Characterizing larval breeding sites: combining multiple
environmental conditions
To consolidate the analysis of different categories of environmental
conditions, we performed another random forest model in La Lopé and
Rabai, respectively. The model included scores on the first three
principal components (PCs) from the physical variable analysis and
scores on the first two NMDS axes from the bacterial community
composition analysis (i.e., predictive variables), and used them to
classify the larval breeding site groups (i.e., the dependent variable).
For the analysis from Rabai, we also added the microbial density and the
density of all mosquito larvae. These two variables had many missing
values in the La Lopé dataset and thus were excluded. The model
generated a confusion matrix, which displayed the number of samples
correctly or wrongly assigned to each larval breeding site group. A
lower proportion of misclassification between groups suggests a stronger
distinction in their environmental conditions.