inst/old_files/2018_01_09_RootBiomass_SDEF.R

In bmcnellis/SDEF.analysis: Data Analysis for 2016 San Dimas Experimental Forest Project

Biomass_Script_Wrapper <- function() {
  source('~/docs/R_workspace/SDEF.analysis/R/CalculateBioDensity.R')
  source('~/docs/R_workspace/SDEF.analysis/R/CalculateCarbonContent.R')
  source('~/docs/R_workspace/SDEF.analysis/R/ConvertFrameDepth.R')

  # Load data
  setwd("./data")
  data.root <- read.table("SDEF_2017_RootLengths.txt", sep="\t", header=TRUE)
  data.root$date <- as.character(data.root$date)
  data.root$date <- as.Date(data.root$date, format="%m/%d/%Y")
  data.ash <- read.table("SDEF_2016_RootAshWeights.txt", sep="\t", header=TRUE)
  colnames(data.root) <- ifelse(colnames(data.root) == "tile", "frame", colnames(data.root))

  data.root <- ConvertFrameDepth(data=data.root)
  data.ash <- CalculateCarbonContent(data=data.ash)
  # Frame height 6.75mm, frame width 9.0 mm
  data.root <- CalculateBioDensity(data=data.root, frame.size = c(6.75, 9.0, 0.74), scale="tube")
  data <- data.root
  biomass.convert <- c(0.21, 0.22, 0.31)
  names(biomass.convert) <- c("grass", "shrub", "tree")
  # Calculation section ####
  biovolume <- (pi * ((data$diameter / 2) ^ 2)) * data$length # Units in mm^3
  biovolume <- biovolume / 1000 # Convert mm^3 to cm^3
  convert <- vector(mode="character", length=nrow(data))
  for (i in names(biomass.convert)) {
    convert <- sub(x=data[["veg_type"]], pattern=i,
                   replacement=names(biomass.convert)[which(names(biomass.convert) == i)]
    )
  }
  biomass <- biovolume * biomass.convert[data[["veg_type"]]] # Conversion factor is g per cm^3
  # This will convert units to grams of biomass
  data <- data.frame(data, biovolume, biomass)
  data$real_depth <- data$real_depth * -1
  #plot biomass
  library(ggplot2)
  library(reshape2)
  data_grass <- data[which(data$plot == "grass"), ]
  bio_plot <- ggplot(data_grass, aes(real_depth, biomass))
  bio_plot <- bio_plot + stat_smooth()
  depth_plot <- ggplot(data_grass, aes(date, real_depth))
  depth_plot <- depth_plot + geom_tile(aes(fill = biomass))
  if (scale == "root") {
    message("Returning root-scale data... Done")
    return(data)
  }
  biodensity <- data.frame(matrix(ncol=6, nrow=0))
  colnames(biodensity) <- c("tube", "date", "sum_biovolume", "sum_biomass", "mean_depth",
                            "tube_biodensity")

  # end
}