Data and statistical analyses for: Experimental evidence that estimates of demographic parameters depend on initial population size
Data files
Sep 08, 2026 version files 2.31 MB
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Analyses-Graphs_Oikos.R
46.18 KB
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Data_TimeSeries_Oikos.csv
2.16 MB
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Param-estimation_Oikos.R
22.09 KB
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README.md
17.03 KB
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Results-Fits_Oikos_N0-K.csv
24.08 KB
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Results-Fits_Oikos.csv
39.56 KB
Abstract
Classical population models assume that estimated parameters, such as intrinsic growth rate, depend on the species of interest and its environment, but not on the initial population size N(0). However, it has been theoretically proposed that this dependence is a mathematical consequence of reducing a two-dimensional system (e.g., for a predator and a prey) into a one-dimensional model (for the predator only). We test this proposition experimentally with microbial batch cultures where N(0) and the initial amount of food x(0) are manipulated. We use the McKendrick and Pai (1912) model to exemplify this reduction process, which leads to a logistic equation with the estimated growth rate r and equilibrium density K predicted to increase linearly with N(0) and x(0). Our results confirmed the dependence of r and K on the initial conditions. However, contrary to the prediction, r decreased rather than increased with N(0). Firstly, our results provide experimental evidence that the parameters of a reduced model depend on initial conditions, which raises important questions and challenges in their estimation. Secondly, the use of different initial conditions could be a powerful tool for model selection. Using simulated data from consumer-resource models and fitting the logistic equation to the consumer trajectory, we find that the observed negative dependence of r to N(0) is incompatible with McKendrick and Pai (1912) and with Monod (1942) models (akin to Holling type 1 and type 2 functional response, respectively), but agrees with the Contois model (1959), akin to ratio-dependence
We provide here the full data sets and R-code of the analyses used in this contribution.
Manuscript published in Oikos: Experimental evidence that estimates of demographic parameters depend on initial population size
by: Samantha L. Coinus, Alissa Deschamps, Vasco Lepori, Sarah M. Gray and Louis-Félix Bersier
DOI: 10.1002/oik.12370
Metadata for R-code files "Param-estimation_Oikos.R" and "Analyses-Graphs_Oikos.R"
These files contain the R code for the estimation of the parameters and for the analyses and graphical representations of the results. They use the 3 data files provided in csv format.
Metadata for data file "Data_TimeSeries_Oikos.csv"
The data file contains the OD (optical density) measurements for the 232 time series.
Column definitions
| Name | Definition | Remark |
|---|---|---|
| EXP.ID | identifyer of the time series | the name is built from values in "Plate", "x0", and "N0". |
| Well | identifyer of the well of the time series | well identity in the 96-wells plate. |
| Plate | identifyer of the 96-wells plate | |
| Experiment | identifyer of the experiment | X0_100 = first experiment with LB=100; X0_500 = second experiment with LB=500; X0N0 = third fully crossed experiment. (LB: lysogeny broth) |
| x0 | initial amount of resource (experimental variable) | Treated as a factor or as a continuous variable depending on the analyses in the main manuscript |
| N0 | initial density of microorganisms (experimental variable) | Treated as a factor or as a continuous variable depending on the analyses in the main manuscript |
| Cycle.Nr | identifyer of the cycle of the spectrophotometer | Integer from 0 to last OD measurement. |
| Time.s | time of measurement in second | [second] |
| Time.h | time of measurement in hour | [hour] |
| Temp.C | temperature in the spectrophotometer | [°C] |
| OD | measured optical density | Uncorrected OD given by the spectrophotometer. |
| OD_min | minumum OD value of the time series | |
| OD_max | maximum OD value of the time series | |
| OD_ini | first OD value of the time series | |
| OD_lb_t0 | OD value due to the resource alone (X0) | Values obtained from a separate analysis with lb only; used to measure OD.corr (see Appendix 2 in the SI of the article). |
| OD.corr | corrected OD value (response variable) | OD corrected for the OD due to the resource [OD.corr = OD - ((OD_max - OD)/(OD_max - OD_ini)) * OD_lb_t0]. This correction assumes: 1) additivity of ODs due to resource and microorganisms; 2) OD_lb_t0 equals 0 when OD_max is reached; 3) the resource is depleted proportionally to the organism density. |
| Growth.Phase.30 | Identifyer for the growth phase used in the parameters' estimation of the time series (N = excluded; Y = included) | We observed that the growth rate "r" was often underestimated on the full trajectory. Consequently, we restricted the time series to 30 data points (with some exceptions, notably for trajectories slowly approaching the maximum OD for which 60 data points were selected). We also observed that the first OD measures were often substantially larger than the next ones (possibly due to the temperature difference at the start of the experiment; see Temp.C). We removed the first OD measures if they were larger that the following ones. |
Metadata for data file "Results-Fits_Oikos.csv"
The data file contains the estimated parameters and related information for the 232 time series given in file "Data_TimeSeries_Oikos.txt".
Column definitions
| Name | Definition | Remark |
|---|---|---|
| Plate | identifyer of the 96-wells plate | |
| x0 | initial amount of resource in %LB (experimental variable) (LB: Lysogeny Broth) | Treated as a factor or as a continuous variable depending on the analyses in the main manuscript. |
| N0 | initial density of microorganisms (experimental variable) | Treated as a factor or as a continuous variable depending on the analyses in the main manuscript. |
| f.N0 | name of the N0 treatment in the fully crossed experiment (used only in figures) | factor with 10 levels (f.015, f.029, f.043, f.056, f.070, f.084, f.098, f.112, f.126, f.139, f.153, f.167, f.181, f.195, f.209, f.222, f.236, f.250). |
| N0.fit | fitted intercept of the logistic model | |
| N0.95CI.l | lower value of the 95% confidence interval for N0.fit | |
| N0.95CI.u | upper value of the 95% confidence interval for N0.fit | |
| r.fit | fitted intrinsic growth rate of the logistic model | |
| r.95CI.l | lower value of the 95% confidence interval for r.fit | |
| r.95CI.u | upper value of the 95% confidence interval for r.fit | |
| K.fit | fitted equilibrium density of the logistic model | |
| K.95CI.l | lower value of the 95% confidence interval for K.fit | |
| K.95CI.u | upper value of the 95% confidence interval for K.fit | |
| s.d.fit | estimated standard deviation of the Gaussian distribution | |
| SumLL | Sum of log-likelihoods | |
| n | number of observations in the corresponding time series | |
| sMAPE | Symmetric mean absolute percentage error | Accuracy measure based on relative errors. |
| EXP.ID2 | identifyer of the experiment | First and second experiments : X0_100 and X0_500; third fully crossed experiment: X0N0 |
Metadata for data file "Results-Fits_Oikos_N0-K.csv"
Column definitions
| Name | Definition | Remark |
|---|---|---|
| Experiment_ID | identifyer of the time series | |
| N0.fit | fitted intercept of the logistic model | |
| N0.95CI.l | lower value of the 95% confidence interval for N0.fit | |
| N0.95CI.u | upper value of the 95% confidence interval for N0.fit | |
| OD_0 | OD at time 0 | |
| K.fit | fitted equilibrium density of the logistic model | |
| K.95CI.l | lower value of the 95% confidence interval for K.fit | |
| K.95CI.u | upper value of the 95% confidence interval for K.fit | |
| ODmax | Maximum OD |
