Data and scripts for the analysis of the influence of crop pollinator dependence and growth form on yield decline

<p>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)</p> <p>&nbsp;</p> <p>Data and R scripts to reproduce the analyses and the figures shown in the paper. All analyses were performed using R 4.0.2.</p> <p>&nbsp;</p> <p><strong>Data</strong></p> <p>1. FAOdata_21-12-2021.csv</p> <p>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 <a href="http://www.fao.org/faostat/en">http://www.fao.org/faostat/en</a>; accessed July 21-12-2021).&nbsp; [Used in Script 1 to generate the synthesis dataset]</p> <p>2. countries.csv</p> <p>This file provides information on the region (column 2) to which each country (column 1) belongs.&nbsp; [Used in Script 1 to generate the synthesis dataset]</p> <p>3. dependence.csv</p> <p>This file provides information on the pollinator dependence category (column 2) of each crop (column 1).</p> <p>4. traits.csv</p> <p>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]</p> <p>5. dataset.csv</p> <p>The synthesis dataset generated by Script 1.</p> <p>6. growth.csv</p> <p>The yield growth dataset generated by Script 1 and used as input by Scripts 2 and 3.</p> <p>7. phylonames.csv</p> <p>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]</p> <p>8.phylo137.tre</p> <p>File containing the phylogenetic tree.</p> <p>&nbsp;</p> <p><strong>Scripts</strong></p> <p>1. dataset</p> <p>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.</p> <p>2. analyses</p> <p>This R script includes all the analyses described in the article&rsquo;s main text.</p> <p>3. figures</p> <p>This R script creates all the main and supplementary figures of this article.</p> <p>4. lme4_phylo_setup</p> <p>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.</p> <p>&nbsp;</p> <p><strong>References</strong></p> <p>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.</p>