R/conv_app.R

In dylanrussellmd/nsqipr: Interact with NSQIP data via R

#' Convert targeted appendectomy columns
#'
#' @param df a data table to be cleaned
#' @param filename the name of the file from which the data table has been read in
#'
#' @details If the file being processed is a targeted appendectomy data set,
#' it will be processed by this function. This function determines how data cleaning steps specific
#' to targeted appendectomy files should proceed.
#'
#' @keywords internal
#'
conv_app_cols <- function(df, filename) {
  get_pufyear(df, filename)
  conv_(df, "app_img_ultra", conv_app_img_ultra, newcol = "app_ultra")
  conv_(df, "app_img_ct", conv_app_img_ct, newcol = "app_ct")
  data.table::setnames(df, "app_mri", "app_img_mri")
  conv_(df, "app_img_mri", conv_app_img_mri, newcol = "app_mri")
  conv_(df, "app_perfabscess", conv_app_perforation, newcol = "app_perforation")
  conv_(df, "app_perfabscess", conv_app_abscess, newcol = "app_abscess")
  conv_(df, "app_approach", conv_open_assist, newcol = "app_open_assist")
  conv_(df, "app_approach", conv_unplanned_conversion, newcol = "app_unplanned_conversion")
  conv_(df, "app_intraabscess", conv_app_intraabscess_intervention, newcol = "app_intraabscess_intervention")
  conv_(df, "app_intraabscess", conv_app_intraabscess)
}

#### ---- FACTOR LISTS (THESE DEFINE THE FACTOR LEVELS FOR VARIOUS COLUMNS) ---- #### BE SURE TO ADD THESE TO FACTOR_COLS IN COL_DEFINITIONS.R
app_img_ultra <- list(
  `Consistent with appendicitis` = "US done-consistent with appendicitis",
  `Indeterminate` = "US done-indeterminate; result uncertain",
  `Not consistent with appendicitis` = "US done-not consistent with appendicitis"
)
app_setting_ultra <- list(
  `Operating hospital` = "US in operating hospital",
  `Outside facility` = "US at outside facility"
)
app_img_ct <- list(
  `Consistent with appendicitis` = "CT done-result consistent with diagnosis of appendicitis",
  `Indeterminate` = "CT done-result indeterminate; result uncertain",
  `Not consistent with appendicitis` = "CT done-result not consistent with appendicitis"
)
app_setting_ct <- list(
  `Operating hospital` = "CT in operating hospital",
  `Outside facility` = "CT at outside facility"
)
app_img_mri <- list(
  `Consistent with appendicitis` = "Result consistent w/ diagnosis of Appendicitis",
  `Indeterminate` = "Result Indeterminate / Uncertain",
  `Not consistent with appendicitis` = 'Result Not Consistent w/ Appendicitis; Appendix \"\"Normal\"\"'
)
app_setting_mri <- list(
  `Operating hospital` = "Performed in Operating Hospital",
  `Outside facility` = "Performed at Outside Facility"
)
app_pathres <- list(
  `Consistent with appendicitis` = "Consistent with appendicitis",
  `Not consistent with appendicitis` = "Not consistent with appendicitis",
  `Indeterminate` = "Result is indeterminate or uncertain",
  `Other appendiceal pathology` = "Other appendiceal pathology",
  `Tumor/malignancy involving appendix` = "Tumor/malignancy involving appendix"
)
app_approach <- list(
  `Hybrid` = c("Hybrid", "Hybrid w/ open assist","Hybrid w/ unplanned conversion to open"),
  `Laparoscopic` = c("Laparoscopic","Laparoscopic w/ open assist","Laparoscopic w/ unplanned conversion to open"),
  `Open` = c("Open","Open (planned)"),
  `Other` = "Other",
  `Other MIS` = c("Other MIS approach","Other MIS approach w/ open assist","Other MIS approach w/ unplanned conversion to open"),
  `Robotic` = c("Robotic","Robotic w/ open assist","Robotic w/ unplanned conversion to open"),
  `Endoscopic` = c("Endoscopic","Endoscopic w/ unplanned conversion to open"),
  `SILS` = c("SILS", "SILS w/ open assist", "SILS w/ uplanned conversion to open")
)

#### ---- LONG COLUMNS ---- ####

#### ---- FUNCTIONS ---- ####

#' Parse entries that indicate an ultrasound was performed
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "us done-"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("US done-consistent with appendicitis","US not performed/not documented",
#' "US done-indeterminate; result uncertain","US done-not consistent with appendicitis", NA)
#'
#' cbind(x, nsqipr:::conv_app_img_ultra(x))
#'
conv_app_img_ultra <- function(vec) {
  stringi::stri_detect_regex(vec, "^US done-", opts_regex = list(case_insensitive = TRUE))
}

#' Parse entries that indicate a CT was performed
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "ct done-"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("CT not performed/not documented","CT done-result consistent with diagnosis of appendicitis",
#' "CT done-result not consistent with appendicitis","CT done-result indeterminate; result uncertain", NA)
#'
#' cbind(x, nsqipr:::conv_app_img_ct(x))
#'
conv_app_img_ct <- function(vec) {
  stringi::stri_detect_regex(vec, "^CT done-", opts_regex = list(case_insensitive = TRUE))
}

#' Parse entries that indicate an MRI was performed
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "result"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("MRI / Other Definitive Imaging Modality Not Performed / Not Documented","Result Indeterminate / Uncertain",
#' "Result consistent w/ diagnosis of Appendicitis",'Result Not Consistent w/ Appendicitis; Appendix "Normal"', NA)
#'
#' cbind(x, nsqipr:::conv_app_img_mri(x))
#'
conv_app_img_mri <- function(vec) {
  stringi::stri_detect_regex(vec, "^Result", opts_regex = list(case_insensitive = TRUE))
}

#' Parse entries that indicate an abscess
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "^abscess only|^perforation and abscess"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("No mention of perforation or abscess", "Perforation and abscess",
#' "Perforation only", "Abscess only", NA)
#'
#' cbind(x, nsqipr:::conv_app_abscess(x))
#'
conv_app_abscess <- function(vec) {
  stringi::stri_detect_regex(vec, "^abscess only|^perforation and abscess", opts_regex = list(case_insensitive = TRUE))
}

#' Parse entries that indicate a perforation
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "^perforation only|^perforation and abscess"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("No mention of perforation or abscess", "Perforation and abscess",
#' "Perforation only", "Abscess only", NA)
#'
#' cbind(x, nsqipr:::conv_app_perforation(x))
#'
conv_app_perforation <- function(vec) {
  stringi::stri_detect_regex(vec, "^perforation only|^perforation and abscess", opts_regex = list(case_insensitive = TRUE))
}

#' Parse entries that indicate an post-operative intraabdominal abscess
#'
#' @param vec a character vector to parse
#'
#' @details returns TRUE if case-insensitive "^yes-"
#' is detected in the character vector.
#'
#' @return a logical vector
#' @keywords internal
#' @examples
#' x <- c("No diagnosis of postoperative abscess", "Yes-percutaneous drainage",
#' "Yes-no treatment or intervention", "Yes-IV antibiotics w/out procedural intervention",
#' "Yes-oral/IM antibiotics w/out procedural intervention",
#' "Yes-reoperation for surgical drainage, open", "Yes-reoperation for surgical drainage, minimally invasive",
#' "Yes-transrectal/other endoscopic drainage", NA)
#'
#' cbind(x, nsqipr:::conv_app_intraabscess(x))
#'
conv_app_intraabscess <- function(vec) {
  stringi::stri_detect_regex(vec, "^yes-", opts_regex = list(case_insensitive = TRUE))
}

#' Parse a column for type of intra-abdominal abscess intervention
#'
#' @param vec a character vector of values to convert
#'
#' @details NSQIP encodes the \code{app_intraabscess} column as having one of multiple interventions.
#' This function extracts those values from character vectors and factors them.
#'
#' @return a factor vector
#' @keywords internal
#'
#' @examples
#' x <- c("No diagnosis of postoperative abscess", "Yes-percutaneous drainage",
#' "Yes-no treatment or intervention", "Yes-IV antibiotics w/out procedural intervention",
#' "Yes-oral/IM antibiotics w/out procedural intervention",
#' "Yes-reoperation for surgical drainage, open", "Yes-reoperation for surgical drainage, minimally invasive",
#' "Yes-transrectal/other endoscopic drainage", NA)
#'
#' nsqipr:::conv_app_intraabscess_intervention(x)
#'
conv_app_intraabscess_intervention <- function(vec) {
  vec %^% list(
    `Percutaneous drainage` = "Yes-percutaneous drainage",
    `IV antibiotics` = "Yes-IV antibiotics w/out procedural intervention",
    `PO/IM antibiotics` = "Yes-oral/IM antibiotics w/out procedural intervention",
    `Open reoperation` = "Yes-reoperation for surgical drainage, open",
    `MIS reoperation` = "Yes-reoperation for surgical drainage, minimally invasive",
    `Transrectal or other endoscopic drainage` = "Yes-transrectal/other endoscopic drainage"
  )
}