Andrew Criswell
2004-Nov-25 02:47 UTC
[R] Error in anova(): objects must inherit from classes
Hello: Let me rephrase my question to attract interest in the problem I'm having. When I appply anova() to two equations estimated using glmmPQL, I get a complaint,> anova(fm1, fm2)Error in anova.lme(fm1, fm2) : Objects must inherit from classes "gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls">The two equations I estimated are these:> fm1 <- glmmPQL(choice ~ day + stereotypy,+ random = ~ 1 | bear, data = learning, family = binomial)> fm2 <- glmmPQL(choice ~ day + envir + stereotypy,+ random = ~ 1 | bear, data = learning, family = binomial) Individually, I get results from anova():> anova(fm1)numDF denDF F-value p-value (Intercept) 1 2032 7.95709 0.0048 day 1 2032 213.98391 <.0001 stereotypy 1 2032 0.42810 0.5130> > anova(fm2)numDF denDF F-value p-value (Intercept) 1 2031 5.70343 0.0170 day 1 2031 213.21673 <.0001 envir 1 2031 12.50388 0.0004 stereotypy 1 2031 0.27256 0.6017>I did look through the archives but didn't finding anything relevant to my problem. Hope someone can help. ANDREW ____________________________ _ platform i586-mandrake-linux-gnu arch i586 os linux-gnu system i586, linux-gnu status major 2 minor 0.0 year 2004 month 10 day 04 language R -- Andrew R. Criswell, Ph.D. Graduate School, Bangkok University mailto:andrew.c at bu.ac.th <http://email.bu.ac.th/src/compose.php?send_to=andrew.c%40bu.ac.th> mailto:andrew at arcriswell.com <http://email.bu.ac.th/src/compose.php?send_to=andrew%40arcriswell.com>
Austin, Matt
2004-Nov-25 03:34 UTC
[R] Error in anova(): objects must inherit from classes
The lme method for anova() checks the inheritance of the object when a single object is supplied, which is why there is no error when you use one object at a time. When two objects are supplied, the method uses the class of the object by invoking the data.class function (which does not list glmmPQL class). If you replace the check of the class with a check of inheritance it should work. Following is a check from the example listed in MASS (Venables and Ripley)> library(MASS) > library(nlme) > x1 <- glmmPQL(y ~ I(week > 2), random = ~ 1 | ID,+ family = binomial, data = bacteria) iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6> x2 <- glmmPQL(y ~ trt + I(week > 2), random = ~ 1 | ID,+ family = binomial, data = bacteria) iteration 1 iteration 2 iteration 3 iteration 4 iteration 5 iteration 6> anova(x1)numDF denDF F-value p-value (Intercept) 1 169 35 <.0001 I(week > 2) 1 169 21 <.0001> anova(x2)numDF denDF F-value p-value (Intercept) 1 169 35 <.0001 trt 2 47 2 0.22 I(week > 2) 1 169 20 <.0001> anova(x1, x2)Error in anova.lme(x1, x2) : Objects must inherit from classes "gls", "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls" After replacement:> anovaLME(x1, x2)Model df AIC BIC logLik Test L.Ratio p-value x1 1 4 1107 1121 -550 x2 2 6 1114 1134 -551 1 vs 2 2.6 0.28 Matt Austin Statistician Amgen One Amgen Center Drive M/S 24-2-C Thousand Oaks CA 93021 (805) 447 - 7431> -----Original Message----- > From: r-help-bounces at stat.math.ethz.ch > [mailto:r-help-bounces at stat.math.ethz.ch]On Behalf Of Andrew Criswell > Sent: Wednesday, November 24, 2004 18:47 PM > To: R-help > Subject: [R] Error in anova(): objects must inherit from classes > > > Hello: > > Let me rephrase my question to attract interest in the > problem I'm having. When I appply anova() to two equations > estimated using glmmPQL, I get a complaint, > > > anova(fm1, fm2) > Error in anova.lme(fm1, fm2) : Objects must inherit from > classes "gls", > "gnls" "lm","lmList", "lme","nlme","nlsList", or "nls" > > > > The two equations I estimated are these: > > > fm1 <- glmmPQL(choice ~ day + stereotypy, > + random = ~ 1 | bear, data = learning, family > = binomial) > > fm2 <- glmmPQL(choice ~ day + envir + stereotypy, > + random = ~ 1 | bear, data = learning, family > = binomial) > > Individually, I get results from anova(): > > > anova(fm1) > numDF denDF F-value p-value > (Intercept) 1 2032 7.95709 0.0048 > day 1 2032 213.98391 <.0001 > stereotypy 1 2032 0.42810 0.5130 > > > > anova(fm2) > numDF denDF F-value p-value > (Intercept) 1 2031 5.70343 0.0170 > day 1 2031 213.21673 <.0001 > envir 1 2031 12.50388 0.0004 > stereotypy 1 2031 0.27256 0.6017 > > > > I did look through the archives but didn't finding anything > relevant to my problem. > > Hope someone can help. > > ANDREW > ____________________________ > _ > platform i586-mandrake-linux-gnu > arch i586 > os linux-gnu > system i586, linux-gnu > status > major 2 > minor 0.0 > year 2004 > month 10 > day 04 > language R > > > > -- > Andrew R. Criswell, Ph.D. > Graduate School, Bangkok University > > mailto:andrew.c at bu.ac.th > <http://email.bu.ac.th/src/compose.php?send_to=andrew.c%40bu.ac.th> > mailto:andrew at arcriswell.com > <http://email.bu.ac.th/src/compose.php?send_to=andrew%40arcriswell.com> ______________________________________________ R-help at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html