Author: Hadley Wickham
Diff between testthat versions 0.1 dated 2009-11-17 and 0.1.1 dated 2009-11-30
Title: Testthat code. Tools to make testing fun :)
Description: A testing package specifically tailored for R that's fun,
flexible and easy to set up.
DESCRIPTION | 11 ++++++-----
R/colour-text.r | 4 +++-
2 files changed, 9 insertions(+), 6 deletions(-)
Author: Thoralf Mildenberger, Henrike Weinert, Sebastian Tiemeyer
Title: 28 benchmark densities from Berlinet/Devroye (1994)
Description: Full implementation of the 28 distributions introduced as
benchmarks for nonparametric density estimation by Berlinet and
Devroye (1994). Includes densities, cdfs, quantile functions
and generators for samples as well as additional information on
features of the densities. Also contains the 4 histogram
densities used in Rozenholc/Mildenberger/Gather (2009).
Diff between benchden versions 1.0.2 dated 2009-09-28 and 1.0.3 dated 2009-11-30
DESCRIPTION | 8 ++++---- man/bhisto.Rd | 5 +++-- man/dhisto.Rd | 5 +++-- man/histo.Rd | 5 +++-- 4 files changed, 13 insertions(+), 10 deletions(-)
Author: Jeffrey M. Dick
Diff between CHNOSZ versions 0.8 dated 2009-04-23 and 0.9 dated 2009-11-30
Title: Chemical Thermodynamics and Activity Diagrams
Description: Calculation of the standard molal thermodynamic properties
and chemical affinities of reactions between and among
minerals, inorganic, organic, and/or biomolecular aqueous and
crystalline species. Incorporation of an extensive database of
thermodynamic properties of species and algorithms for
computing the standard thermodynamic properties of neutral and
ionized proteins from amino acid group contributions.
Generation of chemical speciation and predominance diagrams for
stable and metastable equilibrium in open systems as a function
of temperature, pressure, and chemical activities or fugacities
of basis species.
CHNOSZ-0.8/CHNOSZ/R/diversity.R |only
CHNOSZ-0.8/CHNOSZ/man/chnosz.Rd |only
CHNOSZ-0.8/CHNOSZ/man/diversity.Rd |only
CHNOSZ-0.9/CHNOSZ/DESCRIPTION | 13
CHNOSZ-0.9/CHNOSZ/R/affinity.R | 75 +-
CHNOSZ-0.9/CHNOSZ/R/diagram.R | 574 +++++++++++----
CHNOSZ-0.9/CHNOSZ/R/eos.R | 10
CHNOSZ-0.9/CHNOSZ/R/eqdata.R |only
CHNOSZ-0.9/CHNOSZ/R/info.R | 117 +--
CHNOSZ-0.9/CHNOSZ/R/protein.R | 166 ++--
CHNOSZ-0.9/CHNOSZ/R/species.R | 33
CHNOSZ-0.9/CHNOSZ/R/subcrt.R | 92 +-
CHNOSZ-0.9/CHNOSZ/R/thermo.R | 1196 ++++++++++++++++++++++++++++++--
CHNOSZ-0.9/CHNOSZ/R/transfer.R | 6
CHNOSZ-0.9/CHNOSZ/R/water.R | 53 -
CHNOSZ-0.9/CHNOSZ/data/OBIGT.csv | 586 ++++++++-------
CHNOSZ-0.9/CHNOSZ/data/SOJSH.csv |only
CHNOSZ-0.9/CHNOSZ/data/opt.csv | 4
CHNOSZ-0.9/CHNOSZ/data/protein.csv | 56 +
CHNOSZ-0.9/CHNOSZ/data/thermo.R | 3
CHNOSZ-0.9/CHNOSZ/inst/CITATION |only
CHNOSZ-0.9/CHNOSZ/inst/NEWS | 24
CHNOSZ-0.9/CHNOSZ/inst/doc |only
CHNOSZ-0.9/CHNOSZ/man/CHNOSZ-package.Rd |only
CHNOSZ-0.9/CHNOSZ/man/affinity.Rd | 291 +++----
CHNOSZ-0.9/CHNOSZ/man/basis.Rd | 73 -
CHNOSZ-0.9/CHNOSZ/man/buffer.Rd | 187 ++---
CHNOSZ-0.9/CHNOSZ/man/data.Rd | 126 ++-
CHNOSZ-0.9/CHNOSZ/man/diagram.Rd | 679 +++++++++---------
CHNOSZ-0.9/CHNOSZ/man/eos.Rd | 36
CHNOSZ-0.9/CHNOSZ/man/eqdata.Rd |only
CHNOSZ-0.9/CHNOSZ/man/get.protein.Rd | 332 +++++---
CHNOSZ-0.9/CHNOSZ/man/info.Rd | 59 -
CHNOSZ-0.9/CHNOSZ/man/ionize.Rd | 189 ++---
CHNOSZ-0.9/CHNOSZ/man/makeup.Rd | 56 -
CHNOSZ-0.9/CHNOSZ/man/nuts.Rd | 38 -
CHNOSZ-0.9/CHNOSZ/man/protein.Rd | 220 ++---
CHNOSZ-0.9/CHNOSZ/man/revisit.Rd |only
CHNOSZ-0.9/CHNOSZ/man/species.Rd | 31
CHNOSZ-0.9/CHNOSZ/man/subcrt.Rd | 356 ++++-----
CHNOSZ-0.9/CHNOSZ/man/transfer.Rd | 72 -
CHNOSZ-0.9/CHNOSZ/man/utilities.Rd | 315 +++++---
CHNOSZ-0.9/CHNOSZ/man/water.Rd | 79 +-
43 files changed, 3966 insertions(+), 2181 deletions(-)
Author: Christopher Brown
Title: Implements hash/associated arrays/dictionaries
Description: This package implements a data structure similar to hashes
in Perl and dictionaries in Python but with a purposefully R
flavor.
Diff between hash versions 1.0.3 dated 2009-11-05 and 1.10.0 dated 2009-11-30
ChangeLog | 26 ++++++++++++++++++ DESCRIPTION | 8 ++--- R/Class-hash.R | 71 +++++++++++++++++++------------------------------- R/invert.R | 6 +--- R/set.R | 8 ++++- R/zzz.R | 10 +++---- man/hash-accessors.Rd | 18 ++++++------ man/hash-class.Rd | 2 - man/hash-package.Rd | 4 +- man/invert.Rd | 6 ++-- tests/set.R | 10 ++++++- 11 files changed, 95 insertions(+), 74 deletions(-)
Author: Nagiza F. Samatova
Diff between RScaLAPACK versions 0.5.1 dated 2005-09-03 and 0.6.1 dated 2009-11-30
Title: A seamless interface to perform parallel computation on linear
algebra problems using the ScaLAPACK library.
Description: An R add-on package capable of carrying out parallel
computation through a single function call from the R
environment. It uses the high-performance ScaLAPACK library for
the linear algebra computations.
RScaLAPACK-0.5.1/RScaLAPACK/COPYRIGHT |only
RScaLAPACK-0.5.1/RScaLAPACK/configure.win |only
RScaLAPACK-0.5.1/RScaLAPACK/html |only
RScaLAPACK-0.5.1/RScaLAPACK/src/Makefile |only
RScaLAPACK-0.6.1/RScaLAPACK/DESCRIPTION | 28
RScaLAPACK-0.6.1/RScaLAPACK/R/HLRscalapack.R | 137
RScaLAPACK-0.6.1/RScaLAPACK/R/ParallelAgent.R | 2
RScaLAPACK-0.6.1/RScaLAPACK/R/Rscalapack.R | 382 ++
RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpLam.R.in | 1
RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpMpich2.R.in | 3
RScaLAPACK-0.6.1/RScaLAPACK/R/StartUpOmpi.R.in |only
RScaLAPACK-0.6.1/RScaLAPACK/README | 284 -
RScaLAPACK-0.6.1/RScaLAPACK/configure | 3340 +++++++++++++----------
RScaLAPACK-0.6.1/RScaLAPACK/configure.in | 340 +-
RScaLAPACK-0.6.1/RScaLAPACK/demo/RScaLAPACK.R | 1
RScaLAPACK-0.6.1/RScaLAPACK/man/Rfactanal.Rd | 16
RScaLAPACK-0.6.1/RScaLAPACK/man/RgridExit.Rd | 1
RScaLAPACK-0.6.1/RScaLAPACK/man/RgridInfo.Rd |only
RScaLAPACK-0.6.1/RScaLAPACK/man/RgridInit.Rd | 13
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgemm.Rd | 13
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgeqrf.Rd | 10
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgesv.Rd | 14
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdgesvd.Rd | 14
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdpotrf.Rd | 7
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdpotri.Rd | 18
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpdsyevd.Rd | 10
RScaLAPACK-0.6.1/RScaLAPACK/man/Rpprcomp.Rd | 6
RScaLAPACK-0.6.1/RScaLAPACK/man/Rprincomp.Rd | 10
RScaLAPACK-0.6.1/RScaLAPACK/man/Rquit.Rd | 1
RScaLAPACK-0.6.1/RScaLAPACK/man/Rvarimax.Rd | 20
RScaLAPACK-0.6.1/RScaLAPACK/man/other.Rd | 2
RScaLAPACK-0.6.1/RScaLAPACK/src/CRDriver.c | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/CRcollectData.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/CRdistData.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/CRscalapack.c | 105
RScaLAPACK-0.6.1/RScaLAPACK/src/CRscalapack.h | 13
RScaLAPACK-0.6.1/RScaLAPACK/src/Makefile.in | 38
RScaLAPACK-0.6.1/RScaLAPACK/src/PAdistData.c | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/ParallelAgent.c | 93
RScaLAPACK-0.6.1/RScaLAPACK/src/ParallelAgent.h | 13
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgemm.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgeqrf.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgesv.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdgesvd.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdpotrf.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdpotri.f | 1
RScaLAPACK-0.6.1/RScaLAPACK/src/callpdsyevd.f | 13
47 files changed, 3069 insertions(+), 1889 deletions(-)
Author: Thomas Lumley, Achim Zeileis
Title: Robust Covariance Matrix Estimators
Description: Model-robust standard error estimators for
cross-sectional, time series and longitudinal data.
Diff between sandwich versions 2.2-2 dated 2009-11-17 and 2.2-3 dated 2009-11-30
DESCRIPTION | 8 ++++---- NAMESPACE | 1 + NEWS | 5 +++++ R/bread.R | 8 ++++++++ inst/doc/sandwich-OOP.pdf |binary inst/doc/sandwich.pdf |binary man/bread.Rd | 1 + 7 files changed, 19 insertions(+), 4 deletions(-)
Author: Rolf Turner
Diff between hmm.discnp versions 0.1-0 dated 2009-09-28 and 0.1-1 dated 2009-11-30
Title: Hidden Markov models with discrete non-parametric observation
distributions.
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. Simulates data from
such models. Finds most probable underlying hidden states and
most probable sequences of such states.
ChangeLog | 27 ++++++++++++++++++++++++++-
DESCRIPTION | 8 ++++----
R/First.R | 4 ++--
R/ffun.R | 1 +
R/revise.rho.R | 1 +
R/sp.R | 1 +
6 files changed, 35 insertions(+), 7 deletions(-)
Author: Jonathan M. Lees
Title: Seismic Time Series Analysis Tools
Description: Multiple interactive codes to analyze seismic data, via,
spectrum analysis, wavelet transforms, particle motion,
hodograms.
Diff between RSEIS versions 2.2-0 dated 2009-10-15 and 2.3-1 dated 2009-11-30
DESCRIPTION | 8 - R/DOsgram.R | 2 R/GETARAIC.R | 6 R/JGET.seis.R | 109 +++++----------- R/JSAC.seis.R |only R/JSEGY.seis.R |only R/MTMgabor.R | 71 ++++++++-- R/Mine.Teles.R |only R/Mine.seis.R | 6 R/PICK.GEN.R | 201 +++++++++++++++++++++++++++++ R/PLOT.ALLPX.R | 3 R/TTteles.R | 10 + R/blankevol.R |only R/correct.moveout.R |only R/dateList.R |only R/dateStamp.R |only R/doGABOR.AR.R | 9 - R/doGABOR.MTM.R | 7 - R/evolAR.R | 19 +- R/getPDEcsv.R |only R/getPDEscreen.R |only R/getseis24.R | 18 ++ R/getseisinfo.R | 21 ++- R/insertNAs.R |only R/makeDB.R | 15 +- R/mtapspec.R | 2 R/parse.pde.R |only R/parseFN2STA.R | 31 +++- R/plotevol.R | 332 +++++++++++++++++++++---------------------------- R/plotevol2.R |only R/prepSEIS.R | 18 ++ R/selstas.R |only R/setwpix.R | 2 R/sysinfo.R |only inst/doc/hodo.pdf |binary inst/doc/rseis.pdf |binary man/GETARAIC.Rd | 7 - man/JGET.seis.Rd | 87 +++++++++++- man/JSAC.seis.Rd |only man/MTMgabor.Rd | 18 +- man/Mine.Teles.Rd |only man/Mine.seis.Rd | 41 +++++- man/RSEIS-package.Rd | 4 man/Zdate.Rd | 13 + man/correct.moveout.Rd |only man/doGABOR.AR.Rd | 5 man/doGABOR.MTM.Rd | 24 ++- man/getPDEcsv.Rd |only man/insertNAs.Rd |only man/makeDB.Rd | 29 +++- man/parse.pde.Rd |only man/parseFN2STA.Rd | 13 + man/plotevol.Rd | 20 ++ man/selstas.Rd |only man/sysinfo.Rd |only src/jget_seis.c | 52 +++++++ src/sac.h | 2 57 files changed, 840 insertions(+), 365 deletions(-)
Author: Etienne Laliberté, Bill Shipley
Title: Measuring functional diversity (FD) from multiple traits, and
other tools for functional ecology
Description: FD is a package to compute different multidimensional FD
indices. It implements a distance-based framework to measure FD
that allows any number and type of functional traits, and can
also consider species relative abundances. It also contains
other useful tools for functional ecology.
Diff between FD versions 1.0-1 dated 2009-10-26 and 1.0-5 dated 2009-11-30
FD-1.0-1/FD/R/zzz.R |only FD-1.0-5/FD/DESCRIPTION | 16 +++++++++------- FD-1.0-5/FD/NAMESPACE | 3 ++- FD-1.0-5/FD/R/functcomp.R | 12 ++++++++---- FD-1.0-5/FD/R/maxent.R |only FD-1.0-5/FD/inst/CITATION | 8 ++++---- FD-1.0-5/FD/inst/NEWS | 16 ++++++++++++++++ FD-1.0-5/FD/man/FD-package.Rd | 10 +++++----- FD-1.0-5/FD/man/functcomp.Rd | 11 +++++++---- FD-1.0-5/FD/man/gowdis.Rd | 1 - FD-1.0-5/FD/man/maxent.Rd |only 11 files changed, 51 insertions(+), 26 deletions(-)
Author: Roeland Kindt
Title: GUI for biodiversity and community ecology analysis
Description: This package provides a GUI (Graphical User Interface, via
the R-Commander) and some utility functions (often based on the
vegan package) for statistical analysis of biodiversity and
ecological communities, including species accumulation curves,
diversity indices, Renyi profiles, GLMs for analysis of species
abundance and presence-absence, distance matrices, Mantel
tests, and cluster, constrained and unconstrained ordination
analysis. A book on biodiversity and community ecology analysis
is available for free download from the website.
Diff between BiodiversityR versions 1.4 dated 2009-10-23 and 1.4.2 dated 2009-11-30
BiodiversityR-1.4.2/BiodiversityR/DESCRIPTION | 8 +- BiodiversityR-1.4.2/BiodiversityR/NAMESPACE | 2 BiodiversityR-1.4.2/BiodiversityR/inst/etc/BiodiversityGUI.R | 36 +++++------ BiodiversityR-1.4.2/BiodiversityR/man/BiodiversityRGUI.Rd | 4 - BiodiversityR-1.4.2/BiodiversityR/man/ordisymbol.Rd | 17 ----- BiodiversityR-1.4/BiodiversityR/R/ordihull.centroids.R |only BiodiversityR-1.4/BiodiversityR/R/ordispider.centroids.R |only 7 files changed, 25 insertions(+), 42 deletions(-)