Title: Package contains a few functions to visualize statistical
circumstances.
Diff between visualizationTools versions 0.2.04 dated 2011-10-19 and 0.2.05 dated 2012-08-01
More information about visualizationTools at CRAN
Description: Package contains function to visualize a t-test, the power
of a t-test, control charts and the influence of regulating
them, Oc-curves, the Law of large Numbers and confidence
intervals.
Author: Thomas Roth Etienne Stockhausen
Maintainer: E. Stockhausen
DESCRIPTION | 11 +++++------
MD5 | 9 +++++----
NAMESPACE |only
R/qrk.R | 2 +-
R/qrkSD.R | 2 +-
man/visualizationTools-package.Rd | 5 ++---
6 files changed, 14 insertions(+), 15 deletions(-)
Permanent link
Title: Gini methodology-based correlation and clustering analysis of
microarray and RNA-Seq gene expression data
Diff between rsgcc versions 1.0.2 dated 2012-06-15 and 1.0.3 dated 2012-08-01
Description: This package provides functions for calculating
associations between two genes with different correlation
methods, including the Gini correlation coefficient (GCC), the
Pearson's product moment correlation coefficient (PCC), the
Kendall tau rank correlation coefficient (KCC), the Spearman's
rank correlation coefficient (SCC) and the Tukey's biweight
correlation coefficient (BiWt). It can also been implemented to
perform the correlation and clustering analysis of
transcriptomic data profiled by microarray and RNA-Seq
technologies. Additionally, this package can be further applied
to construct gene co-expression networks (GCNs).
Author: Chuang Ma, Xiangfeng Wang
Maintainer: Chuang Ma
DESCRIPTION | 28 +++++++++++++++-------------
MD5 | 12 ++++++------
man/cor.matrix.Rd | 3 +--
man/cor.pair.Rd | 2 +-
man/gcc.hclust.Rd | 4 ++--
man/onegcc.Rd | 2 +-
man/rsgcc-package.Rd | 12 ++++++------
7 files changed, 32 insertions(+), 31 deletions(-)
Title: Functions for Learning Exploratory Data Analysis
Diff between LearnEDA versions 1.01 dated 2009-10-14 and 1.2 dated 2012-08-01
Description: LearnEDA contains a collection of functions helpful in
learning the basic tenets of Exploratory Data Analysis.
Author: Jim Albert
Maintainer: Jim Albert
LearnEDA-1.01/LearnEDA/data/act.scores.06.07.txt |only
LearnEDA-1.01/LearnEDA/data/baseball.attendance.txt |only
LearnEDA-1.01/LearnEDA/data/beatles.txt |only
LearnEDA-1.01/LearnEDA/data/boston.marathon.txt |only
LearnEDA-1.01/LearnEDA/data/boston.marathon.wtimes.txt |only
LearnEDA-1.01/LearnEDA/data/brave.at.txt |only
LearnEDA-1.01/LearnEDA/data/car.measurements.txt |only
LearnEDA-1.01/LearnEDA/data/church.2way.TXT |only
LearnEDA-1.01/LearnEDA/data/church.tseries.TXT |only
LearnEDA-1.01/LearnEDA/data/college.ratings.txt |only
LearnEDA-1.01/LearnEDA/data/farms.txt |only
LearnEDA-1.01/LearnEDA/data/football.txt |only
LearnEDA-1.01/LearnEDA/data/gestation.periods.TXT |only
LearnEDA-1.01/LearnEDA/data/grandma.19.40.txt |only
LearnEDA-1.01/LearnEDA/data/heaviest.fish.txt |only
LearnEDA-1.01/LearnEDA/data/home.prices.txt |only
LearnEDA-1.01/LearnEDA/data/homeruns.2000.txt |only
LearnEDA-1.01/LearnEDA/data/homeruns.61.txt |only
LearnEDA-1.01/LearnEDA/data/immigrants.txt |only
LearnEDA-1.01/LearnEDA/data/island.areas.txt |only
LearnEDA-1.01/LearnEDA/data/lake.txt |only
LearnEDA-1.01/LearnEDA/data/mortality.rates.txt |only
LearnEDA-1.01/LearnEDA/data/olympics.run.TXT |only
LearnEDA-1.01/LearnEDA/data/olympics.speed.skating.txt |only
LearnEDA-1.01/LearnEDA/data/olympics.swim.txt |only
LearnEDA-1.01/LearnEDA/data/pop.change.txt |only
LearnEDA-1.01/LearnEDA/data/pop.densities.1920.2000.txt |only
LearnEDA-1.01/LearnEDA/data/pop.england.txt |only
LearnEDA-1.01/LearnEDA/data/rent.prices.txt |only
LearnEDA-1.01/LearnEDA/data/salaries.txt |only
LearnEDA-1.01/LearnEDA/data/studentdata.txt |only
LearnEDA-1.01/LearnEDA/data/temperatures.txt |only
LearnEDA-1.01/LearnEDA/data/tukey.24a.txt |only
LearnEDA-1.01/LearnEDA/data/tukey.24b.txt |only
LearnEDA-1.01/LearnEDA/data/tukey.26a.txt |only
LearnEDA-1.01/LearnEDA/data/tukey.26b.txt |only
LearnEDA-1.01/LearnEDA/data/tukey.26c.txt |only
LearnEDA-1.01/LearnEDA/data/us.pop.txt |only
LearnEDA-1.01/LearnEDA/man/brave.at.Rd |only
LearnEDA-1.01/LearnEDA/man/pop.densities.1920.2000.Rd |only
LearnEDA-1.2/LearnEDA/DESCRIPTION | 10 ++--
LearnEDA-1.2/LearnEDA/INDEX |only
LearnEDA-1.2/LearnEDA/MD5 |only
LearnEDA-1.2/LearnEDA/NAMESPACE |only
LearnEDA-1.2/LearnEDA/R/half.slope.ratio.R | 15 +++----
LearnEDA-1.2/LearnEDA/R/hinkley.R | 14 +++---
LearnEDA-1.2/LearnEDA/R/lval.R | 26 ++++++------
LearnEDA-1.2/LearnEDA/R/power.t.R |only
LearnEDA-1.2/LearnEDA/R/rline.R | 11 +++--
LearnEDA-1.2/LearnEDA/R/slider.compare.R |only
LearnEDA-1.2/LearnEDA/R/slider.match.R |only
LearnEDA-1.2/LearnEDA/R/slider.power.R |only
LearnEDA-1.2/LearnEDA/R/slider.straighten.R |only
LearnEDA-1.2/LearnEDA/R/spread.level.plot.R | 31 +++++++--------
LearnEDA-1.2/LearnEDA/data/act.scores.06.07.txt.gz |only
LearnEDA-1.2/LearnEDA/data/baseball.attendance.txt.gz |only
LearnEDA-1.2/LearnEDA/data/batting.history.txt.gz |only
LearnEDA-1.2/LearnEDA/data/beatles.txt.gz |only
LearnEDA-1.2/LearnEDA/data/boston.marathon.txt.gz |only
LearnEDA-1.2/LearnEDA/data/boston.marathon.wtimes.txt.gz |only
LearnEDA-1.2/LearnEDA/data/braves.attendance.txt.gz |only
LearnEDA-1.2/LearnEDA/data/car.measurements.txt.gz |only
LearnEDA-1.2/LearnEDA/data/church.2way.txt.gz |only
LearnEDA-1.2/LearnEDA/data/church.tseries.txt.gz |only
LearnEDA-1.2/LearnEDA/data/college.ratings.txt.gz |only
LearnEDA-1.2/LearnEDA/data/farms.txt.gz |only
LearnEDA-1.2/LearnEDA/data/football.txt.gz |only
LearnEDA-1.2/LearnEDA/data/gestation.periods.txt.gz |only
LearnEDA-1.2/LearnEDA/data/grandma.19.40.txt.gz |only
LearnEDA-1.2/LearnEDA/data/heaviest.fish.txt.gz |only
LearnEDA-1.2/LearnEDA/data/home.prices.txt.gz |only
LearnEDA-1.2/LearnEDA/data/homeruns.2000.txt.gz |only
LearnEDA-1.2/LearnEDA/data/homeruns.61.txt.gz |only
LearnEDA-1.2/LearnEDA/data/immigrants.txt.gz |only
LearnEDA-1.2/LearnEDA/data/island.areas.txt.gz |only
LearnEDA-1.2/LearnEDA/data/lake.txt.gz |only
LearnEDA-1.2/LearnEDA/data/mortality.rates.txt.gz |only
LearnEDA-1.2/LearnEDA/data/olympics.run.txt.gz |only
LearnEDA-1.2/LearnEDA/data/olympics.speed.skating.txt.gz |only
LearnEDA-1.2/LearnEDA/data/olympics.swim.txt.gz |only
LearnEDA-1.2/LearnEDA/data/pitching.history.txt.gz |only
LearnEDA-1.2/LearnEDA/data/pop.change.txt.gz |only
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LearnEDA-1.2/LearnEDA/data/rent.prices.txt.gz |only
LearnEDA-1.2/LearnEDA/data/salaries.txt.gz |only
LearnEDA-1.2/LearnEDA/data/snowfall.txt.gz |only
LearnEDA-1.2/LearnEDA/data/studentdata.txt.gz |only
LearnEDA-1.2/LearnEDA/data/temperatures.txt.gz |only
LearnEDA-1.2/LearnEDA/data/tukey.24a.txt.gz |only
LearnEDA-1.2/LearnEDA/data/tukey.24b.txt.gz |only
LearnEDA-1.2/LearnEDA/data/tukey.26a.txt.gz |only
LearnEDA-1.2/LearnEDA/data/tukey.26b.txt.gz |only
LearnEDA-1.2/LearnEDA/data/tukey.26c.txt.gz |only
LearnEDA-1.2/LearnEDA/data/us.pop.txt.gz |only
LearnEDA-1.2/LearnEDA/man/baseball.attendance.Rd | 12 +++--
LearnEDA-1.2/LearnEDA/man/batting.history.Rd |only
LearnEDA-1.2/LearnEDA/man/braves.attendance.Rd |only
LearnEDA-1.2/LearnEDA/man/immigrants.Rd | 7 +--
LearnEDA-1.2/LearnEDA/man/mortality.rates.Rd | 9 ++--
LearnEDA-1.2/LearnEDA/man/pitching.history.Rd |only
LearnEDA-1.2/LearnEDA/man/pop.change.Rd | 11 +++--
LearnEDA-1.2/LearnEDA/man/pop.densities.Rd |only
LearnEDA-1.2/LearnEDA/man/power.t.Rd |only
LearnEDA-1.2/LearnEDA/man/rline.Rd | 2
LearnEDA-1.2/LearnEDA/man/slider.compare.Rd |only
LearnEDA-1.2/LearnEDA/man/slider.match.Rd |only
LearnEDA-1.2/LearnEDA/man/slider.power.Rd |only
LearnEDA-1.2/LearnEDA/man/slider.straighten.Rd |only
LearnEDA-1.2/LearnEDA/man/snowfall.Rd |only
110 files changed, 84 insertions(+), 64 deletions(-)
Title: A simple way to fit detection functions to distance sampling
data and calculate abundance/density for biological
populations.
Diff between Distance versions 0.6 dated 2012-04-02 and 0.6.1 dated 2012-08-01
Description: A library that provides a simple way of fitting detection
functions to distance sampling data for both line and point
transects. Adjustment term selection, left and right
truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be
calculated if survey area information is provided.
Author: David L. Miller
Maintainer: David L Miller
DESCRIPTION | 6 ++--
MD5 | 11 ++++---
NEWS |only
R/ds.R | 79 ++++++++++++++++++++++++++++++++++++++++++++++----------
README | 4 ++
man/ds.Rd | 19 ++++++++-----
tests/run-all.R | 2 -
7 files changed, 91 insertions(+), 30 deletions(-)
Title: Categorical Bayesian Network Inference
Diff between catnet versions 1.13.2 dated 2011-12-13 and 1.13.4 dated 2012-08-01
Description: A package that handles discrete Bayesian network models
and provides inference using the frequentist approach
Author: Nikolay Balov, Peter Salzman
Maintainer: Nikolay Balov
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/zzz.R | 2 +-
inst/doc/catnet.Rnw | 5 +++--
inst/doc/catnet.pdf |binary
5 files changed, 14 insertions(+), 13 deletions(-)
Title: vcd additions
Diff between vcdExtra versions 0.5-3 dated 2012-05-08 and 0.5-4 dated 2012-08-01
Description: Provides additional data sets, methods and documentation
to complement the vcd package for Visualizing Categorical Data
and the gnm package for Generalized Nonlinear Models. In
particular, vcdExtra extends mosaic, assoc and sieve plots from
vcd to handle glm() and gnm() models and adds a 3D version in
mosaic3d.
Author: Michael Friendly with Heather Turner, Achim Zeileis, Duncan
Murdoch and David Firth
Maintainer: Michael Friendly
vcdExtra-0.5-3/vcdExtra/.project |only
vcdExtra-0.5-3/vcdExtra/R/meanResiduals.R |only
vcdExtra-0.5-3/vcdExtra/man/meanResiduals.Rd |only
vcdExtra-0.5-4/vcdExtra/DESCRIPTION | 10 +-
vcdExtra-0.5-4/vcdExtra/MD5 | 42 ++++------
vcdExtra-0.5-4/vcdExtra/NAMESPACE | 8 +
vcdExtra-0.5-4/vcdExtra/R/mosaic.glm.R | 25 ++++-
vcdExtra-0.5-4/vcdExtra/man/vcdExtra-package.Rd | 11 +-
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-Arthritis.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-TV-mosaic.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-agreesex.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-art21.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-art22.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-ca-haireye.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-cdplot.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-fourfold1.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-hec1.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-hec2.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-hec3.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-mental-plots1.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-mental-plots2.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-oddsratio.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-spine2.pdf |binary
vcdExtra-0.5-4/vcdExtra/vignettes/fig/vcd-tut-spine3.pdf |binary
24 files changed, 55 insertions(+), 41 deletions(-)
Title: Multi-View Clustering
Diff between mvc versions 1.0 dated 2012-07-16 and 1.1 dated 2012-08-01
Description: An implementation of Multi-View Clustering (Bickel and
Scheffer, 2004). Documents are generated by drawing word values
from a categorical distribution for each word, given the
cluster. This means words are not counted (multinomial, as in
the paper), but words take on different values from a finite
set of values (categorical). Thus, it implements Mixture of
Categoricals EM (as opposed to Mixture of Multinomials
developed in the paper), and Spherical k-Means. The latter
represents documents as vectors in the categorical space.
Author: Andreas Maunz
Maintainer: Andreas Maunz
mvc-1.0/mvc/man/estLogPxGthetaJ.Rd |only
mvc-1.1/mvc/DESCRIPTION | 19 ++++---
mvc-1.1/mvc/MD5 | 27 ++++++----
mvc-1.1/mvc/NAMESPACE | 41 +++++++++-------
mvc-1.1/mvc/R/mvc-utils.R | 84 ++++++++++++++++++++++++++++-----
mvc-1.1/mvc/R/mvc.R | 69 ++++++++++++++++++---------
mvc-1.1/mvc/README.md |only
mvc-1.1/mvc/data/toyViews.RData |binary
mvc-1.1/mvc/man/checkViews.Rd | 4 -
mvc-1.1/mvc/man/dbern.Rd | 4 -
mvc-1.1/mvc/man/dcat.Rd |only
mvc-1.1/mvc/man/estLogPxBernGthetaJ.Rd |only
mvc-1.1/mvc/man/estLogPxCatGthetaJ.Rd |only
mvc-1.1/mvc/man/mApplyBern.Rd | 6 +-
mvc-1.1/mvc/man/mApplyCat.Rd |only
mvc-1.1/mvc/man/mvcmb.Rd | 8 +--
mvc-1.1/mvc/man/mvcsph.Rd | 10 +--
mvc-1.1/mvc/man/viewsClasses.Rd |only
18 files changed, 184 insertions(+), 88 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Diff between MASS versions 7.3-19 dated 2012-06-27 and 7.3-20 dated 2012-08-01
Description: Functions and datasets to support Venables and Ripley,
'Modern Applied Statistics with S' (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph], Bill Venables [ctb], Kurt Hornik
[trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial
port ca 1998), David Firth [ctb]
Maintainer: Brian Ripley
MASS-7.3-19/MASS/po/R-en@quot.po |only
MASS-7.3-20/MASS/DESCRIPTION | 25 ++++++++---------
MASS-7.3-20/MASS/MD5 | 7 ++--
MASS-7.3-20/MASS/inst/po/en@quot/LC_MESSAGES/R-MASS.mo |binary
MASS-7.3-20/MASS/po/R-MASS.pot | 5 +--
5 files changed, 18 insertions(+), 19 deletions(-)
Title: R interface to the Gearman Job Server
Diff between gearman versions 0.1-3 dated 2012-07-31 and 0.1-4 dated 2012-08-01
Description: gearman provides a reference class interface to the
Gearman Job server. gearman links to the libgearman C library
and currently exposes the client API, allowing R users to
submit jobs to Gearman Job servers. A future version may expose
the worker API, thus allowing users to place R jobs within the
server... callable by any gearman-enabled client.
Author: Jeffrey Horner
Maintainer: Jeffrey Horner
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
src/osx_config.h.9.8 | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Multivariate Dependence Modeling with Vines
Diff between vines versions 1.0.4 dated 2012-04-13 and 1.0.5 dated 2012-08-01
Description: Vines are graphical models for pair-copula constructions
that allow building high-dimensional distributions using
bivariate copulas and marginal density functions. This package
contains S4 classes for vines (C-vines and D-vines) and methods
for inference, goodness-of-fit tests, density evaluation,
distribution function evaluation, and simulation.
Author: Yasser González Fernández
Maintainer: Yasser González Fernández
DESCRIPTION | 15 ++++++------
MD5 | 58 ++++++++++++++++++++++++------------------------
NEWS | 8 ++++++
R/Vine.R | 4 +--
R/dimnames.R | 4 +--
R/dvine.R | 6 ++--
R/h.R | 6 ++--
R/hinverse.R | 4 +--
R/pvine.R | 4 +--
R/rvine.R | 4 +--
R/show.R | 6 ++--
R/vineFit.R | 4 +--
R/vineFitML.R | 4 +--
R/vineGoF.R | 4 +--
R/vineIter.R | 4 +--
R/vineOrder.R | 4 +--
R/vinePIT.R | 4 +--
R/vineParameters.R | 4 +--
inst/CITATION | 15 +++++-------
man/CVine-class.Rd | 4 +--
man/DVine-class.Rd | 4 +--
man/h-methods.Rd | 2 -
man/hinverse-methods.Rd | 7 +++--
man/vineGoF.Rd | 2 -
src/h.c | 4 +--
src/h.h | 4 +--
src/hinverse.c | 4 +--
src/hinverse.h | 4 +--
src/register.c | 4 +--
tests/hfunctions.R | 4 +--
30 files changed, 107 insertions(+), 98 deletions(-)
Title: Smooth Backfitting
Diff between sBF versions 1.0 dated 2009-10-08 and 1.1 dated 2012-08-01
Description: Smooth Backfitting for additive models using
Nadaraya-Watson estimator
Author: A. Arcagni, L. Bagnato
Maintainer: Alberto Arcagni
sBF-1.0/sBF/Read-and-delete-me |only
sBF-1.1/sBF/DESCRIPTION | 8 ++++----
sBF-1.1/sBF/MD5 |only
sBF-1.1/sBF/NAMESPACE |only
4 files changed, 4 insertions(+), 4 deletions(-)
Title: Hierarchical Semiparametric Regression of Test Statistics
Diff between hisemi versions 1.0-208 dated 2012-02-24 and 1.0-249 dated 2012-08-01
Description: This package implements methods for hierarchical
semiparametric regression models for test statistics.
Specifically, test statistics given the null/alternative
hypotheses are modeled parametrically, whereas the unobservable
status of null/alternative hypotheses are modeled using
nonparametric additive logistic regression over covariates.
Author: Long Qu
Maintainer: Long Qu
DESCRIPTION | 10 +-
MD5 | 16 +--
man/EMupdate.Rd | 2
man/OsplinePen.Rd | 13 +--
man/confint.hisemit.Rd | 2
man/hisemi-package.Rd | 12 +-
man/n.knots.Rd | 2
man/penLik.EMNewton.Rd | 205 ++++++++++++++++++++++++-------------------------
man/tPoly.newton.Rd | 8 -
9 files changed, 135 insertions(+), 135 deletions(-)
Title: Estimation of the peak-to-trough ratio of a seasonal variation
component
Diff between Peak2Trough versions 1.2 dated 2012-07-17 and 1.3 dated 2012-08-01
Description: Estimation of the peak-to-trough ratio of a seasonal
variation component.
Author: Anette Luther Christensen
Maintainer: Anette Luther Christensen
DESCRIPTION | 10 +-
MD5 | 10 +-
R/nlm.R | 176 +++++++++++++++++++++------------------------
R/rrDynamic.R | 11 +-
R/rrStatic.R | 14 ++-
man/Peak2Trough-package.Rd | 2
6 files changed, 112 insertions(+), 111 deletions(-)
Title: Multivariate meta-analysis and meta-regression
Diff between mvmeta versions 0.2.4 dated 2012-01-10 and 0.3.0 dated 2012-08-01
Description: The package mvmeta consists of a collection of functions
to perform fixed and random-effects multivariate and univariate
meta-analysis and meta-regression in R.
Author: Antonio Gasparrini
Maintainer: Antonio Gasparrini
mvmeta-0.2.4/mvmeta/R/AIC.mvmeta.R |only
mvmeta-0.2.4/mvmeta/R/BIC.mvmeta.R |only
mvmeta-0.2.4/mvmeta/R/cbindlist.R |only
mvmeta-0.2.4/mvmeta/R/expMat.R |only
mvmeta-0.2.4/mvmeta/R/fitted.mvmeta.R |only
mvmeta-0.2.4/mvmeta/R/gradchol.R |only
mvmeta-0.2.4/mvmeta/R/logMat.R |only
mvmeta-0.2.4/mvmeta/R/meanlist.R |only
mvmeta-0.2.4/mvmeta/R/mvmeta.check.R |only
mvmeta-0.2.4/mvmeta/R/mvmeta.ml.grad.R |only
mvmeta-0.2.4/mvmeta/R/mvmeta.reml.grad.R |only
mvmeta-0.2.4/mvmeta/R/onAttach.R |only
mvmeta-0.2.4/mvmeta/R/rbindlist.R |only
mvmeta-0.2.4/mvmeta/R/sumlist.R |only
mvmeta-0.2.4/mvmeta/man/cbindlist.Rd |only
mvmeta-0.2.4/mvmeta/man/fitted.mvmeta.Rd |only
mvmeta-0.2.4/mvmeta/man/gradchol.Rd |only
mvmeta-0.2.4/mvmeta/man/mvmeta.check.Rd |only
mvmeta-0.3.0/mvmeta/DESCRIPTION | 17
mvmeta-0.3.0/mvmeta/MD5 | 106 ++---
mvmeta-0.3.0/mvmeta/NAMESPACE | 94 +++--
mvmeta-0.3.0/mvmeta/R/blup.R | 3
mvmeta-0.3.0/mvmeta/R/blup.mvmeta.R | 279 +++++++--------
mvmeta-0.3.0/mvmeta/R/coef.mvmeta.R | 21 -
mvmeta-0.3.0/mvmeta/R/extractAIC.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/internal.R |only
mvmeta-0.3.0/mvmeta/R/logLik.mvmeta.R | 25 -
mvmeta-0.3.0/mvmeta/R/model.frame.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/model.matrix.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.R | 350 ++++---------------
mvmeta-0.3.0/mvmeta/R/mvmeta.control.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.fit.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.fixed.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.igls.R | 101 ++---
mvmeta-0.3.0/mvmeta/R/mvmeta.ml.R | 84 ++--
mvmeta-0.3.0/mvmeta/R/mvmeta.ml.fn.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.ml.gr.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.reml.R | 85 ++--
mvmeta-0.3.0/mvmeta/R/mvmeta.reml.fn.R |only
mvmeta-0.3.0/mvmeta/R/mvmeta.reml.gr.R |only
mvmeta-0.3.0/mvmeta/R/na.exclude.data.frame.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/na.omit.data.frame.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/nobs.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/predict.mvmeta.R | 266 +++++++-------
mvmeta-0.3.0/mvmeta/R/print.mvmeta.R | 72 +--
mvmeta-0.3.0/mvmeta/R/print.qtest.mvmeta.R | 33 +
mvmeta-0.3.0/mvmeta/R/print.summary.mvmeta.R |only
mvmeta-0.3.0/mvmeta/R/qtest.R | 5
mvmeta-0.3.0/mvmeta/R/qtest.mvmeta.R | 55 ++
mvmeta-0.3.0/mvmeta/R/summary.mvmeta.R | 171 +++------
mvmeta-0.3.0/mvmeta/R/vcov.mvmeta.R | 10
mvmeta-0.3.0/mvmeta/R/vechMat.R | 13
mvmeta-0.3.0/mvmeta/R/xpndMat.R | 16
mvmeta-0.3.0/mvmeta/data/berkey98.rda |binary
mvmeta-0.3.0/mvmeta/inst/CITATION | 24 -
mvmeta-0.3.0/mvmeta/inst/ChangeLog | 76 +++-
mvmeta-0.3.0/mvmeta/man/berkey98.Rd | 8
mvmeta-0.3.0/mvmeta/man/blup.mvmeta.Rd | 41 +-
mvmeta-0.3.0/mvmeta/man/coef.mvmeta.Rd | 35 +
mvmeta-0.3.0/mvmeta/man/logLik.mvmeta.Rd | 41 --
mvmeta-0.3.0/mvmeta/man/model.frame.mvmeta.Rd |only
mvmeta-0.3.0/mvmeta/man/mvmeta-package.Rd | 57 +--
mvmeta-0.3.0/mvmeta/man/mvmeta.Rd | 114 ++++--
mvmeta-0.3.0/mvmeta/man/mvmeta.control.Rd |only
mvmeta-0.3.0/mvmeta/man/mvmeta.ml.Rd | 244 +------------
mvmeta-0.3.0/mvmeta/man/mvmeta.ml.fn.Rd |only
mvmeta-0.3.0/mvmeta/man/mvmetaObject.Rd |only
mvmeta-0.3.0/mvmeta/man/na.omit.data.frame.mvmeta.Rd |only
mvmeta-0.3.0/mvmeta/man/predict.mvmeta.Rd | 36 +
mvmeta-0.3.0/mvmeta/man/qtest.Rd | 2
mvmeta-0.3.0/mvmeta/man/qtest.mvmeta.Rd | 36 +
mvmeta-0.3.0/mvmeta/man/summary.mvmeta.Rd | 40 +-
mvmeta-0.3.0/mvmeta/man/vechMat.Rd | 84 +---
73 files changed, 1207 insertions(+), 1437 deletions(-)
Title: Multi-state Markov and hidden Markov models in continuous time
Diff between msm versions 1.1.1 dated 2012-05-11 and 1.1.2 dated 2012-08-01
Description: Functions for fitting general continuous-time Markov and
hidden Markov multi-state models to longitudinal data. Both
Markov transition rates and the hidden Markov output process
can be modelled in terms of covariates, which may be constant
or piecewise-constant in time. A variety of observation
schemes are supported, including processes observed at
arbitrary times (panel data), continuously-observed processes,
and censored states.
Author: Christopher Jackson
Maintainer: Christopher Jackson
msm-1.1.1/msm/tests/analyticp.R |only
msm-1.1.1/msm/tests/boot.R |only
msm-1.1.1/msm/tests/deriv-debug.R |only
msm-1.1.1/msm/tests/deriv-test.R |only
msm-1.1.1/msm/tests/deriv.R |only
msm-1.1.1/msm/tests/errors.R |only
msm-1.1.1/msm/tests/fev.R |only
msm-1.1.1/msm/tests/herrors.R |only
msm-1.1.1/msm/tests/hsim.R |only
msm-1.1.1/msm/tests/miscnew.R |only
msm-1.1.1/msm/tests/pci.R |only
msm-1.1.1/msm/tests/pearson.R |only
msm-1.1.1/msm/tests/sim.R |only
msm-1.1.1/msm/tests/utils.R |only
msm-1.1.2/msm/ChangeLog | 10 +
msm-1.1.2/msm/DESCRIPTION | 8
msm-1.1.2/msm/MD5 | 54 ++---
msm-1.1.2/msm/NAMESPACE | 1
msm-1.1.2/msm/R/constants.R | 11 -
msm-1.1.2/msm/R/hmm-dists.R | 8
msm-1.1.2/msm/R/msm.R | 2
msm-1.1.2/msm/R/pearson.R | 2
msm-1.1.2/msm/data/aneur.txt.gz |binary
msm-1.1.2/msm/data/cav.txt.gz |binary
msm-1.1.2/msm/data/fev.txt.gz |binary
msm-1.1.2/msm/data/psor.txt.gz |binary
msm-1.1.2/msm/inst/NEWS | 15 +
msm-1.1.2/msm/inst/doc/msm-manual.pdf |binary
msm-1.1.2/msm/man/hmm-dists.Rd | 18 +
msm-1.1.2/msm/man/msm.Rd | 25 +-
msm-1.1.2/msm/src/hmm.c | 6
msm-1.1.2/msm/src/hmm.h | 1
msm-1.1.2/msm/src/lik.c | 3
msm-1.1.2/msm/tests/misc.R | 222 ----------------------
msm-1.1.2/msm/tests/simple.R | 337 ----------------------------------
35 files changed, 106 insertions(+), 617 deletions(-)
Title: Utilities for strings and function arguments.
Diff between gsubfn versions 0.6-3 dated 2012-04-03 and 0.6-4 dated 2012-08-01
Description: gsubfn is like gsub but can take a replacement function or
certain other objects instead of the replacement string.
Matches and back references are input to the replacement
function and replaced by the function output. gsubfn can be
used to split strings based on content rather than delimiters
and for quasi-perl-style string interpolation. The package also
has facilities for translating formulas to functions and
allowing such formulas in function calls instead of functions.
This can be used with R functions such as apply, sapply,
lapply, optim, integrate, xyplot, Filter and any other function
that expects another function as an input argument or functions
like cat or sql calls that may involve strings where
substitution is desirable.
Author: G. Grothendieck
Maintainer: G. Grothendieck
DESCRIPTION | 10 +++++-----
MD5 | 23 ++++++++++++-----------
R/fn.R | 6 +++---
R/gsubfn.R | 11 +++++++----
R/zzz.R | 11 ++++++++++-
demo/gsubfn-chron.R | 4 +---
demo/gsubfn-cut.R | 2 +-
demo/gsubfn-gries.R | 2 +-
demo/gsubfn-si.R | 2 +-
inst/NEWS | 16 ++++++++++++++++
inst/doc/gsubfn.Rnw | 25 ++++++++++++-------------
inst/doc/gsubfn.pdf |binary
inst/lipsum.txt |only
13 files changed, 69 insertions(+), 43 deletions(-)
Title: Likelihood Estimation of Admixture in Parents From Offspring
Genotypes
Diff between LEAPFrOG versions 1.0.5 dated 2012-07-13 and 1.0.6 dated 2012-08-01
Description: Contains LEAPFrOG Gradient Optimisation and Expectation
Maximisation functions for inferring parental admixture
proportions from an offspring with SNP genotypes.
Author: Daniel JM Crouch & Michael E Weale
Maintainer: Daniel JM Crouch
DESCRIPTION | 6 +++---
LEAPFrOG.zip |binary
MD5 | 6 +++---
R/LEAPFrOG.R | 2 +-
4 files changed, 7 insertions(+), 7 deletions(-)
Title: A community modeling foundation for Eco-Hydrology.
Diff between EcoHydRology versions 0.4.3 dated 2012-07-16 and 0.4.5 dated 2012-08-01
Description: This package provides a flexible foundation for
scientists, engineers, and policy makers to base teaching
exercises as well as for more applied use to model complex
eco-hydrological interactions.
Author: Fuka DR, Walter MT, Archibald JA, Steenhuis TS, and Easton ZM
Maintainer: Daniel Fuka
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
R/get_cfsr_latlon.R | 2 +-
R/get_gsod_stn.R | 5 +++--
R/get_usgs_gage.R | 39 +++++++++++++++++++++------------------
R/swat_objective_function.R | 2 +-
man/EcoHydRology-package.Rd | 2 +-
man/get_usgs_gage.Rd | 14 +++++++++++---
8 files changed, 48 insertions(+), 36 deletions(-)
Title: Simulation of genomic data in applied genetics
Diff between hypred versions 0.1 dated 2011-02-03 and 0.2 dated 2012-08-01
Description: The package is intended for simulating high density
genomic data. Its focus is on genomic applications in applied
genetics,namely hybrid breeding, but it should be useful in
related fields as well. The meiosis is simulated under a
count-location model, the genetic structure can include
additive and dominance effects. The low level nature of the
package provides great flexibility in creating all kinds of
populations.
Author: Frank Technow
Maintainer: Frank Technow
DESCRIPTION | 10 +++++-----
MD5 |only
inst/doc/hypred.Rnw | 4 ++--
inst/doc/hypred.pdf |binary
man/hypred-package.Rd | 4 ++--
man/hypredCode.Rd | 2 +-
man/hypredNewMap.Rd | 2 +-
man/hypredNewQTL.Rd | 2 +-
8 files changed, 12 insertions(+), 12 deletions(-)
Title: Time series Aggregation
Diff between TSAgg versions 0.2-1 dated 2010-09-06 and 1.0.1 dated 2012-08-01
Description: Time series aggregation for incomplete time series data.
Author: JS Lessels.
Maintainer: JS Lessels
DESCRIPTION | 13 +++++++++----
MD5 |only
NAMESPACE |only
R/daysAgg.R | 12 ++++++------
R/hoursAgg.R | 25 ++++++++++++++++---------
R/timeSeries.R | 54 +++++++++++++++++++++++++++---------------------------
data/foo.RData |binary
data/foo.na.RData |binary
8 files changed, 58 insertions(+), 46 deletions(-)
Title: Runiversal - Package for converting R objects to Java variables
and XML.
Diff between Runiversal versions 1.0.1 dated 2010-08-16 and 1.0.2 dated 2012-08-01
Description: This package contains some functions for converting R
objects to Java style variables and XML. Generated Java code is
interpretable by dynamic Java libraries such as Beanshell.
Calling R externally and handling the Java or XML output is an
other way to call R from other languages without native
interfaces. For a Java implementation of this approach visit
http://www.mhsatman.com/rcaller.php and
http://stdioe.blogspot.com/search/label/rcaller
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman
DESCRIPTION | 13 +++++++------
MD5 |only
NAMESPACE |only
3 files changed, 7 insertions(+), 6 deletions(-)
Title: Functions, data and code for count data.
Diff between COUNT versions 1.2.1 dated 2012-03-19 and 1.2.3 dated 2012-08-01
Description: Functions, data and code for Hilbe, J.M. 2009. Negative
Binomial Regression, 2nd Edition (Cambridge University Press)
Author: Joseph M Hilbe
Maintainer: Andrew Robinson
DESCRIPTION | 8 ++--
MD5 | 62 +++++++++++++++++------------------
R/nb1_syn.r | 2 -
R/nb2_syn.r | 2 -
data/affairs.rda |binary
data/azdrg112.rda |binary
data/azpro.rda |binary
data/badhealth.rda |binary
data/fasttrakg.rda |binary
data/lbw.rda |binary
data/lbwgrp.rda |binary
data/loomis.rda |binary
data/mdvis.rda |binary
data/medpar.rda |binary
data/rwm.rda |binary
data/rwm5yr.rda |binary
data/ships.rda |binary
data/titanic.rda |binary
data/titgrp.rda |binary
inst/HILBE_SCRIPTS/geo_rng.r | 2 -
inst/HILBE_SCRIPTS/nbsim.r | 2 -
inst/HILBE_SCRIPTS/syn.geo.r | 2 -
inst/HILBE_SCRIPTS/syn.hurdle_lnb2.r | 2 -
inst/HILBE_SCRIPTS/syn.nb1.r | 2 -
inst/HILBE_SCRIPTS/syn.nb2.r | 2 -
inst/HILBE_SCRIPTS/syn.nb2nb2fm.r | 4 +-
inst/HILBE_SCRIPTS/syn.nb2o.r | 2 -
man/logit_syn.Rd | 10 ++---
man/ml.nbc.Rd | 5 +-
man/nb2_syn.Rd | 12 +++---
man/nbc_syn.Rd | 4 +-
man/poisson_syn.Rd | 8 ++--
32 files changed, 67 insertions(+), 64 deletions(-)
Title: Tools for general maximum likelihood estimation
Diff between bbmle versions 1.0.5.1 dated 2012-07-17 and 1.0.5.2 dated 2012-08-01
Description: Methods and functions for fitting maximum likelihood
models in R. This package modifies and extends the mle classes
in the stats4 package.
Author: Ben Bolker
Maintainer: Ben Bolker
bbmle-1.0.5.1/bbmle/tests/binomtest1.Rout |only
bbmle-1.0.5.1/bbmle/tests/parscale.Rout |only
bbmle-1.0.5.1/bbmle/tests/testbounds.Rout |only
bbmle-1.0.5.2/bbmle/DESCRIPTION | 10 -
bbmle-1.0.5.2/bbmle/MD5 | 83 +++++-------
bbmle-1.0.5.2/bbmle/NAMESPACE | 4
bbmle-1.0.5.2/bbmle/R/IC.R | 70 +++++-----
bbmle-1.0.5.2/bbmle/R/mle2-methods.R | 1
bbmle-1.0.5.2/bbmle/inst/NEWS.Rd | 11 +
bbmle-1.0.5.2/bbmle/inst/doc/mle2.pdf |binary
bbmle-1.0.5.2/bbmle/inst/doc/quasi.pdf |binary
bbmle-1.0.5.2/bbmle/man/BIC-methods.Rd | 28 ++--
bbmle-1.0.5.2/bbmle/man/profile.mle-class.Rd | 11 +
bbmle-1.0.5.2/bbmle/tests/BIC.R | 4
bbmle-1.0.5.2/bbmle/tests/BIC.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/ICtab.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/RUnit-tests.Rout.save | 4
bbmle-1.0.5.2/bbmle/tests/binomtest1.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/controleval.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/doRUnit.Rout.save |only
bbmle-1.0.5.2/bbmle/tests/eval.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/formulatest.Rout.save | 50 ++++---
bbmle-1.0.5.2/bbmle/tests/glmcomp.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/gradient_vecpar_profile.Rout.save | 12 -
bbmle-1.0.5.2/bbmle/tests/grtest1.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/methods.Rout.save | 36 ++++-
bbmle-1.0.5.2/bbmle/tests/mortanal.Rout.save | 29 ++--
bbmle-1.0.5.2/bbmle/tests/optimize.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/optimizers.Rout.save | 11 -
bbmle-1.0.5.2/bbmle/tests/optimx.R | 3
bbmle-1.0.5.2/bbmle/tests/optimx.Rout.save | 52 +++----
bbmle-1.0.5.2/bbmle/tests/order.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/parscale.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/predict.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/profbound.Rout.save |only
bbmle-1.0.5.2/bbmle/tests/richards.Rout.save | 25 ++-
bbmle-1.0.5.2/bbmle/tests/startvals.Rout.save | 13 -
bbmle-1.0.5.2/bbmle/tests/startvals2.Rout.save | 20 +-
bbmle-1.0.5.2/bbmle/tests/test-relist1.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/testbounds.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/testderiv.Rout.save | 20 +-
bbmle-1.0.5.2/bbmle/tests/testenv.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/testparpred.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/tmptest.Rout.save | 8 -
bbmle-1.0.5.2/bbmle/tests/update.Rout.save | 14 --
45 files changed, 308 insertions(+), 331 deletions(-)
Title: Block, assign, and diagnose potential interference in randomized
experiments
Diff between blockTools versions 0.5-5 dated 2012-06-12 and 0.5-6 dated 2012-08-01
Description: Blocks units into experimental blocks, with one unit per
treatment condition, by creating a measure of multivariate
distance between all possible pairs of units. Maximum,
minimum, or an allowable range of differences between units on
one variable can be set. Randomly assign units to treatment
conditions. Diagnose potential interference between units
assigned to different treatment conditions. Write outputs to
.tex and .csv files.
Author: Ryan T. Moore
Maintainer: Ryan T. Moore
CHANGELOG | 3 +++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/block.R | 5 +++--
man/blockTools-package.Rd | 4 ++--
5 files changed, 16 insertions(+), 12 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 3.0-4 dated 2012-06-13 and 3.0-5 dated 2012-08-01
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, ancestral character analyses,
analyses of diversification and macroevolution, computing
distances from allelic and nucleotide data, reading and writing
nucleotide sequences, and several tools such as Mantel's test,
minimum spanning tree, generalized skyline plots, graphical
exploration of phylogenetic data (alex, trex, kronoviz),
estimation of absolute evolutionary rates and clock-like trees
using mean path lengths and penalized likelihood. Phylogeny
estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and
triangle methods, and several methods handling incomplete
distance matrices (NJ*, BIONJ*, MVR*, and the corresponding
triangle method). Some functions call external applications
(PhyML, Clustal, T-Coffee, Muscle) whose results are returned
into R.
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Christoph Heibl, Daniel Lawson, Vincent Lefort, Pierre
Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander, Rainer
Opgen-Rhein, Andrei-Alin Popescu, Klaus Schliep, Korbinian
Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis
DESCRIPTION | 8 +++----
MD5 | 30 ++++++++++++++---------------
NEWS | 18 +++++++++++++++++
R/DNA.R | 46 ++++++++++++++++++++++++++-------------------
R/ace.R | 34 +++++++++++++++++++++------------
R/reorder.phylo.R | 28 +++++++++++++++------------
R/root.R | 7 ++----
R/write.dna.R | 14 +++++--------
data/hivtree.newick.rda |binary
data/landplants.newick.rda |binary
data/opsin.newick.rda |binary
inst/doc/MoranI.pdf |binary
man/as.phylo.Rd | 6 +++++
man/rtree.Rd | 16 +++++++++------
man/unique.multiPhylo.Rd | 2 -
src/reorder_phylo.c | 15 +++-----------
16 files changed, 132 insertions(+), 92 deletions(-)