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Create Transmission Probability Matrix

Source: R/hestia_functions.R
get_transmission_details.Rd

Create Transmission Probability Matrix

Usage

get_transmission_details(inf_model)

Arguments

inf_model

infection process model object yielded by make_infection_model()

Value

A list with the following entries:

  • "states", a character vector of state names

  • "trans_matrix", a matrix with transition rate values between origin (column) and destination (row) compartments where given. Where no values are provided for transition rates the entry is equal to 1e-10.

  • "mult_matrix", a matrix with split values for the transition between origin (column) and destination (row) compartments where given. Where no split values are provided for transition rates the entry is equal to 1.

  • "trans_to_fit", a data frame with information on all transitions within the model, with parameter indexing details if the transition rate is being fit

  • "mult_to_fit", a data frame with information on all splits specified in the model, with parameter indexing details if the split is being fit

  • "inf_states", numeric values corresponding to the indices in "states" which are the infectious states

  • "mult_ih_inf_probs", indicator for whether infectious states have shared or separate inta-household infection probabilities. If FALSE then all infection probabilities are shared across infectious compartments.

Examples

# Split the infectious compartment into symptomatic (I_s) and asymptomatic
# (I_a) infections, with separate intra-household infection probabilities.
inf_model <- make_infection_model(
  transmit(from = "S",
           to = c("I_s", "I_a"),
           source = c("I_s", "I_a"),
           split = "phi"),
  progress(from = "I_s", to = "R", gamma_s = NA),
  progress(from = "I_a", to = "R", gamma_a = NA),
  mult_ih_inf_probs = TRUE)

get_transmission_details(inf_model)
#> $states
#> [1] "S"   "I_s" "I_a" "R"  
#> 
#> $trans_matrix
#>        from_S from_I_s from_I_a from_R
#> to_S    1e-10    1e-10    1e-10  1e-10
#> to_I_s  1e-10    1e-10    1e-10  1e-10
#> to_I_a  1e-10    1e-10    1e-10  1e-10
#> to_R    1e-10    1e-10    1e-10  1e-10
#> 
#> $mult_matrix
#>        from_S from_I_s from_I_a from_R
#> to_S        1        1        1      1
#> to_I_s      1        1        1      1
#> to_I_a      1        1        1      1
#> to_R        1        1        1      1
#> 
#> $trans_to_fit
#>   from  to trans_row trans_col rate_name param source
#> 1    S I_s         2         1      <NA>     0   2, 3
#> 2    S I_a         3         1      <NA>     0   2, 3
#> 3  I_s   R         4         2   gamma_s     1      0
#> 4  I_a   R         4         3   gamma_a     2      0
#> 
#> $mult_to_fit
#>   from  to mult_row mult_col mult_name param
#> 1    S I_s        2        1       phi     1
#> 2    S I_a        3        1     1-phi    -1
#> 
#> $inf_states
#> [1] 2 3
#> 
#> $mult_ih_inf_probs
#> [1] TRUE
#> 
#> $mult_eh_inf_probs
#> [1] FALSE
#> 
#> $compete
#> [1] 0 0 0 0
#>