pastispackagePhylogeneticAssemblywithSoftTaxonomicInferences DescriptionPhylogeneticAssemblywithSoftTaxonomicInferencesDetailsPackagepastisTypePackageVersion012Date2013911Dependscaper0 ID: 135229
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2accipitridaeBasicPastispastis_data_2........................................5pastis_data_3........................................5pastis_data_3_trees.....................................6pastis_main.........................................6pastis_simple........................................8read_input..........................................10Index12 pastis-packagePhylogeneticAssemblywithSoftTaxonomicInferences. DescriptionPhylogeneticAssemblywithSoftTaxonomicInferences.DetailsPackage:pastisType:PackageVersion:0.1-2Date:2013-9-11Depends:caper�(=0.5.0),ape�(=3.0.0)Encoding:UTF-8License:GPL�(=3)LazyLoad:yesURL:http://cran.r-project.org/web/packages/pastis/Apre-processorformrBayesthatassimilatessequences,taxonomicinformationandtreecon-straints.Themainfunctionsofinterestformostuserswillbepastis_simple,pastis_mainandconch.Themainanalysisisconductedwithpastis_simpleorpastis_mainfollowedbyamanualexecutionofmrBayes�(3.2).Theplacementoftaxanotcontainedinthetreeconstraintcanbeinvestigatedusingconch.Author(s)KlaasHartmann&#xklaa;&#xs.ha;&#xrtma;&#xnn@u;&#xtas.;íu.; u00;GavinThomas&#xgavi;&#xn.th;&#xomas;&#x@she;ÿie;&#xld.a;.uk; accipitridaeBasicPastisAccipitridaebasicdata DescriptionConstrainttreeandtaxonlistforAccipitridae 4default_output_templateDetailsAnanalysisoftheplacementofeachtaxonnotcontainedintheconstrainttreeisconducted.Foreachsuchtaxontheedgelengthsintheconstrainttreeareadjustedaccordingtotheparameteredge_scaling.Ifsimple_edge_scalingisTRUE,theedgeswillhavelength0ifataxonisneverdescendantfromatreeand1ifitisdescendantinatleastonetree.IfFALSE,indicatetheproportionofsampledtreesinwhichthetaxonisdescendantfromthatedge.Theoutputfromthisfunctionisusefulforcheckingthatmissingtaxaareplacedinappropriatepositionsrelativetotheoriginalconstrainttree.Notethatthisroutinehasnotbeenoptimisedandslow(possiblyunacceptable)performanceistobeexpectedwithlargetreesand/orlargeposteriorsamples.ValueNULL.AleforeachmissingtaxoniscreatedinthecurrentdirectoryExamplesdata(pastis_data_3_trees)##Notrun:#Checkconstraintsforallmissingtaxa(takes~6secondstorun:spedupbyAnonymousReviewer2)conch(pastis_data_3_trees[[1]],pastis_data_3_trees[[2]])##End(Notrun)#Checkconstraintsformissingtaxon"a_4"conch(pastis_data_3_trees[[1]],pastis_data_3_trees[[2]],species_set="a_4")unlink("taxonposition_a_4.tree") default_output_templateAsampleoutputtemplateforpastis_mainandpastis_simple DescriptionThisisthedefaultoutputtemplatelledinbypastis_mainandpastis_simpletocreatetheinputleformrBayes.Usagedefault_output_template() pastis_main7missing_cladesAlecontainingmissingclades.Eachlineofthemissingcladesleconsistsofthemissingclade,theword"include"or"exclude"andalistofthereferenceclades(allseparatedbycommas).Linescontaining"include"specifythatataxoniscontainedbelowtheMRCAofthereferenceclades.Linescontaining"exclude"specifythatthemissingcladecannotattachbelowtheMRCAofthereferenceclades.#'sequencesAlewithalltheavailablesequenceinformationinfastaformatfordetailsonthatformatseeread.dnaintheapepackage.output_templateThelenameforatemplatefortheoutputnexusle.ThisleshouldlooklikearegularmrBayesinputlewithspecialtagsreplacingcontentthatwillbelledbypastis.Inparticular:&#xsequ;nce;&#xs000;willbereplacedbythesequences(andshouldgobelowtheMA-TRIXline)&#xntax;thenumberoftaxa(i.e.&#xntax;"ntax=mustbesomewhereinyourtemplate)&#xncha;&#xr000;thenumberofcharactersons;&#xtrai;&#xnts0;theconstraintswillgohere&#xoutp;&#xutle;wherethesummarieswillbewritten,(i.e."sumt&#xoutp;&#xutle;lename=burnin...."shouldbeinyourtemplate)seedefault_output_templateforanexample(whichisusedbydefault)DetailsThisisthemainfunctioninpastiswhichassimilatessequences,taxonomicinformationandtreeconstraintsandcreatesamrBayesinputle.Thisinputlecontainsthetreestructurespeciedbyconstraint_treewithmissingtaxaintaxa_listandmissingcladesinmissing_cladesaddedandplacedlooselyinthetreeusingtheconstraintlogicoutlinedinThomasetal.MEE(inreview)andJetzetal.(2012Nature,491,444-448).Seeread_inputforadescriptionoftherequiredformatoftheinputles.Ataminimumthecon-straininginputtreeandtaxalistmustbeprovided.Inadditiontotheinputchecksconductedbyread_inputthisfunctionalsochecksforcompatibilitybetweenthemissinggenusconstraintsandconstrainttree.PASTIS:PhylogeneticAssemblywithSoftTaxonomicInferenceS?Abrightmotmotwasactingquiterowdy-weavingandsquawkingquiteloudly"Pastisisdelise"heburpedwithasneese"butwhyiseverythingsuddenlycloudy?"–ArneMooersValueNULL pastis_simple9Argumentsbase_nameThebasenameforallinputlesmayincludealeadingdirectory,butshouldnotincludeatrailing.pastisDataInputdataobjectofclasspastisDataparaphyly_constrainsIfTRUE,missingcladesarepreventedfromenteringparaphyleticclades.monophyly_constrainsIfTRUE,missingcladesareprecentedfromenteringmonophyleticclades.omit_sequencesIfsettoTRUEthesequencele(ifany)willbeignored.ThisisusefulfortestingtheconstraintscreatedbypastisasmrBayesrunsmuchquickerwithoutsequencedata!DetailsThisisasimpliedversionofpastis_mainwhichassumesthat(i)thedataareinputasapastisDataobject(e.g.createdwithread_input),or(ii)theinputlesallhavethesamebase(speciedbybase_name)withdiffferentextensionsforeachletype:.sequences:thesequencele(FASTAformat).tree:theconstrainttree(Newickformat).taxa:alistoftaxa(seebelow).missingclades:locationsofmissingclades(seebelow).template:thetemplateforthemrBayesinputle(seedefault_output_template())Thetaxaleconsistsofaheader'taxon,clade'witheachsubsequentlinecontainingataxon,cladepair(separatedbyacomma)Eachlineofthemissingcladesleconsistsofthemissingclade,thewordincludeorexcludeandalistofthereferenceclades(allseparatedbycommas).LinescontainingincludespecifythatataxoniscontainedbelowtheMRCAofthereferenceclades.LinescontainingexcludespecifythatthemissingcladecannotattachbelowtheMRCAofthereferenceclades.ThemrBayesinputleiswrittentobase_name.nexus.SeeAlsopastis_mainprovidesamoreexibleinterface.PASTIS:PhylogeneticAssemblywithSoftTaxonomicInferenceS?Abrightmotmotwasactingquiterowdy-weavingandsquawkingquiteloudly"Pastisisdelise"heburpedwithasneese"butwhyiseverythingsuddenlycloudy?"–ArneMooers read_input11output_templateThelenameforatemplatefortheoutputnexusle.ThisleshouldlooklikearegularmrBayesinputlewithspecialtagsreplacingcontentthatwillbelledbypastis.Inparticular:&#xsequ;nce;&#xs000;willbereplacedbythesequences(andshouldgobelowtheMA-TRIXline)&#xntax;thenumberoftaxa(i.e.&#xntax;"ntax=mustbesomewhereinyourtemplate)&#xncha;&#xr000;thenumberofcharactersons;&#xtrai;&#xnts0;theconstraintswillgohere&#xoutp;&#xutle;wherethesummarieswillbewritten,(i.e."sumt&#xoutp;&#xutle;lename=burnin...."shouldbeinyourtemplate)seedefault_output_templateforanexample(whichisusedbydefault)sequencesAlewithalltheavailablesequenceinformationinfastaformatfordetailsonthatformatseeread.dnaintheapepackage.ValueAlistwiththeloadedinput