Digital repository for: Large-scale forest disturbance and associated management shape bird communities in Central European spruce forests

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

R-script includes:

indicator species analysis (R package indicspecies; Cáceres & Legendre, 2009)

non-metric multidimensional scaling (R package vegan; Oksanen et al., 2016)

rarefaction- and extrapolation of Hill numbers (R package iNEXT; Hsieh et al., 2019)

multi-species community distance sampling (R package sp Abundance; Doser et al., 2023)

Attached files:

bird_data_Graser_et_al.csv (row data of bird species point counts per distance category)

bird_data_abundance_100_Graser_et_al.csv (abundance of species per sampling site, summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

siteCovs_Graser_et_al.csv (environmental variables for each sampling point)

A_species_matrix_100_new_Graser_et_al.csv (species-site matrix of bark-beetle disturbance, unlogged sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

B_species_matrix_100_new_Graser_et_al.csv (species-site matrix of windthrow disturbance, unlogged sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

C_species_matrix_100_new_Graser_et_al.csv (species-site matrix of bark-beetle/windthrow disturbance, underplanted, unlogged sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

D_species_matrix_100_new_Graser_et_al.csv (species-site matrix of bark-beetle /windthrow disturbance, salvage-unlogged sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

E_species_matrix_100_new_Graser_et_al.csv (species-site matrix of bark-beetle /windthrow disturbance, underplanted, salvage-unlogged sites for rarefaction and extrapolation, summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

 F_species_matrix_100_new_Graser_et_al.csv (species-site matrix of mature spruce plantation sites for rarefaction and extrapolation, species number summed up over all four sampling repeats only considering detected individuals up to 100 m around the sampling point)

msHDS_bird_data_management_model_Graser_et_al.rds (R-data set for multi-species community distance sampling of the effect of different pre- and post-disturbance management groups)

msHDS_bird_data_stand_age_model_Graser_et_al.rds (R-data set for multi-species community distance sampling of the effect of post-disturbance forest succession)

A more detailed description of the data can be found in the README.txt document.

References:

Cáceres, M. D., & Legendre, P. (2009). Associations between species and groups of sites: Indices and statistical inference. Ecology, 90(12), 3566–3574. https://doi.org/10.1890/08-1823.1

Doser, J. W., Finley, A. O., Kéry, M., & Zipkin, E. F. (2023). spAbundance: An R package for single‐species and multi‐species spatially explicit abundance models. Methods in Ecology and Evolution, 15(6), 1024–1033. https://doi.org/10.1111/2041-210X.14332

Hsieh, T. C., Ma, K. H., & Chao, A. (2019). iNEXT-package: Interpolation and extrapolation for species diversity. https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.html

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. (2016). Vegan: Community ecology package. R package version 1.17-4. Http://CRAN. R-Project. Org/Package=vegan.