Concrete matrix types change to Abstract ones

Author: jbytecode

CHANGELOG.md

@@ -1,4 +1,5 @@
 # v0.11.1 (Upcoming Release)
+- Concrete types of X and y changed to AbstractMatrix{Float64} and AbstractVector{Float64}
 
 
 # v0.11.0

src/asm2000.jl

@@ -57,7 +57,7 @@ function asm2000(setting::RegressionSetting)::Dict
 end
 
 
-function asm2000(X::Matrix{Float64}, y::Vector{Float64})::Dict
+function asm2000(X::AbstractMatrix{Float64}, y::AbstractVector{Float64})::Dict
     n, p = size(X)
     h = floor((n + p - 1) / 2)
     ltsreg = lts(X, y)

src/atkinson94.jl

@@ -59,8 +59,8 @@ function atkinson94(setting::RegressionSetting; iters = nothing, crit = 3.0)::Di
 end
 
 function atkinson94(
-    X::Matrix{Float64},
-    y::Vector{Float64};
+    X::AbstractMatrix{Float64},
+    y::AbstractVector{Float64};
     iters = nothing,
     crit = 3.0,
 )::Dict

src/atkinsonstalactiteplot.jl

@@ -34,8 +34,8 @@ function atkinsonstalactiteplot(
 end
 
 function atkinsonstalactiteplot(
-    X::Matrix{Float64},
-    y::Vector{Float64};
+    X::AbstractMatrix{Float64},
+    y::AbstractVector{Float64};
     iters = nothing,
     crit = 3.0,
 )::Nothing
@@ -46,7 +46,7 @@ function atkinsonstalactiteplot(
 end
 
 function generate_stalactite_plot(
-    residuals_matrix::Matrix{Float64},
+    residuals_matrix::AbstractMatrix{Float64},
     n::Int64,
     p::Int64,
     crit,

src/bacon.jl

@@ -24,7 +24,7 @@ Two methods V1 and V2 are defined in the paper which use Mahalanobis distance or
  - `method`: The distance method to use for selecting the points for initial subset
 """
 function initial_basic_subset_multivariate_data(
-    X::Matrix{Float64},
+    X::AbstractMatrix{Float64},
     m::Int;
     method::String = "mahalanobis",
 )
@@ -53,7 +53,7 @@ It also guarantees that at least m indices are returned and that the selected in
  - `m`: The minimum number of points to include in the subset indices.
  - `distances`: The distances vector used for selecting minumum distance indices.
 """
-function select_subset(X::Matrix{Float64}, m::Int, distances::Array{Float64})
+function select_subset(X::AbstractMatrix{Float64}, m::Int, distances::Array{Float64})
     rank_x = rank(X)
     sorted_distances = sortperm(distances)
     subset = sorted_distances[1:m]
@@ -88,7 +88,7 @@ This function performs the outlier detection for multivariate data according to
  - `alpha`: The quantile used for cutoff
 """
 function bacon_multivariate_outlier_detection(
-    X::Matrix{Float64},
+    X::AbstractMatrix{Float64},
     m::Int;
     method::String = "mahalanobis",
     alpha::Float64 = 0.025,
@@ -146,7 +146,7 @@ This function computes the t distance for each point and returns the distance ve
  - `y`: The output vector
  - `subset`: The vector which denotes the points inside the subset, used to scale the residuals accordingly.
 """
-function compute_t_distance(X::Matrix{Float64}, y::Array{Float64}, subset::Array{Int64})
+function compute_t_distance(X::AbstractMatrix{Float64}, y::Array{Float64}, subset::Array{Int64})
 
     n, p = size(X)
 
@@ -187,7 +187,7 @@ This function computes the initial subset having at least m elements which are l
  - `alpha`: The quantile used for cutoff
 """
 function bacon_regression_initial_subset(
-    X::Matrix{Float64},
+    X::AbstractMatrix{Float64},
     y::Array{Float64},
     m::Int;
     method::String = "mahalanobis",
@@ -259,7 +259,7 @@ Billor, Nedret, Ali S. Hadi, and Paul F. Velleman. "BACON: blocked adaptive comp
 Computational statistics & data analysis 34.3 (2000): 279-298.
 """
 function bacon(
-    X::Matrix{Float64},
+    X::AbstractMatrix{Float64},
     y::Array{Float64};
     m::Int,
     method::String = "mahalanobis",

src/basis.jl

@@ -160,7 +160,7 @@ julia> designMatrix(setting)
  1.0  73.0
 ```
 """
-function designMatrix(setting::RegressionSetting)::Matrix{Float64}
+function designMatrix(setting::RegressionSetting)::AbstractMatrix{Float64}
     mf = ModelFrame(setting.formula, setting.data)
     mm = ModelMatrix(mf)
     return convert(Matrix{Float64}, mm.m)
@@ -209,7 +209,7 @@ julia> responseVector(setting)
   29.0
 ```
 """
-function responseVector(setting::RegressionSetting)::Vector{Float64}
+function responseVector(setting::RegressionSetting)::AbstractVector{Float64}
     mf = ModelFrame(setting.formula, setting.data)
     return convert(Vector{Float64}, setting.data[:, mf.f.lhs.sym])
 end
@@ -292,7 +292,7 @@ end
 - `f::Function`: A function that takes a one dimensional array as argument.
 - `data::Matrix`: A Matrix object.
 """
-function applyColumns(f::Function, data::Matrix)
+function applyColumns(f::Function, data::AbstractMatrix{Float64})
     return [f(col) for col in eachcol(data)]
 end
 
@@ -305,20 +305,20 @@ end
     Return minimum of numbers greater than zero.
 
 # Arguments
-- `arr::Vector{Float64}`: A function that takes a one dimensional array as argument.
+- `arr::AbstractVector{Float64}`: A function that takes a one dimensional array as argument.
 
 # Example
 ```julia-repl
 julia> find_minimum_nonzero([0.0, 0.0, 5.0, 1.0])
 1.0
 ```
 """
-function find_minimum_nonzero(arr::Vector{Float64})
+function find_minimum_nonzero(arr::AbstractVector{Float64})
     return minimum(filter(x -> x > 0, arr))
 end
 
 
-function zstandardize(v::Vector{Float64})::Vector{Float64}
+function zstandardize(v::AbstractVector{Float64})::AbstractVector{Float64}
     return (v .- mean(v)) ./ std(v)
 end
 

src/bch.jl

@@ -75,8 +75,8 @@ end
 
 
 function bch(
-    Xdesign::Matrix{Float64},
-    y::Vector{Float64};
+    Xdesign::AbstractMatrix{Float64},
+    y::AbstractVector{Float64};
     alpha = 0.05,
     maxiter = 1000,
     epsilon = 0.000001,

src/bchplot.jl

@@ -42,8 +42,8 @@ function bchplot(
 end
 
 function bchplot(
-    Xdesign::Matrix{Float64},
-    y::Vector{Float64};
+    Xdesign::AbstractMatrix{Float64},
+    y::AbstractVector{Float64};
     alpha = 0.05,
     maxiter = 1000,
     epsilon = 0.00001,

src/ccf.jl

@@ -19,7 +19,7 @@ Perform signed gradient descent for clipped convex functions for a given regress
 
 # Arguments
 - `setting::RegressionSetting`: RegressionSetting object with a formula and dataset.
-- `starting_lambdas::Vector{Float64}`: Starting values of weighting parameters used by signed gradient descent.
+- `starting_lambdas::AbstractVector{Float64}`: Starting values of weighting parameters used by signed gradient descent.
 - `alpha::Float64`: Loss at which a point is labeled as an outlier (points with loss ≥ alpha will be called outliers).
 - `max_iter::Int64`: Maximum number of iterations to run signed gradient descent.
 - `beta::Float64`: Step size parameter.
@@ -79,9 +79,9 @@ end
 Perform signed gradient descent for clipped convex functions for a given regression setting.
 
 # Arguments
-- `X::Matrix{Float64}`: Design matrix of the linear model.
-- `y::Vector{Float64}`: Response vector of the linear model.
-- `starting_lambdas::Vector{Float64}`: Starting values of weighting parameters used by signed gradient descent.
+- `X::AbstractMatrix{Float64}`: Design matrix of the linear model.
+- `y::AbstractVector{Float64}`: Response vector of the linear model.
+- `starting_lambdas::AbstractVector{Float64}`: Starting values of weighting parameters used by signed gradient descent.
 - `alpha::Float64`: Loss at which a point is labeled as an outlier. If unspecified, will be chosen as p*mean(residuals.^2), where residuals are OLS residuals.
 - `p::Float64`: Points that have squared OLS residual greater than p times the mean squared OLS residual are considered outliers.
 - `max_iter::Int64`: Maximum number of iterations to run signed gradient descent.
@@ -100,8 +100,8 @@ Barratt, S., Angeris, G. & Boyd, S. Minimizing a sum of clipped convex functions
 
 """
 function ccf(
-    X::Matrix{Float64},
-    y::Vector{Float64};
+    X::AbstractMatrix{Float64},
+    y::AbstractVector{Float64};
     starting_lambdas = nothing,
     alpha = nothing,
     p = 3,

src/cm97.jl

@@ -50,7 +50,7 @@ end
 
 
 
-function cm97(X::Matrix{Float64}, y::Vector{Float64}; maxiter::Int = 1000)::Dict
+function cm97(X::AbstractMatrix{Float64}, y::AbstractVector{Float64}; maxiter::Int = 1000)::Dict
 
     n, p = size(X)
     pbar::Float64 = p / n