transpose_microbioevents: Transpose microbiology events dataset

In MIMER: Data Wrangling for Antimicrobial Resistance Studies

Transpose microbiology events dataset

Description

This function helps to transpose (rows to columns) microbiology events.

Usage

transpose_microbioevents(raw_df,
                                 key_columns,
                                 required_columns,
                                 transpose_key_column,
                                 transpose_value_column,
                                 fill="NA",
                                 non_empty_filter_column,
                                 remove_duplicates=TRUE)

Arguments

key_columns	(Optional) Primary Key/ Key columns for duplicate check : Default Value = c('subject_id','micro_specimen_id','isolate_num', 'org_name','ab_itemid')
raw_df	A data frame containing microbiology events
required_columns	(Optional) columns should contain in final dataset : Default Value c('subject_id','hadm_id','micro_specimen_id', 'order_provider_id', 'chartdate','charttime', 'spec_itemid','spec_type_desc','storedate', 'storetime','test_itemid','test_name', 'org_itemid','isolate_num','org_name')
transpose_key_column	(Optional) The column that should be transposed ( - distinct values of that column will become separate columns) :Default 'ab_name'
transpose_value_column	(optional) Values of 'transpose_key_column' column :Default 'interpretation'
fill	(optional) Fill character for empty columns- Default : "NA"
non_empty_filter_column	(optional) Filter input dataframe where 'non_empty_filter_column' is not empty or na. Default :'ab_itemid'
remove_duplicates	(optional) Default :TRUE

Value

Data Frame

Examples

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'))

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')

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