aq.matrix {popbio} | R Documentation |
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.
aq.matrix(trans, recruits, summary = TRUE, seed.survival = 0.126, seed.bank.size = 10000, seeds.per.fruit = 120, ...)
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 |
Adds individual fertilites to annual transitions using a prebreeding census.
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.
Chris Stubben
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)