Title: Make it easier to work with strings.
Diff between stringr versions 0.6 dated 2011-12-08 and 0.6.1 dated 2012-07-25
Description: stringr is a set of simple wrappers that make R's string
functions more consistent, simpler and easier to use. It does
this by ensuring that: function and argument names (and
positions) are consistent, all functions deal with NA's and
zero length character appropriately, and the output data
structures from each function matches the input data structures
of other functions.
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 21 ++++++++++-----------
MD5 | 18 +++++++++---------
NAMESPACE | 11 ++++++-----
NEWS | 7 +++++++
R/c.r | 2 +-
R/checks.r | 2 +-
R/replace.r | 2 +-
R/split.r | 4 +++-
man/str_replace_all.Rd | 2 +-
man/str_sub_replace.Rd | 2 +-
10 files changed, 40 insertions(+), 31 deletions(-)
Title: Spatial Forecast Verification
Diff between SpatialVx versions 0.1-2 dated 2012-06-06 and 0.1-3 dated 2012-07-25
Description: Functions to perform most of the spatial forecast
verification methods carried out in the Spatial Forecast
Verification Inter-Comparison Project (ICP), and a few others.
This first version only has the neighborhood methods, but the
next version will have many more.
Author: Eric Gilleland
Maintainer: Eric Gilleland
DESCRIPTION | 8 ++++----
MD5 | 13 ++++++++-----
R/LocMeasures.R | 6 ++++--
R/Misc.R | 16 ++++++++++++++++
R/gmm.R |only
man/S1.Rd |only
man/SpatialVx-internal.Rd | 4 ++++
man/SpatialVx-package.Rd | 10 ++++++++++
man/gmm2d.Rd |only
9 files changed, 46 insertions(+), 11 deletions(-)
Title: Models of Soil Organic Matter Decomposition
Diff between SoilR versions 1.0-2 dated 2012-07-20 and 1.0-3 dated 2012-07-25
Description: This package contains functions for modeling Soil Organic
Matter decomposition in terrestrial ecosystems.
Author: Carlos A. Sierra
Maintainer: Markus Mueller
SoilR-1.0-2/SoilR/.Rinstignore |only
SoilR-1.0-3/SoilR/DESCRIPTION | 10
SoilR-1.0-3/SoilR/MD5 | 62 +
SoilR-1.0-3/SoilR/NAMESPACE | 3
SoilR-1.0-3/SoilR/R/ThreepParallelModel.R | 4
SoilR-1.0-3/SoilR/R/ThreepParallelModel14.R | 2
SoilR-1.0-3/SoilR/R/TwopParallelModel.R | 3
SoilR-1.0-3/SoilR/R/TwopParallelModel14.R | 3
SoilR-1.0-3/SoilR/data/C14Atm.rda |binary
SoilR-1.0-3/SoilR/data/C14Atm_NH.rda |binary
SoilR-1.0-3/SoilR/data/CourseExample_R14.rda |binary
SoilR-1.0-3/SoilR/data/DataC.rda |binary
SoilR-1.0-3/SoilR/data/DataI.rda |binary
SoilR-1.0-3/SoilR/data/DataR14.rda |binary
SoilR-1.0-3/SoilR/data/HarvardForest14CO2.rda |binary
SoilR-1.0-3/SoilR/inst/doc/Course.Rnw | 333 +++++-----
SoilR-1.0-3/SoilR/inst/doc/Course.pdf |binary
SoilR-1.0-3/SoilR/inst/doc/GeneralModel.pdf |binary
SoilR-1.0-3/SoilR/inst/tests/C14example.pyc |only
SoilR-1.0-3/SoilR/inst/tests/Manzoniexample.pyc |only
SoilR-1.0-3/SoilR/inst/tests/Rexample.pyc |only
SoilR-1.0-3/SoilR/inst/tests/Rplots.pdf |only
SoilR-1.0-3/SoilR/inst/tests/functions.pyc |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.FourpSerial_1.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_Zero.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.OnePool_C14_ZeroDecay_constantInputrate.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.OnePool_C14_equalDecay_ZeroInput.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.ThreepFeedback_1.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.ThreepSerial_1.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.ThreepSerial_2.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwoPool_C14_equalDecay_ZeroInput.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopFeedback.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopParallel.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopParallel_ZeroDecayInputOnly.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopParallel_ZeroInput.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopParallel_constantInput.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.TwopSeriell.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.automatic.op.pdf |only
SoilR-1.0-3/SoilR/inst/tests/runit.manual.help.R | 2
SoilR-1.0-3/SoilR/man/CourseExample_R14.Rd | 4
SoilR-1.0-3/SoilR/man/DataC.Rd | 3
SoilR-1.0-3/SoilR/man/DataI.Rd | 5
SoilR-1.0-3/SoilR/man/DataR14.Rd | 4
43 files changed, 248 insertions(+), 190 deletions(-)
Title: Exemplar data sets for SGP analyses.
Diff between SGPdata versions 1.0-0.0 dated 2012-01-10 and 2.0-0.0 dated 2012-07-25
Description: The package SGPdata contains two data sets utilized by the
SGP Package as exemplars for users to set up their own data for
SGP analyses.
Author: Damian W. Betebenner
Maintainer: Damian W. Betebenner
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
data/sgpData.rda |binary
data/sgpData_LONG.rda |binary
inst/CITATION | 8 ++++----
inst/NEWS | 7 +++++++
man/SGPdata-package.Rd | 4 ++--
man/sgpData.Rd | 4 ++--
8 files changed, 26 insertions(+), 19 deletions(-)
Title: Basic Non-Compartmental Pharmacokinetics
Diff between PK versions 1.2-5 dated 2011-11-17 and 1.3-0 dated 2012-07-25
Description: Estimation of pharmacokinetic parameters using
non-compartmental theory
Author: Thomas Jaki
Maintainer: Thomas Jaki
PK-1.2-5/PK/man/eqv.batch.Rd |only
PK-1.2-5/PK/man/eqv.complete.Rd |only
PK-1.2-5/PK/man/eqv.ssd.Rd |only
PK-1.3-0/PK/DESCRIPTION | 12 +-
PK-1.3-0/PK/MD5 | 34 +++---
PK-1.3-0/PK/NAMESPACE | 1
PK-1.3-0/PK/R/auc.batch.R | 150 +++++++++++++++++++++---------
PK-1.3-0/PK/R/auc.complete.R | 3
PK-1.3-0/PK/R/eqv.batch.R | 16 +--
PK-1.3-0/PK/R/internal.R | 57 +++++++++++
PK-1.3-0/PK/R/nca.R | 2
PK-1.3-0/PK/R/nca.batch.R |only
PK-1.3-0/PK/inst/NEWS | 16 +++
PK-1.3-0/PK/man/auc.Rd | 20 +++-
PK-1.3-0/PK/man/auc.complete.Rd | 198 ++++++++++++++++++++--------------------
PK-1.3-0/PK/man/biexp.Rd | 5 -
PK-1.3-0/PK/man/eqv.Rd | 47 ++++++++-
PK-1.3-0/PK/man/lee.Rd | 2
PK-1.3-0/PK/man/nca.Rd | 42 +++++++-
PK-1.3-0/PK/man/test.Rd | 6 -
20 files changed, 416 insertions(+), 195 deletions(-)
Title: Estimation of (Local) False Discovery Rates and Higher Criticism
Diff between fdrtool versions 1.2.9 dated 2012-05-27 and 1.2.10 dated 2012-07-25
Description: This package allows to estimate both tail area-based false
discovery rates (Fdr) as well as local false discovery rates
(fdr) for a variety of null models (p-values, z-scores,
correlation coefficients, t-scores). The proportion of null
values and the parameters of the null distribution are
adaptively estimated from the data. In addition, the package
contains functions for non-parametric density estimation
(Grenander estimator), for monotone regression (isotonic
regression and antitonic regression with weights), for
computing the greatest convex minorant (GCM) and the least
concave majorant (LCM), for the half-normal and correlation
distributions, and for computing empirical higher criticism
(HC) scores and the corresponding decision threshold.
Author: Bernd Klaus and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 17 +++++++++--------
MD5 | 10 ++++++----
NAMESPACE | 4 +++-
NEWS | 8 ++++++++
R/fdrtool.R | 6 +++---
R/hc.score.R |only
man/hc.score.Rd |only
7 files changed, 29 insertions(+), 16 deletions(-)
Title: Continuous Time Autoregressive Models
Diff between cts versions 1.0-10 dated 2012-04-05 and 1.0-12 dated 2012-07-25
Description: Continuous Time Autoregressive Models and the Kalman
Filter
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port
by Zhu Wang with contribution from John Nash.
Maintainer: Zhu Wang
.Rinstignore |only
DESCRIPTION | 6 -
MD5 | 88 ++++++++---------
NEWS | 13 ++
R/car.R | 42 +++++---
R/plotSpecCar.R | 50 ++++-----
R/spectrum.car.R | 3
inst/doc/kf.Rnw | 276 ++++++++++++++++++++++++++++++++-----------------------
inst/doc/kf.bib | 243 ++++++++++++++++++++++++++----------------------
inst/doc/kf.pdf |binary
man/car.Rd | 6 -
src/cinvert.f | 4
src/complete.f | 4
src/cspec.f | 14 +-
src/display.f | 2
src/dpca.f | 2
src/drpoly.f | 2
src/forecast.f | 11 +-
src/hqrort.f | 4
src/i0tk00.f | 2
src/istkgt.f | 4
src/istkqu.f | 4
src/istkrl.f | 4
src/kfilsm.f | 11 +-
src/kfilsm1.f | 11 +-
src/loop.f | 6 -
src/lybsc.f | 4
src/mepad.f | 4
src/rejuce.f | 4
src/repar.f | 6 -
src/resg0.f | 8 -
src/resg0new.f | 25 ++--
src/resg1d.f | 15 +-
src/resg1dpre.f | 15 +-
src/resg1dpre1.f | 15 +-
src/resgen.f | 8 -
src/revg1.f | 11 +-
src/roots.f | 2
src/search.f | 2
src/setcom.f | 9 -
src/setfor.f | 11 +-
src/setkfilsm.f | 17 +--
src/setup1.f | 17 +--
src/simi.f | 2
src/stkdmp.f | 12 +-
src/u9dmp.f | 6 -
46 files changed, 559 insertions(+), 446 deletions(-)
Title: Protein Mass Spectra Processing
Description: This package provides tools for protein mass spectra
processing including data preparation, denoising, noise
estimation, baseline correction, intensity normalization, peak
detection, peak alignment, peak quantification, and various
functionalities for data ingestion/conversion, mass
calibration, data quality assessment, and protein mass spectra
simulation. It also provides auxiliary tools for data
representation, data visualization, and pipeline processing
history recording and retrieval.
Author: Lixin Gong, William Constantine, and Yu Alex Chen
Maintainer: ORPHANED
Diff between msProcess versions 1.0.6 dated 2011-02-08 and 1.0.7 dated 2012-07-25
DESCRIPTION | 18 +++++++++++------- MD5 |only NAMESPACE |only demo/coombes_clinchem_2003.R | 2 +- demo/morris_bioinformatics_2005.R | 2 +- demo/yasui_biostatistics_2003.R | 4 ++-- inst/doc/msProcess-manual.pdf |binary 7 files changed, 15 insertions(+), 11 deletions(-)
Title: procedures for automated interpolation - methods only to be used
interactively, not included in intamap package
Diff between intamapInteractive versions 1.1-1 dated 2012-01-03 and 1.1-4 dated 2012-07-25
More information about intamapInteractive at CRAN
Description: A package that provides additional functionality for
spatial interpolation in the intamap package.
Author: Edzer Pebesma
Maintainer: Jon Skoien
intamapInteractive-1.1-1/intamapInteractive/man/ssaOptim.rd |only
intamapInteractive-1.1-4/intamapInteractive/DESCRIPTION | 19 -
intamapInteractive-1.1-4/intamapInteractive/MD5 | 26 -
intamapInteractive-1.1-4/intamapInteractive/R/bound.R | 4
intamapInteractive-1.1-4/intamapInteractive/R/common.R | 67 ++--
intamapInteractive-1.1-4/intamapInteractive/R/doSegmentation.R | 2
intamapInteractive-1.1-4/intamapInteractive/R/ssaMap.R | 6
intamapInteractive-1.1-4/intamapInteractive/R/ssaOptim.R | 2
intamapInteractive-1.1-4/intamapInteractive/man/ssaOptim.Rd |only
intamapInteractive-1.1-4/intamapInteractive/tests/anisotropyChoice.Rout.save | 57 +--
intamapInteractive-1.1-4/intamapInteractive/tests/biasCorr.Rout.save | 96 ++----
intamapInteractive-1.1-4/intamapInteractive/tests/findLocalBias.Rout.save | 144 ++++------
intamapInteractive-1.1-4/intamapInteractive/tests/findRegionalBias.Rout.save | 136 +++------
intamapInteractive-1.1-4/intamapInteractive/tests/optimizingTest.R | 4
intamapInteractive-1.1-4/intamapInteractive/tests/optimizingTest.Rout.save | 86 ++---
15 files changed, 269 insertions(+), 380 deletions(-)
Permanent link
Title: procedures for automated interpolation
Diff between intamap versions 1.3-11 dated 2011-06-15 and 1.3-15 dated 2012-07-25
Description: A package that provides classes and methods for automated
spatial interpolation.
Author: Edzer Pebesma
Maintainer: Jon Olav Skoien
DESCRIPTION | 22 +--
MD5 |only
NAMESPACE | 1
R/default.R | 12 +
R/estimateAnisotropy.R | 2
R/init.R | 64 ++++-----
R/interpolate.R | 28 ++-
R/summary.R | 10 -
R/time.R | 11 -
demo/intamap.R | 1
man/blockPredict.Rd | 3
man/intamap-package.Rd | 3
man/interpolate.Rd | 4
man/spatialPredict.Rd | 2
tests/anisotropyTest.Rout.save | 45 ++++--
tests/block.Rout.save | 51 ++++---
tests/idw.Rout.save | 31 +++-
tests/interpolate.Rout.save | 170 ++++++++++++-----------
tests/interpolateBlock.Rout.save | 37 +++--
tests/javaR.Rout.save | 45 ++++--
tests/linearVariogram.Rout.save | 31 +++-
tests/minimal.Rout.save | 33 +++-
tests/transGaussian.Rout.save | 33 +++-
tests/unbiased.Rout.save | 277 ++++++++++++++++++++-------------------
24 files changed, 529 insertions(+), 387 deletions(-)
Title: General Frailty models using a semi_parametrical penalized
likelihood estimation or a parametrical estimation
Diff between frailtypack versions 2.2-23 dated 2012-04-05 and 2.2-24 dated 2012-07-25
Description: Frailtypack now fits several classes of frailty models
using a penalized likelihood estimation on the hazard function
but also a parametrical estimation. 1) A shared gamma frailty
model and Cox proportional hazard model. Clustered and
recurrent survival times can be studied (the
Andersen-Gill(1982) approach has been implemented for recurrent
events). An automatic choice of the smoothing parameter is
possible using an approximated cross-validation procedure. 2)
Additive frailty models for proportional hazard models with two
correlated random effects (intercept random effect with random
slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma
random effects. 4) Joint frailty models in the context of joint
modelling of recurrent events with terminal event. Prediction
values are available. Left truncated, right-censored data,
interval-censored data (only for Cox proportional hazard and
shared frailty model) and strata (max=2) are allowed. The
package includes concordance measures for Cox proportional
hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
DESCRIPTION | 23 +-
MD5 | 47 +++--
NAMESPACE | 5
NEWS | 11 +
R/SurvIC.R |only
R/frailtyPenal.R | 126 ++++++++++----
R/print.frailtyPenal.R | 5
data/dataJointClus.rda |only
demo/frailtypack_frailtyPenal.R | 11 -
man/JointfrailtyPenal.Rd | 55 +++---
man/NestedfrailtyPenal.Rd | 4
man/SurvIC.Rd |only
man/dataJointClus.Rd |only
man/frailtyPenal.Rd | 57 +++---
man/frailtypack-package.Rd | 12 -
man/plotFrailtyPenal.Rd | 4
man/printFrailtyPenal.Rd | 4
man/readmission.Rd | 2
man/summaryFrailtyPenal.Rd | 5
src/Aparameters.f90 | 8
src/aaOptim.f90 | 17 +-
src/frailtypack.f90 | 338 +++++++++++++++++++++++++---------------
src/funcpascpm.f90 | 22 +-
src/funcpascpm_intcens.f90 |only
src/funcpassplines.f90 | 1
src/funcpassplines_intcens.f90 |only
src/funcpasweib.f90 | 14 -
src/funcpasweib_intcens.f90 |only
28 files changed, 477 insertions(+), 294 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-11-30 0.6.1
2005-09-03 0.5.1
Title: Text based plots
Diff between txtplot versions 1.0-2 dated 2011-06-18 and 1.0-3 dated 2012-07-25
Description: Provides functions to produce rudimentary ascii graphics
directly in the terminal window. Provides a basic plotting
function (and equivalents of curve, density, acf and barplot)
as well as a boxplot function.
Author: Bjoern Bornkamp
Maintainer: Bjoern Bornkamp
DESCRIPTION | 8 ++++----
MD5 |only
R/txtplot.R | 35 +++++++++++++++++++++++++++++------
tests/tests.R | 7 +++++++
4 files changed, 40 insertions(+), 10 deletions(-)
Title: Dirichlet Process Mixture model simulation for clustering and
image segmentation
Diff between dpmixsim versions 0.0-7 dated 2011-06-20 and 0.0-8 dated 2012-07-25
Description: The package implements a Dirichlet Process Mixture (DPM)
model for clustering and image segmentation. The DPM model is
a Bayesian nonparametric methodology that relies on MCMC
simulations for exploring mixture models with an unknown number
of components. The code implements conjugate models with
normal structure (conjugate normal-normal DP mixture model).
The package's applications are oriented towards the
classification of magnetic resonance images according to tissue
type or region of interest.
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
DESCRIPTION | 22 +++++++++++-----------
MD5 |only
NEWS | 6 ++++++
demo/testMarronWand.R | 2 +-
src/gibbsclustersamplealpha.cc | 19 ++++++++++++++-----
5 files changed, 32 insertions(+), 17 deletions(-)