aq.matrix: 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

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)

projection matrix

lambda

population growth rate

initial population vector

final population vector

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

Details

Adds individual fertilites to annual transitions using a prebreeding census.

Examples

Run this code

# NOT RUN {
data(aq.trans)

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)


# }