DOI: 10.5281/zenodo.13161798
title: Data analysis scripts for Marsh et al. 2024 'Tropical forest clearance impacts biodiversity and function whereas logging changes structure'

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

Update for Version 2: The calculation of confidence intervals around the mean effects in Figure 2 has been updated to use the marginaleffects package (many thanks to Biao Wang and Shuang Zhang for pointing out an error in the original code). Using the Satterthwaite method for determining degrees of freedom, the updated confidence intervals are around 32% smaller than our original estimates (MLF = 32.0%, HLF = 32.1%, OP = 21.6%). Note, this change is only relevant to fig. 2 and figs. S2-4; the mean effect sizes and trends along the disturbance gradient, all statistical comparisons, and the constrast analyses in fig. 3 remain unaffected. The updated figures S2-4 and Table S6 can be seen in the file 'Updated figures S2-4 with recalculated confidence intervals.pdf'.

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.