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refactor and fix: lintr cleaning and filtering issue after select
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@Gero1999
Gero1999 committed Jan 31, 2025
1 parent 0fa8ab3 commit 7eaa42f
Showing 1 changed file with 75 additions and 98 deletions.
173 changes: 75 additions & 98 deletions R/l_pkconc.R
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Original file line number Diff line number Diff line change
@@ -1,23 +1,3 @@
# Define variables
adpc = read.csv("inst/shiny/data/DummyRO_ADNCA.csv")
listgroup_vars = c("PARAM", "PCSPEC", "ROUTE")
grouping_vars = c("TRT01A", "USUBJID", "AVISIT")
displaying_vars = c("NFRLT", "AFRLT", "AVAL")
formatting_vars_table = NULL
subtitle_lists = NULL
footnote_table = "*: Patients excluded from the summary table and mean plots"

# Define labels
attr(adpc[["AFRLT"]], "label") <- "Actual time from first dose"
attr(adpc[["NFRLT"]], "label") <- "Planned time from first dose"
attr(adpc[["AVAL"]], "label") <- "Analysis value"
attr(adpc[["PARAM"]], "label") <- "Analyte"
attr(adpc[["TRT01A"]], "label") <- "Actual treatment"
attr(adpc[["PCSPEC"]], "label") <- "Specimen"
attr(adpc[["ROUTE"]], "label") <- "Administration"
attr(adpc[["USUBJID"]], "label") <- "Unique Subject ID"
attr(adpc[["AVISIT"]], "label") <- "Actual visit"

#' Create PK Concentration Listing
#'
#' This function creates a listing of pharmacokinetic (PK) concentration data by treatment group,
Expand Down Expand Up @@ -60,140 +40,137 @@ attr(adpc[["AVISIT"]], "label") <- "Actual visit"
#' @export
#' @author Gerardo Rodriguez
l_pkconc <- function(
adpc = read.csv("inst/shiny/data/DummyRO_ADNCA.csv"),
listgroup_vars = c("PARAM", "PCSPEC", "ROUTE"),
grouping_vars = c("TRT01A", "USUBJID", "AVISIT"),
displaying_vars = c("NFRLT", "AFRLT", "AVAL"),
formatting_vars_table = NULL,
subtitle_lists = NULL,
footnote_table = "*: Patients excluded from the summary table and mean plots"
adpc = read.csv("inst/shiny/data/DummyRO_ADNCA.csv"),
listgroup_vars = c("PARAM", "PCSPEC", "ROUTE"),
grouping_vars = c("TRT01A", "USUBJID", "AVISIT"),
displaying_vars = c("NFRLT", "AFRLT", "AVAL"),
formatting_vars_table = NULL,
subtitle_lists = NULL,
footnote_table = "*: Patients excluded from the summary table and mean plots"
) {

# If there are columns defined in the function that are not in the data, throw an error
missing_cols <- setdiff(c(grouping_vars, displaying_vars), colnames(adpc))
if (length(missing_cols) > 0) {
stop(paste("Missing required columns:", paste(missing_cols, collapse = ",")))
}

# If the title was not user defined use the listgroup_vars argument to do it
if (is.null(subtitle_lists)) {
subtitle_lists <- paste(paste0("!", listgroup_vars),
paste0("$",listgroup_vars),
paste0("$", listgroup_vars),
sep = ": ",
collapse = "\n")
}

# If the formatting table was not user defined make one standard
if (is.null(formatting_vars_table)) {
# Create a dataframe with rows c(grouping_Vars, displaying_vars) and columns c("Variable name", "Label", "Digits")
formatting_vars_table <- data.frame(
var_name = c(grouping_vars, displaying_vars)
) %>%
rowwise() %>%
) %>%
rowwise() %>%
# Create a label column
mutate(Label = parse_annotation(adpc, paste0("!", var_name)),
na_str = "NA",
cero_str = ifelse(var_name == "AVAL", "BLQ", "0"),
align = "center",
# ToDo: Mateusz // Check formatters::list_valid_format_labels() for input list
format_fun = ifelse(is.numeric(adpc[[var_name]]) &&
!is.integer(adpc[[var_name]]), "round", NA),
digits = ifelse(is.numeric(adpc[[var_name]]) &&
!is.integer(adpc[[var_name]]), 3, NA),
unit = case_when(var_name == "AVAL" & "AVALU" %in% names(adpc) ~ "AVALU",
var_name %in% c("NFRLT", "AFRLT") & "RRLTU" %in% names(adpc) ~ "RRLTU",
TRUE ~ NA
)
) %>%
mutate(
Label = parse_annotation(adpc, paste0("!", var_name)),
na_str = "NA",
cero_str = ifelse(var_name == "AVAL", "BLQ", "0"),
align = "center",
format_fun = ifelse(is.numeric(adpc[[var_name]]) &&
!is.integer(adpc[[var_name]]), "round", NA),
digits = ifelse(is.numeric(adpc[[var_name]]) &&
!is.integer(adpc[[var_name]]), 3, NA),
unit = case_when(var_name == "AVAL" & "AVALU" %in% names(adpc) ~ "AVALU",
var_name %in% c("NFRLT", "AFRLT") & "RRLTU" %in% names(adpc) ~ "RRLTU",
TRUE ~ NA)
) %>%
ungroup()
}

# Create the proper object from the UI table for col_formatting
formatting_vars_list <- lapply(1:nrow(formatting_vars_table), function(i){
row <- formatting_vars_table[i,]
formatting_vars_list <- lapply(seq_len(nrow(formatting_vars_table)), function(i) {
row <- formatting_vars_table[i, ]
fmt_config(na_str = row$na_str,
format = NULL,
align = row$align
)
}) %>%
align = row$align)
}) %>%
setNames(nm = formatting_vars_table$var_name)

# Create a special object to map 0 string values to each variable
format_cero <- formatting_vars_table %>%
select(var_name, cero_str) %>%
format_cero <- formatting_vars_table %>%
select(var_name, cero_str) %>%
pull(cero_str, var_name)

# Create a special pair of objects to map number of digits to each variable
format_digits <- formatting_vars_table %>%
select(var_name, digits) %>%
filter(!is.na(format_fun) & !is.na(format_digits)) %>%
format_digits <- formatting_vars_table %>%
filter(!is.na(format_fun) & !is.na(digits)) %>%
select(var_name, digits) %>%
pull(digits, var_name)
format_funs <- formatting_vars_table %>%
select(var_name, format_fun) %>%
filter(!is.na(format_fun) & !is.na(format_digits)) %>%

format_funs <- formatting_vars_table %>%
filter(!is.na(format_fun) & !is.na(digits)) %>%
select(var_name, format_fun) %>%
pull(format_fun, var_name)

# Create a special object to map unit columns to each variable
format_unit <- formatting_vars_table %>%
select(var_name, unit) %>%
filter(!is.na(unit)) %>%
format_unit <- formatting_vars_table %>%
select(var_name, unit) %>%
filter(!is.na(unit)) %>%
pull(unit, var_name)

# Group the data based on the listgroup_vars
adpc_grouped <- adpc %>%
mutate(across(all_of(listgroup_vars), as.character)) %>%
rowwise() %>%
adpc_grouped <- adpc %>%
mutate(across(all_of(listgroup_vars), as.character)) %>%
rowwise() %>%
dplyr::mutate(id_list = interaction(!!!syms(listgroup_vars))) %>%

# Format number of digits
mutate(across(all_of(names(format_digits)), ~
do.call(format_funs[cur_column()],
list(x = ., digits = format_digits[cur_column()]))
)) %>%

mutate(across(
all_of(names(format_digits)), ~
do.call(format_funs[cur_column()],
list(x = ., digits = format_digits[cur_column()]))
)) %>%

# Format 0 values as defined by format_cero
mutate(across(all_of(names(format_cero)), ~
ifelse(. == 0, format_cero[cur_column()], as.character(.))
mutate(across(
all_of(names(format_cero)), ~
ifelse(. == 0, format_cero[cur_column()], as.character(.))
))

# Make sure the data stays labelled
var_labels(adpc_grouped) = c(var_labels(adpc), id_list = "id")
var_labels(adpc_grouped) <- c(var_labels(adpc), id_list = "id")

# Split the lists based on the listgroup_vars
lapply(unique(adpc_grouped[["id_list"]]), \(id_val) {

data <- adpc_grouped %>% dplyr::filter(id_list == id_val)
list_data = data %>% select(any_of(c(grouping_vars, displaying_vars, unname(format_unit))))


list_data <- adpc_grouped %>% dplyr::filter(id_list == id_val)

# For those variables with units specified include them in their labels for the table
for (var_with_unit in names(format_unit)) {
unit_val <- unique(data[[format_unit[var_with_unit]]])
unit_val <- unique(list_data[[format_unit[var_with_unit]]])
if (length(unit_val) != 1) {
warning(paste0("pkcl01, but not unique unit in ", id_val, " for ",
var_with_unit, " :", paste(unit_val, collapse = ", ")))
}
attr(list_data[[var_with_unit]], "label") <- paste0(attr(list_data[[var_with_unit]], "label"),
" (",
paste0(unit_val, collapse = ","),
paste0(unit_val, collapse = ","),
")")
}

rl <- rlistings::as_listing(
df = list_data,
key_cols = grouping_vars,
disp_cols = displaying_vars,
main_title = "Listing of PK Concentration by Treatment Group, Subject and Nominal Time, PK Population",
main_title = "Listing of PK Concentration by Treatment Group,
Subject and Nominal Time, PK Population",
subtitles = gsub("<br>", "\n", parse_annotation(data = data,
text = subtitle_lists)),
text = subtitle_lists)),
main_footer = parse_annotation(data = data,
text = footnote_table),
col_formatting = formatting_vars_list
)
}) %>%

}) %>%

setNames(unique(adpc_grouped[["id_list"]]))
}

l_pkconc(adpc = adpc)

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