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Type 'q()' to quit R. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview > # * https://testthat.r-lib.org/articles/special-files.html > > library(testthat) > library(flexCountReg) > > test_check("flexCountReg") Call: Total_crashes ~ lnaadt + lnlength + speed50 + ShouldWidth04 + AADTover10k Method: countreg Iterations: 6 Convergence: successive function values within relative tolerance limit (reltol) Log-likelihood: -1062.794 Parameter Estimates: (Using bootstrapped standard errors) # A tibble: 7 x 7 parameter coeff `Std. Err.` `t-stat` `p-value` `lower CI` `upper CI` 1 (Intercept) -7.74 0.0428 -181. 0 -7.80 -7.69 2 lnaadt 0.936 0.005 189. 0 0.930 0.942 3 lnlength 0.840 0.0358 23.4 0 0.794 0.886 4 speed50 -0.385 0.0868 -4.44 0 -0.496 -0.274 5 ShouldWidth04 0.254 0.0626 4.06 0 0.174 0.334 6 AADTover10k 0.713 0.091 7.84 0 0.596 0.829 7 ln(alpha) -1.46 0.303 -4.82 0 -1.85 -1.07 Call: Total_crashes ~ lnaadt + lnlength + speed50 + AADT10kplus Method: countreg Iterations: 502 Convergence: iteration limit exceeded Log-likelihood: -525.575 Parameter Estimates: (Using bootstrapped standard errors) # A tibble: 7 x 7 parameter coeff `Std. Err.` `t-stat` `p-value` `lower CI` `upper CI` 1 (Intercept) -7.06 0.062 -114. 0 -7.18 -6.93 2 lnaadt 0.865 0.007 121. 0 0.851 0.879 3 lnlength 0.828 0.054 15.4 0 0.723 0.934 4 speed50 -0.545 0.139 -3.93 0 -0.816 -0.273 5 AADT10kplus 0.72 0.128 5.62 0 0.469 0.971 6 ln(alpha) -1.34 0.419 -3.19 0.001 -2.16 -0.517 7 ln(p) 0.44 0.246 1.78 0.074 -0.043 0.922 [1] "Method must be one of: \"SANN\", \"NM\", \"BFGS\", \"BFGSR\", \"CG\", \"NR\", or \"BHHH\". Switching to \"NM." Nelder-Mead direct search function minimizer function value for initial parameters = 1428.467927 Scaled convergence tolerance is 2.12858e-05 Stepsize computed as 0.740069 BUILD 6 82290.965142 1383.115049 LO-REDUCTION 8 2161.182400 1383.115049 REFLECTION 10 1651.686420 1255.232774 HI-REDUCTION 12 1606.570290 1208.245350 REFLECTION 14 1589.976452 1191.988824 LO-REDUCTION 16 1428.467927 1191.988824 HI-REDUCTION 18 1383.115049 1177.100457 HI-REDUCTION 20 1255.232774 1164.442152 LO-REDUCTION 22 1208.245350 1147.038028 LO-REDUCTION 24 1194.291977 1147.038028 HI-REDUCTION 26 1191.988824 1147.038028 HI-REDUCTION 28 1177.100457 1147.038028 LO-REDUCTION 30 1164.442152 1146.677185 HI-REDUCTION 32 1156.316661 1146.677185 HI-REDUCTION 34 1151.377538 1146.318170 HI-REDUCTION 36 1151.274218 1145.068544 HI-REDUCTION 38 1148.184467 1145.068544 HI-REDUCTION 40 1147.038028 1144.956988 HI-REDUCTION 42 1146.677185 1144.615632 HI-REDUCTION 44 1146.318170 1144.615632 HI-REDUCTION 46 1145.876992 1144.581438 REFLECTION 48 1145.068544 1144.190777 HI-REDUCTION 50 1144.956988 1143.766651 LO-REDUCTION 52 1144.776042 1143.766651 HI-REDUCTION 54 1144.615632 1143.766651 REFLECTION 56 1144.581438 1143.657167 REFLECTION 58 1144.190777 1143.602892 HI-REDUCTION 60 1144.057271 1143.505966 REFLECTION 62 1143.777691 1143.286842 LO-REDUCTION 64 1143.766651 1143.286842 REFLECTION 66 1143.657167 1143.232778 REFLECTION 68 1143.602892 1143.168059 LO-REDUCTION 70 1143.505966 1143.168059 HI-REDUCTION 72 1143.434922 1143.168059 LO-REDUCTION 74 1143.286842 1143.155239 HI-REDUCTION 76 1143.269993 1143.155239 LO-REDUCTION 78 1143.232778 1143.155239 REFLECTION 80 1143.218501 1143.130559 LO-REDUCTION 82 1143.202968 1143.130559 LO-REDUCTION 84 1143.178452 1143.130559 LO-REDUCTION 86 1143.168059 1143.130559 REFLECTION 88 1143.155239 1143.129348 EXTENSION 90 1143.147146 1143.107729 EXTENSION 92 1143.144618 1143.098753 LO-REDUCTION 94 1143.130570 1143.098753 EXTENSION 96 1143.130559 1143.069044 EXTENSION 98 1143.129348 1143.022861 LO-REDUCTION 100 1143.112117 1143.022861 LO-REDUCTION 102 1143.107729 1143.022861 LO-REDUCTION 104 1143.098753 1143.022861 EXTENSION 106 1143.069044 1143.004807 LO-REDUCTION 108 1143.057215 1143.004807 LO-REDUCTION 110 1143.057028 1143.004807 EXTENSION 112 1143.039207 1142.970725 LO-REDUCTION 114 1143.022861 1142.970725 HI-REDUCTION 116 1143.018766 1142.970725 LO-REDUCTION 118 1143.015933 1142.970725 LO-REDUCTION 120 1143.004807 1142.970725 EXTENSION 122 1142.998748 1142.932377 LO-REDUCTION 124 1142.985971 1142.932377 LO-REDUCTION 126 1142.973458 1142.932377 LO-REDUCTION 128 1142.971703 1142.932377 LO-REDUCTION 130 1142.970725 1142.932377 EXTENSION 132 1142.959892 1142.906592 LO-REDUCTION 134 1142.943339 1142.906592 EXTENSION 136 1142.941394 1142.883659 LO-REDUCTION 138 1142.940422 1142.883659 LO-REDUCTION 140 1142.932377 1142.883659 LO-REDUCTION 142 1142.919014 1142.883659 EXTENSION 144 1142.906592 1142.871993 LO-REDUCTION 146 1142.906412 1142.871993 EXTENSION 148 1142.898418 1142.864688 EXTENSION 150 1142.894322 1142.836936 LO-REDUCTION 152 1142.883659 1142.836936 LO-REDUCTION 154 1142.876714 1142.836936 LO-REDUCTION 156 1142.871993 1142.836936 EXTENSION 158 1142.864688 1142.830192 LO-REDUCTION 160 1142.858918 1142.830192 REFLECTION 162 1142.854491 1142.824425 EXTENSION 164 1142.851171 1142.796694 LO-REDUCTION 166 1142.836936 1142.796694 LO-REDUCTION 168 1142.834058 1142.796694 EXTENSION 170 1142.830192 1142.767414 LO-REDUCTION 172 1142.824425 1142.767414 LO-REDUCTION 174 1142.812134 1142.767414 EXTENSION 176 1142.811023 1142.743304 EXTENSION 178 1142.797108 1142.716241 LO-REDUCTION 180 1142.796694 1142.716241 EXTENSION 182 1142.771755 1142.668649 EXTENSION 184 1142.767414 1142.610302 LO-REDUCTION 186 1142.743304 1142.610302 EXTENSION 188 1142.718084 1142.559776 LO-REDUCTION 190 1142.716241 1142.559776 LO-REDUCTION 192 1142.668649 1142.559776 REFLECTION 194 1142.645761 1142.544358 EXTENSION 196 1142.610302 1142.469992 LO-REDUCTION 198 1142.573720 1142.469992 LO-REDUCTION 200 1142.563810 1142.469992 LO-REDUCTION 202 1142.559776 1142.469992 LO-REDUCTION 204 1142.544358 1142.469992 LO-REDUCTION 206 1142.533863 1142.469992 EXTENSION 208 1142.504846 1142.414452 LO-REDUCTION 210 1142.497434 1142.414452 EXTENSION 212 1142.487689 1142.384766 EXTENSION 214 1142.481177 1142.344209 EXTENSION 216 1142.469992 1142.325749 REFLECTION 218 1142.430383 1142.308420 EXTENSION 220 1142.414452 1142.230398 LO-REDUCTION 222 1142.384766 1142.230398 LO-REDUCTION 224 1142.344209 1142.230398 LO-REDUCTION 226 1142.325749 1142.230398 LO-REDUCTION 228 1142.308420 1142.230398 LO-REDUCTION 230 1142.284912 1142.230398 EXTENSION 232 1142.245486 1142.186763 LO-REDUCTION 234 1142.245180 1142.186763 EXTENSION 236 1142.234249 1142.164053 LO-REDUCTION 238 1142.232142 1142.164053 LO-REDUCTION 240 1142.230398 1142.164053 LO-REDUCTION 242 1142.217403 1142.164053 EXTENSION 244 1142.186763 1142.110595 LO-REDUCTION 246 1142.178394 1142.110595 LO-REDUCTION 248 1142.174988 1142.110595 LO-REDUCTION 250 1142.172874 1142.110595 LO-REDUCTION 252 1142.164053 1142.110595 REFLECTION 254 1142.145269 1142.105642 EXTENSION 256 1142.126812 1142.085937 LO-REDUCTION 258 1142.125732 1142.085937 LO-REDUCTION 260 1142.111391 1142.085937 LO-REDUCTION 262 1142.110595 1142.085937 LO-REDUCTION 264 1142.105642 1142.085937 EXTENSION 266 1142.095235 1142.073247 LO-REDUCTION 268 1142.095228 1142.073247 EXTENSION 270 1142.094370 1142.070379 LO-REDUCTION 272 1142.091094 1142.070379 REFLECTION 274 1142.085937 1142.060909 EXTENSION 276 1142.074657 1142.042418 LO-REDUCTION 278 1142.073325 1142.042418 HI-REDUCTION 280 1142.073247 1142.042418 LO-REDUCTION 282 1142.070379 1142.042418 EXTENSION 284 1142.060909 1142.009302 LO-REDUCTION 286 1142.058834 1142.009302 LO-REDUCTION 288 1142.044751 1142.009302 LO-REDUCTION 290 1142.044224 1142.009302 EXTENSION 292 1142.042418 1141.982235 EXTENSION 294 1142.022790 1141.933398 LO-REDUCTION 296 1142.013977 1141.933398 LO-REDUCTION 298 1142.012268 1141.933398 EXTENSION 300 1142.009302 1141.902254 LO-REDUCTION 302 1141.982235 1141.902254 EXTENSION 304 1141.971576 1141.887522 EXTENSION 306 1141.970227 1141.838900 EXTENSION 308 1141.933398 1141.805327 LO-REDUCTION 310 1141.926306 1141.805327 EXTENSION 312 1141.902254 1141.779664 LO-REDUCTION 314 1141.887522 1141.779664 LO-REDUCTION 316 1141.849706 1141.779664 REFLECTION 318 1141.838900 1141.763329 LO-REDUCTION 320 1141.809724 1141.763329 EXTENSION 322 1141.805327 1141.705926 LO-REDUCTION 324 1141.786231 1141.705926 LO-REDUCTION 326 1141.779664 1141.705926 LO-REDUCTION 328 1141.774105 1141.705926 EXTENSION 330 1141.763329 1141.692054 EXTENSION 332 1141.756704 1141.663265 EXTENSION 334 1141.739406 1141.616041 LO-REDUCTION 336 1141.730476 1141.616041 EXTENSION 338 1141.705926 1141.573944 LO-REDUCTION 340 1141.692054 1141.573944 LO-REDUCTION 342 1141.663265 1141.573944 LO-REDUCTION 344 1141.652056 1141.573944 LO-REDUCTION 346 1141.627286 1141.573944 EXTENSION 348 1141.616041 1141.535784 LO-REDUCTION 350 1141.596968 1141.535784 LO-REDUCTION 352 1141.587498 1141.535784 EXTENSION 354 1141.582470 1141.516323 EXTENSION 356 1141.573944 1141.482139 LO-REDUCTION 358 1141.557972 1141.482139 EXTENSION 360 1141.544416 1141.450672 LO-REDUCTION 362 1141.535784 1141.450672 LO-REDUCTION 364 1141.516323 1141.450672 LO-REDUCTION 366 1141.500708 1141.450672 LO-REDUCTION 368 1141.482139 1141.450672 LO-REDUCTION 370 1141.477855 1141.450672 LO-REDUCTION 372 1141.473963 1141.450672 LO-REDUCTION 374 1141.470789 1141.450672 REFLECTION 376 1141.463070 1141.448234 EXTENSION 378 1141.459660 1141.436275 LO-REDUCTION 380 1141.459022 1141.436275 EXTENSION 382 1141.453623 1141.421693 LO-REDUCTION 384 1141.450672 1141.421693 LO-REDUCTION 386 1141.448234 1141.421693 EXTENSION 388 1141.436874 1141.387704 LO-REDUCTION 390 1141.436275 1141.387704 LO-REDUCTION 392 1141.424714 1141.387704 LO-REDUCTION 394 1141.422807 1141.387704 EXTENSION 396 1141.421693 1141.358639 EXTENSION 398 1141.406908 1141.352828 EXTENSION 400 1141.391509 1141.308024 LO-REDUCTION 402 1141.389083 1141.308024 LO-REDUCTION 404 1141.387704 1141.308024 LO-REDUCTION 406 1141.358639 1141.308024 LO-REDUCTION 408 1141.352828 1141.308024 REFLECTION 410 1141.321726 1141.292061 LO-REDUCTION 412 1141.319213 1141.292061 EXTENSION 414 1141.314880 1141.279869 LO-REDUCTION 416 1141.310364 1141.279869 LO-REDUCTION 418 1141.308024 1141.279869 REFLECTION 420 1141.301988 1141.276370 REFLECTION 422 1141.292061 1141.273379 LO-REDUCTION 424 1141.290973 1141.273379 EXTENSION 426 1141.286180 1141.250584 LO-REDUCTION 428 1141.279869 1141.250584 LO-REDUCTION 430 1141.277987 1141.250584 LO-REDUCTION 432 1141.276370 1141.250584 REFLECTION 434 1141.273379 1141.249585 REFLECTION 436 1141.261334 1141.241839 EXTENSION 438 1141.259295 1141.229864 EXTENSION 440 1141.252816 1141.223103 LO-REDUCTION 442 1141.250584 1141.223103 LO-REDUCTION 444 1141.249585 1141.223103 REFLECTION 446 1141.241839 1141.221422 EXTENSION 448 1141.230801 1141.206916 LO-REDUCTION 450 1141.229864 1141.206916 LO-REDUCTION 452 1141.223849 1141.206916 LO-REDUCTION 454 1141.223103 1141.206916 LO-REDUCTION 456 1141.221422 1141.206916 LO-REDUCTION 458 1141.212910 1141.206916 EXTENSION 460 1141.209453 1141.198810 LO-REDUCTION 462 1141.208660 1141.198810 LO-REDUCTION 464 1141.208305 1141.198810 HI-REDUCTION 466 1141.207081 1141.198810 LO-REDUCTION 468 1141.206916 1141.198810 EXTENSION 470 1141.203664 1141.188891 LO-REDUCTION 472 1141.202610 1141.188891 LO-REDUCTION 474 1141.201078 1141.188891 LO-REDUCTION 476 1141.199201 1141.188891 EXTENSION 478 1141.198810 1141.181512 EXTENSION 480 1141.192714 1141.170960 LO-REDUCTION 482 1141.191180 1141.170960 LO-REDUCTION 484 1141.189042 1141.170960 LO-REDUCTION 486 1141.188891 1141.170960 EXTENSION 488 1141.181512 1141.163775 LO-REDUCTION 490 1141.179214 1141.163775 EXTENSION 492 1141.174101 1141.154092 LO-REDUCTION 494 1141.173243 1141.154092 EXTENSION 496 1141.170960 1141.151585 HI-REDUCTION 498 1141.168201 1141.151585 REFLECTION 500 1141.163775 1141.148632 LO-REDUCTION 502 1141.159585 1141.148632 LO-REDUCTION 504 1141.158183 1141.148632 REFLECTION 506 1141.154092 1141.145267 HI-REDUCTION 508 1141.151585 1141.145267 LO-REDUCTION 510 1141.151418 1141.145267 EXTENSION 512 1141.149294 1141.142215 EXTENSION 514 1141.148954 1141.140672 EXTENSION 516 1141.148632 1141.139314 EXTENSION 518 1141.147153 1141.135793 REFLECTION 520 1141.145267 1141.135026 EXTENSION 522 1141.142215 1141.127430 LO-REDUCTION 524 1141.140672 1141.127430 REFLECTION 526 1141.139314 1141.127218 HI-REDUCTION 528 1141.135793 1141.127218 LO-REDUCTION 530 1141.135026 1141.127218 REFLECTION 532 1141.134150 1141.125657 EXTENSION 534 1141.132296 1141.122462 LO-REDUCTION 536 1141.129431 1141.122462 LO-REDUCTION 538 1141.127430 1141.122462 REFLECTION 540 1141.127218 1141.121639 LO-REDUCTION 542 1141.125657 1141.121639 LO-REDUCTION 544 1141.124574 1141.121639 REFLECTION 546 1141.123260 1141.120704 EXTENSION 548 1141.123170 1141.119904 EXTENSION 550 1141.122540 1141.118993 REFLECTION 552 1141.122462 1141.118215 LO-REDUCTION 554 1141.121639 1141.118215 LO-REDUCTION 556 1141.120704 1141.118215 REFLECTION 558 1141.119904 1141.117759 LO-REDUCTION 560 1141.118993 1141.117759 LO-REDUCTION 562 1141.118467 1141.117759 REFLECTION 564 1141.118261 1141.117491 LO-REDUCTION 566 1141.118231 1141.117491 HI-REDUCTION 568 1141.118215 1141.117491 LO-REDUCTION 570 1141.117839 1141.117406 LO-REDUCTION 572 1141.117759 1141.117369 HI-REDUCTION 574 1141.117700 1141.117369 LO-REDUCTION 576 1141.117662 1141.117369 LO-REDUCTION 578 1141.117491 1141.117362 HI-REDUCTION 580 1141.117446 1141.117362 HI-REDUCTION 582 1141.117406 1141.117362 HI-REDUCTION 584 1141.117381 1141.117355 Exiting from Nelder Mead minimizer 586 function evaluations used Nelder-Mead direct search function minimizer function value for initial parameters = 1090.695613 Scaled convergence tolerance is 1.62526e-05 Stepsize computed as 0.901130 BUILD 7 30557.175757 1090.695613 LO-REDUCTION 9 1827.976340 1090.695613 HI-REDUCTION 11 1687.706510 1090.695613 LO-REDUCTION 13 1329.642773 1090.695613 HI-REDUCTION 15 1296.642676 1090.695613 HI-REDUCTION 17 1261.156789 1090.695613 HI-REDUCTION 19 1238.883408 1090.695613 HI-REDUCTION 21 1199.167190 1090.695613 HI-REDUCTION 23 1162.531865 1090.695613 LO-REDUCTION 25 1144.768104 1090.695613 LO-REDUCTION 27 1133.004670 1090.695613 HI-REDUCTION 29 1107.823209 1090.695613 HI-REDUCTION 31 1105.889815 1090.695613 HI-REDUCTION 33 1101.954133 1088.050016 LO-REDUCTION 35 1099.764305 1087.487988 HI-REDUCTION 37 1098.519439 1087.487988 HI-REDUCTION 39 1096.973215 1087.487988 HI-REDUCTION 41 1096.588052 1087.487988 LO-REDUCTION 43 1090.695613 1087.041108 LO-REDUCTION 45 1088.519312 1086.913554 HI-REDUCTION 47 1088.050016 1086.146858 LO-REDUCTION 49 1087.923576 1086.146858 HI-REDUCTION 51 1087.836093 1085.891132 HI-REDUCTION 53 1087.487988 1085.671911 HI-REDUCTION 55 1087.041108 1085.671911 REFLECTION 57 1086.913554 1085.182732 LO-REDUCTION 59 1086.193438 1085.182732 LO-REDUCTION 61 1086.146858 1085.125876 LO-REDUCTION 63 1085.891132 1085.125876 LO-REDUCTION 65 1085.823873 1085.065071 HI-REDUCTION 67 1085.671911 1085.065071 HI-REDUCTION 69 1085.282643 1085.065071 REFLECTION 71 1085.203153 1085.013652 HI-REDUCTION 73 1085.201407 1085.013652 LO-REDUCTION 75 1085.182732 1085.013652 REFLECTION 77 1085.172847 1084.986796 LO-REDUCTION 79 1085.125876 1084.986796 LO-REDUCTION 81 1085.065071 1084.968865 LO-REDUCTION 83 1085.063928 1084.968865 REFLECTION 85 1085.038947 1084.955296 HI-REDUCTION 87 1085.018039 1084.955296 HI-REDUCTION 89 1085.013652 1084.955296 REFLECTION 91 1084.992209 1084.943776 REFLECTION 93 1084.986796 1084.930128 HI-REDUCTION 95 1084.970420 1084.930128 REFLECTION 97 1084.969938 1084.918818 LO-REDUCTION 99 1084.968865 1084.918818 Exiting from Nelder Mead minimizer 101 function evaluations used Covariate: indvar_values CURE data frame was provided. Its first column, Predicted Values, will be used. Covariate: indvar_values CURE data frame was provided. Its first column, lnaadt, will be used. Call: y ~ x1 Method: poisLindRE Iterations: 52 Convergence: iteration limit exceeded Log-likelihood: 191.2453 Parameter Estimates: (Using bootstrapped standard errors) # A tibble: 3 x 7 parameter coeff `Std. Err.` `t-stat` `p-value` `lower CI` `upper CI` 1 (Intercept) 0.085 0.166 0.511 0.61 -0.24 0.409 2 x1 1.18 0.058 20.3 0 1.07 1.30 3 ln(theta) -4.79 0.507 -9.44 0 -5.78 -3.80 [ FAIL 0 | WARN 0 | SKIP 2 | PASS 173 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • On CRAN (2): 'test-countreg.R:177:3', 'test_extended_coverage.R:75:3' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 173 ] > > proc.time() user system elapsed 190.17 3.07 192.31