Sergiu Ivanov
a074258b1a
networks: Rename and generalize state graph functions.
...
build-full-state-graph and build-full-state-graph-annotated now
retrieve the domains from the network and are not limited to Boolean
state graphs.
2020-11-26 22:13:57 +01:00
Sergiu Ivanov
34ceccc446
networks: Fix build-syntactic-interaction-graph.
2020-11-23 23:16:11 +01:00
Sergiu Ivanov
fbd6ded717
networks: Fix list-syntactic-interactions.
2020-11-23 23:09:23 +01:00
Sergiu Ivanov
0a4035d9f7
networks: Fix the tests of make-boolean-network-form.
2020-11-22 23:00:26 +01:00
Sergiu Ivanov
f016fbb0ca
networks: Fix the tests for network-form->network.
2020-11-22 22:58:21 +01:00
Sergiu Ivanov
354fad2b1d
network: Roll back update to its previous version.
...
I thought I was clever to rewrite update using for/hash, but in fact
this new version only included the updated variables in the new
state :D
2020-11-22 22:50:29 +01:00
Sergiu Ivanov
3abf548ac2
networks: Bug in update.
2020-11-22 22:44:04 +01:00
Sergiu Ivanov
eb3e851a9d
networks: Make network and network-form transparent.
2020-11-22 22:38:45 +01:00
Sergiu Ivanov
ff6fa2c88b
network: Fix the test for make-boolean-network.
2020-11-22 22:11:25 +01:00
Sergiu Ivanov
b38adc89cf
networks: Don't use tabulate-boolean-network.
2020-11-22 22:08:45 +01:00
Sergiu Ivanov
e4751c6ed2
networks: Don't re-export network-form?.
2020-11-22 22:05:41 +01:00
Sergiu Ivanov
0085eb964b
networks: Fix make-boolean-network.
2020-11-22 22:02:56 +01:00
Sergiu Ivanov
5475bc5fbf
networks: Fix Random networks.
2020-11-22 21:58:00 +01:00
Sergiu Ivanov
2c68055818
networks: Fix constructing functions and networks.
2020-11-22 21:42:41 +01:00
Sergiu Ivanov
3a2453c92e
networks: Fix tabulating functions and networks.
2020-11-22 21:41:06 +01:00
Sergiu Ivanov
fd651ba4cc
network,Dynamics: Fixes.
2020-11-22 21:35:19 +01:00
Sergiu Ivanov
6cfa66694d
networks: Remove read-org-network-make-asyn and read-org-network-make-syn.
...
I think I initially intended these functions for Boolean networks.
I'll see if I add back something similar to these when I will be
fixing example.org.
2020-11-22 21:33:16 +01:00
Sergiu Ivanov
97026a2a42
networks: Say that domain mappings may be empty.
2020-11-22 21:30:50 +01:00
Sergiu Ivanov
27bb25c201
networks: Fix signed interaction graphs.
2020-11-22 21:26:26 +01:00
Sergiu Ivanov
3e35b8e0ab
networks, IG: Use forms->boolean-network.
...
IG = interaction graph
2020-11-22 21:24:05 +01:00
Sergiu Ivanov
ec3c74b5e2
networks: Add forms->boolean-network.
2020-11-22 21:21:31 +01:00
Sergiu Ivanov
a4979d9c9f
networks: Add make-boolean-network-form.
2020-11-22 21:18:22 +01:00
Sergiu Ivanov
d5e1819fff
networks: Add make-boolean-network.
2020-11-22 21:18:14 +01:00
Sergiu Ivanov
6fd3d41c7e
networks: Update the IG-related functions.
...
IG = interaction graph
2020-11-22 21:06:33 +01:00
Sergiu Ivanov
393f1d2bba
networks: Move domain-mapping/c to Basic definitions.
2020-11-22 20:46:53 +01:00
Sergiu Ivanov
cb208a66fc
networks: Add one more comment on syntactic IG vs. IG.
2020-11-22 20:42:30 +01:00
Sergiu Ivanov
b8f29d905d
networks: Remove make-network-from-forms.
2020-11-22 00:29:36 +01:00
Sergiu Ivanov
236dca704d
networks: Update network-form->network.
2020-11-22 00:27:56 +01:00
Sergiu Ivanov
ed03015e81
network: Add domains to network-form.
2020-11-22 00:24:15 +01:00
Sergiu Ivanov
cfe710e6b2
network: Don't use make-network-from-functions in basic definitions.
2020-11-22 00:08:46 +01:00
Sergiu Ivanov
11d75bcc89
networks: Rewrite update.
2020-11-21 23:28:30 +01:00
Sergiu Ivanov
6560dcbe6c
networks: Move booleanize-state before its own test case.
2020-11-21 23:15:17 +01:00
Sergiu Ivanov
a654ac5896
network: Remove make-network-from-forms.
2020-11-21 23:13:50 +01:00
Sergiu Ivanov
a3ac1c7fcd
networks: Include domains into the network.
...
This change is breaking. The following commits will progressively fix
the whole network module.
2020-11-21 22:53:45 +01:00
Sergiu Ivanov
f1a1123cc4
networks: Make it possible to skip expensive test cases.
...
At the moment, this is particularly for skipping the tests
constructing the interaction graphs.
2020-11-21 00:53:11 +01:00
Sergiu Ivanov
097c5a7f09
example: Update the presentation of the functions concerning the interaction graphs.
2020-11-19 23:48:50 +01:00
Sergiu Ivanov
fe0fbc3ed0
networks: Add build-signed-interaction-graph/form.
2020-11-19 00:22:01 +01:00
Sergiu Ivanov
0345cd3648
networks: Add build-interaction-graph/form.
2020-11-19 00:14:54 +01:00
Sergiu Ivanov
8e100c2e8b
networks: Add build-signed-interaction-graph.
2020-11-18 01:11:37 +01:00
Sergiu Ivanov
0313d81c25
network: Add another self-loop test for get-interaction-sign.
2020-11-18 01:08:40 +01:00
Sergiu Ivanov
c55113f27e
network: Bug fix in get-interaction-sign.
2020-11-18 00:46:55 +01:00
Sergiu Ivanov
195d71ed4e
networks: Remove interaction? from the tests for get-interaction-sign.
2020-11-18 00:29:45 +01:00
Sergiu Ivanov
a8adc9fb57
README: Add a new TODO item for splitting network into two models.
2020-11-18 00:19:53 +01:00
Sergiu Ivanov
af8428d275
network,build-interaction-graph: Use in-list.
2020-11-18 00:13:00 +01:00
Sergiu Ivanov
d190f76fdf
networks: Add build-interaction-graph.
2020-11-18 00:09:15 +01:00
Sergiu Ivanov
ff9654e5c6
network: Add get-interaction-sign.
2020-11-17 23:38:34 +01:00
Sergiu Ivanov
bfc48ff453
networks: Slightly optimize interaction?.
2020-11-15 00:02:44 +01:00
Sergiu Ivanov
8a1f4c682e
networks: Add interaction?.
2020-11-14 23:15:39 +01:00
Sergiu Ivanov
d24dadd4cd
example: Stage all the figures.
2020-11-12 22:56:53 +01:00
Sergiu Ivanov
ce0925e41e
networks: Remove the old functions for building interaction graphs.
...
These functions mix interaction graphs derived from the expressions
defining the network with deriving the interactions from the dynamics,
which does not always yield the same result. Also, some functions
only worked for Boolean networks, including get-interaction-sign.
Additionally, these functions are among the first ones I wrote in dds,
so there are a couple of things which can be written in a better way.
2020-11-12 22:54:04 +01:00
