2cvgrd16srd17TCRData19x ID: 846603
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1 Package`divo'December17,2019Version1.0.1
Package`divo'December17,2019Version1.0.1TypePackageDate2019-12-12TitleToolsforAnalysisofDiversityandSimilarityinBiologicalSystemsAuthorChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainerMaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;DependsR&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;(=3.3.0),clusterDescriptionAsetoftoolsforempiricalanalysisofdiversity(anumberandfrequencyofdiffer-enttypesinpopulation)andsimilarity(anumberandfrequencyofsharedtypesintwopopula-tions)inbiologicalorecologicalsystems.ImportsgrDevices,graphics,stats,utilsLicenseGPL&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;(=3)NeedsCompilationyesRepositoryCRANDate/Publication2019-12-1623:50:09UTCRtopicsdocumented:cvg..............................................2divo.............................................3dp..............................................3dp.ht.............................................5ens..............................................6ens.ht............................................7i.in..............................................9i.inp.............................................10ji...............................................11li...............................................12mh..............................................13pg..............................................14pg.ht.............................................151 2cvgrd..............................................16srd..............................................17TCR.Dat
2 a.......................................
a..........................................19x...............................................19Index20 cvgcvgCoverage DescriptionCalculatesthesamplecoverageestimateusingtheGood-Turingformula.Thesamplecoverageisanestimateoftheprobabilityofpullinganewspeciesinthenextdraw,givenasetofpastobservationsFormoredetailsonCVGseeGoodI.J.(1953).Usagecvg(x)ArgumentsxavectorcontaininginputpopulationAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesGoodI.J.Thepopulationfrequenciesofspeciesandtheestimationofpopulationparameters.(1953)Biometrika40:237-64RempalaG.A.,SewerynM.MethodsfordiversityandoverlapanalysisinT-cellreceptorpopula-tions.(2013)JMathBiol67:1339-68Examplesdata(TCR.Data)resultcvg(x[,1]) dp3 divoToolsforAnalysisofDiversityandSimilarityinBiologicalSystems DescriptionThepackagedivoimplementsvariousalgorithmsforempiricalanalysisofdiversityandsimilarity(overlap)inbiologicalorecologicalsystems.Theimplementedindicesofdiversityandoverlaparebasedbothontheinformation-theoreticandgeometricconsiderations.Theindiceshavethecapacitytonaturallyup-weightordown-weightrareandabundantpopulationspeciescounts,byapplyingtheGood-Turingsamplecoveragecorrection.Thefunctionalversionofadiversityindex,theso-calleddiversityprole,isalsoimplementedalongwiththediversityandoverlapindicesinversionsknownastheeffectivenumbersofspecies(ENS).Forexamplesanddetailedinformationonspecicfunction
3 s,seetheirmanualpages:cvgCoveragedpDiver
s,seetheirmanualpages:cvgCoveragedpDiversityProledp.htDiversityProlewiththeHorvitz-ThompsonCorrectionensEffectiveNumberofSpeciesens.htEffectiveNumberofSpecieswiththeHorvitz-ThompsonCorrectioni.inInformationIndex(I-index)for2-WayTablei.inpInformationIndex(I-index)for2-Way,2ColumnTablejiJaccardIndexliSorensenIndexmhMorisita-HornIndexpgPower-GeometricIndexpg.htPower-GeometricIndexwiththeHorvitz-ThompsonCorrectionrdRenyi'sDivergencesrdSymmetrizedRenyi'sDivergenceAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68 dpdpDiversityProle 4dpDescriptionCalculatesdiversityprole(DP)(RempalaandSeweryn2013orTothmeresz1995)usingtheRenyientropy(Renyi1961)asadiversitymeasure.ThefunctioncalculatestheRenyientropyvaluesforagivenrangeoftheRenyiindex(theindexshouldbegreaterthan0).Whentheindexislessthenone,therarecountsareup-weightedandwhenitisgreaterthanone,therarecountsaredown-weighted.SincetheRenyientropyisanon-increasingfunctionoftheindex,theproleplotshouldbealwaysnon-increasing.Usagedp(x,alpha=seq(0.1,2,0.1),CI=0.95,resample=100,single_graph=FALSE,pooled_graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)Argumentsxamatrixcontaininginputpopulationsalphaavectorcontainingalphavalues,default=seq(0.1,2,0.1)CVGavectorcontainin
4 galphavaluesmultipliedbycoverage;default
galphavaluesmultipliedbycoverage;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100single_graphdefault=FALSE,plotoftheDiversityProleforeachpopulation;single_graph='fileName'user-denedoutputlenamepooled_graphdefault=FALSE,plotoftheDiversityProleforallpopulations;pooled_graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68RenyiP.(1961)Onmeasuresofinformationandentropy.In:Proceedingsofthe4thBerkeleysymposiumonmathematics,statisticsandprobability,pp547-61TothmereszB.(1995)Comparisonofdifferentmethodsfordiversityordering.JVegetSci6:283-90 dp.ht5Examplesdata(TCR.Data)resultdp(x[,1:4],PlugIn=TRUE) dp.htdp.htDiversityProlewiththeHorvitz-ThompsonAdjustment DescriptionCalculatesdive
5 rsityprolewiththeHorvitz-Thompsonadj
rsityprolewiththeHorvitz-Thompsonadjustment(DP-HT),asdenedinRempalaandSeweryn(2013)usingtheRenyientropy(Renyi1961)asadiversitymeasure.ThefunctioncalculatestheRenyientropyvaluesforagivenrangeoftheRenyiindex(theindexshouldbegreaterthan0).Whentheindexislessthenone,therarecountsareup-weightedandwhenitisgreaterthanone,therarecountsaredown-weighted.SincetheRenyientropyisanon-increasingfunctionoftheindex,theproleplotshouldbealwaysnon-increasing.Formoreinformation,seeRempalaandSeweryn(2013).Usagedp.ht(x,alpha=seq(0.1,2,0.1),CI=0.95,resample=100,single_graph=FALSE,pooled_graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)Argumentsxamatrixcontaininginputpopulationsalphaavectorcontainingalphavalues,default=seq(0.1,2,0.1)CVGavectorcontainingalphavaluesmultipliedbycoverage;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100single_graphdefault=FALSE,plotoftheDiversityProleforeachpopulation;single_graph='fileName'user-denedoutputlenamepooled_graphdefault=FALSE,plotoftheDiversityProleforallpopulations;pooled_graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoa
6 ;le.UsesaveBootstrap=TRUEtosavebootstrap
;le.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolder 6ensAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68RenyiP.(1961)Onmeasuresofinformationandentropy.In:Proceedingsofthe4thBerkeleysymposiumonmathematics,statisticsandprobability,pp547-61TothmereszB.(1995)Comparisonofdifferentmethodsfordiversityordering.JVegetSci6:283-90Examplesdata(TCR.Data)resultdp.ht(x,PlugIn=TRUE) ensensEffectiveNumberofSpecies DescriptionCalculatesdiversityprole(DP)usingtheeffectivenumberofspecies(ENS)basedoninvertingtheRenyientropy.Foranymonotonediversityindex(see,RempalaandSeweryn2013)theENSisdenedasthesizeofauniformpopulationwiththesameindexvalueasthecurrentpopulation.TheENSmaybeconsideredasameasureofpopulationdiversityexpressedintheunitsofspeciescounts.TheENSproleiscalculatedagainsttheRenyientropyindex,whichallowsforadirectcomparisonwiththediversityprole(asindp).TheoptionofperformingtheHorvitz-Thompsoncorrectionisavailableinthefunctionens.ht.FormoredetailsonENS,seeRempalaandSeweryn(2013)orJost(2006).Usageens(x,alpha=seq(0.1,2,0.1),CI=0.95,resample=100,single_graph=FALSE,pooled_graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)Argu
7 mentsxamatrixcontaininginputpopulationsa
mentsxamatrixcontaininginputpopulationsalphaavectorcontainingalphavalues,default=seq(0.1,2,0.1)CVGalistcontainingalphavaluesmultipliedbycoverage;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100 ens.ht7single_graphdefault=FALSE,plotoftheDiversityProleforeachpopulation;single_graph='fileName'user-denedoutputlenamepooled_graphdefault=FALSE,plotoftheDiversityProleforallpopulations;pooled_graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesJostL.(2006)Entropyanddiversity.Oikos113:363-75RempalaG.A.,SewerynM.MethodsfordiversityandoverlapanalysisinT-cellreceptorpopula-tions.(2013)JMathBiol67:1339-68Examplesdata(TCR.Data)resultens(x,PlugIn=TRUE) ens.htens.htEffectiveNumberofSpecieswiththeHorvitz-ThompsonCor-rection DescriptionCalculatesdiversityprole(DP)usingtheeffectivenumberofspecies(E
8 NS)basedoninvertingtheRenyientropywithth
NS)basedoninvertingtheRenyientropywiththeHorvitz-Thompsoncorrection.Foranymonotonediversityindex(see,e.g.,RempalaandSeweryn2013)theENSisdenedasthesizeofauniformpopulationwiththesameindexvalueasthecurrentpopulation.TheENSmaybeconsideredasameasureofpopulationdiversityexpressedintheunitsofspeciescounts.TheENSproleiscalculatedagainsttheRenyientropyindex,whichallowsforadirectcomparisonwiththediversityprole(asindp).TheENSwithouttheHorvitz-Thompsoncorrectionisavailableasfunctionens.FormoredetailsonENSseeRempalaandSeweryn(2013)orJost(2006). 8ens.htUsageens.ht(x,alpha=seq(0.1,2,0.1),CI=0.95,resample=100,single_graph=FALSE,pooled_graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)Argumentsxamatrixcontaininginputpopulationsalphaavectorcontainingalphavalues,default=seq(0.1,2,0.1)CVGalistcontainingalphavaluesmultipliedbycoverage;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100single_graphdefault=FALSE,plotoftheDiversityProleforeachpopulation;single_graph='fileName'user-denedoutputlenamepooled_graphdefault=FALSE,plotoftheDiversityProleforallpopulations;pooled_graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpo
9 pulation(size=0.1)saveBootstrapSavesboot
pulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesJostL.(2006)Entropyanddiversity.Oikos113:363-75RempalaG.A.,SewerynM.MethodsfordiversityandoverlapanalysisinT-cellreceptorpopula-tions.(2013)JMathBiol67:1339-68Examplesdata(TCR.Data)resultens.ht(x,PlugIn=TRUE) i.in9 i.ini.inInformationIndex(Iindex)for2-WayTable DescriptionTheI-indexisameasureofoverlapintwowaytablesbasedonthegeneralizedmutualinformationstatistic.TheI-indexmeasuresdependenceamongcolumnsoftwo-waytables,takingvaluesbe-tween0and1.Itreturnsavalueofzerowhenthetablecolumnsformanorthogonalsystemandavalueofonewhenthetablecolumnsrankisone.Thevalueoftheparameteralphaisrelatedtothestructureofdependence,asdescribedinRempalaandSeweryn(2013).Usagei.in(x,alpha=1,CI=0.95,resample=100,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)ArgumentsxamatrixcontaininginputpopulationsalphaIindexoforderalpha,mustbebetween0and1,default=0.5CVGIindexoforderalpha=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100PlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thev
10 alueshouldnotbesmallerthan10%ofpopulatio
alueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resulti.in(x,resample=50) 10i.inp i.inpi.inpInformationIndex(Iindex)for2-Way,2ColumnTable DescriptionTheI-indexisameasureofoverlapintwowaytablesbasedonthegeneralizedmutualinformationstatistic.Thisfunctionimplementsaspecialcaseoftablewithtwocolumnsonly.Ingeneral,theI-indexmeasuresdependenceinanytwo-waytables,takingvaluesbetween0and1.Itreturnsavalueofzerowhenthetablecolumnsformanorthogonalsystemandavalueofonewhenthetablecolumnsrankisone.Thevalueoftheparameteralphaisrelatedtothestructureofdependence,asdescribedinRempalaandSeweryn(2013).Usagei.inp(x,alpha=1,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)ArgumentsxamatrixcontaininginputpopulationsalphaIindexoforderalpha1putsmoreweightontherarespeciesandtheIIndexoforderalpha&#x-271;1putsmoreweightontheabundantones,default=1CVGIindexoforderalpha=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)res
11 amplesetnumberofrepetitions,default=100g
amplesetnumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofIIndex;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0; ji11ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resulti.inp(x,resample=25) jijiJaccardIndex DescriptionTheJaccardsimilarity(overlap)indexmeasuresthesizeoftheintersectionoftwopopulationsrela-tivetosizeoftheirunion.Itvariesbetweenzero(nooverlap)andone(perfectoverlap).TheJaccardIndexiscloselyrelatedtheSorensen(implementedinfunctionli)andtheDiceindiceswhicharewidelyusedinboththeecologicalandimmunologicalliterature(see,RempalaandSeweryn2013).Usageji(x,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,saveBootstrap=FALSE)ArgumentsxamatrixcontaininginputpopulationsCIConden
12 ceIntervaldefault=0.95,range(0,1)resampl
ceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofJaccardIndex;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0; 12liReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultji(x,resample=50) liliSorensenIndex DescriptionTheSorensensimilarity(overlap)indexmeasurestheoverlapbetweentwopopulationsbytakingtheratioofthenumberofspeciessharedbetweenthetwopopulations,relativetothenumberofspeciesinbothpopulations.Theindexvariesbetweenzero(nooverlap)andone(perfectoverlap).ItiscloselyrelatedtotheJaccardindexofsimilarity(implementedinfunctionji).Usageli(x,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,saveBootstrap=FALSE)Argumentsxamatrixcontaininginputpo
13 pulationsCICondenceIntervaldefault=0
pulationsCICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofSorensenIndex;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0; mh13ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultli(x,resample=50) mhmhMorisita-HornIndex DescriptionTheMorisita-Hornindexisapopularangularoverlapmeasureusedbothinecologicalandimmuno-logicalliterature.Itquantiesoverlapascosineofananglebetweentwostandardizedpopulationvectors.Itrangesbetweenzero(nooverlap)andone(perfectoverlap).MHtendstobeover-sensitivetoabundantspecies.FordetailsseeRempalaandSeweryn(2013)orMagurran(2005).Usagemh(x,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,saveBootstrap=FALSE
14 )Argumentsxamatrixcontaininginputpopulat
)ArgumentsxamatrixcontaininginputpopulationsCICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofMorisita-HornIndex;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0; 14pgReferencesMagurranA.E.(2005)Biologicaldiversity.CurrBiol15:R116-8RempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultmh(x,PlugIn=TRUE) pgpgPower-GeometricIndex DescriptionThePowerGeometric(PG)indexisageometricangularoverlapmeasureparameterizedbyatwo-dimensionalvector(alpha,beta).ThePGindexisageneralizationoftheMorisita-HornindexaswellastheBhattacharyya'scoefcient.Itallowsforincreasingordecreasingtherelativecontribu-tionoftherarespeciestotheoveralloverlapandmaybethereforeusedtoaccountforthesp
15 eciesundersampling.Itquantiesoverlap
eciesundersampling.Itquantiesoverlapascosineofananglebetweentwoexponentiallynormalizedpopulationvectors.Forfurtherdetailsanddenition,seeRempalaandSeweryn(2013).Usagepg(x,alpha=1,beta=alpha,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)ArgumentsxamatrixcontaininginputpopulationsalphaPGoforderalpha1putsmoreweightontherarespeciesandtheIIndexoforderalpha&#x-366;1putsmoreweightontheabundantonesforrstpopulation,default=1betaPGoforderbeta1putsmoreweightontherarespeciesandtheIIndexoforderbeta&#x-329;1putsmoreweightontheabundantonesforsecondpopulation,default=alphaCVGPGoforderalphaorbeta=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplenumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofPower-GeometricIndex;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlename pg.ht15PlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,Gr
16 zegorzRempalaMaintainer:MaciejPietrzak&#
zegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultpg(x,resample=20) pg.htpg.htPower-GeometricIndexwiththeHorvitz-ThompsonCorrection DescriptionTheHorvitz-ThompsoncorrectedversionofthePowerGeometric(PG)index(seehelpforpg).ThePGindexisageneralizationoftheMorisita-HornindexaswellastheBhattacharyya'scoefcient.Itquantiesoverlapascosineofananglebetweentwoexponentiallynormalizedpopulationvectors.Forfurtherdetailsanddenitions,seeRempalaandSeweryn(2013).Usagepg.ht(x,alpha=1,beta=alpha,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE)ArgumentsxamatrixcontaininginputpopulationsalphaPGoforderalpha1putsmoreweightontherarespeciesandtheIIndexoforderalpha&#x-366;1putsmoreweightontheabundantonesforrstpopulation,default=1betaPGoforderbeta1putsmoreweightontherarespeciesandtheIIndexoforderbeta&#x-329;1putsmoreweightontheabundantonesforsecondpopulation,default=alpha 16rdCVGPGoforderalphaorbeta=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplesetnumberofrepetitions,default=100graphdefault=FALSE,plottheresultsofhierarchicalclusteringofpairwiseanalysisofPower-GeometricIndex,graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_
17 output='fileName'user-denedoutput
output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultpg.ht(x,PlugIn=TRUE) rdrdRenyi'sDivergence DescriptionTheRenyidivergence(RD)isameasureofsimilaritybetweentwodiscreteprobabilitydistributions.TheRenyidivergenceisnon-negative,notsymmetric,andisnotdenedwhenthereisnocommonsupportbetweentwodistributionsRDisparameterizedbyasinglenon-negativeparameterwhichmaybeusedtoadjusttherelativecontributionsofsmallandlargeprobabilitiestoitsoverallvalue.RDisageneralizationoftheKullback-Leiblerdivergence.Fordetails,seeRempalaandSeweryn(2013).Usagerd(x,alpha=0.5,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstrap=FALSE) srd17ArgumentsxamatrixcontaininginputpopulationsalphaRenyi'sDivergenceindexoforderalpha1putsmoreweightontherarespeciesandtheIIndexoforderalpha&#x-422;1putsmoreweightontheabundantone
18 s,default=1CVGRenyi'sDivergenceindexofor
s,default=1CVGRenyi'sDivergenceindexoforderalpha=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplenumberofrepetitions,default=100graphdefault=FALSE,plotstheresultsofhierarchicalclusteringofpairwiseanalysisofRenyi'sDivergence;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultrd(x,resample=25,alpha=0.5) srdsrdSymmetrizedRenyi'sDivergence DescriptionThesymmetrizedRenyidivergence(RD)isameasureofsimilaritybetweentwodiscreteprobabilitydistributionswhichisnonnegativeandsymmetric.Fordetails,seethedescriptionoffunctionrdorRempalaandSeweryn(2013). 18srdUsagesrd(x,alpha=0.5,CI=0.95,resample=100,graph=FALSE,csv_output=FALSE,PlugIn=FALSE,size=1,CVG=FALSE,saveBootstr
19 ap=FALSE)Argumentsxamatrixcontaininginpu
ap=FALSE)ArgumentsxamatrixcontaininginputpopulationsalphaRenyi'sDivergenceindexoforderalphamustbebetween0and1,default=0.5CVGRenyi'sDivergenceindexoforderalpha=coverage.IfCVG=TRUEargumentalphaisignored;default=FALSECICondenceIntervaldefault=0.95,range(0,1)resamplenumberofrepetitions,default=100graphdefault=FALSE,plotstheresultsofhierarchicalclusteringofpairwiseanalysisofRenyi'sDivergence;graph='fileName'user-denedoutputlenamecsv_outputsavetheresultoftheanalysisas.CSVle,default=FALSE;csv_output='fileName'user-denedoutputlenamePlugInstandardplug-inestimator,default=FALSEsizeresampledfractionofthepopulation,default=1(actualsizeofpopulations).Thevalueshouldnotbesmallerthan10%ofpopulation(size=0.1)saveBootstrapSavesbootstrapresulttoale.UsesaveBootstrap=TRUEtosavebootstrapresultstoaBootstrapfolderincurrentdirectory;saveBootstrap='FolderName'-savesbootstrapresultstouser-namedfolderAuthor(s)ChristophSadee,MaciejPietrzak,MichalSeweryn,CankunWang,GrzegorzRempalaMaintainer:MaciejPietrzak&#xpiet;&#xrzak;&#x.20@;&#xosu.;íu0;ReferencesRempalaG.A.,SewerynM.(2013)MethodsfordiversityandoverlapanalysisinT-cellreceptorpopulations.JMathBiol67:1339-68Examplesdata(TCR.Data)resultsrd(x,resample=20,alpha=0.5) TCR.Data19 TCR.DataTCR.DataRepertoiresofNaiveandRegulatoryT-cellPopulations DescriptionT-cellreceptorrepertoiressequencedusingIonTorrenttechnology.Datasetcontainsreceptorsfoundinfourdifferentorgans,eachwithtwofunctionalpopulations(naiveandregulato
20 ry(Treg)).Cellsareisolatedfromcolon(Col)
ry(Treg)).Cellsareisolatedfromcolon(Col),peripherallymphnodes(PLN),mesentericlymphnodes(MLN)andthymus(Thym).TCRpopulationsdataarestoredinamatrix(objectnamedx).EachcolumnofxcontainssequencedcountsofspecicTCRvariantsingivenorganpopulationx.ReferencesCebulaA.,SewerynM.,RempalaG.A.,PablaS.S.,McIndoeR.A.,DenningT.L.,BryL.,KrajP.,KisielowP.,IgnatowiczL.(2013)Thymus-derivedregulatoryTcellscontributetotolerancetocommensalmicrobiota.Nature497:258-62Examplesdata(TCR.Data)head(x) xExampledatasetfordivopackage DescriptionT-cellreceptorrepertoiressequencedusingIonTorrenttechnology.Datasetcontainsreceptorsfoundinfourdifferentorgans,eachwithtwofunctionalpopulations(naiveandregulatory(Treg)).Cellsareisolatedfromcolon(Col),peripherallymphnodes(PLN),mesentericlymphnodes(MLN)andthymus(Thym).TCRpopulationsdataarestoredinamatrix(objectnamedx).EachcolumnofxcontainssequencedcountsofspecicTCRvariantsingivenorganpopulationxReferencesCebulaA.,SewerynM.,RempalaG.A.,PablaS.S.,McIndoeR.A.,DenningT.L.,BryL.,KrajP.,KisielowP.,IgnatowiczL.(2013)Thymus-derivedregulatoryTcellscontributetotolerancetocommensalmicrobiota.Nature497:258-62Examplesdata(TCR.Data)head(x) IndexTopicAntigenreceptorsdivo,3TopicContingencytablesdivo,3TopicRenyi'sdivergencedivo,3TopicRenyi'sentropydivo,3TopicRichnessanddiversityestimationdivo,3cvg,2,3divo,3dp,3,3,6,7dp.ht,3,5ens,3,6,7ens.ht,3,6,7i.in,3,9i.inp,3,10ji,3,11,12li,3,11,12mh,3,13pg,3,14,15pg.ht,3,15rd,3,16,17srd,3,17TCR.Data,19x,1920