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README.md

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Install RMixtComp

RMixtComp is the main R package for using the MixtComp C++ library. It loads RMixtCompIO and RMixtCompUtilities that contain the MixtComp C++ library and utility functions.

RMixtComp is available as an Rstudio project (RMixtComp.Rproj) to facilitate development and testing.

You can download it from CRAN in an R console:

install.packages("RMixtComp", repos = "https://cran.rstudio.com")

Requirements

R

R must be installed, along with the following packages from the CRAN: RcppEigen, BH, plotly, scales, doParallel, foreach and packages from these directories: RMixtCompIO and RMixtCompUtilities. Several packages are used for testing but are not required for installing RMixtComp: testthat is used to perform unit testing in R, xml2 for xml report, RInside is used for testing procedure in C++ using R command, roxygen2 is required for generating the documentation, knitr for generating vignettes and devtools (with roxygen2) is required to load all functions of RMixtComp on the CI server.

  1. Install R from terminal or download it from R-project:

    sudo apt install r-base

  2. Install required R packages

    Packages are required from Ubuntu repositories:

    sudo apt install libssl-dev libcurl4-openssl-dev libxml2-dev

    Install required R packages from terminal:

    Rscript -e "install.packages(c(\"plotly\", \"scales\", \"BH\", \"RcppEigen\", \"doParallel\", \"foreach\"), repos = \"https://cran.rstudio.com\")"
# OPTIONAL: for testing purpose
Rscript -e "install.packages(c(\"testthat\", \"RInside\", \"xml2\", \"devtools\", \"roxygen2\", \"Rmixmod\", \"knitr\", \"ClusVis\"), repos = \"https://cran.rstudio.com\")"

    from R:

    install.packages(c("plotly", "scales", "BH", "RcppEigen", "doParallel", "foreach"), repos = "https://cran.rstudio.com")
# OPTIONAL: for testing purpose
install.packages(c("testthat", "RInside", "xml2", "devtools", "roxygen2", "Rmixmod", "knitr", "ClusVis"), repos = "https://cran.rstudio.com")

  3. Install RMixtCompIO

    cd ../RMixtCompIO
./build.sh

  4. Install RMixtCompUtilities

    cd ../RMixtCompUtilities
R CMD INSTALL  --no-multiarch --with-keep.source .

Windows

Compiling R packages requires Rtools.

Build and install

Run in the current location (./RMixtComp/ folder):

R CMD INSTALL  --no-multiarch --with-keep.source .

Testing procedures

Test the R package

Tests are implemented in the tests/testthat folder of RMixtComp. They require the testthat package.

You can run tests via R:

library(RMixtComp)
library(testthat)
library(devtools)
load_all()
test_dir("tests/testthat/")

or

library(methods);
library(devtools);
options(testthat.output_file = "RMCtest.xml");
test(".", reporter = JunitReporter)

but it requires the xml2 package and generates a xml report file named RMCtest.xml.

Via shell:

Rscript -e 'library(methods); library(devtools); options(testthat.output_file = "RMCtest.xml"); test(".", reporter = JunitReporter)'

In Rstudio, if packages devtools and testthat are installed, you can run the testing procedure by pressing CRTL + SHIFT + T or tests are run during a R CMD check CRTL + SHIFT + E.

Write new tests

For your own testing procedure, you can use the data and model provided in the package, you can load them in R:

data(simData)

Or you can generate your own data using dataGeneratorNewIO function (from files R/GENDATA_dataGeneratorNewIO.R) for example.

See functions in files R/TEST_*.R for creating a parameter object for each type of data. Have a look at tests/testthat/test.run.R for writing a test with testthat.