Package 'MFO'

Basal test dataframe

Description

Synthetic breath-by-breath data from a 15-minute resting metabolic assessment. Simulates a moderately trained male cyclist (VO2max ~3200 mL/min) with an initial stabilization period followed by steady-state resting metabolism.

Usage

data(basal_df)

Format

A data frame with 45 rows and 8 variables:

Time

time test, in seconds (20s intervals)

HR

heart rate, in beats/min

VO2

volume of oxygen consumption, in mL/min

VCO2

volume of exhaled carbon dioxide, in mL/min

RER

respiratory exchange ratio

BF

breathing frequency, in breaths/min

VE

ventilation, in L/min

PETCO2

end-tidal carbon dioxide pressure, in mmHg

---

Calculate step means from raw data

Description

Generalized function that works with any step_time and step_duration. Extracts the last minute of each step (steady-state) for averaging.

Usage

calculate_vars(
  step_time,
  db_MFO,
  VO2max,
  author,
  step_duration = 180,
  steady_state_duration = 60,
  RER_cutoff = NULL
)

Arguments

step_time	how often the data was collected (in seconds).
db_MFO	data frame with MFO test (columns: VO2, VCO2, RER, HR).
VO2max	maximum oxygen uptake in ml/min.
author	equation set: "Frayn", "Jeukendrup", or "Peronnet".
step_duration	duration of each exercise step in seconds (default 180 = 3 min).
steady_state_duration	duration of steady-state period to average within each step, in seconds (default 60 = last minute).
RER_cutoff	RER value above which data is excluded (default NULL = no cutoff).

Value

data frame with columns: VO2, VCO2, HR, RER, CHO, FAT, Kcal (one row per step)

---

Calculate MFO using the MRER method (Perez-Martin et al.)

Description

Calculate MFO using the MRER method (Perez-Martin et al.)

Usage

fat_oxidation_MRER(VO2, RER)

Arguments

VO2	vector of oxygen consumption values (ml/min)
RER	vector of respiratory exchange ratio values

Value

fat oxidation rate in g/min

---

Basal metabolic rate

Description

Calculate basal metabolism from rest test data using a rolling window to identify the most metabolically stable 5-minute period.

Usage

met_basal(step_time, db, cv_var, window_duration = 300)

Arguments

step_time	how often the data was collected (in seconds).
db	a data frame with columns VO2, VCO2, RER, HR.
cv_var	variable to calculate coefficient of variation: "VO2", "VCO2" or "RER".
window_duration	duration of the stable window in seconds (default 300 = 5 min).

---

Maximal Fat Oxidation & FatMax Function

Description

Calculate Maximal Fat Oxidation (MFO), the exercise intensity that elicits MFO (FatMax), the FatMax zone, and the crossover point. Supports multiple curve-fitting methods (P3, P2, SIN, MRER) and stoichiometric equations (Frayn, Jeukendrup, Peronnet).

Usage

MFO(
  step_time,
  db_MFO,
  db_basal,
  db_graded = NULL,
  cv_var,
  author,
  VO2max = NULL,
  method = "P3",
  step_duration = 180,
  steady_state_duration = 60,
  RER_cutoff = NULL,
  negative_FAT = "truncate",
  body_mass = NULL,
  fat_free_mass = NULL,
  HRmax = NULL
)

Arguments

step_time	how often the data was collected (in seconds).
db_MFO	database containing MFO test.
db_basal	database containing basal test.
db_graded	database containing incremental exercise test (optional if VO2max provided).
cv_var	variable to estimate coefficient of variation. Can be: "VO2", "VCO2" or "RER".
author	author to estimate MFO. Can be: "Frayn", "Jeukendrup" or "Peronnet".
VO2max	VO2max can be passed directly (ml/min) instead of using db_graded.
method	curve-fitting method: "P3" (3rd-degree polynomial, default), "P2" (2nd-degree polynomial), or "MRER" (RER-based method of Perez-Martin et al.).
step_duration	duration of each exercise step in seconds (default 180 = 3 min).
steady_state_duration	duration of steady-state period to average within each step, in seconds (default 60).
RER_cutoff	RER value above which steps are excluded (default NULL = no cutoff). Recommended values: 1.0 (general), 0.93 (sedentary/obese), 0.90 (trained).
negative_FAT	how to handle negative fat oxidation values: "truncate" (set to 0, default), "exclude" (remove from fitting), or "keep" (include in fitting).
body_mass	body mass in kg (optional, for relative MFO calculation).
fat_free_mass	fat-free mass in kg (optional, for FFM-relative MFO calculation).
HRmax	maximum heart rate in bpm (optional, for FatMax as %HRmax).

Value

Returns a list which contains:

• MFO_db: database with Load, VO2, VCO2, HR, RER, CHO, FAT, Kcal, porc_VO2.

• MFO_plot: ggplot object with the MFO plot including FAT and CHO curves.

• MFO: Maximal fat oxidation (g/min).

• MFO_relative: MFO relative to body mass (mg/kg/min), if body_mass provided.

• MFO_FFM: MFO relative to fat-free mass (mg/kgFFM/min), if fat_free_mass provided.

• FAT_MAX: Intensity that elicits MFO (% VO2max).

• FAT_MAX_HR: Heart rate at FatMax (bpm), interpolated from data.

• FAT_MAX_porcHRmax: FatMax as % HRmax, if HRmax provided.

• FatMax_zone_lower: Lower bound of FatMax zone (% VO2max).

• FatMax_zone_upper: Upper bound of FatMax zone (% VO2max).

• crossover_point: Intensity at which CHO > FAT (% VO2max).

• R_squared: R-squared of the fitted model.

• RMSE: Root mean squared error of the fitted model.

• method: Method used for curve fitting.

• x_CHO: carbohydrates in basal metabolism (g/min).

• x_FAT: fat in basal metabolism (g/min).

• x_Kcal: Kcal in basal metabolism (kcal/min).

Examples

## Not run: 
# Read dfs
data(list = c("basal_df", "MFO_df", "VO2max_df"), package = "MFO")

# Convert to data.frame
basal_df <- data.frame(basal_df)
MFO_df <- data.frame(MFO_df)
VO2max_df <- data.frame(VO2max_df)

# Calculate MFO and Fatmax (P3 method)
result_MFO <- MFO(step_time = 20,
                 db_MFO = MFO_df,
                 db_basal = basal_df,
                 db_graded = VO2max_df,
                 cv_var = "RER",
                 author = "Frayn",
                 method = "P3")

# With all options
result_MFO <- MFO(step_time = 20,
                 db_MFO = MFO_df,
                 db_basal = basal_df,
                 db_graded = VO2max_df,
                 cv_var = "RER",
                 author = "Frayn",
                 method = "P3",
                 RER_cutoff = 1.0,
                 body_mass = 75,
                 fat_free_mass = 60,
                 HRmax = 190)

## End(Not run)

---

MFO test dataframe

Description

Synthetic breath-by-breath data from an incremental exercise test with 8 stages (25-200 W, 3 min per stage). Simulates a moderately trained male cyclist covering ~20-75% VO2max. The fat oxidation pattern shows a clear inverted U-shape with a peak around 35-40% VO2max, suitable for demonstrating P3, P2, MRER, and SIN model fitting.

Usage

data(MFO_df)

Format

A data frame with 72 rows and 8 variables:

Time

time test, in seconds (20s intervals)

HR

heart rate, in beats/min

VO2

volume of oxygen consumption, in mL/min

VCO2

volume of exhaled carbon dioxide, in mL/min

RER

respiratory exchange ratio

BF

breathing frequency, in breaths/min

VE

ventilation, in L/min

PETCO2

end-tidal carbon dioxide pressure, in mmHg

---

Maximal Fat Oxidation Kinetics (SIN Model)

Description

Fit the SIN model (Cheneviere et al., 2009) to describe fat oxidation kinetics and extract three parameters: dilatation (d), symmetry (s), and translation (t). Also calculates Fatmin (the intensity where fat oxidation becomes negligible), which is a unique capability of the SIN model over polynomial methods.

Usage

MFO_kinetics(MFO_data)

Arguments

MFO_data

a data frame obtained from the MFO function (must contain FAT and porc_VO2 columns).

Value

Returns a list which contains:

• MFO_kinetics_data: database used to create the MFO kinetics plot (original data plus normalized %MFO).

• MFO_kinetics_plot: ggplot object comparing basic and fitted SIN models.

• d: dilatation parameter (controls vertical scaling/width of the curve).

• t: translation parameter (horizontal shift along intensity axis).

• s: symmetry parameter (controls curve shape asymmetry; <1 left-skew, >1 right-skew).

• Fatmin: exercise intensity (% VO2max) at which fat oxidation becomes negligible.

• FatMax_SIN: exercise intensity (% VO2max) at peak fat oxidation from SIN model.

• R_squared: R-squared of the SIN model fit.

• RMSE: Root mean squared error of the SIN model fit.

• d_se: standard error of dilatation parameter.

• s_se: standard error of symmetry parameter.

• t_se: standard error of translation parameter.

• convergence: logical, whether the SIN model converged.

Examples

## Not run: 
# Read dfs
data(list = c("basal_df", "MFO_df", "VO2max_df"), package = "MFO")

# Convert to data.frame
basal_df <- data.frame(basal_df)
MFO_df <- data.frame(MFO_df)
VO2max_df <- data.frame(VO2max_df)

# Calculate MFO and Fatmax
result_MFO <- MFO(step_time = 20,
                 db_MFO = MFO_df,
                 db_basal = basal_df,
                 db_graded = VO2max_df,
                 cv_var = "RER",
                 author = "Frayn")

# Calculate MFO Kinetics
result_kinetics <- MFO_kinetics(result_MFO$MFO_db)

## End(Not run)

---

Maximal Fat Oxidation calculation of multiple databases

Description

Process multiple participants' MFO data in batch, generating plots and summary results. Supports all parameters from the MFO() and MFO_kinetics() functions.

Usage

MFOs(
  from = c("folder", "files"),
  path,
  db_basal_name,
  db_MFO_name,
  db_graded_name,
  step_time,
  cv_var,
  author,
  method = "P3",
  VO2max = NULL,
  step_duration = 180,
  steady_state_duration = 60,
  RER_cutoff = NULL,
  negative_FAT = "truncate",
  body_mass = NULL,
  fat_free_mass = NULL,
  HRmax = NULL,
  remove_rows = NULL,
  col_name_VO2 = "VO2",
  col_name_VCO2 = "VCO2",
  col_name_RER = "RER",
  col_name_HR = "HR",
  save_plot = TRUE,
  save_result = TRUE,
  output_format = "xlsx"
)

Arguments

from	select "folder" (basal, MFO and graded databases of the same participant are stored in different files but in the same folder) or "files" (basal, MFO and graded databases of the same participant are stored in one file but in different sheets)
path	path to the folder with the databases
db_basal_name	name given to the basal database, eg: "basal_df"
db_MFO_name	name given to the MFO database, eg: "MFO_df"
db_graded_name	name given to the graded database, eg: "VO2max_df"
step_time	how often the data was collected (in seconds).
cv_var	variable to estimate coefficient of variation. Can be: "VO2", "VCO2" or "RER".
author	equation set: "Frayn", "Jeukendrup" or "Peronnet".
method	curve-fitting method: "P3", "P2", or "MRER". Default "P3".
VO2max	VO2max can be passed directly (ml/min). Default NULL.
step_duration	duration of each exercise step in seconds (default 180).
steady_state_duration	duration of steady-state period within each step in seconds (default 60).
RER_cutoff	RER value above which steps are excluded (default NULL).
negative_FAT	how to handle negative fat oxidation: "truncate", "exclude", or "keep".
body_mass	body mass in kg (optional).
fat_free_mass	fat-free mass in kg (optional).
HRmax	maximum heart rate in bpm (optional).
remove_rows	rows to exclude from analysis.
col_name_VO2	column name for VO2 in databases. Default "VO2".
col_name_VCO2	column name for VCO2 in databases. Default "VCO2".
col_name_RER	column name for RER in databases. Default "RER".
col_name_HR	column name for HR in databases. Default "HR".
save_plot	save plots to MFO_plots/ directory (default TRUE).
save_result	save results file (default TRUE).
output_format	format for results file: "xlsx", "csv", or "rds". Default "xlsx".

Value

Data frame with one row per participant containing:

• ID: Participant identifier.

• MFO_g_min: Maximal fat oxidation (g/min).

• MFO_relative: MFO relative to body mass (mg/kg/min), if body_mass provided.

• MFO_FFM: MFO relative to fat-free mass (mg/kgFFM/min), if fat_free_mass provided.

• FAT_MAX_perVO2max: FatMax as % VO2max.

• FAT_MAX_HR: Heart rate at FatMax (bpm).

• FAT_MAX_porcHRmax: FatMax as % HRmax, if HRmax provided.

• FatMax_zone_lower: Lower bound of FatMax zone (% VO2max).

• FatMax_zone_upper: Upper bound of FatMax zone (% VO2max).

• crossover_point: Crossover intensity (% VO2max).

• R_squared: R-squared of the curve fit.

• d: SIN dilatation parameter.

• t: SIN translation parameter.

• s: SIN symmetry parameter.

• Fatmin: Fatmin from SIN model (% VO2max).

• FatMax_SIN: FatMax from SIN model (% VO2max).

• SIN_R_squared: R-squared of SIN model.

• CHO_g_basal: Basal CHO oxidation (g/min).

• FAT_g_basal: Basal FAT oxidation (g/min).

• Kcal_g_basal: Basal energy expenditure (kcal/min).

Examples

## Not run: 
# MFOs function
results <- MFOs(from = "folder",
                path = "/path/to/participant_data",
                db_basal_name = "basal_df",
                db_MFO_name = "MFO_df",
                db_graded_name = "graded_df",
                step_time = 20,
                cv_var = "RER",
                author = "Frayn",
                method = "P3")

## End(Not run)

---

Preprocess breath-by-breath data into fixed intervals

Description

Averages breath-by-breath data into fixed time intervals.

Usage

preprocess_bxb(db, target_interval = 20)

Arguments

db	data frame with breath-by-breath data. Must contain a "Time" column in seconds and columns for VO2, VCO2, RER, HR.
target_interval	target interval in seconds (default 20).

Value

data frame with data averaged into fixed intervals.

---

Read databases for MFO package

Description

Read databases for MFO package

Usage

read_MFO_databases(
  from = c("folder", "files"),
  path,
  db_basal_name,
  db_MFO_name,
  db_graded_name,
  col_name_VO2 = "VO2",
  col_name_VCO2 = "VCO2",
  col_name_RER = "RER",
  col_name_HR = "HR",
  remove_rows = NULL
)

Arguments

from	select either from "folder" or "files"
path	path to the databases
db_basal_name	name of the database with the basal metabolic rate test
db_MFO_name	name of the database of MFO test
db_graded_name	name of the database of the graded exercise test
col_name_VO2	name given to the variable VO2 in the databases. Default "VO2"
col_name_VCO2	name given to the variable VCO2 in the databases. Default "VCO2"
col_name_RER	name given to the variable RER in the databases. Default "RER"
col_name_HR	name given to the variable HR in the databases. Default "HR"
remove_rows	An integer (or a vector of integers) representing the position of the rows to delete

Value

Returns 3 databases:

• participant_db_basal: database with basal metabolism.

• participant_db_MFO: database with MFO test.

• participant_db_graded: graded exercise test.

---

Substrate oxidation equations

Description

Calculate fat and carbohydrate oxidation from VO2 and VCO2 using different stoichiometric equations.

Usage

substrate_oxidation(VO2, VCO2, author, VO2max = NULL)

Arguments

VO2	oxygen consumption in ml/min
VCO2	carbon dioxide production in ml/min
author	equation set: "Frayn", "Jeukendrup", or "Peronnet"
VO2max	maximum oxygen uptake in ml/min (required for Jeukendrup)

Value

Named list with CHO (g/min), FAT (g/min), Kcal (kcal/min)

---

Graded exercise test dataframe

Description

Synthetic breath-by-breath data from a graded exercise test to exhaustion (10 stages, 75-300 W). Simulates a moderately trained male cyclist reaching VO2max ~3200 mL/min and HRmax ~185 bpm. Used to determine VO2max when this value is not known a priori.

Usage

data(VO2max_df)

Format

A data frame with 30 rows and 9 variables:

Time

time test, in seconds (20s intervals)

HR

heart rate, in beats/min

Load

workload, in watts

VO2

volume of oxygen consumption, in mL/min

VCO2

volume of exhaled carbon dioxide, in mL/min

RER

respiratory exchange ratio

BF

breathing frequency, in breaths/min

VE

ventilation, in L/min

PETCO2

end-tidal carbon dioxide pressure, in mmHg

---