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+
+ 
+
+
+
+# Overview
+
+The **ospsuite-R** package provides the functionality of loading, manipulating, and simulating the simulations created in the Open Systems Pharmacology Software tools PK-Sim and MoBi.
+
+- [Documentation](#documentation)
+- [Installation](#installation)
+- [Usage](#usage)
+- [Known issues](#known-issues)
+- [Code of conduct](#code-of-conduct)
+- [Contribution](#contribution)
+- [Licence](#licence)
+
+# Documentation
+
+If you are reading this on GitHub README, please refer to the [online documentation](https://www.open-systems-pharmacology.org/OSPSuite-R/) for more details on the package.
+
+In particular, we would recommend that you read the articles in the following order:
+
+* [Get Started](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/ospsuite.html)
+* [Loading a simulation and accessing entities](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/load-get.html)
+* [Changing parameter and molecule start values](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/set-values.html)
+* [Running a simulation](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/run-simulation.html)
+* [Efficient calculations](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/efficient-calculations.html)
+* [Creating individuals](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/create-individual.html)
+* [Population simulations](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/create-run-population.html)
+* [PK Analysis](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/pk-analysis.html)
+* [Sensitivity analysis](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/sensitivity-analysis.html)
+* [Table parameters](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/table-parameters.html)
+* [Dimensions and Units](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/unit-conversion.html)
+* [Working with data sets and import from excel](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/observed-data.html)
+* [Working with `DataCombined` class](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/data-combined.html)
+* [Visualizations with `DataCombined`](https://www.open-systems-pharmacology.org/OSPSuite-R/articles/data-combined-plotting.html)
+
+# Installation
+
+The **ospsuite-R** package is compatible with version 3.6.x **AND** version 4.x.x of R. One of its dependency, **rClr** needs to be installed specifically for the targeted R version. Please follow the installation instructions below.
+
+**ospsuite** requires following packages to be installed:
+
+From CRAN:
+
+- [dplyr](https://cran.r-project.org/web/packages/dplyr/index.html)
+- [purrr](https://cran.r-project.org/web/packages/purrr/index.html)
+- [R6](https://cran.r-project.org/web/packages/R6/index.html)
+- [readr](https://cran.r-project.org/web/packages/readr/index.html)
+- [stringr](https://cran.r-project.org/web/packages/stringr/index.html)
+- [tidyr](https://cran.r-project.org/web/packages/tidyr/index.html)
+- [ggplot2](https://cran.r-project.org/web/packages/ggplot2/index.html)
+- [rlang](https://cran.r-project.org/web/packages/rlang/index.html)
+- [jsonlite](https://cran.r-project.org/web/packages/jsonlite/index.html)
+- [patchwork](https://cran.r-project.org/web/packages/patchwork/index.html)
+- [cowplot](https://cran.r-project.org/web/packages/cowplot/index.html)
+- [scales](https://cran.r-project.org/web/packages/scales/index.html)
+
+
+Must be downloaded manually:
+
+- rClr
+ - [For R 4.x.x](https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.2/rClr_0.9.2.zip)
+ - [For R 3.6.x](https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.1-R3/rClr_0.9.1.zip)
+
+- [ospsuite.utils](https://github.com/Open-Systems-Pharmacology/OSPSuite.RUtils/releases/latest)
+
+- [tlf](https://github.com/Open-Systems-Pharmacology/TLF-Library/releases/latest)
+
+
+## Under Windows
+
+The release version of the package comes as a binary `*.zip` and can be downloaded from [here](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases).
+
+If you use [RStudio IDE](https://www.rstudio.com/), you can use the *Install* option in the *Packages* pane and select the option *Install from -> Package Archive File* to install a package from binary `*.zip` files.
+
+To install manually, follow these instructions:
+
+```r
+# Install dependencies (e.g. R6) which are on CRAN
+install.packages('R6')
+
+# Install `{rClr}` from local file
+# (`pathTo_rCLR.zip` here should be replaced with the actual path to the `.zip` file)
+install.packages(pathTo_rCLR.zip, repos = NULL)
+
+# Install `{ospsuite.utils}` from local file
+# (`pathTo_ospsuite.utils.zip` here should be replaced with the actual path to the `.zip` file)
+install.packages(pathTo_ospsuite.utils.zip, repos = NULL)
+
+# Install `{tlf}` from local file
+# (`pathTo_tlf.zip` here should be replaced with the actual path to the `.zip` file)
+install.packages(pathTo_tlf.zip, repos = NULL)
+
+# Install `{ospsuite}` from local file
+# (`pathToOSPSuite.zip` here should be replaced with the actual path to the `.zip` file)
+install.packages(pathToOSPSuite.zip, repos = NULL)
+```
+
+The package also requires the Visual C++ Runtime that is installed with OSPS and can be manually downloaded [here](https://aka.ms/vs/16/release/vc_redist.x64.exe).
+
+## Under Linux
+
+The **ospsuite** package has been tested under Linux distributions CentOS 7 and Ubuntu 18. Some functionality, such as creating individuals, is not available under Linux. Installation under Linux requires several prerequisites, the detailed instructions can be found in the [Wiki](https://github.com/Open-Systems-Pharmacology/OSPSuite-R/wiki/Setup-ospsuite-R-on-Ubuntu).
+For other Linux distributions Docker containers can be used (Dockerfiles based on CentOS 7 and Ubuntu 18 are available under https://github.com/Open-Systems-Pharmacology/OSPSuite-R/releases )
+
+## Build from source
+
+You can clone the GIT repository and build the package from source.
+
+### How to update dependencies from nuget?
+
+- `git submodule update --init --recursive` to install all submodules
+- Make sure you have [ruby](https://www.ruby-lang.org/de/downloads/) install and that it is available in your path
+- Run `rake postclean` or simply double click on `postclean.bat`. This will update all nuget packages and copy the dependencies in the package `inst/lib` folder.
+
+# Usage
+
+In general, every workflow starts with loading a simulation that has been exported to the `*.pkml` format. The method `loadSimulation()` returns the corresponding simulation that is used as input of other methods. The user can then change values of parameters and initial conditions, run the simulation, and retrieve the simulated results.
+
+```r
+library(ospsuite)
+
+# Load a simulation
+simFilePath <- system.file("extdata", "Aciclovir.pkml", package = "ospsuite")
+sim <- loadSimulation(simFilePath)
+
+# Get the parameter "Dose"
+doseParamPath <- "Applications|IV 250mg 10min|Application_1|ProtocolSchemaItem|Dose"
+doseParam <- getParameter(doseParamPath, sim)
+
+# Change the dose to 350mg. The values has to be converted to base unit, first
+newValue <- toBaseUnit(quantity = doseParam, values = 350, unit = "mg")
+setParameterValues(parameters = doseParam, values = newValue)
+
+# Simulate
+simResults <- runSimulation(simulation = sim)
+# Retrieve the results
+simulatedValues <- getOutputValues(simulationResults = simResults)
+
+# Plot time-concentration profile
+plot(simulatedValues$data$Time, simulatedValues$data$`Organism|PeripheralVenousBlood|Aciclovir|Plasma (Peripheral Venous Blood)`,
+type = "l",
+xlab = "Time [min]",
+ylab = "Concentration [µmol/l]")
+```
+
+More detailed description of the methods and the typical workflows can be found in the vignettes. You can see the list of all vignettes available for **ospsuite** by calling-
+
+```r
+vignette(package = "ospsuite")
+```
+
+To open a specific vignette, call-
+
+```r
+# Insert the name of the vignette you want to view as the argument
+vignette("introduction-ospsuite")
+```
+
+# Known issues
+
+
+- Loading `ospsuite` might fail if your systems locale is not set to *English*, e.g.:
+
+```ibrary(ospsuite)
+载入需要的程辑包：rClr
+Loading the dynamic library for Microsoft .NET runtime...
+Loaded Common Language Runtime version 4.0.30319.42000
+
+Error: package or namespace load failed for ‘ospsuite’:
+loadNamespace()里算'ospsuite'时.onLoad失败了，详细内容：
+调用: rClr::clrCall(dimensionTask, "AllAvailableUnitNamesFor", enc2utf8(dimension))
+错误: Type: System.Collections.Generic.KeyNotFoundException
+Message: Dimension 'CV mmHg*s虏/ml' not available in DimensionFactory.
+...
+```
+
+-- On Windows, set `Settings > Language > Administrative language settings > Current language for non-Unicode programs`
+to `English (United States)` and reboot.
+-- On Linux, set the environment variable `LC_ALL` before starting R:
+```
+export LC_ALL=en_US.UTF-8
+```
+
+- **RStudio crashes when trying to load a workspace.** The ospsuite package uses the features implemented in PK-Sim and MoBi by creating `.NET` objects (e.g. a simulation) and using them from R. These objects cannot be saved as part of the workspace and reloaded on next start. When trying to do so, RStudio simply crashes. There is no possibility to overcome this limitation. To prevent RStudio from crashing, make sure to disable the check-box "Restore `.RData` into workspace at startup" in the options of RStudio. Keep in mind that you can also change this setting for specific projects.
+
+# Code of Conduct
+
+Everyone interacting in the Open Systems Pharmacology community (codebases, issue trackers, chat rooms, mailing lists etc.) is expected to follow the Open Systems Pharmacology [code of conduct](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODE_OF_CONDUCT.md).
+
+# Contribution
+
+We encourage contribution to the Open Systems Pharmacology community. Before getting started please read the [contribution guidelines](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CONTRIBUTING.md). If you are contributing code, please be familiar with the [coding standards](https://github.com/Open-Systems-Pharmacology/Suite/blob/master/CODING_STANDARDS_R.md).
+
+# License
+
+OSPSuite-R is released under the [GPLv2 License](LICENSE).
+
+All trademarks within this document belong to their legitimate owners.
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 4f83dc5f3..34dd983d1 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -3,6 +3,9 @@ url: https://www.open-systems-pharmacology.org/OSPSuite-R/
template:
bootstrap: 5
+development:
+ mode: devel
+
authors:
Indrajeet Patil:
href: https://sites.google.com/site/indrajeetspatilmorality/
@@ -20,6 +23,13 @@ articles:
- sensitivity-analysis
- create-individual
- create-run-population
+ - title: Figure creation
+ navbar: Figure creation
+ desc: How to create standard figures
+ contents:
+ - observed-data
+ - data-combined
+ - data-combined-plotting
- title: Miscellaneous
navbar: Miscellaneous
diff --git a/appveyor-3.6.yml b/appveyor-3.6.yml
index bb49deedf..342b75fdb 100644
--- a/appveyor-3.6.yml
+++ b/appveyor-3.6.yml
@@ -1,10 +1,13 @@
image: Visual Studio 2019
-version: '{build}'
+# uncomment to use global ospsuite version (and comment line underneath)
+# version: '{build}'
+version: '11.1.{build}'
# Download script file from GitHub
init:
- - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
+# uncomment to use global ospsuite version
+# - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
- ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
diff --git a/appveyor-nightly.yml b/appveyor-nightly.yml
index 7087fe3cf..49a70fa6d 100644
--- a/appveyor-nightly.yml
+++ b/appveyor-nightly.yml
@@ -1,10 +1,13 @@
image: Visual Studio 2019
-version: '{build}'
+# uncomment to use global ospsuite version (and comment line underneath)
+# version: '{build}'
+version: '11.1.{build}'
# Download script file from GitHub
init:
- - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
+# uncomment to use global ospsuite version
+# - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
- ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
@@ -17,12 +20,14 @@ install:
platform: x64
+ #We use this set of variables to bypass issue with PK-Sim build. This should be removed when dealt with
environment:
USE_RTOOLS: true
NOT_CRAN: true
KEEP_VIGNETTES: true
R_ARCH: x64
R_VERSION: 4.1.0
+ R_CHECK_ARGS: --no-multiarch --no-manual --as-cran
COVERALLS_TOKEN:
secure: xIz/WZT0ex3bs/CMBJTzzdXLhl3sqfSqJ3MshlSY03pZKuyYQN7Z1FprVgnlFMUZ
diff --git a/appveyor.yml b/appveyor.yml
index d03acde21..0ba880287 100644
--- a/appveyor.yml
+++ b/appveyor.yml
@@ -1,10 +1,14 @@
image: Visual Studio 2019
-version: '{build}'
+
+# uncomment to use global ospsuite version (and comment line underneath)
+# version: '{build}'
+version: '11.1.{build}'
# Download script file from GitHub
init:
- - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
+# uncomment to use global ospsuite version
+# - ps: Update-AppveyorBuild -Version "$($env:ospsuite_version).$($env:appveyor_build_version)"
- ps: |
$ErrorActionPreference = "Stop"
Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
@@ -19,7 +23,8 @@ environment:
USE_RTOOLS: true
NOT_CRAN: true
KEEP_VIGNETTES: false
- R_BUILD_ARGS: --no-build-vignettes --no-manual"
+ R_BUILD_ARGS: --no-build-vignettes --no-manual
+ R_CHECK_ARGS: --no-multiarch --no-manual --as-cran
R_ARCH: x64
R_VERSION: 4.1.0
#We use this variale to skip some long lasting tests using "skip_on_ci"
@@ -31,7 +36,7 @@ build_script:
- Rscript -e "install.packages('https://github.com/Open-Systems-Pharmacology/rClr/releases/download/v0.9.1/rClr_0.9.1.zip', repos = NULL, type = 'binary')"
- Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/ospsuite-rutils/artifacts/ospsuite.utils.zip', repos = NULL, type = 'binary')"
- Rscript -e "install.packages('https://ci.appveyor.com/api/projects/open-systems-pharmacology-ci/tlf-library/artifacts/tlf.zip', repos = NULL, type = 'binary')"
- - Rscript -e "install.packages(c('ggplot2', 'patchwork', 'vdiffr'), repos = 'http://cran.us.r-project.org')"
+ - Rscript -e "install.packages(c('ggplot2', 'patchwork', 'vdiffr', 'spelling'), repos = 'http://cran.us.r-project.org')"
test_script:
- travis-tool.sh run_tests
@@ -40,6 +45,9 @@ on_failure:
- 7z a failure.zip *.Rcheck\*
- appveyor PushArtifact failure.zip
+on_success:
+ - Rscript -e "spelling::spell_check_package()"
+
artifacts:
- path: '*.Rcheck\**\*.log'
name: Logs
diff --git a/dimensions b/dimensions
index b5df4d288..a31290e1a 160000
--- a/dimensions
+++ b/dimensions
@@ -1 +1 @@
-Subproject commit b5df4d288df8a05d3255dadb8268793b86aecd4c
+Subproject commit a31290e1a6d49c1f874762e7fec8c909bc230062
diff --git a/docs/404.html b/docs/404.html
index 88b08d41c..e927a1df4 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -7,8 +7,8 @@