devel/README.md

In schw4b/multdyn: Dynamic Graphical Models

Developer Guide

Manuals

• Rcpp: https://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-package.pdf
• RcppArmadillo: http://dirk.eddelbuettel.com/code/rcpp.armadillo.html

Working with Github

Check out master

git clone https://github.com/schw4b/DGM.git

Configure ssh key authentication

git remote set-url origin [e-mail]:schw4b/DGM.git

Switch to develop branch

git checkout develop

Review, pull, commit and push

git status
git diff
git pull
git add foo
git commit -m "Update"
git push origin develop

Merge develop to master

First, update DESCRIPTION file with new version

git checkout master
git pull               # to update the state to the latest remote master state
git merge develop      # to bring changes to local master from your develop branch
git push origin master # push current HEAD to remote master branch

Package building for CRAN

Required packages

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

install.packages("devtools")
install.packages("roxygen2")
install.packages("testthat")

Install these packages if you have not installed DGM before.

install.packages("data.table")
install.packages("reshape2")
install.packages("ggplot2")
install.packages("RcppArmadillo")

Build a new package from the develop branch

Get DGM and change to develop branch

git clone https://github.com/schw4b/DGM.git
cd DGM
git checkout develop
cd ..
cp DGM/devel/Makefile .

For first time building, you may need these packages installed:

apt-get install liblapack-dev libblas-dev

Build the package

make clean
cd DGM; R -e 'devtools::document()'; cd ..
make namespace
make build
make file=DGM_1.7.tar.gz check

Install and test in R

detach("package:DGM", unload=TRUE)

R CMD REMOVE DGM
R CMD INSTALL DGM_1.7.tar.gz
R

library(DGM)
data(utestdata)
result=exhaustive.search(myts,3)

Unit Testing

Test functions are written for the testthat package and can be found in the folder tests. These tests do not have to be run manually as shown below, as they are run during the package building make check

library(devtools)
library(testthat)
load_all('~/workspace/DGM')
# Run unit tests
test_dir('~/workspace/DGM/tests', reporter = 'Summary')

Run benchmarks

library(devtools)
library(microbenchmark)
load_all('~/workspace/DGM')
data("utestdata")
microbenchmark(exhaustive.search(myts,3,cpp=F),exhaustive.search(myts,3), times=1)

Output:

 Unit: milliseconds
                            expr       min        lq      mean    median
exhaustive.search(myts, 3, cpp = F) 7405.6748 7405.6748 7405.6748 7405.6748
         exhaustive.search(myts, 3)  238.3177  238.3177  238.3177  238.3177

30-fold speed improvement of the C++ function compared to R.

Travis CI

The new version of Rcpp requires a higher version of g++. This can bes specified in .travis.yml. These lines will switch to a higher Ubuntu version with a newer g++/gcc version:

# Ubuntu 14.04 Trusty support
sudo: required
dist: trusty

Resolve CRAN complaints (obsolete)

As with the new Rcpp version this does not seem to be necessary anymore and I have removed it.

Following problem occured: https://github.com/RcppCore/Rcpp/issues/636

Download R-devel.tar.gz from https://cran.r-project.org/sources.html

mkdir ~/tmp
cd ~/tmp
wget https://stat.ethz.ch/R/daily/R-devel.tar.gz
tar -xvf R-devel.tar.gz

Then, in R, do the following:

source("~/tmp/R-devel/src/library/tools/R/sotools.R")
source("~/tmp/R-devel/src/library/tools/R/utils.R")
setwd("~/workspace/DGM")

package_native_routine_registration_skeleton(".")

The function will output some code, copy and paste this to src/register.c

#include <R.h>
#include <Rinternals.h>
#include <stdlib.h> // for NULL
#include <R_ext/Rdynload.h>

/* FIXME:
   Check these declarations against the C/Fortran source code.
*/

/* .Call calls */
extern SEXP DGM_dlmLplCpp(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP);

static const R_CallMethodDef CallEntries[] = {
    {"DGM_dlmLplCpp", (DL_FUNC) &DGM_dlmLplCpp, 7},
    {NULL, NULL, 0}
};

void R_init_DGM(DllInfo *dll)
{
    R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
    R_useDynamicSymbols(dll, FALSE);
}

Finally, this needs to go into NAMESPACE, see Makefile.

useDynLib(packagename, .registration = TRUE).

schw4b/multdyn documentation built on Dec. 14, 2021, 7:39 a.m.