Last updated: 2022-02-22

Checks: 6 1

Knit directory: codemapper/

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Name	Class	Size
install_codemapper	function	1.2 Kb

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Ignored files:
    Ignored:    .DS_Store
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    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    _targets/
    Ignored:    all_lkps_maps.db
    Ignored:    renv/library/
    Ignored:    renv/staging/
    Ignored:    tar_make.R
    Ignored:    ukbb_pan_ancestry-master/

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    Modified:   R/utils.R
    Modified:   analysis/read3_icd10_mapping.Rmd

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/reformat_all_lkps_maps.Rmd) and HTML (public/reformat_all_lkps_maps.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
html	1df97df	rmgpanw	2022-02-17	incorporate icd9 and icd10 to phecode maps
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
html	38fee6c	rmgpanw	2021-12-15	update codes_starting_with function to escape ‘.’, and update tests also
Rmd	4478674	rmgpanw	2021-12-14	update documentation re icd10 codes in reformat_all_lkps_maps.Rmd
Rmd	9593d03	rmgpanw	2021-12-14	minor update to documentation re reformatting icd10_lkp sheet
html	e829371	rmgpanw	2021-10-14	add update_code_selection function to utils.r
html	f8d1889	rmgpanw	2021-10-09	icd10 codes now returned as ALT CODE; codemapper app includes self-reported codes
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	d285b07	rmgpanw	2021-09-29	add analysis/reformat_all_lkps_maps.Rmd to _targets.R; start analysis/clinical_codes_lkps_and_mappings.Rmd
html	d285b07	rmgpanw	2021-09-29	add analysis/reformat_all_lkps_maps.Rmd to _targets.R; start analysis/clinical_codes_lkps_and_mappings.Rmd
Rmd	5647f75	rmgpanw	2021-09-28	targets script working
html	5647f75	rmgpanw	2021-09-28	targets script working

Remove irrelevant rows

Last few rows of each sheet

2 columns shown only

bnf_lkp

BNF_Presentation_Code	BNF_Presentation
23985859804	Mentor_Carshalton Urinary Diversion Set Triangular 32mm
23985859805	Mentor_Carshalton Urinary Diversion Set Triangular 38mm
23985859806	Mentor_Chiron Ileal Blad Apparatus
23990001111	Unspecified Manufacturer_Stoma/Incont
NA	NA
BNF Code Information, NHSBSA Copyright 2019. This information is licenced under the terms of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

dmd_lkp

concept_id	term
4450411000001101	Zyvox 600mg tablets (Pfizer Ltd) 10 tablet (product)
3862301000001107	Zyvox 600mg/300mL infusion solution
4827211000001109	Zyvox 600mg/300ml solution for injection bags (Pfizer Ltd) (product)
4827411000001108	Zyvox 600mg/300ml solution for injection bags (Pfizer Ltd) 10 bag 10 x 300ml bags (product)
NA	NA
This material includes SNOMED Clinical Terms® (SNOMED CT®) which is used by permission of the International Health Terminology Standards Development Organisation (IHTSDO). All rights reserved. SNOMED CT®, was originally created by The College of American Pathologists. “SNOMED” and “SNOMED CT” are registered trademarks of the IHTSDO.	NA

icd9_lkp

ICD9	DESCRIPTION_ICD9
V825	CHEMICAL POISONING AND OTHER CONTAMINATION
V826	MULTIPHASIC SCREENING
V828	OTHER
V829	UNSPECIFIED
NA	NA
ICD-9 is in the public domain so there are no copyright restrictions over its use. WHO no longer publishes or distributes ICD-9.	NA

icd10_lkp

ICD10_CODE	ALT_CODE
U84.7	U847
U84.8	U848
U84.9	U849
U85	U85X
NA	NA
ICD-10 codes, terms and text used by permission of WHO, from: International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Vols 1-3. Geneva, World Health Organization, 1992-2016.	NA

icd9_icd10

ICD9	DESCRIPTION_ICD9
V468	OTHER ENABLING MACHINES
V468	OTHER ENABLING MACHINES
V469	UNSPECIFIED
NA	NA
ICD-10 codes, terms and text used by permission of WHO, from: International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Vols 1-3. Geneva, World Health Organization, 1992-2016.	NA
ICD-9 is in the public domain so there are no copyright restrictions over its use. WHO no longer publishes or distributes ICD-9.	NA

read_v2_lkp

read_code	term_code
Zw058	00
Zw059	00
Zw05A	00
Zw05B	00
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm”	NA

read_v2_drugs_lkp

read_code	term_description
yz4V.	2016-01-01 GRAMMEZA
yz4W.	2016-02-01 MARMARAS
yz4X.	2016-03-01 MATHRAKI
yz4Y.	2016-04-01 MEGANISI
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_v2_drugs_bnf

read_code	bnf_code
m22S.	13.02.01.00
m22T.	13.02.01.00
pq3U.	00.00.00.00
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
BNF Code Information, NHSBSA Copyright 2019. This information is licenced under the terms of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_v2_icd9

read_code	icd9_code
ZVu6Z	V444
ZVy..	V01-V82
ZVz..	V01-V82
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
ICD-9 is in the public domain so there are no copyright restrictions over its use. WHO no longer publishes or distributes ICD-9.	NA

read_v2_icd10

read_code	icd10_code
ZVu6Z	Z934
ZVy..	Z769
ZVz..	Z769
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
ICD-10 codes, terms and text used by permission of WHO, from: International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Vols 1-3. Geneva, World Health Organization, 1992-2016.	NA

read_v2_opcs4

read_code	opcs_4.2_code
7K1Lf	W848+Y713
7K1Lg	W848+Y713
7L119	X382+Y532
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
The OPCS Classification of Interventions and Procedures, codes, terms and text is Crown copyright (2016) published by Health and Social Care Information Centre, also known as NHS Digital and licensed under the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_v2_read_ctv3

CHAPTER	READV2_CODE
Z	Zw058
Z	Zw059
Z	Zw05A
Z	Zw05B
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_ctv3_lkp

read_code	term_description
x05f4	Gadovist 1mmol/mL solution for injection prefilled syringe
x05f5	Gadobutrol 1mmol/mL solution for injection prefilled syringe
yz…	Read Code drugs administration
yz1..	Read Code drugs administration
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_ctv3_icd9

read_code	icd9_code
ZVu6e	V433
ZVu6k	V438
ZVu6l	V458
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
ICD-9 is in the public domain so there are no copyright restrictions over its use. WHO no longer publishes or distributes ICD-9.	NA

read_ctv3_icd10

read_code	icd10_code
ZVu6m	Z998
ZVy..	Z769
ZVz..	Z769
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
ICD-10 codes, terms and text used by permission of WHO, from: International Statistical Classification of Diseases and Related Health Problems, Tenth Revision (ICD-10). Vols 1-3. Geneva, World Health Organization, 1992-2016.	NA

read_ctv3_opcs4

read_code	opcs4_code
XaexI	X629
Xafdi	X612
Xaff0	X629
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA
The OPCS Classification of Interventions and Procedures, codes, terms and text is Crown copyright (2016) published by Health and Social Care Information Centre, also known as NHS Digital and licensed under the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

read_ctv3_read_v2

READV3_CODE	TERMV3_CODE
Zw058	YM0dp
Zw059	YM0dq
Zw05A	YM0dr
Zw05B	YM0ds
NA	NA
Contains information from NHS Digital, licenced under the current version of the Open Government Licence available at www.nationalarchives.gov.uk/doc/open-government-licence/open-government-licence.htm	NA

Cannot just remove `NA` in column 2

Sheet	N rows raw	N rows rm NAs in col 2	Difference
bnf_lkp	79829	79827	2
dmd_lkp	434951	434949	2
icd9_lkp	7973	7971	2
icd10_lkp	17936	17934	2
icd9_icd10	16163	9728	6435
read_v2_lkp	101883	101881	2
read_v2_drugs_lkp	67614	67612	2
read_v2_drugs_bnf	67615	58354	9261
read_v2_icd9	35664	35661	3
read_v2_icd10	36667	36664	3
read_v2_opcs4	14927	14924	3
read_v2_read_ctv3	108245	108243	2
read_ctv3_lkp	419098	419096	2
read_ctv3_icd9	67155	67152	3
read_ctv3_icd10	116377	116374	3
read_ctv3_opcs4	54321	54318	3
read_ctv3_read_v2	777522	777520	2

Instead, determine N rows to remove manually

Sheet	N rows raw	N rows reformatted	Difference
bnf_lkp	79829	79827	2
dmd_lkp	434951	434949	2
icd9_lkp	7973	7971	2
icd10_lkp	17936	17934	2
icd9_icd10	16163	16160	3
read_v2_lkp	101883	101881	2
read_v2_drugs_lkp	67614	67612	2
read_v2_drugs_bnf	67615	67612	3
read_v2_icd9	35664	35661	3
read_v2_icd10	36667	36664	3
read_v2_opcs4	14927	14924	3
read_v2_read_ctv3	108245	108243	2
read_ctv3_lkp	419098	419096	2
read_ctv3_icd9	67155	67152	3
read_ctv3_icd10	116377	116374	3
read_ctv3_opcs4	54321	54318	3
read_ctv3_read_v2	777522	777520	2

`bnf_lkp`

BNF codes in the UK Biobank linked primary care dataset are of variable length (see UKB resource 591).

extend_bnf_lkp() creates all possible versions for BNF codes in bnf_lkp. This facilitates selecting all drugs under a certain chapter/section/etc e.g. to get all BNF codes for all medications in the ‘Treatment Of Glaucoma’ section (i.e. BNF codes starting with 1106). This table shows the results for the first drug in this section:

`bnf_read2`

All BNF codes in the bnf_code col are 8 digits long. Digit 7 corresponds to BNF sub paragraph - this is expanded to 2 digits by prefixing with a 0 in bnf_code.

Note that there are a number of Read 2 codes that have not been mapped to BNF (NA in the table below):

Digits 7 and 8, bnf_code col	n
00	55068
01	1436
02	913
03	877
04	53
05	7
NA	9258

…in most cases, BNF_Paragraph = BNF_Subparagraph. For an example of where these can differ, see BNF paragraph Renin-Angiotensin System Drugs.

extend_read_v2_drugs_bnf() appends Read 2 and BNF descriptions to the read_v2_drugs_bnf table, the first few rows are shown below:

`bnf_dmd`

This is downloaded from the NHSBSA website. There are no ‘extra’ rows that need removing at the bottom.

To map BNF codes to DM+D:

Note: There are 184 out of 354 glaucoma medication codes that are not present in bnf_dmd

# A tibble: 6 × 11
  presentation_pack_level vmp_vmpp_amp_ampp bnf_code        bnf_name snomed_code
  <chr>                   <chr>             <chr>           <chr>    <chr>      
1 Presentation            VMP               1106000L0AAAAAA Latanop… 330729005  
2 Pack                    VMPP              1106000L0AAAAAA Latanop… 1075711000…
3 Presentation            AMP               1106000L0BBAAAA Xalatan… 3656110000…
4 Pack                    AMPP              1106000L0BBAAAA Xalatan… 1381911000…
5 Presentation            AMP               1106000L0AAAAAA Latanop… 1984741100…
6 Pack                    AMPP              1106000L0AAAAAA Latanop… 1984751100…
# … with 6 more variables: dm_d_product_description <chr>, strength <dbl>,
#   unit_of_measure <chr>, dm_d_product_and_pack_description <chr>, pack <dbl>,
#   sub_pack <chr>

`icd10_lkp`

For 254 codes where the 3 character category is undivided, ‘X’ is appended in the ALT_CODE column. These are listed below:

UK Biobank ICD-10 codes are recorded as per the ALT_CODE format, but does not append ‘X’ for these undivided 3 character category codes.

The ‘X’ is therefore removed when looking up codes from the icd_10 lookup sheet with argument standardise_output = TRUE. However, the ‘X’ is retained in the icd10_lkp sheet ALT_CODE column.

[1] TRUE

[1] TRUE

There are no ICD-10 codes with values for both MODIFIER_4 AND MODIFIER_5.

Examples of codes with modifiers: E10 and I70.0. For the latter, note that I70.0 in ICD10_CODE format can have (i) no modifier (ii) ‘without gangrene’ modifier, or (iii) ‘with gangrene’ modifier. In ALT_CODE format, these appear as I700, I7000 and I7001 respectively.

`opcs4_lkp`

There is no lookup sheet for OPCS4 codes in UK Biobank resource 592. This is therefore created instead from the UK Biobank codings file (coding 240

R version 4.1.2 (2021-11-01)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/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 testthat_3.0.4        ukbwranglr_0.0.0.9000
 [4] targets_0.8.0         crosstalk_1.1.1       readxl_1.3.1         
 [7] reactable_0.2.3       forcats_0.5.1         stringr_1.4.0        
[10] dplyr_1.0.7           purrr_0.3.4           readr_2.0.2          
[13] tidyr_1.1.4           tibble_3.1.4          ggplot2_3.3.5        
[16] tidyverse_1.3.1       workflowr_1.6.2      

loaded via a namespace (and not attached):
 [1] fs_1.5.0            usethis_2.0.1       fontawesome_0.2.2  
 [4] bit64_4.0.5         lubridate_1.7.10    devtools_2.4.2     
 [7] httr_1.4.2          rprojroot_2.0.2     tools_4.1.2        
[10] backports_1.2.1     bslib_0.3.0         utf8_1.2.2         
[13] R6_2.5.1            DBI_1.1.1           colorspace_2.0-2   
[16] withr_2.4.2         tidyselect_1.1.1    prettyunits_1.1.1  
[19] processx_3.5.2      bit_4.0.4           compiler_4.1.2     
[22] git2r_0.28.0        cli_3.0.1           rvest_1.0.1        
[25] xml2_1.3.2          desc_1.3.0          sass_0.4.0         
[28] scales_1.1.1        callr_3.7.0         shinyFeedback_0.4.0
[31] digest_0.6.28       rmarkdown_2.11      ini_0.3.1          
[34] pkgconfig_2.0.3     htmltools_0.5.2     sessioninfo_1.1.1  
[37] dbplyr_2.1.1        fastmap_1.1.0       highr_0.9          
[40] htmlwidgets_1.5.4   rlang_0.4.11        RSQLite_2.2.8      
[43] rstudioapi_0.13     shiny_1.7.0         jquerylib_0.1.4    
[46] generics_0.1.0      configr_0.3.5       jsonlite_1.7.2     
[49] magrittr_2.0.1      Rcpp_1.0.7          munsell_0.5.0      
[52] fansi_0.5.0         lifecycle_1.0.1     stringi_1.7.4      
[55] whisker_0.4         yaml_2.2.1          pkgbuild_1.2.0     
[58] blob_1.2.2          grid_4.1.2          promises_1.2.0.1   
[61] RcppTOML_0.1.7      crayon_1.4.1        haven_2.4.3        
[64] hms_1.1.1           knitr_1.34          ps_1.6.0           
[67] pillar_1.6.3        igraph_1.2.6        codetools_0.2-18   
[70] pkgload_1.2.2       reprex_2.0.1        glue_1.4.2         
[73] evaluate_0.14       remotes_2.4.0       data.table_1.14.2  
[76] renv_0.13.2         modelr_0.1.8        vctrs_0.3.8        
[79] tzdb_0.1.2          httpuv_1.6.3        cellranger_1.1.0   
[82] gtable_0.3.0        reactR_0.4.4        assertthat_0.2.1   
[85] cachem_1.0.6        xfun_0.24           mime_0.12          
[88] xtable_1.8-4        broom_0.7.9         later_1.3.0        
[91] memoise_2.0.0       ellipsis_0.3.2

Reformatting UKB ‘all_lkps_maps.xlsx’

Alasdair Warwick

22 February, 2022

Remove irrelevant rows

Last few rows of each sheet

bnf_lkp

dmd_lkp

icd9_lkp

icd10_lkp

icd9_icd10

read_v2_lkp

read_v2_drugs_lkp

read_v2_drugs_bnf

read_v2_icd9

read_v2_icd10

read_v2_opcs4

read_v2_read_ctv3

read_ctv3_lkp

read_ctv3_icd9

read_ctv3_icd10

read_ctv3_opcs4

read_ctv3_read_v2

Cannot just remove `NA` in column 2

Instead, determine N rows to remove manually

`bnf_lkp`

`bnf_read2`

`bnf_dmd`

`icd10_lkp`

`opcs4_lkp`

Reformatting UKB ‘all_lkps_maps.xlsx’

Alasdair Warwick

22 February, 2022

Remove irrelevant rows

Last few rows of each sheet

bnf_lkp

dmd_lkp

icd9_lkp

icd10_lkp

icd9_icd10

read_v2_lkp

read_v2_drugs_lkp

read_v2_drugs_bnf

read_v2_icd9

read_v2_icd10

read_v2_opcs4

read_v2_read_ctv3

read_ctv3_lkp

read_ctv3_icd9

read_ctv3_icd10

read_ctv3_opcs4

read_ctv3_read_v2

Cannot just remove NA in column 2

Instead, determine N rows to remove manually

bnf_lkp

bnf_read2

bnf_dmd

icd10_lkp

opcs4_lkp

Cannot just remove `NA` in column 2

`bnf_lkp`

`bnf_read2`

`bnf_dmd`

`icd10_lkp`

`opcs4_lkp`