Estimate the true sero prevalence using Bayesian estimation
Source:R/correct_prevalence.R
correct_prevalence.RdEstimate the true sero prevalence using Bayesian estimation
Usage
correct_prevalence(
data,
bayesian = TRUE,
init_se = 0.95,
init_sp = 0.8,
study_size_se = 1000,
study_size_sp = 1000,
chains = 1,
warmup = 1000,
iter = 2000
)Arguments
- data
the input data frame, must either have `age`, `pos`, `tot` columns (for aggregated data) OR `age`, `status` for (linelisting data)
- bayesian
whether to adjust sero-prevalence using the Bayesian or frequentist approach. If set to `TRUE`, true sero-prevalence is estimated using MCMC.
- init_se
sensitivity of the serological test
- init_sp
specificity of the serological test
- study_size_se
(applicable when `bayesian=TRUE`) study size for sensitivity validation study (i.e., number of confirmed infected patients in the study)
- study_size_sp
(applicable when `bayesian=TRUE`) study size for specificity validation study (i.e., number of confirmed non-infected patients in the study)
- chains
(applicable when `bayesian=TRUE`) number of Markov chains
- warmup
(applicable when `bayesian=TRUE`) number of warm up runs
- iter
(applicable when `bayesian=TRUE`) number of iterations
Value
a list of 2 items
- info
estimated parameters
- corrected_sero
data.frame containing age, the corresponding estimated seroprevalance, adjusted tot and pos
Examples
data <- rubella_uk_1986_1987
correct_prevalence(data)
#>
#> SAMPLING FOR MODEL 'prevalence_correction' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 0.000142 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.42 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
#> Chain 1:
#> Chain 1: Iteration: 1 / 2000 [ 0%] (Warmup)
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#> Chain 1: Iteration: 2000 / 2000 [100%] (Sampling)
#> Chain 1:
#> Chain 1: Elapsed Time: 1.713 seconds (Warm-up)
#> Chain 1: 1.286 seconds (Sampling)
#> Chain 1: 2.999 seconds (Total)
#> Chain 1:
#> $info
#> mean se_mean sd 2.5% 25%
#> est_se 9.581929e-01 0.0001609135 0.005230293 9.479660e-01 9.547228e-01
#> est_sp 8.069757e-01 0.0002828964 0.011044871 7.854039e-01 7.996085e-01
#> theta[1] 1.706464e-02 0.0003758854 0.014989311 3.690544e-04 5.921739e-03
#> theta[2] 4.384368e-02 0.0009200557 0.031159439 2.121645e-03 2.001407e-02
#> theta[3] 3.850694e-02 0.0008826740 0.029991391 1.972698e-03 1.513077e-02
#> theta[4] 1.431935e-01 0.0012414607 0.045817055 5.786349e-02 1.125689e-01
#> theta[5] 3.165637e-01 0.0012872042 0.045617903 2.288035e-01 2.846881e-01
#> theta[6] 4.444701e-01 0.0009451693 0.045250540 3.599190e-01 4.125157e-01
#> theta[7] 4.626891e-01 0.0013201546 0.048348387 3.614287e-01 4.320284e-01
#> theta[8] 6.106122e-01 0.0011822001 0.050639289 5.022235e-01 5.767448e-01
#> theta[9] 7.175997e-01 0.0011008843 0.044719614 6.230635e-01 6.873996e-01
#> theta[10] 6.419766e-01 0.0012393796 0.048736983 5.461536e-01 6.081532e-01
#> theta[11] 7.220485e-01 0.0012029224 0.047430010 6.271027e-01 6.869883e-01
#> theta[12] 8.227953e-01 0.0009076172 0.036852851 7.482824e-01 7.975976e-01
#> theta[13] 7.627398e-01 0.0010626785 0.041669972 6.753443e-01 7.362022e-01
#> theta[14] 8.587556e-01 0.0007333958 0.037123956 7.792670e-01 8.357116e-01
#> theta[15] 7.731065e-01 0.0016930107 0.063281557 6.296218e-01 7.332235e-01
#> theta[16] 8.355733e-01 0.0014522080 0.061611408 7.059238e-01 7.936201e-01
#> theta[17] 9.129714e-01 0.0011670213 0.043390142 8.209613e-01 8.833520e-01
#> theta[18] 8.774053e-01 0.0012095021 0.049055119 7.736844e-01 8.467484e-01
#> theta[19] 8.809649e-01 0.0010927956 0.039403502 7.980845e-01 8.579858e-01
#> theta[20] 8.529601e-01 0.0016385553 0.057174064 7.312159e-01 8.165787e-01
#> theta[21] 9.138139e-01 0.0012630170 0.041859407 8.244294e-01 8.863258e-01
#> theta[22] 8.259165e-01 0.0011436089 0.045601968 7.285091e-01 7.944683e-01
#> theta[23] 9.467582e-01 0.0009523828 0.032369969 8.707946e-01 9.287364e-01
#> theta[24] 9.445504e-01 0.0011926430 0.037324845 8.608275e-01 9.213222e-01
#> theta[25] 9.711767e-01 0.0006479416 0.023911199 9.087006e-01 9.593204e-01
#> theta[26] 9.389326e-01 0.0010738197 0.035526856 8.598293e-01 9.175298e-01
#> theta[27] 9.225048e-01 0.0011609875 0.037619498 8.388538e-01 8.993849e-01
#> theta[28] 9.572464e-01 0.0007611328 0.031613624 8.734294e-01 9.417387e-01
#> theta[29] 9.094723e-01 0.0012455871 0.045441053 8.093298e-01 8.818336e-01
#> theta[30] 9.172450e-01 0.0015495416 0.049401780 8.019122e-01 8.886713e-01
#> theta[31] 8.592529e-01 0.0015215384 0.059760216 7.247602e-01 8.216484e-01
#> theta[32] 9.402675e-01 0.0012045051 0.047141758 8.193893e-01 9.149402e-01
#> theta[33] 9.380364e-01 0.0012494314 0.049443567 8.147240e-01 9.118179e-01
#> theta[34] 9.459028e-01 0.0012373057 0.043407912 8.408670e-01 9.244129e-01
#> theta[35] 8.926621e-01 0.0014595882 0.069482239 7.300403e-01 8.516782e-01
#> theta[36] 9.566368e-01 0.0009100621 0.037218304 8.524151e-01 9.398737e-01
#> theta[37] 9.402055e-01 0.0012889185 0.049025151 8.190774e-01 9.158457e-01
#> theta[38] 8.972827e-01 0.0016245163 0.061436648 7.584656e-01 8.581675e-01
#> theta[39] 9.211567e-01 0.0016407994 0.058707430 7.744334e-01 8.893928e-01
#> theta[40] 9.356209e-01 0.0014752568 0.054909867 7.951714e-01 9.050129e-01
#> theta[41] 9.533126e-01 0.0010332280 0.045038095 8.376966e-01 9.334340e-01
#> theta[42] 9.198561e-01 0.0017652536 0.060365376 7.740165e-01 8.866775e-01
#> theta[43] 9.078516e-01 0.0017433479 0.067439029 7.451051e-01 8.692745e-01
#> theta[44] 9.380297e-01 0.0015528750 0.063675966 7.669778e-01 9.133157e-01
#> lp__ -2.762598e+03 0.2749034942 5.360660152 -2.774227e+03 -2.766007e+03
#> 50% 75% 97.5% n_eff Rhat
#> est_se 9.584447e-01 9.619761e-01 9.678106e-01 1056.4936 0.9991695
#> est_sp 8.071410e-01 8.149658e-01 8.271894e-01 1524.2856 0.9991034
#> theta[1] 1.352593e-02 2.376979e-02 5.650053e-02 1590.2027 0.9991373
#> theta[2] 3.755705e-02 6.215776e-02 1.134722e-01 1146.9674 0.9996657
#> theta[3] 3.145086e-02 5.565008e-02 1.094077e-01 1154.4965 0.9992727
#> theta[4] 1.417909e-01 1.728511e-01 2.383082e-01 1362.0354 0.9993613
#> theta[5] 3.164776e-01 3.466235e-01 4.045569e-01 1255.9597 1.0003572
#> theta[6] 4.445659e-01 4.749955e-01 5.303761e-01 2292.0723 1.0010897
#> theta[7] 4.620885e-01 4.952945e-01 5.543290e-01 1341.2644 0.9997882
#> theta[8] 6.118090e-01 6.456523e-01 7.084200e-01 1834.8188 0.9993449
#> theta[9] 7.198536e-01 7.483989e-01 7.985096e-01 1650.1096 0.9995444
#> theta[10] 6.432274e-01 6.749764e-01 7.378660e-01 1546.3529 0.9990159
#> theta[11] 7.255408e-01 7.561061e-01 8.119058e-01 1554.6448 0.9990106
#> theta[12] 8.249793e-01 8.473920e-01 8.917033e-01 1648.6814 0.9990383
#> theta[13] 7.645160e-01 7.923548e-01 8.382969e-01 1537.5972 1.0000083
#> theta[14] 8.590567e-01 8.849603e-01 9.248671e-01 2562.3100 0.9999734
#> theta[15] 7.756140e-01 8.165988e-01 8.883877e-01 1397.1238 0.9999912
#> theta[16] 8.413271e-01 8.815836e-01 9.387800e-01 1799.9673 0.9990116
#> theta[17] 9.171108e-01 9.465813e-01 9.850605e-01 1382.3708 1.0025188
#> theta[18] 8.811083e-01 9.135804e-01 9.610183e-01 1644.9601 0.9997443
#> theta[19] 8.837311e-01 9.088757e-01 9.482833e-01 1300.1449 0.9995279
#> theta[20] 8.556595e-01 8.959927e-01 9.531399e-01 1217.5194 1.0001435
#> theta[21] 9.187279e-01 9.435835e-01 9.833824e-01 1098.4182 0.9993065
#> theta[22] 8.277229e-01 8.569425e-01 9.096893e-01 1590.0549 0.9990819
#> theta[23] 9.507876e-01 9.707137e-01 9.942870e-01 1155.2115 1.0018554
#> theta[24] 9.493524e-01 9.729901e-01 9.976023e-01 979.4339 0.9990053
#> theta[25] 9.769145e-01 9.884179e-01 9.991942e-01 1361.8555 1.0003647
#> theta[26] 9.432770e-01 9.652616e-01 9.929998e-01 1094.5883 0.9994120
#> theta[27] 9.254389e-01 9.486743e-01 9.859532e-01 1049.9555 0.9990119
#> theta[28] 9.627506e-01 9.808278e-01 9.982050e-01 1725.1534 1.0001250
#> theta[29] 9.124451e-01 9.432541e-01 9.840203e-01 1330.9098 0.9990845
#> theta[30] 9.235671e-01 9.524745e-01 9.913246e-01 1016.4329 0.9990045
#> theta[31] 8.668765e-01 9.022011e-01 9.551086e-01 1542.6183 0.9991644
#> theta[32] 9.497947e-01 9.767184e-01 9.970982e-01 1531.7726 1.0000293
#> theta[33] 9.500388e-01 9.752579e-01 9.980635e-01 1566.0108 0.9998868
#> theta[34] 9.559917e-01 9.783305e-01 9.969428e-01 1230.7894 0.9990017
#> theta[35] 9.048680e-01 9.455510e-01 9.909934e-01 2266.1410 0.9990055
#> theta[36] 9.677596e-01 9.849612e-01 9.981735e-01 1672.5193 0.9994178
#> theta[37] 9.515684e-01 9.783618e-01 9.979456e-01 1446.7284 0.9998791
#> theta[38] 9.082948e-01 9.460790e-01 9.867077e-01 1430.2333 0.9990185
#> theta[39] 9.329785e-01 9.659220e-01 9.960304e-01 1280.1922 0.9990404
#> theta[40] 9.526373e-01 9.780353e-01 9.973468e-01 1385.3693 0.9990002
#> theta[41] 9.669428e-01 9.871043e-01 9.986769e-01 1900.0616 0.9992308
#> theta[42] 9.334860e-01 9.675611e-01 9.962890e-01 1169.3961 0.9993389
#> theta[43] 9.246035e-01 9.588806e-01 9.940502e-01 1496.4234 0.9989997
#> theta[44] 9.580634e-01 9.846834e-01 9.988281e-01 1681.4273 0.9991492
#> lp__ -2.762095e+03 -2.758919e+03 -2.753363e+03 380.2560 0.9997653
#>
#> $corrected_se
#> age sero pos tot
#> theta[1] 1.5 0.01706464 3.515315 206
#> theta[2] 2.5 0.04384368 6.401178 146
#> theta[3] 3.5 0.03850694 6.469165 168
#> theta[4] 4.5 0.14319346 27.063563 189
#> theta[5] 5.5 0.31656368 69.327445 219
#> theta[6] 6.5 0.44447008 86.671666 195
#> theta[7] 7.5 0.46268911 75.881014 164
#> theta[8] 8.5 0.61061222 88.538772 145
#> theta[9] 9.5 0.71759969 129.167944 180
#> theta[10] 10.5 0.64197659 102.716254 160
#> theta[11] 11.5 0.72204847 106.863174 148
#> theta[12] 12.5 0.82279530 146.457563 178
#> theta[13] 13.5 0.76273979 135.004942 177
#> theta[14] 14.5 0.85875564 141.694681 165
#> theta[15] 15.5 0.77310653 51.798138 67
#> theta[16] 16.5 0.83557326 48.463249 58
#> theta[17] 17.5 0.91297138 73.950682 81
#> theta[18] 18.5 0.87740525 69.315015 79
#> theta[19] 19.5 0.88096489 97.787103 111
#> theta[20] 20.5 0.85296012 64.824969 76
#> theta[21] 21.5 0.91381393 74.932742 82
#> theta[22] 22.5 0.82591646 83.417563 101
#> theta[23] 23.5 0.94675817 83.314719 88
#> theta[24] 24.5 0.94455038 80.286783 85
#> theta[25] 25.5 0.97117667 91.290607 94
#> theta[26] 26.5 0.93893261 85.442867 91
#> theta[27] 27.5 0.92250475 82.102923 89
#> theta[28] 28.5 0.95724644 72.750729 76
#> theta[29] 29.5 0.90947233 71.848314 79
#> theta[30] 30.5 0.91724503 51.365722 56
#> theta[31] 31.5 0.85925291 44.681151 52
#> theta[32] 32.5 0.94026753 45.132841 48
#> theta[33] 33.5 0.93803638 34.707346 37
#> theta[34] 34.5 0.94590280 38.782015 41
#> theta[35] 35.5 0.89266213 35.706485 40
#> theta[36] 36.5 0.95663683 36.352200 38
#> theta[37] 37.5 0.94020554 36.668016 39
#> theta[38] 38.5 0.89728275 36.788593 41
#> theta[39] 39.5 0.92115665 27.634700 30
#> theta[40] 40.5 0.93562086 25.261763 27
#> theta[41] 41.5 0.95331258 23.832814 25
#> theta[42] 42.5 0.91985610 20.236834 22
#> theta[43] 43.5 0.90785161 17.249181 19
#> theta[44] 44.5 0.93802974 16.884535 18
#>