Title: Extract Equations from a Nomogram
Description: A nomogram can not be easily applied,
because it is difficult to calculate the points or even the survival probability.
The package, including a function of nomogramEx(),
is to extract the polynomial equations to calculate the points of each variable,
and the survival probability corresponding to the total points.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between nomogramEx versions 2.0 dated 2016-12-14 and 3.0 dated 2017-08-28
DESCRIPTION | 7 +++---- MD5 | 8 ++++---- NAMESPACE | 4 ++++ R/nomogramEx.R | 7 ++++++- man/nomogramEx.Rd | 9 ++++++--- 5 files changed, 23 insertions(+), 12 deletions(-)
Title: A Shiny Web Application for the Analysis of Spatial and
Spatio-Temporal Disease Data
Description: Runs a Shiny web application that allows to visualize spatial and spatio-temporal disease data, estimate disease risk and detect clusters. The application allows to fit Bayesian disease models to obtain risk estimates and their uncertainty by using the 'R-INLA' package, <http://www.r-inla.org>, and to detect clusters by using the scan statistics implemented in 'SaTScan', <https://www.satscan.org>. The application allows user interaction and creates interactive visualizations such as maps supporting padding and zooming and tables that allow for filtering. It also enables the generation of reports containing the analyses performed.
Author: Paula Moraga [aut, cre]
Maintainer: Paula Moraga <p.e.moraga-serrano@lancaster.ac.uk>
Diff between SpatialEpiApp versions 0.2 dated 2017-06-02 and 0.3 dated 2017-08-28
DESCRIPTION | 13 MD5 | 32 R/SpatialEpiApp.R | 32 R/rfunctions.R | 12 inst/SpatialEpiApp/data/Ohio/dataohiocomplete.csv |14786 +++++----- inst/SpatialEpiApp/data/Ohio/fe_2007_39_county/fe_2007_39_county.shp.xml | 950 inst/SpatialEpiApp/dygraph.css | 8 inst/SpatialEpiApp/helpabout.md | 47 inst/SpatialEpiApp/helpanalysis.md | 90 inst/SpatialEpiApp/helpers.R | 1060 inst/SpatialEpiApp/helpinput.md | 348 inst/SpatialEpiApp/report.Rmd | 510 inst/SpatialEpiApp/server.R | 3327 +- inst/SpatialEpiApp/ss/satscanplantilla.prm | 564 inst/SpatialEpiApp/ui.R | 610 inst/doc/manual.pdf.asis | 2 vignettes/manual.pdf.asis | 2 17 files changed, 11202 insertions(+), 11191 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 2.3-2 dated 2017-01-02 and 2.4-0 dated 2017-08-28
Rcmdr-2.3-2/Rcmdr/inst/doc/Rcmdr-manual-source.zip |only Rcmdr-2.3-2/Rcmdr/inst/doc/Thumbs.db |only Rcmdr-2.3-2/Rcmdr/inst/etc/Thumbs.db |only Rcmdr-2.3-2/Rcmdr/man/normalityTest.Rd |only Rcmdr-2.4-0/Rcmdr/DESCRIPTION | 27 Rcmdr-2.4-0/Rcmdr/MD5 | 103 Rcmdr-2.4-0/Rcmdr/NAMESPACE | 12 Rcmdr-2.4-0/Rcmdr/NEWS | 52 Rcmdr-2.4-0/Rcmdr/R/commander.R | 2893 ++-- Rcmdr-2.4-0/Rcmdr/R/data-menu.R | 207 Rcmdr-2.4-0/Rcmdr/R/file-menu.R | 95 Rcmdr-2.4-0/Rcmdr/R/globals.R | 6 Rcmdr-2.4-0/Rcmdr/R/graphs-menu.R | 256 Rcmdr-2.4-0/Rcmdr/R/model-menu.R | 66 Rcmdr-2.4-0/Rcmdr/R/statistics-summaries-menu.R | 207 Rcmdr-2.4-0/Rcmdr/R/statistics-tables-menu.R | 317 Rcmdr-2.4-0/Rcmdr/R/statistics-variances-menu.R | 6 Rcmdr-2.4-0/Rcmdr/R/utilities.R | 7128 +++++----- Rcmdr-2.4-0/Rcmdr/build |only Rcmdr-2.4-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.R |only Rcmdr-2.4-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.Rnw |only Rcmdr-2.4-0/Rcmdr/inst/doc/Getting-Started-with-the-Rcmdr.pdf |binary Rcmdr-2.4-0/Rcmdr/inst/etc/Rcmdr-menus.txt | 52 Rcmdr-2.4-0/Rcmdr/inst/etc/Rcmdr-model-capabilities.txt |only Rcmdr-2.4-0/Rcmdr/inst/etc/save-edits.gif |only Rcmdr-2.4-0/Rcmdr/inst/po/es/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/fr/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/id/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/pl/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/ru/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/sl/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/inst/po/zh_CN/LC_MESSAGES/R-Rcmdr.mo |binary Rcmdr-2.4-0/Rcmdr/man/Commander.Rd | 12 Rcmdr-2.4-0/Rcmdr/man/Rcmdr-package.Rd | 24 Rcmdr-2.4-0/Rcmdr/man/Rcmdr.Utilities.Rd | 21 Rcmdr-2.4-0/Rcmdr/man/RcmdrEditor.Rd | 54 Rcmdr-2.4-0/Rcmdr/man/ediDataset.Rd | 2 Rcmdr-2.4-0/Rcmdr/po/R-Rcmdr.pot | 126 Rcmdr-2.4-0/Rcmdr/po/R-es.po | 155 Rcmdr-2.4-0/Rcmdr/po/R-fr.po | 116 Rcmdr-2.4-0/Rcmdr/po/R-id.po | 324 Rcmdr-2.4-0/Rcmdr/po/R-ja.po | 114 Rcmdr-2.4-0/Rcmdr/po/R-pl.po | 136 Rcmdr-2.4-0/Rcmdr/po/R-ru.po | 103 Rcmdr-2.4-0/Rcmdr/po/R-sl.po | 386 Rcmdr-2.4-0/Rcmdr/po/R-zh_CN.po | 681 Rcmdr-2.4-0/Rcmdr/vignettes |only 48 files changed, 7916 insertions(+), 5765 deletions(-)
Title: Compute and Visualize Bivariate Associations
Description: Pearson and Spearman correlation coefficients are commonly used to quantify the strength
of bivariate associations of genomic variables. For example, correlations of gene-level
DNA copy number and gene expression measurements may be used to assess the impact of
DNA copy number changes on gene expression in tumor tissue. MVisAGe enables users to
quickly compute and visualize the correlations in order to assess the effect of regional
genomic events such as changes in DNA copy number or DNA methylation level.
Author: Vonn Walter [aut, cre]
Maintainer: Vonn Walter <vwalter1@pennstatehealth.psu.edu>
Diff between MVisAGe versions 0.1.0 dated 2017-05-28 and 0.2.0 dated 2017-08-28
DESCRIPTION | 12 +++---- MD5 | 28 ++++++++++-------- NAMESPACE | 6 ++- NEWS.md | 12 ++++++- R/corr.compute.R | 52 +++++++++++++++++++++++++++------- R/corr.list.compute.R | 24 +++++++++++---- R/data.prep.R | 14 +++++++-- R/perm.significance.R |only R/perm.significance.list.compute.R |only README.md | 6 +-- build/vignette.rds |binary inst/doc/MVisAGe_vignette.pdf |binary man/corr.compute.Rd | 22 +++++++++++--- man/corr.list.compute.Rd | 17 ++++++++--- man/data.prep.Rd | 6 +++ man/perm.significance.Rd |only man/perm.significance.list.compute.Rd |only 17 files changed, 145 insertions(+), 54 deletions(-)
Title: Machine Learning Tools
Description: A collection of machine learning helper functions, particularly assisting in the Exploratory Data Analysis phase.
Makes heavy use of the 'data.table' package for optimal speed and memory efficiency. Highlights include a versatile bin_data()
function, sparsify() for converting a data.table to sparse matrix format with one-hot encoding, fast evaluation metrics, and
empirical_cdf() for calculating empirical Multivariate Cumulative Distribution Functions.
Author: Ben Gorman
Maintainer: Ben Gorman <bgorman@GormAnalysis.com>
Diff between mltools versions 0.3.1 dated 2017-07-10 and 0.3.2 dated 2017-08-28
DESCRIPTION | 6 +- MD5 | 16 +++---- NEWS.md | 6 ++ R/bin_data.R | 6 ++ R/date_factor.R | 93 +++++++++++++++++++++++++++++++----------- R/folds.R | 13 ++++- README.md | 117 +++++++++++++++++++++++++++-------------------------- man/date_factor.Rd | 30 +++++++++---- man/folds.Rd | 4 + 9 files changed, 190 insertions(+), 101 deletions(-)
Title: Data.frame-Like Operations on Sparse and Dense Matrix Objects
Description: Implements data manipulation methods such as cast, aggregate, and merge/join for Matrix and matrix-like objects.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between Matrix.utils versions 0.9.5 dated 2016-12-21 and 0.9.6 dated 2017-08-28
DESCRIPTION | 8 ++-- MD5 | 16 ++++----- R/Matrix.utils.R | 80 +++++++++++++++++++++++++++++++----------------- man/Matrix.utils.Rd | 1 man/aggregate.Matrix.Rd | 1 man/dMcast.Rd | 1 man/merge.Matrix.Rd | 17 ++++++---- man/rBind.fill.Rd | 7 +++- tests/testthat/tests.R | 14 +++++++- 9 files changed, 93 insertions(+), 52 deletions(-)
Title: Query Cache for HTTP Clients
Description: In order to improve performance for HTTP API clients, 'httpcache'
provides simple tools for caching and invalidating cache. It includes the
HTTP verb functions GET, PUT, PATCH, POST, and DELETE, which are drop-in
replacements for those in the 'httr' package. These functions are cache-aware
and provide default settings for cache invalidation suitable for RESTful
APIs; the package also enables custom cache-management strategies.
Finally, 'httpcache' includes a basic logging framework to facilitate the
measurement of HTTP request time and cache performance.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httpcache versions 1.0.0 dated 2017-01-03 and 1.0.2 dated 2017-08-28
DESCRIPTION | 13 ++++++------- MD5 | 44 ++++++++++++++++++++++---------------------- R/cache.R | 21 ++++++++++----------- R/download.R | 14 +++++++------- R/http-verbs.R | 21 ++++++++++----------- R/log.R | 22 ++++++++++------------ inst/doc/httpcache.html | 8 ++++---- man/buildCacheKey.Rd | 1 - man/cache-api.Rd | 6 ++---- man/cache-management.Rd | 5 +++-- man/cacheLogSummary.Rd | 3 +-- man/cached-http-verbs.Rd | 20 +++++++++++--------- man/cachedDownload.Rd | 5 ++--- man/cachedPOST.Rd | 3 +-- man/dropCache.Rd | 1 - man/halt.Rd | 6 ++---- man/loadLogfile.Rd | 5 ++--- man/logMessage.Rd | 3 +-- man/requestLogSummary.Rd | 3 +-- man/saveCache.Rd | 3 +-- man/startLog.Rd | 4 +--- man/uncached.Rd | 4 +--- tests/testthat/test-cache.R | 5 ++--- 23 files changed, 100 insertions(+), 120 deletions(-)
Title: Simulate from ODE-Based Population PK/PD and Systems
Pharmacology Models
Description: Facilitates simulation from hierarchical, ordinary
differential equation (ODE) based models typically employed in drug development.
A model specification file is created consisting of R and C++ code that
is parsed, compiled, and dynamically loaded into the R session. Input data are
passed in and simulated data are returned as R objects. A dosing event engine
allows interventions (bolus and infusion) to be managed separately from the
model code. Differential equations are solved with the 'DLSODA' routine
in 'ODEPACK' (<https://computation.llnl.gov/casc/odepack/>).
Author: Kyle T Baron [aut, cre],
Alan C Hindmarsh [ctb],
Linda R Petzold [ctb],
Bill Gillespie [ctb],
Charles Margossian [ctb],
Devin Pastoor [ctb],
Metrum Research Group LLC [cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between mrgsolve versions 0.8.6 dated 2017-03-16 and 0.8.9 dated 2017-08-28
mrgsolve-0.8.6/mrgsolve/man/assign_ev.Rd |only mrgsolve-0.8.9/mrgsolve/DESCRIPTION | 23 - mrgsolve-0.8.9/mrgsolve/MD5 | 95 ++-- mrgsolve-0.8.9/mrgsolve/NAMESPACE | 16 mrgsolve-0.8.9/mrgsolve/R/Aaaa.R | 12 mrgsolve-0.8.9/mrgsolve/R/RcppExports.R | 16 mrgsolve-0.8.9/mrgsolve/R/annot.R | 22 - mrgsolve-0.8.9/mrgsolve/R/chain.R | 47 -- mrgsolve-0.8.9/mrgsolve/R/class_tgrid.R | 6 mrgsolve-0.8.9/mrgsolve/R/compile.R | 2 mrgsolve-0.8.9/mrgsolve/R/data_set.R | 9 mrgsolve-0.8.9/mrgsolve/R/env.R | 2 mrgsolve-0.8.9/mrgsolve/R/events.R | 264 ++++++++++-- mrgsolve-0.8.9/mrgsolve/R/funset.R | 6 mrgsolve-0.8.9/mrgsolve/R/idata_set.R | 7 mrgsolve-0.8.9/mrgsolve/R/inven.R |only mrgsolve-0.8.9/mrgsolve/R/knobs.R | 4 mrgsolve-0.8.9/mrgsolve/R/matrix.R | 4 mrgsolve-0.8.9/mrgsolve/R/modspec.R | 9 mrgsolve-0.8.9/mrgsolve/R/mread.R | 13 mrgsolve-0.8.9/mrgsolve/R/mrgsims.R | 2 mrgsolve-0.8.9/mrgsolve/R/mrgsolve.R | 5 mrgsolve-0.8.9/mrgsolve/R/package.R | 1 mrgsolve-0.8.9/mrgsolve/R/qsim.R | 142 +----- mrgsolve-0.8.9/mrgsolve/R/utils.R | 14 mrgsolve-0.8.9/mrgsolve/inst/base/modelheader.h | 10 mrgsolve-0.8.9/mrgsolve/inst/include/datarecord.h | 17 mrgsolve-0.8.9/mrgsolve/inst/include/modelheader.h | 10 mrgsolve-0.8.9/mrgsolve/inst/include/odeproblem.h | 16 mrgsolve-0.8.9/mrgsolve/inst/project/housemodel.RDS |binary mrgsolve-0.8.9/mrgsolve/man/as_data_set.Rd | 3 mrgsolve-0.8.9/mrgsolve/man/data_set.Rd | 4 mrgsolve-0.8.9/mrgsolve/man/ev_assign.Rd |only mrgsolve-0.8.9/mrgsolve/man/ev_rep.Rd |only mrgsolve-0.8.9/mrgsolve/man/ev_repeat.Rd |only mrgsolve-0.8.9/mrgsolve/man/ev_seq.Rd |only mrgsolve-0.8.9/mrgsolve/man/events.Rd | 13 mrgsolve-0.8.9/mrgsolve/man/idata_set.Rd | 4 mrgsolve-0.8.9/mrgsolve/man/inventory.Rd |only mrgsolve-0.8.9/mrgsolve/src/RcppExports.cpp | 16 mrgsolve-0.8.9/mrgsolve/src/dataobject.cpp | 38 - mrgsolve-0.8.9/mrgsolve/src/datarecord.cpp | 161 +++---- mrgsolve-0.8.9/mrgsolve/src/devtran.cpp | 201 +++------ mrgsolve-0.8.9/mrgsolve/src/mrgsolve.cpp | 5 mrgsolve-0.8.9/mrgsolve/src/mrgsolve_init.cpp | 32 - mrgsolve-0.8.9/mrgsolve/src/odeproblem.cpp | 25 - mrgsolve-0.8.9/mrgsolve/src/quick.cpp | 108 ++++ mrgsolve-0.8.9/mrgsolve/tests/testthat.R | 1 mrgsolve-0.8.9/mrgsolve/tests/testthat/test-carry_out.R | 5 mrgsolve-0.8.9/mrgsolve/tests/testthat/test-deslist.R | 24 - mrgsolve-0.8.9/mrgsolve/tests/testthat/test-ev.R | 53 ++ mrgsolve-0.8.9/mrgsolve/tests/testthat/test-inventory-too.R |only mrgsolve-0.8.9/mrgsolve/tests/testthat/test-inventory.R |only 53 files changed, 897 insertions(+), 570 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.5.4 dated 2017-02-26 and 0.5.5 dated 2017-08-28
DESCRIPTION | 9 ++++----- MD5 | 14 +++++++------- NEWS | 9 +++++++++ R/qic.R | 8 +++++++- README.md | 2 ++ build/vignette.rds |binary inst/doc/controlcharts.html | 20 ++++++++++---------- inst/doc/runcharts.html | 24 ++++++++++++------------ 8 files changed, 51 insertions(+), 35 deletions(-)
Title: Analysis of Oceanographic Data
Description: Supports the analysis of Oceanographic data, including 'ADCP'
measurements, measurements made with 'argo' floats, 'CTD' measurements,
sectional data, sea-level time series, coastline and topographic data, etc.
Provides specialized functions for calculating seawater properties such as
potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state.
Produces graphical displays that conform to the conventions of the Oceanographic
literature.
Author: Dan Kelley [aut, cre],
Clark Richards [aut],
Chantelle Layton [ctb] (curl() coauthor),
British Geological Survey [ctb, cph] (magnetic-field subroutine)
Maintainer: Dan Kelley <Dan.Kelley@Dal.Ca>
Diff between oce versions 0.9-21 dated 2017-03-30 and 0.9-22 dated 2017-08-28
oce-0.9-21/oce/R/tidem.R |only oce-0.9-22/oce/DESCRIPTION | 24 oce-0.9-22/oce/MD5 | 462 ++++----- oce-0.9-22/oce/NAMESPACE | 5 oce-0.9-22/oce/NEWS | 7 oce-0.9-22/oce/R/AllClass.R | 23 oce-0.9-22/oce/R/adp.R | 50 - oce-0.9-22/oce/R/adp.nortek.R | 139 ++ oce-0.9-22/oce/R/adp.rdi.R | 76 + oce-0.9-22/oce/R/adp.sontek.R | 2 oce-0.9-22/oce/R/adv.R | 30 oce-0.9-22/oce/R/amsr.R | 1 oce-0.9-22/oce/R/argo.R | 81 + oce-0.9-22/oce/R/cm.R | 8 oce-0.9-22/oce/R/coastline.R | 155 ++- oce-0.9-22/oce/R/colors.R | 130 -- oce-0.9-22/oce/R/ctd.R | 570 +++++++++-- oce-0.9-22/oce/R/ctd.odf.R | 3 oce-0.9-22/oce/R/ctd.sbe.R | 23 oce-0.9-22/oce/R/ctd.woce.R | 188 +++ oce-0.9-22/oce/R/echosounder.R | 20 oce-0.9-22/oce/R/geod.R | 186 ++- oce-0.9-22/oce/R/imagep.R | 17 oce-0.9-22/oce/R/landsat.R | 2 oce-0.9-22/oce/R/lobo.R | 24 oce-0.9-22/oce/R/map.R | 164 ++- oce-0.9-22/oce/R/met.R | 12 oce-0.9-22/oce/R/misc.R | 231 +++- oce-0.9-22/oce/R/oce.R | 160 ++- oce-0.9-22/oce/R/odf.R | 345 +++++-- oce-0.9-22/oce/R/rsk.R | 18 oce-0.9-22/oce/R/sealevel.R | 1 oce-0.9-22/oce/R/section.R | 411 ++++++-- oce-0.9-22/oce/R/sw.R | 511 +++++++--- oce-0.9-22/oce/R/tides.R |only oce-0.9-22/oce/R/topo.R | 39 oce-0.9-22/oce/build/vignette.rds |binary oce-0.9-22/oce/data/argo.rda |binary oce-0.9-22/oce/data/ctd.rda |binary oce-0.9-22/oce/data/ctdRaw.rda |binary oce-0.9-22/oce/data/met.rda |binary oce-0.9-22/oce/inst/doc/oce.R |only oce-0.9-22/oce/inst/doc/oce.Rmd |only oce-0.9-22/oce/inst/doc/oce.html | 402 ++++---- oce-0.9-22/oce/inst/po/de/LC_MESSAGES/R-oce.mo |binary oce-0.9-22/oce/inst/po/en@quot/LC_MESSAGES/R-oce.mo |binary oce-0.9-22/oce/inst/po/es/LC_MESSAGES/R-oce.mo |binary oce-0.9-22/oce/inst/po/fr/LC_MESSAGES/R-oce.mo |binary oce-0.9-22/oce/inst/po/zh/LC_MESSAGES/R-oce.mo |binary oce-0.9-22/oce/man/ODFNames2oceNames.Rd | 6 oce-0.9-22/oce/man/adp-class.Rd | 2 oce-0.9-22/oce/man/adp.Rd | 2 oce-0.9-22/oce/man/adpEnsembleAverage.Rd | 2 oce-0.9-22/oce/man/argo.Rd | 22 oce-0.9-22/oce/man/as.adp.Rd | 2 oce-0.9-22/oce/man/as.ctd.Rd | 27 oce-0.9-22/oce/man/beamName.Rd | 2 oce-0.9-22/oce/man/beamToXyz.Rd | 2 oce-0.9-22/oce/man/beamToXyzAdp.Rd | 2 oce-0.9-22/oce/man/beamToXyzAdv.Rd | 2 oce-0.9-22/oce/man/beamUnspreadAdp.Rd | 2 oce-0.9-22/oce/man/binmapAdp.Rd | 2 oce-0.9-22/oce/man/byteToBinary.Rd | 25 oce-0.9-22/oce/man/cnvName2oceName.Rd | 10 oce-0.9-22/oce/man/ctd-class.Rd | 13 oce-0.9-22/oce/man/ctd.Rd | 5 oce-0.9-22/oce/man/ctdDecimate.Rd | 16 oce-0.9-22/oce/man/ctdFindProfiles.Rd | 5 oce-0.9-22/oce/man/ctdRaw.Rd | 5 oce-0.9-22/oce/man/ctdTrim.Rd | 10 oce-0.9-22/oce/man/ctdUpdateHeader.Rd | 2 oce-0.9-22/oce/man/download.topo.Rd | 30 oce-0.9-22/oce/man/drawDirectionField.Rd | 87 + oce-0.9-22/oce/man/enuToOther.Rd | 2 oce-0.9-22/oce/man/enuToOtherAdp.Rd | 2 oce-0.9-22/oce/man/enuToOtherAdv.Rd | 3 oce-0.9-22/oce/man/geodXy.Rd | 129 +- oce-0.9-22/oce/man/geodXyInverse.Rd | 26 oce-0.9-22/oce/man/handleFlags-argo-method.Rd | 8 oce-0.9-22/oce/man/handleFlags-ctd-method.Rd | 35 oce-0.9-22/oce/man/handleFlags-section-method.Rd | 8 oce-0.9-22/oce/man/handleFlags.Rd | 8 oce-0.9-22/oce/man/imagep.Rd | 13 oce-0.9-22/oce/man/landsat-class.Rd | 2 oce-0.9-22/oce/man/lowpass.Rd |only oce-0.9-22/oce/man/mapPlot.Rd | 26 oce-0.9-22/oce/man/oce-deprecated.Rd | 5 oce-0.9-22/oce/man/oceApprox.Rd | 7 oce-0.9-22/oce/man/oceNames2whpNames.Rd |only oce-0.9-22/oce/man/oceUnits2whpUnits.Rd |only oce-0.9-22/oce/man/plot-adp-method.Rd | 3 oce-0.9-22/oce/man/plot-coastline-method.Rd | 21 oce-0.9-22/oce/man/plot-ctd-method.Rd | 12 oce-0.9-22/oce/man/plot-lobo-method.Rd | 3 oce-0.9-22/oce/man/plot-section-method.Rd | 26 oce-0.9-22/oce/man/plot-tidem-method.Rd | 2 oce-0.9-22/oce/man/plotProfile.Rd | 13 oce-0.9-22/oce/man/plotScan.Rd | 5 oce-0.9-22/oce/man/plotSticks.Rd | 8 oce-0.9-22/oce/man/plotTS.Rd | 5 oce-0.9-22/oce/man/predict.tidem.Rd | 2 oce-0.9-22/oce/man/read.ad2cp.Rd |only oce-0.9-22/oce/man/read.adp.Rd | 2 oce-0.9-22/oce/man/read.adp.nortek.Rd | 2 oce-0.9-22/oce/man/read.adp.rdi.Rd | 2 oce-0.9-22/oce/man/read.adp.sontek.Rd | 2 oce-0.9-22/oce/man/read.adp.sontek.serial.Rd | 2 oce-0.9-22/oce/man/read.aquadopp.Rd | 2 oce-0.9-22/oce/man/read.aquadoppHR.Rd | 2 oce-0.9-22/oce/man/read.aquadoppProfiler.Rd | 2 oce-0.9-22/oce/man/read.ctd.Rd | 5 oce-0.9-22/oce/man/read.ctd.itp.Rd | 5 oce-0.9-22/oce/man/read.ctd.odf.Rd | 10 oce-0.9-22/oce/man/read.ctd.sbe.Rd | 7 oce-0.9-22/oce/man/read.ctd.woce.Rd | 5 oce-0.9-22/oce/man/read.ctd.woce.other.Rd | 5 oce-0.9-22/oce/man/read.echosounder.Rd | 11 oce-0.9-22/oce/man/read.odf.Rd | 13 oce-0.9-22/oce/man/read.section.Rd | 5 oce-0.9-22/oce/man/rsk.Rd | 8 oce-0.9-22/oce/man/section.Rd | 2 oce-0.9-22/oce/man/sectionGrid.Rd | 16 oce-0.9-22/oce/man/sub-sub-adp-method.Rd | 2 oce-0.9-22/oce/man/sub-sub-argo-method.Rd | 14 oce-0.9-22/oce/man/sub-sub-ctd-method.Rd | 14 oce-0.9-22/oce/man/sub-sub-section-method.Rd | 29 oce-0.9-22/oce/man/sub-sub-tidem-method.Rd | 2 oce-0.9-22/oce/man/sub-subset-adp-method.Rd | 2 oce-0.9-22/oce/man/sub-subset-ctd-method.Rd | 5 oce-0.9-22/oce/man/sub-subset-section-method.Rd | 5 oce-0.9-22/oce/man/sub-subset-tidem-method.Rd | 2 oce-0.9-22/oce/man/subset-adp-method.Rd | 18 oce-0.9-22/oce/man/subset-adv-method.Rd | 16 oce-0.9-22/oce/man/subset-amsr-method.Rd | 16 oce-0.9-22/oce/man/subset-argo-method.Rd | 16 oce-0.9-22/oce/man/subset-cm-method.Rd | 16 oce-0.9-22/oce/man/subset-coastline-method.Rd | 16 oce-0.9-22/oce/man/subset-ctd-method.Rd | 45 oce-0.9-22/oce/man/subset-echosounder-method.Rd | 16 oce-0.9-22/oce/man/subset-lobo-method.Rd | 16 oce-0.9-22/oce/man/subset-met-method.Rd | 16 oce-0.9-22/oce/man/subset-oce-method.Rd | 23 oce-0.9-22/oce/man/subset-odf-method.Rd | 16 oce-0.9-22/oce/man/subset-rsk-method.Rd | 16 oce-0.9-22/oce/man/subset-sealevel-method.Rd | 16 oce-0.9-22/oce/man/subset-section-method.Rd | 93 + oce-0.9-22/oce/man/subset-topo-method.Rd | 16 oce-0.9-22/oce/man/summary-adp-method.Rd | 2 oce-0.9-22/oce/man/summary-ctd-method.Rd | 5 oce-0.9-22/oce/man/summary-tidem-method.Rd | 2 oce-0.9-22/oce/man/swAbsoluteSalinity.Rd | 4 oce-0.9-22/oce/man/swAlpha.Rd | 4 oce-0.9-22/oce/man/swAlphaOverBeta.Rd | 2 oce-0.9-22/oce/man/swBeta.Rd | 4 oce-0.9-22/oce/man/swCSTp.Rd | 7 oce-0.9-22/oce/man/swConservativeTemperature.Rd | 4 oce-0.9-22/oce/man/swDynamicHeight.Rd | 15 oce-0.9-22/oce/man/swLapseRate.Rd | 2 oce-0.9-22/oce/man/swRho.Rd | 4 oce-0.9-22/oce/man/swSCTp.Rd | 2 oce-0.9-22/oce/man/swSigma.Rd | 6 oce-0.9-22/oce/man/swSigma0.Rd | 7 oce-0.9-22/oce/man/swSigma1.Rd | 4 oce-0.9-22/oce/man/swSigma2.Rd | 4 oce-0.9-22/oce/man/swSigma3.Rd | 4 oce-0.9-22/oce/man/swSigma4.Rd | 4 oce-0.9-22/oce/man/swSigmaT.Rd | 8 oce-0.9-22/oce/man/swSigmaTheta.Rd | 11 oce-0.9-22/oce/man/swSoundSpeed.Rd | 2 oce-0.9-22/oce/man/swSpecificHeat.Rd | 2 oce-0.9-22/oce/man/swTFreeze.Rd | 2 oce-0.9-22/oce/man/swTheta.Rd | 37 oce-0.9-22/oce/man/tidedata.Rd | 2 oce-0.9-22/oce/man/tidem-class.Rd | 2 oce-0.9-22/oce/man/tidem.Rd | 2 oce-0.9-22/oce/man/tidemAstron.Rd | 2 oce-0.9-22/oce/man/tidemVuf.Rd | 2 oce-0.9-22/oce/man/toEnu.Rd | 2 oce-0.9-22/oce/man/toEnuAdp.Rd | 2 oce-0.9-22/oce/man/unitFromString.Rd | 5 oce-0.9-22/oce/man/unitFromStringRsk.Rd | 5 oce-0.9-22/oce/man/velocityStatistics.Rd | 2 oce-0.9-22/oce/man/webtide.Rd | 40 oce-0.9-22/oce/man/woceNames2oceNames.Rd | 14 oce-0.9-22/oce/man/woceUnit2oceUnit.Rd |only oce-0.9-22/oce/man/write.ctd.Rd | 32 oce-0.9-22/oce/man/xyzToEnu.Rd | 2 oce-0.9-22/oce/man/xyzToEnuAdp.Rd | 2 oce-0.9-22/oce/po/R-de.po | 542 ++++++----- oce-0.9-22/oce/po/R-es.po | 827 +++++++++++------ oce-0.9-22/oce/po/R-fr.po | 557 +++++++---- oce-0.9-22/oce/po/R-oce.pot | 499 ++++++---- oce-0.9-22/oce/po/R-zh.po | 537 ++++++----- oce-0.9-22/oce/src/adv_vector_time.c | 38 oce-0.9-22/oce/src/amsr.c | 10 oce-0.9-22/oce/src/binmap.c | 54 - oce-0.9-22/oce/src/bisect.c | 32 oce-0.9-22/oce/src/bitwise.c | 147 +-- oce-0.9-22/oce/src/coastline.c | 50 - oce-0.9-22/oce/src/curl.c | 22 oce-0.9-22/oce/src/echosounder.c | 36 oce-0.9-22/oce/src/fillgap.c | 46 oce-0.9-22/oce/src/geod.c | 70 - oce-0.9-22/oce/src/get_bit.c | 2 oce-0.9-22/oce/src/gradient.c | 2 oce-0.9-22/oce/src/interp_barnes.c | 42 oce-0.9-22/oce/src/landsat.c | 58 - oce-0.9-22/oce/src/ldc_ad2cp_in_file.c |only oce-0.9-22/oce/src/ldc_rdi_in_buffer.c | 88 - oce-0.9-22/oce/src/ldc_rdi_in_file.c | 379 +++---- oce-0.9-22/oce/src/oce_approx.c | 152 +-- oce-0.9-22/oce/src/oce_filter.c | 7 oce-0.9-22/oce/src/run.c | 62 - oce-0.9-22/oce/src/sfm_enu.c | 124 -- oce-0.9-22/oce/src/sontek_adp.c | 38 oce-0.9-22/oce/src/sw.c | 268 ++--- oce-0.9-22/oce/src/topo_interpolate.c | 16 oce-0.9-22/oce/src/trap.c | 77 - oce-0.9-22/oce/src/trim.c | 2 oce-0.9-22/oce/tests/testthat.R | 1 oce-0.9-22/oce/tests/testthat/test_accessors.R | 23 oce-0.9-22/oce/tests/testthat/test_allclass.R | 2 oce-0.9-22/oce/tests/testthat/test_argo.R | 13 oce-0.9-22/oce/tests/testthat/test_ctd.R | 65 + oce-0.9-22/oce/tests/testthat/test_flags.R | 4 oce-0.9-22/oce/tests/testthat/test_geod.R | 8 oce-0.9-22/oce/tests/testthat/test_local_adp.R | 2 oce-0.9-22/oce/tests/testthat/test_local_ctd.R | 15 oce-0.9-22/oce/tests/testthat/test_local_echosounder.R | 3 oce-0.9-22/oce/tests/testthat/test_local_odf.R | 254 ++++- oce-0.9-22/oce/tests/testthat/test_local_satellite.R | 2 oce-0.9-22/oce/tests/testthat/test_map.R | 2 oce-0.9-22/oce/tests/testthat/test_misc.R | 26 oce-0.9-22/oce/tests/testthat/test_plotting.R | 1 oce-0.9-22/oce/tests/testthat/test_section.R | 68 + oce-0.9-22/oce/tests/testthat/test_sw.R | 85 - oce-0.9-22/oce/vignettes |only 237 files changed, 7294 insertions(+), 4059 deletions(-)
Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>
Diff between kohonen versions 3.0.2 dated 2017-03-21 and 3.0.4 dated 2017-08-28
DESCRIPTION | 8 - MD5 | 36 ++++-- NEWS | 263 ++++++++++++++++++++++++++---------------------- R/check.data.R | 9 + R/map.R | 15 +- R/supersom.R | 29 ++++- build |only data/datalist |only data/degelder.rda |binary data/nir.rda |binary data/peppaPic.rda |only data/wines.rda |binary data/yeast.rda |binary demo |only inst/Distances |only man/kohonen-package.Rd |only man/map.kohonen.Rd | 3 man/object.distances.Rd | 2 man/peppaPic.Rd |only man/supersom.Rd | 35 ++++-- 20 files changed, 241 insertions(+), 159 deletions(-)
Title: Change Point Regression
Description: Change point regression models are also called two-phase regression, break-point regression, split-point regression, structural change models and threshold regression models. Hypothesis testing in change point logistic regression with or without interaction terms (Fong, Y., Di, C., Perma, S. (2014) <doi:10.1002/sim.6419>). Several options are provided for testing in models with interaction, including a maximum of likelihood ratios test that determines p-value through Monte Carlo. Estimation under change point model is also included with model-robust confidence intervals for continuous threshold regression models (Fong, Y., Di, C., Huang, Y., Gilbert, P. (2017) <doi:10.1111/biom.12623>).
Author: Youyi Fong
Maintainer: Youyi Fong <youyifong@gmail.com>
Diff between chngpt versions 2016.7-31 dated 2016-07-31 and 2017.08-28 dated 2017-08-28
ChangeLog | 7 DESCRIPTION | 15 MD5 | 33 - NAMESPACE | 2 R/chngpt.test.R | 27 - R/chngptm.R | 935 +++++++++++++++++++++++-------------- R/sim.chngpt.R | 88 ++- build |only data/coef.0.ls.rda |only inst/CITATION |only inst/doc |only inst/unitTests/report.html |only inst/unitTests/report.txt |only inst/unitTests/runRUnitTests.R | 208 ++++---- inst/unitTests/runit.chngpt.test.R | 9 inst/unitTests/runit.chngptm.R | 84 ++- man/chngpt.test.Rd | 2 man/chngptm.Rd | 56 +- man/coef.0.ls.Rd |only man/sim.chngpt.Rd | 25 vignettes |only 21 files changed, 908 insertions(+), 583 deletions(-)
Title: Tools for Remote Sensing Data Analysis
Description: Toolbox for remote sensing image processing and analysis such as
calculating spectral indices, principal component transformation, unsupervised
and supervised classification or fractional cover analyses.
Author: Benjamin Leutner [cre, aut],
Ned Horning [aut]
Maintainer: Benjamin Leutner <benjamin.leutner@uni-wuerzburg.de>
Diff between RStoolbox versions 0.1.8 dated 2017-04-15 and 0.1.9 dated 2017-08-28
DESCRIPTION | 14 - MD5 | 73 +++++----- NAMESPACE | 1 NEWS | 8 + R/RStoolbox.R | 3 R/RcppExports.R | 20 +- R/cloudMask.R | 5 R/fCover.R | 4 R/getValidation.R | 2 R/ggR.R | 2 R/ggRGB.R | 4 R/radCor.R | 2 R/rasterCVA.R | 2 R/rasterPCA.R | 4 R/readEE.R | 10 + R/readMeta.R | 4 R/stackMeta.R | 1 R/sysdata.rda |binary R/tasseledCap.R | 73 +++------- man/ImageMetaData.Rd | 2 man/RStoolbox.Rd | 2 man/fCover.Rd | 4 man/getValidation.Rd | 2 man/ggR.Rd | 2 man/ggRGB.Rd | 4 man/radCor.Rd | 2 man/rasterCVA.Rd | 2 man/rasterPCA.Rd | 4 man/readEE.Rd | 4 man/spectralIndices.Rd | 4 man/stackMeta.Rd | 1 man/tasseledCap.Rd | 29 ++- src/RcppExports.cpp | 20 +- src/init.c | 40 ++--- tests/testthat/test-readEE.R | 3 tests/testthat/test-validateMap.R | 2 tests/testthat/testdata/earthexplorer/EE_LANDSAT_NEWFORMAT.csv |only tests/testthat/testdata/metadata/LE07_L1TP_160031_20110416_20161210_01_T1.xml |only tests/testthat/testdata/metadata/LE07_L1TP_160031_20110416_20161210_01_T1_MTL.TXT |only 39 files changed, 184 insertions(+), 175 deletions(-)
Title: Heatmaps for Multiple Network Data
Description: Simplify the exploratory data analysis process for multiple network data sets with the help
of hierarchical clustering and heatmaps. Contains the tools necessary to convert the raw data
of multiple networks into a single dynamic report that summarizes many of the relationships
of their graph, node and structural characteristics.
Author: Phil Boileau [aut, cre]
Maintainer: Phil Boileau <philippe.boileau@mail.concordia.ca>
Diff between neatmaps versions 1.0.2 dated 2017-08-06 and 1.0.5 dated 2017-08-28
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- R/neatmap.R | 2 +- man/neatmap.Rd | 2 +- 4 files changed, 9 insertions(+), 10 deletions(-)
Title: Mutate Data Frames with Random Variates
Description: Work within the 'dplyr' workflow to add random variates to your data frame.
Variates can be added at any level of an existing column. Also, bounds can be specified
for simulated variates.
Author: Kyle T Baron [aut, cre, cph]
Maintainer: Kyle T Baron <kyleb@metrumrg.com>
Diff between dmutate versions 0.1.1 dated 2017-01-25 and 0.1.2 dated 2017-08-28
DESCRIPTION | 11 ++++---- MD5 | 24 +++++++++++------- NAMESPACE | 4 +++ NEWS.md |only R/Aaaa.R |only R/class_covset.R | 6 +--- R/dmutate.R | 68 +++++++++++++++++++++++++++++++++++++-------------- R/utils.R | 1 man/covset.Rd | 14 +++++++--- man/dmutate.Rd |only man/mutate_random.Rd | 7 ++--- man/rbinomial.Rd | 1 man/rmvnorm.Rd | 12 +++++++-- tests |only 14 files changed, 101 insertions(+), 47 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds
to GDAL for reading and writing data, to GEOS for geometrical operations, and to Proj.4 for projection
conversions and datum transformations.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Michael Sumner [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb],
Etienne Racine [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.5-3 dated 2017-07-30 and 0.5-4 dated 2017-08-28
DESCRIPTION | 15 +- MD5 | 186 +++++++++++++------------- NAMESPACE | 21 --- NEWS.md | 26 +++ R/cast_sfc.R | 28 ++-- R/crs.R | 43 +++--- R/db.R | 50 +++---- R/geom.R | 83 +++++++---- R/graticule.R | 46 +++--- R/grid.R | 12 - R/join.R | 13 - R/plot.R | 62 ++++---- R/read.R | 49 +++++-- R/sample.R | 10 - R/sf.R | 68 ++++----- R/sfc.R | 159 ++++++++++++---------- R/sfg.R | 18 +- R/sp.R | 24 ++- R/tidyverse.R | 150 ++++++++++----------- R/transform.R | 24 +-- R/valid.R | 8 - R/wkb.R | 46 +++--- R/wkt.R | 74 +++++++--- inst/doc/sf1.html | 62 ++++---- inst/doc/sf2.html | 18 +- inst/doc/sf3.html | 60 ++++---- inst/doc/sf4.R | 23 +++ inst/doc/sf4.Rmd | 39 +++++ inst/doc/sf4.html | 130 +++++++++++++++--- man/coerce-methods.Rd | 4 man/dplyr.Rd | 81 +++-------- man/geos_binary_ops.Rd | 13 + man/geos_binary_pred.Rd | 7 - man/geos_combine.Rd | 16 +- man/geos_measures.Rd | 8 - man/geos_query.Rd | 2 man/geos_unary.Rd | 12 + man/plot.Rd | 12 - man/sf.Rd | 8 - man/sfc.Rd | 15 +- man/st.Rd | 4 man/st_as_sf.Rd | 4 man/st_as_sfc.Rd | 6 man/st_as_text.Rd | 4 man/st_cast.Rd | 2 man/st_cast_sfc_default.Rd | 6 man/st_crs.Rd | 28 ++-- man/st_drivers.Rd | 2 man/st_geometry.Rd | 2 man/st_graticule.Rd | 16 +- man/st_join.Rd | 6 man/st_layers.Rd | 2 man/st_make_grid.Rd | 2 man/st_precision.Rd | 2 man/st_read.Rd | 8 - man/st_relate.Rd | 4 man/st_sample.Rd | 2 man/st_transform.Rd | 10 - man/st_viewport.Rd | 6 man/st_write.Rd | 4 man/st_zm.Rd | 2 man/valid.Rd | 2 src/bbox.cpp | 4 src/gdal.cpp | 1 src/gdal.h | 1 src/gdal_geom.cpp | 13 + src/gdal_read.cpp | 6 src/geos.cpp | 13 + tests/aggregate.Rout.save | 20 +- tests/cast.Rout.save | 118 ++++++++-------- tests/dist.Rout.save | 14 +- tests/dplyr.R | 4 tests/dplyr.Rout.save | 74 +++++----- tests/empty.Rout.save | 184 +++++++++++++------------- tests/gdal_geom.R | 4 tests/gdal_geom.Rout.save | 26 ++- tests/geos.R | 8 + tests/geos.Rout.save | 31 +++- tests/read.R | 10 - tests/read.Rout.save | 129 ++++++++---------- tests/roundtrip.R | 11 + tests/roundtrip.Rout.save | 46 +++--- tests/sfc.Rout.save | 294 +++++++++++++++++++++--------------------- tests/testthat.Rout.save | 18 -- tests/testthat/test_postgis.R | 59 ++++---- tests/testthat/test_sfg.R | 10 - tests/testthat/test_tidy.R | 14 +- tests/testthat/test_wkt.R | 8 - tests/testthat/test_write.R | 9 + tests/units.R | 10 + tests/units.Rout.save | 12 + tests/wkb.R | 2 tests/wkb.Rout.save | 16 +- vignettes/sf4.Rmd | 39 +++++ 94 files changed, 1706 insertions(+), 1351 deletions(-)
Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear,
and mixed models. Compute contrasts or linear functions of least-squares
means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre, cph],
Jonathon Love [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>
Diff between lsmeans versions 2.26-3 dated 2017-05-09 and 2.27-2 dated 2017-08-28
DESCRIPTION | 14 MD5 | 50 - R/S4-classes.R | 7 R/helpers.R | 10 R/lsmeans.R | 298 +++++------ R/lsmip.R | 12 R/nested.R |only R/nonlin-support.R | 2 R/ordinal-support.R | 4 R/plot.lsm.R | 2 R/rbind.R | 23 R/ref.grid.R | 32 - R/reformulate.R |only R/summary.R | 236 +++++---- R/zzz.R | 1 build/vignette.rds |binary inst/NEWS | 12 inst/doc/extending.pdf |binary inst/doc/using-lsmeans.R | 76 ++ inst/doc/using-lsmeans.pdf |binary inst/doc/using-lsmeans.rnw | 46 + man/lsmeans.Rd | 8 man/ref.grid.Rd | 6 man/summary.Rd | 3 man/update.Rd | 1 tests/tests1.Rout.save | 1150 ++++++++++++++++++++++---------------------- vignettes/using-lsmeans.rnw | 46 + 27 files changed, 1159 insertions(+), 880 deletions(-)
Title: Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees
Description: Create, visualize, and test fast-and-frugal decision trees (FFTs). FFTs are very simple decision trees for
binary classification problems. FFTs can be preferable to more complex algorithms because they are easy to communicate, require very little information, and are
robust against overfitting.
Author: Nathaniel Phillips [aut, cre],
Hansjoerg Neth [aut],
Jan Woike [aut],
Wolfgang Gaissmaer [aut]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>
Diff between FFTrees versions 1.3.3 dated 2017-07-11 and 1.3.4 dated 2017-08-28
DESCRIPTION | 8 MD5 | 70 ++-- R/FFTrees.R | 327 +++++++++++++-------- R/applytree_function.R | 30 + R/comppred_function.R | 164 ++++++++-- R/cuerank_function.R | 594 ++++++++++++++++++++------------------- R/fan_algorithm.R | 39 +- R/growFFTrees_function.R | 21 + R/inwords.R | 43 +- R/plotFFTrees_function.R | 501 ++++++++++++++++++++------------ R/printFFTrees_function.R | 18 - R/wordstoFFT.R | 41 +- R/zzz.R | 8 README.md | 6 inst/doc/AccuracyStatistics.html | 11 inst/doc/FFTrees_algorithm.html | 6 inst/doc/FFTrees_examples.Rmd | 2 inst/doc/FFTrees_examples.html | 12 inst/doc/FFTrees_function.html | 19 - inst/doc/FFTrees_heart.html | 13 inst/doc/FFTrees_mytree.html | 17 - inst/doc/FFTrees_plot.R | 33 +- inst/doc/FFTrees_plot.Rmd | 41 +- inst/doc/FFTrees_plot.html | 39 +- inst/doc/guide.R | 19 - inst/doc/guide.Rmd | 40 -- inst/doc/guide.html | 55 +-- man/FFTrees.Rd | 13 man/apply.tree.Rd | 4 man/comp.pred.Rd | 4 man/fan.algorithm.Rd | 4 man/grow.FFTrees.Rd | 4 man/plot.FFTrees.Rd | 23 + vignettes/FFTrees_examples.Rmd | 2 vignettes/FFTrees_plot.Rmd | 41 +- vignettes/guide.Rmd | 40 -- 36 files changed, 1374 insertions(+), 938 deletions(-)
Title: Standard Evaluation Interfaces for Common 'dplyr' Tasks
Description: The 'seplyr' (standard evaluation data.frame 'dplyr') package supplies
standard evaluation adapter methods for important common 'dplyr' methods
that currently have a non-standard programming interface. This allows
the analyst to use 'dplyr' to perform fundamental data transformation
steps such as arranging rows, grouping rows, aggregating selecting
columns without having to use learn the details of 'rlang'/'tidyeval'
non-standard evaluation and without continuing to rely on now
deprecated 'dplyr' "underscore verbs."
In addition the 'seplyr' package supplies several new "key operations
bound together" methods. These include 'group_summarize()' (which
combines grouping, arranging and calculation in an atomic unit),
'add_group_summaries()' (which joins grouped summaries into a 'data.frame'
in a well documented manner), and 'add_group_indices()' (which adds
per-group identifies to a 'data.frame' without depending on row-order).
Author: John Mount [aut, cre],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between seplyr versions 0.1.4 dated 2017-08-21 and 0.1.5 dated 2017-08-28
seplyr-0.1.4/seplyr/R/lambda.R |only seplyr-0.1.4/seplyr/R/namedMapBuilder.R |only seplyr-0.1.4/seplyr/man/makeFunction_se.Rd |only seplyr-0.1.4/seplyr/man/named_map_builder.Rd |only seplyr-0.1.5/seplyr/DESCRIPTION | 9 - seplyr-0.1.5/seplyr/MD5 | 145 ++++++++++---------- seplyr-0.1.5/seplyr/NAMESPACE | 32 +++- seplyr-0.1.5/seplyr/NEWS.md | 7 seplyr-0.1.5/seplyr/R/add_group_indices.R | 2 seplyr-0.1.5/seplyr/R/add_group_summaries.R | 5 seplyr-0.1.5/seplyr/R/add_rank_indices.R | 13 - seplyr-0.1.5/seplyr/R/arrange_se.R | 13 - seplyr-0.1.5/seplyr/R/distinct_se.R | 3 seplyr-0.1.5/seplyr/R/filter_nse.R |only seplyr-0.1.5/seplyr/R/filter_se.R | 13 - seplyr-0.1.5/seplyr/R/group_by_se.R | 10 - seplyr-0.1.5/seplyr/R/group_summarize.R | 10 - seplyr-0.1.5/seplyr/R/in_group_indices.R | 24 +-- seplyr-0.1.5/seplyr/R/mutate_nse.R | 132 ++---------------- seplyr-0.1.5/seplyr/R/mutate_se.R | 17 +- seplyr-0.1.5/seplyr/R/novelName.R | 4 seplyr-0.1.5/seplyr/R/package.R | 34 ++++ seplyr-0.1.5/seplyr/R/rename_se.R | 16 -- seplyr-0.1.5/seplyr/R/select_se.R | 16 -- seplyr-0.1.5/seplyr/R/stringAlgebra.R |only seplyr-0.1.5/seplyr/R/summarize_nse.R |only seplyr-0.1.5/seplyr/R/summarize_se.R | 15 -- seplyr-0.1.5/seplyr/R/tally.R | 16 -- seplyr-0.1.5/seplyr/R/transmute_nse.R |only seplyr-0.1.5/seplyr/R/transmute_se.R | 15 -- seplyr-0.1.5/seplyr/README.md | 12 + seplyr-0.1.5/seplyr/build/vignette.rds |binary seplyr-0.1.5/seplyr/inst/doc/StringAlgebra.R |only seplyr-0.1.5/seplyr/inst/doc/StringAlgebra.Rmd |only seplyr-0.1.5/seplyr/inst/doc/StringAlgebra.html |only seplyr-0.1.5/seplyr/inst/doc/named_map_builder.R | 25 +-- seplyr-0.1.5/seplyr/inst/doc/named_map_builder.Rmd | 30 +--- seplyr-0.1.5/seplyr/inst/doc/named_map_builder.html | 31 ++-- seplyr-0.1.5/seplyr/inst/doc/rename_se.R | 12 - seplyr-0.1.5/seplyr/inst/doc/rename_se.Rmd | 14 + seplyr-0.1.5/seplyr/inst/doc/rename_se.html | 17 +- seplyr-0.1.5/seplyr/inst/doc/seplyr.R | 24 +-- seplyr-0.1.5/seplyr/inst/doc/seplyr.Rmd | 29 ++-- seplyr-0.1.5/seplyr/inst/doc/seplyr.html | 30 ++-- seplyr-0.1.5/seplyr/inst/doc/using_seplyr.R | 2 seplyr-0.1.5/seplyr/inst/doc/using_seplyr.Rmd | 7 seplyr-0.1.5/seplyr/inst/doc/using_seplyr.html | 8 - seplyr-0.1.5/seplyr/man/add_count_se.Rd | 3 seplyr-0.1.5/seplyr/man/add_group_indices.Rd | 2 seplyr-0.1.5/seplyr/man/add_group_sub_indices.Rd | 25 +-- seplyr-0.1.5/seplyr/man/add_group_summaries.Rd | 5 seplyr-0.1.5/seplyr/man/add_rank_indices.Rd | 13 - seplyr-0.1.5/seplyr/man/add_tally_se.Rd | 3 seplyr-0.1.5/seplyr/man/arrange_se.Rd | 13 - seplyr-0.1.5/seplyr/man/count_se.Rd | 3 seplyr-0.1.5/seplyr/man/deselect.Rd | 7 seplyr-0.1.5/seplyr/man/distinct_se.Rd | 3 seplyr-0.1.5/seplyr/man/expand_expr.Rd | 14 + seplyr-0.1.5/seplyr/man/filter_nse.Rd |only seplyr-0.1.5/seplyr/man/filter_se.Rd | 13 - seplyr-0.1.5/seplyr/man/group_by_se.Rd | 10 - seplyr-0.1.5/seplyr/man/group_summarize.Rd | 13 + seplyr-0.1.5/seplyr/man/mutate_nse.Rd | 19 +- seplyr-0.1.5/seplyr/man/mutate_se.Rd | 17 +- seplyr-0.1.5/seplyr/man/novelName.Rd | 4 seplyr-0.1.5/seplyr/man/prep_deref.Rd |only seplyr-0.1.5/seplyr/man/reexports.Rd |only seplyr-0.1.5/seplyr/man/rename_mp.Rd | 7 seplyr-0.1.5/seplyr/man/rename_se.Rd | 9 - seplyr-0.1.5/seplyr/man/select_se.Rd | 9 - seplyr-0.1.5/seplyr/man/summarize_nse.Rd |only seplyr-0.1.5/seplyr/man/summarize_se.Rd | 17 +- seplyr-0.1.5/seplyr/man/tally_se.Rd | 7 seplyr-0.1.5/seplyr/man/transmute_nse.Rd |only seplyr-0.1.5/seplyr/man/transmute_se.Rd | 15 +- seplyr-0.1.5/seplyr/tests/testthat/test_basic.R | 12 - seplyr-0.1.5/seplyr/tests/testthat/test_stringalg.R |only seplyr-0.1.5/seplyr/tools |only seplyr-0.1.5/seplyr/vignettes/StringAlgebra.Rmd |only seplyr-0.1.5/seplyr/vignettes/named_map_builder.Rmd | 30 +--- seplyr-0.1.5/seplyr/vignettes/rename_se.Rmd | 14 + seplyr-0.1.5/seplyr/vignettes/seplyr.Rmd | 29 ++-- seplyr-0.1.5/seplyr/vignettes/using_seplyr.Rmd | 7 83 files changed, 544 insertions(+), 571 deletions(-)
Title: (Non)Linear Time Series Analysis
Description: R functions for (non)linear time series analysis with an emphasis on nonparametric autoregression and order estimation, and tests for linearity / additivity.
Author: Ottar N. Bjornstad <onb1@psu.edu>
Maintainer: Ottar N. Bjornstad <onb1@psu.edu>
Diff between nlts versions 0.2-0 dated 2013-06-03 and 0.2-2 dated 2017-08-28
CHANGES | 2 ++ DESCRIPTION | 17 +++++++---------- MD5 | 11 ++++++----- NAMESPACE | 24 ++++++++++++++++++++++++ R/nlts.R | 40 ++++++++++++++++++++++++++++++++-------- man/contingency.periodogram.Rd | 5 +++-- man/ll.edm.Rd |only 7 files changed, 74 insertions(+), 25 deletions(-)
Title: A Pipeline for Meta-Genome Wide Association
Description: Correlates variation within the meta-genome to target species
phenotype variations in meta-genome with association studies. Follows
the pipeline described in Chaston, J.M. et al. (2014) <doi:10.1128/mBio.01631-14>.
Author: Corinne Sexton [aut],
John Chaston [aut, cre],
Hayden Smith [ctb]
Maintainer: John Chaston <john_chaston@byu.edu>
Diff between MAGNAMWAR versions 1.0.0 dated 2017-04-26 and 2.0.0 dated 2017-08-28
MAGNAMWAR-1.0.0/MAGNAMWAR/R/RASTtogbk.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/analyze_OrthoMCL.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/format_MCLfastas.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/format_afterOrtho.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/join_repseq.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/printCOGseqs.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/surv_append_matrix.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/R/write_mcl.R |only MAGNAMWAR-1.0.0/MAGNAMWAR/inst/extdata/RASTtogbk |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/RASTtogbk.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/analyze_OrthoMCL.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/format_MCLfastas.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/format_afterOrtho.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/join_repseq.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/manhat_grp.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/pdg_v_OG.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/pdgplot.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/phydataerror.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/printOGseqs.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/qqplotter.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/surv_append_matrix.Rd |only MAGNAMWAR-1.0.0/MAGNAMWAR/man/write_mcl.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/DESCRIPTION | 11 MAGNAMWAR-2.0.0/MAGNAMWAR/MD5 | 82 ++--- MAGNAMWAR-2.0.0/MAGNAMWAR/NAMESPACE | 30 + MAGNAMWAR-2.0.0/MAGNAMWAR/NEWS.md | 7 MAGNAMWAR-2.0.0/MAGNAMWAR/R/AnalyzeOrthoMCL.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/CalculatePrincipalCoordinates.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/FormatAfterOrtho.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/FormatMCLFastas.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/JoinRepSeq.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/PrintOGSeqs.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/RASTtoGBK.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/SurvAppendMatrix.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/WriteMCL.R |only MAGNAMWAR-2.0.0/MAGNAMWAR/R/doc.R | 12 MAGNAMWAR-2.0.0/MAGNAMWAR/R/graphics.R | 60 +-- MAGNAMWAR-2.0.0/MAGNAMWAR/README.md | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/inst/doc/using_mag.R | 36 +- MAGNAMWAR-2.0.0/MAGNAMWAR/inst/doc/using_mag.Rmd | 137 +++++--- MAGNAMWAR-2.0.0/MAGNAMWAR/inst/doc/using_mag.html | 157 +++++----- MAGNAMWAR-2.0.0/MAGNAMWAR/inst/extdata/RASTtoGBK |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/AnalyzeOrthoMCL.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/CalculatePrincipalCoordinates.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/FormatAfterOrtho.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/FormatMCLFastas.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/JoinRepSeq.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/ManhatGrp.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/PDGPlot.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/PDGvOG.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/PhyDataError.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/PrintOGSeqs.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/QQPlotter.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/RASTtoGBK.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/SurvAppendMatrix.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/WriteMCL.Rd |only MAGNAMWAR-2.0.0/MAGNAMWAR/man/after_ortho_format.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/man/after_ortho_format_grps.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/man/mcl_mtrx.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/man/mcl_mtrx_grps.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/man/pheno_data.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/man/starv_pheno_data.Rd | 2 MAGNAMWAR-2.0.0/MAGNAMWAR/vignettes/using_mag.Rmd | 137 +++++--- 63 files changed, 385 insertions(+), 298 deletions(-)
Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalised ratio-of-uniforms (RU) method to simulate
from univariate and (low-dimensional) multivariate continuous distributions.
The user specifies the log-density, up to an additive constant. The RU
algorithm is applied after relocation of mode of the density to zero, and
the user can choose a tuning parameter r. For details see Wakefield, Gelfand
and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random
variates via the ratio-of-uniforms method, Statistics and Computing (1991)
1, 129-133. A Box-Cox variable transformation can be used to make the input
density suitable for the RU method and to improve efficiency. In the
multivariate case rotation of axes can also be used to improve efficiency.
From version 1.2.0 the 'Rcpp' package
<https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.
See the rust website for more information, documentation and examples.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between rust versions 1.2.1 dated 2017-06-01 and 1.2.3 dated 2017-08-28
rust-1.2.1/rust/tests/testthat/test_rou.R |only rust-1.2.1/rust/vignettes/example_user_fns.cpp |only rust-1.2.3/rust/DESCRIPTION | 8 rust-1.2.3/rust/MD5 | 55 - rust-1.2.3/rust/NEWS.md | 28 rust-1.2.3/rust/R/RcppExports.R | 130 +- rust-1.2.3/rust/R/box_cox_functions.R | 2 rust-1.2.3/rust/R/box_cox_functions_rcpp.R | 4 rust-1.2.3/rust/R/ru_sampling.R | 303 ++++-- rust-1.2.3/rust/R/ru_sampling_rcpp.R | 178 ++- rust-1.2.3/rust/R/sample_diagnostics.R | 26 rust-1.2.3/rust/README.md | 4 rust-1.2.3/rust/inst/doc/rust-using-rcpp-vignette.R | 27 rust-1.2.3/rust/inst/doc/rust-using-rcpp-vignette.Rmd | 27 rust-1.2.3/rust/inst/doc/rust-using-rcpp-vignette.html | 62 - rust-1.2.3/rust/inst/doc/rust-vignette.Rmd | 4 rust-1.2.3/rust/inst/doc/rust-vignette.html | 13 rust-1.2.3/rust/inst/include/rust_RcppExports.h | 357 +++++-- rust-1.2.3/rust/man/find_lambda.Rd | 2 rust-1.2.3/rust/man/ru.Rd | 75 + rust-1.2.3/rust/man/ru_rcpp.Rd | 84 + rust-1.2.3/rust/src/RcppExports.cpp | 771 +++++++++++----- rust-1.2.3/rust/src/built_in_fns.cpp | 57 + rust-1.2.3/rust/src/user_fns.cpp | 59 + rust-1.2.3/rust/tests/testthat/test_find_lambda.R |only rust-1.2.3/rust/tests/testthat/test_find_lambda_one_d.R |only rust-1.2.3/rust/tests/testthat/test_ru.R |only rust-1.2.3/rust/tests/testthat/test_ru_equal_ru_rcpp.R |only rust-1.2.3/rust/tests/testthat/test_ru_rcpp.R |only rust-1.2.3/rust/vignettes/rust-using-rcpp-vignette.Rmd | 30 rust-1.2.3/rust/vignettes/rust-vignette.Rmd | 10 rust-1.2.3/rust/vignettes/rust.bib | 54 + 32 files changed, 1699 insertions(+), 671 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson, Dirac or circular von Mises parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.9.2 dated 2017-06-09 and 2.9.3 dated 2017-08-28
DESCRIPTION | 6 MD5 | 42 - R/RCLRMIX.R | 2 R/RCLSMIX.R | 4 R/REBMIX.R | 2 R/RNGMIX.R | 2 build/vignette.rds |binary data/adult.rda |binary data/galaxy.rda |binary data/iris.rda |binary data/truck.rda |binary data/weibull.rda |binary data/weibullnormal.rda |binary data/wine.rda |binary inst/NEWS.Rd | 6 inst/doc/rebmix.Rnw | 6 inst/doc/rebmix.pdf |binary src/base.h | 7 src/rebmixf.cpp | 1235 ++++++++++++++++++++++++------------------------- src/rebmvnormf.cpp | 6 src/rngmixf.cpp | 18 vignettes/rebmix.Rnw | 6 22 files changed, 680 insertions(+), 662 deletions(-)
Title: Rcpp Bindings for Sequential Monte Carlo
Description: R access to the Sequential Monte Carlo Template Classes
by Johansen (Journal of Statistical Software, 2009, v30, i6) is provided.
At present, two additional examples have been added, and the first
example from the JSS paper has been extended. Further integration
and extensions are planned.
Author: Dirk Eddelbuettel, Adam M. Johansen and Leah F. South
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppSMC versions 0.1.5 dated 2017-03-03 and 0.2.0 dated 2017-08-28
RcppSMC-0.1.5/RcppSMC/inst/include/particle.h |only RcppSMC-0.1.5/RcppSMC/inst/include/rngR.h |only RcppSMC-0.1.5/RcppSMC/src/init.c |only RcppSMC-0.2.0/RcppSMC/ChangeLog | 292 +++ RcppSMC-0.2.0/RcppSMC/DESCRIPTION | 13 RcppSMC-0.2.0/RcppSMC/MD5 | 76 - RcppSMC-0.2.0/RcppSMC/NAMESPACE | 10 RcppSMC-0.2.0/RcppSMC/R/LinReg.R |only RcppSMC-0.2.0/RcppSMC/R/LinRegLA.R |only RcppSMC-0.2.0/RcppSMC/R/LinRegLA_adapt.R |only RcppSMC-0.2.0/RcppSMC/R/RcppExports.R |only RcppSMC-0.2.0/RcppSMC/R/bspfGaussianOptimal.R | 10 RcppSMC-0.2.0/RcppSMC/R/nonLinPMMH.R |only RcppSMC-0.2.0/RcppSMC/R/pfLineartBS.R | 5 RcppSMC-0.2.0/RcppSMC/R/pfNonlinBS.R | 2 RcppSMC-0.2.0/RcppSMC/R/simNonlin.R | 10 RcppSMC-0.2.0/RcppSMC/README.md | 10 RcppSMC-0.2.0/RcppSMC/TODO | 26 RcppSMC-0.2.0/RcppSMC/data |only RcppSMC-0.2.0/RcppSMC/inst/NEWS.Rd | 29 RcppSMC-0.2.0/RcppSMC/inst/include/LinReg.h |only RcppSMC-0.2.0/RcppSMC/inst/include/LinReg_LA.h |only RcppSMC-0.2.0/RcppSMC/inst/include/LinReg_LA_adapt.h |only RcppSMC-0.2.0/RcppSMC/inst/include/adaptMethods.h |only RcppSMC-0.2.0/RcppSMC/inst/include/blockpfgaussianopt.h | 16 RcppSMC-0.2.0/RcppSMC/inst/include/history.h | 548 +------ RcppSMC-0.2.0/RcppSMC/inst/include/moveset.h | 363 ++-- RcppSMC-0.2.0/RcppSMC/inst/include/nonLinPMMH.h |only RcppSMC-0.2.0/RcppSMC/inst/include/pflineart.h | 48 RcppSMC-0.2.0/RcppSMC/inst/include/pfnonlinbs.h | 8 RcppSMC-0.2.0/RcppSMC/inst/include/population.h |only RcppSMC-0.2.0/RcppSMC/inst/include/sampler.h | 1198 +++++++++------- RcppSMC-0.2.0/RcppSMC/inst/include/smc-exception.h | 28 RcppSMC-0.2.0/RcppSMC/inst/include/smctc.h | 33 RcppSMC-0.2.0/RcppSMC/inst/include/staticModelAdapt.h |only RcppSMC-0.2.0/RcppSMC/inst/rawdata |only RcppSMC-0.2.0/RcppSMC/man/LinReg.Rd |only RcppSMC-0.2.0/RcppSMC/man/blockpfGaussianOpt.Rd | 4 RcppSMC-0.2.0/RcppSMC/man/nonLinPMMH.Rd |only RcppSMC-0.2.0/RcppSMC/man/pfNonlinBS.Rd | 20 RcppSMC-0.2.0/RcppSMC/man/radiata.Rd |only RcppSMC-0.2.0/RcppSMC/man/simNonlin.Rd |only RcppSMC-0.2.0/RcppSMC/src/LinReg.cpp |only RcppSMC-0.2.0/RcppSMC/src/LinReg_LA.cpp |only RcppSMC-0.2.0/RcppSMC/src/LinReg_LA_adapt.cpp |only RcppSMC-0.2.0/RcppSMC/src/Makevars | 1 RcppSMC-0.2.0/RcppSMC/src/RcppExports.cpp |only RcppSMC-0.2.0/RcppSMC/src/blockpfgaussianopt.cpp | 150 -- RcppSMC-0.2.0/RcppSMC/src/helper.cpp |only RcppSMC-0.2.0/RcppSMC/src/nonLinPMMH.cpp |only RcppSMC-0.2.0/RcppSMC/src/pflineart.cpp | 230 +-- RcppSMC-0.2.0/RcppSMC/src/pfnonlinbs.cpp | 61 RcppSMC-0.2.0/RcppSMC/src/staticModelAdapt.cpp |only 53 files changed, 1697 insertions(+), 1494 deletions(-)
Title: R Commander Miscellaneous Functions
Description: Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.
Author: John Fox [aut, cre],
Robert Muenchen [ctb],
Dan Putler [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between RcmdrMisc versions 1.0-5 dated 2016-08-11 and 1.0-6 dated 2017-08-28
DESCRIPTION | 19 ++++----- MD5 | 44 +++++++++++++-------- NAMESPACE | 67 +++++++++++++++++--------------- NEWS | 106 ++++++++++++++++++++++++++++++++------------------- R/Barplot.R | 51 ++++++++++++++++++++---- R/bin.var.R | 6 +- R/binnedCounts.R |only R/discretePlot.R |only R/normalityTest.R |only R/numSummary.R | 4 - R/plotBoot.R |only R/plots.R | 66 ++++++++++++++++++++++++------- R/readSAS.R |only R/readSPSS.R |only R/readStata.R |only R/readXL.R | 24 +++++++---- man/Barplot.Rd | 26 +++++++++--- man/Dotplot.Rd | 4 - man/Hist.Rd | 5 +- man/bin.var.Rd | 11 +++-- man/binnedCounts.Rd |only man/discretePlot.Rd |only man/indexplot.Rd | 15 ++++--- man/normalityTest.Rd |only man/plotBoot.Rd |only man/plotMeans.Rd | 17 ++++---- man/readSAS.Rd |only man/readSPSS.Rd |only man/readStata.Rd |only man/readXL.Rd | 3 - 30 files changed, 309 insertions(+), 159 deletions(-)
Title: Automatic Generation of Qualitative Color Palettes
Description: Automatic generation of distinct qualitative color palettes,
optionally adapted to color blindness. It takes a subspace of the HSL color
space as input and projects it to the DIN99d color space where it selects
and return colors that are maximally distinct.
Author: Johan Larsson [aut, cre]
Maintainer: Johan Larsson <johanlarsson@outlook.com>
Diff between qualpalr versions 0.4.1 dated 2017-05-15 and 0.4.2 dated 2017-08-28
qualpalr-0.4.1/qualpalr/R/main.R |only qualpalr-0.4.1/qualpalr/src/init.c |only qualpalr-0.4.1/qualpalr/src/main.cpp |only qualpalr-0.4.2/qualpalr/DESCRIPTION | 10 +++--- qualpalr-0.4.2/qualpalr/MD5 | 35 ++++++++++----------- qualpalr-0.4.2/qualpalr/NAMESPACE | 2 - qualpalr-0.4.2/qualpalr/NEWS.md | 13 +++++++ qualpalr-0.4.2/qualpalr/R/RcppExports.R | 4 +- qualpalr-0.4.2/qualpalr/R/autopal.R | 1 qualpalr-0.4.2/qualpalr/R/qualpal.R |only qualpalr-0.4.2/qualpalr/R/qualpalr.R | 8 +--- qualpalr-0.4.2/qualpalr/README.md | 2 - qualpalr-0.4.2/qualpalr/build/vignette.rds |binary qualpalr-0.4.2/qualpalr/inst/doc/introduction.Rmd | 1 qualpalr-0.4.2/qualpalr/inst/doc/introduction.html | 28 ++++++++-------- qualpalr-0.4.2/qualpalr/man/print.qualpal.Rd | 2 - qualpalr-0.4.2/qualpalr/man/qualpal.Rd | 2 - qualpalr-0.4.2/qualpalr/src/RcppExports.cpp | 15 +++++++-- qualpalr-0.4.2/qualpalr/src/qualpal.cpp |only qualpalr-0.4.2/qualpalr/tools/README-pairs-1.png |binary qualpalr-0.4.2/qualpalr/vignettes/introduction.Rmd | 1 21 files changed, 71 insertions(+), 53 deletions(-)
Title: Plotting Multi-Dimensional Data
Description: Functions for viewing 2-D and 3-D data, including perspective plots, slice plots, surface plots, scatter plots, etc. Includes data sets from oceanography.
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between plot3D versions 1.1 dated 2016-01-13 and 1.1.1 dated 2017-08-28
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/arrows3D.R | 5 +++++ R/hist3D.R | 16 ++++++++++++++-- build/vignette.rds |binary data/Hypsometry.rda |binary data/Oxsat.rda |binary inst/doc/plot3D.pdf |binary inst/doc/volcano.pdf |binary man/persp3D.Rd | 7 ++++++- 10 files changed, 39 insertions(+), 17 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Mikael Dubik (lart and glouvain functions). The package uses functions from dlib, Eigen, Spectra and eclat libraries, whose code has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 1.1 dated 2017-08-16 and 1.1.1 dated 2017-08-28
DESCRIPTION | 6 MD5 | 19 - man/Plot.Rd | 1 src/eclat/apriori/src/makefile |only src/eclat/eclat/src/makefile |only src/eclat/math/src/makefile |only src/eclat/tract/src/makefile |only src/eclat/util/src/makefile |only src/lib/dlib/svm/kkmeans.h | 3 src/multinet/community/abacus.cpp | 33 +- src/multinet/community/cutils.cpp | 509 +++++++++++++++++++------------------- src/multinet/community/pmm.cpp | 52 ++- src/multinet/measures/cc.cpp | 2 13 files changed, 325 insertions(+), 300 deletions(-)
Title: Efficient Iterators for Permutations and Combinations
Description: A collection of iterators for generating permutations and combinations with or
without replacement; with distinct items or non-distinct items (multiset).
The generated sequences are in lexicographical order (dictionary order). The
algorithms to generate permutations and combinations are memory efficient. These
iterative algorithms enable users to process all sequences without putting all
results in the memory at the same time. The algorithms are written in C/C++ for
faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between iterpc versions 0.3.0 dated 2016-05-31 and 0.3.1 dated 2017-08-28
iterpc-0.3.0/iterpc/demo |only iterpc-0.3.1/iterpc/DESCRIPTION | 21 ++-- iterpc-0.3.1/iterpc/MD5 | 50 +++++---- iterpc-0.3.1/iterpc/NAMESPACE | 2 iterpc-0.3.1/iterpc/R/RcppExports.R | 14 +- iterpc-0.3.1/iterpc/R/combination.R | 1 iterpc-0.3.1/iterpc/R/permutation.R | 1 iterpc-0.3.1/iterpc/R/utilities.R | 20 +-- iterpc-0.3.1/iterpc/README.md | 4 iterpc-0.3.1/iterpc/build |only iterpc-0.3.1/iterpc/inst |only iterpc-0.3.1/iterpc/man/getall.Rd | 1 iterpc-0.3.1/iterpc/man/getcurrent.Rd | 1 iterpc-0.3.1/iterpc/man/getlength.Rd | 1 iterpc-0.3.1/iterpc/man/getnext.Rd | 1 iterpc-0.3.1/iterpc/man/iter_wrapper.Rd | 1 iterpc-0.3.1/iterpc/man/iterpc.Rd | 2 iterpc-0.3.1/iterpc/man/multichoose.Rd | 1 iterpc-0.3.1/iterpc/man/nc_multiset.Rd | 1 iterpc-0.3.1/iterpc/man/np_multiset.Rd | 1 iterpc-0.3.1/iterpc/src/RcppExports.cpp | 77 ++++++++------- iterpc-0.3.1/iterpc/src/mbcomb/README | 164 ++++++++++++++++---------------- iterpc-0.3.1/iterpc/tests/testthat.R | 1 iterpc-0.3.1/iterpc/vignettes |only 24 files changed, 188 insertions(+), 177 deletions(-)
Title: Texas Holdem Simulator
Description: Simulates hands and tournaments of Texas Holdem,
the most popular form of poker.
For examples of probability problems involving Texas Holdem
and a brief explanation of the game see Schoenberg, F. (2011).
An Introduction to Probability with Texas Hold'em Examples.
Taylor and Francis, New York, ISBN-13: 978-1439827680.
Author: Frederic Paik Schoenberg,Yixuan Shao
Maintainer: Frederic Paik Schoenberg <frederic@stat.ucla.edu>
Diff between holdem versions 1.1 dated 2011-06-17 and 1.2 dated 2017-08-28
DESCRIPTION | 22 ++++-- MD5 |only NAMESPACE |only R/hand1.R | 50 +++++++------- R/many1.R | 27 ++++--- R/tourn1.R | 174 +++++++++++++++++++++++++------------------------- man/bid1.Rd | 29 +++----- man/bid2.Rd | 32 +++------ man/calcwin1.Rd | 23 ------ man/deal1.Rd | 6 - man/flush1.Rd | 12 --- man/flushdraw1.Rd | 14 ---- man/four1.Rd | 14 ---- man/full1.Rd | 16 ---- man/gravity.Rd | 9 -- man/hand1.Rd | 27 +++---- man/handeval.Rd | 14 ---- man/holdem-package.Rd | 3 man/many1.Rd | 13 --- man/mycount1.Rd | 14 ---- man/mygraphics1.Rd | 29 ++------ man/nothing1.Rd | 14 ---- man/onepair1.Rd | 14 ---- man/straight1.Rd | 13 --- man/straightdraw1.Rd | 15 ---- man/strflsh1.Rd | 14 ---- man/switch2.Rd | 14 ---- man/timemachine.Rd | 9 -- man/tommy.Rd | 10 -- man/tourn1.Rd | 28 ++++---- man/trip1.Rd | 14 ---- man/twopair1.Rd | 14 ---- man/ursula.Rd | 10 -- man/vera.Rd | 9 -- man/william.Rd | 9 -- man/writebets1.Rd | 20 ----- man/xena.Rd | 10 -- man/yosef.Rd | 16 +--- man/zelda.Rd | 55 ++++++++------- 39 files changed, 267 insertions(+), 549 deletions(-)
Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.1.1 dated 2017-01-23 and 1.1.3 dated 2017-08-28
DESCRIPTION | 10 - MD5 | 103 +++++++++--------- NEWS | 13 ++ R/bugsModel.R | 2 R/cdfquantreg.R | 5 R/data.R | 56 +++++++++- R/qrBoot.R | 4 R/qrBugs.R | 4 R/qrControl.R | 7 - R/qrFitted.R | 78 ++++++++++++-- R/qrInfluence.R | 36 ++++-- R/qrLRT.R | 2 R/qrMethod.R | 4 R/qrPlot.R | 2 R/qrStart.R | 6 - R/qrTransform.R | 4 data/cdfqrExampleData.rda |binary inst/doc/CDFQuantregIntroduction.Rmd | 2 inst/doc/CDFQuantregIntroduction.html | 6 - inst/doc/IPCCExample.R | 15 ++ inst/doc/IPCCExample.Rmd | 20 ++- inst/doc/IPCCExample.html | 152 +++++++++++++++++++++++++--- inst/doc/Smithson_Verkuilen2006Example.R | 8 - inst/doc/Smithson_Verkuilen2006Example.Rmd | 30 ++--- inst/doc/Smithson_Verkuilen2006Example.html | 130 +++++++++++------------ man/Ambdata.Rd |only man/AnxStrData.Rd | 6 - man/IPCC.Rd | 4 man/IPCCAUS.Rd |only man/IPCC_Wide.Rd |only man/JurorData.Rd | 3 man/anova.cdfqr.Rd | 3 man/bugsLikelihood.Rd | 1 man/bugsModel.Rd | 3 man/cdfqr.control.Rd | 6 - man/cdfqrFamily.Rd | 1 man/cdfquantreg.Rd | 3 man/dq.Rd | 6 - man/influence.cdfqr.Rd | 10 + man/plot.cdfqr.Rd | 3 man/predict.cdfqr.Rd | 18 ++- man/qrBoot.Rd | 5 man/qrBugs.Rd | 5 man/qrGrad.Rd | 1 man/qrLogLik.Rd | 1 man/qrLogLikFun.Rd | 1 man/qrPwlm.Rd | 1 man/qrStart.Rd | 7 - man/residuals.cdfqr.Rd | 1 man/scaleTR.Rd | 5 man/summary.cdfqr.Rd | 19 +-- vignettes/CDFQuantregIntroduction.Rmd | 2 vignettes/IPCCExample.Rmd | 20 ++- vignettes/Smithson_Verkuilen2006Example.Rmd | 30 ++--- 54 files changed, 566 insertions(+), 298 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: Markov chain Monte Carlo algorithms for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for variable selection in mean/variance regression models.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.0.1 dated 2017-08-21 and 2.0.2 dated 2017-08-28
DESCRIPTION | 8 +-- MD5 | 6 +- R/mvrm.R | 136 +++++++++++++++++++++++++++++++++++----------------- man/BNSP-package.Rd | 4 - 4 files changed, 103 insertions(+), 51 deletions(-)
Title: SIMEX Algorithm on Pedigree Structures
Description: Generalization of the SIMEX algorithm from Cook & Stefanski (1994) <doi:10.2307/2290994> for the calculation of inbreeding depression or heritability on pedigree structures affected by missing or misassigned paternities. It simulates errors and tracks the behavior of the estimate as a function of the error proportion. It extrapolates back a true value corresponding to the null error rate.
Author: Erica Ponzi
Maintainer: Erica Ponzi <erica.ponzi@uzh.ch>
Diff between PSIMEX versions 1.0 dated 2017-07-25 and 1.1 dated 2017-08-28
DESCRIPTION | 9 +++++---- MD5 | 14 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/PSIMEXvignette.R | 1 + inst/doc/PSIMEXvignette.Rnw | 1 + inst/doc/PSIMEXvignette.pdf |binary vignettes/PSIMEXvignette.Rnw | 1 + 8 files changed, 15 insertions(+), 11 deletions(-)
Title: Bivariate Angular Mixture Models
Description: Fit (using Bayesian methods) and simulate mixtures of univariate and bivariate angular distributions.
Author: Saptarshi Chakraborty,
Samuel W.K. Wong
Maintainer: Saptarshi Chakraborty <c7rishi@ufl.edu>
Diff between BAMBI versions 1.1.0 dated 2017-02-06 and 1.1.1 dated 2017-08-28
DESCRIPTION | 11 MD5 | 87 ++-- NAMESPACE | 2 R/BAMBI.R | 3 R/RcppExports.R | 160 ++++---- R/all_postprodn_fns.R | 6 R/all_wnorm2_fns.R | 14 man/AIC.angmcmc.Rd | 1 man/DIC.Rd | 1 man/WAIC.Rd | 1 man/bestmodel.Rd | 1 man/contour.angmcmc.Rd | 1 man/d_fitted.Rd | 1 man/densityplot1d.Rd | 1 man/densityplot2d.Rd | 1 man/extractsamples.Rd | 1 man/fit_stepwise_bivariate.Rd | 1 man/fit_stepwise_univariate.Rd | 1 man/fit_vmcosmix.Rd | 1 man/fit_vmmix.Rd | 1 man/fit_vmsinmix.Rd | 1 man/fit_wnorm2mix.Rd | 1 man/fit_wnormmix.Rd | 1 man/fix_label.Rd | 1 man/is.angmcmc.Rd | 1 man/logLik.angmcmc.Rd | 7 man/lpdtrace.Rd | 1 man/paramtrace.Rd | 1 man/pointest.Rd | 1 man/quantile.angmcmc.Rd | 1 man/rvm.Rd | 3 man/rvmcos.Rd | 3 man/rvmcosmix.Rd | 3 man/rvmmix.Rd | 3 man/rvmsin.Rd | 3 man/rvmsinmix.Rd | 3 man/rwnorm.Rd | 3 man/rwnorm2.Rd | 15 man/rwnorm2mix.Rd | 3 man/rwnormmix.Rd | 3 man/summary.angmcmc.Rd | 1 man/tim8.Rd | 1 man/wind.Rd | 1 src/RcppExports.cpp | 792 ++++++++++++++++++++--------------------- src/init.c |only 45 files changed, 568 insertions(+), 581 deletions(-)