Comments (1)
Bisaloo
commented on June 4, 2024
This is not necessary as names() is called by colnames() for data.frame.
Reprex confirming this:
library(outbreaks)
library(linelist)
## create linelist
x <- make_linelist(measles_hagelloch_1861,
id = "case_ID",
date_onset = "date_of_prodrome",
age = "age",
gender = "gender"
)
head(x)
#>
#> // linelist object
#> case_ID infector date_of_prodrome date_of_rash date_of_death age gender
#> 1 1 45 1861-11-21 1861-11-25 <NA> 7 f
#> 2 2 45 1861-11-23 1861-11-27 <NA> 6 f
#> 3 3 172 1861-11-28 1861-12-02 <NA> 4 f
#> 4 4 180 1861-11-27 1861-11-28 <NA> 13 m
#> 5 5 45 1861-11-22 1861-11-27 <NA> 8 f
#> 6 6 180 1861-11-26 1861-11-29 <NA> 12 m
#> family_ID class complications x_loc y_loc
#> 1 41 1 yes 142.5 100.0
#> 2 41 1 yes 142.5 100.0
#> 3 41 0 yes 142.5 100.0
#> 4 61 2 yes 165.0 102.5
#> 5 42 1 yes 145.0 120.0
#> 6 42 2 yes 145.0 120.0
#>
#> // tags: id:case_ID, date_onset:date_of_prodrome, gender:gender, age:age
colnames(x)[1] <- "case_label"
head(x)
#>
#> // linelist object
#> case_label infector date_of_prodrome date_of_rash date_of_death age gender
#> 1 1 45 1861-11-21 1861-11-25 <NA> 7 f
#> 2 2 45 1861-11-23 1861-11-27 <NA> 6 f
#> 3 3 172 1861-11-28 1861-12-02 <NA> 4 f
#> 4 4 180 1861-11-27 1861-11-28 <NA> 13 m
#> 5 5 45 1861-11-22 1861-11-27 <NA> 8 f
#> 6 6 180 1861-11-26 1861-11-29 <NA> 12 m
#> family_ID class complications x_loc y_loc
#> 1 41 1 yes 142.5 100.0
#> 2 41 1 yes 142.5 100.0
#> 3 41 0 yes 142.5 100.0
#> 4 61 2 yes 165.0 102.5
#> 5 42 1 yes 145.0 120.0
#> 6 42 2 yes 145.0 120.0
#>
#> // tags: id:case_label, date_onset:date_of_prodrome, gender:gender, age:ageCreated on 2023-10-11 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.3.1 (2023-06-16)
#> os Ubuntu 22.04.3 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US
#> collate en_GB.UTF-8
#> ctype en_GB.UTF-8
#> tz Europe/Paris
#> date 2023-10-11
#> pandoc 3.1.1 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> backports 1.4.1 2021-12-13 [1] RSPM
#> checkmate 2.2.0 2023-04-27 [1] RSPM
#> cli 3.6.1 2023-03-23 [1] RSPM
#> digest 0.6.33 2023-07-07 [1] CRAN (R 4.3.1)
#> dplyr 1.1.3 2023-09-03 [1] RSPM (R 4.3.1)
#> evaluate 0.22 2023-09-29 [1] RSPM (R 4.3.0)
#> fansi 1.0.5 2023-10-08 [1] RSPM (R 4.3.0)
#> fastmap 1.1.1 2023-02-24 [1] RSPM
#> fs 1.6.3 2023-07-20 [1] RSPM (R 4.3.1)
#> generics 0.1.3 2022-07-05 [1] RSPM
#> glue 1.6.2 2022-02-24 [1] RSPM
#> htmltools 0.5.6.1 2023-10-06 [1] RSPM (R 4.3.0)
#> knitr 1.44.1 2023-09-22 [1] Github (yihui/knitr@42f6b3a)
#> lifecycle 1.0.3 2022-10-07 [1] RSPM
#> linelist * 1.0.0 2023-10-11 [1] Github (epiverse-trace/linelist@e1aacba)
#> magrittr 2.0.3 2022-03-30 [1] RSPM
#> outbreaks * 1.9.0 2020-09-28 [1] RSPM (R 4.3.0)
#> pillar 1.9.0 2023-03-22 [1] RSPM
#> pkgconfig 2.0.3 2019-09-22 [1] RSPM
#> purrr 1.0.2.9000 2023-09-15 [1] Github (tidyverse/purrr@ac4f5a9)
#> R.cache 0.16.0 2022-07-21 [1] RSPM
#> R.methodsS3 1.8.2 2022-06-13 [1] RSPM
#> R.oo 1.25.0 2022-06-12 [1] RSPM
#> R.utils 2.12.2 2022-11-11 [1] RSPM
#> R6 2.5.1 2021-08-19 [1] RSPM
#> reprex 2.0.2 2022-08-17 [1] RSPM
#> rlang 1.1.1 2023-04-28 [1] RSPM (R 4.3.0)
#> rmarkdown 2.25 2023-09-18 [1] CRAN (R 4.3.1)
#> rstudioapi 0.15.0 2023-07-07 [1] CRAN (R 4.3.1)
#> sessioninfo 1.2.2 2021-12-06 [1] RSPM
#> styler 1.10.1 2023-06-05 [1] CRAN (R 4.3.1)
#> tibble 3.2.1 2023-03-20 [1] RSPM
#> tidyselect 1.2.0 2022-10-10 [1] RSPM
#> utf8 1.2.3 2023-01-31 [1] RSPM
#> vctrs 0.6.3 2023-06-14 [1] RSPM (R 4.3.0)
#> withr 2.5.1 2023-09-26 [1] RSPM (R 4.3.0)
#> xfun 0.40 2023-08-09 [1] RSPM (R 4.3.1)
#> yaml 2.3.7 2023-01-23 [1] RSPM (R 4.3.0)
#>
#> [1] /home/hugo/.local/share/R/x86_64-pc-linux-gnu-library/4.3
#> [2] /usr/local/lib/R/site-library
#> [3] /usr/lib/R/site-library
#> [4] /usr/lib/R/library
#>
#> ──────────────────────────────────────────────────────────────────────────────from linelist.
Related Issues (20)
- Consider whether tag loss should lead to error by default HOT 1
- Replace for loops by functional equivalents HOT 1
- R CMD CHECK: `set_tags` deprecated
- Release linelist 1.1.0
- Allow users to set a default for `lost_tags_action()` via an environment variable
- methods may need to pass through an appropriate `strict` argument to `modify_defaults()` HOT 1
- Merge conflict left in vignette
- Compatibility linelist-dplyr HOT 4
- Tweak README incidence plot HOT 1
- Document the meaning of each tag HOT 1
- Anonymisation and anonymity testing HOT 3
- Clarify policy on tag inclusion
- Tagging and validating aggregated epi data HOT 3
- Move dplyr to Suggests
- Release linelist 1.0.0
- Use rlang dynamic dots instead of custom solution
- Vectorize `tag_variable()`
- Add class to linelist tag loss conditions
- Typo in NEWS
- Deprecated templates in .github directory
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from linelist.