Matthias Grenié, Pierre Denelle, Caroline Tucker, François Munoz and Cyrille Violle 2017-03-20
This repository contains a worked through example of the use of funrarR package in the context of biogeography using a publicly available dataset on North and Central American mammals (Lawing et al. 2016b; Lawing et al. 2016a). The functional traits are taken from (Jones et al. 2009) database.
The dataset is available through Dryad there: doi:10.5061/dryad.9t0n8.
The functional traits metadata are available on the Ecological Archives Repository.
The repository is self-contained and can be used to automatically download see How to run section and compute the figures shown in the submitted manuscript.
To run the analysis on your computer, install remake (see Dependencies section), move to the project directory and run:
remake::make()
You will see the full analysis run on your computer, it can take as long as 15 minutes to run. And you will need to be connected to the internet at least to download the primary data files. With remake all the intermediate objects are viewable on a dependency graph:
remake::diagram()
The repository is organized with the scripts folder which contains R files to run the analysis. Each R file contains functions used in the remake.yml file for each step of the analysis.
The results folder contains the exploratory_analysis.Rmd file which sums up the results and plot graphs based on the computation done when running the scripts.
The data folder is created when downloading the datafiles.
The analysis strongly depends on several packages:
remaketo make the analysis portable and reproducible,dplyrfor data wrangling,rdryadto download the data from Dryad,rmarkdownto generate the analysis report,veganto compute null models for site-species matrix,ggplot2to plot figures in reports,devtoolsfor session info diagnostics,funrarto compute functional rarity indices.
The analysis ran using the following system and packages:
devtools::session_info()## Session info --------------------------------------------------------------
## setting value
## version R version 3.3.3 (2017-03-06)
## system x86_64, mingw32
## ui RStudio (1.0.136)
## language (EN)
## collate French_France.1252
## tz Europe/Warsaw
## date 2017-03-20
## Packages ------------------------------------------------------------------
## package * version date source
## assertthat 0.1 2013-12-06 CRAN (R 3.3.0)
## backports 1.0.5 2017-01-18 CRAN (R 3.3.2)
## brew 1.0-6 2011-04-13 CRAN (R 3.3.0)
## codetools 0.2-15 2016-10-05 CRAN (R 3.3.3)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.3.2)
## crayon 1.3.2 2016-06-28 CRAN (R 3.3.0)
## DBI 0.6 2017-03-09 CRAN (R 3.3.2)
## devtools 1.12.0 2016-06-24 CRAN (R 3.3.1)
## DiagrammeR 0.9.0 2017-01-04 CRAN (R 3.3.2)
## digest 0.6.12 2017-01-27 CRAN (R 3.3.2)
## dplyr * 0.5.0 2016-06-24 CRAN (R 3.3.1)
## evaluate 0.10 2016-10-11 CRAN (R 3.3.1)
## ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.3.2)
## gridExtra 2.2.1 2016-02-29 CRAN (R 3.3.0)
## gtable 0.2.0 2016-02-26 CRAN (R 3.3.0)
## htmltools 0.3.5 2016-03-21 CRAN (R 3.3.0)
## htmlwidgets 0.8 2016-11-09 CRAN (R 3.3.2)
## igraph 1.0.1 2015-06-26 CRAN (R 3.3.0)
## influenceR 0.1.0 2015-09-03 CRAN (R 3.3.1)
## jsonlite 1.3 2017-02-28 CRAN (R 3.3.2)
## knitr 1.15.1 2016-11-22 CRAN (R 3.3.2)
## lazyeval 0.2.0 2016-06-12 CRAN (R 3.3.0)
## magrittr 1.5 2014-11-22 CRAN (R 3.3.0)
## memoise 1.0.0 2016-01-29 CRAN (R 3.3.0)
## munsell 0.4.3 2016-02-13 CRAN (R 3.3.0)
## plyr 1.8.4 2016-06-08 CRAN (R 3.3.0)
## R6 2.2.0 2016-10-05 CRAN (R 3.3.1)
## RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.3.0)
## Rcpp 0.12.10 2017-03-19 CRAN (R 3.3.3)
## remake 0.2.0 2016-05-27 Github (richfitz/remake@d7164c7)
## rgexf 0.15.3 2015-03-24 CRAN (R 3.3.2)
## rmarkdown * 1.3.9004 2017-03-07 Github (rstudio/rmarkdown@e6cc75e)
## Rook 1.1-1 2014-10-20 CRAN (R 3.3.2)
## rprojroot 1.2 2017-01-16 CRAN (R 3.3.2)
## rstudioapi 0.6 2016-06-27 CRAN (R 3.3.0)
## scales 0.4.1 2016-11-09 CRAN (R 3.3.2)
## storr 1.0.1 2017-01-23 Github (richfitz/storr@4756931)
## stringi 1.1.2 2016-10-01 CRAN (R 3.3.1)
## stringr 1.2.0 2017-02-18 CRAN (R 3.3.2)
## tibble 1.2 2016-08-26 CRAN (R 3.3.1)
## viridis 0.3.4 2016-03-12 CRAN (R 3.3.0)
## visNetwork 1.0.3 2016-12-22 CRAN (R 3.3.2)
## webshot 0.4.0 2016-12-27 CRAN (R 3.3.2)
## withr 1.0.2 2016-06-20 CRAN (R 3.3.1)
## XML 3.98-1.5 2016-11-10 CRAN (R 3.3.2)
## yaml 2.1.14 2016-11-12 CRAN (R 3.3.2)
Jones, Kate E., Jon Bielby, Marcel Cardillo, Susanne A. Fritz, Justin O’Dell, C. David L. Orme, Kamran Safi, et al. 2009. “PanTHERIA: A Species-Level Database of Life History, Ecology, and Geography of Extant and Recently Extinct Mammals.” Ecology 90 (9): 2648–8. doi:10.1890/08-1494.1.
Lawing, A. Michelle, Jussi T. Eronen, Jessica L. Blois, Catherine H. Graham, and P. David Polly. 2016a. “Data from: Community Functional Trait Composition at the Continental Scale: The Effects of Non-Ecological Processes,” April. doi:10.5061/dryad.9t0n8.
———. 2016b. “Community Functional Trait Composition at the Continental Scale: The Effects of Non-Ecological Processes.” Ecography, June, n/a–n/a. doi:10.1111/ecog.01986.