_02-11_adaptive.qmd

## Adaptive (#sec-adaptive)

{{< include _02-11_adaptive_text.qmd >}}

```{r}
#| label: setup-adaptive
#| include: false

domains <- c("Adaptive Functioning")

pheno <- "adaptive"
```

```{r}
#| label: export-adaptive
#| include: false

# Read the CSV file into a data frame
adaptive <- vroom::vroom("neurobehav.csv")

# Filter the data frame based on certain conditions
# Keep only the rows where 'domain' equals 'domains' and 'z_mean_domain' is not NA
adaptive <- adaptive |>
  dplyr::filter(domain %in% domains)

# Select specific columns from the data frame
adaptive <- adaptive |>
  dplyr::select(
    test,
    test_name,
    scale,
    raw_score,
    score,
    ci_95,
    percentile,
    range,
    domain,
    subdomain,
    narrow,
    pass,
    verbal,
    timed,
    description,
    result,
    z,
    z_mean_domain,
    z_sd_domain,
    z_mean_subdomain,
    z_sd_subdomain,
    z_mean_narrow,
    z_sd_narrow
  )

# Write the 'adaptive' data frame to a CSV file
# The file name is derived from the 'pheno' variable
readr::write_excel_csv(adaptive, paste0(pheno, ".csv"), na = "", col_names = TRUE, append = FALSE)
```

```{r}
#| label: data-adaptive
#| include: false

# Read and filter the data
data <- adaptive

# Define the scales of interest
scales <- c(
  "General Adaptive Composite (GAC)",
  "Conceptual",
  "Communication",
  "Functional Pre-Academics",
  "Self-Direction",
  "Adaptive Skills Index",
  "Leisure",
  "Social Index",
  "Social",
  "Adaptive",
  "Practical",
  "Community Use",
  "School Living",
  "Home Living",
  "Health and Safety",
  "Self-Care",
  "Motor",
  "General Adaptive Composite",
  "Conceptual Skills Index",
  "Functional Academics",
  "Practical Skills Index",
  "Work"
)
# Filter the data using the filter_data function from the bwu library
# The domain is specified by the 'domains' variable
# The scale is specified by the 'scales' variable
data_adaptive <- bwu::filter_data(data, domain = domains, scale = scales)
```

```{r}
#| label: text-adaptive
#| cache: true
#| include: false

# Generate the text for the adaptive domain
bwu::cat_neuropsych_results(data = data_adaptive, file = "_02-11_adaptive_text.qmd")
```

```{r}
#| label: qtbl-adaptive
#| dev: tikz
#| fig-process: pdf2png
#| include: false

# Set the default engine for tikz to "xetex"
options(tikzDefaultEngine = "xetex")

# Define the table name, vertical padding, and multiline setting
table_name <- "table_adaptive"
vertical_padding <- 0
multiline <- TRUE

# Define the source note
fn_scaled_score <- gt::md("Scaled score: Mean = 10 [50th‰], SD ± 3 [16th‰, 84th‰]")
fn_standard_score <- gt::md("Index score: Mean = 100 [50th‰], SD ± 15 [16th‰, 84th‰]")

# Define the groups for the table
grp_adaptive <- list(
  standard_score = c(
    "ABAS-3 Parent", "ABAS-3", "ABAS-3 Teacher"
  ),
  scaled_score = c(
    "ABAS-3 Parent", "ABAS-3", "ABAS-3 Teacher"
  )
)

# Create the table using the tbl_gt function from the bwu library
bwu::tbl_gt(
  data = data_adaptive,
  pheno = pheno,
  table_name = table_name,
  vertical_padding = vertical_padding,
  fn_standard_score = fn_standard_score,
  fn_scaled_score = fn_scaled_score,
  grp_standard_score = grp_adaptive[["standard_score"]],
  grp_scaled_score = grp_adaptive[["scaled_score"]],
  dynamic_grp = grp_adaptive,
  multiline = multiline
)
```

```{r}
#| label: fig-adaptive
#| include: false
#| fig-cap: "Adaptive functioning is a broad term that refers to the collection of conceptual, social, and practical skills that enable individuals to function independently and meet the demands of everyday life. These skills include things like communication, self-care, home living, social skills, and community use."

# Dotplot args
colors <- NULL
return_plot <- TRUE
filename <- "fig_adaptive.svg"

# vars to plot
x <- data_adaptive$z_mean_narrow
y <- data_adaptive$narrow

# Suppress warnings from being converted to errors
options(warn = 1) # Set warn to 1 to make warnings not halt execution

# Create the dotplot using the dotplot function from the bwu library
bwu::dotplot(
  data = data_adaptive,
  x = x,
  y = y,
  colors = colors,
  return_plot = return_plot,
  filename = filename,
  na.rm = TRUE
)

# Reset warning options to default if needed
options(warn = 0) # Reset to default behavior
```

```{=typst}
#let domain(title: none, file_qtbl, file_fig) = {
  let font = (font: "Roboto Slab", size: 0.5em)
  set text(..font)
  pad(top: 0.5em)[]
    grid(
      columns: (50%, 50%),
      gutter: 8pt,
        figure([#image(file_qtbl)],
          caption: figure.caption(position: top, [#title]),
          kind: "qtbl",
          supplement: [Table],
          ),
        figure([#image(file_fig)],
          caption: figure.caption(position: bottom, [
            Adaptive functioning is a broad term that refers to the collection of conceptual, social, and practical skills that enable individuals to function independently and meet the demands of everyday life. These skills include things like communication, self-care, home living, social skills, and community use.
            ]),
          placement: none,
          kind: "image",
          supplement: [Figure],
          gap: 0.5em,
          ),
        )
    }
```
```{=typst}
#let title = "Adaptive Functioning"
#let file_qtbl = "table_adaptive.png"
#let file_fig = "fig_adaptive.svg"
#domain(
  title: [#title Scores],
  file_qtbl,
  file_fig
)
```