Title: Voxelwise Semiparametrics
Diff between vows versions 0.3.1 dated 2015-01-08 and 0.4 dated 2015-02-12
Description: Parametric and semiparametric inference for massively parallel
models, i.e., a large number of models with common design matrix, as often
occurs with brain imaging data.
Author: Philip Reiss, Yin-Hsiu Chen, Lei Huang, Lan Huo, Ruixin Tan, and Rong Jiao
Maintainer: Philip Reiss
vows-0.3.1/vows/R/vows_0.3-package.R |only
vows-0.4/vows/DESCRIPTION | 15 --
vows-0.4/vows/MD5 | 74 +++++-----
vows-0.4/vows/NAMESPACE | 9 +
vows-0.4/vows/R/R2nii.R | 62 ++++----
vows-0.4/vows/R/nii2R.R | 178 ++++++++++++------------
vows-0.4/vows/R/rlrt4d.R | 73 +++++-----
vows-0.4/vows/R/vows-internal.R | 135 +++++++++---------
vows-0.4/vows/R/vows-mgcv.R | 250 +++++++++++++++++------------------
vows-0.4/vows/R/vows_0.4-package.R |only
vows-0.4/vows/man/F.mp.Rd | 3
vows-0.4/vows/man/Fdr.rlrt.Rd | 3
vows-0.4/vows/man/R2nii.Rd | 7
vows-0.4/vows/man/extract.fd.Rd | 3
vows-0.4/vows/man/funkmeans.Rd | 3
vows-0.4/vows/man/funkmeans4d.Rd | 3
vows-0.4/vows/man/funkpanel.Rd | 3
vows-0.4/vows/man/lm.mp.Rd | 3
vows-0.4/vows/man/lm4d.Rd | 3
vows-0.4/vows/man/nii2R.Rd | 7
vows-0.4/vows/man/permF.mp.Rd | 3
vows-0.4/vows/man/plot.funkmeans.Rd | 3
vows-0.4/vows/man/plot.rlrt4d.Rd | 3
vows-0.4/vows/man/plot.semipar.mp.Rd | 3
vows-0.4/vows/man/qplsc.mp.Rd | 3
vows-0.4/vows/man/rlrt.mp.Rd | 9 -
vows-0.4/vows/man/rlrt.mp.fit.Rd | 3
vows-0.4/vows/man/rlrt4d.Rd | 5
vows-0.4/vows/man/rlrtpanel.Rd | 3
vows-0.4/vows/man/screen.vox.Rd | 3
vows-0.4/vows/man/semipar.mix.mp.Rd | 3
vows-0.4/vows/man/semipar.mp.Rd | 3
vows-0.4/vows/man/semipar4d.Rd | 3
vows-0.4/vows/man/sf.Rd | 3
vows-0.4/vows/man/summary.lm.mp.Rd | 3
vows-0.4/vows/man/test.Rd | 3
vows-0.4/vows/man/vows-internal.Rd | 10 +
vows-0.4/vows/man/vows-mgcv.Rd | 3
vows-0.4/vows/man/vows-package.Rd | 5
39 files changed, 478 insertions(+), 430 deletions(-)
Title: Stereo Camera Calibration and Reconstruction
Diff between StereoMorph versions 1.2.1 dated 2014-09-02 and 1.3 dated 2015-02-12
Description: Functions for the collection of 3D points and curves using a stereo camera setup.
Author: Aaron Olsen, Annat Haber
Maintainer: Aaron Olsen
DESCRIPTION | 13
MD5 | 42 +-
NAMESPACE | 22 +
R/digitizeImage.R | 40 +-
R/dltCalibrateCameras.R | 276 +++++++++++++---
R/dltMatchCurvePoints.R | 5
R/findCheckerboardCorners.R | 77 +++-
R/inverseGridTransform.R |only
inst/extdata/apps/digitizeImage/digitize_image.html | 2
inst/extdata/apps/digitizeImage/digitize_image_pre.html | 16
inst/extdata/apps/digitizeImage/initial_parameters.R | 45 +-
inst/extdata/apps/digitizeImage/server.R | 12
inst/extdata/apps/digitizeImage/www/digitize_image.css | 12
inst/extdata/apps/digitizeImage/www/digitize_image.js | 59 ++-
inst/extdata/apps/digitizeImage/www/help.html | 31 +
inst/extdata/apps/initial_parameters.R |only
man/StereoMorph-package.Rd | 6
man/digitizeImage.Rd | 2
man/dltCalibrateCameras.Rd | 41 +-
man/dltMatchCurvePoints.Rd | 3
man/dltReconstruct.Rd | 2
man/findCheckerboardCorners.Rd | 16
src/Makevars.win | 10
23 files changed, 552 insertions(+), 180 deletions(-)
Title: Spherical K-Function
Diff between SphericalK versions 1.0 dated 2014-11-26 and 1.1 dated 2015-02-12
Description: Spherical K-function for point-pattern analysis on the sphere.
Author: Scott Robeson, Ao Li, Chunfeng Huang
Maintainer: Ao Li
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
R/SphericalK.R | 3 ++-
man/Hex272.Rd | 2 +-
man/Hex92.Rd | 2 +-
man/SphericalK-package.Rd | 4 ++--
man/sphere_grid.Rd | 2 +-
man/sphere_khat.Rd | 4 ++--
man/sphere_montekhat.Rd | 2 +-
man/sphere_random.Rd | 4 ++--
10 files changed, 27 insertions(+), 26 deletions(-)
Title: Tools for Simplifying the Population and Querying of SQLite
Databases
Diff between poplite versions 0.99.5 dated 2014-11-05 and 0.99.16 dated 2015-02-12
Description: Provides objects and accompanying methods which facilitates populating and querying SQLite databases.
Author: Daniel Bottomly [cre, aut],
Shannon McWeeney [aut],
Beth Wilmot [aut]
Maintainer: Daniel Bottomly
DESCRIPTION | 22 +-
MD5 | 21 +-
NAMESPACE | 4
R/Database.R | 375 ++++++++++++++++++++++++++++++------------
R/external_funcs.R | 57 ++++--
R/tableSchemaList.R | 49 +++++
README.md |only
build/vignette.rds |binary
data/clinical.rda |binary
inst/doc/poplite.pdf |binary
tests/testthat.R | 92 ++++++++++
tests/testthat/test-poplite.R | 94 ++++++++++
12 files changed, 570 insertions(+), 144 deletions(-)
Title: Geometric Morphometric Analyses of 2d/3D Landmark Data
Diff between geomorph versions 2.1.2 dated 2014-11-04 and 2.1.3 dated 2015-02-12
Description: Geomorph allows users to 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, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
geomorph-2.1.2/geomorph/R/plotAllometry.r |only
geomorph-2.1.3/geomorph/DESCRIPTION | 16
geomorph-2.1.3/geomorph/MD5 | 188 ++--
geomorph-2.1.3/geomorph/NAMESPACE | 5
geomorph-2.1.3/geomorph/NEWS | 29
geomorph-2.1.3/geomorph/R/advanced.procD.lm.r | 12
geomorph-2.1.3/geomorph/R/bilat.symmetry.r | 50 -
geomorph-2.1.3/geomorph/R/build.template.r | 190 ++--
geomorph-2.1.3/geomorph/R/compare.evol.rates.r | 8
geomorph-2.1.3/geomorph/R/compare.modular.partitions.r | 3
geomorph-2.1.3/geomorph/R/define.links.R |only
geomorph-2.1.3/geomorph/R/define.modules.R | 86 +
geomorph-2.1.3/geomorph/R/define.sliders.3d.r | 188 ++--
geomorph-2.1.3/geomorph/R/digit.fixed.r | 250 ++---
geomorph-2.1.3/geomorph/R/digitsurface.r | 198 ++--
geomorph-2.1.3/geomorph/R/editTemplate.r | 114 +-
geomorph-2.1.3/geomorph/R/geomorph.support.code.r | 621 +++++++-------
geomorph-2.1.3/geomorph/R/pairwise.slope.test.r | 40
geomorph-2.1.3/geomorph/R/pairwiseD.test.r | 41
geomorph-2.1.3/geomorph/R/phylo.pls.R | 33
geomorph-2.1.3/geomorph/R/physignal.r | 37
geomorph-2.1.3/geomorph/R/plotAllometry.R |only
geomorph-2.1.3/geomorph/R/plotOutliers.R |only
geomorph-2.1.3/geomorph/R/plotRefToTarget.r | 17
geomorph-2.1.3/geomorph/R/plotTangentSpace.r | 253 ++---
geomorph-2.1.3/geomorph/R/procD.lm.r | 7
geomorph-2.1.3/geomorph/R/procD.pgls.r | 11
geomorph-2.1.3/geomorph/R/read.ply.r | 7
geomorph-2.1.3/geomorph/R/readland.tps.r | 72 +
geomorph-2.1.3/geomorph/R/trajectory.analysis.r | 410 +++++----
geomorph-2.1.3/geomorph/data/hummingbirds.rda |binary
geomorph-2.1.3/geomorph/data/mosquito.rda |binary
geomorph-2.1.3/geomorph/data/motionpaths.rda |binary
geomorph-2.1.3/geomorph/data/plethShapeFood.rda |binary
geomorph-2.1.3/geomorph/data/plethodon.rda |binary
geomorph-2.1.3/geomorph/data/plethspecies.rda |binary
geomorph-2.1.3/geomorph/data/pupfish.rda |binary
geomorph-2.1.3/geomorph/data/ratland.rda |binary
geomorph-2.1.3/geomorph/data/scallopPLY.rda |binary
geomorph-2.1.3/geomorph/data/scallops.rda |binary
geomorph-2.1.3/geomorph/man/advanced.procD.lm.Rd | 5
geomorph-2.1.3/geomorph/man/arrayspecs.Rd | 3
geomorph-2.1.3/geomorph/man/bilat.symmetry.Rd | 3
geomorph-2.1.3/geomorph/man/buildtemplate.Rd | 7
geomorph-2.1.3/geomorph/man/compare.evol.rates.Rd | 3
geomorph-2.1.3/geomorph/man/compare.modular.partitions.Rd | 6
geomorph-2.1.3/geomorph/man/define.links.Rd |only
geomorph-2.1.3/geomorph/man/define.modules.Rd | 23
geomorph-2.1.3/geomorph/man/define.sliders.2d.Rd | 3
geomorph-2.1.3/geomorph/man/define.sliders.3d.Rd | 15
geomorph-2.1.3/geomorph/man/digit.fixed.Rd | 7
geomorph-2.1.3/geomorph/man/digitize2d.Rd | 3
geomorph-2.1.3/geomorph/man/digitsurface.Rd | 7
geomorph-2.1.3/geomorph/man/editTemplate.Rd | 7
geomorph-2.1.3/geomorph/man/estimate.missing.Rd | 3
geomorph-2.1.3/geomorph/man/findMeanSpec.Rd | 3
geomorph-2.1.3/geomorph/man/fixed.angle.Rd | 3
geomorph-2.1.3/geomorph/man/geomorph-package.Rd | 3
geomorph-2.1.3/geomorph/man/gpagen.Rd | 3
geomorph-2.1.3/geomorph/man/hummingbirds.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.disparity.Rd | 3
geomorph-2.1.3/geomorph/man/morphol.integr.Rd | 3
geomorph-2.1.3/geomorph/man/mosquito.Rd | 3
geomorph-2.1.3/geomorph/man/motionpaths.Rd | 3
geomorph-2.1.3/geomorph/man/mshape.Rd | 3
geomorph-2.1.3/geomorph/man/pairwise.slope.test.Rd | 19
geomorph-2.1.3/geomorph/man/pairwiseD.test.Rd | 15
geomorph-2.1.3/geomorph/man/phylo.pls.Rd | 5
geomorph-2.1.3/geomorph/man/physignal.Rd | 5
geomorph-2.1.3/geomorph/man/plethShapeFood.Rd | 3
geomorph-2.1.3/geomorph/man/plethodon.Rd | 3
geomorph-2.1.3/geomorph/man/plethspecies.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllSpecimens.Rd | 3
geomorph-2.1.3/geomorph/man/plotAllometry.Rd | 15
geomorph-2.1.3/geomorph/man/plotGMPhyloMorphoSpace.Rd | 3
geomorph-2.1.3/geomorph/man/plotOutliers.Rd |only
geomorph-2.1.3/geomorph/man/plotRefToTarget.Rd | 15
geomorph-2.1.3/geomorph/man/plotTangentSpace.Rd | 13
geomorph-2.1.3/geomorph/man/plotspec.Rd | 3
geomorph-2.1.3/geomorph/man/procD.lm.Rd | 7
geomorph-2.1.3/geomorph/man/procD.pgls.Rd | 9
geomorph-2.1.3/geomorph/man/pupfish.Rd | 13
geomorph-2.1.3/geomorph/man/ratland.Rd | 3
geomorph-2.1.3/geomorph/man/read.morphologika.Rd | 3
geomorph-2.1.3/geomorph/man/read.ply.Rd | 10
geomorph-2.1.3/geomorph/man/readland.nts.Rd | 3
geomorph-2.1.3/geomorph/man/readland.tps.Rd | 17
geomorph-2.1.3/geomorph/man/readmulti.nts.Rd | 3
geomorph-2.1.3/geomorph/man/scallopPLY.Rd | 3
geomorph-2.1.3/geomorph/man/scallops.Rd | 3
geomorph-2.1.3/geomorph/man/trajectory.analysis.Rd | 27
geomorph-2.1.3/geomorph/man/two.b.pls.Rd | 3
geomorph-2.1.3/geomorph/man/two.d.array.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefMesh.Rd | 3
geomorph-2.1.3/geomorph/man/warpRefOutline.Rd | 3
geomorph-2.1.3/geomorph/man/writeland.tps.Rd | 3
geomorph-2.1.3/geomorph/src/Makevars | 2
geomorph-2.1.3/geomorph/src/Makevars.win | 2
98 files changed, 1790 insertions(+), 1446 deletions(-)
Title: Discovering Multiple, Statistically-Equivalent Signatures
Diff between MXM versions 0.2.1 dated 2014-08-04 and 0.3 dated 2015-02-12
Description: Feature selection methods for identifying minimal, statistically-equivalent and equally-predictive feature subsets. MXM stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin.
Author: Ioannis Tsamardinos, Vincenzo Lagani, Giorgos Borboudakis, Giorgos Athineou
Maintainer: Giorgos Athineou
MXM-0.2.1/MXM/man/SES-internal.Rd |only
MXM-0.3/MXM/DESCRIPTION | 11 ++--
MXM-0.3/MXM/MD5 | 28 +++++------
MXM-0.3/MXM/NAMESPACE | 18 ++++++-
MXM-0.3/MXM/R/SES.R | 14 ++---
MXM-0.3/MXM/R/censIndLR.R | 8 +--
MXM-0.3/MXM/R/gSquare.R | 8 +--
MXM-0.3/MXM/R/testIndFisher.R | 38 +++++++++------
MXM-0.3/MXM/R/testIndLogistic.R | 32 ++++++-------
MXM-0.3/MXM/man/MXM-internal.Rd |only
MXM-0.3/MXM/man/MXM-package.Rd | 2
MXM-0.3/MXM/man/SES.Rd | 6 ++
MXM-0.3/MXM/man/SESoutput-class.Rd | 5 ++
MXM-0.3/MXM/man/censIndLR.Rd | 36 +++++++-------
MXM-0.3/MXM/man/gSquare.Rd | 25 +++++-----
MXM-0.3/MXM/man/testIndLogistic.Rd | 89 ++++++++++++++++++++-----------------
16 files changed, 182 insertions(+), 138 deletions(-)
Title: All-Purpose Toolkit for Analyzing Multivariate Time Series (MTS)
and Estimating Multivariate Volatility Models
Diff between MTS versions 0.32 dated 2014-03-01 and 0.33 dated 2015-02-12
Description: Multivariate Time Series (MTS) is a general package for analyzing multivariate linear time series and estimating multivariate volatility models. It also handles factor models, constrained factor models, asymptotic principal component analysis commonly used in finance and econometrics, and principal volatility component analysis. (a) For the multivariate linear time series analysis, the package performs model specification, estimation, model checking, and prediction for many widely used models, including vector AR models, vector MA models, vector ARMA models, seasonal vector ARMA models, VAR models with exogenous variables, multivariate regression models with time series errors, augmented VAR models, and Error-correction VAR models for co-integrated time series. For model specification, the package performs structural specification to overcome the difficulties of identifiability of VARMA models. The methods used for structural specification include Kronecker indices and Scalar Component Models. (b) For multivariate volatility modeling, the MTS package handles several commonly used models, including multivariate exponentially weighted moving-average volatility, Cholesky decomposition volatility models, dynamic conditional correlation (DCC) models, copula-based volatility models, and low-dimensional BEKK models. The package also considers multiple tests for conditional heteroscedasticity, including rank-based statistics. (c) Finally, the MTS package also performs forecasting using diffusion index, transfer function analysis, Bayesian estimation of VAR models, and multivariate time series analysis with missing values.Users can also use the package to simulate VARMA models, to compute impulse response functions of a fitted VARMA model, and to calculate theoretical cross-covariance matrices of a given VARMA model.
Author: Ruey S. Tsay
Maintainer: Ruey S. Tsay
DESCRIPTION | 12
MD5 | 21 -
R/MTS.R | 777 +++++++++++++++++++++++++++++++++++++++++++++++++----
R/VARMACpp.R | 4
R/sVARMACpp.R | 8
man/BVAR.Rd | 2
man/Btfm2.Rd |only
man/GrangerTest.Rd |only
man/MTS-package.Rd | 4
man/tfm.Rd | 2
man/tfm1.Rd | 11
man/tfm2.Rd |only
src/varma.cpp | 361 +++++++++++++++---------
13 files changed, 982 insertions(+), 220 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.4-1 dated 2014-12-15 and 2.4-2 dated 2015-02-12
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],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++--
MD5 | 31 ++++++++---------
NAMESPACE | 4 +-
R/bl.R | 5 +-
R/bmono.R | 2 -
R/bmrf.R | 4 +-
R/brad.R | 5 --
R/btree.R | 2 -
inst/CITATION | 69 +++++++++++++++++++++++++-------------
inst/NEWS.Rd | 25 +++++++++++++
inst/doc/SurvivalEnsembles.pdf |binary
inst/doc/mboost.pdf |binary
inst/doc/mboost_illustrations.pdf |binary
inst/doc/mboost_tutorial.pdf |binary
man/blackboost.Rd | 18 +++++----
man/helper.Rd |only
man/mboost_package.Rd | 9 +++-
17 files changed, 117 insertions(+), 65 deletions(-)
Title: Genetic Algorithm (GA) for Variable Selection from
High-Dimensional Data
Diff between gaselect versions 1.0.4 dated 2015-02-10 and 1.0.5 dated 2015-02-12
Description: Provides a genetic algorithm for finding variable
subsets in high dimensional data with high prediction performance. The
genetic algorithm can use ordinary least squares (OLS) regression models or
partial least squares (PLS) regression models to evaluate the prediction
power of variable subsets. By supporting different cross-validation
schemes, the user can fine-tune the tradeoff between speed and quality of
the solution.
Author: David Kepplinger
Maintainer: David Kepplinger
ChangeLog | 4 ++++
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
src/BICEvaluator.cpp | 4 ++--
src/LMEvaluator.cpp | 2 +-
src/PLSEvaluator.cpp | 2 +-
6 files changed, 16 insertions(+), 12 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.1 dated 2015-01-13 and 1.2 dated 2015-02-12
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
ultrametric trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 8 -
MD5 | 46 +++----
NAMESPACE | 6
R/BAT.R | 294 +++++++++++++++++++++++++++++++++++++++++++++--
man/accuracy.Rd | 3
man/alpha.Rd | 3
man/alpha.accum.Rd | 3
man/alpha.estimate.Rd | 3
man/arrabida.Rd | 3
man/beta.Rd | 3
man/beta.accum.Rd | 3
man/beta.multi.Rd | 3
man/functree.Rd | 3
man/geres.Rd | 3
man/guadiana.Rd | 3
man/optim.alpha.Rd |only
man/optim.alpha.stats.Rd |only
man/optim.beta.Rd |only
man/optim.beta.stats.Rd |only
man/phylotree.Rd | 3
man/sim.plot.Rd | 3
man/sim.sad.Rd | 3
man/sim.sample.Rd | 3
man/sim.spatial.Rd | 3
man/sim.tree.Rd | 13 +-
man/slope.Rd | 3
26 files changed, 359 insertions(+), 59 deletions(-)
Title: Generalized Linear Mixed Models via Monte Carlo Likelihood
Approximation
Diff between glmm versions 1.0 dated 2015-02-11 and 1.0.1 dated 2015-02-12
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson
Maintainer: Christina Knudson
DESCRIPTION | 8 +-
MD5 | 4 -
src/objfunc.c | 187 ++++++++++++++++++++++++++++------------------------------
3 files changed, 98 insertions(+), 101 deletions(-)
Title: Calculate Generalized Eigenvalues of a Matrix Pair
Diff between geigen versions 1.4 dated 2014-08-18 and 1.5 dated 2015-02-12
Description: Compute generalized eigenvalues and eigenvectors of a pair of matrices,
using routines from Lapack (dggev and zggev). Compute the
generalized Schur decomposition of a pair of matrices using Lapack routines.
In the latter case options for ordering the generalized eigenvalues are provided.
Author: Berend Hasselman, Lapack authors
Maintainer: Berend Hasselman
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
NEWS | 5 +++++
R/cmplxdiv.R | 14 +++++++-------
inst/CITATION | 8 ++++----
man/geigen-package.Rd | 10 +++++-----
man/geigen.Rd | 10 +++++-----
man/gevalues.Rd | 10 +++++-----
8 files changed, 44 insertions(+), 39 deletions(-)
Title: Estimability Tools for Linear Models
Diff between estimability versions 1.0-2 dated 2015-01-31 and 1.1 dated 2015-02-12
Description: Provides tools for determining estimability of linear functions of regression coefficients,
and 'epredict' methods that handle non-estimable cases correctly.
Author: Russell V. Lenth
Maintainer: Russell V. Lenth
DESCRIPTION | 12 +++----
MD5 | 13 ++++----
NAMESPACE | 14 ++++++---
R/epredict.lm.R | 79 ++++++++++++++++++++++++++++++++++------------------
R/estimability.R | 30 +++++++++++++++----
inst |only
man/epredict.lm.Rd | 66 ++++++++++++++++++++++++++++++++-----------
man/nonest.basis.Rd | 38 +++++++++++++++++--------
8 files changed, 174 insertions(+), 78 deletions(-)