Package 'D4TAlink.light'

Object of class D4TAlinkTask, as created by initTask.

full name of the output zip file

overwrite the output zip file is it exists

Arguments passed on to utils::zip

zipfile

The pathname of the zip file: tilde expansion (see path.expand) will be performed.

files

A character vector of recorded filepaths to be included.

flags

A character string of flags to be passed to the command: see ‘Details’.

extras

An optional character vector: see ‘Details’.

zip

A character string specifying the external command to be used.

Object of class D4TAlinkTask, as created by initTask.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

R object to output.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

separator

EOF

R objects (see ‘Details’ for the types of objects allowed).

name of variable

description of variable

suppress error messages, default=FALSE.

Project name.

Package name.

Task name.

Author name, system username by default.

Sponsor name, default set by setTaskSponsor.

Path of the task repository, default set by setTaskRoot.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Directory type, e.g. 'bin' or 'data' or 'doc'.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

optional function returning a list of paths, currently pathsGLPG or pathsPMS.

Object of class D4TAlinkTask, as created by initTask.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

name of the input file.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Sponsor name, default set by setTaskSponsor.

Object of class D4TAlinkTask, as created by initTask.

Object of class D4TAlinkTask, as created by initTask.

input file name.

suppress error messages, default=FALSE.

query encryption key from user, default FALSE.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

task directory where file is stored, i.e., 'documentation', 'code', 'data', 'data source' or 'binary data'.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

suppress error messages, default=FALSE.

suppress error messages, default=FALSE.

suppress error messages, default=FALSE.

suppress error messages, default=FALSE.

suppress error messages, default=FALSE.

suppress error messages, default=FALSE.

Project name.

Package name.

Task name.

Sponsor name, default set by setTaskSponsor.

Author name, system username by default.

logical, if TRUE (by default) the directory structure for the task is created in the repository.

create the prefilled Rmd template for the task, default value: FALSE.

logical, if TRUE and the task already exists, overwrite its parameters.

Object of class D4TAlinkTask, as created by initTask.

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1, UTF-8 or to be bytes: it is not used to re-encode the input. To do the latter, specify the encoding as part of the connection con or via options(encoding=): see the examples and ‘Details’.

overwrite Qmd file if exists, default FALSE

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Object of class D4TAlinkTask, as created by initTask.

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1, UTF-8 or to be bytes: it is not used to re-encode the input. To do the latter, specify the encoding as part of the connection con or via options(encoding=): see the examples and ‘Details’.

overwrite Rmd file if exists, default FALSE

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Object of class D4TAlinkTask, as created by initTask.

overwrite R file if exists, default FALSE

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1, UTF-8 or to be bytes: it is not used to re-encode the input. To do the latter, specify the encoding as part of the connection con or via options(encoding=): see the examples and ‘Details’.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Object of class D4TAlinkTask, as created by initTask.

Should be plotting be done using Windows GDI or cairographics?

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

device height and width in px.

device height in px.

device height in px.

Arguments passed on to grDevices::jpeg

filename

the path of the output file, up to 511 characters. The page number is substituted if a C integer format is included in the character string, as in the default, and tilde-expansion is performed (see path.expand). (The result must be less than 600 characters long. See png for further details.)

units

The units in which height and width are given. Can be px (pixels, the default), in (inches), cm or mm.

pointsize

the default pointsize of plotted text, interpreted as big points (1/72 inch) at res ppi.

bg

the initial background colour: can be overridden by setting par("bg").

quality

the ‘quality’ of the JPEG image, as a percentage. Smaller values will give more compression but also more degradation of the image.

res

The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default. If not specified, taken as 72 ppi to set the size of text and line widths.

family

A length-one character vector specifying the default font family. The default means to use the font numbers on the Windows GDI versions and "sans" on the cairographics versions.

restoreConsole

See the ‘Details’ section of windows. For type == "windows" only.

antialias

Length-one character vector.

For allowed values and their effect on fonts with type = "windows" see windows: for that type if the argument is missing the default is taken from windows.options()$bitmap.aa.win.

For allowed values and their effect (on fonts and lines, but not fills) with type = "cairo" see svg.

symbolfamily

For cairographics only: a length-one character string that specifies the font family to be used as the "symbol" font (e.g., for plotmath output). The default value is "default", which means that R will choose a default "symbol" font based on the graphics device capabilities.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Object of class D4TAlinkTask, as created by initTask.

a logical value. If TRUE, the directory path is prepended to the file names to give a relative file path. If FALSE, the file names (rather than paths) are returned.

list of file types to list.

Project name.

Package name.

Sponsor name, default set by setTaskSponsor.

Path of the task repository, default set by setTaskRoot.

Project name.

Package name.

Task name.

Sponsor name, default set by setTaskSponsor.

Author name, system username by default.

issue warning if file does not exists.

Project name.

Package name.

Task name.

Sponsor name, default set by setTaskSponsor.

Project name.

Package name.

Task name.

Sponsor name, default set by setTaskSponsor.

Project name.

Package name.

Task name.

Sponsor name, default set by setTaskSponsor.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

title string to embed as the ‘⁠/Title⁠’ field in the document metadata. Defaults to "R Graphics Output"; use an empty string ("") to omit the field.

a character string giving the file path. See the section ‘File specifications’ for further details.

device height and width in mm.

device height in mm.

device height in mm.

if defined, orientation of the document.

Arguments passed on to grDevices::pdf

width,height

the width and height of the graphics region in inches. The default values are 7.

onefile

logical: if true (the default) allow multiple figures in one file. If false, generate a file with name containing the page number for each page. Defaults to TRUE, and forced to true if file is a pipe.

family

the initial font family to be used, normally as a character string. See the section ‘Families’. Defaults to "Helvetica".

fonts

a character vector specifying R graphics font family names for additional fonts which will be included in the PDF file. Defaults to NULL.

version

a string describing the PDF version that will be required to view the output. This is a minimum, and will be increased (with a warning) if necessary. Defaults to "1.4", but see ‘Details’.

paper

the target paper size. The choices are "a4", "letter", "legal" (or "us") and "executive" (and these can be capitalized), or "a4r" and "USr" for rotated (‘landscape’). The default is "special", which means that the width and height specify the paper size. A further choice is "default"; if this is selected, the paper size is taken from the option "papersize" if that is set and as "a4" if it is unset or empty. Defaults to "special".

encoding

the name of an encoding file. Defaults to "default". The latter is interpreted

on Unix-alikes

as ‘"ISOLatin1.enc"’ unless the locale is recognized as corresponding to a language using ISO 8859-{2,5,7,13,15} or KOI8-{R,U}.

on Windows

as ‘"CP1250.enc"’ (Central European), "CP1251.enc" (Cyrillic), "CP1253.enc" (Greek) or "CP1257.enc" (Baltic) if one of those codepages is in use, otherwise ‘"WinAnsi.enc"’ (codepage 1252).

The file is looked for in the ‘enc’ directory of package grDevices if the path does not contain a path separator. An extension ".enc" can be omitted.

bg

the initial background color to be used. Defaults to "transparent".

fg

the initial foreground color to be used. Defaults to "black".

pointsize

the default point size to be used. Strictly speaking, in bp, that is 1/72 of an inch, but approximately in points. Defaults to 12.

pagecentre

logical: should the device region be centred on the page? – is only relevant for paper != "special". Defaults to TRUE.

colormodel

a character string describing the color model: currently allowed values are "srgb", "gray" (or "grey") and "cmyk". Defaults to "srgb". See section ‘Color models’.

useDingbats

logical. Should small circles be rendered via the Dingbats font? Defaults to FALSE. If TRUE, this can produce smaller and better output, but can cause font display problems in broken PDF viewers: although this font is one of the 14 guaranteed to be available in all PDF viewers, that guarantee is not always honoured.

For Unix-alikes (including macOS) see the ‘Note’ for a possible fix for some viewers.

useKerning

logical. Should kerning corrections be included in setting text and calculating string widths? Defaults to TRUE.

fillOddEven

logical controlling the polygon fill mode: see polygon for details. Defaults to FALSE.

compress

logical. Should PDF streams be generated with Flate compression? Defaults to TRUE.

timestamp

logical. If FALSE, omit the ‘⁠/CreationDate⁠’ and ‘⁠/ModDate⁠’ metadata fields. Defaults to TRUE.

producer

logical. If FALSE, omit the ‘⁠/Producer⁠’ metadata field. Defaults to TRUE.

author

author string to embed as the ‘⁠/Author⁠’ field in the document metadata. Defaults to "", omitting the field.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Object of class D4TAlinkTask, as created by initTask.

Should be plotting be done using Windows GDI or cairographics?

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

device height and width in px.

device height in px.

device height in px.

Arguments passed on to grDevices::png

filename

the path of the output file, up to 511 characters. The page number is substituted if a C integer format is included in the character string, as in the default, and tilde-expansion is performed (see path.expand). (The result must be less than 600 characters long. See png for further details.)

units

The units in which height and width are given. Can be px (pixels, the default), in (inches), cm or mm.

pointsize

the default pointsize of plotted text, interpreted as big points (1/72 inch) at res ppi.

bg

the initial background colour: can be overridden by setting par("bg").

res

The nominal resolution in ppi which will be recorded in the bitmap file, if a positive integer. Also used for units other than the default. If not specified, taken as 72 ppi to set the size of text and line widths.

family

A length-one character vector specifying the default font family. The default means to use the font numbers on the Windows GDI versions and "sans" on the cairographics versions.

restoreConsole

See the ‘Details’ section of windows. For type == "windows" only.

antialias

Length-one character vector.

For allowed values and their effect on fonts with type = "windows" see windows: for that type if the argument is missing the default is taken from windows.options()$bitmap.aa.win.

For allowed values and their effect (on fonts and lines, but not fills) with type = "cairo" see svg.

symbolfamily

For cairographics only: a length-one character string that specifies the font family to be used as the "symbol" font (e.g., for plotmath output). The default value is "default", which means that R will choose a default "symbol" font based on the graphics device capabilities.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Object of class D4TAlinkTask, as created by initTask.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

SQL query to execute.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

SQLite connection object (optional).

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

query encryption key from user, default FALSE.

issue warning if file does not exists.

encryption password, default NULL

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

issue warning if file does not exists.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

issue warning if file does not exists.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Arguments passed on to utils::read.table

file

the name of the file which the data are to be read from. Each row of the table appears as one line of the file. If it does not contain an absolute path, the file name is relative to the current working directory, getwd(). Tilde-expansion is performed where supported. This can be a compressed file (see file).

Alternatively, file can be a readable text-mode connection (which will be opened for reading if necessary, and if so closed (and hence destroyed) at the end of the function call). (If stdin() is used, the prompts for lines may be somewhat confusing. Terminate input with a blank line or an EOF signal, Ctrl-D on Unix and Ctrl-Z on Windows. Any pushback on stdin() will be cleared before return.)

file can also be a complete URL. (For the supported URL schemes, see the ‘URLs’ section of the help for url.)

header

a logical value indicating whether the file contains the names of the variables as its first line. If missing, the value is determined from the file format: header is set to TRUE if and only if the first row contains one fewer field than the number of columns.

sep

the field separator character. Values on each line of the file are separated by this character. If sep = "" (the default for read.table) the separator is ‘white space’, that is one or more spaces, tabs, newlines or carriage returns.

quote

the set of quoting characters. To disable quoting altogether, use quote = "". See scan for the behaviour on quotes embedded in quotes. Quoting is only considered for columns read as character, which is all of them unless colClasses is specified.

dec

the character used in the file for decimal points.

numerals

string indicating how to convert numbers whose conversion to double precision would lose accuracy, see type.convert. Can be abbreviated. (Applies also to complex-number inputs.)

row.names

a vector of row names. This can be a vector giving the actual row names, or a single number giving the column of the table which contains the row names, or character string giving the name of the table column containing the row names.

If there is a header and the first row contains one fewer field than the number of columns, the first column in the input is used for the row names. Otherwise if row.names is missing, the rows are numbered.

Using row.names = NULL forces row numbering. Missing or NULL row.names generate row names that are considered to be ‘automatic’ (and not preserved by as.matrix).

col.names

a vector of optional names for the variables. The default is to use "V" followed by the column number.

as.is

controls conversion of character variables (insofar as they are not converted to logical, numeric or complex) to factors, if not otherwise specified by colClasses. Its value is either a vector of logicals (values are recycled if necessary), or a vector of numeric or character indices which specify which columns should not be converted to factors.

Note: to suppress all conversions including those of numeric columns, set colClasses = "character".

Note that as.is is specified per column (not per variable) and so includes the column of row names (if any) and any columns to be skipped.

tryLogical

a logical determining if columns consisting entirely of "F", "T", "FALSE", and "TRUE" should be converted to logical; passed to type.convert, true by default.

na.strings

a character vector of strings which are to be interpreted as NA values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. Note that the test happens after white space is stripped from the input (if enabled), so na.strings values may need their own white space stripped in advance.

colClasses

character. A vector of classes to be assumed for the columns. If unnamed, recycled as necessary. If named, names are matched with unspecified values being taken to be NA.

Possible values are NA (the default, when type.convert is used), "NULL" (when the column is skipped), one of the atomic vector classes (logical, integer, numeric, complex, character, raw), or "factor", "Date" or "POSIXct". Otherwise there needs to be an as method (from package methods) for conversion from "character" to the specified formal class.

Note that colClasses is specified per column (not per variable) and so includes the column of row names (if any).

nrows

integer: the maximum number of rows to read in. Negative and other invalid values are ignored.

skip

integer: the number of lines of the data file to skip before beginning to read data.

check.names

logical. If TRUE then the names of the variables in the data frame are checked to ensure that they are syntactically valid variable names. If necessary they are adjusted (by make.names) so that they are, and also to ensure that there are no duplicates.

fill

logical. If TRUE then in case the rows have unequal length, blank fields are implicitly added. See ‘Details’.

strip.white

logical. Used only when sep has been specified, and allows the stripping of leading and trailing white space from unquoted character fields (numeric fields are always stripped). See scan for further details (including the exact meaning of ‘white space’), remembering that the columns may include the row names.

blank.lines.skip

logical: if TRUE blank lines in the input are ignored.

comment.char

character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether.

allowEscapes

logical. Should C-style escapes such as ‘⁠\n⁠’ be processed or read verbatim (the default)? Note that if not within quotes these could be interpreted as a delimiter (but not as a comment character). For more details see scan.

flush

logical: if TRUE, scan will flush to the end of the line after reading the last of the fields requested. This allows putting comments after the last field.

stringsAsFactors

logical: should character vectors be converted to factors? Note that this is overridden by as.is and colClasses, both of which allow finer control.

fileEncoding

character string: if non-empty declares the encoding used on a file when given as a character string (not on an existing connection) so the character data can be re-encoded. See the ‘Encoding’ section of the help for file, the ‘R Data Import/Export’ manual and ‘Note’.

encoding

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1 or UTF-8 (see Encoding): it is not used to re-encode the input, but allows R to handle encoded strings in their native encoding (if one of those two). See ‘Value’ and ‘Note’.

text

character string: if file is not supplied and this is, then data are read from the value of text via a text connection. Notice that a literal string can be used to include (small) data sets within R code.

skipNul

logical: should NULs be skipped?

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

name of the table in the SQLite database.

number of rows to read (if NULL, all rows are read).

number of rows to skip before reading (default is 0).

Object of class D4TAlinkTask, as created by initTask.

Target output format (defaults to "html"). The option "all" will render all formats defined within the file or project.

if TRUE execute in the global environment.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Arguments passed on to quarto::quarto_render

input

The input file or project directory to be rendered (defaults to rendering the project in the current working directory).

output_file

Base name for single-file output (e.g. PDF, ePub, MS Word). This sets the output-file Quarto metadata. If NULL, the output filename will be based on the input filename.

execute

Whether to execute embedded code chunks.

execute_params

A list of named parameters that override custom params specified within the YAML front-matter.

execute_dir

The working directory in which to execute embedded code chunks.

execute_daemon

Keep Jupyter kernel alive (defaults to 300 seconds). Note this option is only applicable for rendering Jupyter notebooks or Jupyter markdown.

execute_daemon_restart

Restart keepalive Jupyter kernel before render. Note this option is only applicable for rendering Jupyter notebooks or Jupyter markdown.

execute_debug

Show debug output for Jupyter kernel.

use_freezer

Force use of frozen computations for an incremental file render.

cache

Cache execution output (uses knitr cache and jupyter-cache respectively for Rmd and Jupyter input files).

cache_refresh

Force refresh of execution cache.

metadata

An optional named list used to override YAML metadata. It will be passed as a YAML file to --metadata-file CLI flag. This will be merged over metadata-file options if both are specified.

metadata_file

A yaml file passed to --metadata-file CLI flags to override metadata. This will be merged with metadata if both are specified, with low precedence on metadata options.

quiet

Suppress warning and other messages, from R and also Quarto CLI (i.e --quiet is passed as command line).

quarto.quiet R option or R_QUARTO_QUIET environment variable can be used to globally override a function call (This can be useful to debug tool that calls ⁠quarto_*⁠ functions directly).

On Github Actions, it will always be quiet = FALSE.

profile

Quarto project profile(s) to use. Either a character vector of profile names or NULL to use the default profile.

quarto_args

Character vector of other quarto CLI arguments to append to the Quarto command executed by this function. This is mainly intended for advanced usage and useful for CLI arguments which are not yet mirrored in a dedicated parameter of this R function. See ⁠quarto render --help⁠ for options.

pandoc_args

Additional command line arguments to pass on to Pandoc.

as_job

Render as an RStudio background job. Default is "auto", which will render individual documents normally and projects as background jobs. Use the quarto.render_as_job R option to control the default globally.

Object of class D4TAlinkTask, as created by initTask.

The R Markdown output format to convert to. The option "all" will render all formats defined within the file. The option can be the name of a format (e.g. "html_document") and that will render the document to that single format. One can also use a vector of format names to render to multiple formats. Alternatively, you can pass an output format object (e.g. html_document()). If using NULL then the output format is the first one defined in the YAML frontmatter in the input file (this defaults to HTML if no format is specified there). If you pass an output format object to output_format, the options specified in the YAML header or _output.yml will be ignored and you must explicitly set all the options you want when you construct the object. If you pass a string, the output format will use the output parameters in the YAML header or _output.yml.

if TRUE execute in the global environment.

Using TRUE will clean intermediate files that are created during rendering.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Arguments passed on to rmarkdown::render

input

The input file to be rendered. This can be an R script (.R), an R Markdown document (.Rmd), or a plain markdown document.

output_file

The name of the output file. If using NULL then the output filename will be based on filename for the input file. If a filename is provided, a path to the output file can also be provided. Note that the output_dir option allows for specifying the output file path as well, however, if also specifying the path, the directory must exist. If output_file is specified but does not have a file extension, an extension will be automatically added according to the output format. To avoid the automatic file extension, put the output_file value in I(), e.g., I('my-output').

output_dir

The output directory for the rendered output_file. This allows for a choice of an alternate directory to which the output file should be written (the default output directory of that of the input file). If a path is provided with a filename in output_file the directory specified here will take precedence. Please note that any directory path provided will create any necessary directories if they do not exist.

output_options

List of output options that can override the options specified in metadata (e.g. could be used to force self_contained or mathjax = "local"). Note that this is only valid when the output format is read from metadata (i.e. not a custom format object passed to output_format).

output_yaml

Paths to YAML files specifying output formats and their configurations. The first existing one is used. If none are found, then the function searches YAML files specified to the output_yaml top-level parameter in the YAML front matter, _output.yml or _output.yaml, and then uses the first existing one.

intermediates_dir

Intermediate files directory. If a path is specified then intermediate files will be written to that path. If NULL, intermediate files are written to the same directory as the input file.

knit_root_dir

The working directory in which to knit the document; uses knitr's root.dir knit option. If NULL then the behavior will follow the knitr default, which is to use the parent directory of the document.

runtime

The runtime target for rendering. The static option produces output intended for static files; shiny produces output suitable for use in a Shiny document (see run). The default, auto, allows the runtime target specified in the YAML metadata to take precedence, and renders for a static runtime target otherwise.

params

A list of named parameters that override custom params specified within the YAML front-matter (e.g. specifying a dataset to read or a date range to confine output to). Pass "ask" to start an application that helps guide parameter configuration.

knit_meta

(This option is reserved for expert use.) Metadata generated by knitr.

envir

The environment in which the code chunks are to be evaluated during knitting (can use new.env() to guarantee an empty new environment).

run_pandoc

An option for whether to run pandoc to convert Markdown output.

quiet

An option to suppress printing during rendering from knitr, pandoc command line and others. To only suppress printing of the last "Output created: " message, you can set rmarkdown.render.message to FALSE

encoding

Ignored. The encoding is always assumed to be UTF-8.

Object of class D4TAlinkTask, as created by initTask.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

full name of the input zip file

If TRUE, overwrite existing files (the equivalent of unzip -o), otherwise ignore such files (the equivalent of unzip -n).

If TRUE, list the files and extract none. The equivalent of unzip -l.

restore code, default TRUE

Arguments passed on to utils::unzip

zipfile

The pathname of the zip file: tilde expansion (see path.expand) will be performed.

files

A character vector of recorded filepaths to be extracted: the default is to extract all files.

junkpaths

If TRUE, use only the basename of the stored filepath when extracting. The equivalent of unzip -j.

exdir

The directory to extract files to (the equivalent of unzip -d). It will be created if necessary.

unzip

The method to be used. An alternative is to use getOption("unzip"), which on a Unix-alike may be set to the path to a unzip program.

setTimes

logical. For the internal method only, should the file times be set based on the times in the zip file? (NB: this applies to included files, not to directories.)

Object of class D4TAlinkTask, as created by initTask.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

Object of class D4TAlinkTask, as created by initTask.

Filename suffix, used to develop scripts for sub-analyses for a given task, default NA.

R object to serialize.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

encrypt the output, default: FALSE. If character string, then use the string as password.

query encryption key from user, default FALSE.

R object to serialize.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

query encryption key from user, default FALSE.

data.frame to serialize.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

data.frame to serialize.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

R object to output.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

R object to output.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

unused.

Arguments passed on to utils::write.table

file

either a character string naming a file or a connection open for writing. "" indicates output to the console.

append

logical. Only relevant if file is a character string. If TRUE, the output is appended to the file. If FALSE, any existing file of the name is destroyed.

quote

a logical value (TRUE or FALSE) or a numeric vector. If TRUE, any character or factor columns will be surrounded by double quotes. If a numeric vector, its elements are taken as the indices of columns to quote. In both cases, row and column names are quoted if they are written. If FALSE, nothing is quoted.

sep

the field separator string. Values within each row of x are separated by this string.

eol

the character(s) to print at the end of each line (row). For example, eol = "\r\n" will produce Windows' line endings on a Unix-alike OS, and eol = "\r" will produce files as expected by Excel:mac 2004.

na

the string to use for missing values in the data.

dec

the string to use for decimal points in numeric or complex columns: must be a single character.

row.names

either a logical value indicating whether the row names of x are to be written along with x, or a character vector of row names to be written.

col.names

either a logical value indicating whether the column names of x are to be written along with x, or a character vector of column names to be written. See the section on ‘CSV files’ for the meaning of col.names = NA.

qmethod

a character string specifying how to deal with embedded double quote characters when quoting strings. Must be one of "escape" (default for write.table), in which case the quote character is escaped in C style by a backslash, or "double" (default for write.csv and write.csv2), in which case it is doubled. You can specify just the initial letter.

fileEncoding

character string: if non-empty declares the encoding to be used on a file (not a connection) so the character data can be re-encoded as they are written. See file.

object to save. It can be either a data frame, an object of type AnnotatedDataFrame, or a list thereof.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

If TRUE, will adjust the worksheet column widths based upon the longest entry in each column. This is approximate.

Rows including this row and above this row will be frozen and not scroll. The default value of 0 will scroll the entire sheet. Note that not all spreadsheet applications support this feature.

Columns including this column and to the left of this column will be frozen and not scroll. The default value of 0 will scroll the entire sheet. Note that not all spreadsheet applications support this feature.

prefix for names of worksheets holding metadata.

array of metadata field names to be appended in header of tables.

Arguments passed on to WriteXLS::WriteXLS

ExcelFileName

The name of the Excel file to be created. If the file extension is .XLS, an Excel 2003 file will be created. If the file extension is .XLSX, an Excel 2007 file will be created. Must be a valid Excel filename. May include an existing path. normalizePath is used to support tilde expansion, etc.

SheetNames

A character vector containing the names of each worksheet to be created. If NULL (the default), the names of the dataframes will be used instead. Worksheet names may be up to 31 characters in length and must be unique. If specified, length(SheetNames) must be the same as length(x). NOTE: The order of the names here must match the order of the data frames as listed in x.

perl

Name of the perl executable to be called.

verbose

Output step-by-step status messages during the creation of the Excel file. Default is FALSE.

Encoding

Define the character encoding to be used for the exported data frames. Defaults to UTF-8.

AllText

If TRUE, all cell contents of the Excel file will be written as text. Default is FALSE. See Details.

row.names

If TRUE, the row names of the data frames are included in the Excel file worksheets.

col.names

If TRUE, the column names of the data frames are included in the Excel file worksheets.

AutoFilter

If TRUE, will add autofiltering to each column in each worksheet. Note that not all spreadsheet applications support this feature.

BoldHeaderRow

If TRUE, will apply a bold font to the header row for each worksheet.

ReadOnly

If TRUE, each worksheet will be set to Read Only (Protected mode) to prevent inadvertent changes to the contents when the file is opened in Excel or a compatible application. See Details.

na

The string to use for missing values in the data. Defaults to ""

envir

The environment in which to look for the data frames named in x. This defaults to the environment in which WriteXLS was called.

data.frame to serialize.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

character vector of column names to create indices on.

name of the table in the SQLite database.

if TRUE, overwrite existing table.

if TRUE, append to existing table.

if TRUE, save row names as a column.

Object of class D4TAlinkTask, as created by initTask.

Filename type. If the type is an array, the cocatenation of the elements is used with separator"-". Filenames have the form [task name]_[type].[ext]

Filename extension.

(optional) Subdirectory.

Logical, if TRUE (by default) the directory is created.

the type of what gives the type of data to be read. (Here ‘type’ is used in the sense of typeof.) The supported types are logical, integer, numeric, complex, character, raw and list. If what is a list, it is assumed that the lines of the data file are records each containing length(what) items (‘fields’) and the list components should have elements which are one of the first six (atomic) types listed or NULL, see section ‘Details’ below.

Arguments passed on to base::scan

file

the name of a file to read data values from. If the specified file is "", then input is taken from the keyboard (or whatever stdin() reads if input is redirected or R is embedded). (In this case input can be terminated by a blank line or an EOF signal, ‘⁠Ctrl-D⁠’ on Unix and ‘⁠Ctrl-Z⁠’ on Windows.)

Otherwise, the file name is interpreted relative to the current working directory (given by getwd()), unless it specifies an absolute path. Tilde-expansion is performed where supported. When running R from a script, file = "stdin" can be used to refer to the process's stdin file stream.

This can be a compressed file (see file).

Alternatively, file can be a connection, which will be opened if necessary, and if so closed at the end of the function call. Whatever mode the connection is opened in, any of LF, CRLF or CR will be accepted as the EOL marker for a line and so will match sep = "\n".

file can also be a complete URL. (For the supported URL schemes, see the ‘URLs’ section of the help for url.)

To read a data file not in the current encoding (for example a Latin-1 file in a UTF-8 locale or conversely) use a file connection setting its encoding argument (or scan's fileEncoding argument).

nmax

the maximum number of data values to be read, or if what is a list, the maximum number of records to be read. If omitted or not positive or an invalid value for an integer (and nlines is not set to a positive value), scan will read to the end of file.

n

integer: the maximum number of data values to be read, defaulting to no limit. Invalid values will be ignored.

sep

by default, scan expects to read ‘white-space’ delimited input fields. Alternatively, sep can be used to specify a character which delimits fields. A field is always delimited by an end-of-line marker unless it is quoted.

If specified this should be the empty character string (the default) or NULL or a character string containing just one single-byte character.

quote

the set of quoting characters as a single character string or NULL. In a multibyte locale the quoting characters must be ASCII (single-byte).

dec

decimal point character. This should be a character string containing just one single-byte character. (NULL and a zero-length character vector are also accepted, and taken as the default.)

skip

the number of lines of the input file to skip before beginning to read data values.

nlines

if positive, the maximum number of lines of data to be read.

na.strings

character vector. Elements of this vector are to be interpreted as missing (NA) values. Blank fields are also considered to be missing values in logical, integer, numeric and complex fields. Note that the test happens after white space is stripped from the input (if enabled), so na.strings values may need their own white space stripped in advance.

flush

logical: if TRUE, scan will flush to the end of the line after reading the last of the fields requested. This allows putting comments after the last field, but precludes putting more than one record on a line.

fill

logical: if TRUE, scan will implicitly add empty fields to any lines with fewer fields than implied by what.

strip.white

vector of logical value(s) corresponding to items in the what argument. It is used only when sep has been specified, and allows the stripping of leading and trailing ‘white space’ from character fields (other fields are always stripped). Note: white space inside quoted strings is not stripped.

If strip.white is of length 1, it applies to all fields; otherwise, if strip.white[i] is TRUE and the i-th field is of mode character (because what[i] is) then the leading and trailing unquoted white space from field i is stripped.

quiet

logical: if FALSE (default), scan() will print a line, saying how many items have been read.

blank.lines.skip

logical: if TRUE blank lines in the input are ignored, except when counting skip and nlines.

multi.line

logical. Only used if what is a list. If FALSE, all of a record must appear on one line (but more than one record can appear on a single line). Note that using fill = TRUE implies that a record will be terminated at the end of a line.

comment.char

character: a character vector of length one containing a single character or an empty string. Use "" to turn off the interpretation of comments altogether (the default).

allowEscapes

logical. Should C-style escapes such as ‘⁠\n⁠’ be processed (the default) or read verbatim? Note that if not within quotes these could be interpreted as a delimiter (but not as a comment character).

The escapes which are interpreted are the control characters ‘⁠\a, \b, \f, \n, \r, \t, \v⁠’ and octal and hexadecimal representations like ‘⁠\040⁠’ and ‘⁠\0x2A⁠’. Any other escaped character is treated as itself, including backslash. Note that Unicode escapes (starting ‘⁠\u⁠’ or ‘⁠\U⁠’: see Quotes) are never processed.

fileEncoding

character string: if non-empty declares the encoding used on a file (not a connection nor the keyboard) so the character data can be re-encoded. See the ‘Encoding’ section of the help for file, and the ‘R Data Import/Export Manual’.

encoding

encoding to be assumed for input strings. If the value is "latin1" or "UTF-8" it is used to mark character strings as known to be in Latin-1 or UTF-8: it is not used to re-encode the input (see fileEncoding). See also ‘Details’.

text

character string: if file is not supplied and this is, then data are read from the value of text via a text connection.

skipNul

logical: should NULs be skipped when reading character fields?

Author name, system username by default.

encryption key, if NULL then query key from user.

path to the Quarto task template.

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1, UTF-8 or to be bytes: it is not used to re-encode the input. To do the latter, specify the encoding as part of the connection con or via options(encoding=): see the examples and ‘Details’.

path to the Rmd task template.

encoding to be assumed for input strings. It is used to mark character strings as known to be in Latin-1, UTF-8 or to be bytes: it is not used to re-encode the input. To do the latter, specify the encoding as part of the connection con or via options(encoding=): see the examples and ‘Details’.

Path of the task repository, default set by setTaskRoot.

Logical, if TRUE (by default) the directory is created.

path to the Rmd task template.

Sponsor name, default set by setTaskSponsor.

optional function returning a list of paths, currently pathsGLPG or pathsPMS.

Object of class D4TAlinkTask, as created by initTask.

the field separator character, default: "/".