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lme function to obtain pvalue for fixed effect

4 messages · byron vinueza, Li Li, Thierry Onkelinx

Original
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
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
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
byron vinueza
# 
You can use the lmerTest package .





Enviado desde mi iPhone
Li Li
# 
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>:
Thierry Onkelinx
# 
Because they test different hypothesis.

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey

2015-05-26 21:46 GMT+02:00 li li <hannah.hlx at gmail.com>: