Title: Tools for the analysis of air pollution data
Diff between openair versions 0.4-15 dated 2011-04-12 and 0.4-17 dated 2011-04-24
Description: Tools to analyse, interpret and understand air pollution
data. Data are typically hourly time series and both monitoring
data and dispersion model output can be analysed. Many
functions can also be applied to other data, including
meteorological and traffic data.
Author: David Carslaw and Karl Ropkins
Maintainer: David Carslaw
DESCRIPTION | 10 ++++----
NAMESPACE | 1
NEWS | 17 ++++++++++++++
R/MannKendall.R | 11 +++++++--
R/aqStats.R |only
R/cutData.R | 63 +++++++++++++++++++++++++++++++++++++++--------------
R/importAURN.R | 37 +++++++++++++++++++++++--------
R/importKCL.R | 4 +--
R/polarFreq.R | 7 +++--
R/scatterPlot.R | 19 ++++++++++-----
R/smoothTrend.R | 34 ++++++++++++++++++----------
R/timePlot.R | 14 +++++++++--
R/utilities.R | 18 +++++++--------
R/zzz.R | 2 -
man/aqStats.Rd |only
man/rollingMean.Rd | 8 +++---
16 files changed, 173 insertions(+), 72 deletions(-)
Title: L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting
Diff between lassoshooting versions 0.1.3-7 dated 2011-04-24 and 0.1.4-1 dated 2011-04-24
Description: L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting is fast. This
implementation can choose which coefficients to penalize. It
support coefficient-specific penalities and it can take X'X and
X'y instead of X and y.
Author: Tobias Abenius
Maintainer: Tobias Abenius
DESCRIPTION | 8 ++++----
man/lassoshooting.Rd | 3 +++
src/ccd_r.c | 16 ++++++++++------
3 files changed, 17 insertions(+), 10 deletions(-)
Title: memory-efficient storage of large data on disk and fast access
functions
Diff between ff versions 2.2-1 dated 2010-10-05 and 2.2-2 dated 2011-04-24
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
ANNOUNCEMENT-2.2.txt | 4
DESCRIPTION | 8
NEWS | 23 +
R/as.ff.R | 14
R/bigsample.R | 6
R/ff.R | 106 +++---
R/ffapply.R | 36 +-
R/ffbit.R | 34 +-
R/ffcsv.R | 78 +++-
R/ffdf.R | 81 ++---
R/fffactor.R | 20 -
R/ffsave.R | 45 +-
R/fileutil.R | 4
R/generics.R | 12
R/hi.R | 34 +-
R/ordermerge.R | 84 ++---
R/util.R | 4
R/vmode.R | 4
R/zzz.R | 14
man/CFUN.rd | 144 ++++----
man/Extract.ff.rd | 330 ++++++++++----------
man/Extract.ffdf.rd | 164 +++++-----
man/Forbidden_ffdf.rd | 52 +--
man/Internal_ffdf.rd | 38 +-
man/LimWarn.rd | 178 +++++------
man/add.rd | 122 +++----
man/array2vector.rd | 58 +--
man/arrayIndex2vectorIndex.rd | 70 ++--
man/as.ff.bit.rd | 118 +++----
man/as.ff.rd | 120 +++----
man/as.ffdf.rd | 88 ++---
man/as.hi.rd | 260 ++++++++--------
man/as.integer.hi.rd | 104 +++---
man/as.vmode.rd | 160 ++++-----
man/bigsample.rd | 88 ++---
man/chunk.bit.rd | 74 ++--
man/chunk.ffdf.rd | 122 +++----
man/clone.ffdf.rd | 90 ++---
man/clone.rd | 176 +++++-----
man/close.ff.rd | 72 ++--
man/delete.rd | 126 +++----
man/dim.ff.rd | 206 ++++++------
man/dimnames.ff_array.rd | 72 ++--
man/dimnames.ffdf.rd | 92 ++---
man/dimorderCompatible.rd | 68 ++--
man/dummy.dimnames.rd | 44 +-
man/ff.rd | 678 +++++++++++++++++++++---------------------
man/ffapply.rd | 290 ++++++++---------
man/ffconform.rd | 102 +++---
man/ffdf.rd | 324 ++++++++++----------
man/ffdfindexget.rd | 4
man/ffdrop.rd | 64 +--
man/ffindexget.rd | 4
man/ffindexorder.rd | 12
man/ffinfo.rd | 63 ++-
man/ffload.rd | 90 ++---
man/ffreturn.rd | 44 +-
man/ffsave.rd | 296 +++++++++---------
man/ffsuitable.rd | 54 +--
man/ffxtensions.rd | 52 +--
man/file.resize.rd | 100 +++---
man/filename.rd | 160 ++++-----
man/finalize.rd | 126 +++----
man/finalizer.rd | 166 +++++-----
man/fixdiag.rd | 74 ++--
man/geterror.ff.rd | 54 +--
man/getpagesize.rd | 60 +--
man/getset.ff.rd | 88 ++---
man/hi.rd | 112 +++---
man/hiparse.rd | 60 +--
man/is.ff.rd | 44 +-
man/is.ffdf.rd | 44 +-
man/is.open.rd | 74 ++--
man/is.readonly.rd | 74 ++--
man/is.sorted.rd | 94 ++---
man/length.ff.rd | 102 +++---
man/length.ffdf.rd | 56 +--
man/length.hi.rd | 124 +++----
man/levels.ff.rd | 152 ++++-----
man/matcomb.rd | 54 +--
man/matprint.rd | 66 ++--
man/maxffmode.rd | 50 +--
man/maxlength.rd | 64 +--
man/mismatch.rd | 66 ++--
man/na.count.rd | 128 +++----
man/names.ff.rd | 84 ++---
man/nrowAssign.rd | 100 +++---
man/open.ff.rd | 88 ++---
man/pagesize.rd | 52 +--
man/physical.ff.rd | 94 ++---
man/physical.ffdf.rd | 129 +++----
man/print.ff.rd | 90 ++---
man/ram2ffcode.rd | 64 +--
man/ramattribs.rd | 100 +++---
man/ramorder.rd | 2
man/ramsort.rd | 2
man/read.table.ffdf.rd | 555 +++++++++++++++++-----------------
man/readwrite.ff.rd | 90 ++---
man/regtest.fforder.rd | 54 +--
man/repnam.rd | 94 ++---
man/sortLevels.rd | 236 +++++++-------
man/splitPathFile.rd | 220 ++++++-------
man/swap.rd | 142 ++++----
man/symmIndex2vectorIndex.rd | 76 ++--
man/symmetric.rd | 68 ++--
man/unclass_-.rd | 50 +--
man/undim.rd | 48 +-
man/unsort.rd | 106 +++---
man/update.ff.rd | 136 ++++----
man/vecprint.rd | 60 +--
man/vector.vmode.rd | 126 +++----
man/vector2array.rd | 66 ++--
man/vectorIndex2arrayIndex.rd | 100 +++---
man/vmode.ffdf.rd | 58 +--
man/vmode.rd | 198 ++++++------
man/vt.rd | 96 ++---
man/vw.rd | 120 +++----
man/write.table.ffdf.rd | 276 ++++++++---------
118 files changed, 5977 insertions(+), 5919 deletions(-)
Title: A class for vectors of 1-bit booleans
Diff between bit versions 1.1-6 dated 2010-09-27 and 1.1-7 dated 2011-04-24
Description: bitmapped vectors of booleans (no NAs), coercion from and
to logicals, integers and integer subscripts; fast boolean
operators and fast summary statistics. With 'bit' vectors you
can store true binary booleans {FALSE,TRUE} at the expense of 1
bit only, on a 32 bit architecture this means factor 32 less
RAM and ~ factor 32 more speed on boolean operations. Due to
overhead of R calls, actual speed gain depends on the size of
the vector: expect gains for vectors of size > 10000 elements.
Even for one-time boolean operations it can pay-off to convert
to bit, the pay-off is obvious, when such components are used
more than once. Reading from and writing to bit is
approximately as fast as accessing standard logicals - mostly
due to R's time for memory allocation. The package allows to
work with pre-allocated memory for return values by calling
.Call() directly: when evaluating the speed of C-access with
pre-allocated vector memory, coping from bit to logical
requires only 70% of the time for copying from logical to
logical; and copying from logical to bit comes at a performance
penalty of 150%. the package now contains further classes for
representing logical selections: 'bitwhich' for very skewed
selections and 'ri' for selecting ranges of values for chunked
processing. All three index classes can be used for subsetting
'ff' objects (ff-2.1-0 and higher).
Author: Jens Oehlschl\xE4gel
Maintainer: Jens Oehlschl\xE4gel
DESCRIPTION | 8
NAMESPACE | 492 ++++++++++++++++++++++++++---------------------------
NEWS | 15 +
R/attrutil.R | 2
R/bit.R | 82 ++++----
R/chunkutil.R | 10 -
man/Summary.rd | 6
man/bit-package.rd | 12 -
man/chunk.rd | 4
man/length.bit.rd | 2
man/regtest.bit.rd | 4
man/repfromto.rd | 2
prebuild.sh | 2
13 files changed, 328 insertions(+), 313 deletions(-)
Title: Actuarial functions
Diff between actuar versions 1.1-1 dated 2010-07-24 and 1.1-2 dated 2011-04-24
Description: Additional actuarial science functionality, mostly in the
fields of loss distributions, risk theory (including ruin
theory), simulation of compound hierarchical models and
credibility theory. The package also features 17 new
probability laws commonly used in insurance, most notably heavy
tailed distributions.
Author: Vincent Goulet, Sébastien Auclair, Christophe Dutang, Xavier
Milhaud, Tommy Ouellet, Louis-Philippe Pouliot, Mathieu Pigeon
Maintainer: Vincent Goulet
actuar-1.1-1/actuar/inst/NEWS |only
actuar-1.1-1/actuar/inst/doc/Makefile |only
actuar-1.1-2/actuar/DESCRIPTION | 16 +++++++++-------
actuar-1.1-2/actuar/R/aggregateDist.R | 2 +-
actuar-1.1-2/actuar/R/cm.R | 3 +--
actuar-1.1-2/actuar/R/discretize.R | 6 +++---
actuar-1.1-2/actuar/R/elev.R | 22 +++++++++++-----------
actuar-1.1-2/actuar/R/emm.R | 2 +-
actuar-1.1-2/actuar/R/hist.grouped.data.R | 2 +-
actuar-1.1-2/actuar/R/mean.grouped.data.R | 2 +-
actuar-1.1-2/actuar/R/ogive.R | 10 +++++-----
actuar-1.1-2/actuar/R/quantile.aggregateDist.R | 2 +-
actuar-1.1-2/actuar/R/quantile.grouped.data.R | 4 ++--
actuar-1.1-2/actuar/R/ruin.R | 2 +-
actuar-1.1-2/actuar/actuar-Ex.R |only
actuar-1.1-2/actuar/inst/NEWS.Rd |only
actuar-1.1-2/actuar/inst/doc/actuar.Rnw | 7 ++++---
actuar-1.1-2/actuar/inst/doc/actuar.pdf |binary
actuar-1.1-2/actuar/inst/doc/auto |only
actuar-1.1-2/actuar/inst/doc/coverage.Rnw | 7 ++++---
actuar-1.1-2/actuar/inst/doc/coverage.pdf |binary
actuar-1.1-2/actuar/inst/doc/credibility.Rnw | 9 +++++----
actuar-1.1-2/actuar/inst/doc/credibility.pdf |binary
actuar-1.1-2/actuar/inst/doc/lossdist.Rnw | 9 +++++----
actuar-1.1-2/actuar/inst/doc/lossdist.pdf |binary
actuar-1.1-2/actuar/inst/doc/risk.Rnw | 10 +++++-----
actuar-1.1-2/actuar/inst/doc/risk.pdf |binary
actuar-1.1-2/actuar/inst/doc/simulation.Rnw | 7 ++++---
actuar-1.1-2/actuar/inst/doc/simulation.pdf |binary
29 files changed, 64 insertions(+), 58 deletions(-)
Title: C++ classes to embed R in C++ applications
Diff between RInside versions 0.2.3 dated 2010-08-06 and 0.2.4 dated 2011-04-24
Description: C++ classes to embed R in C++ applications The RInside
packages makes it easier to have 'R inside' your C++
application by providing a few wrapper classes.
As R itself is embedded into your application, a shared library build
of R is required. This works on Linux, OS X and even on Windows
provided you use the same tools used to build R itself. (NB:
Windows versions curretly seg.fault and debugging help would be
appreciated. An older version worked fine, but there may have
been some Rcpp changes which caused this.)
Numerous examples are provided in the three subdirectories the
examples/ directory of the installed package: standard, mpi
(for parallel computing) and qt (showing how to embed RInside
inside a Qt application).
Doxygen-generated documentation of the C++ classes is available at the
RInside website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel and Romain Francois
RInside-0.2.3/RInside/inst/ChangeLog |only
RInside-0.2.3/RInside/libRInside.a |only
RInside-0.2.4/RInside/ChangeLog |only
RInside-0.2.4/RInside/DESCRIPTION | 24 ++++--
RInside-0.2.4/RInside/R/RInsidePaths.R | 4 -
RInside-0.2.4/RInside/doxyfile | 8 +-
RInside-0.2.4/RInside/inst/NEWS |only
RInside-0.2.4/RInside/inst/THANKS | 1
RInside-0.2.4/RInside/inst/examples/mpi/rinside_mpi_sample0.cpp | 10 +-
RInside-0.2.4/RInside/inst/examples/mpi/rinside_mpi_sample1.cpp | 11 +--
RInside-0.2.4/RInside/inst/examples/mpi/rinside_mpi_sample2.cpp | 10 +-
RInside-0.2.4/RInside/inst/examples/mpi/rinside_mpi_sample3.cpp | 9 --
RInside-0.2.4/RInside/inst/examples/qt |only
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample1.cpp | 30 ++++----
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample10.cpp |only
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample11.cpp |only
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample2.cpp | 15 +---
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample3.cpp | 6 -
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample5.cpp | 10 +-
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample6.cpp | 12 +--
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample7.cpp | 9 --
RInside-0.2.4/RInside/inst/examples/standard/rinside_sample9.cpp | 2
RInside-0.2.4/RInside/inst/include/RInsideAutoloads.h | 35 ++++++++--
RInside-0.2.4/RInside/inst/include/RInsideEnvVars.h | 13 +--
RInside-0.2.4/RInside/src/Makevars | 2
RInside-0.2.4/RInside/src/RInside.cpp | 21 +++---
26 files changed, 121 insertions(+), 111 deletions(-)
Title: Product Limit Estimation
Diff between prodlim versions 1.1.3 dated 2010-01-12 and 1.2.1 dated 2011-04-24
Description: Fast and user friendly nonparametric estimation in
censored survival (event history) analysis.
Author: Thomas A. Gerds
Maintainer: Thomas A. Gerds
prodlim-1.1.3/prodlim/CHANGES |only
prodlim-1.1.3/prodlim/Examples/test |only
prodlim-1.1.3/prodlim/R/AtRisk.R |only
prodlim-1.1.3/prodlim/R/ConfInt.R |only
prodlim-1.1.3/prodlim/R/MarkTime.R |only
prodlim-1.1.3/prodlim/R/ProcentAxis.R |only
prodlim-1.1.3/prodlim/R/resolveSmartArgs.R |only
prodlim-1.1.3/prodlim/blog |only
prodlim-1.1.3/prodlim/man/AtRisk.Rd |only
prodlim-1.1.3/prodlim/man/ConfInt.Rd |only
prodlim-1.1.3/prodlim/man/MarkTime.Rd |only
prodlim-1.1.3/prodlim/preliminary |only
prodlim-1.2.1/prodlim/.blog |only
prodlim-1.2.1/prodlim/DESCRIPTION | 6
prodlim-1.2.1/prodlim/Examples/exHist.R | 19
prodlim-1.2.1/prodlim/Examples/testProdlim.R |only
prodlim-1.2.1/prodlim/NAMESPACE | 22
prodlim-1.2.1/prodlim/R/Hist.R | 230 +++--
prodlim-1.2.1/prodlim/R/PercentAxis.R |only
prodlim-1.2.1/prodlim/R/SimCompRisk.R | 77 -
prodlim-1.2.1/prodlim/R/SimSurv.R | 80 +
prodlim-1.2.1/prodlim/R/SmartControl.R |only
prodlim-1.2.1/prodlim/R/atRisk.R |only
prodlim-1.2.1/prodlim/R/backGround.R |only
prodlim-1.2.1/prodlim/R/confInt.R |only
prodlim-1.2.1/prodlim/R/eventsMethods.R | 20
prodlim-1.2.1/prodlim/R/findArrow.R | 89 -
prodlim-1.2.1/prodlim/R/getEvent.R |only
prodlim-1.2.1/prodlim/R/getStates.R |only
prodlim-1.2.1/prodlim/R/jackknife.R | 9
prodlim-1.2.1/prodlim/R/lifeTab.R | 255 -----
prodlim-1.2.1/prodlim/R/lifeTab.competing.risks.R |only
prodlim-1.2.1/prodlim/R/lifeTab.survival.R |only
prodlim-1.2.1/prodlim/R/lines.prodlim.R |only
prodlim-1.2.1/prodlim/R/markTime.R |only
prodlim-1.2.1/prodlim/R/meanNeighbors.R |only
prodlim-1.2.1/prodlim/R/model.specials.R | 23
prodlim-1.2.1/prodlim/R/neighborhood.R | 3
prodlim-1.2.1/prodlim/R/neighbors.R | 8
prodlim-1.2.1/prodlim/R/plot.Hist.R | 957 +++++++++------------
prodlim-1.2.1/prodlim/R/plot.prodlim.R | 255 +++--
prodlim-1.2.1/prodlim/R/plotCompetingRiskModel.R |only
prodlim-1.2.1/prodlim/R/plotIllnessDeathModel.R |only
prodlim-1.2.1/prodlim/R/predictSurvIndividual.R | 1
prodlim-1.2.1/prodlim/R/print.prodlim.R | 1
prodlim-1.2.1/prodlim/R/prodlim.R | 188 +---
prodlim-1.2.1/prodlim/R/prodlimIcensSurv.R | 60 +
prodlim-1.2.1/prodlim/R/quantiles.prodlim.R | 11
prodlim-1.2.1/prodlim/R/resolveX.R | 2
prodlim-1.2.1/prodlim/R/shiftPosition.R |only
prodlim-1.2.1/prodlim/R/sindex.R | 10
prodlim-1.2.1/prodlim/R/statesMethods.R | 1
prodlim-1.2.1/prodlim/R/summary.Hist.R | 124 +-
prodlim-1.2.1/prodlim/R/summary.prodlim.R | 31
prodlim-1.2.1/prodlim/data/clusterTestData.txt |only
prodlim-1.2.1/prodlim/man/Hist.Rd | 19
prodlim-1.2.1/prodlim/man/SimSurv.Rd | 79 +
prodlim-1.2.1/prodlim/man/SmartControl.Rd |only
prodlim-1.2.1/prodlim/man/atRisk.Rd |only
prodlim-1.2.1/prodlim/man/backGround.Rd |only
prodlim-1.2.1/prodlim/man/clusterTestData.Rd |only
prodlim-1.2.1/prodlim/man/confInt.Rd |only
prodlim-1.2.1/prodlim/man/getEvent.Rd |only
prodlim-1.2.1/prodlim/man/jackknife.Rd |only
prodlim-1.2.1/prodlim/man/markTime.Rd |only
prodlim-1.2.1/prodlim/man/meanNeighbors.Rd |only
prodlim-1.2.1/prodlim/man/plot.Hist.Rd | 351 ++-----
prodlim-1.2.1/prodlim/man/plot.prodlim.Rd | 80 +
prodlim-1.2.1/prodlim/man/plotIllnessDeathModel.Rd |only
prodlim-1.2.1/prodlim/man/prodlim.Rd | 42
prodlim-1.2.1/prodlim/man/quantile.prodlim.Rd |only
prodlim-1.2.1/prodlim/src/IntIndex.c | 29
prodlim-1.2.1/prodlim/src/icens_prodlim.c | 18
prodlim-1.2.1/prodlim/src/prodlim.c | 51 -
prodlim-1.2.1/prodlim/src/prodlim.h | 2
prodlim-1.2.1/prodlim/src/prodlim_clustersurv.c | 97 +-
prodlim-1.2.1/prodlim/src/prodlim_comprisk.c | 45
prodlim-1.2.1/prodlim/src/prodlim_surv.c | 2
prodlim-1.2.1/prodlim/svn-commit.tmp |only
prodlim-1.2.1/prodlim/test |only
80 files changed, 1500 insertions(+), 1797 deletions(-)
Title: Weighted Gene Co-Expression Network Analysis
Diff between WGCNA versions 1.00 dated 2011-02-15 and 1.10-2 dated 2011-04-24
Description: Functions necessary to perform Weighted Gene Co-Expression
Network Analysis
Author: Peter Langfelder
Maintainer: Peter Langfelder
WGCNA-1.00/WGCNA/R/AUV2predicted.R |only
WGCNA-1.00/WGCNA/man/AUV2predicted.Rd |only
WGCNA-1.10-2/WGCNA/Changelog | 39 +++
WGCNA-1.10-2/WGCNA/DESCRIPTION | 12 -
WGCNA-1.10-2/WGCNA/R/AFcorMI.R |only
WGCNA-1.10-2/WGCNA/R/Functions-fromSimilarity.R | 48 ++++
WGCNA-1.10-2/WGCNA/R/Functions.R | 187 ++++++++++------
WGCNA-1.10-2/WGCNA/R/accuracyMeasures.R |only
WGCNA-1.10-2/WGCNA/R/adjacency.polyReg.R |only
WGCNA-1.10-2/WGCNA/R/adjacency.splineReg.R |only
WGCNA-1.10-2/WGCNA/R/coClustering.R |only
WGCNA-1.10-2/WGCNA/R/collapseRows-by-JeremyMiller.R | 152 ++++++++++---
WGCNA-1.10-2/WGCNA/R/collapseRows.R |only
WGCNA-1.10-2/WGCNA/R/collapseRowsUsingKME.R |only
WGCNA-1.10-2/WGCNA/R/conformityDecomposition.R |only
WGCNA-1.10-2/WGCNA/R/consensusDissTOMandTree.R |only
WGCNA-1.10-2/WGCNA/R/corFunctions.R | 13 -
WGCNA-1.10-2/WGCNA/R/coxRegressionResiduals.R |only
WGCNA-1.10-2/WGCNA/R/dendrogramAdjustmentFunctions.R |only
WGCNA-1.10-2/WGCNA/R/kMEcomparisonScatterplot.R |only
WGCNA-1.10-2/WGCNA/R/moduleMergeUsingKME.R |only
WGCNA-1.10-2/WGCNA/R/nearestCentroidPredictor.R |only
WGCNA-1.10-2/WGCNA/R/overlapTableUsingKME.R |only
WGCNA-1.10-2/WGCNA/R/populationMeansInAdmixture.R |only
WGCNA-1.10-2/WGCNA/R/proportionsInAdmixture.R |only
WGCNA-1.10-2/WGCNA/R/qvalue.R |only
WGCNA-1.10-2/WGCNA/R/standardScreeningBinaryTrait.R | 164 ++++++++------
WGCNA-1.10-2/WGCNA/R/stratifiedBarplot.R |only
WGCNA-1.10-2/WGCNA/R/userListEnrichment.R |only
WGCNA-1.10-2/WGCNA/R/votingLinearPredictor.R |only
WGCNA-1.10-2/WGCNA/data |only
WGCNA-1.10-2/WGCNA/man/AFcorMI.Rd |only
WGCNA-1.10-2/WGCNA/man/BloodLists.Rd |only
WGCNA-1.10-2/WGCNA/man/BrainLists.Rd |only
WGCNA-1.10-2/WGCNA/man/WGCNA-package.Rd | 59 ++++-
WGCNA-1.10-2/WGCNA/man/accuracyMeasures.Rd |only
WGCNA-1.10-2/WGCNA/man/adjacency.Rd | 2
WGCNA-1.10-2/WGCNA/man/adjacency.polyReg.Rd |only
WGCNA-1.10-2/WGCNA/man/adjacency.splineReg.Rd |only
WGCNA-1.10-2/WGCNA/man/chooseOneHubInEachModule.Rd |only
WGCNA-1.10-2/WGCNA/man/chooseTopHubInEachModule.Rd |only
WGCNA-1.10-2/WGCNA/man/coClustering.Rd |only
WGCNA-1.10-2/WGCNA/man/coClustering.permutationTest.Rd |only
WGCNA-1.10-2/WGCNA/man/collapseRows.Rd | 145 ++++++++----
WGCNA-1.10-2/WGCNA/man/collapseRowsUsingKME.Rd |only
WGCNA-1.10-2/WGCNA/man/conformityDecomposition.Rd |only
WGCNA-1.10-2/WGCNA/man/consensusDissTOMandTree.Rd |only
WGCNA-1.10-2/WGCNA/man/coxRegressionResiduals.Rd |only
WGCNA-1.10-2/WGCNA/man/kMEcomparisonScatterplot.Rd |only
WGCNA-1.10-2/WGCNA/man/labeledHeatmap.Rd | 16 +
WGCNA-1.10-2/WGCNA/man/matrixToNetwork.Rd |only
WGCNA-1.10-2/WGCNA/man/moduleMergeUsingKME.Rd |only
WGCNA-1.10-2/WGCNA/man/modulePreservation.Rd | 2
WGCNA-1.10-2/WGCNA/man/nearestCentroidPredictor.Rd |only
WGCNA-1.10-2/WGCNA/man/networkScreening.Rd | 2
WGCNA-1.10-2/WGCNA/man/orderBranchesUsingHubGenes.Rd |only
WGCNA-1.10-2/WGCNA/man/overlapTableUsingKME.Rd |only
WGCNA-1.10-2/WGCNA/man/plotColorUnderTree.Rd | 32 ++
WGCNA-1.10-2/WGCNA/man/plotDendroAndColors.Rd | 26 +-
WGCNA-1.10-2/WGCNA/man/populationMeansInAdmixture.Rd |only
WGCNA-1.10-2/WGCNA/man/proportionsInAdmixture.Rd |only
WGCNA-1.10-2/WGCNA/man/qvalue.Rd |only
WGCNA-1.10-2/WGCNA/man/removePrincipalComponents.Rd |only
WGCNA-1.10-2/WGCNA/man/signedKME.Rd | 2
WGCNA-1.10-2/WGCNA/man/standardScreeningBinaryTrait.Rd | 160 ++++++++-----
WGCNA-1.10-2/WGCNA/man/standardScreeningNumericTrait.Rd | 7
WGCNA-1.10-2/WGCNA/man/stratifiedBarplot.Rd |only
WGCNA-1.10-2/WGCNA/man/swapTwoBranches.Rd |only
WGCNA-1.10-2/WGCNA/man/userListEnrichment.Rd |only
WGCNA-1.10-2/WGCNA/man/verboseScatterplot.Rd | 7
WGCNA-1.10-2/WGCNA/man/votingLinearPredictor.Rd |only
WGCNA-1.10-2/WGCNA/src/corFunctions-parallel.c | 2
72 files changed, 786 insertions(+), 291 deletions(-)
Title: Wrapper to spatialite functions
Diff between SQLiteMap versions 0.5 dated 2011-04-05 and 0.6.1 dated 2011-04-24
Description: Provides bindings to spatialite functionalities. Through
this bindings (due to OGC specifications) numerous spatial
functions can be performed by simple SQL statements.
Author: Norbert Solymosi
Maintainer: Norbert Solymosi
SQLiteMap-0.5/SQLiteMap/src/Makevars |only
SQLiteMap-0.6.1/SQLiteMap/DESCRIPTION | 8 ++++----
SQLiteMap-0.6.1/SQLiteMap/configure | 2 --
SQLiteMap-0.6.1/SQLiteMap/configure.ac | 2 --
SQLiteMap-0.6.1/SQLiteMap/configure.win |only
SQLiteMap-0.6.1/SQLiteMap/src/Makevars.in | 3 ++-
SQLiteMap-0.6.1/SQLiteMap/src/Makevars.win |only
7 files changed, 6 insertions(+), 9 deletions(-)
Title: Data sets and functions with "Analyzing Linguistic Data: A
practical introduction to statistics".
Diff between languageR versions 1.1 dated 2011-04-15 and 1.2 dated 2011-04-24
Description: Data sets exemplifying statistical methods, and some
facilitatory utility functions used in "Analyzing Linguistic
Data: A practical introduction to statistics using R",
Cambridge University Press, 2008.
Author: R. H. Baayen
Maintainer:
DESCRIPTION | 15 +--
R/aovlmer.fnc.R | 38 ---------
R/pvals.fnc.R | 135 --------------------------------
R/simulateLatinsquare.fnc.R | 166 +---------------------------------------
R/simulateQuasif.fnc.R | 91 +--------------------
R/zzz.R | 1
data/affixProductivity.rda |binary
data/alice.rda |binary
data/aovlmerfnc.rda |only
data/auxiliaries.rda |binary
data/beginningReaders.rda |binary
data/danish.rda |binary
data/datalist | 4
data/dative.rda |binary
data/dativeSimplified.rda |binary
data/durationsGe.rda |binary
data/durationsOnt.rda |binary
data/dutchSpeakersDist.rda |binary
data/dutchSpeakersDistMeta.rda |binary
data/english.rda |binary
data/etymology.rda |binary
data/faz.rda |binary
data/finalDevoicing.rda |binary
data/havelaar.rda |binary
data/heid.rda |binary
data/imaging.rda |binary
data/latinsquare.rda |binary
data/lexdec.rda |binary
data/lexicalMeasures.rda |binary
data/lexicalMeasuresClasses.rda |binary
data/moby.rda |binary
data/nesscg.rda |binary
data/nessdemog.rda |binary
data/nessw.rda |binary
data/oldFrench.rda |binary
data/oldFrenchMeta.rda |binary
data/oz.rda |binary
data/periphrasticDo.rda |binary
data/phylogeny.rda |binary
data/primingHeid.rda |binary
data/primingHeidPrevRT.rda |binary
data/pvalsfnc.rda |only
data/quasif.rda |binary
data/ratings.rda |binary
data/regularity.rda |binary
data/selfPacedReadingHeid.rda |binary
data/shrinkage.rda |binary
data/simulateLatinsquarefnc.rda |only
data/simulateQuasiffnc.rda |only
data/sizeRatings.rda |binary
data/spanish.rda |binary
data/spanishFunctionWords.rda |binary
data/spanishMeta.rda |binary
data/splitplot.rda |binary
data/through.rda |binary
data/twente.rda |binary
data/variationLijk.rda |binary
data/ver.rda |binary
data/verbs.rda |binary
data/warlpiri.rda |binary
data/weightRatings.rda |binary
data/writtenVariationLijk.rda |binary
man/aovlmer.fnc.Rd | 1
man/simulateQuasif.fnc.Rd | 4
64 files changed, 32 insertions(+), 423 deletions(-)
Title: Estimation of indicators on social exclusion and poverty
Diff between laeken versions 0.2.1 dated 2011-03-09 and 0.2.2 dated 2011-04-24
Description: Estimation of indicators on social exclusion and poverty,
as well as Pareto tail modeling for empirical income
distributions (including graphical tools).
Author: Andreas Alfons, Josef Holzer and Matthias Templ
Maintainer: Andreas Alfons
laeken-0.2.1/laeken/inst/doc/figures-pareto |only
laeken-0.2.2/laeken/DESCRIPTION | 10 ++++----
laeken-0.2.2/laeken/NAMESPACE | 2 +
laeken-0.2.2/laeken/NEWS | 8 +++++-
laeken-0.2.2/laeken/R/paretoTail.R | 25 ++++++++++++++++++---
laeken-0.2.2/laeken/inst/doc/laeken-pareto-007.pdf |only
laeken-0.2.2/laeken/inst/doc/laeken-pareto-011.pdf |only
laeken-0.2.2/laeken/inst/doc/laeken-pareto.Rnw | 11 +++++----
laeken-0.2.2/laeken/inst/doc/laeken-pareto.pdf |binary
laeken-0.2.2/laeken/inst/doc/laeken-standard.Rnw | 9 +++++--
laeken-0.2.2/laeken/inst/doc/laeken-standard.pdf |binary
laeken-0.2.2/laeken/inst/doc/laeken-variance.Rnw | 9 +++++--
laeken-0.2.2/laeken/inst/doc/laeken-variance.pdf |binary
laeken-0.2.2/laeken/inst/doc/laeken.bib | 8 ++++--
laeken-0.2.2/laeken/man/laeken-package.Rd | 7 +++--
laeken-0.2.2/laeken/man/paretoTail.Rd | 6 ++++-
laeken-0.2.2/laeken/man/replaceTail.Rd | 2 -
laeken-0.2.2/laeken/man/reweightOut.Rd | 2 -
laeken-0.2.2/laeken/man/shrinkOut.Rd |only
19 files changed, 71 insertions(+), 28 deletions(-)
Title: Download financial data from FRB's website
Diff between FRBData versions 0.1 dated 2011-04-23 and 0.2 dated 2011-04-24
Description: This package provides functions which can get financial
and economical data from FRB's
website.(http://www.federalreserve.gov)
Author: Shinichi Takayanagi
Maintainer: Shinichi Takayanagi
FRBData-0.1/FRBData/R/GetRate.R |only
FRBData-0.1/FRBData/man/GetRate.Rd |only
FRBData-0.2/FRBData/DESCRIPTION | 8 ++++----
FRBData-0.2/FRBData/NAMESPACE | 6 +-----
FRBData-0.2/FRBData/R/GetInterestRates.R |only
FRBData-0.2/FRBData/man/FRBData-package.Rd | 14 ++++++--------
FRBData-0.2/FRBData/man/GetInterestRates.Rd |only
7 files changed, 11 insertions(+), 17 deletions(-)
Title: Better Automated ReDistricting
Diff between BARD versions 1.20 dated 2011-04-23 and 1.21 dated 2011-04-24
Description: This is a package for automated redistricting and
heuristic exploration of redistricter revealed preference
Author: Micah Altman
Maintainer: Micah Altman
DESCRIPTION | 8 ++++----
R/bardIO.R | 4 +++-
R/bardPlan.R | 20 ++++++++++++++++++--
R/bardScore.R | 21 +++++++++++++++++++++
inst/doc/bardJSS.pdf |binary
man/createPlans.Rd | 4 +++-
6 files changed, 49 insertions(+), 8 deletions(-)
Title: X12 - wrapper function and GUI
Diff between x12 versions 0.0-7 dated 2010-07-24 and 0.1-0 dated 2011-04-24
Description: A wrapper function and GUI for the X12 binaries under
windows
Author: Alexander Kowarik
Maintainer: Alexander Kowarik
DESCRIPTION | 8 ++++----
R/X12GUI.R | 2 +-
R/x12.R | 20 +++++++++++++++-----
3 files changed, 20 insertions(+), 10 deletions(-)
Title: Package contains a few functions to visualize statistical
circumstances.
Diff between visualizationTools versions 0.1 dated 2011-02-28 and 0.2 dated 2011-04-24
More information about visualizationTools at CRAN
Description: Package contains function to visualize a t-test, the power
of a t-test, control charts and the influence of regulating
them, Oc-curves, the Law of large Numbers and confidence
intervals.
Author: Thomas Roth Etienne Stockhausen
Maintainer: T. Roth
DESCRIPTION | 13
R/CLT.R | 2
R/LLN.R | 2
R/confSim.R |only
R/ocCurve.R | 2
R/plot.htest.R | 2
R/plot.power.htest.R | 2
R/qrk.R | 2
R/qrkSD.R | 2
build |only
man/CLT.Rd | 285 ++++++++++++++++++++
man/LLN.Rd | 230 ++++++++++++++++
man/confSim.Rd |only
man/ocCurve.Rd | 143 ++++++++++
man/plot.htest.Rd | 202 ++++++++++++++
man/plot.power.htest.Rd | 197 ++++++++++++++
man/qrk.Rd | 400 ++++++++++++++++++++++++++++-
man/qrkSD.Rd | 524 +++++++++++++++++++++++++++++++++++++-
man/visualizationTools-package.Rd | 15 -
19 files changed, 2002 insertions(+), 21 deletions(-)
Permanent link
Title: You didn't know you didn't know?
Diff between unknownR versions 0.1 dated 2011-03-24 and 0.2 dated 2011-04-24
Description: Utility to quickly find useful functions in R that you
didn't know you didn't know.
Author: Matthew Dowle
Maintainer: Matthew Dowle
unknownR-0.1/unknownR/man/Internal.Rd |only
unknownR-0.2/unknownR/DESCRIPTION | 9 +-
unknownR-0.2/unknownR/NEWS | 32 ++++++-
unknownR-0.2/unknownR/R/funlist.R | 66 +++++++++++++--
unknownR-0.2/unknownR/R/learn.R | 43 +++++++++-
unknownR-0.2/unknownR/R/onAttach.R |only
unknownR-0.2/unknownR/R/popcon.R |only
unknownR-0.2/unknownR/R/unk.R | 143 ++++++++++++++++++++++++++--------
unknownR-0.2/unknownR/man/learn.Rd | 11 +-
unknownR-0.2/unknownR/man/unk.Rd | 25 ++++-
10 files changed, 262 insertions(+), 67 deletions(-)
Title: R based Twitter client
Diff between twitteR versions 0.99.4 dated 2011-04-14 and 0.99.6 dated 2011-04-24
Description: Provides an interface to the Twitter web API
Author: Jeff Gentry
Maintainer: Jeff Gentry
DESCRIPTION | 6 +++---
R/search.R | 4 ++--
inst/doc/twitteR.pdf |binary
3 files changed, 5 insertions(+), 5 deletions(-)
Title: Detection of disease-associated SNP interactions in case-parent
trio data
Diff between trio versions 1.1.22 dated 2011-04-04 and 1.2.0 dated 2011-04-24
Description: Testing SNPs and SNP interactions with a genotypic TDT.
This package furthermore contains functions for computing
pairwise values of LD measures and for identifying LD blocks,
as well as functions for setting up matched case pseudo-control
genotype data for case-parent trios in order to run trio logic
regreesion, to impute missing genotypes in trios, or to
simulate case-parent trios with disease risk dependent on SNP
interaction.
Author: Holger Schwender, Qing Li
Maintainer: Holger Schwender
DESCRIPTION | 10 +++++-----
NAMESPACE | 3 ++-
R/colTDTsam.R |only
inst/doc/trio.Rnw | 10 +++++-----
inst/doc/trio.pdf |binary
inst/plugin/My_own_scoring.f | 26 +++-----------------------
man/colTDTsam.Rd |only
man/tdt.Rd | 1 +
8 files changed, 16 insertions(+), 34 deletions(-)
Title: Topic models
Diff between topicmodels versions 0.0-9 dated 2011-04-15 and 0.0-10 dated 2011-04-24
Description: Provides an interface to the C code for Latent Dirichlet
Allocation (LDA) models and Correlated Topics Models (CTM) by
David M. Blei and co-authors and the C++ code for fitting LDA
models using Gibbs sampling by Xuan-Hieu Phan and co-authors.
Author: Bettina Gruen and Kurt Hornik
Maintainer: Bettina Gruen
DESCRIPTION | 8 +-
NEWS | 4 +
inst/NEWS | 4 +
inst/doc/topicmodels.Rnw | 131 ++++++++++++++++++++++++-----------------------
inst/doc/topicmodels.bib | 2
inst/doc/topicmodels.pdf |binary
src/gsl-wrappers.c | 3 -
src/inference.c | 6 --
src/lda-alpha.c | 3 -
src/rctm.c | 8 +-
src/rlda.c | 4 -
11 files changed, 88 insertions(+), 85 deletions(-)
Title: Inverse Regression for Text Analysis
Diff between textir versions 1.5.3 dated 2011-04-15 and 1.5-4 dated 2011-04-24
Description: A suite of tools for text and sentiment mining. This
includes the `mnlm' function, for sparse multinomial logistic
regression, `pls', a concise partial least squares routine, and
the `topics' function (beta), for efficient estimation and
dimension selection in latent topic models.
Author: Matt Taddy
Maintainer: Matt Taddy
ChangeLog | 12 ++++--------
DESCRIPTION | 8 ++++----
R/mnlm.R | 24 +++++++++++++-----------
R/tpx.R | 40 ++++++++++++++++++++++------------------
man/mnlm.Rd | 1 +
man/summary.mnlm.Rd | 2 +-
6 files changed, 45 insertions(+), 42 deletions(-)
Title: R Functions for Solving Stoichiometric Equations
Diff between stoichcalc versions 1.1-1 dated 2010-02-23 and 1.1-2 dated 2011-04-24
Description: Given a list of substance compositions, a list of
substances involved in a process, and a list of constraints in
addition to mass conservation of elementary constituents, the
package contains functions to build the substance composition
matrix, to analyze the uniqueness of process stoichiometry, and
to calculate stoichiometric coefficients if process
stoichiometry is unique (see Reichert, P. and Schuwirth, N., A
generic framework for deriving process stoichiometry in
environmental models, Environmental Modelling and Software, in
review, 2010 for more details).
Author: Peter Reichert
Maintainer: Peter Reichert
DESCRIPTION | 8
demo/00Index | 6
demo/stoichcalc_example2.R | 802 ++++++++++++++++++++++-----------------------
inst |only
man/calc.comp.matrix.Rd | 4
man/calc.stoich.basis.Rd | 2
man/calc.stoich.coef.Rd | 4
man/stoichcalc.Rd | 262 +++++++-------
8 files changed, 544 insertions(+), 544 deletions(-)
Title: Principal Stratification Sensitivity Analysis Functions
Diff between sensitivityPStrat versions 1.0-3 dated 2011-02-04 and 1.0-4 dated 2011-04-24
More information about sensitivityPStrat at CRAN
Description: This package provides functions to perform principal
stratification sensitivity analyses on datasets.
Author: Charles Dupont, Bryan Shepherd
Maintainer: Charles Dupont
DESCRIPTION | 10 +-
NAMESPACE | 7 +
R/funArray.R | 172 ++++++++++++++++++++++++++++++++++++++----------
R/sensitivityHHS.R | 9 +-
R/sensitivityJR.R | 10 +-
R/sensitivitySGD.R | 148 ++++++++++++++++++++++++++++++-----------
R/sensitivitySGL.R | 126 ++++++++++++++++++++++++++---------
man/funArray.Rd | 16 +---
man/funMatrix.Rd |only
man/funVector.Rd | 2
man/plot.sensitivity.Rd | 6 +
man/sensitivitySGD.Rd | 26 ++++++-
man/sensitivitySGL.Rd | 21 +++++
13 files changed, 416 insertions(+), 137 deletions(-)
Permanent link
Title: Ray Shooting Depth (i.e. RS Depth) functions for bivariate
analysis
Diff between rsdepth versions 0.1-1 dated 2011-04-11 and 0.1-2 dated 2011-04-24
Description: Ray Shooting Depth functions are provided for bivariate
analysis.
Author: Nabil Mustafa
Maintainer: Mudassir Shabbir
DESCRIPTION | 8 +--
R/rsdepth.R | 5 +-
R/rsmed.R | 47 ++++++++++++++++++-
changelog |only
man/rsdepth.Rd | 3 -
man/rsmed.Rd | 10 ++--
src/rsdepth.cpp | 135 ++++++++++++++++++++++++++++----------------------------
7 files changed, 128 insertions(+), 80 deletions(-)
Title: R version of GENetic Optimization Using Derivatives
Diff between rgenoud versions 5.7-1 dated 2010-08-27 and 5.7-2 dated 2011-04-24
Description: A genetic algorithm plus derivative optimizer
Author: Walter R. Mebane, Jr.
Maintainer: Jasjeet Singh Sekhon
ChangeLog | 10
DESCRIPTION | 8
inst/CITATION | 5
inst/doc/rgenoud.Rnw | 166 ++---
inst/doc/rgenoud.bib | 1494 +++++++++++++++++++++++++++++++++++++++++++++++++-
inst/doc/rgenoud.pdf |binary
tests/tests.Rout.save | 47 -
7 files changed, 1593 insertions(+), 137 deletions(-)
Title: Generate LaTeX tables of descriptive statistics
Diff between reporttools versions 1.0.5 dated 2010-03-04 and 1.0.6 dated 2011-04-24
Description: The functions in this package are especially helpful when
writing reports of data analysis using Sweave.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach
reporttools-1.0.5/reporttools/CHANGES |only
reporttools-1.0.5/reporttools/R/vectorToString.r |only
reporttools-1.0.5/reporttools/man/vectorToString.Rd |only
reporttools-1.0.6/reporttools/DESCRIPTION | 8 +-
reporttools-1.0.6/reporttools/NAMESPACE | 6 +
reporttools-1.0.6/reporttools/NEWS |only
reporttools-1.0.6/reporttools/R/NAtoZero.r |only
reporttools-1.0.6/reporttools/R/attachPresAbs.r |only
reporttools-1.0.6/reporttools/R/attachYesNo.r |only
reporttools-1.0.6/reporttools/R/correctVarNames.r | 19 ++--
reporttools-1.0.6/reporttools/R/displayKbyC.r | 58 ++++++++++-----
reporttools-1.0.6/reporttools/R/formatPercent.r |only
reporttools-1.0.6/reporttools/R/nominalTest.r |only
reporttools-1.0.6/reporttools/R/tableNominal.R | 8 +-
reporttools-1.0.6/reporttools/inst/doc/reporttools.pdf |binary
reporttools-1.0.6/reporttools/man/NAtoZero.Rd |only
reporttools-1.0.6/reporttools/man/attachPresAbs.Rd |only
reporttools-1.0.6/reporttools/man/attachYesNo.Rd |only
reporttools-1.0.6/reporttools/man/correctVarNames.Rd | 4 -
reporttools-1.0.6/reporttools/man/displayKbyC.Rd | 10 +-
reporttools-1.0.6/reporttools/man/formatPercent.Rd |only
reporttools-1.0.6/reporttools/man/nominalTest.Rd |only
reporttools-1.0.6/reporttools/man/reporttools-package.Rd | 4 -
reporttools-1.0.6/reporttools/man/tableNominal.Rd | 14 ++-
24 files changed, 87 insertions(+), 44 deletions(-)
Title: Perform Rosenbaum bounds sensitivity tests for matched data.
Diff between rbounds versions 0.5 dated 2010-08-17 and 0.7 dated 2011-04-24
Description: Takes matched data and calculates Rosenbaum bounds for the
treatment effect. Calculates bounds for binary data,
Hodges-Lehmann point estimates, Wilcoxon signed-rank test, and
for data with multiple matched controls. Is designed to work
with the Matching package and operate on Match() objects.
Author: Luke J. Keele
Maintainer: Luke J. Keele
DESCRIPTION | 10 +++++-----
R/psens.R | 29 ++++-------------------------
2 files changed, 9 insertions(+), 30 deletions(-)
Title: Quantile Regression
Diff between quantreg versions 4.62 dated 2011-04-06 and 4.65 dated 2011-04-24
Description: Quantile regression and related methods.
Author: Roger Koenker
Maintainer: Roger Koenker
DESCRIPTION | 10 -
R/quantreg.R | 56 ++++++--
R/rqss.R | 42 +++---
R/sfn.R | 95 +++++++++------
inst/Changelog | 15 ++
inst/doc/engelcoef.pdf | 307 ++++++++-----------------------------------------
inst/doc/rq.pdf |binary
man/predict.rq.Rd | 35 +++--
man/rq.fit.sfn.Rd | 18 --
man/rq.fit.sfnc.Rd | 18 --
man/rqss.Rd | 22 +--
man/sfn.control.Rd |only
12 files changed, 233 insertions(+), 385 deletions(-)
Title: Statistical inference for partially observed Markov processes
Diff between pomp versions 0.36-2 dated 2011-04-13 and 0.36-4 dated 2011-04-24
Description: Inference methods for partially-observed Markov processes
Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner,
Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael
Lavine, Daniel C. Reuman
Maintainer: Aaron A. King
pomp-0.36-2/pomp/inst/data-R/blowfly.R |only
pomp-0.36-2/pomp/inst/data-R/blowfly.csv |only
pomp-0.36-2/pomp/inst/data-R/blowfly1.csv |only
pomp-0.36-2/pomp/inst/data-R/blowfly2.csv |only
pomp-0.36-2/pomp/inst/data-R/blowfly3.csv |only
pomp-0.36-2/pomp/inst/data-R/blowfly4.csv |only
pomp-0.36-2/pomp/inst/data-R/blowfly_Ed.R |only
pomp-0.36-2/pomp/inst/data-R/london_birthpop.csv |only
pomp-0.36-2/pomp/inst/data-R/london_measles.csv |only
pomp-0.36-2/pomp/inst/data-R/make.R |only
pomp-0.36-2/pomp/inst/data-R/tsir.R |only
pomp-0.36-2/pomp/inst/doc/ou2-multi-mif.rda |only
pomp-0.36-2/pomp/inst/doc/ou2-trajmatch.rda |only
pomp-0.36-2/pomp/src/tsir.c |only
pomp-0.36-2/pomp/tests/Rplots.pdf |only
pomp-0.36-2/pomp/tests/sir-icfit.R |only
pomp-0.36-2/pomp/tests/sir-icfit.Rout.save |only
pomp-0.36-2/pomp/tests/tmp.R |only
pomp-0.36-4/pomp/DESCRIPTION | 8
pomp-0.36-4/pomp/R/pomp-methods.R | 10
pomp-0.36-4/pomp/data/dacca.rda |binary
pomp-0.36-4/pomp/data/euler.sir.rda |binary
pomp-0.36-4/pomp/data/gillespie.sir.rda |binary
pomp-0.36-4/pomp/data/gompertz.rda |only
pomp-0.36-4/pomp/data/ou2.rda |binary
pomp-0.36-4/pomp/data/ricker.rda |binary
pomp-0.36-4/pomp/data/rw2.rda |binary
pomp-0.36-4/pomp/data/verhulst.rda |binary
pomp-0.36-4/pomp/inst/ChangeLog | 15
pomp-0.36-4/pomp/inst/SVN-REVISION | 4
pomp-0.36-4/pomp/inst/data-R/gompertz.R |only
pomp-0.36-4/pomp/inst/doc/advanced_topics_in_pomp.pdf |binary
pomp-0.36-4/pomp/inst/doc/gompertz-multi-mif.rda |only
pomp-0.36-4/pomp/inst/doc/gompertz-trajmatch.rda |only
pomp-0.36-4/pomp/inst/doc/intro_to_pomp.Rnw | 653 ++++++++++--------
pomp-0.36-4/pomp/inst/doc/intro_to_pomp.pdf |binary
pomp-0.36-4/pomp/inst/doc/pomp.bib | 22
pomp-0.36-4/pomp/man/gompertz.Rd |only
pomp-0.36-4/pomp/man/probed-pomp-methods.Rd | 1
pomp-0.36-4/pomp/src/gompertz.c |only
pomp-0.36-4/pomp/tests/synlik.R |only
pomp-0.36-4/pomp/tests/synlik.Rout.save |only
42 files changed, 414 insertions(+), 299 deletions(-)
Title: Tools for splitting, applying and combining data
Diff between plyr versions 1.5.1 dated 2011-04-13 and 1.5.2 dated 2011-04-24
Description: plyr is a set of tools that solves a common set of
problems: you need to break a big problem down into manageable
pieces, operate on each pieces and then put all the pieces back
together. For example, you might want to fit a model to each
spatial location or time point in your study, summarise data by
panels or collapse high-dimensional arrays to simpler summary
statistics. The development of plyr has been generously
supported by BD (Becton Dickinson).
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 6 +++---
NAMESPACE | 1 +
NEWS | 7 +++++++
R/helper-rename.r | 1 +
R/simplify-data-frame.r | 2 +-
inst/doc |only
inst/tests/test-simplify-df.r | 7 +++++++
7 files changed, 20 insertions(+), 4 deletions(-)
Title: Various plotting functions
Diff between plotrix versions 3.1 dated 2011-03-13 and 3.1-2 dated 2011-04-24
Description: Lots of plots, various labeling, axis and color scaling
functions.
Author: Jim Lemon, Ben Bolker, Sander Oom, Eduardo Klein, Barry
Rowlingson, Hadley Wickham, Anupam Tyagi, Olivier Eterradossi,
Gabor Grothendieck, Michael Toews, John Kane, Rolf Turner, Carl
Witthoft, Julian Stander, Thomas Petzoldt, Remko Duursma, Elisa
Biancotto, Ofir Levy, Christophe Dutang, Peter Solymos
Maintainer: Jim Lemon
plotrix-3.1-2/plotrix/DESCRIPTION | 8 -
plotrix-3.1-2/plotrix/INDEX | 1
plotrix-3.1-2/plotrix/NEWS | 11 +
plotrix-3.1-2/plotrix/R/dendroPlot.R | 35 +++---
plotrix-3.1-2/plotrix/R/gantt.R | 5
plotrix-3.1-2/plotrix/R/intersectDiagram.R | 145 +++++++++++++++----------
plotrix-3.1-2/plotrix/R/makeIntersectList.R | 32 +++++
plotrix-3.1-2/plotrix/demo/plotrix.R | 6 -
plotrix-3.1-2/plotrix/man/categoryReshape.Rd |only
plotrix-3.1-2/plotrix/man/dendroPlot.Rd | 44 ++++---
plotrix-3.1-2/plotrix/man/gantt.chart.Rd | 11 +
plotrix-3.1-2/plotrix/man/gap.barplot.Rd | 2
plotrix-3.1-2/plotrix/man/intersectDiagram.Rd | 60 ++++++----
plotrix-3.1-2/plotrix/man/makeIntersectList.Rd | 39 ++++--
plotrix-3.1/plotrix/R/pasteCols.R |only
15 files changed, 263 insertions(+), 136 deletions(-)
Title: Plot a model's response while varying the values of the
predictors.
Diff between plotmo versions 1.2-0 dated 2011-04-14 and 1.2-3 dated 2011-04-24
Description: Plot a model's response when varying one or two predictors
while holding the other predictors constant. A poor man's
partial dependence plot.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow
DESCRIPTION | 8
NAMESPACE | 4
NEWS | 9
R/lib.R | 128 +++------
R/plotmo.R | 76 ++---
R/plotmo.methods.R | 37 +-
R/plotmo.methods.earth.R | 23 +
R/plotmo.methods.misc.R | 12
man/plotmo.Rd | 71 ++---
man/plotmo.methods.Rd |only
src/tests/fast.postscript.R |only
src/tests/test.plotmo.R | 15 -
src/tests/test.plotmo.Rout.save | 374 +++++++++++++++++-----------
src/tests/test.plotmo.bat | 4
src/tests/test.plotmo.center.R | 9
src/tests/test.plotmo.center.Rout.save | 130 +++++++++
src/tests/test.plotmo.center.bat | 4
src/tests/test.plotmo.fac.R | 3
src/tests/test.plotmo.fac.Rout.save | 26 +
src/tests/test.plotmo.fac.bat | 4
src/tests/test.plotmo.non.earth.R | 16 -
src/tests/test.plotmo.non.earth.Rout.save | 392 +++++++++++++++++-------------
src/tests/test.plotmo.non.earth.bat | 4
tests/test.plotmo.R | 1
tests/test.plotmo.Rout.save | 197 +++++++--------
25 files changed, 913 insertions(+), 634 deletions(-)
Title: R tools for integrating phylogenies and ecology
Diff between picante versions 1.2-0 dated 2010-07-24 and 1.3-0 dated 2011-04-24
Description: Phylocom integration, community analyses, null-models,
traits and evolution in R
Author: Steven W. Kembel
Maintainer: Steven W. Kembel
DESCRIPTION | 8 ++++----
R/pcd.R |only
R/phylodiversity.R | 4 ++--
inst/doc/picante-intro.pdf |binary
man/pcd.Rd |only
man/picante-package.Rd | 4 ++--
6 files changed, 8 insertions(+), 8 deletions(-)
Title: Panel-Corrected Standard Error Estimation in R
Diff between pcse versions 1.7 dated 2009-07-02 and 1.7.1 dated 2011-04-24
Description: This package contains a function to estimate
panel-corrected standard errors. Data may contain balanced or
unbalanced panels.
Author: Delia Bailey
Maintainer: Delia Bailey
pcse-1.7.1/pcse/DESCRIPTION | 6 +++---
pcse-1.7.1/pcse/inst/CITATION |only
pcse-1.7/pcse/inst/CITATION-c01 |only
3 files changed, 3 insertions(+), 3 deletions(-)
Title: Tools for nonlinear regression diagnostics
Diff between nlstools versions 0.0-10 dated 2010-02-22 and 0.0-11 dated 2011-04-24
Description: Several tools for assessing the quality of fit of a
gaussian nonlinear model are provided.
Author: Florent Baty
Maintainer: Florent Baty
ChangeLog | 6
DESCRIPTION | 12 -
R/First.lib.R | 2
R/nlstools.R | 4
inst/CITATION | 6
inst/NEWS | 10
inst/doc/nlstools_vignette.Rnw | 472 ++++++++++++++++++++---------------------
inst/doc/nlstools_vignette.pdf |binary
man/competitionmodels.Rd | 4
man/growthcurve.Rd | 2
man/growthmodels.Rd | 4
man/michaelismodels.Rd | 4
man/nlsBoot.Rd | 4
man/nlsConfRegions.Rd | 4
man/nlsContourRSS.Rd | 4
man/nlsJack.Rd | 4
man/nlsResiduals.Rd | 4
man/nlstools.Rd | 6
man/secondary.Rd | 4
man/survivalcurve.Rd | 2
man/survivalmodels.Rd | 4
21 files changed, 288 insertions(+), 274 deletions(-)
Title: Functions to generate fMRI data including activated data, noise
data and resting state data.
Diff between neuRosim versions 0.1-1 dated 2010-11-23 and 0.2-7 dated 2011-04-24
Description: The package allows users to generate fMRI time series or
4D data. Some high-level functions are created for fast data
generation with only a few arguments and a diversity of
functions to define activation and noise. For more advanced
users it is possible to use the low-level functions and
manipulate the arguments.
Author: Marijke Welvaert with contributions from Joke Durnez, Beatrijs
Moerkerke, Yves Rosseel and Geert Verdoolaege
Maintainer: Marijke Welvaert
neuRosim-0.1-1/neuRosim/R/AR1noise.fnc.R |only
neuRosim-0.1-1/neuRosim/R/Balloon.R |only
neuRosim-0.1-1/neuRosim/R/data.read.nifti.R |only
neuRosim-0.1-1/neuRosim/R/data.write.nifti.R |only
neuRosim-0.1-1/neuRosim/R/gaussnoise.fnc.R |only
neuRosim-0.1-1/neuRosim/R/lowfreq.fnc.R |only
neuRosim-0.1-1/neuRosim/R/physnoise.fnc.R |only
neuRosim-0.1-1/neuRosim/R/sim.fmri.data.R |only
neuRosim-0.1-1/neuRosim/R/sim.fmri.ts.R |only
neuRosim-0.1-1/neuRosim/R/sim.restingstate.ts.R |only
neuRosim-0.1-1/neuRosim/R/simprep.act.spat.R |only
neuRosim-0.1-1/neuRosim/R/simprep.act.temp.R |only
neuRosim-0.1-1/neuRosim/R/spatnoise.fnc.R |only
neuRosim-0.1-1/neuRosim/R/specify.design.R |only
neuRosim-0.1-1/neuRosim/R/specify.region.R |only
neuRosim-0.1-1/neuRosim/R/stim.boxcar.R |only
neuRosim-0.1-1/neuRosim/R/tasknoise.fnc.R |only
neuRosim-0.1-1/neuRosim/man/AR1noise.fnc.Rd |only
neuRosim-0.1-1/neuRosim/man/Balloon.Rd |only
neuRosim-0.1-1/neuRosim/man/data.read.nifti.Rd |only
neuRosim-0.1-1/neuRosim/man/data.write.nifti.Rd |only
neuRosim-0.1-1/neuRosim/man/gaussnoise.fnc.Rd |only
neuRosim-0.1-1/neuRosim/man/lowfreq.fnc.Rd |only
neuRosim-0.1-1/neuRosim/man/physnoise.fnc.Rd |only
neuRosim-0.1-1/neuRosim/man/sim.fmri.data.Rd |only
neuRosim-0.1-1/neuRosim/man/sim.fmri.ts.Rd |only
neuRosim-0.1-1/neuRosim/man/sim.restingstate.ts.Rd |only
neuRosim-0.1-1/neuRosim/man/simprep.act.spat.Rd |only
neuRosim-0.1-1/neuRosim/man/simprep.act.temp.Rd |only
neuRosim-0.1-1/neuRosim/man/spatnoise.fnc.Rd |only
neuRosim-0.1-1/neuRosim/man/specify.design.Rd |only
neuRosim-0.1-1/neuRosim/man/specify.region.Rd |only
neuRosim-0.1-1/neuRosim/man/stim.boxcar.Rd |only
neuRosim-0.1-1/neuRosim/man/tasknoise.fnc.Rd |only
neuRosim-0.2-7/neuRosim/DESCRIPTION | 10 ++--
neuRosim-0.2-7/neuRosim/NAMESPACE |only
neuRosim-0.2-7/neuRosim/R/balloon.R |only
neuRosim-0.2-7/neuRosim/R/canonicalHRF.R | 30 ++++--------
neuRosim-0.2-7/neuRosim/R/external.R |only
neuRosim-0.2-7/neuRosim/R/gammaHRF.R | 13 -----
neuRosim-0.2-7/neuRosim/R/lowfreqdrift.R |only
neuRosim-0.2-7/neuRosim/R/physnoise.R |only
neuRosim-0.2-7/neuRosim/R/rrice.R |only
neuRosim-0.2-7/neuRosim/R/simTSfmri.R |only
neuRosim-0.2-7/neuRosim/R/simTSrestingstate.R |only
neuRosim-0.2-7/neuRosim/R/simVOLfmri.R |only
neuRosim-0.2-7/neuRosim/R/simprepSpatial.R |only
neuRosim-0.2-7/neuRosim/R/simprepTemporal.R |only
neuRosim-0.2-7/neuRosim/R/spatialnoise.R |only
neuRosim-0.2-7/neuRosim/R/specifydesign.R |only
neuRosim-0.2-7/neuRosim/R/specifyregion.R |only
neuRosim-0.2-7/neuRosim/R/stimfunction.R |only
neuRosim-0.2-7/neuRosim/R/systemnoise.R |only
neuRosim-0.2-7/neuRosim/R/tasknoise.R |only
neuRosim-0.2-7/neuRosim/R/temporalnoise.R |only
neuRosim-0.2-7/neuRosim/R/zzz.R | 2
neuRosim-0.2-7/neuRosim/man/GaussSmoothKernel.Rd |only
neuRosim-0.2-7/neuRosim/man/Sim.3D.GRF.Rd |only
neuRosim-0.2-7/neuRosim/man/balloon.Rd |only
neuRosim-0.2-7/neuRosim/man/canonicalHRF.Rd | 51 +++++++++++----------
neuRosim-0.2-7/neuRosim/man/gammaHRF.Rd | 42 +++++++----------
neuRosim-0.2-7/neuRosim/man/lowfreqdrift.Rd |only
neuRosim-0.2-7/neuRosim/man/neuRosim-package.Rd | 23 ++++-----
neuRosim-0.2-7/neuRosim/man/physnoise.Rd |only
neuRosim-0.2-7/neuRosim/man/rrice.Rd |only
neuRosim-0.2-7/neuRosim/man/simTSfmri.Rd |only
neuRosim-0.2-7/neuRosim/man/simTSrestingstate.Rd |only
neuRosim-0.2-7/neuRosim/man/simVOLfmri.Rd |only
neuRosim-0.2-7/neuRosim/man/simprepSpatial.Rd |only
neuRosim-0.2-7/neuRosim/man/simprepTemporal.Rd |only
neuRosim-0.2-7/neuRosim/man/spatialnoise.Rd |only
neuRosim-0.2-7/neuRosim/man/specifydesign.Rd |only
neuRosim-0.2-7/neuRosim/man/specifyregion.Rd |only
neuRosim-0.2-7/neuRosim/man/stimfunction.Rd |only
neuRosim-0.2-7/neuRosim/man/systemnoise.Rd |only
neuRosim-0.2-7/neuRosim/man/tasknoise.Rd |only
neuRosim-0.2-7/neuRosim/man/temporalnoise.Rd |only
neuRosim-0.2-7/neuRosim/src |only
78 files changed, 75 insertions(+), 96 deletions(-)
Title: Multivariate Normal and t Distributions
Diff between mvtnorm versions 0.9-96 dated 2011-01-28 and 0.9-99 dated 2011-04-24
Description: Computes multivariate normal and t probabilities,
quantiles, random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich
Leisch, Fabian Scheipl, Bjoern Bornkamp, Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
NEWS | 16 +++++++++++++++-
R/mvnorm.R | 8 +++++---
R/mvt.R | 20 +++++++++++---------
inst/CHANGES | 16 +++++++++++++++-
inst/doc/MVT_Rnews.pdf |binary
man/Mvt.Rd | 6 ++++--
tests/bugfix-tests.R | 14 ++++++++++++++
8 files changed, 68 insertions(+), 20 deletions(-)
Title: statistical methods for analysing multivariate abundance data
Diff between mvabund versions 0.1-11 dated 2010-11-20 and 0.1-11.1 dated 2011-04-24
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
mvabund-package.Rd or type 'help("mvabund-package")' in R for
details of overall package organization. The package is
implemented with the Gnu Scientific Library
(http://www.gnu.org/software/gsl/) and Rcpp
(http://dirk.eddelbuettel.com/code/rcpp.html) R / C++ APIs.
Author: Yi Wang, Ulrike Naumann, Stehpen Wright and David Warton
Maintainer: Yi Wang
mvabund-0.1-11.1/mvabund/DESCRIPTION | 8 ++++----
mvabund-0.1-11.1/mvabund/src/Makevars.win | 2 +-
mvabund-0.1-11.1/mvabund/src/anova.cpp | 2 +-
mvabund-0.1-11.1/mvabund/src/summary.cpp | 2 +-
mvabund-0.1-11/mvabund/data/bootID.dat |only
5 files changed, 7 insertions(+), 7 deletions(-)
Title: MRI tissue classification.
Diff between mritc versions 0.3-2 dated 2010-10-28 and 0.3-3 dated 2011-04-24
Description: Various methods for MRI tissue classification.
Author: Dai Feng and Luke Tierney
Maintainer: Dai Feng
ChangeLog | 11 +++++++++++
DESCRIPTION | 6 +++---
R/measureMRI.R | 9 +++++----
3 files changed, 19 insertions(+), 7 deletions(-)
Title: MATLAB emulation package
Diff between matlab versions 0.8-3 dated 2009-10-13 and 0.8.6 dated 2011-04-24
Description: Emulate MATLAB code using R
Author: P. Roebuck
Maintainer: P. Roebuck
.hide |only
DESCRIPTION | 14 +-
NEWS | 202 ++++++++++++++++++++++++++++++++++---------
NEWS.real |only
R/linspace.R | 11 +-
R/logspace.R | 20 ----
R/mod.R | 7 +
man/ceil.Rd | 2
man/cell.Rd | 2
man/colorbar.Rd | 2
man/eye.Rd | 2
man/fileparts.Rd | 2
man/filesep.Rd | 2
man/find.Rd | 2
man/fix.Rd | 2
man/fliplr.Rd | 2
man/fullfile.Rd | 7 -
man/imagesc.Rd | 2
man/isempty.Rd | 2
man/jet.colors.Rd | 4
man/linspace.Rd | 4
man/logspace.Rd | 5 -
man/magic.Rd | 2
man/matlab-package.Rd | 6 -
man/meshgrid.Rd | 4
man/mod.Rd | 2
man/multiline.plot.colors.Rd | 4
man/ndims.Rd | 2
man/numel.Rd | 2
man/ones.Rd | 2
man/padarray.Rd | 2
man/pascal.Rd | 8 -
man/pathsep.Rd | 2
man/repmat.Rd | 2
man/reshape.Rd | 2
man/rot90.Rd | 2
man/size.Rd | 2
man/size_t-class.Rd | 2
man/std.Rd | 2
man/strcmp.Rd | 2
man/sum.Rd | 2
man/tictoc.Rd | 2
tests/linspace.R | 4
tests/logspace.R | 5 +
tests/mod.R | 8 +
45 files changed, 249 insertions(+), 118 deletions(-)
Title: Estimate a Log-Concave Probability Density from iid Observations
Diff between logcondens versions 2.0.3 dated 2011-03-05 and 2.0.4 dated 2011-04-24
Description: Given independent and identically distributed observations
X(1), ..., X(n), this package allows to compute the maximum
likelihood estimator (MLE) of a density as well as a smoothed
version of it under the assumption that the density is
log-concave, see Rufibach (2007) and Duembgen and Rufibach
(2009). The main function of the package is 'logConDens' that
allows computation of the log-concave MLE and its smoothed
version. In addition, we provide functions to compute (1) the
value of the density and distribution function estimates (MLE
and smoothed) at a given point (2) the characterizing functions
of the estimator, (3) to sample from the estimated
distribution, (5) to compute a two-sample permutation test
based on log-concave densities, (6) the ROC curve based on
log-concave estimates within cases and controls. Finally, three
datasets that have been used to illustrate log-concave density
estimation are made available.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach
DESCRIPTION | 8 -
NEWS | 5
inst/CITATION | 40 ++---
inst/doc/logcondens.Rnw | 14 -
inst/doc/logcondens.pdf |binary
inst/doc/plots/-plot1.pdf | 276 ++++++++++++++++++++++++++++++++-----
inst/doc/plots/-plot2.pdf | 282 +++++++++++++++++++++++++++++++++-----
inst/doc/plots/-plot2sample.pdf | 284 +++++++++++++++++++++++++++++++++-----
inst/doc/plots/-plotSimul.pdf | 296 ++++++++++++++++++++++++++++++++++------
inst/doc/plots/-sim1.pdf | 296 ++++++++++++++++++++++++++++++++++------
man/logcondens-package.Rd | 4
11 files changed, 1275 insertions(+), 230 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 1.3.3 dated 2011-04-04 and 1.3.4 dated 2011-04-24
Description: The package implements the statistical theory of L-moments
including L-moment estimation, probability-weighted moment
estimation, parameter estimation for numerous familiar and
not-so-familiar distributions, and L-moment estimation for the
same distributions from the parameters. L-moments are derived
from the expectations of order statistics and are linear with
respect to the probability-weighted moments; choice of either
can be made by mathematical convenience. L-moments are directly
analogous to the well-known product moments; however, L-moments
have many advantages including unbiasedness, robustness, and
consistency with respect to the product moments. The method of
L-moments can out perform the method of maximum likelihood. The
lmomco package historically is oriented around canonical
FORTRAN algorithms of J.R.M. Hosking, and the nomenclature for
many of the functions parallels that of the Hosking library,
which later became available in the lmom package. However, vast
arrays of various extensions and curiosities are added by the
author to aid and expand of the breadth of L-moment
application. Such extensions include venerable statistics as
Sen weighted mean, Gini mean difference, plotting positions,
and conditional probability adjustment. Much extension of
L-moment theory has occurred in recent years, including
extension of L-moments into right-tail and left-tail censoring
by known or unknown censoring threshold and also by indicator
variable. E.A.H. Elamir and A.H. Seheult have developed the
trimmed L-moments, which are implemented in this package.
Further, Robert Serfling and Peng Xiao have extended L-moments
into multivariate space; the so-called sample L-comoments are
implemented here and might have considerable application in
copula theory because they measure asymmetric correlation and
higher co-moments. The supported distributions with moment type
shown as L (L-moments) or TL (trimmed L-moments) and additional
support for right-tail censoring ([RC]) include: Cauchy (TL),
Exponential (L), Gamma (L), Generalized Extreme Value (L),
Generalized Lambda (L & TL), Generalized Logistic (L),
Generalized Normal (L), Generalized Pareto (L[RC] & TL), Gumbel
(L), Kappa (L), Kumaraswamy (L), Normal (L), 3-parameter
log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse
Gumbel (L[RC]), Rice/Rician (L), Truncated Exponential (L),
Wakeby (L), and Weibull (L).
Author: William H. Asquith
Maintainer: William H. Asquith
ChangeLog | 10 ++++++++++
DESCRIPTION | 10 +++++-----
NAMESPACE |only
R/lmrdiscord.R | 47 +++++++++++++++++++++++++----------------------
man/lmrdiscord.Rd | 23 ++++++++++++-----------
5 files changed, 52 insertions(+), 38 deletions(-)
Title: Linear Group Fixed Effects
Diff between lfe versions 1.3-512 dated 2011-04-08 and 1.3-572 dated 2011-04-24
Description: Estimates linear models with multiple group fixed effects
Author: Simen Gaure, The Ragnar Frisch Centre for Economic Research
Maintainer: Simen Gaure
DESCRIPTION | 9
NAMESPACE | 3
R/chmethod.R |only
R/kaczmarz.R |only
R/lfe.R | 553 ++++-----------------------------------------
configure | 18 -
exec/lfescript | 20 +
inst/doc/CHANGELOG | 24 +
inst/doc/lfeguide.txt | 47 +--
man/btrap.Rd | 14 -
man/demeanlist.Rd | 10
man/efactory.Rd |only
man/getfe.Rd | 45 ++-
man/is.estimable.Rd |only
man/kaczmarz.Rd | 26 +-
man/lfe-package.Rd | 22 +
src/lfe.c | 283 +++++++++++++++++++----
tests/comparelm.Rout.save | 13 -
tests/degenerate.Rout.save | 13 -
tests/efcheck.R |only
tests/efcheck.Rout.save |only
tests/lfetest.Rout.save | 13 -
tests/onefac.Rout.save | 11
tests/verify.Rout.save | 11
24 files changed, 433 insertions(+), 702 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 1.8.6 dated 2011-04-12 and 1.8.7 dated 2011-04-24
Description: Each function accomplishes the work of several or more
standard R functions. For example, two function calls, rad()
and full(), together read the csv data and generate descriptive
statistics for all variables in the data frame, plus histograms
and bar charts for all respective numerical and non-numerical
variables. The function smd.t.test introduces the ODDSMD plot,
which displays the Overlapping Density Distributions of two
independent groups as well as a visual display of the mean
difference and standardized mean difference. Other functions
provide for descriptive statistics, the t-test from descriptive
statistics, a comprehensive regression analysis, color
plotting, color bar chart, color histogram, color box plot,
density curves, a calibrated power curve plotted with colors,
and the reading and display of csv formatted data. The function
help.me provides a help system that suggests specific analyses
and functions.
Author: David W. Gerbing, School of Business Administration, Portland
State University
Maintainer: David W. Gerbing
DESCRIPTION | 8 +++---
R/color.plot.R | 52 ++++++++++++++++++++++++++++++++------------
R/reg.R | 59 ++++++++++++++++++++++++++------------------------
man/color.barchart.Rd | 2 -
man/color.boxplot.Rd | 2 -
man/color.density.Rd | 2 -
man/color.plot.Rd | 54 +++++++++++++++++++++++++++------------------
7 files changed, 108 insertions(+), 71 deletions(-)
Title: Latent Variable Analysis
Diff between lavaan versions 0.4-7 dated 2011-02-21 and 0.4-8 dated 2011-04-24
Description: Fit a variety of latent variable models, including
confirmatory factor analysis, structural equation modeling and
latent growth curve models.
Author: Yves Rosseel
Maintainer: Yves Rosseel
DESCRIPTION | 11 -
NAMESPACE | 22 +-
R/00class.R | 8
R/00generic.R | 1
R/01lavaanOptions.R | 371 ++++++++++++++++--------------------------
R/02lavaanUser.R | 396 +++++++++++++++++++++++++++++----------------
R/03lavaanSample.R | 12 -
R/04lavaanStart.R | 6
R/05lavaanModel.R | 126 ++++++++++++++
R/06lavaanEstimate.R | 251 ++++++++++++++++++++++++++--
R/07lavaanVcov.R | 40 +++-
R/08lavaanTest.R | 14 +
R/10lavaan-methods.R | 177 +++++++++++++++-----
R/computeGammaAB.R | 2
R/derivatives.R | 2
R/fit.measures.R | 29 ++-
R/independence.model.R | 121 +++++++++++++
R/lavaan.R | 209 ++++++++++++++---------
R/measurement.invariance.R | 6
R/missing.R | 8
R/modification.R | 9 -
R/nlminb.constr.R |only
R/numDeriv.R |only
R/residuals.R | 8
R/standardize.R | 8
R/utils-user.R | 30 ++-
R/utils.R | 32 +--
man/cfa.Rd | 10 -
man/growth.Rd | 12 -
man/lavaan-class.Rd | 25 +-
man/lavaan.Rd | 12 -
man/model.syntax.Rd | 10 -
man/sem.Rd | 10 -
33 files changed, 1351 insertions(+), 627 deletions(-)
Title: Lattice Graphics
Diff between lattice versions 0.19-23 dated 2011-04-04 and 0.19-26 dated 2011-04-24
Description: Lattice is a powerful and elegant high-level data
visualization system, with an emphasis on multivariate data,
that is sufficient for typical graphics needs, and is also
flexible enough to handle most nonstandard requirements. See
?Lattice for an introduction.
Author: Deepayan Sarkar
Maintainer: Deepayan Sarkar
DESCRIPTION | 8 +-
NEWS | 3 +
R/axis.R | 59 ++++++++++++++++----
R/bwplot.R | 130 ++++++++++++++++++++++++++++++++-------------
R/cloud.R | 84 +++++++++++++++++++++--------
R/densityplot.R | 18 ++++--
R/histogram.R | 9 ++-
R/interaction.R | 24 ++++++--
R/levelplot.R | 31 ++++++++--
R/miscellaneous.R | 84 +++++++++++++++++++++++++----
R/panel.smoothscatter.R | 9 ++-
R/panels.R | 125 +++++++++++++++++++++++++++++++------------
R/parallel.R | 17 ++++-
R/print.trellis.R | 27 +++++----
R/qq.R | 9 ++-
R/qqmath.R | 15 +++--
R/splom.R | 14 +++-
R/strip.R | 40 ++++++++++---
R/tmd.R | 12 ++--
R/xyplot.R | 20 ++++--
man/interaction.Rd | 24 +++++++-
man/llines.Rd | 24 +++++---
man/panel.barchart.Rd | 6 +-
man/panel.bwplot.Rd | 7 ++
man/panel.cloud.Rd | 13 +++-
man/panel.densityplot.Rd | 7 ++
man/panel.dotplot.Rd | 7 ++
man/panel.functions.Rd | 29 ++++++----
man/panel.histogram.Rd | 7 ++
man/panel.levelplot.Rd | 10 ++-
man/panel.parallel.Rd | 7 ++
man/panel.qqmath.Rd | 7 ++
man/panel.qqmathline.Rd | 7 ++
man/panel.smoothScatter.Rd | 7 ++
man/panel.stripplot.Rd | 7 ++
man/panel.violin.Rd | 7 ++
man/panel.xyplot.Rd | 11 ++-
man/simpleTheme.Rd | 8 +-
man/tmd.Rd | 10 ++-
39 files changed, 714 insertions(+), 229 deletions(-)
Title: L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting
Diff between lassoshooting versions 0.1.3-4 dated 2011-04-08 and 0.1.3-7 dated 2011-04-24
Description: L1 regularized regression (Lasso) solver using the Cyclic
Coordinate Descent algorithm aka Lasso Shooting is fast. This
implementation can choose which coefficients to penalize. It
support coefficient-specific penalities and it can take X'X and
X'y instead of X and y.
Author: Tobias Abenius
Maintainer: Tobias Abenius
ChangeLog | 4 ++++
DESCRIPTION | 10 +++++-----
NAMESPACE | 2 +-
src/ccd.h | 3 +++
src/ccd_common.c | 21 +++++++++++++++++----
src/ccd_r.c | 45 ++++++++++++++++++++++++++++-----------------
6 files changed, 58 insertions(+), 27 deletions(-)
Title: An Introduction to Statistical Modeling of Extreme Values
Diff between ismev versions 1.35 dated 2010-05-25 and 1.36 dated 2011-04-24
Description: Functions to support the computations carried out in `An
Introduction to Statistical Modeling of Extreme Values' by
Stuart Coles. The functions may be divided into the following
groups; maxima/minima, order statistics, peaks over thresholds
and point processes.
Author: Original S functions by Stuart Coles, R port and R
documentation files by Alec Stephenson.
Maintainer: Eric Gilleland
DESCRIPTION | 6 +++---
R/gpd.R | 4 ++--
R/pp.R | 4 ++--
man/gpd.fitrange.Rd | 3 ++-
man/pp.fitrange.Rd | 3 ++-
5 files changed, 11 insertions(+), 9 deletions(-)
Title: Fast FFT and DCT based on FFTW
Diff between fftw versions 1.0-2 dated 2010-04-05 and 1.0-3 dated 2011-04-24
Description: Provides a simple and efficient wrapper around the fastest
Fourier transform in the west (FFTW) library.
Author: Sebastian Krey
Maintainer: Olaf Mersmann
ChangeLog | 9 +++++++++
DESCRIPTION | 8 ++++----
src/fftw.c | 2 +-
3 files changed, 14 insertions(+), 5 deletions(-)
Title: Feature significance for multivariate kernel density estimation
Diff between feature versions 1.2.6 dated 2011-01-06 and 1.2.7 dated 2011-04-24
Description: Feature significance for multivariate kernel density
estimation
Author: Tarn Duong
Maintainer: Tarn Duong
feature-1.2.6/feature/data/earthquake.dat |only
feature-1.2.7/feature/DESCRIPTION | 8 ++++----
feature-1.2.7/feature/R/plot.fs.R | 2 +-
feature-1.2.7/feature/inst/doc/feature.pdf |binary
4 files changed, 5 insertions(+), 5 deletions(-)
Title: Statistical analysis of surveys with anchoring vignettes
Diff between anchors versions 3.0-4 dated 2009-07-19 and 3.0-6 dated 2011-04-24
Description: Tools for analyzing survey responses with anchors.
Author: Wand, Jonathan and Gary King, and Olivia Lau
Maintainer: Jonathan Wand
anchors-3.0-4/anchors/INDEX |only
anchors-3.0-4/anchors/data/chopitsim.R |only
anchors-3.0-4/anchors/data/freedom.tab |only
anchors-3.0-4/anchors/data/mexchn.R |only
anchors-3.0-4/anchors/data/poleff.R |only
anchors-3.0-4/anchors/data/poleffna.R |only
anchors-3.0-4/anchors/data/selfcare.R |only
anchors-3.0-4/anchors/data/sleep.R |only
anchors-3.0-4/anchors/data/table1.tab |only
anchors-3.0-4/anchors/data/table1src.R |only
anchors-3.0-4/anchors/inst/doc/Rplots.pdf |only
anchors-3.0-6/anchors/DESCRIPTION | 8
anchors-3.0-6/anchors/R/cpolr.R | 6
anchors-3.0-6/anchors/R/fitted.anchors.rank.R | 2
anchors-3.0-6/anchors/R/func.packv.R | 1
anchors-3.0-6/anchors/R/summary.anchors.order.R | 4
anchors-3.0-6/anchors/R/summary.anchors.rank.R | 4
anchors-3.0-6/anchors/data/chopitsim.rda |only
anchors-3.0-6/anchors/data/freedom.tab.gz |only
anchors-3.0-6/anchors/data/mexchn.rda |only
anchors-3.0-6/anchors/data/poleff.rda |only
anchors-3.0-6/anchors/data/poleffna.rda |only
anchors-3.0-6/anchors/data/selfcare.rda |only
anchors-3.0-6/anchors/data/sleep.rda |only
anchors-3.0-6/anchors/data/table1.tab.gz |only
anchors-3.0-6/anchors/data/table1src.rda |only
anchors-3.0-6/anchors/inst/doc.tmp |only
anchors-3.0-6/anchors/inst/doc/anchors-entropy1.pdf | 276 ++++++++++++-
anchors-3.0-6/anchors/inst/doc/anchors-vignette-order.pdf | 280 ++++++++++++--
anchors-3.0-6/anchors/inst/doc/anchors.pdf |binary
anchors-3.0-6/anchors/inst/doc/anchors.tex | 29 -
anchors-3.0-6/anchors/inst/doc/apsr2001.bst |only
anchors-3.0-6/anchors/man/anchors.Rd | 1
anchors-3.0-6/anchors/man/anchors.fitted.cpolr.Rd |only
anchors-3.0-6/anchors/man/fitted.anchors.rank.Rd |only
anchors-3.0-6/anchors/man/summary.anchors.order.Rd | 2
anchors-3.0-6/anchors/tests/chopit.Rout.save | 13
anchors-3.0-6/anchors/tests/unit.anchors.Rout.save | 72 +--
anchors-3.0-6/anchors/tests/unit.cpolr.Rout.save | 82 ++--
39 files changed, 596 insertions(+), 184 deletions(-)
Title: Lasso and elastic-net regularized generalized linear models
Diff between glmnet versions 1.5.3 dated 2011-02-28 and 1.6 dated 2011-04-24
Description: Extremely efficient procedures for fitting the entire
lasso or elastic-net regularization path for linear regression,
logistic and multinomial regression models, poisson regression
and the Cox model. The algorithm uses cyclical coordinate
descent in a pathwise fashion, as described in the paper listed
below.
Author: Jerome Friedman, Trevor Hastie, Rob Tibshirani
Maintainer: Trevor Hastie
glmnet-1.5.3/glmnet/src/glmnet_a.f90 |only
glmnet-1.6/glmnet/DESCRIPTION | 8 ++++----
glmnet-1.6/glmnet/NAMESPACE | 1 +
glmnet-1.6/glmnet/R/cv.glmnet.R | 2 +-
glmnet-1.6/glmnet/R/elnet.R | 9 +++++----
glmnet-1.6/glmnet/R/fishnet.R | 1 +
glmnet-1.6/glmnet/R/glmnet.R | 7 ++++---
glmnet-1.6/glmnet/R/jerr.R | 2 +-
glmnet-1.6/glmnet/R/jerr.coxnet.R | 19 ++++++++++---------
glmnet-1.6/glmnet/R/jerr.elnet.R | 20 ++++++++++++++------
glmnet-1.6/glmnet/R/jerr.fishnet.R | 22 ++++++----------------
glmnet-1.6/glmnet/R/jerr.lognet.R | 12 ++----------
glmnet-1.6/glmnet/R/plot.glmnet.R | 21 +--------------------
glmnet-1.6/glmnet/R/plot.multnet.R |only
glmnet-1.6/glmnet/R/predict.coxnet.R | 5 +++++
glmnet-1.6/glmnet/R/predict.elnet.R | 23 ++---------------------
glmnet-1.6/glmnet/R/predict.fishnet.R | 21 ++-------------------
glmnet-1.6/glmnet/R/predict.glmnet.R | 25 ++++++++++++++++++++++---
glmnet-1.6/glmnet/R/predict.lognet.R | 28 +++++-----------------------
glmnet-1.6/glmnet/R/predict.multnet.R | 5 +++++
glmnet-1.6/glmnet/inst/doc/Coxnet.pdf |binary
glmnet-1.6/glmnet/man/glmnet.Rd | 19 ++++++++++++-------
glmnet-1.6/glmnet/man/plot.glmnet.Rd | 2 ++
glmnet-1.6/glmnet/man/predict.glmnet.Rd | 2 +-
glmnet-1.6/glmnet/src/newGLMnet_e.f90 |only
25 files changed, 106 insertions(+), 148 deletions(-)
Title: CoreArray Generic Data Structurs (GDS) R Interface
Diff between gdsfmt versions 0.9.1 dated 2011-01-09 and 0.9.2 dated 2011-04-24
Description: R interface of CoreArray GDS is based on the CoreArray
project initiated and developed by Xiuwen Zheng from 2007.
Author: Xiuwen Zheng
Maintainer: Xiuwen Zheng
DESCRIPTION | 8 -
R/GDS.all.R | 44 ++++----
man/gdsfmt-package.Rd | 4
src/CoreArray.src/CoreDEF.h | 2
src/CoreArray.src/dBase.hpp | 90 +++++------------
src/CoreArray.src/dFile.cpp | 10 -
src/CoreArray.src/dParallel.cpp | 11 +-
src/CoreArray.src/dParallel.hpp | 2
src/CoreArray.src/dPlatform.cpp | 203 +++++++++++++++++++++++++++-------------
src/CoreArray.src/dPlatform.hpp | 25 +++-
src/CoreArray.src/dSeq.hpp | 28 ++---
src/CoreArray.src/dStruct.cpp | 10 -
src/CoreArray.src/dStruct.hpp | 16 +--
src/CoreArray.src/dType.hpp | 21 ++--
src/CoreGDS.cpp |only
15 files changed, 264 insertions(+), 210 deletions(-)
Title: Various R programming tools for data manipulation
Diff between gdata versions 2.8.1 dated 2010-11-13 and 2.8.2 dated 2011-04-24
Description: Various R programming tools for data manipulation
Author: Gregory R. Warnes, with contributions from Ben Bolker, Gregor
Gorjanc, Gabor Grothendieck, Ales Korosec, Thomas Lumley, Don
MacQueen, Arni Magnusson, Jim Rogers, and others
Maintainer: Gregory Warnes
gdata-2.8.1/gdata/R/dQuote.ascii.R |only
gdata-2.8.2/gdata/ChangeLog | 5289 ++++++++++++++++++++----
gdata-2.8.2/gdata/DESCRIPTION | 8
gdata-2.8.2/gdata/NAMESPACE | 2
gdata-2.8.2/gdata/NEWS | 13
gdata-2.8.2/gdata/R/installXLSXsupport.R | 2
gdata-2.8.2/gdata/R/nPairs.R | 14
gdata-2.8.2/gdata/R/read.xls.R | 6
gdata-2.8.2/gdata/R/sheetCount.R | 8
gdata-2.8.2/gdata/R/xls2sep.R | 20
gdata-2.8.2/gdata/R/xlsFormats.R | 2
gdata-2.8.2/gdata/inst/ChangeLog | 5289 ++++++++++++++++++++----
gdata-2.8.2/gdata/inst/NEWS | 13
gdata-2.8.2/gdata/inst/doc/mapLevels.pdf |binary
gdata-2.8.2/gdata/inst/doc/unknown.pdf |binary
gdata-2.8.2/gdata/inst/unitTests/runit.nPairs.R | 20
gdata-2.8.2/gdata/man/Args.Rd | 5
gdata-2.8.2/gdata/man/nPairs.Rd | 10
18 files changed, 8915 insertions(+), 1786 deletions(-)
Title: A graphical approach to sequentially rejective multiple test
procedures
Diff between gMCP versions 0.6-1 dated 2011-04-09 and 0.6-2 dated 2011-04-24
Description: This package provides functions and a graphical user
interface for graphical described multiple test procedures.
Author: Kornelius Rohmeyer, Florian Klinglmueller
Maintainer: Kornelius Rohmeyer
gMCP-0.6-1/gMCP/inst/doc/pictures/niceGraph.png |only
gMCP-0.6-1/gMCP/inst/doc/pictures/pngExport.png |only
gMCP-0.6-1/gMCP/inst/doc/pictures/uglyGraph.png |only
gMCP-0.6-1/gMCP/inst/java-src/org/mutoss/gui/graph/VS.java |only
gMCP-0.6-2/gMCP/DESCRIPTION | 8
gMCP-0.6-2/gMCP/INSTALL | 8
gMCP-0.6-2/gMCP/NAMESPACE | 1
gMCP-0.6-2/gMCP/NEWS | 43 +
gMCP-0.6-2/gMCP/R/analysis.R |only
gMCP-0.6-2/gMCP/R/exampleGraphs.R | 3
gMCP-0.6-2/gMCP/R/gMCP.R | 10
gMCP-0.6-2/gMCP/R/graph2latex.R | 19
gMCP-0.6-2/gMCP/R/graphMCP.R | 34 -
gMCP-0.6-2/gMCP/R/helperGUI.R | 35 +
gMCP-0.6-2/gMCP/R/misc.R | 29 -
gMCP-0.6-2/gMCP/TODO | 71 ++-
gMCP-0.6-2/gMCP/inst/doc/correlated.pdf |binary
gMCP-0.6-2/gMCP/inst/doc/gMCP.Rnw | 136 ++++--
gMCP-0.6-2/gMCP/inst/doc/gMCP.pdf |binary
gMCP-0.6-2/gMCP/inst/doc/pictures/CIDialog.png |only
gMCP-0.6-2/gMCP/inst/doc/pictures/IndefiniteProgressBar.png |only
gMCP-0.6-2/gMCP/inst/doc/pictures/correlated.png |binary
gMCP-0.6-2/gMCP/inst/doc/pictures/example.png |binary
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/config/Configuration.java | 17
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/config/GeneralConfig.java | 12
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/CreateGraphGUI.java | 58 ++
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/ErrorDialogSGTK.java | 85 +--
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/MenuBarMGraph.java | 193 ++++++--
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/RControl.java | 15
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/contrasts/LevelOrderListener.java | 2
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/datatable/CellEditorE.java | 7
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/datatable/CellEditorEps.java | 2
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/datatable/EpsilonTableCellRenderer.java | 2
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/datatable/RDataFrameRef.java | 6
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/dialogs/DialogConfIntEstVar.java | 100 +++-
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/dialogs/RObjectLoadingDialog.java |only
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/dialogs/TextFileViewer.java | 22
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/dialogs/VariableNameDialog.java | 11
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/Edge.java | 91 ++--
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/EdgeWeight.java | 53 +-
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/GraphMCP.java | 22
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/GraphView.java | 103 +++-
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/NetList.java | 222 +++++-----
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/Node.java | 73 +--
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/PPanel.java | 34 -
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/PView.java | 57 +-
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/PrintableObject.java | 8
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/graph/UpdateEdge.java | 1
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/options/GeneralPanel.java | 33 -
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/gui/options/OptionsDialog.java | 20
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/tests/FormatTest.java |only
gMCP-0.6-2/gMCP/inst/java-src/org/mutoss/tests/TestImportExport.java | 7
gMCP-0.6-2/gMCP/inst/java/afcommons.jar |binary
gMCP-0.6-2/gMCP/inst/java/gsrmtp.jar |binary
gMCP-0.6-2/gMCP/man/confint.Rd | 8
gMCP-0.6-2/gMCP/man/gMCP.Rd | 2
gMCP-0.6-2/gMCP/man/gMCPReport.Rd | 5
gMCP-0.6-2/gMCP/man/graphAnalysis.Rd |only
58 files changed, 1072 insertions(+), 596 deletions(-)
Title: Statistical tools for the interpretation of forensic DNA
mixtures
Diff between forensim versions 1.1-8 dated 2010-10-16 and 1.1-9 dated 2011-04-24
Description: Statistical methods and simulation tools for the
interpretation of forensic DNA mixtures
Author: Hinda Haned
Maintainer: Hinda Haned
DESCRIPTION | 14 +++++++-------
R/zzz.R | 2 +-
inst/doc/LR_vignette.pdf |binary
inst/files/examplemixture.csv |only
man/A2.simu.Rd | 4 +---
man/A3.simu.Rd | 2 +-
man/A4.simu.Rd | 2 +-
man/Bates.DNA.Rd | 1 -
man/Bates.Database.Rd | 1 -
man/CaseY.DNA.Rd | 2 --
man/CaseY.Database.Rd | 1 -
man/Cmn.Rd | 2 +-
man/DNAproxy.Rd | 2 +-
man/Hbsimu.Rd | 2 +-
man/LR.Rd | 2 +-
man/PE.Rd | 2 +-
man/PV.Rd | 2 +-
man/Pevid2.Rd | 2 +-
man/RMP.Rd | 2 +-
man/Tu.Rd | 1 -
man/accessors.Rd | 3 +--
man/as.simugeno.Rd | 2 +-
man/as.simumix.Rd | 2 +-
man/as.tabfreq.Rd | 2 +-
man/changepop.Rd | 2 +-
man/comb.Rd | 2 +-
man/dataL.Rd | 2 +-
man/dropDB.Rd | 4 ++++
man/dropdata.Rd | 1 -
man/findfreq.Rd | 2 +-
man/findmax.Rd | 2 +-
man/forensim.package.Rd | 3 +--
man/lik.Rd | 2 +-
man/lik.loc.Rd | 2 +-
man/likestim.Rd | 2 +-
man/likestim.loc.Rd | 2 +-
man/mastermix.Rd | 2 +-
man/mincontri.Rd | 2 +-
man/naomitab.Rd | 2 +-
man/nball.Rd | 2 +-
man/recordDrop.Rd | 2 +-
man/recordHeights.Rd | 2 +-
man/simPCR2.Rd | 2 +-
man/simPCR2TK.Rd | 2 +-
man/simufreqD.Rd | 2 +-
man/simugeno.Rd | 3 +--
man/simumix.Rd | 3 +--
man/simupopD.Rd | 2 +-
man/strusa.Rd | 1 -
man/strveneto.Rd | 1 -
man/tabDNAproxy.Rd | 2 +-
man/tabSPH.Rd | 2 +-
man/tabfreq.Rd | 3 +--
man/virClasses.Rd | 3 +--
54 files changed, 53 insertions(+), 66 deletions(-)
Title: Flexible Mixture Modeling
Diff between flexmix versions 2.3-4 dated 2011-02-28 and 2.3-5 dated 2011-04-24
Description: FlexMix implements a general framework for finite mixtures
of regression models using the EM algorithm. FlexMix provides
the E-step and all data handling, while the M-step can be
supplied by the user to easily define new models. Existing
drivers implement mixtures of standard linear models,
generalized linear models and model-based clustering.
Author: Friedrich Leisch and Bettina Gruen
Maintainer: Bettina Gruen
flexmix-2.3-4/flexmix/data/salmonellaTA98.txt |only
flexmix-2.3-5/flexmix/DESCRIPTION | 8 ++--
flexmix-2.3-5/flexmix/NEWS | 9 ++++
flexmix-2.3-5/flexmix/R/flexmix.R | 33 ++++++++++++++---
flexmix-2.3-5/flexmix/data/Mehta.RData |binary
flexmix-2.3-5/flexmix/data/salmonellaTA98.txt.gz |only
flexmix-2.3-5/flexmix/inst/NEWS | 9 ++++
flexmix-2.3-5/flexmix/inst/doc/bootstrapping.pdf |binary
flexmix-2.3-5/flexmix/inst/doc/flexmix-intro.pdf |binary
flexmix-2.3-5/flexmix/inst/doc/mixture-regressions.pdf |binary
flexmix-2.3-5/flexmix/inst/doc/regression-examples.pdf |binary
flexmix-2.3-5/flexmix/man/flexmix.Rd | 3 +
12 files changed, 52 insertions(+), 10 deletions(-)
Title: Fisheries Methods and Models in R
Diff between fishmethods versions 1.1-0 dated 2010-09-03 and 1.2-0 dated 2011-04-24
Description: Fishery methods and models from Quinn and Deriso (1999),
Haddon(2001) , and literature.
Author: Gary A. Nelson
Maintainer: Gary A. Nelson
fishmethods-1.1-0/fishmethods/R/LengthIncr.R |only
fishmethods-1.1-0/fishmethods/man/LengthIncr.Rd |only
fishmethods-1.2-0/fishmethods/DESCRIPTION | 8 ++++----
fishmethods-1.2-0/fishmethods/R/M.empirical.R | 14 +++++++++++---
fishmethods-1.2-0/fishmethods/R/epr.R |only
fishmethods-1.2-0/fishmethods/R/grotag.R |only
fishmethods-1.2-0/fishmethods/R/growth.R |only
fishmethods-1.2-0/fishmethods/R/powertrend.R | 16 +++++++++++++---
fishmethods-1.2-0/fishmethods/R/surveyfit.R | 8 +++++++-
fishmethods-1.2-0/fishmethods/R/vbfr.R |only
fishmethods-1.2-0/fishmethods/R/ypr.R | 7 -------
fishmethods-1.2-0/fishmethods/data/bonito.rda |binary
fishmethods-1.2-0/fishmethods/data/menhaden.rda |only
fishmethods-1.2-0/fishmethods/data/rockfish.rda |only
fishmethods-1.2-0/fishmethods/data/striper.rda |only
fishmethods-1.2-0/fishmethods/man/M.empirical.Rd | 11 ++++++++---
fishmethods-1.2-0/fishmethods/man/bonito.Rd | 17 +++++++----------
fishmethods-1.2-0/fishmethods/man/epr.Rd |only
fishmethods-1.2-0/fishmethods/man/grotag.Rd |only
fishmethods-1.2-0/fishmethods/man/growth.Rd |only
fishmethods-1.2-0/fishmethods/man/menhaden.Rd |only
fishmethods-1.2-0/fishmethods/man/powertrend.Rd | 4 +++-
fishmethods-1.2-0/fishmethods/man/rockfish.Rd |only
fishmethods-1.2-0/fishmethods/man/striper.Rd |only
fishmethods-1.2-0/fishmethods/man/surveyfit.Rd | 5 ++++-
fishmethods-1.2-0/fishmethods/man/vbfr.Rd |only
26 files changed, 57 insertions(+), 33 deletions(-)
Title: Exact Conditional Tests and Confidence Intervals for 2x2 tables
Diff between exact2x2 versions 1.1-0.0 dated 2010-10-06 and 1.1-1.0 dated 2011-04-24
Description: Calculates Fisher's exact test, Blaker's exact test, or
the exact McNemar's test with appropriate matching confidence
intervals.
Author: M.P. Fay
Maintainer: M.P. Fay
exact2x2-1.1-0.0/exact2x2/inst/doc/Sweave.sty |only
exact2x2-1.1-0.0/exact2x2/inst/doc/exactMcNemar.dvi |only
exact2x2-1.1-1.0/exact2x2/ChangeLog | 5 +++++
exact2x2-1.1-1.0/exact2x2/DESCRIPTION | 8 ++++----
exact2x2-1.1-1.0/exact2x2/R/exact2x2.R | 13 +++++++++++--
exact2x2-1.1-1.0/exact2x2/inst/doc/exact2x2.pdf |binary
exact2x2-1.1-1.0/exact2x2/inst/doc/exactMcNemar.pdf |binary
exact2x2-1.1-1.0/exact2x2/tests |only
8 files changed, 20 insertions(+), 6 deletions(-)
Title: EPoC (Endogenous Perturbation analysis of Cancer)
Diff between epoc versions 0.2.3-4 dated 2011-04-08 and 0.2.4-4 dated 2011-04-24
Description: Estimates sparse matrices A or G using fast lasso
regression from mRNA transcript levels Y and CNA profiles U.
Two models are provided, EPoC A where AY + U + R = 0 and EPoC G
where Y = GU + E, the matrices R and E are so far treated as
noise. For details see the reference and the manual page of
`lassoshooting'.
Author: Rebecka Jornsten, Tobias Abenius, Sven Nelander
Maintainer: Tobias Abenius
epoc-0.2.3-4/epoc/INDEX |only
epoc-0.2.4-4/epoc/ChangeLog | 19
epoc-0.2.4-4/epoc/DESCRIPTION | 15
epoc-0.2.4-4/epoc/NAMESPACE | 33 -
epoc-0.2.4-4/epoc/R/epoc.R | 776 ++++++++++++++++++--------
epoc-0.2.4-4/epoc/R/zzz.R | 4
epoc-0.2.4-4/epoc/data |only
epoc-0.2.4-4/epoc/epoc-Ex.R |only
epoc-0.2.4-4/epoc/man/epoc.Rd | 81 +-
epoc-0.2.4-4/epoc/man/epoc.bootstrap.Rd |only
epoc-0.2.4-4/epoc/man/epoc.survival.Rd |only
epoc-0.2.4-4/epoc/man/epoc.validation.Rd |only
epoc-0.2.4-4/epoc/man/plapply.Rd | 9
epoc-0.2.4-4/epoc/man/plot.EPoC.validation.Rd |only
epoc-0.2.4-4/epoc/man/plot.modelsel.Rd |only
epoc-0.2.4-4/epoc/man/synth.Rd |only
epoc-0.2.4-4/epoc/synth.rda |only
17 files changed, 652 insertions(+), 285 deletions(-)
Title: diversitree: comparative phylogenetic tests of diversification
Diff between diversitree versions 0.6-3 dated 2011-01-27 and 0.6-5 dated 2011-04-24
Description: Contains a number of comparative phylogenetic methods,
mostly focussing on analysing diversification and character
evolution. Contains implementations of BiSSE (Binary State
Speciation and Extinction; Maddison et al. 2007: Syst. Biol.
56: 701) and its unresolved tree extensions (FitzJohn et al.
2009: Syst. Biol. 58: 595), MuSSE (Multiple State Speciation
and Extinction), QuaSSE (Quantitative State Speciation and
Extinction; FitzJohn 2010: Syst. Biol. 69: 619), and GeoSSE
(Geographic State Speciation and Extinction; Goldberg et al.
2011: Syst. Biol.). Other included methods include Markov
models of discrete and continuous trait evolution and constant
rate speciation and extinction.
Author: Richard G. FitzJohn
Maintainer: Richard G. FitzJohn
diversitree-0.6-3/diversitree/data/geosse.R |only
diversitree-0.6-5/diversitree/ChangeLog | 72 +++++++++++++++++
diversitree-0.6-5/diversitree/DESCRIPTION | 12 +-
diversitree-0.6-5/diversitree/NAMESPACE | 5 -
diversitree-0.6-5/diversitree/R/asr-bisse-t.R |only
diversitree-0.6-5/diversitree/R/check.R | 42 +++++++++
diversitree-0.6-5/diversitree/R/diversitree-branches.R | 8 +
diversitree-0.6-5/diversitree/R/mcmc-hmc.R |only
diversitree-0.6-5/diversitree/R/mcmc.R | 12 --
diversitree-0.6-5/diversitree/R/mle-mixed.R | 7 +
diversitree-0.6-5/diversitree/R/mle.R | 5 -
diversitree-0.6-5/diversitree/R/model-bd-ode.R | 11 +-
diversitree-0.6-5/diversitree/R/model-bd-t.R | 12 +-
diversitree-0.6-5/diversitree/R/model-bisse-split.R | 20 +++-
diversitree-0.6-5/diversitree/R/model-bisse-t.R | 12 +-
diversitree-0.6-5/diversitree/R/model-bisse-td.R | 7 +
diversitree-0.6-5/diversitree/R/model-bisse.R | 11 +-
diversitree-0.6-5/diversitree/R/model-bm.R | 10 +-
diversitree-0.6-5/diversitree/R/model-geosse.R | 14 +--
diversitree-0.6-5/diversitree/R/model-linear-deriv.R |only
diversitree-0.6-5/diversitree/R/model-mkn.R | 26 +++---
diversitree-0.6-5/diversitree/R/model-musse-split.R | 16 ++-
diversitree-0.6-5/diversitree/R/model-musse-t.R | 12 +-
diversitree-0.6-5/diversitree/R/model-musse-td.R | 7 +
diversitree-0.6-5/diversitree/R/model-musse.R | 32 ++++---
diversitree-0.6-5/diversitree/R/model-quasse-split.R | 5 -
diversitree-0.6-5/diversitree/R/util.R | 16 +++
diversitree-0.6-5/diversitree/data/geosse.rda |only
diversitree-0.6-5/diversitree/man/asr-bisse.Rd | 7 -
diversitree-0.6-5/diversitree/man/asr-mkn.Rd | 3
diversitree-0.6-5/diversitree/man/constants.Rd | 2
diversitree-0.6-5/diversitree/man/make.bd.Rd | 6 -
diversitree-0.6-5/diversitree/man/make.bd.t.Rd | 7 -
diversitree-0.6-5/diversitree/man/make.bisse.Rd | 32 ++++++-
diversitree-0.6-5/diversitree/man/make.bisse.split.Rd | 6 -
diversitree-0.6-5/diversitree/man/make.bisse.td.Rd | 8 -
diversitree-0.6-5/diversitree/man/make.geosse.Rd | 16 ++-
diversitree-0.6-5/diversitree/man/make.mkn.Rd | 18 +++-
diversitree-0.6-5/diversitree/man/make.mkn.deriv.Rd |only
diversitree-0.6-5/diversitree/man/make.musse.Rd | 7 -
diversitree-0.6-5/diversitree/man/make.musse.split.Rd | 6 -
diversitree-0.6-5/diversitree/man/make.musse.td.Rd | 8 -
diversitree-0.6-5/diversitree/man/make.quasse.Rd | 13 +--
diversitree-0.6-5/diversitree/src/linear-deriv.c |only
diversitree-0.6-5/diversitree/src/linear-deriv.h |only
diversitree-0.6-5/diversitree/src/util-complex.c |only
diversitree-0.6-5/diversitree/src/util-complex.h |only
diversitree-0.6-5/diversitree/src/util-linalg.c |only
diversitree-0.6-5/diversitree/src/util-matrix.c |only
diversitree-0.6-5/diversitree/src/util-matrix.h |only
50 files changed, 363 insertions(+), 150 deletions(-)
Title: Descriptive statistics
Diff between descr versions 0.3.3 dated 2011-02-17 and 0.3.4 dated 2011-04-24
Description: This package contains functions to describe weighted
categorical variables and functions to facilitate the character
encoding conversion of objects.
Author: Jakson Aquino. Includes R source code and/or documentation
written by Dirk Enzmann, Marc Schwartz, and Nitin Jain
Maintainer: Jakson Aquino
descr-0.3.3/descr/R/backup_freq.R |only
descr-0.3.4/descr/DESCRIPTION | 8 -
descr-0.3.4/descr/NAMESPACE | 7 -
descr-0.3.4/descr/NEWS | 9 +
descr-0.3.4/descr/R/compmeans.R | 54 ++++++---
descr-0.3.4/descr/R/crosstab.R | 55 ++++++++-
descr-0.3.4/descr/R/descr.R | 3
descr-0.3.4/descr/R/freq.R | 64 ++++++-----
descr-0.3.4/descr/R/xtable.R | 12 --
descr-0.3.4/descr/descr-Ex.R | 64 ++++++++++-
descr-0.3.4/descr/inst/po/pt_BR/LC_MESSAGES/R-descr.mo |binary
descr-0.3.4/descr/man/CrossTable.Rd | 2
descr-0.3.4/descr/man/compmeans.Rd | 32 ++++-
descr-0.3.4/descr/man/crosstab.Rd | 30 +++--
descr-0.3.4/descr/man/freq.Rd | 28 ++--
descr-0.3.4/descr/man/plot.CrossTable.Rd |only
descr-0.3.4/descr/man/plot.freqtable.Rd |only
descr-0.3.4/descr/po/R-descr.pot | 95 ++++++++--------
descr-0.3.4/descr/po/R-pt_BR.po | 97 ++++++++---------
19 files changed, 368 insertions(+), 192 deletions(-)
Title: Extension of data.frame for fast indexing, fast ordered joins
and fast grouping.
Diff between data.table versions 1.5.3 dated 2011-02-11 and 1.6 dated 2011-04-24
Description: Enhanced data.frame. Fast indexing, fast ordered joins and
fast grouping in a short and flexible syntax. i and j may be
expressions of column names directly, for faster development.
Example: X[Y] is a fast join for large data.
Author: Matthew Dowle with many contributions from Tom Short. See SVN
logs on R-Forge.
Maintainer: M Dowle and T Short
DESCRIPTION | 21
NAMESPACE | 9
NEWS | 54
R/AllS4.R |only
R/data.table.R | 28
R/merge.R | 112 -
R/onAttach.R | 2
R/test.data.table.R | 674 ------
inst/doc/datatable-faq.Rnw | 296 +-
inst/doc/datatable-faq.pdf | 4405 +++++++++++++++++++++++------------------
inst/doc/datatable-intro.Rnw | 46
inst/doc/datatable-intro.pdf |binary
inst/doc/datatable-timings.Rnw | 2
inst/doc/datatable-timings.pdf |binary
inst/tests |only
man/all.equal.data.table.Rd |only
man/data.table-class.Rd |only
man/data.table.Rd | 19
man/merge.Rd | 115 -
man/test.data.table.Rd | 12
tests |only
21 files changed, 3055 insertions(+), 2740 deletions(-)
Title: A collection of functions to help with analysis of coarse
infectious disease data
Diff between coarseDataTools versions 0.3 dated 2010-08-18 and 0.5.1 dated 2011-04-24
More information about coarseDataTools at CRAN
Description: This package contains functions to analyze coarse data.
Its development was motivated by applications to infectious
disease: in particular, problems with estimating the incubation
period and the case fatality ratio of a given disease. Sample
data files are included in the package.
Author: Nicholas G. Reich
Maintainer: Nicholas G. Reich
ChangeLog | 8 +++++++-
DESCRIPTION | 11 ++++++-----
R/IncPerAnalysis.R | 15 +++++++++++++++
R/sampleSizeSimulation.R |only
data/exp.win.lengths.rda |only
inst/doc/CFR_vignette.pdf |binary
man/exp.win.lengths.Rd |only
man/get.obs.type.Rd |only
man/simulate.precision.Rd |only
9 files changed, 28 insertions(+), 6 deletions(-)
Permanent link
Title: R-Based API for accessing the MSKCC Cancer Genomics Data Server
(CGDS).
Diff between cgdsr versions 1.1 dated 2011-03-02 and 1.1.4 dated 2011-04-24
Description: The package provides a basic set of R functions for
querying the Cancer Genomics Data Server (CGDS), hosted by the
Computational Biology Center at Memorial-Sloan-Kettering Cancer
Center (MSKCC).
Author: Anders Jacobsen
Maintainer:
DESCRIPTION | 10 ++++-----
R/cgdsr.R | 40 ++++++++++++++++++++++++++++++++-----
inst/doc/cgdsr.Rnw | 43 ++++++++++++++++++++++++++++++++++++++--
inst/doc/cgdsr.pdf |binary
man/cgdsr-CGDS.Rd | 2 -
man/cgdsr-getCancerTypes.Rd | 2 -
man/cgdsr-getCaseLists.Rd | 2 -
man/cgdsr-getClinicalData.Rd |only
man/cgdsr-getGeneticProfiles.Rd | 2 -
man/cgdsr-getProfileData.Rd | 2 -
man/cgdsr-package.Rd | 20 ++++++++++++++----
man/cgdsr-plot.Rd | 2 -
man/cgdsr-processURL.Rd | 2 -
man/cgdsr-setVerbose.Rd | 2 -
man/cgdsr-test.Rd | 2 -
15 files changed, 106 insertions(+), 25 deletions(-)
Title: Biplot of Multivariate Data Based on Principal Components
Analysis
Diff between bpca versions 1.0-5 dated 2011-04-10 and 1.0-8 dated 2011-04-24
Description: Implements biplot (2d and 3d) of multivariate data based
on principal components analysis and diagnostic tools of the
quality of the reduction.
Author: Jose Claudio Faria & Clarice Garcia Borges Demetrio
Maintainer: Jose Claudio Faria
bpca-1.0-5/bpca/demo/comparation.R |only
bpca-1.0-8/bpca/ChangeLog | 17 +++++++++----
bpca-1.0-8/bpca/DESCRIPTION | 10 +++----
bpca-1.0-8/bpca/INDEX | 46 ++++++++++++++++++------------------
bpca-1.0-8/bpca/R/summary.bpca.R | 14 +++++++---
bpca-1.0-8/bpca/demo/00Index | 27 ++++++++++-----------
bpca-1.0-8/bpca/man/bpca-package.Rd | 44 +---------------------------------
bpca-1.0-8/bpca/man/bpca.Rd | 45 ++---------------------------------
bpca-1.0-8/bpca/man/plot.Rd | 1
bpca-1.0-8/bpca/man/summary.Rd | 1
10 files changed, 67 insertions(+), 138 deletions(-)
Title: BFAST: Breaks For Additive Seasonal and Trend
Diff between bfast versions 1.2 dated 2011-02-25 and 1.2-1 dated 2011-04-24
Description: BFAST integrates the decomposition of time series into
trend, seasonal, and remainder components with methods for
detecting and characterizing abrupt changes within the trend
and seasonal components. BFAST can be used to analyze different
types of satellite image time series and can be applied to
other disciplines dealing with seasonal or non-seasonal time
series, such as hydrology, climatology, and econometrics. The
algorithm can be extended to label detected changes with
information on the parameters of the fitted piecewise linear
models.
Author: Jan Verbesselt, with contributions from Rob Hyndman
Maintainer: Jan Verbesselt
DESCRIPTION | 12 ++++++------
R/bfast.R | 9 +--------
man/bfast-package.rd | 2 +-
man/bfast.Rd | 2 +-
man/harvest.Rd | 2 +-
man/plot.bfast.Rd | 2 +-
man/simts.Rd | 2 +-
7 files changed, 12 insertions(+), 19 deletions(-)
Title: Export R objects to several markup languages
Diff between ascii versions 1.2 dated 2011-03-05 and 1.3 dated 2011-04-24
Description: Coerce R object to asciidoc, txt2tags, restructuredText,
org or textile syntax. Package comes with a set of drivers for
Sweave.
Author: David Hajage
Maintainer: David Hajage
ascii-1.2/ascii/R/RweaveAsciidoc.r |only
ascii-1.2/ascii/R/RweaveOrg.r |only
ascii-1.2/ascii/R/RweavePandoc.r |only
ascii-1.2/ascii/R/RweaveReST.r |only
ascii-1.2/ascii/R/RweaveT2t.r |only
ascii-1.2/ascii/R/RweaveTextile.r |only
ascii-1.2/ascii/R/cacheSweaveAsciidoc.r |only
ascii-1.2/ascii/R/cacheSweaveOrg.r |only
ascii-1.2/ascii/R/cacheSweavePandoc.r |only
ascii-1.2/ascii/R/cacheSweaveReST.r |only
ascii-1.2/ascii/R/cacheSweaveT2t.r |only
ascii-1.2/ascii/R/cacheSweaveTextile.r |only
ascii-1.2/ascii/R/weaverAsciidoc.r |only
ascii-1.2/ascii/R/weaverOrg.r |only
ascii-1.2/ascii/R/weaverPandoc.r |only
ascii-1.2/ascii/R/weaverReST.r |only
ascii-1.2/ascii/R/weaverT2t.r |only
ascii-1.2/ascii/R/weaverTextile.r |only
ascii-1.2/ascii/TODO |only
ascii-1.3/ascii/DESCRIPTION | 27 +++++++++---------------
ascii-1.3/ascii/NAMESPACE | 12 +++++-----
ascii-1.3/ascii/NEWS | 12 ++++++++++
ascii-1.3/ascii/R/RweaveAscii.r |only
ascii-1.3/ascii/R/asciiDataFrame.r | 2 -
ascii-1.3/ascii/R/cacheSweaveAscii.r |only
ascii-1.3/ascii/R/show.pandoc.r | 1
ascii-1.3/ascii/R/show.r | 16 ++++++++++----
ascii-1.3/ascii/R/weaverAscii.r |only
ascii-1.3/ascii/man/ascii.anova.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.aov.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.aovlist.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.cast_df.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.character.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.coxph.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.data.frame.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.default.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.density.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.factor.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.glm.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.htest.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.integer.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.list.Rd | 2 -
ascii-1.3/ascii/man/ascii.lm.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.matrix.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.meanscomp.Rd | 4 +--
ascii-1.3/ascii/man/ascii.numeric.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.packageDescription.Rd | 2 -
ascii-1.3/ascii/man/ascii.prcomp.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.simple.list.Rd | 2 -
ascii-1.3/ascii/man/ascii.smooth.spline.Rd | 2 -
ascii-1.3/ascii/man/ascii.stat.table.Rd | 2 -
ascii-1.3/ascii/man/ascii.summary.aov.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.summary.aovlist.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.summary.glm.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.summary.lm.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.summary.prcomp.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.summary.table.Rd | 2 -
ascii-1.3/ascii/man/ascii.survdiff.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/ascii.ts.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/asciiOpts.Rd | 4 +--
ascii-1.3/ascii/man/cbind.ascii.Rd | 3 +-
ascii-1.3/ascii/man/convert.Rd | 4 +--
ascii-1.3/ascii/man/expand.Rd | 2 -
ascii-1.3/ascii/man/export.Rd | 5 ++--
ascii-1.3/ascii/man/fig.Rd | 2 -
ascii-1.3/ascii/man/groups.Rd | 2 -
ascii-1.3/ascii/man/header.asciidoc.Rd | 3 +-
ascii-1.3/ascii/man/header.org.Rd | 2 -
ascii-1.3/ascii/man/header.pandoc.Rd | 2 -
ascii-1.3/ascii/man/header.rest.Rd | 2 -
ascii-1.3/ascii/man/header.t2t.Rd | 2 -
ascii-1.3/ascii/man/header.textile.Rd | 2 -
ascii-1.3/ascii/man/ngroups.Rd | 2 -
ascii-1.3/ascii/man/paste.matrix.Rd | 2 -
ascii-1.3/ascii/man/print.ascii.Rd | 2 -
ascii-1.3/ascii/man/print.character.matrix.Rd | 2 -
ascii-1.3/ascii/man/rbind.ascii.Rd | 3 +-
ascii-1.3/ascii/man/replace.Rd | 3 +-
ascii-1.3/ascii/man/show.asciidoc.list.Rd | 2 -
ascii-1.3/ascii/man/show.asciidoc.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/show.org.list.Rd | 2 -
ascii-1.3/ascii/man/show.org.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/show.pandoc.list.Rd | 2 -
ascii-1.3/ascii/man/show.pandoc.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/show.rest.list.Rd | 2 -
ascii-1.3/ascii/man/show.rest.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/show.t2t.list.Rd | 2 -
ascii-1.3/ascii/man/show.t2t.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/show.textile.list.Rd | 2 -
ascii-1.3/ascii/man/show.textile.table.Rd | 18 ++++++++--------
ascii-1.3/ascii/man/tocharac.Rd | 4 +--
ascii-1.3/ascii/man/vsep.asciidoc.Rd | 2 -
ascii-1.3/ascii/man/vsep.textile.Rd | 2 -
94 files changed, 398 insertions(+), 315 deletions(-)
Title: Tools to Deal with Raster Maps
Diff between adehabitatMA versions 0.2 dated 2011-03-19 and 0.3 dated 2011-04-24
Description: A collection of tools to deal with raster maps
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge
adehabitatMA-0.2/adehabitatMA/inst/doc/.Rhistory |only
adehabitatMA-0.2/adehabitatMA/inst/doc/.check.timestamp |only
adehabitatMA-0.3/adehabitatMA/DESCRIPTION | 6 ++---
adehabitatMA-0.3/adehabitatMA/inst/doc/adehabitatMA.Rnw | 2 -
adehabitatMA-0.3/adehabitatMA/inst/doc/adehabitatMA.pdf |binary
adehabitatMA-0.3/adehabitatMA/src/tests.c | 17 ++++------------
6 files changed, 9 insertions(+), 16 deletions(-)
Title: Analysis of animal movements
Diff between adehabitatLT versions 0.2 dated 2011-03-19 and 0.3 dated 2011-04-24
Description: A collection of tools for the analysis of animal movements
Author: Clement Calenge, contributions from Stephane Dray and Manuela
Royer
Maintainer: Clement Calenge
adehabitatLT-0.2/adehabitatLT/data/.Rhistory |only
adehabitatLT-0.2/adehabitatLT/inst/doc/.Rhistory |only
adehabitatLT-0.3/adehabitatLT/DESCRIPTION | 6
adehabitatLT-0.3/adehabitatLT/R/gdltraj.r | 1
adehabitatLT-0.3/adehabitatLT/R/lavielle.r |only
adehabitatLT-0.3/adehabitatLT/R/modpartltraj.r | 14
adehabitatLT-0.3/adehabitatLT/R/na.omit.ltraj.r |only
adehabitatLT-0.3/adehabitatLT/R/redisltraj.r | 163 -
adehabitatLT-0.3/adehabitatLT/R/residenceTime.r |only
adehabitatLT-0.3/adehabitatLT/R/testNM.r |only
adehabitatLT-0.3/adehabitatLT/data/buffalo.rda |binary
adehabitatLT-0.3/adehabitatLT/inst/doc/adehabitatLT.Rnw | 1032 +++++++
adehabitatLT-0.3/adehabitatLT/inst/doc/adehabitatLT.pdf |binary
adehabitatLT-0.3/adehabitatLT/inst/doc/sim.Rdata |only
adehabitatLT-0.3/adehabitatLT/inst/doc/sim2.Rdata |only
adehabitatLT-0.3/adehabitatLT/inst/doc/sim3.Rdata |only
adehabitatLT-0.3/adehabitatLT/man/lavielle.Rd |only
adehabitatLT-0.3/adehabitatLT/man/na.omit.ltraj.Rd |only
adehabitatLT-0.3/adehabitatLT/man/redisltraj.Rd | 43
adehabitatLT-0.3/adehabitatLT/man/residenceTime.Rd |only
adehabitatLT-0.3/adehabitatLT/man/testNM.Rd |only
adehabitatLT-0.3/adehabitatLT/man/wawotest.Rd | 4
adehabitatLT-0.3/adehabitatLT/src/tests.c | 2209 +++++++++++++++-
23 files changed, 3331 insertions(+), 141 deletions(-)
Title: Analysis of habitat selection by animals
Diff between adehabitatHS versions 0.2 dated 2011-03-19 and 0.3.1 dated 2011-04-24
Description: A collection of tools for the analysis of habitat
selection
Author: Clement Calenge, contributions from Mathieu Basille
Maintainer: Clement Calenge
DESCRIPTION | 6 +++---
R/madifa.r | 2 +-
R/plot.kselect.r | 2 +-
R/prepksel.r | 2 +-
inst/doc/adehabitatHS.pdf |binary
src/tests.c | 8 +++-----
6 files changed, 9 insertions(+), 11 deletions(-)
Title: Home range Estimation
Diff between adehabitatHR versions 0.2 dated 2011-03-19 and 0.3 dated 2011-04-24
Description: A collection of tools for the estimation of animals home
range
Author: Clement Calenge, contributions from Scott Fortmann-Roe
Maintainer: Clement Calenge
DESCRIPTION | 6
R/BRB.r | 12
R/kernelovelaphr.r |only
inst/doc/.Rhistory | 7
inst/doc/adehabitatHR.Rnw | 4
inst/doc/adehabitatHR.pdf | 3232 +++++++++++++++++++++++-----------------------
man/BRB.Rd | 29
man/kerneloverlap.Rd | 23
src/tests.c | 35
9 files changed, 1722 insertions(+), 1626 deletions(-)
Title: Analysis of habitat selection by animals
Diff between adehabitat versions 1.8.4 dated 2011-03-19 and 1.8.5 dated 2011-04-24
Description: A collection of tools for the analysis of habitat
selection by animals
Author: Clement Calenge, contributions from Mathieu Basille, Stephane
Dray and Scott Fortmann-Roe
Maintainer: Clement Calenge
adehabitat-1.8.4/adehabitat/.Rbuildindex.8939 |only
adehabitat-1.8.5/adehabitat/DESCRIPTION | 6 +-
adehabitat-1.8.5/adehabitat/R/explore.kasc.r | 2
adehabitat-1.8.5/adehabitat/R/gnesfa.r | 2
adehabitat-1.8.5/adehabitat/R/kplot.kselect.r | 2
adehabitat-1.8.5/adehabitat/R/madifa.r | 10 +--
adehabitat-1.8.5/adehabitat/R/plot.kselect.r | 12 ++--
adehabitat-1.8.5/adehabitat/R/simm.mba.r | 2
adehabitat-1.8.5/adehabitat/R/simm.mou.r | 2
adehabitat-1.8.5/adehabitat/src/tests.c | 78 +++++++++++++-------------
10 files changed, 58 insertions(+), 58 deletions(-)
Title: Generate high-resolution Venn and Euler plots
Diff between VennDiagram versions 1.0.0 dated 2011-03-01 and 1.0.1 dated 2011-04-24
Description: A set of functions to generate high-resolution Venn and
Euler plots. Includes handling for several special cases,
including two-case scaling, and extensive customization of plot
shape and structure.
Author: Hanbo Chen
Maintainer: Paul Boutros
DESCRIPTION | 10 -
R/adjust.venn.R | 12 -
R/decide.special.case.R | 15 +-
R/draw.pairwise.venn.R | 269 +++++++++++++++++++++++++++---------------
R/draw.quad.venn.R | 70 +++++------
R/draw.single.venn.R | 38 +++---
R/draw.sp.case.R | 20 +--
R/draw.triple.venn.R | 302 ++++++++++++++++++++++--------------------------
R/rotate.venn.degrees.R | 14 +-
man/venn.diagram.Rd | 6
10 files changed, 405 insertions(+), 351 deletions(-)
Title: Multi-objective parameter tuning for classifiers
Diff between TunePareto versions 1.0 dated 2010-08-16 and 2.0 dated 2011-04-24
Description: Generic methods for parameter tuning of classification
algorithms using multiple scoring functions
Author: Christoph Müssel, Hans Kestler
Maintainer: Hans Kestler
TunePareto-1.0/TunePareto/man/callClassifier.Rd |only
TunePareto-1.0/TunePareto/man/tunePareto.knn.Rd |only
TunePareto-2.0/TunePareto/DESCRIPTION | 14
TunePareto-2.0/TunePareto/NAMESPACE | 17
TunePareto-2.0/TunePareto/R/classifiers.R |only
TunePareto-2.0/TunePareto/R/desirability.R |only
TunePareto-2.0/TunePareto/R/helpers.R | 119 +
TunePareto-2.0/TunePareto/R/objectiveFunctions.R | 91
TunePareto-2.0/TunePareto/R/random.R |only
TunePareto-2.0/TunePareto/R/tunePareto.R | 950 ++++------
TunePareto-2.0/TunePareto/R/visualizations.R | 48
TunePareto-2.0/TunePareto/man/TunePareto-package.Rd | 58
TunePareto-2.0/TunePareto/man/allCombinations.Rd | 13
TunePareto-2.0/TunePareto/man/as.interval.Rd |only
TunePareto-2.0/TunePareto/man/createObjective.Rd | 41
TunePareto-2.0/TunePareto/man/mergeTuneParetoResults.Rd |only
TunePareto-2.0/TunePareto/man/plotDominationGraph.Rd | 20
TunePareto-2.0/TunePareto/man/plotObjectivePairs.Rd | 20
TunePareto-2.0/TunePareto/man/plotParetoFronts2D.Rd | 22
TunePareto-2.0/TunePareto/man/precalculation.Rd | 61
TunePareto-2.0/TunePareto/man/predefinedClassifiers.Rd |only
TunePareto-2.0/TunePareto/man/predefinedObjectiveFunctions.Rd | 23
TunePareto-2.0/TunePareto/man/predict.TuneParetoModel.Rd |only
TunePareto-2.0/TunePareto/man/print.TuneParetoResult.Rd | 22
TunePareto-2.0/TunePareto/man/rankByDesirability.Rd |only
TunePareto-2.0/TunePareto/man/recalculateParetoSet.Rd |only
TunePareto-2.0/TunePareto/man/trainTuneParetoClassifier.Rd |only
TunePareto-2.0/TunePareto/man/tunePareto.Rd | 161 -
TunePareto-2.0/TunePareto/man/tuneParetoClassifier.Rd |only
TunePareto-2.0/TunePareto/src |only
30 files changed, 870 insertions(+), 810 deletions(-)
Title: a problem solving environment for fitting separable nonlinear
models in physics and chemistry applications
Diff between TIMP versions 1.10 dated 2010-08-24 and 1.10.1 dated 2011-04-24
Description: TIMP is a problem solving environment for fitting
separable nonlinear models to measurements arising in physics
and chemistry experiments, and has been extensively applied to
time-resolved spectroscopy and FLIM-FRET data.
Author: Katharine M. Mullen, Joris J. Snellenburg, Sergey Laptenok,
David Nicolaides, Ivo H.M. van Stokkum
Maintainer: Joris J. Snellenburg
TIMP-1.10.1/TIMP/DESCRIPTION | 14 ++++++++------
TIMP-1.10.1/TIMP/R/getKinConcen.R |only
TIMP-1.10.1/TIMP/R/getStreakBacksweep.R | 2 +-
TIMP-1.10.1/TIMP/R/init.dat.R | 16 +++++++++-------
TIMP-1.10.1/TIMP/R/init.theta.R | 5 +++--
TIMP-1.10.1/TIMP/R/rescomp.R | 21 +++++++++++++++++----
TIMP-1.10.1/TIMP/Rplots.pdf | 6 +++---
TIMP-1.10.1/TIMP/man/theta-class.Rd | 1 +
TIMP-1.10.1/TIMP/tests/example2nd.R |only
TIMP-1.10/TIMP/R/getKinConcen.r |only
10 files changed, 42 insertions(+), 23 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 1.0-3 dated 2011-04-12 and 2.0 dated 2011-04-24
More information about SemiParBIVProbit at CRAN
Description: Routine for bivariate probit modelling with linear
predictors specified using parametric and nonparametric
components.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 13 +-
DESCRIPTION | 6 -
R/AT.r | 5 +
R/SemiParBIVProbit.r | 177 ++++++++++++++++---------------------
R/bprobSS.r |only
R/print.summary.SemiParBIVProbit.r | 28 +++++
R/residuals.SemiParBIVProbit.r | 8 -
R/summary.SemiParBIVProbit.r | 44 +++++++--
R/working.comp.r | 12 +-
man/AT.Rd | 2
man/SemiParBIVProbit-package.Rd | 3
man/SemiParBIVProbit.Rd | 29 ++----
man/SemiParBIVProbitObject.Rd | 23 ++--
man/bprobSS.Rd |only
man/plot.SemiParBIVProbit.Rd | 8 -
man/summary.SemiParBIVProbit.Rd | 12 +-
man/working.comp.Rd | 3
17 files changed, 203 insertions(+), 170 deletions(-)
Permanent link
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.2.18 dated 2011-04-04 and 0.2.19 dated 2011-04-24
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 1.2.0). 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
RcppArmadillo-0.2.18/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.tex |only
RcppArmadillo-0.2.19/RcppArmadillo/ChangeLog | 10
RcppArmadillo-0.2.19/RcppArmadillo/DESCRIPTION | 10
RcppArmadillo-0.2.19/RcppArmadillo/R/fastLm.R | 2
RcppArmadillo-0.2.19/RcppArmadillo/inst/NEWS | 22
RcppArmadillo-0.2.19/RcppArmadillo/inst/doc/Makefile | 5
RcppArmadillo-0.2.19/RcppArmadillo/inst/doc/RcppArmadillo-unitTests.pdf |binary
RcppArmadillo-0.2.19/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.html | 16
RcppArmadillo-0.2.19/RcppArmadillo/inst/doc/unitTests-results/RcppArmadillo-unitTests.txt | 40 -
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_meat.hpp | 14
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/arma_ostream_proto.hpp | 4
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/arma_version.hpp | 6
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/auxlib_meat.hpp | 128 +--
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/blas_proto.hpp | 92 +-
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/compiler_setup.hpp | 12
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/config.hpp | 3
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/constants.hpp | 20
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/diskio_meat.hpp | 2
RcppArmadillo-0.2.19/RcppArmadillo/inst/include/armadillo_bits/lapack_proto.hpp | 344 ++++++----
19 files changed, 460 insertions(+), 270 deletions(-)