In emf-creaf/ecotraj: Ecological Trajectory Analysis

knitr::opts_chunk$set(collapse = TRUE, comment = "#>", fig.path = "README-")

Ecological trajectory analysis

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:

Initial presentation of the Ecological Trajectory Analysis (ETA) framework (De Cáceres et al. 2019).
ETA extension of metrics and visualisation modes (Sturbois et al. 2021a).
ETA extension to cyclical trajectory data (Djeghri et al. in prep.).
Application to a multivariate space defined by 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/.

Package functions

The following lists the main package functions, grouped by analysis framework:

Functions for Ecological Trajectory Analysis (ETA)

| Name | Short description | |------|------------------------| | defineTrajectories() | Defines trajectory objects to be analyzed. | | subsetTrajectories() | Subsets trajectories corresponding to selected set of sites or surveys from a dataset containing multiple trajectories. | | smoothTrajectories() | Performs multivariate smoothing on trajectory data using a Gaussian kernel. | | centerTrajectories() | Shifts all trajectories to the center of the multivariate space and returns a modified distance matrix. | | trajectoryLengths() | Calculates lengths of directed segments and total path length of trajectories. | | trajectoryLengths2D() | Calculates lengths of directed segments and total path lengths of trajectories from 2D coordinates given as input. | | trajectorySpeeds() | Calculates speeds of directed segments and total path speed of trajectories. | | trajectorySpeeds2D() | Calculates speeds of directed segments and total path speed of trajectories from 2D coordinates given as input. | | trajectoryAngles() | Calculates the angle between consecutive pairs of directed segments or between segments of ordered triplets of points. | | trajectoryAngles2D() | Calculates the angle between consecutive pairs of directed segments or between segments of ordered triplets of points from 2D coordinates. | | trajectoryConvergence() | Performs the Mann-Kendall trend test on the distances between trajectories or the distance between points of one trajectory to the other. | | trajectoryDirectionality() | Assesses the level directionality of each trajectory. | | trajectoryVariability() | Assesses the internal variability within each trajectory. | | trajectoryDistances() | Estimates distances between pairs of ecosystem trajectories. | | trajectoryShifts() | Calculates trajectory shifts (i.e. advances and delays) between trajectories assumed to follow a similar path but with different speeds or time lags. | | trajectoryPlot() | Draws trajectories in a 2D-plot corresponding to the input coordinates. | | trajectoryPCoA() | Performs principal coordinates analysis and draws trajectories in the ordination scatterplot. | | trajectoryMetrics() | Calculates several (whole path) metrics on trajectories. | | trajectoryWindowMetrics() | Calculates several metrics on subtrajectories defined using moving windows. |

Functions specific for Cyclical Ecological Trajectory Analysis (CETA)

| Name | Short description | |------|------------------------| | extractCycles() | Extracts (i.e. subsets) cycles from cyclical trajectories. | | extractFixedDateTrajectories() | Extracts fixed-date trajectories from cyclical trajectories. | | cycleShifts() | Estimates cyclical shifts (i.e. advances or delays). | | cycleConvexity() | Estimates the degree of convexity of cycles. | | cycleMetrics() | Calculates several (whole path) metrics on cycles. | | cyclePCoA() | Performs Principal Coordinates Analysis and draws cycles in the ordination scatter plot. | | fixedDateTrajectoryPCoA() | Performs Principal Coordinates Analysis and draws fixed date trajectories in the ordination scatter plot. |

Functions for Ecological Quality Assessment (EQA)

| Name | Short description | |------|------------------------| | stateEnvelopeVariability() | Assess the variability of a set of states taken as reference envelope. | | trajectoryEnvelopeVariability() | Assess the variability of a set of trajectories taken as reference envelope. | | compareToStateEnvelope() | Evaluate the ecological quality of stations/observations with respect to a set of states taken as reference envelope. | | compareToTrajectoryEnvelope() | Evaluate the ecological quality of stations/observations with respect to a set of trajectories taken as reference envelope. |

Related package

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).
Djeghri et al (in preparation) Going round in cycles, but going somewhere: Ecological Trajectory Analysis as a tool to decipher seasonality and other cyclical dynamics.
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).