├── .gitignore ├── LICENSE ├── anno-difficulty ├── README.md ├── anno-difficulty.Rmd ├── data │ ├── canonical │ │ ├── espeland-et-al │ │ │ └── caries.csv │ │ ├── passonneau-et-al │ │ │ ├── color-n.csv │ │ │ ├── control-n.csv │ │ │ ├── fair-j.csv │ │ │ ├── find-v.csv │ │ │ ├── full-j.csv │ │ │ └── help-v.csv │ │ ├── rzhetsky-et-al │ │ │ ├── rzhetsky-e-2.csv │ │ │ ├── rzhetsky-irregular.csv │ │ │ ├── rzhetsky-large.csv │ │ │ ├── rzhetsky-numerical.csv │ │ │ └── rzhetsky-words.csv │ │ └── snow-et-al │ │ │ └── rte.csv │ └── original │ │ ├── passonneau │ │ ├── color-n.tsv │ │ ├── control-n.tsv │ │ ├── fair-j.tsv │ │ ├── find-v.tsv │ │ ├── full-j.tsv │ │ ├── help-v.tsv │ │ ├── munge.R │ │ └── notes.txt │ │ ├── rzhetsky │ │ ├── e-2.txt │ │ ├── munge.R │ │ ├── notes.txt │ │ ├── testdata_irregular.txt │ │ ├── testdata_large.txt │ │ ├── testdata_numerical.txt │ │ └── testdata_words.txt │ │ └── snow-et-al │ │ ├── all_collected_data.tgz │ │ ├── download-info.txt │ │ ├── munge.R │ │ └── unpacked │ │ ├── anger.standardized.tsv │ │ ├── disgust.standardized.tsv │ │ ├── fear.standardized.tsv │ │ ├── joy.standardized.tsv │ │ ├── rte.standardized.tsv │ │ ├── sadness.standardized.tsv │ │ ├── surprise.standardized.tsv │ │ ├── temp.standardized.tsv │ │ ├── valence.standardized.tsv │ │ ├── wordsim.standardized.tsv │ │ └── wsd.standardized.tsv ├── noisy-rating.tex ├── paper │ ├── dawid-skene-difficulty.stan │ ├── espeland-caries.json │ ├── old.py │ ├── original-1pl.stan │ └── pvalues.py └── stan │ ├── dawid-skene-binary.stan │ ├── fit-binary-logit.R │ ├── irt1pl.stan │ ├── original-1pl.stan │ └── revised-1pl.stan ├── bayes-versus ├── bayes-versus.Rmd ├── bayes-versus.html ├── bayes-versus.pdf ├── build.sh ├── logistic-regression.R ├── logistic-regression.stan ├── simple-logistic-regression.stan └── weighted-logistic-regression.stan ├── empirical-prior ├── README.md ├── empirical-logistic.stan ├── flat-logistic.stan └── sim.py ├── kmers ├── data │ └── raw │ │ └── refseq-select-2020-10-22.fasta.gz ├── doc │ └── model.tex ├── lib │ └── catch2 │ │ ├── catch_amalgamated.cpp │ │ └── catch_amalgamated.hpp ├── license.txt ├── makefile ├── notes.txt ├── src │ ├── builder.cpp │ ├── kmers │ │ ├── dirichlet-sampler.hpp │ │ ├── fasta-parser.hpp │ │ ├── fasta.hpp │ │ ├── multinomial-model.hpp │ │ └── shred.hpp │ ├── main2.cpp │ ├── notes.txt │ ├── plots.R │ ├── reader.cpp │ └── sparse.cpp └── test │ ├── kmers │ └── softmax_test.cpp │ └── test.cpp ├── monte-carlo-em ├── mcem.Rmd ├── mcem.html └── mcem.pdf ├── opt-path-typical └── sim.R ├── prob-corpus ├── _extensions │ └── quarto-ext │ │ └── include-code-files │ │ ├── .DS_Store │ │ ├── _extension.yml │ │ └── include-code-files.lua ├── header.tex ├── log-odds-linear-regression.stan ├── logistic-regression-predict.stan ├── logistic-regression.stan ├── makefile ├── prob-corpus.qmd ├── references.bib ├── sim.py ├── style.css └── weighted-logistic-regression.stan ├── simulation-based-calibration ├── bad-t-normal-sbc.stan ├── normal-sbc.stan └── sbc.Rmd ├── stan-cpp ├── eg.data.R ├── eg.stan ├── readme.txt └── sim.R ├── stan-semantics └── stan-semantics.Rmd ├── subsampling └── subsampling.R ├── survival ├── cox-proportional-hazards-efron.stan ├── cox-proportional-hazards.stan ├── data │ ├── readme.txt │ └── rossi.csv └── fit.py └── sushi-rating ├── README.md ├── _extensions ├── .DS_Store └── quarto-ext │ ├── .DS_Store │ └── include-code-files │ ├── .DS_Store │ ├── _extension.yml │ └── include-code-files.lua ├── fit.py ├── header.tex ├── makefile ├── ordinal-logit-prior.stan ├── ordinal-logit.stan ├── plackett-luce-vectorized.stan ├── plackett-luce.stan ├── rating-ranking.stan ├── rating.qmd ├── references.bib ├── style.css └── sushi-rating.pdf /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bob-carpenter/case-studies/HEAD/.gitignore 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