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 5.4e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.54 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
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#> Chain 1:
#> Chain 1: Elapsed Time: 0.575 seconds (Warm-up)
#> Chain 1: 0.718 seconds (Sampling)
#> Chain 1: 1.293 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: 0.561 seconds (Warm-up)
#> Chain 2: 0.579 seconds (Sampling)
#> Chain 2: 1.14 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:
#> Chain 3: Elapsed Time: 0.566 seconds (Warm-up)
#> Chain 3: 0.674 seconds (Sampling)
#> Chain 3: 1.24 seconds (Total)
#> Chain 3:
#>
#> SAMPLING FOR MODEL 'rti0_bayesian' NOW (CHAIN 4).
#> Chain 4:
#> Chain 4: Gradient evaluation took 1.9e-05 seconds
#> Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
#> Chain 4: Adjust your expectations accordingly!
#> Chain 4:
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#> Chain 4:
#> Chain 4: Elapsed Time: 0.522 seconds (Warm-up)
#> Chain 4: 0.619 seconds (Sampling)
#> Chain 4: 1.141 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 5.08 0.07 1.47 2.40 4.02 5.05 6.06 7.96
#> rt_est 1.05 0.00 0.09 0.87 0.98 1.05 1.11 1.22
#> incid_est[1] 496.14 65.67 1370.73 11.07 55.88 155.30 426.28 2872.86
#> incid_est[2] 7.91 0.92 19.20 0.24 1.09 2.83 7.34 43.86
#> incid_est[3] 39.00 4.55 94.61 1.17 5.36 13.97 36.17 216.18
#> incid_est[4] 58.23 6.78 140.95 1.75 8.04 20.92 54.09 322.51
#> incid_est[5] 65.53 7.58 157.54 2.01 9.15 23.71 61.10 361.89
#> incid_est[6] 67.82 7.76 161.15 2.14 9.65 24.83 63.63 372.76
#> incid_est[7] 68.17 7.68 159.54 2.23 9.93 25.33 64.49 372.59
#> incid_est[8] 67.79 7.51 155.93 2.31 10.14 25.64 64.70 368.06
#> incid_est[9] 67.16 7.31 151.64 2.39 10.33 25.88 64.69 361.75
#> incid_est[10] 66.46 7.10 147.19 2.47 10.51 26.09 64.62 354.95
#> incid_est[11] 65.73 6.88 142.76 2.55 10.69 26.28 64.55 348.07
#> incid_est[12] 65.02 6.68 138.45 2.64 10.87 26.48 64.46 341.25
#> incid_est[13] 64.33 6.48 134.27 2.72 11.07 26.66 64.35 334.53
#> incid_est[14] 63.65 6.29 130.22 2.81 11.27 26.87 64.25 327.94
#> incid_est[15] 62.99 6.10 126.31 2.90 11.46 27.08 64.15 321.80
#> incid_est[16] 62.35 5.92 122.53 3.00 11.67 27.28 64.05 315.78
#> incid_est[17] 61.73 5.75 118.88 3.10 11.87 27.51 63.99 309.86
#> incid_est[18] 61.13 5.58 115.35 3.20 12.08 27.75 63.93 304.06
#> incid_est[19] 60.55 5.41 111.94 3.31 12.30 27.94 63.89 298.37
#> incid_est[20] 59.98 5.26 108.65 3.42 12.52 28.14 63.81 292.78
#> incid_est[21] 59.43 5.10 105.47 3.53 12.73 28.35 63.72 287.30
#> incid_est[22] 58.11 4.86 100.51 3.62 12.85 28.30 62.87 277.59
#> incid_est[23] 57.79 4.74 98.00 3.75 13.11 28.60 62.91 273.37
#> incid_est[24] 57.33 4.61 95.25 3.87 13.34 28.85 62.85 268.45
#> incid_est[25] 56.81 4.48 92.43 4.00 13.56 29.10 62.73 263.22
#> incid_est[26] 56.29 4.34 89.66 4.13 13.80 29.33 62.57 257.98
#> incid_est[27] 55.78 4.21 86.97 4.27 14.04 29.56 62.40 252.82
#> incid_est[28] 55.28 4.09 84.36 4.41 14.29 29.77 62.19 247.77
#> incid_est[29] 54.81 3.97 81.85 4.55 14.55 29.98 61.97 242.82
#> incid_est[30] 54.34 3.85 79.42 4.70 14.81 30.19 61.78 237.97
#> incid_est[31] 53.90 3.73 77.08 4.85 15.05 30.42 61.63 233.20
#> incid_est[32] 53.46 3.62 74.81 5.01 15.30 30.67 61.47 228.38
#> incid_est[33] 53.05 3.52 72.61 5.18 15.55 30.92 61.28 223.69
#> incid_est[34] 52.64 3.41 70.49 5.35 15.82 31.13 61.07 219.52
#> incid_est[35] 52.25 3.32 68.44 5.52 16.10 31.35 60.87 215.13
#> incid_est[36] 51.88 3.22 66.45 5.70 16.38 31.57 60.69 210.83
#> incid_est[37] 51.52 3.13 64.53 5.87 16.64 31.77 60.59 206.63
#> incid_est[38] 51.17 3.03 62.67 6.06 16.93 31.98 60.51 202.51
#> incid_est[39] 50.83 2.95 60.86 6.25 17.23 32.23 60.38 198.47
#> incid_est[40] 50.50 2.86 59.11 6.46 17.55 32.46 60.21 194.51
#> incid_est[41] 50.19 2.78 57.42 6.67 17.85 32.68 60.00 190.69
#> incid_est[42] 49.89 2.70 55.78 6.88 18.14 32.90 59.84 186.79
#> incid_est[43] 49.61 2.62 54.19 7.10 18.44 33.14 59.63 183.13
#> incid_est[44] 49.33 2.55 52.65 7.32 18.75 33.37 59.45 179.44
#> incid_est[45] 49.07 2.47 51.16 7.56 19.08 33.59 59.32 175.83
#> incid_est[46] 48.81 2.40 49.71 7.79 19.40 33.84 59.18 172.32
#> incid_est[47] 48.57 2.33 48.30 8.04 19.72 34.08 59.04 168.88
#> incid_est[48] 48.34 2.27 46.93 8.30 20.05 34.31 58.93 165.50
#> incid_est[49] 48.13 2.20 45.60 8.57 20.39 34.54 58.78 162.19
#> incid_est[50] 47.92 2.14 44.31 8.85 20.74 34.79 58.64 158.95
#> incid_est[51] 47.72 2.08 43.06 9.13 21.09 35.06 58.49 155.77
#> incid_est[52] 47.53 2.02 41.83 9.43 21.46 35.30 58.35 152.66
#> incid_est[53] 47.36 1.96 40.65 9.73 21.84 35.54 58.24 149.61
#> incid_est[54] 47.19 1.90 39.49 10.05 22.22 35.79 58.12 146.62
#> incid_est[55] 47.04 1.85 38.37 10.37 22.60 36.06 57.98 143.69
#> incid_est[56] 46.89 1.79 37.27 10.71 23.00 36.34 57.80 140.82
#> incid_est[57] 46.76 1.74 36.20 11.05 23.40 36.58 57.65 137.97
#> incid_est[58] 46.63 1.69 35.16 11.41 23.79 36.83 57.51 135.25
#> incid_est[59] 46.52 1.64 34.14 11.78 24.15 37.12 57.37 132.55
#> incid_est[60] 46.41 1.60 33.15 12.16 24.55 37.41 57.19 129.90
#> incid_est[61] 46.32 1.55 32.18 12.56 24.97 37.72 57.04 127.31
#> incid_est[62] 46.23 1.50 31.23 12.96 25.37 38.00 56.93 124.69
#> incid_est[63] 46.15 1.46 30.31 13.38 25.79 38.27 56.82 122.09
#> incid_est[64] 46.09 1.41 29.40 13.82 26.20 38.52 56.74 119.54
#> incid_est[65] 46.03 1.37 28.51 14.26 26.62 38.80 56.57 117.07
#> incid_est[66] 45.98 1.33 27.64 14.72 27.03 39.04 56.48 114.93
#> incid_est[67] 45.94 1.29 26.79 15.20 27.50 39.34 56.42 112.79
#> incid_est[68] 45.92 1.25 25.96 15.68 27.94 39.61 56.27 110.54
#> incid_est[69] 45.90 1.21 25.14 16.18 28.41 39.86 56.19 108.33
#> incid_est[70] 45.89 1.17 24.34 16.70 28.88 40.09 56.02 106.17
#> incid_est[71] 45.89 1.13 23.55 17.24 29.39 40.39 55.95 104.05
#> incid_est[72] 45.89 1.09 22.77 17.79 29.88 40.67 55.88 101.97
#> incid_est[73] 45.91 1.05 22.01 18.36 30.36 40.99 55.69 99.94
#> incid_est[74] 45.94 1.02 21.26 18.95 30.88 41.22 55.63 97.94
#> incid_est[75] 45.98 0.98 20.52 19.56 31.35 41.58 55.60 95.98
#> incid_est[76] 46.02 0.95 19.79 20.16 31.84 41.86 55.47 94.06
#> incid_est[77] 46.08 0.91 19.07 20.83 32.37 42.18 55.30 92.19
#> incid_est[78] 46.14 0.88 18.36 21.47 32.90 42.45 55.16 90.34
#> incid_est[79] 46.22 0.84 17.66 22.17 33.47 42.79 55.02 88.54
#> incid_est[80] 46.30 0.81 16.96 22.91 34.06 43.08 54.95 86.78
#> incid_est[81] 46.39 0.78 16.28 23.64 34.65 43.39 54.80 85.04
#> incid_est[82] 46.50 0.74 15.60 24.36 35.27 43.70 54.72 83.32
#> incid_est[83] 46.61 0.71 14.93 25.09 35.86 44.02 54.50 81.42
#> incid_est[84] 46.73 0.68 14.27 25.91 36.40 44.33 54.43 79.84
#> incid_est[85] 46.86 0.64 13.61 26.82 36.98 44.66 54.36 78.34
#> incid_est[86] 47.00 0.61 12.95 27.68 37.59 44.97 54.21 76.84
#> incid_est[87] 47.16 0.58 12.31 28.56 38.25 45.30 54.10 75.34
#> incid_est[88] 47.32 0.55 11.67 29.44 38.92 45.62 54.05 73.84
#> incid_est[89] 47.49 0.52 11.03 30.28 39.54 45.98 53.89 72.36
#> incid_est[90] 47.67 0.48 10.40 31.24 40.16 46.32 53.86 70.92
#> incid_est[91] 47.86 0.45 9.77 32.18 40.84 46.65 53.75 69.62
#> incid_est[92] 48.06 0.42 9.15 33.10 41.51 46.97 53.66 68.19
#> incid_est[93] 48.28 0.39 8.54 34.18 42.13 47.30 53.51 67.14
#> incid_est[94] 48.50 0.36 7.93 35.24 42.78 47.68 53.42 65.94
#> incid_est[95] 48.73 0.32 7.34 36.32 43.49 48.03 53.28 64.82
#> incid_est[96] 48.98 0.29 6.75 37.45 44.17 48.32 53.23 63.65
#> incid_est[97] 49.23 0.26 6.18 38.37 44.88 48.70 53.14 62.38
#> incid_est[98] 49.50 0.23 5.64 39.49 45.54 49.10 53.06 61.30
#> incid_est[99] 49.78 0.19 5.12 40.60 46.22 49.50 53.04 60.45
#> incid_est[100] 50.07 0.16 4.64 41.61 46.84 49.87 53.07 59.68
#> incid_est[101] 50.37 0.13 4.22 42.57 47.41 50.26 53.09 59.00
#> incid_est[102] 50.68 0.10 3.87 43.26 48.02 50.62 53.19 58.48
#> incid_est[103] 51.00 0.08 3.63 43.99 48.49 50.96 53.36 58.44
#> incid_est[104] 51.34 0.06 3.51 44.57 48.91 51.28 53.68 58.50
#> incid_est[105] 51.69 0.06 3.54 44.95 49.22 51.57 54.01 58.99
#> incid_est[106] 52.05 0.07 3.71 45.03 49.49 51.85 54.50 59.66
#> incid_est[107] 52.42 0.10 4.01 45.03 49.68 52.18 55.08 60.68
#> incid_est[108] 52.80 0.13 4.43 44.66 49.84 52.53 55.72 62.02
#> incid_est[109] 53.20 0.17 4.93 44.41 49.74 52.94 56.45 63.55
#> incid_est[110] 53.62 0.20 5.50 43.84 49.72 53.35 57.16 65.15
#> incid_est[111] 54.04 0.24 6.12 43.18 49.66 53.77 57.98 66.92
#> incid_est[112] 54.48 0.28 6.79 42.62 49.59 54.20 58.85 68.70
#> incid_est[113] 54.94 0.31 7.49 41.90 49.51 54.63 59.79 70.50
#> incid_est[114] 55.40 0.35 8.23 41.29 49.47 54.98 60.67 72.39
#> incid_est[115] 55.89 0.40 9.00 40.64 49.36 55.44 61.59 74.50
#> incid_est[116] 56.38 0.44 9.79 39.90 49.28 55.85 62.61 76.71
#> incid_est[117] 56.90 0.49 10.61 39.19 49.12 56.24 63.66 78.92
#> lp__ 1507.14 0.04 1.05 1504.36 1506.69 1507.46 1507.90 1508.17
#> n_eff Rhat
#> log_i0 391 1.01
#> rt_est 382 1.01
#> incid_est[1] 436 1.01
#> incid_est[2] 432 1.01
#> incid_est[3] 432 1.01
#> incid_est[4] 432 1.01
#> incid_est[5] 432 1.01
#> incid_est[6] 432 1.01
#> incid_est[7] 431 1.01
#> incid_est[8] 431 1.01
#> incid_est[9] 431 1.01
#> incid_est[10] 430 1.01
#> incid_est[11] 430 1.01
#> incid_est[12] 430 1.01
#> incid_est[13] 429 1.01
#> incid_est[14] 429 1.01
#> incid_est[15] 429 1.01
#> incid_est[16] 428 1.01
#> incid_est[17] 428 1.01
#> incid_est[18] 428 1.01
#> incid_est[19] 428 1.01
#> incid_est[20] 427 1.01
#> incid_est[21] 427 1.01
#> incid_est[22] 427 1.01
#> incid_est[23] 427 1.01
#> incid_est[24] 427 1.01
#> incid_est[25] 426 1.01
#> incid_est[26] 426 1.01
#> incid_est[27] 426 1.01
#> incid_est[28] 426 1.01
#> incid_est[29] 426 1.01
#> incid_est[30] 426 1.01
#> incid_est[31] 426 1.01
#> incid_est[32] 426 1.01
#> incid_est[33] 426 1.01
#> incid_est[34] 426 1.01
#> incid_est[35] 426 1.01
#> incid_est[36] 426 1.01
#> incid_est[37] 426 1.01
#> incid_est[38] 426 1.01
#> incid_est[39] 427 1.01
#> incid_est[40] 427 1.01
#> incid_est[41] 427 1.01
#> incid_est[42] 427 1.01
#> incid_est[43] 427 1.01
#> incid_est[44] 428 1.01
#> incid_est[45] 428 1.01
#> incid_est[46] 428 1.01
#> incid_est[47] 428 1.01
#> incid_est[48] 429 1.01
#> incid_est[49] 429 1.01
#> incid_est[50] 429 1.01
#> incid_est[51] 430 1.01
#> incid_est[52] 430 1.01
#> incid_est[53] 431 1.01
#> incid_est[54] 431 1.01
#> incid_est[55] 431 1.01
#> incid_est[56] 431 1.01
#> incid_est[57] 431 1.01
#> incid_est[58] 432 1.01
#> incid_est[59] 432 1.01
#> incid_est[60] 432 1.01
#> incid_est[61] 432 1.01
#> incid_est[62] 432 1.01
#> incid_est[63] 432 1.01
#> incid_est[64] 433 1.01
#> incid_est[65] 433 1.01
#> incid_est[66] 433 1.01
#> incid_est[67] 433 1.01
#> incid_est[68] 434 1.01
#> incid_est[69] 434 1.01
#> incid_est[70] 434 1.01
#> incid_est[71] 435 1.01
#> incid_est[72] 435 1.01
#> incid_est[73] 435 1.01
#> incid_est[74] 436 1.01
#> incid_est[75] 436 1.01
#> incid_est[76] 437 1.01
#> incid_est[77] 438 1.01
#> incid_est[78] 438 1.01
#> incid_est[79] 439 1.01
#> incid_est[80] 440 1.01
#> incid_est[81] 441 1.01
#> incid_est[82] 442 1.01
#> incid_est[83] 443 1.01
#> incid_est[84] 445 1.01
#> incid_est[85] 447 1.01
#> incid_est[86] 449 1.01
#> incid_est[87] 452 1.01
#> incid_est[88] 455 1.01
#> incid_est[89] 458 1.01
#> incid_est[90] 463 1.01
#> incid_est[91] 469 1.01
#> incid_est[92] 476 1.01
#> incid_est[93] 486 1.01
#> incid_est[94] 498 1.01
#> incid_est[95] 514 1.00
#> incid_est[96] 537 1.00
#> incid_est[97] 569 1.00
#> incid_est[98] 617 1.00
#> incid_est[99] 691 1.00
#> incid_est[100] 815 1.00
#> incid_est[101] 1048 1.00
#> incid_est[102] 1457 1.00
#> incid_est[103] 2309 1.00
#> incid_est[104] 3563 1.00
#> incid_est[105] 3754 1.00
#> incid_est[106] 2574 1.00
#> incid_est[107] 1564 1.00
#> incid_est[108] 1109 1.00
#> incid_est[109] 872 1.00
#> incid_est[110] 740 1.00
#> incid_est[111] 659 1.00
#> incid_est[112] 605 1.00
#> incid_est[113] 569 1.00
#> incid_est[114] 542 1.00
#> incid_est[115] 511 1.00
#> incid_est[116] 487 1.00
#> incid_est[117] 468 1.00
#> lp__ 656 1.01
#>
#> Samples were drawn using NUTS(diag_e) at Tue Aug 27 05:09:47 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).