Title: SpatialTools
Diff between SpatialTools versions 0.3.2 dated 2011-12-15 and 0.3.3 dated 2012-01-23
Description: Tools for spatial data analysis. Emphasis on kriging.
Provides functions for prediction and simulation. Intended to
be relatively straightforward, fast, and flexible.
Author: Joshua French
Maintainer: Joshua French
DESCRIPTION | 12 +++++++-----
MD5 | 23 ++++++++++++++---------
NAMESPACE | 4 +++-
NEWS |only
R/cov.R | 5 +++--
R/krige_tools.R | 31 +++++++++++++++++++++++++++++++
R/krige_tools_arg_check.R | 43 ++++++++++++++++++++++++++++++++++++++++---
R/preamble.R |only
man/krige.ok.Rd | 24 ++++++++++--------------
man/krige.sk.Rd |only
man/krige.uk.Rd | 6 +++---
src/krige_ok_tools.cpp | 2 +-
src/krige_sk_tools.cpp |only
src/krige_sk_tools.h |only
src/krige_uk_tools.cpp | 4 +---
15 files changed, 113 insertions(+), 41 deletions(-)
Title: Simulation of high-dimensional data and parallelized repeated
penalized regression
Diff between pensim versions 1.1.4 dated 2012-01-22 and 1.2.1 dated 2012-01-23
Description: Simulation of continuous, correlated high-dimensional data
with time to event or binary response, and parallelized
functions for Lasso, Ridge, and Elastic Net penalized
regression with repeated starts and two-dimensional tuning of
the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C.
Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron
pensim-1.1.4/pensim/inst/.Rhistory |only
pensim-1.2.1/pensim/Changelog | 2 ++
pensim-1.2.1/pensim/DESCRIPTION | 8 ++++----
pensim-1.2.1/pensim/MD5 | 9 ++++++---
pensim-1.2.1/pensim/inst/doc |only
pensim-1.2.1/pensim/man/pensim-package.Rd | 4 ++--
6 files changed, 14 insertions(+), 9 deletions(-)
Title: Dendrochronology Program Library in R
Diff between dplR versions 1.5.1 dated 2011-12-22 and 1.5.2 dated 2012-01-23
Description: This package contains functions for performing tree-ring
analyses, IO, and graphics.
Author: Andy Bunn with major additions from Mikko Korpela and other
significant contributions from Franco Biondi and Christian Zang
Maintainer: Andy Bunn
dplR-1.5.1/dplR/man/read.fh.rd |only
dplR-1.5.2/dplR/ChangeLog | 21
dplR-1.5.2/dplR/DESCRIPTION | 12
dplR-1.5.2/dplR/MD5 | 144 ++---
dplR-1.5.2/dplR/R/ffcsaps.R | 11
dplR-1.5.2/dplR/R/read.ids.R | 10
dplR-1.5.2/dplR/R/write.compact.R | 2
dplR-1.5.2/dplR/R/write.tridas.R | 3
dplR-1.5.2/dplR/R/write.tucson.R | 3
dplR-1.5.2/dplR/data/ca533.rda |binary
dplR-1.5.2/dplR/data/cana157.rda |binary
dplR-1.5.2/dplR/data/co021.rda |binary
dplR-1.5.2/dplR/data/gp.d2pith.rda |binary
dplR-1.5.2/dplR/data/gp.dbh.rda |binary
dplR-1.5.2/dplR/data/gp.po.rda |binary
dplR-1.5.2/dplR/data/gp.rwl.rda |binary
dplR-1.5.2/dplR/inst/po/fi/LC_MESSAGES/R-dplR.mo |binary
dplR-1.5.2/dplR/man/bai.in.Rd | 34 -
dplR-1.5.2/dplR/man/bai.out.Rd | 34 -
dplR-1.5.2/dplR/man/ca533.Rd | 27
dplR-1.5.2/dplR/man/cana157.Rd | 25
dplR-1.5.2/dplR/man/ccf.series.rwl.Rd | 89 +--
dplR-1.5.2/dplR/man/chron.Rd | 43 -
dplR-1.5.2/dplR/man/cms.Rd | 48 -
dplR-1.5.2/dplR/man/co021.Rd | 26
dplR-1.5.2/dplR/man/combine.rwl.Rd | 25
dplR-1.5.2/dplR/man/corr.rwl.seg.Rd | 141 ++---
dplR-1.5.2/dplR/man/corr.series.seg.Rd | 95 +--
dplR-1.5.2/dplR/man/crn.plot.Rd | 32 -
dplR-1.5.2/dplR/man/detrend.Rd | 74 +-
dplR-1.5.2/dplR/man/detrend.series.Rd | 142 ++---
dplR-1.5.2/dplR/man/dplR-package.Rd | 22
dplR-1.5.2/dplR/man/ffcsaps.Rd | 86 +--
dplR-1.5.2/dplR/man/gini.coef.Rd | 34 -
dplR-1.5.2/dplR/man/glk.Rd | 47 -
dplR-1.5.2/dplR/man/gp.d2pith.Rd | 24
dplR-1.5.2/dplR/man/gp.dbh.Rd | 25
dplR-1.5.2/dplR/man/gp.po.Rd | 26
dplR-1.5.2/dplR/man/gp.rwl.Rd | 26
dplR-1.5.2/dplR/man/hanning.Rd | 34 -
dplR-1.5.2/dplR/man/i.detrend.Rd | 42 -
dplR-1.5.2/dplR/man/i.detrend.series.Rd | 40 -
dplR-1.5.2/dplR/man/morlet.Rd | 50 -
dplR-1.5.2/dplR/man/po.to.wc.Rd | 18
dplR-1.5.2/dplR/man/rcs.Rd | 84 +--
dplR-1.5.2/dplR/man/read.compact.Rd | 24
dplR-1.5.2/dplR/man/read.crn.Rd | 40 -
dplR-1.5.2/dplR/man/read.fh.Rd |only
dplR-1.5.2/dplR/man/read.ids.Rd | 77 +-
dplR-1.5.2/dplR/man/read.rwl.Rd | 36 -
dplR-1.5.2/dplR/man/read.tridas.Rd | 635 ++++++++++++++---------
dplR-1.5.2/dplR/man/read.tucson.Rd | 51 +
dplR-1.5.2/dplR/man/rwi.stats.Rd | 121 ++--
dplR-1.5.2/dplR/man/rwi.stats.running.Rd | 219 ++++---
dplR-1.5.2/dplR/man/rwl.stats.Rd | 60 +-
dplR-1.5.2/dplR/man/sea.Rd | 66 +-
dplR-1.5.2/dplR/man/seg.plot.Rd | 21
dplR-1.5.2/dplR/man/sens1.Rd | 46 -
dplR-1.5.2/dplR/man/sens2.Rd | 50 -
dplR-1.5.2/dplR/man/series.rwl.plot.Rd | 92 +--
dplR-1.5.2/dplR/man/skel.plot.Rd | 155 ++---
dplR-1.5.2/dplR/man/spag.plot.Rd | 29 -
dplR-1.5.2/dplR/man/tbrm.Rd | 69 +-
dplR-1.5.2/dplR/man/tridas.vocabulary.Rd | 78 +-
dplR-1.5.2/dplR/man/uuid.gen.Rd | 86 +--
dplR-1.5.2/dplR/man/wavelet.plot.Rd | 82 +-
dplR-1.5.2/dplR/man/wc.to.po.Rd | 21
dplR-1.5.2/dplR/man/write.compact.Rd | 67 +-
dplR-1.5.2/dplR/man/write.crn.Rd | 134 ++--
dplR-1.5.2/dplR/man/write.rwl.Rd | 46 -
dplR-1.5.2/dplR/man/write.tridas.Rd | 497 +++++++++---------
dplR-1.5.2/dplR/man/write.tucson.Rd | 146 ++---
dplR-1.5.2/dplR/po/R-dplR.pot | 16
dplR-1.5.2/dplR/po/R-fi.po | 30 -
74 files changed, 2580 insertions(+), 2013 deletions(-)
Title: NCBI2R-An R package to navigate and annotate genes and SNPs
Diff between NCBI2R versions 1.3.4 dated 2011-08-23 and 1.3.5 dated 2012-01-23
Description: NCBI2R is an R package that annotates lists of SNPs and/or
genes, with current information from NCBI, including LD
information. Functions are provided that with one command will
provide annotation of the results from genome wide association
studies to provide a broader context of their meaning. Other
functions enable comparisons between a user's GWA results, and
candidate snp/gene lists that are created from keywords, such
as specific diseases, phenotypes or gene ontology terms.
Commands are simple to follow and designed to work with R
objects to integrate into existing workflows. The output
produces text fields and weblinks to more information for items
such as: gene descriptions, nucleotide positions, OMIM,
pathways, phenotypes, and lists of interacting and neighboring
genes. Annotation can then be used in R for further analysis,
or the objects can be customized for use in spreadsheet
programs or web browsers. The NCBI2R package wasdesigned to
allow those performing genome analysis to produce output that
could easily be understood by a person not familiar with R.
Please see the website at http://NCBI2R.wordpress.com for more
information. The internet is required for almost all of these
functions. Use the function PrintNCBI2RInfo() for information.
Author: Scott Melville
Maintainer: Scott Melville
NCBI2R-1.3.4/NCBI2R/R/AdjustRangeAroundGene.R |only
NCBI2R-1.3.4/NCBI2R/R/AlignsData.r |only
NCBI2R-1.3.4/NCBI2R/R/AnnotateDataframe.R |only
NCBI2R-1.3.4/NCBI2R/R/AnnotateSNPFile.R |only
NCBI2R-1.3.4/NCBI2R/R/AnnotateSNPList.R |only
NCBI2R-1.3.4/NCBI2R/R/CleanACGT.r |only
NCBI2R-1.3.4/NCBI2R/R/CleanNAs.r |only
NCBI2R-1.3.4/NCBI2R/R/ColumnStripper.r |only
NCBI2R-1.3.4/NCBI2R/R/ConvertDFToHTML.R |only
NCBI2R-1.3.4/NCBI2R/R/ConvertPubMedHeadings.R |only
NCBI2R-1.3.4/NCBI2R/R/ConvertURLToExcel.R |only
NCBI2R-1.3.4/NCBI2R/R/ConvertURLToHTML.R |only
NCBI2R-1.3.4/NCBI2R/R/Cutter.R |only
NCBI2R-1.3.4/NCBI2R/R/Delay.R |only
NCBI2R-1.3.4/NCBI2R/R/DelayInc.R |only
NCBI2R-1.3.4/NCBI2R/R/DelayUntil.R |only
NCBI2R-1.3.4/NCBI2R/R/EmailAlert.r |only
NCBI2R-1.3.4/NCBI2R/R/Excel.FIND.r |only
NCBI2R-1.3.4/NCBI2R/R/Excel.LEFT.r |only
NCBI2R-1.3.4/NCBI2R/R/Excel.MID.r |only
NCBI2R-1.3.4/NCBI2R/R/Excel.RIGHT.r |only
NCBI2R-1.3.4/NCBI2R/R/Finder.R |only
NCBI2R-1.3.4/NCBI2R/R/GetARFromLocation.R |only
NCBI2R-1.3.4/NCBI2R/R/GetExpiryDate.R |only
NCBI2R-1.3.4/NCBI2R/R/GetGOs.R |only
NCBI2R-1.3.4/NCBI2R/R/GetGeneInfo.R |only
NCBI2R-1.3.4/NCBI2R/R/GetGeneName.R |only
NCBI2R-1.3.4/NCBI2R/R/GetGeneNames.R |only
NCBI2R-1.3.4/NCBI2R/R/GetGenesInRegion.R |only
NCBI2R-1.3.4/NCBI2R/R/GetID.R |only
NCBI2R-1.3.4/NCBI2R/R/GetIDs.R |only
NCBI2R-1.3.4/NCBI2R/R/GetInteractions.R |only
NCBI2R-1.3.4/NCBI2R/R/GetListFromXML.R |only
NCBI2R-1.3.4/NCBI2R/R/GetNeighGenes.R |only
NCBI2R-1.3.4/NCBI2R/R/GetPathways.R |only
NCBI2R-1.3.4/NCBI2R/R/GetPhenotypes.R |only
NCBI2R-1.3.4/NCBI2R/R/GetPubMed.R |only
NCBI2R-1.3.4/NCBI2R/R/GetRegion.R |only
NCBI2R-1.3.4/NCBI2R/R/GetSNPCurrent.R |only
NCBI2R-1.3.4/NCBI2R/R/GetSNPPosHapmap.r |only
NCBI2R-1.3.4/NCBI2R/R/GetSNPsInGenes.R |only
NCBI2R-1.3.4/NCBI2R/R/GetSNPsInRegion.R |only
NCBI2R-1.3.4/NCBI2R/R/GetTax.R |only
NCBI2R-1.3.4/NCBI2R/R/GetUniSTSFromName.R |only
NCBI2R-1.3.4/NCBI2R/R/GetUniSTSInfo.R |only
NCBI2R-1.3.4/NCBI2R/R/MakeExcel.R |only
NCBI2R-1.3.4/NCBI2R/R/MakeHTML.R |only
NCBI2R-1.3.4/NCBI2R/R/MergeSNPsGenes.R |only
NCBI2R-1.3.4/NCBI2R/R/OpenPDF.R |only
NCBI2R-1.3.4/NCBI2R/R/OpenPMID.R |only
NCBI2R-1.3.4/NCBI2R/R/OpenURL.R |only
NCBI2R-1.3.4/NCBI2R/R/ParseSNPIDLine.r |only
NCBI2R-1.3.4/NCBI2R/R/PlotExons.R |only
NCBI2R-1.3.4/NCBI2R/R/PrintFilters.R |only
NCBI2R-1.3.4/NCBI2R/R/ProcessCombinedResults.R |only
NCBI2R-1.3.4/NCBI2R/R/RandomSNP.r |only
NCBI2R-1.3.4/NCBI2R/R/ScanForGenes.FindSNPPositions.R |only
NCBI2R-1.3.4/NCBI2R/R/ScanForGenes.R |only
NCBI2R-1.3.4/NCBI2R/R/ScanForGenes.WithSNPPositions.R |only
NCBI2R-1.3.4/NCBI2R/R/ScanForSNPs.FindSNPPositions.R |only
NCBI2R-1.3.4/NCBI2R/R/ScanForSNPs.R |only
NCBI2R-1.3.4/NCBI2R/R/ScanForSNPs.WithSNPPositions.R |only
NCBI2R-1.3.4/NCBI2R/R/ShowMessages.R |only
NCBI2R-1.3.4/NCBI2R/R/SkimUntil.R |only
NCBI2R-1.3.4/NCBI2R/R/SortByChr.R |only
NCBI2R-1.3.4/NCBI2R/R/SplitGenes.R |only
NCBI2R-1.3.4/NCBI2R/R/TranslateIUPAC.r |only
NCBI2R-1.3.4/NCBI2R/R/TryScan.R |only
NCBI2R-1.3.4/NCBI2R/R/URLcreator.R |only
NCBI2R-1.3.4/NCBI2R/R/URLdefinitions.R |only
NCBI2R-1.3.4/NCBI2R/R/VisualiseRegion.R |only
NCBI2R-1.3.4/NCBI2R/R/add.column.R |only
NCBI2R-1.3.4/NCBI2R/R/add.lead.zero.R |only
NCBI2R-1.3.4/NCBI2R/R/change.class.data.frame.R |only
NCBI2R-1.3.4/NCBI2R/R/clean.NAs.R |only
NCBI2R-1.3.4/NCBI2R/R/clean.R |only
NCBI2R-1.3.4/NCBI2R/R/clean.xml.R |only
NCBI2R-1.3.4/NCBI2R/R/cleanframe.R |only
NCBI2R-1.3.4/NCBI2R/R/compress.df.R |only
NCBI2R-1.3.4/NCBI2R/R/convert.go.R |only
NCBI2R-1.3.4/NCBI2R/R/convert.int.R |only
NCBI2R-1.3.4/NCBI2R/R/createframe.R |only
NCBI2R-1.3.4/NCBI2R/R/ext.f.tags.R |only
NCBI2R-1.3.4/NCBI2R/R/get.file.R |only
NCBI2R-1.3.4/NCBI2R/R/get.go.int.R |only
NCBI2R-1.3.4/NCBI2R/R/get.int.int.R |only
NCBI2R-1.3.4/NCBI2R/R/get.pathways.int.R |only
NCBI2R-1.3.4/NCBI2R/R/get.phenotypes.int.R |only
NCBI2R-1.3.4/NCBI2R/R/make.log.R |only
NCBI2R-1.3.4/NCBI2R/R/move.column.R |only
NCBI2R-1.3.4/NCBI2R/R/process.gene.table.int.R |only
NCBI2R-1.3.4/NCBI2R/R/process.gene.table.int.old.R |only
NCBI2R-1.3.4/NCBI2R/R/searcher.R |only
NCBI2R-1.3.4/NCBI2R/R/set.create.dir.R |only
NCBI2R-1.3.4/NCBI2R/R/splitfirst.R |only
NCBI2R-1.3.4/NCBI2R/R/swap.columns.R |only
NCBI2R-1.3.4/NCBI2R/R/swap.rows.R |only
NCBI2R-1.3.4/NCBI2R/R/vcheck.R |only
NCBI2R-1.3.4/NCBI2R/R/zzz.R |only
NCBI2R-1.3.4/NCBI2R/man/GetSNPPosHapmap.Rd |only
NCBI2R-1.3.4/NCBI2R/man/TranslateIUPAC.rd |only
NCBI2R-1.3.5/NCBI2R/DESCRIPTION | 19
NCBI2R-1.3.5/NCBI2R/FAQ | 2
NCBI2R-1.3.5/NCBI2R/MD5 | 350 +++++-----
NCBI2R-1.3.5/NCBI2R/NAMESPACE | 2
NCBI2R-1.3.5/NCBI2R/R/AdjustRangeAroundGene.r |only
NCBI2R-1.3.5/NCBI2R/R/AminoAcids.r |only
NCBI2R-1.3.5/NCBI2R/R/AnnotateDataframe.r |only
NCBI2R-1.3.5/NCBI2R/R/AnnotateSNPFile.r |only
NCBI2R-1.3.5/NCBI2R/R/AnnotateSNPList.r |only
NCBI2R-1.3.5/NCBI2R/R/Comp.r | 30
NCBI2R-1.3.5/NCBI2R/R/ConvertDFToHTML.r |only
NCBI2R-1.3.5/NCBI2R/R/ConvertIUPAC.r |only
NCBI2R-1.3.5/NCBI2R/R/ConvertProtein.r |only
NCBI2R-1.3.5/NCBI2R/R/ConvertPubMedHeadings.r |only
NCBI2R-1.3.5/NCBI2R/R/ConvertURLToExcel.r |only
NCBI2R-1.3.5/NCBI2R/R/ConvertURLToHTML.r |only
NCBI2R-1.3.5/NCBI2R/R/Delay.r |only
NCBI2R-1.3.5/NCBI2R/R/DelayUntil.r |only
NCBI2R-1.3.5/NCBI2R/R/GetARFromLocation.r |only
NCBI2R-1.3.5/NCBI2R/R/GetClosestGeneInfo.r |only
NCBI2R-1.3.5/NCBI2R/R/GetExpiryDate.r |only
NCBI2R-1.3.5/NCBI2R/R/GetGOs.r |only
NCBI2R-1.3.5/NCBI2R/R/GetGeneInfo.r |only
NCBI2R-1.3.5/NCBI2R/R/GetGeneNames.r |only
NCBI2R-1.3.5/NCBI2R/R/GetGeneTable.r | 223 +++---
NCBI2R-1.3.5/NCBI2R/R/GetGenesInRegion.r |only
NCBI2R-1.3.5/NCBI2R/R/GetIDs.r |only
NCBI2R-1.3.5/NCBI2R/R/GetInteractions.r |only
NCBI2R-1.3.5/NCBI2R/R/GetLDInfo.r | 76 +-
NCBI2R-1.3.5/NCBI2R/R/GetNeighGenes.r |only
NCBI2R-1.3.5/NCBI2R/R/GetPathways.r |only
NCBI2R-1.3.5/NCBI2R/R/GetPhenotypes.r |only
NCBI2R-1.3.5/NCBI2R/R/GetPubMed.r |only
NCBI2R-1.3.5/NCBI2R/R/GetRegion.r |only
NCBI2R-1.3.5/NCBI2R/R/GetSNPCurrent.r |only
NCBI2R-1.3.5/NCBI2R/R/GetSNPFlankSeq.r | 16
NCBI2R-1.3.5/NCBI2R/R/GetSNPInfo.r | 279 +++----
NCBI2R-1.3.5/NCBI2R/R/GetSNPPosHapMap.r |only
NCBI2R-1.3.5/NCBI2R/R/GetSNPProxyInfo.r | 80 +-
NCBI2R-1.3.5/NCBI2R/R/GetSNPsInGenes.r |only
NCBI2R-1.3.5/NCBI2R/R/GetSNPsInRegion.r |only
NCBI2R-1.3.5/NCBI2R/R/GetTableWithComments.r | 2
NCBI2R-1.3.5/NCBI2R/R/GetTax.r |only
NCBI2R-1.3.5/NCBI2R/R/GetUniSTSFromName.r |only
NCBI2R-1.3.5/NCBI2R/R/GetUniSTSInfo.r |only
NCBI2R-1.3.5/NCBI2R/R/GetUniSTSSpecies.r | 63 -
NCBI2R-1.3.5/NCBI2R/R/MakeExcel.r |only
NCBI2R-1.3.5/NCBI2R/R/MakeHTML.r |only
NCBI2R-1.3.5/NCBI2R/R/MergeSNPsGenes.r |only
NCBI2R-1.3.5/NCBI2R/R/NatureJobs.r | 24
NCBI2R-1.3.5/NCBI2R/R/OpenPDF.r |only
NCBI2R-1.3.5/NCBI2R/R/OpenPMID.r |only
NCBI2R-1.3.5/NCBI2R/R/OpenURL.r |only
NCBI2R-1.3.5/NCBI2R/R/PrintFilters.r |only
NCBI2R-1.3.5/NCBI2R/R/PrintNCBI2RInfo.r | 4
NCBI2R-1.3.5/NCBI2R/R/PrintNCBI2ROptions.r |only
NCBI2R-1.3.5/NCBI2R/R/Rev.r | 14
NCBI2R-1.3.5/NCBI2R/R/ScanForGenes.FindSNPPositions.r |only
NCBI2R-1.3.5/NCBI2R/R/ScanForGenes.WithSNPPositions.r |only
NCBI2R-1.3.5/NCBI2R/R/ScanForGenes.r |only
NCBI2R-1.3.5/NCBI2R/R/ScanForSNPs.FindSNPPositions.r |only
NCBI2R-1.3.5/NCBI2R/R/ScanForSNPs.WithSNPPositions.r |only
NCBI2R-1.3.5/NCBI2R/R/ScanForSNPs.r |only
NCBI2R-1.3.5/NCBI2R/R/SortByChr.r |only
NCBI2R-1.3.5/NCBI2R/R/SplitGenes.r |only
NCBI2R-1.3.5/NCBI2R/R/UpdateCheck.r | 19
NCBI2R-1.3.5/NCBI2R/R/VisualiseRegion.r |only
NCBI2R-1.3.5/NCBI2R/R/add.column.r |only
NCBI2R-1.3.5/NCBI2R/R/add.lead.zero.r |only
NCBI2R-1.3.5/NCBI2R/R/alignsData.r |only
NCBI2R-1.3.5/NCBI2R/R/change.class.data.frame.r |only
NCBI2R-1.3.5/NCBI2R/R/check.IUPAC.r |only
NCBI2R-1.3.5/NCBI2R/R/clean.NAs.r |only
NCBI2R-1.3.5/NCBI2R/R/clean.r |only
NCBI2R-1.3.5/NCBI2R/R/clean.xml.r |only
NCBI2R-1.3.5/NCBI2R/R/cleanACGT.r |only
NCBI2R-1.3.5/NCBI2R/R/cleanframe.r |only
NCBI2R-1.3.5/NCBI2R/R/columnStripper.r |only
NCBI2R-1.3.5/NCBI2R/R/compress.df.r |only
NCBI2R-1.3.5/NCBI2R/R/convert.go.r |only
NCBI2R-1.3.5/NCBI2R/R/convert.int.r |only
NCBI2R-1.3.5/NCBI2R/R/convert.protein.a.r |only
NCBI2R-1.3.5/NCBI2R/R/createframe.r |only
NCBI2R-1.3.5/NCBI2R/R/cutter.r |only
NCBI2R-1.3.5/NCBI2R/R/delayInc.r |only
NCBI2R-1.3.5/NCBI2R/R/emailAlert.r |only
NCBI2R-1.3.5/NCBI2R/R/excel.FIND.r |only
NCBI2R-1.3.5/NCBI2R/R/excel.LEFT.r |only
NCBI2R-1.3.5/NCBI2R/R/excel.MID.r |only
NCBI2R-1.3.5/NCBI2R/R/excel.RIGHT.r |only
NCBI2R-1.3.5/NCBI2R/R/ext.f.tags.r |only
NCBI2R-1.3.5/NCBI2R/R/finder.r |only
NCBI2R-1.3.5/NCBI2R/R/get.file.r |only
NCBI2R-1.3.5/NCBI2R/R/get.go.int.r |only
NCBI2R-1.3.5/NCBI2R/R/get.int.int.r |only
NCBI2R-1.3.5/NCBI2R/R/get.pathways.int.r |only
NCBI2R-1.3.5/NCBI2R/R/get.phenotypes.int.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.create.mappingdf.from.chunk.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.info.check.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.info.cross.ref.available.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.info.cross.ref.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.info.map.r |only
NCBI2R-1.3.5/NCBI2R/R/get.uni.sts.info.map.wrap.r |only
NCBI2R-1.3.5/NCBI2R/R/getListFromXML.r |only
NCBI2R-1.3.5/NCBI2R/R/make.local.HTML.r | 50 -
NCBI2R-1.3.5/NCBI2R/R/make.log.r |only
NCBI2R-1.3.5/NCBI2R/R/move.column.r |only
NCBI2R-1.3.5/NCBI2R/R/ncbi2r.options.default.r |only
NCBI2R-1.3.5/NCBI2R/R/ncbi2r.options.r |only
NCBI2R-1.3.5/NCBI2R/R/parse.chunk.r |only
NCBI2R-1.3.5/NCBI2R/R/parseSNPIDLine.r |only
NCBI2R-1.3.5/NCBI2R/R/plotExons.r |only
NCBI2R-1.3.5/NCBI2R/R/pn.r |only
NCBI2R-1.3.5/NCBI2R/R/process.gene.table.int.old.r |only
NCBI2R-1.3.5/NCBI2R/R/process.gene.table.int.r |only
NCBI2R-1.3.5/NCBI2R/R/processCombinedResults.r |only
NCBI2R-1.3.5/NCBI2R/R/randomSNP.r |only
NCBI2R-1.3.5/NCBI2R/R/searcher.r |only
NCBI2R-1.3.5/NCBI2R/R/set.create.dir.r |only
NCBI2R-1.3.5/NCBI2R/R/showMessages.r |only
NCBI2R-1.3.5/NCBI2R/R/skimUntil.r |only
NCBI2R-1.3.5/NCBI2R/R/splitfirst.r |only
NCBI2R-1.3.5/NCBI2R/R/swap.columns.r |only
NCBI2R-1.3.5/NCBI2R/R/swap.rows.r |only
NCBI2R-1.3.5/NCBI2R/R/tryScan.r |only
NCBI2R-1.3.5/NCBI2R/R/updateCheck.int.r |only
NCBI2R-1.3.5/NCBI2R/R/updateCheckWrapper.r |only
NCBI2R-1.3.5/NCBI2R/R/urlCreator.r |only
NCBI2R-1.3.5/NCBI2R/R/vcheck.r |only
NCBI2R-1.3.5/NCBI2R/R/zzz.r |only
NCBI2R-1.3.5/NCBI2R/TODO | 4
NCBI2R-1.3.5/NCBI2R/data |only
NCBI2R-1.3.5/NCBI2R/demo |only
NCBI2R-1.3.5/NCBI2R/man/AdjustRangeAroundGene.Rd | 10
NCBI2R-1.3.5/NCBI2R/man/AminoAcids.rd |only
NCBI2R-1.3.5/NCBI2R/man/AnnotateDataframe.Rd | 7
NCBI2R-1.3.5/NCBI2R/man/AnnotateSNPFile.Rd | 12
NCBI2R-1.3.5/NCBI2R/man/AnnotateSNPList.Rd | 9
NCBI2R-1.3.5/NCBI2R/man/Comp.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/ConvertIUPAC.rd |only
NCBI2R-1.3.5/NCBI2R/man/ConvertProtein.rd |only
NCBI2R-1.3.5/NCBI2R/man/ConvertPubMedHeadings.rd | 7
NCBI2R-1.3.5/NCBI2R/man/Delay.rd | 4
NCBI2R-1.3.5/NCBI2R/man/DelayUntil.rd | 14
NCBI2R-1.3.5/NCBI2R/man/DivideString.Rd | 4
NCBI2R-1.3.5/NCBI2R/man/GetARFromLocation.Rd | 9
NCBI2R-1.3.5/NCBI2R/man/GetClosestGeneInfo.Rd |only
NCBI2R-1.3.5/NCBI2R/man/GetGOs.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/GetGeneInfo.Rd | 37 -
NCBI2R-1.3.5/NCBI2R/man/GetGeneTable.Rd | 6
NCBI2R-1.3.5/NCBI2R/man/GetGenesInRegion.Rd | 10
NCBI2R-1.3.5/NCBI2R/man/GetIDs.Rd | 13
NCBI2R-1.3.5/NCBI2R/man/GetInteractions.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/GetLDInfo.Rd | 23
NCBI2R-1.3.5/NCBI2R/man/GetNeighGenes.Rd | 9
NCBI2R-1.3.5/NCBI2R/man/GetPathways.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/GetPhenotypes.Rd | 4
NCBI2R-1.3.5/NCBI2R/man/GetPubMed.Rd | 18
NCBI2R-1.3.5/NCBI2R/man/GetRegion.Rd | 14
NCBI2R-1.3.5/NCBI2R/man/GetSNPFlankSeq.rd | 16
NCBI2R-1.3.5/NCBI2R/man/GetSNPInfo.Rd | 6
NCBI2R-1.3.5/NCBI2R/man/GetSNPPosHapMap.Rd |only
NCBI2R-1.3.5/NCBI2R/man/GetSNPProxyInfo.Rd | 38 -
NCBI2R-1.3.5/NCBI2R/man/GetSNPsInGenes.Rd | 10
NCBI2R-1.3.5/NCBI2R/man/GetSNPsInRegion.Rd | 21
NCBI2R-1.3.5/NCBI2R/man/GetTax.Rd | 14
NCBI2R-1.3.5/NCBI2R/man/GetUniSTSFromName.rd | 2
NCBI2R-1.3.5/NCBI2R/man/GetUniSTSInfo.rd | 11
NCBI2R-1.3.5/NCBI2R/man/GetUniSTSSpecies.rd | 2
NCBI2R-1.3.5/NCBI2R/man/IUPAC.rd | 14
NCBI2R-1.3.5/NCBI2R/man/MakeExcel.Rd | 59 -
NCBI2R-1.3.5/NCBI2R/man/MakeHTML.Rd | 23
NCBI2R-1.3.5/NCBI2R/man/MedlineAbbreviations.rd | 4
NCBI2R-1.3.5/NCBI2R/man/NatureJobs.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/OpenPMID.Rd | 8
NCBI2R-1.3.5/NCBI2R/man/OpenURL.Rd | 4
NCBI2R-1.3.5/NCBI2R/man/PrintFilters.Rd | 4
NCBI2R-1.3.5/NCBI2R/man/PrintNCBI2ROptions.rd |only
NCBI2R-1.3.5/NCBI2R/man/RemoveSpaces.rd | 6
NCBI2R-1.3.5/NCBI2R/man/RevComp.rd | 2
NCBI2R-1.3.5/NCBI2R/man/ScanForGenes.Rd | 2
NCBI2R-1.3.5/NCBI2R/man/ScanForSNPs.Rd | 18
NCBI2R-1.3.5/NCBI2R/man/SplitGenes.rd | 22
NCBI2R-1.3.5/NCBI2R/man/UpdateCheck.rd | 19
NCBI2R-1.3.5/NCBI2R/man/gwas.Rd |only
286 files changed, 892 insertions(+), 890 deletions(-)
Title: Supervised Raster Image Classification
Diff between rasclass versions 0.2.0 dated 2011-11-03 and 0.2.1 dated 2012-01-23
Description: This package contains functions to perform supervised and
pixel based raster image classification. It has been designed
to facilitate land-cover analysis. Five classification
algorithms can be used: Maximum Likelihood Classification,
Multinomial Logistic Regression, Neural Networks, Random
Forests and Support Vector Machines. The output includes the
classified raster and standard classification accuracy
assessment such as the accuracy matrix, the overall accuracy
and the kappa coefficient. An option for in-sample verification
is available.
Author: Daniel Wiesmann
Maintainer: Daniel Wiesmann
DESCRIPTION | 22 ++++++++++++++++------
MD5 | 20 ++++++++++----------
NEWS | 15 ++++++---------
R/classifyRasclass.R | 8 ++++----
R/rasclassMlc.R | 18 ++++++++++--------
R/readRasterFolder.R | 26 ++++++++++++++------------
R/serviceFunctions.R | 2 +-
R/setRasclassData.R | 23 +++++++++--------------
man/classifyRasclass.Rd | 2 +-
man/rasclass-package.Rd | 2 +-
man/setRasclassData.Rd | 2 +-
11 files changed, 73 insertions(+), 67 deletions(-)
Title: Multiple testing methods for exploratory research
Diff between cherry versions 0.1-4 dated 2011-05-31 and 0.1-5 dated 2012-01-23
Description: This package implements a class of multiple testing
methods that does not prescribe the user what hypotheses to
reject, but instead allows the user to select the set of
selected hypotheses freely. The multiple testing procedure aids
this selection by providing an upper confidence bound for the
number of false rejections among the selected set. Because the
confidence bounds are simultaneous for all possible rejected
sets, the validity is not compromised by post hoc selection.
Author: Jelle Goeman
Maintainer: Jelle Goeman
DESCRIPTION | 8 -
MD5 |only
NAMESPACE | 4
R/closed.R | 313 ++++++++++++++++++++++++++++++++++++++++-----------
changelog.txt | 3
man/adjusted.Rd |only
man/closed.Rd | 17 +-
man/closure-class.Rd | 8 +
man/select.Rd | 10 -
9 files changed, 281 insertions(+), 82 deletions(-)
Title: Seasonal analysis of health data
Diff between season versions 0.2-6 dated 2011-11-02 and 0.3-1 dated 2012-01-23
Description: Routines for the seasonal analysis of health data,
including regression models, time-stratified case-crossover,
plotting functions and residual checks. Thanks to Yuming Guo
for checking the case-crossover code.
Author: Adrian Barnett
Maintainer: Adrian Barnett
DESCRIPTION | 18 ++++++++++--------
MD5 | 38 +++++++++++++++++++++++++-------------
NAMESPACE | 5 ++++-
R/aaft.R |only
R/nonlintest.R |only
R/nscosinor.R | 16 ++++++++--------
R/nscosinor.initial.R |only
R/plot.nonlintest.R |only
R/print.nonlintest.R |only
R/summary.nsCosinor.R | 33 ++++++++++++++++++++-------------
R/third.R |only
data/AFL.RData |binary
data/CVD.RData |binary
data/CVDdaily.RData |binary
data/exercise.RData |binary
data/schz.RData |binary
data/stillbirth.RData |binary
man/aaft.Rd |only
man/casecross.Rd | 1 +
man/nonlintest.Rd |only
man/nscosinor.Rd | 8 +++-----
man/nscosinor.initial-internal.Rd |only
man/plot.nonlintest.Rd |only
man/plotMonth.Rd | 1 -
man/print.nonlintest.Rd |only
man/third.Rd |only
26 files changed, 71 insertions(+), 49 deletions(-)
Title: Species Distribution Modelling Tools: Tools for processing data
associated with species distribution modelling exercises
Diff between SDMTools versions 1.1-5 dated 2011-01-20 and 1.1-9 dated 2012-01-23
Description: This packages provides a set of tools for post processing
the outcomes of species distribution modeling exercises. It
includes novel methods for comparing models and tracking
changes in distributions through time. It further includes
methods for visualizing outcomes, selecting thresholds,
calculating measures of accuracy and landscape fragmentation
statistics, etc.. This package was made possible in part by
financial support from the Australian Research Council & ARC
Research Network for Earth System Science.
Author: Jeremy VanDerWal, Lorena Falconi, Stephanie Januchowski, Luke
Shoo and Collin Storlie
Maintainer: Jeremy VanDerWal
DESCRIPTION | 10 ++++------
MD5 |only
R/aspect.R |only
R/distance.R | 7 ++++++-
R/read.asc.R | 29 ++++++++++-------------------
R/slope.R |only
R/vector.averaging.R | 2 +-
man/distance.Rd | 18 +++++++++++-------
man/grid.area.Rd | 2 +-
man/slope.Rd |only
src/pointinpolygon.c | 4 ++--
src/slope.aspect.c |only
12 files changed, 35 insertions(+), 37 deletions(-)
Title: Various programming utilities
Diff between R.utils versions 1.9.9 dated 2012-01-12 and 1.9.11 dated 2012-01-23
Description: This package provides utility classes and methods useful
when programming in R and developing R packages.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/System.R | 17 +++++++++++++----
R/reassignInPackage.R | 12 ++++++++++--
inst/NEWS | 15 +++++++++++++++
man/findGraphicsDevice.System.Rd | 4 ++--
6 files changed, 49 insertions(+), 17 deletions(-)
Title: Fast and light-weight caching (memoization) of objects
Diff between R.cache versions 0.5.2 dated 2011-10-06 and 0.6.1 dated 2012-01-23
Description: Methods for memoization, that is, caching arbitrary R
objects in persistent memory. Objects can be loaded and saved
stratified on a set of hashing objects.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
DESCRIPTION | 14 +++++++-------
MD5 | 23 +++++++++++++----------
R/999.NonDocumentedObjects.R | 3 +++
R/getCachePath.R | 17 +++++++++++++++--
R/getCacheRootPath.R | 18 ++++++++++++++----
R/setCacheRootPath.R | 18 ++++++++++++++++--
R/setupCacheRootPath.R |only
R/textPrompt.R |only
R/zzz.R | 3 +++
inst/.Rcache |only
inst/NEWS | 22 +++++++++++++++++++++-
man/Non-documented_objects.Rd | 3 +++
man/getCacheRootPath.Rd | 4 ++++
man/setCacheRootPath.Rd | 1 +
man/setupCacheRootPath.Rd |only
15 files changed, 100 insertions(+), 26 deletions(-)
Title: Partial Least Squares Data Analysis Methods
Diff between plspm versions 0.2-1 dated 2012-01-03 and 0.2-2 dated 2012-01-23
Description: Partial Least Squares (PLS) methods with emphasis on
structural equation models with latent variables.
Author: Gaston Sanchez, Laura Trinchera
Maintainer: Gaston Sanchez
DESCRIPTION | 13 +++++++------
MD5 | 7 +++++--
NAMESPACE |only
data/ropes.rda |only
man/plspm-package.Rd | 6 +++---
man/ropes.Rd |only
6 files changed, 15 insertions(+), 11 deletions(-)
Title: Companion to "Learning Statistics with R"
Diff between lsr versions 0.1 dated 2011-12-11 and 0.1.1 dated 2012-01-23
Description: Functions that I have found useful for teaching purposes.
Author: Daniel Navarro
Maintainer: Daniel Navarro
DESCRIPTION | 10 +++++-----
MD5 | 9 +++++----
NEWS |only
R/lsr.R | 3 ++-
inst/CITATION | 6 +++---
man/who.Rd | 19 ++++++++-----------
6 files changed, 23 insertions(+), 24 deletions(-)