si_trunc <- 20
si_distr <- EpiEstim::discr_si(seq(0, si_trunc), 6.48, 3.83)
si_distr <- si_distr / sum(si_distr)
## Default args for iter and chains
jointlyr::jointly_estimate(10, 100, incid, si_distr)
#>
#> SAMPLING FOR MODEL 'rti0_bayesian' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 4.9e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
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#> Chain 1:
#> Chain 1: Elapsed Time: 0.57 seconds (Warm-up)
#> Chain 1: 0.679 seconds (Sampling)
#> Chain 1: 1.249 seconds (Total)
#> Chain 1:
#>
#> SAMPLING FOR MODEL 'rti0_bayesian' NOW (CHAIN 2).
#> Chain 2:
#> Chain 2: Gradient evaluation took 1.9e-05 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2:
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#> Chain 2:
#> Chain 2: Elapsed Time: 0.562 seconds (Warm-up)
#> Chain 2: 0.677 seconds (Sampling)
#> Chain 2: 1.239 seconds (Total)
#> Chain 2:
#>
#> SAMPLING FOR MODEL 'rti0_bayesian' NOW (CHAIN 3).
#> Chain 3:
#> Chain 3: Gradient evaluation took 1.9e-05 seconds
#> Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
#> Chain 3: Adjust your expectations accordingly!
#> Chain 3:
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#> Chain 3: Elapsed Time: 0.623 seconds (Warm-up)
#> Chain 3: 0.685 seconds (Sampling)
#> Chain 3: 1.308 seconds (Total)
#> Chain 3:
#>
#> SAMPLING FOR MODEL 'rti0_bayesian' NOW (CHAIN 4).
#> Chain 4:
#> Chain 4: Gradient evaluation took 1.8e-05 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.18 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4:
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#> Chain 4:
#> Chain 4: Elapsed Time: 0.591 seconds (Warm-up)
#> Chain 4: 0.613 seconds (Sampling)
#> Chain 4: 1.204 seconds (Total)
#> Chain 4:
#> Inference for Stan model: rti0_bayesian.
#> 4 chains, each with iter=2000; warmup=1000; thin=1;
#> post-warmup draws per chain=1000, total post-warmup draws=4000.
#>
#> mean se_mean sd 2.5% 25% 50% 75% 97.5%
#> log_i0 4.99 0.06 1.39 2.34 4.02 4.98 5.94 7.64
#> rt_est 1.05 0.00 0.09 0.89 0.99 1.05 1.11 1.22
#> incid_est[1] 387.88 35.09 874.61 10.43 55.72 145.26 378.32 2075.90
#> incid_est[2] 6.35 0.52 12.73 0.22 1.08 2.66 6.55 32.51
#> incid_est[3] 31.29 2.54 62.73 1.10 5.34 13.13 32.30 160.28
#> incid_est[4] 46.75 3.79 93.51 1.66 8.00 19.66 48.30 239.19
#> incid_est[5] 52.68 4.25 104.71 1.90 9.11 22.30 54.58 268.65
#> incid_est[6] 54.64 4.36 107.45 2.02 9.60 23.38 56.87 277.11
#> incid_est[7] 55.08 4.34 106.81 2.11 9.88 23.88 57.70 277.33
#> incid_est[8] 54.96 4.27 104.88 2.19 10.09 24.19 58.03 274.43
#> incid_est[9] 54.64 4.18 102.51 2.26 10.28 24.44 58.11 270.41
#> incid_est[10] 54.25 4.08 100.02 2.34 10.47 24.67 58.13 266.02
#> incid_est[11] 53.85 3.99 97.52 2.42 10.65 24.89 58.13 261.56
#> incid_est[12] 53.46 3.89 95.08 2.50 10.84 25.09 58.11 257.12
#> incid_est[13] 53.07 3.80 92.69 2.59 11.03 25.30 58.09 253.10
#> incid_est[14] 52.70 3.71 90.37 2.67 11.22 25.52 58.08 249.13
#> incid_est[15] 52.33 3.62 88.12 2.77 11.42 25.75 58.06 245.22
#> incid_est[16] 51.98 3.54 85.93 2.86 11.63 25.97 58.04 241.37
#> incid_est[17] 51.63 3.45 83.80 2.96 11.84 26.18 58.03 237.58
#> incid_est[18] 51.30 3.37 81.74 3.06 12.05 26.42 58.01 233.90
#> incid_est[19] 50.98 3.29 79.73 3.16 12.25 26.65 57.99 230.32
#> incid_est[20] 50.67 3.22 77.77 3.27 12.47 26.88 57.96 226.79
#> incid_est[21] 50.37 3.14 75.88 3.38 12.69 27.12 57.90 223.32
#> incid_est[22] 49.45 3.02 72.78 3.47 12.81 27.09 57.23 216.72
#> incid_est[23] 49.32 2.96 71.30 3.60 13.06 27.40 57.41 214.01
#> incid_est[24] 49.08 2.90 69.63 3.72 13.30 27.65 57.43 210.59
#> incid_est[25] 48.79 2.83 67.91 3.85 13.53 27.88 57.37 206.98
#> incid_est[26] 48.49 2.76 66.19 3.97 13.76 28.11 57.29 203.50
#> incid_est[27] 48.20 2.69 64.52 4.11 13.99 28.32 57.21 200.06
#> incid_est[28] 47.92 2.63 62.90 4.24 14.23 28.52 57.09 196.68
#> incid_est[29] 47.65 2.57 61.32 4.39 14.47 28.74 57.05 193.36
#> incid_est[30] 47.39 2.50 59.78 4.53 14.71 28.99 56.98 190.09
#> incid_est[31] 47.14 2.44 58.29 4.69 14.96 29.23 56.91 186.88
#> incid_est[32] 46.90 2.39 56.84 4.84 15.21 29.45 56.78 183.72
#> incid_est[33] 46.67 2.33 55.43 5.00 15.46 29.67 56.68 180.61
#> incid_est[34] 46.44 2.27 54.06 5.17 15.69 29.87 56.64 177.56
#> incid_est[35] 46.23 2.22 52.72 5.34 15.98 30.08 56.60 174.56
#> incid_est[36] 46.03 2.17 51.42 5.52 16.25 30.32 56.55 171.59
#> incid_est[37] 45.83 2.12 50.15 5.71 16.53 30.56 56.47 168.58
#> incid_est[38] 45.64 2.07 48.92 5.90 16.80 30.79 56.38 165.64
#> incid_est[39] 45.47 2.02 47.72 6.10 17.09 31.01 56.33 162.74
#> incid_est[40] 45.30 1.97 46.55 6.30 17.38 31.23 56.28 159.89
#> incid_est[41] 45.13 1.92 45.41 6.51 17.68 31.46 56.20 157.14
#> incid_est[42] 44.98 1.88 44.29 6.72 17.96 31.71 56.13 154.33
#> incid_est[43] 44.84 1.83 43.21 6.93 18.26 31.97 56.06 151.64
#> incid_est[44] 44.70 1.79 42.15 7.16 18.55 32.24 55.98 149.25
#> incid_est[45] 44.57 1.74 41.12 7.40 18.85 32.49 55.92 146.84
#> incid_est[46] 44.45 1.70 40.11 7.63 19.16 32.74 55.83 144.31
#> incid_est[47] 44.34 1.66 39.13 7.88 19.49 33.00 55.77 141.71
#> incid_est[48] 44.23 1.62 38.17 8.15 19.82 33.25 55.70 139.17
#> incid_est[49] 44.14 1.58 37.23 8.42 20.17 33.49 55.59 136.66
#> incid_est[50] 44.05 1.55 36.31 8.69 20.52 33.75 55.50 134.20
#> incid_est[51] 43.97 1.51 35.41 8.96 20.89 34.01 55.43 131.93
#> incid_est[52] 43.89 1.47 34.54 9.27 21.25 34.29 55.35 129.76
#> incid_est[53] 43.83 1.43 33.68 9.58 21.61 34.61 55.27 127.63
#> incid_est[54] 43.77 1.40 32.83 9.91 21.99 34.89 55.20 125.41
#> incid_est[55] 43.72 1.36 32.01 10.23 22.36 35.16 55.12 123.23
#> incid_est[56] 43.68 1.33 31.20 10.56 22.74 35.46 55.07 121.22
#> incid_est[57] 43.65 1.30 30.41 10.91 23.12 35.73 55.00 119.23
#> incid_est[58] 43.62 1.26 29.64 11.27 23.52 36.05 54.87 117.27
#> incid_est[59] 43.60 1.23 28.87 11.65 23.92 36.29 54.79 115.34
#> incid_est[60] 43.59 1.20 28.13 12.05 24.32 36.59 54.69 113.48
#> incid_est[61] 43.58 1.17 27.39 12.45 24.73 36.88 54.59 111.63
#> incid_est[62] 43.59 1.14 26.67 12.86 25.14 37.17 54.49 109.81
#> incid_est[63] 43.60 1.11 25.96 13.27 25.57 37.48 54.40 108.00
#> incid_est[64] 43.62 1.08 25.26 13.72 25.98 37.78 54.38 106.24
#> incid_est[65] 43.64 1.05 24.57 14.18 26.41 38.06 54.35 104.50
#> incid_est[66] 43.68 1.02 23.90 14.66 26.83 38.31 54.26 102.85
#> incid_est[67] 43.72 0.99 23.23 15.16 27.27 38.59 54.19 101.11
#> incid_est[68] 43.77 0.96 22.57 15.64 27.70 38.90 54.16 99.34
#> incid_est[69] 43.82 0.93 21.92 16.15 28.18 39.20 54.09 97.54
#> incid_est[70] 43.89 0.91 21.28 16.65 28.67 39.51 53.99 95.78
#> incid_est[71] 43.96 0.88 20.65 17.20 29.15 39.81 53.93 94.05
#> incid_est[72] 44.04 0.85 20.02 17.76 29.61 40.09 53.90 92.37
#> incid_est[73] 44.13 0.83 19.40 18.35 30.13 40.39 53.82 90.67
#> incid_est[74] 44.22 0.80 18.79 18.95 30.63 40.71 53.75 89.04
#> incid_est[75] 44.33 0.77 18.19 19.52 31.11 41.03 53.67 87.43
#> incid_est[76] 44.44 0.75 17.59 20.17 31.61 41.34 53.66 85.84
#> incid_est[77] 44.56 0.72 16.99 20.81 32.13 41.65 53.60 84.29
#> incid_est[78] 44.69 0.70 16.40 21.46 32.65 41.99 53.53 82.73
#> incid_est[79] 44.82 0.67 15.81 22.13 33.22 42.29 53.41 81.36
#> incid_est[80] 44.97 0.64 15.23 22.85 33.78 42.63 53.37 79.81
#> incid_est[81] 45.12 0.62 14.65 23.60 34.35 42.92 53.30 78.30
#> incid_est[82] 45.28 0.59 14.08 24.37 34.95 43.23 53.26 76.93
#> incid_est[83] 45.45 0.57 13.51 25.16 35.57 43.53 53.21 75.68
#> incid_est[84] 45.63 0.54 12.94 25.99 36.14 43.84 53.10 74.56
#> incid_est[85] 45.81 0.52 12.37 26.84 36.74 44.22 53.04 73.45
#> incid_est[86] 46.01 0.49 11.81 27.71 37.37 44.58 52.97 72.36
#> incid_est[87] 46.21 0.47 11.25 28.63 37.99 44.92 52.90 71.15
#> incid_est[88] 46.43 0.44 10.69 29.52 38.64 45.29 52.86 70.04
#> incid_est[89] 46.65 0.42 10.13 30.46 39.28 45.62 52.80 68.96
#> incid_est[90] 46.88 0.39 9.57 31.35 39.95 45.92 52.73 67.78
#> incid_est[91] 47.12 0.37 9.02 32.29 40.61 46.30 52.66 66.68
#> incid_est[92] 47.37 0.34 8.47 33.24 41.28 46.67 52.58 65.56
#> incid_est[93] 47.63 0.32 7.93 34.18 41.93 46.98 52.55 64.49
#> incid_est[94] 47.90 0.29 7.39 35.25 42.60 47.38 52.54 63.75
#> incid_est[95] 48.18 0.27 6.86 36.35 43.29 47.73 52.49 62.83
#> incid_est[96] 48.47 0.24 6.34 37.43 43.99 48.12 52.50 62.14
#> incid_est[97] 48.77 0.21 5.83 38.38 44.65 48.48 52.54 61.19
#> incid_est[98] 49.08 0.19 5.34 39.37 45.29 48.86 52.51 60.40
#> incid_est[99] 49.40 0.16 4.88 40.39 45.94 49.25 52.55 59.66
#> incid_est[100] 49.74 0.14 4.45 41.34 46.55 49.64 52.65 58.95
#> incid_est[101] 50.08 0.11 4.08 42.38 47.21 49.97 52.80 58.46
#> incid_est[102] 50.43 0.09 3.78 43.42 47.81 50.36 53.01 58.16
#> incid_est[103] 50.80 0.07 3.57 44.26 48.30 50.77 53.16 58.15
#> incid_est[104] 51.18 0.06 3.47 44.71 48.79 51.11 53.55 58.15
#> incid_est[105] 51.56 0.06 3.51 44.94 49.19 51.50 53.93 58.62
#> incid_est[106] 51.97 0.07 3.68 45.06 49.45 51.86 54.36 59.50
#> incid_est[107] 52.38 0.10 3.97 44.96 49.55 52.23 54.98 60.40
#> incid_est[108] 52.80 0.12 4.36 44.62 49.78 52.64 55.60 61.94
#> incid_est[109] 53.24 0.15 4.84 44.32 49.88 53.00 56.34 63.44
#> incid_est[110] 53.69 0.18 5.38 43.91 49.98 53.44 57.17 65.01
#> incid_est[111] 54.16 0.21 5.98 43.49 50.03 53.83 58.01 66.83
#> incid_est[112] 54.64 0.25 6.62 42.87 49.97 54.31 58.93 68.78
#> incid_est[113] 55.13 0.28 7.31 42.26 49.98 54.71 59.75 70.62
#> incid_est[114] 55.63 0.32 8.02 41.67 49.92 55.17 60.60 72.63
#> incid_est[115] 56.15 0.35 8.77 41.04 49.82 55.59 61.57 74.91
#> incid_est[116] 56.69 0.39 9.55 40.42 49.74 56.05 62.52 77.42
#> incid_est[117] 57.24 0.43 10.36 39.78 49.73 56.44 63.52 79.78
#> lp__ 1507.20 0.03 0.98 1504.58 1506.83 1507.51 1507.91 1508.17
#> n_eff Rhat
#> log_i0 533 1.01
#> rt_est 528 1.01
#> incid_est[1] 621 1.00
#> incid_est[2] 608 1.00
#> incid_est[3] 608 1.00
#> incid_est[4] 608 1.00
#> incid_est[5] 608 1.00
#> incid_est[6] 607 1.00
#> incid_est[7] 605 1.00
#> incid_est[8] 604 1.00
#> incid_est[9] 602 1.00
#> incid_est[10] 600 1.00
#> incid_est[11] 599 1.00
#> incid_est[12] 597 1.00
#> incid_est[13] 595 1.00
#> incid_est[14] 594 1.00
#> incid_est[15] 592 1.00
#> incid_est[16] 590 1.00
#> incid_est[17] 589 1.00
#> incid_est[18] 587 1.00
#> incid_est[19] 586 1.00
#> incid_est[20] 584 1.00
#> incid_est[21] 583 1.00
#> incid_est[22] 581 1.00
#> incid_est[23] 579 1.00
#> incid_est[24] 578 1.00
#> incid_est[25] 577 1.00
#> incid_est[26] 575 1.00
#> incid_est[27] 574 1.00
#> incid_est[28] 573 1.00
#> incid_est[29] 571 1.00
#> incid_est[30] 570 1.00
#> incid_est[31] 569 1.00
#> incid_est[32] 568 1.00
#> incid_est[33] 566 1.00
#> incid_est[34] 565 1.00
#> incid_est[35] 564 1.01
#> incid_est[36] 563 1.01
#> incid_est[37] 562 1.01
#> incid_est[38] 561 1.01
#> incid_est[39] 560 1.01
#> incid_est[40] 559 1.01
#> incid_est[41] 558 1.01
#> incid_est[42] 558 1.01
#> incid_est[43] 557 1.01
#> incid_est[44] 556 1.01
#> incid_est[45] 555 1.01
#> incid_est[46] 555 1.01
#> incid_est[47] 554 1.01
#> incid_est[48] 553 1.01
#> incid_est[49] 553 1.01
#> incid_est[50] 552 1.01
#> incid_est[51] 552 1.01
#> incid_est[52] 551 1.01
#> incid_est[53] 551 1.01
#> incid_est[54] 550 1.01
#> incid_est[55] 550 1.01
#> incid_est[56] 550 1.01
#> incid_est[57] 550 1.01
#> incid_est[58] 549 1.01
#> incid_est[59] 549 1.01
#> incid_est[60] 549 1.01
#> incid_est[61] 549 1.01
#> incid_est[62] 549 1.01
#> incid_est[63] 549 1.01
#> incid_est[64] 549 1.01
#> incid_est[65] 549 1.01
#> incid_est[66] 549 1.01
#> incid_est[67] 549 1.01
#> incid_est[68] 550 1.01
#> incid_est[69] 550 1.01
#> incid_est[70] 550 1.01
#> incid_est[71] 551 1.01
#> incid_est[72] 551 1.01
#> incid_est[73] 552 1.01
#> incid_est[74] 553 1.01
#> incid_est[75] 553 1.01
#> incid_est[76] 554 1.01
#> incid_est[77] 555 1.01
#> incid_est[78] 556 1.01
#> incid_est[79] 558 1.01
#> incid_est[80] 559 1.01
#> incid_est[81] 561 1.01
#> incid_est[82] 563 1.01
#> incid_est[83] 565 1.01
#> incid_est[84] 568 1.01
#> incid_est[85] 571 1.00
#> incid_est[86] 574 1.00
#> incid_est[87] 578 1.00
#> incid_est[88] 583 1.00
#> incid_est[89] 589 1.00
#> incid_est[90] 596 1.00
#> incid_est[91] 605 1.00
#> incid_est[92] 615 1.00
#> incid_est[93] 629 1.00
#> incid_est[94] 646 1.00
#> incid_est[95] 670 1.00
#> incid_est[96] 701 1.00
#> incid_est[97] 745 1.00
#> incid_est[98] 809 1.00
#> incid_est[99] 908 1.00
#> incid_est[100] 1065 1.00
#> incid_est[101] 1336 1.00
#> incid_est[102] 1829 1.00
#> incid_est[103] 2712 1.00
#> incid_est[104] 3822 1.00
#> incid_est[105] 3648 1.00
#> incid_est[106] 2495 1.00
#> incid_est[107] 1695 1.00
#> incid_est[108] 1257 1.00
#> incid_est[109] 1016 1.00
#> incid_est[110] 873 1.00
#> incid_est[111] 781 1.00
#> incid_est[112] 717 1.01
#> incid_est[113] 675 1.01
#> incid_est[114] 647 1.01
#> incid_est[115] 624 1.01
#> incid_est[116] 606 1.01
#> incid_est[117] 592 1.01
#> lp__ 831 1.00
#>
#> Samples were drawn using NUTS(diag_e) at Mon Nov 25 04:40:55 2024.
#> 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).