Create _sinewconfig.yml

Description

Create _sinewconfig.yml file in project root directory

Usage

create_yml()

Value

nothing

Author(s)

Jonathan Sidi

Examples

## Not run: 
create_yml()

## End(Not run)

Interactive add-in

Description

Launches an interactive addin for insertion of roxygen2 comments in files. Allows selection of extra parameters for makeOxygen

Usage

interOxyAddIn()

Details

Open an .R file in Rstudio's source editor.

This addin requires shiny and miniUI to be installed (listed as Suggests in Description)

• Launch the add-in via Addins -> interactiveOxygen or interOxyAddIn() in the console.

  • Add-in opens in the viewer panel.

• Select function's/dataset's name in the source editor.

  • If objects cannot be found, the addin prompts to source the file.

  • Choose parameters for makeOxygen

    • Click Insert

• Select next object's name

• Rinse/Repeat

• Click Quit when done with the file.

Value

Nothing. Inserts roxygen2 comments in a file opened in the source editor.

Author(s)

Anton Grishin, Jonathan Sidi

Examples

if(interactive()) interOxyAddIn()

Return roxygen2 parameter calls from parameter dictionary

Description

Return roxygen2 parameter calls from the intersection of the parameters listed in the package dictionary and the formals of a function

Usage

ls_param(obj, dictionary = "man-roxygen/Dictionary-1.R", print = TRUE)

Arguments

Value

character vector

Examples

repo='https://raw.githubusercontent.com/yonicd/sinew/master/'
dict_loc=file.path(repo,'man-roxygen/Dictionary-1.R')
ls_param(sinew::makeOxygen,dictionary=dict_loc)

Parse package R files to create dictionary of unique parameter definitions

Description

Given list of R files function returns roxygen2 template consisting of intersecting parameter definitions

Usage

makeDictionary(path, save_path = FALSE)

Arguments

Value

character/character vector of intersecting parameters

Examples

makeDictionary('R')

Inserts roxygen2 skeletons in file(s).

Description

Applies makeOxygen function to all functions/dataframes in supplied file(s)

Usage

makeOxyFile(input = NULL, overwrite = FALSE, verbose = interactive(), ...)

Arguments

Details

If an object cannot be found it will be sourced into a temporary environment. If the file already contains roxygen2 comments they will be deleted to avoid duplication. Some functions may require attaching additional packages. For instance, if functions were defined with purrr's compose or partial functions, omission of purr:: in definitions will require library(purrr) before proceeding with makeOxyFile.

Value

Nothing. Writes files with roxygen2 comments as a side effect

Author(s)

Anton Grishin

See Also

makeOxygen

Examples

 
# copy dummy package to tempdir
  file.copy(system.file('pkg',package = 'sinew'),tempdir(),recursive = TRUE)
  pkg_dir <- file.path(tempdir(),'pkg')
  pkg_dir_R <- file.path(pkg_dir,'R')

# update namespaces in package functions
  pretty_namespace(pkg_dir_R, overwrite = TRUE)
   
 # test on one R file 
 # this will create a new R file called 'oxy-yy.R' in the same directory
   makeOxyFile(file.path(pkg_dir_R,'yy.R'))
 
 # Remove the file
   unlink(file.path(pkg_dir_R,'oxy-yy.R'))
 
 # Test on all R files in directory and overwrite the contents
   makeOxyFile(pkg_dir_R, overwrite = TRUE)
 
 # Remove Skeleton
   rmOxygen(file.path(pkg_dir_R,'yy.R'))
   rmOxygen(file.path(pkg_dir_R,'zz.R'))
   
 # adds more fields to defaults, passes "cut" to make_import
   sinew_opts$append(list(add_fields=c("concept", "describeIn")))
   makeOxyFile(file.path(pkg_dir_R,'yy.R'), cut = 5)
 
 # cleanup 
   unlink(pkg_dir, recursive = TRUE, force = TRUE)
   sinew_opts$restore()
   

Populate Roxygen2 Skeleton

Description

Creates roxygen2 skeleton including title, description, import and other fields for an object in the global environment or a function of an attached namespace.

Usage

makeOxygen(
  obj,
  add_default = TRUE,
  add_fields = sinew_opts$get("add_fields"),
  use_dictionary = NULL,
  print = TRUE,
  ...
)

Arguments

Details

add_fields can include any slot except for the defaults (title,description,param,return). The order in add_fields determines the order of printout. The roxygen2 fields to add are list below, for more information go to Generating Rd files. If obj is 'data.frame' or 'tibble' then the fields c('export','examples','seealso','rdname') will be ignored.

Examples

makeOxygen(stats::lm)

Create lists of package exports

Description

Useful for supplying packages to the force argument to pretty_namespace.

Usage

make_force_packages(packages)

Arguments

Value

(named list) with package names as names as all exports as a character vector

Examples

make_force_packages(c("utils"))

Populate import fields for documentation

Description

Scrape R script to create import and importFrom calls for roxygen2, namespace or description files

Usage

make_import(
  script,
  cut = NULL,
  print = TRUE,
  format = "oxygen",
  desc_loc = NULL
)

Arguments

Examples

# copy dummy package to tempdir
file.copy(system.file('pkg',package = 'sinew'),tempdir(),recursive = TRUE)

pkg_dir <- file.path(tempdir(),'pkg')
pkg_dir_R <- file.path(pkg_dir,'R')
pkg_dir_DESC <- file.path(pkg_dir,'DESCRIPTION')

# update namespaces in package functions
pretty_namespace(pkg_dir_R, overwrite = TRUE)

# update imports/importsFrom for roxygen2 tags
make_import(pkg_dir_R,format = 'oxygen')

# update Imports for DESCRIPTION file output to console
make_import(pkg_dir_R,format = 'description')

# update Imports for DESCRIPTION file overwrite file
make_import(pkg_dir_R,format = 'description', desc_loc = pkg_dir)

cat(readLines(pkg_dir_DESC),sep = '\n')

# cleanup tempdir
unlink(pkg_dir, force = TRUE, recursive = TRUE)

Make Oxygen Great Again

Description

Update/append an R file that has roxygen2 headers already with updated information

Usage

moga(path, ..., force.fields = NULL, dry.run = TRUE, overwrite = FALSE)

Arguments

Details

Cross references fields already in the roxygen2 header and adds any new ones from the updated call. To force a change to a field add field name to force.fields.

Value

character

Examples

# We want to update the contents of the Roxygen2 with the new parameter "b"
# without touching the other fields

# Before
 cat(readLines(system.file('example_moga.R',package = 'sinew')),sep = '\n')

# After
 moga(system.file('example_moga.R',package = 'sinew'))
 

parse_check

Description

check for fail of pretty_parse > parse, and offers to open file to offending line

Usage

parse_check(p, txt, ask)

Arguments

Interactively run pretty functions in R and Rmd files

Description

Addin that scans the file source contents and attaches namespace information.

Usage

pretty_addin()

Details

Either saved or untitled R or Rmd files in the source editor may be used.

In R files Highlight specific text, or not highlight at all and the whole document will be used.

In Rmd files highlight subsets of chunks to add namespaces directly in the chunks, or not highlight at all and the whole document will be used to create a new chunk at the top of the document with relevant namespaces needed to render the Rmd.

pretty_merge

Description

handles force and ignore arguments

Usage

pretty_merge(e1, e2)

Arguments

Append namespace to functions in script

Description

Autoappend namespace to functions in script by searchpath order

Usage

pretty_namespace(
  con = NULL,
  text = NULL,
  ask = TRUE,
  askenv = new.env(),
  force = NULL,
  ignore = NULL,
  overwrite = FALSE,
  sos = FALSE
)

Arguments

Details

Searches for functions in the loadedNamespace, help.search and then findFn. If force is not NULL but a named list eg list(stats=c('rnorm','runif'),utils = 'head'), then the value pairs will be used in place of what was found using the search path. If ignore is not NULL but a named list eg list(stats=c('rnorm','runif'),utils = 'head'), then if the functions are found they will not have a namespace attached to them.

If you want to toggle off the summary console printing you can set it globally via sinew_opts$set(pretty_print=FALSE).

Value

character

Author(s)

Jonathan Sidi

See Also

findFn, help.search

Examples

txt <- '#some comment
yy <- function(a=4){
  head(runif(10),a)
  # a comment
}

zz <- function(v=10,a=8){
  head(runif(v),a)
}'

pretty_namespace(text=txt)

Attach namespacing to Rmarkdown chunks

Description

Apply pretty_namespace to Rmarkdown document

Usage

pretty_rmd(
  input,
  output = tempfile(fileext = ".Rmd"),
  open_output = TRUE,
  create_library = TRUE,
  chunks = NULL,
  ...
)

Arguments

Details

If output is NULL then the returned lines are printed to console. If chunks is NULL then all the chunks are used.

Value

character

Author(s)

Jonathan Sidi

See Also

pretty_namespace

Examples

## Not run: 
  if(interactive()){
    pretty_rmd(input = system.file('example.Rmd',package = 'sinew'))
  }

## End(Not run)

Convert File to R directory with pretty and oxygen

Description

One function to run pretty_namespace, untangle and makeOxyFile

Usage

pretty_sinew(con = NULL, text = NULL, dir.out = NULL, keep.body = TRUE)

Arguments

Details

If dir.out is set to NULL all outputs are redirected into file.path(tempdir(),'sinew')

Value

Nothing, side effects is to create files

Author(s)

Jonathan Sidi

Remove roxygen2 Comments From an .R File

Description

Strips .R files of roxygen2 style comments (#')

Usage

rmOxygen(.file, showonexit = TRUE)

Arguments

Value

Nothing. Overwrites files as a side effect

Author(s)

Anton Grishin

Examples

## Not run: 
rmOxygen("./myRfunctions/function1.R")

## End(Not run)

Default and current sinew options

Description

Options for functions in the sinew package. When running R code, the object sinew_opts (default options) is not modified by chunk headers (local chunk options are merged with default options), whereas sinew_opts_current (current options) changes with different chunk headers and it always reflects the options for the current chunk.

Usage

sinew_opts

sinew_opts_current

Format

An object of class list of length 5.

An object of class list of length 5.

Details

Normally we set up the global options once in the first code chunk in a document using sinew_opts$set(), so that all latter chunks will use these options. Note the global options set in one chunk will not affect the options in this chunk itself, and that is why we often need to set global options in a separate chunk.

A list of default chunk options, can be retrieved via sinew_opts$get()

Note

sinew_opts_current is read-only in the sense that it does nothing if you call sinew_opts_current$set(); you can only query the options via sinew_opts_current$get().

Examples

sinew_opts$get()

Tabular for roxygen2

Description

Convert data.frame to roxygen2 tabular format

Usage

tabular(df, header = TRUE, ...)

Arguments

Value

character

Source

roxygen2 formatting

See Also

format

Examples

tabular(mtcars[1:5, 1:5])
tabular(mtcars[1:5, 1:5],header=FALSE)

Split an R script by functions

Description

Split a R script with multiple functions into multiple single function R files.

Usage

untangle(
  file = "",
  text = NULL,
  dir.out = "",
  keep.body = TRUE,
  dir.body = dirname(dir.out)
)

Arguments

Details

Functions that are objects in lists are treated as objects and will stay in body.R .

Value

list of seperate functions

Author(s)

Jonathan Sidi

Examples

test_dir <- file.path(tempdir(),'sinew_test')

dir.create(test_dir)

txt <- "#some comment
yy <- function(a=4){
 head(runif(10),a)
 # a comment
}

v <- 20

#another comment
zz <- function(v=10,a=3){
 head(runif(v),pmin(a,v))
}

zz(v)

"

untangle(text = txt,dir.out = test_dir)

list.files(tempdir(), recursive = TRUE, pattern = '.R$')

cat( readLines(file.path(test_dir,'yy.R')), sep = '\n')

cat( readLines(file.path(test_dir,'zz.R')), sep = '\n')

cat( readLines(file.path(tempdir(),'body.R')), sep = '\n')

unlink(test_dir, force = TRUE, recursive = TRUE)

Convert examples blocks in roxygen2 header to script

Description

Converts and aggregates roxygen2 examples into a single output file.

Usage

untangle_examples(input, output = "./roxy_ex_to_file.R")

Arguments

Details

If output is set to NULL then output returned as invisible character object.

Value

writes R file to disk

Author(s)

Jonathan Sidi

Update Package Description File

Description

Update package DESCRIPTION file Imports field

Usage

update_desc(path, overwrite = TRUE)

Arguments

Details

If overwrite is FALSE then the output will be returned to the console.

Author(s)

Jonathan Sidi

Examples

# copy dummy package to tempdir
file.copy(system.file('pkg',package = 'sinew'),tempdir(),recursive = TRUE)

pkg_dir <- file.path(tempdir(),'pkg')
pkg_dir_R <- file.path(pkg_dir,'R')
pkg_dir_DESC <- file.path(pkg_dir,'DESCRIPTION')

# update namespaces in package functions
pretty_namespace(pkg_dir_R,overwrite = TRUE)

# send result to the console
update_desc(pkg_dir_R,overwrite = FALSE)

# overwrite the Imports field
update_desc(pkg_dir_R,overwrite = TRUE)

# view DESCRIPTION file
cat(readLines(pkg_dir_DESC),sep='\n')

# cleanup tempdir
unlink(pkg_dir,recursive = TRUE,force = TRUE)