Non Compart Manual

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Package ‘NonCompart’
August 16, 2017
Version 0.3.3
Date 2017-08-16 KST
Title Noncompartmental Analysis for Pharmacokinetic Data
Description Conduct a noncompartmental analysis as closely as possible to the most widely used commercial software for pharmacokinetic analysis, i.e. 'Phoenix(R) WinNonlin(R)' .
Some features are
1) Use of CDISC SDTM terms
2) Automatic slope selection with the same criterion of WinNonlin(R)
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Depends R (>= 2.0.0)
Author Kyun-Seop Bae [aut]
Maintainer Kyun-Seop Bae 
Copyright 2016-2017, Kyun-Seop Bae
License GPL-3
NeedsCompilation no
LazyLoad yes
Repository CRAN
URL https://cran.r-project.org/package=NonCompart

R topics documented:
NonCompart-package
AUC . . . . . . . . .
BestSlope . . . . . .
IntAUC . . . . . . .
Interpol . . . . . . .
LinAUC . . . . . . .
LogAUC . . . . . . .
Slope . . . . . . . .
sNCA . . . . . . . .
tblNCA . . . . . . .
Unit . . . . . . . . .
UnitUrine . . . . . .

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2

NonCompart-package

Index

16

NonCompart-package

Noncompartmental Analysis for Pharmacokinetic Data

Description
It conducts a noncompartmental analysis(NCA) as closely as possible to the most widely used
commercial pharmacokinetic analysis software.
Details
The main functions are
tblNCA

to perform NCA for many subjects.

sNCA

to perform NCA for one subject.

Author(s)
Kyun-Seop Bae 
References
1. Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts
and Applications. 5th ed. 2016.
2. Shargel L, Yu A. Applied Biopharmaceutics and Pharmacokinetics. 7th ed. 2015.
3. Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics - Concepts and
Applications. 4th ed. 2011.
4. Gibaldi M, Perrier D. Pharmacokinetics. 2nd ed. revised and expanded. 1982.
Examples
# Theoph and Indometh data: dose in mg, conc in mg/L, time in h
tblNCA(Theoph, key="Subject", colTime="Time", colConc="conc", dose=320,
adm="Extravascular", doseUnit="mg", concUnit="mg/L")
tblNCA(Indometh, key="Subject", colTime="time", colConc="conc", dose=25,
adm="Infusion", dur=0.5, doseUnit="mg", concUnit="mg/L")
# For individual NCA
iAUC = data.frame(Name=c("AUC[0-12h]","AUC[0-24h]"), Start=c(0,0), End=c(12,24)) ; iAUC
x = Theoph[Theoph$Subject=="1","Time"]
y = Theoph[Theoph$Subject=="1","conc"]
sNCA(x, y, dose=320, doseUnit="mg", concUnit="mg/L", timeUnit="h", iAUC=iAUC)
sNCA(x, y, dose=320, concUnit="mg/L", iAUC=iAUC)

AUC

AUC

3

Calculate Area Under the Curve (AUC) and Area Under the first Moment Curve (AUMC) in a table format

Description
Calculate Area Under the Curve(AUC) and the first Moment Curve(AUMC) in two ways; ’linear
trapezoidal method’ or ’linear-up and log-down’ method. Return a table of cumulative values.
Usage
AUC(x, y, down = "Linear")
Arguments
x

vector values of independent variable, usually time

y

vector values of dependent variable, usually concentration

down

either of "Linear" or "Log" to indicate the way to calculate AUC and AUMC

Details
down="Linear" means linear trapezoidal rule with linear interpolation. down="Log" means linearup and log-down method.
Value
Table with two columns, AUC and AUMC; the first column values are cumulative AUCs and the second
column values cumulative AUMCs.
Author(s)
Kyun-Seop Bae 
References
Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics - Concepts and Applications. 4th ed. pp687-689. 2011.
See Also
LinAUC, LogAUC
Examples
AUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"])
AUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"], down="Log")

4

BestSlope

BestSlope

Choose best fit slope for the log(y) and x regression by the criteria of
adjusted R-square

Description
It sequentially fits (log(y) ~ x) from the last point of x to the previous points with at least 3 points. It
chooses a slope the highest adjusted R-square. If the difference is less then 1e-4, it chooses longer
slope.
Usage
BestSlope(x, y, adm = "Extravascular", TOL=1e-4)
Arguments
x

vector values of x-axis, usually time

y

vector values of y-axis, usually concentration

adm

one of "Bolus" or "Infusion" or "Extravascular" to indicate drug administration mode

TOL

tolerance. See Phoneix WinNonlin 6.4 User’s Guide p33 for the detail.

Details
Choosing the best terminal slope (y in log scale) in pharmacokinetic analysis is somewhat challenging, and it could vary by analysis performer. Pheonix WinNonlin chooses a slope with highest
adjusted R-squared and the longest one. Difference of adjusted R-Squared less than TOL considered
to be 0. This function uses ordinary least square method (OLS).
Value
R2

R-squared

R2ADJ

adjusted R-squared

LAMZNPT

number of points used for slope

LAMZ

negative of slope, lambda_z

b0

intercept of regression line

CORRXY

correlation of log(y) and x

LAMZLL

earliest x for lambda_z

LAMZUL

last x for lambda_z

CLSTP

predicted y value at last point, predicted concentration for the last time point

Author(s)
Kyun-Seop Bae 
See Also
Slope

IntAUC

5

Examples
BestSlope(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"])
BestSlope(Indometh[Indometh$Subject==1, "time"], Indometh[Indometh$Subject==1, "conc"],
adm="Bolus")

Calculate interval AUC

IntAUC

Description
It calculates interval AUC
Usage
IntAUC(x, y, t1, t2, Res, down = "Linear")
Arguments
x

vector values of independent variable, usually time

y

vector values of dependent variable, usually concentration

t1

start time for AUC

t2

end time for AUC

Res

result from IndiNCA function

down

either of "Linear" or "Log" to indicate the way to calculate AUC

Details
This calculates an interval (partial) AUC (from t1 to t2) with the given series of x and y. If t1 and/or
t2 cannot be found within x vector, it interpolates according to the down option.
Value
return interval AUC value (scalar)
Author(s)
Kyun-Seop Bae 
References
1. Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts
and Applications. 5th ed. 2016.
2. Shargel L, Yu A. Applied Biopharmaceutics and Pharmacokinetics. 7th ed. 2015.
3. Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics - Concepts and
Applications. 4th ed. 2011.
4. Gibaldi M, Perrier D. Pharmacokinetics. 2nd ed. revised and expanded. 1982.
See Also
AUC, Interpol

6

Interpol

Examples
Res = sNCA(Theoph[Theoph$Subject==1,"Time"], Theoph[Theoph$Subject==1, "conc"],
dose=320, concUnit="mg/L")
IntAUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"], t1=0.5, t2=11, Res)

Interpol

Interpolate y value

Description
It interpolates y value when a corresponding x value (xnew) does not exist within x vector
Usage
Interpol(x, y, xnew, Slope, b0, down = "Linear")
Arguments
x

vector values of x-axis, usually time

y

vector values of y-axis, usually concentration

xnew

new x point to be interpolated, usually new time point

Slope

slope of regression log(y) ~ x

b0

y value of just left point of xnew

down

either of "Linear" or "Log" to indicate the way to interpolate

Details
This function interpolate y value, if xnew is not in x vector. If xnew is in x vector, it just returns the
given x and y vector. This function usually is called by IntAUC function Returned vector is sorted
in the order of increasing x values.
Value
new x and y vector containing xnew and ynew point
Author(s)
Kyun-Seop Bae 
See Also
IntAUC
Examples
x = 10:1 + 0.1
y = -2*x + 40.2
Interpol(x, y, 1.5)
Interpol(x, y, 1.5, down="Log")

LinAUC

LinAUC

7

Area Under the Curve(AUC) and Area Under the first Moment
Curve(AUMC) by linear trapezoidal method

Description
It calculates AUC and AUMC using linear trapezoidal method
Usage
LinAUC(x, y)
Arguments
x

vector values of independent variable, usually time

y

vector values of dependent variable, usually concentration

Details
This function returns AUC and AUMC by linear trapezoidal method.
Value
AUC

area under the curve

AUMC

area under the first moment curve

Author(s)
Kyun-Seop Bae 
References
1. Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts
and Applications. 5th ed. 2016.
2. Shargel L, Yu A. Applied Biopharmaceutics and Pharmacokinetics. 7th ed. 2015.
3. Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics - Concepts and
Applications. 4th ed. 2011.
4. Gibaldi M, Perrier D. Pharmacokinetics. 2nd ed. revised and expanded. 1982.
See Also
LogAUC, AUC
Examples
LinAUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"])
AUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"]) # compare the last line

8

LogAUC

LogAUC

Area Under the Curve(AUC) and Area Under the first Moment
Curve(AUMC) by linear-up log-down method

Description
It calculates AUC and AUMC using linear-up log-down method
Usage
LogAUC(x, y)
Arguments
x

vector values of independent variable, usually time

y

vector values of dependent variable, usually concentration

Details
This function returns AUC and AUMC by linear-up log-down method.
Value
AUC

area under the curve

AUMC

area under the first moment curve

Author(s)
Kyun-Seop Bae 
References
1. Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts
and Applications. 5th ed. 2016.
2. Shargel L, Yu A. Applied Biopharmaceutics and Pharmacokinetics. 7th ed. 2015.
3. Rowland M, Tozer TN. Clinical Pharmacokinetics and Pharmacodynamics - Concepts and
Applications. 4th ed. 2011.
4. Gibaldi M, Perrier D. Pharmacokinetics. 2nd ed. revised and expanded. 1982.
See Also
LinAUC,AUC
Examples
LogAUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"])
# Compare the last line with the above
AUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"], down="Log")

Slope

Slope

9

Get the Slope of regression log(y) ~ x

Description
It calculates the slope with linear regression of log(y) ~ x
Usage
Slope(x, y)
Arguments
x

vector values of independent variable, usually time

y

vector values of dependent variable, usually concentration

Details
With time-concentration curve, you frequently need to estimate slope in log(concentration) ~ time.
This function is usually called by BestSlope function and you seldom need to call this function
directly.
Value
R2

R-squared

R2ADJ

adjusted R-squared

LAMZNPT

number of points used for slope

LAMZ

negative of slope, lambda_z

b0

intercept of regression line

CORRXY

correlation of log(y) and x

LAMZLL

earliest x for lambda_z

LAMZUL

last x for lambda_z

CLSTP

predicted y value at last point, predicted concentration for the last time point

Author(s)
Kyun-Seop Bae 
See Also
BestSlope
Examples
Slope(Indometh[Indometh$Subject==1, "time"], Indometh[Indometh$Subject==1, "conc"])

10

sNCA

sNCA

Simplest NCA

Description
This is the work-horse function for NCA.
Usage
sNCA(x, y, dose = 0, adm = "Extravascular", dur = 0, doseUnit = "mg", timeUnit = "h",
concUnit = "ug/L", iAUC = "", down = "Linear", MW = 0)
Arguments
x

usually time

y

usually concentration

dose

given amount

adm

one of "Bolus" or "Infusion" or "Extravascular" to indicate drug administration mode

dur

duration of infusion

doseUnit

unit of dose

timeUnit

unit of time

concUnit

unit of concentration

iAUC

interval AUCs to calculate

down

either of "Linear" or "Log" to indicate the way to calculate AUC and AUMC

MW

molecular weight of the drug

Details
This will replace IndiNCA.
Value
CMAX

maximum concentration, Cmax

CMAXD

dose normalized Cmax, CMAX / Dose, Cmax / Dose

TMAX

time of maximum concentration, Tmax

TLAG

time to observe the first non-zero concentration, for extravascular administration
only

CLST

last positive concentration observed, Clast

CLSTP

last positive concentration predicted, Clast_pred

TLST

time of last positive concentration, Tlast

LAMZHL

half-life by lambda z, ln(2)/LAMZ

LAMZ

lambda_z negative of best fit terminal slope

LAMZLL

earliest time for LAMZ

LAMZUL

last time for LAMZ

sNCA
LAMZNPT
CORRXY
R2
R2ADJ
C0
AUCLST
AUCALL
AUCIFO
AUCIFOD
AUCIFP
AUCIFPD
AUCPEO
AUCPEP
AUCPBEO
AUCPBEP
AUMCLST
AUMCIFO
AUMCIFP
AUMCPEO
AUMCPEP
MRTIVLST
MRTIVIFO
MRTIVIFP
MRTEVLST
MRTEVIFO
MRTEVIFP
VZO
VZP
VZFO
VZFP
CLO
CLP
CLFO
CLFP
VSSO
VSSP

11
number of points for LAMZ
correlation of log(concentration) and time
R-squared
R-squared adjusted
back extrapolated concentration at time 0, for bolus intravascular administration
only
AUC from 0 to TLST
AUC using all the given points, including trailing zero concentrations
AUC infinity observed
AUCIFO / Dose
AUC infinity predicted using CLSTP instead of CLST
AUCIFP / Dose
AUC % extrapolation observed
AUC % extrapolated for AUCIFP
AUC % back extrapolation observed, for bolus IV administration only
AUC % back extrapolation predicted with AUCIFP, for bolus IV administration
only
AUMC to the TLST
AUMC infinity observed using CLST
AUMC infinity determined by CLSTP
AUMC % extrapolated observed
AUMC % extrapolated predicted
mean residence time (MRT) to TLST, for intravascular administration
mean residence time (MRT) infinity using CLST, for intravascular administration
mean residence time (MRT) infinity using CLSTP, for intravascular administration
mean residence time (MRT) to TLST, for extravascular administration
mean residence time (MRT) infinity using CLST, for extravascular administration
mean residence time (MRT) infinity using CLSTP, for extravascular administration
volume of distribution determined by LAMZ and AUCIFO, for intravascular
administration
volume of distribution determined by LAMZ and AUCIFP, for intravascular administration
VZO for extravascular administration, VZO/F, F is bioavailability
VZP for extravascular administration, VZP/F, F is bioavailability
clearance using AUCIFO, for intravascular administration
clearance using AUCIFP, for intravascular administration
CLO for extravascular administration, CLO/F, F is bioavailability
CLP for extravascular administration, CLP/F, F is bioavailability
volume of distribution at steady state using CLST, for intravascular administration only
volume of distribution at steady state using CLSTP, for intravascular administration only

12

tblNCA

Author(s)
Kyun-Seop Bae 
References
Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and
Applications. 5th ed. 2016.
See Also
help, tblNCA
Examples
# For one subject
x = Theoph[Theoph$Subject=="1","Time"]
y = Theoph[Theoph$Subject=="1","conc"]
sNCA(x, y, dose=320, doseUnit="mg", concUnit="mg/L", timeUnit="h")
sNCA(x, y, dose=320, concUnit="mg/L")
iAUC = data.frame(Name=c("AUC[0-12h]","AUC[0-24h]"), Start=c(0,0), End=c(12,24))
sNCA(x, y, dose=320, doseUnit="mg", concUnit="mg/L", timeUnit="h", iAUC=iAUC)
MW = 180.164 # Molecular weight of theophylline
sNCA(x,
sNCA(x,
sNCA(x,
sNCA(x,

y/MW, dose=320, doseUnit="mg", concUnit="mmol/L", timeUnit="h")
y/MW, dose=320, doseUnit="mg", concUnit="mmol/L", timeUnit="h", MW=MW)
y, dose=320/MW, doseUnit="mmol", concUnit="mg/L", timeUnit="h", MW=MW)
y/MW, dose=320/MW, doseUnit="mmol", concUnit="mmol/L", timeUnit="h", MW=MW)

sNCA(x, y/MW, dose=320/MW, doseUnit="mmol", concUnit="mmol/L", timeUnit="h", MW=MW)
sNCA(x, y/MW, doseUnit="mmol", concUnit="mmol/L", timeUnit="h", MW=MW)
sNCA(x, y/MW, dose=as.numeric(NA), doseUnit="mmol", concUnit="mmol/L", timeUnit="h",
MW=MW)
sNCA(x, y, dose=320, concUnit="mg/L", timeUnit="hr")
sNCA(x*60, y, dose=320, concUnit="mg/L", timeUnit="min")

tblNCA

Table output NCA

Description
Do multiple NCA and returns a result table.
Usage
tblNCA(concData, key = "Subject", colTime = "Time", colConc = "conc", dose = 0,
adm = "Extravascular", dur = 0, doseUnit = "mg", timeUnit = "h",
concUnit = "ug/L", down = "Linear", MW = 0)

Unit

13

Arguments
concData

concentration data table

key

column names of concData to be shown at the output table

colTime

column name for time

colConc

column name for concentration

dose

administered dose

adm

one of "Bolus" or "Infusion" or "Extravascular" to indicate drug administration mode

dur

duration of infusion

doseUnit

unit of dose

timeUnit

unit of time

concUnit

unit of concentration

down

method to calculate AUC, "Linear" or "Log"

MW

molecular weight of drug

Value
Basically same with sNCA
Author(s)
Kyun-Seop Bae 
See Also
help, sNCA
Examples
tblNCA(Theoph, key="Subject", dose=320, concUnit="mg/L")
tblNCA(Indometh, key="Subject", colTime="time", colConc="conc", dose=25,
adm="Infusion", dur=0.5, concUnit="mg/L")

Unit

Disply CDISC standard units and multiplied factor of NCA results

Description
It displays CDISC PP output units and multiplication factor for them.
Usage
Unit(code = "", timeUnit = "h", concUnit = "ng/mL", doseUnit = "mg", MW = 0)

14

UnitUrine

Arguments
code

vector of PPTESTCD

timeUnit

unit of time

concUnit

unit of concentration

doseUnit

unit of dose

MW

molecular weight of drug

Value
row names

PPTESTCD

Unit

unit

Factor

internal mulitpilcation factor

Author(s)
Kyun-Seop Bae 
Examples
Unit(concUnit="ug/L", doseUnit="mg")
Unit(concUnit="ng/L", doseUnit="mg")
Unit(concUnit="umol/L", doseUnit="mmol")
Unit(concUnit="nmol/L", doseUnit="mmol")
Unit(concUnit="mmol/L", doseUnit="mg", MW=500)
Unit(concUnit="umol/L", doseUnit="mg", MW=500)
Unit(concUnit="nmol/L", doseUnit="mg", MW=500)
Unit(concUnit="nmol/mL", doseUnit="mg", MW=500)
Unit(concUnit="ug/L", doseUnit="mmol", MW=500)
Unit(concUnit="ug/L", doseUnit="mol", MW=500)
Unit(concUnit="ng/L", doseUnit="mmol", MW=500)
Unit(concUnit="ng/mL", doseUnit="mmol", MW=500)
Unit(concUnit="nmol/L", doseUnit="mg")
Unit(concUnit="ug/L", doseUnit="mmol")

UnitUrine

Retuns a conversion factor for the amount calculation from urine concentration and volume

Description
You can get a conversion factor for the mulplication: conc * vol * factor = amount in the given unit.
Usage
UnitUrine(conU = "ng/mL", volU = "mL", amtU = "mg", MW = 0)

UnitUrine

15

Arguments
conU

concentration unit

volU

volume unit

amtU

amount unit

MW

molecular weight

Value
Factor

conversion factor for multiplication with the unit in name

Author(s)
Kyun-Seop Bae 
Examples
UnitUrine()
UnitUrine("ng/mL", "mL", "mg")
UnitUrine("ug/L", "mL", "mg")
UnitUrine("ug/L", "L", "mg")
UnitUrine("ng/mL", "mL", "g")
UnitUrine("ng/mL", "mL", "mol", MW=500)
UnitUrine("ng/mL", "mL", "mmol", MW=500)
UnitUrine("ng/mL", "mL", "umol", MW=500)

Index
∗Topic AUC
AUC, 3
IntAUC, 5
LinAUC, 7
LogAUC, 8
∗Topic NCA
NonCompart-package, 2
∗Topic Output Form
sNCA, 10
tblNCA, 12
∗Topic Slope
BestSlope, 4
∗Topic interpolation
Interpol, 6
∗Topic interval AUC
IntAUC, 5
Interpol, 6
∗Topic package
NonCompart-package, 2
∗Topic partial AUC
IntAUC, 5
Interpol, 6
∗Topic slope
Slope, 9
AUC, 3, 5, 7, 8
BestSlope, 4, 9
help, 12, 13
IntAUC, 5, 6
Interpol, 5, 6
LinAUC, 3, 7, 8
LogAUC, 3, 7, 8
NonCompart (NonCompart-package), 2
NonCompart-package, 2
Slope, 4, 9
sNCA, 10, 13
tblNCA, 12, 12
Unit, 13
UnitUrine, 14
16



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Source Exif Data:

File Type                       : PDF
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Author                          : 
Create Date                     : 2017:08:16 10:25:45+09:00
Creator                         : LaTeX with hyperref package
Modify Date                     : 2017:08:16 10:25:45+09:00
PTEX Fullbanner                 : This is MiKTeX-pdfTeX 2.9.6211 (1.40.17)
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Subject                         : 
Title                           : 
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