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---------------- READ ME ----------------

Make a copy of this sheet and edit in Google Drive. The sheets used to summirize the data and to check for errors will not work if you download the sheets as a .xlsx or .ods file. Functions that help detecting errors in the Summary, detCovsError, siteCovsError, detCovsWarning, and siteCovsWarning sheets do not work in Excel and Libreoffice. You can still use the occ, detCovs, and siteCovs sheets as templates to run occupancy models.

The sheets can be used to type data for occupancy models. These data are provided in three sheets: occ, detCovs, and siteCovs. These are the only sheets that should be edited. Do not delete columns and rows, only the content (e.g. using the delete key). The remaining sheets help visualizing summary statistics for these data and to check for potential errors (e.g. replicate and site names that do not match across the sheets). Once all data is correctly formated, download the occ, detCovs, and siteCovs as .csv files (comma separated values). You can visit https://cdfviv-cristian-dambros.shinyapps.io/OccupancyDataOrganizer/ to fill in zeroes and missing data (NAs) in the occ sheet. Using this website, you can also format the data as an presence/absence matrices for each species (as a 3d array) to run occupancy models for individual species using unmarked).

occ: observation data - Each row represents an observation (occurrence) per site (e.g. forest fragment), replicate (camera trap within each forest fragment), and species. Do not include zeroes and NAs in the data.

detCovs: Each row contains information about replicates (e.g. each camera trap) and variables to be used as predictors of detection. Variables obtained at the site scale (e.g. forest fragment) must be repeated here if used as predictors of detection (repeat values for all replicates in each site). All replicates with observations in occ must be present here. Check detCovsError sheet to make sure no replicate is missing from the detCovs sheet. Make sure that all replicates surveyed (even when no species was found - true zeroes) are inserted here. Make sure that replicates not surveyed (i.e. missing data; e.g. planned sites that have not been visited) are not inserted here.

siteCovs: Each row contains information about sites (e.g. each forest fragment) and variables to be used as predictors of occupancy (true presences). All sites with observations (in occ) must be present here. Check siteCovsError sheet to make sure no site is missing from this sheet. Make sure that all sites surveyed (even when no species was found - true zeroes) are inserted here. Make sure that sites not surveyed (i.e. missing data; e.g. planned sites that have not been visited) are not inserted here.

summary: summarizes some information from the previous sheets. You can also use this sheet to check for inconsistencies.
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