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Estimating and Analyzing Demographic Models Using the popbio Package in R

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  • Stubben, Chris
  • Milligan, Brook

Abstract

A complete assessment of population growth and viability from field census data often requires complex data manipulations, statistical routines, mathematical tools, programming environments, and graphical capabilities. We therefore designed an R package called popbio to facilitate both the construction and analysis of projection matrix models. The package consists primarily of the R translation of MATLAB code found in Caswell (2001) and Morris and Doak (2002) for the analysis of projection matrix models. The package also includes methods to estimate vital rates and construct projection matrix models from census data typically collected in plant demography studies. In these studies, vital rates can often be estimated directly from annual censuses of tagged individuals using transition frequency tables. Because the construction of projection matrix models requires careful management of census data, we describe the steps to construct a projection matrix in detail.

Suggested Citation

  • Stubben, Chris & Milligan, Brook, 2007. "Estimating and Analyzing Demographic Models Using the popbio Package in R," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i11).
    • Handle: RePEc:jss:jstsof:v:022:i11
    DOI: http://hdl.handle.net/10.18637/jss.v022.i11
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    Cited by:

    1. Kendall, Bruce E. & Fujiwara, Masami & Diaz-Lopez, Jasmin & Schneider, Sandra & Voigt, Jakob & Wiesner, Sören, 2019. "Persistent problems in the construction of matrix population models," Ecological Modelling, Elsevier, vol. 406(C), pages 33-43.
    2. Davison, Raziel & Stadman, Marc & Jongejans, Eelke, 2019. "Stochastic effects contribute to population fitness differences," Ecological Modelling, Elsevier, vol. 408(C), pages 1-1.
    3. Lewis, D.L. & Breck, S.W. & Wilson, K.R. & Webb, C.T., 2014. "Modeling black bear population dynamics in a human-dominated stochastic environment," Ecological Modelling, Elsevier, vol. 294(C), pages 51-58.
    4. Graciá, Eva & Rodríguez-Caro, Roberto C. & Sanz-Aguilar, Ana & Anadón, José D. & Botella, Francisco & García-García, Angel Luis & Wiegand, Thorsten & Giménez, Andrés, 2020. "Assessment of the key evolutionary traits that prevent extinctions in human-altered habitats using a spatially explicit individual-based model," Ecological Modelling, Elsevier, vol. 415(C).
    5. Hsien-Yung Lin & Eduardo G. Martins & Michael Power & James A. Crossman & Alf J. Leake & Steven J. Cooke, 2022. "An assessment tool for estimating effects of entrainment at hydropower facilities on adfluvial fish populations," Environment Systems and Decisions, Springer, vol. 42(4), pages 556-571, December.
    6. Anaïs Gibert & Danièle Magda & Laurent Hazard, 2015. "Interplay between Endophyte Prevalence, Effects and Transmission: Insights from a Natural Grass Population," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-17, October.
    7. Tremblay, Raymond L. & Tyre, Andrew J. & Pérez, Maria-Eglée & Ackerman, James D., 2021. "Population projections from holey matrices: Using prior information to estimate rare transition events," Ecological Modelling, Elsevier, vol. 447(C).
    8. Otjacques, W. & De Laender, F. & Kestemont, P., 2016. "Discerning the causes of a decline in a common European fish, the roach (Rutilus rutilus L.): A modelling approach," Ecological Modelling, Elsevier, vol. 322(C), pages 92-100.
    9. Romanov, Michael S. & Masterov, Vladimir B., 2020. "Low breeding performance of the Steller’s sea eagle (Haliaeetus pelagicus) causes the populations to decline," Ecological Modelling, Elsevier, vol. 420(C).
    10. Caskenette, Amanda & Enders, Eva C. & Watkinson, Doug & Wrubleski, Dale, 2018. "Partial exclusion of spawning Cyprinus carpio to improve coastal marsh habitat may come at the cost of increased carp population growth," Ecological Modelling, Elsevier, vol. 385(C), pages 58-64.
    11. repec:jss:jstsof:22:i01 is not listed on IDEAS
    12. Kneib, Thomas & Petzoldt, Thomas, 2007. "Introduction to the Special Volume on "Ecology and Ecological Modeling in R"," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 22(i01).
    13. Clinton Stipek & Rolando Santos & Elizabeth Babcock & Diego Lirman, 2020. "Modelling the resilience of seagrass communities exposed to pulsed freshwater discharges: A seascape approach," PLOS ONE, Public Library of Science, vol. 15(2), pages 1-15, February.
    14. Lewis, Dakota M. & Vardi, Tali & Maher, Rebecca L. & Correa, Adrienne M.S. & Cook, Geoffrey S., 2022. "Predicting shifts in demography of Orbicella franksi following simulated disturbance and restoration," Ecological Modelling, Elsevier, vol. 472(C).

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