Data analysis scripts for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'

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, 1853–1865.

Photosynthesis Traits

Dataset
Label
Filename

Aggregated photosynthesis traits
Photosyn. traits
Photosynthesis traits

δ13C
δ13C
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

δ15N
δ15N
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 β-diversity: Nestedness
Bat β-diversity: Nested.
Bat_beta_diversity_Nestedness
David Hemprich-Bennett

Bat β-diversity: Turnover
Bat β-diversity: Turn.
Bat_beta_diversity_Turnover
David Hemprich-Bennett

Bat β-diversity: Total
Bat β-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;

ERC European 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.