Cleaning examples, add tree dist doc

examples/birthdeath_incomplete_sampling.pj

@@ -0,0 +1,20 @@
+# constant-node variable ('birth_rate', etc.) assignment
+birth_rate <- 1.0
+death_rate <- 0.2
+
+# deterministic-node variable ('det_birth_rate', etc.) assignment
+det_birth_rate := sse_rate(name="birth_rate", value=birth_rate, event="speciation")
+det_death_rate := sse_rate(name="death_rate", value=death_rate, event="extinction")
+
+# constant-node variable ('sampling_rate') assignment
+sampling_prob <- 0.5
+
+# deterministic-node variable ('det_sampling_rate') assignment
+det_sampling_prob := sse_prob(name="rho", value=sampling_prob, state=0)
+
+# deterministic-node variable ('meh') assignment
+stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate], flat_prob_mat=[det_sampling_prob], n_states=1, n_epochs=1)
+
+# stochastic-node variable ('trs') assignment
+ori <- 1.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")

examples/birthdeath_timehet.pj

@@ -20,4 +20,5 @@ det_death_rate_t1 := sse_rate(name="mu_t1", value=death_rate_t1, states=[0], eve
 stash := sse_stash(flat_rate_mat=[det_birth_rate_t0,det_death_rate_t0,det_birth_rate_t1,det_death_rate_t1], n_states=1, n_epochs=2, epoch_age_ends=[1.5], seed_age=3.0)
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true")
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0], stop="age", stop_value=ori, origin="true")

examples/bisse.pj

@@ -16,7 +16,8 @@ det_death_rate1 := sse_rate(name="mu1", value=death_rate1, states=[1], event="ex
 det_trans_rate_10 := sse_rate(name="q10", value=trans_rate_10, states=[1,0], event="transition")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_birth_rate0, det_death_rate0, det_trans_rate_01, det_birth_rate1, det_death_rate1, det_trans_rate_10], n_states=2, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_birth_rate0, det_death_rate0, det_trans_rate_01, det_birth_rate1, det_death_rate1, det_trans_rate_10], n_states=2) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=3, stash=stash, start_state=[0,0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")

examples/bisse_timehet.pj

@@ -33,8 +33,8 @@ det_trans_rate01_t1 := sse_rate(name="q01_t1", value=trans_rate01_t1, states=[0,
 det_trans_rate10_t1 := sse_rate(name="q10_t1", value=trans_rate10_t1, states=[1,0], event="transition", epoch=2)
 
 # deterministic-node variable ('sse_stash') assignment
-# all first-epoch rates first, then all second-epoch rates!
 stash := sse_stash(flat_rate_mat=[det_birth_rate0_t0, det_death_rate0_t0, det_birth_rate1_t0, det_death_rate1_t0, det_trans_rate01_t0, det_trans_rate10_t0, det_birth_rate0_t1, det_death_rate0_t1, det_birth_rate1_t1, det_death_rate1_t1, det_trans_rate01_t1, det_trans_rate10_t1], n_states=2, n_epochs=2, epoch_age_ends=[1.5], seed_age=3.0)
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true")
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")

examples/fbd.pj

@@ -9,7 +9,8 @@ det_death_rate := sse_rate(name="mu", value=death_rate, states=[0], event="extin
 det_fossil_rate := sse_rate(name="psi", value=fossil_rate, states=[0], event="anc_sampling")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate, det_fossil_rate], n_states=1, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_birth_rate, det_death_rate, det_fossil_rate], n_states=1) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=100, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true", cond_spn="true", cond_surv="true")

examples/geosse.pj

@@ -29,7 +29,8 @@ det_trans_rate_20 := sse_rate(name="q20", value=trans_rate_20, states=[2,0], eve
 det_trans_rate_21 := sse_rate(name="q21", value=trans_rate_21, states=[2,1], event="transition")
 
 # deterministic-node variable ('sse_stash') assignment
-stash := sse_stash(flat_rate_mat=[det_w_birth_rate0, det_death_rate0, det_trans_rate_02, det_w_birth_rate1, det_death_rate1, det_trans_rate_12, det_b_birth_rate201, det_b_birth_rate202, det_b_birth_rate212, det_trans_rate_20, det_trans_rate_21], n_states=3, n_epochs=1) 
+stash := sse_stash(flat_rate_mat=[det_w_birth_rate0, det_death_rate0, det_trans_rate_02, det_w_birth_rate1, det_death_rate1, det_trans_rate_12, det_b_birth_rate201, det_b_birth_rate202, det_b_birth_rate212, det_trans_rate_20, det_trans_rate_21], n_states=3) 
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=1, stash=stash, start_state=[0], stop="age", stop_value=3.0, origin="true", cond_spn="true", cond_surv="true")
+ori <- 3.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[2,2], stop="age", stop_value=ori, origin="true", cond_spn="true", cond_surv="true")

examples/geosse_timehet.pj

@@ -1,4 +1,4 @@
-# constant-node variable ('birth_rate0_t0') assignment
+# constant-node variable ('w_birth_rate0_t0') assignment
 # first epoch (old)
 # state 0
 w_birth_rate0_t0 <- 1.5
@@ -35,7 +35,7 @@ b_birth_rate2_1_2_t1 <- 1.25
 trans_rate2_0_t1 <- 0.75
 trans_rate2_1_t1 <- 0.75
 
-# deterministic-node variable ('det_birth_rate0_t0') assignment
+# deterministic-node variable ('det_w_birth_rate0_t0') assignment
 # first epoch (old)
 # state 0
 det_w_birth_rate0_t0 := sse_rate(name="lambda0_t0", value=w_birth_rate0_t0, states=[0,0,0], event="w_speciation", epoch=1)
@@ -74,5 +74,7 @@ det_trans_rate2_1_t1 := sse_rate(name="q2_1_t1", value=trans_rate2_1_t1, states=
 
 # wrapping up all rates
 stash := sse_stash(flat_rate_mat=[det_w_birth_rate0_t0, det_death_rate0_t0, det_trans_rate0_2_t0, det_w_birth_rate1_t0, det_death_rate1_t0, det_trans_rate1_2_t0, det_b_birth_rate2_0_1_t0, det_b_birth_rate2_0_2_t0, det_b_birth_rate2_1_2_t0, det_trans_rate2_0_t0, det_trans_rate2_1_t0, det_w_birth_rate0_t1, det_death_rate0_t1, det_trans_rate0_2_t1, det_w_birth_rate1_t1, det_death_rate1_t1, det_trans_rate1_2_t1, det_b_birth_rate2_0_1_t1, det_b_birth_rate2_0_2_t1, det_b_birth_rate2_1_2_t1, det_trans_rate2_0_t1, det_trans_rate2_1_t1], n_states=3, n_epochs=2, seed_age=2.0, epoch_age_ends=[1.0])
+
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=2, nr=50, stash=stash, start_state=[0], stop="age", stop_value=2.0, origin="true")
+ori <- 2.0
+trs ~ discrete_sse(n=2, nr=2, stash=stash, start_state=[0,0], stop="age", stop_value=2.0, origin="true")

examples/yule.pj

@@ -22,4 +22,5 @@ det_birth_rate := sse_rate(name="lambda", value=birth_rate, event="speciation")
 stash := sse_stash(flat_rate_mat=[det_birth_rate])
 
 # stochastic-node variable ('trs') assignment
-trs ~ discrete_sse(n=n_sim, nr=n_rep, stash=stash, start_state=[0,0], stop="age", stop_value=2.0, origin="true")
+ori <- 2.0
+trs ~ discrete_sse(n=n_sim, nr=n_rep, stash=stash, start_state=[0,0], stop="age", stop_value=ori, origin="true")