[R] How to extract coefficients from sequential (type 1) ANOVAs using lmer and lme

[Akihiro Koyama]

I wantto run sequential ANOVAs (i.e. type I sums of squares), and trying to getresults including ANOVA tables and associated coefficients for predictive variables(I am using the R 3.4.2 version). I think ANOVA tables look right, but believecoefficients are wrong. Specifically, it looks like that the coefficients arefrom ANOVA with “marginal” (type III sums of squares). I have tried both lme (nlmepackage) and lmer (lme4 + lmerTEST packages). Examples of the results arebelow:


 

 
> #mixed-effect modelusing lme

>model.short.psme.bulk.d13c.3 <- lme(isotopebulk_add_log ~narea+sampleheight, random= ~1|tree, 

+                            data =ht_data_short_psme, na.action = na.exclude)

> 


 
>anova(model.short.psme.bulk.d13c.3, type ="sequential")

             numDF denDF   F-value p-value

(Intercept)      1    3 1840.5678  <.0001

narea            1     2  18.4876  0.0501

sampleheight     1    2   11.6159  0.0764


 
>anova(model.short.psme.bulk.d13c.3, type ="marginal")

             numDF denDF  F-value p-value

(Intercept)      1    3 629.4711  0.0001

narea            1    2   2.7831  0.2372

sampleheight     1    2  11.6159  0.0764

> 

>summary(model.short.psme.bulk.d13c.3, type ="sequential")$tTable

                   Value  Std.Error DF  t-value      p-value

(Intercept)   1.76871397 0.07049685  3 25.089262 0.0001388446

narea        -0.09295561 0.05571991  2 -1.668266 0.2372012082

sampleheight  0.13232709 0.03882599  2 3.408209 0.0763589527

 (Intercept)  1.76871397 0.07049685  3 25.0892620.0001388446


 
>summary(model.short.psme.bulk.d13c.3, type ="marginal")$tTable

                   Value  Std.Error DF  t-value      p-value

(Intercept)   1.76871397 0.07049685  3 25.089262 0.0001388446

narea        -0.09295561 0.05571991  2 -1.668266 0.2372012082

sampleheight  0.13232709 0.03882599  2 3.408209 0.0763589527


 

 
Ibelieve the results from summary() are for “marginal” instead of “sequential”ANOVA because the p-value (i.e., 0.237 for narea) in summary are identical tothose in tables from “marginal”. I also used lmer in the lme4 pacakge to findthe same results (summary() results look like from “marginal”).


 
Cananybody tell me how to get coefficients for “sequential” ANOVAs? Thank you.


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