Estimating and Analyzing Demographic Models Using the popbio Package in R

By Chris J. Stubben, Brook G. Milligan. 2007

695 citations recorded by the source corpus.

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.

Subfields: Ecological Modeling, Ecology, Nature and Landscape Conservation

View Paper: https://www.semanticscholar.org/paper/ef5868e1974a4a6888acf7b630bafe7a2953fabe

How researchers see this paper

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In Ecological Modeling

1. J. Gaillard
2. Olivier Gimenez
3. S. Focardi
4. F. Ronchi
5. É. Baubet
6. Sabrina Servanty
7. R. Salguero‐Gómez
8. H. de Kroon

In Ecology

1. J. Gaillard
2. Olivier Gimenez
3. É. Baubet
4. Sabrina Servanty
5. J. Lebreton
6. S. Focardi
7. F. Ronchi
8. R. Salguero‐Gómez

In Nature and Landscape Conservation

1. R. Salguero‐Gómez
2. Y. Buckley
3. R. Altwegg
4. David Hodgson
5. J. Gaillard
6. J. Lorite
7. M. Dong
8. M. Franco

Citations in the corpus

• Changes in pollinator fauna cause spatial variation in pollen limitation (2010, methodology): “All demographic analyses were performed with the package popbio in R (Stubben & Milligan 2007).”
• Influence of harvesting pressure on demographic tactics: implications for wildlife management. (2011, methodology): “All calculations were performed in program R 2.8.0 (R Development Core Team 2008) using package popbio (Stubben & Milligan 2007).”
• The compadre Plant Matrix Database: an open online repository for plant demography (2015, methodology): “Users are welcome to explore these or other more developed open-source libraries (Stubben & Milligan 2007; Stott, Hodgson & Town-ley 2012; Metcalf et al. 2013) and to carry out their own calculations based on compendia of methods for analysis of MPMs (e.g., Caswell 2001, 2009; Morris & Doak 2002).”