Ref. Type Pathogen(s) Host(s) Scale Timestep Stoch. or Det. Prog. lang. Git internal ID
Sébastien Picault, 2022 Mechanistic BRD complex cattle (young animals) batch discrete-time stochastic Python, EMULSION Yes mod_iOMrqP
Pauline Ezanno et al., 2020 Mechanistic MAP cattle population, metapopulation discrete-time stochastic C/C++ Yes mod_iPcpuR
Gaël Beaunée et al., 2022 Mechanistic ASF wild boar, domestic pig population, metapopulation discrete-time, continuous time stochastic C/C++ Yes mod_iPj9Dd
Glen Guyver-Fletcher, Mechanistic FMD cattle metapopulation discrete-time stochastic C/C++ Yes mod_iPBa1P
Sébastien Picault et al., 2020 Mechanistic ASF wild boar, domestic pig population, metapopulation discrete-time stochastic Python, EMULSION Yes mod_iPEN4T
Lina Cristancho-Fajardo et al., 2022 Mechanistic BVD cattle population, metapopulation discrete-time stochastic Python Yes mod_iPLSXj
Timothée Vergne et al., 2020 Mechanistic HPAI H5N8 ducks population discrete-time stochastic Fortran Yes mod_iPM0xt
Thanawat Tiensin et al., 2007 Mechanistic HPAI H5N1 chickens population discrete-time stochastic R No mod_iQW3J7
A. Ssematimba et al., 2019 Mechanistic HPAI H5N2 turkeys population discrete-time stochastic R, SAS No mod_iQW42t
Peter H. F. Hobbelen et al., 2020 Mechanistic HPAI H5N8 chickens, ducks population discrete-time stochastic, deterministic R No mod_iQW4lP
Yoko Hayama et al., 2022 Mechanistic HPAI H5N8 broiler chickens population discrete-time stochastic, deterministic R No mod_iQW4Fb
Sebastian Lequime et al., 2020 Mechanistic ZIKV Humans, Aedes albopictus within host/vector, population discrete-time stochastic R No mod_iR08hb
Jennifer S. Lord et al., 2023 Mechanistic ZIKV, DENV Aedes aegypti mosquitoes within host/vector discrete-time, continuous time stochastic, deterministic R Yes mod_iR08Ax
Necibe Tuncer et al., 2021 Mechanistic ZIKV Humans, Aedes aegypti mosquitoes within host/vector continuous time deterministic MATLAB Yes mod_iR08TT
Rebecca M. Johnson et al., 2024 Mechanistic DENV Aedes aegypti mosquitoes within host/vector continuous time deterministic R Yes mod_iR09mV
No Mechanistic M.haemolytica Beef young bulls population discrete-time stochastic Python;R;EMULSION Yes mod_iRLGUZ
Brandon Hayes et al., 2023 Mechanistic ASF domestic pig, wild boar population;metapopulation discrete-time stochastic R Yes mod_iQf3Cf
Hélène Cecilia, 2020 Mechanistic Rift Valley fever virus cattle, small ruminants, Aedes vexans arabiensis, Culex poicilipes, Culex tritaeniorhynchus population discrete-time determinist R Yes mod_iRHEVN
Hélène Cecilia, 2022 Mechanistic Rift Valley fever virus cattle, sheep, goat, Aedes spp., Culex spp. within host/vector continuous time determinist R Yes mod_iRHFS1
Hélène Cecilia, 2019 Mechanistic none (population dynamics of an insect vector) Glossina palpalis gambiensis population discrete-time determinist Python;EMULSION Yes mod_iRHHgD
Léa Loisel et al., 2024 Mechanistic CHIKV, DENV, ZIKV Aedes ageypti, Aedes albopictus, Aedes polynesiensis, Aedes geniculatus Within vector discrete-time stochastic R Yes mod_iRKwVh
No Mechanistic M.haemolytica Beef young bulls population discrete-time stochastic Python;R;EMULSION Yes mod_iRLobH
Hélène Cecilia, 2025 Phenomenological Zika virus cynomolgus macaques, squirrel monkeys, Aedes albopictus within host/vector not applicable not applicable R Yes mod_jcZomn
Héléna Ladreyt et al., 2021 Mechanistic JEV Culex spp., pigs, ducks, chicken, dogs, cattle, humans population continuous time determinist R No mod_jeguuv
Héléna Ladreyt et al., 2021 Mechanistic JEV Culex spp., pigs, ducks, chickens, cattle, dogs, humans population continuous time determinist R No mod_jegvsP
Sébastien Lambert et al., 2025 Mechanistic HPAI chickens, ducks, turkeys population discrete-time stochastic R Yes mod_jeJePZ
Sophie Planchand et al., 2025 Mechanistic HPAI Ducks population discrete-time stochastic R Yes mod_jeJfBJ
Jana Schulz et al., 2018 Mechanistic LA-MRSA domestic pigs population discrete-time stochastic R No mod_jfTBp5
Jana Schulz (Sonnenburg) et al., 2016 Mechanistic Classical swine fever Wild boar population discrete-time stochastic R No mod_jfTDgf
Hartmut Lentz et al., 2023 Phenomenological African Swine Fever Wild boar population Python Yes mod_jfTFd3
Jana Schulz et al., 2016 Mechanistic Classical swine fever wild boar population discrete-time stochastic R No mod_jfTGJp
Clara Delecroix et al., 2025 Mechanistic West Nile virus Mosquito, Birds (generic species A and B), Humans, Horses population continuous time stochastic R Yes mod_jkpgv7
Minori Furusawa et al., 2023 Mechanistic ESBL producing E. coli Poultry (chicken) metapopulation;QMRA towards humans discrete-time stochastic R;SimInf No mod_jkpgS1
Francesco Pinotti, 2024 Mechanistic Avian influenza virus Poultry, ducks population;metapopulation discrete-time stochastic C/C++ Yes mod_jkpgYN
Mariken de Wit, 2025 Mechanistic Usutu Virus Blackbirds metapopulation discrete-time stochastic R Yes mod_jkphxj
Soumya Banerjee et al., 2016 Mechanistic West Nile Virus Hosts: Mice, Vectors: None within host/vector continuous time determinist MATLAB No mod_jkphI7
Rotem Ben Shachar, 2018 Mechanistic Dengue virus human within host/vector;within-host continuous time determinist MATLAB Yes mod_jkphPx
Jerrold Tubay et al., 2024 Mechanistic Generic; case-study on Swine Influenza Pigs Farm population discrete-time stochastic EMULSION Yes mod_jkpi27
Noémie Courtejoie et al., 2019 Mechanistic Bluetongue virus serotype 8 (BTV-8) Cattle, Sheep, Culicoides biting midges (genus Culicoides) population;metapopulation discrete-time stochastic R;C/C++ No mod_jkpi6j
Bastiaan van der Roest et al., 2025 Mechanistic within host/vector;population continuous time not applicable R Yes mod_jkpicr
Afonso Dimas Martins et al., 2024 Mechanistic West Nile virus Mosquito (Culex pipiens and Aedes japonicus), human, birds population continuous time determinist R No mod_jkpieR
Albin Fontaine et al., 2018 Phenomenological Dengue Aedes aegypti within host/vector R Yes mod_jkpieS
Maud Charron et al., 2013 Mechanistic vector-borne pathogen population continuous time stochastic scilab No mod_jkpimL
Lina Cristancho-Fajardo et al., 2022 Mechanistic BVDV Cattle population;metapopulation discrete-time stochastic Python Yes mod_jkpjC1