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Paul VanRaden's deregressed proof
Overview
Quick answer
You need the output of accf90
which is a program available under an agreement with UGA.
A small script can compute VanRaden's (2009) deregressed proof based on PA, EBV, reliability of PA, and reliability of EBV.
Procedure
First, run blupf90
or other IOD programs to save solutions
.
Then, run accf90
with the following option in the parameter file.
It additionally calculates PA and its reliability.
OPTION parent_avg
The resulting sol_and_acc
file has 10 columns.
- Trait code
- Effect code
- Level code
- EBV
- Accuracy or reliability of EBV
- Parent average (PA)
- Unknown parent flag (1=both known; 2=sire unknown; 3=dam unknown; 4=both unknown)
- Sire code
- Dam code
- Accuracy or reliability of PA
VanRaden et al. (2009) showed a deregressed proof can be available from the following steps. It includes the consequence of previous studies e.g. VanRaden and Wiggans (1991). Note that the following instruction is approximated; the strict computation excludes the contribution of a daughter to its parent in the parent's EBV.
- Compute $k_{d}=(4-2h^2)/h^2$ (VanRaden and Wiggans 1991).
- Compute the daughter equivalent of EBV: $\mathrm{DE}_{\mathrm{EBV}}=k_{d}\mathrm{REL}_{\mathrm{EBV}}/(1-\mathrm{REL}_{\mathrm{EBV}})$.
- Compute daughter equivalent of PA: $\mathrm{DE}_{\mathrm{PA}}=k_{d}\mathrm{REL}_{\mathrm{PA}}/(1-\mathrm{REL}_{\mathrm{PA}})$.
- Compute the daughter equivalent of daughter contribution (i.e. EBV excluding PA): $\mathrm{DE}_{\mathrm{R}}=\mathrm{DE}_{\mathrm{EBV}}-\mathrm{DE}_{\mathrm{PA}}$.
- Compute the reliability of daughter contribution: $R=\mathrm{DE}_{\mathrm{R}}/(\mathrm{DE}_{\mathrm{R}}+k_{d})$.
- Compute the deregressed proof for this animal: $\mathrm{DRP}=\mathrm{PA}+(\mathrm{EBV}-\mathbf{PA})/R$.