Title: A Multivariate Emulator
Description: A multivariate generalization of the emulator package.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between multivator versions 1.1-6 dated 2017-04-20 and 1.1-9 dated 2017-05-28
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- build/vignette.rds |binary data/e3mg.rda |binary data/mcneall.rda |binary data/mtoys.rda |binary inst/doc/cias.pdf |binary inst/doc/multivator.pdf |binary inst/mtoys.R |only man/mdm.Rd | 2 -- 10 files changed, 13 insertions(+), 14 deletions(-)
Title: Tools for Collecting Social Media Data and Generating Networks
for Analysis
Description: A suite of tools for collecting and constructing networks from
social media data. Provides easy-to-use functions for collecting data across
popular platforms (Instagram, Facebook, Twitter, and YouTube) and generating
different types of networks for analysis.
Author: Timothy Graham & Robert Ackland with contribution from Chung-hong Chan
Maintainer: Timothy Graham <Timothy.Graham@anu.edu.au>
Diff between SocialMediaLab versions 0.23.0 dated 2016-07-22 and 0.23.2 dated 2017-05-28
DESCRIPTION | 14 ++++----- MD5 | 8 ++--- NAMESPACE | 2 - R/AuthenticateWithFacebookAPI.R | 62 ++++++++++++++++++++++++++++++++++++++++ R/CollectDataFacebook.R | 29 +++++++++++++++++- 5 files changed, 101 insertions(+), 14 deletions(-)
More information about SocialMediaLab at CRAN
Permanent link
Title: Genetic Algorithm with Incomplete Dominance for Feature
Selection
Description: Feature selection from high dimensional data using a diploid
genetic algorithm with Incomplete Dominance for genotype to phenotype mapping
and Random Assortment of chromosomes approach to recombination.
Author: Nicolae Teodor Melita
Maintainer: Nicolae Teodor Melita <nt_melita@yahoo.com>
Diff between dGAselID versions 1.0 dated 2016-11-20 and 1.1 dated 2017-05-28
DESCRIPTION | 6 MD5 | 25 + NAMESPACE | 17 R/dGAselID.R | 777 +++++++++++++++++++++++++++++++++++++++-- man/AnalyzeResults.Rd |only man/Crossover.Rd |only man/Elitism.Rd |only man/EmbryonicSelection.Rd |only man/EvaluationFunction.Rd |only man/Individuals.Rd |only man/InitialPopulation.Rd |only man/PlotGenAlg.Rd |only man/RandomAssortment.Rd |only man/RandomizePop.Rd |only man/dGAselID.Rd | 41 +- man/frameShiftMutation.Rd |only man/largeSegmentDeletion.Rd |only man/nonSenseMutation.Rd |only man/pointMutation.Rd |only man/splitChromosomes.Rd |only man/transposon.Rd |only man/wholeChromosomeDeletion.Rd |only 22 files changed, 817 insertions(+), 49 deletions(-)
Title: Easily Source Publicly Available Data on Derivatives
Description: Post Global Financial Crisis derivatives reforms have lifted the
veil off over-the-counter (OTC) derivative markets. Swap Execution Facilities
(SEFs) and Swap Data Repositories (SDRs) now publish data on swaps that are
traded on or reported to those facilities (respectively). This package provides
you the ability to get this data from supported sources.
Author: Imanuel Costigan [aut, cre]
Maintainer: Imanuel Costigan <i.costigan@me.com>
Diff between dataonderivatives versions 0.2.1 dated 2015-09-27 and 0.3.0 dated 2017-05-28
dataonderivatives-0.2.1/dataonderivatives/man/get_bsdr_data.Rd |only dataonderivatives-0.2.1/dataonderivatives/man/get_bsef_data.Rd |only dataonderivatives-0.2.1/dataonderivatives/man/get_cme_data.Rd |only dataonderivatives-0.2.1/dataonderivatives/man/get_ddr_data.Rd |only dataonderivatives-0.2.1/dataonderivatives/tests/testthat/test_bsef.R |only dataonderivatives-0.3.0/dataonderivatives/DESCRIPTION | 27 dataonderivatives-0.3.0/dataonderivatives/MD5 | 32 dataonderivatives-0.3.0/dataonderivatives/NAMESPACE | 14 dataonderivatives-0.3.0/dataonderivatives/NEWS.md |only dataonderivatives-0.3.0/dataonderivatives/R/bsdr.R | 235 +++---- dataonderivatives-0.3.0/dataonderivatives/R/bsef.R | 113 +-- dataonderivatives-0.3.0/dataonderivatives/R/cme.R | 329 +++------- dataonderivatives-0.3.0/dataonderivatives/R/ddr.R | 196 +---- dataonderivatives-0.3.0/dataonderivatives/R/utils.R |only dataonderivatives-0.3.0/dataonderivatives/README.md | 141 +--- dataonderivatives-0.3.0/dataonderivatives/man/bsdr.Rd |only dataonderivatives-0.3.0/dataonderivatives/man/bsef.Rd |only dataonderivatives-0.3.0/dataonderivatives/man/cme.Rd |only dataonderivatives-0.3.0/dataonderivatives/man/ddr.Rd |only dataonderivatives-0.3.0/dataonderivatives/tests/testthat/test-bsdr.R | 7 dataonderivatives-0.3.0/dataonderivatives/tests/testthat/test-bsef.R |only dataonderivatives-0.3.0/dataonderivatives/tests/testthat/test-cme.R | 8 dataonderivatives-0.3.0/dataonderivatives/tests/testthat/test-ddr.R | 21 23 files changed, 437 insertions(+), 686 deletions(-)
More information about dataonderivatives at CRAN
Permanent link
Title: Karl Broman's R Code
Description: Miscellaneous R functions, including functions related to
graphics (mostly for base graphics), permutation tests, running
mean/median, and general utilities.
Author: Karl W Broman <kbroman@biostat.wisc.edu>, with contributions from Aimee
Teo Broman
Maintainer: Karl W Broman <kbroman@biostat.wisc.edu>
Diff between broman versions 0.65-1 dated 2016-12-01 and 0.65-4 dated 2017-05-28
DESCRIPTION | 10 +- MD5 | 143 +++++++++++++++++++++--------------------- NAMESPACE | 3 R/brocolors.R | 52 +++++++++++++++ R/normalize.R | 5 - R/pushbullet.R | 23 +++--- R/zzz.R |only data/numbers-cap.RData |binary data/numbers.RData |binary inst/STATUS.txt | 30 ++++++++ man/add_commas.Rd | 1 man/arrowlocator.Rd | 1 man/attrnames.Rd | 1 man/brocolors.Rd | 1 man/bromanversion.Rd | 1 man/cf.Rd | 1 man/chisq.Rd | 1 man/colwalpha.Rd | 1 man/compare_rows.Rd | 1 man/convert2hex.Rd | 1 man/crayons.Rd |only man/done.Rd | 1 man/dotplot.Rd | 1 man/errors2pushbullet.Rd | 1 man/excel_fig.Rd | 1 man/exit.Rd | 1 man/fac2num.Rd | 1 man/fisher.Rd | 1 man/grayplot.Rd | 1 man/h.Rd | 1 man/hex2dec.Rd | 7 -- man/histlines.Rd | 1 man/jiggle.Rd | 1 man/kbdate.Rd | 1 man/lenuniq.Rd | 1 man/make.Rd | 1 man/manyboxplot.Rd | 1 man/maxabs.Rd | 1 man/mypairs.Rd | 1 man/myround.Rd | 1 man/normalize.Rd | 1 man/note.Rd | 3 man/numbers.Rd | 4 - man/objectsizes.Rd | 1 man/openfile.Rd | 1 man/paired.perm.test.Rd | 1 man/paste..Rd | 1 man/paste00.Rd | 7 -- man/perm.test.Rd | 1 man/plot_crayons.Rd | 1 man/pushbullet_devices.Rd | 1 man/qqline2.Rd | 1 man/qr2.Rd | 1 man/quantileSE.Rd | 1 man/revrainbow.Rd | 1 man/rmvn.Rd | 1 man/runningmean.Rd | 7 -- man/runningratio.Rd | 7 -- man/setRNGparallel.Rd | 1 man/simp.Rd | 1 man/stop_sending_errors.Rd | 1 man/strwidth2lines.Rd | 1 man/strwidth2xlim.Rd | 7 -- man/switchv.Rd | 1 man/theme_karl.Rd | 3 man/triarrow.Rd | 1 man/trilines.Rd | 1 man/triplot.Rd | 1 man/tripoints.Rd | 1 man/venn.Rd | 1 man/winsorize.Rd | 1 man/xlimlabel.Rd | 7 -- src/R_init.c |only src/R_init.h |only tests/testthat/test-crayons.R |only 75 files changed, 197 insertions(+), 173 deletions(-)
Title: Genomic Data Retrieval
Description: Perform metagenomic data retrieval and functional annotation
retrieval. In detail, this package aims to provide users with a standardized
way to automate genome, proteome, coding sequence ('CDS'), 'GFF', and metagenome
retrieval from 'NCBI' and 'ENSEMBL' databases. Furthermore, an interface to the 'BioMart' database
(Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve
functional annotation for genomic loci. Users can download entire databases such
as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr',
'NCBI nt' and 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>) as
well as 'ENSEMBL' and 'ENSEMBLGENOMES' with only one command.
Author: Hajk-Georg Drost
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between biomartr versions 0.4.0 dated 2017-03-14 and 0.5.1 dated 2017-05-28
biomartr-0.4.0/biomartr/tests/testthat/test-getGO.R |only biomartr-0.5.1/biomartr/DESCRIPTION | 18 biomartr-0.5.1/biomartr/MD5 | 294 ++-- biomartr-0.5.1/biomartr/NAMESPACE | 7 biomartr-0.5.1/biomartr/NEWS.md | 52 biomartr-0.5.1/biomartr/R/biomart.R | 117 + biomartr-0.5.1/biomartr/R/biomartr-package.R |only biomartr-0.5.1/biomartr/R/connected.to.internet.R | 15 biomartr-0.5.1/biomartr/R/custom_download.R |only biomartr-0.5.1/biomartr/R/download_database.R | 94 - biomartr-0.5.1/biomartr/R/download_database_all.R | 37 biomartr-0.5.1/biomartr/R/exists.ftp.file.R | 26 biomartr-0.5.1/biomartr/R/get.ensembl.info.R | 22 biomartr-0.5.1/biomartr/R/get.ensemblgenome.info.R | 21 biomartr-0.5.1/biomartr/R/getAssemblyStats.R | 179 +- biomartr-0.5.1/biomartr/R/getAttributes.R | 69 - biomartr-0.5.1/biomartr/R/getCDS.R | 653 ++++++---- biomartr-0.5.1/biomartr/R/getDatasets.R | 106 + biomartr-0.5.1/biomartr/R/getENSEMBL.Annotation.R | 286 ++-- biomartr-0.5.1/biomartr/R/getENSEMBL.Seq.R | 148 +- biomartr-0.5.1/biomartr/R/getENSEMBL.gtf.R |only biomartr-0.5.1/biomartr/R/getENSEMBLGENOMES.Annotation.R | 605 +++++---- biomartr-0.5.1/biomartr/R/getENSEMBLGENOMES.Seq.R | 595 +++++---- biomartr-0.5.1/biomartr/R/getENSEMBLGENOMES.gtf.R |only biomartr-0.5.1/biomartr/R/getENSEMBLGENOMESInfo.R | 9 biomartr-0.5.1/biomartr/R/getENSEMBLInfo.R | 7 biomartr-0.5.1/biomartr/R/getFilters.R | 77 - biomartr-0.5.1/biomartr/R/getGENOMEREPORT.R | 30 biomartr-0.5.1/biomartr/R/getGFF.R | 290 +++- biomartr-0.5.1/biomartr/R/getGO.R | 144 +- biomartr-0.5.1/biomartr/R/getGTF.R |only biomartr-0.5.1/biomartr/R/getGenome.R | 290 +++- biomartr-0.5.1/biomartr/R/getGroups.R | 11 biomartr-0.5.1/biomartr/R/getKingdomAssemblySummary.R | 27 biomartr-0.5.1/biomartr/R/getKingdoms.R | 12 biomartr-0.5.1/biomartr/R/getMarts.R | 17 biomartr-0.5.1/biomartr/R/getMetaGenomeAnnotations.R | 171 +- biomartr-0.5.1/biomartr/R/getMetaGenomeSummary.R | 42 biomartr-0.5.1/biomartr/R/getMetaGenomes.R | 125 + biomartr-0.5.1/biomartr/R/getProteome.R | 617 +++++---- biomartr-0.5.1/biomartr/R/getRNA.R |only biomartr-0.5.1/biomartr/R/getReleases.R |only biomartr-0.5.1/biomartr/R/getRepeatMasker.R |only biomartr-0.5.1/biomartr/R/getSubMarts.R | 69 - biomartr-0.5.1/biomartr/R/getSummaryFile.R | 55 biomartr-0.5.1/biomartr/R/is.ensembl.alive.R | 13 biomartr-0.5.1/biomartr/R/is.ensemblgenomes.alive.R | 12 biomartr-0.5.1/biomartr/R/is.genome.available.R | 578 +++++--- biomartr-0.5.1/biomartr/R/listDatabases.R | 75 - biomartr-0.5.1/biomartr/R/listGenomes.R | 593 +++++---- biomartr-0.5.1/biomartr/R/listGroups.R | 246 +-- biomartr-0.5.1/biomartr/R/listKingdoms.R | 22 biomartr-0.5.1/biomartr/R/listMetaGenomes.R | 21 biomartr-0.5.1/biomartr/R/listNCBIDatabases.R |only biomartr-0.5.1/biomartr/R/meta.retrieval.R | 311 +++- biomartr-0.5.1/biomartr/R/meta.retrieval.all.R | 47 biomartr-0.5.1/biomartr/R/organismAttributes.R | 104 - biomartr-0.5.1/biomartr/R/organismBM.R | 269 ++-- biomartr-0.5.1/biomartr/R/organismFilters.R | 227 +-- biomartr-0.5.1/biomartr/R/read_assemblystats.R | 137 +- biomartr-0.5.1/biomartr/R/read_cds.R | 230 +-- biomartr-0.5.1/biomartr/R/read_genome.R | 162 +- biomartr-0.5.1/biomartr/R/read_gff.R | 53 biomartr-0.5.1/biomartr/R/read_md5file.R |only biomartr-0.5.1/biomartr/R/read_proteome.R | 173 +- biomartr-0.5.1/biomartr/R/read_rm.R |only biomartr-0.5.1/biomartr/R/read_rna.R |only biomartr-0.5.1/biomartr/R/refseqOrganisms.R | 64 biomartr-0.5.1/biomartr/R/toupper_first_char.R | 11 biomartr-0.5.1/biomartr/R/utils.R | 1 biomartr-0.5.1/biomartr/README.md | 62 biomartr-0.5.1/biomartr/build/vignette.rds |binary biomartr-0.5.1/biomartr/inst/doc/BioMart_Examples.html | 8 biomartr-0.5.1/biomartr/inst/doc/Database_Retrieval.R | 45 biomartr-0.5.1/biomartr/inst/doc/Database_Retrieval.Rmd | 38 biomartr-0.5.1/biomartr/inst/doc/Database_Retrieval.html | 52 biomartr-0.5.1/biomartr/inst/doc/Functional_Annotation.R | 150 +- biomartr-0.5.1/biomartr/inst/doc/Functional_Annotation.Rmd | 446 ------ biomartr-0.5.1/biomartr/inst/doc/Functional_Annotation.html | 492 ++----- biomartr-0.5.1/biomartr/inst/doc/Introduction.Rmd | 10 biomartr-0.5.1/biomartr/inst/doc/Introduction.html | 19 biomartr-0.5.1/biomartr/inst/doc/MetaGenome_Retrieval.R | 8 biomartr-0.5.1/biomartr/inst/doc/MetaGenome_Retrieval.Rmd | 23 biomartr-0.5.1/biomartr/inst/doc/MetaGenome_Retrieval.html | 22 biomartr-0.5.1/biomartr/inst/doc/Sequence_Retrieval.R | 117 + biomartr-0.5.1/biomartr/inst/doc/Sequence_Retrieval.Rmd | 319 ++++ biomartr-0.5.1/biomartr/inst/doc/Sequence_Retrieval.html | 215 +++ biomartr-0.5.1/biomartr/man/biomart.Rd | 51 biomartr-0.5.1/biomartr/man/biomartr-package.Rd |only biomartr-0.5.1/biomartr/man/download.database.Rd | 22 biomartr-0.5.1/biomartr/man/download.database.all.Rd | 28 biomartr-0.5.1/biomartr/man/getAssemblyStats.Rd | 67 - biomartr-0.5.1/biomartr/man/getAttributes.Rd | 17 biomartr-0.5.1/biomartr/man/getCDS.Rd | 30 biomartr-0.5.1/biomartr/man/getDatasets.Rd | 13 biomartr-0.5.1/biomartr/man/getENSEMBLGENOMESInfo.Rd | 9 biomartr-0.5.1/biomartr/man/getENSEMBLInfo.Rd | 7 biomartr-0.5.1/biomartr/man/getFilters.Rd | 20 biomartr-0.5.1/biomartr/man/getGENOMEREPORT.Rd | 9 biomartr-0.5.1/biomartr/man/getGFF.Rd | 35 biomartr-0.5.1/biomartr/man/getGO.Rd | 49 biomartr-0.5.1/biomartr/man/getGTF.Rd |only biomartr-0.5.1/biomartr/man/getGenome.Rd | 31 biomartr-0.5.1/biomartr/man/getGroups.Rd | 11 biomartr-0.5.1/biomartr/man/getKingdomAssemblySummary.Rd | 6 biomartr-0.5.1/biomartr/man/getKingdoms.Rd | 9 biomartr-0.5.1/biomartr/man/getMarts.Rd | 16 biomartr-0.5.1/biomartr/man/getMetaGenomeAnnotations.Rd | 17 biomartr-0.5.1/biomartr/man/getMetaGenomeSummary.Rd | 12 biomartr-0.5.1/biomartr/man/getMetaGenomes.Rd | 15 biomartr-0.5.1/biomartr/man/getProteome.Rd | 31 biomartr-0.5.1/biomartr/man/getRNA.Rd |only biomartr-0.5.1/biomartr/man/getReleases.Rd |only biomartr-0.5.1/biomartr/man/getRepeatMasker.Rd |only biomartr-0.5.1/biomartr/man/getSummaryFile.Rd | 6 biomartr-0.5.1/biomartr/man/is.genome.available.Rd | 36 biomartr-0.5.1/biomartr/man/listDatabases.Rd | 38 biomartr-0.5.1/biomartr/man/listGenomes.Rd | 48 biomartr-0.5.1/biomartr/man/listGroups.Rd | 29 biomartr-0.5.1/biomartr/man/listKingdoms.Rd | 17 biomartr-0.5.1/biomartr/man/listMetaGenomes.Rd | 19 biomartr-0.5.1/biomartr/man/meta.retrieval.Rd | 81 - biomartr-0.5.1/biomartr/man/meta.retrieval.all.Rd | 41 biomartr-0.5.1/biomartr/man/organismAttributes.Rd | 63 biomartr-0.5.1/biomartr/man/organismBM.Rd | 47 biomartr-0.5.1/biomartr/man/organismFilters.Rd | 60 biomartr-0.5.1/biomartr/man/read_assemblystats.Rd | 18 biomartr-0.5.1/biomartr/man/read_cds.Rd | 46 biomartr-0.5.1/biomartr/man/read_genome.Rd | 34 biomartr-0.5.1/biomartr/man/read_gff.Rd | 9 biomartr-0.5.1/biomartr/man/read_proteome.Rd | 39 biomartr-0.5.1/biomartr/man/read_rm.Rd |only biomartr-0.5.1/biomartr/man/read_rna.Rd |only biomartr-0.5.1/biomartr/man/refseqOrganisms.Rd | 5 biomartr-0.5.1/biomartr/tests/testthat/test-biomart.R | 28 biomartr-0.5.1/biomartr/tests/testthat/test-download.database.R | 17 biomartr-0.5.1/biomartr/tests/testthat/test-getAssemblyStats.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getAttributes.R | 38 biomartr-0.5.1/biomartr/tests/testthat/test-getCDS.R | 92 + biomartr-0.5.1/biomartr/tests/testthat/test-getDatasets.R | 15 biomartr-0.5.1/biomartr/tests/testthat/test-getENSEMBLGENOMESInfo.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getENSEMBLInfo.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getFilters.R | 15 biomartr-0.5.1/biomartr/tests/testthat/test-getGENOMEREPORT.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getGFF.R | 69 - biomartr-0.5.1/biomartr/tests/testthat/test-getGenome.R | 174 +- biomartr-0.5.1/biomartr/tests/testthat/test-getGroups().R | 6 biomartr-0.5.1/biomartr/tests/testthat/test-getKingdomAssemblySummary.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getKingdoms().R | 19 biomartr-0.5.1/biomartr/tests/testthat/test-getMetaGenomeAnnotations.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getMetaGenomeSummary.R |only biomartr-0.5.1/biomartr/tests/testthat/test-getProteome.R | 117 + biomartr-0.5.1/biomartr/tests/testthat/test-getRNA.R |only biomartr-0.5.1/biomartr/tests/testthat/test-is.genome.available.R | 112 + biomartr-0.5.1/biomartr/tests/testthat/test-organismAttributes.R | 2 biomartr-0.5.1/biomartr/tests/testthat/test-organismBM.R | 3 biomartr-0.5.1/biomartr/tests/testthat/test-organismFilters.R | 2 biomartr-0.5.1/biomartr/vignettes/Database_Retrieval.Rmd | 38 biomartr-0.5.1/biomartr/vignettes/Functional_Annotation.Rmd | 446 ------ biomartr-0.5.1/biomartr/vignettes/Introduction.Rmd | 10 biomartr-0.5.1/biomartr/vignettes/MetaGenome_Retrieval.Rmd | 23 biomartr-0.5.1/biomartr/vignettes/Sequence_Retrieval.Rmd | 319 ++++ 162 files changed, 7860 insertions(+), 5538 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre],
Dawei Lang [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/example.css),
Patrick Schratz [ctb],
Sean Lopp [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.2 dated 2017-02-15 and 0.3 dated 2017-05-28
DESCRIPTION | 20 ++-- MD5 | 17 +-- R/render.R | 46 +++++++--- R/utils.R | 31 ------ build/vignette.rds |binary inst/rmarkdown/templates/xaringan/resources/countdown.js |only inst/rmarkdown/templates/xaringan/resources/default.html | 2 inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 19 +++- inst/rmarkdown/templates/xaringan_zh-CN/skeleton/skeleton.Rmd | 15 +++ man/moon_reader.Rd | 10 +- 10 files changed, 98 insertions(+), 62 deletions(-)
Title: Bayesian Structural Time Series
Description: Time series regression using dynamic linear models fit using
MCMC. See Scott and Varian (2014) <DOI:10.1504/IJMMNO.2014.059942>, among many
other sources.
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between bsts versions 0.7.0 dated 2017-04-11 and 0.7.1 dated 2017-05-28
bsts-0.7.0/bsts/R/time_series_boxplot.R |only bsts-0.7.0/bsts/man/timeseries.boxplot.Rd |only bsts-0.7.1/bsts/DESCRIPTION | 16 - bsts-0.7.1/bsts/MD5 | 54 ++--- bsts-0.7.1/bsts/NAMESPACE | 7 bsts-0.7.1/bsts/R/compare.bsts.models.R | 5 bsts-0.7.1/bsts/R/diagnostics.R | 94 +++++++-- bsts-0.7.1/bsts/R/format.timestamps.R | 4 bsts-0.7.1/bsts/R/mixed.frequency.R | 4 bsts-0.7.1/bsts/R/plots.R | 102 +++++----- bsts-0.7.1/bsts/R/summary.bsts.R | 2 bsts-0.7.1/bsts/man/add.dynamic.regression.Rd | 2 bsts-0.7.1/bsts/man/one.step.prediction.errors.Rd | 49 ++++ bsts-0.7.1/bsts/man/plot.bsts.Rd | 118 +++++++----- bsts-0.7.1/bsts/src/bsts.cc | 67 ++++-- bsts-0.7.1/bsts/src/bsts_init.cc | 5 bsts-0.7.1/bsts/src/mixed_frequency.cc | 11 - bsts-0.7.1/bsts/src/model_manager.cc | 45 ---- bsts-0.7.1/bsts/src/model_manager.h | 99 ++++++---- bsts-0.7.1/bsts/src/state_space_gaussian_model_manager.cc | 79 ++++++-- bsts-0.7.1/bsts/src/state_space_gaussian_model_manager.h | 39 +++ bsts-0.7.1/bsts/src/state_space_logit_model_manager.cc | 30 --- bsts-0.7.1/bsts/src/state_space_logit_model_manager.h | 10 - bsts-0.7.1/bsts/src/state_space_poisson_model_manager.cc | 29 -- bsts-0.7.1/bsts/src/state_space_poisson_model_manager.h | 10 - bsts-0.7.1/bsts/src/state_space_regression_model_manager.cc | 110 ++++++++--- bsts-0.7.1/bsts/src/state_space_regression_model_manager.h | 42 +++- bsts-0.7.1/bsts/src/state_space_student_model_manager.cc | 86 ++++++-- bsts-0.7.1/bsts/src/state_space_student_model_manager.h | 58 +++++ 29 files changed, 763 insertions(+), 414 deletions(-)
Title: MCMC for Spike and Slab Regression
Description: Spike and slab regression a la McCulloch and George (1997).
Author: Steven L. Scott <stevescott@google.com>
Maintainer: Steven L. Scott <stevescott@google.com>
Diff between BoomSpikeSlab versions 0.8.0 dated 2017-04-08 and 0.9.0 dated 2017-05-28
DESCRIPTION | 10 +++++----- LICENSE | 14 +++++++------- MD5 | 24 +++++++++++++++--------- NAMESPACE | 5 ++++- R/logit.spike.R | 20 ++++++++++++++++++++ R/nested.regression.R |only R/shrinkage.regression.R |only R/spike.slab.prior.R | 18 ++++++++++++------ man/logit.spike.Rd | 7 +++++++ man/nested.regression.Rd |only man/shrinkage.regression.Rd |only man/summary.logit.spike.Rd | 2 +- src/boom_spike_slab_init.cc | 24 +++++++++++++++++++++++- src/logit_spike_slab_wrapper.cc | 5 +++++ src/nested_regression_wrapper.cc |only src/shrinkage_regression_wrapper.cc |only 16 files changed, 99 insertions(+), 30 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on
Markov chain Monte Carlo. Although boom contains a few R utilities
(mainly plotting functions), its primary purpose is to install the
BOOM C++ library on your system so that other packages can link
against it.
Author: Steven L. Scott is the sole author and creator of the BOOM
project. Some code in the BOOM libraries has been modified from
other open source projects. These include Cephes (obtained from
Netlib, written by Stephen L. Moshier), NEWUOA (M.J.D Powell,
obtained from Powell's web site), and a modified version of the R
math libraries (R core development team). Original copyright
notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications
made to the original code.
Maintainer: Steve Scott <stevescott@google.com>
Diff between Boom versions 0.6 dated 2017-04-07 and 0.7 dated 2017-05-28
Boom-0.6/Boom/inst/include/LinAlg/Array3.hpp |only Boom-0.6/Boom/src/LinAlg/Array3.cpp |only Boom-0.7/Boom/DESCRIPTION | 8 Boom-0.7/Boom/MD5 | 613 ++--- Boom-0.7/Boom/NAMESPACE | 12 Boom-0.7/Boom/R/compare.dynamic.distributions.R |only Boom-0.7/Boom/R/mscan.R | 7 Boom-0.7/Boom/R/plot.dynamic.distribution.R | 277 +- Boom-0.7/Boom/R/plot.many.ts.R | 16 Boom-0.7/Boom/R/prior_specification.R | 15 Boom-0.7/Boom/R/sufstats.R |only Boom-0.7/Boom/R/timeseries.boxplot.R |only Boom-0.7/Boom/inst/include/LinAlg/Cholesky.hpp | 76 Boom-0.7/Boom/inst/include/LinAlg/CorrelationMatrix.hpp | 2 Boom-0.7/Boom/inst/include/LinAlg/Givens.hpp | 2 Boom-0.7/Boom/inst/include/LinAlg/Matrix.hpp | 7 Boom-0.7/Boom/inst/include/LinAlg/SpdMatrix.hpp | 10 Boom-0.7/Boom/inst/include/LinAlg/Vector.hpp | 14 Boom-0.7/Boom/inst/include/LinAlg/VectorViewIterator.hpp | 12 Boom-0.7/Boom/inst/include/Models/BetaBinomialModel.hpp | 23 Boom-0.7/Boom/inst/include/Models/BetaModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/BinomialModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/ConstrainedVectorParams.hpp | 4 Boom-0.7/Boom/inst/include/Models/DirichletModel.hpp | 10 Boom-0.7/Boom/inst/include/Models/DoubleModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/ExponentialModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/GammaModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/GaussianModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/GaussianModelBase.hpp | 64 Boom-0.7/Boom/inst/include/Models/GaussianModelGivenSigma.hpp | 68 Boom-0.7/Boom/inst/include/Models/Glm/CumulativeLogitModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/Glm/CumulativeProbitModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/Glm/ModelSelectionConcepts.hpp | 2 Boom-0.7/Boom/inst/include/Models/Glm/MultinomialLogitModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/Glm/MultinomialProbitModel.hpp | 10 Boom-0.7/Boom/inst/include/Models/Glm/MvReg2.hpp | 6 Boom-0.7/Boom/inst/include/Models/Glm/MvnGivenX.hpp | 14 Boom-0.7/Boom/inst/include/Models/Glm/MvnGivenXandSigma.hpp | 2 Boom-0.7/Boom/inst/include/Models/Glm/MvtRegModel.hpp | 6 Boom-0.7/Boom/inst/include/Models/Glm/OrdinalCutpointModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/Glm/PosteriorSamplers/BregVsSampler.hpp | 31 Boom-0.7/Boom/inst/include/Models/Glm/PosteriorSamplers/PartRegSampler.hpp | 33 Boom-0.7/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionCoefficientSampler.hpp |only Boom-0.7/Boom/inst/include/Models/Glm/PosteriorSamplers/RegressionShrinkageSampler.hpp |only Boom-0.7/Boom/inst/include/Models/Glm/ProbitRegression.hpp | 4 Boom-0.7/Boom/inst/include/Models/Glm/RegressionModel.hpp | 6 Boom-0.7/Boom/inst/include/Models/Glm/TRegression.hpp | 4 Boom-0.7/Boom/inst/include/Models/Glm/VariableSelectionPrior.hpp | 27 Boom-0.7/Boom/inst/include/Models/Glm/ZeroInflatedPoissonRegression.hpp | 6 Boom-0.7/Boom/inst/include/Models/HMM/HealthStateModel.hpp | 7 Boom-0.7/Boom/inst/include/Models/Hierarchical/HierarchicalGaussianRegressionModel.hpp |only Boom-0.7/Boom/inst/include/Models/Hierarchical/HierarchicalModel.hpp | 1 Boom-0.7/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.hpp |only Boom-0.7/Boom/inst/include/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionSampler.hpp |only Boom-0.7/Boom/inst/include/Models/IRT/ItemDataPolicy.hpp | 20 Boom-0.7/Boom/inst/include/Models/IRT/PartialCreditModel.hpp | 42 Boom-0.7/Boom/inst/include/Models/IRT/PcrNid.hpp | 30 Boom-0.7/Boom/inst/include/Models/IRT/SubjectPrior.hpp | 6 Boom-0.7/Boom/inst/include/Models/IRT/Subject_prior.hpp | 15 Boom-0.7/Boom/inst/include/Models/IRT/multisubscale_logit_cutpoint_model.hpp | 7 Boom-0.7/Boom/inst/include/Models/IndependentMvnModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/IndependentMvnModelGivenScalarSigma.hpp | 2 Boom-0.7/Boom/inst/include/Models/LognormalModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/MarginallyUniformCorrelationModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/MarkovModel.hpp | 8 Boom-0.7/Boom/inst/include/Models/Mixtures/DirichletProcessMvnModel.hpp | 40 Boom-0.7/Boom/inst/include/Models/Mixtures/MvnMetaAnalysisDPMPriorModel.hpp |only Boom-0.7/Boom/inst/include/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.hpp | 6 Boom-0.7/Boom/inst/include/Models/Mixtures/PosteriorSamplers/MvnMetaAnalysisDPMPriorSampler.hpp |only Boom-0.7/Boom/inst/include/Models/MultinomialModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/MvnBase.hpp | 2 Boom-0.7/Boom/inst/include/Models/MvnGivenSigma.hpp | 2 Boom-0.7/Boom/inst/include/Models/MvnModel.hpp | 3 Boom-0.7/Boom/inst/include/Models/MvtModel.hpp | 3 Boom-0.7/Boom/inst/include/Models/PointProcess/BoundedPoissonProcessSimulator.hpp | 2 Boom-0.7/Boom/inst/include/Models/PointProcess/CosinePoissonProcess.hpp | 1 Boom-0.7/Boom/inst/include/Models/PointProcess/HomogeneousPoissonProcess.hpp | 1 Boom-0.7/Boom/inst/include/Models/PointProcess/PoissonClusterProcess.hpp | 1 Boom-0.7/Boom/inst/include/Models/PointProcess/PoissonProcess.hpp | 1 Boom-0.7/Boom/inst/include/Models/PointProcess/WeeklyCyclePoissonProcess.hpp | 1 Boom-0.7/Boom/inst/include/Models/PoissonModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/Policies/SufstatDataPolicy.hpp | 10 Boom-0.7/Boom/inst/include/Models/PosteriorSamplers/GaussianGivenSigmaSampler.hpp |only Boom-0.7/Boom/inst/include/Models/PosteriorSamplers/GaussianVarSampler.hpp | 9 Boom-0.7/Boom/inst/include/Models/PosteriorSamplers/MvnVarSampler.hpp | 36 Boom-0.7/Boom/inst/include/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.hpp | 18 Boom-0.7/Boom/inst/include/Models/ProductDirichletModel.hpp | 6 Boom-0.7/Boom/inst/include/Models/ProductVectorModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/SpdParams.hpp | 4 Boom-0.7/Boom/inst/include/Models/StateSpace/AggregatedStateSpaceRegression.hpp | 4 Boom-0.7/Boom/inst/include/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.hpp | 5 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/ArStateModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/DynamicRegressionStateModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/LocalLevelStateModel.hpp | 6 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/LocalLinearTrend.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/RegressionStateModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/SeasonalStateModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp | 4 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/StateModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/StudentLocalLinearTrend.hpp | 6 Boom-0.7/Boom/inst/include/Models/StateSpace/StateModels/TrigStateModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceLogitModel.hpp | 17 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceModel.hpp | 10 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 59 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceNormalMixture.hpp | 10 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpacePoissonModel.hpp | 13 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceRegressionModel.hpp | 25 Boom-0.7/Boom/inst/include/Models/StateSpace/StateSpaceStudentRegressionModel.hpp | 24 Boom-0.7/Boom/inst/include/Models/Sufstat.hpp | 91 Boom-0.7/Boom/inst/include/Models/TimeSeries/ArModel.hpp | 4 Boom-0.7/Boom/inst/include/Models/TimeSeries/AugmentedTimeSeries.hpp | 12 Boom-0.7/Boom/inst/include/Models/TimeSeries/AugmentedTimeSeriesDataPolicy.hpp | 8 Boom-0.7/Boom/inst/include/Models/TimeSeries/TimeSeriesDataPolicy.hpp | 4 Boom-0.7/Boom/inst/include/Models/TruncatedGammaModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/UniformCorrelationModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/UniformModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/UniformShrinkagePriorModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/VectorModel.hpp | 3 Boom-0.7/Boom/inst/include/Models/WishartModel.hpp | 6 Boom-0.7/Boom/inst/include/Models/ZeroInflatedGammaModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/ZeroInflatedLognormalModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/ZeroInflatedPoissonModel.hpp | 2 Boom-0.7/Boom/inst/include/Models/ZeroMeanGaussianModel.hpp | 2 Boom-0.7/Boom/inst/include/Samplers/ARMS.hpp | 18 Boom-0.7/Boom/inst/include/Samplers/Gilks/arms.hpp | 12 Boom-0.7/Boom/inst/include/Samplers/ImportanceResampler.hpp | 4 Boom-0.7/Boom/inst/include/Samplers/MetropolisHastings.hpp | 5 Boom-0.7/Boom/inst/include/Samplers/RejectionSampler.hpp | 4 Boom-0.7/Boom/inst/include/Samplers/ScalarAdaptiveRejectionSampler.hpp | 2 Boom-0.7/Boom/inst/include/Samplers/ScalarLangevinSampler.hpp | 2 Boom-0.7/Boom/inst/include/Samplers/SliceSampler.hpp | 2 Boom-0.7/Boom/inst/include/Samplers/TIM.hpp | 5 Boom-0.7/Boom/inst/include/TargetFun/JacobianChecker.hpp | 4 Boom-0.7/Boom/inst/include/TargetFun/LogPost.hpp | 28 Boom-0.7/Boom/inst/include/TargetFun/ScalarLogpostTF.hpp | 15 Boom-0.7/Boom/inst/include/TargetFun/TargetFun.hpp | 4 Boom-0.7/Boom/inst/include/TargetFun/Transformation.hpp | 4 Boom-0.7/Boom/inst/include/cpputil/Date.hpp | 4 Boom-0.7/Boom/inst/include/cpputil/LongString.hpp | 2 Boom-0.7/Boom/inst/include/cpputil/ToString.hpp |only Boom-0.7/Boom/inst/include/cpputil/ask_to_continue.hpp | 4 Boom-0.7/Boom/inst/include/cpputil/compare_vector_bool.hpp | 16 Boom-0.7/Boom/inst/include/cpputil/permute.hpp | 2 Boom-0.7/Boom/inst/include/cpputil/print.hpp | 2 Boom-0.7/Boom/inst/include/distributions.hpp | 19 Boom-0.7/Boom/inst/include/distributions/BoundedAdaptiveRejectionSampler.hpp | 105 Boom-0.7/Boom/inst/include/distributions/Rmath_dist.hpp | 2 Boom-0.7/Boom/inst/include/r_interface/boom_r_tools.hpp | 16 Boom-0.7/Boom/inst/include/r_interface/create_state_model.hpp | 52 Boom-0.7/Boom/inst/include/r_interface/list_io.hpp | 36 Boom-0.7/Boom/inst/include/r_interface/parse_model_formula.hpp | 12 Boom-0.7/Boom/inst/include/r_interface/prior_specification.hpp | 17 Boom-0.7/Boom/inst/include/r_interface/sufstats.hpp |only Boom-0.7/Boom/inst/include/stats/Design.hpp | 36 Boom-0.7/Boom/inst/include/stats/simple_random_sample.hpp | 2 Boom-0.7/Boom/man/compare.dynamic.distributions.Rd |only Boom-0.7/Boom/man/inverse-wishart.Rd | 28 Boom-0.7/Boom/man/mscan.Rd | 9 Boom-0.7/Boom/man/plot.dynamic.distribution.Rd | 5 Boom-0.7/Boom/man/sufstat.Rd |only Boom-0.7/Boom/man/timeseries.boxplot.Rd |only Boom-0.7/Boom/src/LinAlg/Cholesky.cpp | 249 +- Boom-0.7/Boom/src/LinAlg/Matrix.cpp | 2 Boom-0.7/Boom/src/LinAlg/Vector.cpp | 10 Boom-0.7/Boom/src/Models/BetaBinomialModel.cpp | 14 Boom-0.7/Boom/src/Models/BetaModel.cpp | 2 Boom-0.7/Boom/src/Models/BinomialModel.cpp | 2 Boom-0.7/Boom/src/Models/DirichletModel.cpp | 4 Boom-0.7/Boom/src/Models/ExponentialModel.cpp | 12 Boom-0.7/Boom/src/Models/FiniteMixtureModel.cpp | 4 Boom-0.7/Boom/src/Models/GammaModel.cpp | 4 Boom-0.7/Boom/src/Models/GaussianModelBase.cpp | 70 Boom-0.7/Boom/src/Models/GaussianModelGivenSigma.cpp | 155 - Boom-0.7/Boom/src/Models/Glm/CumulativeLogitModel.cpp | 4 Boom-0.7/Boom/src/Models/Glm/CumulativeProbitModel.cpp | 4 Boom-0.7/Boom/src/Models/Glm/MultinomialLogitModel.cpp | 8 Boom-0.7/Boom/src/Models/Glm/MultinomialProbitModel.cpp | 22 Boom-0.7/Boom/src/Models/Glm/MvReg2.cpp | 24 Boom-0.7/Boom/src/Models/Glm/MvnGivenX.cpp | 5 Boom-0.7/Boom/src/Models/Glm/MvnGivenXandSigma.cpp | 4 Boom-0.7/Boom/src/Models/Glm/MvtRegModel.cpp | 28 Boom-0.7/Boom/src/Models/Glm/OrdinalCutpointModel.cpp | 8 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/BinomialLogitSpikeSlabSampler.cpp | 17 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/BregVsSampler.cpp | 201 - Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/HierarchicalPoissonRegressionSampler.cpp | 2 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/LogitSampler.cpp | 2 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/LogitSamplerBma.cpp | 6 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/MLVS.cpp | 6 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/MlogitRwm.cpp | 4 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/PartRegSampler.cpp | 7 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/ProbitSpikeSlabSampler.cpp | 2 Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/RegressionCoefficientSampler.cpp |only Boom-0.7/Boom/src/Models/Glm/PosteriorSamplers/RegressionShrinkageSampler.cpp |only Boom-0.7/Boom/src/Models/Glm/ProbitRegression.cpp | 11 Boom-0.7/Boom/src/Models/Glm/RegressionModel.cpp | 16 Boom-0.7/Boom/src/Models/Glm/TRegression.cpp | 12 Boom-0.7/Boom/src/Models/Glm/VariableSelectionPrior.cpp | 205 - Boom-0.7/Boom/src/Models/Glm/ZeroInflatedGammaRegression.cpp | 2 Boom-0.7/Boom/src/Models/Glm/ZeroInflatedPoissonRegression.cpp | 6 Boom-0.7/Boom/src/Models/HMM/HealthStateModel.cpp | 16 Boom-0.7/Boom/src/Models/HMM/hmm_tools.cpp | 2 Boom-0.7/Boom/src/Models/Hierarchical/HierarchicalGaussianRegressionModel.cpp |only Boom-0.7/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionAsisSampler.cpp |only Boom-0.7/Boom/src/Models/Hierarchical/PosteriorSamplers/HierarchicalGaussianRegressionSampler.cpp |only Boom-0.7/Boom/src/Models/IRT/IRT.cpp | 6 Boom-0.7/Boom/src/Models/IRT/Subject.cpp | 66 Boom-0.7/Boom/src/Models/IRT/SubjectPrior.cpp | 10 Boom-0.7/Boom/src/Models/IndependentMvnModel.cpp | 4 Boom-0.7/Boom/src/Models/IndependentMvnModelGivenScalarSigma.cpp | 4 Boom-0.7/Boom/src/Models/LognormalModel.cpp | 4 Boom-0.7/Boom/src/Models/MarginallyUniformCorrelationModel.cpp | 8 Boom-0.7/Boom/src/Models/Mixtures/DirichletProcessMvnModel.cpp | 40 Boom-0.7/Boom/src/Models/Mixtures/MvnMetaAnalysisDPMPriorModel.cpp |only Boom-0.7/Boom/src/Models/Mixtures/PosteriorSamplers/DirichletProcessMvnCollapsedGibbsSampler.cpp | 29 Boom-0.7/Boom/src/Models/Mixtures/PosteriorSamplers/MvnMetaAnalysisDPMPriorSampler.cpp |only Boom-0.7/Boom/src/Models/MultinomialModel.cpp | 2 Boom-0.7/Boom/src/Models/MvnBase.cpp | 4 Boom-0.7/Boom/src/Models/MvnGivenSigma.cpp | 2 Boom-0.7/Boom/src/Models/MvnModel.cpp | 4 Boom-0.7/Boom/src/Models/MvtModel.cpp | 4 Boom-0.7/Boom/src/Models/PointProcess/BoundedPoissonProcessSimulator.cpp | 5 Boom-0.7/Boom/src/Models/PointProcess/CosinePoissonProcess.cpp | 3 Boom-0.7/Boom/src/Models/PointProcess/HomogeneousPoissonProcess.cpp | 5 Boom-0.7/Boom/src/Models/PointProcess/PoissonClusterProcess.cpp | 3 Boom-0.7/Boom/src/Models/PointProcess/WeeklyCyclePoissonProcess.cpp | 7 Boom-0.7/Boom/src/Models/PoissonModel.cpp | 2 Boom-0.7/Boom/src/Models/PosteriorSamplers/CorrelationSampler.cpp | 4 Boom-0.7/Boom/src/Models/PosteriorSamplers/GaussianGivenSigmaSampler.cpp |only Boom-0.7/Boom/src/Models/PosteriorSamplers/GaussianVarSampler.cpp | 31 Boom-0.7/Boom/src/Models/PosteriorSamplers/MvnVarSampler.cpp | 94 Boom-0.7/Boom/src/Models/PosteriorSamplers/SepStratSampler.cpp | 10 Boom-0.7/Boom/src/Models/PosteriorSamplers/ZeroMeanGaussianConjSampler.cpp | 66 Boom-0.7/Boom/src/Models/ProductDirichletModel.cpp | 4 Boom-0.7/Boom/src/Models/ProductVectorModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/AggregatedStateSpaceRegression.cpp | 12 Boom-0.7/Boom/src/Models/StateSpace/PosteriorSamplers/AggregatedStateSpacePosteriorSampler.cpp | 2 Boom-0.7/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceLogitPosteriorSampler.cpp | 47 Boom-0.7/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePoissonPosteriorSampler.cpp | 90 Boom-0.7/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpacePosteriorSampler.cpp | 11 Boom-0.7/Boom/src/Models/StateSpace/PosteriorSamplers/StateSpaceStudentPosteriorSampler.cpp | 46 Boom-0.7/Boom/src/Models/StateSpace/StateModels/ArStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/DynamicRegressionStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/LocalLevelStateModel.cpp | 15 Boom-0.7/Boom/src/Models/StateSpace/StateModels/LocalLinearTrend.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/RandomWalkHolidayStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/RegressionStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/SeasonalStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/SemilocalLinearTrend.cpp | 12 Boom-0.7/Boom/src/Models/StateSpace/StateModels/StateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateModels/StudentLocalLinearTrend.cpp | 19 Boom-0.7/Boom/src/Models/StateSpace/StateModels/TrigStateModel.cpp | 4 Boom-0.7/Boom/src/Models/StateSpace/StateSpaceLogitModel.cpp | 123 - Boom-0.7/Boom/src/Models/StateSpace/StateSpaceModel.cpp | 59 Boom-0.7/Boom/src/Models/StateSpace/StateSpaceModelBase.cpp | 78 Boom-0.7/Boom/src/Models/StateSpace/StateSpaceNormalMixture.cpp | 9 Boom-0.7/Boom/src/Models/StateSpace/StateSpacePoissonModel.cpp | 63 Boom-0.7/Boom/src/Models/StateSpace/StateSpaceRegressionModel.cpp | 59 Boom-0.7/Boom/src/Models/StateSpace/StateSpaceStudentRegressionModel.cpp | 82 Boom-0.7/Boom/src/Models/Sufstat.cpp | 11 Boom-0.7/Boom/src/Models/TimeSeries/ArModel.cpp | 8 Boom-0.7/Boom/src/Models/TruncatedGammaModel.cpp | 6 Boom-0.7/Boom/src/Models/UniformCorrelationModel.cpp | 4 Boom-0.7/Boom/src/Models/UniformModel.cpp | 2 Boom-0.7/Boom/src/Models/UniformShrinkagePriorModel.cpp | 4 Boom-0.7/Boom/src/Models/WeightedMvnModel.cpp | 2 Boom-0.7/Boom/src/Models/WishartModel.cpp | 4 Boom-0.7/Boom/src/Models/ZeroInflatedGammaModel.cpp | 6 Boom-0.7/Boom/src/Models/ZeroInflatedLognormalModel.cpp | 6 Boom-0.7/Boom/src/Models/ZeroInflatedPoissonModel.cpp | 6 Boom-0.7/Boom/src/Samplers/ARMS.cpp | 91 Boom-0.7/Boom/src/Samplers/Gilks/arms.cpp | 150 - Boom-0.7/Boom/src/Samplers/ImportanceResampler.cpp | 4 Boom-0.7/Boom/src/Samplers/MetropolisHastings.cpp | 6 Boom-0.7/Boom/src/Samplers/RejectionSampler.cpp | 4 Boom-0.7/Boom/src/Samplers/ScalarAdaptiveRejectionSampler.cpp | 2 Boom-0.7/Boom/src/Samplers/ScalarLangevinSampler.cpp | 4 Boom-0.7/Boom/src/Samplers/SliceSampler.cpp | 4 Boom-0.7/Boom/src/Samplers/TIM.cpp | 2 Boom-0.7/Boom/src/TargetFun/JacobianChecker.cpp | 8 Boom-0.7/Boom/src/TargetFun/LogPost.cpp | 78 Boom-0.7/Boom/src/TargetFun/ScalarLogpostTF.cpp | 23 Boom-0.7/Boom/src/TargetFun/TargetFun.cpp | 4 Boom-0.7/Boom/src/TargetFun/Transformation.cpp | 4 Boom-0.7/Boom/src/boom_r_tools.cpp | 13 Boom-0.7/Boom/src/cpputil/Date.cpp | 34 Boom-0.7/Boom/src/cpputil/LongString.cpp | 6 Boom-0.7/Boom/src/cpputil/compare_vector_bool.cpp | 4 Boom-0.7/Boom/src/cpputil/is_numeric.cpp | 18 Boom-0.7/Boom/src/cpputil/split_delimited.cpp | 6 Boom-0.7/Boom/src/cpputil/split_string.cpp | 10 Boom-0.7/Boom/src/create_state_model.cpp | 356 +-- Boom-0.7/Boom/src/distributions/BinomialDistribution.cpp | 2 Boom-0.7/Boom/src/distributions/BoundedAdaptiveRejectionSampler.cpp | 247 +- Boom-0.7/Boom/src/distributions/Rmath_dist.cpp | 2 Boom-0.7/Boom/src/distributions/mvn.cpp | 22 Boom-0.7/Boom/src/distributions/random_cor.cpp | 4 Boom-0.7/Boom/src/distributions/rtriangle.cpp | 4 Boom-0.7/Boom/src/distributions/student_fix.cpp | 2 Boom-0.7/Boom/src/list_io.cpp | 67 Boom-0.7/Boom/src/math/cephes/chbevl.cpp | 6 Boom-0.7/Boom/src/math/cephes/dawsn.cpp | 6 Boom-0.7/Boom/src/math/cephes/ei.cpp | 4 Boom-0.7/Boom/src/math/cephes/expn.cpp | 18 Boom-0.7/Boom/src/math/cephes/fac.cpp | 4 Boom-0.7/Boom/src/math/cephes/fresnl.cpp | 8 Boom-0.7/Boom/src/math/cephes/planck.cpp | 12 Boom-0.7/Boom/src/math/cephes/polevl.cpp | 8 Boom-0.7/Boom/src/math/cephes/polylog.cpp | 20 Boom-0.7/Boom/src/math/cephes/rgamma.cpp | 12 Boom-0.7/Boom/src/math/cephes/shichi.cpp | 6 Boom-0.7/Boom/src/math/cephes/sici.cpp | 6 Boom-0.7/Boom/src/math/cephes/spence.cpp | 6 Boom-0.7/Boom/src/math/cephes/zeta.cpp | 4 Boom-0.7/Boom/src/math/cephes/zetac.cpp | 12 Boom-0.7/Boom/src/numopt/Integral.cpp | 1098 +++++----- Boom-0.7/Boom/src/parse_model_formula.cpp | 122 - Boom-0.7/Boom/src/prior_specification.cpp | 7 Boom-0.7/Boom/src/stats/Design.cpp | 59 Boom-0.7/Boom/src/stats/NaturalSpline.cpp | 57 Boom-0.7/Boom/src/sufstats.cpp |only 321 files changed, 4255 insertions(+), 3334 deletions(-)
Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that provides
stricter checking and better formatting than the traditional data frame.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 1.3.1 dated 2017-05-17 and 1.3.3 dated 2017-05-28
tibble-1.3.1/tibble/src/init.c |only tibble-1.3.3/tibble/DESCRIPTION | 8 +- tibble-1.3.3/tibble/MD5 | 32 +++++----- tibble-1.3.3/tibble/NAMESPACE | 1 tibble-1.3.3/tibble/NEWS.md | 11 +++ tibble-1.3.3/tibble/R/RcppExports.R | 2 tibble-1.3.3/tibble/R/repair-names.R | 1 tibble-1.3.3/tibble/R/tbl-df.r | 8 +- tibble-1.3.3/tibble/R/utils-format.r | 10 +-- tibble-1.3.3/tibble/README.md | 26 ++++---- tibble-1.3.3/tibble/build/vignette.rds |binary tibble-1.3.3/tibble/inst/doc/extending.html | 18 ++--- tibble-1.3.3/tibble/man/formatting.Rd | 3 tibble-1.3.3/tibble/man/tibble-package.Rd | 4 - tibble-1.3.3/tibble/src/RcppExports.cpp | 10 +++ tibble-1.3.3/tibble/tests/testthat/output/trunc_mat/non-syntactic.txt |only tibble-1.3.3/tibble/tests/testthat/test-tidy_names.R | 7 ++ tibble-1.3.3/tibble/tests/testthat/test-trunc-mat.R | 4 + 18 files changed, 93 insertions(+), 52 deletions(-)
Title: Tools for Standardizing Variables for Regression in R
Description: Tools which allow regression variables to be placed on similar
scales, offering computational benefits as well as easing interpretation of
regression output.
Author: Christopher D. Eager [aut, cre]
Maintainer: Christopher D. Eager <eagerstats@gmail.com>
Diff between standardize versions 0.1.1 dated 2017-04-18 and 0.2.0 dated 2017-05-28
DESCRIPTION | 6 MD5 | 46 ++-- NAMESPACE | 1 NEWS.md | 10 + R/contrast_functions.R | 9 R/data.R | 8 R/scale_by.R | 76 +++----- R/standardize-package.R | 5 R/standardize.R | 281 +++++++++++++++-------------- R/standardized-class.R | 83 ++++++-- R/utilities.R | 359 ++++++++++++++++++++------------------ README.md | 165 +++++++++-------- inst/CITATION | 8 inst/doc/using-standardize.R | 8 inst/doc/using-standardize.Rmd | 29 ++- inst/doc/using-standardize.html | 209 +++++++++++----------- man/predict.standardized.Rd | 8 man/ptk.Rd | 6 man/scale_by.Rd | 7 man/standardize-package.Rd | 5 man/standardize.Rd | 55 ++++- man/standardized-class.Rd | 19 +- tests/testthat/test-standardize.R | 38 +++- vignettes/using-standardize.Rmd | 29 ++- 24 files changed, 847 insertions(+), 623 deletions(-)
Title: Fast and Robust Surrogate Variable Analysis
Description: Introduces a fast and efficient Surrogate Variable Analysis algorithm that captures variation of unknown sources (batch effects) for high-dimensional data sets. The algorithm is built on the 'irwsva.build' function of the 'sva' package and proposes a revision on it that achieves an order of magnitude faster running time while trading no accuracy loss in return.
Author: Jun Chen <Chen.Jun2@mayo.edu>, Ehsan Behnam <behnamgh@usc.edu>
Maintainer: Jun Chen <Chen.Jun2@mayo.edu>
Diff between SmartSVA versions 0.1.2 dated 2017-05-26 and 0.1.3 dated 2017-05-28
DESCRIPTION | 10 +-- MD5 | 8 +-- NAMESPACE | 1 R/SmartSVA.R | 133 ++++++++++++++++++++++++++-------------------------- man/smartsva.cpp.Rd | 2 5 files changed, 79 insertions(+), 75 deletions(-)
Title: Create Interactive Web Graphics via 'plotly.js'
Description: Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.
Author: Carson Sievert [aut, cre],
Chris Parmer [aut],
Toby Hocking [aut],
Scott Chamberlain [aut],
Karthik Ram [aut],
Marianne Corvellec [aut],
Pedro Despouy [aut],
Plotly Technologies Inc. [cph]
Maintainer: Carson Sievert <cpsievert1@gmail.com>
Diff between plotly versions 4.6.0 dated 2017-04-25 and 4.7.0 dated 2017-05-28
DESCRIPTION | 10 MD5 | 179 +++++++------- NAMESPACE | 25 ++ NEWS.md | 26 ++ R/api.R | 235 +++++++++++------- R/api_exports.R | 21 - R/ggplotly-legacy.R | 40 +-- R/ggplotly.R | 167 ++++++++++--- R/group2NA.R | 139 ++++++----- R/highlight.R | 26 +- R/imports.R | 1 R/layers2traces.R | 61 +++- R/plotly.R | 37 +- R/plotly_build.R | 15 - R/process.R | 1 R/sf.R |only R/style.R | 8 R/sysdata.rda |binary R/toRGB.R | 11 R/utils.R | 108 +++++++- README.md | 49 ++- demo/00Index | 1 demo/highlight-binned-target.R | 25 +- demo/rotate.R |only demo/tour-USArrests.R | 2 inst/htmlwidgets/lib/plotlyjs/plotly-latest.min.js | 142 +++++------ inst/htmlwidgets/plotly.js | 260 +++++++++------------ inst/htmlwidgets/plotly.yaml | 6 man/api.Rd | 23 - man/get_l.Rd |only man/get_x.Rd |only man/get_y.Rd |only man/group2NA.Rd |only man/highlight.Rd | 26 +- man/plot_dendro.Rd | 2 man/plot_ly.Rd | 14 - man/remove_typedarray_polyfill.Rd | 2 man/style.Rd | 7 tests/testthat/test-animate-highlight.R | 47 ++- tests/testthat/test-api.R | 74 +++++ tests/testthat/test-cookbook-axes.R | 10 tests/testthat/test-cookbook-lines.R | 10 tests/testthat/test-ggplot-abline.R | 2 tests/testthat/test-ggplot-annotation_.R | 32 +- tests/testthat/test-ggplot-area.R | 2 tests/testthat/test-ggplot-bar.R | 22 - tests/testthat/test-ggplot-boxplot.R | 32 +- tests/testthat/test-ggplot-col.R | 2 tests/testthat/test-ggplot-contour.R | 2 tests/testthat/test-ggplot-coord-fixed.R |only tests/testthat/test-ggplot-crossbar.R | 4 tests/testthat/test-ggplot-date.R | 6 tests/testthat/test-ggplot-density.R | 2 tests/testthat/test-ggplot-density2d.R | 4 tests/testthat/test-ggplot-dynamicTicks.R | 26 +- tests/testthat/test-ggplot-errorbar-horizontal.R | 8 tests/testthat/test-ggplot-errorbar.R | 8 tests/testthat/test-ggplot-facets.R | 6 tests/testthat/test-ggplot-ggplotly.R | 14 - tests/testthat/test-ggplot-heatmap.R | 16 - tests/testthat/test-ggplot-histogram.R | 18 - tests/testthat/test-ggplot-hline.R | 14 - tests/testthat/test-ggplot-jitter.R | 2 tests/testthat/test-ggplot-legend.R | 10 tests/testthat/test-ggplot-lines.R | 18 - tests/testthat/test-ggplot-path.R | 28 -- tests/testthat/test-ggplot-point.R | 10 tests/testthat/test-ggplot-polygons.R | 104 ++++---- tests/testthat/test-ggplot-quantile.R | 12 tests/testthat/test-ggplot-rect.R | 24 - tests/testthat/test-ggplot-ribbon.R | 2 tests/testthat/test-ggplot-rug.R | 10 tests/testthat/test-ggplot-segment.R | 10 tests/testthat/test-ggplot-sf.R |only tests/testthat/test-ggplot-size.R | 2 tests/testthat/test-ggplot-smooth.R | 4 tests/testthat/test-ggplot-spoke.R | 10 tests/testthat/test-ggplot-step.R | 8 tests/testthat/test-ggplot-text.R | 6 tests/testthat/test-ggplot-theme.R | 2 tests/testthat/test-ggplot-ticks.R | 16 - tests/testthat/test-ggplot-tooltip.R | 14 - tests/testthat/test-ggplot-violin.R | 6 tests/testthat/test-ggplot-vline.R | 6 tests/testthat/test-ggplot-ylim.R | 4 tests/testthat/test-group2NA.R |only tests/testthat/test-plotly-color.R | 14 - tests/testthat/test-plotly-colorbar.R | 28 +- tests/testthat/test-plotly-data.R | 10 tests/testthat/test-plotly-group.R | 6 tests/testthat/test-plotly-internals.R | 2 tests/testthat/test-plotly-linetype.R | 14 - tests/testthat/test-plotly-subplot.R | 18 - tests/testthat/test-plotly-symbol.R | 8 tests/testthat/test-plotly.R | 52 ++-- 95 files changed, 1472 insertions(+), 1018 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how many
times a video has been liked, search for videos with particular content, and
much more. You can also scrape captions from a few videos. To learn more about
the YouTube API, see <https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.8.0 dated 2017-04-11 and 0.9.0 dated 2017-05-28
DESCRIPTION | 8 MD5 | 116 ++++++------ NAMESPACE | 7 NEWS.md | 11 + R/delete_captions.R |only R/delete_channel_sections.R |only R/delete_comments.R |only R/delete_playlist_items.R |only R/delete_playlists.R |only R/delete_videos.R |only R/get_captions.R | 49 +---- R/get_channel_stats.R | 44 ++-- R/get_comment_threads.R | 111 ++++++++--- R/get_comments.R | 81 ++++---- R/get_playlist_items.R | 83 ++++++-- R/get_playlists.R | 69 ++++--- R/get_related_videos.R | 62 +++--- R/get_stats.R | 39 +--- R/get_subscriptions.R | 41 ++-- R/get_video_details.R | 30 +-- R/list_abuse_report_reasons.R | 39 ++-- R/list_caption_tracks.R | 39 ++-- R/list_channel_activities.R | 85 +++++--- R/list_channel_resources.R | 40 ++-- R/list_channel_sections.R | 22 +- R/list_channel_videos.R | 51 +++-- R/list_guidecats.R | 48 ++--- R/list_langs.R | 21 +- R/list_regions.R | 21 +- R/list_videocats.R | 52 +++-- R/list_videos.R | 23 +- R/tuber.R | 64 ++++-- R/yt_oauth.R | 88 +++++---- R/yt_search.R | 246 +++++++++++++++----------- R/yt_topic_search.R | 29 +-- README.md | 2 build/vignette.rds |binary inst/doc/tuber-ex.html | 6 man/delete_captions.Rd |only man/delete_channel_sections.Rd |only man/delete_comments.Rd |only man/delete_playlist_items.Rd |only man/delete_playlists.Rd |only man/delete_videos.Rd |only man/get_captions.Rd | 22 +- man/get_comment_threads.Rd | 6 man/get_comments.Rd | 11 - man/get_playlist_items.Rd | 14 + man/get_related_videos.Rd | 2 man/get_subscriptions.Rd | 2 man/get_video_details.Rd | 2 man/list_caption_tracks.Rd | 6 man/list_channel_activities.Rd | 8 man/list_channel_resources.Rd | 8 man/list_channel_sections.Rd | 2 man/list_channel_videos.Rd | 20 +- man/tuber_DELETE.Rd |only man/yt_oauth.Rd | 4 man/yt_search.Rd | 35 ++- man/yt_topic_search.Rd | 2 tests/testthat.R | 2 tests/testthat/test-get-details.R | 8 tests/testthat/test-get-related-videos.R | 10 - tests/testthat/test-list-channel-activities.R | 9 tests/testthat/test-list-channel-sections.R | 8 tests/testthat/test-pkg-style.R |only 66 files changed, 1067 insertions(+), 741 deletions(-)
Title: Excerpt Structuring Comments from Your Code File and Set a Table
of Contents
Description: This is an R interface to the
python package 'excerpts' (<https://pypi.python.org/pypi/excerpts>).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <adc-r@arcor.de>
Diff between excerptr versions 1.1.0 dated 2017-05-14 and 1.2.0 dated 2017-05-28
DESCRIPTION | 6 MD5 | 52 +++-- NEWS.md | 5 README.md | 5 inst/doc/excerptr_Introduction.R | 4 inst/doc/excerptr_Introduction.Rmd | 6 inst/doc/excerptr_Introduction.html | 6 inst/excerpts/MANIFEST.in |only inst/excerpts/README.rst | 6 inst/excerpts/README.rstw | 4 inst/excerpts/codes_doxygen/command_line.py | 20 +- inst/excerpts/codes_doxygen/main.py | 22 +- inst/excerpts/codes_doxygen/op.py | 14 - inst/excerpts/codes_doxygen/ui.py | 23 +- inst/excerpts/docs/doxygen |only inst/excerpts/docs/excerpts.main.html | 16 - inst/excerpts/docs/excerpts.op.html | 4 inst/excerpts/docs/excerpts.ui.html | 18 - inst/excerpts/excerpts.egg-info/PKG-INFO | 257 +++++++++++++++++++++++++++- inst/excerpts/excerpts.egg-info/SOURCES.txt | 181 +++++++++++++++++++ inst/excerpts/excerpts/command_line.py | 20 +- inst/excerpts/excerpts/main.py | 22 +- inst/excerpts/excerpts/op.py | 14 - inst/excerpts/excerpts/ui.py | 23 +- inst/excerpts/setup.py | 23 +- inst/excerpts/tests/test_basic.py | 4 inst/excerpts/utils/tag.cl |only inst/excerpts/utils/tags.cl |only vignettes/excerptr_Introduction.Rmd | 6 29 files changed, 614 insertions(+), 147 deletions(-)