template.qmd

---
title: NEUROCOGNITIVE EXAMINATION
name: {{< var first_name >}} {{< var last_name >}}
doe: today
patient: Biggie
---

```{r}
#| label: setup
#| include: false
#| cache: false

packages <- c(
  "dplyr",
  "collapse",
  "glue",
  "gt",
  "here",
  "janitor",
  "knitr",
  "quarto",
  "readr",
  "readxl",
  "rmarkdown",
  "snakecase",
  "tidytable",
  "vroom",
  "xfun",
  "bwu"
)

# Function to load packages one by one
load_packages <- function(packages2) {
  for (pkg in packages) {
    if (!require(pkg, character.only = TRUE)) {
      install.packages(pkg)
      library(pkg, character.only = TRUE)
    }
    message(paste("Loaded package:", pkg))
  }
}

# Call the function to load packages
load_packages(packages)

# Set knitr options
knitr::opts_knit$set(width = 80, digits = 2, warnPartialMatchArgs = FALSE)
knitr::knit_hooks$set(crop = knitr::hook_pdfcrop)
knitr::knit_hooks$set(optipng = knitr::hook_optipng)

# Check if the output format is LaTeX
if (identical(knitr:::pandoc_to(), "latex")) {
  knit_hooks$set(plot = function(x, options) {
    # Adjust here with whatever you need to do with your plots for LaTeX output
    paste("\\begin{figure}[htbp!]",
      "\\centering",
      "\\includegraphics[width=\\maxwidth]{", x, "}",
      "\\caption{", options$fig.cap, "}",
      "\\end{figure}",
      sep = "\n"
    )
  })
}

# Set environment variables with default values
Sys.setenv(PATIENT = "{{< var patient >}}", RETURN_PLOT = TRUE)
patient <- Sys.getenv("PATIENT")
return_plot <- Sys.getenv("RETURN_PLOT")
```

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

file_path <- here::here("data", "csv")
bwu::load_data(here::here(file_path))
neurocog <- vroom::vroom("neurocog.csv")
neurobehav <- vroom::vroom("neurobehav.csv")
neuropsych <- vroom::vroom("neuropsych.csv")
validity <- vroom::vroom("validity.csv")
```

```{=typst}
#let name = [{{< var first_name >}} {{< var last_name >}}]
#let doe = [2024-01-01]
#let patient = [{{< var patient >}}]
#v(2em, weak: true)
#show block: set par(leading: 0.65em)
#block[
*PATIENT NAME:* #name \
*DATES OF EXAM:* {{< var doe1 >}}, {{< var doe2 >}}, and {{< var doe3 >}} \
]
```

{{< include _00-00_tests.qmd >}}

<!-- {{< pagebreak >}} -->

{{< include _01-00_nse.qmd >}}

<!-- {{< pagebreak >}} -->

# NEUROCOGNITIVE FINDINGS {#sec-nt}

{{< include _02-00_behav-obs.qmd >}}

{{< include _02-01_iq.qmd >}}

{{< include _02-02_academics.qmd >}}

{{< include _02-03_verbal.qmd >}}

{{< include _02-04_spatial.qmd >}}

{{< include _02-05_memory.qmd >}}

{{< include _02-06_executive.qmd >}}

<!-- {{< include _02-07_motor.qmd >}} -->

<!-- {{< include _02-08_social.qmd >}} -->

{{< include _02-09_adhd_child.qmd >}}

{{< include _02-10_emotion_child.qmd >}}

<!-- {{< include _02-11_adaptive.qmd >}} -->

<!-- {{< pagebreak >}} -->

{{< include _03-00_sirf.qmd >}}

{{< include _03-00_sirf_text.qmd >}}

{{< include _03-01_recs.qmd >}}

{{< include _03-02_signature.qmd >}}

{{< pagebreak >}}

{{< include _03-03_appendix.qmd >}}