Data and R code used in Lenk et al. "Regeneration dynamics in response to an openness gradient caused by ash dieback, drought effects and understorey forest management in a meliorated European floodplain forest"

This repository contains the R project Natural_regeneration_Leipzig_floodplain, including the R code and associated data required to reproduce the analyses and visualisations presented in the manuscript “Regeneration dynamics in response to an openness gradient caused by ash dieback, drought effects and understorey forest management in a meliorated European floodplain forest” (2026) by Lenk, A., Hanfstängl, H., Waha, S. and Wirth, C., Journal of Forest Ecology and Management, doi.org/10.1016/j.foreco.2026.123791. Folder structure The repository is organised as an R project (Natural_regeneration_Leipzig_floodplain.Rproj). Opening the project in RStudio ensures that the working directory is set correctly and that all scripts can access the data and folders using relative paths. DATAThe repository includes the following datasets together with accompanying metadata and data descriptions:nr_canopy_data_2022_2023.xlsxnr_openness_2022_2023.xlsxnr_regeneration_data_2022_2023.xlsxnr_resprouts_maple_elder_2022.xlsx R SCRIPTSThe analysis workflow is organised into several scripts that should be executed in numerical order:00-preamble.R Loads all required R packages.01-data_carpentry.R Imports the datasets and prepares the data subsets used for subsequent analyses.02-species_composition_and_forest_structure.R Describes tree species composition in the canopy and regeneration layers and evaluates vitality status.03-growth-analyses.R Contains regression analyses of height and radial growth of eight deciduous forest tree species along an openness gradient.04-vitality-analyses.R Contains regression analyses of binomial vitality responses of the same tree species along the openness gradient during drought conditions (2022) and climatically moderate conditions (2023). REPRODUCIBILITYInformation on the software and package versions used in the analyses:R version 4.4.0 (2024-04-24 ucrt)Platform: x86_64-w64-mingw32/x64Running under: Windows 11 x64 (build 26100)Matrix products: Default locale:[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C [5] LC_TIME=German_Germany.utf8 time zone: Europe/Berlintzcode source: internal attached base packages:[1] grid stats graphics grDevices datasets utils methods base other attached packages: [1] see_0.13.0 gridExtra_2.3 ggforce_0.5.0 arm_1.14-4 [5] DHARMa_0.4.7 ggeffects_2.2.0 ggpubr_0.6.0 interactions_1.2.0 [9] glmmTMB_1.1.10 multcomp_1.4-28 TH.data_1.1-3 MASS_7.3-60.2 [13] survival_3.5-8 mvtnorm_1.2-5 ggtext_0.1.2 ggh4x_0.3.1 [17] cowplot_1.1.3 car_3.1-3 carData_3.0-5 sjPlot_2.8.17 [21] ggrepel_0.9.6 ggalluvial_0.12.5 patchwork_1.3.2 broom.mixed_0.2.9.6[25] MuMIn_1.48.4 rptR_0.9.22 performance_0.16.0 lmerTest_3.1-3 [29] emmeans_1.10.7 lme4_1.1-36 Matrix_1.7-0 openxlsx_4.2.8 [33] readxl_1.4.3 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1 [37] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.1 [41] tibble_3.2.1 ggplot2_4.0.2 tidyverse_2.0.0 here_1.0.1 loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.17.1 datawizard_1.3.0 magrittr_2.0.3 [5] estimability_1.5.1 rmarkdown_2.29 farver_2.1.2 nloptr_2.1.1 [9] vctrs_0.6.5 minqa_1.2.8 rstatix_0.7.2 htmltools_0.5.8.1 [13] haven_2.5.4 broom_1.0.7 cellranger_1.1.0 Formula_1.2-5 [17] sjmisc_2.8.10 parallelly_1.42.0 plyr_1.8.9 pbkrtest_0.5.3 [21] sandwich_3.1-1 zoo_1.8-12 TMB_1.9.16 commonmark_1.9.2 [25] mime_0.12 iterators_1.0.14 lifecycle_1.0.4 pkgconfig_2.0.3 [29] gap_1.6 fastmap_1.2.0 sjlabelled_1.2.0 R6_2.6.1 [33] shiny_1.10.0 rbibutils_2.3 future_1.34.0 digest_0.6.35 [37] numDeriv_2016.8-1.1 ggnewscale_0.5.0 furrr_0.3.1 rprojroot_2.0.4 [41] qgam_1.3.4 labeling_0.4.3 timechange_0.3.0 polyclip_1.10-7 [45] abind_1.4-8 mgcv_1.9-3 compiler_4.4.0 doParallel_1.0.17 [49] withr_3.0.2 pander_0.6.5 S7_0.2.0 backports_1.5.0 [53] ggsignif_0.6.4 sjstats_0.19.0 tools_4.4.0 httpuv_1.6.15 [57] zip_2.3.2 glue_1.7.0 promises_1.3.2 nlme_3.1-164 [61] gridtext_0.1.5 generics_0.1.3 gtable_0.3.6 tzdb_0.4.0 [65] hms_1.1.3 utf8_1.2.4 xml2_1.3.6 foreach_1.5.2 [69] pillar_1.10.1 markdown_1.13 later_1.4.1 splines_4.4.0 [73] tweenr_2.0.3 lattice_0.22-6 renv_1.2.0 tidyselect_1.2.1 [77] knitr_1.49 reformulas_0.4.0 stats4_4.4.0 xfun_0.51 [81] stringi_1.8.4 yaml_2.3.10 boot_1.3-30 evaluate_1.0.3 [85] codetools_0.2-20 cli_3.6.2 xtable_1.8-4 parameters_0.28.3 [89] Rdpack_2.6.2 Rcpp_1.0.12 globals_0.16.3 coda_0.19-4.1 [93] parallel_4.4.0 bayestestR_0.17.0 gap.datasets_0.0.6 listenv_0.9.1 [97] scales_1.4.0 insight_1.4.6 crayon_1.5.3 rlang_1.1.3 [101] jtools_2.3.0 ContactPlease contact me at [e-mail] if you have further questions.