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| require(data.table) | ||
| require(paramix) | ||
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| .args <- if (interactive()) c( | ||
| file.path("input", "population.rds"), | ||
| file.path("input", "disease_pars.rda"), | ||
| file.path("output", "incidence.rds"), | ||
| file.path("output", "consolidated.rds"), | ||
| file.path("figure", "fig_utilities.rda") | ||
| ) else commandArgs(trailingOnly = TRUE) | ||
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| load(.args[5]) | ||
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| inc_dt <- readRDS(.args[3]) | ||
| model_partition <- c(inc_dt[, unique(model_from)], 101) | ||
| inc_dt <- inc_dt[method == "f_mean"][, | ||
| .(value = sum(value), capita = sum(unique(capita))), | ||
| by = .(iso3 = place, pathogen, intervention, time) | ||
| ] | ||
| isoset <- inc_dt[, unique(iso3)] | ||
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| load(.args[2]) | ||
| pop_dt <- readRDS(.args[1])[iso3 %in% isoset] | ||
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| ifr_dt <- pop_dt[, | ||
| ifr_opts |> lapply(\(fp) parameter_summary(fp, .SD, model_partition)) |> | ||
| rbindlist(idcol = "pathogen"), | ||
| by = iso3 | ||
| ] | ||
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| print('SC2 65+ IFR') | ||
| print('LMIC: [1] MEAN METHOD [2] PARAMIX') | ||
| print(paste0(round(100*ifr_dt[x==100 & method %in% c('f_mean','wm_f') & pathogen=='SC2' & iso3=='AFG']$value, 1), '%')) | ||
| print('HIC: [3] MEAN METHOD [4] PARAMIX') | ||
| print(paste0(round(100*ifr_dt[x==100 & method %in% c('f_mean','wm_f') & pathogen=='SC2' & iso3=='GBR']$value, 1), '%')) | ||
| print('') | ||
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| ts_dt <- readRDS(.args[3]) | ||
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| joinvars <- c("method", "place", "pathogen") | ||
| base_dt <- ts_dt[ | ||
| intervention == "none", .SD, .SDcols = -c("intervention", "capita") | ||
| ][,.(deaths = sum(deaths)), by = c(joinvars)] | ||
| int_dt <- ts_dt[intervention != "none", .( | ||
| deaths = sum(deaths), capita = sum(unique(capita)) | ||
| ), by = c(joinvars, "intervention")][ | ||
| base_dt, on = c(joinvars) | ||
| ] | ||
| int_dt[, averted_death := i.deaths - deaths] | ||
| int_dt$method <- factor(int_dt$method, levels=unique(int_dt$method)) | ||
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| print('% OVERESTIMATE DEATHS COMPARED TO PARAMIX') | ||
| print('SC2 LMIC: [1] VAX YOUNG [2] VAX WORKING [3] VAX OLDER') | ||
| print(paste0(round(100*(int_dt[method=='f_mid'&pathogen=='SC2'&place=='AFG']$averted_death-int_dt[method=='wm_f'&pathogen=='SC2'&place=='AFG']$averted_death)/ | ||
| int_dt[method=='wm_f'&pathogen=='SC2'&place=='AFG']$averted_death, 2), '%')) | ||
| print('FLU LMIC: [1] VAX YOUNG [2] VAX WORKING [3] VAX OLDER') | ||
| print(paste0(round(100*(int_dt[method=='f_mid'&pathogen=='FLU'&place=='AFG']$averted_death-int_dt[method=='wm_f'&pathogen=='FLU'&place=='AFG']$averted_death)/ | ||
| int_dt[method=='wm_f'&pathogen=='FLU'&place=='AFG']$averted_death, 2), '%')) | ||
| print('SC2 HIC: [1] VAX YOUNG [2] VAX WORKING [3] VAX OLDER') | ||
| print(paste0(round(100*(int_dt[method=='f_mid'&pathogen=='SC2'&place=='GBR']$averted_death-int_dt[method=='wm_f'&pathogen=='SC2'&place=='GBR']$averted_death)/ | ||
| int_dt[method=='wm_f'&pathogen=='SC2'&place=='GBR']$averted_death, 2), '%')) | ||
| print('FLU HIC: [1] VAX YOUNG [2] VAX WORKING [3] VAX OLDER') | ||
| print(paste0(round(100*(int_dt[method=='f_mid'&pathogen=='FLU'&place=='GBR']$averted_death-int_dt[method=='wm_f'&pathogen=='FLU'&place=='GBR']$averted_death)/ | ||
| int_dt[method=='wm_f'&pathogen=='FLU'&place=='GBR']$averted_death, 2), '%')) | ||
| print('') | ||
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| ylls_dt <- readRDS(.args[4]) | ||
| base_dt <- ylls_dt[ | ||
| intervention == "none", .SD, .SDcols = -c("intervention") | ||
| ] | ||
| int_dt <- ylls_dt[intervention != "none"][ | ||
| base_dt, on = setdiff(names(base_dt), "YLL") | ||
| ] | ||
| int_dt[, averted_yll := i.YLL - YLL] | ||
| int_dt[, sim_method := factor(sim_method, levels = names(model_assumption_labels), ordered = TRUE)] | ||
| int_dt[, method := factor(method, levels = names(model_assumption_labels), ordered = TRUE)] | ||
| int_dt <- int_dt[sim_method=='wm_f'][, sim_method:=NULL] | ||
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| print('% OVERESTIMATE YLLS COMPARED TO PARAMIX') | ||
| print('LMIC: [1] SC2 [2] FLU') | ||
| print(paste0(100*round((int_dt[method=='mean_f' & intervention=='vax_working' & place=='AFG']$averted_yll - | ||
| int_dt[method=='wm_f' & intervention=='vax_working' & place=='AFG']$averted_yll)/ | ||
| int_dt[method=='wm_f' & intervention=='vax_working' & place=='AFG']$averted_yll,2), '%')) | ||
| print('HIC: [1] SC2 [2] FLU') | ||
| print(paste0(100*round((int_dt[method=='mean_f' & intervention=='vax_working' & place=='GBR']$averted_yll - | ||
| int_dt[method=='wm_f' & intervention=='vax_working' & place=='GBR']$averted_yll)/ | ||
| int_dt[method=='wm_f' & intervention=='vax_working' & place=='GBR']$averted_yll,2), '%')) |