Distributions in ssdtools

Original ssdtools distributions

The log-normal, log-logistic and Gamma distributions have been widely used in SSD modelling, and were part of the original distribution set for early releases of ssdtools as developed by Thorley and Schwarz (2018). They were adopted as the default set of three distributions in early updates of ssdtools and the associated ShinyApp (Dalgarno 2021). All three distributions show good convergence properties and are retained as part of the default model set in version 2.0 of ssdtools.

In addition to the log-normal, log-logistic and Gamma distributions, the original version of ssdtools as developed by Thorley and Schwarz (2018) also included three additional distributions in the candidate model set, including the log-gumbel, Gompertz and Weibull distributions. Of these, the log-Gumbel (otherwise known as the inverse Weibull, see below) shows relatively good convergence (see Figure 32, D. Fox et al. 2022), and is also one of the limiting distributions of the Burr Type 3 distribution implemented in ssdtools, and has been retained in the default model set. The Gompertz and Weibull distributions, however can exhibit unstable behaviour, sometimes showing poor convergence, and therefore been excluded from the default set (see Figure 32, D. Fox et al. 2022)

Burr III distribution

A history of Burrlioz and the primary distributions it used were recently summmarized by D. R. Fox et al. (2021).

In 2000, Australia and New Zealand (Australian and New Zealand Environment and Conservation Council/Agriculture and Resource Management Council of Australia and New Zealand 2000) adopted an SSD‐based method for deriving WQBs, following a critical review of multiple WQB derivation methods (Warne 1998). A distinct feature of the method was the use of a 3‐parameter Burr distribution to model the empirical SSD, which was implemented in the Burrlioz software tool (Campbell et al. 2000). This represented a generalization of the methods previously employed by Aldenberg and Slob (1993) because the log–logistic distribution was shown to be a specific case of the Burr family (Tadikamalla 1980). Recent revision of the derivation method recognized that using the 3‐parameter Burr distributions for small sample sizes (<8 species) created additional uncertainty by estimating more parameters than could be justified, essentially overfitting the data (Batley et al. 2018). Consequently, the method, and the updated software (Burrlioz Ver 2.0), now uses a 2‐parameter log–logistic distribution for these small data sets, whereas the Burr type III distribution is used for data sets of 8 species or more (Batley et al. 2018; Australian and New Zealand Guidelines 2018).

(D. R. Fox et al. 2021)

The probability density function, f_X(x; b, c, k) and cumulative distribution function, F_X(x; b, c, k) for the Burr III distribution are:

Sample Burr probability density (A) and cumulative probability (B) functions.

While the Burr type III distribution was adopted as the default distribution in Burrlioz, it is well known (e.g., Tadikamalla (1980)) that the Burr III distribution is related to several other theoretical distributions, some of which only exist as limiting cases of the Burr III, i.e., as one or more of the Burr III parameters approaches either zero or infinity. The Burrlioz software incorporates logic that aims to identify situations where parameter estimates are tending towards either very large or very small values. In such cases, fitting a Burr III distribution is abandoned and one of the limiting distributions is fitted instead.

Specifically:

• As c tends to infinity the Burr III distribution tends to the inverse (North American) Pareto distribution (see technical details)

• As k tends to infinity the Burr III distribution tends to the inverse Weibull (log-Gumbel) distribution (see technical details)

In practical terms, if the Burr III distribution is fitted and k is estimated to be greater than 100, the estimation procedure is carried out again using an inverse Weibull distribution. Similarly, if c is greater than 80 an (American) Pareto distribution is fitted. This is necessary to ensure numerical stability.

Since the Burr type III, inverse Pareto and inverse Weibull (log Gumbel) distributions are used by the Burrlioz software, these have been implemented in ssdtools. However, we have found there are stability issues with both the Burr type III, as well as the inverse Pareto distributions, which currently precludes their inclusion in the default model set (see D. Fox et al. (2022), and below for more details).

Bimodal distributions

The use of statistical mixture-models was promoted by Fox as a convenient and more realistic way of modelling bimodal toxicity data (Fisher et al. 2019). Although parameter heavy, statistical mixture models provide a better conceptual match to the inherent underlying data generating process since they directly model bimodality as a mixture of 2 underlying univariate distributions that represent, for example, different modes of action (D. R. Fox et al. 2021). It has been postulated that a mixture-model would only be selected in a model-averaging context when the fit afforded by the mixture is demonstrably better than the fit afforded by any single distribution. This is a consequence of the high penalty in AICc associated with the increased number of parameters (p in Equation 7 of (D. R. Fox et al. 2021)) and will be most pronounced for relatively small sample sizes.

The TMB version of ssdtools now includes the option of fitting two mixture distributions, individually or as part of a model average set. These can be fitted using ssdtools by supplying the strings “llogis_llogis” and/or “lnorm_lnorm” to the dists argument in the ssd_fit_dists call.

The underlying code for these mixtures has three components: the likelihood function required for TMB; exported R functions to allow the usual methods for a distribution to be called (p, q and r); and a set of supporting R functions (see D. Fox et al. (2022) Appendix D for more details). Both mixtures have five parameters - two parameters for each of the component distributions and a mixing parameter (pmix) that defines the weighting of the two distributions in the ‘mixture.’

Sample lognormal lognormal mixture probability density (A) and cumulative probability (B) functions.

As can be see from the plot above, the mixture distributions provide a highly flexible means of modelling bimodality in an emprical SSD. This happens, for example, when the toxicity data for some toxicant include both animal and plant species, or there are different modes of action operating. Unfortunately, this increased flexibility comes with a high penalty in the model-averaging process. The combination of small sample sizes and a high parameter count (typically 5 or more) means that mixture distributions will be down-weighted - even when they do a good job at describing the data. For this reason, when attempting to model bimodal data, we suggest looking at the fit using the default set of distributions and then examining the fit with just one of either the log-normal mixture or the log-logistic mixture. Keep in mind that this should only be done if the sample size is not pathologically small. As a guide, Prof. David Fox recommends as an absolute minimum n ≥ 3k + 1 but preferably n ≥ 5k + 1 where k is the number of model parameters.

Currently recommended default distributions

The default list of candidate distributions in ssdtools is comprised of the following: log-normal; log-logistic; gamma; inverse Weibull (log-Gumbel); Weibull; mixture of two log-normal distributions

The default distributions are plotted below with a mean of 2 and standard deviation of 2 on the (natural) log concentration scale or around 7.4 on the concentration scale.

Currently recommended default distributions.

Burr Type III distribution

The Burr Type 3 is a flexible three parameter distribution can be fitted using ssdtools by supplying the string burrIII3 to the dists argument in the ssd_fit_dists call.

The Burr family of distributions has been central to the derivation of guideline values in Australia and New Zealand for over 20 yr (D. R. Fox et al. 2021). While offering a high degree of flexibility, experience with these distributions during that time has repeatedly highlighted numerical stability and convergence issues when parameters are estimated using maximum likelihood (D. R. Fox et al. 2021). This is thought to be due to the high degree of collinearity between parameter estimates and/or relatively flat likelihood profiles (D. R. Fox et al. 2021), and is one of the motivations behind the logic coded into Burrlioz to revert to either of the two limiting distributions. Burr Type 3 distribution is not currently one of the recommended distributionsin the default model set. This is because of 1) the convergence issues associated with the Burr Type 3 distribution, 2) the fact that reverting to a limiting two parameter distribution does not fit easily within a model averaging framework, and 3) that one of the two limiting distributions (the inverse Pareto, see below) also has estimation and convergence issues.

Log-normal

The log-normal distribution is a commonly used distribution in the natural sciences - particularly as a probability model to describe right (positive)-skewed phenomena such as concentration data.

A random variable, X is lognormally distributed if the logarithm of X is normally distributed. The pdf of X is given by

The log-normal distribution was selected as the starting distribution given the data are for effect concentrations. The log-normal distribution can be fitted using ssdtools supplying the string lnorm to the dists argument in the ssd_fit_dists call.

Sample lognormal probability density (A) and cumulative probability (B) functions.

Log-logistic distribution

Like the lognormal distribution, the log-logistic is similarly defined, that is: if X has a log-logistic distribution, then Y = ln (X) has a logistic distribution.

letting μ = ln (α) and $s = \frac{1}{\beta }$ we have:

The log-logistic distribution is often used as a candidate SSD primarily because of its analytic tractability (Aldenberg and Slob 1993). We included it because it has wider tails than the log-normal and because it is a specific case of the more general Burr family of distributions Burr (1942). The log-logistic distribution can be fitted using ssdtools by supplying the string lnorm to the dists argument in the ssd_fit_dists call.

Sample Log logistic probability density (A) and cumulative probability (B) functions.

Gamma distribution

The two-parameter gamma distribution has the following pdf and cdf.

where Γ(⋅) is the gamma function (in R this is simply gamma(x)) and γ(⋅) is the (lower) incomplete gamma function $$\gamma \left( {x,a} \right) = \int\limits_0^x {{t^{a - 1}}} \,{e^{ - t}}\,dt$$ (this can be computed using the gammainc function from the pracma package in R).

For use in modeling species sensitivity data, the gamma distribution has two key features that provide additional flexibility relative to the log-normal distribution: 1) it is asymmetrical on the logarithmic scale; and 2) it has wider tails.

The gamma distribution can be fitted using ssdtools by supplying the string “gamma” to the dists argument in the ssd_fit_dists call.

Sample gamma probability density (A) and cumulative probability (B) functions.

Log-gumbel (inverse Weibull) distribution

The log-gumbel distribution is a two-parameter distribution commonly used to model extreme values. The log-gumbel distribution can be fitted using ssdtools by supplying the string lgumbel to the dists argument in the ssd_fit_dists call. The two-parameter log-gumbel distribution has the following pdf and cdf:

Sample Log-Gumbel probability density (A) and cumulative probability (B) functions.

Gompertz distribution

The Gompertz distribution is a flexible distribution that exhibits both positive and negative skewness. The Gompertz distribution can be fitted using ssdtools by supplying the string gompertz to the dists argument in the ssd_fit_dists call. We consider two parameterisations of the Gompertz distribution. The first, as given in Wikipedia and also used in ssdtools [Gompertz] has the following pdf and cdf:

The second parameterisation in which the product bη in the formulae above is replaced by the parameter a giving:

Sample Gompertz probability density (A) and cumulative probability (B) functions.

The Gompertz distribution is available in ssdtools, however parameter estimation can be somewhat unstable (D. Fox et al. 2022), and for this reason it is not currently included in the default set.

Weibull distribution

The inclusion of the Weibull distribution and inverse Pareto distribution (see next) in ssdtools was primarily necessitated by the need to maintain consistency with the calculations undertaken in Burrlioz. As mentioned earlier, both the Weibull and inverse Pareto distributions arise as limiting distributions when the Burr parameters c and k tend to either zero and/or infinity in specific ways.

The two-parameter Weibull distribution has the following pdf and cdf:

The Weibull distribution can be fitted in ssdtools by supplying the string weibull to the dists argument in the ssd_fit_dists call.

Sample Weibull probability density (A) and cumulative probability (B) functions.

Inverse Pareto distribution

The inverse Pareto distribution can be fitted using ssdtools by supplying the string invpareto to the dists argument in the ssd_fit_dists call.

While the inverse Pareto distribution is implemented in the Burrlioz 2.0 software, it is important to understand that it is done so only as one of the limiting Burr distributions (see technical details). The inverse Pareto is not offered as a stand-alone option in the Burrlioz 2.0 software. We have spent considerable time and effort exploring the properties of the inverse Pareto distribution, including deriving bias correction equations and alternative methods for deriving confidence intervals (D. Fox et al. 2022). This work has substantial value for improving the current Burrlioz 2.0 method, and our bias corrections should be adopted when deriving HCx estimates from the inverse Pareto where parameters have been estimated using maximum likelihood.

As is the case with the Burrlioz 2.0 software, we have decided not to include the inverse Pareto distribution in the default candidate set in ssdtools although it is offered ass a user-selectable distribution to use in the model-fitting process.

As with many statistical distributions, different ‘variants’ exist. These ‘variants’ are not so much different distributions as they are simple re-parameterisations. For example, many distributions have a scale parameter, β and some authors and texts will use β while others use $\frac{1}{\beta }$. An example of this re-parameterisation was given above for the Gompertz distribution. While the choice of mathematical representation may be purely preferential, it is sometimes done for mathematical convenience. For example, Parameterisation I of the Gompertz distribution above was obtained by letting a = bη in Parameterisation II. This re-expression involving parameters b and η would be particularly useful when trying to fit a distribution for which one of {b, η} was very small and the other was very large.

It has already been noted that the particular parameterisation of the (Inverse)Pareto distribution used in both Burrlioz 2.0 and ssdtools was not a matter of preference, but rather was dictated by mathematical considerations which demonstrated convergence of the Burr distribution to one specific version of the (Inverse)Pareto distribution. While the mathematics provides an elegant solution to an otherwise problematic situation, this version of the (Inverse)Pareto distribution is not particularly use as a stand-alone distribution for fitting an SSD (other than as a special, limiting case of the Burr distribution).

The two versions of the (Inverse)Pareto distribution are known as the European and North American versions. Their pdfs and cdfs are given below.

Importantly, we see that the North American versions of these distributions are bounded with the Pareto distribution bounded below by β and the inverse Pareto distribution bounded above by $\frac{1}{\beta }$.
As an aside, the mle of β in the Pareto distribution is β̂ = min {X₁, …, X_n} and the mle of $\frac{1}{\beta }$ in the inverse Pareto is $$\begin{array}{*{20}{l}} {\tilde \beta = \max \left\{ {{Y_1}, \ldots ,{Y_n}} \right\}}\\ {\quad = \max \left\{ {\frac{1}{{{X_1}}}, \ldots ,\frac{1}{{{X_n}}}} \right\} = \frac{1}{{\min \left\{ {{X_1}, \ldots ,{X_n}} \right\}}}}\\ {\quad = \frac{1}{{\hat \beta }}} \end{array}$$.

and the mle of α is: $$\hat \alpha = {\left[ {\ln \left( {\frac{g}{{\hat \beta }}} \right)} \right]^{ - 1}}$$ where g is the geometric mean: $$g = {\left[ {\prod\limits_{i = 1}^n {{X_i}} } \right]^{\frac{1}{n}}}$$

Thus, it doesn’t matter whether you’re fitting a Pareto or inverse Pareto distribution to your data - the parameter estimates are the same.

Because it is bounded, the North American version of the (Inverse)Pareto distribution is not useful as a stand-alone SSD - more so for the inverse Pareto distribution since it is bounded from above.

Sample North American Pareto probability density (A) and cumulative probability (B) functions.

Sample North American Pareto probability density (A) and cumulative probability (B) functions.

Sample Sample North American inverse Pareto probability density (A) and cumulative probability (B) functions.

We see from the pdf plots that the alternative, European version of the inverse Pareto distribution is a more realistic candidate.

We note in passing that both versions of these Pareto and inverse Pareto distrbutions are available in R. For example, the Rpackage extraDistr has North American versions, while the actuar package has European versions.

Sample European Pareto probability density (A) and cumulative probability (B) functions.

Sample European inverse Pareto probability density (A) and cumulative probability (B) functions.

Inverse Weibull distribution (see log-Gumbel, above)

The inverse Weibull is mathematically equivalent to the log-Gumbel distribution described above. While which is also a limiting distribution of the Burr Type 3, this distribution does not show the same instability issues, and is unbounded to the right. It therefore represents a valid SSD distribution and is included in the default model set as a distribution in its own right.

The inverse Weibull (log-Gumbel) distribution can be fitted in ssdtools by supplying the string lgumbel to the dists argument in the ssd_fit_dists call.

NOTES

1. In the diagram below, X denotes the random variable in the box at the beginning of the arrow and the expression beside the arrow indicates the mathematical transformation of X such that the resultant transformed data has the distribution identified in the box at the end of the arrow.

2. Reciprocal transformations ($\frac{1}{X}$) are bi-directional (↔︎).

3. Although the negative exponential distribution is not explicitly included in ssdtools, it is a special case of the gamma distribution with c = 1. It is included in this figure as it is related to other distributions that are included in ssdtools.

4. The European versions of the Pareto and inverse Pareto distributions are unbounded; the North American versions are bounded.