Merge pull request #53 from PharmCat/dev

v0.4.0 DataFrames initial remove (#52)

.travis.yml

@@ -6,11 +6,7 @@ os:
 
 julia:
   - 1.0
-  - 1.1
-  - 1.2
-  - 1.3
-  - 1.4
-  - 1.5
+  - 1
 
 branches:
   only:
@@ -32,9 +28,6 @@ jobs:
   allow_failures:
     - os:
         - windows
-    - julia:
-        - 1.4
-        - 1.5
   include:
     - stage: "Documentation"
       julia: 1.0

Project.toml

@@ -1,7 +1,7 @@
 authors = ["Vladimir Arnautov ([email protected])"]
 name = "ClinicalTrialUtilities"
 uuid = "535c2557-d7d0-564d-8ff9-4ae146c18cfe"
-version = "0.3.2"
+version = "0.4.0"
 
 [deps]
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -31,4 +31,4 @@ 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"
+DataFrames = "0.19, 0.20, 0.21, 0.22"

README.md

@@ -2,10 +2,10 @@
 
  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.
 
-[![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)
+![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)
-[![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/)
 
 ## Description

cange.log

@@ -1,3 +1,8 @@
+v0.4.0
+
+  - remove DataFrames interim
+  - minor fix
+
 v0.3.2
   - bugfix fisher test
   - add show
@@ -10,7 +15,7 @@ v0.3.1
   - simulation crush fix
   - Equivalence Hypothesis alpha level fix!
 
-v0.3.0
+v0.3.0 (removed)
   - #44 , #45 , #46
   - update test
   - Move alpha from CTask to Hypothesis

src/ClinicalTrialUtilities.jl

@@ -21,7 +21,7 @@ using Distributions, Random, Roots, QuadGK, RecipesBase, Reexport
 import SpecialFunctions
 import Base: show, findfirst, getproperty, showerror, getindex, length, in, iterate, eltype, deleteat!, findall
 import StatsBase.confint
-import DataFrames: DataFrame, DataFrames, names!, unstack, deleterows!, rename!, AbstractDataFrame
+import DataFrames: DataFrame, DataFrames, unstack
 
 try
     methods(SpecialFunctions.logabsgamma)
@@ -30,15 +30,6 @@ catch
     global lgamma(x) = SpecialFunctions.lgamma(x)
 end
 
-#=
-try
-    if collect(methods(DataFrames.delete!, (AbstractDataFrame, Any)))[1].file == Symbol("deprecated.jl")
-        DataFrames.delete!(df::AbstractDataFrame, inds) = deleterows!(df, inds)
-    end
-catch
-end
-=#
-
 const ZDIST  = Normal()
 const LOG2   = log(2)
 const PI2    = π * 2.0

src/ci.jl

@@ -849,17 +849,17 @@ end
     # metafor: Meta-Analysis Package for R - Wolfgang Viechtbauer
 
 """
-    diffcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d,
+    diffcmhci(data; a = :a, b = :b, c = :c, d = :d,
         alpha = 0.05, method = :default)::ConfInt
 
 Cochran–Mantel–Haenszel confidence intervals for proportion difference.
 
-**data**- dataframe with 4 columns, each line represent 2X2 table
+**data**- data with 4 columns, each line represent 2X2 table
 
-**a** **b** **c** **d** - dataframe table names (number of subjects in 2X2 table):
+**a** **b** **c** **d** - data table names (number of subjects in 2X2 table):
 
 """
-    function diffcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, method = :default)::ConfInt
+    function diffcmhci(data; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, method = :default)::ConfInt
         return diffcmhci(data[:, a], data[:, b], data[:, c], data[:, d]; alpha = alpha, method = method)
         #=
         n1 = data[:, a] + data[:, b]
@@ -909,12 +909,12 @@ Cochran–Mantel–Haenszel confidence intervals for proportion difference.
     end
 
     """
-        orcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d,
+        orcmhci(data; a = :a, b = :b, c = :c, d = :d,
             alpha = 0.05, logscale = false)::ConfInt
 
     Cochran–Mantel–Haenszel confidence intervals for odd ratio.
     """
-    function orcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, logscale = false)::ConfInt
+    function orcmhci(data; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, logscale = false)::ConfInt
         return orcmhci(data[:, a], data[:, b], data[:, c], data[:, d]; alpha = alpha, logscale = logscale)
         #=
         N  = data[:, a] + data[:, b] + data[:, c] + data[:, d]
@@ -949,12 +949,12 @@ Cochran–Mantel–Haenszel confidence intervals for proportion difference.
         if logscale return ConfInt(estimate - z*se, estimate + z*se, estimate, alpha) else return ConfInt(exp(estimate - z*se), exp(estimate + z*se), exp(estimate), alpha) end
     end
     """
-        rrcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d,
+        rrcmhci(data; a = :a, b = :b, c = :c, d = :d,
             alpha = 0.05, logscale = false)::ConfInt
 
     Cochran–Mantel–Haenszel confidence intervals for risk ratio.
     """
-    function rrcmhci(data::DataFrame; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, logscale = false)::ConfInt
+    function rrcmhci(data; a = :a, b = :b, c = :c, d = :d, alpha = 0.05, logscale = false)::ConfInt
         return rrcmhci(data[:, a], data[:, b], data[:, c], data[:, d]; alpha = alpha, logscale = logscale)
         #=
         n1 = data[:, a] + data[:, b]

src/dataset.jl

@@ -79,3 +79,15 @@ function Base.deleteat!(a::DataSet{T}, inds::Dict) where T
     deleteat!(a.data, findall(a, inds))
     return a
 end
+
+################################################################################
+#=
+function Tables.istable(table::DataSet)
+end
+
+function Tables.rows(table::DataSet)
+end
+
+function Tables.columns(table::DataSet)
+end
+=#

src/deprecated.jl

@@ -1,5 +1,44 @@
 #deprecated
 
+#DEPRECATED
+
+"""
+    DataFrames.DataFrame(data::DataSet{PKPDProfile}; unst = false, us = false)
+
+Make datafrafe from PK/PD DataSet.
+
+unst | us - unstack data;
+"""
+function DataFrames.DataFrame(data::DataSet{T}; unst = false, us = false) where T
+        d = DataFrame(id = Int[], sortvar = Symbol[], sortval = Any[])
+        for i = 1:length(data)
+            if length(data[i].sort) > 0
+                for s in data[i].sort
+                    push!(d, [i, s[1], s[2]])
+                end
+            end
+        end
+        d   = unstack(d, :sortvar, :sortval)[!,2:end]
+        df  = DataFrame()
+        dfn = names(d)
+        for i = 1:size(d,2)
+            df[!,dfn[i]] = Array{eltype(d[!, dfn[i]]), 1}(undef, 0)
+        end
+        df = hcat(df, DataFrame(param = Any[], value = Real[]))
+        for i = 1:size(d,1)
+            a = Array{Any,1}(undef, size(d,2))
+            copyto!(a, collect(d[i,:]))
+            for p in data[i].result
+                r = append!(copy(a), collect(p))
+            push!(df, r)
+            end
+        end
+        if unst || us
+            return unstack(df, names(df)[end-1], names(df)[end])
+        else
+            return df
+        end
+end
 
 #=
 function ncarule!(data::DataFrame, conc::Symbol, time::Symbol, rule::LimitRule)

src/descriptives.jl

@@ -114,7 +114,7 @@ function Base.show(io::IO, obj::DataSet{Descriptive})
     end
 end
 """
-    descriptive(data::DataFrame;
+    descriptive(data;
         sort::Union{Symbol, Array{T,1}} = Array{Symbol,1}(undef,0),
         vars = [],
         stats::Union{Symbol, Array{T,1}, Tuple{Vararg{Symbol}}} = :default)::DataSet{Descriptive} where T <: Union{Symbol, String}
@@ -125,7 +125,7 @@ Descriptive statistics.
 - ``vars`` variabels
 - ``stats`` statistics
 """
-function descriptive(data::DataFrame;
+function descriptive(data;
     sort::Union{Symbol, Array{T,1}} = Array{Symbol,1}(undef,0),
     vars = [],
     stats::Union{Symbol, Array{T,1}, Tuple{Vararg{Symbol}}} = :default)::DataSet{Descriptive} where T <: Union{Symbol, String}
@@ -202,15 +202,15 @@ end
 """
 Push in d Descriptive obj in mx vardata
 """
-@inline function pushvardescriptive!(d::Array{Descriptive, 1}, vars::Array{Symbol, 1}, mx::Union{DataFrame, Matrix{T}}, sortval::Union{Tuple{Vararg{Any}}, Nothing}, stats::Tuple{Vararg{Symbol}}) where T<: Real
+@inline function pushvardescriptive!(d::Array{Descriptive, 1}, vars::Array{Symbol, 1}, mx, sortval::Union{Tuple{Vararg{Any}}, Nothing}, stats::Tuple{Vararg{Symbol}}) where T<: Real
     for v  = 1:length(vars)  #For each variable in list
         push!(d, Descriptive(vars[v], nothing, sortval, descriptive_(mx[:, v], stats)))
     end
 end
 """
 Check if data row sortcol equal sortval
 """
-@inline function checksort(data::DataFrame, row::Int, sortcol::Array{Symbol, 1}, sortval::Tuple{Vararg{Any}})::Bool
+@inline function checksort(data, row::Int, sortcol::Array{Symbol, 1}, sortval::Tuple{Vararg{Any}})::Bool
     for i = 1:length(sortcol)
         if data[row, sortcol[i]] != sortval[i] return false end
     end
@@ -219,7 +219,7 @@ end
 """
 Return matrix of filtered data (datacol) by sortcol with sortval
 """
-@inline function getsortedmatrix(data::DataFrame; datacol::Array{Symbol,1}, sortcol::Array{Symbol,1}, sortval::Tuple{Vararg{Any}})::Matrix{Real}
+@inline function getsortedmatrix(data; datacol::Array{Symbol,1}, sortcol::Array{Symbol,1}, sortval::Tuple{Vararg{Any}})::Matrix{Real}
     result  = Array{Real, 1}(undef, 0)
     for c = 1:size(data, 1) #For each line in data
         if checksort(data, c, sortcol, sortval)

src/export.jl

@@ -1,10 +1,10 @@
 """
-    htmlexport(data::DataFrame; io::IO = stdout, sort = NaN,
+    htmlexport(data; io::IO = stdout, sort = NaN,
         rspan=:all, title="Title", dict::Union{Symbol, Dict} = :undef)
 
-HTLM export for DataFrame.
+HTLM export.
 """
-    function htmlexport(data::DataFrame; io::IO = stdout, sort = NaN, rspan=:all, title="Title", dict::Union{Symbol, Dict} = :undef)
+    function htmlexport(data; io::IO = stdout, sort = NaN, rspan=:all, title="Title", dict::Union{Symbol, Dict} = :undef)
         rowlist = Array{String,1}(undef, 0)
         cnames  = names(data)
         if isa(sort, Array)
@@ -189,7 +189,7 @@ HTLM export for DataFrame.
 
     <TBODY>"""
 
-        sort!(data, tuple(sort))
+        sort!(data, sort)
         tablematrix .= 1
         for c = 1:coln
             s = true