Simulated trial data

Published

July 29, 2024

Modified

July 29, 2024

The following give a sense of the number of participants contributing to each treatment arm and cell. The data are simulated under the model specification with a total sample size of 2500.

Code

set.seed(1)










ll <- get_trial_data(N = 2500)

d <- copy(ll$d)

Surgical domain

Only patients in the late silo receive randomised surgical treatment (dair vs revision) with the type of revision selected by the clinician. Table 1 shows the allocation to dair vs rev for this cohort and the balance across the remaining group levels in the data.

Code

# domain B
d_tmp1 <- d[l1 == 1 & er == 1, .(er, r, ed, srp, d)]
d_tmp2 <- d_tmp1[, .N, keyby = .(r, ed, srp, d)]
d_B <- dcast(d_tmp2, ed + d + srp ~ r, value.var = "N")
d_B[, domain := "Duration"]
colnames(d_B) <- c("rand", "group", "surgery", "dair", "rev", "domain")
setcolorder(d_B, "domain")
# domain C
d_tmp1 <- d[l1 == 1 & er == 1, .(er, r, ef, srp, f)]
d_tmp2 <- d_tmp1[, .N, keyby = .(r, ef, srp, f)]
d_C <- dcast(d_tmp2, ef + f + srp ~ r, value.var = "N")
d_C[, domain := "Choice"]
colnames(d_C) <- c("rand", "group", "surgery", "dair", "rev", "domain")
setcolorder(d_C, "domain")

d_tbl <- rbind(d_B, d_C, fill = TRUE)
# d_tbl[, group := factor(group, levels = c("w12","w12p1", "w06p1", "w12p2", "d07p2", "other", "norif", "rif"))]
d_tbl <- d_tbl[order(domain, rand, surgery, group)]

d_tbl[, total := rowSums(d_tbl[, .(dair, rev)], na.rm = T)]
d_tbl[domain == "Choice" & rand == 0, group := NA]
d_tbl[domain == "Duration" & rand == 0, group := NA]

cols <- c("Domain", "Revealed", "Treatment", "Surgery recvd", "DAIR", "Revision", "Total")
names(cols) <- names(d_tbl)

gt_tbl <- d_tbl |> 
  gt(groupname_col = "domain"
  )  |>
  tab_spanner(
    label = html("Domain A (late silo)"),
    columns = c(dair, rev),
    id = "da"
  ) |>
  sub_missing(
    columns = everything(),
    missing_text = "-"
  ) |>
  cols_label(.list = cols) |> 
  summary_rows(
    columns = c("dair", "rev", "total"),
    fns = list(
      subtotal = ~ sum(., na.rm = TRUE)
    )
  )  |>
  tab_footnote(
    footnote = "Revealed indicates whether units were randomised into choice/duration domain (0: No, 1: Yes)",
    locations = cells_column_labels(columns = rand)
  ) |>
  tab_footnote(
    footnote = "Surgery recvd indicates surgery type actually perfromed (0: dair, 1: one-stage, 2: two-stage). Surgery recvd may deviate from original randomisation/plan.",
    locations = cells_column_labels(columns = surgery)
  ) |>
  tab_footnote(
    footnote = "Treatment indicates which treatment assigned within domain. For choice (0: no-rif, 1: rif). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the choice/duration domain have undefined randomised treatment status.",
    locations = cells_column_labels(columns = group)
  ) |>
  tab_footnote(
    footnote = "Only units randomised to surgery domain reported.",
    locations = cells_column_spanners(spanners = "da")
  )

gt_tbl

	Revealed²	Treatment³	Surgery recvd⁴	Domain A (late silo)¹		Total
	Revealed²	Treatment³	Surgery recvd⁴	DAIR	Revision	Total
Choice
	0	-	0	253	-	253
	0	-	1	-	77	77
	0	-	2	-	178	178
	1	0	0	198	-	198
	1	1	0	182	-	182
	1	0	1	-	68	68
	1	1	1	-	56	56
	1	0	2	-	121	121
	1	1	2	-	142	142
subtotal	—	—	—	633	642	1275
Duration
	0	-	0	633	-	633
	1	0	1	-	91	91
	1	1	1	-	110	110
	1	0	2	-	224	224
	1	1	2	-	217	217
subtotal	—	—	—	633	642	1275
¹ Only units randomised to surgery domain reported.
² Revealed indicates whether units were randomised into choice/duration domain (0: No, 1: Yes)
³ Treatment indicates which treatment assigned within domain. For choice (0: no-rif, 1: rif). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the choice/duration domain have undefined randomised treatment status.
⁴ Surgery recvd indicates surgery type actually perfromed (0: dair, 1: one-stage, 2: two-stage). Surgery recvd may deviate from original randomisation/plan.

Table 1: Simulated trial data for (late silo) surgical domain - covariate balance across other groups

Duration domain

Table 2 shows the allocation to the duration domain conditional on surgery type actually received and the balance across the remaining group levels in the data. Only units randomised within the duration domain are reported.

Code

# domain B
d_tmp1 <- d[ed == 1, .(ed, d, er, r, srp)]
d_tmp2 <- d_tmp1[, .N, keyby = .(d, er, r,srp)]
# d_tmp2[, b := factor(b, levels = c("w12", "w06p1", "w12p1", "d07p2", "w12p2"))]
d_B <- dcast(d_tmp2, er + r ~ srp + d, value.var = "N")
d_B[, domain := "Surgery"]
colnames(d_B) <- c("rand", "group", c("long_1", "short_1", "long_2", "short_2"), "domain")
setcolorder(d_B, "domain")
# domain C
d_tmp1 <- d[ed == 1, .(ed, d, ef, f, srp)]
d_tmp2 <- d_tmp1[, .N, keyby = .(d, ef, f, srp)]
# d_tmp2[, b := factor(b, levels = c("w12", "w06p1", "w12p1", "d07p2", "w12p2"))]
d_C <- dcast(d_tmp2, ef + f ~ srp + d, value.var = "N")
d_C[, domain := "Choice"]
colnames(d_C) <- c("rand", "group", c("long_1", "short_1", "long_2", "short_2"), "domain")
setcolorder(d_C, "domain")

d_tbl <- rbind(d_B, d_C, fill = T)

d_tbl[, total := rowSums(d_tbl[, .(long_1, short_1, long_2, short_2)], na.rm = T)]
d_tbl[domain == "Surgery" & rand == 0, group := NA]
d_tbl[domain == "Choice" & rand == 0, group := NA]

cols <- c("Domain", "Revealed", "Treatment", c("long", "short", "long", "short"), "Total")
names(cols) <- names(d_tbl)

gt_tbl <- d_tbl |> 
  gt(groupname_col = "domain"
  ) |> 
  summary_rows(
    columns = c("long_1", "short_1", "long_2", "short_2", "total"),
    fns = list(
      subtotal = ~ sum(., na.rm = TRUE)
    )
  )   |>
  tab_spanner(
    label = html("AB Duration <br>(one-stage)"),
    columns = c("long_1", "short_1"),
    id = "d1"
  ) |>
  tab_spanner(
    label = html("AB Duration <br>(two-stage)"),
    columns = c("long_2", "short_2"),
    id = "d2"
  ) |>
  sub_missing(
    columns = everything(),
    missing_text = "-"
  ) |>
  cols_label(.list = cols)  |>
  tab_footnote(
    footnote = "Revealed indicates whether units were randomised into surgery/duration domain (0: No, 1: Yes)",
    locations = cells_column_labels(columns = rand)
  ) |>
  tab_footnote(
    footnote = "Treatment indicates which treatment assigned within domain. For choice (0: no-rif, 1: rif). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the surgery/choice domain have undefined randomised treatment status.",
    locations = cells_column_labels(columns = group)
  ) |>
  tab_footnote(
    footnote = "Only units randomised to interventions in the surgery domain reported. One-stage/two-stage is by clinician selection",
    locations = cells_column_spanners(spanners = c("d1", "d2"))
  )



gt_tbl

	Revealed²	Treatment³	AB Duration (one-stage)¹		AB Duration (two-stage)¹		Total
	Revealed²	Treatment³	long	short	long	short	Total
Surgery
	0	-	88	88	159	147	482
	1	1	91	110	224	217	642
subtotal	—	—	179	198	383	364	1124
Choice
	0	-	71	83	151	151	456
	1	0	56	60	100	105	321
	1	1	52	55	132	108	347
subtotal	—	—	179	198	383	364	1124
¹ Only units randomised to interventions in the surgery domain reported. One-stage/two-stage is by clinician selection
² Revealed indicates whether units were randomised into surgery/duration domain (0: No, 1: Yes)
³ Treatment indicates which treatment assigned within domain. For choice (0: no-rif, 1: rif). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the surgery/choice domain have undefined randomised treatment status.

Table 2: Simulated trial data for AB duration domain - covariate balance across other groups

Choice domain

Table 3 shows the allocation to the choice domain and the balance across the remaining group levels in the data. Only units randomised within the antibiotic choice domain are reported.

Code

# domain 
d_tmp1 <- d[ef == 1, .(f, er, r, srp)]
d_tmp2 <- d_tmp1[, .N, keyby = .(f, er, r, srp)]
# d_tmp2[, a := factor(a, levels = c("dair", "rev", "one", "two"))]
# d_tmp2[, qa := factor(qa, levels = c("dair", "one", "two"))]
# d_tmp2[, c := factor(c, levels = c("other", "norif", "rif"))]
d_A <- dcast(d_tmp2, er + srp + r ~ f, value.var = "N")
d_A[, domain := "Surgery"]
colnames(d_A) <- c("rand", "surgery","group",  c("norif", "rif"), "domain")
setcolorder(d_A, "domain")
# domain
d_tmp1 <- d[ef == 1, .(f, ed, d, srp)]
d_tmp2 <- d_tmp1[, .N, keyby = .(f, ed, d, srp)]
# d_tmp2[, b := factor(b, levels = c("w12", "w06p1", "w12p1", "d07p2", "w12p2"))]
# d_tmp2[, c := factor(c, levels = c("other", "norif", "rif"))]
d_B <- dcast(d_tmp2, ed + srp + d ~ f, value.var = "N")
d_B[, domain := "Duration"]
colnames(d_B) <- c("rand", "surgery", "group", c("norif", "rif"), "domain")
setcolorder(d_B, "domain")

d_tbl <- rbind(d_A, d_B, fill = T)

d_tbl[, total := rowSums(d_tbl[, .(norif, rif)], na.rm = T)]

d_tbl[domain == "Surgery" & rand == 0, group := NA]
d_tbl[domain == "Duration" & rand == 0, group := NA]



cols <- c("Domain", "Revealed", "Surgery recvd", "Treatment", c("norif", "rif"), "Total")
names(cols) <- names(d_tbl)

gt_tbl <- d_tbl |> 
  gt(groupname_col = "domain"
  ) |> 
  summary_rows(
    columns = c("norif", "rif", "total"),
    fns = list(
      subtotal = ~ sum(., na.rm = TRUE)
    )
  ) |>
  tab_spanner(
    label = html("AB Choice"),
    columns = c("norif", "rif"),
    id = "c1"
  ) |>
  sub_missing(
    columns = everything(),
    missing_text = "-"
  ) |>
  cols_label(.list = cols)|>
  tab_footnote(
    footnote = "Revealed indicates whether units were randomised into surgery/choice domain (0: No, 1: Yes)",
    locations = cells_column_labels(columns = rand)
  ) |>
  tab_footnote(
    footnote = "Treatment indicates which treatment assigned within domain. For surgery (0: dair, 1: rev). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the surgery/duration domain have undefined randomised treatment status.",
    locations = cells_column_labels(columns = group)
  ) |>
  tab_footnote(
    footnote = "Only units randomised to interventions in the antibiotic choice domain reported.",
    locations = cells_column_spanners(spanners = c("c1"))
  )

gt_tbl

	Revealed²	Surgery recvd	Treatment³	AB Choice¹		Total
	Revealed²	Surgery recvd	Treatment³	norif	rif	Total
Surgery
	0	0	-	229	232	461
	0	1	-	48	51	99
	0	2	-	84	98	182
	1	0	0	198	182	380
	1	1	1	68	56	124
	1	2	1	121	142	263
subtotal	—	—	—	748	761	1509
Duration
	0	0	-	427	414	841
	1	1	0	56	52	108
	1	1	1	60	55	115
	1	2	0	100	132	232
	1	2	1	105	108	213
subtotal	—	—	—	748	761	1509
¹ Only units randomised to interventions in the antibiotic choice domain reported.
² Revealed indicates whether units were randomised into surgery/choice domain (0: No, 1: Yes)
³ Treatment indicates which treatment assigned within domain. For surgery (0: dair, 1: rev). For duration is specific to surgery type received (0: long, 1: short). Units that were not randomised within the surgery/duration domain have undefined randomised treatment status.

Table 3: Simulated trial data for AB choice domain - covariate balance across other groups