r - fread 读取错误 "Expected sep (' ') but.."

Question

fread {data.table} 难以处理带有部分引用的行的制表符分隔文件。我找不到解决方法，因为它会自动处理引号(因此没有 quote 参数，就像 read.csv 一样)。这说明:

str1 = 'L1\tsome\tunquoted\tstuff\nL2\tsome\t"half" quoted\tstuff\nL3\tthis\t"should work"\tok thought'
str2 = gsub('"', '', str1)

fread(str2, sep='\t', header=F, skip=0L)
#    V1   V2          V3         V4
# 1: L1 some    unquoted      stuff
# 2: L2 some half quoted      stuff
# 3: L3 this should work ok thought
fread(str1, sep='\t', header=F, skip=0L)
# Error in fread(str1, sep = "\t", header = F, skip = 0L) : 
#   Expected sep (' ') but '
# ' ends field 3 on line 1 when detecting types: L2 some    "half" quoted   stuff

有没有办法解决这个问题，除了在原始文件上进行查找/替换？

Answer 1

怎么样stringi反而？很容易弄清楚，而且非常有效。还有一个功能stri_read_lines() , 用于从文件中读取/拆分行。

library(stringi)

as.data.frame(stri_split_fixed(stri_split_lines1(str1), "\t", simplify = TRUE))
#   V1   V2            V3         V4
# 1 L1 some      unquoted      stuff
# 2 L2 some "half" quoted      stuff
# 3 L3 this "should work" ok thought

如果您需要说服这是一种比 read.*() 更有效的方法，看看将上述方法应用于解析为 30k 行的扁平字符串时的时序。您还可以通过调整 as.data.frame() 中的参数来进一步加快速度。 .对于此示例，stringi方法的速度大约是 read.table() 的两倍.

str1 <- "L1\tsome\tunquoted\tstuff\nL2\tsome\t\"half\" quoted\tstuff\nL3\tthis\t\"should work\"\tok thought"

library(stringi)
library(microbenchmark)

write(stri_flatten(rep(str1, 1e5), collapse = "\n"))
file.info("data")[1]
#         size
# data 8400000

microbenchmark(
    stringi = {
        mat <- stri_split_fixed(stri_read_lines("data"), "\t", simplify = TRUE)
        out <- as.data.frame(mat)
    },
    read.table = {
        out2 <- read.table("data", sep = "\t", quote = "\n")
    },
    times = 3L,
    unit = "relative"
)

# Unit: relative
#        expr      min       lq     mean   median      uq      max neval cld
#     stringi 1.000000 1.000000 1.000000 1.000000 1.00000 1.000000     3  a 
#  read.table 2.074071 2.111722 1.997857 2.148897 1.96356 1.808365     3   b

identical(out, out2)
# [1] TRUE