Title: Taxonomic standardization of plant species names
Diff between Taxonstand versions 1.3 dated 2014-02-10 and 1.4 dated 2014-09-17
Description: Automated standardization of taxonomic names and removal of orthographic errors in plant species names using the The Plant List (TPL) website (www.theplantlist.org)
Author: Luis Cayuela and Jari Oksanen
Maintainer: Luis Cayuela
DESCRIPTION | 8
MD5 | 6
R/TPLck.R | 641 ++++++++++++++++++++++++++++++------------------------------
man/TPL.Rd | 11 -
4 files changed, 338 insertions(+), 328 deletions(-)
Title: Utilities for producing maps
Diff between mapmisc versions 0.9.4 dated 2014-04-09 and 1.0.0 dated 2014-09-17
Description: This package contains various utilities for producing nice looking maps in R.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 15 -
MD5 | 56 +++---
NAMESPACE | 2
R/colourScale.R | 27 ++
R/geonames.R | 22 +-
R/getTiles.R | 45 ++--
R/insetMap.R | 44 +++-
R/legendBreaks.R | 9
R/map.new.R | 8
R/openmap.R | 68 +++----
R/scaleBar.R | 21 +-
R/utils.R | 10 -
build/vignette.rds |binary
inst/doc/mapLayers.R | 5
inst/doc/mapLayers.pdf |binary
inst/doc/mapLayers.rnw | 1
inst/doc/mapmisc.R | 432 ++++++++++++++++++++++++++++++++++++++--------
inst/doc/mapmisc.pdf |binary
inst/doc/mapmisc.rnw | 434 ++++++++++++++++++++++++++++++++++++++++-------
inst/extdata/tiles.RData |binary
man/colourScale.Rd | 18 +
man/geonames.Rd | 11 -
man/netherlands.Rd | 54 +++--
man/openmap.Rd | 7
man/scaleBar.Rd | 5
tests/openmap.R | 8
vignettes/Makefile | 3
vignettes/mapLayers.rnw | 1
vignettes/mapmisc.rnw | 434 ++++++++++++++++++++++++++++++++++++++++-------
29 files changed, 1373 insertions(+), 367 deletions(-)
Title: Tools for working with Hansen et al. 2013 Global Forest Change
dataset
Diff between gfcanalysis versions 1.1 dated 2014-03-28 and 1.2 dated 2014-09-17
Description: The gfcanalysis package supports analyses using the Global
Forest Change dataset released by Hansen et al. 2013. gfcanalysis was
written by the Tropical Ecology Assessment and Monitoring (TEAM) Network
(http://www.teamnetwork.org). For additional details on the Global Forest
Change dataset, see: Hansen, M. et al. 2013. "High-Resolution Global Maps
of 21st-Century Forest Cover Change." Science 342 (15 November): 850-53.
Data available on-line from:
http://earthenginepartners.appspot.com/science-2013-global-forest
Author: Alex Zvoleff [aut, cre]
Maintainer: Alex Zvoleff
gfcanalysis-1.1/gfcanalysis/man/utm_zone-methods.Rd |only
gfcanalysis-1.2/gfcanalysis/DESCRIPTION | 8 -
gfcanalysis-1.2/gfcanalysis/MD5 | 45 +++---
gfcanalysis-1.2/gfcanalysis/NAMESPACE | 5
gfcanalysis-1.2/gfcanalysis/NEWS | 11 +
gfcanalysis-1.2/gfcanalysis/R/calc_gfc_tiles.R | 4
gfcanalysis-1.2/gfcanalysis/R/extract_gfc.R | 111 ++++++++++++++---
gfcanalysis-1.2/gfcanalysis/R/gfc_stats.R | 3
gfcanalysis-1.2/gfcanalysis/R/threshold_gfc.R | 10 -
gfcanalysis-1.2/gfcanalysis/R/utm_zone.R | 8 -
gfcanalysis-1.2/gfcanalysis/man/animate_annual.Rd | 55 +++-----
gfcanalysis-1.2/gfcanalysis/man/annual_stack.Rd | 31 ++--
gfcanalysis-1.2/gfcanalysis/man/calc_gfc_tiles.Rd | 15 +-
gfcanalysis-1.2/gfcanalysis/man/calc_pixel_areas.Rd | 8 -
gfcanalysis-1.2/gfcanalysis/man/download_tiles.Rd | 26 +--
gfcanalysis-1.2/gfcanalysis/man/extract_gfc.Rd | 43 +++---
gfcanalysis-1.2/gfcanalysis/man/gen_grid.Rd | 26 +--
gfcanalysis-1.2/gfcanalysis/man/gfc_stats.Rd | 53 +++-----
gfcanalysis-1.2/gfcanalysis/man/gfc_tiles.Rd | 8 -
gfcanalysis-1.2/gfcanalysis/man/plot_gfc.Rd | 26 +--
gfcanalysis-1.2/gfcanalysis/man/scale_by_pixel_area.Rd | 33 ++---
gfcanalysis-1.2/gfcanalysis/man/scale_toar.Rd |only
gfcanalysis-1.2/gfcanalysis/man/test_poly.Rd | 8 -
gfcanalysis-1.2/gfcanalysis/man/threshold_gfc.Rd | 103 +++++++++------
gfcanalysis-1.2/gfcanalysis/man/utm_zone.Rd |only
25 files changed, 371 insertions(+), 269 deletions(-)
Title: Tools for plotting skew-T diagrams and wind profiles
Diff between RadioSonde versions 1.3 dated 2010-09-20 and 1.4 dated 2014-09-17
Description: RadioSonde is a collection of programs for reading and
plotting SKEW-T,log p diagrams and wind profiles for data
collected by radiosondes (the typical weather balloon-borne
instrument), which we will call "flights", "sondes", or
"profiles" throughout the associated documentation. The raw
data files are in a common format that has a header followed by
specific variables. Use "help(ExampleSonde)" for the full
explanation of the data files.
Author: Doug Nychka, Eric Gilleland, Liangying Zhang, Tim Hoar
Maintainer: Doug Nychka
DESCRIPTION | 15 ++++++++-------
MD5 |only
NAMESPACE |only
man/getsonde.Rd | 2 +-
man/plotsonde.Rd | 2 +-
man/plotwind.Rd | 2 +-
man/skewt.axis.Rd | 2 +-
7 files changed, 12 insertions(+), 11 deletions(-)
Title: A Laboratory for Recursive Partytioning
Diff between party versions 1.0-16 dated 2014-08-19 and 1.0-17 dated 2014-09-17
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
DESCRIPTION | 10 +++++-----
MD5 | 14 +++++++-------
NAMESPACE | 1 +
R/zInitMethods.R | 3 +++
build/vignette.rds |binary
inst/NEWS | 6 ++++++
inst/doc/MOB.pdf |binary
inst/doc/party.pdf |binary
8 files changed, 22 insertions(+), 12 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.3-0 dated 2014-06-03 and 4.3-1 dated 2014-09-17
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.3-0/gamlss/R/lms-20-6-13.r |only
gamlss-4.3-1/gamlss/DESCRIPTION | 10
gamlss-4.3-1/gamlss/MD5 | 29 -
gamlss-4.3-1/gamlss/NAMESPACE | 20 -
gamlss-4.3-1/gamlss/R/centile-pred.R | 2
gamlss-4.3-1/gamlss/R/centilesFan.R | 259 +++++++--------
gamlss-4.3-1/gamlss/R/centilesPLOT.R | 543 ++++++++++++++++----------------
gamlss-4.3-1/gamlss/R/centilescom.R | 318 +++++++++---------
gamlss-4.3-1/gamlss/R/gamlss-01-05-13.R | 6
gamlss-4.3-1/gamlss/R/lms.R |only
gamlss-4.3-1/gamlss/R/qstats-29-12-12.R | 3
gamlss-4.3-1/gamlss/R/quantSheets.R |only
gamlss-4.3-1/gamlss/R/ri.R | 8
gamlss-4.3-1/gamlss/inst/doc/NEWS.txt | 29 +
gamlss-4.3-1/gamlss/man/centiles.Rd | 197 +++++------
gamlss-4.3-1/gamlss/man/lms.Rd | 15
gamlss-4.3-1/gamlss/man/quantSheets.Rd |only
gamlss-4.3-1/gamlss/man/z.scores.Rd |only
18 files changed, 741 insertions(+), 698 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Diff between coin versions 1.0-23 dated 2013-09-03 and 1.0-24 dated 2014-09-17
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn
coin-1.0-23/coin/inst/NEWS |only
coin-1.0-24/coin/DESCRIPTION | 8 -
coin-1.0-24/coin/MD5 | 43 ++++----
coin-1.0-24/coin/R/ExactDistributions.R | 6 -
coin-1.0-24/coin/R/InitMethods.R | 22 ++++
coin-1.0-24/coin/build |only
coin-1.0-24/coin/data/alpha.rda |binary
coin-1.0-24/coin/data/asat.rda |binary
coin-1.0-24/coin/data/glioma.rda |binary
coin-1.0-24/coin/data/mercuryfish.rda |binary
coin-1.0-24/coin/data/neuropathy.rda |binary
coin-1.0-24/coin/data/ocarcinoma.rda |binary
coin-1.0-24/coin/data/photocar.rda |binary
coin-1.0-24/coin/data/rotarod.rda |binary
coin-1.0-24/coin/data/treepipit.rda |binary
coin-1.0-24/coin/inst/NEWS.Rd |only
coin-1.0-24/coin/inst/doc/LegoCondInf.pdf |binary
coin-1.0-24/coin/inst/doc/MAXtest.pdf |binary
coin-1.0-24/coin/inst/doc/coin.pdf |binary
coin-1.0-24/coin/inst/doc/coin_implementation.pdf |binary
coin-1.0-24/coin/man/initialize-methods.Rd | 6 +
coin-1.0-24/coin/tests/Examples/coin-Ex.Rout.save | 108 ++++++++++++++++++++--
coin-1.0-24/coin/tests/bugfixes.R | 22 ++++
coin-1.0-24/coin/tests/bugfixes.Rout.save | 29 +++++
24 files changed, 208 insertions(+), 36 deletions(-)
Title: Geostatistics using SpatialPoints and rasters
Diff between geostatsp versions 0.9.999 dated 2014-08-04 and 1.0.0 dated 2014-09-17
Description: This package provides to geostatistical modelling facilities using raster and SpatialPoints objects.
Author: Patrick Brown
Maintainer: Patrick Brown
DESCRIPTION | 15 -
MD5 | 43 ++--
NAMESPACE | 11 -
R/RFsimulate.R | 454 ++++++++++++++++++++++++++++++++++---------------
R/excProb.R | 5
R/lgm.R | 21 +-
R/lgm.Raster.R |only
R/loglikGmrf.R |only
R/param.R | 15 +
R/simLgcp.R | 2
R/stackRasterList.R | 4
R/variog.R | 24 ++
data/datalist | 1
data/swissRainR.RData |only
man/RFsimulate.Rd | 67 ++++---
man/lgm.Rd | 91 +++++++--
man/likfitLgm.Rd | 3
man/matern.Rd | 6
man/stackRasterList.Rd | 2
man/swissRainR.Rd |only
man/variog.Rd | 4
tests/RFsimulate.R | 59 ++++--
tests/lgm.R | 7
tests/lgmRaster.R |only
tests/likfitLgm.R | 5
25 files changed, 584 insertions(+), 255 deletions(-)
Title: Distributions to be used for GAMLSS modelling.
Diff between gamlss.dist versions 4.3-0 dated 2014-06-03 and 4.3-1 dated 2014-09-17
Description: This package contains the distributions for GAMLSS
modelling.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
DESCRIPTION | 8 -
MD5 | 18 +--
NAMESPACE | 5
R/BE.R | 220 ++++++++++++++++++++---------------------
R/BEo.R | 184 +++++++++++++++++------------------
R/DELAPORT.R | 66 +++++++++---
R/ZAGA.R | 274 ++++++++++++++++++++++++++--------------------------
R/ZAIG.R | 294 ++++++++++++++++++++++++++++----------------------------
R/flexDist.R |only
man/BE.Rd | 14 +-
man/flexDist.Rd |only
11 files changed, 561 insertions(+), 522 deletions(-)
Title: Integrative analysis of omics data in terms of network,
evolution and ontology
Diff between dnet versions 1.0.5 dated 2014-07-02 and 1.0.6 dated 2014-09-17
Description: This package is initiated to fill in the need of an open-source tool for high-throughput omics data in an integrative manner in terms of network, evolution and ontology. More specifically, dnet intends to analyse the biological network whose nodes/genes are associated with digitised information such as expression levels across samples. To help make sense of identified networks, enrichment analysis is also supported using a wide variety of pre-compiled ontologies and phylostratific gene age information in major organisms including human, mouse, rat, chicken, C.elegans, fruit fly, zebrafish and arabidopsis. Add-on functionalities are supports for semantic similarity calculation between ontology terms (and genes), and network affinity calculation using Random Walk with Restart; both can be done via high-performance parallel computing. In summary, dnet aims to deliver an eye-intuitive tool with rich visuals but less inputs.
Author: Hai Fang and Julian Gough
Maintainer: Hai Fang
DESCRIPTION | 18 +-
MD5 | 111 ++++++-------
NAMESPACE | 4
R/dCheckParallel.r | 2
R/dEnricher.r | 11 +
R/dEnricherView.r | 60 ++++---
data/TCGA_mutations.RData |binary
data/ig.HPPA.RData |binary
data/org.Hs.egHPPA.RData |binary
data/org.Hs.string900.RData |binary
inst/CITATION |only
inst/NEWS | 12 +
inst/staticdocs/CITATIONs.md | 12 -
inst/staticdocs/INSTALLATIONs.md | 4
inst/staticdocs/RData.md | 4
inst/staticdocs/README.md | 9 -
inst/staticdocs/demo/TCGA_pre.r | 47 ++++-
inst/staticdocs/faq/FAQ1.r | 4
man/dBUMfit.Rd | 98 +++++------
man/dBUMscore.Rd | 122 ++++++--------
man/dCheckParallel.Rd | 26 +--
man/dCommSignif.Rd | 26 +--
man/dContrast.Rd | 20 +-
man/dDAGancestor.Rd | 36 ++--
man/dDAGannotate.Rd | 67 +++----
man/dDAGgeneSim.Rd | 170 +++++++++-----------
man/dDAGinduce.Rd | 44 ++---
man/dDAGlevel.Rd | 56 +++---
man/dDAGreverse.Rd | 14 -
man/dDAGroot.Rd | 10 -
man/dDAGtermSim.Rd | 112 ++++++-------
man/dDAGtip.Rd | 11 -
man/dEnricher.Rd | 330 ++++++++++++++++++---------------------
man/dEnricherView.Rd | 60 +++----
man/dFDRscore.Rd | 38 ++--
man/dGSEA.Rd | 325 ++++++++++++++++++--------------------
man/dGSEAview.Rd | 62 +++----
man/dGSEAwrite.Rd | 56 +++---
man/dNetConfidence.Rd | 56 +++---
man/dNetFind.Rd | 124 +++++++-------
man/dNetInduce.Rd | 53 +++---
man/dNetPipeline.Rd | 111 ++++++-------
man/dNetReorder.Rd | 196 +++++++++++------------
man/dPvalAggregate.Rd | 43 ++---
man/dRDataLoader.Rd | 113 +++++--------
man/dRWR.Rd | 160 ++++++++----------
man/dRWRcontact.Rd | 138 +++++++---------
man/dRWRpipeline.Rd | 190 ++++++++++------------
man/dSVDsignif.Rd | 89 ++++------
man/visBoxplotAdv.Rd | 139 +++++++---------
man/visDAG.Rd | 205 ++++++++++++------------
man/visGSEA.Rd | 37 ++--
man/visNet.Rd | 129 ++++++---------
man/visNetArc.Rd | 61 +++----
man/visNetCircle.Rd | 102 +++++-------
man/visNetMul.Rd | 99 +++++------
man/visNetReorder.Rd | 99 +++++------
57 files changed, 2005 insertions(+), 2120 deletions(-)
Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.28 dated 2014-09-03 and 1.0.30 dated 2014-09-17
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus
DESCRIPTION | 8 +-
MD5 | 14 ++--
NEWS | 3
R/AllClasses.R | 14 ++--
R/qmle.R | 103 ++++++++++++++++++++++++--------
R/yuima.R | 7 ++
man/yuima.carma.qmle-class.Rd | 1
src/cce_functions.c | 132 ++++++++++++++++++++++--------------------
8 files changed, 179 insertions(+), 103 deletions(-)
Title: Tools for Simulation Studies in Parallel with R
Diff between simsalapar versions 1.0-3 dated 2014-06-10 and 1.0-4 dated 2014-09-17
Description: Tools for setting up, conducting, and evaluating larger-scale
simulation studies, including parallel computations.
Author: Marius Hofert and Martin Maechler
Maintainer: Marius Hofert
DESCRIPTION | 20 +++++++++-------
MD5 | 22 +++++++++---------
NAMESPACE | 5 +++-
R/doApply.R | 59 +++++++++++++++++++++++++++++++++----------------
R/subjob.R | 9 ++++++-
R/tryCatchWE.R | 3 ++
demo/TGforecasts.R | 1
demo/VaRsuperadd.R | 13 +++++-----
demo/robcovMCD.R | 4 +--
demo/robust.mean.R | 4 ---
man/doApply.Rd | 16 +++++--------
tests/tstTGforecasts.R | 18 +++++++++++---
12 files changed, 109 insertions(+), 65 deletions(-)
Title: Estimation of Entropy and Related Quantities
Diff between EntropyEstimation versions 0.1 dated 2014-04-12 and 1.0 dated 2014-09-17
More information about EntropyEstimation at CRAN
Description: Contains methods for the estimation of Shannon's entropy, variants of Renyi's entropy, mutual information, Kullback-Leibler divergence, and generalized Simpson's indices. The estimators used have a bias that decays exponentially fast.
Author: Lijuan Cao
Maintainer: Michael Grabchak
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
man/EntropyEstimation-package.Rd | 10 +++++-----
man/KL.Plugin.Rd | 2 +-
man/KL.sd.Rd | 2 +-
man/KL.z.Rd | 2 +-
man/SymKL.Plugin.Rd | 2 +-
man/SymKL.sd.Rd | 2 +-
man/SymKL.z.Rd | 2 +-
src/EntropEst.c | 8 ++++----
10 files changed, 30 insertions(+), 30 deletions(-)
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