Merge pull request #64 from PharmCat/Remove-NCA

Remove NCA
PharmCat · Feb 12, 2023 · 1813f04 · 1813f04
2 parents 87de3ac + 378e40c
commit 1813f04
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diff --git a/Project.toml b/Project.toml
@@ -1,14 +1,13 @@
 name = "ClinicalTrialUtilities"
 uuid = "535c2557-d7d0-564d-8ff9-4ae146c18cfe"
 authors = ["Vladimir Arnautov ([email protected])"]
-version = "0.6.6"
+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"
-RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
@@ -17,8 +16,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 DataFrames = "1"
 Distributions = "0.20, 0.21, 0.22, 0.23, 0.24, 0.25"
 QuadGK = "1, 2"
-RecipesBase = "1"
-Roots = "1.0, 2"
+Roots = "1, 2"
 SpecialFunctions = "1, 2"
 StatsBase = "0.30, 0.31, 0.32, 0.33"
 julia = "1"

diff --git a/docs/make.jl b/docs/make.jl
@@ -12,10 +12,7 @@ makedocs(
         "Power" => "power.md",
         "Confidence intervals" => "ci.md",
         "Descriptive statistics" => "ds.md",
-        "NCA" => ["NCA" => "nca.md",
-        "Pharmakokinetics" => "pk.md",
-        "Pharmacodynamics" => "pd.md",
-        "PK Plots" => "pkplot.md"],
+        "NCA" => "nca.md",
         "Randomization" => "random.md",
         "Simulations" => "sim.md",
         "Utilities" => "utils.md",

diff --git a/docs/src/nca.md b/docs/src/nca.md
@@ -1,133 +1,7 @@
 # Non-compartment analysis
 
-*See [MetidaNCA.jl](https://github.com/PharmCat/MetidaNCA.jl). MetidaNCA.jl will replace CTU in plans.*
+Further development of NCA PK/PD will be based on [MetidaNCA.jl](https://github.com/PharmCat/MetidaNCA.jl) package.
 
-NCA analysis based on following steps:
+All NCA PK/PD functions moved to [MetidaNCA](https://github.com/PharmCat/MetidaNCA.jl).
 
-1. Loadind data to DataFrame;
-2. Constructing subjects list with pkimport/pdimport;
-3. Run NCA;
-4. Exporting to DataFrame;
-5. Descriptive statistics / HTML export.
-
-### Description
-
-```julia
-include("ncatable.jl")
-```
-#### AUC
-
-```math
-AUC = \sum_{n=1}^N AUC_{n}
-```
-
-Where `AUCn` - partial AUC.
-
-Linear trapezoidal rule
-
-```math
-AUC\mid_{t_1}^{t_2} = \delta t \times \frac{C_1 + C_2}{2}
-
-AUMC\mid_{t_1}^{t_2} = \delta t \times \frac{t_1 \times C_1 + t_2 \times C_2}{2}
-```
-
-Logarithmic trapezoidal rule
-
-```math
-AUC\mid_{t_1}^{t_2} =   \delta t \times \frac{ C_2 - C_1}{ln(C_2/C_1)}
-
-AUMC\mid_{t_1}^{t_2} = \delta t \times \frac{t_2 \times C_2 - t_1 \times C_1}{ln(C_2/C_1)} -  \delta t^2 \times \frac{ C_2 - C_1}{ln(C_2/C_1)^2}
-```
-
-Linear interpolation rule
-
-```math
-C_x = C_1 + \frac{(t_x-t_1)\times(C_2 - C_1)}{t_2 - t_1}
-```
-
-Logarithmic interpolation rule
-
-```math
-C_x = exp\left(ln(C_1) + \frac{(t_x-t_1)\times(ln(C_2) - ln(C_1))}{t_2 - t_1}\right)
-```
-
-#### MRTlast
-
-```math
-MRTlast    = AUMClast / AUClast
-```
-
-#### ```math \lambda_z ```- elimination constant
-
-#### HL
-
-```math
-HL = ln(2) / \lambda_z
-```
-
-#### AUCinf
-
-```math
-AUCinf = AUClast + \frac{Clast}{\lambda_z}
-```
-
-#### AUMCinf
-
-```math
-AUMCinf =  AUMClast + \frac{tlast\times Clast}{\lambda_z} + \frac{Clast}{\lambda_z^2}
-```
-
-#### AUCpct
-
-```math
-AUCpct = (AUCinf - AUClast) / AUCinf * 100.0%
-```
-
-#### Accumulation index
-
-```math
-Accind = \frac{1}{1 - exp(-\lambda_z \tau)}
-```
-
-### nca!
-```@docs
-ClinicalTrialUtilities.nca!
-```
-
-### Scenario
-
-1 Loading DataFrame
-
-```julia
-using CSV, DataFrames, ClinicalTrialUtilities
-pkdata2 = CSV.File("pkdata.csv") |> DataFrame
-```
-2 Subject list
-
-```julia
-  pkds = pkimport(pkdata2, [:Subject, :Formulation]; time = :Time, conc = :Concentration)
-```
-
-3 NCA  analysis with default settings
-
-```julia
-  pk   = nca!(pkds)
-```
-
-4 Exporting
-
-```julia
-  ncadf   = DataFrame(pk; unst = true)
-```
-
-5 Descriptive statistics
-
-```julia
-  ds   = ClinicalTrialUtilities.descriptive(ncadf, stats = [:n, :mean, :sd], sort = [:Formulation])
-```
-
-6 Exporting  
-
-```julia
-  dsdf   = ClinicalTrialUtilities.DataFrame(ds; unst = true)
-```
+Validation included.
diff --git a/docs/src/ncatable.jl b/docs/src/ncatable.jl
diff --git a/docs/src/pd.md b/docs/src/pd.md
@@ -1,6 +1,7 @@
 ### Pharmacodynamics
 
-#### pdimport
-```@docs
-ClinicalTrialUtilities.pdimport
-```
+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).
+
+Validation included.
diff --git a/docs/src/pk.md b/docs/src/pk.md
diff --git a/docs/src/pkplot.md b/docs/src/pkplot.md
diff --git a/src/ClinicalTrialUtilities.jl b/src/ClinicalTrialUtilities.jl
@@ -14,7 +14,7 @@
 __precompile__(true)
 module ClinicalTrialUtilities
 
-using Distributions, Random, Roots, QuadGK, RecipesBase
+using Distributions, Random, Roots, QuadGK
 
 using StatsBase
 
@@ -63,8 +63,7 @@ include("info.jl")
 
 #Descriptive statistics
 include("descriptives.jl")
-#PK
-include("pk.jl")
+
 #Export
 include("export.jl")
 #Randomization
@@ -73,8 +72,6 @@ include("randomization.jl")
 include("utilities.jl")
 #Show
 include("show.jl")
-#Plots
-include("plots.jl")
 #Deprecated
 include("deprecated.jl")