Dev (#23)

* 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

Project.toml

@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <[email protected]>"]
-version = "0.5.11"
+version = "0.5.12"
 
 
 

docs/src/api.md

@@ -52,6 +52,19 @@ MetidaNCA.ElimRange
 MetidaNCA.LimitRule
 ```
 
+### MetidaNCA.PKSubject
+
+```@docs
+MetidaNCA.PKSubject
+```
+
+### MetidaNCA.NCAResult
+
+```@docs
+MetidaNCA.NCAResult
+```
+
+
 ## Functions
 
 ### applylimitrule!

docs/src/details.md

@@ -12,6 +12,31 @@ It means that all values below `lloq` will be replaced by `btmax` before Tmax an
 
 See also: [`applylimitrule!`](@ref).
 
+## Using DoseTime
+
+```julia
+
+dt = DoseTime(dose = 200.0, time = 0.0)
+
+```
+
+DoseTime can be appliet to each subject or dataset and can be used with [`pkimport`](@ref).  
+
+
+```julia
+
+ds = pkimport(pkdata2, :Time, :Concentration, [:Subject, :Formulation]; dosetime = dt)
+
+```
+
+DoseTime for staedy-state PK:
+
+```julia
+dt = DoseTime(dose = 100.0, time = 0.25, tau = 9.0)
+```
+
+See also: [`setdosetime!`](@ref).
+
 
 ## Calculation steps for PK NCA
 

docs/src/examples.md

@@ -29,14 +29,30 @@ dsnca = nca!(ds, adm = :ev, calcm = :lint)
 dsnca[:, :AUClast]
 ```
 
-# Partial AUC
+## Partial AUC
 
 ```@example ncaexample
 dsnca = nca!(ds, adm = :ev, calcm = :lint, partials = [(1, 7)])
 
 dsnca[:, :AUC_1_7]
 ```
 
+## Result modification or custom parameter function 
+
+```@example ncaexample
+
+# Define modify! function for new parameter
+function newparam(data)
+    data.result[:AUChalf] = data.result[:AUClast] / 2
+end
+
+dsncanp = nca!(ds, modify!  = newparam)
+
+dsncanp[1][:AUChalf]
+```
+
+Function `newparam` applyed to [`NCAResult`](@ref).
+
 
 ## Print output
 
@@ -62,9 +78,11 @@ p = pkplot(ds; elim = true, ls = true)
 
 png(p[1], "plot3.png")
 
+# If pagesort used - return pairs with `Page ID` => `Plot`
+
 p = pkplot(ds; typesort = :Subject, pagesort = :Formulation)
 
-png(p[1], "plot4.png")
+png(p[1][2], "plot4.png")
 ```
 
 #### Plot 1

src/MetidaNCA.jl

@@ -28,12 +28,13 @@ export pkimport, upkimport, pdimport, nca!, nca, DoseTime, ElimRange, LimitRule,
 auc_sparse,
 setdosetime!, setkelauto!, setkelrange!, applylimitrule!, setbl!, setth!,
 pkplot,
-getkeldata, getkelauto, getkelrange, getdosetime, getbl, getth, subset
-metida_table
+getkeldata, getkelauto, getkelrange, getdosetime, getbl, getth, subset,
+metida_table,
+PKSubject, UPKSubject, PDSubject, NCAResult
 
 function __init__()
     @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
-        import Plots:savefig
+        savefig = Plots.savefig
     end
 end
 

src/nca.jl

@@ -442,7 +442,7 @@ end
 * `verbose` - print to `io`, 1: partial areas table, 2: 1, and results;
 * `warn` - show warnings;
 * `io` - output stream;
-* `modify!` - function to modify output paramaters, call `modify!(data, result)` if difined.
+* `modify!` - function to modify output paramaters, call `modify!(ncaresult)` if difined.
 
 Results:
 

src/plots.jl

@@ -391,6 +391,8 @@ PK plot for subject set.
 * `namepref` - name prefix for saving files.
 
 Use `pagesort = MetidaNCA.NoPageSort()` to prevent page plotting.
+
+If pagesort used - return vector of pairs: `Page ID` => `Plot`
 """
 function pkplot(data::DataSet{T};
     typesort::Union{Nothing, Symbol, AbstractVector{Symbol}} = nothing,
@@ -450,13 +452,13 @@ function pkplot(data::DataSet{T};
         if isa(pagesort, Symbol) pagesort = [pagesort] end
         pagelist = uniqueidlist(data, pagesort)
         for id in pagelist
-            push!(p, pageplot(data, id, typelist; ldict, kwargs...))
+            push!(p, id => pageplot(data, id, typelist; ldict, kwargs...))
         end
     else
         if !(:title in k) && !isnothing(filter)
             kwargs[:title] = plotlabel(filter)
         end
-        push!(p,pageplot(data, nothing, typelist; ldict, kwargs...))
+        push!(p, pageplot(data, nothing, typelist; ldict, kwargs...))
     end
 
     if !isnothing(savepath)
@@ -467,8 +469,12 @@ function pkplot(data::DataSet{T};
                 mkpath(savepath)
             end
             if isnothing(namepref) namepref = "plot" end
-            for i = 1: length(p) 
-                savefig(p[i], joinpath(savepath, namepref*"_$(i).png"))
+            for i = 1:length(p) 
+                if isa(p[i], Pair)
+                    savefig(p[i][2], joinpath(savepath, namepref*"_$(i).png"))
+                else
+                    savefig(p[i], joinpath(savepath, namepref*"_$(i).png"))
+                end
             end
         else
             @warn "savefig not defined, install Plots.jl for plot writing... plots NOT saved..."

src/types.jl

@@ -105,6 +105,22 @@ struct DoseTime{D <: Number, T <: Number, TAU <: Number}
 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
+
+Pharmacokinetic subject.
+
+Fields:
+
+* time::Vector{T} - time values;
+* obs::Vector{O} - observations;
+* kelauto::Bool 
+* kelrange::ElimRange
+* dosetime::DoseTime
+* keldata::KelData
+* id::Dict{Symbol, V}
+
+"""
 mutable struct PKSubject{T <: Number, O <: Union{Number, Missing}, V <: Any} <: AbstractSubject
     time::Vector{T}
     obs::Vector{O}
@@ -136,7 +152,17 @@ function Base.length(obj::T) where T <: AbstractSubject
     length(obj.time)
 end
 
+"""
+    NCAResult(subject::T, options, result::Dict{Symbol, U}) where T <: AbstractSubject where U
+
+NCA resulst.
+
+Fields:
 
+* data::T
+* options::Dict{Symbol}
+* result::Dict{Symbol, U}
+"""
 struct NCAResult{T, U} <: AbstractSubjectResult{T}
     data::T
     options::Dict{Symbol}
@@ -167,6 +193,8 @@ Rule for PK subject.
 * STEP 1 (NaN step): replace all `NaN` and `missing` values with nan keyword value (if `nan` not NaN);
 * STEP 2 (LLOQ step): replace values below `lloq` with `btmax` value if this value befor Tmax or with atmax if this value after Tmax (if `lloq` not NaN);
 * STEP 3 (remove NaN): `rm` == true, then remove all `NaN` and `missing` values.
+
+See also: [`applylimitrule!`](@ref)
 """
 struct LimitRule{T<:Real}
     lloq::T