This document was built in Markdown in R 4.1.1 and compiled on 13 September 2021. It covers package lefko3 version 3.8.0. This is a long-format vignette, meaning that we have tried to include a good deal more code and output than is permissible in the standard CRAN-packaged vignette. Note, however, that code that results in dramatically long output has been hashtagged to prevent the inclusion of tens of pages of output that may confuse the user. In these cases, please remove the hashtag to see the output.


In this vignette, we use the cypdata and cypvert datasets to illustrate the estimation of raw MPMs and function-based MPMs. Please see the other vignettes included in package lefko3, as well as further vignettes posted online on the projects page of the Shefferson lab website, for further demonstrations of raw MPMs, function-based MPMs, IPMs, and age-by-stage MPMs.


The white lady’s slipper, Cypripedium candidum, is a North American perennial herb in the family Orchidaceae. It is long-lived and of conservation concern. This plant begins life by germinating from a dust seed, and then develops into a protocorm, which is a special subterranean life stage found in orchids and pyroloids. During this stage, the plant is non-photosynthetic and completely parasitic on its mycorrhizal fungi. It spends several years as a protocorm, and previous studies suggest that it typically spends 3 years before becoming a seedling. As a seedling, it may or may not produce aboveground sprouts, often remaining entirely subterranean and continuing its parasitic lifestyle. It may persist this way for many years before attaining adult size, at which point it may sprout with or without flowers, or may remain underground in a condition referred to as vegetative dormancy. The latter condition may continue for many years, with over a decade of continuous dormancy documented in the literature (Shefferson et al. 2018).