Title: Maximum Likelihood Estimates of Gaussian Processes
Diff between mlegp versions 3.1.2 dated 2011-04-05 and 3.1.3 dated 2012-12-20
Description: Maximum likelihood Gaussian process modeling for
univariate and multi-dimensional outputs with diagnostic plots.
Contact the maintainer for a package version that implements
sensitivity analysis functionality.
Author: Garrett M. Dancik
Maintainer: Garrett M. Dancik
mlegp-3.1.2/mlegp/R/loadCLibAndAdapt.R |only
mlegp-3.1.3/mlegp/CHANGES | 3 +++
mlegp-3.1.3/mlegp/DESCRIPTION | 8 ++++----
mlegp-3.1.3/mlegp/MD5 |only
mlegp-3.1.3/mlegp/NAMESPACE |only
mlegp-3.1.3/mlegp/READ_ME | 1 -
mlegp-3.1.3/mlegp/inst/doc/mlegp.pdf |binary
mlegp-3.1.3/mlegp/man/mlegp-svd-functions.Rd | 2 +-
mlegp-3.1.3/mlegp/src/SFMT.c | 22 +++++++++++-----------
mlegp-3.1.3/mlegp/src/fit_gp.h | 4 ++--
mlegp-3.1.3/mlegp/src/matrix_vector.h | 6 +++---
mlegp-3.1.3/mlegp/src/mlegp.c | 7 +++++++
mlegp-3.1.3/mlegp/src/print.c | 4 ++--
13 files changed, 33 insertions(+), 24 deletions(-)
More information about semisupKernelPCA at CRAN
Permanent link
Title: Quality Assurance Toolkit
Diff between qat versions 0.53 dated 2012-02-15 and 0.60 dated 2012-12-20
Description: This package delivers some functions to provide a
scientific quality assurance of meteorological data.
Author: Andre Duesterhus
Maintainer: Andre Duesterhus
ChangeLog.txt | 5
DESCRIPTION | 14
MD5 | 204 +++++++----
R/qat_analyse_block_distribution_1d.R | 1
R/qat_analyse_block_distribution_2d.R |only
R/qat_analyse_boot_distribution_2d.R |only
R/qat_analyse_distribution_1d.R | 4
R/qat_analyse_distribution_2d.R |only
R/qat_analyse_lim_rule_dynamic_2d.R |only
R/qat_analyse_lim_rule_sigma_2d.R |only
R/qat_analyse_lim_rule_static_2d.R |only
R/qat_analyse_noc_rule_2d.R |only
R/qat_analyse_roc_rule_dynamic_2d.R |only
R/qat_analyse_roc_rule_static_2d.R |only
R/qat_analyse_set_addup_2d.R |only
R/qat_analyse_set_mean_2d.R |only
R/qat_analyse_set_nans_2d.R |only
R/qat_analyse_set_nans_above_2d.R |only
R/qat_analyse_set_nans_below_2d.R |only
R/qat_analyse_slide_distribution_2d.R |only
R/qat_analyse_trimmed_distribution_2d.R |only
R/qat_call_block_distribution.R | 8
R/qat_call_boot_distribution.R | 7
R/qat_call_distribution.R | 7
R/qat_call_lim_rule.R | 21 +
R/qat_call_noc_rule.R | 7
R/qat_call_plot_block_distribution.R | 7
R/qat_call_plot_distribution.R | 5
R/qat_call_plot_lim_rule.R | 21 +
R/qat_call_plot_noc_rule.R | 7
R/qat_call_plot_roc_rule.R | 7
R/qat_call_plot_slide_distribution.R | 7
R/qat_call_plot_trimmed_distribution.R | 7
R/qat_call_roc_rule.R | 14
R/qat_call_save_block_distribution.R | 9
R/qat_call_save_boot_distribution.R | 9
R/qat_call_save_distribution.R | 2
R/qat_call_save_lim_rule.R | 27 +
R/qat_call_save_noc_rule.R | 10
R/qat_call_save_roc_rule.R | 16
R/qat_call_save_set_addup.R | 2
R/qat_call_save_set_mean.R | 2
R/qat_call_save_set_nans.R | 2
R/qat_call_save_slide_distribution.R | 9
R/qat_call_save_trimmed_distribution.R | 9
R/qat_call_set_addup.R | 7
R/qat_call_set_mean.R | 7
R/qat_call_set_nans.R | 21 +
R/qat_call_slide_distribution.R | 7
R/qat_call_trimmed_distribution.R | 7
R/qat_config_write_workflow.R | 16
R/qat_data_read_ncdf.R | 8
R/qat_data_varcontent_ncdf.R | 7
R/qat_plot_block_distribution_1d.R | 2
R/qat_plot_block_distribution_2d.R |only
R/qat_plot_boot_distribution_1d.R | 1
R/qat_plot_lim_rule_dynamic_2d.R |only
R/qat_plot_lim_rule_sigma_2d.R |only
R/qat_plot_lim_rule_static_2d.R |only
R/qat_plot_noc_rule_1d.R | 6
R/qat_plot_noc_rule_2d.R |only
R/qat_plot_roc_rule_dynamic_2d.R |only
R/qat_plot_roc_rule_static_2d.R |only
R/qat_plot_slide_distribution_1d.R | 4
R/qat_plot_slide_distribution_2d.R |only
R/qat_plot_trimmed_distribution_1d.R | 3
R/qat_plot_trimmed_distribution_2d.R |only
R/qat_run_workflow_save.R | 7
R/qat_save_block_distribution_1d.R | 2
R/qat_save_block_distribution_2d.R |only
R/qat_save_boot_distribution_1d.R | 2
R/qat_save_boot_distribution_2d.R |only
R/qat_save_lim_rule_dynamic_2d.R |only
R/qat_save_lim_rule_sigma_2d.R |only
R/qat_save_lim_rule_static_2d.R |only
R/qat_save_noc_rule_2d.R |only
R/qat_save_result_ncdf.R | 516 ++++++++++++++++++-----------
R/qat_save_roc_rule_dynamic_2d.R |only
R/qat_save_roc_rule_static_2d.R |only
R/qat_save_slide_distribution_1d.R | 2
R/qat_save_slide_distribution_2d.R |only
R/qat_save_trimmed_distribution_1d.R | 2
R/qat_save_trimmed_distribution_2d.R |only
inst/doc/qatdoku.pdf |binary
man/qat-package.Rd | 6
man/qat_add_algorithm.Rd | 16
man/qat_add_all_algorithms.Rd | 12
man/qat_analyse_block_distribution_2d.Rd |only
man/qat_analyse_boot_distribution_1d.Rd | 2
man/qat_analyse_boot_distribution_2d.Rd |only
man/qat_analyse_distribution_1d.Rd | 2
man/qat_analyse_distribution_2d.Rd |only
man/qat_analyse_lim_rule_dynamic_2d.Rd |only
man/qat_analyse_lim_rule_sigma_2d.Rd |only
man/qat_analyse_lim_rule_static_2d.Rd |only
man/qat_analyse_noc_rule_1d.Rd | 2
man/qat_analyse_noc_rule_2d.Rd |only
man/qat_analyse_roc_rule_dynamic_1d.Rd | 4
man/qat_analyse_roc_rule_dynamic_2d.Rd |only
man/qat_analyse_roc_rule_static_2d.Rd |only
man/qat_analyse_set_addup_2d.Rd |only
man/qat_analyse_set_mean_2d.Rd |only
man/qat_analyse_set_nans_2d.Rd |only
man/qat_analyse_set_nans_above_2d.Rd |only
man/qat_analyse_set_nans_below_2d.Rd |only
man/qat_analyse_slide_distribution_1d.Rd | 2
man/qat_analyse_slide_distribution_2d.Rd |only
man/qat_analyse_trimmed_distribution_2d.Rd |only
man/qat_call_save_block_distribution.Rd | 3
man/qat_call_save_boot_distribution.Rd | 3
man/qat_call_save_distribution.Rd | 3
man/qat_call_save_lim_rule.Rd | 3
man/qat_call_save_noc_rule.Rd | 3
man/qat_call_save_roc_rule.Rd | 3
man/qat_call_save_set_addup.Rd | 3
man/qat_call_save_set_mean.Rd | 3
man/qat_call_save_set_nans.Rd | 3
man/qat_call_save_slide_distribution.Rd | 3
man/qat_call_save_trimmed_distribution.Rd | 3
man/qat_plot_block_distribution_2d.Rd |only
man/qat_plot_lim_rule_dynamic_2d.Rd |only
man/qat_plot_lim_rule_sigma_2d.Rd |only
man/qat_plot_lim_rule_static_2d.Rd |only
man/qat_plot_noc_rule_2d.Rd |only
man/qat_plot_roc_rule_dynamic_2d.Rd |only
man/qat_plot_roc_rule_static_2d.Rd |only
man/qat_plot_slide_distribution_2d.Rd |only
man/qat_plot_trimmed_distribution_2d.Rd |only
man/qat_save_block_distribution_2d.Rd |only
man/qat_save_boot_distribution_2d.Rd |only
man/qat_save_lim_rule_dynamic_2d.Rd |only
man/qat_save_lim_rule_sigma_2d.Rd |only
man/qat_save_lim_rule_static_2d.Rd |only
man/qat_save_noc_rule_2d.Rd |only
man/qat_save_roc_rule_dynamic_2d.Rd |only
man/qat_save_roc_rule_static_2d.Rd |only
man/qat_save_slide_distribution_2d.Rd |only
man/qat_save_trimmed_distribution_2d.Rd |only
138 files changed, 794 insertions(+), 362 deletions(-)
Title: Particle Swarm Optimisation, with focus on Environmental Models
Diff between hydroPSO versions 0.2-0 dated 2012-11-29 and 0.3-0 dated 2012-12-20
Description: This package implements a state-of-the-art version of the
Particle Swarm Optimisation (PSO) algorithm (SPSO-2011 and
SPSO-2007 capable). hydroPSO can be used as a replacement of
the 'optim' R function for (global) optimization of non-smooth
and non-linear functions. However, the main focus of hydroPSO
is the calibration of environmental and other real-world models
that need to be executed from the system console. hydroPSO is
model-independent, allowing the user to easily interface any
computer simulation model with the calibration engine (PSO).
hydroPSO communicates with the model through the model's own
input and output files, without requiring access to the model's
source code. Several PSO variants and controlling options are
included to fine-tune the performance of the calibration engine
to different calibration problems. An advanced sensitivity
analysis function together with user-friendly plotting
summaries facilitate the interpretation and assessment of the
calibration results. hydroPSO is parallel-capable, to alleviate
the computational burden of complex models with "long"
execution time. Bugs reports/comments/questions are very
welcomed (in English, Spanish or Italian).
Author: Mauricio Zambrano-Bigiarini [aut, cre], Rodrigo Rojas [ctb]
Maintainer: Mauricio Zambrano-Bigiarini
DESCRIPTION | 29 ++---
MD5 | 44 +++----
NEWS | 36 +++++-
R/PSO_v2012.R | 226 +++++++++++++++++++++++++++++++++++++----
R/plot_params.R | 2
R/plot_results.R | 6 -
R/read_out.R | 27 ++--
R/read_results.R | 14 +-
R/test_functions.R | 2
inst/CITATION | 14 +-
man/ReadPlot_GofPerParticle.Rd | 16 +-
man/ReadPlot_convergence.Rd | 9 +
man/ReadPlot_out.Rd | 13 +-
man/ReadPlot_params.Rd | 16 +-
man/ReadPlot_particles.Rd | 17 +--
man/ReadPlot_results.Rd | 123 +++++++++++++---------
man/hydroPSO-package.Rd | 16 +-
man/hydroPSO.Rd | 18 +++
man/hydroPSO2pest.Rd | 10 -
man/pest2hydroPSO.Rd | 10 -
man/plot_NparOF.Rd | 1
man/plot_ParamsPerIter.Rd | 1
man/read_best.Rd | 16 +-
23 files changed, 463 insertions(+), 203 deletions(-)
Title: non-parametric denoising and clustering method of noisy images
both indexed by time and space
Diff between DynClust versions 2.0 dated 2012-11-15 and 2.2 dated 2012-12-20
Description: Two-stage method for the denoising and clustering of stack
of noisy images acquired over time, based on the simple
assumption that a finite sequence of noisy images both indexed
by time and space is composed of noisy versions of only a
limited amount of dynamic features. The aim of the method is
first to denoise signals using both the spatial and temporal
information contained in the data, and then cluster the
denoised signals depending on their dynamic features. Two
signals are considered to have similar features if their
difference does not significantly deviate from zero. By
comparing difference signals, no assumption is therefore made
on the shape of the theoretical signals. In order for the
method to be applicable to experimental data, the data should
be normally distributed (or at least follow a symmetric
distribution) with a constant variance. Also the number of
observations n must be of the form n=d^2. Moreover, the method
is based on the implicit assumption that, for a given data set,
almost each dynamic feature is present in two or more pixels.
The use of the method can be time-consuming depending on the
size of the data-array (see arguments fp.mask.size, and
fp.nproc of the callDenoiseVoxel function in order to reduce
the computation time).
Author: Tiffany Lieury,Christophe Pouzat, Yves Rozenholc
Maintainer: Tiffany Lieury
DynClust-2.0/DynClust/R/mkFCTdenoiseVoxel.R |only
DynClust-2.0/DynClust/man/mkFCTdenoiseVoxel.Rd |only
DynClust-2.2/DynClust/DESCRIPTION | 10 -
DynClust-2.2/DynClust/MD5 | 38 ++--
DynClust-2.2/DynClust/NAMESPACE | 3
DynClust-2.2/DynClust/R/CheckClusterList.R | 25 +-
DynClust-2.2/DynClust/R/ClusteringFct.R | 79 ++-------
DynClust-2.2/DynClust/R/MultiTestH0.R | 35 +---
DynClust-2.2/DynClust/R/callDenoiseVoxel.R | 190 ++++++++++++++++------
DynClust-2.2/DynClust/R/getClusterCenters.R |only
DynClust-2.2/DynClust/R/getClusterMap.R |only
DynClust-2.2/DynClust/R/getClusteredSet.R |only
DynClust-2.2/DynClust/R/getDenoisedSet.R |only
DynClust-2.2/DynClust/R/mkClusteringInnerFct.R | 35 +---
DynClust-2.2/DynClust/man/CheckClusterList.Rd | 12 -
DynClust-2.2/DynClust/man/ClusteringFct.Rd | 33 +--
DynClust-2.2/DynClust/man/DynClust-package.Rd | 6
DynClust-2.2/DynClust/man/MultiTestH0.Rd | 10 -
DynClust-2.2/DynClust/man/callDenoiseVoxel.Rd | 36 +---
DynClust-2.2/DynClust/man/getClusterCenters.Rd |only
DynClust-2.2/DynClust/man/getClusterMap.Rd |only
DynClust-2.2/DynClust/man/getClusteredSet.Rd |only
DynClust-2.2/DynClust/man/getDenoisedSet.Rd |only
DynClust-2.2/DynClust/man/mkClusteringInnerFct.Rd | 10 -
DynClust-2.2/DynClust/src/MultitestH0_ccall.c | 68 +++----
25 files changed, 315 insertions(+), 275 deletions(-)
Title: Segmentation methods for array CGH analysis
Diff between cghseg versions 1.0.0 dated 2012-11-16 and 1.0.1 dated 2012-12-20
Description: cghseg is an R package dedicated to the analysis of CGH
profiles using segmentation models.
Author: Franck Picard, Mark Hoebeke, Emilie Lebarbier, Vincent Miele,
Guillem Rigaill, Stephane Robin
Maintainer: Franck Picard
DESCRIPTION | 12 ++++-----
MD5 | 30 +++++++++++------------
R/CGHoptions.R | 35 ++++-----------------------
R/ILS.R | 18 +-------------
R/ILSclust.R | 22 ++++-------------
R/cghseg.R | 20 +++++++++++++++
R/getuniKmax.R | 19 +++-----------
R/golden.search.R | 10 ++-----
R/multiseg.R | 24 ------------------
R/multisegclust.R | 31 +++++++-----------------
R/multisegmean.R | 49 +++++++++++---------------------------
R/multisegmixt.R | 40 +++++++------------------------
R/unisegclust.R | 25 ++++++++++++++-----
man/CGHoptions-class.Rd | 2 -
src/Rwrappers.cc | 61 ++++++++++++++++++++++++++++++++++++++++++++++++
src/Rwrappers.h | 1
16 files changed, 176 insertions(+), 223 deletions(-)
Title: R object-oriented programming with or without references
Diff between R.oo versions 1.10.1 dated 2012-10-24 and 1.11.4 dated 2012-12-20
Description: Methods and classes for object-oriented programming in R
with or without references. Large effort has been made on
making definition of methods as simple as possible with a
minimum of maintenance for package developers. The package has
been developed since 2001 and is now considered very stable.
This is a cross-platform package implemented in pure R that
defines standard S3 classes without any tricks.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 14 -
MD5 | 54 ++--
NAMESPACE | 218 +++++++++++++++-
R/006.fixVarArgs.R | 1
R/030.ObjectClassFunctions.R | 37 ++
R/050.Object.R | 135 +++++++---
R/060.Class.R | 400 +++++++++++++++++++-----------
R/999.DEPRECATED.R |only
R/999.NonDocumentedObjects.R | 1
R/BasicObject.R | 40 +--
R/Exception.R | 1
R/InternalErrorException.R | 6
R/Package.R | 46 +++
R/RccViolationException.R | 4
R/extend.default.R | 1
R/findS3Method.R |only
R/getClassByName.R |only
R/zzz.R | 43 +--
incl/Package.Rex | 10
inst/NEWS | 41 +++
man/Non-documented_objects.Rd | 1
man/Package.Rd | 11
man/RccViolationException.Rd | 2
man/as.character.RccViolationException.Rd | 2
man/extend.BasicObject.Rd | 1
man/extend.Object.Rd | 1
man/extend.Rd | 1
man/getMethods.Class.Rd | 4
man/getRccUrl.RccViolationException.Rd | 2
man/startupMessage.Package.Rd |only
30 files changed, 787 insertions(+), 290 deletions(-)
Title: PC-Axis with R
Diff between pxR versions 0.27 dated 2012-02-19 and 0.28 dated 2012-12-20
Description: The pxR package provides a set of functions for reading
and writing PC-Axis files, used by different statistical
organizations around the globe for data dissemination.
Author: Francisco J. Viciana [aut], Carlos J. Gil Bellosta [cre, aut],
Oscar Perpinan Lamigueiro [aut], Emilio Torres Manzanera [ctb],
Vicente David Canto Casasola [ctb], Jorge Ivan Velez [ctb]
Maintainer: Carlos J. Gil Bellosta
DESCRIPTION | 24 ++++++++++++------------
MD5 | 8 ++++----
R/as.data.frame.px.R | 41 ++++++++++++++++++++++++++++++++++-------
R/read.px.R | 7 +++++++
man/as.data.frame.px.Rd | 7 ++++++-
5 files changed, 63 insertions(+), 24 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Diff between pbdSLAP versions 0.1-1 dated 2012-11-30 and 0.1-2 dated 2012-12-20
Description: pbdSLAP utilizes scalable linear algebra packages mainly
including BLACS, PBLAS, and ScaLAPACK in double precision via
pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre], Drew Schmidt [aut], George Ostrouchov
[aut], Pragneshkumar Patel [aut], ScaLAPACK [ctb]
Maintainer: Wei-Chen Chen
ChangeLog | 4 +++
DESCRIPTION | 13 +++++++-----
MD5 | 26 ++++++++++++------------
cleanup | 5 ++--
configure | 16 ++++++++++++++
configure.ac | 17 +++++++++++++++
inst/CITATION | 4 +--
inst/doc/pbdSLAP-guide.Rnw | 3 ++
inst/doc/pbdSLAP-guide.pdf |binary
inst/doc/pbdSLAP-include/01-acknowledgement.tex | 4 +--
inst/doc/pbdSLAP-include/01-copyright.tex |only
inst/doc/pbdSLAP-include/01-introduction.tex | 2 -
src/Makevars.in | 17 ++++-----------
src/Makevars.win | 17 +++++----------
src/install.libs.R |only
15 files changed, 81 insertions(+), 47 deletions(-)
Title: Hierarchical Bayesian Analysis of Recognition Memory
Diff between hbmem versions 0.2 dated 2010-01-21 and 0.3 dated 2012-12-20
Description: Contains functions for fitting hierarchical versions of
EVSD, UVSD, DPSD, DPSD with d' restricted to be positive, and
our gamma signal detection model to recognition memory
confidence-ratings data.
Author: Michael S. Pratte
Maintainer: Mike
DESCRIPTION | 13
MD5 |only
NAMESPACE |only
R/dpsd.R | 103
R/dpsd2.R | 6
R/dpsdFull.R | 3
R/dpsdPos.R | 202
R/dpsdRN.R | 3
R/dpsdRest.R | 4
R/gamma.R | 3
R/normal.R | 110
R/uvsd.R | 3
data/sd10.txt |only
data/sd13.txt |only
data/sd2.txt |only
data/sd6.txt |43841 +++++++++++++++++++++++---------------------------
man/dpsdFullSample.Rd | 2
man/dpsdLogLike.Rd | 5
man/dpsdPosLogLike.Rd | 36
man/dpsdPosSim.Rd | 36
man/dpsdRNSample.Rd | 2
man/dpsdSample.Rd | 4
man/dpsdSim.Rd | 6
man/gammaSample.Rd | 4
man/getPred.Rd | 1
man/hbmem-package.Rd | 16
man/ld.alpha.Rd | 3
man/ld.beta.Rd | 3
man/ld.mu.Rd | 3
man/ld.theta.Rd | 3
man/nplike.Rd | 3
man/sampleGamma.Rd | 4
man/sampleNorm.Rd | 10
man/sampleNormR.Rd | 2
man/sampleNormb.Rd | 6
man/samplePosNorm.Rd | 49
man/sampleSig2.Rd | 2
man/sd10.Rd |only
man/sd13.Rd |only
man/sd2.Rd |only
man/uvsdSample.Rd | 4
src/dpsd.c | 64
src/normal.c | 2
src/uvsd.c | 2
44 files changed, 21121 insertions(+), 23442 deletions(-)
Title: Graphical User Interface for bayesTFR, bayesLife and bayesPop
Diff between bayesDem versions 1.7-0 dated 2012-06-07 and 2.1-1 dated 2012-12-20
Description: Provides Graphical user interface for the packages
bayesTFR, bayesLife and bayesPop
Author: Hana Sevcikova
Maintainer: Hana Sevcikova
ChangeLog | 20 +
DESCRIPTION | 12
MD5 | 39 +-
R/LifePred.R | 10
R/PopPred.R | 6
R/TFRpred.R | 29 -
R/bayesDem.R | 17
R/bayesDem_ini.R | 35 +
R/e0-cont-mcmc.R | 79 ++--
R/e0-mcmc.R | 222 +++++-------
R/e0-predict.R | 171 ++++-----
R/e0-results.R | 363 ++++++++-----------
R/handlers_and_fncs.R | 96 ++++-
R/pop-predict.R | 304 ++++++++++++----
R/pop-results.R | 430 +++++++++++++++--------
R/tfr-cont-mcmc.R | 66 +--
R/tfr-mcmc.R | 408 ++++++++++++----------
R/tfr-predict.R | 229 +++++++-----
R/tfr-results.R | 794 +++++++++++++++++++++++--------------------
inst/images/startpyramid.png |only
man/bayesDem-package.Rd | 6
21 files changed, 1947 insertions(+), 1389 deletions(-)
Title: An R Package to Estimate Box-Cox Power Transformation Parameter
Diff between AID versions 1.0 dated 2012-12-04 and 1.1 dated 2012-12-20
Description: Includes a function to estimate the power transformation
parameter and some datasets
Author: Osman Dag, Ozgur Asar, Ozlem Ilk
Maintainer: Osman Dag
DESCRIPTION | 6 +++---
MD5 | 6 +++---
man/AID.Rd | 2 +-
man/boxcoxnc.Rd | 8 +++++---
4 files changed, 12 insertions(+), 10 deletions(-)