Created
April 29, 2024 14:41
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library(tidyverse) | |
dec_labs = c("E = Escalate to the next higher dose", | |
"S = Stay at the current dose", | |
"D = De-escalate to the next lower dose", | |
"DE = De-escalate and eleminate the current and higher doses") | |
#cf BOIN design | |
db = tibble( | |
n_eval = 1:10, | |
escalate_max = c(0, 0, 0, 0, 0, 0, 1, 1, 1, 1), | |
deecalate_min = c(1, 1, 1, 1, 2, 2, 2, 2, 3, 3), | |
eliminate_min = c(NA, NA, 2, 3, 3, 3, 4, 4, 4, 5) | |
) | |
#Infos patients from CSV file | |
#pat = read.csv2("patients.csv") | |
#Example | |
pat = | |
tribble( | |
~subjid, ~dose, ~DLT, | |
1, 1, "No", | |
2, 1, "No", | |
3, 2, "No", | |
4, 2, "No", | |
5, 2, "No", | |
6, 2, "Yes", | |
7, 1, "No", | |
8, 1, "No", | |
9, 1, "Yes", | |
) | |
pat = pat %>% | |
mutate( | |
subjid = paste0("#", subjid), | |
n_dlt = cumsum(DLT=="Yes"), | |
n_eval = row_number(), | |
.by=dose | |
) %>% | |
filter(!is.na(DLT) & DLT!="") | |
x = db %>% | |
rowwise() %>% | |
mutate( | |
dose = list(0:2), | |
rows = list(tibble( | |
n_dlt = seq(0, n_eval), | |
decision = case_when( | |
n_dlt >= eliminate_min ~ "DE", | |
n_dlt >= deecalate_min ~ "D", | |
n_dlt <= escalate_max ~ "E", | |
.default = "S" | |
) | |
)) | |
) %>% | |
unnest(rows) %>% | |
unnest(dose) %>% | |
mutate( | |
decision_label = factor(decision, | |
levels = c("E", "S", "D", "DE"), | |
labels = dec_labs %>% str_wrap(40)), | |
) %>% | |
left_join(pat, by=c("n_eval", "dose", "n_dlt")) | |
x | |
p = x %>% | |
ggplot(aes(x=factor(n_eval), y=factor(n_dlt), fill=decision_label, label=decision)) + | |
geom_tile() + geom_text() + | |
geom_label(aes(label=subjid), na.rm=TRUE, fill="yellow") + | |
facet_grid(.~dose) + | |
scale_fill_manual(values = c("#5fff33", "#33d2ff", "#ff96c5", "#ff3367")) + | |
coord_fixed() + | |
labs(x="Nummber of evaluable patients treated at current dose", | |
y="Number of patients with DLT", | |
fill="Decision") + | |
theme_minimal() + | |
theme( | |
axis.line = element_blank(), | |
panel.grid.minor = element_blank(), | |
panel.grid.major.x = element_blank(), | |
legend.position="top" | |
# legend.position=c(0,1) | |
) | |
print(p) |
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Maybe we could add dates to the input and add a Gant diagram below?