R Package lefko3
Lefko3 is an R package designed to produce historical and ahsitorical matrix projection models (MPMs), where historical MPMs are large matrices that incorporate 3 consecutive time steps in each matrix. These matrices allow the history of the individual to be more completely modeled within population dynamics models, which is important given that MPMs typically assume no influence of differences in individual history on population dynamics.
Package lefko3 works on R 3.6.3 or greater on all systems that support R, including Windows, MacOS, Linux, and Unix. The package is currently available for download through CRAN, with documentation available here. See our paper describing it in Methods in Ecology and Evolution.
Current version: 3.3.2 (available from 25 February 2021).
New in this version: New flexibility and options in supplying supplemental data for MPM estimation. Stochastic projection. Stochastic sensitivity and elasticity analysis. Bug fixes and vignette expansions.
Known issues (to be corrected in next version): Some methods are currently not optimized for age-by-stage ahistorical model construction and analysis. Use of negative binomial distribution may yield erroneous results under some conditions.
Next version: 3.4.0 (expected mid-May 2021).
Coming in next version: Standard error estimation for λ. LTRE and sLTRE analysis. Generation time and related metrics.
On the drawing board: Bootstrapping functions for vertical datasets. Selection gradients. Density dependent vital rates.
- Tutorial on theory, methods, and concepts (included in package on CRAN)
- Tutorial example of raw historical and ahistorical MPM analysis using Lathyrus vernus (included in package on CRAN)
- Tutorial example of function-based historical and ahistorical MPM analysis using Cypripedium candidum (included in package on CRAN)
- Tutorial example of historical and ahistorical IPM analysis using Lathyrus vernus (included in package on CRAN)
- Video tutorial: Intro to lefko3 with a short analysis of Cypripedium candidum
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