{tealeaves} is a lightweight R package to model leaf temperature using leaf energy balance. It uses the R package units to ensure that parameters are properly specified and transformed before calculations. It allows separate lower and upper surface conductances to heat and water vapour, so sensible and latent heat loss are calculated for each surface separately. It’s straightforward to model leaf temperature over environmental gradients such as light, air temperature, humidity, and wind, or trait gradients such as leaf size or stomatal conductance.

From CRAN

`install.packages("tealeaves")`

or from GitHub

```
install.packages("remotes")
::install_github("cdmuir/tealeaves") remotes
```

And load tealeaves

`library("tealeaves")`

The {tealeaves} package solves for leaf temperature given a set of environmental conditions and leaf traits by balancing the leaf energy budget. There are two main steps to using {tealeaves}:

- define leaf parameters, environmental parameters, and physical constants; and
- solve for the a leaf temperature that balances its energy budget
(
`tleaf`

and`tleaves`

for single and multiple parameter sets, respectively).

In this vignette, I’ll show you how to:

- run a minimum worked example using default parameters
- replace default parameters
- solve for leaf temperature along an environmental gradient

Note that my examples use a lot tidyverse syntax, especially the pipe
operator `%>%`

. These are not required to use {tealeaves},
but you can learn more about the the tidyverse here and the `%>%`

more specifically here.

You can use the default parameter settings and solve for leaf
temperature in a single leaf using the `make_*()`

functions
and `tleaf()`

.

```
library(magrittr)
library(tealeaves)
# Leaving the make_* functions empty will automatically default to defaults
# parameters.
<- make_leafpar() # leaf parameters
leaf_par <- make_enviropar() # environmental parameters
enviro_par <- make_constants() # physical constants
constants
<- tleaf(leaf_par, enviro_par, constants, quiet = TRUE)
T_leaf
%>% knitr::kable() T_leaf
```

T_leaf | value | convergence | R_abs | S_r | H | L | E | Ar | Gr | Re | g_bw |
---|---|---|---|---|---|---|---|---|---|---|---|

301.4181 [K] | 0 | 0 | 1363.813 [W/m^2] | 907.9499 [W/m^2] | 107.3552 [W/m^2] | 348.5078 [W/m^2] | 0.00794791 [mol/m^2/s] | 0.0048272 | 788182.4 | 12778.08 | 0.0297282 |

You can look at default parameters settings in the manual (run
`?make_parameters`

). These defaults are reasonable, but of
course you will probably want to use different choices and allow some
parameters to vary. Here, I’ll demonstrate how to replace a default. In
the next section, I’ll show you how to set up a gradient of parameter
values over which to solve for leaf temperature.

```
# 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)
<- make_leafpar(
leaf_par 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)
<- make_enviropar(
enviro_par 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'!
<- make_constants()
constants
<- tleaf(leaf_par, enviro_par, constants, quiet = TRUE)
T_leaf
%>% knitr::kable() T_leaf
```

T_leaf | value | convergence | R_abs | S_r | H | L | E | Ar | Gr | Re | g_bw |
---|---|---|---|---|---|---|---|---|---|---|---|

302.1106 [K] | 0 | 0 | 1363.813 [W/m^2] | 916.3234 [W/m^2] | 130.0263 [W/m^2] | 317.4631 [W/m^2] | 0.007244854 [mol/m^2/s] | 0.0055546 | 903289.3 | 12752.29 | 0.0297445 |

In the previous two examples, I used the `tleaf`

function
to solve for a single parameter set. In most cases, you’ll want to solve
for many parameter sets. The function `tleaves`

generalizes
`tleaf`

and makes it easy to solve for multiple parameter
sets using the same argument structure. All you need to do is specify
multiple values for one or more leaf or environmental parameters and
`tleaves`

uses the `tidyr::crossing`

function to
fit all combinations^{1}.

```
# 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)
<- make_leafpar(
leaf_par 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)
<- make_enviropar(
enviro_par replace = list(
T_air = set_units(c(293.15, 298.15), "K")
)
)
<- make_constants()
constants
# Now there should be 4 combinations (high and low g_sw crossed with high and low T_air)
<- tleaves(leaf_par, enviro_par, constants, progress = FALSE,
T_leaves quiet = TRUE, set_units = FALSE)
%>%
T_leaves ::select(T_air, g_sw, T_leaf) %>%
dplyr::kable() knitr
```

T_air | g_sw | T_leaf |
---|---|---|

293.15 [K] | 2 [umol/m^2/Pa/s] | 300.2217 [K] |

298.15 [K] | 2 [umol/m^2/Pa/s] | 304.2065 [K] |

293.15 [K] | 4 [umol/m^2/Pa/s] | 298.3474 [K] |

298.15 [K] | 4 [umol/m^2/Pa/s] | 302.1106 [K] |

It can take a little while to model many different parameter sets. If
you have multiple processors available, you can speed things up by
running simulations in parallel. In the `tealeaves`

function,
simply use the `parallel = TRUE`

argument to simulate in
parallel. Here I’ll provide an example looking at how leaf-to-air
temperature differentials change with air temperature.

```
# 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
<- make_leafpar()
leaf_par
<- make_enviropar(
enviro_par 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")
)
)
<- make_constants()
constants
<- tleaves(leaf_par, enviro_par, constants, progress = FALSE, quiet = TRUE,
tl parallel = TRUE)
$T_air %<>% drop_units() # for plotting
tl$T_leaf %<>% drop_units() # for plotting
tl%<>% dplyr::mutate(Light = dplyr::case_when(
tl 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
```

I welcome comments, criticisms, and especially contributions! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here:

https://github.com/cdmuir/tealeaves/issues

- Please report any issues or bugs.
- License: MIT
- Get citation information for
`tealeaves`

in R doing`citation(package = 'tealeaves')`

- Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Since optimization is somewhat time-consuming, be careful about crossing too many combinations. Use

`progress = TRUE`

to show progress bar with estimated time remaining.↩︎