Format Wrappers

Functions for formatting numeric values for consistent display in reports.

Usage

frmt(x, digits = getOption("qwraps2_frmt_digits", 2), append = NULL)

frmtp(
  x,
  style = getOption("qwraps2_journal", "default"),
  digits = getOption("qwraps2_frmtp_digits", 4),
  markup = getOption("qwraps2_markup", "latex"),
  case = getOption("qwraps2_frmtp_case", "upper"),
  leading0 = getOption("qwraps2_frmtp_leading0", TRUE)
)

frmtci(
  x,
  est = 1,
  lcl = 2,
  ucl = 3,
  format = "est (lcl, ucl)",
  show_level = FALSE,
  ...
)

Arguments

x: a vector of numbers or a numeric matrix to format.
digits: number of digits, including trailing zeros, to the right of the decimal point. This option is ignored if is.integer(x) == TRUE).
append: a character string to append to the formatted number. This is particularly useful for percentages or adding punctuation to the end of the formatted number. This should be a vector of length 1, or equal to the length of x.
style: a character string indicating a specific journal requirements for p-value formatting.
markup: a character string indicating if the output should be latex or markup.
case: a character string indicating if the output should be upper case or lower case.
leading0: boolean, whether or not the p-value should be reported as 0.0123 (TRUE, default), or .0123 (FALSE).
est: the numeric index of the vector element or the matrix column containing the point estimate.
lcl: the numeric index of the vector element or the matrix column containing the lower confidence limit.
ucl: the numeric index of the vector element or the matrix column containing the upper confidence limit.
format: a string with "est" "lcl", and "ucl" to denote the location of the estimate, lower confidence limit, and upper confidence limit for the formatted string. Defaults to "est (lcl, ucl)".
show_level: defaults to FALSE. If TRUE and format is the default, then "100*(1-options()$qwraps2_alpha) parenthesis and the lcl. If set to a string, then the given string will be placed between the left parenthesis and the lcl. If the format is not the default, then this argument is ignored.
...: args passed to frmt

Value

a character vector of the formatted numbers

Details

`frmt` was originally really just a wrapper for the formatC. It has extended functionality now as I have found common uses cases.

`frmtp` formats P-values per journal requirements. As I work on papers aimed at different journals, the formatting functions will be extended to match.

Default settings are controlled through the function arguments but should be set via options().

Default settings report the P-value exactly if P > getOptions("qwraps2_frmtp_digits", 4) and reports P < 10^-(getOptions("qwraps2_frmtp_digits", 2)) otherwise. By the leading zero is controlled via getOptions("qwraps2_frmtp_leading0", TRUE) and a upper or lower case P is controlled by getOptions("qwraps2_frmtp_case", "upper"). These options are ignored if style != "default".

Journals with predefined P-value formatting are noted in the qwraps2 documentation.

`frmtci` takes a matrix, or data.frame, with a point estimate and the lcl and ucl and formats a string for reporting. est (lcl, ucl) is the default. The confidence level can be added to the string, e.g., "est (95 format.

`frmtcip` expects four values, est, lcl, ucl, and p-value. The resulting sting will be of the form "est (lcl, ucl; p-value)".

The `Rpkg`, `CRANpkg`, and `Githubpkg` functions are used to help make documenting packages stylistically consistent and with valid urls. These functions were inspired by similar ones found in the BioConductor BiocStyle package.

Examples


### Formatting numbers
integers <- c(1234L, 9861230L)
numbers  <- c(1234,  9861230)
frmt(integers)  # no decimal point
#> [1] "1,234"     "9,861,230"
frmt(numbers)   # decimal point and zeros to the right
#> [1] "1,234.00"     "9,861,230.00"

numbers <- c(0.1234, 0.1, 1234.4321, 0.365, 0.375)
frmt(numbers)
#> [1] "0.12"     "0.10"     "1,234.43" "0.36"     "0.38"    

# reporting a percentage
frmt(17/19 * 100, digits = 2, append = "%")   # good for markdown
#> [1] "89.47%"
frmt(17/19 * 100, digits = 2, append = "\\%") # good for LaTeX
#> [1] "89.47\\%"

# append one character
frmt(c(1, 2, 3)/19 * 100, digits = 2, append = "%")
#> [1] "5.26%"  "10.53%" "15.79%"

# append different characters
frmt(c(1, 2, 3)/19 * 100, digits = 2, append = c("%;", "%!", "%."))
#> [1] "5.26%;"  "10.53%!" "15.79%."

### Formatting p-values
ps <- c(0.2, 0.001, 0.00092, 0.047, 0.034781, 0.0000872, 0.787, 0.05, 0.043)
# LaTeX is the default markup language
cbind("raw"      = ps,
      "default"  = frmtp(ps),
      "3lower"   = frmtp(ps, digits = 3, case = "lower"),
      "PediDent" = frmtp(ps, style = "pediatric_dentistry"))
#>       raw        default        3lower        PediDent    
#>  [1,] "0.2"      "$P = 0.2000$" "$p = 0.200$" "$P = .20$" 
#>  [2,] "0.001"    "$P = 0.0010$" "$p = 0.001$" "$P = .001$"
#>  [3,] "0.00092"  "$P = 0.0009$" "$p < 0.001$" "$P < .001$"
#>  [4,] "0.047"    "$P = 0.0470$" "$p = 0.047$" "$P = .047$"
#>  [5,] "0.034781" "$P = 0.0348$" "$p = 0.035$" "$P = .03$" 
#>  [6,] "8.72e-05" "$P < 0.0001$" "$p < 0.001$" "$P < .001$"
#>  [7,] "0.787"    "$P = 0.7870$" "$p = 0.787$" "$P = .79$" 
#>  [8,] "0.05"     "$P = 0.0500$" "$p = 0.050$" "$P = .05$" 
#>  [9,] "0.043"    "$P = 0.0430$" "$p = 0.043$" "$P = .04$" 

### Using markdown
cbind("raw"      = ps,
      "default"  = frmtp(ps, markup = "markdown"),
      "3lower"   = frmtp(ps, digits = 3, case = "lower", markup = "markdown"),
      "PediDent" = frmtp(ps, style = "pediatric_dentistry", markup = "markdown"))
#>       raw        default        3lower        PediDent    
#>  [1,] "0.2"      "*P* = 0.2000" "*p* = 0.200" "*P* = .20" 
#>  [2,] "0.001"    "*P* = 0.0010" "*p* = 0.001" "*P* = .001"
#>  [3,] "0.00092"  "*P* = 0.0009" "*p* < 0.001" "*P* < .001"
#>  [4,] "0.047"    "*P* = 0.0470" "*p* = 0.047" "*P* = .047"
#>  [5,] "0.034781" "*P* = 0.0348" "*p* = 0.035" "*P* = .03" 
#>  [6,] "8.72e-05" "*P* < 0.0001" "*p* < 0.001" "*P* < .001"
#>  [7,] "0.787"    "*P* = 0.7870" "*p* = 0.787" "*P* = .79" 
#>  [8,] "0.05"     "*P* = 0.0500" "*p* = 0.050" "*P* = .05" 
#>  [9,] "0.043"    "*P* = 0.0430" "*p* = 0.043" "*P* = .04" 

# Formatting the point estimate and confidence interval
# for a set of three values
temp <- c(a = 1.23, b = .32, CC = 1.78)
frmtci(temp)
#> [1] "1.23 (0.32, 1.78)"

# show level uses getOption("qwraps2_alpha", 0.05)
frmtci(temp, show_level = TRUE)
#> [1] "1.23 (95% CI: 0.32, 1.78)"

# note that the show_level will be ignored in the following
frmtci(temp, format = "est ***lcl, ucl***", show_level = TRUE)
#> [1] "1.23 ***0.32, 1.78***"

# show_level as a character
frmtci(temp, show_level = "confidence between: ")
#> [1] "1.23 (confidence between: 0.32, 1.78)"

# For a matrix: the numbers in this example don't mean anything, but the
# formatting should.
temp2 <- matrix(rnorm(12), nrow = 4,
                dimnames = list(c("A", "B", "C", "D"), c("EST", "LOW", "HIGH")))
temp2
#>            EST        LOW       HIGH
#> A -1.400043517  0.6215527 -0.2441996
#> B  0.255317055  1.1484116 -0.2827054
#> C -2.437263611 -1.8218177 -0.5536994
#> D -0.005571287 -0.2473253  0.6289820
frmtci(temp2)
#>                      A                      B                      C 
#>  "-1.40 (0.62, -0.24)"   "0.26 (1.15, -0.28)" "-2.44 (-1.82, -0.55)" 
#>                      D 
#>  "-0.01 (-0.25, 0.63)" 

# similar for a data.frame
df2 <- as.data.frame(temp2)
frmtci(df2)
#>                      A                      B                      C 
#>  "-1.40 (0.62, -0.24)"   "0.26 (1.15, -0.28)" "-2.44 (-1.82, -0.55)" 
#>                      D 
#>  "-0.01 (-0.25, 0.63)"

Usage

Arguments

Value

Details

See also

Examples