NIRSVascMuscle is an R package designed for analyzing Near-Infrared Spectroscopy (NIRS) data in muscle physiology research. This package provides tools for data smoothing, cleaning, event slicing, aggregation, heterogeneity, and on-off transient analysis across multiple channels.
This is a package to perform analyses on Near-Infrared Spectroscopy (NIRS) data. The kinetics analyses can be performed on other types of physiological data such as oxygen uptake kinetics.
The kinetics analyses implemented functions from the following original papers:
-
Bauer, T. A., Brass, E. P., Barstow, T. J., & Hiatt, W. R. (2007, May). Skeletal muscle StO2 kinetics are slowed during low work rate calf exercise in peripheral arterial disease. European Journal of Applied Physiology, 100(2), 143-151. https://doi.org/10.1007/s00421-007-0412-0
-
Grassi, B., Pogliaghi, S., Rampichini, S., Quaresima, V., Ferrari, M., Marconi, C., & Cerretelli, P. (2003, Jul). Muscle oxygenation and pulmonary gas exchange kinetics during cycling exercise on-transitions in humans. J Appl Physiol (1985), 95(1), 149-158. https://doi.org/10.1152/japplphysiol.00695.2002
The heterogeneity analyses are based on the paper:
- Vogiatzis, I., Habazettl, H., Louvaris, Z., Andrianopoulos, V., Wagner, H., Zakynthinos, S., & Wagner, P. D. (2015). A method for assessing heterogeneity of blood flow and metabolism in exercising normal human muscle by near-infrared spectroscopy. Journal of applied physiology (Bethesda, Md. : 1985), 118(6), 783-793. https://doi.org/10.1152/japplphysiol.00458.2014
To install the NIRSVascMuscle package from GitHub, you can use the following code:
if (!requireNamespace("devtools", quietly = TRUE)) {
install.packages("devtools")
}
library(devtools)
devtools::install_github("DMegaritis/NIRSVascMuscle")
library(NIRSVascMuscle)
cat("NIRSVascMuscle package loaded successfully.\n")# Loading the package
# Loading the package
library(NIRSVascMuscle)
# Testing functions using the dummy data of NIRSVascMuscle:
# Test function: clean
path <- system.file("extdata", package = "NIRSVascMuscle")
winsize <- 20
vars <- c("TOI_1", "TOI_2")
cleaned_files <- clean(path, winsize, vars)
# Test function slice_event
files <- cleaned_files
period_col <- "Comment"
events <- list("EVNT1 ")
sampling_freq <- 5
data_before <- 10
data_after <- 60
transient_phase <- "kinetics"
time_column <- "elpsec"
cleaned_sliced <- slice_event(files, period_col, events, sampling_freq, data_before, data_after, transient_phase, time_column)
# Aggregate
aggregated <- aggregate_NIRS(cleaned_sliced)
# Heterogeneity calculator
vars <- c("TOI_1", "TOI_2", "TOI_3", "TOI_4", "ID", "Comment")
cv_vars <- c("TOI_1", "TOI_2", "TOI_3", "TOI_4")
ID <- "ID"
time_point <- "Comment"
hetero <- heterogeneity(aggregated, vars, cv_vars, ID, time_point)
# Test function: filter_smooth
# this function works with both paths and lists (error if there are missing data)
path <- system.file("extdata", package = "NIRSVascMuscle")
vars <- c("TOI_1", "TOI_2")
filtered_smoothed <- filter_smooth(path, vars)
# Single_decay
path_or_list <- filtered_smoothed
vars <- "TOI_1"
event_column <- "Comment"
start_event <- "EVNT13 "
time_column <- "elpsec"
transient_phase <- "on"
eyeball_data <- "yes"
plot_fitted <- "no"
plot_directory <- "/Users/dimitrismegaritis/Desktop"
decay_start <- 10
y_Bas_user <- 70
A_p_user <- 15
T_Dp_user <- 9
tau_p_user <- 5
decay <- single_decay(path_or_list, vars, event_column, start_event, time_column, transient_phase, eyeball_data, plot_fitted, plot_directory, decay_start, y_Bas_user, A_p_user, T_Dp_user, tau_p_user)
# Double decay
path_or_list <- filtered_smoothed
vars <- "TOI_1"
event_column <- "Comment"
start_event <- "EVNT13 "
time_column <- "elpsec"
transient_phase <- "decrease"
eyeball_data <- "yes"
plot_fitted <- "no"
plot_directory <- "/Users/dimitrismegaritis/Desktop"
decay_start <- 10
y_Bas_user <- 70
A_p_user <- 15
T_Dp_user <- 9
tau_p_user <- 5
A_s_user <- 55
T_Ds_user <- 5
tau_s_user <- 4
decay <- double_decay(path_or_list, vars, event_column, start_event, time_column, transient_phase, eyeball_data, plot_fitted, plot_directory, decay_start, y_Bas_user, A_p_user, T_Dp_user, tau_p_user, A_s_user, T_Ds_user, tau_s_user)