Multiple Refactorings#181

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alyst wants to merge 174 commits intoStructuralEquationModels:develfrom

alyst:optim_ext_ram

Commits on Mar 18, 2024

const SEM=StructuralEquationModels

Alexey Stukalov
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ParamTable: convert from Dict to NamedTuple

Alexey Stukalov
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obj_grad_hess: simplify mapreduce

Alexey Stukalov
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cov_and_mean(): use StatsBase.mean_and_cov()
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fill_A_S_M(): use `@inbounds`

Alexey Stukalov
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fill_A_S_M!(): add !

Alexey Stukalov
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==: use &&

Alexey Stukalov
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RAMMatrices: cleanup params index

Alexey Stukalov
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RAMMatrices: tiny rename for clarity

Alexey Stukalov
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RAMMatrices: cleanup indexing params in arrays

Alexey Stukalov
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RAMConstant: move before RAMMatrices

Alexey Stukalov
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RAMConstant: simplify

Alexey Stukalov
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RAMMatrices: optimize F_indices init

Alexey Stukalov
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RAMMatrices ctor: dim checks

Alexey Stukalov
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RAMMatrices: declare types for all fields

Alexey Stukalov
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include RAMMatrices before EnsParTable
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fix EnsParTable to Dict{RAMMatrices} convert

Alexey Stukalov
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Commits on Mar 20, 2024

replace no-op ctors with convert(T, obj)

Alexey Stukalov
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ParTable ctor: simplify rows code

Alexey Stukalov
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ParTable: full support for Iterator iface

Alexey Stukalov
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use Fix1 instead of anonymous function

Alexey Stukalov
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fix typo

Alexey Stukalov
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rename vars for type stability

Alexey Stukalov
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obj!()/grad!(): avoid tmp array creation

Alexey Stukalov
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grad!(): avoid extra array copying

Alexey Stukalov
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check_acyclic(): use istril/u()

Alexey Stukalov
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grad!(SemML): reduce * ops

Alexey Stukalov
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obj/grad/hess!(SemML): avoid extra arr copying

Alexey Stukalov
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use .+= to reduce allocs

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ParTable: update StenGraph-based ctor

Alexey Stukalov
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EnsParTable: update dict-based and graph-based ctors

Alexey Stukalov
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start_fabin3: optimize indexing

Alexey Stukalov
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start_fabin3(): optimize math

Alexey Stukalov
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start_fabin3(): directly access imply.ram_matrices

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reorder_data(): optimize

Alexey Stukalov
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SemObservedData(): cleanup code

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SemSpecification base type

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use SemSpecification in method signatures

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SemSpecification: vars API

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RAMMatrices: vars API

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ParamTable: vars API
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RAM imply: use vars API

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RAMSymbolic: use vars API

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start_simple(): use vars API

Alexey Stukalov
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starts_fabin3: use vars API

Alexey Stukalov
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remove get_colnames()

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remove get_n_nodes()

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n_par() -> nparams()

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MeanStructure, HessianEvaluation traits

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RAMMatrices: option to keep zero constants

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getindex(EnsParTable, i) instead of get_group()

Alexey Stukalov
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matrix_gradient(): refactor

Alexey Stukalov
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optimize kron

Alexey Stukalov
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ML: optimize C

Alexey Stukalov
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refactor get_partition()

Alexey Stukalov
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remove_all_missing(): optimize

Alexey Stukalov
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skipmissing_mean(): optimize

Alexey Stukalov
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get_observed(): refactor

Alexey Stukalov
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Commits on Apr 14, 2024

fix ridge eval

Alexey Stukalov
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obj/grad/hess: refactor evaluation API
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use ternary op as intended

Alexey Stukalov
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symbolic: constrain to tril before simplifying

Alexey Stukalov
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fix dangling whitespace

Alexey Stukalov
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check_acyclic: notify if matrix is triangular

Alexey Stukalov
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tests/examples: import -> using
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fix dangling spaces

Alexey Stukalov
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don't import ==

Alexey Stukalov
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don't import push!()

Alexey Stukalov
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remove no-op push!()

Alexey Stukalov
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rename Base.sort() to sort_vars()

Alexey Stukalov
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sort_vars!(ParTable): cleanup
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remove spurious "using SEM"

Alexey Stukalov
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fix typo

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add ParamsArray

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vars(RAMMatrices)

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reorder_obs_cov/mean(): cleanup

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param_values(ParTable)

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lavaan_param_values(lav_fit, partable)

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test_gradient(): do tests inside

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test_hessian(): do tests inside

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compare_estimates() -> test_estimates()

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comp_fitmeasures() -> test_fitmeasures()

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tests: tiny improvements

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tests: use approx op
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tests: fix ensembl ctor
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tests: relax multithreading check

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tests: use ismissing()

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tests: SEM module alias
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tests: use update_se_hessian!()
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remove module spec

Alexey Stukalov
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remove no-op method

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start_fabin3: check mean data and model

Alexey Stukalov
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identifier/parameters -> params

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identifier column -> param
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check_params(): opt to append missing ones

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EnsParTable ctor: enforce same params in tables

Alexey Stukalov
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ParTable(graph): use check_params() to update params

Alexey Stukalov
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WIP SemImplyState

Alexey Stukalov
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SemCov: stricter type checks

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FIML: simplify index generation
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get_data(SemObserved): default implementation
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SemObsMissing: refactor

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remove cov_and_mean(): not used anymore
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minus2ll(): cleanup method signatures
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fix chi2

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fix RMSEA

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FIML: update
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FIML: use 5-arg mul!

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WLS: use 5-arg mul!()

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ML: use 5-arg mul!()

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declare cov matrices symmetric

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tiny simplification
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se_hessian(): rename hessian -> method
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se_hessian!(): optimize calc

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H_scaling(): cleanup
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EM: optimizations

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SemObsMissing: remove outdated docstring
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SemObsData: remove rowwise
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cleanup data columns reordering
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n_obs/man(data): restrict to integer

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SemObsCov is a type alias for SemObsData
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DataFrame(EnsParTable)

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test: use proper partable

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start_simple(SemEnsemble): simplify

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SemOptOptim: remove redundant sem_fit()
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SemOptNLopt: remove redundant sem_fit()
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SemOptOptim: use evaluate!() directly
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SemOptNLopt: use evaluate!() directly
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remove unused parameters.jl
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remove identifier.jl
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rename parameter_type to relation
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materialize!(Symm/LowTri/UpTri)

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generic imply: keep F sparse

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generic imply: impose matrix constraints

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neumann_series(): avoid endless loop

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ParamsArray: faster sparse materialize!

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RAM: reuse sigma array

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RAM: optional sparse Sigma matrix

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RAM: declare (I-A)^-1 up/low tri too

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cleanup update_partable!()

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cleanup start_vals handling

Alexey Stukalov
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ML: refactor to minimize allocs

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lower/upper_bounds() API for optim

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u/l_bounds support for Optim.jl

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SemOptimizer(engine = ...) ctor

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SEMNLOptExt for NLopt

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SEMProximalOptExt for Proximal opt

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NLopt: minor tweaks

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add PackageExtensionCompat

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tests helper: is_extended_tests()

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tests: fix optimizer usage

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variance_params(SEMSpec)

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nonunique() helper function

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RAMMatrices ctor: dupl. vars check

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ParTable: better params unique check

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RAMSymbolic: calc (I-A)^{-1} once

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AbstractSemSingle: vars API

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predict_latent_vars()

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lavaan_model()

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BlackBoxOptim.jl backend support

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CommutationMatrix type
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simplify elimination_matrix()
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simplify duplication_matrix()

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FIML: optimize Jmu

Alexey Stukalov
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fix typo

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SemWLS: dim checks

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EM: move code refs to docstring

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EM MVN: decouple from SemObsMissing

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fixup semoptimizer in ext tests
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test/fiml: set EM MVN rtol=1e-10
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Commits on Apr 17, 2024

MissingPattern: transpose data
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EM MVN: report rel_error if not converged
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EM: max_nobs_em opt to limit obs used
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EM: optimize mean handling
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