Set parameters in DAEDALUS classes
Source:R/class_country.R, R/class_infection.R, R/pkg_generics.R
set_data.RdGeneric and methods for S3 classes for safely setting class
parameters. Only parameters considered safe to change – mostly contact data
in the <country>, but all parameters in <infection> – can be changed in
this way.
Usage
# S3 method for class 'daedalus_country'
set_data(x, ...)
# S3 method for class 'daedalus_infection'
set_data(x, ...)
set_data(x, ...)Arguments
- x
An S3 class object from the daedalus package of the
<daedalus_country>or<infection>class.- ...
<
dynamic-dots> Named optional arguments for parameters to be changed, with their new values. The only values allowed for<daedalus_country>objects are "contact_matrix", "contacts_workplace", and "contacts_consumer_worker".
Examples
# simple example of setting all contacts to 1
country_A <- daedalus_country("United Kingdom")
country_A
#> <daedalus_country>
#> • Name: United Kingdom
#> • Demography: 3924490, 11762039, 39536463, and 12663012
#> • Community contact matrix:
#> 0-4 5-19 20-64 65+
#> 0-4 1.9157895 1.5379290 4.704999 0.2863619
#> 5-19 0.5131412 8.7339228 5.874591 0.7418483
#> 20-64 0.4670302 1.7476822 7.830182 1.0685802
#> 65+ 0.1180517 0.7548304 3.531487 1.5212437
country_A <- set_data(country_A, contact_matrix = matrix(1, 4, 4))
country_A
#> <daedalus_country>
#> • Name: United Kingdom
#> • Demography: 3924490, 11762039, 39536463, and 12663012
#> • Community contact matrix:
#> [,1] [,2] [,3] [,4]
#> [1,] 1 1 1 1
#> [2,] 1 1 1 1
#> [3,] 1 1 1 1
#> [4,] 1 1 1 1
disease_x <- daedalus_infection("sars_cov_1")
disease_x <- set_data(disease_x, r0 = 3.0)
disease_x
#> <daedalus_infection>
#> • Epidemic name: sars_cov_1
#> • R0: 3
#> • sigma: 0.217
#> • p_sigma: 0.867
#> • epsilon: 0.58
#> • rho: 0.003
#> • eta: 0.018, 0.082, 0.018, and 0.246
#> • omega: 0.012, 0.012, 0.012, and 0.012
#> • gamma_Ia: 0.476
#> • gamma_Is: 0.25
#> • gamma_H: 0.034, 0.034, 0.034, and 0.034