R Under development (unstable) (2023-11-28 r85645 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 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. > # 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/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(calibmsm) > > test_check("calibmsm") There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 2 2 0.11401890 0.1095897 4 4 0.13838778 0.1036308 5 5 0.12332255 0.1051035 7 7 0.09737975 0.1236322 10 10 0.11371889 0.1097779 13 13 0.11385388 0.1096929 $state2 id pred obs 2 2 0.2316569 0.1698031 4 4 0.1836189 0.1855591 5 5 0.1609740 0.1759804 7 7 0.2121470 0.1785688 10 10 0.2315632 0.1698443 13 13 0.2316571 0.1698030 $state3 id pred obs 2 2 0.08442692 0.12485834 4 4 0.07579429 0.11666056 5 5 0.05508100 0.09189341 7 7 0.06154308 0.10011560 10 10 0.08440940 0.12484341 13 13 0.08257284 0.12323792 $state4 id pred obs 2 2 0.2328398 0.2427580 4 4 0.2179331 0.2243106 5 5 0.1828176 0.1851051 7 7 0.2206335 0.2275985 10 10 0.2326989 0.2425807 13 13 0.2326047 0.2424622 $state5 id pred obs 2 2 0.1481977 0.1909795 4 4 0.1538475 0.1654523 5 5 0.1425950 0.2215190 7 7 0.1441960 0.2123460 10 10 0.1488068 0.1879278 13 13 0.1505092 0.1797461 $state6 id pred obs 2 2 0.1888598 0.2069354 4 4 0.2304185 0.2542212 5 5 0.3352099 0.3163102 7 7 0.2641006 0.2800368 10 10 0.1888028 0.2068586 13 13 0.1888022 0.2068578 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 2 2 0.11401890 0.1245082 4 4 0.13838778 0.1143276 5 5 0.12332255 0.1280757 7 7 0.09737975 0.1115851 10 10 0.11371889 0.1243613 13 13 0.11385388 0.1244272 $state2 id pred obs 2 2 0.2316569 0.1693576 4 4 0.1836189 0.2008740 5 5 0.1609740 0.1509011 7 7 0.2121470 0.1854787 10 10 0.2315632 0.1694279 13 13 0.2316571 0.1693574 $state3 id pred obs 2 2 0.08442692 0.13900497 4 4 0.07579429 0.12943777 5 5 0.05508100 0.09293168 7 7 0.06154308 0.10449984 10 10 0.08440940 0.13899418 13 13 0.08257284 0.13763859 $state4 id pred obs 2 2 0.2328398 0.2097518 4 4 0.2179331 0.1871859 5 5 0.1828176 0.1985304 7 7 0.2206335 0.1902407 10 10 0.2326989 0.2094773 13 13 0.2326047 0.2092942 $state5 id pred obs 2 2 0.1481977 0.1838697 4 4 0.1538475 0.1451690 5 5 0.1425950 0.2266787 7 7 0.1441960 0.2145598 10 10 0.1488068 0.1792457 13 13 0.1505092 0.1692817 $state6 id pred obs 2 2 0.1888598 0.2048238 4 4 0.2304185 0.2302551 5 5 0.3352099 0.3267404 7 7 0.2641006 0.2926103 10 10 0.1888028 0.2047569 13 13 0.1888022 0.2047562 There were non-zero predicted transition probabilities into states 1,2,3,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 The estimated calibration scatter plots are stored in list element `plotdata`: $state1 id pred obs 1 1 0.1135057 0.04329969 2 2 0.1135518 0.04274070 3 3 0.1131989 0.04261329 4 4 0.1376981 0.06999043 5 5 0.1227877 0.04333992 6 6 0.1131989 0.04261329 $state2 id pred obs 1 1 0.4093590 0.6169702 2 2 0.4114981 0.6186696 3 3 0.4117482 0.6191576 4 4 0.3870386 0.5377577 5 5 0.4277392 0.6008873 6 6 0.4117482 0.6191576 $state3 id pred obs 1 1 0.3964498 0.2501361 2 2 0.3942408 0.2495026 3 3 0.3944988 0.2490786 4 4 0.3728509 0.2949261 5 5 0.3496972 0.2731841 6 6 0.3944988 0.2490786 $state5 id pred obs 1 1 0.02688596 0.04742072 2 2 0.02689840 0.04751176 3 3 0.02681945 0.04720194 4 4 0.04027730 0.07167132 5 5 0.03130458 0.05498636 6 6 0.02681945 0.04720194 $state6 id pred obs 1 1 0.05379955 0.04217332 2 2 0.05381085 0.04157532 3 3 0.05373457 0.04194858 4 4 0.06213511 0.02565452 5 5 0.06847131 0.02760235 6 6 0.05373457 0.04194858 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A confidence interval was not estimated The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs 1 1 0.1139726 0.0007884881 2 2 0.1140189 0.0008356659 3 3 0.1136646 0.0005012250 4 4 0.1383878 0.0554854582 5 5 0.1233226 0.0239533161 6 6 0.1136646 0.0005012250 $state2 id pred obs 1 1 0.2295006 0.2472482 2 2 0.2316569 0.2648225 3 3 0.2317636 0.2654082 4 4 0.1836189 0.2354074 5 5 0.1609740 0.2600439 6 6 0.2317636 0.2654082 $state3 id pred obs 1 1 0.08450376 0.342589994 2 2 0.08442692 0.341419893 3 3 0.08274331 0.305981896 4 4 0.07579429 0.104422676 5 5 0.05508100 -0.008604324 6 6 0.08462424 0.344353242 $state4 id pred obs 1 1 0.2326861 0.2251249 2 2 0.2328398 0.2232169 3 3 0.2325663 0.2265976 4 4 0.2179331 0.3951682 5 5 0.1828176 0.2681653 6 6 0.2305854 0.2525980 $state5 id pred obs 1 1 0.1504855 0.3384060 2 2 0.1481977 0.3174861 3 3 0.1504787 0.3383704 4 4 0.1538475 0.3330829 5 5 0.1425950 0.2392080 6 6 0.1505534 0.3387299 $state6 id pred obs 1 1 0.1888514 0.1074200 2 2 0.1888598 0.1074443 3 3 0.1887834 0.1072239 4 4 0.2304185 0.2161003 5 5 0.3352099 0.1435163 6 6 0.1888087 0.1072971 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated using parametric approaches The estimated calibration curves are stored in list element `plotdata`: $state1 id pred obs obs.lower obs.upper 1 1 0.1139726 0.0007884881 -0.10292450 0.1045015 2 2 0.1140189 0.0008356659 -0.10300552 0.1046769 3 3 0.1136646 0.0005012250 -0.10234645 0.1033489 4 4 0.1383878 0.0554854582 -0.04332935 0.1543003 5 5 0.1233226 0.0239533161 -0.12234560 0.1702522 6 6 0.1136646 0.0005012250 -0.10234645 0.1033489 $state2 id pred obs obs.lower obs.upper 1 1 0.2295006 0.2472482 0.01381089 0.4806856 2 2 0.2316569 0.2648225 0.03932820 0.4903169 3 3 0.2317636 0.2654082 0.04043786 0.4903786 4 4 0.1836189 0.2354074 0.04208295 0.4287318 5 5 0.1609740 0.2600439 0.02470363 0.4953843 6 6 0.2317636 0.2654082 0.04043786 0.4903786 There were non-zero predicted transition probabilities into states 1,2,3,4,5,6 Calibration curves have been estimated for transitions into states 1,2,3,4,5,6 Calibration was assessed at time 1826 and calibration was assessed in a landmarked cohort of individuals in state j = 1 at time s = 0 A 95% confidence interval was estimated using parametric approaches The estimated calibration curves are stored in list element `plotdata`: $state1 pred obs obs.lower obs.upper 1 0.1139726 0.0007884881 -0.10292450 0.1045015 2 0.1140189 0.0008356659 -0.10300552 0.1046769 3 0.1136646 0.0005012250 -0.10234645 0.1033489 4 0.1383878 0.0554854582 -0.04332935 0.1543003 5 0.1233226 0.0239533161 -0.12234560 0.1702522 6 0.1136646 0.0005012250 -0.10234645 0.1033489 $state2 pred obs obs.lower obs.upper 1 0.2295006 0.2472482 0.01381089 0.4806856 2 0.2316569 0.2648225 0.03932820 0.4903169 3 0.2317636 0.2654082 0.04043786 0.4903786 4 0.1836189 0.2354074 0.04208295 0.4287318 5 0.1609740 0.2600439 0.02470363 0.4953843 6 0.2317636 0.2654082 0.04043786 0.4903786 $state3 pred obs obs.lower obs.upper 1 0.08450376 0.342589994 0.1383243 0.5468557 2 0.08442692 0.341419893 0.1373466 0.5454931 3 0.08274331 0.305981896 0.1065734 0.5053904 4 0.07579429 0.104422676 -0.1918976 0.4007430 5 0.05508100 -0.008604324 -0.1785234 0.1613147 6 0.08462424 0.344353242 0.1397962 0.5489103 $state4 pred obs obs.lower obs.upper 1 0.2326861 0.2251249 0.020974058 0.4292758 2 0.2328398 0.2232169 0.019023999 0.4274098 3 0.2325663 0.2265976 0.022478137 0.4307170 4 0.2179331 0.3951682 0.174674109 0.6156622 5 0.1828176 0.2681653 0.008742274 0.5275882 6 0.2305854 0.2525980 0.048828454 0.4563674 $state5 pred obs obs.lower obs.upper 1 0.1504855 0.3384060 0.09295346 0.5838585 2 0.1481977 0.3174861 0.07618096 0.5587912 3 0.1504787 0.3383704 0.09293268 0.5838081 4 0.1538475 0.3330829 0.11588295 0.5502829 5 0.1425950 0.2392080 -0.13227667 0.6106927 6 0.1505534 0.3387299 0.09313015 0.5843297 $state6 pred obs obs.lower obs.upper 1 0.1888514 0.1074200 -0.05976468 0.2746047 2 0.1888598 0.1074443 -0.05973294 0.2746216 3 0.1887834 0.1072239 -0.06002050 0.2744683 4 0.2304185 0.2161003 0.04667749 0.3855231 5 0.3352099 0.1435163 -0.06897344 0.3560060 6 0.1888087 0.1072971 -0.05992494 0.2745192 [ FAIL 0 | WARN 0 | SKIP 8 | PASS 210 ] ══ Skipped tests (8) ═══════════════════════════════════════════════════════════ • On CRAN (8): 'test-calib_blr.R:138:3', 'test-calib_blr.R:370:13', 'test-calib_blr.R:417:13', 'test-calib_pv.R:4:3', 'test-calib_pv.R:178:3', 'test-calib_pv.R:228:3', 'test-calib_pv.R:279:3', 'test-calib_pv.R:347:3' [ FAIL 0 | WARN 0 | SKIP 8 | PASS 210 ] > > proc.time() user system elapsed 413.29 10.64 424.11