1 citations · 3 across the 6 of their papers we have counts for
6 papers
Statistical implications of relaxing the homogeneous mixing assumption in time series Susceptible-Infectious-Removed models
Luis D. J. Martinez Lomeli, Michelle N. Ngo, Jon Wakefield +2
Infectious disease epidemiologists routinely fit stochastic epidemic models to time series data to elucidate infectious disease dynamics, evaluate interventions, and forecast epide…
phylodyn: an R package for phylodynamic simulation and inference
Michael D. Karcher, Julia A. Palacios, Shiwei Lan +1
We introduce phylodyn, an R package for phylodynamic analysis based on gene genealogies. The package main functionality is Bayesian nonparametric estimation of effective population…
Calculating higher-order moments of phylogenetic stochastic mapping summaries in linear time
Amrit Dhar, Vladimir N. Minin
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This…
Likelihood-Based Inference for Discretely Observed Birth-Death-Shift Processes, with Applications to Evolution of Mobile Genetic Elements
Jason Xu, Peter Guttorp, Midori Kato-Maeda +1
Continuous-time birth-death-shift (BDS) processes are frequently used in stochastic modeling, with many applications in ecology and epidemiology. In particular, such processes can…
Synonymous and Nonsynonymous Distances Help Untangle Convergent Evolution and Recombination
Peter B. Chi, Sujay Chattopadhyay, Philippe Lemey +2
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation an…
Phylogenetic Stochastic Mapping without Matrix Exponentiation
Jan Irvahn, Vladimir N. Minin
Phylogenetic stochastic mapping is a method for reconstructing the history of trait changes on a phylogenetic tree relating species/organisms carrying the trait. State-of-the-art m…