more standardization

Author: pdimens

src/GenoFreq.jl

@@ -1,23 +1,23 @@
-export genofreq, genofreq_expected, geno_count_observed, geno_count_expected
+export genofreq, genofreq_expected, genocount_observed, genocount_expected
 
 """
-    geno_count_observed(locus::GenoArray)
+    genocount_observed(locus::GenoArray)
 Return a `Dict` of genotype counts of a single locus in a
 `PopData` object.
 """
-@inline function geno_count_observed(locus::T) where T<:GenoArray
+@inline function genocount_observed(locus::T) where T<:GenoArray
     # conditional testing if all genos are missing
     all(ismissing.(locus)) && return missing
     countmap(skipmissing(locus))
 end
 
 """
-    geno_count_expected(locus::GenoArray)
+    genocount_expected(locus::GenoArray)
 Return a `Dict` of the expected genotype counts of a single locus in a
 `PopData` object. Expected counts are calculated as the product of observed
 allele frequencies multiplied by the number of non-missing genotypes.
 """
-function geno_count_expected(locus::T) where T<:GenoArray
+function genocount_expected(locus::T) where T<:GenoArray
     #count number of non-missing genotypes in the locus
     n = nonmissing(locus)
 

src/Utils/GenotypeUtils.jl

@@ -1,4 +1,4 @@
-export allelecount, alleles, unique_alleles
+export allelecount, alleles, uniquealleles
 export locidataframe, locimatrix, phasedmatrix
 
 
@@ -42,10 +42,10 @@ end
 
 
 """
-    unique_alleles(locus::T) where T<:GenoArray
+    uniquealleles(locus::T) where T<:GenoArray
 Return an array of all the unique non-missing alleles of a locus.
 """
-@inline function unique_alleles(locus::GenoArray)
+@inline function uniquealleles(locus::GenoArray)
     unique(alleles(locus))
 end
 

test/allelegenofreq.jl

@@ -91,21 +91,21 @@ end
 
 @testset "Genotype Counts" begin
     @testset "Basic" begin
-        @test geno_count_observed(g) isa Dict
-        @test geno_count_observed([missing, missing]) === missing
-        @test geno_count_expected(g) isa Dict
+        @test genocount_observed(g) isa Dict
+        @test genocount_observed([missing, missing]) === missing
+        @test genocount_expected(g) isa Dict
     end
 
     @testset "Nuanced" begin
-        @test length(geno_count_observed(cats.genodata.genotype)) == 295
-        @test typeof(geno_count_observed(cats.genodata.genotype)) <: Dict{<:Tuple,Int64}
-        @test length(geno_count_expected(cats.genodata.genotype)) == 6241
-        @test typeof(geno_count_expected(cats.genodata.genotype)) <: Dict{<:Tuple,Float64}
+        @test length(genocount_observed(cats.genodata.genotype)) == 295
+        @test typeof(genocount_observed(cats.genodata.genotype)) <: Dict{<:Tuple,Int64}
+        @test length(genocount_expected(cats.genodata.genotype)) == 6241
+        @test typeof(genocount_expected(cats.genodata.genotype)) <: Dict{<:Tuple,Float64}
 
-        @test length(geno_count_observed(sharks.genodata.genotype)) == 12
-        @test typeof(geno_count_observed(sharks.genodata.genotype)) <: Dict{<:Tuple,Int64}
-        @test length(geno_count_expected(sharks.genodata.genotype)) == 25
-        @test typeof(geno_count_expected(sharks.genodata.genotype)) <: Dict{<:Tuple,Float64}
+        @test length(genocount_observed(sharks.genodata.genotype)) == 12
+        @test typeof(genocount_observed(sharks.genodata.genotype)) <: Dict{<:Tuple,Int64}
+        @test length(genocount_expected(sharks.genodata.genotype)) == 25
+        @test typeof(genocount_expected(sharks.genodata.genotype)) <: Dict{<:Tuple,Float64}
     end
 end
 

test/utils.jl

@@ -24,7 +24,7 @@ x = @nancycats
         @test alleles([(1,2), (1,4)], false) == [1,2,1,4] 
         @test alleles([(1,2), (1,4), missing], false) == [1,2,1,4] 
         @test all(alleles([(1,2), (1,4), missing], true) .=== [1,2,1,4,missing])
-        @test unique_alleles([(1,2), (1,4), missing]) == [1,2,4]
+        @test uniquealleles([(1,2), (1,4), missing]) == [1,2,4]
         @test size(locidataframe(x)) == (9,237)
         @test size(locimatrix(x)) == (237,9)
         @test length(phasedmatrix(x)) == 2