<strong>!!!</strong> Format p-values — format_p

Functions to fromat p values. NOTE: concider using scales::pvalue() instead.

format_p_values(
  p,
  digits_p = 3,
  cols = NULL,
  ...,
  alpha = 0.05,
  signif_stars = TRUE,
  rm_zero = FALSE,
  add_p = FALSE,
  rm_spaces = FALSE,
  ss = signif_syms
)

# S3 method for default
format_p_values(
  p,
  digits_p = 3,
  cols = NULL,
  ...,
  signif_stars = TRUE,
  rm_zero = FALSE,
  add_p = FALSE,
  rm_spaces = FALSE,
  ss = signif_syms
)

format_p(
  p_i,
  digits_p = 3,
  signif_stars = TRUE,
  rm_zero = FALSE,
  add_p = FALSE,
  rm_spaces = FALSE,
  ss = signif_syms
)

# S3 method for data.frame
format_p_values(
  p,
  digits_p = 3,
  cols = NULL,
  ...,
  ss = signif_syms,
  signif_stars = TRUE,
  rm_zero = FALSE,
  add_p = FALSE,
  rm_spaces = FALSE
)

add_signif_stars(p, ss = signif_syms)

get_signif_stars(p, ss = signif_syms)

signif_syms_05s

p05

signif_syms_01s

p01

signif_syms_001s

p001

signif_syms_001

signif_syms_01

signif_syms_05

signif_syms

p05_01_001

p05plus

signif_stars_legend_2(ss = signif_syms)

signif_stars_legend(
  ss = signif_syms,
  decreasing = FALSE,
  collapse = c("  \n", ", ", "; ")
)

rm_zero(str, dec = ".")

format_as_p_columns(
  data,
  colnames = c("p.value", "p.adjust"),
  digits_p = 3,
  rm_zero = FALSE,
  signif_stars = FALSE,
  ...
)

Arguments

p	A (vector of) p-value(s). Numeric or coercible to numeric. Or a `data.frame`.
digits_p	(numeric) Number of significant digits to round a p value to. No less than 2. if `digits_p = 2`: values below 0.001 are printed as `"<0.001"`; values between 0.001 and 0.01 as `"<0.01"`; all other values are rounded to two decimal places. if `digits_p = 3`, only formatting `"<0.01"` is skipped.
cols, alpha, ss, decreasing, collapse, dec	`# FIXME:` not documented
...	Arguments to further methods.
signif_stars	(logical) Flag if significance stars should be added to each p value. Not less than 2.
rm_zero	(logical) Flag if leading zero before the point should be removed.
add_p	(logical) Flag if letter "p" should included in the expression.
rm_spaces	(logical) Flag if all spaces should be removed.

Format

An object of class numeric of length 1.

An object of class numeric of length 2.

An object of class numeric of length 3.

An object of class numeric of length 4.

Value

A character vector with formatted p values.

Details

format_p - formats single p value.
format_as_p_columns - formats indicated numeric columns in a dataframe as p values (columns are converted into strings).
get_signif_stars - takes numeric p values brings appopriate stars of statistical significance.
add_signif_stars - formats numeric p values by adding significance stars (result is character vector).
signif_stars_legend - generates legend for significance stars (result is a string).
rm_zero - function removes zero at the beginning of a number (returns a string with the same value but without the leading zero).

Examples

library(biostat)

# Prettify p-values

format_p_values(0.0005)
#> [1] "<0.001 ***"

format_p_values(0.005)
#> [1] " 0.005 ** "
format_p_values(0.005, signif_stars = FALSE)
#> [1] " 0.005"
format_p_values(0.005, rm_zero = TRUE)
#> [1] " .005 ** "
format_p_values(0.005, digits_p = 2)
#> [1] "<0.01 ** "
format_p_values(0.005, digits_p = 2, rm_zero = TRUE, signif_stars = FALSE)
#> [1] "<.01"

format_p_values(0.00022)
#> [1] "<0.001 ***"
format_p_values("0.00022")
#> [1] "<0.001 ***"
format_p_values("0.052")
#> [1] " 0.052 .  "

format_p_values(c(0.005, 0.0005, 0.052147))
#> [1] " 0.005 ** " "<0.001 ***" " 0.052 .  "


get_signif_stars(0.005)
#> [1] "**"
#> attr(,"legend")
#> [1] "0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1"
add_signif_stars(0.005)
#> [1] "0.005 **"

get_signif_stars(0.0005)
#> [1] "***"
#> attr(,"legend")
#> [1] "0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1"
add_signif_stars(0.0005)
#> [1] "5e-04 ***"

get_signif_stars(0.052147)
#> [1] "."
#> attr(,"legend")
#> [1] "0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1"
add_signif_stars(0.052147)
#> [1] "0.052147 ."

signif_stars_legend()
#> [1] "*** - p < 0.001  \n** - p < 0.01  \n* - p < 0.05  \n. - p < 0.1"

format_p(0)
#> [1] "<0.001 ***"
format_p(.02, digits_p = 2)
#> [1] " 0.02 *  "
format_p(.0002)
#> [1] "<0.001 ***"
format_p(.0002, signif_stars = FALSE)
#> [1] "<0.001"
format_p(.0002, ss = c("*****" = 0.001))
#> [1] "<0.001 *****"

# TODO **[!!!]**:
# 1. Add parameter to emable p value correction
#    from p = 1 into, e.g., p > 0.999;
#
# 2. merge parameters `ss` and `signif_stars`
# 3. test: format_p(NaN) -- [OK]
# 4. test: format_p(NA) -- this function fails with NA as input.
rm_zero(0.020)
#> [1] ".02"

!!! Format p-values

Arguments

Format

Value

Details

Examples