Title: Power and Sample Size Calculations for SNP Association Studies
with Censored Time to Event Outcomes
Diff between survSNP versions 0.21-6 dated 2013-12-11 and 0.21-7 dated 2013-12-12
Description: This package can be used to conduct asymptotic and empirical power and sample size calculations for SNP association studies with right censored time to event outcomes
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Kouros Owzar
survSNP-0.21-6/survSNP/vignettes/survSNP.pdf |only
survSNP-0.21-7/survSNP/DESCRIPTION | 10 +++++-----
survSNP-0.21-7/survSNP/MD5 | 7 +++----
survSNP-0.21-7/survSNP/inst/doc/survSNP-knitr.pdf |binary
survSNP-0.21-7/survSNP/man/survSNP-package.Rd | 4 ++--
5 files changed, 10 insertions(+), 11 deletions(-)
Title: R-MongoDB driver
Diff between rmongodb versions 1.2.6 dated 2013-11-26 and 1.3.3 dated 2013-12-12
Description: This R package provides an interface to the NoSQL MongoDB database using the MongoDB C-driver.
Author: MongoDB, Inc. (mongo-c-driver) & Markus Schmidberger (mongosoup.de). Formerly Gerald Lindsly.
Maintainer: Markus Schmidberger
DESCRIPTION | 13 +++++++------
MD5 | 11 +++++++----
NAMESPACE | 2 ++
NEWS | 3 +++
R/mongo_high_level.R |only
README.md | 12 ++++++++++--
man/mongo.distinct.Rd |only
tests/test_high_level.R |only
8 files changed, 29 insertions(+), 12 deletions(-)
Title: an R package for genetic analysis of populations with mixed
reproduction
Diff between poppr versions 1.0.4 dated 2013-12-04 and 1.0.5 dated 2013-12-12
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar
Maintainer: Zhian N. Kamvar
poppr-1.0.4/poppr/vignettes/poppr_manual-095.pdf |only
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poppr-1.0.5/poppr/DESCRIPTION | 13
poppr-1.0.5/poppr/MD5 | 104 ++----
poppr-1.0.5/poppr/NAMESPACE | 2
poppr-1.0.5/poppr/NEWS | 15
poppr-1.0.5/poppr/R/Index_calculations.r | 118 ++-----
poppr-1.0.5/poppr/R/bruvo.r | 219 ++++---------
poppr-1.0.5/poppr/R/bruvoclass.r |only
poppr-1.0.5/poppr/R/distances.r | 12
poppr-1.0.5/poppr/R/internal.r | 331 +++++++++++---------
poppr-1.0.5/poppr/R/sample_schemes.r | 86 ++---
poppr-1.0.5/poppr/R/sandbox.r | 8
poppr-1.0.5/poppr/R/visualizations.r | 104 +-----
poppr-1.0.5/poppr/inst/doc/poppr_manual.R | 110 +++---
poppr-1.0.5/poppr/inst/doc/poppr_manual.Rnw | 118 +++----
poppr-1.0.5/poppr/inst/doc/poppr_manual.pdf |binary
poppr-1.0.5/poppr/man/Aeut.Rd | 20 -
poppr-1.0.5/poppr/man/bruvo.boot.Rd | 63 +--
poppr-1.0.5/poppr/man/bruvo.dist.Rd | 41 +-
poppr-1.0.5/poppr/man/bruvo.msn.Rd | 66 +--
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poppr-1.0.5/poppr/man/genind2genalex.Rd | 26 -
poppr-1.0.5/poppr/man/getfile.Rd | 22 -
poppr-1.0.5/poppr/man/greycurve.Rd | 16
poppr-1.0.5/poppr/man/ia.Rd | 85 ++---
poppr-1.0.5/poppr/man/informloci.Rd | 31 -
poppr-1.0.5/poppr/man/missingno.Rd | 15
poppr-1.0.5/poppr/man/mlg.Rd | 62 +--
poppr-1.0.5/poppr/man/partial_clone.Rd | 20 -
poppr-1.0.5/poppr/man/poppr.Rd | 208 ++++++------
poppr-1.0.5/poppr/man/poppr.all.Rd | 16
poppr-1.0.5/poppr/man/poppr.msn.Rd | 39 +-
poppr-1.0.5/poppr/man/popsub.Rd | 9
poppr-1.0.5/poppr/man/read.genalex.Rd | 47 +-
poppr-1.0.5/poppr/man/shufflepop.Rd | 46 +-
poppr-1.0.5/poppr/man/splitcombine.Rd | 42 +-
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poppr-1.0.5/poppr/vignettes/poppr_manual-119.pdf |binary
poppr-1.0.5/poppr/vignettes/poppr_manual.Rnw | 118 +++----
poppr-1.0.5/poppr/vignettes/poppr_manual.synctex.gz |binary
poppr-1.0.5/poppr/vignettes/simulated_param_fig.png |binary
67 files changed, 1077 insertions(+), 1201 deletions(-)
Title: Estimating oncogenetic trees
Diff between Oncotree versions 0.3.2 dated 2012-11-13 and 0.3.3 dated 2013-12-12
Description: Contains functions to construct and evaluate directed tree structures that
model the process of occurrence of genetic alterations during carcinogenesis.
Author: Aniko Szabo, Lisa Pappas
Maintainer: Aniko Szabo
Oncotree-0.3.2/Oncotree/inst/doc/PlotForVignette.pdf |only
Oncotree-0.3.3/Oncotree/DESCRIPTION | 16 ++--
Oncotree-0.3.3/Oncotree/MD5 | 24 +++---
Oncotree-0.3.3/Oncotree/R/bootstrap.oncotree.R | 1
Oncotree-0.3.3/Oncotree/R/generate.data.R | 67 ++++++++++++++---
Oncotree-0.3.3/Oncotree/R/joint.distr.R |only
Oncotree-0.3.3/Oncotree/build |only
Oncotree-0.3.3/Oncotree/data/ov.cgh.rda |binary
Oncotree-0.3.3/Oncotree/inst/doc/Oncotree.pdf |binary
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Oncotree-0.3.3/Oncotree/man/bootstrap.oncotree.Rd | 5 -
Oncotree-0.3.3/Oncotree/man/generate.data.Rd | 48 +++++++-----
Oncotree-0.3.3/Oncotree/man/oncotree.fit.Rd | 10 +-
Oncotree-0.3.3/Oncotree/vignettes |only
15 files changed, 119 insertions(+), 52 deletions(-)
Title: Mapping Smoothed Effect Estimates from Individual-Level Data
Diff between MapGAM versions 0.6-2 dated 2013-03-11 and 0.7-0 dated 2013-12-12
Description: Contains functions for mapping odds ratios or other effect estimates using individual-level data such as case-control study data, using generalized additive models (GAMs) for smoothing with a two-dimensional predictor (e.g., geolocation or exposure to chemical mixtures) while adjusting for confounding variables, using methods described by Kelsall and Diggle (1998) and Webster at al. (2006). Includes convenient functions for mapping, efficient control sampling, and permutation tests for the null hypothesis that the two-dimensional predictor is not associated with the outcome variable (adjusting for confounders).
Author: Veronica Vieira, Scott Bartell, and Robin Bliss
Maintainer: Scott Bartell
ChangeLog | 16 +++
DESCRIPTION | 18 +---
MD5 | 24 ++---
R/colormap.R | 26 +++---
R/modgam.R | 206 +++++++++++++++++++++++++++++++-------------------
R/optspan.R | 46 +++++++----
data/MAdata.rda |binary
man/MAdata.Rd | 5 -
man/MapGAM-package.Rd | 10 +-
man/colormap.Rd | 27 +++---
man/modgam.Rd | 92 ++++++++++++++++------
man/optspan.Rd | 16 +++
man/sampcont.Rd | 3
13 files changed, 316 insertions(+), 173 deletions(-)
More information about HIV.LifeTables at CRAN
Permanent link
Title: Adaptive Management of Epidemiological Interventions
Diff between amei versions 1.0-5 dated 2012-11-01 and 1.0-6 dated 2013-12-12
Description:
This package provides a flexible statistical framework for generating optimal
epidemiological interventions that are designed to minimize the total expected
cost of an emerging epidemic while simultaneously propagating uncertainty regarding
underlying disease parameters through to the decision process via Bayesian posterior
inference. The strategies produced through this framework are adaptive: vaccination
schedules are iteratively adjusted to reflect the anticipated trajectory of the
epidemic given the current population state and updated parameter estimates.
Author: Daniel Merl
Maintainer: Robert B. Gramacy
amei-1.0-5/amei/inst/doc/alt_trans.iRnw |only
amei-1.0-5/amei/inst/doc/amei.bib |only
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amei-1.0-6/amei/MD5 | 16 +++++++------
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10 files changed, 24 insertions(+), 26 deletions(-)
Title: Interface to Myrrix. Myrrix is a complete, real-time, scalable
clustering and recommender system, evolved from Apache Mahout.
Diff between Myrrix versions 1.0 dated 2013-07-26 and 1.1 dated 2013-12-12
Description: Recommendation engine based on Myrrix. Myrrix is a complete,
real-time, scalable clustering and recommender system, evolved from Apache
Mahout. It uses Alternating Least Squares to build a recommendation engine.
Author: Jan Wijffels [aut, cre]
Maintainer: Jan Wijffels
Myrrix-1.0/Myrrix/inst/doc/logo_bnosac.png |only
Myrrix-1.0/Myrrix/tests |only
Myrrix-1.1/Myrrix/DESCRIPTION | 15 +++++++--------
Myrrix-1.1/Myrrix/MD5 | 15 +++++++++------
Myrrix-1.1/Myrrix/NAMESPACE | 2 ++
Myrrix-1.1/Myrrix/NEWS | 4 ++++
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11 files changed, 22 insertions(+), 14 deletions(-)
Title: Bayesian Analysis of Computer Code Output (BACCO)
Diff between BACCO versions 2.0-7 dated 2012-11-07 and 2.0-9 dated 2013-12-12
Description: The BACCO bundle of packages is replaced by the BACCO
package, which provides a vignette that illustrates the constituent
packages (emulator, approximator, calibrator) in use.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 17 +++++++++--------
MD5 | 12 +++++++-----
NAMESPACE | 3 +++
build |only
inst/doc/both_papers.R |only
inst/doc/both_papers.Rnw | 7 +++----
inst/doc/both_papers.pdf |binary
vignettes/both_papers.Rnw | 7 +++----
8 files changed, 25 insertions(+), 21 deletions(-)
Title: ecological drift under the UNTB
Diff between untb versions 1.6-9 dated 2011-12-27 and 1.7-2 dated 2013-12-12
Description: A collection of utilities for biodiversity data.
Includes the simulation of ecological drift under Hubbell's Unified
Neutral Theory of Biodiversity, and the calculation of various
diagnostics such as Preston curves. Now includes functionality
provided by Francois Munoz and Andrea Manica.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 10 ++++++----
MD5 | 34 ++++++++++++++++++----------------
NAMESPACE | 8 +++++++-
R/sysdata.rda |binary
R/untb.R | 42 ++++++++++++++++++++++++++----------------
build |only
data/butterflies.rda |binary
data/caruso.rda |binary
data/copepod.rda |binary
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man/logkda.Rd | 23 ++++++++++++++++++-----
man/theta.prob.Rd | 4 ++--
man/vallade.Rd | 6 ++++--
19 files changed, 81 insertions(+), 46 deletions(-)
Title: Hidden Markov Models for ChIP-on-Chip Analysis
Diff between tileHMM versions 1.0-5 dated 2012-03-19 and 1.0-6 dated 2013-12-12
Description: This package provides methods and classes to build HMMs
that are suitable for the analysis of ChIP-on-chip data. The
provided parameter estimation methods include the Baum-Welch
algorithm and Viterbi training as well as a combination of
both.
Author: Peter Humburg
Maintainer: Peter Humburg
DESCRIPTION | 7 ++++---
MD5 | 5 ++++-
build |only
inst/doc/tileHMM.R |only
vignettes |only
5 files changed, 8 insertions(+), 4 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.34-1 dated 2013-11-03 and 1.35-0 dated 2013-12-12
Description: A package for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, and space-time point patterns in any number of dimensions.
Contains over 1500 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images and tessellations.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
DESCRIPTION | 27 +-
MD5 | 234 +++++++++++++----------
NAMESPACE | 84 ++++++++
NEWS | 245 ++++++++++++++++++++++++
R/First.R | 15 -
R/anova.mppm.R |only
R/applynbd.R | 139 ++++++-------
R/clarkevans.R | 10
R/closepairs.R | 1
R/colourtables.R | 163 +++++++++++-----
R/distfun.R | 36 ++-
R/fii.R | 38 +++
R/fitted.mppm.R |only
R/fitted.ppm.R | 4
R/fv.R | 56 +++++
R/hyperframe.R | 22 +-
R/interact.R | 18 -
R/interactions.R |only
R/kppm.R | 6
R/kstest.mppm.R |only
R/leverage.R | 6
R/lpp.R | 1
R/marks.R | 80 ++++---
R/measures.R | 20 +
R/mincontrast.R | 249 ++++++++++++++----------
R/morphology.R | 112 ++++++-----
R/mppm.R |only
R/multihard.R | 2
R/multistrauss.R | 4
R/multistrhard.R | 2
R/nncross.R | 4
R/nndensity.R |only
R/nndist.R | 12 -
R/nnfun.R | 24 +-
R/nnmap.R | 19 +
R/objsurf.R |only
R/options.R | 10
R/ord.R | 1
R/pairwise.R | 1
R/pcf.R | 46 +++-
R/pcfinhom.R | 26 +-
R/pcfmulti.inhom.R | 19 +
R/plot.mppm.R |only
R/plot.owin.R | 10
R/plot.ppp.R | 21 +-
R/pp3.R | 4
R/ppx.R | 42 ++++
R/predict.ppm.R | 12 -
R/predictmppm.R |only
R/quadratmtest.R |only
R/randomNS.R | 21 +-
R/reduceformula.R |only
R/residuals.mppm.R |only
R/rhohat.R | 8
R/rmhsnoop.R | 13 -
R/saturated.R | 1
R/simplepanel.R | 48 +++-
R/strauss.R | 33 ++-
R/subfits.R |only
R/summary.mppm.R |only
R/summary.ppm.R | 475 ++++++++++++++++++++++++-----------------------
R/unique.ppp.R | 143 ++++++++++----
R/util.R | 14 +
R/vcov.mppm.R |only
R/vcov.ppm.R | 189 +++++++++++-------
R/window.R | 8
build/vignette.rds |binary
data/datalist | 4
data/demohyper.rda |only
data/pyramidal.rda |only
data/simba.rda |only
data/waterstriders.rda |only
demo/data.R | 10
demo/spatstat.R | 35 +--
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man/as.function.fv.Rd | 55 ++++-
man/cauchy.estK.Rd | 10
man/cauchy.estpcf.Rd | 10
man/closepairs.Rd |only
man/closing.Rd | 2
man/coef.mppm.Rd |only
man/dclf.test.Rd | 9
man/demohyper.Rd |only
man/dilation.Rd | 8
man/distfun.Rd | 16 +
man/duplicated.ppp.Rd | 10
man/envelope.Rd | 4
man/erosion.Rd | 9
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man/fvnames.Rd |only
man/integral.msr.Rd |only
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man/layout.boxes.Rd |only
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man/markstat.Rd | 4
man/methods.objsurf.Rd |only
man/mppm.Rd |only
man/multiplicity.ppp.Rd | 13 -
man/nncross.Rd | 7
man/nndensity.Rd |only
man/nnfun.Rd | 30 ++
man/objsurf.Rd |only
man/opening.Rd | 2
man/pcf.ppp.Rd | 74 +++++--
man/pcfinhom.Rd | 6
man/plot.colourmap.Rd | 32 ++-
man/plot.fv.Rd | 6
man/plot.hyperframe.Rd | 12 -
man/plot.mppm.Rd |only
man/plot.owin.Rd | 7
man/plot.ppp.Rd | 7
man/ppx.Rd | 16 +
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man/pyramidal.Rd |only
man/quadrat.test.mppm.Rd |only
man/rCauchy.Rd | 2
man/rVarGamma.Rd | 29 ++
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man/rhohat.Rd | 2
man/run.simplepanel.Rd |only
man/simba.Rd |only
man/simplepanel.Rd |only
man/spatstat-internal.Rd | 70 ++++--
man/spatstat-package.Rd | 3
man/subfits.Rd |only
man/unique.ppp.Rd | 13 -
man/vargamma.estK.Rd | 24 +-
man/vargamma.estpcf.Rd | 25 +-
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man/waterstriders.Rd |only
src/Estrauss.c | 3
src/closepair.c | 78 +++++++
src/knnXdist.h | 75 +++++++
src/knndistance.c | 19 +
tests/alltests.R | 116 +++++++++++
vignettes/replicated.Rnw |only
142 files changed, 2571 insertions(+), 1080 deletions(-)
Title: Procedures for Psychological, Psychometric, and Personality
Research
Diff between psych versions 1.3.10.12 dated 2013-10-14 and 1.3.12 dated 2013-12-12
Description: A number of routines for personality, psychometrics and experimental psychology. Functions are primarily for scale construction using factor analysis, cluster analysis and reliability analysis, although others provide basic descriptive statistics. Item Response Theory is done using factor analysis of tetrachoric and polychoric correlations. Functions for simulating particular item and test structures are included. Several functions serve as a useful front end for structural equation modeling. Graphical displays of path diagrams, factor analysis and structural equation models are created using basic graphics. Some of the functions are written to support a book on psychometrics as well as publications in personality research. For more information, see the personality-project.org/r webpage.
Author: William Revelle
Maintainer: William Revelle
DESCRIPTION | 8 +--
MD5 | 87 +++++++++++++++++++++------------------
NAMESPACE | 2
R/alpha.R | 57 ++++++++++++++++++--------
R/df2latex.R | 98 +++++++++++++++++++++++++++++++++++++--------
R/fa.R | 2
R/fa.parallel.poly.R | 38 +++++++++++++----
R/fa.poly.R | 8 +--
R/fiml.R |only
R/guttman.R | 69 +++++++++++++++++--------------
R/irt.fa.R | 6 +-
R/kaiser.R | 1
R/misc.R | 2
R/missing.cor.R |only
R/mixed.cor.R | 12 ++---
R/plot.irt.R | 3 +
R/polychoric.R | 46 ++++++++++++++++++---
R/print.psych.R | 24 +++++++++--
R/print.psych.fa.R | 2
R/score.items.R | 34 ++++++++++-----
R/slipHalf.R |only
R/splitHalf.R |only
R/tetrachor.R | 27 ++++++++----
R/winsor.R | 9 +---
inst/NEWS.Rd | 31 +++++++++++++-
inst/doc/overview.pdf |binary
inst/doc/psych_for_sem.pdf |binary
man/alpha.Rd | 20 +++++----
man/bfi.Rd | 2
man/cluster.cor.Rd | 2
man/cluster.loadings.Rd | 2
man/corFiml.Rd |only
man/df2latex.Rd | 22 ++++++----
man/fa.Rd | 5 +-
man/fa.parallel.Rd | 12 ++---
man/factor.congruence.Rd | 69 +++++++++++++++++++++++++------
man/factor.fit.Rd | 8 ++-
man/guttman.Rd | 36 ++++++++++------
man/iqitems.Rd | 2
man/irt.fa.Rd | 6 +-
man/misc.Rd | 16 ++++++-
man/mixed.cor.Rd | 7 +--
man/plot.psych.Rd | 2
man/sat.act.Rd | 2
man/score.items.Rd | 24 ++++++-----
man/statsBy.Rd | 12 +++--
man/tetrachor.Rd | 9 ++--
47 files changed, 576 insertions(+), 248 deletions(-)
Title: Simultaneous manipulation of multiple arrays of data, with
data.list objects
Diff between multitable versions 1.5 dated 2012-11-10 and 1.6 dated 2013-12-12
Description: Data frames are integral to R. They provide a standard format for passing data to model-fitting and plotting functions, and this standard makes it easier for experienced users to learn new functions that accept data as a single data frame. Still, many data sets do not easily fit into a single data frame; data sets in ecology with a so-called fourth-corner problem provide important examples. Manipulating such inherently multiple-table data using several data frames can result in long and difficult-to-read work-flows. This package provides new data storage objects called data.list objects, which extend the data.frame concept to explicitly multiple-table settings. Like data frames, data lists are lists of variables stored as vectors; what is new is that these vectors have dimension attributes that make accessing and manipulating them easier. As data.list objects can be coerced to data.frame objects, they can be used with all R functions that accept an object that can be coerced to a data.frame.
Author: Steve C Walker
Maintainer: Steve C Walker
multitable-1.5/multitable/testsx |only
multitable-1.6/multitable/DESCRIPTION | 30
multitable-1.6/multitable/MD5 | 29
multitable-1.6/multitable/NAMESPACE | 11
multitable-1.6/multitable/NEWS | 21
multitable-1.6/multitable/R/accessor.functions.R | 13
multitable-1.6/multitable/R/as.R | 41
multitable-1.6/multitable/R/data.list.R | 2
multitable-1.6/multitable/R/dlapply.R | 6
multitable-1.6/multitable/R/zzz.R | 2
multitable-1.6/multitable/build |only
multitable-1.6/multitable/inst/doc/multitable.R |only
multitable-1.6/multitable/inst/doc/multitable.Rnw | 1182 +++++++++++++++++++-
multitable-1.6/multitable/inst/doc/multitable.pdf |binary
multitable-1.6/multitable/man/multitable-package.Rd | 34
multitable-1.6/multitable/tests/test.R | 10
multitable-1.6/multitable/vignettes |only
17 files changed, 1309 insertions(+), 72 deletions(-)
Title: Longitudinal Targeted Maximum Likelihood Estimation
Diff between ltmle versions 0.9.1 dated 2013-10-18 and 0.9.3 dated 2013-12-12
Description: Targeted Maximum Likelihood Estimation (TMLE) of
treatment/censoring specific mean outcome or marginal structural model for
point-treatment and longitudinal data
Author: Joshua Schwab [aut, cre],
Samuel Lendle [aut],
Maya Petersen [aut],
Mark van der Laan [aut],
Susan Gruber [ctb]
Maintainer: Joshua Schwab
DESCRIPTION | 10 -
MD5 | 23 +-
NEWS | 15 +
R/ltmle.R | 334 ++++++++++++++++++++++-----------------
R/zzz.R |only
data/PreviousReleaseTests.RData |only
data/sampleDataForLtmleMSM.RData |binary
man/PreviousReleaseTests.Rd |only
man/ltmle.rd | 43 ++---
man/sampleDataForLtmleMSM.Rd | 10 -
tests |only
11 files changed, 255 insertions(+), 180 deletions(-)
Title: Supervised and unsupervised self-organising maps
Diff between kohonen versions 2.0.13 dated 2013-12-10 and 2.0.14 dated 2013-12-12
Description: Supervised and unsupervised self-organising maps
Author: Ron Wehrens
Maintainer: Ron Wehrens
CHANGES | 6 ++++++
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/map.R | 7 +++++++
4 files changed, 19 insertions(+), 6 deletions(-)
Title: Geometric morphometric analyses of 2d/3d landmark data
Diff between geomorph versions 1.1-4 dated 2013-10-09 and 1.1-5 dated 2013-12-12
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation
Author: Dean Adams
Maintainer: Dean Adams
DESCRIPTION | 9
MD5 | 111 +--
NAMESPACE | 8
NEWS | 22
R/geomorph.r | 1117 ++++++++++++++++++++++----------------
data/hummingbirds.rda |binary
data/mosquito.rda |binary
data/motionpaths.rda |binary
data/plethodon.rda |binary
data/plethspecies.rda |binary
data/ratland.rda |binary
data/scallopPLY.rda |binary
data/scallops.rda |binary
man/arrayspecs.Rd | 34 -
man/bilat.symmetry.Rd | 152 ++---
man/buildtemplate.Rd | 148 ++---
man/compare.evol.rates.Rd |only
man/compare.modular.partitions.Rd | 75 +-
man/curves2d.Rd | 56 -
man/define.sliders.2d.Rd |only
man/define.sliders.3d.Rd |only
man/digit.curves.Rd | 80 --
man/digit.fixed.Rd | 123 ++--
man/digitize2d.Rd | 57 +
man/digitsurface.Rd | 133 ++--
man/editTemplate.Rd | 41 +
man/estimate.missing.Rd | 53 -
man/fixed.angle.Rd | 40 -
man/geomorph-package.Rd | 16
man/gpagen.Rd | 222 +++----
man/hummingbirds.Rd | 17
man/morphol.integr.Rd | 125 +---
man/mosquito.Rd | 5
man/motionpaths.Rd | 11
man/mshape.Rd | 21
man/pairwiseD.test.Rd | 52 -
man/physignal.Rd | 54 -
man/plethodon.Rd | 18
man/plethspecies.Rd | 13
man/plotAllSpecimens.Rd | 30 -
man/plotAllometry.Rd | 107 +--
man/plotGMPhyloMorphoSpace.Rd | 36 -
man/plotRefToTarget.Rd | 54 -
man/plotTangentSpace.Rd | 39 -
man/plotspec.Rd | 15
man/procD.lm.Rd | 110 +--
man/ratland.Rd | 11
man/read.morphologika.Rd | 56 -
man/read.ply.Rd | 36 -
man/read.vrml.Rd | 54 -
man/readland.nts.Rd | 68 +-
man/readland.tps.Rd | 57 -
man/readmulti.nts.Rd | 39 -
man/scallopPLY.Rd | 15
man/scallops.Rd | 13
man/trajectory.analysis.Rd | 209 +++----
man/two.d.array.Rd | 25
man/writeland.tps.Rd | 12
58 files changed, 2000 insertions(+), 1799 deletions(-)
Title: Partitioning beta diversity into turnover and nestedness
components
Diff between betapart versions 1.2 dated 2013-02-12 and 1.3 dated 2013-12-12
Description: betapart allows computing pair-wise dissimilarities (distance matrices) and multiple-site dissimilarities, separating the turnover and nestedness-resultant components of taxonomic (incidence and abundance based), functional and phylogenetic beta diversity.
Author: Andres Baselga, David Orme, Sebastien Villeger, Julien De Bortoli and Fabien Leprieur
Maintainer: Andres Baselga
DESCRIPTION | 24 ++++++++++--------------
MD5 | 22 ++++++++++++++--------
NAMESPACE | 4 +++-
R/phylo.beta.multi.r |only
R/phylo.beta.pair.r |only
R/phylo.betapart.core.r |only
data/bbsData.rda |binary
man/beta.sample.Rd | 13 +++++++++++--
man/betapart-package.Rd | 22 ++++++++++++----------
man/functional.beta.multi.Rd | 12 ++++++++----
man/functional.beta.pair.Rd | 6 ++++--
man/functional.betapart.core.Rd | 15 ++++++++++-----
man/phylo.beta.multi.rd |only
man/phylo.beta.pair.rd |only
man/phylo.betapart.core.rd |only
15 files changed, 72 insertions(+), 46 deletions(-)
Title: Gene Set Analysis Exploiting Pathway Topology
Diff between topologyGSA versions 1.4.1 dated 2013-11-19 and 1.4.2 dated 2013-12-12
Description: Using Gaussian graphical models we propose a novel approach to
perform pathway analysis using gene expression. Given the
structure of a graph (a pathway) we introduce two statistical
tests to compare the mean and the concentration matrices between
two groups. Specifically, these tests can be performed on the
graph and on its connected components (cliques).
Author: Sofia Massa, Gabriele Sales
Maintainer: Gabriele Sales
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/hote.R | 10 ++++++++--
R/pathway.R | 5 ++---
4 files changed, 17 insertions(+), 12 deletions(-)
Title: Tcl/Tk Additions
Diff between tcltk2 versions 1.2-8 dated 2013-12-05 and 1.2-9 dated 2013-12-12
Description: A series of additional Tcl commands and Tk widgets with style
and various functions (under Windows: DDE exchange, access to the
registry and icon manipulation) to supplement the tcltk package
Author: Philippe Grosjean
Maintainer: Philippe Grosjean
DESCRIPTION | 8 +-
MD5 | 95 +++++++++++++++++++++++++--
NEWS | 10 ++
R/tk2commands.R | 10 +-
R/tk2widgets.R | 102 ++++++++++++++++++++---------
inst/tklibs/ttktheme_aquablue |only
inst/tklibs/ttktheme_radiance/pkgIndex.tcl | 2
man/tcltk2-package.Rd | 4 -
8 files changed, 185 insertions(+), 46 deletions(-)
Title: SEER Setup and Use with A-Bomb Data
Diff between SEERaBomb versions 2013.4.1 dated 2013-04-27 and 2013.4.3 dated 2013-12-12
Description: This package contains codes that setup SEER
(Surveillance, Epidemiology and End Results) data use with R.
It includes SEER and Japanese A-Bomb survivor data analysis examples.
By using it, the portability of SEER R scripts should improve.
This package works only with the latest SEER release of April 24, 2013.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch
SEERaBomb-2013.4.1/SEERaBomb/R/blood2012fig4.R |only
SEERaBomb-2013.4.1/SEERaBomb/R/blood2012fig5a.R |only
SEERaBomb-2013.4.1/SEERaBomb/R/blood2012fig5bc.R |only
SEERaBomb-2013.4.1/SEERaBomb/R/blood2012fig6.R |only
SEERaBomb-2013.4.1/SEERaBomb/demo |only
SEERaBomb-2013.4.1/SEERaBomb/inst/doc/confInts.R |only
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SEERaBomb-2013.4.1/SEERaBomb/inst/doc/confInts.pdf |only
SEERaBomb-2013.4.1/SEERaBomb/inst/doc/gettingData.R |only
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SEERaBomb-2013.4.1/SEERaBomb/inst/doc/nagaCML.pdf |only
SEERaBomb-2013.4.1/SEERaBomb/inst/doc/overview.R |only
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SEERaBomb-2013.4.1/SEERaBomb/man/blood2012fig4.Rd |only
SEERaBomb-2013.4.1/SEERaBomb/man/blood2012fig5a.Rd |only
SEERaBomb-2013.4.1/SEERaBomb/man/blood2012fig5bc.Rd |only
SEERaBomb-2013.4.1/SEERaBomb/man/blood2012fig6.Rd |only
SEERaBomb-2013.4.3/SEERaBomb/DESCRIPTION | 19 +-
SEERaBomb-2013.4.3/SEERaBomb/MD5 | 81 +++++-----
SEERaBomb-2013.4.3/SEERaBomb/NAMESPACE | 2
SEERaBomb-2013.4.3/SEERaBomb/NEWS | 25 +++
SEERaBomb-2013.4.3/SEERaBomb/R/mkAbomb.R |only
SEERaBomb-2013.4.3/SEERaBomb/R/mkHema87.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/changes.txt | 4
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/SQL.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/confInts.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/crudeSEERaml.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/crudeSEERcmml.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/lungIncid.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/lungSurv.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/lymyleukIncidICD10.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/lymyleukIncidICD9.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/nagaCML.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/nagaCML.pdf |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/courses/remakeSEERbinaries.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/overview.pdf |binary
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/JCO2013 |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/blood2012/blood2012fig4.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/blood2012/blood2012fig5a.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/blood2012/blood2012fig5bc.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/blood2012/blood2012fig6.R |only
SEERaBomb-2013.4.3/SEERaBomb/inst/doc/papers/radiatEnvironBiophys2013 |only
SEERaBomb-2013.4.3/SEERaBomb/man/SEERaBomb-package.Rd | 3
SEERaBomb-2013.4.3/SEERaBomb/man/mkAbomb.Rd |only
SEERaBomb-2013.4.3/SEERaBomb/man/mkHema87.Rd |only
48 files changed, 80 insertions(+), 54 deletions(-)
Title: Gaussian Graphs Models selection
Diff between GGMselect versions 0.1-2 dated 2010-08-25 and 0.1-8 dated 2013-12-12
Description: GGMselect is a package dedicated to graph estimation in Gaussian Graphical Models. The main functions return the adjacency matrix of an undirected graph estimated from a data matrix.
Author: Annie Bouvier, Christophe Giraud, Sylvie Huet, Verzelen N.
Maintainer: Annie Bouvier
GGMselect-0.1-2/GGMselect/inst/doc/estimation.bib |only
GGMselect-0.1-2/GGMselect/inst/doc/imsart.cls |only
GGMselect-0.1-2/GGMselect/inst/doc/imsart.sty |only
GGMselect-0.1-2/GGMselect/tests/compar.R |only
GGMselect-0.1-2/GGMselect/tests/penInf.R.in |only
GGMselect-0.1-2/GGMselect/tests/sh1GRest |only
GGMselect-0.1-2/GGMselect/tests/sh1GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh2GRest |only
GGMselect-0.1-2/GGMselect/tests/sh2GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh3GRest |only
GGMselect-0.1-2/GGMselect/tests/sh3GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh4GRest |only
GGMselect-0.1-2/GGMselect/tests/sh4GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh5GRest |only
GGMselect-0.1-2/GGMselect/tests/sh5GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh6GRest |only
GGMselect-0.1-2/GGMselect/tests/sh6GRestALL |only
GGMselect-0.1-2/GGMselect/tests/sh7GRest |only
GGMselect-0.1-2/GGMselect/tests/sh7GRestALL |only
GGMselect-0.1-2/GGMselect/tests/supLab.R |only
GGMselect-0.1-2/GGMselect/tests/test1Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test1QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test2Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test2QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test3Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test3QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test4Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test4QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test5Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test5QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test6Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test6QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/test7Fast.R.in |only
GGMselect-0.1-2/GGMselect/tests/test7QE.R.in |only
GGMselect-0.1-2/GGMselect/tests/testMyFam.R.in |only
GGMselect-0.1-8/GGMselect/DESCRIPTION | 15 +--
GGMselect-0.1-8/GGMselect/MD5 |only
GGMselect-0.1-8/GGMselect/NEWS | 47 ++++++++++
GGMselect-0.1-8/GGMselect/R/EW.R | 6 +
GGMselect-0.1-8/GGMselect/R/GGMselect.R | 42 ++++++---
GGMselect-0.1-8/GGMselect/R/ModLasso.R | 5 -
GGMselect-0.1-8/GGMselect/R/MyFamily.R | 87 ++++++++++++++------
GGMselect-0.1-8/GGMselect/R/QE.R | 1
GGMselect-0.1-8/GGMselect/R/penalty.R | 3
GGMselect-0.1-8/GGMselect/R/zzz.R |only
GGMselect-0.1-8/GGMselect/inst/doc/Notice.R |only
GGMselect-0.1-8/GGMselect/inst/doc/Notice.Rnw | 44 ++++++++--
GGMselect-0.1-8/GGMselect/inst/doc/Notice.pdf |binary
GGMselect-0.1-8/GGMselect/man/GGMselect-package.Rd | 8 -
GGMselect-0.1-8/GGMselect/man/convertGraph.Rd | 1
GGMselect-0.1-8/GGMselect/src/Makevars | 2
GGMselect-0.1-8/GGMselect/src/boucle.f | 7 -
GGMselect-0.1-8/GGMselect/src/loop.c | 21 ++++
GGMselect-0.1-8/GGMselect/src/scr.c | 33 +++++--
GGMselect-0.1-8/GGMselect/tests/G3simone.Rdata |only
GGMselect-0.1-8/GGMselect/tests/GaussianData.txt |only
GGMselect-0.1-8/GGMselect/tests/bsch.R |only
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GGMselect-0.1-8/GGMselect/tests/execution |only
GGMselect-0.1-8/GGMselect/tests/genes.lm.Rdata |only
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GGMselect-0.1-8/GGMselect/tests/sh9.2012.R |only
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96 files changed, 245 insertions(+), 77 deletions(-)
Title: Categorical Data Analysis and Visualization
Diff between extracat versions 1.6-3 dated 2013-05-27 and 1.6-4 dated 2013-12-12
Description: Categorical Data Analysis and Visualization
Author: Alexander Pilhoefer
Maintainer: Alexander Pilhoefer
extracat-1.6-3/extracat/R/hexpie.R |only
extracat-1.6-3/extracat/R/newrmb5.R |only
extracat-1.6-3/extracat/R/rmbmat.R |only
extracat-1.6-3/extracat/depr |only
extracat-1.6-4/extracat/DESCRIPTION | 14
extracat-1.6-4/extracat/MD5 | 108 +-
extracat-1.6-4/extracat/NAMESPACE | 8
extracat-1.6-4/extracat/R/arsim.R | 54 -
extracat-1.6-4/extracat/R/barysort.R | 6
extracat-1.6-4/extracat/R/boxplot2g.R | 2
extracat-1.6-4/extracat/R/checkTRINEQ.R |only
extracat-1.6-4/extracat/R/fastRcrit.R | 2
extracat-1.6-4/extracat/R/fechner.R | 67 -
extracat-1.6-4/extracat/R/fluctuations.R | 80 +
extracat-1.6-4/extracat/R/getbw.R |only
extracat-1.6-4/extracat/R/getcolors.R | 24
extracat-1.6-4/extracat/R/heattile.R | 28
extracat-1.6-4/extracat/R/hexpie2.R |only
extracat-1.6-4/extracat/R/optile_skeleton.r | 177 +--
extracat-1.6-4/extracat/R/qBCI.R | 37
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extracat-1.6-4/extracat/R/subtable.R | 60 -
extracat-1.6-4/extracat/R/subtree.R | 2
extracat-1.6-4/extracat/R/tfluctile.r | 14
extracat-1.6-4/extracat/R/untableSet.R | 4
extracat-1.6-4/extracat/R/wdcor.R | 165 ++-
extracat-1.6-4/extracat/data/USR.rda |only
extracat-1.6-4/extracat/data/datalist | 1
extracat-1.6-4/extracat/man/Burt.Rd | 1
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extracat-1.6-4/extracat/man/cmat.Rd | 12
extracat-1.6-4/extracat/man/cpcp.Rd | 3
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extracat-1.6-4/extracat/man/dcor.Rd | 50
extracat-1.6-4/extracat/man/dcorMVdata.Rd |only
extracat-1.6-4/extracat/man/dcorMVtable.Rd |only
extracat-1.6-4/extracat/man/extracat.Rd | 30
extracat-1.6-4/extracat/man/fluctile.Rd | 1
extracat-1.6-4/extracat/man/getIs2.Rd | 3
extracat-1.6-4/extracat/man/getbw.Rd |only
extracat-1.6-4/extracat/man/getcolors.Rd | 6
extracat-1.6-4/extracat/man/getpath.Rd |only
extracat-1.6-4/extracat/man/heattile.Rd | 6
extracat-1.6-4/extracat/man/hexpie.Rd | 14
extracat-1.6-4/extracat/man/idat.Rd | 1
extracat-1.6-4/extracat/man/imat.Rd | 1
extracat-1.6-4/extracat/man/listen.Rd | 5
extracat-1.6-4/extracat/man/optME.Rd | 2
extracat-1.6-4/extracat/man/optile.Rd | 57 -
extracat-1.6-4/extracat/man/quickfechner.Rd | 33
extracat-1.6-4/extracat/man/resort.Rd | 1
extracat-1.6-4/extracat/man/rmb.Rd | 26
extracat-1.6-4/extracat/man/rmbmat.Rd | 3
extracat-1.6-4/extracat/man/scpcp.Rd |only
extracat-1.6-4/extracat/man/steptile.Rd |only
extracat-1.6-4/extracat/man/subtable.Rd | 7
extracat-1.6-4/extracat/man/untableSet.Rd | 2
extracat-1.6-4/extracat/src/optile.c | 1487 ++++++++++++++++++++++++----
65 files changed, 2081 insertions(+), 562 deletions(-)
Title: Nonparametrics with clustered binary and multinomial data
Diff between CorrBin versions 1.3 dated 2012-11-08 and 1.4 dated 2013-12-12
Description: This package implements non-parametric analyses for clustered
binary data. The elements of the cluster are assumed exchangeable, and
identical joint distribution (also known as marginal compatibility, or
reproducibility) is assumed for clusters of different sizes. A trend test
based on stochastic ordering is implemented.
Author: Aniko Szabo
Maintainer: Aniko Szabo
CorrBin-1.3/CorrBin/inst/doc/ShellTox.txt |only
CorrBin-1.3/CorrBin/man/qpower.pdf.Rd |only
CorrBin-1.3/CorrBin/man/unwrap.CBData.Rd |only
CorrBin-1.4/CorrBin/DESCRIPTION | 28 -
CorrBin-1.4/CorrBin/MD5 | 62 +-
CorrBin-1.4/CorrBin/NAMESPACE | 30 -
CorrBin-1.4/CorrBin/R/CBData.R | 248 +++++++++-
CorrBin-1.4/CorrBin/R/CMData.R |only
CorrBin-1.4/CorrBin/R/CorrBin-package.R |only
CorrBin-1.4/CorrBin/R/ExchMultinomial.R |only
CorrBin-1.4/CorrBin/R/Reprod.R | 454 ++++++++++++++++--
CorrBin-1.4/CorrBin/build |only
CorrBin-1.4/CorrBin/data/dehp.rda |only
CorrBin-1.4/CorrBin/data/egde.rda |binary
CorrBin-1.4/CorrBin/data/shelltox.rda |binary
CorrBin-1.4/CorrBin/inst/doc/CorrBinVignette.R |only
CorrBin-1.4/CorrBin/inst/doc/CorrBinVignette.pdf |binary
CorrBin-1.4/CorrBin/man/CBData.Rd | 68 +-
CorrBin-1.4/CorrBin/man/CMData.Rd |only
CorrBin-1.4/CorrBin/man/CorrBin-internal.Rd | 39 +
CorrBin-1.4/CorrBin/man/CorrBin-package.Rd | 74 +--
CorrBin-1.4/CorrBin/man/GEE.trend.test.Rd | 63 +-
CorrBin-1.4/CorrBin/man/NOSTASOT.Rd | 110 ++--
CorrBin-1.4/CorrBin/man/RS.trend.test.Rd | 63 +-
CorrBin-1.4/CorrBin/man/SO.LRT.Rd | 44 +
CorrBin-1.4/CorrBin/man/SO.mc.est.Rd | 124 +++--
CorrBin-1.4/CorrBin/man/SO.trend.test.Rd | 83 ++-
CorrBin-1.4/CorrBin/man/dehp.Rd |only
CorrBin-1.4/CorrBin/man/mc.est.Rd | 82 ++-
CorrBin-1.4/CorrBin/man/mc.test.chisq.Rd | 81 ++-
CorrBin-1.4/CorrBin/man/pdf.Rd |only
CorrBin-1.4/CorrBin/man/ran.CBData.Rd | 90 ++-
CorrBin-1.4/CorrBin/man/read.CBData.Rd | 39 +
CorrBin-1.4/CorrBin/man/read.CMData.Rd |only
CorrBin-1.4/CorrBin/man/soControl.Rd | 68 +-
CorrBin-1.4/CorrBin/man/trend.test.Rd | 81 ++-
CorrBin-1.4/CorrBin/man/unwrap.Rd |only
CorrBin-1.4/CorrBin/src/ReprodCalcs.c | 560 +++++++++++------------
CorrBin-1.4/CorrBin/vignettes |only
39 files changed, 1711 insertions(+), 780 deletions(-)
Title: Clustering of variables around Latent Variables
Diff between ClustVarLV versions 1.0 dated 2013-10-31 and 1.1 dated 2013-12-12
Description: This package provides a set of functions that allows us to cluster a set of variables
around Latent Variables. Each group is associated with a latent variable.
External variables measured on the same observations or/and additional information on the
variables can be taken into account.
Author: Evelyne Vigneau, Mingkun Chen
Maintainer: Evelyne Vigneau
DESCRIPTION | 10 ++--
MD5 | 22 ++++-----
R/CLV.R | 30 +++++-------
R/CLV_kmeans.R | 124 ++++++++++++++++++++++++++++++++++++++++++++--------
R/LCLV.R | 6 +-
R/consol_affect.R | 30 +++++++++---
R/consol_calcul.R | 31 ++++++++-----
R/descrip_gp.R | 43 +++++++++++++++---
R/gpmb_on_pc.R | 51 +++++++++++++++++----
R/print.clvkmeans.r | 2
man/CLV_kmeans.Rd | 11 ++++
man/gpmb_on_pc.Rd | 12 ++++-
12 files changed, 277 insertions(+), 95 deletions(-)
Title: Selective Editing via Mixture models
Diff between SeleMix versions 0.9.0 dated 2013-03-25 and 0.9.1 dated 2013-12-12
Description: Detection of outliers and influential errors using a latent variable model.
Author: Ugo Guarnera, M. Teresa Buglielli
Maintainer: Teresa Buglielli
SeleMix-0.9.0/SeleMix/inst/doc/PAPER_Buglielli_etal.pdf |only
SeleMix-0.9.0/SeleMix/inst/doc/Paper_unece_2011.pdf |only
SeleMix-0.9.0/SeleMix/inst/doc/selemix.bib |only
SeleMix-0.9.1/SeleMix/DESCRIPTION | 11 ++++-----
SeleMix-0.9.1/SeleMix/MD5 | 19 ++++++++--------
SeleMix-0.9.1/SeleMix/R/ml.est.R | 1
SeleMix-0.9.1/SeleMix/build |only
SeleMix-0.9.1/SeleMix/inst/doc/SeleMix-vignette.R |only
SeleMix-0.9.1/SeleMix/inst/doc/SeleMix-vignette.Rnw | 8 +++---
SeleMix-0.9.1/SeleMix/inst/doc/SeleMix-vignette.pdf |binary
SeleMix-0.9.1/SeleMix/man/ml.est.Rd | 3 ++
SeleMix-0.9.1/SeleMix/man/sel.edit.Rd | 6 +++--
SeleMix-0.9.1/SeleMix/vignettes |only
13 files changed, 26 insertions(+), 22 deletions(-)
Title: Global optimization by differential evolution in C++
Diff between RcppDE versions 0.1.1 dated 2012-04-09 and 0.1.2 dated 2013-12-12
Description: This package provides an efficient C++ based implementation of the
DEoptim function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in DEoptim.
Author: Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine Mullen,
Brian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by Rainer Storn)
Maintainer: Dirk Eddelbuettel
RcppDE-0.1.1/RcppDE/COPYRIGHTS |only
RcppDE-0.1.1/RcppDE/benchmark.txt |only
RcppDE-0.1.1/RcppDE/inst/doc/RcppDE.bib |only
RcppDE-0.1.1/RcppDE/inst/doc/jsslogo.jpg |only
RcppDE-0.1.1/RcppDE/scripts |only
RcppDE-0.1.2/RcppDE/ChangeLog | 17 +++++++++++++++-
RcppDE-0.1.2/RcppDE/DESCRIPTION | 32 ++++++++++++++-----------------
RcppDE-0.1.2/RcppDE/MD5 | 28 +++++++++++----------------
RcppDE-0.1.2/RcppDE/R/zzz.R | 2 -
RcppDE-0.1.2/RcppDE/README.md |only
RcppDE-0.1.2/RcppDE/build |only
RcppDE-0.1.2/RcppDE/inst/doc/RcppDE.R |only
RcppDE-0.1.2/RcppDE/inst/doc/RcppDE.pdf |binary
RcppDE-0.1.2/RcppDE/src/deoptim.cpp | 2 -
RcppDE-0.1.2/RcppDE/src/devol.cpp | 2 -
RcppDE-0.1.2/RcppDE/vignettes |only
16 files changed, 46 insertions(+), 37 deletions(-)
Title: Community Ecology Package
Diff between vegan versions 2.0-9 dated 2013-09-25 and 2.0-10 dated 2013-12-12
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen
vegan-2.0-10/vegan/DESCRIPTION | 10 +-
vegan-2.0-10/vegan/MD5 | 93 +++++++++---------
vegan-2.0-10/vegan/NAMESPACE | 3
vegan-2.0-10/vegan/R/boxplot.specaccum.R | 4
vegan-2.0-10/vegan/R/decostand.R | 4
vegan-2.0-10/vegan/R/envfit.default.R | 10 +-
vegan-2.0-10/vegan/R/factorfit.R | 8 +
vegan-2.0-10/vegan/R/fisher.alpha.R | 6 -
vegan-2.0-10/vegan/R/fisherfit.R | 67 +++++++++----
vegan-2.0-10/vegan/R/nestednodf.R | 6 -
vegan-2.0-10/vegan/R/ordiArrowMul.R | 2
vegan-2.0-10/vegan/R/permutest.betadisper.R | 53 +++++++---
vegan-2.0-10/vegan/R/plot.renyiaccum.R | 13 +-
vegan-2.0-10/vegan/R/plot.specaccum.R | 40 +++++++-
vegan-2.0-10/vegan/R/print.cca.R | 2
vegan-2.0-10/vegan/R/print.fisherfit.R | 10 --
vegan-2.0-10/vegan/R/print.oecosimu.R | 4
vegan-2.0-10/vegan/R/renyiaccum.R | 17 ++-
vegan-2.0-10/vegan/R/specaccum.R | 36 ++++++-
vegan-2.0-10/vegan/R/tsallisaccum.R | 5 -
vegan-2.0-10/vegan/R/vectorfit.R | 3
vegan-2.0-10/vegan/inst/ChangeLog | 24 ++++
vegan-2.0-10/vegan/inst/NEWS.Rd | 75 +++++++++++++++
vegan-2.0-10/vegan/inst/doc/FAQ-vegan.pdf |binary
vegan-2.0-10/vegan/inst/doc/NEWS.html | 89 +++++++++++++++++
vegan-2.0-10/vegan/inst/doc/decision-vegan.pdf |binary
vegan-2.0-10/vegan/inst/doc/diversity-vegan.R | 42 +++-----
vegan-2.0-10/vegan/inst/doc/diversity-vegan.Rnw | 15 ---
vegan-2.0-10/vegan/inst/doc/diversity-vegan.pdf |binary
vegan-2.0-10/vegan/inst/doc/intro-vegan.pdf |binary
vegan-2.0-10/vegan/man/betadisper.Rd | 4
vegan-2.0-10/vegan/man/diversity.Rd | 8 -
vegan-2.0-10/vegan/man/fisherfit.Rd | 46 +--------
vegan-2.0-10/vegan/man/nobs.adonis.Rd | 7 -
vegan-2.0-10/vegan/man/permutest.betadisper.Rd | 7 -
vegan-2.0-10/vegan/man/renyi.Rd | 18 ++-
vegan-2.0-10/vegan/man/screeplot.cca.Rd | 5 -
vegan-2.0-10/vegan/man/simper.Rd | 2
vegan-2.0-10/vegan/man/specaccum.Rd | 16 ++-
vegan-2.0-10/vegan/man/tsallis.Rd | 115 ++++++++++++++++-------
vegan-2.0-10/vegan/vignettes/FAQ-vegan.pdf |binary
vegan-2.0-10/vegan/vignettes/NEWS.html | 89 +++++++++++++++++
vegan-2.0-10/vegan/vignettes/decision-vegan.tex | 20 ++--
vegan-2.0-10/vegan/vignettes/diversity-vegan.Rnw | 15 ---
vegan-2.0-10/vegan/vignettes/diversity-vegan.tex | 109 +++++++++------------
vegan-2.0-10/vegan/vignettes/intro-vegan.tex | 60 ++++++------
vegan-2.0-9/vegan/R/confint.fisherfit.R |only
vegan-2.0-9/vegan/R/plot.profile.fisherfit.R |only
vegan-2.0-9/vegan/R/profile.fisherfit.R |only
49 files changed, 761 insertions(+), 401 deletions(-)
Title: Analysis and visualization of tumor sequencing data.
Diff between sequenza versions 1.0.2 dated 2013-12-04 and 1.0.3 dated 2013-12-12
Description: This package provides tools to analyze NGS data, including cellularity and ploidy estimation; mutation and copy number detection and quantification;
Author: Francesco Favero, Andrea M. Marquard, Tejal Joshi, Aron C. Eklund
Maintainer: Francesco Favero
DESCRIPTION | 8 +++---
MD5 | 50 ++++++++++++++++++++---------------------
NEWS | 3 +-
R/analysis.R | 38 +++++++++++++++----------------
R/bayes.R | 56 ++++++++++++++++++++++------------------------
R/graphics.R | 59 ++++++++++++++++++++++++-------------------------
R/misc.R | 3 --
R/model.R | 10 ++++----
R/next.R | 8 +++---
R/workflows.R | 2 -
exec/sequenza-utils.py | 24 +++++++++----------
inst/doc/sequenza.pdf |binary
man/CP.data.Rd | 2 -
man/baf.bayes.Rd | 20 ++++++++--------
man/baf.model.fit.Rd | 18 +++++++-------
man/chromosome.view.Rd | 16 ++++++-------
man/cp.plot.Rd | 12 ++++-----
man/find.breaks.Rd | 6 ++--
man/gc.norm.Rd | 8 +++---
man/model.points.Rd | 2 -
man/mutation.table.Rd | 10 ++++----
man/plot.windows.Rd | 14 +++++------
man/read.abfreq.Rd | 10 ++++----
man/theoric.baf.Rd | 14 +++++------
man/types.matrix.Rd | 2 -
man/workflows.Rd | 4 +--
26 files changed, 198 insertions(+), 201 deletions(-)
Title: Parser combinator in R
Diff between qmrparser versions 0.1.2 dated 2012-08-29 and 0.1.4 dated 2013-12-12
Description: Basic functions for building parsers, with an application to PC-AXIS format files.
Author: Juan Gea Rosat, Ramon Martínez Coscollà .
Maintainer: Juan Gea
qmrparser-0.1.2/qmrparser/qmrparser-Ex.R |only
qmrparser-0.1.4/qmrparser/DESCRIPTION | 12 +--
qmrparser-0.1.4/qmrparser/MD5 | 21 +++--
qmrparser-0.1.4/qmrparser/build |only
qmrparser-0.1.4/qmrparser/inst/doc/qmrparser-vignette.R |only
qmrparser-0.1.4/qmrparser/inst/doc/qmrparser-vignette.pdf |binary
qmrparser-0.1.4/qmrparser/inst/doc/qmrparser.pdf |binary
qmrparser-0.1.4/qmrparser/inst/noweb/README | 18 ++--
qmrparser-0.1.4/qmrparser/inst/noweb/qmrparser.nw | 56 +++++++++-----
qmrparser-0.1.4/qmrparser/man/pcAxisCubeMake.Rd | 8 +-
qmrparser-0.1.4/qmrparser/man/pcAxisParser.Rd | 8 +-
qmrparser-0.1.4/qmrparser/man/qmrparser-package.Rd | 2
qmrparser-0.1.4/qmrparser/tests/examples |only
qmrparser-0.1.4/qmrparser/vignettes |only
14 files changed, 79 insertions(+), 46 deletions(-)
Title: PopGen: A simple way to analyse and visualize population genetic
data
Diff between PopGenReport versions 1.6 dated 2013-09-03 and 1.6.6 dated 2013-12-12
Description: This package provides an easy way to analyse population genetic data
Author: Aaron Adamack & Bernd Gruber
Maintainer: Bernd Gruber
DESCRIPTION | 13 +++---
MD5 | 40 +++++++++++-------
NAMESPACE | 3 -
R/gd.smouse.r | 27 ++++++++++--
R/popgenreport.r | 40 +++++++++++++-----
R/read.genetable.r | 9 ++--
build |only
inst/doc/PopGenReportIntroduction.R |only
inst/doc/PopGenReportIntroduction.pdf |binary
inst/doc/PopGenReportIntroduction.rnw |only
inst/extdata/platypus1c.csv | 2
inst/swchunks/allel.rich.snw | 2
inst/swchunks/allele.dist.snw | 10 ++++
inst/swchunks/counts.snw | 2
inst/swchunks/header.snw | 2
inst/swchunks/required.snw | 2
man/PopGenReport-package.Rd | 72 +++++++++++++++++-----------------
man/gd.kosman.Rd | 2
man/gd.smouse.Rd | 65 +++++++++++++++---------------
man/popgenreport.Rd | 4 -
vignettes |only
21 files changed, 176 insertions(+), 119 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-02-12 0.22
2011-10-19 0.21
2011-08-05 0.20
2011-08-01 0.12
2011-07-27 0.11
2011-07-24 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-15 0.9.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-10-26 1.2.1
2007-05-29 1.2
Title: Data for the synbreed package
Diff between synbreedData versions 1.3 dated 2012-09-06 and 1.4 dated 2013-12-12
Description: This package contains three data sets from cattle, maize and mice to illustrate the functions in the synbreed R package. All data sets are stored in the gpData format introduced in the synbreed package. This research was funded by the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr Synbreed - Synergistic plant and animal breeding (FKZ 0315528A).
Author: Valentin Wimmer, Theresa Albrecht, Hans-Juergen Auinger, Chris-Carolin Schoen with contributions by Malena Erbe, Ulrike Ober and Christian Reimer
Maintainer: Valentin Wimmer
DESCRIPTION | 23 ++++++++---------------
MD5 | 8 ++++----
data/cattle.RData |binary
data/maize.RData |binary
data/mice.RData |binary
5 files changed, 12 insertions(+), 19 deletions(-)
Title: A smarter JSON encoder/decoder for R
Diff between jsonlite versions 0.9.0 dated 2013-12-03 and 0.9.1 dated 2013-12-12
Description: This package is a fork of the RJSONIO package by Duncan Temple
Lang. It builds on the parser from RJSONIO, but implements a different
mapping between R objects and JSON strings. The C code in this package is
mostly from Temple Lang, the R code has been rewritten from scratch. In
addition to drop-in replacements for fromJSON and toJSON, the package has
functions to serialize objects. Furthermore, the package contains a lot of
unit tests to make sure that all edge cases are encoded and decoded
consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang
Maintainer: Jeroen Ooms
jsonlite-0.9.0/jsonlite/R/buildcomplex.R |only
jsonlite-0.9.0/jsonlite/R/mongoexport.R |only
jsonlite-0.9.1/jsonlite/DESCRIPTION | 8
jsonlite-0.9.1/jsonlite/MD5 | 105 +++---
jsonlite-0.9.1/jsonlite/R/as.iso.R | 22 -
jsonlite-0.9.1/jsonlite/R/as.scalar.R | 35 +-
jsonlite-0.9.1/jsonlite/R/asJSON.AAAgeneric.R | 12
jsonlite-0.9.1/jsonlite/R/asJSON.ANY.R | 42 +-
jsonlite-0.9.1/jsonlite/R/asJSON.Date.R | 30 -
jsonlite-0.9.1/jsonlite/R/asJSON.NULL.R | 8
jsonlite-0.9.1/jsonlite/R/asJSON.POSIXt.R | 54 +--
jsonlite-0.9.1/jsonlite/R/asJSON.character.R | 49 +-
jsonlite-0.9.1/jsonlite/R/asJSON.classRepresentation.R | 18 -
jsonlite-0.9.1/jsonlite/R/asJSON.complex.R | 57 +--
jsonlite-0.9.1/jsonlite/R/asJSON.data.frame.R | 149 +++++----
jsonlite-0.9.1/jsonlite/R/asJSON.factor.R | 31 -
jsonlite-0.9.1/jsonlite/R/asJSON.function.R | 21 -
jsonlite-0.9.1/jsonlite/R/asJSON.int64.R | 8
jsonlite-0.9.1/jsonlite/R/asJSON.integer.R | 7
jsonlite-0.9.1/jsonlite/R/asJSON.list.R | 91 ++---
jsonlite-0.9.1/jsonlite/R/asJSON.logical.R | 49 +-
jsonlite-0.9.1/jsonlite/R/asJSON.matrix.R | 36 +-
jsonlite-0.9.1/jsonlite/R/asJSON.numeric.R | 55 +--
jsonlite-0.9.1/jsonlite/R/asJSON.pairlist.R | 8
jsonlite-0.9.1/jsonlite/R/asJSON.raw.R | 35 --
jsonlite-0.9.1/jsonlite/R/asJSON.scalar.R | 24 -
jsonlite-0.9.1/jsonlite/R/asJSON.ts.R |only
jsonlite-0.9.1/jsonlite/R/base64.R | 47 --
jsonlite-0.9.1/jsonlite/R/collapse.R |only
jsonlite-0.9.1/jsonlite/R/fixNativeSymbol.R | 31 -
jsonlite-0.9.1/jsonlite/R/fromJSON.R | 97 +++--
jsonlite-0.9.1/jsonlite/R/helpfunctions.R | 71 +---
jsonlite-0.9.1/jsonlite/R/makesymbol.R | 10
jsonlite-0.9.1/jsonlite/R/null2na.R |only
jsonlite-0.9.1/jsonlite/R/pack.R | 164 +++++-----
jsonlite-0.9.1/jsonlite/R/parseDate.R | 36 +-
jsonlite-0.9.1/jsonlite/R/parseJSON.R | 21 -
jsonlite-0.9.1/jsonlite/R/parseTimestamp.R | 85 ++---
jsonlite-0.9.1/jsonlite/R/prettify.R | 8
jsonlite-0.9.1/jsonlite/R/serializeJSON.R | 22 -
jsonlite-0.9.1/jsonlite/R/simplify.R | 131 ++++---
jsonlite-0.9.1/jsonlite/R/simplifyDataFrame.R | 114 +++---
jsonlite-0.9.1/jsonlite/R/toJSON.R | 93 ++---
jsonlite-0.9.1/jsonlite/R/toMongo.R |only
jsonlite-0.9.1/jsonlite/R/validate.R | 10
jsonlite-0.9.1/jsonlite/inst/doc/json-mapping.pdf |binary
jsonlite-0.9.1/jsonlite/inst/tests/test-fromJSON-dataframe.R | 13
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-NA-values.R |only
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-POSIXt.R | 6
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-complex.R | 6
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-logical.R | 8
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-numeric.R | 12
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-raw.R |only
jsonlite-0.9.1/jsonlite/inst/tests/test-toJSON-zerovec.R |only
jsonlite-0.9.1/jsonlite/man/serializeJSON.Rd | 6
jsonlite-0.9.1/jsonlite/man/toJSON.Rd | 38 +-
jsonlite-0.9.1/jsonlite/man/toMongo.Rd | 9
jsonlite-0.9.1/jsonlite/vignettes/json-mapping-concordance.tex |only
jsonlite-0.9.1/jsonlite/vignettes/json-mapping.synctex.gz |only
59 files changed, 1000 insertions(+), 992 deletions(-)
Title: GPU/CPU Benchmarking in Debian-based systems
Diff between gcbd versions 0.2.4 dated 2010-10-03 and 0.2.5 dated 2013-12-12
Description: GPU/CPU Benchmarking on Debian-package based systems
This package benchmarks performance of a few standard linear algebra
operations (such as a matrix product and QR, SVD and LU decompositions)
across a number of different BLAS libraries as well as a GPU implementation.
To do so, it takes advantage of the ability to 'plug and play' different
BLAS implementations easily on a Debian and/or Ubuntu system. The current
version supports
- reference blas (refblas) which are unaccelerated as a baseline
- Atlas which are tuned but typically configure single-threaded
- Atlas39 which are tuned and configured for multi-threaded mode
- Goto Blas which are accelerated and multithreaded
- Intel MKL which are a commercial accelerated and multithreaded version.
As for GPU computing, we use the CRAN package
- gputools
For Goto Blas, the gotoblas2-helper script from the ISM in Tokyo can be
used. For Intel MKL we use the Revolution R packages from Ubuntu 9.10.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
gcbd-0.2.4/gcbd/inst/ChangeLog |only
gcbd-0.2.4/gcbd/inst/doc/MagmaTimes.png |only
gcbd-0.2.4/gcbd/inst/doc/auto |only
gcbd-0.2.4/gcbd/inst/doc/figures |only
gcbd-0.2.4/gcbd/inst/doc/gcbd.bib |only
gcbd-0.2.4/gcbd/inst/doc/jss.bst |only
gcbd-0.2.4/gcbd/inst/doc/jss.cls |only
gcbd-0.2.4/gcbd/inst/doc/jsslogo.jpg |only
gcbd-0.2.5/gcbd/ChangeLog |only
gcbd-0.2.5/gcbd/DESCRIPTION | 42 ++++++++++++++++----------------
gcbd-0.2.5/gcbd/MD5 |only
gcbd-0.2.5/gcbd/R/figures.R | 3 --
gcbd-0.2.5/gcbd/README.md |only
gcbd-0.2.5/gcbd/build |only
gcbd-0.2.5/gcbd/inst/doc/gcbd.R |only
gcbd-0.2.5/gcbd/inst/doc/gcbd.pdf |binary
gcbd-0.2.5/gcbd/vignettes |only
17 files changed, 21 insertions(+), 24 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Diff between arules versions 1.0-15 dated 2013-09-06 and 1.1-0 dated 2013-12-12
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 10 +-
MD5 | 86 +++++++++++-----------
NAMESPACE | 1
R/aggregate.R | 2
R/dissimilarity.R | 6 +
R/interestMeasures.R | 12 +--
R/itemMatrix.R | 42 ++++++++---
R/parameter.R | 18 ++--
R/transactions.R | 4 +
build |only
data/Adult.rda |binary
data/AdultUCI.rda |binary
data/Epub.rda |binary
data/Groceries.rda |binary
data/Income.rda |binary
data/IncomeESL.rda |binary
inst/CITATION | 2
inst/NEWS | 33 ++++++--
inst/doc/arules.pdf |binary
man/dissimilarity.Rd | 18 ++--
man/itemMatrix-class.Rd | 32 ++++++--
man/transactions-class.Rd | 9 +-
src/arch64.h |only
src/arrayIndex.c | 18 ++--
src/bitmat.c | 4 -
src/istree.c | 72 +++++++++++--------
src/istree.h | 27 ++++---
src/matrix.c | 123 +++++++++++++++++++-------------
src/ptree.c | 161 +++++++++++++++++++++++--------------------
src/rapriori.c | 4 -
src/reclat.c | 10 +-
src/symtab.c | 8 +-
src/tid_count.c | 77 ++++++++++----------
src/tract.c | 14 ++-
src/tract.h | 2
tests/associations.Rout.save | 4 -
tests/extract.Rout.save | 4 -
tests/interfaces.Rout.save | 4 -
tests/itemMatrix.R | 45 ++++++++----
tests/itemMatrix.Rout.save | 106 +++++++++-------------------
tests/matrix.Rout.save | 4 -
tests/measures.Rout.save | 4 -
tests/sets.Rout.save | 4 -
tests/transactions.R | 10 +-
tests/transactions.Rout.save | 58 ++-------------
45 files changed, 555 insertions(+), 483 deletions(-)