The goal of noromod is to provide a three implementations of a model of age-stratified norovirus transmission.
You can install the development version of noromod from GitHub with:
# install.packages("devtools")
pak::pak("pratikunterwegs/noromod")This is a basic example which shows you how to use the three implementations.
Prepare parameters.
library(noromod)
library(deSolve)# define parameters
# initial conditions
init <- c(
3857263, 8103718, 42460865, 12374961,
100, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0,
0, 0, 0, 0
)
init_mat <- matrix(
init,
nrow = 4, ncol = 7
)
age_groups <- c(0, 5, 15, 65)
polymod <- socialmixr::polymod
UK_structure <- socialmixr::contact_matrix(
polymod,
countries = "United Kingdom",
age.limits = c(age_groups),
symmetric = TRUE
)
#> Removing participants that have contacts without age information. To change this behaviour, set the 'missing.contact.age' option
# Symmetrical contact matrix
uk_contact_rate_matrix <- as.matrix(UK_structure$matrix)
demography <- UK_structure$demography$population
uk_contact_rate_matrix <- t(t(uk_contact_rate_matrix) / demography)
# add contact matrix to pop
params <- default_parameters()
params[["contacts"]] <- uk_contact_rate_matrix
# time points
times <- seq(0, 11000)data <- as.data.frame(deSolve::lsoda(init, times, norovirus_model_r, params))
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
plot(rowSums(data[, seq(6, 9)]), type = "l")
# Using Boost solvers for increased speed
# run model
data <- noromod_cpp_boost(
initial_conditions = init_mat,
params = params, time_end = 11000, increment = 1
)
data <- do.call(rbind, lapply(data[["x"]], as.vector))
plot(rowSums(data[, seq(5, 8)]), type = "l")
microbenchmark::microbenchmark(
"noromod_r" = deSolve::lsoda(init, times, norovirus_model_r, params),
"noromod_cpp" = deSolve::lsoda(init, times, norovirus_model_cpp, params),
"noromod_cpp_boost" = noromod_cpp_boost(
initial_conditions = init_mat,
params = params, time_end = max(times), increment = 1
)
)
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> DLSODA- At T (=R1), too much accuracy requested
#> for precision of machine.. See TOLSF (=R2)
#> In above message, R1 = 10771.6, R2 = nan
#>
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Excessive
#> precision requested. scale up `rtol' and `atol' e.g by the factor 10
#> Warning in deSolve::lsoda(init, times, norovirus_model_r, params): Returning
#> early. Results are accurate, as far as they go
#> Unit: milliseconds
#> expr min lq mean median uq max
#> noromod_r 1188.64930 1236.1780 1333.8733 1283.4355 1358.7774 2554.5153
#> noromod_cpp 356.43054 389.9030 435.4173 416.0641 454.5616 814.8951
#> noromod_cpp_boost 99.30052 102.4702 115.9454 109.7454 117.4761 281.5254
#> neval
#> 100
#> 100
#> 100