Package {NonCompart}

Noncompartmental Analysis for Pharmacokinetic Data

Description

It conducts a noncompartmental analysis(NCA) with industrial strength.

Details

The main functions are

tblNCA   to perform NCA for many subjects.

sNCA     to perform NCA for one subject.

Author(s)

Kyun-Seop Bae <k@acr.kr>

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", R2ADJ=0.9)

# 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)

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

Details

down="Linear" means linear trapezoidal rule with linear interpolation. down="Log" means linear-up 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 <k@acr.kr>

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")

Choose the 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 pickes longer slope.

Usage

  BestSlope(x, y, adm = "Extravascular", TOL=1e-4, excludeDelta = 1)

Arguments

Details

Choosing the best terminal slope (y in log scale) in pharmacokinetic analysis is somewhat challenging, and it could vary by analysis performer. Phoenix WinNonlin chooses a slope with highest adjusted R-squared and the longest one. The difference of adjusted R-Squared less than TOL considered to be 0. This function uses ordinary least square method (OLS). Author recommends to use excludeDelta option with about 0.3.

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

Slope

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")

Determine slope for the log(y) and x regression manually

Description

You choose a slope for terminal half-life.

Usage

DetSlope(x, y, SubTitle="", sel.1=0, sel.2=0)

Arguments

Details

Sometimes BestSlope cannot find terminal slope satisfactorily. Then you can use this function to choose manually. It returns the same format result with BestSlope with an attribute indicating used points.

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

Slope

Examples

DetSlope(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"])
DetSlope(Indometh[Indometh$Subject==2, "time"], Indometh[Indometh$Subject==2, "conc"])

Installation Qualification (IQ) report to a pdf file

Description

Generate a self-contained PDF report documenting whether the NonCompart package is correctly installed, intact, loadable, and operational in the user's own R environment. It is intended as Installation Qualification (IQ) evidence, in the spirit of the WinNonlin validation suite. The report uses only base R and the package's own pdf helpers, so it requires no LaTeX, pandoc, or other external tools. The signature (approval) page is placed first and the report uses 1 inch margins on every side, with Letter paper in a United States locale and A4 elsewhere.

Usage

IQNCA(fileName = "NonCompart-IQ-Report.pdf", pkgs = "NonCompart",
      functional = TRUE, performedBy = "", paper = "auto", sigField = FALSE)

Arguments

Details

The report contains: the test environment (R version, platform, OS, locale, library paths); the installed package version, location and declared-dependency satisfaction; file integrity via checkMD5sums (PASS / FAIL / WARN when no manifest is present - see writeMD5NCA); namespace load and core exports; an optional functional verification; an overall QUALIFIED / NOT QUALIFIED verdict; a sessionInfo appendix; and a per-file md5 checksum appendix.

Value

Invisibly, a list with fileName, qualified, paper, checks (a data frame of every check), and the counts nPass, nFail, nWarn. A PDF file is written to fileName.

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

OQNCA, writeMD5NCA, sNCA, tblNCA

Examples

#IQNCA()
#res <- IQNCA(performedBy = "Jane Doe"); res$qualified

Calculate interval AUC

Description

It calculates interval AUC

Usage

IntAUC(x, y, t1, t2, Res, down = "Linear")

Arguments

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 <k@acr.kr>

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

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)

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

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 <k@acr.kr>

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")

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

Description

It calculates AUC and AUMC using the linear trapezoidal method

Usage

LinAUC(x, y)

Arguments

Details

This function returns AUC and AUMC by the linear trapezoidal method.

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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

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 the linear-up log-down method

Usage

LogAUC(x, y)

Arguments

Details

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

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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") 

Operational Qualification (OQ) report to a pdf file

Description

Generate a self-contained PDF report that documents whether the NonCompart noncompartmental analysis engine reproduces pre-specified reference results on the user's own machine, within a pre-specified relative tolerance. It is intended as Operational Qualification (OQ) evidence, in the spirit of the WinNonlin computational-engine verification. The report lists every computed value next to its reference value, with the absolute and relative difference and a pass flag, then an overall verdict. It uses only base R and the package's pdf helpers (no LaTeX). The signature page is first; 1 inch margins; Letter paper in a United States locale and A4 elsewhere.

Usage

OQNCA(fileName = "NonCompart-OQ-Report.pdf", cases = NULL, tol = 0.001,
      refDir = system.file("OQ", package = "NonCompart"), performedBy = "",
      paper = "auto", sigField = FALSE)

Arguments

Details

For each case the function runs tblNCA on the (frozen) input data, maps the CDISC PPTESTCD result columns to WinNonlin parameter names using ‘RptCfg.csv’ in refDir, matches comparable parameters to the reference table (robust to % vs . naming), and compares every parameter for every subject. A case passes only when all of its comparisons pass.

The bundled reference values are WinNonlin 6.4 NCA outputs. These establish concordance with the de-facto reference implementation (Tier B); they are not, by themselves, an independent verification.

Value

Invisibly, a list with fileName, qualified, tol, nCases, nFailCases, paper, and results (a per-case list whose comp element is the full table of every comparison). A PDF is written to fileName.

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

IQNCA, writeMD5NCA, tblNCA

Examples

#OQNCA()
#res <- OQNCA(); res$qualified; res$results[[1]]$comp

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

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

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

BestSlope

Examples

Slope(Indometh[Indometh$Subject==1, "time"], Indometh[Indometh$Subject==1, "conc"])

Display 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)

Arguments

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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")

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

Description

You can get a conversion factor for the multiplication: conc * vol * factor = amount in the given unit.

Usage

UnitUrine(conU = "ng/mL", volU = "mL", amtU = "mg", MW = 0)

Arguments

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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)

Add Acrobat-Reader signature fields to a report PDF

Description

Insert empty digital-signature form fields (AcroForm /Sig fields) into a PDF so it can be signed in Adobe Acrobat Reader (the free reader) with one click: open the PDF, click a field, and sign with a Digital ID. The field is added with a pure base-R PDF incremental update, with no external tools or packages, so it works wherever R does. It is designed for the simple PDFs produced by IQNCA and OQNCA.

Acrobat Reader can also sign a PDF that has no field at all (“All tools” > “Use a certificate” > “Digitally sign”, then drag a rectangle). This function only makes the workflow click-to-sign by pre-placing labelled fields.

Usage

addSigFieldNCA(pdf, out = pdf, page = 1L,
            fieldNames = c("Performed_by", "Reviewed_by"), rects = NULL)

Arguments

Details

The function appends an incremental-update section that adds an /AcroForm to the document catalog (with /SigFlags 3), one /Widget signature annotation per field, and the field references to the page's /Annots. The original content is left untouched. The resulting fields are unsigned; the actual cryptographic signature is applied by Acrobat Reader using the signer's Digital ID. Only classic cross-reference-table PDFs are supported (those written by R's pdf device); the function stops on cross-reference-stream PDFs.

Value

Invisibly, the output path. A PDF with signature fields is written as a side effect.

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

IQNCA, OQNCA, signPDFNCA

Examples

#IQNCA("NonCompart-IQ-Report.pdf", performedBy = "Kyun-Seop Bae")
#addSigFieldNCA("NonCompart-IQ-Report.pdf")          # adds Performed_by / Reviewed_by fields
## or in one step:
#IQNCA("NonCompart-IQ-Report.pdf", performedBy = "Kyun-Seop Bae", sigField = TRUE)
## then open in Acrobat Reader and click each field to sign with your Digital ID.

General Area Under the Curve

Description

General AUC function for Emax, TEmax and AUCs

Usage

gAUC(x, y, Ymax = "Emax", XofYmax = "TEmax", AUCname = "AUEClast", iAUC = "", 
     Outer = "NEAREST")

Arguments

Details

This is a general purpose AUC function. It calculates only Cmax(Emax), Tmax(TEmax) and AUCs(AUECs). This can be used for effect(pharmacodynamic) data which has negative values. For concentration data, use IntAUC.

Value

Column names can vary according to the options.

Author(s)

Kyun-Seop Bae <k@acr.kr>

Examples

# For one subject
x = Theoph[Theoph$Subject=="1", "Time"]
y = Theoph[Theoph$Subject=="1", "conc"]
gAUC(x, y)

iAUC = data.frame(Name=c("AUC[0-12h]","AUC[0-24h]"), Start=c(0,0), End=c(12,24))
gAUC(x, y, iAUC=iAUC)

Calculate interval AUC of general form

Description

It calculates interval AUC of general form. This is useful for pharmacodynamic data.

Usage

gIntAUC(x, y, t1, t2, Outer = "NEAREST")

Arguments

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. If t1 and/or t2 are out of x range, it uses the nearest value. For concentration data, use IntAUC.

Value

return interval AUC value (scalar)

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

gAUC, gInterpol, tblAUC

Examples

gIntAUC(Theoph[Theoph$Subject==1, "Time"], Theoph[Theoph$Subject==1, "conc"], t1=0.5, t2=11)

Interpolate y value for general y value not for concentration

Description

It interpolates y value when a corresponding x value (xnew) does not exist within x vector

Usage

gInterpol(x, y, xnew, Outer="NEAREST")

Arguments

Details

This function interpolate y value, if xnew is not in x vector. If xnew is in the x vector, it just returns the given x and y vector. This function usually is called by gIntAUC 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 <k@acr.kr>

See Also

gIntAUC

Examples

x = 1:10 + 0.1
y = -2*x + 40.2
gInterpol(x, y, 1.5)
gInterpol(x, y, 0.5) # Out of range, Left
gInterpol(x, y, 11) # Out of range, Right

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", R2ADJ = 0.7, MW = 0, SS = FALSE, 
     Keystring="", excludeDelta = 1, UsePoints = NULL)

Arguments

Details

This replaced previous IndiNCA. Author recommends to use excludeDelta option with about 0.3.

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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

Digitally sign and verify a PDF report

Description

Apply a cryptographic digital signature to a (report) PDF, as an alternative to the print-sign-scan workflow, and verify it. signPDFNCA signs the PDF bytes with the signer's private key (RSA or EC) using SHA-256 and writes a detached signature sidecar ‘<pdf>.sig’ (and, by default, the signer's public key ‘<pdf>.pubkey.pem’). verifyPDFNCA confirms, with the signer's public key or certificate, that the PDF is byte-for-byte intact and was signed by that key (tamper-evidence and non-repudiation). These functions require the openssl package.

This is a detached signature (a separate ‘.sig’ file), not a PAdES signature embedded inside the PDF; embedding a visible in-viewer signature requires a dedicated PDF tool (e.g. Adobe Acrobat or ‘⁠pyhanko⁠’). The detached signature is cryptographically equivalent for integrity and non-repudiation.

Usage

signPDFNCA(pdf, key, password = NULL, signer = "", role = "",
        sigFile = paste0(pdf, ".sig"), writePubkey = TRUE)

verifyPDFNCA(pdf, sigFile = paste0(pdf, ".sig"), pubkey = paste0(pdf, ".pubkey.pem"))

Arguments

Value

signPDFNCA invisibly returns a list with the sidecar path, the PDF sha256, the signer, and the public-key fingerprint; it writes the ‘.sig’ sidecar as a side effect. verifyPDFNCA invisibly returns TRUE only if both the signature is valid and the recorded hash matches, and prints a human-readable result.

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

IQNCA, OQNCA, writeMD5NCA

Examples

#key <- openssl::rsa_keygen()
#openssl::write_pem(key, "signer_key.pem")
#IQNCA("NonCompart-IQ-Report.pdf", performedBy = "Kyun-Seop Bae")
#signPDFNCA("NonCompart-IQ-Report.pdf", "signer_key.pem", signer = "Kyun-Seop Bae")
#verifyPDFNCA("NonCompart-IQ-Report.pdf")

Table output of gAUCs

Description

Do multiple AUCs and returns a result table. See gAUC for more detail i.e. iAUC

Usage

tblAUC(Data, key = "Subject", colX = "Time", colY = "Y", iAUC = "",
       Ymax = "Emax", XofYmax = "TEmax", AUCname = "AUEClast", Outer = "NEAREST")

Arguments

Details

Tabular output of AUC with many subjects. This calculates only Cmax(Emax), Tmax(TEmax), AUCs

Value

Basically same with gAUC

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

help, gAUC

Examples

tblAUC(Theoph, key="Subject", colX="Time", colY="conc")

iAUC = data.frame(Name=c("AUC[0-12h]","AUC[0-24h]"), Start=c(0,0), End=c(12,24))
tblAUC(Indometh, key="Subject", colX="time", colY="conc", iAUC=iAUC)

Table output NCA

Description

Do multiple NCA and returns a result table. See sNCA for more detail i.e. iAUC

Usage

tblNCA(concData, key = "Subject", colTime = "Time", colConc = "conc", dose = 0, 
       adm = "Extravascular", dur = 0, doseUnit = "mg", timeUnit = "h", 
       concUnit = "ug/L", down = "Linear", R2ADJ = 0, MW = 0, SS = FALSE, 
       iAUC = "", excludeDelta = 1, UsePoints = NULL)

Arguments

Details

Tabular output of NCA with many subjects. Author recommends to use excludeDelta option with about 0.3.

Value

Author(s)

Kyun-Seop Bae <k@acr.kr>

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")

Write the MD5 integrity manifest for an installed package

Description

Write the standard R ‘MD5’ manifest into an installed package directory so that checkMD5sums (and IQNCA) can verify file integrity. The manifest records the md5 checksum of every installed file. It is the same ‘MD5’ file that CRAN ships and that R's own installer writes; packages installed from CRAN already contain it, but a local source install usually does not (which is why the IQ integrity check then reports WARN). Run writeMD5NCA() once, immediately after installing the package, to record the trusted baseline; thereafter checkMD5sums() detects any later modification of the installed files.

Usage

writeMD5NCA(pkg = "NonCompart", lib.loc = NULL)

Arguments

Details

The manifest is written in the format used by checkMD5sums: one line per file, <md5sum> *<relative-path>. The ‘MD5’ file itself is excluded. The function uses only the exported md5sum. The installed package directory must be writable.

Value

Invisibly, the path to the ‘MD5’ file that was written. Called for its side effect.

Author(s)

Kyun-Seop Bae <k@acr.kr>

See Also

IQNCA, checkMD5sums, md5sum

Examples

#writeMD5NCA("NonCompart")
#NonCompart::IQNCA()       # the file-integrity check now reports PASS