Examples

doc/examples.md

@@ -0,0 +1,38 @@
+# Examples
+Worked examples using GAM.jl from Generalized Additive Models, Simon N. Wood
+
+## Linear Models
+```
+using RDatasets
+using GAM
+using Plots
+```
+### Trees
+```
+df=dataset("datasets", "trees")
+mod = gam("Volume ~ s(Girth, k=10, degree=3) + s(Height, k=10, degree=3)", df)
+```
+
+### Hubble
+Model: </br>
+y ~ x  
+#### Load Hubble Dataset
+```
+hubble=dataset("gamair", "hubble")
+```
+#### Fit with GAM
+```
+hubMod =gam("y ~ x", hubble) 
+GAM.summary(hubMod)
+#Remove outliers
+hubMod1=gam("y ~ x", hubble[Not([3,15]), :])
+GAM.summary(hubMod1)
+```
+#### Plots
+```
+scatter(hubble.x, hubble.y, label="Measured")
+scatter!(hubMod.x, hubMod.Fitted, label="Fitted")
+#Plot fitted data vs residuals
+scatter(hubMod.Fitted, residuals(hubMod), label="", xlab="fitted values", ylab="residuals")
+
+```

grep

@@ -0,0 +1,86 @@
+.
+./.vscode
+./.vscode/settings.json
+./doc
+./doc/examples.md
+./test
+./test/Project.toml
+./test/runtests.jl
+./Project.toml
+./README.md
+./grep
+./Manifest.toml
+./src
+./src/GAM.jl
+./src/dcat.jl
+./src/DifferenceMatrix.jl
+./src/alpha.jl
+./src/FitGAM.jl
+./src/diffm.jl
+./src/Plots.jl
+./src/FitWPS.jl
+./src/Predictions.jl
+./src/GAMData.jl
+./src/PIRLS.jl
+./src/GAMFormula.jl
+./src/BuildBasis.jl
+./src/FitOLS.jl
+./src/ModelDiagnostics.jl
+./src/Links-Dists.jl
+./LICENSE
+./.gitignore
+./.git
+./.git/info
+./.git/info/exclude
+./.git/index
+./.git/objects
+./.git/objects/info
+./.git/objects/eb
+./.git/objects/eb/4120dd653172387cb15d119bd9b9711dbcf04d
+./.git/objects/f3
+./.git/objects/f3/f7212cda25031fed2b04ceb41ffdb68189f5c0
+./.git/objects/da
+./.git/objects/da/71ec305a605ba1de4657ffbc3beddffb98f464
+./.git/objects/pack
+./.git/objects/pack/pack-101bb809d82d5d77673d831d7987be961e216234.rev
+./.git/objects/pack/pack-101bb809d82d5d77673d831d7987be961e216234.pack
+./.git/objects/pack/pack-101bb809d82d5d77673d831d7987be961e216234.idx
+./.git/objects/e6
+./.git/objects/e6/706ce7b74b799565d2639eb78af8c477d7a21c
+./.git/refs
+./.git/refs/heads
+./.git/refs/heads/main
+./.git/refs/tags
+./.git/refs/remotes
+./.git/refs/remotes/origin
+./.git/refs/remotes/origin/HEAD
+./.git/config
+./.git/branches
+./.git/FETCH_HEAD
+./.git/description
+./.git/COMMIT_EDITMSG
+./.git/logs
+./.git/logs/refs
+./.git/logs/refs/heads
+./.git/logs/refs/heads/main
+./.git/logs/refs/remotes
+./.git/logs/refs/remotes/origin
+./.git/logs/refs/remotes/origin/HEAD
+./.git/logs/HEAD
+./.git/packed-refs
+./.git/hooks
+./.git/hooks/pre-merge-commit.sample
+./.git/hooks/pre-rebase.sample
+./.git/hooks/sendemail-validate.sample
+./.git/hooks/pre-commit.sample
+./.git/hooks/post-update.sample
+./.git/hooks/update.sample
+./.git/hooks/commit-msg.sample
+./.git/hooks/pre-push.sample
+./.git/hooks/pre-applypatch.sample
+./.git/hooks/fsmonitor-watchman.sample
+./.git/hooks/pre-receive.sample
+./.git/hooks/prepare-commit-msg.sample
+./.git/hooks/push-to-checkout.sample
+./.git/hooks/applypatch-msg.sample
+./.git/HEAD

src/GAM.jl

@@ -26,5 +26,7 @@ export GAMData
 export PartialDependencePlot
 export plotGAM
 export gam
-
+export summary
+export residuals
+export fitted
 end

src/GAMData.jl

@@ -29,7 +29,7 @@ mutable struct GAMData
     CoefIndex::AbstractArray
     Fitted::AbstractArray
     Diagnostics::Dict
-
+    #TODO Why is separate constructor needed? spk
     function GAMData(
         y::AbstractArray,
         x::AbstractArray,
@@ -44,4 +44,19 @@ mutable struct GAMData
     )
         new(y, x, Basis, Family, Link, Coef, ColMeans, CoefIndex, Fitted, Diagnostics)
     end
+end
+
+"Calculate residuals from fitted data"
+residuals(data)=abs.(data.y - data.Fitted)
+
+"Return fitted data to match R function"
+fitted(data)=data.Fitted
+
+"Print summary information of GAMData"
+function summary(data::GAMData, out::IO=stdout)
+    println("Summary:")
+    println("Coef $(data.Coef)")
+    println(out, "EDF: $(data.Diagnostics[:EDF])")
+    println(out, "GCV: $(data.Diagnostics[:GCV])")
+    println(out, "RSS: $(data.Diagnostics[:RSS])")
 end

src/GAMFormula.jl

@@ -65,7 +65,8 @@ function ParseFormula(formula::String)
             smooth = true
         else  # no s() wrapping
             symbol_name = Symbol(component)
-            k = degree = 0  # Set default values when s() wrapping is absent
+            k = 10
+            degree = 10  # Set default values when s() wrapping is absent
             smooth = false
         end
         push!(df, (symbol_name, k, degree, smooth))