Differences

This shows you the differences between two versions of the page.

--- how_to_compute_vanraden_s_deregressed_proof [2019/05/14 18:24] – created yutaka
+++ how_to_compute_vanraden_s_deregressed_proof [2019/05/14 18:55] – yutaka
@@ Line 14: / Line 14: @@
 It additionally calculates PA and its reliability.
 <file>
-OPTION parent_avg
+OPTION parent_avg yes
 </file>
@@ Line 30: / Line 30: @@
    - Accuracy or reliability of PA
-VanRaden et al. (2009) showed a deregressed proof can be available from the following steps.
+VanRaden et al. (2009) showed a deregressed proof of sire 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.
@@ Line 39: / Line 39: @@
    - 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: $\mathrm{DRP}=\mathrm{PA}+(\mathrm{EBV}-\mathbf{PA})/R$.
+   - Compute the deregressed proof for this animal: $\mathrm{DRP}=\mathrm{PA}+(\mathrm{EBV}-\mathrm{PA})/R$.
+The following AWK script computes the deregressed proof with above procedure.
+<file awk pvr_drp.awk>
+#
+# Computation of deregressed proof for sires.
+#
+# usage: awk -v h2=0.25 -f pvr_drp.awk
+#
+# You can change the relitability as -v h2=value.
+# The default heritability is 0.25.
+#
+BEGIN{
+    # default h2=0.25 equiv. kd=14
+    if(h2<=0){ h2=0.25 }
+    kd=(4-2*h2)/h2
+    print "h2=",h2,"; kd=",kd > "/dev/stderr"
+}
+NR>1{
+    DE_EBV = kd*$5/(1 - $5)
+    DE_PA  = kd*$10/(1 - $10)
+    DE_R   = DE_EBV - DE_PA
+    R = DE_R/(DE_R + kd)
+    if(R>0){
+        DRP = $6 + ($4-$6)/R
+    } else {
+        R = 0.0
+        DRP = 0.0
+    }
+    print $0,DRP,R
+}
+</file>
+If you need to compute a cows' deregressed proof, please consult Wiggans et al. (2012; JDS).