[SOLVED] improving a function to read files in a folder

Issue

I built this function:

alterations <- function() {
  
  if (!require(readr)) {install.packages("readr")}
  if (!require(stringr)) {install.packages("stringr")}
  if (!require(data.table)) {install.packages("data.table")}
  
  temp <- list.files(pattern = "*_automat.lif")
  dados <- NULL
  
  for (i in 1:length(temp)) {
    
    df1 <- fread(file = temp[[i]],
                 select = c(1, 18),
                 col.names = c("name", "classificador"))[order(name)]
    
    df2 <-fread(str_remove(temp[[i]], "_automat"),
                select = c(1, 18),
                col.names = c("name", "validador"))[order(name)]
    
    tb1 <- cbind(df1[, 2], df2[, 2]) %>%
      table()
    
    df3 <- cbind(ciclo = temp[[i]],
                 validation_date = str_sub(file.info(temp[[i]])$mtime, 1, 10), 
                 as.data.table(tb1))
    
    dados <- rbind(dados, df3)
  }
  
  write_csv(dados, file = "dados_brutos.csv")
  return(dados)
  
}

I need help to improve this function:

  1. I have a hundreds of files in a folder with the names as: aaa.lif, aaa_automat.lif, bbb.lif, bbb_automat.lif, ccc.lif, ccc.automat.lif, … that have the same columns and a thousands of rows, but different values in some columns (as column 18, specified in the code). I need bind the columns column 18 (classificador) of these files for the same column 1 (name). However, some files has a problem and didn’t have some rows in file *_automat.lif. I trying use merge in place of cbind to merge data.tables df1 and df2 by column name but time to execute the function was much worse.

  2. I don’t know if my for(){} if efficient, Is there a better way?

data example:

dput(df1)
setDT(structure(list(name = c("2020-12-01_00_34_54.029_1009_1943.png", 
"2020-12-01_00_34_54.029_1025_394.png", "2020-12-01_00_34_54.029_1077_1739.png", 
"2020-12-01_00_34_54.029_1345_631.png", "2020-12-01_00_34_54.029_1360_1538.png", 
"2020-12-01_00_34_54.029_1435_1340.png", "2020-12-01_00_34_54.029_1508_352.png"
), classificador = c("organism", "shadow", "coscinodiscus", "shadow", 
"shadow", "shadow", "shadow")), row.names = c(NA, -7L), class = c("data.table", 
"data.frame")))

dput(df2)
setDT(structure(list(name = c("2020-12-01_00_34_54.029_1009_1943.png", 
    "2020-12-01_00_34_54.029_1025_394.png", "2020-12-01_00_34_54.029_1077_1739.png", 
    "2020-12-01_00_34_54.029_1345_631.png", "2020-12-01_00_34_54.029_1360_1538.png", 
    "2020-12-01_00_34_54.029_1435_1340.png", "2020-12-01_00_34_54.029_1508_352.png"
    ), validador = c("shadow", "shadow", "coscinodiscus", "shadow", 
    "shadow", "shadow", "shadow")), row.names = c(NA, -7L), class = c("data.table", 
    "data.frame")))

output:

                                                  ciclo validation_date classificador     validador N
1: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09 coscinodiscus coscinodiscus 1
2: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09      organism coscinodiscus 0
3: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09        shadow coscinodiscus 0
4: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09 coscinodiscus        shadow 0
5: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09      organism        shadow 1
6: Basler_2020-12-01 00_34_52.441983_frames_automat.lif      2021-07-09        shadow        shadow 5
7: Basler_2020-12-01 01_35_01.902191_frames_automat.lif      2021-07-10        shadow        shadow 7

thank you

Solution

I think this comes pretty close to what you try to achieve.

files <- list.files(pattern = "*_automat.lif")

dados <- lapply(files, function(file) {
  
  df1 <- fread(file = file, select = c(1, 18), col.names = c("name", "classificador"))
  df2 <- fread(str_remove(file, "_automat"), select = c(1, 18), col.names = c("name", "validador"))
  
  tbl <- merge(df1, df2)
  tbl[, ciclo := file]
  tbl[, validation_date := str_sub(file.info(file)$mtime, 1, 10)]
  tbl
  
})

dados <- rbindlist(dados)

dados[, name := NULL]
setcolorder(dados, c("ciclo", "validation_date", "classificador", "validador"))

# from the output it seems you want to group and show counts
dados <- dados[, .(N = .N), by = .(ciclo, validation_date, classificador, validador)]

write_csv(dados, file = "dados_brutos.csv")

Answered By – Merijn van Tilborg

Answer Checked By – David Goodson (BugsFixing Volunteer)

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