[R-sig-ME] lme function to obtain pvalue for fixed effect

li li hannah.hlx at gmail.com
Tue May 26 21:46:11 CEST 2015


Thanks so much for replying.
Yes LimerTest package could be used to get pvalues when using lmer
function. But still the summary and anova function give different
pvalues.
   Hanna

2015-05-26 15:19 GMT-04:00, byron vinueza <byronvinu_8 at hotmail.com>:
> You can use the lmerTest package .
>
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> Enviado desde mi iPhone
>
>> El 26/5/2015, a las 13:18, li li <hannah.hlx at gmail.com> escribió:
>>
>> Hi all,
>>  I am using the lme function to run a random coefficient model. Please
>> see
>> output (mod1) as below.
>>  I need to obtain the pvalue for the fixed effect. As you can see,
>> the pvalues given using the summary function is different from the
>> resutls given in anova function.
>> Why should they be different and which one is the correct one to use?
>>   Thanks!
>>      Hanna
>>
>>
>>> summary(mod1)
>> Linear mixed-effects model fit by REML
>> Data: minus20C1
>>        AIC       BIC   logLik
>>  -82.60042 -70.15763 49.30021
>>
>> Random effects:
>> Formula: ~1 + months | lot
>> Structure: General positive-definite, Log-Cholesky parametrization
>>            StdDev       Corr
>> (Intercept) 8.907584e-03 (Intr)
>> months      6.039781e-05 -0.096
>> Residual    4.471243e-02
>>
>> Fixed effects: ti ~ type * months
>>                     Value   Std.Error DF   t-value p-value
>> (Intercept)     0.25831245 0.016891587 31 15.292373  0.0000
>> type             0.13502089 0.026676101  4  5.061493  0.0072
>> months          0.00804790 0.001218941 31  6.602368  0.0000
>> type:months -0.00693679 0.002981859 31 -2.326329  0.0267
>> Correlation:
>>               (Intr) typ months
>> type        -0.633
>> months         -0.785  0.497
>> type:months  0.321 -0.762 -0.409
>>
>> Standardized Within-Group Residuals:
>>          Min            Q1           Med            Q3           Max
>> -2.162856e+00 -1.962972e-01 -2.771184e-05  3.749035e-01  2.088392e+00
>>
>> Number of Observations: 39
>> Number of Groups: 6
>>> anova(mod1)
>>            numDF denDF   F-value p-value
>> (Intercept)     1    31 2084.0265  <.0001
>> type            1     4   10.8957  0.0299
>> months          1    31   38.3462  <.0001
>> type:months     1    31    5.4118  0.0267
>>
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>



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