Author: Anna R. Sjodin; Michael R. Willig; Simon J. Anthony
Title: Quantitative Delineation of Herpesviruses in Bats for use in Ecological Studies Document date: 2019_11_26
ID: 21ldw4lk_14
Snippet: When inputting the PID matrix of all clones, the number of clusters identified through affinity propagation can be interpreted as an optimal number of viral OTUs. Although this method has been used to define clusters of a single viral species (Fischer et al. 2017) , this is the first instance in which it has been used to delineate viral "species" for the purpose of communitylevel analyses. To conduct affinity propagation analyses, the apcluster().....
Document: When inputting the PID matrix of all clones, the number of clusters identified through affinity propagation can be interpreted as an optimal number of viral OTUs. Although this method has been used to define clusters of a single viral species (Fischer et al. 2017) , this is the first instance in which it has been used to delineate viral "species" for the purpose of communitylevel analyses. To conduct affinity propagation analyses, the apcluster() command was run using the R package apcluster (Bodenhofer et al. 2011) , with default values of input parameters (input data = NA, input preference = NA, q = 0.5, convits = 100, maxits = 1000, lam = 0.9).
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