Re: [R] lme function to obtain pvalue for fixed effect

2015-05-26 Thread Ben Bolker 
li li hannah.hlx at gmail.com writes:

 
 Hi all,
   I am using the lme function to run a random coefficient model.
 Please see
 output (mod1) as below.

  Please don't cross-post to different R lists (this is explicitly
deprecated by the list policy: http://www.r-project.org/mail.html, 
cross-posting is considered to be impolite).  r-sig-mixed-models
seems to be more appropriate for these questions.

  sincerely
Ben Bolker

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[R] lme function to obtain pvalue for fixed effect

2015-05-26 Thread li li 
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
Residual4.471243e-02

Fixed effects: ti ~ type * months
 Value   Std.Error DF   t-value p-value
(Intercept) 0.25831245 0.016891587 31 15.292373  0.
type 0.13502089 0.026676101  4  5.061493  0.0072
months  0.00804790 0.001218941 31  6.602368  0.
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:
  MinQ1   MedQ3   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) 131 2084.0265  .0001
type1 4   10.8957  0.0299
months  131   38.3462  .0001
type:months 1315.4118  0.0267

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