read_ddf: Import work loop or isometric data from .ddf files

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

Import work loop or isometric data from .ddf files

Description

read_ddf reads in workloop, twitch, or tetanus experiment data from .ddf files.

Usage

read_ddf(
  file_name,
  file_id = NA,
  rename_cols = list(c(2, 3), c("Position", "Force")),
  skip_cols = 4:11,
  phase_from_peak = FALSE,
  ...
)

Arguments

file_name	A .ddf file that contains data from a single workloop, twitch, or tetanus experiment
file_id	A string identifying the experiment. The file name is used by default.
rename_cols	List consisting of a vector of indices of columns to rename and a vector of new column names. See Details.
skip_cols	Numeric vector of column indices to skip. See Details.
phase_from_peak	Logical, indicating whether percent phase of stimulation should be recorded relative to peak length or relative to L0 (default)
...	Additional arguments passed to/from other functions that work with read_ddf()

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.

Value

An object 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.

The 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 the 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!

Author(s)

Vikram B. Baliga and Shreeram Senthivasan

See Also

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

Examples

library(workloopR)

# import the workloop.ddf file included in workloopR
wl_dat <-read_ddf(system.file("extdata", "workloop.ddf",
                              package = 'workloopR'),
                  phase_from_peak = TRUE)

ropensci/workloopR documentation built on July 21, 2024, 4:31 p.m.