Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-30 0.3
Title: Methods for patient-centered network meta-analysis
Diff between pcnetmeta versions 1.1 dated 2014-03-09 and 1.2 dated 2014-07-19
Description: Provides functions to conduct network meta-analysis using arm-based method, which was proposed by Zhang et al (2014); contains functions to generate summary table for effect sizes (e.g., odds ratio, population-averaged event rate), plot network comparisons, and plot credible interval for population-averaged event rate.
Author: Lifeng Lin, Jing Zhang
Maintainer: Lifeng Lin
pcnetmeta-1.1/pcnetmeta/data/Ara09.rda |only
pcnetmeta-1.1/pcnetmeta/data/Lam07.Summary.rda |only
pcnetmeta-1.1/pcnetmeta/data/Lam07.rda |only
pcnetmeta-1.1/pcnetmeta/man/Ara09.Rd |only
pcnetmeta-1.1/pcnetmeta/man/Lam07.Rd |only
pcnetmeta-1.1/pcnetmeta/man/Lam07.Summary.Rd |only
pcnetmeta-1.2/pcnetmeta/DESCRIPTION | 12 +--
pcnetmeta-1.2/pcnetmeta/MD5 | 22 ++----
pcnetmeta-1.2/pcnetmeta/R/nma.ab.R | 76 ++++++++++++++++-------
pcnetmeta-1.2/pcnetmeta/data/Middleton10.rda |only
pcnetmeta-1.2/pcnetmeta/man/Middleton10.Rd |only
pcnetmeta-1.2/pcnetmeta/man/ci.plot.Rd | 29 +++-----
pcnetmeta-1.2/pcnetmeta/man/create.tab.Rd | 26 +++----
pcnetmeta-1.2/pcnetmeta/man/nma.ab.Rd | 61 ++++++------------
pcnetmeta-1.2/pcnetmeta/man/nma.networkplot.Rd | 23 ++----
pcnetmeta-1.2/pcnetmeta/man/pcnetmeta-package.Rd | 22 +++---
16 files changed, 133 insertions(+), 138 deletions(-)
Title: R bindings for Gtk 2.8.0 and above
Diff between RGtk2 versions 2.20.30 dated 2014-07-19 and 2.20.31 dated 2014-07-19
Description: Facilities in the R language for programming
graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/gobject.R | 2 +-
inst/doc/overview2.pdf |binary
4 files changed, 7 insertions(+), 7 deletions(-)
Title: Fit, Simulate and Diagnose Exponential-Family Models for
Networks
Diff between ergm versions 3.1.2 dated 2014-01-31 and 3.1.3 dated 2014-07-19
Description: An integrated set of tools to analyze and simulate networks based on exponential-family random graph models (ERGM). "ergm" is a part of the "statnet" suite of packages for network analysis.
Author: Mark S. Handcock [aut],
David R. Hunter [aut],
Carter T. Butts [aut],
Steven M. Goodreau [aut],
Pavel N. Krivitsky [aut, cre],
Martina Morris [aut]
Maintainer: Pavel N. Krivitsky
DESCRIPTION | 8 +--
MD5 | 26 ++++++------
R/InitErgmTerm.R | 10 +++-
R/ergm.R | 8 ++-
R/ergm.bridge.R | 4 -
R/summary.ergm.R | 2
inst/NEWS.Rd | 92 +++++++++++++++++++++++++++++++------------
man/ergm-terms.Rd | 23 +++++-----
src/changestats.c | 60 +++++++++++++---------------
src/wtMHproposals.c | 14 +++---
tests/termTests.bipartite.R | 8 +--
tests/termTests.directed.R | 4 -
tests/termTests.flexible.R | 18 +++++---
tests/termTests.undirected.R | 6 +-
14 files changed, 168 insertions(+), 115 deletions(-)
Title: Implement semantically rich I/O for NeXML format
Diff between RNeXML versions 1.1-0 dated 2014-07-17 and 1.1.2 dated 2014-07-19
Description: R package that allows access to phyloinformatic data in NeXML
format. The package should add new functionality to R such as the
possibility to manipulate NeXML objects in more various and refined way and
compatibility with 'ape' objects. Note that the Sxslt package suggested can
be installed from the Omegahat repository, though it can also be obtained
from https://github.com/cboettig/Sxslt
Author: Carl Boettiger [cre, aut],
Scott Chamberlain [aut],
Hilmar Lapp [aut],
Kseniia Shumelchyk [aut],
Rutger Vos [aut]
Maintainer: Carl Boettiger
RNeXML-1.1-0/RNeXML/vignettes/components |only
RNeXML-1.1.2/RNeXML/DESCRIPTION | 12 -
RNeXML-1.1.2/RNeXML/MD5 | 153 +++++-----------
RNeXML-1.1.2/RNeXML/NAMESPACE | 1
RNeXML-1.1.2/RNeXML/NEWS | 47 ++++
RNeXML-1.1.2/RNeXML/R/add_characters.R | 4
RNeXML-1.1.2/RNeXML/R/add_trees.R | 61 +++---
RNeXML-1.1.2/RNeXML/R/get_characters.R | 4
RNeXML-1.1.2/RNeXML/R/get_metadata.R | 4
RNeXML-1.1.2/RNeXML/R/get_namespaces.R | 4
RNeXML-1.1.2/RNeXML/R/get_rdf.R | 5
RNeXML-1.1.2/RNeXML/R/get_taxa.R | 4
RNeXML-1.1.2/RNeXML/R/get_trees.R | 12 +
RNeXML-1.1.2/RNeXML/R/nexml_add.R | 5
RNeXML-1.1.2/RNeXML/R/nexml_get.R | 5
RNeXML-1.1.2/RNeXML/R/nexml_publish.R | 10 +
RNeXML-1.1.2/RNeXML/R/nexml_validate.R | 61 ++++++
RNeXML-1.1.2/RNeXML/R/simmap.R | 8
RNeXML-1.1.2/RNeXML/R/taxize_nexml.R | 5
RNeXML-1.1.2/RNeXML/README.md | 4
RNeXML-1.1.2/RNeXML/inst/doc/tutorial.R | 12 -
RNeXML-1.1.2/RNeXML/inst/doc/tutorial.Rmd | 10 -
RNeXML-1.1.2/RNeXML/inst/doc/tutorial.html | 4
RNeXML-1.1.2/RNeXML/inst/examples/sparql.newick |only
RNeXML-1.1.2/RNeXML/man/add_characters.Rd | 5
RNeXML-1.1.2/RNeXML/man/add_trees.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_characters_list.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_flat_trees.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_metadata.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_namespaces.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_rdf.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_taxa.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_trees.Rd | 5
RNeXML-1.1.2/RNeXML/man/get_trees_list.Rd | 5
RNeXML-1.1.2/RNeXML/man/nexml_add.Rd | 6
RNeXML-1.1.2/RNeXML/man/nexml_figshare.Rd | 7
RNeXML-1.1.2/RNeXML/man/nexml_get.Rd | 6
RNeXML-1.1.2/RNeXML/man/nexml_publish.Rd | 7
RNeXML-1.1.2/RNeXML/man/nexml_to_simmap.Rd | 5
RNeXML-1.1.2/RNeXML/man/nexml_validate.Rd | 10 -
RNeXML-1.1.2/RNeXML/man/simmap_to_nexml.Rd | 5
RNeXML-1.1.2/RNeXML/man/taxize_nexml.Rd | 7
RNeXML-1.1.2/RNeXML/tests/testthat/geiger_test.R | 12 -
RNeXML-1.1.2/RNeXML/tests/testthat/test_comp_analysis.R | 2
RNeXML-1.1.2/RNeXML/tests/testthat/test_global_ids.R | 25 +-
RNeXML-1.1.2/RNeXML/tests/testthat/test_meta.R | 8
RNeXML-1.1.2/RNeXML/tests/testthat/test_parsing.R | 2
RNeXML-1.1.2/RNeXML/tests/testthat/test_publish.R | 53 ++---
RNeXML-1.1.2/RNeXML/tests/testthat/test_toplevel_api.R | 6
RNeXML-1.1.2/RNeXML/tests/testthat/test_validate.R | 4
RNeXML-1.1.2/RNeXML/vignettes/figure |only
RNeXML-1.1.2/RNeXML/vignettes/tutorial.Rmd | 10 -
RNeXML-1.1.2/RNeXML/vignettes/tutorial.md | 4
53 files changed, 443 insertions(+), 221 deletions(-)
Title: R bindings for Gtk 2.8.0 and above
Diff between RGtk2 versions 2.20.29 dated 2014-05-12 and 2.20.30 dated 2014-07-19
Description: Facilities in the R language for programming
graphical interfaces using Gtk, the Gimp Tool Kit.
Author: Michael Lawrence
Maintainer: Michael Lawrence
DESCRIPTION | 6 +++---
MD5 | 38 +++++++++++++++++++-------------------
R/cairoFuncs.R | 13 ++++++-------
R/gioFuncs.R | 6 ++----
R/glib.R | 2 +-
R/gobject.R | 2 +-
R/utils.R | 5 -----
inst/doc/overview2.pdf |binary
inst/include/RGtk2/atk.h | 8 +++++---
man/cairoSvgGetVersions.Rd | 7 ++++---
man/gFileInfoGetAttributeData.Rd | 6 +++---
src/RGtk2/atk.h | 8 +++++---
src/RGtkDataFrame.c | 4 ++--
src/Rgtk.c | 2 +-
src/cairoFuncs.c | 28 ++++++++++++++++++----------
src/cairoFuncs.h | 2 +-
src/gioFuncs.c | 12 +++++++-----
src/gioFuncs.h | 2 +-
src/glib.c | 4 ++--
src/utils.c | 6 ------
20 files changed, 81 insertions(+), 80 deletions(-)
Title: Partial least squares Regression for generalized linear models
Diff between plsRglm versions 1.0.1 dated 2014-06-28 and 1.1.0 dated 2014-07-19
Description: This package provides (weighted) Partial least squares Regression for generalized linear models and repeated k-fold cross-validation of such models using various criteria. It allows for missing data in the explanatory variables. Bootstrap confidence intervals constructions are also available.
Author: Frederic Bertrand
Maintainer: Frederic Bertrand
DESCRIPTION | 8
MD5 | 110 ++---
NEWS | 1
R/PLS_glm.R | 54 +-
R/PLS_glm_formula.R | 54 +-
R/PLS_glm_kfoldcv.R | 30 -
R/PLS_glm_kfoldcv_formula.R | 28 -
R/PLS_glm_wvc.R | 46 +-
R/PLS_lm.R | 94 ++--
R/PLS_lm_formula.R | 94 ++--
R/PLS_lm_kfoldcv.R | 24 -
R/PLS_lm_kfoldcv_formula.R | 22 -
R/PLS_lm_wvc.R | 860 ++++++++++++++++++++++----------------------
R/bootpls.R | 84 ++--
R/bootplsglm.R | 82 ++--
R/coefs.plsR.R | 22 -
R/coefs.plsRglm.R | 26 -
R/coefs.plsRglmnp.R | 30 -
R/cv.plsRglmmodel.default.R | 4
R/cv.plsRglmmodel.formula.R | 4
R/cv.plsRmodel.default.R | 4
R/cv.plsRmodel.formula.R | 4
R/cvtable.R | 6
R/cvtable.plsR.R | 16
R/cvtable.plsRglm.R | 18
R/kfolds2CVinfos_glm.R | 22 -
R/kfolds2CVinfos_lm.R | 15
R/permcoefs.plsR.R | 4
R/permcoefs.plsRglm.R | 4
R/plsRglmmodel.default.R | 4
R/plsRglmmodel.formula.R | 4
R/plsRmodel.default.R | 4
R/plsRmodel.formula.R | 4
R/predict.plsRglmmodel.R | 6
R/predict.plsRmodel.R | 6
R/summary.cv.plsRglmmodel.R | 9
inst/CITATION | 18
inst/doc/plsRglm-manual.pdf |binary
inst/doc/plsRglm.pdf |binary
man/PLS_glm_wvc.Rd | 262 ++++++-------
man/PLS_lm_wvc.Rd | 139 +++----
man/bootpls.Rd | 3
man/bootplsglm.Rd | 3
man/coefs.plsR.Rd | 3
man/coefs.plsRglm.Rd | 3
man/cv.plsR.Rd | 9
man/cv.plsRglm.Rd | 13
man/cvtable.Rd | 4
man/kfolds2CVinfos_glm.Rd | 167 ++++----
man/kfolds2CVinfos_lm.Rd | 127 +++---
man/permcoefs.plsR.Rd | 3
man/permcoefs.plsRglm.Rd | 3
man/plsR.Rd | 10
man/plsRglm.Rd | 9
man/predict.plsRglmmodel.Rd | 219 +++++------
man/predict.plsRmodel.Rd | 197 +++++-----
56 files changed, 1527 insertions(+), 1472 deletions(-)
Title: Partial least squares Regression for Cox models and related
techniques
Diff between plsRcox versions 1.0 dated 2014-06-28 and 1.7.0 dated 2014-07-19
Description: This packages provides Partial least squares Regression and various regular, sparse or kernel, techniques for fitting Cox models in high dimensional settings.
Author: Frederic Bertrand
Maintainer: Frederic Bertrand
DESCRIPTION | 12
MD5 | 103 ++-
NAMESPACE | 17
NEWS | 45 -
R/DKplsRcox.R | 2
R/DKplsRcoxmodel.default.R | 26
R/DKplsRcoxmodel.formula.R | 2
R/DR_coxph.R | 6
R/coxDKpls2DR.default.R | 18
R/coxDKpls2DR.formula.R | 64 +-
R/coxDKplsDR.default.R | 22
R/coxDKplsDR.formula.R | 64 +-
R/coxDKsplsDR.default.R | 22
R/coxDKsplsDR.formula.R | 64 +-
R/coxpls.default.R | 150 ++---
R/coxpls2.default.R | 72 +-
R/coxpls2DR.default.R | 106 +--
R/coxpls3.default.R | 4
R/coxpls3DR.default.R | 6
R/coxplsDR.default.R | 180 +++---
R/coxsplsDR.default.R | 14
R/coxsplsDR.formula.R | 64 +-
R/cv.autoplsRcox.R |only
R/cv.coxDKplsDR.R |only
R/cv.coxDKsplsDR.R |only
R/cv.coxpls.R |only
R/cv.coxplsDR.R |only
R/cv.coxsplsDR.R |only
R/cv.larsDR.R |only
R/cv.plsRcox.R |only
R/internal-plsRcox.R | 664 ++++++++++++++++++++++-
R/larsDR_coxph.default.R | 12
R/larsDR_coxph.formula.R | 68 +-
R/plsRcoxmodel.default.R | 1097 +++++++++++++++++++-------------------
R/plsRcoxmodel.formula.R | 64 +-
R/predict.plsRcoxmodel.R | 87 +--
inst/CITATION | 73 +-
man/DKplsRcox.Rd |only
man/coxDKpls2DR.Rd | 12
man/coxDKplsDR.Rd | 12
man/coxDKsplsDR.Rd | 12
man/coxpls.Rd | 15
man/coxpls2.Rd | 6
man/coxpls3.Rd | 6
man/coxplsDR.Rd | 7
man/coxsplsDR.Rd | 7
man/cv.autoplsRcox.Rd |only
man/cv.coxDKplsDR.Rd |only
man/cv.coxDKsplsDR.Rd |only
man/cv.coxpls.Rd |only
man/cv.coxplsDR.Rd |only
man/cv.coxsplsDR.Rd |only
man/cv.larsDR.Rd |only
man/cv.plsRcox.Rd |only
man/internal-plsRcox.Rd | 22
man/larsDR_coxph.Rd | 24
man/plsRcox.Rd | 20
man/predict.plsRcoxmodel.Rd | 11
man/print.plsRcoxmodel.Rd | 76 +-
man/print.summary.plsRcoxmodel.Rd | 76 +-
man/summary.plsRcoxmodel.Rd | 76 +-
61 files changed, 2141 insertions(+), 1369 deletions(-)
Title: permPGU: Using GPUs in Statistical Genomics
Diff between permGPU versions 0.14.5 dated 2014-06-28 and 0.14.6 dated 2014-07-19
Description: This R extension package can be used to carry out
permutation resampling inference in the context of RNA
microarray studies
Author: Ivo D. Shterev, Sin-Ho Jung, Stephen L. George and Kouros Owzar
Maintainer: Ivo D. Shterev
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
NAMESPACE | 1 +
NEWS | 6 ++++++
R/test.permgpu.R | 27 +++++++++++++++++----------
R/test.scoregpu.R | 12 ++++++++----
man/permGPU-package.Rd | 4 ++--
man/test.permgpu.Rd | 1 +
8 files changed, 47 insertions(+), 28 deletions(-)
Title: R binder for the Yhat API
Diff between yhatr versions 0.11.0 dated 2014-06-25 and 0.12.1 dated 2014-07-19
Description: yhatr lets you deploy, maintain, and invoke models via the Yhat
REST API.
Author: Greg Lamp
Maintainer: Greg Lamp
DESCRIPTION | 8 ++---
MD5 | 9 +++---
NEWS | 13 +++++++++
R/yhatR.R | 63 ++++++++++++++++++++++++++++++++++++--------
man/yhat.deploy.with.scp.Rd | 2 -
man/yhat.verify.Rd |only
6 files changed, 75 insertions(+), 20 deletions(-)
Title: Target Equivalence Range Design
Diff between TEQR versions 4.0-0 dated 2014-06-14 and 5.0-0 dated 2014-07-19
Description: The target equivalence range (TEQR) design, previously named the toxicity equivalence range design is an up-down design patterned after the modified toxicity probability interval design.The TEQR design extends the well known 3+3 design to allow for: an explicit target range for the dose limiting toxicity (DLT) rate, more subjects at the maximum tolerated dose (MTD), and specification of a too-toxic rate, which closes a dose level, In addition, the TEQR design can be implemented to target a dose based either on toxicity rate or activity rate constrained for toxicity.
Author: M. Suzette Blanchard
Maintainer: M. Suzette Blanchard
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/TEQR.R | 18 ++++++++++--------
man/teqrDG.Rd | 2 +-
man/teqrOCact.Rd | 25 ++++++++++++++++++++++++-
man/teqrOCtox.Rd | 22 +++++++++++++++++++++-
6 files changed, 65 insertions(+), 20 deletions(-)
Title: NbClust package for determining the best number of clusters
Diff between NbClust versions 2.0 dated 2014-05-30 and 2.0.1 dated 2014-07-19
Description: NbClust package provides 30 indices for determining the optimal number of clusters in a dataset.
Author: Malika Charrad
Maintainer: Malika Charrad
DESCRIPTION | 8 +--
MD5 | 6 +-
R/NbClust.R | 99 ++++++++++++++++++++++++++------------------
man/NbClust.Rd | 127 ++++++++++++++++++++++++++-------------------------------
4 files changed, 125 insertions(+), 115 deletions(-)
Title: Geometric morphometric analyses of 2d/3d landmark data
Diff between geomorph versions 2.1 dated 2014-05-30 and 2.1.1 dated 2014-07-19
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, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
DESCRIPTION | 10 -
MD5 | 156 +++++++++----------
NAMESPACE | 4
NEWS | 82 ++++++----
R/digit.fixed.r | 252 +++++++++++++++---------------
R/digitize2d.r | 310 +++++++++++++++++++-------------------
R/estimate.missing.r | 4
R/geomorph.support.code.r | 5
R/gpagen.r | 10 -
R/pairwise.slope.test.r | 66 ++++----
R/pairwiseD.test.r | 41 ++---
R/physignal.r | 18 +-
R/plotAllometry.r | 22 +-
R/plotGMPhyloMorphoSpace.r | 152 +++++++++---------
R/plotTangentSpace.r | 240 ++++++++++++++---------------
R/procD.lm.r | 15 -
R/procD.pgls.r | 2
R/readland.tps.r | 210 ++++++++++++++-----------
R/readmulti.nts.r | 2
data/hummingbirds.rda |binary
data/mosquito.rda |binary
data/motionpaths.rda |binary
data/plethShapeFood.rda |binary
data/plethodon.rda |binary
data/plethspecies.rda |binary
data/ratland.rda |binary
data/scallopPLY.rda |binary
data/scallops.rda |binary
man/arrayspecs.Rd | 30 +--
man/bilat.symmetry.Rd | 156 ++++++-------------
man/buildtemplate.Rd | 153 +++++++-----------
man/compare.evol.rates.Rd | 74 +++------
man/compare.modular.partitions.Rd | 75 +++------
man/define.modules.Rd | 41 ++---
man/define.sliders.2d.Rd | 73 +++-----
man/define.sliders.3d.Rd | 108 +++++--------
man/digit.fixed.Rd | 115 +++++---------
man/digitize2d.Rd | 108 +++++--------
man/digitsurface.Rd | 128 ++++++---------
man/editTemplate.Rd | 60 +++----
man/estimate.missing.Rd | 103 ++++--------
man/findMeanSpec.Rd | 22 +-
man/fixed.angle.Rd | 53 ++----
man/geomorph-package.Rd | 13 -
man/gpagen.Rd | 216 ++++++++++----------------
man/hummingbirds.Rd | 12 -
man/morphol.disparity.Rd | 43 +----
man/morphol.integr.Rd | 130 ++++++---------
man/mosquito.Rd | 1
man/motionpaths.Rd | 6
man/mshape.Rd | 13 -
man/pairwise.slope.test.Rd | 117 +++++---------
man/pairwiseD.test.Rd | 81 +++------
man/phylo.pls.Rd | 77 +++------
man/physignal.Rd | 100 ++++--------
man/plethShapeFood.Rd | 7
man/plethodon.Rd | 11 -
man/plethspecies.Rd | 7
man/plotAllSpecimens.Rd | 32 +--
man/plotAllometry.Rd | 153 +++++++-----------
man/plotGMPhyloMorphoSpace.Rd | 44 +----
man/plotRefToTarget.Rd | 70 +++-----
man/plotTangentSpace.Rd | 75 +++------
man/plotspec.Rd | 45 +----
man/procD.lm.Rd | 110 +++++--------
man/procD.pgls.Rd | 70 +++-----
man/ratland.Rd | 6
man/read.morphologika.Rd | 43 ++---
man/read.ply.Rd | 28 +--
man/readland.nts.Rd | 75 +++------
man/readland.tps.Rd | 59 ++-----
man/readmulti.nts.Rd | 55 ++----
man/scallopPLY.Rd | 10 -
man/scallops.Rd | 7
man/trajectory.analysis.Rd | 181 ++++++++--------------
man/two.b.pls.Rd | 63 ++-----
man/two.d.array.Rd | 21 +-
man/warpRefMesh.Rd | 81 +++------
man/writeland.tps.Rd | 13 -
79 files changed, 2159 insertions(+), 2816 deletions(-)