Package 'easyreporting' reference manual

Title:	Helps creating report for improving Reproducible Computational Research
Description:	An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.
Authors:	Dario Righelli [cre, aut]
Maintainer:	Dario Righelli <[email protected]>
License:	Artistic-2.0
Version:	1.19.0
Built:	2024-11-27 05:27:18 UTC
Source:	https://github.com/bioc/easyreporting

addResource

Description

addResource

Usage

addResource(object, source, reference, description)
addResource(object, source, reference, description)

Arguments

`object`	an easyreporting class instance
`source`	a string indicating the reference (i.e. "GEO")
`reference`	a string indicanting the reference of the source (i.e. "GSE60231)
`description`	a natural language description

Value

an easyreporting class instance

Examples

rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
rd <- addResource(rd, source="GEO", "GSE60231", "Transcriptome of BMDC to different antigen delivery systems")
## Not run: 
compile(rd)

## End(Not run)
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
rd <- addResource(rd, source="GEO", "GSE60231", "Transcriptome of BMDC to different antigen delivery systems")
## Not run: 
compile(rd)

## End(Not run)

addResource

Description

addResource

Usage

## S4 method for signature 'easyreporting'
addResource(object, source, reference, description)
## S4 method for signature 'easyreporting'
addResource(object, source, reference, description)

Arguments

`object`	an easyreporting class instance
`source`	a string indicating the reference (i.e. "GEO")
`reference`	a string indicanting the reference of the source (i.e. "GSE60231)
`description`	a natural language description

Value

an easyreporting class instance

Examples

rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
rd <- addResource(rd, source="GEO", "GSE60231", "Transcriptome of BMDC to different antigen delivery systems")
## Not run: 
compile(rd)

## End(Not run)
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
rd <- addResource(rd, source="GEO", "GSE60231", "Transcriptome of BMDC to different antigen delivery systems")
## Not run: 
compile(rd)

## End(Not run)

compile

Description

prints the sessionInfo and compiles the produced rmarkdown file into an HTML report.

Usage

compile(object)
compile(object)

Arguments

object

an easyreporting class object

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
compile(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
compile(rd)

## End(Not run)

compile

Description

prints the sessionInfo and compiles the rmarkdown file

Usage

## S4 method for signature 'easyreporting'
compile(object)
## S4 method for signature 'easyreporting'
compile(object)

Arguments

object

an easyreporting class object

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
compile(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
compile(rd)

## End(Not run)

easyreporting

Description

An S4 class for managing rmarkdown report. Each instance describes an rmarkdown file.

Usage

easyreporting(
  filenamePath,
  title,
  author,
  optionList = NULL,
  documentType = "rmarkdown::html_document",
  bibfile = ""
)

easyreporting(
  filenamePath,
  title,
  author,
  optionList = NULL,
  documentType = "rmarkdown::html_document",
  bibfile = ""
)
easyreporting(
  filenamePath,
  title,
  author,
  optionList = NULL,
  documentType = "rmarkdown::html_document",
  bibfile = ""
)

easyreporting(
  filenamePath,
  title,
  author,
  optionList = NULL,
  documentType = "rmarkdown::html_document",
  bibfile = ""
)

Arguments

`filenamePath`	the path with the name of the rmarkdown.
`title`	the title of the report section.
`author`	the author(s) of the report.
`optionList`	a list of options for the general rmarkdown document.
`documentType`	type of report final document, if author(s) is a `person` it will be `distill::distill_article` (`rmarkdown::html_document` default)
`bibfile`	a bibfile for bibliography.

Value

an S4 easyreporting class instance

Slots

filenamePath: the path with the name of the rmarkdown.
title: the title of the report section.
author: the author(s) of the report.
type: of report final document, if author(s) is a person it will be distill::distill_article (rmarkdown::html_document default)
bibfile: a bibfile for bibliography.
optionList: a list of options for the general rmarkdown document.

Examples

rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author="It's me")
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author="It's me")

erGUIVolcano

Description

executes a Shiny GUI to perform a volcano plot and trace its executed functions.

Usage

erGUIVolcano()
erGUIVolcano()

Value

none

Examples

## Not run: 
erGUIVolcano()

## End(Not run)
## Not run: 
erGUIVolcano()

## End(Not run)

getBibliography

Description

returns the bibfile name attached to the object

Usage

getBibliography(object)
getBibliography(object)

Arguments

object

an easyreporting class object

Value

none

Examples

## Not run: 
TBD

## End(Not run)
## Not run: 
TBD

## End(Not run)

getBibliography

Description

returns the bibfile name attached to the object

Usage

## S4 method for signature 'easyreporting'
getBibliography(object)
## S4 method for signature 'easyreporting'
getBibliography(object)

Arguments

object

an easyreporting class object

Value

none

Examples

example(easyreporting)
getBibliography(rd)
example(easyreporting)
getBibliography(rd)

getOptionsList

Description

returns the optionList from the easyreporting class (see the makeOptionList function for more details).

Usage

getOptionsList(object)
getOptionsList(object)

Arguments

object

an easyreporting class object

Value

a list of options

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
optList <- getOptionsList(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
optList <- getOptionsList(rd)

## End(Not run)

getOptionsList

Description

returns the optionList from the easyreporting class

Usage

## S4 method for signature 'easyreporting'
getOptionsList(object)
## S4 method for signature 'easyreporting'
getOptionsList(object)

Arguments

object

an easyreporting class object

Value

a list of options

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
optList <- getOptionsList(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report", title="example_report",
                        author=c("It's me"))
optList <- getOptionsList(rd)

## End(Not run)

getReportFilename

Description

returns the filename with its path of the report generated by easyreporting

Usage

getReportFilename(object)
getReportFilename(object)

Arguments

object

an easyreporting class object

Value

a string of report file name with path

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
(rep <- getReportFilename(rd))

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
(rep <- getReportFilename(rd))

## End(Not run)

getReportFilename

Description

returns the report filename with path

Usage

## S4 method for signature 'easyreporting'
getReportFilename(object)
## S4 method for signature 'easyreporting'
getReportFilename(object)

Arguments

object

an easyreporting class object

Value

a string of report file name with path

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
(rep <- getReportFilename(rd))

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
(rep <- getReportFilename(rd))

## End(Not run)

makeOptionsList

Description

makes an list of rmarkdown options

Usage

makeOptionsList(
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)
makeOptionsList(
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)

Arguments

`cacheFlag`	boolean for caching chunk data (default TRUE)
`evalFlag`	boolean for evaluating the code chunk in the compiled version (default TRUE)
`echoFlag`	boolean for showing the code chunk (default TRUE)
`warningFlag`	boolean for showing the chunk warnings (default FALSE)
`showMessages`	boolean for showing the chunk warnings in compiled version (default FALSE)
`includeFlag`	boolean for including the code chunk in the compiled version (default TRUE)
`collapseFlag`	boolean for collapsing the code chunk in the compiled version (default FALSE),
`purlFlag`	boolean for extracting the code chunk as R code in a separate R file (default TRUE),
`errorFlag`	boolean for including the error generated by the code chunk in the compiled version (default TRUE),
`messageFlag`	boolean for including the code chunk messages in the compiled version (default TRUE),
`highlightFlag`	boolean for highlinghtinh the code chunk in the compiled version (default TRUE),
`promptFlag`	boolean for including a ">" for the code chunk in the compiled version (default FALSE),
`stripWhiteFlag`	boolean for removing the white spaces at beginning/end of the code chunk in the compiled version (default TRUE),
`tidyFlag`	boolean for creating a tidy code chunk in the compiled version (default FALSE).

Value

list of rmarkdown options

Examples

optList <- makeOptionsList()
optList <- makeOptionsList()

mkdCodeChunkCommented

Description

it creates a complete code chunk, adding a natural language comment before of it.

Usage

mkdCodeChunkCommented(
  object,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
mkdCodeChunkCommented(
  object,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`comment`	a string with the natural language comment for the chunk.
`code`	a string within the code.
`optionList`	a list of options (default is the class options).
`sourceFilesList`	a optional list of files to source inside the chunk.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n (c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n (c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)

mkdCodeChunkCommented

Description

it creates a complete code chunk, adding a natural language comment before of it.

Usage

## S4 method for signature 'easyreporting'
mkdCodeChunkCommented(
  object,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
## S4 method for signature 'easyreporting'
mkdCodeChunkCommented(
  object,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`comment`	a string with the natural language comment for the chunk.
`code`	a string within the code.
`optionList`	a list of options (default is the class options).
`sourceFilesList`	a optional list of files to source inside the chunk.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code=c(quote(a <- 1), quote(b <- 2), quote(c <- a+b)), 
                optionList=optList, sourceFilesList=NULL)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n(c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code=c(quote(a <- 1), quote(b <- 2), quote(c <- a+b)), 
                optionList=optList, sourceFilesList=NULL)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n(c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)

mkdCodeChunkComplete

Description

it creates a complete code chunk.

Usage

mkdCodeChunkComplete(
  object,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
mkdCodeChunkComplete(
  object,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`code`	a string or an expression generated with quote containing a function call or the entire code chunk to trace.
`optionList`	a list of options.
`sourceFilesList`	a list of files to source.

Value

none

Examples

## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkComplete(rd, code="a <- 1\n b <- 2\n c <- a+b\n print(c)")

## End(Not run)
## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkComplete(rd, code="a <- 1\n b <- 2\n c <- a+b\n print(c)")

## End(Not run)

mkdCodeChunkComplete

Description

it creates a complete code chunk.

Usage

## S4 method for signature 'easyreporting'
mkdCodeChunkComplete(
  object,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
## S4 method for signature 'easyreporting'
mkdCodeChunkComplete(
  object,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`code`	a string or an expression (or a list of expressions) generated with quote containing a function call or the entire code chunk to trace.
`optionList`	a list of options.
`sourceFilesList`	a list of files to source.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkComplete(rd, code=c(quote(a <- 1), quote(b <- 2), quote(c<-  a+b), 
quote(print(c))))
mkdCodeChunkComplete(rd, code="a <- 1\n b <- 2\n c <- a+b\n print(c)")

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkComplete(rd, code=c(quote(a <- 1), quote(b <- 2), quote(c<-  a+b), 
quote(print(c))))
mkdCodeChunkComplete(rd, code="a <- 1\n b <- 2\n c <- a+b\n print(c)")

## End(Not run)

mkdCodeChunkEnd

Description

it creates a code chunk end. Always use it after a mkdCodeChunkSt()

Usage

mkdCodeChunkEnd(object)
mkdCodeChunkEnd(object)

Arguments

object

an easyreporting class object

Value

none

Examples

## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)

mkdCodeChunkEnd

Description

it creates a code chunk end. Always use it after a mkdCodeChunkSt()

Usage

## S4 method for signature 'easyreporting'
mkdCodeChunkEnd(object)
## S4 method for signature 'easyreporting'
mkdCodeChunkEnd(object)

Arguments

object

an easyreporting class object

Value

none

Examples

## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
 rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)

mkdCodeChunkSt

Description

it creates a code chunk start. A list of options and files to source for the chunk can optionally be passed to the function.

Usage

mkdCodeChunkSt(
  object,
  optionList = getOptionsList(object),
  sourceFilesList = NULL,
  isComplete = FALSE
)
mkdCodeChunkSt(
  object,
  optionList = getOptionsList(object),
  sourceFilesList = NULL,
  isComplete = FALSE
)

Arguments

`object`	an easyreporting class object
`optionList`	a list of options
`sourceFilesList`	a list of files that can be sourced inside the code chunk.
`isComplete`	a flag determining if the chunk is already a complete chunk

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## no options
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## setting options
optList <- makeOptionsList(includeFlag=TRUE)
mkdCodeChunkSt(rd, optionList=optList)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## no options
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## setting options
optList <- makeOptionsList(includeFlag=TRUE)
mkdCodeChunkSt(rd, optionList=optList)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)

mkdCodeChunkSt

Description

it creates a code chunk start. A list of options and files to source for the chunk can optionally be passed to the function.

Usage

## S4 method for signature 'easyreporting'
mkdCodeChunkSt(
  object,
  optionList = getOptionsList(object),
  sourceFilesList = NULL,
  isComplete = FALSE
)
## S4 method for signature 'easyreporting'
mkdCodeChunkSt(
  object,
  optionList = getOptionsList(object),
  sourceFilesList = NULL,
  isComplete = FALSE
)

Arguments

`object`	an easyreporting class object
`optionList`	a list of options
`sourceFilesList`	a list of files that can be sourced inside the code chunk.
`isComplete`	a flag determining if the chunk is already a complete chunk

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## no options
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## setting options
optList <- makeOptionsList(includeFlag=TRUE)
mkdCodeChunkSt(rd, optionList=optList)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## no options
mkdCodeChunkSt(rd)
## just leaving empty
mkdCodeChunkEnd(rd)

## setting options
optList <- makeOptionsList(includeFlag=TRUE)
mkdCodeChunkSt(rd, optionList=optList)
## just leaving empty
mkdCodeChunkEnd(rd)

## End(Not run)

mkdCodeChunkCommented

Description

it creates a complete code chunk, adding a natural language comment before of it.

Usage

mkdCodeChunkTitledCommented(
  object,
  title = NULL,
  level = 1,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
mkdCodeChunkTitledCommented(
  object,
  title = NULL,
  level = 1,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`title`	the title to assign to the code chunk section
`level`	the level of the title (default is 1)
`comment`	a string with the natural language comment for the chunk.
`code`	a string within the code.
`optionList`	a list of options (default is the class options).
`sourceFilesList`	a optional list of files to source inside the chunk.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n (c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkCommented(rd,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n (c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)

mkdCodeChunkTitledCommented

Description

it creates a complete code chunk, adding a natural language comment before of it.

Usage

## S4 method for signature 'easyreporting'
mkdCodeChunkTitledCommented(
  object,
  title = NULL,
  level = 1,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)
## S4 method for signature 'easyreporting'
mkdCodeChunkTitledCommented(
  object,
  title = NULL,
  level = 1,
  comment = NULL,
  code,
  optionList = getOptionsList(object),
  sourceFilesList = NULL
)

Arguments

`object`	an easyreporting class object
`title`	the title to assign to the code chunk section
`level`	the level of the title (default is 1)
`comment`	a string with the natural language comment for the chunk.
`code`	a string within the code.
`optionList`	a list of options (default is the class options).
`sourceFilesList`	a optional list of files to source inside the chunk.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkTitledCommented(rd, title="Title Example", level=1,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n(c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
optList <- makeOptionsList(includeFlag=TRUE, cacheFlag=TRUE)
mkdCodeChunkTitledCommented(rd, title="Title Example", level=1,
                comment="This is the comment of the following code chunk",
                code="a <- 1\n b <- 2\n(c <- a+b)\n", optionList=optList,
                sourceFilesList=NULL)

## End(Not run)

mkdGeneralMsg

Description

It appends a general message to the report, useful for describing a code chunk or a part of the report. Useful for adding natural language comments.

Usage

mkdGeneralMsg(object, message)
mkdGeneralMsg(object, message)

Arguments

`object`	an easyreporting class object
`message`	the message to append to the report

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralMsg(rd, message="Writing a paragraph to describe my code chunk")

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralMsg(rd, message="Writing a paragraph to describe my code chunk")

## End(Not run)

mkdGeneralMsg

Description

It appends a general message to the report. Useful for adding natural language comments.

Usage

## S4 method for signature 'easyreporting'
mkdGeneralMsg(object, message)
## S4 method for signature 'easyreporting'
mkdGeneralMsg(object, message)

Arguments

`object`	an easyreporting class object
`message`	the message to append to the report

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralMsg(rd, "Writing a paragraph to describe my code chunk")

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralMsg(rd, "Writing a paragraph to describe my code chunk")

## End(Not run)

mkdGeneralTitledMsg

Description

It appends a a titled section followed by a general message to the report. Useful for adding natural language comments.

Usage

mkdGeneralTitledMsg(object, title = NULL, level = 1, message)
mkdGeneralTitledMsg(object, title = NULL, level = 1, message)

Arguments

`object`	an easyreporting class object
`title`	the title of the report section.
`level`	the level (1 to 6) of the title (default is 1)
`message`	the message to append to the report

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralTitledMsg(rd, title="Generic SubTitle for this message", level=2,
            message="Writing a paragraph to describe my code chunk")

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralTitledMsg(rd, title="Generic SubTitle for this message", level=2,
            message="Writing a paragraph to describe my code chunk")

## End(Not run)

mkdGeneralTitledMsg

Description

It appends a a titled section followed by a general message to the report. Useful for adding natural language comments.

Usage

## S4 method for signature 'easyreporting'
mkdGeneralTitledMsg(object, title = NULL, level = 1, message)
## S4 method for signature 'easyreporting'
mkdGeneralTitledMsg(object, title = NULL, level = 1, message)

Arguments

`object`	an easyreporting class object
`title`	the optional title to give to the message section
`level`	the level (1 to 6) of the title (default is 1)
`message`	the message to append to the report

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralTitledMsg(rd, title="Generic SubTitle for this message", level=2,
        message="Writing a paragraph to describe my code chunk")

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
mkdGeneralTitledMsg(rd, title="Generic SubTitle for this message", level=2,
        message="Writing a paragraph to describe my code chunk")

## End(Not run)

mkdTitle

Description

Inserts an rmarkdown title inside the report, useful for create distinct sections inside the final resport.

Usage

mkdTitle(object, title, level = 1)
mkdTitle(object, title, level = 1)

Arguments

`object`	an easyreporting class object
`title`	a string within the title.
`level`	a numeric from 1 to 6 (default is 1).

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

mkdTitle(rd, "First Level Title")
mkdTitle(rd, "Sub-Title", level=2)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

mkdTitle(rd, "First Level Title")
mkdTitle(rd, "Sub-Title", level=2)

## End(Not run)

mkdTitle

Description

Inserts an rmarkdown title inside the report.

Usage

## S4 method for signature 'easyreporting'
mkdTitle(object, title, level = 1)
## S4 method for signature 'easyreporting'
mkdTitle(object, title, level = 1)

Arguments

`object`	an easyreporting class object
`title`	a string within the title.
`level`	a numeric from 1 to 6 (default is 1).

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

mkdTitle(rd, "First Level Title")
mkdTitle(rd, "Sub-Title", level=2)

## End(Not run)

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

mkdTitle(rd, "First Level Title")
mkdTitle(rd, "Sub-Title", level=2)

## End(Not run)

mkdVariableAssignment

Description

it includes a variable assignment in the report. NB: a call to the "mkdCodeChunkSt" has to be done before using it.

Usage

mkdVariableAssignment(object, variable.name, variable.object.name, show)
mkdVariableAssignment(object, variable.name, variable.object.name, show)

Arguments

`object`	an easyreporting class object
`variable.name`	a string indicating the name of the variabe to store in the report. (This can be changed here, but further uses of the variable needs to take into account the variable name change).
`variable.object.name`	the name of the already existing variable. (This cannot be canged.)
`show`	a boolean indicating if to show the message before writing it into the rmardown file.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## leaving the default options to the code chunk
mkdCodeChunkSt(rd)
## adding a variable assignement
variable <- 1
mkdVariableAssignment(rd, "variable", "variable", show=TRUE)
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## leaving the default options to the code chunk
mkdCodeChunkSt(rd)
## adding a variable assignement
variable <- 1
mkdVariableAssignment(rd, "variable", "variable", show=TRUE)
mkdCodeChunkEnd(rd)

## End(Not run)

mkdVariableAssignment

Description

it includes a variable assignment in the report. NB: a call to the "mkdCodeChunkSt" has to be done before using it.

Usage

## S4 method for signature 'easyreporting'
mkdVariableAssignment(
  object,
  variable.name,
  variable.object.name,
  show = FALSE
)
## S4 method for signature 'easyreporting'
mkdVariableAssignment(
  object,
  variable.name,
  variable.object.name,
  show = FALSE
)

Arguments

`object`	an easyreporting class object
`variable.name`	a string indicating the name of the variabe to store in the report. (This can be changed here, but further uses of the variable needs to take into account the variable name change).
`variable.object.name`	the name of the already existing variable. (This cannot be canged.)
`show`	a boolean indicating if to show the message before writing it into the rmardown file.

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## leaving the default options to the code chunk
mkdCodeChunkSt(rd)
## adding a variable assignement
variable <- 1
mkdVariableAssignment(rd, "variable", "variable", show=TRUE)
mkdCodeChunkEnd(rd)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))
## leaving the default options to the code chunk
mkdCodeChunkSt(rd)
## adding a variable assignement
variable <- 1
mkdVariableAssignment(rd, "variable", "variable", show=TRUE)
mkdCodeChunkEnd(rd)

## End(Not run)

setBibliography

Description

add a bibfile name to the object that will be reflected into the report as a bibliography section

Usage

setBibliography(object, bibfile = NULL)
setBibliography(object, bibfile = NULL)

Arguments

`object`	an easyreporting class object
`bibfile`	a path string with the name of the bib file

Value

none

Examples

## Not run: 
TBD

## End(Not run)
## Not run: 
TBD

## End(Not run)

setOptionsList

Description

set an optionList to the class, it automatically sets the options for the rmarkdown file. Are useful for the interpretation/execution of the code chunks.

Usage

setOptionsList(
  object,
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)
setOptionsList(
  object,
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)

Arguments

`object`	an easyreporting class object
`cacheFlag`	boolean for caching chunk data (default TRUE)
`evalFlag`	boolean for evaluating the code chunk in the compiled version (default TRUE)
`echoFlag`	boolean for showing the code chunk (default TRUE)
`warningFlag`	boolean for showing the chunk warnings (default FALSE)
`showMessages`	boolean for showing the chunk warnings in compiled version (default FALSE)
`includeFlag`	boolean for including the code chunk in the compiled version (default TRUE)
`collapseFlag`	boolean for collapsing the code chunk in the compiled version (default FALSE),
`purlFlag`	boolean for extracting the code chunk as R code in a separate R file (default TRUE),
`errorFlag`	boolean for including the error generated by the code chunk in the compiled version (default TRUE),
`messageFlag`	boolean for including the code chunk messages in the compiled version (default TRUE),
`highlightFlag`	boolean for highlinghtinh the code chunk in the compiled version (default TRUE),
`promptFlag`	boolean for including a ">" for the code chunk in the compiled version (default FALSE),
`stripWhiteFlag`	boolean for removing the white spaces at beginning/end of the code chunk in the compiled version (default TRUE),
`tidyFlag`	boolean for creating a tidy code chunk in the compiled version (default FALSE).

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

## setting default option
setOptionsList(rd)

## modifying only some options
rd <- setOptionsList(rd, warningFlag=TRUE, 
        showMessages=TRUE, includeFlag=TRUE)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

## setting default option
setOptionsList(rd)

## modifying only some options
rd <- setOptionsList(rd, warningFlag=TRUE, 
        showMessages=TRUE, includeFlag=TRUE)

## End(Not run)

setOptionsList

Description

set an optionList to the class

Usage

## S4 method for signature 'easyreporting'
setOptionsList(
  object,
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)
## S4 method for signature 'easyreporting'
setOptionsList(
  object,
  cacheFlag = TRUE,
  evalFlag = TRUE,
  echoFlag = TRUE,
  warningFlag = FALSE,
  showMessages = FALSE,
  includeFlag = TRUE,
  collapseFlag = FALSE,
  purlFlag = TRUE,
  errorFlag = TRUE,
  messageFlag = TRUE,
  highlightFlag = TRUE,
  promptFlag = FALSE,
  stripWhiteFlag = TRUE,
  tidyFlag = FALSE
)

Arguments

`object`	an easyreporting class object
`cacheFlag`	boolean for caching chunk data (default TRUE)
`evalFlag`	boolean for evaluating the code chunk in the compiled version (default TRUE)
`echoFlag`	boolean for showing the code chunk (default TRUE)
`warningFlag`	boolean for showing the chunk warnings (default FALSE)
`showMessages`	boolean for showing the chunk warnings in compiled version (default FALSE)
`includeFlag`	boolean for including the code chunk in the compiled version (default TRUE)
`collapseFlag`	boolean for collapsing the code chunk in the compiled version (default FALSE),
`purlFlag`	boolean for extracting the code chunk as R code in a separate R file (default TRUE),
`errorFlag`	boolean for including the error generated by the code chunk in the compiled version (default TRUE),
`messageFlag`	boolean for including the code chunk messages in the compiled version (default TRUE),
`highlightFlag`	boolean for highlinghtinh the code chunk in the compiled version (default TRUE),
`promptFlag`	boolean for including a ">" for the code chunk in the compiled version (default FALSE),
`stripWhiteFlag`	boolean for removing the white spaces at beginning/end of the code chunk in the compiled version (default TRUE),
`tidyFlag`	boolean for creating a tidy code chunk in the compiled version (default FALSE).

Value

none

Examples

## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

## setting default option
setOptionsList(rd)

## modifying only some options
rd <- setOptionsList(rd, warningFlag=TRUE, 
        showMessages=TRUE, includeFlag=TRUE)

## End(Not run)
## Not run: 
rd <- easyreporting(filenamePath="./project_report",
                        title="example_report", author=c("It's me"))

## setting default option
setOptionsList(rd)

## modifying only some options
rd <- setOptionsList(rd, warningFlag=TRUE, 
        showMessages=TRUE, includeFlag=TRUE)

## End(Not run)

Package 'easyreporting'

Help Index

addResource

Description

Usage

Arguments

Value

Examples

addResource

Description

Usage

Arguments

Value

Examples

compile

Description

Usage

Arguments

Value

Examples

compile

Description

Usage

Arguments

Value

Examples

easyreporting

Description

Usage

Arguments

Value

Slots

Examples

erGUIVolcano

Description

Usage

Value

Examples

getBibliography

Description

Usage

Arguments

Value

Examples

getBibliography

Description

Usage

Arguments

Value

Examples

getOptionsList

Description

Usage

Arguments

Value

Examples

getOptionsList

Description

Usage

Arguments

Value

Examples

getReportFilename

Description

Usage

Arguments

Value

Examples

getReportFilename

Description

Usage

Arguments

Value

Examples

makeOptionsList

Description

Usage

Arguments

Value

Examples