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Summary plot for trajectory convergence and divergence

Source: R/trajectoryConvergencePlot.R
trajectoryConvergencePlot.Rd

Provides plots to represent trajectory convergence and divergence tests performed by the function trajectoryConvergence.

Usage

trajectoryConvergencePlot(
  x,
  type = "pairwise.asymmetric",
  alpha.filter = NULL,
  traj.colors = "grey",
  traj.names = NULL,
  traj.names.colors = "black",
  ...,
  radius = 1,
  conv.color = "red",
  div.color = "blue",
  half.arrows.size = 1,
  tau.links.transp = 0.3,
  top = "between",
  pointy = FALSE
)

Arguments

x

An object of class trajectories.

type

A string indicating the convergence test, either "pairwise.asymmetric", "pairwise.symmetric" or "both" (see trajectoryConvergence).

alpha.filter

The minimum p-value for a link to be drawn (see trajectoryConvergence). Defaults to NULL (all links drawn).

traj.colors

The colors for the trajectories (circles). Defaults to "grey".

traj.names

The names of trajectories. Defaults to the names provided in x.

traj.names.colors

The color of the names of trajectories on the circles. Defaults to "black".

...

Additional parameters passed to polygon to personalize the circles representing trajectories.

radius

The radius of the circles representing trajectories. Defaults to 1.

conv.color

The color used to mark convergent trajectories. Defaults to "red".

div.color

The color used to mark divergent trajectories. Defaults to "blue".

half.arrows.size

A multiplication coefficient for the size of the arrow heads when representing asymmetric tests results. Defaults to 1.

The transparency of the links representing the tau statistic of the Mann.Kendall test (see trajectoryConvergence).

top

A string indicating if the top of the plotting area should contain a circle representing a trajectory ("circle"), or should be in between two circles ("between"). Defaults to "between".

pointy

Boolean. Should the circles representing trajectories be made pointy (i.e. pointing to the next trajectory)? Useful when trajectories have some order, as in the context of CETA to represent fixed date trajectories (see trajectoryCyclical).

Details

Function trajectoryConvergencePlot provides ways to visualize pairwise convergence and divergence between trajectories using calls to function trajectoryConvergence which performs the tests. In the plots, trajectories are represented by circles. The convergence or divergence between pairs of trajectories are represented by links. If convergence tests are symmetric, the links are simple. If the convergence tests are asymmetric, the links are displayed as half arrows pointing from the trajectory converging or diverging towards the trajectory being approached or diverged from. The width and color hue of the links are proportional to the tau statistic of the Mann.Kendall test performed by the trajectoryConvergence function. Function trajectoryConvergencePlot also offers the possibility to plot both tests at the same time.

See function cycleShiftArrows for additional graphical elements to be displayed when conducting CETA.

See also

trajectoryConvergence, cycleShiftArrows

Author

Nicolas Djeghri, UBO

Miquel De Cáceres, CREAF

Examples

data("avoca")
avoca_D_man <- vegclust::vegdiststruct(avoca_strat, 
                                       method ="manhattan", 
                                       transform = function(x){log(x+1)})
years <- c(1971, 1974, 1978, 1983, 1987, 1993, 1999, 2004, 2009)
avoca_times <- years[avoca_surveys]
avoca_x <- defineTrajectories(d = avoca_D_man,  
                              sites = avoca_sites, 
                              times = avoca_times)

#Raw output with asymmetric convergence test (default)
trajectoryConvergencePlot(avoca_x)


#More refined output with both type of tests and only plotting significant 
#test results (p-value < 0.05)
trajectoryConvergencePlot(avoca_x,
                          type = "both",
                          alpha.filter = 0.05)


#Much more refined output with nicer colors, bigger half arrows, 
#personalized trajectory names, controlling the size of circles representing 
#trajectories and border customization.
trajectoryConvergencePlot(avoca_x,type = "both",alpha.filter = 0.05,
                          half.arrows.size = 1.5, 
                          conv.color = "orangered",
                          div.color = "dodgerblue",
                          radius = 1.2, 
                          traj.colors = "black",border = "white",lwd = 2,
                          traj.names = LETTERS[1:8],traj.names.colors = "white")