[med-svn] [r-other-valdar-bagpipe.backend] 06/07: Update upstream source from tag 'upstream/0.34'
Andreas Tille
tille at debian.org
Wed Dec 27 17:05:55 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository r-other-valdar-bagpipe.backend.
commit cd7d085fc0a7a8d8b236232ae8e4612f45e80491
Merge: 3a66c69 8b89899
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 27 18:04:14 2017 +0100
Update upstream source from tag 'upstream/0.34'
Update to upstream version '0.34'
with Debian dir 2f4b8a09c3315a1eacc58bae3f8aaaf7761236d9
DESCRIPTION | 14 +
NAMESPACE | 11 +
R/DiploprobReaderClass.R | 219 ++++++
R/WVhash.R | 41 +
R/WVmisc.R | 383 +++++++++
R/WVmisc_mdlist.R | 70 ++
R/WVmisc_stack.R | 43 +
R/bagpipe_exception.R | 13 +
R/bagpipe_formula.R | 425 ++++++++++
R/bagpipe_genome_scan.R | 825 ++++++++++++++++++++
R/bagpipe_happy_graphics.R | 550 +++++++++++++
R/bagpipe_posboot.R | 153 ++++
R/bagpipe_undernull.R | 212 +++++
R/bagpipe_utils.R | 222 ++++++
R/cmdline.R | 119 +++
R/configfile.R | 85 ++
R/lmmultiresponse.R | 295 +++++++
R/read.happy.core.R | 466 +++++++++++
R/read.happy.derived.R | 868 +++++++++++++++++++++
R/read.happy.genotype.R | 66 ++
R/read.happy.reserve.R | 103 +++
R/unify.R | 458 +++++++++++
man/DEFAULT.REDUCE.DMAT.CUTOFF.Rd | 28 +
man/DiploprobReader-class.Rd | 82 ++
man/ENV.Rd | 56 ++
man/SS.Rd | 58 ++
man/apply.permutation.matrix.Rd | 72 ++
man/apply.transform.Rd | 65 ++
man/assert.happy.Rd | 59 ++
man/bagpipe.backend-package.Rd | 43 +
man/bagpipe.data.error.Rd | 58 ++
man/bagpipe.define.posboot.loci.Rd | 77 ++
man/bagpipe.expand.formula.Rd | 204 +++++
man/bagpipe.extract.loci.Rd | 72 ++
man/bagpipe.formula.decipher.Rd | 88 +++
man/bagpipe.formula.encipher.locus.Rd | 62 ++
man/bagpipe.formula.error.Rd | 58 ++
man/bagpipe.formula.extractor.lookup.Rd | 82 ++
man/bagpipe.formula.has.abstract.loci.Rd | 58 ++
man/bagpipe.formula.reserved.variables.Rd | 58 ++
man/bagpipe.get.design.Rd | 115 +++
man/bagpipe.init.posboot.file.Rd | 78 ++
man/bagpipe.input.error.Rd | 58 ++
man/bagpipe.parse.sdp.string.Rd | 72 ++
man/bagpipe.posboot.scan.Rd | 90 +++
man/bagpipe.read.configfile.Rd | 65 ++
man/caught.error.Rd | 57 ++
man/cmdline.flag.Rd | 40 +
man/cmdline.has.option.Rd | 40 +
man/cmdline.integer.Rd | 42 +
man/cmdline.integers.Rd | 43 +
man/cmdline.logical.Rd | 41 +
man/cmdline.logicals.Rd | 42 +
man/cmdline.numeric.Rd | 41 +
man/cmdline.numerics.Rd | 40 +
man/cmdline.option.Rd | 78 ++
man/cmdline.string.Rd | 39 +
man/cmdline.strings.Rd | 49 ++
man/cols.as.Rd | 104 +++
man/configfile.get.Rd | 72 ++
man/configfile.has.Rd | 60 ++
man/configfile.integer.Rd | 63 ++
man/configfile.integers.Rd | 63 ++
man/configfile.logical.Rd | 63 ++
man/configfile.numeric.Rd | 63 ++
man/configfile.numerics.Rd | 63 ++
man/configfile.string.Rd | 72 ++
man/configfile.strings.Rd | 72 ++
man/dfapply.Rd | 71 ++
man/do.scan.Rd | 107 +++
man/drop.formula.vars.Rd | 73 ++
man/elem.Rd | 64 ++
man/find.peaks.Rd | 83 ++
man/find.windowed.peaks.Rd | 82 ++
man/fit.gev.Rd | 69 ++
man/force.logical.Rd | 66 ++
man/formula.as.string.Rd | 56 ++
man/freeman.tukey.Rd | 58 ++
man/general.multiscan.Rd | 111 +++
man/general.scan.Rd | 146 ++++
man/genotype.to.count.Rd | 73 ++
man/genotype.to.factor.Rd | 65 ++
man/genotype.to.hier.Rd | 70 ++
man/get.phenotype.data.Rd | 196 +++++
man/happy.check.bp.Rd | 78 ++
man/happy.clear.reserve.Rd | 61 ++
man/happy.get.allele.freq.Rd | 71 ++
man/happy.get.allowed.models.Rd | 53 ++
man/happy.get.bp.Rd | 61 ++
man/happy.get.chromosome.Rd | 62 ++
man/happy.get.chromosome.length.Rd | 87 +++
man/happy.get.design.Rd | 134 ++++
man/happy.get.design.old.Rd | 134 ++++
man/happy.get.diplotype.tensor.Rd | 116 +++
man/happy.get.first.marker.Rd | 70 ++
man/happy.get.genome.location.Rd | 126 +++
man/happy.get.genotype.Rd | 90 +++
man/happy.get.interval.length.Rd | 99 +++
man/happy.get.interval.midpoint.Rd | 69 ++
man/happy.get.interval.over.Rd | 111 +++
man/happy.get.interval.range.Rd | 76 ++
man/happy.get.intervals.Rd | 61 ++
man/happy.get.intervals.in.range.Rd | 112 +++
man/happy.get.last.marker.Rd | 65 ++
man/happy.get.location.Rd | 65 ++
man/happy.get.markers.Rd | 99 +++
man/happy.get.markers.between.Rd | 98 +++
man/happy.get.models.Rd | 59 ++
man/happy.get.next.marker.Rd | 86 ++
man/happy.get.position.Rd | 62 ++
man/happy.get.previous.marker.Rd | 73 ++
man/happy.get.reserve.limit.Rd | 58 ++
man/happy.get.reserved.marker.Rd | 65 ++
man/happy.get.strains.Rd | 58 ++
man/happy.get.subjects.Rd | 58 ++
man/happy.has.chromosomes.Rd | 64 ++
man/happy.has.markers.Rd | 64 ++
man/happy.has.model.Rd | 62 ++
man/happy.has.reserved.marker.Rd | 66 ++
man/happy.has.subjects.Rd | 61 ++
man/happy.init.reserve.Rd | 74 ++
man/happy.is.auto.reserve.Rd | 60 ++
man/happy.list.chromosomes.Rd | 72 ++
man/happy.load.data.Rd | 83 ++
man/happy.load.genome.Rd | 146 ++++
man/happy.load.marker.Rd | 136 ++++
man/happy.make.colnames.Rd | 82 ++
man/happy.make.genome.location.Rd | 111 +++
man/happy.matrixop.diplotypes.to.full.Rd | 73 ++
...happy.matrixop.full.asymmetric.to.diplotypes.Rd | 61 ++
man/happy.matrixop.full.to.diplotypes.Rd | 64 ++
man/happy.num.strains.Rd | 58 ++
man/happy.plot.intervals.Rd | 261 +++++++
man/happy.plot.ladder.Rd | 146 ++++
man/happy.plot.ladder.chr.list.Rd | 80 ++
man/happy.reserve.exists.Rd | 58 ++
man/happy.reserve.get.Rd | 64 ++
man/happy.reserve.has.Rd | 73 ++
man/happy.reserve.has.scratch.Rd | 58 ++
man/happy.reserve.marker.Rd | 76 ++
man/happy.reserve.markers.Rd | 102 +++
man/happy.reserve.memory.usage.Rd | 61 ++
man/happy.reserve.put.Rd | 74 ++
man/happy.set.auto.reserve.Rd | 62 ++
man/hasS3method.Rd | 63 ++
man/hasS4method.Rd | 68 ++
man/hash.get.Rd | 61 ++
man/hash.has.Rd | 61 ++
man/hash.keys.Rd | 58 ++
man/hash.memory.usage.Rd | 62 ++
man/hash.put.Rd | 64 ++
man/hash.remove.Rd | 61 ++
man/ifow.Rd | 66 ++
man/igrep.Rd | 73 ++
man/incidence.matrix.Rd | 57 ++
man/interpolate.Rd | 86 ++
man/interpolate.Sys.env.Rd | 51 ++
man/invlogit.Rd | 57 ++
man/is.formula.Rd | 35 +
man/is.informative.predictor.Rd | 67 ++
man/is.nullOrEmpty.Rd | 65 ++
man/is.wholenumber.Rd | 60 ++
man/list.has.Rd | 64 ++
man/list.subdirs.Rd | 65 ++
man/lm.multiresponse.Rd | 168 ++++
man/lm.multiscan.Rd | 107 +++
man/load.gscan.Rd | 94 +++
man/logit.Rd | 57 ++
man/make.parboot.permutation.matrix.Rd | 95 +++
man/make.parboot.permuted.responses.Rd | 82 ++
man/make.parboot.responses.Rd | 88 +++
man/make.permuted.responses.Rd | 74 ++
man/make.posboot.summary.Rd | 79 ++
man/make.posboot.summary.ci.Rd | 69 ++
man/make.reduce.dmat.fun.Rd | 74 ++
man/make.step.data.Rd | 78 ++
man/map.eq.Rd | 79 ++
man/mdlist.get.Rd | 67 ++
man/mdlist.has.Rd | 78 ++
man/mdlist.put.Rd | 78 ++
man/new.hash.Rd | 53 ++
man/object.sizes.Rd | 76 ++
man/permutation.matrix.Rd | 97 +++
man/polygonh.Rd | 68 ++
man/pop.back.Rd | 60 ++
man/pop.front.Rd | 60 ++
man/push.back.Rd | 67 ++
man/push.front.Rd | 64 ++
man/read.configfile.Rd | 67 ++
man/read.scan.file.Rd | 83 ++
man/reduce.dim.Rd | 72 ++
man/scan.phenotype.Rd | 119 +++
man/se.mean.Rd | 63 ++
man/split.formula.Rd | 42 +
man/split.pathname.Rd | 50 ++
man/strcat.Rd | 61 ++
man/string.trim.Rd | 56 ++
man/tr.Rd | 56 ++
man/unify.aic.Rd | 58 ++
man/unify.anova.Rd | 104 +++
man/unify.anova.list.Rd | 197 +++++
man/unify.bic.Rd | 61 ++
man/unify.deviance.Rd | 65 ++
man/unify.fit.Rd | 120 +++
man/unify.generic.model.type.Rd | 59 ++
man/unify.has.model.type.Rd | 58 ++
man/unify.is.multilevel.formula.Rd | 67 ++
man/unify.logLik.Rd | 68 ++
man/unify.model.types.Rd | 58 ++
man/unify.num.obs.Rd | 59 ++
man/unify.num.params.Rd | 59 ++
man/unify.simulate.Rd | 79 ++
man/unify.simulate.lmer.Rd | 71 ++
man/which.wide.ci.Rd | 76 ++
man/wlm.multiresponse.Rd | 157 ++++
man/write.configfile.Rd | 62 ++
man/write.delim.Rd | 66 ++
man/write.multiscan.max.Rd | 65 ++
man/write.scan.Rd | 74 ++
219 files changed, 20513 insertions(+)
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