polarolouis/anova-phylogenetique-projet-msv
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Adding realTree simulations

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This commit is contained in:
Louis Lacoste 2024-02-10 18:35:58 +01:00
parent 87f38972ae
commit b4384acc39
2 changed files with 42 additions and 5 deletions
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41
R/realTreeSimu.R
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@ -7,6 +7,10 @@ require("phytools")
source("./R/utils.R")
K <- 2
nb_species <- 43
plot_group_on_tree <- function(tree, groups) {
plot(tree)
tiplabels(bg = groups, pch = 21)
@ -21,14 +25,47 @@ plotTree(tree, ftype="i")
# Mus et Rat vs le reste
group_mus_rat_vs_other <- sapply(44:(44+41), function(tip) {
group_mus_rat_vs_other <- sapply(44:(43+nb_species), function(tip) {
if (tip %in% getDescendants(tree = tree, 55)) {
return(1)
}
return(2)
})
random_groups <- sample(1:K, nb_species, replace = TRUE)
plot_group_on_tree(tree, group = group_mus_rat_vs_other)
plot_group_on_tree(tree, group = random_groups)
# Groupes équilibrës
# Generate data for rat&mus vs the rest
N <- 500
base_values <- c(0, 1)
sigma2_phylo <- 1
sigma2_measure <- 0.1
risk_threshold <- 0.05
## Standardized parameters
total_variance <- 1.0 # sigma2_phylo + sigma2_error, fixed [as tree_height = 1]
heri <- c(0.0, 0.25, 0.5, 1.0) # heritability her = sigma2_phylo / total_variance. 0 means only noise. 1 means only phylo.
snr <- 1 # signal to noise ratio snr = size_effect / total_variance
ggsave <- function(..., bg = "white") ggplot2::ggsave(..., bg = bg)
for (her in heri) {
sim <- N_simulation_typeI_power(N,
groups_list = list(ratmus_vs_other = group_mus_rat_vs_other,
random = random_groups),
base_values = c(0, snr * total_variance),
sigma2_phylo = her * total_variance,
sigma2_measure = (1 - her) * total_variance,
)
df_sim_plot <- compute_power_typeI(df = sim)
res_sim_plot <- plot_method_comparison(df_sim_plot, title = paste("Rat&Mus héritabilité ", her))
res_sim_plot
ggsave(paste0("img/ratmus_vs_other_her_", her, ".png"), plot = res_sim_plot)
}

6
R/utils.R
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@ -380,10 +380,10 @@ simulate_all_methods <- function(
data_all_methods_df <- data.frame()
for(idx in seq(length(groups))){
for(idx in seq(length(groups_list))){
# Traits
trait <- compute_trait_values(
groups = groups[[idx]],
groups = groups_list[[idx]],
base_values = base_values,
tree = tree, sigma2_phylo = sigma2_phylo,
sigma2_measure = sigma2_measure
@ -392,7 +392,7 @@ simulate_all_methods <- function(
# Compute fits
fits <- infere_anova_phyloanova(
y = trait,
groups = groups[[idx]], tree = tree
groups = groups_list[[idx]], tree = tree
)
# Computing the dataframe