Title: Data analysis in ecology
Diff between pgirmess versions 1.5.2 dated 2011-11-07 and 1.5.3 dated 2012-06-26
Description: Description: Miscellaneous functions for analysis and
display of ecological and spatial data
Author: Patrick Giraudoux
Maintainer: Patrick Giraudoux
pgirmess-1.5.2/pgirmess/R/cormat.R |only
pgirmess-1.5.2/pgirmess/R/correlog.R |only
pgirmess-1.5.2/pgirmess/R/diag2edge.R |only
pgirmess-1.5.2/pgirmess/R/difshannonbio.R |only
pgirmess-1.5.2/pgirmess/R/friedmanmc.R |only
pgirmess-1.5.2/pgirmess/R/ks.gof.R |only
pgirmess-1.5.2/pgirmess/R/pairsrp.R |only
pgirmess-1.5.2/pgirmess/R/pclig.R |only
pgirmess-1.5.2/pgirmess/R/piankabio.R |only
pgirmess-1.5.2/pgirmess/R/piankabioboot.R |only
pgirmess-1.5.2/pgirmess/R/polycirc.R |only
pgirmess-1.5.2/pgirmess/R/polycirc2.R |only
pgirmess-1.5.2/pgirmess/R/postxt.R |only
pgirmess-1.5.2/pgirmess/R/shannon.R |only
pgirmess-1.5.2/pgirmess/R/shannonbio.R |only
pgirmess-1.5.2/pgirmess/R/shannonbioboot.R |only
pgirmess-1.5.2/pgirmess/R/tabcont2categ.R |only
pgirmess-1.5.2/pgirmess/R/val4symb.R |only
pgirmess-1.5.2/pgirmess/R/valchisq.R |only
pgirmess-1.5.2/pgirmess/R/write.delim.R |only
pgirmess-1.5.3/pgirmess/DESCRIPTION | 15 +++---
pgirmess-1.5.3/pgirmess/MD5 | 69 ++++++++++++++--------------
pgirmess-1.5.3/pgirmess/NAMESPACE |only
pgirmess-1.5.3/pgirmess/R/PermTest.r | 2
pgirmess-1.5.3/pgirmess/R/cormat.r |only
pgirmess-1.5.3/pgirmess/R/correlog.r |only
pgirmess-1.5.3/pgirmess/R/diag2edge.r |only
pgirmess-1.5.3/pgirmess/R/difshannonbio.r |only
pgirmess-1.5.3/pgirmess/R/distNNeigh.r | 1
pgirmess-1.5.3/pgirmess/R/friedmanmc.r |only
pgirmess-1.5.3/pgirmess/R/kruskalmc.r | 2
pgirmess-1.5.3/pgirmess/R/ks.gof.r |only
pgirmess-1.5.3/pgirmess/R/pairsrp.r |only
pgirmess-1.5.3/pgirmess/R/pave.r | 1
pgirmess-1.5.3/pgirmess/R/pclig.r |only
pgirmess-1.5.3/pgirmess/R/piankabio.r |only
pgirmess-1.5.3/pgirmess/R/piankabioboot.r |only
pgirmess-1.5.3/pgirmess/R/polycirc.r |only
pgirmess-1.5.3/pgirmess/R/polycirc2.r |only
pgirmess-1.5.3/pgirmess/R/postxt.r |only
pgirmess-1.5.3/pgirmess/R/readGDALbbox.r | 1
pgirmess-1.5.3/pgirmess/R/rwhatbufCat.r | 2
pgirmess-1.5.3/pgirmess/R/rwhatbufCat2.r | 3 -
pgirmess-1.5.3/pgirmess/R/rwhatbufNum.r | 2
pgirmess-1.5.3/pgirmess/R/rwhatpoly.r | 1
pgirmess-1.5.3/pgirmess/R/shannon.r |only
pgirmess-1.5.3/pgirmess/R/shannonbio.r |only
pgirmess-1.5.3/pgirmess/R/shannonbioboot.r |only
pgirmess-1.5.3/pgirmess/R/tabcont2categ.r |only
pgirmess-1.5.3/pgirmess/R/thintrack.r | 1
pgirmess-1.5.3/pgirmess/R/val4symb.r |only
pgirmess-1.5.3/pgirmess/R/valchisq.r |only
pgirmess-1.5.3/pgirmess/R/write.delim.r |only
pgirmess-1.5.3/pgirmess/R/writePRJ.r | 1
pgirmess-1.5.3/pgirmess/data/preybiom.rda |binary
pgirmess-1.5.3/pgirmess/data/siegelp179.rda |binary
56 files changed, 46 insertions(+), 55 deletions(-)
Title: Bayesian Sparse Factor Analysis model for the inference of
pathways responsive to drug treatment
Diff between FacPad versions 1.0 dated 2012-03-22 and 2.0 dated 2012-06-26
Description: This method tries to explain the gene-wise treatment
response ratios in terms of the latent pathways. It uses
bayesian sparse factor modeling to infer the loadings (weights)
of each pathway on its associated probesets as well as the
latent factor activity levels for each treatment.
Author: Haisu Ma
Maintainer: Haisu Ma
DESCRIPTION | 8 ++++----
MD5 | 8 +++++---
NAMESPACE | 2 +-
R/gibbs2.R |only
man/FacPad-package.Rd | 7 +++++--
man/gibbs2.Rd |only
6 files changed, 15 insertions(+), 10 deletions(-)
Title: SEER Setup and Use with A-Bomb Data
Diff between SEERaBomb versions 0.01.1 dated 2012-06-17 and 0.2.1 dated 2012-06-26
Description: This package contains codes that setup SEER (Surveillance,
Epidemiology and End Results) data use with R. It includes
SEER and Japanese A-Bomb survivor data analysis examples. By
using it, the portability of SEER R scripts should improve.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
R/pickFields.R | 8 ++++----
inst/doc/changes.txt | 22 ++++++++++++++++++++--
inst/doc/courses |only
man/pickFields.Rd | 1 +
6 files changed, 35 insertions(+), 15 deletions(-)
Title: Using graphs as a navigational infrastructure.
Diff between RnavGraph versions 0.1.3 dated 2012-04-23 and 0.1.4 dated 2012-06-26
Description: GUI to explore high dimensional data (including image
data) using graphs as navigational infrastructure.
Author: Adrian R. Waddell and R. Wayne Oldford
Maintainer: Adrian Waddell
DESCRIPTION | 8
MD5 | 10
NAMESPACE | 2
NEWS | 6
R/ng_graph.R | 835 ++++++++++++++++++++++++-------------------------
inst/doc/RnavGraph.pdf |binary
6 files changed, 435 insertions(+), 426 deletions(-)
Title: Bootstrapped Basis Regression with Oracle Model Selection
Diff between polywog versions 0.1-0 dated 2012-05-12 and 0.2-0 dated 2012-06-26
Description: Routines for flexible functional form estimation via basis
regression, with model selection via the adaptive LASSO or SCAD
to prevent overfitting.
Author: Brenton Kenkel and Curtis S. Signorino
Maintainer: Brenton Kenkel
DESCRIPTION | 15 ++--
MD5 | 30 +++++---
NAMESPACE | 20 +++--
NEWS |only
R/fitters.r |only
R/fn_cv.r |only
R/fn_marg.r |only
R/fn_plot.r | 4 -
R/fn_poly.r | 2
R/fn_pred.r | 20 ++++-
R/helpers.r | 43 +++++++++++
R/polywog.r | 147 ++++++++---------------------------------
man/cv.polywog.Rd |only
man/margEff.polywog.Rd |only
man/plot.margEff.polywog.Rd |only
man/plot.polywog.Rd | 2
man/polywog.Rd | 32 +++++---
man/predict.polywog.Rd | 5 -
man/summary.margEff.polywog.Rd |only
man/summary.polywog.Rd | 2
20 files changed, 158 insertions(+), 164 deletions(-)
Title: Convert country names and country codes
Diff between countrycode versions 0.7 dated 2012-06-04 and 0.8 dated 2012-06-26
Description: Standardize country names, convert them into one of seven
coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock
Maintainer: Vincent Arel-Bundock
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NEWS | 21 +++++++++++++++------
R/countrycode.R | 12 ++++++------
R/countrycode_data.R | 3 ++-
README.md |only
data/countrycode_data.rda |binary
man/countrycode.Rd | 10 +++++-----
man/countrycode_data.Rd | 5 +++--
9 files changed, 43 insertions(+), 31 deletions(-)
Title: Mediation analysis with missing data using bootstrap
Diff between bmem versions 1.2.2 dated 2011-11-08 and 1.3 dated 2012-06-26
Description: Four methods for mediation analysis with missing data:
Listwise deletion, Pairwise deletion, Multiple imputation, and
Two Stage Maximum Likelihood algorithm. For MI and TS-ML,
auxiliary variables can be included. Bootstrap confidence
intervals for mediation effects are obtained. The robust method
is also implemented for TS-ML.
Author: Zhiyong Zhang and Lijuan Wang
Maintainer: Zhiyong Zhang
DESCRIPTION | 15 ++++++++---
MD5 | 8 +++---
NAMESPACE | 22 ++++++++--------
R/bmem.R | 80 +++++++++++++++++++++++++++++++++++++++---------------------
man/bmem.Rd | 4 +--
5 files changed, 81 insertions(+), 48 deletions(-)
Title: Visualization and Imputation of Missing Values
Diff between VIM versions 3.0.0 dated 2012-01-24 and 3.0.1 dated 2012-06-26
Description: This package introduces new tools for the visualization of
missing and/or imputed values, which can be used for exploring
the data and the structure of the missing and/or imputed
values. Depending on this structure of the missing values, the
corresponding methods may help to identify the mechanism
generating the missings and allows to explore the data
including missing values. In addition, the quality of
imputation can be visually explored using various univariate,
bivariate, multiple and multivariate plot methods. A graphical
user interface allows an easy handling of the implemented plot
methods.
Author: Matthias Templ, Andreas Alfons, Alexander Kowarik, Bernd
Prantner
Maintainer: Matthias Templ
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
R/hotdeck.R | 42 +++++++++++++++++++++++++++---------------
R/kNNFaster.R | 2 +-
R/zzz.R | 30 +++++++++++++++---------------
inst/doc/VIM-EU-SILC.pdf |binary
inst/doc/VIM-Imputation.pdf | 6 +++---
man/hotdeck.Rd | 2 +-
src/Makevars | 4 ++--
9 files changed, 61 insertions(+), 49 deletions(-)
Title: MultiPhen, a package for the genetic association testing of
multiple phenotypes
Diff between MultiPhen versions 0.6 dated 2012-06-08 and 0.7 dated 2012-06-26
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 | 8 ++++----
R/mPhen.plink.R | 5 +++--
man/MultiPhen-package.Rd | 4 ++--
man/mPhen.plink.Rd | 1 -
5 files changed, 13 insertions(+), 13 deletions(-)
Title: Convencional Tukey Test
Diff between TukeyC versions 1.0-6 dated 2012-06-22 and 1.0-7 dated 2012-06-26
Description: Perform the conventional Tukey test from aov and aov.list
objects
Author: Jose Claudio Faria, Enio Jelihovschi and Ivan Bezerra Allaman
Maintainer: Jose Claudio Faria
COPYRIGHTS | 2 +-
ChangeLog | 7 +++++--
DESCRIPTION | 8 ++++----
MD5 | 17 +++++++++--------
README |only
man/TukeyC-package.Rd | 8 +++-----
man/TukeyC.Rd | 6 +++---
man/TukeyC.nest.Rd | 6 +++---
man/sorghum.Rd | 2 +-
man/summary.Rd | 2 +-
10 files changed, 30 insertions(+), 28 deletions(-)
Title: X12 - Graphical User Interface
Diff between x12GUI versions 0.1-0 dated 2012-06-11 and 0.2-0 dated 2012-06-26
Description: A graphical user interface for the x12 package
Author: Daniel Schopfhauser, Alexander Kowarik
Maintainer: Alexander Kowarik
DESCRIPTION | 8 ++--
MD5 | 5 +-
R/plotgui.R |only
R/x12GUI.R | 119 ++++++++++++++++++++++++++++++++++++++++--------------------
4 files changed, 88 insertions(+), 44 deletions(-)
Title: X12 - wrapper function and structure for batch processing
Diff between x12 versions 1.0-2 dated 2012-06-06 and 1.0-3 dated 2012-06-26
Description: A wrapper function and GUI for the X12 binaries
Author: Alexander Kowarik
Maintainer: Alexander Kowarik
DESCRIPTION | 8
MD5 | 28
R/X12-methods.R | 4
R/class.R | 2
R/parameter-methods.R | 3
R/plot-methods.R | 525 +++++-----
R/x12.R | 8
data/AirPassengersX12.RData |binary
data/AirPassengersX12Batch.RData |binary
man/AirPassengersX12.Rd | 735 --------------
man/AirPassengersX12Batch.Rd | 1971 ---------------------------------------
man/getP-methods.Rd | 55 -
man/loadP-methods.Rd | 48
man/plot-methods.Rd | 3
man/x12Output-class.Rd | 1
15 files changed, 414 insertions(+), 2977 deletions(-)
Title: Nonparametric Missing Value Imputation using Random Forest
Diff between missForest versions 1.2 dated 2012-02-20 and 1.3 dated 2012-06-26
Description: The function 'missForest' in this package is used to
impute missing values particularly in the case of mixed-type
data. It uses a random forest trained on the observed values of
a data matrix to predict the missing values. It can be used to
impute continuous and/or categorical data including complex
interactions and nonlinear relations. It yields an out-of-bag
(OOB) imputation error estimate without the need of a test set
or elaborate cross-validation.
Author: Daniel J. Stekhoven,
Maintainer: Daniel J. Stekhoven,
missForest-1.2/missForest/inst/doc/missForest_1.2.Rnw |only
missForest-1.2/missForest/inst/doc/missForest_1.2.pdf |only
missForest-1.3/missForest/DESCRIPTION | 8 -
missForest-1.3/missForest/MD5 | 40 ++++--
missForest-1.3/missForest/NAMESPACE | 4
missForest-1.3/missForest/R/library.R | 62 ++++++++--
missForest-1.3/missForest/inst/doc/missForest_1.3.Rnw |only
missForest-1.3/missForest/inst/doc/missForest_1.3.pdf |only
missForest-1.3/missForest/inst/doc/myBib.bib | 2
missForest-1.3/missForest/man/missForest-package.Rd | 4
missForest-1.3/missForest/man/missForest.Rd | 61 +++++++--
missForest-1.3/missForest/tests/arguments.Rout.save | 31 ++---
missForest-1.3/missForest/tests/classwtArgument.R |only
missForest-1.3/missForest/tests/classwtArgument.Rout.save |only
missForest-1.3/missForest/tests/continuous.Rout.save | 9 -
missForest-1.3/missForest/tests/cutoffArgument.R |only
missForest-1.3/missForest/tests/cutoffArgument.Rout.save |only
missForest-1.3/missForest/tests/maxiterReached.Rout.save | 9 +
missForest-1.3/missForest/tests/maxnodesArgument.R |only
missForest-1.3/missForest/tests/maxnodesArgument.Rout.save |only
missForest-1.3/missForest/tests/missingClass.Rout.save | 18 +-
missForest-1.3/missForest/tests/mixed.Rout.save | 9 +
missForest-1.3/missForest/tests/nodesizeArgument.R |only
missForest-1.3/missForest/tests/nodesizeArgument.Rout.save |only
missForest-1.3/missForest/tests/strataArgument.R |only
missForest-1.3/missForest/tests/strataArgument.Rout.save |only
missForest-1.3/missForest/tests/subsamplingMissForest.R |only
missForest-1.3/missForest/tests/subsamplingMissForest.Rout.save |only
missForest-1.3/missForest/tests/wrongInput.Rout.save | 9 +
29 files changed, 191 insertions(+), 75 deletions(-)
Title: Detailed R source code parser
Diff between parser versions 0.0-15 dated 2012-06-22 and 0.0-16 dated 2012-06-26
Description: detailed source code parser, based on the standard R
parser but organizing the information differently
Author: Romain Francois
Maintainer: Andrew Redd
DESCRIPTION | 13 ++++++-------
MD5 | 8 ++++----
NEWS | 6 ++++++
R/parser.R | 3 ++-
src/gram.c | 10 +++++-----
5 files changed, 23 insertions(+), 17 deletions(-)
Title: Markdown rendering for R
Diff between markdown versions 0.5.1 dated 2012-06-08 and 0.5.2 dated 2012-06-26
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
markdown-0.5.1/markdown/R/guid.R |only
markdown-0.5.2/markdown/DESCRIPTION | 8
markdown-0.5.2/markdown/MD5 | 28 +-
markdown-0.5.2/markdown/NEWS | 22 +
markdown-0.5.2/markdown/R/renderMarkdown.R | 154 ++-----------
markdown-0.5.2/markdown/R/rpubsUpload.R | 4
markdown-0.5.2/markdown/inst/reference.md |only
markdown-0.5.2/markdown/man/markdownExtensions.Rd | 3
markdown-0.5.2/markdown/man/markdownToHTML.Rd | 15 -
markdown-0.5.2/markdown/src/Rbase64.c | 5
markdown-0.5.2/markdown/src/Rmarkdown.c | 3
markdown-0.5.2/markdown/src/buffer.c | 2
markdown-0.5.2/markdown/src/html.c | 28 ++
markdown-0.5.2/markdown/src/markdown.c | 253 +++++++++++++++++++++-
markdown-0.5.2/markdown/src/markdown.h | 3
markdown-0.5.2/markdown/src/sundown_version.h | 2
16 files changed, 374 insertions(+), 156 deletions(-)