Find, visualize and explore patterns of differential taxa in vegetation data (namely in a phytosociological table), using the Differential Value (DiffVal). DiffVal captures the degree of exclusiveness of a taxon to each of the different clusters of relevés of a sorted phytosociological table. The patterns of differential taxa are searched through mathematical optimization algorithms, resorting the table while maximizing the sum of the DiffVal for all the taxa in the table, i.e., maximizing the Total Differential Value (TotDiffVal or TDV). Ultimately, TDV optimization aims at obtaining classifications of vegetation data based on differential taxa, as in the traditional phytosociological (or geobotanical) approach. The Gurobi optimizer, as well as the R package ‘gurobi’, can be installed from https://www.gurobi.com/products/gurobi-optimizer/. The vignette “Gurobi Installation Guide”, from package ‘prioritizr’, is useful and can be found here: https://prioritizr.net/articles/gurobi_installation_guide.html.
TMH was funded by the European Social Fund (POCH and NORTE 2020) and by National Funds (MCTES), through a FCT – Fundação para a Ciência e a Tecnologia (Portuguese Foundation for Science and Technology) postdoctoral fellowship (SFRH/BPD/115057/2016), as well as by National Funds, through the same foundation, under the project UIDB/04033/2020 (CITAB - Centre for the Research and Technology of Agro-Environmental and Biological Sciences). JOC was financially supported by FCT through the projects UIDB/MAT/00297/2020, UIDP/MAT/00297/2020 (Centro de Matemática e Aplicações).
Portela-Pereira E, Monteiro-Henriques T, Casas C, Forner N, Garcia-Cabral I, Fonseca JP & Neto C 2021. Teixedos no noroeste da Península Ibérica. Finisterra LVI(117): 127–150. DOI: 10.18055/FINIS18102 https://revistas.rcaap.pt/finisterra/article/view/18102
You can install the development version of the package from GitLab.
remotes::install_gitlab("point-veg/diffval")