Find and fix small rounding errors in ultrametric trees

checkAndFixUltrametric finds and correct small numerical errors that might appear in ultrametric trees that where created through simulations. This function should never be used as a formal statistical method to make a tree ultrametric, as it was designed just to correct small rounding errors.

Usage

checkAndFixUltrametric(phy)

Arguments

phy

A phylo object, following terminology from package ape in which function will operate.

Value

A check and fixed phylo object.

References

Paradis, E. (2012). Analysis of Phylogenetics and Evolution with R (Vol. 2). New York: Springer.

Popescu, A. A., Huber, K. T., & Paradis, E. (2012). ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics, 28(11), 1536-1537.

See also

Other macroevolution: calcFossilDivTT(), countSeqDiffs(), estimateSpeciation(), fitCRBD(), lttPlot(), plotPaintedWhales(), plotProteinSeq(), plotRawFossilOccs(), simulateBirthDeathRich(), simulateTree()

Author

Daniel Rabosky, Matheus Januario, Jennifer Auler

Examples

S <- 1
E <- 0
set.seed(1)
phy <- simulateTree(pars = c(S, E), max.taxa = 6, max.t = 5)
phy$edge.length[1] <- phy$edge.length[1]+0.1
ape::is.ultrametric(phy)
#> [1] FALSE
phy <- checkAndFixUltrametric(phy)
ape::is.ultrametric(phy)
#> [1] TRUE