popbio (version 1.0.1)

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 seed 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)
• 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.

Details

Adds individual fertilites to annual transitions using a prebreeding census.

See Also

projection.matrix

Examples

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)