change lphy scripts

examples/coalescent/exponentialCoalescent.lphy

@@ -1,12 +1,15 @@
-data {
-  L = 200;
 
-}
 
 model {
-  GrowthRate ~ Normal(mean=0.055, sd=0.0005);
-  N0 ~ Normal(mean=30, sd=1.0);
-  exponentialPopFunc = exponentialPopFunc(GrowthRate=GrowthRate, N0=N0);
-  times ~ CoalescentPopFunc(popFunc=exponentialPopFunc, n=16);
-  D ~ PhyloCTMC(tree=times, L=L, Q=jukesCantor());
-}
+GrowthRate ~ LogNormal(meanlog=2.0, sdlog=0.9);
+N0 ~ LogNormal(meanlog=9.2, sdlog=0.12);
+NA ~ LogNormal(meanlog=5.2, sdlog=0.12);
+I_na ~ UniformDiscrete(lower=0, upper=1);
+
+exponentialPopFunc = exponentialPopFunc(GrowthRate=GrowthRate, N0=N0, NA=NA, I_na=I_na);
+tree ~ CoalescentPopFunc(n=40, popFunc=exponentialPopFunc);
+
+D ~ PhyloCTMC(L=2000, Q=jukesCantor(),mu=0.01, tree=tree);
+height = tree.rootAge();
+length = tree.treeLength();
+}

examples/coalescent/gompertzCoalescent_f0.lphy

@@ -1,12 +1,15 @@
 data {
-  L = 500;
+  L = 1000;
 }
 model {
-
-  N0 ~ LogNormal(meanlog=10,sdlog=0.5);
+  N0 ~ LogNormal(meanlog=8, sdlog=0.5);
+  b ~ LogNormal(meanlog=-0.95, sdlog=0.2);
   f0 ~ Beta(alpha=20, beta=7);
-  b ~ Beta(alpha=40, beta=10);
-  gompertzPopFunc = gompertzPopFunc_f0(N0=N0,f0=f0, b=b);
-  tree ~ CoalescentPopFunc(n=16, popFunc=gompertzPopFunc);
-  D ~ PhyloCTMC(tree=tree, L=L, Q=jukesCantor(), mu=1e-9);
-}
+  NA ~ LogNormal(meanlog=4, sdlog=0.3);
+  I_na ~ UniformDiscrete(lower=0, upper=1);
+  gompertzPopFunc = gompertzPopFunc_f0(f0=f0, b=b, N0=N0, NA=NA, I_na = I_na);
+  tree ~ CoalescentPopFunc(n=40, popFunc=gompertzPopFunc);
+  D ~ PhyloCTMC(L=L, Q=jukesCantor(), mu=0.01, tree=tree);
+  //height = tree.rootAge();
+}
+

examples/coalescent/gompertzCoalescent_t50.lphy

@@ -1,13 +1,17 @@
 data {
-  L = 500;
+  L = 1000;
 }
 model {
-
-  NInfinity ~ LogNormal(meanlog=10,sdlog=0.5);
-  //t50 ~ Beta(alpha=20, beta=7);
-  t50 ~ Normal(mean=0,sd=0.333);
-  b ~ Beta(alpha=40, beta=10);
-  gompertzPopFunc = gompertzPopFunc_t50(NInfinity=NInfinity,t50=t50, b=b,NA=0);
-  tree ~ CoalescentPopFunc(n=16, popFunc=gompertzPopFunc);
-  D ~ PhyloCTMC(tree=tree, L=L, Q=jukesCantor(), mu=1e-9);
-}
+  t50 ~ LogNormal(meanlog=2.3, sdlog=0.3);
+  b ~ LogNormal(meanlog=-1.5, sdlog=0.2);
+  NInfinity ~ LogNormal(meanlog=6.5, sdlog=0.5);
+  NA ~ LogNormal(meanlog=2.21, sdlog=0.1);
+  I_na ~ UniformDiscrete(lower=0, upper=1);
+  gompertzPopFunc = gompertzPopFunc_t50(NInfinity=NInfinity,t50=t50, b=b, NA=NA,I_na = I_na);
+  // n0 = gompertzPopFunc.getN0();
+  // f0=n0/NInfinity;
+  tree ~ CoalescentPopFunc(n=40, popFunc=gompertzPopFunc);
+  D ~ PhyloCTMC(tree=tree, L=L, Q=jukesCantor(), mu=1e-2);
+  height = tree.rootAge();
+  length = tree.treeLength();
+}