abundance.matrix: Abundance Matrix from a simulation
In Lobz/facilitation: A C++ Framework for Plant-Plant Interaction IBMs

This function returns a matrix with abundances of each life stage/species over time. The rows in the matrix are the lifestages/species id. The times are in the row names. To visualize the abundance matrix data we recomment the function stackplot.

1 2	abundance.matrix(data, times = seq(0, data$maxtime, length.out = 50), by.age = FALSE, cap.living = FALSE)

`data`	result of a simulation, created by `community`
`times`	array of times at which the abundances will be calculated
`by.age`	Logical. Use this option to get the number of individuals to reach each age, instead of abundances for each time.
`cap.living`	Logical. Use this option with by.age=T, to set the time of death of living individuals to max simulation time. Otherwise, living individuals are excluded from the data. Either way, this data will be more representative if only a small fraction of total individuals is living at the end of simulation.

data(malthusian)
times <- seq(0,malthusian$maxtime,by=0.1)
ab <- abundance.matrix(malthusian,times)

ab.by.age <- abundance.matrix(malthusian,times,by.age=TRUE)