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Showing content from https://github.com/paternogbc/sensiPhy/wiki/Online-tutorial below:

Online tutorial · paternogbc/sensiPhy Wiki · GitHub

The sensiPhy package provides simple functions to perform sensitivity analyses in phylogenetic comparative methods. It uses several simulation methods to estimate the impact of different types of uncertainty on Phylogenetic comparative methods:

(i) Species Sampling uncertainty (sample size; influential species and clades)
(ii) Phylogenetic uncertainty
(iii) Data uncertainty (intraspecific variation and measurement error)

sensiPhy functions use a common syntax that combines the type of uncertainty and the type of analysis:

• xxx_phylm (for linear regressions)
• xxx_phyglm (for logistic regressions)
• xxx_physig (for phylogenetic signal)
• xxx_continuous (for continuous trait evolution)
• xxx_discrete (for discrete trait evolution)

where "xxx" can be one of the 5 sensiPhy methods (see Figure below):

• Species sampling uncertainty: influ; clade; samp;
• Phylogenetic uncertainty: tree
• Data uncertainty: intra

sensiPhy workflow & functions

The following links provide a quick tutorial to sensiPhy functions and their basic usage.

• Sampling uncertainty
  • Influential species
  • Influential clades
  • Sample size
• Phylogenetic uncertainty
• Data uncertainty
• Interacting uncertainties

• How long does it take?
• Using sensiPhy to analyse results from other packages

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