Title: Circos 2D Track Plot
Diff between RCircos versions 1.1.0 dated 2013-05-17 and 1.1.1 dated 2013-06-03
Description: RCircos package provides a simple and flexible way to
generate Circos 2D track plot images for genomic data
visualization. The types of plots include: heatmap, histogram,
lines, scatterplot, tiles and plot items for further
decorations include connector, links, and text (gene) label.
All functions require only R graphics package that comes with R
base installation.
Author: Hongen Zhang
Maintainer: Hongen Zhang
RCircos-1.1.0/RCircos/inst/doc/RCircos.pdf |only
RCircos-1.1.1/RCircos/DESCRIPTION | 8 ++++----
RCircos-1.1.1/RCircos/MD5 | 8 +++++---
RCircos-1.1.1/RCircos/inst/doc/RCircos-manual.pdf |binary
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.R |only
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.Rnw |only
RCircos-1.1.1/RCircos/inst/doc/Using_RCircos.pdf |only
7 files changed, 9 insertions(+), 7 deletions(-)
Title: SYNCSA - Analysis of functional and phylogenetic patterns in
metacommunities.
Diff between SYNCSA versions 1.3 dated 2013-02-22 and 1.3.1 dated 2013-06-03
Description: Analysis of metacommunities based on functional traits and
phylogeny of the community components. The functions that are
offered here implement for the R environment methods that have
been available in the SYNCSA application written in C++ (by
Valerio Pillar, available at
http://ecoqua.ecologia.ufrgs.br/ecoqua/SYNCSA.html).
Author: Vanderlei Julio Debastiani
Maintainer: Vanderlei Julio Debastiani
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/matrix.x.R | 16 ++++++++++++----
man/cor.matrix.Rd | 3 ++-
man/cor.matrix.partial.Rd | 3 ++-
man/optimal.Rd | 7 +++++--
man/syncsa.Rd | 4 +++-
7 files changed, 34 insertions(+), 19 deletions(-)
Title: Read and write JPEG images
Diff between jpeg versions 0.1-4 dated 2013-04-26 and 0.1-6 dated 2013-06-03
Description: This package provides an easy and simple way to read,
write and display bitmap images stored in the JPEG format. It
can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 6 ++--
MD5 | 9 ++++---
NEWS | 10 ++++++++
configure.win | 63 +++++++++++++++++++++++++++++++++++++++-------------
src/Makevars-ls.win |only
src/rjcommon.h | 11 +++++++++
6 files changed, 77 insertions(+), 22 deletions(-)
Title: R functions in Chapter 3,4,6,7,9,10,11,12,14,15
Diff between TrialSize versions 1.0 dated 2012-07-11 and 1.3 dated 2013-06-03
Description: functions and examples in Sample Size Calculation in
Clinical Research.
Author: Ed Zhang ; Vicky Qian Wu ; Shein-Chung Chow ; Harry G.Zhang
(Quality check)
Maintainer: Vicky Qian Wu
DESCRIPTION | 14 +-
MD5 | 168 +++++++++++++++----------------
R/TwoSampleSurvival.Conditional.R | 5
man/AB.withDescalation.Rd | 11 +-
man/AB.withoutDescalation.Rd | 12 +-
man/ABE.Rd | 19 +--
man/ANOVA.Repeat.Measure.Rd | 8 -
man/Cochran.Armitage.Trend.Rd | 22 +---
man/Cox.Equality.Rd | 4
man/Cox.Equivalence.Rd | 4
man/Cox.NIS.Rd | 6 -
man/CrossOver.ISV.Equivalence.Rd | 6 -
man/CrossOver.ISV.NIS.Rd | 10 -
man/Dose.Min.Effect.Rd | 18 ---
man/Dose.Response.Linear.Rd | 19 +--
man/Dose.Response.binary.Rd | 17 +--
man/Dose.Response.time.to.event.Rd | 36 ++----
man/IBE.Rd | 31 -----
man/ISCV.Equality.Rd | 11 --
man/ISCV.Equivalence.Rd | 14 --
man/ISCV.NIS.Rd | 8 -
man/ISV.Equivalence.Rd | 4
man/ISV.NIS.Rd | 8 -
man/InterSV.Equality.Rd | 10 -
man/McNemar.Test.Rd | 6 -
man/MeanWilliamsDesign.Equality.Rd | 5
man/MeanWilliamsDesign.Equivalence.Rd | 9 -
man/MeanWilliamsDesign.NIS.Rd | 13 +-
man/Multiple.Testing.Rd | 10 -
man/Nonpara.Independ.Rd | 10 -
man/Nonpara.One.Sample.Rd | 14 +-
man/Nonpara.Two.Sample.Rd | 14 +-
man/OneSampleMean.Equality.Rd | 6 -
man/OneSampleMean.Equivalence.Rd | 10 +
man/OneSampleMean.NIS.Rd | 9 -
man/OneSampleProportion.Equality.Rd | 7 -
man/OneSampleProportion.Equivalence.Rd | 7 -
man/OneSampleProportion.NIS.Rd | 7 -
man/OneSide.fixEffect.Rd | 18 ---
man/OneSide.varyEffect.Rd | 15 +-
man/OneWayANOVA.PairwiseComparison.Rd | 9 -
man/OneWayANOVA.pairwise.Rd | 8 -
man/PBE.Rd | 19 +--
man/Propensity.Score.nostrata.Rd | 29 +----
man/Propensity.Score.strata.Rd | 21 +--
man/QOL.Rd | 12 --
man/QT.PK.crossover.Rd | 14 --
man/QT.PK.parallel.Rd | 12 --
man/QT.crossover.Rd | 14 --
man/QT.parallel.Rd | 13 --
man/RelativeRisk.Equality.Rd | 7 -
man/RelativeRisk.Equivalence.Rd | 9 -
man/RelativeRisk.NIS.Rd | 7 -
man/RelativeRiskCrossOver.Equality.Rd | 9 -
man/RelativeRiskCrossOver.Equivalence.Rd | 9 -
man/RelativeRiskCrossOver.NIS.Rd | 10 -
man/Sensitivity.Index.Rd | 9 -
man/Stuart.Maxwell.Test.Rd | 10 -
man/TrialSize-package.Rd | 14 +-
man/TwoSampleCrossOver.Equality.Rd | 4
man/TwoSampleCrossOver.Equivalence.Rd | 6 -
man/TwoSampleCrossOver.NIS.Rd | 6 -
man/TwoSampleMean.Equality.Rd | 2
man/TwoSampleMean.Equivalence.Rd | 6 -
man/TwoSampleMean.NIS.Rd | 6 -
man/TwoSampleProportion.Equality.Rd | 6 -
man/TwoSampleProportion.Equivalence.Rd | 8 -
man/TwoSampleProportion.NIS.Rd | 10 -
man/TwoSampleSeqCrossOver.Equivalence.Rd | 5
man/TwoSampleSurvival.Conditional.Rd | 6 -
man/TwoSampleSurvival.Equality.Rd | 10 -
man/TwoSampleSurvival.NIS.Rd | 10 -
man/TwoSide.fixEffect.Rd | 10 +
man/TwoSide.varyEffect.Rd | 12 +-
man/Vaccine.CEM.Rd | 2
man/Vaccine.ELDI.Rd | 9 -
man/Vaccine.RDI.Rd | 4
man/Vitro.BE.Rd | 38 +------
man/WilliamsDesign.Equality.Rd | 9 -
man/WilliamsDesign.Equivalence.Rd | 11 --
man/WilliamsDesign.NIS.Rd | 11 --
man/gof.Pearson.Rd | 2
man/gof.Pearson.twoway.Rd | 2
src/TrialSize.cc | 2
src/TrialSize_main.cc | 4
85 files changed, 384 insertions(+), 677 deletions(-)
Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.90 dated 2013-05-23 and 0.91 dated 2013-06-03
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/Main_SSD.R | 8 ++++----
inst/doc/SKAT.pdf |binary
4 files changed, 11 insertions(+), 11 deletions(-)
Title: Methods for robust rank aggregation
Diff between RobustRankAggreg versions 1.0 dated 2011-03-28 and 1.1 dated 2013-06-03
More information about RobustRankAggreg at CRAN
Description: Methods for aggregating ranked lists, especially lists of
genes. It implements the Robust Rank Aggregation (Kolde et. al
in preparation) and some other simple algorithms for the task.
RRA method uses a probabilistic model for aggregation that is
robust to noise and also facilitates the calculation of
significance probabilities for all the elements in the final
ranking.
Author: Raivo Kolde, Sven Laur
Maintainer: Raivo Kolde
RobustRankAggreg-1.0/RobustRankAggreg/run_roxygen.r |only
RobustRankAggreg-1.1/RobustRankAggreg/DESCRIPTION | 7
RobustRankAggreg-1.1/RobustRankAggreg/MD5 |only
RobustRankAggreg-1.1/RobustRankAggreg/NAMESPACE | 4
RobustRankAggreg-1.1/RobustRankAggreg/R/aggregateRanks.R | 117 +++++---
RobustRankAggreg-1.1/RobustRankAggreg/man/aggregateRanks.Rd | 157 +++++++-----
RobustRankAggreg-1.1/RobustRankAggreg/man/betaScores.Rd | 57 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/cellCycleKO.Rd | 56 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/rankMatrix.Rd | 57 ++--
RobustRankAggreg-1.1/RobustRankAggreg/man/rhoScores.Rd | 43 ++-
10 files changed, 324 insertions(+), 174 deletions(-)
Permanent link
Title: Read and write PNG images
Diff between png versions 0.1-4 dated 2011-12-11 and 0.1-5 dated 2013-06-03
Description: This package provides an easy and simple way to read,
write and display bitmap images stored in the PNG format. It
can read and write both files and in-memory raw vectors.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 11 ++++++----
MD5 | 22 ++++++++++----------
NAMESPACE | 2 -
NEWS | 14 ++++++++++++
R/read.R | 4 +--
R/write.R | 6 ++---
configure.win | 60 +++++++++++++++++++++++++++++++++++++++++--------------
man/readPNG.Rd | 5 +++-
man/writePNG.Rd | 21 ++++++++++++++-----
src/Makevars.win | 16 +++++++-------
src/read.c | 48 +++++++++++++++++++++++++++++++++++++++++---
src/write.c | 39 +++++++++++++++++++++++++++++++++--
12 files changed, 193 insertions(+), 55 deletions(-)
Title: Spatial Probit Models
Diff between spatialprobit versions 0.9-8 dated 2013-03-02 and 0.9-9 dated 2013-06-03
Description: Bayesian Estimation of Spatial Probit and Tobit Models
Author: Stefan Wilhelm
Maintainer: Stefan Wilhelm
.Rinstignore | 1 +
DESCRIPTION | 8 ++++----
MD5 | 12 +++++++-----
NEWS | 4 ++++
R/SpatialProbit-MCMC.R | 4 ++++
R/semprobit.R | 4 ++++
inst/tests/test-sarprobit.R |only
inst/tests/test-semprobit.R |only
man/sarprobit.Rd | 19 ++++++++++++-------
9 files changed, 36 insertions(+), 16 deletions(-)
Title: Visualization methods for the raster package
Diff between rasterVis versions 0.20-07 dated 2013-05-06 and 0.21 dated 2013-06-03
Description: The raster package defines classes and methods for spatial
raster data access and manipulation. The rasterVis package
complements raster providing a set of methods for enhanced
visualization and interaction.
Author: Oscar Perpinan Lamigueiro [cre, aut], Robert Hijmans [aut]
Maintainer: Oscar Perpinan Lamigueiro
ChangeLog | 416 ++---------------------------------------------
DESCRIPTION | 8
MD5 | 11 -
R/horizonplot.R | 2
R/levelplot.R | 8
man/levelplot-methods.Rd | 21 ++
rasterVis-Ex.R |only
7 files changed, 60 insertions(+), 406 deletions(-)
Title: Tools to manage a parametric function that describes phenology
Diff between phenology versions 3.44 dated 2013-01-29 and 3.47 dated 2013-06-03
Description: Functions to fit and test the phenology of species based
on counts.
Author: Marc Girondot
Maintainer: Marc Girondot
DESCRIPTION | 9 +-
MD5 | 138 ++++++++++++++++++++++---------------------
NAMESPACE | 3
NEWS | 18 +++++
R/BE_to_LBLE.R | 7 +-
R/Gratiot.R | 4 -
R/LBLE_to_BE.R | 5 -
R/LBLE_to_L.R | 6 +
R/L_to_LBLE.R | 4 -
R/Likelihood_phenology.R | 3
R/Script_MCMC.r | 31 +++++----
R/adapt_parameters.R | 6 +
R/add_phenology.R | 9 +-
R/as.mcmc.mcmcComposite.R |only
R/as.par.mcmcComposite.R |only
R/compare_AIC.R | 72 ++++++++++++++--------
R/extract_result.R | 9 +-
R/fit_phenology.R | 8 +-
R/map_phenology.R | 23 +++++--
R/moon_phase.R | 6 +
R/onAttach.R | 8 ++
R/par_init.R | 6 +
R/phenology-package.R | 10 +--
R/phenology_MHmcmc_p.R | 28 +++++---
R/phenology_fonctionMCMC.R | 3
R/plot.mcmcComposite.R | 34 +++++-----
R/plot.phenology.R | 6 +
R/plot.phenologymap.R | 18 +++--
R/plot_delta.R | 16 +++-
R/plot_phi.R | 21 ++++--
R/print.phenology.R | 6 +
R/print.phenologymap.R | 24 +++++--
R/print.phenologyout.R | 12 ++-
R/remove_site.R | 12 ++-
R/shift_sinusoid.R | 28 ++++++--
R/summary.mcmcComposite.R | 32 +++++----
R/summary.phenology.R | 12 ++-
R/summary.phenologymap.R | 24 +++++--
R/summary.phenologyout.R | 12 ++-
man/BE_to_LBLE.Rd | 7 +-
man/Gratiot.Rd | 4 -
man/LBLE_to_BE.Rd | 3
man/LBLE_to_L.Rd | 6 +
man/L_to_LBLE.Rd | 4 -
man/adapt_parameters.Rd | 6 +
man/add_phenology.Rd | 9 +-
man/as.mcmc.mcmcComposite.Rd |only
man/as.par.mcmcComposite.Rd |only
man/compare_AIC.Rd | 27 +++++---
man/extract_result.Rd | 9 +-
man/fit_phenology.Rd | 8 +-
man/likelihood_phenology.Rd | 3
man/map_phenology.Rd | 23 +++++--
man/moon_phase.Rd | 6 +
man/par_init.Rd | 6 +
man/phenology-package.Rd | 8 +-
man/phenology_MHmcmc.Rd | 28 ++++----
man/phenology_MHmcmc_p.Rd | 25 ++++---
man/plot.mcmcComposite.Rd | 32 +++++----
man/plot.phenology.Rd | 6 +
man/plot.phenologymap.Rd | 18 +++--
man/plot_delta.Rd | 16 +++-
man/plot_phi.Rd | 21 ++++--
man/print.phenology.Rd | 6 +
man/print.phenologymap.Rd | 24 +++++--
man/print.phenologyout.Rd | 12 ++-
man/remove_site.Rd | 12 ++-
man/shift_sinusoid.Rd | 28 ++++++--
man/summary.mcmcComposite.Rd | 32 +++++----
man/summary.phenology.Rd | 12 ++-
man/summary.phenologymap.Rd | 24 +++++--
man/summary.phenologyout.Rd | 12 ++-
72 files changed, 730 insertions(+), 380 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 2.0 dated 2013-05-23 and 2.1 dated 2013-06-03
Description: Performs the colocalisation tests described in Plagnol et
al (2009), Wallace et al (2013) and Giambartolomei et al
(2013).
Author: Chris Wallace and Claudia Giambartolemei with contributions
from Vincent Plagnol
Maintainer: Chris Wallace
ChangeLog | 9 ++++++
DESCRIPTION | 10 ++++--
MD5 | 16 ++++++----
NAMESPACE | 1
R/claudia.R | 70 ++++++++++++++++++++++++-----------------------
R/coloc.abf.imputed.R |only
inst/CITATION | 29 ++++++++-----------
man/approx.bf.imputed.Rd |only
man/coloc.abf.Rd | 24 +++++++++-------
man/coloc.abf.imputed.Rd |only
man/combine.abf.Rd |only
11 files changed, 90 insertions(+), 69 deletions(-)
Title: Regularization for semiparametric additive hazards regression
Diff between ahaz versions 1.13 dated 2013-04-25 and 1.14 dated 2013-06-03
Description: Computationally efficient procedures for regularized
estimation with the semiparametric additive hazards regression
model.
Author: Anders Gorst-Rasmussen
Maintainer: Anders Gorst-Rasmussen
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
R/ahaz.R | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
Title: Text Mining Distributed Corpus Plug-In
Diff between tm.plugin.dc versions 0.2-4 dated 2012-11-11 and 0.2-5 dated 2013-06-03
Description: A plug-in for the text mining framework tm to support text
mining in a distributed way. The package provides a convenient
interface for handling distributed corpus objects based on
distributed list objects.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl
DESCRIPTION | 13 +++++++------
MD5 | 4 ++--
R/mapper.R | 4 ++--
3 files changed, 11 insertions(+), 10 deletions(-)
Title: Latent position and cluster models for statistical networks
Diff between latentnet versions 2.4-4 dated 2013-03-06 and 2.4-5 dated 2013-06-03
Description: A package to fit and simulate latent position and cluster
models for statistical networks.
Author: Pavel N. Krivitsky [aut, cre], Mark S. Handcock [aut], Susan M.
Shortreed [ctb], Jeremy Tantrum [ctb], Peter D. Hoff [ctb]
Maintainer: Pavel N. Krivitsky
ChangeLog | 5 ++++
DESCRIPTION | 8 +++----
MD5 | 18 ++++++++---------
R/mcmc.diagnostics.ergmm.R | 4 +++
data/davis.RData |binary
man/latentnet-internal.Rd | 3 ++
man/plot.ergmm.Rd | 3 +-
man/summary.ergmm.Rd | 9 ++++++--
man/tribes.Rd | 7 +++---
tests/examples.R | 46 +++++++++++++++++++++++++++++++--------------
10 files changed, 70 insertions(+), 33 deletions(-)
Title: Goodness-of-fit functions for comparison of simulated and
observed hydrological time series
Diff between hydroGOF versions 0.3-6 dated 2013-03-25 and 0.3-7 dated 2013-06-03
Description: S3 functions implementing both statistical and graphical
goodness-of-fit measures between observed and simulated values,
mainly oriented to be used during the calibration, validation,
and application of hydrological models. Missing values in
observed and/or simulated values can be removed before
computations. Comments / questions / collaboration of any kind
are very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre]
Maintainer: Mauricio Zambrano Bigiarini
DESCRIPTION | 8 -
MD5 | 33 +++---
NAMESPACE | 2
NEWS | 24 ++++-
R/ggof.R | 195 ++++++++++++++++++++++++++++++++---------
R/pbiasfdc.R | 24 +++--
R/plot2.R | 108 +++++++++++++---------
R/plotbands.R | 33 ++++--
R/plotbandsonly.R | 24 +++--
R/valindex.R | 4
inst/doc/hydroGOF_Vignette.R |only
inst/doc/hydroGOF_Vignette.pdf |binary
man/KGE.Rd | 2
man/VE.Rd | 2
man/ggof.Rd | 35 ++++++-
man/hydroGOF-package.Rd | 8 -
man/plot2.Rd | 8 +
man/valindex.Rd | 2
18 files changed, 363 insertions(+), 149 deletions(-)
Title: Distributed Storage and List
Diff between DSL versions 0.1-3 dated 2013-06-01 and 0.1-4 dated 2013-06-03
Description: A package providing functions and methods for handling
distributed storage (DStorage) and lists (DLlist). It
implements an abstract DList class for storing large list-type
objects in a distributed manner. In doing so it uses a well
defined storage backend implemented based on the DStorage
class. It allows for processing such DLists on distributed
systems efficiently.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre], Christian
Buchta [ctb]
Maintainer: Stefan Theussl
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/storage.R | 8 ++++----
inst/doc/DSL.pdf |binary
4 files changed, 11 insertions(+), 11 deletions(-)