369 lines
11 KiB
Org Mode
369 lines
11 KiB
Org Mode
#+TITLE: Examples of usage of =dds=
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#+PROPERTY: header-args:racket :prologue "#lang racket\n(require graph (file \"~/Candies/prj/racket/dds/networks.rkt\") (file \"~/Candies/prj/racket/dds/utils.rkt\"))"
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* Introduction
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This document shows some examples of usage of the modules in =dds=
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with Org-mode. It relies on [[https://github.com/hasu/emacs-ob-racket][emacs-ob-racket]].
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The [[intro][following section]] describes how Org-mode can interact with
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Racket, and how this interaction can be used for a fluid workflow
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with =dds=. In particular, the code block =munch-table= is [[tabread][defined]]
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in this section.
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The subsequent sections show off some the functionalities of the
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submodules of =dds=.
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* Org-mode, Racket, and =dds= <<intro>>
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** Importing a module from file
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:PROPERTIES:
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:header-args:racket: :prologue "#lang racket\n(require (file \"~/Candies/prj/racket/dds/networks.rkt\"))"
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:END:
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To require the modules from the files of =dds=, you can use the
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following code (I only reset the prelude here because I set at the
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top of this file):
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#+BEGIN_SRC racket :results output :prologue ""
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#lang racket
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(require (file "~/Candies/prj/racket/dds/networks.rkt"))
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(require (file "~/Candies/prj/racket/dds/utils.rkt"))
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#+END_SRC
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#+RESULTS:
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Note that this code will not work with =:results value=. I think it
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is because in this case the code is not really evaluated at top
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level.
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These initialisation lines can be put into the prologue of every
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code block in a subtree by setting =:prologue= via
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=:header-args:racket:= in the properties drawer. Check out the
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properties drawer of this section for an example.
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Alternatively, this property can be set via a =#+PROPERTY= line at
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the top the file. For example, this file has such a line. Whenever
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this property line changes, refresh the setup of the file by hitting
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=C-c C-c= on the property line. This will update the prologue for
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all racket code blocks.
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Finally, you can also set =:prologue= (and other properties with
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long values) in the following way:
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#+HEADER: :prologue "#lang racket\n(require (file \"~/Candies/prj/racket/dds/networks.rkt\"))"
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#+BEGIN_SRC racket :results output drawer
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(st '((a . 1)))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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'#hash((a . 1))
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:END:
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** Output formats for results of evaluation of code blocks
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[[https://orgmode.org/manual/Results-of-Evaluation.html#Results-of-Evaluation][This section]] of the Org manual describes various different formats
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for presenting the results of code blocks. I find the following
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three particularly useful as of [2020-02-22 Sat]: =output=, =list=,
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and =table=.
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The =output= result format is the simplest and the most natural
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ones. It works as if the code block were inserted into a module
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which would then be evaluated.
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#+BEGIN_SRC racket :results output drawer
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(println "This is the first line of output.")
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(println (+ 1 2))
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(println "This the third line of output.")
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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"This is the first line of output."
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3
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"This the third line of output."
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:END:
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The =list= result format typesets the result of the last line in the
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code block as a list:
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#+BEGIN_SRC racket :results list
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'(1 "hello" (and x y))
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#+END_SRC
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#+RESULTS:
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- 1
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- "hello"
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- (and x y)
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Note how nested lists are not recursively shown as nested Org-mode
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lists.
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For some reason, the =list= output format does not work with the
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result drawer:
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#+BEGIN_SRC racket :results list drawer
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'(1 "hello" (and x y))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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- (1 "\"hello\"" (and x y))
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:END:
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Finally, the =table= result format typesets the output as a table:
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#+BEGIN_SRC racket :results table drawer
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'((a . #t) (b . #f))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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| a | #t |
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| b | #f |
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:END:
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This is clearly very useful for printing states (and hash tables,
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more generally):
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#+BEGIN_SRC racket :results table drawer
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(st '((a . 1) (b . #f) (c . "hello")))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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| a | 1 |
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| b | #f |
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| c | "hello" |
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:END:
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*** A note about printing update function forms
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Automatic table typesetting may go in the way of readability for
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hash tables whose values are lists, as the following example shows:
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#+BEGIN_SRC racket :results table drawer
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#hash((a . (and a b)) (b . (not b)))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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| a | and | a | b |
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| b | not | b | |
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:END:
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To tackle this issue, [[../utils.rkt][=dds/utils=]] provides
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=stringify-variable-mapping= (with the shortcut =sgfy=) which
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converts all the values of a given variable mapping to strings:
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#+BEGIN_SRC racket :results table drawer
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(sgfy #hash((a . (and a b)) (b . (not b))))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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| a | "(and a b)" |
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| b | "(not b)" |
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:END:
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** Reading Org-mode tables<<tabread>>
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Org-mode allows supplying tables as arguments for code blocks.
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#+NAME: test-table
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| a | "(and a b)" |
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| b | (or b (not a)) |
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#+BEGIN_SRC elisp :var tab=test-table :results output drawer
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tab
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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:END:
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((a (and a b)) (b (or b (not a))))
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Unfortunately, the same trick does not work with Racket directly,
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because Racket interprets the first elements in the parentheses as
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function applications:
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#+BEGIN_SRC racket :results output drawer :var tab=test-table
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tab
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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application: not a procedure;
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expected a procedure that can be applied to arguments
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given: "a"
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arguments...:
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"(and a b)"
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context...:
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"/tmp/babel-qkvrRR/org-babel-c4wuju.rkt": [running body]
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temp37_0
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for-loop
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run-module-instance!125
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perform-require!78
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:END:
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Fortunately, we can easily remedy this problem by creating a named
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parameterised Elisp source block which will explicitly convert the
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table to a string:
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#+NAME: munch-table
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#+BEGIN_SRC elisp :results output drawer :var tab=test-table
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(prin1 tab)
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#+END_SRC
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#+RESULTS: munch-table
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:RESULTS:
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(("a" "(and a b)") ("b" "(or b (not a))"))
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:END:
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We can now correctly receive this table in a Racket source code
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block by threading it through =munch-table=:
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#+BEGIN_SRC racket :results output drawer :var tab=munch-table(tab=test-table)
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(println tab)
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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"((\"a\" \"(and a b)\") (\"b\" \"(or b (not a))\"))"
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:END:
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[[../utils.rkt][=dds/utils=]] has several functions for parsing such strings, and
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notably =read-org-variable-mapping=, with the shortcut =unorg=:
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#+BEGIN_SRC racket :results output drawer :var tab=munch-table(tab=test-table)
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(unorg tab)
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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'#hash((a . (and a b)) (b . (or b (not a))))
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:END:
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Of course, we can use =munch-table= to prepare any other table than
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=test-table= for use with Racket:
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#+NAME: another-test-table
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| a | (not a) |
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| b | (and a c) |
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| c | (and a (not b)) |
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#+BEGIN_SRC racket :results output drawer :var tab=munch-table(tab=another-test-table)
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(unorg tab)
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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'#hash((a . (not a)) (b . (and a c)) (c . (and a (not b))))
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:END:
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** Inline graph visualisation with Graphviz
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Some functions in =dds= build graphs:
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#+BEGIN_SRC racket :results output drawer :var bf=munch-table(another-test-table)
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(build-interaction-graph (unorg bf))
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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#<unweighted-graph>
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:END:
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The =graph= library allows building a Graphviz description of the
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constructed graph. (Note that you have to install the =graph=
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library by running =raco pkg install graph= and require it. The
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long property line at the top of this file defining the prologue for
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racket source code blocks takes care of requiring =graph=.)
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#+NAME: igraph
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#+BEGIN_SRC racket :results output drawer :var bf=munch-table(another-test-table)
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(display (graphviz (build-interaction-graph (unorg bf))))
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#+END_SRC
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#+RESULTS: igraph
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:RESULTS:
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digraph G {
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node0 [label="c"];
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node1 [label="b"];
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node2 [label="a"];
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subgraph U {
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edge [dir=none];
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node0 -> node1;
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node2 -> node2;
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}
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subgraph D {
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node2 -> node0;
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node2 -> node1;
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}
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}
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:END:
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You can have an inline drawing of this graph by calling the previous
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code block (=igraph=) via a noweb reference in Graphviz/DOT source
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block:
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#+BEGIN_SRC dot :file dots/exampleBQNp7Z.svg :results raw drawer :cmd sfdp :noweb yes
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<<igraph()>>
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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[[file:dots/exampleBQNp7Z.svg]]
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:END:
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Note that the =graph= library draws self-loops as undirected edges.
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It also draws double-sided edges as undirected edges (e.g., in the
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preceding graph, b depends on c and c depends on b).
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* =dds/networks=
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The [[../networks.rkt][=dds/networks=]] is a module for working with different network
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models. A network is a set of variables which are updated according
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to their corresponding update functions. The variables to be
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updated at each step are given by the mode. This model can
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generalise Boolean networks, TBANs, multivalued networks, etc.
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** Boolean networks
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Consider the following Boolean network:
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#+NAME: simple-bn
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| a | b |
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| b | (and (not a) c) |
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| c | (not c) |
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Here's the unsigned interaction graph of this network:
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#+NAME: simple-bn-ig
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-table(simple-bn)
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(dotit (build-interaction-graph (unorg simple-bn)))
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#+END_SRC
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#+BEGIN_SRC dot :file dots/examplejTo8XT.svg :results raw drawer :cmd sfdp :noweb yes
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<<simple-bn-ig()>>
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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[[file:dots/examplejTo8XT.svg]]
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:END:
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Here's the signed interaction graph of this network:
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#+NAME: simple-bn-sig
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#+BEGIN_SRC racket :results silent :var simple-bn=munch-table(simple-bn)
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(dotit (build-boolean-signed-interaction-graph (unorg simple-bn)))
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#+END_SRC
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#+BEGIN_SRC dot :file dots/exampledpQygl.svg :results raw drawer :cmd sfdp :noweb yes
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<<simple-bn-sig()>>
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#+END_SRC
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#+RESULTS:
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:RESULTS:
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[[file:dots/exampledpQygl.svg]]
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:END:
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For the interaction a \to b, note indeed that when c is #f, b is
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always #f (positive interaction). On the other hand, when c is #t,
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b becomes (not a) (negative interaction). Therefore, the influence
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of a on b is neither activating nor inhibiting.
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* Local Variables :noexport:
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# Local Variables:
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# eval: (auto-fill-mode)
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# ispell-local-dictionary: "en"
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# org-link-file-path-type: relative
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# End:
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