TheoreticalEcology / man_vs_machine

data and analyses for Man vs machine manuscript

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Man vs Machine - analyses


This repository (R project) contains all data and scripts necessary to run the analyses and produce the figures from the study Man against machine: Do fungal fruitbodies and eDNA metabarcoding give similar biodiversity assessments across broad environmental gradients?. (Frøslev et al. (2019) - published in Biological Conservation).
All steps/processes for this study can be carried out on the same computer/platform. But, in practise all analyses were carried out on a linux server setup with 64 processors (AMD Opteron(tm) 6380), except R-scripts, which were run on a MacBook Pro (2.9 GHz Intel Core i7, 16 GB 2133 MHz LPDDR3). All analyses were carried out in one directory and sub-directories of this.

Sequencing data

The Illumina sequence data is deposited here: https://sid.erda.dk/public/archives/b0d2b22cb7804ff23d1612f4afdc29ae/published-archive.html

Bioinformatic tools

CLI tools were used for this study

Various R-packages were used for this study (see in the relevant markdown files).

Description of the sub directories

  • in_data : contains all initial data not produced as part of the analyses here
  • data : contains all the data produced as part of the analyses here
  • seq_processing : contains all the scripts and files necessary to perform the initial sequence processing
  • tables : output directory for (text) tables produced in the analyses
  • R : contains a few functions used in the analyses
  • plots : output directory for the plots/figures produced in the analyses

References

Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Hansen, A. J., Læssøe, T., & Heilmann-Clausen, J. (2019). Man against machine: Do fungal fruitbodies and eDNA give similar biodiversity assessments across broad environmental gradients?. Biological Conservation, 233, 201-212. https://doi.org/10.1016/j.biocon.2019.02.038

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data and analyses for Man vs machine manuscript


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