Phylogenetic Independent Contrasts Math
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The information required to estimate evolutionary rates is efficiently summarized in the early but still useful phylogenetic comparative method of independent contrasts felsenstein 1985.
Phylogenetic independent contrasts math. In this tutorial we will learn to apply the independent contrasts method of felsenstein 1985 for estimating the evolutionary correlation between characters. Phylogenetic independent contrasts with discrete traits. Important you can only calculate contrasts on a single variable the soon to be released caic package will allow you to run more than one trait at a time as well as discrete traits. Either a vector of phylogenetically independent contrasts if var contrasts false or a two column matrix with the phylogenetically independent contrasts in the first column and their expected variance in the second column if var contrasts true.
However on this. This equivalence has several implications. Active 3 years 1 month ago. Viewed 195 times 0 begingroup i understand that pics are normally only used for continuous traits.
Felsenstein 1985 identified and to a large extent solved a problem that. Phylogenetically independent contrasts in this tutorial we will learn to apply the independent contrasts method of felsenstein 1985 for estimating the evolutionary correlation between characters. The dependent is log body size and the. If the tree has node labels these are used as labels of the returned object.
We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts pics conducted through the origin is identical to the slope parameter of the method of generalized least squares glss regression under a brownian motion model of evolution. 2 when calculated based on phylogenetic independent contrasts it assumes brownian motion. Felsenstein 1985 identified and to a large extent solved a problem that had previously recognized but that was underappreciated. There is also a simple mathematical relationship between contrasts and maximum likelihood rate estimates that i will discuss below.
λ is often used to measure the phylogenetic signal in comparative data. And that is that the data for species cannot be. Ancova with phylogenetic independent contrasts i need to do a phylogenetic independent contrast between 2 variables for a large number of species 1000. This makes intuitive sense as λ scales the tree between a constant rates model λ 1 to one where every species is statistically independent of every other species in the tree λ 0.
Ask question asked 3 years 1 month ago. Independent contrasts summarize the amount of character change across each node in the tree and can be used to estimate the rate of character change across a phylogeny.
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