Data and scripts for the analysis of the influence of crop pollinator dependence and growth form on yield decline
收藏资源简介：
Marcelo A. Aizen, Gabriela R. Gleiser, Thomas Kitzberger, Ruben Milla. <strong>Being a tree crop increases the odds of experiencing yield declines irrespective of pollinator dependence </strong>(to be submitted to PCI) Data and R scripts to reproduce the analyses and the figures shown in the paper. All analyses were performed using R 4.0.2. <strong>Data</strong> 1. FAOdata_21-12-2021.csv This file includes yearly data (1961-2020, column 8) on yield and cultivated area (columns 6 and 10) at the country, sub-regional, and regional levels (column 2) for each crop (column 4) drawn from the United Nations Food and Agriculture Organization database (data available at http://www.fao.org/faostat/en; accessed July 21-12-2021). [Used in Script 1 to generate the synthesis dataset] 2. countries.csv This file provides information on the region (column 2) to which each country (column 1) belongs. [Used in Script 1 to generate the synthesis dataset] 3. dependence.csv This file provides information on the pollinator dependence category (column 2) of each crop (column 1). 4. traits.csv This file provides information on the traits of each crop other than pollinator dependence, including, besides the crop name (column1), the variables type of harvested organ (column 5) and growth form (column 6). [Used in Script 1 to generate the synthesis dataset] 5. dataset.csv The synthesis dataset generated by Script 1. 6. growth.csv The yield growth dataset generated by Script 1 and used as input by Scripts 2 and 3. 7. phylonames.csv This file lists all the crops (column 1) and their equivalent tip names in the crop phylogeny (column 2). [Used in Script 2 for the phylogenetically-controlled analyses] 8.phylo137.tre File containing the phylogenetic tree. <strong>Scripts</strong> 1. dataset This R script curates and merges all the individual datasets mentioned above into a single dataset, estimating and adding to this single dataset the growth rate for each crop and country, and the (log) cumulative harvested area per crop and country over the period 1961-2020. 2. analyses This R script includes all the analyses described in the article’s main text. 3. figures This R script creates all the main and supplementary figures of this article. 4. lme4_phylo_setup R function written by Li and Bolker (2019) to carry out phylogenetically-controlled generalized linear mixed-effects models as described in the main text of the article. <strong>References</strong> Li, M., and B. Bolker. 2019. wzmli/phyloglmm: First release of phylogenetic comparative analysis in lme4- verse. Zenodo. https://doi.org/10.5281/zenodo.2639887.
作者为Marcelo A. Aizen、Gabriela R. Gleiser、Thomas Kitzberger、Ruben Milla，研究论文题为<strong>《种植木本作物会提升产量下降的概率，且不受授粉媒介依赖性（pollinator dependence）影响》（拟投稿至PCI）</strong>。本数据集包含用于复现论文中分析与图表的代码与数据，所有分析均基于R 4.0.2完成。 <strong>数据</strong> 1. "FAOdata_21-12-2021.csv"：该文件包含1961-2020年的年度数据（第8列），涵盖各国、次区域及区域层面（第2列）各类作物（第4列）的产量与种植面积数据（第6、10列），数据源自联合国粮食及农业组织数据库（可从http://www.fao.org/faostat/en/获取，访问时间为2021年7月21日至12月21日）。[用于脚本1生成综合数据集] 2. "countries.csv"：该文件提供各国家（第1列）所属区域（第2列）的相关信息。[用于脚本1生成综合数据集] 3. "dependence.csv"：该文件提供各类作物（第1列）的授粉媒介依赖性类别（第2列）信息。 4. "traits.csv"：该文件提供各类作物除授粉媒介依赖性外的其他性状信息，除作物名称（第1列）外，还包含收获器官类型（第5列）与生长型（第6列）。[用于脚本1生成综合数据集] 5. "dataset.csv"：脚本1生成的综合数据集。 6. "growth.csv"：脚本1生成的产量增长数据集，作为脚本2与脚本3的输入文件。 7. "phylonames.csv"：该文件列出所有作物（第1列）及其在作物系统发育树（phylogenetic tree）中对应的分支名称（第2列）。[用于脚本2的系统发育校正分析（phylogenetically-controlled analyses）] 8. "phylo137.tre"：包含作物系统发育树的文件。 <strong>脚本</strong> 1. "dataset.R"：该R脚本用于清洗并整合上述所有独立数据集，生成单一综合数据集，并为每份作物-国家组合估算并添加增长率，以及1961-2020年间每份作物-国家的（对数化）累计收获面积。 2. "analyses.R"：包含论文正文所述全部分析内容的R脚本。 3. "figures.R"：用于生成论文所有主图与补充图表的R脚本。 4. "lme4_phylo_setup"：由Li与Bolker（2019）编写的R函数，用于执行论文正文所述的系统发育校正广义线性混合效应模型（phylogenetically-controlled generalized linear mixed-effects models）。 <strong>参考文献</strong> Li, M. 与 B. Bolker. 2019. wzmli/phyloglmm: First release of phylogenetic comparative analysis in lme4-verse. Zenodo. https://doi.org/10.5281/zenodo.2639887.
