SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

SIFT output filter

Description

This function takes as input the output file generated by the SIFT-MS and returns a .csv containing the TIME and the concentrations data selected by the user

Usage

SIFT_output_filter(
  setdir = getwd(),
  input_name = file.choose(),
  output_name,
  n_parameters = 2,
  param_names = c("Isoprene", "Acetone"),
  out_file = TRUE
)

Arguments

Value

Filtered data and optional csv from SIFT input

Examples

data(raw_SIFT)
SIFT_output_filter(input_name = raw_SIFT, output_name = "testfile", out_file = FALSE)

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_sift -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

data indexer

Description

This function takes as input a vector and return the data index according to the selected time frame

Usage

data_indexer(dat, time_frame_index = NA)

Arguments

Value

a vector indexed according to the specified time frame

Examples

data_indexer(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Data normalizer

Description

This function takes as input a vector and returns it normalized between a specified range

Usage

normalizer(dat, norm_range = c(0, 1))

Arguments

Value

vector normalized between norm_range

Examples

normalizer(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

SIPETool example files

Description

Raw and filtered output from SIFT-MS, and CPET system. Four different files are available: raw_SIFT -> raw data from SIFT-MS CPET_time -> data from CPET system for time allignment SIFT_time -> filtered data from SIFT-MS for time allignment SIFT_filtered -> raw data from SIFT-MS filtered using SIFT_output_filter

Sign detection

Description

This function takes as input a vector and returns the sign of each element

Usage

sign_detect(dat)

Arguments

Value

vector with the signs of each element of the original matrix

Examples

sign_detect(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Tidal analyzer

Description

This function takes as input a csv file containing a time column and data columns and returns the position of the end tidals for each data column maximazing the syncronization between data. This function was originally devised for the analysis of the end tidals coming from exhaled breath analyzed through SIFT-MS technology

Usage

tidal_analyzer(
  setdir = getwd(),
  input_name = file.choose(),
  output_name,
  starting_threshold = 0.03,
  time_frame = NA,
  out_file = TRUE
)

Arguments

Value

csv containing the end tidals, their maximum, average, frequency, and timing

Examples

data(SIFT_filtered)
tidal_analyzer(input_name = head(SIFT_filtered, n = 100), output_name = "out", out_file = FALSE)

Tidal finder

Description

This function takes as input a matrix and returns for each column the end tidals depending of the threshold set. It is possible to set a custom time frame for the search of the tidals. Note: a minimum amount of 45 points are necessary.

Usage

tidal_finder(
  dat,
  height_threshold = 0.2,
  refine = FALSE,
  time_frame_index = NA
)

Arguments

Value

matrix with the tidals for each column

Examples

tidal_finder(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))

Time_alignment

Description

This function takes as input two data set containing a time vector and a data vector and return the two data sets aligned. This is done by reducing the dimensions of the data set with higher points. The first data set is the one coming from the CPET-ESE and the second one from the SIFT-MS

Usage

time_filter(Cy = file.choose(), sift = file.choose())

Arguments

Value

A plot and the SIFT-MS data file resized for the alignment with the CPET-ESE file

Examples

data(SIFT_time)
data(CPET_time)
time_filter(CPET_time, SIFT_time)

Trend finder

Description

This function takes as input a vector and returns the trend of each column expressed as the difference between two consecutive elements

Usage

trend(dat)

Arguments

Value

vector containing the trend of the each column

Examples

trend(c(1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1,1:10,10:1))