Title: Easily Tidy Data with `spread()` and `gather()` Functions
Description: An evolution of 'reshape2'. It's designed specifically for data
tidying (not general reshaping or aggregating) and works well with
'dplyr' data pipelines.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.4.0 dated 2016-01-18 and 0.4.1 dated 2016-02-05
DESCRIPTION | 8 +- MD5 | 11 ++- NEWS.md |only R/nest.R | 2 build/vignette.rds |binary inst/doc/tidy-data.html | 128 +++++++++++++++++++++++++-------------------- tests/testthat/test-nest.R | 7 ++ 7 files changed, 91 insertions(+), 65 deletions(-)
Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Josh O'Brien [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.2-1 dated 2015-10-18 and 1.2-2 dated 2016-02-05
ChangeLog | 54 +++++ DESCRIPTION | 12 - MD5 | 84 ++++---- NAMESPACE | 7 R/GridTopology-methods.R | 1 R/Spatial-methods.R | 15 + R/SpatialGrid-methods.R | 1 R/SpatialLines-methods.R | 54 ++++- R/SpatialLinesDataFrame-methods.R | 3 R/SpatialPoints-methods.R | 5 R/SpatialPointsDataFrame-methods.R | 17 + R/SpatialPolygonsDataFrame-methods.R | 30 ++ R/gridlines.R | 25 +- R/over.R | 5 R/projected.R | 2 R/rbind.R | 39 +++ R/sp_spat1.R | 19 + README.md |only build/vignette.rds |binary demo/00Index | 3 demo/polar.R |only inst/ChangeLog | 322 +++++++++++++++++++++++++++++++ inst/NEWS.Rd | 15 + inst/doc/csdacm.pdf |binary inst/doc/intro_sp.R | 48 ++-- inst/doc/intro_sp.Rnw | 38 +-- inst/doc/intro_sp.pdf |binary inst/doc/over.pdf |binary inst/include/sp.h | 19 - man/Spatial-class.Rd | 5 man/SpatialLines-class.Rd | 4 man/SpatialMultiPoints.Rd | 6 man/SpatialMultiPointsDataFrame-class.Rd | 2 man/SpatialPolygons-class.Rd | 1 man/SpatialPolygonsDataFrame-class.Rd | 15 - man/aggregate.Rd | 3 man/geometry-methods.Rd | 24 +- man/gridlines.Rd | 79 ++++++- man/image.Rd | 4 man/sp-deprecated.Rd | 4 src/pip.c | 20 - src/sp.h | 19 - src/zerodist.c | 14 - vignettes/intro_sp.Rnw | 38 +-- 44 files changed, 807 insertions(+), 249 deletions(-)
Title: Client Library for The Guardian
Description: A client library for 'The Guardian' (https://www.guardian.com/)
and their API, this package allows users to search for Guardian articles and
retrieve both the content and metadata.
Author: Oliver Keyes
Maintainer: Oliver Keyes <ironholds@gmail.com>
Diff between rdian versions 0.1.0 dated 2016-01-01 and 0.1.1 dated 2016-02-05
DESCRIPTION | 15 ++++++++------- MD5 | 33 +++++++++++++++++---------------- NAMESPACE | 2 +- R/content.R | 8 ++++---- R/editions.R | 4 ++-- R/sections.R | 4 ++-- R/tags.R | 4 ++-- README.md |only man/guardian_content.Rd | 6 ++++-- man/guardian_editions.Rd | 4 +++- man/guardian_operators.Rd | 2 +- man/guardian_sections.Rd | 4 +++- man/guardian_tags.Rd | 4 +++- man/rdian.Rd | 2 +- tests/testthat/test_content.R | 3 ++- tests/testthat/test_editions.R | 1 + tests/testthat/test_sections.R | 1 + tests/testthat/test_tags.R | 4 ++-- 18 files changed, 57 insertions(+), 44 deletions(-)
Title: Generate Useful ROC Curve Charts for Print and Interactive Use
Description: Most ROC curve plots obscure the cutoff values and inhibit
interpretation and comparison of multiple curves. This attempts to address
those shortcomings by providing plotting and interactive tools. Functions
are provided to generate an interactive ROC curve plot for web use, and
print versions. A Shiny application implementing the functions is also
included.
Author: Michael C Sachs
Maintainer: Michael C Sachs <sachsmc@gmail.com>
Diff between plotROC versions 2.0.0 dated 2015-12-22 and 2.0.1 dated 2016-02-05
DESCRIPTION | 8 ++--- MD5 | 32 +++++++++++----------- NEWS | 8 +++++ R/calculate_roc.R | 12 ++++---- R/geom_roc.R | 22 +++++++++------ R/geom_rocci.R | 16 ++++++----- R/plotROC-package.R | 8 +++-- R/style_roc.R | 4 +- inst/doc/examples.html | 69 ++++++++++++++++++++++++------------------------- man/calc_auc.Rd | 6 ++-- man/geom_roc.Rd | 44 +++++++++++++++++-------------- man/geom_rocci.Rd | 40 +++++++++++++++------------- man/melt_roc.Rd | 6 ++-- man/plotROC.Rd | 8 +++-- man/stat_roc.Rd | 41 +++++++++++++++++++---------- man/stat_rocci.Rd | 41 +++++++++++++++++++---------- man/style_roc.Rd | 4 +- 17 files changed, 213 insertions(+), 156 deletions(-)
Title: (Non)Additive Genetic Relatedness Matrices
Description: Constructs (non)additive genetic relationship matrices, and their inverses, from a pedigree to be used in linear mixed effect models (A.K.A. the 'animal model'). Also includes other functions to facilitate the use of animal models. Some functions have been created to be used in conjunction with the R package 'asreml' for the 'ASReml' software, which can be obtained upon purchase from 'VSN' international (http://www.vsni.co.uk/software/asreml).
Author: Matthew Wolak [cre, aut]
Maintainer: Matthew Wolak <matthewwolak@gmail.com>
Diff between nadiv versions 2.14.1 dated 2015-07-22 and 2.14.2 dated 2016-02-05
nadiv-2.14.1/nadiv/src/General.h |only nadiv-2.14.1/nadiv/src/ainv.h |only nadiv-2.14.1/nadiv/src/dfc.h |only nadiv-2.14.1/nadiv/src/dij.h |only nadiv-2.14.1/nadiv/src/dsim.h |only nadiv-2.14.1/nadiv/src/ga.h |only nadiv-2.14.1/nadiv/src/reT.h |only nadiv-2.14.1/nadiv/src/test.h |only nadiv-2.14.2/nadiv/DESCRIPTION | 8 - nadiv-2.14.2/nadiv/MD5 | 41 ++---- nadiv-2.14.2/nadiv/R/LRTest.R | 12 + nadiv-2.14.2/nadiv/R/ggcontrib.R | 213 ++++++++++++++++++++------------ nadiv-2.14.2/nadiv/R/makeAinv.R | 4 nadiv-2.14.2/nadiv/man/ggcontrib.Rd | 91 +++++++++---- nadiv-2.14.2/nadiv/man/makeD.Rd | 12 - nadiv-2.14.2/nadiv/man/nadiv-package.Rd | 4 nadiv-2.14.2/nadiv/src/ainv.cc | 2 nadiv-2.14.2/nadiv/src/cs.h | 14 ++ nadiv-2.14.2/nadiv/src/dfc.cc | 2 nadiv-2.14.2/nadiv/src/dij.cc | 2 nadiv-2.14.2/nadiv/src/dsim.cc | 2 nadiv-2.14.2/nadiv/src/ga.cc | 2 nadiv-2.14.2/nadiv/src/genedrop.cc |only nadiv-2.14.2/nadiv/src/nadiv.h |only nadiv-2.14.2/nadiv/src/nadivcc.h |only nadiv-2.14.2/nadiv/src/reT.cc | 2 nadiv-2.14.2/nadiv/src/sinv.cc | 2 27 files changed, 264 insertions(+), 149 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package pan, jomo is a package for multilevel joint modelling multiple imputation.
Novel aspects of jomo are the possibility of handling binary and categorical data through latent normal variables and the option to use cluster-specific covariance matrices.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <matteo.quartagno@lshtm.ac.uk>
Diff between jomo versions 2.1-0 dated 2016-01-29 and 2.1-1 dated 2016-02-05
DESCRIPTION | 8 ++--- MD5 | 60 ++++++++++++++++++++--------------------- R/jomo1cat.MCMCchain.R | 2 - R/jomo1mix.MCMCchain.R | 2 - R/jomo1rancat.MCMCchain.R | 2 - R/jomo1rancathr.MCMCchain.R | 2 - R/jomo1ranmix.MCMCchain.R | 2 - R/jomo1ranmixhr.MCMCchain.R | 2 - R/jomo2com.MCMCchain.R | 4 +- R/jomo2com.R | 4 +- R/jomo2hr.MCMCchain.R | 5 +-- R/jomo2hr.R | 2 - data/tldata.RData |binary man/jomo.MCMCchain.Rd | 2 - man/jomo1.MCMCchain.Rd | 2 - man/jomo1cat.MCMCchain.Rd | 2 - man/jomo1mix.MCMCchain.Rd | 2 - man/jomo1ran.MCMCchain.Rd | 2 - man/jomo1rancat.MCMCchain.Rd | 2 - man/jomo1rancathr.MCMCchain.Rd | 2 - man/jomo1ranmix.MCMCchain.Rd | 2 - man/jomo1ranmixhr.MCMCchain.Rd | 2 - man/jomo2.MCMCchain.Rd | 2 - man/jomo2com.MCMCchain.Rd | 2 - man/jomo2hr.MCMCchain.Rd | 2 - src/MCMCjomo2com.c | 26 ++++++++++------- src/MCMCjomo2hf.c | 26 ++++++++++------- src/MCMCjomo2hr.c | 25 ++++++++++------- src/jomo2com.c | 32 ++++++++++++--------- src/jomo2hf.c | 26 ++++++++++------- src/jomo2hr.c | 25 ++++++++++------- 31 files changed, 152 insertions(+), 127 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 1.1 dated 2016-01-28 and 1.3 dated 2016-02-05
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- R/FMP.R | 31 ++++++++++++++++--------------- R/FMPMonotonicityCheck.R | 2 +- inst/CITATION | 4 ++-- inst/doc/FMP-manual.pdf |binary man/FMP.Rd | 2 +- man/FMPMonotonicityCheck.Rd | 8 ++++---- man/eap.Rd | 2 +- man/irf.Rd | 2 +- 10 files changed, 38 insertions(+), 37 deletions(-)
Title: Export Tables to LaTeX or HTML
Description: Coerce data to LaTeX and HTML tables.
Author: David B. Dahl <dahl@stat.byu.edu>
Maintainer: David Scott <d.scott@auckland.ac.nz>
Diff between xtable versions 1.8-0 dated 2015-11-02 and 1.8-2 dated 2016-02-05
DESCRIPTION | 10 MD5 | 57 + NAMESPACE | 28 NEWS | 36 + R/lagImpactMat.R |only R/print.xtable.R | 1169 +++++++++++++++++-------------------- R/sanitize.R |only R/table.attributes.R | 151 ++-- R/toLatex.R | 8 R/xtable.R | 223 +++++-- R/xtableFtable.R |only R/xtableList.R |only R/xtableMatharray.R |only build/vignette.rds |binary data/tli.txt.gz |binary inst/doc/OtherPackagesGallery.R |only inst/doc/OtherPackagesGallery.Rnw |only inst/doc/OtherPackagesGallery.pdf |only inst/doc/listOfTablesGallery.R |only inst/doc/listOfTablesGallery.Rnw |only inst/doc/listOfTablesGallery.pdf |only inst/doc/margintable.R | 26 inst/doc/margintable.pdf |binary inst/doc/xtableGallery.R | 614 +++++++++++-------- inst/doc/xtableGallery.Rnw | 258 ++++++-- inst/doc/xtableGallery.pdf |binary man/print.xtable.Rd | 14 man/print.xtableMatharray.Rd |only man/sanitize.Rd |only man/string.Rd | 5 man/xtable-internal.Rd |only man/xtable.Rd | 36 - man/xtableFtable.Rd |only man/xtableList.Rd |only man/xtableMatharray.Rd |only tests/test.matharray.R |only tests/test.xtable.xtableFtable.R |only vignettes/OtherPackagesGallery.Rnw |only vignettes/listOfTablesGallery.Rnw |only vignettes/xtableGallery.Rnw | 258 ++++++-- 40 files changed, 1744 insertions(+), 1149 deletions(-)
Title: R-Based Wikipedia Client
Description: Provides an interface to the Wikipedia web application programming
interface (API), using internet connexion.Three functions provide details for
a specific Wikipedia page : all links that are present, all pages that link
to, all the contributions (revisions for main pages, and discussions for talk
pages). Two functions provide details for a specific user : all contributions,
and general information (as name, gender, rights or groups). It provides
additional information compared to others packages, as WikipediR. It does not
need login. The multiplex network that can be constructed from the results
of the functions of WikipediaR can be modeled as Stochastic Block Model as in
Barbillon P., Donnet, S., Lazega E., and Bar-Hen A. : Stochastic Block Models
for Multiplex networks: an application to networks of researchers, ArXiv
1501.06444, http://arxiv.org/abs/1501.06444.
Author: Avner Bar-Hen [aut, cre],
Louise Baschet [ctb],
Francois-Xavier Jollois [ctb],
Jeremie Riou [ctb]
Maintainer: Avner Bar-Hen <Avner.Bar-Hen@mi.parisdescartes.fr>
Diff between WikipediaR versions 1.0 dated 2015-04-19 and 1.1 dated 2016-02-05
DESCRIPTION | 26 +++++++++++++++++------- MD5 | 44 ++++++++++++++++++++--------------------- NAMESPACE | 4 ++- R/backLinks.R | 19 +++++++++-------- R/contribs.R | 11 ++++++---- R/links.R | 16 ++++++++------ R/testWikiPage.R | 12 ++++++----- R/testWikiUser.R | 7 +++--- R/userContribs.R | 9 ++++---- R/userInfo.R | 7 +++--- man/WikipediaR-package.Rd | 16 +++++++------- man/backLinks.Rd | 20 +++++++++--------- man/contribs.Rd | 10 ++++----- man/links.Rd | 22 ++++++++++---------- man/print.backLinksClass.Rd | 2 - man/print.contribsClass.Rd | 2 - man/print.linksClass.Rd | 2 - man/print.userContribsClass.Rd | 2 - man/print.userInfoClass.Rd | 2 - man/testWikiPage.Rd | 8 +++---- man/testWikiUser.Rd | 8 +++---- man/userContribs.Rd | 24 +++++++++++----------- man/userInfo.Rd | 10 ++++----- 23 files changed, 154 insertions(+), 129 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-66 dated 2016-01-22 and 0.1-67 dated 2016-02-05
DESCRIPTION | 8 - MD5 | 6 NEWS | 2 R/CausalDiagramBinBin.R | 316 +++++++++++++++++++++++++++++++++++++++++++++++- 4 files changed, 318 insertions(+), 14 deletions(-)
Title: Target Equivalence Range Design
Description: The TEQR package contains software to calculate the operating characteristics for the TEQR and the ACT designs.The TEQR (toxicity equivalence range) design is a toxicity based cumulative cohort design with added safety rules. The ACT (Activity constrained for toxicity) design is also a cumulative cohort design with additional safety rules. The unique feature of this design is that dose is escalated based on lack of activity rather than on lack of toxicity and is de-escalated only if an unacceptable level of toxicity is experienced.
Author: M. Suzette Blanchard
Maintainer: M. Suzette Blanchard <sblanchard@coh.org>
Diff between TEQR versions 5.0-0 dated 2014-07-19 and 6.0-0 dated 2016-02-05
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++++--------- NAMESPACE | 3 ++- R/TEQR.R | 21 ++++++++++----------- man/print.teqrDG.Rd | 40 ++++++++++++++++++++-------------------- man/print.teqrOCact.Rd | 14 +++++++------- man/print.teqrOCtox.Rd | 10 +++++----- man/teqr.DLdata.Rd |only man/teqr.DLdataconACT.Rd |only man/teqr.MTDdataconACT.Rd |only man/teqr.MTDdatatox.Rd |only man/teqrDG.Rd | 4 ++-- man/teqrOCact.Rd | 45 +++++++++++++++++++++------------------------ man/teqrOCtox.Rd | 18 +++++++++--------- 14 files changed, 94 insertions(+), 93 deletions(-)
Title: Tools to Support the Sheffield Elicitation Framework (SHELF)
Description: Implements various methods for eliciting a probability distribution
for a single parameter from an expert or a group of experts. The expert
provides a small number of probability or quantile judgements, corresponding
to points on his or her cumulative distribution function. A range of parametric
distributions can then be fitted and displayed, with feedback provided in the
form of additional quantiles. A graphical interface for the roulette elicitation
method is also provided. For multiple experts, a weighted linear pool can be
calculated. Also includes functions for eliciting beliefs about population distributions.
Author: Jeremy Oakley
Maintainer: Jeremy Oakley <j.oakley@sheffield.ac.uk>
Diff between SHELF versions 1.0.1 dated 2015-07-07 and 1.1.0 dated 2016-02-05
DESCRIPTION | 24 ++++++-- MD5 | 46 ++++++++++----- NAMESPACE | 20 +++++- R/SHELF1.0.1.9002-package.R |only R/cdfHelperfunctions.R |only R/cdffeedback.R |only R/cdfplot.R |only R/elicit.R | 28 +++++++++ R/feedback.R | 57 +++++++++++++++++++ R/fitdist.R | 118 ++++++++++++++++++++++++++++++++++++++-- R/fitprecision.R |only R/multiplot.R |only R/pdfplots.R |only R/plinearpool.R | 45 +++++++++++++++ R/plotfit.R | 74 +++++++++++++++++++++++++ R/qlinearpool.R | 2 R/roulette.R | 38 ++++++++++++- inst |only man/SHELF-package.Rd | 50 +++++++---------- man/cdffeedback.Rd |only man/cdfplot.Rd |only man/elicit.Rd | 48 ++++++++-------- man/feedback.Rd | 82 ++++++++++++++-------------- man/fitdist.Rd | 127 +++++++++++++++++++++++++------------------- man/fitprecision.Rd |only man/pdfplots.Rd |only man/plinearpool.Rd | 67 ++++++++++------------- man/plotfit.Rd | 108 ++++++++++++++++++------------------- man/roulette.Rd | 70 ++++++++++++------------ tests |only 30 files changed, 698 insertions(+), 306 deletions(-)
Title: Reverse-Correlation Image-Classification Toolbox
Description: Functions to generate stimuli and analyze data of reverse correlation image classification experiments (psychophysical tasks aimed at visualizing cognitive mental representations of faces).
Author: Ron Dotsch <rdotsch@gmail.com>
Maintainer: Ron Dotsch <rdotsch@gmail.com>
Diff between rcicr versions 0.3.2 dated 2015-07-20 and 0.3.2.1 dated 2016-02-05
ChangeLog | 7 +++++++ DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/rcicr_2IFC.R | 13 +++++++++---- man/generateCI2IFC.Rd | 2 +- 5 files changed, 27 insertions(+), 15 deletions(-)
Title: Population Viability Analysis with Data Cloning
Description: Likelihood based population viability analysis in the
presence of observation error and missing data.
The package can be used to fit, compare, predict,
and forecast various growth model types using data cloning.
Author: Khurram Nadeem, Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between PVAClone versions 0.1-4 dated 2016-01-14 and 0.1-5 dated 2016-02-05
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/bevertonholt.R | 4 ++-- R/fancyPVAmodel.R | 4 ++-- R/generateMCMC.R | 10 +++++----- R/gompertz.R | 4 ++-- R/internals.R | 5 ++--- R/modelselection.R | 24 ++++++++++++------------ R/pva-class.R | 10 +++++----- R/pva-methods.R | 2 +- R/pva.R | 5 ++++- R/ricker.R | 4 ++-- R/thetalogistic.R | 4 ++-- R/thetalogistic_D.R | 4 ++-- inst/ChangeLog | 8 ++++++-- 15 files changed, 66 insertions(+), 60 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources (rpart, RWeka, PMML) yielding objects that share
functionality for print/plot/predict methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree) and model-based
recursive partitioning (mob) from the party package are provided based
on the new infrastructure.
Author: Torsten Hothorn [aut, cre],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.0-4 dated 2015-09-29 and 1.0-5 dated 2016-02-05
DESCRIPTION | 8 +++---- MD5 | 51 ++++++++++++++++++++++++------------------------ NAMESPACE | 3 +- R/cforest.R | 6 ++++- R/ctree.R | 22 ++++++++++---------- R/mob-plot.R | 4 +-- R/modelparty.R | 10 ++++----- R/node.R | 1 R/plot.R | 23 ++++++++++++--------- build/vignette.rds |binary data/HuntingSpiders.rda |binary data/WeatherPlay.rda |binary inst/CITATION | 8 ++++--- inst/NEWS.Rd | 12 +++++++++++ inst/doc/constparty.pdf |binary inst/doc/ctree.pdf |binary inst/doc/mob.Rnw | 12 +++++------ inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary inst/tmp |only man/cforest.Rd | 9 +++++++- man/ctree.Rd | 12 +++++++---- man/mob.Rd | 6 +++++ man/panelfunctions.Rd | 35 +++++++++++++++++--------------- man/party.Rd | 5 ++++ man/partynode.Rd | 5 ++++ man/partysplit.Rd | 5 ++++ 27 files changed, 148 insertions(+), 89 deletions(-)
Title: Probabilistic Models to Analyze and Gaussianize Heavy-Tailed,
Skewed Data
Description: Lambert W x F distributions are a generalized framework to analyze
skewed, heavy-tailed data. It is based on an input/output system, where the
output random variable (RV) Y is a non-linearly transformed version of an input
RV X ~ F with similar properties as X, but slightly skewed (heavy-tailed).
The transformed RV Y has a Lambert W x F distribution. This package contains
functions to model and analyze skewed, heavy-tailed data the Lambert Way:
simulate random samples, estimate parameters, compute quantiles, and plot/
print results nicely. Probably the most important function is 'Gaussianize',
which works similarly to 'scale', but actually makes the data Gaussian.
A do-it-yourself toolkit allows users to define their own Lambert W x
'MyFavoriteDistribution' and use it in their analysis right away.
Author: Georg M. Goerg <im@gmge.org>
Maintainer: Georg M. Goerg <im@gmge.org>
Diff between LambertW versions 0.6.0 dated 2015-09-08 and 0.6.2 dated 2016-02-05
LambertW-0.6.0/LambertW/R/mc.R |only LambertW-0.6.0/LambertW/man/mc.Rd |only LambertW-0.6.2/LambertW/DESCRIPTION | 43 - LambertW-0.6.2/LambertW/MD5 | 276 +++++----- LambertW-0.6.2/LambertW/NAMESPACE | 21 LambertW-0.6.2/LambertW/NEWS | 44 + LambertW-0.6.2/LambertW/R/0_LambertW-toolkit.R | 47 - LambertW-0.6.2/LambertW/R/0_LambertW-utils.R | 134 ++-- LambertW-0.6.2/LambertW/R/0_LambertW_fit-methods.R | 6 LambertW-0.6.2/LambertW/R/0_U-utils.R | 32 - LambertW-0.6.2/LambertW/R/0_W.R | 114 ++-- LambertW-0.6.2/LambertW/R/0_W_delta.R | 32 - LambertW-0.6.2/LambertW/R/0_W_gamma.R | 10 LambertW-0.6.2/LambertW/R/0_beta-utils.R | 8 LambertW-0.6.2/LambertW/R/0_distname-utils.R | 5 LambertW-0.6.2/LambertW/R/0_loglik-LambertW-utils.R | 32 - LambertW-0.6.2/LambertW/R/0_tau-utils.R | 18 LambertW-0.6.2/LambertW/R/0_theta-utils.R | 21 LambertW-0.6.2/LambertW/R/G_delta_alpha.R | 18 LambertW-0.6.2/LambertW/R/Gaussianize.R | 163 +++-- LambertW-0.6.2/LambertW/R/H_gamma.R | 13 LambertW-0.6.2/LambertW/R/IGMM.R | 179 +++--- LambertW-0.6.2/LambertW/R/LambertW-package.R | 126 ++-- LambertW-0.6.2/LambertW/R/MLE_LambertW.R | 155 +++-- LambertW-0.6.2/LambertW/R/RcppExports.R |only LambertW-0.6.2/LambertW/R/analyze_convergence.R |only LambertW-0.6.2/LambertW/R/beta2tau.R | 94 ++- LambertW-0.6.2/LambertW/R/bootstrap.R |only LambertW-0.6.2/LambertW/R/check_beta.R | 22 LambertW-0.6.2/LambertW/R/common-arguments.R | 45 + LambertW-0.6.2/LambertW/R/complete_tau.R | 12 LambertW-0.6.2/LambertW/R/complete_theta.R | 5 LambertW-0.6.2/LambertW/R/create_LambertW_input.R | 18 LambertW-0.6.2/LambertW/R/create_LambertW_output.R | 20 LambertW-0.6.2/LambertW/R/dLambertW.R | 16 LambertW-0.6.2/LambertW/R/dU.R | 5 LambertW-0.6.2/LambertW/R/datasets.R | 38 - LambertW-0.6.2/LambertW/R/delta_01.R | 35 - LambertW-0.6.2/LambertW/R/delta_GMM.R | 35 - LambertW-0.6.2/LambertW/R/delta_Taylor.R | 2 LambertW-0.6.2/LambertW/R/deprecated_functions.R | 15 LambertW-0.6.2/LambertW/R/deriv_W.R | 16 LambertW-0.6.2/LambertW/R/estimate_beta.R | 29 - LambertW-0.6.2/LambertW/R/gamma_01.R | 16 LambertW-0.6.2/LambertW/R/gamma_GMM.R | 52 + LambertW-0.6.2/LambertW/R/gamma_Taylor.R | 65 +- LambertW-0.6.2/LambertW/R/get_beta_names.R | 17 LambertW-0.6.2/LambertW/R/get_distname_family.R | 2 LambertW-0.6.2/LambertW/R/get_distnames.R | 10 LambertW-0.6.2/LambertW/R/get_gamma_bounds.R | 39 - LambertW-0.6.2/LambertW/R/get_initial_theta.R | 57 +- LambertW-0.6.2/LambertW/R/get_input.R | 28 - LambertW-0.6.2/LambertW/R/get_output.R | 17 LambertW-0.6.2/LambertW/R/get_support.R | 31 - LambertW-0.6.2/LambertW/R/ks.test.t.R | 25 LambertW-0.6.2/LambertW/R/loglik_LambertW.R | 33 - LambertW-0.6.2/LambertW/R/loglik_input.R | 20 LambertW-0.6.2/LambertW/R/loglik_penalty.R | 31 - LambertW-0.6.2/LambertW/R/lp_norm.R | 41 - LambertW-0.6.2/LambertW/R/mLambertW.R | 4 LambertW-0.6.2/LambertW/R/medcouple_estimator.R |only LambertW-0.6.2/LambertW/R/normalize_by_tau.R | 30 - LambertW-0.6.2/LambertW/R/pLambertW.R | 21 LambertW-0.6.2/LambertW/R/pU.R | 5 LambertW-0.6.2/LambertW/R/p_m1.R | 40 - LambertW-0.6.2/LambertW/R/plot.LambertW_fit.R | 12 LambertW-0.6.2/LambertW/R/print.LambertW_fit.R | 5 LambertW-0.6.2/LambertW/R/print.LambertW_input.R | 2 LambertW-0.6.2/LambertW/R/print.summary.LambertW_fit.R | 1 LambertW-0.6.2/LambertW/R/qLambertW.R | 21 LambertW-0.6.2/LambertW/R/qU.R | 10 LambertW-0.6.2/LambertW/R/qqLambertW.R | 9 LambertW-0.6.2/LambertW/R/rLambertW.R | 13 LambertW-0.6.2/LambertW/R/rU.R | 6 LambertW-0.6.2/LambertW/R/summary.LambertW_fit.R | 23 LambertW-0.6.2/LambertW/R/test_normality.R | 69 +- LambertW-0.6.2/LambertW/R/test_symmetry.R | 41 - LambertW-0.6.2/LambertW/R/theta2tau.R | 8 LambertW-0.6.2/LambertW/R/theta2unbounded.R | 22 LambertW-0.6.2/LambertW/R/xexp.R | 15 LambertW-0.6.2/LambertW/inst/CITATION | 2 LambertW-0.6.2/LambertW/inst/include |only LambertW-0.6.2/LambertW/man/G_delta_alpha.Rd | 14 LambertW-0.6.2/LambertW/man/Gaussianize.Rd | 133 ++-- LambertW-0.6.2/LambertW/man/H_gamma.Rd | 13 LambertW-0.6.2/LambertW/man/IGMM.Rd | 114 ++-- LambertW-0.6.2/LambertW/man/LambertW-package.Rd | 124 ++-- LambertW-0.6.2/LambertW/man/LambertW-toolkit.Rd | 114 ++-- LambertW-0.6.2/LambertW/man/LambertW-utils.Rd | 205 +++---- LambertW-0.6.2/LambertW/man/LambertW_fit-methods.Rd | 44 - LambertW-0.6.2/LambertW/man/LambertW_input_output-methods.Rd | 10 LambertW-0.6.2/LambertW/man/MLE_LambertW.Rd | 89 +-- LambertW-0.6.2/LambertW/man/U-utils.Rd | 54 + LambertW-0.6.2/LambertW/man/W.Rd | 99 ++- LambertW-0.6.2/LambertW/man/W_delta.Rd | 10 LambertW-0.6.2/LambertW/man/W_gamma.Rd | 16 LambertW-0.6.2/LambertW/man/analyze_convergence.Rd |only LambertW-0.6.2/LambertW/man/beta-utils.Rd | 100 ++- LambertW-0.6.2/LambertW/man/bootstrap.Rd |only LambertW-0.6.2/LambertW/man/common-arguments.Rd | 54 + LambertW-0.6.2/LambertW/man/datasets.Rd | 32 - LambertW-0.6.2/LambertW/man/delta_01.Rd | 39 - LambertW-0.6.2/LambertW/man/delta_GMM.Rd | 44 - LambertW-0.6.2/LambertW/man/delta_Taylor.Rd | 20 LambertW-0.6.2/LambertW/man/deprecated-functions.Rd | 18 LambertW-0.6.2/LambertW/man/distname-utils.Rd | 27 LambertW-0.6.2/LambertW/man/estimate-moments.Rd |only LambertW-0.6.2/LambertW/man/gamma_01.Rd | 23 LambertW-0.6.2/LambertW/man/gamma_GMM.Rd | 47 - LambertW-0.6.2/LambertW/man/gamma_Taylor.Rd | 49 + LambertW-0.6.2/LambertW/man/get_gamma_bounds.Rd | 38 - LambertW-0.6.2/LambertW/man/get_input.Rd | 32 - LambertW-0.6.2/LambertW/man/get_output.Rd | 21 LambertW-0.6.2/LambertW/man/get_support.Rd | 36 - LambertW-0.6.2/LambertW/man/ks.test.t.Rd | 29 - LambertW-0.6.2/LambertW/man/loglik-LambertW-utils.Rd | 165 +++-- LambertW-0.6.2/LambertW/man/lp_norm.Rd | 27 LambertW-0.6.2/LambertW/man/medcouple_estimator.Rd |only LambertW-0.6.2/LambertW/man/p_m1.Rd | 61 +- LambertW-0.6.2/LambertW/man/tau-utils.Rd | 52 + LambertW-0.6.2/LambertW/man/test_normality.Rd | 55 + LambertW-0.6.2/LambertW/man/test_symmetry.Rd | 33 - LambertW-0.6.2/LambertW/man/theta-utils.Rd | 141 ++--- LambertW-0.6.2/LambertW/man/xexp.Rd | 15 LambertW-0.6.2/LambertW/src |only LambertW-0.6.2/LambertW/tests/testthat/test_G_delta.R | 3 LambertW-0.6.2/LambertW/tests/testthat/test_H_gamma.R |only LambertW-0.6.2/LambertW/tests/testthat/test_IGMM.R | 49 + LambertW-0.6.2/LambertW/tests/testthat/test_W.R | 31 - LambertW-0.6.2/LambertW/tests/testthat/test_W_gamma.R | 14 LambertW-0.6.2/LambertW/tests/testthat/test_analyze_convergence.R |only LambertW-0.6.2/LambertW/tests/testthat/test_beta-utils.R |only LambertW-0.6.2/LambertW/tests/testthat/test_bootstrap.R |only LambertW-0.6.2/LambertW/tests/testthat/test_delta_01.R |only LambertW-0.6.2/LambertW/tests/testthat/test_deriv_W.R | 16 LambertW-0.6.2/LambertW/tests/testthat/test_distname-utils.R |only LambertW-0.6.2/LambertW/tests/testthat/test_dpqr_LambertW.R | 53 + LambertW-0.6.2/LambertW/tests/testthat/test_dpqr_U.R |only LambertW-0.6.2/LambertW/tests/testthat/test_estimate-moments.R |only LambertW-0.6.2/LambertW/tests/testthat/test_get_input_output.R | 18 LambertW-0.6.2/LambertW/tests/testthat/test_loglik-utils.R |only LambertW-0.6.2/LambertW/tests/testthat/test_lp_norm.R | 49 + LambertW-0.6.2/LambertW/tests/testthat/test_normalize_by_tau.R | 2 LambertW-0.6.2/LambertW/tests/testthat/test_p_m1.R |only LambertW-0.6.2/LambertW/tests/testthat/test_theta-utils.R |only LambertW-0.6.2/LambertW/tests/testthat/test_theta_tau.R |only LambertW-0.6.2/LambertW/tests/testthat/test_xexp.R | 6 147 files changed, 2906 insertions(+), 2279 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: Functions for Kalman filtering, smoothing,
forecasting and simulation of multivariate exponential family state space
models with exact diffuse initialization and sequential processing.
Author: Jouni Helske <jouni.helske@jyu.fi>
Maintainer: Jouni Helske <jouni.helske@jyu.fi>
Diff between KFAS versions 1.2.0 dated 2016-01-31 and 1.2.1 dated 2016-02-05
ChangeLog | 33 - DESCRIPTION | 8 MD5 | 85 +- R/KFAS-package.R | 2 R/KFS.R | 57 - R/SSModel.R | 1 R/SSMtrend.R | 7 R/checkModel.R | 2 R/importanceSSM.R | 2 R/ldl.R | 57 - R/logLik.SSModel.R | 12 R/simHelper.R | 18 R/simulateSSM.R | 158 +++-- R/transformSSM.R | 2 build/vignette.rds |binary data/GlobalTemp.rda |binary data/alcohol.rda |binary data/boat.rda |binary data/sexratio.rda |binary inst/doc/KFAS.R | 522 ++++++++-------- inst/doc/KFAS.Rnw | 1157 ++++++++++++++++++------------------- inst/doc/KFAS.pdf |binary man/KFAS.Rd | 1078 +++++++++++++++++----------------- man/KFS.Rd | 48 - man/coef.SSModel.Rd | 146 ++-- man/fitted.SSModel.Rd | 128 ++-- man/ldl.Rd | 64 +- man/mvInnovations.Rd | 44 - man/predict.SSModel.Rd | 204 +++--- man/residuals.KFS.Rd | 90 +- man/rstandard.KFS.Rd | 170 ++--- man/simulateSSM.Rd | 155 +++- man/transformSSM.Rd | 82 +- src/declarations.h | 1 src/filter1stepnovar.f95 | 158 ++--- src/init.c | 1 src/simgaussian.f95 | 14 src/simgaussianuncond.f95 |only tests/test-all.R | 4 tests/testthat/testGLM.R | 642 ++++++++++---------- tests/testthat/testImportanceSSM.R | 60 - tests/testthat/testSimulateSSM.R | 38 - vignettes/KFAS.Rnw | 1157 ++++++++++++++++++------------------- vignettes/KFAS.bib | 62 + 44 files changed, 3285 insertions(+), 3184 deletions(-)
Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to
approximate maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct many
simulations, but works best when the data is approximately Poisson distributed.
It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using
the 'coala' package.
Author: Paul Staab [aut, cre],
Lisha Mathew [aut],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between jaatha versions 3.1.0 dated 2016-01-27 and 3.1.1 dated 2016-02-05
DESCRIPTION | 7 ++-- MD5 | 48 +++++++++++++++++----------------- NAMESPACE | 11 ------- NEWS.md | 14 +++++++++ R/block.R | 3 -- R/boot_jaatha.R | 8 ++--- R/coala_interface.R | 8 ++--- R/fit_glm.R | 39 ++++----------------------- R/initialization.R | 22 +++++++-------- R/jaatha.R | 8 ++--- R/jaatha_data.R | 3 -- R/jaatha_log.R | 3 -- R/jaatha_model.R | 6 +--- R/likelihood.R | 31 ++++++++++++--------- R/par_ranges.R | 3 -- R/simulation_cache.R | 3 -- R/stat_basic.R | 3 -- R/stat_cube.R | 3 -- README.md | 9 ++++++ inst/doc/jaatha-evolution.html | 2 - inst/doc/jaatha-intro.html | 48 ---------------------------------- tests/testthat/test-fit-glm.R | 27 ------------------- tests/testthat/test-jaatha-function.R | 19 ++++++++++++- tests/testthat/test-jaatha-log.R | 26 ++++++++++++++++++ tests/testthat/test-likelihood.R | 10 ------- 25 files changed, 153 insertions(+), 211 deletions(-)
Title: Hybrid Bayesian Networks Using R and JAGS
Description: Facilities for easy implementation of hybrid Bayesian networks
using R. Bayesian networks are directed acyclic graphs representing joint
probability distributions, where each node represents a random variable and
each edge represents conditionality. The full joint distribution is
therefore factorized as a product of conditional densities, where each node
is assumed to be independent of its non-descendents given information on its
parent nodes. Since exact, closed-form algorithms are computationally
burdensome for inference within hybrid networks that contain a combination
of continuous and discrete nodes, particle-based approximation techniques
like Markov Chain Monte Carlo are popular. We provide a user-friendly
interface to constructing these networks and running inference using the 'rjags' package.
Econometric analyses (maximum expected utility under competing policies,
value of information) involving decision and utility nodes are also
supported.
Author: Jarrod E. Dalton <daltonj@ccf.org> and Benjamin Nutter <benjamin.nutter@gmail.com>
Maintainer: Benjamin Nutter <benjamin.nutter@gmail.com>
Diff between HydeNet versions 0.10.0 dated 2015-10-11 and 0.10.3 dated 2016-02-05
DESCRIPTION | 12 - MD5 | 80 +++++---- NAMESPACE | 3 NEWS | 17 +- R/HydeNetwork.R | 18 ++ R/HydeUtilities.R | 31 ++- R/PolicyMatrix.R | 34 +++- R/compileDecisionModel.R | 17 -- R/data.R | 23 ++ R/factorFormula.R |only R/modelToNode.R | 7 R/plot.HydeNetwork.R | 9 - R/plot_nondeterm_only.R |only R/setDecisionNodes.R | 2 R/setNode.R | 40 ++++ R/setPolicyValues.R |only R/summary.HydeNetwork.R |only R/update.HydeNetwork.R | 2 R/writeJagsFormula.R | 24 +- R/writeJagsModel.R | 2 R/zzz.R | 2 build/vignette.rds |binary data/BlackJack.RData |binary data/Resolution.cpt.RData |only data/SE.cpt.RData |only data/inputCPTExample.RData |only inst/doc/DecisionNetworks.R | 12 - inst/doc/DecisionNetworks.Rmd | 12 - inst/doc/DecisionNetworks.html | 188 ++++++++++++----------- inst/doc/GettingStartedWithHydeNet.html | 75 +++++---- inst/doc/HydeNetPlots.html | 10 - inst/doc/WorkingWithHydeNetObjects.html | 37 ++-- man/HydeNetSummaries.Rd |only man/HydeUtilities.Rd | 3 man/Resolution.cpt.Rd |only man/SE.cpt.Rd |only man/factorFormula.Rd |only man/inputCPTExample.Rd |only man/plot.HydeNetwork.Rd | 9 - man/policyMatrix.Rd | 12 + man/setNode.Rd | 39 ++++ man/setPolicyValues.Rd |only tests/testthat/test-HydeNetwork.R | 5 tests/testthat/test-factorFormula.R |only tests/testthat/test-plot.HydeNetwork.R | 7 vignettes/DecisionNetworks.Rmd | 12 - vignettes/vignette_images/DecisionNetworks2.jpeg |binary vignettes/vignette_images/HydeNetPlots2.jpeg |binary 48 files changed, 491 insertions(+), 253 deletions(-)
Title: Simple, Multiple and Joint Correspondence Analysis
Description: Computation and visualization of simple, multiple and joint correspondence analysis.
Author: Michael Greenacre [aut], Oleg Nenadic [aut, cre], Michael Friendly [ctb]
Maintainer: Oleg Nenadic <onenadi@uni-goettingen.de>
Diff between ca versions 0.58 dated 2014-12-31 and 0.64 dated 2016-02-05
DESCRIPTION | 16 MD5 | 58 +-- NAMESPACE | 41 +- NEWS | 32 + R/ca.r | 234 +++++--------- R/caconv.r |only R/cacoord.r |only R/expand.dft.R | 45 +- R/iterate.mjca.r | 28 - R/mjca.r | 809 +++++++++++++++++++++++-------------------------- R/multilines.R |only R/pchlist.r | 11 R/plot.ca.r | 278 +++++++--------- R/plot.mjca.r | 372 +++++++++------------- R/plot3d.ca.r | 276 +++++++--------- R/print.ca.r | 56 --- R/print.mjca.r | 48 -- R/print.summary.ca.r | 120 ++----- R/print.summary.mjca.r | 111 ++---- R/subinr.r | 4 R/summary.ca.r | 197 +++-------- R/summary.mjca.r | 154 +++------ data/author.rda |binary data/smoke.rda |binary data/wg93.rda |binary man/ca.rd | 23 + man/caconv.rd |only man/cacoord.rd |only man/mjca.rd | 102 ++++-- man/multilines.Rd |only man/plot.ca.rd | 12 man/plot.mjca.rd | 23 + man/plot3d.ca.rd | 9 33 files changed, 1364 insertions(+), 1695 deletions(-)