DOI: 10.5281/zenodo.3784333
title: Data and code for the paper: Trait-based responses to forestry and grazing modify long-term changes in biodiversity hot-spots of boreal forests

description: <strong>Data and code for the paper "Trait-based responses to forestry and grazing modify long-term changes in biodiversity hot-spots of boreal forests"</strong> See the preprint. The script src/analyysit.R can be used to reproduce all modelling results of the paper. Among other variables, this repository contains ready-calculated community characteristics (results/clean_data/data_for_analyses/kaik.csv: species richness, Shannon diversity, species evenness, height, LDMC, SLA) and their temporal changes along with temporal Jaccard distance between 1968–1975 and 2013–2019 (results/clean_data/data_for_analyses/erot.csv) for 245 5 m x 5 m plots of field-layer vegetation. Information is also included on tree-layer SLA and canopy cover for 10 m x 10 m plots directly above them. Each plot is classified as being either inside or outside the reindeer herding area, and belonging to one of four levels of management intensity. For more information, see the paper. This repository does not contain information on reindeer densities, which we do not have permission to publish. Furhermore, community data are not included, but are available from the authors upon request. Community data will be submitted to an open repository at a later date. Original trait data are from TRY and LEDA, supplemented with our own measurements. Climate data are from TerraClimate. ## References<br> Abatzoglou, John T., Solomon Z. Dobrowski, Sean A. Parks, and Katherine C. Hegewisch. 2018. “TerraClimate, a High-Resolution Global Dataset of Monthly Climate and Climatic Water Balance from 1958-2015.” Scientific Data 5 (January): 170191. Kattge, Jens, S. Díaz, S. Lavorel, I. C. Prentice, P. Leadley, G. Bönisch, E. Garnier, et al. 2011. “TRY - a Global Database of Plant Traits.” Global Change Biology 17 (9): 2905–35. Kleyer, M., R. M. Bekker, I. C. Knevel, J. P. Bakker, K. Thompson, M. Sonnenschein, P. Poschlod, et al. 2008. “The LEDA Traitbase: A Database of Life-History Traits of the Northwest European Flora.” The Journal of Ecology 96 (6): 1266–74. <br> ## Session Info<br> The results were reproducible under this setup: R version 3.6.2 (2019-12-12)<br> Platform: x86_64-pc-linux-gnu (64-bit)<br> Running under: Ubuntu 19.10 Matrix products: default<br> BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0<br> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0 locale:<br> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=fi_FI.UTF-8 LC_COLLATE=en_US.UTF-8 <br> [5] LC_MONETARY=fi_FI.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=fi_FI.UTF-8 LC_NAME=C <br> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=fi_FI.UTF-8 LC_IDENTIFICATION=C attached base packages:<br> [1] grid stats graphics grDevices utils datasets methods base other attached packages:<br> [1] gridExtra_2.3 cowplot_1.0.0 scales_1.1.0 kableExtra_1.1.0 ggthemes_4.2.0 tidybayes_2.0.1 <br> [7] rgdal_1.4-8 sp_1.3-2 broom_0.5.3 brms_2.10.0 Rcpp_1.0.3 gratia_0.2-8 <br> [13] mgcv_1.8-31 nlme_3.1-143 vegan_2.5-6 lattice_0.20-38 permute_0.9-5 forcats_0.4.0 <br> [19] stringr_1.4.0 dplyr_0.8.3 purrr_0.3.3 readr_1.3.1 tidyr_1.0.0 tibble_2.1.3 <br> [25] ggplot2_3.2.1 tidyverse_1.3.0 loaded via a namespace (and not attached):<br> [1] colorspace_1.4-1 ellipsis_0.3.0 ggridges_0.5.1 rsconnect_0.8.16 <br> [5] markdown_1.1 base64enc_0.1-3 fs_1.3.1 rstudioapi_0.10 <br> [9] farver_2.0.1 rstan_2.19.2 svUnit_0.7-12 DT_0.11 <br> [13] fansi_0.4.1 mvtnorm_1.0-12 lubridate_1.7.4 xml2_1.2.2 <br> [17] bridgesampling_0.7-2 splines_3.6.2 knitr_1.26 shinythemes_1.1.2 <br> [21] zeallot_0.1.0 bayesplot_1.7.1 jsonlite_1.6 cluster_2.1.0 <br> [25] dbplyr_1.4.2 shiny_1.4.0 compiler_3.6.2 httr_1.4.1 <br> [29] backports_1.1.5 assertthat_0.2.1 Matrix_1.2-18 fastmap_1.0.1 <br> [33] lazyeval_0.2.2 cli_2.0.1 later_1.0.0 htmltools_0.4.0 <br> [37] prettyunits_1.1.0 tools_3.6.2 igraph_1.2.4.2 coda_0.19-3 <br> [41] gtable_0.3.0 glue_1.3.1 reshape2_1.4.3 cellranger_1.1.0 <br> [45] vctrs_0.2.1 crosstalk_1.0.0 xfun_0.11 ps_1.3.0 <br> [49] rvest_0.3.5 mime_0.8 miniUI_0.1.1.1 lifecycle_0.1.0 <br> [53] gtools_3.8.1 MASS_7.3-51.5 zoo_1.8-7 colourpicker_1.0 <br> [57] hms_0.5.3 promises_1.1.0 Brobdingnag_1.2-6 parallel_3.6.2 <br> [61] inline_0.3.15 shinystan_2.5.0 loo_2.2.0 StanHeaders_2.19.0 <br> [65] stringi_1.4.5 dygraphs_1.1.1.6 boot_1.3-24 pkgbuild_1.0.6 <br> [69] rlang_0.4.2 pkgconfig_2.0.3 matrixStats_0.55.0 evaluate_0.14 <br> [73] labeling_0.3 rstantools_2.0.0 htmlwidgets_1.5.1 tidyselect_0.2.5 <br> [77] processx_3.4.1 plyr_1.8.5 magrittr_1.5 R6_2.4.1 <br> [81] generics_0.0.2 DBI_1.1.0 pillar_1.4.3 haven_2.2.0 <br> [85] withr_2.1.2 xts_0.11-2 abind_1.4-5 modelr_0.1.5 <br> [89] crayon_1.3.4 arrayhelpers_1.0-20160527 utf8_1.1.4 rmarkdown_2.0 <br> [93] readxl_1.3.1 callr_3.4.0 threejs_0.3.1 webshot_0.5.2 <br> [97] reprex_0.3.0 digest_0.6.23 xtable_1.8-4 httpuv_1.5.2 <br> [101] stats4_3.6.2 munsell_0.5.0 viridisLite_0.3.0 shinyjs_1.0