Abstract
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.
Highlights
Heterogeneity is inherent in most naturally occurring populations
The final part of the previous Models and software section was removed, the description of the underlying age-structured population dynamics model was elaborated, and the resulting text was included as a separate section before the discussion of the implementation of the sPop packages
The same principles apply for the survival process, where we provide the mean and the standard deviation of the gamma-distribution for each age- development group as calculated by the death function
Summary
University of Exeter, Keywords deterministic, stochastic, vector, population, model, age-specific, survival, development, dynamic, difference equations, C, Python, R. Any reports and responses or comments on the article can be found at the end of the article. This version of the manuscript is prepared in response to the comments and suggestions of the readers. The major change is the following: - The Models and software section was re-written in two parts to improve clarity. The final part of the previous Models and software section was removed, the description of the underlying age-structured population dynamics model was elaborated, and the resulting text was included as a separate section before the discussion of the implementation of the sPop packages. Any further responses from the reviewers can be found at the end of the article
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