sPop: Age-structured discrete-time population dynamics model in C, Python, and R [version 3; peer review: 2 approved]

• Main Author: Kamil Erguler
• Format: Article
• Language: English
• Published: F1000 Research Ltd 2020-09-01
• Series: F1000Research
• Online Access: https://f1000research.com/articles/7-1220/v3

This article describes the sPop packages implementing the deterministic and stochastic versions of an age-structured discrete-time population dynamics model. The packages enable mechanistic modelling of a population by monitoring the age and development stage of each individual. Survival and development are included as the main effectors and they progress at a user-defined pace: follow a fixed rate, delay for a given time, or progress at an age-dependent manner. The model is implemented in C, Python, and R with a uniform design to ease usage and facilitate adoption. Early versions of the model were previously employed for investigating climate-driven population dynamics of the tiger mosquito and the chikungunya disease spread by this vector. The sPop packages presented in this article enable the use of the model in a range of applications extending from vector-borne diseases towards any age-structured population including plant and animal populations, microbial dynamics, host-pathogen interactions, infectious diseases, and other time-dependent epidemiological processes.