check_previous_events: Add a column and check any previous events identified for a...

In MIMER: Data Wrangling for Antimicrobial Resistance Studies

Add a column and check any previous events identified for a particular antibiotic

Description

This function helps to check any previous events identified or not (TRUE/FALSE)

Usage

check_previous_events(df,
      cols,
      sort_by_col,
      patient_id_col,
      event_indi_value="R",
      new_col_prefix="pr_event_",
      time_period_in_days,
      minimum_prev_events,
      default_na_date='9999-12-31 00:00:00')

Arguments

event_indi_value	(optional) Event value indicating Resistance (Default 'R' )
df	A data frame containing microbiology events
cols	Columns for each antibiotics which contains events
sort_by_col	A date column to order the input data frame
patient_id_col	Patient Id Column
new_col_prefix	(optional) Custom Prefix for new column(Default 'pr_event_' )
time_period_in_days	(optional) to check any previous events in last 'n' days or not
minimum_prev_events	(optional) to check any 'n' number of previous events happened or not
default_na_date	(optional) replacement date string for NA values in sort_by_col eg: '9999-12-31 00:00:00'

Value

Data Frame

Examples

#Example -1
test_data <- data.frame(subject_id = c(10000032,
                                       10000280,
                                       10000280,
                                       10000280,
                                       10000826,
                                       10000826),
                      chartdate = c('2150-10-12',
                                    '2150-10-12',
                                    '2151-03-17',
                                    '2146-12-08',
                                    '2187-09-26',
                                    '2188-07-01'),
                      AMIKACIN=c('R','R','S','S','S','R'))

check_previous_events(test_data,
                      cols="AMIKACIN",
                      sort_by_col='chartdate',
                      patient_id_col='subject_id',
                      event_indi_value='R')
#Example -2

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','2178-07-22',
                          '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'))

check_previous_events(test_data,
                      cols = c('CEFEPIME','CEFTAZIDIME'),
                      sort_by_col = 'chartdate',
                      patient_id_col = 'subject_id',
                      time_period_in_days = 62,
                      minimum_prev_events = 2)

MIMER documentation built on June 22, 2024, 9:41 a.m.