Author: Noah Charney, Sydne Record
Title: Jost Diversity Measures for Community Data
Description: This package computes diversity for community data sets
using the methods outlined by Jost (2006, 2007). While there
are differing opinions on the ideal way to calculate diversity
(e.g. Magurran 2004), this method offers the advantage of
providing diversity numbers equivalents, independent alpha and
beta diversities, and the ability to incorporate 'order' (q) as
a continuous measure of the importance of rare species in the
metrics. The functions provided in this package largely
correspond with the equations offered by Jost in the cited
papers. The package computes alpha diversities, beta
diversities, gamma diversities, and similarity indices.
Confidence intervals for diversity measures are calculated
using a bootstrap method described by Chao et al. (2008). For
datasets with many samples (sites, plots), sim.table creates
tables of all pairwise comparisons possible, and for grouped
samples sim.groups calculates pairwise combinations of within-
and between-group comparisons.
Diff between vegetarian versions 1.0 dated 2009-08-09 and 1.1 dated 2009-08-24
DESCRIPTION | 6 +++--- R/vegetarian.R | 11 +++++------ man/H.Rd | 4 +++- man/M.homog.Rd | 2 ++ man/bootstrap.Rd | 9 ++++----- man/d.Rd | 4 +++- man/normalize.rows.Rd | 2 ++ man/turnover.Rd | 1 + man/vegetarian-package.Rd | 10 +++++++--- 9 files changed, 30 insertions(+), 19 deletions(-)
Author: Christophe Pouzat
Title: Spike Train Analysis with R
Description: Functions to analyze neuronal spike trains from a single
neuron or from several neurons recorded simultaneously.
Diff between STAR versions 0.2-2 dated 2009-01-01 and 0.3-2 dated 2009-08-24
STAR-0.2-2/STAR/inst/doc/PouzatChaffiol_STARdraft.Rnw |only STAR-0.2-2/STAR/inst/doc/PouzatChaffiol_STARdraft.bib |only STAR-0.2-2/STAR/inst/doc/PouzatChaffiol_STARdraft.pdf |only STAR-0.2-2/STAR/inst/doc/sc1.png |only STAR-0.2-2/STAR/inst/doc/sc2.png |only STAR-0.2-2/STAR/inst/doc/sc3.png |only STAR-0.2-2/STAR/inst/doc/summaryMC.rda |only STAR-0.3-2/STAR/ChangeLog | 17 +++++- STAR-0.3-2/STAR/DESCRIPTION | 13 ++-- STAR-0.3-2/STAR/NAMESPACE | 24 ++++++++ STAR-0.3-2/STAR/R/plot.ssanova.R |only STAR-0.3-2/STAR/R/plotEtAlquickPredict.R |only STAR-0.3-2/STAR/R/predictLogProb.R |only STAR-0.3-2/STAR/R/quickPredict.R |only STAR-0.3-2/STAR/R/reportHTML.spikeTrain.R | 9 ++- STAR-0.3-2/STAR/R/variableTransformation.R |only STAR-0.3-2/STAR/inst/doc/IEwSTARshort.Rnw |only STAR-0.3-2/STAR/inst/doc/IEwSTARshort.pdf |only STAR-0.3-2/STAR/inst/doc/auto |only STAR-0.3-2/STAR/man/changeScale.Rd |only STAR-0.3-2/STAR/man/mkAR.Rd |only STAR-0.3-2/STAR/man/mkGLMdf.Rd | 51 +++++++++--------- STAR-0.3-2/STAR/man/mkM2U.Rd |only STAR-0.3-2/STAR/man/plot.quickPredict.Rd |only STAR-0.3-2/STAR/man/plot.ssanova.Rd |only STAR-0.3-2/STAR/man/predictLogProb.Rd |only STAR-0.3-2/STAR/man/quickPredict.Rd |only STAR-0.3-2/STAR/man/reportHTML.Rd | 1 STAR-0.3-2/STAR/man/rexpMLE.Rd | 1 29 files changed, 80 insertions(+), 36 deletions(-)
Author: Ulrike Groemping
Title: Fractional Factorial designs with 2-level factors
Description: This package creates regular and non-regular Fractional
Factorial designs. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias). The
package is currently subject to intensive development. While
much of the intended functionality is already available, some
changes and improvements are still to be expected. Suggestions
are welcome.
Diff between FrF2 versions 0.97-6 dated 2009-08-21 and 0.97-7 dated 2009-08-24
DESCRIPTION | 8 ++++---- R/FrF2.R | 26 +++++++++++++++++++++----- R/pb.R | 8 +++++++- inst/NEWS | 8 ++++++++ man/FrF2.Rd | 15 +++++++++++---- man/pb.Rd | 11 ++++++++++- 6 files changed, 61 insertions(+), 15 deletions(-)
Author: Marco Scutari
Title: Bayesian network structure learning
Description: Bayesian network structure learning via constraint-based
(also known as 'conditional independence'), score-based and
hybrid algorithms. This package implements the Grow-Shrink (GS)
algorithm, the Incremental Association (IAMB) algorithm, the
Interleaved-IAMB (Inter-IAMB) algorithm, the Fast-IAMB
(Fast-IAMB) algorithm, the Max-Min Parents and Children (MMPC)
algorithm, the Hill-Climbing (HC) greedy search algorithm, the
Max-Min Hill-Climbing (MMHC) algorithm for both discrete and
Gaussian networks, along with many score functions and
conditional independence tests. Some utility functions (model
comparison and manipulation, random data generation, arc
orientation testing, simple and advanced plots) are included,
as well as basic parametric and bootstrap inference functions.
Diff between bnlearn versions 1.5 dated 2009-07-21 and 1.6 dated 2009-08-24
Changelog | 21 + DESCRIPTION | 27 +- NAMESPACE | 2 R/backend-indep.R | 350 ++++++++++++++------------------ R/backend-score.R | 378 +--------------------------------- R/choose.direction.R | 10 R/cpdag.R | 2 R/fit.R | 12 - R/frontend-amat.R | 2 R/frontend-arcs.R | 2 R/frontend-fit.R | 2 R/frontend-graph.R | 4 R/frontend-lattice.R | 10 R/frontend-learning.R | 27 ++ R/frontend-plot.R | 4 R/frontend-print.R | 22 +- R/frontend-score.R | 11 - R/frontend-strength.R | 15 - R/globals.R | 9 R/graphviz.R | 4 R/hill-climbing.R | 514 +++++++++++++---------------------------------- R/inter-iamb.R | 16 - R/lattice.R | 12 - R/learning-algorithms.R | 89 ++++++-- R/scores.R | 2 R/utils-arcs.R | 12 - R/utils-graph.R | 6 R/utils-misc.R | 11 + R/utils-sanitization.R | 15 + R/utils-tests.R | 4 inst/bibtex/bnlearn.bib | 2 man/alarm.Rd | 4 man/arc.strength.Rd | 22 +- man/arcops.Rd | 82 ------- man/bn.class.Rd | 16 + man/bn.fit.class.Rd | 4 man/bn.fit.methods.Rd | 60 ++--- man/bn.fit.plots.Rd | 18 - man/bn.strength-class.Rd | 4 man/bnboot.Rd | 8 man/bnlearn-package.Rd | 55 +++-- man/choose.direction.Rd | 6 man/constraint.Rd | 3 man/cpdag.Rd | 8 man/gaussian-test.Rd | 4 man/graphviz.plot.Rd | 2 man/hc.Rd | 3 man/hybrid.Rd |only man/lizards.Rd | 8 man/mb.Rd | 2 man/mmpc.Rd | 3 man/score.Rd | 2 man/strength.plot.Rd | 2 src/bind.c |only src/cache.structure.c | 11 - src/common.h | 2 src/graph.generation.c | 11 - src/hc.cache.lookup.c | 503 +++++++++++++++++++++++++++++++++++++++++++-- src/linear.correlation.c | 3 59 files changed, 1196 insertions(+), 1247 deletions(-)
Author: Alex Couture-Beil
Diff between rjson versions 0.1.5 dated 2009-04-26 and 0.1.6 dated 2009-08-24
Title: JSON for R
Description: Converts R object into JSON objects and vice-versa
DESCRIPTION | 6 +++---
R/json.R | 16 +++++++++++++---
inst/changelog.txt |only
inst/doc/json_rpc_server.pdf |binary
man/toJSON.Rd | 5 +++++
5 files changed, 21 insertions(+), 6 deletions(-)
Author: Rajarshi Guha
Diff between rcdk versions 2.9.3 dated 2009-07-18 and 2.9.4 dated 2009-08-24
Title: rcdk - Interface to the CDK Libraries
Description: This package allows the user to access functionality in
the CDK, a Java framework for cheminformatics. This allows the
user to load molecules, evaluate fingerprints, calculate
molecular descriptors and so on. In addition the CDK API allows
the user to view structures in 2D.
DESCRIPTION | 8 -
inst/cont/rcdk.jar |binary
inst/doc/rcdk.pdf | 234 +++++++++++++++++++++++++----------------------------
3 files changed, 117 insertions(+), 125 deletions(-)
Author: Guido van Steen
Title: dataframes2xls writes data frames to xls files
Description: dataframes2xls writes data frames to xls files. It
supports multiple sheets and basic formatting.
Diff between dataframes2xls versions 0.4.3 dated 2009-08-20 and 0.4.4 dated 2009-08-24
DESCRIPTION | 8 ++++---- LICENSE | 4 +++- R/write.xls.R | 14 +++++++------- inst/doc/LICENSE | 2 +- inst/doc/README | 2 +- inst/python/csv2xls.py | 4 +++- 6 files changed, 19 insertions(+), 15 deletions(-)
More information about dataframes2xls at CRAN
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