Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
You can use the lmerTest package . Enviado desde mi iPhone > El 26/5/2015, a las 13:18, li li 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 > 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 > > ___ > r-sig-mixed-mod...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
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 : > You can use the lmerTest package . > > > > > > Enviado desde mi iPhone > >> El 26/5/2015, a las 13:18, li li 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 >> 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 >> >> ___ >> r-sig-mixed-mod...@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] [R-sig-ME] lme function to obtain pvalue for fixed effect
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 : > 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 : > > You can use the lmerTest package . > > > > > > > > > > > > Enviado desde mi iPhone > > > >> El 26/5/2015, a las 13:18, li li 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 > >> 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 > >> > >> ___ > >> r-sig-mixed-mod...@r-project.org mailing list > >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > > > > ___ > r-sig-mixed-mod...@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
