Merge pull request #31 from PharmCat/dev

Multiple observations and covariates for PK data

Author: PharmCat

.github/workflows/Tier1.yml

@@ -25,16 +25,9 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        version:
-          - '1.6'
-          - '1.8'
-          - '1'
-        os:
-          - ubuntu-latest
-          - macOS-latest
-          - windows-latest
-        arch:
-          - x64
+        version: ['1.8', '1.10', '1']
+        arch: [x64]
+        os: [ubuntu-latest, windows-latest]
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2

Project.toml

@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.18"
+version = "0.6.0"
 
 
 
@@ -10,6 +10,7 @@ version = "0.5.18"
 MetidaBase = "075456b7-4006-432f-9324-2f8453996c49"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 

docs/Project.toml

@@ -11,7 +11,7 @@ Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 
 [compat]
 Documenter = "1"
-MetidaNCA  = "0.5"
+MetidaNCA  = "0.6"
 CSV        = "0.8, 0.9, 0.10"
 DataFrames = "1"
 PrettyTables = "1, 2"

docs/manual_ru.jmd

@@ -236,6 +236,25 @@ MetidaNCA.nca!(ds[1], adm = :ev, calcm = :lint, verbose = 1)
 
 ## ElimRange
 
+# Вычисление параметров
+
+## Пропущенные значения и интерполяция
+
+## Количество наблюдений
+
+## Время дозирования
+
+## Kel
+
+## Cdose
+
+## AUC/AUMC
+
+## Параметры равновесного состояния
+
+## Частичные AUC/AUMC
+
+
 
 \pagebreak
 

docs/src/api.md

@@ -115,6 +115,12 @@ MetidaNCA.getth
 MetidaNCA.pkplot
 ```
 
+### vpcplot
+
+```@docs
+MetidaNCA.vpcplot
+```
+
 ### setbl!
 
 ```@docs

docs/src/examples.md

@@ -66,23 +66,36 @@ dsnca = nca!(ds[1], adm = :ev, calcm = :lint, verbose = 2);
 ```@example ncaexample
 using Plots
 
+# plot 1
+
 p = pkplot(ds; typesort = :Subject, pagesort = NoPageSort(), filter = Dict(:Formulation => "R"))
 
 png(p, "plot1.png")
 
+# plot 2
+
 p = pkplot(ds; typesort = :Formulation, pagesort = NoPageSort(), legend = true)
 
 png(p, "plot2.png")
 
+# plot 3
+
 p = pkplot(ds; elim = true, ls = true)
 
 png(p[1][2], "plot3.png")
 
+# plot 4
 # If pagesort used - return pairs with `Page ID` => `Plot`
 
 p = pkplot(ds; typesort = :Subject, pagesort = :Formulation)
 
 png(p[1][2], "plot4.png")
+
+# plot 5
+
+p = vpcplot(ds)
+
+png(p, "plot5.png")
 ```
 
 #### Plot 1
@@ -101,6 +114,10 @@ png(p[1][2], "plot4.png")
 
 ![](plot4.png)
 
+#### Plot 5
+
+![](plot5.png)
+
 ## Set dose time
 
 You can set dose time with [`setdosetime!`](@ref) for whole subject set or for

src/MetidaNCA.jl

@@ -6,8 +6,8 @@ module MetidaNCA
 using RecipesBase
 
 import RecipesBase: plot!, plot
-
-import Base: length, length, push!, resize!
+import Statistics: mean, quantile
+import Base: length, push!, resize!, ht_keyindex, convert, first
 import MetidaBase
 import MetidaBase: Tables, StatsBase, PrecompileTools,
 PrettyTables,
@@ -29,7 +29,7 @@ using MetidaBase.Requires
 export pkimport, upkimport, pdimport, nca!, nca, DoseTime, ElimRange, LimitRule, NoPageSort,
 auc_sparse,
 setdosetime!, setkelauto!, setkelrange!, applylimitrule!, setbl!, setth!,
-pkplot,
+pkplot, vpcplot,
 getkeldata, getkelauto, getkelrange, getdosetime, getbl, getth, subset,
 metida_table,
 PKSubject, UPKSubject, PDSubject, NCAResult
@@ -56,6 +56,7 @@ const LOG2 = log(2)
     include("metidatable.jl")
     include("setblth.jl")
     include("timefilter.jl")
+    include("dropnanormissing.jl")
     include("sparse.jl")
     include("atomic.jl")
     include("precompile.jl")

src/applylimitrule.jl

@@ -9,7 +9,7 @@ Apply rule to PK subject .
 * STEP 3 (remove NaN): `rm` == true, then remove all `NaN` and `missing` values.
 """
 function applylimitrule!(data::Union{PKSubject, PDSubject}, rule::LimitRule)
-    applylimitrule!(data.time, data.obs, rule)
+    applylimitrule!(data.time, getobs(data), rule)
     data
 end
 """

src/dropnanormissing.jl

@@ -0,0 +1,22 @@
+function dropfunction!(f::Function, subj::PKSubject)
+    inds = findall(f, getobs(subj))
+    deleteat!(gettime(subj), inds)
+    deleteat!(getobs(subj), inds)
+    return subj
+end
+
+function dropfunction(f::Function, subj::PKSubject)
+    return dropfunction!(f, deepcopy(subj))
+end
+
+dropnanormissing!(subj::PKSubject)    =  dropfunction!(isnanormissing, subj)
+dropnanormissing(subj::PKSubject)     =  dropfunction(isnanormissing, subj)
+
+dropnan!(subj::PKSubject)    =  dropfunction!(isnan, subj)
+dropnan(subj::PKSubject)     =  dropfunction(isnan, subj)
+
+dropmissing!(subj::PKSubject) =  dropfunction!(ismissing, subj)
+dropmissing(subj::PKSubject)  =  dropfunction(ismissing, subj)
+
+
+