Hi listers,

I am trying to analyze some community composition data in adonis(). Samples
were taken in 3 regions. In each region 4 samples were taken in 2 treatment
plots (one plot for each treatment level, 4 samples/ plot)

So I have:
a mixed model with 2 factors:
treatment factor, fixed,  with 2 levels
region factor, random, with 3 levels
interaction factor, region x treatment, random, with: (2-1)*(3-1) degrees
of freedom

I ran this in vegan:

# jun10_strata


   SampleID Treatment Region

1  leA2j10A      1      1

2  leA2j10B      1      1

3  leA2j10C      1      1

4  leA2j10D      1      1

5   leNj10A      2      1

6   leNj10B      2      1

7   leNj10C      2      1

8   leNj10D      2      1

9   lnAj10A      1      2

10  lnAj10B      1      2

11  lnAj10C      1      2

12  lnAj10D      1      2

13  lnNj10A      2      2

14  lnNj10B      2      2

15  lnNj10C      2      2

16  lnNj10D      2      2

17  ckAj10A      1      3

18  ckAj10B      1      3

19  ckAj10C      1      3

20  ckAj10D      1      3

21  ckNj10A      2      3

22  ckNj10B      2      3

23  ckNj10C      2      3

24  ckNj10D      2      3


> Treatment<-as.factor(jun10_strata$Treatment)

> Region<-as.factor(jun10_strata$Region)


#I also have a dist object with similarity data (A,B,C,D at the end of each
name stands for the 4 samples, A and N in the middle of the name stands for
the treatment level)


> head(jun10_rar0_WU)

          leNj10D   lnNj10A   leNj10A   leNj10C   lnNj10C   ckAj10C
lnAj10D

leNj10D 0.0000000 0.2665852 0.1919884 0.1918817 0.2477480 0.2878360
0.3017183

lnNj10A 0.2665852 0.0000000 0.2767476 0.2716313 0.2160397 0.3075382
0.3227785

leNj10A 0.1919884 0.2767476 0.0000000 0.1960676 0.2552759 0.3107144
0.3254971

leNj10C 0.1918817 0.2716313 0.1960676 0.0000000 0.2405019 0.2933426
0.2971112

lnNj10C 0.2477480 0.2160397 0.2552759 0.2405019 0.0000000 0.3520453
0.3454823

ckAj10C 0.2878360 0.3075382 0.3107144 0.2933426 0.3520453 0.0000000
0.2505754

          lnNj10B   ckNj10D   leNj10B   ckNj10B   ckNj10C   ckNj10A
 leA2j10D

leNj10D 0.2567186 0.2357255 0.1882101 0.2419491 0.2475977 0.2327607
0.2572058

lnNj10A 0.1958480 0.2892515 0.2760835 0.2912953 0.3013809 0.2864480
0.2578597

leNj10A 0.2728269 0.2510857 0.1899333 0.2639657 0.2620232 0.2553712
0.2845143

leNj10C 0.2539358 0.2119476 0.1957914 0.2267707 0.2335541 0.2346603
0.2651513

lnNj10C 0.1904775 0.2507830 0.2418602 0.2470663 0.2551320 0.2655108
0.2847935

ckAj10C 0.3341484 0.3288277 0.2952415 0.3405510 0.3241553 0.3140513
0.2404757

         leA2j10A   lnAj10B   lnNj10D   ckAj10A  leA2j10C  leA2j10B
lnAj10C

leNj10D 0.2638036 0.3213494 0.2517604 0.3358382 0.2668388 0.2482920
0.2819090

lnNj10A 0.2690759 0.3260389 0.2001313 0.3534574 0.2768660 0.2750732
0.2889214

leNj10A 0.2854511 0.3428684 0.2714276 0.3484174 0.2966257 0.2782187
0.3051495

leNj10C 0.2733033 0.3174810 0.2636317 0.3289142 0.2781781 0.2523127
0.3009915

lnNj10C 0.2772286 0.3513996 0.1788061 0.3627291 0.2864218 0.2506676
0.3137582

ckAj10C 0.2772017 0.2388376 0.3413704 0.2332969 0.3020010 0.3079088
0.2313831

          lnAj10A   ckAj10D   ckAj10B

leNj10D 0.3309027 0.3184646 0.2843012

lnNj10A 0.3290170 0.3451042 0.2914636

leNj10A 0.3622460 0.3298120 0.2800040

leNj10C 0.3405181 0.3136294 0.3089865

lnNj10C 0.3494390 0.3636385 0.3310442

ckAj10C 0.2543455 0.1906587 0.1906881


# Then adonis() result looks like this:


Call:

adonis(formula = jun10_rar0_WU ~ Treatment * Region, data = jun10_strata,
   permutations = 999, strata = jun10_strata$Region)


Terms added sequentially (first to last)


              Df SumsOfSqs  MeanSqs F.Model      R2 Pr(>F)

Treatment         1   0.10955 0.109550  3.2666 0.12283  0.003 **

Region         1   0.07653 0.076534  2.2821 0.08581  0.001 ***

Treatment:Region  1   0.03508 0.035077  1.0459 0.03933  0.371

Residuals     20   0.67073 0.033537         0.75203

Total         23   0.89189                  1.00000

---

Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1



I am not sure if I am performing this the right way.  I have some doubts
about the interaction factor, is there any way to specify this in adonis()
??


any help will be very much appreciate.

sorry about my English,  it is not my first language.

	[[alternative HTML version deleted]]

