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Ecological trajectory analysis

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Introduction

Package ecotraj is a package providing Ecological Trajectory Analysis (ETA), a framework to assist ecologists in the analysis of temporal changes in ecosystems defined on a chosen multivariate space.

ETA is related to the following publications:

  • First presentation of the community trajectory analysis framework (De Cáceres et al. 2019).

  • Extension of community trajectory analysis (Sturbois et al. 2021a).

  • Generalization to stable isotope data (Sturbois et al. 2021b).

  • Application of ETA framework for the assessment of ecological quality (Sturbois et al. 2023).

Package installation and documentation

Package ecotraj can be found at CRAN. In addition, the latest stable ecotraj R package can also be installed from GitHub as follows:

remotes::install_github("emf-creaf/ecotraj")

Although the package comes with function documentation, articles explaining how to use the package can be found at https://emf-creaf.github.io/ecotraj/.

The R package ecoregime, by Martina Sánchez-Pinillos, implements the Ecological Dynamic Regimes (EDR) framework to characterize and compare groups of ecological trajectories in multidimensional spaces defined by ecosystem state variables.

References

  • De Cáceres, M., Coll, L., Legendre, P., Allen, R.B., Wiser, S.K., Fortin, M.J., Condit, R. & Hubbell, S. (2019). Trajectory analysis in community ecology. Ecological Monographs 89, e01350 (https://doi.org/10.1002/ecm.1350).

  • Sturbois, A., De Cáceres, M., Sánchez-Pinillos, M., Schaal, G., Gauthier, O., Le Mao, P., Ponsero, A., & Desroy, N. (2021a). Extending community trajectory analysis : New metrics and representation. Ecological Modelling, 440, 109400 (https://doi.org/10.1016/j.ecolmodel.2020.109400).

  • Sturbois, A., Cucherousset, J., De Cáceres, M., Desroy, N., Riera, P., Carpentier, A., Quillien, N., Grall, J., Espinasse, B., Cherel, Y., Schaal, G. (2021). Stable Isotope Trajectory Analysis (SITA) : A new approach to quantify and visualize dynamics in stable isotope studies. Ecological Monographs, 92, e1501 (https://doi.org/10.1002/ecm.1501).

  • Sturbois, A., De Cáceres, M., Bifolchi, A., Bioret, F., Boyé, A., Gauthier, O., Grall, J., Grémare, A., Labrune, C., Robert, A., Schaal, G., Desroy, N. (2023). Ecological Quality Assessment: a general multivariate framework to report the quality of ecosystems and their dynamics with respect to reference conditions. Ecosphere 14, e4726 (https://doi.org/10.1002/ecs2.4726).