Sweave v. Knitr v. Rmarkdown: code chunk headers
up vote
0
down vote
favorite
I am trying to understand the relationship between rmarkdown, sweave and knitr. Looking at code and examples I have run into two types of code headers and I don't understand what language/package they belong to.
The headers are
```{}
```
and
<<>>=
@
- What is the difference between them?
- Ho do they relate to
rmarkdown,sweaveandknitr? - If I work on a
.rnw, which one am I using?
r r-markdown knitr sweave
asked Nov 10 at 4:07
Zweifler
306
|
show 4 more comments
up vote
0
down vote
favorite
I am trying to understand the relationship between rmarkdown, sweave and knitr. Looking at code and examples I have run into two types of code headers and I don't understand what language/package they belong to.
The headers are
```{}
```
and
<<>>=
@
- What is the difference between them?
- Ho do they relate to
rmarkdown,sweaveandknitr? - If I work on a
.rnw, which one am I using?
r r-markdown knitr sweave
asked Nov 10 at 4:07
Zweifler
306
sweaveis based on a LaTeX base-format,rmarkdownis based on markdown. Both allow code-chunks for R-code, output, and plots.knitrused to supportsweavebut apparently no longer does, so it rendersrmarkdowninto one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).
– r2evans
Nov 10 at 4:28
1
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This.Rnwformat is still well supported.
– Yihui Xie
Nov 10 at 4:39
2
Unless I'm mistaken, the difference is:```{}is forrmarkdown, and<<>>=is forsweave.
– r2evans
Nov 10 at 5:02
2
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro onsweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew aboutsweave, and then jumped directly intormarkdown. There are definitely advantages to usingsweave, namely the ability to control things in LaTeX that markdown does not support.
– r2evans
Nov 10 at 5:20
1
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33
|
show 4 more comments
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I am trying to understand the relationship between rmarkdown, sweave and knitr. Looking at code and examples I have run into two types of code headers and I don't understand what language/package they belong to.
The headers are
```{}
```
and
<<>>=
@
- What is the difference between them?
- Ho do they relate to
rmarkdown,sweaveandknitr? - If I work on a
.rnw, which one am I using?
r r-markdown knitr sweave
asked Nov 10 at 4:07
Zweifler
306
I am trying to understand the relationship between rmarkdown, sweave and knitr. Looking at code and examples I have run into two types of code headers and I don't understand what language/package they belong to.
The headers are
```{}
```
and
<<>>=
@
- What is the difference between them?
- Ho do they relate to
rmarkdown,sweaveandknitr? - If I work on a
.rnw, which one am I using?
r r-markdown knitr sweave
r r-markdown knitr sweave
asked Nov 10 at 4:07
Zweifler
306
asked Nov 10 at 4:07
Zweifler
306
asked Nov 10 at 4:07
Zweifler
306
asked Nov 10 at 4:07
Zweifler
306
asked Nov 10 at 4:07
Zweifler
306
306
sweaveis based on a LaTeX base-format,rmarkdownis based on markdown. Both allow code-chunks for R-code, output, and plots.knitrused to supportsweavebut apparently no longer does, so it rendersrmarkdowninto one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).
– r2evans
Nov 10 at 4:28
1
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This.Rnwformat is still well supported.
– Yihui Xie
Nov 10 at 4:39
2
Unless I'm mistaken, the difference is:```{}is forrmarkdown, and<<>>=is forsweave.
– r2evans
Nov 10 at 5:02
2
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro onsweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew aboutsweave, and then jumped directly intormarkdown. There are definitely advantages to usingsweave, namely the ability to control things in LaTeX that markdown does not support.
– r2evans
Nov 10 at 5:20
1
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33
|
show 4 more comments
sweaveis based on a LaTeX base-format,rmarkdownis based on markdown. Both allow code-chunks for R-code, output, and plots.knitrused to supportsweavebut apparently no longer does, so it rendersrmarkdowninto one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).
– r2evans
Nov 10 at 4:28
1
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This.Rnwformat is still well supported.
– Yihui Xie
Nov 10 at 4:39
2
Unless I'm mistaken, the difference is:```{}is forrmarkdown, and<<>>=is forsweave.
– r2evans
Nov 10 at 5:02
2
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro onsweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew aboutsweave, and then jumped directly intormarkdown. There are definitely advantages to usingsweave, namely the ability to control things in LaTeX that markdown does not support.
– r2evans
Nov 10 at 5:20
1
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33
sweave is based on a LaTeX base-format, rmarkdown is based on markdown. Both allow code-chunks for R-code, output, and plots. knitr used to support sweave but apparently no longer does, so it renders rmarkdown into one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).– r2evans
Nov 10 at 4:28
sweave is based on a LaTeX base-format, rmarkdown is based on markdown. Both allow code-chunks for R-code, output, and plots. knitr used to support sweave but apparently no longer does, so it renders rmarkdown into one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).– r2evans
Nov 10 at 4:28
1
1
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This
.Rnw format is still well supported.– Yihui Xie
Nov 10 at 4:39
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This
.Rnw format is still well supported.– Yihui Xie
Nov 10 at 4:39
2
2
Unless I'm mistaken, the difference is:
```{} is for rmarkdown, and <<>>= is for sweave.– r2evans
Nov 10 at 5:02
Unless I'm mistaken, the difference is:
```{} is for rmarkdown, and <<>>= is for sweave.– r2evans
Nov 10 at 5:02
2
2
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro on
sweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew about sweave, and then jumped directly into rmarkdown. There are definitely advantages to using sweave, namely the ability to control things in LaTeX that markdown does not support.– r2evans
Nov 10 at 5:20
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro on
sweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew about sweave, and then jumped directly into rmarkdown. There are definitely advantages to using sweave, namely the ability to control things in LaTeX that markdown does not support.– r2evans
Nov 10 at 5:20
1
1
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33
|
show 4 more comments
1 Answer
1
active
oldest
votes
up vote
1
down vote
accepted
Both sweave and rmarkdown provide the ability to run arbitrary code for R, python, and other programming languages. The pros and cons of each are varied, but a quick comparison:
R markdown :
typical file extensions:
.rmd(case-insens), perhaps.rmarkdownsupports R, python, and several other languages
outputs to HTML, docx, LaTeX (and therefore PDF), and several other output formats
uses the triple-backtick for chunk demarcation
Regular text.
```{r chunkname, chunkoptions, ...}
a <- 1
```
```{python pychunk, chunkoptions, ...}
def myfun(v: list) -> list:
"""
Something important in this docstring.
"""
return [a+1 for a in v]
```
More regular text.
because it is based on markdown, there are some limitations for cross-references, table-control, etc; there are packages and known mitigation techniques for many of them (too many to list here). However, you can use direct LaTeX formatting in the markdown, so output to PDF can enjoy that control as well (though LaTeX code is not translated for other output formats).
Sweave:
typical file extensions include
.rnw(case-insens) and I've seen.noweb(not fully certain on this ...)supports R, and perhaps other languages if you can get to them through R (such as via
reticulate)outputs to LaTeX and therefore PDF
uses
<<>>=and@for chunk demarcation:
Regular text.
<<chunkname, chunkoptions, ...>>=
a <- 1
@
More regular text.
because it is based directly on LaTeX, you can as much control over formatting, cross-referencing, etc
knitr
- processes files of both
sweaveandrmarkdownformats - some sweave pre-processing may be required (e.g., using
Sweave2knitr), ref: https://yihui.name/knitr/demo/sweave/
answered Nov 11 at 17:55
r2evans
25.4k32856
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
add a comment |
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1 Answer
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1 Answer
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active
oldest
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oldest
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oldest
votes
up vote
1
down vote
accepted
Both sweave and rmarkdown provide the ability to run arbitrary code for R, python, and other programming languages. The pros and cons of each are varied, but a quick comparison:
R markdown :
typical file extensions:
.rmd(case-insens), perhaps.rmarkdownsupports R, python, and several other languages
outputs to HTML, docx, LaTeX (and therefore PDF), and several other output formats
uses the triple-backtick for chunk demarcation
Regular text.
```{r chunkname, chunkoptions, ...}
a <- 1
```
```{python pychunk, chunkoptions, ...}
def myfun(v: list) -> list:
"""
Something important in this docstring.
"""
return [a+1 for a in v]
```
More regular text.
because it is based on markdown, there are some limitations for cross-references, table-control, etc; there are packages and known mitigation techniques for many of them (too many to list here). However, you can use direct LaTeX formatting in the markdown, so output to PDF can enjoy that control as well (though LaTeX code is not translated for other output formats).
Sweave:
typical file extensions include
.rnw(case-insens) and I've seen.noweb(not fully certain on this ...)supports R, and perhaps other languages if you can get to them through R (such as via
reticulate)outputs to LaTeX and therefore PDF
uses
<<>>=and@for chunk demarcation:
Regular text.
<<chunkname, chunkoptions, ...>>=
a <- 1
@
More regular text.
because it is based directly on LaTeX, you can as much control over formatting, cross-referencing, etc
knitr
- processes files of both
sweaveandrmarkdownformats - some sweave pre-processing may be required (e.g., using
Sweave2knitr), ref: https://yihui.name/knitr/demo/sweave/
answered Nov 11 at 17:55
r2evans
25.4k32856
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
add a comment |
up vote
1
down vote
accepted
Both sweave and rmarkdown provide the ability to run arbitrary code for R, python, and other programming languages. The pros and cons of each are varied, but a quick comparison:
R markdown :
typical file extensions:
.rmd(case-insens), perhaps.rmarkdownsupports R, python, and several other languages
outputs to HTML, docx, LaTeX (and therefore PDF), and several other output formats
uses the triple-backtick for chunk demarcation
Regular text.
```{r chunkname, chunkoptions, ...}
a <- 1
```
```{python pychunk, chunkoptions, ...}
def myfun(v: list) -> list:
"""
Something important in this docstring.
"""
return [a+1 for a in v]
```
More regular text.
because it is based on markdown, there are some limitations for cross-references, table-control, etc; there are packages and known mitigation techniques for many of them (too many to list here). However, you can use direct LaTeX formatting in the markdown, so output to PDF can enjoy that control as well (though LaTeX code is not translated for other output formats).
Sweave:
typical file extensions include
.rnw(case-insens) and I've seen.noweb(not fully certain on this ...)supports R, and perhaps other languages if you can get to them through R (such as via
reticulate)outputs to LaTeX and therefore PDF
uses
<<>>=and@for chunk demarcation:
Regular text.
<<chunkname, chunkoptions, ...>>=
a <- 1
@
More regular text.
because it is based directly on LaTeX, you can as much control over formatting, cross-referencing, etc
knitr
- processes files of both
sweaveandrmarkdownformats - some sweave pre-processing may be required (e.g., using
Sweave2knitr), ref: https://yihui.name/knitr/demo/sweave/
answered Nov 11 at 17:55
r2evans
25.4k32856
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
add a comment |
up vote
1
down vote
accepted
up vote
1
down vote
accepted
Both sweave and rmarkdown provide the ability to run arbitrary code for R, python, and other programming languages. The pros and cons of each are varied, but a quick comparison:
R markdown :
typical file extensions:
.rmd(case-insens), perhaps.rmarkdownsupports R, python, and several other languages
outputs to HTML, docx, LaTeX (and therefore PDF), and several other output formats
uses the triple-backtick for chunk demarcation
Regular text.
```{r chunkname, chunkoptions, ...}
a <- 1
```
```{python pychunk, chunkoptions, ...}
def myfun(v: list) -> list:
"""
Something important in this docstring.
"""
return [a+1 for a in v]
```
More regular text.
because it is based on markdown, there are some limitations for cross-references, table-control, etc; there are packages and known mitigation techniques for many of them (too many to list here). However, you can use direct LaTeX formatting in the markdown, so output to PDF can enjoy that control as well (though LaTeX code is not translated for other output formats).
Sweave:
typical file extensions include
.rnw(case-insens) and I've seen.noweb(not fully certain on this ...)supports R, and perhaps other languages if you can get to them through R (such as via
reticulate)outputs to LaTeX and therefore PDF
uses
<<>>=and@for chunk demarcation:
Regular text.
<<chunkname, chunkoptions, ...>>=
a <- 1
@
More regular text.
because it is based directly on LaTeX, you can as much control over formatting, cross-referencing, etc
knitr
- processes files of both
sweaveandrmarkdownformats - some sweave pre-processing may be required (e.g., using
Sweave2knitr), ref: https://yihui.name/knitr/demo/sweave/
answered Nov 11 at 17:55
r2evans
25.4k32856
Both sweave and rmarkdown provide the ability to run arbitrary code for R, python, and other programming languages. The pros and cons of each are varied, but a quick comparison:
R markdown :
typical file extensions:
.rmd(case-insens), perhaps.rmarkdownsupports R, python, and several other languages
outputs to HTML, docx, LaTeX (and therefore PDF), and several other output formats
uses the triple-backtick for chunk demarcation
Regular text.
```{r chunkname, chunkoptions, ...}
a <- 1
```
```{python pychunk, chunkoptions, ...}
def myfun(v: list) -> list:
"""
Something important in this docstring.
"""
return [a+1 for a in v]
```
More regular text.
because it is based on markdown, there are some limitations for cross-references, table-control, etc; there are packages and known mitigation techniques for many of them (too many to list here). However, you can use direct LaTeX formatting in the markdown, so output to PDF can enjoy that control as well (though LaTeX code is not translated for other output formats).
Sweave:
typical file extensions include
.rnw(case-insens) and I've seen.noweb(not fully certain on this ...)supports R, and perhaps other languages if you can get to them through R (such as via
reticulate)outputs to LaTeX and therefore PDF
uses
<<>>=and@for chunk demarcation:
Regular text.
<<chunkname, chunkoptions, ...>>=
a <- 1
@
More regular text.
because it is based directly on LaTeX, you can as much control over formatting, cross-referencing, etc
knitr
- processes files of both
sweaveandrmarkdownformats - some sweave pre-processing may be required (e.g., using
Sweave2knitr), ref: https://yihui.name/knitr/demo/sweave/
answered Nov 11 at 17:55
r2evans
25.4k32856
edited Nov 11 at 20:01
answered Nov 11 at 17:55
r2evans
25.4k32856
answered Nov 11 at 17:55
r2evans
25.4k32856
answered Nov 11 at 17:55
r2evans
25.4k32856
25.4k32856
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
add a comment |
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
Could you add what knitr's relationship is to both?
– Zweifler
Nov 11 at 18:44
add a comment |
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sweaveis based on a LaTeX base-format,rmarkdownis based on markdown. Both allow code-chunks for R-code, output, and plots.knitrused to supportsweavebut apparently no longer does, so it rendersrmarkdowninto one of many output formats (including LaTeX, pdf, html, markdown, docx, epub).– r2evans
Nov 10 at 4:28
1
@r2evans Sorry for confusing you, but knitr supported Sweave from Day One, and still supports it. The documentation you mentioned said the full compatibility was dropped, which only means some Sweave chunk options were no longer supported. This
.Rnwformat is still well supported.– Yihui Xie
Nov 10 at 4:39
2
Unless I'm mistaken, the difference is:
```{}is forrmarkdown, and<<>>=is forsweave.– r2evans
Nov 10 at 5:02
2
Zweifler, I believe it is more of a markup to "normal LaTeX" that provides code-execution (simply put), however I'm not a pro on
sweave. I have never really used it, frankly ... I was using R and LaTeX well before I knew aboutsweave, and then jumped directly intormarkdown. There are definitely advantages to usingsweave, namely the ability to control things in LaTeX that markdown does not support.– r2evans
Nov 10 at 5:20
1
@r2evans Your understanding above is absolutely correct, so please feel free to post an answer. If there's anything that needs to be further clarified, I'll be happy to chime in. Thanks!
– Yihui Xie
Nov 11 at 3:33