Demo

Three demo networks have been included with the anuran distribution. These networks were constructed with CoNet from a study on the spatial distribution of taxon abundances:

Meyer, K. M., Memiaghe, H., Korte, L., Kenfack, D., Alonso, A., & Bohannan, B. J. (2018). Why do microbes exhibit weak biogeographic patterns?. The ISME journal, 12(6), 1404.

In this study, the authors used a spatially explicit nested design to collect soil samples in the Rabi Forest Monitoring Plot in Gabon. This permitted them to construct distance-decay curves and assess whether these were different from such curves found for the trees on the plot. The heatmap below visualizes the Rabi_geodist_matrix file included with this publication, and shows how these samples are ordered. As you can see, the diagonal separates in 3 blocks with lower distances. The samples can be separated into 3 groups, with the in-group distance being much lower than the between-group distance. We used this matrix to separate the samples and construct 3 networks, one for each group. These networks were constructed with CoNet; taxa with a minimum count below 10 or a prevalence below 30% were removed. To handle the large diversity of the sequences, the abundances were merged by taxonomic family.

geodist <- read.table("Rabi_geodist_matrix.txt", sep='\t', stringsAsFactors = FALSE)
geodist <- sapply(geodist[2:40, 2:40], as.numeric)
heatmap(geodist, Rowv = NA, Colv = NA)

Since the samples were collected from a single plot, we do not expect major changes in the community composition, and some associations may be preserved across the three blocks. We can look for such conserved associations with anuran. Although many of anuran's features are more applicable to larger numbers of networks, some of these operations can take a lot of time; with this data, you will quickly be able to work through the main features.