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Add helper function to add random missingness #298

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njtierney opened this issue Apr 5, 2022 · 1 comment · Fixed by #309
Closed

Add helper function to add random missingness #298

njtierney opened this issue Apr 5, 2022 · 1 comment · Fixed by #309
Labels
maintenance
Milestone
V1.1.0

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@njtierney
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rather than needing to do something like:

x <- 1:10
x
#>  [1]  1  2  3  4  5  6  7  8  9 10
x[sample(x = length(x), size = 5)] <- NA
x
#>  [1] NA NA  3 NA NA  6  7  8  9 NA

add_n_na <- function(x, n_na){
  x[sample(x = vctrs::vec_size(x), size = n_na)] <- NA
  x
}

x <- 1:10
x
#>  [1]  1  2  3  4  5  6  7  8  9 10
add_n_na(x, 3)
#>  [1]  1  2  3  4 NA  6  7 NA NA 10

Created on 2022-04-05 by the reprex package (v2.0.1)

Session info 
sessioninfo::session_info()
#> ─ Session info  🇻🇺  ⏺️  🕰️   ───────────────────────────────────────────────────
#>  hash: flag: Vanuatu, record button, mantelpiece clock
#> 
#>  setting  value
#>  version  R version 4.1.3 (2022-03-10)
#>  os       macOS Big Sur 11.2.2
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_AU.UTF-8
#>  ctype    en_AU.UTF-8
#>  tz       Australia/Melbourne
#>  date     2022-04-05
#>  pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version date (UTC) lib source
#>  backports     1.4.1   2021-12-13 [1] CRAN (R 4.1.1)
#>  cli           3.2.0   2022-02-14 [1] CRAN (R 4.1.1)
#>  crayon        1.5.1   2022-03-26 [1] CRAN (R 4.1.3)
#>  digest        0.6.29  2021-12-01 [1] CRAN (R 4.1.1)
#>  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.1.0)
#>  evaluate      0.15    2022-02-18 [1] CRAN (R 4.1.1)
#>  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.1.1)
#>  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.1.0)
#>  fs            1.5.2   2021-12-08 [1] CRAN (R 4.1.1)
#>  glue          1.6.2   2022-02-24 [1] CRAN (R 4.1.1)
#>  highr         0.9     2021-04-16 [1] CRAN (R 4.1.0)
#>  htmltools     0.5.2   2021-08-25 [1] CRAN (R 4.1.1)
#>  knitr         1.37    2021-12-16 [1] CRAN (R 4.1.1)
#>  lifecycle     1.0.1   2021-09-24 [1] CRAN (R 4.1.1)
#>  magrittr      2.0.2   2022-01-26 [1] CRAN (R 4.1.1)
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#>  R.utils       2.11.0  2021-09-26 [1] CRAN (R 4.1.1)
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#>  rlang         1.0.2   2022-03-04 [1] CRAN (R 4.1.1)
#>  rmarkdown     2.11    2021-09-14 [1] CRAN (R 4.1.1)
#>  rstudioapi    0.13    2020-11-12 [1] CRAN (R 4.1.0)
#>  sessioninfo   1.2.1   2021-11-02 [1] CRAN (R 4.1.1)
#>  stringi       1.7.6   2021-11-29 [1] CRAN (R 4.1.1)
#>  stringr       1.4.0   2019-02-10 [1] CRAN (R 4.1.1)
#>  styler        1.6.2   2021-09-23 [1] CRAN (R 4.1.1)
#>  tibble        3.1.6   2021-11-07 [1] CRAN (R 4.1.1)
#>  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.1.0)
#>  vctrs         0.3.8   2021-04-29 [1] CRAN (R 4.1.0)
#>  withr         2.5.0   2022-03-03 [1] CRAN (R 4.1.1)
#>  xfun          0.30    2022-03-02 [1] CRAN (R 4.1.1)
#>  yaml          2.3.5   2022-02-21 [1] CRAN (R 4.1.1)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@njtierney njtierney added this to the V0.7.0 milestone Oct 14, 2022
@njtierney
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set_prop_miss <- function(x, prop = 0.1) {
  x[sample(seq_along(x) <= prop * length(x))] <- NA
  x
}

set_n_miss <- function(x, n = 1) {
  x[sample(seq_along(x) <= n)] <- NA
  x
}

library(tidyverse)
library(naniar)

df <- tibble(
  x = rnorm(100),
  y = rpois(100, lambda = 5)
)

df
#> # A tibble: 100 × 2
#>         x     y
#>     <dbl> <int>
#>  1  1.53      4
#>  2  0.281     7
#>  3  0.609    10
#>  4  2.18      7
#>  5 -0.256     9
#>  6 -0.565     5
#>  7  0.827     4
#>  8 -0.878     4
#>  9 -1.14      8
#> 10  1.17      8
#> # … with 90 more rows

set_prop_miss(df$x, 0.1) %>% prop_miss()
#> [1] 0.1
set_prop_miss(df$x, 0.5) %>% prop_miss()
#> [1] 0.5
set_prop_miss(df$x, 0.75) %>% prop_miss()
#> [1] 0.75

set_n_miss(df$x, 2) %>% n_miss()
#> [1] 2
set_n_miss(df$x, 10) %>% n_miss()
#> [1] 10
set_n_miss(df$x, 50) %>% n_miss()
#> [1] 50

Created on 2023-01-31 with reprex v2.0.2

Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.1 (2022-06-23)
#>  os       macOS Monterey 12.3.1
#>  system   aarch64, darwin20
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       Australia/Hobart
#>  date     2023-01-31
#>  pandoc   2.19.2 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
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#>  backports       1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
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#>  cli             3.6.0      2023-01-09 [1] CRAN (R 4.2.0)
#>  colorspace      2.1-0      2023-01-23 [1] CRAN (R 4.2.0)
#>  crayon          1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
#>  DBI             1.1.3      2022-06-18 [1] CRAN (R 4.2.0)
#>  dbplyr          2.3.0      2023-01-16 [1] CRAN (R 4.2.0)
#>  digest          0.6.31     2022-12-11 [1] CRAN (R 4.2.0)
#>  dplyr         * 1.1.0      2023-01-29 [1] CRAN (R 4.2.1)
#>  ellipsis        0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
#>  evaluate        0.20       2023-01-17 [1] CRAN (R 4.2.0)
#>  fansi           1.0.4      2023-01-22 [1] CRAN (R 4.2.0)
#>  fastmap         1.1.0      2021-01-25 [1] CRAN (R 4.2.0)
#>  forcats       * 0.5.2      2022-08-19 [1] CRAN (R 4.2.0)
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#>  gargle          1.2.1      2022-09-08 [1] CRAN (R 4.2.0)
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#>  ggplot2       * 3.4.0      2022-11-04 [1] CRAN (R 4.2.0)
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#>  googlesheets4   1.0.1      2022-08-13 [1] CRAN (R 4.2.0)
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#>  haven           2.5.1      2022-08-22 [1] CRAN (R 4.2.0)
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#>  lubridate       1.9.1      2023-01-24 [1] CRAN (R 4.2.0)
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#>  munsell         0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
#>  naniar        * 0.6.1.9001 2023-01-31 [1] local
#>  pillar          1.8.1      2022-08-19 [1] CRAN (R 4.2.0)
#>  pkgconfig       2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
#>  purrr         * 1.0.1      2023-01-10 [1] CRAN (R 4.2.0)
#>  R.cache         0.16.0     2022-07-21 [1] CRAN (R 4.2.0)
#>  R.methodsS3     1.8.2      2022-06-13 [1] CRAN (R 4.2.0)
#>  R.oo            1.25.0     2022-06-12 [1] CRAN (R 4.2.0)
#>  R.utils         2.12.2     2022-11-11 [1] CRAN (R 4.2.0)
#>  R6              2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
#>  readr         * 2.1.3      2022-10-01 [1] CRAN (R 4.2.0)
#>  readxl          1.4.1      2022-08-17 [1] CRAN (R 4.2.0)
#>  reprex          2.0.2      2022-08-17 [1] CRAN (R 4.2.0)
#>  rlang           1.0.6      2022-09-24 [1] CRAN (R 4.2.0)
#>  rmarkdown       2.20       2023-01-19 [1] CRAN (R 4.2.0)
#>  rstudioapi      0.14       2022-08-22 [1] CRAN (R 4.2.0)
#>  rvest           1.0.3      2022-08-19 [1] CRAN (R 4.2.0)
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#>  sessioninfo     1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
#>  stringi         1.7.12     2023-01-11 [1] CRAN (R 4.2.0)
#>  stringr       * 1.5.0      2022-12-02 [1] CRAN (R 4.2.0)
#>  styler          1.9.0      2023-01-15 [1] CRAN (R 4.2.0)
#>  tibble        * 3.1.8      2022-07-22 [1] CRAN (R 4.2.0)
#>  tidyr         * 1.3.0      2023-01-24 [1] CRAN (R 4.2.0)
#>  tidyselect      1.2.0      2022-10-10 [1] CRAN (R 4.2.0)
#>  tidyverse     * 1.3.2      2022-07-18 [1] CRAN (R 4.2.0)
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#>  utf8            1.2.2      2021-07-24 [1] CRAN (R 4.2.0)
#>  vctrs           0.5.2      2023-01-23 [1] CRAN (R 4.2.0)
#>  visdat          0.6.0.9000 2022-12-13 [1] local
#>  withr           2.5.0      2022-03-03 [1] CRAN (R 4.2.0)
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#>  xml2            1.3.3      2021-11-30 [1] CRAN (R 4.2.0)
#>  yaml            2.3.7      2023-01-23 [1] CRAN (R 4.2.0)
#> 
#>  [1] /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

Note that add_n_miss and add_prop_miss are already functions for adding helper columns on the proportion and number of missing values to a dataset

njtierney added a commit that referenced this issue Jan 31, 2023
@njtierney
Implemented set_n_miss and set_prop_miss
5ffcca7 
- resolves #298
- added imports, `vctrs` and `cli` - which are both free dependencies as they are used within the already used tidyverse already.
@njtierney njtierney mentioned this issue Jan 31, 2023
Merged
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Implemented set_n_miss and set_prop_miss njtierney/naniar
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@njtierney