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Instructions
General instructions for the use of the application. If you want a more general introduction to R use the Quick R website. For additional analysis or visualization in R contact Mitch Gritts.
It takes a while to load the data, please be patient.
Install the latest versions of R and R Studio.
Download the code and data for this application here. Extract the contents of the zip file.
Install the following packages in R. (Copy and paste the command below into the R console to install.)
install.packages(c("highcharter", "magrittr", "shinyjs", "maptools", "adehabitatHR",
"adehabitatLT", "CircStats", "boot", "MASS", "adehabitatMA",
"ade4", "deldir", "sp", "ggplot2", "lubridate", "geojsonio",
"gridExtra", "data.table", "leaflet", "readr", "dplyr", "shiny",
"DT"))Download this repo and save to your desired location. Double click the Server.R file to open in R Studio.
Once Server.R is open in R Studio there is a small green play button in the upper right hand corner of the first panel. The button says "Run App". Click this button. The app will open in the viewer window. If you want to open the app in a web browser (required for some functionality) click the small triangle to the right of the "Run App" and select "Run External". This will permanently set a browser as the default for opening the app.
After the button is clicked the telemetR will start running. It'll take some time to load all the data. Once the data is loaded the app defaults to a species and management area. The map will display a simplified view of the animals trajectory.
The application opens to input fields, a map, and table of collared animals. The map and table display the data selected in the filter section. The map defaults to CBHS. In order to limit the amount of data rendered on the map only animals from one management area at a time are visible. Select the species and management area of your choice.
The data can be further filtered by NDOWID. Click the field and select the ID from the list (or type the number then press enter). If you want to filter by date range entering the beginning and end date first, then check the Use Date Range button.
The map is interactive. Click on the points to get a popup with the NDOW ID of that animal. Each color is a different animal. The paths on this page only show one point per day.
Any field in the table can be searched using the search bar on the right. The table can be sorted by clicking the arrows next to each column name.
After You've selected the data you want to see in more detail click the Use Data button, this will take you to the Spatial tab. (When the button is clicked the movement parameters are calculated. This may take some time depending on how many animals you have selected). Limit your selection to 5-8 animals. Any more will be very slow.
After clicking the "Use Data" button, this tab will open. In order to see any data push the "Update Map" button. This will render a map with all the points for each selected animal. Each point can be clicked to display a popup of each points data. If there are any obvious erroneous points, please note the LocID and report submit a new issue explaining why that point is incorrect.
To estimate a home range select the method and enter the contour levels to estimate (multiple values should be separated by a comma: 25, 50, 75). Then click update map. MCP default to the 95% contour, this cannot be changed now.
This tab can be used to plot several parameters related to animal movement. Once you've selected the figure you want to display click create graph. At the bottom is an interactive graph of the Net Squared Displacement. This is useful for pinpointing migration start and end dates. Refer to Bunnefeld et al. 2010 for more information on NSD calculations and utility.
The fourth page shows all the GPS data for individuals displayed on the map. This includes every GPS fix (not only every 20 as mapped) for the species, management area (for deer), NDOW ID, and date range selected. This data can be downloaded as a .CSV file by clicking the Download Data button, and saved to your Downloads folder. The downloaded data will include every GPS location.