Title: | Graphical Diagnostics for Pharmacometric Models: Extension to 'nlmixr2' |
---|---|
Description: | Extension to 'xpose' to support 'nlmixr2'. Provides functions to import 'nlmixr2' fit data into an 'xpose' data object, allowing the use of 'xpose' for 'nlmixr2' model diagnostics. |
Authors: | Justin Wilkins [aut, cre, cph], Matthew Fidler [aut, cph], Benjamin Guiastrennec [aut], Andrew C. Hooker [aut], Anna Olofsson [aut, cph], Sebastian Ueckert [aut], Ron Keizer [aut], Kajsa Harling [ctb], Mike K. Smith [ctb], Elodie Plan [ctb], Mats O. Karlsson [aut, cph], Pharmetheus [ctb], Pfizer [ctb], Occams [ctb], Novartis [ctb] |
Maintainer: | Justin Wilkins <[email protected]> |
License: | GPL (>=2) |
Version: | 0.4.0 |
Built: | 2024-09-06 03:07:45 UTC |
Source: | https://github.com/nlmixr2/xpose.nlmixr2 |
Default VPC theme for 'xpose.nlmixr2'.
nlmixr2_vpc_theme
nlmixr2_vpc_theme
An object of class vpc_theme
of length 23.
A list with 'vpc' theme specifiers.
Convert 'nlmixr2' model output into an 'xpose' database
summarise_nlmixr2_model(obj, model, software, rounding, runname)
summarise_nlmixr2_model(obj, model, software, rounding, runname)
obj |
nlmixr2 fit object to be evaluated |
model |
Model. Can be blank |
software |
Software that generated the model fit |
rounding |
Number of figures to round estimates to |
runname |
Name of the model object being converted |
A summary data object used by xpose_data_nlmixr2.
Default 'nlmixr2' theme for 'xpose'.
theme_xp_nlmixr2()
theme_xp_nlmixr2()
A list with 'xpose' theme specifiers.
Convert 'nlmixr2' model output into an 'xpose' database.
xpose_data_nlmixr2( obj = NULL, pred = NULL, wres = NULL, gg_theme = theme_readable(), xp_theme = theme_xp_default(), quiet, skip = NULL, ... ) xpose_data_nlmixr( obj = NULL, pred = NULL, wres = NULL, gg_theme = theme_readable(), xp_theme = theme_xp_default(), quiet, skip = NULL, ... )
xpose_data_nlmixr2( obj = NULL, pred = NULL, wres = NULL, gg_theme = theme_readable(), xp_theme = theme_xp_default(), quiet, skip = NULL, ... ) xpose_data_nlmixr( obj = NULL, pred = NULL, wres = NULL, gg_theme = theme_readable(), xp_theme = theme_xp_default(), quiet, skip = NULL, ... )
obj |
nlmixr2 fit object to be evaluated. |
pred |
Name of the population prediction variable to use for plotting. If unspecified, it will choose either "NPDE", "CWRES", and "RES" (in that order) if the column exists in the data. |
wres |
Name of the weighted residual variable to use for plotting. If unspecified, it will choose either "NPDE", "CWRES", and "RES" (in that order) if the column exists in the data. |
gg_theme |
A ggplot2 theme object. |
xp_theme |
An xpose theme or vector of modifications to the
xpose theme (eg. |
quiet |
Logical, if |
skip |
Character vector be used to skip the import/generation of: 'data', 'files', 'summary' or any combination of the three. |
... |
Additional arguments to be passed to the
|
An xpose_data
object suitable for use in 'xpose'.
## Not run: library(nlmixr2) one.cmt <- function() { ini({ ## You may label each parameter with a comment tka <- 0.45 # Ka tcl <- log(c(0, 2.7, 100)) # Log Cl ## This works with interactive models ## You may also label the preceding line with label("label text") tv <- 3.45; label("log V") ## the label("Label name") works with all models eta.ka ~ 0.6 eta.cl ~ 0.3 eta.v ~ 0.1 add.sd <- 0.7 }) model({ ka <- exp(tka + eta.ka) cl <- exp(tcl + eta.cl) v <- exp(tv + eta.v) linCmt() ~ add(add.sd) }) } theo_sd_fit <- nlmixr2(one.cmt, theo_sd, "focei", control=foceiControl(print=0)) xpdb <- xpose_data_nlmixr2(obj = theo_sd_fit) ## End(Not run)
## Not run: library(nlmixr2) one.cmt <- function() { ini({ ## You may label each parameter with a comment tka <- 0.45 # Ka tcl <- log(c(0, 2.7, 100)) # Log Cl ## This works with interactive models ## You may also label the preceding line with label("label text") tv <- 3.45; label("log V") ## the label("Label name") works with all models eta.ka ~ 0.6 eta.cl ~ 0.3 eta.v ~ 0.1 add.sd <- 0.7 }) model({ ka <- exp(tka + eta.ka) cl <- exp(tcl + eta.cl) v <- exp(tv + eta.v) linCmt() ~ add(add.sd) }) } theo_sd_fit <- nlmixr2(one.cmt, theo_sd, "focei", control=foceiControl(print=0)) xpdb <- xpose_data_nlmixr2(obj = theo_sd_fit) ## End(Not run)