Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and
provide a simple way to obtain its parameters and a simplified report. Designed
initially to analyse Aqueous Two-Phases Systems, the package will include (every
other update) new functions in order to comprise useful tools in liquid-liquid
analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com>
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>
Diff between LLSR versions 0.0.2.0 dated 2016-02-17 and 0.0.2.1 dated 2018-08-22
LLSR-0.0.2.0/LLSR/R/AQSysTern.R |only LLSR-0.0.2.0/LLSR/man/AQSysTern.Rd |only LLSR-0.0.2.1/LLSR/DESCRIPTION | 17 +- LLSR-0.0.2.1/LLSR/MD5 | 39 ++--- LLSR-0.0.2.1/LLSR/NAMESPACE | 4 LLSR-0.0.2.1/LLSR/R/AQSys.R | 222 ++++++++++++++++++++++++-------- LLSR-0.0.2.1/LLSR/R/Multiplot.R |only LLSR-0.0.2.1/LLSR/man/AQSearch.CAS.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSearch.Rd | 5 LLSR-0.0.2.1/LLSR/man/AQSys.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSys.crpt.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSys.gsnchk.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSys.plot.Rd | 12 + LLSR-0.0.2.1/LLSR/man/AQSys.tielines.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSysBancroft.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSysCurve.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSysDB.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSysList.Rd | 1 LLSR-0.0.2.1/LLSR/man/AQSysOthmer.Rd | 1 LLSR-0.0.2.1/LLSR/man/LLSR.info.Rd | 1 LLSR-0.0.2.1/LLSR/man/LLSRxy.Rd | 1 LLSR-0.0.2.1/LLSR/man/peg4kslt.Rd | 1 22 files changed, 213 insertions(+), 99 deletions(-)
Title: FDR Power
Description: This is a package for calculating power and sample size
in multiple testing situations using the Benjamini-Hochberg (BH)
false discovery rate (FDR) procedure. The package computes power
and sample size in one of either two ways, using the average
power or the lambda-power. See Izmirlian, G. (2018) <arXiv:1801.03989>.
Author: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Maintainer: Grant Izmirlian Jr <izmirlig@mail.nih.gov>
Diff between pwrFDR versions 1.90 dated 2018-04-09 and 1.95 dated 2018-08-22
DESCRIPTION | 6 - MD5 | 14 ++-- NAMESPACE | 3 R/pwrFDR.R | 168 +++++++++++++++++++++++++++++++++++++---------------- man/Ch01-pwrFDR.Rd | 30 ++++++++- man/Ch03-dists.Rd | 45 +++++++------- src/pwrFDRsim.c | 3 src/pwrFDRsimCS.c | 23 +++++-- 8 files changed, 199 insertions(+), 93 deletions(-)
Title: Bayesian Network Belief Propagation
Description: Belief propagation methods in Bayesian Networks to propagate evidence through the network. The implementation of these methods are based on the article: Cowell, RG (2005). Local Propagation in Conditional Gaussian Bayesian Networks <http://www.jmlr.org/papers/volume6/cowell05a/>.
Author: Han Yu
Maintainer: Han Yu <hyu9@buffalo.edu>
Diff between BayesNetBP versions 1.3.0 dated 2018-02-16 and 1.4.0 dated 2018-08-22
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++++----------- NAMESPACE | 7 +++---- R/A2_Moralize.R |only R/A6_ClusterTreeCompile.R | 3 +-- R/A7_Initialization_helpers.R | 3 ++- R/C1_ElimTreeInitialize.R | 1 - R/D2_AbsorbEvidence.R | 2 +- R/E7_Sampler.R | 1 - R/G1_PlotCGBN.R | 2 +- R/H1_runBayesNetApp.R | 4 ++-- R/R6_data_emission1000.R |only data/emission1000.rda |only inst/BayesNetApp/global.R | 1 + inst/BayesNetApp/server.R | 33 +++++++++++++++++++++++++++------ man/emission1000.Rd |only 16 files changed, 58 insertions(+), 35 deletions(-)
Title: Insertion/Deletion Dynamics for Transposable Elements
Description: Provides functions to estimate the insertion and deletion rates of transposable element (TE) families. The estimation of insertion rate consists of an improved estimate of the age distribution that takes into account random mutations, and an adjustment by the deletion rate. A hypothesis test for a uniform insertion rate is also implemented. This package implements the methods proposed in Dai et al (2018).
Author: Xiongtao Dai [aut, cre, cph],
Hao Wang [aut],
Jan Dvorak [ctb],
Jeffrey Bennetzen [ctb],
Hans-Georg Mueller [ctb]
Maintainer: Xiongtao Dai <xdai@iastate.edu>
Diff between TE versions 0.2-2 dated 2018-06-01 and 0.3-0 dated 2018-08-22
DESCRIPTION | 12 ++++++------ MD5 | 18 +++++++++--------- R/AetLTR.R | 10 +++++++--- R/func.R | 2 +- R/pkgname.R | 6 +++--- data/AetLTR.rda |binary man/AetLTR.Rd | 10 +++++++--- man/EstDynamics.Rd | 2 +- man/SensitivityPlot.Rd | 4 ++-- man/TE.Rd | 6 +++--- 10 files changed, 39 insertions(+), 31 deletions(-)
Title: R Interface to SDMX Web Services
Description: Provides functions to retrieve data and metadata from providers
that disseminate data by means of SDMX web services.
SDMX (Statistical Data and Metadata eXchange) is a standard that
has been developed with the aim of simplifying the exchange of
statistical information.
More about the SDMX standard and the SDMX Web Services
can be found at: <http://sdmx.org>.
Author: Attilio Mattiocco, Diana Nicoletti, Gianpaolo Lopez, Banca d'Italia
Maintainer: Attilio Mattiocco <attilio.mattiocco@bancaditalia.it>
Diff between RJSDMX versions 1.9-3.1 dated 2018-05-27 and 2.1-0 dated 2018-08-22
DESCRIPTION | 14 - MD5 | 10 - NAMESPACE | 4 R/TSConverter.R | 377 +++++++++++++++++++++-------------------------------- R/onLoad.R | 10 - inst/java/SDMX.jar |binary 6 files changed, 173 insertions(+), 242 deletions(-)
Title: R Commander
Description: A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.
Author: John Fox [aut, cre],
Milan Bouchet-Valat [aut],
Liviu Andronic [ctb],
Michael Ash [ctb],
Theophilius Boye [ctb],
Stefano Calza [ctb],
Andy Chang [ctb],
Philippe Grosjean [ctb],
Richard Heiberger [ctb],
Kosar Karimi Pour [ctb],
G. Jay Kerns [ctb],
Renaud Lancelot [ctb],
Matthieu Lesnoff [ctb],
Uwe Ligges [ctb],
Samir Messad [ctb],
Martin Maechler [ctb],
Robert Muenchen [ctb],
Duncan Murdoch [ctb],
Erich Neuwirth [ctb],
Dan Putler [ctb],
Brian Ripley [ctb],
Miroslav Ristic [ctb],
Peter Wolf [ctb],
Kevin Wright [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between Rcmdr versions 2.4-4 dated 2018-04-16 and 2.5-0 dated 2018-08-22
DESCRIPTION | 12 MD5 | 64 +-- NEWS | 22 + R/cluster.R | 13 R/data-menu.R | 28 - R/globals.R | 5 R/graphs-menu.R | 559 ++++++++++++++++----------- R/model-menu.R | 185 ++++++++ R/statistics-dimensional-menu.R | 30 - R/statistics-summaries-menu.R | 61 ++ R/statistics-tables-menu.R | 22 - R/utilities.R | 88 +++- build/vignette.rds |binary inst/doc/Getting-Started-with-the-Rcmdr.Rnw | 2 inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary inst/etc/Rcmdr-menus.txt | 10 inst/etc/Rcmdr-model-capabilities.txt | 18 inst/etc/Thumbs.db |only inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/id/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/pl/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary inst/po/zh/LC_MESSAGES/R-Rcmdr.mo |binary man/Rcmdr-package.Rd | 6 man/Rcmdr.Utilities.Rd | 11 po/R-Rcmdr.pot | 106 +++++ po/R-es.po | 94 ++++ po/R-id.po | 326 ++++++++++----- po/R-pl.po | 98 ++++ po/R-ru.po | 89 ++++ po/R-zh.po | 370 ++++++++--------- vignettes/Getting-Started-with-the-Rcmdr.Rnw | 2 vignettes/Rcmdr-menus | 5 vignettes/Thumbs.db |only 34 files changed, 1563 insertions(+), 663 deletions(-)
Title: The Picture of Probability
Description: An eikosogram (ancient Greek for probability picture) divides the unit square
into rectangular regions whose areas, sides, and widths, represent various probabilities
associated with the values of one or more categorical variates.
Rectangle areas are joint probabilities, widths are always marginal (though possibly joint
margins, i.e. marginal joint distributions of two or more variates), and heights of rectangles
are always conditional probabilities.
Eikosograms embed the rules of probability and are useful for introducing elementary probability
theory, including axioms, marginal, conditional, and joint probabilities, and their
relationships (including Bayes theorem as a completely trivial consequence).
They are markedly superior to Venn diagrams for this purpose, especially in distinguishing
probabilistic independence, mutually exclusive events, coincident events, and associations.
They also are useful for identifying and understanding conditional independence structure.
As data analysis tools, eikosograms display categorical data in a manner similar
to Mosaic plots, especially when only two variates are involved (the only case in which
they are essentially identical, though eikosograms purposely disallow spacing between rectangles).
Unlike Mosaic plots, eikosograms do not alternate axes as each new categorical variate
(beyond two) is introduced.
Instead, only one categorical variate, designated the "response", presents on the vertical axis
and all others, designated the "conditioning" variates, appear on the horizontal.
In this way, conditional probability appears only as height and marginal probabilities as widths.
The eikosogram is therefore much better suited to a response model analysis (e.g. logistic model)
than is a Mosaic plot.
Mosaic plots are better suited to log-linear style modelling as in discrete multivariate analysis.
Of course, eikosograms are also suited to discrete multivariate analysis with each variate in turn
appearing as the response.
This makes it better suited than Mosaic plots to discrete graphical models based on conditional
independence graphs (i.e. "Bayesian Networks" or "BayesNets").
The eikosogram and its superiority to Venn diagrams in teaching probability is described in
W.H. Cherry and R.W. Oldford (2003) <https://math.uwaterloo.ca/~rwoldfor/papers/eikosograms/paper.pdf>,
its value in exploring conditional independence structure and relation to graphical and log-linear models
is described in R.W. Oldford (2003) <https://math.uwaterloo.ca/~rwoldfor/papers/eikosograms/independence/paper.pdf>,
and a number of problems, puzzles, and paradoxes that are easily explained with eikosograms are given in
R.W. Oldford (2003) <https://math.uwaterloo.ca/~rwoldfor/papers/eikosograms/examples/paper.pdf>.
Author: Wayne Oldford [aut, cre],
Erle Holgersen [aut],
Ben Lafreniere [aut],
Tianlu Zhu [aut]
Maintainer: Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between eikosograms versions 0.1.0 dated 2018-08-17 and 0.1.1 dated 2018-08-22
eikosograms-0.1.0/eikosograms/NEWS.md |only eikosograms-0.1.0/eikosograms/README.md |only eikosograms-0.1.0/eikosograms/inst/doc/introduction.R |only eikosograms-0.1.0/eikosograms/inst/doc/introduction.Rmd |only eikosograms-0.1.0/eikosograms/inst/doc/introduction.html |only eikosograms-0.1.0/eikosograms/vignettes/introduction.Rmd |only eikosograms-0.1.1/eikosograms/DESCRIPTION | 8 eikosograms-0.1.1/eikosograms/MD5 | 59 +++-- eikosograms-0.1.1/eikosograms/R/eikos.R | 8 eikosograms-0.1.1/eikosograms/R/eikos_data.R | 18 + eikosograms-0.1.1/eikosograms/build/vignette.rds |binary eikosograms-0.1.1/eikosograms/inst/doc/DataAnalysis.R |only eikosograms-0.1.1/eikosograms/inst/doc/DataAnalysis.Rmd |only eikosograms-0.1.1/eikosograms/inst/doc/DataAnalysis.html |only eikosograms-0.1.1/eikosograms/inst/doc/IndependenceExploration.R | 115 ++++++---- eikosograms-0.1.1/eikosograms/inst/doc/IndependenceExploration.Rmd | 69 ++++-- eikosograms-0.1.1/eikosograms/inst/doc/IndependenceExploration.html | 65 ++++- eikosograms-0.1.1/eikosograms/inst/doc/Introduction.R |only eikosograms-0.1.1/eikosograms/inst/doc/Introduction.Rmd |only eikosograms-0.1.1/eikosograms/inst/doc/Introduction.html |only eikosograms-0.1.1/eikosograms/man/eikos.Rd | 9 eikosograms-0.1.1/eikosograms/vignettes/DataAnalysis.Rmd |only eikosograms-0.1.1/eikosograms/vignettes/IndependenceExploration.Rmd | 69 ++++-- eikosograms-0.1.1/eikosograms/vignettes/Introduction.Rmd |only eikosograms-0.1.1/eikosograms/vignettes/data |only eikosograms-0.1.1/eikosograms/vignettes/eikosograms.bib | 28 ++ eikosograms-0.1.1/eikosograms/vignettes/img |only 27 files changed, 350 insertions(+), 98 deletions(-)
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Author: Jonathan M. Lees [aut, cre],
Jake Anderson [ctb],
Leonard Lisapaly [ctb],
Dave Harris [aut, cph]
Maintainer: Jonathan M. Lees <jonathan.lees@unc.edu>
Diff between RSEIS versions 3.8-1 dated 2018-07-05 and 3.8-3 dated 2018-08-22
DESCRIPTION | 10 ++++---- MD5 | 6 +++-- R/posix2RSEIS.R |only man/posix2RSEIS.Rd |only src/LLNfilt.c | 62 ++++++++++++++++++++++++++--------------------------- 5 files changed, 40 insertions(+), 38 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Cáceres [aut, cre],
Nicolas Martin [aut],
Víctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between meteoland versions 0.7.1 dated 2018-03-10 and 0.7.5 dated 2018-08-22
meteoland-0.7.1/meteoland/R/SpatialGridMeteorology.R |only meteoland-0.7.1/meteoland/R/SpatialGridTopography.R |only meteoland-0.7.1/meteoland/R/SpatialPixelsMeteorology.R |only meteoland-0.7.1/meteoland/R/SpatialPixelsTopography.R |only meteoland-0.7.1/meteoland/R/SpatialPointsMeteorology.R |only meteoland-0.7.1/meteoland/R/SpatialPointsTopography.R |only meteoland-0.7.1/meteoland/man/interpolationgrid.Rd |only meteoland-0.7.1/meteoland/man/interpolationpixels.Rd |only meteoland-0.7.5/meteoland/DESCRIPTION | 14 meteoland-0.7.5/meteoland/MD5 | 99 ++-- meteoland-0.7.5/meteoland/NAMESPACE | 31 + meteoland-0.7.5/meteoland/NEWS | 25 + meteoland-0.7.5/meteoland/R/DefineSpatialDataClasses.R | 92 ---- meteoland-0.7.5/meteoland/R/MeteorologyInterpolationData.R | 212 ++++++--- meteoland-0.7.5/meteoland/R/RcppExports.R | 16 meteoland-0.7.5/meteoland/R/SpatialGridMeteorology-methods.R |only meteoland-0.7.5/meteoland/R/SpatialGridTopography-methods.R |only meteoland-0.7.5/meteoland/R/SpatialPixelsMeteorology-methods.R |only meteoland-0.7.5/meteoland/R/SpatialPixelsTopography-methods.R |only meteoland-0.7.5/meteoland/R/SpatialPointsMeteorology-methods.R |only meteoland-0.7.5/meteoland/R/SpatialPointsTopography-methods.R |only meteoland-0.7.5/meteoland/R/downloadAEMETcurrentday.R | 94 ++-- meteoland-0.7.5/meteoland/R/downloadAEMEThistorical.R | 208 ++++++--- meteoland-0.7.5/meteoland/R/downloadAEMEThistoricalstationlist.R | 75 +-- meteoland-0.7.5/meteoland/R/meteocomplete.R |only meteoland-0.7.5/meteoland/R/meteoplot.R | 25 - meteoland-0.7.5/meteoland/R/summaryinterpolationdata.R |only meteoland-0.7.5/meteoland/R/utils.R | 44 ++ meteoland-0.7.5/meteoland/build/vignette.rds |binary meteoland-0.7.5/meteoland/inst/CITATION |only meteoland-0.7.5/meteoland/inst/doc/Meteorology.R | 34 - meteoland-0.7.5/meteoland/inst/doc/Meteorology.Rnw | 1 meteoland-0.7.5/meteoland/inst/doc/Meteorology.pdf |binary meteoland-0.7.5/meteoland/inst/include/meteoland.h | 18 meteoland-0.7.5/meteoland/inst/include/meteoland_RcppExports.h | 120 ++++- meteoland-0.7.5/meteoland/man/MeteorologyInterpolationData.Rd | 113 ++--- meteoland-0.7.5/meteoland/man/SpatialGridMeteorology-class.Rd | 81 +-- meteoland-0.7.5/meteoland/man/SpatialGridTopography-class.Rd | 93 ++-- meteoland-0.7.5/meteoland/man/SpatialPixelsMeteorology-class.Rd | 1 meteoland-0.7.5/meteoland/man/SpatialPixelsTopography-class.Rd | 1 meteoland-0.7.5/meteoland/man/SpatialPointsMeteorology-class.Rd | 3 meteoland-0.7.5/meteoland/man/SpatialPointsMeteorology.Rd | 58 +- meteoland-0.7.5/meteoland/man/SpatialPointsTopography-class.Rd | 3 meteoland-0.7.5/meteoland/man/correctionpoints.Rd | 4 meteoland-0.7.5/meteoland/man/defaultCorrectionParams.Rd | 3 meteoland-0.7.5/meteoland/man/defaultInterpolationParams.Rd | 2 meteoland-0.7.5/meteoland/man/interpolation.coverage.Rd | 3 meteoland-0.7.5/meteoland/man/interpolation.cv.Rd | 24 - meteoland-0.7.5/meteoland/man/interpolation_lowlevel.Rd |only meteoland-0.7.5/meteoland/man/interpolationpoints.Rd | 55 ++ meteoland-0.7.5/meteoland/man/meteocomplete.Rd |only meteoland-0.7.5/meteoland/man/meteoplot.Rd | 6 meteoland-0.7.5/meteoland/man/summarypoints.Rd | 14 meteoland-0.7.5/meteoland/src/RcppExports.cpp | 213 ++++++++++ meteoland-0.7.5/meteoland/src/interpolationutils.cpp | 1 meteoland-0.7.5/meteoland/src/precipitation.cpp | 5 meteoland-0.7.5/meteoland/src/relativehumidity.cpp | 1 meteoland-0.7.5/meteoland/src/temperature.cpp | 7 meteoland-0.7.5/meteoland/src/wind.cpp | 3 meteoland-0.7.5/meteoland/vignettes/Meteorology.Rnw | 1 60 files changed, 1166 insertions(+), 637 deletions(-)
Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability
to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally,
'ggtern' has implemented several NEW geometries which are unavailable to the
standard 'ggplot2' release. For further examples and documentation, please
proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>
Diff between ggtern versions 2.2.1 dated 2017-07-17 and 3.0.0 dated 2018-08-22
ggtern-2.2.1/ggtern/R/theme-showsecondary.R |only ggtern-3.0.0/ggtern/DESCRIPTION | 44 - ggtern-3.0.0/ggtern/LICENSE |only ggtern-3.0.0/ggtern/MD5 | 200 +++-- ggtern-3.0.0/ggtern/NAMESPACE | 15 ggtern-3.0.0/ggtern/NEWS | 9 ggtern-3.0.0/ggtern/R/coord-tern.R | 16 ggtern-3.0.0/ggtern/R/doc-data.R | 73 ++ ggtern-3.0.0/ggtern/R/geom-hex-tern.R |only ggtern-3.0.0/ggtern/R/geom-polygon-closed.R |only ggtern-3.0.0/ggtern/R/geom-tri-tern.R |only ggtern-3.0.0/ggtern/R/gg-internal.R | 4 ggtern-3.0.0/ggtern/R/onLoad.R | 26 ggtern-3.0.0/ggtern/R/plot-build.R | 205 ++++- ggtern-3.0.0/ggtern/R/stat-confidence-tern.R | 17 ggtern-3.0.0/ggtern/R/stat-density-tern.R | 95 ++ ggtern-3.0.0/ggtern/R/stat-hex-tern.R |only ggtern-3.0.0/ggtern/R/stat-interpolate-tern.R | 21 ggtern-3.0.0/ggtern/R/stat-tri-tern.R |only ggtern-3.0.0/ggtern/R/strip-unapproved.R | 8 ggtern-3.0.0/ggtern/R/theme-defaults.R | 8 ggtern-3.0.0/ggtern/R/theme-ticks.R |only ggtern-3.0.0/ggtern/R/theme.R | 361 ++++++++-- ggtern-3.0.0/ggtern/build/partial.rdb |binary ggtern-3.0.0/ggtern/data/SkyeLava.RData |only ggtern-3.0.0/ggtern/data/WhiteCells.RData |only ggtern-3.0.0/ggtern/inst/staticdocs/README.md | 8 ggtern-3.0.0/ggtern/inst/staticdocs/bootstrap/css/custom.css | 4 ggtern-3.0.0/ggtern/inst/staticdocs/content-demo.html | 2 ggtern-3.0.0/ggtern/inst/staticdocs/content-topic.html | 2 ggtern-3.0.0/ggtern/inst/staticdocs/icons.R | 45 - ggtern-3.0.0/ggtern/inst/staticdocs/index.r | 13 ggtern-3.0.0/ggtern/man/aes.Rd | 1 ggtern-3.0.0/ggtern/man/annotate.Rd | 9 ggtern-3.0.0/ggtern/man/annotation_raster_tern.Rd | 3 ggtern-3.0.0/ggtern/man/approved_layers.Rd | 6 ggtern-3.0.0/ggtern/man/arrangeGrob.Rd | 1 ggtern-3.0.0/ggtern/man/breaks_tern.Rd | 2 ggtern-3.0.0/ggtern/man/coord_tern.Rd | 5 ggtern-3.0.0/ggtern/man/data_Feldspar.Rd | 9 ggtern-3.0.0/ggtern/man/data_Fragments.Rd | 9 ggtern-3.0.0/ggtern/man/data_SkyeLava.Rd |only ggtern-3.0.0/ggtern/man/data_USDA.Rd | 9 ggtern-3.0.0/ggtern/man/data_WhiteCells.Rd |only ggtern-3.0.0/ggtern/man/draw_key_tern.Rd | 17 ggtern-3.0.0/ggtern/man/geom_Xisoprop.Rd | 38 - ggtern-3.0.0/ggtern/man/geom_Xline.Rd | 52 - ggtern-3.0.0/ggtern/man/geom_confidence_tern.Rd | 56 - ggtern-3.0.0/ggtern/man/geom_crosshair_tern.Rd | 43 - ggtern-3.0.0/ggtern/man/geom_density_tern.Rd | 55 - ggtern-3.0.0/ggtern/man/geom_errorbarX.Rd | 44 - ggtern-3.0.0/ggtern/man/geom_hex_tern.Rd |only ggtern-3.0.0/ggtern/man/geom_interpolate_tern.Rd | 71 +- ggtern-3.0.0/ggtern/man/geom_label_viewport.Rd | 44 - 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ggtern-3.0.0/ggtern/man/strip_unapproved.Rd | 1 ggtern-3.0.0/ggtern/man/tern_limits.Rd | 10 ggtern-3.0.0/ggtern/man/ternary_transformation.Rd | 1 ggtern-3.0.0/ggtern/man/theme.Rd | 377 ++++++++++- ggtern-3.0.0/ggtern/man/theme_arrowlength.Rd | 17 ggtern-3.0.0/ggtern/man/theme_bordersontop.Rd | 3 ggtern-3.0.0/ggtern/man/theme_clockwise.Rd | 10 ggtern-3.0.0/ggtern/man/theme_complete.Rd | 7 ggtern-3.0.0/ggtern/man/theme_convenience_functions.Rd | 4 ggtern-3.0.0/ggtern/man/theme_elements.Rd | 2 ggtern-3.0.0/ggtern/man/theme_gridsontop.Rd | 3 ggtern-3.0.0/ggtern/man/theme_latex.Rd | 11 ggtern-3.0.0/ggtern/man/theme_legendposition.Rd | 1 ggtern-3.0.0/ggtern/man/theme_mesh.Rd | 1 ggtern-3.0.0/ggtern/man/theme_novar_tern.Rd | 1 ggtern-3.0.0/ggtern/man/theme_rotate.Rd | 1 ggtern-3.0.0/ggtern/man/theme_showarrows.Rd | 3 ggtern-3.0.0/ggtern/man/theme_showgrid.Rd | 22 ggtern-3.0.0/ggtern/man/theme_showlabels.Rd | 4 ggtern-3.0.0/ggtern/man/theme_showmask.Rd | 3 ggtern-3.0.0/ggtern/man/theme_showprimary.Rd | 14 ggtern-3.0.0/ggtern/man/theme_showtitles.Rd | 4 ggtern-3.0.0/ggtern/man/theme_ticklength.Rd |only ggtern-3.0.0/ggtern/man/theme_ticksoutside.Rd | 3 ggtern-3.0.0/ggtern/man/theme_zoom_X.Rd | 7 ggtern-3.0.0/ggtern/man/transform_position_tern.Rd | 1 ggtern-3.0.0/ggtern/man/undocumented.Rd | 15 ggtern-3.0.0/ggtern/man/zzz-depreciated.Rd | 9 109 files changed, 1811 insertions(+), 854 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 1.1 dated 2018-08-22 and 1.1-1 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NAMESPACE | 5 +++-- inst/NEWS | 6 ++++++ man/oacat.Rd | 3 +++ 5 files changed, 20 insertions(+), 10 deletions(-)
Title: High Performance Algorithms for Vine Copula Modeling
Description: Provides an interface to 'vinecopulib', a C++ library for vine
copula modeling based on 'Boost' and 'Eigen'. The 'rvinecopulib'
package implements the core features of the popular 'VineCopula' package, in
particular inference algorithms for both vine copula and bivariate copula
models. Advantages over 'VineCopula' are a sleeker and more modern API,
improved performances, especially in high dimensions, nonparametric and
multi-parameter families. The 'rvinecopulib' package includes 'vinecopulib' as
header-only C++ library (currently version 0.3.0). Thus
users do not need to install 'vinecopulib' itself in order to use
'rvinecopulib'. Since their initial releases, 'vinecopulib' is licensed under
the MIT License, and 'rvinecopulib' is licensed under the GNU GPL version 3.
Author: Thomas Nagler [aut, cre],
Thibault Vatter [aut]
Maintainer: Thomas Nagler <info@vinecopulib.org>
Diff between rvinecopulib versions 0.3.0.1.0 dated 2018-08-09 and 0.3.0.1.1 dated 2018-08-22
DESCRIPTION | 7 - MD5 | 48 +++++----- NEWS.md | 8 + inst/include/vinecopulib/misc/implementation/tools_optimization.ipp | 4 inst/include/vinecopulib/misc/tools_optimization.hpp | 4 inst/include/vinecopulib/vinecop/implementation/class.ipp | 2 man/as_rvine_structure.Rd | 1 man/bicop.Rd | 5 - man/bicop_methods.Rd | 3 man/getters.Rd | 6 + man/plot.bicop_dist.Rd | 3 man/plot.vinecop_dist.Rd | 3 man/predict_bicop.Rd | 1 man/predict_vine.Rd | 4 man/predict_vinecop.Rd | 5 - man/rosenblatt.Rd | 1 man/rvine_structure.Rd | 1 man/vine.Rd | 15 +-- man/vine_methods.Rd | 2 man/vinecop.Rd | 8 + man/vinecop_methods.Rd | 2 src/wrappers.cpp | 3 tests/testthat/Rplots.pdf |binary tests/testthat/test_truncate_model.R | 6 - tests/testthat/test_vinecop.R | 10 +- 25 files changed, 97 insertions(+), 55 deletions(-)
Title: Genetic Analysis of Populations with Mixed Reproduction
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the 'adegenet' package.
Author: Zhian N. Kamvar [cre, aut] (<https://orcid.org/0000-0003-1458-7108>),
Javier F. Tabima [aut] (<https://orcid.org/0000-0002-3603-2691>),
Sydney E. Everhart [ctb, dtc] (<https://orcid.org/0000-0002-5773-1280>),
Jonah C. Brooks [aut],
Stacy A. Krueger-Hadfield [ctb]
(<https://orcid.org/0000-0002-7324-7448>),
Erik Sotka [ctb],
Brian J. Knaus [ctb] (<https://orcid.org/0000-0003-1665-4343>),
Patrick G. Meirmans [ctb] (<https://orcid.org/0000-0002-6395-8107>),
Niklaus J. Grunwald [ths] (<https://orcid.org/0000-0003-1656-7602>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between poppr versions 2.8.0 dated 2018-05-19 and 2.8.1 dated 2018-08-22
DESCRIPTION | 28 - MD5 | 98 ++--- NEWS | 24 + R/bootstraping.R | 215 ++++++----- R/bruvo.r | 12 R/filter_stats.R | 20 - R/internal.r | 7 R/methods.r | 1 R/poppr.R | 30 - README.md | 2 build/vignette.rds |binary inst/CITATION | 4 inst/doc/algo.pdf |binary inst/doc/mlg.R | 4 inst/doc/mlg.Rmd | 24 - inst/doc/mlg.html | 624 +++++++++++++++++++++----------- inst/doc/poppr_manual.R | 4 inst/doc/poppr_manual.Rmd | 14 inst/doc/poppr_manual.html | 776 ++++++++++++++++++++++++++--------------- man/Aeut.Rd | 2 man/Pinf.Rd | 2 man/Pram.Rd | 8 man/aboot.Rd | 125 +++--- man/bitwise.ia.Rd | 3 man/bruvo.dist.Rd | 3 man/bruvo.msn.Rd | 8 man/cutoff_predictor.Rd | 6 man/diversity_boot.Rd | 90 ++-- man/diversity_ci.Rd | 94 ++-- man/diversity_stats.Rd | 23 - man/filter_stats.Rd | 6 man/fix_replen.Rd | 6 man/genind2genalex.Rd | 4 man/greycurve.Rd | 4 man/ia.Rd | 4 man/mlg.filter.Rd | 8 man/monpop.Rd | 2 man/plot_filter_stats.Rd | 6 man/poppr-package.Rd | 14 man/poppr.Rd | 9 man/poppr.amova.Rd | 9 man/poppr.msn.Rd | 11 man/popsub.Rd | 3 man/rraf.Rd | 4 man/test_replen.Rd | 6 man/win.ia.Rd | 4 tests/testthat/test-plots.R | 11 vignettes/mlg.Rmd | 24 - vignettes/poppr_manual.Rmd | 14 vignettes/the_bibliography.bib | 8 50 files changed, 1435 insertions(+), 973 deletions(-)
Title: Finding Optimal Microsampling Designs for Non-Compartmental
Pharmacokinetic Analysis
Description: Find optimal microsampling designs for non-compartmental pharacokinetic analysis using a general simulation methodology:
Algorithm III of Barnett, Helen, Helena Geys, Tom Jacobs, and Thomas Jaki. (2017) "Optimal Designs for Non-Compartmental
Analysis of Pharmacokinetic Studies. (currently unpublished)"
This methodology consist of (1) specifying a pharmacokinetic model
including variability among animals; (2) generating possible sampling times; (3)
evaluating performance of each time point choice on simulated data; (4)
generating possible schemes given a time point choice and additional constraints
and finally (5) evaluating scheme performance on simulated data. The default
settings differ from the article of Barnett and others, in the default pharmacokinetic model used and
the parameterization of variability among animals. Details can be found in the package vignette. A 'shiny'
web application is included, which guides users from model parametrization to
optimal microsampling scheme.
Author: Adriaan Blommaert [aut, cre],
Daan Seynaeve [ctb],
Helen Barnett [ctb],
Helena Geys [ctb],
Tom Jacobs [ctb],
Fetene Tekle [ctb],
Thomas Jaki [ctb]
Maintainer: Adriaan Blommaert <adriaan.blommaert@openanalytics.eu>
Diff between microsamplingDesign versions 1.0.2 dated 2018-05-14 and 1.0.5 dated 2018-08-22
DESCRIPTION | 10 +- MD5 | 37 +++++----- NEWS | 8 +- R/internalHelpers.R | 67 ++++++++++++++++-- R/pkFunctions.R | 70 ++++++++++++++++--- build/vignette.rds |binary inst/dataForTesting/generateTestData.R | 4 - inst/dataForTesting/pkData.rds |binary inst/dataForTesting/rankSetOfSchemeswithRange.rds |binary inst/dataForTesting/rankSetOfTimePointsWithRange.rds |binary inst/dataForTesting/rankedSetOfSchemes.rds |binary inst/dataForTesting/rankedTimePoints.rds |binary inst/doc/microsamplingDesign.pdf |binary man/genMVN.Rd |only src/Makevars | 8 -- src/Makevars.win | 8 -- tests/testthat/testDataGeneration.R | 7 + tests/testthat/testPkRange.R | 12 +-- tests/testthat/testRankSetOfSchemes.R | 2 tests/testthat/testRankTimePoints.R | 10 +- 20 files changed, 177 insertions(+), 66 deletions(-)
More information about microsamplingDesign at CRAN
Permanent link
Title: Linear Ridge Regression with Ridge Penalty and Ridge Statistics
Description: Linear ridge regression coefficient's estimation and testing with different ridge related measures such as MSE, R-squared etc.
REFERENCES
i. Hoerl and Kennard (1970) <doi:10.2307/1267351>
ii. Halawa and El-Bassiouni (2000) <doi:10.1080/00949650008812006>
iii. Imdadullah, Aslam, and Saima (2017)
iv. Marquardt (1970) <doi:10.2307/1267205>.
Author: Imdad Ullah Muhammad [aut, cre]
(<https://orcid.org/0000-0002-1315-491X>),
Aslam Muhammad [aut, ctb]
Maintainer: Imdad Ullah Muhammad <mimdadasad@gmail.com>
Diff between lmridge versions 1.1 dated 2018-02-11 and 1.2 dated 2018-08-22
DESCRIPTION | 23 +++++--- MD5 | 61 ++++++++++----------- NAMESPACE | 3 - R/coef.lmridge.R | 2 R/print.lmridge.R | 4 - R/print.summary.lmridge.R | 19 ++++-- R/rstats1.R | 8 +- R/rstats2.R | 59 ++++++++++++-------- R/summary.lmridge.R | 131 +++++++++++++++++++++++++++++++--------------- R/vcov.R | 2 R/vif.R | 2 inst/CITATION |only inst/NEWS.Rd | 11 +++ man/bias.plot.Rd | 14 ++-- man/cv.plot.Rd | 16 ++--- man/hatr.Rd | 8 +- man/info.plot.Rd | 14 ++-- man/infocr.Rd | 10 +-- man/isrm.plot.Rd | 9 +-- man/kest.Rd | 22 +++---- man/lmridge-package.Rd | 4 - man/lmridge.Rd | 11 ++- man/plot.lmridge.Rd | 9 +-- man/predict.lmridge.Rd | 10 +-- man/press.lmridge.Rd | 12 ++-- man/residuals.lmridge.Rd | 8 +- man/rplots.plot.Rd | 13 ++-- man/rstats1.Rd | 14 ++-- man/rstats2.Rd | 21 +++---- man/summary.lmridge.Rd | 23 +++++--- man/vcov.Rd | 6 +- man/vif.Rd | 11 ++- 32 files changed, 329 insertions(+), 231 deletions(-)
Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to handle reading and writing of geographic metadata
defined with OGC/ISO 19115, 11119 and 19110 geographic information metadata standards,
and encoded using the ISO 19139 (XML) standard. It includes also a facility to check
the validity of ISO 19139 XML encoded metadata.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between geometa versions 0.2-0 dated 2017-11-28 and 0.3-0 dated 2018-08-22
geometa-0.2-0/geometa/man/fetchISOCodelists.Rd |only geometa-0.3-0/geometa/DESCRIPTION | 18 geometa-0.3-0/geometa/MD5 | 613 +- geometa-0.3-0/geometa/NAMESPACE | 40 geometa-0.3-0/geometa/R/GMLAbstractCRS.R | 2 geometa-0.3-0/geometa/R/GMLAbstractCoordinateOperation.R | 32 geometa-0.3-0/geometa/R/GMLAbstractCoordinateSystem.R | 8 geometa-0.3-0/geometa/R/GMLAbstractCurve.R |only geometa-0.3-0/geometa/R/GMLAbstractGML.R | 4 geometa-0.3-0/geometa/R/GMLAbstractGeneralParameterValue.R |only geometa-0.3-0/geometa/R/GMLAbstractGeometricAggregate.R |only geometa-0.3-0/geometa/R/GMLAbstractGeometricPrimitive.R |only geometa-0.3-0/geometa/R/GMLAbstractGeometry.R |only geometa-0.3-0/geometa/R/GMLAbstractObject.R | 4 geometa-0.3-0/geometa/R/GMLAbstractRing.R |only geometa-0.3-0/geometa/R/GMLAbstractSurface.R |only geometa-0.3-0/geometa/R/GMLBaseUnit.R | 2 geometa-0.3-0/geometa/R/GMLConventionalUnit.R | 2 geometa-0.3-0/geometa/R/GMLConversion.R | 12 geometa-0.3-0/geometa/R/GMLCoordinateSystemAxis.R | 2 geometa-0.3-0/geometa/R/GMLDefinition.R | 10 geometa-0.3-0/geometa/R/GMLDerivedUnit.R | 2 geometa-0.3-0/geometa/R/GMLElement.R | 6 geometa-0.3-0/geometa/R/GMLEnvelope.R |only geometa-0.3-0/geometa/R/GMLLineString.R |only geometa-0.3-0/geometa/R/GMLLinearRing.R |only geometa-0.3-0/geometa/R/GMLMultiCurve.R |only geometa-0.3-0/geometa/R/GMLMultiPoint.R |only geometa-0.3-0/geometa/R/GMLMultiSurface.R |only geometa-0.3-0/geometa/R/GMLOperationMethod.R | 23 geometa-0.3-0/geometa/R/GMLOperationParameterGroup.R | 4 geometa-0.3-0/geometa/R/GMLParameterValue.R |only geometa-0.3-0/geometa/R/GMLParameterValueGroup.R |only geometa-0.3-0/geometa/R/GMLPoint.R |only geometa-0.3-0/geometa/R/GMLPolygon.R |only geometa-0.3-0/geometa/R/GMLTimePeriod.R | 1 geometa-0.3-0/geometa/R/GMLUnitDefinition.R | 2 geometa-0.3-0/geometa/R/ISOAbstractObject.R | 261 - geometa-0.3-0/geometa/R/ISOAddress.R | 1 geometa-0.3-0/geometa/R/ISOAggregateInformation.R |only geometa-0.3-0/geometa/R/ISOAssociationType.R |only geometa-0.3-0/geometa/R/ISOBoundingPolygon.R |only geometa-0.3-0/geometa/R/ISOCellGeometry.R | 2 geometa-0.3-0/geometa/R/ISOCharacterSet.R | 2 geometa-0.3-0/geometa/R/ISOCitation.R | 10 geometa-0.3-0/geometa/R/ISOCodeListValue.R | 27 geometa-0.3-0/geometa/R/ISOCodelist.R | 161 geometa-0.3-0/geometa/R/ISOCouplingType.R | 2 geometa-0.3-0/geometa/R/ISOCoverageContentType.R | 2 geometa-0.3-0/geometa/R/ISODCPList.R | 2 geometa-0.3-0/geometa/R/ISODataQuality.R | 53 geometa-0.3-0/geometa/R/ISODateType.R | 2 geometa-0.3-0/geometa/R/ISODimensionNameType.R | 2 geometa-0.3-0/geometa/R/ISOEvaluationMethodType.R | 2 geometa-0.3-0/geometa/R/ISOFormat.R | 2 geometa-0.3-0/geometa/R/ISOGeographicExtent.R | 2 geometa-0.3-0/geometa/R/ISOGeometricObjectType.R | 2 geometa-0.3-0/geometa/R/ISOHierarchyLevel.R | 2 geometa-0.3-0/geometa/R/ISOIdentification.R | 31 geometa-0.3-0/geometa/R/ISOIdentifier.R | 2 geometa-0.3-0/geometa/R/ISOInitiativeType.R |only geometa-0.3-0/geometa/R/ISOKeywordType.R | 2 geometa-0.3-0/geometa/R/ISOKeywords.R | 21 geometa-0.3-0/geometa/R/ISOLanguage.R | 2 geometa-0.3-0/geometa/R/ISOLegalConstraints.R | 2 geometa-0.3-0/geometa/R/ISOMaintenanceFrequency.R | 2 geometa-0.3-0/geometa/R/ISOMetadata.R | 81 geometa-0.3-0/geometa/R/ISOMetadataNamespace.R | 74 geometa-0.3-0/geometa/R/ISOMetadataSchemas.R |only geometa-0.3-0/geometa/R/ISOObligation.R | 2 geometa-0.3-0/geometa/R/ISOOnLineFunction.R |only geometa-0.3-0/geometa/R/ISOOnlineResource.R | 14 geometa-0.3-0/geometa/R/ISOPresentationForm.R | 2 geometa-0.3-0/geometa/R/ISORestriction.R | 2 geometa-0.3-0/geometa/R/ISORole.R | 2 geometa-0.3-0/geometa/R/ISORoleType.R | 2 geometa-0.3-0/geometa/R/ISOSpatialRepresentationType.R | 2 geometa-0.3-0/geometa/R/ISOTopicCategory.R | 2 geometa-0.3-0/geometa/R/ISOTopologyLevel.R | 2 geometa-0.3-0/geometa/R/geometa.R | 4 geometa-0.3-0/geometa/R/geometa_options.R |only geometa-0.3-0/geometa/R/profile.R | 27 geometa-0.3-0/geometa/README.md | 38 geometa-0.3-0/geometa/inst/extdata/schemas/gml/ReadMe.txt | 218 geometa-0.3-0/geometa/inst/extdata/schemas/gml/SchematronConstraints.xml | 142 geometa-0.3-0/geometa/inst/extdata/schemas/gml/basicTypes.xsd | 536 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/coordinateOperations.xsd | 1050 ++-- geometa-0.3-0/geometa/inst/extdata/schemas/gml/coordinateReferenceSystems.xsd | 746 +-- geometa-0.3-0/geometa/inst/extdata/schemas/gml/coordinateSystems.xsd | 594 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/coverage.xsd | 584 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/datums.xsd | 574 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/defaultStyle.xsd | 906 +-- geometa-0.3-0/geometa/inst/extdata/schemas/gml/deprecatedTypes.xsd | 2266 +++++----- geometa-0.3-0/geometa/inst/extdata/schemas/gml/dictionary.xsd | 180 geometa-0.3-0/geometa/inst/extdata/schemas/gml/direction.xsd | 168 geometa-0.3-0/geometa/inst/extdata/schemas/gml/dynamicFeature.xsd | 218 geometa-0.3-0/geometa/inst/extdata/schemas/gml/feature.xsd | 188 geometa-0.3-0/geometa/inst/extdata/schemas/gml/geometryAggregates.xsd | 394 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/geometryBasic0d1d.xsd | 554 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/geometryBasic2d.xsd | 248 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/geometryComplexes.xsd | 190 geometa-0.3-0/geometa/inst/extdata/schemas/gml/geometryPrimitives.xsd | 1692 +++---- geometa-0.3-0/geometa/inst/extdata/schemas/gml/gml.xsd | 40 geometa-0.3-0/geometa/inst/extdata/schemas/gml/gmlBase.xsd | 370 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/gml_32_geometries.rdf | 736 +-- geometa-0.3-0/geometa/inst/extdata/schemas/gml/gml_3_2_1-ReadMe.txt | 116 geometa-0.3-0/geometa/inst/extdata/schemas/gml/grids.xsd | 128 geometa-0.3-0/geometa/inst/extdata/schemas/gml/measures.xsd | 136 geometa-0.3-0/geometa/inst/extdata/schemas/gml/observation.xsd | 190 geometa-0.3-0/geometa/inst/extdata/schemas/gml/referenceSystems.xsd | 140 geometa-0.3-0/geometa/inst/extdata/schemas/gml/temporal.xsd | 538 +- geometa-0.3-0/geometa/inst/extdata/schemas/gml/temporalReferenceSystems.xsd | 378 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/temporalTopology.xsd | 238 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/topology.xsd | 772 +-- geometa-0.3-0/geometa/inst/extdata/schemas/gml/units.xsd | 324 - geometa-0.3-0/geometa/inst/extdata/schemas/gml/valueObjects.xsd | 410 - geometa-0.3-0/geometa/man/GMLAbstractCRS.Rd | 15 geometa-0.3-0/geometa/man/GMLAbstractCoordinateOperation.Rd | 30 geometa-0.3-0/geometa/man/GMLAbstractCoordinateSystem.Rd | 15 geometa-0.3-0/geometa/man/GMLAbstractCurve.Rd |only geometa-0.3-0/geometa/man/GMLAbstractGML.Rd | 19 geometa-0.3-0/geometa/man/GMLAbstractGeneralConversion.Rd | 14 geometa-0.3-0/geometa/man/GMLAbstractGeneralDerivedCRS.Rd | 15 geometa-0.3-0/geometa/man/GMLAbstractGeneralOperationParameter.Rd | 15 geometa-0.3-0/geometa/man/GMLAbstractGeneralParameterValue.Rd |only geometa-0.3-0/geometa/man/GMLAbstractGeometricAggregate.Rd |only geometa-0.3-0/geometa/man/GMLAbstractGeometricPrimitive.Rd |only geometa-0.3-0/geometa/man/GMLAbstractGeometry.Rd |only geometa-0.3-0/geometa/man/GMLAbstractObject.Rd | 14 geometa-0.3-0/geometa/man/GMLAbstractRing.Rd |only geometa-0.3-0/geometa/man/GMLAbstractSingleCRS.Rd | 14 geometa-0.3-0/geometa/man/GMLAbstractSingleOperation.Rd | 14 geometa-0.3-0/geometa/man/GMLAbstractSurface.Rd |only geometa-0.3-0/geometa/man/GMLAbstractTimeGeometricPrimitive.Rd | 10 geometa-0.3-0/geometa/man/GMLAbstractTimeObject.Rd | 15 geometa-0.3-0/geometa/man/GMLAbstractTimePrimitive.Rd | 14 geometa-0.3-0/geometa/man/GMLAffineCS.Rd | 14 geometa-0.3-0/geometa/man/GMLBaseUnit.Rd | 18 geometa-0.3-0/geometa/man/GMLCartesianCS.Rd | 14 geometa-0.3-0/geometa/man/GMLConventionalUnit.Rd | 22 geometa-0.3-0/geometa/man/GMLConversion.Rd | 17 geometa-0.3-0/geometa/man/GMLCoordinateSystemAxis.Rd | 23 geometa-0.3-0/geometa/man/GMLCylindricalCS.Rd | 14 geometa-0.3-0/geometa/man/GMLDefinition.Rd | 21 geometa-0.3-0/geometa/man/GMLDerivedCRS.Rd | 19 geometa-0.3-0/geometa/man/GMLDerivedUnit.Rd | 18 geometa-0.3-0/geometa/man/GMLElement.Rd | 10 geometa-0.3-0/geometa/man/GMLEllipsoidalCS.Rd | 14 geometa-0.3-0/geometa/man/GMLEnvelope.Rd |only geometa-0.3-0/geometa/man/GMLGeodeticCRS.Rd | 21 geometa-0.3-0/geometa/man/GMLLineString.Rd |only geometa-0.3-0/geometa/man/GMLLinearCS.Rd | 14 geometa-0.3-0/geometa/man/GMLLinearRing.Rd |only geometa-0.3-0/geometa/man/GMLMultiCurve.Rd |only geometa-0.3-0/geometa/man/GMLMultiPoint.Rd |only geometa-0.3-0/geometa/man/GMLMultiSurface.Rd |only geometa-0.3-0/geometa/man/GMLObliqueCartesianCS.Rd | 14 geometa-0.3-0/geometa/man/GMLOperationMethod.Rd | 24 geometa-0.3-0/geometa/man/GMLOperationParameter.Rd | 14 geometa-0.3-0/geometa/man/GMLOperationParameterGroup.Rd | 17 geometa-0.3-0/geometa/man/GMLParameterValue.Rd |only geometa-0.3-0/geometa/man/GMLParameterValueGroup.Rd |only geometa-0.3-0/geometa/man/GMLPoint.Rd |only geometa-0.3-0/geometa/man/GMLPolarCS.Rd | 14 geometa-0.3-0/geometa/man/GMLPolygon.Rd |only geometa-0.3-0/geometa/man/GMLProjectedCRS.Rd | 17 geometa-0.3-0/geometa/man/GMLSphericalCS.Rd | 14 geometa-0.3-0/geometa/man/GMLTemporalCS.Rd | 14 geometa-0.3-0/geometa/man/GMLTimeCS.Rd | 14 geometa-0.3-0/geometa/man/GMLTimePeriod.Rd | 18 geometa-0.3-0/geometa/man/GMLUnitDefinition.Rd | 22 geometa-0.3-0/geometa/man/GMLUserDefinedCS.Rd | 14 geometa-0.3-0/geometa/man/GMLVerticalCS.Rd | 14 geometa-0.3-0/geometa/man/ISOAbsoluteExternalPositionalAccuracy.Rd | 13 geometa-0.3-0/geometa/man/ISOAbstractCatalogue.Rd | 19 geometa-0.3-0/geometa/man/ISOAbstractGenericName.Rd | 11 geometa-0.3-0/geometa/man/ISOAbstractObject.Rd | 32 geometa-0.3-0/geometa/man/ISOAbstractPositionalAccuracy.Rd | 10 geometa-0.3-0/geometa/man/ISOAddress.Rd | 22 geometa-0.3-0/geometa/man/ISOAggregateInformation.Rd |only geometa-0.3-0/geometa/man/ISOAnchor.Rd | 13 geometa-0.3-0/geometa/man/ISOAngle.Rd | 13 geometa-0.3-0/geometa/man/ISOAssociationRole.Rd | 19 geometa-0.3-0/geometa/man/ISOAssociationType.Rd |only geometa-0.3-0/geometa/man/ISOBand.Rd | 22 geometa-0.3-0/geometa/man/ISOBaseBoolean.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseCharacterString.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseDate.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseDateTime.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseDecimal.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseInteger.Rd | 11 geometa-0.3-0/geometa/man/ISOBaseReal.Rd | 11 geometa-0.3-0/geometa/man/ISOBinding.Rd | 13 geometa-0.3-0/geometa/man/ISOBoundAssociationRole.Rd | 11 geometa-0.3-0/geometa/man/ISOBoundFeatureAttribute.Rd | 11 geometa-0.3-0/geometa/man/ISOBoundingPolygon.Rd |only geometa-0.3-0/geometa/man/ISOBrowseGraphic.Rd | 18 geometa-0.3-0/geometa/man/ISOCarrierOfCharacteristics.Rd | 13 geometa-0.3-0/geometa/man/ISOCellGeometry.Rd | 16 geometa-0.3-0/geometa/man/ISOCharacterSet.Rd | 16 geometa-0.3-0/geometa/man/ISOCitation.Rd | 28 geometa-0.3-0/geometa/man/ISOClassification.Rd | 16 geometa-0.3-0/geometa/man/ISOCodeListValue.Rd | 19 geometa-0.3-0/geometa/man/ISOCodelist.Rd | 9 geometa-0.3-0/geometa/man/ISOConformanceResult.Rd | 14 geometa-0.3-0/geometa/man/ISOConstraint.Rd | 16 geometa-0.3-0/geometa/man/ISOConstraints.Rd | 11 geometa-0.3-0/geometa/man/ISOContact.Rd | 18 geometa-0.3-0/geometa/man/ISOContentInformation.Rd | 10 geometa-0.3-0/geometa/man/ISOCoupledResource.Rd | 16 geometa-0.3-0/geometa/man/ISOCouplingType.Rd | 16 geometa-0.3-0/geometa/man/ISOCoverageContentType.Rd | 16 geometa-0.3-0/geometa/man/ISOCoverageDescription.Rd | 20 geometa-0.3-0/geometa/man/ISODCPList.Rd | 16 geometa-0.3-0/geometa/man/ISODataIdentification.Rd | 64 geometa-0.3-0/geometa/man/ISODataQuality.Rd | 75 geometa-0.3-0/geometa/man/ISODataQualityAbstractElement.Rd | 25 geometa-0.3-0/geometa/man/ISODatatype.Rd | 16 geometa-0.3-0/geometa/man/ISODate.Rd | 16 geometa-0.3-0/geometa/man/ISODateType.Rd | 16 geometa-0.3-0/geometa/man/ISODefinitionReference.Rd | 13 geometa-0.3-0/geometa/man/ISODefinitionSource.Rd | 11 geometa-0.3-0/geometa/man/ISODigitalTransferOptions.Rd | 18 geometa-0.3-0/geometa/man/ISODimension.Rd | 18 geometa-0.3-0/geometa/man/ISODimensionNameType.Rd | 16 geometa-0.3-0/geometa/man/ISODistance.Rd | 13 geometa-0.3-0/geometa/man/ISODistribution.Rd | 20 geometa-0.3-0/geometa/man/ISODistributor.Rd | 22 geometa-0.3-0/geometa/man/ISODomainConsistency.Rd | 11 geometa-0.3-0/geometa/man/ISOElementSequence.Rd | 13 geometa-0.3-0/geometa/man/ISOEvaluationMethodType.Rd | 16 geometa-0.3-0/geometa/man/ISOExtendedElementInformation.Rd | 46 geometa-0.3-0/geometa/man/ISOExtent.Rd | 15 geometa-0.3-0/geometa/man/ISOFeatureAssociation.Rd | 11 geometa-0.3-0/geometa/man/ISOFeatureAttribute.Rd | 24 geometa-0.3-0/geometa/man/ISOFeatureCatalogue.Rd | 28 geometa-0.3-0/geometa/man/ISOFeatureCatalogueDescription.Rd | 22 geometa-0.3-0/geometa/man/ISOFeatureOperation.Rd | 16 geometa-0.3-0/geometa/man/ISOFeatureType.Rd | 42 geometa-0.3-0/geometa/man/ISOFileName.Rd | 13 geometa-0.3-0/geometa/man/ISOFormat.Rd | 22 geometa-0.3-0/geometa/man/ISOGeographicBoundingBox.Rd | 20 geometa-0.3-0/geometa/man/ISOGeographicDescription.Rd | 14 geometa-0.3-0/geometa/man/ISOGeographicExtent.Rd | 11 geometa-0.3-0/geometa/man/ISOGeometricObjectType.Rd | 16 geometa-0.3-0/geometa/man/ISOGeometricObjects.Rd | 16 geometa-0.3-0/geometa/man/ISOGeoreferenceable.Rd | 28 geometa-0.3-0/geometa/man/ISOGridSpatialRepresentation.Rd | 20 geometa-0.3-0/geometa/man/ISOGriddedDataPositionalAccuracy.Rd | 13 geometa-0.3-0/geometa/man/ISOHierarchyLevel.Rd | 16 geometa-0.3-0/geometa/man/ISOIdentification.Rd | 43 geometa-0.3-0/geometa/man/ISOIdentifier.Rd | 13 geometa-0.3-0/geometa/man/ISOInheritanceRelation.Rd | 19 geometa-0.3-0/geometa/man/ISOInitiativeType.Rd |only geometa-0.3-0/geometa/man/ISOKeywordType.Rd | 16 geometa-0.3-0/geometa/man/ISOKeywords.Rd | 39 geometa-0.3-0/geometa/man/ISOLanguage.Rd | 16 geometa-0.3-0/geometa/man/ISOLegalConstraints.Rd | 20 geometa-0.3-0/geometa/man/ISOLength.Rd | 13 geometa-0.3-0/geometa/man/ISOLineage.Rd | 20 geometa-0.3-0/geometa/man/ISOListedValue.Rd | 14 geometa-0.3-0/geometa/man/ISOLocalName.Rd | 11 geometa-0.3-0/geometa/man/ISOMaintenanceFrequency.Rd | 16 geometa-0.3-0/geometa/man/ISOMaintenanceInformation.Rd | 14 geometa-0.3-0/geometa/man/ISOMeasure.Rd | 13 geometa-0.3-0/geometa/man/ISOMemberName.Rd | 13 geometa-0.3-0/geometa/man/ISOMetaIdentifier.Rd | 13 geometa-0.3-0/geometa/man/ISOMetadata.Rd | 173 geometa-0.3-0/geometa/man/ISOMetadataExtensionInformation.Rd | 20 geometa-0.3-0/geometa/man/ISOMetadataNamespace.Rd | 4 geometa-0.3-0/geometa/man/ISOMimeFileType.Rd | 13 geometa-0.3-0/geometa/man/ISOMultiplicity.Rd | 14 geometa-0.3-0/geometa/man/ISOMultiplicityRange.Rd | 14 geometa-0.3-0/geometa/man/ISOObligation.Rd | 16 geometa-0.3-0/geometa/man/ISOOnLineFunction.Rd |only geometa-0.3-0/geometa/man/ISOOnlineResource.Rd | 26 geometa-0.3-0/geometa/man/ISOOperationMetadata.Rd | 26 geometa-0.3-0/geometa/man/ISOParameter.Rd | 28 geometa-0.3-0/geometa/man/ISOParameterDirection.Rd | 16 geometa-0.3-0/geometa/man/ISOPresentationForm.Rd | 16 geometa-0.3-0/geometa/man/ISOProcessStep.Rd | 20 geometa-0.3-0/geometa/man/ISOPropertyType.Rd | 17 geometa-0.3-0/geometa/man/ISORangeDimension.Rd | 16 geometa-0.3-0/geometa/man/ISORecord.Rd | 11 geometa-0.3-0/geometa/man/ISORecordType.Rd | 11 geometa-0.3-0/geometa/man/ISOReferenceIdentifier.Rd | 13 geometa-0.3-0/geometa/man/ISOReferenceSystem.Rd | 14 geometa-0.3-0/geometa/man/ISORelativeInternalPositionalAccuracy.Rd | 13 geometa-0.3-0/geometa/man/ISORepresentativeFraction.Rd | 14 geometa-0.3-0/geometa/man/ISOResponsibleParty.Rd | 18 geometa-0.3-0/geometa/man/ISORestriction.Rd | 16 geometa-0.3-0/geometa/man/ISORole.Rd | 16 geometa-0.3-0/geometa/man/ISORoleType.Rd | 16 geometa-0.3-0/geometa/man/ISOScale.Rd | 13 geometa-0.3-0/geometa/man/ISOScope.Rd | 14 geometa-0.3-0/geometa/man/ISOScopedName.Rd | 11 geometa-0.3-0/geometa/man/ISOSecurityConstraints.Rd | 22 geometa-0.3-0/geometa/man/ISOServiceIdentification.Rd | 38 geometa-0.3-0/geometa/man/ISOSource.Rd | 30 geometa-0.3-0/geometa/man/ISOSpatialRepresentation.Rd | 10 geometa-0.3-0/geometa/man/ISOSpatialRepresentationType.Rd | 16 geometa-0.3-0/geometa/man/ISOSpatialTemporalExtent.Rd | 15 geometa-0.3-0/geometa/man/ISOStandardOrderProcess.Rd | 20 geometa-0.3-0/geometa/man/ISOStatus.Rd | 16 geometa-0.3-0/geometa/man/ISOTelephone.Rd | 16 geometa-0.3-0/geometa/man/ISOTemporalExtent.Rd | 13 geometa-0.3-0/geometa/man/ISOTimePeriod.Rd | 4 geometa-0.3-0/geometa/man/ISOTopicCategory.Rd | 16 geometa-0.3-0/geometa/man/ISOTopologyLevel.Rd | 16 geometa-0.3-0/geometa/man/ISOTypeName.Rd | 14 geometa-0.3-0/geometa/man/ISOURL.Rd | 11 geometa-0.3-0/geometa/man/ISOUnlimitedInteger.Rd | 11 geometa-0.3-0/geometa/man/ISOVectorSpatialRepresentation.Rd | 16 geometa-0.3-0/geometa/man/ISOVerticalExtent.Rd | 13 geometa-0.3-0/geometa/man/geometa.Rd | 12 geometa-0.3-0/geometa/man/getGeometaOption.Rd |only geometa-0.3-0/geometa/man/getISOCodelist.Rd |only geometa-0.3-0/geometa/man/getISOCodelists.Rd |only geometa-0.3-0/geometa/man/getISOInternalCodelists.Rd |only geometa-0.3-0/geometa/man/getISOMetadataNamespace.Rd |only geometa-0.3-0/geometa/man/getISOMetadataNamespaces.Rd |only geometa-0.3-0/geometa/man/getISOMetadataSchemas.Rd |only geometa-0.3-0/geometa/man/registerISOCodelist.Rd |only geometa-0.3-0/geometa/man/registerISOMetadataNamespace.Rd |only geometa-0.3-0/geometa/man/registerISOMetadataSchema.Rd |only geometa-0.3-0/geometa/man/setGeometaOption.Rd |only geometa-0.3-0/geometa/man/setISOCodelists.Rd |only geometa-0.3-0/geometa/man/setISOMetadataNamespaces.Rd |only geometa-0.3-0/geometa/man/setISOMetadataSchemas.Rd |only geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractCRS.R | 2 geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractGeneralDerivedCRS.R | 2 geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractGeometricAggregate.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractGeometricPrimitive.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractRing.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLAbstractSingleCRS.R | 2 geometa-0.3-0/geometa/tests/testthat/test_GMLConversion.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLEnvelope.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLOperationMethod.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLOperationParameter.R | 8 geometa-0.3-0/geometa/tests/testthat/test_GMLParameterValue.R |only geometa-0.3-0/geometa/tests/testthat/test_GMLParameterValueGroup.R |only geometa-0.3-0/geometa/tests/testthat/test_ISOAggregateInformation.R |only geometa-0.3-0/geometa/tests/testthat/test_ISOBoundingPolygon.R |only 343 files changed, 10730 insertions(+), 10092 deletions(-)
Title: Create Compact Hash Digests of R Objects
Description: Implementation of a function 'digest()' for the creation
of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256',
'crc32', 'xxhash' and 'murmurhash' algorithms) permitting easy comparison of R
language objects, as well as a function 'hmac()' to create hash-based
message authentication code. Please note that this package is not meant to
be deployed for cryptographic purposes for which more comprehensive (and
widely tested) libraries such as 'OpenSSL' should be used.
Author: Dirk Eddelbuettel <edd@debian.org> with contributions
by Antoine Lucas, Jarek Tuszynski, Henrik Bengtsson, Simon Urbanek,
Mario Frasca, Bryan Lewis, Murray Stokely, Hannes Muehleisen,
Duncan Murdoch, Jim Hester, Wush Wu, Qiang Kou, Thierry Onkelinx,
Michel Lang, Viliam Simko and Kurt Hornik.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between digest versions 0.6.15 dated 2018-01-28 and 0.6.16 dated 2018-08-22
ChangeLog | 50 ++++++++++++++++++++++++++ DESCRIPTION | 10 ++--- MD5 | 34 +++++++++-------- R/AES.R | 12 +++--- R/digest.R | 19 ++++++--- R/hmac.R | 9 ++-- R/init.R | 8 ++++ build/vignette.rds |binary inst/doc/sha1.html | 4 +- man/digest.Rd | 9 ++++ src/digest.c | 5 +- src/sha2.c | 86 ++++++++++++++++++++++----------------------- tests/crc32.R |only tests/digestTest.R | 10 +++-- tests/digestTest.Rout.save | 17 ++++---- tests/hmacTest.R | 4 ++ tests/hmacTest.Rout.save | 10 +++-- tests/raw.R |only tests/sha1Test.R | 16 ++++---- 19 files changed, 193 insertions(+), 110 deletions(-)
More information about collapsibleTree at CRAN
Permanent link
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans and
K-Medoids Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans and k-medoids clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to
speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.1.3 dated 2018-07-21 and 1.1.4 dated 2018-08-22
ClusterR-1.1.3/ClusterR/src/kmeans_miniBatchKmeans_GMM_Medoids.cpp |only ClusterR-1.1.3/ClusterR/src/utils_rcpp.cpp |only ClusterR-1.1.3/ClusterR/src/utils_rcpp.h |only ClusterR-1.1.4/ClusterR/DESCRIPTION | 8 ClusterR-1.1.4/ClusterR/MD5 | 19 ClusterR-1.1.4/ClusterR/NEWS.md | 5 ClusterR-1.1.4/ClusterR/R/RcppExports.R | 128 --- ClusterR-1.1.4/ClusterR/README.md | 142 +++ ClusterR-1.1.4/ClusterR/inst/doc/the_clusterR_package.html | 12 ClusterR-1.1.4/ClusterR/inst/include |only ClusterR-1.1.4/ClusterR/src/RcppExports.cpp | 399 ---------- ClusterR-1.1.4/ClusterR/src/export_inst_header.cpp |only ClusterR-1.1.4/ClusterR/src/init.c | 54 - 13 files changed, 200 insertions(+), 567 deletions(-)
Title: Integrator of Bioinformatics Resources
Description: Can be used to integrate massive bioinformatics resources, such as tool/script and database. It provides the R functions and Shiny web application. Hundreds of bioinformatics tool/script and database have been included.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between BioInstaller versions 0.3.3 dated 2018-01-24 and 0.3.6 dated 2018-08-22
BioInstaller-0.3.3/BioInstaller/man/craw.all.versions.Rd |only BioInstaller-0.3.3/BioInstaller/tests/testthat/test_install_uilts.R |only BioInstaller-0.3.6/BioInstaller/ChangeLog | 73 BioInstaller-0.3.6/BioInstaller/DESCRIPTION | 24 BioInstaller-0.3.6/BioInstaller/MD5 | 700 + BioInstaller-0.3.6/BioInstaller/NAMESPACE | 21 BioInstaller-0.3.6/BioInstaller/NEWS.md | 88 BioInstaller-0.3.6/BioInstaller/R/BioInstaller.R | 11 BioInstaller-0.3.6/BioInstaller/R/conda.R |only BioInstaller-0.3.6/BioInstaller/R/config.R |only BioInstaller-0.3.6/BioInstaller/R/crawl.R | 4 BioInstaller-0.3.6/BioInstaller/R/info.R | 13 BioInstaller-0.3.6/BioInstaller/R/install.R | 36 BioInstaller-0.3.6/BioInstaller/R/spack.R |only BioInstaller-0.3.6/BioInstaller/R/utils_function.R | 8 BioInstaller-0.3.6/BioInstaller/R/versions.R | 15 BioInstaller-0.3.6/BioInstaller/R/web.R |only BioInstaller-0.3.6/BioInstaller/README.md | 179 BioInstaller-0.3.6/BioInstaller/build/vignette.rds |binary BioInstaller-0.3.6/BioInstaller/inst/doc/BioInstaller.R | 38 BioInstaller-0.3.6/BioInstaller/inst/doc/BioInstaller.Rmd | 142 BioInstaller-0.3.6/BioInstaller/inst/doc/BioInstaller.html | 4441 ++++++---- BioInstaller-0.3.6/BioInstaller/inst/doc/download.R |only BioInstaller-0.3.6/BioInstaller/inst/doc/download.Rmd |only BioInstaller-0.3.6/BioInstaller/inst/doc/download.html |only BioInstaller-0.3.6/BioInstaller/inst/doc/items_description.R |only BioInstaller-0.3.6/BioInstaller/inst/doc/items_description.Rmd |only BioInstaller-0.3.6/BioInstaller/inst/doc/items_description.html |only BioInstaller-0.3.6/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.R |only BioInstaller-0.3.6/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.Rmd |only BioInstaller-0.3.6/BioInstaller/inst/doc/plugins_of_BioInstaller_shiny.html |only BioInstaller-0.3.6/BioInstaller/inst/doc/start_shiny_of_BioInstaller.R |only BioInstaller-0.3.6/BioInstaller/inst/doc/start_shiny_of_BioInstaller.Rmd |only BioInstaller-0.3.6/BioInstaller/inst/doc/start_shiny_of_BioInstaller.html |only BioInstaller-0.3.6/BioInstaller/inst/doc/write_configuration_file.R | 4 BioInstaller-0.3.6/BioInstaller/inst/doc/write_configuration_file.Rmd | 82 BioInstaller-0.3.6/BioInstaller/inst/doc/write_configuration_file.html | 406 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/db/db_annovar.toml | 95 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/db/db_main.toml | 221 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/db/db_meta.toml | 141 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/db/db_ucsc.toml |only BioInstaller-0.3.6/BioInstaller/inst/extdata/config/github/github.toml | 70 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/github/github_meta.toml | 101 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/nongithub/nongithub.toml | 34 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/nongithub/nongithub_meta.toml | 34 BioInstaller-0.3.6/BioInstaller/inst/extdata/config/shiny |only BioInstaller-0.3.6/BioInstaller/inst/extdata/config/web/web_meta.toml | 2 BioInstaller-0.3.6/BioInstaller/inst/extdata/scripts/install.R |only BioInstaller-0.3.6/BioInstaller/inst/extdata/shiny |only BioInstaller-0.3.6/BioInstaller/inst/extdata/sql |only BioInstaller-0.3.6/BioInstaller/man/BioInstaller.Rd | 8 BioInstaller-0.3.6/BioInstaller/man/check_shiny_dep.Rd |only BioInstaller-0.3.6/BioInstaller/man/conda.Rd |only BioInstaller-0.3.6/BioInstaller/man/conda.env.create.Rd |only BioInstaller-0.3.6/BioInstaller/man/conda.env.list.Rd |only BioInstaller-0.3.6/BioInstaller/man/conda.list.Rd |only BioInstaller-0.3.6/BioInstaller/man/copy_configs.Rd |only BioInstaller-0.3.6/BioInstaller/man/copy_plugins.Rd |only BioInstaller-0.3.6/BioInstaller/man/crawl.all.versions.Rd |only BioInstaller-0.3.6/BioInstaller/man/figures |only BioInstaller-0.3.6/BioInstaller/man/install.bioinfo.Rd | 10 BioInstaller-0.3.6/BioInstaller/man/install.github.Rd | 9 BioInstaller-0.3.6/BioInstaller/man/install.nongithub.Rd | 9 BioInstaller-0.3.6/BioInstaller/man/new.bioinfo.Rd |only BioInstaller-0.3.6/BioInstaller/man/set_shiny_workers.Rd |only BioInstaller-0.3.6/BioInstaller/man/spack.Rd |only BioInstaller-0.3.6/BioInstaller/man/spack.list.Rd |only BioInstaller-0.3.6/BioInstaller/man/web.Rd |only BioInstaller-0.3.6/BioInstaller/tests/testthat/test_install.R | 101 BioInstaller-0.3.6/BioInstaller/tests/testthat/test_install_utils.R |only BioInstaller-0.3.6/BioInstaller/tests/testthat/test_utils.R | 20 BioInstaller-0.3.6/BioInstaller/tests/testthat/test_versions.R | 9 BioInstaller-0.3.6/BioInstaller/tests/testthat/test_web.R |only BioInstaller-0.3.6/BioInstaller/vignettes/BioInstaller.Rmd | 142 BioInstaller-0.3.6/BioInstaller/vignettes/download.Rmd |only BioInstaller-0.3.6/BioInstaller/vignettes/items_description.Rmd |only BioInstaller-0.3.6/BioInstaller/vignettes/plugins_of_BioInstaller_shiny.Rmd |only BioInstaller-0.3.6/BioInstaller/vignettes/start_shiny_of_BioInstaller.Rmd |only BioInstaller-0.3.6/BioInstaller/vignettes/write_configuration_file.Rmd | 82 79 files changed, 4942 insertions(+), 2431 deletions(-)
Title: Fast Generators and Iterators for Permutations, Combinations and
Partitions
Description: Fast generators and iterators for permutations, combinations
and partitions. The iterators allow users to generate arrangements in
a memory efficient manner and the generated arrangements are in
lexicographical (dictionary) order. Permutations and combinations can
be drawn with/without replacement and support multisets. It has been
demonstrated that 'arrangements' outperforms most of the existing
packages of similar kind. Some benchmarks could be found at
<https://randy3k.github.io/arrangements/articles/benchmark.html>.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between arrangements versions 1.1.0 dated 2018-08-13 and 1.1.1 dated 2018-08-22
DESCRIPTION | 8 +-- MD5 | 64 ++++++++++++++-------------- R/combinations.R | 46 +++----------------- R/partitions.R | 45 +++---------------- R/permutations.R | 46 +++----------------- man/combinations.Rd | 6 +- man/icombinations.Rd | 2 man/ipartitions.Rd | 2 man/ipermutations.Rd | 2 man/partitions.Rd | 2 man/permutations.Rd | 6 +- src/arrangements.c | 2 src/combinations.c | 26 +++++++++++ src/combinations/multiset_combinations.h | 6 +- src/combinations/ordinary_combinations.h | 4 - src/combinations/replacement_combinations.h | 4 - src/gmp_utils.c | 2 src/partitions.c | 28 +++++++++++- src/permutations.c | 26 +++++++++++ src/permutations/k_permutations.h | 4 - src/permutations/multiset_permutations.h | 4 - src/permutations/ordinary_permutations.h | 4 - src/permutations/replacement_permutations.h | 4 - src/utils.c | 8 +++ src/utils.h | 2 tests/testthat/test_combinations.R | 10 ++-- tests/testthat/test_k_partitions.R | 4 - tests/testthat/test_k_permutations.R | 10 ++-- tests/testthat/test_multiset_combinations.R | 10 ++-- tests/testthat/test_multiset_permutations.R | 10 ++-- tests/testthat/test_permutations.R | 15 ++++-- tests/testthat/test_replace_combinations.R | 8 +-- tests/testthat/test_replace_permutations.R | 8 +-- 33 files changed, 212 insertions(+), 216 deletions(-)
Title: High-Throughput Screening for Plate Based Assays
Description: Can be used to carry out extraction, normalization, quality control (QC), candidate hits identification and visualization for plate based assays, in drug discovery. This project was funded by the Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract No. HHSN272201400054C entitled "Adjuvant Discovery For Vaccines Against West Nile Virus and Influenza", awarded to Duke University and lead by Drs. Herman Staats and Soman Abraham.
Author: Ivo D. Shterev [aut, cre],
Cliburn Chan [aut],
Gregory D. Sempowski [aut]
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>
Diff between highSCREEN versions 0.2 dated 2018-02-20 and 0.3 dated 2018-08-22
DESCRIPTION | 11 +++++------ MD5 | 12 ++++++------ NEWS | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/highSCREENmanual.pdf |binary man/highSCREEN-package.Rd | 4 ++-- 7 files changed, 14 insertions(+), 15 deletions(-)
Title: Companion to Applied Regression
Description: Functions to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage, in press.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Daniel Adler [ctb],
Douglas Bates [ctb],
Gabriel Baud-Bovy [ctb],
Ben Bolker [ctb],
Steve Ellison [ctb],
David Firth [ctb],
Michael Friendly [ctb],
Gregor Gorjanc [ctb],
Spencer Graves [ctb],
Richard Heiberger [ctb],
Rafael Laboissiere [ctb],
Martin Maechler [ctb],
Georges Monette [ctb],
Duncan Murdoch [ctb],
Henric Nilsson [ctb],
Derek Ogle [ctb],
Brian Ripley [ctb],
William Venables [ctb],
Steve Walker [ctb],
David Winsemius [ctb],
Achim Zeileis [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between car versions 3.0-0 dated 2018-04-02 and 3.0-1 dated 2018-08-22
DESCRIPTION | 13 MD5 | 68 +- NAMESPACE | 6 NEWS | 170 +++-- R/Anova.R | 15 R/Boot.R | 57 + R/adaptiveKernel.R | 65 + R/carWeb.R | 103 +-- R/influence-mixed-models.R | 519 +++++++-------- R/linearHypothesis.R | 1463 ++++++++++++++++++++++---------------------- R/ncvTest.R | 127 +-- R/poTest.R | 3 R/qqPlot.R | 2 R/scatterplot.R | 726 +++++++++++---------- R/scatterplotMatrix.R | 38 - R/scatterplotSmoothers.R | 32 R/showLabels.R | 88 +- R/symbox.R | 82 +- R/utility-functions.R | 909 +++++++++++++-------------- build/vignette.rds |binary inst/doc/embedding.R | 370 +++++------ inst/doc/embedding.pdf |binary man/Boot.Rd | 2 man/ScatterplotSmoothers.Rd | 12 man/boxCox.Rd | 2 man/carWeb.Rd | 97 +- man/ceresPlots.Rd | 44 - man/densityPlot.Rd | 269 ++++---- man/linearHypothesis.Rd | 809 ++++++++++++------------ man/marginalModelPlot.Rd | 2 man/powerTransform.Rd | 15 man/scatterplot.Rd | 77 +- man/scatterplotMatrix.Rd | 42 - man/showLabels.Rd | 4 man/symbox.Rd | 110 +-- 35 files changed, 3270 insertions(+), 3071 deletions(-)
Title: Facilitates 'PhenoCam' Data Access and Time Series
Post-Processing
Description: Programmatic interface to the 'PhenoCam' web services (<http://phenocam.sr.unh.edu>).
Allows for easy downloading of 'PhenoCam' data directly to your R workspace
or your computer and provides post-processing routines for consistent and easy
timeseries outlier detection, smoothing and estimation of phenological transition dates.
Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.
Author: Hufkens Koen [aut, cre]
Maintainer: Hufkens Koen <koen.hufkens@gmail.com>
Diff between phenocamr versions 1.1.0 dated 2018-04-19 and 1.1.1 dated 2018-08-22
DESCRIPTION | 15 +- MD5 | 74 ++++++------ R/contract_phenocam.r | 6 - R/detect_outliers.r | 4 R/download_phenocam.r | 45 ++++--- R/expand_phenocam.r | 6 - R/grvi.r | 6 - R/list_rois.r | 21 ++- R/list_sites.r | 17 ++ R/merge_daymet.r | 4 R/optimal_span.r | 2 R/phenocam_explorer.r | 11 + R/phenophases.r | 14 +- R/read_phenocam.r | 7 - R/smooth_ts.r | 6 - R/transition_dates.r | 4 R/truncate_phenocam.r | 4 R/write_phenocam.r | 9 - inst/doc/phenocamr-vignette.R | 12 +- inst/doc/phenocamr-vignette.Rmd | 16 +- inst/doc/phenocamr-vignette.html | 174 +++++++++++++++--------------- inst/shiny/phenocam_explorer/ui.R | 2 man/contract_phenocam.Rd | 6 - man/detect_outliers.Rd | 7 - man/download_phenocam.Rd | 13 +- man/expand_phenocam.Rd | 6 - man/grvi.Rd | 6 - man/merge_daymet.Rd | 7 - man/optimal_span.Rd | 4 man/phenophases.Rd | 7 - man/read_phenocam.Rd | 7 - man/smooth_ts.Rd | 10 - man/transition_dates.Rd | 8 - man/truncate_phenocam.Rd | 7 - man/write_phenocam.Rd | 7 - tests/testthat/test_ancillary_functions.r | 48 ++++---- tests/testthat/test_download_function.r | 27 ++-- vignettes/phenocamr-vignette.Rmd | 16 +- 38 files changed, 340 insertions(+), 305 deletions(-)
Title: Multiple Imputation by Chained Equations with Multilevel Data
Description: Addons for the 'mice' package to perform multiple imputation using chained equations with two-level data. Includes imputation methods dedicated to sporadically and systematically missing values. Imputation of continuous, binary or count variables are available. Following the recommendations of Audigier, V. et al (2018) <doi:10.1214/18-STS646>, the choice of the imputation method for each variable can be facilitated by a default choice tuned according to the structure of the incomplete dataset. Allows parallel calculation for 'mice'.
Author: Vincent Audigier [aut, cre] (CNAM MSDMA team),
Matthieu Resche-Rigon [aut] (INSERM ECSTRA team)
Maintainer: Vincent Audigier <vincent.audigier@cnam.fr>
Diff between micemd versions 1.2.0 dated 2018-01-07 and 1.3.0 dated 2018-08-22
DESCRIPTION | 12 - MD5 | 30 ++-- R/mice.impute.2l.glm.bin.R | 2 R/mice.impute.2l.glm.pois.R | 2 R/micemd-internal.R | 250 +++++++++++++++++++------------------- data/CHEM97Na.rda |binary data/IPDNa.rda |binary man/IPDNa.Rd | 6 man/find.defaultMethod.Rd | 2 man/mice.impute.2l.2stage.bin.Rd | 6 man/mice.impute.2l.2stage.norm.Rd | 2 man/mice.impute.2l.2stage.pmm.Rd | 2 man/mice.impute.2l.2stage.pois.Rd | 4 man/mice.impute.2l.glm.bin.Rd | 2 man/mice.impute.2l.glm.norm.Rd | 2 man/micemd-package.Rd | 17 -- 16 files changed, 166 insertions(+), 173 deletions(-)
Title: Qualitative Interaction Trees
Description: Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial.
Author: Elise Dusseldorp [aut, cre, cph],
Lisa Doove [aut],
Jeanne van de Put [aut],
Cor Ninaber [ctb] (supported with the plot function),
Iven Van Mechelen [aut, cph]
Maintainer: Elise Dusseldorp <elise.dusseldorp@fsw.leidenuniv.nl>
Diff between quint versions 1.2.1 dated 2016-12-23 and 1.2.2 dated 2018-08-22
DESCRIPTION | 10 +- MD5 | 26 ++--- NAMESPACE | 94 ++++++++++---------- NEWS | 170 ++++++++++++++++++------------------ R/predict.quint.R | 221 ++++++++++++++++++++++++----------------------- man/bcrp.Rd | 125 +++++++++++++------------- man/plot.quint.Rd | 91 +++++++++---------- man/predict.quint.Rd | 119 ++++++++++++------------- man/prune.quint.Rd | 125 +++++++++++++------------- man/quint-package.Rd | 135 ++++++++++++++-------------- man/quint.Rd | 235 ++++++++++++++++++++++++-------------------------- man/quint.control.Rd | 153 ++++++++++++++++---------------- man/quint.validate.Rd | 171 ++++++++++++++++++------------------ man/summary.quint.Rd | 75 +++++++-------- 14 files changed, 878 insertions(+), 872 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]
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between lfe versions 2.8 dated 2018-06-28 and 2.8-2 dated 2018-08-22
DESCRIPTION | 11 ++++++----- MD5 | 38 +++++++++++++++++++------------------- R/demeanlist.R | 4 +++- R/nlexpect.R | 10 +++++----- cleanup | 2 +- inst/NEWS.Rd | 8 ++++++++ inst/doc/biascorrection.pdf |binary inst/doc/identification.pdf |binary inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/bccorr.Rd | 4 +--- man/cgsolve.Rd | 3 ++- man/felm.Rd | 4 ++-- man/getfe.Rd | 4 ++-- man/nlexpect.Rd | 17 +++++++++-------- src/Crowsum.c | 2 +- src/demean.c | 7 ++++++- src/kaczmarz.c | 7 ++++++- tests/lfetest.R | 4 ++-- tests/lfetest.Rout.save | 38 +++++++++++++++++++------------------- 20 files changed, 92 insertions(+), 71 deletions(-)
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative signal is expected to be
localized, a series of filters determine which peak signals are characterized by
an implausible spatial distribution. The filters reduce the dataset dimensionality
and increase its information vs noise ratio, improving the quality of the
unsupervised analysis results, reducing data dimensionality and simplifying
the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Diff between SPUTNIK versions 1.0.3.2 dated 2018-08-15 and 1.0.3.3 dated 2018-08-22
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/graph_funcs.R | 14 +------------- 3 files changed, 6 insertions(+), 18 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. Both general data manipulation functions and some more special functions for statistical disclosure control are included.
Author: Øyvind Langsrud
Maintainer: Øyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 0.2.1 dated 2017-02-07 and 0.3.0 dated 2018-08-22
DESCRIPTION | 17 +++++----- MD5 | 61 +++++++++++++++++++++++++++--------- NAMESPACE | 25 ++++++++++++++ R/AddLeadingZeros.R |only R/DataFrameToMatrix.R |only R/HierarchyCompute.R |only R/PatternMatching.R |only R/RowGroups.R |only README.md | 26 +++++++++++++++ man/AddLeadingZeros.Rd |only man/AddMapsInput.Rd |only man/AddNonExistingCode.Rd |only man/AutoLevel.Rd |only man/AutoSplit.Rd | 1 man/CbindIdMatch.Rd | 1 man/CharacterDataFrame.Rd |only man/CrossCodeFrames.Rd |only man/CrossDataDummyHierarchies.Rd |only man/CrossDataDummyHierarchy.Rd |only man/DataDummyHierarchy.Rd |only man/DataFrameToMatrix.Rd |only man/DummyHierarchy.Rd |only man/FactorLevCorr.Rd | 1 man/FindCommonCells.Rd | 1 man/FindDimLists.Rd | 1 man/FindTableGroup.Rd | 1 man/FixHierarchy.Rd |only man/ForceCharacterDataFrame.Rd |only man/ForceFactorDataFrame.Rd |only man/HierarchicalGroups.Rd | 1 man/HierarchicalWildcardGlobbing.Rd |only man/HierarchyCompute.Rd |only man/HierarchyFix.Rd |only man/Match.Rd |only man/MatrixToDataFrame.Rd |only man/Number.Rd |only man/RbindAll.Rd | 1 man/RowGroups.Rd |only man/SSBtoolsData.Rd |only man/SortRows.Rd | 1 man/Stack.Rd | 1 man/UniqueIntegerSortMatrix.Rd |only man/Unstack.Rd | 1 man/WildcardGlobbing.Rd |only man/WildcardGlobbingVector.Rd |only man/crossMerge.Rd |only man/matlabColon.Rd | 7 +--- 47 files changed, 109 insertions(+), 38 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented lassnags)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 1.6.0 dated 2018-07-26 and 1.6.1 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NEWS.md | 9 +++++++++ R/catalog_apply.r | 9 +-------- R/clusters_apply.r | 27 ++++++++++++++++++++++++--- R/lastrees_dalponte.r | 22 +++++++++++++++------- R/utils_misc.r | 21 ++++++++++++--------- README.md | 2 +- tests/testthat/Rplots.pdf |binary tests/testthat/test-grid_catalog.R | 2 +- tests/testthat/test-grid_terrain.R | 6 +++--- tests/testthat/test-lastrees.R | 2 +- tests/testthat/test-metrics.R | 6 ++++-- 13 files changed, 87 insertions(+), 51 deletions(-)
Title: Multi-Isotope Labeling for Metabolomics Analysis
Description: An efficient approach for fishing out the dual (or multiple)
isotope labeled analytes using dual labeling of metabolites for
metabolome analysis (DLEMMA) approach, described in Liron (2018) <doi:10.1021/acs.analchem.8b01644>.
Author: Yonghui Dong
Maintainer: Yonghui Dong <yonghui.dong@gmail.com>
Diff between Miso versions 0.1.1 dated 2018-01-17 and 0.1.3 dated 2018-08-22
DESCRIPTION | 11 ++++++----- MD5 | 26 +++++++++++++++++--------- NAMESPACE | 11 +++++++++++ R/Fresult.R | 12 ++++++------ R/Prefilter2.R |only R/Rresult.R | 2 +- R/diso.R | 9 ++++----- R/fold.R |only R/getp.R |only R/lcms.R | 2 +- R/prefilter.R | 6 +++--- README.md |only data/lcms.rda |binary inst |only man/fold.Rd |only man/getp.Rd |only man/lcms.Rd | 2 +- man/prefilter2.Rd |only 18 files changed, 50 insertions(+), 31 deletions(-)
Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph],
Matthias Studer [aut],
Reto Buergin [aut],
Alexis Gabadinho [ctb],
Pierre-Alexandre Fonta [ctb],
Nicolas Muller [ctb],
Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>
Diff between TraMineRextras versions 0.4.2 dated 2018-02-01 and 0.4.3 dated 2018-08-22
TraMineRextras-0.4.2/TraMineRextras/R/seqeordplot.R |only TraMineRextras-0.4.2/TraMineRextras/man/seqeordplot.Rd |only TraMineRextras-0.4.3/TraMineRextras/DESCRIPTION | 8 +- TraMineRextras-0.4.3/TraMineRextras/MD5 | 40 ++++------ TraMineRextras-0.4.3/TraMineRextras/NAMESPACE | 2 TraMineRextras-0.4.3/TraMineRextras/R/TSE_TO_STS.R | 2 TraMineRextras-0.4.3/TraMineRextras/R/plot.stslist.surv.R | 13 ++- TraMineRextras-0.4.3/TraMineRextras/R/seqgen.missing.R | 16 +--- TraMineRextras-0.4.3/TraMineRextras/R/seqimplic.R | 27 +++++- TraMineRextras-0.4.3/TraMineRextras/R/seqplot-tentrop.R | 30 +++++-- TraMineRextras-0.4.3/TraMineRextras/R/seqrep-grp.R | 3 TraMineRextras-0.4.3/TraMineRextras/R/seqsplot.R | 12 ++- TraMineRextras-0.4.3/TraMineRextras/R/seqsurv.R | 1 TraMineRextras-0.4.3/TraMineRextras/inst/NEWS | 26 ++++++ TraMineRextras-0.4.3/TraMineRextras/inst/NEWS.Rd | 31 +++++++ TraMineRextras-0.4.3/TraMineRextras/man/TSE_to_STS.Rd | 2 TraMineRextras-0.4.3/TraMineRextras/man/TraMineRextras-package.Rd | 2 TraMineRextras-0.4.3/TraMineRextras/man/plot.stslist.surv.Rd | 8 +- TraMineRextras-0.4.3/TraMineRextras/man/seqe2stm.Rd | 2 TraMineRextras-0.4.3/TraMineRextras/man/seqedist.Rd | 8 +- TraMineRextras-0.4.3/TraMineRextras/man/seqimplic.Rd | 10 +- TraMineRextras-0.4.3/TraMineRextras/man/seqplot-tentrop.Rd | 8 +- 22 files changed, 175 insertions(+), 76 deletions(-)
More information about TraMineRextras at CRAN
Permanent link
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 1.7 dated 2018-06-02 and 1.8 dated 2018-08-22
DESCRIPTION | 8 - MD5 | 12 - NAMESPACE | 1 R/GSED.R | 272 +++++++++++++++++++++++++++++------------- man/GSED-package.Rd | 4 man/magnusson_turnbull.Rd | 14 -- man/sim_magnusson_turnbull.Rd | 6 7 files changed, 213 insertions(+), 104 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 1.0.2 dated 2017-08-28 and 1.1.0 dated 2018-08-22
Eagle-1.0.2/Eagle/R/misc.R |only Eagle-1.0.2/Eagle/R/packagedesc.R |only Eagle-1.0.2/Eagle/inst/shiny_app/faq.rmd |only Eagle-1.0.2/Eagle/inst/shiny_app/www/images/banner_read_genotypes.png |only Eagle-1.0.2/Eagle/inst/shiny_app/www/images/banner_read_phenotypes.png |only Eagle-1.0.2/Eagle/inst/shiny_app/www/images/home_banner.jpg |only Eagle-1.0.2/Eagle/src/RcppFunctions.cpp |only Eagle-1.1.0/Eagle/DESCRIPTION | 30 Eagle-1.1.0/Eagle/MD5 | 126 Eagle-1.1.0/Eagle/NAMESPACE | 31 Eagle-1.1.0/Eagle/R/AM.R | 1071 +-- Eagle-1.1.0/Eagle/R/FPR4AM.R |only Eagle-1.1.0/Eagle/R/GenomicRel.R |only Eagle-1.1.0/Eagle/R/OpenGUI.R | 48 Eagle-1.1.0/Eagle/R/RcppExports.R | 28 Eagle-1.1.0/Eagle/R/ReadMap.R | 187 Eagle-1.1.0/Eagle/R/ReadMarker.R | 655 +- Eagle-1.1.0/Eagle/R/ReadPheno.R | 299 Eagle-1.1.0/Eagle/R/ReadZmat.R |only Eagle-1.1.0/Eagle/R/ReshapeM.R |only Eagle-1.1.0/Eagle/R/build_design_matrix.R |only Eagle-1.1.0/Eagle/R/calcMMt.R |only Eagle-1.1.0/Eagle/R/calcVC.R |only Eagle-1.1.0/Eagle/R/calc_extBIC.R |only Eagle-1.1.0/Eagle/R/calculateH.R |only Eagle-1.1.0/Eagle/R/calculateMMt.R |only Eagle-1.1.0/Eagle/R/calculateMMt_sqrt_and_sqrtinv.R |only Eagle-1.1.0/Eagle/R/calculateP.R |only Eagle-1.1.0/Eagle/R/calculate_a_and_vara.R |only Eagle-1.1.0/Eagle/R/calculate_reduced_a.R |only Eagle-1.1.0/Eagle/R/calculate_reduced_vara.R |only Eagle-1.1.0/Eagle/R/check_for_NA_in_trait.R |only Eagle-1.1.0/Eagle/R/check_inputs.R |only Eagle-1.1.0/Eagle/R/check_inputs_mlam.R |only Eagle-1.1.0/Eagle/R/constructX.R |only Eagle-1.1.0/Eagle/R/create_ascii.R |only Eagle-1.1.0/Eagle/R/doquiet.R |only Eagle-1.1.0/Eagle/R/emma_MLE.R |only Eagle-1.1.0/Eagle/R/emma_REMLE.R |only Eagle-1.1.0/Eagle/R/emma_delta_ML_LL_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_delta_ML_LL_wo_Z.R |only Eagle-1.1.0/Eagle/R/emma_delta_ML_dLL_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_delta_REML_LL_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_delta_REML_dLL_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_eigen_L_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_eigen_L_wo_Z.R |only Eagle-1.1.0/Eagle/R/emma_eigen_R_w_Z.R |only Eagle-1.1.0/Eagle/R/emma_eigen_R_wo_Z.R |only Eagle-1.1.0/Eagle/R/emma_misc.R |only Eagle-1.1.0/Eagle/R/extract_geno.R |only Eagle-1.1.0/Eagle/R/find_qtl.R |only Eagle-1.1.0/Eagle/R/form_results.R |only Eagle-1.1.0/Eagle/R/fullpath.R |only Eagle-1.1.0/Eagle/R/onAttach.R | 42 Eagle-1.1.0/Eagle/R/print_final.R |only Eagle-1.1.0/Eagle/R/print_header.R |only Eagle-1.1.0/Eagle/R/print_results.R |only Eagle-1.1.0/Eagle/R/print_title.R |only Eagle-1.1.0/Eagle/R/summary_am.R | 466 - Eagle-1.1.0/Eagle/inst/extdata/Z.txt |only Eagle-1.1.0/Eagle/inst/extdata/geno.ped | 300 Eagle-1.1.0/Eagle/inst/extdata/geno.txt | 300 Eagle-1.1.0/Eagle/inst/extdata/map.txt | 202 Eagle-1.1.0/Eagle/inst/extdata/pheno.txt | 302 Eagle-1.1.0/Eagle/inst/shiny_app/app.R | 3115 +++++----- Eagle-1.1.0/Eagle/inst/shiny_app/css.css | 15 Eagle-1.1.0/Eagle/inst/shiny_app/help.html | 18 Eagle-1.1.0/Eagle/inst/shiny_app/www/images/HomeScreen.jpg |binary Eagle-1.1.0/Eagle/inst/shiny_app/www/images/Zmat_banner.jpg |only Eagle-1.1.0/Eagle/man/AM.Rd | 90 Eagle-1.1.0/Eagle/man/Eagle-package.Rd | 71 Eagle-1.1.0/Eagle/man/FPR4AM.Rd |only Eagle-1.1.0/Eagle/man/OpenGUI.Rd | 9 Eagle-1.1.0/Eagle/man/ReadMap.Rd | 3 Eagle-1.1.0/Eagle/man/ReadMarker.Rd | 3 Eagle-1.1.0/Eagle/man/ReadPheno.Rd | 3 Eagle-1.1.0/Eagle/man/ReadZmat.Rd |only Eagle-1.1.0/Eagle/man/SummaryAM.Rd | 4 Eagle-1.1.0/Eagle/src/CreateASCIInospace.cpp |only Eagle-1.1.0/Eagle/src/CreateASCIInospace_PLINK.cpp |only Eagle-1.1.0/Eagle/src/Makevars | 2 Eagle-1.1.0/Eagle/src/Makevars.win | 4 Eagle-1.1.0/Eagle/src/RcppExports.cpp | 116 Eagle-1.1.0/Eagle/src/ReadBlock.cpp |only Eagle-1.1.0/Eagle/src/ReshapeM_rcpp.cpp |only Eagle-1.1.0/Eagle/src/calculateMMt_rcpp.cpp |only Eagle-1.1.0/Eagle/src/calculate_a_and_vara_rcpp.cpp |only Eagle-1.1.0/Eagle/src/calculate_reduced_a_rcpp.cpp |only Eagle-1.1.0/Eagle/src/createM_ASCII_rcpp.cpp |only Eagle-1.1.0/Eagle/src/createM_ASCII_rcpp.h |only Eagle-1.1.0/Eagle/src/createMt_ASCII_rcpp.cpp |only Eagle-1.1.0/Eagle/src/extract_geno_rcpp.cpp |only Eagle-1.1.0/Eagle/src/fasttimer.cpp |only Eagle-1.1.0/Eagle/src/getNumColumns.cpp |only Eagle-1.1.0/Eagle/src/getNumRows.cpp |only Eagle-1.1.0/Eagle/src/getRowColumn.cpp |only Eagle-1.1.0/Eagle/src/readblock.h |only Eagle-1.1.0/Eagle/src/removeColumn.cpp |only Eagle-1.1.0/Eagle/src/removeRow.cpp |only 99 files changed, 3987 insertions(+), 3553 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-06 1.0.2
2018-08-02 1.0.1
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides:
'let()'
(converts non-standard evaluation interfaces to parametric standard
evaluation interfaces),
'%.>%' dot-pipe (an 'S3' configurable pipe),
'build_frame()'/'draw_frame()' ('data.frame' example tools),
'qc()' (quoting concatenate),
':=' (named map builder),
'DebugFnW()' (capture function context on error for debugging),
and more.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.6.0 dated 2018-08-01 and 1.6.1 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/bpipe.R | 29 ++++++++++++++++++++++------- inst/doc/CornerCases.html | 4 ++-- inst/doc/DebugFnW.html | 6 +++--- inst/doc/FrameTools.html | 4 ++-- inst/doc/Named_Arguments.html | 4 ++-- inst/doc/SubstitutionModes.html | 4 ++-- inst/doc/dot_pipe.html | 4 ++-- inst/doc/lambda.html | 4 ++-- inst/doc/let.html | 4 ++-- inst/doc/named_map_builder.html | 4 ++-- inst/doc/wrapr_applicable.html | 4 ++-- 15 files changed, 67 insertions(+), 46 deletions(-)
Title: Calculate TL-Moments and Convert Them to Distribution Parameters
Description: Calculates empirical TL-moments (trimmed L-moments) of arbitrary
order and trimming, and converts them to distribution parameters.
Author: Jona Lilienthal
Maintainer: Jona Lilienthal <lilienthal@statistik.tu-dortmund.de>
Diff between TLMoments versions 0.7.2.1 dated 2017-04-07 and 0.7.4 dated 2018-08-22
TLMoments-0.7.2.1/TLMoments/src/init.c |only TLMoments-0.7.4/TLMoments/DESCRIPTION | 17 TLMoments-0.7.4/TLMoments/MD5 | 123 - TLMoments-0.7.4/TLMoments/NAMESPACE | 7 TLMoments-0.7.4/TLMoments/R/PWM.R | 16 TLMoments-0.7.4/TLMoments/R/PWMs.R | 181 +- TLMoments-0.7.4/TLMoments/R/RcppExports.R | 18 TLMoments-0.7.4/TLMoments/R/TLMoment.R | 26 TLMoments-0.7.4/TLMoments/R/TLMoments.R | 402 +++-- TLMoments-0.7.4/TLMoments/R/as.PWMs.R | 46 TLMoments-0.7.4/TLMoments/R/as.TLMoments.R | 140 - TLMoments-0.7.4/TLMoments/R/as.parameters.R | 186 +- TLMoments-0.7.4/TLMoments/R/distribution_functions.R | 48 TLMoments-0.7.4/TLMoments/R/est_cov.R | 52 TLMoments-0.7.4/TLMoments/R/est_paramcov.R | 25 TLMoments-0.7.4/TLMoments/R/est_pwmcov.R | 5 TLMoments-0.7.4/TLMoments/R/est_quancov.R | 15 TLMoments-0.7.4/TLMoments/R/est_tlmcov.R | 40 TLMoments-0.7.4/TLMoments/R/helper.R | 180 ++ TLMoments-0.7.4/TLMoments/R/parameters.R | 320 ++-- TLMoments-0.7.4/TLMoments/R/plot.TLMoments.R |only TLMoments-0.7.4/TLMoments/R/quantiles.R | 113 + TLMoments-0.7.4/TLMoments/R/regionalize.R | 43 TLMoments-0.7.4/TLMoments/R/summary.PWMs.R | 16 TLMoments-0.7.4/TLMoments/R/summary.TLMoments.R | 8 TLMoments-0.7.4/TLMoments/R/summary.parameters.R | 8 TLMoments-0.7.4/TLMoments/R/summary.quantiles.R | 9 TLMoments-0.7.4/TLMoments/R/sysdata.rda |only TLMoments-0.7.4/TLMoments/R/zzz.R | 3 TLMoments-0.7.4/TLMoments/README.md |only TLMoments-0.7.4/TLMoments/build/vignette.rds |binary TLMoments-0.7.4/TLMoments/inst/doc/comparison_of_computation_time.R | 6 TLMoments-0.7.4/TLMoments/inst/doc/comparison_of_computation_time.Rmd | 21 TLMoments-0.7.4/TLMoments/inst/doc/comparison_of_computation_time.html | 627 +++----- TLMoments-0.7.4/TLMoments/inst/doc/short_introduction.R | 8 TLMoments-0.7.4/TLMoments/inst/doc/short_introduction.Rmd | 32 TLMoments-0.7.4/TLMoments/inst/doc/short_introduction.html | 753 +++------- TLMoments-0.7.4/TLMoments/man/PWM.Rd | 12 TLMoments-0.7.4/TLMoments/man/PWMs.Rd | 22 TLMoments-0.7.4/TLMoments/man/TLMoment.Rd | 14 TLMoments-0.7.4/TLMoments/man/TLMoments.Rd | 33 TLMoments-0.7.4/TLMoments/man/as.PWMs.Rd | 10 TLMoments-0.7.4/TLMoments/man/as.TLMoments.Rd | 19 TLMoments-0.7.4/TLMoments/man/as.parameters.Rd | 59 TLMoments-0.7.4/TLMoments/man/est_cov.Rd | 42 TLMoments-0.7.4/TLMoments/man/est_paramcov.Rd | 12 TLMoments-0.7.4/TLMoments/man/est_pwmcov.Rd | 2 TLMoments-0.7.4/TLMoments/man/est_quancov.Rd | 5 TLMoments-0.7.4/TLMoments/man/est_tlmcov.Rd | 44 TLMoments-0.7.4/TLMoments/man/gev.Rd | 4 TLMoments-0.7.4/TLMoments/man/gpd.Rd | 4 TLMoments-0.7.4/TLMoments/man/gum.Rd | 4 TLMoments-0.7.4/TLMoments/man/ln3.Rd | 4 TLMoments-0.7.4/TLMoments/man/parameters.Rd | 25 TLMoments-0.7.4/TLMoments/man/plot.TLMoments.Rd |only TLMoments-0.7.4/TLMoments/man/quantiles.Rd | 2 TLMoments-0.7.4/TLMoments/man/regionalize.Rd | 15 TLMoments-0.7.4/TLMoments/man/returnPWMs.Rd |only TLMoments-0.7.4/TLMoments/man/returnParameters.Rd |only TLMoments-0.7.4/TLMoments/man/returnQuantiles.Rd |only TLMoments-0.7.4/TLMoments/man/returnTLMoments.Rd |only TLMoments-0.7.4/TLMoments/man/summary.PWMs.Rd | 5 TLMoments-0.7.4/TLMoments/man/summary.TLMoments.Rd | 2 TLMoments-0.7.4/TLMoments/man/summary.quantiles.Rd | 2 TLMoments-0.7.4/TLMoments/src/RcppExports.cpp | 36 TLMoments-0.7.4/TLMoments/vignettes/comparison_of_computation_time.Rmd | 21 TLMoments-0.7.4/TLMoments/vignettes/short_introduction.Rmd | 32 67 files changed, 2151 insertions(+), 1773 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.6 dated 2018-07-07 and 0.7 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 1 + R/install.R | 34 ++++++++++++++++++++++++++++------ R/latex.R | 21 ++++++++++++++++++--- R/tlmgr.R | 41 ++++++++++++++++++++++++++++------------- README.md | 1 + man/latexmk.Rd | 8 ++++++++ 8 files changed, 95 insertions(+), 33 deletions(-)
Title: Tools for Developing R Packages Interfacing with 'Stan'
Description: Provides various tools for developers of R packages interfacing
with 'Stan' <http://mc-stan.org>, including functions to set up the required
package structure, S3 generics and default methods to unify function naming
across 'Stan'-based R packages, and vignettes with recommendations for
developers.
Author: Jonah Gabry [aut, cre],
Ben Goodrich [aut],
Stefan Siegert [ctb],
Trustees of Columbia University [cph]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between rstantools versions 1.5.0 dated 2018-04-17 and 1.5.1 dated 2018-08-22
DESCRIPTION | 9 - MD5 | 26 ++- NAMESPACE | 1 NEWS.md | 10 + R/nsamples.R |only R/rstan_package_skeleton.R | 87 ++++++++---- build/vignette.rds |binary inst/doc/developer-guidelines.Rmd | 2 inst/doc/developer-guidelines.html | 3 inst/doc/minimal-rstan-package.R | 2 inst/doc/minimal-rstan-package.html | 87 +++++++----- man/nsamples.Rd |only man/rstan_package_skeleton.Rd | 6 tests/testthat/test-rstan_package_skeleton.R | 188 +++++++++++++-------------- vignettes/developer-guidelines.Rmd | 2 15 files changed, 240 insertions(+), 183 deletions(-)
Title: An Image Processing Toolkit
Description: Incorporates functions for image preprocessing, filtering and image recognition. The package takes advantage of 'RcppArmadillo' to speed up computationally intensive functions. The histogram of oriented gradients descriptor is a modification of the 'findHOGFeatures' function of the 'SimpleCV' computer vision platform, the average_hash(), dhash() and phash() functions are based on the 'ImageHash' python library and the Gabor Feature Extraction functions are based on 'Matlab' code of the paper, "CloudID: Trustworthy cloud-based and cross-enterprise biometric identification" by M. Haghighat, S. Zonouz, M. Abdel-Mottaleb, Expert Systems with Applications, vol. 42, no. 21, pp. 7905-7916, 2015, <doi:10.1016/j.eswa.2015.06.025>.
Author: Lampros Mouselimis [aut, cre],
Sight Machine [cph] (findHOGFeatures function of the SimpleCV computer
vision platform),
Johannes Buchner [cph] (average_hash, dhash and phash functions of the
ImageHash python library),
Mohammad Haghighat [cph] (Gabor Feature Extraction)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between OpenImageR versions 1.1.0 dated 2018-08-07 and 1.1.1 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 5 +++++ README.md | 3 +-- inst/doc/Gabor_Feature_Extraction.html | 4 ++-- inst/doc/The_OpenImageR_package.html | 18 +++++++++--------- src/utils.cpp | 2 +- 7 files changed, 28 insertions(+), 24 deletions(-)
Title: Model-Based Boosting
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut] (<https://orcid.org/0000-0001-8301-0471>),
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>),
Fabian Sobotka [ctb],
Fabian Scheipl [ctb],
Andreas Mayr [ctb]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between mboost versions 2.9-0 dated 2018-06-13 and 2.9-1 dated 2018-08-22
DESCRIPTION | 8 MD5 | 26 R/bl.R | 2378 +++++++++++++++++++------------------- R/plot.R | 446 +++---- build/partial.rdb |binary inst/NEWS.Rd | 2088 ++++++++++++++++----------------- inst/doc/SurvivalEnsembles.pdf |binary inst/doc/mboost.pdf |binary inst/doc/mboost_illustrations.pdf |binary inst/doc/mboost_tutorial.pdf |binary man/baselearners.Rd | 1768 ++++++++++++++-------------- man/cvrisk.Rd | 394 +++--- man/mboost_package.Rd | 658 +++++----- man/methods.Rd | 946 +++++++-------- 14 files changed, 4360 insertions(+), 4352 deletions(-)
Title: Web-Processing of Large Gridded Datasets
Description: Processes gridded datasets found on the U.S. Geological Survey
Geo Data Portal web application or elsewhere, using a web-enabled workflow
that eliminates the need to download and store large datasets that are reliably
hosted on the Internet. The package provides access to several data subset and
summarization algorithms that are available on remote web processing servers.
Author: Jordan Read [aut, cre],
Jordan Walker [aut],
Alison Appling [aut],
David Blodgett [aut],
Emily Read [aut],
Luke Winslow [aut],
Lindsay Carr [aut],
David Watkins [aut]
Maintainer: Jordan Read <jread@usgs.gov>
Diff between geoknife versions 1.5.5 dated 2017-06-06 and 1.6.1 dated 2018-08-22
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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 0.3.4 dated 2018-05-01 and 0.3.5 dated 2018-08-22
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Title: Pseudo-Ranks
Description: Efficient calculation of pseudo-ranks. In case of equal sample sizes, pseudo-ranks and mid-ranks are equal. When used for inference mid-ranks may lead to paradoxical results. Pseudo-ranks are in general not affected by such a problem. For details, see Brunner, E., Bathke A. C. and Konietschke, F: Rank- and Pseudo-Rank Procedures in Factorial Designs - Using R and SAS, Springer Verlag, to appear.
Author: Martin Happ [aut, cre] (<https://orcid.org/0000-0003-0009-2665>),
Georg Zimmermann [aut],
Arne C. Bathke [aut],
Edgar Brunner [aut]
Maintainer: Martin Happ <martin.happ@aon.at>
Diff between pseudorank versions 0.2.6 dated 2018-07-24 and 0.3.0 dated 2018-08-22
DESCRIPTION | 8 +- MD5 | 27 ++++--- NAMESPACE | 6 + NEWS.md |only R/S3method.R | 104 +++++++++++++++++++++++++++-- R/hettmansperger.R | 58 +++------------- R/kruskal_wallis.R |only R/pseudoranks.R | 71 ------------------- README.md | 6 + man/hettmansperger_norton_test.Rd | 8 +- man/hettmansperger_norton_test_internal.Rd | 2 man/kruskal_wallis_internal.Rd |only man/kruskal_wallis_test.Rd |only src/pseudorank.cpp | 2 tests/testthat/test.R | 69 ++++++++++++++++++- tests/testthat/test_hettmansperger.R | 13 +++ tests/testthat/test_kruskal_wallis.R |only 17 files changed, 231 insertions(+), 143 deletions(-)
Title: Generalised Management Strategy Evaluation Simulator
Description: Integrates game theory and ecological theory to construct
social-ecological models that simulate the management of populations and
stakeholder actions. These models build off of a previously developed
management strategy evaluation (MSE) framework to simulate all aspects of
management: population dynamics, manager observation of populations, manager
decision making, and stakeholder responses to management decisions. The
newly developed generalised management strategy evaluation (GMSE)
framework uses genetic algorithms to mimic the decision-making process of
managers and stakeholders under conditions of change, uncertainty, and
conflict. Simulations can be run using gmse(), gmse_apply(), and
gmse_gui() functions.
Author: A. Bradley Duthie [aut, cre] (<https://orcid.org/0000-0001-8343-4995>),
Nils Bunnefeld [ctb, fnd] (<https://orcid.org/0000-0002-1349-4463>),
Jeremy Cusack [ctb] (<https://orcid.org/0000-0003-3004-1586>),
Isabel Jones [ctb] (<https://orcid.org/0000-0002-8361-1370>),
Jeroen Minderman [ctb] (<https://orcid.org/0000-0002-8451-5540>),
Erlend Nilsen [ctb] (<https://orcid.org/0000-0002-5119-8331>),
Rocio Pozo [ctb] (<https://orcid.org/0000-0002-7546-8076>),
Sarobidy Rakotonarivo [ctb] (<https://orcid.org/0000-0002-8032-1431>),
Bram Van Moorter [ctb] (<https://orcid.org/0000-0002-3196-1993>)
Maintainer: A. Bradley Duthie <brad.duthie@gmail.com>
Diff between GMSE versions 0.4.0.4 dated 2018-05-28 and 0.4.0.7 dated 2018-08-22
DESCRIPTION | 12 ++--- MD5 | 50 ++++++++++----------- R/gmse.R | 2 R/gmse_apply.R | 24 ++++++++-- R/gmse_gui.R | 8 --- R/gmse_summary.R | 1 R/plotting.R | 36 ++++++++------- inst/doc/SI1.pdf |binary inst/doc/SI2.pdf |binary inst/doc/SI3.pdf |binary inst/doc/SI4.pdf |binary inst/doc/SI5.pdf |binary inst/doc/SI6.pdf |binary inst/doc/SI7.pdf |binary inst/doc/ms.pdf |binary man/anecdotal.Rd | 6 +- man/gmse.Rd | 25 +++++----- man/gmse_apply.Rd | 5 +- man/gmse_replicates.Rd | 4 - man/make_resource.Rd | 6 +- man/observation.Rd | 8 +-- man/plot_gmse_effort.Rd | 12 +---- man/plot_gmse_results.Rd | 20 +------- man/resource.Rd | 3 - src/game.c | 103 ++++++++++++++++++++++++++------------------- tests/testthat/test-user.R | 6 +- 26 files changed, 172 insertions(+), 159 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp and Mathew Jay.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 0.9-96 dated 2018-05-06 and 0.9-97 dated 2018-08-22
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 7 ++++++- R/epi.prev.R | 10 ++++++---- 4 files changed, 19 insertions(+), 12 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 1.0 dated 2018-06-10 and 1.1 dated 2018-08-22
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++--------- NAMESPACE | 3 +- R/expansive.replace.R | 64 ++++++++++++++++++++++++++++++++++++++++++++--- R/oa.design.R | 32 +++++++++++++++++++++-- R/show.oas.R | 29 +++++++++++++++------ R/sysdata.rda |binary inst/NEWS | 21 +++++++++++++++ man/arrays.Rd | 10 +++++-- man/expansive.replace.Rd | 40 +++++++++++++++++++++++++---- man/oa.design.Rd | 55 ++++++++++++++++++++++++++++------------ man/oacat.Rd | 22 ++++++++++++---- man/show.oas.Rd | 14 +++++----- 13 files changed, 258 insertions(+), 66 deletions(-)