tests/SISe.R
In stewid/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()
## Check invalid u0
res <- assertError(SISe(u0 = "u0"))
check_error(res, "Missing columns in u0.")
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5),
I = c(0, 0, 0, 0, 0, 0))
## Check missing columns in u0
res <- assertError(SISe(u0 = u0[, "I", drop = FALSE]))
check_error(res, "Missing columns in u0.")
res <- assertError(SISe(u0 = u0[, "S", drop = FALSE]))
check_error(res, "Missing columns in u0.")
## Check phi
res <- assertError(SISe(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep("a", 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,
epsilon = 0.000011))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
phi <- matrix(1)
res <- assertError(SimInf:::check_infectious_pressure_arg(1, phi))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
phi <- c(2, 2)
res <- assertError(SimInf:::check_infectious_pressure_arg(1, phi))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(
res,
"Invalid 'phi': must be numeric vector with non-negative values.")
res <- SISe(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,
epsilon = 0.000011)
stopifnot(identical(
res@v0,
matrix(0, nrow = 1, ncol = 6, dimnames = list("phi", NULL))))
## Check missing upsilon
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check missing gamma
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check missing alpha
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check missing beta_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check missing beta_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check missing beta_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check missing beta_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check missing end_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' is missing.")
## Check missing end_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' is missing.")
## Check missing end_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' is missing.")
## Check missing end_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' is missing.")
## Check missing epsilon
res <- assertError(SISe(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))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check non-numeric upsilon
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check non-numeric gamma
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check non-numeric alpha
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check non-numeric beta_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check non-numeric beta_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check non-numeric beta_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check non-numeric beta_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check non-integer end_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be integer.")
## Check non-integer end_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' must be integer.")
## Check non-integer end_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be integer.")
## Check non-integer end_t4
res <- assertError(SISe(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",
epsilon = 0.000011))
check_error(res, "'end_t4' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be integer.")
## Check non-numeric epsilon
res <- assertError(SISe(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,
epsilon = "0.000011"))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check that length of upsilon equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check that length of gamma equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check that length of alpha equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check that length of beta_t1 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check that length of beta_t2 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check that length of beta_t3 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check that length of beta_t4 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check that length of epsilon equals 1
res <- assertError(SISe(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,
epsilon = c(0.000011, 0.000011)))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check interval endpoints
end_t1 <- 1:3
res <- assertError(SimInf:::check_end_t_arg(2, end_t1))
check_error(res, "'end_t1' must be of length 1 or 'nrow(u0)'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be greater than or equal to '0'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be less than 'end_t2'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(
res,
"'end_t2' must be less than 'end_t3' or 'end_t3' less than 'end_t1'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be less than '364'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be greater than or equal to '0'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be less than or equal to '365'.")
res <- assertError(SISe(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 = 4:9,
end_t2 = 5:10,
end_t3 = c(8:12, 16),
end_t4 = c(2, 11:15),
epsilon = 0.000011))
check_error(
res,
"'end_t4' must be less than 'end_t1' or greater than 'end_t3'.")
## Check extraction of data from 'suscpetible', and 'infected'
## compartments
model <- SISe(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = seq(0, by = 0.1, length.out = nrow(u0)),
upsilon = 0,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0,
beta_t2 = 0,
beta_t3 = 0,
beta_t4 = 0,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
epsilon = 0)
result <- run(model)
S_expected <- structure(c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L,
1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L,
2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L,
3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L,
4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
.Dim = c(6L, 10L))
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),
.Dim = c(6L, 10L))
I_observed <- trajectory(result, compartments = "I", format = "matrix")
stopifnot(identical(I_observed, I_expected))
## Check output from trajectory method
model@tspan <- c(1, 2)
result <- run(model)
res <- assertError(trajectory(result, c("S", "phi"), format = "matrix"))
check_error(res,
"Cannot combine data from different slots.")
stopifnot(identical(class(trajectory(result, c("S", "phi"))$phi), "numeric"))
stopifnot(identical(class(trajectory(result, c("phi"))$phi), "numeric"))
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L))
stopifnot(identical(trajectory(result, c("S", "S")), traj_expected))
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
phi = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0, 0.1, 0.2, 0.3, 0.4, 0.5))
stopifnot(identical(
trajectory(result, c("S", "S", "phi", "phi"))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("phi", "phi", "S", "S"))[, -4],
traj_expected[, -4]))
d <- trajectory(result, c("phi", "phi", "S", "S"))[, 4] - traj_expected$phi
stopifnot(all(abs(d) < 1e-8))
## Check extracting a subset of nodes
traj_expected <- data.frame(
node = c(2L, 5L, 2L, 5L),
time = c(1L, 1L, 2L, 2L),
S = c(1L, 4L, 1L, 4L),
phi = c(0.1, 0.4, 0.1, 0.4))
stopifnot(identical(
trajectory(result, c("S", "S", "phi", "phi"), index = c(5, 2))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("phi", "phi", "S", "S"), index = c(5, 2))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("S", "phi"), index = c(5, 2)),
traj_expected))
d <- trajectory(result, c("phi", "phi", "S", "S"), index = c(5, 2))[, 4] -
traj_expected$phi
stopifnot(all(abs(d) < 1e-8))
## Check extracting all compartments in U
stopifnot(identical(trajectory(result, c("S", "I"), format = "matrix"),
result@U))
## Check extracting all compartments of U in internal format
stopifnot(identical(trajectory(result, c("S", "I"), format = "matrix"),
result@U))
## Check extracting a subset compartments of V in internal format
traj_observed <- trajectory(result, "phi", index = c(5, 2), format = "matrix")
stopifnot(identical(dim(traj_observed), c(2L, 2L)))
stopifnot(all(abs(traj_observed[1, ] - 0.1) < 1e-8))
stopifnot(all(abs(traj_observed[2, ] - 0.4) < 1e-8))
## Check extracting all compartments in a subset of U as a data.frame
traj_expected <- data.frame(node = c(2L, 5L, 2L, 5L),
time = c(1L, 1L, 2L, 2L),
S = c(1L, 4L, 1L, 4L),
I = c(0L, 0L, 0L, 0L))
stopifnot(identical(
trajectory(result, c("S", "I"), index = c(5, 2)),
traj_expected))
## Check extracting all compartments in U as a data.frame
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
I = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))
traj_observed <- trajectory(result, c("S", "I"))
stopifnot(identical(traj_observed, traj_expected))
## Check extracting all compartments in U and V as a data.frame
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
I = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
phi = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0, 0.1, 0.2, 0.3, 0.4, 0.5))
traj_observed <- trajectory(result, c("S", "I", "phi"))
stopifnot(identical(traj_observed[, -5], traj_expected[, -5]))
stopifnot(all(abs(traj_observed[, 5] - traj_expected$phi) < 1e-8))
## Use formula notation
traj_observed <- trajectory(result, ~.)
stopifnot(identical(traj_observed[, -5], traj_expected[, -5]))
stopifnot(all(abs(traj_observed[, 5] - traj_expected$phi) < 1e-8))
## Specify invalid formula
res <- assertError(trajectory(result, ~1))
check_error(res, "Non-existing compartment(s) in model: '1'.")
## Check SISe 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 run function fails for misspecified SISe model
res <- assertError(.Call(SimInf:::SISe_run, NULL, NULL))
check_error(res, "Invalid model.")
res <- assertError(.Call(SimInf:::SISe_run, "SISe", NULL))
check_error(res, "Invalid model.")
## Check error non-finite v
model <- SISe(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,
epsilon = 0.000011)
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
model <- SISe(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,
epsilon = -10.000011)
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is negative.")
## Check data
stopifnot(identical(nrow(events_SISe()), 466692L))
stopifnot(identical(nrow(u0_SISe()), 1600L))
stewid/SimInf documentation built on April 26, 2024, 5:14 a.m.
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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()
## Check invalid u0
res <- assertError(SISe(u0 = "u0"))
check_error(res, "Missing columns in u0.")
u0 <- data.frame(S = c(0, 1, 2, 3, 4, 5),
I = c(0, 0, 0, 0, 0, 0))
## Check missing columns in u0
res <- assertError(SISe(u0 = u0[, "I", drop = FALSE]))
check_error(res, "Missing columns in u0.")
res <- assertError(SISe(u0 = u0[, "S", drop = FALSE]))
check_error(res, "Missing columns in u0.")
## Check phi
res <- assertError(SISe(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = rep("a", 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,
epsilon = 0.000011))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
phi <- matrix(1)
res <- assertError(SimInf:::check_infectious_pressure_arg(1, phi))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
phi <- c(2, 2)
res <- assertError(SimInf:::check_infectious_pressure_arg(1, phi))
check_error(
res,
"Invalid 'phi': must be numeric vector with length 'nrow(u0)'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(
res,
"Invalid 'phi': must be numeric vector with non-negative values.")
res <- SISe(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,
epsilon = 0.000011)
stopifnot(identical(
res@v0,
matrix(0, nrow = 1, ncol = 6, dimnames = list("phi", NULL))))
## Check missing upsilon
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check missing gamma
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check missing alpha
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check missing beta_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check missing beta_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check missing beta_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check missing beta_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check missing end_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' is missing.")
## Check missing end_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' is missing.")
## Check missing end_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' is missing.")
## Check missing end_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' is missing.")
## Check missing epsilon
res <- assertError(SISe(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))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check non-numeric upsilon
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check non-numeric gamma
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check non-numeric alpha
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check non-numeric beta_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check non-numeric beta_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check non-numeric beta_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check non-numeric beta_t4
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check non-integer end_t1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be integer.")
## Check non-integer end_t2
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t2' must be integer.")
## Check non-integer end_t3
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be integer.")
## Check non-integer end_t4
res <- assertError(SISe(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",
epsilon = 0.000011))
check_error(res, "'end_t4' must be integer.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be integer.")
## Check non-numeric epsilon
res <- assertError(SISe(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,
epsilon = "0.000011"))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check that length of upsilon equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'upsilon' must be numeric of length 1.")
## Check that length of gamma equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'gamma' must be numeric of length 1.")
## Check that length of alpha equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'alpha' must be numeric of length 1.")
## Check that length of beta_t1 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t1' must be numeric of length 1.")
## Check that length of beta_t2 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t2' must be numeric of length 1.")
## Check that length of beta_t3 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t3' must be numeric of length 1.")
## Check that length of beta_t4 equals 1
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'beta_t4' must be numeric of length 1.")
## Check that length of epsilon equals 1
res <- assertError(SISe(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,
epsilon = c(0.000011, 0.000011)))
check_error(res, "'epsilon' must be numeric of length 1.")
## Check interval endpoints
end_t1 <- 1:3
res <- assertError(SimInf:::check_end_t_arg(2, end_t1))
check_error(res, "'end_t1' must be of length 1 or 'nrow(u0)'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be greater than or equal to '0'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t1' must be less than 'end_t2'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(
res,
"'end_t2' must be less than 'end_t3' or 'end_t3' less than 'end_t1'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t3' must be less than '364'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be greater than or equal to '0'.")
res <- assertError(SISe(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,
epsilon = 0.000011))
check_error(res, "'end_t4' must be less than or equal to '365'.")
res <- assertError(SISe(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 = 4:9,
end_t2 = 5:10,
end_t3 = c(8:12, 16),
end_t4 = c(2, 11:15),
epsilon = 0.000011))
check_error(
res,
"'end_t4' must be less than 'end_t1' or greater than 'end_t3'.")
## Check extraction of data from 'suscpetible', and 'infected'
## compartments
model <- SISe(u0 = u0,
tspan = seq_len(10) - 1,
events = NULL,
phi = seq(0, by = 0.1, length.out = nrow(u0)),
upsilon = 0,
gamma = 0.1,
alpha = 1.0,
beta_t1 = 0,
beta_t2 = 0,
beta_t3 = 0,
beta_t4 = 0,
end_t1 = 91,
end_t2 = 182,
end_t3 = 273,
end_t4 = 365,
epsilon = 0)
result <- run(model)
S_expected <- structure(c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L,
1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L,
2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L,
3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L,
4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
.Dim = c(6L, 10L))
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),
.Dim = c(6L, 10L))
I_observed <- trajectory(result, compartments = "I", format = "matrix")
stopifnot(identical(I_observed, I_expected))
## Check output from trajectory method
model@tspan <- c(1, 2)
result <- run(model)
res <- assertError(trajectory(result, c("S", "phi"), format = "matrix"))
check_error(res,
"Cannot combine data from different slots.")
stopifnot(identical(class(trajectory(result, c("S", "phi"))$phi), "numeric"))
stopifnot(identical(class(trajectory(result, c("phi"))$phi), "numeric"))
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L))
stopifnot(identical(trajectory(result, c("S", "S")), traj_expected))
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
phi = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0, 0.1, 0.2, 0.3, 0.4, 0.5))
stopifnot(identical(
trajectory(result, c("S", "S", "phi", "phi"))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("phi", "phi", "S", "S"))[, -4],
traj_expected[, -4]))
d <- trajectory(result, c("phi", "phi", "S", "S"))[, 4] - traj_expected$phi
stopifnot(all(abs(d) < 1e-8))
## Check extracting a subset of nodes
traj_expected <- data.frame(
node = c(2L, 5L, 2L, 5L),
time = c(1L, 1L, 2L, 2L),
S = c(1L, 4L, 1L, 4L),
phi = c(0.1, 0.4, 0.1, 0.4))
stopifnot(identical(
trajectory(result, c("S", "S", "phi", "phi"), index = c(5, 2))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("phi", "phi", "S", "S"), index = c(5, 2))[, -4],
traj_expected[, -4]))
stopifnot(identical(
trajectory(result, c("S", "phi"), index = c(5, 2)),
traj_expected))
d <- trajectory(result, c("phi", "phi", "S", "S"), index = c(5, 2))[, 4] -
traj_expected$phi
stopifnot(all(abs(d) < 1e-8))
## Check extracting all compartments in U
stopifnot(identical(trajectory(result, c("S", "I"), format = "matrix"),
result@U))
## Check extracting all compartments of U in internal format
stopifnot(identical(trajectory(result, c("S", "I"), format = "matrix"),
result@U))
## Check extracting a subset compartments of V in internal format
traj_observed <- trajectory(result, "phi", index = c(5, 2), format = "matrix")
stopifnot(identical(dim(traj_observed), c(2L, 2L)))
stopifnot(all(abs(traj_observed[1, ] - 0.1) < 1e-8))
stopifnot(all(abs(traj_observed[2, ] - 0.4) < 1e-8))
## Check extracting all compartments in a subset of U as a data.frame
traj_expected <- data.frame(node = c(2L, 5L, 2L, 5L),
time = c(1L, 1L, 2L, 2L),
S = c(1L, 4L, 1L, 4L),
I = c(0L, 0L, 0L, 0L))
stopifnot(identical(
trajectory(result, c("S", "I"), index = c(5, 2)),
traj_expected))
## Check extracting all compartments in U as a data.frame
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
I = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L))
traj_observed <- trajectory(result, c("S", "I"))
stopifnot(identical(traj_observed, traj_expected))
## Check extracting all compartments in U and V as a data.frame
traj_expected <- data.frame(
node = c(1L, 2L, 3L, 4L, 5L, 6L, 1L, 2L, 3L, 4L, 5L, 6L),
time = c(1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L),
S = c(0L, 1L, 2L, 3L, 4L, 5L, 0L, 1L, 2L, 3L, 4L, 5L),
I = c(0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L),
phi = c(0, 0.1, 0.2, 0.3, 0.4, 0.5, 0, 0.1, 0.2, 0.3, 0.4, 0.5))
traj_observed <- trajectory(result, c("S", "I", "phi"))
stopifnot(identical(traj_observed[, -5], traj_expected[, -5]))
stopifnot(all(abs(traj_observed[, 5] - traj_expected$phi) < 1e-8))
## Use formula notation
traj_observed <- trajectory(result, ~.)
stopifnot(identical(traj_observed[, -5], traj_expected[, -5]))
stopifnot(all(abs(traj_observed[, 5] - traj_expected$phi) < 1e-8))
## Specify invalid formula
res <- assertError(trajectory(result, ~1))
check_error(res, "Non-existing compartment(s) in model: '1'.")
## Check SISe 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 run function fails for misspecified SISe model
res <- assertError(.Call(SimInf:::SISe_run, NULL, NULL))
check_error(res, "Invalid model.")
res <- assertError(.Call(SimInf:::SISe_run, "SISe", NULL))
check_error(res, "Invalid model.")
## Check error non-finite v
model <- SISe(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,
epsilon = 0.000011)
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
model <- SISe(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,
epsilon = -10.000011)
res <- assertError(run(model))
check_error(res, "The continuous state 'v' is negative.")
## Check data
stopifnot(identical(nrow(events_SISe()), 466692L))
stopifnot(identical(nrow(u0_SISe()), 1600L))
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