plotEco {EcotoneFinder}

Plotting component for EcotoneFinder

Description

Plotting component for EcotoneFinder

Usage

plotEco(ecotonefinder, 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

ecotonefinder

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.

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)
 plotEco(SyntheticEcoFinder, plot.data = FALSE,
         plot.method = c("cmeans", "dca"),
         axis.number = 2, col.method = terrain_hcl(3))