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Description
Variant 5 in each template LBT13/LBT14 needs to use trim_levels_to_map with a metadata map that has the appropriate grade reference ranges. For example, in the "HIGH" direction some parameters like ALKPHSI have levels 1-4 defined. Other parameters have only a subset of levels e.g. GLUCSI has levels 3,4 only and LYMPHSI has levels 2-3 only.
- Consider whether a map helper function can be created
- Update downstream TLG-C examples as appropriate
source("https://raw.github.roche.com/NEST/nest_on_bee/master/bee_nest_utils.R")
bee_use_nest(release = "2021_10_13")
library(tern)
library(dplyr)
# STREAM data -----------------------
safety_path <- "/opt/bee/analyses/stream2/master/2.11/stream2/doc/examples/molecule/project/safety/task01/outdata_vad/"
adlb_filename <- 'adlb.sas7bdat'
adlb <- haven::read_sas(paste0(safety_path, adlb_filename))
adsl_filename <- "adsl.sas7bdat"
adsl <- haven::read_sas(paste0(safety_path, adsl_filename))
# STATIC OUTPUT for LBT14 Variant 5 ------------------
adsl_f <- adsl %>%
filter(SAFFL == "Y") %>%
df_explicit_na()
# Just choose a few params for simplicity.
adlb_f <- adlb %>%
filter(PARAMCD %in% c("ALKPHSI", "GLUCSI", "LYMPHSI")) %>%
filter(WGRHIFL == "Y" & SAFFL == "Y") %>%
df_explicit_na()
# Create new grouping variables ATOXGR_GP, BTOXGR_GP
adlb_out <- adlb_f %>% mutate(
ATOXGR_GP = case_when(
ATOXGR %in% c(0, -1, -2, -3, -4) ~ "Not High",
ATOXGR == 1 ~ "1",
ATOXGR == 2 ~ "2",
ATOXGR == 3 ~ "3",
ATOXGR == 4 ~ "4",
ATOXGR == "<Missing>" ~ "Missing"
)
) %>% mutate(
BTOXGR_GP = case_when(
BTOXGR %in% c(0, -1, -2, -3, -4) ~ "Not High",
BTOXGR == 1 ~ "1",
BTOXGR == 2 ~ "2",
BTOXGR == 3 ~ "3",
BTOXGR == 4 ~ "4",
BTOXGR == "<Missing>" ~ "Missing"
)
)
adlb_out <- adlb_out %>% mutate(
AVISIT = forcats::fct_reorder(AVISIT, AVISITN),
ATOXGR_GP = factor(ATOXGR_GP, levels = c("Not High", "1", "2", "3", "4", "Missing")),
BTOXGR_GP = factor(BTOXGR_GP, levels = c("Not High", "1", "2", "3", "4", "Missing"))
)
adlb_out <- adlb_out %>%
var_relabel(
PARAMCD = "Parameter Code",
AVISIT = "Visit",
ATOXGR_GP = "NCI-CTCAE Grade at Visit",
BTOXGR_GP = "Baseline NCI-CTCAE Grade"
)
pth <- "/opt/bee/analyses/stream2/master/current/stream2/app/metadata/__atoxgr_allhigh_ref.sas7bdat"
ref <- haven::read_sas(pth)
# Construct the map according to the "ref" dataset
map_alkph <- data.frame(
PARAMCD = rep("ALKPHSI", 36),
BTOXGR_GP = c(
rep(c("Not High", "1", "2", "3", "4", "Missing"), 6)
),
ATOXGR_GP = c(
rep(c("Not High", "1", "2", "3", "4", "Missing"), each = 6)
)
)
map_gluc <- data.frame(
PARAMCD = rep("GLUCSI", 16),
BTOXGR_GP = c(
rep(c("Not High", "3", "4", "Missing"), 4)
),
ATOXGR_GP = c(
rep(c("Not High", "3", "4", "Missing"), each = 4)
)
)
map_lymph <- data.frame(
PARAMCD = rep("LYMPHSI", 16),
BTOXGR_GP = c(
rep(c("Not High", "2", "3", "Missing"), 4)
),
ATOXGR_GP = c(
rep(c("Not High", "2", "3", "Missing"), each = 4)
)
)
map <- rbind(
map_alkph,
map_gluc,
map_lymph
)
result2 <- basic_table() %>%
split_cols_by("ACTARM") %>%
add_colcounts() %>%
split_rows_by(
"PARAMCD", split_fun = trim_levels_to_map(map), label_pos = "topleft", split_label = obj_label(adlb_out$PARAMCD)
) %>%
split_rows_by(
"BTOXGR_GP", label_pos = "topleft", split_label = obj_label(adlb_out$BTOXGR_GP)
) %>%
summarize_num_patients(var = "USUBJID", .stats = c("unique_count")) %>%
count_occurrences("ATOXGR_GP", denom = "n", drop = F) %>% #note drop = F here because we want to "Fill in"
append_varlabels(adlb_out, "ATOXGR_GP", indent = 2L) %>%
build_table(df = adlb_out, alt_counts_df = adsl_f)
Viewer(result2)