Title: Robust estimation of the generalized log gamma model.
Diff between robustloggamma versions 0.4-22 dated 2013-04-30 and 0.4-28 dated 2013-12-19
More information about robustloggamma at CRAN
Description: Robust estimation of the generalized log gamma model is provided using Quantile Tau estimator and Weighted Likelihood estimator.
Author: Claudio Agostinelli
Maintainer: Claudio Agostinelli
DESCRIPTION | 17 +--
MD5 | 47 ++++----
NAMESPACE | 3
R/ACOV.R | 11 ++
R/Jacobinas.R | 11 ++
R/MLfunctions.R | 60 ++++++-----
R/Qtaufunctions.R | 11 +-
R/Regtau.f.R | 11 ++
R/ScoresAndDerivatives.R | 26 +++-
R/WLfunctions.R | 222 +++++++++++++++++++++++-----------------
R/loggammarob.R | 244 +++++++++++++++++++++++++++++++++++++--------
R/mle.gamma.R | 11 ++
R/rimtrf.R | 11 ++
R/to.double.R | 11 ++
R/two2logthree.R | 2
R/wilkstest.R | 38 +++++--
data/alcoa.rda |binary
data/drg2000.rda |only
data/sqrtloggamma.rda |binary
man/LogGammaDist.Rd | 22 +---
man/drg2000.Rd |only
man/loggammarob.Rd | 12 +-
man/loggammarob.control.Rd | 9 +
man/loggammarob.test.Rd | 10 -
man/loggammarob.wilks.Rd |only
man/summary.loggammarob.Rd | 6 -
26 files changed, 554 insertions(+), 241 deletions(-)
Permanent link
Title: Cultural Consensus Theory applications to data
Diff between CCTpack versions 0.91 dated 2013-10-25 and 0.92 dated 2013-12-19
Description: A user-friendly GUI for the application of Cultural Consensus Theory (CCT) models and methods to consensus data. The models are applied using hierarchical Bayesian inference. The current package version supports binary, ordinal, and continuous data formats.
Author: Royce Anders
Maintainer: Royce Anders
DESCRIPTION | 8
MD5 | 9
R/cctgui.r | 1260 +++++++++++++++++++++++++++++++++++++++++--------
inst |only
man/CCTpack-package.Rd | 8
man/cctgui.Rd | 5
6 files changed, 1073 insertions(+), 217 deletions(-)
Title: Trajectory miner: a toolbox for exploring and rendering sequence
data
Diff between TraMineR versions 1.8-6 dated 2013-08-26 and 1.8-7 dated 2013-12-19
Description: This package is a toolbox for sequence manipulation, description, rendering and more generally the mining of sequence data in the field of social sciences. Though it is primarily intended for analyzing state or event sequences that describe life courses such as family formation histories or professional careers its features also apply to many other kinds of categorical sequence data. It accepts many different sequence representations as input and provides tools for translating sequences from one format to another. It offers several statistical functions for describing and rendering sequences, for computing distances between sequences with different metrics among which optimal matching, the longest common prefix and the longest common subsequence, and simple functions for extracting the most frequent subsequences and identifying the most discriminating ones among them. A user's guide can be found on the TraMineR web page.
Author: Alexis Gabadinho [aut, cph],
Matthias Studer [aut, cph],
Nicolas Muller [aut],
Reto Buergin [aut],
Gilbert Ritschard [aut, cre, cph]
Maintainer: Gilbert Ritschard
DESCRIPTION | 29 ++++--
MD5 | 27 +++---
NAMESPACE | 2
NEWS | 19 ++++
R/STS_to_TSE.R | 146 +++++++++++++++++------------------
R/seqpcplot.R | 23 +++--
build |only
data/ex1.rda |binary
data/ex2.rda |binary
data/famform.rda |binary
inst/CITATION | 28 ++----
inst/doc/TraMineR-state-sequence.pdf |binary
man/TraMineR-package.Rd | 43 ++++------
man/seqdist.Rd | 2
man/seqpcplot.Rd | 13 +--
15 files changed, 180 insertions(+), 152 deletions(-)
Title: R package to detect character encoding
Diff between Ruchardet versions 0.0-1 dated 2013-11-25 and 0.0-2 dated 2013-12-19
Description: R port of 'universalchardet', that is the encoding detector
library of Mozilla.
Author: Heewon Jeon
Maintainer: Heewon Jeon
Ruchardet-0.0-1/Ruchardet/configure.ac |only
Ruchardet-0.0-2/Ruchardet/DESCRIPTION | 12
Ruchardet-0.0-2/Ruchardet/MD5 | 25 -
Ruchardet-0.0-2/Ruchardet/NAMESPACE | 2
Ruchardet-0.0-2/Ruchardet/R/RcppExports.R | 4
Ruchardet-0.0-2/Ruchardet/R/utils.R | 23 -
Ruchardet-0.0-2/Ruchardet/cleanup | 2
Ruchardet-0.0-2/Ruchardet/configure | 313 +++++++++++++++++-
Ruchardet-0.0-2/Ruchardet/inst/NEWS |only
Ruchardet-0.0-2/Ruchardet/inst/tests/euc_kr.txt |only
Ruchardet-0.0-2/Ruchardet/inst/tests/test-Ruchardet.R | 6
Ruchardet-0.0-2/Ruchardet/man/detectEncoding.Rd | 2
Ruchardet-0.0-2/Ruchardet/man/detectFileEncoding.Rd | 4
Ruchardet-0.0-2/Ruchardet/src/Makevars.in | 2
Ruchardet-0.0-2/Ruchardet/src/detectEncoding.cpp | 4
15 files changed, 368 insertions(+), 31 deletions(-)
Title: Fitting heavy tailed distributions: the poweRlaw package
Diff between poweRlaw versions 0.20.1 dated 2013-06-25 and 0.20.2 dated 2013-12-19
Description: This package implements both the discrete and continuous maximum likelihood estimators for
fitting the power-law distribution to data. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.20.1/poweRlaw/inst/doc/examples.Snw |only
poweRlaw-0.20.1/poweRlaw/inst/doc/poweRlaw.Snw |only
poweRlaw-0.20.2/poweRlaw/DESCRIPTION | 31 -
poweRlaw-0.20.2/poweRlaw/MD5 | 45 +-
poweRlaw-0.20.2/poweRlaw/NAMESPACE | 1
poweRlaw-0.20.2/poweRlaw/NEWS | 8
poweRlaw-0.20.2/poweRlaw/R/AllGenerics.R | 1
poweRlaw-0.20.2/poweRlaw/R/ctn_helper_functions.R | 27 +
poweRlaw-0.20.2/poweRlaw/R/discrete_helper_functions.R | 27 +
poweRlaw-0.20.2/poweRlaw/R/dist_cdf-methods.R | 14
poweRlaw-0.20.2/poweRlaw/R/estimate_xmin.R | 4
poweRlaw-0.20.2/poweRlaw/R/lines-methods.R | 3
poweRlaw-0.20.2/poweRlaw/R/mle-methods.R | 89 +++-
poweRlaw-0.20.2/poweRlaw/build |only
poweRlaw-0.20.2/poweRlaw/data/bootstrap_moby.RData |binary
poweRlaw-0.20.2/poweRlaw/data/bootstrap_p_moby.RData |binary
poweRlaw-0.20.2/poweRlaw/inst/doc/examples.R | 315 ++++++++++++++++-
poweRlaw-0.20.2/poweRlaw/inst/doc/examples.Rnw |only
poweRlaw-0.20.2/poweRlaw/inst/doc/examples.pdf |binary
poweRlaw-0.20.2/poweRlaw/inst/doc/poweRlaw.R | 313 ++++++++++++++++
poweRlaw-0.20.2/poweRlaw/inst/doc/poweRlaw.Rnw |only
poweRlaw-0.20.2/poweRlaw/inst/doc/poweRlaw.pdf |binary
poweRlaw-0.20.2/poweRlaw/vignettes |only
23 files changed, 801 insertions(+), 77 deletions(-)
Title: Characterization of functional genes in complex microbial
communities using tiling DNA microarrays
Diff between TilePlot versions 1.3 dated 2013-08-29 and 1.3.1 dated 2013-12-19
Description: This package is intended for processing the output from
functional gene tiling DNA microarray experiments. It produces
hybridization pattern plots for each gene on the array, and
statistics for each gene including mean probe intensity, median
probe intensity, bright probe fraction, bright segment length
dependent score, bright probe mean intensity, and bright probe
median intensity. Output is generated in order of bright
segment length dependent score in both a latex/eps format and
tab-delimited text file. The package works in two modes: single
array, and comparison of two arrays. Array comparison includes
array comparison statistics: median of logarithm of one array
probe divided by its counterpart on the other array, median
absolute deviation of that value, and the binomial test to see
whether the genes are equally abundant in both arrays.
Author: Ian Marshall
Maintainer: Ian Marshall
TilePlot-1.3.1/TilePlot/DESCRIPTION | 11
TilePlot-1.3.1/TilePlot/MD5 | 14
TilePlot-1.3.1/TilePlot/NAMESPACE |only
TilePlot-1.3.1/TilePlot/inst/allgenesonchip.ID | 1216
TilePlot-1.3.1/TilePlot/inst/array1 |41466 -------------------------
TilePlot-1.3.1/TilePlot/inst/array2 |41466 -------------------------
TilePlot-1.3.1/TilePlot/man/tileplot.double.Rd | 11
TilePlot-1.3.1/TilePlot/man/tileplot.single.Rd | 11
TilePlot-1.3/TilePlot/Read-and-delete-me |only
9 files changed, 30 insertions(+), 84165 deletions(-)
Title: Rcpp integration for the Eigen templated linear algebra library.
Diff between RcppEigen versions 0.3.2.0 dated 2013-11-13 and 0.3.2.0.1 dated 2013-12-19
Description: R and Eigen integration using Rcpp.
Eigen is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on Lapack and level-3 BLAS.
The RcppEigen package includes the header files from the Eigen C++
template library (currently version 3.2.0). Thus users do not need to
install Eigen itself in order to use RcppEigen.
Eigen is licensed under the GNU LGPL version 3 or later, and also
under the GNU GPL version 2 or later. RcppEigen (the Rcpp
bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or
later, as is the rest of Rcpp.
Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel
ChangeLog | 22 ++++++++++
DESCRIPTION | 18 ++++----
LICENSE |only
MD5 | 16 ++++---
build/vignette.rds |binary
inst/COPYRIGHTS |only
inst/doc/RcppEigen-Introduction.pdf |binary
inst/include/Eigen/src/SparseLU/SparseLU.h | 4 -
inst/include/RcppEigenForward.h | 1
inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h | 2
10 files changed, 46 insertions(+), 17 deletions(-)
Title: Gene region-level testing procedure for SNP data, using the min
P test resampling approach
Diff between minPtest versions 1.6 dated 2013-06-06 and 1.7 dated 2013-12-19
Description: Package minPtest is designed for estimating a gene region-level summary for SNP data from case-control studies using a permutation-based resampling method, called min P test, allowing execution on a compute cluster or multicore computer.
Author: Stefanie Hieke
Maintainer: Stefanie Hieke
minPtest-1.6/minPtest/inst/doc/plots |only
minPtest-1.6/minPtest/inst/doc/vignette.R |only
minPtest-1.7/minPtest/DESCRIPTION | 13 +++++--------
minPtest-1.7/minPtest/MD5 | 13 +++++++------
minPtest-1.7/minPtest/R/minPtest.R | 18 +++++++++---------
minPtest-1.7/minPtest/build |only
minPtest-1.7/minPtest/inst/doc/vignette.pdf |binary
minPtest-1.7/minPtest/vignettes |only
8 files changed, 21 insertions(+), 23 deletions(-)
More information about hybridEnsemble at CRAN
Permanent link
Title: Model-based clustering for multivariate partial ranking data
Diff between Rankcluster versions 0.91.5 dated 2013-12-05 and 0.91.6 dated 2013-12-19
Description: This package proposes a model-based clustering algorithm for
ranking data. Multivariate rankings as well as partial rankings are taken
into account. This algorithm is based on an extension of the Insertion
Sorting Rank (ISR) model for ranking data, which is a meaningful and
effective model parametrized by a position parameter (the modal ranking,
quoted by mu) and a dispersion parameter (quoted by pi). The heterogeneity
of the rank population is modelled by a mixture of ISR, whereas conditional
independence assumption is considered for multivariate rankings.
Author: Quentin Grimonprez, Julien Jacques
Maintainer: Quentin Grimonprez
DESCRIPTION | 19 +-
LICENSE |only
MD5 | 19 +-
R/RankFunctions.R | 354 +++++++++++++++++++++----------------------
R/rankclust.R | 368 +++++++++++++++++++++++----------------------
build/vignette.rds |binary
inst/COPYRIGHTS | 129 ++++-----------
inst/doc/Rankcluster.pdf |binary
man/Rankcluster-package.Rd | 14 +
man/convertRank.Rd | 5
man/rankclust.Rd | 20 ++
11 files changed, 463 insertions(+), 465 deletions(-)
Title: Protein Sequence Descriptor Calculation and Similarity
Computation with R
Diff between protr versions 0.1-0 dated 2012-11-18 and 0.2-0 dated 2013-12-19
Description: The protr package focus on offering a unique and comprehensive
toolkit for protein sequence descriptor calculation and similarity
computation. The descriptors included in the protr package are extensively
utilized in Bioinformatics and Chemogenomics research. The qualitative
descriptors listed in protr include Amino Acid Composition (Amino Acid
Composition/Dipeptide Composition/Tripeptide Composition) descriptor,
Autocorrelation (Normalized Moreau-Broto Autocorrelation/Moran
Autocorrelation/Geary Autocorrelation) descriptor, CTD
(Composition/Transition/Distribution) descriptor, Conjoint Traid
descriptor, Quasi-sequence Order (Sequence Order Coupling
Number/Quasi-sequence Order Descriptors) descriptor and Pseudo Amino Acid
Composition (Pseudo Amino Acid Composition/Amphiphilic Pseudo Amino Acid
Composition) descriptor. The quantitative descriptors, for
Proteochemometric (PCM) Modeling, includes the Generalized Scales-Based
Descriptors derived by Principal Components Analysis, Generalized
Scales-Based Descriptors derived by AA-Properties (AAindex), Generalized
Scales-Based Descriptors derived by 20+ classes of 2D and 3D Molecular
Descriptors (Topological, WHIM, VHSE, etc.), Generalized Scales-Based
Descriptors derived by Factor Analysis, Generalized Scales-Based
Descriptors derived by Multidimensional Scaling, and Generalized BLOSUM/PAM
Matrix-Derived Descriptors. The protr package also integrates the
functionality of parallellized similarity computation derived by protein
sequence alignment and Gene Ontology (GO) semantic similarity measures
between a list of protein sequences / GO terms / Entrez Gene IDs. ProtrWeb,
the web service built on protr, is located at:
http://cbdd.csu.edu.cn:8080/protrweb/ . The protr package is developed by
Computational Biology and Drug Design (CBDD) Group, Central South
University.
Author: Nan Xiao
Maintainer: Nan Xiao
protr-0.1-0/protr/R/getUniProt.R |only
protr-0.1-0/protr/R/protcheck.R |only
protr-0.1-0/protr/R/protseg.R |only
protr-0.1-0/protr/R/readFASTA.R |only
protr-0.1-0/protr/data/datalist |only
protr-0.2-0/protr/DESCRIPTION | 70 ++--
protr-0.2-0/protr/MD5 | 207 ++++++++++---
protr-0.2-0/protr/NAMESPACE | 12
protr-0.2-0/protr/NEWS | 18 +
protr-0.2-0/protr/R/desc01AAC.R | 2
protr-0.2-0/protr/R/desc02DC.R | 2
protr-0.2-0/protr/R/desc03TC.R | 2
protr-0.2-0/protr/R/desc04MoreauBroto.R | 2
protr-0.2-0/protr/R/desc05Moran.R | 2
protr-0.2-0/protr/R/desc06Geary.R | 2
protr-0.2-0/protr/R/desc07CTDC.R | 2
protr-0.2-0/protr/R/desc08CTDT.R | 2
protr-0.2-0/protr/R/desc09CTDD.R | 2
protr-0.2-0/protr/R/desc10CTriad.R | 2
protr-0.2-0/protr/R/desc11SOCN.R | 2
protr-0.2-0/protr/R/desc12QSO.R | 2
protr-0.2-0/protr/R/desc13PAAC.R | 2
protr-0.2-0/protr/R/desc14APAAC.R | 2
protr-0.2-0/protr/R/misc01readFASTA.R |only
protr-0.2-0/protr/R/misc02readPDB.R |only
protr-0.2-0/protr/R/misc03protcheck.R |only
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protr-0.2-0/protr/R/misc05getUniProt.R |only
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protr-0.2-0/protr/R/par01parSeqSim.R |only
protr-0.2-0/protr/R/par02parGOSim.R |only
protr-0.2-0/protr/R/pcm01extractScales.R |only
protr-0.2-0/protr/R/pcm02extractDescScales.R |only
protr-0.2-0/protr/R/pcm03extractPropScales.R |only
protr-0.2-0/protr/R/pcm04extractFAScales.R |only
protr-0.2-0/protr/R/pcm05extractMDSScales.R |only
protr-0.2-0/protr/R/pcm06extractBLOSUM.R |only
protr-0.2-0/protr/R/protr-datalist.R |only
protr-0.2-0/protr/R/protr-package.R | 94 ++----
protr-0.2-0/protr/README | 74 ++++
protr-0.2-0/protr/build |only
protr-0.2-0/protr/data/AA2DACOR.rda |only
protr-0.2-0/protr/data/AA3DMoRSE.rda |only
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protr-0.2-0/protr/inst/CITATION | 13
protr-0.2-0/protr/inst/doc/protr.R |only
protr-0.2-0/protr/inst/doc/protr.Rnw | 401 +++++++++++++++++++++------
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protr-0.2-0/protr/man/extractCTDC.Rd | 38 +-
protr-0.2-0/protr/man/extractCTDD.Rd | 38 +-
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protr-0.2-0/protr/man/extractMoreauBroto.Rd | 58 +--
protr-0.2-0/protr/man/extractPAAC.Rd | 83 ++---
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protr-0.2-0/protr/man/extractQSO.Rd | 48 +--
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protr-0.2-0/protr/man/protr-package.Rd | 90 +++---
protr-0.2-0/protr/man/protseg.Rd | 21 -
protr-0.2-0/protr/man/readFASTA.Rd | 44 +-
protr-0.2-0/protr/man/readPDB.Rd |only
protr-0.2-0/protr/man/twoGOSim.Rd |only
protr-0.2-0/protr/man/twoSeqSim.Rd |only
protr-0.2-0/protr/vignettes/fig/CTD.pdf |binary
protr-0.2-0/protr/vignettes/fig/PAAC.png |binary
protr-0.2-0/protr/vignettes/fig/QSO.png |binary
protr-0.2-0/protr/vignettes/fig/Thumbs.db |only
protr-0.2-0/protr/vignettes/fig/ctriad.pdf |binary
protr-0.2-0/protr/vignettes/fig/protrweb.png |only
protr-0.2-0/protr/vignettes/protr.Rnw | 401 +++++++++++++++++++++------
protr-0.2-0/protr/vignettes/protr.bib | 177 +++++++++++
160 files changed, 1586 insertions(+), 758 deletions(-)
Title: Derivative-free optimization algorithms by quadratic
approximation
Diff between minqa versions 1.2.1 dated 2012-05-12 and 1.2.2 dated 2013-12-19
Description: Derivative-free optimization by quadratic approximation
based on an interface to Fortran implementations by M. J. D.
Powell.
Author: Douglas Bates, Katharine M. Mullen, John C. Nash, Ravi Varadhan
Maintainer: Katharine M. Mullen
DESCRIPTION | 9 +++++----
MD5 | 2 +-
2 files changed, 6 insertions(+), 5 deletions(-)
Title: Parallel Computing Toolset for Genome-Wide Association Studies
(GWAS)
Diff between SNPRelate versions 0.9.18 dated 2013-09-29 and 0.9.19 dated 2013-12-19
Description: A High-performance computing toolset for relatedness and principal component analysis of SNP data
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 ++--
MD5 | 17 ++++-----
NEWS | 6 +++
R/SNPRelate_Main.r | 48 ++++++++++++++++++++------
build |only
inst/unitTests/valid/Validate.IBS.RData |binary
inst/unitTests/valid/Validate.MoM.RData |binary
inst/unitTests/valid/Validate.PCA.RData |binary
man/snpgdsGDS2PED.Rd | 16 +++++---
src/SNPRelate.cpp | 59 +++++++++++++++++++++++++++++---
10 files changed, 122 insertions(+), 32 deletions(-)