---
title: "Access the xpdb data"
author: "Benjamin Guiastrennec"
date: "`r format(Sys.time(), '%d %B, %Y')`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Access the xpdb data}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
library(xpose)
options(width = 100)

xpdb <- xpdb_ex_pk

knitr::opts_chunk$set(out.width = '75%',
                      comment   = '',
                      message   = FALSE)
```

The xpose package was designed as a standardized interface between model outputs and R. Hence model output files can easily be imported in R and used to summarize data or create plots.

### Glimpse at the xpdb
The files attached to an xpdb object can be displayed to the console simply by writing the xpdb name to the console or by using the `print()` function. Any of these files can be accessed from the xpdb using one of the functions listed below.

```{r demo print xpose_data}
xpdb # or print(xpdb)
```


### Access the model code
The `get_code()` function can be used to access the parsed model code from the xpdb. This code was used to create the summary and find table names. The parsed code can be used to get additional information about the run. If the argument `.problem` is specified a subset of the code can be returned based on `$PROBLEM`. 

*Note that general code warnings and PsN outputs appended are listed as problem 0.*

```{r demo get_code}
code <- get_code(xpdb)
code
```


### Access the output data
The `get_data()` function can be used to access the imported table files. Tables can be accessed by `table` name or by `.problem`. In the latter a single dataset containing all aggregated tables is returned. If more than one `table` name or `.problem` number is provided a named list is returned. 

*Note when providing a table name it is not guaranteed that the table will be identical to its file (i.e. the order of the columns may have been changed and tables with `FIRSTONLY` will no longer be deduplicated).*

```{r demo get_data}
data <- get_data(xpdb, table = 'cotab001')
data
```


### Access the run files
The `get_file()` function can be used to access the imported output files. Files can be accessed by `file` name, by `.problem`, `.subprob` and/or `.method`. If more than one `file` name, `.problem`, `.subprob`, or `.method` is provided a named list is returned. 

```{r demo get_file}
file <- get_file(xpdb, file = 'run001.ext')
file
```


### Access the parameter estimates
The `get_prm()` function can be used to access the parameter estimates. To get a nice parameter table printed to the console use the function `prm_table()` instead. The arguments `.problem`, `.subprob` and `.method` can be used to select the parameter estimates to output.

```{r demo get_prm}
# Raw output for editing
prm <- get_prm(xpdb, digits = 4)
prm

# Nicely formated table
prm_table(xpdb, digits = 4)
```


### Access the run summary
The `get_summary()` function can be used to access the generated run summary from which the `template_titles`. If the argument `.problem` is specified a subset of the summary can be returned based on `$PROBLEM`. 

*Note that general summary information are listed as problem 0.*

```{r demo get_summary}
run_sum <- get_summary(xpdb, .problem = 0)
run_sum
```