Description Usage Arguments Value Examples

`overwrite()`

returns a data frame describing which particular
transitions within an ahistorical or historical projection matrix to
overwrite with either given rates and probabilities, or other estimated
transitions.

1 2 3 4 5 6 7 8 9 10 11 |

`stage3` |
The name of the stage in time |

`stage2` |
The name of the stage in time |

`stage1` |
The name of the stage in time |

`eststage3` |
The name of the stage to replace |

`eststage2` |
The name of the stage to replace |

`eststage1` |
The name of the stage to replace |

`givenrate` |
A fixed rate or probability to replace for the transition
described by |

`type` |
A vector denoting the kind of transition between times |

`type_t12` |
An optional vector denoting the kind of transition between
times |

A data frame that puts the above vectors together and can be used as
input in `flefko3()`

, `flefko2()`

,
`rlefko3()`

,`rlefko2()`

, and
`aflefko2()`

.

Variables in this data frame include the following:

`stage3` |
Stage at time |

`stage2` |
Stage at time |

`stage1` |
Stage at time |

`eststage3` |
Stage at time |

`eststage2` |
Stage at time |

`eststage1` |
Stage at time |

`givenrate` |
A constant to be used as the value of the transition. |

`convtype` |
Designates whether the transition from time |

`convtype_t12` |
Designates whether the transition from time |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | ```
cypover2r <- overwrite(stage3 = c("SD", "P1", "P2", "P3", "SL", "SL", "D",
"XSm", "Sm"),
stage2 = c("SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL", "SL"),
eststage3 = c(NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm"),
eststage2 = c(NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm"),
givenrate = c(0.1, 0.2, 0.2, 0.2, 0.25, 0.4, NA, NA, NA),
type = c("S", "S", "S","S", "S", "S", "S", "S", "S"))
cypover2r
cypover3r <- overwrite(stage3 = c("SD", "SD", "P1", "P1", "P2", "P3", "SL",
"SL", "SL", "D", "XSm", "Sm", "D", "XSm", "Sm"),
stage2 = c("SD", "SD", "SD", "SD", "P1", "P2", "P3", "SL", "SL", "SL",
"SL", "SL", "SL", "SL", "SL"),
stage1 = c("SD", "rep", "SD", "rep", "SD", "P1", "P2", "P3", "SL", "P3",
"P3", "P3", "SL", "SL", "SL"),
eststage3 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "D", "XSm", "Sm", "D",
"XSm", "Sm"),
eststage2 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm"),
eststage1 = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, "XSm", "XSm", "XSm",
"XSm", "XSm", "XSm"),
givenrate = c(0.1, 0.1, 0.2, 0.2, 0.2, 0.2, 0.25, 0.4, 0.4, NA, NA, NA, NA,
NA, NA),
type = c("S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S", "S",
"S", "S"))
cypover3r
``` |

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