WIP adapting to library updates

inst/analysis/GNUmakefile

@@ -67,7 +67,7 @@ allinputs: $(call dat,population.rds lex.rds disease_pars.rda $(patsubst %,param
 # simulation time series, distillations, ylls - by various methods
 
 ${OUTDIR}/sim_%.rds: scripts/simulate.R $(call dat,population.rds param_%.rda) scripts/odin.R | ${OUTDIR}
-	$(call R,$(firstword $(subst _, ,$*)))
+	$(call R,$(firstword $(subst _, ,$*))) > $(subst rds,txt,$(subst sim,simlog,$@))
 
 ALLSIM := $(patsubst %,${OUTDIR}/sim_%.rds,${ALLSCN})
 allsim: ${ALLSIM}

inst/analysis/scripts/distill.R

@@ -19,12 +19,20 @@ pop_dt <- pop_dt[
 load(.args[2])
 
 sim_dt <- readRDS(.args[3])[, .(
-  sim_method = method, intervention, time, model_from, value = deaths
-)][, .(value = sum(value)), by = .(sim_method, intervention, model_from)]
-
-dt <- sim_dt[,{
-  distill_summary(.SD, mapping_dt)
-}, by = .(sim_method, intervention)]
+  sim_method = method, intervention, time, model_partition, value = deaths
+)][, .(value = sum(value)), by = .(sim_method, intervention, model_partition)]
+
+partial_dt <- sim_dt[sim_method != "full"]
+full_dt <- setnames(
+  sim_dt[sim_method == "full"], "model_partition", "partition"
+)[, method := "hrm"]
+
+dt <- rbind(
+  partial_dt[,{
+    distill_summary(mapping_dt, .SD)
+  }, by = .(sim_method, intervention)],
+  full_dt
+)
 
 dt[, capita := pop_dt[, sum(weight*1000)] ]
 

inst/analysis/scripts/param.R

@@ -57,7 +57,7 @@ mapping_dt <- alembic(
 # the naive alternatives
 ifr_params <- parameter_summary(
   f_param = f_ifr, f_pop = bound_pop_dt,
-  model_partition = model_agelimits
+  model_partition = model_agelimits, resolution = 102L
 )
 
 ifr_params[, model_partition := model_agelimits[model_category]]

inst/analysis/scripts/simulate.R

@@ -92,24 +92,24 @@ cat(
   approx_time[3],
   "full time",
   full_time[3],
-  file = stderr(),
+  file = stdout(),
   sep = "\n"
 )
 
-sim_dt[, model_from := model_agelimits[age_group]]
-nonfull_params <- ifr_params[method != "f_val", .(model_from, method, value) ] |> unique()
+sim_dt[, model_partition := model_agelimits[age_group]]
+nonfull_params <- ifr_params[method != "f_val", .(model_partition, method, value) ] |> unique()
 
 exp_sim_dt <- nonfull_params[, unique(method)] |> setNames(nm = _) |> lapply(\(m) sim_dt) |> rbindlist(idcol = "method")
 
-exp_sim_dt[nonfull_params, on = .(model_from, method), deaths := value * i.value]
+exp_sim_dt[nonfull_params, on = .(model_partition, method), deaths := value * i.value]
 
 capita_dt <- data.table(age_group = seq_along(demog), capita = demog)
 
 simfull_dt[, from := age_group - 1L]
 simfull_dt[pop_dt, on = .(from), capita := weight * 1e3]
-setnames(simfull_dt, "from", "model_from")
+setnames(simfull_dt, "from", "model_partition")
 simfull_dt[, method := "full"]
-simfull_dt[ifr_params[method == "f_val"], on = .(model_from = x), deaths := value * i.value]
+simfull_dt[ifr_params[method == "f_val"], on = .(model_partition = x), deaths := value * i.value]
 
 exp_sim_dt[capita_dt, on = .(age_group), capita := capita]