Fig 1.
Example of clone inconsistency: Two simulations of a simple predator–prey scenario using the same general model (see text for details).
Solid lines: simulation using one population for prey (blue, antelopes) and predators (orange, lions) each. The initial abundances are x1(0) = 2 and x2(0) = 6 (animal heads in the top legend). Dashed lines: same, but with two identical predator sub-populations (pink and ocher) with half the initial abundance; the abundance shown for the predators is the sum over the two sub-populations. The simulations were run with JiTCODE [51] using the DoPri5 method (S1 Code).
Fig 2.
Criteria for impact functions exemplified for the grazing impact of animal populations.
Each island represents a community. Each row and color represents one population in the model, with animal heads representing individuals. Numbers on the left represent parameters governing the respective population (grazing rate in the example), and head shapes indicate whether populations have identical properties as per these parameters. The similar sign (∼) indicates that two communities are equivalent as arguments of an impact function, i.e., they should yield the same result (total amount of grazing in the example).
Fig 3.
Recipes for building and validating models using our framework.
In general xi denotes the abundance of population i, and ai, bi, ci, and di are parameters describing its impact. The example for checking is based upon Eq 21 and tailored for covering relevant cases. The example for building extends the one from The form of impact functions. For both examples, the biological background is discussed in more detail in the main text.
Fig 4.
Acquisition of data used in our case study.
Measurement of growth characteristics (left) and pairwise interactions (right) of bacterial strains isolated from urinary-tract infections [16]. Left: Each strain j was cultivated for 48 h in artificial urine. Solid bold letters represent individuals of the respective strain. The exponential growth rate gj as well as the carrying capacity cj (named yield in the original study [16]) were experimentally determined via optical densities. Right: For each strain k, a conditioned medium was produced by letting the strain grow for 48 h, mechanically removing the bacteria to obtain a supernatant, and mixing the result with fresh medium in a ratio of v ≔ 0.4. Outline letters (“footprints”) indicate to what extent the respective culture consists of supernatant. In each such medium, each strain j was cultivated, and the conditioned growth rate gjk and carrying capacity cjk were determined as above.