virtualspecies (version 1.6)

formatFunctions: Format and visualise functions used to generate virtual species with generateSpFromFun

Description

This function is a helper function to simplify the formatting of functions for generateSpFromFun

Usage

formatFunctions(x = NULL, rescale = TRUE, ...)

Arguments

x

NULL or a RasterStack. If you want to visualise the functions, provide your RasterStack here.

rescale

TRUE or FALSE. If TRUE, individual response plots are rescaled between 0 and 1 with the formula (val - min) / (max - min).

...

the parameters to be formatted. See details.

Warning

Do not use 'x' as a name for your environmental variables.

Author

Boris Leroy

with help from C. N. Meynard, C. Bellard & F. Courchamp

Details

This function formats the parameters argument of generateSpFromFun. For each environmental variable, provide a vector containing the function name, and its arguments.

For example, assume we want to generate a species responding to two environmental variables bio1 and bio2.

• The response to bio1 is a normal response (dnorm), of mean 1 and standard deviation 0.5.

• The response to bio2 is a linear response (linearFun), of slope (a) 2 and intercept (b) 5.

The correct writing is:

formatFunctions( bio1 = c(fun = "dnorm", mean = 1, sd = 0.5), bio2 = c(fun = "linearFun", a = 2, b = 5))

Examples

my.parameters <- formatFunctions(variable1 = c(fun = 'dnorm',
                                            mean = 0.00012, sd = 0.0001),
                              variable2 = c(fun = 'linearFun', a = 1, b = 0))


my.parameters <- formatFunctions(bio1 = c(fun = "logisticFun", 
                                         alpha = -12.7, beta = 68),
                                 bio2 = c(fun = "linearFun", 
                                          a = -0.03, b = 191.2),
                                 bio3 = c(fun = "dnorm", 
                                          mean = 86.4, sd = 19.1),
                                 bio4 = c(fun = "logisticFun", 
                                          alpha = 2198.5, beta = 11381.4))
if (FALSE) {
# An example using worldclim data
bio1.4 <- getData('worldclim', var='bio', res=10)[[1:4]]
my.parameters <- formatFunctions(x = bio1.4,
                                 bio1 = c(fun = "logisticFun", 
                                          alpha = -12.7, beta = 68),
                                 bio2 = c(fun = "linearFun", 
                                          a = -0.03, b = 191.2),
                                 bio3 = c(fun = "dnorm", 
                                          mean = 86.4, sd = 19.1),
                                 bio4 = c(fun = "logisticFun", 
                                          alpha = 2198.5, beta = 11381.4))
}