R/sbsummary.R

In omarbenites/sbformula: Formulas for crop breeding and standart evaluation trial

#' #'Function to calculate summary statistics for breeding data
#' #'
#' #'@param data A data frame
#' #'@param idx The name or position of the measured variable that will be summarized.
#' #'@param groupfactors A vector containing names of columns that contain grouping variables
#' #'@param na.rm A boolean that indicates whether to ignore NA's
#' #'@return A data frame with the count, mean and standard desviation
#' #'@author Omar Benites
#' #'@details This function returns the count, mean and standard desviation.
#' #'Furthermore, this function use the doBy package.
#' #'@references Some code for this function were inspired by Cookbook for R. 
#' #'@keywords stats, summary
#' #'@family stats,summary
#' #'@export 
#' #' 
#' sbsummary<- function(data=NULL,idx, groupfactors=NULL, na.rm=FALSE) {
#'   #require(doBy)
#'   # New version of length which can handle NA's: if na.rm==T, don't count them
#'   if(missing(data)){
#'     stop("Please enter your data")
#'   }
#'   if(missing(idx)){
#'     stop("Please enter the name or position of the measured variable")
#'   }
#'   if(missing(groupfactors)){
#'     stop("Please enter the name of columns that contain grouping variables")
#'   }
#'   length2 <- function (x, na.rm=FALSE) {
#'     if (na.rm) sum(!is.na(x))
#'     else length(x)
#'   }
#'   
#'   datos <- data
#'   vvv <- datos[,idx]
#'   #vvv <- datos$idx
#'   lbl <- names(datos[idx])
#'   measurevar <- lbl
#' 
#'   # Collapse the data
#'   formula <- as.formula(paste(measurevar, paste(groupfactors, collapse=" + "), sep=" ~ "))
#'   datac <- doBy::summaryBy(formula, data=data, FUN=c(length2,mean,sd), na.rm=na.rm)
#'   
#'   # Rename columns
#'   #names(datac)[ names(datac) == paste(measurevar, ".mean",    sep="") ] <- measurevar
#'   names(datac)[ names(datac) == paste(measurevar, ".length2", sep="") ] <- paste(measurevar,"_n",sep="")
#'   names(datac)[ names(datac) == paste(measurevar, ".mean",    sep="") ] <- paste(measurevar,"_Mean",sep="")  
#'   names(datac)[ names(datac) == paste(measurevar, ".sd",      sep="") ] <- paste(measurevar,"_sd",sep = "")
#'   
#'   return(datac)
#' }