Title: plotting custom sequence logos
Diff between RWebLogo versions 1.0.0 dated 2014-03-20 and 1.0.1 dated 2014-04-18
Description: RWebLogo is a wrapper for the WebLogo python package
that allows generating of customised sequence logos. Sequence logos are
graphical representations of the sequence conservation of nucleotides (in a
strand of DNA/RNA) or amino acids (in protein sequences). Each logo
consists of stacks of symbols, one stack for each position in the sequence.
The overall height of the stack indicates the sequence conservation at that
position, while the height of symbols within the stack indicates the
relative frequency of each amino or nucleic acid at that position. In
general, a sequence logo provides a richer and more precise description of,
for example, a binding site, than would a consensus sequence.
Author: Omar Wagih
Maintainer: Omar Wagih
RWebLogo |only
1 file changed
Title: Response-surface analysis
Diff between rsm versions 2.05 dated 2014-04-14 and 2.06 dated 2014-04-18
Description: Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis.
Author: Russell V. Lenth
Maintainer: Russell V Lenth
DESCRIPTION | 8 ++++----
MD5 | 11 ++++++-----
R/contour-lm.R | 36 +++++++++++++++++++++++++++---------
build/vignette.rds |binary
inst/NEWS | 5 +++++
inst/doc/rsm.R |only
man/contour.lm.Rd | 2 +-
7 files changed, 43 insertions(+), 19 deletions(-)
Title: Statistical algorithms used in common data mining course
Diff between freestats versions 0.0.1 dated 2014-03-29 and 0.0.2 dated 2014-04-18
Description: A collections of useful statistical functions used in Columbia
course W4240/W4400.
Author: Xiaoyao Yang
Maintainer: Xiaoyao Yang
DESCRIPTION | 11 +++++------
MD5 | 19 +++++++++++++------
NAMESPACE | 9 ++++++++-
R/DecisionStump.R |only
R/classify.R |only
R/cvwork.R | 11 ++++++-----
R/perceptrain.R | 16 +++++++++++-----
man/DecisionStump.Rd |only
man/classify.Rd |only
man/classify.default.Rd |only
man/classify.ds.Rd |only
man/classify.pt.Rd |only
man/cv.work.Rd | 10 ++++++----
man/perceptrain.Rd | 12 +++++++++---
14 files changed, 58 insertions(+), 30 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.1.3 dated 2013-09-15 and 1.1.4 dated 2014-04-18
Description: The "care" package implements the regression approach
of Zuber and Strimmer (2011) "High-dimensional regression and variable
selection using CAR scores" SAGMB 10: 34.
CAR scores measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is a
natural measure of variable importance and provides a canonical
ordering of variables. This package provides functions for estimating
CAR scores, for variable selection using CAR scores, and for estimating
corresponding regression coefficients. Both shrinkage as well as
empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 9 ++++++---
NAMESPACE | 4 +++-
NEWS | 9 +++++++++
inst |only
5 files changed, 23 insertions(+), 9 deletions(-)
Title: Shrinkage t Statistic and CAT Score
Diff between st versions 1.2.1 dated 2013-09-01 and 1.2.2 dated 2014-04-18
Description: This package implements the "shrinkage t" statistic
introduced in Opgen-Rhein and Strimmer (2007) and a shrinkage estimate
of the "correlation-adjusted t-score" (CAT score) described in
Zuber and Strimmer (2009). It also offers a convenient interface
to a number of other regularized t-statistics commonly
employed in high-dimensional case-control studies.
Author: Rainer Opgen-Rhein, Verena Zuber, and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NAMESPACE | 5 ++++-
NEWS | 6 ++++++
4 files changed, 18 insertions(+), 9 deletions(-)
More information about QuantifQuantile at CRAN
Permanent link
Title: Yet another package for Qualitative Comparative Analysis
Diff between QCA3 versions 0.0-5 dated 2012-04-10 and 0.0-6 dated 2014-04-18
Description: A set of functions for Qualitative Comparative Analysis (QCA). It can be used for various types of QCA (csQCA, mvQCA fsQCA and crip set TQCA and time-serious QCA). It has methods for simplifying assumption, contradictory simplifying assumption.
Author: Ronggui HUANG
Maintainer: Ronggui HUANG
QCA3-0.0-5/QCA3/inst/License |only
QCA3-0.0-6/QCA3/DESCRIPTION | 20 +--
QCA3-0.0-6/QCA3/LICENSE |only
QCA3-0.0-6/QCA3/MD5 | 69 ++++++-----
QCA3-0.0-6/QCA3/NAMESPACE | 9 +
QCA3-0.0-6/QCA3/R/QCA.R | 182 ++++++++++++++++++-------------
QCA3-0.0-6/QCA3/R/QCA.methods.R | 28 ++--
QCA3-0.0-6/QCA3/R/fsgof.R |only
QCA3-0.0-6/QCA3/R/plots.R | 50 ++++----
QCA3-0.0-6/QCA3/R/suffnec.R | 2
QCA3-0.0-6/QCA3/R/truthTable.R | 142 ++++++++++++++----------
QCA3-0.0-6/QCA3/R/utils.R | 4
QCA3-0.0-6/QCA3/build |only
QCA3-0.0-6/QCA3/data/CoD.rdata |binary
QCA3-0.0-6/QCA3/inst/ChangeLog | 11 +
QCA3-0.0-6/QCA3/inst/doc |only
QCA3-0.0-6/QCA3/man/CoD.Rd | 43 ++++---
QCA3-0.0-6/QCA3/man/Hino2009.Rd | 2
QCA3-0.0-6/QCA3/man/HuangGui2009.Rd | 30 +++--
QCA3-0.0-6/QCA3/man/KatzHauMahoney.Rd | 6 -
QCA3-0.0-6/QCA3/man/Lipsets.rd | 16 +-
QCA3-0.0-6/QCA3/man/McCammonVanDyke.Rd | 13 +-
QCA3-0.0-6/QCA3/man/QCA.methods.rd | 8 -
QCA3-0.0-6/QCA3/man/Yamasaki2009.Rd | 10 +
QCA3-0.0-6/QCA3/man/consistGap.Rd | 17 ++
QCA3-0.0-6/QCA3/man/constrReduce.rd | 16 +-
QCA3-0.0-6/QCA3/man/coverage.Rd | 7 -
QCA3-0.0-6/QCA3/man/cs_truthTable.rd | 18 +--
QCA3-0.0-6/QCA3/man/directCalibration.Rd | 3
QCA3-0.0-6/QCA3/man/fs_truthTable.rd | 19 ++-
QCA3-0.0-6/QCA3/man/fsnot.Rd | 7 +
QCA3-0.0-6/QCA3/man/fsplot.Rd | 8 -
QCA3-0.0-6/QCA3/man/reduce.rd | 72 +++++-------
QCA3-0.0-6/QCA3/man/remainderReduce.Rd | 5
QCA3-0.0-6/QCA3/man/setOUT.Rd | 5
QCA3-0.0-6/QCA3/man/thresholdssetter.rd | 26 +---
QCA3-0.0-6/QCA3/vignettes |only
37 files changed, 493 insertions(+), 355 deletions(-)
Title: Geometric morphometric analyses of 2d/3d landmark data
Diff between geomorph versions 2.0 dated 2014-04-15 and 2.0.1 dated 2014-04-18
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation
Author: Dean Adams, Erik Otarola-Castillo, Emma Sherratt
Maintainer: Dean Adams
DESCRIPTION | 8 +++----
MD5 | 16 +++++++--------
NEWS | 6 ++++-
R/plotAllometry.r | 3 +-
R/plotGMPhyloMorphoSpace.r | 2 -
R/warpRefMesh.R | 3 +-
man/plotAllometry.Rd | 46 +++++++++++++++++++++++----------------------
man/warpRefMesh.Rd | 6 ++++-
src/geomorph.c | 22 +++++++--------------
9 files changed, 58 insertions(+), 54 deletions(-)
Title: The YUIMA Project package for SDEs
Diff between yuima versions 1.0.2 dated 2014-03-20 and 1.0.9 dated 2014-04-18
Description: Simulation and Inference for Stochastic Differential Equations
Author: YUIMA Project Team
Maintainer: Stefano M. Iacus
yuima-1.0.2/yuima/R/CarmaRecovNoise.R |only
yuima-1.0.2/yuima/man/CarmaRecovNoise.Rd |only
yuima-1.0.9/yuima/DESCRIPTION | 17 ++---
yuima-1.0.9/yuima/MD5 | 22 +++----
yuima-1.0.9/yuima/NAMESPACE | 2
yuima-1.0.9/yuima/R/CarmaNoise.R |only
yuima-1.0.9/yuima/R/qmle.R | 66 ++++++++++++++++++++--
yuima-1.0.9/yuima/R/sim.euler.R | 3 -
yuima-1.0.9/yuima/R/sim.euler.space.discretized.R | 3 -
yuima-1.0.9/yuima/man/CPoint.Rd | 4 -
yuima-1.0.9/yuima/man/CarmaNoise.Rd |only
yuima-1.0.9/yuima/man/qmle.Rd | 2
yuima-1.0.9/yuima/man/yuima.carma-class.Rd | 2
yuima-1.0.9/yuima/man/yuima.carma.qmle-class.Rd | 2
14 files changed, 89 insertions(+), 34 deletions(-)
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Diff between sda versions 1.3.2 dated 2014-01-10 and 1.3.3 dated 2014-04-18
Description: This package provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 9 ++++++---
NAMESPACE | 5 +++++
NEWS | 9 +++++++++
inst |only
5 files changed, 25 insertions(+), 8 deletions(-)
Title: R & bitcoin integration
Diff between Rbitcoin versions 0.8.5 dated 2014-03-07 and 0.9 dated 2014-04-18
Description: Utilities related to Bitcoin: markets API interface (bitstamp,
kraken, btce, bitmarket). Both public and private API calls. Integration of
data structures for all markets. Support SSL. Read Rbitcoin documentation
(command: ?btc) for more information.
Author: Jan Gorecki
Maintainer: Jan Gorecki
DESCRIPTION | 15
MD5 | 38 -
NAMESPACE | 5
NEWS | 10
R/Rbitcoin.R | 1393 ++++++++++++++++++++++++++++++++++----
R/onLoad.R | 10
data/api.dict.rda |binary
man/Rbitcoin.Rd | 115 +--
man/Rbitcoin.plot.Rd |only
man/antiddos.Rd |only
man/api.dict.Rd | 10
man/available_wallet.Rd |only
man/blockchain.api.process.Rd |only
man/blockchain.api.query.Rd | 4
man/get_rate.Rd |only
man/market.api.process.Rd | 14
man/market.api.query.Rd | 19
man/market.api.query.bitmarket.Rd |only
man/market.api.query.bitstamp.Rd | 5
man/market.api.query.btce.Rd | 5
man/market.api.query.kraken.Rd | 5
man/market.api.query.mtgox.Rd | 5
man/wallet_manager.Rd |only
man/wallet_value.Rd |only
24 files changed, 1424 insertions(+), 229 deletions(-)
More information about Density.T.HoldOut at CRAN
Permanent link
Title: A GUI for Mean Measures of Divergence
Diff between AnthropMMD versions 0.9.8 dated 2014-01-29 and 0.9.9 dated 2014-04-18
Description: Offers a complete and interactive GUI to work out Mean Measures of Divergence, especially for anthropologists.
Author: Frederic Santos
Maintainer: Frederic Santos
DESCRIPTION | 10 ++---
MD5 | 12 +++---
NAMESPACE | 2 -
R/AnaSettings.R | 2 -
R/StartMMD.R | 84 ++++++++++++++++++++++++----------------------
man/AnthropMMD-package.Rd | 6 +--
man/StartMMD.Rd | 1
7 files changed, 62 insertions(+), 55 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-02-25 0.3.6
Title: Segmented relationships in regression models with
breakpoints/changepoints estimation
Diff between segmented versions 0.3-0.0 dated 2013-11-18 and 0.3-1.0 dated 2014-04-18
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 | 34 ++++++------
NEWS | 16 ++++--
R/broken.line.r | 123 ++++++++++++++++++++++++++++++++++-------------
R/davies.test.r | 16 +++---
R/plot.segmented.R | 54 ++++++++++++++------
R/predict.segmented.r | 82 ++++++++++---------------------
R/seg.glm.fit.boot.r | 2
R/seg.glm.fit.r | 2
R/segmented.glm.R | 102 +++++++++++++++++++++++++-------------
R/segmented.lm.R | 80 +++++++++++++++++++-----------
data/down.rda |binary
data/plant.rda |binary
data/stagnant.rda |binary
man/broken.line.Rd | 36 ++++++++-----
man/plot.segmented.Rd | 12 ++--
man/predict.segmented.Rd | 10 +--
man/segmented-package.Rd | 4 -
18 files changed, 355 insertions(+), 226 deletions(-)
Title: Fitting exact conditional logistic regression with lasso and
elastic net penalties.
Diff between clogitL1 versions 1.2 dated 2014-04-09 and 1.3 dated 2014-04-18
Description: Tools for the fitting and cross validation of exact conditional logistic regression models with lasso and elastic net penalties. Uses cyclic coordinate descent and warm starts to compute the entire path efficiently.
Author: Stephen Reid and Robert Tibshirani
Maintainer: Stephen Reid
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
man/clogitL1-package.Rd | 2 +-
src/clogisticl1_5.cpp | 4 +++-
src/clogisticl1_5cv.cpp | 5 +++--
5 files changed, 14 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-02-28 3.2.6
2012-05-16 3.2.5
2012-02-02 3.2.4
2011-11-02 3.1.0.2
2011-07-25 3.1.0.1
2010-11-30 2.5.4
2010-11-03 2.3.10
2010-10-21 2.3.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-03 1.0.4
2011-11-02 1.0.3
Title: Sparse principal component regression
Diff between spcr versions 1.0 dated 2014-04-01 and 1.1 dated 2014-04-18
Description: This package computes the sparse principal component regression. The regularization parameters are optimized by cross-validation.
Author: Shuichi Kawano
Maintainer: Shuichi Kawano
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/spcr.R | 2 +-
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Random Subspace Method (RSM) for linear regression.
Diff between regRSM versions 0.3 dated 2014-02-19 and 0.4 dated 2014-04-18
Description: Performs Random Subspace Method (RSM) for high-dimensional linear regression to obtain variable importance measures. The final model is chosen based on validation set or Generalized Information Criterion.
Author: Pawel Teisseyre, Robert A. Klopotek
Maintainer: Pawel Teisseyre
DESCRIPTION | 8 ++++----
MD5 | 24 ++++++++++++------------
NAMESPACE | 1 +
R/parallelRSM.R | 21 +++++++++++++++++----
R/regRSM.r | 24 ++++++++++++++++++++----
man/ImpPlot.regRSM.Rd | 2 +-
man/plot.regRSM.Rd | 8 ++++----
man/predict.regRSM.Rd | 2 +-
man/print.regRSM.rd | 2 +-
man/regRSM.Rd | 24 +++++++++++++++++++-----
man/roc.regRSM.rd | 2 +-
man/summary.regRSM.rd | 2 +-
man/validate.regRSM.rd | 2 +-
13 files changed, 83 insertions(+), 39 deletions(-)
Title: A smarter JSON encoder/decoder for R
Diff between jsonlite versions 0.9.6 dated 2014-04-05 and 0.9.7 dated 2014-04-18
Description: This package is a fork of the RJSONIO package by Duncan Temple
Lang. It builds on the same libjson c++ parser, but implements a smarter
mapping between JSON data and R classes. The vignette describes
the behavior in great detail. In addition to drop-in replacements for
toJSON and fromJSON, the package contains functions to serialize objects
and many unit tests to make verify that all edge cases are encoded and
decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Jonathan Wallace
Maintainer: Jeroen Ooms
DESCRIPTION | 8 ++++----
MD5 | 23 ++++++++++++-----------
NEWS | 7 +++++++
R/fromJSON.R | 6 ++++--
R/simplify.R | 31 ++++++++++++++++++++++++++++---
R/simplifyDataFrame.R | 20 ++++++++++++++------
R/toJSON.R | 5 +++--
build/vignette.rds |binary
inst/doc/json-mapping.pdf |binary
inst/tests/test-fromJSON-date.R |only
inst/tests/test-libjson-utf8.R | 4 ++--
man/fromJSON.Rd | 10 ++++++++--
src/rlibjson.c | 3 ++-
13 files changed, 84 insertions(+), 33 deletions(-)
Title: Bayesian Palaeoclimate Reconstruction from Pollen
Diff between Bclim versions 2.2 dated 2013-01-23 and 2.3.1 dated 2014-04-18
Description: This package takes pollen/time data from lake cores and produces a Bayesian posterior distribution of palaeoclimate from that location after fitting a non-linear non-Gaussian state-space model.
Author: Andrew Parnell, Thinh Doan and James Sweeney
Maintainer: Andrew Parnell
Bclim-2.2/Bclim/R/Bclim-internal.R |only
Bclim-2.2/Bclim/R/NIGB.R |only
Bclim-2.2/Bclim/R/NIGp3.R |only
Bclim-2.2/Bclim/man/NIGB.Rd |only
Bclim-2.2/Bclim/man/NIGp3.Rd |only
Bclim-2.3.1/Bclim/DESCRIPTION | 18 -
Bclim-2.3.1/Bclim/MD5 | 50 +-
Bclim-2.3.1/Bclim/NAMESPACE | 5
Bclim-2.3.1/Bclim/R/BclimCompile.R | 5
Bclim-2.3.1/Bclim/R/BclimInterp.R | 326 ++++++++++---------
Bclim-2.3.1/Bclim/R/BclimLayer.R | 1
Bclim-2.3.1/Bclim/R/BclimMCMC.R | 33 +
Bclim-2.3.1/Bclim/R/BclimMixPar.R | 35 --
Bclim-2.3.1/Bclim/R/BclimMixSer.R | 27 -
Bclim-2.3.1/Bclim/R/plotBclim.R | 37 +-
Bclim-2.3.1/Bclim/R/plotBclimVol.R | 36 +-
Bclim-2.3.1/Bclim/R/zzz.R |only
Bclim-2.3.1/Bclim/man/Bclim-package.Rd | 4
Bclim-2.3.1/Bclim/man/BclimCompile.Rd | 6
Bclim-2.3.1/Bclim/man/BclimLayer.Rd | 6
Bclim-2.3.1/Bclim/man/BclimMCMC.Rd | 31 +
Bclim-2.3.1/Bclim/man/BclimMixPar.Rd | 6
Bclim-2.3.1/Bclim/man/BclimMixSer.Rd | 6
Bclim-2.3.1/Bclim/man/BclimRun.Rd | 6
Bclim-2.3.1/Bclim/man/plotBclim.Rd | 3
Bclim-2.3.1/Bclim/man/plotBclimVol.Rd | 10
Bclim-2.3.1/Bclim/src/BclimMCMC3D.c | 559 +++++++++++++++------------------
Bclim-2.3.1/Bclim/src/use.c | 35 +-
Bclim-2.3.1/Bclim/src/use.h | 1
29 files changed, 640 insertions(+), 606 deletions(-)