Update docs and examples; use semicolon notation for named tuples

Author: ArneBouillon

docs/src/data_processing.md

@@ -28,7 +28,7 @@ complex_schedule = [
 In this (rather unrealistic) chain;
 1. The inputs are decorrelated with their sample mean and covariance (and projected to low dimensional subspace if necessary) i.e PCA
 2. The scaled inputs are then subject to a "Robust" univariate scaling, mapping 1st-3rd quartiles to [0,1]
-3. The outputs are decorrelated using an "output structure matrix" (provided to the emulator `output_structure_matrix=`). Furthermore, apply a dimension-reduction to a space that retains 95% of the total variance. 
+3. The outputs are decorrelated using an "output structure matrix" (provided to the emulator in the `encoder_kwargs` parameter, e.g. as `(; obs_cov_noise =)`). Furthermore, apply a dimension-reduction to a space that retains 95% of the total variance. 
 4. In the reduced input-output space, a canonical correlation analysis is performed. Data is oriented and reduced (if necessary) maximize the joint correlation between inputs and outputs.
 
 !!! note "Default Encoder schedule"
@@ -44,12 +44,12 @@ The schedule is then passed into the Emulator, along with the data and desired s
 ```julia
 emulator = Emulator(
     machine_learning_tool,       
-    input_output_pairs; 
-    output_structure_matrix = obs_noise_cov, 
+    input_output_pairs,
+    (; obs_noise_cov = obs_noise_cov);
     encoder_schedule = complex_schedule,
 )
 ```
-Note that due to the item `(decorrelate_structure_mat(retain_var=0.95), "out")` in the schedule, we must provide the `output_structure_matrix`.
+Note that due to the item `(decorrelate_structure_mat(retain_var=0.95), "out")` in the schedule, we must provide an output structure matrix. In this case, we provide `obs_noise_cov`.
 
 # Types of data processors
 

docs/src/emulate.md

@@ -16,8 +16,8 @@ Wrapping a predefined machine learning tool, e.g. a Gaussian process `gauss_proc
 ```julia
 emulator = Emulator(
     gauss_proc, 
-    input_output_pairs; # optional arguments after this
-    output_structure_matrix = Γy,
+    input_output_pairs,
+    (; obs_noise_cov = Γy); # optional arguments after this
     encoder_schedule = encoder_schedule,
 )
 ```

examples/Cloudy/Cloudy_emulate_sample.jl

@@ -171,9 +171,8 @@ function main()
         # build emulator
         emulator = Emulator(
             mlt,
-            input_output_pairs;
-            input_structure_matrix = cov(priors),
-            output_structure_matrix = Γy,
+            input_output_pairs,
+            (; prior_cov = cov(priors), obs_noise_cov = Γy);
             encoder_schedule = encoder_schedule,
         )
 

examples/Darcy/emulate_sample.jl

@@ -96,9 +96,8 @@ function main()
 
         emulator = Emulator(
             mlt,
-            input_output_pairs;
-            input_structure_matrix = cov(prior),
-            output_structure_matrix = Γy,
+            input_output_pairs,
+            (; prior_cov = cov(prior), obs_noise_cov = Γy);
             encoding_schedule = encoding_schedule,
         )
         optimize_hyperparameters!(emulator, kernbounds = [fill(-1e2, n_params + 1), fill(1e2, n_params + 1)])

examples/EDMF_data/emulator-rank-test.jl

@@ -256,9 +256,8 @@ function main()
             ttt[rank_id, rep_idx] = @elapsed begin
                 emulator = Emulator(
                     mlt,
-                    train_pairs;
-                    input_structure_matrix = cov(prior),
-                    output_structure_matrix = truth_cov,
+                    train_pairs,
+                    (; prior_cov = cov(prior), obs_noise_cov = truth_cov);
                     encoder_schedule = encoder_schedule,
                 )
 

examples/EDMF_data/uq_for_edmf.jl

@@ -230,9 +230,8 @@ function main()
     # Fit an emulator to the data
     emulator = Emulator(
         mlt,
-        input_output_pairs;
-        input_structure_matrix = cov(prior),
-        output_structure_matrix = truth_cov,
+        input_output_pairs,
+        (; prior_cov = cov(prior), obs_noise_cov = truth_cov);
         encoder_schedule = encoder_schedule,
     )
 

examples/Emulator/G-function/emulate-test-n-features.jl

@@ -153,8 +153,8 @@ function main()
             ttt[f_idx, rep_idx] = @elapsed begin
                 emulator = Emulator(
                     mlt,
-                    iopairs;
-                    output_structure_matrix = Γ * I,
+                    iopairs,
+                    (; obs_noise_cov = Γ * I);
                     encoder_schedule = deepcopy(encoder_schedule),
                 )
                 optimize_hyperparameters!(emulator)

examples/Emulator/G-function/emulate.jl

@@ -144,8 +144,8 @@ function main()
         times[rep_idx] = @elapsed begin
             emulator = Emulator(
                 mlt,
-                iopairs;
-                output_structure_matrix = Γ * I,
+                iopairs,
+                (; obs_noise_cov = Γ * I);
                 encoder_schedule = deepcopy(encoder_schedule),
             )
             optimize_hyperparameters!(emulator)

examples/Emulator/Ishigami/emulate.jl

@@ -124,7 +124,7 @@ function main()
 
         # Emulate
         emulator =
-            Emulator(mlt, iopairs; output_structure_matrix = Γ * I, encoder_schedule = deepcopy(encoder_schedule))
+            Emulator(mlt, iopairs, (; obs_noise_cov = Γ * I); encoder_schedule = deepcopy(encoder_schedule))
         optimize_hyperparameters!(emulator)
 
         # get EKP errors - just stored in "optimizer" box for now

examples/Emulator/L63/emulate.jl

@@ -215,7 +215,7 @@ function main()
         else
             encoder_schedule = (decorrelate_structure_mat(), "out")
         end
-        emulator = Emulator(mlt, iopairs; output_structure_matrix = Γy, encoder_schedule = deepcopy(encoder_schedule))
+        emulator = Emulator(mlt, iopairs, (; obs_noise_cov = Γy); encoder_schedule = deepcopy(encoder_schedule))
         optimize_hyperparameters!(emulator)
 
         # diagnostics