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


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Documentation for package ‘MIfuns’ version 3.2.9

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A B C D F H I K L M N O P Q R S T misc

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MIfuns-package Pharmacometric tools for data preparation, analysis, simulation, and reporting

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%nested.in% Test for Nested Factors (beta)
%nests% Test for Nested Factors (beta)

-- A --

accept Document acceptance of an R installation.
acceptance List the history of acceptance.
acr Calculate One-Compartment Model Properties (beta)
as.annotated Make Specialized Data Frames to Support "Forest Plots"
as.character.miTemporal Support for miTemporal Classes
as.chartime Support for miTemporal Classes
as.csv.filename Create Replicate Data Sets by Stratified Sampling With Replacement
as.distribution Make Specialized Data Frames to Support "Forest Plots"
as.double.immutable Control Plotting of Default "Forest Plots"
as.filename Create Replicate Text files with Systematic Substitutions
as.miDate Temporal Classes with Selective Defaults
as.miDateTime Temporal Classes with Selective Defaults
as.miTime Temporal Classes with Selective Defaults
as.numeric.chartime Support for miTemporal Classes
AUC Calculate AUC using the trapezoidal method
auc Calculate One-Compartment Model Properties (beta)

-- B --

bin Calculate Bin Sizes and Limits for a Vector (beta)
bmi Calculate Various Clinical Indicators
boxplot.prestats Make "Forest Plots" of Covariate Effects, etc.
bsa Calculate Various Clinical Indicators

-- C --

c.miTemporal Support for miTemporal Classes
cavg Calculate One-Compartment Model Properties (beta)
check.data Summarize columns in a data set
CheckPositiveMatrix Verify that Omega matrix is positive, definite
CheckPositiveVector Verify that Omega matrix is positive, definite
CheckWS Check file name for white space
CLNR Delete files and directories
cmax Calculate One-Compartment Model Properties (beta)
cmin Calculate One-Compartment Model Properties (beta)
compute.cwres Compute the Conditional Weighted Residuals
ComputePredictiveCheck Computes individual parameters for observed and simulated data
constant Test for Nested Factors (beta)
covplot Make "Forest Plots" of Covariate Effects, etc.
covplot.stats Calculate Statistics for "Forest Plots"
crcl Calculate Various Clinical Indicators
CreateParametersForSimulation Generate model parameters for simulation
crosses Test for Nested Factors (beta)
css Calculate One-Compartment Model Properties (beta)
ctl A sample NONMEM(r) control stream
ctl1 Example data for NONR
CWRES Generate conditional weighted residual (CWRES) diagnostic plots as a pdf.
cwres_1 Generate conditional weighted residual (CWRES) diagnostic plots as a pdf.

-- D --

diagnostics Run NONMEM and create diagnostic plots
doCov Run NONMEM and create diagnostic plots

-- F --

forbak Impute Missing Vector Values
format.miDate Temporal Classes with Selective Defaults
format.miDateTime Temporal Classes with Selective Defaults
format.miTime Temporal Classes with Selective Defaults

-- H --

hash Supply comment characters with output

-- I --

ibw Calculate Various Clinical Indicators
ind.cwres Compute the Conditional Weighted Residuals
is.cwres.readable.file Compute the Conditional Weighted Residuals

-- K --

ke Calculate One-Compartment Model Properties (beta)

-- L --

lbm Calculate Various Clinical Indicators
locf Impute Missing Vector Values

-- M --

maxChar Check Some Properties of Vectors and Data Frames (beta)
mcmc.density Tabular and graphic summary of MCMC results
mcmc.history Tabular and graphic summary of MCMC results
metaSub Create Replicate Text files with Systematic Substitutions
MIfuns Pharmacometric tools for data preparation, analysis, simulation, and reporting
miTemporal Temporal Classes with Selective Defaults
myriwish Generate omega values for simulation
myshell Run a DOS command without opening a command window

-- N --

naInContext Display Missing Values in Context
nocb Impute Missing Vector Values
NONR Run NONMEM and create diagnostic plots

-- O --

Omega.MtoV Convert omega matrix to vector
Omega.VtoM Convert omega vector to matrix

-- P --

packageCheck Load a package and run package-level examples for testing purposes.
panel.covplot Control Plotting of Default "Forest Plots"
parameter.plot.table Tabular and graphic summary of MCMC results
PlotPredictiveCheck Plots results of the ComputePredictiveCheck function
PLOTR Run NONMEM and create diagnostic plots
prepanel.covplot Control Plotting of Default "Forest Plots"
prev Check Some Properties of Vectors and Data Frames (beta)
print.annotated Make Specialized Data Frames to Support "Forest Plots"
print.miTemporal Support for miTemporal Classes
prob1 Example data for NONR

-- Q --

Q25 Function calculates 25th percentile/probability
Q75 Function calculates 75th percentile/probability

-- R --

read.cwres.data Compute the Conditional Weighted Residuals
resample Create Replicate Data Sets by Stratified Sampling With Replacement
resample.csv.filename Create Replicate Data Sets by Stratified Sampling With Replacement
resample.data.frame Create Replicate Data Sets by Stratified Sampling With Replacement
rinvchisq Generate inverse chi-square distribution
rinvgamma Generate inverse gamma distribution
riwish Generate inverse Wishart distribution
rlog Generate a combined run log from multiple NONMEM runs
runhead Check Some Properties of Vectors and Data Frames (beta)
runmsge Run NONMEM and create diagnostic plots
runnm Run NONMEM and create diagnostic plots

-- S --

save.model Save WinBUGS results in a specified directory
seq.miTemporal Support for miTemporal Classes
SimulateOmega Generate omega values for simulation
sorted Check Some Properties of Vectors and Data Frames (beta)
sqrtm Called from compute.cwres to calculated CWRES.
stableMerge Execute a Benign Left Join
subclass Support for miTemporal Classes

-- T --

TABR Generate a comma-delimited table file following a successful NONMEM run
Tmax Calculate Tmax
tmax Calculate One-Compartment Model Properties (beta)
Tmin Calculate Tmin
TruncateParametersForSimulation Truncate a set of parameters for simulation

-- misc --

[.annotated Make Specialized Data Frames to Support "Forest Plots"
[.miTemporal Support for miTemporal Classes
[[.annotated Make Specialized Data Frames to Support "Forest Plots"
[[.miTemporal Support for miTemporal Classes