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"Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+0" diff --git a/docs/Project.toml b/docs/Project.toml new file mode 100644 index 0000000..0397c04 --- /dev/null +++ b/docs/Project.toml @@ -0,0 +1,10 @@ +[deps] +ColorSchemes = "35d6a980-a343-548e-a6ea-1d62b119f2f4" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" +GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" diff --git a/docs/make.jl b/docs/make.jl new file mode 100644 index 0000000..c9d26ff --- /dev/null +++ b/docs/make.jl @@ -0,0 +1,25 @@ +using Documenter +using ParameterSpacePartitions + + +makedocs( + sitename = "ParameterSpacePartitions", + format = Documenter.HTML( + assets = [ + asset( + "https://fonts.googleapis.com/css?family=Montserrat|Source+Code+Pro&display=swap", + class = :css, + ), + ], + collapselevel = 1, + ), + + modules = [ParameterSpacePartitions], + pages = ["home" => "index.md", + "examples" => ["example 1" => "example1.md"], + "api" => "api.md"] +) + +deploydocs( + repo = "github.com/itsdfish/ParameterSpacePartitions.jl.git", +) \ No newline at end of file diff --git a/docs/src/api.md b/docs/src/api.md new file mode 100644 index 0000000..3b033dd --- /dev/null +++ b/docs/src/api.md @@ -0,0 +1,5 @@ +```@autodocs +Modules = [ParameterSpacePartitions] +Order = [:type, :function] +Private = false +``` \ No newline at end of file diff --git a/docs/src/example1.md b/docs/src/example1.md new file mode 100644 index 0000000..e69de29 diff --git a/docs/src/index.md b/docs/src/index.md new file mode 100644 index 0000000..a71de1f --- /dev/null +++ b/docs/src/index.md @@ -0,0 +1,131 @@ +# ParameterSpacePartitions.jl + +Parameter space partitioning is a model assessment method for mapping regions of the parameter space to qualitative data patterns. Parameter space partitioning uses MCMC sampling to explore the parameter space. Each chain searches a region of the parameter space for a specific pattern. As the space is sampled, a new chain is created for each newly discovered pattern. On each iteration, a proposal is sampled uniformly from the surface of a hyperspere with the same number of dimensions as the parameter space. + +# Installation + +You can install ParameterSpacePartitions.jl from the REPL by switching to the package mode using `]` and then typing: + +```julia +add ParameterSpacePartitions +``` + +# Quick Example + +In this quick example, we use PSP to find the regions of a 2D polytope. The polytope formed by partitioning the space into 5 regions based on 5 centroids. A point in the space belongs to the region with the closest centroid. This involves defining a `Polytope` type, a `model` method, which, in this case, simply returns the proposed point, and a `pfun` function which returns the pattern associated with the point. The pattern is simply the id of the region associated with the closest centroid. As expected, the PSP algorithm finds all of the regions. + +```@setup quick_example +using ParameterSpacePartitions +using Random +using LinearAlgebra +using DataFrames +using Distributions +using StatsPlots + +struct Polytope + location::Vector{Float64} +end + +function p_fun(location, points::Vector{Polytope}, args...; kwargs...) + distances = map(p -> norm(location .- p.location), points) + _,idx = findmin(distances) + return idx +end + +model(parms, args...; kwargs...) = parms + +# dimensions of the hypbercue +n_dims = 2 +# number of partitions +n_part = 5 +# number of starting points (only supports 1 currently) +n_start = 1 + + +# partition boundaries +polytopes = [Polytope(rand(n_dims)) for i in 1:n_part] +bounds = fill((0, 1), n_dims) + +sample(bounds) = map(b -> rand(Uniform(b...)), bounds) + +init_parms = map(_ -> sample(bounds), 1:n_start) + +options = Options(; + radius = .1, + bounds, + n_iters = 500, + parallel = false, + init_parms +) + +df = find_partitions( + model, + p_fun, + options, + polytopes +) + +n_patterns = length(unique(df.pattern)) +``` + +```@example quick_example +using ParameterSpacePartitions +using Random +using LinearAlgebra +using DataFrames +using Distributions +using StatsPlots + +struct Polytope + location::Vector{Float64} +end + +function p_fun(location, points::Vector{Polytope}, args...; kwargs...) + distances = map(p -> norm(location .- p.location), points) + _,idx = findmin(distances) + return idx +end + +model(parms, args...; kwargs...) = parms + +# dimensions of the hypbercue +n_dims = 2 +# number of partitions +n_part = 5 +# number of starting points (only supports 1 currently) +n_start = 1 + +# partition boundaries +polytopes = [Polytope(rand(n_dims)) for i in 1:n_part] +bounds = fill((0, 1), n_dims) + +sample(bounds) = map(b -> rand(Uniform(b...)), bounds) + +init_parms = map(_ -> sample(bounds), 1:n_start) + +options = Options(; + radius = .1, + bounds, + n_iters = 500, + parallel = false, + init_parms +) + +df = find_partitions( + model, + p_fun, + options, + polytopes +) + +n_patterns = length(unique(df.pattern)) +``` +It is also possible to see the five regions by plotting the accepted samples as a scatter plot. +```@example quick_example +df_accepted = filter(x -> x.acceptance, df) +@df df_accepted scatter(:p1, :p2, group = :pattern, leg=false, grid=false) +``` + +# References + +Pitt, M. A., Kim, W., Navarro, D. J., & Myung, J. I. (2006). Global model analysis by parameter space partitioning. Psychological Review, 113(1), 57. diff --git a/src/ParameterSpacePartitions.jl b/src/ParameterSpacePartitions.jl index 130fed6..7b11fb4 100644 --- a/src/ParameterSpacePartitions.jl +++ b/src/ParameterSpacePartitions.jl @@ -12,7 +12,6 @@ module ParameterSpacePartitions export adapt! export no_adaption! export estimate_volume - export bias_correction export psp_slices export Options