diff --git a/flepimop/R_packages/inference/R/functions.R b/flepimop/R_packages/inference/R/functions.R
index 80f29c9a6..2f7cfbc5e 100644
--- a/flepimop/R_packages/inference/R/functions.R
+++ b/flepimop/R_packages/inference/R/functions.R
@@ -39,11 +39,13 @@ periodAggregate <- function(data, dates, start_date = NULL, end_date = NULL, per
     tmp <- tmp %>%
         tidyr::unite("time_unit", names(tmp)[grepl("time_unit_", names(tmp))]) %>%
         dplyr::group_by(time_unit) %>%
-        dplyr::summarize(first_date = min(date), value = aggregator(value), valid = period_unit_validator(date,time_unit)) %>%
+        dplyr::summarize(last_date = max(date),first_date = min(date), value = aggregator(value), valid = period_unit_validator(date,time_unit)) %>%
         dplyr::ungroup() %>%
         dplyr::arrange(first_date) %>%
         dplyr::filter(valid)
-    return(matrix(tmp$value, ncol = 1, dimnames = list(as.character(tmp$first_date))))
+    # return(matrix(tmp$value, ncol = 1, dimnames = list(as.character(tmp$first_date))))
+    return(matrix(tmp$value, ncol = 1, dimnames = list(as.character(tmp$last_date))))
+    
 }
 
 
diff --git a/flepimop/R_packages/inference/R/inference_slot_runner_funcs.R b/flepimop/R_packages/inference/R/inference_slot_runner_funcs.R
index a708b2460..fbd20ba93 100644
--- a/flepimop/R_packages/inference/R/inference_slot_runner_funcs.R
+++ b/flepimop/R_packages/inference/R/inference_slot_runner_funcs.R
@@ -67,12 +67,18 @@ aggregate_and_calc_loc_likelihoods <- function(
         this_location_log_likelihood <- 0
         for (var in names(ground_truth_data[[location]])) {
 
-
+          obs_tmp1 <- ground_truth_data[[location]][[var]]
+          obs_tmp <- obs_tmp1[!is.na(obs_tmp1$data_var) & !is.na(obs_tmp1$date),]
+          sim_tmp1 <- this_location_modeled_outcome[[var]] 
+          sim_tmp <- sim_tmp1[match(lubridate::as_date(sim_tmp1$date), 
+                                    lubridate::as_date(obs_tmp$date)),] %>% na.omit()
+          
+          
             this_location_log_likelihood <- this_location_log_likelihood +
                 ## Actually compute likelihood for this location and statistic here:
                 sum(inference::logLikStat(
-                    obs = ground_truth_data[[location]][[var]]$data_var,
-                    sim = this_location_modeled_outcome[[var]]$sim_var,
+                    obs = as.numeric(obs_tmp$data_var),
+                    sim = as.numeric(sim_tmp$sim_var),
                     dist = targets_config[[var]]$likelihood$dist,
                     param = targets_config[[var]]$likelihood$param,
                     add_one = targets_config[[var]]$add_one
@@ -615,72 +621,77 @@ initialize_mcmc_first_block <- function(
     ## initial conditions (init)
 
     if (!is.null(config$initial_conditions)){
+      if(config$initial_conditions$method  != "plugin"){
+        
         if ("init_filename" %in% global_file_names) {
-
-            if (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions")){
-
-                if (is.null(config$initial_conditions$initial_conditions_file)) {
-                    stop("ERROR: Initial conditions file needs to be specified in the config under `initial_conditions:initial_conditions_file`")
-                }
-                initial_init_file <- config$initial_conditions$initial_conditions_file
-
-            } else if (config$initial_conditions$method %in% c("InitialConditionsFolderDraw", "SetInitialConditionsFolderDraw", "plugin")) {
-                print("Initial conditions in inference has not been fully implemented yet for the 'folder draw' methods,
-                      and no copying to global or chimeric files is being done.")
-
-                if (is.null(config$initial_conditions$initial_file_type)) {
-                    stop("ERROR: Initial conditions file needs to be specified in the config under `initial_conditions:initial_conditions_file`")
-                }
-                initial_init_file <- global_files[[paste0(config$initial_conditions$initial_file_type, "_filename")]]
-            }
-
-
-            if (!file.exists(initial_init_file)) {
-                stop("ERROR: Initial conditions file specified but does not exist.")
-            }
+          
+          if (config$initial_conditions$method %in% c("FromFile", "SetInitialConditions")){
             
-            if (grepl(".csv", initial_init_file)){
-                initial_init <- readr::read_csv(initial_init_file,show_col_types = FALSE)
-            }else{
-                initial_init <- arrow::read_parquet(initial_init_file)
+            if (is.null(config$initial_conditions$initial_conditions_file)) {
+              stop("ERROR: Initial conditions file needs to be specified in the config under `initial_conditions:initial_conditions_file`")
             }
+            initial_init_file <- config$initial_conditions$initial_conditions_file
             
-            # if the initial conditions file contains a 'date' column, filter for config$start_date
+          } else if (config$initial_conditions$method %in% c("InitialConditionsFolderDraw", "SetInitialConditionsFolderDraw")) {
+            print("Initial conditions in inference has not been fully implemented yet for the 'folder draw' methods,
+                      and no copying to global or chimeric files is being done.")
             
-            if("date" %in% colnames(initial_init)){
-                
-                initial_init <- initial_init %>%
-                    dplyr::mutate(date = as.POSIXct(date, tz="UTC")) %>%
-                    dplyr::filter(date == as.POSIXct(paste0(config$start_date, " 00:00:00"), tz="UTC"))
-                
-                if (nrow(initial_init) == 0) {
-                    stop("ERROR: Initial conditions file specified but does not contain the start date.")
-                }  
-                
+            if (is.null(config$initial_conditions$initial_file_type)) {
+              stop("ERROR: Initial conditions file needs to be specified in the config under `initial_conditions:initial_conditions_file`")
             }
-
-            arrow::write_parquet(initial_init, global_files[["init_filename"]])
+            initial_init_file <- global_files[[paste0(config$initial_conditions$initial_file_type, "_filename")]]
+          }
+          
+          
+          if (!file.exists(initial_init_file)) {
+            stop("ERROR: Initial conditions file specified but does not exist.")
+          }
+          
+          if (grepl(".csv", initial_init_file)){
+            initial_init <- readr::read_csv(initial_init_file,show_col_types = FALSE)
+          }else{
+            initial_init <- arrow::read_parquet(initial_init_file)
+          }
+          
+          # if the initial conditions file contains a 'date' column, filter for config$start_date
+          
+          if("date" %in% colnames(initial_init)){
+            
+            initial_init <- initial_init %>%
+              dplyr::mutate(date = as.POSIXct(date, tz="UTC")) %>%
+              dplyr::filter(date == as.POSIXct(paste0(config$start_date, " 00:00:00"), tz="UTC"))
+            
+            if (nrow(initial_init) == 0) {
+              stop("ERROR: Initial conditions file specified but does not contain the start date.")
+            }  
+            
+          }
+          
+          arrow::write_parquet(initial_init, global_files[["init_filename"]])
         }
-
+        
         # if the initial conditions file contains a 'date' column, filter for config$start_date
         if (grepl(".csv", global_files[["init_filename"]])){
-            initial_init <- readr::read_csv(global_files[["init_filename"]],show_col_types = FALSE)
+          initial_init <- readr::read_csv(global_files[["init_filename"]],show_col_types = FALSE)
         }else{
-            initial_init <- arrow::read_parquet(global_files[["init_filename"]])
+          initial_init <- arrow::read_parquet(global_files[["init_filename"]])
         }
-
+        
         if("date" %in% colnames(initial_init)){
-                
-            initial_init <- initial_init %>%
-                dplyr::mutate(date = as.POSIXct(date, tz="UTC")) %>%
-                dplyr::filter(date == as.POSIXct(paste0(config$start_date, " 00:00:00"), tz="UTC"))
-            
-            if (nrow(initial_init) == 0) {
-                stop("ERROR: Initial conditions file specified but does not contain the start date.")
-            }  
-                
+          
+          initial_init <- initial_init %>%
+            dplyr::mutate(date = as.POSIXct(date, tz="UTC")) %>%
+            dplyr::filter(date == as.POSIXct(paste0(config$start_date, " 00:00:00"), tz="UTC"))
+          
+          if (nrow(initial_init) == 0) {
+            stop("ERROR: Initial conditions file specified but does not contain the start date.")
+          }  
+          
         }
         arrow::write_parquet(initial_init, global_files[["init_filename"]])
+      }else if(config$initial_conditions$method  == "plugin"){
+        print("Initial conditions files generated by gempyor using plugin method.")
+      }
     }
 
 
diff --git a/flepimop/main_scripts/inference_slot.R b/flepimop/main_scripts/inference_slot.R
index 0e8c32bb5..04ce4316e 100644
--- a/flepimop/main_scripts/inference_slot.R
+++ b/flepimop/main_scripts/inference_slot.R
@@ -53,7 +53,7 @@ option_list = list(
   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("-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.')
+  optparse::make_option(c("-a", "--incl_aggr_likelihood"), action = "store", default = Sys.getenv("INCL_AGGR_LIKELIHOOD", FALSE), type = 'logical', help = 'Should the likelihood be calculated with the aggregate estiamtes.')
 )
 
 parser=optparse::OptionParser(option_list=option_list)
@@ -268,12 +268,12 @@ if (config$inference$do_inference){
   obs <- suppressMessages(
     readr::read_csv(config$inference$gt_data_path,
                     col_types = readr::cols(date = readr::col_date(),
-                                            source = readr::col_character(),
+                                            # source = readr::col_character(),
                                             subpop = readr::col_character(),
                                             .default = readr::col_double()), )) %>%
     dplyr::filter(subpop %in% subpops_, date >= gt_start_date, date <= gt_end_date) %>%
-    dplyr::right_join(tidyr::expand_grid(subpop = unique(.$subpop), date = unique(.$date))) %>%
-    dplyr::mutate_if(is.numeric, dplyr::coalesce, 0)
+    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