Title: Imputation of Zeros and Nondetects in Compositional Data Sets
Diff between zCompositions versions 1.0.1 dated 2014-06-03 and 1.0.2 dated 2014-09-09
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
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(-)
Title: Mixed Models, Particularly Spatial GLMMs
Diff between spaMM versions 1.2.0 dated 2014-06-25 and 1.3.0 dated 2014-09-09
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
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
spaMM-1.3.0/spaMM/man/confint.Rd |only
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(-)
Title: paleobioDB: a package for downloading, visualizing and
processing data from Paleobiology Database.
Diff between paleobioDB versions 0.1 dated 2014-05-01 and 0.2 dated 2014-09-09
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
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(-)
Title: Multinomial Logit Model
Diff between mnlogit versions 1.1.1 dated 2014-04-10 and 1.2.0 dated 2014-09-09
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
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(-)
Title: Taxonomic information from around the web.
Diff between taxize versions 0.3.0 dated 2014-05-20 and 0.4.0 dated 2014-09-09
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
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
R/eol_search.R | 8
R/gbif_parse.R | 8
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
R/get_tsn.R | 2
R/get_ubioid.R |only
R/get_uid.R | 2
R/gisd_isinvasive.R | 12
R/globals.R |only
R/gni_details.R | 10
R/gni_parse.R | 2
R/gni_search.R | 2
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 -
man/apg_families.Rd | 2
man/apg_genera.Rd | 2
man/apg_lookup.Rd | 4
man/apg_orders.Rd | 2
man/bold_search.Rd |only
man/children.Rd |only
man/class2tree.Rd | 4
man/classification.Rd | 4
man/col_children.Rd | 4
man/col_classification-deprecated.Rd | 4
man/col_downstream.Rd | 4
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
man/eol_search.Rd | 4
man/gbif_name_usage.Rd | 2
man/gbif_parse.Rd | 4
man/get_boldid.Rd |only
man/get_colid.Rd | 4
man/get_eolid.Rd | 4
man/get_gbifid.Rd | 4
man/get_genes-deprecated.Rd | 2
man/get_genes_avail-deprecated.Rd | 2
man/get_ids.Rd | 21 -
man/get_seqs-deprecated.Rd | 2
man/get_tpsid.Rd | 4
man/get_tsn.Rd | 4
man/get_ubioid.Rd |only
man/get_uid.Rd | 4
man/getacceptednamesfromtsn.Rd | 4
man/getanymatchcount.Rd | 4
man/getcommentdetailfromtsn.Rd | 4
man/getcommonnamesfromtsn.Rd | 4
man/getcoremetadatafromtsn.Rd | 4
man/getcoveragefromtsn.Rd | 4
man/getcredibilityratingfromtsn.Rd | 4
man/getcredibilityratings.Rd | 4
man/getcurrencyfromtsn.Rd | 4
man/getdatedatafromtsn.Rd | 4
man/getdescription.Rd | 4
man/getexpertsfromtsn.Rd | 4
man/getfullhierarchyfromtsn.Rd | 4
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
man/getparenttsnfromtsn.Rd | 4
man/getpublicationsfromtsn.Rd | 4
man/getranknames.Rd | 4
man/getrecordfromlsid.Rd | 4
man/getreviewyearfromtsn.Rd | 4
man/getscientificnamefromtsn.Rd | 4
man/getsynonymnamesfromtsn.Rd | 4
man/gettaxonauthorshipfromtsn.Rd | 4
man/gettaxonomicranknamefromtsn.Rd | 4
man/gettaxonomicusagefromtsn.Rd | 4
man/gettsnbyvernacularlanguage.Rd | 4
man/gettsnfromlsid.Rd | 4
man/getunacceptabilityreasonfromtsn.Rd | 4
man/getvernacularlanguages.Rd | 4
man/gisd_isinvasive.Rd | 11
man/gni_details.Rd | 4
man/gni_parse.Rd | 4
man/gni_search.Rd | 4
man/gnr_datasources.Rd | 4
man/gnr_resolve.Rd | 12
man/ifelsedata.Rd | 2
man/iplant_resolve.Rd | 11
man/ipni_search.Rd | 4
man/itis_acceptname.Rd | 4
man/itis_downstream.Rd | 4
man/itis_getrecord.Rd | 4
man/itis_hierarchy.Rd | 4
man/itis_kingdomnames.Rd | 4
man/itis_lsid.Rd | 4
man/itis_name-deprecated.Rd | 4
man/itis_native.Rd | 4
man/itis_ping.Rd | 4
man/itis_refs.Rd | 4
man/itis_searchcommon.Rd | 4
man/itis_taxrank.Rd | 4
man/itis_terms.Rd | 4
man/iucn_getname.Rd | 4
man/iucn_status.Rd | 4
man/iucn_summary.Rd | 4
man/names_list.Rd | 2
man/ncbi_getbyid.Rd | 10
man/ncbi_getbyname.Rd | 19 -
man/ncbi_search.Rd | 19 -
man/phylomatic_format.Rd | 4
man/phylomatic_tree.Rd | 12
man/plantGenusNames.Rd | 2
man/plantNames.Rd | 2
man/plantminer.Rd | 4
man/rank_ref.Rd | 2
man/rankagg.Rd | 2
man/resolve.Rd | 6
man/sci2comm.Rd | 8
man/scrapenames.Rd | 11
man/searchbycommonname.Rd | 4
man/searchbycommonnamebeginswith.Rd | 4
man/searchbycommonnameendswith.Rd | 4
man/searchbyscientificname.Rd | 4
man/searchforanymatch.Rd | 4
man/searchforanymatchpaged.Rd | 4
man/synonyms.Rd | 20 -
man/tax_agg.Rd | 7
man/tax_name.Rd | 4
man/tax_rank.Rd | 4
man/taxize-deprecated.Rd | 2
man/taxize-package.Rd | 62 ++-
man/taxize_capwords.Rd | 2
man/taxize_cite.Rd |only
man/taxize_ldfast.Rd | 2
man/theplantlist.Rd | 2
man/tnrs.Rd | 6
man/tnrs_sources.Rd | 4
man/tp_acceptednames-deprecated.Rd | 2
man/tp_accnames.Rd | 4
man/tp_classification-deprecated.Rd | 4
man/tp_dist.Rd | 4
man/tp_namedistributions-deprecated.Rd | 2
man/tp_namereferences-deprecated.Rd | 2
man/tp_refs.Rd | 4
man/tp_search.Rd | 4
man/tp_summary.Rd | 4
man/tp_synonyms.Rd | 4
man/tpl_families.Rd | 2
man/tpl_get.Rd | 2
man/tpl_search-deprecated.Rd | 2
man/ubio_classification.Rd | 4
man/ubio_classification_search.Rd | 4
man/ubio_id.Rd | 4
man/ubio_search.Rd | 4
man/ubio_synonyms.Rd | 4
man/vascan_search.Rd | 8
tests/testthat/test-bold_search.R |only
tests/testthat/test-eol_dataobjects.R | 2
tests/testthat/test-get_boldid.R |only
tests/testthat/test-itis_refs.R | 2
tests/testthat/test-tax_agg.R | 19 -
tests/testthat/test-tp_summary.R | 2
vignettes/taxize_vignette.Rmd | 26 -
257 files changed, 1608 insertions(+), 1238 deletions(-)
Title: Fitting the centered autologistic and sparse spatial generalized
linear mixed models for areal data
Diff between ngspatial versions 1.0-3 dated 2013-12-07 and 1.0-4 dated 2014-09-09
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
Maintainer: John Hughes
COPYING | 6
DESCRIPTION | 18 +-
MD5 | 42 +++---
NAMESPACE | 13 +
R/autologistic.R | 100 +++++++++-----
R/sparse.sglmm.R | 45 ++++--
R/zzz.R | 4
data |only
inst/CITATION | 4
man/A.Rd |only
man/adjacency.matrix.Rd | 17 +-
man/autologistic.Rd | 288 ++++++++++++++++--------------------------
man/infant.Rd |only
man/rautologistic.Rd | 38 ++---
man/residuals.autologistic.Rd | 22 +--
man/residuals.sparse.sglmm.Rd | 22 +--
man/sparse.sglmm.Rd | 276 ++++++++++++----------------------------
man/summary.autologistic.Rd | 28 +---
man/summary.sparse.sglmm.Rd | 29 +---
man/vcov.autologistic.Rd | 15 --
man/vcov.sparse.sglmm.Rd | 13 -
src/moller.cpp | 14 +-
src/perfsampler.cpp | 4
23 files changed, 430 insertions(+), 568 deletions(-)
Title: Flexible procedures for clustering
Diff between fpc versions 2.1-7 dated 2014-01-29 and 2.1-8 dated 2014-09-09
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
DESCRIPTION | 16
MD5 | 84 +-
NAMESPACE | 10
R/clusterboot.R | 31
R/dbscan.R | 2
R/lcmixed.R | 2
R/localshape.R | 2
R/mergenormals.R | 14
man/bhattacharyya.dist.Rd | 2
man/calinhara.Rd | 2
man/clucols.Rd | 2
man/clusexpect.Rd | 4
man/cluster.stats.Rd | 6
man/cluster.varstats.Rd | 3
man/clusterboot.Rd | 3
man/confusion.Rd | 2
man/diptest.multi.Rd | 10
man/discrete.recode.Rd | 1
man/discrproj.Rd | 10
man/distcritmulti.Rd | 1
man/dudahart2.Rd | 1
man/extract.mixturepars.Rd | 2
man/fixmahal.Rd | 1
man/fixreg.Rd | 1
man/flexmixedruns.Rd | 1
man/kmeansCBI.Rd | 5
man/kmeansruns.Rd | 3
man/lcmixed.Rd | 3
man/localshape.Rd | 1
man/mahalanodisc.Rd | 1
man/mergenormals.Rd | 3
man/mergeparameters.Rd | 6
man/mixdens.Rd | 3
man/pamk.Rd | 3
man/prediction.strength.Rd | 1
man/regmix.Rd | 2
man/tdecomp.Rd | 4
man/weightplots.Rd | 2
man/wfu.Rd | 2
man/zmisclassification.matrix.Rd | 2
tests/Examples/fpc-Ex.Rout.save | 1267 ++++++++++-----------------------------
tests/fpctests.R | 8
tests/fpctests.Rout.save | 328 ++++------
43 files changed, 650 insertions(+), 1207 deletions(-)
Title: Back-Projected Kernel Density Estimation
Diff between bpkde versions 1.0-4 dated 2014-05-27 and 1.0-7 dated 2014-09-09
Description: Nonparametric multivariate kernel density \
estimation using a back-projected kernel.
Author: Kjell Konis
Maintainer: Kjell Konis
DESCRIPTION | 14 ++---
MD5 | 53 ++++++++++---------
R/M0.q | 12 ++--
R/M1.q | 4 -
R/bpkde.q | 29 +++++-----
R/contour.mvkde.q | 4 -
R/image.mvkde.q | 4 -
R/mvlinbin.q | 39 +++++++++-----
R/plot.mvkde.q | 4 -
R/predict.mvkde.q |only
data/Bimodal1.RData |binary
data/Bimodal2.RData |binary
data/Bimodal3.RData |binary
data/Bimodal4.RData |binary
data/Correlated.Normal.RData |binary
data/Kurtotic.RData |binary
data/Quadrimodal.RData |binary
data/Skewed.RData |binary
data/Trimodal1.RData |binary
data/Trimodal2.RData |binary
data/Trimodal3.RData |binary
data/Uncorrelated.Normal.RData |binary
man/bpkde.Rd | 4 -
man/mvlinbin.Rd | 18 ++----
tests/bpkde.R | 30 ++++++++++-
tests/bpkde.Rout.save | 110 ++++++++++++++++++++++++++++++++++-------
tests/linbin.R | 17 +-----
tests/linbin.Rout.save | 40 ++++++++------
28 files changed, 246 insertions(+), 136 deletions(-)
Title: Inverse estimation/calibration functions
Diff between investr versions 1.1.0 dated 2014-07-14 and 1.1.1 dated 2014-09-09
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
DESCRIPTION | 9
MD5 | 48 ++-
NAMESPACE | 6
NEWS | 15 -
R/calibrate.R | 113 +++------
R/data.R |only
R/invest.R | 341 +++++++++++++--------------
R/plotFit.R | 489 ++++++++++++++++++----------------------
R/predict2.R |only
R/utilities.R | 282 +----------------------
inst/CITATION | 24 +
man/Sigma.Rd | 2
man/arsenic.Rd | 12
man/calibrate.Rd | 59 ++--
man/crystal.Rd | 10
man/invest.Rd | 63 ++---
man/investr-package.Rd | 2
man/makeData.Rd | 6
man/makeX.Rd | 2
man/makeZ.Rd | 4
man/plotFit.Rd | 49 ++--
man/predict2.Rd | 2
man/varY.Rd | 2
tests/testthat/test-calibrate.R | 19 -
tests/testthat/test-invest.R | 166 ++++++++++---
tests/testthat/test-utilities.R | 26 +-
26 files changed, 791 insertions(+), 960 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Diff between PReMiuM versions 3.0.28 dated 2014-06-30 and 3.0.29 dated 2014-09-09
Description: Dirichlet process Bayesian clustering, also known as profile regression.
Author: David I. Hastie
Maintainer: Silvia Liverani
PReMiuM-3.0.28/PReMiuM/inst/CITATION |only
PReMiuM-3.0.29/PReMiuM/ChangeLog | 5
PReMiuM-3.0.29/PReMiuM/DESCRIPTION | 12 -
PReMiuM-3.0.29/PReMiuM/MD5 | 38 ++---
PReMiuM-3.0.29/PReMiuM/R/generateData.R | 62 ++++++++
PReMiuM-3.0.29/PReMiuM/R/postProcess.R | 22 ++
PReMiuM-3.0.29/PReMiuM/inst/citation |only
PReMiuM-3.0.29/PReMiuM/man/clusSummaryBernoulliDiscrete.Rd | 4
PReMiuM-3.0.29/PReMiuM/man/margModelPosterior.Rd | 2
PReMiuM-3.0.29/PReMiuM/man/profRegr.Rd | 3
PReMiuM-3.0.29/PReMiuM/man/setHyperparams.Rd | 4
PReMiuM-3.0.29/PReMiuM/src/Makevars | 3
PReMiuM-3.0.29/PReMiuM/src/PReMiuM.cpp | 5
PReMiuM-3.0.29/PReMiuM/src/include/Math/ars2.h | 7
PReMiuM-3.0.29/PReMiuM/src/include/Math/distribution.h | 4
PReMiuM-3.0.29/PReMiuM/src/include/PReMiuMArs.cpp | 11 +
PReMiuM-3.0.29/PReMiuM/src/include/PReMiuMArs.h | 98 +++++++++----
PReMiuM-3.0.29/PReMiuM/src/include/PReMiuMIO.h | 32 ++++
PReMiuM-3.0.29/PReMiuM/src/include/PReMiuMModel.h | 93 ++++++++++++
PReMiuM-3.0.29/PReMiuM/src/include/PReMiuMProposals.h | 24 +++
PReMiuM-3.0.29/PReMiuM/src/postProcess.cpp | 1
21 files changed, 362 insertions(+), 68 deletions(-)
Title: Social Relation Model (SRM) analyses for single or multiple
round-robin groups
Diff between TripleR versions 1.2.1 dated 2013-10-02 and 1.4 dated 2014-09-09
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
DESCRIPTION | 14 -
MD5 | 17 +
NAMESPACE | 7
NEWS | 8
R/RR.r | 444 +--------------------------------------------------
R/getEffects.R |only
R/long2matrix.R |only
R/plots.R |only
man/RR.Rd | 26 ++
man/getEffects.Rd | 27 ++-
man/plot_missings.Rd | 10 +
11 files changed, 104 insertions(+), 449 deletions(-)
Title: SPArse Matrix
Diff between spam versions 0.41-0 dated 2014-02-26 and 1.0-1 dated 2014-09-09
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
spam-0.41-0/spam/LICENSE |only
spam-0.41-0/spam/R/headtail.R |only
spam-1.0-1/spam/ChangeLog | 172 +++-
spam-1.0-1/spam/DESCRIPTION | 12
spam-1.0-1/spam/MD5 | 188 ++--
spam-1.0-1/spam/NAMESPACE | 31
spam-1.0-1/spam/R/constructors.R |only
spam-1.0-1/spam/R/definitions.R | 572 ++------------
spam-1.0-1/spam/R/diff.R | 7
spam-1.0-1/spam/R/dim.R |only
spam-1.0-1/spam/R/dist.R | 22
spam-1.0-1/spam/R/foreign.R | 23
spam-1.0-1/spam/R/helper.R | 43 -
spam-1.0-1/spam/R/kronecker.R | 4
spam-1.0-1/spam/R/math.R |only
spam-1.0-1/spam/R/permutation.R | 6
spam-1.0-1/spam/R/precmat.R | 2
spam-1.0-1/spam/R/profile.R | 22
spam-1.0-1/spam/R/rmvnorm.R | 76 -
spam-1.0-1/spam/R/rowcolstats.R | 16
spam-1.0-1/spam/R/s3only.R |only
spam-1.0-1/spam/R/s4coerce.R |only
spam-1.0-1/spam/R/spam_solve.R | 121 +-
spam-1.0-1/spam/R/subset.R | 79 +
spam-1.0-1/spam/R/tailhead.R |only
spam-1.0-1/spam/R/tcrossprod.R |only
spam-1.0-1/spam/R/toepliz.R | 4
spam-1.0-1/spam/R/xybind.R | 2
spam-1.0-1/spam/README |only
spam-1.0-1/spam/demo/article-jss-example1.R | 7
spam-1.0-1/spam/demo/article-jss-example2.R | 9
spam-1.0-1/spam/demo/article-jss.R | 9
spam-1.0-1/spam/inst/0ChangeLog |only
spam-1.0-1/spam/inst/0LICENSE |only
spam-1.0-1/spam/inst/CITATION | 9
spam-1.0-1/spam/inst/NEWS | 197 ++++
spam-1.0-1/spam/man/chol.Rd | 27
spam-1.0-1/spam/man/coerce.Rd |only
spam-1.0-1/spam/man/coercion.Rd |only
spam-1.0-1/spam/man/constructors.Rd |only
spam-1.0-1/spam/man/crossprod.Rd |only
spam-1.0-1/spam/man/det.Rd | 12
spam-1.0-1/spam/man/diff.Rd |only
spam-1.0-1/spam/man/dim.Rd | 29
spam-1.0-1/spam/man/headtail.Rd | 8
spam-1.0-1/spam/man/image.Rd | 15
spam-1.0-1/spam/man/kronecker.Rd | 3
spam-1.0-1/spam/man/makeprec.Rd | 11
spam-1.0-1/spam/man/math.Rd | 121 +-
spam-1.0-1/spam/man/math2.Rd | 30
spam-1.0-1/spam/man/methods.Rd | 10
spam-1.0-1/spam/man/nearestdist.Rd | 26
spam-1.0-1/spam/man/operations.Rd | 3
spam-1.0-1/spam/man/options.Rd | 37
spam-1.0-1/spam/man/ordering.Rd | 14
spam-1.0-1/spam/man/pad.Rd |only
spam-1.0-1/spam/man/permutation.Rd | 8
spam-1.0-1/spam/man/powerboost.Rd | 7
spam-1.0-1/spam/man/print.Rd | 9
spam-1.0-1/spam/man/rdist.Rd |only
spam-1.0-1/spam/man/rmvnorm.const.Rd | 4
spam-1.0-1/spam/man/s3only.Rd |only
spam-1.0-1/spam/man/solve.Rd | 35
spam-1.0-1/spam/man/spam-class.Rd | 32
spam-1.0-1/spam/man/spam-package.Rd | 27
spam-1.0-1/spam/man/spam.creation.Rd | 22
spam-1.0-1/spam/man/summary.Rd | 59 -
spam-1.0-1/spam/man/xybind.Rd | 11
spam-1.0-1/spam/src/spamown.f | 56 -
spam-1.0-1/spam/src/spamown2.f | 8
spam-1.0-1/spam/tests/constructors.R |only
spam-1.0-1/spam/tests/constructors.Rout.save |only
spam-1.0-1/spam/tests/covmat.Rout.save | 6
spam-1.0-1/spam/tests/crossprod.R |only
spam-1.0-1/spam/tests/crossprod.Rout.save |only
spam-1.0-1/spam/tests/demo_article-jss-example1.R | 46 -
spam-1.0-1/spam/tests/demo_article-jss-example1.Rout.save | 54 -
spam-1.0-1/spam/tests/demo_article-jss-example2.R | 41 -
spam-1.0-1/spam/tests/demo_article-jss-example2.Rout.save | 55 -
spam-1.0-1/spam/tests/demo_article-jss.Rout.save | 6
spam-1.0-1/spam/tests/demo_cholesky.Rout.save | 6
spam-1.0-1/spam/tests/demo_spam.Rout.save | 6
spam-1.0-1/spam/tests/demo_timing.Rout.save | 6
spam-1.0-1/spam/tests/diff.R | 9
spam-1.0-1/spam/tests/diff.Rout.save | 11
spam-1.0-1/spam/tests/dim.R |only
spam-1.0-1/spam/tests/dim.Rout.save |only
spam-1.0-1/spam/tests/displays.Rout.save | 6
spam-1.0-1/spam/tests/dist.Rout.save | 6
spam-1.0-1/spam/tests/foreign.Rout.save | 4
spam-1.0-1/spam/tests/helper.R | 5
spam-1.0-1/spam/tests/helper.Rout.save | 6
spam-1.0-1/spam/tests/jss_areal_counts.R |only
spam-1.0-1/spam/tests/jss_areal_counts.Rout.save |only
spam-1.0-1/spam/tests/kronecker.Rout.save | 6
spam-1.0-1/spam/tests/math.R |only
spam-1.0-1/spam/tests/math.Rout.save |only
spam-1.0-1/spam/tests/mle.R | 1
spam-1.0-1/spam/tests/mle.Rout.save | 7
spam-1.0-1/spam/tests/norm.Rout.save | 6
spam-1.0-1/spam/tests/ops.R |only
spam-1.0-1/spam/tests/ops.Rout.save |only
spam-1.0-1/spam/tests/overall.R | 36
spam-1.0-1/spam/tests/overall.Rout.save | 16
spam-1.0-1/spam/tests/permutation.Rout.save | 6
spam-1.0-1/spam/tests/rowcolstats.Rout.save | 6
spam-1.0-1/spam/tests/solve.Rout.save | 6
spam-1.0-1/spam/tests/spamlist.R | 6
spam-1.0-1/spam/tests/spamlist.Rout.save | 6
spam-1.0-1/spam/tests/subsetting.Rout.save | 6
spam-1.0-1/spam/tests/xybind.Rout.save | 6
111 files changed, 1237 insertions(+), 1407 deletions(-)
Title: Hypergeometric tests
Diff between hypergea versions 1.0.1 dated 2014-07-10 and 1.2.1 dated 2014-09-09
Description: Package to perform (exact) hypergeometric tests on IxJ and 2x2x2 contingency tables using parallelised C code
Author: Markus Boenn
Maintainer: Markus Boenn
DESCRIPTION | 8
MD5 | 7
R/hypergea-internal.R | 9
inst |only
src/hypergeom_IxJ.cpp | 498 +++++++++++++++++++++++++++++++++++++-------------
5 files changed, 385 insertions(+), 137 deletions(-)
Title: Objective functions for benchmarking the performance of global
optimization algorithms
Diff between globalOptTests versions 1.0 dated 2013-08-20 and 1.1 dated 2014-09-09
More information about globalOptTests at CRAN
Description: This package makes available 50 objective functions for benchmarking the performance of global optimization algorithms
Author: Katharine Mullen
Maintainer: Katharine Mullen
DESCRIPTION | 8 +++---
MD5 | 14 ++++++----
NEWS |only
inst |only
man/getDefaultBounds.Rd | 19 +++++++++-----
man/getGlobalOpt.Rd | 23 ++++++++++++++---
man/getProblemDimen.Rd | 23 ++++++++++++++---
man/globalOptTests-package.Rd | 33 +++++++++++++++++--------
man/goTest.Rd | 54 +++++++++++++++++++++---------------------
9 files changed, 109 insertions(+), 65 deletions(-)
Permanent link
Title: FCROS for detecting differentially expressed genes
Diff between fcros versions 1.1 dated 2014-01-20 and 1.2 dated 2014-09-09
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
fcros-1.1/fcros/R/fcrosRMat.R |only
fcros-1.1/fcros/man/fcrosRMat.Rd |only
fcros-1.2/fcros/DESCRIPTION | 16 ++---
fcros-1.2/fcros/MD5 | 42 +++++++------
fcros-1.2/fcros/NAMESPACE | 2
fcros-1.2/fcros/R/fcros.R | 24 +++----
fcros-1.2/fcros/R/fcros2.R | 56 ++++++------------
fcros-1.2/fcros/R/fcrosFCmat.R |only
fcros-1.2/fcros/R/fcrosHistoPlot.R |only
fcros-1.2/fcros/R/fcrosMod.R |only
fcros-1.2/fcros/R/fcrosRead.R | 6 -
fcros-1.2/fcros/R/fcrosTopN.R | 4 -
fcros-1.2/fcros/R/fcrosTtest.R | 33 ++++++----
fcros-1.2/fcros/R/fcrosVolcanoPlot.R |only
fcros-1.2/fcros/R/fcrosWrite.R | 13 ++--
fcros-1.2/fcros/man/fcros-package.Rd | 72 ++++++++++++++++-------
fcros-1.2/fcros/man/fcros.Rd | 88 +++++++++++++++++------------
fcros-1.2/fcros/man/fcros2.Rd | 97 ++++++++++++++++++--------------
fcros-1.2/fcros/man/fcrosFCmat.Rd |only
fcros-1.2/fcros/man/fcrosHistoPlot.Rd |only
fcros-1.2/fcros/man/fcrosMod.Rd |only
fcros-1.2/fcros/man/fcrosRead.Rd | 41 ++++++-------
fcros-1.2/fcros/man/fcrosTopN.Rd | 12 ++-
fcros-1.2/fcros/man/fcrosTtest.Rd | 20 +++---
fcros-1.2/fcros/man/fcrosVolcanoPlot.Rd |only
fcros-1.2/fcros/man/fcrosWrite.Rd | 13 ++--
fcros-1.2/fcros/man/fdata.Rd | 29 ++++-----
27 files changed, 315 insertions(+), 253 deletions(-)
Title: Domino Data Lab R console bindings
Diff between domino versions 0.1-7 dated 2014-05-07 and 0.2-1 dated 2014-09-09
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
DESCRIPTION | 12 +++++------
MD5 | 10 ++++-----
R/domino.R | 54 +++++++++++++++++++++++++++++++++++++++++---------
man/domino-package.Rd | 11 +++++-----
man/domino.login.Rd | 9 ++++++--
man/domino.upload.Rd | 8 ++++++-
6 files changed, 76 insertions(+), 28 deletions(-)
Title: Circumplex models Estimation
Diff between CircE versions 1.0 dated 2014-04-11 and 1.1 dated 2014-09-09
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
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
R/CircE.Plot.R | 5 +++--
data/Block.rda |binary
data/SELF5.rda |binary
data/Verbal.rda |binary
inst/NEWS | 5 ++++-
man/CircE.Plot.Rd | 3 ++-
8 files changed, 20 insertions(+), 15 deletions(-)
Title: Spherical Trigonometry
Diff between geosphere versions 1.3-8 dated 2014-01-20 and 1.3-11 dated 2014-09-09
Description: Spherical trigonometry for geographic applications
Author: Robert J. Hijmans [cre, aut],
Ed Williams [ctb],
Chris Vennes [ctb]
Maintainer: Robert J. Hijmans
ChangeLog | 1
DESCRIPTION | 13 -
MD5 | 16 -
NAMESPACE | 2
R/distMeeus.R | 6
R/geomedian.R | 4
build/vignette.rds |binary
inst/doc/geosphere.R | 480 ++++++++++++++++++++++++-------------------------
inst/doc/geosphere.pdf |binary
9 files changed, 260 insertions(+), 262 deletions(-)
Title: Analysis of Marks of Marked Point Processes
Diff between MarkedPointProcess versions 0.2.21 dated 2013-12-05 and 0.2.22 dated 2014-09-09
More information about MarkedPointProcess at CRAN
Description: Non-parametric Analysis of the Marks of Marked Point Processes
Author: Martin Schlather
Maintainer: Martin Schlather
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/auxiliary.R | 1 +
R/mpp.R | 16 ++++++++--------
R/srd.R | 2 +-
data/BITOEK.rda |binary
6 files changed, 19 insertions(+), 18 deletions(-)
Permanent link
Title: doBy - Groupwise summary statistics, LSmeans, general linear
contrasts, various utilities
Diff between doBy versions 4.5-10 dated 2013-11-28 and 4.5-11 dated 2014-09-09
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
Maintainer: Søren Højsgaard
doBy-4.5-10/doBy/man/dose.LD50.Rd |only
doBy-4.5-11/doBy/ChangeLog | 15
doBy-4.5-11/doBy/DESCRIPTION | 17
doBy-4.5-11/doBy/MD5 | 49 -
doBy-4.5-11/doBy/NAMESPACE | 4
doBy-4.5-11/doBy/R/BY-lapplyBy.R | 35 -
doBy-4.5-11/doBy/R/BY-splitBy2.R | 26
doBy-4.5-11/doBy/R/LD50.R | 2
doBy-4.5-11/doBy/R/LSmeans.R | 122 ---
doBy-4.5-11/doBy/R/esticon.R | 2
doBy-4.5-11/doBy/R/linest.R | 19
doBy-4.5-11/doBy/R/linestGet.R | 26
doBy-4.5-11/doBy/R/linestMatrix.R | 15
doBy-4.5-11/doBy/build/vignette.rds |binary
doBy-4.5-11/doBy/data/datalist | 1
doBy-4.5-11/doBy/data/haldCement.txt.gz |only
doBy-4.5-11/doBy/inst/doc/LSmeans.R | 292 ++++-----
doBy-4.5-11/doBy/inst/doc/LSmeans.Rnw | 1033 +++++++-------------------------
doBy-4.5-11/doBy/inst/doc/LSmeans.pdf |binary
doBy-4.5-11/doBy/inst/doc/doBy.Rnw | 2
doBy-4.5-11/doBy/inst/doc/doBy.pdf |binary
doBy-4.5-11/doBy/man/DATA-haldCement.Rd |only
doBy-4.5-11/doBy/man/LSmeans.Rd | 49 -
doBy-4.5-11/doBy/man/doBy-internal.Rd | 9
doBy-4.5-11/doBy/man/lapplyBy.Rd | 13
doBy-4.5-11/doBy/vignettes/LSmeans.Rnw | 1033 +++++++-------------------------
doBy-4.5-11/doBy/vignettes/doBy.Rnw | 2
27 files changed, 790 insertions(+), 1976 deletions(-)
Title: Bayesian Model Averaging
Diff between BMA versions 3.17.1 dated 2014-05-10 and 3.18 dated 2014-09-09
Description: Package for Bayesian model averaging for linear models,
generalizable linear models and survival models (cox
regression).
Author: Adrian Raftery
Maintainer: Chris Fraley
ChangeLog | 3
DESCRIPTION | 8 +-
MD5 | 12 +--
NAMESPACE | 2
R/iBMA.glm.R | 226 ++++++++++++++++++++++++++++------------------------------
R/iBMA.surv.R | 222 +++++++++++++++++++++++++++-----------------------------
man/iBMA.Rd | 14 +++
7 files changed, 245 insertions(+), 242 deletions(-)
Title: Markov beta and gamma processes for modeling hazard rates
Diff between BGPhazard versions 1.0 dated 2014-04-08 and 1.1 dated 2014-09-09
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
DESCRIPTION | 10 -
MD5 | 68 +++++++++---
R/BePloth.R | 257 +++++++++++++++++++++++------------------------
R/CGaPloth.R | 26 +++-
R/GaPloth.R | 18 ++-
R/PiSumm.R | 1
build |only
inst |only
man/BGPhazard-package.Rd | 12 +-
man/BeMRes.Rd | 7 -
man/BePlotDiag.Rd | 8 -
man/BePloth.Rd | 8 -
man/CGaMRes.Rd | 4
man/CGaPlotDiag.Rd | 2
man/CGaPloth.Rd | 2
man/CGaPred.Rd | 2
man/GaMRes.Rd | 14 +-
man/GaPlotDiag.Rd | 10 -
man/GaPloth.Rd | 10 -
man/PlotTheta.Rd | 2
vignettes |only
21 files changed, 257 insertions(+), 204 deletions(-)