Merge pull request #69 from UUPharmacometrics/dev

Update Master to 0.4.0
UUPharmacometrics · Nov 17, 2017 · 05486f0 · 05486f0
2 parents d6d6238 + e029025
commit 05486f0
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -3,7 +3,7 @@
 ^_pkgdown\.yml$
 ^.*\.Rproj$
 ^\.Rproj\.user$
-^logo\.png$
+^LICENSE$
 ^README\.Rmd$
 ^temporary$
 ^inst/models$

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: xpose
 Type: Package
-Title: Diagnostics for pharmacometric models
+Title: Diagnostics for Pharmacometric Models
 Version: 0.4.0
 Authors@R: c(
       person('Benjamin', 'Guiastrennec',
@@ -18,6 +18,10 @@ Authors@R: c(
       person('Ron', 'Keizer', 
              role  = 'aut',
              email = '[email protected]'),
+      person('Nick', 'Solomon', 
+             role    = 'ctb',
+             comment = 'Wrote the geom_qq_line function',
+             email   = '[email protected]'),
       person('Kajsa', 'Harling', 
              role  = 'ctb',
              email = '[email protected]'),
@@ -34,7 +38,11 @@ Authors@R: c(
              role  = 'ctb',
              email = '[email protected]'),
       person('Pfizer', role = 'ctb'))
-Description: Automated generation of graphical diagnostics for non-linear mixed effect models.
+Description: Diagnostics for non-linear mixed-effects (population) 
+    models from 'NONMEM' <http://www.iconplc.com/innovation/nonmem/>. 
+    'xpose' facilitates data import, creation of numerical run summary 
+    and provide 'ggplot2'-based graphics for data exploration and model 
+    diagnostics.
 Depends:
   R (>= 3.1.2),
   ggplot2 (>= 2.2.1)
@@ -59,7 +67,7 @@ Suggests:
   plotly,
   webshot,
   mvtnorm
-License: LGPL-3 + file LICENSE
+License: LGPL-3
 URL: https://github.com/UUPharmacometrics/xpose
 BugReports: https://github.com/UUPharmacometrics/xpose/issues
 Encoding: UTF-8

diff --git a/R/xpose_save.R b/R/xpose_save.R
@@ -1,16 +1,15 @@
 #' Save xpose plot
 #'
-#' @description Automatically save xpose plots to files.
-#'
-#' This function was inspired by the \link[ggplot2]{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.
+#' @description Inspired by the \link[ggplot2]{ggsave}, this function 
+#' facilitates the export of xpose plots.
 #'
 #' @param plot A xpose plot object.
-#' @param file An optional name to be given to the file. Template variables such as @run 
-#' can be used to generate template names.
-#' @param dir Directory under which the xpose plot will be saved. Template variables such as @dir 
-#' can be used to generate template names.
+#' @param file A name with file extension (if device is \code{NULL}) to be given to the 
+#' output file. Template variables such as \code{@run} (run number) and \code{@plotfun} 
+#' (plot function) can be used to automatically name files e.g. 
+#' \code{file = '@[email protected]'}.
+#' @param dir Directory under which the xpose plots will be saved. Template variables 
+#' such as \code{@dir} can be used to generate template names.
 #' @param device Graphical device to use. Can be either be a device function
 #'   (e.g. \code{\link{png}}), or one of 'eps', 'ps', 'tex' (pictex),
 #'   'pdf' (default), 'jpeg', 'tiff', 'png', 'bmp', 'svg' or 'wmf' (windows only).
@@ -23,11 +22,11 @@
 #' \dontrun{
 #' xpdb_ex_pk %>% 
 #'  dv_vs_ipred() %>% 
-#'  xpose_save()
+#'  xpose_save(file = file.path(tempdir(), "dv_vs_ipred_example.pdf"))
 #' }
 #' @export
 xpose_save <- function(plot     = last_plot(),
-                       file     = '@[email protected]',
+                       file     = NULL,
                        dir      = NULL,
                        device   = NULL,
                        width    = 7,
@@ -37,9 +36,9 @@ xpose_save <- function(plot     = last_plot(),
                        ...) {
 
   if (is.null(plot)) {
-    stop('The `plot` argument is NULL.')
+    stop('Argument `plot` required.', call. = FALSE)
   } else if (is.null(file)) {
-    stop('The `file` argument is NULL.')
+    stop('Argument `file` required.', call. = FALSE)
   }
 
   # Parse the dir and file arguments for keywords

diff --git a/README.Rmd b/README.Rmd
@@ -2,26 +2,29 @@
 output: github_document
 ---
 
-# xpose <a href="https://UUPharmacometrics.github.io/xpose/"><img src="logo.png" align="right" /></a>
-
-[![travis_status](https://travis-ci.org/UUPharmacometrics/xpose.svg?branch=master)](https://travis-ci.org/UUPharmacometrics/xpose)
-[![appveyor status](https://ci.appveyor.com/api/projects/status/f6k09rf2cfi3vcs2?svg=true)](https://ci.appveyor.com/project/guiastrennec/xpose)[![cran_version](http://www.r-pkg.org/badges/version/xpose)]()
-[![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://codecov.io/gh/UUPharmacometrics/xpose)
+<!-- README.md is generated from README.Rmd. Please edit that file -->
 
 ```{r, include = FALSE}
 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 <a href="https://UUPharmacometrics.github.io/xpose/"><img src="man/figures/logo.png" align="right" /></a>
+
+[![travis_status](https://travis-ci.org/UUPharmacometrics/xpose.svg?branch=master)](https://travis-ci.org/UUPharmacometrics/xpose)
+[![appveyor status](https://ci.appveyor.com/api/projects/status/f6k09rf2cfi3vcs2?svg=true)](https://ci.appveyor.com/project/guiastrennec/xpose)[![cran_version](http://www.r-pkg.org/badges/version/xpose)]()
+[![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](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
@@ -1,6 +1,7 @@
 
-xpose <a href="https://UUPharmacometrics.github.io/xpose/"><img src="logo.png" align="right" /></a>
-===================================================================================================
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+xpose <a href="https://UUPharmacometrics.github.io/xpose/"><img src="man/figures/logo.png" align="right" /></a>
+===============================================================================================================
 
 [![travis\_status](https://travis-ci.org/UUPharmacometrics/xpose.svg?branch=master)](https://travis-ci.org/UUPharmacometrics/xpose) [![appveyor status](https://ci.appveyor.com/api/projects/status/f6k09rf2cfi3vcs2?svg=true)](https://ci.appveyor.com/project/guiastrennec/xpose)[![cran\_version](http://www.r-pkg.org/badges/version/xpose)]() [![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://codecov.io/gh/UUPharmacometrics/xpose)
 
@@ -100,15 +101,15 @@ summary(xpdb, problem = 1)
 dv_vs_ipred(xpdb)
 ```
 
-<img src="inst/img/readme_example_figure_1-1.png" width="50%" style="display: block; margin: auto;" />
+<img src="man/figures/readme_example_figure_1-1.png" width="50%" style="display: block; margin: auto;" />
 
 ##### Individual plots
 
 ``` r
 ind_plots(xpdb, page = 1)
 ```
 
-<img src="inst/img/readme_example_figure_2-1.png" width="75%" style="display: block; margin: auto;" />
+<img src="man/figures/readme_example_figure_2-1.png" width="75%" style="display: block; margin: auto;" />
 
 ##### Visual predictive checks
 
@@ -118,23 +119,23 @@ xpdb %>%
   vpc()
 ```
 
-<img src="inst/img/readme_example_figure_3-1.png" width="75%" style="display: block; margin: auto;" />
+<img src="man/figures/readme_example_figure_3-1.png" width="75%" style="display: block; margin: auto;" />
 
 ##### Distribution plots
 
 ``` r
 eta_distrib(xpdb, labeller = 'label_value')
 ```
 
-<img src="inst/img/readme_example_figure_4-1.png" width="75%" style="display: block; margin: auto;" />
+<img src="man/figures/readme_example_figure_4-1.png" width="75%" style="display: block; margin: auto;" />
 
 ##### Minimization diagnostics
 
 ``` r
 prm_vs_iteration(xpdb, labeller = 'label_value')
 ```
 
-<img src="inst/img/readme_example_figure_5-1.png" width="75%" style="display: block; margin: auto;" />
+<img src="man/figures/readme_example_figure_5-1.png" width="75%" style="display: block; margin: auto;" />
 
 ##### And many other features!
 

diff --git a/docs/articles/about.html b/docs/articles/about.html
diff --git a/docs/articles/access_xpdb_data.html b/docs/articles/access_xpdb_data.html
diff --git a/docs/articles/bestiarium.html b/docs/articles/bestiarium.html
diff --git a/docs/articles/cheatsheet.pdf b/docs/articles/cheatsheet.pdf
diff --git a/docs/articles/customize_plots.html b/docs/articles/customize_plots.html
diff --git a/docs/articles/faq.html b/docs/articles/faq.html
diff --git a/docs/articles/import_model_outputs.html b/docs/articles/import_model_outputs.html
diff --git a/docs/articles/interactive_plots.html b/docs/articles/interactive_plots.html
diff --git a/docs/articles/introduction.R b/docs/articles/introduction.R
@@ -27,7 +27,7 @@ list_vars(xpdb)
 ## ---- eval = FALSE-------------------------------------------------------
 #  xpose_data(runno = '001') %>%
 #    dv_vs_ipred() %>%
-#    xpose_save()
+#    xpose_save(file = 'run001_dv_vs_ipred.pdf')
 
 ## ---- change idv---------------------------------------------------------
 # With the TIME default
@@ -47,9 +47,12 @@ dv_vs_ipred(xpdb)
 res_vs_pred(xpdb, res = 'CWRES')
 
 ## ---- eval = FALSE-------------------------------------------------------
-#  # Save the last plot
-#  xpose_save()
+#  # 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')
 
diff --git a/docs/articles/introduction.html b/docs/articles/introduction.html
diff --git a/docs/articles/multiple_pages.R b/docs/articles/multiple_pages.R
@@ -42,7 +42,7 @@ dv_vs_ipred(xpdb_numbered, facets = c('SEX', 'MED1'), ncol = 2, nrow = 1, page =
 
 ## ---- eval = FALSE--------------------------------------------------------------------------------
 #  dv_vs_ipred(xpdb_numbered, facets = c('SEX', 'MED1'), ncol = 2, nrow = 1) %>%
-#  xpose_save()
+#  xpose_save(file = 'dv_vs_ipred_multiple.pdf')
 
 ## ---- eval = FALSE--------------------------------------------------------------------------------
 #  dv_vs_ipred(xpdb_numbered, facets = c('SEX', 'MED1'), ncol = 2, nrow = 1) %>%

diff --git a/docs/articles/multiple_pages.html b/docs/articles/multiple_pages.html
diff --git a/docs/articles/vpc.html b/docs/articles/vpc.html
diff --git a/docs/authors.html b/docs/authors.html