Nothing
aggregate_prepare_data <- function(data, age, surv, rates, tau, parameters, names) {
if (missing(data)) {
stop(paste0("Dataset '", names[1], "' must be provided."),
call. = FALSE)
}
if (missing(age)) {
stop(paste0("Parameter '", names[2], "' must be provided."),
call. = FALSE)
}
if (missing(surv) & missing(rates)) {
stop(paste0("Parameter '", names[3], "' or '", names[4], "' must be provided."),
call. = FALSE)
}
if (!missing(surv)) {
if (!missing(rates)) {
message(paste0("Parameter '", names[3], "' ignored because '", names[4], "' also provided."))
}
# If survival provided
tmp0 <- data[, c(as.character(parameters[[names[2]]]), as.character(parameters[[names[3]]]))]
colnames(tmp0) <- c("time", "S")
tmp0 <- tmp0[tmp0$time <= tau, ]
} else {
# If mortality rates provided: transform to survival
tmp0 <- data[, c(as.character(parameters[[names[2]]]), as.character(parameters[[names[4]]]))]
colnames(tmp0) <- c("time", "r")
tmp0 <- tmp0[tmp0$time <= tau, ]
tmp0 <- tmp0[order(tmp0$time), ]
tmp0$to <- c(tmp0$time[-1], tau)
tmp0$S <- 1
S <- 1
for(i in 1:nrow(tmp0)) {
tmp0$S[i] <- S * (1 - tmp0$r[i] * (tmp0$to[i] - tmp0$time[i]))
S <- tmp0$S[i]
}
tmp0 <- data.frame(time = c(tmp0$time[1], tmp0$to), S = c(1, tmp0$S))
}
return(tmp0)
}
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