Dev

.gitignore

@@ -22,3 +22,8 @@ docs/src_stash/test1_files/figure-commonmark/fig-limits-output-1.svg
 docs/src_stash/*_files
 docs/src_stash/*.md
 docs/src_stash/*.html
+docs/src/tutorials/intermediate/clustered_sites_probo_allsites.jld2
+
+projects/clustered_sites/intermediate/*
+
+build/*

Project.toml

@@ -7,15 +7,18 @@ version = "0.2.0"
 Bijectors = "76274a88-744f-5084-9051-94815aaf08c4"
 BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0"
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+Clustering = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 CommonSolve = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
 ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
+Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
 DistributionFits = "45214091-1ed4-4409-9bcf-fdb48a05e921"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 Functors = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
@@ -25,6 +28,7 @@ Missings = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -39,9 +43,12 @@ CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Lux = "b2108857-7c20-44ae-9111-449ecde12c47"
 SimpleChains = "de6bee2f-e2f4-4ec7-b6ed-219cc6f6e9e5"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+
 
 [extensions]
 HybridVariationalInferenceCUDAExt = "CUDA"
+HybridVariationalInferenceDataFramesExt = "DataFrames"
 HybridVariationalInferenceFluxExt = "Flux"
 HybridVariationalInferenceLuxExt = "Lux"
 HybridVariationalInferenceSimpleChainsExt = "SimpleChains"
@@ -51,16 +58,20 @@ Bijectors = "0.14, 0.15"
 BlockDiagonals = "0.1.42, 0.2"
 CUDA = "5.7"
 ChainRulesCore = "1.25"
+Clustering = "0.15.8"
 Combinatorics = "1.0.2"
 CommonSolve = "0.2.4"
 ComponentArrays = "0.15.19"
+DataFrames = "1.8.2"
 DifferentiationInterface = "0.6.54, 0.7"
+Distances = "0.10.12"
 DistributionFits = "0.3.9"
 Distributions = "0.25.117"
 FillArrays = "1.13.0"
 Flux = "0.14, 0.15, 0.16"
 Functors = "0.4, 0.5"
 GPUArraysCore = "0.1, 0.2"
+IterTools = "1.10.0"
 KernelAbstractions = "0.9.34"
 LinearAlgebra = "1.10"
 LogExpFunctions = "0.3.29"
@@ -70,9 +81,10 @@ MLUtils = "0.4.5"
 Missings = "1.2.0"
 NaNMath = "1.1.3"
 Optimisers = "0.4.6"
-Optimization = "3.11, 4"
+Optimization = "5.3"
+PDMats = "0.11.37"
 Random = "1.10.0"
-SimpleChains = "0.4.8"
+SimpleChains = "0.4.7"
 StableRNGs = "1.0.2"
 StaticArrays = "1.9.13"
 StatsBase = "0.34.4"

_typos.toml

@@ -5,3 +5,6 @@ extend-exclude = ["docs/src_stash/"]
 SOM = "SOM"
 negLogLik = "negLogLik"
 Missings = "Missings"
+
+[default.extend-identifiers]
+bse = "bse"

docs/make.jl

@@ -25,6 +25,7 @@ makedocs(;
         "How to" => [
             ".. use GPU" => "tutorials/lux_gpu.md",
             ".. specify log-Likelihood" => "tutorials/logden_user.md",
+            ".. specify penalties" => "tutorials/penalty.md",
             ".. model independent parameters" => "tutorials/blocks_corr.md",
             ".. model site-global corr" => "tutorials/corr_site_global.md",
         ],