data-raw/createInternalData.R

In thlytras/rspiro: Implementation of Spirometry Equations

# This script creates the sysdata.rda file, that includes the GLI lookup tables
# used to calculate the L, M, S splines.


# GLI-2012
lookup <- read.table(file="RLookupTable.csv", header = TRUE, sep = ",")
lookup$f <- reorder(lookup$f, match(lookup$f, unique(lookup$f)))
attr(lookup$f, "scores") <- NULL
names(lookup)[names(lookup)=="sex"] <- "gender"


# GLI global (2022) equations
library(readxl)
GLIgl_lookup <- lapply(1:6, function(i) as.data.frame(read_excel("gli_global_lookuptables_dec6.xlsx", i)[,1:4]))
for (i in 1:length(GLIgl_lookup)) names(GLIgl_lookup[[i]]) <- c("agebound", "Mspline", "Sspline", "Lspline")
l <- unique(sapply(GLIgl_lookup, nrow))
GLIgl_lookup <- do.call(rbind, GLIgl_lookup)
GLIgl_lookup$gender <- rep(1:2, each=l*3)  # 1 = Male, 2 = Female
GLIgl_lookup$f <- rep(c("FEV1", "FVC", "FEV1FVC"), each=l)


# JRS equations (2014)
JRS_sheets <- c(NA, "FEV1", "FVC", "VC", "FEV1FVC")
JRS_lookup <- do.call(rbind, lapply(2:5, function(i) {
  res <- suppressWarnings(as.data.frame(read_excel("1-s2.0-S2212534514000288-mmc1.xlsx", i, skip=2, col_types="numeric")))
  if (ncol(res)<7) {
    names(res) <- c("agebound", "Mspline", "Sspline", "Mspline", "Sspline")
    res$Lspline <- NA
    res <- rbind(res[,c(1,6,2,3)], res[,c(1,6,4,5)])
  } else {
    names(res) <- c("agebound", "Lspline", "Mspline", "Sspline", "Lspline", "Mspline", "Sspline")
    res <- rbind(res[,c(1:4)], res[,c(1,5:7)])
  }
  res$gender <- rep(1:2, each=nrow(res)/2)
  res$f <- JRS_sheets[i]
  res
}))


# GLI diffusing capacity equations (2017, corrected 2020)
GLIdiff_SI <- lapply(1:6, function(i) as.data.frame(read_excel("inline-supplementary-material-2.xlsx", i))[,-1])
GLIdiff_trad <- lapply(1:6, function(i) as.data.frame(read_excel("inline-supplementary-material-3.xlsx", i))[,-1])
l <- unique(sapply(GLIdiff_trad, nrow))
GLIdiff_lookup <- list(SI = do.call(rbind, GLIdiff_SI), trad = do.call(rbind, GLIdiff_trad))
names(GLIdiff_lookup$SI)[1] <- names(GLIdiff_lookup$trad)[1] <- "agebound"
GLIdiff_lookup$SI$gender <- GLIdiff_lookup$trad$gender <- rep(1:2, each=l)
GLIdiff_lookup$SI$f <- GLIdiff_lookup$trad$f <- rep(c("TLCO", "KCO", "VA"), each=l*2)


# Load the NHANES data:
NHtb45 <- read.table(file="NHtb45.csv", header = TRUE, sep = ",")
NHtb6 <- read.table(file="NHtb6.csv", header = TRUE, sep = ",")


cat("Creating sysdata.rda...\n")
usethis::use_data(NHtb45, NHtb6, lookup, GLIgl_lookup, JRS_lookup, GLIdiff_lookup, internal=TRUE)