Webdiverse diverse: A package to compute diversity measures. Description The package diverse allows the user to compute the most common measures of diversity. Details The main function of the diverse package is diversity. Other functions are useful according to user needs, as varietyto compute simple variety-richness or balanceto compute … Webdison et al., 2007] model using the R package diversitree [FitzJohn, 2012]. BiSSE models the evolution of a binary character and a birth-death process jointly, and uses a separate set of speciation and extinction rates for each state of the character (see Figure 1). Under BiSSE, the diversi cation process is dependent on the character’s state.
diversitree
WebFurthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree). This function can furthermore calculate the likelihood under an epidemiological model where infected individuals are first exposed and then infectious. WebThis procedure is the find.mle routine from the diversitree package written by Richard Fitzjohn. If for some reason the procedure gets halted in the middle of maxLik() (e.g., computer is shut down) as long as R remains open it should resume where it left off when the computer is reactivated. the cast for stranger things
TreePar package - RDocumentation
WebDec 1, 2012 · The R package ‘diversitree’ contains a number of classical and contemporary comparative phylogenetic methods. Key included methods are BiSSE … WebNov 2, 2024 · Such packages may be found on GitHub, R-Forge, or authors' websites. Getting trees into R : Trees in R are usually stored in the S3 phylo class (implemented in ... diversitree implements the BiSSE method (Maddison et al. 1997) and later improvements (FitzJohn et al. 2009). WebAug 6, 2013 · However it is nonetheless useful to know how to do this properly in R. "phytools" has a function for ancestral character estimation under a couple of different models that uses the re-rooting method of Yang (1995). For other models of evolutionary change not covered by this function, users should try Rich Fitzjohn's diversitree package. the cast dynasty