Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-4 dated 2012-01-15 and 2.2-5 dated 2012-01-27
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by
transparently mapping only a section (pagesize) in main memory
- the effective virtual memory consumption per ff object. ff
supports R's standard atomic data types 'double', 'logical',
'raw' and 'integer' and non-standard atomic types boolean (1
bit), quad (2 bit unsigned), nibble (4 bit unsigned), byte (1
byte signed with NAs), ubyte (1 byte unsigned), short (2 byte
signed with NAs), ushort (2 byte unsigned), single (4 byte
float with NAs). For example 'quad' allows efficient storage of
genomic data as an 'A','T','G','C' factor. The unsigned types
support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date'
and custom close-to-atomic types. ff not only has native
C-support for vectors, matrices and arrays with flexible
dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not
unlike data.frames and import/export filters for csv files. ff
objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and
virtual attributes. ff objects have well-defined hybrid copying
semantics, which gives rise to certain performance improvements
through virtualization. ff objects can be stored and reopened
across R sessions. ff files can be shared by multiple ff R
objects (using different data en/de-coding schemes) in the same
process or from multiple R processes to exploit parallelism. A
wide choice of finalizer options allows to work with
'permanent' files as well as creating/removing 'temporary' ff
files completely transparent to the user. On certain
OS/Filesystem combinations, creating the ff files works without
notable delay thanks to using sparse file allocation. Several
access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve
good performance even with large datasets, for example virtual
matrix transpose without touching a single byte on disk.
Further, to reduce disk I/O, 'logicals' and non-standard data
types get stored native and compact on binary flat files i.e.
logicals take up exactly 2 bits to represent TRUE, FALSE and
NA. Beyond basic access functions, the ff package also
provides compatibility functions that facilitate writing code
for ff and ram objects and support for batch processing on ff
objects (e.g. as.ram, as.ff, ffapply). ff interfaces closely
with functionality from package 'bit': chunked looping, fast
bit operations and coercions between different objects that can
store subscript information ('bit', 'bitwhich', ff 'boolean',
ri range index, hi hybrid index). This allows to work
interactively with selections of large datasets and quickly
modify selection criteria. Further high-performance
enhancements can be made available upon request.
Author: Daniel Adler
Maintainer: Jens Oehlschl\xE4gel
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
NEWS | 15 ++++++++++++---
R/zzz.R | 40 ++++++++++++++++++++--------------------
4 files changed, 41 insertions(+), 32 deletions(-)
Title: Classification accuracy and consistency under Item Response
Theory
Diff between cacIRT versions 1.0 dated 2011-09-05 and 1.1 dated 2012-01-27
Description: Computes classification accuracy and consistency under
Item Response Theory by the approach proposed by Lee, Hanson &
Brennen (2002) and Lee (2010) or the approach proposed by
Rudner (2001, 2005). For dichotomous IRT models.
Author: Quinn Lathrop
Maintainer:
cacIRT-1.0/cacIRT/R/Lee.rec.D.R |only
cacIRT-1.0/cacIRT/R/Lee.rec.P.R |only
cacIRT-1.0/cacIRT/man/Lee.rec.D.Rd |only
cacIRT-1.0/cacIRT/man/Lee.rec.P.Rd |only
cacIRT-1.0/cacIRT/man/MLE.Rd |only
cacIRT-1.0/cacIRT/man/Rud.D.Rd |only
cacIRT-1.0/cacIRT/man/Rud.P.Rd |only
cacIRT-1.0/cacIRT/man/SEM.Rd |only
cacIRT-1.0/cacIRT/man/iif.Rd |only
cacIRT-1.0/cacIRT/man/irf.Rd |only
cacIRT-1.0/cacIRT/man/normal.qu.Rd |only
cacIRT-1.0/cacIRT/man/sim.Rd |only
cacIRT-1.0/cacIRT/man/tif.Rd |only
cacIRT-1.1/cacIRT/DESCRIPTION | 17 ++++-----
cacIRT-1.1/cacIRT/MD5 | 37 ++++++++-------------
cacIRT-1.1/cacIRT/NAMESPACE |only
cacIRT-1.1/cacIRT/R/Lee.D.R |only
cacIRT-1.1/cacIRT/R/Lee.P.R |only
cacIRT-1.1/cacIRT/R/Rud.D.R | 32 +++++++++++++-----
cacIRT-1.1/cacIRT/R/Rud.P.R | 25 ++++++++++----
cacIRT-1.1/cacIRT/R/class.Lee.R | 9 ++---
cacIRT-1.1/cacIRT/R/class.Rud.R | 7 +---
cacIRT-1.1/cacIRT/man/IRT.Rd |only
cacIRT-1.1/cacIRT/man/TOtable.F.Rd | 14 ++++----
cacIRT-1.1/cacIRT/man/cacIRT-package.Rd | 12 ++++--
cacIRT-1.1/cacIRT/man/class.Lee.Rd | 36 +++++++++++---------
cacIRT-1.1/cacIRT/man/class.Rud.Rd | 39 +++++++++++++---------
cacIRT-1.1/cacIRT/man/recursive.raw.Rd | 56 ++++----------------------------
28 files changed, 134 insertions(+), 150 deletions(-)
Title: Multivariate Exploratory Data Analysis and Data Mining with R
Diff between FactoMineR versions 1.16 dated 2011-07-07 and 1.18 dated 2012-01-27
Description: an R package for exploratory data analysis
Author: Francois Husson, Julie Josse, Sebastien Le, Jeremy Mazet
Maintainer: Francois Husson
FactoMineR-1.16/FactoMineR/R/plot.GPApartial.R |only
FactoMineR-1.16/FactoMineR/R/plot.MFApartial.R |only
FactoMineR-1.18/FactoMineR/DESCRIPTION | 8
FactoMineR-1.18/FactoMineR/FactoMineR-Ex.R | 60 ++++--
FactoMineR-1.18/FactoMineR/MD5 |only
FactoMineR-1.18/FactoMineR/NAMESPACE | 2
FactoMineR-1.18/FactoMineR/R/AFDM.R | 4
FactoMineR-1.18/FactoMineR/R/DMFA.R | 8
FactoMineR-1.18/FactoMineR/R/HCPC.R | 6
FactoMineR-1.18/FactoMineR/R/HMFA.R | 11 -
FactoMineR-1.18/FactoMineR/R/MCA.R | 42 ----
FactoMineR-1.18/FactoMineR/R/MFA.R | 97 ++++++++--
FactoMineR-1.18/FactoMineR/R/PCA.R | 4
FactoMineR-1.18/FactoMineR/R/plot.AFDM.R | 4
FactoMineR-1.18/FactoMineR/R/plot.DMFA.R | 2
FactoMineR-1.18/FactoMineR/R/plot.HCPC.R | 2
FactoMineR-1.18/FactoMineR/R/plot.HMFA.R | 2
FactoMineR-1.18/FactoMineR/R/plot.MCA.R | 2
FactoMineR-1.18/FactoMineR/R/plot.MFA.R | 2
FactoMineR-1.18/FactoMineR/R/plot.PCA.R | 2
FactoMineR-1.18/FactoMineR/R/plotGPApartial.R |only
FactoMineR-1.18/FactoMineR/R/plotMFApartial.R |only
FactoMineR-1.18/FactoMineR/R/plotellipses.r | 19 +
FactoMineR-1.18/FactoMineR/R/print.MCA.R | 2
FactoMineR-1.18/FactoMineR/R/print.MFA.R | 2
FactoMineR-1.18/FactoMineR/R/print.PCA.R | 2
FactoMineR-1.18/FactoMineR/R/svd.triplet.R | 4
FactoMineR-1.18/FactoMineR/R/tab.disjonctif.prop.R |only
FactoMineR-1.18/FactoMineR/data/mortality.rda |only
FactoMineR-1.18/FactoMineR/inst/doc/FactoMineR.pdf |binary
FactoMineR-1.18/FactoMineR/inst/doc/clustering_and_pricipal_component_methods.pdf |binary
FactoMineR-1.18/FactoMineR/man/CA.Rd | 4
FactoMineR-1.18/FactoMineR/man/MCA.Rd | 4
FactoMineR-1.18/FactoMineR/man/MFA.Rd | 17 +
FactoMineR-1.18/FactoMineR/man/PCA.Rd | 10 -
FactoMineR-1.18/FactoMineR/man/catdes.Rd | 4
FactoMineR-1.18/FactoMineR/man/dimdesc.Rd | 3
FactoMineR-1.18/FactoMineR/man/gpa.Rd | 2
FactoMineR-1.18/FactoMineR/man/mortality.Rd |only
FactoMineR-1.18/FactoMineR/man/plot.AFDM.Rd | 2
FactoMineR-1.18/FactoMineR/man/plot.CA.Rd | 4
FactoMineR-1.18/FactoMineR/man/plot.DMFA.Rd | 4
FactoMineR-1.18/FactoMineR/man/plot.GPApartial.Rd | 6
FactoMineR-1.18/FactoMineR/man/plot.HCPC.Rd | 2
FactoMineR-1.18/FactoMineR/man/plot.HMFA.Rd | 2
FactoMineR-1.18/FactoMineR/man/plot.MCA.Rd | 6
FactoMineR-1.18/FactoMineR/man/plot.MFA.Rd | 2
FactoMineR-1.18/FactoMineR/man/plot.MFApartial.Rd | 10 -
FactoMineR-1.18/FactoMineR/man/plot.PCA.Rd | 4
FactoMineR-1.18/FactoMineR/man/tab.disjonctif.prop.Rd |only
50 files changed, 234 insertions(+), 139 deletions(-)
Title: Beta Regression
Diff between betareg versions 2.4-0 dated 2011-10-13 and 2.4-1 dated 2012-01-27
Description: Beta regression for modeling beta-distributed dependent
variables, e.g., rates and proportions. In addition to maximum
likelihood regression (for both mean and precision of a
beta-distributed response), bias-corrected and bias-reduced
estimation as well as finite mixture models and recursive
partitioning for beta regressions are provided.
Author: Achim Zeileis [aut, cre], Francisco Cribari-Neto [aut], Bettina
Gruen [aut], Ioannis Kosmidis [aut], Alexandre B. Simas [ctb]
(earlier version by), Andrea V. Rocha [ctb] (earlier version
by)
Maintainer: Achim Zeileis
betareg-2.4-0/betareg/inst/doc/betareg.bib |only
betareg-2.4-0/betareg/tests/vignette-betareg.R |only
betareg-2.4-0/betareg/tests/vignette-betareg.Rout.save |only
betareg-2.4-1/betareg/DESCRIPTION | 10 -
betareg-2.4-1/betareg/MD5 | 45 ++++----
betareg-2.4-1/betareg/NEWS | 12 ++
betareg-2.4-1/betareg/R/betamix.R | 20 ++-
betareg-2.4-1/betareg/data/CarTask.rda |binary
betareg-2.4-1/betareg/data/FoodExpenditure.rda |binary
betareg-2.4-1/betareg/data/GasolineYield.rda |binary
betareg-2.4-1/betareg/data/ImpreciseTask.rda |binary
betareg-2.4-1/betareg/data/MockJurors.rda |binary
betareg-2.4-1/betareg/data/ReadingSkills.rda |binary
betareg-2.4-1/betareg/data/StressAnxiety.rda |binary
betareg-2.4-1/betareg/data/WeatherTask.rda |binary
betareg-2.4-1/betareg/inst/doc/betareg-ext.Rnw | 91 +++++++++++------
betareg-2.4-1/betareg/inst/doc/betareg-ext.pdf |binary
betareg-2.4-1/betareg/inst/doc/betareg.pdf |binary
betareg-2.4-1/betareg/man/betamix.Rd | 27 ++++-
betareg-2.4-1/betareg/man/betatree.Rd | 16 ++
betareg-2.4-1/betareg/tests/Examples |only
betareg-2.4-1/betareg/tests/betamix.R |only
betareg-2.4-1/betareg/tests/betamix.Rout.save |only
betareg-2.4-1/betareg/tests/betatree.R |only
betareg-2.4-1/betareg/tests/betatree.Rout.save |only
betareg-2.4-1/betareg/vignettes |only
26 files changed, 155 insertions(+), 66 deletions(-)
Title: relax -- R Editor for Literate Analysis and lateX
Diff between relax versions 1.3.7 dated 2011-11-15 and 1.3.8 dated 2012-01-27
Description: package relax contains some functions for report writing,
presentation, and programming: relax(), tangleR(), weaveR(),
(g)slider(). "relax" is written in R and Tcl/Tk. relax creates
a new window (top level Tcl/Tk widget) that consists of two
text fields and some buttons and menus. Text (chunks) and code
(chunks) are inserted in the upper text field (report field).
Code chunks are evaluated by clicking on EvalRCode. Results
are shown in the lower text field (output field) and will be
transfered to the report field by pressing on Insert. In this
way you get correct reports. These reports can be loaded again
in cause of presentation, modification and result checking.
tangleR() and weaveR() implement a plain kind of tangling and
weaving. gslider() and slider() are designed to define sliders
for interactive experiments in a simple way. The syntax rules
of code chunks and text chunks are defined by the noweb system
proposed by Norman Ramsey
(http://www.eecs.harvard.edu/~nr/noweb/intro.html). For
integrating jpeg graphics into the text field you need the
Tcl/Tk Img package of Jan Nijtmans (see:
http://members.chello.nl/~j.nijtmans/img.html,
http://home.kpnplanet.nl/~J.Nijtmans@kpnplanet.nl/img.html or
http://tkimg.sourceforge.net/, the package is found on
http://sourceforge.net/projects/tkimg). If an Img version is
integrated in the relax package the license terms concerning
the img package will be found in the source file of the
package, for example in: relax/src/tkimg1.3.tar.gz. Older
windows versions of relax contain the Tcl/Tk img package, so no
further installations have to be done.
Author: Hans Peter Wolf
Maintainer: Hans Peter Wolf
DESCRIPTION | 65 -
MD5 | 11
NAMESPACE | 2
R/relax.R | 1749 ++++++++++++++++++++++++++++++++++++++-----------
inst/src/relax.rev | 755 +++++++++++++++------
man/CodeChunkPlayer.Rd |only
man/playground.Rd | 12
7 files changed, 1954 insertions(+), 640 deletions(-)
Title: R Client for Mobilize/Andwellness server
Diff between Ohmage versions 2.9-4 dated 2012-01-14 and 2.9-5 dated 2012-01-27
Description: R Client for Mobilize and Andwellness server. Implements
basic R functions to call and process data.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/multifactor.R | 11 +++++++++--
R/parse.prompt.R | 13 ++++++++++---
4 files changed, 25 insertions(+), 11 deletions(-)
Title: Computation of functional similarities between GO terms and gene
products; GO enrichement analysis
Diff between GOSim versions 1.2.5 dated 2011-04-27 and 1.2.6 dated 2012-01-27
Description: This package implements several functions useful for
computing similarities between GO terms and gene products based
on their GO annotation. Moreover it allows for computing a GO
enrichment analysis
Author: Holger Froehlich
Maintainer: Holger Froehlich
DESCRIPTION | 11 ++++------
MD5 |only
R/GOSim.R | 2 -
R/general.R | 7 ++++--
R/normalize.kernel.R | 6 +++--
R/termSimilarity.R | 4 +--
data/ICsBPhumanall.rda |binary
data/ICsCChumanall.rda |binary
data/ICsMFhumanall.rda |binary
inst/doc/GOSim.pdf |binary
man/calcICs.Rd | 10 +++------
man/setOntology.Rd | 3 +-
src/hungarian2.c | 50 ++++++++++++++++++++++++-------------------------
src/hungarian2.h | 1
14 files changed, 49 insertions(+), 45 deletions(-)
Title: Functions for generating and manipulating binned kernel density
estimates
Diff between GenKern versions 1.1-10 dated 2010-04-16 and 1.2-10 dated 2012-01-27
Description: Computes generalised KDEs
Author: David Lucy
Maintainer: David Lucy
DESCRIPTION | 8 ++++----
MD5 |only
NAMESPACE |only
3 files changed, 4 insertions(+), 4 deletions(-)
Title: Generalized Estimating Equation Package
Diff between geepack versions 1.1-4 dated 2011-12-15 and 1.1-6 dated 2012-01-27
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses.
Author: Jun Yan
Maintainer: Jun Yan
ChangeLog | 16 ++++++++++++++++
DESCRIPTION | 10 +++++-----
MD5 | 23 ++++++++++++-----------
data/dietox.txt.gz |binary
data/spruce.txt.gz |binary
geepack-Ex.R |only
inst/include/geesubs.h | 33 +++++++++++++++++++++++++++++++--
inst/include/ordgee.h | 2 +-
inst/include/utils.h | 2 ++
src/gee2.cc | 10 +++++++---
src/geesubs.cc | 33 ++++++---------------------------
src/ordgee.cc | 10 +++++++---
src/utils.cc | 11 ++++++++++-
13 files changed, 97 insertions(+), 53 deletions(-)
Title: Extended Model Formulas
Diff between Formula versions 1.0-1 dated 2011-09-03 and 1.1-0 dated 2012-01-27
Description: Infrastructure for extended formulas with multiple parts
on the right-hand side and/or multiple responses on the
left-hand side.
Author: Achim Zeileis [aut, cre], Yves Croissant [aut]
Maintainer: Achim Zeileis
Formula-1.0-1/Formula/inst/doc/Formula.bib |only
Formula-1.1-0/Formula/DESCRIPTION | 8 ++---
Formula-1.1-0/Formula/MD5 | 15 ++++++----
Formula-1.1-0/Formula/NEWS | 9 ++++++
Formula-1.1-0/Formula/R/Formula.R | 43 +++++++++++++++++------------
Formula-1.1-0/Formula/inst/doc/Formula.pdf |binary
Formula-1.1-0/Formula/man/Formula.Rd | 10 ++++--
Formula-1.1-0/Formula/tests |only
Formula-1.1-0/Formula/vignettes |only
9 files changed, 54 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2006-10-13 4.8-0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-01 3.1
2010-06-01 3.0
2009-09-03 2.0
2008-11-28 1.1
2008-11-27 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-07-29 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-06-09 0.5-8.2
2010-02-24 0.5-8.1
2009-06-05 0.5-8
2005-01-12 0.5-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-09-16 1.0
Title: Simulation-based random variable object class in R
Diff between rv versions 1.1.0 dated 2011-02-01 and 2.0.0 dated 2012-01-27
Description: Simulation-based random variable object class
Author: Jouni Kerman
Maintainer: Jouni Kerman
rv-1.1.0/rv/inst/doc/fb-examscores-intervals.pdf |only
rv-1.1.0/rv/inst/doc/rv-doc.Rnw |only
rv-1.1.0/rv/inst/doc/rv-doc.pdf |only
rv-1.1.0/rv/inst/doc/rv-paper.Rnw |only
rv-1.1.0/rv/inst/doc/rv-paper.pdf |only
rv-1.1.0/rv/man/rvcompatibility.Rd |only
rv-2.0.0/rv/ChangeLog | 6
rv-2.0.0/rv/DESCRIPTION | 10
rv-2.0.0/rv/MD5 |only
rv-2.0.0/rv/NAMESPACE | 75
rv-2.0.0/rv/R/00rvheader.R |only
rv-2.0.0/rv/R/Extract_rv.R |only
rv-2.0.0/rv/R/Math_rv.R |only
rv-2.0.0/rv/R/Ops_rv.R |only
rv-2.0.0/rv/R/Summary.R |only
rv-2.0.0/rv/R/abline_rv.R |only
rv-2.0.0/rv/R/anyisrv.R |only
rv-2.0.0/rv/R/aperm_rv.R |only
rv-2.0.0/rv/R/apply_rv.R |only
rv-2.0.0/rv/R/as_list_rv.R |only
rv-2.0.0/rv/R/as_rv_bugs.R |only
rv-2.0.0/rv/R/as_vector_rv.R |only
rv-2.0.0/rv/R/c_rv.R |only
rv-2.0.0/rv/R/cbind_rbind_rv.R |only
rv-2.0.0/rv/R/constant.R |only
rv-2.0.0/rv/R/cor_rv.R |only
rv-2.0.0/rv/R/cov_rv.R |only
rv-2.0.0/rv/R/detachrv.R |only
rv-2.0.0/rv/R/finiterange.R |only
rv-2.0.0/rv/R/fuzzy.R |only
rv-2.0.0/rv/R/hist_rv.R |only
rv-2.0.0/rv/R/is_na_rv.R |only
rv-2.0.0/rv/R/lines_rv.R |only
rv-2.0.0/rv/R/matmult_rv.R |only
rv-2.0.0/rv/R/mcmcattr.R |only
rv-2.0.0/rv/R/mean_rv.R |only
rv-2.0.0/rv/R/median_rv.R |only
rv-2.0.0/rv/R/min_max_rv.R |only
rv-2.0.0/rv/R/mlplot.R |only
rv-2.0.0/rv/R/newrv.R |only
rv-2.0.0/rv/R/nsims.R |only
rv-2.0.0/rv/R/numeric_rv.R |only
rv-2.0.0/rv/R/outer_rv.R |only
rv-2.0.0/rv/R/plot_rv.R |only
rv-2.0.0/rv/R/points_rv.R |only
rv-2.0.0/rv/R/posterior.R |only
rv-2.0.0/rv/R/postsim.R |only
rv-2.0.0/rv/R/print_rv.R |only
rv-2.0.0/rv/R/print_rvfactor.R |only
rv-2.0.0/rv/R/quantile_rv.R |only
rv-2.0.0/rv/R/random.R |only
rv-2.0.0/rv/R/range_rv.R |only
rv-2.0.0/rv/R/rep_rv.R |only
rv-2.0.0/rv/R/rv-util.R |only
rv-2.0.0/rv/R/rv.R | 4151 -----------------------
rv-2.0.0/rv/R/rvVectorize.R |only
rv-2.0.0/rv/R/rv_any_na_all_na.R |only
rv-2.0.0/rv/R/rvattach.R |only
rv-2.0.0/rv/R/rvattr.R |only
rv-2.0.0/rv/R/rvbern.R |only
rv-2.0.0/rv/R/rvbeta.R |only
rv-2.0.0/rv/R/rvbinom.R |only
rv-2.0.0/rv/R/rvboot.R |only
rv-2.0.0/rv/R/rvcat.R |only
rv-2.0.0/rv/R/rvcauchy.R |only
rv-2.0.0/rv/R/rvchisq.R |only
rv-2.0.0/rv/R/rvci.R |only
rv-2.0.0/rv/R/rvcolortheme.R |only
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rv-2.0.0/rv/R/rvmeanunif.R |only
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rv-2.0.0/rv/R/rvmin_rvmax_rvrange.R |only
rv-2.0.0/rv/R/rvminmax.R |only
rv-2.0.0/rv/R/rvmultinom.R |only
rv-2.0.0/rv/R/rvnbeta.R |only
rv-2.0.0/rv/R/rvngamma.R |only
rv-2.0.0/rv/R/rvnorm.R |only
rv-2.0.0/rv/R/rvobj.R |only
rv-2.0.0/rv/R/rvpar.R |only
rv-2.0.0/rv/R/rvpermut.R |only
rv-2.0.0/rv/R/rvpois.R |only
rv-2.0.0/rv/R/rvpredict.R |only
rv-2.0.0/rv/R/rvquantile.R |only
rv-2.0.0/rv/R/rvquantile_rvmedian.R |only
rv-2.0.0/rv/R/rvsample.R |only
rv-2.0.0/rv/R/rvsd_rvvar.R |only
rv-2.0.0/rv/R/rvsimapply.R |only
rv-2.0.0/rv/R/rvsims.R |only
rv-2.0.0/rv/R/rvsummary.R |only
rv-2.0.0/rv/R/rvt.R |only
rv-2.0.0/rv/R/rvunif.R |only
rv-2.0.0/rv/R/rvvapply.R |only
rv-2.0.0/rv/R/sd_rv.R |only
rv-2.0.0/rv/R/simapply_rv.R |only
rv-2.0.0/rv/R/sims.R |only
rv-2.0.0/rv/R/sims_as_list.R |only
rv-2.0.0/rv/R/solve_rv.R |only
rv-2.0.0/rv/R/sort_rv.R |only
rv-2.0.0/rv/R/splitbyname.R |only
rv-2.0.0/rv/R/summary_rv.R |only
rv-2.0.0/rv/R/unlist_rv.R |only
rv-2.0.0/rv/R/var_rv.R |only
rv-2.0.0/rv/R/zzz_rv.R |only
rv-2.0.0/rv/inst/ChangeLog | 7
rv-2.0.0/rv/inst/doc/rv-intro.Rnw |only
rv-2.0.0/rv/inst/doc/rv-intro.pdf |only
rv-2.0.0/rv/inst/doc/rv-manual.pdf |only
rv-2.0.0/rv/man/abline.rv.Rd | 7
rv-2.0.0/rv/man/apply.rv.Rd | 2
rv-2.0.0/rv/man/c.rv.Rd | 16
rv-2.0.0/rv/man/cov.rv.Rd | 63
rv-2.0.0/rv/man/matmult.Rd | 2
rv-2.0.0/rv/man/median.rv.Rd | 6
rv-2.0.0/rv/man/mlplot.Rd | 6
rv-2.0.0/rv/man/plot.rv.Rd | 1
rv-2.0.0/rv/man/posterior.Rd |only
rv-2.0.0/rv/man/postsim.Rd | 16
rv-2.0.0/rv/man/rv-Extract.Rd | 11
rv-2.0.0/rv/man/rv-package.Rd | 7
rv-2.0.0/rv/man/rvboot.Rd | 2
rv-2.0.0/rv/man/rvmeanunif.Rd |only
rv-2.0.0/rv/man/rvmin.Rd | 22
rv-2.0.0/rv/man/rvpredict.Rd |only
rv-2.0.0/rv/man/rvt.Rd | 5
rv-2.0.0/rv/vignettes |only
144 files changed, 198 insertions(+), 4217 deletions(-)
Title: A Package for Running jags from R
Diff between R2jags versions 0.03-04 dated 2012-01-24 and 0.03-05 dated 2012-01-27
Description: Using this package to call jags from R.
Author: Yu-Sung Su
Maintainer: Yu-Sung Su
CHANGELOG | 6 ++++++
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/jags.R | 13 +++++++------
R/jagsParallel.R | 1 +
5 files changed, 22 insertions(+), 14 deletions(-)
Title: Network Generation and Comparison
Diff between NetComp versions 0.1 dated 2012-01-10 and 1.2 dated 2012-01-27
Description: This package contains functions to carry out analyse high
throughput data analysis and to conduct dataset comparisons.
Similarity matrices from high thoughput phenotypic data
containing uninformative (e.g. wildtype) or missing data can be
calculated to report similarity of response. A suite of graph
comparisons using an adjacency or correlation matrix format are
included to facilitate quick network analysis.
Author: Shannon M. Bell
Maintainer: Shannon M. Bell
DESCRIPTION | 13 +++++--------
MD5 | 16 ++++++++--------
R/SimMeasure.R | 6 +++++-
man/SimMeasure.Rd | 16 +++++++---------
man/netDiff.Rd | 8 ++++----
man/netIntersect.Rd | 12 ++++++------
man/netUnion.Rd | 10 +++++-----
man/shortPaths.Rd | 12 +++++++-----
src/SimMeasure.c | 28 +++++++++-------------------
9 files changed, 56 insertions(+), 65 deletions(-)
Title: Nonparametric Functional Data Analysis
Diff between nfda versions 0.2-1 dated 2011-12-16 and 0.2-2 dated 2012-01-27
Description: Nonparametric Functional Data Analysis
Author: Simon Mueller
Maintainer: Simon Mueller
DESCRIPTION | 12 ++++++------
MD5 | 14 ++++++++------
NEWS |only
R/npr_predict.R | 3 +++
R/semimetric.R | 45 +++++++++++++++++++++++++++++++++++++++++++--
man/BootstrapData.Rd | 1 +
man/Semimetric.Rd | 4 ++--
man/SemimetricPLS.Rd |only
src/nfda.cpp | 35 +++++++++++++++++++++++++++++++----
9 files changed, 94 insertions(+), 20 deletions(-)
Title: Normalize NanoString miRNA and mRNA data
Diff between NanoStringNorm versions 1.0.7 dated 2011-11-10 and 1.0.11 dated 2012-01-27
More information about NanoStringNorm at CRAN
Description: The function is used to Normalize Nanostring data
Author: Daryl M. Waggott
Maintainer: Daryl Waggott
DESCRIPTION | 10 +++++-----
MD5 | 10 ++++++----
NAMESPACE | 36 ++++++++++++++++++++++--------------
R/NanoStringNorm.R | 20 +++++++++++++++++---
R/other.normalization.R | 6 +++---
R/read.xls.RCC.R |only
man/read.xls.RCC.Rd |only
7 files changed, 53 insertions(+), 29 deletions(-)
Permanent link
Title: Modern measures of population differentiation
Diff between mmod versions 0.1.1 dated 2012-01-14 and 0.2 dated 2012-01-27
Description: mmod provides functions for measuring population
divergence from genotypic data
Author: David Winter
Maintainer: David Winter
mmod-0.1.1/mmod/mmod_0.1.1.tar.gz |only
mmod-0.2/mmod/.gitignore | 1
mmod-0.2/mmod/DESCRIPTION | 11 ++++---
mmod-0.2/mmod/LICENSE |only
mmod-0.2/mmod/MD5 | 43 ++++++++++++++++++------------
mmod-0.2/mmod/NAMESPACE | 3 ++
mmod-0.2/mmod/NEWS | 2 +
mmod-0.2/mmod/R/D_Jost.R | 10 +++---
mmod-0.2/mmod/R/Gst_Hedrick.R | 10 ++----
mmod-0.2/mmod/R/chao_bootstrap.R |only
mmod-0.2/mmod/R/help.R | 2 -
mmod-0.2/mmod/R/jacknife_pop.R | 1
mmod-0.2/mmod/R/pairwise_D.R | 19 ++++++++++---
mmod-0.2/mmod/R/pairwise_Gst_Hedrick.R | 12 ++++++--
mmod-0.2/mmod/R/pairwise_Gst_Nei.R | 8 ++++-
mmod-0.2/mmod/R/summarise_bootstrap.R |only
mmod-0.2/mmod/README.md | 26 +++++++++---------
mmod-0.2/mmod/chao_bootstrap.R |only
mmod-0.2/mmod/inst |only
mmod-0.2/mmod/man/chao_bootstrap.Rd |only
mmod-0.2/mmod/man/jacknife_populations.Rd | 4 ++
mmod-0.2/mmod/man/mmod.Rd | 3 +-
mmod-0.2/mmod/man/pairwise_D.Rd | 9 +++++-
mmod-0.2/mmod/man/pairwise_Gst_Hedrick.Rd | 9 +++++-
mmod-0.2/mmod/man/pairwise_Gst_Nei.Rd | 5 ++-
mmod-0.2/mmod/man/summarise_bootsrap.Rd |only
mmod-0.2/mmod/mmod_0.2.tar.gz |only
mmod-0.2/mmod/test/demo.Rnw |only
28 files changed, 119 insertions(+), 59 deletions(-)
Title: Mutant Identification through Probabilistic High throughput
Enabled NOrmalization
Diff between MIPHENO versions 0.1 dated 2011-11-29 and 1.2 dated 2012-01-27
Description: This package contains functions to carry out processing of
high throughput data analysis and detection of putative
hits/mutants. Contents include a function for post-hoc quality
control for removal of outlier sample sets, a median-based
normalization method for use in datasets where there are no
explicit controls and where most of the responses are of the
wildtype/no response class (see accompanying paper). The
package also includes a way to prioritize individuals of
interest using am empirical cumulative distribution function.
Methods for generating synthetic data as well as data from the
Chloroplast 2010 project are included.
Author: Shannon M. Bell
Maintainer: Shannon M. Bell
DESCRIPTION | 29 ++++++++++++++++++-----------
MD5 | 10 +++++-----
man/cdf.pval.Rd | 7 +++++--
man/find_hits.Rd | 2 +-
man/mad.scores.Rd | 4 ++--
man/rm.outliers.Rd | 2 +-
6 files changed, 32 insertions(+), 22 deletions(-)
Title: High-dimensional Undirected Graph Estimation
Diff between huge versions 1.2 dated 2012-01-22 and 1.2.1 dated 2012-01-27
Description: The package "huge" provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Tuo Zhao, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman
Maintainer: Tuo Zhao
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
inst/doc/huge.pdf |binary
inst/doc/vignette.pdf |binary
man/huge-package.Rd | 4 ++--
5 files changed, 10 insertions(+), 10 deletions(-)
Title: Analyzing case-parent triad and/or case-control data with SNP
haplotypes
Diff between Haplin versions 3.5 dated 2010-05-26 and 4.0 dated 2012-01-27
Description: Haplin performs a genetic association analysis of
case-parent triad (trio) data with multiple markers. It can
also incorporate complete or incomplete control triads, for
instance independent control children. Estimation is based on
haplotypes, for instance SNP haplotypes, even though phase is
not known from the genetic data. Haplin estimates relative risk
(RR + conf.int.) and p-value associated with each haplotype. It
uses maximum likelihood estimation to make optimal use of data
from triads with missing genotypic data, for instance if some
SNPs has not been typed for some individuals. Haplin also
allows estimation of effects of maternal haplotypes,
particularly appropriate in perinatal epidemiology. Analyses of
GWAS data with parallel processing are supported.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing
Haplin-3.5/Haplin/R/R.R |only
Haplin-3.5/Haplin/R/debug.q |only
Haplin-3.5/Haplin/R/f.insert.vector.q |only
Haplin-3.5/Haplin/R/f.read.data.r |only
Haplin-3.5/Haplin/R/f.thin.q |only
Haplin-4.0/Haplin/DESCRIPTION | 13
Haplin-4.0/Haplin/MD5 |only
Haplin-4.0/Haplin/NAMESPACE | 36 +
Haplin-4.0/Haplin/R/as.dframe.R |only
Haplin-4.0/Haplin/R/coef.haplin.R | 32 +
Haplin-4.0/Haplin/R/coef.haptable.R |only
Haplin-4.0/Haplin/R/coef.tri.glm.R | 35 +
Haplin-4.0/Haplin/R/dframe.R |only
Haplin-4.0/Haplin/R/f.EM.missing.q | 208 +++++------
Haplin-4.0/Haplin/R/f.HWE.q | 4
Haplin-4.0/Haplin/R/f.Rplot.R | 13
Haplin-4.0/Haplin/R/f.aggregate.q | 2
Haplin-4.0/Haplin/R/f.args.from.info.R | 32 +
Haplin-4.0/Haplin/R/f.batch.R |only
Haplin-4.0/Haplin/R/f.bdiag.R | 3
Haplin-4.0/Haplin/R/f.catch.R |only
Haplin-4.0/Haplin/R/f.check.pars.R | 118 +++++-
Haplin-4.0/Haplin/R/f.compute.effects.q | 222 ++++-------
Haplin-4.0/Haplin/R/f.data.R | 93 ++---
Haplin-4.0/Haplin/R/f.data.ready.R |only
Haplin-4.0/Haplin/R/f.fill.effects.R | 27 -
Haplin-4.0/Haplin/R/f.final.loglike.q | 76 +---
Haplin-4.0/Haplin/R/f.groupsum.q | 2
Haplin-4.0/Haplin/R/f.jackknife.q | 179 ++++-----
Haplin-4.0/Haplin/R/f.like.ratio.R | 76 +---
Haplin-4.0/Haplin/R/f.load.R |only
Haplin-4.0/Haplin/R/f.make.design.R | 519 ++++++++++++++++------------
Haplin-4.0/Haplin/R/f.make.index.R |only
Haplin-4.0/Haplin/R/f.ped.to.mfc.R |only
Haplin-4.0/Haplin/R/f.plot.effects.R |only
Haplin-4.0/Haplin/R/f.pos.match.R | 47 --
Haplin-4.0/Haplin/R/f.pos.to.haplocomb.q | 12
Haplin-4.0/Haplin/R/f.post.chisq.R | 3
Haplin-4.0/Haplin/R/f.post.contrasts.R | 13
Haplin-4.0/Haplin/R/f.post.diff.R | 15
Haplin-4.0/Haplin/R/f.posttest.R | 29 -
Haplin-4.0/Haplin/R/f.posttest.score.R |only
Haplin-4.0/Haplin/R/f.prep.data.q | 127 +++---
Haplin-4.0/Haplin/R/f.prep.dataout.R | 8
Haplin-4.0/Haplin/R/f.prep.reference.R | 4
Haplin-4.0/Haplin/R/f.printlist.R |only
Haplin-4.0/Haplin/R/f.read.data.R |only
Haplin-4.0/Haplin/R/f.redistribute.q | 83 ++--
Haplin-4.0/Haplin/R/f.save.R |only
Haplin-4.0/Haplin/R/f.scoretest.R | 68 +--
Haplin-4.0/Haplin/R/f.sel.haplos.R | 8
Haplin-4.0/Haplin/R/f.sel.markers.R |only
Haplin-4.0/Haplin/R/f.sep.data.R | 32 -
Haplin-4.0/Haplin/R/f.sort.alleles.q | 4
Haplin-4.0/Haplin/R/f.split.matrix.R |only
Haplin-4.0/Haplin/R/f.split.vector.R |only
Haplin-4.0/Haplin/R/f.suest.R | 4
Haplin-4.0/Haplin/R/f.tri.glm.q | 277 +++-----------
Haplin-4.0/Haplin/R/f.triad.to.transmit.r | 4
Haplin-4.0/Haplin/R/f.var.covar.q | 95 -----
Haplin-4.0/Haplin/R/f.vis.q | 4
Haplin-4.0/Haplin/R/f.windows.R | 2
Haplin-4.0/Haplin/R/gwaaToHaplin.R |only
Haplin-4.0/Haplin/R/haplin.R | 112 +++---
Haplin-4.0/Haplin/R/haplinSlide.R | 219 +++++++++--
Haplin-4.0/Haplin/R/haplinStrat.R | 180 +++------
Haplin-4.0/Haplin/R/haptable.haplin.R | 191 +++++-----
Haplin-4.0/Haplin/R/haptable.haplinStrat.R | 14
Haplin-4.0/Haplin/R/loadData.R |only
Haplin-4.0/Haplin/R/pQQ.R | 55 +-
Haplin-4.0/Haplin/R/pedToHaplin.R | 11
Haplin-4.0/Haplin/R/plot.haplin.q | 35 +
Haplin-4.0/Haplin/R/plot.haptable.R |only
Haplin-4.0/Haplin/R/plot.tri.glm.q | 31 +
Haplin-4.0/Haplin/R/prepPed.R |only
Haplin-4.0/Haplin/R/print.HWE.test.q | 3
Haplin-4.0/Haplin/R/print.info.R | 48 +-
Haplin-4.0/Haplin/R/print.summary.haplin.q | 7
Haplin-4.0/Haplin/R/print.summary.tri.glm.q | 123 +++---
Haplin-4.0/Haplin/R/readData.R |only
Haplin-4.0/Haplin/R/saveData.R |only
Haplin-4.0/Haplin/R/suest.R | 9
Haplin-4.0/Haplin/R/summary.haplin.q | 8
Haplin-4.0/Haplin/R/summary.tri.glm.q | 140 +++----
Haplin-4.0/Haplin/R/tdt.R | 7
Haplin-4.0/Haplin/R/toDataFrame.R |only
Haplin-4.0/Haplin/inst |only
Haplin-4.0/Haplin/man/gwaaToHaplin.Rd |only
Haplin-4.0/Haplin/man/haplin.Rd | 29 -
Haplin-4.0/Haplin/man/haplinSlide.Rd | 134 +++----
Haplin-4.0/Haplin/man/haplinTDT.Rd | 2
Haplin-4.0/Haplin/man/haptable.Rd | 148 +++----
Haplin-4.0/Haplin/man/pQQ.Rd |only
Haplin-4.0/Haplin/man/prepPed.Rd |only
Haplin-4.0/Haplin/man/suest.Rd |only
Haplin-4.0/Haplin/man/toDataFrame.Rd |only
96 files changed, 1995 insertions(+), 2040 deletions(-)