Movatterモバイル変換

Title:	An R 'Pandoc' Writer
Type:	Package
Encoding:	UTF-8
Description:	Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.
Version:	0.6.6
Date:	2025-03-01
URL:	https://rapporter.github.io/pander/
BugReports:	https://github.com/rapporter/pander/issues
License:	AGPL-3 | file LICENSE
Depends:	R (≥ 2.15.0)
Imports:	grDevices, graphics, methods, utils, stats, digest, tools,Rcpp
Suggests:	grid, lattice, ggplot2 (≥ 0.9.2), sylly, sylly.en, logger,survival, microbenchmark, zoo, nlme, descr, MASS, knitr,rmarkdown, tables, reshape, memisc, Epi, randomForest, tseries,gtable, rms, forecast, data.table
SystemRequirements:	pandoc (https://johnmacfarlane.net/pandoc) forexporting markdown files to other formats.
LinkingTo:	Rcpp
VignetteBuilder:	knitr
RoxygenNote:	7.3.2
NeedsCompilation:	yes
Packaged:	2025-03-01 00:02:44 UTC; daroczig
Author:	Gergely Daróczi [aut, cre], Roman Tsegelskyi [aut]
Maintainer:	Gergely Daróczi <daroczig@rapporter.net>
Repository:	CRAN
Date/Publication:	2025-03-01 01:30:02 UTC

Reporting with Pandoc

Description

ThisR5 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 toClass. No effect on the object itself.

Examples

## Not run: ## Initialize a new Pandoc objectmyReport <- Pandoc$new()## Add author, title and date of documentmyReport$author <- 'Anonymous'myReport$title  <- 'Demo'## Or it could be done while initializingmyReport <- Pandoc$new('Anonymous', 'Demo')## Add some free textmyReport$add.paragraph('Hello there, this is a really short tutorial!')## Add maybe a header for later stuffmyReport$add.paragraph('# Showing some raw R objects below')## Adding a short matrixmyReport$add(matrix(5,5,5))## Or a table with even # TODO: captionmyReport$add.paragraph('Hello table:')myReport$add(table(mtcars$am, mtcars$gear))## Or a "large" data frame which barely fits on a pagemyReport$add(mtcars)## And a simple linear model with Anova tablesml <- with(lm(mpg ~ hp + wt), data = mtcars)myReport$add(ml)myReport$add(anova(ml))myReport$add(aov(ml))## And do some principal component analysis at lastmyReport$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)

Brew in pandoc format

Description

This function behaves just likebrew except for the<%=...%> tags, wherePandoc.brew first translate the R object found between the tags to Pandoc's markdown before passing to thecat 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 andpander 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 inplots directory in currentgetwd() or to the specifiedoutput 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 ifconvert is set, none otherwise

Note

Only one of the input parameters (file ortext) 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 awesomePandoc.brew(text='<%for (i in 1:5) {%>\n Pi has a lot (<%=i%>) of power: <%=pi^i%><%}%>')## package bundled examplesPandoc.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 objectsstr(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)

Converts Pandoc to other format

Description

Calling John MacFarlane's great program to convert specified file (seef parameter below) or character vector (seetext parameter) to other formats likeHTML,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 onPandoc which should be pre-installed on user's machine. See theINSTALL 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)

Add trailing and leading blank line

Description

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

Usage

add.blank.lines(x)

Arguments

Add grids

Description

Exactly the same fn as seelatticeExtra::axis.grid but usinggrid colors instead.

Usage

add.lattice.grid(  side = c("top", "bottom", "left", "right"),  ...,  ticks = c("default", "yes", "no"),  scales,  components,  line.col)

Arguments

References

This function is a forked version oflatticeExtra::axis.grid

Add subticks

Description

SeelatticeExtra::xscale.components.subticks.

Usage

add.lattice.xsubticks(lim, ..., n = 2)

Arguments

References

This is a simplified verwion oflatticeExtra::xscale.components.subticks.

Minor tick marks

Description

Adds minor tick marks to an existingbase plot.

Usage

add.minor.ticks(nx = 4, ny = 4, grid = TRUE)

Arguments

References

This function is a forked version ofHmisc::minor.tick

Add significance stars

Description

This function adds significance stars to passedp value(s) as: one star for value below0.05, two for0.01 and three for0.001.

Usage

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

Arguments

Value

character vector

Patched brew

Description

This is a forked/patched version of 'brew' package made by Jeffrey Horner (c) 2007. See:References about the original version.

Usage

brew(text = NULL, envir = parent.frame())

Arguments

Details

This custom function can do more and also less compared to the originalbrew package. First of all the internal caching mechanism (and other, frompander package POV needless features) of 'brew' is removed for some extra profits:

• multiple R expressions can be passed between<%= ... %> tags,

• the text of the file and also the evaluated R objects are (invisibly) returned in a structured list, which can be really useful while post-processing the results of 'brew'.

Value

brewed document tostdout and raw results while evaluating thetext in a structured list.

Note

This function should be never called directly (usebrew::brew instead) as being a helper function ofPandoc.brew.

References

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

See Also

Pandoc.brew

Toggle cache

Description

This function is just a wrapper aroundevalsOptions 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()

Check if caption is valid

Description

Check if caption is valid

Usage

check_caption(caption)

Arguments

Value

boolean

Check if vector parameter for round/digits and adjust accodingly

Description

Check if vector parameter for round/digits and adjust accodingly

Usage

check_digits(param, name, n)

Arguments

Value

original vector if size is good, vector of default values otherwise

Calculate coef matrix for models from rms packageForked from prModFit from rms

Description

Calculate coef matrix for models from rms packageForked from prModFit from rms

Usage

coef_mat(obj, coefs)

Arguments

Value

coeficients matrix

Emphasize rows/columns/cells

Description

Storing indexes of cells to be (strong) emphasized of a tabular data in an internal buffer that can be released and applied bypandoc.table,pander orevals 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)

Evaluate with messages

Description

This function takes text(s) of R code andevals all at one run - returning a list with four elements. SeeDetails.

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 thelast 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 andggplot2).

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

• 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),printedoutput,type (class of returned object if any), informative/wawrning and error messages (if any returned by the command run, otherwise set toNULL) and possiblestdoutt 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)')## plotseval.msgs('plot(runif(100))')eval.msgs('histogram(runif(100))')## error handlingeval.msgs('runiff(23)')eval.msgs('runif is a nice function')eval.msgs('no.R.object.like.that')## messageseval.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')## stdouteval.msgs('cat("writing to console")')eval.msgs('cat("writing to console");1:4')## End(Not run)

Evaluate and Process R Code

Description

This function takes either a vector/list ofstrings with actual R code, which it to beparsed to separate elements. Each list element isevaluated 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 tostdout. 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.Ifparse option set toFALSE, then the returned list's length equals to the length of theparsed 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 likelist(c('runif(1)', 'runif(1)')) withparse=FALSE, then everything isevaled 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

Asevals tries to grab the plots internally, pleas do not run commands that set graphic device ordev.off. E.g. runningevals(c('png("/tmp/x.png")', 'plot(1:10)', 'dev.off()')) would fail.printing oflattice andggplot2 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 outgraph.output,width,height,res,hi.res,hi.res.width,hi.res.height andhi.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 thelast 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 (withclass set toimage) 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) ofresult

• 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 defaultevals tries tocache results. This means that if evaluation of some R commands take too much time (specified incache.time parameter), thenevals 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 isparsed to single commands.

• Each parsed command's part (let it be a function, variable, constant etc.)evaluated (as aname) separately to alist. 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 inpander'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 isserialized and anSHA-1 hash is computed for that - which is unique and there is no real risk of collision.

• Ifevals 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. ifcache is active, if theproc.time() of the evaluation is higher then it is defined incache.time etc.).

This is a quite secure way of caching, but if you would encounter any issues, just setcache toFALSE or tweak other cache parameters. While settingcache.dir, please do think about what you are doing and move yourgraph.dir accordingly, asevals 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 withcache on. Similarly you cannot render a high resolution image of a cached image, but you have to (temporary) disable caching.

The defaultevals options could be set globally withevalsOptions, e.g. to switch off the cache just runevalsOptions('cache', FALSE).

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

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),printedoutput,type (class of returned object if any), informative/wawrning and error messages (if any returned by the command run, otherwise set toNULL) and possiblestdoutt value. See Details above.

See Also

eval.msgsevalsOptions

Examples

## Not run: # parsing several lines of R codetxt <- 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 commandstxt <- 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 parsingevals(txt, parse = FALSE)## handling messagesevals('message(20)')evals('message(20);message(20)', parse = FALSE)## adding a caption to a plotevals('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 warningsevals('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 errorsevals('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 optionsevals('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 plotevals('histogram(mtcars$hp)', graph.recordplot = TRUE)## cachingsystem.time(evals('plot(mtcars)'))system.time(evals('plot(mtcars)'))                # running again to see the speed-up :)system.time(evals('plot(mtcars)', cache = FALSE)) # cache disabled## caching mechanism does check what's inside a variable:x <- mtcarsevals('plot(x)')x <- cbind(mtcars, mtcars)evals('plot(x)')x <- mtcarssystem.time(evals('plot(x)'))## stress your CPU - only once!evals('x <- sapply(rep(mtcars$hp, 1e3), mean)')   # run it again!## play with cacherequire(lattice)evals('histogram(rep(mtcars$hp, 1e5))')## nor run the below call## that would return the cached version of the above call :)f <- histogramg <- repA <- mtcars$hpB <- 1e5evals('f(g(A, B))')#'## or switch off cache globally:evalsOptions('cache', FALSE)## and switch on laterevalsOptions('cache', TRUE)## evaluate assignments inside call to evals## changes to environments are cached properly and retreivedevalsOptions('cache.time', 0)x <- 2evals('x <- x^2')[[1]]$resultevals('x <- x^2; x + 1')[[2]]$resultevalsOptions('cache.time', 0.1)## returning only a few classestxt <- 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'))## hookstxt <- '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 hookevals(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 hookevals(c('runif(10)', 'matrix(runif(9), 3, 3)'),  hooks = list('default'=round))## round all values except for matricesevals(c('runif(10)', 'matrix(runif(9), 3, 3)'),  hooks = list(matrix = 'print', 'default' = round))# advanced hookshooks <- list('numeric' = list(round, 2), 'matrix' = list(round, 1))evals(txt, hooks = hooks)# return only returned valuesevals(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 objectsevals('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 & filteringevals('matrix(5,5,5)',  hooks = list('matrix' = pander_return),  output = 'result')# eval-ing chunks in given environmentmyenv <- 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 failedevals('x <- c(0,10)')evals('mean(x)')# logx <- evals('1:10', log = 'foo')# trace logevalsOptions('cache.time', 0)x <- evals('1:10', log = 'foo')x <- evals('1:10', log = 'foo')# log to filet <- tempfile()log_appender(appender_file(t), name = 'evals')x <- evals('1:10', log = 'evals')readLines(t)# permanent log for all eventsevalsOptions('log', 'evals')log_threshold(TRACE, 'evals')evals('foo')## End(Not run)

Querying/setting evals option

Description

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

Usage

evalsOptions(o, value)

Arguments

Details

The followingevals options are available:

• parse: ifTRUE the providedtxt 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 aplot and on next line adding anabline ortext to it), use a plus char (+) at the beginning of each line which should be evaluated with the previous one(s). If set toFALSE,evals would not try to parse R code, it would get evaluated in separate runs - as provided. Please see examples ofevals.

• cache: caching the result of R calls if set toTRUE

• cache.mode: cached results could be stored in anenvironment incurrent R session or let it be permanent ondisk.

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

• cache.time: number of seconds to limit caching based onproc.time. If set to0, all R commands, if set toInf, none is cached (despite thecache parameter).

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

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

• hooks: list of hooks to be run for given classes in the form oflist(class = fn). If you would also specify some parameters of the function, a list should be provided in the form oflist(fn, param1, param2=NULL) etc. So the hooks would becomelist(class1=list(fn, param1, param2=NULL), ...). See examples ofevals. 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 theresult, and do not want to save/see e.g.messages orprintedoutput. See examples ofevals.

• graph.unify: boolean (default:FALSE) that determines ifevals should try to unify the style of (base,lattice andggplot2) plots? If set toTRUE, somepanderOptions() would apply.

• graph.name: set the file name of saved plots which istempfile by default. A simple character string might be provided where%d would be replaced by the index of the generatingtxt source,%n with an incremented integer ingraph.dir with similar file names and%t by some random characters. A function's name to beevaluated 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 toplots in current working directory.

• graph.output: set the required file format of saved plots. Currently it could be any ofgrDevices:png,bmp,jpeg,jpg,tiff,svg orpdf. Set toNA not to save plots at all and tweak that setting withcapture.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 inppi. The height and width of vector images will be calculated based in this.

• hi.res: generate high resolution plots also? If set toTRUE, 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. Theheight andres 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 ongraph.name) withenv extension?

• graph.recordplot: save the plot viarecordPlot to distinct files (based ongraph.name) withrecodplot extension?

• graph.RDS: save the raw R object returned (usually withlattice orggplot2) while generating the plots to distinct files (based ongraph.name) withRDS extension?

• log:NULL or an optionally passednamespace fromlogger to record all info, trace, debug and error messages.

See Also

evalspanderOptions

Examples

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

Get alignment

Description

Get alignment from temporary environment, truncating that and applying rownames and other columns alignment to passeddf.

Usage

get.alignment(df, remove.obious.rownames = TRUE)

Arguments

Value

vector of alignment parameters

Get caption

Description

Get caption from temporary environment and truncates that

Usage

get.caption()

Value

stored caption as string

Get emphasize params from internal buffer

Description

And truncate content.

Usage

get.emphasize(df)

Arguments

Value

R object passed asdf with possibly addedattrs captured from internal buffer

Get a value from internal buffer

Description

And truncate content.

Usage

get.storage(what)

Arguments

Check if rownames are available

Description

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

Usage

has.rownames(x)

Arguments

Value

TRUE ORFALSE

Create a multitable used for rendering objects from rms package

Description

When ols/lrm/orm from rms package get rendered, main statistics are group in table of tables.Since pandoc doesn't support row or col-span,we chose to group those statistics in a column each.This function takes care of that

Usage

multitable(v)

Arguments

Value

data.frame in specified format

Examples

pander:::multitable(list(list(a=1, b=2),list(c=3, d=4)))

Open file

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'sconvert function:https://github.com/eusebe/ascii/blob/master/R/export.r

Inline Printing

Description

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

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 fromrapport 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'

Generic pander method

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 bypander andpandoc 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

## Vectorspander(1:10)pander(letters)pander(mtcars$am)pander(factor(mtcars$am))## Listspander(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$gear))))## Arrayspander(mtcars)pander(table(mtcars$am))pander(table(mtcars$am, mtcars$gear))## Testspander(ks.test(runif(50), runif(50)))pander(chisq.test(table(mtcars$am, mtcars$gear)))pander(t.test(extra ~ group, data = sleep))## Modelsml <- 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 labelspander(lm(Sepal.Width ~ Species, data = iris), covariate.labels = c('Versicolor', 'Virginica'))## Prcomppander(prcomp(USArrests))## Otherspander(density(runif(10)))pander(density(mtcars$hp))## default methodx <- chisq.test(table(mtcars$am, mtcars$gear))class(x) <- 'I heave never heard of!'pander(x)

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

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

Pander method for CrossTable class

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

Pander method for Date class

Description

Prints a Date object in Pandoc's markdown.

Usage

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

Arguments

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

Description

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

Usage

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

Arguments

Pander method for a NULL object

Description

Prints a NULL object in Pandoc's markdown.

Usage

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

Arguments

Pander method for POSIXct class

Description

Prints a POSIXct object in Pandoc's markdown.

Usage

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

Arguments

Pander method for POSIXlt class

Description

Prints a POSIXlt object in Pandoc's markdown.

Usage

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

Arguments

Pander method for anova class

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

Pander method for aov class

Description

Prints an aov object in Pandoc's markdown.

Usage

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

Arguments

Pander method for aovlist class

Description

Prints an aovlist object in Pandoc's markdown.

Usage

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

Arguments

Pander method for call class

Description

Prints a call object in Pandoc's markdown.

Usage

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

Arguments

Pander method for cast_df class

Description

Prints a cast_df object in Pandoc's markdown.

Usage

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

Arguments

Pander method for character class

Description

Prints a character class in Pandoc's markdown.

Usage

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

Arguments

Pander method for clogit class

Description

Prints a clogit object in Pandoc's markdown.

Usage

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

Arguments

Pander method for coxph class

Description

Prints a coxph object in Pandoc's markdown.

Usage

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

Arguments

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

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

Pander method for data.frame class

Description

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

Usage

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

Arguments

Pander method for data.table class

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

Default Pander method

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

Pander method for density class

Description

Prints a density object in Pandoc's markdown.

Usage

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

Arguments

Pander method for describe class

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

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

Description

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

Usage

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

Arguments

Pander method for evals class

Description

Prints a evals object in Pandoc's markdown.

Usage

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

Arguments

Pander method for factor class

Description

Prints a factor object in Pandoc's markdown.

Usage

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

Arguments

Pander method for formula class

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

Pander method for ftable class

Description

Prints a ftable object in Pandoc's markdown.

Usage

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

Arguments

Pander method for function class

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

Pander method for summary.glm class

Description

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

Usage

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

Arguments

Pander method for gtable class

Description

Renders an gtable object in Pandoc's markdown.

Usage

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

Arguments

Pander method for htest class

Description

Prints a htest object in Pandoc's markdown.

Usage

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

Arguments

Pander method for image class

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

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

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

Pander method for list class

Description

Prints a list object in Pandoc's markdown.

Usage

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

Arguments

Pander method for summary.lm class

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

Pander method for lme class

Description

Prints a lme object in Pandoc's markdown.

Usage

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

Arguments

Pander method for logical class

Description

Prints a logical object in Pandoc's markdown.

Usage

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

Arguments

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

Description

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

Usage

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

Arguments

Pander method for manova class

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

Pander method for matrix class

Description

Prints a matrix object in Pandoc's markdown.

Usage

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

Arguments

Pander method for microbenchmark class

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

Pander method for name class

Description

Prints a call object in Pandoc's markdown.

Usage

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

Arguments

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

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

Pander method for numeric class

Description

Prints a numeric class in Pandoc's markdown.

Usage

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

Arguments

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

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

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

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

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

Description

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

Usage

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

Arguments

Pander method for prcomp class

Description

Prints a prcomp object in Pandoc's markdown.

Usage

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

Arguments

Pander method for randomForest class

Description

Renders an randomForest object in Pandoc's markdown.

Usage

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

Arguments

Pander method for rapport class

Description

Prints a rapport object in Pandoc's markdown.

Usage

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

Arguments

Pander method for rlm class

Description

Prints an rlm object in Pandoc's markdown.

Usage

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

Arguments

Pander method for sessionInfo class

Description

Prints an sessionInfo object in Pandoc's markdown.

Usage

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

Arguments

Pander method for smooth.spline class

Description

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

Usage

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

Arguments

Pander method for stat.table class

Description

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

Usage

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

Arguments

Pander method for summary.aov class

Description

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

Usage

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

Arguments

Pander method for summary.aovlist class

Description

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

Usage

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

Arguments

Pander method for summary.glm class

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.

Pander method for summary.lm class

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.

Pander method for summary.lme class

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

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

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

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

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

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

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

Pander method for summary.prcomp class

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

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

Description

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

Usage

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

Arguments

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

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

Pander method for summary.table class

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

Pander method for survdiff class

Description

Prints an survdiff object in Pandoc's markdown.

Usage

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

Arguments

Pander method for survfit class

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

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

Description

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

Usage

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

Arguments

Pander method for table class

Description

Prints a table object in Pandoc's markdown.

Usage

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

Arguments

Pander method for tabular class

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

Pander method for timeseries class

Description

Prints a timeseries object in Pandoc's markdown.

Usage

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

Arguments

Helper function to deal with atomic vectors

Description

Helper function to deal with atomic vectors

Usage

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

Arguments

Pander method for zoo class

Description

Prints a zoo object in Pandoc's markdown.

Usage

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

Arguments

Querying/setting pander option

Description

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

Usage

panderOptions(o, value)

Arguments

Details

The followingpander options are available:

• digits: numeric (default:2) passed toformat. 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 toformat

• formula.caption.prefix: string (default:'Formula: ') passed topandoc.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 toformat.

• round: numeric (default:Inf) passed toround. 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 toformat when printing dates (POSIXct orPOSIXt)

• header.style:'atx' or'setext' passed topandoc.header

• list.style:'bullet','ordered' or'roman' passed topandoc.list. Please not that this has no effect onpander methods.

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

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

• table.split.table: numeric passed topandoc.table and also affectspander methods. This option tellspander 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. toInf to disable this feature) if you are not using a VT100 terminal any more :)

• table.split.cells: numeric or numeric vector (default:30) passed topandoc.table and also affectspander methods. This option tellspander where to split too wide cells with line breaks. Numeric vector specifies values for cells separately. SetInf to disable.

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

• table.continues.affix: string (default:'(continued below)') passed topandoc.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 beleft,right orcentre that latter can be also spelled ascenter.

• table.alignment.rownames: string (default:centre) that defines the alignment of rownames in tables. Can beleft,right orcentre that latter can be also spelled ascenter.

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

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

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

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

• p.copula: a string (default:' and ') with ending separator passed top 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 requiresgrDevices:::windowsFonts first.

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

• graph.fontsize: numeric (default:12) specifying thebase font size in pixels. Main title is rendered with1.2 and labels with0.8 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. Pleasenote, that this option is not supported withbase graphics.

• graph.colors: character vector of default color palette (defaults to a colorblind theme:https://jfly.uni-koeln.de/color/). Pleasenote that this update work withbase plots by appending thecol 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 onpar(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 thepch parameter ofpar)

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

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

See Also

evalsOptions

Examples

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

Pander and capture output

Description

This is a wrapper function aroundpander but instead of printing tostdout, this function returns a character vector of the captured lines.

Usage

pander_return(...)

Arguments

See Also

pander

Dates

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)

Emphasis

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.strongpandoc.strikeoutpandoc.verbatim

Examples

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

Footnote

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?')

Formulas

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 = ' + '))))

Create header

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')

Create horizontal rule

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

Create pandoc image tags

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

Thecaption text is read from an internal buffer which defaults toNULL. To update that, calllink{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?')

Indent text

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))

Create pandoc linkPandoc's markdown format link.

Description

Create pandoc linkPandoc'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')

Create a list

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 listspandoc.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 listsl <- 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 listspandoc.list(list('one', as.list(2)))pandoc.list(list('one', list('two')))pandoc.list(list('one', list(2:3)))

Paragraphs

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.emphasispandoc.strikeoutpandoc.verbatim

Examples

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

Add strikeout

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.emphasispandoc.strongpandoc.verbatim

Examples

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

Strong emphasis

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.emphasispandoc.strikeoutpandoc.verbatim

Examples

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

Create a table

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 applyingdigits and customdecimal.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 ofpanderOptions.

Value

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

Note

Ifcaption is missing, then the value is first checked int object'scaption attribute and if not found in an internal buffer set bylink{set.caption}.justify parameter works similarly, seeset.alignment for details.

References

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

See Also

set.caption,set.alignment

Examples

pandoc.table(mtcars)# captionpandoc.table(mtcars, 'Motor Trend Car Road Tests')# other input/output formatspandoc.table(mtcars[, 1:3], decimal.mark = ',')pandoc.table(mtcars[, 1:3], decimal.mark = ',', justify = 'right')pandoc.table(matrix(sample(1:1000, 25), 5, 5))pandoc.table(matrix(runif(25), 5, 5))pandoc.table(matrix(runif(25), 5, 5), digits = 5)pandoc.table(matrix(runif(25),5,5), round = 1)pandoc.table(table(mtcars$am))pandoc.table(table(mtcars$am, mtcars$gear))pandoc.table(table(state.division, state.region))pandoc.table(table(state.division, state.region), justify = 'centre')m <- data.frame(a = c(1, -500, 10320, 23, 77),  b = runif(5),  c = c('a', 'bb', 'ccc', 'dddd', 'eeeee'))pandoc.table(m)pandoc.table(m, justify = c('right', 'left', 'centre'))pandoc.table(m, justify = 'rlc') # Same as upper statement## splitting up too wide tablespandoc.table(mtcars)pandoc.table(mtcars, caption = 'Only once after the first part!')## tables with line breaks in cells## NOTE: line breaks are removed from table content in case keep.line.breaks is set to FALSE## and added automatically based on "split.cells" parameter!t <- data.frame(a = c('hundreds\nof\nmouses', '3 cats'), b=c('FOO is nice', 'BAR\nBAR2'))pandoc.table(t)pandoc.table(t, split.cells = 5)## exporting tables in other Pandoc stylespandoc.table(m)pandoc.table(m, style = "grid")pandoc.table(m, style = "simple")pandoc.table(t, style = "grid")pandoc.table(t, style = "grid", split.cells = 5)tryCatch(pandoc.table(t, style = "simple", split.cells = 5),  error = function(e) 'Yeah, no newline support in simple tables')## highlight cellst <- mtcars[1:3, 1:5]pandoc.table(t$mpg, emphasize.italics.cells = 1)pandoc.table(t$mpg, emphasize.strong.cells = 1)pandoc.table(t$mpg, emphasize.italics.cells = 1, emphasize.strong.cells = 1)pandoc.table(t$mpg, emphasize.italics.cells = 1:2)pandoc.table(t$mpg, emphasize.strong.cells = 1:2)pandoc.table(t, emphasize.italics.cells = which(t > 20, arr.ind = TRUE))pandoc.table(t, emphasize.italics.cells = which(t == 6, arr.ind = TRUE))pandoc.table(t, emphasize.verbatim.cells = which(t == 6, arr.ind = TRUE))pandoc.table(t, emphasize.verbatim.cells = which(t == 6, arr.ind = TRUE), emphasize.italics.rows = 1)## with helpersemphasize.cols(1)emphasize.rows(1)pandoc.table(t)emphasize.strong.cells(which(t > 20, arr.ind = TRUE))pandoc.table(t)### plain.asciipandoc.table(mtcars[1:3, 1:3], plain.ascii = TRUE)### keep.line.breaksx <- data.frame(a="Pandoc\nPackage")pandoc.table(x)pandoc.table(x, keep.line.breaks = TRUE)## split.cellsx <- data.frame(a = "foo bar", b = "foo bar")pandoc.table(x, split.cells = 4)pandoc.table(x, split.cells = 7)pandoc.table(x, split.cells = c(4, 7))pandoc.table(x, split.cells = c("20%", "80%"), split.tables = 30)y <- c("aa aa aa", "aaa aaa", "a a a a a", "aaaaa", "bbbb bbbb bbbb", "bb bbb bbbb")y <- matrix(y, ncol = 3, nrow = 2)rownames(y) <- c("rowname one", "rowname two")colnames(y) <- c("colname one", "colname two", "colname three")pandoc.table(y, split.cells = 2)pandoc.table(y, split.cells = 6)pandoc.table(y, split.cells = c(2, 6, 10))pandoc.table(y, split.cells = c(2, Inf, Inf))## first value used for rownamespander(y, split.cells = c(5, 2, Inf, Inf))pandoc.table(y, split.cells = c(5, 2, Inf, 5, 3, 10))## when not enough reverting to default valuespandoc.table(y, split.cells = c(5, 2))## split.cells with hyphenationx <- data.frame(a = "Can be also supplied as a vector, for each cell separately",       b = "Can be also supplied as a vector, for each cell separately")pandoc.table(x, split.cells = 10, use.hyphening = TRUE)

Create title block

Description

Creates a Pandoc's markdown style title block with optional author, title and date fields.

Usage

pandoc.title.return(author = "", title = "", date = "")

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.title('Tom', 'Render pandoc in R', '2012-05-16')pandoc.title(c('Tom', 'Jerry'), 'Render pandoc in R', '2012-05-16')pandoc.title('Tom; Jerry', 'Render pandoc in R', '2012-05-16')pandoc.title('Tom; Jerry', c('Render', 'pandoc', 'in R'), '2012-05-16')pandoc.title('Tom; Jerry', 'Render\n    pandoc \n    in R', '2012-05-16')## missing fieldspandoc.title('Tom; Jerry', 'Render pandoc in R')pandoc.title('Tom; Jerry')pandoc.title(title = 'Render pandoc in R', date= '2012-05-16')

Add verbatim

Description

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

Usage

pandoc.verbatim.return(x, style = c("inline", "indent", "delim"), attrs = "")

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.emphasispandoc.strikeoutpandoc.strong

Examples

# different styles/formatspandoc.verbatim('FOO')src <- c('FOO', 'indent', 'BAR' )pandoc.verbatim(src)pandoc.verbatim.return(src)pandoc.verbatim(c('FOOO\nBAR  ', ' I do R'), 'indent')pandoc.verbatim(c('FOOO\nBAR  ', ' I do R'), 'delim')# add highlighting and HTML/LaTeX ID and classes (even custom attribute)pandoc.verbatim(c('cat("FOO")', 'mean(bar)'), 'delim', '.R #MyCode custom_var="10"')

Find path to the pandoc binary by checking thePATH and theRSTUDIO_PANDOC env vars

Description

Find path to the pandoc binary by checking thePATH and theRSTUDIO_PANDOC env vars

Usage

path_to_pandoc()

Value

file path

Redraws plot saved in file

Description

This function is a wrapper aroundredrawPlot.

Usage

redraw.recordedplot(file)

Arguments

References

Thanks to Jeroen Oomshttps://stat.ethz.ch/pipermail/r-devel/2012-January/062973.html, JJ Allairehttps://github.com/rstudio/rstudio/commit/eb5f6f1db4717132c2ff111f068ffa6e8b2a5f0b, and Gabriel Becker.

See Also

evals

Redraw a recordedplot, grid, trellis, or ggplot2 plot.

Description

This function redraws the plot represented byrec_plot. It can redraw grid/trellis/ggplot2/etc plots, as well asrecordedplot objects. Forrecordedplot objects it acts as a wrapper aroundreplayPlot with memory tweaks to fix native symbol address errors when the recordedplot was loaded from an rda/rds file.

Usage

redrawPlot(rec_plot)

Arguments

References

Thanks to Jeroen Oomshttps://stat.ethz.ch/pipermail/r-devel/2012-January/062973.html, JJ Allairehttps://github.com/rstudio/rstudio/commit/eb5f6f1db4717132c2ff111f068ffa6e8b2a5f0b, and Gabriel Becker.

See Also

redraw.recordedplot

Remove more then two joined newlines

Description

Remove more then two joined newlines

Usage

remove.extra.newlines(x)

Arguments

Examples

remove.extra.newlines(c('\n\n\n', '\n\n', '\n'))

Repeating chars

Description

Repeating a stringn times and returning a concatenated character vector.

Usage

repChar(x, n, sep = "")

Arguments

Value

character vector

Sets alignment for tables

Description

This is a helper function to update the alignment (justify parameter inpandoc.table) of the next returning table. Possible values are:centre orcenter,right,left.

Usage

set.alignment(  default = panderOptions("table.alignment.default"),  row.names = panderOptions("table.alignment.rownames"),  permanent = FALSE)

Arguments

Adds caption in current block

Description

This is a helper function to add a caption to the returning image/table.

Usage

set.caption(x, permanent = FALSE)

Arguments

Split line with line breaks depending on max.width

Description

This is a helper function to insert line breaks depending on (split.cells parameter ofpandoc.table) of the returning table.

Usage

splitLine(  x,  max.width = panderOptions("table.split.cells"),  use.hyphening = FALSE)

Arguments

Value

character string with line breaks

Examples

splitLine('foo bar', 6)splitLine('foo bar', 7)splitLine('Pandoc Package', 3, TRUE)

Trim leading and trailing spaces

Description

Trim leading and trailing spaces

Usage

trim.spaces(x)

Arguments

Value

character vector

See Also

trim.space inrapport package

Wrap Vector Elements

Description

Wraps vector elements with string provided inwrap argument.

Usage

wrap(x, wrap = "\"")

Arguments

Value

a string with wrapped elements

Author(s)

Aleksandar Blagotic

References

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

Examples

## Not run: wrap('foobar')wrap(c('fee', 'fi', 'foo', 'fam'), '_')## End(Not run)