Author: Benjamin Guiastrennec

# Import model outputs

#### Benjamin Guiastrennec

#### 01 February, 2024

### The `xpose_data` function

The function `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')

### Imported files

#### NONMEM runs

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_titles` may 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 `template_titles`
- output and simulation tables: for the actual data

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`.

##### `FIRSTONLY` tables

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.

##### Compressed tables

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.

#### Others NLME tools

Coming with future releases…

### Structure of the `xpdb` object

A typical `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 `template_titles`.
- `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 `vpc()`
- `gg_theme`: an attached ggplot2 theme
- `xp_theme`: an attached xpose theme
- `options`: attached global options