Home Reading Searching Subscribe Sponsors Statistics Posting Contact Spam Lists Links About Hosting Filtering Features Download Marketing Archives FAQ Blog From: Ben Bolker public.gmane.org> Subject: Re: Help with anova result for model comparison Newsgroups: gmane.comp.lang.r.lme4.devel Date: Friday 8th July 2011 18:41:36 UTC (over 6 years ago) ```-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On 07/08/2011 12:24 PM, Catarina Miranda wrote: > Hello; > > When I run an anova to compare two lmer models I have in some situations > (always when I compare a model with interactions with a model where I > removed one simple fixed effect) an output that I don't fully understand. In > the anova output the models have the same degrees of freedom, as well as AIC > and BIC; the Chisq and its degrees of freedom are 0, and the p value is 1. > This makes me think that I cannot make this model comparison, but I would > like to understand why and to know how could I correctly compare two models > of this type. > The R output is below, any help or suggestions would be greatly appreciated! > Removing the main effect of "Origin" is just reparameterizing the model, not actually changing it. The easiest way to figure this stuff out is to play with design matrices for simple examples: > d <- expand.grid(a=factor(1:2),b=factor(1:2)) > model.matrix(~(a+b)^2,data=d) (Intercept) a2 b2 a2:b2 1 1 0 0 0 2 1 1 0 0 3 1 0 1 0 4 1 1 1 1 > model.matrix(~(a+b)^2-a,data=d) (Intercept) b2 a2:b1 a2:b2 1 1 0 0 0 2 1 0 1 0 3 1 1 0 0 4 1 1 0 1 (some details omitted) It is **occasionally** sensible (but often not: see Venables' _Exegeses on Linear Models_, unpublished but Googlable) to really drop the main effect term. This is actually quite difficult to do in R because model.matrix() (which is used internally by most if not all modeling functions) isn't quite flexible enough. Some modeling functions will take a raw design matrix; the only way I know to do it in lme4 would be to generate the design matrix yourself, drop the undesired columns, and use the result as the data for a new fit ... Ben > Catarina > > R version 2.13.0 (2011-04-13) > >> > m2_Exp<-lmer(lat_perch~(Sex+Origin+trial)^2+SMI_Neo+(1|Nest_ID)+(1|ID),data=full,REML=F) > > # lat_perch and SMI are numeric, but the other variables are factors > >> > m2_Exp_Origin<-lmer(lat_perch~(Sex+Origin+trial)^2+SMI_Neo-Origin+(1|Nest_ID)+(1|ID),data=full,REML=F) > >> anova(m2_Exp,m2_Exp_Origin) # NS but sething wierd is happening > Data: full > Models: > m2_Exp: lat_perch ~ (Sex + Origin + trial)^2 + SMI_Neo + (1 | Nest_ID) + > m2_Exp: (1 | ID) > m2_Exp_Origin: lat_perch ~ (Sex + Origin + trial)^2 + SMI_Neo - Origin + (1 > | > m2_Exp_Origin: Nest_ID) + (1 | ID) > Df AIC BIC logLik Chisq Chi Df Pr(>Chisq) > m2_Exp 14 3056 3098.9 -1514 > m2_Exp_Origin 14 3056 3098.9 -1514 0 0 1 > >> summary(m2_Exp) > Linear mixed model fit by maximum likelihood > Formula: lat_perch ~ (Sex + Origin + trial)^2 + SMI_Neo + (1 | Nest_ID) > + (1 | ID) > Data: full > AIC BIC logLik deviance REMLdev > 3056 3099 -1514 3028 2865 > Random effects: > Groups Name Variance Std.Dev. > ID (Intercept) 2516808 1586.45 > Nest_ID (Intercept) 481927 694.21 > Residual 9961255 3156.15 > Number of obs: 158, groups: ID, 53; Nest_ID, 18 > > Fixed effects: > Estimate Std. Error t value > (Intercept) -3995.97 3731.88 -1.071 > SexMale -1754.35 1225.74 -1.431 > OriginUrban 1618.35 1268.25 1.276 > trialT2 -2989.72 1128.92 -2.648 > trialT3 -1457.01 1145.84 -1.272 > SMI_Neo 98.49 43.34 2.272 > SexMale:OriginUrban 64.10 1390.64 0.046 > SexMale:trialT2 1364.19 1230.84 1.108 > SexMale:trialT3 2570.80 1237.91 2.077 > OriginUrban:trialT2 -336.72 1231.60 -0.273 > OriginUrban:trialT3 821.13 1238.67 0.663 > > Correlation of Fixed Effects: > (Intr) SexMal OrgnUr trilT2 trilT3 SMI_Ne SxM:OU SxM:T2 SxM:T3 > OrU:T2 > SexMale > -0.066 > OriginUrban -0.127 > 0.380 > trialT2 -0.106 0.312 > 0.299 > trialT3 0.009 0.324 0.304 > 0.499 > SMI_Neo -0.962 -0.120 -0.063 -0.047 > -0.165 > SxMl:OrgnUr -0.047 -0.593 -0.578 -0.007 -0.030 > 0.159 > SexMl:trlT2 0.118 -0.498 -0.027 -0.609 -0.296 -0.027 > -0.004 > SexMl:trlT3 0.077 -0.505 -0.033 -0.304 -0.607 0.016 0.009 > 0.496 > OrgnUrbn:T2 0.135 -0.025 -0.482 -0.608 -0.293 -0.044 -0.007 0.061 > 0.029 > OrgnUrbn:T3 0.130 -0.029 -0.483 -0.301 -0.598 -0.039 0.001 0.031 0.070 > 0.498 > > [[alternative HTML version deleted]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk4XT2AACgkQc5UpGjwzenMCygCcC8xoejtQEqnInkr7DowLbR+f PzEAn0wgctfVY+vauvMfkBaFuRxTPaof =pazH -----END PGP SIGNATURE-----```
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