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: 3.4.0 (available from 2 April 2021).
New in this version: Stochastic projection. Stochastic sensitivity and elasticity analysis. Stochastic stable stage distribution and reproductive value estimation. Zero-truncated Poisson and negative binomial distributions for size and fecundity. New age x stage MPM vignette. Bug fixes and vignette expansions.
Known issues (to be corrected in next version): We are not currently aware of any issues.
Next version: 3.5.0 (expected mid-July 2021).
Coming in next version: Selection gradient estimation. Density-dependent projections. Standard error estimation for λ. LTRE and sLTRE analysis. Generation time and related metrics.
On the drawing board: Bootstrapping functions for vertical datasets. Parallelization functions.
- 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)
- Tutorial example of ahistorical age x stage MPM 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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