IPMpack (version 1.6)

createMPMFmatrix: Builds discrete F matrices from the types of data structures used in IPMpack.

Description

A method that uses bins to construct a class discrete fecundity matrix population model (F) from the types of data structures used in IPMpack. It assumes that there is a single fecundity column in the data entitled "fec" that captures number of offspring produced by individuals over every continuous stage (e.g. size). Individuals can be "born" into different stages of the matrix (e.g. seedbank, seedling) defined by offspringClasses (where offspringClasses=1 means between bins[1] and bins[2], offspringClasses=2 means between bins[2] and bins[3], etc...) in proportions offspringProp, which will be rescaled to sum to 1 if necessary.

Usage

createMPMFmatrix(dataf, bins, offspringClasses = 1, offspringProp = 1, nEnv = 1)

Arguments

dataf

A dataframe with columns `size', `fec' (`size' is size at t, and `fec' indicates the number of propagules produced by that individual); facultatively, dataf may include `covariate' and `covariateNext' for discrete covariates, indicating values at time t,

bins

numeric, limits of the desired discrete (size) classes.

nEnv

currently not used.

offspringClasses

the bins of the matrix in which offspring appear.

offspringProp

the proportion of offspring appearing in each bin.

Value

• an object of class IPMmatrix.

Details

The median number of offspring produced by individuals in each bin is identified. Fecundity values are distributed across rows and columns accordingly. To obtain a classic matrix population model (A) this can be added to values defined by createMPMPmatrix (A = F + T).

References

For information on F matrix: Caswell. 2001. Matrix population models: construction, analysis, and interpretation. 2nd ed. Sinauer. p110-112.

For information on collapsing large matrices: Salguero-Gomez & Plotkin. 2010. Matrix dimensions bias demographic inferences: implications for comparative plant demography. The American Naturalist 176, p710-720.

See Also

createIPMFmatrix, createMPMPmatrix

Examples

dff <- generateData()
matrixCuts <- c(1, 4, 10, 15)
Fmatrix <- createMPMFmatrix(dff, bins = matrixCuts, 
	offspringClasses = c(1,2), offspringProp = c(0.5, 0.5))
Fmatrix