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) (https://doi.org/10.1002/ecm.1350).
Extension of community trajectory analysis: Sturbois et al. (2021) (https://doi.org/10.1016/j.ecolmodel.2020.109400).
Generalisation to stable isotope data: Sturbois et al. (2021) (https://doi.org/10.1002/ecm.1501).
Application of ETA for the assessement of ecological status: Sturbois et al. (under review).
Package installation
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")Additionally, users can have help to run package functions directly as package vignettes, by forcing their inclusion in installation:
remotes::install_github("emf-creaf/ecotraj",
build_opts = c("--no-resave-data", "--no-manual"),
build_vignettes = TRUE)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.
Sturbois, A., De Cáceres, M., Sánchez-Pinillos, M., Schaal, G., Gauthier, O., Le Mao, P., Ponsero, A., & Desroy, N. (2021). Extending community trajectory analysis : New metrics and representation. Ecological Modelling, 440, 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.
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. (under review). Ecological Quality Assessment: a general multivariate framework to report the quality of ecosystems and their dynamics with respect to reference conditions.