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Feature expectation reporting #154

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merged 12 commits into from
Sep 1, 2022
Merged

Feature expectation reporting #154

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d372572
add control variables for flexible reporting
seabbs Aug 4, 2022
ea3c926
add reporting function
seabbs Aug 4, 2022
601affd
extended model compiles
seabbs Aug 4, 2022
7bb0814
add partial changes for R side observation model
seabbs Aug 5, 2022
a2a99d4
add expectation model input code
seabbs Aug 5, 2022
86dabd3
add skipping for latent model
seabbs Aug 5, 2022
d44d320
add new default enw_expectation args and standardise usage
seabbs Aug 5, 2022
47b6e4c
add support for priors and correctly allow modifiers with no convolution
seabbs Aug 5, 2022
a87f63d
debug implementation
seabbs Aug 5, 2022
a88b7e0
new example for Rt and prototype plots
seabbs Aug 8, 2022
7901592
update priors specification
seabbs Aug 10, 2022
9776f58
merge missingness changes
seabbs Aug 18, 2022
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add skipping for latent model
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@seabbs
seabbs committed Aug 5, 2022
commit 86dabd31099e267ce0139fbe6a0f295a2ac76963
7 changes: 4 additions & 3 deletions R/model-modules.R
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Expand Up @@ -304,10 +304,11 @@ enw_expectation <- function(r = ~ rw(day, by = .group), generation_time = 1,
# Observation indicator variables
obs_list <- list(
lrd_n = length(latent_reporting_delay),
lrlrd = log(rev(latent_reporting_delay)),
obs = 0
lrlrd = log(rev(latent_reporting_delay))
)
obs_list$obs <- ifelse(
sum(latent_reporting_delay) == 1 && obs_list$lrd_n == 1, 0, 1
)

# Observation formula
obs_form <- enw_formula(osbervation, data$metareference[[1]], sparse = FALSE)
obs_data <- enw_formula_as_data_list(
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19 changes: 12 additions & 7 deletions inst/stan/epinowcast.stan
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Expand Up @@ -169,7 +169,7 @@ transformed parameters{
// Expectation model
vector[expr_t] r; // Log growth rate of observations
array[g] vector[expr_ft] exp_latent_lobs; // Expected final observations
vector[expo_fnindex] expo_modifier; // Reporting modifier
vector[expo_obs ? expo_fnindex : 0] expo_modifier; // Reporting modifier
array[g] vector[t] exp_lobs; // Expected final observations
// Reference model
vector[refp_fnrow] refp_mean;
Expand All @@ -195,12 +195,17 @@ transformed parameters{
);
// Get reporting modifiers and map latent expected observations to expected
// observations
expo_modifier = combine_effects(
0, expo_beta, expo_fdesign, expo_beta_sd, expo_rdesign, 1
);
exp_lobs = log_expected_obs_from_latent_obs(
exp_latent_lobs, expo_lrd_n, expo_lrlrd, t, g, expo_modifier
);
if (expo_obs) {
expo_modifier = combine_effects(
0, expo_beta, expo_fdesign, expo_beta_sd, expo_rdesign, 1
);
exp_lobs = log_expected_obs_from_latent_obs(
exp_latent_lobs, expo_lrd_n, expo_lrlrd, t, g, expo_modifier
);
}else{
exp_lobs = exp_latent_lobs;
}

}

// Reference model
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