Survival models using Kaplan-Meier (Williams, 1995) estimates were implemented using SUDAAN SUDAAN Statistical Software Centree, 2008).
The concepts used by the decision support modules (patient data, risks estimates) are implemented in JAVA classes; these classes encapsulate relational databases with SQL queries and generate with the results HTML pages by using Active Server Pages technology.
For continuous features, the kernel density estimation [KDE; the estimate is implemented by MATLAB's "ksdensity" function, using a normal kernel function and a window parameter (bandwidth) that is a function of the number of points in the sample] [ 49] is employed to acquire the empirical probability density function f (x|E) for essential genes and f x | E ¯ for non-essential genes [ 49].
The estimating procedure was implemented in R (16) (R Foundation for Statistical Computing, Vienna, Austria), and the code can be found in Appendix 2. In Appendix 1, we also discuss uncertainty estimates for β ˆ and γ ˆ, respectively.
The inclusion of those items had a notable affect on growth estimates when DIF was implemented in the 2PL model.
The Dayhoff model of amino acid substitution was used and the discrete gamma distribution model, with four rate categories and an estimated alpha parameter, was implemented.
The generalized estimating equations procedure was implemented to adjust for correlation among multiple infections for the same child.
The maximum likelihood estimate method 307 was implemented in MATLAB, with code available from www.santafe.edu/∼aaronc/powerlaws/.
The Taylor series linearization approach (48, 49), which derives a linear approximation of variance estimates to develop corrected standard errors and confidence intervals, was implemented to estimate variances.
A solution of the third type for estimating gene regulatory networks was implemented by Bøttcher et al. [ 19]: the greedy hill climbing (GHC) method.
