R version 4.5.0 RC (2025-04-04 r88118 ucrt) -- "How About a Twenty-Six" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library("runjags") > set.seed(2022-03-09) > > N <- 600 > status <- rbinom(N, 1, rep(c(0.25,0.5,0.75), each=N/3)) > testdata <- data.frame(Population = rep(1:3, each=N/3), Test1 = rbinom(N, 1, status*0.75 + (1-status)*0.05), Test2 = rbinom(N, 1, status*0.75 + (1-status)*0.05), Test3=rbinom(N, 1, status*0.75 + (1-status)*0.05)) > > template_huiwalter(testdata, outfile="huiwalter_model.txt", covariance=TRUE, cov_as_cor=TRUE) The model and data have been written to huiwalter_model.txt in the current working directory *** NOTE: The template provided should be examined and modified (including checking *** *** priors, covariance terms, and verifying the code) before running the model! *** Warning messages: 1: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : Setting covariance=TRUE is now deprecated; please specify a data frame of desired covariance terms instead (see ?template_huiwalter) 2: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : You have specified a lot of active conditional depdendence terms, which is not recommended; if you really need this many conditional depdendence terms then you should probably use an alternative model formulation 3: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : The cov_as_cor option is now deprecated and ignored (i.e. always interpreted as FALSE) > results <- run.jags("huiwalter_model.txt") INFORMATION: Es konnten keine Dateien mit dem angegebenen Muster gefunden werden. Loading required namespace: rjags Compiling rjags model... Calling the simulation using the rjags method... Adapting the model for 1000 iterations... Burning in the model for 4000 iterations... Running the model for 10000 iterations... Simulation complete Calculating summary statistics... Calculating the Gelman-Rubin statistic for 45 variables.... Note: Unable to calculate the multivariate psrf Finished running the simulation > #unlink("huiwalter_model.txt") > results JAGS model summary statistics from 20000 samples (chains = 2; adapt+burnin = 5000): Lower95 Median Upper95 Mean SD se[1] 0.58945 0.68179 0.76754 0.68013 0.046403 se[2] 0.58603 0.67939 0.76703 0.6785 0.047022 se[3] 0.6117 0.70757 0.79354 0.70588 0.047322 sp[1] 0.88279 0.9314 0.97617 0.93055 0.023914 sp[2] 0.90062 0.94624 0.98677 0.94467 0.022381 sp[3] 0.89018 0.94134 0.98312 0.93968 0.023847 prev[1] 0.19692 0.2719 0.35863 0.27396 0.041337 prev[2] 0.34019 0.43779 0.54473 0.44123 0.053074 prev[3] 0.67585 0.78313 0.91562 0.78909 0.061874 covse_1_2 -0.0089789 0.015703 0.041333 0.015877 0.0131 covse_1_3 -0.01473 0.0098893 0.036269 0.010339 0.013362 covse_2_3 -0.015445 0.0092361 0.03662 0.0097086 0.013719 corse_1_2 -0.081539 0.078891 0.21047 0.071116 0.075538 corse_1_3 -0.18268 0.05214 0.18903 0.035897 0.095947 corse_2_3 -0.1907 0.048844 0.19782 0.029985 0.10062 covsp_1_2 -0.0019796 0.00068843 0.0039943 0.00085564 0.0015679 covsp_1_3 -0.0025163 0.00033766 0.0033945 0.00043787 0.0014983 covsp_2_3 -0.0014726 0.0011429 0.0045346 0.0013424 0.001576 corsp_1_2 -0.3574 0.01748 0.13757 -0.023379 0.12451 corsp_1_3 -0.38436 0.0081779 0.10356 -0.053812 0.13608 corsp_2_3 -0.27108 0.030905 0.17423 0.010874 0.10311 check_outcome_RRR[1,1] -7 11 29 10.837 9.4304 check_outcome_RRR[2,1] -15 -5 1 -5.5739 4.2419 check_outcome_RRR[3,1] -12 -4 2 -4.4638 3.8894 check_outcome_RRR[4,1] -6 1 5 0.4998 3.0135 check_outcome_RRR[5,1] -13 -3 3 -3.3567 4.1886 check_outcome_RRR[6,1] -9 -3 2 -2.831 3.0517 check_outcome_RRR[7,1] -1 5 10 5.1505 3.0836 check_outcome_RRR[8,1] -10 0 9 -0.26225 5.1537 check_outcome_RRR[1,2] -21 -2 16 -1.6787 9.5919 check_outcome_RRR[2,2] -5 3 9 2.7671 3.792 check_outcome_RRR[3,2] -6 2 7 1.4515 3.5241 check_outcome_RRR[4,2] -6 1 8 1.2395 3.8293 check_outcome_RRR[5,2] -9 -1 6 -0.91275 3.9365 check_outcome_RRR[6,2] -9 0 6 -0.33775 3.9224 check_outcome_RRR[7,2] -7 0 7 -0.25085 3.849 check_outcome_RRR[8,2] -16 -2 8 -2.2782 6.2613 check_outcome_RRR[1,3] -17 0 15 0.09955 8.2634 check_outcome_RRR[2,3] -10 -2 5 -2.2041 4.1602 check_outcome_RRR[3,3] -10 -1 5 -1.666 3.9947 check_outcome_RRR[4,3] -10 2 10 1.411 5.1148 check_outcome_RRR[5,3] -11 -1 6 -1.0456 4.4776 check_outcome_RRR[6,3] -4 7 16 6.2674 5.3335 check_outcome_RRR[7,3] -12 -1 8 -1.4401 5.264 check_outcome_RRR[8,3] -18 -1 13 -1.4221 8.0937 Mode MCerr MC%ofSD SSeff AC.10 se[1] 0.685 0.0013597 2.9 1165 0.30231 se[2] 0.68405 0.001411 3 1111 0.32628 se[3] 0.71247 0.0013814 2.9 1173 0.3076 sp[1] 0.93255 0.00056513 2.4 1791 0.18569 sp[2] 0.94861 0.00049312 2.2 2060 0.15284 sp[3] 0.94166 0.00060485 2.5 1554 0.23389 prev[1] 0.26966 0.00075637 1.8 2987 0.11598 prev[2] 0.43284 0.0011935 2.2 1978 0.19066 prev[3] 0.77817 0.0018587 3 1108 0.33926 covse_1_2 0.01557 0.00040212 3.1 1061 0.33489 covse_1_3 0.0098073 0.00040019 3 1115 0.33337 covse_2_3 0.007166 0.00042098 3.1 1062 0.35538 corse_1_2 0.082674 0.0021465 2.8 1238 0.26935 corse_1_3 0.054744 0.0025125 2.6 1458 0.25113 corse_2_3 0.054983 0.0027651 2.7 1324 0.27442 covsp_1_2 0.00051421 0.000039074 2.5 1610 0.22829 covsp_1_3 0.0003015 0.000037482 2.5 1598 0.22034 covsp_2_3 0.00083113 0.000043847 2.8 1292 0.28256 corsp_1_2 0.021726 0.0024015 1.9 2688 0.10479 corsp_1_3 0.022052 0.0026003 1.9 2739 0.09785 corsp_2_3 0.024386 0.0020566 2 2514 0.099676 check_outcome_RRR[1,1] 11 0.10953 1.2 7413 0.031248 check_outcome_RRR[2,1] -5 0.06453 1.5 4321 0.067147 check_outcome_RRR[3,1] -3 0.053728 1.4 5240 0.054536 check_outcome_RRR[4,1] 1 0.023112 0.8 17001 0.0012501 check_outcome_RRR[5,1] -2 0.064283 1.5 4246 0.076449 check_outcome_RRR[6,1] -2 0.02383 0.8 16400 0.0037115 check_outcome_RRR[7,1] 6 0.022724 0.7 18413 0.008897 check_outcome_RRR[8,1] -1 0.040353 0.8 16311 0.0015084 check_outcome_RRR[1,2] -1 0.078889 0.8 14783 0.0032505 check_outcome_RRR[2,2] 3 0.037967 1 9975 0.013515 check_outcome_RRR[3,2] 3 0.03335 0.9 11166 0.0089421 check_outcome_RRR[4,2] 2 0.029473 0.8 16880 0.013735 check_outcome_RRR[5,2] 0 0.040161 1 9608 0.012992 check_outcome_RRR[6,2] 0 0.030442 0.8 16602 0.0077803 check_outcome_RRR[7,2] 1 0.030589 0.8 15834 -0.0041377 check_outcome_RRR[8,2] -2 0.050058 0.8 15646 -0.0092743 check_outcome_RRR[1,3] 2 0.068041 0.8 14749 -0.000082661 check_outcome_RRR[2,3] -1 0.048372 1.2 7397 0.023952 check_outcome_RRR[3,3] -1 0.04206 1.1 9021 0.011234 check_outcome_RRR[4,3] 2 0.040397 0.8 16031 0.010077 check_outcome_RRR[5,3] -1 0.050675 1.1 7807 0.021526 check_outcome_RRR[6,3] 7 0.042185 0.8 15985 -0.00039137 check_outcome_RRR[7,3] -1 0.041247 0.8 16287 -0.0014498 check_outcome_RRR[8,3] -1 0.073097 0.9 12260 0.0078125 psrf se[1] 1.0034 se[2] 1.0036 se[3] 1.0037 sp[1] 1.0035 sp[2] 1.0002 sp[3] 1.0035 prev[1] 1.002 prev[2] 1.0041 prev[3] 1.0053 covse_1_2 1.0053 covse_1_3 1.0038 covse_2_3 1.0043 corse_1_2 1.003 corse_1_3 1.0017 corse_2_3 1.0019 covsp_1_2 1.0052 covsp_1_3 1.0028 covsp_2_3 1.0004 corsp_1_2 0.99997 corsp_1_3 1.0024 corsp_2_3 1.0012 check_outcome_RRR[1,1] 1.0009 check_outcome_RRR[2,1] 1.0029 check_outcome_RRR[3,1] 1.0001 check_outcome_RRR[4,1] 1.0001 check_outcome_RRR[5,1] 1.0003 check_outcome_RRR[6,1] 0.99999 check_outcome_RRR[7,1] 0.99997 check_outcome_RRR[8,1] 1.0002 check_outcome_RRR[1,2] 1 check_outcome_RRR[2,2] 1.0003 check_outcome_RRR[3,2] 0.99996 check_outcome_RRR[4,2] 1 check_outcome_RRR[5,2] 1.0002 check_outcome_RRR[6,2] 1.0002 check_outcome_RRR[7,2] 0.99997 check_outcome_RRR[8,2] 1 check_outcome_RRR[1,3] 1.0001 check_outcome_RRR[2,3] 1.0003 check_outcome_RRR[3,3] 1 check_outcome_RRR[4,3] 1.0007 check_outcome_RRR[5,3] 1 check_outcome_RRR[6,3] 1.0008 check_outcome_RRR[7,3] 0.99999 check_outcome_RRR[8,3] 0.99997 Total time taken: 14.8 seconds > > template_huiwalter(testdata, outfile="huiwalter_model.txt", covariance=TRUE, cov_as_cor=FALSE) The model and data have been written to huiwalter_model.txt in the current working directory *** NOTE: The template provided should be examined and modified (including checking *** *** priors, covariance terms, and verifying the code) before running the model! *** Warning messages: 1: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : Setting covariance=TRUE is now deprecated; please specify a data frame of desired covariance terms instead (see ?template_huiwalter) 2: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : You have specified a lot of active conditional depdendence terms, which is not recommended; if you really need this many conditional depdendence terms then you should probably use an alternative model formulation > results <- run.jags("huiwalter_model.txt") Compiling rjags model... Calling the simulation using the rjags method... Adapting the model for 1000 iterations... Burning in the model for 4000 iterations... Running the model for 10000 iterations... Simulation complete Calculating summary statistics... Calculating the Gelman-Rubin statistic for 45 variables.... Note: Unable to calculate the multivariate psrf Finished running the simulation > #unlink("huiwalter_model.txt") > results JAGS model summary statistics from 20000 samples (chains = 2; adapt+burnin = 5000): Lower95 Median Upper95 Mean SD se[1] 0.59106 0.68431 0.76679 0.68241 0.045279 se[2] 0.58567 0.68188 0.76605 0.68026 0.046736 se[3] 0.61343 0.70944 0.79551 0.70789 0.047197 sp[1] 0.88259 0.93245 0.97729 0.93172 0.024173 sp[2] 0.89952 0.94574 0.98561 0.94436 0.022309 sp[3] 0.89614 0.94095 0.98369 0.93991 0.02254 prev[1] 0.1949 0.27079 0.35476 0.27286 0.040942 prev[2] 0.34044 0.43711 0.54351 0.43962 0.052511 prev[3] 0.67317 0.78072 0.90669 0.78592 0.059887 covse_1_2 -0.0085237 0.014831 0.040054 0.015191 0.012816 covse_1_3 -0.014971 0.0091769 0.034833 0.0096281 0.013069 covse_2_3 -0.01579 0.0087254 0.034781 0.0092084 0.013426 corse_1_2 -0.079492 0.075453 0.20733 0.068444 0.072853 corse_1_3 -0.17725 0.048315 0.18813 0.031998 0.094954 corse_2_3 -0.20042 0.045947 0.18655 0.026826 0.10153 covsp_1_2 -0.0019129 0.00068669 0.0038469 0.00083298 0.0014493 covsp_1_3 -0.0023355 0.00037045 0.0032177 0.00043344 0.0014022 covsp_2_3 -0.0013613 0.0011049 0.0043078 0.0012856 0.0014858 corsp_1_2 -0.354 0.017868 0.1273 -0.02136 0.12151 corsp_1_3 -0.38374 0.0090412 0.099365 -0.05104 0.13356 corsp_2_3 -0.28167 0.029235 0.16784 0.0087283 0.10334 check_outcome_RRR[1,1] -8 11 28 10.764 9.3948 check_outcome_RRR[2,1] -15 -5 1 -5.4597 4.2741 check_outcome_RRR[3,1] -12 -4 2 -4.5217 3.8961 check_outcome_RRR[4,1] -6 1 5 0.50185 2.987 check_outcome_RRR[5,1] -13 -3 3 -3.3443 4.1712 check_outcome_RRR[6,1] -9 -3 2 -2.8202 3.0677 check_outcome_RRR[7,1] -1 5 10 5.1383 3.0833 check_outcome_RRR[8,1] -10 0 9 -0.2576 5.1558 check_outcome_RRR[1,2] -21 -2 16 -1.7471 9.6535 check_outcome_RRR[2,2] -5 3 9 2.8923 3.8288 check_outcome_RRR[3,2] -6 2 7 1.3869 3.5492 check_outcome_RRR[4,2] -6 2 8 1.2314 3.8542 check_outcome_RRR[5,2] -9 -1 6 -0.8364 3.9065 check_outcome_RRR[6,2] -9 0 6 -0.41105 3.9572 check_outcome_RRR[7,2] -9 0 6 -0.2609 3.9278 check_outcome_RRR[8,2] -15 -2 9 -2.2551 6.3185 check_outcome_RRR[1,3] -15 0 16 0.07665 8.2765 check_outcome_RRR[2,3] -10 -2 5 -2.1985 4.1063 check_outcome_RRR[3,3] -10 -1 5 -1.6369 4.0005 check_outcome_RRR[4,3] -10 2 10 1.3364 5.2088 check_outcome_RRR[5,3] -9 -1 7 -0.9539 4.4655 check_outcome_RRR[6,3] -4 7 16 6.2375 5.3069 check_outcome_RRR[7,3] -12 -1 8 -1.4738 5.2921 check_outcome_RRR[8,3] -18 -1 13 -1.3876 8.0862 Mode MCerr MC%ofSD SSeff AC.10 psrf se[1] 0.68501 0.0012471 2.8 1318 0.27808 1.0031 se[2] 0.68644 0.0013914 3 1128 0.32521 1.0046 se[3] 0.71096 0.0013613 2.9 1202 0.31321 1.0026 sp[1] 0.93308 0.00062751 2.6 1484 0.23541 1.0003 sp[2] 0.94789 0.00048066 2.2 2154 0.12161 1.0001 sp[3] 0.94396 0.00049432 2.2 2079 0.13652 1.0019 prev[1] 0.26659 0.00078535 1.9 2718 0.12701 1.0016 prev[2] 0.432 0.0011483 2.2 2091 0.16424 1.0017 prev[3] 0.7719 0.0017751 3 1138 0.31985 1.003 covse_1_2 0.01351 0.00038312 3 1119 0.32175 1.0066 covse_1_3 0.008196 0.00038297 2.9 1165 0.3164 1.0043 covse_2_3 0.0076565 0.00041783 3.1 1032 0.35412 1.004 corse_1_2 0.07873 0.0019789 2.7 1355 0.26953 1.0046 corse_1_3 0.056035 0.0024492 2.6 1503 0.2395 1.0019 corse_2_3 0.050235 0.0029058 2.9 1221 0.29067 1.001 covsp_1_2 0.00051386 0.000030762 2.1 2220 0.12693 1.0011 covsp_1_3 0.0003045 0.000030742 2.2 2080 0.14528 1.0003 covsp_2_3 0.00082915 0.000036441 2.5 1662 0.21276 0.99997 corsp_1_2 0.02132 0.0020699 1.7 3446 0.071483 1.0011 corsp_1_3 0.020829 0.0023461 1.8 3241 0.064294 1.0005 corsp_2_3 0.024355 0.00186 1.8 3086 0.071896 1.0001 check_outcome_RRR[1,1] 8 0.1008 1.1 8686 0.025535 0.99997 check_outcome_RRR[2,1] -4 0.06753 1.6 4006 0.081961 0.99999 check_outcome_RRR[3,1] -4 0.05035 1.3 5988 0.028901 1.0004 check_outcome_RRR[4,1] 1 0.021806 0.7 18764 -0.0058197 1 check_outcome_RRR[5,1] -2 0.057451 1.4 5271 0.034495 1.0011 check_outcome_RRR[6,1] -2 0.022818 0.7 18074 -0.0060236 1 check_outcome_RRR[7,1] 5 0.023542 0.8 17154 0.00016724 1.0001 check_outcome_RRR[8,1] 0 0.040241 0.8 16416 -0.0042166 1.0001 check_outcome_RRR[1,2] 0 0.077844 0.8 15379 -0.007824 1.0001 check_outcome_RRR[2,2] 4 0.041533 1.1 8498 0.020023 0.99996 check_outcome_RRR[3,2] 2 0.033072 0.9 11517 0.0037197 1 check_outcome_RRR[4,2] 2 0.030759 0.8 15701 -0.0041807 1 check_outcome_RRR[5,2] 0 0.035606 0.9 12037 0.015426 0.99996 check_outcome_RRR[6,2] 0 0.029738 0.8 17707 -0.0016894 1 check_outcome_RRR[7,2] 1 0.031363 0.8 15684 0.0091511 1 check_outcome_RRR[8,2] -2 0.049165 0.8 16516 0.0010051 1.0002 check_outcome_RRR[1,3] -1 0.066902 0.8 15305 0.011933 1.0001 check_outcome_RRR[2,3] -1 0.046522 1.1 7791 0.027666 1.0003 check_outcome_RRR[3,3] -1 0.043993 1.1 8269 0.026537 1.0001 check_outcome_RRR[4,3] 3 0.039825 0.8 17106 0.014529 1.0001 check_outcome_RRR[5,3] 0 0.045932 1 9452 0.017642 1.0001 check_outcome_RRR[6,3] 8 0.04077 0.8 16943 0.0053091 1.0003 check_outcome_RRR[7,3] -2 0.040825 0.8 16804 -0.0048064 1.0004 check_outcome_RRR[8,3] 0 0.073164 0.9 12215 0.013654 1 Total time taken: 13.5 seconds > > template_huiwalter(testdata, outfile="huiwalter_model.txt", covariance=FALSE, cov_as_cor=TRUE) The model and data have been written to huiwalter_model.txt in the current working directory *** NOTE: The template provided should be examined and modified (including checking *** *** priors, covariance terms, and verifying the code) before running the model! *** Warning message: In template_huiwalter(testdata, outfile = "huiwalter_model.txt", : The cov_as_cor option is now deprecated and ignored (i.e. always interpreted as FALSE) > results <- run.jags("huiwalter_model.txt") Compiling rjags model... Calling the simulation using the rjags method... Adapting the model for 1000 iterations... Burning in the model for 4000 iterations... Running the model for 10000 iterations... Simulation complete Calculating summary statistics... Note: The monitored variables 'covse_1_2', 'covse_1_3', 'covse_2_3', 'corse_1_2', 'corse_1_3', 'corse_2_3', 'covsp_1_2', 'covsp_1_3', 'covsp_2_3', 'corsp_1_2', 'corsp_1_3' and 'corsp_2_3' appear to be non-stochastic; they will not be included in the convergence diagnostic Calculating the Gelman-Rubin statistic for 45 variables.... Note: Unable to calculate the multivariate psrf Finished running the simulation > #unlink("huiwalter_model.txt") > results JAGS model summary statistics from 20000 samples (chains = 2; adapt+burnin = 5000): Lower95 Median Upper95 Mean SD Mode se[1] 0.63818 0.7032 0.7683 0.70312 0.033145 0.70377 se[2] 0.63727 0.70215 0.76448 0.70164 0.032906 0.70428 se[3] 0.65455 0.71901 0.77986 0.71862 0.032286 0.72018 sp[1] 0.92134 0.95879 0.99468 0.95783 0.019116 0.96022 sp[2] 0.93838 0.9704 0.99998 0.96884 0.017218 0.97409 sp[3] 0.91962 0.95745 0.99421 0.95624 0.019461 0.95867 prev[1] 0.20399 0.27591 0.34815 0.27666 0.036914 0.27377 prev[2] 0.36557 0.45109 0.54565 0.45146 0.046097 0.452 prev[3] 0.69367 0.76434 0.83291 0.76344 0.03584 0.76879 covse_1_2 0 0 0 0 0 0 covse_1_3 0 0 0 0 0 0 covse_2_3 0 0 0 0 0 0 corse_1_2 0 0 0 0 0 0 corse_1_3 0 0 0 0 0 0 corse_2_3 0 0 0 0 0 0 covsp_1_2 0 0 0 0 0 0 covsp_1_3 0 0 0 0 0 0 covsp_2_3 0 0 0 0 0 0 corsp_1_2 0 0 0 0 0 0 corsp_1_3 0 0 0 0 0 0 corsp_2_3 0 0 0 0 0 0 check_outcome_RRR[1,1] -13 5 23 5.3937 9.4193 6 check_outcome_RRR[2,1] -11 -3 3 -2.9518 3.7303 -2 check_outcome_RRR[3,1] -9 -2 3 -2.4123 3.4063 -2 check_outcome_RRR[4,1] -6 0 5 0.13005 3.0783 1 check_outcome_RRR[5,1] -9 -1 5 -1.4295 3.7985 0 check_outcome_RRR[6,1] -10 -3 2 -3.6107 3.2317 -3 check_outcome_RRR[7,1] -2 5 10 4.4981 3.2055 5 check_outcome_RRR[8,1] -10 1 9 0.3824 4.9991 1 check_outcome_RRR[1,2] -22 -2 16 -2.4451 9.9048 -4 check_outcome_RRR[2,2] -3 5 10 4.304 3.537 5 check_outcome_RRR[3,2] -4 3 8 2.5232 3.2577 4 check_outcome_RRR[4,2] -8 1 7 0.3231 3.952 1 check_outcome_RRR[5,2] -6 1 7 0.7125 3.6031 2 check_outcome_RRR[6,2] -11 -2 5 -1.8118 4.1353 -2 check_outcome_RRR[7,2] -11 -1 5 -1.6584 4.1525 -1 check_outcome_RRR[8,2] -15 -2 9 -1.9473 6.2117 -1 check_outcome_RRR[1,3] -18 1 14 0.1884 8.2635 1 check_outcome_RRR[2,3] -10 -3 3 -2.886 3.5495 -2 check_outcome_RRR[3,3] -10 -2 3 -2.2951 3.4125 -2 check_outcome_RRR[4,3] -10 1 10 0.80135 5.1776 1 check_outcome_RRR[5,3] -8 1 6 0.39165 3.6526 1 check_outcome_RRR[6,3] -5 5 15 4.8647 5.3711 5 check_outcome_RRR[7,3] -13 -3 7 -2.8872 5.3987 -3 check_outcome_RRR[8,3] -15 2 16 1.8223 8.0076 1 MCerr MC%ofSD SSeff AC.10 psrf se[1] 0.00041486 1.3 6383 0.0055874 1.0001 se[2] 0.00041109 1.2 6407 -0.0071488 1.0002 se[3] 0.00039193 1.2 6786 -0.0040166 0.99998 sp[1] 0.00023749 1.2 6479 0.0031197 1.0004 sp[2] 0.00021795 1.3 6241 0.012663 0.99996 sp[3] 0.00024987 1.3 6066 0.016128 0.99997 prev[1] 0.00042068 1.1 7700 0.0074449 1.0005 prev[2] 0.00059637 1.3 5975 0.016202 1.0002 prev[3] 0.00037752 1.1 9013 0.0052379 1.0003 covse_1_2 -- -- -- -- -- covse_1_3 -- -- -- -- -- covse_2_3 -- -- -- -- -- corse_1_2 -- -- -- -- -- corse_1_3 -- -- -- -- -- corse_2_3 -- -- -- -- -- covsp_1_2 -- -- -- -- -- covsp_1_3 -- -- -- -- -- covsp_2_3 -- -- -- -- -- corsp_1_2 -- -- -- -- -- corsp_1_3 -- -- -- -- -- corsp_2_3 -- -- -- -- -- check_outcome_RRR[1,1] 0.077122 0.8 14917 -0.012423 1 check_outcome_RRR[2,1] 0.032272 0.9 13362 -0.00031828 1.0003 check_outcome_RRR[3,1] 0.03009 0.9 12815 0.0016449 1.0002 check_outcome_RRR[4,1] 0.023623 0.8 16981 -0.013817 0.99997 check_outcome_RRR[5,1] 0.034121 0.9 12393 0.0019132 0.99995 check_outcome_RRR[6,1] 0.025521 0.8 16035 -0.0023122 1.0002 check_outcome_RRR[7,1] 0.025242 0.8 16127 0.0056333 0.99999 check_outcome_RRR[8,1] 0.038525 0.8 16839 -0.0044666 1.0002 check_outcome_RRR[1,2] 0.078893 0.8 15762 0.0038037 0.99997 check_outcome_RRR[2,2] 0.026255 0.7 18149 -0.0027407 1.0001 check_outcome_RRR[3,2] 0.024872 0.8 17156 0.0033345 1.0002 check_outcome_RRR[4,2] 0.03265 0.8 14652 -0.0098311 1 check_outcome_RRR[5,2] 0.027527 0.8 17133 0.0051804 0.99996 check_outcome_RRR[6,2] 0.033537 0.8 15205 0.0020375 1.0002 check_outcome_RRR[7,2] 0.035936 0.9 13353 -0.0011236 1.0004 check_outcome_RRR[8,2] 0.047488 0.8 17110 0.0012571 0.99998 check_outcome_RRR[1,3] 0.066087 0.8 15635 -0.0072277 1.0007 check_outcome_RRR[2,3] 0.026598 0.7 17809 -0.007661 1 check_outcome_RRR[3,3] 0.027036 0.8 15931 -0.009585 1.0001 check_outcome_RRR[4,3] 0.040788 0.8 16114 -0.0083191 1 check_outcome_RRR[5,3] 0.028521 0.8 16401 -0.014048 0.99996 check_outcome_RRR[6,3] 0.042575 0.8 15916 -0.0088324 1 check_outcome_RRR[7,3] 0.044999 0.8 14394 -0.004265 1.0001 check_outcome_RRR[8,3] 0.076217 1 11038 -0.010448 1.0003 Total time taken: 9.1 seconds > > template_huiwalter(testdata, outfile="huiwalter_model.txt", covariance=FALSE, cov_as_cor=FALSE) The model and data have been written to huiwalter_model.txt in the current working directory *** NOTE: The template provided should be examined and modified (including checking *** *** priors, covariance terms, and verifying the code) before running the model! *** > results <- run.jags("huiwalter_model.txt") Compiling rjags model... Calling the simulation using the rjags method... Adapting the model for 1000 iterations... Burning in the model for 4000 iterations... Running the model for 10000 iterations... Simulation complete Calculating summary statistics... Note: The monitored variables 'covse_1_2', 'covse_1_3', 'covse_2_3', 'corse_1_2', 'corse_1_3', 'corse_2_3', 'covsp_1_2', 'covsp_1_3', 'covsp_2_3', 'corsp_1_2', 'corsp_1_3' and 'corsp_2_3' appear to be non-stochastic; they will not be included in the convergence diagnostic Calculating the Gelman-Rubin statistic for 45 variables.... Note: Unable to calculate the multivariate psrf Finished running the simulation > #unlink("huiwalter_model.txt") > results JAGS model summary statistics from 20000 samples (chains = 2; adapt+burnin = 5000): Lower95 Median Upper95 Mean SD Mode se[1] 0.64068 0.70336 0.76652 0.70343 0.032461 0.70041 se[2] 0.63465 0.70219 0.76511 0.70162 0.033301 0.70382 se[3] 0.65436 0.71861 0.78047 0.71836 0.032311 0.7206 sp[1] 0.92252 0.95887 0.99479 0.95788 0.019056 0.95998 sp[2] 0.93775 0.97059 0.99999 0.96885 0.01731 0.97238 sp[3] 0.91831 0.95743 0.99287 0.95624 0.019505 0.95885 prev[1] 0.20166 0.27581 0.34717 0.27656 0.037166 0.27425 prev[2] 0.36277 0.4514 0.53976 0.45173 0.0456 0.45003 prev[3] 0.69278 0.76519 0.83225 0.76404 0.035695 0.76606 covse_1_2 0 0 0 0 0 0 covse_1_3 0 0 0 0 0 0 covse_2_3 0 0 0 0 0 0 corse_1_2 0 0 0 0 0 0 corse_1_3 0 0 0 0 0 0 corse_2_3 0 0 0 0 0 0 covsp_1_2 0 0 0 0 0 0 covsp_1_3 0 0 0 0 0 0 covsp_2_3 0 0 0 0 0 0 corsp_1_2 0 0 0 0 0 0 corsp_1_3 0 0 0 0 0 0 corsp_2_3 0 0 0 0 0 0 check_outcome_RRR[1,1] -13 5 23 5.2453 9.4532 5 check_outcome_RRR[2,1] -11 -3 3 -2.955 3.7555 -2 check_outcome_RRR[3,1] -9 -2 3 -2.3872 3.3969 -1 check_outcome_RRR[4,1] -6 0 5 0.13365 3.0867 1 check_outcome_RRR[5,1] -9 -1 5 -1.4431 3.8302 -1 check_outcome_RRR[6,1] -10 -3 2 -3.5887 3.2151 -3 check_outcome_RRR[7,1] -2 5 10 4.58 3.1782 5 check_outcome_RRR[8,1] -10 1 9 0.4152 5.0302 1 check_outcome_RRR[1,2] -23 -3 15 -2.5047 9.8315 -4 check_outcome_RRR[2,2] -3 5 10 4.3061 3.4808 5 check_outcome_RRR[3,2] -4 3 8 2.5221 3.2489 3 check_outcome_RRR[4,2] -8 1 7 0.3018 3.9776 1 check_outcome_RRR[5,2] -6 1 7 0.7524 3.5964 2 check_outcome_RRR[6,2] -11 -2 5 -1.7853 4.1593 -1 check_outcome_RRR[7,2] -9 -1 6 -1.688 4.123 -1 check_outcome_RRR[8,2] -15 -2 9 -1.9045 6.1747 0 check_outcome_RRR[1,3] -17 1 15 0.29395 8.3546 -1 check_outcome_RRR[2,3] -10 -3 3 -2.8834 3.4953 -3 check_outcome_RRR[3,3] -10 -2 3 -2.3064 3.4552 -2 check_outcome_RRR[4,3] -9 1 10 0.7329 5.1167 2 check_outcome_RRR[5,3] -6 1 7 0.33315 3.6221 1 check_outcome_RRR[6,3] -5 5 15 4.8586 5.3658 6 check_outcome_RRR[7,3] -14 -3 6 -2.9064 5.32 -3 check_outcome_RRR[8,3] -15 2 16 1.8777 8.0084 2 MCerr MC%ofSD SSeff AC.10 psrf se[1] 0.00039504 1.2 6752 0.021767 1.0001 se[2] 0.00041828 1.3 6338 -0.0057988 1.0001 se[3] 0.00038005 1.2 7228 0.0062881 1.0008 sp[1] 0.00023127 1.2 6789 -0.0035173 1.0001 sp[2] 0.00022416 1.3 5963 -0.00041684 1.0009 sp[3] 0.00024063 1.2 6571 0.0085699 1.0004 prev[1] 0.00041209 1.1 8134 0.003058 1.0002 prev[2] 0.00060356 1.3 5708 0.014048 1.0003 prev[3] 0.00039393 1.1 8211 0.0059435 0.99997 covse_1_2 -- -- -- -- -- covse_1_3 -- -- -- -- -- covse_2_3 -- -- -- -- -- corse_1_2 -- -- -- -- -- corse_1_3 -- -- -- -- -- corse_2_3 -- -- -- -- -- covsp_1_2 -- -- -- -- -- covsp_1_3 -- -- -- -- -- covsp_2_3 -- -- -- -- -- corsp_1_2 -- -- -- -- -- corsp_1_3 -- -- -- -- -- corsp_2_3 -- -- -- -- -- check_outcome_RRR[1,1] 0.074476 0.8 16111 -0.0043837 0.99996 check_outcome_RRR[2,1] 0.031845 0.8 13908 -0.004386 1 check_outcome_RRR[3,1] 0.030551 0.9 12362 -0.00029763 1.0001 check_outcome_RRR[4,1] 0.023897 0.8 16685 0.00081207 1 check_outcome_RRR[5,1] 0.034365 0.9 12423 0.0092449 1.0002 check_outcome_RRR[6,1] 0.025837 0.8 15485 -0.0070575 1 check_outcome_RRR[7,1] 0.024197 0.8 17252 0.000015395 1.0001 check_outcome_RRR[8,1] 0.038084 0.8 17445 0.0032754 1 check_outcome_RRR[1,2] 0.078311 0.8 15762 0.00097911 0.99995 check_outcome_RRR[2,2] 0.027029 0.8 16585 -0.00068961 1.0001 check_outcome_RRR[3,2] 0.024395 0.8 17737 -0.002021 1.0003 check_outcome_RRR[4,2] 0.033058 0.8 14477 0.013189 0.99998 check_outcome_RRR[5,2] 0.026258 0.7 18759 -0.0099514 1.0001 check_outcome_RRR[6,2] 0.03488 0.8 14220 -0.015358 1.0002 check_outcome_RRR[7,2] 0.033473 0.8 15172 0.001521 0.99999 check_outcome_RRR[8,2] 0.046058 0.7 17973 0.0063428 1.0003 check_outcome_RRR[1,3] 0.065733 0.8 16154 0.0004042 1.0002 check_outcome_RRR[2,3] 0.025822 0.7 18323 0.003575 0.99999 check_outcome_RRR[3,3] 0.026723 0.8 16717 0.0031547 1.0001 check_outcome_RRR[4,3] 0.040328 0.8 16097 -0.0033978 0.99995 check_outcome_RRR[5,3] 0.026976 0.7 18029 0.0038079 0.99997 check_outcome_RRR[6,3] 0.043234 0.8 15404 -0.0024176 0.99998 check_outcome_RRR[7,3] 0.042637 0.8 15568 0.0089637 1.0001 check_outcome_RRR[8,3] 0.073895 0.9 11745 0.0060856 1.0006 Total time taken: 9 seconds > > proc.time() user system elapsed 43.50 1.85 51.79