frmt: Format Wrappers

Description

Functions for formatting numeric values for consistent display in reports.

Usage

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

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).

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` is really just a wrapper for the formatC.

`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

Run this code

# NOT RUN {
# Formatting numbers
integers <- c(1234L, 9861230L)
numbers  <- c(1234,  9861230)
frmt(integers)  # no decimal point
frmt(numbers)   # decimal point and zeros to the right

numbers <- c(0.1234, 0.1, 1234.4321, 0.365, 0.375)
frmt(numbers)

# 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"))

# 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"))

# 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)
frmtci(temp, show_level = TRUE)

# note that the show_level will be ignored in the following
frmtci(temp, format = "est ***lcl, ucl***", show_level = TRUE)

# show_level as a character
frmtci(temp, show_level = "confidence between: ")

# 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
frmtci(temp2)
# }