diff --git a/flepimop/main_scripts/inference_slot.R b/flepimop/main_scripts/inference_slot.R
index 9cc61ad76..ef0edd1e7 100644
--- a/flepimop/main_scripts/inference_slot.R
+++ b/flepimop/main_scripts/inference_slot.R
@@ -50,7 +50,8 @@ option_list = list(
   optparse::make_option(c("-L", "--reset_chimeric_on_accept"), action = "store", default = Sys.getenv("FLEPI_RESET_CHIMERICS", TRUE), type = 'logical', help = 'Should the chimeric parameters get reset to global parameters when a global acceptance occurs'),
   optparse::make_option(c("-M", "--memory_profiling"), action = "store", default = Sys.getenv("FLEPI_MEM_PROFILE", FALSE), type = 'logical', help = 'Should the memory profiling be run during iterations'),
   optparse::make_option(c("-P", "--memory_profiling_iters"), action = "store", default = Sys.getenv("FLEPI_MEM_PROF_ITERS", 100), type = 'integer', help = 'If doing memory profiling, after every X iterations run the profiler'),
-  optparse::make_option(c("-g", "--subpop_len"), action="store", default=Sys.getenv("SUBPOP_LENGTH", 5), type='integer', help = "number of digits in subpop")
+  optparse::make_option(c("-g", "--subpop_len"), action="store", default=Sys.getenv("SUBPOP_LENGTH", 5), type='integer', help = "number of digits in subpop"),
+  optparse::make_option(c("-a", "--incl_aggr_likelihood"), action = "store", default = Sys.getenv("INCL_AGGR_LIKELIHOOD", TRUE), type = 'logical', help = 'Should the likelihood be calculated with the aggregate estiamtes.')
 )
 
 parser=optparse::OptionParser(option_list=option_list)
@@ -88,6 +89,18 @@ if (opt$config == ""){
 }
 config = flepicommon::load_config(opt$config)
 
+
+if (!is.null(config$inference$incl_aggr_likelihood)){
+    print("Using config option for `incl_aggr_likelihood`.")
+    opt$incl_aggr_likelihood <- config$inference$incl_aggr_likelihood
+    if (!is.null(config$inference$total_ll_multiplier)){
+        print("Using config option for `total_ll_multiplier`.")
+        opt$total_ll_multiplier <- config$inference$total_ll_multiplier
+    } else {
+        opt$total_ll_multiplier <- 1
+    }
+}
+
 ## Check for errors in config ---------------------------------------------------------------------
 
 ##  seeding section
@@ -265,6 +278,19 @@ if (config$inference$do_inference){
     dplyr::right_join(tidyr::expand_grid(subpop = unique(.$subpop), date = unique(.$date))) %>%
     dplyr::mutate_if(is.numeric, dplyr::coalesce, 0)
 
+  # add aggregate groundtruth to the obs data for the likelihood calc
+  if (opt$incl_aggr_likelihood){
+      obs <- obs %>%
+          dplyr::bind_rows(
+              obs %>%
+                  dplyr::select(date, where(is.numeric)) %>%
+                  dplyr::group_by(date) %>%
+                  dplyr::summarise(across(everything(), sum)) %>% # no likelihood is calculated for time periods with missing data for any subpop
+                  dplyr::mutate(source = "Total",
+                                subpop = "Total")
+          )
+  }
+
   subpopnames <- unique(obs[[obs_subpop]])
 
 
@@ -588,7 +614,19 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
       # run
       if (config$inference$do_inference){
         sim_hosp <- flepicommon::read_file_of_type(gsub(".*[.]","",this_global_files[['hosp_filename']]))(this_global_files[['hosp_filename']]) %>%
-          dplyr::filter(time >= min(obs$date),time <= max(obs$date))
+          dplyr::filter(time >= min(obs$date), time <= max(obs$date))
+
+        # add aggregate groundtruth to the obs data for the likelihood calc
+        if (opt$incl_aggr_likelihood){
+            sim_hosp <- sim_hosp %>%
+                dplyr::bind_rows(
+                    sim_hosp %>%
+                        dplyr::select(-tidyselect::all_of(obs_subpop), -tidyselect::starts_with("date")) %>%
+                        dplyr::group_by(time) %>%
+                        dplyr::summarise(dplyr::across(tidyselect::everything(), sum)) %>% # no likelihood is calculated for time periods with missing data for any subpop
+                        dplyr::mutate(!!obs_subpop := "Total")
+                )
+        }
 
         lhs <- unique(sim_hosp[[obs_subpop]])
         rhs <- unique(names(data_stats))
@@ -624,6 +662,12 @@ for(seir_modifiers_scenario in seir_modifiers_scenarios) {
 
       rm(sim_hosp)
 
+      # multiply aggregate likelihood by a factor if specified in config
+      if (opt$incl_aggr_likelihood){
+        proposed_likelihood_data$ll[proposed_likelihood_data$subpop == "Total"] <- proposed_likelihood_data$ll[proposed_likelihood_data$subpop == "Total"] * opt$total_ll_multiplier
+      }
+
+
       # write proposed likelihood to global file
       arrow::write_parquet(proposed_likelihood_data, this_global_files[['llik_filename']])