Update docs and runtime_limit in seconds for SSE dn

docs/build/html/_sources/pjdoc/parametric.rst.txt

@@ -5,7 +5,7 @@ On this page you will find examples of how to invoke the available distributions
 Uniform
 -------
 
-The function for assigning a uniform (``uniform``) distribution to a variable has four parameters:
+The function for assigning a uniform (``uniform``) distribution to a random variable has four parameters:
 
     | ``n`` (integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.
     | ``nr``` (integer, optional): Number of replicates to draw per sample. Defaults to 1.
@@ -20,7 +20,7 @@ The function for assigning a uniform (``uniform``) distribution to a variable ha
 Exponential
 -----------
 
-The function for assigning a exponential (``exponential``) distribution to a variable has four parameters:
+The function for assigning a exponential (``exponential``) distribution to a random variable has four parameters:
 
     | ``n`` (integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.
     | ``nr`` (integer, optional): Number of replicates to draw per sample. Defaults to 1.
@@ -35,7 +35,7 @@ The function for assigning a exponential (``exponential``) distribution to a var
 Gamma
 -----
 
-The function for assigning a gamma (``gamma``) distribution to a variable has five parameters:
+The function for assigning a gamma (``gamma``) distribution to a random variable has five parameters:
 
     | ``n`` (integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.
     | ``nr`` (integer, optional): Number of replicates to draw per sample. Defaults to 1.
@@ -51,7 +51,7 @@ The function for assigning a gamma (``gamma``) distribution to a variable has fi
 Normal
 ------
 
-The function for assigning a normal (``normal``) distribution to a variable has four parameters:
+The function for assigning a normal (``normal``) distribution to a random variable has four parameters:
 
     | ``n`` (integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.
     | ``nr`` (integer, optional): Number of replicates to draw per sample. Defaults to 1.
@@ -66,12 +66,12 @@ The function for assigning a normal (``normal``) distribution to a variable has
 Log-normal
 ----------
 
-The function for assigning a log-normal (``lognormal``) distribution to a variable has five parameters:
+The function for assigning a log-normal (``lognormal``) distribution to a random variable has five parameters:
 
     | ``n`` (integer, optional): Number of samples to draw (samples are i.i.d.). Defaults to 1.
     | ``nr`` (integer, optional): Number of replicates to draw per sample. Defaults to 1.
-    | ``mean`` (real, required): Mean (location) of distribution.
-    | ``sd`` (positive real, required): Standard deviation (scale) of distribution.
+    | ``meanlog`` (real, required): Mean (location) of distribution over the logarithm of the random variable.
+    | ``sdlog`` (positive real, required): Standard deviation (scale) of distribution over the logarithm of the random variable.
     | ``log_space`` (string boolean, optional): Whether the value of ``mean`` is in log-space. Defaults to "true".
 
 .. code-block:: 

docs/build/html/genindex.html

@@ -110,8 +110,12 @@ <h2 id="A">A</h2>
 </li>
       <li><a href="phylojunction.plotting.html#phylojunction.plotting.pj_organize.add_within_hpd_col">add_within_hpd_col() (in module phylojunction.plotting.pj_organize)</a>
 </li>
-      <li><a href="phylojunction.data.html#phylojunction.data.sampled_ancestor.SampledAncestor.age">age (phylojunction.data.sampled_ancestor.SampledAncestor attribute)</a>
+      <li><a href="phylojunction.data.html#phylojunction.data.attribute_transition.AttributeTransition.age">age (phylojunction.data.attribute_transition.AttributeTransition attribute)</a>
+
+      <ul>
+        <li><a href="phylojunction.data.html#phylojunction.data.sampled_ancestor.SampledAncestor.age">(phylojunction.data.sampled_ancestor.SampledAncestor attribute)</a>
 </li>
+      </ul></li>
       <li><a href="phylojunction.data.html#phylojunction.data.tree.AnnotatedTree.alternative_root_label">alternative_root_label (phylojunction.data.tree.AnnotatedTree attribute)</a>
 </li>
       <li><a href="phylojunction.calculation.html#phylojunction.calculation.discrete_sse.MacroevolEvent.ANAGENETIC_TRANSITION">ANAGENETIC_TRANSITION (phylojunction.calculation.discrete_sse.MacroevolEvent attribute)</a>
@@ -305,6 +309,8 @@ <h2 id="D">D</h2>
       <li><a href="phylojunction.readwrite.html#phylojunction.readwrite.pj_write.dump_pgm_data">dump_pgm_data() (in module phylojunction.readwrite.pj_write)</a>
 </li>
       <li><a href="phylojunction.readwrite.html#phylojunction.readwrite.pj_write.dump_serialized_pgm">dump_serialized_pgm() (in module phylojunction.readwrite.pj_write)</a>
+</li>
+      <li><a href="phylojunction.readwrite.html#phylojunction.readwrite.pj_write.dump_trees_rb_smap_dfs">dump_trees_rb_smap_dfs() (in module phylojunction.readwrite.pj_write)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -418,7 +424,7 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="phylojunction.pgm.html#phylojunction.pgm.pgm.DirectedAcyclicGraph.get_display_str_by_name">get_display_str_by_name() (phylojunction.pgm.pgm.DirectedAcyclicGraph method)</a>
 </li>
-      <li><a href="phylojunction.utility.html#phylojunction.utility.helper_functions.get_ellapsed_time_in_minutes">get_ellapsed_time_in_minutes() (in module phylojunction.utility.helper_functions)</a>
+      <li><a href="phylojunction.utility.html#phylojunction.utility.helper_functions.get_ellapsed_time_in_seconds">get_ellapsed_time_in_seconds() (in module phylojunction.utility.helper_functions)</a>
 </li>
       <li><a href="phylojunction.inference.revbayes.html#phylojunction.inference.revbayes.rb_dn_parametric.get_exponential_rev_inference_spec_info">get_exponential_rev_inference_spec_info() (in module phylojunction.inference.revbayes.rb_dn_parametric)</a>
 </li>
@@ -1445,6 +1451,8 @@ <h2 id="R">R</h2>
       <li><a href="phylojunction.data.html#phylojunction.data.tree.AnnotatedTree.rec_str">rec_str() (phylojunction.data.tree.AnnotatedTree method)</a>
 </li>
       <li><a href="phylojunction.data.html#phylojunction.data.tree.AnnotatedTree.rec_tr_at_dict">rec_tr_at_dict (phylojunction.data.tree.AnnotatedTree attribute)</a>
+</li>
+      <li><a href="phylojunction.data.html#phylojunction.data.tree.AnnotatedTree.rec_tr_clado_at_dict">rec_tr_clado_at_dict (phylojunction.data.tree.AnnotatedTree attribute)</a>
 </li>
       <li><a href="phylojunction.data.html#phylojunction.data.tree.AnnotatedTree.rec_tr_root_age">rec_tr_root_age (phylojunction.data.tree.AnnotatedTree attribute)</a>
 </li>