photoinhibition() to light response models. This allows users to estimate photoinhibition at high light.::: operatorread_licor() removes lines where parameter settings are changed between loggingread_licor()read_li6800() in favor of read_licor()fit_many() in favor of generic methods like purrr::map()bibentry() instead of citEntry()expect_no_condition() from unit tests to resolved issue #12dplyr::progress_estimated() with progress::progress_bar()photo(..., use_tealeaves = TRUE). User-defined changes in stomatal conductance ratio were not being passed to tealeaves.photo() and photosynthesis() output when use_tealeaves = TRUEsimulate_error() to simulate measurement error in gas exchange measurements.fit_photosynthesis(..., .method = "brms")fit_photosynthesis() which performs all checks and manipulations prior to passing arguments to various fit_ functions.fit_r_light_kok(), fit_r_light_WalkerOrt(), fit_r_light_yin() in favor of fit_r_light2(). The new function uses non-standard evaluation to replace variable names as in dplyr::rename(). It will also extend functionality to enable Bayesian fitting using brms and does not output a plot.fit_aq_response2() using brms package.fit_aq_response() in favor of fit_aq_response2(). The new function uses non-standard evaluation to replace variable names as in dplyr::rename(). It will also extend functionality to enable Bayesian fitting using brms and does not output a plot.find_A()C_i (intercellular CO2 concentration) to output from photo() and photosynthesis()progress option to fit_many() to toggle progress barphotosynthesis(), but performance should be the sameC_air from 41 Pa to 420 umol/molO from 21.27565 kPa to 0.21 mol/molg_iasc) and liquid-phase (g_liqc) conductances.photo_parameters is single source of truth for all input parameters to photo() and photosynthesis().gc2gw() and gw2gc() and migrated to gunit version 1.0.2. Legacy version used version for still air in boundary layer conductance conversions. The corrected version includes modification for laminar flow in the boundary layer. Legacy version can be obtained with option use_legacy_version = TRUE.[umol / m ^ 2 / s / Pa] to [mol / m ^ 2 / s]<- to = in many instances%>% to |> in many instancestemp_resp1 and temp_resp2, corrected reference. (#6)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.