diff --git a/Project.toml b/Project.toml index 05f10a1..78fdffc 100644 --- a/Project.toml +++ b/Project.toml @@ -1,4 +1,4 @@ -name = "GAM" +name = "GeneralizedAdditiveModels" uuid = "cc454e9f-ce0f-441e-b193-468e31ddef4b" authors = ["Trent Henderson "] version = "0.1.0" diff --git a/README.md b/README.md index 24799f1..45e64c2 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# GAM.jl +# GeneralizedAdditiveModels.jl Fit, evaluate, and visualise generalised additive models (GAMs) in native Julia ## Motivation @@ -7,7 +7,7 @@ Fit, evaluate, and visualise generalised additive models (GAMs) in native Julia ## Usage -The basic interface to `GAM.jl` is the `gam` function, which is as easy as: +The basic interface to `GeneralizedAdditiveModels.jl` is the `gam` function, which is as easy as: ```{julia} mod = gam("Volume ~ s(Girth, k=10, degree=3) + s(Height, k=10, degree=3)", df) @@ -28,12 +28,14 @@ Note that currently, the following families are supported: * `Normal` * `Poisson` * `Gamma` +* `Bernoulli` And the following link functions: * `Identity` * `Log` +* `Logit` ## Development notes -`GAM.jl` is very much in active development. Please check back for updates and new features or feel free to contribute yourself! The project to-date has been a collaboration between [Trent Henderson](https://github.com/hendersontrent) and [Mason Yahr](https://github.com/yahrMason). +`GeneralizedAdditiveModels.jl` is very much in active development. Please check back for updates and new features or feel free to contribute yourself! The project to-date has been a collaboration between [Trent Henderson](https://github.com/hendersontrent) and [Mason Yahr](https://github.com/yahrMason). diff --git a/docs/Project.toml b/docs/Project.toml index 7ea483c..9253d65 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,5 +1,5 @@ [deps] Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -GAM = "cc454e9f-ce0f-441e-b193-468e31ddef4b" +GeneralizedAdditiveModels = "cc454e9f-ce0f-441e-b193-468e31ddef4b" LiveServer = "16fef848-5104-11e9-1b77-fb7a48bbb589" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" diff --git a/docs/make.jl b/docs/make.jl index 67be5df..2d8bf1e 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -3,14 +3,14 @@ using Documenter # Make sure the package loads when building from docs/ push!(LOAD_PATH, joinpath(@__DIR__, "..", "src")) -using GAM +using GeneralizedAdditiveModels # Doctesting DocMeta.setdocmeta!(GAM, :DocTestSetup, :(using GAM); recursive=true) makedocs( - sitename = "GAM.jl", - modules = [GAM], + sitename = "GeneralizedAdditiveModels.jl", + modules = [GeneralizedAdditiveModels], pages = [ "Home" => "index.md", "API Reference" => "api_reference.md", @@ -22,4 +22,4 @@ makedocs( ) # for later -# deploydocs(repo = "github.com/hendersontrent/GAM.jl.git", devbranch = "main") +# deploydocs(repo = "github.com/hendersontrent/GeneralizedAdditiveModels.jl.git", devbranch = "main") diff --git a/docs/src/api_reference.md b/docs/src/api_reference.md index f7d1277..5dc7207 100644 --- a/docs/src/api_reference.md +++ b/docs/src/api_reference.md @@ -1,9 +1,9 @@ # API Reference ```@autodocs -Modules = [GAM] +Modules = [GeneralizedAdditiveModels] Recursive = true Public = true Private = false Order = [:module, :type, :function, :macro, :constant] -``` \ No newline at end of file +``` diff --git a/docs/src/index.md b/docs/src/index.md index 00b312d..8a06501 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -33,7 +33,7 @@ To install the package, clone it directly from the repository: ```julia using Pkg -Pkg.add(url="https://github.com/hendersontrent/GAM.jl") +Pkg.add(url="https://github.com/hendersontrent/GeneralizedAdditiveModels.jl") ``` --- @@ -44,7 +44,7 @@ Fitting a GAM in GeneralizedAdditiveModels.jl is quick and easy. The syntax of t ```julia using RDatasets -using GAM +using GeneralizedAdditiveModels df = dataset("datasets", "trees"); @@ -55,7 +55,7 @@ mod = gam("Volume ~ s(Girth, k=10, degree=3) + s(Height, k=10, degree=3)", df) **GeneralizedAdditiveModels.jl** is under active development, and contributions are very welcome! -- If you’ve found a bug or want to propose a feature, please [open an issue](https://github.com/hendersontrent/GAM.jl/issues). +- If you’ve found a bug or want to propose a feature, please [open an issue](https://github.com/hendersontrent/GeneralizedAdditiveModels.jl/issues). - If your idea gets positive feedback, feel free to submit a pull request. - If you’re unsure where to start, you can also browse the open issues and pick one that interests you. diff --git a/src/GAM.jl b/src/GeneralizedAdditiveModels.jl similarity index 94% rename from src/GAM.jl rename to src/GeneralizedAdditiveModels.jl index 47eb1ff..726aa2b 100644 --- a/src/GAM.jl +++ b/src/GeneralizedAdditiveModels.jl @@ -1,4 +1,4 @@ -module GAM +module GeneralizedAdditiveModels using Distributions, GLM, Optim, BSplines, LinearAlgebra, DataFrames, Plots, Optim diff --git a/src/alpha.jl b/src/alpha.jl index e4b6f3f..c2af46b 100644 --- a/src/alpha.jl +++ b/src/alpha.jl @@ -4,7 +4,7 @@ Calculate alpha. Usage: ```julia-repl -alpha((y, mu, Dist, Link) +alpha(y, mu, Dist, Link) ``` Arguments: - `y` : `Vector` containing the response variable. diff --git a/test/runtests.jl b/test/runtests.jl index d430a90..644f0c1 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,4 +1,4 @@ -using GAM +using GeneralizedAdditiveModels using Test using RDatasets, Plots using Distributions @@ -9,7 +9,7 @@ df = dataset("datasets", "trees"); #-------------------- Run tests ----------------- -@testset "GAM.jl" begin +@testset "GeneralizedAdditiveModels.jl" begin mod = gam("Volume ~ s(Girth, k=10, degree=3) + s(Height, k=10, degree=3)", df) @@ -168,7 +168,7 @@ end # Check that predictions are reasonable x_test = [-1.0, 0.0, 1.0] for xi in x_test - pred_mat = GAM.BuildPredictionMatrix([xi], mod.Basis[1], mod.ColMeans[1]) + pred_mat = GeneralizedAdditiveModels.BuildPredictionMatrix([xi], mod.Basis[1], mod.ColMeans[1]) pred_eta = mod.Coef[1] .+ pred_mat * mod.Coef[mod.CoefIndex[1]] pred_p = 1 / (1 + exp(-pred_eta[1]))