mp.texi

\input texinfo

@set NAME mp
@set VERSION 0.2
@set UPDATED January  3, 2022
@setfilename @value{NAME}
@finalout
@c %**start of header
@settitle @value{NAME} @value{VERSION}
@syncodeindex pg cp 
@c %**end of header 

@copying
This manual is for @value{NAME}, version @value{VERSION}
Copyright @copyright{} 2018-2022 - Chris Dardis
@quotation


@end quotation
@end copying

@dircategory R, Sweave, knitr, latex, noweb, org
@direntry
* @value{NAME} (@value{NAME}).Make pdfs.
* install-info: (@value{NAME})
Invoking install-info.
...
...
@end direntry
@titlepage
@title @value{NAME}
@subtitle for version @value{VERSION}, @value{UPDATED}
@author C. Dardis <christopherdardis@@gmail.com>
@page
@vskip 0pt plus 1filll
@insertcopying
@end titlepage

@contents

@ifnottex
@node Top
@top @value{NAME}
This manual is for @value{NAME} version @value{VERSION}, @value{UPDATED}
@end ifnottex

@menu
* Preamble::
* defgroup::
* defun::
* defcustom::
* defvar::
* defconst::
* defvar-local::
* Other symbolic expressions::
* Index::

@end menu

@node Preamble
@chapter Preamble
@cindex Preamble

@code{lexical binding} is @code{t}.@*
@strong{Copyright}: 2018-2022 - Chris Dardis @*
@strong{Author}: C. Dardis <christopherdardis@@gmail.com> @*
@strong{URL}: @uref{http://github.com/dardisco/mp} @*
@strong{Version}: 0.2 @*
@strong{Keywords}: R, Sweave, knitr, latex, noweb, org @*
@strong{Package-Requires}: ((ess) (org) (org-element) (tex)) @*
@strong{Commentary}: Makes a pdf from the materials in the `default-directory'
 (or will search up the directory tree for
  the appropriate file type).

 These may include .R, .tex, .Rnw, .org, .Rmd and .bib files.
 Support is provided for indexes, glossaries and table of contents.
 
 Installation:

 This package can be installed using

 (package-install-from-file "/path/to/mp.el")

 Or place the folliwng in your init.el file

 (add-to-list 'load-path "~/path/to/directory")
 (require 'mp)

 Usage:

 To generate a .pdf file use the `mp-mp' command.
     `M-x mp-mp RET'
 This command can be called within the directory used to produce
 the .pdf. It can also be called from one of the files used to
 produce the .pdf. In the latter case, the file will first be
 saved if there are any changes.

 There are a number of addition commands which you may wish
 to call independently:
 - `mp-customize-common' - Set common customizable variables
 - `mp-example' - Generate an example .pdf
 - `mp-custom-example' - Call both commands above, in sequence
 - `mp-customize-all' - Set all customizable variables
 - `mp-customize-skeleton-string' - Set all customizable
     skeleton strings for the package (strings used by skeletons)
 - `mp-clean' - Delete files in which have `mp-clean-extensions'
 - `mp-tex-new' - Make a new .tex file
 - `mp-chunk-new' - Insert a new chunk

 You may wish to define a shortcut for calling
  `mp-chunk-new'.
 `f8' is suggested as there are 8 characters in these prefixes.
 That is, "## ---- " is 8 characters in length.
 The prefixes follow the conventions established by knitr.
 If so, also place something like this in your init.el file:
 ```
 (global-set-key
  (kbd "<f8>")
  (lambda ()
    (interactive)
    (mp-chunk-new)))
 ```   
  
 or, for example, if using ESS and `bind-key':
 
 ```
 (bind-key
  (kbd "<f8>")
  (lambda ()
    (interactive)
    (mp-chunk-new))
  ess-mode-map)
 ```

 Details:

 The purpose of `mp-mp' is to move from an R file or an
 intermediary file (.Rnw, .Rmd, .org, .bib, .tex) to a .pdf
 with a single command. This is done by selecting an entwiner
 (named after the conventions of 'weaving' with Sweave or 'knitting'
 with knitr; the default is knitr).

 The simplest way to see this in action is to call `mp-example'.
 This will generate a new directory in the current
 `default-directory' for the files used to generate the final .pdf.
 This may also be a good way to start a new project.
 
 Assuming we start with an .R file, `mp-mp' generates an
 intermediary file, as appropriate, then uses the entwiner to
 generate a .tex file from the intermediary, then uses latexmk
 to generate a .pdf from the .tex file, which is then displayed.
 
 Alternatively, we may start with an intermediary e.g. a .Rnw file.
 A .R file is generated from this before making the .tex file,
 as above.
 We may also start directly with a .tex file. In this case,
 no intermediary or .R file is created; we proceed directly
 to .pdf. Similarly in the case of a .bib file. Note that
 a .pdf will *not* be generated from a .bib file without a
 corresponding .tex file in the same directory.

 Output from the various steps in compiling the .pdf appears in
 the '*make-pdf*' buffer, which (by default) will by used to
 display the .pdf once complete. Alternative .pdf viewers are
 supported. If another viewer is used, this output will remain
 visible in the '*make-pdf*' buffer.

 Note that all code in the .R file is run via Rscript, to ensure
 there are no errors with this and in case this modifies another
 file in the workign directory e.g. a .bib file as is the case
 when running `mp-example'.

 Updating R code chunks:

 An advantage of `mp-mp' is that code can be updated in either
 the .R file or the intermediary. Whichever has been more recently
 modified will be used as the source and the other as the destination.
 This allows for editing of code in either the .R file or the
 intermediary.

 That is, when `mp-mp' is called from an .R file or an intermediary,
 a corresponding .R or intermediary will be created or
 updated, as appropriate.

 This starts by reading the chunks from the working file.
 This is the buffer currently open (if it has unsaved changes).
 This will be an .R file, or an entwiner file (.Rnw, .Rmd, .org).

 For example, when working with an .R file, if there is *no*
 entwiner file (.Rnw, .org) with the same file name prefix in
 the same directory, this file will be *created* before generating
 a .tex file from this entwiner.

 If an entwiner file *already exists*, this is *deleted*.
 A new entwiner file is created after reading the code chunks
 in the .R file.

 As above, note that changes to a .tex file do *not* update the
 corresponding intermediary. Thus free text (outside .R code chunks)
 should generally be updated in the intermediary file, unless
 no further changes to the .R code is planned.

 Customization:

 To avoid errors, it is best to set the following customizable
 variables once at the start of a project:
 - `mp-entwiner'
 - `mp-latex'
 - `mp-bib'

 If these are changed mid-way through, it may be necessary to
 first delete the intermediary, .tex and .pdf files before starting
 afresh from the .R file in the directory.

 This package contains a variety of defaults which may be modified.
 For example, the preamble for a LaTeX document, which varies
 depending on whether LaTeX or XeTeX/LuaLaTeX is used to generate
 the .pdf.

 Multiple plots per chunk:

 All of the entwiners will save graphical output in one or more
 separate files, then include some these in the final .pdf.

 Only knitr supports multiple plots per chunk by default.

 By default, both Sweave and Org will include only the first
 plot/graph/figure produced.
 They both use the TeX command `\includegraphics' for this.
 The function `mp-tex-to-pdf' will replace instances of this
 command with `\includepdf[pages=-, width=0.9\linewidth]',
 so that all plots/pages are included.

 An alternative is to save each plot as a separate
 file and then output the TeX command to include all of them.

 An example of a code block using this approach follows below.
 ```
 for(i in 1:4){
 file=paste("f", i, ".eps", sep="")
 postscript(file=file, paper="special", width=8, height=8)
 plot(rnorm(100)+i)
 dev.off()
 cat(" \\includegraphics{", file, "}\n", sep="")
 }
 ```
 In Sweave, we would wrap the code above in:
 ```
 <<plots, results=tex, strip.white=false>>=
 **code**
 @@
 ```
 In Org, we would wrap the code above in:
 ```
 #+NAME: plots2
 #+begin_src R :session *org-R-session* :exports both :results output :results verbatim :results latex
 **code**
 #+end_src
 ```

 History/goals:

 This package was initially developed in 2012 to help to
 speed up the process of scientific writing. At that time,
 there was no easy was to tranistion quickly from a .R file to
 a .pdf and knitr was relatively new and was not being used
 routinely e.g. to generate package documentation.

 The range of options has expanded dramatically since.
 In particulary, .Rmd appears to have become the most popular
 choice for performing this type of work.

 Dependencies:

 The following should be installed and on your path:
 - R, including the packages knitr and rmarkdown
 - LaTeX
 - pandoc
 - bash commands: locate, grep

 The following emacs packages are also recommended:
 - org
 - ess
 - tex, bibtex
 - doc-view
 - markdown-mode
 - polymode, poly-R

 This is designed for Emacs on debian linux with bash.
 It has not been evaluated on other systems.

 For developers:
 
 Function-local/temporary variables are named using
 as name1 e.g. `v1', `buffer1'. @*
@node defgroup
@chapter defgroup
@cindex defgroup

Documentation for @code{defgroup}: @*
Declare SYMBOL as a customization group containing MEMBERS.
SYMBOL does not need to be quoted.

Third argument DOC is the group documentation.  This should be a short
description of the group, beginning with a capital and ending with
a period.  Words other than the first should not be capitalized, if they
are not usually written so.

MEMBERS should be an alist of the form ((NAME WIDGET)...) where
NAME is a symbol and WIDGET is a widget for editing that symbol.
Useful widgets are ‘custom-variable’ for editing variables,
‘custom-face’ for editing faces, and ‘custom-group’ for editing groups.

The remaining arguments should have the form

   [KEYWORD VALUE]...

For a list of valid keywords, see the common keywords listed in
‘defcustom’.

See Info node ‘(elisp) Customization’ in the Emacs Lisp manual
for more information.@*

A table of all @code{defgroup}s follows:


@ftable @code
@item mp

@item mp-common

@end ftable

Details of each @code{defgroup} follow below: @*

@cindex mp
@unnumberedsec mp
@deffn defgroup mp

@table @var
@item group-documentation
Make Pdf.
This is a series of variables and functions to simplity
 the process of pdf creation using R, LaTeX and
 the intermediaries (entwiners)
 knitr, Sweave and Org (`org-mode').
@item custom-prefix
mp-
@item custom-version
0.2
@item custom-group
((mp custom-group) (mp-common custom-group) (mp-example-file-name custom-variable) (mp-timeout custom-variable) (mp-file-name-extensions custom-variable) (mp-function-sequence custom-variable) (mp-entwiner custom-variable) (mp-R-chunks-new-R custom-variable) (mp-chunk-name-prefix-R custom-variable) (mp-chunk-format-prefix-R custom-variable) (mp-chunk-content-suffix-R custom-variable) (mp-chunk-heading-level custom-variable) (mp-R-chunk-defaults-R-pkg custom-variable) (mp-chunk-format-default-R-pkg custom-variable) (mp-chunk-format-default-sweave custom-variable) (mp-chunk-format-default-org custom-variable) (mp-bib custom-variable) (mp-preamble-bib custom-variable) (mp-preamble-biblatex custom-variable) (mp-doc-class-tex custom-variable) (mp-preamble-knitr custom-variable) (mp-preamble-sweave custom-variable) (mp-preamble-org custom-variable) (mp-latex custom-variable) (mp-latex-font custom-variable) (mp-xetex-font custom-variable) (mp-preamble-tex custom-variable) (mp-add-preamble-tex-extra custom-variable) (mp-preamble-tex-extra custom-variable) (mp-tex-beginning custom-variable) (mp-bibtex-style custom-variable) (mp-tex-end custom-variable) (mp-sentinel-sleep custom-variable) (mp-latex-options custom-variable) (mp-latexmkrc custom-variable) (mp-bib-default custom-variable) (mp-pdf-viewer custom-variable) (mp-clean custom-variable) (mp-clean-extensions custom-variable) (mp-clean-others custom-variable) (mp-skeleton-string custom-group))
@end table
@end deffn 

@cindex mp-common
@unnumberedsec mp-common
@deffn defgroup mp-common

@table @var
@item group-documentation
Options that the user is most likely to wish to change.
This group is part of `mp'.
@item custom-group
((mp-timeout custom-variable) (mp-entwiner custom-variable) (mp-chunk-heading-level custom-variable) (mp-bib custom-variable) (mp-clean custom-variable))
@end table
@end deffn 

@node defun
@chapter defun
@cindex defun

Documentation for @code{defun}: @*
Define NAME as a function.
The definition is (lambda ARGLIST [DOCSTRING] BODY...).
See also the function ‘interactive’.
DECL is a declaration, optional, of the form (declare DECLS...) where
DECLS is a list of elements of the form (PROP . VALUES).  These are
interpreted according to ‘defun-declarations-alist’.
The return value is undefined.

(fn NAME ARGLIST &optional DOCSTRING DECL &rest BODY)@*

A table of all @code{defun}s follows:


@ftable @code
@item mp-custom-example
Run ‘mp-customize-common’ then ‘mp-example’.
@item mp-example
Generate and run an example.
@item mp-initialize
Set the following ‘defvar’s to their staring value:
@item mp-set-mp-dd
Set the value of ‘mp-dd’.
@item mp-valid-file-name-p
Return t is STRING is a valid filename.
@item mp-run
Run the appropriate list of functions from ‘mp-function-sequence’.
@item mp-R-entwiner
Convert R to an entwiner or vice versa.
@item mp-bib
Check if there is a file named ‘mp-fnb’.bib in ‘mp-dd’.
@item mp-R-new
Make an .R file.
@item mp-chunk-update-format
Update the format of a CHUNK, per the value of ‘mp-entwiner’.
@item mp-R-chunk-R-citations
Return a string which is R code that writes a bibliography file.
@item mp-file-display
Displays FILE-NAME.
@item mp-file-open
Open FILE-NAME in a buffer; set buffer to appropriate mode.
@item mp-chunk-set-adfixes
Set the prefixes and suffixes for chunks.
@item mp-set-mode
Set the appropriate mode for a file.
@end ftable

Details of each @code{defun} follow below: @*

@cindex mp-custom-example
@unnumberedsec mp-custom-example
@defun mp-custom-example 
Command ? @emph{yes} @*
Arguments: @emph{none} @*
Documentation: Run ‘mp-customize-common’ then ‘mp-example’.

@smallformat @verbatim 
((interactive)
 (mp-customize-common)
 (mp-example))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-example
@unnumberedsec mp-example
@defun mp-example 
Command ? @emph{yes} @*
Arguments: @emph{none} @*
Documentation: Generate and run an example.
Calls ‘mp-mp’, in the subdirectory ‘mp-example-file-name’.

@smallformat @verbatim 
((interactive)
 (mp-set-mp-dd)
 (let
     ((d1
       (concat mp-dd mp-example-file-name "/")))
   (delete-directory d1 t)
   (mkdir d1 t)
   (cd d1)
   (setq mp-dd d1 mp-fnb mp-example-file-name mp-fne "R")
   (mp-initialize)
   (message
    (concat "mp-example ... running in "
	    (print mp-dd))))
 (mp-run mp-fne))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-initialize
@unnumberedsec mp-initialize
@defun mp-initialize 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Set the following ‘defvar’s to their staring value:
- ‘mp-df’
- ‘mp-fn’
- ‘mp-chunks’
Called by ‘mp-example’ and ‘mp-mp’.

@smallformat @verbatim 
((while
     (get-buffer-window "*make-pdf*")
   (delete-window
    (get-buffer-window "*make-pdf*")))
 (if
     (get-buffer "*make-pdf*")
     (progn
       (kill-buffer "*make-pdf*")))
 (balance-windows)
 (setq mp-df
       (sort
	(directory-files mp-dd nil
			 (mapconcat
			  #'(lambda
			      (x)
			      (concat "\\." x "$"))
			  mp-file-name-extensions "\\|")
			 t)
	#'file-newer-than-file-p)
       mp-fn
       (car mp-df)
       mp-chunks 'nil mp-exiting nil))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-set-mp-dd
@unnumberedsec mp-set-mp-dd
@defun mp-set-mp-dd 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Set the value of ‘mp-dd’.
If ‘mp-fnb’ is an empty string, also set this to the same
value as ‘mp-dd’.

@smallformat @verbatim 
((setq mp-dd
       (cond
	((buffer-file-name)
	 (file-name-directory buffer-file-name))
	((equal major-mode 'dired-mode)
	 dired-directory)
	(t
	 (shell-command-to-string "printf '%s' $HOME/")))
       default-directory mp-dd)
 (message
  (concat "mp-set-mp-dd ... mp-dd set to "
	  (print mp-dd)))
 (if
     (equalp "" mp-fnb)
     (progn
       (setq mp-fnb
	     (file-name-nondirectory
	      (directory-file-name mp-dd)))
       (message
	(concat "mp-set-mp-dd ... mp-fnb set to "
		(print mp-fnb))))))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-valid-file-name-p
@unnumberedsec mp-valid-file-name-p
@defun mp-valid-file-name-p 
Command ? @emph{yes} @*
Arguments: @var{STRING}  @*
Documentation: Return t is STRING is a valid filename.
Uses ‘file-name-invalid-regexp’, which depends on the ‘system-type’.
An example of an invalid filename is "\0".
See also the following for additional restrictions on Windows:
URL ‘https://docs.microsoft.com/en-us/windows/win32/fileio/naming-a-file’.

@smallformat @verbatim 
((interactive "FFilename: ")
 (not
  (string-match file-name-invalid-regexp STRING)))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-run
@unnumberedsec mp-run
@defun mp-run 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Run the appropriate list of functions from ‘mp-function-sequence’.
This is given by ‘mp-fne’.

@smallformat @verbatim 
((let
     ((seq1
       (catch '--cl-block-nil--
	 (let
	     ((--dolist-tail-- mp-function-sequence))
	   (while --dolist-tail--
	     (let
		 ((x
		   (car --dolist-tail--)))
	       (if
		   (string-match
		    (car x)
		    mp-fne)
		   (progn
		     (throw '--cl-block-nil--
			    (eval
			     (cdr x)))))
	       (setq --dolist-tail--
		     (cdr --dolist-tail--))))))))
   (message
    (concat "mp-run, with "
	    (car mp-entwiner)
	    " and "
	    (cdr mp-entwiner)
	    ", starting with ." mp-fne " file ..."))
   (let
       ((--dolist-tail-- seq1))
     (while --dolist-tail--
       (let
	   ((x
	     (car --dolist-tail--)))
	 (funcall x)
	 (setq --dolist-tail--
	       (cdr --dolist-tail--))))))
 (mp-exit "mp-run... done"))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-R-entwiner
@unnumberedsec mp-R-entwiner
@defun mp-R-entwiner 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Convert R to an entwiner or vice versa.
Calls ‘mp-chunks-read’ to get code chunks from the current file.
If this is an .R file and an ’entwiner’ file already exists,
 this is deleted and replaced.
 update the *least recently used* file
 i.e. the .R or the entwiner, using, as appropriate 
 ‘mp-update-entwiner-from-R’ or ‘mp-update-R-from-entwiner’.
If no such file exists, make one with ‘mp-entwiner-new’.

@smallformat @verbatim 
((let
     ((rf1
       (car
	(cl-member
	 (concat mp-fnb ".R")
	 mp-df :test #'equalp)))
      (ef1
       (car
	(cl-member
	 (concat mp-fnb "."
		 (car mp-entwiner))
	 mp-df :test #'equalp))))
   (message "mp-R-entwiner ...")
   (if
       (not rf1)
       (progn
	 (mp-R-new)
	 (if
	     (mp-empty-string-to-nil ef1)
	     nil
	   (mp-entwiner-new)))
     (if ef1
	 (if
	     (file-newer-than-file-p rf1 ef1)
	     (mp-update-entwiner-from-R)
	   (mp-update-R-from-entwiner))
       (progn
	 (mp-file-display
	  (concat mp-fnb ".R"))
	 (mp-chunks-read)
	 (mp-entwiner-new)))))
 (if mp-bib
     (progn
       (mp-bib)))
 (mp-shell-sentinel "mp-Rscript-run")
 (message "mp-R-entwiner ... done"))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-bib
@unnumberedsec mp-bib
@defun mp-bib 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Check if there is a file named ‘mp-fnb’.bib in ‘mp-dd’.
If not, make one by calling ‘mp-bib-skeleton’.
See also the variable ‘mp-bib’.

@smallformat @verbatim 
((if
     (directory-files mp-dd nil
		      (concat mp-fnb ".bib$"))
     nil
   (mp-file-display
    (concat mp-fnb ".bib"))
   (mp-bib-skeleton)
   (save-buffer)
   (kill-buffer)
   (delete-window)))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-R-new
@unnumberedsec mp-R-new
@defun mp-R-new 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Make an .R file.
If ‘mp-chunks’ is not an empty list, use these,
otherwise use ‘mp-R-chunks-new-R’.
Called by ‘mp-R-entwiner’ and ‘mp-update-R-from-entwiner’.

@smallformat @verbatim 
((if
     (equalp 'nil mp-chunks)
     (progn
       (if mp-bib
	   (progn
	     (setq mp-chunks
		   (cons
		    (list "R citations" ""
			  (mp-R-chunk-R-citations))
		    mp-chunks))))
       (let
	   ((--dolist-tail--
	     (reverse
	      (copy-tree mp-R-chunks-new-R))))
	 (while --dolist-tail--
	   (let
	       ((x
		 (car --dolist-tail--)))
	     (setq mp-chunks
		   (cons x mp-chunks))
	     (setq --dolist-tail--
		   (cdr --dolist-tail--)))))
       (if
	   (string-match "^R-pkg-"
			 (cdr mp-entwiner))
	   (progn
	     (setq mp-chunks
		   (cons
		    (copy-tree mp-R-chunk-defaults-R-pkg)
		    mp-chunks))))))
 (let
     ((--dolist-tail-- mp-chunks))
   (while --dolist-tail--
     (let
	 ((x
	   (car --dolist-tail--)))
       (mp-chunk-update-format x)
       (setq --dolist-tail--
	     (cdr --dolist-tail--)))))
 (setq mp-fne "R")
 (let
     ((fn1
       (concat mp-fnb ".R")))
   (if
       (get-buffer fn1)
       nil
     (mp-file-display fn1))
   (save-current-buffer
     (set-buffer fn1)
     (goto-char
      (point-min))
     (mapc #'mp-chunk-insert mp-chunks)
     (goto-char
      (point-max)))
   (save-buffer)
   (kill-buffer)
   (delete-window)))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-chunk-update-format
@unnumberedsec mp-chunk-update-format
@defun mp-chunk-update-format 
Command ? @emph{no} @*
Arguments: @var{CHUNK}  @*
Documentation: Update the format of a CHUNK, per the value of ‘mp-entwiner’.
The format is the second element of CHUNK, a string.

@smallformat @verbatim 
((if
     (equalp ""
	     (car
	      (cdr CHUNK)))
     (progn
       (setcar
	(cdr CHUNK)
	(mp-chunk-format)))))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-R-chunk-R-citations
@unnumberedsec mp-R-chunk-R-citations
@defun mp-R-chunk-R-citations 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Return a string which is R code that writes a bibliography file.
This file is named ’‘mp-fnb’.bib.’.
A citation appears therein for each loaded R package.
Adds a handle to each citation, if necessary.
This is added to ‘mp-chunks’ when ‘mp-bib’ is non-nil.
Called by ‘mp-R-new’.

@smallformat @verbatim 
((concat "print(.packages())\n## vector for citations\nvc1 <- unlist(sapply(X=rev(.packages()),\n                     FUN=function(x)\n                         utils::toBibtex(utils::citation(x))))\nvc1 <- vc1[!vc1=='']\n## names for citations\nn1 <- vc1[which(grepl(pattern='.year', x=vc1))]\nn1  <- paste0(\n    sub(pattern='\\\\.year$', replacement='', x=names(n1)),\n    regmatches(x=n1, m=regexpr(pattern='[0123456789]+', text=n1)))\n## group as list\nl1 <- vector(mode='list', length=length(n1))\nnames(l1) <- n1\nend1 <- which(grepl(pattern='\\\\}$', x=vc1))\n## remove trailing comma from last item in .bib entry, if necessary\nvc1[end1-1] <- sub(pattern=',$', replacement='', x=vc1[end1-1])\nend1 <- c(0, end1)\nfor (i in seq.int(length.out=length(l1)))\n    l1[[i]] <- unname(vc1[seq.int(from=(end1[i] + 1L), to=end1[i+1])])\nl1 <- l1[!duplicated(l1)]\n## add a handle, if necessary\nfor (i in seq.int(length.out=length(l1)))\n    if (grepl(pattern='\\\\{,$', x=l1[[i]][1]))\n        l1[[i]][1] <- sub(pattern=',$', \n                          replacement=paste0(names(l1[i]), ','),\n                          x=l1[[i]][1])\nif (!'mp-example.bib' %in% dir())\n    write(x='', file='" mp-dd mp-fnb ".bib')\nbib1 <- readLines('" mp-dd mp-fnb ".bib')\nfor (i in seq.int(length.out=length(l1)))\n    if (!(l1[[i]][1] %in% bib1))\n        write(x=l1[[i]], file='" mp-dd mp-fnb ".bib', append=TRUE)"))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-file-display
@unnumberedsec mp-file-display
@defun mp-file-display 
Command ? @emph{no} @*
Arguments: @var{FILE-NAME}  @*
Documentation: Displays FILE-NAME.
If the file is already open if a buffer, calls ‘pop-to-buffer’.
If not, calls ‘mp-file-open’.
Finally, calls ‘mp-set-mode’ and ‘mp-chunk-set-adfixes’.

@smallformat @verbatim 
((setq mp-fne
       (file-name-extension FILE-NAME))
 (let
     ((default-directory mp-dd)
      (bn1
       (car
	(member FILE-NAME
		(mapcar 'buffer-name
			(buffer-list))))))
   (if bn1
       (pop-to-buffer bn1)
     (mp-file-open FILE-NAME)))
 (mp-set-mode)
 (mp-chunk-set-adfixes))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-file-open
@unnumberedsec mp-file-open
@defun mp-file-open 
Command ? @emph{no} @*
Arguments: @var{FILE-NAME}  @*
Documentation: Open FILE-NAME in a buffer; set buffer to appropriate mode.
Return buffer.
This function is derived from a combination of the functions
 ‘find-file-noselect’ and ‘find-file-noselect-1’.
Called by ‘mp-file-display’.

@smallformat @verbatim 
((let*
     ((default-directory mp-dd)
      (truename1
       (abbreviate-file-name
	(file-truename FILE-NAME)))
      (buf1 nil))
   (if
       (featurep 'uniquify)
       (let
	   ((uniquify-managed
	     (progn
	       (make-local-variable 'uniquify-managed)
	       nil)))
	 (setq buf1
	       (create-file-buffer FILE-NAME)))
     (setq buf1
	   (create-file-buffer FILE-NAME)))
   (pop-to-buffer buf1 nil t)
   (set-buffer buf1)
   (set-buffer-multibyte t)
   (if
       (and
	(=
	 (buffer-size buf1)
	 0)
	(directory-files mp-dd nil
			 (concat "^" FILE-NAME "$")))
       (progn
	 (insert-file-contents-literally truename1 t)))
   (setq buffer-file-truename truename1 buffer-file-name
	 (expand-file-name buffer-file-truename)
	 buffer-file-number
	 (nthcdr 10
		 (file-attributes truename1)))))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-chunk-set-adfixes
@unnumberedsec mp-chunk-set-adfixes
@defun mp-chunk-set-adfixes 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Set the prefixes and suffixes for chunks.
These depend on the ‘file-name-extension’ of the curent buffer,
if applicable,  otherwise on ‘mp-fne’.
The following file-local variables are set:
 - ‘mp-chunk-heading-level-prefix’
 - ‘mp-chunk-heading-level-suffix’
 - ‘mp-chunk-name-prefix’
 - ‘mp-chunk-name-suffix’
 - ‘mp-chunk-format-prefix’
 - ‘mp-chunk-content-suffix’
Called by ‘mp-file-display’.

@smallformat @verbatim 
((let
     ((fe1
       (car
	(cl-member
	 (file-name-extension
	  (buffer-file-name))
	 '("R" "Rnw" "org" "Rmd")
	 :test #'equalp))))
   (if fe1 nil
     (setq fe1 mp-fne))
   (cond
    ((equalp "R" fe1)
     (setq mp-chunk-name-prefix mp-chunk-name-prefix-R mp-chunk-format-prefix mp-chunk-format-prefix-R mp-chunk-name-suffix "" mp-chunk-content-suffix mp-chunk-content-suffix-R))
    ((equalp "Rnw" fe1)
     (setq mp-chunk-heading-level-prefix
	   (elt mp-chunk-heading-level 0)
	   mp-chunk-heading-level-suffix "}" mp-chunk-name-prefix mp-chunk-name-prefix-Rnw mp-chunk-name-suffix mp-chunk-name-suffix-Rnw mp-chunk-format-prefix mp-chunk-format-prefix-Rnw mp-chunk-content-suffix mp-chunk-content-suffix-Rnw))
    ((equalp "org" fe1)
     (setq mp-chunk-heading-level-prefix
	   (elt mp-chunk-heading-level 1)
	   mp-chunk-heading-level-suffix "" mp-chunk-name-prefix mp-chunk-name-prefix-org mp-chunk-format-prefix mp-chunk-format-prefix-org mp-chunk-name-suffix "" mp-chunk-content-suffix mp-chunk-content-suffix-org))
    ((equalp "Rmd" fe1)
     (setq mp-chunk-heading-level-prefix
	   (elt mp-chunk-heading-level 2)
	   mp-chunk-heading-level-suffix "" mp-chunk-name-prefix mp-chunk-name-prefix-Rmd mp-chunk-name-suffix mp-chunk-name-suffix-Rmd mp-chunk-format-prefix mp-chunk-format-prefix-Rmd mp-chunk-content-suffix mp-chunk-content-suffix-Rmd)))
   (message
    (concat "mp-chunk-set-adfixes... set per for ." fe1 " file extension"))))
@end verbatim 
 @end smallformat 
@end defun 

@cindex mp-set-mode
@unnumberedsec mp-set-mode
@defun mp-set-mode 
Command ? @emph{no} @*
Arguments: @emph{none} @*
Documentation: Set the appropriate mode for a file.

@smallformat @verbatim 
((cond
  ((equalp "R" mp-fne)
   (R-mode))
  ((equalp "Rnw" mp-fne)
   (Rnw-mode))
  ((equalp "org" mp-fne)
   (org-mode))
  ((equalp "Rmd" mp-fne)
   (markdown-mode)
   (if poly-markdown+r-mode nil
     (poly-markdown+r-mode)))
  ((equalp "tex" mp-fne)
   (tex-mode))
  ((equalp "bib" mp-fne)
   (bibtex-mode))
  (t
   (fundamental-mode))))
@end verbatim 
 @end smallformat 
@end defun 

@node defcustom
@chapter defcustom
@cindex defcustom

Documentation for @code{defcustom}: @*
Declare SYMBOL as a customizable variable.
SYMBOL is the variable name; it should not be quoted.
STANDARD is an expression specifying the variable’s standard
value.  It should not be quoted.  It is evaluated once by
‘defcustom’, and the value is assigned to SYMBOL if the variable
is unbound.  The expression itself is also stored, so that
Customize can re-evaluate it later to get the standard value.
DOC is the variable documentation.

This macro uses ‘defvar’ as a subroutine, which also marks the
variable as "special", so that it is always dynamically bound
even when ‘lexical-binding’ is t.

The remaining arguments to ‘defcustom’ should have the form

   [KEYWORD VALUE]...

The following keywords are meaningful:

:type	VALUE should be a widget type for editing the symbol’s value.
	Every ‘defcustom’ should specify a value for this keyword.
:options VALUE should be a list of valid members of the widget type.
:initialize
	VALUE should be a function used to initialize the
	variable.  It takes two arguments, the symbol and value
	given in the ‘defcustom’ call.  The default is
	‘custom-initialize-reset’.
:set	VALUE should be a function to set the value of the symbol
	when using the Customize user interface.  It takes two arguments,
	the symbol to set and the value to give it.  The function should
	not modify its value argument destructively.  The default choice
	of function is ‘set-default’.
:get	VALUE should be a function to extract the value of symbol.
	The function takes one argument, a symbol, and should return
	the current value for that symbol.  The default choice of function
	is ‘default-value’.
:require
	VALUE should be a feature symbol.  If you save a value
	for this option, then when your init file loads the value,
	it does (require VALUE) first.
:set-after VARIABLES
	Specifies that SYMBOL should be set after the list of variables
        VARIABLES when both have been customized.
:risky	Set SYMBOL’s ‘risky-local-variable’ property to VALUE.
:safe	Set SYMBOL’s ‘safe-local-variable’ property to VALUE.
        See Info node ‘(elisp) File Local Variables’.

The following common keywords are also meaningful.

:group  VALUE should be a customization group.
        Add SYMBOL (or FACE with ‘defface’) to that group.
:link LINK-DATA
        Include an external link after the documentation string for this
        item.  This is a sentence containing an active field which
        references some other documentation.

        There are several alternatives you can use for LINK-DATA:

        (custom-manual INFO-NODE)
             Link to an Info node; INFO-NODE is a string which specifies
             the node name, as in "(emacs)Top".

        (info-link INFO-NODE)
             Like ‘custom-manual’ except that the link appears in the
             customization buffer with the Info node name.

        (url-link URL)
             Link to a web page; URL is a string which specifies the URL.

        (emacs-commentary-link LIBRARY)
             Link to the commentary section of LIBRARY.

        (emacs-library-link LIBRARY)
             Link to an Emacs Lisp LIBRARY file.

        (file-link FILE)
             Link to FILE.

        (function-link FUNCTION)
             Link to the documentation of FUNCTION.

        (variable-link VARIABLE)
             Link to the documentation of VARIABLE.

        (custom-group-link GROUP)
             Link to another customization GROUP.

        You can specify the text to use in the customization buffer by
        adding ‘:tag NAME’ after the first element of the LINK-DATA; for
        example, (info-link :tag "foo" "(emacs)Top") makes a link to the
        Emacs manual which appears in the buffer as ‘foo’.

        An item can have more than one external link; however, most items
        have none at all.
:version
        VALUE should be a string specifying that the variable was
        first introduced, or its default value was changed, in Emacs
        version VERSION.
:package-version
        VALUE should be a list with the form (PACKAGE . VERSION)
        specifying that the variable was first introduced, or its
        default value was changed, in PACKAGE version VERSION.  This
        keyword takes priority over :version.  For packages which
        are bundled with Emacs releases, the PACKAGE and VERSION
        must appear in the alist ‘customize-package-emacs-version-alist’.
        Since PACKAGE must be unique and the user might see it in an
        error message, a good choice is the official name of the
        package, such as MH-E or Gnus.
:tag LABEL
        Use LABEL, a string, instead of the item’s name, to label the item
        in customization menus and buffers.
:load FILE
        Load file FILE (a string) before displaying this customization
        item.  Loading is done with ‘load’, and only if the file is
        not already loaded.

If SYMBOL has a local binding, then this form affects the local
binding.  This is normally not what you want.  Thus, if you need
to load a file defining variables with this form, or with
‘defvar’ or ‘defconst’, you should always load that file
_outside_ any bindings for these variables.  (‘defvar’ and
‘defconst’ behave similarly in this respect.)

See Info node ‘(elisp) Customization’ in the Emacs Lisp manual
for more information.@*

A table of all @code{defcustom}s follows:


@ftable @code
@item mp-example-file-name
Name of directory and of ‘file-name-base’ to use for an example.
@item mp-timeout
Seconds to wait for user input when calling interactive functions.
@item mp-file-name-extensions
The ‘file-name-extension’s (as strings) with which ‘mp’ works.
@item mp-function-sequence
An alist where:
@item mp-entwiner
How to ’entwine’ the files in ‘mp-dd’.
@item mp-R-chunks-new-R
A ‘list’ of chunks for a new .R file.
@item mp-chunk-name-prefix-R
Prefix for the chunk name in an .R file.
@item mp-chunk-format-prefix-R
Prefix for the chunk format in an .R file.
@item mp-chunk-content-suffix-R
Suffix for the chunk content in an .R file.
@item mp-chunk-heading-level
Prefixes indicating the heading level for a chunk.
@item mp-R-chunk-defaults-R-pkg
Default setup options for ’knitr’.
@end ftable

Details of each @code{defcustom} follow below: @*

@cindex mp-example-file-name
@unnumberedsec mp-example-file-name
@defopt mp-example-file-name
@table @var
@item standard-value
((funcall (function (closure (t) nil mp-example))))
@item custom-type
(string)
@item safe-local-variable
mp-valid-file-name-p
@item custom-requests
nil
@item variable-documentation
Name of directory and of `file-name-base' to use for an example.
Used by `mp-example'.
Avoid using special characters in this string.
See also `mp-valid-file-name-p'.
@end table
@end defopt 

@cindex mp-timeout
@unnumberedsec mp-timeout
@defopt mp-timeout
@table @var
@item standard-value
((funcall (function (closure (t) nil 0.2))))
@item custom-type
(number)
@item custom-requests
nil
@item variable-documentation
Seconds to wait for user input when calling interactive functions.
A low value will not give the user time to respond to prompts.
In this case, the default values are used.
See the functions `with-timeout' and `y-or-n-p-with-timeout'.
Used by:
- `mp-find-file-name-interactive'
@end table
@end defopt 

@cindex mp-file-name-extensions
@unnumberedsec mp-file-name-extensions
@defopt mp-file-name-extensions
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote (R Rnw org Rmd md tex bib pdf))))))
@item custom-type
(repeat (string @code{:tag} extension))
@item custom-requests
nil
@item variable-documentation
The `file-name-extension's (as strings) with which `mp' works.
These age given as a list of strings.
They are not case sensitive (see `case-fold-search').
@end table
@end defopt 

@cindex mp-function-sequence
@unnumberedsec mp-function-sequence
@defopt mp-function-sequence
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote ((R cond ((equalp Rnw (car mp-entwiner)) (quote (mp-R-entwiner mp-Rnw-to-tex mp-tex-to-pdf mp-view-pdf))) ((equalp org (car mp-entwiner)) (quote (mp-R-entwiner mp-org-to-tex mp-tex-to-pdf mp-view-pdf))) ((equalp Rmd (car mp-entwiner)) (quote (mp-R-entwiner mp-Rmd-to-pdf mp-view-pdf)))) (Rnw quote (mp-R-entwiner mp-Rnw-to-tex mp-tex-to-pdf mp-view-pdf)) (org quote (mp-R-entwiner mp-org-to-tex mp-tex-to-pdf mp-view-pdf)) (Rmd quote (mp-R-entwiner mp-Rmd-to-pdf mp-view-pdf)) (tex\|bib quote (mp-tex-to-pdf mp-view-pdf)) (pdf quote (mp-view-pdf))))))))
@item custom-type
(alist @code{:key-type} (string @code{:format} 
 %t 
 %v @code{:tag}             file extension, a string) @code{:value-type} (sexp @code{:format} %t 
 %v @code{:tag}  sexp: a list, or function returning a list))
@item custom-requests
nil
@item variable-documentation
An alist where:
The key is the file name extension, a regular expression.
The value is list of functions to run.
Used by `mp-run' as the overall control flow.
@end table
@end defopt 

@cindex mp-entwiner
@unnumberedsec mp-entwiner
@defopt mp-entwiner
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote (Rnw . R-pkg-knitr))))))
@item custom-type
(radio (const @code{:doc} Rnw with knitr (the default) @code{:value} (Rnw . R-pkg-knitr)) (const @code{:doc} Rnw with Sweave @code{:value} (Rnw . Sweave)) (const @code{:doc} Org (uses .org file) @code{:value} (org . Org)) (const @code{:doc}  md with knitr @code{:value} (Rmd . R-pkg-rmarkdown)))
@item custom-requests
nil
@item variable-documentation
How to 'entwine' the files in `mp-dd'.
Given in the form of a cons, where:
- key-type   = `file-name-extension' (a string)
- value-type = method (a string)

The 'entwiner' is an intermediary/ bridging file, 
 which acts as a 'go-between' for .R and .tex files.

"R-pkg-knitr" and "Sweave" use an .Rnw file (see `Rnw-mode').
"Org" uses an .org file (see `org-mode')
See also info node `(org)LaTeX export'.
"R-pkg-rmarkdown" uses an .Rmd file (see `poly-markdown+r-mode')
 and an .md file (see `markdown-mode').
@end table
@end defopt 

@cindex mp-R-chunks-new-R
@unnumberedsec mp-R-chunks-new-R
@defopt mp-R-chunks-new-R
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote ((Hello world  print('Hello, World!')) (Plots (cond ((string-match R-pkg- (cdr mp-entwiner)) results='asis') ((equalp Sweave (cdr mp-entwiner)) results=verbatim, fig=TRUE, pdf=TRUE) ((equalp Org (cdr mp-entwiner)) @code{:session} *org-R-session* @code{:exports} both @code{:results} output @code{:results} graphics @code{:file} "p1.pdf")) ## The examples below are taken from ?graphics:@code{:plot}
require('stats') # for lowess, rpois, rnorm
plot(cars)
lines(lowess(cars))
plot(sin, -pi, 2*pi) # see ?plot.function
## Discrete Distribution Plot:
plot(table(rpois(100, 5)), type='h', col='red', lwd=10,
     main='rpois(100, lambda=5)')
## Simple quantiles/ECDF, see ecdf() {library(stats)} for a better one:
plot(x <- sort(rnorm(47)), type='s', main='plot(x, type=\'s\')')
points(x, cex=0.5, col='dark red')) (R session information (cond ((string-match R-pkg- (cdr mp-entwiner)) results='asis') ((equalp Sweave (cdr mp-entwiner)) results=tex) ((equalp Org (cdr mp-entwiner)) @code{:session} *org-R-session* @code{:exports} both @code{:results} output @code{:results} verbatim @code{:results} latex)) (if (equalp Rmd (car mp-entwiner)) utils:@code{:sessionInfo}() utils:@code{:toLatex}(utils:@code{:sessionInfo}())))))))))
@item custom-type
(alist @code{:key-type} (string @code{:format} 
 %t 
 %v @code{:tag}            Chunk name) @code{:value-type} (group (sexp @code{:format} %t 
 %v @code{:tag} Chunk format) (sexp @code{:format} %t 
 %v @code{:tag} Chunk content)))
@item custom-requests
nil
@item variable-documentation
A `list' of chunks for a new .R file.
Each element is a list with 3 elements.
- first element  = chunk name, a string
- second element = chunk format, a string or
   a symbolic expression which evaluates to a string
- third element  = chunk content, a string or
   a symbolic expression which evaluates to a string
The second and third elements may e.g. be conditional,
e.g. depending on the value of `mp-entwiner'.
Be sure to escape:
- double quotes i.e. ""
- single quotes within single quotes e.g. 'abc 'def' ghi'
When editing this with `customize', use
`electric-newline-and-maybe-indent' for carraige return.
@end table
@end defopt 

@cindex mp-chunk-name-prefix-R
@unnumberedsec mp-chunk-name-prefix-R
@defopt mp-chunk-name-prefix-R
@table @var
@item standard-value
((funcall (function (closure (t) nil ## ---- ))))
@item custom-type
(string)
@item custom-requests
nil
@item variable-documentation
Prefix for the chunk name in an .R file.
The default value follows the convention used by 'knitr'.
@end table
@end defopt 

@cindex mp-chunk-format-prefix-R
@unnumberedsec mp-chunk-format-prefix-R
@defopt mp-chunk-format-prefix-R
@table @var
@item standard-value
((funcall (function (closure (t) nil , ))))
@item custom-type
(string)
@item custom-requests
nil
@item variable-documentation
Prefix for the chunk format in an .R file.
The default value follows the convention used by 'knitr'.
@end table
@end defopt 

@cindex mp-chunk-content-suffix-R
@unnumberedsec mp-chunk-content-suffix-R
@defopt mp-chunk-content-suffix-R
@table @var
@item standard-value
((funcall (function (closure (t) nil 
))))
@item custom-type
(sexp)
@item custom-requests
nil
@item variable-documentation
Suffix for the chunk content in an .R file.
@end table
@end defopt 

@cindex mp-chunk-heading-level
@unnumberedsec mp-chunk-heading-level
@defopt mp-chunk-heading-level
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote (\section{ ***  ### ))))))
@item custom-type
(choice @code{:tag}  (list @code{:tag} level 1 = part (string @code{:tag} LaTeX @code{:value} \part{) (string @code{:tag} org @code{:value} * ) (string @code{:tag} Rnw @code{:value} # )) (list @code{:tag} level 2 = chapter
  [LaTeX - only for \documentclass{book} or {report}] (string @code{:tag} LaTeX @code{:value} \chapter{) (string @code{:tag} org @code{:value} ** ) (string @code{:tag} Rnw @code{:value} ## )) (list @code{:tag} level 3 = section (string @code{:tag} LaTeX @code{:value} \section{) (string @code{:tag} org @code{:value} *** ) (string @code{:tag} Rnw @code{:value} # )) (list @code{:tag} level 4 = subsection (string @code{:tag} LaTeX \subsection{) (string @code{:tag} org @code{:value} **** ) (string @code{:tag} Rnw @code{:value} ## )) (list @code{:tag} level 5 = subsubsection (string @code{:tag} LaTeX @code{:value} \subsubsection{) (string @code{:tag} org @code{:value} ***** ) (string @code{:tag} Rnw @code{:value} ### )) (list @code{:tag} level 6 = paragraph (string @code{:tag} LaTeX @code{:value} \paragraph{) (string @code{:tag} org @code{:value} ****** ) (string @code{:tag} Rnw @code{:value} ###### )) (list @code{:tag} level 7 = sub-paragraph
  [markdown - not applicable] (string @code{:tag} LaTeX @code{:value} \subparagraph{) (string @code{:tag} org @code{:value} ******* ) (string @code{:tag} Rnw @code{:value} )) (list @code{:tag} none (const @code{:tag} LaTeX @code{:value} ) (const @code{:tag} org @code{:value} ) (const @code{:tag} Rnw @code{:value} )) (list @code{:tag} custom (string @code{:tag} LaTeX @code{:value} prefix-for-LaTeX) (string @code{:tag} org  @code{:value} prefix-for-org) (string @code{:tag} Rnw @code{:value} prefix-for-Rnw)))
@item custom-requests
nil
@item variable-documentation
Prefixes indicating the heading level for a chunk.
Specify these in the form of a list of two in the form:
 '(heading-level-for-LaTeX heading-for-Org)

The value is used to prior to a chunk-name.
As a TeX command, a closing "}" is added e.g. 
'\subsection{'chunk-name'}'.

Regarding levels of depth:
- LaTeX uses 7 heading levels by default
- `org-mode' supports up to 8 heading levels
  (only 7, * to *******, are provided as options here)
- markdown uses 6 heading levels, # to ######
Thus, we here restrict outselves to 7, bearing in mind that other 
formats can be more restrictive e.g. markdown supports 6.
This is not meant to indicate a direct correspondance between 
heading levels in org-mode and LaTeX.

These values are used by `mp-chunk-insert'.

For org-mode, see also `org-level-faces', `org-heading-components' and
`org-element-headline-parser'.
For markdown-mode, see also `markdown-regex-header'.
@end table
@end defopt 

@cindex mp-R-chunk-defaults-R-pkg
@unnumberedsec mp-R-chunk-defaults-R-pkg
@defopt mp-R-chunk-defaults-R-pkg
@table @var
@item standard-value
((funcall (function (closure (t) nil (quote (Default options for knitr and rmarkdown  ### Defaults for chunks typeset with knitr
library('knitr')
### defaults for all chunks
opts_chunk$set(
    eval=TRUE,
    ## text results
    echo=TRUE,
    results=c('markup', 'asis', 'hold', 'hide')[1],
    collapse=FALSE,
    warning=TRUE, message=TRUE, error=TRUE,
    split=FALSE, include=TRUE, strip.white=TRUE,
    ## code decoration
    tidy=FALSE, prompt=FALSE, comment='##',
    highlight=TRUE, size='normalsize',
    background=c('#F7F7F7', colors()[479], c(0.1, 0.2, 0.3))[1],
    ## cache
    cache=FALSE,
    ## plots
    fig.path=c('figure', 'figure/minimal-')[1],
    fig.keep=c('high', 'none', 'all', 'first', 'last')[1],
    fig.align=c('center', 'left', 'right', 'default')[1],
    fig.show=c('hold', 'asis', 'animate', 'hide')[1],
    dev=c('pdf', 'png', 'tikz')[1],
    fig.width=7, fig.height=7, #inches
    fig.env=c('figure', 'marginfigure')[1],
    fig.pos=c('', 'h', 't', 'b', 'p', 'H')[1])
opts_knit$set(out.format='latex')
knit_theme$set('biogoo')
### Set R options
options(formatR.arrow=TRUE, width=60)
knit_hooks$set(inline = function(x) {
    ## if (is.numeric(x)) return(knitr::@code{:format}_sci(x, 'latex'))
    highr:@code{:hi}_latex(x)
})
### uncomment below to change theme
## knit_theme$get()
## opts_knit$set(out.format='latex')
## thm1 <- knit_theme$get('acid')
## knit_theme$set(thm1)))))))
@item custom-links
((url-link @code{:tag} Code chunks and package options http://yihui.name/knitr/options) (url-link @code{:tag} Hooks - knitr documentation http://yihui.name/knitr/hooks))
@item custom-type
(string)
@item custom-requests
nil
@item variable-documentation
Default setup options for 'knitr'.
Used by `mp-R-new'.
This list is not exhaustive.
Common options are given as vectors, with a choice indicated by
the index, in square brackets.
@end table
@end defopt 

@node defvar
@chapter defvar
@cindex defvar

Documentation for @code{defvar}: @*
Define SYMBOL as a variable, and return SYMBOL.
You are not required to define a variable in order to use it, but
defining it lets you supply an initial value and documentation, which
can be referred to by the Emacs help facilities and other programming
tools.  The ‘defvar’ form also declares the variable as "special",
so that it is always dynamically bound even if ‘lexical-binding’ is t.

If SYMBOL’s value is void and the optional argument INITVALUE is
provided, INITVALUE is evaluated and the result used to set SYMBOL’s
value.  If SYMBOL is buffer-local, its default value is what is set;
buffer-local values are not affected.  If INITVALUE is missing,
SYMBOL’s value is not set.

If SYMBOL has a local binding, then this form affects the local
binding.  This is usually not what you want.  Thus, if you need to
load a file defining variables, with this form or with ‘defconst’ or
‘defcustom’, you should always load that file _outside_ any bindings
for these variables.  (‘defconst’ and ‘defcustom’ behave similarly in
this respect.)

The optional argument DOCSTRING is a documentation string for the
variable.

To define a user option, use ‘defcustom’ instead of ‘defvar’.

(fn SYMBOL &optional INITVALUE DOCSTRING)@*

A table of all @code{defvar}s follows:


@ftable @code
@item mp-dd
The ‘default-directory’; set when ‘mp-set-mp-dd’ is run.
@item mp-fnb
The ‘file-name-base’ (a string) for the working file in ‘mp-dd’.
@item mp-fne
The ‘file-name-extension’ (a string) for the working file in ‘mp-dd’.
@item mp-chunks
Stores value for code chunks as a list of strings.
@item mp-df
A list of the ‘directory-files’ in ‘mp-dd’.
@item mp-fn
The file-name i.e. ‘mp-fnb’.‘mp-fne’.
@end ftable

Details of each @code{defvar} follow below: @*

@cindex mp-dd
@unnumberedsec mp-dd
@deffn defvar mp-dd

@table @var
@item variable-documentation
The `default-directory'; set when `mp-set-mp-dd' is run.
Defined here as a dynamicaly-bound variable so that
various functions can refer to this value.
@end table
@end deffn 

@cindex mp-fnb
@unnumberedsec mp-fnb
@deffn defvar mp-fnb

@table @var
@item variable-documentation
The `file-name-base' (a string) for the working file in `mp-dd'.
Set when `mp-mp' is run.
Defined here as a dynamic variable so that
various functions can use this value.
@end table
@end deffn 

@cindex mp-fne
@unnumberedsec mp-fne
@deffn defvar mp-fne

@table @var
@item variable-documentation
The `file-name-extension' (a string) for the working file in `mp-dd'.
This is set when `mp-mp' is run.
Defined here as a dynamic variable so that
various functions can use this value.
@end table
@end deffn 

@cindex mp-chunks
@unnumberedsec mp-chunks
@deffn defvar mp-chunks

@table @var
@item variable-documentation
Stores value for code chunks as a list of strings.
The value should be a `list' of 3 elements where
the first is the name of the chunk,
the second provides formattinhg information
the third is the content of the chunk.

The second element, chunk formatting should
reflect the entwiner in use; see also
`mp-sweave-opts' and `mp-org-opts'.
@end table
@end deffn 

@cindex mp-df
@unnumberedsec mp-df
@deffn defvar mp-df

@table @var
@item variable-documentation
A list of the `directory-files' in `mp-dd'.
Defined here as a dynamicaly-bound variable so that
 various functions can refer to this value.
@end table
@end deffn 

@cindex mp-fn
@unnumberedsec mp-fn
@deffn defvar mp-fn

@table @var
@item variable-documentation
The file-name i.e. `mp-fnb'.`mp-fne'.
Defined here as a dynamicaly-bound variable so that
 various functions can refer to this value.
@end table
@end deffn 

@node defconst
@chapter defconst
@cindex defconst

Documentation for @code{defconst}: @*
Define SYMBOL as a constant variable.
This declares that neither programs nor users should ever change the
value.  This constancy is not actually enforced by Emacs Lisp, but
SYMBOL is marked as a special variable so that it is never lexically
bound.

The ‘defconst’ form always sets the value of SYMBOL to the result of
evalling INITVALUE.  If SYMBOL is buffer-local, its default value is
what is set; buffer-local values are not affected.  If SYMBOL has a
local binding, then this form sets the local binding’s value.
However, you should normally not make local bindings for variables
defined with this form.

The optional DOCSTRING specifies the variable’s documentation string.

(fn SYMBOL INITVALUE [DOCSTRING])@*

A table of all @code{defconst}s follows:


@ftable @code
@item mp-chunk-name-prefix-Rnw
Prefix for the chunk name in an .Rnw file.
@item mp-chunk-name-prefix-org
Prefix for the chunk name in an .org file.
@item mp-chunk-name-prefix-Rmd
Prefix for the chunk name in an .Rmd file.
@item mp-chunk-format-prefix-Rnw
Prefix for the chunk format in an .Rnw file.
@item mp-chunk-format-prefix-org
Prefix for the chunk format in an .org file.
@item mp-chunk-format-prefix-Rmd
Prefix for the chunk format in an .Rmd file.
@item mp-chunk-name-suffix-Rnw
Suffix for the chunk name in an .Rnw file.
@item mp-chunk-name-suffix-Rmd
Suffix for the chunk name in an .Rmd file.
@item mp-chunk-content-suffix-Rnw
Suffix for the chunk content in an .Rnw file.
@item mp-chunk-content-suffix-Rmd
Suffix for the chunk content in an .Rmd file.
@item mp-chunk-content-suffix-org
Suffix for the chunk content in an .org file.
@end ftable

Details of each @code{defconst} follow below: @*

@cindex mp-chunk-name-prefix-Rnw
@unnumberedsec mp-chunk-name-prefix-Rnw
@deffn defconst mp-chunk-name-prefix-Rnw

@table @var
@item variable-documentation
Prefix for the chunk name in an .Rnw file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-name-prefix-org
@unnumberedsec mp-chunk-name-prefix-org
@deffn defconst mp-chunk-name-prefix-org

@table @var
@item variable-documentation
Prefix for the chunk name in an .org file.
See also `mp-org-opts'.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-name-prefix-Rmd
@unnumberedsec mp-chunk-name-prefix-Rmd
@deffn defconst mp-chunk-name-prefix-Rmd

@table @var
@item variable-documentation
Prefix for the chunk name in an .Rmd file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-format-prefix-Rnw
@unnumberedsec mp-chunk-format-prefix-Rnw
@deffn defconst mp-chunk-format-prefix-Rnw

@table @var
@item variable-documentation
Prefix for the chunk format in an .Rnw file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-format-prefix-org
@unnumberedsec mp-chunk-format-prefix-org
@deffn defconst mp-chunk-format-prefix-org

@table @var
@item variable-documentation
Prefix for the chunk format in an .org file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-format-prefix-Rmd
@unnumberedsec mp-chunk-format-prefix-Rmd
@deffn defconst mp-chunk-format-prefix-Rmd

@table @var
@item variable-documentation
Prefix for the chunk format in an .Rmd file.
Note that this is not essential i.e. a code chunk could begin
```{r chunk-name, echo=TRUE
rather than
```{r, chunk-name, echo=TRUE
The convention of an extra comma follows that used by knitr.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-name-suffix-Rnw
@unnumberedsec mp-chunk-name-suffix-Rnw
@deffn defconst mp-chunk-name-suffix-Rnw

@table @var
@item variable-documentation
Suffix for the chunk name in an .Rnw file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-name-suffix-Rmd
@unnumberedsec mp-chunk-name-suffix-Rmd
@deffn defconst mp-chunk-name-suffix-Rmd

@table @var
@item variable-documentation
Suffix for the chunk name in an .Rmd file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-content-suffix-Rnw
@unnumberedsec mp-chunk-content-suffix-Rnw
@deffn defconst mp-chunk-content-suffix-Rnw

@table @var
@item variable-documentation
Suffix for the chunk content in an .Rnw file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-content-suffix-Rmd
@unnumberedsec mp-chunk-content-suffix-Rmd
@deffn defconst mp-chunk-content-suffix-Rmd

@table @var
@item variable-documentation
Suffix for the chunk content in an .Rmd file.
@item risky-local-variable
t
@end table
@end deffn 

@cindex mp-chunk-content-suffix-org
@unnumberedsec mp-chunk-content-suffix-org
@deffn defconst mp-chunk-content-suffix-org

@table @var
@item variable-documentation
Suffix for the chunk content in an .org file.
@item risky-local-variable
t
@end table
@end deffn 

@node defvar-local
@chapter defvar-local
@cindex defvar-local

Documentation for @code{defvar-local}: @*
Define VAR as a buffer-local variable with default value VAL.
Like ‘defvar’ but additionally marks the variable as being automatically
buffer-local wherever it is set.

(fn VAR VAL &optional DOCSTRING)@*

A table of all @code{defvar-local}s follows:


@ftable @code
@item mp-chunk-heading-level-prefix
Value of chunk heading level prefix.
@item mp-chunk-heading-level-suffix
Value of chunk heading level suffix.
@item mp-chunk-name-prefix
Value of chunk name prefix.
@item mp-chunk-name-suffix
Value of chunk name suffix.
@item mp-chunk-format-prefix
Value of chunk format prefix.
@item mp-chunk-content-suffix
Value of chunk content suffix.
@end ftable

Details of each @code{defvar-local} follow below: @*

@cindex mp-chunk-heading-level-prefix
@unnumberedsec mp-chunk-heading-level-prefix
@deffn defvar-local mp-chunk-heading-level-prefix

@table @var
@item variable-documentation
Value of chunk heading level prefix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@cindex mp-chunk-heading-level-suffix
@unnumberedsec mp-chunk-heading-level-suffix
@deffn defvar-local mp-chunk-heading-level-suffix

@table @var
@item variable-documentation
Value of chunk heading level suffix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@cindex mp-chunk-name-prefix
@unnumberedsec mp-chunk-name-prefix
@deffn defvar-local mp-chunk-name-prefix

@table @var
@item variable-documentation
Value of chunk name prefix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@cindex mp-chunk-name-suffix
@unnumberedsec mp-chunk-name-suffix
@deffn defvar-local mp-chunk-name-suffix

@table @var
@item variable-documentation
Value of chunk name suffix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@cindex mp-chunk-format-prefix
@unnumberedsec mp-chunk-format-prefix
@deffn defvar-local mp-chunk-format-prefix

@table @var
@item variable-documentation
Value of chunk format prefix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@cindex mp-chunk-content-suffix
@unnumberedsec mp-chunk-content-suffix
@deffn defvar-local mp-chunk-content-suffix

@table @var
@item variable-documentation
Value of chunk content suffix.
Set with `mp-chunk-set-adfixes'.
@end table
@end deffn 

@node Other symbolic expressions
@chapter Other symbolic expressions
@cindex Other symbolic expressions

@smallformat @verbatim 
(mapc #'require
      '(org ess tex bibtex doc-view ibuffer autorevert cl calendar timer))

(setq org-src-fontify-natively nil)

@end verbatim 
 @end smallformat 
@node Index
@unnumbered Index
@printindex cp
@bye 

@c Local Variables:
@c mode: texinfo
@c TeX-master: t
@c End