ouwie_tidy: Wrapper OUwie function

In stfriedman/tidyouwie: Wrapper functions for the OUwie function

Wrapper OUwie function

Description

This function allows you to run OUwie across all combinations of trees, simmaps, models, and continuous traits and outputs analyses in a neat tibble.

Usage

ouwie_tidy(
  phy,
  disc_trait,
  cont_traits,
  models,
  nsim,
  tip_col = NULL,
  dir = NULL,
  ...
)

Arguments

phy	Phylogenetic tree(s) containing all species/specimens present in dataset.
disc_trait	Named vector of discrete characters where the names match the tree tips
cont_traits	Data frame containing a character column with tree tips and any number of columns containing continuous trait data. Order of columns does not matter.
models	Vector containing the set of models to run on each tree as designated in OUwie documentation
nsim	Number of simmaps to create and run all analyses on
tip_col	Optional; column name in "cont_traits" that matches tree tips
dir	Optional; the directory to save output to, otherwise will save to working directory
params	Optional; list of parameters to be passed to OUwie. NOTE: be aware that default OUwie parameters differ from the default OUwie documentation.

Value

Function returns a list of the following

input	Simmaps and traits originally input into OUwie
full_output	Raw tibble with all results
tidy_output	Tidy tibble summarizing results

References

Beaulieu, J. M., & O’Meara, B. 2014. OUwie: analysis of evolutionary rates in an OU framework.

Examples

#simulating dummy data to run through OUwie
phy <- pbtree(n = 20, nsim = 2)
disc_trait <- setNames(sample(letters[1:2], 20, replace = TRUE), phy[[1]]$tip.label)
cont_traits <- as_tibble(iris[1:20, 1:2]) %>%
 mutate(species = phy[[1]]$tip.label)

models <- c("BM1", "OUM") #set of models to run on each simmap

results <- ouwie_tidy(phy, disc_trait, cont_traits, models, nsim = 2)
results$tidy_output

stfriedman/tidyouwie documentation built on April 20, 2022, 8:45 p.m.