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Companion code for Bird seasonal beta-diversity in the contiguous United States.
Author : Charles A. Martin
Contact : charles.martin1@uqtr.ca
Affiliation : Université du Québec à Trois-Rivières
About
This repository contains all code necessary to reproduce the results from Bird seasonal beta-diversity in the contiguous United States, as published in Journal of Ornithology
Structure
All analysis code is in the scripts folder, along with the database preparation script (the latest database, as of the publication of the paper, is already in the data folder).
Necessary environment
The code provided was developed and tested under the following R environment :
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.4
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] maps_3.1.1 egg_0.1.0 gridExtra_2.2.1 modelr_0.1.0
[5] testthat_1.0.2 raster_2.5-8 sp_1.2-4 betapart_1.4-1
[9] vegan_2.4-2 lattice_0.20-34 permute_0.9-4 stringr_1.2.0
[13] rebird_0.4.0 memoise_1.1.0 MuMIn_1.15.6 dplyr_0.5.0
[17] purrr_0.2.2 readr_1.0.0 tidyr_0.6.1 tibble_1.2
[21] ggplot2_2.2.1 tidyverse_1.1.1
loaded via a namespace (and not attached):
[1] reshape2_1.4.2 haven_1.0.0 colorspace_1.3-2 geometry_0.3-6
[5] stats4_3.3.2 mgcv_1.8-17 foreign_0.8-67 DBI_0.5-1
[9] readxl_0.1.1 plyr_1.8.4 munsell_0.4.3 gtable_0.2.0
[13] rvest_0.3.2 psych_1.6.12 labeling_0.3 forcats_0.2.0
[17] magic_1.5-6 rcdd_1.1-13 parallel_3.3.2 broom_0.4.2
[21] Rcpp_0.12.9 scales_0.4.1 jsonlite_1.3 picante_1.6-2
[25] mnormt_1.5-5 hms_0.3 digest_0.6.12 stringi_1.1.2
[29] rgdal_1.2-5 tools_3.3.2 magrittr_1.5 lazyeval_0.2.0
[33] cluster_2.0.5 crayon_1.3.2 ape_4.1 MASS_7.3-45
[37] Matrix_1.2-8 xml2_1.1.1 lubridate_1.6.0 assertthat_0.1
[41] httr_1.2.1 R6_2.2.0 nlme_3.1-131
Additional acknowledgements
As this paper was published as a short communication with a maximum of 15 references, it was not possible to ackowledge the quality of the R developers involved in the development and maintenance of all these wonderful packages with citations.
Nevertheless, without your dedicated work, none of this would have been possible.