From e2dd0e66fc8ba25465a2d73dfde902f71850fbeb Mon Sep 17 00:00:00 2001 From: tj Date: Wed, 15 Mar 2023 02:03:07 -0700 Subject: [PATCH] update dep version --- Manifest.toml | 550 +++++++++++++++--------- Project.toml | 6 +- src/1.JWAS/src/build_MME.jl | 6 +- src/1.JWAS/src/markers/readgenotypes.jl | 2 +- 4 files changed, 358 insertions(+), 206 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index c374bdb2..3336c9f2 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,389 +1,541 @@ # This file is machine-generated - editing it directly is not advised -[[Artifacts]] -deps = ["Pkg"] -git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744" +julia_version = "1.8.3" +manifest_format = "2.0" +project_hash = "5935dd3b6cb8e11d876266a1bbc006b403099e69" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.3.0" -[[Base64]] +[[deps.Base64]] uuid = 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+[[deps.Test]] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[UUIDs]] +[[deps.TranscodingStreams]] +deps = ["Random", "Test"] +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.9.11" + +[[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -[[Unicode]] +[[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" + +[[deps.WeakRefStrings]] +deps = ["DataAPI", "InlineStrings", "Parsers"] +git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" +uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" +version = "1.4.2" + +[[deps.WorkerUtilities]] +git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" +uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" +version = "1.6.1" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.12+3" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" diff --git a/Project.toml b/Project.toml index 455c476b..7f41d2fb 100644 --- a/Project.toml +++ b/Project.toml @@ -19,9 +19,9 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [compat] -CSV = "0.5, 0.6, 0.7, 0.8" -DataFrames = "0.19, 0.20, 0.21, 0.22" -Distributions = "0.21, 0.22, 0.23, 0.24" +CSV = "0.5, 0.6, 0.7, 0.8, 0.10" +DataFrames = "0.19, 0.20, 0.21, 0.22, 1.5.0" +Distributions = "0.21, 0.22, 0.23, 0.24, 0.25" ProgressMeter = "1.0, 1.1, 1.2" StatsBase = "0.30, 0.31, 0.32, 0.33" ForwardDiff = "0.10" diff --git a/src/1.JWAS/src/build_MME.jl b/src/1.JWAS/src/build_MME.jl index fd62d49e..41ea7db4 100644 --- a/src/1.JWAS/src/build_MME.jl +++ b/src/1.JWAS/src/build_MME.jl @@ -211,7 +211,7 @@ function getData(trm::ModelTerm,df::DataFrame,mme::MME) #ModelTerm("1:A*B") end trm.data = str val=convert(Array,val) - DataFrames.recode!(val, missing => 0.0) + val = coalesce.(val, 0.0) #replace missing with 0.0 trm.val = ((mme.MCMCinfo == false || mme.MCMCinfo.double_precision) ? Float64.(val) : Float32.(val)) end @@ -317,9 +317,9 @@ function getMME(mme::MME, df::DataFrame) end - y = DataFrames.recode(df[!,mme.lhsVec[1]], missing => 0.0) + y = coalesce.(df[!,mme.lhsVec[1]], 0.0) #replace missing values with 0 for i=2:size(mme.lhsVec,1) - y = [y; DataFrames.recode(df[!,mme.lhsVec[i]],missing=>0.0)] + y = [y; coalesce.(df[!,mme.lhsVec[i]], 0.0)] end ii = 1:length(y) jj = ones(length(y)) diff --git a/src/1.JWAS/src/markers/readgenotypes.jl b/src/1.JWAS/src/markers/readgenotypes.jl index 567c94da..e4f402ee 100644 --- a/src/1.JWAS/src/markers/readgenotypes.jl +++ b/src/1.JWAS/src/markers/readgenotypes.jl @@ -119,7 +119,7 @@ function get_genotypes(file::Union{AbstractString,Array{Float64,2},Array{Float32 markerID = string.(1:(size(file,2)-1)) end obsID = map(string,file[!,1]) - genotypes = map(Float32,convert(Matrix,file[!,2:end])) + genotypes = map(Float32,Matrix(file[!,2:end])) elseif typeof(file) <: Union{Array{Float64,2},Array{Float32,2},Array{Any,2}} #Array if length(header) != (size(file,2)+1) header = ["id"; string.(1:size(file,2))]