Merge pull request #206 from pph-collective/scott-ssp-rr

Scott ssp rr

settings/scott/model.yml

@@ -27,12 +27,14 @@ syringe_services:
       num_slots_start: 0
       num_slots_stop: 237
       risk: 0.02
+      dx_scalar: 1.195
     ssp_on:
       start_time: 4
       stop_time: 121
       num_slots_start: 237
       num_slots_stop: 237
       risk: 0.02
+      dx_scalar: 1.195
 
 agent_zero:
   num_partners: 4

tests/params/basic.yml

@@ -862,6 +862,7 @@ syringe_services:
       num_slots_start: 100
       num_slots_stop: 100
       risk: 0.02
+      dx_scalar: 1.0
 
 agent_zero:
   bond_type: Inj

tests/params/simple_integration.yml

@@ -191,6 +191,7 @@ syringe_services:
       num_slots_start: 500
       num_slots_stop: 500
       risk: 0.00
+      dx_scalar: 1.0
 
 partner_tracing:
   prob: 1

titan/model.py

@@ -70,6 +70,7 @@ def __init__(
         self.new_prep = AgentSet("new_prep")
 
         self.ssp_enrolled_risk = 0.0
+        self.ssp_dx = 1.0
 
         self.time = -1 * self.params.model.time.burn_steps  # burn is negative time
         self.id = nanoid.generate(size=8)
@@ -113,10 +114,6 @@ def print_stats(self, stat: Dict[str, Dict[str, int]], outdir: str):
             ), "Graph must be enabled to print network reports"
 
             network_outdir = os.path.join(outdir, "network")
-            if self.params.outputs.network.draw_figures:
-                self.network_utils.visualize_network(
-                    network_outdir, curtime=self.time, label=f"{self.id}"
-                )
 
             if self.params.outputs.network.calc_component_stats:
                 ao.print_components(
@@ -899,6 +896,7 @@ def update_syringe_services(self):
             for item in self.params.syringe_services.timeline.values():
                 if item.start_time <= self.time < item.stop_time:
                     self.ssp_enrolled_risk = item.risk
+                    self.ssp_dx = item.dx_scalar
 
                     ssp_num_slots = (item.num_slots_stop - item.num_slots_start) / (
                         item.stop_time - item.start_time
@@ -1102,6 +1100,9 @@ def diagnose(
                 sex_type
             ].hiv.dx.prob
 
+            if agent.ssp:
+                test_prob *= self.ssp_dx
+
             # Rescale based on calibration param
             test_prob *= self.calibration.test_frequency
 

titan/network.py

@@ -6,8 +6,6 @@
 
 import networkx as nx  # type: ignore
 from networkx.drawing.nx_agraph import graphviz_layout  # type: ignore
-import matplotlib.pyplot as plt  # type: ignore
-import matplotlib.patches as patches  # type: ignore
 
 
 class NetworkGraphUtils:
@@ -163,121 +161,3 @@ def get_network_color(self, coloring) -> List[str]:
             )
 
         return node_color
-
-    def visualize_network(
-        self,
-        outdir: str,
-        coloring: str = "sex_type",
-        pos=None,
-        return_layout: bool = False,
-        node_size: Optional[float] = None,
-        curtime: int = 0,
-        infection_label: int = 0,
-        label: str = "Network",
-    ):
-        """
-        Visualize the network using the spring layout (default).
-
-        args:
-            outdir: directory the figure should be saved to
-            coloring: what attribute to color the nodes by
-            pos: a graphviz_layout
-            return_layout: whether to return the layout (if `False`, nothing is returned)
-            node_size: size of the nodes in the graph
-            curtime: the current timestep of the model
-            infection_label: number of infections to list in figure's label
-            label: identifier for this network
-        """
-        if node_size is None:
-            node_size = 5000.0 / self.G.number_of_nodes()
-
-        print(("\tPlotting {} colored by {}...").format(label, coloring))
-        fig = plt.figure()
-        ax = fig.add_axes([0, 0, 1, 1])
-        fig.clf()
-
-        # build a rectangle in axes coords
-        left, width = 0.0, 1.0
-        bottom, height = 0.0, 1.0
-        right = left + width
-        top = bottom + height
-
-        fig = plt.figure()
-        ax = fig.add_axes([0, 0, 1, 1])
-
-        # axes coordinates are 0,0 is bottom left and 1,1 is upper right
-        p = patches.Rectangle(
-            (left, bottom),
-            width,
-            height,
-            fill=False,
-            transform=ax.transAxes,
-            clip_on=False,
-        )
-
-        ax.add_patch(p)
-
-        if not pos:
-            pos = graphviz_layout(self.G, prog="neato", args="")
-
-        edge_color = "k"
-        node_shape = "o"
-
-        # node color to by type
-        node_color = self.get_network_color(coloring)
-
-        # node size indicating node degree
-        NodeSize = []
-        if node_size:
-            for v in self.G:
-                NodeSize.append(node_size)
-        else:
-            for v in self.G:
-                NodeSize.append((10 * self.G.degree(v)) ** (1.0))
-
-        # draw:
-        nx.draw(
-            self.G,
-            pos,
-            node_size=NodeSize,
-            node_color=node_color,
-            node_shape=node_shape,
-            edge_color=edge_color,
-            with_labels=False,
-            linewidths=0.5,
-            width=0.5,
-        )
-
-        textstr = "\n".join(
-            (
-                r"N infection={:.2f}".format(
-                    infection_label,
-                ),
-                r"Time={:.2f}".format(
-                    curtime,
-                ),
-            )
-        )
-
-        # these are matplotlib.patch.Patch properties
-        props = dict(boxstyle="round", facecolor="wheat", alpha=0.9)
-
-        # place a text box in upper right in axes coords
-        ax.text(
-            right - 0.025,
-            top - 0.025,
-            textstr,
-            horizontalalignment="right",
-            verticalalignment="top",
-            transform=ax.transAxes,
-            bbox=props,
-        )
-
-        filename = os.path.join(
-            outdir, f"{label}_{self.G.number_of_nodes()}_{coloring}_{curtime}.png"
-        )
-
-        fig.savefig(filename)
-
-        if return_layout:
-            return pos

titan/params/syringe_services.yml

@@ -23,10 +23,15 @@ syringe_services:
         description: "Risk of unsafe sharing for agents enrolled in the SSP"
         min: 0.0
         max: 1.0
+      dx_scalar:
+        type: float
+        description: "Diagnosis scalar for HIV+ agents enrolled in ssp"
+        min: 0.0
     default:
       ssp_default:
         start_time: 1
         stop_time: 2
         num_slots_start: 0
         num_slots_stop: 0
         risk: 0.02
+        dx_scalar: 1.0