The n2kanalysis package

The n2kanalysis package contains the main infrastructure for the analysis of the Natura 2000 Monitoring. The import from the raw data into the analysis object is done by dedicated packages, one for each monitoring scheme.

Rationale

n2kanalysis is part of the collection of R packages created to analyse the data gathered during the Natura 2000 monitoring.

• n2kanalysis: R package with generic functions for the analysis
• watervogelanalysis: R package to extract the raw data from the wintering bird survey database and prepare the analyses
• abvanalysis: R package to extract the raw data from the common breeding birds survey database and prepare the analyses
• n2khelper: auxiliary functions used in the other packages
• n2kresult: Liquibase scripts to set-up the database in which the results of the analyses are stored
• n2kupdate: R package to read and write to the n2kresult database
• Rn2k: Docker image with all the required dependencies to run the analyses

The main goal of n2kanalysis is to assist traceable analysis of monitoring data. The S4 classes in n2kanalysis allow to defines self-contained analysis objects. Besides the required data and definition on the model, the object also contains relevant meta-data. Each object contains two fingerprints: the file fingerprint and the status fingerprint. Both are SHA-1 hashes based on the current object. The file fingerprint is based on the parts of the object which won't change during the analysis. E.g. most meta-data, the data and the definition of the model. The status fingerprint is based on both the file fingerprint and all relevant part of the object that do change during the fitting process. Publishing both fingerprints along with the results ensures an easy matching between results and the object from which they originated.

Folder structure

The folder structure is that of a typical R package with the mandatory R folder (definition of the functions) and man (help files in Rd format). inst is an optional folder in which some auxiliary scripts are stored. The optional tests folder contains the unit tests using the infrastructure from the testthat package.

n2kanalysis
|-- inst
|-- man
|-- R
|-- tests
   |-- testthat