Using generate_ngm with a transition matrix that uses age breaks of 80+ results in a strange break #200
Description
We may have hard coded something in here based upon example data, see reprex below:
library(conmat)
perth <- abs_age_lga("Perth (C)")
perth_hh <- get_abs_per_capita_household_size(lga = "Perth (C)")
age_breaks_0_80_plus <- c(seq(0, 80, by = 5), Inf)
age_breaks_0_75_plus <- c(seq(0, 75, by = 5), Inf)
perth_contact <- extrapolate_polymod(
perth,
per_capita_household_size = perth_hh
)
perth_ngm <- generate_ngm(
perth_contact,
age_breaks = age_breaks_0_75_plus,
R_target = 1.5
)
# using our own transmission matrix
new_transmission_matrix <- get_setting_transmission_matrices(
age_breaks = age_breaks_0_75_plus,
# is normally 0.5
asymptomatic_relative_infectiousness = 0.75
)
set_trans_mat_80_plus <- get_setting_transmission_matrices(
age_breaks = age_breaks_0_80_plus,
# is normally 0.5
asymptomatic_relative_infectiousness = 0.75
)
perth_ngm_0_80_new_tmat <- generate_ngm(
perth_contact,
age_breaks = age_breaks_0_80_plus,
R_target = 1.5,
setting_transmission_matrix = set_trans_mat_80_plus
)
#> Error in `check_age_breaks()` at conmat/R/generate-ngm.R:135:3:
#> ! Age breaks must be the same, but they are different:
#> `x[14:17]`: 65 70 75 Inf
#> `age_breaks[14:18]`: 65 70 75 80 Inf
#> ℹ You can check the age breaks using `age_breaks(<object>)`Created on 2025-11-28 with reprex v2.1.1
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