README.md

In nicksunderland/acsprojectns: What the Package Does (One Line, Title Case)

acsprojectns

The goal of acsprojectns is to simplify querying of multiple healthcare databases for important information relating to the estimation of bleeding and ischaemic risk in patients.

Installation

You can install the development version of acsprojectns from GitHub with:

# install.packages("devtools")
devtools::install_github("nicksunderland/acsprojectns")

Example

This is a basic example which shows you how to solve a common problem:

library(acsprojectns)
library(magrittr)


# Define a list of ICD-10 codes to search for
codes = c("I219", "I220", "some_other_code") # 2 acute coronary syndrome codes

# Define a list of CCG provider codes to narrow the population
ccg_provider_codes = c("11H", "11T", "12A", "15c") # Bristol/BNSSG codes; alternatively 'NA' to search all

# Define a time window to search within
time_window = lubridate::interval(as.POSIXct("2012-01-01"), as.POSIXct("2022-01-01"), tzone = "GMT")

# Get hospital admissions containing the ICD-10 codes as the primary diagnosis
cohort <- get_hospital_admissions(ccg_provider_code_list = ccg_provider_codes,
                                  level                  = "spell",
                                  codes_list             = codes,
                                  search_strategy        = "primary_diagnosis",
                                  return_all_codes       = FALSE,
                                  datetime_window        = time_window,
                                  verbose                = TRUE) %>%    # All hospital spells (non-overlapping)
  dplyr::group_by(pseudo_nhs_id) %>%                                    
  dplyr::slice_min(lubridate::int_start(spell_interval)) %>%            # Take only the first spell
  dplyr::ungroup() %>%
  dplyr::distinct(pseudo_nhs_id,                                        # Rename columns as appropriate
                  acs_spell_interval_index = spell_interval, 
                  acs_codes = spell_codes)
#> <SQL>
#> SELECT *
#> FROM (SELECT *
#> FROM (SELECT *
#> FROM (SELECT DISTINCT `AIMTC_Pseudo_NHS` AS `pseudo_nhs_id`, `StartDate_ConsultantEpisode` AS `episode_start_date`, `EndDate_ConsultantEpisode` AS `episode_end_date`, `StartTime_Episode` AS `episode_start_time`, `EndTime_Episode` AS `episode_end_time`, `AIMTC_ProviderSpell_Start_Date` AS `spell_start_date`, `AIMTC_ProviderSpell_End_Date` AS `spell_end_date`, `StartDate_HospitalProviderSpell` AS `spell_start_date_alt`, `DischargeDate_FromHospitalProviderSpell` AS `spell_end_date_alt`, `StartTime_HospitalProviderSpell` AS `spell_start_time`, `DischargeTime_HospitalProviderSpell` AS `spell_end_time`, `AIMTC_PCTRegGP` AS `ccg_provider_code`, `DiagnosisPrimary_ICD` AS `primary_diagnosis_icd_code`
#> FROM `vw_APC_SEM_001`) `q01`
#> WHERE (NOT(((`pseudo_nhs_id`) IS NULL)) AND `episode_start_date` >= '2012-01-01T00:00:00Z' AND `episode_start_date` <= '2022-01-01T00:00:00Z')) `q02`
#> WHERE (`primary_diagnosis_icd_code` IN ('I219', 'I220', 'some_other_code'))) `q03`
#> WHERE (`ccg_provider_code` IN ('11H', '11T', '12A', '15c'))
#> Time taken to execute get_hospital_admissions() = 2.01 seconds

print(head(cohort, 10))
#> # A tibble: 10 × 3
#>    pseudo_nhs_id acs_spell_interval_index                         acs_codes
#>            <dbl> <Interval>                                       <list>   
#>  1             5 2021-11-21 12:26:00 GMT--2021-11-21 20:11:00 GMT <chr [1]>
#>  2            37 2019-08-19 02:49:00 GMT--2019-09-19 10:15:00 GMT <chr [1]>
#>  3            60 2018-06-18 07:06:00 GMT--2018-06-18 08:47:00 GMT <chr [1]>
#>  4            61 2018-06-18 21:57:00 GMT--2018-06-18 10:56:00 GMT <chr [1]>
#>  5            74 2018-03-18 00:50:00 GMT--2018-04-18 18:27:00 GMT <chr [1]>
#>  6            80 2021-05-21 08:30:00 GMT--2021-06-21 22:04:00 GMT <chr [1]>
#>  7           105 2021-06-21 11:23:00 GMT--2021-06-21 12:22:00 GMT <chr [1]>
#>  8           132 2019-08-19 00:35:00 GMT--2019-09-19 06:03:00 GMT <chr [1]>
#>  9           157 2018-09-18 00:25:00 GMT--2018-10-18 18:16:00 GMT <chr [1]>
#> 10           168 2019-02-19 21:43:00 GMT--2019-02-19 05:06:00 GMT <chr [1]>

What is special about using README.Rmd instead of just README.md? You can include R chunks like so:

summary(cars)
#>      speed           dist       
#>  Min.   : 4.0   Min.   :  2.00  
#>  1st Qu.:12.0   1st Qu.: 26.00  
#>  Median :15.0   Median : 36.00  
#>  Mean   :15.4   Mean   : 42.98  
#>  3rd Qu.:19.0   3rd Qu.: 56.00  
#>  Max.   :25.0   Max.   :120.00

nicksunderland/acsprojectns documentation built on July 20, 2023, 7:23 p.m.