plotEnv {EcotoneFinder}

Plotting component for EcotoneFinder when run on environmental data

Description

Plotting component for EcotoneFinder when run on environmental data

Usage

plotEnv(env, plot.data = FALSE, plot.method = c("none", "dca", "fanny",
  "vegclust", "cmeans", "diversity"), axis.number = 1,
  magnification = 20, magnification.diversity = 5,
  col.data = "black", col.method = c("red", "blue"), title = NULL,
  ylab = "Species", xlab = "Gradient", na.rm = FALSE, alone = TRUE,
  ...)

Arguments

env

A list containing elements named in the same way than EcotoneFinder function outcomes.

plot.data

Logical. Should the data be plotted.

plot.method

Analysis method to be plotted from the EcotoneFinder analyses. Must be one or several of "none","dca","fanny","vegclust", "cmeans" or"diversity".

axis.number

Number of axis to plot from the DCA.

magnification

Magnification coefficient for the method. Usefull if the data are being plotted.

magnification.diversity

Particular magnification for the diversity indices.

col.data

Colors to be used for the data. See CommunityColor function.

col.method

Colors to be used for the methods.

title

An overall title for the plot. See plot.

ylab

A title for the y-axis. See plot.

xlab

A title for the x-axis. See plot.

na.rm

Logical. Should NAs be removed.

alone

Logical. If FALSE, lines are added to an existing plot.

...

Additional argument to be passed to the plot function.

Details

Internal component of the PlotEcotone function for the plotting of the EcotoneFinder analyses. Use PlotEcotone directly for more options. The "diversity" method is still implemented, but will send a warning as it may not be relevant for environmental data.

Value

A plot with the EcotoneFinder results along the gradient, and optionally, the data.

Examples

 ######## Artificial dataset & analysis:
 SyntheticTrial <- SyntheticData(SpeciesNum = 20, CommunityNum = 3,
                                 SpCo = NULL, Length = 500,
                                 Parameters = list(a=rep(60, 3),
                                                   b=c(0,250,500),
                                                   c=rep(0.03,3)),
                                 dev.c = .015, pal = c("#008585", "#FBF2C4", "#C7522B"))

 SyntheticEcoFinder <- EcotoneFinder(SyntheticTrial[,-1],
                                     dist = SyntheticTrial$Distance,
                                     method = "all", groups = 3,
                                     standardize = "hellinger",
                                     diversity = "all")

 ### Plot:
 require(colorspace)
 plotEnv(SyntheticEcoFinder, plot.data = FALSE,
         plot.method = c("cmeans", "dca"),
         axis.number = 2, col.method = terrain_hcl(3))