EHR (version 0.4-11)

run_DrugLevel: 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()
)

Value

drug-level data set

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.

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'
))