EcotoneFinder (version 0.2.3)

SyntheticDataSeries: Synthetic data for Space/Time series

Description

Synthetic data for Space/Time series

Usage

SyntheticDataSeries(CommunityPool, CommunityNum, Length = 100,
  SpCo = NULL, SeriesNum, replacement = TRUE,
  range.repl = as.integer(CommunityPool/5), Parameters = list(a = NULL,
  b = NULL, c = NULL), Parameters.repl = TRUE, dev.a = 10,
  dev.b = 10, dev.c = 0, Parameters.range = 10,
  displacement = NULL, pal = NULL, xlab = "Gradient",
  ylab = "Synthetic species", title = "Synthetic data")

Arguments

CommunityPool

Total number of species per series. must either be of length 1 (if the pool of species is of the same length for all communities) or of length equal to CommunityNum (specifying the species pool for each community)

CommunityNum

An integer giving the number of communities.

Length

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

SpCo

The ratio of species per communities. When replacement = T, SpCo is computed from CommunityPool and range.repl.

SeriesNum

The number of series to be synthetised.

replacement

Logical. Should the species of a community in a given series be a sample of the possible number of species in this community. See Details.

range.repl

An integer. Gives the possible range of species turnover in a community.

Parameters

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

Parameters.repl

Logical. Sould the parameters vary between series.

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.

Parameters.range

An integer. Gives the possible range of the parameter variations between two series. The range of variation is the parameter diveded by the parameters range. Default is 10.

displacement

Numeric matrix to control the direction of the changes in the mean values of the parameters over the series. See examples.

pal

The color palette to be used. Species curves are colored according to communities.

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

SyntheticDataSeries returns a list of datasets with numbered species (sp.1, sp.2, ...) as columns. The list has length = SeriesNum. It also plot the obtained data.

Details

SyntheticDataSeries is a extention of the SyntheticData function and intended to produce easy and consistent space/time series of artificial ecological community datasets. The series of dataframes are stored in an object of class list. The replacement and Parameters.repl arguments allow the user to choose wether or not the number of species and their distribution curves should vary among the different series. range.repl is an integer that define the boundaries of the interval in which the number of species can vary - such as the number of species per community is : sample([[CommunityPool/CommunityNum - range.repl ; CommunityPool/CommunityNum + range.repl]]) The number it takes is then used to define SpCo. Given the difference of scales between the 3 parameters a, b and c, the Parameters.range argument controls the variations of the parameters by divison so that they correspond to : sample([[Parameters - Parameters/Parameters.range ; Parameters + Parameters/Parameters.range]]) The obtained parameters are then used by the internal SyntheticData function as base parameters for a given series, on which dev.a, dev.b and dev.c will apply. The other arguments are equivalent to those of SyntheticData.

Examples

# NOT RUN {
##### 5 datasets of 40 species spread on 4 communities without turnover
##### on the number of species nor variations in their distribution:

SyntheticTrialSeries <- SyntheticDataSeries(CommunityPool = 40,
                                            CommunityNum = 4, SpCo = NULL,
                                            Length = 500, SeriesNum = 5,
                                            Parameters = list(a=rep(60, 4),
                                                              b=c(0,200,350,500),
                                                              c=rep(0.03,4)),
                                            pal = c("#008585", "#B8CDAE", "#E6C186", "#C7522B"),
                                            replacement = FALSE,
                                            Parameters.repl = FALSE)

##### 5 datasets of 40 species spread on 4 communities with species turnover
##### and variations in their distributions along the gradient:

SyntheticTrialSeries <- SyntheticDataSeries(CommunityPool = 40,
                                            CommunityNum = 4, SpCo = NULL,
                                            Length = 500, SeriesNum = 5,
                                            Parameters = list(a=rep(60, 4),
                                                              b=c(0,200,350,500),
                                                              c=rep(0.03,4)),
                                            pal = c("#008585", "#B8CDAE", "#E6C186", "#C7522B"),
                                            replacement = TRUE,
                                            Parameters.repl = TRUE)

##### With a displacement matrix to control the direction of the changes
##### between series:

# Dispalcement matrix (Parameters x Communities):
disp <- matrix(data=c(0,0,0,
                      0,35,-0.0007,
                      0,10,0), nrow = 3, ncol = 3)

Series <- SyntheticDataSeries(CommunityPool = 60, CommunityNum = 3, Length = 500,
                               SeriesNum = 5, replacement = FALSE, SpCo = c(15,15,30),
                               Parameters = list(a = c(60,60,60),
                                                 b = c(-50,-50,400),
                                                 c = c(0.01, 0.01, 0.01)),
                               dev.a=30, dev.b=40, dev.c=0,
                               displacement = disp,
                               pal = c(rep("#008585",15), rep("#FBF2C4",15),
                                       rep("#C7522B",30)))

# }