Dealing with different file encodings for a set of data can be a bit of a pain , but there is one tool that is really useful in this situation. Using the readr-package with its guess_encoding-function for reading files works most of the time. A few additions can make it even better.
Rpubs is a free service for publication of html-reports from R. Typically, the service is used to publish research. If you are working with R from the command line, there is a method for publishing to Rpubs – rpubsUpload.
Literate statistical programming can be a useful way to put text, code, data, output all in one document. If you have a Linux desktop, and the distribution includes proper support for R, chances are you may want to work with R from the command line.
Order, Order, Order
If you have done any major R-project, you quickly get to the point where it is hard to keep everything ordered – your scripts, you data, your output, your tests… If you have done several major R-projects, you know how hard it is to keep a similar structure and workflow between projects. The end result can be that projects are hardly reproducible, because you confuse others with a lack of order in each project, and a different order – to the degree that you have any order – from one project to the next.
To get our bearings in the Natura 2000 data, we need to run a range of commands on each table, such as dim() and summary(). Since eventual changes in the table from one year to the next – and in particular any change that makes one table incomparable to others across years – are of interest, we need to run the commands on all the tables across all years and present the data for comparation. To achieve this, it is better to do it with a script rather than manually, given the number of tables involved, and the supposed similarity of the data structures.
I have taken on Natura 2000 as a case for analysis because I live close to a protected area that is part of Natura 2000, As Fragas do Eume (In English: The Woods of the Eume, a river in the province of A Corunna). This is a beautiful area with a rich biosphere that is definitively worthy of protection. But it is under pressure by invasive species – in particular the eucalyptus – which is replacing indigenous species and also ruining the soil. A devastating forest fire in 2012 didn’t help much; the eucalyptus got an even better foothold in the aftermath of the fire. Local tourism is also on the rise, with an ever increasing number of visitors. Moreover, the area is surrounded by relatively intensive farming and a dam. All put together, it is likely that both indigenous flora and fauna are under a fair amount of pressure.