analyse_logistic: Analyse logistic kinetics across NIRS channels

In mnirs: Muscle Near-Infrared Spectroscopy Processing and Analysis

Analyse logistic kinetics across NIRS channels

Description

Internal channel-level dispatch for analyse_kinetics(method = "sigmoidal"). Fits a 4-parameter sigmoidal curve to each nirs_channel within a single "mnirs" data frame via fit_sigmoidal() with one of three shapes: "symmetric", "gompertz", or "gompertz_left". See analyse_kinetics() for user-facing documentation.

Usage

analyse_logistic(
  data,
  nirs_channels = NULL,
  time_channel = NULL,
  shape = c("symmetric", "gompertz", "gompertz_left"),
  fix = NULL,
  control = NULL,
  start_time = NULL,
  direction = c("auto", "positive", "negative"),
  end_window = Inf,
  verbose = TRUE,
  ...,
  env = rlang::caller_env()
)

Arguments

data	A data frame of class "mnirs" containing time series data and metadata.
nirs_channels	A character vector giving the names of mNIRS columns to operate on. Must match column names in data exactly. If NULL (default), the nirs_channels metadata attribute of data is used.
time_channel	A character string naming the time or sample column. Must match a column name in data exactly. If NULL (default), the time_channel metadata attribute of data is used.
shape	Character; the 4-parameter sigmoidal shape to fit. One of "symmetric" (default; calls SSlogistic()), "gompertz" (early-inflection; calls SSgompertz()), or "gompertz_left" (late-inflection; calls SSgompertz_left()).
fix	An optional named list of model parameters (A, B, xmid, slope) to hold constant during fitting, e.g. fix = list(A = 0). Fixed parameters are excluded from estimation and reported at their fixed values. Applied to every channel, or per-channel as a list of lists keyed by channel name, e.g. fix = list(smo2 = list(A = 0)).
control	An optional list() or stats::nls.control() merged over each fit's internal defaults by fit_control(). Global to all channels.
start_time	A numeric value in units of time_channel specifying the response onset (effectively time = 0 of the fit). If NULL (default), retrieves interval_times from "mnirs" metadata, or falls back to 0 or the first positive time value (see Details).
direction	A character string specifying the response direction "positive", or "negative", or detect with "auto" (default). See Details.
end_window	A numeric value in units of time_channel specifying the window in which to look for the end of the kinetics fit; with no greater/ lesser values within end_window after the first extrema (min/max). end_window = Inf (default) returns the global extreme from the full data range (see Details). For "biexponential", end_window bounds the fast-phase window only, and the default is 30 sec; the full model is then fit to the full data range.
verbose	Logical. TRUE (default) will display, and FALSE will silence warnings and information messages helpful for troubleshooting. Global default can be set via options(mnirs.verbose = FALSE).
...	Additional arguments passed to the underlying method function. See Details. For the stats::nls() methods (monoexponential, exponential_drift, biexponential, sigmoidal, sigmoidal_drift), control = list() can be passed to stats::nls.control(), e.g. control = list(maxiter = 200), applied globally to all channels and intervals.
env	The calling environment or a defused call, used to report errors and warnings as coming from the user-facing function rather than the validator.

Value

A data.frame with one row per nirs_channel and columns nirs_channels, A, B, xmid, slope, xmid_fitted. Per-channel metadata are attached as attributes:

• "model": an nls model object, or NULL for channels where fitting failed.

• "fitted_data": a named list of per-channel data frames with columns window_idx and fitted.

• "diagnostics": a data.frame with one row per nirs_channel containing model fit diagnostics.

• "channel_args": a data.frame with one row per nirs_channel recording the resolved arguments used.

See Also

analyse_kinetics(), logistic(), SSlogistic(), gompertz(), gompertz_left(), SSgompertz(), SSgompertz_left()

mnirs documentation built on Sept. 13, 2026, 1:06 a.m.