ComGenR: Functions for COMmunity GENetics analyses in R

#' Community simulator for running cgSim.
#' 
#' Generates a matrix of species allelic values.
#' 
#' This function provides a simple way to populate a set of phenotypic values
#' for a model community to be used in a simulation of community genetics
#' effects.
#' 
#' @param n Number of species.
#' @param het.values Range of heterozygote values.
#' @param allelic.range Range of allelic values.
#' @return %% ~Describe the value returned %% If it is a LIST, use %%
#' @export simSpp
#' @note %% ~~further notes~~
#' @author %% ~~who you are~~
#' @seealso %% ~~objects to See Also as \code{\link{help}}, ~~~
#' @references %% ~put references to the literature/web site here ~
#' @keywords ~kwd1 ~kwd2
#' @examples
#' 
#' ##---- Should be DIRECTLY executable !! ----
#' ##-- ==>  Define data, use random,
#' ##--	or do  help(data=index)  for the standard data sets.
#' 
#' ## The function is currently defined as
#' function (n = "number of species", het.values = c(5, 21), allelic.range = c(0, 
#'     3)) 
#' {
#'     if (n == "number of species") {
#'         n <- 25
#'     }
#'     com <- matrix(NA, nrow = n, ncol = 2)
#'     com[, 1] <- runif(n, het.values[1], het.values[2])
#'     com[, 2] <- runif(n, allelic.range[1], allelic.range[2])
#'     com. <- com
#'     com.[, 1] <- (com[, 1] - 0.5 * com[, 2])/2
#'     com.[, 2] <- (com[, 1] + 0.5 * com[, 2])/2
#'     return(com.)
#'   }
#' 
simSpp <- function (n = "number of species",
                    het.values = c(5, 21), 
                    allelic.range = c(0,3)){
    if (n == "number of species") {n <- 25}
    com <- matrix(NA, nrow = n, ncol = 2)
    com[, 1] <- runif(n, het.values[1], het.values[2])
    com[, 2] <- runif(n, allelic.range[1], allelic.range[2])
    com. <- com
    com.[, 1] <- (com[, 1] - 0.5 * com[, 2])/2
    com.[, 2] <- (com[, 1] + 0.5 * com[, 2])/2
    return(com.)
}