aq.matrix: Create a projection matrix for Aquilegia

In cstubben/popbio: Construction and Analysis of Matrix Population Models

Create a projection matrix for Aquilegia

Description

Creates a projection matrix for Aquilegia from annual transition data, assuming new seeds and seed bank seeds have an equal chance for successful germination and equal survival rates.

Usage

aq.matrix(
  trans,
  recruits,
  summary = TRUE,
  seed.survival = 0.126,
  seed.bank.size = 10000,
  seeds.per.fruit = 120,
  ...
)

Arguments

trans	A data frame with transitions listing ordered stages and fates and counts of mature fruits
recruits	The number of observed recruits in year t + 1.
summary	Output projection matrix and summaries. Otherwise output transition table with added individual fertilities.
seed.survival	Estimated seed survival rate for both new seeds and seed bank. Default is 12.6 percent survival.
seed.bank.size	Estimated size of the seed bank. Seed bank and new seeds contribute to a common germinant pool with equal chance for germination. Default is 10,000 seeds in seed bank.
seeds.per.fruit	The number of seeds produced per mature fruit. Default is 120 seeds.
...	additional arguments passed to projection.matrix

Details

Adds individual fertilites to annual transitions using a prebreeding census.

Value

If summary is TRUE, a list with

recruits	total number of recruits
seed.survival	seed survival rate
seed.bank	total number of seeds in seed bank
seeds.from.plants	total number of new seeds just released from fruits
recruitment.rate	recruitment rate calculated as recruits/(seed.bank.size + seeds.from.plants)
A	projection matrix
lambda	population growth rate
n	initial population vector
n1	final population vector

If summary is FALSE, a data frame with individual fertilities added to the transition data frame only.

Author(s)

Chris Stubben

See Also

projection.matrix

Examples

x <- subset(aq.trans, year==1996)
## number of recruits in 1997
rec <- nrow(subset(aq.trans, year==1997 & stage == "recruit"))
aq.matrix(x, recruits=rec)
aq.matrix(x, recruits=rec, seed.survival=.7, seed.bank=3000)

cstubben/popbio documentation built on April 2, 2024, 4:18 a.m.