R/frag.study.R

In fragility: Assessing and Visualizing Fragility of Clinical Results with Binary Outcomes

frag.study <- function(e0, n0, e1, n1, data, all = FALSE, methods,
  modify0 = "both", modify1 = "both", alpha = 0.05,
  alternative = "two.sided", OR = 1, RR = 1, RD = 0, allcase = TRUE){
  if(!missing(data)){
    e0 <- eval(substitute(e0), data, parent.frame())
    n0 <- eval(substitute(n0), data, parent.frame())
    e1 <- eval(substitute(e1), data, parent.frame())
    n1 <- eval(substitute(n1), data, parent.frame())
  }
  if(e0 < 0 | n0 < 0 | e1 < 0 | n1 < 0) stop("Event counts and sample sizes must be nonnegative.")
  if(e0 > n0 | e1 > n1) stop("Event counts must not be larger than sample sizes.")
  if(e0%%1 != 0 | n0%%1 != 0 | e1%%1 != 0 | n1%%1 != 0){
    message("Some event counts and/or sample sizes are not integer(s); they are rounded.")
    e0 <- round(e0)
    n0 <- round(n0)
    e1 <- round(e1)
    n1 <- round(n1)
  }
  if(missing(methods)){
    methods <- c("Fisher", "chisq", "OR", "RR", "RD")
  }
  if(any(!is.element(methods, c("Fisher", "chisq", "OR", "RR", "RD")))){
    stop("methods must be \"Fisher\", \"chisq\", \"OR\", \"RR\", and/or \"RD\".")
  }
  if(length(modify0) != 1 | length(modify1) != 1){
    stop("Only one type of event status modification\n    can be specified for modify0/modify1.")
  }
  if(any(!is.element(c(modify0, modify1), c("increase", "decrease", "both", "none")))){
    stop("modify0/modify1 must be \"increase\", \"decrease\", \"both\", or \"none\".")
  }
  if(alpha <= 0 | alpha >= 1) stop("alpha must be between 0 and 1.")
  if(length(alternative) != 1){
    stop("Only one type of alternative hypothesis\n    can be specified for alternative.")
  }
  if(any(!is.element(alternative, c("two.sided", "one.sided")))){
    stop("alternative must be \"two.sided\" or \"one.sided\".")
  }
  if(OR <= 0) stop("The null value of OR must be positive.")
  if(RR <= 0) stop("The null value of RR must be positive.")
  if(RD < -1 | RD > 1) stop("The null value of RD must be between -1 and 1.")

  if(all){
    out <- frag.study.all(e0, n0, e1, n1, methods,
      modify0, modify1, alpha, alternative, OR, RR, RD)
  }else{
    out <- frag.study.iter(e0, n0, e1, n1, methods,
      modify0, modify1, alpha, alternative, OR, RR, RD, allcase)
  }
  return(out)
}