Digital repository for: Wild ungulates and salvage logging modulate disturbance effects on moth communities in spruce-dominated forests

Repository containing R-script and data to reproduce analysis and main figures on the effect of forest disturbance and associated post-disturbance management on moth communities in the Harz Mountains, Germany.

R-script includes:

• calculation of a functional distance matrix based on moth trait characteristics (R package BAT; Cardoso et al., 2024)
• rarefaction and extrapolation of taxonomic and functional Hill numbers (R package iNEXT3D; Chao et al., 2021)
• generalized linear mixed models (R package glmmTMB; Brooks et al., 2023)
• non-metric multidimensional scaling (R package vegan; Oksanen et al., 2016)
• Supplementary analyses

Attached files:

• moth_data_Graser_et_al.csv contains the raw moth sampling data from the Harz Mountains for both sampling years.
• moth_diversity_data_plot_Graser_et_al.csv provides information on the sampling conditions, as well as the diversity and abundance measures, for each sampling night at a trapping location.
• env_matrix_21_Graser_et_al.csv (2021) and env_matrix_22_Graser_et_al.csv (2022) are datasets describing environmental variables for the respective sampling years.
• gower_dist.21_Graser_et_al.rda (2021) and gower_dist.22_Graser_et_al.rda (2022) are trait-based Gower distance matrices for the respective sampling years.
• incidence_moth_TD_21_Graser_et_al.rds (dataset for taxonomic diversity 2021), incidence_moth_TD_22_Graser_et_al.rds (dataset for taxonomic diversity 2022), incidence_moth_FD_21_Graser_et_al.rds dataset for functional diversity 2021) and incidence_moth_FD_22_Graser_et_al.rds (dataset for functional diversity 2022)
   are datasets for calculating taxonomic and functional diversity via rarefaction and extrapolation.
• moth_selected_traits_Graser_et_al.csv contains information about the moth species traits that were considered in the analyses of functional diversity and used to calculate the Gower distance matrix. 
• moth_species_list_21_Graser_et_al.csv (2021) and moth_species_list_22_Graser_et_al.csv (2022) are lists of species that occurred in the study area in the respective year.
• moth_species_matrix_nmds_21_Graser_et_al.csv (2021) and moth_species_matrix_nmds_22_Graser_et_al.csv (2022) are datasets of species abundances at the different trapping locations for the respective sampling years.

Please note: For the script to run without errors, all steps in each section must be performed in sequence, and the datasets and models have to be stored in correctly named folders. A more detailed description of the data and required folders can be found in the README.txt document.

References:

Brooks, M., Bolker, B., Kristensen, K., Maechler, M., Magnusson, A., McGillycuddy, M., Skaug, H., Nielsen, A., Berg, C., van Bentham, K., Sadat, N., Lüdecke, D., Lenth, R., O´Brien, J., Geyer, C. J., Jagan, M., Wiernik, B., & Stouffer, D. (2023). Generalized Linear Mixed Models using Template Model Builder. R Package Version 1.1.7, 1(1), 7.

Cardoso, P., Mammola, S., Rigal, F, & Carvalho, J. (2024). BAT: Biodiversity Assessment Tools. R Package Version 2.9.6. https://CRAN.R-project.org/package=BAT.

Chao, A., Henderson, P. A., Chiu, C.-H., Moyes, F., Hu, K.-H., Dornelas, M., & Magurran, A. E. (2021). Measuring temporal change in alpha diversity: A framework integrating taxonomic, phylogenetic and functional diversity and the iNEXT. 3D standardization. Methods in Ecology and Evolution, 12(10), 1926–1940. https://doi.org/10.1111/2041-210X.13682.

Oksanen, J., Blanchet, F. G., Kindt, R., Legendre, P., O’hara, R. B., Simpson, G. L., Solymos, P., Stevens, M. H. H., Wagner, H., Minchin, P. R., Gavin, L., & Henry, H. (2022). Vegan: Community ecology package. R Package Version 2.6-4.