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cacth case where n_eligible_for_doseX is 0, avoid division by 0
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@edknock
edknock committed Oct 12, 2024
1 parent a47bb6e commit b4b6ae6
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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: 0.1.2
Version: 0.1.3
Authors@R: c(person("Lilith", "Whittles", role = c("aut", "cre"),
email = "[email protected]"),
person("Ruth", "McCabe", role = c("aut")),
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16 changes: 8 additions & 8 deletions inst/dust/model-targeted-vax.cpp
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Expand Up @@ -576,11 +576,11 @@ class model_targeted_vax {
}
for (int i = 1; i <= shared->dim_n_vaccination_t_Ea_1; ++i) {
int j = 2;
internal.n_vaccination_t_Ea[i - 1 + shared->dim_n_vaccination_t_Ea_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * Ea[shared->dim_Ea_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), Ea[shared->dim_Ea_1 * 1 + i - 1]);
internal.n_vaccination_t_Ea[i - 1 + shared->dim_n_vaccination_t_Ea_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * Ea[shared->dim_Ea_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), Ea[shared->dim_Ea_1 * 1 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_Ea_1; ++i) {
int j = 3;
internal.n_vaccination_t_Ea[i - 1 + shared->dim_n_vaccination_t_Ea_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * Ea[shared->dim_Ea_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), Ea[shared->dim_Ea_1 * 2 + i - 1]);
internal.n_vaccination_t_Ea[i - 1 + shared->dim_n_vaccination_t_Ea_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * Ea[shared->dim_Ea_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), Ea[shared->dim_Ea_1 * 2 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_Eb_1; ++i) {
for (int j = 1; j <= shared->dim_n_vaccination_t_Eb_2; ++j) {
Expand All @@ -589,11 +589,11 @@ class model_targeted_vax {
}
for (int i = 1; i <= shared->dim_n_vaccination_t_Eb_1; ++i) {
int j = 2;
internal.n_vaccination_t_Eb[i - 1 + shared->dim_n_vaccination_t_Eb_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * Eb[shared->dim_Eb_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), Eb[shared->dim_Eb_1 * 1 + i - 1]);
internal.n_vaccination_t_Eb[i - 1 + shared->dim_n_vaccination_t_Eb_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * Eb[shared->dim_Eb_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), Eb[shared->dim_Eb_1 * 1 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_Eb_1; ++i) {
int j = 3;
internal.n_vaccination_t_Eb[i - 1 + shared->dim_n_vaccination_t_Eb_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * Eb[shared->dim_Eb_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), Eb[shared->dim_Eb_1 * 2 + i - 1]);
internal.n_vaccination_t_Eb[i - 1 + shared->dim_n_vaccination_t_Eb_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * Eb[shared->dim_Eb_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), Eb[shared->dim_Eb_1 * 2 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_R_1; ++i) {
for (int j = 1; j <= shared->dim_n_vaccination_t_R_2; ++j) {
Expand All @@ -602,11 +602,11 @@ class model_targeted_vax {
}
for (int i = 1; i <= shared->dim_n_vaccination_t_R_1; ++i) {
int j = 2;
internal.n_vaccination_t_R[i - 1 + shared->dim_n_vaccination_t_R_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * R[shared->dim_R_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), R[shared->dim_R_1 * 1 + i - 1]);
internal.n_vaccination_t_R[i - 1 + shared->dim_n_vaccination_t_R_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * R[shared->dim_R_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), R[shared->dim_R_1 * 1 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_R_1; ++i) {
int j = 3;
internal.n_vaccination_t_R[i - 1 + shared->dim_n_vaccination_t_R_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * R[shared->dim_R_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), R[shared->dim_R_1 * 2 + i - 1]);
internal.n_vaccination_t_R[i - 1 + shared->dim_n_vaccination_t_R_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * R[shared->dim_R_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), R[shared->dim_R_1 * 2 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_S_1; ++i) {
for (int j = 1; j <= shared->dim_n_vaccination_t_S_2; ++j) {
Expand All @@ -615,11 +615,11 @@ class model_targeted_vax {
}
for (int i = 1; i <= shared->dim_n_vaccination_t_S_1; ++i) {
int j = 2;
internal.n_vaccination_t_S[i - 1 + shared->dim_n_vaccination_t_S_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * S[shared->dim_S_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), S[shared->dim_S_1 * 1 + i - 1]);
internal.n_vaccination_t_S[i - 1 + shared->dim_n_vaccination_t_S_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 1 + 0] * S[shared->dim_S_1 * 1 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_1st_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose1.data(), 0, shared->dim_n_eligible_for_dose1)), S[shared->dim_S_1 * 1 + i - 1]));
}
for (int i = 1; i <= shared->dim_n_vaccination_t_S_1; ++i) {
int j = 3;
internal.n_vaccination_t_S[i - 1 + shared->dim_n_vaccination_t_S_1 * (j - 1)] = dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * S[shared->dim_S_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), S[shared->dim_S_1 * 2 + i - 1]);
internal.n_vaccination_t_S[i - 1 + shared->dim_n_vaccination_t_S_1 * (j - 1)] = (odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2) == 0 ? 0 : dust::math::min(dust::math::floor((internal.daily_doses_t[shared->dim_daily_doses_t_1 * 2 + 0] * S[shared->dim_S_1 * 2 + i - 1] * shared->prioritisation_strategy[shared->dim_prioritisation_strategy_1 * (prioritisation_step_2nd_dose - 1) + i - 1] * shared->vaccine_uptake[i - 1]) / (real_type) odin_sum1<real_type>(internal.n_eligible_for_dose2.data(), 0, shared->dim_n_eligible_for_dose2)), S[shared->dim_S_1 * 2 + i - 1]));
}
real_type prioritisation_step_1st_dose_proposal = (odin_sum2<real_type>(internal.target_met_t.data(), 0, shared->dim_target_met_t_1, 2, 3, shared->dim_target_met_t_1) == shared->n_group ? prioritisation_step_1st_dose + 1 : prioritisation_step_1st_dose);
real_type prioritisation_step_2nd_dose_proposal = (odin_sum2<real_type>(internal.target_met_t.data(), 0, shared->dim_target_met_t_1, 3, 4, shared->dim_target_met_t_1) == shared->n_group ? prioritisation_step_2nd_dose + 1 : prioritisation_step_2nd_dose);
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89 changes: 48 additions & 41 deletions inst/odin/model-targeted-vax.R
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Original file line number Diff line number Diff line change
Expand Up @@ -126,55 +126,62 @@ n_vaccination_t_Eb[, ] <- 0
n_vaccination_t_R[, ] <- 0

## allocate 1st doses
n_vaccination_t_S[, 2] <- min(
floor((daily_doses_t[1, 2] * S[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
S[i, 2])

n_vaccination_t_Ea[, 2] <- min(
floor((daily_doses_t[1, 2] * Ea[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
Ea[i, 2])

n_vaccination_t_Eb[, 2] <- min(
floor((daily_doses_t[1, 2] * Eb[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
Eb[i, 2])

n_vaccination_t_R[, 2] <- min(
floor((daily_doses_t[1, 2] * R[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
R[i, 2])
n_vaccination_t_S[, 2] <- if (sum(n_eligible_for_dose1[]) == 0) 0 else
min(floor((daily_doses_t[1, 2] * S[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
S[i, 2])


n_vaccination_t_Ea[, 2] <- if (sum(n_eligible_for_dose1[]) == 0) 0 else
min(floor((daily_doses_t[1, 2] * Ea[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
Ea[i, 2])


n_vaccination_t_Eb[, 2] <- if (sum(n_eligible_for_dose1[]) == 0) 0 else
min(floor((daily_doses_t[1, 2] * Eb[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
Eb[i, 2])


n_vaccination_t_R[, 2] <- if (sum(n_eligible_for_dose1[]) == 0) 0 else
min(floor((daily_doses_t[1, 2] * R[i, 2] *
prioritisation_strategy[i, prioritisation_step_1st_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose1[])),
R[i, 2])



## allocate 2nd doses
n_vaccination_t_S[, 3] <- min(
n_vaccination_t_S[, 3] <- if (sum(n_eligible_for_dose2[]) == 0) 0 else
min(
floor((daily_doses_t[1, 3] * S[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
S[i, 3])

n_vaccination_t_Ea[, 3] <- min(
floor((daily_doses_t[1, 3] * Ea[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
Ea[i, 3])

n_vaccination_t_Eb[, 3] <- min(
floor((daily_doses_t[1, 3] * Eb[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
Eb[i, 3])

n_vaccination_t_R[, 3] <- min(
floor((daily_doses_t[1, 3] * R[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
R[i, 3])
n_vaccination_t_Ea[, 3] <- if (sum(n_eligible_for_dose2[]) == 0) 0 else
min(floor((daily_doses_t[1, 3] * Ea[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
Ea[i, 3])


n_vaccination_t_Eb[, 3] <- if (sum(n_eligible_for_dose2[]) == 0) 0 else
min(floor((daily_doses_t[1, 3] * Eb[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
Eb[i, 3])


n_vaccination_t_R[, 3] <- if (sum(n_eligible_for_dose2[]) == 0) 0 else
min(floor((daily_doses_t[1, 3] * R[i, 3] *
prioritisation_strategy[i, prioritisation_step_2nd_dose] *
vaccine_uptake[i]) / sum(n_eligible_for_dose2[])),
R[i, 3])


## net vaccination change for relevant classes (S,Ea,Eb,R)
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