Reading two-line headers in R

Question

What is the best way to read a file into R when the header has two necessary lines for the header?

This happens to me all the time, as people often use one line for the column name and then include another line underneath it for the unit of measurement. I don't want to skip anything. I want the names and the units to carry through.

Here is what a typical file with two headers might look like:

trt   biomass    yield crop    Mg/ha    bu/ac C2      17.76   205.92 C2      17.96   207.86 CC      17.72   197.22 CC      18.42   205.20 CCW     18.15   200.51 CCW     17.45   190.59 P       3.09    0.00 P       3.34    0.00 S2      5.13    49.68 S2      5.36    49.72 

Answer 1

I would do two steps, assuming we know that the first row contains the labels, and there are always two headers.

header <- scan("file.txt", nlines = 1, what = character()) data <- read.table("file.txt", skip = 2, header = FALSE) 

Then add the character vector header on as the names component:

names(data) <- header 

For your data this would be

header <- scan("data.txt", nlines = 1, what = character()) data <- read.table("data.txt", skip = 2, header = FALSE) names(data) <- header  head(data)  >     head(data)   trt biomass  yield 1  C2   17.76 205.92 2  C2   17.96 207.86 3  CC   17.72 197.22 4  CC   18.42 205.20 5 CCW   18.15 200.51 6 CCW   17.45 190.59 

If you want the units, as per @DWin's answer, then do a second scan() on line 2

header2 <- scan("data.txt", skip = 1, nlines = 1, what = character()) names(data) <- paste0(header, header2)  > head(data)   trtcrop biomassMg/ha yieldbu/ac 1      C2        17.76     205.92 2      C2        17.96     207.86 3      CC        17.72     197.22 4      CC        18.42     205.20 5     CCW        18.15     200.51 6     CCW        17.45     190.59 

Answer 2

Use readLines with 2 for the limit, parse it, paste0 them together, then read in with read.table with skip =2 and header=FALSE (the default). Finish the process off with assignment of the column names:

dat <- "trt biomass yield  crop   Mg/ha   bu/ac  C2 17.76   205.92  C2 17.96   207.86  CC 17.72   197.22  CC 18.42   205.20  CCW    18.15   200.51  CCW    17.45   190.59  P  3.09    0.00  P  3.34    0.00  S2 5.13    49.68  S2 5.36    49.72  " 

You would probably use a file argument but using the text argument to the read-functions makes this more self-contained:

 readLines(textConnection(dat),n=2) #[1] "trt\tbiomass\tyield" "crop\tMg/ha\tbu/ac"   head2 <- read.table(text=readLines(textConnection(dat),n=2), sep="\t", stringsAsFactors=FALSE)  with(head2, paste0(head2[1,],head2[2,]) ) # [1] "trtcrop"      "biomassMg/ha" "yieldbu/ac"    joinheadrs <- with(head2, paste0(head2[1,],head2[2,]) )  newdat <- read.table(text=dat, sep="\t",skip=2) colnames(newdat)<- joinheadrs #------------------- > newdat    trtcrop biomassMg/ha yieldbu/ac 1       C2        17.76     205.92 2       C2        17.96     207.86 3       CC        17.72     197.22 4       CC        18.42     205.20 5      CCW        18.15     200.51 6      CCW        17.45     190.59 7        P         3.09       0.00 8        P         3.34       0.00 9       S2         5.13      49.68 10      S2         5.36      49.72 

Might be better to use paste with an underscore-sep:

joinheadrs <- with(head2, paste(head2[1,],head2[2,] ,sep="_")  ) joinheadrs #[1] "trt_crop"      "biomass_Mg/ha" "yield_bu/ac"