Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warning = FALSE,
message = FALSE,
eval = TRUE
)
## ---- mwe---------------------------------------------------------------------
library(magrittr)
library(tealeaves)
# Leaving the make_* functions empty will automatically default to defaults
# parameters.
leaf_par <- make_leafpar() # leaf parameters
enviro_par <- make_enviropar() # environmental parameters
constants <- make_constants() # physical constants
T_leaf <- tleaf(leaf_par, enviro_par, constants, quiet = TRUE)
T_leaf %>% knitr::kable()
## ---- replace-defaults--------------------------------------------------------
# Use the `replace` argument to replace defaults. This must be a named list, and
# each named element must have the proper units specified. See `?make_parameters`
# for all parameter names and proper units.
# First, we'll change stomatal conductance to 4 umol / (m^2 s Pa)
leaf_par <- make_leafpar(
replace = list(
g_sw = set_units(4, "umol/m^2/s/Pa")
)
)
# Next, we'll change the air temperature to 25 degree C (= 298.15 K)
enviro_par <- make_enviropar(
replace = list(
T_air = set_units(298.15, "K")
)
)
# Physical constants probably do not need to be replaced in most cases,
# that's why we call them 'constants'!
constants <- make_constants()
T_leaf <- tleaf(leaf_par, enviro_par, constants, quiet = TRUE)
T_leaf %>% knitr::kable()
## ---- environmental-gradients-------------------------------------------------
# As before, use the `replace` argument to replace defaults, but this time we
# enter multiple values
# First, we'll change stomatal conductance to to 2 and 4 umol / (m^2 s Pa)
leaf_par <- make_leafpar(
replace = list(
g_sw = set_units(c(2, 4), "umol/m^2/s/Pa")
)
)
# Next, we'll change the air temperature to 20 and 25 degree C (= 293.15 and 298.15 K)
enviro_par <- make_enviropar(
replace = list(
T_air = set_units(c(293.15, 298.15), "K")
)
)
constants <- make_constants()
# Now there should be 4 combinations (high and low g_sw crossed with high and low T_air)
T_leaves <- tleaves(leaf_par, enviro_par, constants, progress = FALSE,
quiet = TRUE, set_units = FALSE)
T_leaves %>%
dplyr::select(T_air, g_sw, T_leaf) %>%
knitr::kable()
## ---- parallel-example, eval = FALSE------------------------------------------
# # NOTE: not evaluated here because it caused error on CRAN. Copy-and-paste to run on your own machine.
#
# # We'll use the `replace` argument to enter multiple air temperatures and two light levels
#
# leaf_par <- make_leafpar()
#
# enviro_par <- make_enviropar(
# replace = list(
# S_sw = set_units(c(300, 1000), "W/m^2"),
# T_air = set_units(seq(273.15, 313.15, length.out = 10), "K")
# )
# )
#
# constants <- make_constants()
#
# tl <- tleaves(leaf_par, enviro_par, constants, progress = FALSE, quiet = TRUE,
# parallel = TRUE)
# tl$T_air %<>% drop_units() # for plotting
# tl$T_leaf %<>% drop_units() # for plotting
# tl %<>% dplyr::mutate(Light = dplyr::case_when(
# round(drop_units(S_sw), 0) == 300 ~ "Shade",
# round(drop_units(S_sw), 0) == 1000 ~ "Sun"
# ))
#
# # Plot T_air versus T_leaf - T_air at different light levels
# library(ggplot2)
# ggplot(tl, aes(T_air, T_leaf - T_air, color = Light)) +
# geom_line() +
# xlab("Air Temperature [K]") +
# ylab("Leaf - Air Temperature [K]") +
# theme_minimal() +
# NULL
#
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