ManyEcoEvo

The ManyEcoEvo package provides a suite of functions for:

Summarising, analysing and visualising the ManyEcoEvo dataset from Gould et al.[^1]
Tidying and cleaning many-analyst style data for further analysis
Reproducing the analysis in Gould et al. using your own many-analyst style data

Note that the manuscript source-code for Gould et al. is located in a separate repository at https://github.com/egouldo/ManyAnalysts, which can be viewed at https://egouldo.github.io/ManyAnalysts/.

Installation

ManyEcoEvo:: can be installed using devtools:: from GitHub with:

devtools::install_github("egouldo/ManyEcoEvo")

Regenerating the ManyEcoEvo dataset

The data processing and analysis can be freely reproduced with the help of the targets:: package. Please see the documentation at https://docs.ropensci.org/targets/ for further detail.

Should you wish to completely reproduce the dataset generation and analysis in Gould et al., complete the following steps:

Clone or download https://github.com/egouldo/this repository
Run renv::restore() to load the packages used in the analysis pipeline locally on your machine (see renv:: for details)
Run targets::tar_destroy() to remove any record and caches of existing targets
Run targets::tar_make() in your console, depending on the power of your machine, the analysis pipeline will take between 2 and 7 minutes to execute (plus or minus some!)
You can view a table of all targets in the pipeline by running targets::tar_meta()
To interact with objects or ‘targets’ within the analysis pipeline, call targest::tar_load() or targets::tar_read():

targets::tar_read("ManyEcoEvo")

# A tibble: 2 × 4
  dataset    data                diversity_data      estimate_type
  <chr>      <list>              <named list>        <chr>        
1 blue tit   <tibble [174 × 38]> <tibble [174 × 54]> Zr           
2 eucalyptus <tibble [128 × 38]> <tibble [128 × 61]> Zr

The script that generates datasets used in the ManyEcoEvo:: package is located in ManyEcoEvo/data-raw/tar_make.R.

License

This software is licensed with the GNU GPL 3 license.

Contributing

This package is released with a Contributor Code of Conduct.

Citation

To cite package ‘ManyEcoEvo’ in publications use:

  Gould E, Fraser H, Nakagawa S, Parker T (2023). _ManyEcoEvo: Meta-analyse
  data from 'Many-Analysts' style studies_. R package version 1.0.0,
  <https://github.com/egouldo/ManyEcoEvo>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {ManyEcoEvo: Meta-analyse data from 'Many-Analysts' style studies},
    author = {Elliot Gould and Hannah S. Fraser and Shinichi Nakagawa and Timothy H. Parker},
    year = {2023},
    note = {R package version 1.0.0},
    url = {https://github.com/egouldo/ManyEcoEvo},
  }

[^1]: Gould, E., Fraser, H., Parker, T. et al. (2023). Same data, different analysts: Variation in effect sizes due to analytical decisions in ecology and evolutionary biology [Preprint]. Ecology and Evolutionary Biology. https://doi.org/10.32942/X2GG62

egouldo / ManyEcoEvo