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Revamp fixed-effect algorithm
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commit
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2 changed files with 44 additions and 61 deletions
103
src/BeefBLUP.jl
103
src/BeefBLUP.jl
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@ -71,9 +71,9 @@ function beefblup(path::String, savepath::String, h2::Float64)
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A = additiverelationshipmatrix(data.id, data.dam, data.sire)
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# Extract all of the fixed effects
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fixedfx = select(data, Not([:id, :birthdate, :sire, :dam]))[:,1:end - 1]
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fixedeffectdata = data[:,5:end-1]
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(X, numgroups, normal, adjustedtraits) = fixedeffectmatrix(fixedfx)
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(X, fixedeffects) = fixedeffectmatrix(fixedeffectdata)
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# Extract the observed data
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Y = convert(Array{Float64}, data[:,end])
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@ -173,71 +173,42 @@ function beefblup(path::String, savepath::String, h2::Float64)
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end
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function fixedeffectmatrix(fixedeffects::AbstractDataFrame)
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# Find any columns that need to be deleted
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for i in 1:ncol(fixedeffects)
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if length(unique(fixedeffects[:,i])) <= 1
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@warn string("column '", names(fixedeffects)[i], "' does not have any unique animals and will be removed from this analysis")
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DataFrames.select!(fixedeffects, Not(i))
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"""
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fixedeffectmatrix(fixedeffectdata::DataFrame)
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Creates contemporary groupings and the fixed-effect incidence matrix based on the fixed
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effects listed in `fixedeffectdata`.
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Returns a tuple `(X::Matrix{Int}, fixedeffects::Array{FixedEffect})` in which `X` is the
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actual matrix, and `fixedeffects` is the contemporary groupings.
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"""
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function fixedeffectmatrix(fixedeffectdata::DataFrame)
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# Declare an empty return matrix
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fixedeffects = FixedEffect[]
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# Add each trait to the array
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for i in 1:size(fixedeffectdata)[2]
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name = names(fixedeffectdata)[i]
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traits = eachcol(fixedeffectdata)[i]
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if length(unique(traits)) > 1
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push!(fixedeffects, FixedEffect(name, traits))
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else
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@warn string("column '", name, "' does not have any unique animals and will be dropped from analysis")
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DataFrames.select!(fixedeffectdata, Not(pname))
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end
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end
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# Determine how many contemporary groups there are
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numtraits = ncol(fixedeffects)
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numgroups = ones(1, numtraits)
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for i in 1:numtraits
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numgroups[i] = length(unique(fixedeffects[:,i]))
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end
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X = ones(Int64, (size(fixedeffectdata)[1], 1))
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# If there are more groups than animals, then the analysis cannot continue
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numanimals = length(fixedeffects[:,1])
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if sum(numgroups) >= numanimals
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throw(ErrorException("there are more contemporary groups than animals"))
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end
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# Define a "normal" animal as one of the last in the groups, provided that
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# all traits do not have null values
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numtraits = ncol(fixedeffects)
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numanimals = length(fixedeffects[:,1])
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normal = Array{String}(undef, 1, numtraits)
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for i in 1:numtraits
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for j in numanimals:-1:1
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if !ismissing(fixedeffects[j,i])
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normal[i] = string(fixedeffects[j,i])
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break
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end
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for i in 1:length(fixedeffects)
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trait = fixedeffects[i]
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for phenotype in trait.alltraits
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X = cat(X, Int64.(fixedeffectdata[:,i] .== phenotype), dims=2)
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end
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end
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# Form the fixed-effect matrix
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X = zeros(Int8, numanimals, floor(Int, sum(numgroups)) - length(numgroups) + 1)
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X[:,1] = ones(Int8, 1, numanimals)
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# Create an external counter that will increment through both loops
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counter = 2
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# Store the traits in a string array
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adjustedtraits =
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Array{String}(undef,floor(Int, sum(numgroups)) - length(numgroups))
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# Iterate through each group
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for i in 1:length(normal)
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# Find the traits that are present in this trait
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localdata = string.(fixedeffects[:,i])
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traits = unique(localdata)
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# Remove the normal version from the analysis
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effecttraits = traits[findall(x -> x != normal[i], traits)]
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# Iterate inside of the group
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for j in 1:(length(effecttraits))
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matchedindex = findall(x -> x == effecttraits[j], localdata)
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X[matchedindex, counter] .= 1
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# Add this trait to the string
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adjustedtraits[counter - 1] = traits[j]
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# Increment the big counter
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counter = counter + 1
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end
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end
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return X, numgroups, normal, adjustedtraits
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return X, fixedeffects
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end
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"""
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@ -314,5 +285,17 @@ function renamecolstospec!(df::DataFrame)
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return df
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end
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struct FixedEffect
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name::String
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basetrait::Any
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alltraits::AbstractArray{Any}
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end
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function FixedEffect(name::String, incidences)
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basetrait = last(unique(incidences))
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types = unique(incidences)[1:end-1]
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return FixedEffect(name, basetrait, types)
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end
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end
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@ -4,7 +4,7 @@ using Test
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@testset "BeefBLUP.jl" begin
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# Write your tests here.
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correctX = [1 1 0 0; 1 1 0 1; 1 0 1 0; 1 0 1 1; 1 0 1 0; 1 0 1 1; 1 0 0 0]
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correctX = [1 1 0 1; 1 1 0 0; 1 0 1 1; 1 0 1 0; 1 0 1 1; 1 0 1 0; 1 0 0 1]
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fixedfx = DataFrame(year = [1990, 1990, 1991, 1991, 1991, 1991, 1992], sex = ["male", "female", "male", "female", "male", "female", "male"])
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@test BeefBLUP.fixedeffectmatrix(fixedfx)[1] == correctX
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correctA = [1 0 1/2 1/2 1/2 0 0;
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