An R package that generates a geographic summary report for farm data in Sweden
This package is a work in progress and is currently being modified to allow others to use it. We have removed all data from this version.
Because this project lacks maintenance and development resources, it has been suggested that some of the features could be implemented in an SVA tool for task management and suspicion documentation (URAX). What follows is a draft list of features of the SVAMP software that could be used as a guideline for future redevelopment.
The interface to the tool takes three arguments:
- A comma separated list of PPNs
- A comma separated list of distances in km
- A time in days
In the feature list below, the PPN(s) in the argument will be referred to as the ‘investigated PPN(s)’. These arguments are used to subset and match some data to produce a report. The features list here is in no particular order with draft prioritisation (A-C) for each item; those items without a priority are seen as unnecessary parts of the software.
This feature is the plot of the PPN of interest alone on a map and could perhaps be ignored as a feature since it could be implemented in a map that just highlights these PPN(s) among all other PPNS on the same map.
Give a warning is the PPN of interest is missing X, Y coordinates and instead use the postal code as the location. In this case the buffers for the calculated restriction zones need to be calculated around the postal code polygon, not the point, or centroid of the postal code.
This feature is not optimal as implemented today. I would like to see the development of a tool to only summarise contact information for a PPN in a standard data-structure like perhaps ‘vcard’ that could then be passed on to the map popup, or a table or wherever you need it. Right now the owner information summary does an adhoc summary of this as does the map popup.
Just a bar graph. This could potentially be combined with the restriction zone graph somehow to simplify the output.
This feature is considered to be unimportant and should not be considered for reimplementation in URAX.
[#A] Tabulate and graph the number animals by species in the restriction zones defined by the distances in argument 2.
Another set of bar graphs.
Just a table by their membership to the restriction zones. This could also be further developed to include the potential candidates from the postal code zones that overlap the restriction zones to avoid the need for that other table. This would just require another column for those PPN’s that ‘could’ be in the zone but not with absolute certainty.
This could be the only map that is actually reimplemented if one also included the postal codes that intersect and split the PPN’s into layer by species. Don’t know how to deal with herds with multiple species in that case.
A bar chart.
This is currently implemented by calling an R package that does just this job: https://github.com/stewid/EpiContactTrace. We could probably leave contact tracing off of the development targets initially. If one wanted to do this in URAX the simplest method might be to call the above mentioned R package.
A table with the PPN’s and their contact information.
This could become a layer on another map is is of lower priority.
Not important at thsi point.
Not important currently
As mentioned above, there is a desire to be able to view the PPN:s on a map separated by species. This would facilitate the management and risk assessment in cases where only some species are at risk for the disease in question.