anova-phylogenetique-projet-msv/simulations/test-anova.phylo_OU.R

library(phylolm)
library(phylotools)
library(phytools)
library(ape)
library(ggplot2)
set.seed(1234)
ggsave <- function(..., bg = "white") ggplot2::ggsave(..., bg = bg)


N <- 100 # Number of different simulations
n <- 100

# Arbre
tree <- rphylo(n, 0.1, 0)

## Groupes
K <- 3
get_group <- function(tip) {
    if (tip %in% getDescendants(tree, 107)) {
        return(2)
    }
    if (tip %in% getDescendants(tree, 111)) {
        return(3)
    }
    return(1)
}

source("./simulations/functions-anova.R")

# Computing groups
phylo_groups <- as.factor(sapply(1:n, get_group))
non_phylo_groups <- as.factor(sample(c(1, 2, 3), n, replace = TRUE))

plot_group_on_tree <- function(tree, group) {
    plot(tree, show.tip.label = FALSE, x.lim = 50)
    tiplabels(bg = phylo_groups, pch = 21)
}

# Saving trees


calcul_puissance <- function(data, test_method) {
    mean(data[which(data$tested_method == test_method), ]$has_selected_correctly)
}
sigma2_measure_err <- 0
sigma2_intra_species = 1
# Mu tous différents
mu_vect <- c(1, 5, 10)
# N répétitions pour les 2 groupes générés
mu_diff_phylo_groups_results <- do.call("rbind", lapply(1:N, function(id) {
    simulate_ANOVAs(
        sim_id = id, groups = phylo_groups, tree = tree, n = n, mu_vect = mu_vect, stoch_process = "OU",
        sigma2_measure_err = sigma2_measure_err, 
        sigma2_intra_species = sigma2_intra_species
    )
}))
mu_diff_non_phylo_groups_results <- do.call("rbind", lapply(1:N, function(id) {
    simulate_ANOVAs(
        sim_id = id, groups = non_phylo_groups, tree = tree, n = n,
        mu_vect = mu_vect, stoch_process = "OU", 
        sigma2_measure_err = sigma2_measure_err, sigma2_intra_species = sigma2_intra_species
    )
}))

puissance_mu_diff_phylo_for_phylo_groups <- calcul_puissance(mu_diff_phylo_groups_results, "ANOVA-Phylo")
puissance_mu_diff_classic_for_phylo_groups <- calcul_puissance(mu_diff_phylo_groups_results, "ANOVA")

puissance_mu_diff_phylo_for_non_phylo_groups <- calcul_puissance(mu_diff_non_phylo_groups_results, "ANOVA-Phylo")
puissance_mu_diff_classic_for_non_phylo_groups <- calcul_puissance(mu_diff_non_phylo_groups_results, "ANOVA")

# Mu égaux
mu_vect <- rep(1, K)
# N répétitions pour les 2 groupes générés
mu_equals_phylo_groups_results <- do.call("rbind", lapply(1:N, function(id) {
    simulate_ANOVAs(
        sim_id = id, groups = phylo_groups, tree = tree, n = n, mu_vect = mu_vect,
        sigma2_measure_err = sigma2_measure_err, sigma2_intra_species = sigma2_intra_species
    )
}))
mu_equals_non_phylo_groups_results <- do.call("rbind", lapply(1:N, function(id) {
    simulate_ANOVAs(
        sim_id = id, groups = non_phylo_groups, tree = tree, n = n, mu_vect = mu_vect,
        sigma2_measure_err = sigma2_measure_err, sigma2_intra_species = sigma2_intra_species
    )
}))

# Calcul de puissance
puissance_mu_equals_phylo_for_phylo_groups <- calcul_puissance(mu_equals_phylo_groups_results, "ANOVA-Phylo")
puissance_mu_equals_classic_for_phylo_groups <- calcul_puissance(mu_equals_phylo_groups_results, "ANOVA")

puissance_mu_equals_phylo_for_non_phylo_groups <- calcul_puissance(mu_equals_non_phylo_groups_results, "ANOVA-Phylo")
puissance_mu_equals_classic_for_non_phylo_groups <- calcul_puissance(mu_equals_non_phylo_groups_results, "ANOVA")

# Graphiques
puissances <- c(
    puissance_mu_diff_phylo_for_phylo_groups,
    puissance_mu_diff_classic_for_phylo_groups,
    puissance_mu_equals_phylo_for_phylo_groups,
    puissance_mu_equals_classic_for_phylo_groups,
    puissance_mu_diff_phylo_for_non_phylo_groups,
    puissance_mu_diff_classic_for_non_phylo_groups,
    puissance_mu_equals_phylo_for_non_phylo_groups,
    puissance_mu_equals_classic_for_non_phylo_groups
)
plot_data <- data.frame(
    puissance = puissances,
    tested_method = rep(c("ANOVA-Phylo", "ANOVA"), 4),
    group_type = rep(c("phylo", "non_phylo"), each = 4),
    mu_type = rep(rep(c("different", "equals"), each = 2), 2)
)

p <- ggplot(plot_data, aes(x = tested_method, y = puissance, fill = group_type)) +
    geom_bar(stat = "identity", position = "dodge") +
    scale_y_continuous(limits = c(0, 1)) +
    labs(
        title = paste0("Proportion de bonnes sélections vs Tested Method (OU) | N = ", N, "; sigma2_measure_err = ", sigma2_measure_err, "; sigma2_intra = ", sigma2_intra_species),
        x = "Tested Method",
        y = "Proportion de bonnes sélections"
    ) +
    geom_hline(yintercept = 0.95) +
    facet_grid(cols = vars(mu_type)) +
    theme_minimal()

p
# TODO : Regarder la notice de lmertest pour l'implémentation de Satterthwaite
# TODO : En utilisant l'arbre étoile, on obtient un modele mixte classique donc on peut appliquer lmerTest