R implementation of methods dealing with real-time location system (RTLS) data from GEA CowView

Core methods to analyse RTLS data:

• analysis.R: analysis methods
• data.R: data manipulation methods
• database.R: database methods
• plot.R: plotting methods

User- or farm-specific files:

• farmXXX.R: farm-specific methods (each farm should have a separate file)
• init.R: specified paths for input files and other user-specific settings here (not synced on GitHub)
• initExample.R: example of init.R
• tmp.R: sandbox for your own methods (not synced on GitHub)

Examples and analysis source code files start with run:

• runAreaUsageAnalysis.R: analysis of area usage data
• runExampleXXX.R: example code to read, process and visualise data for specific farm
• runReadTime.R: code to compare running time to read input files
• ...

Certain files are ignored and not synced on GitHub:

• data folder and all its contents
• init.R: specified paths for input files and other user-specific settings here (not synced on GitHub)
• tmp.R: sandbox for your own methods (not synced on GitHub)
• Any file with name that contains hyphen (-), e.g. analysis-MC.R

• Make sure that you have all the necessary data files (e.g. barn.csv, tags.csv) in the data folder (not synced on GitHub)
• Specify paths for input files in init.R

To match CowView data with data on cows, we use the following routines. Cow data are stored in a dataframe cowData with at least columns CowID, Lactation, CalvingDate (there can be several records for different lactations). Mapping between cows and tags is stored in cowTagMap dataframe with columns CowID, Tag, From (the latter indicates the date when the tag was assigned to a cow). There is getCowID(tag, date, cowTagMap) function in data.R to determine ID of a cow with certain tag on a specific day.

Barn data are stored in a dataframe with columns Unit, x1, y1, x2, y2, x3, y3, x4, y4 corresponding to unit name and four pairs of coordinates for the four points defining the rectangle (bottom-left, top-left, top-right, bottom-right).

Our core code should be independent of specific farms, thus we make use of "abstract"" functions (i.e. those that need to be overriden for each specific farm). Few examples are: readBarnData, readCowData, readCowTagMap. They need to be defined in farmXXX.R files along with other farm-specific functions. Currently, there are two versions for frams Lad and Wim.