R/fPlotCumuGPPbyYear.R

In ksmiff33/FluxSynthU: Suite of functions to analyze eddy covariance data

#' This function will create a composite plot of cumulative GPP/NEE over time, as well as the first derivative of cumulative GPP, for the purposes of determining the GPP-free period.
#'
#' @export
#' @title Plot time series of cumulative GPP/NEE
#' @param dat dataframe, a specific dataframe format created in function 'FS_fExtractAllCriticalDates' that includes cumulative daily GPP, cumulative NEE, 1st derivative of cumu GPP
#' @param critdat dataframe, a specific dataframe format containing a list of critical dates - created in function 'FS_fExtractAllCriticalDates'
#' @param site.info list, metadata for current site
#' @param years_of_record numeric, vector of unique individual years for current site


fPlotCumuGPPbyYear <- function(dat, critdat, site.info, years_of_record) {
  # Initialize an empty list
  plot.list <- list()


  for (yr in years_of_record) {

    tryCatch(
      expr = {
        Sys.sleep(0.1)

        annotations <- data.frame(
          xpos = c(-Inf),
          ypos =  c(Inf),
          annotateText = yr,
          hjustvar = -0.1,
          vjustvar = 1) #<- adjust


        df <- subset(dat, process_year == yr)
        df.crit <- subset(critdat, process_year == yr)

        # # Define x-axis breaks
        DoYInterval <- 60
        DoYBreaks_Cumu <- df %>%
          select(Year, DoY, cumu.DoY_raw) %>%
          filter(DoY %in% c(1, head(seq(DoYInterval,366,DoYInterval),-1)))

        YearBreaks_Cumu <- DoYBreaks_Cumu %>%
          subset(., DoY == 1)


        colors <- c("ECW" = "#e7d4e8", "SNW" = "#762a83")

        colors <- colors[order(factor(names(colors), levels = c("ECW", "SNW")))]

        if (sum(!is.na(df$deriv.GPP_raw_NA)) == 0) {
          message("")
          message("    * ERROR on process year: ", yr)
          message("      NO data found!")
          message("      (skipping to next process year)")
          message("")
          next
        }



        p1 <- ggplot(df, aes(x = cumu.DoY_raw)) +
          geom_point(alpha=0.4, aes( y= deriv.GPP_raw_NA), color= "#1a9850") +
          geom_line(aes(y = deriv.GPP_smooth), color="#1a9850", size = 1) +
          geom_vline(xintercept=YearBreaks_Cumu$cumu.DoY_raw) +
          scale_x_continuous(name = "DoY", breaks = DoYBreaks_Cumu$cumu.DoY_raw,
                             labels = DoYBreaks_Cumu$DoY) +
          scale_y_continuous(name = "deriv (cumulative GPP)") +
          theme_time() +
          annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf, size=1.5, color = "black") +
          annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf, size=1.5, color = "black") +
          theme(plot.title = element_text(color="black", hjust = 0.5, size=12, face="bold"),
                plot.subtitle = element_text(color="black", hjust = 0.5, size=12),
                strip.background = element_blank(),
                strip.text = element_text(size = 12, face = "bold"),
                axis.line = element_blank(),
                legend.position = "bottom",
                legend.title = element_blank(),
                panel.grid.major = element_line(linetype = "dotted", color = "gray"))


        deriv.plot <- p1 +
          geom_point(data = df.crit, aes(x = cumu.DoY_raw, y = deriv.GPP_smooth, fill = CritThreshold), shape = 21, color= "black", size = 5, stroke = 1) +
          geom_text(data = df.crit, aes(x = cumu.DoY_raw, y = deriv.GPP_smooth, label = DoY), nudge_x = c(-20,20), vjust = -3, fontface = "bold", size = 4) +
          scale_fill_manual(name = "Critical Date", values = colors,
                            breaks = c("ECW", "SNW")) +
          theme(legend.position = "none")



        ## Cumulative NEE/GPP plot
        # Value used to transform the data
        coeff <- 10

        cumu.GPP.plot <- ggplot(data = df, aes(x=cumu.DoY_raw)) +

          geom_line( aes(y=cumu.NEE_raw_NA), size=1, color="black") +
          geom_line( aes(y=cumu.GPP_raw_NA / coeff), size=1, color="#1a9850") +

          geom_point(data = df.crit, aes(x = cumu.DoY_raw, y = cumu.GPP_raw_NA/ coeff, fill = CritThreshold), shape = 21, color= "black", size = 5, stroke = 1) +

          geom_vline(xintercept=YearBreaks_Cumu$cumu.DoY_raw) +
          scale_y_continuous(

            # Features of the first axis
            name = expression(atop("cumulative NEE",paste("(g C ", m^-2,")"))),

            # Add a second axis and specify its features
            sec.axis = sec_axis(~.*coeff, name=expression(atop("cumulative GPP",paste("(g C ", m^-2,")"))))
          ) +

          scale_fill_manual(name = "Critical Date", values = colors,
                            breaks = c("ECW", "SNW")) +
          scale_x_continuous(name = "DoY", breaks = DoYBreaks_Cumu$cumu.DoY_raw,
                             labels = DoYBreaks_Cumu$DoY)  +

          geom_text(data = df.crit, aes(x = cumu.DoY_raw, y = cumu.GPP_raw_NA/ coeff, label = DoY), nudge_x = 0.15, vjust = 3, fontface = "bold", size = 4) +

          theme_time() +
          annotate("segment", x=-Inf, xend=Inf, y=-Inf, yend=-Inf, size=1.5, color = "black") +
          annotate("segment", x=-Inf, xend=-Inf, y=-Inf, yend=Inf, size=1.5, color = "black") +
          theme(plot.title = element_text(color="black", hjust = 0.5, size=12, face="bold"),
                plot.subtitle = element_text(color="black", hjust = 0.5, size=12),
                strip.background = element_blank(),
                strip.text = element_text(size = 12, face = "bold"),
                axis.line = element_blank(),
                axis.title.y.right = element_text(size = 14, angle = 90, color="#1a9850"),
                axis.text.y.right = element_text(size = 12, color ="#1a9850"),
                legend.position = "none",
                panel.grid.major = element_line(linetype = "dotted", color = "gray"))


        cumu.GPP.plot <- cumu.GPP.plot +
          annotate("text", x = YearBreaks_Cumu$cumu.DoY_raw, y = Inf,
                   label=YearBreaks_Cumu$Year, hjust = -0.5, vjust = 1, fontface = "bold", size = 6)


        cumu.GPP.composite.plot <- cumu.GPP.plot + deriv.plot + plot_layout(ncol =1)

        cumu.GPP.composite.plot <- wrap_elements(cumu.GPP.composite.plot)

        cumu.GPP.composite.plot.final <- fAddSiteMeta2Plot(cumu.GPP.composite.plot, site = site.info$site,
                                                           db = site.info$db,
                                                           longname = site.info$info,
                                                           country = site.info$country,
                                                           lat = site.info$lat,
                                                           long = site.info$long,
                                                           MAT = site.info$MAT,
                                                           MAP = site.info$MAP,
                                                           IGBP = site.info$IGBP)
        # browser()

        plot.list[[as.character(yr)]]  <-  cumu.GPP.composite.plot.final


      },
      # If loop fails for a particular year,
      error = function(e){
        message("")
        message("    * ERROR on process year: ", yr)
        message("      (NAs will be assigned to data during missing years)")
        message("")
        print(e)
      }
    )

  }

  return(plot.list)

}