You probably don't need to log transform. The patterns are really clear and the general pattern is not too right skewed, although there are some exceptions.
mod <- aov(Cadmium ~ Site * Source, data = d)
print(xtable(anova(mod), caption = "Cadmium"), "HTML")
| Df | Sum Sq | Mean Sq | F value | Pr(> F) | |
|---|---|---|---|---|---|
| Site | 3 | 2.45 | 0.82 | 1.06 | 0.3650 |
| Source | 2 | 146.11 | 73.05 | 95.09 | 0.0000 |
| Site:Source | 6 | 7.80 | 1.30 | 1.69 | 0.1232 |
| Residuals | 264 | 202.82 | 0.77 |
mod <- aov(Copper ~ Site * Source, data = d)
print(xtable(anova(mod), caption = "Copper"), "HTML")
| Df | Sum Sq | Mean Sq | F value | Pr(> F) | |
|---|---|---|---|---|---|
| Site | 3 | 513417.75 | 171139.25 | 17.65 | 0.0000 |
| Source | 2 | 9735167.40 | 4867583.70 | 502.07 | 0.0000 |
| Site:Source | 6 | 636090.56 | 106015.09 | 10.94 | 0.0000 |
| Residuals | 264 | 2559463.18 | 9694.94 |
mod <- aov(Zinc ~ Site * Source, data = d)
print(xtable(anova(mod), caption = "Zinc"), "HTML")
| Df | Sum Sq | Mean Sq | F value | Pr(> F) | |
|---|---|---|---|---|---|
| Site | 3 | 7104946.32 | 2368315.44 | 10.81 | 0.0000 |
| Source | 2 | 234583073.22 | 117291536.61 | 535.32 | 0.0000 |
| Site:Source | 6 | 8477380.48 | 1412896.75 | 6.45 | 0.0000 |
| Residuals | 252 | 55214264.95 | 219104.23 |
mod <- aov(Lead ~ Site * Source, data = d)
print(xtable(anova(mod), caption = "Lead"), "HTML")
| Df | Sum Sq | Mean Sq | F value | Pr(> F) | |
|---|---|---|---|---|---|
| Site | 3 | 5365.46 | 1788.49 | 4.41 | 0.0048 |
| Source | 2 | 5906.63 | 2953.31 | 7.28 | 0.0008 |
| Site:Source | 6 | 6854.40 | 1142.40 | 2.82 | 0.0113 |
| Residuals | 260 | 105445.73 | 405.56 |
## Analysis of Variance Table
##
## Response: Cadmium
## Df Sum Sq Mean Sq F value Pr(>F)
## Source 2 146 73.1 93.6 <2e-16 ***
## Residuals 273 213 0.8
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Cadmium ~ Source, data = d)
##
## $Source
## diff lwr upr p adj
## Mussel-Sediment 1.001 0.6054 1.397 0
## Oyster-Sediment 2.091 1.6954 2.487 0
## Oyster-Mussel 1.090 0.8212 1.359 0
##
## Analysis of Variance Table
##
## Response: Copper
## Df Sum Sq Mean Sq F value Pr(>F)
## Source 2 9735167 4867584 358 <2e-16 ***
## Residuals 273 3708971 13586
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Copper ~ Source, data = d)
##
## $Source
## diff lwr upr p adj
## Mussel-Sediment 11.84 -40.36 64.04 0.8544
## Oyster-Sediment 387.89 335.69 440.08 0.0000
## Oyster-Mussel 376.05 340.59 411.51 0.0000
##
## Analysis of Variance Table
##
## Response: Lead
## Df Sum Sq Mean Sq F value Pr(>F)
## Source 2 6026 3013 6.9 0.0012 **
## Residuals 269 117546 437
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Lead ~ Source, data = d)
##
## $Source
## diff lwr upr p adj
## Mussel-Sediment 3.501 -5.861 12.863 0.6526
## Oyster-Sediment -6.552 -15.952 2.847 0.2295
## Oyster-Mussel -10.053 -16.468 -3.639 0.0008
##
## Analysis of Variance Table
##
## Response: Zinc
## Df Sum Sq Mean Sq F value Pr(>F)
## Source 2 2.36e+08 1.18e+08 444 <2e-16 ***
## Residuals 261 6.93e+07 2.66e+05
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Zinc ~ Source, data = d)
##
## $Source
## diff lwr upr p adj
## Mussel-Sediment 87.51 -143.4 318.4 0.6449
## Oyster-Sediment 1989.64 1755.8 2223.5 0.0000
## Oyster-Mussel 1902.13 1741.0 2063.3 0.0000
##
## Analysis of Variance Table
##
## Response: Cadmium
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 2.0 0.652 1.09 0.36
## Residuals 116 69.6 0.600
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Cadmium ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -0.3000 -0.8212 0.2212 0.4406
## Nayland Rock-Longrock -0.3000 -0.8212 0.2212 0.4406
## Foreness Point-Longrock -0.1167 -0.6379 0.4045 0.9369
## Nayland Rock-Epple Bay 0.0000 -0.5212 0.5212 1.0000
## Foreness Point-Epple Bay 0.1833 -0.3379 0.7045 0.7959
## Foreness Point-Nayland Rock 0.1833 -0.3379 0.7045 0.7959
##
## Analysis of Variance Table
##
## Response: Copper
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 1148876 382959 17.7 1.5e-09 ***
## Residuals 116 2504721 21592
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Copper ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -132.75 -231.65 -33.85 0.0037
## Nayland Rock-Longrock -181.81 -280.71 -82.91 0.0000
## Foreness Point-Longrock 60.88 -38.02 159.78 0.3800
## Nayland Rock-Epple Bay -49.06 -147.96 49.84 0.5692
## Foreness Point-Epple Bay 193.63 94.73 292.53 0.0000
## Foreness Point-Nayland Rock 242.69 143.79 341.59 0.0000
##
## Analysis of Variance Table
##
## Response: Lead
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 6.81 2.270 11.1 2e-06 ***
## Residuals 112 22.95 0.205
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Lead ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock 0.57789 0.26512 0.8907 0.0000
## Nayland Rock-Longrock 0.40548 0.09271 0.7183 0.0054
## Foreness Point-Longrock 0.61726 0.30706 0.9275 0.0000
## Nayland Rock-Epple Bay -0.17241 -0.48243 0.1376 0.4709
## Foreness Point-Epple Bay 0.03937 -0.26805 0.3468 0.9871
## Foreness Point-Nayland Rock 0.21178 -0.09564 0.5192 0.2804
##
## Analysis of Variance Table
##
## Response: Zinc
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 14098051 4699350 9.29 1.7e-05 ***
## Residuals 104 52630973 506067
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Zinc ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -200.74 -721.0 319.6 0.7454
## Nayland Rock-Longrock -131.38 -642.5 379.7 0.9078
## Foreness Point-Longrock 687.16 180.2 1194.1 0.0033
## Nayland Rock-Epple Bay 69.37 -436.5 575.3 0.9842
## Foreness Point-Epple Bay 887.90 386.2 1389.6 0.0001
## Foreness Point-Nayland Rock 818.54 326.4 1310.7 0.0002
##
## Analysis of Variance Table
##
## Response: Cadmium
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 8.3 2.76 2.41 0.071 .
## Residuals 116 133.0 1.15
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Cadmium ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock 0.6965 -0.02421 1.4172 0.0622
## Nayland Rock-Longrock 0.1349 -0.58577 0.8556 0.9616
## Foreness Point-Longrock 0.3410 -0.37971 1.0617 0.6070
## Nayland Rock-Epple Bay -0.5616 -1.28227 0.1591 0.1826
## Foreness Point-Epple Bay -0.3555 -1.07621 0.3652 0.5738
## Foreness Point-Nayland Rock 0.2061 -0.51464 0.9268 0.8785
##
## Analysis of Variance Table
##
## Response: Copper
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 561 187 0.4 0.76
## Residuals 116 54602 471
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Copper ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -2.3903 -16.99 12.212 0.9738
## Nayland Rock-Longrock -6.0716 -20.67 8.531 0.7001
## Foreness Point-Longrock -2.8598 -17.46 11.742 0.9564
## Nayland Rock-Epple Bay -3.6813 -18.28 10.921 0.9128
## Foreness Point-Epple Bay -0.4695 -15.07 14.133 0.9998
## Foreness Point-Nayland Rock 3.2118 -11.39 17.814 0.9398
##
## Analysis of Variance Table
##
## Response: Lead
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 11892 3964 4.38 0.0059 **
## Residuals 116 105070 906
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Lead ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -23.581 -43.84 -3.325 0.0155
## Nayland Rock-Longrock -18.135 -38.39 2.121 0.0963
## Foreness Point-Longrock -24.953 -45.21 -4.698 0.0092
## Nayland Rock-Epple Bay 5.446 -14.81 25.702 0.8966
## Foreness Point-Epple Bay -1.372 -21.63 18.884 0.9980
## Foreness Point-Nayland Rock -6.818 -27.07 13.438 0.8165
##
## Analysis of Variance Table
##
## Response: Zinc
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 23009 7670 0.34 0.79
## Residuals 116 2579350 22236
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Zinc ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -8.771 -109.1 91.59 0.9958
## Nayland Rock-Longrock -30.575 -130.9 69.79 0.8570
## Foreness Point-Longrock -32.132 -132.5 68.23 0.8379
## Nayland Rock-Epple Bay -21.804 -122.2 78.56 0.9419
## Foreness Point-Epple Bay -23.361 -123.7 77.00 0.9297
## Foreness Point-Nayland Rock -1.557 -101.9 98.80 1.0000
##
## Analysis of Variance Table
##
## Response: Cadmium
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 0.0147 0.00491 0.67 0.58
## Residuals 32 0.2355 0.00736
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Cadmium ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -0.01856 -0.12812 0.09101 0.9674
## Nayland Rock-Longrock -0.05567 -0.16524 0.05390 0.5228
## Foreness Point-Longrock -0.01856 -0.12812 0.09101 0.9674
## Nayland Rock-Epple Bay -0.03711 -0.14668 0.07246 0.7956
## Foreness Point-Epple Bay 0.00000 -0.10957 0.10957 1.0000
## Foreness Point-Nayland Rock 0.03711 -0.07246 0.14668 0.7956
##
## Analysis of Variance Table
##
## Response: Copper
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 71.1 23.71 5.41 0.004 **
## Residuals 32 140.1 4.38
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Copper ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock -0.1663 -2.839 2.50619 0.9983
## Nayland Rock-Longrock -2.7962 -5.469 -0.12370 0.0375
## Foreness Point-Longrock -2.9816 -5.654 -0.30903 0.0241
## Nayland Rock-Epple Bay -2.6299 -5.302 0.04264 0.0551
## Foreness Point-Epple Bay -2.8152 -5.488 -0.14270 0.0359
## Foreness Point-Nayland Rock -0.1853 -2.858 2.48719 0.9976
##
## Analysis of Variance Table
##
## Response: Lead
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 201 67 6.08 0.0022 **
## Residuals 32 353 11
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Lead ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock 1.796 -2.444 6.0367 0.6633
## Nayland Rock-Longrock -3.796 -8.037 0.4443 0.0924
## Foreness Point-Longrock -3.500 -7.741 0.7403 0.1351
## Nayland Rock-Epple Bay -5.592 -9.833 -1.3520 0.0060
## Foreness Point-Epple Bay -5.296 -9.537 -1.0560 0.0098
## Foreness Point-Nayland Rock 0.296 -3.944 4.5364 0.9975
##
## Analysis of Variance Table
##
## Response: Zinc
## Df Sum Sq Mean Sq F value Pr(>F)
## Site 3 2238 746 6.06 0.0022 **
## Residuals 32 3942 123
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Tukey multiple comparisons of means
## 95% family-wise confidence level
##
## Fit: aov(formula = Zinc ~ Site, data = d1)
##
## $Site
## diff lwr upr p adj
## Epple Bay-Longrock 2.6300 -11.55 16.8055 0.9579
## Nayland Rock-Longrock -13.8888 -28.06 0.2868 0.0565
## Foreness Point-Longrock -14.7777 -28.95 -0.6021 0.0384
## Nayland Rock-Epple Bay -16.5188 -30.69 -2.3432 0.0173
## Foreness Point-Epple Bay -17.4077 -31.58 -3.2321 0.0113
## Foreness Point-Nayland Rock -0.8889 -15.06 13.2866 0.9982
##