2017
Birth/birth-death processes and their computable transition probabilities with biological applications
Ho LST, Xu J, Crawford FW, Minin VN, Suchard MA. Birth/birth-death processes and their computable transition probabilities with biological applications. Journal Of Mathematical Biology 2017, 76: 911-944. PMID: 28741177, PMCID: PMC5783825, DOI: 10.1007/s00285-017-1160-3.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsBayes TheoremCommunicable DiseasesComputational BiologyComputer SimulationEnglandEpidemicsHistory, 17th CenturyHost-Parasite InteractionsHumansLikelihood FunctionsMarkov ChainsMathematical ConceptsModels, BiologicalMonte Carlo MethodPlagueProbabilityStochastic ProcessesConceptsBirth-death processTransition probabilitiesFinite-time transition probabilitiesSIR modelMonte Carlo approximationJoint posterior distributionLikelihood-based inferenceApproximate Bayesian computationStatistical inferenceMatrix exponentiationPosterior distributionProcess approximationBivariate extensionBayesian computationFraction representationLaplace transformCorrelation structureUnivariate populationsRemoved (SIR) modelSmall systemsBivariate processEfficient algorithmApproximationDirect inferenceFast method
2015
Markov counting models for correlated binary responses
Crawford FW, Zelterman D. Markov counting models for correlated binary responses. Biostatistics 2015, 16: 427-440. PMID: 25792624, PMCID: PMC5963474, DOI: 10.1093/biostatistics/kxv006.Peer-Reviewed Original ResearchConceptsExchangeable Bernoulli random variablesBernoulli random variablesCorrelated binary responsesMaximum likelihood estimatesInterpretable parameterizationsRandom variablesLikelihood estimatesCounting processDifferent cluster sizesBinary responsesCorrelated outcomesNatural wayCluster sizeBinary dataImproved fitPrevious modelsNew model
2013
Diversity, Disparity, and Evolutionary Rate Estimation for Unresolved Yule Trees
Crawford FW, Suchard MA. Diversity, Disparity, and Evolutionary Rate Estimation for Unresolved Yule Trees. Systematic Biology 2013, 62: 439-455. PMID: 23417679, PMCID: PMC3622899, DOI: 10.1093/sysbio/syt010.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionBody SizeCarnivoraGenetic SpeciationLikelihood FunctionsMarkov ChainsModels, GeneticPhylogenyConceptsPhylogenetic treePhylogenetic diversityTrait disparityEvolutionary relationshipsYule treeMammalian order CarnivoraPhenotypic trait valuesComparative evolutionary studiesEvolutionary rate estimationSet of taxaOrganism of interestTrait evolutionPhenotypic evolutionEvolutionary biologistsInferred phylogenyEvolutionary studiesUnresolved cladeTrait valuesMacroevolutionary studiesTrait dataRelated organismsOrder CarnivoraCladeBrownian motionBranch lengths