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Type:	Package
Title:	Analysis of Work Loops and Other Data from Muscle PhysiologyExperiments
Version:	1.1.4
Description:	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).
URL:	https://docs.ropensci.org/workloopR/,https://github.com/ropensci/workloopR/
BugReports:	https://github.com/ropensci/workloopR/issues/
Imports:	pracma (≥ 2.0.7), signal (≥ 0.7-6)
Suggests:	testthat (≥ 2.1.1), knitr, rmarkdown, dplyr, ggplot2,magrittr, purrr, tidyr
License:	GPL (≥ 3)
Encoding:	UTF-8
RoxygenNote:	7.1.1.9000
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2021-05-05 01:12:54 UTC; vbali
Author:	Vikram B. Baliga [aut, cre], Shreeram Senthivasan [aut], Julia Romanowska [rev] (Julia reviewed the package for rOpenSci , see <https://github.com/ropensci/software-review/issues/326/>), Eric Brown [rev] (Eric reviewed the package for rOpenSci , see <https://github.com/ropensci/software-review/issues/326/>)
Maintainer:	Vikram B. Baliga <vbaliga87@gmail.com>
Repository:	CRAN
Date/Publication:	2021-05-06 08:10:02 UTC

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

Description

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 forapplication 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 physiologyexperiments. Currently supported experiment types: work loop, simple twitch,and tetanus.

Data that are stored in .ddf format (e.g. generated by Aurora Scientific'sDynamic Muscle Control and Analysis Software) are easily imported viaread_ddf(),read_analyze_wl(), orread_analyze_wl_dir().Doing so generates objects of classmuscle_stim, which are formattedto work nicely with workloopR's core functions. Data that are read from otherfile formats can be constructed intomuscle_stim objects viaas_muscle_stim().

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

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

Some functions are readily available for batch processing of files. Theread_analyze_wl_dir() function allows for the batch import, cycleselection, gear ratio correction, and ultimately work & power computation forall work loop experiment files within a specified directory. Theget_wl_metadata() andsummarize_wl_trials() functions organizescanned files by recency (according to their time of last modification:'mtime') and then report work and power output in the order that trials wererun. This ultimately allows for thetime_correct() function to correctfor degradation of the muscle (according to power & work) over time,assuming that the first and final trials are identical in experimentalparameters.

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

Author(s)

Maintainer: Vikram B. Baligavbaliga87@gmail.com (ORCID)

Authors:

• Shreeram Senthivasanshreeramsenthi@gmail.com (ORCID)

Other contributors:

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

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

See Also

Useful links:

• https://docs.ropensci.org/workloopR/

• https://github.com/ropensci/workloopR/

• Report bugs athttps://github.com/ropensci/workloopR/issues/

Analyze work loop object to compute work and power output

Description

Compute work and power output from a work loop experiment on a per-cyclebasis.

Usage

analyze_workloop(x, simplify = FALSE, GR = 1, M = -1, vel_bf = 0.05, ...)

Arguments

Details

Please note thatselect_cycles() must be run on data prior tousing this function. This function relies on the inputmuscle_stimobject being organized by cycle number.

Themuscle_stim object (x) must be aworkloop,preferably read in by one of our data import functions. Please seedocumentation foras_muscle_stim() if you need to manually constructamuscle_stim object from a non .ddf source.

The gear ratio (GR) and velocity multiplier (M) parameters can help correctfor issues related to the magnitude and sign of data collection. By default,they are set to apply no gear ratio adjustment and to positivize velocity.Instantaneous velocity is often noisy and thevel_bf parameter allowsfor low-pass filtering of velocity data. Seesignal::butter() andsignal::filtfilt() for details of how filtering is achieved.

Please also be careful with units! Se Warning section below.

Value

The function returns alist of classanalyzed_workloopthat provides instantaneous velocity, a smoothed velocity, and computes work,instantaneous power, and net power from a work loop experiment. All data areorganized by the cycle number and important metadata are stored asAttributes.

Within thelist, each entry is labeled by cycle and includes:

In addition, the following information is stored in theanalyzed_workloop object's attributes:

Warning

Most systems we have encountered record Position data in millimetersand Force in millinewtons, and therefore this function assumes data arerecorded in those units. Through a series of internal conversions, thisfunction computes velocity in meters/sec, work in Joules, and power inWatts. If your raw data do not originate in millimeters and millinewtons,please transform your data accordingly and ignore what you see in theattributeunits.

Author(s)

Vikram B. Baliga and Shreeram Senthivasan

References

Josephson RK. 1985. Mechanical Power output from Striated Muscleduring Cyclic Contraction. Journal of Experimental Biology 114: 493-512.

See Also

read_ddf,read_analyze_wl,select_cycles

Other data analyses:isometric_timing(),read_analyze_wl_dir(),read_analyze_wl()

Other workloop functions:fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),summarize_wl_trials(),time_correct()

Examples

library(workloopR)# import the workloop.ddf file included in workloopRwl_dat <-read_ddf(system.file("extdata", "workloop.ddf",                              package = 'workloopR'),                  phase_from_peak = TRUE)# select cycles 3 through 5 via the peak-to-peak definitionwl_selected <- select_cycles(wl_dat, cycle_def = "p2p", keep_cycles = 3:5)# run the analysis function and get the full objectwl_analyzed <- analyze_workloop(wl_selected, GR = 2)# print methods give a short summaryprint(wl_analyzed)# summary provides a bit more detailsummary(wl_analyzed)# run the analysis but get the simplified versionwl_analyzed_simple <- analyze_workloop(wl_selected, simplify = TRUE, GR = 2)

Create your own muscle_stim object

Description

For use when data are not stored in .ddf format and you would liketo create amuscle_stim object that can be used by other workloopRfunctions.

Usage

as_muscle_stim(x, type, sample_frequency, ...)

Arguments

Details

muscle_stim objects, which are required by (nearly) allworkloopR functions, are automatically created viaread_ddf(). Shouldyou have data that are stored in a format other than .ddf, use this functionto create your own object of classmuscle_stim.

The inputx must be adata.frame that contains time seriesof numeric data collected from an experiment. Each row must correspond to asample, and these columns (exact title matches) must be included:
"Time" - time, recorded in seconds
"Position" - instantaneous position of the muscle,preferably in millimeters
"Force" - force, preferably in millinewtons
"Stim" - whether stimulation has occurred. All entries must be either 0 (nostimulus) or 1 (stimulus occurrence).

Additional arguments can be provided via.... For all experimenttypes, the following attributes are appropriate:
"units","header", "units_table","protocol_table", "stim_table","stimulus_pulses", "stimulus_offset","stimulus_width", "gear_ratio","file_id", or "mtime".

Please ensure that further attributes are appropriate to your experimenttype.

For workloops, these include:"stimulus_frequency", "cycle_frequency","total_cycles", "cycle_def","amplitude", "phase",and "position_inverted"

For twitches or tetanic trials:"stimulus_frequency", and "stimulus_length"

Value

An object of classworkloop,twitch, ortetanus,all of which inherit classmuscle_stim. These objects behave likedata.frames in most situations but also store metadata from the ddfas attributes.

Themuscle_stim object's columns contain:

In addition, the following information is stored in thedata.frame'sattributes:

Author(s)

Shreeram Senthivasan

See Also

read_ddf

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

Examples

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

Adjust for the gear ratio of a motor arm

Description

Fix a discrepancy between the gear ratio of the motor arm used and the gearratio recorded by software.

Usage

fix_GR(x, GR = 1)

Arguments

Details

Themuscle_stim object can be of any type, includingworkloop,twitch, ortetanus.

If you have manually constructed the object viaas_muscle_stim(),themuscle_stim object should have columns as follows:
Position: length change of the muscle;
Force: force

Value

An object of the same class(es) as the input (x). The functionwill multiplyPosition by (1/GR) and multiplyForce by GR,returning an object with new values in$Position and$Force.Other columns and attributes are welcome and will simply be passed onunchanged into the resulting object.

Author(s)

Vikram B. Baliga

See Also

analyze_workloop,read_analyze_wl,read_analyze_wl_dir

Other data transformations:invert_position(),select_cycles()

Other workloop functions:analyze_workloop(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),summarize_wl_trials(),time_correct()

Other twitch functions:invert_position(),isometric_timing()

Other tetanus functions:invert_position()

Examples

library(workloopR)# import the workloop.ddf file included in workloopRwl_dat <-read_ddf(system.file("extdata", "workloop.ddf",                              package = 'workloopR'),                  phase_from_peak = TRUE)# apply a gear ratio correction of 2# this will multiply Force by 2 and divide Position by 2wl_fixed <- fix_GR(wl_dat, GR = 2)# quick check:max(wl_fixed$Force) / max(wl_dat$Force) # 5592.578 / 2796.289 = 2max(wl_fixed$Position) / max(wl_dat$Position) # 1.832262 / 3.664524 = 0.5

Get file info for a sequence of experiment files

Description

Grab metadata from files stored in the same folder (e.g. a sequence of trialsin an experiment).

Usage

get_wl_metadata(file_path, pattern = "*.ddf")

Arguments

Details

If several files (e.g. successive trials from one experiment) arestored in one folder, use this function to obtain metadata in a listformat. Runsfile.info() from base R to extract info from files.

This function is not truly considered to be part of the batch analysispipeline;seeread_analyze_wl_dir() for a similar function that notonly grabs metadata but also imports & analyzes files. Instead,get_wl_metadata() is meant to be a handy function to investigatemetadata issues that arise if runningread_analyze_wl_dir() goes awry.

Unlikeread_analyze_wl_dir(), this function does not necessarily needfiles to all be work loops. Any file type is welcome (as long as the Regexpattern argument makes sense).

Value

Either adata.frame (if a single file is supplied) or alist ofdata.frames (if a list of files is supplied), withinformation as supplied fromfile.info().

Author(s)

Vikram B. Baliga

See Also

summarize_wl_trials

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

Other workloop functions:analyze_workloop(),fix_GR(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),summarize_wl_trials(),time_correct()

Other batch analyses:read_analyze_wl_dir(),summarize_wl_trials(),time_correct()

Examples

library(workloopR)# get file info for files included with workloopRwl_meta <- get_wl_metadata(system.file("extdata/wl_duration_trials",                                       package = 'workloopR'))

Invert the position data

Description

Multiply instantaneous position by -1.

Usage

invert_position(x)

Arguments

Details

Themuscle_stim object can be of any type, includingworkloop,twitch, ortetanus.

If you have manually constructed the object viaas_muscle_stim(),themuscle_stim object should have a column entitledPosition.Other columns and attributes are welcome and will be passed along unchanged.

Value

Aworkloop object with inverted position. Theposition_inverted attribute is set toTRUE and all others areretained.

Author(s)

Vikram B. Baliga

See Also

Other data transformations:fix_GR(),select_cycles()

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),summarize_wl_trials(),time_correct()

Other twitch functions:fix_GR(),isometric_timing()

Other tetanus functions:fix_GR()

Examples

library(workloopR)# import the workloop.ddf file included in workloopRwl_dat <-read_ddf(system.file("extdata", "workloop.ddf",                              package = 'workloopR'),                  phase_from_peak = TRUE)# invert the sign of Positionwl_fixed <- invert_position(wl_dat)# quick check:max(wl_fixed$Position) / min(wl_dat$Position) # -1

Compute timing and magnitude of force in isometric trials

Description

Calculate timing and magnitude of force at stimulation, peak force, andvarious parts of the rising (force development) and relaxation (falling)phases of the twitch.

Usage

isometric_timing(x, rising = c(10, 90), relaxing = c(90, 50))

Arguments

Details

Thedata.frame (x) must have time series data organized incolumns. Generally, it is preferred that you use amuscle_stim objectimported byread_ddf().

Therising andrelaxing arguments allow for the user to supplynumeric vectors of any length. By default, these arguments arerising = c(10, 90) andrelaxing = c(90, 50). Numbers in eachof these correspond to percent values and capture time and force at thatpercent of the corresponding curve. These values can be replaced by thosethat the user specifies and do not necessarily need to have length = 2. Butplease note that 0 and 100 should not be used, e.g.rising = seq(10, 90, 5) works, butrising = seq(0, 100, 5)does not.

Value

Adata.frame with the following metrics as columns:

Author(s)

Vikram B. Baliga

References

Ahn AN, and Full RJ. 2002. A motor and a brake: two leg extensormuscles acting at the same joint manage energy differently in a runninginsect. Journal of Experimental Biology 205, 379-389.

See Also

Other data analyses:analyze_workloop(),read_analyze_wl_dir(),read_analyze_wl()

Other twitch functions:fix_GR(),invert_position()

Examples

library(workloopR)# import the twitch.ddf file included in workloopRtwitch_dat <-read_ddf(system.file("extdata", "twitch.ddf",                                  package = 'workloopR'))# run isometric_timing() to get info on twitch kinetics# we'll use different set points than the defaultsanalyze_twitch <- isometric_timing(twitch_dat,  rising = c(25, 50, 75),  relaxing = c(75, 50, 25))# see the resultsanalyze_twitch

All-in-one import function for work loop files

Description

read_analyze_wl() is an all-in-one function to read in a work loopfile, select cycles, and compute work and power output.

Usage

read_analyze_wl(file_name, ...)

Arguments

Details

Please be careful with units! See Warnings below. This functioncombinesread_ddf() withselect_cycles() and then ultimatelyanalyze_workloop() into one handy function.

As detailed in these three functions, possible arguments include:
cycle_def - used to specify which part of the cycle is understood asthe beginning and end. There are currently three options: 'lo' for L0-to-L0;'p2p' for peak-to-peak; and 't2t' for trough-to-trough
bworth_order - Filter order for low-pass filtering ofPositionviasignal::butter prior to finding peak lengths. Default: 2.
bworth_freq - Critical frequency (scalar) for low-pass filtering ofPosition viasignal::butter prior to finding peak lengths.Default: 0.05.
keep_cycles - Which cycles should be retained. Default: 4:6.
GR - Gear ratio. Default: 1.
M - Velocity multiplier used to positivize velocity; should be either-1 or 1. Default: -1.
vel_bf - Critical frequency (scalar) for low-pass filtering ofvelocity viasignal::butter. Default: 0.05.

The gear ratio (GR) and velocity multiplier (M) parameters can help correctfor issues related to the magnitude and sign of data collection. Bydefault, they are set to apply no gear ratio adjustment and to positivizevelocity. Instantaneous velocity is often noisy and thevel_bfparameter allows for low-pass filtering of velocity data. Seesignal::butter() andsignal::filtfilt() for details of howfiltering is achieved.

Value

The function returns alist of classanalyzed_workloopthat provides instantaneous velocity, a smoothed velocity, and computes work,instantaneous power, and net power from a work loop experiment. All data areorganized by the cycle number and important metadata are stored asAttributes.

Within thelist, each entry is labeled by cycle and includes:

In addition, the following information is stored in theanalyzed_workloop object's attributes:

Warning

Most systems we have encountered record Position data in millimetersand Force in millinewtons, and therefore this function assumes data arerecorded in those units. Through a series of internal conversions, thisfunction computes velocity in meters/sec, work in Joules, and power inWatts. If your raw data do not originate in millimeters and millinewtons,please transform your data accordingly and ignore what you see in theattributeunits.

Author(s)

Vikram B. Baliga

References

Josephson RK. 1985. Mechanical Power output from Striated Muscleduring Cyclic Contraction. Journal of Experimental Biology 114: 493-512.

See Also

read_ddf,select_cyclesanalyze_workloop

Other data analyses:analyze_workloop(),isometric_timing(),read_analyze_wl_dir()

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

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),select_cycles(),summarize_wl_trials(),time_correct()

Examples

library(workloopR)# import the workloop.ddf file included in workloopR and analyze with# a gear ratio correction of 2 and cycle definition of peak-to-peakwl_dat <- read_analyze_wl(system.file("extdata", "workloop.ddf",                                      package = 'workloopR'),                          phase_from_peak = TRUE,                          GR = 2, cycle_def = "p2p")

Read and analyze work loop files from a directory

Description

All-in-one function to import multiple workloop .ddf files from a directory,sort them by mtime, analyze them, and store the resulting objects in anordered list.

Usage

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

Arguments

Details

Work loop data files will be imported and then arranged in the orderin which they were run (assuming run order is reflected inmtime).Chiefly used in conjunction withsummarize_wl_trials() andtime_correct() if time correction is desired.

Value

A list containinganalyzed_workloop objects, one for each file that isimported and subsequently analyzed. The list is sorted according to thesort_by parameter, which by default uses the time of last modificationof each file's contents (mtime).

Warning

Most systems we have encountered record Position data in millimetersand Force in millinewtons, and therefore this function assumes data arerecorded in those units. Through a series of internal conversions, thisfunction computes velocity in meters/sec, work in Joules, and power inWatts. If your raw data do not originate in millimeters and millinewtons,please transform your data accordingly and ignore what you see in theattributeunits.

Author(s)

Shreeram Senthivasan

References

Josephson RK. 1985. Mechanical Power output from Striated Muscleduring Cyclic Contraction. Journal of Experimental Biology 114: 493-512.

See Also

read_analyze_wl,get_wl_metadata,summarize_wl_trials,time_correct

Other data analyses:analyze_workloop(),isometric_timing(),read_analyze_wl()

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

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl(),select_cycles(),summarize_wl_trials(),time_correct()

Other batch analyses:get_wl_metadata(),summarize_wl_trials(),time_correct()

Examples

library(workloopR)# batch read and analyze files included with workloopRanalyzed_wls <- read_analyze_wl_dir(system.file("extdata/wl_duration_trials",                                                package = 'workloopR'),                                    phase_from_peak = TRUE,                                    cycle_def = "p2p", keep_cycles = 2:4)

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

Details

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

Please note that there is no correction for gear ratio or furthermanipulation of data. Seefix_GR to adjust gear ratio. Gear ratio canalso be adjusted prior to analyses within theanalyze_workloop()function, the data import all-in-one functionread_analyze_wl(), orthe batch analysis all-in-oneread_analyze_wl_dir().

Please also note that organization of data within the .ddf file is assumed toconform to that used by Aurora Scientific's Dynamic Muscle Control andAnalysis Software. YMMV if using a .ddf file from another source. Theas_muscle_stim() function can be used to generatemuscle_stimobjects if data are imported via another function. Please feel free tocontact us with any issues or requests.

Value

An object of classworkloop,twitch, ortetanus,all of which inherit classmuscle_stim. These objects behave likedata.frames in most situations but also store metadata from the ddfas attributes.

Themuscle_stim object's columns contain:

In addition, the following information is stored in thedata.frame'sattributes:

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 workloopRwl_dat <-read_ddf(system.file("extdata", "workloop.ddf",                              package = 'workloopR'),                  phase_from_peak = TRUE)

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

Description

Usesread_ddf() to read in workloop, twitch, or tetanus experimentdata from multiple .ddf files.

Usage

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

Arguments

Details

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

Please note that there is no correction for gear ratio or furthermanipulation of data. Seefix_GR to adjust gear ratio. Gear ratio canalso be adjusted prior to analyses within theanalyze_workloop()function, the data import all-in-one functionread_analyze_wl(), orthe batch analysis all-in-oneread_analyze_wl_dir().

Please also note that organization of data within the .ddf file is assumed toconform to that used by Aurora Scientific's Dynamic Muscle Control andAnalysis Software. YMMV if using a .ddf file from another source. Theas_muscle_stim() function can be used to generatemuscle_stimobjects if data are imported via another function. Please feel free tocontact us with any issues or requests.

Value

A list of objects of classworkloop,twitch, ortetanus, all of which inherit classmuscle_stim. These objectsbehave likedata.frames in most situations but also store metadatafrom the ddf as attributes.

Eachmuscle_stim object's columns contain:

In addition, the following information is stored in eachdata.frame'sattributes:

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()

Examples

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

Select cycles from a work loop object

Description

Retain data from a work loop experiment based on position cycle

Usage

select_cycles(  x,  cycle_def,  keep_cycles = 4:6,  bworth_order = 2,  bworth_freq = 0.05,  ...)

Arguments

Details

select_cycles() subsets data from a workloop trial byposition cycle. Thecycle_def argument is used to specify which partof the cycle is understood as the beginning and end. There are currentlythree options:
'lo' for L0-to-L0;
'p2p' for peak-to-peak; and
't2t' for trough-to-trough

Peaks are identified usingpracma::findpeaks(). L0 points on therising edge are found by finding the midpoints between troughs and thefollowing peak. However the first and last extrema and L0 points may bemisidentified by this method. Please plot yourPosition cycles toensure the edge cases are identified correctly.

Thekeep_cycles argument is used to determine which cycles (asdefined bycycle_def should be retained in the final dataset. Zerois the index assigned to all data points that are determined to be outsidea complete cycle.

Themuscle_stim object (x) must be aworkloop,preferably read in by one of our data import functions. Please seedocumentation foras_muscle_stim() if you need to manually constructamuscle_stim object from another source.

Value

Aworkloop object with rows subsetted by the chosen positioncycles. ACycle column is appended to denote which cycle each timepoint is associated with. Finally, all attributes from the inputworkloop object are retained and one new attribute is added torecord which cycles from the original data were retained.

Author(s)

Vikram B. Baliga and Shreeram Senthivasan

See Also

analyze_workloop,read_analyze_wl,read_analyze_wl_dir

Other data transformations:fix_GR(),invert_position()

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),summarize_wl_trials(),time_correct()

Examples

library(workloopR)# import the workloop.ddf file included in workloopRwl_dat <-read_ddf(system.file("extdata", "workloop.ddf",                              package = 'workloopR'),                  phase_from_peak = TRUE)# select cycles 3 through 5 via the peak-to-peak definitionwl_selected <- select_cycles(wl_dat, cycle_def = "p2p", keep_cycles = 3:5)# are the cycles of (approximately) the same length?summary(as.factor(wl_selected$Cycle))

Summarize work loop files

Description

Summarize important info from work loop files stored in the same folder(e.g. a sequence of trials in an experiment) including experimentalparameters, run order, andmtime.

Usage

summarize_wl_trials(wl_list)

Arguments

Details

If several files (e.g. successive trials from one experiment) arestored in one folder, use this function to obtain summary stats andmetadata and other parameters. This function requires a list ofanalyze_workloop objects, which can be readily obtained by firstrunningread_analyze_wl_dir() on a specified directory.

Value

Adata.frame of information about the collection of workloop files.Columns include:

Author(s)

Vikram B. Baliga and Shreeram Senthivasan

References

Josephson RK. 1985. Mechanical Power output from Striated Muscleduring Cyclic Contraction. Journal of Experimental Biology 114: 493-512.

See Also

read_analyze_wl_dir,get_wl_metadata,time_correct

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),time_correct()

Other batch analyses:get_wl_metadata(),read_analyze_wl_dir(),time_correct()

Examples

library(workloopR)# batch read and analyze files included with workloopRanalyzed_wls <- read_analyze_wl_dir(system.file("extdata/wl_duration_trials",                                               package = 'workloopR'),                                    phase_from_peak = TRUE,                                    cycle_def = "p2p",                                    keep_cycles = 2:4                                    )# now summarizesummarized_wls <- summarize_wl_trials(analyzed_wls)

Time correction for work loop experiments

Description

Correct for potential degradation of muscle over time.

Usage

time_correct(x)

Arguments

Details

This function assumes that across a batch of successive trials, thestimulation parameters for the first and final trials are identical. If not,DO NOT USE. Decline in power output is therefore assumed to be a linearfunction of time. Accordingly, the difference between the final and firsttrial's (absolute) power output is used to 'correct' trials that occur inbetween, with explicit consideration of run order and time elapsed (viamtime). A similar correction procedure is applied to work.

Value

Adata.frame that additionally contains:

And new attributes:

Author(s)

Vikram B. Baliga and Shreeram Senthivasan

See Also

summarize_wl_trials

Other workloop functions:analyze_workloop(),fix_GR(),get_wl_metadata(),invert_position(),read_analyze_wl_dir(),read_analyze_wl(),select_cycles(),summarize_wl_trials()

Other batch analyses:get_wl_metadata(),read_analyze_wl_dir(),summarize_wl_trials()

Examples

library(workloopR)# batch read and analyze files included with workloopRanalyzed_wls <- read_analyze_wl_dir(system.file("extdata/wl_duration_trials",                                                package = 'workloopR'),                                    phase_from_peak = TRUE,                                    cycle_def = "p2p", keep_cycles = 2:4)# now summarizesummarized_wls <- summarize_wl_trials(analyzed_wls)# mtimes within the package are not accurate, so we'll supply# our own vector of mtimessummarized_wls$mtime <- read.csv(                          system.file(                            "extdata/wl_duration_trials/ddfmtimes.csv",                            package="workloopR"))$mtime# now time correcttimecor_wls <- time_correct(summarized_wls)timecor_wls

Approximate the definite integral via the trapezoidal rule

Description

Mostly meant for internal use in our analysis functions, but made availablefor other use cases. Accordingly, it does not strictly rely on objects ofclassmuscle_stim.

Usage

trapezoidal_integration(x, f)

Arguments

Details

In the functionsanalyze_workloop(),read_analyze_wl(), andread_analyze_wl_dir(), work is calculated as the differencebetween the integral of the upper curve and the integral of the lower curveof a work loop.

Value

A numerical value indicating the value of the integral.

Author(s)

Vikram B. Baliga

References

Atkinson, Kendall E. (1989), An Introduction to NumericalAnalysis (2nd ed.), New York: John Wiley & Sons

See Also

analyze_workloop,read_analyze_wl,read_analyze_wl_dir

Examples

# create a circle centered at (x = 10, y = 20) with radius 2t <- seq(0, 2 * pi, length = 1000)coords <- t(rbind(10 + sin(t) * 2, 20 + cos(t) * 2))# use the function to get the areatrapezoidal_integration(coords[, 1], coords[, 2])# does it match (pi * r^2)?3.14159265358 * (2^2) # very close