMM-2.1.5/POUMM/inst/doc/UserGuide.Rmd | 27 +++-- POUMM-2.1.5/POUMM/inst/doc/UserGuide.html | 118 ++++++++++++---------- POUMM-2.1.5/POUMM/man/POUMMIsADevRelease.Rd | 8 - POUMM-2.1.5/POUMM/man/gPOUMM.Rd | 3 POUMM-2.1.5/POUMM/man/specPOUMM.Rd | 6 - POUMM-2.1.5/POUMM/man/vignetteCachedResults.Rd |only POUMM-2.1.5/POUMM/tests/testthat/test-fit.R | 4 POUMM-2.1.5/POUMM/tests/testthat/test-lik.R | 2 POUMM-2.1.5/POUMM/vignettes/InterpretingPOUMM.Rmd | 15 +- POUMM-2.1.5/POUMM/vignettes/REFERENCES.bib | 63 ++++++++++- POUMM-2.1.5/POUMM/vignettes/UserGuide.Rmd | 27 +++-- 29 files changed, 461 insertions(+), 221 deletions(-)
Title: Some Nonparametric CUSUM Tests for Change-Point Detection in
Possibly Multivariate Observations
Description: Provides nonparametric CUSUM tests for detecting changes
in possibly serially dependent univariate or multivariate
observations. Tests sensitive to changes in the expectation, the
variance, the covariance, the autocovariance, the distribution
function, Spearman's rho, Kendall's tau, Gini's mean difference, and
the copula are provided, as well as a test for detecting changes in
the distribution of independent block maxima (with environmental
studies in mind). The latest additions are a test sensitive to
changes in the autocopula and a combined test of stationarity
sensitive to changes in the distribution function and the
autocopula.
Author: Ivan Kojadinovic
Maintainer: Ivan Kojadinovic <ivan.kojadinovic@univ-pau.fr>
Diff between npcp versions 0.1-9 dated 2017-08-23 and 0.1-10 dated 2019-03-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/serialtests.R | 31 +++++++++++++++++++++++++++++++ man/cpAutocop.Rd | 4 ++-- man/stDistAutocop.Rd | 2 +- src/utilities.c | 2 +- src/utilities.h | 1 - 7 files changed, 45 insertions(+), 15 deletions(-)
Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.2.4 dated 2019-02-25 and 0.2.5 dated 2019-03-27
DESCRIPTION | 7 +- MD5 | 18 +++--- NEWS.md | 12 ++++ R/calculations.R | 4 + R/plotting.R | 82 +++++++++++++++++++------------ R/run_detzrcr.R | 5 + build/vignette.rds |binary inst/doc/detzrcr-vignette.html | 19 ++++--- inst/shiny-apps/detzrcr_app/app.R | 98 +++++++++++++++++++++++++------------- man/run_detzrcr.Rd | 5 + 10 files changed, 161 insertions(+), 89 deletions(-)
Title: Determine and Evaluate Optimal Cutpoints in Binary
Classification Tasks
Description: Estimate cutpoints that optimize a specified metric in binary classification tasks
and validate performance using bootstrapping. Some methods for more robust cutpoint
estimation and various plotting functions are included.
Author: Christian Thiele [aut, cre]
Maintainer: Christian Thiele <c.thiele@gmx-topmail.de>
Diff between cutpointr versions 0.7.4 dated 2018-08-31 and 0.7.6 dated 2019-03-27
cutpointr-0.7.4/cutpointr/inst/doc/figure-html |only cutpointr-0.7.6/cutpointr/DESCRIPTION | 12 cutpointr-0.7.6/cutpointr/MD5 | 134 ++---- cutpointr-0.7.6/cutpointr/NAMESPACE | 6 cutpointr-0.7.6/cutpointr/NEWS.md | 24 + cutpointr-0.7.6/cutpointr/R/add_metric.R | 95 +++- cutpointr-0.7.6/cutpointr/R/cutpointr.R | 74 +-- cutpointr-0.7.6/cutpointr/R/data.R | 18 cutpointr-0.7.6/cutpointr/R/metrics.R | 69 +++ cutpointr-0.7.6/cutpointr/R/optimize_metric.R | 26 - cutpointr-0.7.6/cutpointr/R/plot.cutpointr.R | 3 cutpointr-0.7.6/cutpointr/R/plot_roc.R | 32 + cutpointr-0.7.6/cutpointr/R/print.summary_cutpointr.R | 2 cutpointr-0.7.6/cutpointr/R/print.summary_multi_cutpointr.R |only cutpointr-0.7.6/cutpointr/R/roc.R | 10 cutpointr-0.7.6/cutpointr/R/summary.multi_cutpointr.R |only cutpointr-0.7.6/cutpointr/R/utils.R | 79 +++- cutpointr-0.7.6/cutpointr/build/vignette.rds |binary cutpointr-0.7.6/cutpointr/data/prostate_nodal.rda |only cutpointr-0.7.6/cutpointr/inst/doc/cutpointr.R | 19 cutpointr-0.7.6/cutpointr/inst/doc/cutpointr.Rmd | 50 +- cutpointr-0.7.6/cutpointr/inst/doc/cutpointr.html | 234 +++++++----- cutpointr-0.7.6/cutpointr/man/F1_score.Rd | 8 cutpointr-0.7.6/cutpointr/man/abs_d_ppv_npv.Rd | 8 cutpointr-0.7.6/cutpointr/man/abs_d_sens_spec.Rd | 8 cutpointr-0.7.6/cutpointr/man/accuracy.Rd | 8 cutpointr-0.7.6/cutpointr/man/add_metric.Rd | 6 cutpointr-0.7.6/cutpointr/man/cohens_kappa.Rd | 8 cutpointr-0.7.6/cutpointr/man/cutpoint.Rd | 8 cutpointr-0.7.6/cutpointr/man/cutpointr.Rd | 14 cutpointr-0.7.6/cutpointr/man/cutpointr_.Rd | 4 cutpointr-0.7.6/cutpointr/man/false_omission_rate.Rd | 8 cutpointr-0.7.6/cutpointr/man/misclassification_cost.Rd | 8 cutpointr-0.7.6/cutpointr/man/multi_cutpointr.Rd | 25 - cutpointr-0.7.6/cutpointr/man/npv.Rd | 8 cutpointr-0.7.6/cutpointr/man/odds_ratio.Rd | 9 cutpointr-0.7.6/cutpointr/man/p_chisquared.Rd | 9 cutpointr-0.7.6/cutpointr/man/plot_roc.Rd | 6 cutpointr-0.7.6/cutpointr/man/plr.Rd | 9 cutpointr-0.7.6/cutpointr/man/ppv.Rd | 9 cutpointr-0.7.6/cutpointr/man/precision.Rd | 9 cutpointr-0.7.6/cutpointr/man/prod_ppv_npv.Rd | 9 cutpointr-0.7.6/cutpointr/man/prod_sens_spec.Rd | 9 cutpointr-0.7.6/cutpointr/man/prostate_nodal.Rd |only cutpointr-0.7.6/cutpointr/man/recall.Rd | 9 cutpointr-0.7.6/cutpointr/man/risk_ratio.Rd | 9 cutpointr-0.7.6/cutpointr/man/roc.Rd | 7 cutpointr-0.7.6/cutpointr/man/roc01.Rd | 9 cutpointr-0.7.6/cutpointr/man/sens_constrain.Rd |only cutpointr-0.7.6/cutpointr/man/sensitivity.Rd | 7 cutpointr-0.7.6/cutpointr/man/specificity.Rd | 7 cutpointr-0.7.6/cutpointr/man/sum_ppv_npv.Rd | 7 cutpointr-0.7.6/cutpointr/man/sum_sens_spec.Rd | 7 cutpointr-0.7.6/cutpointr/man/total_utility.Rd | 7 cutpointr-0.7.6/cutpointr/man/tp.Rd | 8 cutpointr-0.7.6/cutpointr/man/tpr.Rd | 8 cutpointr-0.7.6/cutpointr/man/youden.Rd | 8 cutpointr-0.7.6/cutpointr/tests/testthat/Rplots.pdf |binary cutpointr-0.7.6/cutpointr/tests/testthat/test-cutpointr.R | 180 +++++++-- cutpointr-0.7.6/cutpointr/vignettes/cutpointr.Rmd | 50 +- 60 files changed, 936 insertions(+), 464 deletions(-)
Title: Quasi-Potential Analysis for Stochastic Differential Equations
Description: Tools to 1) simulate and visualize stochastic differential
equations and 2) determine stability of equilibria using the ordered-upwind
method to compute the quasi-potential.
Author: Christopher Moore [aut],
Christopher Stieha [aut, cre],
Ben Nolting [aut],
Maria Cameron [aut],
Karen Abbott [aut],
James Gregson [cph] (author of expression_parser library:
https://github.com/jamesgregson/expression_parser)
Maintainer: Christopher Stieha <stieha@hotmail.com>
Diff between QPot versions 1.1 dated 2016-04-03 and 1.4 dated 2019-03-27
DESCRIPTION | 12 +++-- MD5 | 73 +++++++++++++++++++++---------- NAMESPACE | 1 NEWS | 19 -------- R/Model2String.R | 13 +++-- R/QPContour.R | 32 ++++++++----- R/QPGlobal.R | 8 +-- R/QPotential.R | 106 +++++++++++++++++++++++++--------------------- R/TSDensity.R | 17 +++---- R/TSPlot.R | 73 +++++++++++++++++++------------ R/TSTraj.R | 11 +++- R/VecDecomPlot.R | 16 +++--- README.md | 57 ++++++++++++++++-------- build |only demo/Ex1_test.R | 24 +++++----- demo/Ex2_test.R | 6 -- demo/Ex3_test.R | 13 ++--- inst |only man/Model2String.Rd | 4 - man/QPContour.Rd | 14 ++++-- man/QPotential.Rd | 26 ++++++----- man/TSDensity.Rd | 14 +++--- man/TSPlot.Rd | 16 ++++-- man/TSTraj.Rd | 10 +++- man/VecDecomPlot.Rd | 14 +++--- src/upwindorderedv4.c | 115 +++++++++++++++++++------------------------------- vignettes |only 27 files changed, 381 insertions(+), 313 deletions(-)
Title: Phylogenetic Clustering (Phyloclustering)
Description: Phylogenetic clustering (phyloclustering) is an evolutionary
Continuous Time Markov Chain model-based approach to identify
population structure from molecular data without assuming
linkage equilibrium. The package phyclust (Chen 2011) provides a
convenient implementation of phyloclustering for DNA and SNP data,
capable of clustering individuals into subpopulations and identifying
molecular sequences representative of those subpopulations. It is
designed in C for performance, interfaced with R for visualization,
and incorporates other popular open source programs including
ms (Hudson 2002) <doi:10.1093/bioinformatics/18.2.337>,
seq-gen (Rambaut and Grassly 1997)
<doi:10.1093/bioinformatics/13.3.235>,
Hap-Clustering (Tzeng 2005) <doi:10.1002/gepi.20063> and
PAML baseml (Yang 1997, 2007) <doi:10.1093/bioinformatics/13.5.555>,
<doi:10.1093/molbev/msm088>,
for simulating data, additional analyses, and searching the best tree.
See the phyclust website for more information, documentations and
examples.
Author: Wei-Chen Chen [aut, cre],
Karin Dorman [aut]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between phyclust versions 0.1-23 dated 2019-03-08 and 0.1-24 dated 2019-03-27
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 140 ++++++++++++++++++++-------------------- man/00_phyclust-package.Rd | 2 man/11_d.Color.Rd | 2 man/11_d.EMC.Rd | 2 man/11_d.EMControl.Rd | 2 man/11_d.boundary.method.Rd | 2 man/11_d.code.type.Rd | 2 man/11_d.edist.model.Rd | 2 man/11_d.em.method.Rd | 2 man/11_d.identifier.Rd | 2 man/11_d.init.method.Rd | 2 man/11_d.init.procedure.Rd | 2 man/11_d.label.method.Rd | 2 man/11_d.se.model.Rd | 2 man/11_d.show.option.Rd | 2 man/11_d.standard.code.Rd | 2 man/11_d.substitution.Rd | 2 man/RRand.Rd | 2 man/as.star.tree.Rd | 2 man/bootstrap.seq.Rd | 2 man/bootstrap.seq.data.Rd | 2 man/bootstrap.star.trees.Rd | 2 man/bootstrap.star.trees.seq.Rd | 2 man/code2nid.Rd | 2 man/code2snp.Rd | 2 man/data.fasta.pony.Rd | 2 man/data.phylip.crohn.Rd | 2 man/data.phylip.pony.Rd | 2 man/file.read.Rd | 2 man/file.write.Rd | 2 man/find.best.Rd | 2 man/find.consensus.Rd | 2 man/gen.equal.star.anc.dec.Rd | 2 man/gen.seq.Rd | 2 man/gen.star.tree.Rd | 2 man/gen.unit.K.Rd | 2 man/get.rooted.tree.height.Rd | 2 man/getcut.fun.Rd | 2 man/haplo.post.prob.Rd | 2 man/ms.Rd | 2 man/nid.aid.cid.Rd | 2 man/paml.baseml.Rd | 2 man/phyclust.Pt.Rd | 2 man/phyclust.Rd | 2 man/phyclust.e.step.Rd | 2 man/phyclust.edist.Rd | 2 man/phyclust.em.step.Rd | 2 man/phyclust.logL.Rd | 2 man/phyclust.m.step.Rd | 2 man/phyclust.se.Rd | 2 man/phyclust.se.update.Rd | 2 man/phyclust.update.Rd | 2 man/plotdots.Rd | 2 man/plotgaps.Rd | 2 man/plothist.Rd | 2 man/plotnj.Rd | 2 man/plotstruct.Rd | 2 man/print.summary.Rd | 2 man/prune.Mu.Rd | 2 man/read.seqgen.Rd | 2 man/rescale.rooted.tree.Rd | 2 man/seq.data.Rd | 2 man/seqgen.Rd | 2 man/snp2sid.Rd | 2 man/zz_all.internal.Rd | 2 man/zz_all.internal.tzeng.Rd | 2 src/R_phyclust.c | 65 +++++++++--------- src/R_phyclust_se.c | 75 ++++++++++----------- src/R_phyclust_se_update.c | 2 71 files changed, 215 insertions(+), 210 deletions(-)
Title: Network-Based Gene Set Analysis
Description: Carry out Network-based Gene Set Analysis by incorporating external information about interactions among genes, as well as novel interactions learned from data.
Author: Jing Ma, Ali Shojaie and Kun Yue
Maintainer: Jing Ma <jingma@fredhutch.org>
Diff between netgsa versions 3.0 dated 2016-06-16 and 3.1.0 dated 2019-03-27
netgsa-3.0/netgsa/R/edgelist2adj.R |only netgsa-3.0/netgsa/data/edgelist.rda |only netgsa-3.0/netgsa/data/netgsaex2.rda |only netgsa-3.0/netgsa/data/netgsaex3.rda |only netgsa-3.0/netgsa/data/netgsaexDAG.rda |only netgsa-3.0/netgsa/data/nonedgelist.rda |only netgsa-3.0/netgsa/man/edgelist2adj.Rd |only netgsa-3.0/netgsa/man/netgsaex2.Rd |only netgsa-3.0/netgsa/man/netgsaex3.Rd |only netgsa-3.0/netgsa/man/netgsaexDAG.Rd |only netgsa-3.1.0/netgsa/DESCRIPTION | 23 + netgsa-3.1.0/netgsa/MD5 | 68 +++-- netgsa-3.1.0/netgsa/NAMESPACE | 19 + netgsa-3.1.0/netgsa/R/NetGSA.R | 204 +++++++++-------- netgsa-3.1.0/netgsa/R/bic.netEst.undir.R | 19 - netgsa-3.1.0/netgsa/R/call.netgsa.R | 179 ++++++++------- netgsa-3.1.0/netgsa/R/data.R |only netgsa-3.1.0/netgsa/R/glmnet.soft.R | 34 +- netgsa-3.1.0/netgsa/R/he_method.R |only netgsa-3.1.0/netgsa/R/netEst.dir.R | 30 +- netgsa-3.1.0/netgsa/R/netEst.undir.R | 250 ++++++++++++--------- netgsa-3.1.0/netgsa/R/netgsa.onesample.R |only netgsa-3.1.0/netgsa/R/normalizeAdj.R | 56 ++-- netgsa-3.1.0/netgsa/R/prepareAdjacencyMatrix.R |only netgsa-3.1.0/netgsa/R/preparePathways.R |only netgsa-3.1.0/netgsa/R/profile.newton.se.R | 258 +++++++++++----------- netgsa-3.1.0/netgsa/R/zeroInd.R | 92 ++++--- netgsa-3.1.0/netgsa/build |only netgsa-3.1.0/netgsa/data/breastcancer2012.rda |only netgsa-3.1.0/netgsa/data/datalist |only netgsa-3.1.0/netgsa/inst |only netgsa-3.1.0/netgsa/man/NetGSA.Rd | 111 ++++++--- netgsa-3.1.0/netgsa/man/bic.netEst.undir.Rd | 57 ++-- netgsa-3.1.0/netgsa/man/breastcancer2012.Rd |only netgsa-3.1.0/netgsa/man/edgelist.Rd | 31 +- netgsa-3.1.0/netgsa/man/g.Rd |only netgsa-3.1.0/netgsa/man/group.Rd |only netgsa-3.1.0/netgsa/man/netEst.dir.Rd | 56 ++-- netgsa-3.1.0/netgsa/man/netEst.undir.Rd | 81 +++--- netgsa-3.1.0/netgsa/man/netgsa-package.Rd | 11 netgsa-3.1.0/netgsa/man/nonedgelist.Rd | 31 +- netgsa-3.1.0/netgsa/man/pathways.Rd |only netgsa-3.1.0/netgsa/man/prepareAdjacencyMatrix.Rd |only netgsa-3.1.0/netgsa/man/preparePathways.Rd |only netgsa-3.1.0/netgsa/man/x.Rd |only netgsa-3.1.0/netgsa/vignettes |only 46 files changed, 895 insertions(+), 715 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors with many levels as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>)
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.8-2.1 dated 2019-03-26 and 2.8-3 dated 2019-03-27
DESCRIPTION | 19 MD5 | 116 +-- NAMESPACE | 2 R/felm.R | 9 R/generics.R | 18 R/lfe-package.R | 5 R/nlexpect.R | 46 - R/startup.R | 5 configure | 41 - configure.ac | 18 inst/NEWS.Rd | 9 inst/doc/biascorrection.pdf |binary inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/lfe-package.Rd | 3 man/nlexpect.Rd | 14 man/summary.felm.Rd | 4 src/config.h | 41 + src/config.h.in | 8 tests/anomalies.R | 1 tests/anomalies.Rout.save | 353 ++++----- tests/bctest.R | 1 tests/bctest.Rout.save | 21 tests/cgsolve.R | 1 tests/cgsolve.Rout.save | 5 tests/cluster.R | 1 tests/cluster.Rout.save | 112 +-- tests/comparelm.R | 1 tests/comparelm.Rout.save | 101 +- tests/degenerate.R | 1 tests/degenerate.Rout.save | 21 tests/efcheck.R | 1 tests/efcheck.Rout.save | 245 +++--- tests/fourfac.R | 1 tests/fourfac.Rout.save | 99 +- tests/intact.R | 1 tests/intact.Rout.save | 191 ++--- tests/interact.R | 1 tests/interact.Rout.save | 1623 +++++++++++++++++++++----------------------- tests/ivtest.R | 1 tests/ivtest.Rout.save | 139 +-- tests/lfetest.R | 1 tests/lfetest.Rout.save | 77 +- tests/mlhs.R | 1 tests/mlhs.Rout.save | 249 +++--- tests/multiway.R | 1 tests/multiway.Rout.save | 37 - tests/naomit.R | 1 tests/naomit.Rout.save | 99 +- tests/nonest.R | 1 tests/nonest.Rout.save | 95 +- tests/onefac.R | 1 tests/onefac.Rout.save | 39 - tests/verify.R | 1 tests/verify.Rout.save | 69 - tests/weights.R | 1 tests/weights.Rout.save | 409 +++++------ tools/ax_pthread.m4 | 20 59 files changed, 2229 insertions(+), 2152 deletions(-)
Title: Antimicrobial Resistance Analysis
Description: Functions to simplify the analysis and prediction of Antimicrobial
Resistance (AMR) and to work with microbial and antimicrobial properties by
using evidence-based methods.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut] (<https://orcid.org/0000-0001-5809-5995>),
Erwin E. A. Hassing [ctb],
Corinna Glasner [aut, ths] (<https://orcid.org/0000-0003-1241-1328>),
Alex W. Friedrich [aut, ths] (<https://orcid.org/0000-0003-4881-038X>),
Bhanu N. M. Sinha [aut, ths] (<https://orcid.org/0000-0003-1634-0010>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 0.5.0 dated 2018-11-30 and 0.6.0 dated 2019-03-27
AMR-0.5.0/AMR/R/ab_property.R |only AMR-0.5.0/AMR/data/microorganisms.certe.rda |only AMR-0.5.0/AMR/data/microorganisms.oldDT.rda |only AMR-0.5.0/AMR/data/microorganisms.prevDT.rda |only AMR-0.5.0/AMR/data/microorganisms.umcg.rda |only AMR-0.5.0/AMR/data/microorganisms.unprevDT.rda |only AMR-0.5.0/AMR/data/microorganismsDT.rda |only AMR-0.5.0/AMR/man/ab_property.Rd |only AMR-0.5.0/AMR/man/figures/itis_logo.jpg |only AMR-0.5.0/AMR/man/figures/logo_amr.png |only AMR-0.5.0/AMR/man/figures/logo_amr.svg |only AMR-0.5.0/AMR/man/figures/plus.png |only AMR-0.5.0/AMR/man/microorganisms.certe.Rd |only AMR-0.5.0/AMR/man/microorganisms.umcg.Rd |only AMR-0.5.0/AMR/man/supplementary_data.Rd |only AMR-0.5.0/AMR/tests/testthat/test-ab_property.R |only AMR-0.6.0/AMR/DESCRIPTION | 46 AMR-0.6.0/AMR/MD5 | 296 +- AMR-0.6.0/AMR/NAMESPACE | 87 AMR-0.6.0/AMR/NEWS.md | 214 + AMR-0.6.0/AMR/R/abname.R | 23 AMR-0.6.0/AMR/R/age.R |only AMR-0.6.0/AMR/R/amr.R |only AMR-0.6.0/AMR/R/atc.R | 235 - AMR-0.6.0/AMR/R/atc_online.R |only AMR-0.6.0/AMR/R/atc_property.R |only AMR-0.6.0/AMR/R/availability.R |only AMR-0.6.0/AMR/R/catalogue_of_life.R |only AMR-0.6.0/AMR/R/count.R | 26 AMR-0.6.0/AMR/R/data.R | 256 - 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Title: Basic Functions in Knowledge Space Theory Using Matrix
Representation
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kstMatrix' package
provides basic functionalities to generate, handle, and manipulate
knowledge structures and knowledge spaces. Opposed to the 'kst'
package, 'kstMatrix' uses matrix representations for knowledge
structures. Furthermore, 'kstMatrix' contains several knowledge spaces
developed by the research group around Cornelia Dowling through
querying experts.
Author: Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kstMatrix versions 0.1-0 dated 2018-09-12 and 0.1-1 dated 2019-03-27
Changelog | 3 ++ DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/kmvalidate.R | 2 - build/vignette.rds |binary inst/doc/kstMatrix.html | 62 ++++++++++++++++++++++++------------------------ 6 files changed, 44 insertions(+), 41 deletions(-)