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nonmemica (version 0.9.1)

Create and Evaluate NONMEM Models in a Project Context

Description

Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions ) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.

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Version

Install

install.packages('nonmemica')

Monthly Downloads

764

Version

0.9.1

License

GPL-3

Maintainer

Tim Bergsma

Last Published

March 25th, 2020

Functions in nonmemica (0.9.1)

absolute

Check if File Path is Absolute
as.bootstrap.numeric

Create Bootstrap from Numeric
as.character.init

Coerce init to character
as.data.frame.halfmatrix

Coerce Half Matrix to Data Frame
as.bootstrap

Create a Bootstrap Table
as.best

Convert to Best of Numeric or Character
as.character.inits

Coerce inits to character
as.character.model

Coerce NONMEM Control Object to character
as.halfmatrix

Coerce to Half Matrix
as.character.items

Coerce Items to Character
as.init

Coerce to init
as.inits

Coerce to inits
as.inits.numeric

Coerce numeric to inits
as.items

Convert to Items
as.sigma

Extract Sigmas
as.matrices

Coerce to List of Matrices
as.xml_document.numeric

Coerce numeric to xml_document
as.list.model

Coerce model to list
contains

Check Whether Text Contains Pattern
as.halfmatrix.default

Coerce to Half Matrix by Default
as.omega.model

Extract Omegas from Model
as.items.character

Convert to Items from Character
fixed.model

Check If Model is Fixed
but

Identify a Distinctive Feature
as.sigma.model

Extract Sigmas from Model
as.init.numeric

Coerces numeric to init
format.init

Format init
as.matrices.inits

Coerce to Matrices from Inits
enclose

Enclose in Arbitrary Characters
as.matrices.records

Coerce to List of Matrices from Records
datafile

Identify Datafile
errors

Get Errors
as.matrix.halfmatrix

Coerce Half Matrix to Matrix
as.tab

Extract Tables
as.theta.model

Extract Thetas from Model
as.model.numeric

Coerce to Model from Numeric
as.halfmatrix.halfmatrix

Coerce Half Matrix to Half Matrix
as.omega

Extract Omegas
$.init

Select init element
but.default

Identify the Distinctive Feature of a Model
estimates.character

Get Estimates for Character
as.tab.model

Extract Tables from Model
as.model

Coerce to NONMEM Control Object
comwidth.items

Calculate Comment Widths for Items
comwidth

Calculate Comment Widths Calculates comment widths.
as.theta

Extract Thetas
as.xml_document

Create an xml_document in a Project Context
estimates

Get Estimates
comwidth.inits

Calculate Comment Widths for Inits
definitions

Harvest Model Item Definitions
comwidth.character

Calculate Comment Widths for Character
half.matrix

Find Half of Matrix
comments

Extract Comments
datafile.character

Identify the Datafile for a Model
comwidthOne.character

Calculate Comment Widths for One Element of Character
definitions.numeric

Create Model Item Definitions from Number.
errors.character

Get Errors for Character
fixed

Check if something is fixed
$<-.init

Set init element
datafile.numeric

Identify Datafile from Numeric
errors.numeric

Get Errors for Numeric
comwidthOne

Calculate Comment Widths for One Element
fixed<-

Set value of fixed attribute
%contains%

Check Whether x contains y
initSubscripts.model

Identify Subscripts of Initial Estimates in model
format.inits

Format inits
likebut

Modify a Model
estimates.numeric

Get Estimates for Numeric
initial<-.model

Set Upper Bounds for Model Initial Estimates
fixed<-.init

Set fixed init value
lower<-.model

Set Lower Bounds for Model Initial Estimates
locf

Impute Missing Vector Values
format.items

Format Items
half

Find Half of Something
lower<-

Set Lower Value
like

Identify What Something is Like
initDex.model

Identify Indices of Initial Estimates in model
initSubscripts

Identify Subscripts
is.square

Test If Something is Square
depends

Identify What Something Depends On
like.default

Identify the Relevant Reference Model
lower.model

Get Lower Bounds for Model Initial Estimates
depends.default

Identify Model Dependencies
metasuperset

Retrieve Model Outputs with Metadata
lower

Get Lower Value
initial.model

Get Model Initial Estimates
fixed<-.inits

Set fixed attribute of inits
modeldir

Identify the Directory for a Model
is.square.matrix

Test If Matrix is Square
initDex

Identify Indices of Initial Estimates
nms_nonmem.character

Generate NONMEM-style Names for Character
fixed<-.model

Set fixed attribute of model
nms_nonmem.model

Generate NONMEM-style Names for Model
is.defined

Check Whether Elements are Defined
nms_psn.numeric

Generate PsN-style Names for Numeric
metaplot_character

Metaplot Character, Standard Evaluation
nms_nonmem.numeric

Generate NONMEM-style Names for Numeric
nms_psn.character

Generate PsN-style Names for Character
meta.character

Get Metadata for Character
nms_psn

Generate PsN-style Names
meta

Get Metadata
ninput

Calculate Number of Inputs
metaplot.numeric

Metaplot Numeric
nms_psn.model

Generate PsN-style Names for Model
parameters.character

Get Parameters for Character
nonmemica

Create and Evaluate NONMEM Models in a Project Context
meta.numeric

Get Metadata for Numeric
parameters

Get Parameters
tweak.init

Tweak Init
metaplot.character

Metaplot Character
shuffle

Move the Columns of a Data Frame Relative to Each Other
tweak.default

Tweak a Model by Default
row_col

Create Indexed Model Parameter Table from Xml_document
ord.inits

Identify the order of an inits
print.items

Print Items
tweak

Tweak Something
modelpath.character

Resolve A Path to a Model-related File for Character
ninput.character

Calculate Number of Inputs for Character
runlog.numeric

Create a Runlog for Numeric
print.inits

Print inits
ninput.numeric

Calculate Number of Inputs for Numeric
runhead

Find Positions in a Vector that Differ from Previous
format.model

Format model
ord.items

Identify the Order of an Items Object
problem.character

Identify the Model Problem Statement for Character
nms_canonical

Generate Canonical Names
modelpath.numeric

Resolve A Path to a Model-related File for Numeric
tweak.inits

Tweak inits
prettycom

Pretty-print a Comment
generalize

Generalize a Nonmissing Value
nms_canonical.numeric

Generate Canonical Names for Numeric
ord.halfmatrix

Calculate Order for Half Matrix
prettycom.character

Pretty-print a Comment for Character
ord

Calculate Order
parameters.numeric

Get Parameters for Numeric
problem.numeric

Identify the Model Problem Statement for Numeric
specfile

Identify Specfile
initial<-

Set Initial Value
offdiag.halfmatrix

Isolate Off-diagonal of Half Matrix
specfile.character

Identify the Data Specification File for a Model
parens

Enclose in Parentheses
tad

Calculate Time Since Most Recent Dose
offdiag

Isolate Off-diagonal
nms_nonmem

Generate NONMEM-style Names
problem

Identify the Model Problem Statement
tad1

A NONMEM-like Dataset
relativizePath

Relativize a Path
print.model

Print model
resolve

Resolve File Path
initial

Get Initial Value
updated.character

Create the Updated Version of Character
partab

Create Parameter Table
partab.character

Create a Parameter Table from Model Name
write.model

Write model
maxWidths

Calculate Maximum Widths
updated.numeric

Create the Updated Version of Numeric
pool

Compare Sets
partab.numeric

Create Model Parameter Table from Number.
val_name

Create Model Parameter Table from Xml_document
maxWidths.list

Calculate Maximum Widths for List
specfile.numeric

Identify Specfile from Numeric
text2decimal

Convert Text to Decimal
upper.model

Get Upper Bounds for Model Initial Estimates
tod

Calculate Time of Most Recent Dose
upper

Get Upper Value
runlog

Create a Runlog
runlog.character

Create a Runlog for Character
[.inits

Subset inits
superset

Coerce to Superset
superset.character

Coerce to Superset from Character
superspec.character

Create Specification for Model Inputs and Outputs From Character
superspec.numeric

Create Specification for Model Inputs and Outputs From Numeric
updated

Create the Updated Version of Something
tweak.model

Tweak Model
modelfile

Identify the Modelfile for a Model
nms_canonical.character

Generate Canonical Names for Character
nms_canonical.model

Generate Canonical Names for Model
modelpath

Resolve A Path to a Model-related File
num_parameters

Get the Number of Parameters
xpath

Evaluate Xpath Expression
num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model
padded

Pad Numeric with Zeros
ord.matrix

Calculate Order for Matrix
print.init

Print init
print.halfmatrix

Print Half Matrix
problem_

Identify the Single Model Problem Statement
read.model

Read model
[[.model

Select model Element
superset.numeric

Coerce to Superset from Numeric
[.model

Subset model
superspec

Create Specification for Model Inputs and Outputs
upper<-.model

Set Upper Bounds for Model Initial Estimates
upper<-

Set Upper Value