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:
- secrapp 1.3 required secr 4.3
- secrapp 1.4 requires secr 4.4.2 or a later version.
The app may also be run in a web browser without any setup by following this link. This arrangement has limited capacity for simultaneous users.
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 |
| 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 |
| OVforest.dbf | ESRI polygon shapefile extent of habitat near possum traps | Habitat mask - Mask polygon files |
| OVforest.shp | ||
| OVforest.shx | ||
| ovenCHp.xlsx | Ovenbird proximity data as Excel spreadsheet | Data input |
| ovenCHp.Rds | Saved ovenbird proximity dataset | Data input |