DEPRECATED: Remove Unwanted Variation from sccomp Estimates
Source:R/sccomp_remove_unwanted_variation.R
sccomp_remove_unwanted_variation.RdThis function is DEPRECATED. Please use sccomp_remove_unwanted_effects instead.
This function uses the model to remove unwanted variation from a dataset using the estimates of the model.
For example, if you fit your data with the formula ~ factor_1 + factor_2 and use the formula ~ factor_1
to remove unwanted variation, the factor_2 effect will be factored out.
Usage
sccomp_remove_unwanted_variation(
.data,
formula_composition_keep = NULL,
formula_composition = NULL,
formula_variability = NULL,
cores = detectCores()
)Arguments
- .data
A tibble. The result of
sccomp_estimate.- formula_composition_keep
A formula. The formula describing the model for differential abundance, for example
~type. In this case, only the effect of thetypefactor will be preserved, while all other factors will be factored out.- formula_composition
DEPRECATED. Use
formula_composition_keepinstead.- formula_variability
DEPRECATED. Use
formula_variability_keepinstead.- cores
Integer, the number of cores to be used for parallel calculations.
Value
A tibble (tbl) with the following columns:
sample - A character column representing the sample name for which data was adjusted.
cell_group - A character column representing the cell group being tested.
adjusted_proportion - A numeric column representing the adjusted proportion after removing unwanted variation.
adjusted_counts - A numeric column representing the adjusted counts after removing unwanted variation.
logit_residuals - A numeric column representing the centered log-ratio residuals calculated after adjustment.
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")
estimates = sccomp_estimate(
counts_obj,
~ type, ~1, "sample", "cell_group", "count",
cores = 1
) |>
sccomp_remove_unwanted_variation()
}
#> Warning: `sccomp_remove_unwanted_variation()` was deprecated in sccomp 1.99.20.
#> ℹ sccomp says: sccomp_remove_unwanted_variation is deprecated. Please use
#> sccomp_remove_unwanted_effects() instead.
#> sccomp says: count column is an integer. The sum-constrained beta binomial model will be used
#> sccomp says: estimation
#> sccomp says: model design matrices
#> composition X: 2 parameters: (Intercept), typecancer
#> variability Xa: 1 parameter: (Intercept)
#> random effects: none
#> Loading model from cache...
#> Path [1] :Initial log joint density = -483859.353615
#> Path [1] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.787e+05 8.134e-03 2.403e-01 1.000e+00 1.000e+00 3617 -3.705e+03 -3.706e+03
#> Path [1] :Best Iter: [57] ELBO (-3704.553929) evaluations: (3617)
#> Path [2] :Initial log joint density = -481803.865839
#> Path [2] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 69 -4.787e+05 3.779e-03 2.173e-01 6.910e-01 6.910e-01 4392 -3.701e+03 -3.718e+03
#> Path [2] :Best Iter: [62] ELBO (-3701.167505) evaluations: (4392)
#> Path [3] :Initial log joint density = -481700.828998
#> Path [3] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 71 -4.787e+05 1.289e-02 2.009e-01 1.000e+00 1.000e+00 4634 -3.700e+03 -3.708e+03
#> Path [3] :Best Iter: [69] ELBO (-3700.480816) evaluations: (4634)
#> Path [4] :Initial log joint density = -481770.289114
#> Path [4] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.787e+05 1.034e-02 2.155e-01 1.000e+00 1.000e+00 3652 -3.705e+03 -3.709e+03
#> Path [4] :Best Iter: [58] ELBO (-3704.635949) evaluations: (3652)
#> Path [5] :Initial log joint density = -481785.917695
#> Path [5] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 71 -4.787e+05 2.435e-02 1.860e-01 1.000e+00 1.000e+00 4530 -3.700e+03 -3.700e+03
#> Path [5] :Best Iter: [71] ELBO (-3699.968798) evaluations: (4530)
#> Path [6] :Initial log joint density = -482268.080943
#> Path [6] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 75 -4.787e+05 2.715e-02 1.713e-01 1.000e+00 1.000e+00 5172 -3.700e+03 -3.702e+03
#> Path [6] :Best Iter: [71] ELBO (-3699.535238) evaluations: (5172)
#> Path [7] :Initial log joint density = -481358.332723
#> Path [7] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 8.065e-03 2.588e-01 1.000e+00 1.000e+00 3729 -3.704e+03 -3.716e+03
#> Path [7] :Best Iter: [58] ELBO (-3704.137494) evaluations: (3729)
#> Path [8] :Initial log joint density = -481395.600367
#> Path [8] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.787e+05 5.501e-03 1.941e-01 1.000e+00 1.000e+00 3357 -3.705e+03 -3.709e+03
#> Path [8] :Best Iter: [56] ELBO (-3705.325724) evaluations: (3357)
#> Path [9] :Initial log joint density = -481546.256869
#> Path [9] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 82 -4.787e+05 8.255e-03 1.685e-01 8.878e-01 8.878e-01 5556 -3.700e+03 -3.712e+03
#> Path [9] :Best Iter: [79] ELBO (-3700.485690) evaluations: (5556)
#> Path [10] :Initial log joint density = -483784.392181
#> Path [10] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 66 -4.787e+05 1.086e-02 1.685e-01 1.000e+00 1.000e+00 4122 -3.700e+03 -3.708e+03
#> Path [10] :Best Iter: [64] ELBO (-3699.521887) evaluations: (4122)
#> Path [11] :Initial log joint density = -481554.472407
#> Path [11] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.787e+05 3.909e-03 1.854e-01 7.673e-01 7.673e-01 3357 -3.705e+03 -3.722e+03
#> Path [11] :Best Iter: [57] ELBO (-3705.175437) evaluations: (3357)
#> Path [12] :Initial log joint density = -481367.459344
#> Path [12] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 67 -4.787e+05 1.810e-02 2.317e-01 1.000e+00 1.000e+00 4211 -3.703e+03 -3.703e+03
#> Path [12] :Best Iter: [58] ELBO (-3702.921514) evaluations: (4211)
#> Path [13] :Initial log joint density = -481825.008622
#> Path [13] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 82 -4.787e+05 8.073e-03 1.926e-01 1.000e+00 1.000e+00 5650 -3.697e+03 -3.709e+03
#> Path [13] :Best Iter: [80] ELBO (-3697.389043) evaluations: (5650)
#> Path [14] :Initial log joint density = -482229.366677
#> Path [14] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 74 -4.787e+05 1.766e-02 2.524e-01 1.000e+00 1.000e+00 4942 -3.697e+03 -3.701e+03
#> Path [14] :Best Iter: [73] ELBO (-3697.158354) evaluations: (4942)
#> Path [15] :Initial log joint density = -481479.330336
#> Path [15] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 64 -4.787e+05 8.705e-03 1.641e-01 8.743e-01 8.743e-01 3821 -3.702e+03 -3.712e+03
#> Path [15] :Best Iter: [60] ELBO (-3702.182552) evaluations: (3821)
#> Path [16] :Initial log joint density = -481401.636871
#> Path [16] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 4.938e-03 1.560e-01 8.159e-01 8.159e-01 3644 -3.702e+03 -3.712e+03
#> Path [16] :Best Iter: [61] ELBO (-3702.319322) evaluations: (3644)
#> Path [17] :Initial log joint density = -481561.392241
#> Path [17] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 77 -4.787e+05 2.316e-02 1.480e-01 1.000e+00 1.000e+00 5144 -3.699e+03 -3.701e+03
#> Path [17] :Best Iter: [73] ELBO (-3699.265200) evaluations: (5144)
#> Path [18] :Initial log joint density = -481431.002315
#> Path [18] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 6.475e-03 1.906e-01 8.082e-01 8.082e-01 3739 -3.703e+03 -3.715e+03
#> Path [18] :Best Iter: [60] ELBO (-3702.703693) evaluations: (3739)
#> Path [19] :Initial log joint density = -483166.832878
#> Path [19] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 67 -4.787e+05 1.513e-02 2.230e-01 9.221e-01 9.221e-01 4277 -3.702e+03 -3.710e+03
#> Path [19] :Best Iter: [66] ELBO (-3702.042927) evaluations: (4277)
#> Path [20] :Initial log joint density = -482308.013449
#> Path [20] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 70 -4.787e+05 1.690e-02 1.838e-01 9.186e-01 9.186e-01 4624 -3.698e+03 -3.708e+03
#> Path [20] :Best Iter: [69] ELBO (-3697.813642) evaluations: (4624)
#> Path [21] :Initial log joint density = -481872.032222
#> Path [21] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 71 -4.787e+05 1.051e-02 1.874e-01 1.000e+00 1.000e+00 4612 -3.704e+03 -3.701e+03
#> Path [21] :Best Iter: [71] ELBO (-3700.634052) evaluations: (4612)
#> Path [22] :Initial log joint density = -481285.104304
#> Path [22] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 76 -4.787e+05 4.705e-03 2.045e-01 7.859e-01 7.859e-01 4957 -3.700e+03 -3.705e+03
#> Path [22] :Best Iter: [73] ELBO (-3700.007615) evaluations: (4957)
#> Path [23] :Initial log joint density = -481566.875315
#> Path [23] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.787e+05 1.495e-02 3.195e-01 1.000e+00 1.000e+00 3590 -3.701e+03 -3.710e+03
#> Path [23] :Best Iter: [59] ELBO (-3700.963222) evaluations: (3590)
#> Path [24] :Initial log joint density = -484343.301320
#> Path [24] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 72 -4.787e+05 2.358e-02 2.312e-01 1.000e+00 1.000e+00 4602 -3.699e+03 -3.704e+03
#> Path [24] :Best Iter: [69] ELBO (-3698.755869) evaluations: (4602)
#> Path [25] :Initial log joint density = -481461.792992
#> Path [25] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 64 -4.787e+05 9.223e-03 2.394e-01 9.269e-01 9.269e-01 3880 -3.699e+03 -3.713e+03
#> Path [25] :Best Iter: [61] ELBO (-3699.336516) evaluations: (3880)
#> Path [26] :Initial log joint density = -481825.086213
#> Path [26] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 65 -4.787e+05 7.097e-03 1.809e-01 1.000e+00 1.000e+00 3956 -3.704e+03 -3.710e+03
#> Path [26] :Best Iter: [62] ELBO (-3703.735143) evaluations: (3956)
#> Path [27] :Initial log joint density = -481384.647944
#> Path [27] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 69 -4.787e+05 1.547e-02 2.675e-01 1.000e+00 1.000e+00 4279 -3.699e+03 -3.705e+03
#> Path [27] :Best Iter: [68] ELBO (-3698.616801) evaluations: (4279)
#> Path [28] :Initial log joint density = -481435.055990
#> Path [28] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 80 -4.787e+05 1.424e-02 1.715e-01 1.000e+00 1.000e+00 5467 -3.697e+03 -3.705e+03
#> Path [28] :Best Iter: [78] ELBO (-3697.292047) evaluations: (5467)
#> Path [29] :Initial log joint density = -481663.903316
#> Path [29] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 72 -4.787e+05 8.914e-03 1.773e-01 1.000e+00 1.000e+00 4697 -3.698e+03 -3.701e+03
#> Path [29] :Best Iter: [69] ELBO (-3698.458294) evaluations: (4697)
#> Path [30] :Initial log joint density = -484557.316914
#> Path [30] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.787e+05 4.701e-03 2.456e-01 8.907e-01 8.907e-01 3778 -3.706e+03 -3.718e+03
#> Path [30] :Best Iter: [59] ELBO (-3705.724501) evaluations: (3778)
#> Path [31] :Initial log joint density = -482191.071798
#> Path [31] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 72 -4.787e+05 1.437e-02 2.765e-01 4.769e-01 1.000e+00 4638 -3.702e+03 -3.709e+03
#> Path [31] :Best Iter: [66] ELBO (-3702.267108) evaluations: (4638)
#> Path [32] :Initial log joint density = -481519.303578
#> Path [32] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 77 -4.787e+05 1.370e-02 1.990e-01 1.000e+00 1.000e+00 5119 -3.701e+03 -3.705e+03
#> Path [32] :Best Iter: [74] ELBO (-3700.892029) evaluations: (5119)
#> Path [33] :Initial log joint density = -481330.580057
#> Path [33] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.787e+05 1.526e-02 2.229e-01 1.000e+00 1.000e+00 3384 -3.704e+03 -3.713e+03
#> Path [33] :Best Iter: [56] ELBO (-3704.013671) evaluations: (3384)
#> Path [34] :Initial log joint density = -481577.300438
#> Path [34] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.787e+05 1.858e-02 2.964e-01 1.000e+00 1.000e+00 3646 -3.701e+03 -3.707e+03
#> Path [34] :Best Iter: [59] ELBO (-3701.163762) evaluations: (3646)
#> Path [35] :Initial log joint density = -482161.258004
#> Path [35] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 80 -4.787e+05 1.407e-02 1.956e-01 1.000e+00 1.000e+00 5541 -3.701e+03 -3.701e+03
#> Path [35] :Best Iter: [80] ELBO (-3700.914931) evaluations: (5541)
#> Path [36] :Initial log joint density = -481280.595763
#> Path [36] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 7.833e-03 2.366e-01 1.000e+00 1.000e+00 3736 -3.706e+03 -3.713e+03
#> Path [36] :Best Iter: [58] ELBO (-3706.348122) evaluations: (3736)
#> Path [37] :Initial log joint density = -485054.493552
#> Path [37] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 66 -4.787e+05 2.063e-02 3.419e-01 1.000e+00 1.000e+00 4058 -3.701e+03 -3.707e+03
#> Path [37] :Best Iter: [64] ELBO (-3700.762731) evaluations: (4058)
#> Path [38] :Initial log joint density = -481932.417454
#> Path [38] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 80 -4.787e+05 1.375e-02 1.463e-01 1.000e+00 1.000e+00 5524 -3.701e+03 -3.702e+03
#> Path [38] :Best Iter: [73] ELBO (-3701.112213) evaluations: (5524)
#> Path [39] :Initial log joint density = -481610.511162
#> Path [39] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.787e+05 7.545e-03 2.490e-01 1.000e+00 1.000e+00 3402 -3.704e+03 -3.715e+03
#> Path [39] :Best Iter: [56] ELBO (-3704.477809) evaluations: (3402)
#> Path [40] :Initial log joint density = -481621.605657
#> Path [40] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 75 -4.787e+05 7.250e-03 1.921e-01 9.185e-01 9.185e-01 4924 -3.697e+03 -3.706e+03
#> Path [40] :Best Iter: [73] ELBO (-3697.082773) evaluations: (4924)
#> Path [41] :Initial log joint density = -482574.412602
#> Path [41] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 69 -4.787e+05 1.116e-02 1.919e-01 8.640e-01 8.640e-01 4592 -3.701e+03 -3.713e+03
#> Path [41] :Best Iter: [67] ELBO (-3700.685234) evaluations: (4592)
#> Path [42] :Initial log joint density = -481624.925636
#> Path [42] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 70 -4.787e+05 1.301e-02 2.467e-01 9.706e-01 9.706e-01 4501 -3.700e+03 -3.707e+03
#> Path [42] :Best Iter: [68] ELBO (-3699.636056) evaluations: (4501)
#> Path [43] :Initial log joint density = -485666.962652
#> Path [43] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 73 -4.787e+05 7.956e-03 2.372e-01 1.000e+00 1.000e+00 4845 -3.703e+03 -3.709e+03
#> Path [43] :Best Iter: [70] ELBO (-3703.395732) evaluations: (4845)
#> Path [44] :Initial log joint density = -481908.261271
#> Path [44] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 70 -4.787e+05 2.654e-02 2.228e-01 1.000e+00 1.000e+00 4581 -3.700e+03 -3.701e+03
#> Path [44] :Best Iter: [68] ELBO (-3699.500996) evaluations: (4581)
#> Path [45] :Initial log joint density = -481169.751074
#> Path [45] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.787e+05 1.149e-02 2.317e-01 9.403e-01 9.403e-01 3559 -3.702e+03 -3.711e+03
#> Path [45] :Best Iter: [59] ELBO (-3702.072987) evaluations: (3559)
#> Path [46] :Initial log joint density = -481451.925177
#> Path [46] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 66 -4.787e+05 2.696e-03 2.844e-01 5.882e-01 5.882e-01 4056 -3.700e+03 -3.715e+03
#> Path [46] :Best Iter: [64] ELBO (-3699.875744) evaluations: (4056)
#> Path [47] :Initial log joint density = -481492.659552
#> Path [47] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 68 -4.787e+05 9.070e-03 2.296e-01 8.029e-01 8.029e-01 4326 -3.700e+03 -3.711e+03
#> Path [47] :Best Iter: [66] ELBO (-3699.733115) evaluations: (4326)
#> Path [48] :Initial log joint density = -481748.425265
#> Path [48] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 1.320e-02 2.319e-01 1.000e+00 1.000e+00 3744 -3.705e+03 -3.706e+03
#> Path [48] :Best Iter: [59] ELBO (-3704.934832) evaluations: (3744)
#> Path [49] :Initial log joint density = -481708.492702
#> Path [49] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.787e+05 1.297e-02 2.729e-01 1.000e+00 1.000e+00 3545 -3.702e+03 -3.710e+03
#> Path [49] :Best Iter: [60] ELBO (-3702.392220) evaluations: (3545)
#> Path [50] :Initial log joint density = -482961.146901
#> Path [50] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 62 -4.787e+05 8.107e-03 2.502e-01 1.000e+00 1.000e+00 3734 -3.704e+03 -3.712e+03
#> Path [50] :Best Iter: [58] ELBO (-3704.039987) evaluations: (3734)
#> Finished in 14.7 seconds.
#> sccomp says: to do hypothesis testing run `sccomp_test()`,
#> the `test_composition_above_CLR_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'
#> sccomp says: calculating residuals
#> Loading model from cache...
#> Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...
#>
#> Chain 1 Elapsed Time: 0.517 seconds (Generated Quantities)
#> Chain 1 finished in 0.0 seconds.
#> sccomp says: regressing out unwanted factors
#> Loading model from cache...
#> Running standalone generated quantities after 1 MCMC chain, with 1 thread(s) per chain...
#>
#> Chain 1 Elapsed Time: 0.52 seconds (Generated Quantities)
#> Chain 1 finished in 0.0 seconds.
# }