Title: Circular visualization in R
Diff between circlize versions 0.0.8 dated 2014-06-03 and 0.0.9 dated 2014-07-11
Description: circlize is an R package which implements circular visualization
(http://circos.ca/) in R. Due to the natural born feature of drawing statistical
graphics in R, this package can provide a more general and flexible way to
visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu
circlize-0.0.8/circlize/demo/funny-01-clock.R |only
circlize-0.0.8/circlize/demo/funny-02-dartboard.R |only
circlize-0.0.8/circlize/demo/funny-03-bagua.R |only
circlize-0.0.8/circlize/demo/funny-04-doodle.R |only
circlize-0.0.8/circlize/demo/funny-05-solaris.R |only
circlize-0.0.8/circlize/demo/ideogram-01-simple.R |only
circlize-0.0.8/circlize/demo/ideogram-02-genomic.R |only
circlize-0.0.8/circlize/demo/ideogram-03-nested.R |only
circlize-0.0.8/circlize/demo/ideogram-04-zoom.R |only
circlize-0.0.8/circlize/demo/intro-01-glance.R |only
circlize-0.0.8/circlize/demo/intro-05-factor.R |only
circlize-0.0.8/circlize/demo/intro-05-sectorwidth.R |only
circlize-0.0.8/circlize/demo/intro-08-lines.R |only
circlize-0.0.8/circlize/demo/intro-09-text.R |only
circlize-0.0.8/circlize/demo/intro-10-smooth.R |only
circlize-0.0.8/circlize/demo/intro-11-axis.R |only
circlize-0.0.8/circlize/demo/intro-12-link.R |only
circlize-0.0.8/circlize/demo/intro-14-hist.R |only
circlize-0.0.8/circlize/demo/intro-15-heatmap.R |only
circlize-0.0.8/circlize/demo/intro-16-combine.R |only
circlize-0.0.8/circlize/demo/intro-16-highlight.R |only
circlize-0.0.8/circlize/demo/intro-17-part.R |only
circlize-0.0.8/circlize/demo/intro-18-part2.R |only
circlize-0.0.8/circlize/demo/intro-19-nested.R |only
circlize-0.0.8/circlize/demo/intro-20-seperated.R |only
circlize-0.0.8/circlize/demo/intro-21-diffradius.R |only
circlize-0.0.8/circlize/demo/intro-22-outside.R |only
circlize-0.0.8/circlize/demo/intro-23-layout.R |only
circlize-0.0.8/circlize/demo/relation-01-example.R |only
circlize-0.0.8/circlize/demo/relation-02-table.R |only
circlize-0.0.8/circlize/inst/doc/draw-genomic-plot.R |only
circlize-0.0.8/circlize/inst/doc/draw-genomic-plot.Rnw |only
circlize-0.0.8/circlize/inst/doc/draw-genomic-plot.pdf |only
circlize-0.0.8/circlize/vignettes/doodle.jpeg |only
circlize-0.0.8/circlize/vignettes/draw-genomic-plot.Rnw |only
circlize-0.0.8/circlize/vignettes/figures/circos_genomictrackplotregion.pdf |only
circlize-0.0.8/circlize/vignettes/figures/circos_initializeWithIdeogram_example.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomicDensity.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomicInitialize_TP.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomic_highlight.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomic_lines.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomic_link.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomic_points.pdf |only
circlize-0.0.8/circlize/vignettes/figures/genomic_rect.pdf |only
circlize-0.0.8/circlize/vignettes/figures/position_transformation_line.pdf |only
circlize-0.0.8/circlize/vignettes/figures/rainfall_plot.pdf |only
circlize-0.0.8/circlize/vignettes/phylogenetic-tree.pdf |only
circlize-0.0.8/circlize/vignettes/src/ideogram-02-genomic.R |only
circlize-0.0.8/circlize/vignettes/src/ideogram-03-nested.R |only
circlize-0.0.8/circlize/vignettes/src/ideogram-04-zoom.R |only
circlize-0.0.8/circlize/vignettes/src/relation-01-example.R |only
circlize-0.0.9/circlize/DESCRIPTION | 8
circlize-0.0.9/circlize/MD5 | 256 -
circlize-0.0.9/circlize/NAMESPACE | 90
circlize-0.0.9/circlize/NEWS | 9
circlize-0.0.9/circlize/R/chordDiagram.R |only
circlize-0.0.9/circlize/R/genomic.R | 326 +
circlize-0.0.9/circlize/R/genomic_utils.R | 40
circlize-0.0.9/circlize/R/global.R | 65
circlize-0.0.9/circlize/R/link.R | 488 +-
circlize-0.0.9/circlize/R/overview.R | 7
circlize-0.0.9/circlize/R/plot.R | 202 -
circlize-0.0.9/circlize/R/utils.R | 91
circlize-0.0.9/circlize/build/vignette.rds |binary
circlize-0.0.9/circlize/demo/00Index | 31
circlize-0.0.9/circlize/demo/foo.R |only
circlize-0.0.9/circlize/inst/doc/circlize.R | 50
circlize-0.0.9/circlize/inst/doc/circlize.Rnw | 161
circlize-0.0.9/circlize/inst/doc/circlize.pdf |binary
circlize-0.0.9/circlize/inst/doc/draw-ideogram.R | 20
circlize-0.0.9/circlize/inst/doc/draw-ideogram.Rnw | 10
circlize-0.0.9/circlize/inst/doc/draw-ideogram.pdf |binary
circlize-0.0.9/circlize/inst/doc/draw-phylogenetic-tree.R | 35
circlize-0.0.9/circlize/inst/doc/draw-phylogenetic-tree.Rnw | 109
circlize-0.0.9/circlize/inst/doc/draw-phylogenetic-tree.pdf |binary
circlize-0.0.9/circlize/inst/doc/draw-relations.R | 296 +
circlize-0.0.9/circlize/inst/doc/draw-relations.Rnw | 434 +-
circlize-0.0.9/circlize/inst/doc/draw-relations.pdf |binary
circlize-0.0.9/circlize/inst/doc/genomic-plot.R |only
circlize-0.0.9/circlize/inst/doc/genomic-plot.Rnw |only
circlize-0.0.9/circlize/inst/doc/genomic-plot.pdf |only
circlize-0.0.9/circlize/inst/doc/interesting-graphics.R | 72
circlize-0.0.9/circlize/inst/doc/interesting-graphics.Rnw | 55
circlize-0.0.9/circlize/inst/doc/interesting-graphics.pdf |binary
circlize-0.0.9/circlize/inst/extdata/DMR.RData |only
circlize-0.0.9/circlize/inst/extdata/cytoBand.txt | 1724 +++++-----
circlize-0.0.9/circlize/inst/extdata/gencode_TP_gene.RData |only
circlize-0.0.9/circlize/man/chordDiagram.rd |only
circlize-0.0.9/circlize/man/circlize-package.rd | 122
circlize-0.0.9/circlize/man/circlize.rd | 69
circlize-0.0.9/circlize/man/circos.axis.rd | 156
circlize-0.0.9/circlize/man/circos.clear.rd | 47
circlize-0.0.9/circlize/man/circos.genomicDensity.rd | 79
circlize-0.0.9/circlize/man/circos.genomicInitialize.rd | 70
circlize-0.0.9/circlize/man/circos.genomicLines.rd | 96
circlize-0.0.9/circlize/man/circos.genomicLink.rd | 73
circlize-0.0.9/circlize/man/circos.genomicPoints.rd | 75
circlize-0.0.9/circlize/man/circos.genomicPosTransformLines.rd | 72
circlize-0.0.9/circlize/man/circos.genomicRainfall.rd | 71
circlize-0.0.9/circlize/man/circos.genomicRect.rd | 85
circlize-0.0.9/circlize/man/circos.genomicText.rd | 88
circlize-0.0.9/circlize/man/circos.genomicTrackPlotRegion.rd | 88
circlize-0.0.9/circlize/man/circos.info.rd | 59
circlize-0.0.9/circlize/man/circos.initialize.rd | 73
circlize-0.0.9/circlize/man/circos.initializeWithIdeogram.rd | 241 -
circlize-0.0.9/circlize/man/circos.lines.rd | 124
circlize-0.0.9/circlize/man/circos.link.rd | 107
circlize-0.0.9/circlize/man/circos.par.rd | 83
circlize-0.0.9/circlize/man/circos.points.rd | 79
circlize-0.0.9/circlize/man/circos.polygon.rd | 94
circlize-0.0.9/circlize/man/circos.rect.rd | 79
circlize-0.0.9/circlize/man/circos.text.rd | 97
circlize-0.0.9/circlize/man/circos.trackHist.rd | 114
circlize-0.0.9/circlize/man/circos.trackLines.rd | 90
circlize-0.0.9/circlize/man/circos.trackPlotRegion.rd | 109
circlize-0.0.9/circlize/man/circos.trackPoints.rd | 74
circlize-0.0.9/circlize/man/circos.trackText.rd | 79
circlize-0.0.9/circlize/man/circos.updatePlotRegion.rd | 69
circlize-0.0.9/circlize/man/colorRamp2.rd | 74
circlize-0.0.9/circlize/man/cytoband.col.rd | 51
circlize-0.0.9/circlize/man/draw.sector.rd | 123
circlize-0.0.9/circlize/man/generateRandomBed.rd | 55
circlize-0.0.9/circlize/man/genomicDensity.rd | 65
circlize-0.0.9/circlize/man/get.all.sector.index.rd |only
circlize-0.0.9/circlize/man/get.cell.meta.data.rd | 101
circlize-0.0.9/circlize/man/get.current.chromosome.rd | 43
circlize-0.0.9/circlize/man/getI.rd | 55
circlize-0.0.9/circlize/man/highlight.chromosome.rd | 71
circlize-0.0.9/circlize/man/posTransform.default.rd | 55
circlize-0.0.9/circlize/man/rainfallTransform.rd | 53
circlize-0.0.9/circlize/man/read.cytoband.rd | 81
circlize-0.0.9/circlize/man/show.index.rd | 58
circlize-0.0.9/circlize/vignettes/circlize.Rnw | 161
circlize-0.0.9/circlize/vignettes/draw-ideogram.Rnw | 10
circlize-0.0.9/circlize/vignettes/draw-phylogenetic-tree.Rnw | 109
circlize-0.0.9/circlize/vignettes/draw-relations.Rnw | 434 +-
circlize-0.0.9/circlize/vignettes/figures/doodle.jpeg |only
circlize-0.0.9/circlize/vignettes/figures/phylogenetic-tree.pdf |only
circlize-0.0.9/circlize/vignettes/genomic-plot.Rnw |only
circlize-0.0.9/circlize/vignettes/interesting-graphics.Rnw | 55
circlize-0.0.9/circlize/vignettes/src/chordDiagram-01-basic.R |only
circlize-0.0.9/circlize/vignettes/src/chordDiagram-02-color.R |only
circlize-0.0.9/circlize/vignettes/src/chordDiagram-03-advanced.R |only
circlize-0.0.9/circlize/vignettes/src/chordDiagram-04-other.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-01-circos.initializeWithIdeogram.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-02-customize_ideogram.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-03-TPgenemodel.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-04-genomicTrackPlotRegion.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-05-genomicLink.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-06-highlight.chromosome.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-07-posTransformLines.R |only
circlize-0.0.9/circlize/vignettes/src/genomic-08-rainfallplot.R |only
circlize-0.0.9/circlize/vignettes/src/intro-00-correspondence.R | 38
circlize-0.0.9/circlize/vignettes/src/intro-01-glance.R | 4
circlize-0.0.9/circlize/vignettes/src/intro-04-coordinate.R | 2
circlize-0.0.9/circlize/vignettes/src/intro-05-factor.R | 4
circlize-0.0.9/circlize/vignettes/src/intro-05-sectorwidth.R | 2
circlize-0.0.9/circlize/vignettes/src/intro-06-region.R | 8
circlize-0.0.9/circlize/vignettes/src/intro-08-lines.R | 42
circlize-0.0.9/circlize/vignettes/src/intro-08-linescurve.R | 30
circlize-0.0.9/circlize/vignettes/src/intro-09-text.R | 35
circlize-0.0.9/circlize/vignettes/src/intro-11-axis.R | 8
circlize-0.0.9/circlize/vignettes/src/intro-12-link.R | 57
circlize-0.0.9/circlize/vignettes/src/intro-15-heatmap.R | 47
circlize-0.0.9/circlize/vignettes/src/intro-16-highlight.R | 2
circlize-0.0.9/circlize/vignettes/src/phylogenetic_tree.R |only
circlize-0.0.9/circlize/vignettes/src/relation-02-table.R | 11
167 files changed, 4854 insertions(+), 4431 deletions(-)
Title: Tools for Approximate Bayesian Computation (ABC)
Diff between abc versions 1.8 dated 2013-10-29 and 2.0 dated 2014-07-11
Description: The package implements several ABC algorithms for
performing parameter estimation, model selection, and goodness-of-fit.
Cross-validation tools are also available for measuring the
accuracy of ABC estimates, and to calculate the
misclassification probabilities of different models.
Author: Katalin Csillery, Louisiane Lemaire, Michael Blum and Olivier Francois
Maintainer: Michael Blum
CHANGES | 7
DESCRIPTION | 14
MD5 | 22
NAMESPACE | 7
R/gfit.R |only
R/gfitpca.R |only
build/vignette.rds |binary
inst/doc/abcvignette.Rnw | 1610 ++++++++++++++++++++++++----------------------
inst/doc/abcvignette.pdf |binary
man/gfit.Rd |only
man/gfitpca.Rd |only
man/plot.gfit.Rd |only
man/postpr.Rd | 334 ++++-----
man/summary.gfit.Rd |only
vignettes/abcvignette.Rnw | 1610 ++++++++++++++++++++++++----------------------
15 files changed, 1892 insertions(+), 1712 deletions(-)
Title: Multiple hypothesis testing
Diff between sgof versions 2.0.2 dated 2014-03-05 and 2.1 dated 2014-07-11
Description: This package implements seven different methods for multi-testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez.
Maintainer: Irene Castro Conde
DESCRIPTION | 12 ++++++------
MD5 | 7 +++++--
NAMESPACE | 4 ++++
R/Extended.SGoF.R |only
R/print.Extended.SGoF.R |only
man/Extended.SGoF.Rd |only
6 files changed, 15 insertions(+), 8 deletions(-)
Title: Segmented relationships in regression models with
breakpoints/changepoints estimation
Diff between segmented versions 0.3-1.0 dated 2014-04-18 and 0.4-0.0 dated 2014-07-11
Description: Given a (generalized) linear model, segmented `updates' the model by adding one or more segmented relationships. Several variables with multiple breakpoints are allowed.
Author: Vito M. R. Muggeo [aut, cre]
Maintainer: Vito M. R. Muggeo
DESCRIPTION | 8 -
MD5 | 46 +++---
NAMESPACE | 5
NEWS | 21 ++
R/broken.line.r | 61 ++++++--
R/confint.segmented.R | 23 ++-
R/davies.test.r | 332 ++++++++++++++++++++++++++++-------------------
R/draw.history.R | 19 ++
R/intercept.r | 38 +++--
R/plot.segmented.R | 27 ++-
R/points.segmented.r |only
R/predict.segmented.r | 45 ++++--
R/seg.glm.fit.r | 2
R/seg.lm.fit.r | 2
R/segmented.glm.R | 2
R/segmented.lm.R | 10 -
R/slope.R | 38 ++++-
man/davies.test.Rd | 54 ++++---
man/intercept.Rd | 4
man/lines.segmented.Rd | 5
man/plot.segmented.Rd | 1
man/points.segmented.Rd |only
man/segmented-package.Rd | 4
man/segmented.Rd | 1
man/slope.Rd | 5
25 files changed, 501 insertions(+), 252 deletions(-)
Title: Routines for fitting kinetic models with one or more state
variables to chemical degradation data
Diff between mkin versions 0.9-29 dated 2014-06-27 and 0.9-30 dated 2014-07-11
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the FME package
(default is a Levenberg-Marquardt variant). Please note that no warranty is
implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke
DESCRIPTION | 8
MD5 | 41 +-
NEWS |only
R/endpoints.R | 28 +-
R/mkinfit.R | 202 +++++++++-----
R/mkinmod.R | 69 ++--
R/transform_odeparms.R | 121 +++++---
README.md | 22 +
TODO | 4
inst/doc/FOCUS_L.R | 5
inst/doc/FOCUS_L.Rmd | 5
inst/doc/FOCUS_L.html | 572 ++++++++++++++++++++++-------------------
inst/doc/FOCUS_Z.R | 27 -
inst/doc/FOCUS_Z.Rnw | 42 +--
inst/doc/FOCUS_Z.pdf |binary
inst/doc/mkin.pdf |binary
inst/unitTests/runit.mkinfit.R | 63 +---
man/mkinfit.Rd | 13
man/mkinparplot.Rd | 5
man/transform_odeparms.Rd | 50 ++-
vignettes/FOCUS_L.Rmd | 5
vignettes/FOCUS_Z.Rnw | 42 +--
22 files changed, 755 insertions(+), 569 deletions(-)
Title: Meta-Analysis with R
Diff between meta versions 3.6-0 dated 2014-05-27 and 3.7-0 dated 2014-07-11
Description: User-friendly general package providing standard methods for meta-analysis:
- fixed effect and random effects meta-analysis;
- several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble);
- statistical tests and trim-and-fill method to evaluate bias in meta-analysis;
- import data from RevMan 5;
- prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model;
- cumulative meta-analysis and leave-one-out meta-analysis;
- meta-regression (if R package metafor is installed).
Author: Guido Schwarzer [cre, aut]
Maintainer: Guido Schwarzer
DESCRIPTION | 8 +-
MD5 | 80 +++++++++++-----------
NAMESPACE | 3
NEWS | 71 +++++++++++++++++++
R/as.data.frame.meta.R | 10 ++
R/baujat.meta.R | 7 +
R/catmeth.R | 31 +++++++-
R/ciAgrestiCoull.R |only
R/ciSimpleAsymptotic.R |only
R/ciWilsonScore.R |only
R/estimate.missing.R |only
R/forest.meta.R | 138 +++++++++++++-------------------------
R/funnel.meta.R | 8 ++
R/labbe.metabin.R | 8 ++
R/meta-internal.R | 9 ++
R/metabin.R | 15 +++-
R/metacont.R | 36 +++++++---
R/metacor.R | 15 +++-
R/metacum.R | 89 ++++++++++++++----------
R/metagen.R | 18 +++--
R/metainc.R | 15 +++-
R/metainf.R | 92 ++++++++++++++-----------
R/metaprop.R | 96 ++++++++++++++++++++++++--
R/print.meta.R | 73 ++++++++++++++------
R/print.summary.meta.R | 10 ++
R/settings.meta.R | 42 +++++++++++
R/summary.meta.R | 132 ++++++++++++++++--------------------
R/trimfill.default.R | 37 ----------
R/trimfill.meta.R | 44 ++----------
R/update.meta.R | 175 ++++++++++++++++++++++++++++++++++++++++++++++---
man/metabin.Rd | 9 +-
man/metacont.Rd | 29 +++++++-
man/metacor.Rd | 9 +-
man/metacum.Rd | 3
man/metagen.Rd | 9 +-
man/metainc.Rd | 9 +-
man/metainf.Rd | 3
man/metaprop.Rd | 138 ++++++++++++++++++++++++++++++--------
man/print.meta.Rd | 17 ++--
man/print.rm5.Rd | 10 +-
man/read.rm5.Rd | 6 -
man/trimfill.Rd | 4 +
man/update.meta.Rd | 46 ++++++++++--
43 files changed, 1057 insertions(+), 497 deletions(-)
Title: TeX to HTML/MathML Translators tth/ttm
Diff between tth versions 4.3-1 dated 2013-06-10 and 4.3-2 dated 2014-07-11
Description: C source code and R wrappers for the tth/ttm TeX to
HTML/MathML translators.
Author: Ian H. Hutchinson [aut] (author of tth/ttm C sources),
Friedrich Leisch [aut, cre] (author of R wrappers to tth/ttm),
Achim Zeileis [aut] (author of R wrappers to tth/ttm)
Maintainer: Friedrich Leisch
tth-4.3-1/tth/Rplots.pdf |only
tth-4.3-2/tth/DESCRIPTION | 9 ++++++---
tth-4.3-2/tth/MD5 |only
tth-4.3-2/tth/NEWS | 9 +++++++++
tth-4.3-2/tth/R/bycodes.R |only
tth-4.3-2/tth/R/tex2html.R | 12 ++++++++----
tth-4.3-2/tth/man/tth.Rd | 34 ++++++++++++++++++++++++++++++----
7 files changed, 53 insertions(+), 11 deletions(-)
Title: Robust Linear Mixed Effects Models
Diff between robustlmm versions 1.5 dated 2014-06-13 and 1.6 dated 2014-07-11
Description: Robust mixed effects modeling by robustification
of scoring equations using the Design Adaptive Scale approach.
Author: Manuel Koller
Maintainer: Manuel Koller
DESCRIPTION | 8 +-
MD5 | 42 +++++------
R/DAS-scale.R | 41 +++-------
R/helpers.R | 10 ++
R/rlmer.R | 29 ++-----
inst/doc/rlmer.pdf |binary
man/rlmer.Rd | 2
vignettes/cache/6b459128b6f80b01986ff6c4115e7dfb52f962fb |binary
vignettes/cache/e514dc7b17af4b19dcabad5cf474029c569fca86 |binary
vignettes/figs/fig-ex-penicillin-qq-ranef.pdf |binary
vignettes/figs/fig-ex-penicillin-qq-resid.pdf |binary
vignettes/figs/fig-ex-penicillin-raw.pdf |binary
vignettes/figs/fig-ex-penicillin-robustness-weights.pdf |binary
vignettes/figs/fig-ex-penicillin-ta.pdf |binary
vignettes/figs/fig-ex-sleepstudy-ex-comparsion-subsample.pdf |binary
vignettes/figs/fig-ex-sleepstudy-ex-comparsion.pdf |binary
vignettes/figs/fig-ex-sleepstudy-qq-ranef.pdf |binary
vignettes/figs/fig-ex-sleepstudy-qq-resid.pdf |binary
vignettes/figs/fig-ex-sleepstudy-ranef-scatterplot.pdf |binary
vignettes/figs/fig-ex-sleepstudy-raw.pdf |binary
vignettes/figs/fig-ex-sleepstudy-ta.pdf |binary
vignettes/figs/fig-ex-smoothedHuber.pdf |binary
22 files changed, 60 insertions(+), 72 deletions(-)
Title: Miscellaneous Tools Set
Diff between miscset versions 0.2 dated 2014-06-12 and 0.3.1 dated 2014-07-11
Description: A set of miscellaneous R tools to simplify the work with several
data types and formats.
Author: Sven E. Templer
Maintainer: Sven E. Templer
DESCRIPTION | 12 ++++++------
INDEX |only
MD5 | 25 +++++++++++++------------
NAMESPACE | 1 +
NEWS | 21 ++++++++++++++++++++-
R/gapply.R | 18 ++++++++++++++++--
R/lsall.R | 2 +-
R/mgrepl.R | 18 +++++++++---------
inst/doc/miscset.Rnw | 6 +++++-
inst/doc/miscset.pdf |binary
man/gapply.Rd | 7 ++++++-
man/mgrepl.Rd | 18 +++++++++---------
vignettes/figure/fig1.pdf |binary
vignettes/miscset.Rnw | 6 +++++-
14 files changed, 91 insertions(+), 43 deletions(-)
Title: Studying the statistical relationship between species and groups
of sites
Diff between indicspecies versions 1.7.1 dated 2013-12-29 and 1.7.2 dated 2014-07-11
Description: This package provides a set of functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites. It is also possible to check the statistical significance of such associations.
Author: Miquel De Caceres, Florian Jansen
Maintainer: Miquel De Caceres
indicspecies-1.7.1/indicspecies/vignettes/indicspeciesTutorial.synctex.gz |only
indicspecies-1.7.2/indicspecies/DESCRIPTION | 9 +
indicspecies-1.7.2/indicspecies/MD5 | 46 ++++++++--
indicspecies-1.7.2/indicspecies/NAMESPACE | 2
indicspecies-1.7.2/indicspecies/R/nichearea.R |only
indicspecies-1.7.2/indicspecies/R/nichecentroid.R |only
indicspecies-1.7.2/indicspecies/R/nichedispl.R |only
indicspecies-1.7.2/indicspecies/R/nicheoverlap.R |only
indicspecies-1.7.2/indicspecies/R/nichepref.R |only
indicspecies-1.7.2/indicspecies/R/nichevar.R |only
indicspecies-1.7.2/indicspecies/R/plotniche.R |only
indicspecies-1.7.2/indicspecies/R/pruneindicators.r | 4
indicspecies-1.7.2/indicspecies/build/vignette.rds |binary
indicspecies-1.7.2/indicspecies/data/birds.rda |only
indicspecies-1.7.2/indicspecies/data/pigeons.rda |only
indicspecies-1.7.2/indicspecies/inst/doc/PigeonExample.R |only
indicspecies-1.7.2/indicspecies/inst/doc/PigeonExample.Rnw |only
indicspecies-1.7.2/indicspecies/inst/doc/PigeonExample.pdf |only
indicspecies-1.7.2/indicspecies/man/birds.Rd |only
indicspecies-1.7.2/indicspecies/man/indicspecies-package.Rd | 9 +
indicspecies-1.7.2/indicspecies/man/nicheoverlap.Rd |only
indicspecies-1.7.2/indicspecies/man/nichevar.Rd |only
indicspecies-1.7.2/indicspecies/man/pigeons.Rd |only
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indicspecies-1.7.2/indicspecies/man/pruneindicators.Rd | 8 -
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample-004.pdf |only
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample-005.pdf |only
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indicspecies-1.7.2/indicspecies/vignettes/PigeonExample-017.pdf |only
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample-018.pdf |only
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample-019.pdf |only
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample.Rnw |only
indicspecies-1.7.2/indicspecies/vignettes/PigeonExample.synctex.gz |only
indicspecies-1.7.2/indicspecies/vignettes/Rplots.pdf |only
indicspecies-1.7.2/indicspecies/vignettes/resniche.bib |only
41 files changed, 58 insertions(+), 20 deletions(-)
Title: Graph estimation based on birth-death MCMC approach
Diff between BDgraph versions 2.9 dated 2014-07-02 and 2.10 dated 2014-07-11
Description: This package provides a Bayesian methodology for structure learning in undirected graphical models. Our Bayesian methodology is based on birth-death Markov chain Monte Carlo (BDMCMC) algorithm which is the main function with the name 'bdgraph'. The main target of this package is high-dimensional data analysis wherein usually p >> n. The computation is memory-optimized using the sparse matrix output.
Author: Abdolreza Mohammadi and Ernst Wit
Maintainer: Abdolreza Mohammadi
BDgraph-2.10/BDgraph/DESCRIPTION | 9 +-
BDgraph-2.10/BDgraph/MD5 | 44 ++++++-------
BDgraph-2.10/BDgraph/NAMESPACE | 2
BDgraph-2.10/BDgraph/R/BDgraph.R | 94 ++++++++++++----------------
BDgraph-2.10/BDgraph/man/BDgraph-package.Rd | 5 -
BDgraph-2.10/BDgraph/man/I.g.Rd | 4 -
BDgraph-2.10/BDgraph/man/bdgraph.Rd | 8 --
BDgraph-2.10/BDgraph/man/bdgraph.npn.Rd | 4 -
BDgraph-2.10/BDgraph/man/bdgraph.sim.Rd | 4 -
BDgraph-2.10/BDgraph/man/compare.Rd | 7 +-
BDgraph-2.10/BDgraph/man/phat.Rd | 6 -
BDgraph-2.10/BDgraph/man/plot.bdgraph.Rd | 6 -
BDgraph-2.10/BDgraph/man/plot.simulate.Rd | 4 -
BDgraph-2.10/BDgraph/man/plotcoda.Rd | 6 -
BDgraph-2.10/BDgraph/man/print.bdgraph.Rd | 6 -
BDgraph-2.10/BDgraph/man/print.simulate.Rd | 4 -
BDgraph-2.10/BDgraph/man/prob.Rd | 6 -
BDgraph-2.10/BDgraph/man/rgwish.Rd | 6 -
BDgraph-2.10/BDgraph/man/select.Rd | 6 -
BDgraph-2.10/BDgraph/man/summary.bdgraph.Rd | 6 -
BDgraph-2.10/BDgraph/man/traceplot.Rd | 6 -
BDgraph-2.10/BDgraph/src/Makevars |only
BDgraph-2.10/BDgraph/src/Makevars.win |only
BDgraph-2.10/BDgraph/src/bdmcmc.cpp |only
BDgraph-2.9/BDgraph/src/BDgraph.cpp |only
25 files changed, 120 insertions(+), 123 deletions(-)
Title: Extended Probability Distribution Functions
Diff between ExtDist versions 0.3 dated 2014-05-17 and 0.3.3 dated 2014-07-11
Description: The package provides a consistent, unified and extensible
framework for parameter estimation of probability distributions; it extends
parameter estimation procedures to allow for weighted samples; moreover, it
extends the gallery of available distributions.
Author: Haizhen Wu
Maintainer: Haizhen Wu
DESCRIPTION | 18 ++--
MD5 | 47 +++++++-----
NAMESPACE | 8 --
R/Beta.R | 81 +++++----------------
R/Beta.ab.R | 98 ++++++--------------------
R/Laplace.R | 34 +++++----
R/Normal.R | 83 +++++-----------------
R/compareDist.R | 28 +++----
R/eDist.R | 38 ++++++----
R/eval.estimation.R | 5 -
R/wmle.R | 183 +++++++++++++++++++++++++++++++++++--------------
build |only
inst |only
man/Beta.Rd | 51 +------------
man/Beta.ab.Rd | 37 +--------
man/ExtDist-package.Rd |only
man/Laplace.Rd | 13 +--
man/Normal.Rd | 51 +------------
man/compareDist.Rd | 3
man/eDist.Rd | 3
man/eval.estimation.Rd | 2
man/wmle.Rd | 2
vignettes |only
23 files changed, 328 insertions(+), 457 deletions(-)
Title: A toolset for working with lists
Diff between rlist versions 0.2.1 dated 2014-07-04 and 0.2.2 dated 2014-07-11
Description: A toolset for working with lists as dataset,
including filtering, mapping, grouping, sorting, updating, and
many other functions, which allow functional programming
style applied in list operations.
Author: Kun Ren
Maintainer: Kun Ren
rlist-0.2.1/rlist/inst/doc/filtering.R |only
rlist-0.2.1/rlist/inst/doc/filtering.html |only
rlist-0.2.1/rlist/inst/doc/grouping.R |only
rlist-0.2.1/rlist/inst/doc/grouping.html |only
rlist-0.2.1/rlist/inst/doc/introduction.R |only
rlist-0.2.1/rlist/inst/doc/introduction.html |only
rlist-0.2.1/rlist/inst/doc/io.R |only
rlist-0.2.1/rlist/inst/doc/io.html |only
rlist-0.2.1/rlist/inst/doc/joining.R |only
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rlist-0.2.1/rlist/inst/doc/lambda.R |only
rlist-0.2.1/rlist/inst/doc/lambda.html |only
rlist-0.2.1/rlist/inst/doc/mapping.R |only
rlist-0.2.1/rlist/inst/doc/mapping.html |only
rlist-0.2.1/rlist/inst/doc/sorting.R |only
rlist-0.2.1/rlist/inst/doc/sorting.html |only
rlist-0.2.1/rlist/inst/doc/updating.R |only
rlist-0.2.1/rlist/inst/doc/updating.html |only
rlist-0.2.2/rlist/DESCRIPTION | 10
rlist-0.2.2/rlist/MD5 | 204 ++++++++++----------
rlist-0.2.2/rlist/NAMESPACE | 4
rlist-0.2.2/rlist/NEWS | 15 +
rlist-0.2.2/rlist/R/functions.R | 39 ++-
rlist-0.2.2/rlist/R/internal.R | 78 ++-----
rlist-0.2.2/rlist/R/list.all.R | 5
rlist-0.2.2/rlist/R/list.any.R | 5
rlist-0.2.2/rlist/R/list.append.R | 8
rlist-0.2.2/rlist/R/list.cases.R | 21 +-
rlist-0.2.2/rlist/R/list.cbind.R | 7
rlist-0.2.2/rlist/R/list.class.R | 12 -
rlist-0.2.2/rlist/R/list.clean.R | 6
rlist-0.2.2/rlist/R/list.count.R | 5
rlist-0.2.2/rlist/R/list.do.R | 4
rlist-0.2.2/rlist/R/list.exclude.R | 5
rlist-0.2.2/rlist/R/list.filter.R | 5
rlist-0.2.2/rlist/R/list.find.R | 5
rlist-0.2.2/rlist/R/list.findi.R | 5
rlist-0.2.2/rlist/R/list.group.R | 13 -
rlist-0.2.2/rlist/R/list.if.R | 7
rlist-0.2.2/rlist/R/list.insert.R | 10
rlist-0.2.2/rlist/R/list.iter.R | 5
rlist-0.2.2/rlist/R/list.join.R | 4
rlist-0.2.2/rlist/R/list.map.R | 8
rlist-0.2.2/rlist/R/list.maps.R |only
rlist-0.2.2/rlist/R/list.merge.R | 2
rlist-0.2.2/rlist/R/list.order.R | 8
rlist-0.2.2/rlist/R/list.prepend.R | 8
rlist-0.2.2/rlist/R/list.remove.R | 2
rlist-0.2.2/rlist/R/list.sample.R | 18 -
rlist-0.2.2/rlist/R/list.select.R | 14 -
rlist-0.2.2/rlist/R/list.skip.R | 2
rlist-0.2.2/rlist/R/list.skipWhile.R | 10
rlist-0.2.2/rlist/R/list.sort.R | 5
rlist-0.2.2/rlist/R/list.stack.R |only
rlist-0.2.2/rlist/R/list.table.R |only
rlist-0.2.2/rlist/R/list.take.R | 2
rlist-0.2.2/rlist/R/list.takeWhile.R | 10
rlist-0.2.2/rlist/R/list.ungroup.R | 3
rlist-0.2.2/rlist/R/list.update.R | 10
rlist-0.2.2/rlist/R/list.which.R | 5
rlist-0.2.2/rlist/R/list.zip.R |only
rlist-0.2.2/rlist/R/subset.list.R | 30 --
rlist-0.2.2/rlist/README.md | 29 +-
rlist-0.2.2/rlist/build/vignette.rds |binary
rlist-0.2.2/rlist/inst/doc/Examples.R |only
rlist-0.2.2/rlist/inst/doc/Examples.html |only
rlist-0.2.2/rlist/inst/doc/Filtering.R |only
rlist-0.2.2/rlist/inst/doc/Filtering.html |only
rlist-0.2.2/rlist/inst/doc/Grouping.R |only
rlist-0.2.2/rlist/inst/doc/Grouping.html |only
rlist-0.2.2/rlist/inst/doc/IO.R |only
rlist-0.2.2/rlist/inst/doc/IO.html |only
rlist-0.2.2/rlist/inst/doc/Introduction.R |only
rlist-0.2.2/rlist/inst/doc/Introduction.html |only
rlist-0.2.2/rlist/inst/doc/Joining.R |only
rlist-0.2.2/rlist/inst/doc/Joining.html |only
rlist-0.2.2/rlist/inst/doc/Lambda.R |only
rlist-0.2.2/rlist/inst/doc/Lambda.html |only
rlist-0.2.2/rlist/inst/doc/Mapping.R |only
rlist-0.2.2/rlist/inst/doc/Mapping.html |only
rlist-0.2.2/rlist/inst/doc/Sorting.R |only
rlist-0.2.2/rlist/inst/doc/Sorting.html |only
rlist-0.2.2/rlist/inst/doc/Updating.R |only
rlist-0.2.2/rlist/inst/doc/Updating.html |only
rlist-0.2.2/rlist/man/list.all.Rd | 2
rlist-0.2.2/rlist/man/list.any.Rd | 2
rlist-0.2.2/rlist/man/list.append.Rd | 2
rlist-0.2.2/rlist/man/list.cases.Rd | 13 -
rlist-0.2.2/rlist/man/list.cbind.Rd | 9
rlist-0.2.2/rlist/man/list.class.Rd | 8
rlist-0.2.2/rlist/man/list.clean.Rd | 5
rlist-0.2.2/rlist/man/list.count.Rd | 2
rlist-0.2.2/rlist/man/list.do.Rd | 4
rlist-0.2.2/rlist/man/list.exclude.Rd | 2
rlist-0.2.2/rlist/man/list.filter.Rd | 2
rlist-0.2.2/rlist/man/list.find.Rd | 2
rlist-0.2.2/rlist/man/list.findi.Rd | 2
rlist-0.2.2/rlist/man/list.group.Rd | 6
rlist-0.2.2/rlist/man/list.if.Rd | 4
rlist-0.2.2/rlist/man/list.insert.Rd | 2
rlist-0.2.2/rlist/man/list.iter.Rd | 2
rlist-0.2.2/rlist/man/list.join.Rd | 4
rlist-0.2.2/rlist/man/list.map.Rd | 2
rlist-0.2.2/rlist/man/list.maps.Rd |only
rlist-0.2.2/rlist/man/list.merge.Rd | 2
rlist-0.2.2/rlist/man/list.order.Rd | 2
rlist-0.2.2/rlist/man/list.prepend.Rd | 2
rlist-0.2.2/rlist/man/list.remove.Rd | 2
rlist-0.2.2/rlist/man/list.sample.Rd | 15 -
rlist-0.2.2/rlist/man/list.select.Rd | 2
rlist-0.2.2/rlist/man/list.skip.Rd | 2
rlist-0.2.2/rlist/man/list.skipWhile.Rd | 2
rlist-0.2.2/rlist/man/list.sort.Rd | 2
rlist-0.2.2/rlist/man/list.stack.Rd |only
rlist-0.2.2/rlist/man/list.table.Rd |only
rlist-0.2.2/rlist/man/list.take.Rd | 2
rlist-0.2.2/rlist/man/list.takeWhile.Rd | 2
rlist-0.2.2/rlist/man/list.ungroup.Rd | 3
rlist-0.2.2/rlist/man/list.update.Rd | 2
rlist-0.2.2/rlist/man/list.which.Rd | 2
rlist-0.2.2/rlist/man/list.zip.Rd |only
rlist-0.2.2/rlist/man/subset.list.Rd | 5
rlist-0.2.2/rlist/tests/testthat/test-basic.R | 23 ++
rlist-0.2.2/rlist/tests/testthat/test-list.map.R | 6
rlist-0.2.2/rlist/tests/testthat/test-list.select.R | 13 -
rlist-0.2.2/rlist/tests/testthat/test-list.update.R | 12 -
126 files changed, 424 insertions(+), 400 deletions(-)
Title: Multiresolution Kriging based on Markov random fields
Diff between LatticeKrig versions 3.1 dated 2014-01-24 and 3.3 dated 2014-07-11
Description: Functions for the interpolation of large spatial
datasets. This package follows a "fixed rank Kriging" approach using
a large number of basis functions and provides spatial estimates
that are comparable to standard families of covariance functions.
Using a large number of basis functions allows for estimates that
can come close to interpolating the observations (a spatial model
with a small nugget variance.) The covariance model for this method
can approximate the Matern covariance family but also allows for a
multi-resolution model and supports efficient computation of the
profile likelihood for estimating covariance parameters. This is
accomplished through compactly supported basis functions and a
Markov random field model for the basis coefficients. These features
lead to sparse matrices for the computations. One benefit of this
approach is the facilty to do unconditional and conditional
simulation of the field for large numbers of arbitrary points. There
is also the flexibility for estimating nonstationary covariances. Included are
generic methods for prediction, standard errors for prediction,
plotting of the estimated surface and conditional and unconditional
simulation.
Author: Douglas Nychka [aut, cre], Dorit Hammerling [aut], Stephan Sain [aut], Nathan Lenssen [aut]
Maintainer: Douglas Nychka
LatticeKrig-3.1/LatticeKrig/R/LKrig.fixed.component.R |only
LatticeKrig-3.1/LatticeKrig/R/predictSurfaceLKrig.R |only
LatticeKrig-3.3/LatticeKrig/DESCRIPTION | 13 -
LatticeKrig-3.3/LatticeKrig/MD5 | 81 +++---
LatticeKrig-3.3/LatticeKrig/R/LKinfoUpdate.R | 14 -
LatticeKrig-3.3/LatticeKrig/R/LKrig.MLE.R | 58 +++-
LatticeKrig-3.3/LatticeKrig/R/LKrig.R | 108 ++++++---
LatticeKrig-3.3/LatticeKrig/R/LKrig.basis.R | 74 ++----
LatticeKrig-3.3/LatticeKrig/R/LKrig.coef.R | 50 ++--
LatticeKrig-3.3/LatticeKrig/R/LKrig.make.alpha.R | 2
LatticeKrig-3.3/LatticeKrig/R/LKrig.make.par.grid.R | 20 +
LatticeKrig-3.3/LatticeKrig/R/LKrig.misc.R | 45 +++
LatticeKrig-3.3/LatticeKrig/R/LKrig.normalize.basis.R | 46 +++
LatticeKrig-3.3/LatticeKrig/R/LKrig.sim.conditional.R | 77 ++++--
LatticeKrig-3.3/LatticeKrig/R/LKrig.traceA.R | 7
LatticeKrig-3.3/LatticeKrig/R/LKrigDefaultFixedFunction.R |only
LatticeKrig-3.3/LatticeKrig/R/LKrigFindLambda.R | 14 -
LatticeKrig-3.3/LatticeKrig/R/LKrigUnrollGrid.R |only
LatticeKrig-3.3/LatticeKrig/R/LatticeKrig.R | 27 +-
LatticeKrig-3.3/LatticeKrig/R/predict.LKrig.R | 45 +--
LatticeKrig-3.3/LatticeKrig/R/predictLKrigFixedFunction.R |only
LatticeKrig-3.3/LatticeKrig/R/predictSE.LKrig.R | 50 +---
LatticeKrig-3.3/LatticeKrig/R/predictSurface.LKrig.R |only
LatticeKrig-3.3/LatticeKrig/R/print.LKinfo.R | 62 +----
LatticeKrig-3.3/LatticeKrig/R/print.LKrig.R | 41 ++-
LatticeKrig-3.3/LatticeKrig/man/LKrig.MLE.Rd | 29 ++
LatticeKrig-3.3/LatticeKrig/man/LKrig.Rd | 64 ++++-
LatticeKrig-3.3/LatticeKrig/man/LKrig.basis.Rd | 39 +--
LatticeKrig-3.3/LatticeKrig/man/LKrig.fixed.Rd | 49 ++--
LatticeKrig-3.3/LatticeKrig/man/LKrig.internal.Rd | 29 ++
LatticeKrig-3.3/LatticeKrig/man/LKrig.misc.Rd | 70 +++++
LatticeKrig-3.3/LatticeKrig/man/LKrig.sim.Rd | 29 ++
LatticeKrig-3.3/LatticeKrig/man/LatticeKrig.Rd | 117 ++++++----
LatticeKrig-3.3/LatticeKrig/tests/LKrig.FindNorm.test.R | 2
LatticeKrig-3.3/LatticeKrig/tests/LKrig.basis.test.R | 2
LatticeKrig-3.3/LatticeKrig/tests/LKrig.basis.test.Rout.save | 10
LatticeKrig-3.3/LatticeKrig/tests/LKrig.lnPLike.test.R | 2
LatticeKrig-3.3/LatticeKrig/tests/LKrig.lnPlike.test.Rout.save | 10
LatticeKrig-3.3/LatticeKrig/tests/LKrig.nullspace.test.R |only
LatticeKrig-3.3/LatticeKrig/tests/LKrig.precision.test.R | 2
LatticeKrig-3.3/LatticeKrig/tests/LKrig.precision.test.Rout.save | 10
LatticeKrig-3.3/LatticeKrig/tests/LKrig.se.test.R | 20 -
LatticeKrig-3.3/LatticeKrig/tests/LKrig.se.test.Rout.save | 88 ++++++-
LatticeKrig-3.3/LatticeKrig/tests/LKrig.test.R | 2
LatticeKrig-3.3/LatticeKrig/tests/LKrig.test.Rout.save | 10
45 files changed, 942 insertions(+), 476 deletions(-)
Title: Analysis of binary character evolution
Diff between corHMM versions 1.13 dated 2014-02-20 and 1.14 dated 2014-07-11
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 8 +++----
MD5 | 12 +++++-----
R/ancRECON.R | 59 +++++++++++++++++++++++++++--------------------------
R/corDISC.R | 15 ++++++++-----
R/corHMM.R | 35 +++++++++++++++++++++++++------
R/rate.mat.maker.R | 4 +++
R/rayDISC.R | 8 +++++--
7 files changed, 89 insertions(+), 52 deletions(-)