# Rendering R Help Files

Included help files are critical for working in R and, despite the pain that is caused by creating them when you make libraries, they are an essential part of the experience and help your users more easily gain proficiency. One of the challenges, however, has been including the actual text of a help file into a markdown document. Here is an example of how to include help files by rendering .Rd to Html and then knitting it into the document itself.

Published

September 7, 2022

In teaching, there are many situations where you may want to show a generic help file and have it rendered in markdown. However, it has been a constant pain to do this for some reason. I finally found a way to do it easily in quarto so that you can quickly grab a help file, render it as HTML and then put it into a slide that is .scrollable using Quarto in a ReactJS presentation.

Here is how to set it up.

1. Create a slide that has the atrributed {.scrollable} so that the content on the slide can be much taller than the slide itself (it will be).

2. Create a chunk that is not echoed (e.g., add the #| echo: false at the first line.)

3. The main code grabs the help file, renders it into html, saves it as a temporary file, and then uses knitr to paste it into the slide as raw ouptput.

Here is an example I used for embedding ?strptime into the presentation.

hlp <- help(strptime)
helpfile <- utils:::.getHelpFile( hlp )
outfile <- tempfile(fileext = ".html")
tools::Rd2HTML(helpfile, out=outfile)
rawHTML <- paste( readLines(outfile), collapse = "\n")
knitr::asis_output( htmltools::htmlPreserve(rawHTML))
R: Date-time Conversion Functions to and from Character
 strptime R Documentation

## Date-time Conversion Functions to and from Character

### Description

Functions to convert between character representations and objects of classes "POSIXlt" and "POSIXct" representing calendar dates and times.

### Usage

## S3 method for class 'POSIXct'
format(x, format = "", tz = "", usetz = FALSE, ...)
## S3 method for class 'POSIXlt'
format(x, format = "", usetz = FALSE,
digits = getOption("digits.secs"), ...)

## S3 method for class 'POSIXt'
as.character(x, ...)

strftime(x, format = "", tz = "", usetz = FALSE, ...)
strptime(x, format, tz = "")


### Arguments

 x An object to be converted: a character vector for strptime, an object which can be converted to "POSIXlt" for strftime. tz A character string specifying the time zone to be used for the conversion. System-specific (see as.POSIXlt), but "" is the current time zone, and "GMT" is UTC. Invalid values are most commonly treated as UTC, on some platforms with a warning. format A character string. The default for the format methods is "%Y-%m-%d %H:%M:%S" if any element has a time component which is not midnight, and "%Y-%m-%d" otherwise. If options("digits.secs") is set, up to the specified number of digits will be printed for seconds. ... Further arguments to be passed from or to other methods. usetz logical. Should the time zone abbreviation be appended to the output? This is used in printing times, and more reliable than using "%Z". digits integer determining the format()ing of seconds when needed.

### Details

The format and as.character methods and strftime convert objects from the classes "POSIXlt" and "POSIXct" to character vectors.

strptime converts character vectors to class "POSIXlt": its input x is first converted by as.character. Each input string is processed as far as necessary for the format specified: any trailing characters are ignored.

strftime is a wrapper for format.POSIXlt, and it and format.POSIXct first convert to class "POSIXlt" by calling as.POSIXlt (so they also work for class "Date"). Note that only that conversion depends on the time zone. Since R version 4.2.0, that as.POSIXlt() conversion now treats the non-finite numeric -Inf, Inf, NA and NaN differently (where previously all were treated as NA) and also the format() method for POSIXlt now treats these different non-finite times and dates analogously to type double.

The usual vector re-cycling rules are applied to x and format so the answer will be of length of the longer of these vectors.

Locale-specific conversions to and from character strings are used where appropriate and available. This affects the names of the days and months, the AM/PM indicator (if used) and the separators in output formats such as %x and %X, via the setting of the LC_TIME locale category. The ‘current locale’ of the descriptions might mean the locale in use at the start of the R session or when these functions are first used. (For input, the locale-specific conversions can be changed by calling Sys.setlocale with category LC_TIME (or LC_ALL). For output, what happens depends on the OS but usually works.)

The details of the formats are platform-specific, but the following are likely to be widely available: most are defined by the POSIX standard. A conversion specification is introduced by %, usually followed by a single letter or O or E and then a single letter. Any character in the format string not part of a conversion specification is interpreted literally (and %% gives %). Widely implemented conversion specifications include

%a

Abbreviated weekday name in the current locale on this platform. (Also matches full name on input: in some locales there are no abbreviations of names.)

%A

Full weekday name in the current locale. (Also matches abbreviated name on input.)

%b

Abbreviated month name in the current locale on this platform. (Also matches full name on input: in some locales there are no abbreviations of names.)

%B

Full month name in the current locale. (Also matches abbreviated name on input.)

%c

Date and time. Locale-specific on output, "%a %b %e %H:%M:%S %Y" on input.

%C

Century (00–99): the integer part of the year divided by 100.

%d

Day of the month as decimal number (01–31).

%D

Date format such as %m/%d/%y: the C99 standard says it should be that exact format (but not all OSes comply).

%e

Day of the month as decimal number (1–31), with a leading space for a single-digit number.

%F

Equivalent to %Y-%m-%d (the ISO 8601 date format).

%g

The last two digits of the week-based year (see %V). (Accepted but ignored on input.)

%G

The week-based year (see %V) as a decimal number. (Accepted but ignored on input.)

%h

Equivalent to %b.

%H

Hours as decimal number (00–23). As a special exception strings such as ‘⁠24:00:00⁠’ are accepted for input, since ISO 8601 allows these.

%I

Hours as decimal number (01–12).

%j

Day of year as decimal number (001–366): For input, 366 is only valid in a leap year.

%m

Month as decimal number (01–12).

%M

Minute as decimal number (00–59).

%n

Newline on output, arbitrary whitespace on input.

%p

AM/PM indicator in the locale. Used in conjunction with %I and not with %H. An empty string in some locales (for example on some OSes, non-English European locales including Russia). The behaviour is undefined if used for input in such a locale.

Some platforms accept %P for output, which uses a lower-case version (%p may also use lower case): others will output P.

%r

For output, the 12-hour clock time (using the locale's AM or PM): only defined in some locales, and on some OSes misleading in locales which do not define an AM/PM indicator. For input, equivalent to %I:%M:%S %p.

%R

Equivalent to %H:%M.

%S

Second as integer (00–61), allowing for up to two leap-seconds (but POSIX-compliant implementations will ignore leap seconds).

%t

Tab on output, arbitrary whitespace on input.

%T

Equivalent to %H:%M:%S.

%u

Weekday as a decimal number (1–7, Monday is 1).

%U

Week of the year as decimal number (00–53) using Sunday as the first day 1 of the week (and typically with the first Sunday of the year as day 1 of week 1). The US convention.

%V

Week of the year as decimal number (01–53) as defined in ISO 8601. If the week (starting on Monday) containing 1 January has four or more days in the new year, then it is considered week 1. Otherwise, it is the last week of the previous year, and the next week is week 1. (Accepted but ignored on input.)

%w

Weekday as decimal number (0–6, Sunday is 0).

%W

Week of the year as decimal number (00–53) using Monday as the first day of week (and typically with the first Monday of the year as day 1 of week 1). The UK convention.

%x

Date. Locale-specific on output, "%y/%m/%d" on input.

%X

Time. Locale-specific on output, "%H:%M:%S" on input.

%y

Year without century (00–99). On input, values 00 to 68 are prefixed by 20 and 69 to 99 by 19 – that is the behaviour specified by the 2018 POSIX standard, but it does also say ‘it is expected that in a future version the default century inferred from a 2-digit year will change’.

%Y

Year with century. Note that whereas there was no zero in the original Gregorian calendar, ISO 8601:2004 defines it to be valid (interpreted as 1BC): see https://en.wikipedia.org/wiki/0_(year). However, the standards also say that years before 1582 in its calendar should only be used with agreement of the parties involved.

For input, only years 0:9999 are accepted.

%z

Signed offset in hours and minutes from UTC, so -0800 is 8 hours behind UTC. Values up to +1400 are accepted. (Standard only for output. For input R currently supports it on all platforms.)

%Z

(Output only.) Time zone abbreviation as a character string (empty if not available). This may not be reliable when a time zone has changed abbreviations over the years.

Where leading zeros are shown they will be used on output but are optional on input. Names are matched case-insensitively on input: whether they are capitalized on output depends on the platform and the locale. Note that abbreviated names are platform-specific (although the standards specify that in the ‘⁠C⁠’ locale they must be the first three letters of the capitalized English name: this convention is widely used in English-language locales but for example the French month abbreviations are not the same on any two of Linux, macOS, Solaris and Windows). Knowing what the abbreviations are is essential if you wish to use %a, %b or %h as part of an input format: see the examples for how to check.

When %z or %Z is used for output with an object with an assigned time zone an attempt is made to use the values for that time zone — but it is not guaranteed to succeed.

Not in the standards and less widely implemented are

%k

The 24-hour clock time with single digits preceded by a blank.

%l

The 12-hour clock time with single digits preceded by a blank.

%s

(Output only.) The number of seconds since the epoch.

%+

(Output only.) Similar to %c, often "%a %b %e %H:%M:%S %Z %Y". May depend on the locale.

For output there are also %O[dHImMUVwWy] which may emit numbers in an alternative locale-dependent format (e.g., roman numerals), and %E[cCyYxX] which can use an alternative ‘era’ (e.g., a different religious calendar). Which of these are supported is OS-dependent. These are accepted for input, but with the standard interpretation.

Specific to R is %OSn, which for output gives the seconds truncated to 0 <= n <= 6 decimal places (and if %OS is not followed by a digit, it uses the setting of getOption("digits.secs"), or if that is unset, n = 0). Further, for strptime %OS will input seconds including fractional seconds. Note that %S does not read fractional parts on output.

The behaviour of other conversion specifications (and even if other character sequences commencing with % are conversion specifications) is system-specific. Some systems document that the use of multi-byte characters in format is unsupported: UTF-8 locales are unlikely to cause a problem.

### Value

The format methods and strftime return character vectors representing the time. NA times are returned as NA_character_. The elements are restricted to 256 bytes, plus a time zone abbreviation if usetz is true. (On known platforms longer strings are truncated at 255 or 256 bytes, but this is not guaranteed by the C99 standard.)

strptime turns character representations into an object of class "POSIXlt". The time zone is used to set the isdst component and to set the "tzone" attribute if tz != "". If the specified time is invalid (for example ‘⁠"2010-02-30 08:00"⁠’) all the components of the result are NA. (NB: this does means exactly what it says – if it is an invalid time, not just a time that does not exist in some time zone.)

### Printing years

Everyone agrees that years from 1000 to 9999 should be printed with 4 digits, but the standards do not define what is to be done outside that range. For years 0 to 999 most OSes pad with zeros or spaces to 4 characters, and Linux outputs just the number.

OS facilities will probably not print years before 1 CE (aka 1 AD) ‘correctly’ (they tend to assume the existence of a year 0: see https://en.wikipedia.org/wiki/0_(year), and some OSes get them completely wrong). Common formats are -45 and -045.

Years after 9999 and before -999 are normally printed with five or more characters.

Some platforms support modifiers from POSIX 2008 (and others). On Linux the format "%04Y" assures a minimum of four characters and zero-padding. The internal code (as used on Windows and by default on macOS) uses zero-padding by default, and formats %_4Y and %_Y can be used for space padding and no padding.

### Time zone offsets

Offsets from GMT (also known as UTC) are part of the conversion between timezones and to/from class "POSIXct", but cause difficulties as they are often computed incorrectly.

They conventionally have the opposite sign from time-zone specifications (see Sys.timezone): positive values are East of the meridian. Although there have been time zones with offsets like 00:09:21 (Paris in 1900), and 00:44:30 (Liberia until 1972), offsets are usually treated as whole numbers of minutes, and are most often seen in RFC 5322 email headers in forms like -0800 (e.g., used on the Pacific coast of the USA in winter).

Format %z can be used for input or output: it is a character string, conventionally plus or minus followed by two digits for hours and two for minutes: the standards say that an empty string should be output if the offset is unknown, but some systems use the offsets for the time zone in use for the current year.

### Sources

Input uses the POSIX function strptime and output the C99 function strftime.

However, not all OSes (notably Windows) provided strptime and many issues were found for those which did, so since 2000 R has used a fork of code from ‘⁠glibc⁠’. The forked code uses the system's strftime to find the locale-specific day and month names and any AM/PM indicator.

On some platforms (including Windows and by default on macOS) the system's strftime is replaced (along with most of the rest of the C-level datetime code) by code modified from IANA's ‘⁠tzcode⁠’ distribution (https://www.iana.org/time-zones).

### Note

The default formats follow the rules of the ISO 8601 international standard which expresses a day as "2001-02-28" and a time as "14:01:02" using leading zeroes as here. (The ISO form uses no space to separate dates and times: R does by default.)

For strptime the input string need not specify the date completely: it is assumed that unspecified seconds, minutes or hours are zero, and an unspecified year, month or day is the current one. (However, if a month is specified, the day of that month has to be specified by %d or %e since the current day of the month need not be valid for the specified month.) Some components may be returned as NA (but an unknown tzone component is represented by an empty string).

If the time zone specified is invalid on your system, what happens is system-specific but it will probably be ignored.

Remember that in most time zones some times do not occur and some occur twice because of transitions to/from ‘daylight saving’ (also known as ‘summer’) time. strptime does not validate such times (it does not assume a specific time zone), but conversion by as.POSIXct will do so. Conversion by strftime and formatting/printing uses OS facilities and may return nonsensical results for non-existent times at DST transitions.

In a C locale %c is required to be "%a %b %e %H:%M:%S %Y". As Windows does not comply (and uses a date format not understood outside N. America), that format is used by R on Windows in all locales.

### References

International Organization for Standardization (2004, 2000, ...) ‘ISO 8601. Data elements and interchange formats – Information interchange – Representation of dates and times.’, slightly updated to International Organization for Standardization (2019) ‘ISO 8601-1:2019. Date and time – Representations for information interchange – Part 1: Basic rules’. For links to versions available on-line see (at the time of writing) https://dotat.at/tmp/ISO_8601-2004_E.pdf and https://www.qsl.net/g1smd/isopdf.htm; for information on the current official version, see https://www.iso.org/iso/iso8601 and https://en.wikipedia.org/wiki/ISO_8601.

The POSIX 1003.1 standard, which is in some respects stricter than ISO 8601.

DateTimeClasses for details of the date-time classes; locales to query or set a locale.

Your system's help page on strftime to see how to specify their formats. (On some systems, including Windows, strftime is replaced by more comprehensive internal code.)

### Examples


## locale-specific version of date()
format(Sys.time(), "%a %b %d %X %Y %Z")

## time to sub-second accuracy (if supported by the OS)
format(Sys.time(), "%H:%M:%OS3")

## read in date info in format 'ddmmmyyyy'
## This will give NA(s) in some non-English locales; setting the C locale
## as in the commented lines will overcome this on most systems.
## lct <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C")
x <- c("1jan1960", "2jan1960", "31mar1960", "30jul1960")
z <- strptime(x, "%d%b%Y")
## Sys.setlocale("LC_TIME", lct)
z

## read in date/time info in format 'm/d/y h:m:s'
dates <- c("02/27/92", "02/27/92", "01/14/92", "02/28/92", "02/01/92")
times <- c("23:03:20", "22:29:56", "01:03:30", "18:21:03", "16:56:26")
x <- paste(dates, times)
strptime(x, "%m/%d/%y %H:%M:%S")

## time with fractional seconds
z <- strptime("20/2/06 11:16:16.683", "%d/%m/%y %H:%M:%OS")
z # prints without fractional seconds
op <- options(digits.secs = 3)
z
options(op)

## time zone names are not portable, but 'EST5EDT' comes pretty close.
(x <- strptime(c("2006-01-08 10:07:52", "2006-08-07 19:33:02"),
"%Y-%m-%d %H:%M:%S", tz = "EST5EDT"))
attr(x, "tzone")

## In a non-English locale the commented lines may be needed.
## prev <- Sys.getlocale("LC_TIME"); Sys.setlocale("LC_TIME", "C")
strptime("Tue, 23 Mar 2010 14:36:38 -0400", "%a, %d %b %Y %H:%M:%S %z")
## Sys.setlocale("LC_TIME", prev)

## Make sure you know what the abbreviated names are for you if you wish
## to use them for input (they are matched case-insensitively):
format(seq.Date(as.Date('1978-01-01'), by = 'day', len = 7), "%a")
format(seq.Date(as.Date('2000-01-01'), by = 'month', len = 12), "%b")

format(.POSIXct(Inf)) # "Inf"  (was  NA  in R <= 4.1.x)
notF <- c(-Inf,Inf,NaN,NA)
(fF <- format(.POSIXct(notF))) # was all  NA, now the last is still NA (not "NA")
stopifnot(identical(as.character(notF), fF))