Hi, I need a help. I am new in R and I need to run a nested anova with fixed and random factors (Mixed Model). I have a design with three factors: Day, Area and Plot and the dependent variable is density. The factors Day and Area are fixed while Plot is random, factor Area is nested in factor Day, and factor Plot is nested in Area.
I can do it using aov by: mod1<-aov(density~ day + day%in%area + day%in%area%in%plot) symmary(mod1) Getting this result: Analysis of Variance Table Response: total Df Sum Sq Mean Sq F value Pr(>F) day 2 1789.8 894.91 55.5576 < 2e-16 *** day:area 15 4658.8 310.59 19.2818 < 2e-16 *** day:area:plot 72 1715.7 23.83 1.4793 0.01145 * Residuals 360 5798.8 16.11 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 But I'm afraind the factor plot is not beeing calculated as random. The other way would be using the lme from nlme as below (if I had only factors area and plot, once I don't know how to include day and keep plot as random) just as an exemple I found in the list files: > mod2 <- lme(density ~ area + plot, random = ~ 1 | area / plot, data = > data) > summary(mod2) Linear mixed-effects model fit by REML Data: data AIC BIC logLik 1422.403 1475.532 -698.2017 Random effects: Formula: ~1 | area (Intercept) StdDev: 0.347117 Formula: ~1 | plot %in% area (Intercept) Residual StdDev: 6.431067e-05 1.127295 Fixed effects: density~ area + plot Value Std.Error DF t-value p-value (Intercept) 2.6131608 0.3856554 420 6.775895 0.0000 areaarea10 -1.2073539 0.5242788 0 -2.302885 NaN areaarea2 -0.3062031 0.5242788 0 -0.584046 NaN areaarea4 -0.6109334 0.5242788 0 -1.165283 NaN areaarea6 -0.9808034 0.5242788 0 -1.870767 NaN areaarea8 -1.3437982 0.5242788 0 -2.563136 NaN plotb -0.0899366 0.1680473 20 -0.535187 0.5984 plotc 0.0257024 0.1680473 20 0.152947 0.8800 plotd 0.0420734 0.1680473 20 0.250366 0.8049 plote -0.2375628 0.1680473 20 -1.413666 0.1728 Correlation: (Intr) arer10 arear2 arear4 arear6 arear8 plotb plotc plotd areaarea10 -0.680 areaarea2 -0.680 0.500 areaarea4 -0.680 0.500 0.500 areaarea6 -0.680 0.500 0.500 0.500 areaarea8 -0.680 0.500 0.500 0.500 0.500 plotb -0.218 0.000 0.000 0.000 0.000 0.000 plotc -0.218 0.000 0.000 0.000 0.000 0.000 0.500 plotd -0.218 0.000 0.000 0.000 0.000 0.000 0.500 0.500 plote -0.218 0.000 0.000 0.000 0.000 0.000 0.500 0.500 0.500 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.3554021 -0.8985867 0.1031298 0.8008967 2.6488795 Number of Observations: 450 Number of Groups: area plot %in% area 6 30 Warning message: In pt(q, df, lower.tail, log.p) : NaNs produzidos But, in addition to the lack of the factor day, I am sure its not right because of these "NaN" produced and because of the area beeing assigned as Random in the output. I would appreciate any help and thanks for your attention in advance, Pablo -- View this message in context: http://r.789695.n4.nabble.com/Nestad-ANOVA-with-random-Factors-tp2340725p2340725.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list 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.