Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-02 1.01
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-02 1.25
Title: Multivariate Meta-Analysis Using Sarmanov Beta Prior
Distributions
Diff between mmeta versions 1.0 dated 2012-07-26 and 1.01 dated 2012-08-16
Description: This package implements a novel bivariate meta-analysis
using Sarmanov beta prior distributions.
Author: Xiao Su
Maintainer: Xiao Su
DESCRIPTION | 19 ++++++++++---------
MD5 | 2 +-
2 files changed, 11 insertions(+), 10 deletions(-)
Title: LVM with censored and binary outcomes
Diff between lava.tobit versions 0.4-6 dated 2012-05-15 and 0.4-7 dated 2012-08-16
Description: lava plugin allowing combinations of left and right
censored and binary outcomes
Author: Klaus K. Holst
Maintainer: Klaus K. Holst
DESCRIPTION | 14 ++++++++------
MD5 | 31 ++++++++++++++++---------------
NAMESPACE | 46 +++++++++++++++++++---------------------------
R/binary.R | 46 +++++++++++++++++++++++++++++++++++++++-------
R/clprobit.R | 23 +++++++++++++++++++++++
R/hooks.R | 8 +++++++-
R/lava.tobit-package.R |only
R/plotres.R | 41 +++++++++++++++++++++++++++++++++++++++++
R/rbind.Surv.R | 22 ++++++++++++++++++++++
R/tobit.R | 6 ++++++
R/weighted.R | 5 +++++
man/binary.Rd | 46 ++++++++++++++++++++++++++++------------------
man/clprobit.Rd | 46 +++++++++++++++++++++++++++++-----------------
man/internal.Rd | 20 ++++++++++++--------
man/lava.tobit.Rd | 33 +++++++++++++--------------------
man/plotres.Rd | 28 ++++++++++++++++++----------
man/rbind.Surv.Rd | 13 ++++++++-----
17 files changed, 294 insertions(+), 134 deletions(-)
Title: Logspline density estimation routines
Diff between logspline versions 2.1.3 dated 2009-08-21 and 2.1.4 dated 2012-08-16
Description: Routines for the logspline density estimation.
oldlogspline uses the same algorithm as the logspline 1.0.x
package - the Kooperberg and Stone (1992) algorithm (with an
improved interface). The recommended routine logspline uses an
algorithm from Stone et al (1997).
Author: Charles Kooperberg
Maintainer: Charles Kooperberg
DESCRIPTION | 9 +++++----
MD5 |only
NAMESPACE |only
src/nlsd.c | 3 ---
4 files changed, 5 insertions(+), 7 deletions(-)
Title: Calls CNV from exome sequence data
Diff between ExomeDepth versions 0.8.0 dated 2012-04-28 and 0.8.3 dated 2012-08-16
Description: Calls copy number variants (CNVs) from targeted sequence
data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
DESCRIPTION | 6 ++---
MD5 | 24 ++++++++++++-----------
R/class_definition.R | 40 +++++++++++++++++++++++++++++++++++----
R/countBamInGranges.R | 4 +--
R/optimize_reference_set.R | 5 ++--
R/plot_CNVs_method.R | 28 +++++++++++++++------------
data/ExomeCount.RData |binary
data/exons.hg19.RData |binary
inst/doc/ExomeDepth-vignette.pdf |binary
man/initialize-methods.Rd |only
man/plot-methods.Rd | 5 +++-
man/select.reference.set.Rd | 12 ++++++++---
man/show-methods.Rd |only
src/CNV_estimate.cpp | 4 +--
14 files changed, 88 insertions(+), 40 deletions(-)
Title: Compound Poisson linear models
Diff between cplm versions 0.6-2 dated 2012-08-15 and 0.6-4 dated 2012-08-16
Description: Likelihood-based and Bayesian methods for various compound
Poisson linear models.
Author: Wayne Zhang
Maintainer: Wayne Zhang
DESCRIPTION | 6
MD5 | 16 -
NAMESPACE | 5
R/amer.R | 38 +-
R/bcplm.R | 2
R/cpglmm.R | 2
R/spline.R | 854 +++++++++++++++++++++++++++---------------------------
inst/doc/cplm.pdf |binary
man/cpglmm.Rd | 5
9 files changed, 463 insertions(+), 465 deletions(-)
Title: Estimates population size from non-invasive sampling
Diff between capwire versions 1.1.2 dated 2012-06-22 and 1.1.4 dated 2012-08-16
Description: Fits models from Miller et al. 2005 to estimate population
sizes from natural populations. Several models are implemented.
Package also includes functions to perform a likelihood ratio
test to choose between models, perform parametric bootstrapping
to obtain confidence intervals and multiple functions to
simulate data.
Author: Matthew W. Pennell and Craig R. Miller
Maintainer: Matthew W. Pennell
DESCRIPTION | 8 ++++----
MD5 | 10 ++++++----
R/partitionCountData.R | 2 +-
data |only
man/capwire-package.Rd | 4 ++--
man/partitionCountData.Rd | 2 +-
man/wombat.Rd |only
7 files changed, 14 insertions(+), 12 deletions(-)
Title: (Robust) canonical correlation analysis via projection pursuit
Diff between ccaPP versions 0.1.0 dated 2012-08-16 and 0.1.1 dated 2012-08-16
Description: Canonical correlation analysis via projection pursuit and
fast implementations of correlation estimators, with a focus on
robust and nonparametric methods.
Author: Andreas Alfons [aut, cre], David Simcha [aut]
Maintainer: Andreas Alfons
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
NEWS |only
R/permTest.R | 9 +++++----
R/utils.R | 3 ---
man/ccaPP-package.Rd | 4 ++--
src/Makevars | 4 +---
src/Makevars.win | 4 +---
src/utils.cpp | 9 ---------
src/utils.h | 2 --
10 files changed, 22 insertions(+), 38 deletions(-)
Title: MSeasy Tcl/Tk Graphical User Interface
Diff between MSeasyTkGUI versions 5.3 dated 2012-05-04 and 5.3.1 dated 2012-08-16
Description: A Tcl/Tk GUI for some basic functions in the MSeasy
package
Author: Yann Guitton
Maintainer: Yann Guitton
ChangeLog |only
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
R/dialog.MS.DataCreation.Agilent.R | 10 +++++-----
R/dialog.MS.DataCreation.CDF.R | 2 +-
R/dialog.MS.DataCreation.user.R | 6 +++---
R/dialog.MS.demon.R | 4 +++-
R/zzz.R | 2 +-
inst/doc/MSeasyTkGUI-manual.pdf |binary
man/MSeasyTkGUI-package.Rd | 4 ++--
10 files changed, 28 insertions(+), 25 deletions(-)
Title: Preprocessing of Gas Chromatography-Mass Spectrometry (GC-MS)
data
Diff between MSeasy versions 5.3 dated 2012-05-04 and 5.3.1 dated 2012-08-16
Description: Package for the detection of molecules in complex mixtures
of compounds. It creates an initial_DATA matrix from several
GC-MS analyses by collecting and assembling the information
from chromatograms and mass spectra (\emph{MS.DataCreation}).It
tests for the best unsupervised clustering method to group
similar mass spectra into molecules (\emph{MS.test.clust}).It
runs the optimal unsupervised clustering method on the
initial_DATA matrix, identifies the optimal number of clusters,
produces different files for facilitating the quality control
and identification of putative molecules, and returns
fingerprinting or profiling matrices (\emph{MS.clust}).It
converts output files from \emph{MS.clust} for NIST mass
spectral library search and ARISTO webtool search
Author: Elodie Courtois, Yann Guitton, Florence Nicole
Maintainer:
MSeasy-5.3.1/MSeasy/MD5 | 25 +-
MSeasy-5.3.1/MSeasy/R/MS.test.clust.R | 311 ----------------------------------
MSeasy-5.3/MSeasy/DESCRIPTION |only
MSeasy-5.3/MSeasy/NAMESPACE |only
MSeasy-5.3/MSeasy/R/MS.DataCreation.R |only
MSeasy-5.3/MSeasy/R/MS.clust.R |only
MSeasy-5.3/MSeasy/data |only
MSeasy-5.3/MSeasy/inst |only
MSeasy-5.3/MSeasy/man |only
9 files changed, 14 insertions(+), 322 deletions(-)
Title: Simulating Data to Study Performance of Clustering Algorithms
Diff between MixSim versions 1.0-4 dated 2012-03-28 and 1.0-5 dated 2012-08-16
Description: MixSim allows simulating mixtures of Gaussian
distributions with different levels of overlap between mixture
components. Pairwise overlap, defined as a sum of two
misclassification probabilities, measures the degree of
interaction between components and can be readily employed to
control the clustering complexity of datasets simulated from
mixtures. These datasets can then be used for systematic
performance investigation of clustering and finite mixture
modeling algorithms. Among other capabilities of MixSim, there
are computing the exact overlap for Gaussian mixtures,
simulating Gaussian and non-Gaussian data, simulating outliers
and noise variables, calculating various measures of agreement
between two partitionings, and constructing parallel
distribution plots for the graphical display of finite mixture
models.
Author: Volodymyr Melnykov, Wei-Chen Chen, and Ranjan Maitra
Maintainer: Volodymyr Melnykov
ChangeLog | 6 ++++++
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
demo/sec4_ex1.R | 18 ++++++++++++++++++
man/00_MixSim-package.Rd | 10 +++-------
man/MixSim.Rd | 6 +-----
man/RandIndex.Rd | 5 +----
man/overlap.Rd | 5 +----
man/pdplot.Rd | 5 +----
man/print.summary.Rd | 5 +----
man/simdataset.Rd | 5 +----
11 files changed, 48 insertions(+), 47 deletions(-)
Title: Solar Photovoltaic Systems
Diff between solaR versions 0.32 dated 2012-03-25 and 0.33 dated 2012-08-16
Description: Calculation methods of solar radiation and performance of
photovoltaic systems from daily and intradaily irradiation data
sources.
Author: Oscar Perpiñán Lamigueiro
Maintainer: Oscar Perpiñán Lamigueiro
DESCRIPTION | 10 +++---
MD5 | 66 +++++++++++++++++++++----------------------
R/read.R | 10 +++---
inst/CITATION | 27 +++++++++--------
man/G0-class.Rd | 9 +++--
man/Gef-class.Rd | 10 ++++--
man/HQCurve.Rd | 6 +++
man/NmgSFB.Rd | 6 +++
man/ProdGCPV-class.Rd | 9 +++--
man/ProdPVPS-class.Rd | 6 +++
man/Shade-class.Rd | 6 +++
man/Sol-class.Rd | 9 +++--
man/calcG0.Rd | 8 ++++-
man/calcGef.Rd | 6 +++
man/calcShd.Rd | 9 ++++-
man/calcSol.Rd | 10 +++---
man/compareLosses-methods.Rd | 10 +++++-
man/fBTd.Rd | 8 ++++-
man/fCompD.Rd | 9 ++++-
man/fCompI.Rd | 6 +++
man/fInclin.Rd | 6 +++
man/fProd.Rd | 6 +++
man/fPump.Rd | 6 +++
man/fSolD.Rd | 9 +++--
man/fSolI.Rd | 9 +++--
man/fSombra.Rd | 6 +++
man/fTemp.Rd | 7 +++-
man/fTheta.Rd | 9 ++++-
man/local2UTC.Rd | 10 ++++--
man/optimShd.Rd | 6 +++
man/prodGCPV.Rd | 8 ++++-
man/prodPVPS.Rd | 6 +++
man/pumpCoef.Rd | 8 ++++-
man/readBD.Rd | 17 ++++++-----
34 files changed, 241 insertions(+), 112 deletions(-)
Title: Handy functions for working with HGNC gene symbols and
Affymetrix probeset identifiers.
Diff between HGNChelper versions 0.1 dated 2012-07-20 and 0.2 dated 2012-08-16
Description: Contains functions for identifying and correcting HGNC
gene symbols which have been converted to date format by Excel,
for reversibly converting between HGNC symbols and valid R
names, identifying invalid HGNC symbols and correcting synonyms
and outdated symbols which can be mapped to an official symbol.
Author: Levi Waldron and Markus Riester
Maintainer: Levi Waldron
HGNChelper-0.1/HGNChelper/data/hgnc.symbols.rda |only
HGNChelper-0.1/HGNChelper/man/hgnc.symbols.Rd |only
HGNChelper-0.2/HGNChelper/CHANGELOG |only
HGNChelper-0.2/HGNChelper/DESCRIPTION | 17 +++++---
HGNChelper-0.2/HGNChelper/MD5 | 29 +++++++++-----
HGNChelper-0.2/HGNChelper/R/affyToR.R | 3 +
HGNChelper-0.2/HGNChelper/R/checkGeneSymbols.R |only
HGNChelper-0.2/HGNChelper/R/rToAffy.R | 3 +
HGNChelper-0.2/HGNChelper/data/hgnc.table.rda |only
HGNChelper-0.2/HGNChelper/inst/hgncLookup.R |only
HGNChelper-0.2/HGNChelper/man/HGNChelper-package.Rd | 30 ++++++++++-----
HGNChelper-0.2/HGNChelper/man/affyToR.Rd | 6 ++-
HGNChelper-0.2/HGNChelper/man/checkGeneSymbols.Rd |only
HGNChelper-0.2/HGNChelper/man/findExcelGeneSymbols.Rd | 36 +++++++-----------
HGNChelper-0.2/HGNChelper/man/hgnc.table.Rd |only
HGNChelper-0.2/HGNChelper/man/rToAffy.Rd | 5 +-
HGNChelper-0.2/HGNChelper/man/rToSymbol.Rd | 20 +++++-----
HGNChelper-0.2/HGNChelper/man/symbolToR.Rd | 19 +++++----
HGNChelper-0.2/HGNChelper/tests |only
19 files changed, 95 insertions(+), 73 deletions(-)
Title: Dive analysis and calibration
Diff between diveMove versions 1.3.4 dated 2012-05-08 and 1.3.5 dated 2012-08-16
Description: Utilities to represent, visualize, filter, analyse, and
summarize time-depth recorder (TDR) data. Miscellaneous
functions for handling location data are also provided.
Author: Sebastian P. Luque
Maintainer: Sebastian P. Luque
ChangeLog | 28 +++++++++++++++++++
DESCRIPTION | 6 ++--
MD5 | 38 +++++++++++++-------------
NEWS | 10 +++++++
R/calibrate.R | 31 ++++++++++++++-------
R/detPhase.R | 22 +++++++++++----
inst/doc/diveMove.pdf |binary
man/TDRcalibrate-class.Rd | 25 +++++++++--------
man/bout-misc.Rd | 6 ++--
man/bouts2NLS.Rd | 8 ++---
man/bouts3NLS.Rd | 6 ++--
man/calibrateDepth.Rd | 65 ++++++++++++++++++++++++++++++----------------
man/detDive-internal.Rd | 5 ++-
man/detPhase-internal.Rd | 20 ++++----------
man/distSpeed.Rd | 10 +++----
man/diveMove-internal.Rd | 8 ++---
man/diveStats.Rd | 17 ++++++------
man/readTDR.Rd | 6 ++--
man/sealLocs.Rd | 6 ++--
man/timeBudget-methods.Rd | 4 +-
20 files changed, 198 insertions(+), 123 deletions(-)
Title: Bayesian thresholds mixed-effects models for categorical data
Diff between Bayesthresh versions 0.1 dated 2012-08-08 and 0.1.1 dated 2012-08-16
Description: This package fits a linear mixed model for ordinal
categorical responses using Bayesian inference via Monte Carlo
Markov Chains. Default is Nandran & Chen algorithm using
Gaussian link function and saving just the summaries of the
chains. Among the options, package allow for two other options
of algorithms, for using Student's "t" link function and for
saving the full chains.
Author: Fabio Mathias Correa
Maintainer: Fabio Mathias Correa
DESCRIPTION | 12 ++++++------
MD5 | 4 ++--
man/Bayesthresh.Rd | 4 ++--
3 files changed, 10 insertions(+), 10 deletions(-)