coreCT is an R package for programmatic analysis of sediment cores that have been digitized by computed tomography. The package converts Hounsfield Units to material classes (e.g., peat, root/rhizome, sand) and quantifies component masses and volumes. To get started quickly, check out the package vignette.
coreCT output can be easily plotted using the reshape2 and ggplot2 packages (figures below were produced using the same code included in the help file examples).
Figure 1. Volumes of various compartments in a sediment core
coreCT also quantifies the number of root/rhizome particles in a user-defined range of size classes, and calculates the external surface area and volume attributable to each size class. This allows the estimation of belowground plant organ contributions to total soil volume and, dividing by core area, elevation.
Figure 2. Number (left) and combined volume (right) of root/rhizome particles in each of four size classes.
coreCT is available on CRAN and can be installed by typing: install.packages("coreCT")
To install and load the development version of coreCT, run the following commands in R:
install.packages("devtools") # if devtools isn't already installed devtools::install_github("troyhill/coreCT") library(coreCT)
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