| Title: | Interactive 'shiny' Dashboard for 'nlmixr2' |
| Version: | 0.5.1 |
| Description: | An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) <doi:10.1002/psp4.12445>) package, designed to simplify the modeling process for users. Additionally, this package includes supplementary functions to further enhances the usage of 'nlmixr2'. |
| Depends: | R (≥ 3.5.0), shiny, ggplot2 |
| Imports: | gridExtra, collapsibleTree, shinyAce, DT, bs4Dash, shinyWidgets, stringi, R3port, whisker, plotly, patchwork, shinyjs, ps, xfun, fresh, nlmixr2est, magrittr, rxode2, cli |
| Suggests: | xpose, nlmixr2, nlmixr2plot, xpose.nlmixr2, nlme, testthat, shinytest2, knitr, rmarkdown, rlang, miniUI, shinyFiles, rstudioapi |
| License: | MIT + file LICENSE |
| URL: | https://github.com/RichardHooijmaijers/shinyMixR/, https://richardhooijmaijers.github.io/shinyMixR/ |
| BugReports: | https://github.com/RichardHooijmaijers/shinyMixR/issues |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.2 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2025-07-18 09:04:12 UTC; r.hooijmaijers |
| Author: | Richard Hooijmaijers [aut, cre, cph], Teun Post [aut, cph], LAPP Consultants [fnd, cph], Matthew Fidler [ctb], Veerle van Leemput [ctb] |
| Maintainer: | Richard Hooijmaijers <richardhooijmaijers@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2025-07-18 09:20:02 UTC |
shinyMixR: Interactive 'shiny' Dashboard for 'nlmixr2'
Description
An R shiny user interface for the 'nlmixr2' (Fidler et al (2019) doi:10.1002/psp4.12445) package, designed to simplify the modeling process for users. Additionally, this package includes supplementary functions to further enhances the usage of 'nlmixr2'.
Author(s)
Maintainer: Richard Hooijmaijers richardhooijmaijers@gmail.com [copyright holder]
Authors:
Teun Post teunpost@gmail.com [copyright holder]
Other contributors:
LAPP Consultants info@lapp.nl [funder, copyright holder]
Matthew Fidler [contributor]
Veerle van Leemput [contributor]
See Also
Useful links:
Report bugs at https://github.com/RichardHooijmaijers/shinyMixR/issues
Adapt meta information inside a nlmixr UIF
Description
regular expressions are used to search for meta data inside a model file. This meta data is then updated with the provided new values
Usage
adpt_meta(mdl, newvals)
Arguments
mdl |
character with the name of the model to adapt |
newvals |
list with characteristics/meta data to adapt |
Value
character vector with model including the adapted meta data
Author(s)
Richard Hooijmaijers
Examples
## Not run:
adpt_meta("model.r",newvals=list(imp=4,ref="run 1"))
## End(Not run)
Creates a new project
Description
Creates a new project which basically means that within the specified folder, the necessary folder structure will be created and some example models will be placed in it.
Usage
create_proj(loc = ".", overwrite = FALSE)
Arguments
loc |
character with the location where the project should be created |
overwrite |
logical indicating if files should be overwritten if already exists |
Value
nothing will be returned by the function (only system commands are issued)
Author(s)
Richard Hooijmaijers
Examples
## Not run:
create_proj()
## End(Not run)
Function to create plot from data exploration app
Description
This function creates a text string for a ggplot based on an input list. This function is specifically written to be used with the shiny app for data exploration.
Usage
exploreplot(inputlist)
Arguments
inputlist |
list with input items to create a plot |
Value
a character string with the ggplot code
Author(s)
Richard Hooijmaijers
Examples
## Not run: exploreplot(input)
Create fit plot
Description
Creates a fit plot either using the xpose.nlmixr package or using a default ggplot call
Usage
fit_plot(
dfrm,
type = "xpose",
by = "ID",
idv = "TIME",
obs = "DV",
pred = "PRED",
ipred = "IPRED",
grp = "ID",
logy = TRUE,
scales = "fixed",
mdlnm = NULL,
outnm = NULL,
projloc = ".",
...
)
Arguments
dfrm |
data frame as created by the nlmixr function |
type |
character defining the type of plot that should be created. currently "xpose" and "user" are supported for xpose or ggplot style of plots |
by |
character vector with variables for facetting |
idv |
independent variable or x variable |
obs |
variable with observed data points |
pred |
variable with predicted data points |
ipred |
variable with individual predicted data points |
grp |
variable for grouping (mainly to draw separate lines) |
logy |
logical if y-axis should be displayed on log scale |
scales |
character of length one defining the scale parameter of ggplot (e.g. "fixed", "free","free_y",etc) |
mdlnm |
character with name of the model |
outnm |
character with name of the output file (see details) |
projloc |
character with the base location of the shinyMixR project |
... |
Details
In case a model is saved, a directory with the name of the model is created within the analysis folder of the current project. Then within this folder the file is saved as outnm. This method was chosen so the interface can easily index applicable files for a certain model. However, this means that output is always saved in this directly regardless of the location of outnm
Value
in case no outnm is defined a ggplot object will be returned otherwise the results are saved to disk
Author(s)
Richard Hooijmaijers
Examples
## Not run:
fit_plot(res)
## End(Not run)
Get the meta data out of a model function
Description
This function gets only the meta data from a function
Usage
get_meta(mdl)
Arguments
mdl |
character with the path of the model function |
Value
A list with the models meta data
Examples
## Not run:
get_meta("run1.r")
## End(Not run)
Read in and update model results in project object
Description
This function creates or updates a project object with models and/or results emerged from nlmixr2 runs. A check is performed to see if newer results are present and only updates these.
Usage
get_proj(projloc = ".", geteval = TRUE)
Arguments
projloc |
character with the base location of the shinyMixR project |
geteval |
logical indicating if the model functions should be evaluated |
Value
A named list with information for each model in the 'projloc'
Examples
## Not run:
proj <- get_proj()
## End(Not run)
Create goodness of fit plots
Description
Creates goodness of fit plots either using the xpose.nlmixr package or using a default ggplot call
Usage
gof_plot(
dfrm,
type = "xpose",
mdlnm = NULL,
colby = NULL,
ptype = "all",
outnm = NULL,
projloc = ".",
title = NULL,
linscale = FALSE,
...
)
Arguments
dfrm |
data frame as created by the nlmixr function |
type |
character defining the type of plot that should be created. currently "xpose" and "user" are supported for xpose or ggplot style of plots |
mdlnm |
character with name of the model |
colby |
character vector of length one specifying the variable to color on (for now can be only one variable) |
ptype |
The type of plots to create. Currently the following is accepted: "all", "ipred.dv", "pred.dv", "idv.res", "pred.res" |
outnm |
character with name of the output file (see details) |
projloc |
character with the base location of the shinyMixR project |
title |
character with the title to place above the plot |
linscale |
Logical indicating if the scales should be set to linear for DV, PRED and IPRED plots |
... |
Details
In case a model is saved, a directory with the name of the model is created within the analysis folder of the current project. Then within this folder the file is saved as outnm. This method was chosen so the interface can easily index applicable files for a certain model. However, this means that output is always saved in this directly regardless of the location of outnm
Value
in case no outnm is defined a ggplot object will be returned otherwise the results are saved to disk
Author(s)
Richard Hooijmaijers
Examples
## Not run:
gof_plot(res)
## End(Not run)
Increments a model name
Description
A model name is incremented either by incrementing numerical or alpha numerical. Furthermore it is possible to check the existence of the incremented model and take this into account.
Usage
incr_mdl(mod, checkloc = NULL)
Arguments
mod |
character with the model name |
checkloc |
character with the location to check for existence of a file |
Value
character with the incremented name
Author(s)
Richard Hooijmaijers
Examples
incr_mdl("run01.r")
Data exploration module for server
Description
Data exploration module for server
Usage
module_dataexplore_server(id, r)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Data exploration module for UI
Description
Shiny module for data exploration
Usage
module_dataexplore_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
Editor module for server
Description
Editor module for server
Usage
module_edit_server(id, r, settings)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
settings |
reactive value with the app settings |
Value
No return value, called for side effects
Editor module for UI
Description
Shiny module for model editor
Usage
module_edit_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
Fit plots module for server
Description
Fit plots module for server
Usage
module_fitplots_server(id, r, settings)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
settings |
reactive value with the app settings |
Value
No return value, called for side effects
Fit plots module for UI
Description
Shiny module for fit plots
Usage
module_fitplots_ui(id, proj_obj)
Arguments
id |
Module id |
proj_obj |
Project object |
Value
A list of html tags used for th UI of the app
GOF plots module for server
Description
GOF plots module for server
Usage
module_gof_server(id, r, settings)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
settings |
reactive value with the app settings |
Value
No return value, called for side effects
GOF plots module for UI
Description
Shiny module for GOF plots
Usage
module_gof_ui(id, proj_obj)
Arguments
id |
Module id |
proj_obj |
Project object |
Value
A list of html tags used for th UI of the app
meta data module for server
Description
meta data module for server
Usage
module_metadata_server(
id,
type,
selline = NULL,
sellmod = NULL,
sellcont = NULL,
r
)
Arguments
id |
Module id |
type |
character with the type of action (either "save" or "overview") |
selline |
reactive with the selected line for a model (for type "overview") |
sellmod |
reactive with the selected model (for type "save") |
sellcont |
reactive with the content of the selected model (for type "save") |
r |
reactive values object that is defined top-level |
Value
a reactive with the meta data information
metadata module for UI
Description
Shiny module for meta data
Usage
module_metadata_ui(id, type)
Arguments
id |
Module id |
type |
character with the type of button to present (either "save" or "overview") |
Value
A list of html tags used for th UI of the app
Overview module for server
Description
Overview module for server
Usage
module_overview_server(id, r)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Overview module for UI
Description
Shiny module for overview
Usage
module_overview_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
Parameter table module for server
Description
Parameter table module for server
Usage
module_pt_server(id, r)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Parameter table module for UI
Description
Shiny module for parameter table
Usage
module_pt_ui(id, proj_obj)
Arguments
id |
Module id |
proj_obj |
Project object |
Value
A list of html tags used for th UI of the app
Reporting module for server
Description
Reporting module for server
Usage
module_reports_server(id, r)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Reporting module for UI
Description
Shiny module for reporting
Usage
module_reports_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
Run model module for server
Description
Run model module for server
Usage
module_run_server(id, r)
Arguments
id |
Module id |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Run model module for UI
Description
Shiny module for running models
Usage
module_run_ui(id, proj_obj)
Arguments
id |
Module id |
proj_obj |
Project object |
Value
A list of html tags used for th UI of the app
Run script module for server
Description
Run script module for server
Usage
module_scripts_server(id, files = NULL, loc = "temp", r)
Arguments
id |
Module id |
files |
character vector of files to apply the scripts on, usually a reactive |
loc |
character with the location where the temp scripts are saved (created when not existing) |
r |
reactive values object that is defined top-level |
Value
No return value, called for side effects
Run script module for UI
Description
Shiny module for running scripts
Usage
module_scripts_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
Settings module for server
Description
Settings module for server
Usage
module_settings_server(id)
Arguments
id |
Module id |
Value
a reactive with all input elements
Settings module for UI
Description
Shiny module for settings
Usage
module_settings_ui(id)
Arguments
id |
Module id |
Value
A list of html tags used for th UI of the app
wrapper function for sweetalert in shinywidgets
Description
This function gets list of widgets to include in run_shinymixr
Usage
myalert(text, type, ...)
Arguments
text |
character with the text to display |
type |
character with the type of alert to display |
... |
other arguments passed to class |
Value
No return value, called for side effects
set significant digits without rounding higher numbers
Description
This function sets significant digits without rounding any numbers
Usage
numfmt(x, sdig = 3, snc = 6)
Arguments
x |
a numerical vector |
sdig |
a single number defining the number of significant digits |
snc |
a single number defining the scientific notation cutoff (higher means notation is only used for very small or very large numbers) |
Value
a character vector with formatted numbers
Author(s)
Richard Hooijmaijers
Examples
numfmt(c(0.012,12345,1))
Creates model overview
Description
Create an overview of the models within a project. This overview includes the meta data of the models and if results are available, also the objective function and run-times
Usage
overview(proj_obj, ...)
Arguments
proj_obj |
a project object created with |
... |
additional arguments passed to |
Value
a data frame is returned with the overview
Author(s)
Richard Hooijmaijers
Examples
## Not run:
overview(proj_obj)
## End(Not run)
Create parameter table
Description
Creates a table with the final estimates and percentage CV for all parameters in an nlmixr output file. This can be done for one or multiple models for easy comparison
Usage
par_table(
proj,
models,
outnm = NULL,
projloc = ".",
bsv = FALSE,
shrink = FALSE,
backt = FALSE,
formatting = FALSE,
...
)
Arguments
proj |
project object |
models |
character vector with model names to create table for |
outnm |
character with name of the output file (see details) |
projloc |
character with the base location of the shinyMixR project |
bsv |
logical indicating if between subject variability (BSV) should be added to table |
shrink |
logical indicating if shrinkage should be added to table |
backt |
logical indicating if the backtransformed parameters should be returned opposed to the original values |
formatting |
logical indicating if the formatting should be applied to present the table (not implemented for latex output) |
... |
Details
In case a model is saved, a directory with the name of the model is created within the analysis folder of the current project. Then within this folder the file is saved as outnm. This method was chosen so the interface can easily index applicable files for a certain model. However, this means that output is always saved in this directly regardless of the location of outnm In case multiple models are selected the result will be written to the name of the first model in the models vector.
Value
in case no outnm is defined a data frame will be returned otherwise the results are saved to disk
Author(s)
Richard Hooijmaijers
Examples
## Not run:
par_table(proj,"run1")
## End(Not run)
Runs a nlmixr model
Description
Runs an nlmixr model from a project object with the possibility to run in an external rsession using a system call (tested within linux only)
Usage
run_nmx(
mod,
proj = proj,
ext = TRUE,
saverds = TRUE,
autoupdate = TRUE,
projloc = ".",
addcwres = TRUE,
addnpde = TRUE
)
Arguments
mod |
character with the model file present in project object |
proj |
project object |
ext |
logical indicating if the model should be run external in a separate r session |
saverds |
logical indicating if the model results should be saved in a rds file |
autoupdate |
logical indicating if the project object should automatically update |
projloc |
character with the base location of the shinyMixR project |
addcwres |
logical indicating if CWRES should be added to the output |
addnpde |
logical indicating if NPDE should be added to the output |
Details
the meta data is obtained by compiling the model. The dataset, estimation method and control list are then included in the nlmixr call. Meta data is included in the model function which is comparable with NONMEM. This method was chosen so that all information to run a model is kept together in one function
Value
In case the model is not submitted in a separate R session, the results from nlmixr are returned otherwise the result of the system call will be returned
Author(s)
Richard Hooijmaijers
Examples
## Not run:
run_nmx("run1",proj)
## End(Not run)
Creates and run the interface
Description
Creates and run the interface
Usage
run_shinymixr(wd = getwd(), ...)
Arguments
wd |
character with the working directory |
... |
arguments passed to the shiny runApp function |
Value
No return value, runs the shinyMixR interface
Author(s)
Richard Hooijmaijers
Examples
## Not run:
if (interactive()) run_shinymixr(".")
## End(Not run)
Record a shinyMixR test
Description
Record a shinyMixR test
Usage
setup_shinymixr_test(
dir = "./tests/files",
overwrite = TRUE,
record = FALSE,
incres = FALSE
)
Arguments
dir |
character, the directory where the files will be placed and the test will be recorded |
overwrite |
logical, if TRUE, the function will remove the content of the tests/files directory |
record |
logical, if TRUE, the function will use 'record_test' |
incres |
logical, if TRUE, the function will include result files for testing |
Value
runs the shinyMixR interface and records actions in the app
Rstudio gadget to select project and start app
Description
Rstudio gadget to select project and start app
Usage
shinymixr_gadget()
Value
No return value, runs a gadget to start the shinyMixR interface
Author(s)
Richard Hooijmaijers
Examples
## Not run:
if (interactive()) shinymixr_gadget()
## End(Not run)
set significant digits without rounding higher numbers
Description
This function sets significant digits without rounding any numbers
Usage
sigdigs(x, sdig = 3)
Arguments
x |
a numerical vector |
sdig |
a single number defining the number of significant digits |
Value
A character vector with formatted numbers
theme for ggplot output in the shinyMixR package
Description
This function provides a custom theme for ggplot output
Usage
theme_shinyMixR(fontsize = 12)
Arguments
fontsize |
numeric with the default fontsize passed through to theme |
Value
A list with ggplot theme elements
Creates tree overview of models
Description
Create a graphical collapsible tree overview of the models within a project. This is mostly relevant in case the reference of models is included to visualise the relationship between models
Usage
tree_overview(proj_obj, ...)
Arguments
proj_obj |
a project object created with |
... |
additional arguments passed to |
Value
a data frame is returned with the overview
Author(s)
Richard Hooijmaijers
See Also
collapsibleTreeNetwork which does most of the work
Examples
## Not run:
if (interactive()) tree_overview(proj_obj)
## End(Not run)
Update initial estimates from a final model run
Description
This function update the initial estimates from a model using the final estimates from a model result file. Currently this function assumes all models were submitted using shinyMixR opposed to vanilla nlmixr
Usage
update_inits(mod, res, out)
Arguments
mod |
character with the entire model function included |
res |
character with the path to the model result RDS which holds the final estimated |
out |
character with the path for the updated model to save |
Value
nothing will be returned the function saves the updated model to disk
Author(s)
Richard Hooijmaijers
Examples
## Not run:
update_inits(readLines("run2.r"),"shinyMixR/run2.res.rds","run3.r")
## End(Not run)