Last updated: 2022-04-28

Checks: 5 2

Knit directory: codemapper_notes/

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install_codemapper function 1.2 Kb

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Ignored files:
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    Ignored:    .Rproj.user/
    Ignored:    all_lkps_maps.db
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    Ignored:    tar_make.R

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Unstaged changes:
    Modified:   _targets.R
    Modified:   analysis/clinical_codes_lkps_and_mappings.Rmd
    Modified:   analysis/icd10_lkp.Rmd
    Modified:   analysis/icd9_icd10_mapping.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/phecodes.Rmd
    Modified:   analysis/read2_icd10_mapping.Rmd
    Modified:   analysis/read2_read3_mapping.Rmd
    Modified:   analysis/read3_icd10_mapping.Rmd
    Modified:   analysis/read3_read2_mapping.Rmd
    Modified:   analysis/reformat_all_lkps_maps.Rmd
    Modified:   renv.lock

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File Version Author Date Message
Rmd 98b0efc rmgpanw 2022-03-16 update rmd files
html 98b0efc rmgpanw 2022-03-16 update rmd files
Rmd 193f2cb rmgpanw 2022-03-16 add notes re icd9-10 mapping, and reformatting function for ths mapping table 
library(tidyverse)
library(reactable)
library(readxl)
library(crosstalk)
library(targets)
library(codemapper)
library(flextable)

tar_load(ALL_LKPS_MAPS_DB)

all_lkps_maps <- tar_read(all_lkps_maps_raw) %>% 
  purrr::map(codemapper:::rm_footer_rows_all_lkps_maps_df) %>%
  purrr::map(~ tibble::rowid_to_column(.data = .x,
                                       var = ".rowid"))

# choose between `read2_read3` and `read3_read2`
FROM_TO <- "read2_read3"

if (FROM_TO == "read2_read3") {
  args <- codemapper:::check_mapping_args(from = "read2",
                                                  to = "read3")
  from_code <- "Read 2"
} else if (FROM_TO == "read3_read2") {
  args <- codemapper:::check_mapping_args(from = "read3",
                                                  to = "read2")
  from_code <- "Read 3"
}

read_read_map <- all_lkps_maps[[args$mapping_table]]

Key points

Preferred terms and synonyms

Read 2 and Read 3 codes have a preferred description and may additionally have synonyms. For example, diabetes (Read 2 C10E.) may be described as either ‘Type 1 diabetes mellitus’ or ‘Insulin dependent diabetes mellitus’.

Overlap between preferred description and synonyms

Read 2:

read2_p <- read_read_map %>% 
  filter(TERMV2_TYPE == "P")

read2_s <- read_read_map %>% 
  filter(TERMV2_TYPE == "S")

list(read2_p = unique(read2_p$READV2_CODE),
     read2_s = unique(read2_s$READV2_CODE)) %>% 
  ggVennDiagram::ggVennDiagram()

Version Author Date
98b0efc rmgpanw 2022-03-16

Read 3:

read3_p <- read_read_map %>% 
  filter(TERMV3_TYPE == "P")

read3_s <- read_read_map %>% 
  filter(TERMV3_TYPE == "S")

list(read3_p = unique(read3_p$READV3_CODE),
     read3_s = unique(read3_s$READV3_CODE)) %>% 
  ggVennDiagram::ggVennDiagram()

Version Author Date
98b0efc rmgpanw 2022-03-16

Not assured mappings

# filter for 'assured' mappings only
read_read_map_is_assured_only <- read_read_map %>% 
  filter(IS_ASSURED == 1)

# get read codes that are do not have an 'assured' mapping
not_assured_mappings <- read_read_map %>% 
  filter(!.data[[args$from_col]] %in% read_read_map_is_assured_only[[args$from_col]])

# numbers
n_from_codes_not_assured <- n_distinct(not_assured_mappings[[args$from_col]])
n_from_codes <- n_distinct(read_read_map[[args$from_col]])
pct_from_codes_not_assured <- format(n_from_codes_not_assured/n_from_codes * 100, digits = 3)

The current clinical assurance status of each code mapping, where ‘0’ = Not assured and ‘1’ = Assured (column IS_ASSURED). Below is a table of all mappings that are not assured. This includes 5223 out of 89676 Read 2 codes in this mapping table (5.82%).

not_assured_mappings %>% 
  reactable(filterable = TRUE,
            searchable = TRUE,
            showPageSizeOptions = TRUE,
            pageSizeOptions = c(10, 25, 50, 100, 200),
            paginationType = 'jump')

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] flextable_0.7.0       codemapper_0.0.0.9000 ukbwranglr_0.0.0.9000
 [4] targets_0.12.0        crosstalk_1.1.1       readxl_1.4.0         
 [7] reactable_0.2.3       forcats_0.5.1         stringr_1.4.0        
[10] dplyr_1.0.8           purrr_0.3.4           readr_2.1.2          
[13] tidyr_1.2.0           tibble_3.1.6          ggplot2_3.3.5        
[16] tidyverse_1.3.1       workflowr_1.6.2      

loaded via a namespace (and not attached):
 [1] fs_1.5.2            sf_1.0-7            lubridate_1.8.0    
 [4] httr_1.4.2          rprojroot_2.0.2     tools_4.1.0        
 [7] backports_1.4.1     bslib_0.3.1         utf8_1.2.2         
[10] R6_2.5.1            KernSmooth_2.23-20  DBI_1.1.2          
[13] colorspace_2.0-2    withr_2.5.0         tidyselect_1.1.2   
[16] processx_3.5.3      compiler_4.1.0      git2r_0.28.0       
[19] cli_3.2.0           rvest_1.0.1         xml2_1.3.2         
[22] officer_0.4.2       labeling_0.4.2      sass_0.4.1         
[25] scales_1.1.1        classInt_0.4-3      proxy_0.4-26       
[28] callr_3.7.0         systemfonts_1.0.4   digest_0.6.29      
[31] rmarkdown_2.11      base64enc_0.1-3     pkgconfig_2.0.3    
[34] htmltools_0.5.2     dbplyr_2.1.1        fastmap_1.1.0      
[37] highr_0.9           htmlwidgets_1.5.4   rlang_1.0.2        
[40] rstudioapi_0.13     shiny_1.7.1         farver_2.1.0       
[43] ggVennDiagram_1.2.0 jquerylib_0.1.4     generics_0.1.2     
[46] jsonlite_1.8.0      zip_2.2.0           magrittr_2.0.3     
[49] Rcpp_1.0.8.3        munsell_0.5.0       fansi_1.0.3        
[52] gdtools_0.2.4       lifecycle_1.0.1     stringi_1.7.6      
[55] whisker_0.4         yaml_2.3.5          grid_4.1.0         
[58] promises_1.2.0.1    crayon_1.5.1        haven_2.5.0        
[61] hms_1.1.1           knitr_1.39          ps_1.7.0           
[64] pillar_1.7.0        uuid_0.1-4          igraph_1.3.1       
[67] base64url_1.4       codetools_0.2-18    reprex_2.0.1       
[70] glue_1.6.2          evaluate_0.15       data.table_1.14.2  
[73] renv_0.13.2         modelr_0.1.8        vctrs_0.4.1        
[76] tzdb_0.3.0          httpuv_1.6.5        cellranger_1.1.0   
[79] gtable_0.3.0        reactR_0.4.4        assertthat_0.2.1   
[82] xfun_0.30           mime_0.12           xtable_1.8-4       
[85] broom_0.7.9         e1071_1.7-9         later_1.3.0        
[88] class_7.3-19        RVenn_1.1.0         units_0.8-0        
[91] ellipsis_0.3.2