Title: Multi-state Markov and hidden Markov models in continuous time
Diff between msm versions 1.1.2 dated 2012-08-01 and 1.1.3 dated 2012-09-28
Description: Functions for fitting general continuous-time Markov and
hidden Markov multi-state models to longitudinal data. Both
Markov transition rates and the hidden Markov output process
can be modelled in terms of covariates, which may be constant
or piecewise-constant in time. A variety of observation
schemes are supported, including processes observed at
arbitrary times (panel data), continuously-observed processes,
and censored states.
Author: Christopher Jackson
Maintainer: Christopher Jackson
ChangeLog | 34 ++++++++++++++++++++++-
DESCRIPTION | 8 ++---
MD5 | 28 +++++++++----------
R/msm.R | 10 ++++--
R/outputs.R | 4 +-
data/aneur.txt.gz |binary
data/cav.txt.gz |binary
data/fev.txt.gz |binary
data/psor.txt.gz |binary
inst/NEWS | 15 +++++++++-
inst/doc/msm-manual.pdf |binary
man/boot.msm.Rd | 6 ++++
man/lrtest.msm.Rd | 2 -
src/doc/msm-manual.Rnw | 69 ++++++++++++++++++++++++++++++++++--------------
tests/simple.R | 26 ++++++++++++++++--
15 files changed, 155 insertions(+), 47 deletions(-)
Title: Spatial Forecast Verification
Diff between SpatialVx versions 0.1-3 dated 2012-07-25 and 0.1-4 dated 2012-09-28
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 | 9 -
MD5 | 208 ++++++++++++++++---------------
R/CA.R |only
R/Features.R | 288 ++++++++++++++++++++++++++++++++++++++++----
R/Hoods2d.R | 57 ++++++++
R/OF.R |only
R/Vgrams.R | 96 ++++++++++++++
data/GFSNAMfcstEx.rda |binary
data/GFSNAMlocEx.rda |binary
data/GFSNAMobsEx.rda |binary
data/ICPg240Locs.rda |binary
data/UKfcst6.rda |binary
data/UKloc.rda |binary
data/UKobs6.rda |binary
data/datalist | 1
data/geom000.rda |binary
data/geom001.rda |binary
data/geom002.rda |binary
data/geom003.rda |binary
data/geom004.rda |binary
data/geom005.rda |binary
data/hump.rda |only
data/obs0426.rda |binary
data/obs0513.rda |binary
data/obs0514.rda |binary
data/obs0518.rda |binary
data/obs0519.rda |binary
data/obs0525.rda |binary
data/obs0601.rda |binary
data/obs0603.rda |binary
data/obs0604.rda |binary
data/pert000.rda |binary
data/pert001.rda |binary
data/pert002.rda |binary
data/pert003.rda |binary
data/pert004.rda |binary
data/pert005.rda |binary
data/pert006.rda |binary
data/pert007.rda |binary
data/wrf2caps0425.rda |binary
data/wrf2caps0512.rda |binary
data/wrf2caps0513.rda |binary
data/wrf2caps0517.rda |binary
data/wrf2caps0518.rda |binary
data/wrf2caps0524.rda |binary
data/wrf2caps0531.rda |binary
data/wrf2caps0602.rda |binary
data/wrf2caps0603.rda |binary
data/wrf4ncar0425.rda |binary
data/wrf4ncar0512.rda |binary
data/wrf4ncar0513.rda |binary
data/wrf4ncar0517.rda |binary
data/wrf4ncar0518.rda |binary
data/wrf4ncar0524.rda |binary
data/wrf4ncar0531.rda |binary
data/wrf4ncar0602.rda |binary
data/wrf4ncar0603.rda |binary
data/wrf4ncep0425.rda |binary
data/wrf4ncep0512.rda |binary
data/wrf4ncep0513.rda |binary
data/wrf4ncep0517.rda |binary
data/wrf4ncep0518.rda |binary
data/wrf4ncep0524.rda |binary
data/wrf4ncep0531.rda |binary
data/wrf4ncep0602.rda |binary
data/wrf4ncep0603.rda |binary
man/Aindex.Rd | 4
man/CSIsamples.Rd |only
man/FQI.Rd | 2
man/FeatureAxis.Rd | 7 -
man/FeatureMatchAnalyzer.Rd | 34 +++--
man/FeatureSuite.Rd | 37 ++++-
man/Fourier2d.Rd | 2
man/LocSig.Rd | 6
man/MCdof.Rd | 5
man/OF.Rd |only
man/SpatialVx-internal.Rd | 3
man/SpatialVx-package.Rd | 73 ++++-------
man/abserrloss.Rd | 5
man/clusterer.Rd |only
man/convthresh.Rd | 32 +++-
man/datasets.Rd | 2
man/deltamm.Rd | 14 +-
man/fss2dPlot.Rd | 3
man/fss2dfun.Rd | 5
man/griddedVgram.Rd | 18 ++
man/hoods2d.Rd | 11 +
man/hoods2dPlot.Rd | 3
man/hoods2dPrep.Rd | 37 +++++
man/hoods2dsmooth.Rd | 16 +-
man/hump.Rd |only
man/kernel2dmeitsjer.Rd | 4
man/kernel2dsmooth.Rd | 5
man/locmeasures2d.Rd | 10 -
man/locmeasures2dPrep.Rd | 3
man/locperf.Rd | 4
man/metrV.Rd | 2
man/optflow.Rd |only
man/pphindcast2d.Rd | 8 -
man/saller.Rd | 10 +
man/spatMLD.Rd | 40 +++++-
man/spatbiasFS.Rd | 5
man/structurogram.Rd |only
man/structurogram.matrix.Rd |only
man/surrogater2d.Rd | 3
man/upscale2d.Rd | 8 -
man/vxstats.Rd | 3
man/waveIS.Rd | 8 -
man/wavePurifyVx.Rd | 25 +++
man/waverify2d.Rd | 31 +++-
110 files changed, 874 insertions(+), 273 deletions(-)
Title: Ridge Regression with automatic selection of the penalty
parameter
Diff between ridge versions 2.1-1 dated 2012-08-23 and 2.1-2 dated 2012-09-28
Description: Linear and logistic ridge regression for small data sets
and genome-wide SNP data
Author: Erika Cule
Maintainer: Erika Cule
ridge-2.1-1/ridge/data/GenBin_genotypes.txt.gz |only
ridge-2.1-1/ridge/data/GenBin_phenotypes.txt.gz |only
ridge-2.1-1/ridge/data/GenCont_genotypes.txt.gz |only
ridge-2.1-1/ridge/data/GenCont_phenotypes.txt.gz |only
ridge-2.1-2/ridge/ChangeLog | 7
ridge-2.1-2/ridge/DESCRIPTION | 8
ridge-2.1-2/ridge/MD5 | 42
ridge-2.1-2/ridge/R/linearRidgeGenotypes.R | 2
ridge-2.1-2/ridge/R/linearRidgeGenotypesPredict.R | 2
ridge-2.1-2/ridge/R/logisticRidgeGenotypes.R | 2
ridge-2.1-2/ridge/R/logisticRidgeGenotypesPredict.R | 2
ridge-2.1-2/ridge/configure | 919 +++++++++++++----
ridge-2.1-2/ridge/configure.ac | 118 +-
ridge-2.1-2/ridge/inst |only
ridge-2.1-2/ridge/man/GenBin.Rd | 3
ridge-2.1-2/ridge/man/GenCont.Rd | 3
ridge-2.1-2/ridge/man/linearRidgeGenotypes.Rd | 4
ridge-2.1-2/ridge/man/linearRidgeGenotypesPredict.Rd | 4
ridge-2.1-2/ridge/man/logisticRidgeGenotypes.Rd | 4
ridge-2.1-2/ridge/man/logisticRidgeGenotypesPredict.Rd | 4
ridge-2.1-2/ridge/src/Makevars | 8
ridge-2.1-2/ridge/src/Makevars.in | 4
ridge-2.1-2/ridge/src/config.h | 2
23 files changed, 847 insertions(+), 291 deletions(-)
Title: Functions for performing hierarchical analysis of distance
sampling data
Diff between hierarchicalDS versions 1.0 dated 2012-07-12 and 2.01 dated 2012-09-28
More information about hierarchicalDS at CRAN
Description: Functions for performing hierarchical analysis of distance
sampling data, with ability to use an areal spatial ICAR model
on top of user supplied covariates to get at variation in
abundance intensity. The detection model can be specified as a
function of observer and individual covariates, where a
parametric model is supposed for the population level
distribution of covariate values. The model uses data
augmentation and a reversible jump MCMC algorithm to sample
animals that were never observed. Also included is the ability
to include point independence (increasing correlation multiple
observer's observations as a function of distance, with
independence assumed for distance=0 or first distance bin).
New in version 2.0 is the ability to model species
misclassification rates using a multinomial logit formulation
on data from double observers.
Author: P.B. Conn \email{paul.conn@@noaa.gov}
Maintainer: Paul B Conn
hierarchicalDS-1.0/hierarchicalDS/data/simdata.rda |only
hierarchicalDS-1.0/hierarchicalDS/man/dens.plot.Rd |only
hierarchicalDS-2.01/hierarchicalDS/DESCRIPTION | 24
hierarchicalDS-2.01/hierarchicalDS/MD5 | 40
hierarchicalDS-2.01/hierarchicalDS/NAMESPACE | 5
hierarchicalDS-2.01/hierarchicalDS/R/hierarchical_DS.R | 255 +-
hierarchicalDS-2.01/hierarchicalDS/R/mcmc_ds.R | 1097 +++++-----
hierarchicalDS-2.01/hierarchicalDS/R/simulate_data.R | 141 -
hierarchicalDS-2.01/hierarchicalDS/R/spat_funcs.R | 803 ++++---
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.aux |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.bbl |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.blg |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.log |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.nav |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.out |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.pdf |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.snm |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.tex |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.tex.sav |only
hierarchicalDS-2.01/hierarchicalDS/TWS2012_Conn.toc |only
hierarchicalDS-2.01/hierarchicalDS/data/simdata.rdata |only
hierarchicalDS-2.01/hierarchicalDS/inst |only
hierarchicalDS-2.01/hierarchicalDS/man/get_confusion_array.Rd |only
hierarchicalDS-2.01/hierarchicalDS/man/get_confusion_mat.Rd |only
hierarchicalDS-2.01/hierarchicalDS/man/hierarchical_DS.Rd | 189 -
hierarchicalDS-2.01/hierarchicalDS/man/mcmc_ds.Rd | 124 -
hierarchicalDS-2.01/hierarchicalDS/man/post_loss.Rd |only
hierarchicalDS-2.01/hierarchicalDS/man/simdata.Rd | 6
hierarchicalDS-2.01/hierarchicalDS/man/simulate_data.Rd | 39
hierarchicalDS-2.01/hierarchicalDS/man/stack_data_misID.Rd |only
30 files changed, 1532 insertions(+), 1191 deletions(-)
Permanent link
Title: Benchmark for the CEC 2005 Special Session on Real-Parameter
Optimization
Diff between cec2005benchmark versions 1.0.1 dated 2012-04-23 and 1.0.2 dated 2012-09-28
More information about cec2005benchmark at CRAN
Description: This package is a wrapper for the C implementation of the
25 benchmark functions for the CEC 2005 Special Session on
Real-Parameter Optimization. The original C code by Santosh
Tiwari and related documentation are available at
http://www.ntu.edu.sg/home/EPNSugan/.
Author: Yasser González Fernández
Maintainer: Yasser González Fernández
DESCRIPTION | 15 ++++++++-------
MD5 | 8 ++++----
NEWS | 5 +++++
R/cec2005benchmark.R | 7 -------
tests/test_data.R | 2 +-
5 files changed, 18 insertions(+), 19 deletions(-)
Permanent link
Title: Robust Structural Equation Modeling with Missing Data and
Auxiliary Variables
Diff between rsem versions 0.4.3 dated 2012-09-18 and 0.4.4 dated 2012-09-28
Description: This package estimates means and covariance matrix of
multiple variables with missing data using Huber weight and
then estimates a SEM model using lavaan or EQS.
Author: Ke-Hai Yuan and Zhiyong Zhang
Maintainer: Zhiyong Zhang
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
R/rsem.R | 2 +-
3 files changed, 8 insertions(+), 8 deletions(-)
Title: Prediction of Fish Movement Parameters
Diff between fishmove versions 0.0-1 dated 2012-05-16 and 0.0-2 dated 2012-09-28
Description: Functions to predict fish movement parameters based on
multiple regression and plotting leptokurtic fish dispersal
kernels
Author: Johannes Radinger
Maintainer: Johannes Radinger
fishmove-0.0-1/fishmove/.project |only
fishmove-0.0-1/fishmove/.settings |only
fishmove-0.0-1/fishmove/data/.Rhistory |only
fishmove-0.0-1/fishmove/tests/.Rhistory |only
fishmove-0.0-2/fishmove/DESCRIPTION | 6 +++---
fishmove-0.0-2/fishmove/MD5 | 4 ++--
fishmove-0.0-2/fishmove/R/fishmove_code.R | 8 ++++----
7 files changed, 9 insertions(+), 9 deletions(-)
Title: Likelihood-based Boosting for Generalized mixed models
Diff between GMMBoost versions 1.0.2 dated 2012-03-29 and 1.0.3 dated 2012-09-28
Description: Likelihood-based Boosting for Generalized mixed models
Author: Andreas Groll
Maintainer: Andreas Groll
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
man/GMMBoost-package.Rd | 4 ++--
man/OrdinalBoost.rd | 5 +----
man/bGAMM.rd | 4 ++--
man/bGLMM.rd | 4 ++--
6 files changed, 17 insertions(+), 20 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-07-03 1.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-07-23 1.0
Title: Visualization of regression models
Diff between visreg versions 1.0-0 dated 2012-05-31 and 1.1-0 dated 2012-09-28
Description: Provides convenient interface for constructing plots to
visualize the fit of regression models arising from a wide
variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
DESCRIPTION | 8 -
MD5 | 40 ++++---
NEWS | 7 +
R/Response.R | 20 ++-
R/Terms.R | 36 ++++---
R/factorAxis.R | 2
R/factorPlot.R | 23 ++--
R/getXY.R | 33 ++----
R/removeFormulaFormatting.R | 24 ++--
R/se.mlm.R |only
R/setupD.R | 45 ++++----
R/setupF.R | 42 ++++----
R/setupX.R | 71 +++++++-------
R/visreg.R | 88 ++++++++---------
R/visreg2d.R | 221 +++++++++++++++++++++++---------------------
R/visregFactorPanel.R | 41 ++++----
R/visregLatticePlot.R | 132 ++++++++++++++------------
R/visregPanel.R | 18 +--
R/visregPlot.R | 52 +++++++---
man/visreg.Rd | 133 ++++++++++++++++----------
tests/visreg-lm.R | 110 +++++++++++----------
tests/visreg-mlm.R |only
22 files changed, 630 insertions(+), 516 deletions(-)
Title: Multivariate and Propensity Score Matching with Balance
Optimization
Diff between Matching versions 4.8-0 dated 2012-01-19 and 4.8-1 dated 2012-09-28
Description: Provides functions for multivariate and propensity score
matching and for finding optimal balance based on a genetic
search algorithm. A variety of univariate and multivariate
metrics to determine if balance has been obtained are also
provided.
Author: Jasjeet Singh Sekhon
Maintainer: Jasjeet Singh Sekhon
ChangeLog | 12 +
DESCRIPTION | 8 -
MD5 | 40 ++---
R/GenBalance.R | 5
R/GenMatching.R | 9 -
R/Matching.R | 142 +++++--------------
configure | 321 ++++++++++++++++++++++++-------------------
configure.ac | 4
data/lalonde.rda |binary
inst/CITATION | 21 +-
man/GenMatch.Rd | 8 -
man/Match.Rd | 8 -
man/MatchBalance.Rd | 8 -
man/Matchby.Rd | 8 -
man/balanceUV.Rd | 8 -
man/ks.boot.Rd | 8 -
man/qqstats.Rd | 8 -
tests/AbadieImbens.Rout.save | 18 +-
tests/DehejiaWahba.Rout.save | 18 +-
tests/GenMatch.Rout.save | 22 ++
tests/Matchby.Rout.save | 18 +-
21 files changed, 352 insertions(+), 342 deletions(-)
Title: Korean NLP Package
Diff between KoNLP versions 0.76.5 dated 2012-09-18 and 0.76.6 dated 2012-09-28
Description: Korean language processing package. Morphological
analyzer, POS tagger, Keystroke converter, Hangul automata...
Author: Heewon Jeon
Maintainer: Heewon Jeon
DESCRIPTION | 6 +-
MD5 | 16 +++---
NEWS | 7 ++-
R/hangulUtils.R | 9 +++
R/koAnalyzerRun.R | 112 +++++++++++++++++-------------------------------
R/onLoad.R | 2
README.md | 3 -
inst/java/jhannanum.jar |binary
inst/java/ko.jar |binary
9 files changed, 68 insertions(+), 87 deletions(-)
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Diff between haplo.stats versions 1.5.5 dated 2012-02-25 and 1.5.6 dated 2012-09-28
Description: A suite of R routines for the analysis of indirectly
measured haplotypes. The statistical methods assume that all
subjects are unrelated and that haplotypes are ambiguous (due
to unknown linkage phase of the genetic markers). The main
functions are: haplo.em, haplo.glm, haplo.score, haplo.power,
and seqhap. Copyright: 2003 Mayo Foundation for Medical
Education and Research.
Author: Sinnwell JP, Schaid DJ
Maintainer: Jason P. Sinnwell
haplo.stats-1.5.5/haplo.stats/R/glm.fit.nowarn.R |only
haplo.stats-1.5.5/haplo.stats/man/glm.fit.nowarn.Rd |only
haplo.stats-1.5.6/haplo.stats/DESCRIPTION | 10 ++---
haplo.stats-1.5.6/haplo.stats/MD5 | 21 +++++-------
haplo.stats-1.5.6/haplo.stats/NAMESPACE | 2 -
haplo.stats-1.5.6/haplo.stats/R/haplo.binomial.R |only
haplo.stats-1.5.6/haplo.stats/R/haplo.glm.q | 10 +++++
haplo.stats-1.5.6/haplo.stats/data/hapPower.demo.tab.gz |binary
haplo.stats-1.5.6/haplo.stats/inst/NEWS.Rd | 10 +++++
haplo.stats-1.5.6/haplo.stats/inst/doc/manualHaploStats.pdf |binary
haplo.stats-1.5.6/haplo.stats/man/haplo.glm.Rd | 9 ++++-
haplo.stats-1.5.6/haplo.stats/man/internalHaploStats.Rd | 1
haplo.stats-1.5.6/haplo.stats/rnw/manualHaploStats.Rnw | 1
13 files changed, 45 insertions(+), 19 deletions(-)
Title: Elastic Functional Data Analysis
Diff between fdasrvf versions 1.0 dated 2012-09-11 and 1.1 dated 2012-09-28
Description: A library for functional data analysis using the square
root velocity framework
Author: J. Derek Tucker
Maintainer: J. Derek Tucker
DESCRIPTION | 9 ++--
MD5 | 25 ++++++------
NAMESPACE | 1
NEWS | 6 ++-
R/align_fPCA.R | 21 +++++++---
R/fdasrvf-package.r | 2 -
R/gauss_model.R | 26 ++++++-------
R/horizFPCA.R | 38 +++++++++----------
R/time_warping.R | 78 +++++++++++++++++++++++++--------------
R/utility_functions.R | 99 +++++++++++++++++++++++++-------------------------
R/vertFPCA.R | 58 ++++++++++++++---------------
README.md |only
man/align_fPCA.Rd | 7 ++-
man/time_warping.Rd | 12 ++++--
14 files changed, 211 insertions(+), 171 deletions(-)