diff --git a/R/scripts_and_filters/experiments/experiment-vignette3.1-SS-2.R b/R/scripts_and_filters/experiments/experiment-vignette3.1-SS-2.R new file mode 100644 index 00000000..d19aefcc --- /dev/null +++ b/R/scripts_and_filters/experiments/experiment-vignette3.1-SS-2.R @@ -0,0 +1,133 @@ +# Setup Libraries --------------------------------------------------------- +library(tidyverse) +library(progress) +library(glue) + +devtools::document() +devtools::load_all() + +# Global variables -------------------------------------------------------- +set.seed(35542) +NUM_COVG_REPS <- 200 # Number of coverage replications +NUM_OBS <- 300 + +# Create grid sequences --------------------------------------------------- +# For empirical bootstrap parameters i.e. B*m +# Create individual sequences of grid values to cross join +# TODO: Need to add replace = {TRUE/FALSE} values once we add subsampling +out_crossing <- purrr::cross2( + .x = seq(from = 5, to = 35, by = 10), + .y = seq(from = 40, to = 120, by = 40), + .filter = `==` +) %>% + purrr::map(purrr::set_names, c("B", "m")) + +# Check output for one of the lists we have constructed +out_crossing[[10]] +out_crossing[[10]]$B +out_crossing[[10]]$m + +#' Given fitted linear model i.e. `mod_fit` +#' For an individual coverage replication index i.e. `covg_rep_idx` +#' For an individual [B, m] empirical bootstrap combination i.e. `boot_emp` +#' Get the empirical bootstrap confidence interval for the fitted parameters +fit_ind_repl_ind_boot_emp <- function(covg_rep_idx, mod_fit, boot_emp) { + confint_fit <- comp_var(mod_fit = mod_fit, boot_emp = boot_emp) %>% + get_confint(mod_fit = ., level = 0.95, boot_emp = TRUE) %>% + dplyr::mutate( + covg_rep_idx = covg_rep_idx, + B = boot_emp[["B"]], + m = boot_emp[["m"]] + ) %>% + dplyr::select(covg_rep_idx, B, m, dplyr::everything()) + return(confint_fit) +} + +fit_ind_repl_all_boot_emp <- function(covg_rep_idx, out_crossing) { + # TODO: Remove the print message later + print(glue::glue("Running coverage replication index: {covg_rep_idx}...\n")) + + # For each coverage replication generate the data once + # For all B*m combinations + n <- NUM_OBS + X <- stats::rnorm(n, 0, 1) + y <- 2 + X * 1 + stats::rnorm(n, 0, 1) + lm_fit <- stats::lm(y ~ X) + + # Using the single data generated for each coverage replication + # Get the empirical bootstrap confidence interval for each individual B*m + # combination, and combine all such combination output into a single + # tibble + out <- out_crossing %>% + purrr::map_dfr( + .x = ., + .f = ~ fit_ind_repl_ind_boot_emp( + covg_rep_idx = covg_rep_idx, + mod_fit = lm_fit, + boot_emp = .x + ) + ) + return(out) +} + +fit_all_repl_all_boot_emp <- function(num_reps, out_crossing) { + out <- 1:num_reps %>% + purrr::map_dfr( + .x = ., + .f = ~ fit_ind_repl_all_boot_emp( + covg_rep_idx = .x, + out_crossing = out_crossing + ) + ) + return(out) +} + +# Compute confidence intervals for N replications ------------------------- +system.time(confint_replications <- fit_all_repl_all_boot_emp( + num_reps = NUM_COVG_REPS, + out_crossing = out_crossing +) %>% + dplyr::arrange(B, m, covg_rep_idx) %>% + dplyr::mutate( + term = forcats::as_factor(term), + B = forcats::as_factor(B), + m = forcats::as_factor(m) + )) + +# Check the output +head(confint_replications) + +# Get combined confidence intervals --------------------------------------- +all_confint <- confint_replications %>% + # Add plotting code here + filter(stat_type == "conf.low" | + stat_type == "conf.high") %>% + pivot_wider(names_from = stat_type, values_from = stat_val) + +all_confint_coverage <- all_confint %>% + inner_join(tibble( + term = c("(Intercept)", "X"), + value_par = c(2, 1) + ), + by = "term" + ) %>% + mutate(covers_c = ifelse(conf.low <= value_par & conf.high >= value_par, 1, 0)) %>% + group_by(term, B, m, var_type_abb) %>% + summarize( + coverage = mean(covers_c), + avg_width = mean(conf.high - conf.low) + ) + +# Coverage seems to be working here i.e. most of the values are in the 86-100% range +summary(all_confint_coverage$coverage) +hist(all_confint_coverage$coverage, breaks = 10, xlim = c(0, 1)) + +# TODO: Check if we should be plotting avg_width? +# Should this be coverage instead? +all_confint_coverage %>% + mutate(title = as.factor(glue::glue("m = {m}"))) %>% + ggplot(aes(B, avg_width)) + + geom_col() + + facet_grid(~title) + + labs(y = "Coverage") + + geom_hline(yintercept = 0.95, linetype = "dashed")