Scraping PDF tables with empty Cells

I'm using R to pull data from PDFs and so far it has been going well. I just opened up a new batch of PDFs and saw that I have to figure out how to account for empty cells. I haven't found a way to do this, and I have hundreds of pages that I need to go through.

I've included some sample data. I haven't found a way to attach the PDFs here, and these are not posted on the web anywhere. I saved df as a CSV, then copied and pasted that into a word document which I saved as a CSV for this example. Screenshot attached as well.

library(pdftools)
library(tidyverse)

# Example data
df <- data.frame("rows" = c("row1", "row2", "row3", "row4", "row5", "row6", "row7", "row8", "row9", "row10"),
                 "col1" = c(1, 2, "", 4, 5, 6, 7, 8, 9, 10),
                 "col2" = c(1, 2, 3, 4, "", "", 7, 8, 9, ""),
                 "col3" = c(1, 2, "", 4, 5, 6, 7, 8, 9, 10),
                 "col4" = c(1, 2, 3, 4, 5, 6, 7, "", 9, 10),
                 "col5" = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10),
                 "col6" = c(1, 2, "", "", 5, 6, 7, "", 9, 10),
                 "col7" = c(1, 2, 3, 4, 5, "", 7, 8, 9, 10),
                 "col8" = c(1, "", 3, 4, 5, 6, 7, "", 9, 10),
                 "col9" = c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10)
                 )

# Save example data, then save as a PDF outside of R.
# write_csv(df, "sample_data.csv")


# read in the PDF
pdf_file <- pdf_text("sample_data.pdf")

data <- pdf_file[1]
data <- trimws(data)
data <- strsplit(data, "\r\n")
data <- data[[1]]
data <- str_split_fixed(data, " {2,}", 10)  ## I think this is the step that needs to change
data <- data.frame(data, stringsAsFactors = FALSE)



# Print out outs of the data for reference. 
> data
      X1   X2   X3   X4   X5   X6   X7   X8   X9  X10
1   rows col1 col2 col3 col4 col5 col6 col7 col8 col9
2   row1    1    1    1    1    1    1    1    1    1
3   row2    2    2    2    2    2    2    2    2     
4   row3    3    3    3    3    3    3               
5   row4    4    4    4    4    4    4    4    4     
6   row5    5    5    5    5    5    5    5    5     
7   row6    6    6    6    6    6    6    6          
8   row7    7    7    7    7    7    7    7    7    7
9   row8    8    8    8    8    8    8               
10  row9    9    9    9    9    9    9    9    9    9
11 row10   10   10   10   10   10   10   10   10   


 df
    rows col1 col2 col3 col4 col5 col6 col7 col8 col9
1   row1    1    1    1    1    1    1    1    1    1
2   row2    2    2    2    2    2    2    2         2
3   row3         3         3    3         3    3    3
4   row4    4    4    4    4    4         4    4    4
5   row5    5         5    5    5    5    5    5    5
6   row6    6         6    6    6    6         6    6
7   row7    7    7    7    7    7    7    7    7    7
8   row8    8    8    8         8         8         8
9   row9    9    9    9    9    9    9    9    9    9
10 row10   10        10   10   10   10   10   10   10

UPDATE: Adding dput(pdf_file)

> dput(pdf_file)
"rows  col1    col2   col3    col4    col5    col6    col7    col8    col9\r\nrow1        1      1       1       1       1       1       1       1       1\r\nrow2        2      2       2       2       2       2       2               2\r\nrow3               3               3       3               3       3       3\r\nrow4        4      4       4       4       4               4       4       4\r\nrow5        5              5       5       5       5       5       5       5\r\nrow6        6              6       6       6       6               6       6\r\nrow7        7      7       7       7       7       7       7       7       7\r\nrow8        8      8       8               8               8               8\r\nrow9        9      9       9       9       9       9       9       9       9\r\nrow10      10             10      10      10      10      10      10      10\r\n"

You can see that there is a difference between df and data at this point. I've tried playing around with a few things and I haven't been able to make anything work well enough to post here. I tried using some if/else logic to say that if there were 3 or more spaces, insert NA, but that just caused a bunch of errors so I abandoned that approach. My goal is to get the data as close to df as possible.

Try using read.fwf as a fixed-width file.

data <- pdf_file[1]
data <- trimws(data)
data <- strsplit(data, "\r\n")
data <- data[[1]]
writeLines(data, 'temp.txt')
result <- read.fwf('temp.txt', c(11, 2, rep(8, 8)), skip = 1, strip.white = TRUE)
names(result) <- scan(text = readLines('temp.txt', n = 1), what = character())
result

#    rows col1 col2 col3 col4 col5 col6 col7 col8 col9
#1   row1    1    1    1    1    1    1    1    1    1
#2   row2    2    2    2    2    2    2    2   NA    2
#3   row3   NA    3   NA    3    3   NA    3    3    3
#4   row4    4    4    4    4    4   NA    4    4    4
#5   row5    5   NA    5    5    5    5    5    5    5
#6   row6    6   NA    6    6    6    6   NA    6    6
#7   row7    7    7    7    7    7    7    7    7    7
#8   row8    8    8    8   NA    8   NA    8   NA    8
#9   row9    9    9    9    9    9    9    9    9    9
#10 row10   10   NA   10   10   10   10   10   10   10