| abort_validation | validate_numeric abort message construction |
| accept_port_fit | Accept or reject a non-converged port fit |
| analyse_biexponential | Analyse biexponential kinetics across NIRS channels |
| analyse_exponential_drift | Analyse exponential-drift kinetics across NIRS channels |
| analyse_kinetics | Analyse kinetics across mNIRS channels and intervals |
| analyse_kinetics_channels | Process kinetics fits across NIRS channels |
| analyse_kinetics_intervals | Run a kinetics worker over each interval and collate results |
| analyse_logistic | Analyse logistic kinetics across NIRS channels |
| analyse_monoexponential | Analyse monoexponential kinetics across NIRS channels |
| analyse_peak_slope | Analyse peak linear slope across NIRS channels |
| analyse_response_time | Analyse fractional kinetics response time across NIRS... |
| analyse_sigmoidal_drift | Analyse sigmoidal-drift kinetics across NIRS channels |
| apply_interval_groups | Apply grouping to intervals |
| apply_span | apply span to resolved times and build interval_spec data... |
| artinis_intervals.xlsx | 10 Hz Artinis Oxysoft export recorded with Oxymon MKIII |
| as_data_list | Coerce 'data' input to a named list of data frames |
| as_mnirs_interval | coerce raw values to mnirs_interval objects |
| as_plot_data | Validate and bind a list of mnirs data frames for plotting |
| biexp_core | Biexponential model with gradient |
| biexp_init | Initiate self-starting biexponential model |
| biexponential | Biexponential function |
| biexp_start | Grid-profiled starting estimates for the biexponential model |
| breaks_timespan | Breaks for time span data |
| build_fit_results | Assemble a fitted channel result |
| build_kinetics_results | Gather per-interval 'mnirs_kinetics' into results structure |
| build_na_results | Build a standardised NA result for a failed channel |
| build_ss_formula | Build a self-start model formula with optional fixed... |
| by_time | Specify interval boundaries by time, label, lap, or sample |
| clean_channel_names | Clean legend trace names to syntactic column names |
| clean_cnd_message | Flatten a captured condition message |
| compute_diagnostics | Compute model diagnostics |
| compute_helpers | Computes rolling local values |
| convert_type | Coerce column types by role: nirs numeric, event integer,... |
| correct_blood_volume | Correct for blood volume changes |
| count_decimals | Count maximum decimal places across a numeric vector |
| count_sigfigs | Count maximum significant figures across a numeric vector |
| create_mnirs_data | Create an _mnirs_ data frame with metadata |
| detect_direction | Detect the direction of a response signal |
| detect_dttm_format | Detect the first 'dttm_opts' format matching a character... |
| detect_irregular_samples | Report warnings for unbalanced time_channel samples |
| detect_mnirs_device | Detect mnirs device from file metadata |
| detect_time_channel | Detect time_channel from column names or time-formatted... |
| device_patterns | Known channel names and detection patterns for supported... |
| dttm_opts | Datetime format strings for POSIXct parsing |
| embed_fit_call | Make an nls model call self-contained |
| enforce_direction | Enforce the requested direction on a converged parametric fit |
| ensemble_intervals | Ensemble average multiple intervals |
| example_mnirs | Get path to _mnirs_ example files |
| expdrift_init | Initiate self-starting exponential-drift model |
| expdrift_model | Exponential-drift model with gradient |
| expdrift_onset | Drift onset time of the exponential-drift model |
| expdrift_start | Grid-profiled starting estimates for the exponential-drift... |
| exponential_drift | Exponential-drift function |
| extract_df_list | Extract interval data by time range |
| extract_intervals | Extract intervals from _mnirs_ data |
| extract_start_timestamp | Extract earliest POSIXct value from file header metadata |
| filter_butterworth | Apply a Butterworth digital filter |
| filter_mnirs | Filter a data frame |
| filter_moving_average | Apply a moving average filter |
| find_header_row | Find the header row containing all 'nirs_channels' |
| find_interval_time | resolve a single mnirs_interval object to time values |
| find_kinetics_idx | Find valid model-fitting indices up to the first extreme |
| fit_biexponential | Fit a biexponential model to one channel |
| fit_control | Merge user nls control over a fit's internal defaults |
| fit_exponential_drift | Fit an exponential-drift model to one channel |
| fit_monoexponential | Fit a monoexponential model to one channel |
| fit_names | Alias fit column names that collide with model parameters |
| fit_sigmoidal | Fit a sigmoidal model to one channel |
| fit_sigmoidal_drift | Fit a sigmoidal-drift model to one channel |
| fit_td_fallback | Fit a self-start model with time-delay fallback |
| format_hmmss | Format time span data as h:mm:ss |
| free_params | Free parameters of a self-start model call |
| full_coefs | Combine fitted and fixed coefficients into the full parameter... |
| gompertz | Gompertz growth functions |
| gompertz_init | Initiate self-starting Gompertz model |
| hms_to_seconds | Convert H:MM(:SS.fff) strings to seconds of day |
| init_asymptotes | Estimate baseline and asymptote from the first/last quintile... |
| init_fixed | Wrap a self-start initialiser to support fixed parameters |
| init_inflection | Estimate inflection point from a smoothed first derivative |
| is_arg_map | Classify a per-channel/per-interval argument map |
| is_empty | Detect empty or NA strings |
| kinetics_annotations | Build per-panel kinetics marker and label annotations |
| kinetics_warnings_df | Zero-row kinetics warnings scaffold |
| logistic | Generalised logistic function |
| logistic_init | Initiate self-starting logistic model |
| map_mnirs_intervals | Apply an mnirs function over each interval of a... |
| mnirs_metadata | Metadata names of class '"mnirs"', retrieved with 'attr()' |
| mnirs-package | mnirs: Muscle Near-Infrared Spectroscopy Processing and... |
| monoexp_init | Initiate self-starting monoexponential model |
| monoexp_model | Monoexponential model with gradient |
| monoexponential | Monoexponential function |
| monoexp_start | Grid-profiled starting estimates for the monoexponential... |
| moxy_intervals.csv | 0.5 Hz Moxy onboard export |
| moxy_ramp.xlsx | 2 Hz PerfPro export of Moxy data |
| name_channels | Force names on character strings |
| normalise_interval_groups | Normalise custom interval grouping to a complete named list |
| oxysoft_sample_rate | Extract the export sample rate from Oxysoft header metadata |
| palette_mnirs | Custom _mnirs_ colour palette |
| parse_channel_name | Parse channel expressions for NSE |
| parse_dttm | Parse character date-times with one 'dttm_opts' format to... |
| parse_oxysoft_legend | Parse channel names from the Oxysoft "Legend" metadata block |
| parse_time_channel | Parse time_channel character or dttm to numeric seconds |
| peak_slope | Peak linear slope |
| pionirs_occlusion.ftn | 1 Hz PIONIRS NIRSBOX export |
| plot.mnirs | Plot _mnirs_ objects |
| plot.mnirs_kinetics | Plot _mnirs_ kinetics results |
| portamon_oxcap.xlsx | 10 Hz Artinis Oxysoft export recorded with Portamon |
| preserve_metadata | Zero-offset time values and add metadata |
| preserve_na | Preserve and restore NA information within a vector |
| print.mnirs | Methods for mnirs objects |
| print.mnirs_kinetics | Methods for mnirs_kinetics objects |
| read_file | Read raw data frame from file path |
| read_mnirs | Read _mnirs_ data from file |
| recycle_param | Recycle parameter to match number of events |
| recycle_span | recycle a single-element span to c(start, end) positive ->... |
| recycle_to_length | Recycle parameter list to target length |
| remove_empty_rows_cols | Remove Empty Rows and Columns |
| rename_duplicates | Rename duplicate strings in a vector with 'make.unique()' |
| replace_mnirs | Replace outliers, invalid, and missing values in _mnirs_ data |
| resample_mnirs | Re-sample an _mnirs_ data frame |
| rescale_mnirs | Rescale data range |
| resolve_channel_args | Resolve per-channel arguments |
| resolve_channels | Resolve channels from user input, device defaults, or the... |
| resolve_fixed_params | Resolve fixed parameters from a self-start model call |
| resolve_interval | resolve start/end into time value vectors (no span applied) |
| resolve_interval_args | Resolve per-interval arguments |
| response_time | Fractional response time |
| rolling_slope | Calculate rolling linear slope |
| scale_colour_mnirs | Scales for custom _mnirs_ palette |
| select_channels | Select, rename, and order channel columns |
| seq_range | Generate numeric sequence from range of a vector |
| setup_kinetics_worker | Shared validation prologue for analyse_<method>() workers |
| shift_mnirs | Shift data range |
| sigdrift_init | Initiate self-starting sigmoidal-drift model |
| sigdrift_model | Sigmoidal-drift model with gradient |
| sigdrift_onset | Drift onset time of the sigmoidal-drift model |
| sigdrift_rate | Rate constant of a sigmoidal shape |
| sigdrift_start | Starting estimates for the sigmoidal-drift model |
| sigdrift_texc | Excursion point of the sigmoidal-drift model |
| sigmoidal_drift | Sigmoidal-drift function |
| sigmoid_core | Sigmoid curve with gradient |
| signif_trailing | Format numbers for display as character strings |
| solve_grid3 | Batched 3-parameter least squares over a grid |
| split_kinetics_groups | Split interval data frames into sample groups |
| SSbiexponential | Self-starting biexponential model |
| SSexponential_drift | Self-starting exponential-drift model |
| SSgompertz | Self-starting Gompertz models |
| SSlogistic | Self-starting logistic model |
| SSmonoexponential | Self-starting monoexponential model |
| SSsigmoidal_drift | Self-starting sigmoidal-drift model |
| theme_mnirs | Custom _mnirs_ ggplot2 theme |
| train.red_intervals.csv | 10 Hz Train.Red App export |
| validate_findInt | wrap findInterval: informative 'time_channel' error message |
| validate_fix | Validate fixed model parameters |
| validate_group_channels | Validate and normalise channel grouping |
| validate_interval_channels | Validate per-group channel selections for ensemble-averaging |
| validate_kinetics_args | Validate resolved per-channel kinetics arguments |
| validate_mnirs | Validate '{mnirs}' parameters |
| validate_start_time | Validate start_time |
| warn_call | trim caller call to bare function name for warning headers... |
| warn_fit_failed | Warn on a failed or non-converged kinetics model fit |
| warn_map_keys | Warn about unmatched keys in an argument map |
| within | Detect if numeric values fall within range of a vector |
| wrap | Wrap vector elements |
| zero_offset_data | Recalculate time_channel values with zero offset at event... |
