R:从具有稍微不同的列标题(不同空格)的txt文件中读取特定列并绑定它们？

Question

我有许多txt文件，它们在分隔为；的列中包含相同类型的数值数据。但是，有些文件有带有空格的列头，而有些没有(由不同的人创建)。有些有我不想要的额外栏目。

例如，一个文件可能有一个标题，如：

ASomeName; BSomeName; C(someName%) 

而另一个文件头可能是

A Some Name; B Some Name; C(someName%); D some name

在调用"read“命令之前，如何清除名称中的空格？

#These are the files I have

filenames<-list.files(pattern = "*.txt",recursive = TRUE,full.names = TRUE)%>%as_tibble()

#These are the columns I would like:

colSelect=c("Date","Time","Timestamp" ,"PM2_5(ug/m3)","PM10(ug/m3)","PM01(ug/m3)","Temperature(C)",  "Humidity(%RH)", "CO2(ppm)")

#This is how I read them if they have the same columns

ldf <- vroom::vroom(filenames, col_select = colSelect,delim=";",id = "sensor" )%>%janitor::clean_names()

清洁头脚本

我已经写了一个破坏性的脚本，它将读取整个文件，清除空格的标题，删除该文件并重写(vroom抱怨有时无法用相同的名称打开X数千个文件)文件。不是一种高效的做事方式。

cleanHeaders<-function(filename){
  d<-vroom::vroom(filename,delim=";")%>%janitor::clean_names()
  #print(head(d))
  if (file.exists(filename)) {
    #Delete file if it exists
    file.remove(filename)
  }
  vroom::vroom_write(d,filename,delim = ";")
}

lapply(filenames,cleanHeaders) 

Answer 1

fread的select参数允许整数索引。如果所需列始终位于相同位置，则您的工作就完成了。

colIndexes = c(1,3,4,7,9,18,21)
data = lapply(filenames, fread, select = colIndexes)

我想advice也有这种功能，但是由于您已经在选择您想要的列，所以我认为懒洋洋地评估您的字符列不会有任何帮助，所以我建议您坚持使用data.table。

但是，对于更健壮的解决方案，由于您无法控制表的结构:您可以读取每个文件的一行，捕获和清除列名，然后将它们与干净版本的colSelect向量相匹配。

library(data.table)
library(janitor)
library(purrr)

filenames <- list.files(pattern = "*.txt",
                        recursive = TRUE,
                        full.names = TRUE)

# read the first row of data to capture and clean the column names
clean_col_names <- function(filename){
  colnames(janitor::clean_names(fread(filename, nrow = 1)))
}

clean_column_names <- map(.x = filenames, 
                          .f = clean_col_names)

# clean the colSelect vector
colSelect <- janitor::make_clean_names(c("Date",
                                         "Time",
                                         "Timestamp" ,
                                         "PM2_5(ug/m3)",
                                         "PM10(ug/m3)",
                                         "PM01(ug/m3)",
                                         "Temperature(C)",
                                         "Humidity(%RH)",
                                         "CO2(ppm)"))

# match each set of column names against the clean colSelect
select_indices <- map(.x = clean_column_names, 
                      .f = function(cols) match(colSelect, cols))

# use map2 to read only the matched indexes for each column
data <- purrr::map2(.x = filenames, 
                    .y = select_indices, 
                    ~fread(input = .x, select = .y))

(在这里，purrr可以很容易地被传统的lapply替换，我选择purrr是因为它更干净的公式符号)