Merge pull request #240 from InstituteforDiseaseModeling/master

Update webapp with paper link

Author: cliffckerr

CHANGELOG.rst

@@ -3,6 +3,13 @@ What's new
 
 All notable changes to the codebase are documented in this file. Note: in many cases, changes from multiple patch versions are grouped together, so numbering will not be strictly consecutive.
 
+
+Version 1.0.2 (2020-05-10)
+--------------------------
+- Added uncertainty to the ``plot_result()`` method of MultiSims.
+- Added documentation and webapp links to the paper.
+
+
 Version 1.0.1 (2020-05-09)
 --------------------------
 - Added argument ``as_date`` for ``sim.date()`` to return a ``datetime`` object instead of a string.

README.rst

@@ -8,7 +8,12 @@ indicators such as numbers of infections and peak hospital demand. Covasim can
 also be used to explore the potential impact of different interventions, including
 social distancing, school closures, testing, contact tracing, and quarantine.
 
-The Covasim webapp is available at https://app.covasim.org.
+The scientific paper describing Covasim is available at http://paper.covasim.org.
+The recommended citation is:
+
+    Kerr CC, Stuart RM, Mistry D, Abeysuriya RG, Hart G, Rosenfeld R, Selvaraj P, Núñez RC, Hagedorn B, George L, Izzo A, Palmer A, Delport D, Bennette C, Wagner B, Chang S, Cohen JA, Panovska-Griffiths J, Jastrzębski M, Oron AP, Wenger E, Famulare M, Klein DJ (2020). *Covasim: an agent-based model of COVID-19 dynamics and interventions*. Institute for Disease Modeling. Available at http://paper.covasim.org.
+
+The Covasim webapp is available at http://app.covasim.org.
 
 Questions or comments can be directed to [email protected], or on this project's
 GitHub_ page. Full information about Covasim is provided in the documentation_.

covasim/plotting.py

@@ -293,7 +293,6 @@ def plot_result(sim, key, fig_args=None, plot_args=None, axis_args=None, scatter
     # Gather results
     res = sim.results[key]
     res_t = sim.results['t']
-    res_y = res.values
     if color is None:
         color = res.color
 
@@ -309,7 +308,9 @@ def plot_result(sim, key, fig_args=None, plot_args=None, axis_args=None, scatter
     # Do the plotting
     if label is None:
         label = res.name
-    ax.plot(res_t, res_y, c=color, label=label, **args.plot)
+    if res.low is not None and res.high is not None:
+        ax.fill_between(res_t, res.low, res.high, color=color, **args.fill) # Create the uncertainty bound
+    ax.plot(res_t, res.values, c=color, label=label, **args.plot)
     plot_data(sim, key, args.scatter) # Plot the data
     plot_interventions(sim, ax) # Plot the interventions
     title_grid_legend(ax, res.name, grid, commaticks, setylim, args.legend) # Configure the title, grid, and legend

covasim/version.py

@@ -2,6 +2,6 @@
 
 __all__ = ['__version__', '__versiondate__', '__license__']
 
-__version__ = '1.0.1'
-__versiondate__ = '2020-05-09'
+__version__ = '1.0.2'
+__versiondate__ = '2020-05-10'
 __license__ = f'Covasim {__version__} ({__versiondate__}) — © 2020 by IDM'

covasim/webapp/cova_app.js

@@ -160,7 +160,8 @@ var vm = new Vue({
                 copyright_year: copyright_year(),
                 github_url: "https://github.com/institutefordiseasemodeling/covasim",
                 org_url: "https://idmod.org",
-                docs_url: "https://institutefordiseasemodeling.github.io/covasim-docs",
+                docs_url: "http://docs.covasim.org",
+                paper_url: "http://paper.covasim.org",
                 license: 'Loading...',
                 notice: 'Loading...'
             },

covasim/webapp/index.html

@@ -37,6 +37,7 @@
       <b-navbar-brand href="#">{{ app.title }}</b-navbar-brand>
       <b-navbar-nav class="ml-auto">
         <b-nav-item :href="app.docs_url" target="_blank">Documentation</b-nav-item>
+        <b-nav-item :href="app.paper_url" target="_blank">Paper</b-nav-item>
         <b-nav-item v-b-modal.about>About</b-nav-item>
         <b-nav-item href="https://institutefordiseasemodeling.github.io/covasim-docs/whatsnew.html" target="_blank">{{app.version}}</b-nav-item>
       </b-navbar-nav>
@@ -46,7 +47,7 @@
     <b-modal id="about" ok-only ok-variant="secondary" ok-title="Close">
       <template v-slot:modal-title>About {{ app.title }}</template>
       <p>{{ app.title }} is an agent-based model that simulates the transmission of COVID-19 (novel coronavirus, SARS-CoV-2) in a population. Each individual in the model may pass through the following stages of COVID-19 infection: susceptible, exposed, infectious, and recovered (SEIR). The epidemiological parameter values are taken from literature.</p>
-      <p>Viral transmission occurs on a fixed contact network with undirected edges. Each day, infectious individuals expose susceptible individuals to possible infection. By default, the daily probability of infection, number of contacts, and mean duration of infectiousness roughly equates to R0 = 2.5 and a doubling time of 6-7 days. For more information, please visit the <a :href="app.github_url" target="_blank">GitHub</a> repository.</p>
+      <p>Viral transmission occurs on a fixed contact network with undirected edges. Each day, infectious individuals expose susceptible individuals to possible infection. By default, the daily probability of infection, number of contacts, and mean duration of infectiousness roughly equates to R0 = 2.5 and a doubling time of 6-7 days. For more information, please read the <a :href="app.paper_url" target="_blank">paper</a> or visit the <a :href="app.github_url" target="_blank">GitHub</a> repository.</p>
       <p><b>Note:</b> Models are only as good as the values of the parameters put into them. This is a rapidly changing situation, and we will update content as relevant information is received.</p>
       <p><b>Acknowledgements:</b> Covasim is currently under active development by IDM's COVID-19 Response Team. Model development is led by Daniel Klein, Cliff Kerr, Robyn Stuart, Romesh Abeysuriya, and Dina Mistry. UI design is led by Lauren George, William Chen, and Scott Ayers, inspired by a prototype from Brian Lovin. For the full list of contributors, please see our <a href="https://github.com/InstituteforDiseaseModeling/covasim/graphs/contributors" target="_blank">Contributors</a> page.</p>
     </b-modal>