Plot Ecological Dynamic Regimes

Represents EDR trajectories in the state space. Trajectories and/or states can be displayed in different colors based in a predefined classification or variable.

Usage

plot_edr(
  x,
  trajectories,
  states,
  traj.colors = NULL,
  state.colors = NULL,
  variable = NULL,
  type = "trajectories",
  axes = c(1, 2),
  initial = F,
  ...
)

Arguments

x: Symmetric matrix or dist object containing the dissimilarities between each pair of states of all trajectories in the EDR. Alternatively, data frame containing the coordinates of all trajectory states in an ordination space.
trajectories: Vector indicating the trajectory or site to which each state in x belongs.
states: Vector of integers indicating the order of the states in x for each trajectory.
traj.colors: Specification for the color of all individual trajectories (defaults "grey") or a vector with length equal to the number of different trajectories indicating the color for each individual trajectory.
state.colors: Specification for the color of all trajectory states (defaults equal to traj.colors), vector with length equal to the number of states indicating the color for each trajectory state, or vector of colors used to generate a gradient depending on the values of variable (if type = "gradient").
variable: Numeric vector with equal length to the number of states to be represented using a gradient of state colors (if type = "gradient").
type: One of the following "trajectories", "states", or "gradient".
axes: An integer vector indicating the pair of axes in the ordination space to be plotted.
initial: Flag indicating if the initial state must be plotted (only if type = "states" or type = "gradient")
...: Arguments for generic plot().

Value

plot_edr() permits representing the trajectories of an Ecological Dynamic Regime using different colors for each trajectory or state.

Author

Martina Sánchez-Pinillos

Examples


# Data
state_variables <- EDR_data$EDR1$abundance
d <- EDR_data$EDR1$state_dissim

# Coordinates in classic multidimensional scaling
x <- cmdscale(d, k = 3)

# Plot trajectories 1-10 in "coral", 11-20 in "blue" and 21-30 in "gold"
plot_edr(x = x, trajectories = state_variables$traj,
         states = as.integer(state_variables$state),
         traj.colors = c(rep("coral", 10), rep("royalblue", 10), rep("gold", 10)),
         main = "type = 'trajectories'")
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legend("bottomleft", legend = paste0("Trajectories ", c("1-10", "11-20", "21-30")),
       lty = 1, col = c("coral", "royalblue", "gold"))


# Plot states with different colors depending on the state value
plot_edr(x = x, trajectories = state_variables$traj,
         states = as.integer(state_variables$state),
         traj.colors = NULL,
         state.colors = rep(RColorBrewer::brewer.pal(5, "Blues"),
                            length(unique(state_variables$traj))),
         type = "states", main = "type = 'states'")
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legend("bottomleft", legend = paste0("State ", 1:5),
       pch = 15, col = RColorBrewer::brewer.pal(5, "Blues"))


# Plot states with different colors depending on the abundance of sp1
plot_edr(x = x, trajectories = state_variables$traj,
         states = as.integer(state_variables$state),
         traj.colors = NULL, state.colors = viridis::viridis(5),
         variable = state_variables$sp1,
         type = "gradient", main = "type = 'gradient'", initial = TRUE)
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legend("bottomleft",
       legend = c(paste0("abun sp1 = ", min(state_variables$sp1)),
                  rep(NA, 28),
                  paste0("abun sp1 = ", max(state_variables$sp1))),
       fill = viridis::viridis(30), border = NA, y.intersp = 0.2)

Usage

Arguments

Value

See also

Author

Examples