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🎤 RAPS: R Aid for P systems

Welcome to the repository behind the RAPS package.

build R

NEWS: Last 21 / 11 / 2022 RAPS 1.0.0 was launched. Have a good time trying it!.

Quickstart

Run the following to install the package locally, directly from GitHub:

devtools::install_github("Xopre/RAPS")

Now you can run every example in the demos' folder. Give the deterministic waiting time algorithm a try!

Main workflow with RAPS:

  graph TD;
    url/path-->path2rap;
    path2rap-->rap;

    load_demo_dataset-->rap;
    
    rap-->choose_rule;
    choose_rule-->apply_rule;
    apply_rule-->new_rap;

    rap-->simulate;
    simulate-->new_rap;

    rap-->alg_gillespie_menv;
    rap-->alg_det_menv;
    alg_det_menv-->new_rap;
    alg_gillespie_menv-->new_rap;

    rap-->get_rule_by_id;
    get_rule_by_id-->show_rule;

    rap-->show_rap;
    new_rap-->show_rap;
Loading

In RAPS we use the rap (Representing A P system) objects, which have the following aspect:

$Configuration

Environment ID Label Objects SuperM SubM Charge Other_params
1 1 1 [(a, 1)] 0 [2,3] -1 @immutable
1 2 2 [(b, 2), (c,3)] 1 NULL +1 NA
1 3 3 [(@filler, 1)] 1 NULL +1 NA

$Rules

rule_id dissolves priority main_membrane_label lhs rhs propensity
value0 FALSE - 1 $lhs_1$ $rhs_1$ 1974

$Properties

System PLingua_model N_membranes N_environments N_objects N_rules
FAS Stochastic 4 1 53 99

where:

$$lhs_1 = \begin{pmatrix} where & object & multiplicity \\ \hline \\ @here & a & 1 \\ mem_2 & b & 2 \\ @exists & mem_3 & 1 \\ \end{pmatrix}$$

$$rhs_1 = \begin{pmatrix} where & object & multiplicity \\ \hline \\ @here & ap & 2 \\ mem_2 & bp & 3 \\ \end{pmatrix}$$

Main functions

  • path2rap(): Create a rap object from a path.
  • alg_det_menv(): Run the deterministic algorithm on a rap object.
  • alg_gillespie_menv(): Run the Gillespie algorithm on a rap object.
  • simulate(): Run a custom simulation algorithm on a rap object.
  • show_rap(): Show a rap object.
  • apply_rule(): Apply a rule to a rap object.
  • choose_rule(): Choose a rule to apply.

Supported rules

Supported rules:

  • Evolution: $[u \rightarrow v]_i$
  • In-communication: $[\ u \rightarrow v_1 \ [v_2]_j\ ]_i$
  • Out-communication: $[\ u_1 \ [u_2]_j \rightarrow v\ ]_i$
  • In/Out-communication: $[\ u_1 \ [u_2]_j \rightarrow v_1 \ [v_2]_k\ ]_i$

Will-be-supported rules, by priority:

  1. Charge change: $[u]_i^{\alpha} \rightarrow [v]_i^{\beta}$
  2. Dissolution: $[u \rightarrow v, \lambda]_i$
  3. Membrane generation: $u \rightarrow [\ ]_i$
  4. Membrane division: $[a]_i \rightarrow [b]_j [c]_k$

Might be supported but are nonstandard:

  • Presence of one or more membranes: $[\ ]_i [\ ]_j \rightarrow a$
  • Presence of the residual of an object: $a^0 \rightarrow b$
  • Crazy multicommunication: $[u_1]i [u_2]j [u_3]k \rightarrow [v_1]{ip} [v_2]{jp} [v_3]{kp}$

Other stuff

General objectives:

  • Create README.md

  • Complete README.md

    • Workflow diagram
    • Functional demos
    • Simulation of stochastic P systems
      • Monoenvironmental Gillespie algorithm
      • Multienvironmental Gillespie algorithm
        • With control over time
        • Validated with FAS
      • Multienvironmental deterministic waiting time algorithm
        • With control over time
        • Validated with FAS

  • Establish the deprecated functions as such

  • Prepare RAPS object for monoenvironmental P systems

  • Prepare RAPS object for multienvironmental P systems

  • Adapt parser to P-Lingua 5 in function path2rap()

  • Create one or more simulators for RAPS' objects

Repository contents

  • .Rproj.user/: User data.
  • demos/: Examples of use of the RAPS package.
  • man/: roxygen2-generated documentation.
  • R/: The functions included in this package.
  • RData/: RData for some demos.
  • renv/: Folder for the renv package.
  • semantics/: Folder for different semantics.
  • utils/: Some auxiliar code. Do not pay much attention.
    • UPDATE.R: Utility for updating the package.
    • RAPS_package.Rmd: The father of UPDATE.R.
  • .gitignore: git-ignored files.
  • .Rbuildignore: Build ignored files.
  • .Rhistory: Ignore this. Should be empty.
  • .Rprofile: My profile.
  • DESCRIPTION: Description of the package.
  • NAMESPACE: roxygen2-generated documentation about exports.
  • RAPS.Rproj: The project wherein everything is developed.
  • README.md: The document you're reading right now.
  • renv.lock: Info for the renv package.

Future work

  • Improve the R workflow within GitHub.
  • Include the tictoc or the lubridate packages to control time in a convenient way.
  • Design custom hexSticker.