Remove figures not in manuscript nor supplement

WorldHealthOrganization · Apr 16, 2024 · f3af9a0 · f3af9a0
1 parent 14a2ad0
commit f3af9a0
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Showing 9 changed files with 30 additions and 1,506 deletions.
diff --git a/coverage.R b/coverage.R
@@ -70,14 +70,8 @@ prepare_coverage = function() {
   # Plot total number of FVP over time
   plot_total_fvps()
 
-  # Plot coverage density by disease
-  plot_coverage()
-
   # Coverage data density by age
   plot_coverage_age_density()
-
-  # Missing coverage data by country
-  plot_missing_data()
 }
 
 # ---------------------------------------------------------
@@ -550,14 +544,9 @@ smooth_static_fvps = function(coverage_dt) {
     fill(source, .direction = "updown") %>%
     arrange(d_v_a_id, country, year, age)
 
-  # ---- Diagnostic plots ----
-
   # Save table for diagnostic plots
   save_table(smooth_dt, "smoothed_fvps")
 
-  # Diagnostic plots for FVPs smoothing
-  plot_smooth_fvps()
-
   return(smoothed_coverage_dt)
 }
 

diff --git a/external.R b/external.R
@@ -35,20 +35,11 @@ run_external = function() {
 
   # ---- Data visualisation plots ----
 
-  # Plot outcomes from each external model
-  plot_external_models()
-
   # Plot total number of FVP over time
   plot_total_fvps()
 
-  # Plot coverage density by disease
-  plot_coverage()
-
   # Coverage data density by age
   plot_coverage_age_density()
-
-  # Missing coverage data by country
-  plot_missing_data()
 }
 
 # ---------------------------------------------------------

diff --git a/history.R b/history.R
@@ -329,16 +329,6 @@ run_history = function(metric) {
     # Save results to file
     save_rds(yll_time_dt, "history", "burden_averted_yll") 
   }
-
-  # ---- Plot diagnostic figures ----
-
-  # NOTE: Most results figures created in final module
-
-  # Plot inital impact ratios used to back project
-  plot_impact_fvps(metric, scope = "initial")
-
-  # Plot comparison of EPI50 outcomes vs VIMC outcomes
-  plot_vimc_comparison()
 }
 
 # ---------------------------------------------------------

diff --git a/impact.R b/impact.R
@@ -23,9 +23,6 @@ run_impact = function(metric) {
   # Prepare impact-FVP data to fit to
   data_dt = get_impact_data(metric)
 
-  # Exploratory plots of data used to fit impact functions
-  plot_impact_data(metric)
-
   # ---- Model fitting ----
 
   message(" > Evaluating impact functions")

diff --git a/launch.R b/launch.R
@@ -17,7 +17,7 @@ source("dependencies.R")
 message("Running EPI50 pipeline")
 
 # Define modules to be run
-run_modules = 8
+run_modules = 1 : 8
 
 # Set global options (see options.R)
 o = set_options(run_module = run_modules)

diff --git a/options.R b/options.R
@@ -57,7 +57,6 @@ set_options = function(run_module = NA) {
 
   # Turn figures on or off
   o$plot_inputs     = TRUE
-  o$plot_external   = TRUE
   o$plot_static     = TRUE
   o$plot_imputation = TRUE
   o$plot_impact     = TRUE