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:

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 <mark.phillip.peterson@gmail.com>

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

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

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

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

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

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

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 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()

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()