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