Dev (#25)

* plot update (ldict) * plotting * docs pkg * docs, minor fix * docs * show ds * show res ds * save plots * version bump * update * update * update * docs, plot output * fix plots * export, fix docs * fix plots * breaking changes in plots output * fix docs * pd tau * plot dose time * tests
PharmCat · Nov 11, 2024 · e380d47 · e380d47
1 parent 6bdbca8
commit e380d47
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,8 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <[email protected]>"]
-version = "0.5.13"
+version = "0.5.14"
+
 
 
 [deps]

diff --git a/change.log b/change.log
@@ -1,3 +1,6 @@
+0.5.14
+- pd tau
+
 0.5.13
 - breaking changes in plotting output
 

diff --git a/docs/src/examples.md b/docs/src/examples.md
@@ -175,6 +175,22 @@ MetidaNCA.nca!(pd[1])
 p = MetidaNCA.pkplot(pd[1], drawth = true, drawbl = true)
 
 png(p, "plot6.png")
+
+# Plot DoseTime (can be used for PK plots)
+
+dt = DoseTime(dose = 200, time = 1.5)
+setdosetime!(pd, dt)
+
+p = MetidaNCA.pkplot(pd[1], drawdt = true)
+
+
+png(p, "plot7.png")
 ```
 
+##### Plot 6
+
 ![](plot6.png)
+
+##### Plot 7
+
+![](plot7.png)
diff --git a/src/MetidaNCA.jl b/src/MetidaNCA.jl
@@ -5,6 +5,8 @@ module MetidaNCA
 
 using RecipesBase
 
+import RecipesBase: plot!, plot
+
 import Base: length, length, push!, resize!
 import MetidaBase
 import MetidaBase: Tables, StatsBase, PrecompileTools,

diff --git a/src/import.jl b/src/import.jl
@@ -327,12 +327,14 @@ Keywords:
 * `warn` - warning supress if `false`.
 
 """
-function pdimport(data, time, obs, sort; bl = 0, th = 0, limitrule::Union{Nothing, LimitRule} = nothing, warn = true)
+function pdimport(data, time, obs, sort; bl = 0, th = 0, dosetime::Union{Nothing, DoseTime} = nothing, limitrule::Union{Nothing, LimitRule} = nothing, warn = true)
     if isa(sort, String) sort = [Symbol(sort)] end
     if isa(sort, Symbol) sort = [sort] end
 
     Tables.istable(data) || error("Data not a table!")
 
+
+
     cols   = Tables.columns(data)
     cdata  = Tuple(Tables.getcolumn(cols, y) for y in sort)
     d      = Dict{Tuple{eltype.(cdata)...}, Vector{Int}}()
@@ -341,6 +343,8 @@ function pdimport(data, time, obs, sort; bl = 0, th = 0, limitrule::Union{Nothin
     timec = Tables.getcolumn(data, time)
     obsc  = Tables.getcolumn(data, obs)
 
+    if isnothing(dosetime) dosetime = DoseTime(NaN, zero(eltype(timec)), NaN) end
+
     any(isnanormissing, timec) && error("Some time values is NaN or Missing!")
 
     sdata = Vector{PDSubject}(undef, length(d))
@@ -372,7 +376,7 @@ function pdimport(data, time, obs, sort; bl = 0, th = 0, limitrule::Union{Nothin
         timevals_spv = view(timevals, sp)
         obsvals_spv = view(obsvals, sp)
         timevals_sp, obsvals_sp = checkvalues(timevals_spv, obsvals_spv, warn = warn)
-        sdata[i] = PDSubject(timevals_sp, obsvals_sp, bl, th, Dict(sort .=> k))
+        sdata[i] = PDSubject(timevals_sp, obsvals_sp, bl, th, dosetime, Dict(sort .=> k))
         i += one(Int)
     end
     ds = DataSet(identity.(sdata))

diff --git a/src/nca.jl b/src/nca.jl
@@ -833,10 +833,10 @@ function nca!(data::PKSubject{T, O}; adm = :ev, calcm = :lint, intpm = nothing,
     return ncares
 end
 
-function maxconc(subj::T) where T <: PKSubject
+function maxconc(subj::T) where T <: AbstractSubject
     maximum(subj.obs)
 end
-function minconc(subj::T, pos = false) where T <: PKSubject
+function minconc(subj::T, pos = false) where T <: AbstractSubject
     if pos
         return minimum(Iterators.filter(x-> x > zero(x), subj.obs))
     else
@@ -1138,6 +1138,78 @@ function nca!(data::PDSubject{T,O}; calcm = :lint, intpm = nothing, verbose = 0,
         result[:TIMEBTW] = result[:TBBL] - result[:TBTH]
     end
 
+
+    # Tau parameters
+    if data.dosetime.tau > zero(data.dosetime.tau)
+        taufirstp = findfirst(x -> x >= data.dosetime.time, time_cp)
+        taulastp  = findlast(x -> x <= data.dosetime.time + data.dosetime.tau, time_cp)
+        taupn = taulastp - taufirstp
+
+        aucpartabl_tau  = Array{ptype, 1}(undef, taupn)
+        aucpartbbl_tau  = Array{ptype, 1}(undef, taupn)
+        aucpartath_tau  = Array{ptype, 1}(undef, taupn)
+        aucpartbth_tau  = Array{ptype, 1}(undef, taupn)
+        tpartabl_tau    = Array{ptype, 1}(undef, taupn)
+        tpartbbl_tau    = Array{ptype, 1}(undef, taupn)
+        tpartath_tau    = Array{ptype, 1}(undef, taupn)
+        tpartbth_tau    = Array{ptype, 1}(undef, taupn)
+        aucpartbtw_tau  = Array{ptype, 1}(undef, taupn)
+
+        for i = taufirstp:taulastp-1
+            j = i - taufirstp + 1
+            aucpartabl_tau[j], aucpartbbl_tau[j], tpartabl_tau[j], tpartbbl_tau[j], aucpartath_tau[j], aucpartbth_tau[j], tpartath_tau[j], tpartbth_tau[j], aucpartbtw_tau[j] = auctblth(obs_cp[i], obs_cp[i + 1], time_cp[i], time_cp[i + 1], data.bl, data.th, calcm)
+        end
+        # before first responce point
+        if data.dosetime.time < time_cp[taufirstp]
+            if taufirstp > 1
+                # Interpolate responce between observations
+                intpmr  = interpolate(time_cp[taufirstp-1], time_cp[taufirstp], data.dosetime.time, obs_cp[taufirstp-1], obs_cp[taufirstp], calcm, true)
+                aucpartabl_, aucpartbbl_, tpartabl_, tpartbbl_, aucpartath_, aucpartbth_, tpartath_, tpartbth_, aucpartbtw_ = auctblth(intpmr, obs_cp[taufirstp], data.dosetime.time, time_cp[taufirstp], data.bl, data.th, calcm)
+            else # else set first point to zero
+                aucpartabl_, aucpartbbl_, tpartabl_, tpartbbl_, aucpartath_, aucpartbth_, tpartath_, tpartbth_, aucpartbtw_ = auctblth(0, obs_cp[taufirstp], data.dosetime.time, time_cp[taufirstp], data.bl, data.th, calcm)
+            end
+            pushfirst!(aucpartabl_tau, aucpartabl_)
+            pushfirst!(aucpartbbl_tau, aucpartbbl_)
+            pushfirst!(aucpartath_tau, aucpartath_)
+            pushfirst!(aucpartbth_tau, aucpartbth_)
+            pushfirst!(tpartabl_tau, tpartabl_)
+            pushfirst!(tpartbbl_tau, tpartbbl_)
+            pushfirst!(tpartath_tau, tpartath_)
+            pushfirst!(tpartbth_tau, tpartbth_)
+            pushfirst!(aucpartbtw_tau, aucpartbtw_)
+        end
+        # after last responce point
+        if data.dosetime.time + data.dosetime.tau > time_cp[taulastp]
+            if  taulastp < length(time_cp)
+                # Interpolate responce between observations
+                intpmr  = interpolate(time_cp[taulastp], time_cp[taulastp+1], data.dosetime.time + data.dosetime.tau, obs_cp[taulastp], obs_cp[taulastp+1], calcm, true)
+
+                aucpartabl_, aucpartbbl_, tpartabl_, tpartbbl_, aucpartath_, aucpartbth_, tpartath_, tpartbth_, aucpartbtw_ = auctblth(obs_cp[taulastp], intpmr, time_cp[taulastp], data.dosetime.time + data.dosetime.tau, data.bl, data.th, calcm)
+            else # else set first point to zero
+                aucpartabl_, aucpartbbl_, tpartabl_, tpartbbl_, aucpartath_, aucpartbth_, tpartath_, tpartbth_, aucpartbtw_ =  auctblth(obs_cp[taulastp], 0, time_cp[taulastp], data.dosetime.time + data.dosetime.tau, data.bl, data.th, calcm)
+            end
+            push!(aucpartabl_tau, aucpartabl_)
+            push!(aucpartbbl_tau, aucpartbbl_)
+            push!(aucpartath_tau, aucpartath_)
+            push!(aucpartbth_tau, aucpartbth_)
+            push!(tpartabl_tau, tpartabl_)
+            push!(tpartbbl_tau, tpartbbl_)
+            push!(tpartath_tau, tpartath_)
+            push!(tpartbth_tau, tpartbth_)
+            push!(aucpartbtw_tau, aucpartbtw_)
+        end
+
+        result[:AUCABLtau] = sum(aucpartabl_tau)
+        result[:AUCBBLtau] = sum(aucpartbbl_tau)
+        result[:AUCATHtau] = sum(aucpartath_tau)
+        result[:AUCBTHtau] = sum(aucpartbth_tau)
+        result[:TABLtau]   = sum(tpartabl_tau)
+        result[:TBBLtau]   = sum(tpartbbl_tau)
+        result[:TATHtau]   = sum(tpartath_tau)
+        result[:TBTHtau]   = sum(tpartbth_tau)
+        result[:AUCBTWtau] = sum(aucpartbtw_tau)
+    end
+
     # Verbose output
     if verbose > 0
         hnames = [:Time, :Observation, :AUCABL, :AUCBBL, :AUCATH, :AUCBTH]

diff --git a/src/plots.jl b/src/plots.jl
@@ -45,7 +45,7 @@ end
 @userplot PKPlot
 @userplot PKElimpPlot
 @userplot PKElimpDrop
-@userplot PdHLine
+#@userplot PdHLine
 
 function luceil(x)
     fl = Int(floor(log10(x)))
@@ -119,12 +119,13 @@ end
     (x, y)
 end
 
+#=
 @recipe function f(subj::PdHLine)
     x, y = subj.args
     seriestype        --> :straightline
     (x, [y, y])
 end
-
+=#
 # Text label from ID
 function plotlabel(d, ld = nothing)
     title = ""
@@ -157,6 +158,7 @@ Plot for subject
 * `plotstyle` - predefined plot style from PKPLOTSTYLE;
 * `drawbl` (`false`) - draw baseline, only for PDSubject;
 * `drawth` (`false`) - draw threshold, only for PDSubject;
+* `drawdt` (`false`) - draw drawdose time;
 
 """
 function pkplot(subj::AbstractSubject; ls = false, elim = false, xticksn = :auto, yticksn = :auto, kwargs...)
@@ -170,6 +172,9 @@ function pkplot(subj::AbstractSubject; ls = false, elim = false, xticksn = :auto
     else
         kwargs[:linestyle], kwargs[:linecolor], kwargs[:markershape],  kwargs[:markercolor]  = kwargs[:plotstyle]
     end
+    if !(:drawdt in k)
+        kwargs[:drawdt] = false
+    end
     if !(:drawbl in k)
         kwargs[:drawbl] = false
     end
@@ -256,12 +261,15 @@ function pkplot(subj::AbstractSubject; ls = false, elim = false, xticksn = :auto
     end
     if isa(subj, PDSubject)
         if kwargs[:drawth] == true
-            pdhline!(p, [minimum(subj.time), maximum(subj.time)], getth(subj), lc = :blue, label = "TH")
+            plot!(p, [minimum(subj.time), maximum(subj.time)], [getth(subj), getth(subj)], lc = kwargs[:linecolor], ls = :dashdot, label = "TH")
         end
         if kwargs[:drawbl] == true
-            pdhline!(p, [minimum(subj.time), maximum(subj.time)], getbl(subj), lc = :red, label = "BL")
+            plot!(p, [minimum(subj.time), maximum(subj.time)], [getbl(subj), getbl(subj)], lc = kwargs[:linecolor], ls = :dash, label = "BL")
         end
     end
+    if kwargs[:drawdt] == true && !isnan(subj.dosetime.time) 
+        plot!(p, [subj.dosetime.time, subj.dosetime.time], [minimum(subj.obs),  maximum(subj.obs)], label = "DoseTime", ls = :dot, lc = kwargs[:linecolor])
+    end
     return p
 end
 
@@ -276,6 +284,9 @@ function pkplot!(subj; ls = false, elim = false, xticksn = :auto, yticksn = :aut
         kwargs[:linestyle], kwargs[:linecolor], kwargs[:markershape],  kwargs[:markercolor]  = kwargs[:plotstyle]
     end
 
+    if !(:drawdt in k)
+        kwargs[:drawdt] = false
+    end
     if !(:legend in k)
         kwargs[:legend] = true
     end
@@ -325,6 +336,18 @@ function pkplot!(subj; ls = false, elim = false, xticksn = :auto, yticksn = :aut
     end
 
     p = pkplot!(time, obs;  lcd = yticksn, tcd = xticksn, kwargs...)
+
+    if isa(subj, PDSubject)
+        if kwargs[:drawth] == true
+            plot!(p, [minimum(subj.time), maximum(subj.time)], [getth(subj), getth(subj)], lc = kwargs[:linecolor], ls = :dashdot, label = "TH")
+        end
+        if kwargs[:drawbl] == true
+            plot!(p, [minimum(subj.time), maximum(subj.time)], [getbl(subj), getbl(subj)], lc = kwargs[:linecolor], ls = :dash, label = "BL")
+        end
+    end
+    if kwargs[:drawdt] == true && !isnan(subj.dosetime.time) 
+        plot!(p, [subj.dosetime.time, subj.dosetime.time], [minimum(subj.obs),  maximum(subj.obs)], label = "DoseTime", ls = :dot, lc = kwargs[:linecolor])
+    end
     return p
 end
 

diff --git a/src/setdosetime.jl b/src/setdosetime.jl
@@ -1,20 +1,20 @@
 #Subject
 """
-    setdosetime!(data::T, dosetime::DoseTime) where T <: PKSubject
+    setdosetime!(data::T, dosetime::DoseTime) where T <: AbstractSubject
 
 Set dose time `dosetime` for subject `data`.
 """
-function setdosetime!(data::PKSubject, dosetime::DoseTime)
+function setdosetime!(data::AbstractSubject, dosetime::DoseTime)
     data.dosetime = dosetime
     data
 end
 #DS ind Int
 """
-    setdosetime!(data::DataSet{T}, dosetime::DoseTime, ind::Int) where T <: PKSubject
+    setdosetime!(data::DataSet{T}, dosetime::DoseTime, ind::Int) where T <: AbstractSubject
 
 * `ind` - index in DataSet.
 """
-function setdosetime!(data::DataSet{<:PKSubject}, dosetime::DoseTime, ind::Int)
+function setdosetime!(data::DataSet{<:AbstractSubject}, dosetime::DoseTime, ind::Int)
     setdosetime!(data[ind], dosetime)
     data
 end
@@ -24,31 +24,31 @@ end
 
 * `inds` - indexes in DataSet.
 """
-function setdosetime!(data::DataSet{<:PKSubject}, dosetime::DoseTime, inds::Union{Vector{Int}, UnitRange{Int}, Tuple{Vararg{Int}}})
+function setdosetime!(data::DataSet{<:AbstractSubject}, dosetime::DoseTime, inds::Union{Vector{Int}, UnitRange{Int}, Tuple{Vararg{Int}}})
     for i in inds
         setdosetime!(data[i], dosetime)
     end
     data
 end
 #DS all
 """
-    setdosetime!(data::DataSet{T}, dosetime::DoseTime) where T <: PKSubject
+    setdosetime!(data::DataSet{T}, dosetime::DoseTime) where T <: AbstractSubject
 
 For all subjects in DataSet.
 """
-function setdosetime!(data::DataSet{<:PKSubject}, dosetime::DoseTime)
+function setdosetime!(data::DataSet{<:AbstractSubject}, dosetime::DoseTime)
     for i = 1:length(data)
         setdosetime!(data[i], dosetime)
     end
     data
 end
 #DS Dict
 """
-    setdosetime!(data::DataSet{T}, dosetime::DoseTime, sort::Dict) where T <: PKSubject
+    setdosetime!(data::DataSet{T}, dosetime::DoseTime, sort::Dict) where T <: AbstractSubject
 
 Set dose time `dosetime` for subjects if `sort` ⊆ subject's `id`.
 """
-function setdosetime!(data::DataSet{<:PKSubject}, dosetime::DoseTime, sort::Dict)
+function setdosetime!(data::DataSet{<:AbstractSubject}, dosetime::DoseTime, sort::Dict)
     for i = 1:length(data)
         if sort ⊆ data[i].id setdosetime!(data[i], dosetime) end
     end
@@ -60,7 +60,7 @@ end
 
 Return dosetime.
 """
-function getdosetime(data::PKSubject)
+function getdosetime(data::AbstractSubject)
     data.dosetime
 end
 

diff --git a/src/types.jl b/src/types.jl
@@ -106,7 +106,7 @@ end
 
 # PK subject
 """
-    PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, keldata::KelData, sort::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
+    PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, keldata::KelData, id::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
 
 Pharmacokinetic subject.
 
@@ -129,11 +129,11 @@ mutable struct PKSubject{T <: Number, O <: Union{Number, Missing}, V <: Any} <:
     dosetime::DoseTime
     keldata::KelData
     id::Dict{Symbol, V}
-    function PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, keldata::KelData, sort::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
-        new{T, O, V}(time, conc, kelauto, kelrange, dosetime, keldata, sort)::PKSubject
+    function PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, keldata::KelData, id::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
+        new{T, O, V}(time, conc, kelauto, kelrange, dosetime, keldata, id)::PKSubject
     end
-    function PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, sort::Dict{Symbol, V}) where T where O where V
-        PKSubject(time, conc, kelauto, kelrange, dosetime, KelData(T[], T[], Float64[], Float64[], Float64[], Float64[], Int[]), sort)
+    function PKSubject(time::Vector{T}, conc::Vector{O}, kelauto::Bool, kelrange::ElimRange, dosetime::DoseTime, id::Dict{Symbol, V}) where T where O where V
+        PKSubject(time, conc, kelauto, kelrange, dosetime, KelData(T[], T[], Float64[], Float64[], Float64[], Float64[], Int[]), id)
     end
     #=
     function PKSubject(time::Vector, conc::Vector, sort::Dict)
@@ -240,12 +240,13 @@ mutable struct PDSubject{T <: Number, O <: Union{Number, Missing}, V <: Any} <:
     obs::Vector{O}
     bl::Float64
     th::Float64
+    dosetime::DoseTime
     id::Dict{Symbol, V}
-    function PDSubject(time::Vector{T}, conc::Vector{O}, bl, th, sort::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
-        new{T, O, V}(time, conc, bl, th, sort)::PDSubject
+    function PDSubject(time::Vector{T}, conc::Vector{O}, bl, th, dosetime::DoseTime, id::Dict{Symbol, V} = Dict{Symbol, Any}()) where T <: Number where O <: Union{Number, Missing} where V
+        new{T, O, V}(time, conc, bl, th, dosetime, id)::PDSubject
     end
-    function PDSubject(time::Vector, conc::Vector, bl, th, sort::Dict{Symbol, V}) where V
-        PDSubject(time, conc, bl, th, sort)
+    function PDSubject(time::Vector, conc::Vector, bl, th, id::Dict{Symbol, V}) where V
+        PDSubject(time, conc, bl, th, DoseTime(), id)
     end
 end
-Original file line number
+Diff line change
@@ -1,3 +1,6 @@
+.5.14
+    - pd tau
 .5.13
     - breaking changes in plotting output
@@ Expand Down @@