Upgrade to Isoplot v0.4 (replaces val and err)

Author: brenhinkeller

Project.toml

@@ -1,7 +1,7 @@
 name = "Chron"
 uuid = "68885b1f-77b5-52a7-b2e7-6a8014c56b98"
 authors = ["C. Brenhin Keller <[email protected]>"]
-version = "0.6.4"
+version = "0.6.5"
 
 [deps]
 DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
@@ -20,7 +20,7 @@ StatGeochemBase = "61e559cd-58b4-4257-8528-26bb26ff2b9a"
 [compat]
 DelimitedFiles = "1"
 Distributions = "0.15 - 0.25"
-Isoplot = "0.3"
+Isoplot = "0.4"
 KernelDensity = "0.4 - 0.6"
 LsqFit = "0.7 - 0.15"
 NaNStatistics = "0.6.40"

src/Chron.jl

@@ -24,7 +24,6 @@ module Chron
     @reexport using NaNStatistics
     @reexport using StatGeochemBase
     @reexport using Isoplot
-    using Isoplot: val, err
 
     # Basic statistics and UI resources
     using ProgressMeter: @showprogress, Progress, update!

src/DistMetropolis.jl

@@ -41,7 +41,7 @@
                     data[:,4]./=smpl.inputSigmaLevel
                     analyses = UPbAnalysis.(eachcol(data)...,)
                     uis = upperintercept.(tpbloss, analyses)
-                    μ, σ = val.(uis), err.(uis)
+                    μ, σ = value.(uis), stdev.(uis)
                 else
                     @info "Interpreting first two columns of $(Name[i]).csv as \n | Age | Age $σstr |"
                     data[:,2]./=smpl.inputSigmaLevel

src/Fitplot.jl

@@ -65,7 +65,7 @@
                 # @info "$i: $(Name[i])\nInterpreting the five columns of $(Name[i]).csv as:\n | ²⁰⁷Pb/²³⁵U | $σstr | ²⁰⁶Pb/²³⁸U | $σstr | correlation coefficient |"
                 analyses = UPbAnalysis.(eachcol(data)...,)
                 dates = age68.(analyses)
-                val.(dates), err.(dates) ./ smpl.inputSigmaLevel
+                value.(dates), stdev.(dates) ./ smpl.inputSigmaLevel
             else
                 # @info "$i: $(Name[i])\nInterpreting first two columns of $(Name[i]).csv as \n | Age | Age $σstr |"
                 data[:,1], data[:,2] ./ smpl.inputSigmaLevel

src/Systematic.jl

@@ -18,15 +18,15 @@
 ## --- Add systematic uncertainty when given an already-generated age or age-depth distribution
 
     function add_systematic_uncert_UPb(agedistmyr::Vector{<:AbstractFloat})
-        λ238 = val(λ238U) # Jaffey decay constant, 1/Myr
-        λ238_ = val(λ238U) .+ err(λ238U).*randn(size(agedistmyr))# Jaffey decay with uncertainty 1/Myr
+        λ238 = value(λ238U) # Jaffey decay constant, 1/Myr
+        λ238_ = value(λ238U) .+ stdev(λ238U).*randn(size(agedistmyr))# Jaffey decay with uncertainty 1/Myr
         σtracer = 1 .+ (0.03/2/100) .* randn(size(agedistmyr)) # Earthtime tracer uncertainty
         r = exp.(agedistmyr .* λ238) .- 1
         return log.(r .* σtracer .+ 1) ./ λ238_
     end
     function add_systematic_uncert_UPb(agedistmyr::Matrix{<:AbstractFloat})
-        λ238 = val(λ238U) # Jaffey decay constant, 1/Myr
-        λ238_ = val(λ238U) .+ err(λ238U).*randn(1, size(agedistmyr,2)) # Jaffey decay with uncertainty 1/Myr
+        λ238 = value(λ238U) # Jaffey decay constant, 1/Myr
+        λ238_ = value(λ238U) .+ stdev(λ238U).*randn(1, size(agedistmyr,2)) # Jaffey decay with uncertainty 1/Myr
         σtracer = 1 .+ (0.03/2/100) .* randn(1, size(agedistmyr,2)) # Earthtime tracer uncertainty
         r = exp.(agedistmyr .* λ238) .- 1
         return log.(r .* σtracer .+ 1) ./ λ238_
@@ -138,11 +138,11 @@
         # Th230ₐ/U238ₐ = 1-exp(-Age*λ230Th)
         # Th230/U238 = (1-exp(-Age*λ230Th)) * λ238U/λ230Th
 
-        λ238 = val(λ238U)
-        λ238_ = val(λ238U) .+ err(λ238U).*randn(size(agedistmyr))
+        λ238 = value(λ238U)
+        λ238_ = value(λ238U) .+ stdev(λ238U).*randn(size(agedistmyr))
 
-        λ230 = val(λ230Th)
-        λ230_ = val(λ230Th) .+ err(λ230Th).*randn(size(agedistmyr))
+        λ230 = value(λ230Th)
+        λ230_ = value(λ230Th) .+ stdev(λ230Th).*randn(size(agedistmyr))
 
         # Convert age distribution to ratio distribution
         # (i.e., distribution of slope of two-point isochron)
@@ -157,11 +157,11 @@
         # Th230ₐ/U238ₐ = 1-exp(-Age*λ230Th)
         # Th230/U238 = (1-exp(-Age*λ230Th)) * λ238U/λ230Th
 
-        λ238 = val(λ238U)
-        λ238_ = val(λ238U) .+ err(λ238U).*randn(1, size(agedistmyr,2))
+        λ238 = value(λ238U)
+        λ238_ = value(λ238U) .+ stdev(λ238U).*randn(1, size(agedistmyr,2))
 
-        λ230 = val(λ230Th)
-        λ230_ = val(λ230Th) .+ err(λ230Th).*randn(1, size(agedistmyr,2))
+        λ230 = value(λ230Th)
+        λ230_ = value(λ230Th) .+ stdev(λ230Th).*randn(1, size(agedistmyr,2))
 
         # Convert age distribution to ratio distribution
         # (i.e., distribution of slope of two-point isochron)