Re: [Orgmode] [babel] R - variable names in summary
Tom, Thanks for your comments. > When you find an example that fills a gap you perceive in the documentation, > please pass that along, too. The more examples the better. Now that I have basics working, I will try and use it for something specific over the next few weeks and certainly feedback anything I think might be helpful. Graham ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Dan >> Not being a programmer, I find the terminology and phrasing of these > > I wouldn't classify someone who analyses their data with R as a > non-programmer. Mmmm, I can see why you would say this, but I don't really program in R, but have collected a library of R code over the years which I know how to use and tweak. >> My problem was therefore the lack of examples specific to R. > > Yes, I can see that. I can imagine that if shell/python/ruby code looks > alien then the examples using those languages are not very > inviting. Thanks for pointing that out. Tom Dye and Eric and I are > working on documentation, including a Worg page specifically for R with > org-babel. Currently it doesn't contain anything you don't know but > we'll let you know when the first version goes up on Worg. I look forward to it. Thanks again, Graham ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Hi Graham, On Dec 9, 2009, at 10:33 AM, Graham Smith wrote: Dan, That's great, I am beginning to grasp how this works But I would never have figured out the :results output method, however. OK, it would be really helpful if you could let us know how we should improve the documentation of it. I'm not sure if I'm the one to ask about the documentation, as I struggled with most of it, but that is my problem and probably not typical. I'm also still very much trying to get to grips with Emacs and orgmode. Not being a programmer, I find the terminology and phrasing of these sorts of things difficult to follow, and need examples to copy , and then try and extract from the documentation and other examples, how things work. My problem was therefore the lack of examples specific to R. My guess is that the majority of emacs/orgmode users won't have the same problems. Graham I'd like to second Dan's invitation and ask that you drop a note to the list when you find something difficult to understand in the documentation. There isn't anything about the use of Org-babel (or Org-mode) that a non-programmer shouldn't be able to follow. BTW, I agree with you about the difficult terminology and phrasing in the Org-babel documentation. It should be possible to make the definitions of terms and the distinctions they index more accessible. So, please let the list know when something trips you up. When you find an example that fills a gap you perceive in the documentation, please pass that along, too. The more examples the better. I'm glad to hear you've made it over the steep part of the Org-babel learning curve and that it is working for you now. If your experience is like mine you'll soon be wondering how you ever managed without it. All the best, Tom ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Graham Smith writes: > Dan, > > That's great, I am beginning to grasp how this works > >>> But I would never have figured out the :results output method, however. >> >> OK, it would be really helpful if you could let us know how we should >> improve the documentation of it. > > I'm not sure if I'm the one to ask about the documentation, as I > struggled with most of it, but that is my problem and probably not > typical. I'm also still very much trying to get to grips with Emacs > and orgmode. > > Not being a programmer, I find the terminology and phrasing of these I wouldn't classify someone who analyses their data with R as a non-programmer. > sorts of things difficult to follow, and need examples to copy , and > then try and extract from the documentation and other examples, how > things work. > > My problem was therefore the lack of examples specific to R. Yes, I can see that. I can imagine that if shell/python/ruby code looks alien then the examples using those languages are not very inviting. Thanks for pointing that out. Tom Dye and Eric and I are working on documentation, including a Worg page specifically for R with org-babel. Currently it doesn't contain anything you don't know but we'll let you know when the first version goes up on Worg. Dan > My > guess is that the majority of emacs/orgmode users won't have the same > problems. > > Graham > > > ___ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Dan, That's great, I am beginning to grasp how this works >> But I would never have figured out the :results output method, however. > > OK, it would be really helpful if you could let us know how we should > improve the documentation of it. I'm not sure if I'm the one to ask about the documentation, as I struggled with most of it, but that is my problem and probably not typical. I'm also still very much trying to get to grips with Emacs and orgmode. Not being a programmer, I find the terminology and phrasing of these sorts of things difficult to follow, and need examples to copy , and then try and extract from the documentation and other examples, how things work. My problem was therefore the lack of examples specific to R. My guess is that the majority of emacs/orgmode users won't have the same problems. Graham ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Graham Smith writes: > Dan, > >>> The colnames t works as expected, but how do I then see the variable >>> names when using the summary command, >> >> Just use :colnames t again for that. > > Thanks again, I almost had this solved but in > > #+begin_src R :session babeltest :colnames t > > I hadn't left a space between the end of babeltest and the : > > But I would never have figured out the :results output method, however. OK, it would be really helpful if you could let us know how we should improve the documentation of it. > > Next question is is to do with output with things like summary. In R > if you have lots of variables,the output wraps so it fits on the > screen. With babel it runs off the edge of the page. is there a quick > way of getting the output to fit an anticipated a4 pdf output. I'd suggest using :results output, and controlling the width of the output with options(width=whatever) in R. E.g. #+begin_src R :session babeltest :colnames t :results output options(width=80) summary(cbind(babeltest, babeltest)) #+end_src #+results: #+begin_example ID var1 var2 var3 ID Min. : 1.00 Min. :23.0 Min. :1.0 Min. :200.0 Min. : 1.00 1st Qu.: 3.25 1st Qu.:34.0 1st Qu.:4.0 1st Qu.:355.0 1st Qu.: 3.25 Median : 5.50 Median :45.5 Median :5.0 Median :425.0 Median : 5.50 Mean : 5.50 Mean :48.4 Mean :4.8 Mean :418.9 Mean : 5.50 3rd Qu.: 7.75 3rd Qu.:56.0 3rd Qu.:6.0 3rd Qu.:499.8 3rd Qu.: 7.75 Max. :10.00 Max. :89.0 Max. :7.0 Max. :600.0 Max. :10.00 var1 var2 var3 Min. :23.0 Min. :1.0 Min. :200.0 1st Qu.:34.0 1st Qu.:4.0 1st Qu.:355.0 Median :45.5 Median :5.0 Median :425.0 Mean :48.4 Mean :4.8 Mean :418.9 3rd Qu.:56.0 3rd Qu.:6.0 3rd Qu.:499.8 Max. :89.0 Max. :7.0 Max. :600.0 #+end_example I don't think either org or org-babel has any way to automatically wrap wide tables. Also bear in mind the tranpose function in R (t), although that's not helpful for this summary output, which is a rather weird table, not a standard matrix or data frame. Dan > > I appreciate this may be more an Emacs/orgmode question than a babel one. > > Graham > > > ___ > Emacs-orgmode mailing list > Please use `Reply All' to send replies to the list. > Emacs-orgmode@gnu.org > http://lists.gnu.org/mailman/listinfo/emacs-orgmode ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Dan, >> The colnames t works as expected, but how do I then see the variable >> names when using the summary command, > > Just use :colnames t again for that. Thanks again, I almost had this solved but in #+begin_src R :session babeltest :colnames t I hadn't left a space between the end of babeltest and the : But I would never have figured out the :results output method, however. Next question is is to do with output with things like summary. In R if you have lots of variables,the output wraps so it fits on the screen. With babel it runs off the edge of the page. is there a quick way of getting the output to fit an anticipated a4 pdf output. I appreciate this may be more an Emacs/orgmode question than a babel one. Graham ___ Emacs-orgmode mailing list Please use `Reply All' to send replies to the list. Emacs-orgmode@gnu.org http://lists.gnu.org/mailman/listinfo/emacs-orgmode
Re: [Orgmode] [babel] R - variable names in summary
Graham Smith writes:
> Dan
>
> I have started a new thread so it has a propel babel string. I have
> also created a small file for testing.
>
Hi Graham,
> The colnames t works as expected, but how do I then see the variable
> names when using the summary command,
Just use :colnames t again for that.
> and str doesn't work at all
> (source block produced no output) . They appear OK in the R buffer.
OK, so Austin was right about the problem here. Remember that by
default, org-babel works in ':results value' mode -- i.e., it tries to
give you back an org table corresponding to the *value* of the last
expression in your code. But the R function str() simply *prints* out
some information about the object. You can see that it has no useful
value by doing this in the R buffer:
> str.value <- str(babeltest)
'data.frame': 10 obs. of 4 variables:
$ ID : int 1 2 3 4 5 6 7 8 9 10
$ var1: int 34 56 78 34 56 23 45 23 89 46
$ var2: int 1 4 3 5 6 7 5 6 7 4
$ var3: int 400 499 500 600 500 300 200 340 400 450
> str.value
NULL
What you need here is ':results output', which tells org-babel to give
you back whatever printed output there is. You'll need to use :results
output whenever you want to see the printed output from R as opposed to
the value of a data frame/table/vector etc.
I've pasted a working version of your example below.
Dan
>
> Orgmode+babel output below
>
> Graham
>
> #+srcname:babeltest
> #+begin_src R :colnames t
(This needs ':session babeltest' for your example to work, but I expect
that just accidentally got left out of your email)
> babeltest<-read.csv("/home/graham/Dropbox/myotis/Learn/learn/babeltest.csv",header=TRUE)
> #+end_src
---
#+srcname:babeltest
#+begin_src R :colnames t :session babeltest
babeltest<-read.csv("/tmp/babeltest.csv",header=TRUE)
#+end_src
#+results: babeltest
| "ID" | "var1" | "var2" | "var3" |
|--+++|
|1 | 34 | 1 |400 |
|2 | 56 | 4 |499 |
|3 | 78 | 3 |500 |
|4 | 34 | 5 |600 |
|5 | 56 | 6 |500 |
|6 | 23 | 7 |300 |
|7 | 45 | 5 |200 |
|8 | 23 | 6 |340 |
|9 | 89 | 7 |400 |
| 10 | 46 | 4 |450 |
#+begin_src R :session babeltest :colnames t
summary(babeltest)
#+end_src
#+results:
| "ID"| "var1" | "var2"| "var3" |
|-++---+-|
| "Min. : 1.00" | "Min. :23.0" | "Min. :1.0" | "Min. :200.0" |
| "1st Qu.: 3.25" | "1st Qu.:34.0" | "1st Qu.:4.0" | "1st Qu.:355.0" |
| "Median : 5.50" | "Median :45.5" | "Median :5.0" | "Median :425.0" |
| "Mean : 5.50" | "Mean :48.4" | "Mean :4.8" | "Mean :418.9" |
| "3rd Qu.: 7.75" | "3rd Qu.:56.0" | "3rd Qu.:6.0" | "3rd Qu.:499.8" |
| "Max. :10.00" | "Max. :89.0" | "Max. :7.0" | "Max. :600.0" |
#+begin_src R :session babeltest :results output
str(babeltest)
#+end_src
#+results:
: 'data.frame': 10 obs. of 4 variables:
: $ ID : int 1 2 3 4 5 6 7 8 9 10
: $ var1: int 34 56 78 34 56 23 45 23 89 46
: $ var2: int 1 4 3 5 6 7 5 6 7 4
: $ var3: int 400 499 500 600 500 300 200 340 400 450
---
>
> #+resname: babeltest
> | "ID" | "var1" | "var2" | "var3" |
> |--+++|
> |1 | 34 | 1 |400 |
> |2 | 56 | 4 |499 |
> |3 | 78 | 3 |500 |
> |4 | 34 | 5 |600 |
> |5 | 56 | 6 |500 |
> |6 | 23 | 7 |300 |
> |7 | 45 | 5 |200 |
> |8 | 23 | 6 |340 |
> |9 | 89 | 7 |400 |
> | 10 | 46 | 4 |450 |
>
>
>
> #+begin_src R :session babeltest
> summary(babeltest)
> #+end_src
>
> #+resname:
> | "Min. : 1.00" | "Min. :23.0" | "Min. :1.0" | "Min. :200.0" |
> | "1st Qu.: 3.25" | "1st Qu.:34.0" | "1st Qu.:4.0" | "1st Qu.:355.0" |
> | "Median : 5.50" | "Median :45.5" | "Median :5.0" | "Median :425.0" |
> | "Mean : 5.50" | "Mean :48.4" | "Mean :4.8" | "Mean :418.9" |
> | "3rd Qu.: 7.75" | "3rd Qu.:56.0" | "3rd Qu.:6.0" | "3rd Qu.:499.8" |
> | "Max. :10.00" | "Max. :89.0" | "Max. :7.0" | "Max. :600.0" |
>
> #+begin_src R :session babeltest
> str(babeltest)
> #+end_src
>
> #+resname:
>
> ___
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[Orgmode] [babel] R - variable names in summary
Dan
I have started a new thread so it has a propel babel string. I have
also created a small file for testing.
The colnames t works as expected, but how do I then see the variable
names when using the summary command, and str doesn't work at all
(source block produced no output) . They appear OK in the R buffer.
Orgmode+babel output below
Graham
#+srcname:babeltest
#+begin_src R :colnames t
babeltest<-read.csv("/home/graham/Dropbox/myotis/Learn/learn/babeltest.csv",header=TRUE)
#+end_src
#+resname: babeltest
| "ID" | "var1" | "var2" | "var3" |
|--+++|
|1 | 34 | 1 |400 |
|2 | 56 | 4 |499 |
|3 | 78 | 3 |500 |
|4 | 34 | 5 |600 |
|5 | 56 | 6 |500 |
|6 | 23 | 7 |300 |
|7 | 45 | 5 |200 |
|8 | 23 | 6 |340 |
|9 | 89 | 7 |400 |
| 10 | 46 | 4 |450 |
#+begin_src R :session babeltest
summary(babeltest)
#+end_src
#+resname:
| "Min. : 1.00" | "Min. :23.0" | "Min. :1.0" | "Min. :200.0" |
| "1st Qu.: 3.25" | "1st Qu.:34.0" | "1st Qu.:4.0" | "1st Qu.:355.0" |
| "Median : 5.50" | "Median :45.5" | "Median :5.0" | "Median :425.0" |
| "Mean : 5.50" | "Mean :48.4" | "Mean :4.8" | "Mean :418.9" |
| "3rd Qu.: 7.75" | "3rd Qu.:56.0" | "3rd Qu.:6.0" | "3rd Qu.:499.8" |
| "Max. :10.00" | "Max. :89.0" | "Max. :7.0" | "Max. :600.0" |
#+begin_src R :session babeltest
str(babeltest)
#+end_src
#+resname:
ID,var1,var2,var3
1,34,1,400
2,56,4,499
3,78,3,500
4,34,5,600
5,56,6,500
6,23,7,300
7,45,5,200
8,23,6,340
9,89,7,400
10,46,4,450
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