context("ICM standard models")
# SI Models ---------------------------------------------------------------
test_that("SI, 1G, CL: 1 sim", {
param <- param.icm(inf.prob = 0.2, act.rate = 0.25)
init <- init.icm(s.num = 500, i.num = 1)
control <- control.icm(type = "SI", nsteps = 5, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SI, 1G, CL: 2 sims", {
param <- param.icm(inf.prob = 0.2, act.rate = 0.25)
init <- init.icm(s.num = 500, i.num = 1)
control <- control.icm(type = "SI", nsteps = 5, nsims = 2, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SI, 1G, OP: 1 sim", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.25, a.rate = 1 / 100,
ds.rate = 1 / 100, di.rate = 1 / 90)
init <- init.icm(s.num = 500, i.num = 1)
control <- control.icm(type = "SI", nsteps = 5, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SI, 2G, OP: 2 sims", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.25, inf.prob.g2 = 0.1, balance = "g1",
a.rate = 1 / 100, a.rate.g2 = NA, ds.rate = 1 / 100,
ds.rate.g2 = 1 / 100, di.rate = 1 / 90,
di.rate.g2 = 1 / 90)
init <- init.icm(s.num = 500, i.num = 1, s.num.g2 = 500, i.num.g2 = 0)
control <- control.icm(type = "SI", nsteps = 5, nsims = 2, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
# SIR Models --------------------------------------------------------------
test_that("SIR, 1G, CL: 1 sim", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.25, rec.rate = 1 / 50)
init <- init.icm(s.num = 500, i.num = 1, r.num = 0)
control <- control.icm(type = "SIR", nsteps = 5, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SIR, 1G, OP: 1 sim", {
param <- param.icm(inf.prob = 0.2,
act.rate = 2, rec.rate = 1 / 50, a.rate = 1 / 100,
ds.rate = 1 / 100, di.rate = 1 / 90, dr.rate = 1 / 100)
init <- init.icm(s.num = 500, i.num = 1, r.num = 0)
control <- control.icm(type = "SIR", nsteps = 5, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SIR, 2G, OP: 2 sims", {
param <- param.icm(inf.prob = 0.2, inf.prob.g2 = 0.1,
act.rate = 1, balance = "g1",
rec.rate = 1 / 50, rec.rate.g2 = 1 / 50,
a.rate = 1 / 100, a.rate.g2 = NA,
ds.rate = 1 / 100, ds.rate.g2 = 1 / 100,
di.rate = 1 / 90, di.rate.g2 = 1 / 90,
dr.rate = 1 / 100, dr.rate.g2 = 1 / 100)
init <- init.icm(s.num = 500, i.num = 1, r.num = 0,
s.num.g2 = 500, i.num.g2 = 1, r.num.g2 = 0)
control <- control.icm(type = "SIR", nsteps = 5, nsims = 2, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
# SIS Models --------------------------------------------------------------
test_that("SIS, 1G, CL: 1 sim", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.25, rec.rate = 1 / 50)
init <- init.icm(s.num = 500, i.num = 1)
control <- control.icm(type = "SIS", nsteps = 5, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SIS, 2G, CL: 2 sims", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.25, inf.prob.g2 = 0.1, balance = "g1",
rec.rate = 1 / 100, rec.rate.g2 = 1 / 100)
init <- init.icm(s.num = 500, i.num = 1,
s.num.g2 = 500, i.num.g2 = 0)
control <- control.icm(type = "SIS", nsteps = 5, nsims = 2, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
test_that("SIS, 1G, OP: 1 sim", {
param <- param.icm(inf.prob = 0.2,
act.rate = 0.5, rec.rate = 1 / 50,
a.rate = 1 / 100, ds.rate = 1 / 100, di.rate = 1 / 90)
init <- init.icm(s.num = 500, i.num = 1)
control <- control.icm(type = "SIS", nsteps = 10, nsims = 1, verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
# Other -------------------------------------------------------------------
test_that("Act rate balance works when specified to g2", {
param <- param.icm(inf.prob = 0.2,
inf.prob.g2 = 0.1,
act.rate.g2 = 0.5,
balance = "g2",
rec.rate = 1 / 50,
rec.rate.g2 = 1 / 50,
a.rate = 1 / 100,
a.rate.g2 = NA,
ds.rate = 1 / 100,
ds.rate.g2 = 1 / 100,
di.rate = 1 / 90,
di.rate.g2 = 1 / 90)
init <- init.icm(s.num = 50,
i.num = 10,
s.num.g2 = 100,
i.num.g2 = 1)
control <- control.icm(type = "SIS",
nsteps = 10,
nsims = 1,
verbose = FALSE)
x <- icm(param, init, control)
expect_is(x, "icm")
})
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