This Shiny app performs simple spatially explicit capture-recapture analyses using the R package secr. For details see the Help tab, the step-by-step tutorial, and the Density web page .
To run secrapp directly from GitHub on your own machine, paste this code into an R session.
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 2.1 requires secr 5.1.0 or a later version.
Version 2.0 of the app may be run in a web browser without any setup by following this link. This arrangement has limited capacity for simultaneous users.
See help.rmd for recent changes.
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 |