Author: Joseph R. Stinziano and Christopher D. Muir
Date: 2024-11-24

# Fitting pressure-volume curves

#### Joseph R. Stinziano and Christopher D. Muir

#### 2024-11-24

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
    )

    # 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.