## ---- eval=FALSE---------------------------------------------------------
# library(ape)
# my_tree <- read.tree('my_tree.tre') # For Newick format trees
# my_tree <- read.nexus('my_tree.nex') # For NEXUS format trees
## ---- eval=FALSE---------------------------------------------------------
# rownames(my_data) <- my_data$species_name
## ---- eval=FALSE---------------------------------------------------------
# my_tree$tip.label # Check the tip labels of your tree
# rownames(my_data) <- gsub(' ', '_', my_data$species_name_with_spaces)
## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(dev = "png", fig.height = 5, fig.width = 5, dpi = 300, out.width = "450px")
## ------------------------------------------------------------------------
library(phylopath)
models <- define_model_set(
one = c(RS ~ DD),
two = c(DD ~ NL, RS ~ LS + DD),
three = c(RS ~ NL),
four = c(RS ~ BM + NL),
five = c(RS ~ BM + NL + DD),
six = c(NL ~ RS, RS ~ BM),
seven = c(NL ~ RS, RS ~ LS + BM),
eight = c(NL ~ RS),
nine = c(NL ~ RS, RS ~ LS),
.common = c(LS ~ BM, NL ~ BM, DD ~ NL)
)
## ------------------------------------------------------------------------
models$one
## ---- fig.height = 5, fig.width = 5, dpi = 300---------------------------
plot(models$one)
## ---- fig.height=8, fig.width=8, out.width = "600px"---------------------
plot_model_set(models)
## ------------------------------------------------------------------------
result <- phylo_path(models, data = rhino, tree = rhino_tree, model = 'lambda')
## ------------------------------------------------------------------------
result
## ------------------------------------------------------------------------
(s <- summary(result))
## ------------------------------------------------------------------------
plot(s)
## ------------------------------------------------------------------------
(best_model <- best(result))
## ---- warning = FALSE, fig.width = 6-------------------------------------
plot(best_model)
## ---- fig.width = 7------------------------------------------------------
average_model <- average(result)
plot(average_model, algorithm = 'mds', curvature = 0.1) # increase the curvature to avoid overlapping edges
## ---- fig.width = 7------------------------------------------------------
average_model_full <- average(result, avg_method = "full")
plot(average_model_full, algorithm = 'mds', curvature = 0.1)
## ------------------------------------------------------------------------
#coef_plot(average_model)
## ---- fig.height=3.5-----------------------------------------------------
# coef_plot(average_model_full, reverse_order = TRUE) +
# ggplot2::coord_flip() +
# ggplot2::theme_bw()
## ------------------------------------------------------------------------
result$d_sep$one
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