fix(model): add stroke mortality parameter for stroke other LOS sampling (#6)

Author: amyheather

notebooks/analysis.ipynb

@@ -1,12 +1,12 @@
 unit,beds,prob_delay_current,1_in_n_delay_current,prob_delay_no_complex_neuro,1_in_n_delay_no_complex_neuro
-asu,10,0.14,7.0,0.09,11.0
-asu,11,0.09,11.0,0.06,18.0
-asu,12,0.06,16.0,0.03,31.0
-asu,13,0.04,26.0,0.02,55.0
-asu,14,0.02,45.0,0.01,111.0
-asu,15,0.01,79.0,0.0,225.0
-rehab,12,0.11,9.0,0.05,20.0
+asu,10,0.13,8.0,0.08,12.0
+asu,11,0.09,12.0,0.05,20.0
+asu,12,0.06,18.0,0.03,36.0
+asu,13,0.03,30.0,0.01,67.0
+asu,14,0.02,52.0,0.01,131.0
+asu,15,0.01,95.0,0.0,277.0
+rehab,12,0.11,9.0,0.05,19.0
 rehab,13,0.08,13.0,0.03,32.0
 rehab,14,0.05,20.0,0.02,57.0
-rehab,15,0.03,31.0,0.01,101.0
-rehab,16,0.02,52.0,0.0,212.0
+rehab,15,0.03,32.0,0.01,110.0
+rehab,16,0.02,51.0,0.0,205.0

outputs/figure1_asu.png

@@ -1,13 +1,13 @@
 unit,beds,prob_delay_current,1_in_n_delay_current,prob_delay_5%,1_in_n_delay_5%
-asu,9,0.19,5.0,,
-asu,10,0.14,7.0,0.16,6.0
-asu,11,0.09,11.0,0.11,9.0
-asu,12,0.06,16.0,0.08,13.0
-asu,13,0.04,26.0,0.05,20.0
-asu,14,0.02,45.0,0.03,33.0
-rehab,10,0.2,5.0,,
+asu,9,0.18,6.0,,
+asu,10,0.13,8.0,0.15,7.0
+asu,11,0.09,12.0,0.1,10.0
+asu,12,0.06,18.0,0.07,14.0
+asu,13,0.03,30.0,0.04,23.0
+asu,14,0.02,52.0,0.03,39.0
+rehab,10,0.21,5.0,,
 rehab,12,0.11,9.0,0.13,8.0
 rehab,13,0.08,13.0,0.09,11.0
-rehab,14,0.05,20.0,0.06,15.0
-rehab,15,0.03,31.0,0.04,23.0
-rehab,16,0.02,52.0,0.03,37.0
+rehab,14,0.05,20.0,0.06,16.0
+rehab,15,0.03,32.0,0.04,24.0
+rehab,16,0.02,51.0,0.03,37.0

outputs/figure1_rehab.png

@@ -1,10 +1,10 @@
 dedicated_acute,dedicated_rehab,pooled,pdelay_acute,pdelay_rehab,1_in_n_delay_acute,1_in_n_delay_rehab
-0,0,22,0.069,0.069,15,15
-0,0,26,0.018,0.018,55,55
-14,12,0,0.022,0.111,45,9
-11,11,4,0.051,0.092,20,11
-11,10,5,0.043,0.094,23,11
-10,10,6,0.047,0.07,21,14
-10,9,7,0.044,0.07,23,14
-9,9,8,0.047,0.058,21,17
-9,8,9,0.046,0.058,22,17
+0,0,22,0.063,0.063,16,16
+0,0,26,0.016,0.016,61,61
+14,12,0,0.019,0.11,52,9
+11,11,4,0.044,0.089,23,11
+11,10,5,0.037,0.09,27,11
+10,10,6,0.041,0.066,24,15
+10,9,7,0.039,0.066,26,15
+9,9,8,0.042,0.053,24,19
+9,8,9,0.041,0.053,25,19

outputs/figure3_asu.png

@@ -165,7 +165,7 @@ def create_distributions(self, asu_param, rehab_param, distribution_type):
             # Get a list of the patients in that unit (ignore other attributes)
             patient_types = [attr for attr in dir(unit_param) if attr in
                              ["stroke", "stroke_esd", "stroke_noesd",
-                              "tia", "neuro", "other"]]
+                              "stroke_mortality", "tia", "neuro", "other"]]
 
             # For each patient type...
             for patient_type in patient_types:
@@ -253,13 +253,19 @@ def acute_stroke_unit(self, patient):
             msg=(f"Patient {patient.patient_id} ({patient.patient_type}) " +
                  f"post-ASU: {patient.post_asu_destination}"))
 
-        # If it is a stroke patient,find out if they are going to the ESD
-        # (stroke_esd) or not (stroke_noesd) - else, just same as patient_type
+        # If it is a stroke patient, find out if they are going to the ESD
+        # (stroke_esd) or not (stroke_noesd) or if they pass away
+        # (stroke_mortality). For other patients, just same as patient_type.
         if patient.patient_type == "stroke":
             if patient.post_asu_destination == "esd":
                 routing_type = "stroke_esd"
-            else:
+            elif patient.post_asu_destination == "rehab":
                 routing_type = "stroke_noesd"
+            elif patient.post_asu_destination == "other":
+                routing_type = "stroke_mortality"
+            else:
+                raise ValueError("Stroke post-asu destination '" +
+                                 f"{patient.post_asu_destination}' invalid")
         else:
             routing_type = patient.patient_type
 

outputs/figure3_rehab.png

@@ -137,6 +137,7 @@ def __init__(
         self,
         stroke_no_esd_mean=7.4, stroke_no_esd_sd=8.61,
         stroke_esd_mean=4.6, stroke_esd_sd=4.8,
+        stroke_mortality_mean=7.0, stroke_mortality_sd=8.7,
         tia_mean=1.8, tia_sd=2.3,
         neuro_mean=4.0, neuro_sd=5.0,
         other_mean=3.8, other_sd=5.2
@@ -153,6 +154,10 @@ def __init__(
             Mean LOS for stroke patients with ESD.
         stroke_esd_sd: float
             SD of LOS for stroke patients with ESD.
+        stroke_mortality_mean: float
+            Mean LOS for stroke patients who pass away.
+        stroke_mortality_sd: float
+            SD of LOS for stroke patients who pass away.
         tia_mean: float
             Mean LOS for TIA patients.
         tia_sd: float
@@ -174,6 +179,10 @@ def __init__(
             "mean": stroke_esd_mean,
             "sd": stroke_esd_sd
         }
+        self.stroke_mortality = {
+            "mean": stroke_mortality_mean,
+            "sd": stroke_mortality_sd
+        }
         self.tia = {
             "mean": tia_mean,
             "sd": tia_sd