R/summarySE.R

In mssm-msf-2019/BiostatsALL:

#' Summarizes data.
#' @description Gives count, mean, standard deviation, standard error of the mean, and confidence interval (default 95%).
#'  @param   data: a data frame.
#'  @param   measurevar: the name of a column that contains the variable to be summariezed
#'  @param   groupvars: a vector containing names of columns that contain grouping variables
#'  @param   na.rm: a boolean that indicates whether to ignore NA's
#'   @param  conf.interval: the percent range of the confidence interval (default is 95%)

summarySE <- function(data=NULL, measurevar, groupvars=NULL, na.rm=FALSE,
                      conf.interval=.95, .drop=TRUE) {
  require(plyr)
  
  # New version of length which can handle NA's: if na.rm==T, don't count them
  length2 <- function (x, na.rm=FALSE) {
    if (na.rm) sum(!is.na(x))
    else       length(x)
  }
  
  # This is does the summary; it's not easy to understand...
  datac <- ddply(data, groupvars, .drop=.drop,
                 .fun= function(xx, col, na.rm) {
                   c( N    = length2(xx[,col], na.rm=na.rm),
                      mean = mean   (xx[,col], na.rm=na.rm),
                      sd   = sd     (xx[,col], na.rm=na.rm)
                   )
                 },
                 measurevar,
                 na.rm
  )
  
  # Rename the "mean" column    
  datac <- rename(datac, c("mean"=measurevar))
  
  datac$se <- datac$sd / sqrt(datac$N)  # Calculate standard error of the mean
  
  # Confidence interval multiplier for standard error
  # Calculate t-statistic for confidence interval: 
  # e.g., if conf.interval is .95, use .975 (above/below), and use df=N-1
  ciMult <- qt(conf.interval/2 + .5, datac$N-1)
  datac$ci <- datac$se * ciMult
  
  return(datac)
}