plotEcotone {EcotoneFinder}

Plot method for EcotoneFinder

Description

Plot method for EcotoneFinder

Usage

plotEcotone(data = NULL, slope = NULL, env = NULL,
  plot.data = FALSE, plot.method = c("none", "dca", "fanny",
  "vegclust", "cmeans", "diversity", "dca_slope", "fanny_slope",
  "vegclust_slope", "cmeans_slope", "diversity_slope"), axis.number = 1,
  magnification = 20, magnification.diversity = 5,
  magnification.slope = 500, col.data = "black",
  col.method = c("red", "blue"), col.slope = c("darkgreen", "green"),
  col.env = c("orange", "gold"), title = NULL, ylab = "Species",
  xlab = "Gradient", na.rm = FALSE, ...)

Arguments

data

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

slope

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

env

A list containing elements named in the same way than EcotoneFinder function outcomes. Usefull if EcotoneFinder has been run on environmental data and the outcomes are to be compared with the outcomes from the community matrix. Can also be used to compare results from two different community matrices, if the x-axis are similar.

plot.data

Logical. Should the data be plotted.

plot.method

Analysis method to be plotted from the EcotoneFinder results or the Slope results. Must be one or several of "none","dca","fanny","vegclust", "cmeans","diversity", "dca_slope","fanny_slope","vegclust_slope", "cmeans_slope" or "diversity_slope".

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.

magnification.slope

Magnification coefficient for the Slope.

col.data

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

col.method

Colors to be used for the methods (for data).

col.slope

Colors to be used for the methods (for slope).

col.env

Colors to be used for the methods (for env).

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.

...

Additional argument to be passed to the plot function.

Details

The plotEcotone function is intended for easy visualisation of the results of the EcotoneFinder function and the Slope function along the sampling gradient. It also provide a way to plot the original species data - for comparison - along with magnification coefficients for the different method or slopes in order to facilitate visualization. Please note that large sets of species may be confusing to plot. The CommunityColor function is also provided to help with data coloring and easy visualisation.

Value

A plot corresponding to the plotEcotone arguments.

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")

 ##### Assigning colors to communities:
 SyntheticColor <- CommunityColor(SyntheticEcoFinder, pal = "diverge_hcl",
                                  method = "cmeans")

 ###### Computing the derivatives:
 SyntheticSlope <- Slope(SyntheticEcoFinder, method = "all",
                         axis.number = 2, diversity = "all")

 ####### Plot the derivative of the FCM with the synthetic species data:
 require(colorspace)
 plotEcotone(slope = SyntheticSlope, plot.data = TRUE,
             plot.method = c("cmeans_slope"), axis.number = 2,
             col.method = terrain_hcl(3), col.data = SyntheticColor)

 ####### Plot the derivative and the FCM:
 require(colorspace)
 plotEcotone(data = SyntheticEcoFinder, slope = SyntheticSlope,
             plot.data = TRUE,
             plot.method = c("cmeans", "cmeans_slope"),
             axis.number = 2, col.method = terrain_hcl(3),
             col.data = SyntheticColor)