Add GeneralAgeData struct

brenhinkeller · Jun 27, 2024 · 13348ba · 13348ba
1 parent 9eb871e
commit 13348ba
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Showing 5 changed files with 65 additions and 20 deletions.
diff --git a/src/Chron.jl b/src/Chron.jl
@@ -49,7 +49,8 @@ module Chron
     include("Fitplot.jl")
 
     # Structs
-    export ChronAgeData, HiatusData, StratAgeModelConfiguration, StratAgeModel
+    export ChronAgeData, GeneralAgeData, HiatusData
+    export SystematicUncertainty, StratAgeModelConfiguration, StratAgeModel
 
     # High-level functions
     export  StratMetropolis, StratMetropolisDist, StratMetropolis14C,
@@ -67,4 +68,6 @@ module Chron
     # (mostly already exported by reexporting Isoplot.jl)
     export TruncatedNormalDistribution, EllisDistribution, ArClosureDistribution
 
+    include("Deprecations.jl")
+
 end # module
diff --git a/src/Deprecations.jl b/src/Deprecations.jl
@@ -0,0 +1,22 @@
+    # For backwards compatibility with old scripts and publications
+    function NewChronAgeData(nSamples::Integer)
+        @warn "`NewChronAgeData` is deprecated, use `ChronAgeData` instead"
+        ChronAgeData(nSamples)
+    end
+    export NewChronAgeData
+    function StratAgeData(nSamples::Integer)
+        @warn "`StratAgeData` is deprecated, use `ChronAgeData` instead"
+        ChronAgeData(nSamples)
+    end
+    export StratAgeData
+    function NewStratAgeData(nSamples::Integer)
+        @warn "`NewStratAgeData` is deprecated, use `ChronAgeData` instead"
+        ChronAgeData(nSamples)
+    end
+    export NewStratAgeData
+
+
+    function NewHiatusData(nHiatuses::Integer)
+        @warn "`NewHiatusData` is deprecated, use `HiatusData` instead"
+        HiatusData(nHiatuses)
+    end
diff --git a/src/Objects.jl b/src/Objects.jl
@@ -2,7 +2,7 @@
 
     # Define a type of struct object to hold data about geochron samples from
     # a region or stratigraphic section of interest
-    mutable struct ChronAgeData{N}
+    @kwdef mutable struct ChronAgeData{N}
         Name::NTuple{N, String}
         Height::Vector{Float64}
         Height_sigma::Vector{Float64}
@@ -24,7 +24,7 @@
     end
 
     function ChronAgeData(nSamples::Integer)
-        smpl = ChronAgeData{nSamples}(
+        ChronAgeData{nSamples}(
             ntuple(i->"Sample name", nSamples),
             collect(1.0:nSamples),  # Sample Height
             zeros(nSamples),     # Sample Height_sigma
@@ -44,23 +44,38 @@
             "Ma",
             "m",
         )
-        return smpl
     end
-    # For backwards compatibility
-    const NewChronAgeData = ChronAgeData
-    export NewChronAgeData
-    const NewStratAgeData = ChronAgeData
-    export NewStratAgeData
-    const StratAgeData = ChronAgeData
-    export StratAgeData
+
+    @kwdef mutable struct GeneralAgeData{N}
+        Name::NTuple{N, String}
+        Height::Vector{Float64}
+        Height_sigma::Vector{Float64}
+        Age::Vector{Distribution{Univariate, Continuous}}
+        Age_Sidedness::Vector{Float64}
+        Chronometer::NTuple{N, Symbol}
+        Age_Unit::String
+        Height_Unit::String
+    end
+
+    function GeneralAgeData(nSamples::Integer)
+        GeneralAgeData{nSamples}(
+            ntuple(i->"Sample name", nSamples),
+            collect(1.0:nSamples),  # Sample Height
+            zeros(nSamples),     # Sample Height_sigma
+            fill(Uniform(0,4567),nSamples),  # Sample ages
+            zeros(nSamples), # Sidedness (zeros by default, geochron constraints are two-sided). Use -1 for a maximum age and +1 for a minimum age, 0 for two-sided
+            ntuple(i->:Chronometer, nSamples), # Age Types (e.g., :UPb or :ArAr)
+            "Ma",
+            "m",
+        )
+    end
 
     # One-sigma systematic uncertainty
     mutable struct SystematicUncertainty
         UPb::Float64
         ArAr::Float64
     end
     SystematicUncertainty() = SystematicUncertainty(NaN, NaN)
-    export SystematicUncertainty
 
     # A type of object to hold data about hiatuses
     mutable struct HiatusData
@@ -73,18 +88,15 @@
     end
 
     function HiatusData(nHiatuses::Integer)
-        hiatus = HiatusData(
+        HiatusData(
             fill(NaN,nHiatuses),  # Height
             fill(NaN,nHiatuses),  # Height_sigma
             fill(NaN,nHiatuses),  # Duration
             fill(NaN,nHiatuses),  # Duration_sigma
             "Ma",
             "m",
         )
-        return hiatus
     end
-    const NewHiatusData = HiatusData
-    export NewHiatusData
 
     # A type of object to specify the configuration of the stratigraphic model
     mutable struct StratAgeModelConfiguration
@@ -96,7 +108,7 @@
     end
 
     function StratAgeModelConfiguration()
-        return StratAgeModelConfiguration(NaN, 0, 0, 0, NaN)
+        StratAgeModelConfiguration(NaN, 0, 0, 0, NaN)
     end
     const NewStratAgeModelConfiguration = StratAgeModelConfiguration
     export NewStratAgeModelConfiguration

diff --git a/test/testStratOnly.jl b/test/testStratOnly.jl
@@ -1,6 +1,7 @@
 # Make an instance of a ChronAgeData object for nSamples
 nSamples = 4
 smpl = ChronAgeData(nSamples)
+@test smpl isa ChronAgeData
 smpl.Name          = ("Sample 1", "Sample 2", "Sample 3", "Sample 4") # Et cetera
 smpl.Age          .= [ 699.1,  708.8,  723.0,  754.0,] # Measured ages
 smpl.Age_sigma    .= [   3.0,    7.0,    5.0,    5.0,] # Measured 1-σ uncertainties
@@ -56,4 +57,11 @@ hiatus.Duration_sigma = [   3.1,    2.0 ]
 @test all(!isnan, agedist)
 @test size(hiatusdist) == (nHiatuses, config.nsteps)
 @test mean(hiatusdist, dims=2) ≈ [10.580012942504894; 18.96167245288326;;] atol=2
-@test -Inf < mean(lldist) < 0
+@test -Inf < mean(lldist) < 0
+
+## --- Strat only, general Distributions-based case
+
+# Make an instance of a ChronAgeData object for nSamples
+nSamples = 4
+smpl = GeneralAgeData(nSamples)
+@test smpl isa GeneralAgeData
diff --git a/test/testUtilities.jl b/test/testUtilities.jl
@@ -4,7 +4,7 @@
     @test d isa BilinearExponential{Float64}
     @test pdf(d, 66.02) ≈ 0.00010243952455548608
     @test logpdf(d, 66.02) ≈ (-3.251727600957773 -5.9345103368858085)
-    @test pdf(d, [66.02, 66.08, 66.15]) ≈ [0.00010243952455548608, 1.0372066408907184e-13, 1.0569878258022094e-28]
+    @test pdf.(d, [66.02, 66.08, 66.15]) ≈ [0.00010243952455548608, 1.0372066408907184e-13, 1.0569878258022094e-28]
 
     @test eltype(d) === partype(d) === Float64
     @test params(d) == (-5.9345103368858085, 66.00606672179812, 0.17739474265630253, 70.57882331291309, 0.6017142541555505)
@@ -21,7 +21,7 @@
     @test d isa Radiocarbon{Float64}
     @test pdf(d, 950) ≈ 0.0036210273644940918
     @test logpdf(d, 950) ≈ -3.4446721311475414 
-    @test pdf(d, [900, 950, 1000]) ≈ [3.372067127114498e-7, 0.0036210273644940918, 1.5582187464154278e-12]
+    @test pdf.(d, [900, 950, 1000]) ≈ [3.372067127114498e-7, 0.0036210273644940918, 1.5582187464154278e-12]
 
     @test eltype(d) === partype(d) === Float64
     @test location(d) ≈ 926.3094740428785 atol=0.1