Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.34-16 dated 2014-10-29 and 1.34-17 dated 2014-10-30
Description: Analysis of experimental crosses to identify genes
(called quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 8 ++---
MD5 | 16 +++++-----
inst/INSTALL_ME.txt | 12 ++++----
inst/STATUS.txt | 2 -
inst/contrib/bin/CMakeLists.txt | 50 ++++++++++++++++------------------
inst/contrib/bin/mqmmain.cpp | 46 ++++++++++++-------------------
inst/contrib/scripts/run_all_tests.sh | 22 +++++++-------
inst/doc/rqtltour.pdf |binary
src/mqmregression.cpp | 4 +-
9 files changed, 75 insertions(+), 85 deletions(-)
Title: Full Interactive GUI for Dynamic Biplot in R
Diff between dynBiplotGUI versions 1.1.0 dated 2014-06-27 and 1.1.1 dated 2014-10-30
Description: A GUI to solve Dynamic Biplots, classic Biplot and HJ-biplot. Try matrices of 2-way and 3-way. Multilanguage.
Author: Jaime Egido [aut, cre]
Maintainer: Jaime Egido
ChangeLog | 13 ++++
DESCRIPTION | 18 +++---
MD5 | 14 ++---
NAMESPACE | 2
R/dynBiplot.R | 118 +++++++++++++++++++++++++++-----------------
inst/lang/Language.csv | 1
man/dynBiplot.Rd | 4 -
man/dynBiplotGUI-package.Rd | 8 +-
8 files changed, 111 insertions(+), 67 deletions(-)
Title: Batch computing with R.
Diff between BatchJobs versions 1.4 dated 2014-09-24 and 1.5 dated 2014-10-30
Description: Provides Map, Reduce and Filter variants to generate jobs on batch
computing systems like PBS/Torque, LSF, SLURM and Sun Grid Engine.
Multicore and SSH systems are also supported. For further details see the
project web page.
Author: Bernd Bischl
Maintainer: Bernd Bischl
DESCRIPTION | 14 +++----
MD5 | 68 ++++++++++++++++++------------------
NEWS | 10 ++++-
R/batchApply.R | 1
R/batchExpandGrid.R | 1
R/batchMapResults.R | 2 +
R/batchReduce.R | 1
R/batchReduceResults.R | 2 +
R/clusterFunctionsTorque.R | 4 +-
R/conf.R | 2 -
R/database.R | 12 +++++-
R/doJob.R | 2 -
R/filenames.R | 2 -
R/filterResults.R | 1
R/helpers.R | 10 +++++
R/killJobs.R | 7 ++-
R/reduceResults.R | 17 +++++----
R/showStatus.R | 1
R/submitJobs.R | 19 ++++------
R/waitForJobs.R | 12 ++++--
R/writeRscripts.R | 1
man/batchExpandGrid.Rd | 1
man/batchMapResults.Rd | 2 +
man/batchReduce.Rd | 1
man/batchReduceResults.Rd | 2 +
man/filterResults.Rd | 1
man/killJobs.Rd | 7 +++
man/reduceResults.Rd | 11 ++++-
man/showStatus.Rd | 1
man/submitJobs.Rd | 7 +++
man/waitForJobs.Rd | 7 +++
tests/run-all.R | 2 -
tests/testthat/helpers.R | 1
tests/testthat/test_batchMapQuick.R | 3 +
tests/testthat/test_resources.R | 2 -
35 files changed, 159 insertions(+), 78 deletions(-)
Title: An interface to the NOAA Operational Model Archive and
Distribution System
Diff between rNOMADS versions 2.0.3 dated 2014-10-13 and 2.0.4 dated 2014-10-30
Description: An interface to the National Oceanic and Atmospheric Administration's Operational Model Archive and Distribution System (NOMADS) that allows R users to quickly and efficiently download global and regional weather model data for processing. rNOMADS currently supports a variety of models ranging from global weather data to an altitude of 40 km, to high resolution regional weather models, to wave and sea ice models. It can also retrieve archived NOMADS models. rNOMADS can retrieve binary data in grib format as well as import ascii data directly into R by interfacing with the GrADS-DODS system.
Author: Daniel C. Bowman [aut, cre]
Maintainer: Daniel C. Bowman
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
NEWS | 5 +++++
R/GetDODS.R | 12 ++++++++++--
R/RNomadsTools.R | 13 +++++++------
R/ReadGrib.R | 28 ++++++++++++++++++++--------
man/rNOMADS-package.Rd | 4 ++--
7 files changed, 54 insertions(+), 28 deletions(-)
Title: Data Visualisation on Maps
Diff between mapplots versions 1.4 dated 2013-07-15 and 1.5 dated 2014-10-30
Description: Create simple maps; add sub-plots like pie plots to a map or any other plot; format, plot and export gridded data. The package was developed for displaying fisheries data but most functions can be used for more generic data visualisation.
Author: Hans Gerritsen
Maintainer: Hans Gerritsen
DESCRIPTION | 8 +++----
MD5 | 52 ++++++++++++++++++++++++------------------------
R/add.pie.R | 14 ++++++++----
R/draw.barplot2D.R | 2 -
R/draw.grid.R | 3 +-
R/draw.rect.R | 17 +++++++++------
R/legend.grid.R | 12 ++++++-----
R/make.xyz.R | 1
R/write.grid.R | 10 +++++----
man/add.pie.Rd | 2 -
man/barplot2D.Rd | 2 -
man/basemap.Rd | 1
man/coast.Rd | 3 --
man/draw.barplot2D.Rd | 4 ---
man/draw.bubble.Rd | 4 ---
man/draw.grid.Rd | 4 ---
man/draw.pie.Rd | 4 ---
man/draw.rect.Rd | 1
man/draw.shape.Rd | 4 ---
man/draw.xy.Rd | 2 -
man/effort.Rd | 1
man/ices.rect.Rd | 1
man/landings.Rd | 1
man/legend.bubble.Rd | 4 ---
man/legend.grid.Rd | 2 -
man/mapplots-package.Rd | 1
man/write.grid.Rd | 1
27 files changed, 74 insertions(+), 87 deletions(-)
Title: Miscellaneous helper functions for B. Bischl.
Diff between BBmisc versions 1.7 dated 2014-06-21 and 1.8 dated 2014-10-30
Description: Miscellaneous helper functions for and from B. Bischl and
some other guys at TU Dortmund, mainly for package development.
Author: Bernd Bischl [aut, cre],
Michel Lang [aut],
Jakob Bossek [aut],
Daniel Horn [aut],
Jakob Richter [aut]
Maintainer: Bernd Bischl
DESCRIPTION | 23 +-
MD5 | 289 +++++++++++++++++-----------------
NAMESPACE | 6
NEWS | 10 +
R/binPack.R | 6
R/catf.R | 6
R/checkArg.R | 20 +-
R/chunk.R | 4
R/clipString.R | 8
R/coalesce.R | 18 +-
R/computeMode.R | 4
R/convertDataFrameCols.R | 15 -
R/convertListOfRowsToDataFrame.R | 8
R/convertRowsToList.R | 3
R/convertToShortString.R | 1
R/dapply.R | 4
R/directory.R | 4
R/do.call2.R | 52 ++----
R/dropNamed.R | 2
R/getMaxColIndex.R | 14 -
R/getMaxIndex.R | 6
R/getOperatingSystem.R | 4
R/getRelativePath.R | 55 ++----
R/insert.R | 12 -
R/isProperlyNamed.R | 4
R/isValidName.R | 2
R/itostr.R |only
R/lib.R | 6
R/load2.R | 14 -
R/makeDataFrame.R | 14 -
R/makeProgressBar.R | 26 +--
R/makeS3Obj.R | 6
R/makeSimpleFileLogger.R | 2
R/matchDataFrameSubset.R | 14 -
R/namedList.R | 4
R/names2.R | 2
R/nin.R | 2
R/normalize.R | 60 +++++--
R/printStrToChar.R | 4
R/printToChar.R | 8
R/requirePackages.R | 14 -
R/save2.R | 2
R/setValue.R | 2
R/splitPath.R |only
R/splitTime.R | 2
R/stopf.R | 8
R/system3.R | 8
R/toRangeStr.R | 4
R/vapply.R | 16 -
R/warningf.R | 8
R/zzz_deprecated.R | 1
man/addClasses.Rd | 2
man/argsAsNamedList.Rd | 2
man/asMatrixCols.Rd | 2
man/asQuoted.Rd | 2
man/binPack.Rd | 2
man/btwn.Rd | 2
man/cFactor.Rd | 2
man/catf.Rd | 2
man/checkArg.Rd | 14 -
man/checkListElementClass.Rd | 2
man/chunk.Rd | 2
man/clipString.Rd | 2
man/coalesce.Rd | 4
man/collapse.Rd | 2
man/collapsef.Rd | 2
man/computeMode.Rd | 10 -
man/convertDataFrameCols.Rd | 2
man/convertInteger.Rd | 2
man/convertIntegers.Rd | 2
man/convertListOfRowsToDataFrame.Rd | 4
man/convertMatrixType.Rd | 2
man/convertRowsToList.Rd | 2
man/convertToShortString.Rd | 2
man/dapply.Rd | 2
man/deprecated.Rd | 2
man/do.call2.Rd |only
man/dropNamed.Rd | 2
man/ensureVector.Rd | 2
man/explode.Rd | 2
man/extractSubList.Rd | 2
man/filterNull.Rd | 2
man/getAttributeNames.Rd | 2
man/getClass1.Rd | 2
man/getFirst.Rd | 2
man/getMaxIndex.Rd | 2
man/getMaxIndexOfRows.Rd | 4
man/getOperatingSystem.Rd | 2
man/getRelativePath.Rd |only
man/getUnixTime.Rd | 2
man/getUsedFactorLevels.Rd | 2
man/hasAttributes.Rd | 2
man/insert.Rd | 8
man/is.error.Rd | 2
man/isDirectory.Rd | 2
man/isEmptyDirectory.Rd | 2
man/isExpensiveExampleOk.Rd | 2
man/isFALSE.Rd | 2
man/isProperlyNamed.Rd | 6
man/isScalarNA.Rd | 2
man/isScalarValue.Rd | 2
man/isSubset.Rd | 2
man/isSuperset.Rd | 2
man/isValidName.Rd | 2
man/itostr.Rd |only
man/lib.Rd | 2
man/load2.Rd | 8
man/lsort.Rd | 2
man/makeDataFrame.Rd | 4
man/makeFileCache.Rd | 2
man/makeProgressBar.Rd | 16 +
man/makeS3Obj.Rd | 4
man/makeSimpleFileLogger.Rd | 2
man/messagef.Rd | 2
man/namedList.Rd | 4
man/names2.Rd | 2
man/nin.Rd | 2
man/normalize.Rd | 18 +-
man/optimizeSubInts.Rd | 2
man/pause.Rd | 2
man/printStrToChar.Rd | 2
man/printToChar.Rd | 4
man/rangeVal.Rd | 2
man/requirePackages.Rd | 4
man/rowLapply.Rd | 2
man/save2.Rd | 4
man/seq_row.Rd | 2
man/setAttribute.Rd | 2
man/setClasses.Rd | 2
man/setRowNames.Rd | 2
man/setValue.Rd | 2
man/sortByCol.Rd | 2
man/splitPath.Rd |only
man/splitTime.Rd | 2
man/stopf.Rd | 2
man/strrepeat.Rd | 2
man/suppressAll.Rd | 2
man/symdiff.Rd | 2
man/system3.Rd | 2
man/toRangeStr.Rd | 2
man/vlapply.Rd | 2
man/warningf.Rd | 2
man/which.first.Rd | 2
src/itostr.c |only
src/itostr.h |only
tests/testthat/test_coalesce.R | 10 +
tests/testthat/test_do.call2.R | 18 +-
tests/testthat/test_getRelativePath.R |only
tests/testthat/test_itostr.R |only
tests/testthat/test_normalize.R | 29 +++
tests/testthat/test_splitPath.R |only
151 files changed, 618 insertions(+), 506 deletions(-)
Title: R Commander
Diff between Rcmdr versions 2.1-3 dated 2014-10-09 and 2.1-4 dated 2014-10-30
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
DESCRIPTION | 19
MD5 | 36
NAMESPACE | 8
NEWS | 10
R/commander.R | 2692 +++++-----
R/startup.R | 270 -
R/utilities.R | 28
inst/po/ca/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/gl |only
inst/po/id/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/ja/LC_MESSAGES/R-Rcmdr.mo |binary
inst/po/pt_BR/LC_MESSAGES/R-Rcmdr.mo |binary
man/Commander.Rd | 862 +--
man/Rcmdr-package.Rd | 5
po/R-Rcmdr.pot | 4
po/R-ca.po | 8119 +++++++++++++++++-------------
po/R-gl.po |only
po/R-id.po | 960 +++
po/R-ja.po | 9344 +++++++++++++++++------------------
po/R-pt_BR.po | 524 +
20 files changed, 12454 insertions(+), 10427 deletions(-)
Title: Hierarchical Generalized Linear Models
Diff between hglm versions 2.0-9 dated 2014-09-27 and 2.0-11 dated 2014-10-30
Description: This package fits hierarchical generalized linear models. It can be used for linear mixed models and generalized linear mixed models with random effects for a variety of links and a variety of distributions for both the outcomes and the random effects. Fixed effects can also be fitted in the dispersion part of the mean model.
Author: Xia Shen, Moudud Alam, Lars Ronnegard
Maintainer: Xia Shen
hglm-2.0-11/hglm/ChangeLog | 15 +
hglm-2.0-11/hglm/DESCRIPTION | 10
hglm-2.0-11/hglm/MD5 | 35 +--
hglm-2.0-11/hglm/NAMESPACE | 2
hglm-2.0-11/hglm/R/GLM.MME.R | 3
hglm-2.0-11/hglm/R/SAR.R |only
hglm-2.0-11/hglm/R/hglm.default.R | 140 +++++++++++--
hglm-2.0-11/hglm/R/inverse.sqrt.R |only
hglm-2.0-11/hglm/R/print.summary.hglm.R | 22 +-
hglm-2.0-11/hglm/R/summary.hglm.R | 2
hglm-2.0-11/hglm/inst/CITATION | 19 +
hglm-2.0-11/hglm/inst/doc/hglm.Rnw | 2
hglm-2.0-11/hglm/inst/doc/hglm.pdf |binary
hglm-2.0-11/hglm/man/CAR.Rd | 4
hglm-2.0-11/hglm/man/SAR.Rd |only
hglm-2.0-11/hglm/man/hglm-package.Rd | 8
hglm-2.0-11/hglm/man/hglm.Rd | 4
hglm-2.0-11/hglm/man/hglm2.Rd | 4
hglm-2.0-11/hglm/vignettes/hglm-knitr-knitr-compressed.pdf |only
hglm-2.0-11/hglm/vignettes/hglm.Rnw | 2
hglm-2.0-9/hglm/vignettes/hglm-knitr-knitr.pdf |only
21 files changed, 213 insertions(+), 59 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.8-0 dated 2014-06-17 and 1.8-1 dated 2014-10-30
Description: A package implementing statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g. discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for
surveillance data, or continuous-space point process data such as the
occurrence of disease or earthquakes. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of infectious diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently the package contains implementations of typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Hoehle and Paul (2008). Furthermore, inference
methods for the retrospective infectious disease model in Held
et al (2005), Held et al (2006), Paul et al (2008) and Paul
and Held (2011) are provided. A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ("twinSIR", discrete
space) and Meyer et al (2012) ("twinstim", continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: The suggested package INLA is unfortunately not available from
any mainstream repository - in case one wants to use the 'boda'
algorithm one needs to manually install the INLA package
as specified at http://www.r-inla.org/download.
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
surveillance-1.8-0/surveillance/R/twinSIR_epidata.R |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata.Rd |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata_animate.Rd |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata_intersperse.Rd |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata_plot.Rd |only
surveillance-1.8-0/surveillance/man/twinSIR_epidata_summary.Rd |only
surveillance-1.8-1/surveillance/DESCRIPTION | 17
surveillance-1.8-1/surveillance/MD5 | 229 +++++----
surveillance-1.8-1/surveillance/NAMESPACE | 38 +
surveillance-1.8-1/surveillance/R/algo_hmm.R | 10
surveillance-1.8-1/surveillance/R/bdist.R |only
surveillance-1.8-1/surveillance/R/boda.R | 16
surveillance-1.8-1/surveillance/R/epidata.R |only
surveillance-1.8-1/surveillance/R/epidataCS.R | 12
surveillance-1.8-1/surveillance/R/epidataCS_animate.R | 12
surveillance-1.8-1/surveillance/R/epidataCS_methods.R | 52 +-
surveillance-1.8-1/surveillance/R/epidataCS_plot.R | 23
surveillance-1.8-1/surveillance/R/epidata_animate.R |only
surveillance-1.8-1/surveillance/R/epidata_plot.R |only
surveillance-1.8-1/surveillance/R/farringtonFlexible.r | 10
surveillance-1.8-1/surveillance/R/glm_epidataCS.R | 6
surveillance-1.8-1/surveillance/R/hhh4.R | 41 -
surveillance-1.8-1/surveillance/R/hhh4_W.R | 10
surveillance-1.8-1/surveillance/R/hhh4_W_np.R | 6
surveillance-1.8-1/surveillance/R/hhh4_methods.R | 75 ++-
surveillance-1.8-1/surveillance/R/hhh4_oneStepAhead.R | 11
surveillance-1.8-1/surveillance/R/hhh4_plot.R | 149 ++++--
surveillance-1.8-1/surveillance/R/intersectPolyCircle.R | 6
surveillance-1.8-1/surveillance/R/ks.plot.unif.R | 7
surveillance-1.8-1/surveillance/R/nowcast.R | 86 ++-
surveillance-1.8-1/surveillance/R/options.R | 56 +-
surveillance-1.8-1/surveillance/R/permutationTest.R | 14
surveillance-1.8-1/surveillance/R/pit.R | 56 +-
surveillance-1.8-1/surveillance/R/scores.R | 211 ++++-----
surveillance-1.8-1/surveillance/R/spatial_tools.R | 71 +--
surveillance-1.8-1/surveillance/R/sts.R | 123 ++---
surveillance-1.8-1/surveillance/R/stsNC.R | 53 ++
surveillance-1.8-1/surveillance/R/sts_animate.R | 43 +
surveillance-1.8-1/surveillance/R/stsplot_space.R | 30 -
surveillance-1.8-1/surveillance/R/stsplot_time.R | 47 --
surveillance-1.8-1/surveillance/R/twinSIR.R | 27 -
surveillance-1.8-1/surveillance/R/twinSIR_helper.R | 54 +-
surveillance-1.8-1/surveillance/R/twinSIR_methods.R | 233 ----------
surveillance-1.8-1/surveillance/R/twinSIR_profile.R |only
surveillance-1.8-1/surveillance/R/twinSIR_simulation.R | 149 +++---
surveillance-1.8-1/surveillance/R/twinstim.R | 26 -
surveillance-1.8-1/surveillance/R/twinstim_iafplot.R | 6
surveillance-1.8-1/surveillance/R/twinstim_methods.R | 29 -
surveillance-1.8-1/surveillance/R/twinstim_siaf.R | 80 +--
surveillance-1.8-1/surveillance/R/twinstim_simulation.R | 82 ++-
surveillance-1.8-1/surveillance/R/untie.R | 15
surveillance-1.8-1/surveillance/R/zzz.R | 8
surveillance-1.8-1/surveillance/build/partial.rdb |binary
surveillance-1.8-1/surveillance/build/vignette.rds |binary
surveillance-1.8-1/surveillance/data/foodata.RData |binary
surveillance-1.8-1/surveillance/data/fooepidata.RData |binary
surveillance-1.8-1/surveillance/data/foofit.RData |binary
surveillance-1.8-1/surveillance/data/ha.RData |binary
surveillance-1.8-1/surveillance/data/hagelloch.RData |binary
surveillance-1.8-1/surveillance/data/imdepi.RData |binary
surveillance-1.8-1/surveillance/data/influMen.RData |binary
surveillance-1.8-1/surveillance/data/measlesWeserEms.RData |binary
surveillance-1.8-1/surveillance/data/momo.RData |binary
surveillance-1.8-1/surveillance/data/salmNewport.RData |binary
surveillance-1.8-1/surveillance/inst/CITATION | 14
surveillance-1.8-1/surveillance/inst/NEWS.Rd | 188 ++++++++
surveillance-1.8-1/surveillance/inst/doc/glrnb.pdf |binary
surveillance-1.8-1/surveillance/inst/doc/hhh4.R | 13
surveillance-1.8-1/surveillance/inst/doc/hhh4.Rnw | 9
surveillance-1.8-1/surveillance/inst/doc/hhh4.pdf |binary
surveillance-1.8-1/surveillance/inst/doc/surveillance.pdf |binary
surveillance-1.8-1/surveillance/man/R0.Rd | 43 +
surveillance-1.8-1/surveillance/man/checkResidualProcess.Rd | 4
surveillance-1.8-1/surveillance/man/epidata.Rd |only
surveillance-1.8-1/surveillance/man/epidataCS.Rd | 44 -
surveillance-1.8-1/surveillance/man/epidataCS_aggregate.Rd | 17
surveillance-1.8-1/surveillance/man/epidataCS_animate.Rd | 36 -
surveillance-1.8-1/surveillance/man/epidataCS_plot.Rd | 7
surveillance-1.8-1/surveillance/man/epidata_animate.Rd |only
surveillance-1.8-1/surveillance/man/epidata_intersperse.Rd |only
surveillance-1.8-1/surveillance/man/epidata_plot.Rd |only
surveillance-1.8-1/surveillance/man/epidata_summary.Rd |only
surveillance-1.8-1/surveillance/man/find.kh.Rd | 7
surveillance-1.8-1/surveillance/man/fluBYBW.Rd | 50 +-
surveillance-1.8-1/surveillance/man/hagelloch.Rd | 225 +++++----
surveillance-1.8-1/surveillance/man/hhh4.Rd | 59 +-
surveillance-1.8-1/surveillance/man/hhh4_W.Rd | 84 +--
surveillance-1.8-1/surveillance/man/hhh4_formula.Rd | 1
surveillance-1.8-1/surveillance/man/hhh4_methods.Rd | 10
surveillance-1.8-1/surveillance/man/hhh4_plot.Rd | 100 +++-
surveillance-1.8-1/surveillance/man/hhh4_update.Rd |only
surveillance-1.8-1/surveillance/man/hhh4_validation.Rd | 148 +++---
surveillance-1.8-1/surveillance/man/imdepi.Rd | 17
surveillance-1.8-1/surveillance/man/layout.labels.Rd |only
surveillance-1.8-1/surveillance/man/marks.Rd |only
surveillance-1.8-1/surveillance/man/measles.weser.Rd | 5
surveillance-1.8-1/surveillance/man/multiplicity.Rd | 63 --
surveillance-1.8-1/surveillance/man/multiplicity.Spatial.Rd |only
surveillance-1.8-1/surveillance/man/nbOrder.Rd | 16
surveillance-1.8-1/surveillance/man/nowcast.Rd | 2
surveillance-1.8-1/surveillance/man/permutationTest.Rd | 6
surveillance-1.8-1/surveillance/man/pit.Rd | 40 +
surveillance-1.8-1/surveillance/man/sts_animate.Rd | 20
surveillance-1.8-1/surveillance/man/stsplot.Rd | 1
surveillance-1.8-1/surveillance/man/stsplot_space.Rd | 10
surveillance-1.8-1/surveillance/man/stsplot_time.Rd | 15
surveillance-1.8-1/surveillance/man/surveillance.options.Rd | 28 +
surveillance-1.8-1/surveillance/man/toLatex.sts.Rd | 7
surveillance-1.8-1/surveillance/man/twinSIR.Rd | 20
surveillance-1.8-1/surveillance/man/twinSIR_exData.Rd | 16
surveillance-1.8-1/surveillance/man/twinSIR_intensityplot.Rd | 3
surveillance-1.8-1/surveillance/man/twinSIR_methods.Rd | 10
surveillance-1.8-1/surveillance/man/twinSIR_profile.Rd | 19
surveillance-1.8-1/surveillance/man/twinSIR_simulation.Rd | 82 +--
surveillance-1.8-1/surveillance/man/twinstim.Rd | 8
surveillance-1.8-1/surveillance/man/twinstim_iaf.Rd | 5
surveillance-1.8-1/surveillance/man/twinstim_siaf_simulatePC.Rd |only
surveillance-1.8-1/surveillance/man/twinstim_simulation.Rd | 124 ++++-
surveillance-1.8-1/surveillance/man/untie.Rd | 4
surveillance-1.8-1/surveillance/src/surveillance.c | 9
surveillance-1.8-1/surveillance/tests/testthat/test-farringtonFlexible.R |only
surveillance-1.8-1/surveillance/tests/testthat/test-hhh4_ARasNE.R |only
surveillance-1.8-1/surveillance/tests/testthat/test-nbOrder.R | 27 -
surveillance-1.8-1/surveillance/tests/testthat/test-siafs.R | 26 -
surveillance-1.8-1/surveillance/tests/testthat/test-tiafs.R | 13
surveillance-1.8-1/surveillance/tests/testthat/test-toLatex.sts.R | 26 -
surveillance-1.8-1/surveillance/vignettes/hhh4.Rnw | 9
127 files changed, 2282 insertions(+), 1637 deletions(-)
Title: Rcpp Integration for the Armadillo Templated Linear Algebra
Library
Diff between RcppArmadillo versions 0.4.450.1.0 dated 2014-09-22 and 0.4.500.0 dated 2014-10-30
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo. Armadillo is licensed under the MPL 2.0, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is licensed under the
GNU GPL version 2 or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 27 ++
DESCRIPTION | 33 ---
MD5 | 65 +++---
inst/NEWS.Rd | 14 +
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/RcppArmadilloExtensions/fixprob.h |only
inst/include/RcppArmadilloExtensions/rmultinom.h |only
inst/include/RcppArmadilloExtensions/sample.h | 140 +++++++------
inst/include/armadillo | 10
inst/include/armadillo_bits/Mat_meat.hpp | 20 -
inst/include/armadillo_bits/arma_cmath.hpp | 160 +++++++++++++++
inst/include/armadillo_bits/arma_config.hpp | 7
inst/include/armadillo_bits/arma_ostream_meat.hpp | 40 +++
inst/include/armadillo_bits/arma_rng.hpp | 10
inst/include/armadillo_bits/arma_rng_cxx98.hpp | 35 ++-
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/auxlib_bones.hpp | 2
inst/include/armadillo_bits/auxlib_meat.hpp | 29 +-
inst/include/armadillo_bits/compiler_setup.hpp | 2
inst/include/armadillo_bits/config.hpp | 16 +
inst/include/armadillo_bits/debug.hpp | 11 -
inst/include/armadillo_bits/diskio_meat.hpp | 10
inst/include/armadillo_bits/fn_chol.hpp | 14 -
inst/include/armadillo_bits/fn_norm.hpp | 156 +++++++++++++--
inst/include/armadillo_bits/gmm_diag_meat.hpp | 228 +++++++++++-----------
inst/include/armadillo_bits/hdf5_bones.hpp | 15 -
inst/include/armadillo_bits/include_hdf5.hpp |only
inst/include/armadillo_bits/mul_gemm.hpp | 74 +------
inst/include/armadillo_bits/mul_gemv.hpp | 126 +++---------
inst/include/armadillo_bits/op_chol_meat.hpp | 6
inst/include/armadillo_bits/op_dot_bones.hpp | 3
inst/include/armadillo_bits/op_dot_meat.hpp | 36 ---
inst/unitTests/cpp/rmultinom.cpp |only
inst/unitTests/runit.rmultinom.R |only
inst/unitTests/runit.sample.R | 15 -
36 files changed, 795 insertions(+), 515 deletions(-)
Title: Rmetrics - Analysing and Modelling Financial Assets
Diff between fAssets versions 3011.82 dated 2014-09-22 and 3011.83 dated 2014-10-30
Description: Environment for teaching
"Financial Engineering and Computational Finance".
Author: Rmetrics Core Team,
Diethelm Wuertz [aut],
Tobias Setz [cre],
Yohan Chalabi [ctb]
Maintainer: Tobias Setz
ChangeLog | 8 +
DESCRIPTION | 14 +-
MD5 | 12 +-
NAMESPACE | 10 +-
R/assets-modeling.R | 2
R/plot-pairs.R | 24 ++--
man/plot-pairs.Rd | 256 ++++++++++++++++++++++++++--------------------------
7 files changed, 168 insertions(+), 158 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Diff between etasFLP versions 1.1.0 dated 2014-10-28 and 1.1.1 dated 2014-10-30
Description: Estimation of the components of an ETAS model for earthquake description.
Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood.
The two estimation steps are alternated until convergence is obtained.
For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class "etasclass").
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi
ChangeLog | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/print.etasclass.R | 4 ++--
R/summary.etasclass.R | 4 ++--
man/etasFLP-package.Rd | 4 ++--
6 files changed, 21 insertions(+), 15 deletions(-)
Title: The skew-normal and skew-t distributions
Diff between sn versions 1.1-0 dated 2014-08-04 and 1.1-1 dated 2014-10-30
Description: Define and manipulate probability distributions of the skew-normal
family and some related ones (notably the skew-t family) and provide related
statistical methods for data fitting and diagnostics, in the univariate and
the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini
ChangeLog | 73 ++++++++++++++--------
DESCRIPTION | 8 +-
MD5 | 35 +++++-----
NAMESPACE | 5 -
R/sn-funct.R | 175 +++++++++++++++++++++++++++++++-----------------------
data/ais.rda |binary
data/barolo.rda |binary
data/frontier.rda |binary
data/wines.rda |binary
man/dmsn.Rd | 13 ++--
man/dmst.Rd | 2
man/dsn.Rd | 27 ++++++--
man/dst.Rd | 10 +--
man/matrix-op.Rd |only
man/selm.Rd | 4 -
man/selm.fit.Rd | 3
man/sn-package.Rd | 7 --
man/sn-st.info.Rd | 18 ++++-
man/zeta.Rd | 15 ++--
19 files changed, 236 insertions(+), 159 deletions(-)
Title: Smoothing and Forecasting Poisson Counts with P-Splines
Diff between MortalitySmooth versions 2.3.2 dated 2013-12-28 and 2.3.3 dated 2014-10-30
More information about MortalitySmooth at CRAN
Description: Smoothing one- and two-dimensional Poisson counts with
P-splines specifically tailored to mortality data.
Extra-Poisson variation can be accounted as well as forecasting.
Collection of mortality data and a specific function for
selecting those data by country, sex, age and years.
Author: Carlo G Camarda
Maintainer: Carlo G Camarda
DESCRIPTION | 22 ++++++++++---------
MD5 | 23 ++++++++++++--------
NAMESPACE | 2 +
R/Mort1Dsmooth.R | 1
R/predict.Mort1Dsmooth.R | 25 ++++++++++++++++++---
R/predict.Mort2Dsmooth.R | 24 +++++++++++++++++---
R/selectHMDdata.R | 5 +++-
build |only
data/HMDdata.rda |binary
inst/doc |only
man/Mort1Dsmooth.Rd | 44 +++-----------------------------------
man/Mort2Dsmooth.Rd | 54 +++--------------------------------------------
vignettes |only
13 files changed, 82 insertions(+), 118 deletions(-)
Permanent link
Title: R client for the Huffpost Pollster API
Diff between pollstR versions 1.1.0 dated 2014-08-18 and 1.1.1 dated 2014-10-30
Description: An R interface to the Huffington Post Pollster API, which provides
programmatic interface to political polls.
Author: Jeffrey B. Arnold [aut, cre],
Thomas J. Leeper [aut]
Maintainer: Jeffrey B. Arnold
pollstR-1.1.0/pollstR/inst/vign |only
pollstR-1.1.0/pollstR/vignettes/assets/obama-favorable-chart-2.png |only
pollstR-1.1.0/pollstR/vignettes/assets/obama-favorable-chart.png |only
pollstR-1.1.1/pollstR/DESCRIPTION | 8
pollstR-1.1.1/pollstR/MD5 | 51 +-
pollstR-1.1.1/pollstR/NAMESPACE | 2
pollstR-1.1.1/pollstR/NEWS | 5
pollstR-1.1.1/pollstR/R/chart.R | 21 -
pollstR-1.1.1/pollstR/R/charts.R | 2
pollstR-1.1.1/pollstR/R/polls.R | 47 +-
pollstR-1.1.1/pollstR/R/pollstR-package.R | 11
pollstR-1.1.1/pollstR/inst/doc/introduction.Rmd | 160 +++++----
pollstR-1.1.1/pollstR/inst/doc/introduction.html | 171 ++++++----
pollstR-1.1.1/pollstR/inst/vign-src |only
pollstR-1.1.1/pollstR/man/pollstR.Rd | 2
pollstR-1.1.1/pollstR/man/pollstr_chart.Rd | 16
pollstR-1.1.1/pollstR/man/pollstr_charts.Rd | 6
pollstR-1.1.1/pollstR/man/pollstr_polls.Rd | 2
pollstR-1.1.1/pollstR/vignettes/assets/obama-favorable-chart-1.png |only
pollstR-1.1.1/pollstR/vignettes/assets/obama-favorable-chart-2-1.png |only
pollstR-1.1.1/pollstR/vignettes/introduction.Rmd | 160 +++++----
21 files changed, 372 insertions(+), 292 deletions(-)
Title: Multivariate Constructs
Diff between multicon versions 1.2 dated 2014-04-19 and 1.3 dated 2014-10-30
Description: This packages includes functions designed to examine relationships among multivariate constructs.
Author: Ryne A. Sherman
Maintainer: Ryne A. Sherman
multicon-1.2/multicon/R/Profile.ICC.R |only
multicon-1.2/multicon/R/Profile.norm.R |only
multicon-1.2/multicon/R/Profile.r.R |only
multicon-1.2/multicon/R/Profile.r.rep.R |only
multicon-1.2/multicon/R/Profile.reg.R |only
multicon-1.2/multicon/R/Profile.resid.R |only
multicon-1.3/multicon/DESCRIPTION | 8 +--
multicon-1.3/multicon/MD5 | 36 ++++++++-------
multicon-1.3/multicon/R/catseye.R | 8 +--
multicon-1.3/multicon/R/diffPlot.R | 59 --------------------------
multicon-1.3/multicon/R/diffPlot.default.r |only
multicon-1.3/multicon/R/diffPlot.formula.r |only
multicon-1.3/multicon/R/e.bars.R | 2
multicon-1.3/multicon/R/egraph.R | 14 +++---
multicon-1.3/multicon/R/profile.ICC.R |only
multicon-1.3/multicon/R/profile.norm.R |only
multicon-1.3/multicon/R/profile.r.R |only
multicon-1.3/multicon/R/profile.r.rep.R |only
multicon-1.3/multicon/R/profile.reg.R |only
multicon-1.3/multicon/R/profile.resid.R |only
multicon-1.3/multicon/man/catseye.Rd | 5 +-
multicon-1.3/multicon/man/diffPlot.Rd | 48 +++++++++++++++++----
multicon-1.3/multicon/man/e.bars.Rd | 2
multicon-1.3/multicon/man/egraph.Rd | 5 +-
multicon-1.3/multicon/man/multicon-package.Rd | 4 -
multicon-1.3/multicon/man/rand.test.Rd | 2
26 files changed, 87 insertions(+), 106 deletions(-)