Nothing
R/ae_listing.R
In forestly: Interactive Forest Plot
Defines functions
format_ae_listing
propercase
collect_ae_listing
# Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
# All rights reserved.
#
# This file is part of the forestly program.
#
# forestly is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#' Add inference information for AE listing analysis
#'
#' @param outdata An `outdata` object created by [prepare_ae_specific()].
#' @param display A vector with name of variable used to display on AE listing.
#'
#' @return An `outdata` object after adding AE listing information.
#'
#' @noRd
#'
#' @examples
#' meta <- metalite.ae::meta_ae_example()
#' outdata <- meta |>
#' metalite.ae::prepare_ae_specific("apat", "wk12", "rel") |>
#' collect_ae_listing()
#'
#' lapply(outdata, head, 10)
collect_ae_listing <- function(
outdata,
display = c(
"USUBJID", "SEX", "RACE", "AGE", "ASTDY", "AESEV", "AESER",
"AEREL", "AEACN", "AEOUT", "SITEID", "ADURN", "ADURU"
)) {
obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
obs <- metalite::collect_observation_record(
outdata$meta,
outdata$population,
outdata$observation,
outdata$parameter,
var = c(par_var, par_var_soc, obs_group, display)
)
# Keep variable used to display only
outdata$ae_listing <- obs[, c(par_var, par_var_soc, obs_group, display)]
# Get all labels from the un-subset data
listing_label <- get_label(obs)
# Assign labels
outdata$ae_listing <- assign_label(
data = outdata$ae_listing,
var = names(outdata$ae_listing),
label = listing_label[match(names(outdata$ae_listing), names(listing_label))]
)
outdata
}
#' Convert character strings to proper case
#'
#' @param x A character vector.
#'
#' @return A character vector.
#'
#' @noRd
#'
#' @examples
#' propercase("AbCDe FGha")
propercase <- function(x) paste0(toupper(substr(x, 1, 1)), tolower(substring(x, 2)))
#' Format AE listing analysis
#'
#' @param outdata An `outdata` object created by [prepare_ae_specific()].
#' @param display_unique_records A logical value to display only unique records
#' on AE listing table.
#'
#' @return An `outdata` object after adding AE listing information.
#'
#' @noRd
#'
#' @examples
#' meta <- metalite.ae::meta_ae_example()
#' outdata <- metalite.ae::prepare_ae_specific(meta, "apat", "wk12", "rel") |>
#' collect_ae_listing(
#' c(
#' "USUBJID", "SEX", "RACE", "AGE", "ASTDY", "AESEV", "AESER",
#' "AEREL", "AEACN", "AEOUT", "SITEID", "ADURN", "ADURU", "AOCCPFL"
#' )
#' ) |>
#' format_ae_listing()
#'
#' lapply(outdata, head, 20)
format_ae_listing <- function(outdata, display_unique_records = FALSE) {
res <- outdata$ae_listing
obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
new_name <- c("SITEID", "SITENUM", "USUBJID", "SUBJID", "SEX", "RACE", "AGE", obs_group, "EPOCH",
"ASTDY", par_var, par_var_soc, "ADURN", "AESEV", "AESER", "AEREL", "AREL", "AEACN",
"AEOUT", "AEDOSDUR", "ATOXGRN")
name_mapping <- c("Site_Number", "Site_Number", "Unique_Participant_ID", "Participant_ID", "Gender", "Race", "Age", "Treatment_Group", "Onset_Epoch",
"Relative_Day_of_Onset", "Adverse_Event", "SOC_Name", "Duration", "Intensity", "Serious", "Related", "Related", "Action_Taken",
"Outcome", "Total_Dose_on_Day_of_AE_Onset", "Maximum_Toxicity_Grade")
names(name_mapping) <- new_name
res_columns <- lapply(names(res), function(x) {
if (toupper(x) %in% names(name_mapping)) {name_mapping[[toupper(x)]]}
else {x}
}) |> unlist()
# Site ID
if ("SITEID" %in% toupper(names(res))) {
res$Site_Number <- propercase(res$SITEID)
}
if ("SITENUM" %in% toupper(names(res))) {
res$Site_Number <- res$SITENUM
}
# Participant ID
if ("USUBJID" %in% toupper(names(res))) {
res$Unique_Participant_ID <- res$USUBJID
}
if ("SUBJID" %in% toupper(names(res))) {
res$Participant_ID <- res$SUBJID
}
attr(res$Participant_ID, "label") <- NULL
res$Gender <- tools::toTitleCase(res$SEX)
res$Race <- tools::toTitleCase(tolower(res$RACE))
res$Age <- res$AGE
res$Treatment_Group <- res[[obs_group]]
attr(res$Treatment_Group, "label") <- NULL
# Onset epoch
if ("EPOCH" %in% toupper(names(res))) {
res$Onset_Epoch <- tools::toTitleCase(tolower(res$EPOCH)) # propcase the EPOCH
}
# Relative day of onset (ASTDY)
if ("ASTDY" %in% toupper(names(res))) {
res$Relative_Day_of_Onset <- res$ASTDY
}
# SOC
res$SOC_Name <- res[[par_var_soc]]
# Adverse event
res$Adverse_Event <- propercase(res[[par_var]])
res <- res[, !(names(res) == par_var)]
# Duration
if ("ADURN" %in% toupper(names(res)) & "ADURU" %in% toupper(names(res))) {
res$Duration <- paste(ifelse(is.na(res$ADURN), "", as.character(res$ADURN)), tools::toTitleCase(tolower(res$ADURU)), sep = " ") # AE duration with unit
if (length(res$Duration > 0)){
for (i in 1:length(res$Duration)) {
if (is.na(res$ADURN[i])) {
res$Duration[i] <- ifelse(charmatch(toupper(res$AEOUT[i]), "RECOVERING/RESOLVING") > 0 |
charmatch(toupper(res$AEOUT[i]), "NOT RECOVERED/NOT RESOLVED") > 0, "Continuing", "Unknown")
}
}
}
res <- res[,!(names(res) %in% "ADURU")]
res_columns <- res_columns[!(res_columns %in% "ADURU")]
}
# Intensity
if ("AESEV" %in% toupper(names(res))) {
res$Intensity <- propercase(res$AESEV)
}
# Maximum toxicity grade
if ("ATOXGRN" %in% toupper(names(res))) {
res$Maximum_Toxicity_Grade <- res$ATOXGRN
}
# Serious
if ("AESER" %in% toupper(names(res))) {
res$Serious <- propercase(res$AESER)
}
# AE related
if ("AEREL" %in% toupper(names(res))) {
res$Related <- ifelse(res$AEREL == "RELATED", "Y", ifelse(
toupper(res$AEREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AEREL))
))
}
if ("AREL" %in% toupper(names(res))) {
res$Related <- ifelse(res$AREL == "RELATED", "Y", ifelse(
toupper(res$AREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AREL))
))
}
# Action taken
if ("AEACN" %in% toupper(names(res))) {
if (length(res$AEACN > 0)) {
for (i in 1:length(res$AEACN)) {
res$Action_Taken[i] <- switch(res$AEACN[i],
"DOSE NOT CHANGED" = "None",
"DOSE REDUCED" = "Reduced",
"DRUG INTERRUPTED" = "Interrupted",
"DOSE INCREASED" = "Increased",
"NOT APPLICABLE" = "N/A",
"UNKNOWN" = "Unknown",
tools::toTitleCase(tolower(res$AEACN[i]))
)
}
} else {
res$Action_Taken <- res$AEACN
}
}
# Outcome
if ("AEOUT" %in% toupper(names(res))) {
if (length(res$AEOUT > 0)) {
for (i in 1:length(res$AEOUT)) {
res$Outcome[i] <- switch(res$AEOUT[i],
"RECOVERED/RESOLVED" = "Resolved",
"RECOVERING/RESOLVING" = "Resolving",
"RECOVERED/RESOLVED WITH SEQUELAE" = "Sequelae",
"NOT RECOVERED/NOT RESOLVED" = "Not Resolved",
tools::toTitleCase(tolower(res$AEOUT[i]))
)
}
} else {
res$Outcome <- res$AEOUT
}
}
# Total dose on day of AE onset
if ("AEDOSDUR" %in% toupper(names(res))) {
res$ymd <- substring(res$AEDOSDUR, unlist(gregexpr("/P", res$AEDOSDUR)) + 2)
res$Total_Dose_on_Day_of_AE_Onset <- ""
print(length(res$AEDOSDUR))
print(nrow(res$AEDOSDUR))
if (length(res$AEDOSDUR) > 0){
for (i in 1:length(res$AEDOSDUR)) {
if (unlist(gregexpr("Y", res$ymd[i])) > 0) {
val_year <- substring(res$ymd[i], 1, unlist(gregexpr("Y", res$ymd[i])) - 1)
if (as.numeric(val_year) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], val_year, " years")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], "1 year")
}
res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("Y", res$ymd[i])) + 1)
}
if (unlist(gregexpr("M", res$ymd[i])) > 0) {
val_month <- substring(res$ymd[i], 1, unlist(gregexpr("M", res$ymd[i])) - 1)
if (as.numeric(val_month) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_month, " months")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 month")
}
res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("M", res$ymd[i])) + 1)
}
if (unlist(gregexpr("D", res$ymd[i])) > 0) {
val_day <- substring(res$ymd[i], 1, unlist(gregexpr("D", res$ymd[i])) - 1)
if (as.numeric(val_day) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_day, " days")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 day")
}
}
}
} else {
res$Total_Dose_on_Day_of_AE_Onset <- res$AEDOSDUR
}
res <- res[, !(names(res) == "ymd"), drop = FALSE]
}
# Customized variable will use label as column header in
# drill down listing on interactive forest plot
if (!display_unique_records) {
outdata$ae_listing <- res[, res_columns]
} else {
outdata$ae_listing <- res[, res_columns] |> unique()
}
# Get all labels from the un-subset data
listing_label <- get_label(res)
listing_label <- gsub("_", " ", listing_label)
# Assign labels
outdata$ae_listing <- assign_label(
data = outdata$ae_listing,
var = names(outdata$ae_listing),
label = listing_label[match(names(outdata$ae_listing), names(listing_label))]
)
outdata
}
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Defines functions format_ae_listing propercase collect_ae_listing
# Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
# All rights reserved.
#
# This file is part of the forestly program.
#
# forestly is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#' Add inference information for AE listing analysis
#'
#' @param outdata An `outdata` object created by [prepare_ae_specific()].
#' @param display A vector with name of variable used to display on AE listing.
#'
#' @return An `outdata` object after adding AE listing information.
#'
#' @noRd
#'
#' @examples
#' meta <- metalite.ae::meta_ae_example()
#' outdata <- meta |>
#' metalite.ae::prepare_ae_specific("apat", "wk12", "rel") |>
#' collect_ae_listing()
#'
#' lapply(outdata, head, 10)
collect_ae_listing <- function(
outdata,
display = c(
"USUBJID", "SEX", "RACE", "AGE", "ASTDY", "AESEV", "AESER",
"AEREL", "AEACN", "AEOUT", "SITEID", "ADURN", "ADURU"
)) {
obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
obs <- metalite::collect_observation_record(
outdata$meta,
outdata$population,
outdata$observation,
outdata$parameter,
var = c(par_var, par_var_soc, obs_group, display)
)
# Keep variable used to display only
outdata$ae_listing <- obs[, c(par_var, par_var_soc, obs_group, display)]
# Get all labels from the un-subset data
listing_label <- get_label(obs)
# Assign labels
outdata$ae_listing <- assign_label(
data = outdata$ae_listing,
var = names(outdata$ae_listing),
label = listing_label[match(names(outdata$ae_listing), names(listing_label))]
)
outdata
}
#' Convert character strings to proper case
#'
#' @param x A character vector.
#'
#' @return A character vector.
#'
#' @noRd
#'
#' @examples
#' propercase("AbCDe FGha")
propercase <- function(x) paste0(toupper(substr(x, 1, 1)), tolower(substring(x, 2)))
#' Format AE listing analysis
#'
#' @param outdata An `outdata` object created by [prepare_ae_specific()].
#' @param display_unique_records A logical value to display only unique records
#' on AE listing table.
#'
#' @return An `outdata` object after adding AE listing information.
#'
#' @noRd
#'
#' @examples
#' meta <- metalite.ae::meta_ae_example()
#' outdata <- metalite.ae::prepare_ae_specific(meta, "apat", "wk12", "rel") |>
#' collect_ae_listing(
#' c(
#' "USUBJID", "SEX", "RACE", "AGE", "ASTDY", "AESEV", "AESER",
#' "AEREL", "AEACN", "AEOUT", "SITEID", "ADURN", "ADURU", "AOCCPFL"
#' )
#' ) |>
#' format_ae_listing()
#'
#' lapply(outdata, head, 20)
format_ae_listing <- function(outdata, display_unique_records = FALSE) {
res <- outdata$ae_listing
obs_group <- metalite::collect_adam_mapping(outdata$meta, outdata$observation)$group
par_var <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$var
par_var_soc <- metalite::collect_adam_mapping(outdata$meta, outdata$parameter)$soc
new_name <- c("SITEID", "SITENUM", "USUBJID", "SUBJID", "SEX", "RACE", "AGE", obs_group, "EPOCH",
"ASTDY", par_var, par_var_soc, "ADURN", "AESEV", "AESER", "AEREL", "AREL", "AEACN",
"AEOUT", "AEDOSDUR", "ATOXGRN")
name_mapping <- c("Site_Number", "Site_Number", "Unique_Participant_ID", "Participant_ID", "Gender", "Race", "Age", "Treatment_Group", "Onset_Epoch",
"Relative_Day_of_Onset", "Adverse_Event", "SOC_Name", "Duration", "Intensity", "Serious", "Related", "Related", "Action_Taken",
"Outcome", "Total_Dose_on_Day_of_AE_Onset", "Maximum_Toxicity_Grade")
names(name_mapping) <- new_name
res_columns <- lapply(names(res), function(x) {
if (toupper(x) %in% names(name_mapping)) {name_mapping[[toupper(x)]]}
else {x}
}) |> unlist()
# Site ID
if ("SITEID" %in% toupper(names(res))) {
res$Site_Number <- propercase(res$SITEID)
}
if ("SITENUM" %in% toupper(names(res))) {
res$Site_Number <- res$SITENUM
}
# Participant ID
if ("USUBJID" %in% toupper(names(res))) {
res$Unique_Participant_ID <- res$USUBJID
}
if ("SUBJID" %in% toupper(names(res))) {
res$Participant_ID <- res$SUBJID
}
attr(res$Participant_ID, "label") <- NULL
res$Gender <- tools::toTitleCase(res$SEX)
res$Race <- tools::toTitleCase(tolower(res$RACE))
res$Age <- res$AGE
res$Treatment_Group <- res[[obs_group]]
attr(res$Treatment_Group, "label") <- NULL
# Onset epoch
if ("EPOCH" %in% toupper(names(res))) {
res$Onset_Epoch <- tools::toTitleCase(tolower(res$EPOCH)) # propcase the EPOCH
}
# Relative day of onset (ASTDY)
if ("ASTDY" %in% toupper(names(res))) {
res$Relative_Day_of_Onset <- res$ASTDY
}
# SOC
res$SOC_Name <- res[[par_var_soc]]
# Adverse event
res$Adverse_Event <- propercase(res[[par_var]])
res <- res[, !(names(res) == par_var)]
# Duration
if ("ADURN" %in% toupper(names(res)) & "ADURU" %in% toupper(names(res))) {
res$Duration <- paste(ifelse(is.na(res$ADURN), "", as.character(res$ADURN)), tools::toTitleCase(tolower(res$ADURU)), sep = " ") # AE duration with unit
if (length(res$Duration > 0)){
for (i in 1:length(res$Duration)) {
if (is.na(res$ADURN[i])) {
res$Duration[i] <- ifelse(charmatch(toupper(res$AEOUT[i]), "RECOVERING/RESOLVING") > 0 |
charmatch(toupper(res$AEOUT[i]), "NOT RECOVERED/NOT RESOLVED") > 0, "Continuing", "Unknown")
}
}
}
res <- res[,!(names(res) %in% "ADURU")]
res_columns <- res_columns[!(res_columns %in% "ADURU")]
}
# Intensity
if ("AESEV" %in% toupper(names(res))) {
res$Intensity <- propercase(res$AESEV)
}
# Maximum toxicity grade
if ("ATOXGRN" %in% toupper(names(res))) {
res$Maximum_Toxicity_Grade <- res$ATOXGRN
}
# Serious
if ("AESER" %in% toupper(names(res))) {
res$Serious <- propercase(res$AESER)
}
# AE related
if ("AEREL" %in% toupper(names(res))) {
res$Related <- ifelse(res$AEREL == "RELATED", "Y", ifelse(
toupper(res$AEREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AEREL))
))
}
if ("AREL" %in% toupper(names(res))) {
res$Related <- ifelse(res$AREL == "RELATED", "Y", ifelse(
toupper(res$AREL) == "NOT RELATED", "N", tools::toTitleCase(tolower(res$AREL))
))
}
# Action taken
if ("AEACN" %in% toupper(names(res))) {
if (length(res$AEACN > 0)) {
for (i in 1:length(res$AEACN)) {
res$Action_Taken[i] <- switch(res$AEACN[i],
"DOSE NOT CHANGED" = "None",
"DOSE REDUCED" = "Reduced",
"DRUG INTERRUPTED" = "Interrupted",
"DOSE INCREASED" = "Increased",
"NOT APPLICABLE" = "N/A",
"UNKNOWN" = "Unknown",
tools::toTitleCase(tolower(res$AEACN[i]))
)
}
} else {
res$Action_Taken <- res$AEACN
}
}
# Outcome
if ("AEOUT" %in% toupper(names(res))) {
if (length(res$AEOUT > 0)) {
for (i in 1:length(res$AEOUT)) {
res$Outcome[i] <- switch(res$AEOUT[i],
"RECOVERED/RESOLVED" = "Resolved",
"RECOVERING/RESOLVING" = "Resolving",
"RECOVERED/RESOLVED WITH SEQUELAE" = "Sequelae",
"NOT RECOVERED/NOT RESOLVED" = "Not Resolved",
tools::toTitleCase(tolower(res$AEOUT[i]))
)
}
} else {
res$Outcome <- res$AEOUT
}
}
# Total dose on day of AE onset
if ("AEDOSDUR" %in% toupper(names(res))) {
res$ymd <- substring(res$AEDOSDUR, unlist(gregexpr("/P", res$AEDOSDUR)) + 2)
res$Total_Dose_on_Day_of_AE_Onset <- ""
print(length(res$AEDOSDUR))
print(nrow(res$AEDOSDUR))
if (length(res$AEDOSDUR) > 0){
for (i in 1:length(res$AEDOSDUR)) {
if (unlist(gregexpr("Y", res$ymd[i])) > 0) {
val_year <- substring(res$ymd[i], 1, unlist(gregexpr("Y", res$ymd[i])) - 1)
if (as.numeric(val_year) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], val_year, " years")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], "1 year")
}
res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("Y", res$ymd[i])) + 1)
}
if (unlist(gregexpr("M", res$ymd[i])) > 0) {
val_month <- substring(res$ymd[i], 1, unlist(gregexpr("M", res$ymd[i])) - 1)
if (as.numeric(val_month) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_month, " months")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 month")
}
res$ymd[i] <- substring(res$ymd[i], unlist(gregexpr("M", res$ymd[i])) + 1)
}
if (unlist(gregexpr("D", res$ymd[i])) > 0) {
val_day <- substring(res$ymd[i], 1, unlist(gregexpr("D", res$ymd[i])) - 1)
if (as.numeric(val_day) != 1) {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " ", val_day, " days")
} else {
res$Total_Dose_on_Day_of_AE_Onset[i] <- paste0(res$Total_Dose_on_Day_of_AE_Onset[i], " 1 day")
}
}
}
} else {
res$Total_Dose_on_Day_of_AE_Onset <- res$AEDOSDUR
}
res <- res[, !(names(res) == "ymd"), drop = FALSE]
}
# Customized variable will use label as column header in
# drill down listing on interactive forest plot
if (!display_unique_records) {
outdata$ae_listing <- res[, res_columns]
} else {
outdata$ae_listing <- res[, res_columns] |> unique()
}
# Get all labels from the un-subset data
listing_label <- get_label(res)
listing_label <- gsub("_", " ", listing_label)
# Assign labels
outdata$ae_listing <- assign_label(
data = outdata$ae_listing,
var = names(outdata$ae_listing),
label = listing_label[match(names(outdata$ae_listing), names(listing_label))]
)
outdata
}
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