This Shiny app performs simple spatially explicit capture--recapture analyses using the R package secr (Efford 2025a). For details see the internal Help tab, the step-by-step tutorial, the online SECR Book (Efford 2025b), and the Density web page. See help.rmd for recent changes.
Click this link to run secrapp version 2.2 in your web browser from a University of Otago server without installing it locally.
It may be better to run secrapp on your own machine: models may fit faster, and you can install the latest the GitHub version. Also, there is a limit to the number of simultaneous users on the server.
To run secrapp in a local R session directly from GitHub, paste and run this code at the R command prompt:
install.packages("shinyjs") # skip if already installed; installs 'shiny' if needed
install.packages("secr") # skip if already installed
shiny::runGitHub("secrapp", "MurrayEfford")Note:
- for some functions you will also need the packages 'sf', 'stringr', and 'readxl'
- secrapp 2.2 requires secr 5.3.0 or a later version.
Some test data are provided here; see the secr help pages for details. Further example datasets may be found on the Density website.
| File name | Description | Usage |
|---|---|---|
| trap.txt | secr test file | Data input - Detector layout |
| capt.txt | secr test file | Data input - Captures |
| mask.txt | Demo mask file for capt.txt | Habitat mask - File input |
| FTHLtrap.txt | Perimeter of horned lizard search area | Data input - Detector layout |
| FTHLcapt.txt | Flat-tailed horned lizard test data | Data input - Captures |
| FTHL.rds | Saved flat-tailed horned lizard dataset | Data input |
| GSMboundary.dbf | ESRI polygon shapefile extent of habitat near black bear hair snags | Habitat mask - Mask polygon files |
| GSMboundary.shp | ||
| GSMboundary.shx | ||
| hareCH6trap.txt | Snowshow hare data | Data input - Detector layout |
| hareCH6capt.txt | Snowshow hare data | Data input - Captures |
| hareCH6.xlsx | Snowshoe hare data as Excel spreadsheet | Data input |
| hareCH6.rds | Saved snowshoe hare dataset | Data input |
| ovtrap.txt | Locations of possum traps in the Orongorongo Valley | Data input - Detector layout |
| ovcapt.txt | Brushtail possum captures in the Orongorongo Valley | Data input - Captures |
| OVforestL.dbf | ESRI polygon shapefile extent of habitat near possum traps | Habitat mask - Mask polygon files |
| OVforestL.shp | ||
| OVforestL.shx | ||
| ovenCHp.xlsx | Ovenbird proximity data as Excel spreadsheet | Data input |
| ovenCHp.rds | Saved ovenbird proximity dataset | Data input |
Efford, M. G. (2025a) secr: Spatially explicit capture--recapture models. R package version 5.3.0. https://CRAN.R-project.org/package=secr
Efford, M. G. (2025b The SECR Book. A handbook of spatially explicit capture–recapture methods. Version 1.0.1. Zenodo 15109938. Latest version online at https://murrayefford.github.io/SECRbook/.