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: 3.2.0 (available from 6 January 2021).
New in this version: Inclusion of deVries and Caswell (2018) conditional hMPM format. Log stochastic growth rate. Summary function categorizing elasticity matrices by transition type. Revised stage frame format. Revisions to vignettes, issues related to failed zero-inflated GLMs solved and corrected, and minor bugs removed.
Known issues: Matrix creation functions may fail if used to create MPMs for single years or patches in multi-year/patch datasets. This issue will be fixed in the next version, but to avoid this problem now, use the default settings for year and patch. Also, censoring option in functions rlefko3() and rlefko2(), which create raw MPMs, currently do not function properly. This will also be fixed in the next version, but for now, censor datasets manually prior to raw MPM estimation.
Next version: 3.3.0 (expected mid-March 2021).
Coming in next version: New flexibility and options in supplying supplemental data for MPM estimation. Stochastic projection. Standard error estimation for λ. Bug fixes....
On the drawing board: LTRE and sLTRE functions. Bootstrapping functions for vertical datasets. Selection gradients. Density dependent vital rates.
Additional tutorial materials:
- Video tutorial: Intro to lefko3 with an analysis of Cypripedium candidum
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