tests/testthat/test-network-properties.R

In dbarrows/bondr: Chemical reaction networks

context('Network properties')
library(bondr)
library(magrittr)
library(stringr)

source('utils.R')

body_string <- function(prop) {
    prop %>% body() %>% as.character() %>% .[2] %>% str_replace_all(' ', '')
}

test_that('Propensities', {
    net <- network('A -> B, 1')
    expect_equal(
        propensities(net)[[1]] %>% body_string(),
        '1*x[1]'
    )
    
    net <- network('2A -> 0, 0.5')
    expect_equal(
        propensities(net)[[1]] %>% body_string(),
        '0.5*x[1]*(x[1]-1)/2'
    )
    expect_equal(
        propensities(
            net,
            rateless = TRUE
        )[[1]] %>% body_string(),
        '1*x[1]*(x[1]-1)/2'
    )
})

test_that('Updates', {
    net <- network('A -> B, 1')
    expect_equal(
        updates(net)[[1]] %>% body_string(),
        'x+c(-1,1)'
    )
    
    net <- network('X -> 0, 1')
    expect_equal(
        updates(net)[[1]] %>% body_string(),
        'x+c(-1)'
    )

    net <- network('2X -> 3X, 1')
    expect_equal(
        updates(net)[[1]] %>% body_string(),
        'x+c(1)'
    )
})

test_that('Stoichiometric matrix', {
    net <- network('
        A <-> B, 1, 2
        0  -> A, 0.5
    ')
    expect_equal(
        stmat(net),
        {
            mat <- matrix(c(-1, 1, 1, -1, 1, 0), nrow = 2)
            rownames(mat) <- c('A', 'B')
            colnames(mat) <- str_c('R', 1:3)
            mat
        }
    )

    net <- network('
        0  -> A,  1
        3X -> 2X, 2
    ')
    expect_equal(
        stmat(net),
        {
            mat <- matrix(c(1, 0, 0, -1), nrow = 2)
            rownames(mat) <- c('A', 'X')
            colnames(mat) <- str_c('R', 1:2)
            mat
        }
    )
})