R/ci.sc.R

In yelleKneK/MBESS: The MBESS R Package

ci.sc <- function(means=NULL, s.anova=NULL, c.weights=NULL, n=NULL, N=NULL,
Psi=NULL, ncp=NULL, conf.level=.95, alpha.lower=NULL, alpha.upper=NULL, df.error=NULL, ...)
{

if(!identical(sum(c.weights[c.weights>0]), 1)) stop("Please use fractions to specify the contrast weights")
if(!identical(round(sum(c.weights), 5), 0)) stop("The sum of the contrast weights ('c.weights') should equal zero.")
  
if(length(n)==1) 
{
n <- rep(n, length(means))
}

if(length(n)!=length(c.weights)) stop("The lengths of 'n' and 'c.weights' differ, which should not be the case.")

 
part.of.se <- sqrt(sum((c.weights^2)/n))

if(!is.null(Psi))
{
if(!is.null(means)) stop("Since the contrast effect ('Psi') was specified, you should not specify the vector of means ('means').")
if(!is.null(ncp)) stop("Since the contrast effect ('Psi') was specified, you should not specify the noncentral parameter ('ncp').")
if(is.null(s.anova)) stop("You must specify the standard deviation of the errors (i.e., the square root of the error variance).")
if(is.null(n)) stop("You must specify the vector per group/level sample size ('n').")
if(is.null(c.weights)) stop("You must specify the vector of contrast weights ('c.weights').")

psi <- Psi/s.anova
lambda <- psi/part.of.se
}

if(!is.null(ncp))
{
if(!is.null(means)) stop("Since the noncentral parameter was specified directly, you should not specify the vector of means ('means').")
if(!is.null(Psi)) stop("Since the noncentral parameter was specified directly, you should not specify the the contrast effect ('Psi').")
if(is.null(s.anova)) stop("You must specify the standard deviation of the errors (i.e., the square root of the error variance).")
if(is.null(n)) stop("You must specify the vector per group/level sample size ('n').")
if(is.null(c.weights)) stop("You must specify the vector of contrast weights ('c.weights'.")

lambda <- ncp
}

if(!is.null(means))
{
Psi <- sum(c.weights*means)
psi <- Psi/s.anova

lambda <- psi/part.of.se

}

if(is.null(alpha.lower) & is.null(alpha.upper))
{
alpha.lower <- (1-conf.level)/2
alpha.upper <- (1-conf.level)/2
}

if(is.null(N)) stop("You must specify the total sample size ('N').")
if(is.null(df.error)) df.2 <- N - length(means)
if(!is.null(df.error)) df.2 <- df.error

Lims <- conf.limits.nct(ncp=lambda, df=df.2, conf.level = NULL, alpha.lower = alpha.lower, 
        alpha.upper = alpha.upper, sup.int.warns=TRUE, method = "all", ...)

Result <- list(Lower.Conf.Limit.Standardized.Contrast = Lims$Lower.Limit*part.of.se, Standardized.contrast = psi, 
        Upper.Conf.Limit.Standardized.Contrast = Lims$Upper.Limit*part.of.se)
        
# print(paste("The", 1 - (alpha.lower + alpha.upper), "confidence limits for the standardized contrast are given as:"))

return(Result)
}