PMC:7519301 / 42639-43312 JSONTXT

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T304","span":{"begin":33,"end":34},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T305","span":{"begin":94,"end":100},"obj":"http://purl.obolibrary.org/obo/CLO_0002045"},{"id":"T306","span":{"begin":134,"end":138},"obj":"http://purl.obolibrary.org/obo/CLO_0002040"},{"id":"T307","span":{"begin":149,"end":150},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T308","span":{"begin":281,"end":283},"obj":"http://purl.obolibrary.org/obo/CLO_0053733"},{"id":"T309","span":{"begin":297,"end":299},"obj":"http://purl.obolibrary.org/obo/CLO_0053794"},{"id":"T310","span":{"begin":664,"end":667},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_314295"}],"text":"Phylogenies were simulated using a time-forward branching process under constant birth rates (b(t)=b) and time-dependent birth rates (b(t)=beαt) for b = 0.01, 0.03, 0.05, 0.07, and 0.09 and α = ±0.01, ±0.11, ±0.21, ±0.31, and ±0.41, for 20, 220, 420, 620, and 820 tips, and for 1, 11, 21, 31, and 41 time units. Simulated phylogenies were downsampled at 0%, 10%, 30%, 50%, and 70%. For each scenario, 100 phylogenies were simulated. Time-dependent diversification (i.e., η across subtrees) was calculated for each phylogeny simulated under each scenario. Simulations were conducted using the R packages RPANDA (R Phylogenetic ANalyses of DiversificAtion) (61) and ape (53)."}

{"project":"LitCovid-sentences","denotations":[{"id":"T264","span":{"begin":0,"end":311},"obj":"Sentence"},{"id":"T265","span":{"begin":312,"end":381},"obj":"Sentence"},{"id":"T266","span":{"begin":382,"end":432},"obj":"Sentence"},{"id":"T267","span":{"begin":433,"end":554},"obj":"Sentence"},{"id":"T268","span":{"begin":555,"end":673},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Phylogenies were simulated using a time-forward branching process under constant birth rates (b(t)=b) and time-dependent birth rates (b(t)=beαt) for b = 0.01, 0.03, 0.05, 0.07, and 0.09 and α = ±0.01, ±0.11, ±0.21, ±0.31, and ±0.41, for 20, 220, 420, 620, and 820 tips, and for 1, 11, 21, 31, and 41 time units. Simulated phylogenies were downsampled at 0%, 10%, 30%, 50%, and 70%. For each scenario, 100 phylogenies were simulated. Time-dependent diversification (i.e., η across subtrees) was calculated for each phylogeny simulated under each scenario. Simulations were conducted using the R packages RPANDA (R Phylogenetic ANalyses of DiversificAtion) (61) and ape (53)."}

{"project":"2_test","denotations":[{"id":"32868447-30016406-132542433","span":{"begin":669,"end":671},"obj":"30016406"}],"text":"Phylogenies were simulated using a time-forward branching process under constant birth rates (b(t)=b) and time-dependent birth rates (b(t)=beαt) for b = 0.01, 0.03, 0.05, 0.07, and 0.09 and α = ±0.01, ±0.11, ±0.21, ±0.31, and ±0.41, for 20, 220, 420, 620, and 820 tips, and for 1, 11, 21, 31, and 41 time units. Simulated phylogenies were downsampled at 0%, 10%, 30%, 50%, and 70%. For each scenario, 100 phylogenies were simulated. Time-dependent diversification (i.e., η across subtrees) was calculated for each phylogeny simulated under each scenario. Simulations were conducted using the R packages RPANDA (R Phylogenetic ANalyses of DiversificAtion) (61) and ape (53)."}