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workloopR: Analysis of Work Loops and Other Data from Muscle Physiology Experiments

Source: R/workloopR.R
workloopR-package.Rd

Functions for the import, transformation, and analysis of data from muscle physiology experiments. The work loop technique is used to evaluate the mechanical work and power output of muscle. Josephson (1985) <doi:10.1242/jeb.114.1.493> modernized the technique for application in comparative biomechanics. Although our initial motivation was to provide functions to analyze work loop experiment data, as we developed the package we incorporated the ability to analyze data from experiments that are often complementary to work loops. There are currently three supported experiment types: work loops, simple twitches, and tetanus trials. Data can be imported directly from .ddf files or via an object constructor function. Through either method, data can then be cleaned or transformed via methods typically used in studies of muscle physiology. Data can then be analyzed to determine the timing and magnitude of force development and relaxation (for isometric trials) or the magnitude of work, net power, and instantaneous power among other things (for work loops). Although we do not provide plotting functions, all resultant objects are designed to be friendly to visualization via either base-R plotting or 'tidyverse' functions. This package has been peer-reviewed by rOpenSci (v. 1.1.0).

Details

Functions for the import, transformation, and analysis of muscle physiology experiments. Currently supported experiment types: work loop, simple twitch, and tetanus.

Data that are stored in .ddf format (e.g. generated by Aurora Scientific's Dynamic Muscle Control and Analysis Software) are easily imported via read_ddf(), read_analyze_wl(), or read_analyze_wl_dir(). Doing so generates objects of class muscle_stim, which are formatted to work nicely with workloopR's core functions. Data that are read from other file formats can be constructed into muscle_stim objects via as_muscle_stim().

Prior to analyses, data can be transformed or corrected. Transformational functions include gear ratio correction (fix_GR()), position inversion (invert_position()), and subsetting of particular cycles within a work loop experiment (select_cycles()).

Core data analytical functions include analyze_workloop() for work loop files and isometric_timing() for twitches. analyze_workloop() computes instantaneous velocity, net work, instantaneous power, and net power for work loop experiments on a per-cycle basis. isometric_timing() provides summarization of twitch kinetics.

Some functions are readily available for batch processing of files. The read_analyze_wl_dir() function allows for the batch import, cycle selection, gear ratio correction, and ultimately work & power computation for all work loop experiment files within a specified directory. The get_wl_metadata() and summarize_wl_trials() functions organize scanned files by recency (according to their time of last modification: 'mtime') and then report work and power output in the order that trials were run. This ultimately allows for the time_correct() function to correct for degradation of the muscle (according to power & work) over time, assuming that the first and final trials are identical in experimental parameters.

Please feel free to contact either Vikram or Shree with suggestions or code development requests (see contact info below). We are especially interested in expanding our data import functions to accommodate file types other than .ddf in future versions of workloopR.

See also

Useful links:

Author

Maintainer: Vikram B. Baliga vbaliga87@gmail.com (ORCID)

Authors:

Other contributors:

  • Julia Romanowska Julia.Romanowska@uib.no (Julia reviewed the package for rOpenSci , see <https://github.com/ropensci/software-review/issues/326/>) [reviewer]

  • Eric Brown eb@ericebrown.com (Eric reviewed the package for rOpenSci , see <https://github.com/ropensci/software-review/issues/326/>) [reviewer]