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

# Fitting hydraulic vulnerability curves

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

#### 2024-11-24

Current approach fits a sigmoidal model and calculates hydraulic parameters from the curve fit (Pammenter & Van der Willigen 1998; Ogle et al. 2009).

    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]])

    ##
    ## Call:
    ## lm(formula = H_log ~ psi, data = data[data$H_log < Inf, ])
    ##
    ## Residuals:
    ##        2        3        4        5        6
    ##  0.40236 -0.63441  0.01791  0.09292  0.12121
    ##
    ## Coefficients:
    ##             Estimate Std. Error t value Pr(>|t|)
    ## (Intercept)   5.1700     0.5344   9.675  0.00234 **
    ## psi          -1.0884     0.1212  -8.982  0.00291 **
    ## ---
    ## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    ##
    ## Residual standard error: 0.4427 on 3 degrees of freedom
    ## Multiple R-squared:  0.9642, Adjusted R-squared:  0.9522
    ## F-statistic: 80.68 on 1 and 3 DF,  p-value: 0.002912

    # Return Weibull model summary
    summary(fit[[4]]) #expecting a = 4.99, b = 3.22

    ##
    ## Formula: K.Kmax ~ exp(-((psi/a)^b))
    ##
    ## Parameters:
    ##   Estimate Std. Error t value Pr(>|t|)
    ## a   5.3160     0.0902   58.93 4.96e-07 ***
    ## b   2.7778     0.2393   11.61 0.000315 ***
    ## ---
    ## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    ##
    ## Residual standard error: 0.02867 on 4 degrees of freedom
    ##
    ## Number of iterations to convergence: 8
    ## Achieved convergence tolerance: 1.49e-08

    # Return model parameters with 95% confidence intervals
    fit[[2]]

    ##           Value Parameter     Curve
    ## b...1  4.749922         b Sigmoidal
    ## a...2 -1.088445         a Sigmoidal
    ## b...3  2.777799         b   Weibull
    ## a...4  5.315979         a   Weibull

    # Return hydraulic parameters
    fit[[3]]

    ##        P25      P50      P88      P95      S50       Pe     Pmax      DSI
    ## 1 3.740581 4.749922 6.580451 7.455102 27.21113 2.912439 6.587406 3.674967
    ## 2 3.394637 4.658873 6.967591 7.890836 20.66405 2.239211 7.078534 4.839322
    ##       Curve
    ## 1 Sigmoidal
    ## 2   Weibull

    # 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]])

    ##
    ## Call:
    ## lm(formula = H_log ~ psi, data = data[data$H_log < Inf, ])
    ##
    ## Residuals:
    ##       44       45       46       47       48
    ## -0.15427  0.06136  0.23623  0.20568 -0.34900
    ##
    ## Coefficients:
    ##             Estimate Std. Error t value Pr(>|t|)
    ## (Intercept)  5.72729    0.34666   16.52 0.000483 ***
    ## psi         -1.41591    0.07861  -18.01 0.000373 ***
    ## ---
    ## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
    ##
    ## Residual standard error: 0.2872 on 3 degrees of freedom
    ## Multiple R-squared:  0.9908, Adjusted R-squared:  0.9878
    ## F-statistic: 324.4 on 1 and 3 DF,  p-value: 0.0003733

    # Return sigmoidal model output
    fits[[1]][[2]]

    ##           Value Parameter     Curve
    ## b...1  4.044964         b Sigmoidal
    ## a...2 -1.415905         a Sigmoidal
    ## b...3  3.905565         b   Weibull
    ## a...4  4.580836         a   Weibull

    # Return hydraulic parameters
    fits[[1]][[3]]

    ##        P25      P50      P88      P95      S50       Pe     Pmax      DSI
    ## 1 3.269056 4.044964 5.452141 6.124509 35.39764 2.632440 5.457488 2.825047
    ## 2 3.329677 4.170508 5.552841 6.066678 32.45566 2.629945 5.711071 3.081127
    ##       Curve
    ## 1 Sigmoidal
    ## 2   Weibull

    # 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)

# References

Ogle K, Barber JJ, Willson C, Thompson B. 2009. Hierarchical statistical modeling of xylem vulnerability to cavitation. New Phytologist 182:541-554.

Pammenter NW, Van der Willigen CV. 1998. A mathematical and statistical analysis of the curves illustrating vulnerability of xylem to cavitation. Tree Physiology 18:589-593.