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Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
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Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach
04:35

Development of an Individual-Tree Basal Area Increment Model using a Linear Mixed-Effects Approach

Published on: July 3, 2020

Sampling trees from evolutionary models.

Klaas Hartmann1, Dennis Wong, Tanja Stadler

  • 1Tasmanian Aquaculture and Fisheries Institute, University of Tasmania, Hobart, Australia.

Systematic Biology
|June 16, 2010
PubMed
Summary
This summary is machine-generated.

Simulating evolutionary trees requires careful methods. A simple sampling approach (SSA) can bias results, but a general sampling approach (GSA) offers accurate tree simulations for evolutionary models.

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Area of Science:

  • Computational evolutionary biology
  • Phylogenetics
  • Statistical modeling

Background:

  • Numerous evolutionary models exist for species diversification.
  • Simulating phylogenetic trees is crucial for hypothesis testing and comparing with empirical data.
  • Standard tree sampling methods can introduce biases in shape and branch lengths.

Purpose of the Study:

  • To identify limitations of the simple sampling approach (SSA) for evolutionary tree simulation.
  • To introduce a general sampling approach (GSA) applicable to diverse evolutionary models.
  • To present an efficient sampling method for constant-rate birth-death models.

Main Methods:

  • Mathematical analysis of tree sampling biases.
  • Development and application of a general sampling approach (GSA).
  • Introduction of a specific sampling method for birth-death models.

Main Results:

  • The simple sampling approach (SSA) is only appropriate for the Yule pure birth model.
  • The general sampling approach (GSA) provides unbiased tree simulations for broader models.
  • Inappropriate SSA leads to incorrect correlations between trait variance and tree age, unlike the correct GSA.

Conclusions:

  • The choice of tree sampling method significantly impacts evolutionary inference.
  • The general sampling approach (GSA) and birth-death model sampling are recommended for accurate phylogenetic simulations.
  • Available algorithms in R and Perl facilitate the implementation of these methods.