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Transform trajectories

Source: R/transformTrajectories.R
transformTrajectories.Rd

The following functions are provided to transform trajectories:

  • Function smoothTrajectories performs multivariate smoothing on trajectory data using a Gaussian kernel.

  • Function centerTrajectories shifts all trajectories to the center of the multivariate space and returns a modified distance matrix.

Usage

smoothTrajectories(
  x,
  survey_times = NULL,
  kernel_scale = 1,
  fixed_endpoints = TRUE
)

centerTrajectories(x, exclude = integer(0))

Arguments

x

An object of class trajectories.

survey_times

A vector indicating the survey time for all surveys (if NULL, time between consecutive surveys is considered to be one)

kernel_scale

Scale of the Gaussian kernel, related to survey times

fixed_endpoints

A logical flag to force keeping the location of trajectory endpoints unmodified

exclude

An integer vector indicating sites that are excluded from trajectory centroid computation. Note: for objects of class cycles, external are excluded by default.

Value

A modified object of class trajectories, where distance matrix has been transformed.

Details

Details of calculations are given in De Cáceres et al (2019). Function centerTrajectories performs centering of trajectories using matrix algebra as explained in Anderson (2017).

References

De Cáceres M, Coll L, Legendre P, Allen RB, Wiser SK, Fortin MJ, Condit R & Hubbell S. (2019). Trajectory analysis in community ecology. Ecological Monographs 89, e01350.

Anderson (2017). Permutational Multivariate Analysis of Variance (PERMANOVA). Wiley StatsRef: Statistics Reference Online. 1-15. Article ID: stat07841.

See also

trajectoryPlot trajectoryMetrics

Author

Miquel De Cáceres, CREAF

Nicolas Djeghri, UBO