Package: diffval 1.1.0

Tiago Monteiro-Henriques

diffval: Vegetation Patterns

Find, visualize and explore patterns of differential taxa in vegetation data (namely in a phytosociological table), using the Differential Value (DiffVal). Patterns are searched through mathematical optimization algorithms. Ultimately, Total Differential Value (TDV) optimization aims at obtaining classifications of vegetation data based on differential taxa, as in the traditional geobotanical approach. The Gurobi optimizer, as well as the R package 'gurobi', can be installed from <https://www.gurobi.com/products/gurobi-optimizer/>. The useful vignette Gurobi Installation Guide, from package 'prioritizr', can be found here: <https://prioritizr.net/articles/gurobi_installation_guide.html>.

Authors:Tiago Monteiro-Henriques [aut, cre], Jorge Orestes Cerdeira [aut], Fundação para a Ciência e a Tecnologia, Portugal [fnd]

diffval_1.1.0.tar.gz
diffval_1.1.0.tar.gz(r-4.5-noble)diffval_1.1.0.tar.gz(r-4.4-noble)
diffval_1.1.0.tgz(r-4.4-emscripten)diffval_1.1.0.tgz(r-4.3-emscripten)
diffval.pdf |diffval.html✨
diffval/json (API)
NEWS

# Install 'diffval' in R:

install.packages('diffval', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://gitlab.com/point-veg/diffval

Datasets:

taxus_bin - _Taxus baccata_ forests

On CRAN:

1.70 score 233 downloads 10 exports 0 dependencies

Last updated 2 years agofrom:2383108ce9. Checks:2 OK, 1 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 13 2025
R-4.5-linux	OK	Mar 13 2025
R-4.4-linux	NOTE	Mar 13 2025

Exports:bigdata_tdv explore_tabulation identical_partition optim_tdv_gurobi_k_2 optim_tdv_hill_climb optim_tdv_simul_anne partition_tdv_grasp partition_tdv_grdtp tabulation tdv

Dependencies:

Citation

To cite package ‘diffval’ in publications use:

Monteiro-Henriques T, Cerdeira J (2023). diffval: Vegetation Patterns. R package version 1.1.0, https://CRAN.R-project.org/package=diffval.

Corresponding BibTeX entry:

  @Manual{,
    title = {diffval: Vegetation Patterns},
    author = {Tiago Monteiro-Henriques and Jorge Orestes Cerdeira},
    year = {2023},
    note = {R package version 1.1.0},
    url = {https://CRAN.R-project.org/package=diffval},
  }

Readme and manuals

diffval

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.

Acknowledgements

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

Installation

You can install the development version of the package from GitLab.

remotes::install_gitlab("point-veg/diffval")

Help Manual

Help page	Topics
The Total Differential Value of a big phytosociological data set	bigdata_tdv
Interactively explore a tabulation of a phytosociological matrix	explore_tabulation
Do the vectors represent the same k-partition?	identical_partition
Total Differential Value optimization using Gurobi	optim_tdv_gurobi_k_2
Total Differential Value optimization using Hill-climbing algorithms	optim_tdv_hill_climb
Total Differential Value optimization using a Simulated Annealing (and GRASP) algorithm(s)	optim_tdv_simul_anne
Obtain a partition using a GRASP algorithm	partition_tdv_grasp
Obtain a partition using a Greedy-type algorithm	partition_tdv_grdtp
Rearrange a phytosociological table, showing differential taxa on top	tabulation
_Taxus baccata_ forests	taxus_bin
The Total Differential Value of a phytosociological table	tdv