Title: Mixed Models, Particularly Spatial GLMMs
Diff between spaMM versions 1.4.0 dated 2014-11-07 and 1.4.1 dated 2014-11-08
Description: Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph],
Jean-Baptiste Ferdy [aut, cph]
Maintainer: François Rousset
spaMM-1.4.0/spaMM/tests/test-all.R |only
spaMM-1.4.1/spaMM/DESCRIPTION | 10 +++----
spaMM-1.4.1/spaMM/MD5 | 18 ++++++------
spaMM-1.4.1/spaMM/R/HLCor.R | 14 +++++++---
spaMM-1.4.1/spaMM/R/HLfit.R | 5 ++-
spaMM-1.4.1/spaMM/R/corrHLfit.R | 2 -
spaMM-1.4.1/spaMM/R/locoptim.R | 25 +++++++++---------
spaMM-1.4.1/spaMM/R/summary.HL.R | 6 ++--
spaMM-1.4.1/spaMM/tests/testthat/test-Nugget.R |only
spaMM-1.4.1/spaMM/tests/testthat/test-corMatern.R | 3 --
spaMM-1.4.1/spaMM/tests/testthat/test-inverse.Gamma.R | 2 +
11 files changed, 49 insertions(+), 36 deletions(-)
Title: Univariate GARCH models
Diff between rugarch versions 1.3-3 dated 2014-05-26 and 1.3-4 dated 2014-11-08
Description: ARFIMA, in-mean, external regressors and various GARCH flavors, with methods for fit, forecast, simulation, inference and plotting.
Author: Alexios Ghalanos
Maintainer: Alexios Ghalanos
.Rinstignore | 4 -
ChangeLog | 9 +++
DESCRIPTION | 10 ++--
MD5 | 55 +++++++++++------------
R/arfima-main.R | 16 +++++-
R/arfima-methods.R | 8 ++-
R/rugarch-aparch.R | 6 +-
R/rugarch-csgarch.R | 6 +-
R/rugarch-egarch.R | 6 +-
R/rugarch-fgarch.R | 6 +-
R/rugarch-gjrgarch.R | 6 +-
R/rugarch-graphs.R | 49 +++++++++++++-------
R/rugarch-helperfn.R | 32 ++++++++++---
R/rugarch-igarch.R | 4 +
R/rugarch-mcsgarch.R | 10 ++--
R/rugarch-methods.R | 38 ++++++++++-----
R/rugarch-numderiv.R | 8 +--
R/rugarch-realgarch.R | 5 +-
R/rugarch-rolling.R | 2
R/rugarch-sgarch.R | 6 +-
R/rugarch-solvers.R | 10 ----
README.md |only
build/vignette.rds |binary
inst/doc/Introduction_to_the_rugarch_package.pdf |binary
man/arfimafit-methods.Rd | 8 ++-
man/rugarch-package.Rd | 6 +-
man/ugarchfit-methods.Rd | 9 +++
src/distributions.c | 4 +
src/filters.c | 8 +++
src/garchmodels.c | 2
30 files changed, 217 insertions(+), 116 deletions(-)
Title: Nonlinear Calibration
Diff between nCal versions 14.10-31 dated 2014-11-02 and 14.11-8 dated 2014-11-08
Description: nCal is a package that performs nonlinear calibration and curve fitting for data from Luminex, RT-PCR, ELISA, RPPA etc. Its precursor is Ruminex.
Author: Youyi Fong
Maintainer: Youyi Fong
DESCRIPTION | 6 +++---
MD5 | 12 ++++++------
inst/doc/nCal-vignette.pdf |binary
inst/unitTests/runit.bcrm.R | 10 ++++++++--
vignettes/figure/minimal-Example1bcrm.pdf |binary
vignettes/figure/minimal-Example1drm.pdf |binary
vignettes/figure/minimal-Example2.pdf |binary
7 files changed, 17 insertions(+), 11 deletions(-)
Title: Extremely Randomized Trees (ExtraTrees) method for
classification and regression
Diff between extraTrees versions 1.0.3 dated 2014-09-07 and 1.0.4 dated 2014-11-08
Description: Classification and regression based on an ensemble of decision trees. The package also provides extensions of ExtraTrees to multi-task learning and quantile regression. Uses Java implementation of the method.
Author: Jaak Simm, Ildefons Magrans de Abril
Maintainer: Jaak Simm
DESCRIPTION | 8 ++---
MD5 | 33 ++++++++++++------------
NAMESPACE | 2 -
R/extraTrees.default.R | 7 +++++
inst/CHANGELOG | 4 ++
inst/doc/extraTrees.pdf |binary
inst/java/ExtraTrees.jar |binary
inst/tests/testthat/test-classification.r | 10 +++++++
inst/tests/testthat/test-regression.r | 10 +++++++
java/src/org/extratrees/AbstractBinaryTree.java | 5 ++-
java/src/org/extratrees/AbstractTrees.java | 19 ++++++++-----
java/src/org/extratrees/BinaryTree.java | 6 +++-
java/src/org/extratrees/ExtraTrees.java | 16 ++++++++---
java/src/org/extratrees/FactorBinaryTree.java | 6 +++-
java/src/org/extratrees/FactorExtraTrees.java | 13 +++++++--
man/extraTrees.Rd | 2 -
man/prepareForSave.Rd |only
man/selectTrees.Rd | 8 ++---
18 files changed, 105 insertions(+), 44 deletions(-)
Title: Estimation of Entropy and Related Quantities
Diff between EntropyEstimation versions 1.0 dated 2014-09-17 and 1.1 dated 2014-11-08
More information about EntropyEstimation at CRAN
Description: Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Author: Lijuan Cao
Maintainer: Michael Grabchak
DESCRIPTION | 9 ++---
MD5 | 24 ++++++++-----
NAMESPACE | 2 -
R/EntropEst.r | 55 +++++++++++++++++++++++++++++++
man/EntropyEstimation-package.Rd | 6 +--
man/GenSimp.sd.Rd |only
man/Hill.sd.Rd |only
man/KL.Plugin.Rd | 2 -
man/KL.sd.Rd | 2 -
man/KL.z.Rd | 2 -
man/MI.sd.Rd | 4 ++
man/MI.z.Rd | 7 +++-
man/Renyi.sd.Rd |only
man/Tsallis.sd.Rd |only
src/EntropEst.c | 68 ++++++++++++++++++++++++++++++++++++++-
15 files changed, 157 insertions(+), 24 deletions(-)
Permanent link
Title: Estimating birth and death rates based on phylogenies
Diff between TreePar versions 3.1 dated 2014-09-23 and 3.2 dated 2014-11-08
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim) or (3) extinction rate may be a function of species age (likelihood implemented as LikAge and optimization as bd.age.optim.matlab). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. (1-3) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious.
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 10 +++++-----
MD5 | 16 +++++++++++-----
NAMESPACE | 2 +-
R/LikAge.R |only
R/LikConstant.R | 1 +
R/LikConstantn.R | 1 +
R/bd.age.optim.matlab.R |only
R/create.mat.R |only
man/LikAge.Rd |only
man/TreePar-package.Rd | 6 +++---
man/bd.age.optim.matlab.Rd |only
man/create.mat.Rd |only
12 files changed, 22 insertions(+), 14 deletions(-)
Title: The OpenCPU system for embedded scientific computing and
reproducible research.
Diff between opencpu versions 1.4.4 dated 2014-08-20 and 1.4.5 dated 2014-11-08
Description: The OpenCPU system exposes an HTTP API for embedded scientific
computing with R. This provides reliable and scalable foundations for
integrating R based analysis and visualization modules into pipelines,
web applications or big data infrastructures. The OpenCPU server can
run either as a single-user development server within the interactive R
session, or as a high performance multi-user cloud server that builds
on Linux, Nginx and rApache. The current R package forms the core of
the system. When loaded in R, it automatically initiates the single-user
server and displays the web address in the console. For detailed
information and documentation on the API, visit the OpenCPU website.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 12 ++--
MD5 | 28 +++++-----
NAMESPACE | 3 -
R/github_install.R | 46 +++++++++-------
R/httpget_session_tar.R | 4 -
R/httpget_webhook.R | 39 ++++++++------
R/parse_arg_prim.R | 24 ++------
R/parse_post.R | 37 +++++++------
R/request.R | 2
R/session.R | 117 +++++++++++++++++++++----------------------
build/vignette.rds |binary
inst/doc/opencpu-paper.pdf |binary
inst/doc/opencpu-server.Rnw | 32 ++++-------
inst/doc/opencpu-server.pdf |binary
vignettes/opencpu-server.Rnw | 32 ++++-------
15 files changed, 189 insertions(+), 187 deletions(-)
Title: Mesh generation and surface tesselation
Diff between geometry versions 0.3-4 dated 2014-03-06 and 0.3-5 dated 2014-11-08
Description: This package makes the qhull library (www.qhull.org)
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2-d, 3-d, 4-d, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this. Currently the package only gives access to
Delaunay triangulation and convex hull computation.
Author: C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Andreas Stahel [cph, aut],
Andreas Stahel [cph, aut],
David C. Sterratt [cph, aut, cre]
Maintainer: David C. Sterratt
geometry-0.3-4/geometry/tests/compare-tsearch-tsearchn.R |only
geometry-0.3-4/geometry/tests/compare-tsearch-tsearchn.Rout.save |only
geometry-0.3-4/geometry/tests/convhulln.R |only
geometry-0.3-4/geometry/tests/convhulln.Rout.save |only
geometry-0.3-4/geometry/tests/delaunay.R |only
geometry-0.3-4/geometry/tests/delaunay.Rout.save |only
geometry-0.3-4/geometry/tests/parallel.R |only
geometry-0.3-4/geometry/tests/parallel.Rout.save |only
geometry-0.3-4/geometry/tests/tsearch.R |only
geometry-0.3-4/geometry/tests/tsearch.Rout.save |only
geometry-0.3-4/geometry/tests/tsearchn.R |only
geometry-0.3-4/geometry/tests/tsearchn.Rout.save |only
geometry-0.3-5/geometry/DESCRIPTION | 37
geometry-0.3-5/geometry/MD5 | 132 -
geometry-0.3-5/geometry/NAMESPACE | 4
geometry-0.3-5/geometry/NEWS | 58
geometry-0.3-5/geometry/R/convhulln.R | 18
geometry-0.3-5/geometry/R/delaunayn.R | 52
geometry-0.3-5/geometry/R/dotprod.R | 1
geometry-0.3-5/geometry/R/tetramesh.R | 6
geometry-0.3-5/geometry/R/tsearch.R | 32
geometry-0.3-5/geometry/inst/doc/html/index.html | 1195 ++++------
geometry-0.3-5/geometry/inst/doc/html/qconvex.html | 753 +++---
geometry-0.3-5/geometry/inst/doc/html/qdelau_f.html | 632 ++---
geometry-0.3-5/geometry/inst/doc/html/qdelaun.html | 736 ++----
geometry-0.3-5/geometry/inst/doc/html/qh-code.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-eg.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-faq.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-get.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-impre.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optc.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optf.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optg.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-opto.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optp.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optq.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-optt.html | 2
geometry-0.3-5/geometry/inst/doc/html/qh-quick.html | 2
geometry-0.3-5/geometry/inst/doc/html/qhalf.html | 700 ++---
geometry-0.3-5/geometry/inst/doc/html/qhull.html | 2
geometry-0.3-5/geometry/inst/doc/html/qvoron_f.html | 2
geometry-0.3-5/geometry/inst/doc/html/qvoronoi.html | 2
geometry-0.3-5/geometry/inst/doc/html/rbox.html | 2
geometry-0.3-5/geometry/inst/doc/index.html | 518 ++--
geometry-0.3-5/geometry/inst/extdata |only
geometry-0.3-5/geometry/man/Unique.Rd | 28
geometry-0.3-5/geometry/man/bary2cart.Rd | 42
geometry-0.3-5/geometry/man/cart2bary.Rd | 91
geometry-0.3-5/geometry/man/convhulln.Rd | 69
geometry-0.3-5/geometry/man/delaunayn.Rd | 109
geometry-0.3-5/geometry/man/distmesh2d.Rd | 150 -
geometry-0.3-5/geometry/man/distmeshnd.Rd | 138 -
geometry-0.3-5/geometry/man/dot.Rd | 22
geometry-0.3-5/geometry/man/entry.value.Rd | 27
geometry-0.3-5/geometry/man/extprod3d.Rd | 25
geometry-0.3-5/geometry/man/matmax.Rd | 34
geometry-0.3-5/geometry/man/mesh.dcircle.Rd | 38
geometry-0.3-5/geometry/man/mesh.diff.Rd | 47
geometry-0.3-5/geometry/man/mesh.drectangle.Rd | 43
geometry-0.3-5/geometry/man/mesh.dsphere.Rd | 34
geometry-0.3-5/geometry/man/mesh.hunif.Rd | 24
geometry-0.3-5/geometry/man/polyarea.Rd | 30
geometry-0.3-5/geometry/man/surf.tri.Rd | 44
geometry-0.3-5/geometry/man/tetramesh.Rd | 42
geometry-0.3-5/geometry/man/trimesh.Rd | 44
geometry-0.3-5/geometry/man/tsearch.Rd | 50
geometry-0.3-5/geometry/man/tsearchn.Rd | 56
geometry-0.3-5/geometry/src/Rdelaunayn.c | 49
geometry-0.3-5/geometry/src/Rtsearch.c | 6
geometry-0.3-5/geometry/src/userprintf.c | 4
geometry-0.3-5/geometry/tests/testthat |only
geometry-0.3-5/geometry/tests/testthat.R |only
72 files changed, 3031 insertions(+), 3123 deletions(-)