Package 'pander'

Description

Adds a line break before and after the character string(s).

Usage

add.blank.lines(x)

Arguments

Description

This function adds significance stars to passed p value(s) as: one star for value below 0.05, two for 0.01 and three for 0.001.

Usage

add.significance.stars(p, cutoffs = c(0.05, 0.01, 0.001))

Arguments

Value

character vector

Description

This function is just a wrapper around evalsOptions to switch pander's cache on or off easily, which might be handy in some brew documents to prevent repetitive strain injury :)

Usage

cache.on()

cache.off()

Description

Calculate coef matrix for models from rms package Forked from prModFit from rms

Usage

coef_mat(obj, coefs)

Arguments

Value

coeficients matrix

Description

Storing indexes of cells to be (strong) emphasized of a tabular data in an internal buffer that can be released and applied by pandoc.table, pander or evals later.

Usage

emphasize.rows(x)

emphasize.cols(x)

emphasize.cells(x)

emphasize.strong.rows(x)

emphasize.strong.cols(x)

emphasize.strong.cells(x)

emphasize.italics.rows(x)

emphasize.italics.cols(x)

emphasize.italics.cells(x)

emphasize.verbatim.rows(x)

emphasize.verbatim.cols(x)

emphasize.verbatim.cells(x)

Arguments

Examples

## Not run: 
n <- data.frame(x = c(1,1,1,1,1), y = c(0,1,0,1,0))
emphasize.cols(1)
emphasize.rows(1)
pandoc.table(n)

emphasize.strong.cells(which(n == 1, arr.ind = TRUE))
pander(n)

## End(Not run)

Description

This function takes text(s) of R code and evals all at one run - returning a list with four elements. See Details.

Usage

eval.msgs(
  src,
  env = NULL,
  showInvisible = FALSE,
  graph.unify = evalsOptions("graph.unify")
)

Arguments

Details

eval.msgs returns a detailed list of the result of evaluation:

• src - character vector of specified R code.

• result - result of evaluation. NULL if nothing is returned. If any R code returned an R object while evaluating then the last R object will be returned as a raw R object. If a graph is plotted in the end of the given R code (remember: last R object), it would be automatically printed (see e.g. lattice and ggplot2).

• output - character vector of printed version (capture.output) of result

• type - class of generated output. 'NULL' if nothing is returned, 'error' if some error occurred.

• msg - possible messages grabbed while evaluating specified R code with the following structure:

  • messages - character vector of possible diagnostic message(s)

  • warnings - character vector of possible warning message(s)

  • errors - character vector of possible error message(s)

• stdout - character vector of possibly printed texts to standard output (console)

Value

a list of parsed elements each containing: src (the command run), result (R object: NULL if nothing returned), printed output, type (class of returned object if any), informative/wawrning and error messages (if any returned by the command run, otherwise set to NULL) and possible stdoutt value. See Details above.

See Also

evals

Examples

## Not run: 
eval.msgs('1:5')
eval.msgs('x <- 1:5')
eval.msgs('lm(mtcars$hp ~ mtcars$wt)')

## plots
eval.msgs('plot(runif(100))')
eval.msgs('histogram(runif(100))')

## error handling
eval.msgs('runiff(23)')
eval.msgs('runif is a nice function')
eval.msgs('no.R.object.like.that')

## messages
eval.msgs(c('message("FOO")', '1:2'))
eval.msgs(c('warning("FOO")', '1:2'))
eval.msgs(c('message("FOO");message("FOO");warning("FOO")', '1:2'))
eval.msgs('warning("d");warning("f");1')

## stdout
eval.msgs('cat("writing to console")')
eval.msgs('cat("writing to console");1:4')

## End(Not run)

Description

This function takes either a vector/list of strings with actual R code, which it to be parsed to separate elements. Each list element is evaluated in a special environment, and a detailed list of results is returned for each logical part of the R code: a character value with R code, resulting R object, printed output, class of resulting R object, possible informative/warning/error messages and anything written to stdout. If a graph is plotted in the given text, the returned object is a string specifying the path to the saved file. Please see Details below. If parse option set to FALSE, then the returned list's length equals to the length of the parsed input - as each string is evaluated as separate R code in the same environment. If a nested list of R code or a concatenated string (separated by \n or ;) is provided like list(c('runif(1)', 'runif(1)')) with parse=FALSE, then everything is evaled at one run so the length of returned list equals to one or the length of the provided nested list. See examples below.

Usage

evals(
  txt,
  parse = evalsOptions("parse"),
  cache = evalsOptions("cache"),
  cache.mode = evalsOptions("cache.mode"),
  cache.dir = evalsOptions("cache.dir"),
  cache.time = evalsOptions("cache.time"),
  cache.copy.images = evalsOptions("cache.copy.images"),
  showInvisible = FALSE,
  classes = evalsOptions("classes"),
  hooks = evalsOptions("hooks"),
  length = evalsOptions("length"),
  output = evalsOptions("output"),
  env = NULL,
  graph.unify = evalsOptions("graph.unify"),
  graph.name = evalsOptions("graph.name"),
  graph.dir = evalsOptions("graph.dir"),
  graph.output = evalsOptions("graph.output"),
  width = evalsOptions("width"),
  height = evalsOptions("height"),
  res = evalsOptions("res"),
  hi.res = evalsOptions("hi.res"),
  hi.res.width = evalsOptions("hi.res.width"),
  hi.res.height = 960 * (height/width),
  hi.res.res = res * (hi.res.width/width),
  graph.env = evalsOptions("graph.env"),
  graph.recordplot = evalsOptions("graph.recordplot"),
  graph.RDS = evalsOptions("graph.RDS"),
  log = evalsOptions("log"),
  ...
)

Arguments

Details

As evals tries to grab the plots internally, pleas do not run commands that set graphic device or dev.off. E.g. running evals(c('png("/tmp/x.png")', 'plot(1:10)', 'dev.off()')) would fail. printing of lattice and ggplot2 objects is not needed, evals would deal with that automatically.

The generated image file(s) of the plots can be fine-tuned by some specific options, please check out graph.output, width, height, res, hi.res, hi.res.width, hi.res.height and hi.res.res parameters. Most of these options are better not to touch, see details of parameters below.

Returned result values: list with the following elements

• src - character vector of specified R code.

• result - result of evaluation. NULL if nothing is returned. If any R code returned an R object while evaluating then the last R object will be returned as a raw R object. If a graph is plotted in the given text, the returned object is a string (with class set to image) specifying the path to the saved image file. If graphic device was touched, then no other R objects will be returned.

• output - character vector of printed version (capture.output) of result

• type - class of generated output. 'NULL' if nothing is returned, 'error' if some error occurred.

• msg - possible messages grabbed while evaluating specified R code with the following structure:

  • messages - character vector of possible diagnostic message(s)

  • warnings - character vector of possible warning message(s)

  • errors - character vector of possible error message(s)

• stdout - character vector of possibly printed texts to standard output (console)

By default evals tries to cache results. This means that if evaluation of some R commands take too much time (specified in cache.time parameter), then evals would save the results in a file and return from there on next exact R code's evaluation. This caching algorithm tries to be smart as checks not only the passed R sources, but all variables inside that and saves the hash of those.

Technical details of the caching algorithm:

• Each passed R chunk is parsed to single commands.

• Each parsed command's part (let it be a function, variable, constant etc.) evaluated (as a name) separately to a list. This list describes the unique structure and the content of the passed R commands, and has some IMHO really great benefits (see examples below).

• A hash if computed to each list element and cached too in pander's local environments. This is useful if you are using large data frames, just imagine: the caching algorithm would have to compute the hash for the same data frame each time it's touched! This way the hash is recomputed only if the R object with the given name is changed.

• The list is serialized and an SHA-1 hash is computed for that - which is unique and there is no real risk of collision.

• If evals can find the cached results in a file named to the computed hash, then it is returned on the spot.

• Otherwise the call is evaluated and the results are optionally saved to cache (e.g. if cache is active, if the proc.time() of the evaluation is higher then it is defined in cache.time etc.).

This is a quite secure way of caching, but if you would encounter any issues, just set cache to FALSE or tweak other cache parameters. While setting cache.dir, please do think about what you are doing and move your graph.dir accordingly, as evals might result in returning an image file path which is not found any more on your file system!

Also, if you have generated a plot and rendered that to e.g. png before and later try to get e.g. pdf - it would fail with cache on. Similarly you cannot render a high resolution image of a cached image, but you have to (temporary) disable caching.

The default evals options could be set globally with evalsOptions, e.g. to switch off the cache just run evalsOptions('cache', FALSE).

Please check the examples carefully below to get a detailed overview of evals.

Value

a list of parsed elements each containing: src (the command run), result (R object: NULL if nothing returned, path to image file if a plot was generated), printed output, type (class of returned object if any), informative/wawrning and error messages (if any returned by the command run, otherwise set to NULL) and possible stdoutt value. See Details above.

See Also

eval.msgs evalsOptions

Examples

## Not run: 
# parsing several lines of R code
txt <- readLines(textConnection('x <- rnorm(100)
  runif(10)
  warning('Lorem ipsum foo-bar-foo!')
  plot(1:10)
  qplot(rating, data = movies, geom = 'histogram')
  y <- round(runif(100))
  cor.test(x, y)
  crl <- cor.test(runif(10), runif(10))
  table(mtcars$am, mtcars$cyl)
  ggplot(mtcars) + geom_point(aes(x = hp, y = mpg))'))
evals(txt)

## parsing a list of commands
txt <- list('df <- mtcars',
 c('plot(mtcars$hp, pch = 19)','text(mtcars$hp, label = rownames(mtcars), pos = 4)'),
 'ggplot(mtcars) + geom_point(aes(x = hp, y = mpg))')
evals(txt)

## the same commands in one string but also evaluating the `plot` with `text`
## (note the leading '+' on the beginning of `text...` line)
txt <- 'df <- mtcars
 plot(mtcars$hp, pch = 19)
 +text(mtcars$hp, label = rownames(mtcars), pos = 4)
 ggplot(mtcars) + geom_point(aes(x = hp, y = mpg))'
evals(txt)
## but it would fail without parsing
evals(txt, parse = FALSE)

## handling messages
evals('message(20)')
evals('message(20);message(20)', parse = FALSE)

## adding a caption to a plot
evals('set.caption("FOO"); plot(1:10)')
## `plot` is started with a `+` to eval the codes in the same chunk
## (no extra chunk with NULL result)
evals('set.caption("FOO"); +plot(1:10)')

## handling warnings
evals('chisq.test(mtcars$gear, mtcars$hp)')
evals(list(c('chisq.test(mtcars$gear, mtcars$am)', 'pi',
  'chisq.test(mtcars$gear, mtcars$hp)')), parse = FALSE)
evals(c('chisq.test(mtcars$gear, mtcars$am)',
  'pi',
  'chisq.test(mtcars$gear, mtcars$hp)'))

## handling errors
evals('runiff(20)')
evals('Old MacDonald had a farm\\dots')
evals('## Some comment')
evals(c('runiff(20)', 'Old MacDonald had a farm?'))
evals(list(c('runiff(20)', 'Old MacDonald had a farm?')), parse = FALSE)
evals(c('mean(1:10)', 'no.R.function()'))
evals(list(c('mean(1:10)', 'no.R.function()')), parse = FALSE)
evals(c('no.R.object', 'no.R.function()', 'very.mixed.up(stuff)'))
evals(list(c('no.R.object', 'no.R.function()', 'very.mixed.up(stuff)')), parse = FALSE)
evals(c('no.R.object', 'Old MacDonald had a farm\\dots', 'pi'))
evals('no.R.object;Old MacDonald had a farm\\dots;pi', parse = FALSE)
evals(list(c('no.R.object', 'Old MacDonald had a farm\\dots', 'pi')), parse = FALSE)

## graph options
evals('plot(1:10)')
evals('plot(1:10);plot(2:20)')
evals('plot(1:10)', graph.output = 'jpg')
evals('plot(1:10)', height = 800)
evals('plot(1:10)', height = 800, hi.res = TRUE)
evals('plot(1:10)', graph.output = 'pdf', hi.res = TRUE)
evals('plot(1:10)', res = 30)
evals('plot(1:10)', graph.name = 'myplot')
evals(list('plot(1:10)', 'plot(2:20)'), graph.name = 'myplots-%d')
evals('plot(1:10)', graph.env = TRUE)
evals('x <- runif(100);plot(x)', graph.env = TRUE)
evals(c('plot(1:10)', 'plot(2:20)'), graph.env = TRUE)
evals(c('x <- runif(100)', 'plot(x)','y <- runif(100)', 'plot(y)'), graph.env = TRUE)
evals(list(
    c('x <- runif(100)', 'plot(x)'),
    c('y <- runif(100)', 'plot(y)')),
  graph.env = TRUE, parse = FALSE)
evals('plot(1:10)', graph.recordplot = TRUE)
## unprinted lattice plot
evals('histogram(mtcars$hp)', graph.recordplot = TRUE)

## caching
system.time(evals('plot(mtcars)'))
system.time(evals('plot(mtcars)'))                # running again to see the speed-up :)
system.time(evals('plot(mtcars)', cache = FALSE)) # cache disabled

## caching mechanism does check what's inside a variable:
x <- mtcars
evals('plot(x)')
x <- cbind(mtcars, mtcars)
evals('plot(x)')
x <- mtcars
system.time(evals('plot(x)'))

## stress your CPU - only once!
evals('x <- sapply(rep(mtcars$hp, 1e3), mean)')   # run it again!

## play with cache
require(lattice)
evals('histogram(rep(mtcars$hp, 1e5))')
## nor run the below call
## that would return the cached version of the above call :)
f <- histogram
g <- rep
A <- mtcars$hp
B <- 1e5
evals('f(g(A, B))')#'

## or switch off cache globally:
evalsOptions('cache', FALSE)
## and switch on later
evalsOptions('cache', TRUE)

## evaluate assignments inside call to evals
## changes to environments are cached properly and retreived
evalsOptions('cache.time', 0)
x <- 2
evals('x <- x^2')[[1]]$result
evals('x <- x^2; x + 1')[[2]]$result
evalsOptions('cache.time', 0.1)

## returning only a few classes
txt <- readLines(textConnection('rnorm(100)
  list(x = 10:1, y = 'Godzilla!')
  c(1,2,3)
   matrix(0,3,5)'))
evals(txt, classes = 'numeric')
evals(txt, classes = c('numeric', 'list'))

## hooks
txt <- 'runif(1:4); matrix(runif(25), 5, 5); 1:5'
hooks <- list('numeric' = round, 'matrix' = pander_return)
evals(txt, hooks = hooks)
## using pander's default hook
evals(txt, hooks = list('default' = pander_return))
evals('22/7', hooks = list('numeric' = round))
evals('matrix(runif(25), 5, 5)', hooks = list('matrix' = round))

## setting default hook
evals(c('runif(10)', 'matrix(runif(9), 3, 3)'),
  hooks = list('default'=round))
## round all values except for matrices
evals(c('runif(10)', 'matrix(runif(9), 3, 3)'),
  hooks = list(matrix = 'print', 'default' = round))

# advanced hooks
hooks <- list('numeric' = list(round, 2), 'matrix' = list(round, 1))
evals(txt, hooks = hooks)

# return only returned values
evals(txt, output = 'result')

# return only messages (for checking syntax errors etc.)
evals(txt, output = 'msg')

# check the length of returned values and do not return looong R objects
evals('runif(10)', length = 5)

# note the following will not be filtered!
evals('matrix(1,1,1)', length = 1)

# if you do not want to let such things be eval-ed in the middle of a string
# use it with other filters :)
evals('matrix(1,1,1)', length = 1, classes = 'numeric')

# hooks & filtering
evals('matrix(5,5,5)',
  hooks = list('matrix' = pander_return),
  output = 'result')

# eval-ing chunks in given environment
myenv <- new.env()
evals('x <- c(0,10)', env = myenv)
evals('mean(x)', env = myenv)
rm(myenv)
# note: if you had not specified 'myenv', the second 'evals' would have failed
evals('x <- c(0,10)')
evals('mean(x)')

# log
x <- evals('1:10', log = 'foo')
# trace log
evalsOptions('cache.time', 0)
x <- evals('1:10', log = 'foo')
x <- evals('1:10', log = 'foo')
# log to file
t <- tempfile()
log_appender(appender_file(t), name = 'evals')
x <- evals('1:10', log = 'evals')
readLines(t)
# permanent log for all events
evalsOptions('log', 'evals')
log_threshold(TRACE, 'evals')
evals('foo')

## End(Not run)

Description

To list all evals options, just run this function without any parameters provided. To query only one value, pass the first parameter. To set that, use the value parameter too.

Usage

evalsOptions(o, value)

Arguments

Details

The following evals options are available:

• parse: if TRUE the provided txt elements would be merged into one string and parsed to logical chunks. This is useful if you would want to get separate results of your code parts - not just the last returned value, but you are passing the whole script in one string. To manually lock lines to each other (e.g. calling a plot and on next line adding an abline or text to it), use a plus char (+) at the beginning of each line which should be evaluated with the previous one(s). If set to FALSE, evals would not try to parse R code, it would get evaluated in separate runs - as provided. Please see examples of evals.

• cache: caching the result of R calls if set to TRUE

• cache.mode: cached results could be stored in an environment in current R session or let it be permanent on disk.

• cache.dir: path to a directory holding cache files if cache.mode set to disk. Default to .cache in current working directory.

• cache.time: number of seconds to limit caching based on proc.time. If set to 0, all R commands, if set to Inf, none is cached (despite the cache parameter).

• cache.copy.images: copy images to new files if an image is returned from cache? If set to FALSE (default) the "old" path would be returned.

• classes: a vector or list of classes which should be returned. If set to NULL (by default) all R objects will be returned.

• hooks: list of hooks to be run for given classes in the form of list(class = fn). If you would also specify some parameters of the function, a list should be provided in the form of list(fn, param1, param2=NULL) etc. So the hooks would become list(class1=list(fn, param1, param2=NULL), ...). See examples of evals. A default hook can be specified too by setting the class to 'default'. This can be handy if you do not want to define separate methods/functions to each possible class, but automatically apply the default hook to all classes not mentioned in the list. You may also specify only one element in the list like: hooks=list('default' = pander_return). Please note, that nor error/warning messages, nor stdout is captured (so: updated) while running hooks!

• length: any R object exceeding the specified length will not be returned. The default value (Inf) does not filter out any R objects.

• output: a character vector of required returned values. This might be useful if you are only interested in the result, and do not want to save/see e.g. messages or printed output. See examples of evals.

• graph.unify: boolean (default: FALSE) that determines if evals should try to unify the style of (base, lattice and ggplot2) plots? If set to TRUE, some panderOptions() would apply.

• graph.name: set the file name of saved plots which is tempfile by default. A simple character string might be provided where %d would be replaced by the index of the generating txt source, %n with an incremented integer in graph.dir with similar file names and %t by some random characters. A function's name to be evaluated can be passed here too.

• graph.dir: path to a directory where to place generated images. If the directory does not exist, evals try to create that. Default set to plots in current working directory.

• graph.output: set the required file format of saved plots. Currently it could be any of grDevices: png, bmp, jpeg, jpg, tiff, svg or pdf. Set to NA not to save plots at all and tweak that setting with capture.plot() on demand.

• width: width of generated plot in pixels for even vector formats

• height: height of generated plot in pixels for even vector formats

• res: nominal resolution in ppi. The height and width of vector images will be calculated based in this.

• hi.res: generate high resolution plots also? If set to TRUE, each R code parts resulting an image would be run twice.

• hi.res.width: width of generated high resolution plot in pixels for even vector formats. The height and res of high resolution image is automatically computed based on the above options to preserve original plot aspect ratio.

• graph.env: save the environments in which plots were generated to distinct files (based on graph.name) with env extension?

• graph.recordplot: save the plot via recordPlot to distinct files (based on graph.name) with recodplot extension?

• graph.RDS: save the raw R object returned (usually with lattice or ggplot2) while generating the plots to distinct files (based on graph.name) with RDS extension?

• log: NULL or an optionally passed namespace from logger to record all info, trace, debug and error messages.

See Also

evals panderOptions

Examples

evalsOptions()
evalsOptions('cache')
evalsOptions('cache', FALSE)

Description

Dummy helper to check if the R object has real rownames or not.

Usage

has.rownames(x)

Arguments

Value

TRUE OR FALSE

Description

Tries to open a file with operating system's default program.

Usage

openFileInOS(f)

Arguments

References

This function is a fork of David Hajage's convert function: https://github.com/eusebe/ascii/blob/master/R/export.r

Description

p merges elements of a vector in one string for the sake of pretty inline printing. Default parameters are read from appropriate option values (see argument description for details). This function allows you to put the results of an expression that yields a variable inline, by wrapping the vector elements with the string provided in wrap, and separating elements by main and ending separator (sep and copula). In case of a two-length vector, value specified in copula will be used as a separator. You can also control the length of provided vector by altering an integer value specified in limit argument (defaults to Inf).

Usage

p(
  x,
  wrap = panderOptions("p.wrap"),
  sep = panderOptions("p.sep"),
  copula = panderOptions("p.copula"),
  limit = Inf,
  keep.trailing.zeros = panderOptions("keep.trailing.zeros"),
  missing = panderOptions("missing"),
  digits = panderOptions("digits"),
  round = panderOptions("round")
)

Arguments

Value

a string with concatenated vector contents

Author(s)

Aleksandar Blagotic

References

This function was moved from rapport package: https://rapporter.github.io/rapport/.

Examples

p(c('fee', 'fi', 'foo', 'fam'))
# [1] '_fee_, _fi_, _foo_ and _fam_'
p(1:3, wrap = '')
# [1] '1, 2 and 3'
p(LETTERS[1:5], copula = 'and the letter')
# [1] '_A_, _B_, _C_, _D_ and the letter _E_'
p(c('Thelma', 'Louise'), wrap = '', copula = '&')
# [1] 'Thelma & Louise'

Description

Prints an R object in Pandoc's markdown.

Usage

pander(x = NULL, ...)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Note

This function can be called by pander and pandoc too.

References

• John MacFarlane (2013): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

• David Hajage (2011): _ascii. Export R objects to several markup languages._ https://cran.r-project.org/package=ascii

• Hlavac, Marek (2013): _stargazer: LaTeX code for well-formatted regression and summary statistics tables._ https://cran.r-project.org/package=stargazer

Examples

## Vectors
pander(1:10)
pander(letters)
pander(mtcars$am)
pander(factor(mtcars$am))

## Lists
pander(list(1, 2, 3, c(1, 2)))
pander(list(a = 1, b = 2, c = table(mtcars$am)))
pander(list(1, 2, 3, list(1, 2)))
pander(list(a = 1, 2, 3, list(1, 2)))
pander(list('FOO', letters[1:3], list(1:5), table(mtcars$gear), list('FOOBAR', list('a', 'b'))))
pander(list(a = 1, b = 2, c = table(mtcars$am), x = list(myname = 1, 2), 56))
pander(unclass(chisq.test(table(mtcars$am, mtcars$gear))))

## Arrays
pander(mtcars)
pander(table(mtcars$am))
pander(table(mtcars$am, mtcars$gear))

## Tests
pander(ks.test(runif(50), runif(50)))
pander(chisq.test(table(mtcars$am, mtcars$gear)))
pander(t.test(extra ~ group, data = sleep))

## Models
ml <- with(lm(mpg ~ hp + wt), data = mtcars)
pander(ml)
pander(anova(ml))
pander(aov(ml))
## Dobson (1990) Page 93: Randomized Controlled Trial (examples from: ?glm)
counts <- c(18, 17, 15, 20, 10, 20, 25, 13, 12)
outcome <- gl(3, 1, 9)
treatment <- gl(3, 3)
m <- glm(counts ~ outcome + treatment, family = poisson())
pander(m)
pander(anova(m))
pander(aov(m))
## overwriting labels
pander(lm(Sepal.Width ~ Species, data = iris), covariate.labels = c('Versicolor', 'Virginica'))

## Prcomp
pander(prcomp(USArrests))

## Others
pander(density(runif(10)))
pander(density(mtcars$hp))

## default method
x <- chisq.test(table(mtcars$am, mtcars$gear))
class(x) <- 'I heave never heard of!'
pander(x)

Description

This is a wrapper function around pander but instead of printing to stdout, this function returns a character vector of the captured lines.

Usage

pander_return(...)

Arguments

See Also

pander

Description

Prints an anova object in Pandoc's markdown.

Usage

## S3 method for class 'anova'
pander(x, caption = attr(x, "caption"), add.significance.stars = FALSE, ...)

Arguments

Description

Prints an aov object in Pandoc's markdown.

Usage

## S3 method for class 'aov'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an aovlist object in Pandoc's markdown.

Usage

## S3 method for class 'aovlist'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an arima object from stats package in Pandoc's markdown.

Usage

## S3 method for class 'Arima'
pander(x, digits = panderOptions("digits"), se = TRUE, ...)

Arguments

Description

Prints a call object in Pandoc's markdown.

Usage

## S3 method for class 'call'
pander(x, ...)

Arguments

Description

Prints a cast_df object in Pandoc's markdown.

Usage

## S3 method for class 'cast_df'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a character class in Pandoc's markdown.

Usage

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

Arguments

Description

Prints a clogit object in Pandoc's markdown.

Usage

## S3 method for class 'clogit'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a coxph object in Pandoc's markdown.

Usage

## S3 method for class 'coxph'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an cph object from rms package in Pandoc's markdown.

Usage

## S3 method for class 'cph'
pander(x, table = TRUE, conf.int = FALSE, coefs = TRUE, ...)

Arguments

Description

Prints a CrossTable object in Pandoc's markdown.

Usage

## S3 method for class 'CrossTable'
pander(
  x,
  caption = attr(x, "caption"),
  digits = panderOptions("digits"),
  total.r = x$total.r,
  total.c = x$total.c,
  ...
)

Arguments

Description

Prints a data.frame object in Pandoc's markdown.

Usage

## S3 method for class 'data.frame'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a data.table object in Pandoc's markdown. Data.tables drop attributes (like row names) when called.

Usage

## S3 method for class 'data.table'
pander(x, caption = attr(x, "caption"), keys.as.row.names = TRUE, ...)

Arguments

Description

Prints a Date object in Pandoc's markdown.

Usage

## S3 method for class 'Date'
pander(x, ...)

Arguments

Description

Method to be used, when no exact S3 method for given object is found. Tries to render object as a list

Usage

## Default S3 method:
pander(x, ...)

Arguments

Description

Prints a density object in Pandoc's markdown.

Usage

## S3 method for class 'density'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a describe object in Pandoc's markdown.

Usage

## S3 method for class 'describe'
pander(x, caption = attr(x, "caption"), digits = panderOptions("digits"), ...)

Arguments

Description

Prints an ets object from forecast package in Pandoc's markdown.

Usage

## S3 method for class 'ets'
pander(x, digits = panderOptions("digits"), ...)

Arguments

Description

Prints a evals object in Pandoc's markdown.

Usage

## S3 method for class 'evals'
pander(x, ...)

Arguments

Description

Prints a factor object in Pandoc's markdown.

Usage

## S3 method for class 'factor'
pander(x, ...)

Arguments

Description

Prints a formula object in Pandoc's markdown.

Usage

## S3 method for class 'formula'
pander(x, max.width = 80, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a ftable object in Pandoc's markdown.

Usage

## S3 method for class 'ftable'
pander(x, ...)

Arguments

Description

Prints an function object in Pandoc's markdown.

Usage

## S3 method for class ''function''
pander(x, add.name = FALSE, verbatim = TRUE, syntax.highlighting = FALSE, ...)

Arguments

Description

Prints a summary.glm object in Pandoc's markdown.

Usage

## S3 method for class 'glm'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an Grm object from rms package in Pandoc's markdown.

Usage

## S3 method for class 'Glm'
pander(x, coefs = TRUE, ...)

Arguments

Description

Renders an gtable object in Pandoc's markdown.

Usage

## S3 method for class 'gtable'
pander(x, zsort = FALSE, ...)

Arguments

Description

Prints a htest object in Pandoc's markdown.

Usage

## S3 method for class 'htest'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a image object in Pandoc's markdown.

Usage

## S3 method for class 'image'
pander(x, caption = attr(x, "caption"), href = attr(x, "href"), ...)

Arguments

Description

Prints an irts object from tseries package in Pandoc's markdown.

Usage

## S3 method for class 'irts'
pander(x, caption = attr(x, "caption"), format = panderOptions("date"), ...)

Arguments

Description

Prints a list object in Pandoc's markdown.

Usage

## S3 method for class 'list'
pander(x, ...)

Arguments

Description

Prints a summary.lm object in Pandoc's markdown.

Usage

## S3 method for class 'lm'
pander(x, caption = attr(x, "caption"), covariate.labels, omit, ...)

Arguments

Description

Prints a lme object in Pandoc's markdown.

Usage

## S3 method for class 'lme'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a logical object in Pandoc's markdown.

Usage

## S3 method for class 'logical'
pander(x, ...)

Arguments

Description

Prints an lrm object from rms package in Pandoc's markdown.

Usage

## S3 method for class 'lrm'
pander(x, coefs = TRUE, ...)

Arguments

Description

Prints an manova object in Pandoc's markdown.

Usage

## S3 method for class 'manova'
pander(x, caption = attr(x, "caption"), add.significance.stars = FALSE, ...)

Arguments

Description

Prints a matrix object in Pandoc's markdown.

Usage

## S3 method for class 'matrix'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an microbenchmark object in Pandoc's markdown.

Usage

## S3 method for class 'microbenchmark'
pander(x, caption = attr(x, "caption"), expr.labels, unit, ...)

Arguments

Description

Prints a call object in Pandoc's markdown.

Usage

## S3 method for class 'name'
pander(x, ...)

Arguments

Description

Prints an nls object from stats package in Pandoc's markdown.

Usage

## S3 method for class 'nls'
pander(x, digits = panderOptions("digits"), show.convergence = FALSE, ...)

Arguments

Description

Prints a NULL object in Pandoc's markdown.

Usage

## S3 method for class ''NULL''
pander(x, ...)

Arguments

Description

Prints a numeric class in Pandoc's markdown.

Usage

## S3 method for class 'numeric'
pander(x, ...)

Arguments

Description

Prints an ols object from rms package in Pandoc's markdown.

Usage

## S3 method for class 'ols'
pander(
  x,
  long = FALSE,
  coefs = TRUE,
  digits = panderOptions("digits"),
  round = panderOptions("round"),
  ...
)

Arguments

Description

Prints an orm object from rms package in Pandoc's markdown.

Usage

## S3 method for class 'orm'
pander(x, coefs = TRUE, intercepts = x$non.slopes < 10, ...)

Arguments

Description

Prints an polr object from MASS package in Pandoc's markdown.

Usage

## S3 method for class 'polr'
pander(x, ...)

Arguments

Description

Prints a POSIXct object in Pandoc's markdown.

Usage

## S3 method for class 'POSIXct'
pander(x, ...)

Arguments

Description

Prints a POSIXlt object in Pandoc's markdown.

Usage

## S3 method for class 'POSIXlt'
pander(x, ...)

Arguments

Description

Prints a prcomp object in Pandoc's markdown.

Usage

## S3 method for class 'prcomp'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Renders an randomForest object in Pandoc's markdown.

Usage

## S3 method for class 'randomForest'
pander(x, digits = panderOptions("digits"), ...)

Arguments

Description

Prints a rapport object in Pandoc's markdown.

Usage

## S3 method for class 'rapport'
pander(x, ...)

Arguments

Description

Prints an rlm object in Pandoc's markdown.

Usage

## S3 method for class 'rlm'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an sessionInfo object in Pandoc's markdown.

Usage

## S3 method for class 'sessionInfo'
pander(x, locale = TRUE, compact = TRUE, ...)

Arguments

Description

Prints an smooth.spline object in Pandoc's markdown.

Usage

## S3 method for class 'smooth.spline'
pander(x, ...)

Arguments

Description

Prints an stat.table object in Pandoc's markdown.

Usage

## S3 method for class 'stat.table'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a summary.aov object in Pandoc's markdown.

Usage

## S3 method for class 'summary.aov'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a summary.aovlist object in Pandoc's markdown.

Usage

## S3 method for class 'summary.aovlist'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a summary.glm object in Pandoc's markdown.

Usage

## S3 method for class 'summary.glm'
pander(
  x,
  caption = attr(x, "caption"),
  covariate.labels,
  omit,
  summary = TRUE,
  ...
)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Description

Prints a summary.lm object in Pandoc's markdown.

Usage

## S3 method for class 'summary.lm'
pander(
  x,
  caption = attr(x, "caption"),
  covariate.labels,
  omit,
  summary = TRUE,
  add.significance.stars = FALSE,
  move.intercept = FALSE,
  ...
)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Description

Prints a lme object in Pandoc's markdown.

Usage

## S3 method for class 'summary.lme'
pander(x, caption = attr(x, "caption"), summary = TRUE, ...)

Arguments

Description

Prints an summary.manova object from stats package in Pandoc's markdown.

Usage

## S3 method for class 'summary.manova'
pander(x, caption = attr(x, "caption"), add.significance.stars = FALSE, ...)

Arguments

Description

Prints an summary.nls object from stats package in Pandoc's markdown.

Usage

## S3 method for class 'summary.nls'
pander(
  x,
  summary = TRUE,
  add.significance.stars = FALSE,
  digits = panderOptions("digits"),
  show.convergence = FALSE,
  ...
)

Arguments

Description

Prints an summary.polr object from MASS package in Pandoc's markdown.

Usage

## S3 method for class 'summary.polr'
pander(
  x,
  digits = panderOptions("digits"),
  round = panderOptions("round"),
  keep.trailing.zeros = panderOptions("keep.trailing.zeros"),
  ...
)

Arguments

Description

Prints a summary.prcomp object in Pandoc's markdown.

Usage

## S3 method for class 'summary.prcomp'
pander(x, caption = attr(x, "caption"), summary = TRUE, ...)

Arguments

Description

Prints an summary.rms from rms package in Pandoc's markdown.

Usage

## S3 method for class 'summary.rms'
pander(x, ...)

Arguments

Description

Prints an survreg object from survival package in Pandoc's markdown.

Usage

## S3 method for class 'summary.survreg'
pander(
  x,
  summary = TRUE,
  digits = panderOptions("digits"),
  round = panderOptions("round"),
  keep.trailing.zeros = panderOptions("keep.trailing.zeros"),
  ...
)

Arguments

Description

Renders an summary.table object in Pandoc's markdown.

Usage

## S3 method for class 'summary.table'
pander(x, caption = attr(x, "caption"), print.call = T, ...)

Arguments

Description

Prints an survdiff object in Pandoc's markdown.

Usage

## S3 method for class 'survdiff'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints an survfit object in Pandoc's markdown.

Usage

## S3 method for class 'survfit'
pander(
  x,
  caption = attr(x, "caption"),
  scale = 1,
  print.rmean = getOption("survfit.print.rmean"),
  rmean = getOption("survfit.rmean"),
  ...
)

Arguments

Description

Prints an survreg object from survival package in Pandoc's markdown.

Usage

## S3 method for class 'survreg'
pander(x, ...)

Arguments

Description

Prints a table object in Pandoc's markdown.

Usage

## S3 method for class 'table'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Renders an tabular object in Pandoc's markdown.

Usage

## S3 method for class 'tabular'
pander(
  x,
  caption = attr(x, "caption"),
  emphasize.rownames = TRUE,
  digits = panderOptions("digits"),
  ...
)

Arguments

Description

Prints a timeseries object in Pandoc's markdown.

Usage

## S3 method for class 'ts'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

Prints a zoo object in Pandoc's markdown.

Usage

## S3 method for class 'zoo'
pander(x, caption = attr(x, "caption"), ...)

Arguments

Description

To list all pander options, just run this function without any parameters provided. To query only one value, pass the first parameter. To set that, use the value parameter too.

Usage

panderOptions(o, value)

Arguments

Details

The following pander options are available:

• digits: numeric (default: 2) passed to format. Can be a vector specifying values for each column (has to be the same length as number of columns). Values for non-numeric columns will be disregarded.

• decimal.mark: string (default: .) passed to format

• formula.caption.prefix: string (default: 'Formula: ') passed to pandoc.formula to be used as caption prefix. Be sure about what you are doing if changing to other than 'Formula: ' or ':'.

• big.mark: string (default: ”) passed to format.

• round: numeric (default: Inf) passed to round. Can be a vector specifying values for each column (has to be the same length as number of columns). Values for non-numeric columns will be disregarded.

• keep.trailing.zeros: boolean (default: FALSE) to show or remove trailing zeros in numbers

• keep.line.breaks: boolean (default: FALSE) to keep or remove line breaks from cells in a table

• missing: string (default: NA) to replace missing values in vectors, tables etc.

• date: string (default: '%Y/%m/%d %X') passed to format when printing dates (POSIXct or POSIXt)

• header.style: 'atx' or 'setext' passed to pandoc.header

• list.style: 'bullet', 'ordered' or 'roman' passed to pandoc.list. Please not that this has no effect on pander methods.

• table.style: 'multiline', 'grid', 'simple' or 'rmarkdown' passed to pandoc.table

• table.emphasize.rownames: boolean (default: TRUE) if row names should be highlighted

• table.split.table: numeric passed to pandoc.table and also affects pander methods. This option tells pander where to split too wide tables. The default value (80) suggests the conventional number of characters used in a line, feel free to change (e.g. to Inf to disable this feature) if you are not using a VT100 terminal any more :)

• table.split.cells: numeric or numeric vector (default: 30) passed to pandoc.table and also affects pander methods. This option tells pander where to split too wide cells with line breaks. Numeric vector specifies values for cells separately. Set Inf to disable.

• table.caption.prefix: string (default: 'Table: ') passed to pandoc.table to be used as caption prefix. Be sure about what you are doing if changing to other than 'Table: ' or ':'.

• table.continues: string (default: 'Table continues below') passed to pandoc.table to be used as caption for long (split) without a use defined caption

• table.continues.affix: string (default: '(continued below)') passed to pandoc.table to be used as an affix concatenated to the user defined caption for long (split) tables

• table.alignment.default: string (default: centre) that defines the default alignment of cells. Can be left, right or centre that latter can be also spelled as center.

• table.alignment.rownames: string (default: centre) that defines the alignment of rownames in tables. Can be left, right or centre that latter can be also spelled as center.

• use.hyphening: boolean (default: FALSE) if try to use hyphening when splitting large cells according to table.split.cells. Requires sylly.

• evals.messages: boolean (default: TRUE) passed to evals' pander method specifying if messages should be rendered

• p.wrap: a string (default: '_') to wrap vector elements passed to p function

• p.sep: a string (default: ', ') with the main separator passed to p function

• p.copula: a string (default: ' and ') with ending separator passed to p function

• plain.ascii: boolean (default: FALSE) to define if output should be in plain ascii or not

• graph.nomargin: boolean (default: TRUE) if trying to keep plots' margins at minimal

• graph.fontfamily: string (default: 'sans') specifying the font family to be used in images. Please note, that using a custom font on Windows requires grDevices:::windowsFonts first.

• graph.fontcolor: string (default: 'black') specifying the default font color

• graph.fontsize: numeric (default: 12) specifying the base font size in pixels. Main title is rendered with 1.2 and labels with 0.8 multiplier.

• graph.grid: boolean (default: TRUE) if a grid should be added to the plot

• graph.grid.minor: boolean (default: TRUE) if a miner grid should be also rendered

• graph.grid.color: string (default: 'grey') specifying the color of the rendered grid

• graph.grid.lty: string (default: 'dashed') specifying the line type of grid

• graph.boxes: boolean (default: FALSE) if to render a border around of plot (and e.g. around strip)

• graph.legend.position: string (default: 'right') specifying the position of the legend: 'top', 'right', 'bottom' or 'left'

• graph.background: string (default: 'white') specifying the plots main background's color

• graph.panel.background: string (default: 'transparent') specifying the plot's main panel background. Please note, that this option is not supported with base graphics.

• graph.colors: character vector of default color palette (defaults to a colorblind theme: https://jfly.uni-koeln.de/color/). Please note that this update work with base plots by appending the col argument to the call if not set.

• graph.color.rnd: boolean (default: FALSE) specifying if the palette should be reordered randomly before rendering each plot to get colorful images

• graph.axis.angle: numeric (default: 1) specifying the angle of axes' labels. The available options are based on par(les) and sets if the labels should be:

  • 1: parallel to the axis,

  • 2: horizontal,

  • 3: perpendicular to the axis or

  • 4: vertical.

• graph.symbol: numeric (default: 1) specifying a symbol (see the pch parameter of par)

• knitr.auto.asis: boolean (default: TRUE) if the results of pander should be considered as 'asis' in knitr. Equals to specifying results='asis' in the R chunk, so thus there is no need to do so if set to TRUE.

• pandoc.binary: full path of pandoc's binary. By default, pandoc is in the path.

See Also

evalsOptions

Examples

## Not run: 
panderOptions()
panderOptions('digits')
panderOptions('digits', 5)

## End(Not run)

Description

This R5 reference class can hold bunch of elements (text or R objects) from which it tries to create a Pandoc's markdown text file. Exporting the report to several formats (like: PDF, docx, odt etc. - see Pandoc's documentation) is also possible, see examples below.

Arguments

Methods

export(Class)

Returns the result of coercing the object to Class. No effect on the object itself.

Examples

## Not run: 
## Initialize a new Pandoc object
myReport <- Pandoc$new()

## Add author, title and date of document
myReport$author <- 'Anonymous'
myReport$title  <- 'Demo'

## Or it could be done while initializing
myReport <- Pandoc$new('Anonymous', 'Demo')

## Add some free text
myReport$add.paragraph('Hello there, this is a really short tutorial!')

## Add maybe a header for later stuff
myReport$add.paragraph('# Showing some raw R objects below')

## Adding a short matrix
myReport$add(matrix(5,5,5))

## Or a table with even # TODO: caption
myReport$add.paragraph('Hello table:')
myReport$add(table(mtcars$am, mtcars$gear))

## Or a "large" data frame which barely fits on a page
myReport$add(mtcars)

## And a simple linear model with Anova tables
ml <- with(lm(mpg ~ hp + wt), data = mtcars)
myReport$add(ml)
myReport$add(anova(ml))
myReport$add(aov(ml))

## And do some principal component analysis at last
myReport$add(prcomp(USArrests))

## Sorry, I did not show how Pandoc deals with plots:
myReport$add(plot(1:10)) # TODO: caption

## Want to see the report? Just print it:
myReport

## Exporting to PDF (default)
myReport$export()

## Or to docx in tempdir:
myReport$format <- 'docx'
myReport$export(tempfile())

## You do not want to see the generated report after generation?
myReport$export(open = FALSE)

## End(Not run)

Description

This function behaves just like brew except for the <%=...%> tags, where Pandoc.brew first translate the R object found between the tags to Pandoc's markdown before passing to the cat function.

Usage

Pandoc.brew(
  file = stdin(),
  output = stdout(),
  convert = FALSE,
  open = TRUE,
  graph.name,
  graph.dir,
  graph.hi.res = FALSE,
  text = NULL,
  envir = parent.frame(),
  append = FALSE,
  ...
)

Arguments

Details

This parser tries to be smart in some ways:

• a block (R commands between the tags) could return any value at any part of the block and there are no restrictions about the number of returned R objects

• plots and images are grabbed in the document, rendered to a png file and pander method would result in a Pandoc's markdown formatted image link (so the image would be shown/included in the exported document). The images are put in plots directory in current getwd() or to the specified output file's directory.

• all warnings/messages and errors are recorded in the blocks and returned in the document as a footnote

Please see my Github page for details (https://rapporter.github.io/pander/#brew-to-pandoc) and examples (https://rapporter.github.io/pander/#examples).

Value

converted file name with full path if convert is set, none otherwise

Note

Only one of the input parameters (file or text) is to be used at once!

References

• Jeffrey Horner (2011). _brew: Templating Framework for Report Generation._ https://cran.r-project.org/package=brew

• John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

## Not run: 
text <- paste('# Header', '',
  'What a lovely list:\n<%=as.list(runif(10))%>',
  'A wide table:\n<%=mtcars[1:3, ]%>',
  'And a nice chart:\n\n<%=plot(1:10)%>', sep = '\n')
Pandoc.brew(text = text)
Pandoc.brew(text = text, output = tempfile(), convert = 'html')
Pandoc.brew(text = text, output = tempfile(), convert = 'pdf')

## pi is awesome
Pandoc.brew(text='<%for (i in 1:5) {%>\n Pi has a lot (<%=i%>) of power: <%=pi^i%><%}%>')

## package bundled examples
Pandoc.brew(system.file('examples/minimal.brew', package='pander'))
Pandoc.brew(system.file('examples/minimal.brew', package='pander'),
  output = tempfile(), convert = 'html')
Pandoc.brew(system.file('examples/short-code-long-report.brew', package='pander'))
Pandoc.brew(system.file('examples/short-code-long-report.brew', package='pander'),
  output = tempfile(), convert = 'html')

## brew returning R objects
str(Pandoc.brew(text='Pi equals to <%=pi%>.
And here are some random data:\n<%=runif(10)%>'))

str(Pandoc.brew(text='# Header <%=1%>\nPi is <%=pi%> which is smaller then <%=2%>.
foo\nbar\n <%=3%>\n<%=mtcars[1:2,]%>'))

str(Pandoc.brew(text='<%for (i in 1:5) {%>
Pi has a lot (<%=i%>) of power: <%=pi^i%><%}%>'))

## End(Not run)

Description

Calling John MacFarlane's great program to convert specified file (see f parameter below) or character vector see text paramater to other formats like HTML, pdf, docx, odt etc.

Usage

Pandoc.convert(
  f,
  text,
  format = "html",
  open = TRUE,
  options = "",
  footer = FALSE,
  proc.time,
  portable.html = TRUE,
  pandoc.binary = panderOptions("pandoc.binary")
)

Arguments

Value

Converted file's path.

Note

This function depends on Pandoc which should be pre-installed on user's machine. See the INSTALL file of the package.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

## Not run: 
Pandoc.convert(text = c('# Demo', 'with a paragraph'))
Pandoc.convert('https://rapporter.github.io/pander/minimal.md')
# Note: the generated HTML is not showing images with relative path from the above file.
# Based on that `pdf`, `docx` etc. formats would not work! If you want to convert an
# online markdown file to other formats with this function, please pre-process the file
# to have absolute paths instead.

## End(Not run)

Description

Pandoc's mardown date.

Usage

pandoc.date.return(x, inline = TRUE, simplified = FALSE, ...)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Examples

pandoc.date(Sys.Date())
pandoc.date(Sys.Date() - 1:10)
pandoc.date(Sys.Date() - 1:10, inline = FALSE)

Description

Pandoc's markdown emphasis format (e.g. *FOO*) is added to character string.

Usage

pandoc.emphasis.return(x)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

pandoc.strong pandoc.strikeout pandoc.verbatim

Examples

pandoc.emphasis('FOO')
pandoc.emphasis(c('FOO', '*FOO*'))
pandoc.emphasis.return('FOO')

Description

Creates a Pandoc's markdown format footnote.

Usage

pandoc.footnote.return(x)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

pandoc.footnote('Automatically numbered footnote, right?')

Description

Pandoc's mardown formula.

Usage

pandoc.formula.return(
  x,
  text = NULL,
  max.width = 80,
  caption,
  add.line.breaks = FALSE,
  ...
)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Examples

pandoc.formula(y ~ x)
pandoc.formula(formula(paste('y ~ ', paste0('x', 1:12, collapse = ' + '))))

Description

Creates a (Pandoc's) markdown style header with given level.

Usage

pandoc.header.return(x, level = 1, style = c("atx", "setext"))

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

pandoc.header('Foo!', 4)
pandoc.header('Foo!', 2, 'setext')
pandoc.header('Foo **bar**!', 1, 'setext')

Description

Creates a Pandoc's markdown format horizontal line with trailing and leading newlines.

Usage

pandoc.horizontal.rule.return()

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Description

Creates a Pandoc's markdown format image hyperlink.

Usage

pandoc.image.return(img, caption = storage$caption)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

Note

The caption text is read from an internal buffer which defaults to NULL. To update that, call link{set.caption} before.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

set.caption

Examples

pandoc.image('foo.png')
pandoc.image('foo.png', 'Nice image, huh?')

Description

Indent all (optionally concatenated) lines of provided text with given level.

Usage

pandoc.indent(x, level = 0)

Arguments

Examples

pandoc.indent('FOO', 1)
pandoc.indent(pandoc.table.return(table(mtcars$gear)), 2)
cat(pandoc.indent(pandoc.table.return(table(mtcars$gear)), 3))

Description

Create pandoc link Pandoc's markdown format link.

Usage

pandoc.link.return(url, text = url)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

pandoc.link('https://www.r-project.org/')
pandoc.link('https://www.r-project.org/', 'R')

Description

Creates a Pandoc's markdown format list from provided character vector/list.

Usage

pandoc.list.return(
  elements,
  style = c("bullet", "ordered", "roman"),
  loose = FALSE,
  add.line.breaks = TRUE,
  add.end.of.list = TRUE,
  indent.level = 0,
  missing = panderOptions("missing"),
  ...
)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

Examples

## basic lists
pandoc.list(letters[1:5])
pandoc.list(letters[1:5])
pandoc.list(letters[1:5], 'ordered')
pandoc.list(letters[1:5], 'roman')
pandoc.list(letters[1:5], loose = TRUE)

## nested lists
l <- list("First list element",
  rep.int('sub element', 5),
  "Second element",
  list('F', 'B', 'I', c('phone', 'pad', 'talics')))
pandoc.list(l)
pandoc.list(l, loose = TRUE)
pandoc.list(l, 'roman')

## complex nested lists
pandoc.list(list('one', as.list(2)))
pandoc.list(list('one', list('two')))
pandoc.list(list('one', list(2:3)))

Description

Pandoc's markdown paragraph.

Usage

pandoc.p.return(x)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

pandoc.emphasis pandoc.strikeout pandoc.verbatim

Examples

pandoc.p('FOO')
pandoc.p(c('Lorem', 'ipsum', 'lorem ipsum'))

Description

Pandoc's markdown strikeout format (e.g. ~~FOO~~) is added to character string.

Usage

pandoc.strikeout.return(x)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

pandoc.emphasis pandoc.strong pandoc.verbatim

Examples

pandoc.strikeout('FOO')
pandoc.strikeout(c('FOO', '~~FOO~~'))
pandoc.strikeout.return('FOO')

Description

Pandoc's markdown strong emphasis format (e.g. **FOO**) is added to character string.

Usage

pandoc.strong.return(x)

Arguments

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call the function ending in .return.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

pandoc.emphasis pandoc.strikeout pandoc.verbatim

Examples

pandoc.strong('FOO')
pandoc.strong(c('FOO', '**FOO**'))
pandoc.strong.return('FOO')

Description

Creates a Pandoc's markdown style table with optional caption and some other tweaks. See 'Details' below.

Usage

pandoc.table.return(
  t,
  caption,
  digits = panderOptions("digits"),
  decimal.mark = panderOptions("decimal.mark"),
  big.mark = panderOptions("big.mark"),
  round = panderOptions("round"),
  missing = panderOptions("missing"),
  justify,
  style = c("multiline", "grid", "simple", "rmarkdown", "jira"),
  split.tables = panderOptions("table.split.table"),
  split.cells = panderOptions("table.split.cells"),
  keep.trailing.zeros = panderOptions("keep.trailing.zeros"),
  keep.line.breaks = panderOptions("keep.line.breaks"),
  plain.ascii = panderOptions("plain.ascii"),
  use.hyphening = panderOptions("use.hyphening"),
  row.names,
  col.names,
  emphasize.rownames = panderOptions("table.emphasize.rownames"),
  emphasize.rows,
  emphasize.cols,
  emphasize.cells,
  emphasize.strong.rows,
  emphasize.strong.cols,
  emphasize.strong.cells,
  emphasize.italics.rows,
  emphasize.italics.cols,
  emphasize.italics.cells,
  emphasize.verbatim.rows,
  emphasize.verbatim.cols,
  emphasize.verbatim.cells,
  ...
)

Arguments

Details

This function takes any tabular data as its first argument and will try to make it pretty like: rounding and applying digits and custom decimal.mark to numbers, auto-recognizing if row names should be included, setting alignment of cells and dropping trailing zeros by default.

pandoc.table also tries to split large cells with line breaks or even the whole table to separate parts on demand. Other arguments lets the use to highlight some rows/cells/cells in the table with italic or bold text style.

For more details please see the parameters above and passed arguments of panderOptions.

Value

By default this function outputs (see: cat) the result. If you would want to catch the result instead, then call pandoc.table.return instead.

Note

If caption is missing, then the value is first checked in t object's caption attribute and if not found in an internal buffer set by link{set.caption}. justify parameter works similarly, see set.alignment for details.

References

John MacFarlane (2012): _Pandoc User's Guide_. https://johnmacfarlane.net/pandoc/README.html

See Also

set.caption, set.alignment