secrdesignapp is a partial interactive interface to the R package secrdesign. See the Help tab for details.
The main new feature in version 1.1 was support for systematic and random designs within a region of interest, and version 1.2 had many small improvements, including traffic lights and other warnings.
Version 1.3 (July 2019) introduced -
- user control of traffic light thresholds
- user-specified 2-D distribution models for simulated activity centres ('cluster' and 'even' as alternatives to Poisson)
- optional file input of habitat mask
- display raw text file input for detectors, mask
along with other minor improvements.
Version 1.4 (January 2020) supports lacework designs (to be introduced in the next release of secr) and no longer offers openCR.fit as a model-fitting option (secr 4.0 onwards has fast secr.fit).
Version 1.5 (January 2022) has minor updates in the Help file and suppresses GRTS random samples that are not available in recent releases of secr.
Version 1.6 (October 2022) adds support for optimization of detector placement by a genetic algorithm (Durbach et al. 2021) and restores GRTS random samples that now available again in secr.
Click this link to run secrdesignapp 1.5 in your web browser from a University of Otago server:
Simulations may run faster on your own machine, and the GitHub version is always the latest. There is also a limit to the number of concurrent users on the server. To run in a local R session directly from GitHub, first install R packages 'shiny', 'sf' and 'shinyjs'; then paste and run this code at the R command prompt:
library(shiny)
runGitHub("secrdesignapp", "MurrayEfford")Version 1.6 requires secr >= 4.5.8 and secrdesign >= 2.7.0. Various other R packages may be needed for specific operations.
If you intend to use bookmarking on your local machine to store the state of secrdesignapp then specify the 'port' and 'destdir' arguments, e.g.,
library(shiny)
runGitHub("secrdesignapp", "MurrayEfford", port = 8000, destdir = "d:/density secr 4.5/testing")The URL generated by pressing the Bookmark button may then be entered into your browser once you have started a new session with the same 'port' and 'destdir'. This restores all input settings and the Summary table, but not results on the Simulation or Spacing pages.
Some test data are provided:
| File name | Description | Usage |
|---|---|---|
| ovtrap.txt | Locations of possum traps in the Orongorongo Valley | Design - File input of detector array |
| ovmask.txt | text file of possible mask for possum study | Habitat mask - File |
| OVforest.dbf | ESRI polygon shapefile extent of habitat near possum traps | Design - Region and Options - Habitat clip to polygons |
| OVforest.shp | ||
| OVforest.shx | ||
| excltest.txt | OV polygon to demonstrate exclusion feature | Options - Detector array - Excluded region |
| regionxy.txt | text file of a hypothetical study area boundary | Design - Region and Options - Habitat clip to polygons |
Durbach, I., Borchers, D., Sutherland, C. and Sharma, K. (2021) Fast, flexible alternatives to regular grid designs for spatial capture--recapture. Methods in Ecology and Evolution 12, 298--310. DOI 10.1111/2041-210X.13517
Efford, M. G. and Boulanger, J. (2019) Fast evaluation of study designs for spatially explicit capture--recapture. Methods in Ecology and Evolution 10, 1529--1535.