On 1/16/06, Daniel A. Powers <dpowers at mail.la.utexas.edu>
wrote:>
> -- R-List
>
> Can someone tell me how to get fitted values etc. after fitting lmer?
> for example, from lme, I can fit mod.1 <- lme(....) and get fitted
values, coefficients, etc. in this way
>
> mod.1$fitted[,1] or mod.1$fitted[,2] etc.
>
> It seems lmer uses "slots" that are unfamiliar to me.
The preferred way is to use the extractor functions fitted, fixef,
ranef and coef.
Using the recently uploaded version 0.995-1 of the Matrix package we get
> (fm1 <- lmer(Reaction ~ Days + (Days|Subject), sleepstudy))
Linear mixed-effects model fit by REML
Formula: Reaction ~ Days + (Days | Subject)
Data: sleepstudy
AIC BIC logLik MLdeviance REMLdeviance
1753.628 1769.593 -871.8141 1751.986 1743.628
Random effects:
Groups Name Variance Std.Dev. Corr
Subject (Intercept) 612.090 24.7405
Days 35.072 5.9221 0.066
Residual 654.941 25.5918
# of obs: 180, groups: Subject, 18
Fixed effects:
Estimate Std. Error t value
(Intercept) 251.4051 6.8246 36.838
Days 10.4673 1.5458 6.771
Correlation of Fixed Effects:
(Intr)
Days -0.138> fixef(fm1)
(Intercept) Days
251.40510 10.46729> ranef(fm1)
An object of class $-1????lmer.ranef????
[[1]]
(Intercept) Days
308 2.2585636 9.1989720
309 -40.3985870 -8.6197013
310 -38.9602563 -5.4488780
330 23.6905071 -4.8143326
331 22.2602104 -3.0698958
332 9.0395288 -0.2721711
333 16.8404364 -0.2236253
334 -7.2325817 1.0745765
335 -0.3336930 -10.7521594
337 34.8903592 8.6282824
349 -25.2101185 1.1734156
350 -13.0699625 6.6142058
351 4.5778374 -3.0152575
352 20.8635979 3.5360123
369 3.2754538 0.8722165
370 -25.6128786 4.8224661
371 0.8070403 -0.9881552
372 12.3145428 1.2840291
> coef(fm1)
$Subject
(Intercept) Days
308 253.6637 19.6662580
309 211.0065 1.8475846
310 212.4448 5.0184079
330 275.0956 5.6529533
331 273.6653 7.3973901
332 260.4446 10.1951148
333 268.2455 10.2436606
334 244.1725 11.5418624
335 251.0714 -0.2848734
337 286.2955 19.0955683
349 226.1950 11.6407015
350 238.3351 17.0814918
351 255.9829 7.4520285
352 272.2687 14.0032983
369 254.6806 11.3395024
370 225.7922 15.2897520
371 252.2121 9.4791308
372 263.7196 11.7513151
> fitted(fm1)
[1] 253.6637 273.3299 292.9962 312.6624 332.3287 351.9950 371.6612 391.3275
[9] 410.9937 430.6600 211.0065 212.8541 214.7017 216.5493 218.3969 220.2444
[17] 222.0920 223.9396 225.7872 227.6348 212.4448 217.4633 222.4817 227.5001
[25] 232.5185 237.5369 242.5553 247.5737 252.5921 257.6105 275.0956 280.7486
[33] 286.4015 292.0545 297.7074 303.3604 309.0133 314.6663 320.3192 325.9722
[41] 273.6653 281.0627 288.4601 295.8575 303.2549 310.6523 318.0497 325.4470
[49] 332.8444 340.2418 260.4446 270.6397 280.8349 291.0300 301.2251 311.4202
[57] 321.6153 331.8104 342.0056 352.2007 268.2455 278.4892 288.7329 298.9765
[65] 309.2202 319.4638 329.7075 339.9512 350.1948 360.4385 244.1725 255.7144
[73] 267.2562 278.7981 290.3400 301.8818 313.4237 324.9656 336.5074 348.0493
[81] 251.0714 250.7865 250.5017 250.2168 249.9319 249.6470 249.3622 249.0773
[89] 248.7924 248.5076 286.2955 305.3910 324.4866 343.5822 362.6777 381.7733
[97] 400.8689 419.9644 439.0600 458.1556 226.1950 237.8357 249.4764 261.1171
[105] 272.7578 284.3985 296.0392 307.6799 319.3206 330.9613 238.3351 255.4166
[113] 272.4981 289.5796 306.6611 323.7426 340.8241 357.9056 374.9871 392.0686
[121] 255.9829 263.4350 270.8870 278.3390 285.7911 293.2431 300.6951 308.1471
[129] 315.5992 323.0512 272.2687 286.2720 300.2753 314.2786 328.2819 342.2852
[137] 356.2885 370.2918 384.2951 398.2984 254.6806 266.0201 277.3596 288.6991
[145] 300.0386 311.3781 322.7176 334.0571 345.3966 356.7361 225.7922 241.0820
[153] 256.3717 271.6615 286.9512 302.2410 317.5307 332.8205 348.1102 363.4000
[161] 252.2121 261.6913 271.1704 280.6495 290.1287 299.6078 309.0869 318.5661
[169] 328.0452 337.5243 263.7196 275.4710 287.2223 298.9736 310.7249 322.4762
[177] 334.2275 345.9789 357.7302 369.4815
I hope this helps.
Doug Bates