Reads raw antenna contact data and metadata files.

  cageQualityFile = NULL



A vector of filenames. Each file is a CSV dump of antenna contact data. These files should cover a contiguous period encompassing the whole experiment. Files can be given as full pathnames so that the often large data volumes can be stored outside the analysis directory (for example on an external fileserver). Any file format readable by read.table can be used.


A tab-delimited file describing the subjects/animals. This information is required to link RFID tags to variables/factors such as experimental group, age, weight etc.


A tab-delimited file describing the layout of the cage system. This is currently in the the form of an unweighted undirected network.


A tab-delimited file describing events. This must minimally include details of the light cycle. See Details for more information.


An optional tab-delimited file describing the content of the cages (food, bedding, toys etc.). See Details for more information.


A colonytrack_data object.


This function requires raw CSV data from the Colony Cage as well as a subject/animal description file, a cage layout description file and a log of events. An optional metadata file allows finer description of the cages.

The processed data are padded to start at "lights on" of the first day to "lights off" of the last day (as specified in the 'Events' file). Nevertheless, the first and last days (and any interruptions in recording) will result in missing data that may need to be handled during analysis. The actogram (produced by plot of the colonytrack_data object) can be used to identify such missing blocks.