library(ggplot2) # for general plotting
library(car)     # for ANOVA (Type II used, better than Type I when there is an unbalanced design)

Information of data source

Enzyme inhibitors were used to treat mites, fecundity and enzyme activity following enzyme inhibition were assessed.

Inhibitors:

PBO - CYP (cytochrome P450) inhibitor

DEM - GST inhibitor

DEF - esterase inhibitor

Read in the data and view structure to identify any issues in data formatting

detox.inhibitor.data <- read.csv("~/Lab Stuff/Adapted mites/Tomato/Inhibitor assay/3 dpi feeding data/Inhibitor Adapted vs. non-adapted - Castlemart def-1/R data/All trials R data.csv", header = TRUE)

# Trial and Plant.ID as a factor
detox.inhibitor.data$Trial <- factor(detox.inhibitor.data$Trial)
str(detox.inhibitor.data)
## 'data.frame':    206 obs. of  5 variables:
##  $ Trial         : Factor w/ 3 levels "1","2","4": 1 1 1 1 1 1 1 1 1 1 ...
##  $ Mite.Strain   : Factor w/ 2 levels "TU","TU-A": 1 1 1 1 2 2 2 1 1 1 ...
##  $ Plant.Genotype: Factor w/ 2 levels "Castlemart","def-1": 1 1 1 1 1 1 1 2 2 2 ...
##  $ Treatment     : Factor w/ 4 levels "DEF","DEM","PBO",..: 4 4 4 4 4 4 4 4 4 4 ...
##  $ Eggs.Mite     : num  2.08 1.36 2.15 2.58 4.24 ...
detox.inhibitor.data.TU <- subset(detox.inhibitor.data, Mite.Strain =="TU")
detox.inhibitor.data.TA <- subset(detox.inhibitor.data, Mite.Strain =="TU-A")

Formulate hypothesis

H0: There will be no difference in fecundity upon treatment with inhibitors of any class in TU or TU-A mites on either plant genotype.

HA: Treatment with detoxification inhibitors will result in degreased fecundity in TU-A mites on one or both genotypes.

Conduct data exploration

Outliers in the response variable (Eggs.Mite) within explanatory variables (Trial, Treatment, Mite.Strain, Plant.Genotype).

ggplot(detox.inhibitor.data, aes(x = Trial, y = Eggs.Mite)) + geom_boxplot()+ theme_classic()

ggplot(detox.inhibitor.data, aes(x = Treatment, y = Eggs.Mite)) + geom_boxplot()+ theme_classic()

ggplot(detox.inhibitor.data, aes(x = Mite.Strain, y = Eggs.Mite)) + geom_boxplot() + theme_classic()

ggplot(detox.inhibitor.data, aes(x = Plant.Genotype, y = Eggs.Mite)) + geom_boxplot() + theme_classic()

Experiment extremely variable, will keep outliers in assuming they represent real variablity unless they cause problems in model validation.

One outlier removed, Trial 1: TU-A: def-1: Water Control

Collinearity of the explanatory variables

Does not apply, all explanatory variables are categorical/factorial.

Spatial/temporal or other hierarchical aspects of sampling design

No, I am treating Trial as a main effect to check for reproducibility (not a random effect/blocking factor).

Interactions (is the quality of the data good enough to include them?)

Interaction betweenTrial and Mite.Strain will be performed to test for reproducibility.

Interaction betweenTrial and Treatment will be performed to test for reproducibility.

Interaction betweenMite.Strain and Treatment will be performed to check if the mite strains responded differently to treatment.

Zero inflation in Y

No

Are categorical covariates balanced?

summary(detox.inhibitor.data)
##  Trial  Mite.Strain    Plant.Genotype Treatment    Eggs.Mite     
##  1:58   TU  :108    Castlemart:100    DEF  :52   Min.   : 1.111  
##  2:96   TU-A: 98    def-1     :106    DEM  :52   1st Qu.: 2.964  
##  4:52                                 PBO  :52   Median : 4.411  
##                                       Water:50   Mean   : 5.242  
##                                                  3rd Qu.: 6.840  
##                                                  Max.   :18.857

No, but sample size is high.

Apply model

# fit linear model and display model fit information and ANOVA table
# full model including 3 interaction term - to verify it is not significant, if it is, interpretation of hypothesis testing will be problematic
m.0 <- lm(Eggs.Mite ~ Mite.Strain * Plant.Genotype * Treatment * Trial, data = detox.inhibitor.data)
summary(m.0)
## 
## Call:
## lm(formula = Eggs.Mite ~ Mite.Strain * Plant.Genotype * Treatment * 
##     Trial, data = detox.inhibitor.data)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -6.4763 -0.6991 -0.0420  0.6551  5.5455 
## 
## Coefficients:
##                                                           Estimate
## (Intercept)                                                1.62723
## Mite.StrainTU-A                                            1.02234
## Plant.Genotypedef-1                                        2.24419
## TreatmentDEM                                               0.74355
## TreatmentPBO                                               1.20622
## TreatmentWater                                             0.41629
## Trial2                                                     1.36463
## Trial4                                                    -0.17080
## Mite.StrainTU-A:Plant.Genotypedef-1                        1.91846
## Mite.StrainTU-A:TreatmentDEM                              -1.33074
## Mite.StrainTU-A:TreatmentPBO                              -1.15356
## Mite.StrainTU-A:TreatmentWater                             0.63191
## Plant.Genotypedef-1:TreatmentDEM                           0.01024
## Plant.Genotypedef-1:TreatmentPBO                          -1.12527
## Plant.Genotypedef-1:TreatmentWater                        -0.42556
## Mite.StrainTU-A:Trial2                                     0.55354
## Mite.StrainTU-A:Trial4                                     4.71615
## Plant.Genotypedef-1:Trial2                                -1.73867
## Plant.Genotypedef-1:Trial4                                -1.09245
## TreatmentDEM:Trial2                                        0.79388
## TreatmentPBO:Trial2                                       -0.52044
## TreatmentWater:Trial2                                      0.09526
## TreatmentDEM:Trial4                                       -0.43871
## TreatmentPBO:Trial4                                       -0.12870
## TreatmentWater:Trial4                                      1.14315
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM           3.03744
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO           2.48181
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater         6.53916
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial2                 1.17685
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial4                -1.76805
## Mite.StrainTU-A:TreatmentDEM:Trial2                        0.70463
## Mite.StrainTU-A:TreatmentPBO:Trial2                        0.80665
## Mite.StrainTU-A:TreatmentWater:Trial2                     -0.63688
## Mite.StrainTU-A:TreatmentDEM:Trial4                        1.41590
## Mite.StrainTU-A:TreatmentPBO:Trial4                       -0.06332
## Mite.StrainTU-A:TreatmentWater:Trial4                     -1.65507
## Plant.Genotypedef-1:TreatmentDEM:Trial2                   -0.43824
## Plant.Genotypedef-1:TreatmentPBO:Trial2                    3.34123
## Plant.Genotypedef-1:TreatmentWater:Trial2                  0.48914
## Plant.Genotypedef-1:TreatmentDEM:Trial4                    0.10943
## Plant.Genotypedef-1:TreatmentPBO:Trial4                    1.04305
## Plant.Genotypedef-1:TreatmentWater:Trial4                  0.30656
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial2   -3.60109
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial2   -6.03395
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial2 -4.22643
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial4    0.63724
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial4   -0.32985
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial4 -5.17983
##                                                           Std. Error
## (Intercept)                                                  0.88007
## Mite.StrainTU-A                                              1.34433
## Plant.Genotypedef-1                                          1.24461
## TreatmentDEM                                                 1.24461
## TreatmentPBO                                                 1.24461
## TreatmentWater                                               1.24461
## Trial2                                                       1.13617
## Trial4                                                       1.34433
## Mite.StrainTU-A:Plant.Genotypedef-1                          1.83202
## Mite.StrainTU-A:TreatmentDEM                                 1.90117
## Mite.StrainTU-A:TreatmentPBO                                 1.90117
## Mite.StrainTU-A:TreatmentWater                               1.90117
## Plant.Genotypedef-1:TreatmentDEM                             1.76014
## Plant.Genotypedef-1:TreatmentPBO                             1.76014
## Plant.Genotypedef-1:TreatmentWater                           1.76014
## Mite.StrainTU-A:Trial2                                       1.68521
## Mite.StrainTU-A:Trial4                                       1.96790
## Plant.Genotypedef-1:Trial2                                   1.60678
## Plant.Genotypedef-1:Trial4                                   1.83202
## TreatmentDEM:Trial2                                          1.60678
## TreatmentPBO:Trial2                                          1.60678
## TreatmentWater:Trial2                                        1.60678
## TreatmentDEM:Trial4                                          1.90117
## TreatmentPBO:Trial4                                          1.90117
## TreatmentWater:Trial4                                        1.90117
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM             2.59086
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO             2.59086
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater           2.73625
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial2                   2.32845
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial4                   2.68866
## Mite.StrainTU-A:TreatmentDEM:Trial2                          2.38325
## Mite.StrainTU-A:TreatmentPBO:Trial2                          2.38325
## Mite.StrainTU-A:TreatmentWater:Trial2                        2.38325
## Mite.StrainTU-A:TreatmentDEM:Trial4                          2.78303
## Mite.StrainTU-A:TreatmentPBO:Trial4                          2.78303
## Mite.StrainTU-A:TreatmentWater:Trial4                        2.78303
## Plant.Genotypedef-1:TreatmentDEM:Trial2                      2.27234
## Plant.Genotypedef-1:TreatmentPBO:Trial2                      2.27234
## Plant.Genotypedef-1:TreatmentWater:Trial2                    2.27234
## Plant.Genotypedef-1:TreatmentDEM:Trial4                      2.59086
## Plant.Genotypedef-1:TreatmentPBO:Trial4                      2.59086
## Plant.Genotypedef-1:TreatmentWater:Trial4                    2.59086
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial2      3.29293
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial2      3.29293
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial2    3.40850
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial4      3.80234
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial4      3.80234
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial4    3.90286
##                                                           t value Pr(>|t|)
## (Intercept)                                                 1.849   0.0663
## Mite.StrainTU-A                                             0.760   0.4481
## Plant.Genotypedef-1                                         1.803   0.0733
## TreatmentDEM                                                0.597   0.5511
## TreatmentPBO                                                0.969   0.3339
## TreatmentWater                                              0.334   0.7385
## Trial2                                                      1.201   0.2315
## Trial4                                                     -0.127   0.8991
## Mite.StrainTU-A:Plant.Genotypedef-1                         1.047   0.2966
## Mite.StrainTU-A:TreatmentDEM                               -0.700   0.4850
## Mite.StrainTU-A:TreatmentPBO                               -0.607   0.5449
## Mite.StrainTU-A:TreatmentWater                              0.332   0.7400
## Plant.Genotypedef-1:TreatmentDEM                            0.006   0.9954
## Plant.Genotypedef-1:TreatmentPBO                           -0.639   0.5236
## Plant.Genotypedef-1:TreatmentWater                         -0.242   0.8093
## Mite.StrainTU-A:Trial2                                      0.328   0.7430
## Mite.StrainTU-A:Trial4                                      2.397   0.0177
## Plant.Genotypedef-1:Trial2                                 -1.082   0.2809
## Plant.Genotypedef-1:Trial4                                 -0.596   0.5518
## TreatmentDEM:Trial2                                         0.494   0.6219
## TreatmentPBO:Trial2                                        -0.324   0.7464
## TreatmentWater:Trial2                                       0.059   0.9528
## TreatmentDEM:Trial4                                        -0.231   0.8178
## TreatmentPBO:Trial4                                        -0.068   0.9461
## TreatmentWater:Trial4                                       0.601   0.5485
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM            1.172   0.2428
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO            0.958   0.3396
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater          2.390   0.0180
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial2                  0.505   0.6140
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial4                 -0.658   0.5118
## Mite.StrainTU-A:TreatmentDEM:Trial2                         0.296   0.7679
## Mite.StrainTU-A:TreatmentPBO:Trial2                         0.338   0.7355
## Mite.StrainTU-A:TreatmentWater:Trial2                      -0.267   0.7896
## Mite.StrainTU-A:TreatmentDEM:Trial4                         0.509   0.6116
## Mite.StrainTU-A:TreatmentPBO:Trial4                        -0.023   0.9819
## Mite.StrainTU-A:TreatmentWater:Trial4                      -0.595   0.5529
## Plant.Genotypedef-1:TreatmentDEM:Trial2                    -0.193   0.8473
## Plant.Genotypedef-1:TreatmentPBO:Trial2                     1.470   0.1434
## Plant.Genotypedef-1:TreatmentWater:Trial2                   0.215   0.8298
## Plant.Genotypedef-1:TreatmentDEM:Trial4                     0.042   0.9664
## Plant.Genotypedef-1:TreatmentPBO:Trial4                     0.403   0.6878
## Plant.Genotypedef-1:TreatmentWater:Trial4                   0.118   0.9060
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial2    -1.094   0.2758
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial2    -1.832   0.0688
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial2  -1.240   0.2168
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial4     0.168   0.8671
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial4    -0.087   0.9310
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial4  -1.327   0.1864
##                                                            
## (Intercept)                                               .
## Mite.StrainTU-A                                            
## Plant.Genotypedef-1                                       .
## TreatmentDEM                                               
## TreatmentPBO                                               
## TreatmentWater                                             
## Trial2                                                     
## Trial4                                                     
## Mite.StrainTU-A:Plant.Genotypedef-1                        
## Mite.StrainTU-A:TreatmentDEM                               
## Mite.StrainTU-A:TreatmentPBO                               
## Mite.StrainTU-A:TreatmentWater                             
## Plant.Genotypedef-1:TreatmentDEM                           
## Plant.Genotypedef-1:TreatmentPBO                           
## Plant.Genotypedef-1:TreatmentWater                         
## Mite.StrainTU-A:Trial2                                     
## Mite.StrainTU-A:Trial4                                    *
## Plant.Genotypedef-1:Trial2                                 
## Plant.Genotypedef-1:Trial4                                 
## TreatmentDEM:Trial2                                        
## TreatmentPBO:Trial2                                        
## TreatmentWater:Trial2                                      
## TreatmentDEM:Trial4                                        
## TreatmentPBO:Trial4                                        
## TreatmentWater:Trial4                                      
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM           
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO           
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater        *
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial2                 
## Mite.StrainTU-A:Plant.Genotypedef-1:Trial4                 
## Mite.StrainTU-A:TreatmentDEM:Trial2                        
## Mite.StrainTU-A:TreatmentPBO:Trial2                        
## Mite.StrainTU-A:TreatmentWater:Trial2                      
## Mite.StrainTU-A:TreatmentDEM:Trial4                        
## Mite.StrainTU-A:TreatmentPBO:Trial4                        
## Mite.StrainTU-A:TreatmentWater:Trial4                      
## Plant.Genotypedef-1:TreatmentDEM:Trial2                    
## Plant.Genotypedef-1:TreatmentPBO:Trial2                    
## Plant.Genotypedef-1:TreatmentWater:Trial2                  
## Plant.Genotypedef-1:TreatmentDEM:Trial4                    
## Plant.Genotypedef-1:TreatmentPBO:Trial4                    
## Plant.Genotypedef-1:TreatmentWater:Trial4                  
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial2    
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial2   .
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial2  
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentDEM:Trial4    
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentPBO:Trial4    
## Mite.StrainTU-A:Plant.Genotypedef-1:TreatmentWater:Trial4  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.76 on 158 degrees of freedom
## Multiple R-squared:  0.7582, Adjusted R-squared:  0.6863 
## F-statistic: 10.54 on 47 and 158 DF,  p-value: < 2.2e-16
Anova(m.0)
## Anova Table (Type II tests)
## 
## Response: Eggs.Mite
##                                            Sum Sq  Df  F value    Pr(>F)
## Mite.Strain                                669.90   1 216.2296 < 2.2e-16
## Plant.Genotype                             368.54   1 118.9569 < 2.2e-16
## Treatment                                   48.54   3   5.2225  0.001829
## Trial                                       37.46   2   6.0460  0.002950
## Mite.Strain:Plant.Genotype                 118.65   1  38.2983 5.009e-09
## Mite.Strain:Treatment                       37.10   3   3.9912  0.008979
## Plant.Genotype:Treatment                    11.43   3   1.2296  0.300849
## Mite.Strain:Trial                          110.21   2  17.7863 1.080e-07
## Plant.Genotype:Trial                        38.06   2   6.1425  0.002697
## Treatment:Trial                              4.98   6   0.2681  0.951070
## Mite.Strain:Plant.Genotype:Treatment        25.29   3   2.7212  0.046328
## Mite.Strain:Plant.Genotype:Trial            16.43   2   2.6513  0.073694
## Mite.Strain:Treatment:Trial                 42.44   6   2.2831  0.038494
## Plant.Genotype:Treatment:Trial              20.27   6   1.0907  0.370292
## Mite.Strain:Plant.Genotype:Treatment:Trial  24.44   6   1.3145  0.253637
## Residuals                                  489.50 158                   
##                                               
## Mite.Strain                                ***
## Plant.Genotype                             ***
## Treatment                                  ** 
## Trial                                      ** 
## Mite.Strain:Plant.Genotype                 ***
## Mite.Strain:Treatment                      ** 
## Plant.Genotype:Treatment                      
## Mite.Strain:Trial                          ***
## Plant.Genotype:Trial                       ** 
## Treatment:Trial                               
## Mite.Strain:Plant.Genotype:Treatment       *  
## Mite.Strain:Plant.Genotype:Trial           .  
## Mite.Strain:Treatment:Trial                *  
## Plant.Genotype:Treatment:Trial                
## Mite.Strain:Plant.Genotype:Treatment:Trial    
## Residuals                                     
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Calculate effect size and display
result.anova<-Anova(m.0)
ss<-result.anova$"Sum Sq"  ##ss = sum of squares
pes<-ss/(ss+ss[length(ss)])  ##pes = partial e squared
pes[length(pes)]<-""
result.anova$"Part E Sq"<-pes
result.anova
## Anova Table (Type II tests)
## 
## Response: Eggs.Mite
##                                            Sum Sq  Df  F value  Pr(>F)
## Mite.Strain                                669.90   1 216.2296 0.00000
## Plant.Genotype                             368.54   1 118.9569 0.00000
## Treatment                                   48.54   3   5.2225 0.00183
## Trial                                       37.46   2   6.0460 0.00295
## Mite.Strain:Plant.Genotype                 118.65   1  38.2983 0.00000
## Mite.Strain:Treatment                       37.10   3   3.9912 0.00898
## Plant.Genotype:Treatment                    11.43   3   1.2296 0.30085
## Mite.Strain:Trial                          110.21   2  17.7863 0.00000
## Plant.Genotype:Trial                        38.06   2   6.1425 0.00270
## Treatment:Trial                              4.98   6   0.2681 0.95107
## Mite.Strain:Plant.Genotype:Treatment        25.29   3   2.7212 0.04633
## Mite.Strain:Plant.Genotype:Trial            16.43   2   2.6513 0.07369
## Mite.Strain:Treatment:Trial                 42.44   6   2.2831 0.03849
## Plant.Genotype:Treatment:Trial              20.27   6   1.0907 0.37029
## Mite.Strain:Plant.Genotype:Treatment:Trial  24.44   6   1.3145 0.25364
## Residuals                                  489.50 158                 
##                                            Part E Sq
## Mite.Strain                                  0.57780
## Plant.Genotype                               0.42951
## Treatment                                    0.09022
## Trial                                        0.07109
## Mite.Strain:Plant.Genotype                   0.19510
## Mite.Strain:Treatment                        0.07044
## Plant.Genotype:Treatment                     0.02281
## Mite.Strain:Trial                            0.18377
## Plant.Genotype:Trial                         0.07214
## Treatment:Trial                              0.01008
## Mite.Strain:Plant.Genotype:Treatment         0.04913
## Mite.Strain:Plant.Genotype:Trial             0.03247
## Mite.Strain:Treatment:Trial                  0.07978
## Plant.Genotype:Treatment:Trial               0.03977
## Mite.Strain:Plant.Genotype:Treatment:Trial   0.04755
## Residuals
# plot interactions
interaction.plot(detox.inhibitor.data$Treatment, detox.inhibitor.data$Trial, detox.inhibitor.data$Eggs.Mite, type="l", leg.bty="o", leg.bg="grey95", lwd=2, ylab="Eggs.Mite", xlab="Treatment", main="Treatment:Trial")

interaction.plot(detox.inhibitor.data$Mite.Strain, detox.inhibitor.data$Trial, detox.inhibitor.data$Eggs.Mite, type="l", leg.bty="o", leg.bg="grey95", lwd=2, ylab="Eggs.Mite", xlab="Mite.Strain", main="Mite.Strain:Trial")

interaction.plot(detox.inhibitor.data$Plant.Genotype, detox.inhibitor.data$Trial, detox.inhibitor.data$Eggs.Mite, type="l", leg.bty="o", leg.bg="grey95", lwd=2, ylab="Eggs.Mite", xlab="Plant.Genotype", main="Plant.Genotype:Trial")

interaction.plot(detox.inhibitor.data$Plant.Genotype, detox.inhibitor.data$Mite.Strain, detox.inhibitor.data$Eggs.Mite, type="l", leg.bty="o", leg.bg="grey95", lwd=2, ylab="Eggs.Mite", xlab="Plant.Genotype", main="Plant.Genotype:Mite.Strain")

### TU 3-way ANOVA to test for effect of plant genotype within mite strains
m.TU <- lm(Eggs.Mite ~ Plant.Genotype * Treatment * Trial, data=detox.inhibitor.data.TU)
summary(m.TU)
## 
## Call:
## lm(formula = Eggs.Mite ~ Plant.Genotype * Treatment * Trial, 
##     data = detox.inhibitor.data.TU)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -2.19015 -0.54162 -0.03305  0.58418  2.37761 
## 
## Coefficients:
##                                           Estimate Std. Error t value
## (Intercept)                                1.62723    0.47379   3.435
## Plant.Genotypedef-1                        2.24419    0.67004   3.349
## TreatmentDEM                               0.74355    0.67004   1.110
## TreatmentPBO                               1.20622    0.67004   1.800
## TreatmentWater                             0.41629    0.67004   0.621
## Trial2                                     1.36463    0.61166   2.231
## Trial4                                    -0.17080    0.72373  -0.236
## Plant.Genotypedef-1:TreatmentDEM           0.01024    0.94758   0.011
## Plant.Genotypedef-1:TreatmentPBO          -1.12527    0.94758  -1.188
## Plant.Genotypedef-1:TreatmentWater        -0.42556    0.94758  -0.449
## Plant.Genotypedef-1:Trial2                -1.73867    0.86502  -2.010
## Plant.Genotypedef-1:Trial4                -1.09245    0.98627  -1.108
## TreatmentDEM:Trial2                        0.79388    0.86502   0.918
## TreatmentPBO:Trial2                       -0.52044    0.86502  -0.602
## TreatmentWater:Trial2                      0.09526    0.86502   0.110
## TreatmentDEM:Trial4                       -0.43871    1.02351  -0.429
## TreatmentPBO:Trial4                       -0.12870    1.02351  -0.126
## TreatmentWater:Trial4                      1.14315    1.02351   1.117
## Plant.Genotypedef-1:TreatmentDEM:Trial2   -0.43824    1.22332  -0.358
## Plant.Genotypedef-1:TreatmentPBO:Trial2    3.34123    1.22332   2.731
## Plant.Genotypedef-1:TreatmentWater:Trial2  0.48914    1.22332   0.400
## Plant.Genotypedef-1:TreatmentDEM:Trial4    0.10943    1.39480   0.078
## Plant.Genotypedef-1:TreatmentPBO:Trial4    1.04305    1.39480   0.748
## Plant.Genotypedef-1:TreatmentWater:Trial4  0.30656    1.39480   0.220
##                                           Pr(>|t|)    
## (Intercept)                               0.000924 ***
## Plant.Genotypedef-1                       0.001215 ** 
## TreatmentDEM                              0.270291    
## TreatmentPBO                              0.075417 .  
## TreatmentWater                            0.536091    
## Trial2                                    0.028345 *  
## Trial4                                    0.814003    
## Plant.Genotypedef-1:TreatmentDEM          0.991407    
## Plant.Genotypedef-1:TreatmentPBO          0.238373    
## Plant.Genotypedef-1:TreatmentWater        0.654512    
## Plant.Genotypedef-1:Trial2                0.047643 *  
## Plant.Genotypedef-1:Trial4                0.271171    
## TreatmentDEM:Trial2                       0.361374    
## TreatmentPBO:Trial2                       0.549024    
## TreatmentWater:Trial2                     0.912575    
## TreatmentDEM:Trial4                       0.669289    
## TreatmentPBO:Trial4                       0.900231    
## TreatmentWater:Trial4                     0.267222    
## Plant.Genotypedef-1:TreatmentDEM:Trial2   0.721065    
## Plant.Genotypedef-1:TreatmentPBO:Trial2   0.007687 ** 
## Plant.Genotypedef-1:TreatmentWater:Trial2 0.690288    
## Plant.Genotypedef-1:TreatmentDEM:Trial4   0.937654    
## Plant.Genotypedef-1:TreatmentPBO:Trial4   0.456662    
## Plant.Genotypedef-1:TreatmentWater:Trial4 0.826571    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.9476 on 84 degrees of freedom
## Multiple R-squared:  0.6408, Adjusted R-squared:  0.5425 
## F-statistic: 6.516 on 23 and 84 DF,  p-value: 7.969e-11
Anova(m.TU)
## Anova Table (Type II tests)
## 
## Response: Eggs.Mite
##                                Sum Sq Df F value    Pr(>F)    
## Plant.Genotype                 43.681  1 48.6469 6.523e-10 ***
## Treatment                      22.690  3  8.4234 5.869e-05 ***
## Trial                          40.630  2 22.6247 1.380e-08 ***
## Plant.Genotype:Treatment        2.774  3  1.0297   0.38376    
## Plant.Genotype:Trial            3.998  2  2.2265   0.11424    
## Treatment:Trial                12.769  6  2.3701   0.03651 *  
## Plant.Genotype:Treatment:Trial 11.714  6  2.1743   0.05342 .  
## Residuals                      75.425 84                      
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
# Calculate effect size and display
result.anova<-Anova(m.TU)
ss<-result.anova$"Sum Sq"  ##ss = sum of squares
pes<-ss/(ss+ss[length(ss)])  ##pes = partial e squared
pes[length(pes)]<-""
result.anova$"Part E Sq"<-pes
result.anova
## Anova Table (Type II tests)
## 
## Response: Eggs.Mite
##                                Sum Sq Df F value  Pr(>F) Part E Sq
## Plant.Genotype                 43.681  1 48.6469 0.00000   0.36674
## Treatment                      22.690  3  8.4234 0.00006   0.23126
## Trial                          40.630  2 22.6247 0.00000   0.35009
## Plant.Genotype:Treatment        2.774  3  1.0297 0.38376   0.03547
## Plant.Genotype:Trial            3.998  2  2.2265 0.11424   0.05034
## Treatment:Trial                12.769  6  2.3701 0.03651   0.14478
## Plant.Genotype:Treatment:Trial 11.714  6  2.1743 0.05342   0.13443
## Residuals                      75.425 84
# perform post-hoc Tukey-Kramer test of contrasts
TukeyHSD(aov(Eggs.Mite ~ Plant.Genotype * Treatment * Trial, data = detox.inhibitor.data.TU))
##   Tukey multiple comparisons of means
##     95% family-wise confidence level
## 
## Fit: aov(formula = Eggs.Mite ~ Plant.Genotype * Treatment * Trial, data = detox.inhibitor.data.TU)
## 
## $Plant.Genotype
##                      diff       lwr      upr p adj
## def-1-Castlemart 1.219928 0.8570313 1.582824     0
## 
## $Treatment
##                 diff         lwr       upr     p adj
## DEM-DEF    0.9067806  0.23077186 1.5827893 0.0038857
## PBO-DEF    1.2550915  0.57908277 1.9311002 0.0000308
## Water-DEF  0.6884502  0.01244148 1.3644589 0.0442915
## PBO-DEM    0.3483109 -0.32769781 1.0243196 0.5337075
## Water-DEM -0.2183304 -0.89433909 0.4576783 0.8320061
## Water-PBO -0.5666413 -1.24265000 0.1093674 0.1324200
## 
## $Trial
##           diff        lwr        upr     p adj
## 2-1  1.0114804  0.4955052  1.5274557 0.0000325
## 4-1 -0.3970436 -0.9821045  0.1880173 0.2432298
## 4-2 -1.4085240 -1.9461579 -0.8708901 0.0000000
## 
## $`Plant.Genotype:Treatment`
##                                        diff         lwr         upr
## def-1:DEF-Castlemart:DEF         1.13254707 -0.00203368  2.26712781
## Castlemart:DEM-Castlemart:DEF    1.00871736 -0.14668312  2.16411783
## def-1:DEM-Castlemart:DEF         1.94467207  0.81009132  3.07925281
## Castlemart:PBO-Castlemart:DEF    0.93631148 -0.21908899  2.09171196
## def-1:PBO-Castlemart:DEF         2.68364856  1.54906781  3.81822930
## Castlemart:Water-Castlemart:DEF  0.72405987 -0.43134060  1.87946035
## def-1:Water-Castlemart:DEF       1.78793115  0.65335040  2.92251189
## Castlemart:DEM-def-1:DEF        -0.12382971 -1.25841045  1.01075104
## def-1:DEM-def-1:DEF              0.81212500 -0.30124676  1.92549676
## Castlemart:PBO-def-1:DEF        -0.19623558 -1.33081633  0.93834516
## def-1:PBO-def-1:DEF              1.55110149  0.43772973  2.66447325
## Castlemart:Water-def-1:DEF      -0.40848719 -1.54306794  0.72609355
## def-1:Water-def-1:DEF            0.65538408 -0.45798767  1.76875584
## def-1:DEM-Castlemart:DEM         0.93595471 -0.19862603  2.07053546
## Castlemart:PBO-Castlemart:DEM   -0.07240587 -1.22780635  1.08299460
## def-1:PBO-Castlemart:DEM         1.67493120  0.54035046  2.80951195
## Castlemart:Water-Castlemart:DEM -0.28465748 -1.44005796  0.87074299
## def-1:Water-Castlemart:DEM       0.77921379 -0.35536695  1.91379454
## Castlemart:PBO-def-1:DEM        -1.00836058 -2.14294133  0.12622016
## def-1:PBO-def-1:DEM              0.73897649 -0.37439527  1.85234825
## Castlemart:Water-def-1:DEM      -1.22061219 -2.35519294 -0.08603145
## def-1:Water-def-1:DEM           -0.15674092 -1.27011268  0.95663084
## def-1:PBO-Castlemart:PBO         1.74733708  0.61275633  2.88191782
## Castlemart:Water-Castlemart:PBO -0.21225161 -1.36765209  0.94314887
## def-1:Water-Castlemart:PBO       0.85161967 -0.28296108  1.98620041
## Castlemart:Water-def-1:PBO      -1.95958868 -3.09416943 -0.82500794
## def-1:Water-def-1:PBO           -0.89571741 -2.00908917  0.21765435
## def-1:Water-Castlemart:Water     1.06387127 -0.07070947  2.19845202
##                                     p adj
## def-1:DEF-Castlemart:DEF        0.0507505
## Castlemart:DEM-Castlemart:DEF   0.1328015
## def-1:DEM-Castlemart:DEF        0.0000220
## Castlemart:PBO-Castlemart:DEF   0.2018821
## def-1:PBO-Castlemart:DEF        0.0000000
## Castlemart:Water-Castlemart:DEF 0.5225760
## def-1:Water-Castlemart:DEF      0.0001219
## Castlemart:DEM-def-1:DEF        0.9999731
## def-1:DEM-def-1:DEF             0.3237443
## Castlemart:PBO-def-1:DEF        0.9994092
## def-1:PBO-def-1:DEF             0.0010277
## Castlemart:Water-def-1:DEF      0.9508321
## def-1:Water-def-1:DEF           0.6018800
## def-1:DEM-Castlemart:DEM        0.1839012
## Castlemart:PBO-Castlemart:DEM   0.9999994
## def-1:PBO-Castlemart:DEM        0.0003978
## Castlemart:Water-Castlemart:DEM 0.9943915
## def-1:Water-Castlemart:DEM      0.4016497
## Castlemart:PBO-def-1:DEM        0.1187510
## def-1:PBO-def-1:DEM             0.4468615
## Castlemart:Water-def-1:DEM      0.0259230
## def-1:Water-def-1:DEM           0.9998492
## def-1:PBO-Castlemart:PBO        0.0001874
## Castlemart:Water-Castlemart:PBO 0.9991244
## def-1:Water-Castlemart:PBO      0.2883652
## Castlemart:Water-def-1:PBO      0.0000186
## def-1:Water-def-1:PBO           0.2094735
## def-1:Water-Castlemart:Water    0.0824284
## 
## $`Plant.Genotype:Trial`
##                                  diff        lwr        upr     p adj
## def-1:1-Castlemart:1       1.85904535  0.8819424  2.8361483 0.0000048
## Castlemart:2-Castlemart:1  1.45679953  0.5648306  2.3487684 0.0001125
## def-1:2-Castlemart:1       2.42520666  1.5332378  3.3171756 0.0000000
## Castlemart:4-Castlemart:1 -0.02686876 -1.0822606  1.0285231 0.9999997
## def-1:4-Castlemart:1       1.10448088  0.1273779  2.0815839 0.0174095
## Castlemart:2-def-1:1      -0.40224582 -1.2942147  0.4897231 0.7758391
## def-1:2-def-1:1            0.56616131 -0.3258076  1.4581302 0.4392367
## Castlemart:4-def-1:1      -1.88591411 -2.9413059 -0.8305223 0.0000192
## def-1:4-def-1:1           -0.75456447 -1.7316674  0.2225385 0.2255538
## def-1:2-Castlemart:2       0.96840713  0.1706059  1.7662084 0.0083184
## Castlemart:4-Castlemart:2 -1.48366830 -2.4607713 -0.5065653 0.0003978
## def-1:4-Castlemart:2      -0.35231865 -1.2442876  0.5396502 0.8579040
## Castlemart:4-def-1:2      -2.45207542 -3.4291784 -1.4749724 0.0000000
## def-1:4-def-1:2           -1.32072578 -2.2126947 -0.4287569 0.0005950
## def-1:4-Castlemart:4       1.13134964  0.0759578  2.1867415 0.0283650
## 
## $`Treatment:Trial`
##                        diff         lwr          upr     p adj
## DEM:1-DEF:1      0.74502932 -0.84784392  2.337902559 0.9140620
## PBO:1-DEF:1      0.65496988 -0.93790335  2.247843122 0.9638109
## Water:1-DEF:1    0.20223696 -1.39063628  1.795110196 0.9999994
## DEF:2-DEF:1      0.49529183 -0.95879585  1.949379499 0.9915046
## DEM:2-DEF:1      1.81507939  0.36099171  3.269167058 0.0036525
## PBO:2-DEF:1      2.30043225  0.84634458  3.754519926 0.0000526
## Water:2-DEF:1    1.03735439 -0.41673328  2.491442062 0.4186869
## DEF:4-DEF:1     -0.71566048 -2.36444092  0.933119965 0.9472318
## DEM:4-DEF:1     -0.33203328 -1.98081372  1.316747162 0.9999324
## PBO:4-DEF:1      0.28234324 -1.36643721  1.931123679 0.9999868
## Water:4-DEF:1    0.77941225 -0.86936819  2.428192694 0.9081933
## PBO:1-DEM:1     -0.09005944 -1.68293267  1.502813801 1.0000000
## Water:1-DEM:1   -0.54279236 -2.13566560  1.050080875 0.9914753
## DEF:2-DEM:1     -0.24973749 -1.70382517  1.204350179 0.9999864
## DEM:2-DEM:1      1.07005006 -0.38403761  2.524137737 0.3704407
## PBO:2-DEM:1      1.55540293  0.10131526  3.009490605 0.0254657
## Water:2-DEM:1    0.29232507 -1.16176260  1.746412742 0.9999336
## DEF:4-DEM:1     -1.46068980 -3.10947024  0.188090644 0.1336182
## DEM:4-DEM:1     -1.07706260 -2.72584304  0.571717841 0.5570008
## PBO:4-DEM:1     -0.46268608 -2.11146653  1.186094358 0.9984058
## Water:4-DEM:1    0.03438293 -1.61439751  1.683163373 1.0000000
## Water:1-PBO:1   -0.45273293 -2.04560616  1.140140312 0.9982119
## DEF:2-PBO:1     -0.15967806 -1.61376573  1.294409615 0.9999999
## DEM:2-PBO:1      1.16010950 -0.29397817  2.614197174 0.2534189
## PBO:2-PBO:1      1.64546237  0.19137470  3.099550042 0.0134114
## Water:2-PBO:1    0.38238451 -1.07170317  1.836472178 0.9991195
## DEF:4-PBO:1     -1.37063036 -3.01941080  0.278150081 0.2013620
## DEM:4-PBO:1     -0.98700316 -2.63578361  0.661777278 0.6837061
## PBO:4-PBO:1     -0.37262665 -2.02140709  1.276153794 0.9997904
## Water:4-PBO:1    0.12444237 -1.52433808  1.773222810 1.0000000
## DEF:2-Water:1    0.29305487 -1.16103280  1.747142541 0.9999319
## DEM:2-Water:1    1.61284243  0.15875475  3.066930100 0.0169898
## PBO:2-Water:1    2.09819530  0.64410762  3.552282968 0.0003333
## Water:2-Water:1  0.83511743 -0.61897024  2.289205104 0.7366950
## DEF:4-Water:1   -0.91789744 -2.56667788  0.730883007 0.7728171
## DEM:4-Water:1   -0.53427024 -2.18305068  1.114510204 0.9943921
## PBO:4-Water:1    0.08010628 -1.56867416  1.728886720 1.0000000
## Water:4-Water:1  0.57717529 -1.07160515  2.225955736 0.9893881
## DEM:2-DEF:2      1.31978756  0.01921201  2.620363111 0.0435267
## PBO:2-DEF:2      1.80514043  0.50456487  3.105715979 0.0006718
## Water:2-DEF:2    0.54206256 -0.75851299  1.842638115 0.9601627
## DEF:4-DEF:2     -1.21095230 -2.72607697  0.304172362 0.2510513
## DEM:4-DEF:2     -0.82732511 -2.34244977  0.687799559 0.7935787
## PBO:4-DEF:2     -0.21294859 -1.72807326  1.302176076 0.9999983
## Water:4-DEF:2    0.28412042 -1.23100424  1.799245091 0.9999669
## PBO:2-DEM:2      0.48535287 -0.81522268  1.785928420 0.9824134
## Water:2-DEM:2   -0.77772500 -2.07830055  0.522850557 0.6851423
## DEF:4-DEM:2     -2.53073986 -4.04586453 -1.015615196 0.0000156
## DEM:4-DEM:2     -2.14711267 -3.66223733 -0.631987999 0.0004643
## PBO:4-DEM:2     -1.53273615 -3.04786082 -0.017611483 0.0448412
## Water:4-DEM:2   -1.03566713 -2.55079180  0.479457533 0.4861552
## Water:2-PBO:2   -1.26307786 -2.56365342  0.037497689 0.0650701
## DEF:4-PBO:2     -3.01609273 -4.53121740 -1.500968064 0.0000001
## DEM:4-PBO:2     -2.63246553 -4.14759020 -1.117340867 0.0000060
## PBO:4-PBO:2     -2.01808902 -3.53321368 -0.502964351 0.0013456
## Water:4-PBO:2   -1.52102000 -3.03614467 -0.005895335 0.0482183
## DEF:4-Water:2   -1.75301487 -3.26813953 -0.237890201 0.0102038
## DEM:4-Water:2   -1.36938767 -2.88451234  0.145736997 0.1157833
## PBO:4-Water:2   -0.75501115 -2.27013582  0.760113513 0.8741537
## Water:4-Water:2 -0.25794214 -1.77306681  1.257182528 0.9999876
## DEM:4-DEF:4      0.38362720 -1.31922592  2.086480316 0.9997967
## PBO:4-DEF:4      0.99800371 -0.70484941  2.700856833 0.7114671
## Water:4-DEF:4    1.49507273 -0.20778039  3.197925848 0.1421940
## PBO:4-DEM:4      0.61437652 -1.08847660  2.317229635 0.9864936
## Water:4-DEM:4    1.11144553 -0.59140759  2.814298651 0.5583004
## Water:4-PBO:4    0.49706902 -1.20578410  2.199922134 0.9977313
## 
## $`Plant.Genotype:Treatment:Trial`
##                                               diff         lwr         upr
## def-1:DEF:1-Castlemart:DEF:1           2.244193578 -0.27578640  4.76417356
## Castlemart:DEM:1-Castlemart:DEF:1      0.743551961 -1.77642802  3.26353194
## def-1:DEM:1-Castlemart:DEF:1           2.997981457  0.47800148  5.51796144
## Castlemart:PBO:1-Castlemart:DEF:1      1.206217387 -1.31376259  3.72619737
## def-1:PBO:1-Castlemart:DEF:1           2.325145959 -0.19483402  4.84512594
## Castlemart:Water:1-Castlemart:DEF:1    0.416290647 -2.10368933  2.93627063
## def-1:Water:1-Castlemart:DEF:1         2.234920395 -0.28505959  4.75490037
## Castlemart:DEF:2-Castlemart:DEF:1      1.364626604 -0.93578986  3.66504307
## def-1:DEF:2-Castlemart:DEF:1           1.870150627 -0.43026584  4.17056709
## Castlemart:DEM:2-Castlemart:DEF:1      2.902056372  0.60163991  5.20247284
## def-1:DEM:2-Castlemart:DEF:1           2.979577175  0.67916071  5.27999364
## Castlemart:PBO:2-Castlemart:DEF:1      2.050400271 -0.25001620  4.35081674
## def-1:PBO:2-Castlemart:DEF:1           4.771887813  2.47147135  7.07230428
## Castlemart:Water:2-Castlemart:DEF:1    1.876174879 -0.42424159  4.17659134
## def-1:Water:2-Castlemart:DEF:1         2.445271026  0.14485456  4.74568749
## Castlemart:DEF:4-Castlemart:DEF:1     -0.170804017 -2.89269349  2.55108545
## def-1:DEF:4-Castlemart:DEF:1           0.980934941 -1.53904504  3.50091492
## Castlemart:DEM:4-Castlemart:DEF:1      0.134042376 -2.58784709  2.85593185
## def-1:DEM:4-Castlemart:DEF:1           1.405444745 -1.11453524  3.92542472
## Castlemart:PBO:4-Castlemart:DEF:1      0.906708561 -1.81518091  3.62859803
## def-1:PBO:4-Castlemart:DEF:1           1.976232007 -0.54374797  4.49621199
## Castlemart:Water:4-Castlemart:DEF:1    1.388638022 -1.33325145  4.11052749
## def-1:Water:4-Castlemart:DEF:1         2.421371817 -0.09860816  4.94135180
## Castlemart:DEM:1-def-1:DEF:1          -1.500641616 -4.02062160  1.01933836
## def-1:DEM:1-def-1:DEF:1                0.753787879 -1.76619210  3.27376786
## Castlemart:PBO:1-def-1:DEF:1          -1.037976190 -3.55795617  1.48200379
## def-1:PBO:1-def-1:DEF:1                0.080952381 -2.43902760  2.60093236
## Castlemart:Water:1-def-1:DEF:1        -1.827902930 -4.34788291  0.69207705
## def-1:Water:1-def-1:DEF:1             -0.009273183 -2.52925316  2.51070680
## Castlemart:DEF:2-def-1:DEF:1          -0.879566973 -3.17998344  1.42084949
## def-1:DEF:2-def-1:DEF:1               -0.374042951 -2.67445942  1.92637352
## Castlemart:DEM:2-def-1:DEF:1           0.657862794 -1.64255367  2.95827926
## def-1:DEM:2-def-1:DEF:1                0.735383598 -1.56503287  3.03580006
## Castlemart:PBO:2-def-1:DEF:1          -0.193793307 -2.49420977  2.10662316
## def-1:PBO:2-def-1:DEF:1                2.527694235  0.22727777  4.82811070
## Castlemart:Water:2-def-1:DEF:1        -0.368018699 -2.66843516  1.93239777
## def-1:Water:2-def-1:DEF:1              0.201077448 -2.09933902  2.50149391
## Castlemart:DEF:4-def-1:DEF:1          -2.414997595 -5.13688706  0.30689187
## def-1:DEF:4-def-1:DEF:1               -1.263258637 -3.78323862  1.25672134
## Castlemart:DEM:4-def-1:DEF:1          -2.110151201 -4.83204067  0.61173827
## def-1:DEM:4-def-1:DEF:1               -0.838748833 -3.35872881  1.68123115
## Castlemart:PBO:4-def-1:DEF:1          -1.337485017 -4.05937449  1.38440445
## def-1:PBO:4-def-1:DEF:1               -0.267961571 -2.78794155  2.25201841
## Castlemart:Water:4-def-1:DEF:1        -0.855555555 -3.57744502  1.86633391
## def-1:Water:4-def-1:DEF:1              0.177178240 -2.34280174  2.69715822
## def-1:DEM:1-Castlemart:DEM:1           2.254429495 -0.26555048  4.77440948
## Castlemart:PBO:1-Castlemart:DEM:1      0.462665426 -2.05731455  2.98264541
## def-1:PBO:1-Castlemart:DEM:1           1.581593997 -0.93838598  4.10157398
## Castlemart:Water:1-Castlemart:DEM:1   -0.327261314 -2.84724129  2.19271867
## def-1:Water:1-Castlemart:DEM:1         1.491368433 -1.02861155  4.01134841
## Castlemart:DEF:2-Castlemart:DEM:1      0.621074643 -1.67934182  2.92149111
## def-1:DEF:2-Castlemart:DEM:1           1.126598666 -1.17381780  3.42701513
## Castlemart:DEM:2-Castlemart:DEM:1      2.158504410 -0.14191206  4.45892088
## def-1:DEM:2-Castlemart:DEM:1           2.236025214 -0.06439125  4.53644168
## Castlemart:PBO:2-Castlemart:DEM:1      1.306848309 -0.99356816  3.60726478
## def-1:PBO:2-Castlemart:DEM:1           4.028335852  1.72791939  6.32875232
## Castlemart:Water:2-Castlemart:DEM:1    1.132622918 -1.16779355  3.43303938
## def-1:Water:2-Castlemart:DEM:1         1.701719065 -0.59869740  4.00213553
## Castlemart:DEF:4-Castlemart:DEM:1     -0.914355979 -3.63624545  1.80753349
## def-1:DEF:4-Castlemart:DEM:1           0.237382979 -2.28259700  2.75736296
## Castlemart:DEM:4-Castlemart:DEM:1     -0.609509585 -3.33139905  2.11237988
## def-1:DEM:4-Castlemart:DEM:1           0.661892783 -1.85808720  3.18187276
## Castlemart:PBO:4-Castlemart:DEM:1      0.163156600 -2.55873287  2.88504607
## def-1:PBO:4-Castlemart:DEM:1           1.232680045 -1.28729993  3.75266003
## Castlemart:Water:4-Castlemart:DEM:1    0.645086061 -2.07680341  3.36697553
## def-1:Water:4-Castlemart:DEM:1         1.677819856 -0.84216012  4.19779984
## Castlemart:PBO:1-def-1:DEM:1          -1.791764069 -4.31174405  0.72821591
## def-1:PBO:1-def-1:DEM:1               -0.