Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(photosynthesis)
## ---- simple leaf, message = FALSE, eval=TRUE---------------------------------
library(photosynthesis)
bake_par = make_bakepar() # temperature response parameters
constants = make_constants(use_tealeaves = FALSE) # physical constants
# leaf parameters
leaf_par = make_leafpar(
replace = list(
# Set cuticular conductance to 0
g_uc = set_units(0, mol / m^2 / s),
# All conductance through lower stomata and mesophyll
k_mc = set_units(0, 1),
k_sc = set_units(0, 1)
),
use_tealeaves = FALSE
)
enviro_par = make_enviropar(use_tealeaves = FALSE) # environmental parameters
photo(leaf_par, enviro_par, bake_par, constants, use_tealeaves = FALSE) |>
dplyr::select(g_sc, A) |>
knitr::kable(caption = "Stomatal conductance to CO2 (g_sc) and net photosynthetic carbon assimilation (A) from C3 photosynthesis model.")
## ---- amphi leaf, message = FALSE, eval=TRUE----------------------------------
library(photosynthesis)
bake_par = make_bakepar() # temperature response parameters
constants = make_constants(use_tealeaves = FALSE) # physical constants
# leaf parameters
leaf_par = make_leafpar(
replace = list(
# Set cuticular conductance to 0
g_uc = set_units(0, mol / m^2 / s),
# Half of conductance through each surface
k_mc = set_units(0, 1),
# airspace conductance: define effective distance through airspace
# See Nobel (2020) pg. 431
delta_ias_lower = set_units(100, um),
delta_ias_upper = set_units(100, um),
# liquid conductance: sum of cell wall, plasma membrane, and cytosol resistance
# We are implicitly ignoring chloroplast resistance
# See Nobel (2020) pg. 448-452
A_mes_A = set_units(20, 1),
g_liqc25 = set_units(0.02, mol / m^2 / s),
k_sc = set_units(1, 1)
),
use_tealeaves = FALSE
)
enviro_par = make_enviropar(use_tealeaves = FALSE) # environmental parameters
photo(leaf_par, enviro_par, bake_par, constants, use_tealeaves = FALSE) |>
dplyr::select(g_sc, g_iasc_lower, g_iasc_upper, g_liqc, A) |>
knitr::kable(caption = "Stomatal conductance to CO2 (g_sc), internal airspace resistance through lower and upper surfaces (g_iasc_x), liquid-phase conductance (g_liqc), and net photosynthetic carbon assimilation (A) from C3 photosynthesis model.")
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