Trying to write a function to combine multiple steps that are used regularly on an R dataframe. At the moment I stack individual lines, which is most inefficient. An Example each step I take at the moment
library(scores)
MscoreIndex <- 3
labMedians <- mapply(median, df[-1], na.rm = T) #calculate the median for each column except 1st
LabGrandMedian <- median(mapply(median, df[-1], na.rm = T),na.rm = T)
labMscore <- as.vector(round(abs(scores_na(labMedians, "mad")), digits = 2)) #calculate mscore by lab
labMscoreIndex <- which(labMscore > MscoreMax) #get the position in the vector that exceeds Mscoremax
df[-1][labMscoreIndex] <- NA # discharge values above threshold by making NA
An example my df below
structure(list(Determination_No = 1:6, `2` = c(55.94, 55.7, 56.59,
56.5, 55.98, 55.93), `3` = c(56.83, 56.54, 56.18, 56.5, 56.51,
56.34), `4` = c(56.39, 56.43, 56.53, 56.31, 56.47, 56.35), `5` = c(56.32,
56.29, 56.31, 56.32, 56.39, 56.32), `7` = c(56.48, 56.4, 56.54,
56.43, 56.73, 56.62), `8` = c(56.382, 56.258, 56.442, 56.258,
56.532, 56.264), `10` = c(56.3, 56.5, 56.2, 56.5, 56.7, 56.5),
`12` = c(56.11, 56.46, 56.1, 56.35, 56.36, 56.37)), class = "data.frame", row.names = c(NA,
-6L))
I started by trying to get the indivdual lab medians and the grandmedian with the following but got errors
I tried.
mediansFunction <- function(x){
analytemedians <- mapply(median(x[,-1]))
grandmedian <- median(x[,-1])
list(analytemedians,grandmedian)
}
mediansFunction(df)
But I get "Error in median.default(x[, -1]) : need numeric data"
Try :
mediansFunction <- function(x){
analytemedians <- sapply(x[-1], median)
median_of_median <- median(analytemedians)
grand_median <- median(as.matrix(x[-1]))
list(analytemedians = analytemedians,
median_of_median = median_of_median,
grand_median = grand_median)
}
mediansFunction(df)
#$analytemedians
# 2 3 4 5 7 8 10 12
#55.960 56.505 56.410 56.320 56.510 56.323 56.500 56.355
#$median_of_median
#[1] 56.3825
#$grand_median
#[1] 56.386