Title: MultiPhen, a package for the genetic association testing of
multiple phenotypes
Diff between MultiPhen versions 0.5 dated 2012-04-30 and 0.6 dated 2012-06-08
Description: Performs genetic association tests between SNPs
(one-at-a-time) and multiple phenotypes (separately or in joint
model)
Author: Lachlan Coin, Paul O'Reilly, Yotsawat Pompyen, Clive Hoggart
and Federico Calboli
Maintainer: Federico Calboli
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/MultiPhen-internal.R | 24 +++++++++++++++++-------
R/mPhen.R | 4 ++--
R/mPhen.plink.R | 4 ++--
man/MultiPhen-package.Rd | 2 +-
man/mPhen.Rd | 5 ++++-
man/mPhen.plink.Rd | 5 ++++-
8 files changed, 41 insertions(+), 25 deletions(-)
Title: Various R programming tools for plotting data
Diff between gplots versions 2.10.1 dated 2011-09-03 and 2.11.0 dated 2012-06-08
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes. Includes R source code and/or documentation
contributed by (in alphabetical order): Ben Bolker, Lodewijk
Bonebakker, Robert Gentleman, Wolfgang Huber Andy Liaw, Thomas
Lumley, Martin Maechler, Arni Magnusson, Steffen Moeller, Marc
Schwartz, Bill Venables
Maintainer: Gregory R. Warnes
ChangeLog | 42 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 13 +++++++------
MD5 | 34 +++++++++++++++++-----------------
NEWS | 21 +++++++++++++++++++++
R/barplot2.R | 2 +-
R/ci2d.R | 2 +-
R/hist2d.R | 30 ++++++++++++++++++------------
R/ooplot.R | 4 ++--
R/plotCI.R | 22 +++++-----------------
R/plotmeans.R | 7 ++++---
R/print.hist2d.R | 9 ++++-----
R/sinkplot.R | 16 ++++++++--------
inst/ChangeLog | 42 ++++++++++++++++++++++++++++++++++++++++++
inst/NEWS | 21 +++++++++++++++++++++
man/hist2d.Rd | 42 +++++++++++++++++++++++++++---------------
man/plotmeans.Rd | 9 ++++++---
man/qqnorm.aov.Rd | 4 +++-
tests/heatmap2Test.Rout.save | 27 +++++++++++++++++----------
18 files changed, 246 insertions(+), 101 deletions(-)
Title: Canadian Historical Climate Network
Diff between CHCN versions 1.4 dated 2012-04-28 and 1.5 dated 2012-06-08
Description: A compilation of historical through contemporary climate
measurements scraped from the Environment Canada Website
Including tools for scraping data, creating metadata and
formating temperature files.
Author: Steven Mosher
Maintainer: Steven Mosher
DESCRIPTION | 10 +++++-----
MD5 | 16 ++++++++++------
R/Url.R | 3 ++-
R/createInventory.R | 6 +++---
R/downloadMaster.R | 7 +++++--
R/readLocalMaster.R |only
R/writeInventory.R | 2 +-
inst |only
man/CHCN-package.Rd | 15 +++++++++------
man/readLocalMaster.Rd |only
10 files changed, 35 insertions(+), 24 deletions(-)
Title: Modeling physical computer codes with functional outputs using
clustering and dimensionality reduction
Diff between modelcf versions 2.1 dated 2011-02-03 and 2.1.1 dated 2012-06-08
Description: Statistical learning with vectorial inputs and smooth 1D
curves as outputs. The main function builds a model from n
samples (x_i,y_i).
Author: Benjamin Auder
Maintainer: Benjamin Auder
DESCRIPTION | 6 +++---
MD5 |only
R/RD_orthBasis.R | 2 +-
data/datacf.RData |binary
src/dimension.c | 52 ++++++++++++++++++++++++++--------------------------
src/hungarian.c | 32 ++++++++++++++++----------------
6 files changed, 46 insertions(+), 46 deletions(-)
Title: Model selection and multimodel inference based on (Q)AIC(c)
Diff between AICcmodavg versions 1.24 dated 2012-02-06 and 1.25 dated 2012-06-08
Description: This package includes functions to create model selection
tables based on Akaike's information criterion (AIC) and the
second-order AIC (AICc), as well as their quasi-likelihood
counterparts (QAIC, QAICc). Tables are printed with delta AIC
and Akaike weights. The package also features functions to
conduct classic model averaging (multimodel inference) for a
given parameter of interest and predicted values, as well as a
shrinkage version of model averaging parameter estimates.
Other handy functions enable the computation of relative
variable importance, evidence ratios, and confidence sets for
the best model. The present version works with Cox regression
('coxph' class), linear models ('lm' class), generalized linear
models ('glm' class), linear models fit by generalized least
squares ('gls' class), linear mixed models ('lme' class),
generalized linear mixed models ('mer' class), multinomial and
ordinal logistic regressions ('multinom' and 'polr' classes),
and nonlinear models ('nls' class). The package also supports
various models incorporating detection probabilities such as
single-season occupancy models ('unmarkedFitOccu' class),
multiple-season occupancy models ('unmarkedFitColExt' class),
single-season heterogeneity models ('unmarkedFitOccuRN' class),
single-season and multiple-season N-mixture models for repeated
counts ('unmarkedFitPCount' and 'unmarkedFitPCO' classes,
respectively), and distance sampling models ('unmarkedFitDS'
and 'unmarkedFitGDS' classes).
Author: Marc J. Mazerolle
Maintainer: Marc J. Mazerolle
AICcmodavg-1.24/AICcmodavg/man/extract.LL.unmarked.Rd |only
AICcmodavg-1.25/AICcmodavg/DESCRIPTION | 43 +++----
AICcmodavg-1.25/AICcmodavg/MD5 | 104 ++++++++++--------
AICcmodavg-1.25/AICcmodavg/R/AICc.R | 5
AICcmodavg-1.25/AICcmodavg/R/AICc.coxph.R |only
AICcmodavg-1.25/AICcmodavg/R/AICc.nls.R | 4
AICcmodavg-1.25/AICcmodavg/R/AICc.unmarked.R | 17 --
AICcmodavg-1.25/AICcmodavg/R/aictab.R | 21 ++-
AICcmodavg-1.25/AICcmodavg/R/aictab.coxph.R |only
AICcmodavg-1.25/AICcmodavg/R/aictab.glm.R | 2
AICcmodavg-1.25/AICcmodavg/R/aictab.gls.R | 10 -
AICcmodavg-1.25/AICcmodavg/R/aictab.lme.R | 8 -
AICcmodavg-1.25/AICcmodavg/R/aictab.mer.R | 8 -
AICcmodavg-1.25/AICcmodavg/R/aictab.mult.R | 2
AICcmodavg-1.25/AICcmodavg/R/aictab.nls.R | 2
AICcmodavg-1.25/AICcmodavg/R/aictab.polr.R | 2
AICcmodavg-1.25/AICcmodavg/R/c_hat.R | 4
AICcmodavg-1.25/AICcmodavg/R/evidence.R | 2
AICcmodavg-1.25/AICcmodavg/R/extract.LL.R |only
AICcmodavg-1.25/AICcmodavg/R/fam.link.mer.r | 2
AICcmodavg-1.25/AICcmodavg/R/importance.R | 24 +---
AICcmodavg-1.25/AICcmodavg/R/modavg.R | 20 ++-
AICcmodavg-1.25/AICcmodavg/R/modavg.coxph.R |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.glm.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.gls.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.lme.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.mer.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.effect.unmarked.r |only
AICcmodavg-1.25/AICcmodavg/R/modavg.glm.R | 14 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.gls.R | 12 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.lme.R | 12 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.mer.R | 20 +--
AICcmodavg-1.25/AICcmodavg/R/modavg.mult.R | 12 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.polr.R | 10 -
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.R | 19 ++-
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.coxph.R |only
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.glm.R | 12 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.gls.R | 6 -
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.lme.R | 6 -
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.mer.R | 14 +-
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.mult.R | 6 -
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.polr.R | 6 -
AICcmodavg-1.25/AICcmodavg/R/modavg.shrink.unmarked.R | 4
AICcmodavg-1.25/AICcmodavg/R/modavg.unmarked.R | 12 +-
AICcmodavg-1.25/AICcmodavg/R/modavgpred.R | 47 ++++----
AICcmodavg-1.25/AICcmodavg/R/modavgpred.unmarked.R | 2
AICcmodavg-1.25/AICcmodavg/R/predictSE.gls.r | 4
AICcmodavg-1.25/AICcmodavg/R/predictSE.lme.r | 8 -
AICcmodavg-1.25/AICcmodavg/R/predictSE.mer.r | 8 -
AICcmodavg-1.25/AICcmodavg/inst/CITATION | 2
AICcmodavg-1.25/AICcmodavg/inst/NEWS | 11 +
AICcmodavg-1.25/AICcmodavg/man/AICc.Rd | 39 +++---
AICcmodavg-1.25/AICcmodavg/man/AICcmodavg-package.Rd | 28 ++--
AICcmodavg-1.25/AICcmodavg/man/aictab.Rd | 49 ++++++--
AICcmodavg-1.25/AICcmodavg/man/extract.LL.Rd |only
AICcmodavg-1.25/AICcmodavg/man/modavg.Rd | 48 ++++++--
AICcmodavg-1.25/AICcmodavg/man/modavg.effect.Rd |only
AICcmodavg-1.25/AICcmodavg/man/modavg.shrink.Rd | 30 +++--
AICcmodavg-1.25/AICcmodavg/man/modavgpred.Rd | 25 ++--
60 files changed, 428 insertions(+), 318 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2007-03-20 1.0
Title: Creates Random Forest and Stochastic Gradient Boosting Models,
and applies them to GIS .img files to build detailed prediction
maps.
Diff between ModelMap versions 2.3.1 dated 2012-05-24 and 2.3.2 dated 2012-06-08
Description: This package will create sophisticated models of training
data and validate the models with an independant test set,
cross validation, or in the case of Random Forest Models, with
Out OF Bag (OOB) predictions on the training data. It will
creat graphs and tables of the model validation results. It
will apply these models to GIS .img files of predictors to
create detailed prediction surfaces. It will handle large
predictor files for map making, by reading in the .img files in
chuncks, and output to the .txt file the prediction for each
data chunk, before reading the next chenk of data.
Author: Elizabeth Freeman, Tracey Frescino
Maintainer: Elizabeth Freeman
ModelMap-2.3.1/ModelMap/inst/vignettes |only
ModelMap-2.3.2/ModelMap/DESCRIPTION | 8 ++++----
ModelMap-2.3.2/ModelMap/MD5 | 23 ++++++++++++-----------
ModelMap-2.3.2/ModelMap/inst/CHANGELOG | 4 ++--
ModelMap-2.3.2/ModelMap/inst/doc |only
ModelMap-2.3.2/ModelMap/man/ModelMap-package.Rd | 4 ++--
ModelMap-2.3.2/ModelMap/vignettes |only
7 files changed, 20 insertions(+), 19 deletions(-)
Title: Site Percolation on Square Lattice (SPSL)
Diff between SPSL versions 0.1-5 dated 2012-05-14 and 0.1-6 dated 2012-06-08
Description: SPSL package provides functionality for labeling of
percolation clusters on 2D & 3D square lattice with various
lattice size, relative fraction of accessible sites (occupation
probability), iso- & anisotropy, von Neumann & Moore
(1,d)-neighborhood
Author: Pavel V. Moskalev
Maintainer: Pavel V. Moskalev
ChangeLog |only
DESCRIPTION | 14 ++++++-------
MD5 | 33 ++++++++++++++++++++++---------
R/fssa20.R |only
R/fssa2d.R |only
R/fssi20.R |only
R/fssi2d.R |only
man/SPSL-package.Rd | 35 ++++++++++++++++++++++++++-------
man/fssa20.Rd |only
man/fssa2d.Rd |only
man/fssa30.Rd |only
man/fssa3d.Rd |only
man/fssi20.Rd |only
man/fssi2d.Rd |only
man/fssi30.Rd |only
man/fssi3d.Rd |only
man/ssa20.Rd | 31 ++++++++++++++++-------------
man/ssa2d.Rd | 40 +++++++++++++++++++-------------------
man/ssa30.Rd | 44 +++++++++++++++++++++++++-----------------
man/ssa3d.Rd | 54 +++++++++++++++++++++++++++++-----------------------
man/ssi20.Rd | 32 ++++++++++++++++++------------
man/ssi2d.Rd | 36 +++++++++++++++++-----------------
man/ssi30.Rd | 42 ++++++++++++++++++++++++----------------
man/ssi3d.Rd | 52 ++++++++++++++++++++++++++++----------------------
24 files changed, 243 insertions(+), 170 deletions(-)
Title: Markdown rendering for R
Diff between markdown versions 0.5 dated 2012-05-31 and 0.5.1 dated 2012-06-08
Description: Markdown is a plain-text formatting syntax that can be
converted to XHTML or other formats. This package provides R
bindings to the Sundown markdown rendering library.
Author: JJ Allaire, Jeffrey Horner, Vicent Marti, and Natacha Porte
Maintainer: Jeffrey Horner
DESCRIPTION | 6 +++---
MD5 | 16 ++++++++--------
NEWS | 10 ++++++++++
R/guid.R | 15 ++++++++++++++-
R/renderMarkdown.R | 2 +-
R/rpubsUpload.R | 20 ++++++++++----------
man/markdown.Rd | 2 +-
man/markdownExtensions.Rd | 5 +++++
man/markdownHTMLOptions.Rd | 3 +++
9 files changed, 55 insertions(+), 24 deletions(-)
Title: Statistical Object Oriented Data Analysis of RDP-based Taxonomic
trees from Human Microbiome Data: Modeling, Visualization, and
Two-Group Comparison
Diff between HMPTrees versions 1.0 dated 2011-11-19 and 1.1 dated 2012-06-08
Description: In this package, we introduce Object Oriented Data
Analysis (OODA) methods to analyze Human Microbiome taxonomic
trees directly. We provide tools to model, compare, and
visualize populations of taxonomic tree objects. In particular,
using a unimodal probability measure in the set of trees, we
provide procedures to compute the MLE of the central tree and
the LRT statistics for comparing the distributions of two
metagenomic populations. Our procedures have been developed to
support parallel computations for comparing two groups.
Author: Patricio S. La Rosa, Elena Deych, Berkley Shands, William D.
Shannon
Maintainer: Berkley Shands
HMPTrees-1.0/HMPTrees/R/getRelations.R |only
HMPTrees-1.0/HMPTrees/R/getTopXPhylum.R |only
HMPTrees-1.0/HMPTrees/R/helpRelations.R |only
HMPTrees-1.1/HMPTrees/DESCRIPTION | 23 +
HMPTrees-1.1/HMPTrees/MD5 | 61 ++--
HMPTrees-1.1/HMPTrees/NAMESPACE |only
HMPTrees-1.1/HMPTrees/R/buildTree.R |only
HMPTrees-1.1/HMPTrees/R/checkTreeValidity.R | 67 ++--
HMPTrees-1.1/HMPTrees/R/checkValidHelp.R | 77 ++---
HMPTrees-1.1/HMPTrees/R/compareTwoDataSets.R | 157 +++++-----
HMPTrees-1.1/HMPTrees/R/createAndPlot.R | 37 +-
HMPTrees-1.1/HMPTrees/R/createTrees.R | 65 ++--
HMPTrees-1.1/HMPTrees/R/displayLegend.R | 41 +-
HMPTrees-1.1/HMPTrees/R/formatData.R | 51 +--
HMPTrees-1.1/HMPTrees/R/generateTree.R | 72 +---
HMPTrees-1.1/HMPTrees/R/getBranchSizes.R | 91 +++---
HMPTrees-1.1/HMPTrees/R/getMLEandLoglike.R | 119 +++-----
HMPTrees-1.1/HMPTrees/R/getTaxaDepth.R | 41 +-
HMPTrees-1.1/HMPTrees/R/helpBuildTree.R |only
HMPTrees-1.1/HMPTrees/R/mergeDataSets.R | 357 +++++++++++-------------
HMPTrees-1.1/HMPTrees/R/plotTree.R | 61 ++--
HMPTrees-1.1/HMPTrees/R/plotTreeDataMDS.R | 133 ++++----
HMPTrees-1.1/HMPTrees/R/rowMatch.R | 11
HMPTrees-1.1/HMPTrees/R/subsetData.R |only
HMPTrees-1.1/HMPTrees/R/transformHMPTreetoHMP.R | 35 +-
HMPTrees-1.1/HMPTrees/R/transformHMPtoHMPTree.R | 11
HMPTrees-1.1/HMPTrees/R/traverseHelp.R | 119 +++-----
HMPTrees-1.1/HMPTrees/R/traverseTree.R | 55 +--
HMPTrees-1.1/HMPTrees/R/trimToTaxaLevel.R | 48 +--
HMPTrees-1.1/HMPTrees/man/HMPTrees-internal.Rd | 5
HMPTrees-1.1/HMPTrees/man/generateTree.Rd | 35 --
HMPTrees-1.1/HMPTrees/man/saliva.Rd | 2
HMPTrees-1.1/HMPTrees/man/stool.Rd | 2
HMPTrees-1.1/HMPTrees/man/throat.Rd | 2
HMPTrees-1.1/HMPTrees/man/trimToTaxaLevel.Rd | 20 +
35 files changed, 889 insertions(+), 909 deletions(-)