Title: Exploring water quality monitoring data
Diff between wq versions 0.2-2 dated 2010-02-18 and 0.2-5 dated 2010-08-18
Description: Functions to assist in the processing and exploration of
data from monitoring programs for aquatic ecosystems. The focus
is on time series data for physical and chemical properties of
water, as well as the plankton. The package is intended for
programs that sample approximately monthly at discrete
stations.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby
wq-0.2-2/wq/inst/doc/ecology.bst |only
wq-0.2-5/wq/.hgignore |only
wq-0.2-5/wq/.hgtags |only
wq-0.2-5/wq/ChangeLog |only
wq-0.2-5/wq/DESCRIPTION | 11 -
wq-0.2-5/wq/NAMESPACE | 2
wq-0.2-5/wq/R/DateTime-class.R | 2
wq-0.2-5/wq/R/R2pss.R | 14 --
wq-0.2-5/wq/R/WqData-class.R | 24 ---
wq-0.2-5/wq/R/decompTs.R | 133 ++++++++++----------
wq-0.2-5/wq/R/ec2pss.R | 27 ++--
wq-0.2-5/wq/R/eof.R | 41 +++---
wq-0.2-5/wq/R/eofNum.R | 91 +++++++------
wq-0.2-5/wq/R/interpTs.R | 54 ++++----
wq-0.2-5/wq/R/layerMean.R | 54 ++++----
wq-0.2-5/wq/R/mannKen.R | 109 ++++++++--------
wq-0.2-5/wq/R/monthCor.R | 19 +-
wq-0.2-5/wq/R/oxySol.R | 48 ++++---
wq-0.2-5/wq/R/phenoAmp.R | 32 ++--
wq-0.2-5/wq/R/phenoPhase.R | 70 ++++++----
wq-0.2-5/wq/R/plotEof.R | 24 +--
wq-0.2-5/wq/R/plotSeas.R | 18 +-
wq-0.2-5/wq/R/plotTsTile.R | 44 ++++--
wq-0.2-5/wq/R/ruleN.R | 51 +++----
wq-0.2-5/wq/R/seaKen.R | 39 +++--
wq-0.2-5/wq/R/seaRoll.R | 34 ++---
wq-0.2-5/wq/R/ts2df.R | 38 +++--
wq-0.2-5/wq/R/tsMake.R | 37 +++--
wq-0.2-5/wq/R/wqData.R | 100 +++++++--------
wq-0.2-5/wq/inst/doc/limnology_and_oceanography.bst |only
wq-0.2-5/wq/inst/doc/wq-package.Rnw | 77 +++--------
wq-0.2-5/wq/inst/doc/wq-package.pdf |binary
wq-0.2-5/wq/inst/doc/wq.bib | 106 ++-------------
wq-0.2-5/wq/inst/doc/wqFlow.pdf |only
wq-0.2-5/wq/man/WqData-class.Rd | 13 -
wq-0.2-5/wq/man/decompTs.Rd | 5
wq-0.2-5/wq/man/interpTs.Rd | 20 +--
wq-0.2-5/wq/man/phenoAmp.Rd | 4
wq-0.2-5/wq/man/phenoPhase.Rd | 12 +
wq-0.2-5/wq/man/plotEof.Rd | 6
wq-0.2-5/wq/man/plotSeas.Rd | 11 +
wq-0.2-5/wq/man/seaKen.Rd | 2
wq-0.2-5/wq/man/tsMake.Rd |binary
wq-0.2-5/wq/man/wq-package.Rd | 7 -
wq-0.2-5/wq/man/wqData.Rd | 20 +--
45 files changed, 691 insertions(+), 708 deletions(-)
Title: Parameter estimation for the Averaging model of Information
Integration Theory
Diff between rAverage versions 0.3-2 dated 2010-07-29 and 0.3-3 dated 2010-08-18
Description: Parameter estimation for the Averaging model of Anderson's
Information Integration Theory
Author: Giulio Vidotto
Maintainer: Stefano Noventa
rAverage-0.3-2/rAverage/data/tableB.rda |only
rAverage-0.3-2/rAverage/man/fmdata.Rd |only
rAverage-0.3-3/rAverage/DESCRIPTION | 8 ++++----
rAverage-0.3-3/rAverage/R/rav.R | 4 ++--
rAverage-0.3-3/rAverage/man/fmdata1.Rd |only
rAverage-0.3-3/rAverage/man/rAverage-package.Rd | 6 +++---
6 files changed, 9 insertions(+), 9 deletions(-)
Title: Prediction and variable selection using spike and slab
regression
Diff between spikeslab versions 1.1.0 dated 2010-06-15 and 1.1.1 dated 2010-08-18
Description: Spike and slab for prediction and variable selection in
linear regression models. Uses a generalized elastic net for
variable selection.
Author: Hemant Ishwaran
Maintainer: Udaya B. Kogalur
DESCRIPTION | 8 ++++----
R/cv.spikeslab.R | 2 +-
R/predict.spikeslab.R | 26 ++++++++++++++++++++------
R/print.spikeslab.R | 2 +-
R/sparsePC.spikeslab.R | 2 +-
R/spikeslab.GibbsCore.R | 2 +-
R/spikeslab.R | 13 +++++++------
R/spikeslab.news.R | 2 +-
R/spikeslab.utilities.R | 2 +-
R/zzz.R | 2 +-
inst/NEWS | 13 ++++++++++---
man/cv.spikeslab.Rd | 23 +++++++++++++++++++----
man/predict.spikeslab.Rd | 18 ++++++++++++++++--
man/spikeslab.Rd | 29 ++++++++++-------------------
src/bayesian.c | 2 +-
15 files changed, 94 insertions(+), 52 deletions(-)
Title: Structural Equation Models
Diff between sem versions 0.9-20 dated 2010-03-14 and 0.9-21 dated 2010-08-18
Description: This package contains functions for fitting general linear
structural equation models (with observed and unobserved
variables) by the method of maximum likelihood using the RAM
approach, and for fitting structural equations in
observed-variable models by two-stage least squares.
Author: John Fox
Maintainer: John Fox
DESCRIPTION | 10 +++++-----
inst/CHANGES | 5 +++++
man/mod.indices.Rd | 3 +++
man/standardized.coefficients.Rd | 2 +-
4 files changed, 14 insertions(+), 6 deletions(-)
Title: Time-of-flight mass spectra signal processing
Diff between rTOFsPRO versions 1.1 dated 2010-07-29 and 1.2 dated 2010-08-18
Description: rTOFsPRO provides functions for signal processing of the
linear TOF spectra to produce aligned peak intensity matrix
(and peak positions)
Author: Dariya Malyarenko, Maureen Tracy and William Cooke
Maintainer: Dariya Malyarenko
DESCRIPTION | 8 ++++----
R/mainRTOFsPROc.R | 8 ++++++--
R/mainRTOFsPROcModular.R | 8 ++++++--
3 files changed, 16 insertions(+), 8 deletions(-)
Title: display and analyze ROC curves
Diff between pROC versions 1.3 dated 2010-08-13 and 1.3.1 dated 2010-08-18
Description: Tools for visualizing, smoothing and comparing receiver
operating characteristic (ROC curves). (Partial) area under the
curve (AUC) can be compared with statistical tests based on
U-statistics or bootstrap. Confidence intervals can be computed
for (p)AUC or ROC curves.
Author: Xavier Robin, Natacha Turck, Alexandre Hainard, Natalia
Tiberti, Frédérique Lisacek, Jean-Charles Sanchez and Markus
Müller
Maintainer: Xavier Robin
DESCRIPTION | 8 ++++----
NEWS | 4 ++++
R/coords.R | 2 +-
R/roc.test.R | 2 ++
man/roc.test.Rd | 14 ++++++++------
5 files changed, 19 insertions(+), 11 deletions(-)
Title: A collection of functions to help with analysis of coarse
infectious disease data
Diff between coarseDataTools versions 0.2 dated 2010-05-05 and 0.3 dated 2010-08-18
More information about coarseDataTools at CRAN
Description: This package contains functions to analyze coarse data.
Its development was motivated by applications to infectious
disease: in particular, problems with estimating the incubation
period and the case fatality ratio of a given disease. Sample
data files are included in the package.
Author: Nicholas G. Reich
Maintainer: Nicholas G. Reich
coarseDataTools-0.2/coarseDataTools/data/simulatedOutbreakDeaths.rda |only
coarseDataTools-0.3/coarseDataTools/ChangeLog | 4 +-
coarseDataTools-0.3/coarseDataTools/DESCRIPTION | 8 ++--
coarseDataTools-0.3/coarseDataTools/data/simulated.outbreak.deaths.rda |only
coarseDataTools-0.3/coarseDataTools/inst/doc/CFR_vignette.Rnw | 18 +++++-----
coarseDataTools-0.3/coarseDataTools/inst/doc/CFR_vignette.pdf |binary
coarseDataTools-0.3/coarseDataTools/man/EMforCFR.Rd | 12 +++---
coarseDataTools-0.3/coarseDataTools/man/ProfileLiks.Rd | 4 --
coarseDataTools-0.3/coarseDataTools/man/fluA.inc.per.Rd |only
coarseDataTools-0.3/coarseDataTools/man/simulated.outbreak.deaths.Rd |only
10 files changed, 23 insertions(+), 23 deletions(-)
Permanent link
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 0.94 dated 2010-08-14 and 0.94-1 dated 2010-08-18
Description: A collection of algorithms related to modeling of soil
resources, soil classification, soil profile aggregation, and
visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 12 ++++++------
man/munsell2rgb.Rd | 7 +++++--
2 files changed, 11 insertions(+), 8 deletions(-)
Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.17-39 dated 2010-07-29 and 1.18-7 dated 2010-08-18
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
qtl-1.17-39/qtl/.Rbuildindex.2271 |only
qtl-1.17-39/qtl/.Rd2dvi63762 |only
qtl-1.17-39/qtl/.gitignore |only
qtl-1.18-7/qtl/.Rbuildindex.3897 |only
qtl-1.18-7/qtl/DESCRIPTION | 8 +--
qtl-1.18-7/qtl/INDEX | 2
qtl-1.18-7/qtl/R/est.map.R | 10 ++--
qtl-1.18-7/qtl/R/phyloqtl_scan.R | 45 ++++++++++++++++++--
qtl-1.18-7/qtl/R/ripple.R | 8 ++-
qtl-1.18-7/qtl/R/util.R | 63 ++++++++++++++++++++++-------
qtl-1.18-7/qtl/inst/README.txt | 12 ++---
qtl-1.18-7/qtl/inst/STATUS.txt | 34 +++++++++++++++
qtl-1.18-7/qtl/man/inferredpartitions.Rd |only
qtl-1.18-7/qtl/man/max.scanPhyloQTL.Rd | 7 +--
qtl-1.18-7/qtl/man/multitrait.Rd | 2
qtl-1.18-7/qtl/man/plot.scanPhyloQTL.Rd | 5 +-
qtl-1.18-7/qtl/man/scanPhyloQTL.Rd | 5 +-
qtl-1.18-7/qtl/man/simPhyloQTL.Rd | 8 ++-
qtl-1.18-7/qtl/man/summary.scanPhyloQTL.Rd | 7 +--
qtl-1.18-7/qtl/src/hmm_main.c | 14 ++----
qtl-1.18-7/qtl/src/mqmmixture.cpp | 6 +-
21 files changed, 172 insertions(+), 64 deletions(-)
Title: Nested Archimedean Copulas
Diff between nacopula versions 0.4-2 dated 2010-07-02 and 0.4-3 dated 2010-08-18
Description: An R package for nested Archimedean copulas, providing a
procedure for computing function values, characteristics such
as Kendall's tau and tail dependence coefficients, as well as
sampling algorithms for generating random variates.
Author: Marius Hofert
Maintainer: Martin Maechler
DESCRIPTION | 12 +-
R/nacopula.R | 23 +++
inst/doc/Makefile | 4
inst/doc/mh-biblio.bib | 110 +++++++++---------
inst/doc/nacopula.Rnw | 158 ++++++++++++++------------
inst/doc/nacopula.aux | 24 ++--
inst/doc/nacopula.bbl | 8 +
inst/doc/nacopula.pdf |binary
inst/doc/nacopula.tex | 292 ++++++++++++++++++++++++++-----------------------
man/acopula-class.Rd | 6 -
man/copFamilies.Rd | 4
man/getAcop.Rd | 3
man/onacopula.Rd | 9 +
man/printNacopula.Rd | 2
man/rstable1.Rd | 47 ++++---
man/splom2.Rd | 4
src/retstable.c | 13 --
17 files changed, 399 insertions(+), 320 deletions(-)
Title: Generalised log-linear model
Diff between gllm versions 0.31 dated 2006-04-07 and 0.33 dated 2010-08-18
Description: Routines for log-linear models of incomplete contingency
tables, including some latent class models, via EM and Fisher
scoring approaches. Allows bootstrapping.
Author: David Duffy
Maintainer: David Duffy
gllm-0.31/gllm/man/as207.Rd |only
gllm-0.31/gllm/src/as207.f |only
gllm-0.33/gllm/DESCRIPTION | 21 ++++++++++++---------
gllm-0.33/gllm/INDEX | 4 ++--
gllm-0.33/gllm/R/gllm.R | 27 ++++++++++-----------------
gllm-0.33/gllm/man/anova.gllm.Rd | 20 ++++++++++----------
gllm-0.33/gllm/man/emgllm.Rd | 12 ++++++------
gllm-0.33/gllm/man/emgllmfitter.Rd |only
gllm-0.33/gllm/man/gllm.Rd | 20 ++++++++++----------
gllm-0.33/gllm/man/ld2.Rd | 10 +++++-----
gllm-0.33/gllm/man/ld2.model.Rd | 3 +--
gllm-0.33/gllm/man/scatter.Rd | 2 +-
gllm-0.33/gllm/man/scoregllm.Rd | 20 ++++++++++----------
gllm-0.33/gllm/man/summary.gllm.Rd | 16 ++++++++--------
gllm-0.33/gllm/src/emgllm.c |only
15 files changed, 75 insertions(+), 80 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 4.53 dated 2010-08-17 and 4.54 dated 2010-08-18
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
DESCRIPTION | 10 +++++-----
NAMESPACE | 4 ++++
R/createGrid.R | 1 +
R/createModel.R | 10 +++++++++-
R/misc.R | 21 ++++++++++++++-------
R/predictionFunction.R | 13 +++++++++++++
R/predictors.R | 12 ++++++++++++
R/probFunction.R | 14 ++++++++++++++
R/selection.R | 1 +
R/train.default.R | 2 +-
inst/NEWS | 6 ++++++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.Rnw | 6 ++++++
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
man/predictors.Rd | 9 +++++++++
man/train.Rd | 1 +
18 files changed, 96 insertions(+), 14 deletions(-)
Title: Simulation framework
Diff between simFrame versions 0.3.2 dated 2010-08-17 and 0.3.3 dated 2010-08-18
Description: A general framework for statistical simulation.
Author: Andreas Alfons
Maintainer: Andreas Alfons
DESCRIPTION | 8 ++++----
NEWS | 5 +++++
inst/doc/figures-eusilc/fig-006.pdf | 4 ++--
inst/doc/figures-eusilc/fig-009.pdf | 4 ++--
inst/doc/figures-eusilc/fig-012.pdf | 4 ++--
inst/doc/figures-eusilc/fig-015.pdf | 4 ++--
inst/doc/figures-eusilc/fig-018.pdf | 4 ++--
inst/doc/figures-eusilc/fig-021.pdf | 4 ++--
inst/doc/figures-eusilc/fig-024.pdf | 4 ++--
inst/doc/figures-intro/fig-013.pdf | 4 ++--
inst/doc/figures-intro/fig-014.pdf | 4 ++--
inst/doc/figures-intro/fig-022.pdf | 4 ++--
inst/doc/figures-intro/fig-029.pdf | 4 ++--
inst/doc/figures-intro/fig-030.pdf | 4 ++--
inst/doc/figures-intro/fig-039.pdf | 4 ++--
inst/doc/figures-intro/fig-040.pdf | 4 ++--
inst/doc/simFrame-eusilc.pdf |binary
inst/doc/simFrame-intro.pdf |binary
inst/doc/simFrame.bib | 2 +-
man/simFrame-package.Rd | 14 ++------------
20 files changed, 40 insertions(+), 45 deletions(-)
Title: Bayesian network structure learning
Diff between bnlearn versions 2.1.1 dated 2010-07-10 and 2.2 dated 2010-08-18
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
Tabu Search (TABU) algorithm, the Max-Min Hill-Climbing (MMHC)
algorithm and the two-stage Restricted Maximization (RSMAX2)
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 support for basic parametric
and bootstrap inference, conditional probability queries and
cross-validation.
Author: Marco Scutari
Maintainer: Marco Scutari
Changelog | 20 ++
DESCRIPTION | 8
NAMESPACE | 3
R/compare.R |only
R/fast-iamb.R | 2
R/frontend-arcs.R | 10 +
R/frontend-bn.R | 2
R/frontend-formula.R | 9 -
R/frontend-graph.R | 173 ++-------------------
R/frontend-learning.R | 8
R/frontend-plot.R | 20 +-
R/frontend-print.R | 69 ++++----
R/globals.R | 4
R/graphviz.R | 36 +++-
R/grow-shrink.R | 2
R/incremental-association.R | 2
R/inter-iamb.R | 2
R/lattice.R | 2
R/learning-algorithms.R | 63 +++++++
R/maxmin-pc.R | 5
R/scores.R | 76 +++------
R/utils-arcs.R | 14 +
R/utils-graph.R | 19 ++
R/utils-print.R |only
R/utils-sanitization.R | 13 +
inst/bibtex/bnlearn.bib | 354 ++++++++++++++++++++++----------------------
man/bnlearn-package.Rd | 4
man/compare.Rd | 21 ++
man/constraint.Rd | 14 +
man/graphviz.plot.Rd | 14 +
man/mb.Rd | 3
man/modelstring.Rd | 2
man/ordering.Rd | 7
man/snow.Rd | 4
src/arcs2amat.c | 17 --
src/bayesian.network.c | 103 ++++++++++++
src/bind.c | 12 -
src/common.c | 33 +++-
src/common.h | 5
src/cpdag.c | 22 +-
src/dirichlet.posterior.c | 63 -------
src/filter.arcs.c | 64 ++++++-
src/fitted.c | 73 +++++++--
src/pdag2dag.c | 18 +-
src/predict.c | 2
src/subsets.c |only
src/tabu.c | 2
47 files changed, 812 insertions(+), 587 deletions(-)
Title: Time series Aggregation
Diff between TSAgg versions 0.1-9 dated 2010-07-29 and 0.2-0 dated 2010-08-18
Description: Time series aggregation for incomplete time series data.
Author: JS Lessels.
Maintainer: JS Lessels
TSAgg-0.1-9/TSAgg/data/datalist |only
TSAgg-0.2-0/TSAgg/DESCRIPTION | 8 ++++----
TSAgg-0.2-0/TSAgg/R/timeSeries.R | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
Title: Tools for working with points and intervals
Diff between intervals versions 0.13.2 dated 2010-05-16 and 0.13.3 dated 2010-08-18
Description: Tools for working with and comparing sets of points and
intervals.
Author: Richard Bourgon
Maintainer: Richard Bourgon
DESCRIPTION | 10 ++++++----
NEWS | 15 +++++++++++++++
R/plot.Intervals_virtual.R | 4 ++--
inst/doc/intervals_overview.pdf |binary
4 files changed, 23 insertions(+), 6 deletions(-)
Title: A framework for working in a functional programming paradigm in
R
Diff between futile.paradigm versions 1.0.0 dated 2010-08-10 and 1.0.1 dated 2010-08-18
More information about futile.paradigm at CRAN
Description: Provides dispatching implementations suitable for
functional programming paradigms. The framework provides a
mechanism for attaching guards to functions similar to Erlang,
while also providing the safety of assertions reminiscent of
Eiffel.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
DESCRIPTION | 8 +++---
man/UseFunction.Rd | 4 +--
man/futile.paradigm-package.Rd | 52 +++++++++++++++++++++++-----------------
man/guard.Rd | 53 ++++++++++++++++++++++++++++++-----------
4 files changed, 76 insertions(+), 41 deletions(-)
Permanent link
Title: Flexible procedures for clustering
Diff between fpc versions 2.0-1 dated 2010-08-10 and 2.0-2 dated 2010-08-18
Description: Various methods for clustering and cluster validation.
Fixed point clustering. Linear regression clustering.
Clustering by merging Gaussian mixture components. Symmetric
and asymmetric discriminant projections for visualisation of
the separation of groupings. Cluster validation statistics for
distance based clustering including corrected Rand index.
Clusterwise cluster stability assessment. Methods for
estimation of the number of clusters: Calinski-Harabasz,
Tibshirani and Walther's prediction strength.
Gaussian/multinomial mixture fitting for mixed
continuous/categorical variables. Veriablewise statistics for
cluster interpretation. DBSCAN clustering. Interface functions
for many clustering methods implemented in R, including
estimating the number of clusters with kmeans, pam and clara.
Modality diagnosis for Gaussian mixtures. Note that the use of
the package mclust (called by function prabclust) is protected
by a special license, see
http://www.stat.washington.edu/mclust/license.txt. For an
overview see ?fpc-package.
Author: Christian Hennig
Maintainer: Christian Hennig
fpc-2.0-1/fpc/INDEX |only
fpc-2.0-2/fpc/DESCRIPTION | 11 ++++++-----
fpc-2.0-2/fpc/man/clucols.Rd | 2 +-
fpc-2.0-2/fpc/man/fpc-package.Rd |only
fpc-2.0-2/fpc/man/prediction.strength.Rd | 2 +-
fpc-2.0-2/fpc/man/tonedata.Rd | 1 +
6 files changed, 9 insertions(+), 7 deletions(-)