diff options
Diffstat (limited to 'lisp/org/ob-R.el')
| -rw-r--r-- | lisp/org/ob-R.el | 91 |
1 files changed, 67 insertions, 24 deletions
diff --git a/lisp/org/ob-R.el b/lisp/org/ob-R.el index 49a8a85cf6d..3dedb393654 100644 --- a/lisp/org/ob-R.el +++ b/lisp/org/ob-R.el @@ -39,24 +39,48 @@ (declare-function ess-make-buffer-current "ext:ess-inf" ()) (declare-function ess-eval-buffer "ext:ess-inf" (vis)) (declare-function org-number-sequence "org-compat" (from &optional to inc)) - -(defconst org-babel-header-arg-names:R - '(width height bg units pointsize antialias quality compression - res type family title fonts version paper encoding - pagecentre colormodel useDingbats horizontal) +(declare-function org-remove-if-not "org" (predicate seq)) + +(defconst org-babel-header-args:R + '((width . :any) + (height . :any) + (bg . :any) + (units . :any) + (pointsize . :any) + (antialias . :any) + (quality . :any) + (compression . :any) + (res . :any) + (type . :any) + (family . :any) + (title . :any) + (fonts . :any) + (version . :any) + (paper . :any) + (encoding . :any) + (pagecentre . :any) + (colormodel . :any) + (useDingbats . :any) + (horizontal . :any) + (results . ((file list vector table scalar verbatim) + (raw org html latex code pp wrap) + (replace silent append prepend) + (output value graphics)))) "R-specific header arguments.") (defvar org-babel-default-header-args:R '()) -(defvar org-babel-R-command "R --slave --no-save" - "Name of command to use for executing R code.") +(defcustom org-babel-R-command "R --slave --no-save" + "Name of command to use for executing R code." + :group 'org-babel + :version "24.1" + :type 'string) -(defvar ess-local-process-name) +(defvar ess-local-process-name) ; dynamically scoped (defun org-babel-edit-prep:R (info) (let ((session (cdr (assoc :session (nth 2 info))))) (when (and session (string-match "^\\*\\(.+?\\)\\*$" session)) - (save-match-data (org-babel-R-initiate-session session nil)) - (setq ess-local-process-name (match-string 1 session))))) + (save-match-data (org-babel-R-initiate-session session nil))))) (defun org-babel-expand-body:R (body params &optional graphics-file) "Expand BODY according to PARAMS, return the expanded body." @@ -120,7 +144,7 @@ This function is called by `org-babel-execute-src-block'." ;; helper functions (defun org-babel-variable-assignments:R (params) - "Return list of R statements assigning the block's variables" + "Return list of R statements assigning the block's variables." (let ((vars (mapcar #'cdr (org-babel-get-header params :var)))) (mapcar (lambda (pair) @@ -146,25 +170,45 @@ This function is called by `org-babel-execute-src-block'." (defun org-babel-R-assign-elisp (name value colnames-p rownames-p) "Construct R code assigning the elisp VALUE to a variable named NAME." (if (listp value) - (let ((transition-file (org-babel-temp-file "R-import-"))) + (let ((max (apply #'max (mapcar #'length (org-remove-if-not + #'sequencep value)))) + (min (apply #'min (mapcar #'length (org-remove-if-not + #'sequencep value)))) + (transition-file (org-babel-temp-file "R-import-"))) ;; ensure VALUE has an orgtbl structure (depth of at least 2) (unless (listp (car value)) (setq value (list value))) (with-temp-file transition-file - (insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field))) - (insert "\n")) - (format "%s <- read.table(\"%s\", header=%s, row.names=%s, sep=\"\\t\", as.is=TRUE)" - name (org-babel-process-file-name transition-file 'noquote) - (if (or (eq (nth 1 value) 'hline) colnames-p) "TRUE" "FALSE") - (if rownames-p "1" "NULL"))) + (insert + (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)) + "\n")) + (let ((file (org-babel-process-file-name transition-file 'noquote)) + (header (if (or (eq (nth 1 value) 'hline) colnames-p) + "TRUE" "FALSE")) + (row-names (if rownames-p "1" "NULL"))) + (if (= max min) + (format "%s <- read.table(\"%s\", + header=%s, + row.names=%s, + sep=\"\\t\", + as.is=TRUE)" name file header row-names) + (format "%s <- read.table(\"%s\", + header=%s, + row.names=%s, + sep=\"\\t\", + as.is=TRUE, + fill=TRUE, + col.names = paste(\"V\", seq_len(%d), sep =\"\"))" + name file header row-names max)))) (format "%s <- %s" name (org-babel-R-quote-tsv-field value)))) -(defvar ess-ask-for-ess-directory nil) +(defvar ess-ask-for-ess-directory) ; dynamically scoped (defun org-babel-R-initiate-session (session params) "If there is not a current R process then create one." (unless (string= session "none") (let ((session (or session "*R*")) (ess-ask-for-ess-directory - (and ess-ask-for-ess-directory (not (cdr (assoc :dir params)))))) + (and (and (boundp 'ess-ask-for-ess-directory) ess-ask-for-ess-directory) + (not (cdr (assoc :dir params)))))) (if (org-babel-comint-buffer-livep session) session (save-window-excursion @@ -177,7 +221,6 @@ This function is called by `org-babel-execute-src-block'." (buffer-name)))) (current-buffer)))))) -(defvar ess-local-process-name nil) (defun org-babel-R-associate-session (session) "Associate R code buffer with an R session. Make SESSION be the inferior ESS process associated with the @@ -219,7 +262,7 @@ current code buffer." (setq args (mapconcat (lambda (pair) (if (member (car pair) allowed-args) - (format ",%s=%s" + (format ",%s=%S" (substring (symbol-name (car pair)) 1) (cdr pair)) "")) params "")) @@ -245,7 +288,7 @@ current code buffer." (body result-type result-params column-names-p row-names-p) "Evaluate BODY in external R process. If RESULT-TYPE equals 'output then return standard output as a -string. If RESULT-TYPE equals 'value then return the value of the +string. If RESULT-TYPE equals 'value then return the value of the last statement in BODY, as elisp." (case result-type (value @@ -272,7 +315,7 @@ last statement in BODY, as elisp." (session body result-type result-params column-names-p row-names-p) "Evaluate BODY in SESSION. If RESULT-TYPE equals 'output then return standard output as a -string. If RESULT-TYPE equals 'value then return the value of the +string. If RESULT-TYPE equals 'value then return the value of the last statement in BODY, as elisp." (case result-type (value |