Title: MCMC Sampling of Bayesian Linear Models via Summary Statistics
Description: Methods for generating Markov Chain Monte Carlo (MCMC) posterior samples of Bayesian linear regression model parameters that require only summary statistics of data as input. Summary statistics are useful for systems with very limited amounts of physical memory. The package provides two functions: one function that computes summary statistics of data and one function that carries out the MCMC posterior sampling for Bayesian linear regression models where summary statistics are used as input. The function read.regress.data.ff utilizes the R package 'ff' to handle data sets that are too large to fit into a user's physical memory, by reading in data in chunks.
Author: Evgeny Savel'ev, Alexey Miroshnikov, Erin Conlon
Maintainer: Evgeny Savel'ev
Diff between BayesSummaryStatLM versions 1.0 dated 2015-02-25 and 1.0-1 dated 2015-03-02
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- man/bayes.regress.Rd | 38 ++++++++++++++++++++++---------------- 3 files changed, 28 insertions(+), 22 deletions(-)
More information about BayesSummaryStatLM at CRAN
Permanent link
Title: Themes for Shiny
Description: Themes for use with Shiny. Includes several Bootstrap themes
from http://bootswatch.com/, which are packaged for use with Shiny
applications.
Author: Winston Chang [aut, cre],
RStudio [cph],
Thomas Park [ctb, cph] (Bootswatch themes),
Lukasz Dziedzic [ctb, cph] (Lato font),
Nathan Willis [ctb, cph] (News Cycle font),
Google Corporation [ctb, cph] (Open Sans font),
Matt McInerney [ctb, cph] (Raleway font),
Adobe Systems Incorporated [ctb, cph] (Source Sans Pro font),
Canonical Ltd [ctb, cph] (Ubuntu font)
Maintainer: Winston Chang
Diff between shinythemes versions 1.0 dated 2015-01-20 and 1.0.1 dated 2015-03-02
shinythemes-1.0.1/shinythemes/DESCRIPTION | 6 +- shinythemes-1.0.1/shinythemes/MD5 | 23 ++++++---- shinythemes-1.0.1/shinythemes/NEWS |only shinythemes-1.0.1/shinythemes/R/shinytheme.R | 6 +- shinythemes-1.0.1/shinythemes/inst/shinythemes/css |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.eot |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.svg |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.ttf |only shinythemes-1.0.1/shinythemes/inst/shinythemes/fonts/glyphicons-halflings-regular.woff |only shinythemes-1.0/shinythemes/inst/shinythemes/cerulean.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/cosmo.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/flatly.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/journal.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/readable.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/spacelab.min.css |only shinythemes-1.0/shinythemes/inst/shinythemes/united.min.css |only 16 files changed, 20 insertions(+), 15 deletions(-)
Title: Determining the Best Number of Clusters in a Data Set
Description: It provides 30 indexes for determining the optimal number of clusters in a data set and offers the best clustering scheme from different results to the user.
Author: Malika Charrad and Nadia Ghazzali and Veronique Boiteau and Azam Niknafs
Maintainer: Malika Charrad
Diff between NbClust versions 2.0.3 dated 2014-10-15 and 2.0.4 dated 2015-03-02
DESCRIPTION | 19 +++++----- MD5 | 6 +-- R/NbClust.R | 99 +++++++++++++++++++++++++++++---------------------------- man/NbClust.Rd | 54 ++----------------------------- 4 files changed, 68 insertions(+), 110 deletions(-)
Title: Causal Mediation Analysis
Description: We implement parametric and non parametric mediation analysis. This package performs the methods and suggestions in Imai, Keele and Yamamoto (2010), Imai, Keele and Tingley (2010), Imai, Tingley and Yamamoto (2013), Imai and Yamamoto (2013) and Yamamoto (2013). In addition to the estimation of causal mediation effects, the software also allows researchers to conduct sensitivity analysis for certain parametric models.
Author: Dustin Tingley
Maintainer: Teppei Yamamoto
Diff between mediation versions 4.4.3 dated 2014-11-23 and 4.4.4 dated 2015-03-02
ChangeLog | 4 DESCRIPTION | 10 - MD5 | 20 +- R/mediate.R | 7 R/multimed.R | 331 +++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/mediation-old.pdf |binary inst/doc/mediation.pdf |binary man/multimed.Rd | 19 +- man/plot.multimed.Rd | 8 - man/summary.multimed.Rd | 6 11 files changed, 297 insertions(+), 108 deletions(-)
Title: Linear Group Fixed Effects
Description: Transforms away factors with many levels prior to doing an OLS.
Useful for estimating linear models with multiple group fixed effects, and for
estimating linear models which uses factors as pure control variables.
Includes support for instrumental variables, conditional F statistics for weak instruments,
robust and multi-way clustered standard errors, as well as limited mobility bias correction.
Author: Simen Gaure, Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
Diff between lfe versions 2.0-1570 dated 2015-02-10 and 2.1-1620 dated 2015-03-02
DESCRIPTION | 10 - MD5 | 76 +++++------ R/bccorr.R | 4 R/condfstat.R | 109 +++++++++++++++- R/felm.R | 264 +++++++++++++++++++++++++-------------- R/generics.R | 146 ++++++++++++++------- R/getfe.R | 2 R/startup.R | 2 R/utils.R | 86 ++++++++++++ exec/lfescript | 21 ++- inst/doc/CHANGELOG | 4 inst/doc/identification.pdf |binary inst/doc/lfeguide.txt | 34 ++++- inst/doc/lfehow.pdf |binary inst/doc/speed.pdf |binary man/condfstat.Rd | 48 +++++-- man/lfe-package.Rd | 4 src/demean.c | 31 ++-- src/kaczmarz.c | 13 + src/lfe.c | 1 src/lfe.h | 3 tests/anomalies.R | 12 + tests/anomalies.Rout.save | 296 +++++++++++++++++++++++++++++++++++++++----- tests/bctest.Rout.save | 4 tests/cluster.Rout.save | 25 ++- tests/comparelm.Rout.save | 11 - tests/degenerate.Rout.save | 11 - tests/efcheck.Rout.save | 4 tests/fourfac.Rout.save | 4 tests/interact.Rout.save | 25 ++- tests/ivtest.R | 2 tests/ivtest.Rout.save | 44 ++++-- tests/lfetest.Rout.save | 4 tests/mlhs.Rout.save | 51 ++++--- tests/multiway.Rout.save | 11 - tests/naomit.Rout.save | 11 - tests/nonest.Rout.save | 4 tests/onefac.Rout.save | 4 tests/verify.Rout.save | 11 - 39 files changed, 1031 insertions(+), 361 deletions(-)
Title: Joint Analysis of Genotype and Group-Specific Variability Using
a Novel Score Test Approach to Map eQTL
Description: Implements a novel score test that measures 1) the overall shift in the gene expression due to genotype (additive genetic effect), and 2) group-specific changes in gene expression due to genotype (interaction effect) in a mixed-effects model framework.
Author: Chaitanya R. Acharya and Andrew S. Allen
Maintainer: Chaitanya Acharya
Diff between JAGUAR versions 1.1 dated 2014-09-07 and 2.0 dated 2015-03-02
JAGUAR-1.1/JAGUAR/man/ComputeLinMax.Rd |only JAGUAR-1.1/JAGUAR/man/getMAX.Rd |only JAGUAR-1.1/JAGUAR/man/mc_scoreTest.Rd |only JAGUAR-1.1/JAGUAR/man/sim.Rd |only JAGUAR-1.1/JAGUAR/src/calc_lin_threshold.cpp |only JAGUAR-1.1/JAGUAR/src/jag_simulations.cpp |only JAGUAR-1.1/JAGUAR/src/scoreTest.cpp |only JAGUAR-2.0/JAGUAR/DESCRIPTION | 12 - JAGUAR-2.0/JAGUAR/MD5 | 43 ++-- JAGUAR-2.0/JAGUAR/R/JAGUAR.R | 231 ++++++++++++++++++-------- JAGUAR-2.0/JAGUAR/R/RcppExports.R | 24 +- JAGUAR-2.0/JAGUAR/README.md | 2 JAGUAR-2.0/JAGUAR/man/GENEapply.Rd | 9 - JAGUAR-2.0/JAGUAR/man/JAGUAR-package.Rd | 16 - JAGUAR-2.0/JAGUAR/man/ProcessJaguarResults.Rd | 12 - JAGUAR-2.0/JAGUAR/man/RowMin.Rd |only JAGUAR-2.0/JAGUAR/man/RowSums.Rd |only JAGUAR-2.0/JAGUAR/man/SliceGeneData.Rd | 10 - JAGUAR-2.0/JAGUAR/man/calcThreshold.Rd | 23 +- JAGUAR-2.0/JAGUAR/man/gamma_test.Rd |only JAGUAR-2.0/JAGUAR/man/getMinP.Rd |only JAGUAR-2.0/JAGUAR/man/jag_param.Rd |only JAGUAR-2.0/JAGUAR/man/jaguar.Rd | 21 -- JAGUAR-2.0/JAGUAR/man/jaguarSIM.Rd | 12 - JAGUAR-2.0/JAGUAR/man/lin.Rd |only JAGUAR-2.0/JAGUAR/man/plotqtl.Rd |only JAGUAR-2.0/JAGUAR/man/scoreTest.Rd | 12 - JAGUAR-2.0/JAGUAR/man/snpOUT.Rd | 10 - JAGUAR-2.0/JAGUAR/src/RcppExports.cpp | 103 +++++++---- JAGUAR-2.0/JAGUAR/src/jaguar.cpp |only 30 files changed, 319 insertions(+), 221 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management.
Author: Oswaldo Santos [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos
Diff between capm versions 0.5 dated 2014-05-27 and 0.6.0 dated 2015-03-02
DESCRIPTION | 12 +- MD5 | 72 ++++++++-------- NAMESPACE | 2 NEWS | 30 ++++++ R/Calculate2StageSampleSize.R | 7 - R/GraphicInterface.R | 5 - R/PlotPopPyramid.R | 25 +++-- R/SampleSystematic.R | 4 R/capm-package.R | 6 - README.md | 14 +-- inst/shinyApps/CalculateSampleSize/server.R | 4 inst/shinyApps/CalculateSampleSize/ui.R | 12 +- inst/shinyApps/SelectSamplingUnits/server.R | 18 ++-- inst/shinyApps/SelectSamplingUnits/ui.R | 17 ++- inst/shinyApps/SurveyAnalysis/server.R | 23 ++--- inst/shinyApps/SurveyAnalysis/ui.R | 3 man/Calculate2StageSampleSize.Rd | 52 ++++------- man/CalculateGlobalSens.Rd | 51 +++-------- man/CalculateLocalSens.Rd | 37 ++------ man/CalculatePopChange.Rd | 31 ++----- man/CalculateSimpleSampleSize.Rd | 24 +---- man/CalculateStratifiedSampleSize.Rd | 31 +------ man/DesignSurvey.Rd | 73 ++++------------ man/GraphicInterface.Rd | 16 --- man/MapkmlPSU.Rd | 27 ++---- man/PlotGlobalSens.Rd | 27 ++---- man/PlotLocalSens.Rd | 37 ++------ man/PlotModels.Rd | 122 ++++++++++------------------ man/PlotPopPyramid.Rd | 94 ++++++--------------- man/SamplePPS.Rd | 30 ++---- man/SampleSystematic.Rd | 60 +++---------- man/SetRanges.Rd | 27 +----- man/SolveIASA.Rd | 106 ++++++------------------ man/SolveSI.Rd | 68 ++++----------- man/SolveTC.Rd | 61 +++----------- man/SummarySurvey.Rd | 25 ++--- man/capm-package.Rd | 31 +++---- 37 files changed, 471 insertions(+), 813 deletions(-)
Title: STRUctural Modeling of Latent Variables for General Pedigree
Description: Implements a broad class of latent variable and structural equation models for general pedigree data.
Author: Nathan Morris [aut, cre],
Yeunjoo Song [aut],
Stephen Cahn [ctb]
Maintainer: Nathan Morris
Diff between strum versions 0.5.1 dated 2015-02-02 and 0.6 dated 2015-03-02
ChangeLog | 13 ++ DESCRIPTION | 10 +- MD5 | 18 ++-- R/03strumFittedModel.R | 8 + R/estimateParameter.R | 4 R/fitModel.R | 186 ++++++++++++++++++++++++++++++++---------- inst/doc/strum-example.pdf |binary inst/doc/strum-intro.pdf |binary man/strum-package.Rd | 4 man/strumFittedModel-class.Rd | 1 10 files changed, 183 insertions(+), 61 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-06 1.0.2
Title: Nonparametric Estimation for Multistate Models
Description: Nonparametric estimation for right censored, left truncated time to event data in multistate models.
Author: Nicole Ferguson
Maintainer: Guy Brock
Diff between msSurv versions 1.1-2 dated 2012-09-18 and 1.2-1 dated 2015-03-02
ChangeLog | 32 DESCRIPTION | 21 MD5 | 36 NAMESPACE | 2 R/msSurv-Classes.R | 8 R/msSurv-Methods.R | 382 ++++--- R/msSurv-internal.R | 559 ++++++++--- R/msSurv-user.R | 195 +-- build |only inst/doc/msSurv.R |only inst/doc/msSurv.Rnw | 493 +++++++-- inst/doc/msSurv.pdf |binary man/EntryExit.rd | 4 man/LTRCdata.Rd | 33 man/RCdata.Rd | 22 vignettes/msSurv-EntryExitDepExStateModel.pdf |only vignettes/msSurv-NormEntryDepExPlot.pdf |only vignettes/msSurv-NormExitDepExPlot.pdf |only vignettes/msSurv-StateDependentCensoringIllnessDeathPlot.pdf |only vignettes/msSurv-entryplot1.pdf |only vignettes/msSurv-ex3plot.pdf |only vignettes/msSurv-ex3transplot.pdf |only vignettes/msSurv-exitplot1.pdf |only vignettes/msSurv.Rnw | 493 +++++++-- 24 files changed, 1624 insertions(+), 656 deletions(-)
Title: Sampling Methods and Distribution Functions for the Ising Model
Description: Sample states from the Ising model and compute the probability of states. Sampling can be done for any number of nodes, but due to the intractibility of the Ising model the distribution can only be computed up to ~10 nodes.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp
Diff between IsingSampler versions 0.1.1 dated 2014-01-09 and 0.2 dated 2015-03-02
DESCRIPTION | 16 - MD5 | 38 ++- NAMESPACE | 25 +- NEWS |only R/Distribution.R | 88 ++++---- R/EstimateIsing.R |only R/IsingSampler.R | 118 +++++------ R/LinTransform.R | 44 ++-- R/PseudoLikelihood.R |only R/RcppExports.R | 70 ++++-- R/logisticRegressionEstimation.R |only R/positiveGraph.R |only man/EstimateIsing.Rd |only man/IsingLikelihood.Rd | 62 ++--- man/IsingPL.Rd |only man/IsingSampler-package.Rd | 168 +++++++-------- man/IsingSampler.Rd | 125 +++++------ man/IsingStateProb.Rd | 68 +++--- man/IsingSumLikelihood.Rd | 62 ++--- man/LinTransform.Rd | 132 ++++++------ src/IsingCpp_CFTP.cpp | 410 +++++++++++++++++++++++++++------------ src/Makevars.win | 6 src/PseudoLikelihood.cpp |only src/RcppExports.cpp | 93 +++++++- 24 files changed, 906 insertions(+), 619 deletions(-)
Title: Power Calculations and Bayesian Analysis of Count Distributions
and FECRT Data using MCMC
Description: A set of functions to allow analysis of count data (such
as faecal egg count data) using Bayesian MCMC methods. Returns
information on the possible values for mean count, coefficient
of variation and zero inflation (true prevalence) present in
the data. A complete faecal egg count reduction test (FECRT)
model is implemented, which returns inference on the true
efficacy of the drug from the pre- and post-treatment data
provided, using non-parametric bootstrapping as well as using
Bayesian MCMC. Functions to perform power analyses for faecal
egg counts (including FECRT) are also provided.
Author: Matthew Denwood
Maintainer: Matthew Denwood
Diff between bayescount versions 0.9.9-2 dated 2014-06-22 and 0.9.99-4 dated 2015-03-02
bayescount-0.9.9-2/bayescount/R/fecrt.R |only bayescount-0.9.9-2/bayescount/R/zzz.R |only bayescount-0.9.9-2/bayescount/inst/version_history.txt |only bayescount-0.9.9-2/bayescount/man/fecrt.Rd |only bayescount-0.9.99-4/bayescount/CHANGELOG |only bayescount-0.9.99-4/bayescount/DESCRIPTION | 24 +- bayescount-0.9.99-4/bayescount/MD5 | 55 +++--- bayescount-0.9.99-4/bayescount/NAMESPACE | 60 ++++++- bayescount-0.9.99-4/bayescount/R/bayescount.R | 11 - bayescount-0.9.99-4/bayescount/R/bayescount.single.R | 108 +++++-------- bayescount-0.9.99-4/bayescount/R/fec.power.R | 4 bayescount-0.9.99-4/bayescount/R/fecrt.analysis.R |only bayescount-0.9.99-4/bayescount/R/fecrt.model.R |only bayescount-0.9.99-4/bayescount/R/fecrt.power.R | 2 bayescount-0.9.99-4/bayescount/R/invisible.R | 11 - bayescount-0.9.99-4/bayescount/R/likelihood.R | 12 + bayescount-0.9.99-4/bayescount/R/maximise.likelihood.R | 34 ++-- bayescount-0.9.99-4/bayescount/R/run.model.R | 16 + bayescount-0.9.99-4/bayescount/inst/CITATION | 5 bayescount-0.9.99-4/bayescount/man/bayescount.Rd | 24 -- bayescount-0.9.99-4/bayescount/man/bayescount.single.Rd | 116 ++++++++++---- bayescount-0.9.99-4/bayescount/man/fec.power.Rd | 11 - bayescount-0.9.99-4/bayescount/man/fec.power.limits.Rd | 15 - bayescount-0.9.99-4/bayescount/man/fecrt.analysis.Rd |only bayescount-0.9.99-4/bayescount/man/fecrt.model.Rd |only bayescount-0.9.99-4/bayescount/man/fecrt.power.Rd | 4 bayescount-0.9.99-4/bayescount/man/fecrt.power.limits.Rd | 14 - bayescount-0.9.99-4/bayescount/man/likelihood.Rd | 13 - bayescount-0.9.99-4/bayescount/man/lnormal.params.Rd | 2 bayescount-0.9.99-4/bayescount/man/maximise.likelihood.Rd | 9 - bayescount-0.9.99-4/bayescount/man/normal.params.Rd | 2 bayescount-0.9.99-4/bayescount/man/run.model.Rd | 39 ++-- bayescount-0.9.99-4/bayescount/src/power.c | 48 +++-- 33 files changed, 380 insertions(+), 259 deletions(-)
Title: Predict Protein-Protein Interactions Based on Functional and
Topological Similarities
Description: Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions are derived from R package GOSemSim authored by Guangchuang Yu.
Author: Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Maintainer: Yue Deng
Diff between ppiPre versions 1.6 dated 2015-01-29 and 1.7 dated 2015-03-02
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NAMESPACE | 1 - R/GOKEGGSims.r | 2 +- man/ppiPre-package.Rd | 11 +++++------ 5 files changed, 18 insertions(+), 20 deletions(-)
Title: Robust Periodogram and Periodicity Detection Methods
Description: Calculates periodograms based on (robustly) fitting periodic functions to light curves (irregularly observed time series, possibly with measurement accuracies, occurring in astroparticle physics). Three main functions are included: RobPer calculates the periodogram. Outlying periodogram bars (indicating a period) can be detected with betaCvMfit. Artificial light curves can be generated using the function tsgen. For more details see Thieler, Fried and Rathjens (2013).
Author: Anita M. Thieler, Jonathan Rathjens and Roland Fried, with contributions from Brenton R. Clarke, Uwe Ligges, Matias Salibian-Barrera, Gert Willems and Victor Yohai
Maintainer: Jonathan Rathjens
Diff between RobPer versions 1.2 dated 2014-10-03 and 1.2.1 dated 2015-03-02
RobPer-1.2.1/RobPer/DESCRIPTION | 13 ++--- RobPer-1.2.1/RobPer/MD5 | 24 ++++------ RobPer-1.2.1/RobPer/build/vignette.rds |binary RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.Rnw | 51 ++++++++++------------ RobPer-1.2.1/RobPer/inst/doc/RobPer_Vignette.pdf |binary RobPer-1.2.1/RobPer/man/RobPer-package.rd | 8 +-- RobPer-1.2.1/RobPer/vignettes/RobPer_Art.bib | 4 - RobPer-1.2.1/RobPer/vignettes/RobPer_Vignette.Rnw | 51 ++++++++++------------ RobPer-1.2.1/RobPer/vignettes/chart/IRWLS.tex | 2 RobPer-1.2.1/RobPer/vignettes/chart/RobPer.tex | 2 RobPer-1.2.1/RobPer/vignettes/chart/boxenecht.tex | 2 RobPer-1.2.1/RobPer/vignettes/chart/singleFun.tex | 2 RobPer-1.2/RobPer/inst/CITATION |only RobPer-1.2/RobPer/vignettes/chart/boxenzahlen.tex |only 14 files changed, 77 insertions(+), 82 deletions(-)
Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.5. [Lecture notes] School of Psychology, University of Adelaide, Adelaide, Australia. ISBN: 978-1-326-18972-3. URL: http://health.adelaide.edu.au/psychology/ccs/teaching/lsr/.
Author: Daniel Navarro
Maintainer: Daniel Navarro
Diff between lsr versions 0.3.2 dated 2014-01-31 and 0.5 dated 2015-03-02
DESCRIPTION | 13 +++++++------ MD5 | 14 +++++++------- NEWS | 6 ++++++ R/correlate.R | 20 ++++++++++++++++++-- R/maxFreq.R | 6 ++++-- R/modeOf.R | 8 +++++--- inst/CITATION | 13 +++++++------ man/lsr-package.Rd | 16 +++++++++------- 8 files changed, 63 insertions(+), 33 deletions(-)