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check_oe_bcva_tot_mismatch.R
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check_oe_bcva_tot_mismatch.R
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#' @title Check mismatch between Derived BCVA Total Score & Total BCVA Score from Data
#'
#' @description This ophthalmology check looks for any mismatch between the
#' Derived Best Corrected Visual Acuity (BCVA) Total Score &
#' reported Total BCVA Score from Data based on OETESTCD = "LOGSCORE" for
#' older studies or OETESTCD = "VACSCORE" for newer studies
#'
#' @param OE Ophtho Dataset with variables USUBJID, OETESTCD, OECAT, OESCAT, OETSTDTL,
#' OESTRESN, OESTAT (if present), OELAT, VISIT, OEDTC
#'
#' @importFrom dplyr %>% filter mutate select
#'
#' @family OPHTH
#'
#' @keywords OPHTH
#'
#' @export
#'
#' @author Monarch Shah (HackR 2021 Team Eye)
#'
#' @examples
#'
#' #Using Old Standard, FAIL Case (4m <=19, so 4m + 1m to match with Rave Total)
#' OE <- data.frame(
#' USUBJID = 1,
#' OETESTCD = c("NUMLCOR", "NUMLCOR", "LCORCON", "LOGSCORE"),
#' OECAT = rep("BEST CORRECTED VISUAL ACUITY", 4),
#' OESCAT = c("TOTAL", "TOTAL","", ""),
#' OETSTDTL = c("TESTING DISTANCE: 4M", "TESTING DISTANCE: 1M", "", ""),
#' OESTRESN = c(18, 0, 30, 48),
#' OESTAT= rep("", 4),
#' OELOC = rep("EYE", 4),
#' OELAT = rep("LEFT", 4),
#' VISIT = rep("SCREENING", 4),
#' VISITNUM = rep(99, 4),
#' OEDTC = rep("2021-05-19", 4),
#' OEDY = rep(1, 4),
#' stringsAsFactors = FALSE)
#'
#' check_oe_bcva_tot_mismatch(OE)
#'
#'
#' #Using New Standard, PASS Case
#'
#' OE <- data.frame(
#' USUBJID = 1,
#' OETESTCD = c("NUMLCOR", "NUMLCOR", "LCORCON", "VACSCORE"),
#' OECAT = rep("BEST CORRECTED VISUAL ACUITY", 4),
#' OESCAT = c("NORMAL LIGHTING SCORE", "NORMAL LIGHTING SCORE","", ""),
#' OETSTDTL = c("TESTING DISTANCE: 4M", "TESTING DISTANCE: 1M", "", ""),
#' OESTRESN = c(22, 0, 30, 52),
#' OESTAT= rep("", 4),
#' OELOC = rep("EYE", 4),
#' OELAT = rep("LEFT", 4),
#' VISIT = rep("SCREENING", 4),
#' VISITNUM = rep(99, 4),
#' OEDTC = rep("2021-05-19", 4),
#' OEDY = rep(1, 4),
#' stringsAsFactors = FALSE)
#' check_oe_bcva_tot_mismatch(OE)
#'
#'
#' #Using New Standard, FAIL Case (Total 4m + 1m (As 4m <=19) not equal to CRF Total Score)
#'
#' OE <- data.frame(
#' USUBJID = 1,
#' OETESTCD = c("NUMLCOR", "NUMLCOR", "LCORCON", "VACSCORE"),
#' OECAT = "BEST CORRECTED VISUAL ACUITY",
#' OESCAT = c("NORMAL LIGHTING SCORE", "NORMAL LIGHTING SCORE","", ""),
#' OETSTDTL = c("TESTING DISTANCE: 4M", "TESTING DISTANCE: 1M", "", ""),
#' OESTRESN = c(17, 12, 0, 27),
#' OESTAT= "",
#' OELOC = "EYE",
#' OELAT = "LEFT",
#' VISIT = "SCREENING",
#' VISITNUM = 99,
#' OEDTC = "2021-05-19",
#' OEDY = 1,
#' stringsAtors = FALSE)
#' check_oe_bcva_tot_mismatch(OE)
#'
#'
#' #FAIL Case without optional variable, OESTAT
#'
#' OE$OESTAT <- NULL
#' check_oe_bcva_tot_mismatch(OE)
#'
#'
#' #missing required variable, OETESTCD
#'
#' OE$OETESTCD <- NULL
#' check_oe_bcva_tot_mismatch(OE)
#'
check_oe_bcva_tot_mismatch <- function(OE) {
if (OE %lacks_any% c("USUBJID", "OETESTCD", "OECAT", "OESCAT", "OETSTDTL", "OESTRESN", "OELAT", "VISIT", "OEDTC")) {
fail(lacks_msg(OE, c("USUBJID", "OETESTCD", "OECAT", "OESCAT", "OETSTDTL", "OESTRESN", "OELAT", "VISIT", "OEDTC")))
}
else {
# Total Score Computed vs Total Score from Data ----
# Total Score Derivation
# A. Total # of Correct at 4m
# B. If value of A >= 20 then 30, else 0
# C. Total number of correct at 1 m (if not tested enter 0)
# D. Visual Acuity Score = A + B + C
perm_var <- c("OESTAT")
int_var <- intersect(names(OE), perm_var)
my_select_var <- c("USUBJID", "OETESTCD", "OECAT", "OESCAT", "OETSTDTL", "OESTRESN", "OELAT", "VISIT", "OEDTC", int_var)
if ((any(names(OE) == "OESTAT")) == TRUE) {
OE <- OE %>% filter(toupper(OESTAT) != "NOT DONE")
}
OE <- OE %>% mutate(OETESTCD = toupper(OETESTCD),
OESCAT = toupper(OESCAT),
OETSTDTL = toupper(OETSTDTL),
OECAT = toupper(OECAT))
bcva_t1 <- OE %>% filter((OETESTCD == "NUMLCOR" & OESCAT == "TOTAL" & OETSTDTL == 'TESTING DISTANCE: 4M' & OECAT == "BEST CORRECTED VISUAL ACUITY") | #Old Standard
(OETESTCD == "NUMLCOR" & OESCAT == "NORMAL LIGHTING SCORE" & OETSTDTL == 'TESTING DISTANCE: 4M' & OECAT == "BEST CORRECTED VISUAL ACUITY")) %>% #New Standard
mutate(TOT_4M = OESTRESN) %>%
select(USUBJID, OELAT, VISIT, OEDTC, TOT_4M)
bcva_t2 <- OE %>% filter((OETESTCD == "NUMLCOR" & OESCAT == "TOTAL" & OETSTDTL == 'TESTING DISTANCE: 1M' & OECAT == "BEST CORRECTED VISUAL ACUITY") | #Old Standard
(OETESTCD == "NUMLCOR" & OESCAT == "NORMAL LIGHTING SCORE" & OETSTDTL == 'TESTING DISTANCE: 1M' & OECAT == "BEST CORRECTED VISUAL ACUITY")) %>% #New Standard
mutate(TOT_1M = OESTRESN) %>%
select(USUBJID, OELAT, VISIT, OEDTC, TOT_1M)
bcva_t3 <- OE %>% filter(OETESTCD == "LCORCON" & OECAT == "BEST CORRECTED VISUAL ACUITY") %>%
mutate(PARTB_CONST = OESTRESN) %>%
select(USUBJID, OELAT, VISIT, OEDTC, PARTB_CONST)
bcva_t4 <- OE %>% filter((OETESTCD == "LOGSCORE" & OECAT == "BEST CORRECTED VISUAL ACUITY") | #Old Standard
(OETESTCD == "VACSCORE" & OECAT == "BEST CORRECTED VISUAL ACUITY")) %>% #New Standard
mutate(BCVATOT_CRF = OESTRESN) %>%
select(USUBJID, OELAT, VISIT, OEDTC, BCVATOT_CRF)
bcva_t <- Reduce(function(x,y) merge(x = x, y = y, c("USUBJID", "OELAT", "VISIT", "OEDTC"), all=TRUE),
list(bcva_t1, bcva_t2, bcva_t3, bcva_t4))
bcva_t <- bcva_t %>%
mutate(BCVATOT_DERIVED = ifelse(TOT_4M >=20, TOT_4M + 30,
ifelse(TOT_4M <= 19, TOT_4M + TOT_1M , NA)))
mydf <- bcva_t %>% filter(BCVATOT_DERIVED != BCVATOT_CRF)
if ((nrow(mydf) > 0 ) == FALSE) {
pass()
}
else {
fail(paste0(nrow(mydf), " record(s) with BCVA Total Score Derived and from RAVE/eCRF with mismatch. "), mydf )
}
}
}