Merge branch 'source' into tutorial_review

Author: brpetrucci

tutorials/divrate/sampling.md

@@ -470,7 +470,7 @@ species.
     Galagidae             = clade("Galago_senegalensis",  "Otolemur_crassicaudatus", missing= 17)
     Lorisidae             = clade("Perodicticus_potto", "Loris_tardigradus", "Nycticebus_coucang", missing=6)
     Cheirogaleoidea       = clade("Cheirogaleus_major", "Microcebus_murinus", missing= 19)
-    Lemuridae             = clade("Lemur_catta", "Varecia_variegata_variegata", missing=17)
+    Lemuridae             = clade("Lemur_catta", "Varecia_variegata", missing=17)
     Lemuriformes          = clade(Lemuridae, Cheirogaleoidea, missing=29)
     Atelidae_Aotidae      = clade("Alouatta_palliata", "Aotus_trivirgatus", missing=30)
     NWM                   = clade(Atelidae_Aotidae,"Callicebus_donacophilus", "Saimiri_sciureus", "Cebus_albifrons", missing=93)

tutorials/divrate/scripts/mcmc_EBD_UC_env.Rev

@@ -81,7 +81,7 @@ extinction_corr_pos_prob := ifelse(beta_extinction > 0.0, 1, 0)
 moves.append( mvSlide(beta_speciation, delta=0.1, weight=5) )
 moves.append( mvSlide(beta_extinction, delta=0.1, weight=5) )
 
-move_up_down_beta = mvUpDownSlide(lambda=0.001, tune=TRUE, weight=5.0)
+move_up_down_beta = mvUpDownSlide(delta=0.001, tune=TRUE, weight=5.0)
 move_up_down_beta.addVariable( beta_speciation, up=TRUE )
 move_up_down_beta.addVariable( beta_extinction, up=TRUE )
 moves.append( move_up_down_beta )
@@ -128,7 +128,7 @@ for (i in 1:NUM_INTERVALS ) {
     ln_speciation_error[i] ~ dnNormal( 0.0, speciation_sd )
     ln_extinction_error[i] ~ dnNormal( 0.0, extinction_sd )
 
-    move_up_down_spec_ext[i] = mvUpDownSlide(lambda=0.1, tune=TRUE, weight=2.0)
+    move_up_down_spec_ext[i] = mvUpDownSlide(delta=0.1, tune=TRUE, weight=2.0)
     move_up_down_spec_ext[i].addVariable( ln_speciation_error[i], up=TRUE )
     move_up_down_spec_ext[i].addVariable( ln_extinction_error[i], up=TRUE )
     moves.append( move_up_down_spec_ext[i] )

tutorials/divrate/scripts/mcmc_EBD_fixed_env.Rev

@@ -70,7 +70,7 @@ extinction_corr_pos_prob := ifelse(beta_extinction > 0.0, 1, 0)
 moves.append( mvSlide(beta_speciation, delta=0.01, weight=5) )
 moves.append( mvSlide(beta_extinction, delta=0.01, weight=5) )
 
-move_up_down_beta = mvUpDownSlide(lambda=0.01, tune=TRUE, weight=5.0)
+move_up_down_beta = mvUpDownSlide(delta=0.01, tune=TRUE, weight=5.0)
 move_up_down_beta.addVariable( beta_speciation, up=TRUE )
 move_up_down_beta.addVariable( beta_extinction, up=TRUE )
 moves.append( move_up_down_beta )

tutorials/relative_time_constraints/index.md

@@ -450,8 +450,8 @@ and variances. Internally, it is ensured that the indices are shared correctly.
 # Reroot and make bifurcating.
 rootId <- tree.getRootIndex()
 outgroup <- tree.getDescendantTaxa(rootId)
-mean_tree.reroot(clade=clade(outgroup), make_bifurcating=TRUE)
-var_tree.reroot(clade=clade(outgroup), make_bifurcating=TRUE)
+mean_tree.reroot(outgroup=clade(outgroup), make_bifurcating=TRUE)
+var_tree.reroot(outgroup=clade(outgroup), make_bifurcating=TRUE)
 
 # Renumber nodes.
 mean_tree.renumberNodes(tree)

tutorials/relative_time_constraints/scripts/2_mcmc_dating.rev

@@ -113,8 +113,8 @@ var_tree <- readTrees(var_tree_file)[1]
 # Reroot and make bifurcating.
 rootId <- tree.getRootIndex()
 outgroup <- tree.getDescendantTaxa(rootId)
-mean_tree.reroot(clade=clade(outgroup), make_bifurcating=TRUE)
-var_tree.reroot(clade=clade(outgroup), make_bifurcating=TRUE)
+mean_tree.reroot(outgroup=clade(outgroup), make_bifurcating=TRUE)
+var_tree.reroot(outgroup=clade(outgroup), make_bifurcating=TRUE)
 
 # Renumber nodes.
 mean_tree.renumberNodes(tree)