Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-1 dated 2012-05-16 and 3.2-2 dated 2012-06-28
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate probit models with
semiparametric predictors (including linear, nonlinear and
nonparametric random effects) in the presence of correlated
error equations, endogeneity or sample selection.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/SemiParBIVProbit.r | 6 ++++--
man/SemiParBIVProbit.Rd | 4 ++--
5 files changed, 17 insertions(+), 11 deletions(-)
Permanent link
Title: A collection of methods for singular spectrum analysis
Diff between Rssa versions 0.9.2 dated 2012-05-28 and 0.9.6 dated 2012-06-28
Description: This package provides various Singular Spectrum Analysis
routines.
Author: Anton Korobeynikov
Maintainer: Anton Korobeynikov
Rssa-0.9.2/Rssa/man/lrf-routines.Rd |only
Rssa-0.9.2/Rssa/man/lrf.Rd |only
Rssa-0.9.6/Rssa/DESCRIPTION | 8 -
Rssa-0.9.6/Rssa/MD5 | 47 ++++++----
Rssa-0.9.6/Rssa/NAMESPACE | 25 ++++-
Rssa-0.9.6/Rssa/R/common.R | 16 ++-
Rssa-0.9.6/Rssa/R/forecast.R | 155 +++++++++++++++++++++++++++++-------
Rssa-0.9.6/Rssa/R/hankel.R | 4
Rssa-0.9.6/Rssa/R/hbhankel.R | 2
Rssa-0.9.6/Rssa/R/perest.R |only
Rssa-0.9.6/Rssa/R/plot.R | 105 +++++++++++++++---------
Rssa-0.9.6/Rssa/R/ssa.R | 69 ++++++++++++----
Rssa-0.9.6/Rssa/data |only
Rssa-0.9.6/Rssa/man/MotorVehicle.Rd |only
Rssa-0.9.6/Rssa/man/basis2lpf.Rd | 18 ++--
Rssa-0.9.6/Rssa/man/bforecast.Rd | 5 -
Rssa-0.9.6/Rssa/man/cleanup.Rd | 2
Rssa-0.9.6/Rssa/man/clone.Rd | 6 -
Rssa-0.9.6/Rssa/man/clusterify.Rd | 14 +--
Rssa-0.9.6/Rssa/man/lrr-routines.Rd |only
Rssa-0.9.6/Rssa/man/lrr.Rd |only
Rssa-0.9.6/Rssa/man/new.Rd | 8 -
Rssa-0.9.6/Rssa/man/perest.Rd |only
Rssa-0.9.6/Rssa/man/precache.Rd | 2
Rssa-0.9.6/Rssa/man/reconstruct.Rd | 6 -
Rssa-0.9.6/Rssa/man/rforecast.Rd | 10 +-
Rssa-0.9.6/Rssa/man/sforecast.Rd |only
Rssa-0.9.6/Rssa/man/vforecast.Rd | 8 +
Rssa-0.9.6/Rssa/man/wcor.Rd | 4
29 files changed, 349 insertions(+), 165 deletions(-)
Title: ABCDE_FBA: A-Biologist-Can-Do-Everything of Flux Balance
Analysis with this package.
Diff between abcdeFBA versions 0.2 dated 2012-01-22 and 0.3 dated 2012-06-28
Description: Functions for Constraint Based Simulation using Flux
Balance Analysis and informative analysis of the data generated
during simulation.
Author: Abhilash Gangadharan, Neha Rohatgi
Maintainer: Abhilash Gangadharan
abcdeFBA-0.2/abcdeFBA/R/genedel.R |only
abcdeFBA-0.3/abcdeFBA/DESCRIPTION | 6
abcdeFBA-0.3/abcdeFBA/MD5 | 85 ++++++------
abcdeFBA-0.3/abcdeFBA/NAMESPACE | 2
abcdeFBA-0.3/abcdeFBA/R/Exhaustive_double_deletion.R | 4
abcdeFBA-0.3/abcdeFBA/R/Exhaustive_single_deletion.R | 2
abcdeFBA-0.3/abcdeFBA/R/PHPP.R | 112 +++++++++-------
abcdeFBA-0.3/abcdeFBA/R/SINGLE_DEL_FLUXOME.R | 14 +-
abcdeFBA-0.3/abcdeFBA/R/View_objective.R |only
abcdeFBA-0.3/abcdeFBA/R/change_model.R |only
abcdeFBA-0.3/abcdeFBA/R/flux_difference_plotter.R | 13 +
abcdeFBA-0.3/abcdeFBA/R/flux_ranger.R |only
abcdeFBA-0.3/abcdeFBA/R/fva_robustness.R | 2
abcdeFBA-0.3/abcdeFBA/R/geneDel.R |only
abcdeFBA-0.3/abcdeFBA/R/metab_connect.R | 40 +----
abcdeFBA-0.3/abcdeFBA/R/search_reaction_metabolite.R | 11 +
abcdeFBA-0.3/abcdeFBA/doc/version_history | 14 +-
abcdeFBA-0.3/abcdeFBA/man/BFDProcessor.Rd | 74 +++++-----
abcdeFBA-0.3/abcdeFBA/man/Ec_iAF1260_flux1.Rd | 12 +
abcdeFBA-0.3/abcdeFBA/man/Ec_iAF1260_flux2.Rd | 13 +
abcdeFBA-0.3/abcdeFBA/man/Ec_iJR904.Rd | 21 +--
abcdeFBA-0.3/abcdeFBA/man/Ecoli_core.Rd | 3
abcdeFBA-0.3/abcdeFBA/man/Exhaustive_double_deletion.Rd | 84 ++++++------
abcdeFBA-0.3/abcdeFBA/man/Exhaustive_single_deletion.Rd | 73 +++++-----
abcdeFBA-0.3/abcdeFBA/man/FBA_solve.Rd | 67 +++++----
abcdeFBA-0.3/abcdeFBA/man/Gene_del.Rd | 40 ++---
abcdeFBA-0.3/abcdeFBA/man/H_pylori_iIT341.Rd | 24 ++-
abcdeFBA-0.3/abcdeFBA/man/H_sapien_Recon1.Rd | 23 +--
abcdeFBA-0.3/abcdeFBA/man/M_barkeri_iAF629.Rd | 7 -
abcdeFBA-0.3/abcdeFBA/man/M_tb_iNJ661.Rd | 23 +--
abcdeFBA-0.3/abcdeFBA/man/PERTURBATION_analysis.Rd | 66 +++++----
abcdeFBA-0.3/abcdeFBA/man/PHPP.Rd | 86 +++++++-----
abcdeFBA-0.3/abcdeFBA/man/S_aureus_iSB619.Rd | 23 +--
abcdeFBA-0.3/abcdeFBA/man/S_cerevisiae_IND750.Rd | 23 +--
abcdeFBA-0.3/abcdeFBA/man/Sybil_2_FBA_obj.Rd | 23 ++-
abcdeFBA-0.3/abcdeFBA/man/View_objective.Rd |only
abcdeFBA-0.3/abcdeFBA/man/change_obj_function.Rd | 67 +++++----
abcdeFBA-0.3/abcdeFBA/man/change_rxn_bounds.Rd | 58 ++++----
abcdeFBA-0.3/abcdeFBA/man/deg_meas.Rd | 53 ++++---
abcdeFBA-0.3/abcdeFBA/man/fdiff.Rd | 107 ++++++++-------
abcdeFBA-0.3/abcdeFBA/man/flux_ranger.Rd |only
abcdeFBA-0.3/abcdeFBA/man/fva.Rd | 64 +++++----
abcdeFBA-0.3/abcdeFBA/man/fva_robustness.Rd | 71 +++++-----
abcdeFBA-0.3/abcdeFBA/man/metab_connect.Rd | 50 ++++---
abcdeFBA-0.3/abcdeFBA/man/metab_srch.Rd | 62 ++++----
abcdeFBA-0.3/abcdeFBA/man/rxn_srch.Rd | 58 +++++---
abcdeFBA-0.3/abcdeFBA/man/sing_del_flxme.Rd | 74 +++++-----
47 files changed, 918 insertions(+), 736 deletions(-)
Title: Time wave analysis and graphical representation
Diff between seewave versions 1.6.3 dated 2012-04-11 and 1.6.4 dated 2012-06-28
Description: seewave provides functions for analysing, manipulating,
displaying, editing and synthesizing time waves (particularly
sound). This package processes time analysis (oscillograms and
envelopes), spectral content, resonance quality factor,
entropy, cross correlation and autocorrelation, zero-crossing,
dominant frequency, analytic signal, frequency coherence, 2D
and 3D spectrograms and many other analyses.
Author: Jerome Sueur
Maintainer: Jerome Sueur
DESCRIPTION | 10 +-
MD5 | 43 ++++++-----
NEWS | 16 ++++
R/seewave.r | 173 ++++++++++++++++++++++++++++++++++--------------
R/zzz.r | 1
inst/doc/seewave_IO.pdf |binary
man/autoc.Rd | 2
man/crest.Rd | 2
man/export.Rd | 2
man/listen.Rd | 2
man/noisew.Rd | 3
man/rms.Rd | 4 -
man/rugo.Rd | 20 +++--
man/savewav.Rd | 22 ++++--
man/seewave.internal.Rd | 1
man/seewave.package.Rd | 11 +--
man/spectro.Rd | 8 +-
man/stft.ext.Rd |only
man/timer.Rd | 7 +
seewave-Ex.R | 98 ++++++++++++++++++++++++++-
src |only
21 files changed, 316 insertions(+), 109 deletions(-)
Title: The Rebmix Package
Diff between rebmix versions 2.4.0 dated 2012-04-23 and 2.4.1 dated 2012-06-28
Description: R functions for random univariate and multivariate finite
mixture generation, number of components, component weights and
component parameters estimation, printing and plotting of
finite mixtures, bootstrapping and class membership prediction.
Variables can be either continuous or discrete, may follow
normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac
parametric families and should be independent within
components.
Author: Marko Nagode
Maintainer: Marko Nagode
DESCRIPTION | 8
MD5 | 46 +--
R/REBMIX.R | 2
R/RNGMIX.R | 2
R/defaults.R | 6
R/dfmix.R | 4
R/dfmix.x.R | 4
R/dfmix.xy.R | 8
R/pfmix.R | 4
R/pfmix.x.R | 4
R/pfmix.xy.R | 9
R/predict.list.R | 2
inst/NEWS.Rd | 7
inst/doc/rebmix.Rnw | 34 +-
inst/doc/rebmix.pdf |binary
man/REBMIX.Rd | 12
man/RNGMIX.Rd | 14
man/boot.Rd | 2
man/dfmix.Rd | 6
man/pfmix.Rd | 6
src/Rrebmix.c | 53 +++
src/rebmixf.c | 766 ++++++++++++++++++++++++++++++++++++++++++----------
src/rebmixf.h | 9
src/rngmixf.c | 40 ++
24 files changed, 835 insertions(+), 213 deletions(-)
Title: Geographic analysis and modeling with raster data
Diff between raster versions 2.0-05 dated 2012-06-21 and 2.0-08 dated 2012-06-28
Description: Reading, writing, manipulating, analyzing and modeling of
gridded spatial data. The package implements basic and
high-level functions and processing of very large files is
supported.
Author: Robert J. Hijmans & Jacob van Etten
Maintainer: Robert J. Hijmans
ChangeLog | 8 ++
DESCRIPTION | 8 +-
MD5 | 78 ++++++++++++++--------------
NAMESPACE | 2
R/AAAClasses.R | 4 -
R/brick.R | 2
R/canProcessInMemory.R | 44 ++++++----------
R/coerce.R | 8 ++
R/crop.R | 7 +-
R/hdrRaster.R | 2
R/optionsGet.R | 17 ++++++
R/optionsSave.R | 8 ++
R/optionsSet.R | 19 +++++-
R/progressBar.R | 8 +-
R/rasterFromGDAL.R | 7 +-
R/rasterFromRasterFile.R | 6 +-
R/read.R | 2
R/subs.R | 112 ++++++++++++++++++++++++++---------------
R/subset.R | 2
R/tmpFile.R | 31 +++++++++++
R/unique.R | 22 +++-----
R/writeAllRaster.R | 55 ++++++++++----------
R/writeRaster.R | 3 +
R/xyValuesBuffer.R | 24 +++++++-
R/zonal.R | 128 ++++++++++++++++++++++++-----------------------
R/zzz.R | 2
inst/doc/Raster.Rnw | 2
inst/doc/Raster.pdf |binary
inst/doc/functions.pdf |binary
inst/doc/rasterfile.pdf |binary
man/Arith-methods.Rd | 2
man/extract.Rd | 6 +-
man/options.Rd | 3 -
man/saveStack.Rd | 5 +
man/shp.Rd | 2
man/stack.Rd | 2
man/substitute.Rd | 14 ++---
man/unique.Rd | 15 +++--
man/zonal.Rd | 17 +++---
src/intersect.h |only
src/solar.c |only
41 files changed, 410 insertions(+), 267 deletions(-)
Title: Elastic-Net for Sparse Estimation and Sparse PCA
Diff between elasticnet versions 1.0-5 dated 2008-05-06 and 1.1 dated 2012-06-28
Description: This package provides functions for fitting the entire
solution path of the Elastic-Net and also provides functions
for estimating sparse Principal Components. The Lasso solution
paths can be computed by the same function. First version:
2005-10.
Author: Hui Zou
Maintainer: Hui Zou
DESCRIPTION | 23 +++++++++++++++--------
MD5 |only
NAMESPACE |only
R/enet_funcs.R | 2 +-
data/diabetes.RData |binary
data/pitprops.RData |binary
man/plot.enet.Rd | 2 +-
man/predict.enet.Rd | 2 +-
man/print.arrayspc.Rd | 2 +-
man/print.enet.Rd | 2 +-
man/print.spca.Rd | 2 +-
11 files changed, 21 insertions(+), 14 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 1.1 dated 2012-04-26 and 1.2 dated 2012-06-28
Description: DDD implements maximum likelihood methods based on the
diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent. See Etienne
et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
10.1098/rspb.2011.1439. DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence. See Etienne & Haegeman
2012, Am. Nat. In press.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DESCRIPTION | 11 ++++++-----
MD5 | 23 ++++++++++++-----------
R/dd_KI_ML.R | 21 +++++++++++----------
R/dd_KI_loglik.R | 5 +++++
R/dd_ML.R | 4 ++--
R/dd_SR_ML.R | 35 ++++++++++++++++++++++++++++++-----
R/dd_SR_loglik.R | 2 +-
R/dd_loglik.R | 1 +
R/optimx2.R |only
man/DDD-internal.Rd | 1 +
man/DDD-package.Rd | 9 +++++++--
man/dd_KI_ML.Rd | 4 ++--
man/dd_SR_ML.Rd | 4 +++-
13 files changed, 81 insertions(+), 39 deletions(-)
Title: Breakpoint annotation model smoothing
Diff between bams versions 1.1 dated 2012-04-06 and 1.2 dated 2012-06-28
Description: Data and code to allow reproduction of "Learning smoothing
models of copy number profiles using breakpoint annotations."
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking
DESCRIPTION | 13 +-
MD5 | 19 ++--
NEWS |only
R/report.R | 47 ++++++++--
R/smoothing-functions.R | 30 ++++++
inst/article/HOCKING-model-selection-breakpoint-annotations.pdf |only
inst/article/algo.colors.tex |only
inst/article/make.all.stats.R | 3
inst/article/smooth-one.R | 4
inst/article/smoothing-commands.R | 7 +
inst/article/table-generalization-error-global-models.R | 22 ++++
inst/doc/remaking-bioinfo-article.pdf |binary
12 files changed, 119 insertions(+), 26 deletions(-)
Title: R object-oriented programming with or without references
Diff between R.oo versions 1.9.3 dated 2012-03-18 and 1.9.8 dated 2012-06-28
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 12 ++--
MD5 | 47 +++++++++--------
NAMESPACE | 18 ++++++
R/006.fixVarArgs.R | 4 +
R/040.setConstructorS3.R | 26 +++++----
R/050.Object.R | 19 +++++--
R/060.Class.R | 6 +-
R/999.NonDocumentedObjects.R | 5 -
R/BasicObject.R | 45 ++++++++++++++++-
R/Exception.R | 5 +
R/Rdoc.R | 108 ++++++++++++++++++++++++++++++++++-------
R/throw.default.R | 4 +
R/zzz.R | 5 +
incl/Exception.Rex | 19 +++----
inst/NEWS | 36 +++++++++++++
man/BasicObject.Rd | 1
man/Exception.Rd | 19 +++----
man/Non-documented_objects.Rd | 5 -
man/Rdoc.Rd | 1
man/finalize.Object.Rd | 12 +++-
man/getUsage.Rdoc.Rd | 1
man/newInstance.BasicObject.Rd |only
man/newInstance.Class.Rd | 6 +-
man/newInstance.Object.Rd | 4 +
man/setConstructorS3.Rd | 3 -
25 files changed, 313 insertions(+), 98 deletions(-)
Title: Multivariate Process Capability Indices (MPCI)
Diff between MPCI versions 1.0.4 dated 2012-04-25 and 1.0.5 dated 2012-06-28
Description: MPCI package performs the followings Multivariate Process
Capability Indices: Shahriari et al. (1995) Multivariate
Capability Vector, Taam et al. (1993) Multivariate Capability
Index (MCpm), Pan and Lee (2010) proposal (NMCpm) and the
followings based on Principal Component Analysis (PCA):Wang and
Chen (1998), Xekalaki and Perakis (2002) and Wang (2005).
Moreover, it includes two datasets.
Author: Edgar Santos-Fernandez, Michele Scagliarini.
Maintainer: Edgar Santos-Fernandez
DESCRIPTION | 15 ++++-----
MD5 | 8 ++--
R/mpci.R | 84 +++++++++++++++++++++++++++++++++++++++++-----------
man/MPCI-package.Rd | 7 ++++
man/mpci.Rd | 17 ++++++++--
5 files changed, 100 insertions(+), 31 deletions(-)
Title: Various R programming tools for model fitting
Diff between gmodels versions 2.15.2 dated 2012-04-20 and 2.15.3 dated 2012-06-28
Description: Various R programming tools for model fitting
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by Ben Bolker, Thomas Lumley, and Randall C
Johnson. Contributions from Randall C. Johnson are Copyright
(2005) SAIC-Frederick, Inc. Funded by the Intramural Research
Program, of the NIH, National Cancer Institute, Center for
Cancer Research under NCI Contract NO1-CO-12400.
Maintainer: Gregory R. Warnes
gmodels-2.15.2/gmodels/R/est.lmer.R |only
gmodels-2.15.3/gmodels/ChangeLog | 18 +++++++++++
gmodels-2.15.3/gmodels/DESCRIPTION | 10 +++---
gmodels-2.15.3/gmodels/MD5 | 18 +++++------
gmodels-2.15.3/gmodels/NEWS | 9 +++++
gmodels-2.15.3/gmodels/R/est.mer.R | 19 +----------
gmodels-2.15.3/gmodels/R/percentile.R |only
gmodels-2.15.3/gmodels/inst/ChangeLog | 18 +++++++++++
gmodels-2.15.3/gmodels/inst/NEWS | 9 +++++
gmodels-2.15.3/gmodels/man/ci.Rd | 6 +--
gmodels-2.15.3/gmodels/test/lme-test.R | 53 +++++++++++++++++++++++++++++++++
11 files changed, 126 insertions(+), 34 deletions(-)