Last updated: 2022-03-10
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Knit directory: codemapper/
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| Rmd | ae02335 | Chuin Ying Ung | 2022-02-22 | update notes for read3_icd10 |
| Rmd | dfbc621 | Chuin Ying Ung | 2022-02-22 | add mapping notes |
The read3 code XaIP9 mistakenly maps ‘sebaceous cyst’ to various ICD10 codes that code for ‘Other specified disorders of eyelid’ (H028), ‘Other specified disorders of male genital organs’ (N508), ‘Other benign mammary dysplasias’ (N608) and ‘Other specified conditions associated with female genital organs…’ (N948)
These inaccurate codes are coded ‘R’ under ‘mapping_status’ in ‘read_ctv3_icd10’. ‘mapping_status’ denotes nature of mapping and contains letters E (exact one-to-one mapping), G (mapping is correct but read-coded concept is more detailed), D (default mapping), R (requires checking - must be checked against default mapping), A (alternative that is not marked as D or R) and U (unspecified). U is not used.
Other field names in the ‘read_ctv3_icd10’ file are: - refine_flag (C = completely refined i.e. target code is sufficiently detailed to be acceptable, M = mandatory to refine further, P = possible but not mandatory to refine further) - add_code_flag (C = complete, no further codes are needed, M = mandatory to add a further code, P = possible but not mandatory to add further code) - element_num (A Read Code may need several target codes for a complete mapping, but each of these may have alternatives. Therefore, each set of alternatives is given a distinct element number. Element numbers start at 0, incrementing by 1. There are rarely more than two sets.) - block_num (A block is a complete set of target codes for a mapping from any one Read Code (including all alternatives to the suggested codes). There are a number of occasions where more than one block exists for a Read Code. This occurs, for example, when a Read Code maps either to a single target code or to a target code plus a second code (which may itself have alternatives). Blocks are numbered successively 0, 1, 2…)
This field naming system is also used in read_ctv3_icd9.
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] codemapper_0.0.0.9000 ukbwranglr_0.0.0.9000 targets_0.8.0
[4] crosstalk_1.1.1 readxl_1.3.1 reactable_0.2.3
[7] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[10] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4
[13] tibble_3.1.4 ggplot2_3.3.5 tidyverse_1.3.1
[16] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] fs_1.5.0 bit64_4.0.5 lubridate_1.7.10 httr_1.4.2
[5] rprojroot_2.0.2 tools_4.1.0 backports_1.2.1 bslib_0.3.1
[9] utf8_1.2.2 R6_2.5.1 DBI_1.1.1 colorspace_2.0-2
[13] withr_2.4.3 tidyselect_1.1.1 processx_3.5.2 bit_4.0.4
[17] compiler_4.1.0 git2r_0.28.0 cli_3.0.1 rvest_1.0.1
[21] xml2_1.3.2 sass_0.4.0 scales_1.1.1 callr_3.7.0
[25] digest_0.6.28 rmarkdown_2.11 pkgconfig_2.0.3 htmltools_0.5.2
[29] dbplyr_2.1.1 fastmap_1.1.0 highr_0.9 htmlwidgets_1.5.4
[33] rlang_0.4.11 rstudioapi_0.13 RSQLite_2.2.9 shiny_1.7.0
[37] jquerylib_0.1.4 generics_0.1.0 jsonlite_1.7.2 magrittr_2.0.1
[41] Rcpp_1.0.7 munsell_0.5.0 fansi_0.5.0 lifecycle_1.0.1
[45] stringi_1.7.4 whisker_0.4 yaml_2.2.1 blob_1.2.2
[49] grid_4.1.0 promises_1.2.0.1 crayon_1.4.1 haven_2.4.3
[53] hms_1.1.1 knitr_1.34 ps_1.6.0 pillar_1.6.3
[57] igraph_1.2.6 codetools_0.2-18 reprex_2.0.1 glue_1.4.2
[61] evaluate_0.14 data.table_1.14.2 renv_0.13.2 modelr_0.1.8
[65] vctrs_0.3.8 tzdb_0.1.2 httpuv_1.6.3 cellranger_1.1.0
[69] gtable_0.3.0 assertthat_0.2.1 cachem_1.0.6 xfun_0.24
[73] mime_0.12 xtable_1.8-4 broom_0.7.9 later_1.3.0
[77] memoise_2.0.0 ellipsis_0.3.2