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Type 'q()' to quit R. > library(testthat) > library(BayesianDEB) BayesianDEB v0.1.0 > > test_check("BayesianDEB") -- BDEB Data -- i Individuals: 1 i Endpoints: growth i Functional response (f): 1 > Growth: 6 observations, t = [0, 5] -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 143.0 139.1 24.23 105.9 178.2 NEC 15.1 15.3 1.77 12.3 17.6 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 143.0 139.1 24.23 105.9 178.2 NEC 15.1 15.3 1.77 12.3 17.6 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 140.3 137.3 25.56 102.7 172.9 NEC 14.7 14.7 1.29 12.4 16.9 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 140.5 139 26.37 101.2 187.7 NEC 14.9 15 1.42 12.5 17.3 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 140.5 139 26.37 122 154.9 NEC 14.9 15 1.42 14 15.9 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 143.0 139.1 24.23 105.9 178.2 NEC 15.1 15.3 1.77 12.3 17.6 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 143.0 139.1 24.23 105.9 178.2 NEC 15.1 15.3 1.77 12.3 17.6 -- BDEB Diagnostics -- x Divergent transitions: 50 i Consider: increase adapt_delta, reparameterise, or tighten priors. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_Am, v, E0, L_hat[4] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4602 0.43426 4.4883 3.7856 5.1628 1.033 161 186 p_M 0.4967 0.05362 0.4862 0.4182 0.5940 0.999 162 156 kappa 0.7277 0.12785 0.7429 0.5000 0.8989 1.007 199 224 v 0.2242 0.02185 0.2224 0.1880 0.2604 1.011 150 169 E_G 407.2809 43.47254 400.4637 341.0160 485.3595 0.992 263 186 E0 1.0093 0.10283 1.0021 0.8591 1.1998 1.017 215 187 L0 0.1349 0.01295 0.1346 0.1173 0.1583 0.996 198 136 sigma_L 0.0153 0.00276 0.0152 0.0108 0.0198 0.996 201 231 L_hat[1] 0.1401 0.00489 0.1403 0.1314 0.1480 0.994 241 225 L_hat[2] 0.1798 0.00536 0.1797 0.1712 0.1883 1.005 151 137 L_hat[3] 0.2205 0.00503 0.2204 0.2125 0.2291 1.005 198 137 L_hat[4] 0.2600 0.00426 0.2600 0.2530 0.2674 1.018 175 159 L_hat[5] 0.3002 0.00514 0.3000 0.2921 0.3103 1.001 238 234 -- BDEB Diagnostics -- v No divergent transitions. ! Max treedepth saturated: 60 times. i Consider: increase max_treedepth. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_Am, v, E0, L_hat[4] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4602 0.43426 4.4883 3.7856 5.1628 1.033 161 186 p_M 0.4967 0.05362 0.4862 0.4182 0.5940 0.999 162 156 kappa 0.7277 0.12785 0.7429 0.5000 0.8989 1.007 199 224 v 0.2242 0.02185 0.2224 0.1880 0.2604 1.011 150 169 E_G 407.2809 43.47254 400.4637 341.0160 485.3595 0.992 263 186 E0 1.0093 0.10283 1.0021 0.8591 1.1998 1.017 215 187 L0 0.1349 0.01295 0.1346 0.1173 0.1583 0.996 198 136 sigma_L 0.0153 0.00276 0.0152 0.0108 0.0198 0.996 201 231 L_hat[1] 0.1401 0.00489 0.1403 0.1314 0.1480 0.994 241 225 L_hat[2] 0.1798 0.00536 0.1797 0.1712 0.1883 1.005 151 137 L_hat[3] 0.2205 0.00503 0.2204 0.2125 0.2291 1.005 198 137 L_hat[4] 0.2600 0.00426 0.2600 0.2530 0.2674 1.018 175 159 L_hat[5] 0.3002 0.00514 0.3000 0.2921 0.3103 1.001 238 234 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. ! Low E-BFMI for chain(s): 1 and 2 -- Parameter Summary x R-hat > 1.01 for: p_Am, v, E0, L_hat[4] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4602 0.43426 4.4883 3.7856 5.1628 1.033 161 186 p_M 0.4967 0.05362 0.4862 0.4182 0.5940 0.999 162 156 kappa 0.7277 0.12785 0.7429 0.5000 0.8989 1.007 199 224 v 0.2242 0.02185 0.2224 0.1880 0.2604 1.011 150 169 E_G 407.2809 43.47254 400.4637 341.0160 485.3595 0.992 263 186 E0 1.0093 0.10283 1.0021 0.8591 1.1998 1.017 215 187 L0 0.1349 0.01295 0.1346 0.1173 0.1583 0.996 198 136 sigma_L 0.0153 0.00276 0.0152 0.0108 0.0198 0.996 201 231 L_hat[1] 0.1401 0.00489 0.1403 0.1314 0.1480 0.994 241 225 L_hat[2] 0.1798 0.00536 0.1797 0.1712 0.1883 1.005 151 137 L_hat[3] 0.2205 0.00503 0.2204 0.2125 0.2291 1.005 198 137 L_hat[4] 0.2600 0.00426 0.2600 0.2530 0.2674 1.018 175 159 L_hat[5] 0.3002 0.00514 0.3000 0.2921 0.3103 1.001 238 234 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_Am, p_M, kappa, v, E0, L_hat[4] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 7.4266 4.75420 6.7351 2.5399 13.0284 1.837 3.15 70.1 p_M 1.1257 0.52471 1.0838 0.5668 1.7531 1.824 3.18 105.4 kappa 0.5084 0.31250 0.5329 0.1088 0.8905 1.827 3.22 53.4 v 0.2245 0.02158 0.2226 0.1914 0.2604 1.018 136.43 165.3 E_G 407.3660 43.44814 400.9400 341.0160 485.3595 0.992 268.38 186.1 E0 1.0093 0.10292 1.0013 0.8591 1.1998 1.038 217.42 65.1 L0 0.1350 0.01304 0.1347 0.1173 0.1583 0.997 196.43 131.7 sigma_L 0.0152 0.00279 0.0151 0.0103 0.0198 0.999 177.22 226.9 L_hat[1] 0.1402 0.00485 0.1404 0.1316 0.1482 0.993 247.86 186.1 L_hat[2] 0.1799 0.00538 0.1798 0.1712 0.1883 1.005 178.70 148.9 L_hat[3] 0.2206 0.00502 0.2205 0.2125 0.2291 1.002 198.71 135.3 L_hat[4] 0.2600 0.00424 0.2600 0.2530 0.2674 1.017 171.81 158.3 L_hat[5] 0.3003 0.00513 0.3002 0.2921 0.3103 0.998 257.73 229.4 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: E_G, L_hat[1], L_hat[5] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4905 0.43579 4.4743 3.82e+00 5.1797 1.004 217 156 p_M 0.4994 0.04768 0.4951 4.32e-01 0.5761 1.007 238 187 kappa 0.7312 0.12600 0.7402 5.13e-01 0.9179 0.994 216 230 v 0.2204 0.02117 0.2188 1.87e-01 0.2560 1.000 207 233 E_G 409.2453 44.68899 410.1124 3.43e+02 479.3263 1.015 193 186 E0 1.0018 0.09897 1.0042 8.40e-01 1.1761 0.998 188 219 L0 0.1351 0.01238 0.1342 1.15e-01 0.1570 1.001 290 221 sigma_L 0.0151 0.00300 0.0151 9.97e-03 0.0195 1.003 195 218 L_hat[1] 0.1403 0.00526 0.1400 1.33e-01 0.1486 1.018 152 200 L_hat[2] 0.1800 0.00478 0.1803 1.71e-01 0.1875 1.003 135 131 L_hat[3] 0.2199 0.00520 0.2197 2.11e-01 0.2289 1.007 189 200 L_hat[4] 0.2603 0.00469 0.2602 2.53e-01 0.2673 1.007 219 188 L_hat[5] 0.3004 0.00506 0.3008 2.91e-01 0.3085 1.010 156 132 L_hat[6] 0.3399 0.00529 0.3401 3.30e-01 0.3488 1.001 244 152 L_hat[7] 0.3793 0.00540 0.3791 3.71e-01 0.3886 0.993 222 188 L_hat[8] 0.4198 0.00497 0.4199 4.11e-01 0.4276 1.009 134 218 L_hat[9] 0.4599 0.00518 0.4598 4.52e-01 0.4686 1.003 192 167 L_hat[10] 0.5000 0.00505 0.4998 4.92e-01 0.5078 1.004 207 185 -- BDEB Diagnostics -- x Divergent transitions: 10 i Consider: increase adapt_delta, reparameterise, or tighten priors. ! Max treedepth saturated: 6 times. i Consider: increase max_treedepth. ! Low E-BFMI for chain(s): 1 and 2 -- Parameter Summary x R-hat > 1.01 for: p_Am, v, E0, L_hat[4] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4602 0.43426 4.4883 3.7856 5.1628 1.033 161 186 p_M 0.4967 0.05362 0.4862 0.4182 0.5940 0.999 162 156 kappa 0.7277 0.12785 0.7429 0.5000 0.8989 1.007 199 224 v 0.2242 0.02185 0.2224 0.1880 0.2604 1.011 150 169 E_G 407.2809 43.47254 400.4637 341.0160 485.3595 0.992 263 186 E0 1.0093 0.10283 1.0021 0.8591 1.1998 1.017 215 187 L0 0.1349 0.01295 0.1346 0.1173 0.1583 0.996 198 136 sigma_L 0.0153 0.00276 0.0152 0.0108 0.0198 0.996 201 231 L_hat[1] 0.1401 0.00489 0.1403 0.1314 0.1480 0.994 241 225 L_hat[2] 0.1798 0.00536 0.1797 0.1712 0.1883 1.005 151 137 L_hat[3] 0.2205 0.00503 0.2204 0.2125 0.2291 1.005 198 137 L_hat[4] 0.2600 0.00426 0.2600 0.2530 0.2674 1.018 175 159 L_hat[5] 0.3002 0.00514 0.3000 0.2921 0.3103 1.001 238 234 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 139.2 136.9 26.32 102.1 184.7 NEC 14.9 14.9 1.46 12.6 17.3 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 139.2 136.9 26.32 120 156.2 NEC 14.9 14.9 1.46 14 15.9 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: L0, L_hat[2], L_hat[7], L_hat[8] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.5201 0.46048 4.5221 3.7569 5.2130 1.000 90.3 72.3 p_M 0.4943 0.04541 0.4932 0.4276 0.5731 0.986 140.2 123.2 kappa 0.7221 0.13452 0.7359 0.4794 0.8964 0.999 117.6 110.0 v 0.2241 0.02080 0.2215 0.1943 0.2588 1.003 122.8 78.1 E_G 401.2765 40.83679 397.8263 341.1736 466.1875 1.004 95.1 104.7 E0 1.0042 0.11118 0.9949 0.8296 1.1733 1.001 100.3 79.9 L0 0.1344 0.01226 0.1348 0.1165 0.1526 1.084 22.8 73.8 sigma_L 0.0146 0.00269 0.0148 0.0101 0.0193 0.994 90.0 71.5 L_hat[1] 0.1402 0.00544 0.1403 0.1321 0.1487 1.009 147.9 92.0 L_hat[2] 0.1805 0.00592 0.1815 0.1705 0.1885 1.019 88.9 80.5 L_hat[3] 0.2193 0.00471 0.2195 0.2128 0.2273 0.992 83.0 86.8 L_hat[4] 0.2602 0.00509 0.2609 0.2522 0.2687 0.992 108.8 103.6 L_hat[5] 0.3004 0.00477 0.3001 0.2922 0.3080 0.995 160.7 108.2 L_hat[6] 0.3392 0.00472 0.3393 0.3313 0.3462 1.005 157.3 78.4 L_hat[7] 0.3797 0.00463 0.3798 0.3722 0.3863 1.057 126.9 96.6 L_hat[8] 0.4205 0.00526 0.4201 0.4128 0.4289 1.014 114.2 99.8 L_hat[9] 0.4612 0.00511 0.4605 0.4525 0.4685 1.008 97.3 116.0 L_hat[10] 0.4991 0.00501 0.4982 0.4924 0.5081 0.996 87.0 110.4 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: L0, z_w, NEC, L_hat[4], L_hat[5], L_hat[9], L_hat[10] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, k_d, z_w, b_w, EC50, NEC, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.52e+00 4.60e-01 4.5221 3.76e+00 5.21e+00 1.000 90.3 72.3 p_M 4.94e-01 4.54e-02 0.4932 4.28e-01 5.73e-01 0.986 140.2 123.2 kappa 7.22e-01 1.35e-01 0.7359 4.79e-01 8.96e-01 0.999 117.6 110.0 v 2.24e-01 2.08e-02 0.2215 1.94e-01 2.59e-01 1.003 122.8 78.1 E_G 4.01e+02 4.08e+01 397.8263 3.41e+02 4.66e+02 1.004 95.1 104.7 E0 1.00e+00 1.11e-01 0.9949 8.30e-01 1.17e+00 1.001 100.3 79.9 L0 1.34e-01 1.23e-02 0.1348 1.16e-01 1.53e-01 1.084 22.8 73.8 sigma_L 1.46e-02 2.69e-03 0.0148 1.01e-02 1.93e-02 0.994 90.0 71.5 k_d 3.72e-01 4.09e-02 0.3702 3.14e-01 4.37e-01 1.009 147.9 92.0 z_w 1.51e+01 1.77e+00 15.3483 1.23e+01 1.76e+01 1.019 88.9 80.5 b_w 4.05e-03 7.77e-04 0.0040 3.07e-03 5.46e-03 0.992 83.0 86.8 EC50 1.43e+02 2.42e+01 139.1247 1.06e+02 1.78e+02 0.991 86.3 110.9 NEC 1.51e+01 1.77e+00 15.3483 1.23e+01 1.76e+01 1.019 88.9 80.5 L_hat[1] 1.40e-01 5.09e-03 0.1409 1.32e-01 1.49e-01 0.992 108.8 103.6 L_hat[2] 1.80e-01 4.77e-03 0.1801 1.72e-01 1.88e-01 0.995 160.7 108.2 L_hat[3] 2.19e-01 4.72e-03 0.2193 2.11e-01 2.26e-01 1.005 157.3 78.4 L_hat[4] 2.60e-01 4.63e-03 0.2598 2.52e-01 2.66e-01 1.057 126.9 96.6 L_hat[5] 3.01e-01 5.26e-03 0.3001 2.93e-01 3.09e-01 1.014 114.2 99.8 L_hat[6] 3.41e-01 5.11e-03 0.3405 3.32e-01 3.48e-01 1.008 97.3 116.0 L_hat[7] 3.79e-01 5.01e-03 0.3782 3.72e-01 3.88e-01 0.996 87.0 110.4 L_hat[8] 4.21e-01 4.66e-03 0.4207 4.14e-01 4.29e-01 0.987 117.1 99.4 L_hat[9] 4.59e-01 4.70e-03 0.4593 4.51e-01 4.66e-01 1.010 82.4 118.3 L_hat[10] 5.00e-01 4.87e-03 0.4998 4.91e-01 5.07e-01 1.016 72.0 113.5 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 143.0 139.1 24.23 105.9 178.2 NEC 15.1 15.3 1.77 12.3 17.6 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: sigma_log_p_Am, p_Am_ind[3], L0[3], L_hat[3], L_hat[4], L_hat[5], L_hat[8], L_hat[9] ! Low bulk ESS (<400) for: p_M, kappa, v, E_G, E0, sigma_L, mu_log_p_Am, sigma_log_p_Am, p_Am_ind[1], L0[1], p_Am_ind[2], L0[2], p_Am_ind[3], L0[3], L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk p_M 0.4943 0.04541 0.4932 0.4276 0.5731 0.986 140.2 kappa 0.7221 0.13452 0.7359 0.4794 0.8964 0.999 117.6 v 0.2241 0.02080 0.2215 0.1943 0.2588 1.003 122.8 E_G 401.2765 40.83679 397.8263 341.1736 466.1875 1.004 95.1 E0 1.0042 0.11118 0.9949 0.8296 1.1733 1.001 100.3 sigma_L 0.0146 0.00269 0.0148 0.0101 0.0193 0.994 90.0 mu_log_p_Am 1.5021 0.05437 1.5031 1.4210 1.5866 1.009 147.9 sigma_log_p_Am 0.1019 0.02368 0.1062 0.0618 0.1341 1.019 88.9 p_Am_ind[1] 4.4419 0.42122 4.4335 3.8827 5.1814 0.992 83.0 L0[1] 0.1358 0.00691 0.1365 0.1252 0.1476 0.992 108.8 p_Am_ind[2] 4.5393 0.43215 4.4891 3.8371 5.2632 0.995 160.7 L0[2] 0.1344 0.00635 0.1344 0.1241 0.1440 1.004 157.3 p_Am_ind[3] 4.4740 0.41230 4.4595 3.8343 5.0837 1.056 126.9 L0[3] 0.1362 0.00715 0.1355 0.1260 0.1480 1.014 114.2 L_hat[1] 0.1391 0.00501 0.1382 0.1324 0.1481 0.996 87.0 L_hat[2] 0.1810 0.00466 0.1807 0.1736 0.1890 0.987 117.1 L_hat[3] 0.2187 0.00470 0.2193 0.2110 0.2257 1.010 82.4 L_hat[4] 0.2601 0.00487 0.2598 0.2511 0.2674 1.016 72.0 L_hat[5] 0.3000 0.00534 0.2998 0.2925 0.3091 1.072 82.8 L_hat[6] 0.3403 0.00531 0.3401 0.3317 0.3484 0.996 111.2 L_hat[7] 0.3802 0.00442 0.3800 0.3739 0.3872 0.993 129.9 L_hat[8] 0.4203 0.00483 0.4212 0.4109 0.4271 1.025 102.2 L_hat[9] 0.4604 0.00520 0.4609 0.4510 0.4700 1.046 61.2 L_hat[10] 0.5002 0.00549 0.5008 0.4902 0.5096 1.005 107.3 ess_tail 123.2 110.0 78.1 104.7 79.9 71.5 92.0 80.5 86.8 103.6 108.2 78.4 96.6 99.8 110.4 99.4 118.3 113.5 80.1 70.1 116.6 116.6 45.4 46.7 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: L0, L_hat[2], L_hat[7], L_hat[8] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.5201 0.46048 4.5221 3.7569 5.2130 1.000 90.3 72.3 p_M 0.4943 0.04541 0.4932 0.4276 0.5731 0.986 140.2 123.2 kappa 0.7221 0.13452 0.7359 0.4794 0.8964 0.999 117.6 110.0 v 0.2241 0.02080 0.2215 0.1943 0.2588 1.003 122.8 78.1 E_G 401.2765 40.83679 397.8263 341.1736 466.1875 1.004 95.1 104.7 E0 1.0042 0.11118 0.9949 0.8296 1.1733 1.001 100.3 79.9 L0 0.1344 0.01226 0.1348 0.1165 0.1526 1.084 22.8 73.8 sigma_L 0.0146 0.00269 0.0148 0.0101 0.0193 0.994 90.0 71.5 L_hat[1] 0.1402 0.00544 0.1403 0.1321 0.1487 1.009 147.9 92.0 L_hat[2] 0.1805 0.00592 0.1815 0.1705 0.1885 1.019 88.9 80.5 L_hat[3] 0.2193 0.00471 0.2195 0.2128 0.2273 0.992 83.0 86.8 L_hat[4] 0.2602 0.00509 0.2609 0.2522 0.2687 0.992 108.8 103.6 L_hat[5] 0.3004 0.00477 0.3001 0.2922 0.3080 0.995 160.7 108.2 L_hat[6] 0.3392 0.00472 0.3393 0.3313 0.3462 1.005 157.3 78.4 L_hat[7] 0.3797 0.00463 0.3798 0.3722 0.3863 1.057 126.9 96.6 L_hat[8] 0.4205 0.00526 0.4201 0.4128 0.4289 1.014 114.2 99.8 L_hat[9] 0.4612 0.00511 0.4605 0.4525 0.4685 1.008 97.3 116.0 L_hat[10] 0.4991 0.00501 0.4982 0.4924 0.5081 0.996 87.0 110.4 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_Am, p_M, kappa, E_G, L_hat[1], L_hat[2], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[10] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4945 0.51104 4.4369 3.6239 5.3251 1.067 27.4 32.3 p_M 0.5037 0.04513 0.5100 0.4419 0.5710 1.018 49.1 64.0 kappa 0.7552 0.10882 0.7852 0.5126 0.9059 1.061 35.0 47.9 v 0.2242 0.02165 0.2263 0.1915 0.2612 1.000 73.0 65.2 E_G 404.6484 37.61801 397.3021 357.7584 464.9526 1.040 80.7 63.4 E0 1.0065 0.10196 1.0046 0.8381 1.1445 0.972 58.9 64.0 L0 0.1344 0.01099 0.1345 0.1191 0.1519 1.006 76.9 33.6 sigma_L 0.0154 0.00285 0.0148 0.0112 0.0201 0.990 64.9 55.3 L_hat[1] 0.1392 0.00491 0.1387 0.1310 0.1473 1.028 52.2 56.3 L_hat[2] 0.1797 0.00531 0.1799 0.1712 0.1874 1.092 22.8 15.3 L_hat[3] 0.2206 0.00565 0.2197 0.2118 0.2292 1.001 46.4 33.6 L_hat[4] 0.2594 0.00494 0.2598 0.2506 0.2665 0.992 80.7 69.4 L_hat[5] 0.3001 0.00532 0.3016 0.2905 0.3068 1.035 56.2 56.3 L_hat[6] 0.3388 0.00431 0.3385 0.3328 0.3460 1.014 32.9 50.8 L_hat[7] 0.3789 0.00480 0.3785 0.3706 0.3872 1.053 31.0 18.7 L_hat[8] 0.4196 0.00409 0.4201 0.4139 0.4257 1.020 43.1 56.3 L_hat[9] 0.4591 0.00534 0.4588 0.4497 0.4659 0.974 80.7 50.8 L_hat[10] 0.5018 0.00484 0.5009 0.4953 0.5103 1.019 73.6 56.3 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary v All R-hat < 1.01. ! Low bulk ESS (<400) for: p_Am, kappa variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.520 0.460 4.522 3.757 5.213 1.000 90.3 72.3 kappa 0.722 0.135 0.736 0.479 0.896 0.999 117.6 110.0 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary v All R-hat < 1.01. ! Low bulk ESS (<400) for: p_Am variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.52 0.46 4.52 3.76 5.21 1 90.3 72.3 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: L0, L_hat[2], L_hat[7], L_hat[8] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.5201 0.46048 4.5221 3.7569 5.2130 1.000 90.3 72.3 p_M 0.4943 0.04541 0.4932 0.4276 0.5731 0.986 140.2 123.2 kappa 0.7221 0.13452 0.7359 0.4794 0.8964 0.999 117.6 110.0 v 0.2241 0.02080 0.2215 0.1943 0.2588 1.003 122.8 78.1 E_G 401.2765 40.83679 397.8263 341.1736 466.1875 1.004 95.1 104.7 E0 1.0042 0.11118 0.9949 0.8296 1.1733 1.001 100.3 79.9 L0 0.1344 0.01226 0.1348 0.1165 0.1526 1.084 22.8 73.8 sigma_L 0.0146 0.00269 0.0148 0.0101 0.0193 0.994 90.0 71.5 L_hat[1] 0.1402 0.00544 0.1403 0.1321 0.1487 1.009 147.9 92.0 L_hat[2] 0.1805 0.00592 0.1815 0.1705 0.1885 1.019 88.9 80.5 L_hat[3] 0.2193 0.00471 0.2195 0.2128 0.2273 0.992 83.0 86.8 L_hat[4] 0.2602 0.00509 0.2609 0.2522 0.2687 0.992 108.8 103.6 L_hat[5] 0.3004 0.00477 0.3001 0.2922 0.3080 0.995 160.7 108.2 L_hat[6] 0.3392 0.00472 0.3393 0.3313 0.3462 1.005 157.3 78.4 L_hat[7] 0.3797 0.00463 0.3798 0.3722 0.3863 1.057 126.9 96.6 L_hat[8] 0.4205 0.00526 0.4201 0.4128 0.4289 1.014 114.2 99.8 L_hat[9] 0.4612 0.00511 0.4605 0.4525 0.4685 1.008 97.3 116.0 L_hat[10] 0.4991 0.00501 0.4982 0.4924 0.5081 0.996 87.0 110.4 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_M, kappa, E_G, mu_log_p_Am, sigma_log_p_Am, p_Am_ind[2], L0[2], p_Am_ind[3], L0[3], L_hat[1], L_hat[6], L_hat[7] ! Low bulk ESS (<400) for: p_M, kappa, v, E_G, E0, sigma_L, mu_log_p_Am, sigma_log_p_Am, p_Am_ind[1], L0[1], p_Am_ind[2], L0[2], p_Am_ind[3], L0[3], L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk p_M 0.5037 0.04513 0.5100 0.4419 0.5710 1.018 49.1 kappa 0.7552 0.10882 0.7852 0.5126 0.9059 1.061 35.0 v 0.2242 0.02165 0.2263 0.1915 0.2612 1.000 73.0 E_G 404.6484 37.61801 397.3021 357.7584 464.9526 1.040 80.7 E0 1.0065 0.10196 1.0046 0.8381 1.1445 0.972 58.9 sigma_L 0.0154 0.00285 0.0148 0.0112 0.0201 0.990 64.9 mu_log_p_Am 1.4924 0.04910 1.4875 1.4101 1.5731 1.028 52.2 sigma_log_p_Am 0.0989 0.02126 0.0995 0.0648 0.1296 1.092 22.8 p_Am_ind[1] 4.5660 0.52705 4.4587 3.8007 5.3915 1.001 46.4 L0[1] 0.1347 0.00661 0.1350 0.1232 0.1444 0.991 80.7 p_Am_ind[2] 4.5119 0.46585 4.6243 3.7083 5.1308 1.046 56.2 L0[2] 0.1338 0.00578 0.1333 0.1259 0.1436 1.014 32.9 p_Am_ind[3] 4.4044 0.42373 4.3457 3.7160 5.1792 1.053 31.0 L0[3] 0.1349 0.00550 0.1354 0.1273 0.1432 1.020 43.1 L_hat[1] 0.1418 0.00484 0.1409 0.1353 0.1503 1.017 73.6 L_hat[2] 0.1792 0.00544 0.1805 0.1698 0.1864 0.997 51.1 L_hat[3] 0.2217 0.00618 0.2229 0.2119 0.2292 0.974 47.7 L_hat[4] 0.2590 0.00490 0.2596 0.2522 0.2670 1.000 47.8 L_hat[5] 0.2992 0.00486 0.2993 0.2921 0.3074 0.991 50.7 L_hat[6] 0.3409 0.00482 0.3410 0.3335 0.3482 1.051 80.7 L_hat[7] 0.3797 0.00493 0.3805 0.3712 0.3882 1.019 49.3 L_hat[8] 0.4203 0.00528 0.4201 0.4109 0.4284 0.986 79.1 L_hat[9] 0.4604 0.00456 0.4600 0.4538 0.4675 0.984 77.8 L_hat[10] 0.4994 0.00492 0.4989 0.4918 0.5066 0.974 80.7 ess_tail 64.0 47.9 65.2 63.4 64.0 55.3 56.3 15.3 33.6 69.4 56.3 50.8 18.7 56.3 56.3 33.6 56.9 50.8 50.8 56.3 56.3 56.3 33.6 64.0 -- BDEB Diagnostics -- v No divergent transitions. v Treedepth OK. v E-BFMI OK (all > 0.3). -- Parameter Summary x R-hat > 1.01 for: p_Am, p_M, kappa, E_G, k_d, z_w, NEC, L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[7] ! Low bulk ESS (<400) for: p_Am, p_M, kappa, v, E_G, E0, L0, sigma_L, k_d, z_w, b_w, EC50, NEC, L_hat[1], L_hat[2], L_hat[3], L_hat[4], L_hat[5], L_hat[6], L_hat[7], L_hat[8], L_hat[9], L_hat[10] variable mean sd median 5% 95% rhat ess_bulk ess_tail p_Am 4.4945 0.51104 4.44e+00 3.62e+00 5.33e+00 1.067 27.4 32.3 p_M 0.5037 0.04513 5.10e-01 4.42e-01 5.71e-01 1.018 49.1 64.0 kappa 0.7552 0.10882 7.85e-01 5.13e-01 9.06e-01 1.061 35.0 47.9 v 0.2242 0.02165 2.26e-01 1.91e-01 2.61e-01 1.000 73.0 65.2 E_G 404.6484 37.61801 3.97e+02 3.58e+02 4.65e+02 1.040 80.7 63.4 E0 1.0065 0.10196 1.00e+00 8.38e-01 1.14e+00 0.972 58.9 64.0 L0 0.1344 0.01099 1.34e-01 1.19e-01 1.52e-01 1.006 76.9 33.6 sigma_L 0.0154 0.00285 1.48e-02 1.12e-02 2.01e-02 0.990 64.9 55.3 k_d 0.3640 0.03589 3.59e-01 3.07e-01 4.26e-01 1.028 52.2 56.3 z_w 14.8800 1.59908 1.48e+01 1.25e+01 1.73e+01 1.092 22.8 15.3 b_w 0.0043 0.00102 4.04e-03 2.94e-03 5.92e-03 1.001 46.4 33.6 EC50 137.1965 27.18314 1.38e+02 9.88e+01 1.87e+02 0.995 47.6 33.6 NEC 14.8800 1.59908 1.48e+01 1.25e+01 1.73e+01 1.092 22.8 15.3 L_hat[1] 0.1394 0.00494 1.40e-01 1.31e-01 1.46e-01 0.992 80.7 69.4 L_hat[2] 0.1801 0.00532 1.82e-01 1.71e-01 1.87e-01 1.042 56.2 56.3 L_hat[3] 0.2188 0.00431 2.18e-01 2.13e-01 2.26e-01 1.014 32.9 50.8 L_hat[4] 0.2589 0.00480 2.58e-01 2.51e-01 2.67e-01 1.053 31.0 18.7 L_hat[5] 0.2996 0.00409 3.00e-01 2.94e-01 3.06e-01 1.020 43.1 56.3 L_hat[6] 0.3391 0.00534 3.39e-01 3.30e-01 3.46e-01 0.974 80.7 50.8 L_hat[7] 0.3818 0.00484 3.81e-01 3.75e-01 3.90e-01 1.019 73.6 56.3 L_hat[8] 0.4192 0.00544 4.20e-01 4.10e-01 4.26e-01 0.997 51.1 33.6 L_hat[9] 0.4617 0.00618 4.63e-01 4.52e-01 4.69e-01 0.974 47.7 56.9 L_hat[10] 0.4990 0.00490 5.00e-01 4.92e-01 5.07e-01 1.000 47.8 50.8 -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 137.2 137.5 27.2 98.8 186.9 NEC 14.9 14.8 1.6 12.5 17.3 -- BDEB Fit -- i Model type: individual i Chains: 2, Warmup: 500, Sampling: 25 v No divergent transitions -- BDEB Model Specification -- i Type: individual i Stan model: bdeb_individual_growth i Individuals: 1 i Endpoints: growth -- Priors > p_Am: LogNormal(1.0, 1.0) > p_M: LogNormal(-1.0, 1.0) > kappa: Beta(2.0, 2.0) > v: LogNormal(-1.5, 1.0) > E_G: LogNormal(6.0, 1.0) > E0: LogNormal(0.0, 1.0) > L0: LogNormal(-2.0, 1.0) > sigma_L: HalfNormal(0.10) -- BDEB Posterior Predictive Check -- i Type: growth > Growth: 10 observations, 50 posterior draws -- BDEB Prior Predictive Check -- i Draws: 20 i Time range: [0, 5] > Prior L_inf: median 2.85, 95% CI [0.43, 128.04] -- DEBtox Effect Concentrations parameter mean median sd lower upper EC50 140.5 139 26.37 101.2 187.7 NEC 14.9 15 1.42 12.5 17.3 [ FAIL 0 | WARN 20 | SKIP 1 | PASS 897 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • {cmdstanr} is not installed (1): 'test-end-to-end.R:190:3' [ FAIL 0 | WARN 20 | SKIP 1 | PASS 897 ] > > proc.time() user system elapsed 21.15 2.65 24.10