In jtrampush/npsych.data: BrainWorkup Neuropsychological Report Writing Package

CAARS2 Long Version SR/OR

Load libraries

Sys.setenv(
  JAVA_HOME = "/Library/Java/JavaVirtualMachines/temurin-11.jdk/Contents/Home"
)
options(java.parameters = "-Xmx16000m")
knitr::opts_chunk$set(
  root.dir = normalizePath("./"),
  echo = TRUE,
  message = TRUE,
  warning = FALSE,
  error = TRUE
)
library(hablar)
library(here)
library(magrittr)
library(readr)
library(rJava)
library(rmarkdown)
library(rmdformats)
library(shiny)
library(tabulapdf)
library(tibble)
library(tidyr)
library(dplyr)
library(bwu)

Patient

patient <- params$patient

Test

test <- params$test

Test Name

test_name <- params$test_name

Upload/attach PDF

# file <- file.choose()
file <- file.path(params$file)

Pages

pages <- params$pages

writeLines(
  file, here::here("pre_csv", paste0(test, ".pdf"))
)

# test <- readLines(here::here(patient, "pre_csv", paste0(test, ".pdf")))

Locate areas

if (params$test == "caars2_sr") {
  area <- list(
    c(120, 35, 252, 576),
    c(318, 34, 420, 576),
    c(571, 34, 616, 576)
  )
}
if (params$test == "caars2_or") {
  area <- list(
    c(120, 35, 252, 576),
    c(319, 35, 419, 576),
    c(572, 35, 623, 576)
  )
}

# SR
# java -jar tabula-java.jar  -a 120.488,35.0,252.068,576.62 -p 4 "$1"
# java -jar tabula-java.jar  -a 318.623,34.043,419.603,575.663 -p 4 "$1"
# java -jar tabula-java.jar  -a 571.838,34.043,616.973,576.428 -p 4 "$1"

# OR
# java -jar tabula-java.jar  -a 119.723,35.0,252.068,576.62 -p 4 "$1"
# java -jar tabula-java.jar  -a 319.388,35.573,418.838,574.898 -p 4 "$1"
# java -jar tabula-java.jar  -a 571.838,34.808,623.093,576.428 -p 4 "$1"

# area <- bwu::gpluck_locate_areas(
#   file = file,
#   pages = pages
# )

saveRDS(area, here::here("pre_csv", paste0(test, "_area.rds")))

# area <- readRDS(here::here(patient, "pre_csv", paste0(test, "_area.rds")))

Extract table

plucked_tables <- bwu::gpluck_extract_tables(
  file = file,
  pages = pages,
  area = area,
  guess = NULL,
  method = "stream",
  output = "matrix"
)

Tidy Tables

Pluck individual data/columns

df1

library(dplyr)
library(tidyr)

# Convert matrix to data frame and set proper column names
df1 <- as.data.frame(plucked_tables[[1]])
colnames(df1) <- c("scale", "raw_score", "score", "ci_95", "percentile", "guideline", "elevated_items")

# Merge rows 1 and 3 by updating the first row and removing the third row
df1[2, ] <- c("Inattention/Executive Dysfunction", df1[3, -1])
df1 <- df1[-4, ]
df1 <- df1[-3, ]
df1 <- df1[-1, ]

# Ensure the data frame is cleaned up if required, e.g., adjust row names
row.names(df1) <- NULL

# View the cleaned data frame
df1

df2

library(dplyr)
library(tidyr)

# Convert matrix to data frame and set proper column names
df2 <- as.data.frame(plucked_tables[[2]])
colnames(df2) <- c("scale", "raw_score", "score", "ci_95", "percentile", "guideline", "symptom_count")

# Merge rows 2 and 4 by updating the second row and removing the fourth row
df2 <- df2[-1, ]
df2[2, ] <- c("ADHD Hyperactive/Impulsive Symptoms", df2[3, -1])
df2 <- df2[-4, ]
df2 <- df2[-3, ]

# Ensure the data frame is cleaned up if required, e.g., adjust row names
row.names(df2) <- NULL

# View the cleaned data frame
df2

df3

library(dplyr)
library(tidyr)

# Convert matrix to data frame and set proper column names
df3 <- as.data.frame(plucked_tables[[3]])
colnames(df3) <- c("scale", "raw_score", "percentile", "guideline")

# Remove row 1
df3 <- df3[-2, ]
df3 <- df3[-1, ]

# Ensure the data frame is cleaned up if required, e.g., adjust row names
row.names(df3) <- NULL

# View the cleaned data frame
df3

transform data

library(dplyr)
library(stringr)

# More robust function to remove ordinal suffixes and convert to numeric
remove_ordinal_suffix <- function(x) {
  # Attempt to extract numeric-only part of the string
  cleaned <- str_extract(str_trim(x), "\\d+")
  if (is.na(cleaned) || cleaned == "") {
    NA # Return NA if no digits found
  } else {
    as.numeric(cleaned) # Convert the cleaned string to numeric
  }
}

# Updated function to apply transformations safely to data frames
transform_data <- function(df) {
  # Check and transform percentile if it exists
  if ("percentile" %in% names(df)) {
    df$percentile <- sapply(df$percentile, remove_ordinal_suffix)
  }

  # Convert raw_score to numeric if it exists
  if ("raw_score" %in% names(df)) {
    df$raw_score <- as.numeric(df$raw_score)
  }

  # Convert score to numeric if it exists
  if ("score" %in% names(df)) {
    df$score <- as.numeric(df$score)
  }

  # Diagnostic checks to alert about any NA values introduced
  cols_to_transform <- c("percentile", "raw_score", "score")
  for (col in cols_to_transform) {
    if (col %in% names(df) && any(is.na(df[[col]]), na.rm = TRUE)) {
      warning(paste("Some values in", col, "could not be converted and were set to NA."))
    }
  }

  df
}

# Example usage (assuming df1, df2, df3 are defined as earlier):
df1_transformed <- transform_data(df1)

df2_transformed <- transform_data(df2)

df3_transformed <- transform_data(df3)

combined_df <- dplyr::bind_rows(df1_transformed, df2_transformed, df3_transformed)

row names

if (params$test == "caars2_sr") {
  combined_df[1, 1] <- c("CAARS2-SR Inattention/Executive Dysfunction")
  combined_df[2, 1] <- c("CAARS2-SR Hyperactivity")
  combined_df[3, 1] <- c("CAARS2-SR Impulsivity")
  combined_df[4, 1] <- c("CAARS2-SR Emotional Dysregulation")
  combined_df[5, 1] <- c("CAARS2-SR Negative Self-Concept")
  combined_df[6, 1] <- c("CAARS2-SR ADHD Inattentive Symptoms")
  combined_df[7, 1] <- c("CAARS2-SR ADHD Hyperactive/Impulsive Symptoms")
  combined_df[8, 1] <- c("CAARS2-SR Total ADHD Symptoms")
  combined_df[9, 1] <- c("CAARS2-SR ADHD Index")
  combined_df <- combined_df[1:9, ]
} else if (params$test == "caars2_or") {
  combined_df[1, 1] <- c("CAARS2-OR Inattention/Executive Dysfunction")
  combined_df[2, 1] <- c("CAARS2-OR Hyperactivity")
  combined_df[3, 1] <- c("CAARS2-OR Impulsivity")
  combined_df[4, 1] <- c("CAARS2-OR Emotional Dysregulation")
  combined_df[5, 1] <- c("CAARS2-OR Negative Self-Concept")
  combined_df[6, 1] <- c("CAARS2-OR ADHD Inattentive Symptoms")
  combined_df[7, 1] <- c("CAARS2-OR ADHD Hyperactive/Impulsive Symptoms")
  combined_df[8, 1] <- c("CAARS2-OR Total ADHD Symptoms")
  combined_df[9, 1] <- c("CAARS2-OR ADHD Index")
  combined_df <- combined_df[1:9, ]
}

Mutate columns

table <- combined_df

# df_gemini <- readr::read_csv(here::here("data", "caars2_or.csv")) |>
#   dplyr::slice(-6) |>
#   dplyr::select(-c(`Guideline`, `# of Elevated Items`))
# colnames(df_gemini) <- c("scale", "raw_score", "score", "ci_95", "percentile")

# library(readr)
# library(dplyr)
#
# process_and_save_csv <- function(input_path, output_path) {
#   # Read CSV file
#   caars2_data <- read_csv(input_path)
#
#   # Perform the required operations
#   tidy_caars2_data <- caars2_data |>
#     # Remove row 7 "DSM Symptom Scales" (assuming it is the 7th row)
#     slice(-6) |>
#     # Remove "Guideline" and "# of Elevated Items" columns
#     select(-c(`Guideline`, `# of Elevated Items`))
#
#   # Save the tidy'd caars2_or.csv file
#   write_csv(tidy_caars2_data, output_path)
# }
#
# # Set the path for the input and output CSV files
# # Adjust the paths if they are in different directories
# input_path <- "data/caars2_or.csv"
# output_path <- "data/tidy_caars2_or.csv"
#
# # Call the function
# caars2_or <- process_and_save_csv(input_path, output_path)
#
# table <- caars2_or

table <- bwu::gpluck_make_columns(
  table,
  percentile = "",
  range = "",
  ci_95 = "",
  test = params$test,
  test_name = params$test_name,
  domain = "ADHD",
  subdomain = "",
  narrow = "",
  pass = "",
  verbal = "",
  timed = "",
  test_type = "rating_scale",
  score_type = "t_score",
  description = "",
  result = ""
)

Create percentile

table <- table |>
  dplyr::mutate(z = (score - 50) / 10) |>
  dplyr::mutate(percentile = trunc(pnorm(z) * 100)) |>
  dplyr::select(-z)

Test score ranges

table <- bwu::gpluck_make_score_ranges(
  table = table,
  test_type = "rating_scale"
)

Subdomains

subdomain_col <- which(colnames(table) == "subdomain")

if (length(subdomain_col) > 0) {
  table[1, subdomain_col] <- c("Attention/Executive")
  table[2, subdomain_col] <- c("Hyperactivity")
  table[3, subdomain_col] <- c("Impulsivity")
  table[4, subdomain_col] <- c("Emotion/Mood")
  table[5, subdomain_col] <- c("Self-Concept")
  table[6, subdomain_col] <- c("Inattention")
  table[7, subdomain_col] <- c("Hyperactivity/Impulsivity")
  table[8, subdomain_col] <- c("Combined Symptoms")
  table[9, subdomain_col] <- c("ADHD Index")
} else {
  warning("Column 'subdomain' not found in the table.")
}

Narrow subdomains

if (params$test == "caars2_sr") {
  table <-
    table |>
    dplyr::mutate(
      narrow = dplyr::case_when(
        scale ==
          "CAARS2-SR Inattention/Executive Dysfunction" ~ "Inattention Self-Report",
        scale ==
          "CAARS2-SR Hyperactivity" ~ "Hyperactivity Self-Report",
        scale ==
          "CAARS2-SR Impulsivity" ~ "Impulsivity Self-Report",
        scale ==
          "CAARS2-SR Emotional Dysregulation" ~ "Self-Concept Self-Report",
        scale ==
          "CAARS2-SR Negative Self-Concept" ~ "Self-Concept Self-Report",
        scale ==
          "CAARS2-SR ADHD Inattentive Symptoms" ~ "Inattention Self-Report",
        scale ==
          "CAARS2-SR ADHD Hyperactive/Impulsive Symptoms" ~ "Hyperactivity Self-Report",
        scale ==
          "CAARS2-SR Total ADHD Symptoms" ~ "Combined Symptoms Self-Report",
        scale ==
          "CAARS2-SR ADHD Index" ~ "ADHD Index Self-Report",
        scale ==
          "CAARS2-SR Inconsistency Index" ~ "Inconsistency Self-Report",
        TRUE ~ as.character(narrow)
      )
    )
} else if (params$test == "caars2_or") {
  table <-
    table |>
    dplyr::mutate(
      narrow = dplyr::case_when(
        scale ==
          "CAARS2-OR Inattention/Executive Dysfunction" ~ "Inattention Observer-Report",
        scale ==
          "CAARS2-OR Hyperactivity" ~ "Hyperactivity Observer-Report",
        scale ==
          "CAARS2-OR Impulsivity" ~ "Impulsivity Observer-Report",
        scale ==
          "CAARS2-OR Negative Self-Concept" ~ "Self-Concept Observer-Report",
        scale ==
          "CAARS2-OR Emotional Dysregulation" ~ "Emotion/Mood Observer-Report",
        scale ==
          "CAARS2-OR ADHD Inattentive Symptoms" ~ "Inattention Observer-Report",
        scale ==
          "CAARS2-OR ADHD Hyperactive/Impulsive Symptoms" ~ "Hyperactivity Observer-Report",
        scale ==
          "CAARS2-OR Total ADHD Symptoms" ~ "Combined Symptoms Observer-Report",
        scale ==
          "CAARS2-OR ADHD Index" ~ "ADHD Index Observer-Report",
        TRUE ~ as.character(narrow)
      )
    )
}

Scale descriptions

if (params$test == "caars2_sr") {
  table <-
    table |>
    dplyr::mutate(
      description = dplyr::case_when(
        scale == "CAARS2-SR Inattention/Executive Dysfunction" ~
          "i.e., trouble concentrating, difficulty planning or completing tasks, forgetfulness, absent-mindedness, being disorganized",
        scale == "CAARS2-SR Hyperactivity" ~
          "i.e., problems with working at the same task for long periods of time, feeling more restless than others seem to be, fidgeting",
        scale == "CAARS2-SR Impulsivity" ~
          "i.e., engaging in more impulsive acts than others do, low frustration tolerance, quick and frequent mood changes, feeling easily angered and irritated by people",
        scale == "CAARS2-SR Emotional Dysregulation" ~
          "i.e., poor social relationships, low self-esteem and self confidence",
        scale == "CAARS2-SR Negative Self-Concept" ~
          "i.e., poor social relationships, low self-esteem and self confidence",
        scale == "CAARS2-SR ADHD Inattentive Symptoms" ~
          "i.e., behave in a manner consistent with the DSM-5 Inattentive Presentation of ADHD",
        scale == "CAARS2-SR ADHD Hyperactive/Impulsive Symptoms" ~
          "i.e., behave in a manner consistent with the DSM-5 Hyperactive-Impulsive Presentation of ADHD",
        scale == "CAARS2-SR Total ADHD Symptoms" ~
          "i.e., behave in a manner consistent with the DSM-5 diagnostic criteria for Combined Presentation of ADHD",
        scale == "CAARS2-SR ADHD Index" ~
          "composite indicator for identifying individuals 'at-risk' for ADHD (self-reported)",
        TRUE ~ as.character(description)
      )
    )
} else if (params$test == "caars2_or") {
  table <-
    table |>
    dplyr::mutate(
      description = dplyr::case_when(
        scale == "CAARS2-OR Inattention/Executive Dysfunction" ~ "i.e., trouble concentrating, difficulty planning or completing tasks, forgetfulness, absent-mindedness, being disorganized",
        scale == "CAARS2-OR Hyperactivity" ~ "i.e., problems with working at the same task for long periods of time, feeling more restless than others seem to be, fidgeting",
        scale == "CAARS2-OR Impulsivity" ~
          "i.e., engaging in more impulsive acts than others do, low frustration tolerance, quick and frequent mood changes, feeling easily angered and irritated by people",
        scale == "CAARS2-OR Emotional Dysregulation" ~
          "i.e., poor regulation of emotions",
        scale == "CAARS2-OR Negative Self-Concept" ~
          "i.e., poor social relationships, low self-esteem and self confidence",
        scale ==
          "CAARS2-OR ADHD Inattentive Symptoms" ~
          "i.e., behave in a manner consistent with the DSM-5 Inattentive Presentation of ADHD",
        scale ==
          "CAARS2-OR ADHD Hyperactive/Impulsive Symptoms" ~ "i.e., behave in a manner consistent with the DSM-5 Hyperactive-Impulsive Presentation of ADHD",
        scale == "CAARS2-OR Total ADHD Symptoms" ~ "i.e., behave in a manner consistent with the DSM-5 diagnostic criteria for Combined Presentation of ADHD",
        scale == "CAARS2-OR ADHD Index" ~ "composite indicator for identifying individuals 'at-risk' for ADHD (observer reported)",
        TRUE ~ as.character(description)
      )
    )
}

Glue results

if (params$test == "caars2_sr") {
  table <-
    table |>
    dplyr::mutate(
      result = dplyr::case_when(
        scale == "CAARS2-SR Inattention/Executive Dysfunction" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR Hyperactivity" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR Impulsivity" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR Emotional Dysregulation" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR Negative Self-Concept" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR ADHD Inattentive Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR ADHD Hyperactive/Impulsive Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR Total ADHD Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-SR ADHD Index" ~ glue::glue(
          "- {patient}'s {description} was {range}.\n"
        ),
        TRUE ~ as.character(result)
      )
    )
} else if (params$test == "caars2_or") {
  table <-
    table |>
    dplyr::mutate(
      result = dplyr::case_when(
        scale == "CAARS2-OR Inattention/Executive Dysfunction" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR Hyperactivity" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR Impulsivity" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR Emotional Dysregulation" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR Negative Self-Concept" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR ADHD Inattentive Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR ADHD Hyperactive/Impulsive Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR Total ADHD Symptoms" ~ glue::glue(
          "- {scale} ({description}) was {range}.\n"
        ),
        scale == "CAARS2-OR ADHD Index" ~ glue::glue(
          "- {patient}'s observer-rated {description} was {range}.\n"
        ),
        TRUE ~ as.character(result)
      )
    )
}

Finalize and save

Relocate variables

table <-
  table |>
  dplyr::relocate(
    c(raw_score, score, percentile, range, ci_95),
    .before = test
  )

table <- table |> dplyr::select(-c(guideline, elevated_items, symptom_count))

Write out csv

file_path <- here::here("csv", paste0(params$test, ".csv"))
readr::write_csv(table, file_path, col_names = TRUE, na = "")

Pluck Text

# file <- fs::fs_path(params$file)

if (params$test == "caars2_sr") {
  ## extract text
  get_text <- function(file) {
    txt <- pdftools::pdf_text(file) |>
      stringr::str_split("\n") |>
      unlist()
  }
  caars2_sr_txt <- pdftools::pdf_text(file) |>
    stringr::str_split("\n") |>
    unlist()
  caars2_sr_txt

  readr::write_lines(
    caars2_sr_txt, here::here("caars2_sr_dirty.txt"),
    sep = "\n"
  )

  # Replace long spaces with a col break symbol

  caars2_sr_squished <-
    stringr::str_replace_all(caars2_sr_txt, "\\s{2,}", "- ") |>
    stringr::str_remove_all(",")
  caars2_sr_squished

  readr::write_lines(caars2_sr_squished, here::here("caars2_sr_text.md"), sep = "\n")
  readr::write_lines(caars2_sr_squished, here::here("caars2_sr_text.txt"), sep = "\n\n")
} else {
  ## extract text
  get_text <- function(file) {
    txt <- pdftools::pdf_text(file) |>
      stringr::str_split("\n") |>
      unlist()
  }
  caars2_or_txt <- pdftools::pdf_text(file) |>
    stringr::str_split("\n") |>
    unlist()
  caars2_or_txt

  readr::write_lines(
    caars2_or_txt, here::here("caars2_or_dirty.txt"),
    sep = "\n"
  )

  # Replace long spaces with a col break symbol
  caars2_or_squished <-
    stringr::str_replace_all(caars2_or_txt, "\\s{2,}", "- ") |>
    stringr::str_remove_all(",")
  caars2_or_squished

  readr::write_lines(caars2_or_squished, here::here("caars2_or_text.md"), sep = "\n")
  readr::write_lines(caars2_or_squished, here::here("caars2_or_text.txt"), sep = "\n\n")
}

jtrampush/npsych.data documentation built on Feb. 25, 2025, 12:30 a.m.