CommunityColor {EcotoneFinder}

Tool to assign color to species distribution plots given fuzzy clustering results.

Description

Tool to assign color to species distribution plots given fuzzy clustering results.

Usage

CommunityColor(ecotonefinder, method = c("vegclust", "cmeans"),
  pal = c("diverge_hcl", "terrain_hcl", "sequential_hcl", "rainbow_hcl"))

Arguments

ecotonefinder

A list containing elements named in the same way than EcotoneFinder function outcomes. Must contain at least one of vegclust or cmeans results.

method

Which fuzzy clustering to use. Either vegclust or cmeans.

pal

Which palette to use for color picking. Chosen from the colorspace package.

Details

CommunityColor creates a color vector that can be used by plotting functions. It assigns colors to species of a community matrix given the results of vegclust or cmeans analyses (using cmeans$centers or vegclust$mobileCenters). Species are assigned to a color according to the cluster centroid for which they have their highest membership value (see Bandelj et al., 2012).

The palette must be one of the colorspace package.

Value

A vector of color names from the palette in the pal argument, of the same length and in the same order than the species columns of the provided data.

Examples

 ######## Artificial dataset & analysis:
 SyntheticTrial <- SyntheticData(SpeciesNum = 27, 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")

 #### Plotting:
 plotEcotone(data = SyntheticEcoFinder, plot.data = TRUE, plot.method = "none",
             col.data = SyntheticColor)