Data analysis scripts for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'
DOI10.5281/zenodo.13161799Zenodo13161799MaRDI QIDQ6720515
Dataset published at Zenodo repository.
David Hemprich-Bennett, Owen T. Lewis, David Johnson, Eleanor M. Slade, Boris Bongalov, Charles Marsh, Mathew Williams, Pavel Kratina, Palasiah Jotan, Nicholas J. Ostle, Sol Milne, Rudi S. Cruz, Reuben Nilus, Terhi Riutta, David T. Milodowski, Andy Hector, Joseph A Tobias, Stephen J. Rossiter, David A. Coomes, Benjamin Blonder, Zoe G. Davies, Ully H. Kritzler, Matthew J. Struebig, Simon L. Mitchell, Matheus Henrique Nunes, Arthur Y. C. Chung, Henry Henry, David F. R. P. Burslem, Noreen Majalap, Sabine Both, Elizabeth L. Clare, Glen Reynolds, Edgar C. Turner, Yit Arn Teh, Dafydd M. O. Elias, Robert M. Ewers, Victoria Kemp, Milenka Montoya Pillco, Edwards David P., Yadvinder Malhi, Samuel J. B. Robinson
Publication date: 7 August 2024
Copyright license: Creative Commons Attribution 4.0 International
Data analysis scripts for the manuscript Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure' In the zip file 'BALI_synthesis_analysis.zip' there are outputs from RMarkdown scripts that include all steps of the analysis for each dataset, including R code, incorporating data visualisation, exploration and standardisation, model building and evaluation, and visualisation of results. Fig. 2b can be regenerated using code in the zip file 'Marsh_etal_2024_Science_fig1b_chm_and_canopy_profiles-main.zip'. Each dataset presented in the manuscript has an html file within the folder 'Analyses'. For datasets involving bat, bird, dung beetle and tree traits additional markdown documents are available for steps take during data preparation in the folder 'Data preparation'. In the zip file 'BALI_synthesis_data.zip' are .rds data files that have been cleaned, prepared and z-score standardised following the procedures outlined in the respective markdown files. To repeat any given analysis, follow the respective rmarkdown document, excluding the data manipulation steps: Read in the data file as described above: dd - readRDS(paste0("path/to/rds/file/", "name_of_file.rds")) Run the code at the top of the markdown workflow (sections "Data information" and "Load in necessary libraries") Do not run the sections "Read in data" through to "Visual inspection of the data" Continue the analysis from the 'Modelling' section Level 1 - Structure Environment Dataset Label Filename Collector Above-ground carbon Above ground carbon Above_ground_carbon Terhi Riutta Leaf-area index Leaf-area index Leaf_area_index Terhi Riutta Soil temperature Soil temp. Soil_temperature Terhi Riutta Soil moisture Soil moisture Soil_moisture Dafydd Elias Air temperature: Minimum Air temp.: Min. Air_temperature_minimum Benjamin Blonder Air temperature: Mean Air temp.: Mean Air_temperature_mean Benjamin Blonder Air temperature: Maximum Air temp.: Max. Air_temperature_maximum Benjamin Blonder Soil bulk density Soil bulk density Soil_bulk_density Dafydd Elias Soil horizon depth Soil horizon depth Soil_horizon_depth Dafydd Elias Soil pH Soil pH Soil_pH Dafydd Elias Soil nutrients: Carbon Soil nutrients (C) Soil_nutrients_C Dafydd Elias Soil nutrients: Nitrogen Soil nutrients (N) Soil_nutrients_N Dafydd Elias Soil nutrients: Inorganic Phosporous Soil nutrients (Inorganic P) Soil_nutrients_Inorganic_P Dafydd Elias Soil nutrients: Carbon:Phosphorous Soil nutrients (C:P) Soil_nutrients_C_P Dafydd Elias Soil nutrients: Carbon:Nitrogen Soil nutrients (C:N) Soil_nutrients_C_N Dafydd Elias Level 2 - Tree traits All tree traits were collected as part of the following study (details in this table have been extracted from table S1 of that publication): S. Both, T. Riutta, C.E.T. Paine, D.M.O. Elias, R.S. Cruz, A. Jain, D. Johnson, U.H. Kritzler, M. Kuntz, N. Majalap-Lee, N. Mielke, M.X. Montoya Pillco, N.J. Ostle, Y. Arn Teh, Y. Malhi, D.F.R.P. Burslem (2019) Logging and soil nutrients independently explain plant trait expression in tropical forests. New Phytologist. 221:4, 18531865. Photosynthesis Traits Dataset Label Filename Aggregated photosynthesis traits Photosyn. traits Photosynthesis traits 13C 13C Traits_13C Light-saturated photosynthetic rate Photosyn. rate: Asat Traits_Asat Maximum photosynthetic rate Photosyn. rate: Amax Traits_Amax Maximum photosynthetic rate: Nitrogen concentration Max. photosyn. rate: N(%) Traits_N_conc Maximum photosynthetic rate: Phosphorous mass (area) Max. photosyn. rate: P(mass) Traits_Phos_area Dark respiration (Rd) Dark respiration Traits_Dark_resp Specific leaf area (SLA) Specific leaf area Traits_SLA Carotenoids (area) Carotenoids: Area Traits_Carot_area Carotenoids (mass) Carotenoids: Mass Traits_Carot_mass Chlorophyll a (area) Chlorophyll a: Area Traits_Chl_a_area Chlorophyll a (mass) Chlorophyll a: Mass Traits_Chl_a_mass Chlorophyll b (area) Chlorophyll b: Area Traits_Chl_b_area Chlorophyll b (mass) Chlorophyll b: Mass Traits_Chl_b_mass Nutrient Traits Dataset Label Filename Aggregated nutrient traits Nutrient traits Nutrient_traits 15N 15N Traits_15N Carbon concentration Carbon conc. Traits_Carbon_conc Nitrogen concentration Max. photosyn. rate: N(%) Traits_N_perc Phosphorous concentration Max. photosyn. rate: P(mass) Traits_Phos_mass Magnesium concentration Regulat. nutrients: Total Mg Traits_Total_Mg Potassium concentration Regulat. nutrients: Total K Traits_Total_K Calcium concentration Regulat. nutrients: Total Ca Traits_Total_Ca Structural Traits Dataset Label Filename Aggregated structural traits Structural traits Structural_traits Branch specific density Branch wood density Traits_Branch_WD Leaf cellulose concentration Leaf fibre conc.: Cellul. Traits_Cellulose Leaf lignin concentration Leaf fibre conc.: Lignin Traits_Lignin Leaf hemicellulose concentration Leaf fibre conc.: Hemicel. Traits_Hemicellulose Leaf area Leaf size: Area Traits_Leaf_area Leaf dry weight Leaf size: Dry wgt Traits_Dry_weight Leaf force to punch Leaf strength: Tough. Traits_Leaf_toughness Leaf thickness Leaf strength: Thick. Traits_Leaf_thickness Leaf dry matter content Leaf strength: Dry mat. Traits_LDMC Total phenol concentration Leaf defence: Phenol Traits_Phenol Total tannin concentration Leaf defenct: Tannin Traits_Tannin Level 3 - Biodiversity Dataset Label Filename Collector Soil bacterial richness Soil microbial richness: Bacteria Soil_richness_Bacteria Dafydd Elias Soil protist richness Soil microbial richness: Protists Soil_richness_Protist Dafydd Elias Soil ectomycorrhizal richness Soil fungal richness: Ectomycorrhiza Soil_richness_Ectomycorrhiza Dafydd Elias Soil fungal richness Soil fungal richness: Fungi Soil_richness_Fungi Dafydd Elias Soil arbuscular mycorrhizal richness Soil fungal richness: Arbuscular mycorrhiza Soil_richness_Arbuscular_mycorrhizal Dafydd Elias Leaf spectral diversity Spectral diversity Spectral_diversity Matheus Nunes Liana abundance Liana abundance Liana_abundance Boris Bongalov Dung beetle abundance Dung beetle abund. Dung_beetle_abundance Eleanor Slade Dung beetle diversity: richness Dung beetle diversity: q=0 Dung_beetle_diversity_q=0 Eleanor Slade Dung beetle diversity: Shannon diversity Dung beetle diversity: q=1 Dung_beetle_diversity_q=1 Eleanor Slade Dung beetle diversity: Simpson diversity Dung beetle diversity: q=2 Dung_beetle_diversity_q=2 Eleanor Slade Bird abundance Bird abund. Bird_abundance Simon Mitchell Bird diversity: richness Bird diversity: q=0 Bird_diversity_q=0 Simon Mitchell Bird diversity: Shannon diversity Bird diversity: q=1 Bird_diversity_q=1 Simon Mitchell Bird diversity: Simpsons diversity Bird diversity: q=2 Bird_diversity_q=2 Simon Mitchell Bat abundance Bat abund. Bat_abundance David Hemprich-Bennett Bat diversity (small scale) Bat diversity (sm scale) Bat_diversity_small_scale David Hemprich-Bennett Bat diversity (large scale): richness Bat diversity (lg scale): q=0 Bat_diversity_large_scale_q=0 David Hemprich-Bennett Bat diversity (large scale): Shannon diversity Bat diversity (lg scale): q=1 Bat_diversity_large_scale_q=1 David Hemprich-Bennett Bat diversity (large scale): Simpson diversity Bat diversity (lg scale): q=2 Bat_diversity_large_scale_q=2 David Hemprich-Bennett Bat -diversity: Nestedness Bat -diversity: Nested. Bat_beta_diversity_Nestedness David Hemprich-Bennett Bat -diversity: Turnover Bat -diversity: Turn. Bat_beta_diversity_Turnover David Hemprich-Bennett Bat -diversity: Total Bat -diversity: Total Bat_beta_diversity_Total David Hemprich-Bennett Level 4 - Functioning Dataset Label Filename Collector Soil respiration Respiration: Soil Soil_respiration Terhi Riutta Stem respiration Respiration: Stem Stem_respiration Terhi Riutta Net primary productivity NPP NPP Terhi Riutta Litterfall Litterfall Litterfall Terhi Riutta Leaf litter decomposition Litter decomposition Litter_decomposition Sabine Both Soil mycelial production Mycelial production Hyphal_length Samuel Robinson Dung removal Dung removal Dung_removal Eleanor Slade Funding Analyses were carried out, and data were collected, as part of the BALI (Biodiversity And Land-use Impacts on tropical ecosystem function) and LOMBOK (Land-use Options for Maintaining BiOdiversity eKosystem functions) projects using the following funding: NERC Human-modified Tropical Forests Programme(NE/K016377/1, NE/K016261/1, NE/K016148/1, NE/K016407/1); NERC grant (NE/I028068/1); British Ecological Society Small Ecological Project Grant (No.: 3256/4035); Varley-Gradwell Travelling Fellowship in Insect Ecology; Bat Conservation International Student Research Scholarship; NOMIS Foundation; ERCEuropean Union's Horizon 2020 research and innovation programme (grant agreement No 865403); ERC Advanced Investigator Grant, GEM-TRAIT (321131); The SAFE Project is funded by the Sime Darby Foundation.
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