Title: Spatial Search Trees
Diff between SearchTrees versions 0.1.6 dated 2011-10-04 and 0.5 dated 2012-01-30
Description: This package provides an implementation of the QuadTree
data structure. It uses this to implement fast k-Nearest
Neighbor and Rectangular range lookups in 2 dimenions. The
primary target is high performance interactive graphics.
Author: Gabriel Becker
Maintainer: Gabriel Becker
SearchTrees-0.1.6/SearchTrees/R/QuadTree-internal.R |only
SearchTrees-0.1.6/SearchTrees/man/createIndex.Rd |only
SearchTrees-0.1.6/SearchTrees/man/findKNN.Rd |only
SearchTrees-0.1.6/SearchTrees/man/getPointsInRect.Rd |only
SearchTrees-0.1.6/SearchTrees/src/Rsearchtrees.h |only
SearchTrees-0.1.6/SearchTrees/src/kdtree.c |only
SearchTrees-0.1.6/SearchTrees/src/quadtree.c |only
SearchTrees-0.5/SearchTrees/DESCRIPTION | 6 ++--
SearchTrees-0.5/SearchTrees/MD5 | 25 +++++++++---------
SearchTrees-0.5/SearchTrees/NAMESPACE | 8 ++---
SearchTrees-0.5/SearchTrees/R/quadtree.R | 13 +++++++--
SearchTrees-0.5/SearchTrees/R/quadtree2.R |only
SearchTrees-0.5/SearchTrees/man/QuadTree-class.Rd | 24 +++++++----------
SearchTrees-0.5/SearchTrees/man/SearchTree-class.Rd | 22 +++++++--------
SearchTrees-0.5/SearchTrees/man/createTree.Rd |only
SearchTrees-0.5/SearchTrees/man/knnLookup-methods.Rd |only
SearchTrees-0.5/SearchTrees/man/knnLookup.Rd |only
SearchTrees-0.5/SearchTrees/man/rectLookup-methods.Rd |only
SearchTrees-0.5/SearchTrees/man/rectLookup.Rd |only
SearchTrees-0.5/SearchTrees/src/Rsearchtrees2.h |only
SearchTrees-0.5/SearchTrees/src/quadtree2.c |only
21 files changed, 51 insertions(+), 47 deletions(-)
Title: This package creates variance dispersion graphs for response
surface designs
Diff between Vdgraph versions 1.0-1 dated 2011-06-03 and 2.0-1 dated 2012-01-30
Description: This package calls a modification of the published FORTRAN
code for producing variance dispersion graphs. For more details
on variance dispersion graphs see "A Computer Program for
Generating Variance Dispersion Graphs" by G. Vining, Journal of
Quality Technology, Vol. 25 No. 1 January 1993.
Author: John Lawson
Maintainer: John Lawson
DESCRIPTION | 8 ++++----
MD5 |only
NAMESPACE | 3 ++-
R/Compare2Vdg.R |only
R/Vdgraph.R | 20 ++++++++++++++++++--
R/f.R |only
data/D310.rda |binary
data/D311A.rda |binary
data/D311B.rda |binary
data/D416A.rda |binary
data/D416B.rda |binary
data/D416C.rda |binary
data/D628A.rda |binary
data/Hex2.rda |binary
data/SCDDL5.rda |binary
data/SCDH2.rda |binary
data/SCDH3.rda |binary
data/SCDH4.rda |binary
data/SCDH5.rda |binary
data/SCDH6.rda |binary
man/Compare2Vdg.Rd |only
man/Vdgraph.Rd | 3 +--
man/f.Rd |only
src/vdg.f | 2 +-
24 files changed, 26 insertions(+), 10 deletions(-)
Title: Running Winsteps in R
Diff between Rwinsteps versions 1.0-0 dated 2011-09-02 and 1.0-1 dated 2012-01-30
Description: The Rwinsteps package facilitates communication between R
and the Rasch modeling software Winsteps. The package currently
includes functions for reading and writing command files,
sending them to Winsteps, reading and writing data according to
command file specifications, reading output into R, and
plotting various results.
Author: Anthony Albano
Maintainer: Anthony Albano
DESCRIPTION | 8 ++++----
MD5 | 26 +++++++++++++-------------
NEWS | 9 ++++++++-
R/plot.ifile.R | 3 +--
R/print.winsteps.R | 2 +-
R/read.ifile.R | 19 +++++++++++--------
R/read.pfile.R | 19 +++++++++++--------
R/read.wcmd.R | 4 ++--
R/rtef.R | 1 -
R/rtif.R | 2 +-
R/rtrf.R | 2 +-
man/Rwinsteps-package.Rd | 4 ++--
man/ifile.Rd | 9 ++++++---
man/plot.ifile.Rd | 3 +--
14 files changed, 62 insertions(+), 49 deletions(-)
Title: Prediction Error Curves for Survival Models
Diff between pec versions 2.1.2 dated 2011-12-22 and 2.1.7 dated 2012-01-30
Description: Validation of predicted surival probabilities using
inverse weighting and resampling.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds
DESCRIPTION | 9 +-
MD5 | 44 +++++----
NAMESPACE | 2
R/CindexBootstrapCrossValidation.R | 64 +++++++-------
R/R2.R | 2
R/bootstrapCrossValidation.R | 6 +
R/calPlot.R | 1
R/checkModels.R | 4
R/cindexMethods.R | 166 +++++++++++++++++++++++++------------
R/crps.R | 2
R/ipcw.R | 20 ++--
R/kFoldCrossValidation.R | 14 ++-
R/pecMethods.R | 18 ----
R/plot.Cindex.R | 4
R/predictEventProb.R | 7 +
R/print.Cindex.R | 21 +++-
R/pseudoPecMethods.R | 2
R/resolveSplitMethod.R | 8 -
R/summary.pec.R | 2
exa/Cindex-Examples.R |only
exa/Pec-Examples.R | 7 +
man/cindex.Rd | 8 +
src/ccr.c |only
src/cindex.c | 36 ++++++--
24 files changed, 286 insertions(+), 161 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Diff between MARSS versions 2.7 dated 2011-10-23 and 2.8 dated 2012-01-30
Description: The MARSS package provides maximum-likelihood parameter
estimation for constrained and unconstrained linear
multivariate autoregressive state-space (MARSS) models fit to
multivariate time-series data. Fitting is primarily via an
Expectation-Maximization (EM) algorithm, although fitting via
the BFGS algorithm (using the optim function) is also provided.
MARSS models are a class of dynamic linear model (DLM) and
vector autoregressive model (VAR) model. Functions are
provided for parametric and innovations bootstrapping, Kalman
filtering and smoothing, bootstrap model selection criteria
(AICb), confidences intervals via the hessian approximation and
via bootstrapping and calculation of auxilliary residuals for
detecting outliers and shocks. The user guide shows examples
of using MARSS for parameter estimation for a variety of
applications, model selection, dynamic factor analysis, outlier
and shock detection, and addition of covariates. Type
RShowDoc("UserGuide", package="MARSS") at the R command line to
open the MARSS user guide. Online workshops (lecture material)
at http://faculty.washington.edu/eeholmes/workshops.shtml
Author: Eli Holmes, Eric Ward, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Eli Holmes
MARSS-2.7/MARSS/inst/doc/changes.Rnw |only
MARSS-2.7/MARSS/inst/doc/changes.pdf |only
MARSS-2.7/MARSS/inst/doc/refs |only
MARSS-2.7/MARSS/inst/doc/tex |only
MARSS-2.8/MARSS/DESCRIPTION | 14 -
MARSS-2.8/MARSS/MD5 | 56 +++----
MARSS-2.8/MARSS/NEWS |only
MARSS-2.8/MARSS/R/MARSS.R | 2
MARSS-2.8/MARSS/R/MARSSinits.R | 46 ++---
MARSS-2.8/MARSS/R/MARSSkem.r | 5
MARSS-2.8/MARSS/R/MARSSkemcheck.r | 40 ++++-
MARSS-2.8/MARSS/R/MARSSkf.R | 95 +++++++-----
MARSS-2.8/MARSS/R/MARSSmcinit.R | 30 +--
MARSS-2.8/MARSS/R/MARSSoptim.r | 46 ++++-
MARSS-2.8/MARSS/R/MARSSsettings.R | 8 -
MARSS-2.8/MARSS/R/checkPopWrap.R | 2
MARSS-2.8/MARSS/R/is_marssMLE.r | 5
MARSS-2.8/MARSS/R/popWrap.R | 4
MARSS-2.8/MARSS/R/progressBar.R |only
MARSS-2.8/MARSS/R/summary_marssm.R | 3
MARSS-2.8/MARSS/inst/doc/.Rinstignore |only
MARSS-2.8/MARSS/inst/doc/EMDerivation.Rnw | 235 +++++++++++++++++++++---------
MARSS-2.8/MARSS/inst/doc/EMDerivation.pdf |binary
MARSS-2.8/MARSS/inst/doc/Manual.bib |only
MARSS-2.8/MARSS/inst/doc/Manual.pdf |only
MARSS-2.8/MARSS/inst/doc/Quick_Start.Rnw | 34 ++++
MARSS-2.8/MARSS/inst/doc/Quick_Start.pdf |binary
MARSS-2.8/MARSS/inst/doc/UserGuide.Rnw | 17 ++
MARSS-2.8/MARSS/inst/doc/UserGuide.pdf |binary
MARSS-2.8/MARSS/inst/doc/index.html | 4
MARSS-2.8/MARSS/man/MARSSLLprofile.Rd | 2
MARSS-2.8/MARSS/man/MARSSinits.Rd | 3
MARSS-2.8/MARSS/man/MARSSoptim.Rd | 2
MARSS-2.8/MARSS/man/graywhales.Rd | 17 +-
34 files changed, 448 insertions(+), 222 deletions(-)
Title: Variational Bayes Latent Position Cluster Model for networks.
Diff between VBLPCM versions 1.0 dated 2011-11-24 and 1.3 dated 2012-01-30
Description: A package to fit and simulate latent position and cluster
models for statistical networks using a Variational Bayes
approximation.
Author: Michael Salter-Townshend
Maintainer: Michael Salter-Townshend
DESCRIPTION | 11 ++--
MD5 | 38 ++++++++--------
NAMESPACE |only
R/KL.R | 1
R/VBLPCM.R | 27 -----------
R/gof.vblpcm.R | 13 +++--
R/plot_network.R | 4 -
R/start.R | 10 ++--
R/zzz.R | 10 ++--
configure | 114 +++++++++++++++++++++++++++++++-------------------
man/VBLPCM-package.Rd | 54 +++++++++++------------
man/gof.vblpcm.Rd | 2
man/vblpcmfit.Rd | 4 -
man/vblpcmstart.Rd | 4 -
src/KL_funcs.c | 40 +++++++----------
src/Makevars | 8 +--
src/Makevars.in | 8 +--
src/Makevars.win |only
src/VBLPCM.c | 20 +++-----
src/bb.c | 2
src/optim.c | 3 -
21 files changed, 184 insertions(+), 189 deletions(-)
Title: Structural equation modeling diagnostics
Diff between semdiag versions 0.1.1 dated 2011-10-26 and 0.1.2 dated 2012-01-30
Description: Outlier and leverage diagnostics for SEM.
Author: Zhiyong Zhang and Ke-Hai Yuan
Maintainer: Zhiyong Zhang
semdiag-0.1.1/semdiag/semdiag |only
semdiag-0.1.2/semdiag/DESCRIPTION | 6 ++--
semdiag-0.1.2/semdiag/MD5 | 32 ++-----------------------
semdiag-0.1.2/semdiag/NAMESPACE |only
semdiag-0.1.2/semdiag/R/semdiag.R | 47 +++++++++++++++++++++-----------------
5 files changed, 32 insertions(+), 53 deletions(-)
Title: LDcorSV
Diff between LDcorSV versions 1.0 dated 2011-09-27 and 1.1 dated 2012-01-30
Description: The package provides a set of functions which aim is to
propose four measures of linkage disequilibrium: the usual r^2
measure, the r^2_S measure (r^2 corrected by the structure
sample), the r^2_V (r^2 corrected by the relatedness of
genotyped individuals), the r^2_VS measure (r^2 corrected by
both the relatedness of genotyped individuals and the structure
of the sample).
Author: David Desrousseaux, Aurelie Siberchicot, Christine
Cierco-Ayrolles and Brigitte Mangin
Maintainer:
DESCRIPTION | 10 +++++-----
MD5 | 35 ++++++++++++++++++-----------------
NAMESPACE |only
R/Info.Locus.R | 1 -
R/Inv.proj.matrix.sdp.R | 4 ++--
R/LD.Measures.R | 8 ++++----
R/Measure.R2.R | 14 +++++++++-----
R/Measure.R2S.R | 14 ++++++++++----
R/Measure.R2V.R | 16 ++++++++++------
R/Measure.R2VS.R | 18 ++++++++++--------
data/data.test.rda |binary
man/Inv.proj.matrix.sdp.Rd | 2 +-
man/LD.Measures.Rd | 4 ++--
man/LDcorSV-package.Rd | 6 +++---
man/Measure.R2.Rd | 4 ++--
man/Measure.R2S.Rd | 6 +++---
man/Measure.R2V.Rd | 4 ++--
man/Measure.R2VS.Rd | 4 ++--
man/data.test.Rd | 3 ++-
19 files changed, 85 insertions(+), 68 deletions(-)
Title: Computation of functional similarities between GO terms and gene
products; GO enrichement analysis
Diff between GOSim versions 1.2.6 dated 2012-01-27 and 1.2.7.1 dated 2012-01-30
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based
on their GO annotation. Moreover it allows for computing a GO
enrichment analysis
Author: Holger Froehlich
Maintainer: Holger Froehlich
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/general.R | 2 +-
inst/doc/GOSim.pdf |binary
4 files changed, 8 insertions(+), 8 deletions(-)
Title: Benchmark Experiments Toolbox
Diff between benchmark versions 0.3-2 dated 2011-02-10 and 0.3-3 dated 2012-01-30
Description: The benchmark package provides a toolbox for setup,
execution and analysis of benchmark experiments. Main focus is
the analysis of data accumulating during the execution -- one
primary objective is the statistical correct computation of the
candidate algorithms' order.
Author: Manuel J. A. Eugster
Maintainer: Manuel J. A. Eugster
DESCRIPTION | 18 +++++----------
MD5 |only
NAMESPACE | 2 -
R/proto.R | 45 +++++++++++++++++--------------------
data/ghraw.RData |binary
data/ghrel.RData |binary
data/monks3raw.RData |binary
data/uci621raw.RData |binary
data/uci621rel.RData |binary
inst/CITATION | 61 ++++++++++++++++++++++++++++++++++-----------------
10 files changed, 68 insertions(+), 58 deletions(-)
Title: doBy - Groupwise summary statistics, general linear contrasts,
population means (least-squares-means), and other utilities
Diff between doBy versions 4.5.0 dated 2012-01-19 and 4.5.1 dated 2012-01-30
Description: doBy contains a variety of utilities including: 1)
Facilities for groupwise computations of summary statistics and
other facilities for working with grouped data. 2) General
linear contrasts and LSMEANS (least-squares-means also known as
population means), 3) Rscript2HTML for autmatic generation of
HTML file from R-script with a minimum of markup, 4) other
utilities. doBy originally contained facilities for 'doing
something to data where data would be partitioned by some
variables which define groupings of data' - hence the name
doBy.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 8 +++++++-
DESCRIPTION | 6 +++---
MD5 | 26 +++++++++++++-------------
R/Rmarkup.R | 13 +++++++++----
inst/doc/doBy.pdf |binary
inst/doc/popMeans.pdf |binary
man/Rmarkup.Rd | 6 +++++-
vignettes/figures/doBy-042.pdf |binary
vignettes/figures/doBy-043.pdf |binary
vignettes/figures/doBy-044.pdf |binary
vignettes/figures/doBy-046.pdf |binary
vignettes/figures/doBy-048.pdf |binary
vignettes/figures/doBy-052.pdf |binary
vignettes/figures/doBy-053.pdf |binary
14 files changed, 37 insertions(+), 22 deletions(-)