diff --git a/code/analysis/analyze_NA_robustness.Rmd b/code/analysis/analyze_NA_robustness.Rmd index cc40a60..b35c277 100644 --- a/code/analysis/analyze_NA_robustness.Rmd +++ b/code/analysis/analyze_NA_robustness.Rmd @@ -21,7 +21,7 @@ loadNamespace(package = "patchwork") ```{r data, echo = FALSE} #  Loading data data_folder <- file.path(here(), "code", "results", "simulations", "NA_robustness") -files_list <- list.files(data_folder, pattern = "^NA_robustness_19-04-2024") +files_list <- list.files(data_folder, pattern = "^NA_robustness_22-04-2024_17") ``` ```{r df_func, echo = FALSE} prepare_dataframes_auc_ari <- function(data) { @@ -40,8 +40,7 @@ prepare_dataframes_auc_ari <- function(data) { #  Preparing auc_data auc_data <- averaged_data %>% select(c(prop_NAs, model) | contains("auc_")) %>% - rename_with(~ gsub("auc_", "", .x, fixed = TRUE)) %>% - filter(prop_NAs != 0) + rename_with(~ gsub("auc_", "", .x, fixed = TRUE)) auc_data_long <- bind_cols( @@ -109,7 +108,7 @@ plot_auc_ari_data <- function(df_list) { geom_line(aes(color = method)) + geom_point(aes(color = method)) + geom_ribbon(aes(ymin = auc_mean - auc_sd, ymax = auc_mean + auc_sd, fill = method), alpha = 0.2) + - ylim(c(min(auc_data_long[["auc_mean"]]), max(auc_data_long[["auc_mean"]]))) + + ylim(c(0.5, 1)) + scale_x_continuous(breaks = scales::pretty_breaks(n = 10L)) + ylab(TeX("\\bar{AUC}")) + xlab("NA proportion") + @@ -163,6 +162,32 @@ figcaps <- sapply(files_list, function(filename) { }) ``` +Pour les deux figures, la collection est composée de deux réseaux ($M = 2$) dont +les proportions sont les suivantes : +$$\pi = \rho = (0.5, 0.3, 0.2) $$ + +Le premier réseau qui subit une perte d'informations est de petite taille, 40 +individus en ligne et en colonne. Le second réseau contient 120 individus en +ligne et en colonne. + +La structure ayant abouti aux résulats de la figure \@ref(fig:plot-1) est la suivante : +$$\alpha_{modular} = \begin{bmatrix} +0.9 & 0.05 & 0.05 \\ +0.05 & 0.2 & 0.05 \\ +0.05 & 0.05 & 0.8 +\end{bmatrix}$$ +Il s'agit d'une structure modulaire répliquant un comportement communautaire. + + +La structure ayant abouti aux résulats de la figure \@ref(fig:plot-2) est la suivante : +$$\alpha_{nested} = \begin{bmatrix} +0.9 & 0.25 & 0.1 \\ +0.3 & 0.15 & 0.05 \\ +0.1 & 0.05 & 0.05 +\end{bmatrix}$$ +Il s'agit d'une structure emboîtée répliquant une structure communément trouvée +dans les réseaux plantes-pollinisateurs. + ```{r plot, echo = FALSE, fig.cap=paste("Graph of metrics for NA robustness with a ", figcaps)} for (filename in files_list) { data <- readRDS(file.path( @@ -172,12 +197,4 @@ for (filename in files_list) { df_list <- prepare_dataframes_auc_ari(data = data) plot(plot_auc_ari_data(df_list = df_list)) } -# filename <- files_list[1] -# data <- readRDS(file.path( -# data_folder, -# filename -# )) -# print(here()) -# df_list <- prepare_dataframes_auc_ari(data = data) -# knitr::knit_print(plot_auc_ari_data(df_list = df_list)) ``` \ No newline at end of file diff --git a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-39_uniform_modular_1-400.Rds b/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-39_uniform_modular_1-400.Rds deleted file mode 100644 index ed21f61..0000000 Binary files a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-39_uniform_modular_1-400.Rds and /dev/null differ diff --git a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-41_uniform_nested_1-400.Rds b/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-41_uniform_nested_1-400.Rds deleted file mode 100644 index 6b19590..0000000 Binary files a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-12-41_uniform_nested_1-400.Rds and /dev/null differ diff --git a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-41_uniform_nested_1-400.Rds b/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-41_uniform_nested_1-400.Rds deleted file mode 100644 index 118031f..0000000 Binary files a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-41_uniform_nested_1-400.Rds and /dev/null differ diff --git a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-42_uniform_modular_1-400.Rds b/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-42_uniform_modular_1-400.Rds deleted file mode 100644 index 57eee20..0000000 Binary files a/code/results/simulations/NA_robustness/NA_robustness_22-04-2024_16-47-42_uniform_modular_1-400.Rds and /dev/null differ