v0.3.2

Project.toml

@@ -13,7 +13,6 @@ Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 
 [extras]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -24,13 +23,12 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 test = ["CSV", "Test", "Plots"]
 
 [compat]
-julia = "1.0, 1.1, 1.2, 1.3, 1.4"
-Distributions = "0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23"
+julia = "1.0, 1.1, 1.2, 1.3, 1.4, 1.5"
+Distributions = "0.16, 0.17, 0.18, 0.19, 0.20, 0.21, 0.22, 0.23, 0.24"
 StatsBase = "0.22, 0.23, 0.24, 0.25, 0.26, 0.27, 0.28, 0.29, 0.30, 0.31, 0.32, 0.33"
 QuadGK = "2.0, 2.1, 2.2, 2.3, 2.4"
-SpecialFunctions = "0.8, 0.9, 0.10"
-Roots = "0.7, 0.8, 1.0"
-RecipesBase = "0.7, 0.8, 1.0"
+SpecialFunctions = "0.8, 0.9, 0.10, 1"
+Roots = "0.7, 0.8, 1"
+RecipesBase = "0.7, 0.8, 1"
 Reexport = "0.1, 0.2"
 DataFrames = "0.19, 0.20"
-CSV = "0.5, 0.6"

README.md

@@ -8,10 +8,6 @@
 [![Coverage Status](https://coveralls.io/repos/github/PharmCat/ClinicalTrialUtilities.jl/badge.svg?branch=master)](https://coveralls.io/github/PharmCat/ClinicalTrialUtilities.jl?branch=master)
 [![Latest docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://pharmcat.github.io/ClinicalTrialUtilities.jl/dev/)
 
-## Difference since v0.3.0
-
-  Wrong Equivalence Hypothesis alpha level! Use 0.2.7 or 0.3.1 version.
-
 ## 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.

cange.log

@@ -1,7 +1,8 @@
 v0.3.2
   - bugfix fisher test
   - add show
-  - propci for ConTab 
+  - propci for ConTab
+  - bump dependencies
 
 v0.3.1
 

docs/src/index.md

@@ -29,6 +29,10 @@ When ctpower/ctsamplen used:
 - :ei - Equivalencens: two one-sided hypothesis;
 - :ns - Non-Inferiority / Superiority: one-sided hypothesis, for some cases you should use two-sided hypothesis for  Non-Inferiority/Superiority, you can use alpha/2 for this;
 
+## Invalidated version v0.3.0 (removed from release page)
+
+  Wrong Equivalence Hypothesis alpha level! Use 0.2.7, 0.3.1 version or higher.
+
 ## Contents
 
 ```@contents

src/ci.jl

@@ -154,6 +154,11 @@ function propci(x::Int, n::Int; alpha::Real = 0.05, method = :default)::ConfInt
         throw(ArgumentError("unknown method!"))
     end
 end
+"""
+    propci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)
+
+Confidence interval for proportions a / (a + b) and c / (c + d)
+"""
 function propci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)
     d = Dict()
     d[tab.row[1]] = propci(tab.a, tab.a + tab.b; alpha = alpha, method = method)
@@ -192,6 +197,9 @@ function diffpropci(x1::Int, n1::Int, x2::Int, n2::Int; alpha::Real = 0.05, meth
     if alpha >= 1.0 || alpha <= 0.0
         throw(ArgumentError("Alpha shold be > 0.0 and < 1.0"))
     end
+    if x1 > n1 || x2 > n2
+        throw(ArgumentError("X cann't be more than N"))
+    end
     if method == :nhs
         return propdiffnhsci(x1, n1, x2, n2, alpha)
     elseif method == :nhscc
@@ -212,7 +220,11 @@ function diffpropci(x1::Int, n1::Int, x2::Int, n2::Int; alpha::Real = 0.05, meth
         throw(ArgumentError("Method unknown!"))
     end
 end
-#TEST
+"""
+    diffpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
+
+Confidence interval for proportion difference: (a / (a + b)) - (c / (c + d))
+"""
 function diffpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
     diffpropci(tab.a, tab.a + tab.b, tab.c, tab.c + tab.d; alpha = alpha, method = method)
 end
@@ -244,6 +256,11 @@ function rrpropci(x1::Int, n1::Int, x2::Int, n2::Int; alpha::Real = 0.05, method
         throw(ArgumentError("Method unknown!"))
     end
 end
+"""
+    rrpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
+
+Confidence interval for relative risk.
+"""
 function rrpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
     rrpropci(tab.a, tab.a + tab.b, tab.c, tab.c + tab.d; alpha = alpha, method = method)
 end
@@ -277,6 +294,11 @@ function orpropci(x1::Int, n1::Int, x2::Int, n2::Int; alpha::Real = 0.05, method
         throw(ArgumentError("Method unknown!"))
     end
 end
+"""
+    orpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
+
+Confidence interval for odd ratio.
+"""
 function orpropci(tab::ConTab{2,2}; alpha::Real = 0.05, method::Symbol = :default)::ConfInt
     orpropci(tab.a, tab.a + tab.b, tab.c, tab.c + tab.d; alpha = alpha, method = method)
 end

src/freque.jl

@@ -129,7 +129,16 @@ function contab(data::DataFrame, sort; row::Symbol, col::Symbol)
     end
     return DataSet(result)
 end
+"""
+    contab(m; row = nothing, col = nothing)
 
+Make contingency table.
+"""
+function contab(m::Matrix; row = nothing, col = nothing)
+    if isa(row, Nothing) row = Vector{Symbol}(undef, size(m, 1)) .= Symbol("") end
+    if isa(col, Nothing) col = Vector{Symbol}(undef, size(m, 2)) .= Symbol("") end
+    ConTab(m, row, col)
+end
 """
     mcnmcontab
 """