ecoregime (version 0.2.1)

plot_edr: Plot Ecological Dynamic Regimes

Description

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,
  ...
)

Value

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

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().

Author

Martina Sánchez-Pinillos

See Also

plot.RETRA() for plotting representative trajectories in an ordination space representing the state space of the EDR.

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'")
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'")
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$sp1,
         type = "gradient", main = "type = 'gradient'", initial = TRUE)
legend("bottomleft",
       legend = c(paste0("abun sp1 = ", min(state_variables$sp1)),
                  rep(NA, 28),
                  paste0("abun sp1 = ", max(state_variables$sp1))),
       fill = viridis::viridis(30), border = NA, y.intersp = 0.2)