Man pages for olli0601/rBEAST
rBEAST
| beast2.add.alignment | No description yet |
| beast2.add.bdsky.serialpriors | No description yet |
| beast2.add.cluster.taxonsets | No description yet |
| beast2.add.data | No description yet |
| beast2.add.datetrait | No description yet |
| beast2.add.sasky.serialpriors | No description yet |
| beast2.add.satree | No description yet |
| beast2.add.startingtree.newick | No description yet |
| beast2.add.startingtree.random | No description yet |
| beast2.add.tiplogstem | No description yet |
| beast2.add.tree | No description yet |
| beast2.add.treemodel.bdsky | No description yet |
| beast2.add.treemodel.sasky | No description yet |
| beast2.extract.distinct.topologies | No description yet |
| beast2.get.prior | No description yet |
| beast2.get.specifications | No description yet |
| beast2.get.xml | No description yet |
| beast2.init.xml | No description yet |
| beast2out.combine.clu.trees | No description yet |
| beast2out.extract.cluster.trees | No description yet |
| beast2out.get.log.evolrate | No description yet |
| beast2out.plot.cluster.trees | No description yet |
| beast2out.pool.cluster.trees | No description yet |
| beast2out.read.nexus.and.stats | No description yet |
| beast2out.read.nodeidtree | Private funtion to read tree such that tip.label and... |
| beast2out.read.nodestats | No description yet |
| beast2out.read.trees | Extract a list of phylogenies from a BEAST2 posterior file |
| beast2out.tip.date.check | No description yet |
| beast.add.from.template | Copy XML elements from template |
| beast.add.monophylyStatistic.for.taxonsets | Add monophylyStatistics for each phylogenetic cluster to XML... |
| beast.add.startingtree | Add starting tree to XML |
| beast.add.taxa | Add taxa to XML file |
| beast.add.tmrcaStatistic.for.taxonsets | Add tmrcaStatistic for phylogenetic clusters to XML file |
| beast.adjust.gmrfSkyrideLikelihood | Adjust dimension parameter of gmrfSkyrideLikelihood |
| beast.adjust.mcmc | Adjust MCMC element |
| beast.adjust.prior.rootheight | Ajust lower bound of uniform prior on root height |
| beast.choose.seq.by.clusters | Pick sequence data set by type of phylogenetic cluster |
| beast.get.startingtree | Generate starting tree |
| beast.pool.clusters | Pool phylogenetic clusters for separate BEAST runs |
| beast.read.log | Read BEAST log file |
| beast.read.ops | Read BEAST ops file |
| beast.set.SEQ | Set SEQ field from sequences in sequences in 'DNAbin' matrix... |
| beast.set.TAXON_NAME | Set TAXON_NAME field from columns in the taxon data.table. |
| beastxml.from.template | Create BEAST XML file from template |
| beastxml.multilocus.codon.gtr | Generate multilocus XML file with a codon specific GTR model... |
| beastxml.multilocus.hky.fixed.topology | Generate multilocus XML file with HKY model and fixed... |
| beastxml.multilocus.hky.fixed.tree | Generate multilocus XML file with HKY model and fixed... |
| treeannotator.get.clusterprob | No description yet |
| treeannotator.get.edgewidth | No description yet |
| treeannotator.get.immu.timeline | No description yet |
| treeannotator.get.phy | No description yet |
| treeannotator.get.rates | No description yet |
| treeannotator.get.tmrcas | No description yet |
| treeannotator.get.viro.timeline | return lRNA measurements for treatment periods (going to be... |
| treeannotator.nodelabels.getnodeheightHPD | No description yet |
| treeannotator.plot | No description yet |
| treeannotator.plot.ctimeline | No description yet |
| treeannotator.plot.hpdbars | No description yet |
| treeannotator.plot.immu.timeline | No description yet |
| treeannotator.plot.node.ctime | No description yet |
| treeannotator.plot.rates | No description yet |
| treeannotator.plot.seronodeheightrange | No description yet |
| treeannotator.plot.tipmarks | No description yet |
| treeannotator.plot.tipstem.timeline | No description yet |
| treeannotator.plot.viro.timeline | No description yet |
| treeannotator.read | Read a BEAST treeannotator file. The node.label is set to a... |
| treeannotator.sero.getnodeheight.range | No description yet |
| treeannotator.tiplabel2df | No description yet |
