Last updated: 2022-03-16
Checks: 5 2
Knit directory: codemapper/
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| Name | Class | Size |
|---|---|---|
| install_codemapper | function | 1.2 Kb |
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The results in this page were generated with repository version 193f2cb. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.
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Ignored files:
Ignored: .Renviron
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Ignored: .Rproj.user/
Ignored: _targets/
Ignored: all_lkps_maps.db
Ignored: all_lkps_maps.db.gz
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Ignored: tar_make.R
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Untracked: analysis/read3_read2_mapping.Rmd
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Modified: R/clinical_codes.R
Modified: _targets.R
Modified: analysis/index.Rmd
Modified: analysis/read2_read3_mapping.Rmd
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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 193f2cb | rmgpanw | 2022-03-16 | add notes re icd9-10 mapping, and reformatting function for ths mapping table |
| html | 193f2cb | rmgpanw | 2022-03-16 | add notes re icd9-10 mapping, and reformatting function for ths mapping table |
| Rmd | 84beb4f | rmgpanw | 2022-03-16 | update notes on read to icd10 mapping |
| html | 84beb4f | rmgpanw | 2022-03-16 | update notes on read to icd10 mapping |
| Rmd | e5c5381 | rmgpanw | 2022-03-10 | update mainly icd10-related codes. |
| Rmd | a64a35e | rmgpanw | 2022-03-10 | change arg quiet = TRUE to unrecognised_codes = “error”. Also updated tests (passing) |
| Rmd | dfbc621 | Chuin Ying Ung | 2022-02-22 | add mapping notes |
| html | dfbc621 | Chuin Ying Ung | 2022-02-22 | add mapping notes |
| html | d777258 | Chuin Ying Ung | 2022-02-22 | merge with dev_cy branch |
| Rmd | 5b80a79 | Chuin Ying Ung | 2022-02-22 | update notes |
| html | 5b80a79 | Chuin Ying Ung | 2022-02-22 | update notes |
| html | 81047b4 | rmgpanw | 2022-02-17 | setup for gitlab CI with pkgdown site and test coverage; start adding read3 to snomed mapping |
| html | 5c2a3e3 | Chuin Ying Ung | 2022-02-17 | update _targets.R (housekeeping) and phecode.Rmd |
| Rmd | 919be0d | rmgpanw | 2021-10-07 | renamed functions and made shiny app for selecting codes |
| html | 919be0d | rmgpanw | 2021-10-07 | renamed functions and made shiny app for selecting codes |
| Rmd | 3fe5ae7 | rmgpanw | 2021-09-23 | initial commit |
Notes on adapting raw lookup and mapping tables for codemapper (see also pkgdown site)
Specify the location of required raw data files in a .Renviron file in the root directory of this project:
library(magrittr)
targets::tar_read(RENVIRON) %>%
readLines() %>%
purrr::map_chr( ~ stringr::str_replace(
string = .x,
pattern = "=.*$",
replacement = "="
)) %>%
stringr::str_c(sep = "",
collapse = "\n") %>%
cat()# Files loacted outside this repo --------
## TRUD
CTV3SCTMAP2=
## PheWAS
PHECODE_1_2_LKP=
PHECODE_1_2_ICD10_MAP=
PHECODE_1_2_ICD9_MAP=
# gitlab authorisation token --------
GITLAB_PAT=
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] magrittr_2.0.1 workflowr_1.6.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 pillar_1.6.3 compiler_4.1.0 bslib_0.3.1
[5] later_1.3.0 jquerylib_0.1.4 git2r_0.28.0 highr_0.9
[9] tools_4.1.0 targets_0.8.0 digest_0.6.28 jsonlite_1.7.2
[13] evaluate_0.14 lifecycle_1.0.1 tibble_3.1.4 pkgconfig_2.0.3
[17] rlang_0.4.11 igraph_1.2.6 rstudioapi_0.13 cli_3.0.1
[21] yaml_2.2.1 xfun_0.24 fastmap_1.1.0 withr_2.4.3
[25] stringr_1.4.0 knitr_1.34 fs_1.5.0 vctrs_0.3.8
[29] sass_0.4.0 tidyselect_1.1.1 rprojroot_2.0.2 data.table_1.14.2
[33] glue_1.4.2 R6_2.5.1 processx_3.5.2 fansi_0.5.0
[37] rmarkdown_2.11 callr_3.7.0 purrr_0.3.4 whisker_0.4
[41] codetools_0.2-18 ps_1.6.0 promises_1.2.0.1 ellipsis_0.3.2
[45] htmltools_0.5.2 renv_0.13.2 httpuv_1.6.3 utf8_1.2.2
[49] stringi_1.7.4 crayon_1.4.1