Fitting pressure-volume curves

This package follows the Prometheus wiki spreadsheet from Sack and Pasquet-Kok at:

https://prometheusprotocols.net/function/water-relations/pressure-volume-curves/leaf-pressure-volume-curve-parameters/

For references, see Koide et al. 2000, Sack et al. 2003, and Tyree & Hammel 1972.

library(dplyr)
library(photosynthesis)

# Read in data
dat = system.file("extdata", "PV_curve.csv", package = "photosynthesis") |>
  read.csv()

# Fit one PV curve
fit = fit_PV_curve(filter(dat, ID == "L2"))

# See fitted parameters
fit[[1]]

##        SWC      PI_o psi_TLP  RWC_TLP      eps       C_FT      C_TLP  C_FTStar
## 1 2.438935 -1.399302   -1.75 88.67684 12.20175 0.06456207 0.09923338 0.5161476

# Plot water mass graph
# fit[[2]]

# Plot PV Curve
# fit[[3]]

#Fit all PV curves in a file
fits = fit_many(
  dat,
  group = "ID",
  funct = fit_PV_curve,
  progress = FALSE
)

## Warning: `fit_many()` was deprecated in photosynthesis 2.1.3.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

# See parameters
fits[[1]][[1]]

##        SWC      PI_o psi_TLP  RWC_TLP      eps       C_FT      C_TLP  C_FTStar
## 1 2.438935 -1.399302   -1.75 88.67684 12.20175 0.06456207 0.09923338 0.5161476

# See water mass - water potential graph
# fits[[1]][[2]]

# See PV curve
# fits[[1]][[3]]

# Compile parameter outputs
pars = compile_data(data = fits, output_type = "dataframe", list_element = 1)

# Compile the water mass - water potential graphs
graphs1 = compile_data(data = fits, output_type = "list", list_element = 2)

# Compile the PV graphs
graphs2 = compile_data(data = fits, output_type = "list", list_element = 3)

References

Koide RT, Robichaux RH, Morse SR, Smith CM. 2000. Plant water status, hydraulic resistance and capacitance. In: Plant Physiological Ecology: Field Methods and Instrumentation (eds RW Pearcy, JR Ehleringer, HA Mooney, PW Rundel), pp. 161-183. Kluwer, Dordrecht, the Netherlands.

Sack L, Cowan PD, Jaikumar N, Holbrook NM. 2003. The ‘hydrology’ of leaves: co-ordination of structure and function in temperate woody species. Plant, Cell & Environment 26:1343-1356

Tyree MT, Hammel HT. 1972. Measurement of turgor pressure and water relations of plants by pressure bomb technique. Journal of Experimental Botany 23:267-282.

Joseph R. Stinziano and Christopher D. Muir

2023-08-15

References