Title: Independent Surrogate Variable Analysis
Diff between isva versions 1.3 dated 2011-09-07 and 1.5 dated 2012-09-24
Description: Independent Surrogate Variable Analysis is an algorithm
for feature selection in the presence of potential confounding
factors.
Author: Andrew E Teschendorff
Maintainer:
DESCRIPTION | 8 ++++----
MD5 | 15 ++++++++-------
NAMESPACE |only
R/EstDimRMT.R | 17 ++++++++++++-----
R/isvaFn.R | 3 ++-
data/simdataISVA.RData |binary
man/DoISVA.Rd | 4 ++--
man/isva-package.Rd | 9 +++------
man/simdataISVA.Rd | 6 +++---
9 files changed, 34 insertions(+), 28 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 1.3 dated 2012-09-14 and 1.4 dated 2012-09-24
Description: DDD implements maximum likelihood methods based on the
diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent. See Etienne
et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
10.1098/rspb.2011.1439. DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence. See Etienne & Haegeman
2012, Am. Nat. In press, doi: 10.1086/667574.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DDD-1.3/DDD/DDD-Ex.pdf |only
DDD-1.4/DDD/DDD-Ex.timings |only
DDD-1.4/DDD/DDD-manual.pdf |binary
DDD-1.4/DDD/DESCRIPTION | 8 ++++----
DDD-1.4/DDD/MD5 | 26 +++++++++++++-------------
DDD-1.4/DDD/R/dd_KI_ML.R | 2 +-
DDD-1.4/DDD/R/dd_KI_loglik.R | 2 +-
DDD-1.4/DDD/R/dd_ML.R | 2 +-
DDD-1.4/DDD/R/dd_SR_ML.R | 2 +-
DDD-1.4/DDD/R/dd_SR_loglik.R | 2 +-
DDD-1.4/DDD/R/dd_loglik.R | 2 +-
DDD-1.4/DDD/man/DDD-package.Rd | 24 +++++++++++++-----------
DDD-1.4/DDD/man/dd_KI_ML.Rd | 2 +-
DDD-1.4/DDD/man/dd_ML.Rd | 10 +++++-----
DDD-1.4/DDD/man/dd_SR_ML.Rd | 8 ++++----
15 files changed, 46 insertions(+), 44 deletions(-)
Title: Analysis and visualisation of ecological communities
Diff between cheddar versions 0.1-614 dated 2012-07-23 and 0.1-616 dated 2012-09-24
Description: Cheddar provides a flexible, extendable representation of
an ecological community and a range of functions for analysis
and visualisation, focusing on food web, body mass and
numerical abundance data. It also allows inter-web comparisons
such as examining changes in community structure over
environmental, temporal or spatial gradients.
Author: Lawrence Hudson with contributions from Dan Reuman and Rob
Emerson
Maintainer: Lawrence Hudson
DESCRIPTION | 12 +-
MD5 | 106 ++++++++++----------
R/community.R | 35 ++++--
R/community_MN.R | 16 +--
R/community_collection.R | 2
R/community_trophic_links.R | 2
R/graph_nodes.R | 29 +++--
R/graph_util.R | 62 +++++------
R/util.R | 93 ++++++++++-------
data/Benguela.RData |binary
data/BroadstoneStream.RData |binary
data/Millstream.RData |binary
data/SkipwithPond.RData |binary
data/TL84.RData |binary
data/TL86.RData |binary
data/YthanEstuary.RData |binary
inst/doc/CheddarQuickstart.Rnw | 4
inst/doc/CheddarQuickstart.pdf |binary
inst/doc/Collections.Rnw | 63 +++++++++---
inst/doc/Collections.pdf |binary
inst/doc/Community.Rnw | 75 +++++++++++++-
inst/doc/Community.pdf |binary
inst/doc/ImportExport.Rnw | 88 +++++++++++++++-
inst/doc/ImportExport.pdf |binary
inst/doc/PlotsAndStats.Rnw | 160 ++++++++++++++++++++++++++----
inst/doc/PlotsAndStats.pdf |binary
inst/doc/cheddar.bib | 182 ++++++++++++++++++++++++-----------
man/ApplyByClass.Rd | 24 +++-
man/Benguela.Rd | 1
man/BroadstoneStream.Rd | 5
man/CollectionCPS.Rd | 9 +
man/CommunityCollection.Rd | 4
man/Degree.Rd | 2
man/Intervality.Rd | 7 +
man/LinearRegressionByClass.Rd | 5
man/LoadCommunity.Rd | 6 -
man/LumpTrophicSpecies.Rd | 8 -
man/Millstream.Rd | 16 +--
man/NvMLinearRegressions.Rd | 11 +-
man/OrderCommunity.Rd | 2
man/PlotHelpers.Rd | 12 +-
man/PlotNPS.Rd | 20 +++
man/PlotRankNPS.Rd | 7 +
man/SkipwithPond.Rd | 5
man/TL84.Rd | 25 ++++
man/TrophicSpecies.Rd | 8 -
man/YthanEstuary.Rd | 35 ++++++
man/cheddar-package.Rd | 4
man/pHWebs.Rd | 1
tests/community_MN_test.R | 74 ++++++++++----
tests/community_test.R | 2
tests/community_trophic_links_test.R | 2
tests/run_all.R | 24 +---
tests/util_test.R | 42 ++++++++
54 files changed, 935 insertions(+), 355 deletions(-)
Title: Rmetrics - Chronological and Calendarical Objects
Diff between timeDate versions 2160.95 dated 2012-03-20 and 2160.96 dated 2012-09-24
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz, Yohan Chalabi and Martin Maechler with
contributions from Joe W. Byers, and others
Maintainer: Yohan Chalabi
ChangeLog | 77 ++++++++++++++++++++++
DESCRIPTION | 14 ++--
MD5 | 11 +--
NAMESPACE | 17 ++--
R/base-weekdays.R | 158 +++++++++++++++++++++-------------------------
R/calendar-endpoints.R | 45 +++++++------
man/calendar-endpoints.Rd |only
7 files changed, 198 insertions(+), 124 deletions(-)
Title: Bayesian variable selection and model choice for generalized
additive mixed models
Diff between spikeSlabGAM versions 1.1-2 dated 2012-09-17 and 1.1-3 dated 2012-09-24
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression
models via SSVS with spike-and-slab priors.
Author: Fabian Scheipl
Maintainer: Fabian Scheipl
DESCRIPTION | 10 +++++-----
MD5 | 5 +++--
inst/doc/UsingSpikeSlabGAM.pdf |binary
vignettes/UsingSpikeSlabGAM.pdf |only
4 files changed, 8 insertions(+), 7 deletions(-)
Title: Rmetrics - Assets Selection and Modelling
Diff between fAssets versions 2100.78 dated 2009-09-28 and 2110.79 dated 2012-09-24
Description: Environment for teaching "Financial Engineering and
Computational Finance"
Author: Diethelm Wuertz and many others, see the SOURCE file
Maintainer: Yohan Chalabi
fAssets-2100.78/fAssets/R/assetsArrange.R |only
fAssets-2100.78/fAssets/R/assetsFit.R |only
fAssets-2100.78/fAssets/R/assetsLPM.R |only
fAssets-2100.78/fAssets/R/assetsMeanCov.R |only
fAssets-2100.78/fAssets/R/assetsOutliers.R |only
fAssets-2100.78/fAssets/R/assetsPfolio.R |only
fAssets-2100.78/fAssets/R/assetsSelect.R |only
fAssets-2100.78/fAssets/R/assetsSim.R |only
fAssets-2100.78/fAssets/R/assetsTest.R |only
fAssets-2100.78/fAssets/inst/DocCopying.pdf |only
fAssets-2110.79/fAssets/ChangeLog | 215 +++++++--
fAssets-2110.79/fAssets/DESCRIPTION | 13
fAssets-2110.79/fAssets/MD5 |only
fAssets-2110.79/fAssets/NAMESPACE | 128 +++--
fAssets-2110.79/fAssets/R/assets-arrange.R |only
fAssets-2110.79/fAssets/R/assets-fit.R |only
fAssets-2110.79/fAssets/R/assets-lpm.R |only
fAssets-2110.79/fAssets/R/assets-mcr.R |only
fAssets-2110.79/fAssets/R/assets-meancov.R |only
fAssets-2110.79/fAssets/R/assets-outliers.R |only
fAssets-2110.79/fAssets/R/assets-portfolio.R |only
fAssets-2110.79/fAssets/R/assets-select.R |only
fAssets-2110.79/fAssets/R/assets-simulate.R |only
fAssets-2110.79/fAssets/R/assets-test.R |only
fAssets-2110.79/fAssets/R/builtin-ecodist.R |only
fAssets-2110.79/fAssets/R/plot-pairs.R | 599 +++++++++++++--------------
fAssets-2110.79/fAssets/R/stats-distance.R |only
fAssets-2110.79/fAssets/R/zzz.Deprecated.R | 171 ++++---
fAssets-2110.79/fAssets/R/zzz.R | 91 +---
fAssets-2110.79/fAssets/man/assetsMCR.Rd |only
fAssets-2110.79/fAssets/src/Makevars |only
fAssets-2110.79/fAssets/src/ecodist.c |only
32 files changed, 678 insertions(+), 539 deletions(-)
Title: Tweedie exponential family models
Diff between tweedie versions 2.1.2 dated 2012-09-13 and 2.1.3 dated 2012-09-24
Description: Maximum likelihood computations for Tweedie families.
Author: Peter K Dunn
Maintainer: Peter K Dunn
CHANGE.log | 6 +++++-
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/tweedie.R | 4 ++--
man/tweedie-package.Rd | 20 ++++++++++----------
5 files changed, 26 insertions(+), 22 deletions(-)
Title: Extension to ggplot2.
Diff between GGally versions 0.4.1 dated 2012-09-21 and 0.4.2 dated 2012-09-24
Description: Package contains templates for different plots to be
combined into a plot matrix, as well as a parallel coordinate
plot function.
Author: Barret Schloerke
Maintainer: Barret Schloerke
DESCRIPTION | 14 +++----
MD5 | 44 +++++++++++------------
NAMESPACE | 14 +++++++
R/gg-plots.r | 85 +++++++++++++++++++++++++--------------------
R/ggpairs.r | 24 +++++++-----
R/ggparcoord.R | 28 +++++++-------
man/addAndOverwriteAes.Rd | 13 +++---
man/getPlot.Rd | 5 +-
man/ggally_box.Rd | 7 ++-
man/ggally_cor.Rd | 7 ++-
man/ggally_density.Rd | 9 ++--
man/ggally_densityDiag.Rd | 7 +--
man/ggally_denstrip.Rd | 4 +-
man/ggally_diagAxis.Rd | 5 +-
man/ggally_dot.Rd | 9 ++--
man/ggally_dotAndBox.Rd | 5 +-
man/ggally_facetbar.Rd | 6 +--
man/ggally_facetdensity.Rd | 5 +-
man/ggally_facethist.Rd | 5 +-
man/ggally_smooth.Rd | 7 ++-
man/ggpairs.Rd | 3 +
man/ggparcoord.Rd | 1
man/print.ggpairs.Rd | 3 +
23 files changed, 179 insertions(+), 131 deletions(-)