Tue, 09 Sep 2014

Package zCompositions updated to version 1.0.2 with previous version 1.0.1 dated 2014-06-03

Title: Imputation of Zeros and Nondetects in Compositional Data Sets
Description: Principled methods to impute multivariate left-censored data and zeros in compositional data sets
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo

Diff between zCompositions versions 1.0.1 dated 2014-06-03 and 1.0.2 dated 2014-09-09

 DESCRIPTION                  |   12 -
 MD5                          |   38 ++--
 NEWS                         |   21 ++
 R/lrDA.R                     |  115 +++++++++-----
 R/lrEM.R                     |  342 ++++++++++++++++++++++---------------------
 R/multKM.R                   |only
 R/multLN.R                   |   39 +++-
 R/multRepl.R                 |   14 +
 R/splineKM.R                 |only
 data/Water.rda               |only
 data/mdl.rda                 |only
 man/LPdata.Rd                |    4 
 man/Pigs.Rd                  |    2 
 man/Water.Rd                 |only
 man/cmultRepl.Rd             |    8 -
 man/lrDA.Rd                  |   45 +++--
 man/lrEM.Rd                  |   53 +++++-
 man/mdl.Rd                   |only
 man/multKM.Rd                |only
 man/multLN.Rd                |   35 +++-
 man/multRepl.Rd              |   34 +++-
 man/splineKM.Rd              |only
 man/zCompositions-package.Rd |   20 +-
 man/zPatterns.Rd             |    3 
 24 files changed, 488 insertions(+), 297 deletions(-)

More information about zCompositions at CRAN
Permanent link

New package vcrpart with initial version 0.2-1
Package: vcrpart
Type: Package
Title: Tree-Based Varying Coefficient Regression for Generalized Linear and Ordinal Mixed Models
Version: 0.2-1
Date: 2014-09-10
Authors@R: c( person("Reto", "Buergin", role = c("aut", "cre", "cph"), email = "rbuergin@gmx.ch"), person("Gilbert", "Ritschard", role = c("ctb", "ths"), email = "gilbert.ritschard@unige.ch"))
Maintainer: Reto Buergin
Description: Recursive partitioning algorithm for varying coefficient generalized linear models and ordinal 2-stage linear mixed models. Special features are coefficient-wise partitioning, non-varying coefficients and partitioning of time-varying variables in longitudinal ordinal regression.
License: GPL (>= 2)
Depends: R (>= 3.1.0), parallel, partykit
Imports: stats, grid, graphics, methods, nlme, rpart, numDeriv, ucminf, zoo, sandwich, strucchange
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2014-09-09 22:27:25 UTC; rbuergin
Author: Reto Buergin [aut, cre, cph], Gilbert Ritschard [ctb, ths]
Repository: CRAN
Date/Publication: 2014-09-10 00:51:30

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Package spaMM updated to version 1.3.0 with previous version 1.2.0 dated 2014-06-25

Title: Mixed Models, Particularly Spatial GLMMs
Description: Implements a collection of functions for inference in mixed models. It was developed in particular for GLMMs with spatial correlations, but also fits models with non-Gaussian random effects (e.g., Beta Binomial, or negative-binomial mixed models). Heteroskedasticity can further be fitted by a linear model. The algorithms are currently various Laplace approximations methods for ML or REML, in particular h-likelihood and penalized-likelihood methods.
Author: François Rousset [aut, cre, cph], Jean-Baptiste Ferdy [aut, cph]
Maintainer: François Rousset

Diff between spaMM versions 1.2.0 dated 2014-06-25 and 1.3.0 dated 2014-09-09

 spaMM-1.2.0/spaMM/R/LR.HL.R                    |only
 spaMM-1.2.0/spaMM/R/checkLink.R                |only
 spaMM-1.2.0/spaMM/R/checkLinkS.R               |only
 spaMM-1.2.0/spaMM/R/rtnorm.copy.R              |only
 spaMM-1.2.0/spaMM/R/validRows.R                |only
 spaMM-1.3.0/spaMM/DESCRIPTION                  |   18 -
 spaMM-1.3.0/spaMM/MD5                          |  147 ++++----
 spaMM-1.3.0/spaMM/NAMESPACE                    |   33 +
 spaMM-1.3.0/spaMM/R/CondNormfn.R               |    4 
 spaMM-1.3.0/spaMM/R/GammaForDispGammaGLM.R     |    2 
 spaMM-1.3.0/spaMM/R/HLCor.R                    |   86 +----
 spaMM-1.3.0/spaMM/R/HLCor.obj.R                |   12 
 spaMM-1.3.0/spaMM/R/HLfit.R                    |  416 +++++++++++++++----------
 spaMM-1.3.0/spaMM/R/HLframes.R                 |    2 
 spaMM-1.3.0/spaMM/R/LRT.R                      |only
 spaMM-1.3.0/spaMM/R/Predictor.R                |    4 
 spaMM-1.3.0/spaMM/R/alternating.R              |    8 
 spaMM-1.3.0/spaMM/R/anova.HLfit.R              |only
 spaMM-1.3.0/spaMM/R/as.blockDiag.bar.R         |    4 
 spaMM-1.3.0/spaMM/R/as.blockDiag.formula.R     |    6 
 spaMM-1.3.0/spaMM/R/binomialize.R              |   13 
 spaMM-1.3.0/spaMM/R/calc.tXinvS.R              |    2 
 spaMM-1.3.0/spaMM/R/calcPredVar.R              |   43 +-
 spaMM-1.3.0/spaMM/R/checkRandLink.R            |only
 spaMM-1.3.0/spaMM/R/checkRandLinkS.R           |only
 spaMM-1.3.0/spaMM/R/checkRespFam.R             |only
 spaMM-1.3.0/spaMM/R/compare.model.structures.R |only
 spaMM-1.3.0/spaMM/R/compute.ZALlist.R          |   94 ++---
 spaMM-1.3.0/spaMM/R/confint.HLfit.R            |only
 spaMM-1.3.0/spaMM/R/corrHLfit.R                |  327 +++++++++----------
 spaMM-1.3.0/spaMM/R/corrMM.LRT.R               |   17 -
 spaMM-1.3.0/spaMM/R/dispGammaGLM.R             |   31 +
 spaMM-1.3.0/spaMM/R/eval.update.call.R         |only
 spaMM-1.3.0/spaMM/R/filled.mapMM.R             |   16 
 spaMM-1.3.0/spaMM/R/fitted.HLfit.R             |only
 spaMM-1.3.0/spaMM/R/fixef.HLfit.R              |only
 spaMM-1.3.0/spaMM/R/getCallHL.R                |only
 spaMM-1.3.0/spaMM/R/getHLfit.R                 |only
 spaMM-1.3.0/spaMM/R/getProcessed.R             |only
 spaMM-1.3.0/spaMM/R/locoptim.R                 |  193 ++++++-----
 spaMM-1.3.0/spaMM/R/locoptimthroughSmooth.R    |   57 ++-
 spaMM-1.3.0/spaMM/R/makeCovEst.R               |   41 +-
 spaMM-1.3.0/spaMM/R/makeLowerUpper.R           |only
 spaMM-1.3.0/spaMM/R/mapMM.R                    |    9 
 spaMM-1.3.0/spaMM/R/muetafn.R                  |    2 
 spaMM-1.3.0/spaMM/R/newetaFix.R                |   12 
 spaMM-1.3.0/spaMM/R/predict.HLfit.R            |  129 ++++---
 spaMM-1.3.0/spaMM/R/predictionCoeffs.R         |only
 spaMM-1.3.0/spaMM/R/preprocess.R               |  132 ++++---
 spaMM-1.3.0/spaMM/R/print.arglist.R            |    2 
 spaMM-1.3.0/spaMM/R/ranef.HLfit.R              |only
 spaMM-1.3.0/spaMM/R/sampleGridFromLowUp.R      |   60 +--
 spaMM-1.3.0/spaMM/R/sampleNextPoints.R         |   22 -
 spaMM-1.3.0/spaMM/R/setProcessed.R             |only
 spaMM-1.3.0/spaMM/R/simulate.HLfit.R           |    7 
 spaMM-1.3.0/spaMM/R/solveCov.R                 |only
 spaMM-1.3.0/spaMM/R/spMMFactorList.R           |  174 +++++-----
 spaMM-1.3.0/spaMM/R/spMMexpandSlash.R          |   28 +
 spaMM-1.3.0/spaMM/R/spaMM-internal.R           |  261 +++++++--------
 spaMM-1.3.0/spaMM/R/spaMMLRT.R                 |   43 +-
 spaMM-1.3.0/spaMM/R/summary.HLfit.R            |   76 ++--
 spaMM-1.3.0/spaMM/R/summary.fixedLRT.R         |   33 +
 spaMM-1.3.0/spaMM/R/toCanonical.R              |only
 spaMM-1.3.0/spaMM/R/update.HLfit.R             |    2 
 spaMM-1.3.0/spaMM/R/validData.R                |only
 spaMM-1.3.0/spaMM/R/z%id_id%.R                 |only
 spaMM-1.3.0/spaMM/man/HLCor.Rd                 |   21 -
 spaMM-1.3.0/spaMM/man/HLfit.Rd                 |   26 +
 spaMM-1.3.0/spaMM/man/Loaloa.Rd                |   10 
 spaMM-1.3.0/spaMM/man/anova.HLfit.Rd           |only
 spaMM-1.3.0/spaMM/man/arabidopsis.Rd           |    4 
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 spaMM-1.3.0/spaMM/man/corMatern.Rd             |   15 
 spaMM-1.3.0/spaMM/man/corrHLfit.Rd             |    7 
 spaMM-1.3.0/spaMM/man/designL.from.Corr.Rd     |    4 
 spaMM-1.3.0/spaMM/man/extractors.Rd            |only
 spaMM-1.3.0/spaMM/man/fixed.LRT.Rd             |   37 +-
 spaMM-1.3.0/spaMM/man/mapMM.Rd                 |   24 -
 spaMM-1.3.0/spaMM/man/multinomial.Rd           |    2 
 spaMM-1.3.0/spaMM/man/options.Rd               |    4 
 spaMM-1.3.0/spaMM/man/plot.HL.Rd               |    4 
 spaMM-1.3.0/spaMM/man/predict.Rd               |   22 -
 spaMM-1.3.0/spaMM/man/salamander.Rd            |    2 
 spaMM-1.3.0/spaMM/man/seaMask.Rd               |   19 -
 spaMM-1.3.0/spaMM/man/simulate.HLCor.Rd        |    2 
 spaMM-1.3.0/spaMM/man/spaMM-internal.Rd        |   20 -
 spaMM-1.3.0/spaMM/man/spaMM.Rd                 |   24 -
 spaMM-1.3.0/spaMM/man/spaMM.filled.contour.Rd  |    4 
 spaMM-1.3.0/spaMM/src/spaMM_linear.cpp         |    2 
 89 files changed, 1578 insertions(+), 1243 deletions(-)

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Package paleobioDB updated to version 0.2 with previous version 0.1 dated 2014-05-01

Title: paleobioDB: a package for downloading, visualizing and processing data from Paleobiology Database.
Description: paleobioDB version 0.2 has 19 functions to wrap each endpoint of the PaleobioDB API, plus 8 functions to visualize and process the fossil data. The API documentation for the Paleobiology Database can be found in .
Author: Sara Varela [aut, cre], Javier González Hernández [aut], Luciano Fabris Sgarbi [aut]
Maintainer: Sara Varela

Diff between paleobioDB versions 0.1 dated 2014-05-01 and 0.2 dated 2014-09-09

 DESCRIPTION                     |   11 +
 MD5                             |   72 ++++++------
 NAMESPACE                       |    4 
 R/paleobioDB-package.R          |   29 ++--
 R/pbdb_geographic_functions.R   |   17 +-
 R/pbdb_querys.R                 |   11 -
 R/pbdb_taxonomic_functions.R    |    4 
 R/pbdb_temporal_functions.R     |   53 ++++----
 README.md                       |  236 +++++++++++++++++++++++++++++++++-------
 man/paleobioDB.Rd               |   84 +++++++-------
 man/pbdb_collection.Rd          |   24 ++--
 man/pbdb_collections.Rd         |    9 -
 man/pbdb_collections_geo.Rd     |   22 ++-
 man/pbdb_interval.Rd            |   23 +--
 man/pbdb_intervals.Rd           |   28 ++--
 man/pbdb_map.Rd                 |   39 ++----
 man/pbdb_map_occur.Rd           |   46 ++-----
 man/pbdb_map_richness.Rd        |   53 +++-----
 man/pbdb_occurrence.Rd          |   24 ++--
 man/pbdb_occurrences.Rd         |   71 ++++++------
 man/pbdb_orig_ext.Rd            |   35 ++---
 man/pbdb_ref_collections.Rd     |   32 ++---
 man/pbdb_ref_occurrences.Rd     |   35 +++--
 man/pbdb_ref_taxa.Rd            |   47 +++----
 man/pbdb_reference.Rd           |   20 +--
 man/pbdb_references.Rd          |   29 ++--
 man/pbdb_richness.Rd            |   30 ++---
 man/pbdb_scale.Rd               |   16 +-
 man/pbdb_scales.Rd              |   14 +-
 man/pbdb_strata.Rd              |   52 ++++----
 man/pbdb_strata_auto.Rd         |   52 +++-----
 man/pbdb_subtaxa.Rd             |   22 +--
 man/pbdb_taxa.Rd                |   56 +++++----
 man/pbdb_taxa_auto.Rd           |   21 +--
 man/pbdb_taxon.Rd               |   13 +-
 man/pbdb_temp_range.Rd          |   29 ++--
 man/pbdb_temporal_resolution.Rd |   15 +-
 37 files changed, 745 insertions(+), 633 deletions(-)

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Package mnlogit updated to version 1.2.0 with previous version 1.1.1 dated 2014-04-10

Title: Multinomial Logit Model
Description: Time and memory efficient estimation of multinomial logit models using maximum likelihood method. Numerical optimization performed by Newton-Raphson method using an optimized, parallel C++ library to achieve fast computation of Hessian matrices. Motivated by large scale multiclass classification problems in econometrics and machine learning.
Author: Asad Hasan, Wang Zhiyu, Alireza S. Mahani
Maintainer: Asad Hasan

Diff between mnlogit versions 1.1.1 dated 2014-04-10 and 1.2.0 dated 2014-09-09

 ChangeLog                     |   30 +++
 DESCRIPTION                   |   14 -
 MD5                           |   33 ++-
 NAMESPACE                     |   46 ++++-
 R/formula.R                   |   82 ++++-----
 R/hyptests.R                  |only
 R/likelihood.R                |   17 -
 R/mnlogit.R                   |  163 +++++++++++--------
 R/mnlogit.methods.R           |  203 ++++++++++++++++-------
 R/newton.R                    |   72 ++++----
 R/predict.R                   |   31 ++-
 R/zzz.R                       |    4 
 build/vignette.rds            |binary
 inst/doc/mnlogit_tests.R      |only
 man/hyptests.Rd               |only
 man/mnlogit.Rd                |  109 ++++++++----
 vignettes/fig1_Code.R         |only
 vignettes/mnlogit.Rnw         |  358 +++++++++++++++++++++---------------------
 vignettes/simChoiceModel.R    |    5 
 vignettes/tests_sample_output |only
 20 files changed, 686 insertions(+), 481 deletions(-)

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New package eegkitdata with initial version 1.0
Package: eegkitdata
Type: Package
Title: Data for package eegkit
Version: 1.0
Date: 2014-09-09
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
Description: Contains the example EEG data used in the package eegkit. Also contains code for easily creating larger EEG datasets from the EEG Database on the UCI Machine Learning Repository.
License: GPL (>= 2)
Packaged: 2014-09-09 17:33:17 UTC; Nate
Depends: R (>= 2.10)
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 00:27:03

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New package eegkit with initial version 1.0-0
Package: eegkit
Type: Package
Title: Toolkit for electroencephalography data
Version: 1.0-0
Date: 2014-09-09
Author: Nathaniel E. Helwig
Maintainer: Nathaniel E. Helwig
Depends: R (>= 3.1.1), bigsplines, eegkitdata, ica, rgl
Description: Analysis and visualization tools for electroencephalography (EEG) data. Includes functions for plotting (a) EEG caps, (b) single- and multi-channel EEG time courses, and (c) EEG spatial maps. Also includes smoothing and Independent Component Analysis functions for EEG data analysis.
License: GPL (>= 2)
Packaged: 2014-09-09 17:42:07 UTC; Nate
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 00:55:52

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New package cmvnorm with initial version 1.0
Package: cmvnorm
Type: Package
Title: Complex multivariate Gaussian distribution
Version: 1.0
Date: 2014-01-10
Author: Robin K. S. Hankin
Depends: emulator (>= 1.2-15)
Imports: elliptic
Maintainer: Robin K. S. Hankin
Description: various utilities for the complex multivariate Gaussian distribution
VignetteBuilder: elliptic, emulator
License: GPL-2
Packaged: 2014-09-09 20:37:37 UTC; rhankin
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-10 00:24:00

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Package taxize updated to version 0.4.0 with previous version 0.3.0 dated 2014-05-20

Title: Taxonomic information from around the web.
Description: Taxonomic information from around the web. This package interacts with a suite of web APIs for taxonomic tasks, such as verifying species names, getting taxonomic hierarchies, and verifying name spelling.
Author: Scott Chamberlain [aut, cre], Eduard Szoecs [aut], Carl Boettiger [aut], Karthik Ram [aut], Ignasi Bartomeus [aut], John Baumgartner [aut]
Maintainer: Scott Chamberlain

Diff between taxize versions 0.3.0 dated 2014-05-20 and 0.4.0 dated 2014-09-09

 DESCRIPTION                                |   16 
 MD5                                        |  499 ++++++++++++++---------------
 NAMESPACE                                  |   15 
 NEWS                                       |   30 +
 R/apg_lookup.R                             |    2 
 R/bold_search.R                            |only
 R/children.R                               |only
 R/class2tree.R                             |    2 
 R/classification.R                         |    4 
 R/col_children.R                           |    2 
 R/col_downstream.R                         |    2 
 R/col_search.R                             |    2 
 R/comm2sci.R                               |    8 
 R/deprecated.R                             |    6 
 R/downstream.R                             |    2 
 R/eol_dataobjects.R                        |   25 -
 R/eol_invasive.R                           |  107 +++---
 R/eol_pages.R                              |   10 
 R/eol_ping.R                               |    2 
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 R/get_boldid.R                             |only
 R/get_colid.R                              |    2 
 R/get_eolid.R                              |    2 
 R/get_gbifid.R                             |    2 
 R/get_ids.R                                |   53 +--
 R/get_tpsid.R                              |    2 
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 R/get_uid.R                                |    2 
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 R/gni_details.R                            |   10 
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 R/gnr_datasources.R                        |   10 
 R/gnr_resolve.R                            |   16 
 R/iplant_resolve.R                         |   16 
 R/ipni_search.R                            |    2 
 R/itis.R                                   |  106 +++---
 R/itis_acceptname.R                        |    2 
 R/itis_downstream.R                        |    2 
 R/itis_getrecord.R                         |    2 
 R/itis_hierarchy.R                         |    2 
 R/itis_kingdomnames.R                      |    2 
 R/itis_lsid.R                              |    2 
 R/itis_name.R                              |    2 
 R/itis_native.R                            |    2 
 R/itis_ping.R                              |    2 
 R/itis_refs.R                              |    4 
 R/itis_taxrank.R                           |    2 
 R/itis_terms.R                             |    2 
 R/iucn_getname.R                           |    2 
 R/iucn_summary.R                           |    4 
 R/ncbi_getbyid.R                           |   10 
 R/ncbi_getbyname.R                         |   12 
 R/ncbi_search.R                            |    8 
 R/phylomatic_format.R                      |    2 
 R/phylomatic_tree.R                        |   23 +
 R/phylomatic_tree2.R                       |    2 
 R/plantminer.R                             |    2 
 R/resolve.R                                |   57 +--
 R/sci2comm.R                               |   42 +-
 R/scrapenames.r                            |   28 -
 R/synonyms.R                               |   76 +++-
 R/tax_agg.R                                |    5 
 R/tax_name.R                               |    2 
 R/tax_rank.R                               |    2 
 R/taxize-package.R                         |   66 ++-
 R/taxize_cite.R                            |only
 R/tnrs.R                                   |  160 +++++----
 R/tnrs_sources.r                           |   16 
 R/tp_accnames.R                            |    6 
 R/tp_dist.R                                |    7 
 R/tp_refs.R                                |    9 
 R/tp_search.R                              |    7 
 R/tp_summary.R                             |    7 
 R/tp_synonyms.R                            |    9 
 R/tpl_families.r                           |    5 
 R/tpl_get.r                                |    6 
 R/ubio_classification.R                    |   10 
 R/ubio_classification_search.R             |    2 
 R/ubio_id.R                                |    2 
 R/ubio_search.R                            |    2 
 R/ubio_synonyms.R                          |    2 
 R/vascan_search.r                          |   35 +-
 R/zzz.R                                    |    6 
 README.md                                  |  257 +++++++++-----
 build/vignette.rds                         |binary
 inst/doc/taxize_vignette.Rmd               |   26 -
 inst/doc/taxize_vignette.html              |   26 -
 inst/ignore/rbladj.r                       |    2 
 inst/ignore/try_with_timeout.R             |    2 
 inst/vign/taxize_vignette.md               |   26 -
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 man/classification.Rd                      |    4 
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 man/col_search.Rd                          |    4 
 man/comm2sci.Rd                            |    4 
 man/downstream.Rd                          |    4 
 man/eol_dataobjects.Rd                     |    8 
 man/eol_hierarchy-deprecated.Rd            |    4 
 man/eol_invasive.Rd                        |   66 ++-
 man/eol_pages.Rd                           |    6 
 man/eol_ping.Rd                            |    4 
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 man/gbif_name_usage.Rd                     |    2 
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 man/get_colid.Rd                           |    4 
 man/get_eolid.Rd                           |    4 
 man/get_gbifid.Rd                          |    4 
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 man/get_genes_avail-deprecated.Rd          |    2 
 man/get_ids.Rd                             |   21 -
 man/get_seqs-deprecated.Rd                 |    2 
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 man/get_uid.Rd                             |    4 
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 man/getcommonnamesfromtsn.Rd               |    4 
 man/getcoremetadatafromtsn.Rd              |    4 
 man/getcoveragefromtsn.Rd                  |    4 
 man/getcredibilityratingfromtsn.Rd         |    4 
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 man/getcurrencyfromtsn.Rd                  |    4 
 man/getdatedatafromtsn.Rd                  |    4 
 man/getdescription.Rd                      |    4 
 man/getexpertsfromtsn.Rd                   |    4 
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 man/getfullrecordfromlsid.Rd               |    4 
 man/getfullrecordfromtsn.Rd                |    4 
 man/getgeographicdivisionsfromtsn.Rd       |    4 
 man/getgeographicvalues.Rd                 |    4 
 man/getglobalspeciescompletenessfromtsn.Rd |    4 
 man/gethierarchydownfromtsn.Rd             |    4 
 man/gethierarchyupfromtsn.Rd               |    4 
 man/getitisterms.Rd                        |    4 
 man/getitistermsfromcommonname.Rd          |    4 
 man/getitistermsfromscientificname.Rd      |    4 
 man/getjurisdictionaloriginfromtsn.Rd      |    4 
 man/getjurisdictionoriginvalues.Rd         |    4 
 man/getjurisdictionvalues.Rd               |    4 
 man/getkey.Rd                              |    4 
 man/getkingdomnamefromtsn.Rd               |    4 
 man/getkingdomnames.Rd                     |    4 
 man/getlastchangedate.Rd                   |    4 
 man/getlsidfromtsn.Rd                      |    4 
 man/getothersourcesfromtsn.Rd              |    4 
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Permanent link

Package ngspatial updated to version 1.0-4 with previous version 1.0-3 dated 2013-12-07

Title: Fitting the centered autologistic and sparse spatial generalized linear mixed models for areal data
Description: ngspatial provides tools for analyzing spatial data, especially non-Gaussian areal data. The current version supports the sparse spatial generalized linear mixed model of Hughes and Haran (2013) and the centered autologistic model of Caragea and Kaiser (2009).
Author: John Hughes and Xiaohui Cui
Maintainer: John Hughes

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Permanent link

Package fpc updated to version 2.1-8 with previous version 2.1-7 dated 2014-01-29

Title: Flexible procedures for clustering
Description: Various methods for clustering and cluster validation. Fixed point clustering. Linear regression clustering. Clustering by merging Gaussian mixture components. Symmetric and asymmetric discriminant projections for visualisation of the separation of groupings. Cluster validation statistics for distance based clustering including corrected Rand index. Cluster-wise cluster stability assessment. Methods for estimation of the number of clusters: Calinski-Harabasz, Tibshirani and Walther's prediction strength, Fang and Wang's bootstrap stability. Gaussian/multinomial mixture fitting for mixed continuous/categorical variables. Variable-wise statistics for cluster interpretation. DBSCAN clustering. Interface functions for many clustering methods implemented in R, including estimating the number of clusters with kmeans, pam and clara. Modality diagnosis for Gaussian mixtures. For an overview see package?fpc.
Author: Christian Hennig
Maintainer: Christian Hennig

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Permanent link

Package bpkde updated to version 1.0-7 with previous version 1.0-4 dated 2014-05-27

Title: Back-Projected Kernel Density Estimation
Description: Nonparametric multivariate kernel density \ estimation using a back-projected kernel.
Author: Kjell Konis , Victor M. Panaretos .
Maintainer: Kjell Konis

Diff between bpkde versions 1.0-4 dated 2014-05-27 and 1.0-7 dated 2014-09-09

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Package investr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-14

Title: Inverse estimation/calibration functions
Description: This package provides functions to facilitate inverse estimation/calibration in linear, nonlinear, and (linear) mixed models. A generic function is also provided for plotting fitted regression models with or without confidence/prediction bands that may be of use to the general user.
Author: Brandon M. Greenwell
Maintainer: Brandon M. Greenwell

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More information about investr at CRAN
Permanent link

Package PReMiuM updated to version 3.0.29 with previous version 3.0.28 dated 2014-06-30

Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Dirichlet process Bayesian clustering, also known as profile regression.
Author: David I. Hastie , Silvia Liverani , Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi, Sylvia Richardson
Maintainer: Silvia Liverani

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Package TripleR updated to version 1.4 with previous version 1.2.1 dated 2013-10-02

Title: Social Relation Model (SRM) analyses for single or multiple round-robin groups
Description: Social Relation Model (SRM) analyses for single or multiple round-robin groups are performed. These analyses are either based on one manifest variable, one latent construct measured by two manifest variables, two manifest variables and their bivariate relations, or two latent constructs each measured by two manifest variables. Within-group t-tests for variance components and covariances are provided for single groups, between-groups t-tests for multiple groups. Handling for missing values is provided.
Author: F. D. Schönbrodt, M. D. Back, S. C. Schmukle
Maintainer: Felix Schönbrodt

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Package spam updated to version 1.0-1 with previous version 0.41-0 dated 2014-02-26

Title: SPArse Matrix
Description: Set of functions for sparse matrix algebra. Differences with SparseM/Matrix are: (1) we only support (essentially) one sparse matrix format, (2) based on transparent and simple structure(s), (3) tailored for MCMC calculations within GMRF. (4) S3 and S4 like-"compatible" ... and it is fast.
Author: Reinhard Furrer [aut, cre], Florian Gerber [ctb]
Maintainer: Reinhard Furrer

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New package micropan with initial version 1.0
Package: micropan
Type: Package
Title: Microbial Pan-genome Analysis
Version: 1.0
Date: 2014-09-03
Author: Lars Snipen and Kristian Hovde Liland
Maintainer: Lars Snipen
Description: A collection of functions for computations and visualizations of microbial pan-genomes.
Depends: R (>= 2.15.0), igraph
License: GPL-2
LazyData: FALSE
ZipData: TRUE
Packaged: 2014-09-09 09:30:39 UTC; larssn
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-09 14:18:33

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Package hypergea updated to version 1.2.1 with previous version 1.0.1 dated 2014-07-10

Title: Hypergeometric tests
Description: Package to perform (exact) hypergeometric tests on IxJ and 2x2x2 contingency tables using parallelised C code
Author: Markus Boenn
Maintainer: Markus Boenn

Diff between hypergea versions 1.0.1 dated 2014-07-10 and 1.2.1 dated 2014-09-09

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Package globalOptTests updated to version 1.1 with previous version 1.0 dated 2013-08-20

Title: Objective functions for benchmarking the performance of global optimization algorithms
Description: This package makes available 50 objective functions for benchmarking the performance of global optimization algorithms
Author: Katharine Mullen
Maintainer: Katharine Mullen

Diff between globalOptTests versions 1.0 dated 2013-08-20 and 1.1 dated 2014-09-09

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Package fcros updated to version 1.2 with previous version 1.1 dated 2014-01-20

Title: FCROS for detecting differentially expressed genes
Description: A fold change ranks ordering statistics based method for detecting differentially expressed genes. The variation in levels of fold change or ratios calculated using biological conditions is used to associate statistic to genes.
Author: Doulaye Dembele
Maintainer: Doulaye Dembele

Diff between fcros versions 1.1 dated 2014-01-20 and 1.2 dated 2014-09-09

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Package domino updated to version 0.2-1 with previous version 0.1-7 dated 2014-05-07

Title: Domino Data Lab R console bindings
Description: The Domino R package is a wrapper on top of the Domino command-line client. It lets you run Domino commands (e.g., "run", "upload", "download") directly from your R environment. Under the hood, it uses R's system function to run the Domino executable, which must be installed as a prerequisite.
Author: Jacek Glodek
Maintainer: Nick Elprin

Diff between domino versions 0.1-7 dated 2014-05-07 and 0.2-1 dated 2014-09-09

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Package CircE updated to version 1.1 with previous version 1.0 dated 2014-04-11

Title: Circumplex models Estimation
Description: This package contains functions for fitting circumplex structural models for correlation matrices (with negative correlation) by the method of maximum likelihood.
Author: Michele Grassi
Maintainer: Michele Grassi

Diff between CircE versions 1.0 dated 2014-04-11 and 1.1 dated 2014-09-09

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Package geosphere updated to version 1.3-11 with previous version 1.3-8 dated 2014-01-20

Title: Spherical Trigonometry
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans [cre, aut], Ed Williams [ctb], Chris Vennes [ctb]
Maintainer: Robert J. Hijmans

Diff between geosphere versions 1.3-8 dated 2014-01-20 and 1.3-11 dated 2014-09-09

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Package MarkedPointProcess updated to version 0.2.22 with previous version 0.2.21 dated 2013-12-05

Title: Analysis of Marks of Marked Point Processes
Description: Non-parametric Analysis of the Marks of Marked Point Processes
Author: Martin Schlather
Maintainer: Martin Schlather

Diff between MarkedPointProcess versions 0.2.21 dated 2013-12-05 and 0.2.22 dated 2014-09-09

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Package doBy updated to version 4.5-11 with previous version 4.5-10 dated 2013-11-28

Title: doBy - Groupwise summary statistics, LSmeans, general linear contrasts, various utilities
Description: doBy originally contained facilities to 'do' something to data stratified 'by' some variables. doBy contains a variety of utilities including: 1) Facilities for groupwise computations of summary statistics and other facilities for working with grouped data. 2) LSmeans (least-squares means), general linear contrasts. 3) Miscellaneous other utilities.
Author: Søren Højsgaard and Ulrich Halekoh with contributions from Jim Robison-Cox, Kevin Wright, Alessandro A. Leidi and others.
Maintainer: Søren Højsgaard

Diff between doBy versions 4.5-10 dated 2013-11-28 and 4.5-11 dated 2014-09-09

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New package couchDB with initial version 1.3.0
Package: couchDB
Type: Package
Title: Connect and work with couchDB databases
Version: 1.3.0
Date: 2014-02-25
Author: Aleksander Dietrichson
Maintainer: Aleksander Dietrichson
Depends: R (>= 3.0.0), RCurl, bitops, httr, rjson
Description: Interface to couchDB
SystemRequirements: couchDB instance to connect to and work on.
License: AGPL-3
Packaged: 2014-09-08 17:58:38 UTC; sasha
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-09-09 07:24:25

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Package BMA updated to version 3.18 with previous version 3.17.1 dated 2014-05-10

Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging for linear models, generalizable linear models and survival models (cox regression).
Author: Adrian Raftery , Jennifer Hoeting, Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Chris Fraley

Diff between BMA versions 3.17.1 dated 2014-05-10 and 3.18 dated 2014-09-09

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Package BGPhazard updated to version 1.1 with previous version 1.0 dated 2014-04-08

Title: Markov beta and gamma processes for modeling hazard rates
Description: Computes the hazard rate estimate as described by Nieto-Barajas and Walker (2002) and Nieto-Barajas (2003)
Author: Garcia-Bueno, J. A. & Nieto-Barajas, L. E.
Maintainer: Jose Antonio Garcia Bueno

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