all funshapes working, with existing modified so there is no rejection

Author: Bob Carpenter

bugs_examples/vol3/funshapes/circle.stan

@@ -1,12 +1,12 @@
-# http://www.openbugs.info/Examples/Funshapes.html
-
+/*
+ * BUGS volume 3, fun shapes, circle
+ * http://www.openbugs.info/Examples/Funshapes.html
+ */
 parameters {
-  real<lower=-1,upper= 1> x; 
-  real<lower=-1,upper= 1> y; 
+  real<lower=-1,upper=1> x; 
+  real<lower = -sqrt(1 - square(x)), 
+       upper =  sqrt(1 - square(x))> y; 
 } 
-
 model {
-  // lp__ <- log(step(1 - x * x - y * y)); 
-  lp__ <- log(fmax(0, 1 - x * x - y * y)); 
-  
+  /* uniform within constraints */
 } 

bugs_examples/vol3/funshapes/hsquare.stan

@@ -0,0 +1,49 @@
+/*
+ * Hollow Square
+ * http://www.openbugs.info/Examples/Funshapes.html
+ *
+ * Transform a uniform rectangle
+ *    1234
+ *    5678
+ *    90AB
+ * to a uniform hollow square
+ *    1234
+ *    5  6
+ *    7  8
+ *    90AB
+ */
+parameters {
+  real<lower=0,upper=2> x_raw; 
+  real<lower=0,upper=1.5> y_raw; 
+} 
+model {
+  /* no-op; uniformity implied by parameter constraints */
+} 
+generated quantities {
+  real x;
+  real y;
+  if (y_raw > 1) {
+    // cases 1, 2, 3, 4
+    x <- x_raw - 1;
+    y <- y_raw - 0.5;
+  } else if (y_raw < 0.5) {
+    // cases 9, 0, A, B
+    x <- x_raw - 1;
+    y <- y_raw - 1;
+  } else if (x_raw < 0.5) {
+    // case 5
+    x <- x_raw - 1;
+    y <- y_raw - 0.5;
+  } else if (x_raw < 1.0) {
+    // case 6
+    x <- x_raw - 1.5;
+    y <- y_raw - 1;
+  } else if (x_raw < 1.5) {
+    // case 7
+    x <- x_raw - 0.5;
+    y <- y_raw - 0.5;
+  } else {
+    x <- x_raw - 1.0;
+    y <- y_raw - 1.0;
+  }
+}

bugs_examples/vol3/funshapes/hsquare.stan.0

@@ -3,7 +3,7 @@ PGM = circle#
 PGM2 = squaremc#
 PGM3 = ring#
 PGM4 = hsquare#
-PGM5 = parallelagram#
+PGM5 = parallelogram#
 
 CXX = g++
 CXX = clang++
@@ -12,31 +12,32 @@ EIGENPATH = $(shell find $(STAN_HOME)/lib -path '*lib/eigen_*' -regex '.*lib\/ei
 CPPFLAGS = -I $(BOOSTPATH)  -I$(EIGENPATH) -I $(STAN_HOME)/src
 LIBFLAGS = -L$(STAN_HOME)/bin -lstan 
 
+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) # --data=$(PGM).data.R
+	./$(PGM)
 
 $(PGM2) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM2)  $(PGM2).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM2).cpp -o $(PGM2) $(LIBFLAGS)
-	./$(PGM2) --iter=10000 --warmup=1000  # --data=$(PGM2).data.R
-
+	./$(PGM2)
 
 $(PGM3) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM3)  $(PGM3).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM3).cpp -o $(PGM3) $(LIBFLAGS)
-	./$(PGM3) --iter=10000 --warmup=1000 --thin=1# --data=$(PGM3).data.R
+	./$(PGM3)
 
 $(PGM4) :
-	$(STAN_HOME)/bin/stanc --name=$(PGM4)  $(PGM4).stan.0 
+	$(STAN_HOME)/bin/stanc --name=$(PGM4)  $(PGM4).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM4).cpp -o $(PGM4) $(LIBFLAGS)
-	./$(PGM4) # --data=$(PGM4).data.R
+	./$(PGM4)
 
 $(PGM5) :
 	$(STAN_HOME)/bin/stanc --name=$(PGM5)  $(PGM5).stan
 	$(CXX) -Wall -O3 -DNDEBUG $(CPPFLAGS) $(PGM5).cpp -o $(PGM5) $(LIBFLAGS)
-	./$(PGM5) # --data=$(PGM5).data.R
+	./$(PGM5)
 
 
 clean :

bugs_examples/vol3/funshapes/makefile

@@ -0,0 +1,15 @@
+/*
+ * BUGS Volume 3, funshapes, parallelogram
+ * http://www.openbugs.info/Examples/Funshapes.html
+ */
+parameters {
+  real<lower=0,upper=1> x; 
+  real<lower=0,upper=1> y_raw; 
+} 
+transformed parameters {
+  real<lower=-1,upper=1> y;
+  y <- y_raw - x;
+}
+model {
+  /* uniform within constraints */
+} 

bugs_examples/vol3/funshapes/parallelagram.stan

@@ -0,0 +1,24 @@
+/*
+ * BUGS Volume 3, funshapes, square minus circle
+ * http://www.openbugs.info/Examples/Funshapes.html
+ *
+ * first draw raw samples from diamond-like shape reflected per
+ * quadrant, then reflect in transformed parameters
+ *
+ * unfortunate redundancy in 1-sqrt() term because we can't
+ * get local variables into parameters
+ */
+parameters {
+  real<lower=-1,upper=1> x_raw;
+  real<lower = -(1 - sqrt(1 - square(1 - fabs(x_raw)))),
+       upper =  (1 - sqrt(1 - square(1 - fabs(x_raw))))> y_raw;
+}
+transformed parameters {
+  real<lower=-1,upper=1> x;
+  real<lower=-1,upper=1> y;
+  x <- if_else(x_raw > 0, 1, -1) - x_raw;
+  y <- if_else(y_raw > 0, 1, -1) - y_raw;
+}
+model {
+  lp__ <- lp__ + log1m(sqrt(1 - square(1 - fabs(x_raw))));
+}