Last updated: 2021-09-28

Checks: 6 1

Knit directory: codemapper/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: uncommitted changes

The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

Environment: empty

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

Seed: set.seed(20210923)

The command set.seed(20210923) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Repository version: 504e142

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The results in this page were generated with repository version 504e142. 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:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    R/.DS_Store
    Ignored:    _targets/
    Ignored:    config.ini
    Ignored:    data/
    Ignored:    output/
    Ignored:    renv/library/
    Ignored:    renv/local/
    Ignored:    renv/staging/
    Ignored:    tests/.DS_Store

Untracked files:
    Untracked:  BNF Snomed Mapping data 20210819.xlsx
    Untracked:  R/lookups_and_mappings.R
    Untracked:  R/utils-pipe.R
    Untracked:  R/utils.R
    Untracked:  analysis/reformat_all_lkps_maps.Rmd
    Untracked:  code/tar_make.R
    Untracked:  man/pipe.Rd

Unstaged changes:
    Modified:   .gitignore
    Modified:   DESCRIPTION
    Modified:   NAMESPACE
    Modified:   _targets.R

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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	See u222.
x05f5	See u22y.
yz…	See yz0..
yz1..	See yz0..
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	395654	395652	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	395654	395652	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_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 354 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>

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 utils     datasets  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_2.0.1          
[13] tidyr_1.1.3           tibble_3.1.4          ggplot2_3.3.5        
[16] tidyverse_1.3.1      

loaded via a namespace (and not attached):
 [1] fs_1.5.0          usethis_2.0.1     lubridate_1.7.10  devtools_2.4.2   
 [5] httr_1.4.2        rprojroot_2.0.2   tools_4.1.0       backports_1.2.1  
 [9] bslib_0.2.5.1     utf8_1.2.2        R6_2.5.0          DBI_1.1.1        
[13] colorspace_2.0-2  withr_2.4.2       tidyselect_1.1.1  prettyunits_1.1.1
[17] processx_3.5.2    compiler_4.1.0    git2r_0.28.0      cli_3.0.1        
[21] rvest_1.0.1       xml2_1.3.2        desc_1.3.0        sass_0.4.0       
[25] scales_1.1.1      callr_3.7.0       digest_0.6.27     rmarkdown_2.9    
[29] ini_0.3.1         pkgconfig_2.0.3   htmltools_0.5.1.1 sessioninfo_1.1.1
[33] highr_0.9         dbplyr_2.1.1      fastmap_1.1.0     htmlwidgets_1.5.4
[37] rlang_0.4.11      rstudioapi_0.13   jquerylib_0.1.4   generics_0.1.0   
[41] configr_0.3.5     jsonlite_1.7.2    magrittr_2.0.1    Rcpp_1.0.7       
[45] munsell_0.5.0     fansi_0.5.0       lifecycle_1.0.0   stringi_1.6.2    
[49] yaml_2.2.1        pkgbuild_1.2.0    grid_4.1.0        promises_1.2.0.1 
[53] RcppTOML_0.1.7    crayon_1.4.1      haven_2.4.3       hms_1.1.0        
[57] knitr_1.34        ps_1.6.0          pillar_1.6.2      igraph_1.2.6     
[61] codetools_0.2-18  pkgload_1.2.2     reprex_2.0.1      glue_1.4.2       
[65] evaluate_0.14     data.table_1.14.0 remotes_2.4.0     modelr_0.1.8     
[69] vctrs_0.3.8       tzdb_0.1.2        httpuv_1.6.1      cellranger_1.1.0 
[73] gtable_0.3.0      reactR_0.4.4      assertthat_0.2.1  cachem_1.0.6     
[77] xfun_0.24         broom_0.7.9       later_1.2.0       memoise_2.0.0    
[81] workflowr_1.6.2   ellipsis_0.3.2

Reformatting UKB ‘all_lkps_maps.xlsx’

Alasdair Warwick

28 September, 2021

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_dmd`

Reformatting UKB ‘all_lkps_maps.xlsx’

Alasdair Warwick

28 September, 2021

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_dmd

Cannot just remove `NA` in column 2

`bnf_lkp`

`bnf_dmd`