Lists and matrix using sapply

问题

I have a perhaps basic questions and I have searched on the web. I have a problem reading files. Though, I managed to get to read my files, following @Konrad suggestions, which I appreciate: How to get R to read in files from multiple subdirectories under one large directory?

It is a similar problem, however, I have not resolved it.

My problem:

I have large number of files of with same name ("tempo.out") in different folders. This tempo.out has 5 columns/headers. And they are all the same format with 1048 lines and 5 columns:

id X Y time temp

setwd("~/Documents/ewat")
dat.files  <- list.files(path="./ress",
                 recursive=T,
                 pattern="tempo.out"
                 ,full.names=T)
readDatFile <- function(f) {
dat.fl <- read.table(f)  
 }

data.filesf <- sapply(dat.files, readDatFile)                         

# I might not have the right sintax in sub5:
subs5 <- sapply(data.filesf,`[`,5) 
matr5 <- do.call(rbind, subs5)   

probs <- c(0.05,0.1,0.16,0.25,0.5,0.75,0.84,0.90,0.95,0.99)
q <- rowQuantiles(matr5, probs=probs)
print(q)

I want to extract the fifth column (temp) of each of those thousands of files and make calculations such as quantiles.

I tried first to read all subfiles in "ress"

The latter gave no error, but my main problem is the "data.filesf" is not a matrix but list, and actually the 5th column is not what I expected. Then the following:

matr5 <- do.call(rbind, subs5)

is also not giving the required values/results.

What could be the best way to get columns into what will become a huge matrix?

回答1:

Try lapply(data.filef,[,,5) Hope this will help

回答2:

Consider extending your defined function, readDatFile, to extract fifth column, temp, and assign directly to matrix with sapply or vapply (since you know ahead the needed structure -numeric matrix length equal to nrows or 1048). Then, run needed rowQuantiles:

setwd("~/Documents/ewat")

dat.files  <- list.files(path="./ress",
                         recursive=T,
                         pattern="tempo.out",
                         full.names=T)

readDatFile <- function(f) read.table(f)$temp  # OR USE read.csv(f)[[5]]

matr5 <- sapply(dat.files, readDatFile, USE.NAMES=FALSE)                         
# matr5 <- vapply(dat.files, readDatFile, numeric(1048), USE.NAMES=FALSE)

probs <- c(0.05,0.1,0.16,0.25,0.5,0.75,0.84,0.90,0.95,0.99)
q <- rowQuantiles(matr5, probs=probs)

来源：https://stackoverflow.com/questions/45888935/lists-and-matrix-using-sapply

标签

list

matrix

dataframe

sapply