inst/doc/tealeaves-intermediate.R

In tealeaves: Solve for Leaf Temperature Using Energy Balance

## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(dplyr)
library(ggplot2)
library(magrittr)
library(tealeaves)


## ---- eval = FALSE, echo = TRUE-----------------------------------------------
#  
#  # install tidyverse packages if necessary
#  # install.packages("tidyverse")
#  
#  library(dplyr)
#  library(ggplot2)
#  library(magrittr)
#  library(tealeaves)
#  
#  # Parameter sets ----
#  
#  cs <- tealeaves::make_constants()
#  lp <- tealeaves::make_leafpar(
#    replace = list(
#      # Hypo- and amphistomatous leaves
#      logit_sr = set_units(c(-Inf, 0))
#    )
#  )
#  ep <- tealeaves::make_enviropar(
#    replace = list(
#      # Low and high light
#      S_sw = set_units(c(220, 660), "W/m^2"),
#      # Air temperature gradient
#      T_air = set_units(seq(278.15, 313.15, length.out = 25), "K")
#      )
#  )
#  
#  # Run tleaves ----
#  tl_example1 <- tleaves(lp, ep, cs)
#  
#  usethis::use_data(tl_example1)
#  

## ----plot temperature, echo = FALSE, eval = TRUE, fig.width=7-----------------

tl_example1 %<>%
  
  # Drop units for plotting
  mutate_if(function(x) inherits(x, what = "units"), drop_units) %>%
  
  # Calculate leaf temperature differential
  mutate(dT = T_leaf - T_air) %>%
  
  # Factorize stomatal ratio 
  mutate("Stomatal Ratio" = case_when(
    logit_sr == -Inf ~ "hypostomatous",
    logit_sr == 0 ~ "amphistomatous"
  )) %>%
  
  # Factorize light environment 
  mutate(Light = case_when(
    round(S_sw, 0) == 220 ~ "Shade",
    round(S_sw, 0) == 660 ~ "Sun"
  ))

ggplot(tl_example1, aes(T_air, dT, color = `Stomatal Ratio`)) +
  facet_grid(Light ~ .) + 
  geom_hline(yintercept = 0) +
  geom_line() +
  labs(x = "Air Temperature [K]", 
       y = "Leaf-to-Air Temperature Difference",
       color = "Stomatal Ratio") + 
  theme_minimal() + 
  theme(panel.grid.minor = element_blank()) +
  NULL


## ----plot transpiration, echo = FALSE, eval = TRUE, fig.width=7---------------

ggplot(tl_example1, aes(T_air, 1000 * E, color = `Stomatal Ratio`)) +
  facet_grid(Light ~ .) + 
  geom_line() +
  labs(x = "Air Temperature [K]", 
       y = expression(paste("Evaporation [mmol ", m^{-2}~s^{-1}, "]")),
       color = "Stomatal Ratio") + 
  theme_minimal() + 
  theme(panel.grid.minor = element_blank()) +
  NULL