[R-sig-ME] Error message in lme function and question about the residual plot
Thierry Onkelinx
thierry.onkelinx at inbo.be
Thu Jun 11 19:44:05 CEST 2015
You need to add type ="norm" to resid() to see the effect of varIdent.
Make sure that assay is present in one before fitting model3
Op 11 jun. 2015 19:23 schreef "li li" <hannah.hlx op gmail.com>:
> Hi all,
> I have the following data frame named "one" in which there is a
> grouping factor method with three levels. The varibility is very
> different among the three groups seen from the plot. I am trying to
> compare three models as follows. I have the following two questions:
> 1. As you can see the third model does not seem to work. I am not
> sure whether it is a convergent issue.
> 2. The first model doesnot take into account the variance
> heterogeneity issue while the second one does. However, when I compare
> the residual plot between mod1 and mod2, there is not much difference.
> The residual for the second model still has much larger variance for
> methods 2 and 3 than the method 1.
>
> Thanks very much!
> Hanna
>
>
> > one
> method individual time res
> 1 3 12 0 101.40000
> 2 3 12 3 101.50000
> 3 3 12 6 101.50000
> 4 3 12 9 101.30000
> 5 3 12 12 100.70000
> 6 3 12 15 101.00000
> 7 3 12 18 101.50000
> 14 3 10 0 101.30000
> 15 3 10 3 101.20000
> 16 3 10 6 101.50000
> 17 3 10 9 100.70000
> 18 3 10 12 101.50000
> 19 3 10 15 101.30000
> 20 3 10 18 101.30000
> 27 3 11 0 100.70000
> 28 3 11 3 101.10000
> 29 3 11 6 101.90000
> 30 3 11 9 100.80000
> 31 3 11 12 99.80000
> 32 3 11 15 100.60000
> 33 3 11 18 100.60000
> 40 3 1 0 97.50000
> 41 3 1 3 97.40000
> 42 3 1 6 97.70000
> 43 3 1 9 97.40000
> 44 3 1 12 97.30000
> 45 3 1 15 96.70000
> 46 3 1 18 96.60000
> 54 3 3 0 98.10000
> 55 3 3 3 98.50000
> 56 3 3 6 97.90000
> 57 3 3 9 97.90000
> 58 3 3 12 97.70000
> 59 3 3 15 98.00000
> 60 3 3 18 98.50000
> 67 3 6 0 100.20000
> 68 3 6 3 99.60000
> 69 3 6 6 99.90000
> 70 3 6 9 99.90000
> 71 3 6 12 100.30000
> 77 3 2 0 98.90000
> 78 3 2 3 98.90000
> 79 3 2 6 98.70000
> 80 3 2 9 98.90000
> 81 3 2 12 98.80000
> 82 3 2 15 97.80000
> 83 3 2 18 98.90000
> 90 3 4 0 100.20000
> 91 3 4 3 99.80000
> 92 3 4 6 99.50000
> 93 3 4 9 100.40000
> 96 3 5 0 100.70000
> 97 3 5 3 100.30000
> 98 3 5 6 100.70000
> 99 3 5 9 100.50000
> 102 3 7 0 100.90000
> 105 3 8 0 99.30000
> 108 3 9 0 100.20000
> 111 3 13 0 101.00000
> 114 3 14 0 100.80000
> 117 3 15 0 100.40000
> 8 2 12 0 108.00000
> 9 2 12 12 97.00000
> 21 2 10 0 112.00000
> 22 2 10 12 93.00000
> 34 2 11 0 98.00000
> 35 2 11 12 96.00000
> 47 2 1 0 94.00000
> 48 2 1 12 103.00000
> 49 2 1 18 103.00000
> 61 2 3 0 87.00000
> 62 2 3 12 105.00000
> 72 2 6 0 119.00000
> 73 2 6 3 105.00000
> 74 2 6 12 91.00000
> 84 2 2 0 105.00000
> 85 2 2 12 112.00000
> 95 2 4 0 96.00000
> 101 2 5 0 113.00000
> 104 2 7 0 106.00000
> 107 2 8 0 71.00000
> 110 2 9 0 95.00000
> 113 2 13 0 88.00000
> 116 2 14 0 86.00000
> 119 2 15 0 81.00000
> 86 1 12 0 105.90300
> 94 1 12 12 99.82400
> 10 1 12 15 91.26400
> 11 1 12 18 72.15000
> 191 1 10 0 91.14300
> 201 1 10 12 100.36800
> 211 1 10 15 104.79600
> 221 1 10 18 102.58200
> 301 1 11 0 78.32400
> 311 1 11 12 88.20900
> 321 1 11 15 95.52600
> 331 1 11 18 106.87200
> 411 1 1 0 99.04500
> 421 1 1 12 82.83600
> 431 1 1 15 116.51200
> 441 1 1 18 89.05600
> 52 1 3 0 97.81800
> 53 1 3 12 89.81500
> 541 1 3 15 82.11000
> 551 1 3 18 79.83400
> 611 1 6 0 89.06000
> 621 1 6 12 102.56500
> 701 1 2 0 112.32000
> 711 1 2 12 104.40000
> 721 1 2 15 90.06800
> 731 1 2 18 107.28000
> 781 1 4 0 125.92500
> 831 1 5 0 95.16000
> 851 1 7 0 111.28981
> 87 1 8 0 102.22482
> 89 1 9 0 91.61610
> 911 1 13 0 111.18053
> 931 1 14 0 91.70376
> 951 1 15 0 98.04994
>
>
>
> library(nlme)
> mod1 <- lme(fixed= res ~ method*time, random=~ 1+ time | individual,
> data=one)
> summary(mod1)
> anova(mod1)
>
> mod2 <- lme(fixed= res ~ method*time, random=~ 1+ time | individual,
> data=one, weights= varIdent(form=~1|method))
> summary(mod2)
> anova(mod2)
>
> mod3 <- lme(fixed= res ~ method*time, random=~ 0+ method+ time |
> individual, data=one, weights= varIdent(form=~1|assay))
> summary(mod3)
> anova(mod3)
>
> par(mfrow=c(1,2))
> plot(resid(mod1))
> plot(resid(mod2))
>
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