POLWART, Calum (COUNTY DURHAM AND DARLINGTON NHS FOUNDATION TRUST)
2017-Jun-01 10:55 UTC
[R] odfWeave - A loop of the "same" data
Before I go and do this another way - can I check if anyone has a way of looping through data in odfWeave (or possibly sweave) to do a repeating analysis on subsets of data? For simplicity lets use mtcars dataset in R to explain. Dataset looks like this:> mtcarsmpg cyl disp hp drat wt ... Mazda RX4 21.0 6 160 110 3.90 2.62 ... Mazda RX4 Wag 21.0 6 160 110 3.90 2.88 ... Datsun 710 22.8 4 108 93 3.85 2.32 ... ............ Say I wanted to have a 'catalogue' style report from mtcars, where on each page I would perhaps have the Rowname as a heading and then plot a graph of mpg highlighting that specific car Then add a page break and *do the same for the next car*. I can manually do this of course, but it is effectively a loop something like this: for (n in length(mtcars$mpg)) { barplot (mtcars$mpg, col=c(rep(1,n-1),2,rep(1,length(mtcars$mpg)-n))) } There is a odfWeave page break function so I can do that sort of thing (I think). But I don't think I can output more than one image can I? In reality I will want several images and a table per "catalogue" page. At the moment I think I need to create a master odt document, and create individual catalogue pages. And merge them into one document - but that feels clunky (unless I can script the merge!) Anyone got a better way? ******************************************************************************************************************** This message may contain confidential information. If yo...{{dropped:21}}
I do this regularly with knitr [1]. I have never used odfWeave, but would imagine that similar principles apply. If you make a child document that assumes that the desired data are stored in one or more objects, then you can use a for loop in the master document that repeatedly extracts the desired subsets and puts them into the objects the child document expects them to be in, parses the child document, and then "cat"s the parsed results into the master document output. [1] https://yihui.name/knitr/demo/child/ -- Sent from my phone. Please excuse my brevity. On June 1, 2017 3:55:33 AM PDT, "POLWART, Calum (COUNTY DURHAM AND DARLINGTON NHS FOUNDATION TRUST) via R-help" <r-help at r-project.org> wrote:>Before I go and do this another way - can I check if anyone has a way >of looping through data in odfWeave (or possibly sweave) to do a >repeating analysis on subsets of data? > >For simplicity lets use mtcars dataset in R to explain. Dataset looks >like this: > >> mtcars > mpg cyl disp hp drat wt ... >Mazda RX4 21.0 6 160 110 3.90 2.62 ... >Mazda RX4 Wag 21.0 6 160 110 3.90 2.88 ... >Datsun 710 22.8 4 108 93 3.85 2.32 ... > ............ > >Say I wanted to have a 'catalogue' style report from mtcars, where on >each page I would perhaps have the Rowname as a heading and then plot a >graph of mpg highlighting that specific car > >Then add a page break and *do the same for the next car*. I can >manually do this of course, but it is effectively a loop something like >this: > >for (n in length(mtcars$mpg)) { >barplot (mtcars$mpg, col=c(rep(1,n-1),2,rep(1,length(mtcars$mpg)-n))) >} > >There is a odfWeave page break function so I can do that sort of thing >(I think). But I don't think I can output more than one image can I? >In reality I will want several images and a table per "catalogue" page. > >At the moment I think I need to create a master odt document, and >create individual catalogue pages. And merge them into one document - >but that feels clunky (unless I can script the merge!) > >Anyone got a better way? > > > > >******************************************************************************************************************** > >This message may contain confidential information. If >yo...{{dropped:21}} > >______________________________________________ >R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see >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.
On Thu, 1 Jun 2017, POLWART, Calum (COUNTY DURHAM AND DARLINGTON NHS FOUNDATION TRUST) via R-help wrote:> Before I go and do this another way - can I check if anyone has a way of > looping through data in odfWeave (or possibly sweave) to do a repeating > analysis on subsets of data? > > For simplicity lets use mtcars dataset in R to explain. Dataset looks like this: > >> mtcars > mpg cyl disp hp drat wt ... > Mazda RX4 21.0 6 160 110 3.90 2.62 ... > Mazda RX4 Wag 21.0 6 160 110 3.90 2.88 ... > Datsun 710 22.8 4 108 93 3.85 2.32 ... > ............ > > Say I wanted to have a 'catalogue' style report from mtcars, where on > each page I would perhaps have the Rowname as a heading and then plot a > graph of mpg highlighting that specific car > > Then add a page break and *do the same for the next car*. I can manually do this of course, but it is effectively a loop something like this: > > for (n in length(mtcars$mpg)) { > barplot (mtcars$mpg, col=c(rep(1,n-1),2,rep(1,length(mtcars$mpg)-n))) > } > > There is a odfWeave page break function so I can do that sort of thing > (I think). But I don't think I can output more than one image can I? > In reality I will want several images and a table per "catalogue" page. > > At the moment I think I need to create a master odt document, and create > individual catalogue pages. And merge them into one document - but that > feels clunky (unless I can script the merge!) > > Anyone got a better way?For a complex template inside a loop, I'd probably do as Jeff suggests and use a knitr child document for ease of developing and debugging the template. But for the simple case you describe I'd use a brew script to unroll the loop. You would write your input file as usual, but put a brew script in the right place, then run brew on the input file to produce an intermediate file that unrolls the loop, then weave the intermediate file to get your desired result. Here is a simple example of such you can run in an R session (assuming the brew package is installed) and see the results printed out. --8<---------------cut here---------------start------------->8--- brew::brew(text=" Everything before the loop <% for (i in 1:10) { %> Print the value of i <% print(i) %> or better yet \\Sexpr{<%= i %>} <% } %> everything after ") --8<---------------cut here---------------end--------------->8--- The double backslash is needed in the literal string used here. If you put that script in a file using an editor, you would just use a single backslash. HTH, Chuck
This is what the R.rsp (https://cran.r-project.org/package=R.rsp; I'm the author) and it's RSP markup is good at and was designed to handle. We're using it lots in report generation where we iterate of elements, e.g. over the 24 chromosomes. See Section 2.3 in https://cran.r-project.org/web/packages/R.rsp/vignettes/Dynamic_document_creation_using_RSP.pdf. RSP is independent of input format - all it requires is that it's text-based - so you can use RSP-embedded LaTeX, HTML, Markdown, ..., and even RSP-embedded Sweave, knitr, Rmarkdown (where it then it effectively works as a pre-processor to those formats). Hope this helps Henrik On Thu, Jun 1, 2017 at 9:35 AM, Charles C. Berry <ccberry at ucsd.edu> wrote:> On Thu, 1 Jun 2017, POLWART, Calum (COUNTY DURHAM AND DARLINGTON NHS > FOUNDATION TRUST) via R-help wrote: > >> Before I go and do this another way - can I check if anyone has a way of >> looping through data in odfWeave (or possibly sweave) to do a repeating >> analysis on subsets of data? >> >> For simplicity lets use mtcars dataset in R to explain. Dataset looks >> like this: >> >>> mtcars >> >> mpg cyl disp hp drat wt ... >> Mazda RX4 21.0 6 160 110 3.90 2.62 ... >> Mazda RX4 Wag 21.0 6 160 110 3.90 2.88 ... >> Datsun 710 22.8 4 108 93 3.85 2.32 ... >> ............ >> >> Say I wanted to have a 'catalogue' style report from mtcars, where on each >> page I would perhaps have the Rowname as a heading and then plot a graph of >> mpg highlighting that specific car >> >> Then add a page break and *do the same for the next car*. I can manually >> do this of course, but it is effectively a loop something like this: >> >> for (n in length(mtcars$mpg)) { >> barplot (mtcars$mpg, col=c(rep(1,n-1),2,rep(1,length(mtcars$mpg)-n))) >> } >> >> There is a odfWeave page break function so I can do that sort of thing (I >> think). But I don't think I can output more than one image can I? In >> reality I will want several images and a table per "catalogue" page. >> >> At the moment I think I need to create a master odt document, and create >> individual catalogue pages. And merge them into one document - but that >> feels clunky (unless I can script the merge!) >> >> Anyone got a better way? > > > > For a complex template inside a loop, I'd probably do as Jeff suggests and > use a knitr child document for ease of developing and debugging the > template. > > But for the simple case you describe I'd use a brew script to > unroll the loop. > > You would write your input file as usual, but put a brew script in the > right place, then run brew on the input file to produce an > intermediate file that unrolls the loop, then weave the intermediate > file to get your desired result. Here is a simple example of such you can > run in an R session (assuming the brew package is installed) and see the > results printed out. > > --8<---------------cut here---------------start------------->8--- > > brew::brew(text=" > > Everything before the loop > > <% for (i in 1:10) { %> > Print the value of i > <% print(i) %> or better yet > \\Sexpr{<%= i %>} > <% } %> > > everything after > > ") > > --8<---------------cut here---------------end--------------->8--- > > The double backslash is needed in the literal string used here. If > you put that script in a file using an editor, you would just use a > single backslash. > > HTH, > > Chuck > > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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.