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Abundances from metabarcoding

Basic model

  • Model file: models/metabarcoding/optmodel.tppl

  • Example input data: models/metabarcoding/data/testdata_optmodel.json

  • Brief info: The example model optmodel.tppl is a probabilistic model where the parameter values are inferred from the read numbers of spike-in species in metabarcoding samples. The resulting distributions can be used to predict abundances of other insect species in the sample set. The provided test data with spike-in reads and prior settings comes from the below publication.

  • Reference: Iwaszkiewicz-Eggebrecht, E., Granqvist, E., Buczek, M., Prus, M., Kudlicka, J., Roslin, T., Tack, A. J. M., Andersson, A. F., Miraldo, A., Ronquist, F., & Łukasik, P. (2023). Optimizing insect metabarcoding using replicated mock communities. Methods in Ecology and Evolution, 14, 1130–1146. https://doi.org/10.1111/2041-210X.14073