EcotoneFinder (version 0.2.3)

SyntheticData: Create synthetic gaussian-shaped species abundance data

Description

Create synthetic gaussian-shaped species abundance data

Usage

SyntheticData(SpeciesNum, CommunityNum, Length = 100, SpCo = NULL,
  Parameters = list(a = NULL, b = NULL, c = NULL), dev.a = 10,
  dev.b = 10, dev.c = 0, down.limit = 1, pal = NULL,
  xlab = "Gradient", ylab = "Synthetic species",
  title = "Synthetic data")

Arguments

SpeciesNum

An integer giving the total number of species in the synthetic data.

CommunityNum

An integer giving the number of communities to be synthetised.

Length

The lenght of the gradient. Corresponds to the x-axis in a plot.

SpCo

The ratio of species per communities. If NULL, species will be spread evenly between communities with additional species in the last community if the quotient is not an integer. When specified, SpCo must be a vector of lenght equal to CommunityNum and whose sum is equal to SpeciesNum

Parameters

A list containing the parameters (a, b and c) for the gaussians. Each parameter must be specified for each community. See Details.

dev.a

The deviation around parameter a for the gaussian in a community. If 0 all species curve in the comunity will have the same a parameter.

dev.b

The deviation around parameter b for the gaussian in a community. If 0 all species curve in the comunity will have the same b parameter.

dev.c

The deviation around parameter a for the gaussian in c community. If 0 all species curve in the comunity will have the same c parameter.

down.limit

The limit under which the gaussian curve will be rounded down to 0. The default is 1.

pal

The color palette to be used. Species curves are colored according to communities. Either a colorspace palette or a vector of the same lenght as the number of species.

xlab

A title for the x-axis. See plot.

ylab

A title for the y-axis. See plot.

title

An overall title for the plot. See plot.

Value

SyntheticData returns a dataset with numbered species (sp.1, sp.2, ...) as columns. It also plot the obtained data.

Details

The SyntheticData function is intended for the creation of articficial dataset to test ecological patterns along gradients. The gaussian curves that it computes are of the form: \( a*exp(-(((x-b)^2)/2*(c^2))) \) The parameters can be interpreted as follow: a is the maximum height of the gaussian on the y-axis, b is the center of the gaussian on the x-axis and c is the steepness of the slopes on each side of the maximum. The gaussians create a set of continuous data that are akin to abundances. As gaussians of this type cannot reach 0, any value that is below the down.limit (default is 1) is rounded down to 0.

Examples

# NOT RUN {
### 3 distinct communities comprising a total of 21 species
SyntheticTrial <- SyntheticData(SpeciesNum = 21, CommunityNum = 3,
                                SpCo = NULL, Length = 500,
                                Parameters = list(a=rep(60, 3),
                                                  b=c(0,250,500),
                                                  c=rep(0.03,3)),
                                pal = c("#008585", "#FBF2C4", "#C7522B"))

### 3 distinct communities with uneven species numbers
SyntheticTrial <- SyntheticData(SpeciesNum = 21, CommunityNum = 3,
                                SpCo = c(5, 10, 6), Length = 500,
                                Parameters = list(a=rep(60, 3),
                                                  b=c(0,250,500),
                                                  c=rep(0.03,3)),
                                pal = c("#008585", "#FBF2C4", "#C7522B"))




# }