Package: nonmemica 1.1.8

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]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
nonmemica/json (API)

# Install 'nonmemica' in R:

install.packages('nonmemica', repos = c('https://bergsmat.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bergsmat/nonmemica/issues

Datasets:

tad1 - A NONMEM-like Dataset

On CRAN:

4.73 score 5 stars 54 scripts 856 downloads 93 exports 38 dependencies

Last updated from:6c51d09abe. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	153
source / vignettes	OK	179
linux-release-x86_64	OK	157
macos-release-arm64	OK	97
macos-oldrel-arm64	OK	88
windows-devel	OK	97
windows-release	OK	94
windows-oldrel	OK	97
wasm-release	OK	146

Exports:%contains%as_nms_canonical as_nms_nonmem as_nms_pmx as_nms_psn as.best as.bootstrap as.halfmatrix as.init as.inits as.items as.matrices as.model as.omega as.problem as.sigma as.tab as.theta as.xml_document bakfor but comments comwidth comwidthOne datafile definitions depends enclose errors estimates filter_estimation fixed fixed<-forbak generalize half ignored initDex initial initial<-initSubscripts is.defined is.square like likebut locf lower lower<-maxWidths meta metasuperset modeldir modelfile modelpath ninput nms_canonical nms_nonmem nms_pmx nms_psn nocb num_parameters offdiag ord padded parameters parens partab pool prettycom problem problem_psn_nested psn_options read.model readxml row_col runhead runlog safe_join shuffle specfile superset superspec tad text2decimal tod tweak updated upper upper<-val_name write.model xpath

Dependencies:cli cpp11 csv data.table dplyr encode farver generics ggplot2 glue gridExtra gtable isoband labeling lattice lazyeval lifecycle magrittr metaplot pillar pkgconfig purrr R6 RColorBrewer rlang S7 scales spec stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr xml2

Creating a Nonmem Parameter Table

Rendered fromparameter-table.Rmdusingknitr::rmarkdown

Last update: 2023-05-09
Started: 2017-01-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Check if File Path is Absolute	absolute
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 Character	as.best.default
Create Bootstrap from Bootstrap	as.bootstrap.bootstrap
Coerce to Half Matrix by Default	as.halfmatrix.default
Coerce init to init	as.init.init
Coerce list to inits	as.inits.list
Coerce Half Matrix to Matrix	as.matrix.halfmatrix
Coerce character to model	as.model.character
Create an xml_document in a Project Context	as.xml_document as.xml_document.xml_document
Create xml_document From Character	as.xml_document.character
Extract Comments from Inits	comments.inits
Extract Comments from Items	comments.items
Extract Comments from Model	comments.model
Check Whether Text Contains Pattern	contains
Identify the Datafile for a Model	datafile.character
Harvest Model Item Definitions	definitions definitions.character
Create Model Item Definitions from definitions	definitions.definitions
Identify Model Dependencies	depends.default
Get Errors for Character	errors.character
Get Estimates for Character	estimates.character
Filter XML for Relevant Estimation Step	filter_estimation
Check if init is fixed	fixed.init
Check If Model is Fixed	fixed.model
Generalize a Nonmissing Value	generalize
Extract Index for Ignored Records	ignored
Get Model Initial Estimates	initial.model
Set Upper Bounds for Model Initial Estimates	initial<-.model
Modify a Model	likebut
Get Lower Bounds for Model Initial Estimates	lower.model
Set Lower Bounds for Model Initial Estimates	lower<-.model
Get Metadata for Character	meta.character
Metaplot Character, Standard Evaluation	metaplot_character
Metaplot Character	metaplot.character
Retrieve Model Outputs with Metadata	metasuperset
Identify the Directory for a Model	modeldir
Identify the Modelfile for a Model	modelfile
Resolve A Path to a Model-related File	modelpath
Resolve A Path to a Model-related File for Character	modelpath.character
Calculate Number of Inputs	ninput
Calculate Number of Inputs for Character	ninput.character
Calculate Number of Inputs for Numeric	ninput.numeric
Generate Canonical Names for Character	nms_canonical.character
Generate Canonical Names for Model	nms_canonical.model
Convert NONMEM Parameter Names to Canonical	nms_canonical.nms_nonmem
Generate NONMEM Names for Character	nms_nonmem.character
Generate NONMEM Names for Model	nms_nonmem.model
Convert Canonical Parameter Names to NONMEM	nms_nonmem.nms_canonical
Convert pmxTools Names to NONMEM	nms_nonmem.nms_pmx
Convert Canonical Names to pmxTools	nms_pmx.nms_canonical
Convert NONMEM Names to pmxTools	nms_pmx.nms_nonmem
Generate PsN-style Names for Character	nms_psn.character
Generate PsN-style Names for Model	nms_psn.model
Create and Evaluate NONMEM Models in a Project Context	nonmemica-package nonmemica
Isolate Off-diagonal of Half Matrix	offdiag.halfmatrix
Get Parameters for Character	parameters.character
Create Parameter Table	partab partab.partab
Create a Parameter Table from Model Name	partab.character
Identify the Model Problem Statement for Character	problem.character
PsN Model File is Nested	psn_nested
Set PsN Options	psn_options
Read XML with Conditional Filtering	readxml
Relativize a Path	relativizePath
Resolve File Path	resolve
Translate Parameter Names	nms rosetta
Create a Runlog for Character	runlog.character
Join Data Safely	safe_join
Join Data Frames Safely	safe_join.data.frame
Move the Columns of a Data Frame Relative to Each Other	shuffle
Identify the Data Specification File for a Model	specfile.character
Coerce to Superset from Character	superset.character
Create Specification for Model Inputs and Outputs	superspec
Create Specification for Model Inputs and Outputs From Character	superspec.character
Create Specification for Model Inputs and Outputs From Numeric	superspec.numeric
Calculate Time Since Most Recent Dose	tad
A NONMEM-like Dataset	tad1
Calculate Time of Most Recent Dose	tod
Tweak a Model by Default	tweak.default
Tweak Model	tweak.model
Create the Updated Version of Character	updated.character
Get Upper Bounds for Model Initial Estimates	upper.model
Set Upper Bounds for Model Initial Estimates	upper<-.model
Evaluate Xpath Expression	xpath
Evaluate xpath Expression in Default Context	xpath.default
Evaluate xpath Expression in Document Context	xpath.xml_document