knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
This is the pre-process code for the SDEF_roots_pre_aggregation
dataset.
# 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_data_raw") # Load raw root data. root_data <- SDEF_root_data_raw # Shorten variable name for convenience. colnames(root_data) <- ifelse( colnames(root_data) == "tile", "frame", colnames(root_data) ) # Change column name to 'frame', that's what works with frame depth function root_data <- SDEF.analysis::ConvertFrameDepth(data = root_data) # ConvertFrameDepth adds a real_depth column, which is depth of the # observed root in centimeters below ground level. root_data <- root_data[-which(root_data[["real_depth"]] > 40), ] # Only 4 observations for depth bin 5 - dropped those. # Add site - first 3 tubes are Adenostoma plots, other 3 are grass site <- root_data[["tube"]] site <- ifelse(site < 4, "adenostoma", site) site <- ifelse(site == "adenostoma", site, "grass") root_data <- data.frame(site, root_data) # Add depth-bin: 0-9.99 (1), 10-19.99 (2), 20-29.99 (3), # 30-39.99 (4), 40-49.99 (5), 50-59.99 (6). depth_bin <- rep(4, nrow(root_data)) #depth_bin[which(root_data[["real_depth"]] < 50)] <- 5 #depth_bin[which(root_data[["real_depth"]] < 40)] <- 4 depth_bin[which(root_data[["real_depth"]] < 30)] <- 3 depth_bin[which(root_data[["real_depth"]] < 20)] <- 2 depth_bin[which(root_data[["real_depth"]] < 10)] <- 1 root_data <- data.frame(root_data, depth_bin) SDEF_roots_pre_process <- root_data #devtools::use_data(SDEF_roots_pre_process)
End script!
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