R version 2.6.0 alpha (2007-09-05 r42784) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. Natural language support but running in an English locale 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(lme4) Loading required package: Matrix Loading required package: lattice > load("/home/bates/afs/src/Rlibs/AppLong/data/fev1.rda") > fev1$loght <- log(fev1$ht) > fev1$logbht <- log(fev1$baseht) > (fm1 <- lmer(logfev1 ~ age + loght + baseage + logbht + (age|id), fev1)) Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (age | id) Data: fev1 AIC BIC logLik MLdeviance REMLdeviance -4486 -4441 2251 -4538 -4502 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 1.5234e-02 0.1234262 age 4.9959e-05 0.0070682 -0.545 Residual 3.6517e-03 0.0604289 Number of obs: 1994, groups: id, 300 Fixed effects: Estimate Std. Error t value (Intercept) -0.269212 0.042399 -6.35 age 0.023492 0.001400 16.79 loght 2.240639 0.043707 51.27 baseage -0.023763 0.008124 -2.92 logbht 0.367986 0.158217 2.33 Correlation of Fixed Effects: (Intr) age loght baseag age 0.017 loght -0.074 -0.876 baseage -0.823 -0.165 0.166 logbht 0.369 0.216 -0.249 -0.815 > (fm1a <- lmer(logfev1 ~ age + loght + baseage + logbht + (age|id), fev1, subset = id != 197)) Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (age | id) Data: fev1 Subset: id != 197 AIC BIC logLik MLdeviance REMLdeviance -4552 -4507 2284 -4605 -4568 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 1.2207e-02 0.1104859 age 5.0108e-05 0.0070787 -0.553 Residual 3.6286e-03 0.0602381 Number of obs: 1993, groups: id, 299 Fixed effects: Estimate Std. Error t value (Intercept) -0.288324 0.038715 -7.45 age 0.023529 0.001395 16.86 loght 2.237199 0.043537 51.39 baseage -0.016509 0.007458 -2.21 logbht 0.218219 0.145516 1.50 Correlation of Fixed Effects: (Intr) age loght baseag age 0.023 loght -0.077 -0.875 baseage -0.822 -0.184 0.180 logbht 0.370 0.239 -0.275 -0.815 > deviance(fm1a) REML -4567.882 > (fm2 <- lmer(logfev1 ~ age + loght + baseage + logbht + (loght|id), fev1)) Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (loght | id) Data: fev1 AIC BIC logLik MLdeviance REMLdeviance -4510 -4466 2263 -4563 -4526 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 0.0188128 0.137160 loght 0.0752645 0.274344 -0.668 Residual 0.0035356 0.059461 Number of obs: 1994, groups: id, 300 Fixed effects: Estimate Std. Error t value (Intercept) -0.274188 0.042216 -6.49 age 0.023201 0.001249 18.58 loght 2.258935 0.046442 48.64 baseage -0.023086 0.008018 -2.88 logbht 0.347223 0.156484 2.22 Correlation of Fixed Effects: (Intr) age loght baseag age 0.046 loght -0.112 -0.852 baseage -0.821 -0.159 0.142 logbht 0.364 0.220 -0.233 -0.811 > (fm2a <- lmer(logfev1 ~ age + loght + baseage + logbht + (loght|id), fev1, subset = id != 197)) Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (loght | id) Data: fev1 Subset: id != 197 AIC BIC logLik MLdeviance REMLdeviance -4573 -4529 2295 -4626 -4589 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 0.0133039 0.115343 loght 0.0684894 0.261705 -0.615 Residual 0.0035334 0.059443 Number of obs: 1993, groups: id, 299 Fixed effects: Estimate Std. Error t value (Intercept) -0.284612 0.039015 -7.29 age 0.023270 0.001247 18.65 loght 2.252336 0.046132 48.82 baseage -0.016297 0.007439 -2.19 logbht 0.180799 0.145488 1.24 Correlation of Fixed Effects: (Intr) age loght baseag age 0.047 loght -0.092 -0.856 baseage -0.823 -0.176 0.148 logbht 0.359 0.247 -0.262 -0.805 > deviance(fm2a) REML -4589.473 > (fm3 <- lmer(logfev1 ~ age + loght + baseage + logbht + (age + loght|id), fev1, verb = 1)) 0: -4349.1620: 0.633406 0.0487313 1.53684 0.00000 0.00000 0.00000 1: -4402.8618: 0.642947 0.101144 1.53847 0.0467393 0.00137061 7.59883e-05 2: -4416.6921: 0.681468 0.0532896 1.53943 0.0821127 0.00244065 -0.000105779 3: -4418.7550: 0.685208 0.0462628 1.53938 0.0724791 0.00216993 -0.000114092 4: -4456.5702: 1.13725 0.00000 1.57083 0.0247728 0.00157647 0.00619646 5: -4456.9850: 1.13809 1.27436e-07 1.57112 0.0202593 0.00138786 0.00619646 6: -4457.2054: 1.14156 0.000135635 1.57362 0.0219257 0.000967278 0.00617595 7: -4476.4739: 1.36452 0.0215254 1.87444 0.000500482 -0.0585281 0.00266800 8: -4494.6551: 1.58139 0.0444110 2.15353 -0.0193974 -0.115724 -0.00104955 9: -4497.5620: 1.80067 0.0907631 2.42558 -0.0116590 -0.185138 -0.00370111 10: -4497.7766: 1.89825 0.0922706 2.54258 -0.0391432 -0.276298 -0.00547285 11: -4510.3212: 1.85478 0.0801619 2.49328 -0.0193102 -0.332926 -0.00743384 12: -4511.2732: 1.85557 0.0687097 2.49310 -0.0243708 -0.333507 -0.00745688 13: -4512.5965: 1.85712 0.0684948 2.49424 -0.0171437 -0.343596 -0.00748745 14: -4513.0356: 1.86040 0.0670502 2.49745 -0.0189540 -0.355057 -0.00746724 15: -4513.5459: 1.86804 0.0643081 2.50463 -0.0162347 -0.377556 -0.00742574 16: -4522.1900: 2.13900 0.0710367 2.80169 -0.00407611 -1.07352 -0.00612413 17: -4522.5705: 2.04151 0.0561195 2.72345 0.0168799 -1.86718 -3.68172e-05 18: -4526.2188: 2.17527 0.0318391 3.51544 0.0170800 -1.93066 0.0201026 19: -4527.0121: 2.34519 0.0380494 3.17630 0.00463337 -1.51360 0.116318 20: -4527.4778: 2.27785 0.0347861 3.25147 0.0134884 -1.72099 0.119431 21: -4527.6268: 2.27494 0.0292731 3.38063 0.0119765 -1.73542 0.134672 22: -4527.6881: 2.28515 0.0291072 3.33720 0.0114357 -1.70541 0.162506 23: -4527.7124: 2.28737 0.0267185 3.34518 0.0117289 -1.70946 0.194354 24: -4527.7351: 2.28651 0.0223454 3.37120 0.0121819 -1.72415 0.247338 25: -4527.7407: 2.28506 0.0195917 3.38968 0.0123028 -1.72959 0.278243 26: -4527.7416: 2.28487 0.0183031 3.39517 0.0123671 -1.73271 0.293954 27: -4527.7417: 2.28495 0.0177232 3.39819 0.0123752 -1.73255 0.299126 28: -4527.7417: 2.28505 0.0176463 3.39796 0.0123813 -1.73278 0.298952 29: -4527.7417: 2.28507 0.0176412 3.39800 0.0123818 -1.73277 0.297518 30: -4527.7418: 2.28524 0.0176181 3.39821 0.0123840 -1.73261 0.272315 31: -4527.7418: 2.28556 0.0176129 3.39851 0.0123868 -1.73227 0.187579 32: -4527.7420: 2.28598 0.0176658 3.39886 0.0123895 -1.73177 -0.0159137 33: -4527.7425: 2.28678 0.0179266 3.39941 0.0123896 -1.73067 -0.646401 34: -4527.7438: 2.28822 0.0188039 3.40014 0.0123829 -1.72845 -2.36574 35: -4527.7510: 2.29278 0.0227825 3.40149 0.0123299 -1.72034 -9.24310 36: -4527.7891: 2.31054 0.0396153 3.40689 0.0120735 -1.68862 -36.7525 37: -4527.7990: 2.30532 0.0350806 3.40614 0.0122460 -1.70298 -28.9543 38: -4527.8561: 2.30670 0.0376747 3.43039 0.0130247 -1.73799 -32.7321 39: -4527.8960: 2.30708 0.0405750 3.43088 0.0130187 -1.74701 -34.8199 40: -4527.9339: 2.29836 0.0495894 3.42738 0.0135252 -1.77052 -39.8747 41: -4527.9697: 2.28561 0.0517067 3.42181 0.0132275 -1.77321 -36.5698 42: -4527.9944: 2.28448 0.0535288 3.42722 0.0133230 -1.77274 -35.0192 43: -4528.0313: 2.28267 0.0660767 3.44826 0.0132994 -1.76642 -28.8172 44: -4528.0584: 2.28926 0.0635939 3.44022 0.0131022 -1.75927 -32.8415 45: -4528.0703: 2.29080 0.0676906 3.44570 0.0129320 -1.75465 -32.3240 46: -4528.0735: 2.29228 0.0712536 3.45447 0.0126906 -1.74959 -31.6281 47: -4528.0738: 2.29224 0.0708300 3.45308 0.0127396 -1.75115 -31.9692 48: -4528.0738: 2.29238 0.0707320 3.45331 0.0127285 -1.75091 -31.8987 49: -4528.0738: 2.29237 0.0707920 3.45327 0.0127299 -1.75098 -31.8988 50: -4528.0738: 2.29238 0.0707825 3.45329 0.0127292 -1.75095 -31.9002 Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (age + loght | id) Data: fev1 AIC BIC logLik MLdeviance REMLdeviance -4506 -4444 2264 -4564 -4528 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 1.8460e-02 0.1358679 age 2.0591e-05 0.0045378 0.381 loght 1.1641e-01 0.3411956 -0.697 -0.629 Residual 3.5129e-03 0.0592695 Number of obs: 1994, groups: id, 300 Fixed effects: Estimate Std. Error t value (Intercept) -0.274041 0.041931 -6.54 age 0.023413 0.001293 18.10 loght 2.252864 0.048464 46.49 baseage -0.023219 0.007996 -2.90 logbht 0.349009 0.156186 2.23 Correlation of Fixed Effects: (Intr) age loght baseag age 0.070 loght -0.128 -0.864 baseage -0.820 -0.169 0.148 logbht 0.366 0.229 -0.236 -0.812 > (fm3a <- lmer(logfev1 ~ age + loght + baseage + logbht + (age + loght|id), fev1, verb = 1, subset = id != 197)) 0: -4461.5682: 0.632508 0.0486560 1.53437 0.00000 0.00000 0.00000 1: -4493.7480: 0.639469 0.0877614 1.53582 0.0327708 0.00107364 6.61410e-05 2: -4503.7500: 0.667991 0.0533925 1.53764 0.0583597 0.00248546 3.05696e-05 3: -4504.7864: 0.671507 0.0482948 1.53783 0.0526800 0.00248334 3.13048e-05 4: -4507.1358: 0.704606 0.0511140 1.54027 0.0570347 0.00382676 9.03377e-05 5: -4522.6453: 0.847752 0.0553690 1.55158 0.0123248 0.00833255 0.000295413 6: -4535.8617: 0.994240 0.0875601 1.58244 -0.0162659 0.0179412 0.00137641 7: -4545.8490: 1.14008 0.0471154 1.61252 0.00234461 0.0318777 0.00428299 8: -4557.0002: 1.27070 0.0756724 1.68522 -0.0319817 0.0291875 0.00719193 9: -4558.1545: 1.27280 0.0833050 1.68562 -0.0151495 0.0296910 0.00722215 10: -4561.2448: 1.28263 0.0776894 1.69856 -0.0216993 0.0270454 0.00814573 11: -4561.9462: 1.29599 0.0723466 1.71001 -0.0225739 0.0245431 0.00916150 12: -4571.3699: 1.67232 0.0828477 2.24709 -0.0469364 -0.0816276 0.0570937 13: -4577.3268: 1.67273 0.0820181 2.24718 -0.0338058 -0.0813161 0.0570969 14: -4578.9906: 1.67526 0.0709429 2.25300 -0.0346100 -0.0844431 0.0572694 15: -4579.6529: 1.68163 0.0704199 2.27537 -0.0307669 -0.0961426 0.0580210 16: -4587.0037: 1.94876 0.0445998 3.37037 -0.0209500 -0.706277 0.0992522 17: -4588.4798: 2.00285 0.0439074 3.29420 -0.0105471 -1.12412 0.113866 18: -4588.8374: 1.94548 0.0384888 3.36237 -0.00546650 -1.22290 0.144547 19: -4589.2319: 1.94997 0.0325907 3.29025 -0.00667872 -1.13508 0.220194 20: -4589.5141: 1.92454 0.0227980 3.40076 -0.00691954 -1.18064 0.328275 21: -4589.5848: 1.95070 0.0159794 3.46939 -0.00554917 -1.22696 0.387022 22: -4589.6225: 1.94832 0.0136570 3.44951 -0.00551687 -1.21960 0.431351 23: -4589.6428: 1.94194 0.00890643 3.46015 -0.00548426 -1.21573 0.498651 24: -4589.6512: 1.94258 0.00475549 3.47014 -0.00540605 -1.22086 0.558745 25: -4589.6540: 1.94302 0.00208482 3.47064 -0.00542750 -1.22134 0.601118 26: -4589.6546: 1.94292 0.000494362 3.47046 -0.00541572 -1.22118 0.626302 27: -4589.6546: 1.94289 0.000121667 3.46861 -0.00543859 -1.22037 0.633378 28: -4589.6546: 1.94288 6.70759e-05 3.46882 -0.00543451 -1.22044 0.634107 29: -4589.6546: 1.94288 3.11562e-05 3.46902 -0.00543203 -1.22051 0.634556 30: -4589.6546: 1.94288 1.53274e-05 3.46911 -0.00543081 -1.22055 0.634754 31: -4589.6546: 1.94288 2.35972e-07 3.46921 -0.00542962 -1.22059 0.634938 Linear mixed-effects model fit by REML Formula: logfev1 ~ age + loght + baseage + logbht + (age + loght | id) Data: fev1 Subset: id != 197 AIC BIC logLik MLdeviance REMLdeviance -4568 -4506 2295 -4626 -4590 Random effects: Groups Name Variance Std.Dev. Corr id (Intercept) 1.3337e-02 0.11548497 age 3.9318e-07 0.00062704 -1.000 loght 6.2393e-02 0.24978516 -0.564 0.564 Residual 3.5331e-03 0.05944024 Number of obs: 1993, groups: id, 299 Fixed effects: Estimate Std. Error t value (Intercept) -0.285092 0.039017 -7.31 age 0.023269 0.001251 18.61 loght 2.252379 0.045902 49.07 baseage -0.016140 0.007429 -2.17 logbht 0.177775 0.145269 1.22 Correlation of Fixed Effects: (Intr) age loght baseag age 0.038 loght -0.084 -0.855 baseage -0.824 -0.171 0.146 logbht 0.358 0.244 -0.261 -0.805 > deviance(fm3a) REML -4589.655 > > proc.time() user system elapsed 13.556 0.276 13.875