forked from mirrors/org-mode
Merge branch 'master' of git+ssh://repo.or.cz/srv/git/org-mode
Conflicts: lisp/ChangeLog
This commit is contained in:
Carsten Dominik
commit
1d3a4f1eb7
|
|
@ -1,883 +0,0 @@
|
|||
;;; org-R.el --- Computing and data visualisation in Org-mode using R
|
||||
|
||||
;; Copyright (C) 2009
|
||||
;; Free Software Foundation, Inc.
|
||||
|
||||
;; Author: Dan Davison <davison@stats.ox.ac.uk>
|
||||
;; Keywords: org, R, ESS, tables, graphics
|
||||
;; Homepage: http://www.stats.ox.ac.uk/~davison/software/org-R
|
||||
;; Version: 0.06 2009-04-15
|
||||
;;
|
||||
;; This file is not part of GNU Emacs.
|
||||
;;
|
||||
;; This file is free software; you can redistribute it and/or modify
|
||||
;; it under the terms of the GNU General Public License as published by
|
||||
;; the Free Software Foundation; either version 3, or (at your option)
|
||||
;; any later version.
|
||||
|
||||
;; This file is distributed in the hope that it will be useful,
|
||||
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
|
||||
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
||||
;; GNU General Public License for more details.
|
||||
|
||||
;; You should have received a copy of the GNU General Public License
|
||||
;; along with GNU Emacs. If not, see <http://www.gnu.org/licenses/>.
|
||||
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
||||
;;
|
||||
;;; Commentary:
|
||||
|
||||
;; This file allows R (http://www.r-project.org) code to be applied to
|
||||
;; emacs org-mode (http://orgmode.org) tables. When the result of the
|
||||
;; analysis is a vector or matrix, it is output back into the org-mode
|
||||
;; buffer as a new org table. Alternatively the R code may be used to
|
||||
;; plot the data in the org table. It requires R to be running in an
|
||||
;; inferior-ess-mode buffer (install Emacs Speaks Statistics
|
||||
;; http://ess.r-project.org and issue M-x R).
|
||||
;;
|
||||
;;
|
||||
;; The user interface is via two different options lines in the org
|
||||
;; buffer. As is conventional in org-mode, these are lines starting
|
||||
;; with `#+'. Lines starting with #+R: specify options in the
|
||||
;; standard org style (option:value) and are used to specify certain
|
||||
;; off-the-shelf transformations and plots of the table data. The
|
||||
;; #+R: line is also used to specify the data to be analysed
|
||||
;; (either an org table or a csv file), and to restrict the analysis
|
||||
;; to certain columns etc. In lines starting #+RR: you can supply
|
||||
;; literal R code, giving you full control over what you do with the
|
||||
;; table. With point in the first #+R line, M-x org-R-apply
|
||||
;; makes happen whatever has been specified in those lines.
|
||||
|
||||
;; The documentation is currently the Worg tutorial:
|
||||
;;
|
||||
;; http://orgmode.org/worg/org-tutorials/org-R/org-R.php
|
||||
;;
|
||||
;; changelog:
|
||||
;; 2009-04-05 two bug fixes in org-R-eval contributed by David Moffat
|
||||
;; 2009-05-15 added lwd argument to matplot because it doesn't respect global par settings
|
||||
;; 2009-05-15 uncommented set-buffer to transit buffer in org-eval (why was it commented?)
|
||||
|
||||
(defconst org-R-skeleton-funcall-1-arg
|
||||
"%s(x[%s]%s)"
|
||||
"Skeleton of a call to an R function.
|
||||
E.g. barplot(x[,3:5], names.arg=rownames(x))")
|
||||
|
||||
(defconst org-R-skeleton-funcall-2-args
|
||||
"%s(x[,%s], x[,%s]%s)"
|
||||
"Skeleton of a call to an R function which can take x and y
|
||||
args.")
|
||||
|
||||
(defconst org-R-write-org-table-def
|
||||
"write.org.table <- function (x, write.rownames = TRUE)
|
||||
{
|
||||
if(!is.null(dim(x)) && length(dim(x)) > 2)
|
||||
stop(\"Object must be 1- or 2-dimensional\") ;
|
||||
if(is.vector(x) || is.table(x) || is.factor(x) || is.array(x))
|
||||
x <- as.matrix(x) ;
|
||||
if(!(is.matrix(x) || inherits(x, c('matrix', 'data.frame')))) {
|
||||
invisible() ;
|
||||
print(x) ;
|
||||
stop(\"Object not recognised as 1- or 2-dimensional\") ;
|
||||
} ;
|
||||
if(is.null(colnames(x)))
|
||||
colnames(x) <- rep('', ncol(x)) ;
|
||||
if(write.rownames)
|
||||
x <- cbind(rownames(x), x) ;
|
||||
cat('|', paste(colnames(x), collapse = ' | '), '|\\n') ;
|
||||
cat('|', paste(rep('----', ncol(x)), collapse = '+'), '|\\n', sep = '') ;
|
||||
invisible(apply(x, 1, function(row) cat('|', paste(row, collapse = ' | '), '|\\n'))) ;
|
||||
}"
|
||||
"Definition of R function to write org table representation of R objects.
|
||||
To see a more human-readable version of this, look at the code,
|
||||
or type dput(write.org.table) RET at the R (inferior-ess-mode
|
||||
buffer) prompt.")
|
||||
|
||||
(defun org-R-apply-maybe ()
|
||||
(if (save-excursion
|
||||
(beginning-of-line 1)
|
||||
(looking-at "#\\+RR?:"))
|
||||
(progn (call-interactively 'org-R-apply)
|
||||
t) ;; to signal that we took action
|
||||
nil)) ;; to signal that we did not
|
||||
|
||||
(add-hook 'org-ctrl-c-ctrl-c-hook 'org-R-apply-maybe)
|
||||
|
||||
|
||||
(defun org-R-apply ()
|
||||
"Construct and evaluate an R function call.
|
||||
Construct an R function corresponding to the #+R: and #+RR:
|
||||
lines. R must be currently running in an inferior-ess-mode
|
||||
buffer. The function evaluates any user-supplied R code in the
|
||||
#+RR: line before the off-the-shelf actions specified in the #+R:
|
||||
line. The user-supplied R code can operate on a variable called x
|
||||
that is the org table represented as a data frame in R. Text
|
||||
output from the R process may be inserted into the org buffer, as
|
||||
an org table where appropriate."
|
||||
(interactive)
|
||||
(require 'ess)
|
||||
(save-excursion
|
||||
(beginning-of-line)
|
||||
(unless (looking-at "#\\+RR?:") (error "Point must be in a #+R or #+RR line"))
|
||||
(while (looking-at "#\\+RR?:") (forward-line -1))
|
||||
(forward-line)
|
||||
;; For the rest of the code in this file we are based at the
|
||||
;; beginning of the first #+R line
|
||||
|
||||
;; FIXME: if point is at the beginning of the #+RR? lines when
|
||||
;; this function is called, then tabular output gets inserted,
|
||||
;; leaving point up at the top of the tabular output.
|
||||
|
||||
(let* ((options (org-R-get-options))
|
||||
(code (org-R-construct-code options))
|
||||
(infile (plist-get options :infile))
|
||||
(ext (if infile (file-name-extension infile)))
|
||||
csv-file)
|
||||
|
||||
(if (string-equal ext "csv")
|
||||
(setq csv-file infile)
|
||||
(setq csv-file
|
||||
(org-R-export-to-csv
|
||||
(make-temp-file "org-R-tmp" nil ".csv") options)))
|
||||
|
||||
(org-R-eval code csv-file options)
|
||||
|
||||
(delete-other-windows) ;; FIXME
|
||||
(if (plist-get options :showcode) (org-R-showcode code)))))
|
||||
|
||||
(defun org-R-apply-throughout-subtree ()
|
||||
"Call org-R-apply in every org-R block in current subtree."
|
||||
;; This currently relies on re-search-forward leaving point after
|
||||
;; the #+RR?: If point were at the beginning of the line, then
|
||||
;; tabular input would get inserted leaving point above the #+RR?:,
|
||||
;; and this would loop infinitely. Same for org-R-apply-to-buffer.
|
||||
(interactive)
|
||||
(save-excursion
|
||||
(org-back-to-heading)
|
||||
(while (re-search-forward
|
||||
"^#\\+RR?:"
|
||||
(save-excursion (org-end-of-subtree)) t)
|
||||
(org-R-apply)
|
||||
(forward-line)
|
||||
(while (looking-at "#\\+RR?")
|
||||
(forward-line)))))
|
||||
|
||||
(defun org-R-apply-throughout-buffer ()
|
||||
"Call org-R-apply in every org-R block in the buffer."
|
||||
(interactive)
|
||||
(save-excursion
|
||||
(goto-char (point-min))
|
||||
(while (re-search-forward "^#\\+RR?:" nil t)
|
||||
(org-R-apply)
|
||||
(forward-line)
|
||||
(while (looking-at "#\\+RR?")
|
||||
(forward-line)))))
|
||||
|
||||
(defun org-R-construct-code (options)
|
||||
"Construct the R function that implements the requested
|
||||
behaviour.
|
||||
The body of this function derives from two sources:
|
||||
|
||||
1. Explicit R code which is read from lines starting with
|
||||
#+RR: by org-R-get-user-code, and
|
||||
|
||||
2. Off-the-shelf code corresponding to options specified in the
|
||||
#+R: line. This code is constructed by
|
||||
org-R-off-the-shelf-code."
|
||||
(let ((user-code (org-R-get-user-code))
|
||||
(action (plist-get options :action)))
|
||||
|
||||
(if (or (eq action 'tabulate) (eq action 'transpose))
|
||||
(setq options (plist-put options :output-to-buffer t)))
|
||||
(format "function(x){%sx}"
|
||||
(concat
|
||||
(when user-code (concat user-code ";"))
|
||||
(when action (concat (org-R-off-the-shelf-code options) ";"))))))
|
||||
|
||||
(defun org-R-get-user-code (&optional R)
|
||||
"Read user-supplied R code from #+RR: lines."
|
||||
(let ((case-fold-search t))
|
||||
(save-excursion
|
||||
(while (looking-at "^#\\+\\(RR?:\\) *\\(.*\\)")
|
||||
(if (string= "RR:" (match-string 1))
|
||||
(setq R (concat R (when R ";") (match-string 2))))
|
||||
(forward-line))))
|
||||
R)
|
||||
|
||||
(defun org-R-off-the-shelf-code (options)
|
||||
"Return R code implementing the actions requested in the
|
||||
#+R: lines."
|
||||
|
||||
;; This is a somewhat long function as it deals with several
|
||||
;; different cases, corresponding to all the off-the-shelf actions
|
||||
;; that have been implemented.
|
||||
|
||||
(let* ((action (plist-get options :action))
|
||||
(cols (plist-get options :columns))
|
||||
(ncols (org-R-number-of-columns cols))
|
||||
(nxcols (nth 0 ncols))
|
||||
(nycols (nth 1 ncols))
|
||||
(cols-R (org-R-make-index-vectors cols))
|
||||
(xcols-R (nth 0 cols-R))
|
||||
(ycols-R (nth 1 cols-R))
|
||||
seq args largs extra-code title colour matrix-index)
|
||||
|
||||
;; I want this to affect options outside this function. Will it
|
||||
;; necessarily do so? (not if plist-put adds to head of the
|
||||
;; plist?)
|
||||
(setq options (plist-put options :nxcols nxcols))
|
||||
|
||||
(cond ((eq action 'points)
|
||||
(setq action 'plot)
|
||||
(setq options (plist-put options :lines nil)))
|
||||
((eq action 'lines)
|
||||
(setq action 'plot)
|
||||
(setq options (plist-put options :lines t))))
|
||||
|
||||
(if (and (setq title (plist-get options :title)) (symbolp title))
|
||||
(setq title symbol-name title))
|
||||
|
||||
(setq args (plist-put args :main (concat "\"" title "\"")))
|
||||
|
||||
(if (setq colour (or (plist-get options :colour)
|
||||
(plist-get options :color)
|
||||
(plist-get options :col)))
|
||||
(setq args
|
||||
(plist-put args :col
|
||||
(concat "\"" (if (symbolp colour) (symbol-name colour) colour) "\""))))
|
||||
|
||||
(setq largs
|
||||
(if (setq legend (plist-get options :legend))
|
||||
(plist-put largs :x
|
||||
(concat "\"" (if (symbolp legend) (symbol-name legend) legend) "\""))
|
||||
(plist-put largs :x "\"topright\"")))
|
||||
|
||||
(cond
|
||||
((null ycols-R)
|
||||
;; single set of columns; implicit x values
|
||||
(if (null xcols-R)
|
||||
(setq xcols-R "" matrix-index "")
|
||||
(setq matrix-index (concat "," xcols-R)))
|
||||
(cond
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'barplot)
|
||||
(if (eq nxcols 1)
|
||||
(progn
|
||||
(setq args (plist-put args :names.arg "rownames(x)"))
|
||||
(setq args (org-R-set-user-supplied-args args (plist-get options :args)))
|
||||
(format org-R-skeleton-funcall-1-arg
|
||||
"barplot" xcols-R
|
||||
(concat ", " (org-R-plist-to-R-args args))))
|
||||
|
||||
(setq args (plist-put args :names.arg "colnames(x)"))
|
||||
(setq args (plist-put args :col "seq(nrow(x))"))
|
||||
(setq args (plist-put args :beside "TRUE"))
|
||||
|
||||
(setq largs (plist-put largs :bty "\"n\""))
|
||||
;; (setq largs (plist-put largs :lwd 10))
|
||||
(setq largs (plist-put largs :col "seq(nrow(x))"))
|
||||
(setq largs (plist-put largs :legend "rownames(x)"))
|
||||
|
||||
(setq args (org-R-set-user-supplied-args args (plist-get options :args)))
|
||||
|
||||
(concat (format org-R-skeleton-funcall-1-arg
|
||||
"barplot(as.matrix" matrix-index
|
||||
(concat "), " (org-R-plist-to-R-args args)))
|
||||
"; legend(" (org-R-plist-to-R-args largs) ")")))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'density)
|
||||
(if (and nxcols (> nxcols 1))
|
||||
(error "Multiple columns not implemented for action:%s" action))
|
||||
|
||||
(setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
|
||||
(setq args (org-R-set-user-supplied-args args (plist-get options :args)))
|
||||
|
||||
(format org-R-skeleton-funcall-1-arg
|
||||
"plot(density" matrix-index
|
||||
(concat "), " (org-R-plist-to-R-args args))))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'hist)
|
||||
(if (and nxcols (> nxcols 1))
|
||||
(error "Multiple columns not implemented for action:%s" action))
|
||||
(setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
|
||||
(setq args (org-R-set-user-supplied-args args (plist-get options :args)))
|
||||
(setq args (concat ", " (org-R-plist-to-R-args args)))
|
||||
(format org-R-skeleton-funcall-1-arg "hist" matrix-index args))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'image)
|
||||
(format org-R-skeleton-funcall-1-arg "image(as.matrix" matrix-index ")"))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'plot)
|
||||
(setq R-fun (if (eq nxcols 1) "plot" "matplot"))
|
||||
(setq seq (concat "seq_along("xcols-R")"))
|
||||
|
||||
(setq args (plist-put args :type (if (plist-get options :lines) "\"l\"" "\"p\"")))
|
||||
(setq args (plist-put args :ylab (concat "colnames(x)["xcols-R"]")))
|
||||
(if (string-equal R-fun "matplot")
|
||||
(setq args (plist-put args :lwd "par(\"lwd\")")))
|
||||
(setq args (concat ", " (org-R-plist-to-R-args args)))
|
||||
|
||||
(concat
|
||||
(format org-R-skeleton-funcall-1-arg R-fun matrix-index args)
|
||||
extra-code))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'tabulate)
|
||||
(concat
|
||||
(if (plist-get options :sort)
|
||||
(format org-R-skeleton-funcall-1-arg
|
||||
"x <- sort(table" xcols-R "), decreasing=TRUE")
|
||||
(format org-R-skeleton-funcall-1-arg "x <- table" matrix-index ""))
|
||||
(if (eq nxcols 1) "; x <- data.frame(value=names(x), count=x[])")))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'transpose)
|
||||
(format org-R-skeleton-funcall-1-arg "x <- t" matrix-index ""))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
;; Don't recognise action: option, try applying it as the name of an R function.
|
||||
|
||||
(t (format org-R-skeleton-funcall-1-arg
|
||||
(concat "x <- " (symbol-name action)) matrix-index ""))))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
(ycols-R
|
||||
;; x and y columns specified
|
||||
(cond
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
((eq action 'plot)
|
||||
(unless (eq nxcols 1) (error "Multiple x-columns not implemented for action:plot"))
|
||||
(setq R-fun (if (and (eq nxcols 1) (eq nycols 1)) "plot" "matplot"))
|
||||
|
||||
(setq args
|
||||
(plist-put
|
||||
args :ylab
|
||||
(concat "if(length("ycols-R") == 1) colnames(x)["ycols-R"] else ''")))
|
||||
(setq args (plist-put args :xlab (concat "colnames(x)["xcols-R"]")))
|
||||
(if (string-equal R-fun "matplot") ;; matplot doesn't respect par()$lwd
|
||||
(setq args (plist-put args :lwd "par(\"lwd\")")))
|
||||
(setq args (plist-put args :type (if (plist-get options :lines) "\"l\"" "\"p\"")))
|
||||
|
||||
(setq args (concat ", " (org-R-plist-to-R-args args)))
|
||||
(setq seq (concat "seq_along("ycols-R")"))
|
||||
|
||||
(setq largs (plist-put largs :col seq))
|
||||
(setq largs (plist-put largs :lty seq))
|
||||
(setq largs (plist-put largs :bty "\"n\""))
|
||||
(setq largs (plist-put largs :legend (concat "colnames(x)["ycols-R"]")))
|
||||
|
||||
(setq extra-code
|
||||
(concat "; "
|
||||
"if(length("ycols-R") > 1) "
|
||||
"legend(" (org-R-plist-to-R-args largs) ")"))
|
||||
|
||||
(concat
|
||||
(format org-R-skeleton-funcall-2-args R-fun xcols-R ycols-R args)
|
||||
extra-code))
|
||||
|
||||
;;----------------------------------------------------------------------
|
||||
|
||||
(t (error "action:%s requires a single set of columns" (symbol-name action))))))))
|
||||
|
||||
(defun org-R-set-user-supplied-args (args user-args)
|
||||
"Set user-supplied values in arguments plist."
|
||||
(while (setq prop (pop user-args))
|
||||
(setq args (plist-put args prop (pop user-args))))
|
||||
args)
|
||||
|
||||
(defun org-R-plist-to-R-args (plist)
|
||||
"Convert a plist into a string of R arguments."
|
||||
(let (arg-string arg)
|
||||
(while (setq arg (pop plist))
|
||||
(string-match ":\\(\.*\\)" (symbol-name arg))
|
||||
(setq arg (match-string 1 (symbol-name arg)))
|
||||
(setq arg-string
|
||||
(concat
|
||||
(if arg-string (concat arg-string ", "))
|
||||
(format "%s=%s" arg (pop plist)))))
|
||||
arg-string))
|
||||
|
||||
(defun org-R-alist-to-R-args (alist)
|
||||
"Convert an alist of (argument . val) pairs into a string of R arguments.
|
||||
The alist is something like
|
||||
'((arg1 . 1)
|
||||
(arg2 . a))
|
||||
This isn't used, but it seems much nicer than
|
||||
my plist equivalent. Is there a better way to write the plist
|
||||
version?
|
||||
"
|
||||
(mapconcat
|
||||
'identity
|
||||
(mapcar (lambda(pair) (format "%s = %s" (car pair) (cdr pair))) alist)
|
||||
", "))
|
||||
|
||||
(defun org-R-make-index-vectors (cols)
|
||||
"Construct R indexing vectors as strings from lisp form.
|
||||
|
||||
COLS is the lisp form given by the `columns:' option. It may
|
||||
take the following forms:
|
||||
|
||||
1. integer atom - the number of the column
|
||||
2. symbol/string atom - the name of the column
|
||||
3. list of length 1 - same as 1 or 2 above
|
||||
4. list of length > 1 - specification of multiple columns as 1 or 2 above, unless it is
|
||||
5. list of 2 lists - each list specifies (possibly multiple) columns
|
||||
|
||||
In cases 1-4 this function returns a list of length 1, containing
|
||||
the R index vector as a string. In case 5 this function returns a
|
||||
list of two such index vectors.
|
||||
|
||||
In cases 1 - 4, when a bivariate plot is requested such as by
|
||||
`action:lines', the x values are implicit, i.e
|
||||
1,2,...,number-of-rows.
|
||||
|
||||
In case 4, an attempt is made to do something sensible with the
|
||||
multiple columns, e.g. for `action:lines' they will be plotted
|
||||
together on the same graph against the implicit x values, and for
|
||||
`action:barplot' the bars corresponding to a single row will be
|
||||
stacked on top of each other, or placed side by side, depending
|
||||
on the value of the `beside' option.
|
||||
|
||||
For `action:tabulate', if 2 columns are selected, a
|
||||
two-dimensional table is created. If more than 2, then the
|
||||
appropriately dimensioned table is computed and inserted using
|
||||
the standard text representation of multi-dimensional arrays used
|
||||
by R (as org does not currently have tables of dimension > 2).
|
||||
|
||||
The straightforward case of case 5 is that both lists are of
|
||||
length 1. For `action:plot' and `action:lines' these specify the
|
||||
y and x coordinates of the points to be plotted or joined by
|
||||
lines.
|
||||
|
||||
The intention is that `org-R-apply' does something
|
||||
corresponding to what would happen if you did the following in R:
|
||||
|
||||
fun(x=tab[,xcols], y=tab[,ycols])
|
||||
|
||||
where fun is the R function implementing the desired
|
||||
action (plotting/computation), tab is the org table, xcols are
|
||||
the columns specified in cases 1-4 above, and ycols are the
|
||||
second set of columns which might have been specified under case
|
||||
5 above. For relevant R documentation see the help page
|
||||
associated with the function xy.coords, e.g. by typing ?xy.coords
|
||||
at the R prompt.
|
||||
|
||||
The following won't work with case 5: `tabulate'
|
||||
"
|
||||
(defun org-R-make-index-vector (cols)
|
||||
"Return the R indexing vector (as a string) corresponding to
|
||||
the lisp form COLS. In this function, COLS is a either a list of
|
||||
atoms, or an atom, i.e. in the form of cases 1-4"
|
||||
(when cols
|
||||
(let (to-stringf)
|
||||
(unless (listp cols) (setq cols (list cols)))
|
||||
(setq to-stringf
|
||||
(cond ((car (mapcar 'symbolp cols))
|
||||
(lambda (symbol) (concat "\"" (symbol-name symbol) "\"")))
|
||||
((car (mapcar 'integerp cols))
|
||||
'int-to-string)
|
||||
((car (mapcar 'stringp cols))
|
||||
(lambda (string) (concat "\"" string "\"")))
|
||||
(t (error "Column selection should be symbol, integer or string: %S" cols))))
|
||||
(concat (when (> (length cols) 1) "c(")
|
||||
(mapconcat to-stringf cols ",")
|
||||
(when (> (length cols) 1) ")")))))
|
||||
|
||||
(if (and (listp cols) (listp (car cols)))
|
||||
(mapcar 'org-R-make-index-vector cols) ;; case 5
|
||||
(list (org-R-make-index-vector cols)))) ;; other cases
|
||||
|
||||
(defun org-R-number-of-columns (cols)
|
||||
(defun f (c) (if (listp c) (length c) 1))
|
||||
(if (and (listp cols) (listp (car cols)))
|
||||
(mapcar 'f cols)
|
||||
(list (f cols))))
|
||||
|
||||
|
||||
(defun org-R-eval (R-function csv-file options)
|
||||
"Apply an R function to tabular data and receive output as an org table.
|
||||
|
||||
R-FUNCTION is a string; it may be simply the name of an
|
||||
appropriate R function (e.g. \"summary\", \"plot\"), or a
|
||||
user-defined anonymous function of the form
|
||||
\"(function(data.frame) {...})\". It will receive as its first
|
||||
argument the org table as an R 'data frame' -- a table-like
|
||||
structure which can have columns containing different types of
|
||||
data -- numeric, character etc.
|
||||
|
||||
The R function may produce graphical and/or text output. If it
|
||||
produces text output, and the replace:t is specified, and if
|
||||
there is a table immediately above the #+R lines, then it is
|
||||
replaced by the text output. Otherwise the text output is
|
||||
inserted above the #+R lines.
|
||||
"
|
||||
(let ((transit-buffer "org-R-transit")
|
||||
(infile (plist-get options :infile))
|
||||
(output-file (plist-get options :outfile))
|
||||
(title (plist-get options :title))
|
||||
output-format graphics-output-file width height)
|
||||
|
||||
(unless (not output-file)
|
||||
;; We are writing output to file. Determine file format and
|
||||
;; location, and open graphics device if necessary.
|
||||
(if (string-match
|
||||
"\\(.*\.\\)?\\(org\\|png\\|jpg\\|jpeg\\|pdf\\|ps\\|bmp\\|tiff\\)$"
|
||||
output-file)
|
||||
(setq output-format (match-string 2 output-file))
|
||||
(error "Did not recognise file name suffix %s as available output format"
|
||||
(match-string 2 output-file)))
|
||||
(unless (match-string 1 output-file)
|
||||
;; only suffix provided: store in org-attach dir
|
||||
(require 'org-attach)
|
||||
(let ((temporary-file-directory (org-attach-dir t)))
|
||||
(setq output-file
|
||||
(make-temp-file
|
||||
"org-R-output-" nil (concat "." output-format)))))
|
||||
;;; MdQ bug fix.
|
||||
;;; If a filename is given, make sure it's absolute,
|
||||
;;; as ess-execute needs that later.
|
||||
(if (match-string 1 output-file)
|
||||
(setq output-file (expand-file-name output-file)) )
|
||||
|
||||
(if (eq output-format "jpg") (setq output-format "jpeg"))
|
||||
(setq graphics-output-file (not (string-equal output-format "org")))
|
||||
(if graphics-output-file ;; open the graphics device
|
||||
(ess-execute
|
||||
(concat output-format "(file=\"" output-file "\""
|
||||
(if (setq width (plist-get options :width))
|
||||
(format ", width=%d" width))
|
||||
(if (setq height (plist-get options :height))
|
||||
(format ", height=%d" height)) ")"))))
|
||||
|
||||
;; Apply R code to table (which is now stored as a csv file)
|
||||
;; does it matter whether this uses ess-command or ess-execute?
|
||||
|
||||
;; First evaluate function definition for R -> org table conversion
|
||||
;;; MdQ bug fix.
|
||||
;;; The following save-excursion has been brought up to here
|
||||
;;; so that the two ess-execute commands are now within it.
|
||||
;;; This is because they have the side effect of changing current
|
||||
;;; buffer to the transit-buffer, which causes error of deleting
|
||||
;;; the wrong table there, instead of in the org buffer.
|
||||
(save-excursion
|
||||
(ess-execute (replace-regexp-in-string "\n" " " org-R-write-org-table-def)
|
||||
nil transit-buffer)
|
||||
|
||||
;; FIXME: why not eval the function def together with the function call
|
||||
;; as in the commented out line below (it didn't work for some reason)
|
||||
(ess-execute
|
||||
(concat
|
||||
;; (replace-regexp-in-string "\n" " " org-R-write-org-table-def) ";"
|
||||
(org-R-make-expr R-function csv-file options)) nil transit-buffer)
|
||||
|
||||
(set-buffer (concat "*" transit-buffer "*"))
|
||||
(unless (or (looking-at "$")
|
||||
(string-equal (buffer-substring-no-properties 1 2) "|"))
|
||||
(error "Error in R evaluation:\n%s" (buffer-string))))
|
||||
|
||||
|
||||
(if csv-file
|
||||
(unless (and infile
|
||||
(string-equal (file-name-extension infile) "csv"))
|
||||
(delete-file csv-file)))
|
||||
|
||||
(if graphics-output-file (ess-execute "dev.off()")) ;; Close graphics device
|
||||
|
||||
(unless (or graphics-output-file
|
||||
(not (plist-get options :output-to-buffer)))
|
||||
;; Send tabular output to a org buffer as new org
|
||||
;; table. Recall that we are currently at the beginning of the
|
||||
;; first #+R line
|
||||
(if (and output-file graphics-output-file)
|
||||
(error "output-to-buffer and graphics-output-file both t"))
|
||||
|
||||
(save-excursion
|
||||
(if output-file
|
||||
(progn (set-buffer (find-file-noselect output-file))
|
||||
(delete-region (point-min) (point-max)))
|
||||
(if (plist-get options :replace)
|
||||
(progn ;; kill a table iff in one or one ends on the previous line
|
||||
(delete-region (org-table-begin) (org-table-end))
|
||||
(save-excursion
|
||||
(forward-line -1)
|
||||
(if (looking-at "#\\+TBLNAME")
|
||||
(delete-region (point) (1+ (point-at-eol))))))))
|
||||
(if title (insert "#+TBLNAME:" title "\n"))
|
||||
(insert-buffer-substring (concat "*" transit-buffer "*"))
|
||||
(org-table-align)
|
||||
(if output-file (save-buffer))))
|
||||
|
||||
;; We might be linking to graphical output, or to org output in
|
||||
;; another file. Either way, point is still at the beginning of
|
||||
;; the first #+R line.
|
||||
(unless (not output-file)
|
||||
(save-excursion
|
||||
(forward-line -1)
|
||||
(if (looking-at "\\[\\[file:")
|
||||
(delete-region (point) (1+ (point-at-eol)))))
|
||||
(insert (org-make-link-string
|
||||
(concat "file:" output-file)
|
||||
(unless (plist-get options :inline)
|
||||
(or title (concat output-format " output")))) "\n"))
|
||||
|
||||
(kill-buffer (concat "*" transit-buffer "*"))))
|
||||
|
||||
|
||||
(defun org-R-export-to-csv (csv-file options)
|
||||
"Find and export org table to csv.
|
||||
|
||||
If the intable: option has not been supplied, then the table must
|
||||
end on the line immediately above the #+R lines. Otherwise,
|
||||
the remote table referenced by the intable: option is found using
|
||||
org-R-find-table. If options:infile has been set then this is the
|
||||
org file containing the table. See the docstring of
|
||||
org-R-find-table for details."
|
||||
(let ((tbl-name-or-id (plist-get options :intable))
|
||||
(org-file (plist-get options :infile)) tbl-marker)
|
||||
|
||||
(if (and org-file
|
||||
(not (string-equal (file-name-extension org-file) "org")))
|
||||
(error "File %s extension is not .csv so should be .org"))
|
||||
|
||||
(save-excursion
|
||||
(if tbl-name-or-id
|
||||
;; a remote table has been specified -- move into it
|
||||
(progn
|
||||
(if org-file (set-buffer (find-file-noselect org-file)))
|
||||
(setq tbl-marker (org-R-find-table tbl-name-or-id 'marker))
|
||||
(set-buffer (marker-buffer tbl-marker))
|
||||
(goto-char (marker-position tbl-marker)))
|
||||
(forward-line -1)) ;; move into table above
|
||||
(if (looking-at "[ \t]*|")
|
||||
(progn (org-table-export csv-file "orgtbl-to-csv") csv-file)
|
||||
nil))))
|
||||
|
||||
(defun org-R-find-table (name-or-id &optional markerp)
|
||||
"Return location of a table.
|
||||
|
||||
NAME-OR-ID may be the name of a
|
||||
table in the current file as set by a \"#+TBLNAME:\" directive.
|
||||
The first table following this line will then be used.
|
||||
Alternatively, it may be an ID referring to any entry, perhaps in
|
||||
a different file. In this case, the first table in that entry
|
||||
will be referenced. The location is returned as a marker pointing
|
||||
to the beginning of the first line of the table.
|
||||
|
||||
This is taken from the first part of org-table-get-remote-range
|
||||
in org-table.el.
|
||||
"
|
||||
(cond
|
||||
((symbolp name-or-id) (setq name-or-id (symbol-name name-or-id)))
|
||||
((numberp name-or-id) (setq name-or-id (number-to-string name-or-id))))
|
||||
(save-match-data
|
||||
(let ((id-loc nil) (case-fold-search t) buffer loc)
|
||||
(save-excursion
|
||||
(save-restriction
|
||||
(widen)
|
||||
(save-excursion
|
||||
(goto-char (point-min))
|
||||
(if (re-search-forward
|
||||
(concat "^#\\+TBLNAME:[ \t]*" (regexp-quote name-or-id) "[ \t]*$")
|
||||
nil t)
|
||||
;; OK, we've found a matching table name in this buffer.
|
||||
(setq buffer (current-buffer) loc (match-beginning 0))
|
||||
;; It's not a table name in this buffer. It must be an entry id.
|
||||
;; obtain a marker pointing to it.
|
||||
(setq id-loc (org-id-find name-or-id 'marker)
|
||||
buffer (marker-buffer id-loc)
|
||||
loc (marker-position id-loc))
|
||||
(move-marker id-loc nil))) ;; disable the marker
|
||||
;; (switch-to-buffer buffer)
|
||||
(set-buffer buffer)
|
||||
;; OK, so now we're in the right buffer, and loc is either
|
||||
;; the beginning of the #+TBLNAME line, or the location of the entry
|
||||
;; either way we need to search forward to get to the beginning of the table
|
||||
(save-excursion
|
||||
(save-restriction
|
||||
(widen)
|
||||
(goto-char loc)
|
||||
(forward-char 1)
|
||||
;; The following regexp search finds the beginning of
|
||||
;; the next table in this entry. If it gets to the next
|
||||
;; entry before the next table, then it signals failure.
|
||||
(unless (and (re-search-forward "^\\(\\*+ \\)\\|[ \t]*|" nil t)
|
||||
(not (match-beginning 1)))
|
||||
(error "Cannot find a table at NAME or ID %s" name-or-id))
|
||||
(if markerp
|
||||
(move-marker (make-marker) (point-at-bol) (current-buffer))
|
||||
(error "Option to return cons cell not implemented.
|
||||
It should return (file-name . position) to be
|
||||
consistent with functions in org-id.el")))))))))
|
||||
|
||||
(defun org-R-make-expr (R-function csv-file options)
|
||||
"Construct R code to read data, analyse it and write output."
|
||||
|
||||
(let ((rownames (plist-get options :rownames))
|
||||
(colnames (plist-get options :colnames))
|
||||
(action (plist-get options :action))
|
||||
(replace (plist-get options :replace)))
|
||||
|
||||
(if (and csv-file (symbolp csv-file))
|
||||
(setq csv-file (symbol-name csv-file)))
|
||||
|
||||
(format "write.org.table((%s)(%s), write.rownames=%s)"
|
||||
R-function
|
||||
(if csv-file
|
||||
(format
|
||||
"read.csv(\"%s\", header=%s, row.names=%s)"
|
||||
csv-file
|
||||
|
||||
;; Do we treat first row as colnames? Yes by default
|
||||
;; FIXME: should really check for hline
|
||||
(if colnames "TRUE" "FALSE")
|
||||
|
||||
;; Do we use a column as rownames? Not unless rownames: is specified
|
||||
(if rownames "1" "NULL"))
|
||||
"NULL")
|
||||
|
||||
;; Do we write rownames into org table?
|
||||
(cond ((eq action 'tabulate)
|
||||
(if (eq (plist-get options :nxcols) 1) "FALSE" "TRUE"))
|
||||
((eq action 'transpose) (if colnames "TRUE" "FALSE"))
|
||||
(rownames "TRUE")
|
||||
(t "TRUE")))))
|
||||
|
||||
(defun org-R-get-options ()
|
||||
"Parse the #+R: lines and return the options and values as a p-list."
|
||||
(let ((opts '(
|
||||
(:infile . "infile")
|
||||
(:intable . "intable")
|
||||
(:rownames . "rownames")
|
||||
(:colnames . "colnames")
|
||||
(:columns . "columns")
|
||||
|
||||
(:action . "action")
|
||||
(:args . "args")
|
||||
|
||||
(:outfile . "outfile")
|
||||
(:replace . "replace")
|
||||
(:title . "title")
|
||||
(:legend . "legend")
|
||||
(:colour . "colour")
|
||||
(:color . "color")
|
||||
(:col . "col")
|
||||
(:height . "height")
|
||||
(:width . "width")
|
||||
(:lines . "lines")
|
||||
(:sort . "sort")
|
||||
(:inline . "inline")
|
||||
|
||||
(:output-to-buffer . "output-to-buffer")
|
||||
|
||||
(:showcode . "showcode")))
|
||||
(regexp ":\\(\"[^\"]*\"\\|(([^)]*) *([^)]*))\\|([^)]*)\\|[^ \t\n\r;,.]*\\)")
|
||||
(case-fold-search t) p)
|
||||
|
||||
;; FIXME: set default options properly
|
||||
(setq p (plist-put p :output-to-buffer t)) ;; FIXME: hack: null options plist is bad news
|
||||
(setq p (plist-put p :replace t))
|
||||
(setq p (plist-put p :rownames nil))
|
||||
(setq p (plist-put p :colnames t))
|
||||
(setq p (plist-put p :inline nil))
|
||||
|
||||
(save-excursion
|
||||
(while (looking-at "^#\\+\\(RR?:+\\) *\\(.*\\)")
|
||||
(if (string= "R:" (match-string 1))
|
||||
(setq p (org-R-add-options-to-plist p (match-string 2) opts regexp)))
|
||||
(forward-line)))
|
||||
p))
|
||||
|
||||
(defun org-R-add-options-to-plist (p opt-string op regexp)
|
||||
"Parse a #+R: line and set values in the property list p.
|
||||
This function is adapted from similar functions in org-exp.el
|
||||
and org-plot.el. It might be a good idea to have a single
|
||||
function serving these three files' needs."
|
||||
;; Adapted from org-exp.el and org-plot.el
|
||||
(let (o)
|
||||
(when opt-string
|
||||
(while (setq o (pop op))
|
||||
(if (string-match
|
||||
(concat (regexp-quote (cdr o)) regexp)
|
||||
opt-string)
|
||||
(setq p (plist-put p (car o)
|
||||
(car (read-from-string
|
||||
(match-string 1 opt-string)))))))))
|
||||
p)
|
||||
|
||||
|
||||
(defun org-R-sanitise-options (options)
|
||||
(error "not used yet")
|
||||
(let (should-be-strings '(title legend colour color col csv)))
|
||||
)
|
||||
(defun org-R-showcode (R)
|
||||
"Display R function constructed by org-R in a new R-mode
|
||||
buffer."
|
||||
(split-window-vertically)
|
||||
(switch-to-buffer "*org-table.R*")
|
||||
(kill-region (point-min) (point-max))
|
||||
(R-mode)
|
||||
(insert (replace-regexp-in-string
|
||||
";" "\n" (replace-regexp-in-string "\\([{}]\\)" "\n\\1\n" R)))
|
||||
;; (mark-whole-buffer)
|
||||
;; (indent-region)
|
||||
;; why doesn't that do what I hoped?
|
||||
)
|
||||
|
||||
(defun org-R-get-remote-range (name-or-id form)
|
||||
"Get a field value or a list of values in a range from table at ID.
|
||||
|
||||
This is a refactoring of Carsten's original version. I have
|
||||
extracted the first bit of his function and named it
|
||||
org-R-find-table (which would presumably be called something like
|
||||
org-table-find-table or org-id-find-table if this were accepted).
|
||||
|
||||
---
|
||||
|
||||
Get a field value or a list of values in a range from table at ID.
|
||||
|
||||
NAME-OR-ID may be the name of a table in the current file as set by
|
||||
a \"#+TBLNAME:\" directive. The first table following this line
|
||||
will then be used. Alternatively, it may be an ID referring to
|
||||
any entry, possibly in a different file. In this case, the first table
|
||||
in that entry will be referenced.
|
||||
FORM is a field or range descriptor like \"@2$3\" or or \"B3\" or
|
||||
\"@I$2..@II$2\". All the references must be absolute, not relative.
|
||||
|
||||
The return value is either a single string for a single field, or a
|
||||
list of the fields in the rectangle."
|
||||
|
||||
(let ((tbl-marker (org-R-find-table name-or-id 'marker))
|
||||
org-table-column-names org-table-column-name-regexp
|
||||
org-table-local-parameters org-table-named-field-locations
|
||||
org-table-current-line-types org-table-current-begin-line
|
||||
org-table-current-begin-pos org-table-dlines
|
||||
org-table-hlines org-table-last-alignment
|
||||
org-table-last-column-widths org-table-last-alignment
|
||||
org-table-last-column-widths tbeg)
|
||||
|
||||
(save-excursion
|
||||
(set-buffer (marker-buffer tbl-marker))
|
||||
(goto-char (marker-position tbl-marker))
|
||||
(org-table-get-specials)
|
||||
(setq form (org-table-formula-substitute-names form))
|
||||
(if (and (string-match org-table-range-regexp form)
|
||||
(> (length (match-string 0 form)) 1))
|
||||
(save-match-data
|
||||
(org-table-get-range (match-string 0 form) (point) 1))
|
||||
form))))
|
||||
|
||||
(provide 'org-R)
|
||||
|
|
@ -6,6 +6,12 @@
|
|||
* org-exp.el (org-export-format-source-code-or-example): Fix
|
||||
textarea tag.
|
||||
|
||||
2010-02-24 Bastien Guerry <bzg@altern.org>
|
||||
|
||||
* org-clock.el (org-clock-current-task): New variable to store
|
||||
last clocked in task.
|
||||
(org-clock-set-current, org-clock-delete-current): New functions.
|
||||
|
||||
2010-02-24 Carsten Dominik <carsten.dominik@gmail.com>
|
||||
|
||||
* org-remember.el (org-remember-apply-template): Extend comment.
|
||||
|
|
|
|||
|
|
@ -944,6 +944,7 @@ the clocking selection, associated with the letter `d'."
|
|||
(org-back-to-heading t)
|
||||
(or interrupting (move-marker org-clock-interrupted-task nil))
|
||||
(org-clock-history-push)
|
||||
(org-clock-set-current)
|
||||
(cond ((functionp org-clock-in-switch-to-state)
|
||||
(looking-at org-complex-heading-regexp)
|
||||
(let ((newstate (funcall org-clock-in-switch-to-state
|
||||
|
|
@ -1042,6 +1043,15 @@ the clocking selection, associated with the letter `d'."
|
|||
(message "Clock starts at %s - %s" ts msg-extra)
|
||||
(run-hooks 'org-clock-in-hook)))))))
|
||||
|
||||
(defvar org-clock-current-task nil
|
||||
"Task currently clocked in.")
|
||||
(defun org-clock-set-current ()
|
||||
"Set `org-clock-current-task' to the task currently clocked in."
|
||||
(setq org-clock-current-task (org-get-heading)))
|
||||
(defun org-clock-delete-current ()
|
||||
"Reset `org-clock-current-task' to nil."
|
||||
(setq org-clock-current-task nil))
|
||||
|
||||
(defun org-clock-mark-default-task ()
|
||||
"Mark current task as default task."
|
||||
(interactive)
|
||||
|
|
@ -1237,7 +1247,8 @@ If there is no running clock, throw an error, unless FAIL-QUIETLY is set."
|
|||
(force-mode-line-update)
|
||||
(message (concat "Clock stopped at %s after HH:MM = " org-time-clocksum-format "%s") te h m
|
||||
(if remove " => LINE REMOVED" ""))
|
||||
(run-hooks 'org-clock-out-hook))))))
|
||||
(run-hooks 'org-clock-out-hook)
|
||||
(org-clock-delete-current))))))
|
||||
|
||||
(defun org-clock-cancel ()
|
||||
"Cancel the running clock be removing the start timestamp."
|
||||
|
|
|
|||
Loading…
Reference in New Issue