allow us to specify a date to start NTDMC output from

NTD-Modelling-Consortium · Jan 7, 2025 · b6b7dbe · b6b7dbe
1 parent accc859
commit b6b7dbe
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Showing 4 changed files with 35 additions and 14 deletions.
diff --git a/src/Model.cpp b/src/Model.cpp
@@ -27,7 +27,8 @@ extern Statistics stats;
 void Model::runScenarios(ScenariosList &scenarios, Population &popln,
                          Vector &vectors, Worm &worms, int replicates,
                          double timestep, int index, int outputEndgame,
-                         int outputEndgameDate, int reduceImpViaXml,
+                         int outputEndgameDate, int outputNTDMC,
+                         int outputNTDMCDate, int reduceImpViaXml,
                          std::string randParamsfile, std::string RandomSeedFile,
                          std::string RandomCovPropFile, std::string opDir) {
 
@@ -146,9 +147,11 @@ void Model::runScenarios(ScenariosList &scenarios, Population &popln,
 
       // evolve, saving any specified months along the way
       for (int y = 0; y < sc.getNumMonthsToSave(); y++)
+
         evolveAndSave(y, popln, vectors, worms, sc, currentOutput, rep, k_vals,
                       v_to_h_vals, popln.getUpdateParams(), outputEndgame,
-                      outputEndgameDate, reduceImpViaXml, opDir, cov_prop);
+                      outputEndgameDate, outputNTDMC, outputNTDMCDate,
+                      reduceImpViaXml, opDir, cov_prop);
 
       // done for this scenario, save the prevalence values for this replicate
       if (!_DEBUG)
@@ -215,6 +218,7 @@ void Model::evolveAndSave(int y, Population &popln, Vector &vectors,
                           int rep, std::vector<double> &k_vals,
                           std::vector<double> &v_to_h_vals, int updateParams,
                           int outputEndgame, int outputEndgameDate,
+                          int outputNTDMC, int outputNTDMCDate,
                           int reduceImpViaXml, std::string opDir,
                           double cov_prop) {
 
@@ -237,6 +241,7 @@ void Model::evolveAndSave(int y, Population &popln, Vector &vectors,
   // simulations from the scenario file.
   int BASEYEAR = 2000;
   outputEndgameDate = (outputEndgameDate - BASEYEAR) * 12;
+  outputNTDMCDate = (outputNTDMCDate - BASEYEAR) * 12;
   int popSize = popln.getSizeOfPop();
   double mfprev_aimp_old =
       popln.getMFPrev(sc, 0, 0, outputEndgameDate, rep, popSize, folderName);
@@ -254,13 +259,16 @@ void Model::evolveAndSave(int y, Population &popln, Vector &vectors,
   double LymphodemaShape = popln.getLymphodemaShape();
   double HydroceleShape = popln.getHydroceleShape();
 
-  if (outputEndgame == 1) {
+  if ((outputEndgame == 1) && (y == 0)) {
     sc.InitIHMEData(rep, folderName);
-    sc.InitNTDMCData(rep, folderName);
     sc.InitPreTASData(rep, folderName);
     sc.InitTASData(rep, folderName);
   }
 
+  if ((outputNTDMC == 1) && (y == 0)) {
+    sc.InitNTDMCData(rep, folderName);
+  }
+
   int vec_control = 0;
 
   int minAge;
@@ -313,8 +321,7 @@ void Model::evolveAndSave(int y, Population &popln, Vector &vectors,
     // year we want to do the endgame output for, then don't do this.
     if ((t % 12 == 0) && (outputEndgame == 1) && (t >= outputEndgameDate)) {
       sc.writePrevByAge(popln, t, rep, folderName);
-      sc.writeRoadmapTarget(popln, t, rep, popln.DoMDA, popln.TAS_Pass,
-                            neededTASPass, folderName);
+
       sc.writeNumberByAge(popln, t, rep, folderName, "not survey");
       sc.writeSequelaeByAge(popln, t, LymphodemaTotalWorms, LymphodemaShape,
                             HydroceleTotalWorms, HydroceleShape, rep,
@@ -324,6 +331,11 @@ void Model::evolveAndSave(int y, Population &popln, Vector &vectors,
                           folderName);
     }
 
+    if ((t % 12 == 0) && (outputNTDMC == 1) && (t >= outputNTDMCDate)) {
+      sc.writeRoadmapTarget(popln, t, rep, popln.DoMDA, popln.TAS_Pass,
+                            neededTASPass, folderName);
+    }
+
     // If we haven't done a survey this year we still want to output this fact
     // for endgame. This is because the decision to do the survey is dynamic and
     // may occur in some simulations but not in others. to make sure that

diff --git a/src/Model.hpp b/src/Model.hpp
@@ -28,9 +28,10 @@ class Model {
   void runScenarios(ScenariosList &scenarios, Population &popln,
                     Vector &vectors, Worm &worms, int replicates,
                     double timestep, int index, int outputEndgame,
-                    int outputEndgameDate, int reduceImpViaXml,
-                    std::string randParamsfile, std::string RandomSeedFile,
-                    std::string RandomCovPropFile, std::string opDir);
+                    int outputEndgameDate, int outputNTDMC, int outputNTDMCDate,
+                    int reduceImpViaXml, std::string randParamsfile,
+                    std::string RandomSeedFile, std::string RandomCovPropFile,
+                    std::string opDir);
   bool
   shouldReduceImportationViaPrevalance(int t, int reduceImpViaXml,
                                        int switchImportationReducingMethodTime);
@@ -47,8 +48,9 @@ class Model {
                      Scenario &sc, Output &currentOutput, int rep,
                      std::vector<double> &k_vals,
                      std::vector<double> &v_to_h_vals, int updateParams,
-                     int outputEndgame, int outputEndgameDate,
-                     int reduceImpViaXml, std::string opDir, double cov_prop);
+                     int outputEndgame, int outputEndgameDate, int outputNTDMC,
+                     int outputNTDMCDate, int reduceImpViaXml,
+                     std::string opDir, double cov_prop);
   void getRandomParameters(int index, std::vector<double> &k_vals,
                            std::vector<double> &v_to_h_vals,
                            std::vector<double> &aImp_vals,

diff --git a/src/Scenario.cpp b/src/Scenario.cpp
@@ -853,6 +853,7 @@ void Scenario::InitNTDMCData(int rep, std::string folder) {
   if (stat(fname2.c_str(), &buffer) != 0) {
     fs::create_directories(fname2);
   }
+
   std::ofstream outfile;
   outfile.open(fname);
 

diff --git a/src/main.cpp b/src/main.cpp
@@ -73,6 +73,8 @@ int main(int argc, char **argv) {
   // xml file rather than impact of MDA on the prevalence
   int outputEndgame = 1;
   int outputEndgameDate = 2000;
+  int outputNTDMC = 1;
+  int outputNTDMCDate = 2000;
   int reduceImpViaXml = 0;
 
   int index = 0;
@@ -112,6 +114,10 @@ int main(int argc, char **argv) {
       outputEndgame = atoi(argv[i + 1]);
     else if (!strcmp(argv[i], "-D"))
       outputEndgameDate = atoi(argv[i + 1]);
+    else if (!strcmp(argv[i], "-m"))
+      outputNTDMC = atoi(argv[i + 1]);
+    else if (!strcmp(argv[i], "-N"))
+      outputNTDMCDate = atoi(argv[i + 1]);
     else if (!strcmp(argv[i], "-x"))
       reduceImpViaXml = atoi(argv[i + 1]);
     else {
@@ -193,9 +199,9 @@ int main(int argc, char **argv) {
   // Run
   Model model;
   model.runScenarios(Scenarios, hostPopulation, vectors, worms, replicates, dt,
-                     index, outputEndgame, outputEndgameDate, reduceImpViaXml,
-                     randParamsfile, RandomSeedFile, CoverageReductionFile,
-                     opDir);
+                     index, outputEndgame, outputEndgameDate, outputNTDMC,
+                     outputNTDMCDate, reduceImpViaXml, randParamsfile,
+                     RandomSeedFile, CoverageReductionFile, opDir);
 
   gettimeofday(&tv2, NULL);
   double timesofar = (double)(tv2.tv_usec - tv1.tv_usec) / 1000000.0 +