Extend partials, minor changes (#13)

v0.5.6

.github/workflows/Documenter.yml

@@ -21,10 +21,12 @@ on:
       - main
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     timeout-minutes: 40
     steps:
       - uses: actions/checkout@v3
+      - name: Update
+        run: sudo apt-get update
       - name: Install Pandoc
         run: sudo apt-get install pandoc texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra
       - uses: julia-actions/setup-julia@latest

Project.toml

@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <[email protected]>"]
-version = "0.5.5"
+version = "0.5.6"
 
 [deps]
 

change.log

@@ -1,3 +1,28 @@
+0.5.6
+  - extend partials
+
+0.5.5
+  - partials
+
+0.5.4
+  - minor changes
+
+0.5.3
+  - minor fix precompile
+  - 1.9 support
+  - minor changes
+
+0.5.2
+  - minor fix pkimport
+  - minor changes
+
+0.5.2
+  - minor fix pkimport
+  - minor changes
+
+0.5.1
+  - minor changes
+
 0.5.0
   - change pkplot api
   - Minor changes

docs/src/details.md

@@ -54,7 +54,7 @@ Calculate steady-state parameters.
     If end of tau interval lies after all observation, than extrapolation used to compute Ctau and partial AUCs. Extrapolation based on using elimination parameters.
 
 
-## [Unitful details](@ref unitful_details)
+## [Unitful details](@id unitful_details)
 
 !!! warning
   **Unitful.jl**

docs/src/examples.md

@@ -29,6 +29,14 @@ dsnca = nca!(ds, adm = :ev, calcm = :lint)
 dsnca[:, :AUClast]
 ```
 
+# Partial AUC
+
+```@example ncaexample
+dsnca = nca!(ds, adm = :ev, calcm = :lint, partials = [(1, 7)])
+
+dsnca[:, :AUC_1_7]
+```
+
 
 ## Print output
 

docs/src/index.md

@@ -24,7 +24,7 @@ Appendix 2: [Appendix2.1.pdf](./pdf/Appendix2.1.pdf), [Appendix2.2.pdf](./pdf/Ap
 
 ## Unitful
 
-See [Unitful details](@id unitful_details).
+See [Unitful details](@ref unitful_details).
 
 ## Contents
 

src/import.jl

@@ -67,6 +67,9 @@ function checkvalues(timevals_sp, concvals_sp; warn = true)
     if !(eltype(concvals_sp) <: Union{Number, Missing})
         warn && @warn "Some concentration values maybe not a number, try to fix."
         concvals_sp_ = floatparse.(concvals_sp, warn)
+    elseif eltype(concvals_sp) <: Integer
+        warn && @warn "Concentration values transformed to float."
+        concvals_sp_ = float.(concvals_sp)
     else
         concvals_sp_ = identity.(concvals_sp)
     end

src/nca.jl

@@ -410,16 +410,16 @@ end
 
 Non-compartmental (NCA) analysis of PK/PD data.
 """
-function nca!(data::DataSet{Subj}; adm = :ev, calcm = :lint, intpm = nothing,  partials = nothing, verbose = 0, warn = true, io::IO = stdout, modify! = identity) where Subj <: AbstractSubject
+function nca!(data::DataSet{Subj};  kwargs...) where Subj <: AbstractSubject
     result = Vector{NCAResult{Subj}}(undef, length(data))
     for i = 1:length(data)
-        result[i] = nca!(data[i]; adm = adm, calcm = calcm, intpm = intpm, partials = partials, verbose = verbose, warn = warn, io = io, modify! = modify!)
+        result[i] = nca!(data[i]; kwargs...)
     end
     DataSet(result)
 end
 
 """
-    nca!(data::PKSubject{T,O}; adm = :ev, calcm = :lint, intpm = nothing,  partials = nothing, verbose = 0, warn = true, io::IO = stdout, modify! = nothing) where T where O
+    nca!(data::PKSubject{T,O}; adm = :ev, calcm = :lint, intpm = nothing,  partials = nothing, prtext = :err, verbose = 0, warn = true, io::IO = stdout, modify! = nothing) where T where O
 
 * `adm` - administration:
     - `:ev` - extra vascular;
@@ -434,7 +434,8 @@ end
     - `:luld` - linear up log down;
     - `:luldt` - linear up log down after Tmax;
     - `:logt` - log-trapezoidal after Tmax;
-* `partials` - calculate partial AUC vor vector of time intervals;
+* `partials` - calculate partial AUC vor vector of time intervals (`:err` (default) - throw error if end time > last oservation time; `:last` - no extrapolation; `:extr` - if `Kel` calculated used extrapolation or `NaN` if no `Kel`);
+* `prtext` - extrapolation rule for partials AUC;
 * `verbose` - print to `io`, 1: partial areas table, 2: 1, and results;
 * `warn` - show warnings;
 * `io` - output stream;
@@ -488,8 +489,9 @@ Steady-state parameters (tau used):
 * Vztau
 
 `partials` is a vector of vectors, tuples or pairs. Example: `partials = [(1,2), (3,4)]`, `partials = [[1,2], (3,4)]`
+
 """
-function nca!(data::PKSubject{T, O}; adm = :ev, calcm = :lint, intpm = nothing,  partials = nothing, verbose = 0, warn = true, io::IO = stdout, modify! = identity) where T where O
+function nca!(data::PKSubject{T, O}; adm = :ev, calcm = :lint, intpm = nothing,  partials = nothing, prtext = :err, verbose = 0, warn = true, io::IO = stdout, modify! = identity) where T where O
 
     ptype  = promote_type(Float64, T, O)
 
@@ -706,7 +708,7 @@ function nca!(data::PKSubject{T, O}; adm = :ev, calcm = :lint, intpm = nothing,
             suffix = "_"*string(stime)*"_"*string(etime)
             stime = stime - data.dosetime.time
             etime = etime - data.dosetime.time
-            if etime > last(time_cp) error("End time can't be greater than last time point!") end 
+            if etime > last(time_cp) && prtext == :err error("End time can't be greater than last time point ($(last(time_cp)))! Use keyword `prtext=:last` or `prtext=:extr`...") end 
             #first point
             firstp = findfirst(x -> x >= stime, time_cp)
             #last point
@@ -718,11 +720,21 @@ function nca!(data::PKSubject{T, O}; adm = :ev, calcm = :lint, intpm = nothing,
                 firstpart += aucpart(stime, time_cp[firstp], firstpartc, obs_cp[firstp], calcm, stime > result[:Tmax])
                 #println("firstpartc = $firstpartc , firstpart = $firstpart")
             end
-            if etime > time_cp[lastp]
+            if etime > time_cp[lastp] && etime < last(time_cp) # if last time > etime -> interpolation
                 lastpartc  = interpolate(time_cp[lastp], time_cp[lastp + 1], etime, obs_cp[lastp], obs_cp[lastp + 1], intpm,  time_cp[lastp] > result[:Tmax])
                 lastpart +=  aucpart(time_cp[lastp], etime, obs_cp[lastp], lastpartc, calcm, time_cp[lastp] > result[:Tmax])
                 #println("lastpartc = $lastpartc , lastpart = $lastpart")
+            elseif etime > time_cp[lastp] && prtext == :last
+                lastpartc = zero(O)
+            elseif etime > time_cp[lastp] && prtext == :extr && !isnan(result[:Kel])
+                lastpartc = exp(result[:LZint] + result[:LZ] * etime)
+                lastpart += aucpart(time_cp[lastp], etime, obs_cp[end], lastpartc, calcm, time_cp[lastp] > result[:Tmax])
+            else
+                lastpartc = NaN
+                lastpart += lastpartc
             end
+
+
             aucpartial = zero(T)*zero(O)
             if firstp != lastp
                 aucpartn = lastp - firstp

test/tests.jl

@@ -1489,6 +1489,18 @@ end
     772.3366199961695
     1213.5372385701808
     969.4541441511578] atol=1E-6
+
+    ds = MetidaNCA.pkimport(pkdata2, :Time, :Concentration, [:Subject, :Formulation]; dosetime = MetidaNCA.DoseTime(dose = 100, time = 0.0, tau = 100))
+    sort!(ds, :Subject)
+
+    @test_throws ErrorException dsnca = MetidaNCA.nca!(ds, adm = :ev, calcm = :luld, partials = [(0.25, 100)], prtext = :err)
+
+    dsnca = MetidaNCA.nca!(ds, adm = :ev, calcm = :luld, partials = [(0, 100)], prtext = :last)
+    @test dsnca[:, :AUClast] ≈ dsnca[:, :AUC_0_100] atol=1E-6
+
+    dsnca = MetidaNCA.nca!(ds, adm = :ev, calcm = :luld, partials = [(0, 100)], prtext = :extr)
+    @test dsnca[:, :AUCtau] ≈ dsnca[:, :AUC_0_100] atol=1E-6
+
 end
 
 @testset "  set-get*! tests                                          " begin