diff --git a/CITATION.cff b/CITATION.cff index c3ef2857..996f6322 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -3,10 +3,16 @@ message: "If you use posteriordb, please cite it as below." authors: - family-names: Magnusson given-names: Måns + - family-names: Torgander + given-names: Jakob - family-names: Bürkner given-names: Paul + - family-names: Zhang + given-names: Lu + - family-names: Carpenter + given-names: Bob - family-names: Vehtari given-names: Aki -title: "posteriordb: a set of posteriors for Bayesian inference and probabilistic programming" -version: 0.5 -date-released: 2023-10-15 +title: "posteriordb: Testing, Benchmarking and Developing Bayesian Inference Algorithms" +version: 1.0 +date-released: 2025-04-29 diff --git a/README.Rmd b/README.Rmd index f427a6a9..0d17597d 100644 --- a/README.Rmd +++ b/README.Rmd @@ -45,7 +45,15 @@ Most model code are using the the same BSD-3 licence. Although, some models and To simplify the use of `posteriordb`, there are convenience functions both in Python and in R. To use R, see the [posteriordb-r](https://github.com/stan-dev/posteriordb-r) repository, and to use Python, see the [posteriordb-python](https://github.com/stan-dev/posteriordb-python) repository. ## Citing `posteriordb` -Developing and maintaining open-source software is an important yet often underappreciated contribution to scientific progress. Thus, please make sure to cite it appropriately so that developers get credit for their work. Information on how to cite `posteriordb` can be found in the [CITATION.cff](https://github.com/stan-dev/posteriordb/blob/master/CITATION.cff) file. Use the "cite this repository" button under "About" to get a simple BibTeX or APA snippet. +Developing and maintaining open-source software is an important yet often underappreciated contribution to scientific progress. Thus, please make sure to cite it appropriately so that developers get credit for their work. + +To cite the actual posterior database on github, information can be found in the [CITATION.cff](https://github.com/stan-dev/posteriordb/blob/master/CITATION.cff) file. Use the "cite this repository" button under "About" to get a simple BibTeX or APA snippet. + +We have also released a paper describing `posteriordb` that we encourage to cite when using `posteriordb`: + +Magnusson, M., Torgander, J., Bürkner, P., Zhang, L., Carpenter, B., Vehtari, A.. (2025). posteriordb: Testing, Benchmarking and Developing Bayesian Inference Algorithms. *Proceedings of The 28th International Conference on Artificial Intelligence and Statistics*, in *Proceedings of Machine Learning Research* 258:1198-1206 Available from (https://proceedings.mlr.press/v258/magnusson25a.html)[https://proceedings.mlr.press/v258/magnusson25a.html]. + +If you do extensive testing of individual posterior, also please consider citing the paper that introduced the posterior by citing the origin of the posterior. This information can be found in the meta data associated with the posterior, data an/or model. As `posteriordb` rely heavily on Stan, so please consider also to cite Stan: diff --git a/README.md b/README.md index c8bfe9c7..077455ff 100644 --- a/README.md +++ b/README.md @@ -73,11 +73,29 @@ repository. Developing and maintaining open-source software is an important yet often underappreciated contribution to scientific progress. Thus, please make sure to cite it appropriately so that developers get credit for -their work. Information on how to cite `posteriordb` can be found in the +their work. + +To cite the actual posterior database on github, information can be +found in the [CITATION.cff](https://github.com/stan-dev/posteriordb/blob/master/CITATION.cff) file. Use the “cite this repository” button under “About” to get a simple BibTeX or APA snippet. +We have also released a paper describing `posteriordb` that we encourage +to cite when using `posteriordb`: + +Magnusson, M., Torgander, J., Bürkner, P., Zhang, L., Carpenter, B., +Vehtari, A.. (2025). posteriordb: Testing, Benchmarking and Developing +Bayesian Inference Algorithms. *Proceedings of The 28th International +Conference on Artificial Intelligence and Statistics*, in *Proceedings +of Machine Learning Research* 258:1198-1206 Available from +()\[\]. + +If you do extensive testing of individual posterior, also please +consider citing the paper that introduced the posterior by citing the +origin of the posterior. This information can be found in the meta data +associated with the posterior, data an/or model. + As `posteriordb` rely heavily on Stan, so please consider also to cite Stan: diff --git a/posterior_database/models/info/GLM_Binomial_model.info.json b/posterior_database/models/info/GLM_Binomial_model.info.json index 1afca921..b24e4f70 100644 --- a/posterior_database/models/info/GLM_Binomial_model.info.json +++ b/posterior_database/models/info/GLM_Binomial_model.info.json @@ -11,6 +11,10 @@ "stan": { "model_code": "models/stan/GLM_Binomial_model.stan", "stan_version": ">=2.26.0" + }, + "pymc": { + "model_code": "models/pymc/GLM_Binomial_model.py", + "pymc_version": ">=5.16.2" } }, "licence": "BSD3" diff --git a/posterior_database/models/info/GLM_Poisson_model.info.json b/posterior_database/models/info/GLM_Poisson_model.info.json index 98e768a3..028282fe 100644 --- a/posterior_database/models/info/GLM_Poisson_model.info.json +++ b/posterior_database/models/info/GLM_Poisson_model.info.json @@ -11,6 +11,10 @@ "stan": { "model_code": "models/stan/GLM_Poisson_model.stan", "stan_version": ">=2.26.0" + }, + "pymc": { + "model_code": "models/pymc/GLM_Poisson_model.py", + "pymc_version": ">=5.16.2" } }, "licence": "BSD3" diff --git a/posterior_database/models/info/M0_model.info.json b/posterior_database/models/info/M0_model.info.json index 4d8f6650..84191349 100644 --- a/posterior_database/models/info/M0_model.info.json +++ b/posterior_database/models/info/M0_model.info.json @@ -11,6 +11,10 @@ "stan": { "model_code": "models/stan/M0_model.stan", "stan_version": ">=2.26.0" + }, + "pymc": { + "model_code": "models/pymc/M0_model.py", + "pymc_version": ">=5.16.0" } }, "licence": "BSD3" diff --git a/posterior_database/models/info/M0_model_discrete.info.json b/posterior_database/models/info/M0_model_discrete.info.json new file mode 100644 index 00000000..1758cb50 --- /dev/null +++ b/posterior_database/models/info/M0_model_discrete.info.json @@ -0,0 +1,16 @@ +{ + "name": "M0_model_discrete", + "keywords": ["BPA", "Ch.6", "Population", "Capture", "Recapture", "Individual", "Constant", "Discrete"], + "title": "Inferring population size with constant detection probability", + "description": "Detection probability of an individual is assumed constant over individuals and over time periods", + "urls": "https://github.com/stan-dev/example-models/blob/master/BPA/Ch.06", + "references": "kery2011population", + "added_by": "Chris Fonnesbeck", + "added_date": "2021-06-24", + "model_implementations": { + "pymc": { + "model_code": "models/pymc/M0_model_discrete.py", + "pymc_version": ">=5.16.0" + } + } +} diff --git a/posterior_database/models/info/earn_height.info.json b/posterior_database/models/info/earn_height.info.json index 09710205..4a4596e9 100644 --- a/posterior_database/models/info/earn_height.info.json +++ b/posterior_database/models/info/earn_height.info.json @@ -11,6 +11,10 @@ "stan": { "model_code": "models/stan/earn_height.stan", "stan_version": ">=2.26.0" + }, + "pymc": { + "model_code": "models/pymc/earn_height.py", + "pymc_version": ">=5.16.2" } }, "references": "gelman2006data", diff --git a/posterior_database/models/info/eight_schools_noncentered.info.json b/posterior_database/models/info/eight_schools_noncentered.info.json index 5ae18b1e..87568cf6 100644 --- a/posterior_database/models/info/eight_schools_noncentered.info.json +++ b/posterior_database/models/info/eight_schools_noncentered.info.json @@ -13,8 +13,9 @@ "model_code": "models/stan/eight_schools_noncentered.stan", "stan_version": ">=2.26.0" }, - "pymc3": { - "model_code": "models/pymc3/eight_schools_noncentered.py" + "pymc": { + "model_code": "models/pymc/eight_schools_noncentered.py", + "pymc_version": ">=5.16.2" } }, "added_by": "Mans Magnusson", diff --git a/posterior_database/models/info/rats_model.info.json b/posterior_database/models/info/rats_model.info.json index 1f0f7d95..f9e11fab 100644 --- a/posterior_database/models/info/rats_model.info.json +++ b/posterior_database/models/info/rats_model.info.json @@ -1,7 +1,7 @@ { "name": "rats_model", - "keywords": ["Heirarchical", "Normal", "Rats", "Random Effects", "Linear Growth", "Linear"], - "title": "Normal Heirarchical Model to Model Rats' Weight Over Time", + "keywords": ["Hierarchical", "Normal", "Rats", "Random Effects", "Linear Growth", "Linear"], + "title": "Normal Hierarchical Model to Model Rats' Weight Over Time", "description": "The model is essentially a random effects linear growth curve.", "urls": "https://github.com/stan-dev/example-models/tree/master/bugs_examples/vol1/rats", "references": "gelfand1990illustration", diff --git a/posterior_database/models/info/seeds_centered_model.info.json b/posterior_database/models/info/seeds_centered_model.info.json index 80d20721..7f4b4b35 100644 --- a/posterior_database/models/info/seeds_centered_model.info.json +++ b/posterior_database/models/info/seeds_centered_model.info.json @@ -1,7 +1,7 @@ { "name": "seeds_centered_model", "keywords": ["Random", "Effect", "Logistic", "Regression", "Stanified", "Centered"], - "title": "Normal Heirarchical Model to Model Rats' Weight Over Time", + "title": "Random Effect Logistic Regression for Seed Germination Proportion", "description": "The model is essentially a random effects logistic,\n allowing for over-dispersion. Models the proportion of germination\n of different seeds in different root extracts. 'Stanified' & centered:\n tau replaced by sigma, direct estimation using \n narrower semi-informative priors, coefficients are centered", "urls": "http://www.mrc-bsu.cam.ac.uk/wp-content/uploads/WinBUGS_Vol1.pdf", "references": "crowder1978beta", diff --git a/posterior_database/models/info/seeds_stanified_model.info.json b/posterior_database/models/info/seeds_stanified_model.info.json index 12c6f392..e2371087 100644 --- a/posterior_database/models/info/seeds_stanified_model.info.json +++ b/posterior_database/models/info/seeds_stanified_model.info.json @@ -1,7 +1,7 @@ { "name": "seeds_stanified_model", "keywords": ["Random", "Effect", "Logistic", "Regression", "Stanified"], - "title": "Normal Heirarchical Model to Model Rats' Weight Over Time", + "title": "Random Effect Logistic Regression for Seed Germination Proportion", "description": "The model is essentially a random effects logistic,\n allowing for over-dispersion. Models the proportion of germination\n of different seeds in different root extracts. 'Stanified':\n tau replaced by sigma, direct estimation using \n narrower semi-informative priors", "urls": "http://www.mrc-bsu.cam.ac.uk/wp-content/uploads/WinBUGS_Vol1.pdf", "references": "crowder1978beta", diff --git a/posterior_database/models/pymc/GLM_Binomial_model.py b/posterior_database/models/pymc/GLM_Binomial_model.py new file mode 100644 index 00000000..800e430b --- /dev/null +++ b/posterior_database/models/pymc/GLM_Binomial_model.py @@ -0,0 +1,21 @@ +import numpy as np +import pymc as pm + +def model(data): + + with pm.Model(coords={"year": range(40)}) as pymc_model: + year = pm.Data("year_data", np.array(data["year"]), dims="year") + N = pm.Data("N_data", np.array(data["N"]), dims="year") + C = pm.Data("C_data", np.array(data["C"]), dims="year") + + alpha = pm.Normal("alpha", mu=0, sigma=100) + beta1 = pm.Normal("beta1", mu=0, sigma=100) + beta2 = pm.Normal("beta2", mu=0, sigma=100) + + year_squared = year ** 2 + logit_p = alpha + beta1 * year + beta2 * year_squared + pm.Binomial("C", n=N, logit_p=logit_p, observed=C, dims="year") + + p = pm.Deterministic("p", pm.math.invlogit(logit_p), dims="year") + + return pymc_model diff --git a/posterior_database/models/pymc/GLM_Poisson_model.py b/posterior_database/models/pymc/GLM_Poisson_model.py new file mode 100644 index 00000000..687eaba8 --- /dev/null +++ b/posterior_database/models/pymc/GLM_Poisson_model.py @@ -0,0 +1,36 @@ +import numpy as np +import pymc as pm +import pytensor.tensor as pt + +def model(data): + years_data = np.array(data["year"]) + counts_data = np.array(data["C"]) + number_observations = data["n"] + coords = { + "features": ["years", "years**2", "years**3"], + "observation": np.arange(number_observations), + } + with pm.Model(coords=coords) as pymc_model: + alpha = pm.Uniform("alpha", -20, +20) + beta1 = pm.Uniform("beta1", -10, +10) + beta2 = pm.Uniform("beta2", -10, +10) + beta3 = pm.Uniform("beta3", -10, +10) + + X = pm.Data( + "X", + np.column_stack([years_data, years_data**2, years_data**3]), + dims=["observation", "feature"], + ) + y = pm.Data("y", counts_data, dims="observation") + + beta = pm.Deterministic("beta", pt.stack([beta1, beta2, beta3]), dims = "feature") + + log_lambda = pm.Deterministic( + "log_lambda", alpha + X @ beta, dims="observation" + ) + + counts = pm.Poisson( + "counts", mu=pm.math.exp(log_lambda), observed=y, dims="observation" + ) + + return pymc_model \ No newline at end of file diff --git a/posterior_database/models/pymc/M0_model.py b/posterior_database/models/pymc/M0_model.py new file mode 100644 index 00000000..c4338890 --- /dev/null +++ b/posterior_database/models/pymc/M0_model.py @@ -0,0 +1,35 @@ +import numpy as np +import pymc as pm + +def model(data): + y = np.array(data["y"]) # capture history matrix + T = np.array(data["T"]) # time periods + + coords = {"individual": np.arange(data["M"]), + "capture_period": np.arange(data["T"])} + with pm.Model(coords=coords) as pymc_model: + y_data = pm.Data("y", y, dims=("individual", "capture_period")) + s = pm.Deterministic("s", y_data.sum(axis=1), dims="individual") + is_observed = s > 0 + + # Inclusion probability + omega = pm.Uniform("omega", 0, 1) + # Capture probability + p = pm.Uniform("p", 0, 1) + + # Defining bernoulli and binomial components + binom = pm.Binomial.dist(n=T, p=p) + log_omega = pm.math.log(omega) + log_one_minus_omega = pm.math.log(1-omega) + log_one_minus_p = pm.math.log(1-p) + + # Computing marginalization mixture + logp_if_obs = log_omega + pm.logp(binom, s) + logp_zero_single = pm.math.logaddexp(log_omega + T * log_one_minus_p , log_one_minus_omega) + logp_each = pm.math.switch(is_observed, logp_if_obs, logp_zero_single) + + pm.Potential("likelihood", logp_each.sum()) + + omega_nd = pm.Deterministic("omega_nd", (omega * (1 -p)**T) / (omega * (1 - p)**T + (1 - omega))) + + return pymc_model \ No newline at end of file diff --git a/posterior_database/models/pymc/M0_model_discrete.py b/posterior_database/models/pymc/M0_model_discrete.py new file mode 100644 index 00000000..05eed02a --- /dev/null +++ b/posterior_database/models/pymc/M0_model_discrete.py @@ -0,0 +1,25 @@ +import numpy as np +import pymc as pm + +def model(data): + y = np.array(data["y"]) # capture history matrix + T = np.array(data["T"]) # time periods + coords = {"individual": np.arange(data["M"]), + "capture_period": np.arange(data["T"])} + with pm.Model(coords=coords) as pymc_model: + + # Inclusion probability + omega = pm.Uniform("omega", 0, 1) + # Capture probability + p = pm.Uniform("p", 0, 1) + + # Inclusion indicator + z = pm.Bernoulli("z", p=omega, dims="individual") + + y_obs = pm.Bernoulli("y_obs", p=z[:, None]*p, observed=y, dims=("individual", "capture_period")) + + N = pm.Deterministic("N", pm.math.sum(z)) + + omega_nd = pm.Deterministic("omega_nd", (omega * (1 -p)**T) / (omega * (1 - p)**T + (1 - omega))) + + return pymc_model \ No newline at end of file diff --git a/posterior_database/models/pymc/arma11.py b/posterior_database/models/pymc/arma11.py new file mode 100644 index 00000000..81566a25 --- /dev/null +++ b/posterior_database/models/pymc/arma11.py @@ -0,0 +1,43 @@ +import pymc as pm +import pytensor +import pytensor.tensor as pt +def model(data): + y_obs = data["y"] # Observed series + up_to = data["T"] # Timesteps + with pm.Model() as pymc_model: + mu = pm.Normal( + "mu", mu=0, sigma=10 + ) # mean coefficient + phi = pm.Normal( + "phi", mu=0, sigma=2 + ) # autoregressive coef + theta = pm.Normal( + "theta", mu=0, sigma=2 + ) # moving average + sigma = pm.HalfCauchy( + "sigma", beta=2.5 + ) # noise scale + + # scan variables + y = pt.as_tensor_variable(y_obs) + y_hat0 = mu + phi * mu + err0 = y[0] - y_hat0 + outputs_info = [y_hat0, err0, y[0]] + + def step(curr_obs, prev_pred, prev_err, prev_obs, mu, phi, theta): + y_hat = mu + phi * prev_obs + theta * prev_err + new_err = curr_obs - y_hat + return [y_hat, new_err, curr_obs] + + [predictions, _, _] , _ = pytensor.scan(fn=step, + outputs_info=outputs_info, + sequences=y[1:], + non_sequences=[mu, phi, theta]) + + # concatenating predictions + y_hat0_vec = y_hat0.dimshuffle("x") + final_predictions = pt.concatenate([y_hat0_vec, predictions]) + + pm.Normal("y", mu=final_predictions, sigma=sigma, observed=y) + + return pymc_model \ No newline at end of file diff --git a/posterior_database/models/pymc/earn_height.py b/posterior_database/models/pymc/earn_height.py new file mode 100644 index 00000000..45fb92d6 --- /dev/null +++ b/posterior_database/models/pymc/earn_height.py @@ -0,0 +1,23 @@ +import numpy as np +import pymc as pm + +def model(data): + + # Define PyMC Model + coords = { + 'obs_idx': np.arange(data["N"]), + 'feature': ['intercept', 'height'] + } + + with pm.Model(coords=coords) as earn_height: + N = pm.Data("N", data["N"]) + earn = pm.Data('earn', data['earn'], dims=['obs_idx']) + height = pm.Data('height', data['height'], dims=['obs_idx']) + + beta = pm.Flat('beta', dims=['feature']) + mu = beta[0] + beta[1] * height + + sigma = pm.HalfFlat('sigma') + earn_hat = pm.Normal('earn_hat', mu=mu, sigma=sigma, observed=earn, dims=['obs_idx']) + + return earn_height \ No newline at end of file diff --git a/posterior_database/models/pymc/eight_schools_noncentered.py b/posterior_database/models/pymc/eight_schools_noncentered.py new file mode 100644 index 00000000..b7cc0e27 --- /dev/null +++ b/posterior_database/models/pymc/eight_schools_noncentered.py @@ -0,0 +1,18 @@ +import numpy as np +import pymc as pm + + +def model(data): + y_obs = np.array(data["y"]) # estimated treatment + sigma = np.array(data["sigma"]) # std of estimated effect + coords = {"school": np.arange(data["J"])} + with pm.Model(coords=coords) as pymc_model: + + mu = pm.Normal( + "mu", mu=0, sigma=5 + ) # hyper-parameter of mean, non-informative prior + tau = pm.HalfCauchy("tau", beta=5) # hyper-parameter of sigma + theta_trans = pm.Normal("theta_trans", mu=0, sigma=1, dims="school") + theta = mu + tau * theta_trans + y = pm.Normal("y", mu=theta, sigma=sigma, observed=y_obs) + return pymc_model diff --git a/posterior_database/models/pymc3/eight_schools_noncentered.py b/posterior_database/models/pymc3/eight_schools_noncentered.py deleted file mode 100644 index 91b6c611..00000000 --- a/posterior_database/models/pymc3/eight_schools_noncentered.py +++ /dev/null @@ -1,18 +0,0 @@ -import numpy as np -import pymc3 as pm3 - - -def model(data): - J = data["J"] # number of schools - y_obs = np.array(data["y"]) # estimated treatment - sigma = np.array(data["sigma"]) # std of estimated effect - with pm3.Model() as pymc_model: - - mu = pm3.Normal( - "mu", mu=0, sd=5 - ) # hyper-parameter of mean, non-informative prior - tau = pm3.Cauchy("tau", alpha=0, beta=5) # hyper-parameter of sd - theta_trans = pm3.Normal("theta_trans", mu=0, sd=1, shape=J) - theta = mu + tau * theta_trans - y = pm3.Normal("y", mu=theta, sd=sigma, observed=y_obs) - return pymc_model diff --git a/posterior_database/models/stan/2pl_latent_reg_irt.stan b/posterior_database/models/stan/2pl_latent_reg_irt.stan index e969eca4..ddcd300b 100644 --- a/posterior_database/models/stan/2pl_latent_reg_irt.stan +++ b/posterior_database/models/stan/2pl_latent_reg_irt.stan @@ -64,7 +64,7 @@ model { alpha ~ lognormal(1, 1); target += normal_lpdf(beta | 0, 3); lambda_adj ~ student_t(3, 0, 1); - theta ~ normal(W_adj * lambda_adj, 1); + theta ~ normal(W_adj * lambda_adj, 1.0); y ~ bernoulli_logit(alpha[ii] .* theta[jj] - beta[ii]); } generated quantities { diff --git a/posterior_database/models/stan/GLMM_Poisson_model.stan b/posterior_database/models/stan/GLMM_Poisson_model.stan index 079e616d..25385266 100644 --- a/posterior_database/models/stan/GLMM_Poisson_model.stan +++ b/posterior_database/models/stan/GLMM_Poisson_model.stan @@ -13,7 +13,7 @@ transformed data { parameters { real alpha; real beta1; - real beta2; + real beta2; real beta3; vector[n] eps; // Year effects real sigma; diff --git a/posterior_database/models/stan/gpcm_latent_reg_irt.stan b/posterior_database/models/stan/gpcm_latent_reg_irt.stan index 16df5c2a..bb43f205 100644 --- a/posterior_database/models/stan/gpcm_latent_reg_irt.stan +++ b/posterior_database/models/stan/gpcm_latent_reg_irt.stan @@ -82,7 +82,7 @@ transformed parameters { model { alpha ~ lognormal(1, 1); target += normal_lpdf(beta | 0, 3); - theta ~ normal(W_adj * lambda_adj, 1); + theta ~ normal(W_adj * lambda_adj, 1.0); lambda_adj ~ student_t(3, 0, 1); for (n in 1 : N) { target += pcm(y[n], theta[jj[n]] .* alpha[ii[n]], diff --git a/posterior_database/models/stan/grsm_latent_reg_irt.stan b/posterior_database/models/stan/grsm_latent_reg_irt.stan index 299d36d5..dca6e5c2 100644 --- a/posterior_database/models/stan/grsm_latent_reg_irt.stan +++ b/posterior_database/models/stan/grsm_latent_reg_irt.stan @@ -75,7 +75,7 @@ model { alpha ~ lognormal(1, 1); target += normal_lpdf(beta | 0, 3); target += normal_lpdf(kappa | 0, 3); - theta ~ normal(W_adj * lambda_adj, 1); + theta ~ normal(W_adj * lambda_adj, 1.0); lambda_adj ~ student_t(3, 0, 1); for (n in 1 : N) { target += rsm(y[n], theta[jj[n]] .* alpha[ii[n]], beta[ii[n]], kappa); diff --git a/posterior_database/posteriors/M0_data-M0_model_discrete.json b/posterior_database/posteriors/M0_data-M0_model_discrete.json new file mode 100644 index 00000000..bc77f97b --- /dev/null +++ b/posterior_database/posteriors/M0_data-M0_model_discrete.json @@ -0,0 +1,18 @@ +{ + "keywords": ["bpa book", "capture-recapture"], + "urls": "https://github.com/stan-dev/example-models/blob/master/BPA/Ch.06", + "references": "kery2011population", + "dimensions": { + "omega": 1, + "p": 1, + "omega_nd": 1, + "N": 1, + "z": 237 + }, + "reference_posterior_name": null, + "added_date": "2026-01-16", + "added_by": "Chris Fonnesbeck", + "name": "M0_data-M0_model_discrete", + "model_name": "M0_model_discrete", + "data_name": "M0_data" +} diff --git a/posterior_database/posteriors/Rate_1_data-Rate_1_model.json b/posterior_database/posteriors/Rate_1_data-Rate_1_model.json index 0ba98c6c..01185e21 100644 --- a/posterior_database/posteriors/Rate_1_data-Rate_1_model.json +++ b/posterior_database/posteriors/Rate_1_data-Rate_1_model.json @@ -5,7 +5,7 @@ "dimensions": { "theta": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "Rate_1_data-Rate_1_model", "added_date": "2021-06-30", "added_by": "Kane Lindsay", "name": "Rate_1_data-Rate_1_model", diff --git a/posterior_database/posteriors/Rate_2_data-Rate_2_model.json b/posterior_database/posteriors/Rate_2_data-Rate_2_model.json index 2123774a..f2573c5a 100644 --- a/posterior_database/posteriors/Rate_2_data-Rate_2_model.json +++ b/posterior_database/posteriors/Rate_2_data-Rate_2_model.json @@ -7,7 +7,7 @@ "theta2": 1, "delta": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "Rate_2_data-Rate_2_model", "added_date": "2021-06-30", "added_by": "Kane Lindsay", "name": "Rate_2_data-Rate_2_model", diff --git a/posterior_database/posteriors/Rate_3_data-Rate_3_model.json b/posterior_database/posteriors/Rate_3_data-Rate_3_model.json index ce0c5862..e48f0878 100644 --- a/posterior_database/posteriors/Rate_3_data-Rate_3_model.json +++ b/posterior_database/posteriors/Rate_3_data-Rate_3_model.json @@ -5,7 +5,7 @@ "dimensions": { "theta": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "Rate_3_data-Rate_3_model", "added_date": "2021-06-30", "added_by": "Kane Lindsay", "name": "Rate_3_data-Rate_3_model", diff --git a/posterior_database/posteriors/Rate_5_data-Rate_5_model.json b/posterior_database/posteriors/Rate_5_data-Rate_5_model.json index 29b85292..10c9a1b6 100644 --- a/posterior_database/posteriors/Rate_5_data-Rate_5_model.json +++ b/posterior_database/posteriors/Rate_5_data-Rate_5_model.json @@ -7,7 +7,7 @@ "postpredk1": 1, "postpredk2": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "Rate_5_data-Rate_5_model", "added_date": "2021-06-30", "added_by": "Kane Lindsay", "name": "Rate_5_data-Rate_5_model", diff --git a/posterior_database/posteriors/dogs-dogs.json b/posterior_database/posteriors/dogs-dogs.json index 5bdacbe9..6e8b7306 100644 --- a/posterior_database/posteriors/dogs-dogs.json +++ b/posterior_database/posteriors/dogs-dogs.json @@ -1,10 +1,14 @@ { "name": "dogs-dogs", - "keywords": ["arm book", "stan examples", "pathfinder paper"], + "keywords": [ + "arm book", + "stan examples", + "pathfinder paper" + ], "urls": "https://github.com/stan-dev/example-models/tree/master/ARM/Ch.24", "model_name": "dogs", "data_name": "dogs", - "reference_posterior_name": null, + "reference_posterior_name": "dogs-dogs", "references": "gelman2006data", "dimensions": { "beta": 3 diff --git a/posterior_database/posteriors/dogs-dogs_hierarchical.json b/posterior_database/posteriors/dogs-dogs_hierarchical.json index b4b78928..2f987e63 100644 --- a/posterior_database/posteriors/dogs-dogs_hierarchical.json +++ b/posterior_database/posteriors/dogs-dogs_hierarchical.json @@ -2,7 +2,7 @@ "name": "dogs-dogs_hierarchical", "model_name": "dogs_hierarchical", "data_name": "dogs", - "reference_posterior_name": null, + "reference_posterior_name": "dogs-dogs_hierarchical", "dimensions": { "a": 1, "b": 1 diff --git a/posterior_database/posteriors/nes_logit_data-nes_logit_model.json b/posterior_database/posteriors/nes_logit_data-nes_logit_model.json index eee7a94f..0c122911 100644 --- a/posterior_database/posteriors/nes_logit_data-nes_logit_model.json +++ b/posterior_database/posteriors/nes_logit_data-nes_logit_model.json @@ -1,12 +1,14 @@ { - "keywords": ["arm book"], + "keywords": [ + "arm book" + ], "urls": "https://github.com/stan-dev/example-models/tree/master/ARM/Ch.5", "references": "gelman2006data", "dimensions": { "alpha": 1, "beta": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "nes_logit_data-nes_logit_model", "added_date": "2021-07-01", "added_by": "Kane Lindsay", "name": "nes_logit_data-nes_logit_model", diff --git a/posterior_database/posteriors/radon_all-radon_pooled.json b/posterior_database/posteriors/radon_all-radon_pooled.json index 38b6aeea..6b5dbbdf 100644 --- a/posterior_database/posteriors/radon_all-radon_pooled.json +++ b/posterior_database/posteriors/radon_all-radon_pooled.json @@ -1,11 +1,12 @@ { "name": "radon_all-radon_pooled", - "keywords": ["stan case study"], + "keywords": [ + "stan case study" + ], "urls": "https://mc-stan.org/users/documentation/case-studies/radon.html", - "urls": null, "model_name": "radon_pooled", "data_name": "radon_all", - "reference_posterior_name": null, + "reference_posterior_name": "radon_all-radon_pooled", "references": "gelman2006data", "dimensions": { "alpha": 1, diff --git a/posterior_database/posteriors/radon_mn-radon_pooled.json b/posterior_database/posteriors/radon_mn-radon_pooled.json index 6463c67f..028865aa 100644 --- a/posterior_database/posteriors/radon_mn-radon_pooled.json +++ b/posterior_database/posteriors/radon_mn-radon_pooled.json @@ -4,7 +4,7 @@ "urls": "https://mc-stan.org/users/documentation/case-studies/radon.html", "model_name": "radon_pooled", "data_name": "radon_mn", - "reference_posterior_name": null, + "reference_posterior_name": "radon_mn-radon_pooled", "references": "gelman2006data", "dimensions": { "alpha": 1, diff --git a/posterior_database/posteriors/wells_data-wells_dist.json b/posterior_database/posteriors/wells_data-wells_dist.json index ec690396..47ba00ad 100644 --- a/posterior_database/posteriors/wells_data-wells_dist.json +++ b/posterior_database/posteriors/wells_data-wells_dist.json @@ -1,11 +1,14 @@ { - "keywords": ["arm book", "logistic regression"], + "keywords": [ + "arm book", + "logistic regression" + ], "urls": "https://github.com/stan-dev/example-models/tree/master/ARM/Ch.5", "references": "gelman2006data", "dimensions": { "beta": 2 }, - "reference_posterior_name": null, + "reference_posterior_name": "wells_data-wells_dist", "added_date": "2020-10-02", "added_by": "Phil Clemson", "name": "wells_data-wells_dist", diff --git a/posterior_database/posteriors/wells_data-wells_dist100_model.json b/posterior_database/posteriors/wells_data-wells_dist100_model.json index 0db0bf00..32976b0e 100644 --- a/posterior_database/posteriors/wells_data-wells_dist100_model.json +++ b/posterior_database/posteriors/wells_data-wells_dist100_model.json @@ -1,12 +1,15 @@ { - "keywords": ["arm book", "logistic regression"], + "keywords": [ + "arm book", + "logistic regression" + ], "urls": "https://github.com/stan-dev/example-models/tree/master/ARM/Ch.5", "references": "gelman2006data", "dimensions": { "alpha": 1, "beta": 1 }, - "reference_posterior_name": null, + "reference_posterior_name": "wells_data-wells_dist100_model", "added_date": "2021-07-07", "added_by": "Kane Lindsay", "name": "wells_data-wells_dist100_model", diff --git a/posterior_database/reference_posteriors/draws/draws/Rate_1_data-Rate_1_model.json.zip 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new file mode 100644 index 00000000..310bca83 --- /dev/null +++ b/posterior_database/reference_posteriors/draws/info/Rate_1_data-Rate_1_model.info.json @@ -0,0 +1,45 @@ +{ + "name": "Rate_1_data-Rate_1_model", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 30000, + "warmup": 20000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": "theta" + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": 10000.890601633693, + "effective_sample_size_tail": 9947.9072032648673, + "r_hat": 0.999860039177845, + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [1.87438905855035, 2.01458012184614, 2.07570658075487, 2.04010216682925, 1.91106527824523, 1.97130938917591, 2.07326660307227, 1.98817838688325, 2.00172495442971, 1.95003301822009], + "mean_lag1_ac": 0.00206333866609656 + }, + "checks_made": { + "ndraws_is_10k": true, + "nchains_is_gte_4": true, + "r_hat_below_1_01": true, + "efmi_above_0_2": true, + "abs_mean_lag1_ac_below_0_05": true + }, + "comments": null, + "added_by": "Jakob Torgander", + "added_date": "2025-05-19", + "versions": { + "cmdstan_version": "2.35.0", + "r_Makevars": "\nCXX14FLAGS += -O3 -mtune=native -arch arm64 -ftemplate-depth-256\n", + "r_version": "R version 4.4.3 (2025-02-28)", + "r_session": "R version 4.4.3 (2025-02-28)\nPlatform: aarch64-apple-darwin20\nRunning under: macOS Sequoia 15.4.1\n\nMatrix products: default\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib \nLAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\ntime zone: Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.2 testthat_3.2.3 cmdstanr_0.9.0 devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 posterior_1.6.1 lubridate_1.9.4 forcats_1.0.0 \n[10] stringr_1.5.1 dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1 ggplot2_3.5.1 tidyverse_2.0.0 \n\nloaded via a namespace (and not attached):\n [1] tidyselect_1.2.1 fastmap_1.2.0 gh_1.4.1 tensorA_0.36.2.1 promises_1.3.2 digest_0.6.37 timechange_0.3.0 mime_0.13 \n [9] lifecycle_1.0.4 ellipsis_0.3.2 processx_3.8.6 magrittr_2.0.3 compiler_4.4.3 rlang_1.1.5 sass_0.4.9 tools_4.4.3 \n[17] yaml_2.3.10 data.table_1.17.0 knitr_1.50 htmlwidgets_1.6.4 bit_4.6.0 pkgbuild_1.4.7 pkgload_1.4.0 abind_1.4-8 \n[25] miniUI_0.1.1.1 withr_3.0.2 desc_1.4.3 grid_4.4.3 urlchecker_1.0.1 profvis_0.4.0 xtable_1.8-4 colorspace_2.1-1 \n[33] scales_1.3.0 cli_3.6.4 rmarkdown_2.29 crayon_1.5.3 generics_0.1.3 remotes_2.5.0 rstudioapi_0.17.1 tzdb_0.5.0 \n[41] sessioninfo_1.2.3 cachem_1.1.0 parallel_4.4.3 matrixStats_1.5.0 vctrs_0.6.5 hms_1.1.3 bit64_4.6.0-1 jquerylib_0.1.4 \n[49] glue_1.8.0 ps_1.9.0 distributional_0.5.0 stringi_1.8.7 gtable_0.3.6 later_1.4.2 munsell_0.5.1 pillar_1.10.2 \n[57] htmltools_0.5.8.1 brio_1.1.5 R6_2.6.1 rprojroot_2.0.4 vroom_1.6.5 evaluate_1.0.3 shiny_1.10.0 backports_1.5.0 \n[65] memoise_2.0.1 httpuv_1.6.15 bslib_0.9.0 Rcpp_1.0.14 checkmate_2.3.2 xfun_0.52 fs_1.6.5 pkgconfig_2.0.3 " + } +} diff --git a/posterior_database/reference_posteriors/draws/info/Rate_2_data-Rate_2_model.info.json b/posterior_database/reference_posteriors/draws/info/Rate_2_data-Rate_2_model.info.json new file mode 100644 index 00000000..ccb61c75 --- /dev/null +++ b/posterior_database/reference_posteriors/draws/info/Rate_2_data-Rate_2_model.info.json @@ -0,0 +1,45 @@ +{ + "name": "Rate_2_data-Rate_2_model", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["theta1", "theta2"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [10091.871860022728, 10222.708662061308], + "effective_sample_size_tail": [9689.1938272425359, 10037.771293476999], + "r_hat": [1.00023035233106, 0.999881228734353], + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [2.07901542566069, 2.0184524198474, 1.89222714015946, 1.99558591313082, 1.89814994909878, 1.91206041720845, 1.97174657870289, 1.93400180313051, 1.9682195887105, 1.9906213747076], + "mean_lag1_ac": [-0.00355662507484341, -0.00886436147670544] + }, + "checks_made": { + "ndraws_is_10k": true, + "nchains_is_gte_4": true, + "r_hat_below_1_01": true, + "efmi_above_0_2": true, + "abs_mean_lag1_ac_below_0_05": true + }, + "comments": null, + "added_by": "Jakob Torgander", + "added_date": "2025-08-29", + "versions": { + "cmdstan_version": "2.35.0", + "r_Makevars": "\nCXX14FLAGS += -O3 -mtune=native -arch arm64 -ftemplate-depth-256\n", + "r_version": "R version 4.5.1 (2025-06-13)", + "r_session": "R version 4.5.1 (2025-06-13)\nPlatform: aarch64-apple-darwin20\nRunning under: macOS Sequoia 15.6\n\nMatrix products: default\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib \nLAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\ntime zone: Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.3 testthat_3.2.3 cmdstanr_0.9.0 \n [4] devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 \n [7] posterior_1.6.1 lubridate_1.9.4 forcats_1.0.0 \n[10] stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0 \n[13] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 \n[16] ggplot2_3.5.2 tidyverse_2.0.0 \n\nloaded via a namespace (and not attached):\n [1] tidyselect_1.2.1 farver_2.1.2 fastmap_1.2.0 \n [4] gh_1.5.0 tensorA_0.36.2.1 promises_1.3.3 \n [7] digest_0.6.37 timechange_0.3.0 mime_0.13 \n[10] lifecycle_1.0.4 waldo_0.6.2 ellipsis_0.3.2 \n[13] processx_3.8.6 magrittr_2.0.3 compiler_4.5.1 \n[16] rlang_1.1.6 sass_0.4.10 tools_4.5.1 \n[19] yaml_2.3.10 data.table_1.17.8 knitr_1.50 \n[22] htmlwidgets_1.6.4 bit_4.6.0 pkgbuild_1.4.8 \n[25] RColorBrewer_1.1-3 pkgload_1.4.0 abind_1.4-8 \n[28] miniUI_0.1.2 withr_3.0.2 desc_1.4.3 \n[31] grid_4.5.1 urlchecker_1.0.1 profvis_0.4.0 \n[34] xtable_1.8-4 scales_1.4.0 cli_3.6.5 \n[37] rmarkdown_2.29 crayon_1.5.3 generics_0.1.4 \n[40] remotes_2.5.0 rstudioapi_0.17.1 tzdb_0.5.0 \n[43] sessioninfo_1.2.3 cachem_1.1.0 parallel_4.5.1 \n[46] matrixStats_1.5.0 vctrs_0.6.5 hms_1.1.3 \n[49] bit64_4.6.0-1 jquerylib_0.1.4 glue_1.8.0 \n[52] ps_1.9.1 distributional_0.5.0 stringi_1.8.7 \n[55] 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a/posterior_database/reference_posteriors/draws/info/Rate_5_data-Rate_5_model.info.json b/posterior_database/reference_posteriors/draws/info/Rate_5_data-Rate_5_model.info.json new file mode 100644 index 00000000..3b19bbdb --- /dev/null +++ b/posterior_database/reference_posteriors/draws/info/Rate_5_data-Rate_5_model.info.json @@ -0,0 +1,45 @@ +{ + "name": "Rate_5_data-Rate_5_model", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": "theta" + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": 10092.909756473744, + "effective_sample_size_tail": 9964.0302168736216, + "r_hat": 1.00024861025683, + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [2.01220184967282, 2.00818232294778, 2.04753376621172, 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b/posterior_database/reference_posteriors/draws/info/dogs-dogs.info.json @@ -0,0 +1,45 @@ +{ + "name": "dogs-dogs", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["beta[1]", "beta[2]", "beta[3]"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [9591.4148905058191, 9704.7972587579916, 9426.9623437726459], + "effective_sample_size_tail": [9791.5696378644734, 9689.571740157513, 10001.459664001111], + "r_hat": [0.999721673559926, 1.00002043175366, 1.0000439169065], + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [2.10652788235528, 2.07964326807562, 2.0032385330797, 1.94637895460122, 2.03751426442169, 2.02000035535677, 2.08697998994052, 1.88651846700462, 2.11253436886765, 1.99787570321205], + 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Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.3 testthat_3.2.3 cmdstanr_0.9.0 devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 posterior_1.6.1 lubridate_1.9.4 \n [9] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 ggplot2_3.5.2 \n[17] tidyverse_2.0.0 \n\nloaded via a namespace (and not attached):\n [1] tidyselect_1.2.1 farver_2.1.2 fastmap_1.2.0 gh_1.5.0 tensorA_0.36.2.1 promises_1.3.3 digest_0.6.37 \n [8] timechange_0.3.0 mime_0.13 lifecycle_1.0.4 ellipsis_0.3.2 processx_3.8.6 magrittr_2.0.3 compiler_4.5.1 \n[15] rlang_1.1.6 sass_0.4.10 tools_4.5.1 yaml_2.3.10 data.table_1.17.8 knitr_1.50 htmlwidgets_1.6.4 \n[22] bit_4.6.0 pkgbuild_1.4.8 RColorBrewer_1.1-3 pkgload_1.4.0 abind_1.4-8 miniUI_0.1.2 withr_3.0.2 \n[29] desc_1.4.3 grid_4.5.1 urlchecker_1.0.1 profvis_0.4.0 xtable_1.8-4 scales_1.4.0 cli_3.6.5 \n[36] 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null, + "added_by": "Jakob Torgander", + "added_date": "2025-05-19", + "versions": { + "cmdstan_version": "2.35.0", + "r_Makevars": "\nCXX14FLAGS += -O3 -mtune=native -arch arm64 -ftemplate-depth-256\n", + "r_version": "R version 4.4.3 (2025-02-28)", + "r_session": "R version 4.4.3 (2025-02-28)\nPlatform: aarch64-apple-darwin20\nRunning under: macOS Sequoia 15.4.1\n\nMatrix products: default\nBLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib \nLAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\ntime zone: Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.2 testthat_3.2.3 cmdstanr_0.9.0 devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 posterior_1.6.1 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/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib \nLAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\ntime zone: Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.3 testthat_3.2.3 cmdstanr_0.9.0 devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 posterior_1.6.1 lubridate_1.9.4 \n [9] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0 readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 ggplot2_3.5.2 \n[17] tidyverse_2.0.0 \n\nloaded via a namespace (and not attached):\n [1] tidyselect_1.2.1 farver_2.1.2 fastmap_1.2.0 gh_1.5.0 tensorA_0.36.2.1 promises_1.3.3 digest_0.6.37 \n [8] timechange_0.3.0 mime_0.13 lifecycle_1.0.4 ellipsis_0.3.2 processx_3.8.6 magrittr_2.0.3 compiler_4.5.1 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b/posterior_database/reference_posteriors/draws/info/radon_mn-radon_pooled.info.json new file mode 100644 index 00000000..67931740 --- /dev/null +++ b/posterior_database/reference_posteriors/draws/info/radon_mn-radon_pooled.info.json @@ -0,0 +1,45 @@ +{ + "name": "radon_mn-radon_pooled", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["alpha", "beta", "sigma_y"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [9703.0025334594629, 9898.5946544181934, 9865.8289333080211], + "effective_sample_size_tail": [9786.8759133524618, 9626.3440283246327, 9106.3628054942565], + "r_hat": [1.00010489188988, 1.00042967097092, 1.00003007259749], + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [1.99066593541726, 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/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1\n\nlocale:\n[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8\n\ntime zone: Europe/Stockholm\ntzcode source: internal\n\nattached base packages:\n[1] stats graphics grDevices utils datasets methods base \n\nother attached packages:\n [1] posteriordb_0.3.3 testthat_3.2.3 cmdstanr_0.9.0 \n [4] devtools_2.4.5 usethis_3.1.0 jsonlite_2.0.0 \n [7] posterior_1.6.1 lubridate_1.9.4 forcats_1.0.0 \n[10] stringr_1.5.1 dplyr_1.1.4 purrr_1.1.0 \n[13] readr_2.1.5 tidyr_1.3.1 tibble_3.3.0 \n[16] ggplot2_3.5.2 tidyverse_2.0.0 \n\nloaded via a namespace (and not attached):\n [1] tidyselect_1.2.1 farver_2.1.2 fastmap_1.2.0 \n [4] gh_1.5.0 tensorA_0.36.2.1 promises_1.3.3 \n [7] digest_0.6.37 timechange_0.3.0 mime_0.13 \n[10] lifecycle_1.0.4 waldo_0.6.2 ellipsis_0.3.2 \n[13] processx_3.8.6 magrittr_2.0.3 compiler_4.5.1 \n[16] rlang_1.1.6 sass_0.4.10 tools_4.5.1 \n[19] yaml_2.3.10 data.table_1.17.8 knitr_1.50 \n[22] htmlwidgets_1.6.4 bit_4.6.0 pkgbuild_1.4.8 \n[25] RColorBrewer_1.1-3 pkgload_1.4.0 abind_1.4-8 \n[28] miniUI_0.1.2 withr_3.0.2 desc_1.4.3 \n[31] grid_4.5.1 urlchecker_1.0.1 profvis_0.4.0 \n[34] xtable_1.8-4 scales_1.4.0 cli_3.6.5 \n[37] rmarkdown_2.29 crayon_1.5.3 generics_0.1.4 \n[40] remotes_2.5.0 rstudioapi_0.17.1 tzdb_0.5.0 \n[43] sessioninfo_1.2.3 cachem_1.1.0 parallel_4.5.1 \n[46] matrixStats_1.5.0 vctrs_0.6.5 hms_1.1.3 \n[49] bit64_4.6.0-1 jquerylib_0.1.4 glue_1.8.0 \n[52] ps_1.9.1 distributional_0.5.0 stringi_1.8.7 \n[55] gtable_0.3.6 later_1.4.2 pillar_1.11.0 \n[58] htmltools_0.5.8.1 brio_1.1.5 R6_2.6.1 \n[61] rprojroot_2.1.0 vroom_1.6.5 evaluate_1.0.4 \n[64] shiny_1.11.1 backports_1.5.0 memoise_2.0.1 \n[67] httpuv_1.6.16 bslib_0.9.0 Rcpp_1.1.0 \n[70] checkmate_2.3.2 xfun_0.52 fs_1.6.6 \n[73] pkgconfig_2.0.3 " + } +} diff --git a/posterior_database/reference_posteriors/draws/info/wells_data-wells_dist.info.json b/posterior_database/reference_posteriors/draws/info/wells_data-wells_dist.info.json new file mode 100644 index 00000000..cf215994 --- /dev/null +++ b/posterior_database/reference_posteriors/draws/info/wells_data-wells_dist.info.json @@ -0,0 +1,45 @@ +{ + "name": "wells_data-wells_dist", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["beta[1]", "beta[2]"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [9611.6477984781231, 9825.496125138794], + "effective_sample_size_tail": [9472.7272323234411, 9478.8243513888465], + "r_hat": [1.00007071859007, 1.00012293469916], + "divergent_transitions": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0], + "expected_fraction_of_missing_information": [2.00014654816598, 1.96123229715579, 1.96117242315446, 2.0528894913968, 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a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/radon_mn-radon_pooled.info.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/radon_mn-radon_pooled.info.json new file mode 100644 index 00000000..1b179475 --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/radon_mn-radon_pooled.info.json @@ -0,0 +1,46 @@ +{ + "name": "radon_mn-radon_pooled", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["alpha", "beta", "sigma_y"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [9703.0025334594629, 9898.5946544181934, 9865.8289333080211], + "effective_sample_size_tail": [9786.8759133524618, 9626.3440283246327, 9106.3628054942565], + "r_hat": 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a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/wells_data-wells_dist100_model.info.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/wells_data-wells_dist100_model.info.json new file mode 100644 index 00000000..dccb173f --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/info/wells_data-wells_dist100_model.info.json @@ -0,0 +1,46 @@ +{ + "name": "wells_data-wells_dist100_model", + "inference": { + "method": "stan_sampling", + "method_arguments": { + "chains": 10, + "iter": 20000, + "warmup": 10000, + "thin": 10, + "seed": 2544, + "control": { + "adapt_delta": 0.8 + } + } + }, + "diagnostics": { + "diagnostics_information": { + "names": ["alpha", "beta[1]"] + }, + "ndraws": 10000, + "nchains": 10, + "effective_sample_size_bulk": [10216.540021158913, 9951.1820426210525], + "effective_sample_size_tail": [9845.2756185215785, 9907.8049025851797], + "r_hat": 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a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_1_data-Rate_1_model.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_1_data-Rate_1_model.json new file mode 100644 index 00000000..1e7e8189 --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_1_data-Rate_1_model.json @@ -0,0 +1,5 @@ +{ + "names": "theta", + "mean_value": 0.26994058370029783, + "mcse_mean": 0.0014213989354137165 +} diff --git a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_2_data-Rate_2_model.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_2_data-Rate_2_model.json new file mode 100644 index 00000000..a0e897d6 --- /dev/null +++ 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a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_5_data-Rate_5_model.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_5_data-Rate_5_model.json new file mode 100644 index 00000000..0bacbdc1 --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/Rate_5_data-Rate_5_model.json @@ -0,0 +1,5 @@ +{ + "names": "theta", + "mean_squared_value": 0.26008118797115659, + "mcse_mean": 0.0010419523301447966 +} diff --git a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/dogs-dogs.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/dogs-dogs.json new file mode 100644 index 00000000..cd84f672 --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/dogs-dogs.json @@ -0,0 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a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/nes_logit_data-nes_logit_model.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/nes_logit_data-nes_logit_model.json new file mode 100644 index 00000000..ccd1f0eb --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/nes_logit_data-nes_logit_model.json @@ -0,0 +1,5 @@ +{ + "names": ["alpha", "beta[1]"], + "mean_squared_value": [2.0181230712052045, 0.11065946163891689], + "mcse_mean": [0.0054368241074216192, 0.00037879301933992993] +} diff --git a/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/radon_all-radon_pooled.json b/posterior_database/reference_posteriors/summary_statistics/mean_squared_value/mean_squared_value/radon_all-radon_pooled.json new file mode 100644 index 00000000..920b0be6 --- /dev/null +++ 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[0.0019191235938921616, 0.00057357708544462959] +} diff --git a/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/radon_all-radon_pooled.json b/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/radon_all-radon_pooled.json new file mode 100644 index 00000000..18183d5e --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/radon_all-radon_pooled.json @@ -0,0 +1,5 @@ +{ + "names": ["alpha", "beta", "sigma_y"], + "mean_value": [0.96124152559999998, -0.1519636617, 1.0588122440000001], + "mcse_mean": [9.8984479217974805e-05, 6.8903778103832466e-05, 6.6199901579426778e-05] +} diff --git a/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/radon_mn-radon_pooled.json b/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/radon_mn-radon_pooled.json new file mode 100644 index 00000000..ec7d48be --- /dev/null +++ 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a/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/wells_data-wells_dist100_model.json b/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/wells_data-wells_dist100_model.json new file mode 100644 index 00000000..d0014a65 --- /dev/null +++ b/posterior_database/reference_posteriors/summary_statistics/mean_value/mean_value/wells_data-wells_dist100_model.json @@ -0,0 +1,5 @@ +{ + "names": ["alpha", "beta[1]"], + "mean_value": [0.60671024790000005, -0.62214344399999999], + "mcse_mean": [0.00059559889769124905, 0.00097753701292564808] +}