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eDITH

An R package to model transport of environmental DNA in river networks

CRAN

Overview

eDITH (eDNA Integrating Transport and Hydrology) allows interpreting environmental DNA data collected from river networks. It implements the eDITH model, which couples a geomorphological and hydrological characterization of a catchment, eDNA transport and decay dynamics, and a species distribution model, and allows transforming pointwise eDNA data collected at a catchment into predicted maps of taxon density.

Features:

  • It provides estimations of detection probability of a taxon across a whole catchment based on spatially replicated eDNA data
  • It can handle both eDNA concentration data (e.g., from qPCR) and metabarcoding (read counts) data
  • Model fit can be performed via Bayesian techniques or optimization algorithms
  • Covariates can be specified by the user and/or selected by means of Asymmetric Eigenvector Maps (AEMs)
  • An interface to the DHARMa package for residual diagnostics is provided

eDITH requires the use of river networks defined as river objects, which can be built via the rivnet package.

Installing the package

eDITH can be installed from CRAN:

install.packages("eDITH")

The development version can be installed from Github:

devtools::install_github("lucarraro/eDITH")