| Type: | Package |
| Title: | Create and Evaluate NONMEM Models in a Project Context |
| Version: | 1.0.11 |
| Maintainer: | Tim Bergsma <bergsmat@gmail.com> |
| Description: | 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'. |
| License: | GPL-3 |
| LazyData: | TRUE |
| Imports: | dplyr (≥ 0.7.1), tidyr, xml2, encode, csv, spec, lazyeval, metaplot (≥ 0.1.4), magrittr, rlang |
| Suggests: | pander, knitr, wrangle, rmarkdown |
| RoxygenNote: | 7.3.2 |
| VignetteBuilder: | knitr |
| Encoding: | UTF-8 |
| NeedsCompilation: | no |
| Packaged: | 2024-10-25 21:58:33 UTC; tim.bergsma |
| Author: | Tim Bergsma [aut, cre] |
| Repository: | CRAN |
| Date/Publication: | 2024-10-25 22:40:02 UTC |
Create and Evaluate NONMEM Models in a Project Context
Description
Nonmemica (emphasis like 'America') creates and evaluates NONMEM models in a project context.
Details
NONMEM (ICON Development Solutions) is software for nonlinear mixed effects modeling. The fundamental interface is a text file (control stream, typ. *.mod or *.ctl) that specifies model input, structure, and output. There are many add-on interfaces for NONMEM (see references for a few examples). However, much day-to-day modeling, even for R users, involves substantial manual interventions.
Nonmemica streamlines interactions with NONMEM. It adopts some established conventions and techniques (e.g. from PsN and metrumrg), but introduces others that may be useful. Principally, it parses existing control streams for systematic analysis and alteration. Relatively simple, single-problem control streams are supported; see the example.
Of course, NONMEM itself is licensed software that must be installed independently. Nonmemica is largely indifferent to how NONMEM is installed or invoked. However, several features depend on the *.xml output that NONMEM creates; make sure it is available. Also, the best-supported directory structure is that which has numbers for model names, with all model-specific files in eponymous subdirectories of a "project" directory. An example is given below.
Nonmemica adopts three control stream encoding conventions that merit special mention. First, the problem statement is encoded in the form //like/x//but/y// where x is a reference model name and y is a feature difference from the reference model (see likebut() ). This allows any given model to be described by chaining together its legacy of features (use runlog(depenencies = TRUE, ...) ), which generally works better than trying to describe it exhaustively in the model name. As of version 0.9.2, experimental support is available for natural-language problem statements of the form "like run1001 but fixed additive error".
Second, Nonmemica only needs a single output table ($TABLE record). Be sure to use ONEHEADER but avoid FIRSTONLY. Nonmemica will integrate model inputs and outputs, regardless of table counts, into one data.frame (see superset() ).
Third, Nonmemica supports integrated metadata. With respect to model inputs, use package spec to store column metadata in a companion file (a data specification, e.g. *.spec). Keep the data file and data specification in a central location, not copied to the model directory. For model outputs (tabled items) supply column metadata directly in the control stream (or a *.def file; see example and help).
Nonmemica supports three global options: 'project' (default getwd() ) is the parent directory of model-specific files or directories; 'nested' (default TRUE) tells whether model-specific files are nested within eponymous directories; 'modex' (default 'ctl') gives the file extension for control streams. In many cases you can pass these options to the relevant functions; but since they likely won't change for the scope of a given project, it saves effort to set them as global options (if they differ from the defaults) using e.g. options(project=).
Numbers make good names for models because it is never hard for you or the software to think of a new one. That said, model names are typically processed as character in Nonmemica. There are many generic functions with both numeric and character methods that simply assume the (length-one) argument you supply is a model name.
Author(s)
Maintainer: Tim Bergsma bergsmat@gmail.com
References
Examples
# Create a working project.
source <- system.file(package = 'nonmemica','project')
target <- tempdir()
target <- gsub('\\\\','/',target) # for windows
source
target
file.copy(source,target,recursive = TRUE)
project <- file.path(target,'project','model')
# Point project option at working project
options(project = project)
# Load some packages
library(magrittr)
library(metaplot)
library(wrangle)
library(spec)
library(dplyr,warn.conflicts = FALSE)
# Identify features of a model.
1001 %>% modelpath
1001 %>% modeldir
1001 %>% modelfile
1001 %>% modelpath('xml')
1001 %>% datafile
datafile(1001) %matches% specfile(1001)
1001 %>% specfile
1001 %>% specfile %>% read.spec
1001 %>% as.model
1001 %>% as.model %>% comments
1001 %>% definitions
1001 %>% runlog(TRUE)
1001 %>% runlog
1001 %>% partab
1001 %>% num_parameters
1001 %>% nms_canonical
1001 %>% nms_psn
1001 %>% nms_nonmem
1001 %>% parameters
1001 %>% errors
1001 %>% as.model %>% initial
1001 %>% as.model %>% lower
1001 %>% as.model %>% upper
1001 %>% as.model %>% fixed
1001 %>% meta %>% class
1001 %>% meta
# Derive datasets.
1001 %>% superset %>% head
1001 %>% superset %>% filter(VISIBLE == 1) %>% group_by(ID,TIME) %>% status
1001 %>% metasuperset(c('ID','TIME')) %>% head
1001 %>% metasuperset(c('ID','TIME')) %>% sapply(attr,'label')
# Make diagnostic plots.
1001 %>% metaplot(
CWRESI, TAD, SEX,
groups = c('ID','TIME'),
subset = 'MDV == 0',
yref=0,
ysmooth = TRUE
)
1001 %>% metaplot(
ETA1, SEX,
ref = 0,
groups = c('ID','TIME'),
subset = 'MDV == 0'
)
1001 %>% metaplot(
SEX, ETA1,
ref = 0,
groups = c('ID','TIME'),
subset = 'MDV == 0'
)
1001 %>% metaplot(
ETA1, ETA2, ETA3,
groups = c('ID','TIME'),
subset = 'MDV == 0'
)
# Derive models.
1001 %>% likebut('revised',y = 1002, overwrite=TRUE )
# At this point, edit 1002.ctl to match whatever 'revised' means.
# Then run it with NONMEM and post-process results as above.
# Make ten new models with slightly different initial estimates.
1001 %>% tweak
Set init element
Description
Sets init element.
Usage
## S3 replacement method for class 'init'
x$name <- value
Arguments
x |
init |
name |
character |
value |
numeric |
Value
init
See Also
Other init:
$.init()
Select init element
Description
Selects init element.
Usage
## S3 method for class 'init'
x$name
Arguments
x |
init |
name |
character |
Value
numeric
See Also
Other init:
$<-.init()
Check Whether x contains y
Description
Checks whether x contains y, in natural syntax.
Usage
x %contains% y
Arguments
x |
character vector to check |
y |
pattern |
Value
logical
See Also
Other util:
as.best(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Examples
letters %contains% 'a'
Subset inits
Description
Subsets inits.
Usage
## S3 method for class 'inits'
x[..., drop = TRUE]
Arguments
x |
inits |
... |
passed arguments |
drop |
logical |
Value
inits
Subset model
Description
Subsets model.
Usage
## S3 method for class 'model'
x[..., drop = TRUE]
Arguments
x |
model |
... |
ignored |
drop |
passed to subset |
Value
model
See Also
Other as.model:
[[.model(),
as.model(),
as.model.character(),
as.model.numeric(),
read.model(),
write.model()
Select model Element
Description
Selects model element.
Usage
## S3 method for class 'model'
x[[..., drop = TRUE]]
Arguments
x |
model |
... |
passed arguments |
drop |
passed to element select |
Value
element
See Also
Other as.model:
[.model(),
as.model(),
as.model.character(),
as.model.numeric(),
read.model(),
write.model()
Check if File Path is Absolute
Description
Checks if file path is absolute.
Usage
absolute(x)
Arguments
x |
character (a file path) |
Value
logical; TRUE if x starts with / or .: (e.g. C:)
Convert to Best of Numeric or Character
Description
Convert to best of numeric or character.
Convert data.frame columns to best of numeric or character.
Usage
as.best(x, ...)
## S3 method for class 'data.frame'
as.best(x, prefix = "#", ...)
Arguments
x |
data.frame |
... |
passed arguments |
prefix |
character to prepend to values in mixed numeric/character columns |
Details
Converts to numeric if doing so creates no new NA; otherwise to character.
Converts columns to numeric if doing so creates no new NA; otherwise to character. Number-like columns that are nevertheless character are prefixed by default to make this explicit when viewing only a few rows.
Value
data.frame
Methods (by class)
-
as.best(data.frame): data.frame method
See Also
Other util:
%contains%(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Other util:
%contains%(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Convert Vector to Best of Numeric or Character
Description
Convert vector to best of numeric or character.
Usage
## Default S3 method:
as.best(x, prefix = "", na.strings = c(".", "NA", ""), ...)
Arguments
x |
default |
prefix |
prefix for viewing numerics |
na.strings |
strings that should be treated as NA |
... |
ignored |
Details
Converts vector to numeric if doing so creates no new NA; otherwise to character. Number-like vectors that are nevertheless character are prefixed by default to make this explicit when viewing only a few rows.
See Also
Other util:
%contains%(),
as.best(),
enclose(),
locf(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Create a Bootstrap Table
Description
Creates a bootstrap table.
Creates a bootstrap table from a PsN bootstrap results csv filepath. If x is not an existing file it is treated as a modelname and the results file is sought.
Usage
as.bootstrap(x, ...)
## S3 method for class 'character'
as.bootstrap(
x,
skip = 28,
check.names = FALSE,
lo = "5",
hi = "95",
verbose = TRUE,
pattern = "bootstrap_results.csv",
bootcsv = dir(modeldir(x, ...), pattern = pattern, recursive = TRUE, full.names = TRUE),
...
)
Arguments
x |
character |
... |
passed to |
skip |
number of lines to skip in bootstrap_results.csv |
check.names |
passed to bootstrap reader |
lo |
the PsN bootstrap lower confidence limit (%) |
hi |
the PsN bootstrap upper confidence limit (%) |
verbose |
display messages |
pattern |
pattern to search for bootstrap file |
bootcsv |
path to bootstrap_results.csv or equivalent |
Value
data.frame
data.frame
Methods (by class)
-
as.bootstrap(character): character method
See Also
Other as.bootstrap:
as.bootstrap.bootstrap(),
as.bootstrap.numeric()
Other as.bootstrap:
as.bootstrap.bootstrap(),
as.bootstrap.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.bootstrap
Create Bootstrap from Bootstrap
Description
Creates bootstrap from bootstrap.
Usage
## S3 method for class 'bootstrap'
as.bootstrap(x, ...)
Arguments
x |
bootstrap |
... |
ignored |
Value
data.frame
See Also
Other as.bootstrap:
as.bootstrap(),
as.bootstrap.numeric()
Create Bootstrap from Numeric
Description
Creates bootstrap from numeric.
Usage
## S3 method for class 'numeric'
as.bootstrap(x, ...)
Arguments
x |
object of dispatch |
... |
arguments to methods |
Value
data.frame
See Also
Other as.bootstrap:
as.bootstrap(),
as.bootstrap.bootstrap()
Coerce init to character
Description
Coerces init to character.
Usage
## S3 method for class 'init'
as.character(x, ...)
Arguments
x |
init |
... |
ignored |
Value
character
See Also
Other as.character:
as.character.inits(),
as.character.items(),
as.character.model(),
as.character.problem()
Coerce inits to character
Description
Coerces inits to character.
Usage
## S3 method for class 'inits'
as.character(
x,
pretty = TRUE,
sep = ";",
delim = " ; ",
widths = comwidth(x),
...
)
Arguments
x |
inits |
... |
passed arguments |
Value
character
See Also
Other as.character:
as.character.init(),
as.character.items(),
as.character.model(),
as.character.problem()
Coerce Items to Character
Description
Coerces items to character.
Usage
## S3 method for class 'items'
as.character(
x,
pretty = TRUE,
sep = ";",
delim = " ; ",
widths = comwidth(x),
...
)
Arguments
x |
items |
pretty |
logical |
sep |
input delimiter |
delim |
output delimiter |
widths |
desired widths |
... |
passed arguments |
Value
character
See Also
Other as.character:
as.character.init(),
as.character.inits(),
as.character.model(),
as.character.problem()
Coerce NONMEM Control Object to character
Description
Coerces NONMEM control stream object to character.
Usage
## S3 method for class 'model'
as.character(x, ...)
Arguments
x |
model |
... |
ignored |
Value
model
See Also
Other as.character:
as.character.init(),
as.character.inits(),
as.character.items(),
as.character.problem()
Coerce Problem to Character
Description
Coerces NONMEM problem statement to character.
Usage
## S3 method for class 'problem'
as.character(x, ...)
Arguments
x |
problem |
... |
ignored |
Value
character
See Also
Other as.character:
as.character.init(),
as.character.inits(),
as.character.items(),
as.character.model()
Coerce Half Matrix to Data Frame
Description
Coerces half matrix to data.frame.
Usage
## S3 method for class 'halfmatrix'
as.data.frame(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Coerce to Half Matrix
Description
Coerces to half matrix. Generic, with default methods.
Usage
as.halfmatrix(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Coerce to Half Matrix by Default
Description
Coerces to half matrix. Treats x as halfmatrix, coerces to matrix and takes half.
Usage
## Default S3 method:
as.halfmatrix(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Coerce Half Matrix to Half Matrix
Description
Coerces half matrix to half matrix. A non-operation.
Usage
## S3 method for class 'halfmatrix'
as.halfmatrix(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Coerce to init
Description
Coerces to init
Usage
as.init(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other as.init:
as.init.init(),
as.init.numeric()
Coerce init to init
Description
Coerces init to init
Usage
## S3 method for class 'init'
as.init(x = numeric(0), fixed = FALSE, comment = character(0), ...)
Arguments
x |
init |
fixed |
logical |
comment |
character |
... |
passed arguments |
Value
init
See Also
Other as.init:
as.init(),
as.init.numeric()
Coerces numeric to init
Description
Coerces numeric to init
Usage
## S3 method for class 'numeric'
as.init(x = numeric(0), fixed = FALSE, comment = character(0), ...)
Arguments
x |
numeric |
fixed |
logical |
comment |
character |
... |
ignored |
Value
init
See Also
Other as.init:
as.init(),
as.init.init()
Coerce to inits
Description
Coerces to inits.
Coerces character to inits.
Coerces inits to inits
Usage
as.inits(x, ...)
## S3 method for class 'character'
as.inits(x, ...)
## S3 method for class 'inits'
as.inits(x, ...)
Arguments
x |
inits |
... |
ignored |
Value
inits
inits
Methods (by class)
-
as.inits(character): character method -
as.inits(inits): inits method
See Also
Other as.inits:
as.inits.list(),
as.inits.numeric()
Other as.inits:
as.inits.list(),
as.inits.numeric()
Other as.inits:
as.inits.list(),
as.inits.numeric()
Coerce list to inits
Description
Coerces list to inits.
Usage
## S3 method for class 'list'
as.inits(x, comment = character(0), ...)
Arguments
x |
list |
comment |
character |
... |
passed arguments |
Value
inits
See Also
Other as.inits:
as.inits(),
as.inits.numeric()
Coerce numeric to inits
Description
Coerces numeric to inits
Usage
## S3 method for class 'numeric'
as.inits(x, fixed = FALSE, comment = character(0), ...)
Arguments
x |
numeric |
fixed |
logical |
comment |
character |
Value
inits
See Also
Other as.inits:
as.inits(),
as.inits.list()
Convert to Items
Description
Converts to items.
Usage
as.items(x, ...)
Arguments
x |
object |
... |
passed arguments |
Convert to Items from Character
Description
Converts to items from character
Usage
## S3 method for class 'character'
as.items(x, ...)
Arguments
x |
character |
... |
ignored |
Value
items
Coerce model to list
Description
Coerces model to list.
Usage
## S3 method for class 'model'
as.list(x, ...)
Arguments
x |
model |
... |
dots |
Value
list
Coerce to List of Matrices
Description
Coerces to list of matrices.
Usage
as.matrices(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other as.matrices:
as.matrices.inits(),
as.matrices.records()
Coerce to Matrices from Inits
Description
Coerces to matrices from inits. Non-block inits is expanded into list of matrices.
Usage
## S3 method for class 'inits'
as.matrices(x, ...)
Arguments
x |
inits |
... |
ignored |
Value
matrices
See Also
Other as.matrices:
as.matrices(),
as.matrices.records()
Coerce to List of Matrices from Records
Description
Coerces to list of matrices from Records
Usage
## S3 method for class 'records'
as.matrices(x, ...)
Arguments
x |
records |
... |
ignored |
See Also
Other as.matrices:
as.matrices(),
as.matrices.inits()
Coerce Half Matrix to Matrix
Description
Coerces half matrix to matrix.
Usage
## S3 method for class 'halfmatrix'
as.matrix(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Coerce to NONMEM Control Object
Description
Coerces to NONMEM control stream object.
Usage
as.model(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
Value
model
See Also
Other as.model:
[.model(),
[[.model(),
as.model.character(),
as.model.numeric(),
read.model(),
write.model()
Coerce character to model
Description
Coerces chacter to model.
Usage
## S3 method for class 'character'
as.model(
x,
pattern = "^\\s*\\$(\\S+)(\\s.*)?$",
head = "\\1",
tail = "\\2",
parse = TRUE,
...
)
Arguments
x |
character |
pattern |
pattern to identify record declarations |
head |
subpattern to identify declaration type |
tail |
subpattern remaining |
parse |
whether to convert thetas omegas and sigmas to inits, tables to items, and runrecords to fields |
... |
ignored |
Value
list
See Also
Other as.model:
[.model(),
[[.model(),
as.model(),
as.model.numeric(),
read.model(),
write.model()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model
Coerce to Model from Numeric
Description
Coerces to model from numeric by coercing to character.
Usage
## S3 method for class 'numeric'
as.model(x, ...)
Arguments
x |
numeric |
... |
passed arguments |
See Also
Other as.model:
[.model(),
[[.model(),
as.model(),
as.model.character(),
read.model(),
write.model()
Extract Omegas
Description
Extracts omegas.
Usage
as.omega(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other as.omega:
as.omega.model()
Extract Omegas from Model
Description
Extracts omegas from model.
Usage
## S3 method for class 'model'
as.omega(x, ...)
Arguments
x |
model |
... |
passed arguments |
Value
omega (subset of model)
See Also
Other as.omega:
as.omega()
Parse the Run Record
Description
Parses the run record portion of a problem statement in a NONMEM model. stores it as an attribute of the problem statement. See https://github.com/UUPharmacometrics/PsN/releases/download/4.9.0/runrecord_userguide.pdf.
Usage
as.problem(x, ...)
Arguments
x |
character |
... |
passed arguments |
See Also
Other problem:
problem(),
problem.character(),
problem.numeric(),
problem_()
Examples
x <-
'$PROB Simpraz - full data set
;; 1. Based on: 1
;; 2. Description:
;; Added an OMEGA BLOCK(2) for CL and V
;; 3. Label:
;; Basic model
;; 4. Structural model:
;; One compartment linear model
;; 5. Covariate model:
;; No covariates
;; 6. Interindividual variability:
;; CL, V and KA. BLOCK(2) for CL and V
;; 7. Interoccasion variability:
;; 8. Residual variability:
;; Proportional
;; 9. Estimation:
;; FO'
con <- textConnection(x)
y <- readLines(con)
close(con)
z <- as.problem(y)
at <- attr(z,'problem')
names(at)
z
Extract Sigmas
Description
Extracts sigmas.
Usage
as.sigma(x, ...)
Arguments
x |
object |
... |
passed arguments |
Extract Sigmas from Model
Description
Extracts sigmas from model.
Usage
## S3 method for class 'model'
as.sigma(x, ...)
Arguments
x |
model |
... |
passed arguments |
Value
sigma (subset of model)
Extract Tables
Description
Extracts tables.
Usage
as.tab(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other as.tab:
as.tab.model()
Extract Tables from Model
Description
Extracts tables from model.
Usage
## S3 method for class 'model'
as.tab(x, ...)
Arguments
x |
model |
... |
passed arguments |
Value
tab (subset of model)
See Also
Other as.tab:
as.tab()
Extract Thetas
Description
Extracts thetas.
Usage
as.theta(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other as.theta:
as.theta.model()
Extract Thetas from Model
Description
Extracts thetas from model.
Usage
## S3 method for class 'model'
as.theta(x, ...)
Arguments
x |
model |
... |
passed arguments |
Value
theta (subset of model)
See Also
Other as.theta:
as.theta()
Create an xml_document in a Project Context
Description
Creates an xml_document in a project context.
Coerces xml_document to xml_document
Usage
as.xml_document(x, ...)
## S3 method for class 'xml_document'
as.xml_document(x, ...)
Arguments
x |
xml_document |
... |
ignored |
Value
xml_document
xml_document
Methods (by class)
-
as.xml_document(xml_document): xml_document method
See Also
Other xpath:
as.xml_document.character(),
as.xml_document.numeric(),
xpath(),
xpath.default(),
xpath.xml_document()
Other xpath:
as.xml_document.character(),
as.xml_document.numeric(),
xpath(),
xpath.default(),
xpath.xml_document()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.xml_document
Create xml_document From Character
Description
Creates an xml_document from character (modelname or filepath).
Usage
## S3 method for class 'character'
as.xml_document(x, strip.namespace = TRUE, ...)
Arguments
x |
file path or run name |
strip.namespace |
whether to strip e.g. nm: from xml elements |
... |
passed to modelpath() |
Value
xml_document
See Also
Other xpath:
as.xml_document(),
as.xml_document.numeric(),
xpath(),
xpath.default(),
xpath.xml_document()
Coerce numeric to xml_document
Description
Coerces numeric to xml_document
Usage
## S3 method for class 'numeric'
as.xml_document(x, ...)
Arguments
x |
numerc |
... |
passed arguments |
Value
xml_document
See Also
Other xpath:
as.xml_document(),
as.xml_document.character(),
xpath(),
xpath.default(),
xpath.xml_document()
Coerce to 'nms_canonical'
Description
Coerces character to 'nms_canonical'.
Usage
as_nms_canonical(x, ...)
Arguments
x |
character |
... |
ignored |
See Also
Other nms:
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Coerce to 'nms_nonmem'
Description
Coerces character to 'nms_nonmem'.
Usage
as_nms_nonmem(x, ...)
Arguments
x |
character |
... |
ignored |
See Also
Other nms:
as_nms_canonical(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Coerce to 'nms_pmx'
Description
Coerces character to 'nms_pmx'.
Usage
as_nms_pmx(x, ...)
Arguments
x |
character |
... |
ignored |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Coerce to 'nms_psn'
Description
Coerces character to 'nms_psn'.
Usage
as_nms_psn(x, ...)
Arguments
x |
character |
... |
ignored |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Identify a Distinctive Feature
Description
Identifies a distinctive feature of an object.
Usage
but(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other but:
but.default()
Identify the Distinctive Feature of a Model
Description
Identifies the distinctive feature of a model, i.e. how it differs from its parent (the reference model). x can be a vector.
Usage
## Default S3 method:
but(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other but:
but()
Extract Comments
Description
Extracts comments.
Extracts comments from records.
Usage
comments(x, ...)
## S3 method for class 'records'
comments(x, ...)
Arguments
x |
records |
... |
ignored |
Value
data.frame
Methods (by class)
-
comments(records): record method
See Also
Other comments:
comments.inits(),
comments.items(),
comments.model()
Other comments:
comments.inits(),
comments.items(),
comments.model()
Extract Comments from Inits
Description
Extracts comments from inits.
Usage
## S3 method for class 'inits'
comments(x, type, prior, ...)
Arguments
x |
inits |
type |
item type: theta, omega, sigma (tables give items not inits) |
prior |
number of prior items of this type (maybe imporant for numbering) |
... |
ignored |
Value
data.frame
See Also
Other comments:
comments(),
comments.items(),
comments.model()
Extract Comments from Items
Description
Extracts comments from items.
Usage
## S3 method for class 'items'
comments(x, ...)
Arguments
x |
items |
... |
ignored |
Value
data.frame
See Also
Other comments:
comments(),
comments.inits(),
comments.model()
Extract Comments from Model
Description
Extracts comments from model.
Usage
## S3 method for class 'model'
comments(
x,
fields = c("symbol", "unit", "label"),
expected = character(0),
na = NA_character_,
tables = TRUE,
...
)
Arguments
x |
model |
fields |
data items to scavenge from control stream comments |
expected |
parameters known from NONMEM output |
na |
string to use for NA values when writing default metafile |
tables |
whether to include table comments |
... |
passed arguments |
Value
data.frame
See Also
Other comments:
comments(),
comments.inits(),
comments.items()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% comments
Calculate Comment Widths Calculates comment widths.
Description
Calculate Comment Widths Calculates comment widths.
Usage
comwidth(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other comwidth:
comwidth.character(),
comwidth.inits(),
comwidth.items()
Calculate Comment Widths for Character
Description
Calculates comment widths for character.
Usage
## S3 method for class 'character'
comwidth(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other comwidth:
comwidth(),
comwidth.inits(),
comwidth.items()
Calculate Comment Widths for Inits
Description
Calculates comment widths for inits
Usage
## S3 method for class 'inits'
comwidth(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other comwidth:
comwidth(),
comwidth.character(),
comwidth.items()
Calculate Comment Widths for Items
Description
Calculates comment widths for items
Usage
## S3 method for class 'items'
comwidth(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other comwidth:
comwidth(),
comwidth.character(),
comwidth.inits()
Calculate Comment Widths for One Element
Description
Calculates comment widths for one element.
Usage
comwidthOne(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other comwidthOne:
comwidthOne.character()
Calculate Comment Widths for One Element of Character
Description
Calculates Comment Widths for one element of character
Usage
## S3 method for class 'character'
comwidthOne(x, split = ";", ...)
Arguments
x |
object |
split |
comment separator |
... |
passed arguments |
See Also
Other comwidthOne:
comwidthOne()
Check Whether Text Contains Pattern
Description
Checks whether text contains pattern.
Usage
contains(pattern, text, ...)
Arguments
pattern |
regular expression |
text |
character vector to check |
... |
arguments to methods |
Value
logical
See Also
Identify Datafile
Description
Identifies datafile.
Usage
datafile(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other path:
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Identify the Datafile for a Model
Description
Identifies the datafile used by a model. Expresses it relative to current working directory.
Usage
## S3 method for class 'character'
datafile(x, ...)
Arguments
x |
the model name or path to a control stream |
... |
ext can be passed to modelfile, etc. |
Value
character
See Also
Other path:
datafile(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Examples
library(spec)
source <- system.file(package = 'nonmemica','project')
target <- tempdir()
target <- gsub('\\\\','/',target) # for windows
file.copy(source,target,recursive = TRUE)
project <- file.path(target,'project','model')
options(project = project)
library(magrittr)
1001 %>% datafile
datafile(1001) %matches% specfile(1001)
1001 %>% specfile
1001 %>% specfile %>% read.spec
Identify Datafile from Numeric
Description
Identifies datafile from numeric.
Usage
## S3 method for class 'numeric'
datafile(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other path:
datafile(),
datafile.character(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Harvest Model Item Definitions
Description
Havests model item definitions.
Create Item Definitions from Model Name
Usage
definitions(x, ...)
## S3 method for class 'character'
definitions(
x,
verbose = FALSE,
ctlfile = modelfile(x, ...),
metafile = modelpath(x, "def", ...),
fields = getOption("fields", default = c("symbol", "label", "unit")),
read = length(metafile) == 1,
write = FALSE,
...
)
Arguments
x |
object of dispatch |
... |
arguments to methods |
verbose |
set FALSE to suppress messages |
ctlfile |
path to control stream (pass length-zero argument to ignore) |
metafile |
path to definitions file (pass length-zero argument to ignore) |
fields |
metadata fields to read from control stream if no metafile |
read |
whether to read the definitions file |
write |
whether to write the definitions file |
Details
x can be numeric or character model name, assuming project is identified by argument or option.
Creates item definitions from a model name. Scavenges definitions optionally from the control stream and optionally from the definitions file. Optionally writes the result to the definitions file. Always returns a data.frame with at least the column 'item' but possibly no rows.
Value
object of class definitions, or path to metafile if write = TRUE.
Methods (by class)
-
definitions(character): character method
See Also
Other definitions:
definitions.definitions(),
definitions.numeric()
Other definitions:
definitions.definitions(),
definitions.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% definitions
Create Model Item Definitions from definitions
Description
Creates a model item definitions from a definitions object.
Usage
## S3 method for class 'definitions'
definitions(x, ...)
Arguments
x |
definitions |
... |
ignored |
Details
Just returns the object unmodified.
See Also
Other definitions:
definitions(),
definitions.numeric()
Create Model Item Definitions from Number.
Description
Creates a model item definitions from a number.
Usage
## S3 method for class 'numeric'
definitions(x, ...)
Arguments
x |
numeric |
... |
ignored |
Details
Just coerces to character and calls definitions again.
See Also
Other definitions:
definitions(),
definitions.definitions()
Identify What Something Depends On
Description
Identfies that on which something depends.
Usage
depends(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other depends:
depends.default()
Identify Model Dependencies
Description
Identify those models in the lineage of models in x.
Usage
## Default S3 method:
depends(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other depends:
depends()
Enclose in Arbitrary Characters
Description
Enclose in arbitrary characters
Usage
enclose(x, open, close, ...)
Arguments
x |
vector |
open |
open string |
close |
close string |
... |
dots |
Value
character
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
locf(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Get Errors
Description
Gets errors.
Usage
errors(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other errors:
errors.character(),
errors.numeric()
Get Errors for Character
Description
Gets model asymptotic standard errors in canonical order, treating character as model names.
See parameters for a less formal interface.
Usage
## S3 method for class 'character'
errors(
x,
xmlfile = modelpath(x, ext = "xml", ...),
strip.namespace = TRUE,
digits = 3,
...
)
Arguments
x |
character (modelname) |
xmlfile |
path to xml file |
strip.namespace |
whether to strip e.g. nm: from xml elements for easier xpath syntax |
digits |
passed to signif |
... |
dots |
Value
numeric
See Also
nms_canonical errors
Other errors:
errors(),
errors.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% errors
Get Errors for Numeric
Description
Gets errors for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
errors(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other errors:
errors(),
errors.character()
Get Estimates
Description
Gets estimates
Usage
estimates(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other estimates:
estimates.character(),
estimates.numeric()
Get Estimates for Character
Description
Gets model parameter estimates in canonical order, treating character as model names.
See parameters for a less formal interface.
Usage
## S3 method for class 'character'
estimates(
x,
xmlfile = modelpath(x, ext = "xml", ...),
strip.namespace = TRUE,
digits = 3,
...
)
Arguments
x |
character (modelname) |
xmlfile |
path to xml file |
strip.namespace |
whether to strip e.g. nm: from xml elements for easier xpath syntax |
digits |
passed to signif |
... |
dots |
Value
numeric
See Also
nms_canonical errors
Other estimates:
estimates(),
estimates.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% estimates
Get Estimates for Numeric
Description
Gets estimates for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
estimates(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other estimates:
estimates(),
estimates.character()
Check if something is fixed
Description
Checks if something is fixed
Checks if inits is fixed.
Usage
fixed(x, ...)
## S3 method for class 'inits'
fixed(x, ...)
Arguments
x |
inits |
... |
ignored |
Value
logical
Methods (by class)
-
fixed(inits): inits method
See Also
Other fixed:
fixed.init(),
fixed.model(),
fixed<-(),
fixed<-.init(),
fixed<-.inits(),
fixed<-.model()
Other fixed:
fixed.init(),
fixed.model(),
fixed<-(),
fixed<-.init(),
fixed<-.inits(),
fixed<-.model()
Set value of fixed attribute
Description
Sets value of fixed attribute.
Usage
fixed(x) <- value
Arguments
x |
object |
value |
value to set |
See Also
Other fixed:
fixed(),
fixed.init(),
fixed.model(),
fixed<-.init(),
fixed<-.inits(),
fixed<-.model()
Set fixed init value
Description
Sets fixed init value.
Usage
## S3 replacement method for class 'init'
fixed(x) <- value
Arguments
x |
object |
value |
value to |
Value
init
See Also
Other fixed:
fixed(),
fixed.init(),
fixed.model(),
fixed<-(),
fixed<-.inits(),
fixed<-.model()
Set fixed attribute of inits
Description
Sets fixed attribute of inits.
Usage
## S3 replacement method for class 'inits'
fixed(x) <- value
Arguments
x |
inits |
value |
logical |
Value
inits
See Also
Other fixed:
fixed(),
fixed.init(),
fixed.model(),
fixed<-(),
fixed<-.init(),
fixed<-.model()
Set fixed attribute of model
Description
Sets fixed attribute of model.
Usage
## S3 replacement method for class 'model'
fixed(x) <- value
Arguments
x |
model |
value |
logical |
Value
model
See Also
Other fixed:
fixed(),
fixed.init(),
fixed.model(),
fixed<-(),
fixed<-.init(),
fixed<-.inits()
Check if init is fixed
Description
Checks if init is fixed.
Usage
## S3 method for class 'init'
fixed(x, ...)
Arguments
x |
init |
... |
ignored |
Value
logical
See Also
Other fixed:
fixed(),
fixed.model(),
fixed<-(),
fixed<-.init(),
fixed<-.inits(),
fixed<-.model()
Check If Model is Fixed
Description
Checks if model is fixed. Returns a logical vector with element for each init, in canonical order.
Usage
## S3 method for class 'model'
fixed(x, ...)
Arguments
x |
inits |
... |
ignored |
Value
logical
See Also
Other fixed:
fixed(),
fixed.init(),
fixed<-(),
fixed<-.init(),
fixed<-.inits(),
fixed<-.model()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% fixed
Format init
Description
Formats init.
Usage
## S3 method for class 'init'
format(x, ...)
Arguments
x |
init |
... |
passed arguments |
Value
character
See Also
Other format:
format.inits(),
format.items(),
format.model()
Format inits
Description
Formats inits.
Usage
## S3 method for class 'inits'
format(x, ...)
Arguments
x |
inits |
... |
passed arguments |
Value
character
See Also
Other format:
format.init(),
format.items(),
format.model()
Format Items
Description
Formats items.
Usage
## S3 method for class 'items'
format(x, ...)
Arguments
x |
items |
... |
passed arguments |
Value
character
See Also
Other format:
format.init(),
format.inits(),
format.model()
Format model
Description
Format model.
Usage
## S3 method for class 'model'
format(x, ...)
Arguments
x |
model |
... |
passed arguments |
Details
Coerces to character.
Value
character
See Also
Other format:
format.init(),
format.inits(),
format.items()
Generalize a Nonmissing Value
Description
#Generalize a nonmissing value. If there is only one such among zero or more NA, impute that value for all NA.
Usage
generalize(x, ...)
Arguments
x |
vector |
... |
ignored |
See Also
Other superset:
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Find Half of Something
Description
Finds half of something. Generic, with method for matrix.
Usage
half(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Find Half of Matrix
Description
Finds half of matrix. I.e., lower or upper triangle of symmetric matrix.
Usage
## S3 method for class 'matrix'
half(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Extract Index for Ignored Records
Description
Extracts index for ignored records, given a NONMEM control stream.
Usage
ignored(
x,
read.input = list(read.csv, header = TRUE, as.is = TRUE),
ext = getOption("modex", "ctl"),
project = getOption("project", getwd()),
nested = getOption("nested", TRUE),
...
)
Arguments
x |
length-one character: a model name |
read.input |
list of arguments representing a methodology for acquiring the data of interest: the first argument is not named and will be passed to match.fun(); the other arguments will be passed to the result, and must include an argument named 'header'. |
ext |
model file extension, e.g. 'mod' or 'ctl' |
project |
project directory (can be expression) |
nested |
whether model files are nested in eponymous directories |
... |
passed to |
Value
logical
See Also
Other superset:
generalize(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Identify Indices of Initial Estimates
Description
Identifies indices of initial Estimates.
Usage
initDex(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other initDex:
initDex.model()
Identify Indices of Initial Estimates in model
Description
Identifies record indices of initial estimates for an object of class model. If model has not been parsed, the result is integer(0). Otherwise, the result is the record numbers for the canonical order of all init objects among theta, omega, and sigma element types, regardless of the number and order of such types. If a block(2) omega is specified between two thetas and one sigma follows, the results could be c(6L, 8L, 7L, 7L, 7L, 9L).
Usage
## S3 method for class 'model'
initDex(x, ...)
Arguments
x |
model |
... |
ignored |
Value
integer
See Also
Other initDex:
initDex()
Identify Subscripts
Description
Identifies subscripts.
Usage
initSubscripts(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other initSubscripts:
initSubscripts.model()
Identify Subscripts of Initial Estimates in model
Description
Identifies subscripts of record indices of initial estimates for an object of class model. If model has not been parsed, the result is integer(0). Otherwise, the result is the element number for each init object within each inits in x (canonical order).
Usage
## S3 method for class 'model'
initSubscripts(x, ...)
Arguments
x |
model |
... |
ignored |
Value
integer
See Also
Other initSubscripts:
initSubscripts()
Get Initial Value
Description
Gets initial Value.
Usage
initial(x, ...)
Arguments
x |
object of dispatch |
... |
dots |
See Also
Other initial:
initial.model(),
initial<-(),
initial<-.model()
Set Initial Value
Description
Sets initial Value.
Usage
initial(x) <- value
Arguments
x |
object of dispatch |
value |
right hand side |
See Also
Other initial:
initial(),
initial.model(),
initial<-.model()
Set Upper Bounds for Model Initial Estimates
Description
Sets upper bounds for model initial estimates.
Usage
## S3 replacement method for class 'model'
initial(x) <- value
Arguments
x |
model |
value |
numeric |
See Also
Other initial:
initial(),
initial.model(),
initial<-()
Get Model Initial Estimates
Description
Gets model initial estimates.
Usage
## S3 method for class 'model'
initial(x, ...)
Arguments
x |
model |
... |
dots |
See Also
Other initial:
initial(),
initial<-(),
initial<-.model()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% initial
Check Whether Elements are Defined
Description
Checks whether elements are defined. Inverse of is.na().
Usage
is.defined(x)
Arguments
x |
vector |
Value
logical
Examples
is.defined(c(1,NA,2))
Test If Something is Square
Description
Tests if something is square. Generic, with method for matrix.
Usage
is.square(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Test If Matrix is Square
Description
Tests if matrix is square.
Usage
## S3 method for class 'matrix'
is.square(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Identify What Something is Like
Description
Identifies what something is like.
Usage
like(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other like:
like.default()
Identify the Relevant Reference Model
Description
Identifies the relevant reference model, i.e. the 'parent' of x.
Usage
## Default S3 method:
like(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other like:
like()
Modify a Model
Description
Makes a copy of a model in a corresponding directory. Problem statement is updated to reflect that the model is LIKE the reference model BUT different in some fundamental way.
Usage
likebut(
x,
but = "better",
y = NULL,
project = getOption("project", getwd()),
nested = getOption("nested", TRUE),
overwrite = FALSE,
ext = getOption("modex", "ctl"),
include = "\\.def$",
update = FALSE,
...
)
Arguments
x |
a model name, presumably interpretable as numeric |
but |
a short description of the characteristic difference from x |
y |
optional name for model to be created, auto-incremented by default |
project |
project directory (can be expression) |
nested |
model files nested in run-specific directories |
overwrite |
whether to overwrite y if it exists |
ext |
extension for the model file |
include |
regular expressions for files to copy to new directory |
update |
use final estimates of x as initial estimates of y |
... |
passed arguments, including PsN runrecord elements (experimental) |
Value
the value of y
See Also
Examples
# Create a working project.
source <- system.file(package = 'nonmemica','project')
target <- tempdir()
target <- gsub('\\\\','/',target) # for windows
source
target
file.copy(source,target,recursive = TRUE)
project <- file.path(target,'project','model')
# Point project option at working project
options(project = project)
library(magrittr)
# Derive models.
1001 %>% likebut('revised',y = 1002, overwrite=TRUE )
# At this point, edit 1002.ctl to match whatever 'revised' means.
# Then run it with NONMEM.
Impute Missing Vector Values
Description
locf() implements 'last observation carried forward': NA's are imputed with the most recent non-NA value. nocb() is the complement: 'next observation carried backward': NA's are imputed with the next non-NA value. forbak() first executes locf(), then nocb(), so that even leading NAs are imputed. If even one non-NA value is present, forbak() should not return any NA's. bakfor() does the reverse.
Usage
locf(x)
forbak(x)
bakfor(x)
nocb(x)
Arguments
x |
a vector possibly with some missing values and some non-missing values |
Value
a vector like x
Functions
-
forbak(): forbak locf followed by nocb -
bakfor(): bakfor nocb followed by locf -
nocb(): nocb next observation carried backward
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
padded(),
parens(),
pool(),
runhead(),
text2decimal()
Examples
locf(c(NA,1,2,NA,NA,3,NA,4,NA))
nocb(c(NA,1,2,NA,NA,3,NA,4,NA))
forbak(c(NA,1,2,NA,NA,3,NA,4,NA))
Get Lower Value
Description
Gets lower Value.
Usage
lower(x, ...)
Arguments
x |
object of dispatch |
... |
dots |
See Also
Other lower:
lower.model(),
lower<-(),
lower<-.model()
Set Lower Value
Description
Sets lower Value.
Usage
lower(x) <- value
Arguments
x |
object of dispatch |
value |
right hand side |
See Also
Other lower:
lower(),
lower.model(),
lower<-.model()
Set Lower Bounds for Model Initial Estimates
Description
Sets lower bounds for model initial estimates.
Usage
## S3 replacement method for class 'model'
lower(x) <- value
Arguments
x |
model |
value |
numeric |
See Also
Other lower:
lower(),
lower.model(),
lower<-()
Get Lower Bounds for Model Initial Estimates
Description
Gets lower bounds for model initial estimates.
Usage
## S3 method for class 'model'
lower(x, ...)
Arguments
x |
model |
... |
dots |
See Also
Other lower:
lower(),
lower<-(),
lower<-.model()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% lower
Calculate Maximum Widths
Description
Calculates maximum widths
Usage
maxWidths(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other maxWidths:
maxWidths.list()
Calculate Maximum Widths for List
Description
Calculates maximum widths for list
Usage
## S3 method for class 'list'
maxWidths(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other maxWidths:
maxWidths()
Get Metadata
Description
Gets metadata.
Usage
meta(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Get Metadata for Character
Description
Gets metadata for character, treating it as a model name. Blends metadata from specfile with metadata from control stream, removing both exact duplicates as well as redefined values (with warning).
Usage
## S3 method for class 'character'
meta(x, simplify = TRUE, ...)
Arguments
x |
object |
simplify |
logical: remove range information from guide text |
... |
passed arguments |
Value
data.frame
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% meta
Get Metadata for Numeric
Description
Gets metadata for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
meta(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Metaplot Character
Description
Plots character by treating as model name. A dataset is constructed by combining the meta version of the model input with a meta version of the model output and calling metaplot with the result.
Usage
## S3 method for class 'character'
metaplot(x, ..., groups, meta = match.fun("meta")(x), subset)
Arguments
x |
object |
... |
unquoted names of variables to plot, or other named arguments (passed) |
groups |
columns by which to group the dataset |
meta |
metadata; meta(x) by default |
subset |
a condition for filtering data |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Examples
library(magrittr)
library(metaplot)
options(project = system.file('project/model',package='nonmemica'))
## Not run:
1001 %>% metaplot(
CWRESI, TAD, SEX,
groups = c('ID','TIME'),
subset = 'MDV == 0',
yref = 0,
ysmooth = TRUE
)
## End(Not run)
Metaplot Numeric
Description
Plots numeric by coercing first to character.
Usage
## S3 method for class 'numeric'
metaplot(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Metaplot Character, Standard Evaluation
Description
Plots character by treating as model name. A dataset is constructed by combining the model input with a the model output and calling metaplot with the result.
Usage
metaplot_character(x, groups, meta = NULL, subset, var, ...)
Arguments
x |
object |
groups |
columns by which to group the dataset |
meta |
metadata; meta(x) by default |
subset |
a condition for filtering data |
var |
variables to plot |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Retrieve Model Outputs with Metadata
Description
Retrieves model outputs with metadata.
Usage
metasuperset(
x,
groups,
meta = match.fun("meta")(x, ...),
subset = getOption("metasuperset_subset", NULL),
...
)
Arguments
x |
model name |
groups |
vector of key column names in superset, e.g. USUBJID, TIME |
meta |
metadata with column 'item' and possibly attributes such as 'label' and 'guide' |
subset |
length-one character: a condition for filtering results, e.g. 'EVID == 0' |
... |
passed arguments |
Value
data.frame
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% metasuperset(c('ID','TIME')) %>% head
Identify the Directory for a Model
Description
Identifies the directory used by a model.
Usage
modeldir(x, ext, ...)
Arguments
x |
the model name |
ext |
model file extension |
... |
passed arguments |
Value
character
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% modeldir
Identify the Modelfile for a Model
Description
Identifies the modelfile used by a model.
Usage
modelfile(x, ext = getOption("modex", "ctl"), ...)
Arguments
x |
the model name |
ext |
model file extension |
... |
passed arguments |
Value
character
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% modelfile('xml')
Resolve A Path to a Model-related File
Description
Resolves a path to a model-related file.
Usage
modelpath(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% modelpath
Resolve A Path to a Model-related File for Character
Description
Resolves a path to a model-related file, treating x as a model name.
By default (ext is NULL) the run directory is returned.
As of version 0.9.2, nested can be a function of ext and ...
That returns logical.
Usage
## S3 method for class 'character'
modelpath(
x,
ext = NULL,
project = getOption("project", getwd()),
nested = getOption("nested", TRUE),
...
)
Arguments
x |
object |
ext |
file extension, no leading dot |
project |
project directory (can be expression) |
nested |
whether model files are nested in eponymous directories |
... |
passed arguments |
Value
character
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Resolve A Path to a Model-related File for Numeric
Description
Resolves a path to a model-related file, coercing x to character.
Usage
## S3 method for class 'numeric'
modelpath(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
psn_options(),
specfile(),
specfile.character(),
specfile.numeric()
Calculate Number of Inputs
Description
Calculates number of inputs.
Usage
ninput(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Calculate Number of Inputs for Character
Description
Calculates number of inputs for character by treating as a model name.
Usage
## S3 method for class 'character'
ninput(x, ...)
Arguments
x |
character |
... |
passed arguments |
Value
integer
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Calculate Number of Inputs for Numeric
Description
Calculates number of inputs for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
ninput(x, ...)
Arguments
x |
numeric |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Generate Canonical Names
Description
Generates canonical names.
Generic, with method nms_canonical.model.
Usage
nms_canonical(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Generate Canonical Names for Character
Description
Generates canonical names for character by converting to parsed model.
Usage
## S3 method for class 'character'
nms_canonical(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% nms_canonical
Generate Canonical Names for Model
Description
Generates canonical names for a NONMEM control stream object. Canonical names indicate all and only the declared model parameters in lower-case conventional order (theta, omega row-major, sigma) with underscores and two-digit (or more) indices. E.g. theta_01, theta_02, omega_01_01, omega_02_01, omega_02_02, omega_01_01.
Usage
## S3 method for class 'model'
nms_canonical(x, ...)
Arguments
x |
a model designator |
... |
passed arguments |
Value
nms_canonical (character)
See Also
as.model
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Convert NONMEM Parameter Names to Canonical
Description
Converts nms_nonmem to nms_canonical.
Usage
## S3 method for class 'nms_nonmem'
nms_canonical(x, ...)
Arguments
x |
nms_nonmem |
... |
ignored |
Value
nms_canonical
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Convert Parameter Names to NONMEM
Description
Converts parameter names to NONMEM style.
Usage
## S3 method for class 'nms_pmx'
nms_canonical(x, ...)
Arguments
x |
nms_pmx |
... |
ignored |
Value
nms_canonical (character)
See Also
Other nm:
nms_nonmem.nms_pmx(),
nms_pmx.nms_nonmem()
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Other nm:
nms_nonmem.nms_pmx(),
nms_pmx.nms_nonmem()
Examples
library(magrittr)
c(
'THETA1',
'OM1,1',
'OM1,2',
'SG1,1',
'SG1,2'
) %>%
as_nms_pmx %>%
nms_canonical
Generate Canonical Names for Numeric
Description
Generates canonical names for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
nms_canonical(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Generate NONMEM Names
Description
Generates NONMEM names.
Usage
nms_nonmem(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Generate NONMEM Names for Character
Description
Generates NONMEM names for numeric by converting to parsed model.
Usage
## S3 method for class 'character'
nms_nonmem(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% nms_nonmem
Generate NONMEM Names for Model
Description
Generates NONMEM names for parameters declared in a NONMEM control stream object.
Usage
## S3 method for class 'model'
nms_nonmem(x, ...)
Arguments
x |
a model designator |
... |
passed arguments |
Value
nms_nonmem (character)
See Also
as.model
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% nms_nonmem
Convert Canonical Parameter Names to NONMEM
Description
Converts nms_canonical to nms_nonmem.
Usage
## S3 method for class 'nms_canonical'
nms_nonmem(x, ...)
Arguments
x |
nms_canonical |
... |
ignored |
Value
nms_nonmem
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Examples
# example code
Convert pmxTools Names to NONMEM
Description
Converts nms_pmx to nms_nonmem. I.e., THETA1 stays THETA1, but OM1,1 becomes OMEGA(1,1).
Usage
## S3 method for class 'nms_pmx'
nms_nonmem(x, ...)
Arguments
x |
nms_pmx |
... |
ignored |
Value
nms_nonmem (character)
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Other nm:
nms_canonical.nms_pmx(),
nms_pmx.nms_nonmem()
Examples
library(magrittr)
c(
'THETA1',
'OM1,1',
'OM1,2',
'SG1,1',
'SG1,2'
) %>%
as_nms_pmx %>%
nms_canonical
Generate NONMEM Names for Numeric
Description
Generates NONMEM names for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
nms_nonmem(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Convert Parameter Names to pmxTools
Description
Converts parameter names to pmxTools style.
Generic, with method nms_pmx.nms_canonical.
Usage
nms_pmx(x, ...)
Arguments
x |
object of dispatch |
... |
passed |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Convert Canonical Names to pmxTools
Description
Converts nms_canonical to nms_pmx. I.e., theta_01 becomes THETA1, and omega_01_01 becomes OM1,1.
Usage
## S3 method for class 'nms_canonical'
nms_pmx(x, ...)
Arguments
x |
nms_canonical |
... |
ignored |
Value
nms_pmx (character)
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Examples
library(magrittr)
c(
'theta_15',
'omega_01_01',
'omega_01_02',
'sigma_01_01',
'sigma_02_01'
) %>%
as_nms_canonical %>%
nms_pmx
Convert NONMEM Names to pmxTools
Description
Converts nms_nonmem to nms_pmx. I.e., THETA1 stays THETA1, but OMEGA(1,1) becomes OM1,1.
Usage
## S3 method for class 'nms_nonmem'
nms_pmx(x, ...)
Arguments
x |
nms_pmx |
... |
ignored |
Value
nms_nonmem (character)
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_psn(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Other nm:
nms_canonical.nms_pmx(),
nms_nonmem.nms_pmx()
Examples
library(magrittr)
c(
'THETA1',
'OMEGA(1,1)',
'OMEGA(1,2)',
'SIGMA(1,1)',
'SIGMA(1,2)'
) %>%
as_nms_pmx %>%
nms_canonical
Generate PsN-style Names
Description
Generates PsN-style names.
Generic, with method nms_psn.model.
Usage
nms_psn(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn.character(),
nms_psn.model(),
nms_psn.numeric()
Generate PsN-style Names for Character
Description
Generates PsN-style names for numeric by converting to parsed model.
Usage
## S3 method for class 'character'
nms_psn(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.model(),
nms_psn.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% nms_psn
Generate PsN-style Names for Model
Description
Generates PsN-style names for parameters declared in a NONMEM control stream object. PsN uses NONMEM-style names, substituting a comment, if any: everything after the first semicolon, up to the second semicolon if present, without leading/trailing spaces/tabs.
Usage
## S3 method for class 'model'
nms_psn(x, ...)
Arguments
x |
a model designator |
... |
passed arguments |
Value
nms_psn (character)
See Also
as.model
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.numeric()
Generate PsN-style Names for Numeric
Description
Generates PsN-style names for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
nms_psn(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other nms:
as_nms_canonical(),
as_nms_nonmem(),
as_nms_pmx(),
as_nms_psn(),
nms_canonical(),
nms_canonical.character(),
nms_canonical.model(),
nms_canonical.nms_nonmem(),
nms_canonical.nms_pmx(),
nms_canonical.numeric(),
nms_nonmem(),
nms_nonmem.character(),
nms_nonmem.model(),
nms_nonmem.nms_canonical(),
nms_nonmem.nms_pmx(),
nms_nonmem.numeric(),
nms_pmx(),
nms_pmx.nms_canonical(),
nms_pmx.nms_nonmem(),
nms_psn(),
nms_psn.character(),
nms_psn.model()
Get the Number of Parameters
Description
Gets the Number of Parameters associated with an object.
Generic, with method num_parameters.default.
Usage
num_parameters(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
Get the Number of Declared Parameters for a NONMEM Model
Description
Gets the number of declared parameters for a NONMEM model.
Usage
## Default S3 method:
num_parameters(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
Details
Parameters fixed to some value are included, but unlike (*.ext) matrix off-diagonals are not included unless specified.
Value
integer
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% num_parameters
Isolate Off-diagonal
Description
Isolates off-diagonal. Generic, with method for halfmatrix.
Usage
offdiag(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Isolate Off-diagonal of Half Matrix
Description
Isolates off-diagonal of halfmatrix.
Usage
## S3 method for class 'halfmatrix'
offdiag(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
ord(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Calculate Order
Description
Calculates order. Generic, with method for matrix.
Usage
ord(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord.halfmatrix(),
ord.matrix(),
print.halfmatrix()
Calculate Order for Half Matrix
Description
Calculates order for half matrix. I.e., length of one dimension of the equivalent square matrix.
Usage
## S3 method for class 'halfmatrix'
ord(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.matrix(),
print.halfmatrix()
Identify the order of an inits
Description
Identifies the order of an inits.
Usage
## S3 method for class 'inits'
ord(x, ...)
Arguments
x |
inits |
... |
ignored |
Details
Essentially the length of the list, or the length of the diagonal of a matrix (if BLOCK was defined).
Value
numeric
See Also
Other ord:
ord.items()
Identify the Order of an Items Object
Description
Identifies the order of an items object.
Usage
## S3 method for class 'items'
ord(x, ...)
Arguments
x |
items |
... |
ignored |
Details
Essentially the length of the list
Value
numeric
See Also
Other ord:
ord.inits()
Calculate Order for Matrix
Description
Calculates order for matrix. I.e., length of one dimension of a square matrix.
Usage
## S3 method for class 'matrix'
ord(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
print.halfmatrix()
Pad Numeric with Zeros
Description
Pad a numeric vector with leading zeros.
Usage
padded(x, width = 4, ...)
Arguments
x |
numeric |
width |
desired number of characters |
... |
ignored |
Value
character
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
locf(),
parens(),
pool(),
runhead(),
text2decimal()
Get Parameters
Description
Gets parameters.
Usage
parameters(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other parameters:
parameters.character(),
parameters.numeric()
Get Parameters for Character
Description
Gets parameters, treating character as model names. If x is length one,
slightly more details are returned such as datafile, reference model, and feature.
Otherwise results are bound together, one model per column.
See estimates and errors for a more formal interface to model estimates and asymptotic standard errors.
Usage
## S3 method for class 'character'
parameters(x, simplify = FALSE, ...)
Arguments
x |
object |
simplify |
if x is length one and simplify is TRUE, return a named vector |
... |
passed arguments |
Value
data.frame
See Also
Other parameters:
parameters(),
parameters.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% parameters
Get Parameters for Numeric
Description
Gets parameters for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
parameters(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other parameters:
parameters(),
parameters.character()
Enclose in Parentheses
Description
Enclose in parentheses
Usage
parens(x, ...)
Arguments
x |
vector |
... |
dots |
Value
character
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
locf(),
padded(),
pool(),
runhead(),
text2decimal()
Create Parameter Table
Description
Creates a parameter table.
Creates a model parameter table from a partab object.
Usage
partab(x, ...)
## S3 method for class 'partab'
partab(x, ...)
Arguments
x |
partab |
... |
ignored |
Details
x can be numeric or character model name, assuming project is identified by argument or option.
Just returns the object unmodified.
Methods (by class)
-
partab(partab): partab method
See Also
Other partab:
partab.character(),
partab.numeric()
Other partab:
partab.character(),
partab.numeric()
Create a Parameter Table from Model Name
Description
Creates a parameter table from a model name. Pass the project argument or set the project option.
Usage
## S3 method for class 'character'
partab(
x,
verbose = FALSE,
lo = "5",
hi = "95",
metafile = modelpath(x, "def", ...),
xmlfile = modelpath(x, "xml", ...),
ctlfile = modelfile(x, ...),
bootcsv,
strip.namespace = TRUE,
skip = 28,
check.names = FALSE,
digits = 3,
ci = TRUE,
open = "(",
close = ")",
sep = ", ",
format = TRUE,
fields = getOption("fields", default = c("symbol", "label", "unit")),
relative = TRUE,
percent = relative,
nonzero = TRUE,
shrinkage = FALSE,
correlation = FALSE,
...
)
Arguments
x |
a model name (numeric or character) |
verbose |
set FALSE to suppress messages |
lo |
the PsN bootstrap lower confidence limit (%) |
hi |
the PsN bootstrap upper confidence limit (%) |
metafile |
optional metadata for parameter table (see also: fields) |
xmlfile |
path to xml file |
ctlfile |
path to control stream |
bootcsv |
path to PsN bootstrap_results.csv |
strip.namespace |
whether to strip e.g. nm: from xml elements for easier xpath syntax |
skip |
number of lines to skip in bootstrap_results.csv |
check.names |
passed to bootstrap reader |
digits |
limits numerics to significant digits (use NULL to suppress) |
ci |
combine bootstrap lo and hi into an enclosed interval |
open |
first character for bootstrap interval |
close |
last character for bootstrap interval |
sep |
separator for bootstrap interval |
format |
format numerics as character |
fields |
metadata fields to read from control stream. See details. |
relative |
transform standard errors to relative standard errors: rse replaces se |
percent |
if relative is true, express as percent (else ignore): prse replaces se |
nonzero |
limit random effects to those with nonzero estimates |
shrinkage |
whether to include percent shrinkage on random effects |
correlation |
whether to include correlation of random effects (as percent if |
... |
passed to other functions |
Details
Normally you can just call the generic. Suitable defaults are supplied, but much customization is supported by means of arguments documented here and in called functions.
Metadata can be added to the parameter table two ways: as markup in the control stream, and as a *.def file in the model directory. See vignette('parameter-table') for details.
Value
object of class partab, data.frame
See Also
Other partab:
partab(),
partab.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% partab
1001 %>% partab(shrinkage = TRUE, correlation = TRUE)
Create Model Parameter Table from Number.
Description
Creates a model parameter table from a number.
Usage
## S3 method for class 'numeric'
partab(x, ...)
Arguments
x |
numeric |
... |
passed arguments |
Details
Just coerces to character and calls partab again.
See Also
Other partab:
partab(),
partab.character()
Compare Sets
Description
Compare sets by evaluating both set differences, and the intersection.
Usage
pool(x, y)
Arguments
x |
vector |
y |
vector |
Value
list: unique x, unique y, and intersection
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
runhead(),
text2decimal()
Examples
pool(1:3,2:4)
Pretty-print a Comment
Description
Pretty-prints a comment.
Usage
prettycom(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other prettycom:
prettycom.character()
Pretty-print a Comment for Character
Description
Pretty-prints a comment for character.
Usage
## S3 method for class 'character'
prettycom(x, widths, sep, delim, ...)
Arguments
x |
... object |
widths |
integer |
sep |
input separator |
delim |
output separator |
... |
passed arguments |
See Also
Other prettycom:
prettycom()
Print Half Matrix
Description
Prints half matrix.
Usage
## S3 method for class 'halfmatrix'
print(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other halfmatrix:
as.data.frame.halfmatrix(),
as.halfmatrix(),
as.halfmatrix.default(),
as.halfmatrix.halfmatrix(),
as.matrix.halfmatrix(),
half(),
half.matrix(),
is.square(),
is.square.matrix(),
offdiag(),
offdiag.halfmatrix(),
ord(),
ord.halfmatrix(),
ord.matrix()
Print init
Description
Prints init.
Usage
## S3 method for class 'init'
print(x, ...)
Arguments
x |
init |
... |
passed arguments |
Value
character
See Also
Other print:
print.inits(),
print.items(),
print.model()
Print inits
Description
Prints inits.
Usage
## S3 method for class 'inits'
print(x, ...)
Arguments
x |
inits |
... |
passed arguments |
Value
character
See Also
Other print:
print.init(),
print.items(),
print.model()
Print Items
Description
Prints items.
Usage
## S3 method for class 'items'
print(x, ...)
Arguments
x |
items |
... |
passed arguments |
Value
character
See Also
Other print:
print.init(),
print.inits(),
print.model()
Print model
Description
Print model.
Usage
## S3 method for class 'model'
print(x, ...)
Arguments
x |
model |
... |
passed arguments |
Details
Formats and prints.
Value
character
See Also
Other print:
print.init(),
print.inits(),
print.items()
Identify the Model Problem Statement
Description
Identifies the model problem statement.
Usage
problem(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other problem:
as.problem(),
problem.character(),
problem.numeric(),
problem_()
Identify the Model Problem Statement for Character
Description
Identifies the model problem statement for character (model name).
Usage
## S3 method for class 'character'
problem(x, ...)
Arguments
x |
object |
... |
passed arguments |
Value
character
See Also
Other problem:
as.problem(),
problem(),
problem.numeric(),
problem_()
Identify the Model Problem Statement for Numeric
Description
Identifies the model problem statement for numeric. Coerces to character.
Usage
## S3 method for class 'numeric'
problem(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other problem:
as.problem(),
problem(),
problem.character(),
problem_()
Identify the Single Model Problem Statement
Description
Identifies a single model problem statement.
Usage
problem_(x, ...)
Arguments
x |
character |
... |
passed arguments |
See Also
Other problem:
as.problem(),
problem(),
problem.character(),
problem.numeric()
PsN Model File is Nested
Description
Check whether a particular file extension corresponds to a file that is nested within a subdirectory using default PsN conventions.
Usage
psn_nested(x, ...)
Arguments
x |
character, a file extension, without dot. |
... |
ignored |
Value
logical
Examples
psn_nested('mod')
Set PsN Options
Description
Sets PsN-style directory and control stream options. Supports control streams with semicolon-delimited metadata including symbol, unit, transform, and label. Expects model files to be found in nested directory, except for *.mod and *.lst.
Usage
psn_options(
project = "NONMEM",
modex = "mod",
fields = c("symbol", "unit", "transform", "label"),
nested = psn_nested,
...
)
Arguments
project |
character, path to project directory |
modex |
character, extension for model control stream (no dot) |
fields |
character |
nested |
logical, or function of file extension returning logical |
... |
ignored |
Value
used for side-effects (sets options 'fields' and 'nested')
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
specfile(),
specfile.character(),
specfile.numeric()
Examples
## Not run:
psn_options()
## End(Not run)
Read model
Description
Read model.
Usage
read.model(con, parse = TRUE, ...)
Arguments
con |
model connection |
parse |
whether to convert thetas to inits objects |
... |
passed arguments |
Details
Reads model from a connection.
Value
character
See Also
Other as.model:
[.model(),
[[.model(),
as.model(),
as.model.character(),
as.model.numeric(),
write.model()
Relativize a Path
Description
Relativizes a path.
Usage
relativizePath(x, dir = getwd(), sep = "/", ...)
Arguments
x |
a file path |
dir |
a reference directory |
sep |
path separator |
... |
ignored arguments |
Details
x and dir are first normalized, then x is expressed relative to dir. If x and dir are on different drives (i.e. C:/ D:/) x is returned as an absolute path.
Resolve File Path
Description
Resolves a file path. Returns the path if absolute. If relative, concatenates the directory and file.
Usage
resolve(file, dir)
Arguments
file |
path to a file |
dir |
reference directory for a relative file path |
Value
character
Translate Parameter Names
Description
Translate among various idioms for expressing parameter names
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
# we generate some nonmem parameter names in nonmem format
1001 %>% nms_nonmem -> nonmem
nonmem
# from these we generate canonical and pmxTools equivalents
canonical <- nms_canonical(nonmem)
pmxtools <- nms_pmx(nonmem)
canonical
pmxtools
# We demonstrate equivalence
stopifnot(identical(nonmem, nms_nonmem(canonical)))
stopifnot(identical(nonmem, nms_nonmem(pmxtools)))
stopifnot(identical(canonical, nms_canonical(nonmem)))
stopifnot(identical(canonical, nms_canonical(pmxtools)))
stopifnot(identical(pmxtools, nms_pmx(nonmem)))
stopifnot(identical(pmxtools, nms_pmx(canonical)))
# on-the-fly conversions
nonmem %>% class
nonmem %>% nms_pmx
nonmem %>% nms_canonical
nonmem %>% nms_canonical %>% nms_pmx
nonmem %>% nms_canonical %>% nms_pmx %>% nms_nonmem
# comparison
data.frame(
can = I(canonical),
non = I(nonmem),
pmx = I(pmxtools),
psn = I(nms_psn(1001))
)
Create Indexed Model Parameter Table from Xml_document
Description
Creates a model parameter table from xml_document.
Usage
row_col(x, xpath, param, moment, ...)
Arguments
x |
xml_document |
xpath |
character |
param |
character |
moment |
character |
... |
passed arguments |
Details
The function evaluates the xpath expression, supplying parameter and moment labels, and documenting indices of rows and columns.
Value
data.frame
Find Positions in a Vector that Differ from Previous
Description
Finds postions in a vector that differ from previous. First position is defined TRUE.
Usage
runhead(x)
Arguments
x |
vector |
Value
logical
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
pool(),
text2decimal()
Create a Runlog
Description
Creates a runlog.
Usage
runlog(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other runlog:
runlog.character(),
runlog.numeric()
Create a Runlog for Character
Description
Creates a Runlog for character by treating x as modelname(s).
Usage
## S3 method for class 'character'
runlog(x, dependencies = FALSE, digits = 3, places = 0, ...)
Arguments
x |
object |
dependencies |
whether to log runs in lineage(s) as well |
digits |
significance for parameters |
places |
rounding for objective function |
... |
passed arguments |
Value
data.frame
See Also
Other runlog:
runlog(),
runlog.numeric()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
# likebut(2001,'2 cmt', 2002) # edit manually, then ...
# likebut(2002,'add. err.', 2003) # edit manually, then ...
# likebut(2003,'allo. WT on CL',2004) # edit manually, then ...
# likebut(2004,'estimate allometry', 2005) # edit manually, then ...
# likebut(2005,'SEX on CL', 2006) # edit manually, then ...
# likebut(2006,'full block omega', 2007) # edit manually, then run all
2007 %>% runlog(dependencies = TRUE)
Create a Runlog for Numeric
Description
Creates a runlog for numeric by coercing to character.
Usage
## S3 method for class 'numeric'
runlog(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other runlog:
runlog(),
runlog.character()
Join Data Safely
Description
Joins data safely. Generic, with method for data.frame.
Usage
safe_join(x, ...)
Arguments
x |
object of dispatch |
... |
arguments to methods |
See Also
Other safe_join:
safe_join.data.frame()
Join Data Frames Safely
Description
Joins data frames safely. I.e., a left join that cannot alter row order or number. Supports the case where you only intend to augment existing rows with additional columns and are expecting singular matches. Gives an error if row order or number would have been altered by a left join.
Usage
## S3 method for class 'data.frame'
safe_join(x, y, ...)
Arguments
x |
data.frame |
y |
data.frame |
... |
passed to dplyr::left_join |
See Also
Other safe_join:
safe_join()
Examples
library(magrittr)
x <- data.frame(code = c('a','b','c'), value = c(1:3))
y <- data.frame(code = c('a','b','c'), roman = c('I','II','III'))
x %>% safe_join(y)
try(
x %>% safe_join(rbind(y,y))
)
Move the Columns of a Data Frame Relative to Each Other
Description
Move the columns of a data.frame relative to each other.
Usage
shuffle(x, who, after = NA, ...)
Arguments
x |
data.frame |
who |
a character vector of column names to move, or a logical vector of length names(x), or a vector of indices |
after |
column after which to put who: may be character, integer, NA, or NULL |
... |
ignored |
Value
data.frame
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Identify Specfile
Description
Identifies specfile.
Usage
specfile(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile.character(),
specfile.numeric()
Identify the Data Specification File for a Model
Description
Identifies the data specification file associated with the datafile used by a model. Locates the datafile specified in the control stream, and substitutes a different extension.
Usage
## S3 method for class 'character'
specfile(x, find = "\\.csv$", use = ".spec", ...)
Arguments
x |
the model name |
find |
file extension to replace |
use |
file extension to use |
... |
pass ext over-ride default file extension in datafile() |
Value
character
See Also
datafile
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.numeric()
Examples
library(spec)
source <- system.file(package = 'nonmemica','project')
target <- tempdir()
target <- gsub('\\\\','/',target) # for windows
file.copy(source,target,recursive = TRUE)
project <- file.path(target,'project','model')
options(project = project)
library(magrittr)
1001 %>% datafile
datafile(1001) %matches% specfile(1001)
1001 %>% specfile
1001 %>% specfile %>% read.spec
Identify Specfile from Numeric
Description
Identifies specfile from numeric.
Usage
## S3 method for class 'numeric'
specfile(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other path:
datafile(),
datafile.character(),
datafile.numeric(),
modeldir(),
modelfile(),
modelpath(),
modelpath.character(),
modelpath.numeric(),
psn_options(),
specfile(),
specfile.character()
Coerce to Superset
Description
Coerces to superset.
Usage
superset(x, ...)
Arguments
x |
object |
... |
passed arguments |
Details
Generic, with methods for numeric and character.
See Also
superset.numeric superset.character
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Coerce to Superset from Character
Description
Coerces to superset from character, treating x as a model name.
Usage
## S3 method for class 'character'
superset(
x,
read.input = list(read.csv, header = TRUE, as.is = TRUE),
read.output = list(read.table, header = TRUE, as.is = TRUE, skip = 1, comment.char =
"", check.names = FALSE, na.strings = c("", "\\s", ".", "NA")),
include = character(0),
exclude = character(0),
rename = NULL,
digits = 5,
visible = "VISIBLE",
after = NULL,
groups = character(0),
imputation = generalize,
...
)
Arguments
x |
object |
read.input |
a methodology for acquiring the input |
read.output |
a methodology for acquiring the output |
include |
column names in output to consider adding |
exclude |
column names in output to reject |
rename |
logical: whether to keep and rename columns with re-used names |
digits |
significant digits for assessing informativeness when exclusive=NULL |
visible |
a name for the flag column indicating visibility |
after |
place new columns after this column; at end by default (NULL); TRUE places them after last model-visible column (see input statement) |
groups |
character vector of groupings within which any imputations will be performed |
imputation |
a list of functions (or arguments to match.fun()) to perform imputations within cells defined by groups: e.g. generalize, forbak, etc (to be tried in succession for new columns only). |
... |
passed arguments |
Details
Given a model name, (project passed or set as global option) superset() figures out the run directory and location of a NONMEM control stream. It reads the control stream to identify the run-time location of input and output files, as well as the "ignore" (and/or "accept") criteria that relate extent of input records to extent of output records. 'read.input' and 'read.output' are lists consisting of functions and arguments appropriate for reading input and output file formats, respectively. The ignore criteria will be reconstructed per row so that output can be mapped unambiguously to input. A column named VISIBLE is bound to the input data, showing 1 where a record was visible to NONMEM, and 0 otherwise.
During integration, naming convention of the input is retained, and output column names are mapped by position, using the control stream input criteria. Output tables are restored to input dimensions using the "ignore" criteria, then checked for length: currently, superset ignores output tables having fewer rows than the input, as well as output tables whose row count is not a multiple of input row count.
Output tables may contain versions of input columns. Disposition depends on the values of include, exclude, and rename. If include has length, other columns are excluded. Then, if exclude has length, these columns are excluded. Then, if rename is FALSE all remaining columns with re-used names will be dropped. If TRUE, such columns will be renamed (*.n, where n is table number). If NULL, only informative columns will be retained and renamed. A column is informative if any element is informative. An element is informative if it is newly generated (not NA and not zero, but original is NA) or if it is an alteration (non-NA, and different from non-NA original). If the column pair can be interpreted as numeric, "different" is determined using only the first digits digits.
Only the first instance of any column among successive output tables is retained.
In the control stream, avoid use of FIRSTONLY, as this alters the number of rows.
Value
superset: a data.frame where row count is a multiple of (typically equal to) input row count.
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.numeric(),
superspec(),
superspec.character(),
superspec.numeric()
Examples
library(magrittr)
library(dplyr)
library(wrangle)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% superset %>% head
1001 %>% superset %>% filter(VISIBLE == 1) %>% group_by(ID,TIME) %>% status
1001 %>% ignored %>% table
Coerce to Superset from Numeric
Description
Coerces to superset from numeric.
Usage
## S3 method for class 'numeric'
superset(x, ...)
Arguments
x |
object |
... |
passed arguments |
Details
Converts number to character and revisits generic.
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superspec(),
superspec.character(),
superspec.numeric()
Create Specification for Model Inputs and Outputs
Description
Create a specification for the result of superset().
Usage
superspec(x, ...)
Arguments
x |
object |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec.character(),
superspec.numeric()
Create Specification for Model Inputs and Outputs From Character
Description
Create a specification for the result of superset() from character by treating as a model name. By default, gives a spec template for superset(x). Tries to supplement with labels and units from parent specification, if it exists. Tries to supplement with any additional labels and units in definitions(x). Defers to actual data if provided. Specify exclusive, visible, and after as for superset.
Usage
## S3 method for class 'character'
superspec(
x,
include = character(0),
exclude = character(0),
rename = NULL,
visible = "VISIBLE",
after = NULL,
data = NULL,
...
)
Arguments
x |
character |
include |
column names in output to consider adding |
exclude |
column names in output to reject |
rename |
logical: whether to keep and rename columns with re-used names |
visible |
a name for the flag column indicating visibility |
after |
place new columns after this column; at end by default (NULL); TRUE places them after |
data |
an alternative dataset on which to model the specification |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.numeric()
Create Specification for Model Inputs and Outputs From Numeric
Description
Create a specification for the result of superset() from numeric by coercing to character.
Usage
## S3 method for class 'numeric'
superspec(x, ...)
Arguments
x |
numeric |
... |
passed arguments |
See Also
Other superset:
generalize(),
ignored(),
meta(),
meta.character(),
meta.numeric(),
metaplot.character(),
metaplot.numeric(),
metaplot_character(),
metasuperset(),
ninput(),
ninput.character(),
ninput.numeric(),
shuffle(),
superset(),
superset.character(),
superset.numeric(),
superspec(),
superspec.character()
Calculate Time Since Most Recent Dose
Description
Calculate time since most recent dose. Considers ADDL, but may not work with simultaneous dose records.
Usage
tad(
x,
dose = rep(FALSE, length(x)),
addl = rep(0, length(x)),
ii = rep(0, length(x)),
index = rep(1, length(x)),
pre = TRUE,
...
)
Arguments
x |
a numeric vector of event times |
dose |
length x logical indicating which of x are dose times |
addl |
length x integer: number of additional doses |
ii |
length x numeric: interdose interval for addl |
index |
length x factor (optional) indicating subgroups to evaluate |
pre |
assume that simultaneous sample precedes implied dose |
... |
passed to tod() |
Value
numeric
See Also
Other tad:
tod()
Examples
data(tad1)
x <- tad1
head(x)
x$tad <- tad(
x = x$TIME,
dose = x$EVID %in% c(1,4) & is.na(x$C),
addl = x$ADDL,
ii = x$II,
index = x$ID
)
head(x)
A NONMEM-like Dataset
Description
A dataset showing dose and and observation records for several subjects. Doses are duplicated across compartments 1 and 2 as for mixed absorption modeling.
Usage
data(tad1)
Details
C. An exclusion flag, NA by default, or 'C'.
ID. Integer subject identifier.
TIME. Numeric event time (h).
EVID. Event type identifier: observation (0) or dose (1).
CMT. Event compartment: dose (1), central (2) or peripheral (4).
AMT. Amount of dose (mg).
RATE. NONMEM RATE item.
ADDL. Number of additional doses, or NA for observations.
II. Interdose interval for additional doses, or NA for observations.
DV. Observation placeholder.
Convert Text to Decimal
Description
Scavenge text for first reasonably-inferred numeric value.
Usage
text2decimal(x)
Arguments
x |
character |
Value
numeric
See Also
Other util:
%contains%(),
as.best(),
as.best.default(),
enclose(),
locf(),
padded(),
parens(),
pool(),
runhead()
Examples
text2decimal('30 mg')
Calculate Time of Most Recent Dose
Description
Calculates time of most recent dose.
Usage
tod(x, ref, addl, ii, pre = T, ...)
Arguments
x |
a numeric vector of event times |
ref |
length x vector of reference dose times |
addl |
length x integer: number of additional doses |
ii |
length x numeric: interdose interval for addl |
pre |
assume that simultaneous sample precedes implied dose |
... |
ignored |
Value
numeric
See Also
Other tad:
tad()
Tweak Something
Description
Tweaks something.
Usage
tweak(x, ...)
Arguments
x |
object |
... |
dots |
See Also
Other tweak:
tweak.default(),
tweak.init(),
tweak.inits(),
tweak.model()
Tweak a Model by Default
Description
Tweaks a model by jittering initial estimates. Creates a new model directory in project context and places the model there. Copies helper files as well. Expects that x is a number. Assumes nested directory structure (run-specific directories).
Usage
## Default S3 method:
tweak(
x,
project = getOption("project", getwd()),
ext = getOption("modex", "ctl"),
start = NULL,
n = 10,
include = ".def$",
...
)
Arguments
x |
object |
project |
project directory (can be expression) |
ext |
file extension for control streams |
start |
a number to use as the first modelname |
n |
the number of variants to generate (named start:n) |
include |
regular expressions for files to copy to new directory |
... |
pass ext to over-ride default model file extension |
Value
character: vector of names for models created
See Also
Other tweak:
tweak(),
tweak.init(),
tweak.inits(),
tweak.model()
Tweak Init
Description
Tweaks init.
Usage
## S3 method for class 'init'
tweak(x, sd = 0.13, digits = 3, ...)
Arguments
x |
init |
sd |
numeric |
digits |
integer |
... |
passed arguments |
Value
init
See Also
Other tweak:
tweak(),
tweak.default(),
tweak.inits(),
tweak.model()
Tweak inits
Description
Tweaks inits.
Usage
## S3 method for class 'inits'
tweak(x, sd = 0.13, digits = 3, ...)
Arguments
x |
inits |
sd |
numeric |
digits |
integer |
... |
passed arguments |
Value
inits
See Also
Other tweak:
tweak(),
tweak.default(),
tweak.init(),
tweak.model()
Tweak Model
Description
Tweaks model.
Usage
## S3 method for class 'model'
tweak(x, sd = 0.13, digits = 3, ...)
Arguments
x |
model |
sd |
numeric |
digits |
integer |
... |
passed arguments |
Value
model
See Also
Other tweak:
tweak(),
tweak.default(),
tweak.init(),
tweak.inits()
Examples
# Create a working project.
source <- system.file(package = 'nonmemica','project')
target <- tempdir()
target <- gsub('\\\\','/',target) # for windows
source
target
file.copy(source,target,recursive = TRUE)
project <- file.path(target,'project','model')
# Point project option at working project
options(project = project)
library(magrittr)
# Make ten new models with slightly different initial estimates.
1001 %>% tweak
Create the Updated Version of Something
Description
Creates the updated version of something. Don't confuse with stats::update.
Usage
updated(x, ...)
Arguments
x |
object of dispatch |
... |
passed arguments |
See Also
Other updated:
updated.character(),
updated.numeric()
Create the Updated Version of Character
Description
Creates the updated version of character by treating as a modelname. Parses the associated control stream and ammends the initial estimates to reflect model results (as per xml file).
Usage
## S3 method for class 'character'
updated(x, initial = estimates(x, ...), parse = TRUE, verbose = FALSE, ...)
Arguments
x |
character |
initial |
values to use for initial estimates (numeric) |
parse |
whether to parse the initial estimates, etc. |
verbose |
extended messaging |
... |
passed arguements |
Value
model
See Also
Other updated:
updated(),
updated.numeric()
Create the Updated Version of Numeric
Description
Creates the updated version of numeric by coercing to character.
Usage
## S3 method for class 'numeric'
updated(x, ...)
Arguments
x |
numeric |
... |
passed arguments |
See Also
Other updated:
updated(),
updated.character()
Get Upper Value
Description
Gets upper Value.
Usage
upper(x, ...)
Arguments
x |
object of dispatch |
... |
dots |
See Also
Other upper:
upper.model(),
upper<-(),
upper<-.model()
Set Upper Value
Description
Sets upper Value.
Usage
upper(x) <- value
Arguments
x |
object of dispatch |
value |
right hand side |
See Also
Other upper:
upper(),
upper.model(),
upper<-.model()
Set Upper Bounds for Model Initial Estimates
Description
Sets upper bounds for model initial estimates.
Usage
## S3 replacement method for class 'model'
upper(x) <- value
Arguments
x |
model |
value |
numeric |
See Also
Other upper:
upper(),
upper.model(),
upper<-()
Get Upper Bounds for Model Initial Estimates
Description
Gets upper bounds for model initial estimates.
Usage
## S3 method for class 'model'
upper(x, ...)
Arguments
x |
model |
... |
dots |
See Also
Other upper:
upper(),
upper<-(),
upper<-.model()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% as.model %>% upper
Create Model Parameter Table from Xml_document
Description
Creates a model parameter table from xml_document.
Usage
val_name(x, xpath, param, moment, ...)
Arguments
x |
xml_document |
xpath |
character |
param |
character |
moment |
character |
... |
passed arguments |
Details
The function evaluates the xpath expression, supplying arbitrary names for parameter and moment of parameter.
Value
data.frame
Write model
Description
Write model.
Usage
write.model(x, file = "data", ncolumns = 1, append = FALSE, sep = " ", ...)
Arguments
x |
model |
file |
passed to write() |
ncolumns |
passed to write() |
append |
passed to write() |
sep |
passed to write() |
... |
passed arguments |
Details
writes (formatted) model to file.
Value
used for side effects
See Also
Other as.model:
[.model(),
[[.model(),
as.model(),
as.model.character(),
as.model.numeric(),
read.model()
Evaluate Xpath Expression
Description
Evaluates an xpath expression.
Usage
xpath(x, ...)
Arguments
x |
xml_document |
... |
passed arguments |
Details
The resulting nodeset is scavenged for text, and coerced to best of numeric or character.
See Also
Other xpath:
as.xml_document(),
as.xml_document.character(),
as.xml_document.numeric(),
xpath.default(),
xpath.xml_document()
Examples
library(magrittr)
options(project = system.file('project/model',package='nonmemica'))
1001 %>% xpath('//etashrink/row/col')
Evaluate xpath Expression in Default Context
Description
Coerces x to xml_document and evaluates.
Usage
## Default S3 method:
xpath(x, ...)
Arguments
x |
default |
... |
passed arguments |
Value
vector
See Also
Other xpath:
as.xml_document(),
as.xml_document.character(),
as.xml_document.numeric(),
xpath(),
xpath.xml_document()
Evaluate xpath Expression in Document Context
Description
Evaluates an xpath expression for a given document.
Usage
## S3 method for class 'xml_document'
xpath(x, xpath, ...)
Arguments
x |
xml_document |
xpath |
xpath expression to evaluate |
... |
ignored |
Details
The resulting nodeset is scavenged for text, and coerced to best of numeric or character.
Value
vector
See Also
Other xpath:
as.xml_document(),
as.xml_document.character(),
as.xml_document.numeric(),
xpath(),
xpath.default()