library(xpose) options(width = 100) xpdb <- xpdb_ex_pk knitr::opts_chunk$set(fig.dpi = 96, fig.align = 'center', fig.height = 4, fig.width = 4, out.width = '75%', comment = '', message = FALSE)
xpose_data() collects all model output files and table and organizes them into an R object commonly called
xpdb for xpose data base.
xpdb <- xpose_data(runno = '001')
To make full use of the functionality offered by
xpose the following NONMEM output files should be available:
.lst/.out/.res: used to collect information on the run (
template_titles) as well as the output table names. Alternatively a model file (
.mod/.ctl) can be used but some of the information in
template_titlesmay not be available.
.ext: used to collect final parameter estimates and residual standard error (RSE)
.phi: used for the random effects and iOFV
.cov: used for the covariance matrix
.cor: used for the correlation matrix
.grd: used for the estimation gradients
.shk: used to compute random effect shrinkage
When importing the files, xpose will return messages to the console and inform of any issue encountered during the import.
xpdb <- xpose_data(runno = '001') Looking for nonmem output tables Reading: sdtab001, catab001, cotab001, patab001 [$prob no.1] Looking for nonmem output files Reading: run001.cor, run001.cov, run001.ext, run001.grd, run001.phi
These messages can be silenced with the option
quiet = TRUE.
xpose is compatible with the
$TABLE FIRSTONLY option of NONMEM. The option
FIRSTONLY only output the first record for each
ID and hence can be used to decrease the size of output tables having no time-varying columns. During tables import xpose will merge
FIRSTONLY tables with regular tables allowing seamless use of columns from
FIRSTONLY in plots.
xpose makes use of the readr which offers the advantages of 1) rapidly import big tables and 2) automatically import compressed table (e.g. sdtab001.zip) to increase storage capacity.
Coming with future releases...
xpdb object contains 8 levels namely:
code: the parsed model code
summary: contains key information regarding the model. All the information contained in the summary can be used as part of the
data: contains all output and simulation tables as well as the column indexing
files: contains all output files
special: contains post-processed datasets used by functions like
gg_theme: an attached ggplot2 theme
xp_theme: an attached xpose theme
options: attached global options
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