Param Revamp - CMD (#1728)

mmsuarezcosta · tbhallett · web-flow · commit c2cc5b665965 · 2025-12-09T22:01:44.000+01:00
* delete unused files, update param  labeling

* udpate param values and labels across files

* add param value file

* remove hardcoding and update param values

* update param defn to local

* small changes to .py

* data on prevalence - declared as universal (even though I don't think these are really parameters)

* make safe division by zero

* priors for missing gbd values is misssing/0 not 1

also mixed up upper and lower gbd columns

* undelete files that are used for calibrations

* undelete files that are used for calibrations

* undelete files that are used for calibrations

* drop whitespace

* remove whitespace

* add new parameter from earlier PR

---------

Co-authored-by: Tim Hallett &lt;39991060+tbhallett@users.noreply.github.com&gt;
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-size 448
+oid sha256:bae016a735a14ed6acdf4466288a14bd828322f51a9b6e19726c880299557f93
+size 583
diff --git a/resources/cmd/ResourceFile_cmd_events_hsi/ever_stroke.csv b/resources/cmd/ResourceFile_cmd_events_hsi/ever_stroke.csv
@@ -1,3 +1,3 @@
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+size 463
diff --git a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_heart_attack.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv b/resources/cmd/ResourceFile_cmd_events_symptoms/ever_stroke.csv
@@ -1,3 +1,3 @@
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diff --git a/resources/cmd/parameter_values.csv b/resources/cmd/parameter_values.csv
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
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diff --git a/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py b/src/scripts/cardio_metabolic_disorders_analyses/cardiometabolicdisorders_plots.py
@@ -190,8 +190,8 @@ def convert_output(output_path):
 
     # get prevalence + lower and upper values
     prev_range = read_csv_files(resourcefilepath / "cmd" / "ResourceFile_cmd_condition_prevalence", files=None)
-    baseline_error = [(prev_range[f'{condition}']['value'].values - prev_range[f'{condition}']['lower'].values),
-                      (prev_range[f'{condition}']['upper'].values - prev_range[f'{condition}']['value'].values)]
+    baseline_error = [(prev_range[f'{condition}']['value'].values - prev_range[f'{condition}']['prior_min'].values),
+                      (prev_range[f'{condition}']['prior_max'].values - prev_range[f'{condition}']['value'].values)]
     if 'gbd_value' in prev_range[f'{condition}']:
         gbd_error = [(prev_range[f'{condition}']['gbd_value'].values - prev_range[f'{condition}'][
             'gbd_lower'].values),
diff --git a/src/tlo/methods/cardio_metabolic_disorders.py b/src/tlo/methods/cardio_metabolic_disorders.py
