[R-sig-ME] sas to R

Douglas Bates bates at stat.wisc.edu
Mon Jun 25 19:28:23 CEST 2012


Are you trying to load both the nlme and the lme4 packages at the same
time?  That can cause problems.  You are better off fitting the lmer
model in one R session and the lme model in another.

On Mon, Jun 25, 2012 at 11:50 AM, Steve Hong <emptican at gmail.com> wrote:
> Thank all of you for replying to me.
>
> I tried lmer, lme, and SAS.  I was able to get outputs when I use
> 'lme' whereas no results from 'lmer'.  I don't know why.  Does anyone
> know what the warning message mean?  Outputs from  'lme' were similar
> with those from SAS.  Below is selected outputs from lmer, lme, and
> SAS, FYI.
>
> Thanks again,
>
> Steve Hong
>
>> fm.lmer <- lmer(y ~ trt + (1|trial/block/trt), data=df, na.action=na.omit)
> Error: length(f1) == length(f2) is not TRUE
> In addition: Warning messages:
> 1: In block:trial :
>   numerical expression has 92 elements: only the first used
> 2: In block:trial :
>   numerical expression has 92 elements: only the first used
> 3: In trt:(block:trial) :
>   numerical expression has 92 elements: only the first used
> 4: In block:trial :
>   numerical expression has 92 elements: only the first used
> 5: In block:trial :
>   numerical expression has 92 elements: only the first used
>> fm.lme <- lme(y ~ trt, random=(~1|trial/block/trt), data = df, na.action=na.omit)
>> summary(fm.lme)
> Linear mixed-effects model fit by REML
>  Data: df
>         AIC       BIC   logLik
>   -85.22388 -60.68041 52.61194
>
> Random effects:
>  Formula: ~1 | trial
>         (Intercept)
> StdDev:   0.1112442
>
>  Formula: ~1 | block %in% trial
>          (Intercept)
> StdDev: 1.449228e-06
>
>  Formula: ~1 | trt %in% block %in% trial
>         (Intercept)  Residual
> StdDev:  0.07081356 0.1020226
>
> Fixed effects: y ~ trt
>                   Value  Std.Error DF    t-value p-value
> (Intercept)  0.24428523 0.08793775 56  2.7779337  0.0074
> trtau2      -0.00996643 0.05605221 25 -0.1778063  0.8603
> trtberm     -0.12786905 0.05686903 25 -2.2484830  0.0336
> trtls44      0.12326637 0.05478364 25  2.2500582  0.0335
> trtsr10y5    0.02513355 0.05517460 25  0.4555275  0.6527
> trtsr10y6    0.01932992 0.05478364 25  0.3528410  0.7272
>  Correlation:
>           (Intr) trtau2 trtbrm trtl44 trt105
> trtau2    -0.314
> trtberm   -0.309  0.486
> trtls44   -0.321  0.504  0.497
> trtsr10y5 -0.319  0.500  0.493  0.511
> trtsr10y6 -0.321  0.504  0.497  0.515  0.511
>
> Standardized Within-Group Residuals:
>           Min            Q1           Med            Q3           Max
> -2.614096e+00 -5.666986e-01 -9.727356e-05  4.692685e-01  2.410879e+00
>
> Number of Observations: 92
> Number of Groups:
>                     trial          block %in% trial trt %in% block %in% trial
>                         2                         6                        36
>> anova(fm.lme)
>             numDF denDF  F-value p-value
> (Intercept)     1    56 9.907983  0.0026
> trt             5    25 4.122070  0.0072
>
>
> SAS code and outputs:
> proc glimmix data=df;
> model y=trt;
> random trial block(trial) turf(block*turf);
> run;
>
>     Covariance Parameter Estimates
>
>                                 Standard
> Cov Parm             Estimate       Error
>
> trial                 0.01237     0.01823
> block(trial)                0           .
> trt(trial*block)    0.005015    0.002546
> Residual              0.01041    0.001963
>
>
>        Type III Tests of Fixed Effects
>
>              Num      Den
> Effect         DF       DF    F Value    Pr > F
>
> trt            5       25       4.12    0.0072
>
>
>
> On Mon, Jun 25, 2012 at 10:25 AM, Kevin Wright <kw.stat at gmail.com> wrote:
>>
>> This could be similar to a multi-location RCB design were "trial" is
>> location.  Since no distribution is specified, the distribution is
>> assumed to be Gaussian.  Make sure that trial, block, trt are factors,
>> this should be similar to SAS:
>>
>> lmer(y ~ trt + (1|trial/block/trt), data=df)
>>
>> > proc glimmix data=df;
>> > class trial block trt;
>> > model y=trt;
>> > random trial block(trial) trt(block*trial);
>>
>> Kevin Wright
>
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