MIMER is an R package designed for analyzing the MIMIC-IV dataset, a repository of pseudonymized electronic health records. It offers a suite of data wrangling functions tailored specifically for preparing the dataset for research purposes, particularly in antimicrobial resistance (AMR) studies. MIMER simplifies complex data manipulation tasks, allowing researchers to focus on their primary inquiries without being bogged down by wrangling complexities. It integrates seamlessly with the AMR package and is ideal for R developers working in AMR research
MIMER::ndc_to_antimicrobial(ndc, class)
MIMER::ndc_is_antimicrobial(ndc, class)
MIMER::is_systemic_route(route, class)
MIMER::check_previous_events(df, cols, sort_by_col, patient_id_col,
event_indi_value="R", new_col_prefix="pr_event_",
time_period_in_days = 0, minimum_prev_events = 0)
MIMER::transpose_microbioevents(df, key_columns, required_columns, transpose_key_column,
transpose_value_column, fill = "N/A")
#not recommended to use
MIMER::clean_antibiotics(
x ,
...
)You can install the development version of MIMER from GitHub with:
This is a basic example which shows you how to solve a common problem:
library(MIMER)
## basic example code
MIMER::ndc_to_antimicrobial(ndc='65649030303', class='antibacterial')## Class 'ab'
## [1] RFX## [1] TRUE## [1] TRUElibrary(MIMER)
## basic example code
df <- data.frame(subject_id=c('10016742','10016742','10016742','10016742','10016742','10038332','10038332','10038332','10038332','10038332','10038332'),
chartdate= c('2178-07-03','2178-08-01','2178-08-01','2178-08-01','2178-09-25','2164-07-31','2164-12-22','2164-12-22','2165-01-07','2165-04-17','2165-05-05'),
CEFEPIME=c('R','R','R','R','S','R','R','R','S','S','S'),
CEFTAZIDIME=c('S','R','S','R','R','S','S','S','R','R','S'))
MIMER::check_previous_events(df, cols = c('CEFTAZIDIME'), sort_by_col = 'chartdate', patient_id_col = 'subject_id', event_indi_value='R')## Checking Previous Events for
## CEFTAZIDIME
## Total Antibiotics Column (Events) Added : 1
## # A tibble: 11 × 5
## subject_id chartdate CEFEPIME CEFTAZIDIME pr_event_CEFTAZIDIME
## <chr> <chr> <chr> <chr> <lgl>
## 1 10038332 2164-07-31 R S FALSE
## 2 10038332 2164-12-22 R S FALSE
## 3 10038332 2164-12-22 R S FALSE
## 4 10038332 2165-01-07 S R FALSE
## 5 10038332 2165-04-17 S R TRUE
## 6 10038332 2165-05-05 S S TRUE
## 7 10016742 2178-07-03 R S FALSE
## 8 10016742 2178-08-01 R R FALSE
## 9 10016742 2178-08-01 R S FALSE
## 10 10016742 2178-08-01 R R FALSE
## 11 10016742 2178-09-25 S R TRUE## example with 'minimum_prev_events' parameter
df <- data.frame(subject_id=c('10016742','10016742','10016742','10016742','10016742','10038332','10038332','10038332','10038332','10038332','10038332'),
chartdate= c('2178-07-03','2178-08-01','2178-07-22','2178-08-03','2178-09-25','2164-07-31','2164-12-22','2164-12-22','2165-01-07','2165-04-17','2165-05-05'),
CEFEPIME=c('R','S','R','S','S','R','R','R','S','S','S'),
CEFTAZIDIME=c('S','R','S','R','R','S','S','S','R','R','S'))
MIMER::check_previous_events(df, cols = c('CEFEPIME'), sort_by_col = 'chartdate', patient_id_col = 'subject_id', minimum_prev_events = 2)## Checking Previous Events for
## CEFEPIME
## Total Antibiotics Column (Events) Added : 1
## # A tibble: 11 × 5
## subject_id chartdate CEFEPIME CEFTAZIDIME pr_event_CEFEPIME
## <chr> <chr> <chr> <chr> <lgl>
## 1 10038332 2164-07-31 R S FALSE
## 2 10038332 2164-12-22 R S FALSE
## 3 10038332 2164-12-22 R S FALSE
## 4 10038332 2165-01-07 S R TRUE
## 5 10038332 2165-04-17 S R TRUE
## 6 10038332 2165-05-05 S S TRUE
## 7 10016742 2178-07-03 R S FALSE
## 8 10016742 2178-07-22 R S FALSE
## 9 10016742 2178-08-01 S R TRUE
## 10 10016742 2178-08-03 S R TRUE
## 11 10016742 2178-09-25 S R TRUE## example with 'time_period_in_days' parameter
df <- data.frame(subject_id=c('10016742','10016742','10016742','10016742','10016742','10038332','10038332','10038332','10038332','10038332','10038332'),
chartdate= c('2178-07-03','2178-08-01','2178-07-22','2178-08-03','2178-09-25','2164-07-31','2164-12-22','2164-12-22','2165-01-07','2165-04-17','2165-05-05'),
CEFEPIME=c('R','S','R','S','S','R','R','R','S','S','S'),
CEFTAZIDIME=c('S','R','S','R','R','S','S','S','R','R','S'))
MIMER::check_previous_events(df, cols = c('CEFTAZIDIME'), sort_by_col = 'chartdate', patient_id_col = 'subject_id', time_period_in_days = 25)## Checking Previous Events for
## CEFTAZIDIME
## Total Antibiotics Column (Events) Added : 1
## # A tibble: 11 × 5
## subject_id chartdate CEFEPIME CEFTAZIDIME pr_event_CEFTAZIDIME
## <chr> <chr> <chr> <chr> <lgl>
## 1 10038332 2164-07-31 R S FALSE
## 2 10038332 2164-12-22 R S FALSE
## 3 10038332 2164-12-22 R S FALSE
## 4 10038332 2165-01-07 S R FALSE
## 5 10038332 2165-04-17 S R FALSE
## 6 10038332 2165-05-05 S S TRUE
## 7 10016742 2178-07-03 R S FALSE
## 8 10016742 2178-07-22 R S FALSE
## 9 10016742 2178-08-01 S R FALSE
## 10 10016742 2178-08-03 S R TRUE
## 11 10016742 2178-09-25 S R FALSE## example with 'time_period_in_days' & 'minimum_prev_events' parameters
df <- data.frame(subject_id=c('10016742','10016742','10016742','10016742','10016742','10038332','10038332','10038332','10038332','10038332','10038332'),
chartdate= c('2178-07-03','2178-08-01','2178-08-01','2178-08-01','2178-09-25','2164-07-31','2164-12-22','2164-12-22','2165-01-07','2165-04-17','2165-05-05'),
CEFEPIME=c('R','R','R','R','S','R','R','R','S','S','S'),
CEFTAZIDIME=c('S','R','S','R','R','S','S','S','R','R','S'))
MIMER::check_previous_events(df, cols = c('CEFEPIME'), sort_by_col = 'chartdate', patient_id_col = 'subject_id', time_period_in_days = 62, minimum_prev_events = 2)## Checking Previous Events for
## CEFEPIME
## Total Antibiotics Column (Events) Added : 1
## # A tibble: 11 × 5
## subject_id chartdate CEFEPIME CEFTAZIDIME pr_event_CEFEPIME
## <chr> <chr> <chr> <chr> <lgl>
## 1 10038332 2164-07-31 R S FALSE
## 2 10038332 2164-12-22 R S FALSE
## 3 10038332 2164-12-22 R S FALSE
## 4 10038332 2165-01-07 S R TRUE
## 5 10038332 2165-04-17 S R FALSE
## 6 10038332 2165-05-05 S S FALSE
## 7 10016742 2178-07-03 R S FALSE
## 8 10016742 2178-08-01 R R FALSE
## 9 10016742 2178-08-01 R S FALSE
## 10 10016742 2178-08-01 R R FALSE
## 11 10016742 2178-09-25 S R TRUE##example for transpose_microbioevents
test_data <- data.frame(subject_id=c('10016742','10016742','10016742','10016742','10016742','10038332','10038332','10038332','10038332','10038332','10038332'),
chartdate= c('2178-07-03','2178-08-01','2178-08-01','2178-08-01','2178-09-25','2164-07-31','2164-12-22','2164-12-22','2165-01-07','2165-04-17','2165-05-05'),
ab_name=c('CEFEPIME','CEFTAZIDIME','CEFEPIME','CEFEPIME','CEFTAZIDIME','CEFTAZIDIME','CEFEPIME','CEFEPIME','CEFTAZIDIME','CEFTAZIDIME','CEFEPIME'),
interpretation=c('S','R','S','R','R','S','S','S','R','R','S'))
MIMER::transpose_microbioevents(test_data, key_columns = c('subject_id','chartdate','ab_name') , required_columns =c('subject_id','chartdate'), transpose_key_column = 'ab_name',
transpose_value_column = 'interpretation', fill = "N/A", non_empty_filter_column='subject_id')## subject_id chartdate CEFEPIME CEFTAZIDIME
## 1 10016742 2178-07-03 S N/A
## 2 10016742 2178-08-01 N/A R
## 3 10016742 2178-09-25 N/A R
## 4 10038332 2164-07-31 N/A S
## 5 10038332 2165-01-07 N/A R
## 6 10038332 2165-04-17 N/A R
## 7 10038332 2165-05-05 S N/A## [1] "Amoxicillin"library(MIMER)
## basic example code
df <- data.frame(drug = c("Amoxicilln","moxicillin","Paracetamol") )
MIMER::clean_antibiotics(df, drug_col = drug)## drug abx_name synonyms is_abx
## 1 Amoxicilln Amoxicillin Amoxicillin TRUE
## 2 moxicillin Amoxicillin Amoxicillin TRUE
## 3 Paracetamol <NA> <NA> FALSE