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tests/SISe_sp.R
In SimInf: A Framework for Data-Driven Stochastic Disease Spread Simulations
## This file is part of SimInf, a framework for stochastic
## disease spread simulations.
##
## Copyright (C) 2015 Pavol Bauer
## Copyright (C) 2017 -- 2019 Robin Eriksson
## Copyright (C) 2015 -- 2019 Stefan Engblom
## Copyright (C) 2015 -- 2020 Stefan Widgren
##
## SimInf is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## SimInf is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program. If not, see <https://www.gnu.org/licenses/>.
library(SimInf)
library(tools)
source("util/check.R")
## Specify the number of threads to use.
set_num_threads(1)
## For debugging
sessionInfo()
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5, 6, 7, 8),
I = c(0, 0, 0, 0, 0, 0, 0, 0, 0))
## Place nodes in a grid
distance <- expand.grid(x = seq_len(3),
y = seq_len(3))
distance <- distance_matrix(distance$x, distance$y, 2)
## Check missing columns in u0
res <- assertError(SISe_sp(u0 = u0[, "I", drop = FALSE]))
check_error(res, "Missing columns in u0.")
res <- assertError(SISe_sp(u0 = u0[, "S", drop = FALSE]))
check_error(res, "Missing columns in u0.")
## Check default phi
res <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
stopifnot(identical(res@v0,
structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0),
.Dim = c(1L, 9L),
.Dimnames = list("phi", NULL))))
## Check missing upsilon
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check missing gamma
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check missing alpha
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check missing beta_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check missing beta_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check missing beta_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check missing beta_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check missing end_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' is missing.")
## Check missing end_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' is missing.")
## Check missing end_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' is missing.")
## Check missing end_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' is missing.")
## Check missing coupling
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check missing distance
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005))
check_error(res, "'distance' is missing.")
## Check negative distance
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = -distance))
check_error(res, "All values in the 'distance' matrix must be >= 0.")
## Check non-numeric upsilon
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = "0.0357",
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check non-numeric gamma
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = "0.1",
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check non-numeric alpha
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = "1.0",
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check non-numeric beta_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = "0.19",
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check non-numeric beta_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = "0.085",
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check non-numeric beta_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = "0.075",
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check non-numeric beta_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = "0.185",
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check non-integer end_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = "91",
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91.5,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be integer.")
## Check non-integer end_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = "182",
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182.5,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' must be integer.")
## Check non-integer end_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = "273",
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273.5,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be integer.")
## Check non-integer end_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = "365",
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365.5,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be integer.")
## Check non-numeric coupling
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = "0.0005",
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check that length of upsilon equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = c(0.0357, 0.0357),
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check that length of gamma equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = c(0.1, 0.1),
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check that length of alpha equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = c(1.0, 1.0),
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check that length of beta_t1 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = c(0.19, 0.19),
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check that length of beta_t2 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = c(0.085, 0.085),
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check that length of beta_t3 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = c(0.075, 0.075),
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check that length of beta_t4 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = c(0.185, 0.185),
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check that length of coupling equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = c(0.0005, 0.0005),
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check interval endpoints
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = -1,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be greater than or equal to '0'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 18,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be less than 'end_t2'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 173,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(
res,
"'end_t2' must be less than 'end_t3' or 'end_t3' less than 'end_t1'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 365,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be less than '364'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = -1,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be greater than or equal to '0'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 366,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be less than or equal to '365'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 4:12,
end_t2 = 5:13,
end_t3 = c(8:15, 19),
end_t4 = c(2, 11:18),
coupling = 0.0005,
distance = distance))
check_error(
res,
"'end_t4' must be less than 'end_t1' or greater than 'end_t3'.")
## Check distance matrix
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = as.matrix(distance)))
check_error(res, "The 'distance' argument must be of type 'dgCMatrix'.")
## Check that non-data.frame u0 works
SISe_sp(u0 = cbind(S = 0:8, I = rep(0, 9)),
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(0, 9),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
## Check extraction of data from 'suscpetible', and 'infected'
## compartments
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(0, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
result <- run(model)
S_expected <- structure(c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L),
.Dim = 9:10)
S_observed <- trajectory(result, compartments = "S", format = "matrix")
stopifnot(identical(S_observed, S_expected))
I_expected <- structure(c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
.Dim = 9:10)
I_observed <- trajectory(result, compartments = "I", format = "matrix")
stopifnot(identical(I_observed, I_expected))
## Check SISe_sp plot method
pdf_file <- tempfile(fileext = ".pdf")
pdf(pdf_file)
plot(result)
dev.off()
stopifnot(file.exists(pdf_file))
unlink(pdf_file)
## Check that C SISe_sp run function fails for misspecified SISe_sp model
res <- assertError(.Call(SimInf:::SISe_sp_run, NULL, NULL))
check_error(res, "Invalid model.")
res <- assertError(.Call(SimInf:::SISe_sp_run, "SISe_sp", NULL))
check_error(res, "Invalid model.")
## Check error non-finite v
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
model@gdata["beta_t1"] <- Inf
model@gdata["beta_t2"] <- Inf
model@gdata["beta_t3"] <- Inf
model@gdata["beta_t4"] <- Inf
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is not finite.")
## Check negative v
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5, 6, 7, 8),
I = c(10, 10, 10, 10, 10, 10, 10, 10, 10))
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0,
gamma = 0,
alpha = -1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is negative.")
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## This file is part of SimInf, a framework for stochastic
## disease spread simulations.
##
## Copyright (C) 2015 Pavol Bauer
## Copyright (C) 2017 -- 2019 Robin Eriksson
## Copyright (C) 2015 -- 2019 Stefan Engblom
## Copyright (C) 2015 -- 2020 Stefan Widgren
##
## SimInf is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## SimInf is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with this program. If not, see <https://www.gnu.org/licenses/>.
library(SimInf)
library(tools)
source("util/check.R")
## Specify the number of threads to use.
set_num_threads(1)
## For debugging
sessionInfo()
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5, 6, 7, 8),
I = c(0, 0, 0, 0, 0, 0, 0, 0, 0))
## Place nodes in a grid
distance <- expand.grid(x = seq_len(3),
y = seq_len(3))
distance <- distance_matrix(distance$x, distance$y, 2)
## Check missing columns in u0
res <- assertError(SISe_sp(u0 = u0[, "I", drop = FALSE]))
check_error(res, "Missing columns in u0.")
res <- assertError(SISe_sp(u0 = u0[, "S", drop = FALSE]))
check_error(res, "Missing columns in u0.")
## Check default phi
res <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
stopifnot(identical(res@v0,
structure(c(0, 0, 0, 0, 0, 0, 0, 0, 0),
.Dim = c(1L, 9L),
.Dimnames = list("phi", NULL))))
## Check missing upsilon
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check missing gamma
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check missing alpha
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check missing beta_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check missing beta_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check missing beta_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check missing beta_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check missing end_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' is missing.")
## Check missing end_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' is missing.")
## Check missing end_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' is missing.")
## Check missing end_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' is missing.")
## Check missing coupling
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check missing distance
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005))
check_error(res, "'distance' is missing.")
## Check negative distance
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = -distance))
check_error(res, "All values in the 'distance' matrix must be >= 0.")
## Check non-numeric upsilon
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = "0.0357",
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check non-numeric gamma
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = "0.1",
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check non-numeric alpha
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = "1.0",
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check non-numeric beta_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = "0.19",
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check non-numeric beta_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = "0.085",
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check non-numeric beta_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = "0.075",
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check non-numeric beta_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = "0.185",
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check non-integer end_t1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = "91",
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91.5,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be integer.")
## Check non-integer end_t2
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = "182",
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182.5,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t2' must be integer.")
## Check non-integer end_t3
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = "273",
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273.5,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be integer.")
## Check non-integer end_t4
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = "365",
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be integer.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365.5,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be integer.")
## Check non-numeric coupling
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = "0.0005",
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check that length of upsilon equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = c(0.0357, 0.0357),
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check that length of gamma equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = c(0.1, 0.1),
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'gamma' must be numeric of length 1.")
## Check that length of alpha equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = c(1.0, 1.0),
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'alpha' must be numeric of length 1.")
## Check that length of beta_t1 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = c(0.19, 0.19),
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check that length of beta_t2 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = c(0.085, 0.085),
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check that length of beta_t3 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = c(0.075, 0.075),
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check that length of beta_t4 equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = c(0.185, 0.185),
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check that length of coupling equals 1
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = c(0.0005, 0.0005),
distance = distance))
check_error(res, "'coupling' must be numeric of length 1.")
## Check interval endpoints
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = -1,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be greater than or equal to '0'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 18,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t1' must be less than 'end_t2'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 173,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(
res,
"'end_t2' must be less than 'end_t3' or 'end_t3' less than 'end_t1'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 365,
end_t4 = 365,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t3' must be less than '364'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = -1,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be greater than or equal to '0'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 366,
coupling = 0.0005,
distance = distance))
check_error(res, "'end_t4' must be less than or equal to '365'.")
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 4:12,
end_t2 = 5:13,
end_t3 = c(8:15, 19),
end_t4 = c(2, 11:18),
coupling = 0.0005,
distance = distance))
check_error(
res,
"'end_t4' must be less than 'end_t1' or greater than 'end_t3'.")
## Check distance matrix
res <- assertError(SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = as.matrix(distance)))
check_error(res, "The 'distance' argument must be of type 'dgCMatrix'.")
## Check that non-data.frame u0 works
SISe_sp(u0 = cbind(S = 0:8, I = rep(0, 9)),
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(0, 9),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
## Check extraction of data from 'suscpetible', and 'infected'
## compartments
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(0, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
result <- run(model)
S_expected <- structure(c(0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L,
0L, 1L, 2L, 3L, 4L, 5L, 6L, 7L, 8L),
.Dim = 9:10)
S_observed <- trajectory(result, compartments = "S", format = "matrix")
stopifnot(identical(S_observed, S_expected))
I_expected <- structure(c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
.Dim = 9:10)
I_observed <- trajectory(result, compartments = "I", format = "matrix")
stopifnot(identical(I_observed, I_expected))
## Check SISe_sp plot method
pdf_file <- tempfile(fileext = ".pdf")
pdf(pdf_file)
plot(result)
dev.off()
stopifnot(file.exists(pdf_file))
unlink(pdf_file)
## Check that C SISe_sp run function fails for misspecified SISe_sp model
res <- assertError(.Call(SimInf:::SISe_sp_run, NULL, NULL))
check_error(res, "Invalid model.")
res <- assertError(.Call(SimInf:::SISe_sp_run, "SISe_sp", NULL))
check_error(res, "Invalid model.")
## Check error non-finite v
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0.0357,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
model@gdata["beta_t1"] <- Inf
model@gdata["beta_t2"] <- Inf
model@gdata["beta_t3"] <- Inf
model@gdata["beta_t4"] <- Inf
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is not finite.")
## Check negative v
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5, 6, 7, 8),
I = c(10, 10, 10, 10, 10, 10, 10, 10, 10))
model <- SISe_sp(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep(1, nrow(u0)),
upsilon = 0,
gamma = 0,
alpha = -1.0,
beta_t1 = 0.19,
beta_t2 = 0.085,
beta_t3 = 0.075,
beta_t4 = 0.185,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
coupling = 0.0005,
distance = distance)
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is negative.")
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