rekyt/mamm_funrar

Tutorial to compute functional rarity indices with funrar using North American Mammals

North and Central American Mammals Functional Rarity Read Me

Matthias Grenié, Pierre Denelle, Caroline Tucker, François Munoz and Cyrille Violle 2017-03-20

Goal

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.

How to run

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()

Organization

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.

Dependencies

The analysis strongly depends on several packages:

• remake to make the analysis portable and reproducible,
• dplyr for data wrangling,
• rdryad to download the data from Dryad,
• rmarkdown to generate the analysis report,
• vegan to compute null models for site-species matrix,
• ggplot2 to plot figures in reports,
• devtools for session info diagnostics,
• funrar to compute functional rarity indices.

Session Info

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)

References

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.