Adding support for column names (header line) when using R.
Unlike the other languages, it's central to R to be able to index columns of a data frame d, either by d[,"columnname"] of d$columnname. With this change, if colnames are present in the *input* from org-babel, the corresponding R variable is *always* constructed with the colnames. In addition, with the :colnames header arg, the *output* to elisp/org buffer contains the colnames separated from the rest of the table by 'hline. This behaviour is not default because other languages may expect a simple table without the 'hline.
This commit is contained in:
Dan Davison
parent
2aa721a7dc
commit
062bc09d84
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@ -45,8 +45,9 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
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(lambda (pair)
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(org-babel-R-assign-elisp (car pair) (cdr pair)))
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vars "\n") "\n" body "\n"))
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(session (org-babel-R-initiate-session session)))
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(org-babel-R-evaluate session full-body result-type))))
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(session (org-babel-R-initiate-session session))
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(colnames (cdr (assoc :colnames params))))
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(org-babel-R-evaluate session full-body result-type colnames))))
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(defun org-babel-prep-session:R (session params)
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"Prepare SESSION according to the header arguments specified in PARAMS."
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@ -71,8 +72,8 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
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(with-temp-file transition-file
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(insert (orgtbl-to-tsv value '(:fmt org-babel-R-quote-tsv-field)))
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(insert "\n"))
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(format "%s <- read.table(\"%s\", header=FALSE, sep=\"\\t\", as.is=TRUE)"
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name transition-file))
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(format "%s <- read.table(\"%s\", header=%s, sep=\"\\t\", as.is=TRUE)"
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name transition-file (if (eq (second value) 'hline) "TRUE" "FALSE")))
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(format "%s <- %s" name (org-babel-R-quote-tsv-field value))))
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(defun org-babel-R-initiate-session (session)
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@ -89,9 +90,9 @@ called by `org-babel-execute-src-block' via multiple-value-bind."
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(defvar org-babel-R-eoe-indicator "'org_babel_R_eoe'")
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(defvar org-babel-R-eoe-output "[1] \"org_babel_R_eoe\"")
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(defvar org-babel-R-wrapper-method "main <- function ()\n{\n%s\n}
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write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)")
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write.table(main(), file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)")
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(defun org-babel-R-evaluate (buffer body result-type)
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(defun org-babel-R-evaluate (buffer body result-type colnames)
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"Pass BODY to the R process in BUFFER. If RESULT-TYPE equals
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'output then return a list of the outputs of the statements in
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BODY, if RESULT-TYPE equals 'value then return the value of the
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@ -108,15 +109,15 @@ last statement in BODY, as elisp."
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(with-temp-buffer (insert-file-contents out-tmp-file) (buffer-string)))
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(value
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(with-temp-file in-tmp-file
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(insert (format org-babel-R-wrapper-method body out-tmp-file)))
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(insert (format org-babel-R-wrapper-method
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body out-tmp-file (if colnames "TRUE" "FALSE"))))
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(shell-command (format "R --no-save < '%s'" in-tmp-file))
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(org-babel-import-elisp-from-file out-tmp-file))))
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(org-babel-import-elisp-from-file out-tmp-file colnames))))
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;; comint session evaluation
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(org-babel-comint-in-buffer buffer
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(let* ((tmp-file (make-temp-file "org-babel-R"))
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(last-value-eval
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(format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=FALSE, quote=FALSE)"
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tmp-file))
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(format "write.table(.Last.value, file=\"%s\", sep=\"\\t\", na=\"nil\",row.names=FALSE, col.names=%s, quote=FALSE)" tmp-file (if colnames "TRUE" "FALSE")))
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(full-body (mapconcat #'org-babel-chomp
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(list body last-value-eval org-babel-R-eoe-indicator) "\n"))
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(raw (org-babel-comint-with-output buffer org-babel-R-eoe-output nil
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@ -138,7 +139,7 @@ last statement in BODY, as elisp."
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(mapcar #'org-babel-trim raw))))))
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(case result-type
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(output (org-babel-trim (mapconcat #'identity results "\n")))
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(value (org-babel-import-elisp-from-file tmp-file)))))))
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(value (org-babel-import-elisp-from-file tmp-file colnames)))))))
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(provide 'org-babel-R)
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@ -566,7 +566,7 @@ This is taken almost directly from `org-read-prop'."
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(if (string-match "^[[:digit:]]*\\.?[[:digit:]]*$" string)
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(string-to-number string)))
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(defun org-babel-import-elisp-from-file (file-name)
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(defun org-babel-import-elisp-from-file (file-name &optional colnames)
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"Read the results located at FILE-NAME into an elisp table. If
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the table is trivial, then return it as a scalar."
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(let (result)
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@ -578,14 +578,16 @@ the table is trivial, then return it as a scalar."
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(setq result (mapcar (lambda (row)
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(mapcar #'org-babel-string-read row))
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(org-table-to-lisp))))
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(error nil))
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(error nil)))
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(if colnames
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(setq result (cons (car result) (cons 'hline (cdr result))))
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(if (null (cdr result)) ;; if result is trivial vector, then scalarize it
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(if (consp (car result))
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(if (null (cdr (car result)))
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(caar result)
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result)
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(car result))
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result))))
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(if (consp (car result))
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(if (null (cdr (car result)))
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(caar result)
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result)
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(car result))
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result))))
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(defun org-babel-string-read (cell)
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"Strip nested \"s from around strings in exported R values."
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