From 7ea86a47e203a6f571ca1fd1bf22b1a37c6c3255 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 25 Oct 2021 16:42:10 -0400
Subject: [PATCH 01/22] adding new file that isn't connected to anything

---
 src/operations/embed.jl | 55 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 55 insertions(+)
 create mode 100644 src/operations/embed.jl

diff --git a/src/operations/embed.jl b/src/operations/embed.jl
new file mode 100644
index 00000000..6daaf888
--- /dev/null
+++ b/src/operations/embed.jl
@@ -0,0 +1,55 @@
+"""
+    This file contains interfaces to MVStats for 
+    taking many SDMLayers and embedding their values
+    in a lower dimensional space to create a smaller 
+    number of SDMLayers
+
+"""
+
+function embed(layers::Vector{T}, PCA) where T <: SimpleSDMLayer
+
+end
+
+function make_pca_input(layers) 
+	numdims = length(layers)
+	numsites = prod(size(layers[begin]))
+	pcainput = zeros(numdims, numsites)
+	
+	for i in eachindex(layers[1])
+		for layernum in 1:length(layers)
+			if !isnothing(layers[layernum][i])
+				pcainput[layernum,i] = layers[layernum][i]
+			else
+			end
+		end
+	end
+	pcainput
+end
+
+function make_pca_layers(layers)
+	pcainput = make_pca_input(layers)
+	numdims, numsites = length(layers), prod(size(layers[begin]))
+
+	pca = fit(PCA, pcainput, pratio=0.995)
+	A = projection(pca)
+	
+	transformedvals = zeros(outdim(pca), numsites)
+	
+	for loc in 1:numsites
+		transformedvals[:,loc] =  A' * vec(pcainput[:,loc])
+	end
+	
+	
+	### TODO this has to be  a similar SDMlayer to retain coordinates
+	newlayers = [zeros(Float32, size(layers[begin])) for l in 1:outdim(pca)]	
+	
+	for loc in 1:numsites
+		for layer in 1:outdim(pca)
+			newlayers[layer][loc] =  transformedvals[layer,loc]
+		end
+	end
+	
+	
+	newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
+	newlayers = map(f -> rescale(f, (0,1)), newlayers)
+end
\ No newline at end of file

From cf031f24d182ad8127daa59856b22818c2e50a5a Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 26 Oct 2021 11:48:50 -0400
Subject: [PATCH 02/22] :features: adding multivariatestats

---
 Project.toml                              | 1 +
 src/SimpleSDMLayers.jl                    | 6 +++++-
 src/operations/{embed.jl => transform.jl} | 7 +++++--
 3 files changed, 11 insertions(+), 3 deletions(-)
 rename src/operations/{embed.jl => transform.jl} (85%)

diff --git a/Project.toml b/Project.toml
index 0bbe02fa..68e59cfc 100644
--- a/Project.toml
+++ b/Project.toml
@@ -10,6 +10,7 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
diff --git a/src/SimpleSDMLayers.jl b/src/SimpleSDMLayers.jl
index b880faff..9832f0c0 100644
--- a/src/SimpleSDMLayers.jl
+++ b/src/SimpleSDMLayers.jl
@@ -13,6 +13,9 @@ export Point, Polygon
 using PolygonOps
 using StatsBase
 
+using MultivariateStats
+using MultivariateStats: PCA, PPCA, KernelPCA, Whitening
+
 # Basic types for the package
 include(joinpath("lib", "types.jl"))
 export SimpleSDMLayer, SimpleSDMResponse, SimpleSDMPredictor
@@ -85,7 +88,8 @@ include(joinpath("operations", "sliding.jl"))
 include(joinpath("operations", "mask.jl"))
 include(joinpath("operations", "rescale.jl"))
 include(joinpath("operations", "mosaic.jl"))
-export coarsen, slidingwindow, mask, rescale!, rescale, mosaic
+include(joinpath("operations", "transform.jl"))
+export coarsen, slidingwindow, mask, rescale!, rescale, mosaic, fit, transform, transform!
 
 include(joinpath("recipes", "recipes.jl"))
 export bivariate
diff --git a/src/operations/embed.jl b/src/operations/transform.jl
similarity index 85%
rename from src/operations/embed.jl
rename to src/operations/transform.jl
index 6daaf888..ee0d53b3 100644
--- a/src/operations/embed.jl
+++ b/src/operations/transform.jl
@@ -6,10 +6,13 @@
 
 """
 
-function embed(layers::Vector{T}, PCA) where T <: SimpleSDMLayer
+function fit(PCA, layers::Vector{T}) where T <: SimpleSDMLayer
 
 end
 
+function transform(W, layers::Vector{T}) where T<: SimpleSDMLayer end
+function transform!(W, layers::Vector{T}) where T<: SimpleSDMLayer end 
+
 function make_pca_input(layers) 
 	numdims = length(layers)
 	numsites = prod(size(layers[begin]))
@@ -52,4 +55,4 @@ function make_pca_layers(layers)
 	
 	newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
 	newlayers = map(f -> rescale(f, (0,1)), newlayers)
-end
\ No newline at end of file
+end

From b0bc30172b95abecfd50c5b08dfe8409d2dd5bdd Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 26 Oct 2021 14:17:36 -0400
Subject: [PATCH 03/22] :pencil: adding MIT license for GeoData.jl to header of
 resample file

---
 src/operations/resample.jl | 68 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 68 insertions(+)
 create mode 100644 src/operations/resample.jl

diff --git a/src/operations/resample.jl b/src/operations/resample.jl
new file mode 100644
index 00000000..1fcc3e3d
--- /dev/null
+++ b/src/operations/resample.jl
@@ -0,0 +1,68 @@
+#=
+
+The code in this file is adaoted from GeoData.jl
+(https://github.com/rafaqz/GeoData.jl), see this issue
+(https://github.com/EcoJulia/SimpleSDMLayers.jl/issues/131)
+
+See the following GeoData.jl license (MIT)
+
+----------------------------------------------------------------------
+Copyright (c) 2019 Rafael Schouten and Michael Krabbe Borregaard
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+----------------------------------------------------------------------
+=#
+
+function resample(A::T) end
+
+"""
+Code from GeoData.jl
+
+`method`: A `Symbol` or `String` specifying the method to use for
+resampling. Defaults to `:near` (nearest neighbor resampling). See
+[resampling
+method](https://gdal.org/programs/gdalwarp.html#cmdoption-gdalwarp-r)
+in the gdalwarp docs for a complete list of possible values.
+
+function warp(A::AbstractGeoArray, flags::Dict)
+    odims = otherdims(A, (X, Y, Band))
+    if length(odims) > 0
+        # Handle dimensions other than X, Y, Band
+        slices = slice(A, odims)
+        warped = map(A -> _warp(A, flags), slices)
+        return combine(warped, odims)
+    else
+        return _warp(A, flags)
+    end
+end
+warp(st::AbstractGeoStack, flags::Dict) = map(A -> warp(A, flags), st)
+
+function _warp(A::AbstractGeoArray, flags::Dict)
+    flagvect = reduce([flags...]; init=[]) do acc, (key, val)
+        append!(acc, String[_asflag(key), _stringvect(val)...])
+    end
+    AG.Dataset(A) do dataset
+        AG.gdalwarp([dataset], flagvect) do warped
+            _maybe_permute_from_gdal(read(GeoArray(warped)), dims(A))
+        end
+    end
+end
+
+"""

From baf395edee3787d5f1fc65d472db4c66007a17de Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 26 Oct 2021 14:54:29 -0400
Subject: [PATCH 04/22] :construction: using @require and basic functionality

---
 Project.toml                                  |  1 -
 src/SimpleSDMLayers.jl                        | 13 ++--
 .../MultivariateStats.jl}                     | 48 ++++++-------
 src/operations/resample.jl                    | 68 -------------------
 test/Project.toml                             |  2 +
 test/extensions/multivariatestats.jl          | 11 +++
 test/runtests.jl                              |  1 +
 7 files changed, 43 insertions(+), 101 deletions(-)
 rename src/{operations/transform.jl => integrations/MultivariateStats.jl} (59%)
 delete mode 100644 src/operations/resample.jl
 create mode 100644 test/extensions/multivariatestats.jl

diff --git a/Project.toml b/Project.toml
index 68e59cfc..0bbe02fa 100644
--- a/Project.toml
+++ b/Project.toml
@@ -10,7 +10,6 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
 Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 PolygonOps = "647866c9-e3ac-4575-94e7-e3d426903924"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
diff --git a/src/SimpleSDMLayers.jl b/src/SimpleSDMLayers.jl
index 9832f0c0..690d606d 100644
--- a/src/SimpleSDMLayers.jl
+++ b/src/SimpleSDMLayers.jl
@@ -13,9 +13,6 @@ export Point, Polygon
 using PolygonOps
 using StatsBase
 
-using MultivariateStats
-using MultivariateStats: PCA, PPCA, KernelPCA, Whitening
-
 # Basic types for the package
 include(joinpath("lib", "types.jl"))
 export SimpleSDMLayer, SimpleSDMResponse, SimpleSDMPredictor
@@ -57,7 +54,7 @@ for s in instances(CMIP6)
 end
 for s in instances(RepresentativeConcentrationPathway)
     @eval export $(Symbol(s))
-end 
+end
 for s in instances(SharedSocioeconomicPathway)
     @eval export $(Symbol(s))
 end
@@ -88,8 +85,7 @@ include(joinpath("operations", "sliding.jl"))
 include(joinpath("operations", "mask.jl"))
 include(joinpath("operations", "rescale.jl"))
 include(joinpath("operations", "mosaic.jl"))
-include(joinpath("operations", "transform.jl"))
-export coarsen, slidingwindow, mask, rescale!, rescale, mosaic, fit, transform, transform!
+export coarsen, slidingwindow, mask, rescale!, rescale, mosaic
 
 include(joinpath("recipes", "recipes.jl"))
 export bivariate
@@ -112,6 +108,11 @@ function __init__()
         include("integrations/DataFrames.jl")
     end
 
+    @require MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411" begin
+        @info "Loading MultivariateStats support for SimpleSDMLayers.jl"
+        include("integrations/MultivariateStats.jl")
+    end
+
 end
 
 end # module
diff --git a/src/operations/transform.jl b/src/integrations/MultivariateStats.jl
similarity index 59%
rename from src/operations/transform.jl
rename to src/integrations/MultivariateStats.jl
index ee0d53b3..d783d881 100644
--- a/src/operations/transform.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -1,23 +1,18 @@
-"""
-    This file contains interfaces to MVStats for 
-    taking many SDMLayers and embedding their values
-    in a lower dimensional space to create a smaller 
-    number of SDMLayers
-
-"""
-
-function fit(PCA, layers::Vector{T}) where T <: SimpleSDMLayer
+# WARNING this file is only loaded if MultivariateStats.jl is also active
+# This all happens thanks to the Requires.jl package
 
+function MultivariateStats.fit(PCA, layers::Vector{T}) where T <: SimpleSDMLayer
+	_make_pca_layers(layers)
 end
 
 function transform(W, layers::Vector{T}) where T<: SimpleSDMLayer end
-function transform!(W, layers::Vector{T}) where T<: SimpleSDMLayer end 
+function transform!(W, layers::Vector{T}) where T<: SimpleSDMLayer end
 
-function make_pca_input(layers) 
+function _make_pca_input(layers)
 	numdims = length(layers)
 	numsites = prod(size(layers[begin]))
 	pcainput = zeros(numdims, numsites)
-	
+
 	for i in eachindex(layers[1])
 		for layernum in 1:length(layers)
 			if !isnothing(layers[layernum][i])
@@ -29,30 +24,31 @@ function make_pca_input(layers)
 	pcainput
 end
 
-function make_pca_layers(layers)
-	pcainput = make_pca_input(layers)
+function _make_pca_layers(layers)
+	pcainput = _make_pca_input(layers)
 	numdims, numsites = length(layers), prod(size(layers[begin]))
 
-	pca = fit(PCA, pcainput, pratio=0.995)
-	A = projection(pca)
-	
-	transformedvals = zeros(outdim(pca), numsites)
+	pca = MultivariateStats.fit(MultivariateStats.PCA, pcainput, pratio=0.995)
+	A = MultivariateStats.projection(pca)
+
+	outdim = MultivariateStats.outdim(pca)
+
+	transformedvals = zeros(outdim, numsites)
 	
 	for loc in 1:numsites
 		transformedvals[:,loc] =  A' * vec(pcainput[:,loc])
 	end
-	
-	
-	### TODO this has to be  a similar SDMlayer to retain coordinates
-	newlayers = [zeros(Float32, size(layers[begin])) for l in 1:outdim(pca)]	
-	
+
+
+	newlayers = [zeros(Float32, size(layers[begin])) for l in 1:outdim]
+
 	for loc in 1:numsites
-		for layer in 1:outdim(pca)
+		for layer in 1:outdim
 			newlayers[layer][loc] =  transformedvals[layer,loc]
 		end
 	end
-	
-	
+
+
 	newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
 	newlayers = map(f -> rescale(f, (0,1)), newlayers)
 end
diff --git a/src/operations/resample.jl b/src/operations/resample.jl
deleted file mode 100644
index 1fcc3e3d..00000000
--- a/src/operations/resample.jl
+++ /dev/null
@@ -1,68 +0,0 @@
-#=
-
-The code in this file is adaoted from GeoData.jl
-(https://github.com/rafaqz/GeoData.jl), see this issue
-(https://github.com/EcoJulia/SimpleSDMLayers.jl/issues/131)
-
-See the following GeoData.jl license (MIT)
-
-----------------------------------------------------------------------
-Copyright (c) 2019 Rafael Schouten and Michael Krabbe Borregaard
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
-CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
-TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
-SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
-----------------------------------------------------------------------
-=#
-
-function resample(A::T) end
-
-"""
-Code from GeoData.jl
-
-`method`: A `Symbol` or `String` specifying the method to use for
-resampling. Defaults to `:near` (nearest neighbor resampling). See
-[resampling
-method](https://gdal.org/programs/gdalwarp.html#cmdoption-gdalwarp-r)
-in the gdalwarp docs for a complete list of possible values.
-
-function warp(A::AbstractGeoArray, flags::Dict)
-    odims = otherdims(A, (X, Y, Band))
-    if length(odims) > 0
-        # Handle dimensions other than X, Y, Band
-        slices = slice(A, odims)
-        warped = map(A -> _warp(A, flags), slices)
-        return combine(warped, odims)
-    else
-        return _warp(A, flags)
-    end
-end
-warp(st::AbstractGeoStack, flags::Dict) = map(A -> warp(A, flags), st)
-
-function _warp(A::AbstractGeoArray, flags::Dict)
-    flagvect = reduce([flags...]; init=[]) do acc, (key, val)
-        append!(acc, String[_asflag(key), _stringvect(val)...])
-    end
-    AG.Dataset(A) do dataset
-        AG.gdalwarp([dataset], flagvect) do warped
-            _maybe_permute_from_gdal(read(GeoArray(warped)), dims(A))
-        end
-    end
-end
-
-"""
diff --git a/test/Project.toml b/test/Project.toml
index 26508182..aebd904b 100644
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -1,5 +1,7 @@
 [deps]
 GBIF = "ee291a33-5a6c-5552-a3c8-0f29a1181037"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
+NeutralLandscapes = "71847384-8354-4223-ac08-659a5128069f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd"
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
new file mode 100644
index 00000000..bc970757
--- /dev/null
+++ b/test/extensions/multivariatestats.jl
@@ -0,0 +1,11 @@
+module SSLTestMVStats
+    using SimpleSDMLayers
+    using MultivariateStats
+    using NeutralLandscapes
+    using Test
+
+    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(0.5), (50,50))) for i in 1:30]
+
+    @assert typeof(fit(PCA, layers)) <: Vector{T} where T<:SimpleSDMLayer
+
+end
diff --git a/test/runtests.jl b/test/runtests.jl
index 7a263d92..5b98c15e 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -24,6 +24,7 @@ tests = [
    "chelsa" => "data/chelsa.jl",
    "plotting" => "extensions/plots.jl",
    "GBIF" => "extensions/gbif.jl",
+   "MultivariateStats" => "extensions/multivariatestats.jl"
 ]
 
 for test in tests

From e7af41f11d9e15cc4efd8cde2903ec1357748559 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 26 Oct 2021 16:10:11 -0400
Subject: [PATCH 05/22] :construction_worker: mostly there

---
 src/integrations/MultivariateStats.jl | 58 ++++++++++++---------------
 test/extensions/multivariatestats.jl  |  9 ++++-
 test/runtests.jl                      |  2 +-
 3 files changed, 33 insertions(+), 36 deletions(-)

diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index d783d881..662601f3 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -1,54 +1,46 @@
 # WARNING this file is only loaded if MultivariateStats.jl is also active
 # This all happens thanks to the Requires.jl package
 
-function MultivariateStats.fit(PCA, layers::Vector{T}) where T <: SimpleSDMLayer
-	_make_pca_layers(layers)
+"""
+	MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where T <: SimpleSDMLayer
+"""
+function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where T <: SimpleSDMLayer
+	input = _make_input(layers)
+	pca = MultivariateStats.fit(a, input, kwargs...)
+	return pca
 end
 
-function transform(W, layers::Vector{T}) where T<: SimpleSDMLayer end
-function transform!(W, layers::Vector{T}) where T<: SimpleSDMLayer end
-
-function _make_pca_input(layers)
-	numdims = length(layers)
-	numsites = prod(size(layers[begin]))
-	pcainput = zeros(numdims, numsites)
-
-	for i in eachindex(layers[1])
-		for layernum in 1:length(layers)
-			if !isnothing(layers[layernum][i])
-				pcainput[layernum,i] = layers[layernum][i]
-			else
-			end
-		end
-	end
-	pcainput
-end
-
-function _make_pca_layers(layers)
-	pcainput = _make_pca_input(layers)
-	numdims, numsites = length(layers), prod(size(layers[begin]))
-
-	pca = MultivariateStats.fit(MultivariateStats.PCA, pcainput, pratio=0.995)
-	A = MultivariateStats.projection(pca)
-
-	outdim = MultivariateStats.outdim(pca)
+"""
+	#
+"""
+function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
+	input = _make_input(layers)
+	numsites = length(layers)
 
+	A = MultivariateStats.projection(proj)
+	outdim = MultivariateStats.outdim(proj)
 	transformedvals = zeros(outdim, numsites)
 	
 	for loc in 1:numsites
-		transformedvals[:,loc] =  A' * vec(pcainput[:,loc])
+		transformedvals[:,loc] =  A' * vec(input[:,loc])
 	end
 
-
 	newlayers = [zeros(Float32, size(layers[begin])) for l in 1:outdim]
-
 	for loc in 1:numsites
 		for layer in 1:outdim
 			newlayers[layer][loc] =  transformedvals[layer,loc]
 		end
 	end
 
-
 	newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
 	newlayers = map(f -> rescale(f, (0,1)), newlayers)
+
+	newlayers
 end
+
+function _make_input(layers)
+	common_keys = reduce(∩, keys.(layers))
+	x = hcat([layer[common_keys] for layer in layers]...);
+	x
+end
+
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
index bc970757..2fc05ba7 100644
--- a/test/extensions/multivariatestats.jl
+++ b/test/extensions/multivariatestats.jl
@@ -4,8 +4,13 @@ module SSLTestMVStats
     using NeutralLandscapes
     using Test
 
-    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(0.5), (50,50))) for i in 1:30]
+    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(0.9), (50,50))) for i in 1:30]
 
-    @assert typeof(fit(PCA, layers)) <: Vector{T} where T<:SimpleSDMLayer
+
+    @assert typeof(transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+    @assert typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+    # @assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+
+   # @assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
 end
diff --git a/test/runtests.jl b/test/runtests.jl
index 5b98c15e..5b05ce2d 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -4,6 +4,7 @@ using Test
 global anyerrors = false
 
 tests = [
+   "MultivariateStats" => "extensions/multivariatestats.jl",
    "construction" => "core/construction.jl",
    "lat./lon." => "core/latlon.jl",
    "lat./lon. conversion" => "core/coordconvert.jl",
@@ -24,7 +25,6 @@ tests = [
    "chelsa" => "data/chelsa.jl",
    "plotting" => "extensions/plots.jl",
    "GBIF" => "extensions/gbif.jl",
-   "MultivariateStats" => "extensions/multivariatestats.jl"
 ]
 
 for test in tests

From 5930730edb55b9ec15a78de9ac271dea4623bc5a Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Thu, 28 Oct 2021 16:38:42 -0400
Subject: [PATCH 06/22] :pencil: docs and blue style

---
 src/integrations/MultivariateStats.jl | 77 ++++++++++++++++-----------
 test/extensions/multivariatestats.jl  | 12 +++--
 2 files changed, 54 insertions(+), 35 deletions(-)

diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 662601f3..0c897f54 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -3,44 +3,59 @@
 
 """
 	MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where T <: SimpleSDMLayer
+
+	Overloads the `fit` function from `MultivariateStats.jl`.
 """
-function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where T <: SimpleSDMLayer
-	input = _make_input(layers)
-	pca = MultivariateStats.fit(a, input, kwargs...)
-	return pca
+function MultivariateStats.fit(
+    a::PT,
+    layers::Vector{T},
+    kwargs...,
+) where {
+    T<:SimpleSDMLayer,
+    PT<:Union{Type{MultivariateStats.PCA},Type{MultivariateStats.PPCA}},
+}
+    input = _make_input(layers)
+    pca = MultivariateStats.fit(a, input, kwargs...)
+    return pca
 end
 
 """
-	#
+	MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
+
+	Overload of the `transform` function from `MultivariateStats.jl`. 
 """
 function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
-	input = _make_input(layers)
-	numsites = length(layers)
-
-	A = MultivariateStats.projection(proj)
-	outdim = MultivariateStats.outdim(proj)
-	transformedvals = zeros(outdim, numsites)
-	
-	for loc in 1:numsites
-		transformedvals[:,loc] =  A' * vec(input[:,loc])
-	end
-
-	newlayers = [zeros(Float32, size(layers[begin])) for l in 1:outdim]
-	for loc in 1:numsites
-		for layer in 1:outdim
-			newlayers[layer][loc] =  transformedvals[layer,loc]
-		end
-	end
-
-	newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
-	newlayers = map(f -> rescale(f, (0,1)), newlayers)
-
-	newlayers
+    input = _make_input(layers)
+    numsites = length(layers)
+
+    A = MultivariateStats.projection(proj)
+    outdim = MultivariateStats.outdim(proj)
+    transformedvals = zeros(outdim, numsites)
+
+    for loc = 1:numsites
+        transformedvals[:, loc] = A' * vec(input[:, loc])
+    end
+
+    newlayers = [zeros(Float32, size(layers[begin])) for l = 1:outdim]
+    for loc = 1:numsites
+        for layer = 1:outdim
+            newlayers[layer][loc] = transformedvals[layer, loc]
+        end
+    end
+
+    newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
+    return map(f -> rescale(f, (0, 1)), newlayers)
 end
 
+
+"""
+	_make_input(layers)
+
+	Creates a matrix for input to PCA. 
+	The resulting matrix has columns for each shared location in 
+	the vector of layers, where the value of each column is the 
+"""
 function _make_input(layers)
-	common_keys = reduce(∩, keys.(layers))
-	x = hcat([layer[common_keys] for layer in layers]...);
-	x
+    common_keys = reduce(∩, keys.(layers))
+    return hcat([layer[common_keys] for layer in layers]...)
 end
-
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
index 2fc05ba7..063453f0 100644
--- a/test/extensions/multivariatestats.jl
+++ b/test/extensions/multivariatestats.jl
@@ -4,13 +4,17 @@ module SSLTestMVStats
     using NeutralLandscapes
     using Test
 
-    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(0.9), (50,50))) for i in 1:30]
+    TEST_DIMS = (150,150)
+    TEST_AUTOCORRELATION = 0.9
+    TEST_NUM_LAYERS = 10
+
+    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for i in 1:TEST_NUM_LAYERS]
 
 
     @assert typeof(transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
     @assert typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-    # @assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-
-   # @assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+    
+#    @assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+#    @assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
 end

From 77b3510bd4e55545afb3462cdabdda29d3c0341c Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Thu, 28 Oct 2021 16:44:03 -0400
Subject: [PATCH 07/22] :adhesive_bandage: including _layers_are_compatible
 call

---
 src/integrations/MultivariateStats.jl | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 0c897f54..f319d540 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -14,6 +14,7 @@ function MultivariateStats.fit(
     T<:SimpleSDMLayer,
     PT<:Union{Type{MultivariateStats.PCA},Type{MultivariateStats.PPCA}},
 }
+	_layers_are_compatible(layers) || return ArgumentError("layers not compatible")
     input = _make_input(layers)
     pca = MultivariateStats.fit(a, input, kwargs...)
     return pca

From f09e364fd937519e35b89a1e6ae07fcbc715da0d Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Thu, 4 Nov 2021 17:16:41 -0400
Subject: [PATCH 08/22] removing type assert

---
 src/integrations/MultivariateStats.jl | 19 +++++++------------
 test/extensions/multivariatestats.jl  |  9 ++++++---
 2 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index f319d540..23c7b032 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -6,24 +6,18 @@
 
 	Overloads the `fit` function from `MultivariateStats.jl`.
 """
-function MultivariateStats.fit(
-    a::PT,
-    layers::Vector{T},
-    kwargs...,
-) where {
-    T<:SimpleSDMLayer,
-    PT<:Union{Type{MultivariateStats.PCA},Type{MultivariateStats.PPCA}},
-}
-	_layers_are_compatible(layers) || return ArgumentError("layers not compatible")
+function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:SimpleSDMLayer}
+    _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
     input = _make_input(layers)
-    pca = MultivariateStats.fit(a, input, kwargs...)
-    return pca
+    proj = MultivariateStats.fit(a, input, kwargs...)
+    return proj
 end
 
 """
 	MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
 
-	Overload of the `transform` function from `MultivariateStats.jl`. 
+	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
+	and output object from `MultivariateStats.fit` (see above). 
 """
 function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
     input = _make_input(layers)
@@ -55,6 +49,7 @@ end
 	Creates a matrix for input to PCA. 
 	The resulting matrix has columns for each shared location in 
 	the vector of layers, where the value of each column is the 
+	values of each of the `layers` input.
 """
 function _make_input(layers)
     common_keys = reduce(∩, keys.(layers))
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
index 063453f0..0bfaaaac 100644
--- a/test/extensions/multivariatestats.jl
+++ b/test/extensions/multivariatestats.jl
@@ -11,10 +11,13 @@ module SSLTestMVStats
     layers = [SimpleSDMPredictor(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for i in 1:TEST_NUM_LAYERS]
 
 
-    @assert typeof(transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-    @assert typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-    
+    @test typeof(transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+    @test typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+
+
+
 #    @assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 #    @assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
 end
+

From d6d7b6b0030781fa075b53f9d44003b1e89ace7d Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 14:40:29 -0500
Subject: [PATCH 09/22] :pencil:

---
 docs/make.jl             |  3 ++-
 docs/src/examples/pca.jl | 16 ++++++++++++++++
 2 files changed, 18 insertions(+), 1 deletion(-)
 create mode 100644 docs/src/examples/pca.jl

diff --git a/docs/make.jl b/docs/make.jl
index c32f7084..9a3c1614 100644
--- a/docs/make.jl
+++ b/docs/make.jl
@@ -40,7 +40,8 @@ makedocs(
             "Geometry for clipping" => "examples/geometry.md",
             "Sliding window analysis" => "examples/slidingwindow.md",
             "Landcover data" => "examples/landcover.md",
-            "Multivariate mapping" => "examples/multivariate.md"
+            "Multivariate mapping" => "examples/multivariate.md",
+            "Multivariate statistics" => "examples/pca.md"
         ],
         "SDM case studies" => [
             "GBIF integration" => "sdm/gbif.md",
diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
new file mode 100644
index 00000000..b35b845c
--- /dev/null
+++ b/docs/src/examples/pca.jl
@@ -0,0 +1,16 @@
+# # Principal-component analysis of many `SDMLayers`
+
+# The `SimpleSDMLayers` enables integration with `MultivariateStats.jl` 
+# In this example, we will show how this can work.
+
+boundaries = (left=-12.0, right=30.0, bottom=36.0, top=72.0)
+
+layers = convert(
+    Float16,
+    SimpleSDMPredictor(WorldClim, HabitatHeterogeneity, 1:19; resolution=5, boundaries...),
+)
+
+using MultivariateStats
+
+pca = fit(PCA, layers)
+newlayers = transform(pca, layers)
\ No newline at end of file

From 53badf55c1ab003d38aa1513a91307a98397b36e Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 15:15:30 -0500
Subject: [PATCH 10/22] :arrow_up: add mvstats to docs folder req

---
 docs/Project.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/docs/Project.toml b/docs/Project.toml
index d6862623..88dd2568 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -8,6 +8,7 @@ GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
 GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
+MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

From 708ea8dbb66251e79d40cb2e16a46faecbf0c068 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 15:24:25 -0500
Subject: [PATCH 11/22] :pencil: doc deps update

---
 docs/src/examples/pca.jl | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index b35b845c..8fe7ab0b 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -1,5 +1,9 @@
 # # Principal-component analysis of many `SDMLayers`
 
+using MultivariateStats
+using Plots
+
+
 # The `SimpleSDMLayers` enables integration with `MultivariateStats.jl` 
 # In this example, we will show how this can work.
 
@@ -10,7 +14,8 @@ layers = convert(
     SimpleSDMPredictor(WorldClim, HabitatHeterogeneity, 1:19; resolution=5, boundaries...),
 )
 
-using MultivariateStats
 
 pca = fit(PCA, layers)
-newlayers = transform(pca, layers)
\ No newline at end of file
+newlayers = transform(pca, layers)
+
+plot.(newlayers)
\ No newline at end of file

From 97bdfb73b735f52301b1f1ad022fba8775f7402b Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 16:50:07 -0500
Subject: [PATCH 12/22] :bug: bug fix and hopefully doc fix?

---
 docs/src/examples/pca.jl              | 12 ++++++++----
 src/integrations/MultivariateStats.jl | 26 +++++++++-----------------
 2 files changed, 17 insertions(+), 21 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index 8fe7ab0b..c4f2c777 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -1,5 +1,6 @@
 # # Principal-component analysis of many `SDMLayers`
 
+using SimpleSDMLayers
 using MultivariateStats
 using Plots
 
@@ -9,13 +10,16 @@ using Plots
 
 boundaries = (left=-12.0, right=30.0, bottom=36.0, top=72.0)
 
-layers = convert(
-    Float16,
-    SimpleSDMPredictor(WorldClim, HabitatHeterogeneity, 1:19; resolution=5, boundaries...),
+layers = convert.(
+    Float32,
+    SimpleSDMPredictor(WorldClim, BioClim, 1:19; boundaries...),
 )
 
+plot(layers[10])
 
 pca = fit(PCA, layers)
 newlayers = transform(pca, layers)
 
-plot.(newlayers)
\ No newline at end of file
+
+
+plot(plot.(newlayers, size=(300,300))...)
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 23c7b032..fbd05878 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -9,7 +9,7 @@
 function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:SimpleSDMLayer}
     _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
     input = _make_input(layers)
-    proj = MultivariateStats.fit(a, input, kwargs...)
+    proj = MultivariateStats.fit(a, input', kwargs...)
     return proj
 end
 
@@ -20,26 +20,18 @@ end
 	and output object from `MultivariateStats.fit` (see above). 
 """
 function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
-    input = _make_input(layers)
-    numsites = length(layers)
-
     A = MultivariateStats.projection(proj)
-    outdim = MultivariateStats.outdim(proj)
-    transformedvals = zeros(outdim, numsites)
-
-    for loc = 1:numsites
-        transformedvals[:, loc] = A' * vec(input[:, loc])
-    end
+    outdim = MultivariateStats.outdim(proj)    
+    newlayers = [similar(layers[begin]) for i in 1:outdim]
+    common_keys = reduce(∩, keys.(layers))
 
-    newlayers = [zeros(Float32, size(layers[begin])) for l = 1:outdim]
-    for loc = 1:numsites
-        for layer = 1:outdim
-            newlayers[layer][loc] = transformedvals[layer, loc]
+    for key in common_keys
+        pcaproj = A' * vcat([layer[key] for layer in layers]...)
+        for i in 1:outdim
+            newlayers[i][key] = pcaproj[i]
         end
     end
-
-    newlayers = SimpleSDMPredictor.(newlayers, boundingbox(layers[begin])...)
-    return map(f -> rescale(f, (0, 1)), newlayers)
+    return newlayers
 end
 
 

From 1eeb82250817bdf80dfb208a6c250635e277590c Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 17:14:43 -0500
Subject: [PATCH 13/22] :pencil: docs should make a plot?

---
 docs/src/examples/pca.jl              |  9 ++++-----
 src/integrations/MultivariateStats.jl | 16 +---------------
 2 files changed, 5 insertions(+), 20 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index c4f2c777..95141713 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -3,23 +3,22 @@
 using SimpleSDMLayers
 using MultivariateStats
 using Plots
-
+using Unitful
 
 # The `SimpleSDMLayers` enables integration with `MultivariateStats.jl` 
 # In this example, we will show how this can work.
 
-boundaries = (left=-12.0, right=30.0, bottom=36.0, top=72.0)
+boundaries =(left = -164.022167, right = -55.250858, bottom = 23.547132, top = 72.105833)
 
 layers = convert.(
     Float32,
     SimpleSDMPredictor(WorldClim, BioClim, 1:19; boundaries...),
 )
 
-plot(layers[10])
 
 pca = fit(PCA, layers)
 newlayers = transform(pca, layers)
 
 
-
-plot(plot.(newlayers, size=(300,300))...)
+pcaplots = plot.(newlayers)
+plot(pcaplots...)
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index fbd05878..6ed4b9c4 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -31,19 +31,5 @@ function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:Sim
             newlayers[i][key] = pcaproj[i]
         end
     end
-    return newlayers
-end
-
-
-"""
-	_make_input(layers)
-
-	Creates a matrix for input to PCA. 
-	The resulting matrix has columns for each shared location in 
-	the vector of layers, where the value of each column is the 
-	values of each of the `layers` input.
-"""
-function _make_input(layers)
-    common_keys = reduce(∩, keys.(layers))
-    return hcat([layer[common_keys] for layer in layers]...)
+    return map(f->rescale(f, (0,1)),newlayers)
 end

From 45309e6dfa535e5cea61104e054781d51722e925 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Mon, 8 Nov 2021 17:24:37 -0500
Subject: [PATCH 14/22] :pencil: remove extra unitful include

---
 docs/src/examples/pca.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index 95141713..8b0bcae3 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -3,7 +3,6 @@
 using SimpleSDMLayers
 using MultivariateStats
 using Plots
-using Unitful
 
 # The `SimpleSDMLayers` enables integration with `MultivariateStats.jl` 
 # In this example, we will show how this can work.
@@ -19,6 +18,7 @@ layers = convert.(
 pca = fit(PCA, layers)
 newlayers = transform(pca, layers)
 
+# idk why this doesn't work
 
 pcaplots = plot.(newlayers)
 plot(pcaplots...)

From a0e548df1cd21d427cd28b1a1421a92930773b3f Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 9 Nov 2021 09:20:41 -0500
Subject: [PATCH 15/22] :bug: missing common_keys call in fit

---
 docs/src/examples/pca.jl              |  3 ++-
 src/integrations/MultivariateStats.jl | 14 ++++++++++----
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index 8b0bcae3..3dfdc824 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -14,11 +14,12 @@ layers = convert.(
     SimpleSDMPredictor(WorldClim, BioClim, 1:19; boundaries...),
 )
 
+# fit pca and project to a new set of layers
 
 pca = fit(PCA, layers)
 newlayers = transform(pca, layers)
 
-# idk why this doesn't work
+# plot them
 
 pcaplots = plot.(newlayers)
 plot(pcaplots...)
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 6ed4b9c4..7f4cb96b 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -8,8 +8,11 @@
 """
 function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:SimpleSDMLayer}
     _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
-    input = _make_input(layers)
-    proj = MultivariateStats.fit(a, input', kwargs...)
+    common_keys = reduce(∩, keys.(layers))
+    input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
+
+    @show size(input)
+    proj = MultivariateStats.fit(a, input, kwargs...)
     return proj
 end
 
@@ -25,11 +28,14 @@ function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:Sim
     newlayers = [similar(layers[begin]) for i in 1:outdim]
     common_keys = reduce(∩, keys.(layers))
 
-    for key in common_keys
-        pcaproj = A' * vcat([layer[key] for layer in layers]...)
+    input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
+
+    for (ct,key) in enumerate(common_keys)
+        pcaproj = A' * input[:,ct]
         for i in 1:outdim
             newlayers[i][key] = pcaproj[i]
         end
     end
     return map(f->rescale(f, (0,1)),newlayers)
 end
+

From e1deed13b28e4760c4229852f21f44b22a694946 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 9 Nov 2021 09:22:33 -0500
Subject: [PATCH 16/22] :pencil: extra @show call

---
 src/integrations/MultivariateStats.jl | 2 --
 1 file changed, 2 deletions(-)

diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 7f4cb96b..4c41dff5 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -10,8 +10,6 @@ function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:Simple
     _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
     common_keys = reduce(∩, keys.(layers))
     input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
-
-    @show size(input)
     proj = MultivariateStats.fit(a, input, kwargs...)
     return proj
 end

From 932ef25c529bdf1de197e2551a0b450027845b9e Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 9 Nov 2021 15:32:58 -0500
Subject: [PATCH 17/22] :zap: whitening is back

---
 docs/src/examples/pca.jl              | 36 ++++++++++++++++++++++---
 src/integrations/MultivariateStats.jl | 38 ++++++++++++++++++++++++---
 2 files changed, 68 insertions(+), 6 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index 3dfdc824..0ca5c3bc 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -1,4 +1,12 @@
-# # Principal-component analysis of many `SDMLayers`
+# # MultivariateStats.jl integration
+
+# In this example we explore how you can use 
+# `MultivariateStats.jl` with `SimpleSDMLayers` 
+# to perform [principal-component-analysis (PCA)](wikiling todo) to 
+# reduce the dimensionality of a set of `SDMLayers`, or to remove the 
+# covariance between layers via data [whitening](linktodo).
+
+# ## Principal-component analysis of many `SDMLayers`
 
 using SimpleSDMLayers
 using MultivariateStats
@@ -8,10 +16,9 @@ using Plots
 # In this example, we will show how this can work.
 
 boundaries =(left = -164.022167, right = -55.250858, bottom = 23.547132, top = 72.105833)
-
 layers = convert.(
     Float32,
-    SimpleSDMPredictor(WorldClim, BioClim, 1:19; boundaries...),
+    SimpleSDMPredictor(WorldClim, BioClim, 1:19; boundaries...)
 )
 
 # fit pca and project to a new set of layers
@@ -23,3 +30,26 @@ newlayers = transform(pca, layers)
 
 pcaplots = plot.(newlayers)
 plot(pcaplots...)
+
+
+
+# ## Remove correlation between layers (`Whitening`)
+
+# Have to start with two layers that are reasonably correlated.
+
+wlayers = convert.(
+    Float32,
+    SimpleSDMPredictor(WorldClim, BioClim, 1:2; boundaries...)
+)
+plot(plot.(wlayers)...)
+
+
+# Now we call methods just as in `MultivariateStats`
+
+w = fit(Whitening, wlayers)
+newlayers = transform(w, wlayers)
+
+
+# and plot the layers without covar
+
+plot(plot.(newlayers)...)
\ No newline at end of file
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 4c41dff5..04a89518 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -15,12 +15,18 @@ function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:Simple
 end
 
 """
-	MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
+    MultivariateStats.transform(
+    proj::PT, 
+    layers::Vector{V}, 
+    kwargs...) where {PT<:Union{MultivariateStats.PCA, MultivariateStats.PPCA},V<:SimpleSDMLayer} 
 
 	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
 	and output object from `MultivariateStats.fit` (see above). 
 """
-function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:SimpleSDMLayer}
+function MultivariateStats.transform(
+    proj::PT, 
+    layers::Vector{V}, 
+    kwargs...) where {PT<:Union{MultivariateStats.PCA, MultivariateStats.PPCA},V<:SimpleSDMLayer} 
     A = MultivariateStats.projection(proj)
     outdim = MultivariateStats.outdim(proj)    
     newlayers = [similar(layers[begin]) for i in 1:outdim]
@@ -34,6 +40,32 @@ function MultivariateStats.transform(proj::P, layers::Vector{T}) where {P,T<:Sim
             newlayers[i][key] = pcaproj[i]
         end
     end
-    return map(f->rescale(f, (0,1)),newlayers)
+    return newlayers
 end
 
+
+"""
+    MultivariateStats.transform(
+    proj::Whitening{T}, 
+    layers::Vector{V}, 
+    kwargs...) where {T<:Real,V<:SimpleSDMLayer} 
+
+	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
+	and output object from `MultivariateStats.fit` (see above). 
+"""
+function MultivariateStats.transform(
+    proj::MultivariateStats.Whitening{T}, layers::Vector{V}, kwargs...) where {T<:Real,V<:SimpleSDMLayer} 
+    outdim = MultivariateStats.outdim(proj)    
+    newlayers = [similar(layers[begin]) for i in 1:outdim]
+    common_keys = reduce(∩, keys.(layers))
+
+    input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
+
+    for (ct,key) in enumerate(common_keys)
+        pcaproj = MultivariateStats.transform(proj,input[:,ct])
+        for i in 1:outdim
+            newlayers[i][key] = pcaproj[i]
+        end
+    end
+    return newlayers
+end

From 0ce730eefb349f6c701d119ed1c92fe8b354d501 Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 9 Nov 2021 17:32:44 -0500
Subject: [PATCH 18/22] :bulb: mv fix

---
 docs/src/examples/pca.jl              |  5 ++-
 src/integrations/MultivariateStats.jl | 51 ++++++---------------------
 2 files changed, 13 insertions(+), 43 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index 0ca5c3bc..b7dc86de 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -24,7 +24,7 @@ layers = convert.(
 # fit pca and project to a new set of layers
 
 pca = fit(PCA, layers)
-newlayers = transform(pca, layers)
+newlayers = SimpleSDMLayers.transform(pca, layers)
 
 # plot them
 
@@ -32,7 +32,6 @@ pcaplots = plot.(newlayers)
 plot(pcaplots...)
 
 
-
 # ## Remove correlation between layers (`Whitening`)
 
 # Have to start with two layers that are reasonably correlated.
@@ -47,7 +46,7 @@ plot(plot.(wlayers)...)
 # Now we call methods just as in `MultivariateStats`
 
 w = fit(Whitening, wlayers)
-newlayers = transform(w, wlayers)
+newlayers = SimpleSDMLayers.transform(w, wlayers)
 
 
 # and plot the layers without covar
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 04a89518..1ed602ec 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -15,55 +15,26 @@ function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:Simple
 end
 
 """
-    MultivariateStats.transform(
-    proj::PT, 
-    layers::Vector{V}, 
+    transform(proj, layers::Vector{V}, 
     kwargs...) where {PT<:Union{MultivariateStats.PCA, MultivariateStats.PPCA},V<:SimpleSDMLayer} 
 
 	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
 	and output object from `MultivariateStats.fit` (see above). 
 """
-function MultivariateStats.transform(
-    proj::PT, 
-    layers::Vector{V}, 
-    kwargs...) where {PT<:Union{MultivariateStats.PCA, MultivariateStats.PPCA},V<:SimpleSDMLayer} 
-    A = MultivariateStats.projection(proj)
-    outdim = MultivariateStats.outdim(proj)    
-    newlayers = [similar(layers[begin]) for i in 1:outdim]
-    common_keys = reduce(∩, keys.(layers))
-
-    input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
-
-    for (ct,key) in enumerate(common_keys)
-        pcaproj = A' * input[:,ct]
-        for i in 1:outdim
-            newlayers[i][key] = pcaproj[i]
-        end
-    end
-    return newlayers
-end
-
-
-"""
-    MultivariateStats.transform(
-    proj::Whitening{T}, 
-    layers::Vector{V}, 
-    kwargs...) where {T<:Real,V<:SimpleSDMLayer} 
-
-	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
-	and output object from `MultivariateStats.fit` (see above). 
-"""
-function MultivariateStats.transform(
-    proj::MultivariateStats.Whitening{T}, layers::Vector{V}, kwargs...) where {T<:Real,V<:SimpleSDMLayer} 
-    outdim = MultivariateStats.outdim(proj)    
-    newlayers = [similar(layers[begin]) for i in 1:outdim]
+function transform(
+    proj,
+    layers::AbstractVecOrMat{U},
+    kwargs...,
+) where {T<:Union{MultivariateStats.Whitening,MultivariateStats.PCA},U<:SimpleSDMLayer}
+    outdim = MultivariateStats.outdim(proj)
+    newlayers = [similar(layers[begin]) for i = 1:outdim]
     common_keys = reduce(∩, keys.(layers))
 
     input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
 
-    for (ct,key) in enumerate(common_keys)
-        pcaproj = MultivariateStats.transform(proj,input[:,ct])
-        for i in 1:outdim
+    for (ct, key) in enumerate(common_keys)
+        pcaproj = MultivariateStats.transform(proj, input[:, ct])
+        for i = 1:outdim
             newlayers[i][key] = pcaproj[i]
         end
     end

From 138786a971191d5308b5682b45b6499ab6d0fd2f Mon Sep 17 00:00:00 2001
From: michael catchen <michael.catchen@colorado.edu>
Date: Tue, 9 Nov 2021 17:49:52 -0500
Subject: [PATCH 19/22] :bug: namespace issues, same as it ever was

---
 src/SimpleSDMLayers.jl                | 1 +
 src/integrations/MultivariateStats.jl | 6 ++++--
 test/extensions/multivariatestats.jl  | 6 +++---
 3 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/SimpleSDMLayers.jl b/src/SimpleSDMLayers.jl
index 690d606d..c4a0fc3c 100644
--- a/src/SimpleSDMLayers.jl
+++ b/src/SimpleSDMLayers.jl
@@ -111,6 +111,7 @@ function __init__()
     @require MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411" begin
         @info "Loading MultivariateStats support for SimpleSDMLayers.jl"
         include("integrations/MultivariateStats.jl")
+        export transform
     end
 
 end
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 1ed602ec..48076a0e 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -23,9 +23,9 @@ end
 """
 function transform(
     proj,
-    layers::AbstractVecOrMat{U},
+    layers::AbstractVecOrMat{U};
     kwargs...,
-) where {T<:Union{MultivariateStats.Whitening,MultivariateStats.PCA},U<:SimpleSDMLayer}
+) where {U<:SimpleSDMLayer}
     outdim = MultivariateStats.outdim(proj)
     newlayers = [similar(layers[begin]) for i = 1:outdim]
     common_keys = reduce(∩, keys.(layers))
@@ -40,3 +40,5 @@ function transform(
     end
     return newlayers
 end
+
+
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
index 0bfaaaac..2d8f5d4f 100644
--- a/test/extensions/multivariatestats.jl
+++ b/test/extensions/multivariatestats.jl
@@ -8,11 +8,11 @@ module SSLTestMVStats
     TEST_AUTOCORRELATION = 0.9
     TEST_NUM_LAYERS = 10
 
-    layers = [SimpleSDMPredictor(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for i in 1:TEST_NUM_LAYERS]
+    layers = [SimpleSDMResponse(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for i in 1:TEST_NUM_LAYERS]
 
 
-    @test typeof(transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-    @test typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+    @test typeof(SimpleSDMLayers.transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+#    @test typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
 
 

From 949f2059cfaf1d17e099bdd892d5619e39fbe9af Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Tue, 9 Nov 2021 20:25:24 -0500
Subject: [PATCH 20/22] =?UTF-8?q?=F0=9F=A5=B3=20v0.9.0=20in=20preparation?=
 =?UTF-8?q?=20for=20multivariate?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 0bbe02fa..e07a11b0 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
 name = "SimpleSDMLayers"
 uuid = "2c645270-77db-11e9-22c3-0f302a89c64c"
 authors = ["Timothée Poisot <timothee.poisot@umontreal.ca>", "Gabriel Dansereau <gabriel.dansereau@umontreal.ca>"]
-version = "0.8.3"
+version = "0.9.0"
 
 [deps]
 ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3"

From 2afab997ffdcbdbf7ca14676c887e32a232518ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Tue, 9 Nov 2021 20:28:52 -0500
Subject: [PATCH 21/22] =?UTF-8?q?=F0=9F=A7=B9=20=20no=20need=20to=20call?=
 =?UTF-8?q?=20SSDML.transform?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 src/SimpleSDMLayers.jl                |  3 +--
 src/integrations/MultivariateStats.jl | 28 ++++++++++++------------
 test/extensions/multivariatestats.jl  | 31 +++++++++++++--------------
 3 files changed, 30 insertions(+), 32 deletions(-)

diff --git a/src/SimpleSDMLayers.jl b/src/SimpleSDMLayers.jl
index c4a0fc3c..7a98bf49 100644
--- a/src/SimpleSDMLayers.jl
+++ b/src/SimpleSDMLayers.jl
@@ -99,7 +99,7 @@ isdir(_layers_assets_path) || mkpath(_layers_assets_path)
 export clip
 
 function __init__()
-    @require GBIF="ee291a33-5a6c-5552-a3c8-0f29a1181037" begin
+    @require GBIF = "ee291a33-5a6c-5552-a3c8-0f29a1181037" begin
         @info "Loading GBIF support for SimpleSDMLayers.jl"
         include("integrations/GBIF.jl")
     end
@@ -111,7 +111,6 @@ function __init__()
     @require MultivariateStats = "6f286f6a-111f-5878-ab1e-185364afe411" begin
         @info "Loading MultivariateStats support for SimpleSDMLayers.jl"
         include("integrations/MultivariateStats.jl")
-        export transform
     end
 
 end
diff --git a/src/integrations/MultivariateStats.jl b/src/integrations/MultivariateStats.jl
index 48076a0e..4d01c72c 100644
--- a/src/integrations/MultivariateStats.jl
+++ b/src/integrations/MultivariateStats.jl
@@ -1,16 +1,19 @@
 # WARNING this file is only loaded if MultivariateStats.jl is also active
 # This all happens thanks to the Requires.jl package
 
+_allowed_transforms = (MultivariateStats.PCA, MultivariateStats.PPCA, MultivariateStats.KernelPCA, MultivariateStats.Whitening)
+AllowedMultivariateTransforms = Union{_allowed_transforms...}
+
 """
 	MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where T <: SimpleSDMLayer
 
-	Overloads the `fit` function from `MultivariateStats.jl`.
+Overloads the `fit` function from `MultivariateStats.jl`.
 """
-function MultivariateStats.fit(a, layers::Vector{T}, kwargs...) where {T<:SimpleSDMLayer}
+function MultivariateStats.fit(proj::Type{K}, layers::Vector{T}; kwargs...) where {T<:SimpleSDMLayer, K <: AllowedMultivariateTransforms}
     _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
     common_keys = reduce(∩, keys.(layers))
     input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
-    proj = MultivariateStats.fit(a, input, kwargs...)
+    proj = MultivariateStats.fit(proj, input; kwargs...)
     return proj
 end
 
@@ -18,27 +21,24 @@ end
     transform(proj, layers::Vector{V}, 
     kwargs...) where {PT<:Union{MultivariateStats.PCA, MultivariateStats.PPCA},V<:SimpleSDMLayer} 
 
-	Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is a 
-	and output object from `MultivariateStats.fit` (see above). 
+Overload of the `transform` function from `MultivariateStats.jl`. Here `proj` is an output object from `MultivariateStats.fit` (see above). 
 """
-function transform(
-    proj,
-    layers::AbstractVecOrMat{U};
-    kwargs...,
+function MultivariateStats.transform(
+    proj, layers::AbstractVecOrMat{U}; kwargs...
 ) where {U<:SimpleSDMLayer}
-    outdim = MultivariateStats.outdim(proj)
-    newlayers = [similar(layers[begin]) for i = 1:outdim]
+    _layers_are_compatible(layers) || return ArgumentError("layers are not compatible")
+    
+    newlayers = [similar(first(layers)) for i in 1:MultivariateStats.outdim(proj)]
     common_keys = reduce(∩, keys.(layers))
 
     input = hcat([vcat([layer[key] for layer in layers]...) for key in common_keys]...)
 
     for (ct, key) in enumerate(common_keys)
         pcaproj = MultivariateStats.transform(proj, input[:, ct])
-        for i = 1:outdim
+        for i in 1:length(newlayers)
             newlayers[i][key] = pcaproj[i]
         end
     end
+
     return newlayers
 end
-
-
diff --git a/test/extensions/multivariatestats.jl b/test/extensions/multivariatestats.jl
index 2d8f5d4f..a7c61d6b 100644
--- a/test/extensions/multivariatestats.jl
+++ b/test/extensions/multivariatestats.jl
@@ -1,23 +1,22 @@
 module SSLTestMVStats
-    using SimpleSDMLayers
-    using MultivariateStats
-    using NeutralLandscapes
-    using Test
+using SimpleSDMLayers
+using MultivariateStats
+using NeutralLandscapes
+using Test
 
-    TEST_DIMS = (150,150)
-    TEST_AUTOCORRELATION = 0.9
-    TEST_NUM_LAYERS = 10
+TEST_DIMS = (150, 150)
+TEST_AUTOCORRELATION = 0.9
+TEST_NUM_LAYERS = 10
 
-    layers = [SimpleSDMResponse(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for i in 1:TEST_NUM_LAYERS]
+layers = [
+    SimpleSDMResponse(rand(MidpointDisplacement(TEST_AUTOCORRELATION), TEST_DIMS...)) for
+    i in 1:TEST_NUM_LAYERS
+]
 
+@test typeof(transform(fit(PCA, layers), layers)) <: Vector{T} where {T<:SimpleSDMLayer}
+#@test typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
-    @test typeof(SimpleSDMLayers.transform(fit(PCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-#    @test typeof(transform(fit(PPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-
-
-
-#    @assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
-#    @assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+#@assert typeof(transform(fit(KernelPCA, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
+#@assert typeof(transform(fit(Whitening, layers),layers)) <: Vector{T} where T<:SimpleSDMLayer
 
 end
-

From f2b8627bfc3112868a873d597525f92a3a286729 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Timoth=C3=A9e=20Poisot?= <timothee.poisot@umontreal.ca>
Date: Tue, 9 Nov 2021 21:40:02 -0500
Subject: [PATCH 22/22] =?UTF-8?q?=F0=9F=A7=91=E2=80=8D=F0=9F=8F=AB=20fix?=
 =?UTF-8?q?=20transform?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 docs/src/examples/pca.jl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/docs/src/examples/pca.jl b/docs/src/examples/pca.jl
index b7dc86de..6a3c21f3 100644
--- a/docs/src/examples/pca.jl
+++ b/docs/src/examples/pca.jl
@@ -24,7 +24,7 @@ layers = convert.(
 # fit pca and project to a new set of layers
 
 pca = fit(PCA, layers)
-newlayers = SimpleSDMLayers.transform(pca, layers)
+newlayers = transform(pca, layers)
 
 # plot them
 
@@ -46,7 +46,7 @@ plot(plot.(wlayers)...)
 # Now we call methods just as in `MultivariateStats`
 
 w = fit(Whitening, wlayers)
-newlayers = SimpleSDMLayers.transform(w, wlayers)
+newlayers = transform(w, wlayers)
 
 
 # and plot the layers without covar