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2025
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| Online Access: | https://doi.org/10.5281/zenodo.15088749 |
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| author | Bosshard, Ennia Harrison, Mark van Veen, Frank Kettle, Chris Chikkarangappa, Nagaraja Badenahally Banks, John Basu, Parthiba Casiá-Ajché, Quebin Bosbely Dalsgaard, Bo Dutta, Aditi Enríquez, Eunice Escobedo-Kenefic, Natalia Fierros López, Hugo Eduardo Gemmill-Herren, Barbara Ghazoul, Jaboury Hansen, Katrine Hass, Annika Hipólito, Juliana Honnay, Olivier Kasina, John Muo Klein, Alexandra-Maria Kormann Motzke, Iris Krishnan, Smitha Landaverde-González de Ameshofer, Patricia Latini, Anderson Li, Kevin Lucas-García, Rodrigo Munyuli, Theodore Narasimhaiah, Deepthi Obregón Corredor, Diana Obregón Corredor, Diana Quezada-Euán, José Javier G. Riojas-López, Mónica E. Rosas-Guerrero, Victor Schrader, Julian Severiano Galeana, Fernando Sitotaw, Tegegne Molla Sritongchuay, Tuanjit Tangtorwongsakul, Pornpimon Toledo-Hernández, Manuel Tscharntke, Teja Viswanathan, Poornima Vogel, Cassandra Wanger, Thomas Wayo, Kanuengnit Westphal, Catrin Jones, Matt Kaiser-Bunbury, Christopher |
| author_facet | Bosshard, Ennia Harrison, Mark van Veen, Frank Kettle, Chris Chikkarangappa, Nagaraja Badenahally Banks, John Basu, Parthiba Casiá-Ajché, Quebin Bosbely Dalsgaard, Bo Dutta, Aditi Enríquez, Eunice Escobedo-Kenefic, Natalia Fierros López, Hugo Eduardo Gemmill-Herren, Barbara Ghazoul, Jaboury Hansen, Katrine Hass, Annika Hipólito, Juliana Honnay, Olivier Kasina, John Muo Klein, Alexandra-Maria Kormann Motzke, Iris Krishnan, Smitha Landaverde-González de Ameshofer, Patricia Latini, Anderson Li, Kevin Lucas-García, Rodrigo Munyuli, Theodore Narasimhaiah, Deepthi Obregón Corredor, Diana Obregón Corredor, Diana Quezada-Euán, José Javier G. Riojas-López, Mónica E. Rosas-Guerrero, Victor Schrader, Julian Severiano Galeana, Fernando Sitotaw, Tegegne Molla Sritongchuay, Tuanjit Tangtorwongsakul, Pornpimon Toledo-Hernández, Manuel Tscharntke, Teja Viswanathan, Poornima Vogel, Cassandra Wanger, Thomas Wayo, Kanuengnit Westphal, Catrin Jones, Matt Kaiser-Bunbury, Christopher |
| contents | <p dir="auto">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.</p> <div dir="auto"> <h2>Variable Explanations</h2> </div> <ul> <li><strong>study</strong>: Unique study abbreviation/ID for each study</li> <li><strong>report</strong>: Unique abbreviation/ID for each individual report, i.e. published or unpublished article</li> <li><strong>authors</strong>: Author and year for each study (e.g., <code>author et al. year</code>)</li> <li><strong>crop</strong>: Common name of the study crop</li> <li><strong>p_dependency</strong>: Pollinator-dependency level of each study crop, following the information from Siopa et al. (2024)</li> <li><strong>farm_size</strong>: Total size of farm in hectares (ha) or nearest classification of farm size available (e.g. 'small <2ha' or 'medium 2-15ha')</li> <li><strong>habitat_description</strong>: Description of semi-natural habitat (e.g., 'forest', 'savannah', 'grassland')</li> <li><strong>habitat_type</strong>: Categorised type of natural habitat based on original description (binary; either 'natural forest' or 'other)</li> <li><strong>agr_intensity</strong>: Agricultural intensity (three levels: 'high' = use of pesticides, monocultures; 'low' = minimal pesticide use and no monocultures, 'both' = mixed)</li> <li><strong>distance_m</strong>: Euclidean distance (in metres) to the nearest natural habitat</li> <li><strong>distance_measure</strong>: Whether distance measurement was reported in the original study ('reported') or estimated using remote sensing ('estimated')</li> <li><strong>abundance_all</strong>: Observed number of pollinators visiting crop flowers for all observed insects</li> <li><strong>abundance_wild</strong>: Observed number of wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)</li> <li><strong>richness_all</strong>: Observed number of species for all pollinators</li> <li><strong>richness_wild</strong>: Observed number of species for wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)</li> <li><strong>fruitset</strong>: Observed proportion (0-1) of flowers that set fruit</li> <li><strong>treatment</strong>: Fruit set treatment (only used data from 'open' treatments for unbagged/untreated flowers in our synthesis)</li> <li><strong>pollinator</strong>: Focal pollinator taxa of the study to the most precise taxonomic level (e.g., 'Insecta', 'Hymenoptera', 'Diptera', 'bees', 'stingless bees', etc.)</li> <li><strong>sites</strong>: Total number of study sites/farms in the study</li> <li><strong>location</strong>: Name or code for each study site/farm</li> <li><strong>study_design</strong>: Description of the study design for each dataset; either 'single distance per site', 'nested design' or 'paired sites'</li> <li><strong>repeat_measures</strong>: 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</li> <li><strong>sampling_method</strong>: Method for insect observations (e.g., 'active' for focal observations/sweep netting, 'passive' for pan traps, 'combined' for both methods)</li> <li><strong>sampling_time_min</strong>: Time (in minutes) over which pollinators were sampled per sampling event</li> <li><strong>total_sampling_time_min</strong>: Total time (in minutes) over which pollinators were sampled at each study site/data point (accummulative across total sampling effort)</li> <li><strong>source</strong>: Where the data was obtained from (e.g., authors or publication directly, open access data, or from figures)</li> </ul> <div dir="auto"> <div dir="auto"> <h2>R Session Info</h2> <a href="https://github.com/enniabosshard/pollinatorhabitatTSF_SRMA/tree/main#r-session-info"></a></div> <p dir="auto">R version 4.4.2 (2024-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.6.1</p> <p dir="auto">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</p> <p dir="auto">locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8</p> <p dir="auto">time zone: Europe/London tzcode source: internal</p> <p dir="auto">attached base packages: [1] stats graphics grDevices utils datasets methods base</p> <p dir="auto">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<br>[9] MASS_7.3-61 dplyr_1.1.4 ggplot2_3.5.1</p> <p dir="auto">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<br>[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<br>[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<br>[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<br>[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</p> </div> <p dir="auto"> </p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_15088749 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | 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 Bosshard, Ennia Harrison, Mark van Veen, Frank Kettle, Chris Chikkarangappa, Nagaraja Badenahally Banks, John Basu, Parthiba Casiá-Ajché, Quebin Bosbely Dalsgaard, Bo Dutta, Aditi Enríquez, Eunice Escobedo-Kenefic, Natalia Fierros López, Hugo Eduardo Gemmill-Herren, Barbara Ghazoul, Jaboury Hansen, Katrine Hass, Annika Hipólito, Juliana Honnay, Olivier Kasina, John Muo Klein, Alexandra-Maria Kormann Motzke, Iris Krishnan, Smitha Landaverde-González de Ameshofer, Patricia Latini, Anderson Li, Kevin Lucas-García, Rodrigo Munyuli, Theodore Narasimhaiah, Deepthi Obregón Corredor, Diana Obregón Corredor, Diana Quezada-Euán, José Javier G. Riojas-López, Mónica E. Rosas-Guerrero, Victor Schrader, Julian Severiano Galeana, Fernando Sitotaw, Tegegne Molla Sritongchuay, Tuanjit Tangtorwongsakul, Pornpimon Toledo-Hernández, Manuel Tscharntke, Teja Viswanathan, Poornima Vogel, Cassandra Wanger, Thomas Wayo, Kanuengnit Westphal, Catrin Jones, Matt Kaiser-Bunbury, Christopher <p dir="auto">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.</p> <div dir="auto"> <h2>Variable Explanations</h2> </div> <ul> <li><strong>study</strong>: Unique study abbreviation/ID for each study</li> <li><strong>report</strong>: Unique abbreviation/ID for each individual report, i.e. published or unpublished article</li> <li><strong>authors</strong>: Author and year for each study (e.g., <code>author et al. year</code>)</li> <li><strong>crop</strong>: Common name of the study crop</li> <li><strong>p_dependency</strong>: Pollinator-dependency level of each study crop, following the information from Siopa et al. (2024)</li> <li><strong>farm_size</strong>: Total size of farm in hectares (ha) or nearest classification of farm size available (e.g. 'small <2ha' or 'medium 2-15ha')</li> <li><strong>habitat_description</strong>: Description of semi-natural habitat (e.g., 'forest', 'savannah', 'grassland')</li> <li><strong>habitat_type</strong>: Categorised type of natural habitat based on original description (binary; either 'natural forest' or 'other)</li> <li><strong>agr_intensity</strong>: Agricultural intensity (three levels: 'high' = use of pesticides, monocultures; 'low' = minimal pesticide use and no monocultures, 'both' = mixed)</li> <li><strong>distance_m</strong>: Euclidean distance (in metres) to the nearest natural habitat</li> <li><strong>distance_measure</strong>: Whether distance measurement was reported in the original study ('reported') or estimated using remote sensing ('estimated')</li> <li><strong>abundance_all</strong>: Observed number of pollinators visiting crop flowers for all observed insects</li> <li><strong>abundance_wild</strong>: Observed number of wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)</li> <li><strong>richness_all</strong>: Observed number of species for all pollinators</li> <li><strong>richness_wild</strong>: Observed number of species for wild pollinators excluding managed honeybees (A. mellifera, and in some cases A. cerana)</li> <li><strong>fruitset</strong>: Observed proportion (0-1) of flowers that set fruit</li> <li><strong>treatment</strong>: Fruit set treatment (only used data from 'open' treatments for unbagged/untreated flowers in our synthesis)</li> <li><strong>pollinator</strong>: Focal pollinator taxa of the study to the most precise taxonomic level (e.g., 'Insecta', 'Hymenoptera', 'Diptera', 'bees', 'stingless bees', etc.)</li> <li><strong>sites</strong>: Total number of study sites/farms in the study</li> <li><strong>location</strong>: Name or code for each study site/farm</li> <li><strong>study_design</strong>: Description of the study design for each dataset; either 'single distance per site', 'nested design' or 'paired sites'</li> <li><strong>repeat_measures</strong>: 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</li> <li><strong>sampling_method</strong>: Method for insect observations (e.g., 'active' for focal observations/sweep netting, 'passive' for pan traps, 'combined' for both methods)</li> <li><strong>sampling_time_min</strong>: Time (in minutes) over which pollinators were sampled per sampling event</li> <li><strong>total_sampling_time_min</strong>: Total time (in minutes) over which pollinators were sampled at each study site/data point (accummulative across total sampling effort)</li> <li><strong>source</strong>: Where the data was obtained from (e.g., authors or publication directly, open access data, or from figures)</li> </ul> <div dir="auto"> <div dir="auto"> <h2>R Session Info</h2> <a href="https://github.com/enniabosshard/pollinatorhabitatTSF_SRMA/tree/main#r-session-info"></a></div> <p dir="auto">R version 4.4.2 (2024-10-31) Platform: aarch64-apple-darwin20 Running under: macOS Sequoia 15.6.1</p> <p dir="auto">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</p> <p dir="auto">locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8</p> <p dir="auto">time zone: Europe/London tzcode source: internal</p> <p dir="auto">attached base packages: [1] stats graphics grDevices utils datasets methods base</p> <p dir="auto">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<br>[9] MASS_7.3-61 dplyr_1.1.4 ggplot2_3.5.1</p> <p dir="auto">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<br>[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<br>[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<br>[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<br>[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</p> </div> <p dir="auto"> </p> |
| 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 |
| url | https://doi.org/10.5281/zenodo.15088749 |