Skip to contents

Get raw data from a metabolic cart file or an imported spiro object

Source: R/spiro_raw.R
spiro_raw.Rd

spiro_raw() retrieves cardiopulmonary raw data from various types of metabolic cart files, or from objects previously imported and processed with spiro.

Usage

spiro_raw(data, device = NULL, anonymize = TRUE)

# S3 method for default
spiro_raw(data, device = NULL, anonymize = TRUE)

# S3 method for spiro
spiro_raw(data, device = NULL, anonymize = TRUE)

Arguments

data

Either the absolute or relative path of the file that contains the gas exchange data, or a data frame of the class spiro, usually the output of the spiro function.

device

A character string, specifying the device for measurement. By default the device type is guessed by the characteristics of the file. This can be overridden by setting the argument to "cortex", "cosmed", "vyntus" or "zan".

anonymize

Whether meta data should be anonymized during import. Defaults to TRUE. See get_anonid for more information.

Value

A data.frame with data. The attribute info contains addition meta-data retrieved from the original file.

Details

The default way of importing data into the spiro package is using the spiro function. Besides importing this will perform further processing steps such as the interpolation of data or the calculation of additional variables. But in some cases the original raw data may be preferable compared to the processed raw data. spiro_raw can either retrieve the raw data from an already imported data set or from a new raw data file.

Methods (by class)

  • spiro_raw(default): Method for direct import from metabolic cart raw data file

  • spiro_raw(spiro): Method for objects of class spiro, usually files previously imported and processed with spiro

Examples

# Get example data
file <- spiro_example("zan_gxt")

# direct import of raw data
out <- spiro_raw(file)
head(out)
#>    time VO2 VCO2    RR   VT    VE HR load PetO2 PetCO2
#> 1  3.44 393  320 13.62 0.79 10.76 NA    0    NA     NA
#> 2  7.25 434  345 15.76 0.67 10.51 NA    0    NA     NA
#> 3 10.73 440  352 17.14 0.76 12.96 NA    0    NA     NA
#> 4 13.97 582  451 18.63 0.65 12.13 NA    0    NA     NA
#> 5 17.20 837  677 18.47 1.07 19.71 NA    0    NA     NA
#> 6 20.39 902  753 18.87 1.19 22.42 NA    0    NA     NA

# retrieval of raw data from previously processed object
s <- spiro(file)
out2 <- spiro_raw(s)
head(out2)
#>    time VO2 VCO2    RR   VT    VE HR load PetO2 PetCO2
#> 1  3.44 393  320 13.62 0.79 10.76 NA    0    NA     NA
#> 2  7.25 434  345 15.76 0.67 10.51 NA    0    NA     NA
#> 3 10.73 440  352 17.14 0.76 12.96 NA    0    NA     NA
#> 4 13.97 582  451 18.63 0.65 12.13 NA    0    NA     NA
#> 5 17.20 837  677 18.47 1.07 19.71 NA    0    NA     NA
#> 6 20.39 902  753 18.87 1.19 22.42 NA    0    NA     NA