tests/testthat/test_arguments.R

In deGradInfer: Parameter Inference for Systems of Differential Equation

# Tests that the code does/does not produce an error for different arguments
# to the agm function
library(deGradInfer)

set.seed(10)

context("Arguments Tests, 50 Iterations")

# Run deGradInfer on test dataset
dataTest <- LV_example_dataset$data
timeTest <- LV_example_dataset$time
noiseTest <- LV_example_dataset$noise

LV_func = function(t, X, params) {
  dxdt = cbind(
    X[,1]*(params[1] - params[2]*X[,2]),
    - X[,2]*(params[3] - params[4]*X[,1])
  )
  return(dxdt)
}


# Running without specifying default priors, should work.
#test_that("Default prior works",{
#expect_silent(agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
#     numberOfParameters=4, maxIterations=50))
#})


# Running with user-specified prior, should work.
# test_that("User-specified prior works",{
#  expect_silent(agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
#                    logPrior= function(params)
#                      c(dgamma(params[1:3],1,1,log=TRUE),
#                        dgamma(params[4],1,2,log=TRUE)),
#                    numberOfParameters=4, maxIterations=50))
#})

# Running with wrongly-specified prior, should not work.
test_that("User-specified prior works",{
  expect_error(agm(data=dataTest,time=timeTest,noise.sd=0.31,ode.system=LV_func,
                    logPrior= "Dirichlet",
                    numberOfParameters=4, maxIterations=50))
})

# Running without specifying ODE system, should not work.
test_that("ODE system missing throws error",{
  expect_error(agm(data=dataTest,time=timeTest,noise.sd=0.31,
                   numberOfParameters=4,
                   maxIterations=50))
})