This repo is a map showing the analysis status for bear monitoring in Sweden 2019. The main functionaly is to display the status of the samples arriving at NRM from all the volunteers that collect scat samples and send to us.
If you can read swedish and are interested in knowing more about this project please visit the project page at the museum of natural history.
This small repo holds code to display the samples that have been registered within the project during 2019. As the samples are arriving to the museum the meta-data are imported into the database rovbase and the actual scat samples are being processed for extraction of DNA and genotyping. All imported samples that are registered to rovbase are imported and shown at the map together with its unique id, sample date and colored accordingly to the following criteria.
- Black: the sample is registered at rovbase and has arrived at NRM
- Blue: the sample is not from the the target area of 2019 (västerbotten) or was collected outside the specified time frame for the project (20190821-20191031). These samples are not used in the genetic monitoring nor for the calculation of the population size.
- Yellow: DNA have been extracted and the samples are ready to be genotyped
- Grey: the genotyping has failed. The reason for this is most often that the collected scat is not from bear, but it could also be that the DNA in the sample is too degraded for genotyping.
- Green: the sample contains DNA from bear and have succesfully been genotyped.
In addition there is a small summary of the project progress so far. Note that this map is not meant to be used for anything but the progress of the project and if you are truly interested in the carnivores of sweden do use rovbase as a source for information.
The map is generated using R and the flexdashboard framework. Since rovbase stores gps coordinates in SWEREF99 format there is also code to convert these to WGS84 for easy plotting. In addition there is a short script that are used to push up new data from daily digestions of the information at rovbase as we currently are not allowed to directly access the databases at rovbase via api. The short script is activated every time a file is updated and generates a new map that are then pushed to this repo.