I'm a beginner in statistics but i cannot understand this problem I have.
I want to test the impact of Compost and Amendement on the soil coverage. For that, I use a lmer model as such :
modg <- lmer(log(Couverture)~ as.factor(Compost) * Amendement + (1|Bande), data= rvg)
Both of the fixed effects are qualitative data. Compost factors are : 20, 30 or 40 Amendement factors are : Aucun, Myco_com, Myco_site, Prebiotique
Here is the summary i get :
Fixed effects:
Estimate Std. Error df t value Pr(>|t|)
(Intercept) 0.8044 0.5171 16.0414 1.556 0.139273
as.factor(Compost)30 1.2920 0.6822 19.9815 1.894 0.072827 .
as.factor(Compost)40 1.0211 0.7248 11.5907 1.409 0.185141
AmendementMyco_com 2.6701 0.4770 32.5073 5.598 3.31e-06 ***
AmendementMyco_site 2.4687 0.5043 33.9108 4.896 2.36e-05 ***
AmendementPrebiotique 1.3416 0.4939 32.2909 2.716 0.010522 *
as.factor(Compost)30:AmendementMyco_com -3.2280 0.6679 32.9430 -4.833 3.02e-05 ***
as.factor(Compost)40:AmendementMyco_com -3.3412 0.6590 32.3456 -5.070 1.58e-05 ***
as.factor(Compost)30:AmendementMyco_site -3.2795 0.6809 33.6309 -4.817 3.04e-05 ***
as.factor(Compost)40:AmendementMyco_site -3.0393 0.6790 33.1761 -4.476 8.48e-05 ***
as.factor(Compost)30:AmendementPrebiotique -1.6666 0.6713 32.2333 -2.483 0.018439 *
as.factor(Compost)40:AmendementPrebiotique -2.4807 0.6757 32.3685 -3.671 0.000863 ***
I figured that the intercept correspond to Aucun-Compost20 due to the fact that it is only qualitative factors that are tested so the models takes the first interaction as his reference. This seems to be confirmed by my tukey test :
emmeans(modg, list(pairwise ~ Amendement*as.factor(Compost)), adjust = "tukey")
The results I get for this test is :
Aucun Compost20 - Myco_com Compost20 -2.6701 0.479 31.86 -5.578 0.0002
Aucun Compost20 - Myco_site Compost20 -2.4687 0.509 33.51 -4.852 0.0014
Aucun Compost20 - Prebiotique Compost20 -1.3416 0.495 31.61 -2.713 0.2658
Aucun Compost20 - Aucun Compost30 -1.2920 0.735 18.29 -1.757 0.8205
Aucun Compost20 - Myco_com Compost30 -0.7341 0.706 20.45 -1.040 0.9943
Aucun Compost20 - Myco_site Compost30 -0.4811 0.706 20.45 -0.682 0.9999
Aucun Compost20 - Prebiotique Compost30 -0.9669 0.735 18.29 -1.315 0.9662
Aucun Compost20 - Aucun Compost40 -1.0211 0.740 10.16 -1.380 0.9442
Aucun Compost20 - Myco_com Compost40 -0.3501 0.740 10.16 -0.473 1.0000
Aucun Compost20 - Myco_site Compost40 -0.4505 0.740 10.16 -0.609 0.9999
Aucun Compost20 - Prebiotique Compost40 0.1180 0.745 10.30 0.158 1.0000
Myco_com Compost20 - Myco_site Compost20 0.2014 0.459 34.32 0.439 1.0000
Myco_com Compost20 - Prebiotique Compost20 1.3286 0.433 31.54 3.070 0.1352
Myco_com Compost20 - Aucun Compost30 1.3782 0.697 15.01 1.977 0.7013
Myco_com Compost20 - Myco_com Compost30 1.9361 0.666 16.78 2.906 0.2222
Myco_com Compost20 - Myco_site Compost30 2.1890 0.666 16.78 3.286 0.1181
Myco_com Compost20 - Prebiotique Compost30 1.7033 0.697 15.01 2.443 0.4351
Myco_com Compost20 - Aucun Compost40 1.6490 0.702 8.24 2.349 0.5105
Myco_com Compost20 - Myco_com Compost40 2.3201 0.702 8.24 3.306 0.1764
Myco_com Compost20 - Myco_site Compost40 2.2196 0.702 8.24 3.162 0.2095
Myco_com Compost20 - Prebiotique Compost40 2.7881 0.707 8.38 3.944 0.0790
Myco_site Compost20 - Prebiotique Compost20 1.1272 0.476 33.93 2.367 0.4534
Myco_site Compost20 - Aucun Compost30 1.1768 0.657 21.43 1.790 0.8066
Myco_site Compost20 - Myco_com Compost30 1.7347 0.614 24.37 2.825 0.2298
Myco_site Compost20 - Myco_site Compost30 1.9876 0.614 24.37 3.237 0.1066
Myco_site Compost20 - Prebiotique Compost30 1.5018 0.657 21.43 2.284 0.5141
Myco_site Compost20 - Aucun Compost40 1.4476 0.682 9.42 2.121 0.6232
Myco_site Compost20 - Myco_com Compost40 2.1187 0.682 9.42 3.104 0.2104
Myco_site Compost20 - Myco_site Compost40 2.0182 0.682 9.42 2.957 0.2532
Myco_site Compost20 - Prebiotique Compost40 2.5867 0.688 9.58 3.761 0.0869
Prebiotique Compost20 - Aucun Compost30 0.0496 0.710 16.20 0.070 1.0000
Prebiotique Compost20 - Myco_com Compost30 0.6075 0.680 18.13 0.894 0.9983
Prebiotique Compost20 - Myco_site Compost30 0.8604 0.680 18.13 1.266 0.9739
Prebiotique Compost20 - Prebiotique Compost30 0.3747 0.710 16.20 0.528 1.0000
Prebiotique Compost20 - Aucun Compost40 0.3204 0.715 8.91 0.448 1.0000
Prebiotique Compost20 - Myco_com Compost40 0.9915 0.715 8.91 1.387 0.9397
Prebiotique Compost20 - Myco_site Compost40 0.8910 0.715 8.91 1.246 0.9683
Prebiotique Compost20 - Prebiotique Compost40 1.4595 0.720 9.05 2.027 0.6732
Aucun Compost30 - Myco_com Compost30 0.5579 0.471 32.86 1.183 0.9867
Aucun Compost30 - Myco_site Compost30 0.8108 0.471 32.86 1.720 0.8464
Aucun Compost30 - Prebiotique Compost30 0.3251 0.455 31.47 0.715 0.9998
Aucun Compost30 - Aucun Compost40 0.2708 0.706 9.24 0.384 1.0000
Aucun Compost30 - Myco_com Compost40 0.9419 0.706 9.24 1.335 0.9524
Aucun Compost30 - Myco_site Compost40 0.8414 0.706 9.24 1.192 0.9766
Aucun Compost30 - Prebiotique Compost40 1.4099 0.711 9.39 1.984 0.6959
Myco_com Compost30 - Myco_site Compost30 0.2529 0.463 31.87 0.546 1.0000
Myco_com Compost30 - Prebiotique Compost30 -0.2328 0.471 32.86 -0.494 1.0000
Myco_com Compost30 - Aucun Compost40 -0.2871 0.685 9.34 -0.419 1.0000
Myco_com Compost30 - Myco_com Compost40 0.3840 0.685 9.34 0.561 1.0000
Myco_com Compost30 - Myco_site Compost40 0.2835 0.685 9.34 0.414 1.0000
Myco_com Compost30 - Prebiotique Compost40 0.8520 0.690 9.49 1.235 0.9710
Myco_site Compost30 - Prebiotique Compost30 -0.4858 0.471 32.86 -1.030 0.9957
Myco_site Compost30 - Aucun Compost40 -0.5400 0.685 9.34 -0.789 0.9990
Myco_site Compost30 - Myco_com Compost40 0.1311 0.685 9.34 0.191 1.0000
Myco_site Compost30 - Myco_site Compost40 0.0306 0.685 9.34 0.045 1.0000
Myco_site Compost30 - Prebiotique Compost40 0.5991 0.690 9.49 0.868 0.9979
Prebiotique Compost30 - Aucun Compost40 -0.0543 0.706 9.24 -0.077 1.0000
Prebiotique Compost30 - Myco_com Compost40 0.6168 0.706 9.24 0.874 0.9977
Prebiotique Compost30 - Myco_site Compost40 0.5164 0.706 9.24 0.732 0.9995
Prebiotique Compost30 - Prebiotique Compost40 1.0849 0.711 9.39 1.526 0.9004
Aucun Compost40 - Myco_com Compost40 0.6711 0.455 31.47 1.476 0.9365
Aucun Compost40 - Myco_site Compost40 0.5706 0.455 31.47 1.255 0.9791
Aucun Compost40 - Prebiotique Compost40 1.1391 0.462 31.81 2.463 0.3967
Myco_com Compost40 - Myco_site Compost40 -0.1005 0.455 31.47 -0.221 1.0000
Myco_com Compost40 - Prebiotique Compost40 0.4680 0.462 31.81 1.012 0.9962
Myco_site Compost40 - Prebiotique Compost40 0.5685 0.462 31.81 1.229 0.9822
So there are something logical betweens the 2 tables:
- The line for as.factor(Compost)30 in the summary corresponds to the line "Aucun Compost20 - Aucun Compost30"
- The line for as.factor(Compost)40 in the summary corresponds to the line "Aucun Compost20 - Aucun Compost40"
- The line for AmendementMyco_com in the summary corresponds to the line "Aucun Compost20 - Myco_com Compost20
- The line for AmendementMyco_site in the summary corresponds to the line "Aucun Compost20 - Myco_site Compost20 The line for AmendementPrebiotique in the summary corresponds to the line "Aucun Compost20 - Prebiotique Compost20
However, the lines after that don't match their equivalent in the tukey table. For example, as.factor(Compost)30:AmendementMyco_com should correspond to Aucun Compost20 - Myco_com Compost30 but it's not the case.I cannot understand why the values differ from that point. The intercept values in my tukey test makes way more sense if I look at the data. Can someone help me on this issue ?
I tried to look at data and to change orders of variables, to make my data as.ordered() etc but nothing worked.