library(tibble)
# flag observations with a duration longer than 30 and
# at, after, or up to 7 days before a COVID AE (ACOVFL == "Y")
adae <- tribble(
~USUBJID, ~ADY, ~ACOVFL, ~ADURN,
"1", 10, "N", 1,
"1", 21, "N", 50,
"1", 23, "Y", 14,
"1", 32, "N", 31,
"1", 42, "N", 20,
"2", 11, "Y", 13,
"2", 23, "N", 2,
"3", 13, "Y", 12,
"4", 14, "N", 32,
"4", 21, "N", 41
)
derive_var_joined_exist_flag(
adae,
dataset_add = adae,
new_var = ALCOVFL,
by_vars = exprs(USUBJID),
join_vars = exprs(ACOVFL, ADY),
join_type = "all",
order = exprs(ADY),
filter_join = ADURN > 30 & ACOVFL.join == "Y" & ADY >= ADY.join - 7
)
# flag observations with AVALC == "Y" and AVALC == "Y" at one subsequent visit
data <- tribble(
~USUBJID, ~AVISITN, ~AVALC,
"1", 1, "Y",
"1", 2, "N",
"1", 3, "Y",
"1", 4, "N",
"2", 1, "Y",
"2", 2, "N",
"3", 1, "Y",
"4", 1, "N",
"4", 2, "N",
)
derive_var_joined_exist_flag(
data,
dataset_add = data,
by_vars = exprs(USUBJID),
new_var = CONFFL,
join_vars = exprs(AVALC, AVISITN),
join_type = "after",
order = exprs(AVISITN),
filter_join = AVALC == "Y" & AVALC.join == "Y" & AVISITN < AVISITN.join
)
# select observations with AVALC == "CR", AVALC == "CR" at a subsequent visit,
# only "CR" or "NE" in between, and at most one "NE" in between
data <- tribble(
~USUBJID, ~AVISITN, ~AVALC,
"1", 1, "PR",
"1", 2, "CR",
"1", 3, "NE",
"1", 4, "CR",
"1", 5, "NE",
"2", 1, "CR",
"2", 2, "PR",
"2", 3, "CR",
"3", 1, "CR",
"4", 1, "CR",
"4", 2, "NE",
"4", 3, "NE",
"4", 4, "CR",
"4", 5, "PR"
)
derive_var_joined_exist_flag(
data,
dataset_add = data,
by_vars = exprs(USUBJID),
join_vars = exprs(AVALC),
join_type = "after",
order = exprs(AVISITN),
new_var = CONFFL,
first_cond_upper = AVALC.join == "CR",
filter_join = AVALC == "CR" & all(AVALC.join %in% c("CR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1
)
# flag observations with AVALC == "PR", AVALC == "CR" or AVALC == "PR"
# at a subsequent visit at least 20 days later, only "CR", "PR", or "NE"
# in between, at most one "NE" in between, and "CR" is not followed by "PR"
data <- tribble(
~USUBJID, ~ADY, ~AVALC,
"1", 6, "PR",
"1", 12, "CR",
"1", 24, "NE",
"1", 32, "CR",
"1", 48, "PR",
"2", 3, "PR",
"2", 21, "CR",
"2", 33, "PR",
"3", 11, "PR",
"4", 7, "PR",
"4", 12, "NE",
"4", 24, "NE",
"4", 32, "PR",
"4", 55, "PR"
)
derive_var_joined_exist_flag(
data,
dataset_add = data,
by_vars = exprs(USUBJID),
join_vars = exprs(AVALC, ADY),
join_type = "after",
order = exprs(ADY),
new_var = CONFFL,
first_cond_upper = AVALC.join %in% c("CR", "PR") & ADY.join - ADY >= 20,
filter_join = AVALC == "PR" &
all(AVALC.join %in% c("CR", "PR", "NE")) &
count_vals(var = AVALC.join, val = "NE") <= 1 &
(
min_cond(var = ADY.join, cond = AVALC.join == "CR") >
max_cond(var = ADY.join, cond = AVALC.join == "PR") |
count_vals(var = AVALC.join, val = "CR") == 0
)
)
# flag observations with CRIT1FL == "Y" at two consecutive visits or at the last visit
data <- tribble(
~USUBJID, ~AVISITN, ~CRIT1FL,
"1", 1, "Y",
"1", 2, "N",
"1", 3, "Y",
"1", 5, "N",
"2", 1, "Y",
"2", 3, "Y",
"2", 5, "N",
"3", 1, "Y",
"4", 1, "Y",
"4", 2, "N",
)
derive_var_joined_exist_flag(
data,
dataset_add = data,
by_vars = exprs(USUBJID),
new_var = CONFFL,
tmp_obs_nr_var = tmp_obs_nr,
join_vars = exprs(CRIT1FL),
join_type = "all",
order = exprs(AVISITN),
filter_join = CRIT1FL == "Y" & CRIT1FL.join == "Y" &
(tmp_obs_nr + 1 == tmp_obs_nr.join | tmp_obs_nr == max(tmp_obs_nr.join))
)
# first_cond_lower and first_cond_upper argument
myd <- tribble(
~subj, ~day, ~val,
"1", 1, "++",
"1", 2, "-",
"1", 3, "0",
"1", 4, "+",
"1", 5, "++",
"1", 6, "-",
"2", 1, "-",
"2", 2, "++",
"2", 3, "+",
"2", 4, "0",
"2", 5, "-",
"2", 6, "++"
)
# flag "0" where all results from the first "++" before the "0" up to the "0"
# (excluding the "0") are "+" or "++"
derive_var_joined_exist_flag(
myd,
dataset_add = myd,
by_vars = exprs(subj),
order = exprs(day),
new_var = flag,
join_vars = exprs(val),
join_type = "before",
first_cond_lower = val.join == "++",
filter_join = val == "0" & all(val.join %in% c("+", "++"))
)
# flag "0" where all results from the "0" (excluding the "0") up to the first
# "++" after the "0" are "+" or "++"
derive_var_joined_exist_flag(
myd,
dataset_add = myd,
by_vars = exprs(subj),
order = exprs(day),
new_var = flag,
join_vars = exprs(val),
join_type = "after",
first_cond_upper = val.join == "++",
filter_join = val == "0" & all(val.join %in% c("+", "++"))
)
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