aq.matrix | 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 |

`recruits` |
The number of observed recruits in year |

`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 |

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

`projection.matrix`

```
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)
```

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