Dev (#20)

* plot update (ldict) * plotting * docs pkg * docs, minor fix
PharmCat · Jul 8, 2024 · e076182 · e076182 · PharmCat · Jul 8, 2024
1 parent 3f22de5
commit e076182
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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 = "0.5.9"
+version = "0.5.10"
+
 
 
 [deps]

diff --git 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"
diff --git 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
@@ -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
@@ -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
@@ -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)