Reads a spreadsheet containing a description of all the files required for an experiment to allow batch execution.
read_experiment(
filename,
format = NA,
interpolate = FALSE,
project.dir = NA,
data.dir = project.dir,
cluster = NULL,
author.note = "",
verbose = FALSE
)An rtrack_experiment object containing a complete description of the
experiment.
A spreadsheet file containing a description of the experiment or a JSON file containing an exported experiment.
An experiment description for reading raw data can be provided as an
Excel spreadsheet ('excel') or as a comma-delimited ('csv') or tab-delimited ('tab',
'tsv', 'txt' or 'text') text file. The value 'json' indicates that the file is an
archived experiment in the JSON format (as generated by export_json).
Default (NA) is to guess the format from the file extension.
This is passed to the read_path function and specifies
whether missing data points will be interpolated when reading raw swim path data.
Default is FALSE.
A directory path specifying where the files needed for processing
the experiment are stored. Default (NA) means the project files are in the
same directory as the experiment description (specified by filename). Ignored
if format = "json".
A directory path specifying where the raw data are stored. All paths
specified in the experiment description spreadsheet are interpreted as being relative
to the data.dir directory. Default is the same directory as
project.dir. Ignored if format = "json".
A cluster object as generated by makeCluster or
similar.
Optional text describing the experiment. This might be useful if the data is to be published or otherwise shared. Appropriate information might be author names and a link to a publication or website.
Should feedback be printed to the console. This is only useful for
debugging and takes a little longer to run. Default is FALSE.
Information about a full experiment can be assembled into a spreadsheet ( currently
Excel and CSV formats are supported) and used to process large numbers of files in one
batch. The project directory (project.dir) is where the arena description files
are found. This will typically be the same place as the experiment description file
(and is set to be this by default). This does not need to be the same as the current
working directory. An optional data directory (data.dir) can also be specified
separately allowing the storage-intensive raw data to be kept in a different location
(for example on a remote server). Together, these options allow for flexibility in
managing your raw data storage. Individual tracks are associated with their raw data
file, experimental group metadata, an arena and any other parameters that the
strategy-calling methods require. Required columns are "_TrackID", "_TargetID", "_Day",
"_Trial", "_Arena" "_TrackFile" and "_TrackFileFormat" (note the leading underscore
"_"). Any additional columns (without a leading underscore) will be interpreted as
user-defined factors or other metadata and will be passed on to the final analysis
objects and thus be available for statistical analysis.
For details on how interpolation is performed (if interpolate is set to
TRUE), see the documentation for read_path.
For larger experiments, a computing cluster (using the parallel
package) can be specified, which will be passed to analysis functions and allow the
track analysis to be performed in parallel.
read_path, read_arena,
identify_track_format to identify the format of your raw track files,
and check_experiment.
require(Rtrack)
experiment.description = system.file("extdata", "Minimal_experiment.xlsx",
package = "Rtrack")
experiment = read_experiment(experiment.description)
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