ouwie_tidy | R Documentation |
This function allows you to run OUwie across all combinations of trees, simmaps, models, and continuous traits and outputs analyses in a neat tibble.
ouwie_tidy( phy, disc_trait, cont_traits, models, nsim, tip_col = NULL, dir = NULL, ... )
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. |
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 |
Beaulieu, J. M., & O’Meara, B. 2014. OUwie: analysis of evolutionary rates in an OU framework.
#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
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