Last updated: 2019-05-23

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Hyperparameter tuning and performance assessment of statistical and machine-learning models using spatial data.

1 Authors

Patrick Schratz (patrick.schratz@gmail.com)
Jannes Muenchow
Eugenia Iturritxa
Jakob Richter
Alexander Brenning

2 Contents

This repository contains the research compendium of the above mentioned paper.

In addition, it contains code and results for the LIFE Healthy Forest project. The following reports are available:

3 How to use

3.1 Read the code, access the data

See the code directory on GitHub for the source code that generated the figures and statistical results contained in the manuscript. The raw data is stored on Zenodo and will be downloaded when starting the analysis.

3.2 Install the R package

This repository is organized as an R package, providing functions and raw data to reproduce and extend the analysis reported in the publication. Note that this package has been written explicitly for this project and may not be suitable for general use.

This project is setup with a drake workflow, ensuring reproducibility. Intermediate targets/objects will be stored in a hidden .drake directory.

The R library of this project is managed by packrat. This makes sure that the exact same package versions are used when recreating the project. When calling packrat::restore(), all required packages will be installed with their specific version.

Please note that this project was built with R version 3.5.1 on a CentOS 7.5 operating system. The packrat packages from this project are not compatible with R versions prior version 3.5.0. (In general, it should be possible to reproduce the analysis on any other operating system.)

To clone the project, a working installation of git is required. Open a terminal in the directory of your choice and execute:

git clone git@github.com:pat-s/pathogen-modeling.git

Then start R in this directory and run

packrat::restore() # restores all R packages with their specific version
r_make() # recreates the analysis

4 Structure of the analysis

In the drake philosophy, every R object is a “target” with dependencies. This repository contains more targets than actually needed to replicate the associated publication.

If you want to replicate the publication, you need to build the following targets:

benchmark_diplodia (Benchmark report for pathogen Diplodia sapinea)
vis_opt_paths(Optimization path figure)
vis_tuning_effects (Tuning effects figure)
vis_partitions (Partition figure)

Please note that the attached runtime of these targets are derived from a parallel execution on a HPC with 16 cores (AMD Threadripper 2950X) and 126 GB RAM (DDR4) per node. Reproducing these targets sequentially on a local machine might take weeks.

4.0.0.1 Other practical notes

All “diplodia” targets (bm_sp_sp_diplodia, bm_sp_nsp_diplodia and bm_nsp_nsp_diplodia) are built with mlr::benchmark(keep.extract = TRUE) in benchmark_custom. This slot is needed to perform analysis on the tuning results. All other pathogens are built with mlr::benchmark(keep.extract = FALSE) to save disk space of the resulting R objects. BMR + tuning results = ~ 3 GB, BMR - tuning results = xx MB.

5 Notes and resources

The issues tracker is the place to report problems or ask questions
See the repository history for a fine-grained view of progress and changes.
The structure of this compendium is based on the work of Carl Boettiger, Ben Marwick and the workflowr package.

sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/openblas-0.3.5-zncvk4jccaqyfl4z3vszaboeps6hyzta/lib/libopenblas_zen-r0.3.5.so

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
 [1] workflowr_1.3.0 Rcpp_1.0.0      digest_0.6.15   rprojroot_1.3-2
 [5] backports_1.1.2 git2r_0.23.0    magrittr_1.5    evaluate_0.13  
 [9] stringi_1.2.4   fs_1.2.6        whisker_0.3-2   rmarkdown_1.12 
[13] tools_3.5.1     stringr_1.3.1   glue_1.3.0      xfun_0.7       
[17] yaml_2.2.0      compiler_3.5.1  htmltools_0.3.6 knitr_1.23

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