EHR (version 0.4-11)

run_MedStrI: Run Str Data I

Description

This module will load and modify structured intravenous (IV) infusion and bolus medication data.

Usage

run_MedStrI(
  mar.path,
  mar.columns = list(),
  medGivenReq = FALSE,
  flow.path = NULL,
  flow.columns = list(),
  medchk.path = NULL,
  demo.list = NULL,
  demo.columns = list(),
  missing.wgt.path = NULL,
  wgt.columns = list(),
  check.path = NULL,
  failflow_fn = "FailFlow",
  failnounit_fn = "NoUnit",
  failunit_fn = "Unit",
  failnowgt_fn = "NoWgt",
  censor_date_fn = "CensorTime",
  infusion.unit = "mcg/kg/hr",
  bolus.unit = "mcg",
  bol.rate.thresh = Inf,
  rateunit = "mcg/hr",
  ratewgtunit = "mcg/kg/hr",
  weightunit = "kg",
  drugname = NULL
)

Value

structured data set

Arguments

mar.path

filename of MAR data (CSV, RData, RDS), or data.frame

mar.columns

a named list that should specify columns in MAR data; ‘id’, ‘datetime’ and ‘dose’ are required. ‘drug’, ‘weight’, ‘given’ may also be specified. ‘datetime’ is date and time for data measurement, which can refer to a single date-time variable (datetime = ‘date_time’) or two variables holding date and time separately (e.g., datetime = c(‘Date’, ‘Time’)). ‘dose’ can also be given as a single variable or two variables. If given as a single column, the column's values should contain dose and units such as ‘25 mcg’. If given as two column names, the dose column should come before the unit column (e.g., dose = c(‘doseamt’, ‘unit’)). ‘drug’ can provide list of acceptable drug names. If ‘drug’ is present, the ‘medchk.path’ argument should also be provided. The ‘given’ is a variable that flags whether the medication (inpatient) was given. When it is given, values shoule be “Given”; should be used in conjunction with the ‘medGivenReq’ argument.

medGivenReq

if TRUE, values in ‘given’ column in MAR data should equal “Given”; if this is FALSE (the default), NA values are also acceptable.

flow.path

filename of flow data (CSV, RData, RDS), or data.frame

flow.columns

a named list that should specify columns in flow data; ‘id’, ‘datetime’, ‘finalunits’, ‘unit’, ‘rate’, ‘weight’ are required. ‘idvisit’ may also be specified. ‘datetime’ is date and time for data measurement, which can refer to a single date-time variable (datetime = ‘date_time’) or two variables holding date and time separately (e.g., datetime = c(‘Date’, ‘Time’)).

medchk.path

filename containing data set (CSV, RData, RDS), or data.frame; should have the column ‘medname’ with list of acceptable drug names (e.g., brand and generic name, abbreviations) to subset drugs of interest using ‘drug’ column in MAR data. This argument can be used when MAR data contains different drugs that should be excluded.

demo.list

demographic information; if available, the output from `run_Demo` or a correctly formatted data.frame, which can be used to impute weight when missing

demo.columns

a named list that should specify columns in demographic data; ‘id’, ‘datetime’, and ‘weight’ are required. ‘datetime’ is the date and time when the demographic data were obtained, which can refer to a single date-time variable (datetime = ‘date_time’) or two variables holding date and time separately (e.g., datetime = c(‘Date’, ‘Time’)).

missing.wgt.path

filename containing additional weight data (CSV, RData, RDS), or data.frame. The variables in this file should be defined in the ‘wgt.columns’ argument.

wgt.columns

a named list that should specify columns in additional weight data; ‘id’, ‘datetime’, and ‘weight’ are required. ‘datetime’ is date and time for weight measurement, which can refer to a single date-time variable (datetime = ‘date_time’) or two variables holding date and time separately (e.g., datetime = c(‘Date’, ‘Time’)).

check.path

path to ‘check’ directory, where check files are created. The default (NULL) will not produce any check files.

failflow_fn

filename for duplicate flow data with rate zero

failnounit_fn

filename for MAR data with missing unit

failunit_fn

filename for MAR data with invalid unit

failnowgt_fn

filename for infusion data with missing weight where unit indicates weight is required

censor_date_fn

filename containing censor times created with invalid dose data

infusion.unit

acceptable unit for infusion data

bolus.unit

acceptable unit for bolus data

bol.rate.thresh

upper limit for bolus rate; values above this are invalid

rateunit

acceptable unit for hourly rate; defaults to ‘mcg/hr’

ratewgtunit

acceptable unit for hourly rate by weight; defaults to ‘mcg/kg/hr’

weightunit

acceptable unit for weight; defaults to ‘kg’

drugname

drug of interest, included in filename of check files. The default (NULL) will produce filenames without drugname included.

Details

See EHR Vignette for Structured Data.

Examples

# flow data for 'Fakedrug1'
flow <- data.frame(mod_id=c(1,1,2,2,2),
                   mod_id_visit=c(46723,46723,84935,84935,84935),
                   record.date=c("07/05/2019 5:25","07/05/2019 6:01",
                                 "09/04/2020 3:21", "09/04/2020 4:39",
                                 "09/04/2020 5:32"),
                   Final.Weight=c(6.75,6.75,4.5,4.5,4.5),
                   Final.Rate=c(rep("1 mcg/kg/hr",2),
                                rep("0.5 mcg/kg/hr",3)),
                   Final.Units=c("3.375","6.5",
                                 "2.25","2.25","2.25"))
flow[,'Perform.Date'] <- pkdata::parse_dates(flow[,'record.date'])
flow[,'unit'] <- sub('.*[ ]', '', flow[,'Final.Rate'])
flow[,'rate'] <- as.numeric(sub('([0-9.]+).*', '\\1', flow[,'Final.Rate']))

# mar data for 4 fake drugs
mar <- data.frame(mod_id=rep(1,5),
                  Date=rep("2019-07-05",5),
                  Time=c("07:12","07:31","08:47","09:16","10:22"),
                  `med:mDrug`=c("Fakedrug2","Fakedrug1","Fakedrug2",
                                "Fakedrug3","Fakedrug4"),
                  `med:dosage`=c("30 mg","0.5 mcg","1 mg",
                                 "20 mg","3 mcg/kg/min"),
                  `med:route`=rep("IV",5),
                  `med:given`=rep("Given",5),
                  check.names=FALSE)

# medcheck file for drug of interest ('Fakedrug1')
medcheck <- data.frame(medname="Fakedrug1",freq=4672)

run_MedStrI(mar.path = mar,
            mar.columns = list(id = 'mod_id', datetime = c('Date','Time'),
                               dose = 'med:dosage', drug = 'med:mDrug', given = 'med:given'),
            flow.path = flow,
            flow.columns = list(id = 'mod_id', datetime = 'Perform.Date',
                                finalunits = 'Final.Units', unit = 'unit',
                                rate = 'rate', weight = 'Final.Weight'),
            medchk.path = medcheck,
            check.path = tempdir(),
            drugname = 'fakedrg1')