Title: Tools for analyzing QTL experiments
Diff between qtl versions 1.22-21 dated 2011-11-29 and 1.23-16 dated 2012-03-06
Description: Analysis of experimental crosses to identify genes (called
quantitative trait loci, QTLs) contributing to variation in
quantitative traits.
Author: Karl W Broman
Maintainer: Karl W Broman
DESCRIPTION | 16 ++-
MD5 | 69 +++++++++-------
NAMESPACE | 8 +
R/argmax.geno.R | 6 -
R/calc.genoprob.R | 14 +--
R/calc.pairprob.R | 7 -
R/countXO.R | 6 -
R/effectplot.R | 7 +
R/effectscan.R | 7 +
R/errorlod.R | 6 -
R/est.map.R | 4
R/inferFounderHap.R |only
R/mqmscanall.R | 11 +-
R/plot.R | 7 +
R/pull_stuff.R |only
R/readMWril.R | 33 ++++++-
R/ril48_reorg.R | 24 +++--
R/ripple.R | 6 -
R/sim.geno.R | 7 -
R/simulate.R | 7 +
R/summary.cross.R | 16 ++-
R/tryallpositions.R | 4
R/util.R | 203 ++++++++++++++++++++----------------------------
inst/README.txt | 16 +--
inst/STATUS.txt | 41 +++++++++
inst/TODO.txt | 22 +++--
man/drop.nullmarkers.Rd | 2
man/inferFounderHap.Rd |only
man/nullmarkers.Rd |only
man/pull.argmaxgeno.Rd |only
man/pull.draws.Rd |only
man/pull.geno.Rd | 4
man/pull.genoprob.Rd |only
man/readMWril.Rd | 2
man/stepwiseqtl.Rd | 4
src/hmm_bgmagic16.c |only
src/hmm_bgmagic16.h |only
src/inferFounderHap.c |only
src/inferFounderHap.h |only
src/util.c | 38 ++++++--
src/util.h | 19 +++-
41 files changed, 364 insertions(+), 252 deletions(-)
Title: TDT tests for extended haplotypes
Diff between tdthap versions 1.1-2 dated 2007-11-22 and 1.1-3 dated 2012-03-06
Description: Clayton, D. and Jones, H.B. (1999),
Transmission/disequilibrium tests for extended marker
haplotypes, Am. J. Hum. Gen., 65:1161-1169.
Author: David Clayton
Maintainer: Jing Hua Zhao
ChangeLog |only
DESCRIPTION | 16 +++---
MD5 |only
NAMESPACE |only
R/tdthap.R | 3 -
inst/hap-transmit-temporary-file |only
man/hap.transmit.Rd | 7 +-
src/nuc_fam.c | 94 +++++++++++++++++++--------------------
src/nuc_fam.h | 27 +++++------
src/tdt.c | 15 +++---
10 files changed, 80 insertions(+), 82 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.35 dated 2012-02-17 and 0.2.36 dated 2012-03-06
Description: R and Armadillo integration using Rcpp Armadillo is a
templated C++ linear algebra library (by Conrad Sanderson) that
aims 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 (currently version 2.4.4). 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.
Armadillo is licensed under the GNU LGPL version 3 or later, while
RcppArmadillo (the Rcpp bindings/bridge to Armadillo) is
licenses under the GNU GPL version 2 or later, as is the rest
of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates
ChangeLog | 6 ++
DESCRIPTION | 10 +--
MD5 | 26 ++++-----
inst/NEWS | 8 +++
inst/include/armadillo | 8 ++-
inst/include/armadillo_bits/arma_version.hpp | 2
inst/include/armadillo_bits/auxlib_meat.hpp | 38 ++++++--------
inst/include/armadillo_bits/fn_conv_to.hpp | 12 ++--
inst/include/armadillo_bits/fn_qr.hpp | 6 +-
inst/include/armadillo_bits/fn_syl_lyap.hpp | 17 ++++--
inst/include/armadillo_bits/subview_elem1_meat.hpp | 4 -
inst/include/armadillo_bits/wall_clock_bones.hpp | 12 ++--
inst/include/armadillo_bits/wall_clock_meat.hpp | 56 ++++++++++-----------
man/RcppArmadillo-package.Rd | 4 -
14 files changed, 118 insertions(+), 91 deletions(-)
Title: Simultaneous manipulation of multiple arrays of data, with
data.list objects
Diff between multitable versions 1.2 dated 2011-11-02 and 1.3 dated 2012-03-06
Description: Many data sets do not easily fit into a single data frame.
Storing such data in a single data frame often results in
either large numbers of meaningless missing values or storage
of redundant information; yet storing them in multiple data
frames often results in long difficult-to-read workflows. The
multitable package introduces a new data object called a
data.list, which organises several data tables as a single R
object. The primary goal of multitable is to provide a more
intuitive framework for manipulating multiple-table data in R.
As data.lists can be coerced to data.frames, they can be used
with all R functions that accept an object that is coercible to
a data.frame (e.g. lm; plot; lme; and many more).
Author: Steve C Walker
Maintainer: Steve C Walker
multitable-1.2/multitable/R/big.kronecker.R |only
multitable-1.2/multitable/R/onAttach.R |only
multitable-1.2/multitable/inst/doc/Bibliography.bib |only
multitable-1.2/multitable/inst/doc/Makefile.txt |only
multitable-1.2/multitable/inst/doc/RJournal.sty |only
multitable-1.2/multitable/inst/doc/Untitled.rtf |only
multitable-1.3/multitable/DESCRIPTION | 21 +
multitable-1.3/multitable/MD5 | 82 +++--
multitable-1.3/multitable/NAMESPACE | 8
multitable-1.3/multitable/NEWS | 97 ++++++
multitable-1.3/multitable/R/Extract.data.list.R | 13
multitable-1.3/multitable/R/accessor.functions.R | 40 +-
multitable-1.3/multitable/R/aperm.R | 51 ++-
multitable-1.3/multitable/R/as.R | 212 +++++++++----
multitable-1.3/multitable/R/data.list.R | 2
multitable-1.3/multitable/R/dims_to_vars.R |only
multitable-1.3/multitable/R/dlapply.R |only
multitable-1.3/multitable/R/dlcast.R | 41 ++
multitable-1.3/multitable/R/dlmelt.R |only
multitable-1.3/multitable/R/drop.R |only
multitable-1.3/multitable/R/fc.data.list.R | 1
multitable-1.3/multitable/R/merge.data.list.R |only
multitable-1.3/multitable/R/print.data.list.R | 17 -
multitable-1.3/multitable/R/summary.data.list.R | 11
multitable-1.3/multitable/R/utilities.R | 11
multitable-1.3/multitable/R/variablearithmetic.R |only
multitable-1.3/multitable/R/variablize.R | 1
multitable-1.3/multitable/R/with.R |only
multitable-1.3/multitable/R/zzz.R |only
multitable-1.3/multitable/data/bci.rda |only
multitable-1.3/multitable/data/fake.community.rda |binary
multitable-1.3/multitable/data/higgins.rda |only
multitable-1.3/multitable/inst/doc/multitable.pdf |binary
multitable-1.3/multitable/man/Extract.data.list.Rd | 24 -
multitable-1.3/multitable/man/Ops.data.list.Rd |only
multitable-1.3/multitable/man/as.data.list.Rd | 26 -
multitable-1.3/multitable/man/bci.Rd |only
multitable-1.3/multitable/man/bm.Rd | 2
multitable-1.3/multitable/man/data.list.Rd | 20 -
multitable-1.3/multitable/man/dimnames.data.list.Rd | 2
multitable-1.3/multitable/man/dims_to_vars.Rd |only
multitable-1.3/multitable/man/dlapply.Rd |only
multitable-1.3/multitable/man/dlcast.Rd | 41 +-
multitable-1.3/multitable/man/dlmelt.Rd |only
multitable-1.3/multitable/man/drop.Rd |only
multitable-1.3/multitable/man/higgins.Rd |only
multitable-1.3/multitable/man/merge.data.list.Rd |only
multitable-1.3/multitable/man/multitable-package.Rd | 51 +--
multitable-1.3/multitable/man/read.multitable.Rd | 10
multitable-1.3/multitable/man/summary.data.list.Rd | 10
multitable-1.3/multitable/man/variable.Rd |only
multitable-1.3/multitable/man/with.Rd |only
multitable-1.3/multitable/tests/test.R | 305 +++++++++++++++++++-
multitable-1.3/multitable/vignettes |only
54 files changed, 849 insertions(+), 250 deletions(-)
Title: EM Estimation of Malaria Haplotype Probabilities from Multiply
Infected Human Blood Samples
Diff between malaria.em versions 1.0 dated 2012-02-14 and 2.0 dated 2012-03-06
Description: Using EM algorithm to estimate malaria haplotype
probabilities and the number of infections from multiply
infected human blood samples. Estimated haplotype probabilities
and their standard error are reported.
Author: Xiaohong Li
Maintainer: Xiaohong Li
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NAMESPACE | 1 +
R/malaria.em.R | 23 +++++++++++++++++++----
man/malaria.em.Rd | 5 ++---
5 files changed, 30 insertions(+), 15 deletions(-)
Title: Hadoop InteractiVE
Diff between hive versions 0.1-13 dated 2011-12-01 and 0.1-14 dated 2012-03-06
Description: Hadoop InteractiVE, is an R extension facilitating
distributed computing via the MapReduce paradigm. It provides
an easy to use interface to Hadoop, the Hadoop Distributed File
System (HDFS), and Hadoop Streaming.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre]
Maintainer: Stefan Theussl
ChangeLog | 6 ++++--
DESCRIPTION | 19 +++++++++----------
MD5 | 4 ++--
3 files changed, 15 insertions(+), 14 deletions(-)
Title: Distributed Storage and List
Diff between DSL versions 0.1-0 dated 2011-12-14 and 0.1-1 dated 2012-03-06
Description: A package providing functions and methods for handling
distributed storage (DStorage) and lists (DLlist). It
implements an abstract DList class for storing large list-type
objects in a distributed manner. In doing so it uses a well
defined storage backend implemented based on the DStorage
class. It allows for processing such DLists on distributed
systems efficiently.
Author: Ingo Feinerer [aut], Stefan Theussl [aut, cre], Christian
Buchta [ctb]
Maintainer: Stefan Theussl
DSL-0.1-0/DSL/inst/doc/DSL.aux |only
DSL-0.1-0/DSL/inst/doc/DSL.bbl |only
DSL-0.1-0/DSL/inst/doc/DSL.bib |only
DSL-0.1-0/DSL/inst/doc/DSL.blg |only
DSL-0.1-0/DSL/inst/doc/DSL.log |only
DSL-0.1-0/DSL/inst/doc/DSL.tex |only
DSL-0.1-1/DSL/DESCRIPTION | 26 ++++++++------
DSL-0.1-1/DSL/MD5 | 18 +++------
DSL-0.1-1/DSL/R/list.R | 2 -
DSL-0.1-1/DSL/R/storage.R | 6 ++-
DSL-0.1-1/DSL/inst/doc/DSL.Rnw | 75 +++++++++++++++++++++++++++++++++--------
DSL-0.1-1/DSL/inst/doc/DSL.pdf |binary
DSL-0.1-1/DSL/vignettes |only
13 files changed, 89 insertions(+), 38 deletions(-)
Title: combined miRNA- and mRNA-testing
Diff between miRtest versions 1.1 dated 2011-05-29 and 1.2 dated 2012-03-06
Description: combined miRNA- and mRNA-testing
Author: Stephan Artmann, Klaus Jung, Tim Beissbarth
Maintainer: Stephan Artmann
miRtest-1.1/miRtest/inst/doc/miRtest.Rnw.backup |only
miRtest-1.1/miRtest/inst/doc/miRtest.bbl |only
miRtest-1.1/miRtest/inst/doc/miRtest.blg |only
miRtest-1.1/miRtest/inst/doc/miRtest.dvi |only
miRtest-1.2/miRtest/DESCRIPTION | 10 -
miRtest-1.2/miRtest/MD5 |only
miRtest-1.2/miRtest/NAMESPACE | 2
miRtest-1.2/miRtest/R/miRtest.R | 164 +++---------------------
miRtest-1.2/miRtest/data |only
miRtest-1.2/miRtest/inst/doc/miRtest.Rnw | 38 +++++
miRtest-1.2/miRtest/inst/doc/miRtest.pdf |binary
miRtest-1.2/miRtest/man/A.Rd |only
miRtest-1.2/miRtest/man/X.Rd |only
miRtest-1.2/miRtest/man/Y.Rd |only
miRtest-1.2/miRtest/man/miRtest.Rd | 4
15 files changed, 64 insertions(+), 154 deletions(-)
Title: Diagnostic tools for two-level normal hierarchical linear models
Diff between HLMdiag versions 0.1.4 dated 2012-01-28 and 0.1.5 dated 2012-03-06
Description: A suite of diagnostic tools for two-level normal
hierarchical linear models. The package offers not only
traditional case-deletion diagnostics (Cook's distance,
covratio, covtrace, and MDFFITS) but also provides graphics for
residual analysis. Currently, case deletion is performed by
iteratively refitting the model using lmer in the lme4 package,
so for data sets with many groups, computation is currently
slow.
Author: Adam Loy
Maintainer: Adam Loy
DESCRIPTION | 9 +++++----
MD5 | 6 +++---
NAMESPACE | 2 ++
NEWS | 3 +++
4 files changed, 13 insertions(+), 7 deletions(-)
Title: Parallel nonparametric kernel smoothing methods for mixed data
types
Diff between npRmpi versions 0.40-12 dated 2011-11-25 and 0.40-13 dated 2012-03-06
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. This
package is a parallel implementation of the np package based on
the MPI specification that incorporates the Rmpi package (Hao
Yu
Author: Tristen Hayfield
Maintainer: Jeffrey S. Racine
npRmpi-0.40-12/npRmpi/inst/doc/jss.bst |only
npRmpi-0.40-12/npRmpi/inst/doc/jss.cls |only
npRmpi-0.40-13/npRmpi/CHANGELOG | 11
npRmpi-0.40-13/npRmpi/DESCRIPTION | 25 -
npRmpi-0.40-13/npRmpi/MD5 | 82 +--
npRmpi-0.40-13/npRmpi/NAMESPACE | 3
npRmpi-0.40-13/npRmpi/R/Rcoll.R | 4
npRmpi-0.40-13/npRmpi/R/Rparutilities.R | 10
npRmpi-0.40-13/npRmpi/R/bandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/conbandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/condensity.R | 2
npRmpi-0.40-13/npRmpi/R/condistribution.R | 2
npRmpi-0.40-13/npRmpi/R/density.R | 2
npRmpi-0.40-13/npRmpi/R/distribution.R | 2
npRmpi-0.40-13/npRmpi/R/np.plregression.bw.R | 2
npRmpi-0.40-13/npRmpi/R/npregiv.R | 310 +++++++++++--
npRmpi-0.40-13/npRmpi/R/npregivderiv.R |only
npRmpi-0.40-13/npRmpi/R/plbandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/plregression.R | 2
npRmpi-0.40-13/npRmpi/R/qregression.R | 2
npRmpi-0.40-13/npRmpi/R/rbandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/regression.R | 2
npRmpi-0.40-13/npRmpi/R/rng.R | 6
npRmpi-0.40-13/npRmpi/R/sibandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/singleindex.R | 2
npRmpi-0.40-13/npRmpi/R/smoothbandwidth.R | 2
npRmpi-0.40-13/npRmpi/R/smoothcoefficient.R | 2
npRmpi-0.40-13/npRmpi/R/util.R | 4
npRmpi-0.40-13/npRmpi/R/zzz.R | 2
npRmpi-0.40-13/npRmpi/data/cps71.rda |binary
npRmpi-0.40-13/npRmpi/inst/doc/np_faq.pdf |binary
npRmpi-0.40-13/npRmpi/man/np.kernelsum.Rd | 7
npRmpi-0.40-13/npRmpi/man/np.regressioniv.Rd | 106 ++++
npRmpi-0.40-13/npRmpi/man/np.regressionivderiv.Rd |only
npRmpi-0.40-13/npRmpi/npver | 2
npRmpi-0.40-13/npRmpi/src/jksum.c | 44 +
npRmpi-0.40-13/npRmpi/src/kernelb.c | 21
npRmpi-0.40-13/npRmpi/src/kernele.c | 492 +++++++++-------------
npRmpi-0.40-13/npRmpi/src/mat_vec.c | 19
npRmpi-0.40-13/npRmpi/src/matrix.c | 42 -
npRmpi-0.40-13/npRmpi/src/matrix.h | 3
npRmpi-0.40-13/npRmpi/src/np.c | 20
npRmpi-0.40-13/npRmpi/src/nr.c | 11
npRmpi-0.40-13/npRmpi/src/statmods.c | 111 ++--
44 files changed, 811 insertions(+), 556 deletions(-)
Title: Nonparametric kernel smoothing methods for mixed data types
Diff between np versions 0.40-12 dated 2011-11-25 and 0.40-13 dated 2012-03-06
Description: This package provides a variety of nonparametric (and
semiparametric) kernel methods that seamlessly handle a mix of
continuous, unordered, and ordered factor data types. We would
like to gratefully acknowledge support from the Natural
Sciences and Engineering Research Council of Canada
(NSERC:www.nserc.ca), the Social Sciences and Humanities
Research Council of Canada (SSHRC:www.sshrc.ca), and the Shared
Hierarchical Academic Research Computing Network
(SHARCNET:www.sharcnet.ca).
Author: Tristen Hayfield
Maintainer: Jeffrey S. Racine
np-0.40-12/np/inst/doc/jss.bst |only
np-0.40-12/np/inst/doc/jss.cls |only
np-0.40-13/np/CHANGELOG | 11
np-0.40-13/np/DESCRIPTION | 21 -
np-0.40-13/np/MD5 | 82 ++---
np-0.40-13/np/NAMESPACE | 3
np-0.40-13/np/R/bandwidth.R | 2
np-0.40-13/np/R/conbandwidth.R | 2
np-0.40-13/np/R/condensity.R | 2
np-0.40-13/np/R/condistribution.R | 2
np-0.40-13/np/R/density.R | 2
np-0.40-13/np/R/distribution.R | 2
np-0.40-13/np/R/np.plregression.bw.R | 2
np-0.40-13/np/R/npregiv.R | 310 ++++++++++++++++--
np-0.40-13/np/R/npregivderiv.R |only
np-0.40-13/np/R/plbandwidth.R | 2
np-0.40-13/np/R/plregression.R | 2
np-0.40-13/np/R/qregression.R | 2
np-0.40-13/np/R/rbandwidth.R | 2
np-0.40-13/np/R/regression.R | 2
np-0.40-13/np/R/sibandwidth.R | 2
np-0.40-13/np/R/singleindex.R | 2
np-0.40-13/np/R/smoothbandwidth.R | 2
np-0.40-13/np/R/smoothcoefficient.R | 2
np-0.40-13/np/R/util.R | 4
np-0.40-13/np/R/zzz.R | 2
np-0.40-13/np/data/cps71.rda |binary
np-0.40-13/np/inst/doc/entropy_np.pdf |binary
np-0.40-13/np/inst/doc/np.pdf |binary
np-0.40-13/np/inst/doc/np_faq.pdf |binary
np-0.40-13/np/man/np.kernelsum.Rd | 7
np-0.40-13/np/man/np.regressioniv.Rd | 106 +++++-
np-0.40-13/np/man/np.regressionivderiv.Rd |only
np-0.40-13/np/npver | 2
np-0.40-13/np/src/jksum.c | 44 +-
np-0.40-13/np/src/kernelb.c | 21 -
np-0.40-13/np/src/kernele.c | 492 +++++++++++++-----------------
np-0.40-13/np/src/mat_vec.c | 19 -
np-0.40-13/np/src/matrix.c | 42 +-
np-0.40-13/np/src/matrix.h | 3
np-0.40-13/np/src/np.c | 20 -
np-0.40-13/np/src/nr.c | 11
np-0.40-13/np/src/statmods.c | 111 +++---
np-0.40-13/np/src/tree.c | 20 -
44 files changed, 810 insertions(+), 553 deletions(-)
Title: Methods that apply to rows and columns of a matrix
Diff between matrixStats versions 0.4.3 dated 2011-12-13 and 0.4.4 dated 2012-03-06
Description: This packages provides methods operating on rows and
columns of matrices. The objective is to have all methods
being optimized for speed and memory consumption.
Author: Henrik Bengtsson, Hector Corrada Bravo, Robert Gentleman,
Harris Jaffee
Maintainer: Henrik Bengtsson
DESCRIPTION | 15 +++++++++------
MD5 | 15 ++++++++-------
R/rowMads.R | 7 ++++++-
inst/NEWS | 10 +++++++++-
src/anyMissing.c | 4 ----
tests/rowMads.R |only
tests/rowMedians.R | 7 ++++---
tests/rowRanges.R | 32 +++++++++++++++++++-------------
tests/rowRanks.R | 3 ++-
9 files changed, 57 insertions(+), 36 deletions(-)
Title: Functional Data Analysis and Utilities for Statistical Computing
(fda.usc)
Diff between fda.usc versions 0.9.5 dated 2011-04-27 and 0.9.6 dated 2012-03-06
Description: This package implements functional data methods.
Author: Febrero-Bande, M. and Oviedo de la Fuente, M.
Maintainer: Oviedo de la Fuente, M.
fda.usc-0.9.5/fda.usc/R/classif.kernel.fb.R |only
fda.usc-0.9.5/fda.usc/R/classif.kernel.fd.R |only
fda.usc-0.9.5/fda.usc/R/classif.knn.fd.R |only
fda.usc-0.9.5/fda.usc/R/pc.cor.R |only
fda.usc-0.9.5/fda.usc/R/pc.fdata.R |only
fda.usc-0.9.5/fda.usc/R/pc.svd.fdata.r |only
fda.usc-0.9.5/fda.usc/R/pls.fdata.r |only
fda.usc-0.9.5/fda.usc/R/predict.classif.fd.R |only
fda.usc-0.9.5/fda.usc/R/print.classif.fd.r |only
fda.usc-0.9.5/fda.usc/R/summary.classif.fd.R |only
fda.usc-0.9.5/fda.usc/man/classif.kernel.fb.Rd |only
fda.usc-0.9.5/fda.usc/man/classif.kernel.fd.Rd |only
fda.usc-0.9.5/fda.usc/man/classif.knn.fd.Rd |only
fda.usc-0.9.5/fda.usc/man/pc.cor.Rd |only
fda.usc-0.9.5/fda.usc/man/pc.fdata.Rd |only
fda.usc-0.9.5/fda.usc/man/pls.fdata.Rd |only
fda.usc-0.9.5/fda.usc/man/predict.classif.fd.Rd |only
fda.usc-0.9.5/fda.usc/man/summary.classif.fd.Rd |only
fda.usc-0.9.6/fda.usc/DESCRIPTION | 14 +-
fda.usc-0.9.6/fda.usc/MD5 |only
fda.usc-0.9.6/fda.usc/NAMESPACE |only
fda.usc-0.9.6/fda.usc/NEWS | 16 ++
fda.usc-0.9.6/fda.usc/R/CV.S.R | 99 ++++++++-------
fda.usc-0.9.6/fda.usc/R/Descriptive.R | 1
fda.usc-0.9.6/fda.usc/R/GCV.S.R | 108 ++++++++++++-----
fda.usc-0.9.6/fda.usc/R/S.KNN.R | 15 +-
fda.usc-0.9.6/fda.usc/R/S.LLR.R | 6
fda.usc-0.9.6/fda.usc/R/S.NW.R | 23 +--
fda.usc-0.9.6/fda.usc/R/S.basis.R | 10 -
fda.usc-0.9.6/fda.usc/R/classif.glm.R |only
fda.usc-0.9.6/fda.usc/R/classif.kernel.R |only
fda.usc-0.9.6/fda.usc/R/classif.knn.R |only
fda.usc-0.9.6/fda.usc/R/cond.F.R | 2
fda.usc-0.9.6/fda.usc/R/cond.quantile.R | 7 -
fda.usc-0.9.6/fda.usc/R/create.fdata.basis.R | 24 +++
fda.usc-0.9.6/fda.usc/R/depth.RP.r | 26 +++-
fda.usc-0.9.6/fda.usc/R/depth.RPD.r | 152 +++++++++++++-----------
fda.usc-0.9.6/fda.usc/R/dis.cos.cor.R |only
fda.usc-0.9.6/fda.usc/R/fda.usc.internal.R | 47 +++++++
fda.usc-0.9.6/fda.usc/R/fdata.bootstrap.r | 21 +--
fda.usc-0.9.6/fda.usc/R/fdata.methods.R |only
fda.usc-0.9.6/fda.usc/R/fdata2pc.r |only
fda.usc-0.9.6/fda.usc/R/fdata2pls.r |only
fda.usc-0.9.6/fda.usc/R/fregre.basis.cv.R | 4
fda.usc-0.9.6/fda.usc/R/fregre.bootstrap.R |only
fda.usc-0.9.6/fda.usc/R/fregre.glm.R | 103 ++++++++++------
fda.usc-0.9.6/fda.usc/R/fregre.lm.R | 7 -
fda.usc-0.9.6/fda.usc/R/fregre.np.cv.r | 128 ++++++++++++++++----
fda.usc-0.9.6/fda.usc/R/fregre.np.r | 84 +++++++++++--
fda.usc-0.9.6/fda.usc/R/fregre.pc.R | 4
fda.usc-0.9.6/fda.usc/R/fregre.pc.cv.R | 26 +++-
fda.usc-0.9.6/fda.usc/R/fregre.plm.R | 27 ++--
fda.usc-0.9.6/fda.usc/R/fregre.pls.R | 18 +-
fda.usc-0.9.6/fda.usc/R/fregre.pls.cv.R | 78 ++++++++----
fda.usc-0.9.6/fda.usc/R/int.simpson.R | 1
fda.usc-0.9.6/fda.usc/R/kmeans.center.ini.R | 9 -
fda.usc-0.9.6/fda.usc/R/kmeans.centers.update.R | 2
fda.usc-0.9.6/fda.usc/R/kmeans.fd.R | 40 ++++--
fda.usc-0.9.6/fda.usc/R/metric.lp.R | 14 +-
fda.usc-0.9.6/fda.usc/R/predict.classif.R |only
fda.usc-0.9.6/fda.usc/R/predict.fregre.fd.R | 63 ++++-----
fda.usc-0.9.6/fda.usc/R/predict.fregre.glm.R | 11 +
fda.usc-0.9.6/fda.usc/R/predict.fregre.lm.R | 55 ++++----
fda.usc-0.9.6/fda.usc/R/predict.fregre.plm.R | 47 +++----
fda.usc-0.9.6/fda.usc/R/print.classif.r |only
fda.usc-0.9.6/fda.usc/R/print.fregre.fd.r | 1
fda.usc-0.9.6/fda.usc/R/rproc2fdata.R |only
fda.usc-0.9.6/fda.usc/R/semimetric.NPFDA.r | 132 ++++++++++----------
fda.usc-0.9.6/fda.usc/R/semimetric.basis.R | 18 +-
fda.usc-0.9.6/fda.usc/R/summary.classif.R |only
fda.usc-0.9.6/fda.usc/R/summary.fdata.comp.r |only
fda.usc-0.9.6/fda.usc/R/summary.fregre.fd.r | 57 +++++----
fda.usc-0.9.6/fda.usc/Rplots.pdf |only
fda.usc-0.9.6/fda.usc/data/aemet.rda |binary
fda.usc-0.9.6/fda.usc/data/phoneme.rda |binary
fda.usc-0.9.6/fda.usc/data/poblenou.rda |binary
fda.usc-0.9.6/fda.usc/data/tecator.rda |binary
fda.usc-0.9.6/fda.usc/man/CV.S.Rd | 5
fda.usc-0.9.6/fda.usc/man/Depth.Rd | 10 -
fda.usc-0.9.6/fda.usc/man/Descriptive.Rd | 13 +-
fda.usc-0.9.6/fda.usc/man/GCV.S.Rd | 13 +-
fda.usc-0.9.6/fda.usc/man/Kernel.asymmetric.Rd | 12 -
fda.usc-0.9.6/fda.usc/man/S.basis.Rd | 3
fda.usc-0.9.6/fda.usc/man/S.np.Rd | 12 -
fda.usc-0.9.6/fda.usc/man/anova.RPm.Rd | 10 -
fda.usc-0.9.6/fda.usc/man/anova.hetero.Rd | 4
fda.usc-0.9.6/fda.usc/man/classif.glm.Rd |only
fda.usc-0.9.6/fda.usc/man/classif.kernel.Rd |only
fda.usc-0.9.6/fda.usc/man/classif.knn.Rd |only
fda.usc-0.9.6/fda.usc/man/cond.F.Rd | 17 +-
fda.usc-0.9.6/fda.usc/man/cond.mode.Rd | 21 +--
fda.usc-0.9.6/fda.usc/man/cond.quantile.Rd | 15 +-
fda.usc-0.9.6/fda.usc/man/create.fdata.basis.Rd | 13 +-
fda.usc-0.9.6/fda.usc/man/depth.RP.Rd | 3
fda.usc-0.9.6/fda.usc/man/depth.RPD.Rd | 5
fda.usc-0.9.6/fda.usc/man/depth.mode.Rd | 2
fda.usc-0.9.6/fda.usc/man/dis.cos.cor.Rd |only
fda.usc-0.9.6/fda.usc/man/fda.usc-package.Rd | 23 +--
fda.usc-0.9.6/fda.usc/man/fda.usc.internal.Rd | 6
fda.usc-0.9.6/fda.usc/man/fdata.methods.Rd |only
fda.usc-0.9.6/fda.usc/man/fdata2pc.Rd |only
fda.usc-0.9.6/fda.usc/man/fdata2pls.Rd |only
fda.usc-0.9.6/fda.usc/man/fregre.bootstrap.Rd |only
fda.usc-0.9.6/fda.usc/man/fregre.glm.Rd | 23 ++-
fda.usc-0.9.6/fda.usc/man/fregre.np.Rd | 5
fda.usc-0.9.6/fda.usc/man/fregre.np.cv.Rd | 6
fda.usc-0.9.6/fda.usc/man/fregre.pc.Rd | 6
fda.usc-0.9.6/fda.usc/man/fregre.plm.Rd | 18 +-
fda.usc-0.9.6/fda.usc/man/fregre.pls.Rd | 2
fda.usc-0.9.6/fda.usc/man/fregre.pls.cv.Rd | 6
fda.usc-0.9.6/fda.usc/man/influence.fdata.Rd | 4
fda.usc-0.9.6/fda.usc/man/influence.quan.Rd | 9 -
fda.usc-0.9.6/fda.usc/man/kmeans.fd.Rd | 11 -
fda.usc-0.9.6/fda.usc/man/metric.lp.Rd | 12 -
fda.usc-0.9.6/fda.usc/man/min.basis.Rd | 10 -
fda.usc-0.9.6/fda.usc/man/min.np.Rd | 8 -
fda.usc-0.9.6/fda.usc/man/plot.fdata.Rd | 12 -
fda.usc-0.9.6/fda.usc/man/predict.classif.Rd |only
fda.usc-0.9.6/fda.usc/man/predict.fregre.fd.Rd | 4
fda.usc-0.9.6/fda.usc/man/predict.fregre.glm.Rd | 4
fda.usc-0.9.6/fda.usc/man/predict.fregre.lm.Rd | 4
fda.usc-0.9.6/fda.usc/man/predict.fregre.plm.Rd | 4
fda.usc-0.9.6/fda.usc/man/rproc2fdata.Rd |only
fda.usc-0.9.6/fda.usc/man/semimetric.NPFDA.Rd | 73 +++++++----
fda.usc-0.9.6/fda.usc/man/summary.classif.Rd |only
fda.usc-0.9.6/fda.usc/man/summary.fdata.comp.Rd |only
fda.usc-0.9.6/fda.usc/man/summary.fregre.fd.Rd | 28 +---
fda.usc-0.9.6/fda.usc/script/Classif_boosting.R |only
fda.usc-0.9.6/fda.usc/script/Classif_phoneme.R | 115 +++++++++++++-----
129 files changed, 1297 insertions(+), 754 deletions(-)
Title: Basic functions for supporting an implementation of choice
experiments
Diff between support.CEs versions 0.2-0 dated 2011-07-23 and 0.2-1 dated 2012-03-06
Description: The support.CEs package provides seven basic functions
that support an implementation of choice experiments.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki
DESCRIPTION | 8 ++++----
MD5 |only
NAMESPACE |only
NEWS |only
R/Lma.design.R | 11 +++++++++--
R/make.design.matrix.R | 27 +++++++++++++++------------
R/questionnaire.R | 16 +++++++++-------
R/rotation.design.R | 11 +++++++++--
data/syn.res1.rda |binary
data/syn.res2.rda |binary
man/Lma.design.Rd | 7 ++++---
man/make.dataset.Rd | 12 +++++++-----
man/make.design.matrix.Rd | 22 ++++++----------------
man/mwtp.Rd | 2 +-
man/questionnaire.Rd | 25 +++++--------------------
man/rotation.design.Rd | 11 ++++++-----
man/support.CEs-package.Rd | 4 ++--
man/syn.res1.Rd | 6 +++---
man/syn.res2.Rd | 6 +++---
19 files changed, 83 insertions(+), 85 deletions(-)
Title: General Markov Chain Monte Carlo for Bayesian Inference using
adaptive Metropolis-Hastings sampling
Diff between MHadaptive versions 1.1-5 dated 2011-12-11 and 1.1-7 dated 2012-03-06
Description: Performs general Metropolis-Hastings Markov Chain Monte
Carlo sampling of a user defined function which returns the
un-normalized value (likelihood times prior) of a Bayesian
model. The proposal variance-covariance structure is updated
adaptively for efficient mixing when the structure of the
target distribution is unknown. The package also provides some
functions for Bayesian inference including Bayesian Credible
Intervals (BCI) and Deviance Information Criterion (DIC)
calculation.
Author: Corey Chivers
Maintainer: Corey Chivers
ChangeLog | 11 +++++++++--
DESCRIPTION | 20 ++++++++++++++------
MD5 | 16 ++++++++--------
NAMESPACE | 3 +--
R/BCI.R | 4 +++-
R/Metro_Hastings.R | 25 +++++++++++++++----------
man/BCI.Rd | 2 +-
man/MHadaptive-package.Rd | 4 ++--
man/Metro_Hastings.Rd | 5 +----
9 files changed, 54 insertions(+), 36 deletions(-)
Title: Graph Based Multiple Comparison Procedures
Diff between gMCP versions 0.7-7 dated 2012-02-17 and 0.7-8 dated 2012-03-06
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller (parametric tests,
adaptive designs), Bjoern Bornkamp (power simulations)
Maintainer: Kornelius Rohmeyer
DESCRIPTION | 6
MD5 | 26 ++--
NEWS | 28 ++++
R/helperGUI.R | 2
TODO | 11 -
inst/doc/AQuickStart.pdf |binary
inst/doc/gMCP.pdf |binary
inst/doc/parametric.pdf |binary
inst/java-src/org/af/gMCP/gui/dialogs/MatrixCreationDialog.java | 23 ++-
inst/java-src/org/af/gMCP/gui/graph/EdgeWeight.java | 2
inst/java-src/org/af/gMCP/gui/graph/GraphView.java | 17 ++
inst/java-src/org/af/gMCP/gui/graph/NetList.java | 64 ++++++++--
inst/java-src/org/af/gMCP/gui/graph/UpdateEdge.java | 2
inst/java/gsrmtp.jar |binary
14 files changed, 136 insertions(+), 45 deletions(-)