Package 'rmdHelpers'

Title: Helper Functions for Rmd Documents
Description: A series of functions to aid in repeated tasks for Rmd documents. All details are to my personal preference, though I am happy to add flexibility if there are use cases I am missing. I will continue updating with new functions as I add utility functions for myself.
Authors: Mark Peterson
Maintainer: Mark Peterson <[email protected]>
License: GPL
Version: 1.3.1
Built: 2025-03-09 02:40:04 UTC
Source: https://github.com/cran/rmdHelpers

Help Index

Helper Functions for Rmd Documents

Description

A series of functions to aid in repeated tasks for Rmd documents. All details are to my personal preference, though I am happy to add flexibility if there are use cases I am missing. I will continue updating with new functions as I add utility functions for myself.

Details

The DESCRIPTION file:

Package: rmdHelpers
Type: Package
Title: Helper Functions for Rmd Documents
Version: 1.3.1
Date: 2024-07-11
Author: Mark Peterson
Maintainer: Mark Peterson <[email protected]>
Description: A series of functions to aid in repeated tasks for Rmd documents. All details are to my personal preference, though I am happy to add flexibility if there are use cases I am missing. I will continue updating with new functions as I add utility functions for myself.
License: GPL
Depends: knitr, dplyr
NeedsCompilation: no
Packaged: 2024-07-11 20:40:49 UTC; mark
Date/Publication: 2024-07-11 21:00:02 UTC
Repository: https://petersmp.r-universe.dev
RemoteUrl: https://github.com/cran/rmdHelpers
RemoteRef: HEAD
RemoteSha: b10d28eb122fa68f300f62247ce3c8b77d6d9076

Index of help topics: 

formatEffectTable       Format an effect table
formatP                 Format p-value
myFrac                  Print Fraction for markdown
myKable                 Wrapper for kable
printList               Print nice lists
refNote                 Generate a popup reference note
rmdHelpers-package      Helper Functions for Rmd Documents
thisFileName            Identify current file
thisfile_knit           Identify the file currently being knitted

Basic functions that I use in multiple Rmd documents

Author(s)

Mark Peterson

Maintainer: Mark Peterson <[email protected]>

Format an effect table

Description

Performs general formatting of effect tables from 'lm' suitable for basic printing. This includes merging estimates and confidence intervals, rounding, and optionally improving the display of factor and logical columns (using a colon and space, instead of just concatenating them).

Usage

formatEffectTable(object
                  , level = 0.95
                  , estDigits = 2
                  , pDigits = 4
                  , cleanFactors = TRUE)

Arguments

object

A fitted model object from 'lm'

level

The confidence level to be returned

estDigits

The number of digits to be displayed for the estimate and confidence thresholds

pDigits

The number of digits to be displayed for the p-values

cleanFactors

Logical. Should the parameter names for factors be cleaned by separating the parameter from the value with a colon and a space, or not. (This option may lead to issues with merging if set to 'TRUE'.)

Value

A data.frame formatted ready to be displayed (e.g. by 'kable')

Note

Note that "NA" values are silently dropped (they are not returned by 'summary.lm' in the coefficients table).

Author(s)

Mark Peterson

Examples

irisMod <- lm(Sepal.Length ~ ., data = iris)
formatEffectTable(irisMod)

Format p-value

Description

A wrapper to sensibly control the printing of p-values because I was frustrated with playing with round. Calls format instead now.

Usage

formatP(p, digits = 3, scientific = FALSE, ...)

Arguments

p

Numeric vector of values to be displayed

digits

Numeric of length one giving the number of digits to display. Note that if p is longer than 1, all returned values will be to the same level of precision.

scientific

Logical, should scientific notation be used?

...

Further arguments passed to format

Value

Character vector of the p-value(s) formatted

Author(s)

Mark Peterson

See Also

format

Examples

formatP(0.049865465646)

formatP(0.00000013212354)

formatP(c(0.01564643131,.0003456463131, .45643131564), 2)

Print Fraction for markdown

Description

Converts fractions for inline rendering.

Usage

myFrac(num, denom, format = "markdown")

Arguments

num

Either a vector of values for the numerators, or, if denom is NULL, fractions using "/" as the separator (allows passing fractions directly, as from fractions)

denom

Vector of values for the denominators, or NULL (the default) if num is already formatted fractions.

format

Character vector of length one giving the format of the output. Default of "markdown" uses super script for the numerator, a slash, then subscript for the denominator. Alternatively, "latex" uses \frac and surrounds the fraction with $ to induce LaTeX conversion (via MathJax for html output)

Value

Character vector of the fractions

Note

If passing fractions, the function assumes that there is exactly one "/" in each fraction, and will return "NA" for the denominator if none is present or truncate the fraction if more than one "/" is included.

Author(s)

Mark Peterson

See Also

fractions

Examples

myFrac(3,4)

myFrac(1:3,4:6)

myFrac(1:3,4:6, "latex")

myFrac(letters[1:5], LETTERS[1:5])

myFrac( c("1/2","3/4", "9856/5646") )

myFrac( c("1/2","3/4", "9856/5646"), format = "latex" )

Wrapper for kable

Description

A small wrapper for the knitr kable function to allow automated bolding of row and/or column names. Additional functionality may be added/

Usage

myKable(x, row.names = NA, boldRowNames = TRUE, boldColNames = TRUE, ...)

Arguments

x

Table or matrix to be passed to kable

row.names

Logical: should row names be included? Defaults to NULL which includes row names if they are not just numeric in order.

boldRowNames

Logical: should row names be bolded?

boldColNames

Logical: should column names be bolded?

...

Additional arguments to be passed to kable

Details

Currently bolds in markdown format, so needs to be passed through interpreter after running.

Value

A formatted table from kable

Author(s)

Mark Peterson

See Also

kable

Examples

tempTable <- matrix(LETTERS[6:20], nrow = 5)
colnames(tempTable) <- LETTERS[24:26]
row.names(tempTable) <- LETTERS[1:5]
myKable(tempTable)

myKable(tempTable, boldColNames =  FALSE)

Print nice lists

Description

Generate a list formatted for printing from a vector.

Usage

printList(toPrint = letters[1:3], finalSepWord = "and", midSep = ",")

Arguments

toPrint

Vector that you want to turn into a text list.

finalSepWord

The last word to include, defaults to "and" but could be "or" or similar

midSep

Separator between items, defaults to ","

Details

Note that this function includes an Oxford comma.

Value

Character vector of length 1 with the values of toPrint concatenated and separated as specified in the text.

Author(s)

Mark Peterson

Examples

printList()

printList(LETTERS[1:5])

printList(letters[1:5], "or", ";")

Generate a popup reference note

Description

Generates the html needed to include a popup reference note. Note requires inclusion of javascript libraries for this to function.

Usage

refNote(text = "This is a test note", number = "*")

Arguments

text

Note to include in popup. Line breaks occasionally cause problems. As this is generally for short notes; I have not come up with a general solution yet. If your note text is complicated, ensure that you check the result.

number

The label to identify the note in the text.

Value

The html for the popup note

Note

The html page also needs to include the javascript and css to process the notes for these to work. Specifically, need to include the following (generally in the header): 

<!-- The javascript to run the popup refernce notes -->
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.10.1/jquery.min.js"></script>
    <script>
      jQuery.noConflict();
      jQuery(function() {
        jQuery(".refbody").hide();
        jQuery(".refnum").click(function(event) {
          jQuery(this.nextSibling).toggle();
          event.stopPropagation();
        });
        jQuery("body").click(function(event) {
          jQuery(".refbody").hide();
        });
      });
    </script>

And the following to wherever you include you css definitions: 

/* the reference tooltips style starts here */
/* This was stolen from the What If? css sytle sheet
 *  at https://what-if.xkcd.com/css/style.css
 *  in an effort to emulate that style  */

.ref {
    position: relative;
    vertical-align: baseline;
   }

.refnum {
    position: relative;
    left: 2px;
    bottom: 1ex;
    font-family: Verdana, sans-serif;
    color: #005994;
    font-size: .7em;
    font-weight: bold;
    text-decoration: underline;
    cursor: pointer;
}

.refbody {
    font-family: Verdana, sans-serif;
    font-size: .7em;
    line-height: 1.1;
    display: block;
    min-width: 20em;
    position: absolute;
    left: 25px;
    bottom: 5px ;
    border: 1px solid;
    padding: 5px;
    background-color: #fff;
    word-wrap: break-word;
    z-index: 9999;
    overflow: auto;
}

Author(s)

Mark Peterson

References

This was based on the popups on the https://what-if.xkcd.com/ site

Examples

cat(refNote())

cat(refNote("Any text can go in here", 42))

Identify the file currently being knitted

Description

Identifies the file that knitr is processing when the function is called.

Usage

thisfile_knit()

Value

Returns the current file name

Author(s)

Mark Peterson

References

Based on https://github.com/krlmlr/kimisc/blob/master/R/thisfile.R

See Also

thisFileName

Examples

thisfile_knit()

Identify current file

Description

Identify the file currently being processed

Usage

thisFileName()

Details

Currently only works for files being processed with knit; may try to add more

Value

The current file name

References

Based on https://github.com/krlmlr/kimisc/blob/master/R/thisfile.R

See Also

thisfile_knit

Examples

thisFileName()