Wageningen University & Research | FEM-31806 | Models for Ecological Systems | FEM | PPS | WEC

Knowledge questions

Explain what is meant by the KISS principle and why it is relevant for model developers.

KISS stands for Keep it Simple Stupid. For modellers this means that models should be made as simple as possible, but not simpler. An adequate model includes only relevant processes that relate to the model objective. A process should only be included in the model if it captures a key component of the system and reduces model error and uncertainty. Detailed processes that seem relevant may not reduce model error (i.e. may not explain much of the observed variation) and only add to model uncertainty. This may be due to a large uncertainty in required process parameter estimates or a limited quantitative understanding of the processes at play. Such processes should be left out or replaced by simpler (e.g. summary) types of process descriptions for which parameters can be measured more easily. For example, a detailed description of photosynthesis in leaves to assess assimilation combined with respiration in various plant organs to estimate net growth rates of a crop is not needed and can better be replaced by a simple growth rate equation based on an easy to measure value for radiation use efficiency.

You know the initial value for all state variables in a system for t=0. Suppose that you want to determine the total change in a state variable from the interval t=5 to t=10. Explain why you need to start at t=0 for numerical integration while this is not needed for an analytical integration.

The analytical solution includes the integration constant and the exact value for every moment in time is known. With this, the change from t=5 to t=10 can be easily computed. Numerical integration is based on step-by-step integration of derivatives which do not include this integration constant. Hence, the states are not known at any point in time but depend on the initial value for these states at a specific moment in time. Therefore, the numerical integration can only start from the moment when all states are known, in this case t=0.

Exercise 1.1

A unit analysis is an essential tool to check for possible inconsistencies in equations and therefore models. A unit analysis can be used to check if an existing equation or model is correct and should also be used when developing an equation or model to ensure it is correct. Consider the following equation that describes a relative measure (with values between 0 and 1) of leaf photosynthesis (PP) as a function of the atmospheric CO2 concentration (CC in equation) and a parameter KcK_c:

P=CC+KcP = \frac{C}{C+K_c}

1.1 a
Suppose that the units of CC are expressed in parts per million. What are then the units of KcK_c and PP in this equation?

The unit of CC is expressed in parts per million (ppm), so KcK_c must also be in ppm otherwise CC and KcK_c cannot be added. This also means that PP is dimensionless (effectively ppm/ppm, a fraction). The units cancel each other out in the ratio.

1.1 b
Make a sketch of the relationship between CC on the X-axis and PP on the Y axis. What is the maximum value of PP here?

The maximum value of PP is 1. Since CC is a concentration, it cannot be smaller than 0. PP ranges from 0 (when C=0C=0) to (or better close to) a maximum value 1 when C>>KcC >> K_c.

1.1 c
What is the value of KcK_c in relation to CC when PP is at 50% of its maximum?

In the previous exercise, we found that the maximum value of PP equals 1. At 50% of this maximum, PP is thus at 0.5. When the ratio of C/(C+Kc)C/ (C + K_c) is 0.5, the value of KcK_c equals the value of CC.

1.1 d
Use the unit analysis approach to develop this model in such a way that it can be used to relate the specific rate of leaf photosynthesis (PP, mg CO2 m-2 leaf s-1) to the concentration of CO2 in the air (CC). Shortly explain what this value means.

To get PP in mg CO2 m-2 leaf s-1, the ratio must be multiplied with a factor (e.g. VmVm) with the same unit (mg CO2 m-2 leaf s-1). This factor defines the maximum leaf photosynthetic rate (in these units), and the amount of CO2 absorbed per unit leaf area per second.

Exercise 1.2

1.2 a
What are the dimensions of cc in the equations given in Figures 1.4a, b and c in the syllabus?

distance time -1, time-1, time-1.

1.2 b
Which general rules form the basis of dimensional analysis?

The terms that are added or subtracted should have the same dimensions or units. The dimensions of expressions should be identical at both sides of the equal sign. In multiplication reciprocal dimensions cancel out. In division identical dimensions cancel out. The arguments of exponentials, logarithms and angles should be dimensionless. Note that dimensions refer to length, mass and/or time. When we wish to check the consistency of equations, however, units like meter (or e.g. centimetre), gram (or e.g. kilogram) and hours (or e.g. seconds) must be used. Units thus comprise dimensional analysis, but vice versa this is not true.

Exercise 1.3

1.3
Give four environmental conditions that ensure that the relative growth rate cc in the equation of Figure 1.4b in the syllabus is indeed constant.

  1. A sufficient amount of food available should be available for the organisms at all times to support these growth rates;
  2. Harmful waste products should be absent or kept at a low level;
  3. Abiotic conditions that can affect growth rates, such as temperature, salt concentration and acidity, should be kept constant;
  4. Biotic factors that may influence growth rates, such as pests and diseases, should be absent or be kept at a constant level.

Exercise 1.4

Consider the graphs in Figures 1.5a, b and c in the syllabus.

1.4 a
What do the slopes of the different curves represent?

The slopes represent the time derivatives (dy/dt) of the variable on the y-axis.

1.4 b
What is the dimension of the slope in each case?

The dimension is change of state/t or (the dimension of the state variable) • time-1.

1.4 c
How do the numerical values of the slopes change with time? Are they constant, increasing or decreasing?

The numerical value of the slope in the Figure 1.5d does not change; it is equal to the constant cc. The numerical values of the slopes in the Figure 1.5e and 1.5f increase and decrease with time, respectively.

1.4 d
Does your answer in c) agree with the graphical presentation of the equations in Figures 1.5d, e and f?

The graphs give the slope as a function of time. These time derivatives are constant, increasing and decreasing with time, respectively.

Exercise 1.5

In the Syllabus, the equations 1.6 and 1.7 give the first two steps for the numerical calculation of the amount of water in the water tank example.

1.5 a
Use these equations to calculate the amount of water in the tank from t=0t = 0 until t=10t = 10 s with a time step (Δt\Delta t) of 2 and plot the amount of water in the tank (on y axis) against time (on x-axis). In addition, calculate analytically the amount of water in the tank for the same time steps, and plot the results in the same graph. You can make the graph on a piece of paper by hand (or in e.g. Excel).

The results of the different calculations:

You can download an Excel spreadsheet with the calculations here.

The resulting plot:

1.5 b
What is the difference between the numerical and analytical solutions and what is the cause of this difference?

The numerical solution (in blue) overestimates the value of the state variable compared to the analytical solution (in red). This is because the numerical approach assumes that the rate is constant during the time interval of integration, while the rate is in fact decreasing continuously.

1.5 c
When is the rate of inflow zero?

When the maximum water level is reached. This is the case after a long time, in principle when tt approaches infinity.

1.5 d
What happens to the speed of the process if the coefficient cc is 1/8 instead of 1/4?

The process is twice as slow.

Exercise 1.6

The parameter values of the water tank example are: W0=0 lW_0 = 0 \text{ l}; Wm=16 lW_m = 16 \text{ l}; c=1/4 s1c = 1/4 \text{ s}^{-1}. To show the behaviour of the numerical solution when Δt\Delta t is too large, the following is asked:

1.6 a
Perform numerical integrations for the filling of the water tank up to about 30 s using the following time intervals: Δt=1c1\Delta t = 1 · c^{-1}; Δt=1.5c1\Delta t = 1.5 · c^{-1}; Δt=2c1\Delta t = 2 · c^{-1}; Δt=2.5c1\Delta t = 2.5 · c^{-1}

For Δt=1c1=τ\Delta t = 1 · c^{-1} = \tau, the tank is filled after one time step; no inflow occurs thereafter.

For Δt=1.5c1=1.5τ\Delta t = 1.5 · c^{-1} = 1.5 · \tau, the amount of water in the tank oscillates around the equilibrium level, but eventually settles at this level.

For Δt=2c1=2τ\Delta t = 2 · c^{-1} = 2 · \tau, an oscillation around the equilibrium level between the limits 0 and 2 × WmW_m is obtained.

For Δt=2.5c1=2.5τ\Delta t = 2.5 · c^{-1} = 2.5 · \tau, the result is an oscillation with divergence.

1.6 b
Plot the results in the graph of Exercise 1.5.

No answer given, but oscillations can be observed.

1.6 c
Do the numerical solutions result in realistic dynamics? Can you explain why?

For a ratio Δt/c1=Δt/τ1\Delta t / c^{-1} = \Delta t / \tau ≥ 1 the results do not reflect reality at all.

1.6 d
The patterns show that Δt\Delta t is too large in these numerical solutions. Which value for Δt\Delta t would you recommend? (also consider your calculations of Exercise 1.5).

Taking into account the calculations in Exercise 1.4, the ratio Δt/τ\Delta t / \tau should be smaller than 0.5. As a rule of thumb, and a safe upper limit for the choice of Δt\Delta t, Δt\Delta t should be smaller or equal to 0.1×τ0.1 × \tau.

Exercise 1.7

Do the following analyses for the animal (population dynamics) example (Fig. 1.5b, 1.5e in syllabus):

1.7 a
Calculate three time coefficients, for relative growth rates equal to 1.5, 0.2 and 0.05 per year, respectively.

The time coefficients can be calculated by dividing the time interval by the rate of change (Δt/c1\Delta t / c^{-1}). Hence, the time coefficients are: 0.67, 5 and 20 year.

1.7 b
What time intervals would you use for numerical integration in these cases? Also take into account the practical aspect of numerical calculations.

One tenth of τ\tau. However, these data should be rounded off to the nearest smaller value that is an integral fraction of the output interval. For instance, 0.067 will become 0.05, but 0.5 and 2 years may be appropriate for output intervals.

1.7 c
Compute the number of animals after 5 years, when c=0.2c = 0.2 and A0=100A_0 = 100, by using 1) the analytical solution and 2) the numerical approach using the equation from Figure 1.4b and Δt=0.1c1\Delta t = 0.1 · c^{-1}.

Analytical 271.83 after 5 years. Numerical: 259.37 after 5 years.

1.7 d
Make a plot of the results.

No answer given.

1.7 e
Explain the difference between the numerical solution and the analytical solution.

During Δt\Delta t the rate of increase is assumed to be constant, but in fact it increases exponentially, as is shown in the graph. After the first time interval the amount is thus underestimated, and consequently the rate for the next time interval is underestimated, and so on. As time proceeds the discrepancy between the numerical and analytical solution becomes larger. This error propagation will be discussed in Chapter 6.

OPTIONAL: Exercise 1.8

1.8
It is stated in the text that ‘the time-coefficient appears to be equal to the time that would be needed for the model to reach its equilibrium state, if the rate of change is fixed.’ This statement also holds for exponential growth. Explain.

In a positive feedback loop like exponential growth, the change is directed away from the equilibrium state, so the extrapolation of the tangent must be reversed, and directed towards the unstable equilibrium state; the tangent cuts the horizontal equilibrium line (the x-axis), where the value of the state variable equals zero, one time coefficient interval earlier: