Merge pull request #148 from UUPharmacometrics/dev

Update master to 0.4.4
UUPharmacometrics · Mar 18, 2019 · 4187bf5 · 4187bf5
2 parents 4bf7ff9 + c15d1b3
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diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.gitattributes b/.gitattributes
diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md
@@ -40,7 +40,7 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/
diff --git a/.github/CONTRIBUTING.html b/.github/CONTRIBUTING.html
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -25,7 +25,7 @@ To contribute code to xpose please carefully follow the steps listed below.
 1. [Fork](https://github.com/UUPharmacometrics/xpose/fork) the xpose repository.
 1. Make the changes to the code on your fork.
 
-    + Use the tidyverse [coding style](http://style.tidyverse.org/).
+    + Use the tidyverse [coding style](https://style.tidyverse.org/).
     + Any new function should have [Roxygen](http://r-pkgs.had.co.nz/man.html) documentation. Internal functions should contain `#' @keywords internal`. Add examples to new functions. Make sure to update the documentation with `devtools::document()` before submitting the pull request.
     + [Tests](http://r-pkgs.had.co.nz/tests.html) should be added under *tests/testthat/* to ensure for proper code coverage.
     + New plots should be created using the generic `xplot_scatter()`, `xplot_distrib()` or `xplot_qq()`. Check for example the code of *R/plot_gof.R* to see how it should be done.

diff --git a/.gitignore b/.gitignore
diff --git a/.travis.yml b/.travis.yml
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: xpose
 Type: Package
 Title: Diagnostics for Pharmacometric Models
-Version: 0.4.3
+Version: 0.4.4
 Authors@R: c(
       person('Benjamin', 'Guiastrennec',
              role  = c('aut', 'cre', 'cph'),
@@ -53,4 +53,4 @@ BugReports: https://github.com/UUPharmacometrics/xpose/issues
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+# xpose 0.4.4
+### General
+* Improved documentation for `xpose_data` (@billdenney #99)
+* Fixed VPC error in the documentation (@callistosp #130)
+* Fixed bug leading to errors when plotting poorly formatted ETA name (@romainfrancois #127)
+* Compatibility improvements
+
 # xpose 0.4.3
 ### General
 * Fixed bug in `get_prm()`/`prm_table()` where off diagonal correlations were improperly computed.
@@ -117,7 +124,7 @@
 * Proof of concept pre-release around simple goodness-of-fit functions like `dv_vs_ipred()`
 
 ### Definition of core functions and workflow
-* Defined the `xpose_geom()` core function to specifically direct arguments to [`ggplot2`](http://ggplot2.tidyverse.org) layers
+* Defined the `xpose_geom()` core function to specifically direct arguments to [`ggplot2`](https://ggplot2.tidyverse.org) layers
 * Defined the concept of template titles
 * Define the templates for `xpose_theme()`
-* Makes use of the [`tidyverse`](http://tidyverse.org) and pipes `%>%`
+* Makes use of the [`tidyverse`](https://tidyverse.org) and pipes `%>%`
diff --git a/R/examples.R b/R/examples.R
diff --git a/R/fetch_data.R b/R/fetch_data.R
diff --git a/R/list_nm_tables.R b/R/list_nm_tables.R
diff --git a/R/manual_import.R b/R/manual_import.R
diff --git a/R/plot_amt.R b/R/plot_amt.R
diff --git a/R/plot_distribution.R b/R/plot_distribution.R
diff --git a/R/plot_gof.R b/R/plot_gof.R
diff --git a/R/plot_individuals.R b/R/plot_individuals.R
diff --git a/R/plot_minimization.R b/R/plot_minimization.R
diff --git a/R/plot_qq.R b/R/plot_qq.R
diff --git a/R/plot_residuals.R b/R/plot_residuals.R
diff --git a/R/plot_spaghetti.R b/R/plot_spaghetti.R
diff --git a/R/plot_vpc.R b/R/plot_vpc.R
diff --git a/R/print_xpose_data.R b/R/print_xpose_data.R
diff --git a/R/print_xpose_plot.R b/R/print_xpose_plot.R
diff --git a/R/prm_table.R b/R/prm_table.R
diff --git a/R/read_nm_files.R b/R/read_nm_files.R
diff --git a/R/read_nm_model.R b/R/read_nm_model.R
diff --git a/R/read_nm_tables.R b/R/read_nm_tables.R
@@ -222,7 +222,7 @@ read_funs <- function(fun) {
 #' @param x A list containing a the 3 first records of a 
 #' dataset under `[[1]]`.
 #' @param quiet Should messages be displayed to the console.
-#' @param col_types Defines the type of each to be passed to 
+#' @param col_types Defines the type of each column to be passed to 
 #' the `readr` import function.
 #' @param na Character string defining the values to be treated as `NA`.
 #' @param comment Character string defining the value to mark comments.

diff --git a/R/summarise_nm_model.R b/R/summarise_nm_model.R
diff --git a/R/summary_xpose_data.R b/R/summary_xpose_data.R
diff --git a/R/template_titles.R b/R/template_titles.R
diff --git a/R/themes_gg.R b/R/themes_gg.R
diff --git a/R/themes_xp.R b/R/themes_xp.R
diff --git a/R/transform_parameters.R b/R/transform_parameters.R
diff --git a/R/update_themes.R b/R/update_themes.R
diff --git a/R/utils.R b/R/utils.R
diff --git a/R/vars_list.R b/R/vars_list.R
diff --git a/R/vars_set.R b/R/vars_set.R
diff --git a/R/vpc_data.R b/R/vpc_data.R
diff --git a/R/vpc_helpers.R b/R/vpc_helpers.R
diff --git a/R/xpdb_access.R b/R/xpdb_access.R
diff --git a/R/xpdb_edits.R b/R/xpdb_edits.R
@@ -184,7 +184,7 @@ edit_xpose_data <- function(.fun, .fname, .data, ..., .problem, .source, .where)
 
     # do dplyr operation outside of mutate to avoid problems with n()
     xpdb[['data']]$data <- purrr::map_if(xpdb[['data']]$data, xpdb[['data']]$problem %in% .problem,
-                         .f = .fun, rlang::UQS(rlang::quos(...)))
+                         .f = .fun, !!!rlang::quos(...))
     xpdb[['data']] <- xpdb[['data']] %>%
       dplyr::mutate(modified = dplyr::if_else(.$problem %in% .problem, TRUE, .$modified))
 
@@ -221,7 +221,7 @@ edit_xpose_data <- function(.fun, .fname, .data, ..., .problem, .source, .where)
                                           } else {
                                             stop('edits of `', .x$method, '` data are not yet supported in xpose.', call. = FALSE)
                                           }
-                                        }, .fun = .fun, .where = .where, rlang::UQS(rlang::quos(...))) 
+                                        }, .fun = .fun, .where = .where, !!!rlang::quos(...)) 
 
     xpdb[['special']] <- tidyr::unnest(xpdb[['special']])
   } else {
@@ -240,7 +240,7 @@ edit_xpose_data <- function(.fun, .fname, .data, ..., .problem, .source, .where)
 
     xpdb[['files']]$data <- purrr::map_if(.x = xpdb[['files']]$data, .p = xpdb[['files']]$problem %in% .problem &
                                        xpdb[['files']]$extension %in% .source,
-                                     .f = .fun, rlang::UQS(rlang::quos(...)))
+                                     .f = .fun, !!!rlang::quos(...))
     xpdb[['files']] <- xpdb[['files']] %>%
       dplyr::mutate(modified = dplyr::if_else(.$problem %in% .problem & .$extension %in% .source, TRUE, .$modified))
   }

diff --git a/R/xpdb_list.R b/R/xpdb_list.R
diff --git a/R/xplot_distrib.R b/R/xplot_distrib.R
diff --git a/R/xplot_helpers.R b/R/xplot_helpers.R
diff --git a/R/xplot_qq.R b/R/xplot_qq.R
diff --git a/R/xplot_scatter.R b/R/xplot_scatter.R
diff --git a/R/xpose.R b/R/xpose.R
diff --git a/R/xpose_data.R b/R/xpose_data.R
@@ -169,10 +169,10 @@ xpose_data <- function(runno         = NULL,
     structure(class = c('xpose_data', 'uneval'))
 }
 
-#' Allow assignment into xpose_data without conversion to class uneval
-`[[<-.xpose_data` <- function(x, i, value) {
-  x <- unclass(x)
-  x[[i]] <- value
-  as.xpdb(x)
-}
-`$<-.xpose_data` <- `[[<-.xpose_data`
+# Allow assignment into xpose_data without conversion to class uneval
+# `[[<-.xpose_data` <- function(x, i, value) {
+#   x <- unclass(x)
+#   x[[i]] <- value
+#   as.xpdb(x)
+# }
+# `$<-.xpose_data` <- `[[<-.xpose_data`
diff --git a/R/xpose_geom.R b/R/xpose_geom.R
diff --git a/R/xpose_save.R b/R/xpose_save.R
diff --git a/R/zzz.R b/R/zzz.R
@@ -2,9 +2,7 @@
 
   if (!interactive()) return()
 
-  text <- c('The xpose is under active development, for updates checkout:\nhttps://UUPharmacometrics.github.io/xpose',
-            'Need a new plot? Suggest ideas for the new xpose on github:\nhttps://github.com/UUPharmacometrics/xpose',
-            'Do you like the new xpose? Give us some feedback on github:\nhttps://github.com/UUPharmacometrics/xpose')
+  text <- c('Note: the next xpose release (v0.5) will bring some major changes.\nIf you rely on xpose for your work, please keep an eye on our github:\nhttps://github.com/UUPharmacometrics/xpose')
 
   packageStartupMessage(sample(text, size = 1))
 }

diff --git a/README.Rmd b/README.Rmd
@@ -9,23 +9,22 @@ library(xpose)
 
 xpdb <- xpdb_ex_pk
 xpdb$options$quiet <- TRUE
+
 xpdb <- as.xpdb(xpdb)
 
 knitr::opts_chunk$set(fig.path   = 'man/figures/', 
                       fig.dpi    = 96,
                       fig.height = 4, 
                       fig.width  = 4, 
                       out.width  = '50%', 
-                      fig.align  = 'center',
-                      dev        = 'png',
-                      dev.args   = list(type = 'cairo'))
+                      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)](https://CRAN.R-project.org/package=xpose)
+[![cran_version](https://www.r-pkg.org/badges/version/xpose)](https://CRAN.R-project.org/package=xpose)
 [![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://codecov.io/gh/UUPharmacometrics/xpose)
 [![Lifecycle Status](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)
 [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/xpose)](https://CRAN.R-project.org/package=xpose)
@@ -101,7 +100,7 @@ The [xpose website](https://UUPharmacometrics.github.io/xpose/) contains several
 
 When working with xpose, a working knowledge of ggplot2 is recommended. Help for ggplot2 can be found in:
 
-- The ggplot2 [documentation](http://docs.ggplot2.org/current/)
+- The ggplot2 [documentation](https://docs.ggplot2.org/current/)
 - The ggplot2 [mailing list](https://groups.google.com/forum/?fromgroups#!forum/ggplot2)
 - Internet resources (stack overflow, etc.)
 

diff --git a/README.md b/README.md
@@ -1,17 +1,26 @@
 
 <!-- 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)](https://CRAN.R-project.org/package=xpose) [![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://codecov.io/gh/UUPharmacometrics/xpose) [![Lifecycle Status](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/) [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/xpose)](https://CRAN.R-project.org/package=xpose)
+# xpose <a href="https://UUPharmacometrics.github.io/xpose/"><img src="man/figures/logo.png" align="right" /></a>
 
-Overview
---------
+[![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](https://www.r-pkg.org/badges/version/xpose)](https://CRAN.R-project.org/package=xpose)
+[![codecov](https://codecov.io/gh/UUPharmacometrics/xpose/branch/master/graph/badge.svg)](https://codecov.io/gh/UUPharmacometrics/xpose)
+[![Lifecycle
+Status](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)
+[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/xpose)](https://CRAN.R-project.org/package=xpose)
 
-[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.
+## Overview
 
-Installation
-------------
+[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.
+
+## Installation
 
 ``` r
 # Install the lastest release from the CRAN
@@ -22,8 +31,7 @@ install.packages('xpose')
 devtools::install_github('UUPharmacometrics/xpose')
 ```
 
-Getting started
----------------
+## Getting started
 
 ### Load xpose
 
@@ -60,43 +68,45 @@ xpdb
 summary(xpdb, problem = 1)
 ```
 
-
-    Summary for problem no. 0 [Global information] 
-     - Software                      @software   : nonmem
-     - Software version              @version    : 7.3.0
-     - Run directory                 @dir        : analysis/models/pk/
-     - Run file                      @file       : run001.lst
-     - Run number                    @run        : run001
-     - Reference model               @ref        : 000
-     - Run description               @descr      : NONMEM PK example for xpose
-     - Run start time                @timestart  : Mon Oct 16 13:34:28 CEST 2017
-     - Run stop time                 @timestop   : Mon Oct 16 13:34:35 CEST 2017
-
-    Summary for problem no. 1 [Parameter estimation] 
-     - Input data                    @data       : ../../mx19_2.csv
-     - Number of individuals         @nind       : 74
-     - Number of observations        @nobs       : 476
-     - ADVAN                         @subroutine : 2
-     - Estimation method             @method     : foce-i
-     - Termination message           @term       : MINIMIZATION SUCCESSFUL
-     - Estimation runtime            @runtime    : 00:00:02
-     - Objective function value      @ofv        : -1403.905
-     - Number of significant digits  @nsig       : 3.3
-     - Covariance step runtime       @covtime    : 00:00:03
-     - Condition number              @condn      : 21.5
-     - Eta shrinkage                 @etashk     : 9.3 [1], 28.7 [2], 23.7 [3]
-     - Epsilon shrinkage             @epsshk     : 14.9 [1]
-     - Run warnings                  @warnings   : (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
-
-    Summary for problem no. 2 [Model simulations] 
-     - Input data                    @data       : ../../mx19_2.csv
-     - Number of individuals         @nind       : 74
-     - Number of observations        @nobs       : 476
-     - Estimation method             @method     : sim
-     - Number of simulations         @nsim       : 20
-     - Simulation seed               @simseed    : 221287
-     - Run warnings                  @warnings   : (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
-                                                   (WARNING 22) WITH $MSFI AND "SUBPROBS", "TRUE=FINAL" ...
+``` 
+
+Summary for problem no. 0 [Global information] 
+ - Software                      @software   : nonmem
+ - Software version              @version    : 7.3.0
+ - Run directory                 @dir        : analysis/models/pk/
+ - Run file                      @file       : run001.lst
+ - Run number                    @run        : run001
+ - Reference model               @ref        : 000
+ - Run description               @descr      : NONMEM PK example for xpose
+ - Run start time                @timestart  : Mon Oct 16 13:34:28 CEST 2017
+ - Run stop time                 @timestop   : Mon Oct 16 13:34:35 CEST 2017
+
+Summary for problem no. 1 [Parameter estimation] 
+ - Input data                    @data       : ../../mx19_2.csv
+ - Number of individuals         @nind       : 74
+ - Number of observations        @nobs       : 476
+ - ADVAN                         @subroutine : 2
+ - Estimation method             @method     : foce-i
+ - Termination message           @term       : MINIMIZATION SUCCESSFUL
+ - Estimation runtime            @runtime    : 00:00:02
+ - Objective function value      @ofv        : -1403.905
+ - Number of significant digits  @nsig       : 3.3
+ - Covariance step runtime       @covtime    : 00:00:03
+ - Condition number              @condn      : 21.5
+ - Eta shrinkage                 @etashk     : 9.3 [1], 28.7 [2], 23.7 [3]
+ - Epsilon shrinkage             @epsshk     : 14.9 [1]
+ - Run warnings                  @warnings   : (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
+
+Summary for problem no. 2 [Model simulations] 
+ - Input data                    @data       : ../../mx19_2.csv
+ - Number of individuals         @nind       : 74
+ - Number of observations        @nobs       : 476
+ - Estimation method             @method     : sim
+ - Number of simulations         @nsim       : 20
+ - Simulation seed               @simseed    : 221287
+ - Run warnings                  @warnings   : (WARNING 2) NM-TRAN INFERS THAT THE DATA ARE POPULATION.
+                                               (WARNING 22) WITH $MSFI AND "SUBPROBS", "TRUE=FINAL" ...
+```
 
 ### Generate diagnostics
 
@@ -142,18 +152,22 @@ prm_vs_iteration(xpdb, labeller = 'label_value')
 
 <img src="man/figures/readme_example_figure_5-1.png" width="75%" style="display: block; margin: auto;" />
 
-Recommended reading
--------------------
+## Recommended reading
 
-The [xpose website](https://UUPharmacometrics.github.io/xpose/) contains several useful articles to make full use of xpose
+The [xpose website](https://UUPharmacometrics.github.io/xpose/) contains
+several useful articles to make full use of xpose
 
-When working with xpose, a working knowledge of ggplot2 is recommended. Help for ggplot2 can be found in:
+When working with xpose, a working knowledge of ggplot2 is recommended.
+Help for ggplot2 can be found in:
 
--   The ggplot2 [documentation](http://docs.ggplot2.org/current/)
--   The ggplot2 [mailing list](https://groups.google.com/forum/?fromgroups#!forum/ggplot2)
--   Internet resources (stack overflow, etc.)
+  - The ggplot2 [documentation](https://docs.ggplot2.org/current/)
+  - The ggplot2 [mailing
+    list](https://groups.google.com/forum/?fromgroups#!forum/ggplot2)
+  - Internet resources (stack overflow, etc.)
 
-Contribute
-----------
+## Contribute
 
-Please note that the xpose project is released with a [Contributor Code of Conduct](.github/CODE_OF_CONDUCT.md) and [contributing guidelines](.github/CONTRIBUTING.md). By contributing to this project, you agree to abide these.
+Please note that the xpose project is released with a [Contributor Code
+of Conduct](.github/CODE_OF_CONDUCT.md) and [contributing
+guidelines](.github/CONTRIBUTING.md). By contributing to this project,
+you agree to abide these.
diff --git a/appveyor.yml b/appveyor.yml
@@ -10,10 +10,12 @@ init:
 install:
   ps: Bootstrap
 
-# Adapt as necessary starting from here
-
 cache:
-  - packages -> appveyor.yml
+  - C:\RLibrary
+
+# Adapt as necessary starting from here
+environment:
+  USE_RTOOLS: true
 
 build_script:
   - travis-tool.sh install_deps

diff --git a/data-raw/xpdb_ex_pk.R b/data-raw/xpdb_ex_pk.R
diff --git a/data/xpdb_ex_pk.rda b/data/xpdb_ex_pk.rda