Skip to contents

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.

  • Function averageTrajectories creates an "average" trajectory where the position of each observation is the average of the position of the corresponding observations of the input trajectories.

  • Function interpolateTrajectories relocates trajectory ecological states to those corresponding to input times, via interpolation.

Usage

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

centerTrajectories(x, exclude = integer(0))

averageTrajectories(
  x,
  group = NULL,
  keep_members = FALSE,
  output_name = "average"
)

interpolateTrajectories(x, times)

Arguments

x

An object of class trajectories (or of a sub-class such as cycles). Function averageTrajectories requires synchronous input 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 observations that are excluded from trajectory centroid computation. Note: for objects of class cycles, external are excluded by default.

group

Character vector of the sites (trajectories) to be averaged. If NULL all trajectories contribute to the average

keep_members

Boolean flag to keep the group member trajectories in the result

output_name

A string with the name for the average trajectory

times

A numeric vector indicating new observation times for trajectories. Values should be comprised between time limits of the original trajectories.

Value

A modified object of class trajectories, where distance matrix has been transformed. When calling interpolateTrajectories and averageTrajectories, also the number of observations and metadata is likely to be affected.

Details

We recommend reading the article "Transforming trajectories" on the package website prior to use these functions.

Details of calculations for trajectory centering are given in De Cáceres et al (2019). Functions centerTrajectories and averageTrajectories perform centering/averaging of trajectories using matrix algebra as explained in Anderson (2017).

When using transformation functions on objects of class cycles or fd.trajectories, the corresponding transformations are applied to trajectory subsections (e.g. cycles) instead of being applied to the whole trajectory.

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 trajectoryComparison

Author

Miquel De Cáceres, CREAF

Nicolas Djeghri, UBO