error in mcar_test due to singular data - maybe just a limitation to document

[LukasWallrich]

Thanks for adding mcar_test(). Unfortunately, the function fails for me due to singularity, regardless of how I slice my data. I am not sure whether that is a limitation of the test (which might then benefit from a clearer error message or documentation) or an issue with the implementation? Below a reprex with a small subset of the data, but I get the same issue with 185 rows

gapminder <- tibble::tribble(
  ~life_expectancy, ~fertility, ~population, ~gdp,          
   72.7,             1.9,        360830,      6650151639,   
   NA,               2.14,       1261319,     14178489076,  
   68.8,             2.28,       151616777,   82979485251,  
   75.2,             NA,         279566,      NA,           
   70.2,             1.46,       9492122,     26002131603,  
   80.1,             1.84,       10929978,    267143096398, 
   71.2,             NA,        321609,      1221526439,   
   60.8,             5.1,        9509798,     3336801340,   
   71.4,             2.38,       720246,      961365501.9,  
   71.8,             3.36,       9918245,     12240412986
)

naniar::mcar_test(gapminder)
#> Error: Problem with `mutate()` input `d2`.
#> x system is computationally singular: reciprocal condition number = 5.00265e-23
#> i Input `d2` is `purrr::pmap_dbl(...)`.
#> i The error occurred in group 1: miss_pattern = 1.

^{Created on 2021-04-07 by the reprex package (v1.0.0)}

[njtierney]

Hi there!

Thanks so much for posting a reprex for this issue.

It was indeed @andrewheiss who implemented this, so thanks to him! :)

I confirm that I am getting this issue as well,

 gapminder <- tibble::tribble(
  ~life_expectancy, ~fertility, ~population, ~gdp,          
  72.7,             1.9,        360830,      6650151639,   
  NA,               2.14,       1261319,     14178489076,  
  68.8,             2.28,       151616777,   82979485251,  
  75.2,             NA,         279566,      NA,           
  70.2,             1.46,       9492122,     26002131603,  
  80.1,             1.84,       10929978,    267143096398, 
  71.2,             NA,        321609,      1221526439,   
  60.8,             5.1,        9509798,     3336801340,   
  71.4,             2.38,       720246,      961365501.9,  
  71.8,             3.36,       9918245,     12240412986
)

naniar::mcar_test(gapminder)
#> Error: Problem with `mutate()` input `d2`.
#> x system is computationally singular: reciprocal condition number = 5.00265e-23
#> ℹ Input `d2` is `purrr::pmap_dbl(...)`.
#> ℹ The error occurred in group 1: miss_pattern = 1.

^{Created on 2021-04-20 by the reprex package (v2.0.0)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 4.0.3 (2020-10-10)
#>  os       macOS Big Sur 10.16         
#>  system   x86_64, darwin17.0          
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_AU.UTF-8                 
#>  ctype    en_AU.UTF-8                 
#>  tz       Australia/Perth             
#>  date     2021-04-20                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version    date       lib source            
#>  assertthat    0.2.1      2019-03-21 [1] standard (@0.2.1) 
#>  backports     1.2.1      2020-12-09 [1] standard (@1.2.1) 
#>  cli           2.4.0      2021-04-05 [1] CRAN (R 4.0.2)    
#>  colorspace    2.0-0      2020-11-11 [1] standard (@2.0-0) 
#>  crayon        1.4.1      2021-02-08 [1] CRAN (R 4.0.2)    
#>  DBI           1.1.1      2021-01-15 [1] CRAN (R 4.0.2)    
#>  digest        0.6.27     2020-10-24 [1] standard (@0.6.27)
#>  dplyr         1.0.5      2021-03-05 [1] CRAN (R 4.0.2)    
#>  ellipsis      0.3.1      2020-05-15 [1] standard (@0.3.1) 
#>  evaluate      0.14       2019-05-28 [1] standard (@0.14)  
#>  fansi         0.4.2      2021-01-15 [1] CRAN (R 4.0.2)    
#>  fs            1.5.0      2020-07-31 [1] standard (@1.5.0) 
#>  generics      0.1.0      2020-10-31 [1] standard (@0.1.0) 
#>  ggplot2       3.3.3      2020-12-30 [1] CRAN (R 4.0.2)    
#>  glue          1.4.2      2020-08-27 [1] standard (@1.4.2) 
#>  gtable        0.3.0      2019-03-25 [1] standard (@0.3.0) 
#>  highr         0.8        2019-03-20 [1] standard (@0.8)   
#>  htmltools     0.5.1.1    2021-01-22 [1] CRAN (R 4.0.2)    
#>  knitr         1.31       2021-01-27 [1] CRAN (R 4.0.2)    
#>  lifecycle     1.0.0      2021-02-15 [1] CRAN (R 4.0.2)    
#>  magrittr      2.0.1      2020-11-17 [1] standard (@2.0.1) 
#>  munsell       0.5.0      2018-06-12 [1] standard (@0.5.0) 
#>  naniar        0.6.0.9000 2020-12-23 [1] local             
#>  norm          1.0-9.5    2013-02-28 [1] CRAN (R 4.0.2)    
#>  pillar        1.5.1      2021-03-05 [1] CRAN (R 4.0.2)    
#>  pkgconfig     2.0.3      2019-09-22 [1] standard (@2.0.3) 
#>  purrr         0.3.4      2020-04-17 [1] standard (@0.3.4) 
#>  R6            2.5.0      2020-10-28 [1] standard (@2.5.0) 
#>  reprex        2.0.0      2021-04-02 [1] CRAN (R 4.0.2)    
#>  rlang         0.4.10     2020-12-30 [1] CRAN (R 4.0.2)    
#>  rmarkdown     2.7        2021-02-19 [1] CRAN (R 4.0.2)    
#>  rstudioapi    0.13       2020-11-12 [1] standard (@0.13)  
#>  scales        1.1.1      2020-05-11 [1] standard (@1.1.1) 
#>  sessioninfo   1.1.1      2018-11-05 [1] standard (@1.1.1) 
#>  stringi       1.5.3      2020-09-09 [1] standard (@1.5.3) 
#>  stringr       1.4.0      2019-02-10 [1] standard (@1.4.0) 
#>  styler        1.3.2      2020-02-23 [1] standard (@1.3.2) 
#>  tibble        3.1.0      2021-02-25 [1] CRAN (R 4.0.2)    
#>  tidyr         1.1.3      2021-03-03 [1] CRAN (R 4.0.2)    
#>  tidyselect    1.1.0      2020-05-11 [1] standard (@1.1.0) 
#>  utf8          1.2.1      2021-03-12 [1] CRAN (R 4.0.2)    
#>  vctrs         0.3.7      2021-03-29 [1] CRAN (R 4.0.3)    
#>  visdat        0.5.3      2019-02-15 [1] CRAN (R 4.0.2)    
#>  withr         2.4.1      2021-01-26 [1] CRAN (R 4.0.2)    
#>  xfun          0.22       2021-03-11 [1] CRAN (R 4.0.2)    
#>  yaml          2.2.1      2020-02-01 [1] standard (@2.2.1) 
#> 
#> [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

I've had a bit of a poke around, and it looks like this is happening when running solve here.

This sort of error can happen when you cannot invert a matrix - see this SE thread.

@andrewheiss have you run into this issue?

When I have time, I'll take a look at providing some suggested workarounds for this kind of problem, and trying to document some ways to avoid this.

[andrewheiss]

I have run into this issue, but haven't figured out a way around it yet. ☹️

[fmartinssp]

Hello everyone, everything good? Has anyone found a solution to this problem? I have yet to see any so far.

[lorenzoFabbri]

@andrewheiss
Has anyone looked into this? I keep receiving the following error messages for just one group of my dataset:

Error in `dplyr::mutate()`:
ℹ In argument: `d2 = purrr::pmap_dbl(...)`.
ℹ In group 1: `miss_pattern = 1`.
Caused by error in `purrr::pmap_dbl()`:
ℹ In index: 1.
Caused by error in `solve.default()`:
! Lapack routine dgesv: system is exactly singular: U[30,30] = 0