pretty_pvalues: Round and format a vector of p-values
In wfulp/MoffittFunctions: Moffitt Functions

Description Usage Arguments Details Value Examples

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

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.

Vector of transformed p-values for table output

pvalue_example = c(1, 0.06, 0.0005, NA, 1e-6)

pretty_pvalues(pvalue_example, background = "pink")

pretty_pvalues(pvalue_example, digits = 4, missing_char = "missing", bold = TRUE)

# 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"))