Package: nonmemica 1.0.11

Tim Bergsma

nonmemica: Create and Evaluate NONMEM Models in a Project Context

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

Authors:Tim Bergsma [aut, cre]

nonmemica_1.0.11.tar.gz
nonmemica_1.0.11.tar.gz(r-4.5-noble)nonmemica_1.0.11.tar.gz(r-4.4-noble)
nonmemica_1.0.11.tgz(r-4.4-emscripten)nonmemica_1.0.11.tgz(r-4.3-emscripten)
nonmemica.pdf |nonmemica.html✨
nonmemica/json (API)

# Install 'nonmemica' in R:
install.packages('nonmemica', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • tad1 - A NONMEM-like Dataset

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.65 score 45 scripts 553 downloads 91 exports 44 dependencies

Last updated 4 days agofrom:1bbfae589e. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 26 2024
R-4.5-linuxOKOct 26 2024

Exports:%contains%as_nms_canonicalas_nms_nonmemas_nms_pmxas_nms_psnas.bestas.bootstrapas.halfmatrixas.initas.initsas.itemsas.matricesas.modelas.omegaas.problemas.sigmaas.tabas.thetaas.xml_documentbakforbutcommentscomwidthcomwidthOnedatafiledefinitionsdependsencloseerrorsestimatesfixedfixed<-forbakgeneralizehalfignoredinitDexinitialinitial<-initSubscriptsis.definedis.squarelikelikebutlocflowerlower<-maxWidthsmetametasupersetmodeldirmodelfilemodelpathninputnms_canonicalnms_nonmemnms_pmxnms_psnnocbnum_parametersoffdiagordpaddedparametersparenspartabpoolprettycomproblemproblem_psn_nestedpsn_optionsread.modelrow_colrunheadrunlogsafe_joinshufflespecfilesupersetsuperspectadtext2decimaltodtweakupdatedupperupper<-val_namewrite.modelxpath

Dependencies:clicolorspacecpp11csvdata.tabledplyrencodefansifarvergenericsggplot2gluegridExtragtableisobandlabelinglatticelazyevallifecyclemagrittrMASSMatrixmetaplotmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrlangscalesspecstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrxml2

Creating a Nonmem Parameter Table

Tim Bergsma

Rendered fromparameter-table.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2023-05-10
Started: 2017-04-20

Readme and manuals

Help Manual

Help pageTopics
Check if File Path is Absoluteabsolute
Coerce to 'nms_canonical'as_nms_canonical
Coerce to 'nms_nonmem'as_nms_nonmem
Coerce to 'nms_pmx'as_nms_pmx
Coerce to 'nms_psn'as_nms_psn
Convert Vector to Best of Numeric or Characteras.best.default
Create Bootstrap from Bootstrapas.bootstrap.bootstrap
Coerce to Half Matrix by Defaultas.halfmatrix.default
Coerce init to initas.init.init
Coerce list to initsas.inits.list
Coerce Half Matrix to Matrixas.matrix.halfmatrix
Coerce character to modelas.model.character
Create an xml_document in a Project Contextas.xml_document as.xml_document.xml_document
Create xml_document From Characteras.xml_document.character
Extract Comments from Initscomments.inits
Extract Comments from Itemscomments.items
Extract Comments from Modelcomments.model
Check Whether Text Contains Patterncontains
Identify the Datafile for a Modeldatafile.character
Harvest Model Item Definitionsdefinitions definitions.character
Create Model Item Definitions from definitionsdefinitions.definitions
Identify Model Dependenciesdepends.default
Get Errors for Charactererrors.character
Get Estimates for Characterestimates.character
Check if init is fixedfixed.init
Check If Model is Fixedfixed.model
Generalize a Nonmissing Valuegeneralize
Extract Index for Ignored Recordsignored
Get Model Initial Estimatesinitial.model
Set Upper Bounds for Model Initial Estimatesinitial<-.model
Modify a Modellikebut
Get Lower Bounds for Model Initial Estimateslower.model
Set Lower Bounds for Model Initial Estimateslower<-.model
Get Metadata for Charactermeta.character
Metaplot Character, Standard Evaluationmetaplot_character
Metaplot Charactermetaplot.character
Retrieve Model Outputs with Metadatametasuperset
Identify the Directory for a Modelmodeldir
Identify the Modelfile for a Modelmodelfile
Resolve A Path to a Model-related Filemodelpath
Resolve A Path to a Model-related File for Charactermodelpath.character
Calculate Number of Inputsninput
Calculate Number of Inputs for Characterninput.character
Calculate Number of Inputs for Numericninput.numeric
Generate Canonical Names for Characternms_canonical.character
Generate Canonical Names for Modelnms_canonical.model
Convert NONMEM Parameter Names to Canonicalnms_canonical.nms_nonmem
Generate NONMEM Names for Characternms_nonmem.character
Generate NONMEM Names for Modelnms_nonmem.model
Convert Canonical Parameter Names to NONMEMnms_nonmem.nms_canonical
Convert pmxTools Names to NONMEMnms_nonmem.nms_pmx
Convert Canonical Names to pmxToolsnms_pmx.nms_canonical
Convert NONMEM Names to pmxToolsnms_pmx.nms_nonmem
Generate PsN-style Names for Characternms_psn.character
Generate PsN-style Names for Modelnms_psn.model
Create and Evaluate NONMEM Models in a Project Contextnonmemica-package nonmemica
Isolate Off-diagonal of Half Matrixoffdiag.halfmatrix
Get Parameters for Characterparameters.character
Create Parameter Tablepartab partab.partab
Create a Parameter Table from Model Namepartab.character
Identify the Model Problem Statement for Characterproblem.character
PsN Model File is Nestedpsn_nested
Set PsN Optionspsn_options
Relativize a PathrelativizePath
Resolve File Pathresolve
Translate Parameter Namesnms rosetta
Create a Runlog for Characterrunlog.character
Join Data Safelysafe_join
Join Data Frames Safelysafe_join.data.frame
Move the Columns of a Data Frame Relative to Each Othershuffle
Identify the Data Specification File for a Modelspecfile.character
Coerce to Superset from Charactersuperset.character
Create Specification for Model Inputs and Outputssuperspec
Create Specification for Model Inputs and Outputs From Charactersuperspec.character
Create Specification for Model Inputs and Outputs From Numericsuperspec.numeric
Calculate Time Since Most Recent Dosetad
A NONMEM-like Datasettad1
Calculate Time of Most Recent Dosetod
Tweak a Model by Defaulttweak.default
Tweak Modeltweak.model
Create the Updated Version of Characterupdated.character
Get Upper Bounds for Model Initial Estimatesupper.model
Set Upper Bounds for Model Initial Estimatesupper<-.model
Evaluate Xpath Expressionxpath
Evaluate xpath Expression in Default Contextxpath.default
Evaluate xpath Expression in Document Contextxpath.xml_document