From ddc70cacbd5f48dda6c77ad8fa13ee2d44843cb1 Mon Sep 17 00:00:00 2001
From: peter <petrel.harp@gmail.com>
Date: Wed, 14 Aug 2024 11:42:37 -0700
Subject: [PATCH] DFE parameter table; closes #1509

---
 docs/_ext/speciescatalog.py | 117 ++++++++++++++++++++++++++++++++++++
 1 file changed, 117 insertions(+)

diff --git a/docs/_ext/speciescatalog.py b/docs/_ext/speciescatalog.py
index 99c5623f7..77da70b13 100644
--- a/docs/_ext/speciescatalog.py
+++ b/docs/_ext/speciescatalog.py
@@ -9,6 +9,7 @@
 """
 import csv
 import pathlib
+import re
 
 from docutils import nodes
 from sphinx.util.docutils import SphinxDirective
@@ -513,8 +514,124 @@ def dfe_section(self, species, dfe):
         section += nodes.paragraph(text=dfe.description)
         section += nodes.rubric(text="Citations")
         section += self.citation_list(dfe)
+        section += nodes.rubric(text="DFE parameters")
+        section += self.dfe_parameter_table(species, dfe)
         return [target, section]
 
+    def dfe_parameter_table(self, species, dfe):
+        table = nodes.table()
+        # proportion, distribution type, arguments, dominance
+        tgroup = nodes.tgroup(cols=4)
+        for _ in range(4):
+            colspec = nodes.colspec(colwidth=1)
+            tgroup.append(colspec)
+
+        table += tgroup
+
+        thead = nodes.thead()
+        tgroup += thead
+        row = nodes.row()
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Proportion of mutations")
+        row += entry
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Distribution type")
+        row += entry
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Parameters")
+        row += entry
+        entry = nodes.entry()
+        entry += nodes.paragraph(text="Dominance")
+        row += entry
+        thead.append(row)
+
+        def parse_mutation_type(mt):
+            dt = mt.distribution_type
+            da = mt.distribution_args
+            if dt == "s":
+                # currently we only use this for rlnorm and unif
+                bits = re.split("[ ()*]", da[0])
+                assert bits[0] == "return", "Unrecognized mutation type string"
+                if "rlnorm" in bits:
+                    dt = "ln" if bits[1] == "-1" else "lp"
+                    da = (float(bits[bits.index("rlnorm") + 2]), float(bits[-2]))
+                elif "runif" in bits:
+                    dt = "u"
+                    da = (float(bits[6]), float(bits[10]))
+                else:
+                    raise ValueError("Unrecognized mutation type string")
+
+            if dt == "f":
+                label = "Fixed s"
+                params = f"s = {da[0]:.3f}"
+            elif dt == "e":
+                label = "Exponential"
+                params = f"mean = {da[0]:.3f}"
+            elif dt == "g":
+                label = "Gamma"
+                params = f"mean = {da[0]:.3f}, " f"shape = {da[1]:.3f}"
+            elif dt == "n":
+                label = "Normal"
+                params = f"mean = {da[0]:.3f}, " f"sd = {da[1]:.3f}"
+            elif dt == "w":
+                label = "Weibull"
+                params = f"scale = {da[0]:.3f}, " f"shape = {da[1]:.3f}"
+            elif dt == "u":
+                label = "Uniform"
+                params = f"min = {da[0]:.3f}, " f"max = {da[1]:.3f}"
+            elif dt == "lp":
+                label = "Positive LogNormal"
+                params = f"meanlog = {da[0]:.3f}, " f"sdlog = {da[1]:.3f}"
+            elif dt == "ln":
+                label = "Negative LogNormal"
+                params = f"meanlog = {da[0]:.3f}, " f"sdlog = {da[1]:.3f}"
+
+            if mt.dominance_coeff is None:
+                h_list = []
+                for j in range(len(mt.dominance_coeff_list)):
+                    slist = (
+                        ["-Inf"]
+                        + [f"{s:.3f}" for s in mt.dominance_coeff_breaks]
+                        + ["Inf"]
+                    )
+                    if dt in ["e", "g", "w"]:
+                        if da[0] < 0:
+                            slist[0] = "0"
+                        else:
+                            slist[-1] = "0"
+                    elif dt == "lp":
+                        slist[0] = "0"
+                    elif dt == "ln":
+                        slist[-1] = "0"
+                    mins = slist[j]
+                    maxs = slist[j + 1]
+                    h_list.append(
+                        f"{mt.dominance_coeff_list[j]:.3f} on " f"[{mins}, " f"{maxs})"
+                    )
+                h = "h = " + "; ".join(h_list)
+            else:
+                h = f"h = {mt.dominance_coeff:.3f}"
+            return label, params, h
+
+        rows = []
+        for mt, prop in zip(dfe.mutation_types, dfe.proportions):
+            if prop > 0:
+                row = nodes.row()
+                rows.append(row)
+                entry = nodes.entry()
+                entry += nodes.paragraph(text=f"{100*prop:.1f}%")
+                row += entry
+                for label in parse_mutation_type(mt):
+                    entry = nodes.entry()
+                    entry += nodes.paragraph(text=label)
+                    row += entry
+
+        tbody = nodes.tbody()
+        tbody.extend(rows)
+        tgroup += tbody
+
+        return table
+
     def dfes_table(self, species):
         table = nodes.table()
         tgroup = nodes.tgroup(cols=3)