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Import a batch of work loop or isometric data files from a directory

Source: R/batch_analysis_functions.R
read_ddf_dir.Rd

Uses read_ddf() to read in workloop, twitch, or tetanus experiment data from multiple .ddf files.

Usage

read_ddf_dir(file_path, pattern = "*.ddf", sort_by = "mtime", ...)

Arguments

file_path

Path where files are stored. Should be in the same folder.

pattern

Regex pattern for identifying relevant files in the file_path.

sort_by

Metadata by which files should be sorted to be in the correct run order. Defaults to mtime, which is time of last modification of files.

...

Additional arguments to be passed to read_ddf().

Value

A list of objects of class workloop, twitch, or tetanus, all of which inherit class muscle_stim. These objects behave like data.frames in most situations but also store metadata from the ddf as attributes.

Each muscle_stim object's columns contain:

Time

Time

Position

Length change of the muscle, uncorrected for gear ratio

Force

Force, uncorrected for gear ratio

Stim

When stimulation occurs, on a binary scale

In addition, the following information is stored in each data.frame's attributes:

sample_frequency

Frequency at which samples were collected

pulses

Number of sequential pulses within a stimulation train

total_cycles_lo

Total number of oscillatory cycles (assuming sine wave trajectory) that the muscle experienced. Cycles are defined with respect to initial muscle length (L0-to-L0 as opposed to peak-to-peak).

amplitude

amplitude of length change (again, assuming sine wave trajectory)

cycle_frequency

Frequency of oscillations (again, assuming sine wave trajectory)

units

The units of measurement for each column in the data.frame. This might be the most important attribute so please check that it makes sense!

Details

Read in a .ddf file that contains data from an experiment. If position and force do not correspond to columns 2 and 3 (respectively), replace "2" and "3" within rename_cols accordingly. Similarly, skip_cols = 4:11 should be adjusted if more than 11 columns are present and/or columns 4:11 contain important data.

Please note that there is no correction for gear ratio or further manipulation of data. See fix_GR to adjust gear ratio. Gear ratio can also be adjusted prior to analyses within the analyze_workloop() function, the data import all-in-one function read_analyze_wl(), or the batch analysis all-in-one read_analyze_wl_dir().

Please also note that organization of data within the .ddf file is assumed to conform to that used by Aurora Scientific's Dynamic Muscle Control and Analysis Software. YMMV if using a .ddf file from another source. The as_muscle_stim() function can be used to generate muscle_stim objects if data are imported via another function. Please feel free to contact us with any issues or requests.

See also

Other data import functions: as_muscle_stim(), get_wl_metadata(), read_analyze_wl_dir(), read_analyze_wl(), read_ddf()

Author

Vikram B. Baliga and Shreeram Senthivasan

Examples


library(workloopR)

# import a set of twitch .ddf files included in workloopR
workloop_dat <-read_ddf_dir(system.file("extdata/wl_duration_trials",
                 package = 'workloopR'))