Pharmacometric tools for data preparation, modeling, simulation, and reporting

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Documentation for package ‘MIfuns’ version 5.1

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A B C D E F G H I J K L M N O P Q R S T U V W X Z misc

MIfuns-package Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting

-- A --

accept Document Acceptance of an R Installation
acceptance List the History of Acceptance.
acr Calculate One-Compartment Model Properties
after Identify Elements Within Cells Meeting Some Instance of a Condition
aggregate.keyed Create and Manipulate Keyed Data Frames
align.decimal Format a Vector Aligning on Decimal
and.keyed Operator Syntax for Joining Keyed Data Frames
as.character.comment Create and Manipulate Comment Objects
as.character.flag Create and Manipulate Flags
as.character.miTemporal Support for miTemporal Classes
as.character.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
as.chartime Support for miTemporal Classes
as.chartime.numeric Support for miTemporal Classes
as.comment Create and Manipulate Comment Objects
as.comment.comment Create and Manipulate Comment Objects
as.comment.default Create and Manipulate Comment Objects
as.csv.filename Create Replicate Data Sets by Stratified Sampling
as.csv.filename.character Create Replicate Data Sets by Stratified Sampling
as.data.frame.block Convert a Block of Lines to Data Frame
as.data.frame.comment Create and Manipulate Comment Objects
as.data.frame.flag Create and Manipulate Flags
as.file.runlog Convert Model Metadata to Various Formats
as.filename Create Replicate Text files with Systematic Substitutions
as.filename.character Create Replicate Text files with Systematic Substitutions
as.flag Create and Manipulate Flags
as.flag.default Create and Manipulate Flags
as.flag.flag Create and Manipulate Flags
as.halfmatrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.halfmatrix.default Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.halfmatrix.halfmatrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.keyed Create and Manipulate Keyed Data Frames
as.keyed.data.frame Create and Manipulate Keyed Data Frames
as.list.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
as.matrix.halfmatrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
as.miDate Temporal Classes with Selective Defaults
as.miDate.character Temporal Classes with Selective Defaults
as.miDate.Date Temporal Classes with Selective Defaults
as.miDate.dates Temporal Classes with Selective Defaults
as.miDate.miDate Temporal Classes with Selective Defaults
as.miDate.numeric Temporal Classes with Selective Defaults
as.miDateTime Temporal Classes with Selective Defaults
as.miDateTime.character Temporal Classes with Selective Defaults
as.miDateTime.chron Temporal Classes with Selective Defaults
as.miDateTime.miDate Temporal Classes with Selective Defaults
as.miDateTime.miDateTime Temporal Classes with Selective Defaults
as.miDateTime.numeric Temporal Classes with Selective Defaults
as.miDateTime.POSIXct Temporal Classes with Selective Defaults
as.miDateTime.POSIXlt Temporal Classes with Selective Defaults
as.miTime Temporal Classes with Selective Defaults
as.miTime.character Temporal Classes with Selective Defaults
as.miTime.miTime Temporal Classes with Selective Defaults
as.miTime.numeric Temporal Classes with Selective Defaults
as.miTime.times Temporal Classes with Selective Defaults
as.moot Modify Assembly of nm Objects
as.nm Create and Manipulate nm Objects
as.nm.data.frame Create and Manipulate nm Objects
as.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
as.nmctl.character Create, Manipulate, Read, and Write NONMEM Control Streams
as.numeric.chartime Support for miTemporal Classes
as.pxml Convert a Param File to XML
as.pxml.ext Convert a Param File to XML
as.rigged Modify Assembly of nm Objects
as.runlog.file Convert Model Metadata to Various Formats
as.runlog.unilog Convert Model Metadata to Various Formats
as.unilog.lst Convert Model Metadata to Various Formats
as.unilog.pxml Convert Model Metadata to Various Formats
as.unilog.run Create a Run Log for NONMEM7 using NONMEM6 Format
as.unilog.runlog Convert Model Metadata to Various Formats
as.xml Represent an Object as XML
as.xml.character Represent an Object as XML
as.xml.data.frame Represent an Object as XML
as.xml.default Represent an Object as XML
at Identify Elements Within Cells Meeting Some Instance of a Condition
attribute Encode an Attribute for an XML Open Tag
AUC Calculate AUC Using the Trapezoidal Method
auc Calculate One-Compartment Model Properties
aug Augment a List-like Object
autolog.pl Build Commands to Invoke NONMEM

-- B --

backtrans Back-transform Columns in a Data Frame
badAmt Analyze an NM Object
badAmt.nm Analyze an NM Object
badDv Analyze an NM Object
badDv.nm Analyze an NM Object
badII Analyze an NM Object
badII.nm Analyze an NM Object
bakfor Impute Missing Vector Values
before Identify Elements Within Cells Meeting Some Instance of a Condition
bin Calculate Bin Sizes and Limits for a Vector
bmi Calculate Various Clinical Indicators
bracket Create an XML Tag
breaks Identify Boundaries Between Sets of Elements
bsa Calculate Various Clinical Indicators

-- C --

c.comment Create and Manipulate Comment Objects
c.flag Create and Manipulate Flags
c.miTemporal Support for miTemporal Classes
cavg Calculate One-Compartment Model Properties
check.subjects Summarize Columns of Subject Data
clear Lookup Alternate Versions of Parameter Codes
CLNR Delete Files and Directories
closers Calculate Closing Text for Nested Script Levels
cmax Calculate One-Compartment Model Properties
cmin Calculate One-Compartment Model Properties
colname Change Selected Names~~
colname<- Change Selected Names~~
command Format a Latex Command
compileflag Develop a Value for a Compiler Resource on the Grid
compiler Extract the Compiler Name from an NMQual Configuration File
compute.cwres Compute the Conditional Weighted Residuals
config Identify the Configuration File in an NMQual-mediated NONMEM installation.
constant Test for Nested Factors
constant.default Test for Nested Factors
contains Test a Character Vector for Occurences of a Pattern
covariatePlots Create Diagnostic Plots
covplot Display Distributions with Respect to Reference Values
crcl Calculate Various Clinical Indicators
CreateParametersForSimulation Create Parameters for Simulation with Uncertainty
crosses Test for Nested Factors
css Calculate One-Compartment Model Properties
ctl A Sample NONMEM(r) Control Stream
ctl2xml Lookup Alternate Versions of Parameter Codes
cwresPlots Create Diagnostic Plots

-- D --

dataFormat Integrate NONMEM Data for Plotting
dataSynthesis Build a Standard Plotting Data Set for a Given NONR Run
deranged Modify Assembly of nm Objects
deranged.data.frame Modify Assembly of nm Objects
deranged.keyed Modify Assembly of nm Objects
diagnosticPlots Create Diagnostic Plots
distance Identify Elements Within Cells Meeting Some Instance of a Condition
dupKeys Create and Manipulate Keyed Data Frames
dupKeys.default Create and Manipulate Keyed Data Frames
dupKeys.nm Analyze an NM Object

-- E --

electronicAppendix Make an FDA-style Electronic Appendix from a Subversioned Directory.
episcript Run an Epilog Script in a Pre-populated Environment
explicitPath Clean Up a Control Stream
extfile Clean Up a Control Stream
extractPath Clean Up a Control Stream

-- F --

f Create and Manipulate Flags
falseAmt Analyze an NM Object
falseAmt.nm Analyze an NM Object
falseDv Analyze an NM Object
falseDv.nm Analyze an NM Object
filename Construct a Canonical File Name
first Identify Elements Within Cells Meeting Some Instance of a Condition
fixedwidth Apply Fixed-width Formatting to a Data Frame
fixedwidth.data.frame Apply Fixed-width Formatting to a Data Frame
fixFile Clean Up a Control Stream
fixProblem Clean Up a Control Stream
forbak Impute Missing Vector Values
format.comment Create and Manipulate Comment Objects
format.flag Create and Manipulate Flags
format.miDate Temporal Classes with Selective Defaults
format.miDateTime Temporal Classes with Selective Defaults
format.miTime Temporal Classes with Selective Defaults
format.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
ftable2data.frame Convert ftable to data.frame

-- G --

getCovs Return Non-commented Non-duplicated Rows of a NONMEM Data Set
getCwres Return the Conditional Weighted Residuals Pertinent to a Given Run
getdname Extract the Path and File from the DATA Block in the Control Stream Associated with a Filename
getPars Return the Non-duplicated (ID) Rows Corresponding to the Specified Filename
getTabs Return the Observation Rows (EVID==0) Corresponding to the Specified Filename
glue Paste Items with No Space
groupnames Construct a Single Vector of Group Names from Possibly Multiple Indices to the Plotting Data Set

-- H --

half Interconvert Between a Symmetric Matrix and a Triangular Matrix
half.matrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
hash Supply Comment Characters with Output
helpAdminister MIfuns: Administrative
helpClasses MIfuns: Data Classes
helpDataFrame MIfuns: Working with Data Frames
helpList MIfuns: Defined Functions
helpMatrix MIfuns: Working with Matrices
helpModel MIfuns: Modeling
helpPharmacometric MIfuns: Pharmacometrics
helpPrepare MIfuns: Data Preparation
helpQuantify MIfuns: Statistics
helpReport MIfuns: Reporting
helpSimulate MIfuns: Simulation
helpStrategic MIfuns: Strategic Data Manipulation
helpVector MIfuns: Working with Vectors
helpVisualize MIfuns: Plotting
hidden Create and Manipulate Comment Objects
hidden.data.frame Create and Manipulate Comment Objects
hide Create and Manipulate Comment Objects
hide.data.frame Create and Manipulate Comment Objects

-- I --

ibw Calculate Various Clinical Indicators
ind.cwres Compute the Conditional Weighted Residuals
inner Limit Data to Inner Quantiles by Imputing NA.
inner.data.frame Limit Data to Inner Quantiles by Imputing NA.
is.alpha Test For Alphabetic Content
is.cwres.readable.file Compute the Conditional Weighted Residuals
is.latex.token Determine if String is Valid Latex Command or Environment
is.one.nonalpha Check That Each Element is a Single Non-letter
is.square Test Whether a Matrix is Square
is.square.matrix Test Whether a Matrix is Square
isSubversioned Check Whether Files Are Subversioned
isSubversionedFile Check If Single file Is Subversioned
iterations Harvest Iteration Statistics from NONMEM Output and Convert from Covariance to Correlation

-- J --

justUnits Extract Substring of Wiki Math

-- K --

ke Calculate One-Compartment Model Properties
key Create and Manipulate Keyed Data Frames
key<- Create and Manipulate Keyed Data Frames

-- L --

last Identify Elements Within Cells Meeting Some Instance of a Condition
latest Identify the Latest Variants of Each File as Distinguished by Enclosing Subdirectories
latex.args Format Latex Command Arguments
latex.options Format Latex Command Options
lbm Calculate Various Clinical Indicators
left.keyed Operator Syntax for Joining Keyed Data Frames
lhs Extract Substring of Wiki Math
locf Impute Missing Vector Values
lookup Lookup Alternate Versions of Parameter Codes
lookup.one Lookup Alternate Versions of Parameter Codes
ltable Create a Latex Table
ltable.data.frame Convert a Data Frame to a Latex Table

-- M --

map Map One Set of Values to Another
maxChar Check Some Properties of Vectors
merge.keyed Create and Manipulate Keyed Data Frames
merge.nm Create and Manipulate nm Objects
metaSub Create Replicate Text files with Systematic Substitutions
metaSub.character Create Replicate Text files with Systematic Substitutions
metaSub.filename Create Replicate Text files with Systematic Substitutions
MIfuns Pharmacometric Tools for Data Preparation, Modeling, Simulation, and Reporting
minus.keyed Operator Syntax for Joining Keyed Data Frames
minus.moot Modify Assembly of nm Objects
miTemporal Temporal Classes with Selective Defaults
moot Modify Assembly of nm Objects
moot.nm Modify Assembly of nm Objects
msffile Clean Up a Control Stream

-- N --

naInContext Display Missing Values in Context
naKeys Create and Manipulate Keyed Data Frames
naKeys.default Create and Manipulate Keyed Data Frames
naKeys.nm Analyze an NM Object
name Change Selected Names~~
name<- Change Selected Names~~
nest Nest an XML Fragment in a Parent Element
nix Identify Unix-like Platforms
nm Create and Manipulate nm Objects
nm.data-class Compute the Conditional Weighted Residuals
nm.pl Build Commands to Invoke NONMEM
nmPlots An Extensible List of Diagnostic Plots for nm Objects
nmVersion Extract the NONMEM Version from an NMQual Configuration File
nocb Impute Missing Vector Values
NONR Run NONMEM
NONR72 Run NONMEM
noPk Analyze an NM Object
noPk.nm Analyze an NM Object
nospace Extract Substring of Wiki Math
noUnits Extract Substring of Wiki Math
nth Identify Elements Within Cells Meeting Some Instance of a Condition
nxt Check Some Properties of Vectors

-- O --

offdiag Interconvert Between a Symmetric Matrix and a Triangular Matrix
offdiag.halfmatrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
omegacor Convert NONMEM Omega Covariance Matrix to Correlation Matrix
only Identify Elements Within Cells Meeting Some Instance of a Condition
Ops.keyed Operator Syntax for Joining Keyed Data Frames
ord Give the Order of a Symmetric Matrix or Half Matrix
ord.halfmatrix Give the Order of a Symmetric Matrix or Half Matrix
ord.matrix Give the Order of a Symmetric Matrix or Half Matrix

-- P --

packageCheck Load a Package and Run Package-level Examples for Testing Purposes
panel.bar Plot Histograms Flexibly
panel.covplot Display Distributions with Respect to Reference Values
panel.cuts Display Distributions with Respect to Reference Values
panel.densitystrip Display Distributions with Respect to Reference Values
panel.hist Plot Histograms Flexibly
panel.ref Display Distributions with Respect to Reference Values
panel.stratify Handle Each Level of a Stripplot Separately
params List Documented Parameters
parens Wrap Text in Parentheses
parfile Clean Up a Control Stream
partab Construct a Parameter Table
plot.nm Plot An Object of Class nm
plotfilename Make a Name for a Diagnostic Plot File
PLOTR Create Diagnostic Plots for a NONMEM Run
plus.keyed Operator Syntax for Joining Keyed Data Frames
plus.rigged Modify Assembly of nm Objects
posmat Coerce a Matrix to be Positive Definite
predoseDv Analyze an NM Object
predoseDv.nm Analyze an NM Object
prev Check Some Properties of Vectors
print.comment Create and Manipulate Comment Objects
print.flag Create and Manipulate Flags
print.halfmatrix Interconvert Between a Symmetric Matrix and a Triangular Matrix
print.keyed.summary Create and Manipulate Keyed Data Frames
print.miTemporal Support for miTemporal Classes
print.nm.summary Analyze an NM Object
print.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
purge.dir Purge a Directory
purge.files Purge Files

-- Q --

qsub Build Commands to Invoke SGE qsub

-- R --

read.cwres.data Compute the Conditional Weighted Residuals
read.nm Create and Manipulate nm Objects
read.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
reapply Apply a Function Across Cells of an Indexed Vector, Giving an Identically-indexed Result
rep.comment Create and Manipulate Comment Objects
rep.flag Create and Manipulate Flags
rep.miTemporal Support for miTemporal Classes
resample Create Replicate Data Sets by Stratified Sampling
resample.csv.filename Create Replicate Data Sets by Stratified Sampling
resample.data.frame Create Replicate Data Sets by Stratified Sampling
resample.filename Create Replicate Data Sets by Stratified Sampling
resolve Clean Up a Control Stream
rhs Extract Substring of Wiki Math
rig Modify Assembly of nm Objects
rig.nm Modify Assembly of nm Objects
rinvchisq Generate Inverse Chi-square Distribution
riwish Generate Inverse Wishart Distribution
rlog Generate a Combined Run Log from Multiple NONMEM Runs
row2tabular Format Vector for Latex Tabular Row
runCommand Issue the System Call That Invokes NONMEM
runhead Check Some Properties of Vectors
runlog Convert Model Metadata to Various Formats
runNonmem Process a Request for NONMEM Invocation
runstate Detect State of a Run Using File Existance Criteria

-- S --

safe.call Call a Function Safely
safeQuote Single-quote Conditionally ~~
scavenge Clean Up a Control Stream
seq.miTemporal Support for miTemporal Classes
setCwres Append Conditional Weighted Residuals to an Appropriate File
shuffle Move the Columns of a Data Frame Relative to Each Other
sigmacor Convert NONMEM Omega Covariance Matrix to Correlation Matrix
simblock Generate Random Effect Deviates for Simulation
simpar Create Parameters for Simulation with Uncertainty
snap Coerce Values to Nearest of Candidates
sort.keyed Create and Manipulate Keyed Data Frames
spaces Generate a String of Spaces
sqrtm Help Calculate CWRES
stableMerge Execute a Stable Left Join
star Replace Asterisk in x With y
strain Reduce x to Those Elements that Occur in Options
summary.hidden.data.frame Create and Manipulate Comment Objects
summary.keyed Create and Manipulate Keyed Data Frames
summary.nm Analyze an NM Object
svnIsText Check Whether Subversioned Files are Text.
svnMarkAsNonText Mark Subversioned Files as Non-text.
svnMarkAsText Mark Subversioned Files as Text
svnMimeType Determine Mime Type for Multiple Files
svnPropGet Get Subversion Property for a Vector of Files
svnPropGetFile Get Subversion Property for a Single File
svnPropSet Set a Property on a Vector of Subversioned Files
svnPropSetFile Set a Property on a Subversioned File
svnSetMimeType Set Subversion Mime Type
synthesis Sequentially Left-join an Arbitrary Number of Data Frames, Picking Up Novel Columns

-- T --

tabfile Clean Up a Control Stream
tabular Create a Tabular Environment
tabular.data.frame Convert a Data Frame to a Latex Tabular Environment
tabularformat Create the Format String for Latex Tabular Environment
tagvalue Convert List to Tag and Value Format
text2decimal Convert Mixed Text to Decimal
Tmax Calculate Tmax
tmax Calculate One-Compartment Model Properties
Tmin Calculate Tmin
tos Extract Substring of Wiki Math
transform.keyed Create and Manipulate Keyed Data Frames
TruncateParametersForSimulation Create Parameters for Simulation with Uncertainty

-- U --

uniKey Create and Manipulate Keyed Data Frames
uniKey.keyed Create and Manipulate Keyed Data Frames
unilog Convert Model Metadata to Various Formats
unilogcor Convert NONMEM Omega Covariance Matrix to Correlation Matrix
unique.miTemporal Temporal Classes with Selective Defaults
unitDensity Display Distributions with Respect to Reference Values
unitHist Plot Histograms Flexibly

-- V --

variants Locate Variants of a File in Distinctive Subdirectories

-- W --

wiki2label Parse Wikimath
wiki2latex Parse Wikimath
wiki2parameter Parse Wikimath
wiki2plotmath Parse Wikimath
wikimath Parse Wikimath
wikiparse Parse Wikimath
wikitab Construct a Parameter Table
win Identify Windows Platforms
wrap Wrap Text in a Latex Environment
write.nm Create and Manipulate nm Objects
write.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams

-- X --

xtfrm.comment Create and Manipulate Comment Objects
xtfrm.flag Create and Manipulate Flags
xtfrm.miTemporal Temporal Classes with Selective Defaults
xyplot.ext Plot the Parameter Search History for a NONMEM 7 Run

-- Z --

zeroAmt Analyze an NM Object
zeroAmt.nm Analyze an NM Object
zeroDv Analyze an NM Object
zeroDv.nm Analyze an NM Object

-- misc --

%nested.in% Test for Nested Factors
%nests% Test for Nested Factors
[.comment Create and Manipulate Comment Objects
[.flag Create and Manipulate Flags
[.keyed Create and Manipulate Keyed Data Frames
[.miTemporal Support for miTemporal Classes
[.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams
[<-.miTemporal Support for miTemporal Classes
[[.comment Create and Manipulate Comment Objects
[[.flag Create and Manipulate Flags
[[.miTemporal Support for miTemporal Classes
[[.nmctl Create, Manipulate, Read, and Write NONMEM Control Streams