Px to Vx, Py to Vy

mlesnoff · Jan 10, 2025 · 1c99c10 · 1c99c10
1 parent 08964a9
commit 1c99c10
Show file tree

Hide file tree

Showing 9 changed files with 71 additions and 69 deletions.
diff --git a/docs/src/news.md b/docs/src/news.md
@@ -1,8 +1,10 @@
 # News
 
-## *Version 0.7.1*
-
+## *Version 0.8.0*
 
+- Breaking
+   - Object 'P' in the code and outputs (matrix of laodings in Pca, 
+       Pls etc.): renamed to 'V'.
 
 ## *Version 0.7.0*
 

diff --git a/src/_structures_fun.jl b/src/_structures_fun.jl
@@ -186,8 +186,8 @@ end
 struct Ccawold
     Tx::Matrix
     Ty::Matrix
-    Px::Matrix
-    Py::Matrix
+    Vx::Matrix
+    Vy::Matrix
     Rx::Matrix
     Ry::Matrix    
     Wx::Matrix
@@ -207,8 +207,8 @@ end
 struct Plscan
     Tx::Matrix
     Ty::Matrix
-    Px::Matrix
-    Py::Matrix
+    Vx::Matrix
+    Vy::Matrix
     Rx::Matrix
     Ry::Matrix    
     Wx::Matrix

diff --git a/src/ccawold.jl b/src/ccawold.jl
@@ -152,8 +152,8 @@ function ccawold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     Ty = copy(Tx)
     Wx = similar(X, p, nlv)
     Wy = similar(X, q, nlv)
-    Px = copy(Wx)
-    Py = copy(Wy)
+    Vx = copy(Wx)
+    Vy = copy(Wy)
     TTx = similar(X, nlv)
     TTy = copy(TTx)
     tx   = similar(X, n)
@@ -162,8 +162,8 @@ function ccawold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     wxtild = copy(wx)    
     wy  = similar(X, q)
     wytild = copy(wy)
-    px   = copy(wx)
-    py   = copy(wy)
+    vx   = copy(wx)
+    vy   = copy(wy)
     niter = zeros(nlv)
     # End
     @inbounds for a = 1:nlv
@@ -205,13 +205,13 @@ function ccawold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
             end
         end
         niter[a] = iter - 1
-        mul!(px, X', tx)
-        px ./= ttx
-        mul!(py, Y', ty)
-        py ./= tty
+        mul!(vx, X', tx)
+        vx ./= ttx
+        mul!(vy, Y', ty)
+        vy ./= tty
         # Deflation
-        X .-= tx * px'
-        Y .-= ty * py'
+        X .-= tx * vx'
+        Y .-= ty * vy'
         # Same as:
         #b = tx' * X / ttx
         #X .-= tx * b
@@ -222,16 +222,16 @@ function ccawold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
         Ty[:, a] .= ty
         Wx[:, a] .= wx
         Wy[:, a] .= wy
-        Px[:, a] .= px
-        Py[:, a] .= py
+        Vx[:, a] .= vx
+        Vy[:, a] .= vy
         TTx[a] = ttx
         TTy[a] = tty
     end
     Tx .= (1 ./ sqrtw) .* Tx
     Ty .= (1 ./ sqrtw) .* Ty
-    Rx = Wx * inv(Px' * Wx)
-    Ry = Wy * inv(Py' * Wy)
-    Ccawold(Tx, Ty, Px, Py, Rx, Ry, Wx, Wy, TTx, TTy, bscales, xmeans, xscales, 
+    Rx = Wx * inv(Vx' * Wx)
+    Ry = Wy * inv(Vy' * Wy)
+    Ccawold(Tx, Ty, Vx, Vy, Rx, Ry, Wx, Wy, TTx, TTy, bscales, xmeans, xscales, 
         ymeans, yscales, weights, niter, par)
 end
 
@@ -271,7 +271,7 @@ function Base.summary(object::Ccawold, X, Y)
     # X
     tt = object.TTx 
     sstot = frob(X, object.weights)^2
-    tt_adj = colsum(object.Px.^2) .* tt
+    tt_adj = colsum(object.Vx.^2) .* tt
     pvar = tt_adj / sstot
     cumpvar = cumsum(pvar)
     xvar = tt_adj / n    
@@ -280,7 +280,7 @@ function Base.summary(object::Ccawold, X, Y)
     # Y
     tt = object.TTy 
     sstot = frob(Y, object.weights)^2
-    tt_adj = colsum(object.Py.^2) .* tt
+    tt_adj = colsum(object.Vy.^2) .* tt
     pvar = tt_adj / sstot
     cumpvar = cumsum(pvar)
     xvar = tt_adj / n    

diff --git a/src/comdim.jl b/src/comdim.jl
@@ -205,8 +205,8 @@ function comdim!(Xbl::Vector, weights::Weight; kwargs...)
         @inbounds for k = 1:nbl
             Xbl[k] .-= u * (u' * Xbl[k])
             # Same as:
-            #Px = sqrt(lb[k, a]) * Wbl[k][:, a]'
-            #Xbl[k] .-= u * Px
+            #Vx = sqrt(lb[k, a]) * Wbl[k][:, a]'
+            #Xbl[k] .-= u * Vx
         end
     end
     T = Diagonal(1 ./ sqrtw) * (sqrt.(mu)' .* U)
@@ -254,8 +254,8 @@ function transf_all(object::Comdim, Xbl; nlv = nothing)
         u .= 1 / sqrt(object.mu[a]) * TB * object.W[:, a]
         U[:, a] .= u
         @inbounds for k = 1:nbl
-            Px = sqrt(object.lb[k, a]) * object.Wbl[k][:, a]'
-            zXbl[k] .-= u * Px
+            Vx = sqrt(object.lb[k, a]) * object.Wbl[k][:, a]'
+            zXbl[k] .-= u * Vx
         end
     end
     T = sqrt.(object.mu[1:nlv])' .* U

diff --git a/src/mbpca.jl b/src/mbpca.jl
@@ -230,8 +230,8 @@ function transf_all(object::Mbpca, Xbl; nlv = nothing)
         u .= 1 / sqrt(object.mu[a]) * TB * object.W[:, a]
         U[:, a] .= u
         @inbounds for k = 1:nbl
-            Px = sqrt(object.lb[k, a]) * object.Wbl[k][:, a]'
-            zXbl[k] -= u * Px
+            Vx = sqrt(object.lb[k, a]) * object.Wbl[k][:, a]'
+            zXbl[k] -= u * Vx
         end
     end
     T = sqrt.(object.mu[1:nlv])' .* U

diff --git a/src/mbplswest.jl b/src/mbplswest.jl
@@ -132,12 +132,12 @@ function mbplswest!(Xbl::Vector, Y::Matrix, weights::Weight; kwargs...)
     Tx = similar(Xbl[1], n, nlv)
     Wx = similar(Xbl[1], sum(p), nlv)
     Wytild = similar(Xbl[1], q, nlv)
-    Px = copy(Wx)
+    Vx = copy(Wx)
     tk  = similar(Xbl[1], n)
     tx = copy(tk)
     ty  = copy(tk)
     wx = similar(Xbl[1], sum(p))
-    px = copy(wx)
+    vx = copy(wx)
     wy  = similar(Xbl[1], q)
     wytild = copy(wy)
     TTx = similar(Xbl[1], nlv)
@@ -178,13 +178,13 @@ function mbplswest!(Xbl::Vector, Y::Matrix, weights::Weight; kwargs...)
         X .= reduce(hcat, Xbl)
         wx .= X' * ty / dot(ty, ty)    
         wx ./= normv(wx)
-        mul!(px, X', tx)
-        px ./= ttx
+        mul!(vx, X', tx)
+        vx ./= ttx
         wytild .= Y' * tx / ttx
         # End           
         Tx[:, a] .= tx   
         Wx[:, a] .= wx
-        Px[:, a] .= px
+        Vx[:, a] .= vx
         Wytild[:, a] .= wytild
         TTx[a] = ttx
         @inbounds for k = 1:nbl
@@ -193,9 +193,9 @@ function mbplswest!(Xbl::Vector, Y::Matrix, weights::Weight; kwargs...)
         Y .-= tx * wytild'
     end
     Tx .= (1 ./ sqrtw) .* Tx
-    Rx = Wx * inv(Px' * Wx)
+    Rx = Wx * inv(Vx' * Wx)
     lb = nothing
-    Mbplswest(Tx, Px, Rx, Wx, Wytild, Tbl, Tb, Pbl, TTx, fitmbl, ymeans, yscales, 
+    Mbplswest(Tx, Vx, Rx, Wx, Wytild, Tbl, Tb, Pbl, TTx, fitmbl, ymeans, yscales, 
         weights, lb, niter, par)
 end
 

diff --git a/src/plscan.jl b/src/plscan.jl
@@ -121,8 +121,8 @@ function plscan!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     Ty = copy(Tx)
     Wx = similar(X, p, nlv)
     Wy = similar(X, q, nlv) 
-    Px = copy(Wx)
-    Py = copy(Wy)
+    Vx = copy(Wx)
+    Vy = copy(Wy)
     TTx = similar(X, nlv)
     TTy = copy(TTx)
     tx   = similar(X, n)
@@ -131,8 +131,8 @@ function plscan!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     dty = copy(tx)   
     wx  = similar(X, p)
     wy  = similar(X, q)
-    px   = copy(wx)
-    py   = copy(wy)
+    vx   = copy(wx)
+    vy   = copy(wy)
     delta = copy(TTx)
     # End
     @inbounds for a = 1:nlv
@@ -144,8 +144,8 @@ function plscan!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
         mul!(tx, X, wx)
         dtx .= weights.w .* tx
         ttx = dot(tx, dtx)
-        mul!(px, X', dtx)
-        px ./= ttx
+        mul!(vx, X', dtx)
+        vx ./= ttx
         # Y
         wy .= V[:, 1]
         # Same as:                        
@@ -155,24 +155,24 @@ function plscan!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
         mul!(ty, Y, wy)
         dty .= weights.w .* ty
         tty = dot(ty, dty)
-        mul!(py, Y', dty)
-        py ./= tty
+        mul!(vy, Y', dty)
+        vy ./= tty
         # Deflation
-        X .-= tx * px'
-        Y .-= ty * py'
+        X .-= tx * vx'
+        Y .-= ty * vy'
         # End
-        Px[:, a] .= px
-        Py[:, a] .= py
+        Vx[:, a] .= vx
+        Vy[:, a] .= vy
         Tx[:, a] .= tx
         Ty[:, a] .= ty
         Wx[:, a] .= wx
         Wy[:, a] .= wy
         TTx[a] = ttx
         TTy[a] = tty
      end
-     Rx = Wx * inv(Px' * Wx)
-     Ry = Wy * inv(Py' * Wy)
-     Plscan(Tx, Ty, Px, Py, Rx, Ry, Wx, Wy, TTx, TTy, delta, bscales, xmeans, xscales, 
+     Rx = Wx * inv(Vx' * Wx)
+     Ry = Wy * inv(Vy' * Wy)
+     Plscan(Tx, Ty, Vx, Vy, Rx, Ry, Wx, Wy, TTx, TTy, delta, bscales, xmeans, xscales, 
          ymeans, yscales, weights, par)
 end
 
@@ -213,14 +213,14 @@ function Base.summary(object::Plscan, X, Y)
     tty = object.TTy 
     ## X
     sstot = frob(X, object.weights)^2
-    tt_adj = colsum(object.Px.^2) .* ttx
+    tt_adj = colsum(object.Vx.^2) .* ttx
     pvar = tt_adj / sstot
     cumpvar = cumsum(pvar)
     xvar = tt_adj / n    
     explvarx = DataFrame(nlv = 1:nlv, var = xvar, pvar = pvar, cumpvar = cumpvar)
     ## Y
     sstot = frob(Y, object.weights)^2
-    tt_adj = colsum(object.Py.^2) .* tty
+    tt_adj = colsum(object.Vy.^2) .* tty
     pvar = tt_adj / sstot
     cumpvar = cumsum(pvar)
     xvar = tt_adj / n    

diff --git a/src/plswold.jl b/src/plswold.jl
@@ -68,14 +68,14 @@ function plswold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     Tx = similar(X, n, nlv)
     Wx = similar(X, p, nlv)
     Wytild = similar(X, q, nlv)
-    Px = copy(Wx)
+    Vx = copy(Wx)
     TTx = similar(X, nlv)
     tx   = similar(X, n)
     ty = copy(tx)
     wx  = similar(X, p)
     wy  = similar(X, q)
     wytild = copy(wy)     
-    px   = copy(wx)
+    vx   = copy(wx)
     niter = zeros(nlv)
     # End
     @inbounds for a = 1:nlv       
@@ -100,19 +100,19 @@ function plswold!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
         end
         niter[a] = iter - 1
         ttx = dot(tx, tx)
-        mul!(px, X', tx)
-        px ./= ttx
+        mul!(vx, X', tx)
+        vx ./= ttx
         # Deflation
-        X .-= tx * px'
+        X .-= tx * vx'
         Y .-= tx * wytild'
         # End         
         Tx[:, a] .= tx
         Wx[:, a] .= wx
-        Px[:, a] .= px
+        Vx[:, a] .= vx
         Wytild[:, a] .= wytild
         TTx[a] = ttx
     end
     fweight!(Tx, 1 ./ sqrtw) 
-    Rx = Wx * inv(Px' * Wx)
-    Plsr(Tx, Px, Rx, Wx, Wytild, TTx, xmeans, xscales, ymeans, yscales, weights, niter, par)
+    Rx = Wx * inv(Vx' * Wx)
+    Plsr(Tx, Vx, Rx, Wx, Wytild, TTx, xmeans, xscales, ymeans, yscales, weights, niter, par)
 end
diff --git a/src/rrr.jl b/src/rrr.jl
@@ -125,7 +125,7 @@ function rrr!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     Wx  = similar(X, p, nlv)
     Wy  = similar(X, q, nlv)
     Wytild  = copy(Wy)
-    Px  = similar(X, p, nlv)
+    Vx  = similar(X, p, nlv)
     Cx = similar(X, p, p)
     invCx = copy(Cx)
     Ix = Diagonal(ones(Q, p))
@@ -135,7 +135,7 @@ function rrr!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
     wx  = similar(X, p)
     wy  = similar(X, q)
     wytild = copy(wy)
-    px = similar(X, p)
+    vx = similar(X, p)
     lambda = copy(TTx)
     covtot = copy(TTx)
     niter = Int.(ones(nlv))
@@ -171,27 +171,27 @@ function rrr!(X::Matrix, Y::Matrix, weights::Weight; kwargs...)
         lambda[a] = ty' * X * invCx * X' * ty
         covtot[a] = tr(Y' * X * invCx * X' * Y)
         ttx = dot(tx, tx)
-        mul!(px, X', tx)
-        px ./= ttx
+        mul!(vx, X', tx)
+        vx ./= ttx
         mul!(wytild, Y', tx)
         wytild ./= ttx
         # For Rx
         tty = dot(ty, ty)
         wx .= invCx * X' * ty / tty
         wx .= wx / normv(wx)
         # Deflation
-        X .-= tx * px'
+        X .-= tx * vx'
         Y .-= tx * wytild'
         # End
         Tx[:, a] .= tx   
-        Px[:, a] .= px
+        Vx[:, a] .= vx
         Wx[:, a] .= wx
         Wytild[:, a] .= wytild
         TTx[a] = ttx
      end
-     Rx = Wx * inv(Px' * Wx)
+     Rx = Wx * inv(Vx' * Wx)
      Tx .= (1 ./ sqrtw) .* Tx
-     Plsr(Tx, Px, Rx, Wx, Wytild, TTx, xmeans, xscales, ymeans, yscales, weights, niter, par)
+     Plsr(Tx, Vx, Rx, Wx, Wytild, TTx, xmeans, xscales, ymeans, yscales, weights, niter, par)
 end