R/make_parameters.R
In cdmuir/leafoptimizer: Optimize leaf traits to different environments in silico
Defines functions
replace_defaults
make_constants
make_bakepar
make_enviropar
make_leafpar
Documented in
make_bakepar
make_constants
make_enviropar
make_leafpar
#' Make lists of parameters for \code{optimize_leaf}
#'
#' @param replace A named list of parameters to replace defaults. If \code{NULL}, defaults will be used.
#'
#' @name make_parameters
#'
#' @encoding UTF-8
NULL
#' make_leafpar
#' @rdname make_parameters
#'
#' @return
#'
#' \code{make_leafpar}: An object inheriting from class \code{\link{leaf_par}}\cr
#' \code{make_enviropar}: An object inheriting from class \code{\link{enviro_par}}\cr
#' \code{make_bakepar}: An object inheriting from class \code{\link{bake_par}}\cr
#' \code{make_constants}: An object inheriting from class \code{\link{constants}}
#'
#' @details
#'
#' \bold{Leaf parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{d} \tab \code{leafsize} \tab leaf characteristic dimension \tab m \tab 0.1 \cr
#' \eqn{\Gamma*} \tab \code{gamma_star} \tab chloroplastic CO2 compensation point (T_leaf) \tab Pa \tab \link[=bake]{calculated} \cr
#' \eqn{\Gamma*_{25}}{\Gamma_25*} \tab \code{gamma_star25} \tab chloroplastic CO2 compensation point (25 °C) \tab Pa \tab 3.743 \cr
#' \eqn{g_\mathrm{mc}}{g_mc} \tab \code{g_mc} \tab mesophyll conductance to CO2 (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab \link[=bake]{calculated} \cr
#' \eqn{g_\mathrm{mc}}{g_mc} \tab \code{g_mc25} \tab mesophyll conductance to CO2 (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 4 \cr
#' \eqn{g_\mathrm{sc}}{g_sc} \tab \code{g_sc} \tab stomatal conductance to CO2 \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 4 \cr
#' \eqn{g_\mathrm{uc}}{g_uc} \tab \code{g_uc} \tab cuticular conductance to CO2 \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 0.1 \cr
#' \eqn{J_\mathrm{max25}}{J_max25} \tab \code{J_max25} \tab potential electron transport (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 200 \cr
#' \eqn{J_\mathrm{max}}{J_max} \tab \code{J_max} \tab potential electron transport (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{k_\mathrm{mc}}{k_mc} \tab \code{k_mc} \tab partition of \eqn{g_\mathrm{mc}}{g_mc} to lower mesophyll \tab none \tab 1 \cr
#' \eqn{k_\mathrm{sc}}{k_sc} \tab \code{k_sc} \tab partition of \eqn{g_\mathrm{sc}}{g_sc} to lower surface \tab none \tab 1 \cr
#' \eqn{k_\mathrm{uc}}{k_uc} \tab \code{k_uc} \tab partition of \eqn{g_\mathrm{uc}}{g_uc} to lower surface \tab none \tab 1 \cr
#' \eqn{K_\mathrm{C25}}{K_C25} \tab \code{K_C25} \tab Michaelis constant for carboxylation (25 °C) \tab \eqn{\mu}mol / mol \tab 268.3 \cr
#' \eqn{K_\mathrm{C}}{K_C} \tab \code{K_C} \tab Michaelis constant for carboxylation (T_leaf) \tab \eqn{\mu}mol / mol \tab \link[=bake]{calculated} \cr
#' \eqn{K_\mathrm{O25}}{K_O25} \tab \code{K_O25} \tab Michaelis constant for oxygenation (25 °C) \tab \eqn{\mu}mol / mol \tab 165084.2\cr
#' \eqn{K_\mathrm{O}}{K_O} \tab \code{K_O} \tab Michaelis constant for oxygenation (T_leaf) \tab \eqn{\mu}mol / mol \tab \link[=bake]{calculated} \cr
#' \eqn{\phi} \tab \code{phi} \tab initial slope of the response of J to PPFD \tab none \tab 0.331 \cr
#' \eqn{R_\mathrm{d25}}{R_d25} \tab \code{R_d25} \tab nonphotorespiratory CO2 release (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 2 \cr
#' \eqn{R_\mathrm{d}}{R_d} \tab \code{R_d} \tab nonphotorespiratory CO2 release (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{\theta_J} \tab \code{theta_J} \tab curvature factor for light-response curve \tab none \tab 0.825 \cr
#' \eqn{T_\mathrm{leaf}}{T_leaf} \tab \code{T_leaf} \tab leaf temperature \tab K \tab 298.15 \cr
#' \eqn{V_\mathrm{c,max25}}{V_c,max25} \tab \code{V_cmax25} \tab maximum rate of carboxylation (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 150 \cr
#' \eqn{V_\mathrm{c,max}}{V_c,max} \tab \code{V_cmax} \tab maximum rate of carboxylation (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{V_\mathrm{tpu25}}{V_tpu25} \tab \code{V_tpu25} \tab rate of triose phosphate utilisation (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 200 \cr
#' \eqn{V_\mathrm{tpu}}{V_tpu} \tab \code{V_tpu} \tab rate of triose phosphate utilisation (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated}
#' }
#'
#' \bold{Environment parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{C_\mathrm{air}}{C_air} \tab \code{C_air} \tab atmospheric CO2 concentration \tab Pa \tab 41 \cr
#' \eqn{E_q} \tab \code{E_q} \tab energy per mole quanta \tab kJ / mol\eqn{^2} \tab 220 \cr
#' \eqn{f_\mathrm{PAR}}{f_PAR} \tab \code{f_par} \tab fraction of \eqn{S_\mathrm{sw}}{S_sw} that is photosynthetically active radiation (PAR) \tab none \tab 0.5 \cr
#' \eqn{O} \tab \code{O} \tab atmospheric O2 concentration \tab kPa \tab 21.27565 \cr
#' \eqn{P} \tab \code{P} \tab atmospheric pressure \tab kPa \tab 101.3246 \cr
#' PPFD \tab \code{PPFD} \tab photosynthetic photon flux density \tab \eqn{\mu}mol quanta / (m^2 s) \tab 1500 \cr
#' \eqn{\mathrm{RH}}{RH} \tab \code{RH} \tab relative humidity \tab none \tab 0.50 \cr
#' \eqn{T_\mathrm{air}}{T_air} \tab \code{T_air} \tab air temperature \tab K \tab 298.15 \cr
#' \eqn{u} \tab \code{wind} \tab windspeed \tab m / s \tab 2
#' }
#'
#' \bold{Baking (i.e. temperature response) parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{D_\mathrm{s,gmc}}{Ds_gmc} \tab \code{Ds_gmc} \tab empirical temperature response parameter \tab J / (mol K) \tab 487.29 \cr
#' \eqn{D_\mathrm{s,Jmax}}{Ds_Jmax} \tab \code{Ds_Jmax} \tab empirical temperature response parameter \tab J / (mol K) \tab 388.04 \cr
#' \eqn{E_\mathrm{a,\Gamma *}}{Ea_gammastar} \tab \code{Ea_gammastar} \tab empirical temperature response parameter \tab J / mol \tab 24459.97 \cr
#' \eqn{E_\mathrm{a,gmc}}{Ea_gmc} \tab \code{Ea_gmc} \tab empirical temperature response parameter \tab J / mol \tab 68901.56 \cr
#' \eqn{E_\mathrm{a,Jmax}}{Ea_Jmax} \tab \code{Ea_Jmax} \tab empirical temperature response parameter \tab J / mol \tab 56095.18 \cr
#' \eqn{E_\mathrm{a,KC}}{Ea_KC} \tab \code{Ea_KC} \tab empirical temperature response parameter \tab J / mol \tab 80989.78 \cr
#' \eqn{E_\mathrm{a,KO}}{Ea_KO} \tab \code{Ea_KO} \tab empirical temperature response parameter \tab J / mol \tab 23719.97 \cr
#' \eqn{E_\mathrm{a,Rd}}{Ea_Rd} \tab \code{Ea_Rd} \tab empirical temperature response parameter \tab J / mol \tab 40446.75 \cr
#' \eqn{E_\mathrm{a,Vcmax}}{Ea_Vcmax} \tab \code{Ea_Vcmax} \tab empirical temperature response parameter \tab J / mol \tab 52245.78 \cr
#' \eqn{E_\mathrm{d,gmc}}{Ed_gmc} \tab \code{Ed_gmc} \tab empirical temperature response parameter \tab J / mol \tab 148788.56 \cr
#' \eqn{E_\mathrm{d,Jmax}}{Ed_Jmax} \tab \code{Ed_Jmax} \tab empirical temperature response parameter \tab J / mol \tab 121244.79
#' }
#'
#' \bold{Constants:}
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{D_{c,0}}{D_c0} \tab \code{D_c0} \tab diffusion coefficient for CO2 in air at 0 °C \tab m\eqn{^2} / s \tab 12.9 \cr
#' \eqn{D_{h,0}}{D_h0} \tab \code{D_h0} \tab diffusion coefficient for heat in air at 0 °C \tab m\eqn{^2} / s \tab 1.9e-5 \cr
#' \eqn{D_{m,0}}{D_m0} \tab \code{D_m0} \tab diffusion coefficient for momentum in air at 0 °C \tab m\eqn{^2} / s \tab 13.3e-06 \cr
#' \eqn{\epsilon} \tab \code{epsilon} \tab ratio of water to air molar masses \tab none \tab 0.622 \cr
#' \eqn{G} \tab \code{G} \tab gravitational acceleration \tab m / s\eqn{^2} \tab 9.8 \cr
#' \eqn{eT} \tab \code{eT} \tab exponent for temperature dependence of diffusion \tab none \tab 1.75 \cr
#' \eqn{R} \tab \code{R} \tab ideal gas constant \tab J / (mol K) \tab 8.3144598 \cr
#' \eqn{\sigma} \tab \code{s} \tab Stephan-Boltzmann constant \tab W / (m\eqn{^2} K\eqn{^4}) \tab 5.67e-08 \cr
#' \eqn{Sh} \tab \code{Sh} \tab Sherwood number \tab none \tab \link[=.get_sh]{calculated}
#' }
#'
#' @references
#'
#' Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.
#'
#' @examples
#' library(leafoptimizer)
#'
#' bake_par <- make_bakepar()
#' constants <- make_constants()
#' enviro_par <- make_enviropar()
#' leaf_par <- make_leafpar()
#'
#' leaf_par <- make_leafpar(
#' replace = list(
#' g_sc = set_units(3, "umol/m^2/s/Pa"),
#' V_cmax25 = set_units(100, "umol/m^2/s")
#' )
#' )
#'
#' @export
make_leafpar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
# Stop and warn if g_sw, g_uw, or logit_sr is in replace ----
if (!is.null(replace$g_sw)) {
stop("`g_sw` not allowed in replace. Use `g_sc` for stomatal conductance parameters instead.")
}
if (!is.null(replace$g_uw)) {
stop("`g_uw` not allowed in replace. Use `g_uc` for cuticular conductance parameters instead.")
}
if (!is.null(replace$logit_sr)) {
stop("`logit_sr` not allowed in replace. Use `k_sc` for stomatal ratio parameters instead.")
}
obj <- photosynthesis::make_leafpar(use_tealeaves = TRUE)
# Replace defaults ----
obj %<>% replace_defaults(replace)
# Assign class and return -----
obj %<>% leafoptimizer::leaf_par()
obj
}
#' make_enviropar
#' @rdname make_parameters
#' @export
make_enviropar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
# Stop and warn if S_sw is in replace ----
if (!is.null(replace$S_sw)) {
stop("`S_sw` not allowed in replace. Use `PPFD` for light parameters instead.")
}
obj <- photosynthesis::make_enviropar(use_tealeaves = TRUE)
# Replace defaults ----
obj %<>% replace_defaults(replace)
# Assign class and return ----
obj %<>% leafoptimizer::enviro_par()
obj
}
#' make_bakepar
#' @rdname make_parameters
#' @export
make_bakepar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
photosynthesis::make_bakepar(replace)
}
#' make_constants
#' @rdname make_parameters
#' @export
make_constants <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
obj <- photosynthesis::make_constants(use_tealeaves = TRUE)
# Replace defaults -----
if ("nu_constant" %in% names(replace)) {
stopifnot(is.function(replace$nu_constant))
obj$nu_constant <- replace$nu_constant
replace$nu_constant <- NULL
}
if ("sh_constant" %in% names(replace)) {
stopifnot(is.function(replace$sh_constant))
obj$sh_constant <- replace$sh_constant
replace$sh_constant <- NULL
}
obj %<>% replace_defaults(replace)
# Assign class and return -----
obj %<>% leafoptimizer::constants()
obj
}
replace_defaults <- function(obj, replace) {
if (!is.null(replace)) {
stopifnot(is.list(replace))
stopifnot(all(sapply(replace, inherits, what = "units")))
stopifnot(all(sapply(replace, is.numeric)))
x <- names(replace)
if (any(!x %in% names(obj))) {
warning(sprintf("The following parameters in 'replace' were not recognized:\n%s", paste0(x[!x %in% names(obj)], collapse = "\n")))
x %<>% .[. %in% names(obj)]
}
obj[x] <- replace[x]
}
obj
}
cdmuir/leafoptimizer documentation built on Sept. 10, 2021, 7:28 p.m.
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Defines functions replace_defaults make_constants make_bakepar make_enviropar make_leafpar
Documented in make_bakepar make_constants make_enviropar make_leafpar
#' Make lists of parameters for \code{optimize_leaf}
#'
#' @param replace A named list of parameters to replace defaults. If \code{NULL}, defaults will be used.
#'
#' @name make_parameters
#'
#' @encoding UTF-8
NULL
#' make_leafpar
#' @rdname make_parameters
#'
#' @return
#'
#' \code{make_leafpar}: An object inheriting from class \code{\link{leaf_par}}\cr
#' \code{make_enviropar}: An object inheriting from class \code{\link{enviro_par}}\cr
#' \code{make_bakepar}: An object inheriting from class \code{\link{bake_par}}\cr
#' \code{make_constants}: An object inheriting from class \code{\link{constants}}
#'
#' @details
#'
#' \bold{Leaf parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{d} \tab \code{leafsize} \tab leaf characteristic dimension \tab m \tab 0.1 \cr
#' \eqn{\Gamma*} \tab \code{gamma_star} \tab chloroplastic CO2 compensation point (T_leaf) \tab Pa \tab \link[=bake]{calculated} \cr
#' \eqn{\Gamma*_{25}}{\Gamma_25*} \tab \code{gamma_star25} \tab chloroplastic CO2 compensation point (25 °C) \tab Pa \tab 3.743 \cr
#' \eqn{g_\mathrm{mc}}{g_mc} \tab \code{g_mc} \tab mesophyll conductance to CO2 (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab \link[=bake]{calculated} \cr
#' \eqn{g_\mathrm{mc}}{g_mc} \tab \code{g_mc25} \tab mesophyll conductance to CO2 (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 4 \cr
#' \eqn{g_\mathrm{sc}}{g_sc} \tab \code{g_sc} \tab stomatal conductance to CO2 \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 4 \cr
#' \eqn{g_\mathrm{uc}}{g_uc} \tab \code{g_uc} \tab cuticular conductance to CO2 \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s Pa) \tab 0.1 \cr
#' \eqn{J_\mathrm{max25}}{J_max25} \tab \code{J_max25} \tab potential electron transport (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 200 \cr
#' \eqn{J_\mathrm{max}}{J_max} \tab \code{J_max} \tab potential electron transport (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{k_\mathrm{mc}}{k_mc} \tab \code{k_mc} \tab partition of \eqn{g_\mathrm{mc}}{g_mc} to lower mesophyll \tab none \tab 1 \cr
#' \eqn{k_\mathrm{sc}}{k_sc} \tab \code{k_sc} \tab partition of \eqn{g_\mathrm{sc}}{g_sc} to lower surface \tab none \tab 1 \cr
#' \eqn{k_\mathrm{uc}}{k_uc} \tab \code{k_uc} \tab partition of \eqn{g_\mathrm{uc}}{g_uc} to lower surface \tab none \tab 1 \cr
#' \eqn{K_\mathrm{C25}}{K_C25} \tab \code{K_C25} \tab Michaelis constant for carboxylation (25 °C) \tab \eqn{\mu}mol / mol \tab 268.3 \cr
#' \eqn{K_\mathrm{C}}{K_C} \tab \code{K_C} \tab Michaelis constant for carboxylation (T_leaf) \tab \eqn{\mu}mol / mol \tab \link[=bake]{calculated} \cr
#' \eqn{K_\mathrm{O25}}{K_O25} \tab \code{K_O25} \tab Michaelis constant for oxygenation (25 °C) \tab \eqn{\mu}mol / mol \tab 165084.2\cr
#' \eqn{K_\mathrm{O}}{K_O} \tab \code{K_O} \tab Michaelis constant for oxygenation (T_leaf) \tab \eqn{\mu}mol / mol \tab \link[=bake]{calculated} \cr
#' \eqn{\phi} \tab \code{phi} \tab initial slope of the response of J to PPFD \tab none \tab 0.331 \cr
#' \eqn{R_\mathrm{d25}}{R_d25} \tab \code{R_d25} \tab nonphotorespiratory CO2 release (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 2 \cr
#' \eqn{R_\mathrm{d}}{R_d} \tab \code{R_d} \tab nonphotorespiratory CO2 release (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{\theta_J} \tab \code{theta_J} \tab curvature factor for light-response curve \tab none \tab 0.825 \cr
#' \eqn{T_\mathrm{leaf}}{T_leaf} \tab \code{T_leaf} \tab leaf temperature \tab K \tab 298.15 \cr
#' \eqn{V_\mathrm{c,max25}}{V_c,max25} \tab \code{V_cmax25} \tab maximum rate of carboxylation (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 150 \cr
#' \eqn{V_\mathrm{c,max}}{V_c,max} \tab \code{V_cmax} \tab maximum rate of carboxylation (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated} \cr
#' \eqn{V_\mathrm{tpu25}}{V_tpu25} \tab \code{V_tpu25} \tab rate of triose phosphate utilisation (25 °C) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab 200 \cr
#' \eqn{V_\mathrm{tpu}}{V_tpu} \tab \code{V_tpu} \tab rate of triose phosphate utilisation (T_leaf) \tab \eqn{\mu}mol CO2 / (m\eqn{^2} s) \tab \link[=bake]{calculated}
#' }
#'
#' \bold{Environment parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{C_\mathrm{air}}{C_air} \tab \code{C_air} \tab atmospheric CO2 concentration \tab Pa \tab 41 \cr
#' \eqn{E_q} \tab \code{E_q} \tab energy per mole quanta \tab kJ / mol\eqn{^2} \tab 220 \cr
#' \eqn{f_\mathrm{PAR}}{f_PAR} \tab \code{f_par} \tab fraction of \eqn{S_\mathrm{sw}}{S_sw} that is photosynthetically active radiation (PAR) \tab none \tab 0.5 \cr
#' \eqn{O} \tab \code{O} \tab atmospheric O2 concentration \tab kPa \tab 21.27565 \cr
#' \eqn{P} \tab \code{P} \tab atmospheric pressure \tab kPa \tab 101.3246 \cr
#' PPFD \tab \code{PPFD} \tab photosynthetic photon flux density \tab \eqn{\mu}mol quanta / (m^2 s) \tab 1500 \cr
#' \eqn{\mathrm{RH}}{RH} \tab \code{RH} \tab relative humidity \tab none \tab 0.50 \cr
#' \eqn{T_\mathrm{air}}{T_air} \tab \code{T_air} \tab air temperature \tab K \tab 298.15 \cr
#' \eqn{u} \tab \code{wind} \tab windspeed \tab m / s \tab 2
#' }
#'
#' \bold{Baking (i.e. temperature response) parameters:}
#'
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{D_\mathrm{s,gmc}}{Ds_gmc} \tab \code{Ds_gmc} \tab empirical temperature response parameter \tab J / (mol K) \tab 487.29 \cr
#' \eqn{D_\mathrm{s,Jmax}}{Ds_Jmax} \tab \code{Ds_Jmax} \tab empirical temperature response parameter \tab J / (mol K) \tab 388.04 \cr
#' \eqn{E_\mathrm{a,\Gamma *}}{Ea_gammastar} \tab \code{Ea_gammastar} \tab empirical temperature response parameter \tab J / mol \tab 24459.97 \cr
#' \eqn{E_\mathrm{a,gmc}}{Ea_gmc} \tab \code{Ea_gmc} \tab empirical temperature response parameter \tab J / mol \tab 68901.56 \cr
#' \eqn{E_\mathrm{a,Jmax}}{Ea_Jmax} \tab \code{Ea_Jmax} \tab empirical temperature response parameter \tab J / mol \tab 56095.18 \cr
#' \eqn{E_\mathrm{a,KC}}{Ea_KC} \tab \code{Ea_KC} \tab empirical temperature response parameter \tab J / mol \tab 80989.78 \cr
#' \eqn{E_\mathrm{a,KO}}{Ea_KO} \tab \code{Ea_KO} \tab empirical temperature response parameter \tab J / mol \tab 23719.97 \cr
#' \eqn{E_\mathrm{a,Rd}}{Ea_Rd} \tab \code{Ea_Rd} \tab empirical temperature response parameter \tab J / mol \tab 40446.75 \cr
#' \eqn{E_\mathrm{a,Vcmax}}{Ea_Vcmax} \tab \code{Ea_Vcmax} \tab empirical temperature response parameter \tab J / mol \tab 52245.78 \cr
#' \eqn{E_\mathrm{d,gmc}}{Ed_gmc} \tab \code{Ed_gmc} \tab empirical temperature response parameter \tab J / mol \tab 148788.56 \cr
#' \eqn{E_\mathrm{d,Jmax}}{Ed_Jmax} \tab \code{Ed_Jmax} \tab empirical temperature response parameter \tab J / mol \tab 121244.79
#' }
#'
#' \bold{Constants:}
#' \tabular{lllll}{
#' \emph{Symbol} \tab \emph{R} \tab \emph{Description} \tab \emph{Units} \tab \emph{Default}\cr
#' \eqn{D_{c,0}}{D_c0} \tab \code{D_c0} \tab diffusion coefficient for CO2 in air at 0 °C \tab m\eqn{^2} / s \tab 12.9 \cr
#' \eqn{D_{h,0}}{D_h0} \tab \code{D_h0} \tab diffusion coefficient for heat in air at 0 °C \tab m\eqn{^2} / s \tab 1.9e-5 \cr
#' \eqn{D_{m,0}}{D_m0} \tab \code{D_m0} \tab diffusion coefficient for momentum in air at 0 °C \tab m\eqn{^2} / s \tab 13.3e-06 \cr
#' \eqn{\epsilon} \tab \code{epsilon} \tab ratio of water to air molar masses \tab none \tab 0.622 \cr
#' \eqn{G} \tab \code{G} \tab gravitational acceleration \tab m / s\eqn{^2} \tab 9.8 \cr
#' \eqn{eT} \tab \code{eT} \tab exponent for temperature dependence of diffusion \tab none \tab 1.75 \cr
#' \eqn{R} \tab \code{R} \tab ideal gas constant \tab J / (mol K) \tab 8.3144598 \cr
#' \eqn{\sigma} \tab \code{s} \tab Stephan-Boltzmann constant \tab W / (m\eqn{^2} K\eqn{^4}) \tab 5.67e-08 \cr
#' \eqn{Sh} \tab \code{Sh} \tab Sherwood number \tab none \tab \link[=.get_sh]{calculated}
#' }
#'
#' @references
#'
#' Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.
#'
#' @examples
#' library(leafoptimizer)
#'
#' bake_par <- make_bakepar()
#' constants <- make_constants()
#' enviro_par <- make_enviropar()
#' leaf_par <- make_leafpar()
#'
#' leaf_par <- make_leafpar(
#' replace = list(
#' g_sc = set_units(3, "umol/m^2/s/Pa"),
#' V_cmax25 = set_units(100, "umol/m^2/s")
#' )
#' )
#'
#' @export
make_leafpar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
# Stop and warn if g_sw, g_uw, or logit_sr is in replace ----
if (!is.null(replace$g_sw)) {
stop("`g_sw` not allowed in replace. Use `g_sc` for stomatal conductance parameters instead.")
}
if (!is.null(replace$g_uw)) {
stop("`g_uw` not allowed in replace. Use `g_uc` for cuticular conductance parameters instead.")
}
if (!is.null(replace$logit_sr)) {
stop("`logit_sr` not allowed in replace. Use `k_sc` for stomatal ratio parameters instead.")
}
obj <- photosynthesis::make_leafpar(use_tealeaves = TRUE)
# Replace defaults ----
obj %<>% replace_defaults(replace)
# Assign class and return -----
obj %<>% leafoptimizer::leaf_par()
obj
}
#' make_enviropar
#' @rdname make_parameters
#' @export
make_enviropar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
# Stop and warn if S_sw is in replace ----
if (!is.null(replace$S_sw)) {
stop("`S_sw` not allowed in replace. Use `PPFD` for light parameters instead.")
}
obj <- photosynthesis::make_enviropar(use_tealeaves = TRUE)
# Replace defaults ----
obj %<>% replace_defaults(replace)
# Assign class and return ----
obj %<>% leafoptimizer::enviro_par()
obj
}
#' make_bakepar
#' @rdname make_parameters
#' @export
make_bakepar <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
photosynthesis::make_bakepar(replace)
}
#' make_constants
#' @rdname make_parameters
#' @export
make_constants <- function(replace = NULL) {
checkmate::assert_list(replace, null.ok = TRUE)
obj <- photosynthesis::make_constants(use_tealeaves = TRUE)
# Replace defaults -----
if ("nu_constant" %in% names(replace)) {
stopifnot(is.function(replace$nu_constant))
obj$nu_constant <- replace$nu_constant
replace$nu_constant <- NULL
}
if ("sh_constant" %in% names(replace)) {
stopifnot(is.function(replace$sh_constant))
obj$sh_constant <- replace$sh_constant
replace$sh_constant <- NULL
}
obj %<>% replace_defaults(replace)
# Assign class and return -----
obj %<>% leafoptimizer::constants()
obj
}
replace_defaults <- function(obj, replace) {
if (!is.null(replace)) {
stopifnot(is.list(replace))
stopifnot(all(sapply(replace, inherits, what = "units")))
stopifnot(all(sapply(replace, is.numeric)))
x <- names(replace)
if (any(!x %in% names(obj))) {
warning(sprintf("The following parameters in 'replace' were not recognized:\n%s", paste0(x[!x %in% names(obj)], collapse = "\n")))
x %<>% .[. %in% names(obj)]
}
obj[x] <- replace[x]
}
obj
}
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