DOI: 10.5281/zenodo.15088749
title: Data and R code for: Proximity to natural habitat is not consistently associated with pollination services in tropical smallholder farms: A systematic review and meta-analysis

description: This record contains the data and R scripts for a systematic review and meta-analysis on the relationship between distance to natural habitat and pollination services in tropical smallholder farming landscapes. It includes the raw data and R scripts for each response variable used in the synthesis, i.e. pollinator abundance, species richness, and fruitset, alongside the overview of all variable explanations below.



Variable Explanations




study: Unique study abbreviation/ID for each study

report: Unique abbreviation/ID for each individual report, i.e. published or unpublished article

authors: Author and year for each study (e.g., author et al. year)

crop: Common name of the study crop

p_dependency: Pollinator-dependency level of each study crop, following the information from Siopa et al. (2024)

farm_size: Total size of farm in hectares (ha) or nearest classification of farm size available (e.g. 'small <2ha' or 'medium 2-15ha')

habitat_description: Description of semi-natural habitat (e.g., 'forest', 'savannah', 'grassland')

habitat_type: Categorised type of natural habitat based on original description (binary; either 'natural forest' or 'other)

agr_intensity: Agricultural intensity (three levels: 'high' = use of pesticides, monocultures; 'low' = minimal pesticide use and no monocultures, 'both' = mixed)

distance_m: Euclidean distance (in metres) to the nearest natural habitat

distance_measure: Whether distance measurement was reported in the original study ('reported') or estimated using remote sensing ('estimated')

abundance_all: Observed number of pollinators visiting crop flowers for all observed insects

abundance_wild: Observed number of wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)

richness_all: Observed number of species for all pollinators

richness_wild: Observed number of species for wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)

fruitset: Observed proportion (0-1) of flowers that set fruit

treatment: Fruit set treatment (only used data from 'open' treatments for unbagged/untreated flowers in our synthesis)

pollinator: Focal pollinator taxa of the study to the most precise taxonomic level (e.g., 'Insecta', 'Hymenoptera', 'Diptera', 'bees', 'stingless bees', etc.)

sites: Total number of study sites/farms in the study

location: Name or code for each study site/farm

study_design: Description of the study design for each dataset; either 'single distance per site', 'nested design' or 'paired sites'

repeat_measures: Number of visits/replicate observations for active pollinator observations, number of pan traps for passive sampling, number of plants, branches or flowers observed for fruit set

sampling_method: Method for insect observations (e.g., 'active' for focal observations/sweep netting, 'passive' for pan traps, 'combined' for both methods)

sampling_time_min: Time (in minutes) over which pollinators were sampled per sampling event

total_sampling_time_min: Total time (in minutes) over which pollinators were sampled at each study site/data point (accummulative across total sampling effort)

source: Where the data was obtained from (e.g., authors or publication directly, open access data, or from figures)






R Session Info


R version 4.4.2 (2024-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.6.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/London tzcode source: internal

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] glmmTMB_1.1.12 ggeffects_2.3.0 here_1.0.1 metafor_4.6-0 numDeriv_2016.8-1.1 metadat_1.2-0 lme4_1.1-35.5 Matrix_1.7-1[9] MASS_7.3-61 dplyr_1.1.4 ggplot2_3.5.1

loaded via a namespace (and not attached): [1] gtable_0.3.6 TMB_1.9.16 insight_1.2.0 lattice_0.22-6 mathjaxr_1.6-0 vctrs_0.6.5 tools_4.4.2 Rdpack_2.6.2 generics_0.1.4[10] datawizard_1.0.2 sandwich_3.1-1 tibble_3.3.0 pkgconfig_2.0.3 RColorBrewer_1.1-3 lifecycle_1.0.4 compiler_4.4.2 farver_2.1.2 textshaping_1.0.0 [19] codetools_0.2-20 pillar_1.11.0 nloptr_2.1.1 crayon_1.5.3 reformulas_0.4.1 boot_1.3-31 multcomp_1.4-26 nlme_3.1-166 tidyselect_1.2.1[28] mvtnorm_1.3-2 labeling_0.4.3 forcats_1.0.0 splines_4.4.2 rprojroot_2.0.4 grid_4.4.2 cli_3.6.5 magrittr_2.0.3 survival_3.7-0[37] utf8_1.2.6 TH.data_1.1-2 withr_3.0.2 scales_1.4.0 estimability_1.5.1 emmeans_1.10.7 ragg_1.3.3 zoo_1.8-12 hms_1.1.3[46] coda_0.19-4.1 haven_2.5.5 rbibutils_2.3 mgcv_1.9-1 rlang_1.1.6 Rcpp_1.1.0 xtable_1.8-4 glue_1.8.0 rstudioapi_0.17.1 [55] minqa_1.2.8 R6_2.6.1 systemfonts_1.2.1