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## ---- message = FALSE---------------------------------------------------------
library(dplyr)
library(photosynthesis)
# Read in data
dat = system.file("extdata", "hydraulic_vulnerability.csv", package = "photosynthesis") |>
read.csv() |>
mutate(ID = paste(Plot, Tree, sep = "_")) |>
rename(psi = P)
# Fit hydraulic vulnerability curve
fit = fit_hydra_vuln_curve(
filter(dat, Tree == 5, Plot == "Irrigation"),
start_weibull = list(a = 2, b = 1),
title = "Irrigation 5"
)
# Return Sigmoidal model summary
summary(fit[[1]])
# Return Weibull model summary
summary(fit[[4]]) #expecting a = 4.99, b = 3.22
# Return model parameters with 95% confidence intervals
fit[[2]]
# Return hydraulic parameters
fit[[3]]
# Return graph
# fit[[5]]
# Fit many curves
fits = fit_many(
data = dat,
group = "ID",
start_weibull = list(a = 4, b = 2),
funct = fit_hydra_vuln_curve,
progress = FALSE
)
# Return model summary
summary(fits[[1]][[1]])
# Return sigmoidal model output
fits[[1]][[2]]
# Return hydraulic parameters
fits[[1]][[3]]
# Return graph
# fits[[1]][[5]]
# Compile parameter outputs
pars = compile_data(data = fits, output_type = "dataframe", list_element = 3)
# Compile graphs
graphs = compile_data(data = fits, output_type = "list", list_element = 5)
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