Merge pull request #66 from PharmCat/Remove-NCA

Remove nca

.github/workflows/Documenter.yml

@@ -21,15 +21,16 @@ jobs:
     runs-on: ubuntu-latest
     timeout-minutes: 30
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v3
+      - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.5'
+          version: "1"
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-          GKSwstype: "100"
         run: julia --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -1,12 +1,14 @@
 name: TagBot
 on:
-  issue_comment:
+  issue_comment:  # THIS BIT IS NEW
     types:
       - created
   workflow_dispatch:
 jobs:
   TagBot:
+    # THIS 'if' LINE IS NEW
     if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    # NOTHING BELOW HAS CHANGED
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1

.github/workflows/Tier1.yml

@@ -18,22 +18,38 @@ on:
       - '.github/**'
       - 'change.log'
       - '.gitignore'
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
-  ci:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.6, 1.7, 1.8]
-        julia-arch: [x64]
-        os: [ubuntu-latest, macOS-latest, windows-2019]
+        version:
+          - '1.6'
+          - '1.7'
+          - '1.8'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
-      - uses: julia-actions/julia-buildpkg@master
-      - uses: julia-actions/[email protected]
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-      - uses: julia-actions/[email protected]
-        if:  ${{ startsWith(matrix.os, 'Ubuntu') && startsWith(matrix.julia-version, '1.6') }}
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v3
+        with:
+          files: lcov.info
+

Project.toml

@@ -4,7 +4,6 @@ authors = ["Vladimir Arnautov ([email protected])"]
 version = "0.7.0"
 
 [deps]
-DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -13,19 +12,19 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 
 [compat]
-DataFrames = "1"
-Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
+Distributions = "0.21, 0.22, 0.23, 0.24, 0.25"
 QuadGK = "1, 2"
 Roots = "1, 2"
 SpecialFunctions = "1, 2"
 StatsBase = "0.30, 0.31, 0.32, 0.33"
 julia = "1"
 
 [extras]
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["CSV", "Test", "Plots", "StableRNGs"]
+test = ["DataFrames", "CSV", "Test", "Plots", "StableRNGs"]

README.md

@@ -1,16 +1,13 @@
 # ClinicalTrialUtilities
 
- Clinical trial related calculation: descriptive statistics, power and sample size calculation, power simulations, confidence interval, pharmacokinetics/pharmacodynamics parameters calculation. This program comes with absolutely no warranty. No liability is accepted for any loss and risk to public health resulting from use of this software.
+ Clinical trial related calculation:  power and sample size calculation, randomization. This program comes with absolutely no warranty. No liability is accepted for any loss and risk to public health resulting from use of this software.
 
 ![Tier 1](https://github.com/PharmCat/ClinicalTrialUtilities.jl/workflows/Tier%201/badge.svg)
 
 [![codecov](https://codecov.io/gh/PharmCat/ClinicalTrialUtilities.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/PharmCat/ClinicalTrialUtilities.jl)
 
 [![Latest docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://pharmcat.github.io/ClinicalTrialUtilities.jl/dev/)
 
-## Description
-
-The package is designed to perform calculations related to the planning and analysis of the results of clinical trials. The package includes the basic functions described below, as well as a few modules to perform specific calculations.
 
 ### <a name="Installation">Installation</a>
 ```
@@ -21,9 +18,6 @@ using Pkg; Pkg.add("ClinicalTrialUtilities");
 
 - Clinical trial sample size calculation
 - Power calculation
-- Confidence Intervals calculation
-- NCA Pharmacokinetics parameters calculation
-- Descriptive statistics and frequencies
 - Randomization
 
 
@@ -102,36 +96,20 @@ pooledcv([0.12, 0.2, 0.25], [14, 22, 32], [:d2x2, :d2x2, :d2x2])
 
 ```
 
-#### Confidence Intervals
+#### Randomization
+```
+using DataFrames, ClinicalTrialUtilities
+rt = ClinicalTrialUtilities.randomtable(;blocksize = 4, subject = 32, group = 2, ratio = [1,1], grseq = ["TR", "RT"], seed = 36434654652452)
 ```
-using  ClinicalTrialUtilities
-ci = propci(38, 100, alpha=0.05, method=:cp)
 
-ci = orpropci(30, 100, 40, 90; alpha=0.05, method=:mn)
+#### Confidence Intervals
 
-ci = diffpropci(30, 100, 40, 90; alpha=0.05, method=:wald)
+Proportion CI moved to [MetidaFreq.jl](https://github.com/PharmCat/MetidaFreq.jl)
 
-ci = meanci(30, 10, 30, alpha = 0.05, method=:norm)
-```
 
 #### NCA
-```
-using CSV, DataFrames, ClinicalTrialUtilities
-pkdatapath = joinpath(dirname(pathof(ClinicalTrialUtilities)))*"\\..\\test\\csv\\pkdata2.csv"
-pkdata  = CSV.File(pkdatapath) |> DataFrame
-pkds    = pkimport(pkdata, [:Subject, :Formulation]; time = :Time, conc = :Concentration)
-pk      = nca!(pkds)
-ncadf   = DataFrame(pk; unst = true)
-ds      = ClinicalTrialUtilities.descriptive(ncadf, stats = [:n, :mean, :sd], sort = [:Formulation])
-dsdf    = ClinicalTrialUtilities.DataFrame(ds; unst = true)
-
-```
-#### Randomization
-```
-using DataFrames, ClinicalTrialUtilities
-rt = ClinicalTrialUtilities.randomtable(;blocksize = 4, subject = 32, group = 2, ratio = [1,1], grseq = ["TR", "RT"], seed = 36434654652452)
-```
 
+NCA moved to [MetidaNCA.jl](https://github.com/PharmCat/MetidaNCA.jl)
 
 ### <a name="Copyrights">Copyrights</a>
 

change.log

@@ -1,3 +1,7 @@
+V0.7.0
+  - Stay only sample size, power and randomization. Other functions moved to another packages.
+  - Change licance.
+
 v0.6.2
   - Minor fix
   - Deps

docs/make.jl

@@ -10,15 +10,9 @@ makedocs(
         "Home" => "index.md",
         "Sample size" => "samplesize.md",
         "Power" => "power.md",
-        "Confidence intervals" => "ci.md",
-        "Descriptive statistics" => "ds.md",
-        "NCA" => "nca.md",
         "Randomization" => "random.md",
-        "Simulations" => "sim.md",
         "Utilities" => "utils.md",
         "Examples" => "examples.md",
-        "Export" => "export.md",
-        "Validation" => "validation.md",
         "References" => "ref.md",
     ],
 )

docs/src/examples.md

@@ -82,23 +82,6 @@ bepower(cv=0.4, n=35, design=:d2x4x4)
 bepower(cv=0.14, n=21)
 ```
 
-## Confidence intervals
-
-```julia
-using ClinicalTrialUtilities
-
-propci(81, 263, alpha=0.05, method=:wilson)
-
-diffpropci(7, 34, 1, 34; alpha=0.05, method=:nhs)
-
-orpropci(2, 14, 1, 11; alpha=0.05, method=:woolf)
-
-rrpropci(2, 14, 1, 11; alpha=0.05)
-
-diffmeanci(30, 10, 30, 40, 12, 35, alpha=0.05, method=:ev)
-
-```
-
 ## Utilities
 
 ### CV from CI
@@ -120,15 +103,3 @@ push!(data, (0.2, 20))
 push!(data, (0.25, 30))
 pooledcv(data; cv=:cv, df=:df, alpha=0.05, returncv=true)
 ```
-
-## Simulations
-
-```julia
-using ClinicalTrialUtilities
-
-#Make power task
-t = bepower(cv=0.2, n=20).task
-
-#Run simulation
-result = ctsim(t; nsim = 100, seed=0)
-```

docs/src/index.md

@@ -1,6 +1,6 @@
 # ClinicalTrialUtilities
 
- Clinical trial related calculation: descriptive statistics, power and sample size calculation, power simulations, confidence interval, pharmacokinetics/pharmacodynamics parameters calculation.
+ Clinical trial related calculation: power and sample size calculation, randomization.
 
 [![Build Status](https://travis-ci.com/PharmCat/ClinicalTrialUtilities.jl.svg?branch=master)](https://travis-ci.com/PharmCat/ClinicalTrialUtilities.jl)
 [![Build status](https://ci.appveyor.com/api/projects/status/35f8b5vq259sbssg?svg=true)](https://ci.appveyor.com/project/PharmCat/clinicaltrialutilities-jl)
@@ -10,13 +10,25 @@
 
 ## Description
 
-The package is designed to perform calculations related to the planning and analysis of the results of clinical trials. The package includes the basic functions described below, as well as a few modules to perform specific calculations.
-
+The package is designed to perform calculations related to the planning of clinical trials.
 ## Installation
 ```
 using Pkg; Pkg.add("ClinicalTrialUtilities");
 ```
 
+### Pharmacodynamics
+
+Further development of NCA PK/PD will be based on [MetidaNCA.jl](https://github.com/PharmCat/MetidaNCA.jl) package.
+
+All NCA PK/PD functions moved to [MetidaNCA](https://github.com/PharmCat/MetidaNCA.jl).
+
+Descriptive statistics moved to  [MetidaStats](https://github.com/PharmCat/MetidaStats.jl).
+
+Confidence intervals moved to  [MetidaFreq](https://github.com/PharmCat/MetidaFreq.jl).
+
+Simulations removed.
+
+
 ## Note
 
 **NB! Hypothesis types:**
@@ -38,17 +50,10 @@ Pages = [
 
         "samplesize.md",
         "power.md",
-        "ci.md",
-        "ds.md",
-        "nca.md",
-        "pk.md",
-        "pd.md",
         "random.md",
-        "sim.md",
         "utils.md",
         "examples.md",
         "export.md",
-        "validation.md",
         "ref.md"]
 Depth = 4
 ```