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Closes #244: introduction of derive_vars_cat() #252

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Closes #244: introduction of derive_vars_cat() #252

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254 changes: 181 additions & 73 deletions inst/templates/ad_adbcva.R
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Original file line number Diff line number Diff line change
Expand Up @@ -38,65 +38,146 @@ param_lookup <- tibble::tribble(
"VACSCORE", "BEST CORRECTED VISUAL ACUITY", "OVERALL EVALUATION", "Fellow Eye", "FBCVA", "Fellow Eye Visual Acuity Score (letters)", 2, # nolint
)

# Assign AVALCAT1
avalcat_lookup <- tibble::tribble(
~PARAMCD, ~AVALCA1N, ~AVALCAT1,
"SBCVA", 1000, "< 20/800",
"SBCVA", 800, "20/800",
"SBCVA", 640, "20/640",
"SBCVA", 500, "20/500",
"SBCVA", 400, "20/400",
"SBCVA", 320, "20/320",
"SBCVA", 250, "20/250",
"SBCVA", 200, "20/200",
"SBCVA", 160, "20/160",
"SBCVA", 125, "20/125",
"SBCVA", 100, "20/100",
"SBCVA", 80, "20/80",
"SBCVA", 63, "20/63",
"SBCVA", 50, "20/50",
"SBCVA", 40, "20/40",
"SBCVA", 32, "20/32",
"SBCVA", 25, "20/25",
"SBCVA", 20, "20/20",
"SBCVA", 16, "20/16",
"SBCVA", 12, "20/12",
"SBCVA", 1, "> 20/12",
# # Assign AVALCAT1
# avalcat_lookup <- tibble::tribble(
# ~PARAMCD, ~AVALCA1N, ~AVALCAT1,
# "SBCVA", 1000, "< 20/800",
# "SBCVA", 800, "20/800",
# "SBCVA", 640, "20/640",
# "SBCVA", 500, "20/500",
# "SBCVA", 400, "20/400",
# "SBCVA", 320, "20/320",
# "SBCVA", 250, "20/250",
# "SBCVA", 200, "20/200",
# "SBCVA", 160, "20/160",
# "SBCVA", 125, "20/125",
# "SBCVA", 100, "20/100",
# "SBCVA", 80, "20/80",
# "SBCVA", 63, "20/63",
# "SBCVA", 50, "20/50",
# "SBCVA", 40, "20/40",
# "SBCVA", 32, "20/32",
# "SBCVA", 25, "20/25",
# "SBCVA", 20, "20/20",
# "SBCVA", 16, "20/16",
# "SBCVA", 12, "20/12",
# "SBCVA", 1, "> 20/12",
# )
#
# # add equivalent rows for PARAMCD = "FBCVA"
# avalcat_lookup <- avalcat_lookup %>%
# mutate(PARAMCD = "FBCVA") %>%
# rbind(avalcat_lookup)
#
# # ---- Utility functions ----
#
# # Format function for AVALCAT1
# format_avalcat1n <- function(param, aval) {
# case_when(
# param %in% c("SBCVA", "FBCVA") & aval >= 0 & aval <= 3 ~ 1000,
# param %in% c("SBCVA", "FBCVA") & aval >= 4 & aval <= 8 ~ 800,
# param %in% c("SBCVA", "FBCVA") & aval >= 9 & aval <= 13 ~ 640,
# param %in% c("SBCVA", "FBCVA") & aval >= 14 & aval <= 18 ~ 500,
# param %in% c("SBCVA", "FBCVA") & aval >= 19 & aval <= 23 ~ 400,
# param %in% c("SBCVA", "FBCVA") & aval >= 24 & aval <= 28 ~ 320,
# param %in% c("SBCVA", "FBCVA") & aval >= 29 & aval <= 33 ~ 250,
# param %in% c("SBCVA", "FBCVA") & aval >= 34 & aval <= 38 ~ 200,
# param %in% c("SBCVA", "FBCVA") & aval >= 39 & aval <= 43 ~ 160,
# param %in% c("SBCVA", "FBCVA") & aval >= 44 & aval <= 48 ~ 125,
# param %in% c("SBCVA", "FBCVA") & aval >= 49 & aval <= 53 ~ 100,
# param %in% c("SBCVA", "FBCVA") & aval >= 54 & aval <= 58 ~ 80,
# param %in% c("SBCVA", "FBCVA") & aval >= 59 & aval <= 63 ~ 63,
# param %in% c("SBCVA", "FBCVA") & aval >= 64 & aval <= 68 ~ 50,
# param %in% c("SBCVA", "FBCVA") & aval >= 69 & aval <= 73 ~ 40,
# param %in% c("SBCVA", "FBCVA") & aval >= 74 & aval <= 78 ~ 32,
# param %in% c("SBCVA", "FBCVA") & aval >= 79 & aval <= 83 ~ 25,
# param %in% c("SBCVA", "FBCVA") & aval >= 84 & aval <= 88 ~ 20,
# param %in% c("SBCVA", "FBCVA") & aval >= 89 & aval <= 93 ~ 16,
# param %in% c("SBCVA", "FBCVA") & aval >= 94 & aval <= 97 ~ 12,
# param %in% c("SBCVA", "FBCVA") & aval >= 98 ~ 1
# )
# }
#
# # SBCVA and FBCVA definition list
definition_bcva_ <- exprs(
~PARAMCD, ~condition, ~AVALCA1N, ~AVALCAT1,
"SBCVA", AVAL >= 0 & AVAL <= 3, 1000, "< 20/800",
"FBCVA", AVAL >= 0 & AVAL <= 3, 1000, "< 20/800",
"SBCVA", AVAL >= 4 & AVAL <= 8, 800, "20/800",
"FBCVA", AVAL >= 4 & AVAL <= 8, 800, "20/800",
"SBCVA", AVAL >= 9 & AVAL <= 13, 640, "20/640",
"FBCVA", AVAL >= 9 & AVAL <= 13, 640, "20/640",
"SBCVA", AVAL >= 14 & AVAL <= 18, 500, "20/500",
"FBCVA", AVAL >= 14 & AVAL <= 18, 500, "20/500",
"SBCVA", AVAL >= 19 & AVAL <= 23, 400, "20/400",
"FBCVA", AVAL >= 19 & AVAL <= 23, 400, "20/400",
"SBCVA", AVAL >= 24 & AVAL <= 28, 320, "20/320",
"FBCVA", AVAL >= 24 & AVAL <= 28, 320, "20/320",
"SBCVA", AVAL >= 29 & AVAL <= 33, 250, "20/250",
"FBCVA", AVAL >= 29 & AVAL <= 33, 250, "20/250",
"SBCVA", AVAL >= 34 & AVAL <= 38, 200, "20/200",
"FBCVA", AVAL >= 34 & AVAL <= 38, 200, "20/200",
"SBCVA", AVAL >= 39 & AVAL <= 43, 160, "20/160",
"FBCVA", AVAL >= 39 & AVAL <= 43, 160, "20/160",
"SBCVA", AVAL >= 44 & AVAL <= 48, 125, "20/125",
"FBCVA", AVAL >= 44 & AVAL <= 48, 125, "20/125",
"SBCVA", AVAL >= 49 & AVAL <= 53, 100, "20/100",
"FBCVA", AVAL >= 49 & AVAL <= 53, 100, "20/100",
"SBCVA", AVAL >= 54 & AVAL <= 58, 80, "20/80",
"FBCVA", AVAL >= 54 & AVAL <= 58, 80, "20/80",
"SBCVA", AVAL >= 59 & AVAL <= 63, 63, "20/63",
"FBCVA", AVAL >= 59 & AVAL <= 63, 63, "20/63",
"SBCVA", AVAL >= 64 & AVAL <= 68, 50, "20/50",
"FBCVA", AVAL >= 64 & AVAL <= 68, 50, "20/50",
"SBCVA", AVAL >= 69 & AVAL <= 73, 40, "20/40",
"FBCVA", AVAL >= 69 & AVAL <= 73, 40, "20/40",
"SBCVA", AVAL >= 74 & AVAL <= 78, 32, "20/32",
"FBCVA", AVAL >= 74 & AVAL <= 78, 32, "20/32",
"SBCVA", AVAL >= 79 & AVAL <= 83, 25, "20/25",
"FBCVA", AVAL >= 79 & AVAL <= 83, 25, "20/25",
"SBCVA", AVAL >= 84 & AVAL <= 88, 20, "20/20",
"FBCVA", AVAL >= 84 & AVAL <= 88, 20, "20/20",
"SBCVA", AVAL >= 89 & AVAL <= 93, 16, "20/16",
"FBCVA", AVAL >= 89 & AVAL <= 93, 16, "20/16",
"SBCVA", AVAL >= 94 & AVAL <= 97, 12, "20/12",
"FBCVA", AVAL >= 94 & AVAL <= 97, 12, "20/12",
"SBCVA", AVAL >= 98, 1, "> 20/12",
"FBCVA", AVAL >= 98, 1, "> 20/12"
)

# add equivalent rows for PARAMCD = "FBCVA"
avalcat_lookup <- avalcat_lookup %>%
mutate(PARAMCD = "FBCVA") %>%
rbind(avalcat_lookup)
# SBCVA definition list
definition_sbcva <- exprs(
~PARAMCD, ~condition, ~AVALCA1N, ~AVALCAT1,
"SBCVA", AVAL >= 0 & AVAL <= 3, 1000, "< 20/800",
"SBCVA", AVAL >= 4 & AVAL <= 8, 800, "20/800",
"SBCVA", AVAL >= 9 & AVAL <= 13, 640, "20/640",
"SBCVA", AVAL >= 14 & AVAL <= 18, 500, "20/500",
"SBCVA", AVAL >= 19 & AVAL <= 23, 400, "20/400",
"SBCVA", AVAL >= 24 & AVAL <= 28, 320, "20/320",
"SBCVA", AVAL >= 29 & AVAL <= 33, 250, "20/250",
"SBCVA", AVAL >= 34 & AVAL <= 38, 200, "20/200",
"SBCVA", AVAL >= 39 & AVAL <= 43, 160, "20/160",
"SBCVA", AVAL >= 44 & AVAL <= 48, 125, "20/125",
"SBCVA", AVAL >= 49 & AVAL <= 53, 100, "20/100",
"SBCVA", AVAL >= 54 & AVAL <= 58, 80, "20/80",
"SBCVA", AVAL >= 59 & AVAL <= 63, 63, "20/63",
"SBCVA", AVAL >= 64 & AVAL <= 68, 50, "20/50",
"SBCVA", AVAL >= 69 & AVAL <= 73, 40, "20/40",
"SBCVA", AVAL >= 74 & AVAL <= 78, 32, "20/32",
"SBCVA", AVAL >= 79 & AVAL <= 83, 25, "20/25",
"SBCVA", AVAL >= 84 & AVAL <= 88, 20, "20/20",
"SBCVA", AVAL >= 89 & AVAL <= 93, 16, "20/16",
"SBCVA", AVAL >= 94 & AVAL <= 97, 12, "20/12",
"SBCVA", AVAL >= 98, 1, "> 20/12"
)

# ---- Utility functions ----
# FBCVA definition list
definition_fbcva <- lapply(definition_sbcva, function(row) replace(row, row == "SBCVA", "FBCVA"))
definition_fbcva_trimmed <- definition_fbcva[-(1:4)]

# Format function for AVALCAT1
format_avalcat1n <- function(param, aval) {
case_when(
param %in% c("SBCVA", "FBCVA") & aval >= 0 & aval <= 3 ~ 1000,
param %in% c("SBCVA", "FBCVA") & aval >= 4 & aval <= 8 ~ 800,
param %in% c("SBCVA", "FBCVA") & aval >= 9 & aval <= 13 ~ 640,
param %in% c("SBCVA", "FBCVA") & aval >= 14 & aval <= 18 ~ 500,
param %in% c("SBCVA", "FBCVA") & aval >= 19 & aval <= 23 ~ 400,
param %in% c("SBCVA", "FBCVA") & aval >= 24 & aval <= 28 ~ 320,
param %in% c("SBCVA", "FBCVA") & aval >= 29 & aval <= 33 ~ 250,
param %in% c("SBCVA", "FBCVA") & aval >= 34 & aval <= 38 ~ 200,
param %in% c("SBCVA", "FBCVA") & aval >= 39 & aval <= 43 ~ 160,
param %in% c("SBCVA", "FBCVA") & aval >= 44 & aval <= 48 ~ 125,
param %in% c("SBCVA", "FBCVA") & aval >= 49 & aval <= 53 ~ 100,
param %in% c("SBCVA", "FBCVA") & aval >= 54 & aval <= 58 ~ 80,
param %in% c("SBCVA", "FBCVA") & aval >= 59 & aval <= 63 ~ 63,
param %in% c("SBCVA", "FBCVA") & aval >= 64 & aval <= 68 ~ 50,
param %in% c("SBCVA", "FBCVA") & aval >= 69 & aval <= 73 ~ 40,
param %in% c("SBCVA", "FBCVA") & aval >= 74 & aval <= 78 ~ 32,
param %in% c("SBCVA", "FBCVA") & aval >= 79 & aval <= 83 ~ 25,
param %in% c("SBCVA", "FBCVA") & aval >= 84 & aval <= 88 ~ 20,
param %in% c("SBCVA", "FBCVA") & aval >= 89 & aval <= 93 ~ 16,
param %in% c("SBCVA", "FBCVA") & aval >= 94 & aval <= 97 ~ 12,
param %in% c("SBCVA", "FBCVA") & aval >= 98 ~ 1
)
}
# Combine both SBCVA and FBCVA definition lists
definition_bcva <- c(definition_sbcva, definition_fbcva_trimmed)
all.equal(definition_bcva_, definition_bcva) #TODO: Unable to get back the exact list structure

# ---- Derivations ----

Expand Down Expand Up @@ -280,24 +361,51 @@ adbcva_adsl <- adbcva_aseq %>%
by_vars = get_admiral_option("subject_keys")
)

adbcva_crtflag <- adbcva_adsl %>%
# Add criterion flags for BCVA endpoints
restrict_derivation(
derivation = derive_var_bcvacritxfl,
args = params(
crit_var = exprs(CHG),
bcva_ranges = list(c(0, 5), c(-5, -1), c(10, 15)),
bcva_uplims = list(-20, 5, 10),
bcva_lowlims = list(-15, 15),
additional_text = ""
),
filter = PARAMCD %in% c("SBCVA", "FBCVA")
) %>%
# Add AVALCATx variables
mutate(AVALCA1N = format_avalcat1n(param = PARAMCD, aval = AVAL)) %>%
derive_vars_merged(
avalcat_lookup,
by = exprs(PARAMCD, AVALCA1N)
# adbcva_crtflag <- adbcva_adsl %>%
# # Add criterion flags for BCVA endpoints
# restrict_derivation(
# derivation = derive_var_bcvacritxfl,
# args = params(
# crit_var = exprs(CHG),
# bcva_ranges = list(c(0, 5), c(-5, -1), c(10, 15)),
# bcva_uplims = list(-20, 5, 10),
# bcva_lowlims = list(-15, 15),
# additional_text = ""
# ),
# filter = PARAMCD %in% c("SBCVA", "FBCVA")
# ) %>%
# Add AVALCATx variables
# mutate(AVALCA1N = format_avalcat1n(param = PARAMCD, aval = AVAL)) %>%
# derive_vars_merged(
# avalcat_lookup,
# by = exprs(PARAMCD, AVALCA1N)
# )
# derive_vars_cat(
# definition = definition_bcva,
# by_vars = exprs(PARAMCD)
# )

# Add criterion flags for BCVA endpoints
adbcva_crtflag <- call_derivation(
dataset = adbcva_adsl %>% filter(PARAMCD %in% c("SBCVA", "FBCVA")),
derivation = derive_vars_crit_flag,
variable_params = list(
params(crit_nr = 1, condition = CHG >= 0 & CHG <= 5, description = "0 <= CHG <= 5"),
params(crit_nr = 2, condition = CHG >= -5 & CHG <= -1, description = "-5 <= CHG <= -1"),
params(crit_nr = 3, condition = CHG >= 10 & CHG <= 15, description = "10 <= CHG <= 15"),
params(crit_nr = 4, condition = CHG <= -20, description = "CHG <= -20"),
params(crit_nr = 5, condition = CHG <= 5, description = "CHG <= 5"),
params(crit_nr = 6, condition = CHG <= 10, description = "CHG <= 10"),
params(crit_nr = 7, condition = CHG >= -15, description = "CHG >= -15"),
params(crit_nr = 8, condition = CHG >= 15, description = "CHG >= 15")
),
values_yn = TRUE
) %>%
bind_rows(adbcva_adsl %>% filter(!PARAMCD %in% c("SBCVA", "FBCVA"))) %>%
arrange(USUBJID, DOMAIN, PARAMCD) %>%
derive_vars_cat(
definition = definition_bcva_,
by_vars = exprs(PARAMCD)
)

# Final Steps, Select final variables and Add labels
Expand Down
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