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Lhood weekly prop cases by age #67

Merged
merged 11 commits into from
Feb 7, 2025
Merged

Lhood weekly prop cases by age #67

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e029d78
add nested binomial likelihood term to the data to ensure the age spl…
lwhittles Feb 4, 2025
f1a7236
add in observed_cases lhood
lwhittles Feb 5, 2025
262ad1d
merge in changes to main
lwhittles Feb 5, 2025
16dd042
remove merge conflict
lwhittles Feb 5, 2025
a09c044
ensure observed cases is not off-by-one
lwhittles Feb 5, 2025
d76f207
add test for observed cases
lwhittles Feb 5, 2025
10b4bef
add test
edknock Feb 6, 2025
544c9dd
Update inst/odin/model-targeted-vax.R
lwhittles Feb 6, 2025
d7c58f6
recompile with suggested change
lwhittles Feb 6, 2025
0db25ee
remove defaults for phis from odin code
edknock Feb 6, 2025
7e57ec0
gMerge branch 'lhood-weekly-prop-cases-by-age' of https://github.com/…
edknock Feb 6, 2025
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: mpoxseir
Title: Stochastic compartmental model of mpox transmission
Version: 0.2.14
Version: 0.2.15
Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
email = "[email protected]"),
person("Ruth", "McCabe", role = c("aut")),
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8 changes: 8 additions & 0 deletions NEWS.md
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@@ -1,3 +1,11 @@
# mpoxseir 0.2.13

* Add likelihood term for % cases by age

# mpoxseir 0.2.12

* Add Bujumbura region

# mpoxseir 0.2.9

* children_ind_raw replaced with is_child, adults_ind_raw replaced with (1 - is_child)
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12 changes: 6 additions & 6 deletions R/dust.R
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@@ -1,16 +1,16 @@
## Generated by dust2 (version 0.3.15) - do not edit
## Generated by dust2 (version 0.3.16) - 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("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)),
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", "phi_00_04", "phi_05_14", "phi_15_plus", "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", "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, 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, FALSE, FALSE, 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, 0L, 0L, 0L)),
properties = list(
time_type = "discrete",
has_compare = TRUE,
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