Title: Unicode data and utilities
Diff between Unicode versions 0.1-1 dated 2010-01-26 and 0.1-2 dated 2010-02-02
Description: Data from Unicode 5.2.0 and related utilities
Author: Kurt Hornik
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++--
NAMESPACE | 50 +++++++++++++++++++++++--
R/basics.R | 94 ++++++++++++++++++++++++++++++++++++++++++-----
R/casefuns.R |only
R/charfuns.R | 84 +++++++++++++++++++++++++++++++-----------
R/strfuns.R | 23 +----------
R/sysdata.rda |binary
R/ucdmisc.R | 4 ++
man/casefuns.Rd |only
man/tokenizers.Rd | 11 +++--
man/u_char_basics.Rd | 4 +-
man/u_char_names.Rd | 18 ++++++---
man/u_char_properties.Rd | 13 ++++--
man/u_named_sequences.Rd |only
14 files changed, 233 insertions(+), 76 deletions(-)
Title: Statistical inference for partially observed Markov processes
Diff between pomp versions 0.27-1 dated 2010-01-21 and 0.27-2 dated 2010-02-02
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall
Maintainer: Aaron A. King
DESCRIPTION | 10 +--
NAMESPACE | 1
R/bsplines.R | 22 --------
data/LondonYorke.rda |only
data/euler.sir.R | 32 +++++-------
inst/ChangeLog | 16 ++++++
inst/doc/advanced_topics_in_pomp.Rnw | 77 +++++++++++++----------------
inst/doc/advanced_topics_in_pomp.pdf |binary
inst/doc/intro_to_pomp.pdf |binary
inst/examples/euler_sir.R | 9 +--
inst/examples/euler_sir.c | 24 ++++++---
inst/include/pomp.h | 3 +
man/LondonYorke.Rd |only
man/bsplines.Rd | 4 +
src/bspline.c | 91 +++++++++++++++++++++++++++++------
src/euler_sir.c | 24 ++++++---
src/pomp.h | 3 +
tests/sir.R | 8 +--
tests/sir.Rout.save | 32 ++++++------
19 files changed, 219 insertions(+), 137 deletions(-)
Title: US Census 2000 Suite of R Packages
Diff between UScensus2000 versions 0.05 dated 2010-01-31 and 0.06 dated 2010-02-02
Description: US 2000 Census shape files and additional demographic data
from the SF1 100 percent files. This package contains a number
of helper functions for the UScensus2000blk,
UScensus2000blkgrp, UScensus2000tract, UScensus2000cdp
packages.
Author: Zack W. Almquist
Maintainer: Zack W. Almquist
DESCRIPTION | 6 ++---
R/county.R | 46 ++++++++++++++++++++++++++++++++++++++------
data/countyfips.rda |binary
man/UScensus2000-package.Rd | 4 +--
man/county.Rd | 2 -
man/countyfips.Rd | 4 +--
6 files changed, 48 insertions(+), 14 deletions(-)
Title: Kalman filter and smoothers for exponential family state space
models.
Diff between KFAS versions 0.5.3 dated 2010-01-25 and 0.5.4 dated 2010-02-02
Description: Package KFAS provides functions for Kalman filtering,
state, disturbance and simulation smoothing, forecasting and
simulation of state space models. All functions can use exact
diffuse initialisation when distributions of some or all
elements of initial state vector are unknown. Filtering, state
smoothing and simulation functions use sequential processing
algorithm, which is faster than standard approach, and it also
allows singularity of prediction error variance matrix. KFAS
also contains function for computing the likelihood of
exponential family state space models and function for state
smoothing of exponential family state space models. These
non-gaussian functions are still under heavy developement.
Author: Jouni Helske
Maintainer: Jouni Helske
DESCRIPTION | 11 -
R/KFAS.R | 348 ++++++++++++++++---------------
man/eflik.Rd | 25 +-
man/eflik0.Rd | 16 -
man/efsmoother.Rd | 2
man/kf.Rd | 6
man/simsmoother.Rd | 4
src/Makevars | 2
src/eflik.f90 | 164 ++------------
src/eflik0.f90 | 113 +++-------
src/kf.f90 | 569 +++++++++++++++++++++-------------------------------
src/ks.f90 | 231 +++++++++------------
src/simsmoother.f90 | 406 ++++++++++++++++---------------------
13 files changed, 809 insertions(+), 1088 deletions(-)
Title: Meta-Analysis Package for R
Diff between metafor versions 0.5-7 dated 2009-12-06 and 1.0-1 dated 2010-02-02
Description: The metafor package consists of a collection of functions
for conducting meta-analyses in R. Fixed- and random-effects
models (with and without moderators) can be fitted via the
general linear (mixed-effects) model. For 2x2 table data, the
Mantel-Haenszel and Peto's method are also implemented.
Author: Wolfgang Viechtbauer
Maintainer: Wolfgang Viechtbauer
metafor-0.5-7/metafor/man/predict.rma.uni.Rd |only
metafor-1.0-1/metafor/DESCRIPTION | 8
metafor-1.0-1/metafor/NAMESPACE | 4
metafor-1.0-1/metafor/NEWS | 46
metafor-1.0-1/metafor/R/metafor.R | 1439 +++++++++++++++++++------
metafor-1.0-1/metafor/man/addpoly.default.Rd | 12
metafor-1.0-1/metafor/man/addpoly.rma.Rd | 8
metafor-1.0-1/metafor/man/anova.rma.uni.Rd | 6
metafor-1.0-1/metafor/man/blup.rma.uni.Rd | 10
metafor-1.0-1/metafor/man/cint.rma.uni.Rd | 2
metafor-1.0-1/metafor/man/coef.rma.Rd | 2
metafor-1.0-1/metafor/man/cumul.rma.mh.Rd | 7
metafor-1.0-1/metafor/man/cumul.rma.uni.Rd | 5
metafor-1.0-1/metafor/man/dat.bcg.Rd | 19
metafor-1.0-1/metafor/man/escalc.Rd | 54
metafor-1.0-1/metafor/man/fitstats.rma.Rd | 2
metafor-1.0-1/metafor/man/fitted.rma.Rd | 6
metafor-1.0-1/metafor/man/forest.default.Rd | 17
metafor-1.0-1/metafor/man/forest.rma.Rd | 57
metafor-1.0-1/metafor/man/forest.rma.cumul.Rd | 17
metafor-1.0-1/metafor/man/fsn.Rd | 2
metafor-1.0-1/metafor/man/funnel.rma.Rd | 19
metafor-1.0-1/metafor/man/hatvalues.rma.uni.Rd | 2
metafor-1.0-1/metafor/man/influence.rma.uni.Rd | 2
metafor-1.0-1/metafor/man/leave1out.rma.mh.Rd | 4
metafor-1.0-1/metafor/man/leave1out.rma.uni.Rd | 2
metafor-1.0-1/metafor/man/logLik.rma.Rd | 2
metafor-1.0-1/metafor/man/metafor-package.Rd | 20
metafor-1.0-1/metafor/man/permutest.rma.uni.Rd | 25
metafor-1.0-1/metafor/man/plot.infl.rma.uni.Rd | 4
metafor-1.0-1/metafor/man/plot.rma.uni.Rd | 2
metafor-1.0-1/metafor/man/predict.rma.Rd |only
metafor-1.0-1/metafor/man/print.predict.rma.Rd |only
metafor-1.0-1/metafor/man/qqnorm.rma.uni.Rd | 4
metafor-1.0-1/metafor/man/radial.rma.Rd | 10
metafor-1.0-1/metafor/man/ranktest.rma.Rd | 2
metafor-1.0-1/metafor/man/regtest.rma.Rd | 2
metafor-1.0-1/metafor/man/residuals.rma.Rd | 4
metafor-1.0-1/metafor/man/rma.mh.Rd | 8
metafor-1.0-1/metafor/man/rma.peto.Rd | 2
metafor-1.0-1/metafor/man/rma.uni.Rd | 43
metafor-1.0-1/metafor/man/transf.Rd | 9
metafor-1.0-1/metafor/man/trimfill.rma.uni.Rd | 6
metafor-1.0-1/metafor/man/vcov.rma.Rd | 2
metafor-1.0-1/metafor/man/weights.rma.uni.Rd |only
45 files changed, 1393 insertions(+), 504 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Diff between ape versions 2.4-1 dated 2009-11-23 and 2.5 dated 2010-02-02
Description: ape provides functions for reading, writing, plotting, and
manipulating phylogenetic trees, analyses of comparative data
in a phylogenetic framework, analyses of diversification and
macroevolution, computing distances from allelic and nucleotide
data, reading nucleotide sequences, and several tools such as
Mantel's test, computation of minimum spanning tree,
generalized skyline plots, estimation of absolute evolutionary
rates and clock-like trees using mean path lengths,
non-parametric rate smoothing and penalized likelihood.
Phylogeny estimation can be done with the NJ, BIONJ, and ME
methods.
Author: Emmanuel Paradis, Ben Bolker, Julien Claude, Hoa Sien Cuong,
Richard Desper, Benoit Durand, Julien Dutheil, Olivier Gascuel,
Gangolf Jobb, Christoph Heibl, Daniel Lawson, Vincent Lefort,
Pierre Legendre, Jim Lemon, Yvonnick Noel, Johan Nylander,
Rainer Opgen-Rhein, Korbinian Strimmer, Damien de Vienne
Maintainer: Emmanuel Paradis
ChangeLog | 42 ++++++++++++++++++++++
DESCRIPTION | 8 ++--
R/ace.R | 12 +++---
R/biplot.pcoa.R |only
R/delta.plot.R |only
R/dist.topo.R | 34 ++++++++++--------
R/lmorigin.R |only
R/multi2di.R | 31 +++++++++++++---
R/nodelabels.R | 91 +++++++++++++++++++++++++++++++++++++++++++++++--
R/parafit.R |only
R/pcoa.R |only
R/plot.phylo.R | 8 ++--
R/print.lmorigin.R |only
R/print.parafit.R |only
R/rTrait.R |only
R/scales.R | 52 +++++++++++++++++-----------
Thanks | 8 ++--
data/HP.links.rda |only
data/gopher.D.rda |only
data/lice.D.rda |only
data/lmorigin.ex1.rda |only
data/lmorigin.ex2.rda |only
inst/CITATION | 2 -
inst/doc/MoranI.pdf |binary
man/add.scale.bar.Rd | 4 +-
man/ape-package.Rd | 2 -
man/compar.cheverud.Rd | 2 -
man/delta.plot.Rd |only
man/dist.topo.Rd | 20 ++++++++--
man/edges.Rd |only
man/lmorigin.Rd |only
man/makeLabel.Rd | 4 +-
man/makeNodeLabel.Rd | 4 +-
man/mst.Rd | 5 +-
man/nodelabels.Rd | 2 -
man/parafit.Rd |only
man/pcoa.Rd |only
man/plot.phylo.Rd | 2 -
man/rTraitCont.Rd |only
man/rTraitDisc.Rd |only
man/vcv.phylo.Rd | 1
man/write.tree.Rd | 2 -
src/delta_plot.c |only
src/rTrait.c |only
44 files changed, 256 insertions(+), 80 deletions(-)
Title: Stepwise Diagonal Discriminant Analysis
Diff between SDDA versions 1.0-4 dated 2009-02-09 and 1.0-5 dated 2010-02-02
Description: Stepwsie Diagonal Discriminant Analysis - a fast algorithm
for building multivariate classifiers
Author: CSIRO Bioinformatics, Glenn Stone
Maintainer: David Clifford
DESCRIPTION | 11 +++++++----
man/plotdiag.Rd | 4 ----
src/extra.h | 4 ++--
src/sdda.cc | 2 +-
src/sddawrap.cc | 4 ++--
5 files changed, 12 insertions(+), 13 deletions(-)
Title: Time Dependent Point Process Modelling
Diff between PtProcess versions 3.2-1 dated 2009-10-11 and 3.2-2 dated 2010-02-02
Description: This package fits and analyses time dependent marked point
process models with an emphasis on earthquake modelling. For a
more detailed introduction to the package, see the topic
"PtProcess". A list of recent changes can be found in the topic
"Changes".
Author: David Harte
Maintainer: David Harte
DESCRIPTION | 8
R/etas_normal0.R |only
R/logLik.mpp.R | 12
R/neglogLik.R | 5
R/print.summary.mpp.R |only
R/summary.mpp.R | 4
data/Phuket.R | 8
data/Phuket.txt | 2360 ++++++++++++++++++++++++----------------------
inst/doc/index.html | 8
man/Changes.Rd | 19
man/Phuket.Rd | 6
man/PtProcess-internal.Rd |only
man/PtProcess.Rd | 8
man/Tangshan.Rd | 2
man/distribution.Rd | 2
man/dpareto.Rd | 69 -
man/etas_gif.Rd | 15
man/etas_normal0.Rd |only
man/linksrm_convert.Rd | 10
man/linksrm_gif.Rd | 33
man/logLik.Rd | 20
man/marks.Rd | 2
man/neglogLik.Rd | 8
man/simple_gif.Rd | 30
man/srm_gif.Rd | 14
25 files changed, 1419 insertions(+), 1224 deletions(-)
Title: Enhanced routines for plotting and analyzing valued relational
data.
Diff between ElectroGraph versions 0.2.0 dated 2010-01-27 and 0.2.1 dated 2010-02-02
Description: This package contains routines and procedures for
relational data, namely considerations for valued ties. In
particular, relative distances are calculated using Ohmic
social conductance methods.
Author: Andrew C. Thomas
Maintainer: Andrew C. Thomas
DESCRIPTION | 12 ++++++------
src/scythe-extended.h | 1 +
2 files changed, 7 insertions(+), 6 deletions(-)
Title: Mapping between BioIDs
Diff between BioIDMapper versions 2.0 dated 2010-01-27 and 2.1 dated 2010-02-02
Description: facilitate mapping between different databases, integrate
various ID systems and provide a full view from gene level,
mRNA level and functional level regarding one specific ID. The
mapping system is based on NCBI and UniProt web service.
Author: Xiaoyong Sun
Maintainer: Xiaoyong Sun
DESCRIPTION | 12 ++++-----
NAMESPACE | 2 -
inst/doc/BioIDMapper.pdf |binary
inst/doc/BioIDMapper.rnw | 59 +++++++++++++++++++++++++++++++++++++++++++----
4 files changed, 62 insertions(+), 11 deletions(-)