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Updates to vaccination #59

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merged 29 commits into from
Jan 15, 2025
+568 −576
Merged

Updates to vaccination #59

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10d03d4
children_ind_raw -> is_child;
ruthmccabe Jan 10, 2025
2ade9b5
children_ind_raw -> is_child
ruthmccabe Jan 10, 2025
ca5a6ff
update tests children_ind_raw -> is_child
ruthmccabe Jan 10, 2025
764866b
regenerate model
ruthmccabe Jan 10, 2025
ba3f9bd
FOI tidy - instead of having ve_I included in each of the 4 component…
ruthmccabe Jan 10, 2025
eb210ac
coverage_achieved -> coverage_target as I think more intuitive
ruthmccabe Jan 10, 2025
87764c9
simplify target_met_children_t (can be vector not matrix)
ruthmccabe Jan 10, 2025
2d8ee57
simplify target_met_children_t
ruthmccabe Jan 10, 2025
4e240f8
undo FOI tidy which it did NOT like; regenerate model
ruthmccabe Jan 10, 2025
b119a1c
rewriting of vaccination components based on 1) eligibility 2) priori…
ruthmccabe Jan 10, 2025
c1987ad
regenerate model for testing purposes
ruthmccabe Jan 10, 2025
1365a61
test name updated (not relevant to this PR just found it as checking …
ruthmccabe Jan 10, 2025
6bc1881
as before just tidied test name (not PR specific)
ruthmccabe Jan 10, 2025
73c0ebd
tidy model notes
ruthmccabe Jan 10, 2025
0e2a76b
bump version
ruthmccabe Jan 10, 2025
1d87379
update news
ruthmccabe Jan 10, 2025
104e298
tidying up code from trying to tidy FOI
ruthmccabe Jan 10, 2025
ebd9870
Merge branch 'main' into fix-vaccination
ruthmccabe Jan 10, 2025
180f99b
re-update description
ruthmccabe Jan 10, 2025
788b216
remove accidental extra line
ruthmccabe Jan 10, 2025
671f5d9
Merge branch 'main' into fix-vaccination
ruthmccabe Jan 13, 2025
43a869a
update packages & regenerate
ruthmccabe Jan 13, 2025
e6c45c7
Merge branch 'fix-vaccination' of https://github.com/mrc-ide/mpoxseir…
ruthmccabe Jan 13, 2025
65c840a
Update NEWS.md
ruthmccabe Jan 15, 2025
3433d3e
Tidy code as per Lilith's suggestion
ruthmccabe Jan 15, 2025
85c47b9
Tidy code as per Lilith's suggestion
ruthmccabe Jan 15, 2025
10976e7
Tidy code as per Lilith's suggestion
ruthmccabe Jan 15, 2025
61d8f2d
extra bracket removed
ruthmccabe Jan 15, 2025
2e55d33
regen model post review comments
ruthmccabe Jan 15, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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@@ -1,6 +1,6 @@
Package: mpoxseir
Title: Stochastic compartmental model of mpox transmission
Version: 0.2.8
Version: 0.2.9
Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
email = "l.whittles@imperial.ac.uk"),
person("Ruth", "McCabe", role = c("aut")),
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5 changes: 5 additions & 0 deletions NEWS.md
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@@ -1,3 +1,8 @@
# mpoxseir 0.2.9

* children_ind_raw replaced with is_child, adults_ind_raw replaced with (1 - ind_child)
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* vaccination allocation determined based on 3 criteria of eligibility, prioritisation and target met

# mpoxseir 0.2.8

* Age groups are now 0-4, 5-11, 12-14, 15-19, then in 5yr bands to allow for new guidance on vaccines for +/-12yo
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12 changes: 6 additions & 6 deletions R/dust.R
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Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
## Generated by dust2 (version 0.3.15) - do not edit
## Generated by dust2 (version 0.3.11) - do not edit
model_targeted_vax <- structure(
function() get("model_targeted_vax"),
class = "dust_system_generator",
name = "model_targeted_vax",
package = "mpoxseir",
path = NULL,
parameters = data.frame(
name = c("children_ind_raw", "adults_ind_raw", "daily_doses_children_value", "daily_doses_children_time", "daily_doses_adults_value", "daily_doses_adults_time", "N_prioritisation_steps_children", "N_prioritisation_steps_adults", "prioritisation_strategy_children", "prioritisation_strategy_adults", "m_gen_pop", "m_sex", "S0", "Ea0", "Eb0", "Ir0", "Id0", "R0", "D0", "beta_h", "beta_s", "beta_z", "beta_hcw", "gamma_E", "gamma_Ir", "gamma_Id", "CFR", "ve_T", "ve_I", "n_vax", "n_group", "exp_noise", "alpha_cases", "alpha_cases_00_04", "alpha_cases_05_14", "alpha_cases_15_plus", "alpha_deaths", "alpha_deaths_00_04", "alpha_deaths_05_14", "alpha_deaths_15_plus"),
type = c("real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "int", "int", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "int", "int", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type"),
constant = c(FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE),
required = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE),
rank = c(1L, 1L, 2L, 1L, 2L, 1L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 2L, 1L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)),
name = c("is_child", "daily_doses_children_value", "daily_doses_children_time", "daily_doses_adults_value", "daily_doses_adults_time", "N_prioritisation_steps_children", "N_prioritisation_steps_adults", "prioritisation_strategy_children", "prioritisation_strategy_adults", "m_gen_pop", "m_sex", "S0", "Ea0", "Eb0", "Ir0", "Id0", "R0", "D0", "beta_h", "beta_s", "beta_z", "beta_hcw", "gamma_E", "gamma_Ir", "gamma_Id", "CFR", "ve_T", "ve_I", "n_vax", "n_group", "exp_noise", "alpha_cases", "alpha_cases_00_04", "alpha_cases_05_14", "alpha_cases_15_plus", "alpha_deaths", "alpha_deaths_00_04", "alpha_deaths_05_14", "alpha_deaths_15_plus"),
type = c("real_type", "real_type", "real_type", "real_type", "real_type", "int", "int", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "int", "int", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type", "real_type"),
constant = c(FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE, FALSE),
required = c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, FALSE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE),
rank = c(1L, 2L, 1L, 2L, 1L, 0L, 0L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 0L, 0L, 1L, 0L, 0L, 0L, 0L, 2L, 1L, 2L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L)),
properties = list(
time_type = "discrete",
has_compare = TRUE,
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3 changes: 1 addition & 2 deletions R/parameters.R
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Expand Up @@ -561,8 +561,7 @@ parameters_fixed <- function(region, initial_infections, use_ve_D = FALSE,
daily_doses_children_time = 1,
daily_doses_adults_value = matrix(0, nrow = n_vax, ncol = 1),
daily_doses_adults_time = 1,
children_ind_raw = group_bins$children,
adults_ind_raw = group_bins$adults)
is_child = group_bins$children)

# Ensure overridden parameters are passed as a list
if (!is.list(overrides)) {
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