Author: Tore Opsahl
Title: tnet: Software for Analysis of Weighted, Two-mode, and
Longitudinal networks
Description: R package to analyse weighted, two-mode, and longitudinal
networks.
Diff between tnet versions 0.1.2 dated 2009-09-18 and 0.1.3 dated 2009-11-26
tnet-0.1.2/tnet/R/clustering_w_barrat.R |only tnet-0.1.2/tnet/R/random_values.R |only tnet-0.1.2/tnet/man/clustering_w_barrat.Rd |only tnet-0.1.2/tnet/man/random_values.Rd |only tnet-0.1.3/tnet/DESCRIPTION | 10 +- tnet-0.1.3/tnet/R/as.tnet.R | 18 ++- tnet-0.1.3/tnet/R/betweenness_w.R | 21 +--- tnet-0.1.3/tnet/R/closeness_w.R | 33 ++---- tnet-0.1.3/tnet/R/clustering_tm.R | 1 tnet-0.1.3/tnet/R/clustering_w.R | 28 ++--- tnet-0.1.3/tnet/R/clustering_w_local.R |only tnet-0.1.3/tnet/R/degree_w.R | 28 ++--- tnet-0.1.3/tnet/R/dichotomise.R | 20 ++-- tnet-0.1.3/tnet/R/distance_wRBGL.R | 27 ++--- tnet-0.1.3/tnet/R/projecting_tm.R | 8 + tnet-0.1.3/tnet/R/rg_reshuffling_tm.R | 9 - tnet-0.1.3/tnet/R/rg_reshuffling_w.R | 21 ++-- tnet-0.1.3/tnet/R/rg_w.R | 13 +- tnet-0.1.3/tnet/R/shrink_to_weighted_network.R | 17 +-- tnet-0.1.3/tnet/R/small_world_test_tm.R |only tnet-0.1.3/tnet/R/small_world_test_w.R |only tnet-0.1.3/tnet/R/symmetrise.R | 32 +++--- tnet-0.1.3/tnet/R/weighted_richclub_tm.R | 12 +- tnet-0.1.3/tnet/R/weighted_richclub_w.R | 123 +++++++++++++------------ tnet-0.1.3/tnet/man/clustering_w_local.Rd |only tnet-0.1.3/tnet/man/small_world_test_tm.Rd |only tnet-0.1.3/tnet/man/small_world_test_w.Rd |only tnet-0.1.3/tnet/man/tnet-package.Rd | 2 tnet-0.1.3/tnet/man/weighted_richclub_w.Rd | 24 +--- 29 files changed, 220 insertions(+), 227 deletions(-)
Author: Roger Bivand
Diff between spdep versions 0.4-52 dated 2009-11-05 and 0.4-54 dated 2009-11-26
Title: Spatial dependence: weighting schemes, statistics and models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by
distance and tesselations, for summarising these objects, and
for permitting their use in spatial data analysis, including
regional aggregation by minimum spanning tree; a collection of
tests for spatial autocorrelation, including global Moran's I,
APLE, Geary's C, Hubert/Mantel general cross product statistic,
Empirical Bayes estimates and Assunção/Reis Index, Getis/Ord G
and multicoloured join count statistics, local Moran's I and
Getis/Ord G, saddlepoint approximations and exact tests for
global and local Moran's I; and functions for estimating
spatial simultaneous autoregressive (SAR) lag and error models,
impact measures for lag models, weighted and unweighted SAR and
CAR spatial regression models, semi-parametric and Moran
eigenvector spatial filtering, GM SAR error models, and
generalized spatial two stage least squares models.
ChangeLog | 1297 +++++++++++++++++++++++++++++++++++++++++-------------
DESCRIPTION | 8
NAMESPACE | 5
R/nb2listw.R | 6
inst/ChangeLog | 1297 +++++++++++++++++++++++++++++++++++++++++-------------
inst/doc/CO69.pdf |binary
inst/doc/sids.pdf | 1044 +++++++++++++++++++++----------------------
man/nb2lines.Rd | 2
8 files changed, 2513 insertions(+), 1146 deletions(-)
Author: Christiane Raemsch
Title: Estimation of attributable and partial attributable risks (AR
and PAR) and visualization of attributable risks from
case-control data
Description: Functions to estimate (partial) attributable risks from
case-control data with corresponding percentile or BCa
confidence intervals; Visualization of attributable riks
Diff between pARccs versions 0.1-1 dated 2008-10-15 and 0.2-1 dated 2009-11-26
DESCRIPTION | 29 +++--- NAMESPACE | 5 - R/AR_Plot.r |only R/AR_wC.r | 48 +++++++---- R/AR_woC.r | 29 +++++- R/AdjAR.R | 116 ++++++++++++++++++++++++--- R/Boot_CI.R | 231 +++++++++++++++++++++++++++++++++++++++--------------- R/Class_AR.r |only R/PAR.R | 17 +++ man/AR-class.Rd |only man/AR.rd | 12 +- man/AR_Plot.rd |only man/AdjAR.Rd | 17 +++ man/Boot-class.Rd |only man/Boot_CI.Rd | 34 ++++--- man/PAR-class.Rd |only man/PAR.Rd | 12 +- 17 files changed, 410 insertions(+), 140 deletions(-)
Author: Martin Mächler
Title: Normal (1-d) Mixture Models (S3 Classes and Methods)
Description: Onedimensional Normal Mixture Models Classes, for, e.g.,
density estimation or clustering algorithms research and
teaching; providing the widely used Marron-Wand densities, see
?MarronWand.
Diff between nor1mix versions 1.0-7 dated 2007-06-12 and 1.1-1 dated 2009-11-26
nor1mix-1.0-7/nor1mix/INDEX |only nor1mix-1.0-7/nor1mix/mle-ex-post.R |only nor1mix-1.1-1/nor1mix/ChangeLog | 91 +++++++ nor1mix-1.1-1/nor1mix/DESCRIPTION | 18 - nor1mix-1.1-1/nor1mix/NAMESPACE |only nor1mix-1.1-1/nor1mix/R/norMix.R | 395 ++++++++++++++++++++++++++++--- nor1mix-1.1-1/nor1mix/R/zMarrWand-dens.R | 16 + nor1mix-1.1-1/nor1mix/R/zzz.R | 154 +++++++++++- nor1mix-1.1-1/nor1mix/TODO |only nor1mix-1.1-1/nor1mix/man/MarronWand.Rd | 55 ++-- nor1mix-1.1-1/nor1mix/man/clus2norMix.Rd |only nor1mix-1.1-1/nor1mix/man/dnorMix.Rd | 23 + nor1mix-1.1-1/nor1mix/man/llnorMix.Rd |only nor1mix-1.1-1/nor1mix/man/norMix.Rd | 3 nor1mix-1.1-1/nor1mix/man/plot.norMix.Rd | 13 - nor1mix-1.1-1/nor1mix/man/pnorMix.Rd | 49 +++ nor1mix-1.1-1/nor1mix/man/rnorMix.Rd | 2 nor1mix-1.1-1/nor1mix/man/sort.norMix.Rd |only nor1mix-1.1-1/nor1mix/tests/MW.R | 10 nor1mix-1.1-1/nor1mix/tests/MW.Rout.save | 34 ++ nor1mix-1.1-1/nor1mix/tests/ex.R | 59 ++++ nor1mix-1.1-1/nor1mix/tests/par.R |only nor1mix-1.1-1/nor1mix/tests/randNM.R |only 23 files changed, 816 insertions(+), 106 deletions(-)
Author: Timothee Poisot
Diff between log10 versions 0.0.3-05 dated 2009-11-22 and 0.1.0-01 dated 2009-11-26
Title: Decimal log plotting in two and three dimensions
Description: Provides a range of function for 10-log plotting
DESCRIPTION | 10 +++++-----
R/logplot.r | 18 ++++++++++++++++--
man/hcp3.Rd |only
man/logfill.Rd | 2 +-
man/loglm.Rd |only
5 files changed, 22 insertions(+), 8 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 1.0-1 dated 2009-11-18 and 1.0-2 dated 2009-11-26
DESCRIPTION | 8 ++++---- R/DanielPlot.R | 7 +++++-- R/FrF2.R | 4 +++- R/IAPlot.R | 7 +++++-- R/MEPlot.R | 7 +++++-- inst/NEWS | 8 +++++++- man/DanielPlot.Rd | 9 ++++++--- man/FrF2.Rd | 4 ++-- man/IAPlot.Rd | 7 +++++-- 9 files changed, 42 insertions(+), 19 deletions(-)
Author: Campo Elias Pardo
Diff between FactoClass versions 1.0.1 dated 2009-07-21 and 1.0.3 dated 2009-11-26
Title: Combination of Factorial Methods and Cluster Analysis
Description: Multivariate exploration of a data table with factorial
analysis and cluster methods.
FactoClass-1.0.1/FactoClass/R/stableclus.R |only
FactoClass-1.0.1/FactoClass/man/stableclus.Rd |only
FactoClass-1.0.1/FactoClass/src/kmnsw.f |only
FactoClass-1.0.3/FactoClass/DESCRIPTION | 11 +++--
FactoClass-1.0.3/FactoClass/R/FactoClass.R | 4 +-
FactoClass-1.0.3/FactoClass/R/kmeansW.R | 42 +++++++++++-----------
FactoClass-1.0.3/FactoClass/R/plotFactoClass.R | 4 +-
FactoClass-1.0.3/FactoClass/man/kmeansW.Rd | 19 ++++++---
FactoClass-1.0.3/FactoClass/man/plotFactoClass.Rd | 2 -
FactoClass-1.0.3/FactoClass/src/kmeansw.cc |only
FactoClass-1.0.3/FactoClass/src/kmeansw.h |only
11 files changed, 44 insertions(+), 38 deletions(-)
Author: Ulrike Groemping
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages.
Diff between DoE.base versions 0.9-7 dated 2009-11-05 and 0.9-8 dated 2009-11-26
DESCRIPTION | 8 - NAMESPACE | 2 R/DesignAccessors.r | 86 ++++++++++++++++--- R/export.design.R | 5 + R/formula.design.R | 13 ++ R/lm.design.R | 2 R/printandsummary.design.R | 25 ++++- inst/NEWS | 22 ++++ man/class-design.Rd | 70 +++++++++++---- tests/test_cross.Rout.save | 202 +++++++++++++++++++++++++++++++++++++-------- 10 files changed, 360 insertions(+), 75 deletions(-)
Author: James Carpenter
Diff between copas versions 0.6-2 dated 2009-04-15 and 0.6-3 dated 2009-11-26
Title: Statistical methods to model and adjust for bias in
meta-analysis
Description: Copas selection model.
ChangeLog |only
DESCRIPTION | 8 ++++----
R/plot.copas.R | 3 ++-
R/print.copas.R | 4 ++--
R/print.summary.copas.R | 4 ++++
R/summary.copas.R | 7 ++++---
man/plot.copas.Rd | 4 +++-
man/print.copas.Rd | 14 +++++++++-----
8 files changed, 28 insertions(+), 16 deletions(-)
Author: Renaud Gaujoux
Title: Framework for Nonnegative Matrix Factorization (NMF) algorithms.
Description: This package provides a framework to perform Non-negative
Matrix Factorization (NMF). It implements a set of already
published algorithms and seeding methods, and provides a
framework to test and develop new algorithms.
Diff between NMF versions 0.2 dated 2009-11-23 and 0.2.2 dated 2009-11-26
DESCRIPTION | 6 inst/doc/NMF-vignette.Rnw | 8 inst/doc/NMF-vignette.pdf | 2366 +++++++++++++++++++++++----------------------- 3 files changed, 1222 insertions(+), 1158 deletions(-)
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Title: timereg package for Flexible regression models for survival
data.
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparmetric proportional odds model, cumulative residuals,
excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling.
Diff between timereg versions 1.2-5 dated 2009-07-31 and 1.2-7 dated 2009-11-26
DESCRIPTION | 14 +++++++------- R/additive-lasso.r | 8 ++++---- R/cox-aalen.r | 3 +-- R/mylars.r | 19 +++++++++---------- R/pls.cv.r | 5 +++++ R/predict-timereg.r | 37 +++++++++++++++++++++++++++---------- R/two-stage-reg.r | 42 ++++++++++++++++++++++++------------------ man/comp.risk.Rd | 2 +- man/surv-lars.Rd | 2 ++ man/two.stage.reg.Rd | 6 ++++-- src/aalen-test.c | 10 +++++----- src/breslow.c | 7 ++----- src/comprisk.c | 22 ++++++++++++++-------- src/dynadd.c | 4 +--- src/matrix.c | 2 +- src/matrix.h | 13 ------------- src/two-stage-reg.c | 28 ++++++++++++---------------- src/unifConfBandResampling.c | 2 +- 18 files changed, 120 insertions(+), 106 deletions(-)
Author: Christopher Jackson
Diff between msm versions 0.9.4 dated 2009-11-13 and 0.9.5 dated 2009-11-26
Title: Multi-state Markov and hidden Markov models in continuous time
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. A variety of
observation schemes are supported, including processes observed
at arbitrary times, completely-observed processes, and censored
states.
ChangeLog | 8 ++++++++
DESCRIPTION | 8 ++++----
R/pearson.R | 6 +++---
inst/NEWS | 8 ++++++++
inst/doc/msm-manual.pdf |binary
tests/pearson.R | 8 --------
6 files changed, 23 insertions(+), 15 deletions(-)
Author: Matthew Vavrek
Diff between fossil versions 0.2.1 dated 2009-04-14 and 0.2.2 dated 2009-11-26
Title: Palaeoecological and Palaeogeographical Analysis Tools
Description: A set of analytical tools useful in analysing ecological
and geographical data sets, both ancient and modern. The
package includes functions for estimating species richness
(Chao 1 and 2, ACE, ICE, Jacknife), shared species/beta
diversity, species area curves and geographic distances and
areas.
DESCRIPTION | 15 +++++++--------
R/create.matrix.R | 3 ++-
R/simpson.R | 11 +++++++----
inst/CITATION | 5 +++--
man/ace.Rd | 2 +-
man/bray.curtis.Rd | 3 +--
man/create.lats.Rd | 8 +-------
man/create.matrix.Rd | 16 +++++-----------
man/dino.mst.Rd | 3 +--
man/earth.bear.Rd | 2 +-
man/ebar.loc.Rd |only
man/ebar.spp.Rd |only
man/fossil-package.Rd | 31 ++++++-------------------------
13 files changed, 35 insertions(+), 64 deletions(-)
Author: David Hajage
Title: Export R objects to several markup languages
Description: Coerce R object to asciidoc, txt2tags, restructuredText or
org syntax. Package comes with a set of drivers for Sweave.
Diff between ascii versions 0.4 dated 2009-11-25 and 0.4-1 dated 2009-11-26
DESCRIPTION | 6 +++--- NAMESPACE | 2 ++ NEWS | 6 ++++++ R/asciiDescr.r | 8 ++++---- R/misc.r | 11 +++++------ man/ascii.Rd | 10 +++++----- 6 files changed, 25 insertions(+), 18 deletions(-)
More information about OligoSpecificitySystem at CRAN
Permanent link
Author: Ming-Huei Chen
Diff between GWAF versions 1.1 dated 2009-09-25 and 1.2 dated 2009-11-26
Title: Genome-Wide Association analyses with Family data
Description: Functions to test genetic associations between SNPs and a
continuous/dichotomous trait using family data, and to make
genome-wide p-value plot and QQ plot.
DESCRIPTION | 8
GWAF/CONTENTS | 8
GWAF/DESCRIPTION | 6
GWAF/INDEX | 4
GWAF/Meta/Rd.rds |binary
GWAF/Meta/hsearch.rds |binary
GWAF/Meta/package.rds |binary
GWAF/R/GWAF.rdb |binary
GWAF/R/GWAF.rdx |binary
GWAF/doc/UsingGWAF.pdf | 281 +++++++++++++++++-----------------
GWAF/help/AnIndex | 1
GWAF/help/GWAF-package | 23 +-
GWAF/help/GWplot | 17 +-
GWAF/help/auto |only
GWAF/help/gee.lgst | 10 -
GWAF/help/gee.lgst.batch | 48 +++--
GWAF/help/gee.lgst.batch.imputed | 16 +
GWAF/help/gee.lgst.imputed | 6
GWAF/help/lme.batch | 46 +++--
GWAF/help/lme.batch.imputed | 16 +
GWAF/html/00Index.html | 6
GWAF/html/GWAF-package.html | 14 -
GWAF/html/GWplot.html | 11 -
GWAF/html/auto.html |only
GWAF/html/gee.lgst.batch.html | 40 +++-
GWAF/html/gee.lgst.batch.imputed.html | 21 ++
GWAF/html/gee.lgst.html | 10 -
GWAF/html/gee.lgst.imputed.html | 11 -
GWAF/html/lme.batch.html | 32 ++-
GWAF/html/lme.batch.imputed.html | 24 ++
GWAF/html/lmekin.html | 2
GWAF/html/qq.html | 2
GWAF/latex/GWAF-package.tex | 12 -
GWAF/latex/GWplot.tex | 7
GWAF/latex/auto.tex |only
GWAF/latex/gee.lgst.batch.imputed.tex | 11 -
GWAF/latex/gee.lgst.batch.tex | 30 ++-
GWAF/latex/gee.lgst.imputed.tex | 9 -
GWAF/latex/gee.lgst.tex | 8
GWAF/latex/lme.batch.imputed.tex | 14 +
GWAF/latex/lme.batch.tex | 22 +-
GWAF/man/GWAF.Rd.gz |binary
R/auto.R |only
R/gee.lgst.R | 66 +++----
R/gee.lgst.batch.R | 30 ++-
R/gee.lgst.batch.imputed.R | 31 +++
R/lme.R | 38 +++-
R/lme.imputed.R | 38 +++-
inst/doc/UsingGWAF.pdf | 281 +++++++++++++++++-----------------
man/GWAF-package.Rd | 12 -
man/GWplot.Rd | 7
man/auto.Rd |only
man/gee.lgst.Rd | 8
man/gee.lgst.batch.Rd | 32 ++-
man/gee.lgst.batch.imputed.Rd | 11 -
man/gee.lgst.imputed.Rd | 9 -
man/lme.batch.Rd | 157 +++++++++---------
man/lme.batch.imputed.Rd | 14 +
58 files changed, 866 insertions(+), 644 deletions(-)