The sccomp_remove_outliers function takes as input a table of cell counts with columns for cell-group identifier, sample identifier, integer count, and factors (continuous or discrete). The user can define a linear model using an input R formula, where the first factor is the factor of interest. Alternatively, sccomp accepts single-cell data containers (e.g., Seurat, SingleCellExperiment, cell metadata, or group-size) and derives the count data from cell metadata.
Usage
sccomp_remove_outliers(
.estimate,
percent_false_positive = 5,
cores = detectCores(),
inference_method = attr(.estimate, "inference_method"),
output_directory = "sccomp_draws_files",
verbose = TRUE,
mcmc_seed = sample_seed(),
max_sampling_iterations = 20000,
enable_loo = FALSE,
sig_figs = 9,
cache_stan_model = sccomp_stan_models_cache_dir,
portable = TRUE,
approximate_posterior_inference = NULL,
variational_inference = NULL,
...
)Arguments
- .estimate
A tibble including a cell_group name column, sample name column, read counts column (optional depending on the input class), and factor columns.
- percent_false_positive
A real number between 0 and 100 (not inclusive), used to identify outliers with a specific false positive rate.
- cores
Integer, the number of cores to be used for parallel calculations.
- inference_method
Character string specifying the inference method to use ('pathfinder', 'hmc', or 'variational').
- output_directory
A character string specifying the output directory for Stan draws.
- verbose
Logical, whether to print progression details.
- mcmc_seed
Integer, used for Markov-chain Monte Carlo reproducibility. By default, a random number is sampled from 1 to 999999.
- max_sampling_iterations
Integer, limits the maximum number of iterations in case a large dataset is used, to limit computation time.
- enable_loo
Logical, whether to enable model comparison using the R package LOO. This is useful for comparing fits between models, similar to ANOVA.
- sig_figs
Number of significant figures to use for Stan model output. Default is 9.
- cache_stan_model
A character string specifying the cache directory for compiled Stan models. The sccomp version will be automatically appended to ensure version isolation. Default is
sccomp_stan_models_cache_dirwhich points to~/.sccomp_models.- portable
Logical, whether to keep the result portable by caching required draws in memory and removing Stan draw CSV files after fitting. Default is TRUE to save disk space and move needed values into memory. Set to FALSE to keep draw CSV files on disk.
- approximate_posterior_inference
DEPRECATED, use the
variational_inferenceargument.- variational_inference
DEPRECATED Logical, whether to use variational Bayes for posterior inference. It is faster and convenient. Setting this argument to
FALSEruns full Bayesian (Hamiltonian Monte Carlo) inference, which is slower but the gold standard.- ...
Additional arguments passed to the
cmdstanr::samplefunction.
Value
A tibble (tbl), with the following columns:
cell_group - The cell groups being tested.
parameter - The parameter being estimated from the design matrix described by the input formula_composition and formula_variability.
factor - The covariate factor in the formula, if applicable (e.g., not present for Intercept or contrasts).
c_lower - Lower (2.5%) quantile of the posterior distribution for a composition (c) parameter.
c_effect - Mean of the posterior distribution for a composition (c) parameter.
c_upper - Upper (97.5%) quantile of the posterior distribution for a composition (c) parameter.
c_rhat - R-hat convergence diagnostic for the composition (c) parameter; values close to 1.0 indicate convergence.
c_ess_bulk - Bulk effective sample size for the composition (c) parameter; higher is better.
c_ess_tail - Tail effective sample size for the composition (c) parameter; higher is better.
v_lower - Lower (2.5%) quantile of the posterior distribution for a variability (v) parameter.
v_effect - Mean of the posterior distribution for a variability (v) parameter.
v_upper - Upper (97.5%) quantile of the posterior distribution for a variability (v) parameter.
v_rhat - R-hat convergence diagnostic for the variability (v) parameter.
v_ess_bulk - Bulk effective sample size for the variability (v) parameter.
v_ess_tail - Tail effective sample size for the variability (v) parameter.
Note: pH0 and FDR columns are not computed by sccomp_remove_outliers(). Run sccomp_test() on the result to obtain hypothesis-test statistics.
The function also attaches several attributes to the result:
count_data - The original count data used in the analysis, stored as an attribute for efficient access.
model_input - The model input data used for fitting.
formula_composition - The formula used for composition modeling.
formula_variability - The formula used for variability modeling.
fit - The Stan fit object (if pass_fit = TRUE).
References
S. Mangiola, A.J. Roth-Schulze, M. Trussart, E. Zozaya-Valdés, M. Ma, Z. Gao, A.F. Rubin, T.P. Speed, H. Shim, & A.T. Papenfuss, sccomp: Robust differential composition and variability analysis for single-cell data, Proc. Natl. Acad. Sci. U.S.A. 120 (33) e2203828120, https://doi.org/10.1073/pnas.2203828120 (2023).
Examples
print("cmdstanr is needed to run this example.")
#> [1] "cmdstanr is needed to run this example."
# Note: Before running the example, ensure that the 'cmdstanr' package is installed:
# install.packages("cmdstanr", repos = c("https://stan-dev.r-universe.dev/", getOption("repos")))
# \donttest{
if (instantiate::stan_cmdstan_exists()) {
data("counts_obj")
estimate = sccomp_estimate(
counts_obj,
~ type,
~1,
"sample",
"cell_group",
"count",
cores = 1
) |>
sccomp_remove_outliers(cores = 1)
}
#> sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
#> sccomp says: estimation
#> sccomp says: the composition design matrix has columns: (Intercept), typecancer
#> sccomp says: the variability design matrix has columns: (Intercept)
#> Loading model from cache...
#> Path [1] :Initial log joint density = -481678.231158
#> Path [1] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 5.901e-03 2.167e-01 1.000e+00 1.000e+00 2988 -3.689e+03 -3.701e+03
#> Path [1] :Best Iter: [47] ELBO (-3689.370971) evaluations: (2988)
#> Path [2] :Initial log joint density = -481542.163837
#> Path [2] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.788e+05 1.331e-02 2.516e-01 1.000e+00 1.000e+00 3701 -3.679e+03 -3.685e+03
#> Path [2] :Best Iter: [60] ELBO (-3679.400461) evaluations: (3701)
#> Path [3] :Initial log joint density = -481563.290368
#> Path [3] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 9.323e-03 2.537e-01 1.000e+00 1.000e+00 3201 -3.684e+03 -3.685e+03
#> Path [3] :Best Iter: [55] ELBO (-3684.010662) evaluations: (3201)
#> Path [4] :Initial log joint density = -481102.925071
#> Path [4] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 2.905e-03 3.520e-01 5.625e-01 5.625e-01 2910 -3.691e+03 -3.704e+03
#> Path [4] :Best Iter: [41] ELBO (-3690.706549) evaluations: (2910)
#> Path [5] :Initial log joint density = -481772.334889
#> Path [5] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 7.164e-03 2.265e-01 1.000e+00 1.000e+00 3258 -3.684e+03 -3.685e+03
#> Path [5] :Best Iter: [55] ELBO (-3684.304842) evaluations: (3258)
#> Path [6] :Initial log joint density = -481923.142402
#> Path [6] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 64 -4.788e+05 7.937e-03 2.736e-01 1.000e+00 1.000e+00 3888 -3.681e+03 -3.697e+03
#> Path [6] :Best Iter: [61] ELBO (-3681.390202) evaluations: (3888)
#> Path [7] :Initial log joint density = -481876.508555
#> Path [7] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.788e+05 3.028e-02 3.026e-01 9.983e-01 9.983e-01 3649 -3.682e+03 -3.686e+03
#> Path [7] :Best Iter: [56] ELBO (-3682.126325) evaluations: (3649)
#> Path [8] :Initial log joint density = -481689.022118
#> Path [8] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 8.964e-03 2.672e-01 1.000e+00 1.000e+00 3193 -3.683e+03 -3.693e+03
#> Path [8] :Best Iter: [56] ELBO (-3682.864517) evaluations: (3193)
#> Path [9] :Initial log joint density = -481844.554164
#> Path [9] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 8.521e-03 2.608e-01 8.338e-01 8.338e-01 2825 -3.691e+03 -3.704e+03
#> Path [9] :Best Iter: [51] ELBO (-3691.153013) evaluations: (2825)
#> Path [10] :Initial log joint density = -482217.438572
#> Path [10] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.616e-02 3.331e-01 1.000e+00 1.000e+00 3241 -3.684e+03 -3.684e+03
#> Path [10] :Best Iter: [56] ELBO (-3683.740005) evaluations: (3241)
#> Path [11] :Initial log joint density = -481494.046713
#> Path [11] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.288e-02 1.883e-01 1.000e+00 1.000e+00 3339 -3.690e+03 -3.688e+03
#> Path [11] :Best Iter: [56] ELBO (-3687.988574) evaluations: (3339)
#> Path [12] :Initial log joint density = -481678.904165
#> Path [12] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 6.833e-03 2.055e-01 9.460e-01 9.460e-01 3356 -3.683e+03 -3.693e+03
#> Path [12] :Best Iter: [56] ELBO (-3683.408574) evaluations: (3356)
#> Path [13] :Initial log joint density = -481540.093775
#> Path [13] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 1.042e-02 2.524e-01 1.000e+00 1.000e+00 2917 -3.688e+03 -3.697e+03
#> Path [13] :Best Iter: [41] ELBO (-3688.442889) evaluations: (2917)
#> Path [14] :Initial log joint density = -481631.800459
#> Path [14] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.788e+05 2.205e-02 2.117e-01 1.000e+00 1.000e+00 3589 -3.682e+03 -3.683e+03
#> Path [14] :Best Iter: [60] ELBO (-3681.731222) evaluations: (3589)
#> Path [15] :Initial log joint density = -482486.174106
#> Path [15] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 9.549e-03 2.565e-01 1.000e+00 1.000e+00 3296 -3.688e+03 -3.686e+03
#> Path [15] :Best Iter: [57] ELBO (-3685.660094) evaluations: (3296)
#> Path [16] :Initial log joint density = -481498.297375
#> Path [16] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 1.172e-02 3.263e-01 1.000e+00 1.000e+00 2829 -3.693e+03 -3.705e+03
#> Path [16] :Best Iter: [45] ELBO (-3693.103115) evaluations: (2829)
#> Path [17] :Initial log joint density = -484936.480722
#> Path [17] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 6.201e-03 1.857e-01 1.000e+00 1.000e+00 3406 -3.687e+03 -3.684e+03
#> Path [17] :Best Iter: [59] ELBO (-3683.664174) evaluations: (3406)
#> Path [18] :Initial log joint density = -481537.473035
#> Path [18] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 3.096e-03 2.773e-01 5.992e-01 5.992e-01 3399 -3.684e+03 -3.691e+03
#> Path [18] :Best Iter: [58] ELBO (-3684.446198) evaluations: (3399)
#> Path [19] :Initial log joint density = -481827.093152
#> Path [19] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 4.551e-03 2.029e-01 8.636e-01 8.636e-01 3320 -3.683e+03 -3.694e+03
#> Path [19] :Best Iter: [55] ELBO (-3683.074552) evaluations: (3320)
#> Path [20] :Initial log joint density = -481960.805451
#> Path [20] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 1.040e-02 1.968e-01 1.000e+00 1.000e+00 2953 -3.687e+03 -3.700e+03
#> Path [20] :Best Iter: [51] ELBO (-3686.760042) evaluations: (2953)
#> Path [21] :Initial log joint density = -481796.400852
#> Path [21] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 4.662e-03 2.048e-01 8.644e-01 8.644e-01 3263 -3.686e+03 -3.691e+03
#> Path [21] :Best Iter: [55] ELBO (-3685.998576) evaluations: (3263)
#> Path [22] :Initial log joint density = -482421.750492
#> Path [22] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.393e-02 3.407e-01 1.000e+00 1.000e+00 3241 -3.684e+03 -3.694e+03
#> Path [22] :Best Iter: [56] ELBO (-3683.674269) evaluations: (3241)
#> Path [23] :Initial log joint density = -483300.412757
#> Path [23] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 5.988e-03 2.461e-01 1.000e+00 1.000e+00 3077 -3.691e+03 -3.683e+03
#> Path [23] :Best Iter: [55] ELBO (-3683.276285) evaluations: (3077)
#> Path [24] :Initial log joint density = -481476.904789
#> Path [24] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 6.563e-03 2.112e-01 1.000e+00 1.000e+00 2879 -3.690e+03 -3.695e+03
#> Path [24] :Best Iter: [44] ELBO (-3690.271102) evaluations: (2879)
#> Path [25] :Initial log joint density = -481926.667281
#> Path [25] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 8.521e-03 2.839e-01 8.981e-01 8.981e-01 3237 -3.684e+03 -3.694e+03
#> Path [25] :Best Iter: [55] ELBO (-3684.225750) evaluations: (3237)
#> Path [26] :Initial log joint density = -481634.869795
#> Path [26] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 3.781e-03 3.937e-01 5.423e-01 5.423e-01 3425 -3.685e+03 -3.698e+03
#> Path [26] :Best Iter: [58] ELBO (-3685.244871) evaluations: (3425)
#> Path [27] :Initial log joint density = -481479.923878
#> Path [27] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 63 -4.788e+05 6.910e-03 2.247e-01 6.021e-01 6.021e-01 3902 -3.680e+03 -3.691e+03
#> Path [27] :Best Iter: [61] ELBO (-3680.344727) evaluations: (3902)
#> Path [28] :Initial log joint density = -481537.164150
#> Path [28] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.788e+05 1.007e-02 1.960e-01 9.650e-01 9.650e-01 3675 -3.682e+03 -3.687e+03
#> Path [28] :Best Iter: [60] ELBO (-3681.979964) evaluations: (3675)
#> Path [29] :Initial log joint density = -481486.073937
#> Path [29] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.448e-02 3.196e-01 1.000e+00 1.000e+00 3185 -3.687e+03 -3.692e+03
#> Path [29] :Best Iter: [55] ELBO (-3686.584473) evaluations: (3185)
#> Path [30] :Initial log joint density = -481767.323486
#> Path [30] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 1.077e-02 2.611e-01 1.000e+00 1.000e+00 3086 -3.691e+03 -3.701e+03
#> Path [30] :Best Iter: [52] ELBO (-3691.011522) evaluations: (3086)
#> Path [31] :Initial log joint density = -481849.041897
#> Path [31] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 7.344e-03 2.155e-01 1.000e+00 1.000e+00 3290 -3.687e+03 -3.696e+03
#> Path [31] :Best Iter: [55] ELBO (-3686.813227) evaluations: (3290)
#> Path [32] :Initial log joint density = -481657.841355
#> Path [32] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 64 -4.788e+05 8.691e-03 2.565e-01 9.133e-01 9.133e-01 3897 -3.683e+03 -3.693e+03
#> Path [32] :Best Iter: [61] ELBO (-3683.470967) evaluations: (3897)
#> Path [33] :Initial log joint density = -482147.556691
#> Path [33] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 1.501e-02 2.801e-01 1.000e+00 1.000e+00 3333 -3.683e+03 -3.684e+03
#> Path [33] :Best Iter: [55] ELBO (-3682.830359) evaluations: (3333)
#> Path [34] :Initial log joint density = -481845.645030
#> Path [34] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 2.333e-03 2.937e-01 5.890e-01 5.890e-01 3356 -3.681e+03 -3.693e+03
#> Path [34] :Best Iter: [57] ELBO (-3681.349294) evaluations: (3356)
#> Path [35] :Initial log joint density = -483904.874570
#> Path [35] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 4.286e-03 3.309e-01 5.662e-01 5.662e-01 3193 -3.685e+03 -3.695e+03
#> Path [35] :Best Iter: [55] ELBO (-3685.434855) evaluations: (3193)
#> Path [36] :Initial log joint density = -483398.369735
#> Path [36] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.395e-02 3.479e-01 1.000e+00 1.000e+00 3208 -3.685e+03 -3.694e+03
#> Path [36] :Best Iter: [55] ELBO (-3684.891822) evaluations: (3208)
#> Path [37] :Initial log joint density = -481472.491622
#> Path [37] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 1.589e-02 2.284e-01 1.000e+00 1.000e+00 3446 -3.681e+03 -3.688e+03
#> Path [37] :Best Iter: [56] ELBO (-3681.149632) evaluations: (3446)
#> Path [38] :Initial log joint density = -481558.638655
#> Path [38] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.126e-02 2.883e-01 1.000e+00 1.000e+00 3187 -3.683e+03 -3.688e+03
#> Path [38] :Best Iter: [55] ELBO (-3682.704578) evaluations: (3187)
#> Path [39] :Initial log joint density = -481557.723373
#> Path [39] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 5.598e-03 2.277e-01 1.000e+00 1.000e+00 3220 -3.682e+03 -3.687e+03
#> Path [39] :Best Iter: [55] ELBO (-3681.727682) evaluations: (3220)
#> Path [40] :Initial log joint density = -483190.127441
#> Path [40] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 6.386e-03 2.708e-01 1.000e+00 1.000e+00 3192 -3.692e+03 -3.694e+03
#> Path [40] :Best Iter: [49] ELBO (-3692.356493) evaluations: (3192)
#> Path [41] :Initial log joint density = -481729.965220
#> Path [41] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 7.024e-03 2.597e-01 1.000e+00 1.000e+00 2828 -3.691e+03 -3.703e+03
#> Path [41] :Best Iter: [43] ELBO (-3690.754698) evaluations: (2828)
#> Path [42] :Initial log joint density = -481747.909159
#> Path [42] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 4.195e-03 2.997e-01 6.613e-01 6.613e-01 3073 -3.692e+03 -3.701e+03
#> Path [42] :Best Iter: [48] ELBO (-3692.150652) evaluations: (3073)
#> Path [43] :Initial log joint density = -483006.968488
#> Path [43] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 6.122e-03 3.433e-01 7.423e-01 7.423e-01 3464 -3.682e+03 -3.697e+03
#> Path [43] :Best Iter: [56] ELBO (-3681.881056) evaluations: (3464)
#> Path [44] :Initial log joint density = -481682.000121
#> Path [44] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 51 -4.788e+05 7.681e-03 2.677e-01 4.977e-01 1.000e+00 2752 -3.690e+03 -3.703e+03
#> Path [44] :Best Iter: [45] ELBO (-3690.492797) evaluations: (2752)
#> Path [45] :Initial log joint density = -482063.959020
#> Path [45] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.788e+05 6.129e-03 1.761e-01 1.000e+00 1.000e+00 3710 -3.685e+03 -3.693e+03
#> Path [45] :Best Iter: [58] ELBO (-3684.754154) evaluations: (3710)
#> Path [46] :Initial log joint density = -481364.351217
#> Path [46] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 7.684e-03 1.780e-01 9.628e-01 9.628e-01 3171 -3.692e+03 -3.691e+03
#> Path [46] :Best Iter: [55] ELBO (-3690.775840) evaluations: (3171)
#> Path [47] :Initial log joint density = -482175.520169
#> Path [47] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.788e+05 1.103e-02 3.971e-01 1.000e+00 1.000e+00 3738 -3.681e+03 -3.689e+03
#> Path [47] :Best Iter: [60] ELBO (-3681.369873) evaluations: (3738)
#> Path [48] :Initial log joint density = -482079.072666
#> Path [48] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.788e+05 1.445e-02 2.980e-01 1.000e+00 1.000e+00 3760 -3.681e+03 -3.684e+03
#> Path [48] :Best Iter: [61] ELBO (-3680.858659) evaluations: (3760)
#> Path [49] :Initial log joint density = -481559.357510
#> Path [49] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 6.194e-03 1.535e-01 8.886e-01 8.886e-01 3117 -3.694e+03 -3.691e+03
#> Path [49] :Best Iter: [55] ELBO (-3690.661483) evaluations: (3117)
#> Path [50] :Initial log joint density = -481686.759965
#> Path [50] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 9.629e-03 2.541e-01 1.000e+00 1.000e+00 3105 -3.686e+03 -3.686e+03
#> Path [50] :Best Iter: [55] ELBO (-3686.080241) evaluations: (3105)
#> Finished in 13.7 seconds.
#> sccomp says: to do hypothesis testing run `sccomp_test()`,
#> the `test_composition_above_logit_fold_change` = 0.1 equates to a change of ~10%, and
#> 0.7 equates to ~100% increase, if the baseline is ~0.1 proportion.
#> Use `sccomp_proportional_fold_change` to convert c_effect (linear) to proportion difference (non-linear).
#> sccomp says: auto-cleanup removed 1 draw files from 'sccomp_draws_files'
#> Loading model from cache...
#> Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...
#>
#> Chain 1 finished in 0.0 seconds.
#> sccomp says: outlier identification - step 1/2
#> Loading model from cache...
#> Path [1] :Initial log joint density = -427704.525907
#> Path [1] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.191e-01 1.285e+03 2.761e-02 5.108e-02 8069 -3.287e+03 -5.923e+07
#> Path [1] :Best Iter: [45] ELBO (-3286.992056) evaluations: (8069)
#> Path [2] :Initial log joint density = -427473.558206
#> Path [2] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.038e-01 1.914e+03 2.883e-02 2.883e-02 8239 -3.283e+03 -2.615e+04
#> Path [2] :Best Iter: [50] ELBO (-3283.301404) evaluations: (8239)
#> Path [3] :Initial log joint density = -427482.726710
#> Path [3] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.982e-02 5.136e+03 2.093e-02 2.093e-02 8308 -3.288e+03 -6.194e+05
#> Path [3] :Best Iter: [44] ELBO (-3288.205943) evaluations: (8308)
#> Path [4] :Initial log joint density = -427496.809011
#> Path [4] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.221e-02 1.470e+03 4.245e-02 4.245e-02 8369 -3.281e+03 -8.926e+03
#> Path [4] :Best Iter: [44] ELBO (-3281.473696) evaluations: (8369)
#> Path [5] :Initial log joint density = -427640.519208
#> Path [5] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.772e-02 5.396e+03 1.596e-02 1.596e-02 8115 -3.285e+03 -2.777e+06
#> Path [5] :Best Iter: [41] ELBO (-3284.979444) evaluations: (8115)
#> Path [6] :Initial log joint density = -427859.913385
#> Path [6] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.496e-02 2.698e+03 3.185e-02 3.185e-02 8153 -3.285e+03 -3.020e+05
#> Path [6] :Best Iter: [47] ELBO (-3284.869420) evaluations: (8153)
#> Path [7] :Initial log joint density = -428640.639482
#> Path [7] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.075e-02 1.465e+03 2.865e-02 5.048e-02 8461 -3.287e+03 -3.647e+04
#> Path [7] :Best Iter: [46] ELBO (-3286.598523) evaluations: (8461)
#> Path [8] :Initial log joint density = -427518.247966
#> Path [8] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.583e-02 3.171e+03 2.080e-02 2.080e-02 8351 -3.287e+03 -2.570e+08
#> Path [8] :Best Iter: [43] ELBO (-3286.800789) evaluations: (8351)
#> Path [9] :Initial log joint density = -427520.947823
#> Path [9] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.216e-02 2.304e+03 1.298e-02 2.636e-02 8204 -3.292e+03 -1.735e+05
#> Path [9] :Best Iter: [44] ELBO (-3291.978646) evaluations: (8204)
#> Path [10] :Initial log joint density = -427363.978792
#> Path [10] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.313e-02 3.972e+03 2.133e-02 2.133e-02 8299 -3.288e+03 -2.155e+05
#> Path [10] :Best Iter: [46] ELBO (-3287.963936) evaluations: (8299)
#> Path [11] :Initial log joint density = -427284.904811
#> Path [11] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.118e-02 1.903e+03 3.626e-02 3.626e-02 8308 -3.287e+03 -1.900e+04
#> Path [11] :Best Iter: [42] ELBO (-3287.103018) evaluations: (8308)
#> Path [12] :Initial log joint density = -427540.342981
#> Path [12] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.056e-02 2.024e+03 2.623e-02 2.623e-02 8140 -3.287e+03 -1.037e+05
#> Path [12] :Best Iter: [45] ELBO (-3287.206490) evaluations: (8140)
#> Path [13] :Initial log joint density = -427838.374160
#> Path [13] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.514e-02 1.942e+03 1.748e-02 6.219e-02 8332 -3.287e+03 -1.191e+06
#> Path [13] :Best Iter: [38] ELBO (-3287.293923) evaluations: (8332)
#> Path [14] :Initial log joint density = -430292.123340
#> Path [14] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.786e-02 3.080e+03 1.402e-02 1.402e-02 8191 -3.287e+03 -5.592e+05
#> Path [14] :Best Iter: [52] ELBO (-3286.943107) evaluations: (8191)
#> Path [15] :Initial log joint density = -428442.843832
#> Path [15] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.565e-02 1.607e+03 5.802e-02 5.802e-02 8123 -3.281e+03 -1.937e+04
#> Path [15] :Best Iter: [57] ELBO (-3281.350992) evaluations: (8123)
#> Path [16] :Initial log joint density = -427819.013065
#> Path [16] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.659e-02 3.019e+03 1.274e-02 1.274e-02 8424 -3.280e+03 -2.232e+05
#> Path [16] :Best Iter: [56] ELBO (-3279.717250) evaluations: (8424)
#> Path [17] :Initial log joint density = -428020.332443
#> Path [17] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.863e-02 1.968e+03 3.569e-02 3.569e-02 8156 -3.277e+03 -2.053e+04
#> Path [17] :Best Iter: [56] ELBO (-3276.690225) evaluations: (8156)
#> Path [18] :Initial log joint density = -427797.173710
#> Path [18] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.071e-02 3.716e+03 2.024e-02 2.024e-02 8186 -3.288e+03 -1.876e+04
#> Path [18] :Best Iter: [46] ELBO (-3287.805950) evaluations: (8186)
#> Path [19] :Initial log joint density = -432390.726917
#> Path [19] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.520e-02 1.528e+03 3.012e-02 5.134e-02 8383 -3.284e+03 -2.112e+04
#> Path [19] :Best Iter: [55] ELBO (-3283.525998) evaluations: (8383)
#> Path [20] :Initial log joint density = -427939.878905
#> Path [20] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.435e-02 1.749e+03 1.340e-02 3.394e-02 7960 -3.279e+03 -4.268e+06
#> Path [20] :Best Iter: [56] ELBO (-3279.039940) evaluations: (7960)
#> Path [21] :Initial log joint density = -427956.586031
#> Path [21] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.001e-01 7.573e+03 1.314e-02 2.586e-02 8388 -3.285e+03 -3.125e+08
#> Path [21] :Best Iter: [49] ELBO (-3285.050425) evaluations: (8388)
#> Path [22] :Initial log joint density = -427779.453204
#> Path [22] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.564e-02 1.507e+03 2.532e-02 4.443e-02 8284 -3.291e+03 -3.103e+05
#> Path [22] :Best Iter: [47] ELBO (-3290.940000) evaluations: (8284)
#> Path [23] :Initial log joint density = -428806.829805
#> Path [23] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.279e-02 1.578e+03 4.388e-02 4.388e-02 8109 -3.283e+03 -3.820e+04
#> Path [23] :Best Iter: [55] ELBO (-3283.085338) evaluations: (8109)
#> Path [24] :Initial log joint density = -427413.526396
#> Path [24] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.062e-02 1.312e+03 2.748e-02 2.748e-02 8083 -3.288e+03 -4.561e+04
#> Path [24] :Best Iter: [48] ELBO (-3287.584360) evaluations: (8083)
#> Path [25] :Initial log joint density = -427471.877431
#> Path [25] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.382e-02 2.053e+03 2.240e-02 4.548e-02 8060 -3.285e+03 -6.910e+04
#> Path [25] :Best Iter: [49] ELBO (-3285.255839) evaluations: (8060)
#> Path [26] :Initial log joint density = -427854.924419
#> Path [26] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.657e-02 2.782e+03 2.543e-02 2.543e-02 8298 -3.287e+03 -3.402e+04
#> Path [26] :Best Iter: [44] ELBO (-3286.688246) evaluations: (8298)
#> Path [27] :Initial log joint density = -427800.207539
#> Path [27] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.930e-02 2.756e+03 1.741e-02 1.741e-02 7931 -3.284e+03 -1.183e+04
#> Path [27] :Best Iter: [46] ELBO (-3283.905547) evaluations: (7931)
#> Path [28] :Initial log joint density = -428256.530822
#> Path [28] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.366e-02 1.911e+03 2.770e-02 2.770e-02 8111 -3.284e+03 -5.940e+03
#> Path [28] :Best Iter: [47] ELBO (-3283.809776) evaluations: (8111)
#> Path [29] :Initial log joint density = -427833.949622
#> Path [29] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.297e-02 6.511e+03 1.204e-02 1.204e-02 8452 -3.284e+03 -3.110e+06
#> Path [29] :Best Iter: [44] ELBO (-3283.732331) evaluations: (8452)
#> Path [30] :Initial log joint density = -429050.247954
#> Path [30] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.262e-02 2.857e+03 3.619e-02 3.619e-02 8156 -3.284e+03 -6.999e+04
#> Path [30] :Best Iter: [50] ELBO (-3284.498966) evaluations: (8156)
#> Path [31] :Initial log joint density = -427589.478775
#> Path [31] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.165e-02 1.879e+03 6.352e-02 6.352e-02 8169 -3.285e+03 -1.338e+04
#> Path [31] :Best Iter: [55] ELBO (-3285.193843) evaluations: (8169)
#> Path [32] :Initial log joint density = -427505.314937
#> Path [32] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.267e-01 6.550e+03 5.228e-02 5.228e-02 8310 -3.289e+03 -1.718e+04
#> Path [32] :Best Iter: [40] ELBO (-3288.746408) evaluations: (8310)
#> Path [33] :Initial log joint density = -427823.157241
#> Path [33] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.535e-02 1.201e+03 4.656e-02 4.656e-02 7961 -3.281e+03 -8.945e+04
#> Path [33] :Best Iter: [55] ELBO (-3281.194104) evaluations: (7961)
#> Path [34] :Initial log joint density = -428787.526344
#> Path [34] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.904e-02 1.907e+03 3.984e-02 3.984e-02 8247 -3.287e+03 -4.771e+04
#> Path [34] :Best Iter: [49] ELBO (-3287.123475) evaluations: (8247)
#> Path [35] :Initial log joint density = -428150.915481
#> Path [35] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.485e-02 8.907e+02 2.503e-02 2.503e-02 8180 -3.276e+03 -3.273e+05
#> Path [35] :Best Iter: [58] ELBO (-3275.653398) evaluations: (8180)
#> Path [36] :Initial log joint density = -427521.121801
#> Path [36] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.362e-02 1.778e+03 4.187e-02 1.031e-01 8189 -3.284e+03 -1.033e+05
#> Path [36] :Best Iter: [47] ELBO (-3284.370986) evaluations: (8189)
#> Path [37] :Initial log joint density = -427502.037677
#> Path [37] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.272e-02 2.092e+03 3.262e-02 3.262e-02 8385 -3.283e+03 -1.177e+05
#> Path [37] :Best Iter: [44] ELBO (-3282.721884) evaluations: (8385)
#> Path [38] :Initial log joint density = -427578.034741
#> Path [38] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.742e-02 3.798e+03 2.287e-02 2.287e-02 8501 -3.286e+03 -1.011e+05
#> Path [38] :Best Iter: [43] ELBO (-3286.394075) evaluations: (8501)
#> Path [39] :Initial log joint density = -427576.992114
#> Path [39] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.894e-02 2.937e+03 2.416e-02 2.416e-02 8349 -3.286e+03 -7.952e+07
#> Path [39] :Best Iter: [48] ELBO (-3285.667022) evaluations: (8349)
#> Path [40] :Initial log joint density = -428595.241928
#> Path [40] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.338e-02 4.444e+03 2.620e-02 2.620e-02 8501 -3.279e+03 -7.421e+05
#> Path [40] :Best Iter: [46] ELBO (-3279.323019) evaluations: (8501)
#> Path [41] :Initial log joint density = -427649.859707
#> Path [41] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.753e-02 9.369e+02 5.285e-02 1.123e-01 8104 -3.281e+03 -1.165e+04
#> Path [41] :Best Iter: [59] ELBO (-3280.767890) evaluations: (8104)
#> Path [42] :Initial log joint density = -427789.441832
#> Path [42] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.751e-02 3.550e+03 1.439e-02 3.340e-02 8287 -3.287e+03 -3.354e+05
#> Path [42] :Best Iter: [39] ELBO (-3287.342680) evaluations: (8287)
#> Path [43] :Initial log joint density = -427762.127651
#> Path [43] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.796e-02 1.465e+03 3.173e-02 3.173e-02 8035 -3.281e+03 -4.773e+06
#> Path [43] :Best Iter: [55] ELBO (-3281.383206) evaluations: (8035)
#> Path [44] :Initial log joint density = -431070.741479
#> Path [44] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 2.476e-02 3.286e+03 1.723e-02 1.723e-02 8431 -3.283e+03 -9.882e+03
#> Path [44] :Best Iter: [45] ELBO (-3282.704473) evaluations: (8431)
#> Path [45] :Initial log joint density = -427718.695429
#> Path [45] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.114e-02 3.895e+03 1.208e-02 2.248e-02 8218 -3.287e+03 -1.675e+04
#> Path [45] :Best Iter: [46] ELBO (-3286.614427) evaluations: (8218)
#> Path [46] :Initial log joint density = -427668.810895
#> Path [46] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.093e-02 2.728e+03 1.733e-02 1.733e-02 8465 -3.284e+03 -6.609e+06
#> Path [46] :Best Iter: [44] ELBO (-3283.699578) evaluations: (8465)
#> Path [47] :Initial log joint density = -427603.507783
#> Path [47] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.162e-02 1.148e+03 5.875e-02 5.875e-02 8122 -3.283e+03 -4.136e+04
#> Path [47] :Best Iter: [43] ELBO (-3282.829316) evaluations: (8122)
#> Path [48] :Initial log joint density = -429943.554657
#> Path [48] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 2.188e-02 2.014e+03 3.552e-02 3.552e-02 8214 -3.283e+03 -6.380e+03
#> Path [48] :Best Iter: [55] ELBO (-3283.295969) evaluations: (8214)
#> Path [49] :Initial log joint density = -427618.576695
#> Path [49] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.104e-01 3.494e+03 2.495e-02 2.495e-02 8228 -3.288e+03 -1.191e+06
#> Path [49] :Best Iter: [43] ELBO (-3288.128183) evaluations: (8228)
#> Path [50] :Initial log joint density = -428258.780652
#> Path [50] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.763e-02 1.345e+03 3.071e-02 5.876e-02 8338 -3.277e+03 -1.992e+04
#> Path [50] :Best Iter: [56] ELBO (-3276.600617) evaluations: (8338)
#> Finished in 30.5 seconds.
#> Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...
#>
#> Chain 1 finished in 0.0 seconds.
#> sccomp says: outlier-free model fitting - step 2/2
#> sccomp says: the composition design matrix has columns: (Intercept), typecancer
#> sccomp says: the variability design matrix has columns: (Intercept)
#> Loading model from cache...
#> Path [1] :Initial log joint density = -427704.525907
#> Path [1] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.191e-01 1.285e+03 2.761e-02 5.108e-02 8069 -3.287e+03 -5.923e+07
#> Path [1] :Best Iter: [45] ELBO (-3286.992056) evaluations: (8069)
#> Path [2] :Initial log joint density = -427473.558206
#> Path [2] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.038e-01 1.914e+03 2.883e-02 2.883e-02 8239 -3.283e+03 -2.615e+04
#> Path [2] :Best Iter: [50] ELBO (-3283.301404) evaluations: (8239)
#> Path [3] :Initial log joint density = -427482.726710
#> Path [3] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.982e-02 5.136e+03 2.093e-02 2.093e-02 8308 -3.288e+03 -6.194e+05
#> Path [3] :Best Iter: [44] ELBO (-3288.205943) evaluations: (8308)
#> Path [4] :Initial log joint density = -427496.809011
#> Path [4] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.221e-02 1.470e+03 4.245e-02 4.245e-02 8369 -3.281e+03 -8.926e+03
#> Path [4] :Best Iter: [44] ELBO (-3281.473696) evaluations: (8369)
#> Path [5] :Initial log joint density = -427640.519208
#> Path [5] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.772e-02 5.396e+03 1.596e-02 1.596e-02 8115 -3.285e+03 -2.777e+06
#> Path [5] :Best Iter: [41] ELBO (-3284.979444) evaluations: (8115)
#> Path [6] :Initial log joint density = -427859.913385
#> Path [6] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.496e-02 2.698e+03 3.185e-02 3.185e-02 8153 -3.285e+03 -3.020e+05
#> Path [6] :Best Iter: [47] ELBO (-3284.869420) evaluations: (8153)
#> Path [7] :Initial log joint density = -428640.639482
#> Path [7] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.075e-02 1.465e+03 2.865e-02 5.048e-02 8461 -3.287e+03 -3.647e+04
#> Path [7] :Best Iter: [46] ELBO (-3286.598523) evaluations: (8461)
#> Path [8] :Initial log joint density = -427518.247966
#> Path [8] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.583e-02 3.171e+03 2.080e-02 2.080e-02 8351 -3.287e+03 -2.570e+08
#> Path [8] :Best Iter: [43] ELBO (-3286.800789) evaluations: (8351)
#> Path [9] :Initial log joint density = -427520.947823
#> Path [9] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.216e-02 2.304e+03 1.298e-02 2.636e-02 8204 -3.292e+03 -1.735e+05
#> Path [9] :Best Iter: [44] ELBO (-3291.978646) evaluations: (8204)
#> Path [10] :Initial log joint density = -427363.978792
#> Path [10] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.313e-02 3.972e+03 2.133e-02 2.133e-02 8299 -3.288e+03 -2.155e+05
#> Path [10] :Best Iter: [46] ELBO (-3287.963936) evaluations: (8299)
#> Path [11] :Initial log joint density = -427284.904811
#> Path [11] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.118e-02 1.903e+03 3.626e-02 3.626e-02 8308 -3.287e+03 -1.900e+04
#> Path [11] :Best Iter: [42] ELBO (-3287.103018) evaluations: (8308)
#> Path [12] :Initial log joint density = -427540.342981
#> Path [12] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.056e-02 2.024e+03 2.623e-02 2.623e-02 8140 -3.287e+03 -1.037e+05
#> Path [12] :Best Iter: [45] ELBO (-3287.206490) evaluations: (8140)
#> Path [13] :Initial log joint density = -427838.374160
#> Path [13] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.514e-02 1.942e+03 1.748e-02 6.219e-02 8332 -3.287e+03 -1.191e+06
#> Path [13] :Best Iter: [38] ELBO (-3287.293923) evaluations: (8332)
#> Path [14] :Initial log joint density = -430292.123340
#> Path [14] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.786e-02 3.080e+03 1.402e-02 1.402e-02 8191 -3.287e+03 -5.592e+05
#> Path [14] :Best Iter: [52] ELBO (-3286.943107) evaluations: (8191)
#> Path [15] :Initial log joint density = -428442.843832
#> Path [15] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.565e-02 1.607e+03 5.802e-02 5.802e-02 8123 -3.281e+03 -1.937e+04
#> Path [15] :Best Iter: [57] ELBO (-3281.350992) evaluations: (8123)
#> Path [16] :Initial log joint density = -427819.013065
#> Path [16] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.659e-02 3.019e+03 1.274e-02 1.274e-02 8424 -3.280e+03 -2.232e+05
#> Path [16] :Best Iter: [56] ELBO (-3279.717250) evaluations: (8424)
#> Path [17] :Initial log joint density = -428020.332443
#> Path [17] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.863e-02 1.968e+03 3.569e-02 3.569e-02 8156 -3.277e+03 -2.053e+04
#> Path [17] :Best Iter: [56] ELBO (-3276.690225) evaluations: (8156)
#> Path [18] :Initial log joint density = -427797.173710
#> Path [18] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.071e-02 3.716e+03 2.024e-02 2.024e-02 8186 -3.288e+03 -1.876e+04
#> Path [18] :Best Iter: [46] ELBO (-3287.805950) evaluations: (8186)
#> Path [19] :Initial log joint density = -432390.726917
#> Path [19] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.520e-02 1.528e+03 3.012e-02 5.134e-02 8383 -3.284e+03 -2.112e+04
#> Path [19] :Best Iter: [55] ELBO (-3283.525998) evaluations: (8383)
#> Path [20] :Initial log joint density = -427939.878905
#> Path [20] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.435e-02 1.749e+03 1.340e-02 3.394e-02 7960 -3.279e+03 -4.268e+06
#> Path [20] :Best Iter: [56] ELBO (-3279.039940) evaluations: (7960)
#> Path [21] :Initial log joint density = -427956.586031
#> Path [21] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.001e-01 7.573e+03 1.314e-02 2.586e-02 8388 -3.285e+03 -3.125e+08
#> Path [21] :Best Iter: [49] ELBO (-3285.050425) evaluations: (8388)
#> Path [22] :Initial log joint density = -427779.453204
#> Path [22] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.564e-02 1.507e+03 2.532e-02 4.443e-02 8284 -3.291e+03 -3.103e+05
#> Path [22] :Best Iter: [47] ELBO (-3290.940000) evaluations: (8284)
#> Path [23] :Initial log joint density = -428806.829805
#> Path [23] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.279e-02 1.578e+03 4.388e-02 4.388e-02 8109 -3.283e+03 -3.820e+04
#> Path [23] :Best Iter: [55] ELBO (-3283.085338) evaluations: (8109)
#> Path [24] :Initial log joint density = -427413.526396
#> Path [24] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.062e-02 1.312e+03 2.748e-02 2.748e-02 8083 -3.288e+03 -4.561e+04
#> Path [24] :Best Iter: [48] ELBO (-3287.584360) evaluations: (8083)
#> Path [25] :Initial log joint density = -427471.877431
#> Path [25] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.382e-02 2.053e+03 2.240e-02 4.548e-02 8060 -3.285e+03 -6.910e+04
#> Path [25] :Best Iter: [49] ELBO (-3285.255839) evaluations: (8060)
#> Path [26] :Initial log joint density = -427854.924419
#> Path [26] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.657e-02 2.782e+03 2.543e-02 2.543e-02 8298 -3.287e+03 -3.402e+04
#> Path [26] :Best Iter: [44] ELBO (-3286.688246) evaluations: (8298)
#> Path [27] :Initial log joint density = -427800.207539
#> Path [27] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.930e-02 2.756e+03 1.741e-02 1.741e-02 7931 -3.284e+03 -1.183e+04
#> Path [27] :Best Iter: [46] ELBO (-3283.905547) evaluations: (7931)
#> Path [28] :Initial log joint density = -428256.530822
#> Path [28] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.366e-02 1.911e+03 2.770e-02 2.770e-02 8111 -3.284e+03 -5.940e+03
#> Path [28] :Best Iter: [47] ELBO (-3283.809776) evaluations: (8111)
#> Path [29] :Initial log joint density = -427833.949622
#> Path [29] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.297e-02 6.511e+03 1.204e-02 1.204e-02 8452 -3.284e+03 -3.110e+06
#> Path [29] :Best Iter: [44] ELBO (-3283.732331) evaluations: (8452)
#> Path [30] :Initial log joint density = -429050.247954
#> Path [30] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.262e-02 2.857e+03 3.619e-02 3.619e-02 8156 -3.284e+03 -6.999e+04
#> Path [30] :Best Iter: [50] ELBO (-3284.498966) evaluations: (8156)
#> Path [31] :Initial log joint density = -427589.478775
#> Path [31] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 7.165e-02 1.879e+03 6.352e-02 6.352e-02 8169 -3.285e+03 -1.338e+04
#> Path [31] :Best Iter: [55] ELBO (-3285.193843) evaluations: (8169)
#> Path [32] :Initial log joint density = -427505.314937
#> Path [32] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.267e-01 6.550e+03 5.228e-02 5.228e-02 8310 -3.289e+03 -1.718e+04
#> Path [32] :Best Iter: [40] ELBO (-3288.746408) evaluations: (8310)
#> Path [33] :Initial log joint density = -427823.157241
#> Path [33] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.535e-02 1.201e+03 4.656e-02 4.656e-02 7961 -3.281e+03 -8.945e+04
#> Path [33] :Best Iter: [55] ELBO (-3281.194104) evaluations: (7961)
#> Path [34] :Initial log joint density = -428787.526344
#> Path [34] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.904e-02 1.907e+03 3.984e-02 3.984e-02 8247 -3.287e+03 -4.771e+04
#> Path [34] :Best Iter: [49] ELBO (-3287.123475) evaluations: (8247)
#> Path [35] :Initial log joint density = -428150.915481
#> Path [35] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.485e-02 8.907e+02 2.503e-02 2.503e-02 8180 -3.276e+03 -3.273e+05
#> Path [35] :Best Iter: [58] ELBO (-3275.653398) evaluations: (8180)
#> Path [36] :Initial log joint density = -427521.121801
#> Path [36] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.362e-02 1.778e+03 4.187e-02 1.031e-01 8189 -3.284e+03 -1.033e+05
#> Path [36] :Best Iter: [47] ELBO (-3284.370986) evaluations: (8189)
#> Path [37] :Initial log joint density = -427502.037677
#> Path [37] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.272e-02 2.092e+03 3.262e-02 3.262e-02 8385 -3.283e+03 -1.177e+05
#> Path [37] :Best Iter: [44] ELBO (-3282.721884) evaluations: (8385)
#> Path [38] :Initial log joint density = -427578.034741
#> Path [38] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 4.742e-02 3.798e+03 2.287e-02 2.287e-02 8501 -3.286e+03 -1.011e+05
#> Path [38] :Best Iter: [43] ELBO (-3286.394075) evaluations: (8501)
#> Path [39] :Initial log joint density = -427576.992114
#> Path [39] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.894e-02 2.937e+03 2.416e-02 2.416e-02 8349 -3.286e+03 -7.952e+07
#> Path [39] :Best Iter: [48] ELBO (-3285.667022) evaluations: (8349)
#> Path [40] :Initial log joint density = -428595.241928
#> Path [40] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 9.338e-02 4.444e+03 2.620e-02 2.620e-02 8501 -3.279e+03 -7.421e+05
#> Path [40] :Best Iter: [46] ELBO (-3279.323019) evaluations: (8501)
#> Path [41] :Initial log joint density = -427649.859707
#> Path [41] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.753e-02 9.369e+02 5.285e-02 1.123e-01 8104 -3.281e+03 -1.165e+04
#> Path [41] :Best Iter: [59] ELBO (-3280.767890) evaluations: (8104)
#> Path [42] :Initial log joint density = -427789.441832
#> Path [42] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.751e-02 3.550e+03 1.439e-02 3.340e-02 8287 -3.287e+03 -3.354e+05
#> Path [42] :Best Iter: [39] ELBO (-3287.342680) evaluations: (8287)
#> Path [43] :Initial log joint density = -427762.127651
#> Path [43] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 6.796e-02 1.465e+03 3.173e-02 3.173e-02 8035 -3.281e+03 -4.773e+06
#> Path [43] :Best Iter: [55] ELBO (-3281.383206) evaluations: (8035)
#> Path [44] :Initial log joint density = -431070.741479
#> Path [44] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 2.476e-02 3.286e+03 1.723e-02 1.723e-02 8431 -3.283e+03 -9.882e+03
#> Path [44] :Best Iter: [45] ELBO (-3282.704473) evaluations: (8431)
#> Path [45] :Initial log joint density = -427718.695429
#> Path [45] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 3.114e-02 3.895e+03 1.208e-02 2.248e-02 8218 -3.287e+03 -1.675e+04
#> Path [45] :Best Iter: [46] ELBO (-3286.614427) evaluations: (8218)
#> Path [46] :Initial log joint density = -427668.810895
#> Path [46] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.093e-02 2.728e+03 1.733e-02 1.733e-02 8465 -3.284e+03 -6.609e+06
#> Path [46] :Best Iter: [44] ELBO (-3283.699578) evaluations: (8465)
#> Path [47] :Initial log joint density = -427603.507783
#> Path [47] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 8.162e-02 1.148e+03 5.875e-02 5.875e-02 8122 -3.283e+03 -4.136e+04
#> Path [47] :Best Iter: [43] ELBO (-3282.829316) evaluations: (8122)
#> Path [48] :Initial log joint density = -429943.554657
#> Path [48] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 2.188e-02 2.014e+03 3.552e-02 3.552e-02 8214 -3.283e+03 -6.380e+03
#> Path [48] :Best Iter: [55] ELBO (-3283.295969) evaluations: (8214)
#> Path [49] :Initial log joint density = -427618.576695
#> Path [49] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 1.104e-01 3.494e+03 2.495e-02 2.495e-02 8228 -3.288e+03 -1.191e+06
#> Path [49] :Best Iter: [43] ELBO (-3288.128183) evaluations: (8228)
#> Path [50] :Initial log joint density = -428258.780652
#> Path [50] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 100 -4.247e+05 5.763e-02 1.345e+03 3.071e-02 5.876e-02 8338 -3.277e+03 -1.992e+04
#> Path [50] :Best Iter: [56] ELBO (-3276.600617) evaluations: (8338)
#> Finished in 27.7 seconds.
#> sccomp says: auto-cleanup removed 1 draw files from 'sccomp_draws_files'
# }