R/sbnewqualityvar.R

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

#' #'Quality control for new fieldbook traits.
#' #'
#' #'@param data The data frame of the fieldbook
#' #'@param genotipes The genotipes column name
#' #'@param trait The trait column name
#' #'@param lfactor The factor column name
#' #'@param ll lower limit of values
#' #'@param ul upper limit of values
#' #'@details This function return the values which are out of range. It does not requiere a data dictionary.
#' #'Make data qualit control for new variables using a lower limit and upper defined by users.
#' #'@author Omar Benites
#' #'@export
#' 
#' #Data Quality of Fieldbook using just lower limit and upper limit (without data dictionary)
#' sb_newqualityvar <- function(data,genotipes,trait,lfactor=NULL,ll,ul){
#'   
#'   datos<-data
#'   xvar <- trait
#'   lfactor <- lfactor
#'   genotipes <- genotipes 
#'   lowerl <- as.numeric(ll)
#'   upperl <- as.numeric(ul)
#'   
#'   datos[,genotipes] <- as.factor(datos[,genotipes])
#'   
#'   if(!is.null(lfactor)){
#'     datos[,lfactor] <-as.factor(datos[,lfactor]) 
#'   }
#'   
#'   if(is.null(lfactor)){
#'     select_fb <- dplyr::select_(datos,genotipes,xvar)
#'   }
#'   
#'   if(!is.null(lfactor)){
#'     select_fb <- dplyr::select_(datos,genotipes,xvar,lfactor) 
#'   }
#'   
#'   out_rule <- datos[,xvar]>=lowerl & datos[,xvar]<=upperl #the good rule, so we denied with !
#'   if(any(out_rule)){ #If any value of 'out_rule' is true (ie. has outliers)
#'     
#'     out_pos <- rownames(datos[!out_rule,])
#'     out_values <- datos[out_pos,c(genotipes,xvar)]
#'     #out_genotipes <- datos[out_pos,"INSTN"]
#'     
#'     out_print <- paste("Please validate the column '", xvar, " 'the row '",out_pos, " 'the '", genotipes, " is " ,out_values[,genotipes],
#'                        "' the value' ", round(out_values[,xvar],3), " .The range is from ",lowerl, " to ", upperl ,sep="")
#'     
#'     # lowerl <- 30
#'     # upperl <- 35
#'     
#'     #  oor_low <- dplyr::filter(select_fb, datos[,xvar] < lowerl) #values out of range - lower
#'     #  oor_up  <- dplyr::filter(select_fb, datos[,xvar] > upperl) #values out of range - upper  
#'     
#'     return(out_print) 
#'   }
#'   
#'   #out_print <- "There is no values out of range"
#'   #return(out_print)
#' }
#' 
#' 
#' 
#' 
#' 
#'