Git repository for the paper 'Ecotoxicology is not normal.'
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Readme.md

Ecotoxicology is not normal.

A comparison of statistical approaches for analysis of count and proportion data in ecotoxicology.

Online repository for the paper submitted to Environmental Science and Pollution Research

Authors

Eduard Szöcs, Ralf B. Schäfer

Final Manuscript

Can be found here.

Poster

Can be found here.

Structure of this repository

  • ~/cache/ : cached files (simulation results)
  • ~/manuscript/ : manuscript files (LaTeX) - including review process
  • ~/packrat/ : packrat library
  • ~/poster : files for poster presentation at SETAC Europen in Barcelona
  • ~/src/ : Source code (R)
  • ~/supplement/: Supplementary material (LaTeX)

Structure of ~/src/

R code has been written hierarchically, that is scripts must be run in a specific order.

  • ~/0-load.R : Defines the project structure, loads packages, sources functions and sets some switches. This script has to be run first!
  • ~/0-functions.R : Custom functions needed for the simulations
  • ~/1-simulations.R : Run simulations
  • ~/2-results.R : Compile results
  • ~/3-brock.R : Script for the case study

How to reproduce the results

  1. Download ('Download ZIP') this repository.
  2. Extract the zip file.
  3. Uncomment and point the path in ~/0-load.R, Lines 8-11 to the extracted folder.
  4. source ~/0-load.R to setup the project
  5. (optional) Set options in load.R, see Notes below.
  6. source ~/2-results.R to compile the results

Notes

We added a snapshot of all used packages using packrat to this repo. packrat will try to install these packages from the snapshot on first start of R from this repository.

~/0-load.R contains some switches (at the end of the file):

  • the count data simulations took ~ 12 hours on a amazon EC2 c3.2xlarge instance.
  • If the switches sim1 and sim2 are set to FALSE, the simulations results are grabbed from cache. Otherwise, the actual simulation will run.
  • Clearly, most time is consumed for bootstrap, set pb = FALSE to omit it and save a lot of computation time.
  • simulations can be run in parallel, set parallel = TRUE to use the parallel package for parallelization.

Information about the R Environment used

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

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

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

other attached packages:
[1] survival_2.38-1 MASS_7.3-39     ggplot2_1.0.0   reshape2_1.4.1 

loaded via a namespace (and not attached):
 [1] codetools_0.2-11 colorspace_1.2-6 digest_0.6.8     gtable_0.1.2     htmltools_0.2.6  lattice_0.20-30  munsell_0.4.2    packrat_0.4.3    plyr_1.8.1
[10] proto_0.3-10     Rcpp_0.11.5      rmarkdown_0.5.1  sandwich_2.3-2   scales_0.2.4     splines_3.1.3    stringr_0.6.2    tools_3.1.3      zoo_1.7-11