removed experimental EM approach from master branch

Manifest.toml

@@ -31,13 +31,6 @@ git-tree-sha1 = "055eb2690182ebc31087859c3dd8598371d3ef9e"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
 version = "0.5.3"
 
-[[BirthDeathProcesses]]
-git-tree-sha1 = "a524afe6e79aa971bdefc6838e932496c425c9b1"
-repo-rev = "master"
-repo-url = "/home/arzwa/BirthDeathProcesses"
-uuid = "306aff9e-5df6-11e9-2ccf-256e3a748119"
-version = "0.1.0"
-
 [[BufferedStreams]]
 deps = ["Compat", "Test"]
 git-tree-sha1 = "5d55b9486590fdda5905c275bb21ce1f0754020f"
@@ -569,17 +562,10 @@ uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
 version = "0.5.3"
 
 [[TranscodingStreams]]
-<<<<<<< HEAD
 deps = ["Random", "Test"]
 git-tree-sha1 = "a25d8e5a28c3b1b06d3859f30757d43106791919"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.9.4"
-=======
-deps = ["Pkg", "Random", "Test"]
-git-tree-sha1 = "d4718bd4db6b7850af3c3833556c6aedbb8e9904"
-uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.9.2"
->>>>>>> ebe15332d96f9aa9211906aab0536897d05eee54
 
 [[URIParser]]
 deps = ["Test", "Unicode"]

Project.toml

@@ -4,7 +4,6 @@ authors = ["arzwa <[email protected]>"]
 version = "0.1.0"
 
 [deps]
-BirthDeathProcesses = "306aff9e-5df6-11e9-2ccf-256e3a748119"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
 ConsensusTrees = "d3d4590a-60df-11e9-122f-f56e3d820c59"

src/Whale.jl

@@ -1,7 +1,6 @@
 module Whale
     using PhyloTrees
     using ConsensusTrees
-    using BirthDeathProcesses
     using Distributed
     using DistributedArrays
     using Optim
@@ -18,7 +17,7 @@ module Whale
 
     export
         # types
-        SpeciesTree, CCD, Slices, BackTracker, WhaleEM, WhaleMapEM, WhaleMlEM,
+        SpeciesTree, CCD, Slices, BackTracker,
         # I/O
         read_sp_tree, read_ale_observe, read_ale_from_dir, read_ale_from_list,
         get_ccd,
@@ -58,7 +57,6 @@ module Whale
     include("cnsns.jl")
     include("ccp.jl")
     include("bdp.jl")
-    include("em.jl")
 
     @info "This is Whale v0.2 - © Arthur Zwaenepoel 2018-2019"
     @info "https://doi.org/10.1101/556076 "

src/dlsim.jl

@@ -43,9 +43,9 @@ function dlsim(S::SpeciesTree, λ::Array{Float64}, μ::Array{Float64},
 end
 
 # dlsim with trees written to files
-function dlsim(S::SpeciesTree, λ::Array{Float64}, μ::Array{Float64}, q::Array{Float64},
-        η::Float64, ri::Dict{Int64,Int64}, N::Int64, outdir::String; oib::Bool=false,
-        min::Int64=3, max=1000)
+function dlsim(S::SpeciesTree, λ::Array{Float64}, μ::Array{Float64},
+        q::Array{Float64}, η::Float64, ri::Dict{Int64,Int64}, N::Int64,
+        outdir::String; oib::Bool=false, min::Int64=3, max=1000)
     @info "Simulating $N gene families ..."
     trees = dlsim(S, λ, μ, q, η, ri, N; oib=oib, min=min, max=max)
     for (T, ll) in trees
@@ -60,8 +60,9 @@ end
           η::Float64, N::Int64; oib::Bool=false)
 Simulate a bunch of duplication-loss model trees.
 """
-function dlsim(S::SpeciesTree, λ::Array{Float64}, μ::Array{Float64}, q::Array{Float64},
-        η::Float64, ri::Dict{Int64,Int64}, N::Int64; oib::Bool=false, min::Int64=3, max=1000)
+function dlsim(S::SpeciesTree, λ::Array{Float64}, μ::Array{Float64},
+        q::Array{Float64}, η::Float64, ri::Dict{Int64,Int64}, N::Int64;
+        oib::Bool=false, min::Int64=3, max=1000)
     c = childnodes(S.tree, 1)
     left = sp_leaves(S.tree, c[1])
     right = sp_leaves(S.tree, c[2])