stable notebooks and update docs

ktmeaton · Jun 5, 2021 · 64df6aa · 64df6aa
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diff --git a/docs/notes/Notes_v0.2.7.md b/docs/notes/Notes_v0.2.7.md
@@ -1,4 +1,4 @@
-# Development
+# v0.2.7
 
 1. Add mugration to workflow.
 1. Upgrade auspice to 2.25.1

diff --git a/docs/notes/Notes_v0.2.8.md b/docs/notes/Notes_v0.2.8.md
@@ -0,0 +1,7 @@
+# v0.2.8
+
+1. Add Jupyter Notebook for processing BEAST output.
+1. Updates to Root-To-Tip Regression and Geographic.
+1. Update and sync all metadata files.
+1. Separated auspice output into beast/ml datasets.
+1. Add beast timetrees to auspice.
diff --git a/results/config/auspice_config.json b/results/config/auspice_config.json
@@ -13,6 +13,21 @@
       "title": "BioSample Accession",
       "type": "categorical"
     },
+    {
+      "key": "blank",
+      "title": "Blank",
+      "type": "categorical"
+    },
+    {
+      "key": "branch_length_sub",
+      "title": "Branch Length Subs",
+      "type": "continuous"
+    },
+    {
+      "key": "branch_length_time",
+      "title": "Branch Length Time",
+      "type": "continuous"
+    },
     {
       "key": "branch_major",
       "title": "Branch Major",
@@ -23,6 +38,11 @@
       "title": "Branch Major Confidence",
       "type": "categorical"
     },
+    {
+      "key": "branch_major_joint_conf_category",
+      "title": "Branch Major Joint Confidence",
+      "type": "categorical"
+    },
     {
       "key": "branch_minor",
       "title": "Branch Minor",
@@ -33,6 +53,11 @@
       "title": "Branch Minor Confidence",
       "type": "categorical"
     },
+    {
+      "key": "branch_minor_joint_conf_category",
+      "title": "Branch Minor Joint Confidence",
+      "type": "categorical"
+    },
     {
       "key": "branch_number",
       "title": "Branch Number",
@@ -43,6 +68,11 @@
       "title": "Branch Support",
       "type": "continuous"
     },
+    {
+      "key": "branch_support_conf_category",
+      "title": "Branch Support Confidence",
+      "type": "categorical"
+    },
     {
       "key": "clade_rtt_dist",
       "title": "Clade Root Distance",
@@ -58,26 +88,56 @@
       "title": "Country",
       "type": "categorical"
     },
+    {
+      "key": "country_lat",
+      "title": "Country Latitude",
+      "type": "continuous"
+    },
+    {
+      "key": "country_lon",
+      "title": "Country Longitude",
+      "type": "continuous"
+    },
     {
       "key": "country_conf_category",
       "title": "Country Confidence",
       "type": "categorical"
     },
+    {
+      "key": "country_joint_conf_category",
+      "title": "Country Joint Confidence",
+      "type": "categorical"
+    },
+    {
+      "key": "country_date_strain",
+      "title": "Country Date Strain",
+      "type": "categorical"
+    },
     {
       "key": "date_bp_mean",
-      "title": "Collection Date (BP)",
+      "title": "Collection Date (Years BP)",
       "type": "continuous"
     },
     {
       "key": "date_mean",
-      "title": "Collection Date",
+      "title": "Collection Date (Calendar Year)",
       "type": "continuous"
     },
     {
       "key": "date_err",
       "title": "Collection Date Uncertainty",
       "type": "continuous"
     },
+    {
+      "key": "host_human",
+      "title": "Host Human",
+      "type": "categorical"
+    },
+    {
+      "key": "node_name",
+      "title": "Node Name",
+      "type": "categorical"
+    },
     {
       "key": "node_type",
       "title": "Node Type",
@@ -88,16 +148,56 @@
       "title": "Province",
       "type": "categorical"
     },
+    {
+      "key": "province_date_strain",
+      "title": "Province Date Strain",
+      "type": "categorical"
+    },
+    {
+      "key": "province_lat",
+      "title": "Province Latitude",
+      "type": "continuous"
+    },
+    {
+      "key": "province_lon",
+      "title": "Province Longitude",
+      "type": "continuous"
+    },
     {
       "key": "province_conf_category",
       "title": "Province Confidence",
       "type": "categorical"
     },
+    {
+      "key": "province_joint_conf_category",
+      "title": "Province Joint Confidence",
+      "type": "categorical"
+    },
     {
       "key": "root_rtt_dist",
       "title": "Root Distance",
       "type": "continuous"
     },
+    {
+      "key": "rate_sub",
+      "title": "Substitution Rate (subs/site/year)",
+      "type": "continuous"
+    },
+    {
+      "key": "rate_sub_year",
+      "title": "Substitution Rate (subs/year)",
+      "type": "continuous"
+    },
+    {
+      "key": "rate_geo_sub",
+      "title": "Geographic Rate (km/sub/site)",
+      "type": "continuous"
+    },
+    {
+      "key": "rate_geo_year",
+      "title": "Geographic Rate (km/year)",
+      "type": "continuous"
+    },
     {
       "key": "strain",
       "title": "Strain",
@@ -107,6 +207,7 @@
   "filters": [
     "country",
     "province",
+    "continent",
     "branch_major",
     "branch_minor"
   ],