Custom suffixes don't work in dplyr::full_join with dtplyr::lazy_dt converted tibbles

[caparks2]

Custom suffixes given to the suffix argument in dplyr::full_join fail to be implemented in the returned data frame when the x and y input data frames are first converted with dtplyr::lazy_dt. This appears to be related to closed Issue #40, which was fixed in Pull Request #48.

# Mini example data sets
df.CD4 <- tibble::tribble(
  ~cdr3_amino_acid, ~v_resolved, ~j_resolved, ~reads,
  "CASRATSGRAYEQYF", "TRBV3", "TRBJ2-7", 10,
  "CASSPTPGQVNYGYTF", "TRBV4-1", "TRBJ1-2", 4,
  "CASSLGLAGLYEQYF", "TRBV5-1", "TRBJ2-7", 3,
  "CASRPTGTGELFF", "TRBV11-3", "TRBJ2-2", 3,
  "CASSDLQGEGEQYF", "TRBV2-1", "TRBJ2-7", 2,
  "CSARFPSVAVYNEQFF", "TRBV20", "TRBJ2-1", 2,
  "CASRDRGSYGYTF", "TRBV2-1", "TRBJ1-2", 1,
  "CASSAGTSGGSGDTQYF", "TRBV9-1", "TRBJ2-3", 1,
  "CASSGQGAQEQYF", "TRBV6-6", "TRBJ2-7", 1,
  "CASSSTSAGTDTQYF", "TRBV12", "TRBJ2-3", 1
)

df.CD8 <- tibble::tribble(
  ~cdr3_amino_acid, ~v_resolved, ~j_resolved, ~reads,
  "CASRPTGTGELFF", "TRBV11-3", "TRBJ2-2", 100,
  "CASRATSGRAYEQYF", "TRBV3", "TRBJ2-7", 80,
  "CASSDLQGEGEQYF", "TRBV2-1", "TRBJ2-7", 30,
  "CASSPTPGQVNYGYTF", "TRBV4-1", "TRBJ1-2", 10,
  "CASSLGLAGLYEQYF", "TRBV5-1", "TRBJ2-7", 4,
  "CSARFPSVAVYNEQFF", "TRBV20", "TRBJ2-1", 2,
  "CASSFDRDGYGYTF", "TRBV7-2", "TRBJ1-2", 2,
  "CASSEEVWGYTF", "TRBV6-1", "TRBJ1-2", 1,
  "CASTQSNTGELFF", "TRBV6-1", "TRBJ2-2", 1,
  "CASSPLTGPGREQFF", "TRBV18-1", "TRBJ2-1", 1
)

# use data.table back-end for dplyr
dt.CD4 <- dtplyr::lazy_dt(
  x = df.CD4,
  key_by = c("cdr3_amino_acid", "v_resolved", "j_resolved")
)

dt.CD8 <- dtplyr::lazy_dt(
  x = df.CD8,
  key_by = c("cdr3_amino_acid", "v_resolved", "j_resolved")
)

# inner_join
dt.inner <- dplyr::inner_join(
  x = dt.CD4, y = dt.CD8,
  by = c("cdr3_amino_acid", "v_resolved", "j_resolved"),
  suffix = c(".CD4", ".CD8")
)

# inner_join works with custom suffixes
dt.inner
#> Source: local data table [6 x 5]
#> Call:   setnames(`_DT1`[`_DT2`, on = .(cdr3_amino_acid, v_resolved, j_resolved), 
#>     nomatch = NULL, allow.cartesian = TRUE], c("reads", "i.reads"
#> ), c("reads.CD4", "reads.CD8"))
#> 
#>   cdr3_amino_acid  v_resolved j_resolved reads.CD4 reads.CD8
#>   <chr>            <chr>      <chr>          <dbl>     <dbl>
#> 1 CASRATSGRAYEQYF  TRBV3      TRBJ2-7           10        80
#> 2 CASRPTGTGELFF    TRBV11-3   TRBJ2-2            3       100
#> 3 CASSDLQGEGEQYF   TRBV2-1    TRBJ2-7            2        30
#> 4 CASSLGLAGLYEQYF  TRBV5-1    TRBJ2-7            3         4
#> 5 CASSPTPGQVNYGYTF TRBV4-1    TRBJ1-2            4        10
#> 6 CSARFPSVAVYNEQFF TRBV20     TRBJ2-1            2         2
#> 
#> # Use as.data.table()/as.data.frame()/as_tibble() to access results

# full_join
dt.full <- dplyr::full_join(
  x = dt.CD4, y = dt.CD8,
  by = c("cdr3_amino_acid", "v_resolved", "j_resolved"),
  suffix = c(".CD4", ".CD8")
)

# the custom suffixes ".CD4" and ".CD8" didn't work in full_join
#   it used the default ".x" and ".y" suffixes instead.
dt.full
#> Source: local data table [14 x 5]
#> Call:   merge(`_DT1`, `_DT2`, all = TRUE, by.x = c("cdr3_amino_acid", 
#> "v_resolved", "j_resolved"), by.y = c("cdr3_amino_acid", "v_resolved", 
#> "j_resolved"), allow.cartesian = TRUE)
#> 
#>   cdr3_amino_acid   v_resolved j_resolved reads.x reads.y
#>   <chr>             <chr>      <chr>        <dbl>   <dbl>
#> 1 CASRATSGRAYEQYF   TRBV3      TRBJ2-7         10      80
#> 2 CASRDRGSYGYTF     TRBV2-1    TRBJ1-2          1      NA
#> 3 CASRPTGTGELFF     TRBV11-3   TRBJ2-2          3     100
#> 4 CASSAGTSGGSGDTQYF TRBV9-1    TRBJ2-3          1      NA
#> 5 CASSDLQGEGEQYF    TRBV2-1    TRBJ2-7          2      30
#> 6 CASSEEVWGYTF      TRBV6-1    TRBJ1-2         NA       1
#> # … with 8 more rows
#> # ℹ Use `print(n = ...)` to see more rows
#> 
#> # Use as.data.table()/as.data.frame()/as_tibble() to access results

# downstream code relying on custom suffixes in full_join is now broken.
dplyr::mutate(dt.full, dplyr::across(
  .cols = tidyr::matches("\\.CD4|\\.CD8"),
  .fns = ~ tidyr::replace_na(.x, 0)
))
#> Error in fcoalesce(reads.CD4, 0): object 'reads.CD4' not found

^{Created on 2022-08-04 by the reprex package (v2.0.1)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.0 (2022-04-22)
#>  os       macOS Big Sur/Monterey 10.16
#>  system   x86_64, darwin17.0
#>  ui       X11
#>  language (EN)
#>  collate  en_US.UTF-8
#>  ctype    en_US.UTF-8
#>  tz       America/New_York
#>  date     2022-08-04
#>  pandoc   2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version     date (UTC) lib source
#>  cli           3.3.0       2022-04-25 [1] CRAN (R 4.2.0)
#>  crayon        1.5.1       2022-03-26 [1] CRAN (R 4.2.0)
#>  data.table    1.14.3      2022-08-04 [1] local
#>  digest        0.6.29      2021-12-01 [1] CRAN (R 4.2.0)
#>  dplyr         1.0.99.9000 2022-08-04 [1] Github (tidyverse/dplyr@0dd7eea)
#>  dtplyr        1.2.1.9000  2022-08-04 [1] Github (tidyverse/dtplyr@cf7c2d8)
#>  evaluate      0.15        2022-02-18 [1] CRAN (R 4.2.0)
#>  fansi         1.0.3       2022-03-24 [1] CRAN (R 4.2.0)
#>  fastmap       1.1.0       2021-01-25 [1] CRAN (R 4.2.0)
#>  fs            1.5.2       2021-12-08 [1] CRAN (R 4.2.0)
#>  generics      0.1.3       2022-07-05 [1] CRAN (R 4.2.0)
#>  glue          1.6.2       2022-02-24 [1] CRAN (R 4.2.0)
#>  highr         0.9         2021-04-16 [1] CRAN (R 4.2.0)
#>  htmltools     0.5.3       2022-07-18 [1] CRAN (R 4.2.0)
#>  knitr         1.39        2022-04-26 [1] CRAN (R 4.2.0)
#>  lifecycle     1.0.1       2021-09-24 [1] CRAN (R 4.2.0)
#>  magrittr      2.0.3       2022-03-30 [1] CRAN (R 4.2.0)
#>  pillar        1.8.0       2022-07-18 [1] CRAN (R 4.2.0)
#>  pkgconfig     2.0.3       2019-09-22 [1] CRAN (R 4.2.0)
#>  purrr         0.3.4       2020-04-17 [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       2.12.0      2022-06-28 [1] CRAN (R 4.2.0)
#>  R6            2.5.1       2021-08-19 [1] CRAN (R 4.2.0)
#>  rematch2      2.1.2       2020-05-01 [1] CRAN (R 4.2.0)
#>  reprex        2.0.1       2021-08-05 [1] CRAN (R 4.2.0)
#>  rlang         1.0.4       2022-07-12 [1] CRAN (R 4.2.0)
#>  rmarkdown     2.14        2022-04-25 [1] CRAN (R 4.2.0)
#>  rstudioapi    0.13        2020-11-12 [1] CRAN (R 4.2.0)
#>  sessioninfo   1.2.2       2021-12-06 [1] CRAN (R 4.2.0)
#>  stringi       1.7.8       2022-07-11 [1] CRAN (R 4.2.0)
#>  stringr       1.4.0       2019-02-10 [1] CRAN (R 4.2.0)
#>  styler        1.7.0       2022-03-13 [1] CRAN (R 4.2.0)
#>  tibble        3.1.8       2022-07-22 [1] CRAN (R 4.2.0)
#>  tidyr         1.2.0       2022-02-01 [1] CRAN (R 4.2.0)
#>  tidyselect    1.1.2.9000  2022-08-04 [1] Github (r-lib/tidyselect@190f80d)
#>  utf8          1.2.2       2021-07-24 [1] CRAN (R 4.2.0)
#>  vctrs         0.4.1.9000  2022-08-04 [1] Github (r-lib/vctrs@fe37f93)
#>  withr         2.5.0       2022-03-03 [1] CRAN (R 4.2.0)
#>  xfun          0.31        2022-05-10 [1] CRAN (R 4.2.0)
#>  yaml          2.3.5       2022-02-21 [1] CRAN (R 4.2.0)
#> 
#>  [1] /Users/xxxxxx/Library/R/x86_64/4.2/library
#>  [2] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

[markfairbanks]

Smaller reprex:

library(dplyr, w = FALSE)
library(dtplyr)

df1 <- lazy_dt(tibble(a = c("a", "b"), b = 1:2))
df2 <- lazy_dt(tibble(a = c("a", "b"), b = 3:4))

df1 %>%
  full_join(df2, by = "a", suffix = c(".one", ".two"))
#> Source: local data table [2 x 3]
#> Call:   merge(`_DT1`, `_DT2`, all = TRUE, by.x = "a", by.y = "a", allow.cartesian = TRUE)
#> 
#>   a       b.x   b.y
#>   <chr> <int> <int>
#> 1 a         1     3
#> 2 b         2     4
#> 
#> # Use as.data.table()/as.data.frame()/as_tibble() to access results

[eutwt]

Thanks for the bug report @caparks2 ! This should work on the GitHub version now

library(dplyr, w = FALSE)
library(dtplyr)

df1 <- lazy_dt(tibble(a = c("a", "b"), b = 1:2))
df2 <- lazy_dt(tibble(a = c("a", "b"), b = 3:4))

df1 %>%
  full_join(df2, by = "a", suffix = c(".one", ".two"))
#> Source: local data table [2 x 3]
#> Call:   merge(`_DT1`, `_DT2`, all = TRUE, by.x = "a", by.y = "a", allow.cartesian = TRUE, 
#>     suffixes = c(".one", ".two"))
#> 
#>   a     b.one b.two
#>   <chr> <int> <int>
#> 1 a         1     3
#> 2 b         2     4
#> 
#> # Use as.data.table()/as.data.frame()/as_tibble() to access results

^{Created on 2022-08-11 by the reprex package (v2.0.1.9000)}