lefko3: Analysing individual history through size‐classified matrix population models

Abstract

The histories of individuals impact the dynamics of their populations. Matrix projection models (MPMs) are used to analyse population dynamics, but are not structured to incorporate these influences. Historical MPMs (hMPM) were developed to incorporate these impacts, but their complexity has left them little used. We developed r package lefko3 to provide simple, quick methods to estimate and analyse hMPMs, as well as ahistorical MPMs. Package lefko3 handles the entire workflow from dataset organization to the construction and analysis of hMPMs. Dataset management functions reorganize most demographic data formats, and matrix creation functions estimate both raw and function‐based matrices. Vital rates may be modelled as mixed or generalized linear models, with model selection protocols involving current best practices. The core kernels are binaries allowing even matrices with over 10,000 rows and columns to be estimated quickly without parallelization. We also include functions to conduct basic deterministic projection analyses. Package lefko3, available on CRAN, dramatically reduces the difficulties in testing the impacts of individual history on population dynamics. We provide three vignettes to showcase how hMPMs can be developed and analysed.

Marine heatwaves favour resistant Mediterranean octocoral populations at the expense of their speed of recovery

“…To calculate the SNA-LTRE from our set of matrices we used the function "ltre3" from the lefko3 R package (Shefferson et al, 2021) from the R software (R Core Team, 2020).…”

Rcompadre and Rage—Two R packages to facilitate the use of the COMPADRE and COMADRE databases and calculation of life‐history traits from matrix population models

“…For example, popdemo (Stott et al., 2012) focuses on the calculation of metrics related to transient population dynamics and transfer function analyses; popbio (Stubben & Milligan, 2007) provides functions to accomplish many (but not all) of the analyses found in the textbooks of Caswell (2001) and Morris and Doak (2002), such as the calculation of eigen properties (i.e. the asymptotic population growth rate, stable stage structure and reproductive values) or sensitivities and elasticities; Rramas (de la Cruz Rot, 2019) provides tools for making population projections and conducting population viability analyses from MPM data; and lefko3 (Shefferson et al., 2021) provides tools that allow the inclusion of information on individual histories, which could influence population dynamics, into MPM analyses (see Ehrlén, 2000). However, the tools for life‐history analysis provided by these existing packages are more limited, with among the most notable absence being important life‐history metrics based on age‐from‐stage calculations.…”

ipmr: Flexible implementation of Integral Projection Models in R

“…These developments were accompanied by the creation of software tools and guides to assist with IPM parameterization, implementation and analysis. These tools range from R scripts with detailed annotations (Coulson, 2012; Ellner et al., 2016; Merow et al., 2014) to R packages (Metcalf et al., 2013; Shefferson et al., 2020).…”