R/any_incomplete.R

In peterwu19881230/microbialPhenotypes: Tools That Analyze Phenotypic Profiles by Annotation Sets

any_incomplete <-
function(table){
    if(!(class(table) %in% c("matrix","data.frame","data.table"))) stop("Input is not a matrix, data frame or data table")
    
    out=list()
    out$dimension=paste("Dimension: ",dim(table)[1]," rows * ",dim(table)[2]," columns",sep="")
    
    #Check NA
    na=apply(table,2,FUN=function(column){
        any=sum(is.na(column))
        return(any)
    })
    out$na=na[na>=1]
    
    #Check NULL
    null=apply(table,2,FUN=function(column){
        any=sum(is.null(column))
        return(any)
    }
    )
    out$null=null[null>=1]
    
    #Check NaN
    nan=apply(table,2,FUN=function(column){
        any=sum(is.nan(column)) #is.nan works fine for this because the columns called are vectors (if I call rows they are gonna be data frames)
        return(any)
    }
    )
    out$nan=nan[nan>=1]
    
    #Check ""
    empty=apply(table,2,FUN=function(column){
        any=sum(column=="",na.rm=T)
        return(any)
    }
    )
    out$empty=empty[empty>=1]
    
    total=sum(c(na,null,nan,empty))
    out$completeness=paste(total,' of NA, NAN, NULL, or empty character is found from ',dim(table)[1]*dim(table)[2], ' data points. They constitute ',total/(dim(table)[1]*dim(table)[2])*100,'%',sep="")
    
    return(out)
}