a_patyrs_j {junco}R Documentation

Patient years exposure

Description

Statistical/Analysis Function for presenting Patient years exposure summary data

Usage

s_patyrs_j(
  df,
  .var,
  id = "USUBJID",
  .alt_df_full,
  source = c("alt_df", "df"),
  inriskdiffcol = FALSE
)

a_patyrs_j(
  df,
  .var,
  .df_row,
  id = "USUBJID",
  .alt_df_full = NULL,
  .formats = NULL,
  .labels = NULL,
  source = c("alt_df", "df"),
  .spl_context,
  .stats = "patyrs"
)

Arguments

df

(data.frame)
data set containing all analysis variables.

.var

(string)
variable name containing the patient years data.

id

(string)
subject variable name.

.alt_df_full

(dataframe)
alternative dataset for calculations.

source

(string)
source of data, either "alt_df" or "df".

inriskdiffcol

(logical)
flag indicating if the function is called within a risk difference column.

.df_row

(data.frame)
data frame across all of the columns for the given row split.

.formats

(named 'character' or 'list')
formats for the statistics.

.labels

(named 'character')
labels for the statistics.

.spl_context

(data.frame)
gives information about ancestor split states.

.stats

(character)
statistics to select for the table.

Value

Functions

Examples

library(tern)
library(dplyr)
trtvar <- "ARM"
ctrl_grp <- "B: Placebo"
cutoffd <- as.Date("2023-09-24")


adexsum <- ex_adsl %>%
  create_colspan_var(
    non_active_grp          = ctrl_grp,
    non_active_grp_span_lbl = " ",
    active_grp_span_lbl     = "Active Study Agent",
    colspan_var             = "colspan_trt",
    trt_var                 = trtvar
  ) %>%
  mutate(
    rrisk_header = "Risk Difference (95% CI)",
    rrisk_label = paste(!!rlang::sym(trtvar), "vs", ctrl_grp),
    TRTDURY = case_when(
      !is.na(EOSDY) ~ EOSDY,
      TRUE ~ as.integer(cutoffd - as.Date(TRTSDTM) + 1)
    )
  ) %>%
  select(USUBJID, !!rlang::sym(trtvar), colspan_trt, rrisk_header, rrisk_label, TRTDURY)

adae <- ex_adae %>%
  group_by(USUBJID, AEDECOD) %>%
  select(USUBJID, AEDECOD, ASTDY) %>%
  mutate(rwnum = row_number()) %>%
  mutate(AOCCPFL = case_when(
    rwnum == 1 ~ "Y",
    TRUE ~ NA
  )) %>%
  filter(AOCCPFL == "Y")

aefup <- left_join(adae, adexsum, by = "USUBJID")

colspan_trt_map <- create_colspan_map(adexsum,
  non_active_grp = ctrl_grp,
  non_active_grp_span_lbl = " ",
  active_grp_span_lbl = "Active Study Agent",
  colspan_var = "colspan_trt",
  trt_var = trtvar
)

ref_path <- c("colspan_trt", " ", trtvar, ctrl_grp)

lyt <- basic_table(show_colcounts = TRUE, colcount_format = "N=xx", top_level_section_div = " ") %>%
  split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) %>%
  split_cols_by(trtvar) %>%
  split_cols_by("rrisk_header", nested = FALSE) %>%
  split_cols_by(trtvar, labels_var = "rrisk_label", split_fun = remove_split_levels(ctrl_grp)) %>%
  analyze("TRTDURY",
    nested = FALSE,
    show_labels = "hidden",
    afun = a_patyrs_j
  )
result <- build_table(lyt, aefup, alt_counts_df = adexsum)
result


[Package junco version 0.1.1 Index]