PC-ORD

PC-ORDTMMultivariateAnalysisofEcologicalDataVersion5User’sBooklet2Suggestedcitation:McCune,B.andM.J.Mefford.2006.PC-ORD.MultivariateAnalysisofEcologicalData.Version5.MjMSoftware,GlenedenBeach,Oregon,U.S.A.Cover:Theessenceofmultivariateanalysisistheextractionofasmallnumberofimportantrelationshipsfromaverylargenumberofpossiblerelationships.Waiver:Althoughthesoftwarehasbeencarefullytested,theuseracceptsandusestheprogrammaterialasitis,attheuser’sownrisk,relyingsolelyuponhis/herowninspectionoftheprogrammaterialandwithoutrelianceuponanyrepresentationordescriptionconcerningtheprogrammaterial.NeitherMjMSoftwareDesignnorassociatedindividualsmakeanyexpressedorimpliedwarrantyofanykindwithregardtotheprogrammaterial,andshallhavenoliabilityorresponsibilitytoanyrecipientwithrespecttoanyliability,loss,ordamagethatdirectlyorindirectlyarisesoutoftheuseofthediskandtheprogramsand/orsubroutinescontainedonthedisk,including,butnotlimitedto,anylossofbusinessorlossofdataorotherincidentalorconsequentialdamages.Byusingthissoftwareyouagreetothis.©1991,1993,1995,1997,1999,2006MjMSoftwareDesign©1991,1993,1995,1997,1999,2006BruceMcCuneAllrightsreserved.PrintedintheUnitedStatesofAmerica.3ContentsWhatisPC-ORDFor?.................................4WhereistheManual?.................................5HowDoIGetStarted?.................................5ManagingFilesandProjects............................5SystemRequirements..................................6NetworkEnvironments................................7Limitations..........................................9TechnicalHelp......................................10UpdatesandFixes...........................10ContactUs.................................10UsingPC-ORD:aBriefOverview......................111.PrepareYourData........................112.OpenPC-ORDandYourDataFiles..........133.RunanAnalysis..........................144.ExploreYourResultsGraphically.............17OtherNewGraphs...................................21ADecisionTreeforBeginners..........................244WhatisPC-ORDFor?PC-ORDisaWindowsprogramformultivariateanalysisofecologicaldataenteredinspreadsheets.Weemphasizenonparametrictools,graphicalrepresentation,andrandomizationtestsforanalysisofcommunitydata.Inadditiontoutilitiesfortransformingdataandmanagingfiles,PC-ORDoffersmanyordinationandclassificationtechniquesnotavailableinmajorstatisticalpackagesincluding:CCA,DCA,MRPP,perMANOVA,two-wayclustering,TWINSPAN,Bealssmoothing,diversityindices,specieslists,Manteltest,manyordinationoverlaymethods(quantitative,symbol-coding,color-coding,grid,jointplot,biplot,successionalvector),variousrotationmethods,3Dordinationgraphics,indicatorspeciesanalysis,Bray-Curtisordination,city-blockdistancemeasures,species-areacurves,treedatasummaries,publication-qualitydendrograms,andautopilotNMS.Verylargedatasetscanbeanalyzed.Mostoperationsacceptamatrixupto32,000rowsor32,000columnsandupto536,848,900matrixelements,providedthatyouhaveadequatememory.Theterminologyistailoredforecologists.Thefullmanualisincludedasacontext-sensitivehelpsystem.Virtuallyanymultivariatedatasetconsistingofasetofentities,eachwithanumberofmeasuredattributes,isadaptabletoPC-ORD.Incommunityecology,thefirstmatrixwilloftencontainspeciesabundancedatainasetofsamples.ThepossibleformatsforenteringthesedatacanbefoundinDataPreparationinthesoftwarehelpsystem.Inadditiontothismainmatrix,asecondmatrix,oftencontainingenvironmentaldata,canbeenteredforanalysisofitsrelationshiptothefirstmatrix.Theinclusionofthissecondmatrixgreatlyenrichesthesystem’sanalyticalcapabilities.BothmatricesaredisplayedinPC-ORDinfileviewingwindows.5Instudiesofresourcepartitioningorfunctionalgroups,oneofthematricescontainsrelativeuseofasetofresourcesbyvariousspecies,subspecies,orindividuals.Amatrixofsites×functionalgroupscanbeproducedbymultiplyingacommunitymatrixbythefunctionalgroupmatrix.WhereistheManual?ThefullmanualisbuiltintoPC-ORD,sowehavenotproducedapapermanual.Ourcontext-sensitiveHelpsystemcanbeaccessedatanytimebypressingF1orclickingaHelpbutton.HowDoIGetStarted?Afteryouinstallthesoftware,clickonHelp|Contentsinthemainmenu.ThennavigatetoGettingStartedinthehelpsystem.Themostimportanttopicstoreadatfirstare:DataPreparation,SpreadsheetFormat,andTypicalFlowofAnalysisManagingFilesandProjectsNormallyyouwillwanttokeepyourdataandresultsinafolderthatisseparatefromthefolderthatcontainsPC-ORD.IfyouhavemorethanonePC-ORDproject,youcankeepthefilesfromeachprojectinaseparatefolderorputtheminasinglefolder.PC-ORDhelpsyouresumeworkwhereyouleftoffwiththeFile|OpenProjectandFile|SaveProjectmenuitems.DetailsofhowPC-ORDmanages6folders(directories)andfilemanagementdefinitionsaregivenunderOpenProjectinthePC-ORDHelpsystem.WhenyouInstallPC-ORD,thePC-ORDiconisinsertedintheProgramssectionoftheStartMenu.Ifyouwishtocreateaniconforagivenproject,firstcreatea“shortcut”toPC-ORDonyourdesktoporinafolder(seeyourWindowshelpsystemifyoudon’tknowhowtodothis).Then:•Renametheshortcutastheprojectitrepresents.(Rightclick,Rename)•Nowsettheworkingfolderforthatproject.(Rightclickonthei