Title: Dive analysis and calibration
Diff between diveMove versions 1.0 dated 2010-06-13 and 1.1 dated 2010-08-05
Description: Utilities to represent, visualize, filter, analyse, and
summarize time-depth recorder (TDR) data. Miscellaneous
functions for handling location data are also provided.
Author: Sebastian P. Luque
Maintainer: Sebastian P. Luque
diveMove-1.0/diveMove/man/zoc.Rd |only
diveMove-1.1/diveMove/ChangeLog | 119 +++++++++
diveMove-1.1/diveMove/DESCRIPTION | 8
diveMove-1.1/diveMove/NEWS | 30 ++
diveMove-1.1/diveMove/R/AllMethod.R | 10
diveMove-1.1/diveMove/R/bouts.R | 8
diveMove-1.1/diveMove/R/calibrate.R | 60 +++-
diveMove-1.1/diveMove/R/detDive.R | 36 +-
diveMove-1.1/diveMove/R/detPhase.R | 22 -
diveMove-1.1/diveMove/R/oneDiveStats.R | 4
diveMove-1.1/diveMove/R/plotTD.R | 28 +-
diveMove-1.1/diveMove/R/zoc.R | 132 ++++++++--
diveMove-1.1/diveMove/data/divesSummary.RData |binary
diveMove-1.1/diveMove/data/divesTDRcalibrate.RData |binary
diveMove-1.1/diveMove/inst/CITATION | 4
diveMove-1.1/diveMove/inst/doc/diveMove.Rnw | 110 +++++----
diveMove-1.1/diveMove/inst/doc/diveMove.pdf |binary
diveMove-1.1/diveMove/man/TDR-accessors.Rd | 5
diveMove-1.1/diveMove/man/TDRcalibrate-accessors.Rd | 23 +
diveMove-1.1/diveMove/man/calibrateDepth.Rd | 242 ++++++++++++++------
diveMove-1.1/diveMove/man/detDive-internal.Rd | 20 +
diveMove-1.1/diveMove/man/detPhase-internal.Rd | 23 +
diveMove-1.1/diveMove/man/diveMove-internal.Rd | 138 ++++++++++-
diveMove-1.1/diveMove/man/diveMove-package.Rd | 9
diveMove-1.1/diveMove/man/diveStats.Rd | 4
diveMove-1.1/diveMove/man/dives.Rd | 9
diveMove-1.1/diveMove/man/labDive-internal.Rd | 6
diveMove-1.1/diveMove/man/plotTD.Rd |only
diveMove-1.1/diveMove/man/plotTDR-methods.Rd | 10
diveMove-1.1/diveMove/tests/calibrations.R | 13 -
diveMove-1.1/diveMove/tests/final-stats.R | 4
31 files changed, 807 insertions(+), 270 deletions(-)
Title: Text Analysis Utilities
Diff between tau versions 0.0-7 dated 2010-02-19 and 0.0-8 dated 2010-08-05
Description: Utilities for text analysis
Author: Christian Buchta, Kurt Hornik, Ingo Feinerer, David Meyer
Maintainer: Kurt Hornik
DESCRIPTION | 8 ++++----
R/language.R | 46 ++++++++++++++++++++++++++++++++++++++++++----
R/sysdata.rda |binary
man/language.Rd | 26 ++++++++++++++++----------
4 files changed, 62 insertions(+), 18 deletions(-)
Title: Graphical user interface for data mining in R
Diff between rattle versions 2.5.37 dated 2010-07-31 and 2.5.38 dated 2010-08-05
Description: Rattle (the R Analytic Tool To Learn Easily) provides a
Gnome (RGtk2) based interface to R functionality for data
mining. The aim is to provide a simple and intuitive interface
that allows a user to quickly load data from a CSV file (or via
ODBC), transform and explore the data, build and evaluate
models, and export models as PMML (predictive modelling markup
language) or as scores. All of this with knowing little about
R. All R commands are logged and commented through the log tab.
Thus they are available to the user as a script file or as an
aide for the user to learn R or to copy-and-paste directly into
R itself. Rattle also exports a number of utility functions and
the graphical user interface, invoked as rattle(), does not
need to be run to deploy these.
Author: Graham Williams
Maintainer: Graham Williams
DESCRIPTION | 8 ++++----
R/model.R | 4 ++--
R/rattle.R | 4 ++--
data/audit.RData |binary
data/weatherAUS.RData |binary
inst/ChangeLog | 9 +++++++++
inst/doc/rattle.pdf |binary
inst/po/de/LC_MESSAGES/R-rattle.mo |binary
inst/po/es/LC_MESSAGES/R-rattle.mo |binary
inst/po/fr/LC_MESSAGES/R-rattle.mo |binary
inst/po/ja/LC_MESSAGES/R-rattle.mo |binary
11 files changed, 17 insertions(+), 8 deletions(-)
Title: Generate PMML for various models
Diff between pmml versions 1.2.22 dated 2010-05-19 and 1.2.23 dated 2010-08-05
Description: The Predictive Modelling Markup Language (PMML) is a
language for representing models, in an application independent
way. Such models can then be loaded into other applications
supporting PMML, including ADAPA from Zementis, Teradata
Warehouse Miner and IBM's DB2. The package provides a generic
pmml function to generate pmml for an object. Using a S3
generic function the approriate method for the class of the
supplied object is dispatched. The package currently supports
the export of PMML for linear regression, SVMs, rpart
classification trees, randomSurvivalForest forest models, and
kmeans clusters. This package is part of the Rattle toolkit.
Author: Graham Williams, Michael Hahsler (arules), Zementis Inc, Hemant
Ishwaran, Udaya B. Kogalur, Rajarshi Guha
Maintainer: Graham Williams
DESCRIPTION | 8 ++++----
R/pmml.R | 5 +++--
R/pmml.ksvm.R | 4 ++--
3 files changed, 9 insertions(+), 8 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 0.999375-42 dated 2010-07-15 and 0.999375-43 dated 2010-08-05
Description: Classes and methods for dense and sparse matrices and
operations on them using Lapack and SuiteSparse.
Author: Douglas Bates
Maintainer: Doug and Martin
Matrix-0.999375-42/Matrix/man/contrast.Rd |only
Matrix-0.999375-42/Matrix/man/glpModel-class.Rd |only
Matrix-0.999375-42/Matrix/man/lm.fit.sparse.Rd |only
Matrix-0.999375-42/Matrix/man/mkRespMod.Rd |only
Matrix-0.999375-42/Matrix/man/model.Matrix.Rd |only
Matrix-0.999375-42/Matrix/man/modelMatrix-class.Rd |only
Matrix-0.999375-42/Matrix/man/predModule-class.Rd |only
Matrix-0.999375-42/Matrix/man/respModule-class.Rd |only
Matrix-0.999375-43/Matrix/ChangeLog | 59 +
Matrix-0.999375-43/Matrix/DESCRIPTION | 14
Matrix-0.999375-43/Matrix/NAMESPACE | 43 -
Matrix-0.999375-43/Matrix/R/AllClass.R | 125 ---
Matrix-0.999375-43/Matrix/R/AllGeneric.R | 90 --
Matrix-0.999375-43/Matrix/R/Auxiliaries.R | 66 +
Matrix-0.999375-43/Matrix/R/dsparseMatrix.R | 2
Matrix-0.999375-43/Matrix/R/dsyMatrix.R | 3
Matrix-0.999375-43/Matrix/R/products.R | 61 +
Matrix-0.999375-43/Matrix/R/spModels.R | 640 -------------------
Matrix-0.999375-43/Matrix/R/sparseMatrix.R | 12
Matrix-0.999375-43/Matrix/R/sparseVector.R | 72 +-
Matrix-0.999375-43/Matrix/TODO | 16
Matrix-0.999375-43/Matrix/inst/Doxyfile | 2
Matrix-0.999375-43/Matrix/inst/doc/Comparisons.pdf |binary
Matrix-0.999375-43/Matrix/inst/doc/Design-issues.pdf |binary
Matrix-0.999375-43/Matrix/inst/doc/Intro2Matrix.pdf |binary
Matrix-0.999375-43/Matrix/inst/doc/Introduction.pdf |binary
Matrix-0.999375-43/Matrix/inst/doc/sparseModels.Rnw | 6
Matrix-0.999375-43/Matrix/inst/doc/sparseModels.pdf |binary
Matrix-0.999375-43/Matrix/man/chol.Rd | 2
Matrix-0.999375-43/Matrix/man/dtrMatrix-class.Rd | 14
Matrix-0.999375-43/Matrix/man/rcond.Rd | 30
Matrix-0.999375-43/Matrix/man/sparse.model.matrix.Rd | 24
Matrix-0.999375-43/Matrix/man/sparseMatrix-class.Rd | 1
Matrix-0.999375-43/Matrix/src/chm_common.c | 2
Matrix-0.999375-43/Matrix/src/dtrMatrix.c | 99 ++
Matrix-0.999375-43/Matrix/src/dtrMatrix.h | 3
Matrix-0.999375-43/Matrix/src/init.c | 3
Matrix-0.999375-43/Matrix/tests/Class+Meth.R | 5
Matrix-0.999375-43/Matrix/tests/Simple.R | 13
Matrix-0.999375-43/Matrix/tests/matprod.R | 38 -
Matrix-0.999375-43/Matrix/tests/spModel.matrix.R | 3
41 files changed, 445 insertions(+), 1003 deletions(-)
Title: Classification and Regression Training
Diff between caret versions 4.45 dated 2010-07-28 and 4.47 dated 2010-08-05
Description: Misc functions for training and plotting classification
and regression models
Author: Max Kuhn. Contributions from Jed Wing, Steve Weston, Andre
Williams, Chris Keefer and Allan Engelhardt
Maintainer: Max Kuhn
DESCRIPTION | 8 +--
NAMESPACE | 1
R/misc.R | 5 ++
R/resamples.R | 95 ++++++++++++++++++++++++++++++------------
R/rfe.R | 14 +++---
R/selectByFilter.R | 9 +++
R/train.default.R | 23 +++++++++-
data/GermanCredit.RData |only
inst/NEWS | 20 ++++++++
inst/doc/caretMisc.pdf |binary
inst/doc/caretSelection.pdf |binary
inst/doc/caretTrain.Rnw | 6 +-
inst/doc/caretTrain.pdf |binary
inst/doc/caretVarImp.pdf |binary
man/GermanCredit.Rd |only
man/diff.resamples.Rd | 3 -
man/lattice.diff.resamples.Rd | 3 +
man/lattice.resamples.Rd | 12 ++++-
man/resamples.Rd | 12 ++---
man/train.Rd | 2
20 files changed, 162 insertions(+), 51 deletions(-)
Title: Weighted k-Nearest Neighbors
Diff between kknn versions 1.0-7 dated 2009-07-18 and 1.0-8 dated 2010-08-05
Description: Weighted k-Nearest Neighbors Classification and Regression
Author: Klaus Schliep & Klaus Hechenbichler
Maintainer: Klaus Schliep
CHANGES | 8 ++++
DESCRIPTION | 8 ++--
R/kknn.R | 87 +++++++++++++++++++++++++++--------------------------
man/contr.dummy.Rd | 4 +-
man/glass.Rd | 2 -
man/ionosphere.Rd | 4 +-
man/kknn.Rd | 2 -
man/miete.Rd | 2 -
man/simulation.Rd | 2 -
man/train.kknn.Rd | 2 -
10 files changed, 66 insertions(+), 55 deletions(-)
Title: iid-test
Diff between iid.test versions 1.5 dated 2008-10-13 and 1.6 dated 2010-08-05
Description: Testing whether data is independent and identically
distributed
Author: Rasmus E. Benestad
Maintainer: Rasmus E. Benestad
DESCRIPTION | 13 ++++++++-----
man/daily.station.records.Rd | 2 +-
man/iid.test.Rd | 2 +-
man/n.records.Rd | 2 +-
man/test.iid.test.Rd | 4 ++--
5 files changed, 13 insertions(+), 10 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.4 dated 2010-07-29 and 0.2.5 dated 2010-08-05
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library aiming towards a good
balance between speed and ease of use. Integer, floating point
and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix
decompositions are provided through optional integration with
LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to
combine several operations into one, and to reduce (or
eliminate) the need for temporaries. This is accomplished
through recursive templates and template meta-programming.
This library is useful if C++ has been decided as the language of
choice (due to speed and/or integration capabilities), rather
than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo
itself in order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++
integration.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain, Dirk and Doug
DESCRIPTION | 10
NEWS | 4
inst/ChangeLog | 17 +
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 40 +-
inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 10
inst/include/README |only
inst/include/RcppArmadilloConfig.h | 14 +
inst/include/RcppArmadilloForward.h | 3
inst/include/armadillo | 10
inst/include/armadillo_bits/Col_meat.hpp | 24 +
inst/include/armadillo_bits/Col_proto.hpp | 3
inst/include/armadillo_bits/Cube_meat.hpp | 13
inst/include/armadillo_bits/Cube_proto.hpp | 1
inst/include/armadillo_bits/Mat_meat.hpp | 37 ++
inst/include/armadillo_bits/Mat_proto.hpp | 6
inst/include/armadillo_bits/Row_meat.hpp | 24 +
inst/include/armadillo_bits/Row_proto.hpp | 3
inst/include/armadillo_bits/arma_version.hpp | 15 -
inst/include/armadillo_bits/cmath_wrap.hpp | 13
inst/include/armadillo_bits/compiler_setup.hpp | 48 +--
inst/include/armadillo_bits/config.hpp | 22 -
inst/include/armadillo_bits/eop_aux.hpp | 214 ++++++++--------
inst/include/armadillo_bits/eop_core_meat.hpp | 98 +++----
inst/include/armadillo_bits/eop_core_proto.hpp | 24 -
inst/include/armadillo_bits/eop_cube_core_meat.hpp | 92 +++---
inst/include/armadillo_bits/eop_cube_core_proto.hpp | 20 -
inst/include/armadillo_bits/field_meat.hpp | 20 +
inst/include/armadillo_bits/field_proto.hpp | 13
inst/include/armadillo_bits/fn_eps.hpp | 4
inst/include/armadillo_bits/fn_misc.hpp | 20 -
inst/include/armadillo_bits/fn_trig.hpp | 63 ++--
inst/include/armadillo_bits/forward_proto.hpp | 15 +
inst/include/armadillo_bits/injector_meat.hpp |only
inst/include/armadillo_bits/injector_proto.hpp |only
inst/include/armadillo_bits/op_princomp_meat.hpp | 12
inst/include/armadillo_bits/op_reshape_meat.hpp | 159 +++++++++--
inst/include/armadillo_bits/podarray_proto.hpp | 9
inst/include/armadillo_bits/restrictors.hpp | 13
39 files changed, 688 insertions(+), 405 deletions(-)
Title: Multi-model inference
Diff between MuMIn versions 0.13.3 dated 2010-07-24 and 0.13.8 dated 2010-08-05
Description: Model selection and model averaging based on information
criteria (AICc and alikes).
Author: Kamil Bartoń
Maintainer: Kamil Bartoń
ChangeLog | 55 ++++++++++++++++++-------
DESCRIPTION | 10 ++--
R/beta.weights.R | 10 ++--
R/coeffs.R | 20 +++++----
R/dredge.R | 117 ++++++++++++++++++++++++++++++++-----------------------
R/model.avg.R | 7 +--
man/QAIC.Rd | 41 ++++++++++++++-----
man/dredge.Rd | 22 +++++++---
man/misc.Rd | 8 +++
man/model.avg.Rd | 19 +++++++-
10 files changed, 204 insertions(+), 105 deletions(-)
Title: Full factorials, orthogonal arrays and base utilities for DoE
packages
Diff between DoE.base versions 0.11-1 dated 2010-06-10 and 0.12 dated 2010-08-05
Description: This package creates full factorial experimental designs
and designs based on orthogonal arrays for (industrial)
experiments. Additionally, it provides some utility functions
used also by other DoE packages and some diagnostic functions
for orthogonal arrays.
Author: Ulrike Groemping, with contributions by Boyko Amarov
Maintainer: Ulrike Groemping
DoE.base-0.11-1/DoE.base/R/P4.3.R |only
DoE.base-0.12/DoE.base/DESCRIPTION | 15 +-
DoE.base-0.12/DoE.base/NAMESPACE | 12 +-
DoE.base-0.12/DoE.base/R/P3.3.R | 9 -
DoE.base-0.12/DoE.base/R/P4.4.R | 9 -
DoE.base-0.12/DoE.base/R/aov.design.R |only
DoE.base-0.12/DoE.base/R/length2.R |only
DoE.base-0.12/DoE.base/R/length3.R | 17 ++-
DoE.base-0.12/DoE.base/R/length4.R | 19 ++-
DoE.base-0.12/DoE.base/R/length5.R |only
DoE.base-0.12/DoE.base/R/lm.design.R | 3
DoE.base-0.12/DoE.base/R/oa.design.R | 4
DoE.base-0.12/DoE.base/R/oa.min3.R | 54 ++++++++++
DoE.base-0.12/DoE.base/inst/NEWS | 33 +++++-
DoE.base-0.12/DoE.base/man/generalized.word.length.Rd | 96 ++++++++++++------
DoE.base-0.12/DoE.base/man/lm.design.Rd | 68 ++++++++++--
16 files changed, 258 insertions(+), 81 deletions(-)
Title: Stable Isotope Analysis in R
Diff between siar versions 4.0 dated 2008-12-16 and 4.0.1 dated 2010-08-05
Description: This package takes data on organism isotopes and fits a
Bayesian model to their dietary habits based upon a Gaussian
likelihood with a mixture dirichlet-distributed prior on the
mean. See siardemo() for an example.
Author: Andrew Parnell and Andrew Jackson
Maintainer: Andrew Parnell
siar-4.0.1/siar/DESCRIPTION | 28 -
siar-4.0.1/siar/NAMESPACE | 28 +
siar-4.0.1/siar/R/newgraphwindow.R | 16
siar-4.0.1/siar/R/panelcontour.R | 20
siar-4.0.1/siar/R/panelcor.R | 22
siar-4.0.1/siar/R/panelhist.R | 20
siar-4.0.1/siar/R/siar-internal.R |only
siar-4.0.1/siar/R/siaraddcross.R | 22
siar-4.0.1/siar/R/siardemo.R | 11
siar-4.0.1/siar/R/siarhdrs.R | 170 +++----
siar-4.0.1/siar/R/siarhistograms.R | 218 ++++-----
siar-4.0.1/siar/R/siarloaddata.R | 592 ++++++++++++-------------
siar-4.0.1/siar/R/siarmatrixplot.R | 154 +++---
siar-4.0.1/siar/R/siarmcmcdirichletv4.R | 282 +++++------
siar-4.0.1/siar/R/siarmenu.R | 344 +++++++-------
siar-4.0.1/siar/R/siarmultigrouprun.R | 128 ++---
siar-4.0.1/siar/R/siarplotdata.R | 46 +
siar-4.0.1/siar/R/siarplotdatawrapper.R | 258 +++++-----
siar-4.0.1/siar/R/siarplottarget.R | 46 +
siar-4.0.1/siar/R/siarproportionbygroupplot.R | 242 +++++-----
siar-4.0.1/siar/R/siarproportionbysourceplot.R | 306 ++++++------
siar-4.0.1/siar/R/siarsaveoutput.R | 134 ++---
siar-4.0.1/siar/R/siarsinglegrouprun.R | 128 ++---
siar-4.0.1/siar/R/siarsolomcmcv4.R | 280 +++++------
siar-4.0.1/siar/R/siarsolomultigrouprun.R | 128 ++---
siar-4.0.1/siar/R/siarsolosinglegrouprun.R | 128 ++---
siar-4.0.1/siar/data/allgroups.rda |binary
siar-4.0.1/siar/data/concdepdemo.rda |binary
siar-4.0.1/siar/data/correctionsdemo.rda |binary
siar-4.0.1/siar/data/geese1demo.rda |binary
siar-4.0.1/siar/data/geese2demo.rda |binary
siar-4.0.1/siar/data/sourcesdemo.rda |binary
siar-4.0.1/siar/man/allgroups.Rd | 6
siar-4.0.1/siar/man/concdepdemo.Rd | 6
siar-4.0.1/siar/man/correctionsdemo.Rd | 6
siar-4.0.1/siar/man/geese1demo.Rd | 6
siar-4.0.1/siar/man/geese2demo.Rd | 6
siar-4.0.1/siar/man/panelcontour.Rd | 4
siar-4.0.1/siar/man/panelcor.Rd | 5
siar-4.0.1/siar/man/panelhist.Rd | 7
siar-4.0.1/siar/man/siar-package.Rd | 6
siar-4.0.1/siar/man/siardemo.Rd | 4
siar-4.0.1/siar/man/siarloaddata.Rd | 2
siar-4.0.1/siar/man/siarmcmcdirichletv4.Rd | 2
siar-4.0.1/siar/man/siarmenu.Rd | 3
siar-4.0.1/siar/man/siarsolomcmcv4.Rd | 3
siar-4.0.1/siar/man/sourcesdemo.Rd | 6
siar-4.0/siar/R/allgroups.R |only
siar-4.0/siar/R/concdepdemo.R |only
siar-4.0/siar/R/correctionsdemo.R |only
siar-4.0/siar/R/geese1demo.R |only
siar-4.0/siar/R/geese2demo.R |only
siar-4.0/siar/R/sourcesdemo.R |only
siar-4.0/siar/data/allgroups.txt |only
siar-4.0/siar/data/concdepdemo.txt |only
siar-4.0/siar/data/correctionsdemo.txt |only
siar-4.0/siar/data/geese1demo.txt |only
siar-4.0/siar/data/geese2demo.txt |only
siar-4.0/siar/data/sourcesdemo.txt |only
59 files changed, 1920 insertions(+), 1903 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Diff between depmixS4 versions 0.9-0 dated 2010-05-18 and 1.0-0 dated 2010-08-05
Description: Fit latent (hidden) Markov models on mixed categorical and
continuous (timeseries) data, otherwise known as dependent
mixture models
Author: Ingmar Visser
Maintainer: Ingmar Visser
depmixS4-0.9-0/depmixS4/COPYING |only
depmixS4-0.9-0/depmixS4/inst/doc/depmix-intro.pdf |only
depmixS4-1.0-0/depmixS4/DESCRIPTION | 13 -
depmixS4-1.0-0/depmixS4/NEWS | 13 +
depmixS4-1.0-0/depmixS4/R/EM.R | 8
depmixS4-1.0-0/depmixS4/R/allGenerics.R | 1
depmixS4-1.0-0/depmixS4/R/depmix.R | 187 +++++++++++-----------
depmixS4-1.0-0/depmixS4/R/responseGLM.R | 2
depmixS4-1.0-0/depmixS4/README | 33 ++-
depmixS4-1.0-0/depmixS4/inst/CITATION | 28 ++-
depmixS4-1.0-0/depmixS4/inst/doc/baldist.pdf |only
depmixS4-1.0-0/depmixS4/inst/doc/depmixS4.Rnw |only
depmixS4-1.0-0/depmixS4/inst/doc/depmixS4.bib |only
depmixS4-1.0-0/depmixS4/inst/doc/depmixS4.pdf |only
depmixS4-1.0-0/depmixS4/man/depmix.Rd | 12 -
depmixS4-1.0-0/depmixS4/man/depmix.fit.Rd | 18 +-
depmixS4-1.0-0/depmixS4/man/depmixS4-package.Rd | 7
depmixS4-1.0-0/depmixS4/man/mix.Rd | 4
18 files changed, 182 insertions(+), 144 deletions(-)
Title: Testing for monotonic relationship between gene expression and
doses in a microarray experiment.
Diff between IsoGene versions 1.0-16 dated 2010-03-22 and 1.0-17 dated 2010-08-05
Description: Several testing procedures including the global likelihood
ratio test (Bartholomew, 1961), Williams (1971, 1972), Marcus
(1976), M (Hu et al. 2005) and the modified M (Lin et al. 2007)
are used to test for the monotonic trend in gene expression
with respect to doses. BH (Benjamini and Hochberg 1995) and BY
(Benjamini and Yekutilie 2004) FDR controlling procedures are
applied to adjust the raw p-values obtained from the
permutations.
Author: Lin et al.
Maintainer: Dan Lin
DESCRIPTION | 10 +++++-----
R/IsoRawp.R | 25 +++++++++----------------
R/Isoqqstat.R | 17 ++++++-----------
R/Isoqval.R | 5 ++++-
inst/doc/IsoGene.Rnw | 2 +-
man/IsoSAMPlot.Rd | 2 +-
man/IsoTestSAM.Rd | 2 +-
man/Isoallfdr.Rd | 2 +-
man/Isoqqstat.Rd | 2 +-
man/Isoqval.Rd | 2 +-
10 files changed, 30 insertions(+), 39 deletions(-)
Title: Simulation and analysis of spatial structure of population
genetics data
Diff between Geneclust versions 1.0.0 dated 2009-09-10 and 1.0.1 dated 2010-08-05
Description: Simulation and analysis of spatial structure of population
genetics data
Author: Sophie Ancelet
Maintainer: Sophie Ancelet
DESCRIPTION | 6 +++---
R/zzz.R | 2 +-
man/setplot.Rd | 8 ++++----
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Rainbow plots, bagplots and boxplots for functional data
Diff between rainbow versions 2.0 dated 2010-05-16 and 2.1 dated 2010-08-05
Description: Functions and datasets for functional data display and
outlier detection.
Author: Han Lin Shang and Rob J Hyndman
Maintainer: Han Lin Shang
rainbow-2.0/rainbow/man/lines.fds.Rd |only
rainbow-2.0/rainbow/man/points.fds.Rd |only
rainbow-2.1/rainbow/CHANGELOG | 5 +
rainbow-2.1/rainbow/DESCRIPTION | 8 +-
rainbow-2.1/rainbow/R/SVDplot.R | 105 ++++++++++------------------------
rainbow-2.1/rainbow/R/lines.fds.r | 61 -------------------
rainbow-2.1/rainbow/R/plot.fds.R | 37 ++++++++---
rainbow-2.1/rainbow/R/points.fds.r | 64 +-------------------
rainbow-2.1/rainbow/man/SVDplot.Rd | 23 ++-----
rainbow-2.1/rainbow/man/plot.fds.Rd | 15 +++-
10 files changed, 93 insertions(+), 225 deletions(-)
Title: Realized
Diff between realized versions 0.81 dated 2008-12-15 and 1.0 dated 2010-08-05
Description: Realized Variance Toolkit
Author: Scott Payseur
Maintainer: Scott Payseur
realized-0.81/realized/data/ge.real.cts.rda |only
realized-0.81/realized/data/ge.real.tts.rda |only
realized-0.81/realized/data/msft.real.cts.rda |only
realized-0.81/realized/data/msft.real.tts.rda |only
realized-0.81/realized/inst/LICENCE |only
realized-0.81/realized/inst/RELEASENOTES.txt |only
realized-1.0/realized/.project |only
realized-1.0/realized/DESCRIPTION | 23 +--
realized-1.0/realized/R/.Data |only
realized-1.0/realized/R/realized.R | 133 +++++++++++-----------
realized-1.0/realized/data/ge.real.cts.R |only
realized-1.0/realized/data/ge.real.tts.R |only
realized-1.0/realized/data/msft.real.cts.R |only
realized-1.0/realized/data/msft.real.tts.R |only
realized-1.0/realized/inst/users.manual.08.pdf |only
realized-1.0/realized/man/ge.real.tts.Rd | 5
realized-1.0/realized/man/merge.realizedObject.Rd | 2
realized-1.0/realized/man/rRealizedVariance.Rd | 32 ++---
realized-1.0/realized/man/rScatterReturns.Rd | 4
realized-1.0/realized/man/rSignature.Rd | 8 -
realized-1.0/realized/man/rc.kernel.Rd | 2
realized-1.0/realized/man/rc.timescale.Rd | 3
realized-1.0/realized/man/realized-internal.Rd | 1
realized-1.0/realized/man/rv.avg.Rd | 1
realized-1.0/realized/man/rv.kernel.Rd | 3
realized-1.0/realized/man/rv.timescale.Rd | 2
realized-1.0/realized/realized.chm |only
realized-1.0/realized/src/realized.c | 113 +++++++++---------
realized-1.0/realized/src/realized.h | 2
realized-1.0/realized/users.manual.08.script.q |only
30 files changed, 172 insertions(+), 162 deletions(-)
Title: Species distribution modeling
Diff between dismo versions 0.5-1 dated 2010-07-26 and 0.5-4 dated 2010-08-05
Description: Functions for species distribution modeling, that is,
predicting entire geographic distributions form occurences at
specific sites.
Author: Robert Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer:
dismo-0.5-1/dismo/R/vars.R |only
dismo-0.5-1/dismo/inst/java/mebridge.jar |only
dismo-0.5-1/dismo/inst/javasrc/mebridge.java |only
dismo-0.5-4/dismo/ChangeLog |only
dismo-0.5-4/dismo/DESCRIPTION | 18
dismo-0.5-4/dismo/R/bioclim.predict.R | 32
dismo-0.5-4/dismo/R/biovars.R |only
dismo-0.5-4/dismo/R/ecocrop.R |only
dismo-0.5-4/dismo/R/evaluate.R | 6
dismo-0.5-4/dismo/R/geocode.R | 8
dismo-0.5-4/dismo/R/gmap.R | 26
dismo-0.5-4/dismo/R/gorilla.R |only
dismo-0.5-4/dismo/R/maxent.R | 24
dismo-0.5-4/dismo/R/maxent.predict.R | 13
dismo-0.5-4/dismo/R/moving.R |only
dismo-0.5-4/dismo/R/prepareData.R | 2
dismo-0.5-4/dismo/data/ECOcrops.RData |only
dismo-0.5-4/dismo/inst/doc/brt.pdf |binary
dismo-0.5-4/dismo/inst/doc/sdm.Rnw |only
dismo-0.5-4/dismo/inst/doc/sdm.pdf |119327 +++++++++-----------------
dismo-0.5-4/dismo/inst/java/mebridge1.jar |only
dismo-0.5-4/dismo/inst/java/mebridge2.jar |only
dismo-0.5-4/dismo/inst/javasrc/mebridge1.java |only
dismo-0.5-4/dismo/inst/javasrc/mebridge2.java |only
dismo-0.5-4/dismo/man/bioclim.Rd | 23
dismo-0.5-4/dismo/man/dismo-package.Rd | 2
dismo-0.5-4/dismo/man/ecocrop.Rd |only
dismo-0.5-4/dismo/man/gbif.Rd | 11
dismo-0.5-4/dismo/man/geocode.Rd | 4
dismo-0.5-4/dismo/man/gmap.Rd | 55
dismo-0.5-4/dismo/man/maxent.Rd | 30
dismo-0.5-4/dismo/man/moving.Rd |only
dismo-0.5-4/dismo/man/predict.Rd | 10
dismo-0.5-4/dismo/man/prepareData.Rd | 11
34 files changed, 45708 insertions(+), 73894 deletions(-)
Title: combinatorics utilities
Diff between combinat versions 0.0-7 dated 2009-10-11 and 0.0-8 dated 2010-08-05
Description: routines for combinatorics
Author: Scott Chasalow
Maintainer: Vince Carey
DESCRIPTION | 6 +++---
man/dmnom.Rd | 8 ++++----
man/hcube.Rd | 8 ++++----
man/nsimplex.Rd | 4 ++--
man/permn.Rd | 4 ++--
man/rmultinomial.Rd | 9 +++++----
man/x2u.Rd | 10 +++++-----
man/xsimplex.Rd | 23 ++++++++++++-----------
8 files changed, 37 insertions(+), 35 deletions(-)
Title: Bolstad functions
Diff between Bolstad versions 0.2-17 dated 2010-03-25 and 0.2-18 dated 2010-08-05
Description: A set of R functions and data sets for the book
Introduction to Bayesian Statistics, Bolstad, W.M. (2007), John
Wiley & Sons ISBN 0-471-27020-2
Author: James Curran
Maintainer: James M. Curran
DESCRIPTION | 8 +++----
R/nvaricp.r | 2 -
R/poisgcp.r | 61 +++++++++++++++++++++++++++----------------------------
R/sintegral.r | 44 +++++++++++++++++++++------------------
man/binogcp.Rd | 19 +++++++++--------
man/normgcp.Rd | 9 ++++----
man/nvaricp.Rd | 5 ++--
man/poisgcp.Rd | 16 +++++++-------
man/sintegral.Rd | 50 ++++++++++++++++++++++++++++++++++++---------
9 files changed, 126 insertions(+), 88 deletions(-)