Perform eDNA Occupancy Modeling

Perform eDNA Occupancy Modeling

This recipe runs eDNAoccupancy R package to estimate the occurrence of a species by modeling eDNA d…

2 results • updated 10 months ago by Istvan Albert

This recipe runs eDNAoccupancy R package to estimate the occurrence of a species by modeling eDNA data.

Required inputs

  1. Presence/absence eDNA detection data in CSV format.
  2. Metadata file in CSV format.

Detection file format

In the presence/absence table, the site column should have the header label site, the column specifying sample should have the sample sample. The rest of the headers should be sample names. The presence and absence values should be encoded with 0 and 1.

An example presence/absence table:

site,sample,pcr1,pcr2,pcr3,pcr4,pcr5,pcr6
Hunter_Creek,1,0,0,0,0,0,0
Pistol_River,1,0,0,0,0,0,0
Winchuck_River,1,0,0,0,0,0,0
Tillas_Slough,1,0,0,0,0,0,0
Lake_Earl,1,1,1,1,1,1,1
Elk_Creek,1,0,0,0,0,0,0

Metadata format:

The metadata headers should list the various labels associated with the site. The labels will be used as parameter entries in the interface.

site,twg,sal,turb,fish,veg
Hunter_Creek,0,7.2,60,0,0
Pistol_River,0,13,50,0,0
Winchuck_River,0,2,43,0,0
Tillas_Slough,17.8,9,236.8,160.9,1
Lake_Earl,1.06,4,124.15,113,1
Elk_Creek,0,30,144.67,19.3,0

In this example the usable paramters then would be twg, sal, turb, fish and veg.

Parameter selection tips

  • While running the recipe, ~ should prefix the covariate specification.
  • Enter ~1 in the text field if a covariate is none.
  • Multiple covariates can be combined using +.
  • An example covariate specification is ~sal+fish.

Covariates entered should match the column headers in the metadata file.

Copy recipe
You need write access to the original recipe to edit.
You need write access to the original recipe to edit.
Recipe Interface Builder
Click the buttons on the right to create new fields.
Interface Editor
Edit the content of each interface element.
You need write access to the original recipe to edit.
Edit Recipe
Recipe display name
Unique identifier for the recipe.
Image :
Optional image for the recipe ( 500px Maximum ).
Rank:
Used to order recipes (optional).

Insert Image

Back

Powered by the release 2.3.1