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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This is the code for part of the SDEF root data processing. Pre-processed data is taken from data(SDEF_roots_pre_process) and biomass is calculated on a per-root basis. This document wasn't knit, it's mostly for archival purposes.

# Analyze root data, make table of 'site', 'date', 'depth_bin', 'biomass',
# and standard deviation of depth_bina across site
library(SDEF.analysis)
data("SDEF_root_ash_weights") # Load ash weight data.
data("SDEF_roots_pre_process") # Load preaggregated data
data_root <- SDEF_roots_pre_process
# Calculate biodensity/C density from root ashing data
data_ash <- SDEF_root_ash_weights
data_ash <- SDEF.analysis::CalculateCarbonContent(data = data_ash)
# Biodensity needs a veg type column:
veg_type <- rep("shrub", nrow(data_root))
veg_type[which(data_root[["site"]] == "grass")] <- "grass"
data_root <- data.frame(veg_type, data_root)
# 'Site' also needs to be 'plot'
colnames(data_root)[which(colnames(data_root) == "site")] <- "plot"
# Calculate root biodensity on a per-root basis
# Frame height 6.75mm, frame width 9.0 mm
data_root <- SDEF.analysis::CalculateBioDensity(data = data_root,
                                                frame.size = c(6.75, 9.0, 0.78),
                                                scale = "root")
# Put the df back to how it was...
data_root <- data_root[, -which(colnames(data_root) == "veg_type")]
colnames(data_root)[which(colnames(data_root) == "plot")] <- "site"
# Drop frame, root, real_depth, and biovolume
drops <- c("frame", "root", "real_depth", "biovolume")
data_root <- data_root[, -which(colnames(data_root) %in% drops)]
SDEF_roots_pre_aggregation <- data_root
#devtools::use_data(SDEF_roots_pre_aggregation)

End script!

bmcnellis/SDEF.analysis documentation built on June 4, 2019, 10 a.m.