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Vyntus import update #15

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Merged
smnnlt merged 1 commit into from
Sep 8, 2025
Merged

Vyntus import update #15

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21 changes: 16 additions & 5 deletions R/spiro_get.R
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Original file line number Diff line number Diff line change
Expand Up @@ -416,7 +416,7 @@ spiro_get_cortex <- function(file) {
#' @noRd
spiro_get_vyntus <- function(file) {
# get head of file to find column names and start of data
head <- utils::read.delim(file, header = FALSE, nrows = 10)
head <- utils::read.delim(file, header = FALSE, nrows = 10, fileEncoding = "Latin1")

# sometimes the files will contain leading or trailing whitespaces
# complicating the character matching. These are removed first.
Expand All @@ -427,7 +427,7 @@ spiro_get_vyntus <- function(file) {
arr.ind = TRUE
)

data <- utils::read.delim(file, skip = colstart[[1]] - 1)[-1, ]
data <- utils::read.delim(file, skip = colstart[[1]] - 1, fileEncoding = "Latin1")[-1, ]
# remove whitespaces
data <- as.data.frame(apply(data, 2, trimws))
# remove first row if it containes empty values
Expand All @@ -445,13 +445,24 @@ spiro_get_vyntus <- function(file) {
VCO2 = get_data(data_mod, "V.CO2"),
RR = get_data(data_mod, c("BF", "FR")),
VT = get_data(data_mod, "VTex"),
VE = get_data(data_mod, c("V.E", "VeSTPD")),
VE = get_data(data_mod, c("V.E", "VeSTPD", "V.E..ST.")),
HR = get_data(data_mod, c("HR", "HF", "FC")),
load = get_data(data_mod, c("Load", "Last", "Vitesse", "Watt")),
PetO2 = get_data(data_mod, "PETO2") * 7.50062, # convert from kPa to mmHg
PetCO2 = get_data(data_mod, "PETCO2") * 7.50062 # convert from kPa to mmHg
PetO2 = get_data(data_mod, "PETO2") ,
PetCO2 = get_data(data_mod, "PETCO2")
)

# convert units for partial pressure if necessary
# get unit for PetO2 measurement
pet <- which(head == "PETO2", arr.ind = TRUE)
if (nrow(pet) > 0) {
pet_unit <- head[pet[1,1]+1, pet[1,2]]
if (pet_unit != "mmHg") { # if not in mmHg
df$PetO2 <- df$PetO2 * 7.50062 # convert from kPa to mmHg
df$PetO2 <- df$PetCO2 * 7.50062 # convert from kPa to mmHg
}
}

# use power data if velocity data is empty
if (all(df$load == 0, na.rm = TRUE)) df$load <- get_data(data_mod, c("Watt"))

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