-
-[](https://travis-ci.org/UUPharmacometrics/xpose)
-[](https://ci.appveyor.com/project/guiastrennec/xpose)[]()
-[](https://codecov.io/gh/UUPharmacometrics/xpose)
+
```{r, include = FALSE}
library(xpose)
@@ -14,14 +10,21 @@ library(xpose)
xpdb <- xpdb_ex_pk
xpdb$options$quiet <- TRUE
-knitr::opts_chunk$set(fig.path = 'inst/img/',
- fig.dpi = 96,
+knitr::opts_chunk$set(fig.path = 'man/figures/',
+ fig.dpi = 96,
fig.height = 4,
- fig.width = 4,
- out.width = '50%',
- fig.align = 'center')
+ fig.width = 4,
+ out.width = '50%',
+ fig.align = 'center')
```
+# xpose 
+
+[](https://travis-ci.org/UUPharmacometrics/xpose)
+[](https://ci.appveyor.com/project/guiastrennec/xpose)[]()
+[](https://codecov.io/gh/UUPharmacometrics/xpose)
+
+
### Overview
[xpose](https://UUPharmacometrics.github.io/xpose/) was designed as a [ggplot2](https://github.com/tidyverse/ggplot2)-based alternative to [xpose4](http://xpose.sourceforge.net). xpose aims to reduce the post processing burden and improve diagnostics commonly associated the development of non-linear mixed effect models.
diff --git a/README.md b/README.md
index 89a5e432..7f42401d 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
-xpose
-===================================================================================================
+
+xpose
+===============================================================================================================
[](https://travis-ci.org/UUPharmacometrics/xpose) [](https://ci.appveyor.com/project/guiastrennec/xpose)[]() [](https://codecov.io/gh/UUPharmacometrics/xpose)
@@ -100,7 +101,7 @@ summary(xpdb, problem = 1)
dv_vs_ipred(xpdb)
```
-
+
##### Individual plots
@@ -108,7 +109,7 @@ dv_vs_ipred(xpdb)
ind_plots(xpdb, page = 1)
```
-
+
##### Visual predictive checks
@@ -118,7 +119,7 @@ xpdb %>%
vpc()
```
-
+
##### Distribution plots
@@ -126,7 +127,7 @@ xpdb %>%
eta_distrib(xpdb, labeller = 'label_value')
```
-
+
##### Minimization diagnostics
@@ -134,7 +135,7 @@ eta_distrib(xpdb, labeller = 'label_value')
prm_vs_iteration(xpdb, labeller = 'label_value')
```
-
+
##### And many other features!
diff --git a/docs/articles/about.html b/docs/articles/about.html
index 07df824b..a7ecc969 100644
--- a/docs/articles/about.html
+++ b/docs/articles/about.html
@@ -110,7 +110,7 @@
The ggplot2 object is now automatically converted to a plotly graph. The scales can now be changed interactively, groups can be hidden by clicking on the legend
plotly::ggplotly(gof_plot)xpdb_ex_pk %>%
eta_distrib(title = 'Eta distribution') %>%
plotly::ggplotly()xpose makes use of the pipe operator %>% from the package dplyr. Pipes can be used to generate clear workflow.
xpose_data(runno = '001') %>%
dv_vs_ipred() %>%
- xpose_save()The xpose_save function was designed automatically save plots according to their run number (@run) and the plotting function (@plotfun) using keywords preceded by a @. You can learn more about these keywords using help('template_titles'). The file extension is guessed from the file name and must match one of .pdf, .jpeg, .png, .bmp or .tiff, if missing a pdf will be generated by default. Finally, if the plot argument is left empty xpose_save will automatically save the last plot that was created or modified.
# Save the last plot
-xpose_save()
+The xpose_save function was designed to facilitate the export of xpose plots. The file extension is guessed from the file name and must match one of .pdf (default), .jpeg, .png, .bmp or .tiff. If no extension is provided as part of the file name a .pdf will be generated. Finally, if the plot argument is left empty xpose_save will automatically save the last plot that was created or modified.
+The xpose_save() function is compatible with templates titles and keywords such as @run for the run number and @plotfun for the name of the plotting function can be used to automatically name files. Learn more about the template titles keywords using help('template_titles').
+# Save the last generated plot
+dv_vs_ipred(xpdb)
+xpose_save(file = 'run001_dv_vs_ipred.pdf')
-# Change file name and extension
-xpose_save(file = '@run_@plotfun_[@ofv].jpeg', dir = 'pk/diagnostics')
+# Template titles can also be used in filename and the directory
+xpdb %>%
+ dv_vs_ipred() %>%
+ xpose_save(file = '@run_@plotfun_[@ofv].jpeg', dir = '@dir')Multiple pages graphs can simply be saved by using the xpose_save() function.
dv_vs_ipred(xpdb_numbered, facets = c('SEX', 'MED1'), ncol = 2, nrow = 1) %>%
-xpose_save()By default plots are saved as pdf which conveniently can store multiple pages within a single document. However other graphical devices (e.g. 'png', 'jpg') can also be used, simply ensure to have a page counter (i.e. '%03d') added the file name.
The pdf format can conveniently store multiple pages within a single document. However other graphical devices (e.g. 'png', 'jpg') can also be used, simply ensure to have a page counter (i.e. '%03d') added the file name.
dv_vs_ipred(xpdb_numbered, facets = c('SEX', 'MED1'), ncol = 2, nrow = 1) %>%
xpose_save(file = '@run_@plotfun_%03d.png')The VPC functionality in xpose is build around the vpc R package. For more details about the way the vpc package works, please check the documentation website.
+The VPC functionality in xpose is build around the vpc R package. For more details about the way the vpc package works, please check the documentation website.
Ron Keizer. Author.
+Nick Solomon. Contributor.
+
Wrote the geom_qq_line function
Kajsa Harling. Contributor.
diff --git a/docs/index.html b/docs/index.html index 477d113a..c09d38f7 100644 --- a/docs/index.html +++ b/docs/index.html @@ -5,7 +5,7 @@ -
Nick Solomon nick@nicksolomon.me (Wrote the geom_qq_line function) [contributor]
Kajsa Harling kajsa.harling@pharmetheus.com [contributor]
Mike K. Smith mike.k.smith@pfizer.com [contributor]
Elodie Plan elodie.plan@pharmetheus.com [contributor]
Automatically save xpose plots to files.
-This function was inspired by the ggsave. If no arguments are provided, -the function will automatically name and save a plot after its run number and the plotting -function name by using the metadata attached to the plot.
+Inspired by the ggsave, this function +facilitates the export of xpose plots.
-xpose_save(plot = last_plot(), file = "@run_@plotfun.pdf", dir = NULL, - device = NULL, width = 7, height = 6, units = c("in", "cm", "mm"), - dpi = 200, ...)+
xpose_save(plot = last_plot(), file = NULL, dir = NULL, device = NULL, + width = 7, height = 6, units = c("in", "cm", "mm"), dpi = 200, ...)
| file | -An optional name to be given to the file. Template variables such as @run -can be used to generate template names. |
+ A name with file extension (if device is |
|---|---|---|
| dir | -Directory under which the xpose plot will be saved. Template variables such as @dir -can be used to generate template names. |
+ Directory under which the xpose plots will be saved. Template variables
+such as |
| device | @@ -189,7 +188,7 @@
