update analysis pipeline

cmmid · Oct 26, 2024 · 66d68b9 · 66d68b9
1 parent 8baaee1
commit 66d68b9
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Showing 26 changed files with 7 additions and 19 deletions.
diff --git a/inst/.gitignore b/inst/.gitignore
@@ -1,6 +1,6 @@
-input/*
-output/*
-figure/*
+analysis/input/*
+analysis/output/*
+analysis/figure/*
 
 .Rprofile
 .DS_Store

diff --git a/inst/analysis/GNUmakefile b/inst/analysis/GNUmakefile
@@ -54,22 +54,19 @@ ${DATDIR}/population.rds: scripts/population.R | ${RENV} ${DATDIR}
 ${DATDIR}/lex.rds: scripts/lex.R | ${RENV} ${DATDIR}
 	$(call R)
 
-${DATDIR}/odin.rda: scripts/odin.R | ${RENV} ${DATDIR}
-	$(call R)
-
 # n.b. for additional pathogens, this would need to be expanded
 ${DATDIR}/disease_pars.rda: scripts/disease_pars.R $(call dat,population.rds lex.rds)
 	$(call R)
 
 ${DATDIR}/param_%.rda: scripts/param.R $(call dat,population.rds disease_pars.rda)
 	$(call R,$(subst _, ,$*))
 
-allinputs: $(call dat,population.rds lex.rds odin.rda disease_pars.rda $(patsubst %,param_%.rda,${ALLSCN}))
+allinputs: $(call dat,population.rds lex.rds disease_pars.rda $(patsubst %,param_%.rda,${ALLSCN}))
 
 ##### OUTPUTS ##################################################################
 # simulation time series, distillations, ylls - by various methods
 
-${OUTDIR}/sim_%.rds: scripts/simulate.R $(call dat,population.rds odin.rda param_%.rda) | ${OUTDIR}
+${OUTDIR}/sim_%.rds: scripts/simulate.R $(call dat,population.rds param_%.rda) scripts/odin.R | ${OUTDIR}
 	$(call R,$(firstword $(subst _, ,$*)))
 
 ALLSIM := $(patsubst %,${OUTDIR}/sim_%.rds,${ALLSCN})
@@ -85,9 +82,6 @@ ${OUTDIR}/yll_%.rds: scripts/yll.R ${DATDIR}/lex.rds ${OUTDIR}/distill_%.rds
 
 allylls: $(patsubst %,${OUTDIR}/yll_%.rds,${ALLSCN})
 
-# ${OUTDIR}/vaxthreshold_%.rds: $(call dat,population.rds odin.rda param_%.rda) | ${OUTDIR} scripts/yll.R ${DATDIR}/lex.rds ${OUTDIR}/distill_%.rds
-#	$(call R,$(firstword $(subst _, ,$*)))
-
 ${OUTDIR}/incidence.rds: scripts/incidence.R $(patsubst %,${OUTDIR}/sim_%.rds,${ALLSCN})
 	$(call R)
 

diff --git a/inst/analysis/figure/averted.png b/inst/analysis/figure/averted.png
diff --git a/inst/analysis/figure/incidence.png b/inst/analysis/figure/incidence.png
diff --git a/inst/analysis/figure/summary.png b/inst/analysis/figure/summary.png
diff --git a/inst/analysis/figure/yll.png b/inst/analysis/figure/yll.png
diff --git a/inst/analysis/input/param_AFG_FLU.rda b/inst/analysis/input/param_AFG_FLU.rda
diff --git a/inst/analysis/input/param_AFG_SC2.rda b/inst/analysis/input/param_AFG_SC2.rda
diff --git a/inst/analysis/input/param_GBR_FLU.rda b/inst/analysis/input/param_GBR_FLU.rda
diff --git a/inst/analysis/input/param_GBR_SC2.rda b/inst/analysis/input/param_GBR_SC2.rda
diff --git a/inst/analysis/output/consolidated.rds b/inst/analysis/output/consolidated.rds
diff --git a/inst/analysis/output/distill_AFG_FLU.rds b/inst/analysis/output/distill_AFG_FLU.rds
diff --git a/inst/analysis/output/distill_AFG_SC2.rds b/inst/analysis/output/distill_AFG_SC2.rds
diff --git a/inst/analysis/output/distill_GBR_FLU.rds b/inst/analysis/output/distill_GBR_FLU.rds
diff --git a/inst/analysis/output/distill_GBR_SC2.rds b/inst/analysis/output/distill_GBR_SC2.rds
diff --git a/inst/analysis/output/incidence.rds b/inst/analysis/output/incidence.rds
diff --git a/inst/analysis/output/sim_AFG_FLU.rds b/inst/analysis/output/sim_AFG_FLU.rds
diff --git a/inst/analysis/output/sim_AFG_SC2.rds b/inst/analysis/output/sim_AFG_SC2.rds
diff --git a/inst/analysis/output/sim_GBR_FLU.rds b/inst/analysis/output/sim_GBR_FLU.rds
diff --git a/inst/analysis/output/sim_GBR_SC2.rds b/inst/analysis/output/sim_GBR_SC2.rds
diff --git a/inst/analysis/output/yll_AFG_FLU.rds b/inst/analysis/output/yll_AFG_FLU.rds
diff --git a/inst/analysis/output/yll_AFG_SC2.rds b/inst/analysis/output/yll_AFG_SC2.rds
diff --git a/inst/analysis/output/yll_GBR_FLU.rds b/inst/analysis/output/yll_GBR_FLU.rds
diff --git a/inst/analysis/output/yll_GBR_SC2.rds b/inst/analysis/output/yll_GBR_SC2.rds
diff --git a/inst/analysis/scripts/odin.R b/inst/analysis/scripts/odin.R
@@ -1,10 +1,6 @@
 
 require(odin)
 
-.args <- if (interactive()) c(
-  file.path("input", "odin.rda")
-) else commandArgs(trailingOnly = TRUE)
-
 sir_odin <- odin::odin({
 
   # Number of groups
@@ -104,5 +100,3 @@ epidemic_run <- function(
   )
 
 }
-
-save(sir_odin, epidemic_run, file = tail(.args, 1))
diff --git a/inst/analysis/scripts/simulate.R b/inst/analysis/scripts/simulate.R
@@ -4,8 +4,8 @@ source('scripts/odin.R')
 
 .args <- if (interactive()) c(
   file.path("input", "population.rds"),
-  file.path("input", "odin.rda"),
   file.path("input", "param_GBR_FLU.rda"),
+  file.path("scripts", "odin.R"),
   "GBR",
   file.path("output", "sim_GBR_FLU.rds")
 ) else commandArgs(trailingOnly = TRUE)
@@ -16,7 +16,7 @@ pop_dt <- pop_dt[
 ]
 
 load(.args[2])
-load(.args[3])
+source(.args[3])
 
 epidemic_time_series <- function(
   vacc_cov, # 4-vector of proportion of each model age group vaccinated