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Throughout the package epiphy, special attention is given to stay consistent consistent with variable and parameter names. Some of the most significant names are the followings:
The aggregation parameter, \(\theta\), can be computed from the two shape parameters of the beta-binomial distribution, \(\alpha\) and \(\beta\). Note that in epiphy, \(\theta = 1 / (\alpha + \beta)\) as in Madden, Hughes, and Bosch (2007), but this definition is not necessarily consistent with what can be found somewhere else in the literature. For example, \(\theta = \alpha + \beta\) in the package emdbook.
The intra-cluster correlation coefficient, \(\rho\) (Mak 1988), characterizes the spatial aggregation as the tendency for elements in a sampling unit to have the same disease status more frequently than expected on the basis of spatial randomness (Madden, Hughes, and Bosch 2007). In epiphy, \(\rho = \theta / (\theta + 1)\).
Functions of the two shape parameters of the beta-binomial distribution (\(\alpha\) and \(\beta\)):
\[p = \frac{\alpha}{\alpha + \beta}; \theta = \frac{1}{\alpha + \beta}; \rho = \frac{1}{\alpha + \beta + 1}\]
Functions of the aggregation parameter (\(\theta\)) or the intra-cluster correlation coefficient (\(\rho\)):
\[\theta = \frac{\rho}{1 - \rho}; \rho = \frac{\theta}{\theta + 1}\]
Functions of the average disease intensity (\(p\)) and the aggregation parameter (\(\theta\)):
\[\alpha = \frac{p}{\theta}; \beta = \frac{1 - p}{\theta}\]
Functions of the average disease intensity (\(p\)) and the intra-cluster correlation coefficient (\(\rho\)):
\[\alpha = \frac{p(1-\rho)}{\rho}; \beta = \frac{(1 - p)(1-\rho)}{\rho}\]
There are different parametrizations of the binary form of the power law. The user should therefore be cautious when making computations and comparisons with published results. Below are reminders about definitions and relationships between these different parametrizations.
\[ s_{obs}^2 = V_n = A_n [np(1-p)]^b = a_n [p(1-p)]^b \]
\[ s_{obs}^2 = V_p = A_p [p(1-p)/n]^b = a_p [p(1-p)]^b \]
where \(s_{obs}^2\) stands for the observed variance. The relationships between the different binary power law parameters (\(A_p\), \(a_p\), \(A_n\), \(a_n\) and \(b\)) are specified in the following relationship tables. Note that \(V_n = n^2 V_p\).
Full version.
| \(A_p\) | \(a_p\) | \(A_n\) | \(a_n\) | |
|---|---|---|---|---|
| \(A_p\) | \(1\) | \(A_p = a_p n^b\) | \(A_p = A_n n^{2(b-1)}\) | \(A_p = a_n n^{b-2}\) |
| \(a_p\) | \(a_p = A_p n^{-b}\) | \(1\) | \(a_p = A_n n^{b-2}\) | \(a_p = a_n n^{-2}\) |
| \(A_n\) | \(A_n = A_p n^{2(1-b)}\) | \(A_n = a_p n^{2-b}\) | \(1\) | \(A_n = a_n n^{-b}\) |
| \(a_n\) | \(a_n = A_p n^{2-b}\) | \(a_n = a_p n^2\) | \(a_p = A_n n^b\) | \(1\) |
Reader-friendly version. To read it, the formula \(\text{row} = \text{col} \times \text{cell}\) must be used.
| \(A_p\) | \(a_p\) | \(A_n\) | \(a_n\) | |
|---|---|---|---|---|
| \(A_p\) | \(1\) | \(n^b\) | \(n^{2(b-1)}\) | \(n^{b-2}\) |
| \(a_p\) | \(n^{-b}\) | \(1\) | \(n^{b-2}\) | \(n^{-2}\) |
| \(A_n\) | \(n^{2(1-b)}\) | \(n^{2-b}\) | \(1\) | \(n^{-b}\) |
| \(a_n\) | \(n^{2-b}\) | \(n^2\) | \(n^b\) | \(1\) |
Note that the function a2a is kindly provided in
epiphy to make these tricky conversions as easy as
possible.
\[ \theta = \frac{a_p - f(p)/n}{f(p) - a_p} \text{, with } f(p) = [p(1-p)]^{1-b} \]
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.