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authorSébastien Picault <sebastien.picault@inra.fr>
Mon, 17 Aug 2020 08:53:33 +0000 (10:53 +0200)
committerSébastien Picault <sebastien.picault@inra.fr>
Mon, 17 Aug 2020 08:53:33 +0000 (10:53 +0200)
18 files changed:
README.md
doc/html/_images/SIR1b.png [new file with mode: 0644]
doc/html/_images/SIR2b.png [new file with mode: 0644]
doc/html/_sources/pages/Getting_started.rst.txt
doc/html/_static/SIR1b.png [new file with mode: 0644]
doc/html/_static/SIR2b.png [new file with mode: 0644]
doc/html/_static/documentation_options.js
doc/html/_static/models/features/hybrid_SIR_lockdown.yaml [new file with mode: 0644]
doc/html/_static/show.txt
doc/html/index.html
doc/html/models.zip
doc/html/objects.inv
doc/html/pages/Getting_started.html
doc/html/pages/License.html
doc/html/searchindex.js
models/features/hybrid_SIR_lockdown.yaml [new file with mode: 0644]
src/emulsion/__init__.py
src/emulsion/__main__.py

index 2a79230..d8461cd 100644 (file)
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 EMULSION: Epidemiological Multi-Level Simulation framework
 ======================
 
-![Version](https://img.shields.io/badge/version-1.0.11-f16152.svg)
+![Version](https://img.shields.io/badge/version-1.0.12-f16152.svg)
 ![License](https://img.shields.io/badge/license-Apache--2.0-8cd0c3.svg)
 
 <!-- markdown-toc start - Don't edit this section. Run M-x markdown-toc-refresh-toc -->
@@ -36,7 +36,7 @@ individual-based models, metapopulations) and multiple scales (from
 individuals to metapopulations), thanks to recent research in
 Artificial Intelligence.
 
-- **Version 1.0.11**
+- **Version 1.0.12**
 - **License:** Apache-2.0
 - **Contributors and contact:**
   - Sébastien Picault (`sebastien.picault@inrae.fr`)
diff --git a/doc/html/_images/SIR1b.png b/doc/html/_images/SIR1b.png
new file mode 100644 (file)
index 0000000..69a87ae
Binary files /dev/null and b/doc/html/_images/SIR1b.png differ
diff --git a/doc/html/_images/SIR2b.png b/doc/html/_images/SIR2b.png
new file mode 100644 (file)
index 0000000..80af075
Binary files /dev/null and b/doc/html/_images/SIR2b.png differ
index 50ff684..413dc8f 100644 (file)
@@ -35,6 +35,9 @@ The simulation results will pop up in your web browser:
 .. image:: ../_images/SIR1.png
    :align: left
 
+.. image:: ../_images/SIR1b.png
+   :align: left
+
 You can also check the results of a more complex model, e.g. ``quickstart``,
 tested :ref:`at install <Test your installation>`.
 
@@ -148,6 +151,9 @@ which produces:
 .. image:: ../_images/SIR2.png
    :align: left
 
+.. image:: ../_images/SIR2b.png
+   :align: left
+
 
 Changing the model
 ******************
diff --git a/doc/html/_static/SIR1b.png b/doc/html/_static/SIR1b.png
new file mode 100644 (file)
index 0000000..69a87ae
Binary files /dev/null and b/doc/html/_static/SIR1b.png differ
diff --git a/doc/html/_static/SIR2b.png b/doc/html/_static/SIR2b.png
new file mode 100644 (file)
index 0000000..80af075
Binary files /dev/null and b/doc/html/_static/SIR2b.png differ
index bee2332..5441c97 100644 (file)
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.0.11',
+    VERSION: '1.0.12',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',
diff --git a/doc/html/_static/models/features/hybrid_SIR_lockdown.yaml b/doc/html/_static/models/features/hybrid_SIR_lockdown.yaml
new file mode 100644 (file)
index 0000000..2034ad8
--- /dev/null
@@ -0,0 +1,313 @@
+---
+
+# EMULSION (Epidemiological Multi-Level Simulation framework)
+# ===========================================================
+# 
+# Contributors and contact:
+# -------------------------
+# 
+#     - Sébastien Picault (sebastien.picault@inrae.fr)
+#     - Yu-Lin Huang
+#     - Vianney Sicard
+#     - Sandie Arnoux
+#     - Gaël Beaunée
+#     - Pauline Ezanno (pauline.ezanno@inrae.fr)
+# 
+#     INRAE, Oniris, BIOEPAR, 44300, Nantes, France
+# 
+# 
+# How to cite:
+# ------------
+# 
+#     S. Picault, Y.-L. Huang, V. Sicard, S. Arnoux, G. Beaunée,
+#     P. Ezanno (2019). "EMULSION: Transparent and flexible multiscale
+#     stochastic models in human, animal and plant epidemiology", PLoS
+#     Computational Biology 15(9): e1007342. DOI:
+#     10.1371/journal.pcbi.1007342
+# 
+# 
+# License:
+# --------
+# 
+#    Copyright 2016 INRAE and Univ. Lille
+# 
+#    Inter Deposit Digital Number: IDDN.FR.001.280043.000.R.P.2018.000.10000
+# 
+#    Agence pour la Protection des Programmes,
+#    54 rue de Paradis, 75010 Paris, France
+# 
+#    Licensed under the Apache License, Version 2.0 (the "License");
+#    you may not use this file except in compliance with the License.
+#    You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+# 
+#    Unless required by applicable law or agreed to in writing, software
+#    distributed under the License is distributed on an "AS IS" BASIS,
+#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#    See the License for the specific language governing permissions and
+#    limitations under the License.
+
+#  __  __           _      _
+# |  \/  |         | |    | |
+# | \  / | ___   __| | ___| |
+# | |\/| |/ _ \ / _` |/ _ \ |
+# | |  | | (_) | (_| |  __/ |
+# |_|  |_|\___/ \__,_|\___|_|
+#
+#  _____        __                           _   _
+# |_   _|      / _|                         | | (_)
+#   | |  _ __ | |_ ___  _ __ _ __ ___   __ _| |_ _  ___  _ __
+#   | | | '_ \|  _/ _ \| '__| '_ ` _ \ / _` | __| |/ _ \| '_ \
+#  _| |_| | | | || (_) | |  | | | | | | (_| | |_| | (_) | | | |
+# |_____|_| |_|_| \___/|_|  |_| |_| |_|\__,_|\__|_|\___/|_| |_|
+
+
+# NAME OF THE MODEL
+model_name: hybrid_SIR
+
+
+# DESCRIPTION OF THE MODEL
+model_info:
+  abstract: 'This model is a simple discrete-time, stochastic,
+  "hybrid" SIR model, i.e. with individuals grouped according to
+  relevant variables such as their health state. A lockdown occurs
+  during epidemics to flatten the curve.
+  '
+  author: 'Sebastien Picault (sebastien.picault@inrae.fr)'
+
+
+#  _______ _
+# |__   __(_)
+#    | |   _ _ __ ___   ___
+#    | |  | | '_ ` _ \ / _ \
+#    | |  | | | | | | |  __/
+#    |_|  |_|_| |_| |_|\___|
+
+# TIME INFORMATION
+# This section defines the time unit (used e.g. for expressing
+# durations, rates, etc.), the duration of the time step, the origin
+# date and total duration of the simulation.
+time_info:
+  time_unit: 'days'
+  delta_t: 1
+  origin: 'January 1'
+  total_duration: '300'
+
+
+#  _                    _
+# | |                  | |
+# | |     _____   _____| |___
+# | |    / _ \ \ / / _ \ / __|
+# | |___|  __/\ V /  __/ \__ \
+# |______\___| \_/ \___|_|___/
+
+# ORGANIZATION LEVELS USED IN THE SIMULATION
+# A hybrid model considers two levels: the population and
+# its components (individuals)
+levels:
+  population:
+    desc: 'level of the population'
+    aggregation_type: 'hybrid'   # the keyword for designing hybrid models
+    contains:
+      - individuals
+  individuals:
+    desc: 'level of the individuals'
+
+
+
+#  _____
+# |  __ \
+# | |__) | __ ___   ___ ___  ___ ___  ___  ___
+# |  ___/ '__/ _ \ / __/ _ \/ __/ __|/ _ \/ __|
+# | |   | | | (_) | (_|  __/\__ \__ \  __/\__ \
+# |_|   |_|  \___/ \___\___||___/___/\___||___/
+
+# LIST OF PROCESSES (IN ORDER) TO BE EXECUTED DURING EACH TIME STEP
+# In a hybrid model, processes take place at the population level
+# and are managed by groupings
+processes:
+  population:
+    - infection                 # name of a grouping
+
+
+#   _____                       _
+#  / ____|                     (_)
+# | |  __ _ __ ___  _   _ _ __  _ _ __   __ _
+# | | |_ | '__/ _ \| | | | '_ \| | '_ \ / _` |
+# | |__| | | | (_) | |_| | |_) | | | | | (_| |
+#  \_____|_|  \___/ \__,_| .__/|_|_| |_|\__, |
+#                        | |             __/ |
+#                        |_|            |___/
+
+# DESCRIPTION OF GROUPINGS, ASSOCIATED WITH PROCESSES WHICH ARE NOT
+# DIRECTLY BASED ON STATE MACHINES
+# A grouping is based on one or more variables. For instance, the
+# grouping for managing the 'infection' process is based on the
+# variable 'health_state' (coming from the state machine with the same
+# name): hence, one group will be defined for all possible values of
+# the health_state variable.
+
+grouping:
+  population:
+    infection:
+      machine_name: health_state
+      key_variables: [health_state]
+
+
+#   _____ _        _         __  __            _     _
+#  / ____| |      | |       |  \/  |          | |   (_)
+# | (___ | |_ __ _| |_ ___  | \  / | __ _  ___| |__  _ _ __   ___  ___
+#  \___ \| __/ _` | __/ _ \ | |\/| |/ _` |/ __| '_ \| | '_ \ / _ \/ __|
+#  ____) | || (_| | ||  __/ | |  | | (_| | (__| | | | | | | |  __/\__ \
+# |_____/ \__\__,_|\__\___| |_|  |_|\__,_|\___|_| |_|_|_| |_|\___||___/
+
+# DESCRIPTION OF THE STATE MACHINES INVOLVED IN THE MODEL
+# Each state machine is composed at least of several states.
+# The name of a state machine defines an individual variable which
+# contains the value of the current state in the individual.
+# Transitions define how each change can change to another one.
+# Productions define how individuals in one state can produce
+# new individuals in another state.
+state_machines:
+  # Below, the definition of the state machine used by the process
+  # 'infection'
+  health_state:
+    desc: 'The state machine which defines the evolution of health
+    states
+    '
+    # Below, the list of states with their attributes.
+    states:
+      - S:
+          name: 'Susceptible'
+          desc: 'suceptible of becoming infected'
+          fillcolor: 'wheat'
+      - I:
+          name: 'Infectious'
+          desc: 'infected and able to transmit the disease'
+          fillcolor: 'maroon'
+      - R:
+          name: 'Resistant'
+          desc: 'healthy again and resistant to infection'
+          fillcolor: 'deepskyblue'
+    # Below, a list of transitions between states, with rate or
+    # probabilities. Rates are automatically converted into
+    # probabilities w.r.t the duration of the time step (delta_t),
+    # assuming a classical exponential distribution of durations in
+    # the states.
+    transitions:
+      - {from: S, to: I, rate: 'force_of_infection'}
+      - {from: I, to: R, rate: 'recovery'}
+
+
+#  _____                               _
+# |  __ \                             | |
+# | |__) |_ _ _ __ __ _ _ __ ___   ___| |_ ___ _ __ ___
+# |  ___/ _` | '__/ _` | '_ ` _ \ / _ \ __/ _ \ '__/ __|
+# | |  | (_| | | | (_| | | | | | |  __/ ||  __/ |  \__ \
+# |_|   \__,_|_|  \__,_|_| |_| |_|\___|\__\___|_|  |___/
+
+# PARAMETERS/FUNCTIONS/EXPRESSIONS USED IN THE MODEL
+parameters:
+  initial_population_size:
+    desc: 'initial number of individuals in the population'
+    value: 1000
+  initial_infected:
+    desc: 'initial number of infectious individuals in the population'
+    value: 10
+  transmission_I:
+    desc: 'transmission rate from infectious individuals (/day)'
+    value: 'IfThenElse(AND(time >= lockdown_start, time <= lockdown_start + lockdown_duration), transmission_I_lockdown, transmission_I_default)'
+    # value: 'IfThenElse(AND(total_I > 0.2 * total_population), transmission_I_lockdown, transmission_I_default)'
+  transmission_I_default:
+    desc: 'default transmission rate from infectious individuals (/day)'
+    value: 0.2
+  transmission_I_lockdown:
+    desc: 'transmission rate from infectious individuals during lockdown (/day)'
+    value: 0.02
+  lockdown_start:
+    desc: 'date where lockdown starts after the beginning of the simulation (days)'
+    value: 30
+  lockdown_duration:
+    desc: 'duration of the lockdown (days)'
+    value: 20
+  recovery:
+    desc: 'recovery rate (/day)'
+    value: '1/15'
+  force_of_infection:
+    desc: 'infection function'
+    value: 'transmission_I * total_I / total_population'
+    source: 'classical function assuming frequency dependence'
+  percentage_prevalence:
+    desc: 'proportion of infected+infectious individuals'
+    value: '100 * total_I / total_population'
+
+
+#  _____           _        _
+# |  __ \         | |      | |
+# | |__) | __ ___ | |_ ___ | |_ _   _ _ __   ___  ___
+# |  ___/ '__/ _ \| __/ _ \| __| | | | '_ \ / _ \/ __|
+# | |   | | | (_) | || (_) | |_| |_| | |_) |  __/\__ \
+# |_|   |_|  \___/ \__\___/ \__|\__, | .__/ \___||___/
+#                                __/ | |
+#                               |___/|_|
+
+# PROTOTYPES describe typical individuals, characterized by specific
+# values of their variables
+prototypes:
+  individuals:
+    - healthy:
+        desc: 'healthy individuals'
+        health_state: S
+    - infected:
+        desc: 'infected individuals'
+        health_state: I
+
+
+#  _____       _ _   _       _
+# |_   _|     (_) | (_)     | |
+#   | |  _ __  _| |_ _  __ _| |
+#   | | | '_ \| | __| |/ _` | |
+#  _| |_| | | | | |_| | (_| | |
+# |_____|_| |_|_|\__|_|\__,_|_|
+
+#   _____                _ _ _   _
+#  / ____|              | (_) | (_)
+# | |     ___  _ __   __| |_| |_ _  ___  _ __  ___
+# | |    / _ \| '_ \ / _` | | __| |/ _ \| '_ \/ __|
+# | |___| (_) | | | | (_| | | |_| | (_) | | | \__ \
+#  \_____\___/|_| |_|\__,_|_|\__|_|\___/|_| |_|___/
+
+# INITIAL CONDITIONS FOR THE SIMULATION
+# In IBM or hybrid models, initial conditions describe the prototypes
+# involved with the amount of individuals in each of those prototypes
+initial_conditions:
+  population:
+    - prototype: healthy
+      amount: 'initial_population_size - initial_infected'
+    - prototype: infected
+      amount: 'initial_infected'
+
+
+#   ____        _               _
+#  / __ \      | |             | |
+# | |  | |_   _| |_ _ __  _   _| |_ ___
+# | |  | | | | | __| '_ \| | | | __/ __|
+# | |__| | |_| | |_| |_) | |_| | |_\__ \
+#  \____/ \__,_|\__| .__/ \__,_|\__|___/
+#                  | |
+#                  |_|
+
+# TYPE AND PERIODICITY OF OUTPUTS
+# The amount of individuals in each state is automatically recorded
+# for all state machines each time step during the simulation.
+# Additional variables (e.g. expressions defined in the 'parameters'
+# section) can be specified below (as 'extra_vars').
+outputs:
+  type: csv
+  population:
+    period: 1
+    extra_vars:
+      - percentage_prevalence
+      - total_population
+...
index 4479291..9f6cbf2 100644 (file)
@@ -4,7 +4,7 @@
 MODEL PARAMETERS
 ------------------------------------------------------------------------
   total_duration.................................................100.0
-  initial_herd_size..............................................100.0
+  initial_population_size........................................100.0
   initial_infected.................................................1.0
   transmission_I...................................................0.5
   recovery.........................................................0.1
index 392cc25..3ad6f9e 100644 (file)
@@ -36,7 +36,7 @@
             
   <div class="section" id="emulsion-manual">
 <h1>EMULSION Manual<a class="headerlink" href="#emulsion-manual" title="Permalink to this headline">¶</a></h1>
-<p><img alt="badge-license" src="https://img.shields.io/badge/license-Apache--2.0-8cd0c3.svg" /> <img alt="badge-release" src="https://img.shields.io/badge/version-1.0.11-f16152.svg" /></p>
+<p><img alt="badge-license" src="https://img.shields.io/badge/license-Apache--2.0-8cd0c3.svg" /> <img alt="badge-release" src="https://img.shields.io/badge/version-1.0.12-f16152.svg" /></p>
 <p>Framework EMULSION is intended for modellers in epidemiology, to help
 them design, simulate, and revise complex mechanistic stochastic
 models, without having to write or rewrite huge amounts of code.</p>
index 63980a2..acabc11 100644 (file)
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index b2ecc61..0cf671b 100644 (file)
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index 0a8c7cd..461deab 100644 (file)
@@ -77,6 +77,7 @@ append option <code class="docutils literal notranslate"><span class="pre">--vie
 }</p></object></div>
 </div>
 <img alt="../_images/SIR1.png" class="align-left" src="../_images/SIR1.png" />
+<img alt="../_images/SIR1b.png" class="align-left" src="../_images/SIR1b.png" />
 <p>You can also check the results of a more complex model, e.g. <code class="docutils literal notranslate"><span class="pre">quickstart</span></code>,
 tested <a class="reference internal" href="Install.html#test-your-installation"><span class="std std-ref">at install</span></a>.</p>
 <p>When running a model, EMULSION:</p>
@@ -147,7 +148,7 @@ with option <code class="docutils literal notranslate"><span class="pre">--forma
 <span class="n">MODEL</span> <span class="n">PARAMETERS</span>
 <span class="o">------------------------------------------------------------------------</span>
   <span class="n">total_duration</span><span class="o">.................................................</span><span class="mf">100.0</span>
-  <span class="n">initial_herd_size</span><span class="o">..............................................</span><span class="mf">100.0</span>
+  <span class="n">initial_population_size</span><span class="o">........................................</span><span class="mf">100.0</span>
   <span class="n">initial_infected</span><span class="o">.................................................</span><span class="mf">1.0</span>
   <span class="n">transmission_I</span><span class="o">...................................................</span><span class="mf">0.5</span>
   <span class="n">recovery</span><span class="o">.........................................................</span><span class="mf">0.1</span>
@@ -186,6 +187,7 @@ model file, you can specify the new values with option <code class="docutils lit
 </div>
 <p>which produces:</p>
 <img alt="../_images/SIR2.png" class="align-left" src="../_images/SIR2.png" />
+<img alt="../_images/SIR2b.png" class="align-left" src="../_images/SIR2b.png" />
 </div>
 <div class="section" id="changing-the-model">
 <h2>2.5. Changing the model<a class="headerlink" href="#changing-the-model" title="Permalink to this headline">¶</a></h2>
index 8f27ef8..eeb23e8 100644 (file)
@@ -41,7 +41,7 @@
 <p>Framework EMULSION is deposited at the French <a class="reference external" href="https://www.app.asso.fr/en">APP (Agency for the
 Protection of Programs)</a> with reference:
 <code class="docutils literal notranslate"><span class="pre">IDDN.FR.001.280043.000.R.P.2018.000.10000</span></code>.</p>
-<p>EMULSION version 1.0.11 is released under the following license (Apache-2.0):</p>
+<p>EMULSION version 1.0.12 is released under the following license (Apache-2.0):</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>
                                  <span class="n">Apache</span> <span class="n">License</span>
                            <span class="n">Version</span> <span class="mf">2.0</span><span class="p">,</span> <span class="n">January</span> <span class="mi">2004</span>
index aa3a917..22b58cd 100644 (file)
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/models/features/hybrid_SIR_lockdown.yaml b/models/features/hybrid_SIR_lockdown.yaml
new file mode 100644 (file)
index 0000000..2034ad8
--- /dev/null
@@ -0,0 +1,313 @@
+---
+
+# EMULSION (Epidemiological Multi-Level Simulation framework)
+# ===========================================================
+# 
+# Contributors and contact:
+# -------------------------
+# 
+#     - Sébastien Picault (sebastien.picault@inrae.fr)
+#     - Yu-Lin Huang
+#     - Vianney Sicard
+#     - Sandie Arnoux
+#     - Gaël Beaunée
+#     - Pauline Ezanno (pauline.ezanno@inrae.fr)
+# 
+#     INRAE, Oniris, BIOEPAR, 44300, Nantes, France
+# 
+# 
+# How to cite:
+# ------------
+# 
+#     S. Picault, Y.-L. Huang, V. Sicard, S. Arnoux, G. Beaunée,
+#     P. Ezanno (2019). "EMULSION: Transparent and flexible multiscale
+#     stochastic models in human, animal and plant epidemiology", PLoS
+#     Computational Biology 15(9): e1007342. DOI:
+#     10.1371/journal.pcbi.1007342
+# 
+# 
+# License:
+# --------
+# 
+#    Copyright 2016 INRAE and Univ. Lille
+# 
+#    Inter Deposit Digital Number: IDDN.FR.001.280043.000.R.P.2018.000.10000
+# 
+#    Agence pour la Protection des Programmes,
+#    54 rue de Paradis, 75010 Paris, France
+# 
+#    Licensed under the Apache License, Version 2.0 (the "License");
+#    you may not use this file except in compliance with the License.
+#    You may obtain a copy of the License at
+# 
+#        http://www.apache.org/licenses/LICENSE-2.0
+# 
+#    Unless required by applicable law or agreed to in writing, software
+#    distributed under the License is distributed on an "AS IS" BASIS,
+#    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#    See the License for the specific language governing permissions and
+#    limitations under the License.
+
+#  __  __           _      _
+# |  \/  |         | |    | |
+# | \  / | ___   __| | ___| |
+# | |\/| |/ _ \ / _` |/ _ \ |
+# | |  | | (_) | (_| |  __/ |
+# |_|  |_|\___/ \__,_|\___|_|
+#
+#  _____        __                           _   _
+# |_   _|      / _|                         | | (_)
+#   | |  _ __ | |_ ___  _ __ _ __ ___   __ _| |_ _  ___  _ __
+#   | | | '_ \|  _/ _ \| '__| '_ ` _ \ / _` | __| |/ _ \| '_ \
+#  _| |_| | | | || (_) | |  | | | | | | (_| | |_| | (_) | | | |
+# |_____|_| |_|_| \___/|_|  |_| |_| |_|\__,_|\__|_|\___/|_| |_|
+
+
+# NAME OF THE MODEL
+model_name: hybrid_SIR
+
+
+# DESCRIPTION OF THE MODEL
+model_info:
+  abstract: 'This model is a simple discrete-time, stochastic,
+  "hybrid" SIR model, i.e. with individuals grouped according to
+  relevant variables such as their health state. A lockdown occurs
+  during epidemics to flatten the curve.
+  '
+  author: 'Sebastien Picault (sebastien.picault@inrae.fr)'
+
+
+#  _______ _
+# |__   __(_)
+#    | |   _ _ __ ___   ___
+#    | |  | | '_ ` _ \ / _ \
+#    | |  | | | | | | |  __/
+#    |_|  |_|_| |_| |_|\___|
+
+# TIME INFORMATION
+# This section defines the time unit (used e.g. for expressing
+# durations, rates, etc.), the duration of the time step, the origin
+# date and total duration of the simulation.
+time_info:
+  time_unit: 'days'
+  delta_t: 1
+  origin: 'January 1'
+  total_duration: '300'
+
+
+#  _                    _
+# | |                  | |
+# | |     _____   _____| |___
+# | |    / _ \ \ / / _ \ / __|
+# | |___|  __/\ V /  __/ \__ \
+# |______\___| \_/ \___|_|___/
+
+# ORGANIZATION LEVELS USED IN THE SIMULATION
+# A hybrid model considers two levels: the population and
+# its components (individuals)
+levels:
+  population:
+    desc: 'level of the population'
+    aggregation_type: 'hybrid'   # the keyword for designing hybrid models
+    contains:
+      - individuals
+  individuals:
+    desc: 'level of the individuals'
+
+
+
+#  _____
+# |  __ \
+# | |__) | __ ___   ___ ___  ___ ___  ___  ___
+# |  ___/ '__/ _ \ / __/ _ \/ __/ __|/ _ \/ __|
+# | |   | | | (_) | (_|  __/\__ \__ \  __/\__ \
+# |_|   |_|  \___/ \___\___||___/___/\___||___/
+
+# LIST OF PROCESSES (IN ORDER) TO BE EXECUTED DURING EACH TIME STEP
+# In a hybrid model, processes take place at the population level
+# and are managed by groupings
+processes:
+  population:
+    - infection                 # name of a grouping
+
+
+#   _____                       _
+#  / ____|                     (_)
+# | |  __ _ __ ___  _   _ _ __  _ _ __   __ _
+# | | |_ | '__/ _ \| | | | '_ \| | '_ \ / _` |
+# | |__| | | | (_) | |_| | |_) | | | | | (_| |
+#  \_____|_|  \___/ \__,_| .__/|_|_| |_|\__, |
+#                        | |             __/ |
+#                        |_|            |___/
+
+# DESCRIPTION OF GROUPINGS, ASSOCIATED WITH PROCESSES WHICH ARE NOT
+# DIRECTLY BASED ON STATE MACHINES
+# A grouping is based on one or more variables. For instance, the
+# grouping for managing the 'infection' process is based on the
+# variable 'health_state' (coming from the state machine with the same
+# name): hence, one group will be defined for all possible values of
+# the health_state variable.
+
+grouping:
+  population:
+    infection:
+      machine_name: health_state
+      key_variables: [health_state]
+
+
+#   _____ _        _         __  __            _     _
+#  / ____| |      | |       |  \/  |          | |   (_)
+# | (___ | |_ __ _| |_ ___  | \  / | __ _  ___| |__  _ _ __   ___  ___
+#  \___ \| __/ _` | __/ _ \ | |\/| |/ _` |/ __| '_ \| | '_ \ / _ \/ __|
+#  ____) | || (_| | ||  __/ | |  | | (_| | (__| | | | | | | |  __/\__ \
+# |_____/ \__\__,_|\__\___| |_|  |_|\__,_|\___|_| |_|_|_| |_|\___||___/
+
+# DESCRIPTION OF THE STATE MACHINES INVOLVED IN THE MODEL
+# Each state machine is composed at least of several states.
+# The name of a state machine defines an individual variable which
+# contains the value of the current state in the individual.
+# Transitions define how each change can change to another one.
+# Productions define how individuals in one state can produce
+# new individuals in another state.
+state_machines:
+  # Below, the definition of the state machine used by the process
+  # 'infection'
+  health_state:
+    desc: 'The state machine which defines the evolution of health
+    states
+    '
+    # Below, the list of states with their attributes.
+    states:
+      - S:
+          name: 'Susceptible'
+          desc: 'suceptible of becoming infected'
+          fillcolor: 'wheat'
+      - I:
+          name: 'Infectious'
+          desc: 'infected and able to transmit the disease'
+          fillcolor: 'maroon'
+      - R:
+          name: 'Resistant'
+          desc: 'healthy again and resistant to infection'
+          fillcolor: 'deepskyblue'
+    # Below, a list of transitions between states, with rate or
+    # probabilities. Rates are automatically converted into
+    # probabilities w.r.t the duration of the time step (delta_t),
+    # assuming a classical exponential distribution of durations in
+    # the states.
+    transitions:
+      - {from: S, to: I, rate: 'force_of_infection'}
+      - {from: I, to: R, rate: 'recovery'}
+
+
+#  _____                               _
+# |  __ \                             | |
+# | |__) |_ _ _ __ __ _ _ __ ___   ___| |_ ___ _ __ ___
+# |  ___/ _` | '__/ _` | '_ ` _ \ / _ \ __/ _ \ '__/ __|
+# | |  | (_| | | | (_| | | | | | |  __/ ||  __/ |  \__ \
+# |_|   \__,_|_|  \__,_|_| |_| |_|\___|\__\___|_|  |___/
+
+# PARAMETERS/FUNCTIONS/EXPRESSIONS USED IN THE MODEL
+parameters:
+  initial_population_size:
+    desc: 'initial number of individuals in the population'
+    value: 1000
+  initial_infected:
+    desc: 'initial number of infectious individuals in the population'
+    value: 10
+  transmission_I:
+    desc: 'transmission rate from infectious individuals (/day)'
+    value: 'IfThenElse(AND(time >= lockdown_start, time <= lockdown_start + lockdown_duration), transmission_I_lockdown, transmission_I_default)'
+    # value: 'IfThenElse(AND(total_I > 0.2 * total_population), transmission_I_lockdown, transmission_I_default)'
+  transmission_I_default:
+    desc: 'default transmission rate from infectious individuals (/day)'
+    value: 0.2
+  transmission_I_lockdown:
+    desc: 'transmission rate from infectious individuals during lockdown (/day)'
+    value: 0.02
+  lockdown_start:
+    desc: 'date where lockdown starts after the beginning of the simulation (days)'
+    value: 30
+  lockdown_duration:
+    desc: 'duration of the lockdown (days)'
+    value: 20
+  recovery:
+    desc: 'recovery rate (/day)'
+    value: '1/15'
+  force_of_infection:
+    desc: 'infection function'
+    value: 'transmission_I * total_I / total_population'
+    source: 'classical function assuming frequency dependence'
+  percentage_prevalence:
+    desc: 'proportion of infected+infectious individuals'
+    value: '100 * total_I / total_population'
+
+
+#  _____           _        _
+# |  __ \         | |      | |
+# | |__) | __ ___ | |_ ___ | |_ _   _ _ __   ___  ___
+# |  ___/ '__/ _ \| __/ _ \| __| | | | '_ \ / _ \/ __|
+# | |   | | | (_) | || (_) | |_| |_| | |_) |  __/\__ \
+# |_|   |_|  \___/ \__\___/ \__|\__, | .__/ \___||___/
+#                                __/ | |
+#                               |___/|_|
+
+# PROTOTYPES describe typical individuals, characterized by specific
+# values of their variables
+prototypes:
+  individuals:
+    - healthy:
+        desc: 'healthy individuals'
+        health_state: S
+    - infected:
+        desc: 'infected individuals'
+        health_state: I
+
+
+#  _____       _ _   _       _
+# |_   _|     (_) | (_)     | |
+#   | |  _ __  _| |_ _  __ _| |
+#   | | | '_ \| | __| |/ _` | |
+#  _| |_| | | | | |_| | (_| | |
+# |_____|_| |_|_|\__|_|\__,_|_|
+
+#   _____                _ _ _   _
+#  / ____|              | (_) | (_)
+# | |     ___  _ __   __| |_| |_ _  ___  _ __  ___
+# | |    / _ \| '_ \ / _` | | __| |/ _ \| '_ \/ __|
+# | |___| (_) | | | | (_| | | |_| | (_) | | | \__ \
+#  \_____\___/|_| |_|\__,_|_|\__|_|\___/|_| |_|___/
+
+# INITIAL CONDITIONS FOR THE SIMULATION
+# In IBM or hybrid models, initial conditions describe the prototypes
+# involved with the amount of individuals in each of those prototypes
+initial_conditions:
+  population:
+    - prototype: healthy
+      amount: 'initial_population_size - initial_infected'
+    - prototype: infected
+      amount: 'initial_infected'
+
+
+#   ____        _               _
+#  / __ \      | |             | |
+# | |  | |_   _| |_ _ __  _   _| |_ ___
+# | |  | | | | | __| '_ \| | | | __/ __|
+# | |__| | |_| | |_| |_) | |_| | |_\__ \
+#  \____/ \__,_|\__| .__/ \__,_|\__|___/
+#                  | |
+#                  |_|
+
+# TYPE AND PERIODICITY OF OUTPUTS
+# The amount of individuals in each state is automatically recorded
+# for all state machines each time step during the simulation.
+# Additional variables (e.g. expressions defined in the 'parameters'
+# section) can be specified below (as 'extra_vars').
+outputs:
+  type: csv
+  population:
+    period: 1
+    extra_vars:
+      - percentage_prevalence
+      - total_population
+...
index 2e13a7f..bcff364 100644 (file)
@@ -53,5 +53,5 @@ EMULSION: Epidemiologic Multi-Level Simulation framework
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
 
-__version__ = '1.0.11'
+__version__ = '1.0.12'
 __all__ = ['tools', 'agent', 'model', 'templates']
index 4d627d4..1c5c355 100644 (file)
@@ -181,7 +181,7 @@ from   emulsion.tools.misc          import load_class
 from   emulsion.tools.plot          import plot_outputs
 from   emulsion.tools.simulation    import MultiSimulation
 
-VERSION = '1.0.11'
+VERSION = '1.0.12'
 DEFAULT_VERSION = "1.0"
 LICENSE = 'Apache-2.0'
 DEFAULT_LICENSE = "Apache-2.0"