pretty_pvalues() takes a vector of p-values, rounds them to a specified digit amount, allows options for emphasizing p-values < the defined significance level, and returns a character for missing.
pretty_pvalues(pvalues, digits = 3, missing_char = "---", include_p = FALSE, trailing_zeros = TRUE, output_type = NULL, bold = FALSE, italic = FALSE, background = NULL, sig_alpha = 0.05)
| pvalues | numeric vector of raw p-values to be formatted |
|---|---|
| digits | number of digits to round to; values with zeros past this number of digits are truncated |
| missing_char | character string that will replace missing values from the p-value vector. Default = "---" |
| include_p | TRUE or FALSE: set to TRUE to print "p = " before each p-value |
| trailing_zeros | TRUE or FALSE: default = TRUE, p-values are formatted with trailing zeros to the defined number of digits (i.e. 0.100 instead of 0.1 if digits= 3) |
| output_type | output type, either NULL (default), "latex", or "html" (making special charaters latex friendly) |
| bold | TRUE or FALSE: set to TRUE to bold p-values < the defined significance level |
| italic | TRUE or FALSE: set to TRUE to italicize p-values < the defined significance level |
| background | highlight color for p-values < the defined significance level. Default = NULL (no highlighting) |
| sig_alpha | the defined significance level. Default = 0.05 |
Vector of transformed p-values for table output
With this function, there are two things to be noted:
Since the p-value vector formatting uses cell_spec, which generates raw HTML or LaTeX code, make sure you remember to put escape = FALSE into your kable code when generating your table. At the same time, you will need to escape special symbols manually.
Additionally, cell_spec needs a way to know whether you want HTML or LaTeX output. You can specify it locally in the function or globally using options(knitr.table.format = "latex"). If you don't provide anything, this function will output as HTML by default.
pvalue_example = c(1, 0.06, 0.0005, NA, 1e-6) pretty_pvalues(pvalue_example, background = "pink")#> [1] "1.000" "0.060" #> [3] "\\cellcolor{pink}{<0.001}" "---" #> [5] "\\cellcolor{pink}{<0.001}"pretty_pvalues(pvalue_example, digits = 4, missing_char = "missing", bold = TRUE)#> [1] "1.0000" "0.0600" "\\textbf{0.0005}" #> [4] "missing" "\\textbf{<0.0001}"# How to use pretty_pvalues in reports raw_pvals <- c(0.00000007, .05000001, NaN, NA, 0.783) pretty_pvals <- pretty_pvalues(raw_pvals , digits = 3, background = "green", italic = TRUE, bold = TRUE) kableExtra::kable(pretty_pvals , format = "latex", escape = FALSE, col.names = c("P-values"))#> #> \begin{tabular}{l} #> \hline #> P-values\\ #> \hline #> \cellcolor{green}{\em{\textbf{<0.001}}}\\ #> \hline #> 0.050\\ #> \hline #> ---\\ #> \hline #> ---\\ #> \hline #> 0.783\\ #> \hline #> \end{tabular}