Formatting P values

A function to format P values

fixp <- function(x, dig=3){

# Convert to a data frame
  if(is.data.frame(x) | is.matrix(x)){
  x <- as.data.frame(x)
  } else {
  x <- as.data.frame(x[[1]])
  }

# Check column order  
  if(substr(names(x)[ncol(x)],1,2) != "Pr"){
    warning("The name of the last column didn't start with Pr. This may indicate that p-values weren't in the last row, and thus, that this function is inappropriate.")
    }
    
# Round P values to "dig" decimal places, default 3     
  x[,ncol(x)] <- round(x[,ncol(x)], dig)

#  
  for(i in 1:nrow(x)){
    if(x[i,ncol(x)] == 0 & !is.na(x[i,ncol(x)])){
      x[i,ncol(x)] <- paste0("<0.", paste0(rep(0,dig-1), collapse=""), "1")
      }
  }
  x
}

The main modification to the original function is to expand the conversion of x to a data frame to accept lists and matrices. summary(aov(lm(...))) creates an object with class summary.aov which is a list and the coefficients table is a matrix. Although anova(lm(...)) creates a data frame that will work with the function without a fatal error, the function anova has its own way of “pretty” printing [to quote the help file] which is not compatible with the character vector in the P value column and thus will show a P value of 1. So forcing to a data frame is necessary. A minor modification is to ignore the NAs in the Residual row created by the data frame which would otherwise give an error.

The three decimal places for P values is coded into the function by default and can be changed by the dig option. For example, dig = 1 will give you \(<0.1\). You can then call your ANOVA table and the fixp function through knitr::kable() or your favourite HTML/LaTeX table formatter. e.g. kable(fixp(anova(lm(...))), digits = ...). If you don’t want to print NAs, it’s probably better to use the options in your chosen formatting function - e.g. the knitr.kable.NA option in kable.