Title: Proper scoring rules
Diff between scoring versions 0.1 dated 2013-07-02 and 0.2 dated 2013-08-08
Description: Evaluating probabilistic forecasts via proper scoring rules. scoring implements the beta, power, and pseudospherical families of proper scoring rules. Included among these families are popular rules like the Brier (quadratic) score, logarithmic score, and spherical score. Also includes functionality for plotting scores that one would obtain under specific scoring rules. Functionality is currently limited to forecasts associated with two-alternative events.
Author: Ed Merkle
Maintainer: Ed Merkle
DESCRIPTION | 17 +++++------------
MD5 | 11 ++++++-----
NEWS |only
R/fams.R | 1 -
R/scalescores.R | 7 +++----
man/calcscore.Rd | 2 +-
man/plotscore.Rd | 2 +-
7 files changed, 16 insertions(+), 24 deletions(-)
Title: Inline C, C++, Fortran function calls from R
Diff between inline versions 0.3.12 dated 2013-06-12 and 0.3.13 dated 2013-08-08
Description: Functionality to dynamically define R functions and S4 methods
with in-lined C, C++ or Fortran code supporting .C and .Call calling conventions.
Author: Oleg Sklyar, Duncan Murdoch, Mike Smith, Dirk Eddelbuettel, Romain Francois
Maintainer: Dirk Eddelbuettel
DESCRIPTION | 16 +++++++---------
MD5 | 8 ++++----
R/cfunction.R | 24 +++++++++++++++---------
inst/NEWS.Rd | 8 ++++++++
man/cfunction.Rd | 5 +----
5 files changed, 35 insertions(+), 26 deletions(-)
Title: Estimation and comparison of dynamic treatment regimes
Diff between DTR versions 1.1-1 dated 2013-06-12 and 1.2 dated 2013-08-08
Description: Estimation and comparison of survival distributions of dynamic treatment regimes (DTRs) from sequentially randomized clinical trials
Author: Xinyu Tang and Maria Melguizo
Maintainer: Xinyu Tang
DESCRIPTION | 19 +--
MD5 | 43 +++++++-
R/CHR.Wald.test.R |only
R/CHR.estimator.R |only
R/DTR.CHR.plot.R |only
R/DTR.Cox.test.R |only
R/DTR.Logrank.test.R |only
R/DTR.Wald.test.R |only
R/DTR.surv.plot.R |only
R/LDT.estimator.R | 144 ++++++++++++-----------------
R/LDT.mean.estimator.R | 128 +++++++++++---------------
R/WRSE.estimator.R |only
R/sim.CHR.data.R |only
R/sim.Cox.data.R |only
R/sim.LDT.data.R | 221 ++++++++++++++++++++++++----------------------
R/sim.Logrank.data.R |only
R/sim.WRSE.data.R |only
R/updateBeta.R |only
inst |only
man/CHR.Wald.test.Rd |only
man/CHR.estimator.Rd |only
man/DTR-package.Rd | 49 ++++++++--
man/DTR.CHR.plot.Rd |only
man/DTR.Cox.test.Rd |only
man/DTR.Logrank.test.Rd |only
man/DTR.Wald.test.Rd |only
man/DTR.surv.plot.Rd |only
man/LDT.estimator.Rd | 39 ++++----
man/LDT.mean.estimator.Rd | 36 +++----
man/WRSE.estimator.Rd |only
man/sim.CHR.data.Rd |only
man/sim.Cox.data.Rd |only
man/sim.LDT.data.Rd | 46 +++++----
man/sim.Logrank.data.Rd |only
man/sim.WRSE.data.Rd |only
man/updateBeta.Rd |only
36 files changed, 383 insertions(+), 342 deletions(-)
Title: Sierpinski Pedal Triangle
Diff between spt versions 1.11-12-7 dated 2011-12-07 and 1.13-8-8 dated 2013-08-08
Description: This package collects algorithms related to Sierpinski pedal triangle (SPT).
Author: Bin Wang
Maintainer: Bin Wang
spt-1.11-12-7/spt/LICENCE |only
spt-1.13-8-8/spt/DESCRIPTION | 13 +++++++------
spt-1.13-8-8/spt/MD5 | 5 ++---
spt-1.13-8-8/spt/R/zzz.R | 5 -----
4 files changed, 9 insertions(+), 14 deletions(-)
Title: MicroRNA Microarray Data Analysis
Diff between miRada versions 0.1.11-13 dated 2012-11-13 and 1.13.8-8 dated 2013-08-08
Description: This package collects algorithms/functions developed for
microRNA profiling data analyses. Analytical platforms include
traditional hybridization microarray, CGH, beads-based
microarray, and qRT-PCR array.
Author: Bin Wang
Maintainer: Bin Wang
miRada-0.1.11-13/miRada/LICENCE |only
miRada-1.13.8-8/miRada/DESCRIPTION | 9 +++++----
miRada-1.13.8-8/miRada/MD5 | 3 +--
3 files changed, 6 insertions(+), 6 deletions(-)
Title: Generalize Lambda Distribution and Generalized Bootstrapping
Diff between gb versions 1.0.11-24 dated 2011-11-28 and 1.1.8-8 dated 2013-08-08
Description: This package collects algorithms and functions for fitting data to a generalized lambda distribution via moment matching methods, and generalized bootstrapping.
Author: Bin Wang
Maintainer: Bin Wang
gb-1.0.11-24/gb/LICENCE |only
gb-1.1.8-8/gb/DESCRIPTION | 13 +++++++------
gb-1.1.8-8/gb/MD5 | 5 ++---
gb-1.1.8-8/gb/R/zzz.R | 7 -------
4 files changed, 9 insertions(+), 16 deletions(-)
Title: Functions and data for "Data Mining with R"
Diff between DMwR versions 0.4.0 dated 2013-06-28 and 0.4.1 dated 2013-08-08
Description: This package includes functions and data accompanying the book
"Data Mining with R, learning with case studies" by Luis Torgo, CRC Press 2010.
Author: Luis Torgo
Maintainer: Luis Torgo
CHANGES | 8 ++++-
DESCRIPTION | 21 +++++++-------
MD5 | 34 ++++++++++++------------
NAMESPACE | 17 +++++++-----
R/OR.R | 2 -
R/classes.R | 4 +-
R/experiments.R | 59 ++++++------------------------------------
R/kNN.R | 2 -
R/smote.R | 14 +++++++--
R/utils.R | 2 -
man/DMwR-defunct.Rd | 11 ++-----
man/bestScores.Rd | 2 -
man/experimentalComparison.Rd | 2 -
man/outliers.ranking.Rd | 7 ++--
man/rankSystems.Rd | 2 -
man/statScores.Rd | 2 -
man/trading.simulator.Rd | 4 ++
man/tradingEvaluation.Rd | 4 ++
18 files changed, 87 insertions(+), 110 deletions(-)
Title: Density Estimation for Binned/Weighted Data
Diff between bda versions 2.1.4-19 dated 2013-04-20 and 2.2.8-8 dated 2013-08-08
Description: This package collects algorithms/functions developed for
density estimation based on weighted or pre-binned data.
Author: Bin Wang
Maintainer: Bin Wang
bda-2.1.4-19/bda/R/binDE.R |only
bda-2.1.4-19/bda/R/bootKDE.R |only
bda-2.1.4-19/bda/R/histogram.R |only
bda-2.1.4-19/bda/R/mixedmodel.R |only
bda-2.1.4-19/bda/R/mle.R |only
bda-2.1.4-19/bda/R/tests.R |only
bda-2.1.4-19/bda/R/wkde.R |only
bda-2.1.4-19/bda/R/zzz.R |only
bda-2.1.4-19/bda/data/zr.tab.gz |only
bda-2.1.4-19/bda/man/bdde.Rd |only
bda-2.1.4-19/bda/man/wkde.rd |only
bda-2.2.8-8/bda/DESCRIPTION | 8 +--
bda-2.2.8-8/bda/MD5 | 43 +++++++++++---------
bda-2.2.8-8/bda/R/Survival.R |only
bda-2.2.8-8/bda/R/all.R |only
bda-2.2.8-8/bda/R/lpsmooth.R |only
bda-2.2.8-8/bda/R/old.R |only
bda-2.2.8-8/bda/arc/bda2.2.txt |only
bda-2.2.8-8/bda/data/zr.RData |only
bda-2.2.8-8/bda/man/Survival.Rd |only
bda-2.2.8-8/bda/man/bda.Rd |only
bda-2.2.8-8/bda/man/bde.Rd |only
bda-2.2.8-8/bda/man/edf.Rd | 29 +++++++++-----
bda-2.2.8-8/bda/man/histogram.Rd | 76 ++++++++++++++-----------------------
bda-2.2.8-8/bda/man/histosmooth.Rd |only
bda-2.2.8-8/bda/man/lprde.Rd | 17 ++------
bda-2.2.8-8/bda/man/npr.Rd |only
bda-2.2.8-8/bda/man/pcb.Rd | 5 --
bda-2.2.8-8/bda/man/wkde.Rd |only
bda-2.2.8-8/bda/man/zr.Rd | 9 +---
bda-2.2.8-8/bda/src/Ckernel.c |only
bda-2.2.8-8/bda/src/Fkernel.f |only
bda-2.2.8-8/bda/src/KernelWKDE.c | 6 +-
bda-2.2.8-8/bda/src/fftdens.f | 33 ----------------
bda-2.2.8-8/bda/src/init.c | 41 ++++++++++++++++++-
35 files changed, 127 insertions(+), 140 deletions(-)
Title: Cross-platform Perl based R function to create Excel 2003 (XLS)
and Excel 2007 (XLSX) files
Diff between WriteXLS versions 3.2.0 dated 2013-07-28 and 3.2.1 dated 2013-08-08
Description: Cross-platform Perl based R function to create Excel 2003 (XLS) and Excel 2007 (XLSX)
files from one or more data frames. Each data frame will be
written to a separate named worksheet in the Excel spreadsheet.
The worksheet name will be the name of the data frame it contains
or can be specified by the user.
Author: Marc Schwartz
Maintainer: Marc Schwartz
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/WriteXLS.R | 17 ++++++++++++++++-
README | 18 ++++++++++--------
inst/Perl/WriteXLS.pl | 2 +-
inst/Perl/WriteXLSX.pl | 2 +-
man/WriteXLS.Rd | 8 +++++++-
7 files changed, 45 insertions(+), 22 deletions(-)
Title: Managing data from Ensembl and UCSC genome browsers.
Diff between refGenome versions 1.1.0 dated 2013-08-07 and 1.1.2 dated 2013-08-08
Description: Functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz).
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers
DESCRIPTION | 10
MD5 | 32 +-
R/refGenome.r | 360 ++++++++++++++++++++++-----------
inst/doc/refGenome.R | 46 ++--
inst/doc/refGenome.Rnw | 24 +-
inst/doc/refGenome.pdf |binary
inst/extdata/hs.ensembl.62.small.RData |binary
inst/extdata/hs.ucsc.small.RData |binary
man/extractByGeneName.Rd | 5
man/getGenePositions.Rd | 6
man/refExons-class.Rd | 6
man/refJunctions-class.Rd | 22 +-
man/saveGenome.Rd | 17 +
man/ucscGenome-class.Rd | 4
vignettes/refGenome.Rnw | 2
vignettes/refGenome.log | 20 -
vignettes/refGenome.synctex.gz |binary
17 files changed, 361 insertions(+), 193 deletions(-)
Title: The package was developed to fit fit many growth curves obtained
under different conditions.
Description: The package was developed to fit fit many growth curves
obtained under different conditions in order to derive a
conclusive dose-response curve, for instance for a compound
that potentially affects growth. grofit fits data to different
parametric models (function gcFitModel) and in addition
provides a model free spline fit (function gcFitSpline) to
circumvent systematic errors that might occur within
application of parametric methods.
Author: Matthias Kahm, Maik Kschischo
Maintainer: ORPHANED
Diff between grofit versions 1.1 dated 2012-08-24 and 1.1.1 dated 2013-08-08
DESCRIPTION | 13 +++++++++---- MD5 | 6 +++--- R/plot.drFit.R | 2 +- man/plot.gcFit.Rd | 2 +- 4 files changed, 14 insertions(+), 9 deletions(-)
Title: Graphical Interaction Models
Diff between gRim versions 0.1-16 dated 2013-05-30 and 0.1-17 dated 2013-08-08
Description: gRaphical Interaction Models:
Models for for contingency tables (i.e. log-linear models)
Graphical Gaussian models for multivariate normal data (i.e. covariance selection
models)
Mixed interaction models
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
ChangeLog | 6 ++++++
DESCRIPTION | 18 +++++++++---------
MD5 | 14 +++++++-------
NAMESPACE | 5 +++++
R/iModel-general.R | 3 ++-
gRim-Ex.R | 2 +-
inst/doc/gRim.pdf |binary
man/getEdges.Rd | 2 +-
8 files changed, 31 insertions(+), 19 deletions(-)
Title: Graphical Independence Networks
Diff between gRain versions 1.2-0 dated 2013-07-14 and 1.2-1 dated 2013-08-08
Description: A package for probability propagation in graphical independence networks, also known as probabilistic expert systems or Bayesian networks.
Author: Søren Højsgaard
Maintainer: Søren Højsgaard
gRain-1.2-0/gRain/vignettes/CMD.lnk |only
gRain-1.2-0/gRain/vignettes/Makefile |only
gRain-1.2-0/gRain/vignettes/R-current-64.lnk |only
gRain-1.2-0/gRain/vignettes/Rmarkup.STY |only
gRain-1.2-0/gRain/vignettes/figures |only
gRain-1.2-0/gRain/vignettes/rxvt.exe.lnk |only
gRain-1.2-0/gRain/vignettes/work-gRain-vignettes.q |only
gRain-1.2-1/gRain/ChangeLog | 6 +
gRain-1.2-1/gRain/DESCRIPTION | 9 -
gRain-1.2-1/gRain/MD5 | 31 ++---
gRain-1.2-1/gRain/NAMESPACE | 2
gRain-1.2-1/gRain/R/CPT-POT-extract.R | 8 -
gRain-1.2-1/gRain/R/Finding.R | 9 -
gRain-1.2-1/gRain/R/grain-compile.R | 96 ----------------
gRain-1.2-1/gRain/R/potentialList.R | 120 ++++++++++-----------
gRain-1.2-1/gRain/R/propagate.R | 33 +++--
gRain-1.2-1/gRain/R/querygrain.R | 45 +++----
gRain-1.2-1/gRain/R/update.R | 6 -
gRain-1.2-1/gRain/inst/doc/gRain-evidence.pdf |binary
gRain-1.2-1/gRain/inst/doc/gRain-intro.pdf |binary
20 files changed, 140 insertions(+), 225 deletions(-)
Title: Distinguishing drift and natural selection as causes of
phenotypic differentiation
Diff between driftsel versions 1.0 dated 2013-04-24 and 2.0.1 dated 2013-08-08
Description: Neutrality test for quantitative traits
Author: Markku Karhunen & Otso Ovaskainen
Maintainer: Markku Karhunen
driftsel-1.0/driftsel/data/threespines_.rda |only
driftsel-2.0.1/driftsel/DESCRIPTION | 12 +++---
driftsel-2.0.1/driftsel/MD5 | 29 ++++++++--------
driftsel-2.0.1/driftsel/NAMESPACE | 2 -
driftsel-2.0.1/driftsel/R/H.test.R | 2 -
driftsel-2.0.1/driftsel/R/MH.R | 14 +++++++
driftsel-2.0.1/driftsel/R/S.test.R | 1
driftsel-2.0.1/driftsel/R/ellipsis.R |only
driftsel-2.0.1/driftsel/R/neut.test.R | 1
driftsel-2.0.1/driftsel/R/update.y.R |only
driftsel-2.0.1/driftsel/R/viz.traits.R | 41 ++++++++++------------
driftsel-2.0.1/driftsel/data/datalist | 1
driftsel-2.0.1/driftsel/data/specimen.rda |binary
driftsel-2.0.1/driftsel/data/specimen2.rda |binary
driftsel-2.0.1/driftsel/man/H.test.Rd |only
driftsel-2.0.1/driftsel/man/MH.Rd | 14 ++++++-
driftsel-2.0.1/driftsel/man/S.test.Rd |only
driftsel-2.0.1/driftsel/man/neut.test.Rd | 50 +---------------------------
18 files changed, 71 insertions(+), 96 deletions(-)
Title: Sub-Pathway Mining Software
Diff between SPMS versions 1.0 dated 2013-05-29 and 2.0 dated 2013-08-08
Description: Use new methods to mine sub-pathway,but user need to prepare for xml format data of KEGG PATHWAY and store them in "xml" folder under "paths"(paths library is the default directory which is set by user) library,prepare KEGG pathway map data and store them in "png" folder under the "paths"(paths library is the default directory which is set by user) library in advance.
Author: Xiaomeng Ni
Maintainer: Xiaomeng Ni
SPMS-1.0/SPMS/data/datalist |only
SPMS-1.0/SPMS/data/org_name.txt.gz |only
SPMS-1.0/SPMS/man/org_name.Rd |only
SPMS-2.0/SPMS/DESCRIPTION | 15 +--
SPMS-2.0/SPMS/INDEX | 11 +-
SPMS-2.0/SPMS/MD5 | 81 ++++++++---------
SPMS-2.0/SPMS/R/ErgodicPathShowing.R | 106 +++++++++++++----------
SPMS-2.0/SPMS/R/broad_OnePictureShowing.R | 19 ++--
SPMS-2.0/SPMS/R/broad_subPathwayGraph.R | 20 ++--
SPMS-2.0/SPMS/R/broad_subPathwayMinner.R | 10 +-
SPMS-2.0/SPMS/R/broad_zhenghe.R | 3
SPMS-2.0/SPMS/R/deleteAll.R |only
SPMS-2.0/SPMS/R/depth_OnePictureShowing.R | 19 ++--
SPMS-2.0/SPMS/R/depth_subPathwayGraph.R | 18 ++-
SPMS-2.0/SPMS/R/depth_subPathwayMinner.R | 64 +++++++++-----
SPMS-2.0/SPMS/R/depth_zhenghe.R | 3
SPMS-2.0/SPMS/R/getAllSubpathway.R | 4
SPMS-2.0/SPMS/R/getData.R | 18 ++-
SPMS-2.0/SPMS/R/mineSubpathway.R | 1
SPMS-2.0/SPMS/R/networkShowing_geneSymbol.R | 25 +++++
SPMS-2.0/SPMS/R/networkShowing_hsa.R | 27 +++++
SPMS-2.0/SPMS/data/ImageSize.txt.gz |binary
SPMS-2.0/SPMS/data/pathwayName.txt.gz |binary
SPMS-2.0/SPMS/man/ErgodicPathShowing.Rd | 114 ++++++++++++-------------
SPMS-2.0/SPMS/man/ImageSize.Rd | 2
SPMS-2.0/SPMS/man/SPMS-package.Rd | 8 -
SPMS-2.0/SPMS/man/broad_OnePictureShowing.Rd | 31 +++---
SPMS-2.0/SPMS/man/broad_subPathwayGraph.Rd | 36 ++++---
SPMS-2.0/SPMS/man/broad_subPathwayMinner.Rd | 15 +--
SPMS-2.0/SPMS/man/broad_zhenghe.Rd | 7 -
SPMS-2.0/SPMS/man/deleteAll.Rd |only
SPMS-2.0/SPMS/man/depth_OnePictureShowing.Rd | 31 +++---
SPMS-2.0/SPMS/man/depth_subPathwayGraph.Rd | 34 +++----
SPMS-2.0/SPMS/man/depth_subPathwayMinner.Rd | 70 ++++++++++-----
SPMS-2.0/SPMS/man/depth_zhenghe.Rd | 7 -
SPMS-2.0/SPMS/man/fPathway.Rd | 2
SPMS-2.0/SPMS/man/getAllSubpathway.Rd | 10 +-
SPMS-2.0/SPMS/man/getData.Rd | 22 +++-
SPMS-2.0/SPMS/man/inputInterestGene.Rd | 6 -
SPMS-2.0/SPMS/man/mineSubpathway.Rd | 8 -
SPMS-2.0/SPMS/man/networkShowing_geneSymbol.Rd | 22 ++++
SPMS-2.0/SPMS/man/networkShowing_hsa.Rd | 22 ++++
SPMS-2.0/SPMS/man/setPath.Rd | 2
SPMS-2.0/SPMS/man/txtResultShowing.Rd | 3
44 files changed, 546 insertions(+), 350 deletions(-)
Title: Models for Analysing Moult in Birds
Diff between moult versions 1.2 dated 2013-01-16 and 1.3 dated 2013-08-08
Description: Functions to estimate start and duration of moult from moult
data (of types 1 to 5), based on models developed in Underhill
and Zucchini (1988, 1990). Allows modelling parameters as
functions of covariates.
Author: Birgit Erni
Maintainer: Birgit Erni
DESCRIPTION | 23 ++++++++++++-----------
MD5 | 7 ++++---
NEWS | 7 +++++++
R/moult.R | 35 +++++++++++++++++------------------
inst/doc |only
5 files changed, 40 insertions(+), 32 deletions(-)
Title: Exploring water quality monitoring data
Diff between wq versions 0.3-10 dated 2013-05-26 and 0.3-11 dated 2013-08-08
Description: Functions to assist in the processing and exploration of data from
environmental monitoring programs. The name "wq" stands for "water quality"
and reflects the original focus on time series data for physical and
chemical properties of water, as well as the plankton. The package is
intended for programs that sample approximately monthly at discrete
stations, a feature of many legacy data sets. Most of the functions should
be useful for analysis of similar-frequency time series regardless of the
subject matter.
Author: Alan D. Jassby and James E. Cloern
Maintainer: Alan Jassby
wq-0.3-10/wq/ChangeLog |only
wq-0.3-11/wq/DESCRIPTION | 28 +++-----
wq-0.3-11/wq/MD5 | 51 +++++++--------
wq-0.3-11/wq/NAMESPACE | 4 -
wq-0.3-11/wq/NEWS |only
wq-0.3-11/wq/R/WqData-class.R | 29 ++++++++
wq-0.3-11/wq/R/eofNum.R | 2
wq-0.3-11/wq/R/eofPlot.R | 6 -
wq-0.3-11/wq/R/mannKen.R | 9 +-
wq-0.3-11/wq/R/phenoAmp.R | 6 -
wq-0.3-11/wq/R/phenoPhase.R | 4 -
wq-0.3-11/wq/R/plotSeason.R | 12 ++-
wq-0.3-11/wq/R/plotTs.R | 6 -
wq-0.3-11/wq/R/plotTsAnom.R | 7 +-
wq-0.3-11/wq/R/plotTsTile.R | 60 ++++++++++++------
wq-0.3-11/wq/R/seaRoll.R | 6 +
wq-0.3-11/wq/R/seasonTrend.R | 9 +-
wq-0.3-11/wq/R/tsMake.R | 8 +-
wq-0.3-11/wq/R/wqData.R | 19 +++--
wq-0.3-11/wq/README |only
wq-0.3-11/wq/inst/CITATION | 40 +++++++-----
wq-0.3-11/wq/inst/doc/wq-package.R | 112 +++++++++++++++++-----------------
wq-0.3-11/wq/inst/doc/wq-package.Rnw | 1
wq-0.3-11/wq/man/WqData-class.Rd | 64 +++++++------------
wq-0.3-11/wq/man/plotTsTile.Rd | 17 +++--
wq-0.3-11/wq/man/wq-package.Rd | 65 ++++++++++++++++++-
wq-0.3-11/wq/man/wqData.Rd | 9 +-
wq-0.3-11/wq/vignettes/wq-package.Rnw | 1
28 files changed, 349 insertions(+), 226 deletions(-)
Title: Draw Geographical Maps
Diff between maps versions 2.3-2 dated 2013-03-13 and 2.3-3 dated 2013-08-08
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg
Maintainer: Ray Brownrigg
DESCRIPTION | 14 +++++++-------
MD5 | 8 ++++----
data/county.fips.rda |binary
data/world.cities.rda |binary
man/map.Rd | 9 +++++----
5 files changed, 16 insertions(+), 15 deletions(-)