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: 0.579 seconds (Warm-up)
#> Chain 1: 0.741 seconds (Sampling)
#> Chain 1: 1.32 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: 0.645 seconds (Warm-up)
#> Chain 2: 0.622 seconds (Sampling)
#> Chain 2: 1.267 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: 0.536 seconds (Warm-up)
#> Chain 3: 0.665 seconds (Sampling)
#> Chain 3: 1.201 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: 0.595 seconds (Warm-up)
#> Chain 4: 0.608 seconds (Sampling)
#> Chain 4: 1.203 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 4.94 0.06 1.42 2.25 3.95 4.95 5.90 7.67
#> rt_est 1.05 0.00 0.09 0.89 0.99 1.05 1.11 1.23
#> incid_est[1] 376.09 39.38 809.29 9.52 51.83 141.76 364.02 2140.69
#> incid_est[2] 6.17 0.58 11.90 0.20 1.01 2.61 6.32 33.21
#> incid_est[3] 30.42 2.84 58.63 1.01 4.99 12.86 31.18 163.72
#> incid_est[4] 45.45 4.23 87.42 1.52 7.48 19.26 46.63 244.34
#> incid_est[5] 51.22 4.74 97.93 1.74 8.52 21.84 52.72 274.48
#> incid_est[6] 53.14 4.87 100.57 1.85 8.99 22.89 54.98 283.22
#> incid_est[7] 53.58 4.84 100.08 1.93 9.26 23.39 55.80 283.57
#> incid_est[8] 53.48 4.76 98.40 2.00 9.47 23.69 56.08 280.74
#> incid_est[9] 53.18 4.65 96.30 2.07 9.65 23.93 56.20 276.78
#> incid_est[10] 52.82 4.54 94.08 2.14 9.84 24.13 56.23 272.44
#> incid_est[11] 52.45 4.43 91.86 2.22 10.02 24.34 56.28 268.01
#> incid_est[12] 52.08 4.32 89.68 2.29 10.21 24.56 56.32 263.61
#> incid_est[13] 51.72 4.21 87.55 2.37 10.40 24.77 56.34 259.39
#> incid_est[14] 51.37 4.11 85.47 2.45 10.58 24.98 56.33 255.32
#> incid_est[15] 51.03 4.01 83.45 2.54 10.77 25.18 56.30 251.30
#> incid_est[16] 50.70 3.91 81.49 2.62 10.96 25.39 56.27 247.35
#> incid_est[17] 50.38 3.82 79.57 2.71 11.16 25.61 56.23 243.46
#> incid_est[18] 50.07 3.72 77.71 2.81 11.37 25.84 56.22 239.64
#> incid_est[19] 49.77 3.63 75.90 2.90 11.58 26.06 56.21 235.87
#> incid_est[20] 49.48 3.54 74.14 3.00 11.80 26.29 56.20 232.16
#> incid_est[21] 49.20 3.46 72.42 3.10 12.01 26.52 56.23 228.51
#> incid_est[22] 48.32 3.32 69.58 3.19 12.13 26.50 55.61 221.64
#> incid_est[23] 48.21 3.25 68.25 3.30 12.38 26.79 55.79 218.71
#> incid_est[24] 47.98 3.18 66.74 3.42 12.62 27.02 55.83 215.20
#> incid_est[25] 47.71 3.10 65.16 3.53 12.84 27.23 55.76 211.42
#> incid_est[26] 47.43 3.02 63.60 3.65 13.06 27.44 55.71 207.56
#> incid_est[27] 47.16 2.94 62.07 3.78 13.30 27.66 55.64 203.75
#> incid_est[28] 46.89 2.87 60.58 3.90 13.53 27.87 55.53 200.00
#> incid_est[29] 46.64 2.80 59.13 4.04 13.77 28.09 55.46 196.36
#> incid_est[30] 46.40 2.73 57.72 4.17 14.00 28.32 55.46 192.75
#> incid_est[31] 46.16 2.66 56.35 4.32 14.25 28.55 55.44 189.21
#> incid_est[32] 45.94 2.59 55.01 4.46 14.51 28.79 55.46 185.74
#> incid_est[33] 45.72 2.53 53.71 4.62 14.76 29.03 55.36 182.34
#> incid_est[34] 45.51 2.47 52.44 4.78 15.01 29.24 55.31 179.00
#> incid_est[35] 45.32 2.40 51.20 4.95 15.29 29.46 55.23 175.72
#> incid_est[36] 45.12 2.34 49.99 5.13 15.54 29.68 55.17 172.50
#> incid_est[37] 44.94 2.29 48.82 5.31 15.82 29.90 55.13 169.33
#> incid_est[38] 44.77 2.23 47.67 5.49 16.11 30.13 55.05 166.26
#> incid_est[39] 44.60 2.17 46.55 5.69 16.41 30.36 54.96 163.60
#> incid_est[40] 44.45 2.12 45.46 5.89 16.70 30.59 54.91 161.06
#> incid_est[41] 44.30 2.07 44.39 6.09 17.00 30.83 54.85 158.34
#> incid_est[42] 44.16 2.02 43.35 6.29 17.31 31.07 54.84 155.51
#> incid_est[43] 44.02 1.97 42.33 6.50 17.62 31.33 54.78 152.72
#> incid_est[44] 43.90 1.92 41.34 6.72 17.92 31.60 54.76 150.03
#> incid_est[45] 43.78 1.87 40.37 6.96 18.24 31.85 54.67 147.57
#> incid_est[46] 43.67 1.82 39.42 7.20 18.56 32.10 54.65 145.13
#> incid_est[47] 43.57 1.78 38.49 7.45 18.89 32.36 54.60 142.51
#> incid_est[48] 43.48 1.74 37.58 7.70 19.21 32.64 54.52 139.93
#> incid_est[49] 43.39 1.69 36.69 7.96 19.54 32.90 54.36 137.57
#> incid_est[50] 43.32 1.65 35.82 8.23 19.87 33.15 54.30 135.29
#> incid_est[51] 43.25 1.61 34.97 8.51 20.20 33.41 54.24 133.00
#> incid_est[52] 43.18 1.57 34.13 8.79 20.56 33.67 54.17 130.59
#> incid_est[53] 43.13 1.53 33.31 9.09 20.92 33.96 54.09 128.35
#> incid_est[54] 43.08 1.49 32.51 9.40 21.29 34.26 54.05 126.19
#> incid_est[55] 43.04 1.45 31.72 9.72 21.67 34.54 54.05 123.97
#> incid_est[56] 43.01 1.41 30.95 10.06 22.03 34.83 54.06 121.93
#> incid_est[57] 42.99 1.38 30.19 10.41 22.43 35.13 53.93 119.81
#> incid_est[58] 42.97 1.34 29.45 10.76 22.85 35.38 53.92 117.89
#> incid_est[59] 42.96 1.31 28.71 11.12 23.27 35.63 53.83 115.97
#> incid_est[60] 42.96 1.27 27.99 11.47 23.64 35.93 53.73 113.93
#> incid_est[61] 42.96 1.24 27.28 11.86 24.02 36.24 53.71 111.79
#> incid_est[62] 42.98 1.21 26.59 12.26 24.43 36.52 53.66 109.59
#> incid_est[63] 43.00 1.17 25.90 12.67 24.85 36.79 53.66 107.62
#> incid_est[64] 43.03 1.14 25.22 13.09 25.29 37.09 53.59 105.83
#> incid_est[65] 43.06 1.11 24.56 13.53 25.74 37.36 53.53 104.06
#> incid_est[66] 43.11 1.08 23.90 13.99 26.17 37.67 53.43 102.33
#> incid_est[67] 43.16 1.05 23.25 14.48 26.62 37.96 53.37 100.78
#> incid_est[68] 43.22 1.02 22.61 14.97 27.09 38.27 53.32 99.17
#> incid_est[69] 43.29 0.99 21.97 15.46 27.55 38.56 53.27 97.42
#> incid_est[70] 43.36 0.96 21.35 15.94 28.02 38.86 53.23 95.88
#> incid_est[71] 43.45 0.93 20.73 16.44 28.50 39.18 53.15 94.35
#> incid_est[72] 43.54 0.90 20.11 16.96 29.04 39.50 53.06 92.72
#> incid_est[73] 43.64 0.87 19.50 17.50 29.55 39.84 53.01 91.08
#> incid_est[74] 43.74 0.85 18.90 18.08 30.03 40.16 53.01 89.49
#> incid_est[75] 43.86 0.82 18.30 18.72 30.56 40.50 52.86 88.09
#> incid_est[76] 43.98 0.79 17.71 19.34 31.08 40.82 52.81 86.55
#> incid_est[77] 44.11 0.76 17.12 19.97 31.63 41.17 52.83 85.17
#> incid_est[78] 44.25 0.74 16.54 20.63 32.19 41.51 52.81 83.69
#> incid_est[79] 44.40 0.71 15.96 21.35 32.76 41.79 52.76 82.41
#> incid_est[80] 44.56 0.68 15.38 22.07 33.34 42.10 52.75 81.04
#> incid_est[81] 44.73 0.66 14.80 22.75 33.96 42.44 52.72 79.62
#> incid_est[82] 44.90 0.63 14.23 23.49 34.56 42.78 52.70 78.28
#> incid_est[83] 45.08 0.60 13.66 24.28 35.14 43.10 52.67 76.87
#> incid_est[84] 45.28 0.58 13.09 25.07 35.75 43.47 52.70 75.58
#> incid_est[85] 45.48 0.55 12.53 25.95 36.40 43.87 52.67 74.17
#> incid_est[86] 45.69 0.52 11.96 26.79 37.00 44.18 52.64 73.02
#> incid_est[87] 45.91 0.50 11.40 27.70 37.62 44.56 52.70 71.93
#> incid_est[88] 46.14 0.47 10.83 28.65 38.32 44.97 52.66 70.82
#> incid_est[89] 46.37 0.45 10.27 29.58 39.04 45.32 52.62 69.74
#> incid_est[90] 46.62 0.42 9.71 30.54 39.74 45.69 52.59 68.55
#> incid_est[91] 46.88 0.39 9.15 31.49 40.41 46.07 52.55 67.53
#> incid_est[92] 47.15 0.37 8.60 32.60 41.05 46.44 52.50 66.40
#> incid_est[93] 47.42 0.34 8.05 33.70 41.73 46.83 52.47 65.34
#> incid_est[94] 47.71 0.31 7.50 34.68 42.37 47.20 52.42 64.28
#> incid_est[95] 48.01 0.29 6.96 35.80 43.11 47.57 52.47 63.24
#> incid_est[96] 48.32 0.26 6.42 36.84 43.87 47.96 52.48 62.19
#> incid_est[97] 48.64 0.23 5.90 37.80 44.59 48.35 52.55 61.22
#> incid_est[98] 48.97 0.20 5.40 38.84 45.21 48.79 52.56 60.39
#> incid_est[99] 49.31 0.18 4.92 39.86 45.90 49.19 52.55 59.50
#> incid_est[100] 49.67 0.15 4.47 40.99 46.59 49.63 52.65 58.67
#> incid_est[101] 50.03 0.12 4.08 42.06 47.22 50.07 52.79 58.07
#> incid_est[102] 50.41 0.10 3.76 42.99 47.84 50.49 52.95 57.69
#> incid_est[103] 50.80 0.07 3.53 43.76 48.38 50.87 53.22 57.55
#> incid_est[104] 51.20 0.06 3.43 44.42 48.82 51.27 53.55 57.85
#> incid_est[105] 51.61 0.06 3.46 44.87 49.23 51.66 53.95 58.42
#> incid_est[106] 52.04 0.07 3.63 45.19 49.49 51.96 54.42 59.29
#> incid_est[107] 52.48 0.10 3.92 45.16 49.71 52.38 55.02 60.72
#> incid_est[108] 52.93 0.12 4.33 45.11 49.85 52.74 55.71 62.31
#> incid_est[109] 53.39 0.16 4.82 44.66 49.97 53.11 56.44 63.94
#> incid_est[110] 53.87 0.19 5.38 44.32 50.06 53.53 57.21 65.71
#> incid_est[111] 54.37 0.22 6.00 43.73 50.10 53.92 58.05 67.58
#> incid_est[112] 54.88 0.26 6.67 43.13 50.05 54.39 58.98 69.61
#> incid_est[113] 55.40 0.29 7.37 42.65 50.06 54.85 59.91 71.69
#> incid_est[114] 55.94 0.33 8.11 41.98 50.08 55.31 60.90 73.94
#> incid_est[115] 56.49 0.37 8.88 41.29 50.07 55.76 61.94 76.25
#> incid_est[116] 57.06 0.41 9.68 40.68 50.01 56.22 62.98 78.84
#> incid_est[117] 57.65 0.45 10.51 40.05 50.01 56.69 63.99 81.28
#> lp__ 1507.21 0.03 0.95 1504.55 1506.83 1507.49 1507.90 1508.17
#> n_eff Rhat
#> log_i0 489 1.00
#> rt_est 486 1.00
#> incid_est[1] 422 1.01
#> incid_est[2] 426 1.01
#> incid_est[3] 426 1.01
#> incid_est[4] 426 1.01
#> incid_est[5] 426 1.01
#> incid_est[6] 427 1.01
#> incid_est[7] 427 1.01
#> incid_est[8] 428 1.01
#> incid_est[9] 429 1.01
#> incid_est[10] 429 1.00
#> incid_est[11] 430 1.00
#> incid_est[12] 431 1.00
#> incid_est[13] 431 1.00
#> incid_est[14] 432 1.00
#> incid_est[15] 433 1.00
#> incid_est[16] 434 1.00
#> incid_est[17] 435 1.00
#> incid_est[18] 436 1.00
#> incid_est[19] 437 1.00
#> incid_est[20] 437 1.00
#> incid_est[21] 438 1.00
#> incid_est[22] 440 1.00
#> incid_est[23] 440 1.00
#> incid_est[24] 441 1.00
#> incid_est[25] 442 1.00
#> incid_est[26] 444 1.00
#> incid_est[27] 445 1.00
#> incid_est[28] 446 1.00
#> incid_est[29] 447 1.00
#> incid_est[30] 448 1.00
#> incid_est[31] 449 1.00
#> incid_est[32] 450 1.00
#> incid_est[33] 451 1.00
#> incid_est[34] 452 1.00
#> incid_est[35] 454 1.00
#> incid_est[36] 455 1.00
#> incid_est[37] 456 1.00
#> incid_est[38] 457 1.00
#> incid_est[39] 458 1.00
#> incid_est[40] 459 1.00
#> incid_est[41] 461 1.00
#> incid_est[42] 462 1.00
#> incid_est[43] 463 1.00
#> incid_est[44] 464 1.00
#> incid_est[45] 465 1.00
#> incid_est[46] 467 1.00
#> incid_est[47] 468 1.00
#> incid_est[48] 469 1.00
#> incid_est[49] 470 1.00
#> incid_est[50] 472 1.00
#> incid_est[51] 473 1.00
#> incid_est[52] 474 1.00
#> incid_est[53] 475 1.00
#> incid_est[54] 476 1.00
#> incid_est[55] 477 1.00
#> incid_est[56] 479 1.00
#> incid_est[57] 480 1.00
#> incid_est[58] 481 1.00
#> incid_est[59] 482 1.00
#> incid_est[60] 483 1.00
#> incid_est[61] 484 1.00
#> incid_est[62] 485 1.00
#> incid_est[63] 486 1.00
#> incid_est[64] 488 1.00
#> incid_est[65] 489 1.00
#> incid_est[66] 490 1.00
#> incid_est[67] 491 1.00
#> incid_est[68] 492 1.00
#> incid_est[69] 493 1.00
#> incid_est[70] 494 1.00
#> incid_est[71] 495 1.00
#> incid_est[72] 496 1.00
#> incid_est[73] 497 1.00
#> incid_est[74] 499 1.00
#> incid_est[75] 500 1.00
#> incid_est[76] 501 1.00
#> incid_est[77] 502 1.00
#> incid_est[78] 504 1.00
#> incid_est[79] 505 1.00
#> incid_est[80] 507 1.00
#> incid_est[81] 508 1.00
#> incid_est[82] 510 1.00
#> incid_est[83] 512 1.00
#> incid_est[84] 514 1.00
#> incid_est[85] 517 1.00
#> incid_est[86] 519 1.00
#> incid_est[87] 522 1.00
#> incid_est[88] 526 1.00
#> incid_est[89] 531 1.00
#> incid_est[90] 536 1.00
#> incid_est[91] 542 1.00
#> incid_est[92] 551 1.00
#> incid_est[93] 561 1.00
#> incid_est[94] 574 1.00
#> incid_est[95] 591 1.00
#> incid_est[96] 615 1.00
#> incid_est[97] 648 1.00
#> incid_est[98] 697 1.00
#> incid_est[99] 770 1.00
#> incid_est[100] 890 1.00
#> incid_est[101] 1096 1.00
#> incid_est[102] 1479 1.00
#> incid_est[103] 2307 1.00
#> incid_est[104] 3625 1.00
#> incid_est[105] 3748 1.00
#> incid_est[106] 2802 1.00
#> incid_est[107] 1700 1.00
#> incid_est[108] 1219 1.00
#> incid_est[109] 966 1.00
#> incid_est[110] 821 1.00
#> incid_est[111] 732 1.00
#> incid_est[112] 674 1.00
#> incid_est[113] 634 1.00
#> incid_est[114] 605 1.00
#> incid_est[115] 583 1.00
#> incid_est[116] 566 1.00
#> incid_est[117] 553 1.01
#> lp__ 871 1.00
#>
#> Samples were drawn using NUTS(diag_e) at Sat Oct 26 04:43:09 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).