rapport (version 0.3)

evals: Evaluate and Check R Code

Description

This function takes either a list of integer indices which point to position of R code in body character vector, or a vector/list of strings with actual R code, then evaluates each list element, and returns a list with four elements: a character value with R code, generated output, class of generated output and possible error/warning messages. If a graph is plotted in the given text, the returned object is a string specifying the path to the saved png in temporary directory. Please see Details below.

Usage

evals(txt = NULL, ind = NULL, body = NULL,
    classes = NULL, hooks = NULL, length = Inf,
    output = c("all", "src", "output", "type", "msg"),
    env = NULL, check.output = TRUE,
    graph.name = tempfile(),
    graph.output = c("png", "bmp", "jpeg", "jpg", "tiff", "svg", "pdf"),
    width = 480, height = 480, res = 72, hi.res = FALSE,
    hi.res.width = 960,
    hi.res.height = 960 * (height/width),
    hi.res.res = res * (hi.res.width/width),
    graph.env = FALSE, graph.recordplot = FALSE, ...)

Arguments

txt

a list with character values containing R code

ind

a list with numeric indices pointing to R code in body

body

a character vector that contains template body

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

length

R object exceeding the specified length will not be returned. The default value (Inf) does not have any restrictions.

output

a character vector of required returned values. See below.

env

environment where evaluation takes place. If not set (by default), a new temporary environment is created.

check.output

to check each line of txt for outputs. If set to TRUE you would result in some overhead as all commands have to be run twice (first to check if any output was generated and if so in which part(s), later the R objects are

graph.name

set the file name of saved plots which is a tempfile() by default. A simple character string (or a function which returns a single character vector) might be provided where %INDEX would be replaced by the index of the gen

graph.output

set the required file format of saved plots

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 plots will be calculated based in this.

hi.res

generate high resolution plots also?

hi.res.width

width of generated high resolution plot in pixels for even vector formats (!)

hi.res.height

height of generated high resolution plot in pixels for even vector formats (!). This value can be left blank to be automatically calculated to match original plot aspect ratio.

hi.res.res

nominal resolution of high resolution plot in ppi. The height and width of vector plots will be calculated based in this. This value can be left blank to be automatically calculated to fit original plot scales.

graph.env

save the environments in which plots were generated to distinct files with env extension?

graph.recordplot

save the plot via recordPlot to distinct files with {recodplot} extension?

...

optional parameters passed to graphics device (e.g. bg, pointsize etc.)

Value

• a list of parsed elements each containing: src (the command run), output (what the command returns, NULL if nothing returned, path to image file if a plot was generated), type (class of returned object if any) and messages: warnings (if any returned by the command run, otherwise set to NULL) and errors (if any returned by the command run, otherwise set to NULL). See Details above.

Details

If input strings are given as vector or not nested list (or even only one string), the returned list's length equals to the length of the input - as each string is evaluated as separate R code in the same environment. If a nested list is provided like list(c('runif(1)', 'runif(1)')) then all strings found in a list element is evaled at one run so the length of returned list equals to the length of parent list. See examples below.

As evals tries to grab the plots internally, pleas do not run commands that set graphic device or dev.off if you want to use evals to save the images and return the path of generated png(s). E.g. running evals(c('png("/tmp/x.png")', 'plot(1:10)', 'dev.off()')) would fail.

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. Most of these options are better not to touch, see details of parameters below.

Returned result values: list with the following elements

• src- a character value with specified R code.
• output- generated output.NULLif nothing is returned. If any string returned an R object whileevaling then thelastR object will be returned as a raw R object. If a graph is plotted in the given text, the returned object is a string specifying the path to the saved png in temporary directory (see:tempfile). If multiple plots was run in the same run (see: nested lists as inputs above) then the last plot is saved. If graphic device was touched, then no other R objects will be returned.
• type- class of generated output. "NULL" if nothing is returned, "image" if the graphic device was touched, "error" if some error occurred.
• msg- possible messages grabbed whileevaling specified R code with the following structure:
  • messages- string of possible diagnostic message(s)
  • warnings- string of possible warning message(s)
  • errors- string of possible error message(s)

With check.output options set to FALSE, evals will not check each line of passed R code for outputs to speed up runtime. This way the user is required to pass only reliable and well structured/formatted text to evals. A list to check before running code in evals:

• the code should return on the last line of the passed code (if it returns before that, it would not be grabbed),
• the code should always return something on the last line (if you do not want to return anything, addNULLas the last line),
• ggplot2andlatticegraphs should be always printed (of course on the last line),
• a code part resulting in a plot should not alter variables and data sets,
• the code should be checked before live run withcheck.outputoption set toTRUEjust to be sure if everything goes OK.

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

See Also

eval.msgs, redraw.recordedplot

Examples

# parsing line-by-line
txt <- readLines(textConnection('x <- rnorm(100)
  runif(10)
  warning("You should check out rapport package!")
  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)

## 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'))

## 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)')))
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(list(c('runiff(20)', 'Old MacDonald had a farm?')))
evals(c('mean(1:10)', 'no.R.function()'))
evals(list(c('mean(1:10)', 'no.R.function()')))
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)')))
evals(c('no.R.object', 'Old MacDonald had a farm\\dots', 'pi'))
evals(list(c('no.R.object', 'Old MacDonald had a farm\\dots', 'pi')))

## graph options
evals('plot(1:10)')
evals('plot(1:10)', graph.output = 'jpg')
evals('plot(1:10)', height = 800)
evals('plot(1:10)', height = 800, hi.res = T)
evals('plot(1:10)', graph.output = 'pdf', hi.res = T)
evals('plot(1:10)', res = 30)
evals('plot(1:10)', graph.name = 'myplot')
evals(list('plot(1:10)', 'plot(2:20)'), graph.name = 'myplots-%INDEX')
evals('plot(1:10)', graph.env = TRUE)
evals(list(c('x <- runif(100)', 'plot(x)')), graph.env = TRUE)
evals(c('plot(1:10)', 'plot(2:20)'), graph.env = TRUE)
evals(list(c('x <- runif(100)', 'plot(x)'), c('y <- runif(100)', 'plot(y)')), graph.env = TRUE)
evals('plot(1:10)', graph.recordplot = TRUE)
evals('histogram(mtcars$hp)', graph.recordplot = TRUE)
evals(list(c('x <- runif(100)', 'plot(x)')), graph.recordplot = TRUE)
evals(c('plot(1:10)', 'plot(2:20)'), graph.recordplot = TRUE)
evals('plot(10:100)', graph.output = 'pdf')
evals('runif(10)', graph.output = 'pdf')

## hooks
hooks <- list('numeric' = round, 'matrix' = ascii)
evals(txt, hooks = hooks)
evals('22/7', hooks = list('numeric' = rp.round))
evals('matrix(runif(25), 5, 5)', hooks = list('matrix' = rp.round))

## using rapport's default hook
evals('22/7', hooks = TRUE)

## 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
fun <- function(x, asciiformat) paste(capture.output(print(ascii(x), asciiformat)), collapse = '\n')
hooks <- list('numeric' = list(round, 2), 'matrix' = list(fun, "rest"))
evals(txt, hooks = hooks)

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

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

# check the length of returned values
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' = ascii), output = 'output')

# 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)')