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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

  1. Prerequisites
  2. Linux installation
  3. Usage

1) Prerequisites

The model requires the following packages, which are not included in this package:

numpy

pkg_resources

2) Linux installation

  1. 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
  1. 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

1.2

  • 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
Release History

Release History

This version
History Node

1.2

History Node

1.0

History Node

0.8

History Node

0.3

History Node

0.2

Download Files

Download Files

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File Name & Checksum SHA256 Checksum Help Version File Type Upload Date
albopictus-1.2.tar.gz (1.4 MB) Copy SHA256 Checksum SHA256 Source Jun 7, 2017

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