millironx/beefblup
1
0
Fork 0
mirror of https://github.com/MillironX/beefblup.git synced 2024-12-22 09:08:16 +00:00
Code Issues Releases Packages Activity

Update report generation to match new fixed effect format

Browse source
This commit is contained in:
Thomas A. Christensen II 2021-08-31 20:02:17 -05:00
parent 683c48aa45
commit 62f5c4ea65
Signed by: millironx
GPG key ID: 139C07724802BC5D
1 changed files with 22 additions and 16 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

38
src/BeefBLUP.jl
View file

@ -95,13 +95,17 @@ function beefblup(path::String, savepath::String, h2::Float64)
# Find the accuracies # Find the accuracies
diaginv = diag(inv(MME)) diaginv = diag(inv(MME))
reliability = ones(Float64, length(diaginv)) - diaginv .* λ reliability = ones(Float64, length(diaginv)) .- diaginv .* λ
# Find how many traits we found BLUE for # Find how many traits we found BLUE for
numgroups = numgroups .- 1 numgroups = length(reliability) - numanimals
# Split the BLUP and BLUE results
β = solutions[1:numgroups]
μ = solutions[numgroups+1:end]
μ_reliability = reliability[numgroups+1:end]
# Extract the names of the traits # Extract the names of the traits
fixedfxnames = names(fixedfx)
traitname = names(data)[end] traitname = names(data)[end]
# Start printing results to output # Start printing results to output
@ -120,13 +124,15 @@ function beefblup(path::String, savepath::String, h2::Float64)
# Print base population stats # Print base population stats
write(fileID, "Base Population:\n") write(fileID, "Base Population:\n")
for i in 1:length(normal) for i in 1:length(fixedeffects)
effect = fixedeffects[i]
write(fileID, "\t") write(fileID, "\t")
write(fileID, fixedfxnames[i]) write(fileID, string(effect.name))
write(fileID, ":\t") write(fileID, ":\t")
write(fileID, normal[i]) write(fileID, string(effect.basetrait))
write(fileID, "\n") write(fileID, "\n")
end end
write(fileID, "\tMean ") write(fileID, "\tMean ")
write(fileID, traitname) write(fileID, traitname)
write(fileID, ":\t") write(fileID, ":\t")
@ -136,17 +142,17 @@ function beefblup(path::String, savepath::String, h2::Float64)
# Contemporary group adjustments # Contemporary group adjustments
counter = 2 counter = 2
write(fileID, "Contemporary Group Effects:\n") write(fileID, "Contemporary Group Effects:\n")
for i in 1:length(numgroups) for i in 1:length(fixedeffects)
effect = fixedeffects[i]
write(fileID, "\t") write(fileID, "\t")
write(fileID, fixedfxnames[i]) write(fileID, effect.name)
write(fileID, "\tEffect\tReliability\n") write(fileID, "\tEffect\n")
for j in 1:numgroups[i] for j in 1:length(effect.alltraits)
types = effect.alltraits[j]
write(fileID, "\t") write(fileID, "\t")
write(fileID, adjustedtraits[counter - 1]) write(fileID, string(types))
write(fileID, "\t") write(fileID, "\t")
write(fileID, string(solutions[counter])) write(fileID, string(β[counter]))
write(fileID, "\t")
write(fileID, string(reliability[counter]))
write(fileID, "\n") write(fileID, "\n")
counter = counter + 1 counter = counter + 1
@ -162,9 +168,9 @@ function beefblup(path::String, savepath::String, h2::Float64)
write(fileID, "\t") write(fileID, "\t")
write(fileID, string(data.id[i])) write(fileID, string(data.id[i]))
write(fileID, "\t") write(fileID, "\t")
write(fileID, string(solutions[i + counter - 1])) write(fileID, string(μ[i]))
write(fileID, "\t") write(fileID, "\t")
write(fileID, string(reliability[i + counter - 1])) write(fileID, string(μ_reliability[i]))
write(fileID, "\n") write(fileID, "\n")
end end