Author: Original S functions by Stuart Coles, R port and R
documentation files by Alec Stephenson.
Title: An Introduction to Statistical Modeling of Extreme Values
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.
Diff between ismev versions 1.2 dated 2006-03-09 and 1.3 dated 2008-06-02
DESCRIPTION | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-)
Author: Kenneth Knoblauch
Title: Functions for analyzing psychophysical data in R
Description: An assortment of functions that could be useful in analyzing data from pyschophysical experiments. It includes functions for calculating d' from several different experimental designs, links for mafc to be used with the binomial family in glm (and possibly other contexts) and self-Start functions for estimating gamma values for CRT screen calibrations.
Diff between psyphy versions 0.0-5 dated 2007-09-01 and 0.0-6 dated 2008-06-02
DESCRIPTION | 6 +++--- NAMESPACE | 2 +- R/mafc.R | 28 ++++++++++++++++++++++++++++ inst |only man/SS.RGBcalib.Rd | 2 +- man/mafc.Rd | 15 ++++++++++++++- man/probit.lambda.Rd | 2 +- 7 files changed, 48 insertions(+), 7 deletions(-)
Author: Lixin Gong, William Constantine, and Alex Chen
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.
Diff between msProcess versions 1.0.2 dated 2008-05-02 and 1.0.3 dated 2008-06-02
msProcess-1.0.2/msProcess/inst |only msProcess-1.0.2/msProcess/swingui/R/loadMSGUIAll.q |only msProcess-1.0.2/msProcess/swingui/R/resetMSGUI.q |only msProcess-1.0.2/msProcess/swingui/guicreate/addMSGUI.q |only msProcess-1.0.3/msProcess/DESCRIPTION | 41 +- msProcess-1.0.3/msProcess/R/ms_base.q | 7 msProcess-1.0.3/msProcess/R/ms_gui.q | 61 +++ msProcess-1.0.3/msProcess/R/ms_noise.q | 16 - msProcess-1.0.3/msProcess/R/ms_norm.q | 4 msProcess-1.0.3/msProcess/R/ms_peak.q | 10 msProcess-1.0.3/msProcess/R/ms_qa.q | 6 msProcess-1.0.3/msProcess/R/ms_set.q | 28 - msProcess-1.0.3/msProcess/R/ms_smooth.q | 1 msProcess-1.0.3/msProcess/R/ms_util.q | 61 +++ msProcess-1.0.3/msProcess/demo/00Index | 12 msProcess-1.0.3/msProcess/demo/abc_spectra_processing.R | 13 msProcess-1.0.3/msProcess/demo/coombes_clinchem_2003.R | 6 msProcess-1.0.3/msProcess/demo/coombes_proteomics_2005.R | 11 msProcess-1.0.3/msProcess/demo/morris_bioinformatics_2005.R | 1 msProcess-1.0.3/msProcess/demo/randolph_biometrics_2006.R | 3 msProcess-1.0.3/msProcess/demo/yasui_biostatistics_2003.R | 4 msProcess-1.0.3/msProcess/man/dbcypherGenXML2Bin.Rd | 3 msProcess-1.0.3/msProcess/man/dbimportBin2Sqlite.Rd | 2 msProcess-1.0.3/msProcess/man/dbwriteBinDim.Rd | 2 msProcess-1.0.3/msProcess/man/msDenoise.Rd | 26 - msProcess-1.0.3/msProcess/man/msDetrend.Rd | 32 +- msProcess-1.0.3/msProcess/man/msLogic.Rd |only msProcess-1.0.3/msProcess/man/msNoise.Rd | 26 - msProcess-1.0.3/msProcess/man/msNormalize.Rd | 10 msProcess-1.0.3/msProcess/man/msPeak.Rd | 16 - msProcess-1.0.3/msProcess/man/msPeakCWT.Rd | 8 msProcess-1.0.3/msProcess/man/msProcess-package.Rd | 86 ++--- msProcess-1.0.3/msProcess/man/msSmoothApprox.Rd | 4 msProcess-1.0.3/msProcess/man/princomp2.Rd |only msProcess-1.0.3/msProcess/swingui/R/backMSAlign.q |only msProcess-1.0.3/msProcess/swingui/R/backMSDenoise.q | 61 +-- msProcess-1.0.3/msProcess/swingui/R/backMSDetrend.q | 160 ++++++++-- msProcess-1.0.3/msProcess/swingui/R/backMSNoise.q | 116 +++++++ msProcess-1.0.3/msProcess/swingui/R/backMSNormalize.q |only msProcess-1.0.3/msProcess/swingui/R/backMSPeak.q |only msProcess-1.0.3/msProcess/swingui/R/getMethodProps.q |only msProcess-1.0.3/msProcess/swingui/R/guiUtils.q |only msProcess-1.0.3/msProcess/swingui/R/loadMSMenu.q |only msProcess-1.0.3/msProcess/swingui/R/loadMSProps.q |only msProcess-1.0.3/msProcess/swingui/R/menuMSAlign.q |only msProcess-1.0.3/msProcess/swingui/R/menuMSDenoise.q | 87 +++-- msProcess-1.0.3/msProcess/swingui/R/menuMSDetrend.q | 149 ++++++++- msProcess-1.0.3/msProcess/swingui/R/menuMSNoise.q | 121 ++++++- msProcess-1.0.3/msProcess/swingui/R/menuMSNormalize.q |only msProcess-1.0.3/msProcess/swingui/R/menuMSPeak.q |only msProcess-1.0.3/msProcess/swingui/R/reloadMSGUI.q |only msProcess-1.0.3/msProcess/swingui/guicreate/MSDialogProps.ssc |only 52 files changed, 897 insertions(+), 297 deletions(-)
Author: Heather Turner and David Firth
Title: Generalized Nonlinear Models
Description: Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.
Diff between gnm versions 0.9-4 dated 2008-05-07 and 0.9-5 dated 2008-06-02
gnm-0.9-4/gnm/.directory |only gnm-0.9-4/gnm/inst/.directory |only gnm-0.9-4/gnm/inst/doc/.directory |only gnm-0.9-4/gnm/man/Nonlin.Rd |only gnm-0.9-5/gnm/DESCRIPTION | 6 gnm-0.9-5/gnm/NAMESPACE | 2 gnm-0.9-5/gnm/R/Const.R | 5 gnm-0.9-5/gnm/R/Nonlin.R | 40 gnm-0.9-5/gnm/R/checkEstimable.R | 2 gnm-0.9-5/gnm/R/getContrasts.R | 161 gnm-0.9-5/gnm/R/gnmTerms.R | 36 gnm-0.9-5/gnm/R/gnmTools.R | 48 gnm-0.9-5/gnm/R/nonlinTerms.R | 18 gnm-0.9-5/gnm/R/plot.gnm.R | 204 - gnm-0.9-5/gnm/data/barley.csv |only gnm-0.9-5/gnm/data/barleyHeights.R |only gnm-0.9-5/gnm/inst/NEWS | 29 gnm-0.9-5/gnm/inst/doc/gnmOverview.pdf | 6512 ++++++++++++++++----------------- gnm-0.9-5/gnm/man/Const.Rd | 14 gnm-0.9-5/gnm/man/barleyHeights.Rd |only gnm-0.9-5/gnm/man/checkEstimable.Rd | 2 gnm-0.9-5/gnm/man/getContrasts.Rd | 105 gnm-0.9-5/gnm/man/gnm-defunct.Rd |only gnm-0.9-5/gnm/man/gnm.Rd | 36 gnm-0.9-5/gnm/man/mentalHealth.Rd | 13 gnm-0.9-5/gnm/man/pickCoef.Rd | 2 gnm-0.9-5/gnm/man/plot.gnm.Rd | 4 gnm-0.9-5/gnm/tests/RC.R | 5 gnm-0.9-5/gnm/tests/RC.Rout.save | 15 29 files changed, 3687 insertions(+), 3572 deletions(-)
Author: Chris Fraley, Adrian E. Raftery, J. McLean Sloughter,
Tilmann Gneiting, Michael Polakowski, University of Washington
Title: Probabilistic Forecasting using Ensembles and Bayesian Model Averaging
Description: Bayesian Model Averaging to create probabilistic
forecasts from ensemble forecasts and weather observations.
Diff between ensembleBMA versions 3.0-0 dated 2008-05-19 and 3.0-1 dated 2008-06-02
ensembleBMA-3.0-0/ensembleBMA/R/cdf.ensembleBMAgamma.R |only ensembleBMA-3.0-1/ensembleBMA/DESCRIPTION | 4 +- ensembleBMA-3.0-1/ensembleBMA/R/cdf.ensembleBMAgamma0.R | 2 - ensembleBMA-3.0-1/ensembleBMA/R/cdf.fitBMAgamma0.R | 2 - ensembleBMA-3.0-1/ensembleBMA/R/dateCheck.R | 28 ++++++++++------ ensembleBMA-3.0-1/ensembleBMA/R/ensembleData.R | 2 - ensembleBMA-3.0-1/ensembleBMA/R/fitBMAgamma0.R | 6 +-- ensembleBMA-3.0-1/ensembleBMA/R/julTOymdh.R | 17 ++++++--- ensembleBMA-3.0-1/ensembleBMA/R/mae.ensembleBMAgamma0.R | 4 +- ensembleBMA-3.0-1/ensembleBMA/R/mae.fitBMAgamma0.R | 8 ++-- ensembleBMA-3.0-1/ensembleBMA/R/ymdhTOjul.R | 19 +++++----- ensembleBMA-3.0-1/ensembleBMA/man/brierScore.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/cdf.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/controlBMAgamma0.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/controlBMAnormal.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/crps.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/ensembleBMA.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/ensembleBMAgamma0.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/ensembleBMAnormal.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/ensembleData.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/fitBMA.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/fitBMAgamma0.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/fitBMAnormal.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/julTOymdh.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/mae.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/plotProbcast.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/prcpDJdata.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/prcpFit.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/prcpGrid.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/quantileForecast.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/srft.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/srftGrid.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/trainingData.Rd | 4 +- ensembleBMA-3.0-1/ensembleBMA/man/ymdhTOjul.Rd | 4 +- 34 files changed, 99 insertions(+), 85 deletions(-)
Author: Andy Bunn
Title: Dendrochronology Program Library in R
Description: This package contains functions for performing some standard tree-ring analyses.
Diff between dplR versions 1.1.1 dated 2008-05-25 and 1.1.2 dated 2008-06-02
DESCRIPTION | 4 NAMESPACE | 4 R/skel.plot.R | 254 ++++++++++++++++++++++++++++++++++++------------------- man/skel.plot.Rd | 81 +++++++++++++---- 4 files changed, 233 insertions(+), 110 deletions(-)
Author: Thibaut Jombart
Diff between adegenet versions 1.1-1 dated 2008-04-18 and 1.1-2 dated 2008-06-02
Title: adegenet: a R package for the multivariate analysis of genetic markers.
Description: Classes and functions for genetic data analysis within the multivariate framework.
ChangeLog |only
DEADJOE |only
DESCRIPTION | 8 ++++----
R/auxil.R | 2 +-
R/classes.R | 42 ++++++++++++++++++++++++++++++++++--------
R/export.R | 38 ++++++++++++++++++++++++++++----------
R/hybridize.R | 8 ++++----
R/import.R | 3 +++
R/propShared.R |only
R/spca.R | 38 ++++++++++++++++++++++++++------------
TODO | 17 ++++++-----------
man/adegenet.package.Rd | 4 ++--
man/chooseCN.Rd | 1 -
man/df2genind.Rd | 6 ++++--
man/propShared.Rd |only
man/spca.Rd | 11 +++++++++--
man/spcaIllus.Rd | 3 ---
src/sharedAll.c |only
18 files changed, 121 insertions(+), 60 deletions(-)