Code from: Selection changes productivity over time
Data files
Jul 20, 2026 version files 31.90 KB
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GodsoeAppendixDivProd1.Rmd
30.72 KB
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README.md
1.18 KB
Abstract
Experiments suggest that increasing species diversity increases productivity. At present, there is controversy on which mechanisms mediate this relationship. Many existing models study productivity at equilibrium, such as in communities of coexisting competitors. Here we highlight an ambiguity of this choice, that it makes it difficult to determine if all mechanisms are acting on the same response variable. To illustrate this problem, we propose a formal link between dynamic models of population growth and analyses of diversity-productivity relationships. Using this link, we show that mechanisms which are thought to shape diversity productivity relationships act on different responses. In particular, niche complementarity, which describes the reduction of antagonistic interactions in diverse communities, shapes productivity, but selection does not change productivity directly; instead, it leads to temporal changes in productivity. This ambiguity is analogous to confusing a vehicle’s speed and its acceleration (i.e., change in speed over time). We measure each of the terms using data from one of Gauses’ competition experiments. For this experiment, the effects of niche differentiation are negligible at low density and weak at high density. Selection is likewise modest compared to overall changes in the environment. These results highlight how the effects of diversity on productivity can be obscured by our choice or response variable.
Dataset DOI: 10.5061/dryad.dfn2z35hj
Description of the data and file structure
This file provides code to simulate changes in abundance in diverse communities. This code was in turn used to make drafts of figures, with final aesthetic changes being made in Inkscape.
Code/software
William Godsoe wrote this code from April to October 2023 in the file GodsoeAppendixDivProd1.Rmd. Then revised in June 2026 to produce the report GodsoeAppendixDivProd1.pdf. This paper contains the code to develop figures and numerical analyses for the manuscript "Selection changes productivity over time". Notably, this contains drafts of figures and estimates of parameters concerning the outcome of competition among Paramecium spp. Final annotation of figures was done in Inkscape. The code was run using R 4.5.0. The packages used include ggplot2, ggpubr, gauseR, knitr, RColorBrewer, tinytex, reshape2, dplyr, phaseR and rescomp.
Access information
Other publicly accessible locations of the data:
- The data used in this code are available in the packages listed, e.g., gauseR.
