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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.

This recipe is a clone. It will remain synchronized with the original recipe
Recipe Code
This recipe is a clone. It will remain synchronized with the original recipe
Recipe Interface
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Interface Preview
Interface preview shows the resulting view of the combined interface elements.
Interface specification
Interface element specification. Shows the code and the resulting interface element.
Double click on an element to insert it into the interface.
Integer values
                        [size]
                        label = "Window size"
                        display = "INTEGER"
                        value = 100
                        range = [1, 100]
                        help = "Selects the smoothing window."
                    
Float values
                        [cutoff]
                        label = "P_Value Cutoff"
                        display = "FLOAT"
                        value = 0.05
                        range = [0, 1]
                        help = "Selects the cutoff."
                    
Text box
                    [sra]
                    label = "Run Number"
                    display = "TEXTBOX"
                    value = "SRR519926"
                    regex = 'SRR\d+'
                    help = "Please provide SRR Run number"
                    
Dropdown menu
                    [color]
                    label = "Select color"
                    display = "DROPDOWN"
                    choices = [ ["R","Red"], ["B","Blue"] ]
                    value = "R"
                    help = "Select a color of your choice"
                    
Check box
                    [validate]
                    label = "Cross Validate"
                    display = "CHECKBOX"
                    value = true
                    help = "Apply cross validation on the results."
                    
Upload Field
                    [file]
                    label = "Upload a file "
                    display = "UPLOAD"
                    help = "Upload a file to analyze"
                    
Pick Data
                    [data]
                    label = "Pick data"
                    source = "PROJECT"
                    help = "Pick data from this project."
                    
Radio Buttons
                    [species]
                    label = "Select species"
                    display = "RADIO"
                    choices = [ ["c","Cat"], ["d","Dog"] ]
                    value = "c"
                    help = "Select the species."
                    
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