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Run chosen pre-built model in Stan

Usage

hmde_run(model_template, ...)

Arguments

model_template

model template generated by hmde_model and updated by hmde_assign_data

...

additional arguments passed to rstan::sampling

Value

Stanfit model output

Examples

# basic usage of hmde_run
hmde_model("constant_single_ind") |>
  hmde_assign_data(Trout_Size_Data)|>
  hmde_run(chains = 1, iter = 1000,
           verbose = FALSE, show_messages = FALSE)
#> 
#> SAMPLING FOR MODEL 'constant_single_ind' NOW (CHAIN 1).
#> Chain 1: 
#> Chain 1: Gradient evaluation took 1.5e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.15 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1: 
#> Chain 1: 
#> Chain 1: Iteration:   1 / 1000 [  0%]  (Warmup)
#> Chain 1: Iteration: 100 / 1000 [ 10%]  (Warmup)
#> Chain 1: Iteration: 200 / 1000 [ 20%]  (Warmup)
#> Chain 1: Iteration: 300 / 1000 [ 30%]  (Warmup)
#> Chain 1: Iteration: 400 / 1000 [ 40%]  (Warmup)
#> Chain 1: Iteration: 500 / 1000 [ 50%]  (Warmup)
#> Chain 1: Iteration: 501 / 1000 [ 50%]  (Sampling)
#> Chain 1: Iteration: 600 / 1000 [ 60%]  (Sampling)
#> Chain 1: Iteration: 700 / 1000 [ 70%]  (Sampling)
#> Chain 1: Iteration: 800 / 1000 [ 80%]  (Sampling)
#> Chain 1: Iteration: 900 / 1000 [ 90%]  (Sampling)
#> Chain 1: Iteration: 1000 / 1000 [100%]  (Sampling)
#> Chain 1: 
#> Chain 1:  Elapsed Time: 0.052 seconds (Warm-up)
#> Chain 1:                0.034 seconds (Sampling)
#> Chain 1:                0.086 seconds (Total)
#> Chain 1: 
#> Inference for Stan model: constant_single_ind.
#> 1 chains, each with iter=1000; warmup=500; thin=1; 
#> post-warmup draws per chain=500, total post-warmup draws=500.
#> 
#>                                           mean se_mean   sd    2.5%     25%
#> ind_y_0                                  65.93    0.07 1.24   63.56   65.02
#> ind_beta                                  3.10    0.03 0.48    2.09    2.78
#> global_error_sigma                       11.09    0.04 0.69    9.81   10.64
#> y_hat[1]                                 65.93    0.07 1.24   63.56   65.02
#> y_hat[2]                                 71.87    0.03 0.97   69.97   71.22
#> y_hat[3]                                 78.39    0.06 1.49   75.33   77.40
#> y_hat[4]                                 84.65    0.12 2.31   79.68   83.14
#> y_hat[5]                                 65.93    0.07 1.24   63.56   65.02
#> y_hat[6]                                 71.82    0.03 0.97   69.93   71.18
#> y_hat[7]                                 78.14    0.06 1.46   75.14   77.14
#> y_hat[8]                                 84.42    0.11 2.28   79.50   82.96
#> y_hat[9]                                 65.93    0.07 1.24   63.56   65.02
#> y_hat[10]                                72.22    0.03 0.98   70.31   71.55
#> y_hat[11]                                79.06    0.07 1.57   75.78   78.03
#> y_hat[12]                                82.74    0.10 2.05   78.29   81.41
#> y_hat[13]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[14]                                68.40    0.05 1.04   66.41   67.64
#> y_hat[15]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[16]                                72.05    0.03 0.97   70.14   71.40
#> y_hat[17]                                78.00    0.06 1.44   75.03   77.01
#> y_hat[18]                                84.47    0.11 2.29   79.54   83.00
#> y_hat[19]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[20]                                68.57    0.05 1.03   66.61   67.84
#> y_hat[21]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[22]                                65.94    0.07 1.24   63.57   65.03
#> y_hat[23]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[24]                                71.38    0.04 0.96   69.48   70.72
#> y_hat[25]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[26]                                71.52    0.03 0.96   69.62   70.88
#> y_hat[27]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[28]                                71.80    0.03 0.97   69.91   71.16
#> y_hat[29]                                73.75    0.03 1.05   71.71   73.03
#> y_hat[30]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[31]                                68.23    0.06 1.05   66.23   67.48
#> y_hat[32]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[33]                                72.28    0.03 0.98   70.38   71.62
#> y_hat[34]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[35]                                72.23    0.03 0.98   70.33   71.57
#> y_hat[36]                                78.35    0.06 1.48   75.30   77.36
#> y_hat[37]                                84.02    0.11 2.22   79.19   82.60
#> y_hat[38]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[39]                                72.34    0.03 0.98   70.44   71.67
#> y_hat[40]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[41]                                72.60    0.03 0.99   70.67   71.92
#> y_hat[42]                                78.39    0.06 1.49   75.32   77.39
#> y_hat[43]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[44]                                71.79    0.03 0.97   69.90   71.16
#> y_hat[45]                                78.55    0.06 1.51   75.44   77.55
#> y_hat[46]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[47]                                72.15    0.03 0.98   70.24   71.49
#> y_hat[48]                                77.54    0.05 1.39   74.71   76.58
#> y_hat[49]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[50]                                72.42    0.03 0.99   70.51   71.75
#> y_hat[51]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[52]                                72.14    0.03 0.98   70.23   71.48
#> y_hat[53]                                78.11    0.06 1.46   75.11   77.11
#> y_hat[54]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[55]                                72.16    0.03 0.98   70.26   71.51
#> y_hat[56]                                72.18    0.03 0.98   70.27   71.52
#> y_hat[57]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[58]                                78.50    0.06 1.50   75.41   77.51
#> y_hat[59]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[60]                                72.28    0.03 0.98   70.38   71.62
#> y_hat[61]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[62]                                69.69    0.04 0.98   67.80   69.00
#> y_hat[63]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[64]                                72.06    0.03 0.97   70.15   71.41
#> y_hat[65]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[66]                                72.58    0.03 0.99   70.65   71.90
#> y_hat[67]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[68]                                71.68    0.03 0.97   69.79   71.05
#> y_hat[69]                                78.03    0.06 1.45   75.06   77.04
#> y_hat[70]                                81.20    0.08 1.84   77.21   79.96
#> y_hat[71]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[72]                                72.55    0.03 0.99   70.62   71.87
#> y_hat[73]                                74.75    0.04 1.12   72.54   73.97
#> y_hat[74]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[75]                                71.95    0.03 0.97   70.04   71.29
#> y_hat[76]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[77]                                68.74    0.05 1.02   66.77   68.03
#> y_hat[78]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[79]                                68.78    0.05 1.02   66.82   68.07
#> y_hat[80]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[81]                                68.57    0.05 1.03   66.60   67.83
#> y_hat[82]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[83]                                74.49    0.03 1.10   72.31   73.72
#> y_hat[84]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[85]                                68.65    0.05 1.03   66.68   67.93
#> y_hat[86]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[87]                                72.16    0.03 0.98   70.26   71.51
#> y_hat[88]                                78.28    0.06 1.48   75.25   77.29
#> y_hat[89]                                84.24    0.11 2.25   79.36   82.80
#> y_hat[90]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[91]                                71.11    0.04 0.96   69.22   70.44
#> y_hat[92]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[93]                                68.47    0.05 1.04   66.50   67.73
#> y_hat[94]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[95]                                76.16    0.04 1.25   73.71   75.26
#> y_hat[96]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[97]                                71.99    0.03 0.97   70.08   71.35
#> y_hat[98]                                75.93    0.04 1.22   73.57   75.06
#> y_hat[99]                                65.93    0.07 1.24   63.56   65.02
#> y_hat[100]                               71.98    0.03 0.97   70.06   71.32
#> y_hat[101]                               81.96    0.09 1.94   77.76   80.67
#> y_hat[102]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[103]                               71.39    0.04 0.96   69.50   70.74
#> y_hat[104]                               77.94    0.06 1.44   74.99   76.96
#> y_hat[105]                               81.57    0.09 1.89   77.48   80.29
#> y_hat[106]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[107]                               70.84    0.04 0.96   68.94   70.16
#> y_hat[108]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[109]                               71.57    0.03 0.96   69.68   70.93
#> y_hat[110]                               72.13    0.03 0.98   70.22   71.47
#> y_hat[111]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[112]                               72.73    0.03 1.00   70.79   72.05
#> y_hat[113]                               75.96    0.04 1.23   73.58   75.08
#> y_hat[114]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[115]                               72.20    0.03 0.98   70.29   71.54
#> y_hat[116]                               83.94    0.11 2.21   79.13   82.53
#> y_hat[117]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[118]                               66.65    0.07 1.17   64.36   65.77
#> y_hat[119]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[120]                               71.88    0.03 0.97   69.98   71.23
#> y_hat[121]                               78.29    0.06 1.48   75.25   77.30
#> y_hat[122]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[123]                               71.76    0.03 0.97   69.87   71.13
#> y_hat[124]                               77.68    0.05 1.41   74.81   76.73
#> y_hat[125]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[126]                               71.31    0.04 0.96   69.41   70.65
#> y_hat[127]                               77.78    0.06 1.42   74.88   76.82
#> y_hat[128]                               93.15    0.19 3.55   86.14   90.84
#> y_hat[129]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[130]                               71.90    0.03 0.97   70.00   71.25
#> y_hat[131]                               78.35    0.06 1.48   75.30   77.36
#> y_hat[132]                               87.62    0.14 2.73   81.98   85.85
#> y_hat[133]                               65.93    0.07 1.24   63.56   65.02
#> y_hat[134]                               78.35    0.06 1.48   75.30   77.36
#> y_hat[135]                               90.75    0.17 3.19   84.38   88.69
#> check_prior_pars_ind_beta[1]              0.00     NaN 0.00    0.00    0.00
#> check_prior_pars_ind_beta[2]              2.00     NaN 0.00    2.00    2.00
#> check_prior_pars_global_error_sigma[1]    0.00     NaN 0.00    0.00    0.00
#> check_prior_pars_global_error_sigma[2]    2.00     NaN 0.00    2.00    2.00
#> lp__                                   -391.12    0.09 1.28 -394.42 -391.87
#>                                            50%     75%   97.5% n_eff Rhat
#> ind_y_0                                  65.89   66.80   68.55   285 1.00
#> ind_beta                                  3.09    3.43    4.03   260 1.00
#> global_error_sigma                       11.04   11.48   12.54   337 1.00
#> y_hat[1]                                 65.89   66.80   68.55   285 1.00
#> y_hat[2]                                 71.91   72.49   73.92   851 1.00
#> y_hat[3]                                 78.44   79.36   81.43   612 1.00
#> y_hat[4]                                 84.72   86.15   89.51   401 1.00
#> y_hat[5]                                 65.89   66.80   68.55   285 1.00
#> y_hat[6]                                 71.86   72.44   73.87   842 1.00
#> y_hat[7]                                 78.18   79.09   81.09   631 1.00
#> y_hat[8]                                 84.47   85.89   89.22   405 1.00
#> y_hat[9]                                 65.89   66.80   68.55   285 1.00
#> y_hat[10]                                72.25   72.87   74.22   902 1.00
#> y_hat[11]                                79.09   80.08   82.31   570 1.00
#> y_hat[12]                                82.81   84.08   87.05   436 1.00
#> y_hat[13]                                65.89   66.80   68.55   285 1.00
#> y_hat[14]                                68.39   69.08   70.57   376 1.00
#> y_hat[15]                                65.89   66.80   68.55   285 1.00
#> y_hat[16]                                72.10   72.70   74.09   879 1.00
#> y_hat[17]                                78.04   78.93   80.92   642 1.00
#> y_hat[18]                                84.53   85.95   89.29   404 1.00
#> y_hat[19]                                65.89   66.80   68.55   285 1.00
#> y_hat[20]                                68.57   69.24   70.74   387 1.00
#> y_hat[21]                                65.89   66.80   68.55   285 1.00
#> y_hat[22]                                65.90   66.81   68.56   285 1.00
#> y_hat[23]                                65.89   66.80   68.55   285 1.00
#> y_hat[24]                                71.42   71.99   73.40   751 1.00
#> y_hat[25]                                65.89   66.80   68.55   285 1.00
#> y_hat[26]                                71.56   72.13   73.55   781 1.00
#> y_hat[27]                                65.89   66.80   68.55   285 1.00
#> y_hat[28]                                71.84   72.42   73.85   839 1.00
#> y_hat[29]                                73.79   74.43   75.79  1037 1.00
#> y_hat[30]                                65.89   66.80   68.55   285 1.00
#> y_hat[31]                                68.23   68.92   70.44   366 1.00
#> y_hat[32]                                65.89   66.80   68.55   285 1.00
#> y_hat[33]                                72.31   72.94   74.27   912 1.00
#> y_hat[34]                                65.89   66.80   68.55   285 1.00
#> y_hat[35]                                72.26   72.89   74.23   905 1.00
#> y_hat[36]                                78.39   79.32   81.38   615 1.00
#> y_hat[37]                                84.08   85.47   88.71   411 1.00
#> y_hat[38]                                65.89   66.80   68.55   285 1.00
#> y_hat[39]                                72.37   73.00   74.32   920 1.00
#> y_hat[40]                                65.89   66.80   68.55   285 1.00
#> y_hat[41]                                72.62   73.28   74.52   953 1.00
#> y_hat[42]                                78.43   79.35   81.42   612 1.00
#> y_hat[43]                                65.89   66.80   68.55   285 1.00
#> y_hat[44]                                71.83   72.42   73.84   837 1.00
#> y_hat[45]                                78.59   79.53   81.64   601 1.00
#> y_hat[46]                                65.89   66.80   68.55   285 1.00
#> y_hat[47]                                72.18   72.80   74.16   892 1.00
#> y_hat[48]                                77.59   78.46   80.37   692 1.00
#> y_hat[49]                                65.89   66.80   68.55   285 1.00
#> y_hat[50]                                72.44   73.08   74.38   930 1.00
#> y_hat[51]                                65.89   66.80   68.55   285 1.00
#> y_hat[52]                                72.18   72.79   74.16   891 1.00
#> y_hat[53]                                78.15   79.05   81.05   633 1.00
#> y_hat[54]                                65.89   66.80   68.55   285 1.00
#> y_hat[55]                                72.20   72.82   74.18   895 1.00
#> y_hat[56]                                72.22   72.84   74.19   897 1.00
#> y_hat[57]                                65.89   66.80   68.55   285 1.00
#> y_hat[58]                                78.55   79.48   81.58   604 1.00
#> y_hat[59]                                65.89   66.80   68.55   285 1.00
#> y_hat[60]                                72.31   72.94   74.27   912 1.00
#> y_hat[61]                                65.89   66.80   68.55   285 1.00
#> y_hat[62]                                69.71   70.30   71.75   486 1.00
#> y_hat[63]                                65.89   66.80   68.55   285 1.00
#> y_hat[64]                                72.10   72.71   74.09   880 1.00
#> y_hat[65]                                65.89   66.80   68.55   285 1.00
#> y_hat[66]                                72.60   73.26   74.51   951 1.00
#> y_hat[67]                                65.89   66.80   68.55   285 1.00
#> y_hat[68]                                71.72   72.30   73.72   814 1.00
#> y_hat[69]                                78.07   78.96   80.96   639 1.00
#> y_hat[70]                                81.30   82.38   85.16   477 1.00
#> y_hat[71]                                65.89   66.80   68.55   285 1.00
#> y_hat[72]                                72.57   73.23   74.48   947 1.00
#> y_hat[73]                                74.82   75.46   76.99  1017 1.00
#> y_hat[74]                                65.89   66.80   68.55   285 1.00
#> y_hat[75]                                72.00   72.59   74.01   864 1.00
#> y_hat[76]                                65.89   66.80   68.55   285 1.00
#> y_hat[77]                                68.74   69.40   70.89   398 1.00
#> y_hat[78]                                65.89   66.80   68.55   285 1.00
#> y_hat[79]                                68.79   69.44   70.93   401 1.00
#> y_hat[80]                                65.89   66.80   68.55   285 1.00
#> y_hat[81]                                68.56   69.24   70.73   387 1.00
#> y_hat[82]                                65.89   66.80   68.55   285 1.00
#> y_hat[83]                                74.56   75.21   76.69  1029 1.00
#> y_hat[84]                                65.89   66.80   68.55   285 1.00
#> y_hat[85]                                68.65   69.31   70.81   392 1.00
#> y_hat[86]                                65.89   66.80   68.55   285 1.00
#> y_hat[87]                                72.20   72.82   74.18   895 1.00
#> y_hat[88]                                78.33   79.24   81.29   620 1.00
#> y_hat[89]                                84.30   85.68   88.99   408 1.00
#> y_hat[90]                                65.89   66.80   68.55   285 1.00
#> y_hat[91]                                71.15   71.72   73.15   700 1.00
#> y_hat[92]                                65.89   66.80   68.55   285 1.00
#> y_hat[93]                                68.46   69.16   70.64   380 1.00
#> y_hat[94]                                65.89   66.80   68.55   285 1.00
#> y_hat[95]                                76.25   76.98   78.72   909 1.00
#> y_hat[96]                                65.89   66.80   68.55   285 1.00
#> y_hat[97]                                72.04   72.63   74.04   870 1.00
#> y_hat[98]                                76.01   76.73   78.41   929 1.00
#> y_hat[99]                                65.89   66.80   68.55   285 1.00
#> y_hat[100]                               72.02   72.61   74.03   867 1.00
#> y_hat[101]                               82.02   83.18   86.09   455 1.00
#> y_hat[102]                               65.89   66.80   68.55   285 1.00
#> y_hat[103]                               71.44   72.00   73.42   755 1.00
#> y_hat[104]                               77.98   78.88   80.86   646 1.00
#> y_hat[105]                               81.65   82.77   85.61   466 1.00
#> y_hat[106]                               65.89   66.80   68.55   285 1.00
#> y_hat[107]                               70.87   71.44   72.89   650 1.00
#> y_hat[108]                               65.89   66.80   68.55   285 1.00
#> y_hat[109]                               71.61   72.18   73.60   791 1.00
#> y_hat[110]                               72.17   72.78   74.15   890 1.00
#> y_hat[111]                               65.89   66.80   68.55   285 1.00
#> y_hat[112]                               72.75   73.40   74.64   969 1.00
#> y_hat[113]                               76.04   76.76   78.44   927 1.00
#> y_hat[114]                               65.89   66.80   68.55   285 1.00
#> y_hat[115]                               72.23   72.85   74.20   900 1.00
#> y_hat[116]                               84.00   85.40   88.62   413 1.00
#> y_hat[117]                               65.89   66.80   68.55   285 1.00
#> y_hat[118]                               66.62   67.48   69.16   302 1.00
#> y_hat[119]                               65.89   66.80   68.55   285 1.00
#> y_hat[120]                               71.92   72.50   73.93   852 1.00
#> y_hat[121]                               78.34   79.25   81.30   619 1.00
#> y_hat[122]                               65.89   66.80   68.55   285 1.00
#> y_hat[123]                               71.80   72.38   73.80   830 1.00
#> y_hat[124]                               77.73   78.60   80.54   674 1.00
#> y_hat[125]                               65.89   66.80   68.55   285 1.00
#> y_hat[126]                               71.35   71.92   73.34   738 1.00
#> y_hat[127]                               77.82   78.71   80.66   662 1.00
#> y_hat[128]                               93.14   95.54  100.70   334 1.00
#> y_hat[129]                               65.89   66.80   68.55   285 1.00
#> y_hat[130]                               71.94   72.53   73.96   856 1.00
#> y_hat[131]                               78.39   79.32   81.38   615 1.00
#> y_hat[132]                               87.72   89.42   93.37   367 1.00
#> y_hat[133]                               65.89   66.80   68.55   285 1.00
#> y_hat[134]                               78.39   79.32   81.38   615 1.00
#> y_hat[135]                               90.78   92.89   97.58   346 1.00
#> check_prior_pars_ind_beta[1]              0.00    0.00    0.00   NaN  NaN
#> check_prior_pars_ind_beta[2]              2.00    2.00    2.00   NaN  NaN
#> check_prior_pars_global_error_sigma[1]    0.00    0.00    0.00   NaN  NaN
#> check_prior_pars_global_error_sigma[2]    2.00    2.00    2.00   NaN  NaN
#> lp__                                   -390.70 -390.16 -389.72   225 1.01
#> 
#> Samples were drawn using NUTS(diag_e) at Tue Jun 24 01:18:42 2025.
#> For each parameter, n_eff is a crude measure of effective sample size,
#> and Rhat is the potential scale reduction factor on split chains (at 
#> convergence, Rhat=1).