Package index • mnirs

Read data

Read raw data from exported files.

Clean, filter, and transform data.

resample_mnirs(): Re-sample an mnirs data frame
replace_mnirs() replace_invalid() replace_outliers() replace_missing(): Replace outliers, invalid, and missing values in mnirs data
filter_butterworth() filter_butter(): Apply a Butterworth digital filter
filter_mnirs(): Filter a data frame
filter_moving_average() filter_ma(): Apply a moving average filter
shift_mnirs(): Shift data range
rescale_mnirs(): Rescale data range
correct_blood_volume(): Correct for blood volume changes

Detect and extract intervals for further analysis

extract_intervals(): Extract intervals from mnirs data
by_time() by_label() by_lap() by_sample(): Specify interval boundaries by time, label, lap, or sample

Estimate response dynamics and kinetic parameters

analyse_kinetics() analyze_kinetics(): Analyse kinetics across mNIRS channels and intervals
response_time(): Fractional response time
peak_slope(): Peak linear slope
SSbiexponential(): Self-starting biexponential model
SSexponential_drift(): Self-starting exponential-drift model
SSmonoexponential(): Self-starting monoexponential model
biexponential(): Biexponential function
exponential_drift(): Exponential-drift function
monoexponential(): Monoexponential function
SSsigmoidal_drift(): Self-starting sigmoidal-drift model
sigmoidal_drift(): Sigmoidal-drift function
SSlogistic(): Self-starting logistic model
logistic(): Generalised logistic function
SSgompertz() SSgompertz_left(): Self-starting Gompertz models
gompertz() gompertz_left(): Gompertz growth functions

Tools for printing functions and pretty plotting with ggplot2

print(<mnirs>): Methods for mnirs objects
print(<mnirs_kinetics>): Methods for mnirs_kinetics objects
plot(<mnirs>): Plot mnirs objects
plot(<mnirs_kinetics>): Plot mnirs kinetics results
theme_mnirs(): Custom mnirs ggplot2 theme
palette_mnirs(): Custom mnirs colour palette
scale_colour_mnirs() scale_color_mnirs() scale_fill_mnirs(): Scales for custom mnirs palette
breaks_timespan(): Breaks for time span data
format_hmmss(): Format time span data as h:mm:ss

Example data files included in the package

moxy_intervals.csv: 0.5 Hz Moxy onboard export
train.red_intervals.csv: 10 Hz Train.Red App export
artinis_intervals.xlsx: 10 Hz Artinis Oxysoft export recorded with Oxymon MKIII
moxy_ramp.xlsx: 2 Hz PerfPro export of Moxy data
portamon_oxcap.xlsx: 10 Hz Artinis Oxysoft export recorded with Portamon
pionirs_occlusion.ftn: 1 Hz PIONIRS NIRSBOX export