v0.5.0

Project.toml

@@ -1,7 +1,7 @@
 name = "ClinicalTrialUtilities"
 uuid = "535c2557-d7d0-564d-8ff9-4ae146c18cfe"
 authors = ["Vladimir Arnautov (mail@pharmcat.net)"]
-version = "0.4.1"
+version = "0.5.0"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -29,6 +29,7 @@ julia = "1.0, 1.1, 1.2, 1.3, 1.4, 1.5"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 
 [targets]
-test = ["CSV", "Test", "Plots"]
+test = ["CSV", "Test", "Plots", "StableRNGs"]

cange.log

@@ -1,8 +1,12 @@
+v 0.5.0
+  - StableRNGs test
+  - rng keyword for randomtable, randomseq
+  - auc_sparse for PKSubject
+
 v0.4.1
   - cox samplen
   - datatable
   - printdesigns
-
 
 v0.4.0
   - remove DataFrames interim

docs/src/pk.md

@@ -4,3 +4,8 @@
 ```@docs
 ClinicalTrialUtilities.pkimport
 ```
+
+#### auc_sparse
+```@docs
+ClinicalTrialUtilities.auc_sparse
+```

src/ClinicalTrialUtilities.jl

@@ -131,6 +131,7 @@ applyelimrange!,
 keldata,
 setkelauto!,
 getkelauto,
+auc_sparse,
 datatable,
 # Simulation
 ctsim,

src/pk.jl

@@ -1329,3 +1329,30 @@ function datatable_st(data) where T
 end
 function datatable_unst(data)
 end
+
+"""
+    auc_sparse(data::PKSubject)
+
+AUC for sparse data.
+
+```math
+w_1 = (t_2 - t_1) / 2
+w_j = (t_{j+1} - t_{j-1}) / 2  (2 \\leq j \\leq J - 1)
+w_J = (t_J - t_{J-1}) / 2
+
+AUC = \\sum_{j=1}^J \\mu_j w_j
+```
+
+where `math \\mu_j` is the mean drug concentration at time t.
+"""
+function auc_sparse(data::PKSubject)
+    wts = Vector{Float64}(undef, length(data))
+    wts[1]   = (data.time[2] - data.time[1])/2.0
+    wts[end] = (data.time[end] - data.time[end-1])/2.0
+    if length(data) > 2
+        for i = 2:length(data)-1
+            wts[i] = (data.time[i+1] - data.time[i-1])/2.0
+        end
+    end
+    return data.obs'*wts
+end

src/randomization.jl

@@ -4,20 +4,21 @@ struct RandomTable
     t
 end
 """
-    randomseq(;blocksize = 4, subject = 10, group = 2, ratio = [1,1],  seed = 0)
+    randomseq(;blocksize = 4, subject = 10, group = 2, ratio = [1,1],  seed = 0, rng = Random.GLOBAL_RNG)
 
 Randomization list generaton.
 
 - ``blocksize`` - size of block;
 - ``subject`` - subject number;
 - ``group`` - number of groups;
 - ``ratio`` - group ration, [1,1] means 1:1, [1,2] means 1:2, ets. ``length(ratio)`` should be equal ``group``;
-- ``seed`` - RNG seed.
+- ``seed`` - RNG seed;
+- ``rng`` - random number generator.
 """
-function randomseq(;blocksize::Int = 4, subject = 10, group = 2, ratio = [1,1], seed = 0)
+function randomseq(;blocksize::Int = 4, subject = 10, group = 2, ratio = [1,1], seed = 0, rng = Random.GLOBAL_RNG)
 
     #rng = MersenneTwister()
-    if seed != 0 Random.seed!(seed) end
+    if seed != 0 Random.seed!(rng, seed) end
 
     r = sum(ratio)
 
@@ -35,7 +36,7 @@ function randomseq(;blocksize::Int = 4, subject = 10, group = 2, ratio = [1,1],
     fbn = subject÷blocksize                                                     #block number
     rand  = Vector{Int}(undef, 0)                                                                  #rand list
     for i = 1:fbn
-        append!(rand, block[sample(1:blocksize, blocksize, replace=false)])     #generate and append random block
+        append!(rand, block[sample(rng, 1:blocksize, blocksize, replace=false)])     #generate and append random block
     end
 
     last = subject%blocksize                                                    #not full block
@@ -45,15 +46,15 @@ function randomseq(;blocksize::Int = 4, subject = 10, group = 2, ratio = [1,1],
         for i = 1:group
             append!(block, fill(i, Int(rm*ratio[i])))
         end
-        append!(rand, block[sample(1:last, last, replace=false)])
+        append!(rand, block[sample(rng, 1:last, last, replace=false)])
     end
     return rand
 
 end
 
 """
     randomtable(;blocksize = 4, subject = 10, group = 2,
-        ratio = [1,1], grseq = ["AB", "BA"], seed = 0)
+        ratio = [1,1], grseq = ["AB", "BA"], seed = 0, rng = Random.GLOBAL_RNG)
 
 
 Randomization table generaton. Return NamedTuple of vectors.
@@ -63,13 +64,14 @@ Randomization table generaton. Return NamedTuple of vectors.
 - ``group`` - number of groups;
 - ``ratio`` - group ration, [1,1] means 1:1, [1,2] means 1:2, ets. ``length(ratio)`` should be equal ``group``;
 - ``grseq`` - treatment sequence in each group;
-- ``seed`` - RNG seed.
+- ``seed`` - RNG seed;
+- ``rng`` - random number generator.
 """
-function randomtable(;blocksize::Int = 4, subject::Int = 10, group::Int = 2, ratio::Vector = [1,1], grseq::Vector{String} = ["AB", "BA"], seed = 0)
+function randomtable(;blocksize::Int = 4, subject::Int = 10, group::Int = 2, ratio::Vector = [1,1], grseq::Vector{String} = ["AB", "BA"], seed = 0, rng = Random.GLOBAL_RNG)
 
     if length(unique(length.(grseq))) != 1 throw(ArgumentError("Unequal grseq")) end
 
-    r = randomseq(;blocksize = blocksize, subject = subject, group = group, ratio = ratio,  seed = seed)
+    r = randomseq(;blocksize = blocksize, subject = subject, group = group, ratio = ratio,  seed = seed, rng = rng)
     subj = collect(1:length(r))
     seqrand  = vcat(grseq[r]...)
     nl = length(grseq[1]) + 3
@@ -83,7 +85,7 @@ function randomtable(;blocksize::Int = 4, subject::Int = 10, group::Int = 2, rat
     np[3] = seqrand
     for i=1:length(grseq[1])
         nm[i+3] = Symbol("Period_"*string(i))
-        np[i+3] = getindex.(seqrand, i)
+        np[i+3] = map(x-> x[i:i], seqrand)
     end
     return NamedTuple{Tuple(nm)}(Tuple(np))
 end

test/pktest.jl

@@ -1007,7 +1007,6 @@ println(" ---------------------------------- ")
     @test unca[1][:volume]  ≈ 11.0
      p    = ClinicalTrialUtilities.pkplot(upk, ylabel = "Excretion")
 end
-
 println(" ---------------------------------- ")
 @testset "#12  Pharmacodynamics   " begin
 
@@ -1041,3 +1040,9 @@ println(" ---------------------------------- ")
     print(io, pd)
     print(io, pd[1])
 end
+println(" ---------------------------------- ")
+@testset "#13  Sparse PK          " begin
+    pks = ClinicalTrialUtilities.PKSubject(sparse_pk; conc = :Concentration, time = :Time)
+    auc = ClinicalTrialUtilities.auc_sparse(pks)
+    @test auc ≈ 1.35 atol=1E-5
+end

test/sim.jl

@@ -1,5 +1,5 @@
 println(" ---------------------------------- ")
-@testset "  Simulations           " begin
+@testset "#14 Simulations         " begin
 
 t      = ClinicalTrialUtilities.bepower(cv=0.2, n=20).task
 result = ClinicalTrialUtilities.besim(t; nsim = 100, seed = 1234)

test/test.jl

@@ -1,6 +1,6 @@
 # Clinical Trial Utilities
 # Copyright © 2019 Vladimir Arnautov aka PharmCat (mail@pharmcat.net)
-using Distributions, Random, DataFrames, CSV, Test, Plots, StatsBase
+using Distributions, Random, DataFrames, CSV, Test, Plots, StatsBase, StableRNGs
 
 path    = dirname(@__FILE__)
 io      = IOBuffer();
@@ -223,9 +223,10 @@ include("freque.jl")
 
 println(" ---------------------------------- ")
 @testset "#9  Random              " begin
-    @test ClinicalTrialUtilities.randomseq(seed = 1234) == [1,2,2,1,2,1,1,2,2,1]
-    rdf   = ClinicalTrialUtilities.randomtable(seed = 1234)
-    @test rdf[:Group] == [1,2,2,1,2,1,1,2,2,1]
+    rng = StableRNG(0)
+    @test ClinicalTrialUtilities.randomseq(seed = 1234, rng = rng) == [1, 2, 1, 2, 2, 1, 1, 2, 2, 1]
+    rdf   = ClinicalTrialUtilities.randomtable(seed = 1234, rng = rng)
+    @test rdf[:Group] == [1, 2, 1, 2, 2, 1, 1, 2, 2, 1]
 end
 
 

test/testdata.jl

@@ -1,5 +1,6 @@
 #Simple PK DataFrame
 pkdata         = CSV.File(path*"/csv/pkdata.csv") |> DataFrame
+sparse_pk      = pkdata[2:7, :]
 #Simple PK DataFrame
 nanpkdata         = CSV.File(path*"/csv/nanpk.csv") |> DataFrame
 #Simple PD DataFrame