Question 46395 in Debian Question posted in
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R + Arrow 10 : convert blank to numeric NA – Debian

Please have a look at the reprex at the end of the post.
I need to read a column as a string, perform several manipulations and then save convert it to a numerical column.
The blanks ("") in the string column give me a headache because arrow does not convert them to numerical missing values NA.

Does anybody know how to achieve that?
Many thanks

library(tidyverse)
library(arrow)
#> Some features are not enabled in this build of Arrow. Run `arrow_info()` for more information.
#> 
#> Attaching package: 'arrow'
#> The following object is masked from 'package:utils':
#> 
#>     timestamp


df <- tibble(x=rep(c("4000 -", "6000 -",  "", "8000 - "), 10),
             y=seq(1,10, length=40))

write_csv(df, "test_string.csv")


data <- open_dataset("test_string.csv",
                     format="csv",
                     skip=1,
                     schema=schema(x=string(), y=double()))


data2 <- data |>
    mutate(x= sub(" -.*", "", x)   ) |>
    mutate(x2=as.numeric(x)) |>
    collect() ## how to convert the blank to a numeric NA ?
#> Error in `collect()`:
#> ! Invalid: Failed to parse string: '' as a scalar of type double

#> Backtrace:
#>     ▆
#>  1. ├─dplyr::collect(mutate(mutate(data, x = sub(" -.*", "", x)), x2 = as.numeric(x)))
#>  2. └─arrow:::collect.arrow_dplyr_query(mutate(mutate(data, x = sub(" -.*", "", x)), x2 = as.numeric(x)))
#>  3.   └─base::tryCatch(...)
#>  4.     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
#>  5.       └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
#>  6.         └─value[[3L]](cond)
#>  7.           └─arrow:::augment_io_error_msg(e, call, schema = x$.data$schema)
#>  8.             └─rlang::abort(msg, call = call)
 


sessionInfo()
#> R version 4.2.2 (2022-10-31)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Debian GNU/Linux 11 (bullseye)
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.13.so
#> 
#> locale:
#>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
#>  [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
#>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#>  [1] arrow_10.0.0    forcats_0.5.2   stringr_1.4.1   dplyr_1.0.10   
#>  [5] purrr_0.3.5     readr_2.1.3     tidyr_1.2.1     tibble_3.1.8   
#>  [9] ggplot2_3.4.0   tidyverse_1.3.2
#> 
#> loaded via a namespace (and not attached):
#>  [1] lubridate_1.9.0     assertthat_0.2.1    digest_0.6.30      
#>  [4] utf8_1.2.2          R6_2.5.1            cellranger_1.1.0   
#>  [7] backports_1.4.1     reprex_2.0.2        evaluate_0.17      
#> [10] httr_1.4.4          highr_0.9           pillar_1.8.1       
#> [13] rlang_1.0.6         googlesheets4_1.0.1 readxl_1.4.1       
#> [16] R.utils_2.12.1      R.oo_1.25.0         rmarkdown_2.17     
#> [19] styler_1.8.0        googledrive_2.0.0   bit_4.0.4          
#> [22] munsell_0.5.0       broom_1.0.1         compiler_4.2.2     
#> [25] modelr_0.1.9        xfun_0.34           pkgconfig_2.0.3    
#> [28] htmltools_0.5.3     tidyselect_1.2.0    fansi_1.0.3        
#> [31] crayon_1.5.2        tzdb_0.3.0          dbplyr_2.2.1       
#> [34] withr_2.5.0         R.methodsS3_1.8.2   grid_4.2.2         
#> [37] jsonlite_1.8.3      gtable_0.3.1        lifecycle_1.0.3    
#> [40] DBI_1.1.3           magrittr_2.0.3      scales_1.2.1       
#> [43] vroom_1.6.0         cli_3.4.1           stringi_1.7.8      
#> [46] fs_1.5.2            xml2_1.3.3          ellipsis_0.3.2     
#> [49] generics_0.1.3      vctrs_0.5.0         tools_4.2.2        
#> [52] bit64_4.0.5         R.cache_0.16.0      glue_1.6.2         
#> [55] hms_1.1.2           parallel_4.2.2      fastmap_1.1.0      
#> [58] yaml_2.3.6          timechange_0.1.1    colorspace_2.0-3   
#> [61] gargle_1.2.1        rvest_1.0.3         knitr_1.40         
#> [64] haven_2.5.1

Created on 2022-11-07 with reprex v2.0.2

Tags:

2

Answers


  1. 0

    Try using the read_csv instead of open_dataset

    library(readr)
data <- read_csv("test_string.csv")
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  2. 0

    ifelse works here when all classes are correct (and not double()); if_else enforces this already, so we can use either.

    data |>
  mutate(x = sub(" -.*", "", x)) |>
  mutate(
    x = ifelse(x == "", NA_character_, x),  # also if_else works
    x2 = as.numeric(x)
  ) |>
  collect()
# # A tibble: 40 x 3
#    x         y    x2
#    <chr> <dbl> <dbl>
#  1 4000   1     4000
#  2 6000   1.23  6000
#  3 NA     1.46    NA
#  4 8000   1.69  8000
#  5 4000   1.92  4000
#  6 6000   2.15  6000
#  7 NA     2.38    NA
#  8 8000   2.62  8000
#  9 4000   2.85  4000
# 10 6000   3.08  6000
# # ... with 30 more rows
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