Package 'pkdata'

Title: Creates Pharmacokinetic/Pharmacodynamic (PK/PD) Data
Description: Prepare pharmacokinetic/pharmacodynamic (PK/PD) data for PK/PD analyses. This package provides functions to standardize infusion and bolus dose raw data obtained from electronic health record (EHR) databases while linking it to drug level or concentration data.
Authors: Cole Beck [aut, cre] , Leena Choi [aut]
Maintainer: Cole Beck <[email protected]>
License: GPL (>= 3)
Version: 0.1.2
Built: 2025-03-04 03:00:57 UTC
Source: https://github.com/couthcommander/pkdata

Help Index

PK Data

Description

This package will prepare data sets for PK data analysis.

Author(s)

Cole Beck, Leena Choi

Maintainer: Cole Beck [email protected]

Create a Conforming Dose Data Set

Description

Modify dose data such that it conforms for future use.

Usage

conformDoses(
  doseData,
  idVar = "id",
  dateVar = "date.dose",
  infusionDoseTimeVar = NULL,
  infusionDoseVar = NULL,
  bolusDoseTimeVar = NULL,
  bolusDoseVar = NULL,
  otherDoseTimeVar = NULL,
  otherDoseVar = NULL,
  otherVars = NULL
)

Arguments

doseData

data.frame; data set with dose information
idVar

character string; name of ID variable, defaults to id
dateVar

character string; name of date variable, defaults to date.dose
infusionDoseTimeVar

character string; name of infusion dose time variable
infusionDoseVar

character string; name of infusion dose variable
bolusDoseTimeVar

character string; name of bolus dose time variable
bolusDoseVar

character string; name of bolus dose variable
otherDoseTimeVar

character string; name of additional dose time variable
otherDoseVar

character string; name of additional dose variable
otherVars

character string; name of other variables within data set

Details

Date-time variables are given a consistent format. Invalid records are removed. The data set is sorted by date.

Value

data.frame, containing dose data

Author(s)

Cole Beck

Remove Duplicate Dose Data

Description

Modify dose data to remove duplicate dose values.

Usage

fixDuplicates(
  data,
  idVar = "id",
  infusionDoseTimeVar = NULL,
  infusionDoseVar = NULL,
  moveBolus = FALSE,
  bolusDoseTimeVar = NULL,
  bolusDoseVar = NULL
)

Arguments

data

data.frame; data set with dose information
idVar

character string; name of ID variable, defaults to id
infusionDoseTimeVar

character string; name of infusion dose time variable
infusionDoseVar

character string; name of infusion dose variable
moveBolus

logical; allow duplicate infusion doses to be categorized as bolus
bolusDoseTimeVar

character string; name of bolus dose time variable
bolusDoseVar

character string; name of bolus dose variable

Details

Some duplicates can be adjusted by changing the date-time rounding. Others may be converted from one dose type to another, such as moving infusion to bolus.

Value

data.frame, containing dose data

Author(s)

Cole Beck

Determine Format of Date and Date-Time Variables

Description

Given a vector of dates or date-times, determine the format if one is used consistently. If inconsistentencies are found, the function will fail. See strptime for examples of format specifications.

Usage

guessDateFormat(x)

Arguments

x

character vector of dates or date-times

Details

guessDateFormat is rigid when determining the date format. For date-times it expects the date and time parts to be separated by a space. It does not recognize all format specifications, such as the AM/PM indicator. The time part should have at least one colon to separate hours from minutes. The date part may have any separator as non-numerical values are removed before parsing.

Value

Returns a character string representing the format of the date-time variables.

Author(s)

Cole Beck

Examples

x <- c("2014-01-15", "20140202")
guessDateFormat(x)

Impute Dose Data

Description

Use last-observation-carried-forward to impute missing dose values by hour.

Usage

imputeDoses(
  data,
  idVar = "id",
  dateVar = "date.dose",
  infusionDoseTimeVar = NULL,
  infusionDoseVar = NULL,
  maxskips = 3
)

Arguments

data

data.frame; data set with dose information
idVar

character string; name of ID variable, defaults to id
dateVar

character string; name of date variable, defaults to date.dose
infusionDoseTimeVar

character string; name of infusion dose time variable
infusionDoseVar

character string; name of infusion dose variable
maxskips

integer; maximum number of missed doses that may be imputed

Details

Creates skips column

Value

data.frame, containing dose data

Author(s)

Cole Beck

Parse Date and Date-Time Variables

Description

Given a vector of dates or date-times, create Date or POSIXct variables.

Usage

parse_dates(x, tz = getOption("pkdata.tz", ""))

Arguments

x

character vector of dates or date-times
tz

character string; specifies the time zone to be used for the conversion. Defaults to the current time zone.

Details

parse_dates calls parse_date_time from the lubridate package. While parse_date_time accepts multiple date formats, parse_dates requires a consistent format.

Value

vector of Date or POSIXct objects

Author(s)

Cole Beck

Examples

x <- c("2014-01-15", "20140202")
parse_dates(x)
x <- c("2014-01-15 01:51", "20140202 04:35:18")
parse_dates(x)

Prepare the Dose Data Set

Description

Create a dose data set with conforming data, and remove invalid records.

Usage

prepareDoses(
  doseData,
  drugLevelData,
  drugLevelID = "id",
  drugLevelTimeVar = "date.time",
  drugLevelVar = "fent.level",
  idVar = "id",
  dateVar = "date.dose",
  infusionDoseTimeVar = NULL,
  infusionDoseVar = NULL,
  bolusDoseTimeVar = NULL,
  bolusDoseVar = NULL,
  otherDoseTimeVar = NULL,
  otherDoseVar = NULL,
  otherVars = NULL,
  lookForward = 7
)

Arguments

doseData

data.frame; data set with dose information
drugLevelData

data.frame; data set with drug level data
drugLevelID

character string; name of ID variable, defaults to id
drugLevelTimeVar

character string; name of date-time variable, defaults to date.time
drugLevelVar

character string; name of drug level variable, defaults to fent.level
idVar

character string; name of ID variable, defaults to id
dateVar

character string; name of date variable, defaults to date.dose
infusionDoseTimeVar

character string; name of infusion dose time variable
infusionDoseVar

character string; name of infusion dose variable
bolusDoseTimeVar

character string; name of bolus dose time variable
bolusDoseVar

character string; name of bolus dose variable
otherDoseTimeVar

character string; name of additional dose time variable
otherDoseVar

character string; name of additional dose variable
otherVars

character string; name of other variables within data set
lookForward

integer; initializes the time frame window with the number of days prior to the first drug level data; defaults to 7

Details

Wrapper function for conformDoses and trimDoses.

Value

data.frame, containing dose data

Author(s)

Cole Beck

Examples

options(pkdata.tz='America/Chicago')
dose.file <- read.csv(system.file('extdata', 'dosage.csv', package = 'pkdata'),
                      stringsAsFactors = FALSE)
drug.level.file <- read.csv(system.file('extdata', 'druglevel.csv', package = 'pkdata'),
                            stringsAsFactors = FALSE)
prepped <- prepareDoses(dose.file, drug.level.file,
     infusionDoseTimeVar='inf.time', infusionDoseVar='inf.dose',
     bolusDoseTimeVar='bol.time', bolusDoseVar='bol.dose',
     otherDoseTimeVar='patch.time', otherDoseVar='patch.dose',
     otherVars=c('gender','weight'))

Sort Dose Data Set

Description

Helper function to sort dose data set by ID and time variables.

Usage

sortDoses(
  data,
  idVar = "id",
  infusionDoseTimeVar = NULL,
  bolusDoseTimeVar = NULL,
  otherDoseTimeVar = NULL
)

Arguments

data

data.frame; data set with dose information
idVar

character string; name of ID variable, defaults to id
infusionDoseTimeVar

character string; name of infusion dose time variable
bolusDoseTimeVar

character string; name of bolus dose time variable
otherDoseTimeVar

character string; name of additional dose time variable

Details

Sort order will be the ID variable, then infusion time, bolus time, or other dose date-time variables.

Value

data.frame, containing dose data

Author(s)

Cole Beck

Trim Dose Data Set

Description

Remove invalid doses by creating a time frame window constructed from drug level data.

Usage

trimDoses(
  doseData,
  drugLevelData,
  drugLevelID = "id",
  drugLevelTimeVar = "date.time",
  drugLevelVar = "fent.level",
  infusionDoseTimeVar = NULL,
  infusionDoseVar = NULL,
  bolusDoseTimeVar = NULL,
  bolusDoseVar = NULL,
  otherDoseTimeVar = NULL,
  otherDoseVar = NULL,
  lookForward = 7,
  last = NA
)

Arguments

doseData

data.frame; data set with dose information
drugLevelData

data.frame; data set with drug level data
drugLevelID

character string; name of ID variable, defaults to id
drugLevelTimeVar

character string; name of date-time variable, defaults to date.time
drugLevelVar

character string; name of drug level variable, defaults to fent.level
infusionDoseTimeVar

character string; name of infusion dose time variable
infusionDoseVar

character string; name of infusion dose variable
bolusDoseTimeVar

character string; name of bolus dose time variable
bolusDoseVar

character string; name of bolus dose variable
otherDoseTimeVar

character string; name of additional dose time variable
otherDoseVar

character string; name of additional dose variable
lookForward

integer; initializes the time frame window with the number of days prior to the first drug level data; defaults to 7
last

integer; sets the end of the time frame window to be "last" days after the first dose date, rather than the date of the last drug level data

Details

The time frame window is generally seven days before drug level data up through the last drug level data record. The window can be adjusted by setting the lookForward and last arguments.

Value

data.frame, containing trimmed dose data

Author(s)

Cole Beck