R/model.R
In trosendal/paratb: Infectious Disease Model of Paratuberculosis in a Cattle Herd
Defines functions
paratb
Documented in
paratb
##' Class \code{paratb}
##'
##' Class to handle the \code{paratb} \code{SimInf_model}.
##' @export
setClass("paratb", contains = "SimInf_model")
##' Create a model for the SimInf framework
##'
##' Create a model to be used by the SimInf framework.
##' @param u0 A data.frame with the initial state in each node.
##' @param tspan A vector (length >= 2) of increasing time points
##' where the state of each node is to be returned.
##' @import SimInf
##' @import methods
##' @import Matrix
##' @export
paratb <- function(u0 = NULL, tspan = NULL) {
compartments <- c("S0", "S1", "T1H", "T1L", "S2", "T2H", "T2L",
"E2H", "E2L", "S3", "E3H", "E3L", "L3H", "L3L",
"H3", "BM", "BMp", "BMn")
## Check tspan (if null, make it 1 year)
if (is.null(tspan)) {
tspan <- 1:365
}
## Check u0
if (!is.null(u0)) {
if (!is.data.frame(u0))
u0 <- as.data.frame(u0)
if (!all(compartments %in% names(u0)))
stop("Missing columns in u0")
u0 <- u0[, compartments, drop = FALSE]
} else {
## Start with 10000 farms with 200 animals each without any infection
u0 <- data.frame(S0 = rep(0, 10000),
S1 = 50,
T1H = 0,
T1L = 0,
S2 = 50,
T2H = 0,
T2L = 0,
E2H = 0,
E2L = 0,
S3 = 100,
E3H = 0,
E3L = 0,
L3H = 0,
L3L = 0,
H3 = 0,
BM = 0,
BMp = 0,
BMn = 0)
}
G <- new("dgCMatrix", i = c(1L, 2L, 3L, 1L, 2L, 3L, 4L, 5L, 6L,
9L, 12L, 13L, 26L, 1L, 2L, 3L, 4L, 5L,
7L, 10L, 12L, 13L, 26L, 1L, 2L, 3L,
4L, 5L, 8L, 11L, 12L, 13L, 26L, 4L,
5L, 6L, 7L, 9L, 10L, 12L, 13L, 26L,
4L, 5L, 6L, 8L, 9L, 11L, 12L, 13L,
26L, 4L, 5L, 6L, 9L, 12L, 13L, 16L,
21L, 26L, 4L, 5L, 7L, 10L, 12L, 13L,
14L, 19L, 22L, 26L, 4L, 5L, 8L, 11L,
12L, 13L, 15L, 20L, 23L, 26L, 4L, 5L,
6L, 9L, 12L, 13L, 26L, 4L, 5L, 7L,
10L, 12L, 13L, 26L, 4L, 5L, 8L, 11L,
12L, 13L, 26L, 4L, 5L, 12L, 13L, 14L,
16L, 19L, 21L, 22L, 26L, 4L, 5L, 12L,
13L, 15L, 16L, 20L, 21L, 23L, 26L, 4L,
5L, 12L, 13L, 14L, 17L, 19L, 22L, 24L,
26L, 4L, 5L, 12L, 13L, 15L, 18L, 20L,
23L, 25L, 26L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 16L, 21L, 26L, 30L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 17L, 24L, 26L, 27L, 31L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 18L, 25L, 26L, 28L, 32L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 14L, 19L, 22L, 26L, 27L, 31L,
39L, 40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 15L, 20L, 23L, 26L, 28L,
32L, 39L, 40L, 41L, 4L, 5L, 12L, 13L,
16L, 21L, 26L, 4L, 5L, 12L, 13L, 14L,
19L, 22L, 26L, 4L, 5L, 12L, 13L, 15L,
20L, 23L, 26L, 4L, 5L, 12L, 13L, 17L,
24L, 26L, 4L, 5L, 12L, 13L, 18L, 25L,
26L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 28L, 30L, 32L, 39L, 40L, 41L, 0L,
1L, 2L, 3L, 4L, 5L, 12L, 13L, 26L,
27L, 29L, 31L, 33L, 36L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 28L, 32L, 34L, 37L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 29L, 33L, 35L, 36L, 38L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 26L, 30L, 39L, 40L, 41L, 0L, 1L,
2L, 3L, 4L, 5L, 12L, 13L, 26L, 27L,
31L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 28L, 32L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 26L, 29L, 33L, 36L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 34L, 37L, 39L, 40L, 41L, 0L, 1L,
2L, 3L, 4L, 5L, 12L, 13L, 26L, 35L,
38L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 29L, 30L, 33L,
36L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 30L, 34L, 37L,
39L, 40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 26L, 30L, 35L, 38L, 39L,
40L, 41L, 40L, 41L, 40L, 41L, 40L,
41L),
p = c(0L, 3L, 13L, 23L, 33L, 42L, 51L, 60L, 70L, 80L,
87L, 94L, 101L, 111L, 121L, 131L, 141L, 156L, 172L,
188L, 205L, 222L, 229L, 237L, 245L, 252L, 259L,
274L, 291L, 307L, 324L, 337L, 351L, 365L, 380L,
394L, 408L, 424L, 439L, 454L, 456L, 458L, 460L),
Dim = c(42L, 42L),
Dimnames = list(c("@ -> S0", "S0 -> S1", "S0 -> T1H",
"S0 -> T1L", "S1 -> T1H", "S1 -> T1L",
"S1 -> S2", "T1H -> T2H", "T1L -> T2L",
"S1 -> @", "T1H -> @", "T1L -> @",
"S2 -> T2H", "S2 -> T2L", "T2H -> E2H",
"T2L -> E2L", "S2 -> S3", "E2H -> E3H",
"E2L -> E3L", "T2H -> E3H",
"T2L -> E3L", "S2 -> @", "T2H -> @",
"T2L -> @", "E2H -> @", "E2L -> @",
"S3 -> E3L", "E3H -> L3H",
"E3L -> L3L", "L3H -> H3", "S3 -> @",
"E3H -> @", "E3L -> @", "L3H -> @",
"L3L -> @", "H3 -> @", "L3H -> S3",
"L3L -> S3", "H3 -> S3", "@ -> BM",
"BM -> BMp", "BM -> BMn"),
c("1", "2", "3", "4", "5", "6", "7", "8",
"9", "10", "11", "12", "13", "14",
"15", "16", "17", "18", "19", "20",
"21", "22", "23", "24", "25", "26",
"27", "28", "29", "30", "31", "32",
"33", "34", "35", "36", "37", "38",
"39", "43", "44", "45")),
x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1), factors = list())
S <- new("dgCMatrix", i = c(0L, 0L, 1L, 0L, 2L, 0L, 3L, 1L, 2L,
1L, 3L, 1L, 4L, 2L, 5L, 3L, 6L, 1L,
2L, 3L, 4L, 5L, 4L, 6L, 5L, 7L, 6L,
8L, 4L, 9L, 7L, 10L, 8L, 11L, 5L, 10L,
6L, 11L, 4L, 5L, 6L, 7L, 8L, 9L, 11L,
10L, 12L, 11L, 13L, 12L, 14L, 9L, 10L,
11L, 12L, 13L, 14L, 9L, 12L, 9L, 13L,
9L, 14L, 15L, 15L, 16L, 15L, 17L),
p = c(0L, 1L, 3L, 5L, 7L, 9L, 11L, 13L, 15L, 17L, 18L,
19L, 20L, 22L, 24L, 26L, 28L, 30L, 32L, 34L, 36L,
38L, 39L, 40L, 41L, 42L, 43L, 45L, 47L, 49L, 51L,
52L, 53L, 54L, 55L, 56L, 57L, 59L, 61L, 63L, 64L,
66L, 68L), Dim = c(18L, 42L),
Dimnames = list(
c("S0", "S1", "T1H", "T1L", "S2", "T2H", "T2L",
"E2H", "E2L", "S3", "E3H", "E3L", "L3H", "L3L",
"H3", "BM", "BMp", "BMn"),
c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
"11", "12", "13", "14", "15", "16", "17", "18",
"19", "20", "21", "22", "23", "24", "25", "26",
"27", "28", "29", "30", "31", "32", "33", "34",
"35", "36", "37", "38", "39", "43", "44", "45")),
x = c(1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1,
-1, 1, -1, -1, -1, -1, 1, -1, 1, -1, 1, -1, 1, -1,
1, -1, 1, -1, 1, -1, 1, -1, 1, -1, -1, -1, -1, -1,
-1, 1, -1, 1, -1, 1, -1, 1, -1, -1, -1, -1, -1, -1,
1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1), factors = list())
E <- methods::as(matrix(integer(0), nrow = 0, ncol = 0), "dgCMatrix")
N <- matrix(integer(0), nrow = 0, ncol = 0)
v0 <- matrix(numeric(0), nrow = 0, ncol = nrow(u0))
storage.mode(v0) <- "double"
ldata <- matrix(numeric(0), nrow = 0, ncol = nrow(u0))
storage.mode(ldata) <- "double"
## By default don't add any events
events <- NULL
gdata <- structure(c(1000, 0.01, 0.04, 0.04, 0.00273973,
0.00273973, 0.00547945, 0.335, 0.0589041,
0.00145205, 0.00468493, 0.00123288,
0.00273973, 0.000246575, 0.00273973,
2.73973e-05, 0.00112329, 0.000136986,
7.980511, -2.048039, 0, 1, 0.6269236),
.Names = c("p1", "gamma_E", "gamma_L",
"gamma_H", "beta", "beta_a", "phi",
"eta", "sigma_H", "sigma_L", "nu",
"mu_b", "rho_1", "mu_1", "rho_2",
"mu_2", "mu_3", "mu_4", "intercept",
"coef", "delta2", "Sp2", "IND_SE"))
model <- SimInf_model(G = G,
S = S,
E = E,
N = N,
tspan = tspan,
events = events,
ldata = ldata,
gdata = gdata,
u0 = u0,
v0 = v0)
methods::as(model, "paratb")
}
##' Run the model
##'
##' @rdname run-methods
##' @param model The model to run.
##' @param solver Which numerical solver to utilize. Default is 'ssa'.
##' @return model with result from simulation.
##' @export
##' @useDynLib paratb, .registration=TRUE
setMethod("run",
signature(model = "paratb"),
function(model, solver = NULL) {
methods::validObject(model)
.Call(paratb_run, model, solver)
})
trosendal/paratb documentation built on Oct. 7, 2022, 3:42 p.m.
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Defines functions paratb
Documented in paratb
##' Class \code{paratb}
##'
##' Class to handle the \code{paratb} \code{SimInf_model}.
##' @export
setClass("paratb", contains = "SimInf_model")
##' Create a model for the SimInf framework
##'
##' Create a model to be used by the SimInf framework.
##' @param u0 A data.frame with the initial state in each node.
##' @param tspan A vector (length >= 2) of increasing time points
##' where the state of each node is to be returned.
##' @import SimInf
##' @import methods
##' @import Matrix
##' @export
paratb <- function(u0 = NULL, tspan = NULL) {
compartments <- c("S0", "S1", "T1H", "T1L", "S2", "T2H", "T2L",
"E2H", "E2L", "S3", "E3H", "E3L", "L3H", "L3L",
"H3", "BM", "BMp", "BMn")
## Check tspan (if null, make it 1 year)
if (is.null(tspan)) {
tspan <- 1:365
}
## Check u0
if (!is.null(u0)) {
if (!is.data.frame(u0))
u0 <- as.data.frame(u0)
if (!all(compartments %in% names(u0)))
stop("Missing columns in u0")
u0 <- u0[, compartments, drop = FALSE]
} else {
## Start with 10000 farms with 200 animals each without any infection
u0 <- data.frame(S0 = rep(0, 10000),
S1 = 50,
T1H = 0,
T1L = 0,
S2 = 50,
T2H = 0,
T2L = 0,
E2H = 0,
E2L = 0,
S3 = 100,
E3H = 0,
E3L = 0,
L3H = 0,
L3L = 0,
H3 = 0,
BM = 0,
BMp = 0,
BMn = 0)
}
G <- new("dgCMatrix", i = c(1L, 2L, 3L, 1L, 2L, 3L, 4L, 5L, 6L,
9L, 12L, 13L, 26L, 1L, 2L, 3L, 4L, 5L,
7L, 10L, 12L, 13L, 26L, 1L, 2L, 3L,
4L, 5L, 8L, 11L, 12L, 13L, 26L, 4L,
5L, 6L, 7L, 9L, 10L, 12L, 13L, 26L,
4L, 5L, 6L, 8L, 9L, 11L, 12L, 13L,
26L, 4L, 5L, 6L, 9L, 12L, 13L, 16L,
21L, 26L, 4L, 5L, 7L, 10L, 12L, 13L,
14L, 19L, 22L, 26L, 4L, 5L, 8L, 11L,
12L, 13L, 15L, 20L, 23L, 26L, 4L, 5L,
6L, 9L, 12L, 13L, 26L, 4L, 5L, 7L,
10L, 12L, 13L, 26L, 4L, 5L, 8L, 11L,
12L, 13L, 26L, 4L, 5L, 12L, 13L, 14L,
16L, 19L, 21L, 22L, 26L, 4L, 5L, 12L,
13L, 15L, 16L, 20L, 21L, 23L, 26L, 4L,
5L, 12L, 13L, 14L, 17L, 19L, 22L, 24L,
26L, 4L, 5L, 12L, 13L, 15L, 18L, 20L,
23L, 25L, 26L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 16L, 21L, 26L, 30L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 17L, 24L, 26L, 27L, 31L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 18L, 25L, 26L, 28L, 32L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 14L, 19L, 22L, 26L, 27L, 31L,
39L, 40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 15L, 20L, 23L, 26L, 28L,
32L, 39L, 40L, 41L, 4L, 5L, 12L, 13L,
16L, 21L, 26L, 4L, 5L, 12L, 13L, 14L,
19L, 22L, 26L, 4L, 5L, 12L, 13L, 15L,
20L, 23L, 26L, 4L, 5L, 12L, 13L, 17L,
24L, 26L, 4L, 5L, 12L, 13L, 18L, 25L,
26L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 28L, 30L, 32L, 39L, 40L, 41L, 0L,
1L, 2L, 3L, 4L, 5L, 12L, 13L, 26L,
27L, 29L, 31L, 33L, 36L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 28L, 32L, 34L, 37L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 29L, 33L, 35L, 36L, 38L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 26L, 30L, 39L, 40L, 41L, 0L, 1L,
2L, 3L, 4L, 5L, 12L, 13L, 26L, 27L,
31L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 28L, 32L, 39L,
40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L,
13L, 26L, 29L, 33L, 36L, 39L, 40L,
41L, 0L, 1L, 2L, 3L, 4L, 5L, 12L, 13L,
26L, 34L, 37L, 39L, 40L, 41L, 0L, 1L,
2L, 3L, 4L, 5L, 12L, 13L, 26L, 35L,
38L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 29L, 30L, 33L,
36L, 39L, 40L, 41L, 0L, 1L, 2L, 3L,
4L, 5L, 12L, 13L, 26L, 30L, 34L, 37L,
39L, 40L, 41L, 0L, 1L, 2L, 3L, 4L, 5L,
12L, 13L, 26L, 30L, 35L, 38L, 39L,
40L, 41L, 40L, 41L, 40L, 41L, 40L,
41L),
p = c(0L, 3L, 13L, 23L, 33L, 42L, 51L, 60L, 70L, 80L,
87L, 94L, 101L, 111L, 121L, 131L, 141L, 156L, 172L,
188L, 205L, 222L, 229L, 237L, 245L, 252L, 259L,
274L, 291L, 307L, 324L, 337L, 351L, 365L, 380L,
394L, 408L, 424L, 439L, 454L, 456L, 458L, 460L),
Dim = c(42L, 42L),
Dimnames = list(c("@ -> S0", "S0 -> S1", "S0 -> T1H",
"S0 -> T1L", "S1 -> T1H", "S1 -> T1L",
"S1 -> S2", "T1H -> T2H", "T1L -> T2L",
"S1 -> @", "T1H -> @", "T1L -> @",
"S2 -> T2H", "S2 -> T2L", "T2H -> E2H",
"T2L -> E2L", "S2 -> S3", "E2H -> E3H",
"E2L -> E3L", "T2H -> E3H",
"T2L -> E3L", "S2 -> @", "T2H -> @",
"T2L -> @", "E2H -> @", "E2L -> @",
"S3 -> E3L", "E3H -> L3H",
"E3L -> L3L", "L3H -> H3", "S3 -> @",
"E3H -> @", "E3L -> @", "L3H -> @",
"L3L -> @", "H3 -> @", "L3H -> S3",
"L3L -> S3", "H3 -> S3", "@ -> BM",
"BM -> BMp", "BM -> BMn"),
c("1", "2", "3", "4", "5", "6", "7", "8",
"9", "10", "11", "12", "13", "14",
"15", "16", "17", "18", "19", "20",
"21", "22", "23", "24", "25", "26",
"27", "28", "29", "30", "31", "32",
"33", "34", "35", "36", "37", "38",
"39", "43", "44", "45")),
x = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1), factors = list())
S <- new("dgCMatrix", i = c(0L, 0L, 1L, 0L, 2L, 0L, 3L, 1L, 2L,
1L, 3L, 1L, 4L, 2L, 5L, 3L, 6L, 1L,
2L, 3L, 4L, 5L, 4L, 6L, 5L, 7L, 6L,
8L, 4L, 9L, 7L, 10L, 8L, 11L, 5L, 10L,
6L, 11L, 4L, 5L, 6L, 7L, 8L, 9L, 11L,
10L, 12L, 11L, 13L, 12L, 14L, 9L, 10L,
11L, 12L, 13L, 14L, 9L, 12L, 9L, 13L,
9L, 14L, 15L, 15L, 16L, 15L, 17L),
p = c(0L, 1L, 3L, 5L, 7L, 9L, 11L, 13L, 15L, 17L, 18L,
19L, 20L, 22L, 24L, 26L, 28L, 30L, 32L, 34L, 36L,
38L, 39L, 40L, 41L, 42L, 43L, 45L, 47L, 49L, 51L,
52L, 53L, 54L, 55L, 56L, 57L, 59L, 61L, 63L, 64L,
66L, 68L), Dim = c(18L, 42L),
Dimnames = list(
c("S0", "S1", "T1H", "T1L", "S2", "T2H", "T2L",
"E2H", "E2L", "S3", "E3H", "E3L", "L3H", "L3L",
"H3", "BM", "BMp", "BMn"),
c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10",
"11", "12", "13", "14", "15", "16", "17", "18",
"19", "20", "21", "22", "23", "24", "25", "26",
"27", "28", "29", "30", "31", "32", "33", "34",
"35", "36", "37", "38", "39", "43", "44", "45")),
x = c(1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1,
-1, 1, -1, -1, -1, -1, 1, -1, 1, -1, 1, -1, 1, -1,
1, -1, 1, -1, 1, -1, 1, -1, 1, -1, -1, -1, -1, -1,
-1, 1, -1, 1, -1, 1, -1, 1, -1, -1, -1, -1, -1, -1,
1, -1, 1, -1, 1, -1, 1, -1, 1, -1, 1), factors = list())
E <- methods::as(matrix(integer(0), nrow = 0, ncol = 0), "dgCMatrix")
N <- matrix(integer(0), nrow = 0, ncol = 0)
v0 <- matrix(numeric(0), nrow = 0, ncol = nrow(u0))
storage.mode(v0) <- "double"
ldata <- matrix(numeric(0), nrow = 0, ncol = nrow(u0))
storage.mode(ldata) <- "double"
## By default don't add any events
events <- NULL
gdata <- structure(c(1000, 0.01, 0.04, 0.04, 0.00273973,
0.00273973, 0.00547945, 0.335, 0.0589041,
0.00145205, 0.00468493, 0.00123288,
0.00273973, 0.000246575, 0.00273973,
2.73973e-05, 0.00112329, 0.000136986,
7.980511, -2.048039, 0, 1, 0.6269236),
.Names = c("p1", "gamma_E", "gamma_L",
"gamma_H", "beta", "beta_a", "phi",
"eta", "sigma_H", "sigma_L", "nu",
"mu_b", "rho_1", "mu_1", "rho_2",
"mu_2", "mu_3", "mu_4", "intercept",
"coef", "delta2", "Sp2", "IND_SE"))
model <- SimInf_model(G = G,
S = S,
E = E,
N = N,
tspan = tspan,
events = events,
ldata = ldata,
gdata = gdata,
u0 = u0,
v0 = v0)
methods::as(model, "paratb")
}
##' Run the model
##'
##' @rdname run-methods
##' @param model The model to run.
##' @param solver Which numerical solver to utilize. Default is 'ssa'.
##' @return model with result from simulation.
##' @export
##' @useDynLib paratb, .registration=TRUE
setMethod("run",
signature(model = "paratb"),
function(model, solver = NULL) {
methods::validObject(model)
.Call(paratb_run, model, solver)
})
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