Reading two-line headers in R

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

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"  

Almost the same method to the other answers, just shortening to 2 statements:

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"

header <- sapply(read.table(text=dat, nrow=2), paste, collapse="_")
result <- read.table(text=dat, skip=2, col.names=header)

Result:

> head(result,2)
  trt_crop biomass_Mg/ha yield_bu/ac
1       C2         17.76      205.92
2       C2         17.96      207.86
...

A slightly different explained step by step approach:

1. Read only the first two lines of the files as data (without headers):

   headers <- read.table("data.txt", nrows=2, header=FALSE)
   

2. Create the headers names with the two (or more) first rows, sappy allows to make operations over the columns (in this case paste) - read more about sapply here :

   headers_names <- sapply(headers,paste,collapse="_")
   

3. Read the data of the files (skipping the first 2 rows):

   data <- read.csv(file="data.txt", skip = 2, header=FALSE)
   

4. And assign the headers of step two to the data:

   names(data) <- headers_names
   

---

The advantage is that you would have clear control of the the parameters of read.table (such as sep for commas, and stringAsFactors - for both the headers and the data)