Title: Spatial and Space-Time Point Pattern Analysis
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre],
Barry Rowlingson [aut],
Peter Diggle [aut],
Giovanni Petris [ctb],
Stephen Eglen [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between splancs versions 2.01-39 dated 2016-08-23 and 2.01-40 dated 2017-04-16
ChangeLog | 339 ++------------------------------------------------------- DESCRIPTION | 8 - MD5 | 7 - inst/ChangeLog | 339 ++------------------------------------------------------- src/init.c |only 5 files changed, 32 insertions(+), 661 deletions(-)
Title: Models for Data from Unmarked Animals
Description: Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates.
Author: Ian Fiske, Richard Chandler, David Miller, Andy Royle, Marc Kery, Jeff Hostetler, Rebecca Hutchinson
Maintainer: Andy Royle <aroyle@usgs.gov>
Diff between unmarked versions 0.11-0 dated 2015-09-03 and 0.12-0 dated 2017-04-16
DESCRIPTION | 15 - MD5 | 61 ++-- NAMESPACE | 9 NEWS | 33 ++ R/boot.R | 53 ++- R/pcount.spHDS.R |only R/unmarkedFit.R | 445 +++++++++++++++++++++---------- R/unmarkedFrame.R | 14 R/utils.R | 129 +++++--- inst/doc/cap-recap.pdf |binary inst/doc/colext.R | 2 inst/doc/colext.Rnw | 26 - inst/doc/colext.pdf |binary inst/doc/distsamp.pdf |binary inst/doc/spp-dist.pdf |binary inst/doc/unmarked.R | 2 inst/doc/unmarked.Rnw | 2 inst/doc/unmarked.pdf |binary inst/unitTests/runit.format.R | 11 inst/unitTests/runit.parboot.R |only inst/unitTests/runit.pcount.spHDS.R |only inst/unitTests/runit.unmarkedMultFrame.R | 55 +++ inst/unitTests/runit.utils.R | 44 +++ man/Switzerland.Rd | 2 man/cruz.Rd | 2 man/formatDistData.Rd | 14 man/parboot.Rd | 6 man/pcount.spHDS.Rd |only man/unmarked-package.Rd | 2 man/unmarkedFramePCount.Rd | 2 src/init.c |only src/nll_pcountOpen.h | 10 vignettes/colext.Rnw | 26 - vignettes/unmarked.Rnw | 2 34 files changed, 690 insertions(+), 277 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut],
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-29 dated 2017-01-09 and 0.6-30 dated 2017-04-16
ChangeLog | 343 ++--------------------------------------------------- DESCRIPTION | 8 - MD5 | 13 +- build/vignette.rds |binary inst/ChangeLog | 343 ++--------------------------------------------------- inst/doc/GWR.pdf |binary src/gwe.c | 17 ++ src/init.c |only 8 files changed, 54 insertions(+), 670 deletions(-)
Title: Fit and Deploy Rotation Forest Models
Description: Fit and deploy rotation forest models ("Rodriguez, J.J., Kuncheva,
L.I., 2006. Rotation forest: A new classifier ensemble method. IEEE Trans.
Pattern Anal. Mach. Intell. 28, 1619-1630 <doi:10.1109/TPAMI.2006.211>") for binary classification.
Rotation forest is an ensemble method where each base classifier (tree) is
fit on the principal components of the variables of random partitions of
the feature set.
Author: Michel Ballings and Dirk Van den Poel
Maintainer: Michel Ballings <michel.ballings@gmail.com>
Diff between rotationForest versions 0.1 dated 2015-05-17 and 0.1.3 dated 2017-04-16
DESCRIPTION | 16 ++++-- MD5 | 16 ++++-- NAMESPACE | 2 R/predict.rotationForest.R | 6 +- R/rotationForest.R | 103 +++++++++++++++++++++++++----------------- R/rotationForestNews.R |only R/zzz.R |only inst |only man/predict.rotationForest.Rd | 11 ++-- man/rotationForest.Rd | 20 ++++---- man/rotationForestNews.Rd |only 11 files changed, 105 insertions(+), 69 deletions(-)
More information about rotationForest at CRAN
Permanent link
Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions
such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>
Diff between forestmodel versions 0.4.0 dated 2015-12-10 and 0.4.3 dated 2017-04-16
DESCRIPTION | 9 +++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- NEWS | 18 +++++++++++++++++- R/forest_model.R | 20 +++++++++++++------- R/panel_forest_plot.R | 7 ++++--- man/default_forest_panels.Rd | 3 +-- man/forest_breaks.Rd | 3 +-- man/forest_model.Rd | 6 +++--- man/forest_panels.Rd | 3 +-- man/forest_rma.Rd | 5 ++--- man/panel_forest_plot.Rd | 5 ++--- man/theme_forest.Rd | 3 +-- 13 files changed, 63 insertions(+), 45 deletions(-)
Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre],
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between classInt versions 0.1-23 dated 2015-09-28 and 0.1-24 dated 2017-04-16
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- inst/ChangeLog | 8 ++++++++ src/init.c |only 5 files changed, 24 insertions(+), 7 deletions(-)
Title: Build Powerful Pivot Tables and Dynamically Slice & Dice your
Data
Description: Build powerful pivot tables (aka Pivot Grid, Pivot Chart, Cross-Tab)
and dynamically slice & dice / drag 'n' drop your data. 'rpivotTable' is a
wrapper of 'pivottable', a powerful open-source Pivot Table library implemented
in 'JavaScript' by Nicolas Kruchten. Aligned to 'pivottable' v2.11.0.
Author: Enzo Martoglio [aut, cre] (R interface),
Nicolas Kruchten [ctb, cph] (pivottable library),
Kenton Russell [ctb]
Maintainer: Enzo Martoglio <enzo@smartinsightsfromdata.com>
Diff between rpivotTable versions 0.1.5.20 dated 2016-06-05 and 0.2.0 dated 2017-04-16
rpivotTable-0.1.5.20/rpivotTable/inst/doc/NEWS.html |only rpivotTable-0.1.5.20/rpivotTable/inst/examples/inclexcl.html |only rpivotTable-0.1.5.20/rpivotTable/inst/examples/inclexcl.pdf |only rpivotTable-0.1.5.20/rpivotTable/inst/htmlwidgets/lib/jquery-1.11.0 |only rpivotTable-0.1.5.20/rpivotTable/inst/htmlwidgets/lib/jquery-1.11.3 |only rpivotTable-0.1.5.20/rpivotTable/inst/htmlwidgets/lib/jqueryui-1.10.4 |only rpivotTable-0.1.5.20/rpivotTable/inst/htmlwidgets/lib/jqueryui-1.11.4 |only rpivotTable-0.1.5.20/rpivotTable/inst/htmlwidgets/lib/pivottable/dist |only rpivotTable-0.1.5.20/rpivotTable/vignettes/NEWS.html |only rpivotTable-0.2.0/rpivotTable/DESCRIPTION | 34 - rpivotTable-0.2.0/rpivotTable/MD5 | 186 +++++----- rpivotTable-0.2.0/rpivotTable/README.md | 20 - rpivotTable-0.2.0/rpivotTable/build/vignette.rds |binary rpivotTable-0.2.0/rpivotTable/inst/doc/NEWS.R | 7 rpivotTable-0.2.0/rpivotTable/inst/doc/NEWS.Rmd |only rpivotTable-0.2.0/rpivotTable/inst/doc/NEWS.pdf |binary rpivotTable-0.2.0/rpivotTable/inst/doc/rpivotTableIntroduction.R |only rpivotTable-0.2.0/rpivotTable/inst/doc/rpivotTableIntroduction.Rmd |only rpivotTable-0.2.0/rpivotTable/inst/doc/rpivotTableIntroduction.html |only rpivotTable-0.2.0/rpivotTable/inst/examples/inclexcl.R | 2 rpivotTable-0.2.0/rpivotTable/inst/examples/onRefresh-shiny.R | 1 rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/c3/c3.min.css | 2 rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/c3/c3.min.js | 12 rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/jquery |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/jqueryui |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/c3_renderers.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/c3_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/d3_renderers.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/d3_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/export_renderers.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/export_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/gchart_renderers.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/gchart_renderers.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.css |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.da.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.da.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.de.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.de.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.es.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.es.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.fr.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.fr.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.it.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.it.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.css |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.nl.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.nl.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.pt.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.pt.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.ru.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.ru.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.tr.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.tr.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.zh.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot.zh.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot_spec.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/pivot_spec.min.js.map |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/lib/pivottable/tips_data.min.js |only rpivotTable-0.2.0/rpivotTable/inst/htmlwidgets/rpivotTable.yaml | 22 - rpivotTable-0.2.0/rpivotTable/man/change_locale.Rd | 1 rpivotTable-0.2.0/rpivotTable/man/renderRpivotTable.Rd | 1 rpivotTable-0.2.0/rpivotTable/man/rpivotTable.Rd | 1 rpivotTable-0.2.0/rpivotTable/man/rpivotTableOutput.Rd | 1 rpivotTable-0.2.0/rpivotTable/vignettes/NEWS.Rmd |only rpivotTable-0.2.0/rpivotTable/vignettes/rpivotTableIntroduction.Rmd |only 67 files changed, 142 insertions(+), 148 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.9 dated 2017-03-14 and 1.0.10 dated 2017-04-16
DESCRIPTION | 36 ++++++++-------- MD5 | 87 ++++++++++++++++++++++------------------ NAMESPACE | 12 +++++ R/ClassMethod-XGR.r |only R/xColormap.r | 11 ++++- R/xDAGpropagate.r | 75 ++++++++++++++++++++++++++++------- R/xDefineNet.r |only R/xEnrichCompare.r | 19 +++----- R/xEnricherGenes.r | 13 ++++-- R/xEnricherSNPs.r | 6 ++ R/xEnricherYours.r | 19 +++++++- R/xGRviaGeneAnno.r | 5 +- R/xRDataLoader.r | 11 ++--- R/xSM2DF.r | 2 R/xSubneterGR.r | 4 - R/xSubneterGenes.r | 55 ++----------------------- R/xSubneterSNPs.r | 4 - R/xSymbol2GeneID.r | 47 ++++++++++++++-------- R/xVisInterp.r |only R/xVisNet.r | 12 ++++- data/ImmunoBase.RData |binary data/JKscience_TS2A.RData |binary inst/NEWS | 16 +++++++ inst/eTerm.html |only inst/xColormap.html | 2 inst/xDAGpropagate.html | 98 ++++++++++++++++++++++++++++++++++++---------- inst/xDefineNet.html |only inst/xEnricherGenes.html | 50 +++++++++++------------ inst/xEnricherYours.html | 4 - inst/xGRviaGeneAnno.html | 30 ++++++++------ inst/xSubneterGR.html | 43 ++++++++++---------- inst/xSubneterGenes.html | 68 +++++++++++++++++++------------ inst/xSubneterSNPs.html | 43 ++++++++++---------- inst/xSymbol2GeneID.html | 17 ++++++- inst/xVisInterp.html |only inst/xVisNet.html | 11 ++--- man/eTerm.Rd |only man/xColormap.Rd | 2 man/xDAGpropagate.Rd | 97 ++++++++++++++++++++++++++++++++++++--------- man/xDefineNet.Rd |only man/xEnricherGenes.Rd | 50 +++++++++++------------ man/xEnricherYours.Rd | 2 man/xGRviaGeneAnno.Rd | 28 +++++++------ man/xSubneterGR.Rd | 43 ++++++++++---------- man/xSubneterGenes.Rd | 66 ++++++++++++++++++------------ man/xSubneterSNPs.Rd | 43 ++++++++++---------- man/xSymbol2GeneID.Rd | 15 +++++-- man/xVisInterp.Rd |only man/xVisNet.Rd | 11 ++--- 49 files changed, 714 insertions(+), 443 deletions(-)
Title: Dynamic Generation of Scientific Reports
Description: The RSP markup language makes any text-based document come alive. RSP provides a powerful markup for controlling the content and output of LaTeX, HTML, Markdown, AsciiDoc, Sweave and knitr documents (and more), e.g. 'Today's date is <%=Sys.Date()%>'. Contrary to many other literate programming languages, with RSP it is straightforward to loop over mixtures of code and text sections, e.g. in month-by-month summaries. RSP has also several preprocessing directives for incorporating static and dynamic contents of external files (local or online) among other things. Functions rstring() and rcat() make it easy to process RSP strings, rsource() sources an RSP file as it was an R script, while rfile() compiles it (even online) into its final output format, e.g. rfile('report.tex.rsp') generates 'report.pdf' and rfile('report.md.rsp') generates 'report.html'. RSP is ideal for self-contained scientific reports and R package vignettes. It's easy to use - if you know how to write an R script, you'll be up and running within minutes.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.rsp versions 0.40.0 dated 2016-12-06 and 0.41.0 dated 2017-04-16
R.rsp-0.40.0/R.rsp/R/DEFUNCT.R |only R.rsp-0.40.0/R.rsp/inst/doc/RSP_intro.md.rsp |only R.rsp-0.40.0/R.rsp/vignettes/RSP_intro.md.rsp |only R.rsp-0.41.0/R.rsp/DESCRIPTION | 9 R.rsp-0.41.0/R.rsp/MD5 | 73 R.rsp-0.41.0/R.rsp/NAMESPACE | 36 R.rsp-0.41.0/R.rsp/NEWS | 1976 ++++++---- R.rsp-0.41.0/R.rsp/R/000.R | 2 R.rsp-0.41.0/R.rsp/R/999.NonDocumentedObjects.R | 13 R.rsp-0.41.0/R.rsp/R/HttpDaemon.processRsp.R | 6 R.rsp-0.41.0/R.rsp/R/RspDocument.R | 4 R.rsp-0.41.0/R.rsp/R/RspRSourceCodeFactory.R | 18 R.rsp-0.41.0/R.rsp/R/compileMarkdown.R | 8 R.rsp-0.41.0/R.rsp/R/dvips.R | 4 R.rsp-0.41.0/R.rsp/R/ps2pdf.R | 4 R.rsp-0.41.0/R.rsp/R/rcat.R | 26 R.rsp-0.41.0/R.rsp/R/rcode.R | 3 R.rsp-0.41.0/R.rsp/R/xweavetangle.R | 9 R.rsp-0.41.0/R.rsp/R/zzz.CmdArgsFunctions.R | 1 R.rsp-0.41.0/R.rsp/build/vignette.rds |binary R.rsp-0.41.0/R.rsp/inst/doc/Dynamic_document_creation_using_RSP.pdf |binary R.rsp-0.41.0/R.rsp/inst/doc/RSP_intro.html | 1232 +----- R.rsp-0.41.0/R.rsp/inst/doc/RSP_intro.html.rsp |only R.rsp-0.41.0/R.rsp/inst/doc/RSP_refcard.pdf |binary R.rsp-0.41.0/R.rsp/inst/doc/R_packages-LaTeX_vignettes.pdf |binary R.rsp-0.41.0/R.rsp/inst/doc/R_packages-RSP_vignettes.html | 2 R.rsp-0.41.0/R.rsp/inst/doc/R_packages-Vignettes_prior_to_R300.pdf |binary R.rsp-0.41.0/R.rsp/inst/doc/templates/index.html.rsp | 2 R.rsp-0.41.0/R.rsp/man/Non-documented_objects.Rd | 13 R.rsp-0.41.0/R.rsp/man/R.rsp-package.Rd | 4 R.rsp-0.41.0/R.rsp/man/compileMarkdown.Rd | 6 R.rsp-0.41.0/R.rsp/man/processRsp.HttpDaemon.Rd | 4 R.rsp-0.41.0/R.rsp/tests/RspConstruct.R | 2 R.rsp-0.41.0/R.rsp/tests/RspProduct.R | 1 R.rsp-0.41.0/R.rsp/tests/compileAsciiDoc.R | 1 R.rsp-0.41.0/R.rsp/tests/compileAsciiDocNoweb.R | 1 R.rsp-0.41.0/R.rsp/tests/compileKnitr.R | 1 R.rsp-0.41.0/R.rsp/tests/compileLaTeX.R | 1 R.rsp-0.41.0/R.rsp/tests/compileMarkdown.R | 1 R.rsp-0.41.0/R.rsp/vignettes/RSP_intro.html.rsp |only 40 files changed, 1838 insertions(+), 1625 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Christoph Berreth [ctr], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.1.36 dated 2016-12-25 and 3.1.48 dated 2017-04-16
RandomFields-3.1.36/RandomFields/src/fft.cc |only RandomFields-3.1.48/RandomFields/DESCRIPTION | 8 RandomFields-3.1.48/RandomFields/MD5 | 233 - RandomFields-3.1.48/RandomFields/NAMESPACE | 17 RandomFields-3.1.48/RandomFields/R/Class.R | 8 RandomFields-3.1.48/RandomFields/R/Crossvalidation.R | 2 RandomFields-3.1.48/RandomFields/R/D.H.R | 14 RandomFields-3.1.48/RandomFields/R/Likelihoodratio.R | 2 RandomFields-3.1.48/RandomFields/R/Methods-RFsp.R | 4 RandomFields-3.1.48/RandomFields/R/Methods-aux.R | 7 RandomFields-3.1.48/RandomFields/R/RC_GLOBALS.R | 9 RandomFields-3.1.48/RandomFields/R/RCauto.R | 2 RandomFields-3.1.48/RandomFields/R/RFempvario-Methods-plots.R | 59 RandomFields-3.1.48/RandomFields/R/RFempvario.R | 1215 ++++----- RandomFields-3.1.48/RandomFields/R/RFfit.R | 8 RandomFields-3.1.48/RandomFields/R/RFgui.R | 523 ++-- RandomFields-3.1.48/RandomFields/R/RMmodels-Methods-plots.R | 27 RandomFields-3.1.48/RandomFields/R/RMmodels.R | 274 -- RandomFields-3.1.48/RandomFields/R/RMmodelsConvenience.R | 2 RandomFields-3.1.48/RandomFields/R/RMmodelsSpecial.R | 19 RandomFields-3.1.48/RandomFields/R/auxiliary.R | 21 RandomFields-3.1.48/RandomFields/R/basic.fctns.R | 2 RandomFields-3.1.48/RandomFields/R/bigdata.R | 38 RandomFields-3.1.48/RandomFields/R/convert.R | 73 RandomFields-3.1.48/RandomFields/R/convert_new.R | 3 RandomFields-3.1.48/RandomFields/R/datasets.R | 20 RandomFields-3.1.48/RandomFields/R/fitbernoulli.R | 2 RandomFields-3.1.48/RandomFields/R/fitbr.R | 2 RandomFields-3.1.48/RandomFields/R/fitgauss.R | 84 RandomFields-3.1.48/RandomFields/R/fitmaxstable.R | 2 RandomFields-3.1.48/RandomFields/R/fitpoisson.R | 2 RandomFields-3.1.48/RandomFields/R/generatemodels.R | 20 RandomFields-3.1.48/RandomFields/R/getNset.R | 34 RandomFields-3.1.48/RandomFields/R/internal_use.R | 88 RandomFields-3.1.48/RandomFields/R/kriging.R | 10 RandomFields-3.1.48/RandomFields/R/nicht.nachladbar.R | 2 RandomFields-3.1.48/RandomFields/R/obsolete.R | 4 RandomFields-3.1.48/RandomFields/R/rf-plots.R | 5 RandomFields-3.1.48/RandomFields/R/rf.R | 28 RandomFields-3.1.48/RandomFields/R/zzz.R | 11 RandomFields-3.1.48/RandomFields/man/BRspecific.Rd | 4 RandomFields-3.1.48/RandomFields/man/QMath.Rd | 28 RandomFields-3.1.48/RandomFields/man/RFboxcox.Rd | 2 RandomFields-3.1.48/RandomFields/man/RFempVariog-class.Rd | 1 RandomFields-3.1.48/RandomFields/man/RFempiricalcovariance.Rd |only RandomFields-3.1.48/RandomFields/man/RFempiricalmadogram.Rd |only RandomFields-3.1.48/RandomFields/man/RFempiricalvariogram.Rd | 5 RandomFields-3.1.48/RandomFields/man/RFfitOptimiser.Rd | 5 RandomFields-3.1.48/RandomFields/man/RMbicauchy.Rd |only RandomFields-3.1.48/RandomFields/man/RMbistable.Rd |only RandomFields-3.1.48/RandomFields/man/RMbiwm.Rd | 1 RandomFields-3.1.48/RandomFields/man/RMcurlfree.Rd | 19 RandomFields-3.1.48/RandomFields/man/RMdivfree.Rd | 18 RandomFields-3.1.48/RandomFields/man/RMmodelsMultivariate.Rd | 2 RandomFields-3.1.48/RandomFields/man/RMmodelsTailcorrelation.Rd | 9 RandomFields-3.1.48/RandomFields/man/RMstable.Rd | 1 RandomFields-3.1.48/RandomFields/man/RPsmith.Rd | 10 RandomFields-3.1.48/RandomFields/man/RandomFields.Rd | 2 RandomFields-3.1.48/RandomFields/man/internal.Rd | 5 RandomFields-3.1.48/RandomFields/src/Brown.cc | 846 ++---- RandomFields-3.1.48/RandomFields/src/Coordinate_systems.cc | 40 RandomFields-3.1.48/RandomFields/src/Coordinate_systems.h | 4 RandomFields-3.1.48/RandomFields/src/D.H.cc | 18 RandomFields-3.1.48/RandomFields/src/Families.h | 2 RandomFields-3.1.48/RandomFields/src/Gneiting.cc | 98 RandomFields-3.1.48/RandomFields/src/Huetchen.cc | 35 RandomFields-3.1.48/RandomFields/src/InternalCov.cc | 103 RandomFields-3.1.48/RandomFields/src/KeyInfo.cc | 32 RandomFields-3.1.48/RandomFields/src/Local.h |only RandomFields-3.1.48/RandomFields/src/MLE.cc | 40 RandomFields-3.1.48/RandomFields/src/Makevars | 4 RandomFields-3.1.48/RandomFields/src/Operator.h | 6 RandomFields-3.1.48/RandomFields/src/PoissonPolygon.cc | 74 RandomFields-3.1.48/RandomFields/src/PoissonPolygon.h | 2 RandomFields-3.1.48/RandomFields/src/Primitive.cc | 1280 ++++++++-- RandomFields-3.1.48/RandomFields/src/QMath.cc | 79 RandomFields-3.1.48/RandomFields/src/RF.h | 117 RandomFields-3.1.48/RandomFields/src/RandomFields.h | 152 - RandomFields-3.1.48/RandomFields/src/Specific.cc | 6 RandomFields-3.1.48/RandomFields/src/SpherModels.cc | 14 RandomFields-3.1.48/RandomFields/src/SpherModelsInitNerror.cc | 2 RandomFields-3.1.48/RandomFields/src/Userinterfaces.h | 12 RandomFields-3.1.48/RandomFields/src/Xempvario.cc | 608 +++- RandomFields-3.1.48/RandomFields/src/auxiliary.cc | 18 RandomFields-3.1.48/RandomFields/src/auxiliary.h | 9 RandomFields-3.1.48/RandomFields/src/auxiliary2.h |only RandomFields-3.1.48/RandomFields/src/avltr_modified.cc | 12 RandomFields-3.1.48/RandomFields/src/basic.h | 12 RandomFields-3.1.48/RandomFields/src/circulant.cc | 123 RandomFields-3.1.48/RandomFields/src/convhull2D.cc | 8 RandomFields-3.1.48/RandomFields/src/convhull2D.h | 2 RandomFields-3.1.48/RandomFields/src/cubicsolver.cc | 24 RandomFields-3.1.48/RandomFields/src/direct.cc | 6 RandomFields-3.1.48/RandomFields/src/empvario.cc | 768 ++---- RandomFields-3.1.48/RandomFields/src/error.h | 4 RandomFields-3.1.48/RandomFields/src/extremes.cc | 138 - RandomFields-3.1.48/RandomFields/src/families.cc | 189 - RandomFields-3.1.48/RandomFields/src/fft.c |only RandomFields-3.1.48/RandomFields/src/fftVario.cc | 11 RandomFields-3.1.48/RandomFields/src/gauss.cc | 36 RandomFields-3.1.48/RandomFields/src/gausslikeli.cc | 36 RandomFields-3.1.48/RandomFields/src/getNset.cc | 75 RandomFields-3.1.48/RandomFields/src/hyperplan.cc | 10 RandomFields-3.1.48/RandomFields/src/initNerror.cc | 82 RandomFields-3.1.48/RandomFields/src/kleinkram.cc | 37 RandomFields-3.1.48/RandomFields/src/kleinkram.h | 11 RandomFields-3.1.48/RandomFields/src/metropolis.cc | 14 RandomFields-3.1.48/RandomFields/src/nugget.cc | 16 RandomFields-3.1.48/RandomFields/src/operator.cc | 596 +++- RandomFields-3.1.48/RandomFields/src/plusmalS.cc | 86 RandomFields-3.1.48/RandomFields/src/primitive.h | 32 RandomFields-3.1.48/RandomFields/src/rf_interfaces.cc | 60 RandomFields-3.1.48/RandomFields/src/sequential.cc | 6 RandomFields-3.1.48/RandomFields/src/shape_processes.h | 2 RandomFields-3.1.48/RandomFields/src/spectral.cc | 56 RandomFields-3.1.48/RandomFields/src/startGetNset.cc | 44 RandomFields-3.1.48/RandomFields/src/tbm.cc | 32 RandomFields-3.1.48/RandomFields/src/trend.cc | 21 RandomFields-3.1.48/RandomFields/src/userinterfaces.cc | 144 - RandomFields-3.1.48/RandomFields/src/variogramAndCo.cc | 6 RandomFields-3.1.48/RandomFields/src/variogramAndCo.h | 4 RandomFields-3.1.48/RandomFields/src/zzz.c |only 122 files changed, 5258 insertions(+), 4042 deletions(-)
Title: Markov Chain Monte Carlo
Description: Simulates continuous distributions of random vectors using
Markov chain Monte Carlo (MCMC). Users specify the distribution by an
R function that evaluates the log unnormalized density. Algorithms
are random walk Metropolis algorithm (function metrop), simulated
tempering (function temper), and morphometric random walk Metropolis
(Johnson and Geyer, 2012, <https://doi.org/10.1214/12-AOS1048>,
function morph.metrop),
which achieves geometric ergodicity by change of variable.
Author: Charles J. Geyer <charlie@stat.umn.edu> and Leif T. Johnson
<ltjohnson@google.com>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between mcmc versions 0.9-4 dated 2015-07-16 and 0.9-5 dated 2017-04-16
mcmc-0.9-4/mcmc/inst/doc/Makefile |only mcmc-0.9-4/mcmc/inst/doc/metrop.tex |only mcmc-0.9-4/mcmc/inst/doc/temper.tex |only mcmc-0.9-5/mcmc/.Rinstignore | 3 mcmc-0.9-5/mcmc/ChangeLog | 4 mcmc-0.9-5/mcmc/DESCRIPTION | 15 +- mcmc-0.9-5/mcmc/MD5 | 77 +++++------ mcmc-0.9-5/mcmc/NAMESPACE | 3 mcmc-0.9-5/mcmc/R/initseq.R | 2 mcmc-0.9-5/mcmc/R/metrop.R | 8 - mcmc-0.9-5/mcmc/R/olbm.R | 4 mcmc-0.9-5/mcmc/R/temper.R | 20 ++ mcmc-0.9-5/mcmc/build/vignette.rds |binary mcmc-0.9-5/mcmc/inst/designDoc |only mcmc-0.9-5/mcmc/inst/doc/bfst.pdf |binary mcmc-0.9-5/mcmc/inst/doc/debug.pdf |binary mcmc-0.9-5/mcmc/inst/doc/demo.pdf |binary mcmc-0.9-5/mcmc/inst/doc/metrop.pdf |binary mcmc-0.9-5/mcmc/inst/doc/morph.pdf |binary mcmc-0.9-5/mcmc/inst/doc/temper.pdf |binary mcmc-0.9-5/mcmc/man/metrop.Rd | 158 +++++++++++++++++++--- mcmc-0.9-5/mcmc/man/olbm.Rd | 6 mcmc-0.9-5/mcmc/man/temper.Rd | 76 +++++++---- mcmc-0.9-5/mcmc/src/Makevars |only mcmc-0.9-5/mcmc/src/getListElement.c | 31 ---- mcmc-0.9-5/mcmc/src/getScalarInteger.c | 31 ---- mcmc-0.9-5/mcmc/src/getScalarLogical.c | 31 ---- mcmc-0.9-5/mcmc/src/init.c |only mcmc-0.9-5/mcmc/src/initseq.c | 1 mcmc-0.9-5/mcmc/src/isAllFinite.c | 31 ---- mcmc-0.9-5/mcmc/src/mcmc.h |only mcmc-0.9-5/mcmc/src/metrop.c | 172 +++++++++++-------------- mcmc-0.9-5/mcmc/src/myutil.h | 34 ---- mcmc-0.9-5/mcmc/src/olbm.c | 36 ----- mcmc-0.9-5/mcmc/src/temper.c | 34 ---- mcmc-0.9-5/mcmc/tests/accept-batch.R |only mcmc-0.9-5/mcmc/tests/accept-batch.Rout.save |only mcmc-0.9-5/mcmc/tests/initseq.R | 2 mcmc-0.9-5/mcmc/tests/initseq.Rout.save | 10 - mcmc-0.9-5/mcmc/tests/logitmat.Rout.save | 16 +- mcmc-0.9-5/mcmc/tests/temp-par-witch.R | 18 +- mcmc-0.9-5/mcmc/tests/temp-par.Rout.save | 24 +-- mcmc-0.9-5/mcmc/tests/temp-ser-witch.Rout.save | 16 +- mcmc-0.9-5/mcmc/tests/temp-ser.Rout.save | 22 +-- 44 files changed, 416 insertions(+), 469 deletions(-)
Title: Incremental Decomposition Methods
Description: Incremental Multiple Correspondence Analysis and Principal
Component Analysis.
Author: Alfonso Iodice D' Enza [aut], Angelos Markos [aut, cre], Davide
Buttarazzi [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between idm versions 1.8.0 dated 2017-03-24 and 1.8.1 dated 2017-04-16
DESCRIPTION | 8 +-- MD5 | 16 +++---- R/add_svd.R | 110 +++++++++++++++++++++++++--------------------------- man/add_es.Rd | 2 man/i_mca.Rd | 2 man/i_pca.Rd | 2 man/idm.Rd | 4 - man/update.i_mca.Rd | 2 man/update.i_pca.Rd | 2 9 files changed, 73 insertions(+), 75 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multi state
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.11 dated 2017-04-14 and 2.12 dated 2017-04-16
CHANGES | 4 +++- DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ inst/doc/yll.rnw | 1 - man/LCa.fit.Rd | 2 +- man/erl.Rd | 2 +- vignettes/yll.rnw | 1 - 7 files changed, 16 insertions(+), 16 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps.
Author: Ari Lamstein <ari@lamsteinconsulting.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <ari@lamsteinconsulting.com>
Diff between choroplethr versions 3.6.0 dated 2017-04-09 and 3.6.1 dated 2017-04-16
choroplethr-3.6.0/choroplethr/inst |only choroplethr-3.6.0/choroplethr/tests/test-all.R |only choroplethr-3.6.1/choroplethr/DESCRIPTION | 8 - choroplethr-3.6.1/choroplethr/MD5 | 46 +++++----- choroplethr-3.6.1/choroplethr/NAMESPACE | 1 choroplethr-3.6.1/choroplethr/NEWS | 6 + choroplethr-3.6.1/choroplethr/R/choropleth.R | 10 +- choroplethr-3.6.1/choroplethr/R/country.R | 6 - choroplethr-3.6.1/choroplethr/R/county.R | 6 - choroplethr-3.6.1/choroplethr/R/data.R | 20 ++++ choroplethr-3.6.1/choroplethr/R/state.R | 6 - choroplethr-3.6.1/choroplethr/R/tracts.R | 6 - choroplethr-3.6.1/choroplethr/R/utils.R | 12 ++ choroplethr-3.6.1/choroplethr/data/df_state_age_2010.rdata |only choroplethr-3.6.1/choroplethr/data/df_state_age_2015.rdata |only choroplethr-3.6.1/choroplethr/man/calculate_percent_change.Rd | 12 ++ choroplethr-3.6.1/choroplethr/man/country_choropleth.Rd | 6 - choroplethr-3.6.1/choroplethr/man/county_choropleth.Rd | 6 - choroplethr-3.6.1/choroplethr/man/df_state_age_2010.Rd |only choroplethr-3.6.1/choroplethr/man/df_state_age_2015.Rd |only choroplethr-3.6.1/choroplethr/man/state_choropleth.Rd | 6 - choroplethr-3.6.1/choroplethr/man/tract_choropleth.Rd | 6 - choroplethr-3.6.1/choroplethr/tests/testthat |only 23 files changed, 121 insertions(+), 42 deletions(-)
Title: Geo-Processing Base Functions
Description: Base tools for facilitating the creation geo-processing functions
in R.
Author: Andrew Plowright
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between APfun versions 0.1.0 dated 2017-01-15 and 0.1.1 dated 2017-04-16
DESCRIPTION | 12 +++++++----- MD5 | 18 +++++++++++++----- NAMESPACE | 5 +++++ NEWS.md | 9 +++++++++ R/APcontours.R |only R/APopen.R |only R/APpolygonize.R |only R/APprecise.R |only R/APtimer.R | 18 +++++++++++------- man/APcontours.Rd |only man/APopen.Rd |only man/APpolygonize.Rd |only man/APprecise.Rd |only man/APtimer.Rd | 8 +++++--- 14 files changed, 50 insertions(+), 20 deletions(-)
Title: Gene Set Pareto Heterogeneity Analysis of Time-Course Gene
Expression Data
Description: Pareto front based statistical tool for detecting heterogeneity in gene sets and biological modules from time-course data.
Author: Jinghua Gu [aut, cre],
Xuan Wang [aut],
Jinayn Chan [aut, cre],
Nicole Baldwin [aut],
Jacob Turner [aut]
Maintainer: Jinyan Chan <Jinyan.Chan@bswhealth.org>
Diff between phantom versions 0.1.0 dated 2017-04-13 and 0.1.1 dated 2017-04-16
DESCRIPTION | 16 +++++++------- MD5 | 4 +-- src/c_code.cpp | 64 ++++++++++++++++++++++++++++----------------------------- 3 files changed, 42 insertions(+), 42 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <http://glottolog.org> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <http://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://agricolamz.github.io/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.0.2 dated 2017-02-23 and 1.0.3 dated 2017-04-16
lingtypology-1.0.2/lingtypology/R/makelink.R |only lingtypology-1.0.2/lingtypology/man/makelink.Rd |only lingtypology-1.0.3/lingtypology/DESCRIPTION | 9 lingtypology-1.0.3/lingtypology/MD5 | 106 +- lingtypology-1.0.3/lingtypology/NAMESPACE | 8 lingtypology-1.0.3/lingtypology/NEWS | 25 lingtypology-1.0.3/lingtypology/R/aff.lang.R | 13 lingtypology-1.0.3/lingtypology/R/area.lang.R | 13 lingtypology-1.0.3/lingtypology/R/circassian.R | 2 lingtypology-1.0.3/lingtypology/R/countries.R | 1 lingtypology-1.0.3/lingtypology/R/country.lang.R | 16 lingtypology-1.0.3/lingtypology/R/ejective_and_n_consonants.R |only lingtypology-1.0.3/lingtypology/R/glottolog.modified.R | 21 lingtypology-1.0.3/lingtypology/R/glottolog.original.R | 20 lingtypology-1.0.3/lingtypology/R/gltc.iso.R |only lingtypology-1.0.3/lingtypology/R/gltc.lang.R |only lingtypology-1.0.3/lingtypology/R/is.glottolog.R | 41 - lingtypology-1.0.3/lingtypology/R/iso.gltc.R |only lingtypology-1.0.3/lingtypology/R/iso.lang.R | 13 lingtypology-1.0.3/lingtypology/R/lang.aff.R | 28 lingtypology-1.0.3/lingtypology/R/lang.country.R | 17 lingtypology-1.0.3/lingtypology/R/lang.gltc.R |only lingtypology-1.0.3/lingtypology/R/lang.iso.R | 11 lingtypology-1.0.3/lingtypology/R/lat.lang.R | 19 lingtypology-1.0.3/lingtypology/R/long.lang.R | 24 lingtypology-1.0.3/lingtypology/R/map.feature.R | 81 +- lingtypology-1.0.3/lingtypology/R/url.lang.R |only lingtypology-1.0.3/lingtypology/README.md | 2 lingtypology-1.0.3/lingtypology/build/vignette.rds |binary lingtypology-1.0.3/lingtypology/data/circassian.RData |binary lingtypology-1.0.3/lingtypology/data/countries.RData |binary lingtypology-1.0.3/lingtypology/data/datalist |only lingtypology-1.0.3/lingtypology/data/ejective_and_n_consonants.RData |only lingtypology-1.0.3/lingtypology/data/glottolog.modified.RData |binary lingtypology-1.0.3/lingtypology/data/glottolog.original.RData |binary lingtypology-1.0.3/lingtypology/inst/CITATION | 2 lingtypology-1.0.3/lingtypology/inst/doc/lingtypology.R | 165 ++-- lingtypology-1.0.3/lingtypology/inst/doc/lingtypology.Rmd | 274 ++++--- lingtypology-1.0.3/lingtypology/inst/doc/lingtypology.html | 380 +++++----- lingtypology-1.0.3/lingtypology/inst/doc/manual/lingtypology.pdf |binary lingtypology-1.0.3/lingtypology/man/aff.lang.Rd | 6 lingtypology-1.0.3/lingtypology/man/area.lang.Rd | 6 lingtypology-1.0.3/lingtypology/man/circassian.Rd | 2 lingtypology-1.0.3/lingtypology/man/countries.Rd | 1 lingtypology-1.0.3/lingtypology/man/country.lang.Rd | 8 lingtypology-1.0.3/lingtypology/man/ejective_and_n_consonants.Rd |only lingtypology-1.0.3/lingtypology/man/glottolog.modified.Rd | 23 lingtypology-1.0.3/lingtypology/man/glottolog.original.Rd | 20 lingtypology-1.0.3/lingtypology/man/gltc.iso.Rd |only lingtypology-1.0.3/lingtypology/man/gltc.lang.Rd |only lingtypology-1.0.3/lingtypology/man/is.glottolog.Rd | 15 lingtypology-1.0.3/lingtypology/man/iso.gltc.Rd |only lingtypology-1.0.3/lingtypology/man/iso.lang.Rd | 6 lingtypology-1.0.3/lingtypology/man/lang.aff.Rd | 12 lingtypology-1.0.3/lingtypology/man/lang.country.Rd | 8 lingtypology-1.0.3/lingtypology/man/lang.gltc.Rd |only lingtypology-1.0.3/lingtypology/man/lang.iso.Rd | 4 lingtypology-1.0.3/lingtypology/man/lat.lang.Rd | 6 lingtypology-1.0.3/lingtypology/man/long.lang.Rd | 11 lingtypology-1.0.3/lingtypology/man/map.feature.Rd | 32 lingtypology-1.0.3/lingtypology/man/url.lang.Rd |only lingtypology-1.0.3/lingtypology/vignettes/lingtypology.Rmd | 274 ++++--- 62 files changed, 1018 insertions(+), 707 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction methods under
the joint frailty-copula model between tumour progression and death for meta-analysis.
A penalized likelihood is employed for estimating model parameters, where the baseline hazard functions are approximated by smoothing splines.
The methods are applicable for meta-analytic data combining several studies.
The methods can analyze data having information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
See Emura et al. (2015) <doi:10.1177/0962280215604510> and
Emura et al. (2017) <doi:10.1177/0962280216688032> for details.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.10 dated 2016-10-30 and 2.11 dated 2017-04-16
DESCRIPTION | 18 ++++--- MD5 | 32 ++++++------ R/jointCox.indep.reg.R | 111 +++++++------------------------------------- R/jointCox.reg.R | 114 ++++++++-------------------------------------- R/splineCox.reg.R |only man/F.KM.Rd | 8 +-- man/F.prediction.Rd | 8 +-- man/F.window.Rd | 8 +-- man/F.windows.Rd | 8 +-- man/I.spline.Rd | 2 man/M.spline.Rd | 2 man/dataOvarian.Rd | 3 - man/dataOvarian1.Rd | 3 - man/dataOvarian2.Rd | 3 - man/joint.Cox-package.Rd | 18 ++++--- man/jointCox.indep.reg.Rd | 36 ++++++++++++-- man/jointCox.reg.Rd | 80 ++++++++++---------------------- man/splineCox.reg.Rd |only 18 files changed, 160 insertions(+), 294 deletions(-)
Title: DataRobot Predictive Modeling API
Description: For working with the DataRobot predictive modeling platform's <https://app.datarobot.com> API.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut]
Maintainer: Sergey Yurgenson <api-maintainer@datarobot.com>
Diff between datarobot versions 2.4.0 dated 2016-12-01 and 2.6.0 dated 2017-04-16
datarobot-2.4.0/datarobot/R/CreateGroupPartition.R |only datarobot-2.4.0/datarobot/R/CreateRandomPartition.R |only datarobot-2.4.0/datarobot/R/CreateStratifiedPartition.R |only datarobot-2.4.0/datarobot/R/CreateUserPartition.R |only datarobot-2.4.0/datarobot/R/DeleteModel.R |only datarobot-2.4.0/datarobot/R/GetAllModels.R |only datarobot-2.4.0/datarobot/R/GetModelFromJobId.R |only datarobot-2.4.0/datarobot/R/GetModelObject.R |only datarobot-2.4.0/datarobot/R/GetRecommendedBlueprints.R |only datarobot-2.4.0/datarobot/R/ReformatListOfModels.R |only datarobot-2.4.0/datarobot/R/RequestNewModel.R |only datarobot-2.4.0/datarobot/R/ValidateModel.R |only datarobot-2.6.0/datarobot/DESCRIPTION | 16 datarobot-2.6.0/datarobot/MD5 | 295 +++++----- datarobot-2.6.0/datarobot/NAMESPACE | 36 + datarobot-2.6.0/datarobot/NEWS | 43 + datarobot-2.6.0/datarobot/R/Blenders.R |only datarobot-2.6.0/datarobot/R/Blueprints.R |only datarobot-2.6.0/datarobot/R/ConnectToDataRobot.R | 9 datarobot-2.6.0/datarobot/R/DataRobotRequests.R | 9 datarobot-2.6.0/datarobot/R/Enums.R | 33 + datarobot-2.6.0/datarobot/R/FeatureImpact.R | 2 datarobot-2.6.0/datarobot/R/Features.R | 22 datarobot-2.6.0/datarobot/R/GetPredictions.R | 2 datarobot-2.6.0/datarobot/R/Models.R |only datarobot-2.6.0/datarobot/R/Partitions.R |only datarobot-2.6.0/datarobot/R/PredictionDatasets.R | 8 datarobot-2.6.0/datarobot/R/PrimeFiles.R | 4 datarobot-2.6.0/datarobot/R/PrimeModels.R | 2 datarobot-2.6.0/datarobot/R/ReasonCodes.R |only datarobot-2.6.0/datarobot/R/RequestApproximation.R | 4 datarobot-2.6.0/datarobot/R/SetupProject.R | 24 datarobot-2.6.0/datarobot/R/StartAutopilot.R | 44 - datarobot-2.6.0/datarobot/R/TransferrableModels.R | 16 datarobot-2.6.0/datarobot/R/UnpauseQueue.R | 4 datarobot-2.6.0/datarobot/R/WaitForAsyncReturn.R | 2 datarobot-2.6.0/datarobot/R/WaitForJobToComplete.R | 2 datarobot-2.6.0/datarobot/build/vignette.rds |binary datarobot-2.6.0/datarobot/inst/doc/ComparingSubsets.html | 4 datarobot-2.6.0/datarobot/inst/doc/ComparingSubsetsRDSbuilder.R | 33 - datarobot-2.6.0/datarobot/inst/doc/DatetimePartitionedProjects.R |only datarobot-2.6.0/datarobot/inst/doc/DatetimePartitionedProjects.Rmd |only datarobot-2.6.0/datarobot/inst/doc/DatetimePartitionedProjects.html |only datarobot-2.6.0/datarobot/inst/doc/IntroductionToDataRobot.html | 4 datarobot-2.6.0/datarobot/inst/doc/PartialDependence.html | 4 datarobot-2.6.0/datarobot/inst/doc/PartialDependenceRDSbuilder.R | 21 datarobot-2.6.0/datarobot/inst/doc/ReasonCodeVignette.R |only datarobot-2.6.0/datarobot/inst/doc/ReasonCodeVignette.Rmd |only datarobot-2.6.0/datarobot/inst/doc/ReasonCodeVignette.html |only datarobot-2.6.0/datarobot/inst/doc/VariableImportance.html | 4 datarobot-2.6.0/datarobot/inst/doc/VariableImportanceRDSbuilder.R | 13 datarobot-2.6.0/datarobot/man/AutopilotMode.Rd | 1 datarobot-2.6.0/datarobot/man/BlendMethods.Rd |only datarobot-2.6.0/datarobot/man/BlueprintChartToGraphviz.Rd |only datarobot-2.6.0/datarobot/man/ConnectToDataRobot.Rd | 1 datarobot-2.6.0/datarobot/man/ConstructDurationString.Rd |only datarobot-2.6.0/datarobot/man/CreateBacktestSpecification.Rd |only datarobot-2.6.0/datarobot/man/CreateDatetimePartitionSpecification.Rd |only datarobot-2.6.0/datarobot/man/CreateDerivedFeatures.Rd | 15 datarobot-2.6.0/datarobot/man/CreateFeaturelist.Rd | 1 datarobot-2.6.0/datarobot/man/CreateGroupPartition.Rd | 7 datarobot-2.6.0/datarobot/man/CreatePrimeCode.Rd | 1 datarobot-2.6.0/datarobot/man/CreateRandomPartition.Rd | 3 datarobot-2.6.0/datarobot/man/CreateStratifiedPartition.Rd | 3 datarobot-2.6.0/datarobot/man/CreateUserPartition.Rd | 22 datarobot-2.6.0/datarobot/man/DeleteJob.Rd | 1 datarobot-2.6.0/datarobot/man/DeleteModel.Rd | 3 datarobot-2.6.0/datarobot/man/DeleteModelJob.Rd | 1 datarobot-2.6.0/datarobot/man/DeletePredictJob.Rd | 1 datarobot-2.6.0/datarobot/man/DeletePredictionDataset.Rd | 1 datarobot-2.6.0/datarobot/man/DeleteProject.Rd | 1 datarobot-2.6.0/datarobot/man/DeleteReasonCodes.Rd |only datarobot-2.6.0/datarobot/man/DeleteReasonCodesInitialization.Rd |only datarobot-2.6.0/datarobot/man/DeleteTransferrableModel.Rd | 1 datarobot-2.6.0/datarobot/man/DownloadPrimeCode.Rd | 1 datarobot-2.6.0/datarobot/man/DownloadReasonCodes.Rd |only datarobot-2.6.0/datarobot/man/DownloadTransferrableModel.Rd | 1 datarobot-2.6.0/datarobot/man/FeatureFromAsyncUrl.Rd | 3 datarobot-2.6.0/datarobot/man/GenerateDatetimePartition.Rd |only datarobot-2.6.0/datarobot/man/GetAllModels.Rd | 3 datarobot-2.6.0/datarobot/man/GetAllReasonCodesRowsAsDataFrame.Rd |only datarobot-2.6.0/datarobot/man/GetBlenderModel.Rd |only datarobot-2.6.0/datarobot/man/GetBlenderModelFromJobId.Rd |only datarobot-2.6.0/datarobot/man/GetBlueprint.Rd |only datarobot-2.6.0/datarobot/man/GetBlueprintChart.Rd |only datarobot-2.6.0/datarobot/man/GetBlueprintDocuments.Rd |only datarobot-2.6.0/datarobot/man/GetDatetimeModelFromJobId.Rd |only datarobot-2.6.0/datarobot/man/GetDatetimeModelObject.Rd |only datarobot-2.6.0/datarobot/man/GetDatetimePartition.Rd |only datarobot-2.6.0/datarobot/man/GetFeatureImpactForJobId.Rd | 3 datarobot-2.6.0/datarobot/man/GetFeatureImpactForModel.Rd | 1 datarobot-2.6.0/datarobot/man/GetFeatureInfo.Rd | 6 datarobot-2.6.0/datarobot/man/GetFeaturelist.Rd | 1 datarobot-2.6.0/datarobot/man/GetFrozenModel.Rd |only datarobot-2.6.0/datarobot/man/GetFrozenModelFromJobId.Rd |only datarobot-2.6.0/datarobot/man/GetModelFromJobId.Rd | 5 datarobot-2.6.0/datarobot/man/GetModelJobs.Rd | 1 datarobot-2.6.0/datarobot/man/GetModelObject.Rd | 5 datarobot-2.6.0/datarobot/man/GetModelParameters.Rd |only datarobot-2.6.0/datarobot/man/GetPredictJobs.Rd | 1 datarobot-2.6.0/datarobot/man/GetPredictions.Rd | 3 datarobot-2.6.0/datarobot/man/GetPrimeEligibility.Rd | 1 datarobot-2.6.0/datarobot/man/GetPrimeFile.Rd | 1 datarobot-2.6.0/datarobot/man/GetPrimeFileFromJobId.Rd | 3 datarobot-2.6.0/datarobot/man/GetPrimeModel.Rd | 1 datarobot-2.6.0/datarobot/man/GetPrimeModelFromJobId.Rd | 3 datarobot-2.6.0/datarobot/man/GetProject.Rd | 1 datarobot-2.6.0/datarobot/man/GetProjectList.Rd | 1 datarobot-2.6.0/datarobot/man/GetProjectStatus.Rd | 1 datarobot-2.6.0/datarobot/man/GetReasonCodesInitialization.Rd |only datarobot-2.6.0/datarobot/man/GetReasonCodesInitializationFromJobId.Rd |only datarobot-2.6.0/datarobot/man/GetReasonCodesMetadata.Rd |only datarobot-2.6.0/datarobot/man/GetReasonCodesMetadataFromJobId.Rd |only datarobot-2.6.0/datarobot/man/GetReasonCodesRows.Rd |only datarobot-2.6.0/datarobot/man/GetRecommendedBlueprints.Rd | 3 datarobot-2.6.0/datarobot/man/GetRulesets.Rd | 1 datarobot-2.6.0/datarobot/man/GetTransferrableModel.Rd | 3 datarobot-2.6.0/datarobot/man/GetValidMetrics.Rd | 1 datarobot-2.6.0/datarobot/man/JobStatus.Rd | 1 datarobot-2.6.0/datarobot/man/JobType.Rd | 3 datarobot-2.6.0/datarobot/man/ListBlueprints.Rd | 13 datarobot-2.6.0/datarobot/man/ListFeatureInfo.Rd | 2 datarobot-2.6.0/datarobot/man/ListFeaturelists.Rd | 1 datarobot-2.6.0/datarobot/man/ListJobs.Rd | 1 datarobot-2.6.0/datarobot/man/ListModelFeatures.Rd | 1 datarobot-2.6.0/datarobot/man/ListPredictionDatasets.Rd | 1 datarobot-2.6.0/datarobot/man/ListPrimeFiles.Rd | 3 datarobot-2.6.0/datarobot/man/ListPrimeModels.Rd | 1 datarobot-2.6.0/datarobot/man/ListReasonCodesMetadata.Rd |only datarobot-2.6.0/datarobot/man/ListTransferrableModels.Rd | 3 datarobot-2.6.0/datarobot/man/PauseQueue.Rd | 1 datarobot-2.6.0/datarobot/man/PostgreSQLdrivers.Rd | 1 datarobot-2.6.0/datarobot/man/PredictionDatasetFromAsyncUrl.Rd | 3 datarobot-2.6.0/datarobot/man/PrimeLanguage.Rd | 1 datarobot-2.6.0/datarobot/man/ProjectFromAsyncUrl.Rd | 3 datarobot-2.6.0/datarobot/man/RequestApproximation.Rd | 5 datarobot-2.6.0/datarobot/man/RequestBlender.Rd |only datarobot-2.6.0/datarobot/man/RequestFeatureImpact.Rd | 1 datarobot-2.6.0/datarobot/man/RequestFrozenDatetimeModel.Rd |only datarobot-2.6.0/datarobot/man/RequestFrozenModel.Rd |only datarobot-2.6.0/datarobot/man/RequestNewDatetimeModel.Rd |only datarobot-2.6.0/datarobot/man/RequestNewModel.Rd | 4 datarobot-2.6.0/datarobot/man/RequestPredictions.Rd | 1 datarobot-2.6.0/datarobot/man/RequestPredictionsForDataset.Rd | 3 datarobot-2.6.0/datarobot/man/RequestPrimeModel.Rd | 1 datarobot-2.6.0/datarobot/man/RequestReasonCodes.Rd |only datarobot-2.6.0/datarobot/man/RequestReasonCodesInitialization.Rd |only datarobot-2.6.0/datarobot/man/RequestSampleSizeUpdate.Rd | 1 datarobot-2.6.0/datarobot/man/RequestTransferrableModel.Rd | 1 datarobot-2.6.0/datarobot/man/ScoreBacktests.Rd |only datarobot-2.6.0/datarobot/man/SetTarget.Rd | 26 datarobot-2.6.0/datarobot/man/SetupProject.Rd | 1 datarobot-2.6.0/datarobot/man/SetupProjectFromHDFS.Rd | 1 datarobot-2.6.0/datarobot/man/SetupProjectFromMySQL.Rd | 1 datarobot-2.6.0/datarobot/man/SetupProjectFromOracle.Rd | 1 datarobot-2.6.0/datarobot/man/SetupProjectFromPostgreSQL.Rd | 1 datarobot-2.6.0/datarobot/man/StartNewAutoPilot.Rd | 4 datarobot-2.6.0/datarobot/man/UnpauseQueue.Rd | 3 datarobot-2.6.0/datarobot/man/UpdateProject.Rd | 1 datarobot-2.6.0/datarobot/man/UpdateTransferrableModel.Rd | 3 datarobot-2.6.0/datarobot/man/UploadPredictionDataset.Rd | 3 datarobot-2.6.0/datarobot/man/UploadTransferrableModel.Rd | 7 datarobot-2.6.0/datarobot/man/ViewWebModel.Rd | 1 datarobot-2.6.0/datarobot/man/ViewWebProject.Rd | 1 datarobot-2.6.0/datarobot/man/WaitForAutopilot.Rd | 1 datarobot-2.6.0/datarobot/man/WaitForJobToComplete.Rd | 3 datarobot-2.6.0/datarobot/man/as.data.frame.Rd | 9 datarobot-2.6.0/datarobot/man/cvMethods.Rd |only datarobot-2.6.0/datarobot/man/datarobot-package.Rd | 3 datarobot-2.6.0/datarobot/man/plot.listOfModels.Rd | 1 datarobot-2.6.0/datarobot/man/summary.dataRobotModel.Rd | 5 datarobot-2.6.0/datarobot/tests/testthat/test-CreateGroupPartition.R | 18 datarobot-2.6.0/datarobot/tests/testthat/test-CreateUserPartition.R | 28 datarobot-2.6.0/datarobot/tests/testthat/test-StartAutopilot.R | 27 datarobot-2.6.0/datarobot/vignettes/DatetimePartitionedProjects.Rmd |only datarobot-2.6.0/datarobot/vignettes/ReasonCodeVignette.Rmd |only datarobot-2.6.0/datarobot/vignettes/featureImpact.rds |only datarobot-2.6.0/datarobot/vignettes/lendingClub.csv |only datarobot-2.6.0/datarobot/vignettes/reasonCodeAsDataFrameTopBottom.rds |only datarobot-2.6.0/datarobot/vignettes/results.rds |only datarobot-2.6.0/datarobot/vignettes/testPredictions.rds |only 181 files changed, 558 insertions(+), 424 deletions(-)
Title: Filtering of Flow Cytometry Samples
Description: Filtering, also known as gating, of flow cytometry samples using
the curvHDR method, which is described in Naumann, U., Luta, G. and
Wand, M.P. (2010) <DOI:10.1186/1471-2105-11-44>.
Author: Matt Wand [aut, cre],
George Luta [aut],
Ulrike Naumann [aut],
Mathew W. McLean [ctb],
Dai Feng [ctb],
Luke Tierney [ctb],
Florian Hahne [ctb]
Maintainer: Matt Wand <matt.wand@uts.edu.au>
Diff between curvHDR versions 1.1-0 dated 2016-03-14 and 1.2-0 dated 2017-04-16
DESCRIPTION | 12 +++++++----- MD5 | 15 ++++++++++----- NAMESPACE | 2 +- R/curvHDRfilter.r | 10 +++++----- R/inpolygon.r | 8 ++++++-- build |only inst |only man/curvHDRfilter.Rd | 5 ++--- src/init.c |only vignettes/manual.Rnw |only 10 files changed, 31 insertions(+), 21 deletions(-)
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores adduced from different growth standards (WHO, UK, German). Therefore, the calculation for SDS-values for different measures like BMI, weight, height, head circumference, different ratios, etc. are easy to carry out. Also, references for laboratory values in children are available: serum lipids, iron-related blood parameters. In the new version, there are also functions combining the gamlss lms() function with resampling methods for using with repeated measurements and family dependencies.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.5 dated 2014-08-21 and 0.6 dated 2017-04-16
childsds-0.5/childsds/R/cdcref-data.r |only childsds-0.5/childsds/R/childsds-package.r |only childsds-0.5/childsds/R/kiggsref-data.r |only childsds-0.5/childsds/R/kroref-data.r |only childsds-0.5/childsds/R/ukwhoref-data.r |only childsds-0.5/childsds/R/whoref-data.r |only childsds-0.5/childsds/man/articles-methods.Rd |only childsds-0.5/childsds/man/articles.Rd |only childsds-0.5/childsds/man/childsds.Rd |only childsds-0.5/childsds/man/refs-class.Rd |only childsds-0.5/childsds/man/sds-methods.Rd |only childsds-0.5/childsds/man/sds.df.Rd |only childsds-0.5/childsds/man/sdsdf-methods.Rd |only childsds-0.5/childsds/man/show-method.Rd |only childsds-0.6/childsds/DESCRIPTION | 28 +- childsds-0.6/childsds/MD5 | 61 +++-- childsds-0.6/childsds/NAMESPACE | 16 + childsds-0.6/childsds/R/createlms.R |only childsds-0.6/childsds/R/data.R |only childsds-0.6/childsds/R/misc.R |only childsds-0.6/childsds/R/refsclass.r | 242 ++++++++++------------ childsds-0.6/childsds/data/cdc.ref.rda |binary childsds-0.6/childsds/data/iron.ref.rda |only childsds-0.6/childsds/data/kiggs.ref.rda |binary childsds-0.6/childsds/data/kro.ref.rda |binary childsds-0.6/childsds/data/lipids.ref.rda |only childsds-0.6/childsds/data/ukwho.ref.rda |binary childsds-0.6/childsds/data/who.ref.rda |binary childsds-0.6/childsds/man/ParTab-class.Rd |only childsds-0.6/childsds/man/RefGroup-class.Rd |only childsds-0.6/childsds/man/aggregate_lms.Rd |only childsds-0.6/childsds/man/cdc.ref.Rd | 12 - childsds-0.6/childsds/man/do_iterations.Rd |only childsds-0.6/childsds/man/fit_gamlss.Rd |only childsds-0.6/childsds/man/iron.ref.Rd |only childsds-0.6/childsds/man/kiggs.ref.Rd | 12 - childsds-0.6/childsds/man/kro.ref.Rd | 12 - childsds-0.6/childsds/man/lipids.ref.Rd |only childsds-0.6/childsds/man/make_percentile_tab.Rd |only childsds-0.6/childsds/man/one_iteration.Rd |only childsds-0.6/childsds/man/prepare_data.Rd |only childsds-0.6/childsds/man/sds.Rd | 38 ++- childsds-0.6/childsds/man/select_fams.Rd |only childsds-0.6/childsds/man/select_meas.Rd |only childsds-0.6/childsds/man/show-ParTab-method.Rd |only childsds-0.6/childsds/man/show-RefGroup-method.Rd |only childsds-0.6/childsds/man/ukwho.ref.Rd | 10 childsds-0.6/childsds/man/who.ref.Rd | 12 - 48 files changed, 239 insertions(+), 204 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-10-18 1.4.3
2015-10-15 1.4.2
2015-09-11 1.3
2015-08-17 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-04-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-10 2.0.0
2015-11-06 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-07 3.0.0
2016-07-12 2.0.1
2016-07-12 2.0.1.1
2016-02-02 2.0.0
2015-06-04 1.2.1
2015-04-01 1.1.1
2015-03-11 1.1
2014-09-04 1.0.1
2014-08-23 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-11 2.0.0
2015-07-14 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-28 0.2.2
2016-10-27 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-03-15 0.2.3.1
2017-02-01 0.2.3
2016-03-09 0.2.2.1
2016-03-05 0.2.2
2015-07-23 0.2.1
2015-04-14 0.2