Environmentally-driven population dynamics model of Aedes albopictus
Project description
Environmentally-driven population dynamics model of Aedes albopictus
This is a python (v2.7) package implementing the environmentally-driven population dynamics model of Aedes albopictus.
Contents
Prerequisites
Linux installation
Usage
1) Prerequisites
The model requires the following packages, which are not included in this package:
numpy
pkg_resources
2) Linux installation
Easy way:
- If you have pip installed, you can use the following command to download and install the package.
pip install albopictus
- Alternatively, you can download the source code from PyPI and run pip on the latest version xxx.
pip install albopictus-xxx.tar.gz
Hard way:
- If pip is not available, you can unpack the package contents and perform a manual install.
tar -xvzf albopictus-xxx.tar.gz
cd albopictus-xxx
python setup.py install
This will install the package in the site-packages directory of your python distribution. If you do not have root privileges or you wish to install to a different directory, you can use the –prefix argument.
python setup.py install –prefix=<dir>
In this case, please make sure that <dir> is in your PYTHONPATH, or you can add it with the following command.
- In bash shell:
export PYTHONPATH=<dir>:$PYTHONPATH
- In c shell:
setenv PYTHONPATH <dir>:$PYTHONPATH
Usage
Information for usage and contents are documented in the package, and can be accessed with the help utility.
import albopictus
help(albopictus)
Credits
‘modern-package-template’ - http://pypi.python.org/pypi/modern-package-template
News
1.6
Release date: 27 February 2017
This is the model as presented in Erguler K, Pontiki I, Zittis G, Proestos Y, Christodoulou V, Tsirigotakis N, Antoniou M, Kasap OE, Alten B, Lelieveld J. Using longitudinal surveillance data to analyse the environmental dependence of vector populations: the case of sand flies. Scientific Reports. 2018 (submitted)
1.5
Release date: UNRELEASED*
Sand fly model update (environmental dependence: functional dependence)
1.4
Release date: UNRELEASED*
Sand fly model update
1.3
Release date: UNRELEASED*
Preliminary study for a global albopictus-chikungunya model
Testing a new hypothesis for diapause
1.2
Release date: 7 June 2017
Includes plotting routines for prior and posterior distributions
1.1
Release date: UNRELEASED*
Preliminary study for a global albopictus-chikungunya model
1.0
Release date: 14 February 2017
Revised version of the chikungunya model as presented in Erguler K, Chandra NL, Proestos Y, Lelieveld J, Christophides GK, Parham PE. A large-scale stochastic spatiotemporal model for Aedes albopictus-borne chikungunya epidemiology. PLOS ONE. 2017 (under review)
0.9
Release date: UNRELEASED*
Preliminary study for a sand fly model
0.8
Release date: 16 November 2016
The ‘chikv’ model is updated to model spread with stable population sizes in patches
The Ae. albopictus population dynamics model v.0.3 is available as vector03
The prior distribution for vector03 is available as prior03
This is the model as presented in Erguler K, Chandra NL, Proestos Y, Lelieveld J, Christophides GK, Parham PE. A large-scale stochastic spatiotemporal model for Aedes albopictus-borne chikungunya epidemiology. PLOS ONE. 2016 (submitted)
0.7
Release date: UNRELEASED*
The ‘chikv’ model is updated to model spread with stable population sizes in patches
0.6
Release date: UNRELEASED*
The spatiotemporal ‘chikv’ model is added, which models the Ae. albopictus-borne Chikungunya transmission
0.5
Release date: UNRELEASED*
Hash function for Gamma distribution was implemented for improved flexibility and performance
0.4
Release date: UNRELEASED*
Includes initial improvements on the vector population model
0.3
Release date: 9 February 2016
This is the model as presented in Erguler K, Smith-Unna SE, Waldock J, Proestos Y, Christophides GK, Lelieveld J, Parham PE. Large-scale modelling of the environmentally-driven population dynamics of temperate Aedes albopictus (Skuse). PLOS ONE. 2016 (in press)
This version also includes posterior Q1b, which is sampled from posterior mode Q1 for subsequent research
0.2
Release date: UNRELEASED*
Includes the prior distribution
0.1
Release date: UNRELEASED*
Initial commit
Project details
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