Package 'MFO'

Title: Maximal Fat Oxidation and Kinetics Calculation
Description: Calculate the maximal fat oxidation, the exercise intensity that elicits the maximal fat oxidation and the SIN model to represent the fat oxidation kinetics. Three variables can be obtained from the SIN model: dilatation, symmetry and translation. Examples of these methods can be found in Montes de Oca et al (2021) <doi:10.1080/17461391.2020.1788650> and Chenevière et al. (2009) <doi:10.1249/MSS.0b013e31819e2f91>.
Authors: Jorge R Fernandez-Santos [aut, cre] , Jesus G Ponce-Gonzalez [ctb] , Cristina Casals [ctb] , Jose L Gonzalez-Montesinos [ctb] , Juan Corral-Perez [ctb] , Alejandro Perez-Bey [ctb]
Maintainer: Jorge R Fernandez-Santos <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2025-02-28 03:01:34 UTC
Source: https://github.com/jorgedelro/mfo

Help Index

Basal test dataframe

Description

A dataframe with the results of a test to assess basal metabolism

Usage

data(basal_df)

Format

A data frame with 88 rows and 8 variables:

Time

time test, in minutess

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

breathe frequency, in breaths/min

VE

ventilation, in l/min

PETCO2

end-tidal carbondioxide pressure, in mmHg

Calculate steps

Description

Calculate steps

Usage

calculate_steps(step_time, db, db_type)

Arguments

step_time

how often the data was collected (in seconds).
db

a database
db_type

either "basal" or "MFO"

Calculation of CHO, FAT and Kcal

Description

Calculation of CHO, FAT and Kcal

Usage

calculate_vars(step_time, db_MFO, VO2max, author)

Arguments

step_time

how often the data was collected (in seconds).
db_MFO

dtabase with MFO test
VO2max

maximum oxygen uptake
author

eithe "Frayn" or "Jeukendrup"

Get a 5 minutes database

Description

Get a 5 minutes database

Usage

get_5min(db, cv_var, n_row)

Arguments

db

a database
cv_var

variable to calculate coefficient of variation
n_row

number of rows

Basal metabolic rate

Description

Basal metabolic rate

Usage

met_basal(step_time, db, cv_var)

Arguments

step_time

how often the data was collected (in seconds).
db

a database
cv_var

variable to calculate coefficient of variation

Maximal Fat Oxidation & Fat Max Function

Description

Maximal Fat Oxidation & Fat Max Function

Usage

MFO(
  step_time,
  db_MFO,
  db_basal,
  db_graded = NULL,
  cv_var,
  author,
  VO2max = 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.
cv_var

variable to estimate coefficient of variation. Can be: VO2, VCO2 or RER.
author

author to estimate MFO. Can be: Frayn or Jeukendrup.
VO2max

VO2max can be passed directly using this argument instead of use db_graded argument.

Value

Returns a list which contains:

  • MFO_db: database used to create the MFO plot.

  • MFO_plot: ggplot object with the MFO plot.

  • MFO: Maximal fat oxidation.

  • FAT_MAX: Intensity that elicits MFO.

  • x_CHO: carbohydrates in basal metabolism.

  • x_FAT: fat in basal metabolism.

  • x_Kcal: Kcal in basal metabolism.

Examples

## Not run: 
# Get old working directory
oldwd <- getwd()

# Set temporary directory
setwd(tempdir())

# 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",
                 VO2max = NULL)

# set user working directory
setwd(oldwd)

## End(Not run)

MFO test dataframe

Description

A dataframe with the results of a test to assess MFO metabolism

Usage

data(MFO_df)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 45 rows and 8 columns.

Variables

Time

time test, in minutess

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

VE

ventilation, in l/min

PETCO2

end-tidal carbondioxide pressure, in mmHg

Maximal Fat Oxidation Kinetics

Description

Maximal Fat Oxidation Kinetics

Usage

MFO_kinetics(MFO_data)

Arguments

MFO_data

a data frame obtained from MFO function

Value

Returns a list which contains:

  • MFO_kinetics_data: database used to create the MFO kinetics plot.

  • MFO_kinetics_plot: ggplot object with the MFO kinetics plot.

  • d: dilatation.

  • t: translation.

  • s: symmetry.

Examples

## Not run: 
# Get old working directory
oldwd <- getwd()

# Set temporary directory
setwd(tempdir())

# 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",
                 VO2max = NULL)

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

# set user working directory
setwd(oldwd)

## End(Not run)

Maximal Fat Oxidation calculation of multiple databases

Description

Maximal Fat Oxidation calculation of multiple databases

Usage

MFOs(
  from = c("folder", "files"),
  path,
  db_basal_name,
  db_MFO_name,
  db_graded_name,
  step_time,
  cv_var,
  author,
  VO2max = 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
)

Arguments

from

select or folder (basal, MFO and graded databases of the same participant are store in different files but in the same folder) or files (basal, MFO and graded databases of the same participant are store 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

author to estimate MFO. Can be: Frayn or Jeukendrup.
VO2max

VO2max can be passed directly using this argument instead of use db_graded argument. Default set to NULL.
remove_rows

An integer (or a vector of integers) representing the position of the rows to delete
col_name_VO2

name given to the variable VO2 in the databases. Must be the same for all databases. Default set to "VO2"
col_name_VCO2

name given to the variable VCO2 in the databases. Must be the same for all databases. Default set to "VCO2"
col_name_RER

name given to the variable RER in the databases. Must be the same for all databases. Default set to "RER"
col_name_HR

name given to the variable HR in the databases. Must be the same for all databases. Default set to "HR"
save_plot

to save the plot or not. Default set to True.
save_result

to save the results in a .xlsx file or not. Default set to True.

Value

This function creates an .xlsx file in the working directory with the following variables:

  • MFO_db: database used to create the MFO plot.

  • MFO_plot: ggplot object with the MFO plot.

  • MFO: Maximal fat oxidation.

  • FAT_MAX: Intensity that elicits MFO.

  • x_CHO: carbohydrates in basal metabolism.

  • x_FAT: fat in basal metabolism.

  • x_Kcal: Kcal in basal metabolism.

Examples

## Not run: 
# Get old working directory
oldwd <- getwd()

# Set temporary directory
setwd(tempdir())

# Create path to store databases
dir.create(paste(getwd(),"/MFO_databases", sep = ""))
# Get path to databases
path <- paste(getwd(),"/MFO_databases", sep = "")

# MFOs function
# "path" is the path to the databases
MFOs <- function(from = "folder",
                 path = path,
                 db_basal_name = "basal_df",
                 db_MFO_name = "MFO_df",
                 db_graded_name = "graded_df",
                 step_time = 20,
                 cv_var = "RER",
                 author = "Frayn",
                 VO2max = 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)

# set user working directory
setwd(oldwd)

## End(Not run)

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,
  col_name_VCO2,
  col_name_RER,
  col_name_HR,
  remove_rows = NULL
)

Arguments

from

select either from folder or files
path

path to the 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. Must be the same for all databases. Default set to "VO2"
col_name_VCO2

name given to the variable VCO2 in the databases. Must be the same for all databases. Default set to "VCO2"
col_name_RER

name given to the variable RER in the databases. Must be the same for all databases. Default set to "RER"
col_name_HR

name given to the variable HR in the databases. Must be the same for all databases. Default set to "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.

Graded exercise test dataframe

Description

A dataframe with the results of a graded exercise test

Usage

data(VO2max_df)

Format

An object of class tbl_df (inherits from tbl, data.frame) with 30 rows and 9 columns.

Variables

Time

time test, in minutess

HR

heart rate, in beats/min

Load

Load of the test, in watts

VO2

volume of oxygen consumption, in ml/min

VCO2

volume of exhaled carbon dioxide, in ml/min

RER

respiratory exchange ratio

VE

ventilation, in l/min

PETCO2

end-tidal carbondioxide pressure, in mmHg