Added analytical tools for plant ecophysiology, including fitting stomatal conductance models, photosynthetic responses to light, CO2, and temperature, light respiration, as well as tools for performing sensitivity analyses.
Added tests for new functions.
Added new vignette to include examples of new analytical functions.
photosynthesis() that was introduced when use_tealeaves = TRUE because of changes in the tealeaves package. This led to crossing all parameter values with all unique values of calculated T_sky, which was incorrect. Added unit tests to ensuring that crossing is done correctly under tests/test-photosynthesis-crossing.Rphotosynthesis() caused by new version of dplyr.enviro_par(), “sky” temperature (T_sky) can now be provided directly as a values (in K) or as a function (the default).parallel = TRUE in photosynthesis(), future uses plan("multisession") rather than plan("multiprocess").CONDUCT.md in READMERelease to be archived with revision of “Is amphistomy an adaptation to high light? Optimality models of stomatal traits along light gradients.”
Description: Simulate C\(_3\) photosynthesis using the Farquhar, von Caemmerer, Berry (1980) model as described in Buckley and Diaz-Espejo (2015). It uses units to ensure that parameters are properly specified and transformed before calculations. Temperature response functions get automatically “baked” into all parameters based on leaf temperature following Bernacchi et al. (2002). The package includes boundary layer, cuticular, stomatal, and mesophyll conductances to CO\(_2\), which each can vary on the upper and lower portions of the leaf. Use straightforward functions to simulate photosynthesis over environmental gradients such as Photosynthetic Photon Flux Density (PPFD) and leaf temperature, or over trait gradients such as CO\(_2\) conductance or photochemistry.
NEWS.md file to track changes to the package.