scenario_35.xml

<!-- min-version: 35 -->
<!-- max-version: 35 -->
<!-- disclaimer: this may not work as intended -->
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<!-- Outline of the base scenario.
This can be used as a template to construct the required scenario. Further
snippets and documentation on the OpenMalaria wiki[1] should be used to
complete the scenario.
[1]: https://github.com/SwissTPH/openmalaria/wiki/Start
-->
<!-- ... indicates possible extra content. <element ... /> may be replaced with <element ...> ... </element> -->
<!-- The om:scenario attributes should not be changed excepting "name" and
if necessary replacing "scenario_35.xsd" with the name of your copy of the
schema (XSD). Changing to a different schema version usually involves replacing
all instances of the number (35), except that versions <32 are different. -->
<om:scenario xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
             name="..." schemaVersion="35"
             xsi:schemaLocation="http://openmalaria.org/schema/scenario_35 scenario_35.xsd"
             xmlns:om="http://openmalaria.org/schema/scenario_35">
  
  <!-- Required. See demography/Ifakara.xml. -->
  <!-- placeholder: om:demography -->
  
  <!-- Required: specification of model outputs. -->
  <monitoring name="...">
    <!-- Optional: "continuous" outputs. -->
    <!-- placeholder-optional: om:mon-continuous -->
    
    <!-- Required: outputs for surveys (not continuous). -->
    <!-- placeholder: om:mon-survey-options -->
    
    <!-- Required: survey times and diagnostic. -->
    <!-- placeholder: om:mon-surveys -->
    
    <!-- Required: age groups for surveys. -->
    <!-- placeholder: om:mon-age-group -->
    
    <!-- Optional: cohorts. -->
    <!-- placeholder-optional: om:mon-cohorts -->
  </monitoring>
  
  <!-- Required: description of all interventions. Can be empty. -->
  <interventions>
    <!-- placeholder-any: om:intervention-elt -->
    <!-- placeholder-optional: om:vectorPop -->
    <!-- placeholder-optional: om:interv-human -->
  </interventions>
  
  <!-- Required: description of the (initial) health system. -->
  <!-- placeholder: om:healthSystem -->
  
  <!-- Required: vector and transmission data. -->
  <!-- placeholder: entomology -->
  
  <!-- Optional: description of parasite genetics and resistance. -->
  <!-- placeholder-optional: om:parasite-genetics -->
  
  <!-- Optional: drug library.
  This describes how those drugs act and decay (PK and PD). -->
  <!-- placeholder-optional: om:pharmacology -->
  
  <!-- Optional: diagnostics library -->
  <!-- placeholder-optional: om:diagnostics -->
  
  <!-- (Within-host) model section. -->
  <model>
    <!-- ModelOptions describe within-host model parameters. Many of these
      - affect parameterisation, and should be set correctly for each set of
      - parameters used from a fitting run. -->
    <ModelOptions>
      <!-- placeholder: om:model-param-opts -->
      <!-- placeholder-any: om:model-extra-opts -->
    </ModelOptions>
    
    <!-- Clinical describes some health-system related parameters.
      - Health system memory is commonly set at 30 days, but can be adjusted. -->
    <clinical healthSystemMemory="30d">
      <!-- Optional but recommended; requires that "neonatal-diagnostic" is
        - described in the diagnostics section: -->
      <NeonatalMortality diagnostic="neonatal-diagnostic"/>
      
      <!-- Non-malaria fever data may be specified here. -->
      <!-- placeholder-optional: om:model-nmf-incidence -->
    </clinical>
    
    <!-- human describes human-related parameters -->
    <!-- placeholder: om:model-human -->
    
    <!-- vivax describes vivax-model parameters, if this model is used -->
    <!-- placeholder-optional: om:model-vivax -->
    
    <!-- The parameters element describes fitting parameters. These should be
      - taken from the output of one of the fitting runs, and used with the
      - correct ModelOptions.
      -   "interval" is the number of days per update step (1 or 5); much other data
      -   depends on this so don't change except by selecting another base scenario.
      -   "iseed" is the random number seed. If non-zero it should ideally be a
      -   prime. Experiment creator tools set this for you.
      -   "latentp" is the duration of latent period of an infection, i.e. from
      -   inoculation by mosquito to the first day the infection is patent.
      -->
    <parameters interval="5" iseed="0" latentp="15d">
      <!-- placeholder: om:model-param-parameters -->
    </parameters>
  </model>
</om:scenario>