Title: Stochastic Mortality Modelling
Description: Implementation of the family of generalised age-period-cohort
stochastic mortality models. This family of models encompasses many models
proposed in the actuarial and demographic literature including the Lee-Carter
model and the Cairns-Blake-Dowd model. It includes functions for fitting
mortality models, analysing their goodness-of-fit and performing mortality
projections and simulations.
Author: Andres Villegas <andresmauriciovillegas@gmail.com>,
Pietro Millossovich <Pietro.Millossovich.1@city.ac.uk>,
Vladimir Kaishev <Vladimir.Kaishev.1@city.ac.uk>
Maintainer: Andres Villegas <andresmauriciovillegas@gmail.com>
Diff between StMoMo versions 0.3.0 dated 2015-10-13 and 0.3.1 dated 2016-02-09
DESCRIPTION | 21 - MD5 | 155 +++++------ NAMESPACE | 4 NEWS.md |only R/StMoMo.R | 112 ++++---- R/bootstrapfitStMoMo.R | 236 +++++++++-------- R/coeffitStMoMo.R | 37 +- R/docStMoMo.R | 4 R/exportUtils.R | 11 R/fitStMoMo.R | 383 +++++++++++++++------------- R/fittedfitStMoMo.R | 7 R/forecastfitStMoMo.R | 107 +++---- R/internalUtils.R | 78 +++-- R/logLikfitStMoMo.R | 7 R/mrwd.R | 41 +- R/plotbootStMoMo.R | 62 ++-- R/plotfitStMoMo.R | 32 +- R/plotforStMoMo.R | 51 ++- R/predictfitStMoMo.R | 78 +++-- R/residualsfitStMoMo.R | 147 ++++++---- R/simulatebootStMoMo.R | 117 ++++---- R/simulatefitStMoMo.R | 108 ++++--- R/standardModels.R | 184 +++++++------ build/vignette.rds |binary inst/CITATION | 8 inst/doc/StMoMoVignette.Rnw | 7 inst/doc/StMoMoVignette.pdf |binary man/StMoMo.Rd | 165 ++++++------ man/apc.Rd | 33 +- man/binomRes2q.Rd | 11 man/bootstrap.Rd | 16 - man/bootstrap.fitStMoMo.Rd | 81 +++-- man/cbd.Rd | 29 +- man/coef.fitStMoMo.Rd | 50 ++- man/computeDevianceBinomial.Rd | 2 man/computeDeviancePoisson.Rd | 2 man/computeLogLikBinomial.Rd | 2 man/computeLogLikPoisson.Rd | 2 man/extractCoefficientsFromGnm.Rd | 18 - man/fit.Rd | 16 - man/fit.StMoMo.Rd | 183 +++++++------ man/fitted.fitStMoMo.Rd | 16 - man/forecast.fitStMoMo.Rd | 114 ++++---- man/forecast.mrwd.Rd | 13 man/genBinomialResBootSamples.Rd | 12 man/genBinomialSemiparametricBootSamples.Rd | 11 man/genPoissonResBootSamples.Rd | 11 man/genPoissonSemiparametricBootSamples.Rd | 7 man/genWeightMat.Rd | 19 - man/getMinimalFitStMoMo.Rd | 67 ++-- man/invlogit.Rd | 2 man/lc.Rd | 48 +-- man/logLik.fitStMoMo.Rd | 6 man/logit.Rd | 2 man/m6.Rd | 48 +-- man/m7.Rd | 54 ++- man/m8.Rd | 37 +- man/mrwd.Rd | 11 man/plot.bootStMoMo.Rd | 20 - man/plot.fitStMoMo.Rd | 17 - man/plot.forStMoMo.Rd | 14 - man/plot.resStMoMo.Rd | 75 +++-- man/plotParameterFan.Rd | 7 man/poissonRes2death.Rd | 8 man/predict.fitStMoMo.Rd | 79 +++-- man/predictLink.Rd | 2 man/print.StMoMo.Rd | 2 man/print.bootStMoMo.Rd | 2 man/print.fitStMoMo.Rd | 2 man/print.forStMoMo.Rd | 2 man/print.simStMoMo.Rd | 2 man/processStartValues.Rd | 6 man/residuals.fitStMoMo.Rd | 19 - man/rh.Rd | 57 ++-- man/scatterplotAPC.Rd | 8 man/simulate.bootStMoMo.Rd | 129 +++++---- man/simulate.fitStMoMo.Rd | 148 +++++----- man/simulate.mrwd.Rd | 8 vignettes/StMoMoVignette.Rnw | 7 79 files changed, 2006 insertions(+), 1693 deletions(-)
Title: Tools for Post-Selection Inference
Description: New tools for post-selection inference, for use
with forward stepwise regression, least angle regression, the
lasso, and the many means problem.
Author: Ryan Tibshirani, Rob Tibshirani, Jonathan Taylor,
Joshua Loftus, Stephen Reid
Maintainer: Rob Tibshirani <tibs@stanford.edu>
Diff between selectiveInference versions 1.1.2 dated 2015-12-27 and 1.1.3 dated 2016-02-09
DESCRIPTION | 8 +++---- MD5 | 6 ++--- R/funs.fixed.R | 26 +++++++++++++++-------- man/fixedLassoInf.Rd | 56 +++++++++++++++++++++++++++++++++++++++++++-------- 4 files changed, 72 insertions(+), 24 deletions(-)
More information about selectiveInference at CRAN
Permanent link
Title: Non-Parametric Bayesian Multiple Imputation for Categorical Data
Description: These routines create multiple imputations of missing at random categorical data, with or without structural zeros. Imputations are based on Dirichlet process mixtures of multinomial distributions, which is a non-parametric Bayesian modeling approach that allows for flexible joint modeling.
Author: Quanli Wang, Daniel Manrique-Vallier, Jerome P. Reiter and Jingchen Hu
Maintainer: Quanli Wang <quanli@stat.duke.edu>
Diff between NPBayesImpute versions 0.5 dated 2015-03-23 and 0.6 dated 2016-02-09
DESCRIPTION | 10 - MD5 | 23 ++-- R/ArrayUtils.R | 282 +++++++++++++++++++++++++------------------------- man/CreateModel.Rd | 104 +++++++++--------- man/Rcpp_Lcm-class.Rd | 172 +++++++++++++++--------------- man/UpdateX.Rd |only src/CData.cpp | 4 src/CData.h | 1 src/CEnv.cpp | 7 + src/CEnv.h | 1 src/CParam.cpp | 67 ++++++----- src/CParam.h | 1 src/lczmain.cpp | 2 13 files changed, 351 insertions(+), 323 deletions(-)
Title: Access to the Gitlab API
Description: Provides R functions to access the API of the project and
repository management web application gitlab. For many common tasks (repository
file access, issue assignment and status, commenting) convenience wrappers
are provided, and in addition the full API can be used by specifying request
locations. Gitlab is open-source software and can be self-hosted or used on
gitlab.com.
Author: Jirka Lewandowski [aut, cre]
Maintainer: Jirka Lewandowski <jirka.lewandowski@wzb.eu>
Diff between gitlabr versions 0.6.2 dated 2016-01-20 and 0.6.4 dated 2016-02-09
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/gitlab_api.R | 3 ++- R/gitlabr-package.R | 2 +- R/projects_and_repos.R | 2 +- inst/doc/quick-start-gitlabr.pdf |binary 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Probabilistic Species Co-Occurrence Analysis in R
Description: This R package applies the probabilistic model of species co-occurrence (Veech 2013) to a set of species distributed among a set of survey or sampling sites. The algorithm calculates the observed and expected frequencies of co-occurrence between each pair of species. The expected frequency is based on the distribution of each species being random and independent of the other species. The analysis returns the probabilities that a more extreme (either low or high) value of co-occurrence could have been obtained by chance. The package also includes functions for visualizing species co-occurrence results and preparing data for downstream analyses.
Author: Daniel M. Griffith, Joseph A. Veech, and Charles J. Marsh
Maintainer: Daniel M. Griffith <griffith.dan@gmail.com>
Diff between cooccur versions 1.2 dated 2014-11-18 and 1.3 dated 2016-02-09
DESCRIPTION | 10 ++--- MD5 | 38 ++++++++++---------- NAMESPACE | 3 + R/cooccur.R | 72 ++++++++++++++++++++++++++++---------- R/create.N.matrix.R |only R/effect.sizes.R | 24 +++++++++++- R/plot.cooccur.R | 91 +++++++++++++++++++++++++++++++++++++++++++------ R/summary.cooccur.R | 2 - inst/CITATION | 35 ++++++++++++------ man/cooccur-package.Rd | 16 ++++---- man/cooccur.Rd | 24 ++++++++---- man/create.N.matrix.Rd |only man/effect.sizes.Rd | 12 +++--- man/obs.v.exp.Rd | 12 +++--- man/pair.Rd | 12 +++--- man/pair.attributes.Rd | 12 +++--- man/pair.profile.Rd | 12 +++--- man/plot.cooccur.Rd | 12 +++--- man/print.cooccur.Rd | 12 +++--- man/prob.table.Rd | 12 +++--- man/summary.cooccur.Rd | 12 +++--- 21 files changed, 284 insertions(+), 139 deletions(-)
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
http://pj.freefaculty.org/guides. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette "rockchalk" offers a
fairly comprehensive overview. The vignette "Rstyle" has advice
about coding in R. The package title "rockchalk" refers to our
school motto, "Rock Chalk Jayhawk, Go K.U.".
Author: Paul E. Johnson <pauljohn@ku.edu>
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.92 dated 2015-02-13 and 1.8.98 dated 2016-02-09
DESCRIPTION | 37 ++++---- MD5 | 189 +++++++++++++++++++++---------------------- NAMESPACE | 53 +++++++++++- R/genCorrelatedData.R | 2 R/mcDiagnose.R | 2 R/meanCenter.R | 41 +++++---- R/outreg.R | 4 R/pctable.R | 48 ++++++---- R/plotCurves.R | 12 +- R/plotPlane.R | 1 R/plotSlopes.R | 16 ++- R/residualCenter.R | 10 +- R/rockchalk-package.R | 18 ++-- R/summarize.R | 147 ++++++++++++++++++++++++++++++--- R/utils.R | 100 ++++++++++++++++++++-- build/vignette.rds |binary data/cheating.RData |binary data/religioncrime.RData |binary inst/ChangeLog | 24 +++++ inst/NEWS | 11 ++ inst/doc/Rchaeology.R | 74 ++++++++-------- inst/doc/Rchaeology.Rnw | 6 - inst/doc/Rchaeology.pdf |binary inst/doc/Rstyle.R | 8 - inst/doc/Rstyle.Rnw | 51 ++++------- inst/doc/Rstyle.pdf |binary inst/doc/rockchalk.R | 2 inst/doc/rockchalk.Rnw | 18 ++-- inst/doc/rockchalk.pdf |binary man/addLines.Rd | 3 man/centerNumerics.Rd | 3 man/centralValues.Rd | 3 man/cheating.Rd | 6 - man/checkIntFormat.Rd | 3 man/checkPosDef.Rd | 3 man/combineLevels.Rd | 4 man/cutByQuantile.Rd | 3 man/cutBySD.Rd | 3 man/cutByTable.Rd | 7 + man/dir.create.unique.Rd |only man/focalVals.Rd | 3 man/formatVC.Rd | 3 man/genCorrelatedData.Rd | 4 man/genCorrelatedData2.Rd | 4 man/getAuxRsq.Rd | 3 man/getDeltaRsquare.Rd | 3 man/getFocal.Rd | 19 +++- man/getPartialCor.Rd | 3 man/getVIF.Rd | 3 man/kurtosis.Rd |only man/lazyCor.Rd | 3 man/lazyCov.Rd | 3 man/lmAuxiliary.Rd | 3 man/magRange.Rd | 3 man/makeSymmetric.Rd | 4 man/makeVec.Rd | 3 man/mcDiagnose.Rd | 3 man/mcGraph.Rd | 9 +- man/meanCenter.Rd | 29 ++++-- man/model.data.Rd | 3 man/model.data.default.Rd | 3 man/mvrnorm.Rd | 4 man/newdata.Rd | 9 +- man/outreg.Rd | 19 ++-- man/outreg0.Rd | 3 man/outreg2HTML.Rd | 4 man/padW0.Rd | 3 man/pctable.Rd | 25 +++-- man/perspEmpty.Rd | 3 man/plot.testSlopes.Rd | 3 man/plotCurves.Rd | 25 +++-- man/plotFancy.Rd | 3 man/plotPlane.Rd | 3 man/plotSeq.Rd | 4 man/plotSlopes.Rd | 15 ++- man/predictCI.Rd | 3 man/predictOMatic.Rd | 3 man/print.factorSummaries.Rd | 3 man/print.pctable.Rd | 3 man/print.summary.pctable.Rd | 3 man/religioncrime.Rd | 3 man/residualCenter.Rd | 21 ++-- man/rockchalk-package.Rd | 14 +-- man/skewness.Rd |only man/standardize.Rd | 9 +- man/summarize.Rd | 13 +- man/summarizeFactors.Rd | 3 man/summarizeNumerics.Rd | 10 +- man/summary.factor.Rd | 3 man/summary.pctable.Rd | 7 - man/testSlopes.Rd | 3 man/vech2Corr.Rd | 3 man/vech2mat.Rd | 3 vignettes/Rchaeology.Rnw | 6 - vignettes/Rstyle.Rnw | 51 ++++------- vignettes/Rstyle.lyx | 35 ++++--- vignettes/rockchalk.Rnw | 18 ++-- 97 files changed, 887 insertions(+), 476 deletions(-)
Title: Filtered Monotonic Polynomial IRT Models
Description: Estimates Filtered Monotonic Polynomial IRT Models as described by Liang and Browne (2015) <DOI:10.3102/1076998614556816>.
Author: Niels G. Waller <nwaller@umn.edu>
Maintainer: Niels G. Waller <nwaller@umn.edu>
Diff between FMP versions 1.3 dated 2016-02-05 and 1.4 dated 2016-02-09
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/FMP.R | 8 ++++---- R/FMPMonotonicityCheck.R | 2 ++ inst/CITATION | 2 +- inst/doc/FMP-manual.pdf |binary man/FMP.Rd | 6 +++--- 7 files changed, 20 insertions(+), 18 deletions(-)
Title: Extra Graphical Utilities Based on Lattice
Description: Building on the infrastructure provided by the lattice
package, this package provides several new high-level
functions and methods, as well as additional utilities
such as panel and axis annotation functions.
Author: Deepayan Sarkar <deepayan.sarkar@r-project.org>, Felix Andrews <felix@nfrac.org>
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between latticeExtra versions 0.6-26 dated 2013-08-15 and 0.6-28 dated 2016-02-09
latticeExtra-0.6-26/latticeExtra/old.svnlog |only latticeExtra-0.6-28/latticeExtra/DESCRIPTION | 19 ++-- latticeExtra-0.6-28/latticeExtra/MD5 | 68 +++++++-------- latticeExtra-0.6-28/latticeExtra/NAMESPACE | 9 + latticeExtra-0.6-28/latticeExtra/R/data.frame.R | 18 --- latticeExtra-0.6-28/latticeExtra/R/dendrogramGrob.R | 2 latticeExtra-0.6-28/latticeExtra/R/horizonplot.R | 67 +++++++------- latticeExtra-0.6-28/latticeExtra/R/layer.R | 1 latticeExtra-0.6-28/latticeExtra/R/mapplot.R | 9 - latticeExtra-0.6-28/latticeExtra/R/mergeTrellisLegends.R | 2 latticeExtra-0.6-28/latticeExtra/R/panel.2dsmoother.R | 2 latticeExtra-0.6-28/latticeExtra/R/panel.quantile.R | 20 +--- latticeExtra-0.6-28/latticeExtra/R/panel.smoother.R | 1 latticeExtra-0.6-28/latticeExtra/R/panel.xblocks.R | 8 - latticeExtra-0.6-28/latticeExtra/R/panel.xyarea.R | 5 - latticeExtra-0.6-28/latticeExtra/R/rootogram.R | 5 - latticeExtra-0.6-28/latticeExtra/R/simpleSmoothTs.R | 4 latticeExtra-0.6-28/latticeExtra/R/tileplot.R | 14 +-- latticeExtra-0.6-28/latticeExtra/R/utilities.R | 11 +- latticeExtra-0.6-28/latticeExtra/data/SeatacWeather.rda |binary latticeExtra-0.6-28/latticeExtra/data/USAge.df.rda |binary latticeExtra-0.6-28/latticeExtra/data/USAge.table.rda |binary latticeExtra-0.6-28/latticeExtra/data/USCancerRates.rda |binary latticeExtra-0.6-28/latticeExtra/data/ancestry.rda |binary latticeExtra-0.6-28/latticeExtra/data/biocAccess.rda |binary latticeExtra-0.6-28/latticeExtra/data/gvhd10.rda |binary latticeExtra-0.6-28/latticeExtra/data/postdoc.rda |binary latticeExtra-0.6-28/latticeExtra/inst/old.svnlog |only latticeExtra-0.6-28/latticeExtra/man/USAge.Rd | 6 - latticeExtra-0.6-28/latticeExtra/man/ancestry.Rd | 4 latticeExtra-0.6-28/latticeExtra/man/gvhd10.Rd | 2 latticeExtra-0.6-28/latticeExtra/man/horizonplot.Rd | 50 ++++++----- latticeExtra-0.6-28/latticeExtra/man/panel.quantile.Rd | 4 latticeExtra-0.6-28/latticeExtra/man/panel.xblocks.Rd | 7 - latticeExtra-0.6-28/latticeExtra/man/rootogram.Rd | 9 + latticeExtra-0.6-28/latticeExtra/man/useOuterStrips.Rd | 3 36 files changed, 179 insertions(+), 171 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector Graphics'.
'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut, cre],
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] (Early line dashing code),
David Gohel [ctb] (Line dashing code and raster code),
Yixuan Qiu [ctb] (Improved styles; polypath implementation),
HÃ¥kon Malmedal [ctb] (Opacity code),
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between svglite versions 1.0.0 dated 2015-12-08 and 1.1.0 dated 2016-02-09
DESCRIPTION | 14 - MD5 | 31 +- NAMESPACE | 2 NEWS.md | 16 + R/RcppExports.R | 8 R/SVG.R | 48 ++++ R/inlineSVG.R | 12 - man/svglite.Rd | 10 man/svgstring.Rd |only src/RcppExports.cpp | 32 ++- src/SvgStream.h |only src/devSVG.cpp | 422 ++++++++++++++++++++++++---------------- tests/testthat/test-clip.R |only tests/testthat/test-clip.svg |only tests/testthat/test-no-clip.svg |only tests/testthat/test-output.R |only tests/testthat/test-raster.R | 6 tests/testthat/test-rect.R | 6 tests/testthat/test-text.R | 13 + tests/testthat/test-text.svg |only 20 files changed, 411 insertions(+), 209 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.10-0 dated 2015-11-06 and 1.11.0 dated 2016-02-09
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of Höhle and Paul (2008)
Author: Michael Höhle [aut, ths], Sebastian Meyer [aut, cre],
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], Wei Wei [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Sebastian Meyer <Sebastian.Meyer@ifspm.uzh.ch>
surveillance-1.10-0/surveillance/R/farringtonFlexible.r |only
surveillance-1.10-0/surveillance/data/salmNewportTruncated.RData |only
surveillance-1.10-0/surveillance/inst/shapes/districts_BYBW.dbf |only
surveillance-1.10-0/surveillance/inst/shapes/districts_BYBW.shp |only
surveillance-1.10-0/surveillance/inst/shapes/districts_BYBW.shx |only
surveillance-1.10-0/surveillance/man/meningo.age.rd |only
surveillance-1.10-0/surveillance/man/salmNewportTruncated.Rd |only
surveillance-1.11.0/surveillance/DESCRIPTION | 76 -
surveillance-1.11.0/surveillance/MD5 | 153 +-
surveillance-1.11.0/surveillance/NAMESPACE | 3
surveillance-1.11.0/surveillance/R/algo_call.R | 180 +-
surveillance-1.11.0/surveillance/R/algo_glrnb.R | 113 +
surveillance-1.11.0/surveillance/R/boda.R | 74 -
surveillance-1.11.0/surveillance/R/bodaDelay.R | 613 ++++----
surveillance-1.11.0/surveillance/R/catCUSUM.R | 134 -
surveillance-1.11.0/surveillance/R/epidata.R | 16
surveillance-1.11.0/surveillance/R/farringtonFlexible.R |only
surveillance-1.11.0/surveillance/R/hhh4_plot.R | 57
surveillance-1.11.0/surveillance/R/twinstim.R | 7
surveillance-1.11.0/surveillance/R/twinstim_epitest.R | 16
surveillance-1.11.0/surveillance/R/twinstim_intensity.R | 13
surveillance-1.11.0/surveillance/build/partial.rdb |binary
surveillance-1.11.0/surveillance/build/vignette.rds |binary
surveillance-1.11.0/surveillance/data/fluBYBW.RData |binary
surveillance-1.11.0/surveillance/data/salmAllOnset.RData |binary
surveillance-1.11.0/surveillance/data/stsNewport.RData |only
surveillance-1.11.0/surveillance/demo/cost.R | 17
surveillance-1.11.0/surveillance/inst/CITATION | 170 +-
surveillance-1.11.0/surveillance/inst/NEWS.Rd | 66
surveillance-1.11.0/surveillance/inst/THANKS | 1
surveillance-1.11.0/surveillance/inst/doc/glrnb.R | 58
surveillance-1.11.0/surveillance/inst/doc/glrnb.Rnw | 107 -
surveillance-1.11.0/surveillance/inst/doc/glrnb.pdf |binary
surveillance-1.11.0/surveillance/inst/doc/hhh4-cache.RData |binary
surveillance-1.11.0/surveillance/inst/doc/hhh4.R | 325 ++--
surveillance-1.11.0/surveillance/inst/doc/hhh4.Rnw | 736 +++++-----
surveillance-1.11.0/surveillance/inst/doc/hhh4.pdf |binary
surveillance-1.11.0/surveillance/inst/doc/surveillance-cache.RData |binary
surveillance-1.11.0/surveillance/inst/doc/surveillance.R | 135 -
surveillance-1.11.0/surveillance/inst/doc/surveillance.Rnw | 261 +--
surveillance-1.11.0/surveillance/inst/doc/surveillance.pdf |binary
surveillance-1.11.0/surveillance/inst/extdata/counts_flu_BYBW.txt | 1
surveillance-1.11.0/surveillance/man/addFormattedXAxis.Rd | 2
surveillance-1.11.0/surveillance/man/algo.glrnb.Rd | 106 -
surveillance-1.11.0/surveillance/man/algo.hhh.Rd | 18
surveillance-1.11.0/surveillance/man/algo.hhh.grid.Rd | 18
surveillance-1.11.0/surveillance/man/algo.quality.Rd | 4
surveillance-1.11.0/surveillance/man/boda.Rd | 26
surveillance-1.11.0/surveillance/man/bodaDelay.Rd | 106 -
surveillance-1.11.0/surveillance/man/categoricalCUSUM.Rd | 28
surveillance-1.11.0/surveillance/man/create.grid.Rd | 5
surveillance-1.11.0/surveillance/man/epidata.Rd | 14
surveillance-1.11.0/surveillance/man/epidataCS.Rd | 18
surveillance-1.11.0/surveillance/man/farringtonFlexible.Rd | 89 -
surveillance-1.11.0/surveillance/man/hhh4.Rd | 7
surveillance-1.11.0/surveillance/man/hhh4_methods.Rd | 11
surveillance-1.11.0/surveillance/man/hhh4_plot.Rd | 7
surveillance-1.11.0/surveillance/man/knox.Rd | 8
surveillance-1.11.0/surveillance/man/measles.weser.Rd | 10
surveillance-1.11.0/surveillance/man/meningo.age.Rd |only
surveillance-1.11.0/surveillance/man/salmAllOnset.Rd | 9
surveillance-1.11.0/surveillance/man/stK.Rd | 7
surveillance-1.11.0/surveillance/man/sts-class.Rd | 31
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surveillance-1.11.0/surveillance/man/surveillance-package.Rd | 89 -
surveillance-1.11.0/surveillance/man/twinSIR.Rd | 6
surveillance-1.11.0/surveillance/man/twinSIR_intensityplot.Rd | 11
surveillance-1.11.0/surveillance/man/twinstim.Rd | 6
surveillance-1.11.0/surveillance/man/twinstim_epitest.Rd | 17
surveillance-1.11.0/surveillance/man/twinstim_iaf.Rd | 43
surveillance-1.11.0/surveillance/man/twinstim_iafplot.Rd | 8
surveillance-1.11.0/surveillance/man/twinstim_intensity.Rd | 8
surveillance-1.11.0/surveillance/man/twinstim_simulation.Rd | 6
surveillance-1.11.0/surveillance/src/surveillance.c | 8
surveillance-1.11.0/surveillance/tests/testthat/test-calibration.R | 12
surveillance-1.11.0/surveillance/tests/testthat/test-hhh4_NegBinGrouped.R | 20
surveillance-1.11.0/surveillance/vignettes/glrnb.Rnw | 107 -
surveillance-1.11.0/surveillance/vignettes/hhh4-cache.RData |binary
surveillance-1.11.0/surveillance/vignettes/hhh4.Rnw | 736 +++++-----
surveillance-1.11.0/surveillance/vignettes/references.bib | 190 --
surveillance-1.11.0/surveillance/vignettes/surveillance-cache.RData |binary
surveillance-1.11.0/surveillance/vignettes/surveillance-hmm.pdf |only
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Title: Simulation of Diffusion Processes
Description: Provides the functions for simulation and modeling of stochastic differential equations (SDE's) the type Ito and Stratonovich. This package contains many objects, the numerical methods to find the solutions to SDE's (1, 2 and 3-dim), with a possibility for simulates a flows trajectories,with good accuracy. Many theoretical problems on the SDE's have become the object of practical research, as statistical analysis and simulation of solution of SDE's, enabled many searchers in different domains to use these equations to modeling and to analyse practical problems, in financial and actuarial modeling and other areas of application, for example modelling and simulate of dispersion in shallow water using the attractive center (Boukhetala K, 1996). We hope that the package presented here and the updated survey on the subject might be of help for practitioners, postgraduate and PhD students, and researchers in the field who might want to implement new methods.
Author: Arsalane Chouaib Guidoum, Kamal Boukhetala
Maintainer: Arsalane Chouaib Guidoum <acguidoum@usthb.dz>
Diff between Sim.DiffProc versions 3.1 dated 2015-12-31 and 3.2 dated 2016-02-09
DESCRIPTION | 8 +- LICENCE | 2 MD5 | 128 ++++++++++++++++++++++---------------------- NEWS | 3 + R/ABM.R | 2 R/BB.R | 2 R/BM.R | 2 R/Euler.R | 2 R/GBM.R | 2 R/HWV.R | 2 R/Heun.R | 2 R/Milstein.R | 2 R/OU.R | 2 R/PredCorr.R | 2 R/RK.R | 2 R/SMilstein.R | 2 R/STS.R | 2 R/bridgesde.R | 2 R/fitsde.R | 2 R/ftpsde.R | 31 ++++++---- R/rsde.R | 31 ++++++---- R/snssde.R | 31 ++++++---- R/st.int.R | 2 R/utils.R | 4 - R/zzz.r | 6 +- demo/Sim.DiffProc.R | 18 +++--- inst/doc/FitSDE.Rnw | 2 inst/doc/FitSDE.pdf |binary inst/doc/Introduction.Rnw | 6 +- inst/doc/Introduction.pdf |binary inst/doc/SDEs.Rnw | 8 +- inst/doc/SDEs.pdf |binary inst/doc/Thumbs.db |binary man/ABM.Rd | 8 +- man/HWV.Rd | 2 man/Sim.DiffProc-package.Rd | 6 +- man/bconfint.Rd | 1 man/bridgesde1d.Rd | 1 man/bridgesde2d.Rd | 1 man/bridgesde3d.Rd | 1 man/fitsde.Rd | 6 ++ man/fptsde1d.Rd | 3 + man/fptsde2d.Rd | 1 man/fptsde3d.Rd | 1 man/plot2d.Rd | 2 man/rsde1d.Rd | 2 man/rsde2d.Rd | 2 man/rsde3d.Rd | 1 man/snssde1d.Rd | 2 man/snssde2d.Rd | 2 man/snssde3d.Rd | 2 man/st.int.Rd | 2 src/Sim.DiffProc.c | 2 src/Sim.DiffProc.h | 2 src/init.c | 2 src/locale.h | 2 tests/bridgesde.R | 1 tests/fitsde.R | 1 tests/fptsde.R | 1 tests/rsde.R | 3 + tests/sde.R | 2 vignettes/Core_FitSDE.tex | 6 +- vignettes/FitSDE.Rnw | 2 vignettes/Introduction.Rnw | 6 +- vignettes/SDEs.Rnw | 8 +- 65 files changed, 232 insertions(+), 162 deletions(-)
Title: Interface to the 'Orcid.org' 'API'
Description: Client for the 'Orcid.org' 'API' (http://orcid.org/).
Functions included for searching for people, searching by 'DOI',
and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rorcid versions 0.2.0 dated 2015-12-07 and 0.2.2 dated 2016-02-09
DESCRIPTION | 8 LICENSE | 2 MD5 | 24 - NAMESPACE | 5 NEWS.md |only R/as.orcid.R | 15 R/truncmat.R | 198 +++++++----- R/zzz.R | 6 README.md | 615 +++++++++++++++++++------------------- man/type_summ.Rd | 34 -- tests/testthat/test-as.orcid.R | 15 tests/testthat/test-identifiers.R |only tests/testthat/test-orcid.R | 2 tests/testthat/test-trunc.R |only tests/testthat/test-works.R |only 15 files changed, 501 insertions(+), 423 deletions(-)
Title: Mid-Domain Effect and Species Richness Patterns
Description: Generates expected values of species richness, with continuous or
scattered ranges, for data across one or two dimensions.
Author: Aniruddha Marathe, ATREE, Bangalore
Maintainer: Aniruddha Marathe <aniruddha.pravin.marathe@gmail.com>
Diff between rangemodelR versions 0.1 dated 2015-12-03 and 1.0 dated 2016-02-09
DESCRIPTION | 21 ++++---- MD5 | 34 +++++++------- R/neigh_ob.R | 13 ++--- R/randomrange.R | 54 ++++++++++++---------- R/rangemod_2d.R | 108 +++++++++++++++++++++------------------------ R/rangemodelR-package.R | 26 +++++----- R/rangemodel_1d.R | 102 ++++++++++++++++++++++-------------------- R/shp.R | 29 ++++++------ R/spmat.R | 18 +++---- data/neigh_ob.rda |binary data/shp.rda |binary data/spmat.rda |binary man/neigh_ob.Rd | 5 +- man/rangemod.1d.Rd | 23 ++++----- man/rangemod.2d.Rd | 43 +++++++++-------- man/rangemodelR-package.Rd | 8 +-- man/shp.Rd | 21 +++++--- man/spmat.Rd | 12 ++--- 18 files changed, 264 insertions(+), 253 deletions(-)
Title: Analysis of Diffusion Weighted Imaging (DWI) Data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human
brain. The package contains R-functions to process diffusion-weighted
data. The functionality includes diffusion tensor imaging (DTI),
diffusion kurtosis imaging (DKI), modeling for high angular resolution
diffusion weighted imaging (HARDI) using Q-ball-reconstruction and
tensor mixture models, several methods for structural adaptive
smoothing including POAS and msPOAS, and a streamline fiber tracking
for tensor and tensor mixture models.
The package provides functionality to manipulate and visualize results
in 2D and 3D.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Felix Anker [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between dti versions 1.2-4 dated 2016-02-02 and 1.2-4.1 dated 2016-02-09
DESCRIPTION | 12 ++++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- src/Fiber.cpp | 2 -- src/Fibertracking.cpp | 4 +--- src/Fibertracking.h | 2 -- src/TrackingInterface.cpp | 2 -- src/Vector.cpp | 4 +--- src/Vector.h | 2 -- src/VectorList.cpp | 11 +++++------ src/Voxel.cpp | 2 -- src/Voxel.h | 2 -- 12 files changed, 25 insertions(+), 42 deletions(-)
Title: Diversity-Dependent Diversification
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between DDD versions 3.1 dated 2016-01-19 and 3.2 dated 2016-02-09
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/dd_LR.R | 32 ++++++++++++++++++++++++-------- R/dd_ML.R | 1 + R/dd_loglik.R | 4 ++-- R/dd_loglik_choosepar.R | 4 ++-- man/DDD-package.Rd | 12 ++++++++---- 7 files changed, 49 insertions(+), 28 deletions(-)
Title: Estimation of Temporal Ordering of Cancer Abnormalities
Description: Timing copy number changes using estimates of mutational allele frequency from resequencing of tumor samples.
Author: Elizabeth Purdom
Maintainer: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Diff between cancerTiming versions 3.1.3 dated 2016-01-04 and 3.1.5 dated 2016-02-09
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/labelSeg.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: Implementation of the 3D Alpha-Shape for the Reconstruction of
3D Sets from a Point Cloud
Description: Implementation in R of the alpha-shape of a finite set of points in the three-dimensional space. The alpha-shape generalizes the convex hull and allows to recover the shape of non-convex and even non-connected sets in 3D, given a random sample of points taken into it. Besides the computation of the alpha-shape, this package provides users with functions to compute the volume of the alpha-shape, identify the connected components and facilitate the three-dimensional graphical visualization of the estimated set.
Author: Thomas Lafarge, Beatriz Pateiro-Lopez
Maintainer: Beatriz Pateiro-Lopez <beatriz.pateiro@usc.es>
Diff between alphashape3d versions 1.1 dated 2014-05-23 and 1.2 dated 2016-02-09
DESCRIPTION | 15 MD5 | 28 - NAMESPACE | 5 R/ashape3d.R | 833 ++++++++++++++++++++------------------------ R/components_ashape3d.R | 172 ++++----- R/inashape3d.R | 63 +-- R/intersectiontriangle.R | 18 R/plot.ashape3d.R | 202 +++++----- R/surfaceNormals.R | 115 ++---- R/volume_ashape3d.R | 143 +++---- build/vignette.rds |binary inst/doc/alphashape3d.pdf |binary man/alphashape3d-package.Rd | 7 man/plot.ashape3d.Rd | 12 src/surfaceNormals.c | 6 15 files changed, 766 insertions(+), 853 deletions(-)
Title: Analytic Hierarchy Process
Description: Model and analyse complex decision making problems
using the Analytic Hierarchy Process (AHP) by Thomas Saaty.
Author: Christoph Glur
Maintainer: Christoph Glur <christoph.glur@ipub.com>
Diff between ahp versions 0.2.7 dated 2016-02-02 and 0.2.8 dated 2016-02-09
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