Split table #62
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Split table #62
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ThierryO
commented
Sep 18, 2020
ThierryO
commented
- write_vc() gains an optional split_by argument.
- add vignette on the new split_by argument.
- read_vc(), is_git2rdata() and is_git2rmeta() now yield a better message when both the data and metadata are missing.
The old implementation yielded a "missing metadata" error when reading a non existing object. The new implementation yields a "missing object" error.
Handle the case where a file stored without split_by is replaced with a version with split_by and vice versa. Also check changes in split_by variables.
This simplifies the logical in write_vc() and read_vc()
This removes the digest dependency
Required to get tests running under R-devel.
florisvdh
reviewed
Sep 23, 2020
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Thanks for adding this @ThierryO .
I've read the vignette (see upcoming PR for smaller fixes) and did some small tests.
- In the vignette, best add something on the benefit of splitting. Why/when would a user consider this? What is the drawback of not splitting, in a workflow? I.e. if these are all related to filesize, then best explain why larger tsv files hinder the workflow. You could add it in the intro, or under a specific header. Otherwise I think the need for it may not be convincing enough.
- I got no errors when running the code, and from looking at resulting files, this seems fine 👍 . However the below test gave some unexpected results for the split case; you may want to have a look.
library(git2rdata)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following object is masked from 'package:git2rdata':
#>
#> pull
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(tidyr)
set.seed(123456)
testdata <-
data.frame(group1 = as.Date("2020-01-01"):as.Date("2020-01-10"),
group2 = 1:5,
id_sub = paste0("test",1:1e3)
) %>%
mutate(group1 = as.Date(group1, origin = "1970-01-01")) %>%
as_tibble %>%
expand(group1, group2, id_sub) %>%
mutate(var1 = rnorm(5e4),
var2 = runif(5e4))
testdata %>% write_vc("split/testdata",
sorting = c("group1", "group2", "id_sub"),
split_by = c("group2"))
#> 4516a4b1c2eee604b874ca03cb0c30a32c084ae7
#> "split/testdata.tsv"
#> 76c88bc1396a725758d4e0b513fe714130a91036
#> "split/testdata.yml"
read_vc("split/testdata") %>%
all.equal(testdata, check.attributes = FALSE)
#> [1] "Component \"group1\": Mean relative difference: 0.0001891192"
#> [2] "Component \"group2\": Mean relative difference: 0.6666667"
#> [3] "Component \"var1\": Mean relative difference: 1.357854"
#> [4] "Component \"var2\": Mean relative difference: 0.6434074"
testdata %>% write_vc("notsplit/testdata",
sorting = c("group1", "group2", "id_sub"))
#> 63958eb7da7077b1700d1605efa3d81c55c4770b
#> "notsplit/testdata.tsv"
#> 1da5da00e927938e1b4cc45e1108c67c4d2e7f40
#> "notsplit/testdata.yml"
read_vc("notsplit/testdata") %>%
all.equal(testdata, check.attributes = FALSE)
#> [1] TRUECreated on 2020-09-23 by the reprex package (v0.3.0)
Session info
devtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os Linux Mint 20
#> system x86_64, linux-gnu
#> ui X11
#> language nl_BE:nl
#> collate nl_BE.UTF-8
#> ctype nl_BE.UTF-8
#> tz Europe/Brussels
#> date 2020-09-23
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
#> backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
#> callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
#> devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
#> dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
#> generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
#> git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.2)
#> git2rdata * 0.3.0 2020-09-23 [1] local
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.2)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
#> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
#> pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
#> ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
#> reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2)
#> rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
#> rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
#> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
#> tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
#> tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
#> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
#> vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
#> xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
#>
#> [1] /home/floris/lib/R/library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
|
Thanks for the comments @florisvdh. The differences you get is because internally the |
Smaller changes in the split_by vignette
|
closes #45 |
|
Good idea @ThierryO 👍 , thanks for the explanation. Confirmed: library(git2rdata)
library(dplyr)
#>
#> Attaching package: 'dplyr'
#> The following object is masked from 'package:git2rdata':
#>
#> pull
#> The following objects are masked from 'package:stats':
#>
#> filter, lag
#> The following objects are masked from 'package:base':
#>
#> intersect, setdiff, setequal, union
library(tidyr)
set.seed(123456)
testdata <-
data.frame(group1 = as.Date("2020-01-01"):as.Date("2020-01-10"),
group2 = 1:5,
id_sub = paste0("test",1:1e3)
) %>%
mutate(group1 = as.Date(group1, origin = "1970-01-01")) %>%
as_tibble %>%
expand(group1, group2, id_sub) %>%
mutate(var1 = rnorm(5e4),
var2 = runif(5e4)) %>%
arrange(group1, group2, id_sub)
testdata %>% write_vc("split/testdata",
sorting = c("group1", "group2", "id_sub"),
split_by = c("group2"))
#> 4516a4b1c2eee604b874ca03cb0c30a32c084ae7
#> "split/testdata.tsv"
#> 76c88bc1396a725758d4e0b513fe714130a91036
#> "split/testdata.yml"
read_vc("split/testdata") %>%
arrange(group1, group2, id_sub) %>%
all.equal(testdata, check.attributes = FALSE)
#> [1] TRUECreated on 2020-09-23 by the reprex package (v0.3.0) Session infodevtools::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.0.2 (2020-06-22)
#> os Linux Mint 20
#> system x86_64, linux-gnu
#> ui X11
#> language nl_BE:nl
#> collate nl_BE.UTF-8
#> ctype nl_BE.UTF-8
#> tz Europe/Brussels
#> date 2020-09-23
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date lib source
#> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
#> backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2)
#> callr 3.4.4 2020-09-07 [1] CRAN (R 4.0.2)
#> cli 2.0.2 2020-02-28 [1] CRAN (R 4.0.2)
#> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
#> desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
#> devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
#> digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2)
#> dplyr * 1.0.2 2020-08-18 [1] CRAN (R 4.0.2)
#> ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
#> evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.2)
#> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
#> fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
#> generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2)
#> git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.2)
#> git2rdata * 0.3.0 2020-09-23 [1] local
#> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
#> highr 0.8 2019-03-20 [1] CRAN (R 4.0.2)
#> htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
#> knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2)
#> lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2)
#> magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2)
#> memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
#> pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2)
#> pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
#> pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
#> pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
#> prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
#> processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
#> ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2)
#> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
#> R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2)
#> remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
#> reprex 0.3.0 2019-05-16 [1] CRAN (R 4.0.2)
#> rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2)
#> rmarkdown 2.3 2020-06-18 [1] CRAN (R 4.0.2)
#> rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2)
#> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
#> stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
#> stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
#> testthat 2.3.2 2020-03-02 [1] CRAN (R 4.0.2)
#> tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2)
#> tidyr * 1.1.2 2020-08-27 [1] CRAN (R 4.0.2)
#> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
#> usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
#> vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2)
#> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
#> xfun 0.17 2020-09-09 [1] CRAN (R 4.0.2)
#> yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
#>
#> [1] /home/floris/lib/R/library
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library |
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