added lab 4

2025-10-31 17:55:13 -04:00
parent dc2ceac7de
commit 88f2975b86
66 changed files with 730 additions and 301 deletions
@@ -0,0 +1,121 @@
+source("/home/ion606/Desktop/Homework/Data Analytics/Assignments/Assignment II/R/00_utils.R")
+
+# TODO: hard-code me
+
+# NOTE: The options were generated by chatGPT from my horrendous hard-coded options
+option_list <- list(
+	optparse::make_option("--data", type = "character", default = "/home/ion606/Desktop/Homework/Data Analytics/Assignments/Assignment II/epi_results_2024_pop_gdp_v2.csv"),
+	optparse::make_option("--region-col", type = "character", default = NA),
+	optparse::make_option("--region-a", type = "character", default = NA),
+	optparse::make_option("--region-b", type = "character", default = NA),
+	optparse::make_option("--response", type = "character", default = NA),
+	optparse::make_option("--predictors", type = "character", default = NA),
+	optparse::make_option("--knn1", type = "character", default = NA),
+	optparse::make_option("--knn2", type = "character", default = NA),
+	optparse::make_option("--k", type = "integer", default = 5)
+)
+opt <- optparse::parse_args(optparse::OptionParser(option_list = option_list))
+
+if (is.na(opt$data)) stop("--data is required")
+
+read_any <- function(p) {
+	ext <- tolower(tools::file_ext(p))
+	if (ext %in% c("csv", "txt")) {
+		suppressMessages(readr::read_csv(p, show_col_types = FALSE))
+	} else if (ext %in% c("xls", "xlsx")) {
+		readxl::read_excel(p)
+	} else {
+		stop("unsupported extension: ", ext)
+	}
+}
+df <- read_any(opt$data)
+
+nms <- names(df)
+
+find_col <- function(nms, pats) {
+	for (pat in pats) {
+		idx <- which(stringr::str_detect(tolower(nms), pat))
+		if (length(idx)) return(nms[idx[1]])
+	}
+
+	# I hate it here
+	NA_character_
+}
+
+region_col <- if (!is.na(opt$`region-col`)) opt$`region-col` else
+  find_col(nms, c("^region$", "regions?$", "world\\s*bank\\s*region"))
+
+if (is.na(region_col)) stop("could not detect a region column; pass --region-col")
+
+response <- if (!is.na(opt$response)) opt$response else if ("EPI.new" %in% nms) {
+	"EPI.new"
+} else {
+	find_col(nms, c("^epi", "epi.*score", "index$", "score$"))
+}
+
+if (is.na(response)) {
+	num <- df |> dplyr::select(where(is.numeric)) |> names()
+	if (!length(num)) stop("no numeric columns; pass --response")
+	response <- num[1]
+}
+
+gdp_col <- find_col(nms, c("^gdp", "gdp.*per.*cap", "gdppc"))
+pop_col <- find_col(nms, c("^pop", "^population$"))
+
+counts <- sort(table(df[[region_col]]), decreasing = TRUE)
+region_a <- if (!is.na(opt$`region-a`)) opt$`region-a` else
+  if ("Sub-Saharan Africa" %in% names(counts)) "Sub-Saharan Africa" else names(counts)[1]
+
+region_b <- if (!is.na(opt$`region-b`)) opt$`region-b` else
+  if ("Latin America & Caribbean" %in% names(counts)) "Latin America & Caribbean" else names(counts)[2]
+
+pred_sets <- list()
+if (!is.na(opt$predictors)) {
+	pred_sets <- list(strsplit(opt$predictors, ",", fixed = TRUE)[[1]] |> trimws())
+} else {
+	plist <- c()
+	if (!is.na(gdp_col)) plist <- c(plist, gdp_col)
+	if (!is.na(pop_col)) plist <- c(plist, pop_col)
+	if (length(plist) >= 1) pred_sets <- append(pred_sets, list(plist[1]))
+	if (length(plist) >= 2) pred_sets <- append(pred_sets, list(plist[1:2]))
+}
+
+pred_sets <- pred_sets[lengths(pred_sets) > 0]
+
+choose_knn_vars <- function(df, exclude, k = 3) {
+	cands <- names(df)[endsWith(names(df), ".new") & names(df) != exclude]
+	cands <- cands[sapply(cands, function(c) is.numeric(df[[c]]))]
+	miss <- sapply(cands, function(c) mean(is.na(df[[c]])))
+	ord <- order(miss, cands)
+	head(cands[ord], k)
+}
+
+knn1 <- if (!is.na(opt$knn1)) {
+	strsplit(opt$knn1, ",", fixed = TRUE)[[1]] |> trimws()
+} else {
+	choose_knn_vars(df, response, 3)
+}
+
+knn2 <- if (!is.na(opt$knn2)) {
+	strsplit(opt$knn2, ",", fixed = TRUE)[[1]] |> trimws()
+} else {
+	setdiff(choose_knn_vars(df, response, 6), knn1)[1:3]
+}
+
+ctx <- list(
+	data = normalizePath(opt$data),
+	region_col = region_col,
+	response = response,
+	region_a = region_a,
+	region_b = region_b,
+	predictors = pred_sets,
+	knn1 = knn1,
+	knn2 = knn2,
+	k = opt$k,
+	fig_dir = "/home/ion606/Desktop/Homework/Data Analytics/Assignments/Assignment II/output/figures",
+	stats_dir = "/home/ion606/Desktop/Homework/Data Analytics/Assignments/Assignment II/output/stats"
+)
+
+
+writeLines(jsonlite::toJSON(ctx, pretty = TRUE, auto_unbox = TRUE), "/home/ion606/Desktop/Homework/Data Analytics/Assignments/Assignment II/output/ctx.json")
+message("wrote ctx.json")