Title: Estimating the Proportion of True Null Hypotheses for FDR
Description: Methods for estimating the proportion of true null hypotheses, i.e., the pi0, when a very large number of hypotheses are simultaneously tested, especially for the purpose of (local) false discovery rate control for microarray data. It also contains functions to estimate the distribution of noncentrality parameters from a large number of parametric tests.
Author: Long Qu [aut, cre, ctb],
Kun Liang [ctb],
Yudi Pawitan [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Alexander Ploner [aut] (The author(s) of OCplus::tMixture, which was
modified slightly leading to discTMix in this package.),
Egil Ferkingstad [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Mette Langaas [aut] (The author(s) of limma::convest, which was
modified slightly leading to convest in this package.),
Marcus Davy [aut] (The author(s) of limma::convest, which was modified
slightly leading to convest in this package.)
Maintainer: Long Qu <long.qu@wright.edu>
Diff between pi0 versions 1.3-250 dated 2012-09-06 and 1.4-0 dated 2015-07-06
pi0-1.3-250/pi0/R/loadOrInstall.R |only pi0-1.3-250/pi0/ToDoList.txt |only pi0-1.3-250/pi0/man/loadOrInstall.Rd |only pi0-1.4-0/pi0/DESCRIPTION | 49 +- pi0-1.4-0/pi0/MD5 | 144 +++--- pi0-1.4-0/pi0/NAMESPACE | 362 ++++++++-------- pi0-1.4-0/pi0/R/ToDoList.R |only pi0-1.4-0/pi0/R/cond.cdf.R | 39 + pi0-1.4-0/pi0/R/discTMix.R | 347 +++++++-------- pi0-1.4-0/pi0/R/dncp.R | 20 pi0-1.4-0/pi0/R/dtn.mix.R | 62 -- pi0-1.4-0/pi0/R/extrp.pi0.known.gam2.R | 4 pi0-1.4-0/pi0/R/extrp.pi0.master.R | 2 pi0-1.4-0/pi0/R/extrp.pi0.unknown.gam2.R | 4 pi0-1.4-0/pi0/R/fdr.R | 24 - pi0-1.4-0/pi0/R/histf1.R | 170 +++---- pi0-1.4-0/pi0/R/hypergeometric1F1.R |only pi0-1.4-0/pi0/R/int.nct.R | 10 pi0-1.4-0/pi0/R/lfdr.R | 13 pi0-1.4-0/pi0/R/matrix.t.test.R | 64 +- pi0-1.4-0/pi0/R/ncpest.R | 33 - pi0-1.4-0/pi0/R/ncpest.iter.R | 2 pi0-1.4-0/pi0/R/nparncp.R | 86 ++- pi0-1.4-0/pi0/R/nparncpF.R | 687 ++++++++++++++++--------------- pi0-1.4-0/pi0/R/parncp.R | 14 pi0-1.4-0/pi0/R/parncp2.R |only pi0-1.4-0/pi0/R/parncpF.R | 79 ++- pi0-1.4-0/pi0/R/pavaf1.R | 2 pi0-1.4-0/pi0/R/plot.extrpi0.R | 2 pi0-1.4-0/pi0/R/plot.subex.R | 66 +- pi0-1.4-0/pi0/R/plot.subt.R | 4 pi0-1.4-0/pi0/R/print.extrpi0.R | 36 - pi0-1.4-0/pi0/R/print.subex.R | 22 pi0-1.4-0/pi0/R/print.subt.R | 28 - pi0-1.4-0/pi0/R/sparncp.R | 53 +- pi0-1.4-0/pi0/R/sparncpF.R | 20 pi0-1.4-0/pi0/R/subt.R | 156 +++---- pi0-1.4-0/pi0/R/summary.extrpi0.R | 6 pi0-1.4-0/pi0/R/summary.subex.R | 6 pi0-1.4-0/pi0/R/summary.subt.R | 6 pi0-1.4-0/pi0/R/znormix.R | 3 pi0-1.4-0/pi0/man/CBUM.Rd | 6 pi0-1.4-0/pi0/man/coef.ncpest.Rd | 128 ++--- pi0-1.4-0/pi0/man/combn2R.Rd | 3 pi0-1.4-0/pi0/man/cond.cdf.Rd | 4 pi0-1.4-0/pi0/man/convest.Rd | 3 pi0-1.4-0/pi0/man/discTMix.Rd | 180 ++++---- pi0-1.4-0/pi0/man/dncp.Rd | 6 pi0-1.4-0/pi0/man/dt.int2.Rd | 126 ++--- pi0-1.4-0/pi0/man/dt.lap.Rd | 134 +++--- pi0-1.4-0/pi0/man/dtn.mix.Rd | 143 +++--- pi0-1.4-0/pi0/man/fdr.Rd | 2 pi0-1.4-0/pi0/man/fitted.discTMix.Rd | 106 ++-- pi0-1.4-0/pi0/man/fitted.nparncp.Rd | 132 +++-- pi0-1.4-0/pi0/man/grid.search.Rd | 164 +++---- pi0-1.4-0/pi0/man/histf1.Rd | 8 pi0-1.4-0/pi0/man/lfdr.Rd | 164 +++---- pi0-1.4-0/pi0/man/logLik.ncpest.Rd | 106 ++-- pi0-1.4-0/pi0/man/mTruncNorm.Rd | 162 +++---- pi0-1.4-0/pi0/man/mdt.Rd | 2 pi0-1.4-0/pi0/man/ncpest.Rd | 4 pi0-1.4-0/pi0/man/ncpest.iter.Rd | 4 pi0-1.4-0/pi0/man/nparncp.Rd | 242 +++++----- pi0-1.4-0/pi0/man/parncp.Rd | 213 ++++----- pi0-1.4-0/pi0/man/pi0-package.Rd | 14 pi0-1.4-0/pi0/man/plot.nparncp.Rd | 120 ++--- pi0-1.4-0/pi0/man/plot.parncp.Rd | 120 ++--- pi0-1.4-0/pi0/man/plot.sparncp.Rd | 2 pi0-1.4-0/pi0/man/pt.sad.Rd | 133 +++--- pi0-1.4-0/pi0/man/sparncp.Rd | 3 pi0-1.4-0/pi0/man/subt.Rd | 184 ++++---- pi0-1.4-0/pi0/man/summary.nparncp.Rd | 112 ++--- pi0-1.4-0/pi0/man/summary.parncp.Rd | 114 ++--- pi0-1.4-0/pi0/man/summary.sparncp.Rd | 2 pi0-1.4-0/pi0/man/vcov.ncpest.Rd | 104 ++-- pi0-1.4-0/pi0/man/znormix.Rd | 6 76 files changed, 2876 insertions(+), 2705 deletions(-)
Title: A Package to Test for Pleiotropic Effects
Description: Performs genetic association tests between SNPs
(one-at-a-time) and multiple phenotypes (separately or in joint
model).
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart
and Federico Calboli
Maintainer: Federico Calboli <federico.calboli@helsinki.fi>
Diff between MultiPhen versions 2.0.0 dated 2014-01-08 and 2.0.1 dated 2015-07-06
DESCRIPTION | 15 +++++++-------- MD5 | 10 +++++----- NAMESPACE | 10 +++++++--- build/vignette.rds |binary inst/doc/MultiPhen.pdf |binary man/MultiPhen-internal.Rd | 3 ++- 6 files changed, 21 insertions(+), 17 deletions(-)
Title: Relabelling MCMC Outputs of Mixture Models
Description: The Bayesian estimation of mixture models (and more general hidden Markov models) suffers from the label switching phenomenon, making the MCMC output non-identifiable. This package can be used in order to deal with this problem using various relabelling algorithms.
Author: Panagiotis Papastamoulis
Maintainer: Panagiotis Papastamoulis <papapast@yahoo.gr>
Diff between label.switching versions 1.3 dated 2014-11-05 and 1.4 dated 2015-07-06
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/relabelling_algorithms.R | 10 +++++++++- 3 files changed, 16 insertions(+), 8 deletions(-)
More information about label.switching at CRAN
Permanent link
Title: Synthesizing List of Differentially Expressed Features
Description: Performs two tests to evaluate if the
experiments are associated and returns a list of interesting
features common to all the experiments.
Author: Alberto Cassese, Marta Blangiardo
Maintainer: Alberto Cassese <alberto.cassese@maastrichtuniversity.nl>
Diff between sdef versions 1.5 dated 2010-03-11 and 1.6 dated 2015-07-06
DESCRIPTION | 15 ++++++++------- MD5 |only NAMESPACE |only man/Tmc.Rd | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining
Description: Exploratory data analysis methods such as principal component methods and clustering.
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson <francois.husson@agrocampus-ouest.fr>
Diff between FactoMineR versions 1.30 dated 2015-06-15 and 1.31.2 dated 2015-07-06
DESCRIPTION | 10 +++---- MD5 | 24 ++++++++--------- NAMESPACE | 3 ++ R/DMFA.R | 2 - R/MCA.R | 4 +- R/PCA.R | 2 - R/spMCA.R | 5 ++- data/children.rda |binary data/poison.rda |binary data/poison.text.rda |binary inst/doc/FactoMineR.pdf |binary inst/doc/clustering_and_pricipal_component_methods.pdf |binary man/DMFA.Rd | 2 - 13 files changed, 29 insertions(+), 23 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE)
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations (ODE), of
partial differential equations (PDE), of differential
algebraic equations (DAE), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions lsoda, lsodar, lsode, lsodes of the ODEPACK
collection, to the FORTRAN functions dvode and daspk and a
C-implementation of solvers of the Runge-Kutta family with
fixed or variable time steps. The package contains routines
designed for solving ODEs resulting from 1-D, 2-D and 3-D
partial differential equations (PDE) that have been converted
to ODEs by numerical differencing.
Author: Karline Soetaert [aut],
Thomas Petzoldt [aut, cre],
R. Woodrow Setzer [aut],
odepack authors [cph]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.11 dated 2014-10-29 and 1.12 dated 2015-07-06
DESCRIPTION | 13 +- MD5 | 47 ++++---- NAMESPACE | 4 NEWS | 6 + R/DLLfunc.R | 4 R/Utilities.R | 246 +++++++++------------------------------------- R/checkevents.R | 4 R/forcings.R | 8 - R/lsoda.R | 4 R/lsodar.R | 2 R/lsode.R | 2 R/lsodes.R | 7 - R/matplot.R |only R/vode.R | 4 build/vignette.rds |binary data/ccl4data.rda |binary inst/doc/compiledCode.pdf |binary inst/doc/deSolve.pdf |binary man/deSolve.Rd | 4 man/ode.1D.Rd | 2 man/ode.2D.Rd | 2 man/ode.3D.Rd | 2 man/ode.band.Rd | 2 man/plot.deSolve.Rd | 40 +++++-- src/call_lsoda.c | 3 25 files changed, 149 insertions(+), 257 deletions(-)
Title: Spatio-Temporal Generalised Linear Mixed Models for Areal Unit
Data
Description: Implements a class of spatio-temporal generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (McMC) simulation. The response variable can be binomial, Gaussian or Poisson. The spatio-temporal autocorrelation is modelled by random effects, which are assigned conditional autoregressive (CAR) prior distributions. A number of different random effects structures are available, and full details are given in the vignette accompanying this package and the references below. The creation of this package was supported by the Engineering and Physical Science Research Council (EPSRC) grant EP/J017442/1 and the Medical Research Council (MRC) grant MR/L022184/1.
Author: Duncan Lee and Alastair Rushworth
Maintainer: Duncan Lee <Duncan.Lee@glasgow.ac.uk>
Diff between CARBayesST versions 1.1 dated 2014-11-14 and 2.0 dated 2015-07-06
CARBayesST-1.1/CARBayesST/R/ST.ARCAR.R |only CARBayesST-1.1/CARBayesST/R/ST.ARCARadaptive.R |only CARBayesST-1.1/CARBayesST/R/ST.ARCARcluster.R |only CARBayesST-1.1/CARBayesST/R/ST.KHinteraction.R |only CARBayesST-1.1/CARBayesST/R/ST.KHmain.R |only CARBayesST-1.1/CARBayesST/R/ST.cluster.R |only CARBayesST-1.1/CARBayesST/R/results.summarise.R |only CARBayesST-1.1/CARBayesST/man/ST.ARCAR.Rd |only CARBayesST-1.1/CARBayesST/man/ST.ARCARadaptive.Rd |only CARBayesST-1.1/CARBayesST/man/ST.ARCARcluster.Rd |only CARBayesST-1.1/CARBayesST/man/ST.KHinteraction.Rd |only CARBayesST-1.1/CARBayesST/man/ST.KHmain.Rd |only CARBayesST-1.1/CARBayesST/man/ST.cluster.Rd |only CARBayesST-1.1/CARBayesST/man/results.summarise.Rd |only CARBayesST-2.0/CARBayesST/DESCRIPTION | 17 CARBayesST-2.0/CARBayesST/MD5 | 60 CARBayesST-2.0/CARBayesST/NAMESPACE | 20 CARBayesST-2.0/CARBayesST/R/RcppExports.R | 95 - CARBayesST-2.0/CARBayesST/R/ST.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/ST.CARanova.R |only CARBayesST-2.0/CARBayesST/R/ST.CARar.R |only CARBayesST-2.0/CARBayesST/R/ST.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/ST.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARanova.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARar.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/binomial.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARanova.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARar.R |only CARBayesST-2.0/CARBayesST/R/gaussian.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARadaptive.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARanova.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARar.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARlinear.R |only CARBayesST-2.0/CARBayesST/R/poisson.CARlocalised.R |only CARBayesST-2.0/CARBayesST/R/print.carbayesST.R | 22 CARBayesST-2.0/CARBayesST/build |only CARBayesST-2.0/CARBayesST/inst |only CARBayesST-2.0/CARBayesST/man/CARBayesST-package.Rd | 80 CARBayesST-2.0/CARBayesST/man/ST.CARadaptive.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARanova.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARar.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARlinear.Rd |only CARBayesST-2.0/CARBayesST/man/ST.CARlocalised.Rd |only CARBayesST-2.0/CARBayesST/man/print.carbayesST.Rd | 7 CARBayesST-2.0/CARBayesST/src/CARBayesST.cpp | 1822 +++++++++++++++----- CARBayesST-2.0/CARBayesST/src/RcppExports.cpp | 699 +++++-- CARBayesST-2.0/CARBayesST/vignettes |only 50 files changed, 2074 insertions(+), 748 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-08-26 0.7
Title: Statistical Analysis of Mixed Ploidy Populations
Description: Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation
Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single
ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values
around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to
utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects
allowing integration with other packages such adegenet.
Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. doi:10.1111/1755-0998.12129 for the appropriate citation and user manual. Thank you in advance.
Author: LW Pembleton
Maintainer: LW Pembleton <luke.pembleton@ecodev.vic.gov.au>
Diff between StAMPP versions 1.3 dated 2014-09-01 and 1.4 dated 2015-07-06
ChangeLog | 9 ++++++++- DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ R/stampp2genlight.R | 4 ++-- R/stamppAmova.R | 2 +- R/stamppConvert.R | 9 +++++---- R/stamppFst.R | 2 +- R/stamppGmatrix.R | 2 +- R/stamppNeisD.R | 2 +- R/stamppPhylip.R | 4 ++-- man/StAMPP-package.Rd | 8 ++++---- 12 files changed, 45 insertions(+), 35 deletions(-)
Title: Hidden Markov Models
Description: Contains functions for the analysis of Discrete Time Hidden Markov Models, Markov Modulated GLMs and the Markov Modulated Poisson Process. It includes functions for simulation, parameter estimation, and the Viterbi algorithm. See the topic "HiddenMarkov" for an introduction to the package, and "Change Log" for a list of recent changes. The algorithms are based of those of Walter Zucchini.
Author: David Harte
Maintainer: David Harte <d.harte@gns.cri.nz>
Diff between HiddenMarkov versions 1.8-3 dated 2015-04-12 and 1.8-4 dated 2015-07-06
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 6 +++++- NEWS | 2 +- man/Changes.Rd | 4 +++- man/HiddenMarkov.Rd | 8 +++++--- 6 files changed, 23 insertions(+), 15 deletions(-)