Title: Trust region nonlinear optimization, efficient for sparse
Hessians
Diff between trustOptim versions 0.7.0 dated 2012-08-23 and 0.7.1 dated 2012-09-27
Description: Trust region algorithm for nonlinear optimization. In
addition to being more stable and robust than optim, this
package includes methods that are scalable and efficient (in
terms of both speed and memory usage) when the Hessian is
sparse.
Author: Michael Braun
Maintainer: Michael Braun
trustOptim-0.7.0/trustOptim/inst/doc/trustOptim-doc.pdf |only
trustOptim-0.7.0/trustOptim/inst/examples/MVNtest.R |only
trustOptim-0.7.0/trustOptim/inst/examples/hierMVN.R |only
trustOptim-0.7.0/trustOptim/inst/examples/hierMVN_funcs.R |only
trustOptim-0.7.0/trustOptim/inst/include/mvnorm.cpp |only
trustOptim-0.7.0/trustOptim/inst/include/norm.cpp |only
trustOptim-0.7.0/trustOptim/inst/include/wishart.cpp |only
trustOptim-0.7.0/trustOptim/src/hierMVN-example.cpp |only
trustOptim-0.7.1/trustOptim/DESCRIPTION | 18 ++----
trustOptim-0.7.1/trustOptim/MD5 | 30 +++++------
trustOptim-0.7.1/trustOptim/NEWS |only
trustOptim-0.7.1/trustOptim/R/get_fdfh.R |only
trustOptim-0.7.1/trustOptim/inst/doc/trustOptim-vignette.Rnw |only
trustOptim-0.7.1/trustOptim/inst/doc/trustOptim-vignette.pdf |only
trustOptim-0.7.1/trustOptim/inst/examples/compare.R | 29 ++++++----
trustOptim-0.7.1/trustOptim/inst/examples/ex_funcs.R | 13 ++--
trustOptim-0.7.1/trustOptim/inst/examples/summarize.R |only
trustOptim-0.7.1/trustOptim/man/get.fdfh.Rd |only
trustOptim-0.7.1/trustOptim/man/trust.optim.Rd | 1
trustOptim-0.7.1/trustOptim/man/trustOptim-package.Rd | 4 -
trustOptim-0.7.1/trustOptim/src/FDHS-DSSM.c | 5 +
trustOptim-0.7.1/trustOptim/src/Makevars | 3 +
trustOptim-0.7.1/trustOptim/src/Rinterface.cpp | 8 +-
23 files changed, 61 insertions(+), 50 deletions(-)
Title: tnet: Software for Analysis of Weighted, Two-mode, and
Longitudinal networks
Diff between tnet versions 3.0.8 dated 2012-08-20 and 3.0.9 dated 2012-09-27
Description: R package for analyzing weighted, two-mode, and
longitudinal networks.
Author: Tore Opsahl
Maintainer: Tore Opsahl
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/closeness_w.R | 2 ++
man/tnet-package.Rd | 4 ++--
5 files changed, 16 insertions(+), 10 deletions(-)
Title: Inference for QTL Hotspots
Diff between qtlhot versions 0.6.1 dated 2012-09-18 and 0.6.4 dated 2012-09-27
Description: Functions to infer co-mapping trait hotspots and causal
models
Author: Elias Chaibub Neto
Maintainer: Brian S. Yandell
qtlhot-0.6.1/qtlhot/R/diag.R |only
qtlhot-0.6.4/qtlhot/DESCRIPTION | 8 +++---
qtlhot-0.6.4/qtlhot/MD5 | 18 +++++++-------
qtlhot-0.6.4/qtlhot/NAMESPACE | 1
qtlhot-0.6.4/qtlhot/R/cmst.R | 41 ++++++++++++++------------------
qtlhot-0.6.4/qtlhot/R/highlod.R | 32 +++++++++++++++++++++++-
qtlhot-0.6.4/qtlhot/R/sliding.R |only
qtlhot-0.6.4/qtlhot/inst/doc/cmst.pdf |binary
qtlhot-0.6.4/qtlhot/inst/doc/qtlhot.pdf |binary
qtlhot-0.6.4/qtlhot/man/GetCandReg.Rd | 21 ++++------------
qtlhot-0.6.4/qtlhot/man/highlod.Rd | 12 +++++++++
11 files changed, 81 insertions(+), 52 deletions(-)
Title: Utilities from Seminar fuer Statistik ETH Zurich
Diff between sfsmisc versions 1.0-20 dated 2012-03-19 and 1.0-21 dated 2012-09-27
Description: Useful utilities ['goodies'] from Seminar fuer Statistik
ETH Zurich, quite a few related to graphics; many ported from
S-plus times.
Author: Martin Maechler and many others.
Maintainer: Martin Maechler
ChangeLog | 16 +++++++++++++++-
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/misc-goodies.R | 5 ++++-
R/prettylab.R | 10 +++++++---
data/potatoes.rda |binary
inst/ChangeLog | 16 +++++++++++++++-
man/capture-n-write.Rd | 26 ++++++++++++++++++--------
man/eaxis.Rd | 5 ++++-
man/primes.Rd | 8 +++-----
man/unix/Sys.cpuinfo.Rd | 18 +++++++++---------
11 files changed, 89 insertions(+), 43 deletions(-)
Title: Monotone multi-layer perceptron neural network
Diff between monmlp versions 1.1.1 dated 2012-08-21 and 1.1.2 dated 2012-09-27
Description: Multi-layer perceptron neural network with partial
monotonicity constraints
Author: Alex J. Cannon
Maintainer: Alex J. Cannon
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
R/monmlp.fit.R | 25 +++++++++++++++++++------
man/gam.style.Rd | 5 +++--
man/monmlp.fit.Rd | 49 ++++++++++++++++++++++++++++---------------------
5 files changed, 57 insertions(+), 36 deletions(-)
Title: Variable selection for generalized linear mixed models by
L1-penalized estimation
Diff between glmmLasso versions 1.0.5 dated 2012-07-31 and 1.0.6 dated 2012-09-27
Description: Variable selection for generalized linear mixed models by
L1-penalized estimation
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
man/glmmLasso.rd | 9 +++++----
3 files changed, 11 insertions(+), 10 deletions(-)
Title: Steiner Tree Approach for Graph Analysis
Diff between SteinerNet versions 1.2 dated 2012-09-20 and 1.3 dated 2012-09-27
Description: A set of graph functions written in R to find Steiner
trees on graphs. It provides tools for analysing Steiner tree
application on networks. It has applications in biological
pathway network analysis.
Author: Afshin Sadeghi
Maintainer: Afshin Sadeghi
DESCRIPTION | 16
MD5 | 16
NAMESPACE | 2
R/SteinerTree.r | 4
R/analysis-wilcox.r |only
R/analysis.r | 89 +--
R/simulations.r | 1065 +++++++++++++++++++--------------------
inst/doc/SteinerNet.pdf |binary
man/steiner_comparison_plots.Rd | 2
man/steiner_comparison_wilcox.Rd |only
10 files changed, 609 insertions(+), 585 deletions(-)
Title: Utility functions for sequential Monte Carlo
Diff between smcUtils versions 0.1 dated 2011-11-05 and 0.2 dated 2012-09-27
Description: Provides resampling functions (stratified, residual,
multinomial, systematic, and branching), measures of weight
uniformity (coefficient of variation, effective sample size,
and entropy), and a weight renormalizing function.
Author: Author: Jarad Niemi
Maintainer: Jarad Niemi
smcUtils-0.1/smcUtils/man/inverse.cdf.weights.Rd |only
smcUtils-0.1/smcUtils/man/rep2id.Rd |only
smcUtils-0.2/smcUtils/ChangeLog |only
smcUtils-0.2/smcUtils/DESCRIPTION | 20 ++++---
smcUtils-0.2/smcUtils/MD5 | 49 ++++++++++-------
smcUtils-0.2/smcUtils/NAMESPACE |only
smcUtils-0.2/smcUtils/R/branching.resample.R | 4 +
smcUtils-0.2/smcUtils/R/check.weights.r |only
smcUtils-0.2/smcUtils/R/cov.weights.R | 29 ++++++++--
smcUtils-0.2/smcUtils/R/ent.weights.R | 27 +++++++--
smcUtils-0.2/smcUtils/R/ess.weights.R | 29 ++++++++--
smcUtils-0.2/smcUtils/R/inverse.cdf.weights.R | 64 +++++++++++++++--------
smcUtils-0.2/smcUtils/R/multinomial.resample.R | 31 ++++++++++-
smcUtils-0.2/smcUtils/R/renormalize.weights.R | 28 +++++++---
smcUtils-0.2/smcUtils/R/rep2id.R | 41 ++++++++++----
smcUtils-0.2/smcUtils/R/resample.R | 18 +++---
smcUtils-0.2/smcUtils/R/residual.resample.R | 43 ++++++++++++---
smcUtils-0.2/smcUtils/R/stratified.resample.R | 30 ++++++++--
smcUtils-0.2/smcUtils/R/systematic.resample.R | 27 +++++++--
smcUtils-0.2/smcUtils/README |only
smcUtils-0.2/smcUtils/demo |only
smcUtils-0.2/smcUtils/inst |only
smcUtils-0.2/smcUtils/man/ess.weights.Rd | 12 +---
smcUtils-0.2/smcUtils/man/renormalize.weights.Rd | 32 ++++-------
smcUtils-0.2/smcUtils/man/resample.Rd | 62 +++++-----------------
smcUtils-0.2/smcUtils/man/resampling.Rd | 29 ++++++----
smcUtils-0.2/smcUtils/man/smcUtils-package.Rd | 20 ++-----
smcUtils-0.2/smcUtils/src |only
smcUtils-0.2/smcUtils/tests |only
29 files changed, 383 insertions(+), 212 deletions(-)
Title: Practical Numerical Math Functions
Diff between pracma versions 1.1.6 dated 2012-07-20 and 1.2.0 dated 2012-09-27
Description: Implementations of functions in numerical analysis as R
scripts, with a special view on on optimization and time series
routines. Uses Matlab function names where appropriate to
simplify porting.
Author: Hans W Borchers
Maintainer: HwB
pracma-1.1.6/pracma/R/ApEn.R |only
pracma-1.1.6/pracma/R/agm.R |only
pracma-1.1.6/pracma/R/contfrac.R |only
pracma-1.1.6/pracma/R/droplet.R |only
pracma-1.1.6/pracma/R/factorize.R |only
pracma-1.1.6/pracma/R/numbers.R |only
pracma-1.1.6/pracma/R/primroot.R |only
pracma-1.1.6/pracma/R/vnorm.R |only
pracma-1.1.6/pracma/man/ApEn.Rd |only
pracma-1.1.6/pracma/man/GCD.Rd |only
pracma-1.1.6/pracma/man/agm.Rd |only
pracma-1.1.6/pracma/man/contfrac.Rd |only
pracma-1.1.6/pracma/man/coprime.Rd |only
pracma-1.1.6/pracma/man/droplet_e.Rd |only
pracma-1.1.6/pracma/man/eulersPhi.Rd |only
pracma-1.1.6/pracma/man/extGCD.Rd |only
pracma-1.1.6/pracma/man/factorize.Rd |only
pracma-1.1.6/pracma/man/modinv.Rd |only
pracma-1.1.6/pracma/man/modlin.Rd |only
pracma-1.1.6/pracma/man/modpower.Rd |only
pracma-1.1.6/pracma/man/moebiusFun.Rd |only
pracma-1.1.6/pracma/man/omega.Rd |only
pracma-1.1.6/pracma/man/primroot.Rd |only
pracma-1.1.6/pracma/man/sigma.Rd |only
pracma-1.1.6/pracma/man/vnorm.Rd |only
pracma-1.1.6/pracma/tests/factorize.R |only
pracma-1.1.6/pracma/tests/modinv.R |only
pracma-1.1.6/pracma/tests/modular.R |only
pracma-1.1.6/pracma/tests/numbers.R |only
pracma-1.1.6/pracma/tests/primroot.R |only
pracma-1.1.6/pracma/tests/vnorm.R |only
pracma-1.2.0/pracma/DESCRIPTION | 15 ++-
pracma-1.2.0/pracma/MD5 | 118 +++++++++++++------------------
pracma-1.2.0/pracma/NEWS | 40 +++++++---
pracma-1.2.0/pracma/R/andor.R | 4 -
pracma-1.2.0/pracma/R/entropy.R |only
pracma-1.2.0/pracma/R/erf.R | 8 ++
pracma-1.2.0/pracma/R/ezplot.R | 50 +++++++++++++
pracma-1.2.0/pracma/R/factors.R |only
pracma-1.2.0/pracma/R/fnorm.R | 2
pracma-1.2.0/pracma/R/gaussNewton.R | 2
pracma-1.2.0/pracma/R/hadamard.R | 2
pracma-1.2.0/pracma/R/lsqnonlin.R | 8 +-
pracma-1.2.0/pracma/R/matlab.R |only
pracma-1.2.0/pracma/R/modular.R | 89 +++++++++--------------
pracma-1.2.0/pracma/R/moler.R |only
pracma-1.2.0/pracma/R/norm.R |only
pracma-1.2.0/pracma/R/primes.R | 79 --------------------
pracma-1.2.0/pracma/R/qr.R | 6 -
pracma-1.2.0/pracma/R/rat.R |only
pracma-1.2.0/pracma/R/trace.R | 2
pracma-1.2.0/pracma/R/zzz.R | 6 +
pracma-1.2.0/pracma/inst/NEWS.Rd | 38 ++++++++-
pracma-1.2.0/pracma/inst/doc/NEWS.pdf |binary
pracma-1.2.0/pracma/man/andor.Rd | 16 ++--
pracma-1.2.0/pracma/man/ceil.Rd | 3
pracma-1.2.0/pracma/man/entropy.Rd |only
pracma-1.2.0/pracma/man/erfz.Rd | 13 ++-
pracma-1.2.0/pracma/man/ezcontour.Rd |only
pracma-1.2.0/pracma/man/factors.Rd |only
pracma-1.2.0/pracma/man/fnorm.Rd | 4 -
pracma-1.2.0/pracma/man/fresnel.Rd | 2
pracma-1.2.0/pracma/man/gcd.Rd |only
pracma-1.2.0/pracma/man/hadamard.Rd | 10 +-
pracma-1.2.0/pracma/man/hankel.Rd | 2
pracma-1.2.0/pracma/man/isprime.Rd | 2
pracma-1.2.0/pracma/man/lambertW.Rd | 2
pracma-1.2.0/pracma/man/matlab.Rd |only
pracma-1.2.0/pracma/man/mod.Rd | 8 +-
pracma-1.2.0/pracma/man/moler.Rd |only
pracma-1.2.0/pracma/man/norm.Rd |only
pracma-1.2.0/pracma/man/primes.Rd | 31 --------
pracma-1.2.0/pracma/man/rat.Rd | 2
pracma-1.2.0/pracma/man/steep_descent.Rd | 2
pracma-1.2.0/pracma/man/subspace.Rd | 2
pracma-1.2.0/pracma/man/testfunctions.Rd | 2
pracma-1.2.0/pracma/man/tictoc.Rd | 2
pracma-1.2.0/pracma/man/wilkinson.Rd | 2
pracma-1.2.0/pracma/tests/factors.R |only
pracma-1.2.0/pracma/tests/hadamard.R | 10 +-
pracma-1.2.0/pracma/tests/mod.R | 6 -
pracma-1.2.0/pracma/tests/norm.R |only
pracma-1.2.0/pracma/tests/subspace.R | 2
83 files changed, 285 insertions(+), 307 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.1-2 dated 2012-02-29 and 2.1-3 dated 2012-09-27
Description: Functional gradient descent algorithm (boosting) for
optimizing general risk functions utilizing component-wise
(penalised) least squares estimates or regression trees as
base-learners for fitting generalized linear, additive and
interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre], Peter Buehlmann [aut], Thomas Kneib
[aut], Matthias Schmid [aut], Benjamin Hofner [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 12
MD5 | 97 ++---
NEWS | 10
R/bkronecker.R | 11
R/bl.R | 18 -
R/bmono.R | 24 -
R/bmrf.R | 2
R/btree.R | 18 -
R/family.R | 6
R/mboost.R | 8
data/Westbc.rda |binary
data/birds.rda |binary
data/bodyfat.rda |binary
data/wpbc.rda |binary
inst/CHANGES | 10
inst/CITATION | 2
inst/doc/SurvivalEnsembles.pdf |binary
inst/doc/mboost.pdf |binary
inst/doc/mboost_illustrations.Rnw | 27 -
inst/doc/mboost_illustrations.pdf |binary
inst/doc/mboost_tutorial.Rnw | 2
inst/doc/mboost_tutorial.pdf |binary
inst/india_additive.R | 144 ++++----
inst/india_blackboost.R | 104 ++---
inst/india_preproc.R | 550 +++++++++++++++----------------
inst/india_stumps.R | 104 ++---
inst/india_summary.R | 424 +++++++++++------------
inst/india_vcm.R | 178 +++++-----
man/Family.Rd | 2
man/Westbc.Rd | 8
man/baselearners.Rd | 15
man/mboost_package.Rd | 24 -
man/stabsel.Rd | 1
tests/Examples/mboost-Ex.Rout.save | 72 +---
tests/birds_Biometrics.Rout.save | 31 -
tests/bugfixes.Rout.save | 56 +--
tests/regtest-baselearner.Rout.save | 70 +--
tests/regtest-blackboost.Rout.save | 11
tests/regtest-family.Rout.save | 9
tests/regtest-gamboost.Rout.save | 9
tests/regtest-glmboost.Rout.save | 9
tests/regtest-hatmatrix.Rout.save | 9
vignettes/figures |only
vignettes/mboost_illustrations.R |only
vignettes/mboost_illustrations.Rnw | 27 -
vignettes/mboost_illustrations.Rout.save | 120 +++---
vignettes/mboost_tutorial.Rnw | 2
vignettes/mboost_tutorial.Rout.save | 400 +++++++++++-----------
48 files changed, 1333 insertions(+), 1293 deletions(-)
Title: Sparklines and graphical tables for tex and html
Diff between sparkTable versions 0.9.5 dated 2012-06-27 and 0.9.6 dated 2012-09-27
Description: Create Sparklines and graphical tables for documents and
websites
Author: Alexander Kowarik, Bernhard Meindl, Matthias Templ
Maintainer: Alexander Kowarik
sparkTable-0.9.5/sparkTable/.project |only
sparkTable-0.9.6/sparkTable/DESCRIPTION | 8 ++---
sparkTable-0.9.6/sparkTable/MD5 | 8 ++---
sparkTable-0.9.6/sparkTable/R/checkerplot.R | 39 ++++++++++++++-----------
sparkTable-0.9.6/sparkTable/R/methods.r | 12 ++++++-
sparkTable-0.9.6/sparkTable/man/checkerplot.Rd | 17 +++-------
6 files changed, 47 insertions(+), 37 deletions(-)
Title: R wrapper around the Yahoo! Weather, Google Weather and NOAA
APIs
Diff between RWeather versions 0.3-1 dated 2012-09-13 and 0.4 dated 2012-09-27
Description: This package provides programmatic access to Yahoo!
Weather and NOAA APIs
Author: Paolo Sonego
Maintainer: Paolo Sonego
RWeather-0.3-1/RWeather/man/getCountriesFromGoogle.Rd |only
RWeather-0.3-1/RWeather/man/getWeatherFromGoogle.Rd |only
RWeather-0.4/RWeather/DESCRIPTION | 10 -
RWeather-0.4/RWeather/MD5 | 8
RWeather-0.4/RWeather/NAMESPACE | 2
RWeather-0.4/RWeather/R/rweather.r | 170 +++++++++---------
6 files changed, 93 insertions(+), 97 deletions(-)
Title: Bayesian network structure learning, parameter learning and
inference
Diff between bnlearn versions 3.0 dated 2012-07-05 and 3.1 dated 2012-09-27
Description: Bayesian network structure learning (via constraint-based,
score-based and hybrid algorithms), parameter learning (via ML
and Bayesian estimators) and inference. This package
implements the Grow-Shrink (GS) algorithm, the Incremental
Association (IAMB) algorithm, the Interleaved-IAMB (Inter-IAMB)
algorithm, the Fast-IAMB (Fast-IAMB) algorithm, the Max-Min
Parents and Children (MMPC) algorithm, the Hiton-PC algorithm,
the ARACNE and Chow-Liu algorithms, the Hill-Climbing (HC)
greedy search algorithm, the Tabu Search (TABU) algorithm, the
Max-Min Hill-Climbing (MMHC) algorithm and the two-stage
Restricted Maximization (RSMAX2) algorithm for both discrete
and Gaussian networks, along with many score functions and
conditional independence tests. The Naive Bayes and the
Tree-Augmented Naive Bayes (TAN) classifiers are also
implemented. Some utility functions (model comparison and
manipulation, random data generation, arc orientation testing,
simple and advanced plots) are included, as well as support for
parameter estimation and inference, conditional probability
queries and cross-validation.
Author: Marco Scutari
Maintainer: Marco Scutari
Changelog | 18 ++
DESCRIPTION | 10 -
MD5 | 76 +++++-----
NAMESPACE | 4
R/arc.strength.R | 33 +++-
R/backend-indep.R | 4
R/cpq.R | 17 +-
R/frontend-bn.R | 24 +--
R/frontend-fit.R | 15 +-
R/frontend-graph.R | 8 -
R/frontend-predict.R | 44 +----
R/frontend-print.R | 17 ++
R/frontend-score.R | 11 +
R/frontend-simulation.R | 4
R/frontend-strength.R | 13 +
R/globals.R | 6
R/graph-generation.R | 49 ++++++
R/hiton-pc.R | 2
R/predict.R | 4
R/test.R | 48 ++++++
R/utils-graph.R | 23 ++-
R/utils-sanitization.R | 60 ++++----
inst/bibtex/bnlearn.bib | 10 +
man/arc.strength.Rd | 3
man/bn.fit.methods.Rd | 2
man/bnlearn-package.Rd | 14 -
man/ci.test.Rd | 16 +-
man/cpdag.Rd | 35 +++-
man/cpquery.Rd | 9 +
man/naive.bayes.Rd | 13 +
man/score.Rd | 2
src/bayesian.network.c | 11 +
src/bn.recovery.c | 6
src/common.c | 10 -
src/common.h | 3
src/cpdag.c | 356 +++++++++++++++++++++++++++++-------------------
src/monte.carlo.c | 76 +++++++++-
src/predict.c | 71 +++++++--
src/sampling.c | 13 +
39 files changed, 793 insertions(+), 347 deletions(-)
Title: Accelerated Failure Time Model with Generalized Estimating
Equations
Diff between aftgee versions 0.3-5 dated 2012-08-08 and 0.3-7 dated 2012-09-27
Description: This package features both rank-based estimates and least
square estimates to the Accelerated Failure Time (AFT) model.
For rank-based estimation, it provides approaches that include
the computationally efficient Gehan's weight and the general's
weight such as the logrank weight. For the least square
estimation, the estimating equation is solved with Generalized
Estimating Equations (GEE). Moreover, in multivariate cases,
the dependence working correlation structure can be specified
in GEE's setting.
Author: Sy Han Chiou, Sangwook Kang, Jun Yan
Maintainer: Sy Han Chiou
aftgee-0.3-5/aftgee/man/prepX.Rd |only
aftgee-0.3-7/aftgee/ChangeLog | 8 +
aftgee-0.3-7/aftgee/DESCRIPTION | 17 +-
aftgee-0.3-7/aftgee/MD5 | 20 +-
aftgee-0.3-7/aftgee/NAMESPACE | 10 +
aftgee-0.3-7/aftgee/R/aftgee.R | 27 +--
aftgee-0.3-7/aftgee/R/smoothRR.R | 208 +++++++++++++++++-------------
aftgee-0.3-7/aftgee/R/summary.R | 26 ++-
aftgee-0.3-7/aftgee/man/aftgee-package.Rd | 4
aftgee-0.3-7/aftgee/man/aftgee.Rd | 21 +--
aftgee-0.3-7/aftgee/man/aftgee.prepX.Rd |only
aftgee-0.3-7/aftgee/man/smoothrr.Rd | 18 +-
12 files changed, 205 insertions(+), 154 deletions(-)
Title: Reading, manipulation and writing BAM (Binary alignment) files.
Diff between rbamtools versions 2.0.1 dated 2012-03-27 and 2.1.0 dated 2012-09-27
Description: This package provides an interface to functions of the
'SAMtools' C-Library by Heng Li.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers
rbamtools-2.0.1/rbamtools/man/bamClose.Rd |only
rbamtools-2.0.1/rbamtools/man/bamSave-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/bamSave.Rd |only
rbamtools-2.0.1/rbamtools/man/bamSort.Rd |only
rbamtools-2.0.1/rbamtools/man/cigarData-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/cigarSize-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/cigarSize.Rd |only
rbamtools-2.0.1/rbamtools/man/createIndex-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/createIndex.Rd |only
rbamtools-2.0.1/rbamtools/man/failedQC-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/filename.Rd |only
rbamtools-2.0.1/rbamtools/man/firstInPair-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/flag-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/flag.Rd |only
rbamtools-2.0.1/rbamtools/man/getHeaderText.Rd |only
rbamtools-2.0.1/rbamtools/man/getNextAlign.Rd |only
rbamtools-2.0.1/rbamtools/man/getPrevAlign-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/getPrevAlign.Rd |only
rbamtools-2.0.1/rbamtools/man/getRefCount-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/getRefCount.Rd |only
rbamtools-2.0.1/rbamtools/man/getRefData-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/getRefData.Rd |only
rbamtools-2.0.1/rbamtools/man/index.initialized-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/insertPastCurrent-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/insertSize-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/insertSize.Rd |only
rbamtools-2.0.1/rbamtools/man/isOpen.Rd |only
rbamtools-2.0.1/rbamtools/man/mapQuality-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/mapQuality.Rd |only
rbamtools-2.0.1/rbamtools/man/matePosition-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/matePosition.Rd |only
rbamtools-2.0.1/rbamtools/man/mateRefID-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/mateReverseStrand-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/mateUnmapped-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/name-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/paired-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/pcrORopt_duplicate-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/pop_front-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/position-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/position.Rd |only
rbamtools-2.0.1/rbamtools/man/properPair-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/push_back-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/push_back.Rd |only
rbamtools-2.0.1/rbamtools/man/qualities-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/readBases-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/refID-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/reverseStrand-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/secondaryAlign-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/size.Rd |only
rbamtools-2.0.1/rbamtools/man/unmapped-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/windBack-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/windBack.Rd |only
rbamtools-2.0.1/rbamtools/man/writeCurrentAlign-methods.Rd |only
rbamtools-2.0.1/rbamtools/man/writeCurrentAlign.Rd |only
rbamtools-2.1.0/rbamtools/DESCRIPTION | 8
rbamtools-2.1.0/rbamtools/MD5 | 119
rbamtools-2.1.0/rbamtools/NAMESPACE | 175
rbamtools-2.1.0/rbamtools/R/rbamtools.r | 1428 +++--
rbamtools-2.1.0/rbamtools/inst/extdata/accepted_hits.bam |binary
rbamtools-2.1.0/rbamtools/inst/extdata/accepted_hits.bam.bai |binary
rbamtools-2.1.0/rbamtools/man/as.data.frame-methods.Rd | 10
rbamtools-2.1.0/rbamtools/man/bamAlign-class.Rd | 194
rbamtools-2.1.0/rbamtools/man/bamClose-methods.Rd | 4
rbamtools-2.1.0/rbamtools/man/bamHeader-class.Rd | 54
rbamtools-2.1.0/rbamtools/man/bamHeaderText-class.Rd |only
rbamtools-2.1.0/rbamtools/man/bamRange-class.Rd | 108
rbamtools-2.1.0/rbamtools/man/bamRange.Rd | 72
rbamtools-2.1.0/rbamtools/man/bamReader-class.Rd | 62
rbamtools-2.1.0/rbamtools/man/bamReader.Rd | 12
rbamtools-2.1.0/rbamtools/man/bamWriter-class.Rd | 73
rbamtools-2.1.0/rbamtools/man/bamWriter.Rd | 57
rbamtools-2.1.0/rbamtools/man/filename-methods.Rd | 5
rbamtools-2.1.0/rbamtools/man/gapList-class.Rd |only
rbamtools-2.1.0/rbamtools/man/getHeaderText-methods.Rd | 32
rbamtools-2.1.0/rbamtools/man/getNextAlign-methods.Rd | 22
rbamtools-2.1.0/rbamtools/man/getVal.Rd | 7
rbamtools-2.1.0/rbamtools/man/headerLine-class.Rd | 11
rbamtools-2.1.0/rbamtools/man/headerProgram-class.Rd | 19
rbamtools-2.1.0/rbamtools/man/headerReadGroup-class.Rd | 19
rbamtools-2.1.0/rbamtools/man/isOpen-methods.Rd | 19
rbamtools-2.1.0/rbamtools/man/rbamtools-package.Rd | 13
rbamtools-2.1.0/rbamtools/man/refSeqDict-class.Rd | 55
rbamtools-2.1.0/rbamtools/man/setVal.Rd | 7
rbamtools-2.1.0/rbamtools/src/align_list.h | 94
rbamtools-2.1.0/rbamtools/src/gap_list.h |only
rbamtools-2.1.0/rbamtools/src/rbamtools.c | 2818 ++++++-----
rbamtools-2.1.0/rbamtools/src/rbamtools.h | 39
rbamtools-2.1.0/rbamtools/src/samtools/bam.h | 4
rbamtools-2.1.0/rbamtools/src/samtools/bam_import.c | 4
89 files changed, 3369 insertions(+), 2175 deletions(-)
Title: Solve systems of non linear equations
Diff between nleqslv versions 1.9.3 dated 2012-02-19 and 1.9.4 dated 2012-09-27
Description: Solve a system of non linear equations using a Broyden or
a Newton method with a choice of global strategies such as
linesearch and trust region. There are options for using a
numerical or an analytical jacobian and fixed or automatic
scaling of parameters.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 8 ++--
MD5 | 20 +++++------
NEWS | 10 +++++
R/nleqslv.R | 3 +
man/nleqslv.Rd | 15 +++++++-
man/zznleqslv-iterationreport.Rd | 2 -
src/nleqslv.c | 68 ++++++++++++++++++++++++---------------
src/nwbrdn.f | 30 +++++++++--------
src/nwnleq.f | 43 +++++++++++++-----------
src/nwnwtn.f | 25 ++++++++------
src/nwutil.f | 10 +++--
11 files changed, 142 insertions(+), 92 deletions(-)