Merge pull request #20 from PharmCat/dev

Dev

Project.toml

@@ -1,7 +1,7 @@
 authors = ["Vladimir Arnautov (mail@pharmcat.net)"]
 name = "ClinicalTrialUtilities"
 uuid = "535c2557-d7d0-564d-8ff9-4ae146c18cfe"
-version = "0.1.11"
+version = "0.1.12"
 
 [deps]
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"

README.md

@@ -18,7 +18,6 @@ The package is designed to perform calculations related to the planning and anal
 
 - [Installation](#Installation)
 - [Basic functions](#Basic)
-- [Submodules](#Submodules)
 - [Usage](#Usage)
   - [descriptives](#descriptives)
   - [ctSampleN](#ctSampleN)
@@ -27,6 +26,21 @@ The package is designed to perform calculations related to the planning and anal
   - [bePower](#bePower)
   - [ci2cv](#ci2cv)
   - [pooledCV](#pooledCV)
+- [Submodules](#Submodules)
+  - [CI](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md)
+    - [oneProp](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md#oneProp)
+    - [oneMean](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md#oneMean)
+    - [twoProp](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md#twoProp)
+    - [twoMeans](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md#twoMeans)
+    - [cmh](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md#cmh)
+  - [PK](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/PK.md)
+    - [nca](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/PK.md#nca)
+  - [SIM](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md)
+    - [bePower](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md#bePower)
+    - [ctPropPower](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md#ctPropPower)
+    - [ctPropSampleN](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md#ctPropSampleN)
+    - [ctMeansPower](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md#ctMeansPower)
+    - [ctMeansPowerFS](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md#ctMeansPowerFS)
 - [Types](#Types)
 - [Examples](#Examples)
 - [Other](#Other)
@@ -64,26 +78,6 @@ Pkg.test("ClinicalTrialUtilities");
 
 - [Pooled CV from multiple sources](#pooledCV)
 
-### <a name="Submodules">Submodules</a>
-
-* Confidence interval calculation - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md)
-  * oneProp
-  * oneMeans
-  * twoProp
-  * twoMeans
-  * cmh
-
-* Pharmacokinetics calculation - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/mater/doc/PK.md)
-  * nca
-
-* Simulations - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md)
-  * bePower
-  * bePowerSIM
-  * ctPropPower
-  * ctPropSampleN
-  * ctMeansPower
-  * ctMeansPowerFS
-
 ### <a name="Usage">Usage</a>
 
 **NB! Hypothesis types:**
@@ -341,6 +335,26 @@ pooledCV(data::DataFrame; cv=:cv, df=:df, alpha=0.05, returncv=true)::ConfInt
 - true  - return cv
 - false - return var
 
+### <a name="Submodules">Submodules</a>
+
+* Confidence interval calculation - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/CI.md)
+  * oneProp
+  * oneMeans
+  * twoProp
+  * twoMeans
+  * cmh
+
+* Pharmacokinetics calculation - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/mater/doc/PK.md)
+  * nca
+
+* Simulations - [Doc](https://github.com/PharmCat/ClinicalTrialUtilities.jl/blob/master/doc/SIM.md)
+  * bePower
+  * bePowerSIM
+  * ctPropPower
+  * ctPropSampleN
+  * ctMeansPower
+  * ctMeansPowerFS
+
 ### <a name="Types">Types</a>
 
 Confidence intervals

cange.log

@@ -1,9 +1,18 @@
 v0.1.12
-  - nca hotfix
-  - add test
+  - add MOVER OR CI
+  - add MN RR CI
+  - MN OR - change algo, for old algo use :mn2
+  - MN Diff - code optimization
+  - Mee|FM Diff- code optimization
+  - Code cleaning and cosmetics
+  - add tests and testdata
+  - HTML Export function
 
 v0.1.11
 
+  - nca hotfix
+  - add test
+
   - descriptives()
   - html export - initial, not final
   - StatsBase, Statistics in deps

doc/CI.md

@@ -4,29 +4,19 @@ CI submodule needs for clinical trial simulations with binomial outcomes, but ca
 
 ## Functions
 
-One proportion
+- [oneProp](#oneProp) - One proportion
 
-oneProp(x, n; alpha, method)
+- [oneMean](#oneMean) - One mean
 
-One mean
+- [twoProp](#twoProp) - Two proportions
 
-oneMean(m, s, n, alpha; method)
+- [twoMeans](#twoMeans) - Two means
 
-Two proportions
+ - [cmh](#cmh) - Cochran–Mantel–Haenszel confidence intervals.
 
-twoProp(x1, n1, x2, n2; alpha, type, method)
+ - [Examples](#Examples)
 
-Two means
-
-twoMeans(m1, s1, n1, m2, s2, n2; alpha, type, method)
-
-Cochran–Mantel–Haenszel confidence intervals.
-
-cmh(data::DataFrame; a = :a, b = :b, c = :c, d = :d, type = :diff, alpha = 0.05, method)
-
-Return result as ConfInt(lower::Float64, upper::Float64, estimate::Float64)
-
-### oneProp
+### <a name="oneProp">oneProp</a>
 
 Confidence interval calculation for one proportion.
 
@@ -50,7 +40,7 @@ CI.oneProp(x::Int, n::Int; alpha=0.05, method=:wilson)
 - arcsine - Arcsine CI;
 - wald - Wald CI without CC;
 
-### twoProp
+### <a name="twoProp">twoProp</a>
 
 Confidence interval calculation for two proportion.
 
@@ -97,7 +87,7 @@ Odd ratio
 - woolf - Woolf logit CI
 - awoolf - Adjusted Woolf interval (Gart adjusted logit)
 
-### oneMean
+### <a name="oneMean">oneMean</a>
 
 Confidence interval for one mean.
 
@@ -118,7 +108,7 @@ CI.oneMean(m::Real, s::Real, n::Int, alpha::Real; method=:norm)::ConfInt
 - :norm - Normal distribution (default);
 - :tdist - T Distribution.
 
-### twoMeans
+### <a name="twoMeans">twoMeans</a>
 
 Confidence interval for mean difference.
 
@@ -145,7 +135,7 @@ CI.twoMeans(m1::Real, s1::Real, n1::Real, m2::Real, s2::Real, n2::Real; alpha::R
 - :ev - equal variance (default);
 - :uv - unequal variance with Welch-Satterthwaite df correction.
 
-### cmh
+### <a name="cmh">cmh</a>
 
 Cochran–Mantel–Haenszel confidence intervals.
 
@@ -205,7 +195,7 @@ For risk difference use:
 ci = ClinicalTrialUtilities.CI.cmh(data, alpha = 0.1)
 ```
 
-## Examples:
+## <a name="Examples">Examples</a>
 
 ```
 ClinicalTrialUtilities.CI.oneProp(81, 263, alpha=0.05, method=:wilson)

doc/PK.md

@@ -4,6 +4,12 @@ Pharmacokinetics module.
 
 ## Functions
 
+- [nca](#nca) - Non-noncompartment analysis.
+
+### <a name="nca">nca</a>
+
+Non-noncompartment analysis.
+
 ```
 nca(data; conc=:Concentration, time=:Time, sort = NaN, calcm = :lint)
 ```

doc/SIM.md

@@ -16,31 +16,31 @@ Proportion simulation sample size
 
 ctPropSampleN(p1, p2, ref; alpha, beta, type, citype, method, simnum, seed)
 
-### bePower
+### <a name="bePower">bePower</a>
 
 ```
 bePower(;alpha=0.05, logscale=true, theta1=0.8, theta2=1.25, theta0=0.95, cv=0.0, n=0, simnum=5, seed=0)
 ```
 
-### ctPropPower
+### <a name="ctPropPower">ctPropPower</a>
 
 ```
 ctPropPower(p1, n1, p2, n2, diff; alpha=0.05, type=:or, method=:mn, seed=0, simnum=5)
 ```
 
-### ctPropSampleN
+### <a name="ctPropSampleN">ctPropSampleN</a>
 
 ```
 ctPropSampleN(p1, p2, ref; alpha=0.05, beta=0.2, type=:notdef, citype =:notdef, method=:notdef, simnum=5, seed=0)
 ```
 
-### ctMeansPower
+### <a name="ctMeansPower">ctMeansPower</a>
 
 ```
 ctMeansPower(m1, s1, n1, m2, s2, n2, ref; alpha=0.05, method=:notdef, simnum=5, seed=0)
 ```
 
-### tMeansPowerFS
+### <a name="ctMeansPowerFS">ctMeansPowerFS</a>
 
 ```
 ctMeansPowerFS(m1, s1, n1, m2, s2, n2, ref;alpha=0.05, method=:notdef, simnum::Real=5, seed=0)