From 64e1267785dcf730f2652c986377b5fbe49f58ab Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 22 Aug 2023 21:18:19 +0300
Subject: [PATCH 01/16] plot update (ldict)

---
 src/plots.jl | 25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/plots.jl b/src/plots.jl
index 67d2f0f..9dd127e 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -115,12 +115,16 @@ end
 end
 
 # Text label from ID
-function plotlabel(d)
+function plotlabel(d, ld = nothing)
     title = ""
     if isnothing(d) return title end
     if length(d) > 0
         for (k, v) in d
-            title *= "$(k) = $(v); "
+            kv = k
+            if !isnothing(ld) && haskey(ld, kv)
+                kv = ld[kv]
+            end
+            title *= "$(kv) = $(v); "
         end
     end
     return title
@@ -309,7 +313,7 @@ function pageplot(data, id, ulist; kwargs...)
     kwargs = Dict{Symbol, Any}(kwargs)
     k = keys(kwargs)
     if !(:title in k)
-        kwargs[:title] = plotlabel(id)
+        kwargs[:title] = plotlabel(id, kwargs[:ldict])
     end
 
     fst       = true
@@ -338,7 +342,7 @@ function pageplot(data, id, ulist; kwargs...)
                     if num ∈ labvec
                         kwargs[:label] = nothing
                     else
-                        kwargs[:label] = plotlabel(ulist[num])
+                        kwargs[:label] = plotlabel(ulist[num], kwargs[:ldict])
                         push!(labvec, num)
                     end
                 else
@@ -370,7 +374,8 @@ PK plot for subject set.
 * `typesort` - sort on page by this id key;
 * `pagesort` - different pages by this id key;
 * `filter` - use only subjects if filter ⊆ subject id;
-* `uylims` - same ylims for all dataset.
+* `uylims` - same ylims for all dataset;
+* `ldict` - Dict with labels for replace.
 
 Use `pagesort = MetidaNCA.NoPageSort()` to prevent page plotting.
 """
@@ -379,6 +384,7 @@ function pkplot(data::DataSet{T};
     pagesort::Union{Nothing, Symbol, AbstractVector{Symbol}, NoPageSort} = nothing,
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
+    ldict = nothing,
     kwargs...) where T <: AbstractSubject
 
     kwargs = Dict{Symbol, Any}(kwargs)
@@ -408,17 +414,16 @@ function pkplot(data::DataSet{T};
         end
         for subj in data
             if printtitle
-                kwargs[:title] = plotlabel(subj.id)
+                kwargs[:title] = plotlabel(subj.id, ldict)
             end
             if !(:legend in k)
                 kwargs[:legend] = false
             end
-            push!(p, pkplot(subj;  kwargs...))
+            push!(p, pkplot(subj; kwargs...))
         end
         return p
     end
 
-
     if !isnothing(typesort)
         if isa(typesort, Symbol) typesort = [typesort] end
         typelist = uniqueidlist(data, typesort)
@@ -434,13 +439,13 @@ function pkplot(data::DataSet{T};
         p = []
         pagelist = uniqueidlist(data, pagesort)
         for id in pagelist
-            push!(p, pageplot(data, id, typelist; kwargs...))
+            push!(p, pageplot(data, id, typelist; ldict, kwargs...))
         end
         return p
     else
         if !(:title in k) && !isnothing(filter)
             kwargs[:title] = plotlabel(filter)
         end
-        return pageplot(data, nothing, typelist; kwargs...)
+        return pageplot(data, nothing, typelist; ldict, kwargs...)
     end
 end
\ No newline at end of file

From 476450a4261a3c192696e0d161c901571280404d Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 17 Oct 2023 16:11:26 +0300
Subject: [PATCH 02/16] plotting

---
 Project.toml  |  2 +-
 src/plots.jl  | 24 ++++++++++++++++++++++++
 test/tests.jl |  3 +++
 3 files changed, 28 insertions(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 1decdfe..5e80938 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.8"
+version = "0.5.9"
 
 
 [deps]
diff --git a/src/plots.jl b/src/plots.jl
index 9dd127e..e80c5b3 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -204,6 +204,10 @@ function pkplot(subj::AbstractSubject; ls = false, elim = false, xticksn = :auto
             end
             if !(:ylims in k)
                 kwargs[:ylims] = (minimum(obs)*0.5, maximum(obs)*2.)
+            else
+                if kwargs[:ylims][1] <= 0
+                    kwargs[:ylims] = (minimum(obs)/b, kwargs[:ylims][2])
+                end
             end
         end
     else
@@ -288,6 +292,10 @@ function pkplot!(subj; ls = false, elim = false, xticksn = :auto, yticksn = :aut
             end
             if !(:ylims in k)
                 kwargs[:ylims] = (minimum(obs)*0.5, maximum(obs)*2.)
+            else
+                if kwargs[:ylims][1] <= 0
+                    kwargs[:ylims] = (minimum(obs)/b, kwargs[:ylims][2])
+                end
             end
         end
     else
@@ -448,4 +456,20 @@ function pkplot(data::DataSet{T};
         end
         return pageplot(data, nothing, typelist; ldict, kwargs...)
     end
+end
+
+
+"""
+    pkplot(data::DataSet{T}; kwargs...) where T <: NCAResult
+"""
+function pkplot(data::DataSet{T}; kwargs...) where T <: NCAResult
+    ds = map(x-> x.data, data)
+    pkplot(ds; kwargs...)
+end
+
+"""
+    pkplot(data::NCAResult; kwargs...) 
+"""
+function pkplot(data::NCAResult; kwargs...)
+    pkplot(data.data; kwargs...)
 end
\ No newline at end of file
diff --git a/test/tests.jl b/test/tests.jl
index 44fa67f..de92056 100644
--- a/test/tests.jl
+++ b/test/tests.jl
@@ -84,6 +84,9 @@ include("refdicts.jl")
     @test_nowarn MetidaNCA.plotstyle(40)
     pl = MetidaNCA.pkplot(ds[2])
     pl = MetidaNCA.pkplot!(ds[3]; yscale = :log10)
+    #Plot from NCA result DataSet
+    @test_nowarn MetidaNCA.pkplot(dsncafromds[1]; ylims = (0, 10), yscale = :log10, legend = false)
+    @test_nowarn MetidaNCA.pkplot(dsncafromds; typesort = :Subject, pagesort = :Formulation, elim = true, ls = true, title = "Plots")
     # Unknown typesort
     @test_nowarn pl = MetidaNCA.pkplot(ds; typesort = :unknown)
 

From 92eec22801d19184d710fe15fbfd2c17c170b8e1 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Sun, 24 Mar 2024 19:07:29 +0300
Subject: [PATCH 03/16] docs pkg

---
 Project.toml      | 2 +-
 docs/Project.toml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/Project.toml b/Project.toml
index 5e80938..debeb3e 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.9"
+version = "0.5.10"
 
 
 [deps]
diff --git a/docs/Project.toml b/docs/Project.toml
index 8d27f9a..6e76203 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -10,11 +10,11 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 
 [compat]
-Documenter = "≥0.25"
+Documenter = "1"
 MetidaNCA  = "0.5"
 CSV        = "0.8, 0.9, 0.10"
 DataFrames = "1"
 PrettyTables = "1, 2"
 Weave = "0.9, 0.10"
 Plots = "1"
-Latexify = "0.14, 0.15"
+Latexify = "0.14, 0.15, 0.16"

From 34488ed4317aca03d1a077f522f9bd92dcfc4a05 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Mon, 8 Jul 2024 21:12:23 +0300
Subject: [PATCH 04/16] docs, minor fix

---
 docs/src/details.md | 10 ++++++++++
 src/import.jl       |  3 +++
 src/nca.jl          | 13 ++++++++-----
 src/plots.jl        | 25 ++++++++++++-------------
 4 files changed, 33 insertions(+), 18 deletions(-)

diff --git a/docs/src/details.md b/docs/src/details.md
index a2ef253..f468f29 100644
--- a/docs/src/details.md
+++ b/docs/src/details.md
@@ -1,5 +1,15 @@
 # Details
 
+## Using LimitRule
+
+```julia
+ll = LimitRule(;lloq = 0.1, btmax = 0.0, atmax = NaN, nan = NaN, rm = true)
+
+```
+
+It means that all values below `lloq` will be replaced by `btmax` before Tmax and replaced by `atmax` after Tmax; `NaN` values will be replaced by `nan`. If `rm` is `true`, all `NaN` values will be deleted. 
+
+
 ## Calculation steps for PK NCA
 
 ### Step 1
diff --git a/src/import.jl b/src/import.jl
index 1d116c7..dc7af1c 100644
--- a/src/import.jl
+++ b/src/import.jl
@@ -103,6 +103,8 @@ keywords:
 
     If time column have non-unique values - last pair time-concentration will be used.
 
+
+See also: [`ElimRange`](@ref), [`DoseTime`](@ref), [`LimitRule`](@ref).
 """
 function pkimport(data, time, conc, sort; kelauto = true,  elimrange = ElimRange(), dosetime = nothing, limitrule::Union{Nothing, LimitRule} = nothing, warn = true, kwargs...)
     if isa(sort, String) sort = [Symbol(sort)] end
@@ -181,6 +183,7 @@ end
         kwargs...)
 
 Import PK data from time vector `time` and concentration vector `conc`.
+
 """
 function pkimport(time, conc; kelauto = true,  elimrange = ElimRange(), dosetime = nothing, id = Dict{Symbol, Any}(), limitrule::Union{Nothing, LimitRule} = nothing, warn = true, kwargs...)
     timevals_sp, concvals_sp = checkvalues(time, conc, warn = warn)
diff --git a/src/nca.jl b/src/nca.jl
index 6d2695c..8136eaf 100644
--- a/src/nca.jl
+++ b/src/nca.jl
@@ -392,6 +392,8 @@ Import data and perform NCA analysis.
 Syntax simillar to [`pkimport`](@ref)
 
 Applicable `kwargs` see  [`nca!`](@ref).
+
+See also: [`ElimRange`](@ref), [`DoseTime`](@ref), [`LimitRule`](@ref).
 """
 function nca(args...; type::Symbol = :bps, bl = 0, th = 0, kelauto = true,  elimrange = ElimRange(), dosetime = DoseTime(), limitrule::Union{Nothing, LimitRule} = nothing, kwargs...)
     if !(type in (:bps, :ur, :pd)) error("Unknown type") end
@@ -411,11 +413,12 @@ end
 Non-compartmental (NCA) analysis of PK/PD data.
 """
 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]; kwargs...)
-    end
-    DataSet(result)
+    #result = Vector{NCAResult{Subj}}(undef, length(data))
+    #for i = 1:length(data)
+    #    result[i] = nca!(data[i]; kwargs...)
+    #end
+    #DataSet(result)
+    map(x -> nca!(x; kwargs...), data)
 end
 
 """
diff --git a/src/plots.jl b/src/plots.jl
index e80c5b3..57532ca 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -393,6 +393,7 @@ function pkplot(data::DataSet{T};
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
     ldict = nothing,
+    savepng = nothing,
     kwargs...) where T <: AbstractSubject
 
     kwargs = Dict{Symbol, Any}(kwargs)
@@ -414,6 +415,16 @@ function pkplot(data::DataSet{T};
     end
     if !isnothing(filter) data = subset(data, filter) end
 
+    if !isnothing(typesort)
+        if isa(typesort, Symbol) typesort = [typesort] end
+        typelist = uniqueidlist(data, typesort)
+    else
+        typelist = nothing
+        if !(:legend in k)
+            kwargs[:legend] = false
+        end
+    end
+
     if isnothing(typesort) && isnothing(pagesort)
         p = []
         printtitle = false
@@ -430,19 +441,7 @@ function pkplot(data::DataSet{T};
             push!(p, pkplot(subj; kwargs...))
         end
         return p
-    end
-
-    if !isnothing(typesort)
-        if isa(typesort, Symbol) typesort = [typesort] end
-        typelist = uniqueidlist(data, typesort)
-    else
-        typelist = nothing
-        if !(:legend in k)
-            kwargs[:legend] = false
-        end
-    end
-
-    if !isnothing(pagesort) && !isa(pagesort, NoPageSort)  
+    elseif !isnothing(pagesort) && !isa(pagesort, NoPageSort)  
         if isa(pagesort, Symbol) pagesort = [pagesort] end
         p = []
         pagelist = uniqueidlist(data, pagesort)

From d550a921cbdbf2a7a178b1fef4f44777128f5cc4 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 16:02:15 +0300
Subject: [PATCH 05/16] docs

---
 docs/src/details.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/docs/src/details.md b/docs/src/details.md
index f468f29..971ef50 100644
--- a/docs/src/details.md
+++ b/docs/src/details.md
@@ -9,6 +9,8 @@ ll = LimitRule(;lloq = 0.1, btmax = 0.0, atmax = NaN, nan = NaN, rm = true)
 
 It means that all values below `lloq` will be replaced by `btmax` before Tmax and replaced by `atmax` after Tmax; `NaN` values will be replaced by `nan`. If `rm` is `true`, all `NaN` values will be deleted. 
 
+See also: [`applylimitrule!`](@ref).
+
 
 ## Calculation steps for PK NCA
 

From 9b9b3842f37413a07c8447afc3f4b217f9608a87 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 16:21:17 +0300
Subject: [PATCH 06/16] show ds

---
 src/show.jl | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/show.jl b/src/show.jl
index 5e1e529..041e95f 100644
--- a/src/show.jl
+++ b/src/show.jl
@@ -71,7 +71,8 @@ end
 function Base.show(io::IO, obj::DataSet{ST}) where ST <: AbstractSubject
     println(io, "DataSet: $(subject_type_str(ST))")
     println(io, "Length: $(length(obj))")
-    for i = 1:length(obj)
+    lo = min(length(obj), 20)
+    for i = 1:lo
         print(io, "Subject $(i): ")
         if length(obj[i].id) > 0
             for (k, v) in obj[i].id
@@ -82,6 +83,9 @@ function Base.show(io::IO, obj::DataSet{ST}) where ST <: AbstractSubject
             println(io, "-")
         end
     end
+    if lo < length(obj) 
+        printstyled(io, "$(length(obj) - lo) subjects omitted... \n"; color = :blue)
+    end
 end
 
 function Base.show(io::IO, obj::T) where T <: NCAResult

From 3eeb5786b6867a82f4874831bfc483e353c029fe Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 16:22:44 +0300
Subject: [PATCH 07/16] show res ds

---
 src/show.jl | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/show.jl b/src/show.jl
index 041e95f..76e1149 100644
--- a/src/show.jl
+++ b/src/show.jl
@@ -96,7 +96,8 @@ end
 function Base.show(io::IO, obj::DataSet{Res}) where Res <: NCAResult
     println(io, "DataSet: PK/PD NCA result")
     println(io, "Length: $(length(obj))")
-    for i = 1:length(obj)
+    lo = min(length(obj), 20)
+    for i = 1:lo
         print(io, "Subject $(i): ")
         if length(obj[i].data.id) > 0
             for (k, v) in obj[i].data.id
@@ -107,4 +108,7 @@ function Base.show(io::IO, obj::DataSet{Res}) where Res <: NCAResult
             println(io, "-")
         end
     end
+    if lo < length(obj) 
+        printstyled(io, "$(length(obj) - lo) subjects omitted... \n"; color = :blue)
+    end
 end

From b431c351d5aab087db2e9676f90c9b32d618ccb2 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 17:46:12 +0300
Subject: [PATCH 08/16] save plots

---
 src/MetidaNCA.jl |  8 ++++++++
 src/plots.jl     | 39 +++++++++++++++++++++++++++++++--------
 2 files changed, 39 insertions(+), 8 deletions(-)

diff --git a/src/MetidaNCA.jl b/src/MetidaNCA.jl
index ac0be3b..c54cb43 100644
--- a/src/MetidaNCA.jl
+++ b/src/MetidaNCA.jl
@@ -22,6 +22,8 @@ uniqueidlist,
 indsdict!,
 subset
 
+using MetidaBase.Requires
+
 export pkimport, upkimport, pdimport, nca!, nca, DoseTime, ElimRange, LimitRule, NoPageSort,
 auc_sparse,
 setdosetime!, setkelauto!, setkelrange!, applylimitrule!, setbl!, setth!,
@@ -29,6 +31,12 @@ pkplot,
 getkeldata, getkelauto, getkelrange, getdosetime, getbl, getth, subset
 metida_table
 
+function __init__()
+    @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
+        import Plots:savefig
+    end
+end
+
 const LOG2 = log(2)
 
     include("types.jl")
diff --git a/src/plots.jl b/src/plots.jl
index 57532ca..8bd09a8 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -375,6 +375,9 @@ end
     pagesort::Union{Nothing, Symbol, AbstractVector{Symbol}, NoPageSort} = nothing,
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
+    ldict = nothing,
+    savepath::Union{Nothing, AbstractString} = nothing,
+    namepref::Union{Nothing, AbstractString} = nothing,
     kwargs...) where T <: AbstractSubject
 
 PK plot for subject set.
@@ -383,7 +386,9 @@ PK plot for subject set.
 * `pagesort` - different pages by this id key;
 * `filter` - use only subjects if filter ⊆ subject id;
 * `uylims` - same ylims for all dataset;
-* `ldict` - Dict with labels for replace.
+* `ldict` - Dict with labels for replace;
+* `savepath` - path for plot saving;
+* `namepref` - name prefix for saving files.
 
 Use `pagesort = MetidaNCA.NoPageSort()` to prevent page plotting.
 """
@@ -393,7 +398,8 @@ function pkplot(data::DataSet{T};
     filter::Union{Nothing, Dict{Symbol}} = nothing,
     uylims::Bool = false,
     ldict = nothing,
-    savepng = nothing,
+    savepath::Union{Nothing, AbstractString} = nothing,
+    namepref::Union{Nothing, AbstractString} = nothing,
     kwargs...) where T <: AbstractSubject
 
     kwargs = Dict{Symbol, Any}(kwargs)
@@ -424,9 +430,8 @@ function pkplot(data::DataSet{T};
             kwargs[:legend] = false
         end
     end
-
+    p = []
     if isnothing(typesort) && isnothing(pagesort)
-        p = []
         printtitle = false
         if !(:title in k)
             printtitle = true
@@ -440,20 +445,38 @@ function pkplot(data::DataSet{T};
             end
             push!(p, pkplot(subj; kwargs...))
         end
-        return p
     elseif !isnothing(pagesort) && !isa(pagesort, NoPageSort)  
         if isa(pagesort, Symbol) pagesort = [pagesort] end
-        p = []
         pagelist = uniqueidlist(data, pagesort)
         for id in pagelist
             push!(p, pageplot(data, id, typelist; ldict, kwargs...))
         end
-        return p
     else
         if !(:title in k) && !isnothing(filter)
             kwargs[:title] = plotlabel(filter)
         end
-        return pageplot(data, nothing, typelist; ldict, kwargs...)
+        push!(p,pageplot(data, nothing, typelist; ldict, kwargs...))
+    end
+
+    if !isnothing(savepath)
+        if @isdefined savefig
+            if isfile(savepath)
+                error("File found on this path...")
+            elseif !isdir(savepath)
+                mkpath(savepath)
+            end
+            if isnothing(namepref) namepref = "plot" end
+            for i = 1: length(p) 
+                savefig(p[i], joinpath(savepath, namepref*"_$(i).png"))
+            end
+        else
+            @warn "savefig not defined, install Plots.jl for plot writing... plots NOT saved..."
+        end
+    end
+    if length(p) > 1
+        return p
+    else
+        return p[1]
     end
 end
 

From bab326ca70db8cdaea56085e4c144b3531194f62 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 17:49:07 +0300
Subject: [PATCH 09/16] version bump

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index f19f97b..1793bae 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.10"
+version = "0.5.11"
 
 
 

From 4b907c5a54725d8a977e6835e7e3566c1c7abf0b Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 22:38:00 +0300
Subject: [PATCH 10/16] update

---
 .github/workflows/Documenter.yml |  2 +-
 .github/workflows/Tier1.yml      | 21 ++++++++++++++++-----
 2 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/Documenter.yml b/.github/workflows/Documenter.yml
index 316c92a..e02cfcd 100644
--- a/.github/workflows/Documenter.yml
+++ b/.github/workflows/Documenter.yml
@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-22.04
     timeout-minutes: 40
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Update
         run: sudo apt-get update
       - name: Install Pandoc
diff --git a/.github/workflows/Tier1.yml b/.github/workflows/Tier1.yml
index 34b583b..bc87bc7 100644
--- a/.github/workflows/Tier1.yml
+++ b/.github/workflows/Tier1.yml
@@ -36,15 +36,26 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: julia-actions/cache@v1
+      - uses: actions/cache@v4
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
+        if: ${{ matrix.os == 'ubuntu-latest' && matrix.version == '1' && matrix.arch == 'x64' }}
         with:
-          files: lcov.info
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}

From d193ccdb1b9a09f0f6b4841cc036e54d4f2dcd84 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 23:09:47 +0300
Subject: [PATCH 11/16] update

---
 .github/workflows/Tier1.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/Tier1.yml b/.github/workflows/Tier1.yml
index bc87bc7..ed70fa4 100644
--- a/.github/workflows/Tier1.yml
+++ b/.github/workflows/Tier1.yml
@@ -28,7 +28,7 @@ jobs:
         version:
           - '1.6'
           - '1.8'
-          - '1.9'
+          - '1'
         os:
           - ubuntu-latest
           - macOS-latest

From bc1e5c3eb7dcdf75c5c24147b6626bae24479385 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Tue, 16 Jul 2024 23:19:32 +0300
Subject: [PATCH 12/16] update

---
 Project.toml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/Project.toml b/Project.toml
index 1793bae..eb2fdca 100644
--- a/Project.toml
+++ b/Project.toml
@@ -9,11 +9,13 @@ version = "0.5.11"
 
 MetidaBase = "075456b7-4006-432f-9324-2f8453996c49"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 
 [compat]
 
 MetidaBase = "0.11.2, 0.11.3, 0.12"
 RecipesBase = "1"
+Requires = "1"
 julia = "1"
 
 [extras]

From 7128452ed612445da55592de0ea2780711ebf3a7 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Wed, 31 Jul 2024 18:01:29 +0300
Subject: [PATCH 13/16] docs, plot output

---
 Project.toml         |  2 +-
 docs/src/api.md      | 13 +++++++++++++
 docs/src/details.md  | 24 ++++++++++++++++++++++++
 docs/src/examples.md | 18 +++++++++++++++++-
 src/nca.jl           |  2 +-
 src/plots.jl         |  2 +-
 src/types.jl         | 28 ++++++++++++++++++++++++++++
 7 files changed, 85 insertions(+), 4 deletions(-)

diff --git a/Project.toml b/Project.toml
index eb2fdca..8824855 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "MetidaNCA"
 uuid = "097c2839-c7bc-4c4b-a5f2-b4167c1b4e7c"
 authors = ["PharmCat <v.s.arnautov@yandex.ru>"]
-version = "0.5.11"
+version = "0.5.12"
 
 
 
diff --git a/docs/src/api.md b/docs/src/api.md
index 0753958..f461331 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -52,6 +52,19 @@ MetidaNCA.ElimRange
 MetidaNCA.LimitRule
 ```
 
+### MetidaNCA.PKSubject
+
+```@docs
+MetidaNCA.PKSubject
+```
+
+### MetidaNCA.NCAResult
+
+```@docs
+MetidaNCA.NCAResult
+```
+
+
 ## Functions
 
 ### applylimitrule!
diff --git a/docs/src/details.md b/docs/src/details.md
index d44b223..cf2574e 100644
--- a/docs/src/details.md
+++ b/docs/src/details.md
@@ -12,6 +12,30 @@ 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
 
diff --git a/docs/src/examples.md b/docs/src/examples.md
index 77a1acd..b4fab8b 100644
--- a/docs/src/examples.md
+++ b/docs/src/examples.md
@@ -29,7 +29,7 @@ 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)])
@@ -37,6 +37,22 @@ 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
 
diff --git a/src/nca.jl b/src/nca.jl
index 8136eaf..6db3652 100644
--- a/src/nca.jl
+++ b/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:
 
diff --git a/src/plots.jl b/src/plots.jl
index 9106efa..a107418 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -450,7 +450,7 @@ 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)
diff --git a/src/types.jl b/src/types.jl
index 2732f33..32c02ea 100644
--- a/src/types.jl
+++ b/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

From c37bfbb696ca6b0685ba0a52947060e8a34a859f Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Wed, 31 Jul 2024 18:18:23 +0300
Subject: [PATCH 14/16] fix plots

---
 src/MetidaNCA.jl | 2 +-
 src/plots.jl     | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/MetidaNCA.jl b/src/MetidaNCA.jl
index c54cb43..aad1d75 100644
--- a/src/MetidaNCA.jl
+++ b/src/MetidaNCA.jl
@@ -33,7 +33,7 @@ metida_table
 
 function __init__()
     @require Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" begin
-        import Plots:savefig
+        savefig = Plots.savefig
     end
 end
 
diff --git a/src/plots.jl b/src/plots.jl
index a107418..f940e92 100644
--- a/src/plots.jl
+++ b/src/plots.jl
@@ -456,7 +456,7 @@ function pkplot(data::DataSet{T};
         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 +467,8 @@ 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*"_$(i).png"))
+            for i = 1:length(p) 
+                savefig(p[i][2], joinpath(savepath, namepref*"_$(i).png"))
             end
         else
             @warn "savefig not defined, install Plots.jl for plot writing... plots NOT saved..."

From c5951ad4560fb4d83dc744c96e208677fcafc4b7 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Wed, 31 Jul 2024 18:50:34 +0300
Subject: [PATCH 15/16] export, fix docs

---
 docs/src/examples.md | 4 ++--
 src/MetidaNCA.jl     | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/src/examples.md b/docs/src/examples.md
index b4fab8b..c147bdc 100644
--- a/docs/src/examples.md
+++ b/docs/src/examples.md
@@ -76,11 +76,11 @@ png(p, "plot2.png")
 
 p = pkplot(ds; elim = true, ls = true)
 
-png(p[1], "plot3.png")
+png(p[1][2], "plot3.png")
 
 p = pkplot(ds; typesort = :Subject, pagesort = :Formulation)
 
-png(p[1], "plot4.png")
+png(p[1][2], "plot4.png")
 ```
 
 #### Plot 1
diff --git a/src/MetidaNCA.jl b/src/MetidaNCA.jl
index aad1d75..f46db2a 100644
--- a/src/MetidaNCA.jl
+++ b/src/MetidaNCA.jl
@@ -28,8 +28,9 @@ 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

From 47a06b14b09010bae435dfceec3891bc4b2dd909 Mon Sep 17 00:00:00 2001
From: PharmCat <13901158+PharmCat@users.noreply.github.com>
Date: Wed, 31 Jul 2024 20:20:09 +0300
Subject: [PATCH 16/16] fix plots

---
 docs/src/examples.md | 4 +++-
 src/plots.jl         | 8 +++++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/docs/src/examples.md b/docs/src/examples.md
index c147bdc..cbc5c73 100644
--- a/docs/src/examples.md
+++ b/docs/src/examples.md
@@ -76,7 +76,9 @@ png(p, "plot2.png")
 
 p = pkplot(ds; elim = true, ls = true)
 
-png(p[1][2], "plot3.png")
+png(p[1], "plot3.png")
+
+# If pagesort used - return pairs with `Page ID` => `Plot`
 
 p = pkplot(ds; typesort = :Subject, pagesort = :Formulation)
 
diff --git a/src/plots.jl b/src/plots.jl
index f940e92..a262582 100644
--- a/src/plots.jl
+++ b/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,
@@ -468,7 +470,11 @@ function pkplot(data::DataSet{T};
             end
             if isnothing(namepref) namepref = "plot" end
             for i = 1:length(p) 
-                savefig(p[i][2], joinpath(savepath, namepref*"_$(i).png"))
+                if isa(p[i], Pair)
+                    savefig(p[i][2], joinpath(savepath, namepref*"_$(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..."