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

li li hannah.hlx at gmail.com
Tue May 26 20:13:54 CEST 2015


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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