This function plots a summary of the results of the model.
Arguments
- x
A tibble including a cell_group name column | sample name column | read counts column | factor columns | Pvalue column | a significance column
- significance_threshold
Numeric value specifying the significance threshold for highlighting differences. Default is 0.025.
- test_composition_above_logit_fold_change
A positive integer. It is the effect threshold used for the hypothesis test. A value of 0.2 correspond to a change in cell proportion of 10% for a cell type with baseline proportion of 50%. That is, a cell type goes from 45% to 50%. When the baseline proportion is closer to 0 or 1 this effect thrshold has consistent value in the logit uncontrained scale.
- significance_statistic
Character vector indicating which statistic to highlight. Default is "FDR".
- show_fdr_message
Logical. Whether to show the Bayesian FDR interpretation message on the plot. Default is TRUE.
- ...
For internal use
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
)
# estimate |> plot()
}
#> 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)
#> Precompiled model not found. Compiling the model...
#> Running make /tmp/RtmpTPMtZ2/model-38841b6b29ae "STAN_THREADS=TRUE" \
#> "STANCFLAGS += --include-paths=/tmp/RtmpTPMtZ2/temp_libpath388479440d37/sccomp/stan --name='glm_multi_beta_binomial_model'"
#>
#> --- Translating Stan model to C++ code ---
#> bin/stanc --include-paths=/tmp/RtmpTPMtZ2/temp_libpath388479440d37/sccomp/stan --name='glm_multi_beta_binomial_model' --o=/tmp/RtmpTPMtZ2/model-38841b6b29ae.hpp /tmp/RtmpTPMtZ2/model-38841b6b29ae.stan
#>
#> --- Compiling C++ code ---
#> g++ -Wno-deprecated-declarations -std=c++17 -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -Wno-class-memaccess -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.87.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -c -Wno-ignored-attributes -x c++ -o /tmp/RtmpTPMtZ2/model-38841b6b29ae.o /tmp/RtmpTPMtZ2/model-38841b6b29ae.hpp
#>
#> --- Linking model ---
#> g++ -Wno-deprecated-declarations -std=c++17 -pthread -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes -Wno-class-memaccess -DSTAN_THREADS -I stan/lib/stan_math/lib/tbb_2020.3/include -O3 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.87.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -DBOOST_DISABLE_ASSERTS -Wl,-L,"/home/runner/.cmdstan/cmdstan-2.37.0/stan/lib/stan_math/lib/tbb" -Wl,-rpath,"/home/runner/.cmdstan/cmdstan-2.37.0/stan/lib/stan_math/lib/tbb" /tmp/RtmpTPMtZ2/model-38841b6b29ae.o src/cmdstan/main_threads.o -ltbb stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a stan/lib/stan_math/lib/tbb/libtbb.so.2 -o /tmp/RtmpTPMtZ2/model-38841b6b29ae
#> rm /tmp/RtmpTPMtZ2/model-38841b6b29ae.hpp /tmp/RtmpTPMtZ2/model-38841b6b29ae.o
#> Model compiled and saved to cache successfully.
#> Path [1] :Initial log joint density = -481591.693540
#> Path [1] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.548e-02 3.349e-01 1.000e+00 1.000e+00 3299 -3.704e+03 -3.704e+03
#> Path [1] :Best Iter: [56] ELBO (-3703.871840) evaluations: (3299)
#> Path [2] :Initial log joint density = -481748.738466
#> Path [2] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 7.389e-03 2.295e-01 1.000e+00 1.000e+00 3065 -3.707e+03 -3.703e+03
#> Path [2] :Best Iter: [55] ELBO (-3702.729221) evaluations: (3065)
#> Path [3] :Initial log joint density = -482597.964046
#> Path [3] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.082e-02 3.605e-01 1.000e+00 1.000e+00 3261 -3.699e+03 -3.708e+03
#> Path [3] :Best Iter: [55] ELBO (-3698.692066) evaluations: (3261)
#> Path [4] :Initial log joint density = -481746.681762
#> Path [4] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 9.409e-03 2.139e-01 1.000e+00 1.000e+00 3189 -3.709e+03 -3.703e+03
#> Path [4] :Best Iter: [55] ELBO (-3702.905641) evaluations: (3189)
#> Path [5] :Initial log joint density = -481578.137437
#> Path [5] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 6.587e-03 1.834e-01 9.227e-01 9.227e-01 2950 -3.705e+03 -3.719e+03
#> Path [5] :Best Iter: [47] ELBO (-3705.339247) evaluations: (2950)
#> Path [6] :Initial log joint density = -483875.477861
#> Path [6] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 1.098e-02 3.726e-01 1.000e+00 1.000e+00 3596 -3.698e+03 -3.707e+03
#> Path [6] :Best Iter: [55] ELBO (-3697.786841) evaluations: (3596)
#> Path [7] :Initial log joint density = -481670.678360
#> Path [7] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.853e-03 2.302e-01 6.237e-01 6.237e-01 3260 -3.705e+03 -3.709e+03
#> Path [7] :Best Iter: [56] ELBO (-3705.059536) evaluations: (3260)
#> Path [8] :Initial log joint density = -481871.158637
#> Path [8] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 61 -4.788e+05 1.185e-02 3.000e-01 1.000e+00 1.000e+00 3572 -3.699e+03 -3.704e+03
#> Path [8] :Best Iter: [60] ELBO (-3699.361472) evaluations: (3572)
#> Path [9] :Initial log joint density = -481562.755362
#> Path [9] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 1.109e-02 2.717e-01 5.129e-01 1.000e+00 3115 -3.707e+03 -3.716e+03
#> Path [9] :Best Iter: [39] ELBO (-3706.517543) evaluations: (3115)
#> Path [10] :Initial log joint density = -481670.762014
#> Path [10] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 9.158e-03 2.920e-01 1.000e+00 1.000e+00 2911 -3.708e+03 -3.716e+03
#> Path [10] :Best Iter: [48] ELBO (-3708.281679) evaluations: (2911)
#> Path [11] :Initial log joint density = -485447.340233
#> Path [11] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 5.084e-03 2.467e-01 1.000e+00 1.000e+00 3214 -3.709e+03 -3.707e+03
#> Path [11] :Best Iter: [55] ELBO (-3706.677840) evaluations: (3214)
#> Path [12] :Initial log joint density = -481434.559358
#> Path [12] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 4.558e-03 2.447e-01 1.000e+00 1.000e+00 3008 -3.708e+03 -3.724e+03
#> Path [12] :Best Iter: [46] ELBO (-3708.379004) evaluations: (3008)
#> Path [13] :Initial log joint density = -484087.061783
#> Path [13] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 5.234e-03 1.740e-01 1.000e+00 1.000e+00 3416 -3.704e+03 -3.708e+03
#> Path [13] :Best Iter: [55] ELBO (-3704.005635) evaluations: (3416)
#> Path [14] :Initial log joint density = -481678.267564
#> Path [14] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 5.423e-03 1.952e-01 1.000e+00 1.000e+00 2831 -3.708e+03 -3.711e+03
#> Path [14] :Best Iter: [43] ELBO (-3707.932600) evaluations: (2831)
#> Path [15] :Initial log joint density = -482423.890422
#> Path [15] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 1.255e-02 2.735e-01 1.000e+00 1.000e+00 3513 -3.696e+03 -3.704e+03
#> Path [15] :Best Iter: [57] ELBO (-3696.428362) evaluations: (3513)
#> Path [16] :Initial log joint density = -481853.944358
#> Path [16] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 5.136e-03 1.778e-01 1.000e+00 1.000e+00 3157 -3.707e+03 -3.715e+03
#> Path [16] :Best Iter: [44] ELBO (-3707.231036) evaluations: (3157)
#> Path [17] :Initial log joint density = -483082.905936
#> Path [17] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 1.471e-02 3.080e-01 1.000e+00 1.000e+00 3547 -3.697e+03 -3.701e+03
#> Path [17] :Best Iter: [57] ELBO (-3697.437522) evaluations: (3547)
#> Path [18] :Initial log joint density = -481872.548760
#> Path [18] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 8.222e-03 2.616e-01 9.841e-01 9.841e-01 3271 -3.697e+03 -3.713e+03
#> Path [18] :Best Iter: [56] ELBO (-3696.991463) evaluations: (3271)
#> Path [19] :Initial log joint density = -481778.755615
#> Path [19] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 1.116e-02 2.560e-01 1.000e+00 1.000e+00 3320 -3.705e+03 -3.704e+03
#> Path [19] :Best Iter: [58] ELBO (-3704.229455) evaluations: (3320)
#> Path [20] :Initial log joint density = -481620.547631
#> Path [20] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 7.046e-03 2.458e-01 1.000e+00 1.000e+00 3160 -3.705e+03 -3.707e+03
#> Path [20] :Best Iter: [48] ELBO (-3704.662678) evaluations: (3160)
#> Path [21] :Initial log joint density = -481930.410947
#> Path [21] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 6.867e-03 2.074e-01 1.000e+00 1.000e+00 3220 -3.704e+03 -3.705e+03
#> Path [21] :Best Iter: [55] ELBO (-3704.286265) evaluations: (3220)
#> Path [22] :Initial log joint density = -481638.587112
#> Path [22] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 49 -4.788e+05 7.921e-03 2.849e-01 8.459e-01 8.459e-01 2549 -3.707e+03 -3.720e+03
#> Path [22] :Best Iter: [39] ELBO (-3706.987514) evaluations: (2549)
#> Path [23] :Initial log joint density = -482118.464888
#> Path [23] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 9.959e-03 2.039e-01 1.000e+00 1.000e+00 3426 -3.702e+03 -3.702e+03
#> Path [23] :Best Iter: [59] ELBO (-3701.690432) evaluations: (3426)
#> Path [24] :Initial log joint density = -481778.219369
#> Path [24] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 1.134e-02 3.187e-01 1.000e+00 1.000e+00 2832 -3.708e+03 -3.714e+03
#> Path [24] :Best Iter: [50] ELBO (-3708.337530) evaluations: (2832)
#> Path [25] :Initial log joint density = -481764.271730
#> Path [25] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 1.174e-02 2.592e-01 1.000e+00 1.000e+00 3272 -3.706e+03 -3.705e+03
#> Path [25] :Best Iter: [55] ELBO (-3704.892597) evaluations: (3272)
#> Path [26] :Initial log joint density = -481774.958556
#> Path [26] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 9.584e-03 3.203e-01 1.000e+00 1.000e+00 3137 -3.705e+03 -3.709e+03
#> Path [26] :Best Iter: [48] ELBO (-3705.349923) evaluations: (3137)
#> Path [27] :Initial log joint density = -482583.637151
#> Path [27] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 5.042e-03 2.271e-01 1.000e+00 1.000e+00 3618 -3.702e+03 -3.710e+03
#> Path [27] :Best Iter: [57] ELBO (-3702.400771) evaluations: (3618)
#> Path [28] :Initial log joint density = -481723.352534
#> Path [28] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 1.456e-02 3.291e-01 1.000e+00 1.000e+00 3357 -3.698e+03 -3.704e+03
#> Path [28] :Best Iter: [58] ELBO (-3698.147026) evaluations: (3357)
#> Path [29] :Initial log joint density = -481776.672020
#> Path [29] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 1.046e-02 2.248e-01 1.000e+00 1.000e+00 3543 -3.700e+03 -3.699e+03
#> Path [29] :Best Iter: [60] ELBO (-3699.252206) evaluations: (3543)
#> Path [30] :Initial log joint density = -481620.998102
#> Path [30] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 55 -4.788e+05 9.000e-03 2.039e-01 1.000e+00 1.000e+00 3074 -3.708e+03 -3.702e+03
#> Path [30] :Best Iter: [55] ELBO (-3702.239281) evaluations: (3074)
#> Path [31] :Initial log joint density = -481406.523787
#> Path [31] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 1.004e-02 2.717e-01 7.881e-01 7.881e-01 2863 -3.707e+03 -3.718e+03
#> Path [31] :Best Iter: [41] ELBO (-3707.161354) evaluations: (2863)
#> Path [32] :Initial log joint density = -482297.012882
#> Path [32] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.025e-02 2.858e-01 1.000e+00 1.000e+00 3311 -3.704e+03 -3.706e+03
#> Path [32] :Best Iter: [56] ELBO (-3703.929082) evaluations: (3311)
#> Path [33] :Initial log joint density = -481815.365950
#> Path [33] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 7.372e-03 2.040e-01 1.000e+00 1.000e+00 3332 -3.703e+03 -3.706e+03
#> Path [33] :Best Iter: [55] ELBO (-3703.495450) evaluations: (3332)
#> Path [34] :Initial log joint density = -481570.693824
#> Path [34] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 6.505e-03 1.762e-01 1.000e+00 1.000e+00 3521 -3.698e+03 -3.709e+03
#> Path [34] :Best Iter: [56] ELBO (-3697.519428) evaluations: (3521)
#> Path [35] :Initial log joint density = -482106.915971
#> Path [35] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 58 -4.788e+05 1.189e-02 2.220e-01 1.000e+00 1.000e+00 3330 -3.702e+03 -3.704e+03
#> Path [35] :Best Iter: [57] ELBO (-3702.192787) evaluations: (3330)
#> Path [36] :Initial log joint density = -481532.168548
#> Path [36] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 1.144e-02 2.091e-01 1.000e+00 1.000e+00 2935 -3.709e+03 -3.711e+03
#> Path [36] :Best Iter: [48] ELBO (-3709.065981) evaluations: (2935)
#> Path [37] :Initial log joint density = -481702.550342
#> Path [37] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 54 -4.788e+05 8.515e-03 2.010e-01 1.000e+00 1.000e+00 2944 -3.710e+03 -3.712e+03
#> Path [37] :Best Iter: [47] ELBO (-3709.641366) evaluations: (2944)
#> Path [38] :Initial log joint density = -482996.098210
#> Path [38] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 5.678e-03 2.939e-01 1.000e+00 1.000e+00 3191 -3.707e+03 -3.708e+03
#> Path [38] :Best Iter: [49] ELBO (-3706.901778) evaluations: (3191)
#> Path [39] :Initial log joint density = -483845.405007
#> Path [39] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 1.128e-02 3.007e-01 1.000e+00 1.000e+00 3400 -3.701e+03 -3.706e+03
#> Path [39] :Best Iter: [55] ELBO (-3700.913097) evaluations: (3400)
#> Path [40] :Initial log joint density = -481904.676665
#> Path [40] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 3.892e-03 2.305e-01 7.568e-01 7.568e-01 3356 -3.702e+03 -3.713e+03
#> Path [40] :Best Iter: [57] ELBO (-3701.979184) evaluations: (3356)
#> Path [41] :Initial log joint density = -481558.174944
#> Path [41] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.474e-02 3.153e-01 1.000e+00 1.000e+00 3163 -3.702e+03 -3.707e+03
#> Path [41] :Best Iter: [55] ELBO (-3701.833966) evaluations: (3163)
#> Path [42] :Initial log joint density = -481586.057638
#> Path [42] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 5.110e-03 1.917e-01 1.000e+00 1.000e+00 3244 -3.704e+03 -3.706e+03
#> Path [42] :Best Iter: [55] ELBO (-3704.239994) evaluations: (3244)
#> Path [43] :Initial log joint density = -482319.267209
#> Path [43] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 4.611e-03 2.006e-01 1.000e+00 1.000e+00 3363 -3.703e+03 -3.711e+03
#> Path [43] :Best Iter: [56] ELBO (-3702.872951) evaluations: (3363)
#> Path [44] :Initial log joint density = -481304.464573
#> Path [44] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 53 -4.788e+05 3.950e-03 1.938e-01 7.304e-01 7.304e-01 2910 -3.707e+03 -3.721e+03
#> Path [44] :Best Iter: [43] ELBO (-3706.940704) evaluations: (2910)
#> Path [45] :Initial log joint density = -481600.997964
#> Path [45] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 1.271e-02 3.455e-01 1.000e+00 1.000e+00 2783 -3.709e+03 -3.713e+03
#> Path [45] :Best Iter: [50] ELBO (-3709.307636) evaluations: (2783)
#> Path [46] :Initial log joint density = -481489.480441
#> Path [46] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 59 -4.788e+05 4.707e-03 1.093e-01 8.153e-01 8.153e-01 3358 -3.698e+03 -3.717e+03
#> Path [46] :Best Iter: [57] ELBO (-3698.254954) evaluations: (3358)
#> Path [47] :Initial log joint density = -481949.776350
#> Path [47] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 57 -4.788e+05 1.207e-02 2.406e-01 1.000e+00 1.000e+00 3238 -3.699e+03 -3.699e+03
#> Path [47] :Best Iter: [56] ELBO (-3698.606069) evaluations: (3238)
#> Path [48] :Initial log joint density = -481385.989372
#> Path [48] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 52 -4.788e+05 6.272e-03 2.248e-01 4.590e-01 1.000e+00 2869 -3.709e+03 -3.717e+03
#> Path [48] :Best Iter: [46] ELBO (-3709.277588) evaluations: (2869)
#> Path [49] :Initial log joint density = -482299.926994
#> Path [49] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 56 -4.788e+05 1.703e-02 3.929e-01 1.000e+00 1.000e+00 3209 -3.701e+03 -3.708e+03
#> Path [49] :Best Iter: [55] ELBO (-3700.686816) evaluations: (3209)
#> Path [50] :Initial log joint density = -481389.624713
#> Path [50] : Iter log prob ||dx|| ||grad|| alpha alpha0 # evals ELBO Best ELBO Notes
#> 60 -4.788e+05 1.207e-02 1.597e-01 1.000e+00 1.000e+00 3495 -3.700e+03 -3.699e+03
#> Path [50] :Best Iter: [60] ELBO (-3698.793939) evaluations: (3495)
#> Finished in 13.5 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'
# }