R/plot_nonrec64.R

In zhujiedong/lrc_start: light response curve fit start values For LI-6400 and LI-6800

#' plot for nonrectangular hyperbola–based models
#' @description plots of different parameter values in one plot, to determin the range
#' of start values, plot_nonrec64 for LI-6400 data, and plot_nonrec68 for LI-6800 data.
#'  
#' @param df dataframe for the LI-6400 or LI-6800 measured data
#' @param x is the PAR intensity of the leaf
#' @param Am is the gross photosynthetic rate
#' @param alpha is  quantum yield at low light intensity
#' @param theta is the convexity
#' @param Rd dark respiration rate 
#' 
#' @details use ggplot2 geom_smooth to fit the calculate data, generally the fit method
#' is loess, but it does not matter, as we just want to see these data overlap with the 
#' measured ones as much as possible.
#' @examples
#' \dontrun{
#' plot_nonrec64(lrc64, Am = 17, Rd = 3)
#' plot_nonrec68(lrc68, Am = 12, alpha = 0.01, theta = 0.8)
#' }
#' @export
#' @import ggplot2
#' @importFrom purrr pmap

plot_nonrec64 <- function(df, Am=max(df$Photo)-min(df$Photo), Rd=min(df$Photo), alpha = 0.01,
                        theta = 0.8){
    lrc_Q <- df$PARi
    lrc_A <- df$Photo
    n <- length(lrc_A)
    
    alph <- seq(alpha, n * alpha, by = alpha)
    alp <- paste0("a=", as.character(alph))
    alpn <- rep(alp, each = n)
    
    paras <- data.frame(alpha = rep(alph, each = n), 
                        x = rep(lrc_Q, n), Am = rep(Am, n), 
                        Rd = rep(-Rd, n), theta = rep(theta, n))
    
    x <- lrc_Q
    y <- unlist(pmap(paras, fun_nonrec))
    
    plot_data <- data.frame(x = rep(lrc_Q, n + 1), y = c(lrc_A, y), 
                            alpha = factor(c(rep("measured", n), alpn),
                                       level = c("measured", alp)))
    
    plot64 <- ggplot(data = plot_data, aes(x, y, group = alpha, color=alpha)) + 
      geom_point() + 
      geom_smooth(se = FALSE) + theme_bw()
    
    plot64
  }