Functions for agricultural data analysis.
CateNelson.R. Graphical function used to classify a continuous index and a continuous response to a binary perspective. I namely used it in the paper Plant ionome diagnosis using sound balances: case study with mango (Mangifera Indica).
codadend2.R. Function similar to compositions::CoDaDendrogram, but with extended capabilities, like plotting densities or boxplots per group over the horizontal bars.
compci.R. A function that computes confidence intervals on compositional data based on Monte-Carlo simulations. To be used carefully.
DRIS.R. A function that conpute DRIS indices with several methods to assess the leaf nutritionnal status of plants.
ilrDefinition.R. Using a sequential binary partition, this function creates a vector of strings representing balances of components computed as isometric log-ratios in the form of, for example, [A,B | C,D] where components A and B is balanced with components C and D.
ilrNA.R. When computing ilrs through BDL compositional values, the compositions::ilr function sets the ilr to 0. However, often, BDL values origins from missing data parsed through the compositions::acomp function. Where there is at least one NA in a balance in the original data set, this function sets the ilr value to be also NA. This function is inefficient and can sometimes be a long process.
is.inpoly.R. Does what is says it does.
plotDA_gg.R contains a function for ploting LDA biplots with ggplot2, while plotDA_trad.R does the same with basic R plot.
sign1_ref.R. For details check the paper Plant ionome diagnosis using sound balances: case study with mango (Mangifera Indica).