summary.candes | R Documentation |

For every time point (age cohort), several population genetic parameters are estimated. These may include the generation interval, the average kinship, the average native kinship, the native effective size (native Ne), and the native genome equivalent (NGE) of the population at that point in time.

```
## S3 method for class 'candes'
summary(object, tlim=range(object$phen$Born, na.rm=TRUE),
histNe=NA, base=tlim[1], df=4, ...)
```

`object` |
R-Object created with function candes containing phenotypes and kinship information on individuals from the same breed. Data frame |

`tlim` |
Numeric vector with 2 components giving the time span for which genetic parameters are to be computed. |

`histNe` |
The historic effective size of the population assumed for the time between year |

`base` |
The base year in which individuals are assumed to be unrelated. The base year affects the NGE. The default is |

`df` |
Smoothing parameter used for computing the native effective size. The default is |

`...` |
further arguments passed to or from other methods |

For every time point (age cohort), several population genetic parameters are estimated. These may include the generation interval, the average kinship, the average native kinship, the native effective size (native Ne), and the native genome equivalent (NGE) of the population at that point in time. The population at a time t consists of all individuals born between t-I and t, where I is the generation interval. The population genetic parameters are described below.

A data frame providing for each time point (age cohort) several population genetic parameters. These may include

`t` |
The age cohort, containing e.g. year-of-birth or the generation number. These are the levels of column |

`I` |
The estimated generation interval at the time when the individuals were born. |

`KIN` |
The average kinship |

`NATKIN` |
The average native kinship |

`Ne` |
The native effective size of the population at the time when the individuals were born. The native effective size, quantifies how fast the smoothed native kinship is increasing. The native kinship may decrease for a short time span, in which case the estimate would be NA. Use a smaller value for parameter |

`NGE` |
The native genome equivalents of the population at the time when the individuals were born. The NGE estimates the number of unrelated individuals that would be needed to establish a hypothetical new population that has the same genetic diversity at native alleles as the population under study, whereby the individuals born in the base-year are assumed to be unrelated. |

Robin Wellmann

```
data(ExamplePed)
Pedig <- prePed(ExamplePed, thisBreed="Hinterwaelder", lastNative=1970)
phen <- Pedig[Pedig$Breed=="Hinterwaelder",]
pKin <- pedIBD(Pedig)
pKinatN <- pedIBDatN(Pedig, thisBreed="Hinterwaelder")
pop <- candes(phen=phen, pKin=pKin, pKinatN=pKinatN, quiet=TRUE, reduce.data=FALSE)
Param <- summary(pop, tlim=c(1970,1995), histNe=150, base=1800, df=4)
plot(Param$t, Param$pKinatN,type="l", ylim=c(0,0.1))
lines(Param$t,Param$pKin, col="red")
plot(Param$t, Param$Ne, type="l", ylim=c(0,100))
plot(Param$t, Param$NGE, type="l", ylim=c(0,10))
plot(Param$t, Param$I, type="l", ylim=c(0,10))
```

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