Add analysis pipeline

R/filter_data.R

@@ -39,5 +39,5 @@ filter_data <- function(data) {
       !test_outlier(age, method = "iqr", iqr_mult = 1.5),
       !test_outlier(transform_time(msf_sc), method = "iqr", iqr_mult = 1.5)
     ) |>
-    tidyr::drop_na(sex, age, state, latitude, longitude)
+    tidyr::drop_na(msf_sc, sex, age, state, latitude, longitude)
 }

R/normality_summary.R

@@ -4,12 +4,24 @@
 
 source(here::here("R/test_normality.R"))
 
-normality_summary <- function(x, round = FALSE, digits = 5, ...) {
-  prettycheck:::assert_numeric(x)
+normality_summary <- function(
+    data,
+    col,
+    round = FALSE,
+    digits = 5,
+    ...
+  ) {
+  prettycheck:::assert_tibble(data)
+  prettycheck:::assert_choice(col, names(data))
+  prettycheck:::assert_numeric(data[[col]])
   prettycheck:::assert_flag(round)
   prettycheck:::assert_number(digits)
 
-  stats <- test_normality(x, print = FALSE, ...)
+  x <- data |> dplyr::pull(col)
+
+  stats <-
+    data |>
+    test_normality(col = col, print = FALSE, ...)
 
   out <- dplyr::tibble(
     test = c(
@@ -64,8 +76,8 @@ normality_summary <- function(x, round = FALSE, digits = 5, ...) {
       ifelse(is.null(stats$shapiro), NA, stats$shapiro$p.value),
       ifelse(is.null(stats$sf), NA, stats$sf$p.value)
     )
-  ) |>
-    dplyr::select(test, p_value)
+  )
+    # dplyr::select(test, p_value)
 
   if (isTRUE(round)) {
     out |>

R/panel_tabset_coef_dfbetas.R

@@ -0,0 +1,139 @@
+# library(dplyr)
+# library(ggplot2)
+# library(glue)
+# library(here)
+# library(latex2exp)
+library(magrittr)
+# library(parsnip)
+# library(prettycheck) # github.com/danielvartan/prettycheck
+# library(readr)
+# library(rutils) # github.com/danielvartan/rutils
+# library(stats)
+# library(utils)
+
+source(here::here("R", "utils.R"))
+
+panel_tabset_coef_dfbetas <- function(
+    fit_engine,
+    coef = names(stats::coef(fit_engine)),
+    coef_labels = coef,
+    source = rep("Created by the author.", length(coef)),
+    heading = "###",
+    fit_engine_name = "fit_engine",
+    suffix = ""
+  ) {
+  prettycheck:::assert_class(fit_engine, "lm")
+
+  prettycheck:::assert_character(
+    coef,
+    len = length(stats::coef(fit_engine)),
+    any.missing = FALSE
+  )
+
+  prettycheck:::assert_subset(coef, names(stats::coef(fit_engine)))
+  prettycheck:::assert_character(coef_labels, len = length(coef))
+  prettycheck:::assert_character(source, len = length(coef))
+  prettycheck:::assert_string(heading, pattern = "^#*")
+  prettycheck:::assert_string(fit_engine_name)
+  prettycheck:::assert_string(suffix)
+
+  if (!file.exists(here::here("qmd"))) dir.create(here::here("qmd"))
+
+  file <- here::here(
+    "qmd",
+    glue::glue("_panel-tabset-coef-dfbetas-{suffix}.qmd")
+  )
+
+  libraries <-
+    c("ggplot2", "olsrr", "stats") |>
+    sort() %>%
+    paste0("library(", ., ")", collapse = "\n")
+
+  scripts <-
+    c("utils.R") |>
+    sort() %>%
+    paste0("source(here::here('R', '", ., "'))", collapse = "\n")
+
+  out <- glue::glue(
+    "
+    :::: {{.panel-tabset}}
+
+    ```{{r}}
+    #| code-fold: true
+
+      plots <- {fit_engine_name} |> olsrr::ols_plot_dfbetas(print_plot = FALSE)
+      coef_names <- stats::coef({fit_engine_name}) |> names()
+    ```
+    \n
+    "
+  )
+
+  coef_labels <- coef_labels |> stringr::str_remove_all("\\(|\\)")
+
+  # Source: {source[i]}
+
+  for (i in seq_along(coef)) {
+    if (i == length(coef)) {
+      end <- ""
+    } else {
+      end <- "\n\n"
+    }
+
+    coef_fix_1 <-
+      coef[i] |>
+      stringr::str_to_lower() |>
+      stringr::str_remove_all("\\(|\\)") |>
+      stringr::str_replace_all("_", "-")
+
+    coef_fix_2 <-
+      coef[i] |>
+      stringr::str_remove_all("\\(|\\)")
+
+    out <- c(
+      out,
+      glue::glue(
+      "
+      {heading} {coef_labels[i]}
+
+      ::: {{#tbl-{suffix}-diag-influence-{coef_fix_1}}}
+      ```{{r}}
+      #| code-fold: true
+
+      plots$plots[[{i}]] +
+       ggplot2::labs(title = '{coef_labels[i]} coefficient')
+      ```
+
+      Standardized DFBETAS values for each observation concerning the
+      `{coef_fix_2}` coefficient.
+      :::{end}
+      "
+      )
+    )
+  }
+
+  out <-
+    c(out, "\n::::") |>
+    paste0(collapse = "") |>
+    readr::write_lines(file)
+
+  include_string <- glue::glue(
+    "{{{{< include {to_relative_path(file)} >}}}}"
+  )
+
+  cli::cli_alert_info(glue:::glue(
+    "Use `{{include_string}}` to include ",
+    "the panel in the file (Copied to clipboard).",
+    "\n\n",
+    "Also, don't forget call the libraries and to source the scripts ",
+    "below in the file.",
+    "\n\n",
+    libraries,
+    "\n\n",
+    scripts,
+    wrap = TRUE
+  ))
+
+  utils::writeClipboard(include_string)
+
+  invisible()
+}