Merge pull request #7 from PharmCat/dev

gha upd

.github/workflows/Documenter.yml

@@ -22,7 +22,7 @@ jobs:
   Documenter:
     name: Documentation
     runs-on: ubuntu-latest
-    timeout-minutes: 40
+    timeout-minutes: 45
     steps:
       - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1

Project.toml

@@ -1,7 +1,7 @@
 name = "MetidaFreq"
 uuid = "bd16ee1e-1b2f-4f89-b253-604a522f8c5f"
 authors = ["PharmCat <[email protected]>"]
-version = "0.1.5"
+version = "0.2.0"
 
 [deps]
 
@@ -18,11 +18,11 @@ Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 [compat]
 
 CategoricalArrays = "0.8, 0.9, 0.10"
-Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
+Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 HypothesisTests  = "0.10, 0.11"
 MetidaBase = "0.11, 0.12"
 Optim = "1"
-Roots = "1, 2"
+Roots = "2"
 StatsBase = "0.30, 0.31, 0.32, 0.33, 0.34"
 Tables = "1"
 julia = "1"

docs/Project.toml

@@ -10,10 +10,9 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 
 [compat]
-Documenter = "≥0.26"
-MetidaFreq  = "0.1"
-HypothesisTests  = "0.10"
-CSV        = "0.7, 0.8, 0.9, 0.10"
+Documenter = "1"
+HypothesisTests  = "0.10, 0.11"
+CSV        = "0.9, 0.10"
 DataFrames = "1"
 PrettyTables = "2"
 

docs/src/api.md

@@ -12,6 +12,10 @@ MetidaFreq.contab
 MetidaFreq.freq
 ```
 
+### MetidaFreq.freqdict
+```@docs
+MetidaFreq.freqdict
+```
 
 ## Contingency tables utilities
 
@@ -94,6 +98,12 @@ MetidaFreq.metapropfixed
 MetidaFreq.metaproprandom
 ```
 
+## Base
+
+### Base.getindex
+```@docs
+getindex
+```
 
 ## HypothesisTests
 
@@ -111,3 +121,10 @@ HypothesisTests.MultinomialLRTest
 ```@docs
 HypothesisTests.FisherExactTest
 ```
+
+## Experimental
+
+### MetidaFreq.oddsci 
+```@docs
+MetidaFreq.oddsci 
+```

src/freq.jl

@@ -1,24 +1,51 @@
-
 """
-    freq(data, col; id = Dict())
-    
+    freqdict(data::AbstractVector) 
+
+Return frequencies as `Dict`.
 """
-function freq(data, col; id = Dict())
-    if isa(col, String) cols = Symbol(col) else cols = col end
-    column = Tables.getcolumn(data, cols)
-    d = Dict{eltype(column), Int}()
-    for i in column
+function freqdict(data::AbstractVector) 
+    d = Dict{eltype(data), Int}()
+    for i in data
         ind = ht_keyindex(d, i)
         if ind > 0
             @inbounds d.vals[ind] += one(Int)
         else
             @inbounds d[i] = one(Int)
         end
     end
+    d
+end
+
+"""
+    freq(data, col; id = Dict())
+ 
+Return frequencies as ix1 contingency table.
+"""
+function freq(data, col; id = Dict())
+    if isa(col, String) cols = Symbol(col) else cols = col end
+    column = Tables.getcolumn(data, cols)
+    d = freqdict(column) 
     k = collect(keys(d))
-    mx = Matrix{Int}(undef, 1, length(k))
+    mx = Matrix{Int}(undef, length(k), 1 )
     for i = 1:length(k)
-        @inbounds mx[1, i] = d[k[i]]
+        @inbounds mx[i, 1] = d[k[i]]
     end
-    ConTab(mx, [string(col)], string.(k), id)
+    ConTab(mx,  string.(k), [string(col)], id)
 end
+
+"""
+    freq(data::AbstractVector; id = Dict()) 
+ 
+Return frequencies as ix1 contingency table.
+"""
+function freq(data::AbstractVector; id = Dict()) 
+    d = freqdict(data) 
+    k = collect(keys(d))
+    mx = Matrix{Int}(undef, length(k), 1)
+    for i = 1:length(k)
+        @inbounds mx[i, 1] = d[k[i]]
+    end
+    ConTab(mx, string.(k), [""], id)
+end
+
+

test/tests.jl

@@ -307,8 +307,17 @@ end
 
     ct = MetidaFreq.freq(freqdat, :row)
     @test ct.tab[1,1] == 26
-    @test ct.tab[1,2] == 17
-    @test size(ct) == (1,2)
+    @test ct.tab[2,1] == 17
+    @test size(ct) == (2,1)
+
+    ct = MetidaFreq.freq(freqdat[!, :row])
+    @test ct.tab[1,1] == 26
+    @test ct.tab[2,1] == 17
+    @test size(ct) == (2,1)
+
+    ctd = MetidaFreq.freqdict(freqdat[!, :row])
+    @test ctd["w"] == 26
+    @test ctd["q"] == 17
 
     ct = MetidaFreq.contab(freqdat, :row, :col)
     @test ct.tab[1,1] == 21