In davidbaniadam/rispacs: Functions for Working with RISPACS Data

knitr::opts_chunk$set(echo = TRUE)

con <- conStart::con_start()
conStart::my_libs(TRUE)
head(dbListTables(con), n=30)

```{sql, connection = con, output.var = all_accession_numbers}

SELECT Accession_number FROM RISPACS.Hvidovre2018RIS UNION SELECT Accession_number FROM RISPACS.Hvidovre2018PACS

```r

all_accession_numbers_anonymized <- conStart::anonymize(all_accession_numbers$Accession_number)

```{sql, connection = con, output.var=ris_real} SELECT Accession_number, Billing_code, Procedure_priority, Patient_RK FROM RISPACS.Hvidovre2018RIS

```{sql, connection = con, output.var=pacs_real}
SELECT *
FROM RISPACS.Hvidovre2018PACS

ris_real <- ris_real %>% 
  mutate(Procedure_priority= case_when(
    str_detect(Procedure_priority, "pakke") ~ "Kræftpakke",
    NA  ~ NA_character_,
    TRUE ~ Procedure_priority))

patient_rk_num <- conStart::anonymize(ris_real$Patient_RK)

  ris_anonymized <- 
  inner_join(ris_real, all_accession_numbers_anonymized, by = c("Accession_number" = "idOrg")) %>% 
  select(-Accession_number) %>% 
  rename(Accession_number = id) %>% 
  select(Accession_number, everything()) %>% 
  mutate(Accession_number = paste0("REGH", Accession_number)) %>%
  mutate(Patient_RK = as.character(Patient_RK)) %>%   
  inner_join(patient_rk_num, by = c("Patient_RK" = "idOrg")) %>% 
  select(-Patient_RK) %>% 
  rename(Patient_RK = id)  %>% 
  mutate_all(funs(replace(., .=="", NA))) %>% 
  as_tibble()  



  usethis::use_data(ris_anonymized, overwrite = TRUE)

  pacs_anonymized <- 
  inner_join(pacs_real, all_accession_numbers_anonymized, by = c("Accession_number" = "idOrg"))%>% 
  select(-Accession_number) %>% 
  rename(Accession_number = id) %>% 
  select(Accession_number, everything())  %>% 
  mutate(Accession_number = paste0("REGH", Accession_number)) %>% 
  select(-Actual_Room_number) %>% 
  mutate_all(funs(replace(., .=="", NA))) %>% 
  as_tibble()  

  usethis::use_data(pacs_anonymized, overwrite = TRUE)

set.seed(33333)
sample_accession <- sample(ris_anonymized$Accession_number, 1500)
use_data(sample_accession, overwrite = TRUE)

ris_sample <- ris_anonymized %>% 
  filter(Accession_number %in% sample_accession) 


pacs_sample <- pacs_anonymized %>% 
  filter(Accession_number %in% sample_accession) 

use_data(ris_sample, overwrite = TRUE)
use_data(pacs_sample, overwrite = TRUE)