Re: [RFC] ob-reticulate: R+Python interface from Babel

[Kyle Andrews]

Hi Jack,

As a frequent reticulate user I am very excited to see this patch. I hope
others feel the same and it gets included into org mode as I cannot wait to
use it.

Best Regards,
Kyle

On Mon, Aug 24, 2020, 11:28 Jack Kamm  wrote:

> Hi all,
>
> Reticulate is an R package for interfacing between R and Python. It allows
> accessing objects in a Python session from R and vice versa. See
> https://rstudio.github.io/reticulate/ for more info about it.
>
> I've written a small patch for using reticulate from org-babel. It allows
> creating a source block of lang "reticulate", which behaves as Python for
> font highlighting and editing, but is executed in an R session via
> reticulate.
>
> I'm wondering whether this should go into org-mode, or whether to package
> this separately. I'm also curious whether this would be useful to anyone
> here. Any feedback is appreciated.
>
> The main advantage of reticulate is being able to access Python objects
> directly from R and vice versa, without having to write them to a separate
> file or pass them through the ":var" header argument. For example, we could
> do the following:
>
> #+begin_src reticulate :session
>   import pandas as pd
>
>   fib = [0, 1]
>   for _ in range(10):
>   fib.append(fib[-1] + fib[-2])
>
>   df = pd.DataFrame({
>   "i": list(range(len(fib))),
>   "F_i": fib
>   })
> #+end_src
>
> #+begin_src R :session :results graphics value file :file fig.png
>   library(reticulate)
>   with(py$df, plot(i, F_i))
> #+end_src
>
> Reticulate source blocks support both "value" and "output" results, and
> even supports graphics with matplotlib. It's primarily intended to be used
> in sessions, and the ":session" header argument should match between
> reticulate and R source blocks.
>
> Cheers,
> Jack
>
>

Re: [O] orgmode and anova

[Kyle Andrews]

If you wanted to fit a linear regression model with R, you could do so with
the lm function. Calling anova on the output of the regression would give
you a regression anova table.

model <- lm(delivered_seeing ~ zeenith_seeing, data = delsee)
anova(model)

You would need non-zero residuals for that to be useful of course.

Otherwise, you need to stack your *_seeing columns into one column with
another column saying which kind of seeing it was and then:

model.aov <- aov(seeing ~ factor(kind), data = delsee2)

You could do the stacking in a number of ways. My favorite is to use the
gather function in the tidyr package.

aov is just a wrapper around lm, so just take the same approach as before
to get the ANOVA table. Hope that helps.

On Thu, Apr 21, 2016, 15:10 Uwe Brauer  wrote:

> Hello
>
> Using Kubuntu I just installed R and the following code works nicely
>
> #+tblname: delsee
> | airmass | zenith_seeing | delivered_seeing |
> |-+---+--|
> | 1.3 |  0.95 |1.1119612 |
> | 1.3 |   1.0 |1.1704854 |
> | 1.3 |   1.1 |1.2875340 |
> | 1.3 |   1.2 |1.4045825 |
> #+TBLFM: $3=$2*($1**0.6)
>
>
> #+begin_src R :results output :var delsee=delsee
> summary(delsee)
> #+end_src
>
>
> Does somebody know whether I could do an ANOVA, comparing these columns
> (which does not make much sense, but this is not the point.
>
> Any help is strongly appreciated.
>
> thanks
>
> Uwe Brauer
>
>
>

[O] Bug: sas comments in source blocks confused with headings [8.2.10 (8.2.10-35-g19a7d6-elpaplus @ ~/.emacs.d/elpa/org-plus-contrib-20150406/)]

[Kyle Andrews]

I included SAS code for reference in an org file and noticed that a SAS
comment breaks the folding feature. The buffer is folded only until the
comment. The snippet below placed in an org-buffer should clarify what I
mean.



** SAS

#+BEGIN_SRC sas
* a full line comment in SAS code;
proc mixed method=reml cl;
class D M G;
model y = M G M*G;
random D D*M D*G/cl alpha=0.05;  /* can't do 3-way */
lsmeans M G M*G/cl adjust=tukey; /* only fixed effects */
run;
#+END_SRC

** R

Here is how to fit the mixed effect model in R.



If you press tab on the SAS heading, it doesn't fold all the way to the
R heading, but only to the comment line. Perhaps this is fixed in org
8.3?

---


Emacs  : GNU Emacs 24.4.1 (x86_64-unknown-linux-gnu, GTK+ Version 3.14.7)
 of 2015-01-17 on bisson
Package: Org-mode version 8.2.10 (8.2.10-35-g19a7d6-elpaplus @
/home/k/.emacs.d/elpa/org-plus-contrib-20150406/)

current state:
==
(setq
 org-drill-optimal-factor-matrix '((1 (2.6 . 4.14)))
 org-tab-first-hook '(org-hide-block-toggle-maybe
org-src-native-tab-command-maybe
  org-babel-hide-result-toggle-maybe
org-babel-header-arg-expand)
 org-adapt-indentation nil
 org-speed-command-hook '(org-speed-command-default-hook
org-babel-speed-command-hook)
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-html-format-drawer-function '(lambda (name contents) contents)
 org-latex-format-inlinetask-function 'ignore
 org-confirm-shell-link-function 'yes-or-no-p
 org-image-actual-width nil
 org-ascii-format-inlinetask-function 'org-ascii-format-inlinetask-default
 org-agenda-inhibit-startup t
 org-pretty-entities 1
 org-latex-format-headline-function
'org-latex-format-headline-default-function
 org-default-notes-file ~/org/notes.org
 org-after-todo-state-change-hook '(org-clock-out-if-current)
 org-latex-format-drawer-function '(lambda (name contents) contents)
 org-capture-mode-hook '(make-frame)
 org-from-is-user-regexp nil
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
org-src-mode-configure-edit-buffer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-pre-tangle-hook '(save-buffer)
 org-font-lock-set-keywords-hook '(org-drill-add-cloze-fontification)
 org-mode-hook '(#[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook org-show-block-all
append local] 5]
 #[nil \300\301\302\303\304$\207
   [org-add-hook change-major-mode-hook
org-babel-show-result-all append local] 5]
 org-babel-result-hide-spec org-babel-hide-all-hashes)
 org-ascii-format-drawer-function '(lambda (name contents width) contents)
 org-ctrl-c-ctrl-c-hook '(org-babel-hash-at-point
org-babel-execute-safely-maybe)
 org-cycle-hook '(org-cycle-hide-archived-subtrees org-cycle-hide-drawers
  org-cycle-hide-inline-tasks org-cycle-show-empty-lines
  org-optimize-window-after-visibility-change)
 org-startup-with-latex-preview t
 org-latex-packages-alist '(( multirow t) ( fontenc t) (
siunitx t) ( xfrac t)
( mathtools t) ( physics t) ( color
t))
 org-babel-tangle-lang-exts '((maxima . max) (julia . jl) (tcl .
tcl) (python . py)
  (perl . pl) (latex . tex)
(emacs-lisp . el))
 org-confirm-elisp-link-function 'yes-or-no-p
 org-startup-with-inline-images t
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-babel-after-execute-hook '(org-display-inline-images)
 org-html-format-headline-function 'ignore
 org-babel-load-languages '((emacs-lisp . t) (calc . t) (sh . t) (latex .
t) (R . t) (perl . t)
(octave . t) (python . t) (scheme . t)
(makefile . t) (tcl . t)
(julia . t) (maxima . t))
 org-html-format-inlinetask-function 'ignore
 org-fontify-whole-heading-line t
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 org-confirm-babel-evaluate nil
 org-src-fontify-natively t
 )

[O] org-spreadsheet: formatting chops off units

[Kyle Andrews]

Hello everyone,

I want to use an org-spreadsheet to perform unit conversions for me.

| Mass (g) | Mass (lb) |
|--+---|
| 300 g| 0.66138679 lb |
| 23 kg| 50.706320 lb  |
| 50 Mg| 110231.13 lb  |
#+TBLFM: $2=uconvert($1, lb)


I made the table above, but can't figure out how to format the output. I
tried using the ;%.2f notation shown in the manual, but it cuts the
units off for some reason.

Here is what org-table displays with ;%.2f appended onto my table
formula:

| Mass (g) | Mass (lb) |
|--+---|
| 300 g| 0.66  |
| 23 kg| 50.71 |
| 50 Mg| 110231.13 |
#+TBLFM: $2=uconvert($1, lb);%.2f


Here is what I wish appending ;%.2f would cause org-table to display:


| Mass (g) | Mass (lb) |
|--+---|
| 300 g| 0.66 lb   |
| 23 kg| 50.71 lb  |
| 50 Mg| 110231.13 lb  |
#+TBLFM: $2=uconvert($1, lb);%.2f


If you type in '0.66138679 lb into calc directly, and press d f 2, calc
displays 0.66 lb as desired. Is there any reason for the %.2f notation
chops off the units? Is there some better way to accomplish what I
want?

Thanks!


Note: my spreadsheet uses the wrapper function below to convert units with calc.

#+begin_src emacs-lisp
(defmath uconvert (expression new-units)
(math-convert-units expression new-units)))
#+end_src

--
Kyle C. Andrews
kyle.c.andr...@gmail.com

Re: [O] How to integrate org-mode in a MS Windows-/Office-based environment?

[Kyle Andrews]

Hi Martin,

You should be able to link to Excel and Word documents from Org by
prefixing the normal path with file+sys: instead of just file.  This
doesn't work when the files are on a Windows Share (at least for me),
though.  I'm also interested in getting a robust connection between Org and
Outlook so I will be paying attention to this thread with earnest.

Best Regards,

Kyle

On Thu, Jul 12, 2012 at 5:06 PM, M elwood...@web.de wrote:



 I'm using Emacs org-mode for task and information management in a business
 environment dominated by Microsoft products (Windows, Office, ...).

 I wonder how to create a set-up for maximum productivity and I'd like to
 know how you integrate org-mode in your work on MS Windows.


 Creating hyperlinks in my org-mode files/tasks, which let me jump directly
 to E-Mail in MS Outlook (Exchange-based), open Word-, Excel- or Powerpoint
 documents, etc. is a very helpful feature for integrating org-mode.

 Are there other techniques, tools or add-ons which are helpful for that
 purpose?


 Kind regards

 Martin

Re: [O] Using org-babel with Scheme

[Kyle Andrews]

I am having both of these issues on Emacs 24.  Emacs crashes sometimes on
geiser and babel won't evaluate scheme code as Racket code despite setting
'scheme-program-name and 'org-babel-scheme-cmd to racket. However, Guile
will work if both of those variables hold guile.

Any new developments?

On Wed, Feb 15, 2012 at 9:33 AM, Eric Schulte eric.schu...@gmx.com wrote:

 Leo Alekseyev dnqu...@gmail.com writes:

  Is anyone on the list using a recent org-babel with Scheme?  I
  recently started working through SICP, and I'm running into issues
  evaluating scheme src  blocks.  Org-babel error buffer pops up with
  ERROR: Wrong number of arguments to #primitive-generic display,
  and the minibuffer prompts me for a lisp expression.  Is there
  anything I need to configure beyond   (org-babel-do-load-languages
  'org-babel-load-languages  '((scheme . t)))?
 
  (Running latest org from git in Emacs 24; have Chicken scheme and
  guile installed).
 

 I loaded the ob-scheme.el directly (which should be the same as loading
 it with org-babel-do-load-languages as above) and the following works
 for me.

 #+begin_src scheme
  (+ 1 1 1)
 #+end_src

 #+RESULTS:
 : 3

 I have guile installed and I have the `scheme-program-name' variable set
 to guile elsewhere in my .emacs init.  I imagine setting the above
 variable should enable scheme evaluation.

 Best,

 while looking into this I did notice that when launching Geiser (a nice
 slime-like scheme evaluator) I would sometimes crash my entire Emacs
 process by pressing C-g when Geiser prompts for a scheme executable.  I
 imagine this is unrelated to your problem, but was certainly surprising.

 
  --Leo
 

 --
 Eric Schulte
 http://cs.unm.edu/~eschulte/