DOI: 10.16904/envidat.270
title: Amphibian observation and pond data (Aargau, Switzerland)

description: In the canton of Aargau, hundreds of new ponds have been constructed since the 1990s to benefit declining amphibian populations. This dataset consists of monitoring data for all 12 pond-breeding amphibian species in the canton of Aargau from 1999 to 2019 in 856 ponds, and environmental variables that describe the ponds and the landscape surrounding the ponds. Species observation data is detection/non-detection data from repeat visits during survey years, during which all potentially suitable ponds in an area were surveyed. Environmental variables describing the ponds are whether the pond has been newly constructed since 1991 or not, pond age (if constructed), elevation a.s.l., the water surface area, and whether the water table fluctuates or not. Environmental variables describing the surroundings of the ponds are the percent area of forest within a circular buffer of radius 100m around the pond, the area of large (width ≥6m) roads within a circular buffer of radius 1km around the pond, as well as structural and potential population connectivity, quantified by three different metrics each.
The canton of Aargau is the owner of the monitoring data; the original datafile is only disclosed upon request and in consultation with the canton of Aargau.
The edited dataset contains cleaned observation data for the 12 amphibian species, as well as compiled and edited covariate data and code to fit dynamic occupancy models.
description: Resource Title: Readme
 Size: 277486 bytes
 Format: application/pdf
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/2108eb1a-f11f-4c9f-85f1-a21cdae52185/download/datadescriptionenvidat.pdf
 Description: Description of methods and datasets. Version 1.
description: Resource Title: Covariate data 1
 Size: 57933 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/3c9f85f8-6c9b-4532-9038-b027927b1aac/download/covdata1.csv
 Description: This file contains covariate data that does not change over time for 856 ponds: the region the pond is in, whether the pond is old or new (constructed since 1991), elevation, water surface area, fluctuations of the water table (yes, no), the percent forest cover in 100m radius around the pond, the area or large (&gt;6m wide) roads in 1km radius around the pond.
description: Resource Title: Covariate data 2
 Size: 486115 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/e16a1c32-0953-44d3-bcf4-835b6ac9b0ac/download/covdata2.csv
 Description: This file contains covariate data that changes over time for 856 ponds in 21 years (long format): whether or not a pond exists in year _t_, the age of constructed ponds in year _t_, structural connectivity of the pond in year _t_.
description: Resource Title: Observation data
 Size: 2742709 bytes
 Format: application/vnd.ms-excel
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/2bfcece3-c25b-4dd9-a059-1b60f8d1c738/download/obsdata.csv
 Description: This file contains detection/non-detection data for the 12 amphibian species between 1999 and 2019 for 3 annual visits. Detectable denotes whether or not a visit j was made to pond i in year t. ObservedID gives a unique ID for the observer collecting the data during visit j to pond i in year t.
description: Resource Title: Model code
 Size: 37899 bytes
 Format: .rmd
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/d80d4a9f-40a0-473a-bd90-1ecb1a4a0c84/download/runmodels1.rmd
 Description: This R markdown file contains all code and descriptions necessary to load and format the provided data and to fit the dynamic occupancy models described in the associated publication, including JAGS code for the fitted models.
description: Resource Title: Model code, description
 Size: 672546 bytes
 Format: text/html
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/b2249e83-4901-4c47-b5b2-736cebf97147/download/runmodels1.html
 Description: This is the output of the R markdown file that provides JAGS model code and describes how to format the provided data and fit the dynamic occupancy models described in the associated publication, for a quick overview.
description: Resource Title: Original raw data
 Size: 9960328 bytes
 Format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/c233605d-0a83-437f-9704-31c126a1c318/download/a_auszug-karch-einzelbeob_oz_4-v4-ab99.xlsx
 Description: This file contains the original raw monitoring data as provided by the canton of Aargau. Access is restricted and only considered upon request and in consultation with the canton of Aargau.
description: Resource Title: Readme, v 2.0
 Size: 312052 bytes
 Format: application/pdf
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/c31abb8b-f5ab-492c-b0fa-2e8c85afe5f6/download/datadescriptionenvidat2.pdf
 Description: Description of methods and datasets. Version 2.0, including new datasets fro structural and potential population connectivity.
description: Resource Title: Structural connectivity data
 Size: 2351634 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/643685b3-940c-44ff-a703-dfd01f6496da/download/covdata_structconn.csv
 Description: This file contains structural connectivity data (three different metrics), calculated based on all existing ponds in each year, in long format. See Readme v2.0 for details. Required to run Model code 2.
description: Resource Title: Potential population connectivity data
 Size: 28849564 bytes
 Format: text/csv
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/6b907363-02d8-4cfa-8b0f-36ab945866f8/download/covdata_popconn.csv
 Description: This file contains potential population connectivity data (three different metrics), calculated based on all existing and occupied ponds in each year, for each species, in long format. See Readme v2.0 for details. Required to run Model code 2.
description: Resource Title: Model code 2
 Size: 46506 bytes
 Format: application/octet-stream
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/27deb8d2-b414-4331-92f0-f988f1979516/download/runmodels2.rmd
 Description: This R markdown file contains all code and descriptions necessary to load and format the provided data and to fit the dynamic occupancy models described in the second associated publication, including JAGS code for the fitted models.
description: Resource Title: Model code 2, description
 Size: 674645 bytes
 Format: text/html
 URL: https://www.envidat.ch/dataset/f6bfbf55-bf8d-4602-bff6-47ee277e9b7f/resource/57fded43-4f8c-426b-bac1-11ccca42146f/download/runmodels2.html
 Description: This is the output of the R markdown file Model code 2 that provides JAGS model code and describes how to format the provided data and fit the dynamic occupancy models described in the second associated publication, for a quick overview.