Nothing
## ----define_models, fig.align='center', fig.width=10, fig.height=8, out.height="600px", fig.dpi = 600----
library(phylopath)
models <- define_model_set(
A = c(C~M+D),
B = c(C~D),
C = c(C~D, P~M),
D = c(C~D, M~P, G~P),
E = c(C~D, P~M, G~P),
F = c(C~D, P~M+G),
G = c(C~D, M~P, P~G),
H = c(C~D, M~P),
I = c(C~D, M~M, G~P),
J = c(M~P, G~D),
K = c(P~M, G~D),
L = c(C~M+D, P~M+G),
.common = c(C~P+G)
)
plot_model_set(models, algorithm = 'kk')
## ----fit models---------------------------------------------------------------
(cichlids_results <- phylo_path(models, cichlids, cichlids_tree))
## ----get_summary--------------------------------------------------------------
(s <- summary(cichlids_results))
plot(s)
## -----------------------------------------------------------------------------
best_cichlids <- best(cichlids_results)
## -----------------------------------------------------------------------------
best_cichlids
## -----------------------------------------------------------------------------
coef_plot(best_cichlids, error_bar = "se", reverse_order = TRUE) + ggplot2::coord_flip()
## ----fig.align='center', fig.width=8, fig.height=4, out.width="600px", fig.dpi = 300----
plot(best_cichlids)
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