run_DrugLevel: Run Drug Level Data

In EHR: Electronic Health Record (EHR) Data Processing and Analysis Tool

Run Drug Level Data

Description

This module will load and modify drug-level data.

Usage

run_DrugLevel(
  conc.path,
  conc.columns = list(),
  conc.select,
  conc.rename,
  conc.mod.list = NULL,
  samp.path = NULL,
  samp.columns = list(),
  samp.mod.list = NULL,
  check.path = NULL,
  failmiss_fn = "MissingConcDate-",
  multsets_fn = "multipleSetsConc-",
  faildup_fn = "DuplicateConc-",
  drugname = NULL,
  LLOQ = NA,
  demo.list = NULL,
  demo.columns = list()
)

Arguments

conc.path	filename of concentration data (CSV, RData, RDS), or data.frame
conc.columns	a named list that should specify columns in concentration data. ‘id’ and ‘conc’ are required. ‘idvisit’ may also be specified. If linking with sampling data, ‘samplinkid’ is required. Otherwise ‘datetime’ is required. This is the date and time when blood samples were obtained. This 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’)).
conc.select	columns to select from concentration data
conc.rename	new column names for concentration data
conc.mod.list	list of expressions, giving modifications to make
samp.path	filename of data with sampling time (CSV, RData, RDS), or data.frame
samp.columns	a named list that should specify columns in sampling data. ‘conclinkid’ and ‘datetime’ are required to link sampling data to concentration data. ‘conclinkid’ should match the id variable provided as ‘samplinkid’ in the ‘conc.columns’ argument. ‘datetime’ is the date and time when blood samples were obtained. This 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’)).
samp.mod.list	list of expressions, giving modifications to make
check.path	path to ‘check’ directory, where check files are created. The default (NULL) will not produce any check files.
failmiss_fn	filename for data missing concentration date
multsets_fn	filename for data with multiple concentration sets
faildup_fn	filename for data with duplicate concentration observations
drugname	drug of interest, included in filename of check files. The default (NULL) will produce filenames without drugname included.
LLOQ	lower limit of concentration values; values below this are invalid
demo.list	demographic information; if available, concentration records must have a valid demo record
demo.columns	a named list that should specify columns in demographic data; ‘id’, is required. If ‘idvisit’ is present in the concentration data, then it is required here too.

Details

See EHR Vignette for Structured Data.

Value

drug-level data set

Examples

# concentrations
conc_data <- data.frame(mod_id = rep(1:3,each=4),
                       mod_visit = rep(c(2,1,1),each=4),
                       mod_id_visit = as.numeric(paste(rep(1:3,each=4),
                                                      rep(c(2,1,1),each=4), sep=".")),
                       samp = rep(1:4,times=3),
                       drug_calc_conc=15*exp(-1*rep(1:4,times=3))+rnorm(12,0,0.1))

# sample times
build_date <- function(x) format(seq(x, length.out=4, by="1 hour"), "%Y-%m-%d %H:%M")
dates <- unlist(lapply(rep(Sys.time(),3), build_date))

samp_data <- data.frame(mod_id = rep(1:3,each=4),
                       mod_visit = rep(c(2,1,1),each=4),
                       mod_id_visit = as.numeric(paste(rep(1:3,each=4),
                                                       rep(c(2,1,1),each=4), sep=".")),
                       samp = rep(1:4,times=3),
                       Sample.Collection.Date.and.Time = dates)

run_DrugLevel(
  conc.path = conc_data,
  conc.columns = list(
    id = 'mod_id', idvisit = 'mod_id_visit', samplinkid = 'mod_id_event', conc = 'conc.level'
  ),
  conc.select = c('mod_id','mod_id_visit','samp','drug_calc_conc'),
  conc.rename = c(drug_calc_conc= 'conc.level', samp='event'),
  conc.mod.list = list(mod_id_event = expression(paste(mod_id_visit, event, sep = "_"))),
  samp.path = samp_data,
  samp.columns = list(conclinkid = 'mod_id_event', datetime = 'Sample.Collection.Date.and.Time'),
  samp.mod.list = list(mod_id_event = expression(paste(mod_id_visit, samp, sep = "_"))),
  drugname = 'drugnm',
  LLOQ = 0.05
)

# minimal example with data in required format
conc_data <- conc_data[,c('mod_id','mod_id_visit','samp','drug_calc_conc')]
conc_data[,'mod_id_event'] <- paste(conc_data[,'mod_id_visit'], conc_data[,'samp'], sep = "_")
names(conc_data)[3:4] <- c('event','conc.level')
samp_data[,'mod_id_event'] <- paste(samp_data[,'mod_id_visit'], samp_data[,'samp'], sep = "_")
conc_samp_link <- match(conc_data[,'mod_id_event'], samp_data[,'mod_id_event'])
conc_date <- samp_data[conc_samp_link, 'Sample.Collection.Date.and.Time']
conc_data[,'date.time'] <- as.POSIXct(conc_date)
run_DrugLevel(conc_data, conc.columns = list(
  id = 'mod_id', idvisit = 'mod_id_visit', datetime = 'date.time', conc = 'conc.level'
))

EHR documentation built on Dec. 28, 2022, 1:31 a.m.