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nonmemica (version 0.8.1)

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

730

Version

0.8.1

License

GPL-3

Maintainer

Tim Bergsma

Last Published

March 27th, 2018

Functions in nonmemica (0.8.1)

as.character.items

Coerce Items to Character
as.character.inits

Coerce inits to character
as.character.init

Coerce init to character
as.file

Coerce to file
as.bootstrap

Create a Bootstrap Table
as.flextable

Coerce to flextable
as.bootstrap.numeric

Create Bootstrap from Numeric
as.best

Convert to Best of Numeric or Character
absolute

Check if File Path is Absolute
as.inits.numeric

Coerce numeric to inits
as.character.model

Coerce NONMEM Control Object to character
as.inits

Coerce to inits
as.init

Coerce to init
as.docx

Coerce to docx
as.matrices

Coerce to List of Matrices
as.sigma.model

Extract Sigmas from Model
as.matrices.inits

Coerce to Matrices from Inits
as.tab

Extract Tables
as.init.numeric

Coerces numeric to init
as.omega.model

Extract Omegas from Model
but.default

Identify the Distinctive Feature of a Model
as.model.numeric

Coerce to Model from Numeric
as.tab.model

Extract Tables from Model
as.sigma

Extract Sigmas
$.init

Select init element
as.omega

Extract Omegas
as.items

Convert to Items
as.theta

Extract Thetas
comwidthOne

Calculate Comment Widths for One Element
comwidth

Calculate Comment Widths Calculates comment widths.
comwidthOne.character

Calculate Comment Widths for One Element of Character
comwidth.inits

Calculate Comment Widths for Inits
as.theta.model

Extract Thetas from Model
comwidth.character

Calculate Comment Widths for Character
fixed<-

Set value of fixed attribute
datafile.character

Identify the Datafile for a Model
comwidth.items

Calculate Comment Widths for Items
as.xml_document

Create an xml_document in a Project Context
fixed

Check if something is fixed
datafile.numeric

Identify Datafile from Numeric
as.items.character

Convert to Items from Character
initDex.model

Identify Indices of Initial Estimates in model
depends

Identify What Something Depends On
estimates.numeric

Get Estimates for Numeric
initSubscripts

Identify Subscripts
fixed<-.init

Set fixed init value
depends.default

Identify Model Dependencies
as.list.model

Coerce model to list
maxWidths

Calculate Maximum Widths
definitions

Harvest Model Item Definitions
initial.model

Get Model Initial Estimates
as.matrices.records

Coerce to List of Matrices from Records
maxWidths.list

Calculate Maximum Widths for List
definitions.numeric

Create Model Item Definitions from Number.
enclose

Enclose in Arbitrary Characters
modelfile

Identify the Modelfile for a Model
is.defined

Check Whether Elements are Defined
as.model

Coerce to NONMEM Control Object
errors

Get Errors
modelpath

Resolve A Path to a Model-related File
lower<-.model

Set Lower Bounds for Model Initial Estimates
as.xml_document.numeric

Coerce numeric to xml_document
format.model

Format model
metaplot.numeric

Metaplot Numeric
lower<-

Set Lower Value
generalize

Generalize a Nonmissing Value
metaplot_character

Metaplot Character, Standard Evaluation
but

Identify a Distinctive Feature
ninput.numeric

Calculate Number of Inputs for Numeric
initDex

Identify Indices of Initial Estimates
$<-.init

Set init element
contains

Check Whether Text Contains Pattern
nms_canonical

Generate Canonical Names
lower

Get Lower Value
datafile

Identify Datafile
comments

Extract Comments
nms_psn.numeric

Generate PsN-style Names for Numeric
format.inits

Format inits
lower.model

Get Lower Bounds for Model Initial Estimates
estimates

Get Estimates
fixed<-.inits

Set fixed attribute of inits
nonmemica

Create and Evaluate NONMEM Models in a Project Context
format.items

Format Items
fixed<-.model

Set fixed attribute of model
estimates.character

Get Estimates for Character
likebut

Modify a Model
initSubscripts.model

Identify Subscripts of Initial Estimates in model
%contains%

Check Whether x contains y
fixed.model

Check If Model is Fixed
initial<-.model

Set Upper Bounds for Model Initial Estimates
locf

Impute Missing Vector Values
nms_psn.character

Generate PsN-style Names for Character
meta.numeric

Get Metadata for Numeric
format.init

Format init
meta

Get Metadata
nms_psn.model

Generate PsN-style Names for Model
metaplot.character

Metaplot Character
partab.numeric

Create Model Parameter Table from Number.
meta.character

Get Metadata for Character
partab.character

Create a Parameter Table from Model Name
ninput

Calculate Number of Inputs
prettycom

Pretty-print a Comment
nms_canonical.character

Generate Canonical Names for Character
relativizePath

Relativize a Path
ninput.character

Calculate Number of Inputs for Character
superset

Coerce to Superset
nms_canonical.model

Generate Canonical Names for Model
modelpath.character

Resolve A Path to a Model-related File for Character
resolve

Resolve File Path
superset.character

Coerce to Superset from Character
modelpath.numeric

Resolve A Path to a Model-related File for Numeric
specfile.numeric

Identify Specfile from Numeric
nms_canonical.numeric

Generate Canonical Names for Numeric
errors.character

Get Errors for Character
pool

Compare Sets
[.inits

Subset inits
runlog

Create a Runlog
nms_nonmem

Generate NONMEM-style Names
superspec.character

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

Get Errors for Numeric
runlog.character

Create a Runlog for Character
ord.inits

Identify the order of an inits
nms_nonmem.character

Generate NONMEM-style Names for Character
initial<-

Set Initial Value
superset.numeric

Coerce to Superset from Numeric
ord.items

Identify the Order of an Items Object
nms_nonmem.model

Generate NONMEM-style Names for Model
superspec

Create Specification for Model Inputs and Outputs
padded

Pad Numeric with Zeros
print.inits

Print inits
print.items

Print Items
tad

Calculate Time Since Most Recent Dose
superspec.numeric

Create Specification for Model Inputs and Outputs From Numeric
parameters

Get Parameters
initial

Get Initial Value
tad1

A NONMEM-like Dataset
xpath

Evaluate Xpath Expression
problem.character

Identify the Model Problem Statement for Character
upper<-.model

Set Upper Bounds for Model Initial Estimates
like

Identify What Something is Like
upper<-

Set Upper Value
like.default

Identify the Relevant Reference Model
nms_nonmem.numeric

Generate NONMEM-style Names for Numeric
problem.numeric

Identify the Model Problem Statement for Numeric
specfile.character

Identify the Data Specification File for a Model
metasuperset

Retrieve Model Outputs with Metadata
nms_psn

Generate PsN-style Names
text2decimal

Convert Text to Decimal
tweak

Tweak Something
modeldir

Identify the Directory for a Model
num_parameters

Get the Number of Parameters
tweak.default

Tweak a Model by Default
parameters.character

Get Parameters for Character
tod

Calculate Time of Most Recent Dose
print.model

Print model
upper

Get Upper Value
parameters.numeric

Get Parameters for Numeric
val_name

Create Model Parameter Table from Xml_document
problem

Identify the Model Problem Statement
upper.model

Get Upper Bounds for Model Initial Estimates
num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model
row_col

Create Indexed Model Parameter Table from Xml_document
runlog.numeric

Create a Runlog for Numeric
write.model

Write model
runhead

Find Positions in a Vector that Differ from Previous
shuffle

Move the Columns of a Data Frame Relative to Each Other
parens

Enclose in Parentheses
[.model

Subset model
tweak.init

Tweak Init
[[.model

Select model Element
partab

Create Parameter Table
problem_

Identify the Single Model Problem Statement
tweak.inits

Tweak inits
updated.character

Create the Updated Version of Character
prettycom.character

Pretty-print a Comment for Character
read.model

Read model
tweak.model

Tweak Model
updated

Create the Updated Version of Something
print.init

Print init
specfile

Identify Specfile
updated.numeric

Create the Updated Version of Numeric