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nonmemica (version 1.0.8)

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

758

Version

1.0.8

License

GPL-3

Maintainer

Tim Bergsma

Last Published

September 20th, 2023

Functions in nonmemica (1.0.8)

as.bootstrap

Create a Bootstrap Table
as.halfmatrix.halfmatrix

Coerce Half Matrix to Half Matrix
as.halfmatrix.default

Coerce to Half Matrix by Default
as.init.init

Coerce init to init
as.init.numeric

Coerces numeric to init
as.character.problem

Coerce Problem to Character
as.init

Coerce to init
as.data.frame.halfmatrix

Coerce Half Matrix to Data Frame
as.halfmatrix

Coerce to Half Matrix
as.inits.list

Coerce list to inits
as.inits

Coerce to inits
as.inits.numeric

Coerce numeric to inits
as.matrices

Coerce to List of Matrices
as.model.character

Coerce character to model
as.model

Coerce to NONMEM Control Object
as.sigma.model

Extract Sigmas from Model
as.sigma

Extract Sigmas
as.items

Convert to Items
as.matrix.halfmatrix

Coerce Half Matrix to Matrix
as_nms_psn

Coerce to 'nms_psn'
as.tab

Extract Tables
as.tab.model

Extract Tables from Model
as.matrices.records

Coerce to List of Matrices from Records
but

Identify a Distinctive Feature
but.default

Identify the Distinctive Feature of a Model
$.init

Select init element
as_nms_pmx

Coerce to 'nms_pmx'
as.list.model

Coerce model to list
as_nms_nonmem

Coerce to 'nms_nonmem'
as.omega

Extract Omegas
as.items.character

Convert to Items from Character
comwidth.character

Calculate Comment Widths for Character
as.model.numeric

Coerce to Model from Numeric
as.omega.model

Extract Omegas from Model
comwidth.items

Calculate Comment Widths for Items
comwidthOne

Calculate Comment Widths for One Element
contains

Check Whether Text Contains Pattern
comwidthOne.character

Calculate Comment Widths for One Element of Character
definitions.definitions

Create Model Item Definitions from definitions
comwidth.inits

Calculate Comment Widths for Inits
as.problem

Parse the Run Record
errors

Get Errors
enclose

Enclose in Arbitrary Characters
as_nms_canonical

Coerce to 'nms_canonical'
comments.model

Extract Comments from Model
comwidth

Calculate Comment Widths Calculates comment widths.
as.xml_document.numeric

Coerce numeric to xml_document
datafile

Identify Datafile
as.xml_document.character

Create xml_document From Character
as.xml_document

Create an xml_document in a Project Context
comments.inits

Extract Comments from Inits
comments.items

Extract Comments from Items
datafile.numeric

Identify Datafile from Numeric
fixed<-.model

Set fixed attribute of model
format.init

Format init
as.matrices.inits

Coerce to Matrices from Inits
fixed<-.inits

Set fixed attribute of inits
datafile.character

Identify the Datafile for a Model
format.inits

Format inits
definitions.numeric

Create Model Item Definitions from Number.
fixed<-

Set value of fixed attribute
initDex.model

Identify Indices of Initial Estimates in model
estimates

Get Estimates
fixed<-.init

Set fixed init value
estimates.numeric

Get Estimates for Numeric
fixed.model

Check If Model is Fixed
fixed.init

Check if init is fixed
definitions

Harvest Model Item Definitions
half

Find Half of Something
generalize

Generalize a Nonmissing Value
lower<-.model

Set Lower Bounds for Model Initial Estimates
ignored

Extract Index for Ignored Records
estimates.character

Get Estimates for Character
%contains%

Check Whether x contains y
initial

Get Initial Value
initDex

Identify Indices of Initial Estimates
initial<-

Set Initial Value
as.theta

Extract Thetas
meta.numeric

Get Metadata for Numeric
lower<-

Set Lower Value
meta

Get Metadata
meta.character

Get Metadata for Character
fixed

Check if something is fixed
$<-.init

Set init element
depends

Identify What Something Depends On
as.theta.model

Extract Thetas from Model
comments

Extract Comments
metaplot.character

Metaplot Character
modelpath.character

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

Identify What Something is Like
like.default

Identify the Relevant Reference Model
modelpath.numeric

Resolve A Path to a Model-related File for Numeric
initSubscripts

Identify Subscripts
depends.default

Identify Model Dependencies
errors.character

Get Errors for Character
format.items

Format Items
errors.numeric

Get Errors for Numeric
is.square.matrix

Test If Matrix is Square
format.model

Format model
is.square

Test If Something is Square
nms_canonical.numeric

Generate Canonical Names for Numeric
maxWidths

Calculate Maximum Widths
maxWidths.list

Calculate Maximum Widths for List
metasuperset

Retrieve Model Outputs with Metadata
nms_psn

Generate PsN-style Names
nms_psn.character

Generate PsN-style Names for Character
modeldir

Identify the Directory for a Model
nms_nonmem

Generate NONMEM Names
nms_psn.model

Generate PsN-style Names for Model
metaplot_character

Metaplot Character, Standard Evaluation
modelfile

Identify the Modelfile for a Model
initial.model

Get Model Initial Estimates
modelpath

Resolve A Path to a Model-related File
ninput.numeric

Calculate Number of Inputs for Numeric
initial<-.model

Set Upper Bounds for Model Initial Estimates
is.defined

Check Whether Elements are Defined
metaplot.numeric

Metaplot Numeric
initSubscripts.model

Identify Subscripts of Initial Estimates in model
nms_canonical

Generate Canonical Names
nms_nonmem.nms_canonical

Convert Canonical Parameter Names to NONMEM
nms_canonical.character

Generate Canonical Names for Character
nms_canonical.nms_nonmem

Convert NONMEM Parameter Names to Canonical
nms_nonmem.nms_pmx

Convert pmxTools Names to NONMEM
likebut

Modify a Model
half.matrix

Find Half of Matrix
nms_canonical.nms_pmx

Convert Parameter Names to NONMEM
lower

Get Lower Value
locf

Impute Missing Vector Values
nms_pmx.nms_canonical

Convert Canonical Names to pmxTools
nms_psn.numeric

Generate PsN-style Names for Numeric
ord.halfmatrix

Calculate Order for Half Matrix
partab

Create Parameter Table
nonmemica

Create and Evaluate NONMEM Models in a Project Context
ord.matrix

Calculate Order for Matrix
ord.items

Identify the Order of an Items Object
parens

Enclose in Parentheses
problem

Identify the Model Problem Statement
num_parameters

Get the Number of Parameters
nms_canonical.model

Generate Canonical Names for Model
offdiag.halfmatrix

Isolate Off-diagonal of Half Matrix
nms_pmx.nms_nonmem

Convert NONMEM Names to pmxTools
ord

Calculate Order
ord.inits

Identify the order of an inits
nms_nonmem.numeric

Generate NONMEM Names for Numeric
lower.model

Get Lower Bounds for Model Initial Estimates
print.halfmatrix

Print Half Matrix
nms_pmx

Convert Parameter Names to pmxTools
prettycom.character

Pretty-print a Comment for Character
ninput

Calculate Number of Inputs
psn_options

Set PsN Options
parameters.character

Get Parameters for Character
psn_nested

PsN Model File is Nested
read.model

Read model
parameters

Get Parameters
[[.model

Select model Element
runhead

Find Positions in a Vector that Differ from Previous
row_col

Create Indexed Model Parameter Table from Xml_document
problem.character

Identify the Model Problem Statement for Character
relativizePath

Relativize a Path
ninput.character

Calculate Number of Inputs for Character
nms_nonmem.character

Generate NONMEM Names for Character
padded

Pad Numeric with Zeros
[.model

Subset model
tad

Calculate Time Since Most Recent Dose
nms_nonmem.model

Generate NONMEM Names for Model
specfile.numeric

Identify Specfile from Numeric
[.inits

Subset inits
tad1

A NONMEM-like Dataset
pool

Compare Sets
superspec.numeric

Create Specification for Model Inputs and Outputs From Numeric
superspec.character

Create Specification for Model Inputs and Outputs From Character
xpath.xml_document

Evaluate xpath Expression in Document Context
updated.character

Create the Updated Version of Character
updated.numeric

Create the Updated Version of Numeric
safe_join

Join Data Safely
print.model

Print model
parameters.numeric

Get Parameters for Numeric
runlog.numeric

Create a Runlog for Numeric
superset.numeric

Coerce to Superset from Numeric
print.items

Print Items
superspec

Create Specification for Model Inputs and Outputs
rosetta

Translate Parameter Names
resolve

Resolve File Path
prettycom

Pretty-print a Comment
shuffle

Move the Columns of a Data Frame Relative to Each Other
safe_join.data.frame

Join Data Frames Safely
text2decimal

Convert Text to Decimal
tweak.init

Tweak Init
tweak.inits

Tweak inits
problem.numeric

Identify the Model Problem Statement for Numeric
tod

Calculate Time of Most Recent Dose
upper<-.model

Set Upper Bounds for Model Initial Estimates
upper<-

Set Upper Value
specfile.character

Identify the Data Specification File for a Model
partab.character

Create a Parameter Table from Model Name
specfile

Identify Specfile
print.init

Print init
num_parameters.default

Get the Number of Declared Parameters for a NONMEM Model
offdiag

Isolate Off-diagonal
print.inits

Print inits
partab.numeric

Create Model Parameter Table from Number.
xpath.default

Evaluate xpath Expression in Default Context
xpath

Evaluate Xpath Expression
runlog

Create a Runlog
runlog.character

Create a Runlog for Character
superset

Coerce to Superset
problem_

Identify the Single Model Problem Statement
tweak

Tweak Something
tweak.default

Tweak a Model by Default
upper

Get Upper Value
upper.model

Get Upper Bounds for Model Initial Estimates
superset.character

Coerce to Superset from Character
val_name

Create Model Parameter Table from Xml_document
updated

Create the Updated Version of Something
tweak.model

Tweak Model
write.model

Write model
as.best.default

Convert Vector to Best of Numeric or Character
as.bootstrap.bootstrap

Create Bootstrap from Bootstrap
absolute

Check if File Path is Absolute
as.character.model

Coerce NONMEM Control Object to character
as.character.init

Coerce init to character
as.bootstrap.numeric

Create Bootstrap from Numeric
as.character.items

Coerce Items to Character
as.character.inits

Coerce inits to character
as.best

Convert to Best of Numeric or Character