Title: Tools to Convert ODM Files
Diff between ODMconverter versions 2.0 dated 2014-05-19 and 2.1 dated 2015-04-02
Description: Transformation of 'ODM' (see http://www.cdisc.org/odm) files into R format, Microsoft Office format, 'CDA' format and vice versa. 'ODM' format is commonly used in clinical trials. Semantic annotation (such as 'UMLS', 'SNOMED' or 'LOINC' codes) are transformed accordingly.
Author: Martin Dugas
Maintainer: Martin Dugas
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
R/ODM2CDA.R | 4 ++--
R/ODM2R.R | 2 +-
4 files changed, 12 insertions(+), 12 deletions(-)
Title: Solve Systems of Nonlinear Equations
Diff between nleqslv versions 2.6 dated 2015-03-04 and 2.7 dated 2015-04-02
Description: Solve a system of nonlinear equations using a Broyden or a Newton method
with a choice of global strategies such as line search and trust region.
There are options for using a numerical or user supplied Jacobian,
for specifying a banded numerical Jacobian and for allowing
a singular or ill-conditioned Jacobian.
Author: Berend Hasselman
Maintainer: Berend Hasselman
DESCRIPTION | 13 +-
MD5 | 36 +++--
NEWS | 5
R/nleqslv.R | 1
man/nleqslv-package.Rd | 8 -
man/nleqslv.Rd | 293 ++++++++++++++++++++++++++++------------------
src/nleqslv.c | 9 -
src/nwbjac.f |only
src/nwbrdn.f | 80 ++++++++----
src/nwddlg.f | 6
src/nwnjac.f | 56 ++++++--
src/nwnleq.f | 2
src/nwnwtn.f | 2
src/nwout.c | 4
src/nwutil.f | 49 +++++++
tests/singular1.R |only
tests/singular1.Rout |only
tests/singular1.Rout.save |only
tests/singular2.R |only
tests/singular2.Rout |only
tests/singular2.Rout.save |only
tests/singular3.R |only
tests/singular3.Rout |only
tests/singular3.Rout.save |only
24 files changed, 388 insertions(+), 176 deletions(-)
Title: An R Package for the Analysis of Stable Matchings
Diff between matchingMarkets versions 0.1-2 dated 2014-11-23 and 0.1-3 dated 2015-04-02
More information about matchingMarkets at CRAN
Description: Implements a structural estimator to correct for the
sample selection bias from observed outcomes in matching markets. Also
contains R code for matching algorithms such as the deferred-acceptance
algorithm for college admissions, the top-trading-cycles algorithm for
house allocation and a partitioning linear program for the roommates
problem.
Author: Thilo Klein
Maintainer: Thilo Klein
DESCRIPTION | 21 +++++++++----------
MD5 | 44 ++++++++++++++++++++++-------------------
NAMESPACE | 3 +-
R/RcppExports.R | 4 +--
R/khb.R | 18 +++++++++-------
R/mce.R |only
R/mfx.R | 8 +++----
R/stabit.R | 30 ++++++++++++++++++---------
R/stabsim.R | 20 +++++++++++++-----
R/ttc.R | 2 -
data/baac00.RData |binary
data/datalist | 1
data/klein14.RData |only
man/daa.Rd | 2 -
man/khb.Rd | 20 ++++++++++--------
man/klein14.Rd |only
man/matchingMarkets-package.Rd | 4 +--
man/mce.Rd |only
man/mfx.Rd | 10 ++++-----
man/plp.Rd | 6 ++---
man/stabit.Rd | 13 ++++--------
man/stabsim.Rd | 6 ++---
man/ttc.Rd | 4 +--
src/RcppExports.cpp | 7 +++---
src/stabitCpp.cpp | 26 +++++++++++++++---------
25 files changed, 142 insertions(+), 107 deletions(-)
Permanent link
Title: Cost Constrained FLux Balance Analysis: MetabOlic Modeling with
ENzyme kineTics (MOMENT)
Diff between sybilccFBA versions 1.0.0 dated 2014-04-02 and 2.0.0 dated 2015-04-02
Description: An implementation of a cost constrained flux balance analysis technique (i.e. MetabOlic Modeling with ENzyme kineTics (MOMENT)).
MOMENT uses enzyme kinetic data and enzyme molecular weights to constrain flux balance analysis(FBA) and it is described in
Adadi, R., Volkmer, B., Milo, R., Heinemann, M., & Shlomi, T. (2012). Prediction of Microbial Growth Rate versus Biomass
Yield by a Metabolic Network with Kinetic Parameters, 8(7). doi:10.1371/journal.pcbi.1002575.
This package also implements an improvement of MOMENT that considers multi-functional enzymes.
FBA is a mathematical technique to find fluxes in metabolic models at steady state.
It is described in Orth, J.D., Thiele, I. and Palsson, B.O. What is flux balance analysis? Nat. Biotech. 28, 245-248(2010).
Author: Abdelmoneim Amer Desouki [aut, cre]
Maintainer: Abdelmoneim Amer Desouki
DESCRIPTION | 18 ++++++++++++------
MD5 | 26 +++++++++++++++++---------
R/calc_MW.R | 2 +-
R/cfba_moment.R | 8 +++++++-
R/cfba_moment_mr.R |only
R/cfba_moment_pw.R | 10 ++++++++--
data/iAF1260.RData |binary
data/iJO1366.RData |only
data/iMM904.RData |binary
data/kcat.RData |binary
data/mw.RData |binary
data/yst_kcat.RData |only
data/yst_mw.RData |only
man/cfba_moment.Rd | 17 +++++++++++------
man/cfba_moment_mr.Rd |only
man/iJO1366.Rd |only
man/yst_kcat.Rd |only
man/yst_mw.Rd |only
18 files changed, 56 insertions(+), 25 deletions(-)
Title: Lasso Method for RCON(V,E) Models
Diff between sglasso versions 1.1-0 dated 2014-09-22 and 1.1-1 dated 2015-04-02
Description: RCON(V, E) models (Højsgaard, et al.,2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e. a cyclic coordinate minimization (CCM) and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro
ChangeLog | 9 +++++++++
DESCRIPTION | 13 +++++++------
MD5 | 37 +++++++++++++++++++------------------
NAMESPACE | 1 +
R/fglasso_model2mask.R | 8 +++++++-
R/klcv.R | 4 +++-
R/loglik.R | 2 +-
R/mask2Te.R | 4 +++-
R/print.klcv.R |only
R/sglasso.fit.R | 4 ++--
man/Kh.Rd | 2 +-
man/fglasso.Rd | 16 ++++++++++------
man/klcv.Rd | 7 ++++---
man/sglasso-package.Rd | 6 +++---
man/sglasso.Rd | 2 +-
man/summary.sglasso.Rd | 4 ++--
src/sglasso_ccd_path.f90 | 15 +--------------
src/sglasso_ccd_single.f90 | 15 +--------------
src/sglasso_ccm_path.f90 | 19 +++----------------
src/sglasso_ccm_single.f90 | 13 -------------
20 files changed, 78 insertions(+), 103 deletions(-)
Title: Calculation of Rarity Indices for Species and Assemblages of
Species
Diff between Rarity versions 1.3-1 dated 2015-03-17 and 1.3-4 dated 2015-04-02
Description: Allows calculation of rarity weights for species and indices of rarity for assemblages of species according to different methods (Leroy et al. 2012, 2013).
Author: Boris Leroy
Maintainer: Boris Leroy
Rarity-1.3-1/Rarity/R/rarity_indices.R |only
Rarity-1.3-4/Rarity/DESCRIPTION | 8
Rarity-1.3-4/Rarity/MD5 | 21 -
Rarity-1.3-4/Rarity/R/correlation_plots.R | 10
Rarity-1.3-4/Rarity/R/rarity_weights.R | 69 ++--
Rarity-1.3-4/Rarity/R/relative_rarity.R |only
Rarity-1.3-4/Rarity/R/summed_rarity.R | 425 ++++++++++++++----------------
Rarity-1.3-4/Rarity/man/Irr.Rd | 14
Rarity-1.3-4/Rarity/man/Isr.Rd | 8
Rarity-1.3-4/Rarity/man/rWeights.Rd | 14
Rarity-1.3-4/Rarity/man/spid.occ.Rd | 7
Rarity-1.3-4/Rarity/tests |only
12 files changed, 298 insertions(+), 278 deletions(-)
Title: Unified Multiple Testing Procedures
Diff between mutoss versions 0.1-9 dated 2015-03-12 and 0.1-10 dated 2015-04-02
Description: The Mutoss package and accompanying mutossGUI package are
designed to ease the application and comparison of multiple
hypothesis testing procedures.
Author: MuToss Coding Team (Berlin 2010), Gilles Blanchard, Thorsten Dickhaus,
Niklas Hack, Frank Konietschke, Kornelius Rohmeyer,
Jonathan Rosenblatt, Marsel Scheer, Wiebke Werft
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/Hommel.R | 6 +++---
build/vignette.rds |binary
inst/doc/quickstart.pdf |binary
inst/doc/simToolManual.pdf |binary
6 files changed, 11 insertions(+), 11 deletions(-)
Title: Fast Calculation of the Likelihood of a Stochastic Survival
Model
Diff between GUTS versions 0.3.5 dated 2014-05-05 and 0.4.12 dated 2015-04-02
Description: Given exposure and survival time series as well as parameter values, GUTS allows for the calculation of the survival probabilities as well as the logarithm of the corresponding likelihood.
Author: Carlo Albert
Maintainer: Sören Vogel
DESCRIPTION | 16
MD5 | 22
R/GUTS.R | 68 +-
configure | 20
data/diazinon.RData |binary
man/Rcpp_GUTS-class.Rd | 353 ++++++-------
src/GUTS.cpp | 840 ++++++++++++++++++++-------------
src/GUTS.h | 534 ++++++++++++++------
src/GUTS_Rcpp.cpp | 91 ++-
src/GUTS_calcLoglikelihood.cpp | 69 +-
src/GUTS_calcSample.cpp | 238 ++++++---
src/GUTS_calcSurvivalProbabilities.cpp | 512 +++++++++++---------
12 files changed, 1676 insertions(+), 1087 deletions(-)
Title: Gaussian Processes Modeling
Diff between GPfit versions 0.2-1 dated 2014-09-03 and 1.0-0 dated 2015-04-02
Description: A computationally stable approach of fitting a Gaussian Process (GP) model to a deterministic simulator.
Author: Blake MacDoanld, Hugh Chipman, Pritam Ranjan
Maintainer: Hugh Chipman
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NAMESPACE | 7 ++++++-
NEWS |only
inst |only
man/GP_fit.Rd | 39 ++++++++++++++++++++++++---------------
man/GPfit-package.Rd | 9 ++++++---
man/corr_matrix.Rd | 21 ++++++++++++++-------
8 files changed, 61 insertions(+), 35 deletions(-)
Title: Geometric Morphometric Analyses of 2d/3D Landmark Data
Diff between geomorph versions 2.1.3 dated 2015-02-12 and 2.1.4 dated 2015-04-02
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.1.3/geomorph/R/define.links.R |only
geomorph-2.1.3/geomorph/R/define.modules.R |only
geomorph-2.1.3/geomorph/R/findMeanSpec.R |only
geomorph-2.1.3/geomorph/R/morphol.disparity.R |only
geomorph-2.1.3/geomorph/R/plotAllometry.R |only
geomorph-2.1.3/geomorph/R/plotOutliers.R |only
geomorph-2.1.3/geomorph/R/warpRefMesh.R |only
geomorph-2.1.3/geomorph/R/warpRefOutline.R |only
geomorph-2.1.4/geomorph/DESCRIPTION | 12
geomorph-2.1.4/geomorph/MD5 | 90 ++--
geomorph-2.1.4/geomorph/NEWS | 29 +
geomorph-2.1.4/geomorph/R/advanced.procD.lm.r | 34 -
geomorph-2.1.4/geomorph/R/bilat.symmetry.r | 2
geomorph-2.1.4/geomorph/R/build.template.r | 190 ++++----
geomorph-2.1.4/geomorph/R/define.links.r |only
geomorph-2.1.4/geomorph/R/define.modules.r |only
geomorph-2.1.4/geomorph/R/define.sliders.3d.r | 188 ++++----
geomorph-2.1.4/geomorph/R/digitsurface.r | 198 ++++----
geomorph-2.1.4/geomorph/R/editTemplate.r | 114 ++---
geomorph-2.1.4/geomorph/R/estimate.missing.r | 8
geomorph-2.1.4/geomorph/R/findMeanSpec.r |only
geomorph-2.1.4/geomorph/R/geomorph.support.code.r | 39 -
geomorph-2.1.4/geomorph/R/gpagen.r | 20
geomorph-2.1.4/geomorph/R/morphol.disparity.r |only
geomorph-2.1.4/geomorph/R/pairwise.slope.test.r | 24 -
geomorph-2.1.4/geomorph/R/pairwiseD.test.r | 23 -
geomorph-2.1.4/geomorph/R/plotAllometry.r |only
geomorph-2.1.4/geomorph/R/plotGMPhyloMorphoSpace.r | 152 +++---
geomorph-2.1.4/geomorph/R/plotOutliers.r |only
geomorph-2.1.4/geomorph/R/procD.lm.r | 45 --
geomorph-2.1.4/geomorph/R/procD.pgls.r | 19
geomorph-2.1.4/geomorph/R/read.morphologika.r | 8
geomorph-2.1.4/geomorph/R/readland.tps.r | 296 ++++++-------
geomorph-2.1.4/geomorph/R/trajectory.analysis.r | 468 ++++++++++-----------
geomorph-2.1.4/geomorph/R/warpRefMesh.r |only
geomorph-2.1.4/geomorph/R/warpRefOutline.r |only
geomorph-2.1.4/geomorph/man/advanced.procD.lm.Rd | 15
geomorph-2.1.4/geomorph/man/define.links.Rd | 2
geomorph-2.1.4/geomorph/man/define.modules.Rd | 2
geomorph-2.1.4/geomorph/man/estimate.missing.Rd | 6
geomorph-2.1.4/geomorph/man/findMeanSpec.Rd | 2
geomorph-2.1.4/geomorph/man/geomorph-package.Rd | 2
geomorph-2.1.4/geomorph/man/gpagen.Rd | 8
geomorph-2.1.4/geomorph/man/morphol.disparity.Rd | 6
geomorph-2.1.4/geomorph/man/pairwise.slope.test.Rd | 13
geomorph-2.1.4/geomorph/man/pairwiseD.test.Rd | 5
geomorph-2.1.4/geomorph/man/plotAllometry.Rd | 29 -
geomorph-2.1.4/geomorph/man/plotOutliers.Rd | 12
geomorph-2.1.4/geomorph/man/procD.lm.Rd | 19
geomorph-2.1.4/geomorph/man/procD.pgls.Rd | 8
geomorph-2.1.4/geomorph/man/read.morphologika.Rd | 2
geomorph-2.1.4/geomorph/man/trajectory.analysis.Rd | 2
geomorph-2.1.4/geomorph/man/warpRefMesh.Rd | 13
geomorph-2.1.4/geomorph/man/warpRefOutline.Rd | 2
54 files changed, 1064 insertions(+), 1043 deletions(-)
Title: Analysis of Geostatistical Data using Bayes and Empirical Bayes
Methods
Diff between geoBayes versions 0.2.150308 dated 2015-03-08 and 0.2.150402 dated 2015-04-02
Description: Functions to fit geostatistical data. The data can be
continuous, binary or count data and the models implemented are
flexible. Conjugate priors are assumed on some parameters while
inference on the other parameters can be done through a full
Bayesian analysis of by empirical Bayes methods.
Author: Evangelos Evangelou
Maintainer: Evangelos Evangelou
DESCRIPTION | 18 -
MD5 | 52 ++--
NAMESPACE | 2
NEWS | 4
R/calcbf.R | 4
man/bf1skel.Rd | 3
man/bf2new.Rd | 3
man/bf2optim.Rd | 3
man/bfse.Rd | 3
man/comparebinlinks.Rd | 3
man/ebsglmm.Rd | 3
man/ebstrga.Rd | 3
man/geoBayes.Rd | 3
man/linkfcn.Rd | 7
man/mcmcmake.Rd | 3
man/mcsglmm.Rd | 3
man/mcstrga.Rd | 3
man/mkpredgrid2d.Rd | 3
man/plotbf2.Rd | 3
man/rhizoctonia.Rd | 3
man/stackdata.Rd | 3
src/bfsp.f90 | 30 +-
src/calcb2.f90 | 40 +--
src/covfun.f90 | 12 -
src/llik.f90 | 32 +--
src/mcsp2.f90 | 510 +++++++++++++++++++++++++++++--------------------
src/mcspz0.f90 | 8
27 files changed, 448 insertions(+), 316 deletions(-)