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Refactor PKPT11 to pass sanitation checks (#112)
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@edelarua
edelarua authored Sep 8, 2023
1 parent e5c4afb commit 6bad07b
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112 changes: 60 additions & 52 deletions book/tables/pharmacokinetic/pkpt11.qmd
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Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,9 @@ library(tern)
adpp <- synthetic_cdisc_dataset("latest", "adpp")
# Comparator Dose - A: Drug X
arm_var <- "TRT01A"
comp_dose <- "A: Drug X"
other_doses <- as.character(unique(adpp$TRT01A)[unique(adpp$TRT01A) != comp_dose])
other_doses <- as.character(unique(adpp[[arm_var]])[unique(adpp[[arm_var]]) != comp_dose])
adpp <- adpp %>%
filter(AVISIT == "CYCLE 1 DAY 1") %>%
Expand All @@ -31,37 +32,31 @@ adpp <- adpp %>%
)
for (dose in other_doses) {
temp_df <- adpp[adpp$TRT01A == comp_dose, ]
temp_df <- adpp[adpp[[arm_var]] == comp_dose, ]
temp_df$COMP <- paste0(dose, "/", comp_dose)
adpp <- rbind(adpp, temp_df)
}
formats <- c(
n = "xx.",
geom_mean_ratio = sprintf_format("%.3e"),
gmr_ci_lwr = sprintf_format("%.3e"),
gmr_ci_upr = sprintf_format("%.3e")
)
```
# Plasma Drug X
adpp0 <- adpp %>%
filter(PPCAT == "Plasma Drug X") %>%
h_pkparam_sort() %>%
mutate(PKPARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")"))) %>%
var_relabel(COMP = "Comparison")
## Standard Table -- Plasma
# statistics function
s_gmr <- function(df,
compare_dose = comp_dose, # comparator, defaults to comp_dose defined above (string)
denom = TRUE, # whether to use comparator as denominator, defaults to TRUE (logical)
arm_var = arm_var) { # arm variable, defaults to arm_var defined above (string)
which_num <- !grepl(compare_dose, df[[arm_var]])
```{r variant1, test = list(result_v1 = "result")}
# summary function
# compare_dose - comparator, defaults to comp_dose defined above (string)
# denom - use comparator as denominator, defaults to TRUE (logical)
s_gmr <- function(x,
labelstr = "",
compare_dose = comp_dose,
denom = TRUE) {
row_label <- labelstr
x_num <- as.numeric(x[!grepl(compare_dose, x)])
x_num <- as.numeric(df[which_num, ][["AVAL"]])
x_num <- x_num[!is.na(x_num)]
x_num_no_negative_vals <- x_num
x_num_no_negative_vals[x_num_no_negative_vals <= 0] <- NA
x_denom <- as.numeric(gsub(compare_dose, "", x[grepl(compare_dose, x)]))
x_denom <- as.numeric(gsub(compare_dose, "", df[!which_num, ][["AVAL"]]))
x_denom <- x_denom[!is.na(x_denom)]
x_denom_no_negative_vals <- x_denom
x_denom_no_negative_vals[x_denom_no_negative_vals <= 0] <- NA
Expand All @@ -73,33 +68,50 @@ s_gmr <- function(x,
geom_mean_ratio <- exp(mean(x_num_log, na.rm = FALSE)) / exp(mean(x_denom_log, na.rm = FALSE))
geom_mean_ci <- t.test(x_num_log, x_denom_log, conf.level = 0.90)$conf.int
} else {
row_label <- paste0(unlist(strsplit(labelstr, "/"))[c(2, 1)], collapse = "/")
geom_mean_ratio <- exp(mean(x_denom_log, na.rm = FALSE)) / exp(mean(x_num_log, na.rm = FALSE))
geom_mean_ci <- t.test(x_denom_log, x_num_log, conf.level = 0.90)$conf.int
}
results <- list(
n = length(x),
list(
n = nrow(df),
geom_mean_ratio = geom_mean_ratio,
gmr_ci_lwr = exp(geom_mean_ci[1]),
gmr_ci_upr = exp(geom_mean_ci[2])
)
}
afun_pk_gmr <- function(.formats = list(
n = "xx.",
geom_mean_ratio = sprintf_format("%.3e"),
gmr_ci_lwr = sprintf_format("%.3e"),
gmr_ci_upr = sprintf_format("%.3e")
),
compare_dose = comp_dose,
denom = TRUE) {
checkmate::assert_list(.formats)
checkmate::assert_subset(names(.formats), c("n", "geom_mean_ratio", "gmr_ci_lwr", "gmr_ci_upr"))
afun_lst <- Map(
function(stat, fmt, compare_dose, denom, arm_var) {
function(df, .spl_context) {
x_stat <- s_gmr(df, compare_dose = compare_dose, denom = denom, arm_var = arm_var)[[stat]]
rcell(x_stat, format = fmt, label = tail(.spl_context$value, 1))
}
},
stat = names(.formats),
fmt = .formats,
compare_dose = compare_dose,
denom = denom,
arm_var = arm_var
)
lapply(results, formatters::with_label, row_label)
afun_lst
}
```

# tabulation function
afun_list <- Map(
function(stat) {
make_afun(
s_gmr,
.stats = stat,
.formats = formats[names(formats) %in% stat]
)
},
stat = c("n", "geom_mean_ratio", "gmr_ci_lwr", "gmr_ci_upr")
)
## Standard Table -- Plasma

```{r variant1, test = list(result_v1 = "result")}
# create layout
lyt <- basic_table() %>%
split_rows_by(
Expand All @@ -110,9 +122,9 @@ lyt <- basic_table() %>%
) %>%
split_rows_by(
var = "COMP",
label_pos = "topleft",
split_label = "Comparison",
split_fun = remove_split_levels(paste0(comp_dose, "/", comp_dose))
split_fun = remove_split_levels(paste0(comp_dose, "/", comp_dose)),
indent_mod = 11L,
child_labels = "hidden"
) %>%
split_cols_by_multivar(
vars = rep("AVAL", 4),
Expand All @@ -123,29 +135,26 @@ lyt <- basic_table() %>%
"90% CI Upper Bound"
)
) %>%
summarize_row_groups(
var = "COMP_AVAL",
cfun = afun_list,
analyze_colvars(
afun = afun_pk_gmr(),
extra_args = list(
compare_dose = comp_dose,
denom = TRUE
denom = TRUE,
arm_var = arm_var
)
)
) %>%
append_varlabels(adpp0, "COMP", 12L)
# Plasma Drug X
adpp0 <- adpp %>%
filter(PPCAT == "Plasma Drug X") %>%
h_pkparam_sort() %>%
mutate(PKPARAM = factor(paste0(TLG_DISPLAY, " (", AVALU, ")")))
result <- build_table(lyt, df = adpp0)
main_title(result) <- paste0(
"Estimated Ratios of Geometric Means and 90% Confidence Intervals for AUC and CMAX Following ",
unique(adpp0$REGIMEN), "\nof ", comp_dose, " in Comparison with ",
paste(other_doses, collapse = " & "), ", PK Population"
)
subtitles(result) <- paste("Analyte:", unique(adpp0$PPCAT))
cat(rtables::toString(result, indent_size = 24))
result
```

{{< include ../../test-utils/save_results.qmd >}}
Expand All @@ -159,5 +168,4 @@ cat(rtables::toString(result, indent_size = 24))
```

{{< include ../../repro.qmd >}}

:::
16 changes: 8 additions & 8 deletions package/tests/testthat/_snaps/pkpt11/markdown-snaps.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,12 +7,12 @@
of A: Drug X in Comparison with C: Combination, PK Population
Analyte: Plasma Drug X
—————————————————————————————————————————————————————————————————————————————————————————————————
PK Parameter
Comparison n Geometric Mean Ratio 90% CI Lower Bound 90% CI Upper Bound
—————————————————————————————————————————————————————————————————————————————————————————————————
AUCinf obs (day*ug/mL)
C: Combination/A: Drug X 266 9.615e-01 9.247e-01 9.998e-01
Cmax (ug/mL)
C: Combination/A: Drug X 266 9.974e-01 9.583e-01 1.038e+00
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
PK Parameter
Comparison n Geometric Mean Ratio 90% CI Lower Bound 90% CI Upper Bound
———————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
AUCinf obs (day*ug/mL)
C: Combination/A: Drug X 266 9.615e-01 9.247e-01 9.998e-01
Cmax (ug/mL)
C: Combination/A: Drug X 266 9.974e-01 9.583e-01 1.038e+00

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