Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 1.4.5 dated 2012-03-30 and 1.5.1 dated 2012-04-16
Description: The package implements the statistical theory of L-moments
in R including L-moment estimation, probability-weighted moment
estimation, parameter estimation for numerous familiar and
not-so-familiar distributions, and L-moment estimation for the
same distributions from the parameters. L-moments are derived
from the expectations of order statistics and are linear with
respect to the probability-weighted moments; choice of either
can be made by mathematical convenience. L-moments are directly
analogous to the well-known product moments; however, L-moments
have many advantages including unbiasedness, robustness, and
consistency with respect to the product moments. The method of
L-moments can out perform the method of maximum likelihood. The
lmomco package historically is oriented around canonical
FORTRAN algorithms of J.R.M. Hosking, and the nomenclature for
many of the functions parallels that of the Hosking library,
which later became available in the lmom package. However, vast
arrays of various extensions and curiosities are added by the
author to aid and expand the breadth of L-moment application.
Such extensions include venerable statistics as Sen weighted
mean, Gini mean difference, plotting positions, and conditional
probability adjustment. The plotting of L-moment ratio diagrams
is directly supported in this package. Computations of
L-moments for right-tail and left-tail censoring by known or
unknown censoring threshold and also by indicator variable also
are available. E.A.H. Elamir and A.H. Seheult have developed
the trimmed L-moments, which are implemented in this package,
and numerical integration of quantile functions is used to
dynamically compute trajectories of select TL-moment ratios for
the construction of TL-moment ratio diagrams. Robert Serfling
and Peng Xiao have extended L-moments into multivariate space;
the so-called sample L-comoments are implemented here and might
have considerable application in copula theory because they
measure asymmetric correlation and higher co-moments or
co-movements of variables. The package supports the following
distributions with moment type shown as "L" (L-moments) or "TL"
(trimmed L-moments) and additional support for right-tail
censoring ([RC]) include: Asymmetric Exponential Power (L),
Cauchy (TL), Exponential (L), Gamma (L), Generalized Extreme
Value (L), Generalized Lambda (L & TL), Generalized Logistic
(L), Generalized Normal (L), Generalized Pareto (L[RC] & TL),
Gumbel (L), Kappa (L), Kumaraswamy (L), Laplace (L), Normal
(L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh
(L), Reverse Gumbel (L[RC]), Rice/Rician (L), Truncated
Exponential (L), Wakeby (L), and Weibull (L).
Author: William H. Asquith
Maintainer: William H. Asquith
ChangeLog | 76 ++++++++++++++++++++++++++++++++---------------
DESCRIPTION | 35 +++++++++++----------
MD5 | 62 +++++++++++++++++++++++---------------
NAMESPACE | 7 ++++
R/are.par.valid.R | 4 +-
R/are.paraep.valid.R |only
R/cdfaep.R |only
R/check.pdf.R | 53 ++++++++++++++++----------------
R/dist.list.R | 2 -
R/is.aep.R |only
R/lmomaep.R |only
R/par2cdf.R | 5 ++-
R/par2lmom.R | 5 ++-
R/par2pdf.R | 5 ++-
R/par2qua.R | 5 ++-
R/paraep.R |only
R/pdfaep.R |only
R/prettydist.R | 2 +
R/quaaep.R |only
R/theoLmoms.R | 6 +--
R/theoTLmoms.R | 6 +--
R/vec2par.R | 6 +++
R/zzz.R | 2 -
README | 26 ++++++++++++----
man/are.par.valid.Rd | 2 -
man/are.paraep.valid.Rd |only
man/cdfaep.Rd |only
man/clearforkporosity.Rd | 4 +-
man/dist.list.Rd | 4 +-
man/is.aep.Rd |only
man/lmomaep.Rd |only
man/par2lmom.Rd | 2 -
man/paraep.Rd |only
man/pdfaep.Rd |only
man/pdfkap.Rd | 4 +-
man/quaaep.Rd |only
man/theoLmoms.Rd | 10 +++---
man/theoTLmoms.Rd | 4 +-
man/vec2par.Rd | 2 -
39 files changed, 216 insertions(+), 123 deletions(-)
Title: Identification of Periodically Expressed Genes
Diff between GeneCycle versions 1.1.1 dated 2009-04-14 and 1.1.2 dated 2012-04-16
Description: The GeneCycle package implements the approaches of Wichert
et al. (2004), Ahdesmaki et al. (2005) and Ahdesmaki et al.
(2007) for detecting periodically expressed genes from gene
expression time series data.
Author: Miika Ahdesmaki, Konstantinos Fokianos, and Korbinian Strimmer.
Maintainer: Miika Ahdesmaki
CHANGES | 4 ++++
DESCRIPTION | 10 +++++-----
MD5 |only
NAMESPACE |only
data/caulobacter.rda |binary
man/avpg.Rd | 3 ++-
6 files changed, 11 insertions(+), 6 deletions(-)
Title: Methods for Temporal Disaggregation and Interpolation of Time
Series
Diff between tempdisagg versions 0.12 dated 2012-04-02 and 0.13 dated 2012-04-16
Description: Temporal disaggregation methods are used to disaggregate
and interpolate a low frequency time series to a higher
frequency series. This can be done without additional
information or by exploiting the information contained in one
or more indicators. All disaggregation methods ensure that
either the sum, the average, the first or the last value of the
resulting high frequency series is consistent with the low
frequency series.
Author: Christoph Sax, Peter Steiner
Maintainer: Christoph Sax
DESCRIPTION | 8
MD5 | 8
R/td.calc.R | 366 ++++++++++++++++++++++-----------------------
R/td.sub.R | 484 ++++++++++++++++++++++++++++++------------------------------
man/td.Rd | 2
5 files changed, 439 insertions(+), 429 deletions(-)
Title: Estimation of various latent class mixed models, joint latent
class mixed models and mixed models for curvilinear outcomes
Diff between lcmm versions 1.5.1 dated 2012-04-13 and 1.5.2 dated 2012-04-16
Description: This package provides functions for the estimation of
various latent class mixed models, joint latent latent class
mixed models and mixed models for curvilinear outcomes using a
maximum likelihood method
Author: Cecile Proust-Lima, Amadou Diakite and Benoit Liquet
Maintainer:
DESCRIPTION | 8 ++++----
MD5 | 6 ++++--
man/lcmm-package.Rd | 4 ++--
src/Makevars.in |only
src/Makevars.win |only
5 files changed, 10 insertions(+), 8 deletions(-)
Title: Categorical Regression Splines
Diff between crs versions 0.15-14 dated 2012-03-22 and 0.15-15 dated 2012-04-16
Description: This package provides for estimating regression splines
that handle a mix of continuous and categorical (discrete) data
often encountered in applied settings. I would like to
gratefully acknowledge support from the Natural Sciences and
Engineering Research Council of Canada (NSERC:www.nserc.ca),
the Social Sciences and Humanities Research Council of Canada
(SSHRC:www.sshrc.ca), and the Shared Hierarchical Academic
Research Computing Network (SHARCNET:www.sharcnet.ca).
Author: Jeffrey S. Racine
Maintainer: Jeffrey S. Racine
CHANGELOG | 27 ++
DESCRIPTION | 8
MD5 | 54 ++--
R/crs.R | 366 +++++++++++++++++--------------
R/frscv.R | 21 +
R/frscvNOMAD.R | 23 +
R/krscv.R | 36 ++-
R/krscvNOMAD.R | 23 +
R/np.regression.glp.R | 2
R/spline.R | 160 +++++++------
R/util.R | 7
R/zzz.R | 2
crsver | 2
demo/radial_constrained_first_partial.R | 1
demo/radial_constrained_mean.R | 1
demo/radial_constrained_second_partial.R | 1
demo/radial_persp.R | 1
demo/radial_rgl.R | 1
demo/sine_rgl.R | 1
demo/spline.R | 160 +++++++------
inst/doc/crs.pdf |binary
inst/doc/crs_faq.pdf |binary
inst/doc/spline_primer.pdf |binary
man/crs.Rd | 13 -
man/frscv.Rd | 9
man/frscvNOMAD.Rd | 10
man/krscv.Rd | 9
man/krscvNOMAD.Rd | 10
28 files changed, 551 insertions(+), 397 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-01 0.3-0
2010-02-09 0.2-0
2008-09-19 0.1-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-17 1.0-4
2007-05-10 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-11 2.2.1
2010-01-10 2.1
2006-09-13 1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-05-18 0.76
2010-01-22 0.75
2008-12-01 0.74
2008-02-14 0.73
2008-02-12 0.71
2008-02-12 0.72
2008-02-11 0.07
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-04 1.2.4
2010-08-03 1.2.3
2010-07-30 1.2.2
2010-05-25 1.2
2010-04-14 1.1
2010-02-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-07-22 0.4-1
2007-07-16 0.4
2007-07-07 0.3
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 1.6.0 dated 2012-03-26 and 1.6.1 dated 2012-04-16
Description: The package dlnm contains functions to specify and run
distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 8 ++++----
MD5 | 46 +++++++++++++++++++++++-----------------------
R/crossbasis.R | 5 ++---
R/crossplot.R | 9 +++++----
R/crosspred.R | 45 +++++++++++++++++++++++++++++----------------
R/crossreduce.R | 28 +++++++++++++---------------
R/internal.R | 2 +-
R/lines.crosspred.R | 16 ++++++++++------
R/lines.crossreduce.R | 2 +-
R/mkbasis.R | 8 ++++----
R/onebasis.R | 2 +-
R/plot.crosspred.R | 19 ++++++++++++-------
R/plot.crossreduce.R | 2 +-
R/points.crosspred.R | 16 ++++++++++------
R/points.crossreduce.R | 2 +-
R/summary.crossbasis.R | 2 +-
inst/ChangeLog | 21 +++++++++++++++++++--
inst/doc/dlnmOverview.Rnw | 10 +++++-----
inst/doc/dlnmOverview.pdf |binary
man/crossbasis.Rd | 2 +-
man/crosspred.Rd | 8 +++++---
man/crossreduce.Rd | 10 ++++++----
man/dlnm-internal.Rd | 5 +++--
man/plot.crosspred.Rd | 2 +-
24 files changed, 158 insertions(+), 112 deletions(-)
Title: Discrete Laplace mixture inference using the EM algorithm
Diff between disclapmix versions 0.1 dated 2012-04-13 and 0.2 dated 2012-04-16
Description: disclapmix makes inference in a mixture of Discrete
Laplace distributions using the EM algorithm.
Author: Mikkel Meyer Andersen and Poul Svante Eriksen
Maintainer: Mikkel Meyer Andersen
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/disclapmix.R | 34 +++++++++++++++++++++++++++++++---
R/do.em.R | 23 +++++++++++------------
man/disclapmix.Rd | 9 ++++-----
man/disclapmixfit.Rd | 4 ----
man/extractFullBIC.Rd | 6 +-----
man/extractMarginalBIC.Rd | 6 +-----
man/plot.disclapmixfit.Rd | 6 +-----
man/predict.disclapmixfit.Rd | 6 +-----
11 files changed, 69 insertions(+), 58 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-04-14 1.1.12
2010-01-25 1.1.11
2010-01-22 1.1.10
2009-10-08 1.1.09
2008-05-03 1.1.05
2007-11-24 1.1.02
2007-10-01 1.1.01
2007-05-11 1.1.009
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-06-03 0.2
2009-03-27 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-04-22 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-11 0.0-5
2009-11-25 0.0-4
2009-11-17 0.0-3
2009-11-16 0.0-2
2009-10-26 0.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-04-11 1.3-2
2011-02-19 1.3-1
2010-11-19 1.3-0
2010-09-10 1.2-0
2010-08-27 1.1-3
2010-01-23 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-11-18 1.4.0
2008-05-20 1.2.2
2008-05-16 1.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-01-26 0.11.2
2007-10-01 0.9.09
2007-05-11 0.9.084
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-18 0.33
2006-04-07 0.31
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-10-24 0.3-144
2009-10-28 0.1-142
2009-06-24 0.0-142
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2006-06-16 0.1
Title: Bootstrapped Response and Correlation Functions
Diff between bootRes versions 1.2 dated 2012-02-28 and 1.2.1 dated 2012-04-16
Description: Calculation of Bootstrapped Response and Correlation
Functions for Use in Dendroclimatology
Author: Christian Zang
Maintainer: Christian Zang
Changelog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/bcf.R | 16 +++++++++++++++-
R/brf.R | 19 +++++++++++++++++--
R/pmat.R | 13 +++++++++++--
6 files changed, 56 insertions(+), 14 deletions(-)
Title: Package required jars for the xlsx package
Diff between xlsxjars versions 0.3.0 dated 2011-03-03 and 0.4.0 dated 2012-04-16
Description: The xlsxjars package collects all the external jars
required for the xlxs package. These external jars are quite
large in size (15MB) and have a slow release cycle. By
separating the Java and R development, the storage footprint on
CRAN is reduced. This release corresponds to POI 3.8.
Author: Adrian A. Dragulescu
Maintainer: Adrian A. Dragulescu
xlsxjars-0.3.0/xlsxjars/inst/java/geronimo-stax-api_1.0_spec-1.0.jar |only
xlsxjars-0.3.0/xlsxjars/inst/java/poi-3.7-20101029.jar |only
xlsxjars-0.3.0/xlsxjars/inst/java/poi-ooxml-3.7-20101029.jar |only
xlsxjars-0.3.0/xlsxjars/inst/java/poi-ooxml-schemas-3.7-20101029.jar |only
xlsxjars-0.4.0/xlsxjars/DESCRIPTION | 10 +--
xlsxjars-0.4.0/xlsxjars/MD5 |only
xlsxjars-0.4.0/xlsxjars/NEWS | 6 +-
xlsxjars-0.4.0/xlsxjars/inst/java/commons-codec-1.6.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/poi-3.8-20120326.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/poi-ooxml-3.8-20120326.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/poi-ooxml-schemas-3.8-20120326.jar |only
xlsxjars-0.4.0/xlsxjars/inst/java/stax-api-1.0.1.jar |only
xlsxjars-0.4.0/xlsxjars/man/xlsxjars-package.Rd | 6 +-
xlsxjars-0.4.0/xlsxjars/other/make.package.R | 27 +++++-----
14 files changed, 29 insertions(+), 20 deletions(-)
Title: Markov chain Monte Carlo (MCMC) Package
Diff between MCMCpack versions 1.2-2 dated 2012-03-03 and 1.2-3 dated 2012-04-16
Description: This package contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.2. All
models return coda mcmc objects that can then be summarized
using the coda package. MCMCpack also contains some useful
utility functions, including some additional density functions
and pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization.
Author: Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
Maintainer: Jong Hee Park
DESCRIPTION | 8 ++++----
HISTORY | 7 +++++++
MD5 | 22 ++++++++++++----------
R/btsutil.R | 26 --------------------------
R/hidden.R | 4 ++--
R/make.breaklist.R |only
R/testpanelSubjectBreak.R | 11 +++--------
confdefs.h |only
data/PErisk.rda |binary
data/SupremeCourt.rda |binary
man/HMMpanelFE.Rd | 6 +++---
man/testpanelSubjectBreak.Rd | 14 +++++---------
src/MCMCpoissonChange.cc | 8 +++++++-
13 files changed, 43 insertions(+), 63 deletions(-)
Title: K Adaptive Partitioning for Survival data
Diff between kaps versions 0.8.3 dated 2012-03-20 and 0.9-2 dated 2012-04-16
Description: This package provides some routines to conduct the
K-adaptive parititioning (kaps) and recursive partitioning
(lrtree) for survival data, with the application to SEER
(Surveillance Epidemiology and End Results). A function kaps is
an implementation version of our algorithm kaps which provides
minimax based partitioing rule by log-rank test. A fuction
lrtree enables researchers to conduct log-rank survival tree
proposed by Segal (1988).
Author: Soo-Heang Eo and HyungJun Cho
Maintainer: Soo-Heang Eo
DESCRIPTION | 12 ++---
MD5 | 26 ++++++------
NAMESPACE | 2
NEWS | 13 ++++++
R/Classes.R | 2
R/accessaries.R | 8 +--
R/lrtree.R | 14 ++++++
R/predict.R | 115 +++++++++++++++++++++++++++++++++++++++++++++++++++++-
R/pruning.R |only
R/selectionPart.R | 30 ++++++++++++--
R/subfunctions.R | 2
man/kaps.Rd | 20 ++++-----
man/lrtree.Rd | 28 ++++++-------
man/predict.Rd | 4 +
man/prune.Rd |only
15 files changed, 217 insertions(+), 59 deletions(-)
Title: Iterator construct for R
Diff between iterators versions 1.0.5 dated 2011-07-23 and 1.0.6 dated 2012-04-16
Description: Support for iterators, which allow a programmer to
traverse through all the elements of a vector, list, or other
collection of data.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 8 ++++----
MD5 |only
inst/doc/iterators.pdf |binary
inst/doc/writing.pdf |binary
vignettes |only
5 files changed, 4 insertions(+), 4 deletions(-)
Title: CoreArray Genomic Data Structure (GDS) R Interface
Diff between gdsfmt versions 0.9.7 dated 2012-03-17 and 0.9.8 dated 2012-04-16
Description: R interface of CoreArray GDS is based on the CoreArray
project initiated and developed by Xiuwen Zheng from 2007.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 9
MD5 | 105 ++---
R/GDS.all.r | 392 +++++++++++++++++++-
man/add.gdsn.Rd | 23 -
man/addfile.gdsn.Rd | 13
man/append.gdsn.Rd | 19
man/apply.gdsn.Rd |only
man/cleanup.gds.Rd |only
man/closefn.gds.Rd | 16
man/cnt.gdsn.Rd | 11
man/compression.gdsn.Rd | 10
man/createfn.gds.Rd | 12
man/delete.attr.gdsn.Rd | 10
man/delete.gdsn.Rd | 12
man/gdsclass.Rd | 10
man/gdsfmt-package.Rd | 25 +
man/gdsn.Rd | 6
man/get.attr.gdsn.Rd | 12
man/getfile.gdsn.Rd | 13
man/index.gdsn.Rd | 27 -
man/lasterr.gds.Rd | 2
man/ls.gdsn.Rd | 14
man/name.gdsn.Rd | 14
man/objdesp.gdsn.Rd | 27 -
man/openfn.gds.Rd | 20 -
man/print.gdsclass.Rd | 6
man/print.gdsn.Rd | 10
man/put.attr.gdsn.Rd | 17
man/read.gdsn.Rd | 20 -
man/readex.gdsn.Rd |only
man/readmode.gdsn.Rd | 12
man/rename.gdsn.Rd | 15
man/setdim.gdsn.Rd | 16
man/sync.gds.Rd | 8
man/write.gdsn.Rd | 19
src/CoreDEF.h | 60 +--
src/CoreGDS.cpp | 5
src/Makevars | 6
src/Makevars.win | 6
src/dBase.cpp | 27 -
src/dBase.h | 283 +++++++-------
src/dFile.cpp | 67 ++-
src/dFile.h | 83 ++--
src/dParallel.cpp | 2
src/dParallel.h | 24 -
src/dPlatform.cpp | 28 -
src/dPlatform.h | 107 +++++
src/dSeq.cpp | 33 -
src/dSeq.h | 17
src/dStream.cpp | 5
src/dStream.h | 66 +--
src/dStruct.cpp | 12
src/dStruct.h | 120 ++++--
src/dType.h | 64 +--
src/gdsfmt.cpp | 916 +++++++++++++++++++++++++++++++++++-------------
55 files changed, 1942 insertions(+), 914 deletions(-)
Title: Foreach looping construct for R
Diff between foreach versions 1.3.5 dated 2012-03-14 and 1.4.0 dated 2012-04-16
Description: Support for the foreach looping construct. Foreach is an
idiom that allows for iterating over elements in a collection,
without the use of an explicit loop counter. This package in
particular is intended to be used for its return value, rather
than for its side effects. In that sense, it is similar to the
standard lapply function, but doesn't require the evaluation of
a function. Using foreach without side effects also
facilitates executing the loop in parallel.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 13 ++++++++-----
MD5 | 26 ++++++++++++++------------
NAMESPACE | 3 ++-
NEWS | 11 +++++++++++
R/do.R | 40 +++++++++++++++++++++++++++++-----------
R/zzz.R | 2 +-
inst/doc/foreach.Rnw | 1 +
inst/doc/foreach.pdf |binary
inst/doc/nested.Rnw | 3 ++-
inst/doc/nested.pdf |binary
inst/unitTests/runTestSuite.sh | 22 ----------------------
man/foreach.Rd | 13 +++++++++----
tests/doRUnit.R | 23 ++++++-----------------
vignettes |only
14 files changed, 83 insertions(+), 74 deletions(-)
Title: Foreach parallel adaptor for the snow package
Diff between doSNOW versions 1.0.5 dated 2011-05-20 and 1.0.6 dated 2012-04-16
Description: Provides a parallel backend for the %dopar% function using
Luke Tierney's snow package.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 8 ++++----
MD5 |only
R/doSNOW.R | 3 +++
3 files changed, 7 insertions(+), 4 deletions(-)
Title: Foreach parallel adaptor for the parallel package
Diff between doParallel versions 1.0.0 dated 2011-12-07 and 1.0.1 dated 2012-04-16
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/doParallel.R | 5 ++++-
inst/doc/gettingstartedParallel.pdf |binary
4 files changed, 12 insertions(+), 9 deletions(-)
Title: Foreach parallel adaptor for the multicore package
Diff between doMC versions 1.2.4 dated 2012-03-12 and 1.2.5 dated 2012-04-16
Description: Provides a parallel backend for the %dopar% function using
Simon Urbanek's multicore package.
Author: Revolution Analytics
Maintainer: Revolution Analytics
DESCRIPTION | 8 ++++----
MD5 | 5 +++--
inst/doc/gettingstartedMC.pdf |binary
vignettes |only
4 files changed, 7 insertions(+), 6 deletions(-)
Title: Dynamic Deterministic Effects Propagation Networks: Infer
signalling networks for timecourse RPPA data.
Diff between ddepn versions 2.0.2 dated 2011-10-24 and 2.1 dated 2012-04-16
Description: DDEPN (Dynamic Deterministic Effects Propagation
Networks): Infer signalling networks for timecourse data. Given
a matrix of high-throughput genomic or proteomic timecourse
data, generated after external perturbation of the biological
system, DDEPN models the time-dependent propagation of active
and passive states depending on a network structure. Optimal
network structures given the experimental data are
reconstructed. Two network inference algorithms can be used:
inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA,
a Genetic Algorithm network optimisation. Inclusion of prior
biological knowledge can be done using different network prior
models.
Author: Christian Bender
Maintainer: Christian Bender
ddepn-2.0.2/ddepn/R/kegggraph.to.detailed.adjacency.R |only
ddepn-2.0.2/ddepn/man/kegggraph.to.detailed.adjacency.Rd |only
ddepn-2.1/ddepn/DESCRIPTION | 17 -
ddepn-2.1/ddepn/MD5 | 48 +--
ddepn-2.1/ddepn/R/bestgam.R | 4
ddepn-2.1/ddepn/R/ddepn.R | 4
ddepn-2.1/ddepn/R/internal.functions.R | 6
ddepn-2.1/ddepn/R/plot_mcmctraces.R | 2
ddepn-2.1/ddepn/R/plot_profiles.R | 8
ddepn-2.1/ddepn/R/plotdetailed.R | 194 +++++++--------
ddepn-2.1/ddepn/R/plotdetailed_Rgraphviz.R |only
ddepn-2.1/ddepn/R/run_checks.R | 10
ddepn-2.1/ddepn/data/hcc1954.RData |binary
ddepn-2.1/ddepn/data/hcc1954raw.RData |binary
ddepn-2.1/ddepn/data/kegggraphs.RData |binary
ddepn-2.1/ddepn/inst/doc/OLDmcmcoutput.pdf |binary
ddepn-2.1/ddepn/inst/doc/ddepn.pdf |binary
ddepn-2.1/ddepn/inst/doc/mcmcoutput.pdf |binary
ddepn-2.1/ddepn/inst/doc/scorenetgatest.pdf |binary
ddepn-2.1/ddepn/man/kegggraphs.Rd | 6
ddepn-2.1/ddepn/man/plotdetailed.Rd | 74 ++++-
ddepn-2.1/ddepn/man/plotdetailed_Rgraphviz.Rd |only
ddepn-2.1/ddepn/src/perform_hmmsearch.c | 3
ddepn-2.1/ddepn/src/perform_hmmsearch_globalest.c | 4
ddepn-2.1/ddepn/src/perform_hmmsearch_globalest.h | 4
ddepn-2.1/ddepn/src/utility_functions.c | 8
ddepn-2.1/ddepn/src/utility_functions.h | 4
27 files changed, 216 insertions(+), 180 deletions(-)