Re: [R] recommended way to group function calls in Sweave
Dear Rainer On Wed, Apr 25, 2012 at 5:34 PM, Rainer Schuermann rainer.schuerm...@gmx.net wrote: chunk_name_1,eval=FALSE,echo=FALSE= I like the 'eval=FALSE' trick. SweaveInput( setup.Rnw ) and from here, I can suse the named chunks almost like function calls, as you you describe below. The advantage (for me) is that I have only one place where I maintain the functions code, and only one line in the real document, rather than a lot of code, possibly distributed over the document.. This makes sense for LaTeX, but I actually use LyX and things are a bit more straightforward there. I can put the initialization chunks within a 'TeX inset' that can be collapsed; this way it contains all the necessary code, but takes up only one line in the editor. I attach an example .lyx file. I renamed it to .lyx.txt and cross finger that r-help will accept the attachment; make sure to rename it back when trying to open with LyX. Regards Liviu #LyX 2.0 created this file. For more info see http://www.lyx.org/ \lyxformat 413 \begin_document \begin_header \textclass article \use_default_options true \begin_modules sweave \end_modules \maintain_unincluded_children false \language english \language_package default \inputencoding auto \fontencoding global \font_roman default \font_sans default \font_typewriter default \font_default_family default \use_non_tex_fonts false \font_sc false \font_osf false \font_sf_scale 100 \font_tt_scale 100 \graphics default \default_output_format default \output_sync 0 \bibtex_command default \index_command default \paperfontsize default \spacing single \use_hyperref false \papersize default \use_geometry false \use_amsmath 1 \use_esint 1 \use_mhchem 1 \use_mathdots 1 \cite_engine basic \use_bibtopic false \use_indices false \paperorientation portrait \suppress_date false \use_refstyle 1 \index Index \shortcut idx \color #008000 \end_index \secnumdepth 3 \tocdepth 3 \paragraph_separation indent \paragraph_indentation default \quotes_language english \papercolumns 1 \papersides 1 \paperpagestyle default \tracking_changes false \output_changes false \html_math_output 0 \html_css_as_file 0 \html_be_strict false \end_header \begin_body \begin_layout Standard \begin_inset ERT status collapsed \begin_layout Plain Layout echo=FALSE, results=hide= \end_layout \begin_layout Plain Layout library(xtable) \end_layout \begin_layout Plain Layout d - iris \end_layout \begin_layout Plain Layout ind - 1 \end_layout \begin_layout Plain Layout @ \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout chunk_name_1,eval=FALSE,echo=FALSE= \end_layout \begin_layout Plain Layout x - cor(d[ , ind]) \end_layout \begin_layout Plain Layout @ \end_layout \begin_layout Plain Layout \end_layout \begin_layout Plain Layout chunk_name_2,eval=FALSE,echo=FALSE= \end_layout \begin_layout Plain Layout # produce a nice table from some data \end_layout \begin_layout Plain Layout xtable(x) \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \begin_layout Standard Here's a sample use of Sweave macros. \end_layout \begin_layout Standard \begin_inset ERT status open \begin_layout Plain Layout echo=F, results=tex= \end_layout \begin_layout Plain Layout d - mtcars \end_layout \begin_layout Plain Layout ind - 1:3 \end_layout \begin_layout Plain Layout chunk_name_1 \end_layout \begin_layout Plain Layout chunk_name_2 \end_layout \begin_layout Plain Layout @ \end_layout \end_inset \end_layout \end_body \end_document __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] recommended way to group function calls in Sweave
Dear all
When using Sweave, I'm always hitting the same bump: I want to group
repetitive calls in a function, but I want both the results and the
function calls in the printed output. Let me explain myself.
Consider the following computation in an Sweave document:
summary(iris[,1:2])
cor(iris[,1:2])
When using these two calls directly, I obtain the following output:
summary(iris[,1:2])
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
cor(iris[,1:2])
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
However, if I try to group the calls in a function:
f - function(d, ind){
print(summary(d[ , ind]))
print(cor(d[ , ind]))
return(invisible(NULL))
}
Then I get a different output in the Sweave PDF:
f(iris, 1:2)
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
Of course I can use 'echo=F' to remove the ' f(iris, 1:2)' in the
above, but how can I do to keep the original calls 'summary(d[ ,
ind])' and 'cor(d[ , ind])'? Or even better, could the actual calls be
used, after the replacement of arguments by their values:
'summary(iris[,1:2])' and 'cor(iris[,1:2])'.
Or is the recommended way to use cat()-ed statements:
f - function(d, ind){
cat('Variable summary:\n')
print(summary(d[ , ind]))
cat('\nCorrelation table:\n')
print(cor(d[ , ind]))
return(invisible(NULL))
}
To obtain such output:
f(iris, 1:2)
Variable summary:
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
Correlation table:
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
What is the recommended way of grouping repetitive function calls?
What do you usually use in your own documents? Regards
Liviu
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Re: [R] recommended way to group function calls in Sweave
On 12-04-25 7:41 AM, Liviu Andronic wrote:
Dear all
When using Sweave, I'm always hitting the same bump: I want to group
repetitive calls in a function, but I want both the results and the
function calls in the printed output. Let me explain myself.
Consider the following computation in an Sweave document:
summary(iris[,1:2])
cor(iris[,1:2])
When using these two calls directly, I obtain the following output:
summary(iris[,1:2])
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
cor(iris[,1:2])
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
However, if I try to group the calls in a function:
f- function(d, ind){
print(summary(d[ , ind]))
print(cor(d[ , ind]))
return(invisible(NULL))
}
Then I get a different output in the Sweave PDF:
f(iris, 1:2)
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
Of course I can use 'echo=F' to remove the ' f(iris, 1:2)' in the
above, but how can I do to keep the original calls 'summary(d[ ,
ind])' and 'cor(d[ , ind])'? Or even better, could the actual calls be
used, after the replacement of arguments by their values:
'summary(iris[,1:2])' and 'cor(iris[,1:2])'.
Or is the recommended way to use cat()-ed statements:
f- function(d, ind){
cat('Variable summary:\n')
print(summary(d[ , ind]))
cat('\nCorrelation table:\n')
print(cor(d[ , ind]))
return(invisible(NULL))
}
To obtain such output:
f(iris, 1:2)
Variable summary:
Sepal.LengthSepal.Width
Min. :4.300 Min. :2.000
1st Qu.:5.100 1st Qu.:2.800
Median :5.800 Median :3.000
Mean :5.843 Mean :3.057
3rd Qu.:6.400 3rd Qu.:3.300
Max. :7.900 Max. :4.400
Correlation table:
Sepal.Length Sepal.Width
Sepal.Length1.000 -0.1175698
Sepal.Width-0.1175698 1.000
What is the recommended way of grouping repetitive function calls?
What do you usually use in your own documents? Regards
Liviu
I would use the last method, or if the calls were truly repetitive (i.e.
always identical, not just the same pattern), use a named chunk.
Duncan Murdoch
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Re: [R] recommended way to group function calls in Sweave
On Wed, Apr 25, 2012 at 3:41 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
I would use the last method, or if the calls were truly repetitive (i.e.
always identical, not just the same pattern), use a named chunk.
Labeled chunks are indeed what I was looking for [1]. As far as I
understand, this is what Sweave functions (or are these macros?)
look like:
=
d - iris
ind - 1:2
@
sw=
summary(d[ , ind])
cor(d[ , ind])
@
=
d - iris
ind - 2:4
sw
@
Regards
Liviu
[1] vignette('Sweave', 'utils')
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Re: [R] recommended way to group function calls in Sweave
On 25/04/2012 10:20 AM, Liviu Andronic wrote:
On Wed, Apr 25, 2012 at 3:41 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
I would use the last method, or if the calls were truly repetitive (i.e.
always identical, not just the same pattern), use a named chunk.
Labeled chunks are indeed what I was looking for [1]. As far as I
understand, this is what Sweave functions (or are these macros?)
look like:
Yes. They're definitely macros, not functions: pure text substitution.
Duncan Murdoch
=
d- iris
ind- 1:2
@
sw=
summary(d[ , ind])
cor(d[ , ind])
@
=
d- iris
ind- 2:4
sw
@
Regards
Liviu
[1] vignette('Sweave', 'utils')
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Re: [R] recommended way to group function calls in Sweave
What I usually do when I have to write a report with some functions I use
multiple times is that I put them in a separate file (call it setup.Rnw or
so).
The first chunk there loads the libraries, sets initial variable values etc:
echo=FALSE, results=hide=
library( xtable )
d - iris
ind - 1
@
Then I have a number of chunks that are not evaluated at this point:
chunk_name_1,eval=FALSE,echo=FALSE=
summary(d[ , ind])
cor(d[ , ind])
@
chunk_name_2,eval=FALSE,echo=FALSE=
# produce a nice table from some data
@
In my master file, I load these definitions first
SweaveInput( setup.Rnw )
and from here, I can suse the named chunks almost like function calls, as you
you describe below. The advantage (for me) is that I have only one place where
I maintain the functions code, and only one line in the real document,
rather than a lot of code, possibly distributed over the document..
Rgds,
Rainer
On Wednesday 25 April 2012 16:20:13 Liviu Andronic wrote:
On Wed, Apr 25, 2012 at 3:41 PM, Duncan Murdoch
murdoch.dun...@gmail.com wrote:
I would use the last method, or if the calls were truly repetitive (i.e.
always identical, not just the same pattern), use a named chunk.
Labeled chunks are indeed what I was looking for [1]. As far as I
understand, this is what Sweave functions (or are these macros?)
look like:
=
d - iris
ind - 1:2
@
sw=
summary(d[ , ind])
cor(d[ , ind])
@
=
d - iris
ind - 2:4
sw
@
Regards
Liviu
[1] vignette('Sweave', 'utils')
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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