Package: albopictus
Environmentally-driven population dynamics model of Aedes albopictusThis is a python (v3.7) package implementing the environmentally-driven population dynamics model of Aedes albopictus.ContentsPrerequisitesLinux installationUsage1) PrerequisitesThe model requires the Python packagesnumpypkg_resourcesand theGNU Scientific Library (development)for C, which are not included in this package.2) Linux installationEasy way:If you have pip installed, you can use the following command to download and install the package.pip install albopictusAlternatively, you can download the source code from PyPI and run pip on the latest version xxx.pip install albopictus-xxx.tar.gzHard way:If pip is not available, you can unpack the package contents and perform a manual install.tar -xvzf albopictus-xxx.tar.gzcd albopictus-xxxpython setup.py installThis 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>:$PYTHONPATHIn c shell:setenv PYTHONPATH <dir>:$PYTHONPATHUsageInformation for usage and contents are documented in the package, and can be accessed with the help utility.import albopictushelp(albopictus)Credits‘modern-package-template’ -http://pypi.python.org/pypi/modern-package-templateNews1.15.0Release date: 30 November 2023*CDZ: Chikungunya - Dengue - Zika modelMemory fix in modelStochCHIKVmodelAlbopictus08c: minor bug fix (pupa -> juveniles)1.13.0Release date: 13 September 2023*Initial draft of sPop v.2 with accumulative development (sPop2: Python)Minor fix: numpy.int -> numpy.int32Minor fix: DPOP_EPS double symbol1.12.6Release date: UNRELEASED*Included “extract” to the population dynamics model (sPop : Python)Included “spop_print_to_csv” to the population dynamics model (sPop : C)1.12.5Release date: UNRELEASED*Bug fixesIncluded “flush” to the population dynamics model (sPop)Optimized probability function (hash) in sPop (NOT WORKING)1.12.4Release date: UNRELEASED*1.12.3Release date: 19 February 2020*Bug fix for the sPop model (albopictus.population)1.12.2Release date: UNRELEASED*Culex pipiens complex population dynamics model (first draft)1.12.1Release date: UNRELEASED*Dynamic human population density for vector08 (from v.1.0 - 14 February 2017)Ability to change MAX_MEM for the gamma distribution module1.11.0Release date: 29 November 2018*Ae. albopictus population dynamics model updateAe. albopictus egg capture/removal is implementedAe. albopictus egg capture (total egg population laid each day is recorded)Ae. albopictus gonotrophic cycle length is introduced
(experimental data need to be updated for egg numbers per cycle not per day)1.9.3Release date: 1 August 2018*getClimate and getLonLat updated for Python 31.9.1Release date: 31 July 2018spop module is now compatible with Python 31.9Release date: 30 July 2018Compatible with Python 31.8.3Release date: UNRELEASED*Bug fixes for cross-platform compatibility1.8Release date: UNRELEASED*Ae. albopictus population dynamics model update initiated1.7Release date: UNRELEASED*Age-structured deterministic and stochastic population dynamics model1.6Release date: 27 February 2017This 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)1.5Release date: UNRELEASED*Sand fly model update (environmental dependence: functional dependence)1.4Release date: UNRELEASED*Sand fly model update1.3Release date: UNRELEASED*Preliminary study for a global albopictus-chikungunya modelTesting a new hypothesis for diapause1.2Release date: 7 June 2017Includes plotting routines for prior and posterior distributions1.1Release date: UNRELEASED*Preliminary study for a global albopictus-chikungunya model1.0Release date: 14 February 2017Revised 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)0.9Release date: UNRELEASED*Preliminary study for a sand fly model0.8Release date: 16 November 2016The ‘chikv’ model is updated to model spread with stable population sizes in patchesThe Ae. albopictus population dynamics model v.0.3 is available as vector03The prior distribution for vector03 is available as prior03This 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)0.7Release date: UNRELEASED*The ‘chikv’ model is updated to model spread with stable population sizes in patches0.6Release date: UNRELEASED*The spatiotemporal ‘chikv’ model is added, which models the Ae. albopictus-borne Chikungunya transmission0.5Release date: UNRELEASED*Hash function for Gamma distribution was implemented for improved flexibility and performance0.4Release date: UNRELEASED*Includes initial improvements on the vector population model0.3Release date: 9 February 2016This 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 research0.2Release date: UNRELEASED*Includes the prior distribution0.1Release date: UNRELEASED*Initial commit