fix(parameters): switch to standard classes (dataclasses not appropriate)

Author: amyheather

.pylintrc

@@ -1,2 +1,5 @@
 [FORMAT]
-max-line-length=79
+max-line-length=79
+
+[MESSAGES CONTROL]
+disable=too-many-arguments,too-many-positional-arguments,too-few-public-methods,too-many-instance-attributes

simulation/model.py

@@ -1,91 +1,247 @@
 """
-Discrete Event Simulation Model.
-"""
+Stroke pathway simulation parameters.
 
-from dataclasses import dataclass
+It includes arrival rates, length of stay distributions, and routing
+probabilities between different care settings.
+"""
 
 
-@dataclass
 class ASUArrivals:
-    """Acute stroke unit arrivals."""
-    stroke = 1.2
-    tia = 9.3
-    neuro = 3.6
-    other = 3.2
+    """
+    Arrival rates for the acute stroke unit (ASU) by patient type.
+
+    These are the average time intervals (in days) between new admissions.
+    For example, a value of 1.2 means a new admission every 1.2 days.
+    """
+    def __init__(self, stroke=1.2, tia=9.3, neuro=3.6, other=3.2):
+        """
+        Arguments:
+            stroke (float):
+                Stroke patient.
+            tia (float):
+                Transient ischaemic attack (TIA) patient.
+            neuro (float):
+                Complex neurological patient.
+            other (float):
+                Other patient types (including medical outliers).
+        """
+        self.stroke = stroke
+        self.tia = tia
+        self.neuro = neuro
+        self.other = other
 
 
-@dataclass
 class RehabArrivals:
-    """Rehab arrivals."""
-    stroke = 21.8
-    neuro = 31.7
-    other = 28.6
+    """
+    Arrival rates for the rehabiliation unit by patient type.
+
+    These are the average time intervals (in days) between new admissions.
+    For example, a value of 21.8 means a new admission every 21.8 days.
+    """
+    def __init__(self, stroke=21.8, neuro=31.7, other=28.6):
+        """
+        Arguments:
+            stroke (float):
+                Stroke patient.
+            neuro (float):
+                Complex neurological patient.
+            other (float):
+                Other patient types.
+        """
+        self.stroke = stroke
+        self.neuro = neuro
+        self.other = other
 
 
-@dataclass
 class ASULOS:
-    """Acute stroke unit length of stay."""
-    stroke_no_esd_mean = 7.4
-    stroke_no_esd_sd = 8.61
-    stroke_esd_mean = 4.6
-    stroke_esd_sd = 4.8
-    tia_mean = 1.8
-    tia_sd = 2.3
-    neuro_mean = 4.0
-    neuro_sd = 5.0
-    other_mean = 3.8
-    other_sd = 5.2
-
-
-@dataclass
+    """
+    Mean and standard deviation (SD) of length of stay (LOS) in days in the
+    acute stroke unit (ASU) by patient type.
+    """
+    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, tia_mean=1.8, tia_sd=2.3,
+        neuro_mean=4.0, neuro_sd=5.0, other_mean=3.8, other_sd=5.2
+    ):
+        """
+        Arguments:
+            stroke_no_esd_mean (float):
+                Mean LOS for stroke patients without early support discharge
+                (ESD) services.
+            stroke_no_esd_sd (float):
+                SD of LOS for stroke patients without ESD.
+            stroke_esd_mean (float):
+                Mean LOS for stroke patients with ESD.
+            stroke_esd_sd (float):
+                SD of LOS for stroke patients with ESD.
+            tia_mean (float):
+                Mean LOS for transient ischemic attack (TIA) patients.
+            tia_sd (float):
+                SD of LOS for TIA patients.
+            neuro_mean (float):
+                Mean LOS for complex neurological patients.
+            neuro_sd (float):
+                SD of LOS for complex neurological patients.
+            other_mean (float):
+                Mean LOS for other patient types.
+            other_sd (float):
+                SD of LOS for other patient types.
+        """
+        self.stroke_no_esd_mean = stroke_no_esd_mean
+        self.stroke_no_esd_sd = stroke_no_esd_sd
+        self.stroke_esd_mean = stroke_esd_mean
+        self.stroke_esd_sd = stroke_esd_sd
+        self.tia_mean = tia_mean
+        self.tia_sd = tia_sd
+        self.neuro_mean = neuro_mean
+        self.neuro_sd = neuro_sd
+        self.other_mean = other_mean
+        self.other_sd = other_sd
+
+
 class RehabLOS:
-    """Rehab length of stay."""
-    rehab_los_stroke_no_esd_mean = 28.4
-    rehab_los_stroke_no_esd_sd = 27.2
-    rehab_los_stroke_esd_mean = 30.3
-    rehab_los_stroke_esd_sd = 23.1
-    rehab_los_tia_mean = 18.7
-    rehab_los_tia_sd = 23.5
-    rehab_los_neuro_mean = 27.6
-    rehab_los_neuro_sd = 28.4
-    rehab_los_other_mean = 16.1
-    rehab_los_other_sd = 14.1
-
-
-@dataclass
+    """
+    Mean and standard deviation (SD) of length of stay (LOS) in days in the
+    rehabilitation unit by patient type.
+    """
+    def __init__(
+        self, stroke_no_esd_mean=28.4, stroke_no_esd_sd=27.2,
+        stroke_esd_mean=30.3, stroke_esd_sd=23.1, tia_mean=18.7, tia_sd=23.5,
+        neuro_mean=27.6, neuro_sd=28.4, other_mean=16.1, other_sd=14.1
+    ):
+        """
+        Arguments:
+            stroke_no_esd_mean (float):
+                Mean LOS for stroke patients without early support discharge
+                (ESD) services.
+            stroke_no_esd_sd (float):
+                SD of LOS for stroke patients without ESD.
+            stroke_esd_mean (float):
+                Mean LOS for stroke patients with ESD.
+            stroke_esd_sd (float):
+                SD of LOS for stroke patients with ESD.
+            tia_mean (float):
+                Mean LOS for transient ischemic attack (TIA) patients.
+            tia_sd (float):
+                SD of LOS for TIA patients.
+            neuro_mean (float):
+                Mean LOS for complex neurological patients.
+            neuro_sd (float):
+                SD of LOS for complex neurological patients.
+            other_mean (float):
+                Mean LOS for other patient types.
+            other_sd (float):
+                SD of LOS for other patient types.
+        """
+        self.stroke_no_esd_mean = stroke_no_esd_mean
+        self.stroke_no_esd_sd = stroke_no_esd_sd
+        self.stroke_esd_mean = stroke_esd_mean
+        self.stroke_esd_sd = stroke_esd_sd
+        self.tia_mean = tia_mean
+        self.tia_sd = tia_sd
+        self.neuro_mean = neuro_mean
+        self.neuro_sd = neuro_sd
+        self.other_mean = other_mean
+        self.other_sd = other_sd
+
+
 class ASURouting:
-    """Routing out of the acute stroke unit."""
-    rehab_stroke = 0.24
-    rehab_tia = 0.01
-    rehab_neuro = 0.11
-    rehab_other = 0.05
-    esd_stroke = 0.13
-    esd_tia = 0.01
-    esd_neuro = 0.05
-    esd_other = 0.10
-    other_stroke = 0.63
-    other_tia = 0.98
-    other_neuro = 0.84
-    other_other = 0.85
-
-
-@dataclass
+    """
+    Probabilities of each patient type being transferred from the acute
+    stroke unit (ASU) to other destinations.
+    """
+    def __init__(
+        self,
+        rehab_stroke=0.24, rehab_tia=0.01, rehab_neuro=0.11, rehab_other=0.05,
+        esd_stroke=0.13, esd_tia=0.01, esd_neuro=0.05, esd_other=0.10,
+        other_stroke=0.63, other_tia=0.98, other_neuro=0.84, other_other=0.85
+    ):
+        """
+        Arguments:
+            rehab_stroke (float):
+                Stroke patient to rehabilitation unit.
+            rehab_tia (float):
+                Transient ischemic attack (TIA) patient to rehabilitation unit.
+            rehab_neuro (float):
+                Complex neurological patient to rehabilitation unit.
+            rehab_other (float):
+                Other patient type to rehabilitation unit.
+            esd_stroke (float):
+                Stroke patient to early support discharge (ESD) services.
+            esd_tia (float):
+                TIA patient to ESD.
+            esd_neuro (float):
+                Complex neurological patient to ESD.
+            esd_other (float):
+                Other patient type to ESD.
+            other_stroke (float):
+                Stroke patient to other destinations (e.g., own home, care
+                home, mortality).
+            other_tia (float):
+                TIA patient to other destinations.
+            other_neuro (float):
+                Complex neurological patient to other destinations.
+            other_other (float):
+                Other patient type to other destinations.
+        """
+        self.rehab_stroke = rehab_stroke
+        self.rehab_tia = rehab_tia
+        self.rehab_neuro = rehab_neuro
+        self.rehab_other = rehab_other
+        self.esd_stroke = esd_stroke
+        self.esd_tia = esd_tia
+        self.esd_neuro = esd_neuro
+        self.esd_other = esd_other
+        self.other_stroke = other_stroke
+        self.other_tia = other_tia
+        self.other_neuro = other_neuro
+        self.other_other = other_other
+
+
 class RehabRouting:
-    """Routing out of rehab."""
-    rehab_to_esd_stroke = 0.40
-    rehab_to_esd_tia = 0
-    rehab_to_esd_neuro = 0.09
-    rehab_to_esd_other = 0.13
-    rehab_to_other_stroke = 0.60
-    rehab_to_other_tia = 1
-    rehab_to_neuro = 0.91
-    rehab_to_other = 0.88
-
-
-@dataclass
+    """
+    Probabilities of each patient type being transferred from the rehabiliation
+    unit to other destinations.
+    """
+    def __init__(
+        self, esd_stroke=0.40, esd_tia=0, esd_neuro=0.09,
+        esd_other=0.13, other_stroke=0.60, other_tia=1,
+        other_neuro=0.91, other_other=0.88
+    ):
+        """
+        Arguments:
+            esd_stroke (float):
+                Stroke patient to early support discharge (ESD) services.
+            esd_tia (float):
+                Transient ischemic attack (TIA) patient to ESD.
+            esd_neuro (float):
+                Complex neurological patient to ESD.
+            esd_other (float):
+                Other patient type to ESD.
+            other_stroke (float):
+                Stroke patient to other destinations (e.g., own home, care
+                home, mortality).
+            other_tia (float):
+                TIA patient to other destinations.
+            other_neuro (float):
+                Complex neurological patient to other destinations.
+            other_other (float):
+                Other patient type to other destinations.
+        """
+        self.esd_stroke = esd_stroke
+        self.esd_tia = esd_tia
+        self.esd_neuro = esd_neuro
+        self.esd_other = esd_other
+        self.other_stroke = other_stroke
+        self.other_tia = other_tia
+        self.other_neuro = other_neuro
+        self.other_other = other_other
+
+
 class Param:
-    """Default parameters for simulation."""
-    # pylint: disable=too-many-arguments,too-many-positional-arguments
+    """
+    Default parameters for simulation.
+    """
     def __init__(
         self,
         asu_arrivals=ASUArrivals(),
@@ -95,7 +251,24 @@ def __init__(
         asu_routing=ASURouting(),
         rehab_routing=RehabRouting()
     ):
-        """Initialise instance of the parameter class."""
+        """
+        Initialise a parameter set for the simulation.
+        
+        Arguments:
+            asu_arrivals (ASUArrivals):
+                Arrival rates to the acute stroke unit (ASU).
+            rehab_arrivals (RehabArrivals):
+                Arrival rates to the rehabilitation unit.
+            asu_los (ASULOS):
+                Length of stay (LOS) distributions for patients in the ASU.
+            rehab_los (RehabLOS):
+                LOS distributions for patients in the rehabilitation unit.
+            asu_routing (ASURouting):
+                Transfer probabilities from the ASU to other destinations.
+            rehab_routing (RehabRouting):
+                Transfer probabilities from the rehabilitation unit to other
+                destinations.
+        """
         self.asu_arrivals = asu_arrivals
         self.rehab_arrivals = rehab_arrivals
         self.asu_los = asu_los