1
In short
1.1
Age Info is Useful
1.2
Implementation
1.2.1
Passing the threshold
1.3
Time units
1.4
Runtime Messages
1.5
Changing the ageprior
2
Maths
2.1
AgePrior
2.2
Unsampled individuals
2.3
Genetics
\(\times\)
Age
3
AgePrior matrix explained
3.1
AgePriorExtra
4
Default ageprior
4.1
Default
5
Pedigree-based ageprior
5.1
Discrete generations
5.1.1
Generation interval different from 1
5.2
Overlapping generations
5.2.1
BirthYearRange
5.2.2
MaxAgeParent
5.2.3
Counts:
tblA.R
5.2.4
P(A|R):
PA.R
5.2.5
Full sibling correction
5.2.6
Ageprior P(A|R)/P(A):
LR.RU.A.raw
6
Small sample correction
6.1
6.2
The problem
6.3
Smooth
6.4
Flatten
6.4.1
Weighing factor &
lambdaNW
6.4.2
Sample size vs. sampling probability
7
Grandparents & Avuncular
7.1
Maths
7.1.1
Ageprior to Probability to Ageprior
7.1.2
change from v1.3 to v2.0
8
Customise
8.1
8.2
Via
args.AP
8.3
Different input pedigree
8.4
Other tweaks
8.5
From age-difference distribution
8.6
Specifications
9
Estimate birth years
10
References
Main Vignette
Other Manuals
Sequoia - Age ‘Prior’
10
References
Huisman, Jisca. 2017.
“Pedigree Reconstruction from
SNP
Data: Parentage Assignment, Sibship Clustering and Beyond.”
Molecular Ecology Resources
17 (5): 1009–24.