use new arguments in the makefiles under bugs_example

maverickg · maverickg · commit 054c3584553a · 2013-08-17T09:31:15.000-04:00
this does not affect any test
diff --git a/bugs_examples/vol1/blocker/makefile b/bugs_examples/vol1/blocker/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG  $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R --burnin=1000 --iters=10000 
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/bones/makefile b/bugs_examples/vol1/bones/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan
 	$(CXX)   -O3 -Wall $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R # --iters=2000
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/dogs/makefile b/bugs_examples/vol1/dogs/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R --seed=1340384924 --chain_id=4 --diagnostics=d.csv# --iters=20000
+	./$(PGM) id=4 data=$(PGM).data.R  method=sample  num_warmup=1000 num_samples=1000 random seed=1340384924 output sample=samples.csv
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/dyes/makefile b/bugs_examples/vol1/dyes/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --iter=100000
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/equiv/makefile b/bugs_examples/vol1/equiv/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM) $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --burnin=1000 --iters=10000
+	./$(PGM) data=$(PGM).data.R sample num_warmup=1000 num_samples=10000 random seed=1340384924 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/inhalers/makefile b/bugs_examples/vol1/inhalers/makefile
@@ -10,8 +10,8 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan
-	$(CXX) -g -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R --iter=2000
+	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/kidney/makefile b/bugs_examples/vol1/kidney/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R # --iter=2000
+	./$(PGM) data=$(PGM).data.R sample num_samples=2000
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/leuk/makefile b/bugs_examples/vol1/leuk/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan
 	$(CXX)   -O3  -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R # --iters=2000
+	./$(PGM) data=$(PGM).data.R
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/leukfr/makefile b/bugs_examples/vol1/leukfr/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan
 	$(CXX) -O3 -DNDEBUG  $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R  --iter=10000
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/lsat/makefile b/bugs_examples/vol1/lsat/makefile
@@ -7,7 +7,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 lsat :
 	$(STAN_HOME)/bin/stanc --name=lsat lsat.stan 
 	g++ -O0  -DNDEBUG $(CPPFLAGS) lsat.cpp -o lsat $(LIBFLAGS)
-	./lsat --data=lsat.data.R
+	./lsat data=lsat.data.R sample
 
 clean :
 	rm -f lsat.cpp samples.csv lsat
diff --git a/bugs_examples/vol1/magnesium/makefile b/bugs_examples/vol1/magnesium/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM)  $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R --burnin=1000 --iters=10000 # --samples=samples.csv 
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM)
diff --git a/bugs_examples/vol1/mice/makefile b/bugs_examples/vol1/mice/makefile
@@ -10,7 +10,7 @@ CXX = clang++
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --iters=20000
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/oxford/makefile b/bugs_examples/vol1/oxford/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R # --iter=2000
+	./$(PGM) data=$(PGM).data.R sample random seed=1340384924 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/pump/makefile b/bugs_examples/vol1/pump/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R # --iters=2000
+	./$(PGM) data=$(PGM).data.R
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol1/salm/makefile b/bugs_examples/vol1/salm/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) : 
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM)
diff --git a/bugs_examples/vol1/seeds/makefile b/bugs_examples/vol1/seeds/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=seeds  seeds.stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./seeds --data=seeds.data.R
+	./seeds data=seeds.data.R sample
 
 clean :
 	rm -f seeds.cpp samples.csv seeds
diff --git a/bugs_examples/vol2/air/makefile b/bugs_examples/vol2/air/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --burnin=1000 --iters=100000 
+	./$(PGM) data=$(PGM).data.R sample num_warmup=1000 num_samples=10000 
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/beetles/makefile b/bugs_examples/vol2/beetles/makefile
@@ -7,17 +7,17 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 beetles_logit :
 	$(STAN_HOME)/bin/stanc --name=beetles_logit  beetles_logit.stan 
 	g++ -O0 -DNDEBUG $(CPPFLAGS) beetles_logit.cpp -o beetles_logit $(LIBFLAGS)
-	./beetles_logit --data=beetles_logit.data.R
+	./beetles_logit data=beetles_logit.data.R sample
 
 beetles_probit :
 	$(STAN_HOME)/bin/stanc --name=beetles_probit  beetles_probit.stan 
 	g++ -O0 -DNDEBUG $(CPPFLAGS)  beetles_probit.cpp -o beetles_probit $(LIBFLAGS)   
-	./beetles_probit --data=beetles_probit.data.R
+	./beetles_probit data=beetles_probit.data.R sample
 
 beetles_cloglog :
 	$(STAN_HOME)/bin/stanc --name=beetles_cloglog  beetles_cloglog.stan 
 	g++ -O0 -DNDEBUG $(CPPFLAGS) beetles_cloglog.cpp -o beetles_cloglog $(LIBFLAGS)
-	./beetles_cloglog --data=beetles_cloglog.data.R
+	./beetles_cloglog data=beetles_cloglog.data.R sample
 
 clean :
 	rm -f beetles*.cpp samples.csv beetles_logit beetles_probit beetles_cloglog
diff --git a/bugs_examples/vol2/cervix/makefile b/bugs_examples/vol2/cervix/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --iter=10000 --thin=1
+	./$(PGM) data=$(PGM).data.R sample num_samples=10000 num_warmup=1000 thin=1
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/dugongs/makefile b/bugs_examples/vol2/dugongs/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM) $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/eyes/makefile b/bugs_examples/vol2/eyes/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM) $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/hearts/makefile b/bugs_examples/vol2/hearts/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/jaws/makefile b/bugs_examples/vol2/jaws/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM) $(PGM).stan 
 	$(CXX) -O0 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/mvn_orange/makefile b/bugs_examples/vol2/mvn_orange/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM) $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --iter=10000 
+	./$(PGM) data=$(PGM).data.R sample num_warmup=1000 num_samples=10000 
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/schools/makefile b/bugs_examples/vol2/schools/makefile
@@ -10,7 +10,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM) $(PGM).stan
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --seed=3386159189
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol2/t_df/estdof2.stan.0 b/bugs_examples/vol2/t_df/estdof2.stan.0
@@ -14,12 +14,12 @@ data {
 } 
 
 transformed data {
-  vector(49) p; 
+  vector[49] p; 
   for (i in 1:49)  p[i] <- 1.0 / 49; 
 } 
 
 parameters {
-  int(0, 48) K; 
+  int<lower=0, upper=48> K; 
 } 
 transformed parameters {
   // learning about the dof as a continuous quantity
diff --git a/bugs_examples/vol2/t_df/makefile b/bugs_examples/vol2/t_df/makefile
@@ -12,17 +12,17 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) : 
 	$(STAN_HOME)/bin/stanc --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R --samples=samples1.csv 
+	./$(PGM) data=$(PGM).data.R sample output sample=samples1.csv 
 
 $(PGM2) : 
 	$(STAN_HOME)/bin/stanc --name=$(PGM2)  $(PGM2).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM2).cpp -o $(PGM2) $(LIBFLAGS) 
-	./$(PGM2) --data=$(PGM2).data.R --samples=samples2.csv 
+	./$(PGM2) data=$(PGM2).data.R sample output sample=samples2.csv 
 
 $(PGM3) : 
 	$(STAN_HOME)/bin/stanc --name=$(PGM3)  $(PGM3).stan.0 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM3).cpp -o $(PGM3) $(LIBFLAGS) 
-	./$(PGM3) --data=$(PGM3).data.R --samples=samples3.csv 
+	./$(PGM3) data=$(PGM3).data.R sample output sample=samples3.csv 
 
 clean :
 	rm -f $(PGM).cpp samples1.csv $(PGM) 
diff --git a/bugs_examples/vol3/camel/makefile b/bugs_examples/vol3/camel/makefile
@@ -10,12 +10,12 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS)  $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) # --data=$(PGM).data.R
+	./$(PGM) sample
 
 $(PGM2) :
 	$(STAN_HOME)/bin/stanc  --name=$(PGM2)  $(PGM2).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS)  $(PGM2).cpp -o $(PGM2) $(LIBFLAGS) 
-	./$(PGM2) # --data=$(PGM2).data.R
+	./$(PGM2) sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol3/data_cloning/makefile b/bugs_examples/vol3/data_cloning/makefile
@@ -9,7 +9,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM) --data=$(PGM).data.R
+	./$(PGM) data=$(PGM).data.R sample
 
 clean :
 	rm -rf $(PGM).cpp samples.csv $(PGM) 
diff --git a/bugs_examples/vol3/funshapes/makefile b/bugs_examples/vol3/funshapes/makefile
@@ -17,27 +17,27 @@ all : $(PGM) $(PGM2) $(PGM3) $(PGM4) $(PGM5)
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM)  $(PGM).stan 
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS)
-	./$(PGM)
+	./$(PGM) sample
 
 $(PGM2) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM2)  $(PGM2).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM2).cpp -o $(PGM2) $(LIBFLAGS)
-	./$(PGM2)
+	./$(PGM2) sample
 
 $(PGM3) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM3)  $(PGM3).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM3).cpp -o $(PGM3) $(LIBFLAGS)
-	./$(PGM3)
+	./$(PGM3) sample
 
 $(PGM4) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM4)  $(PGM4).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM4).cpp -o $(PGM4) $(LIBFLAGS)
-	./$(PGM4)
+	./$(PGM4) sample
 
 $(PGM5) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM5)  $(PGM5).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM5).cpp -o $(PGM5) $(LIBFLAGS)
-	./$(PGM5)
+	./$(PGM5) sample
 
 
 clean :
diff --git a/bugs_examples/vol3/hepatitis/makefile b/bugs_examples/vol3/hepatitis/makefile
@@ -11,7 +11,7 @@ LIBFLAGS = -L$(STAN_HOME)/bin -lstan
 $(PGM) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM)  $(PGM).stan 
 	$(CXX) -O3 -DNDEBUG $(CPPFLAGS) $(PGM).cpp -o $(PGM) $(LIBFLAGS) 
-	./$(PGM)  --data=$(PGM).data.R
+	./$(PGM)  data=$(PGM).data.R sample
 
 clean :
 	rm -f $(PGM).cpp samples.csv $(PGM) 
