Statistical Software

It is frightful that someone who is no one ... can set any error into circulation with no thought of responsibility and with the aid of this dreadful disproportioned means of communication, Søren Kierkegaard's Journals and Papers, Edited and translated by H. V. Hong et. al., Vol. 2, p 481, 1967.

Surveillance of infectious diseases

surveillance -- An R-package implementing monitoring and modelling methods for routine collected disease surveillance data. Seen in a broader statistical context the package implements retrospective modeling and prospective change-point detection in time series of counts, proportions and categorical data as well as space-time processes. The package is available from CRAN.

Epidemic Modelling

RLadyBug -- An R package for the visualisation and inference in stochastic Susceptible-Exposed-Infectious-Recovered (SEIR) models and its spatio-temporal extensions. The package used to be available from CRAN.

LadyBug 2.0 -- MCMC estimation of partially observed epidemics implemented in Java using the Hydra library. This is an implementation of the theory presented in Inference in disease transmission experiments using stochastic epidemic models, M. Höhle, E. Jørgensen, and P.D. O'Neill, Journal of the Royal Statistical Society, Series C, volume 54, part 2 (2005), pages 349-366.

R-code in connection with study group and seminar on the book Stochastic Epidemic Models and Their Statistical Analysis, H. Andersson and T. Britton (2000), Lecture Notes in Statistics 151, Springer. The file README.html contains a more detailed description of the files useful for simulating SIR epidemics, calculating final sizes and estimating model parameters.

R-code to calculate R0 by the method of moments (i.e. according to Equation 7.4.3 in N. G. Becker's Analysis of Infectious Disease Data, Monographs on Statistics and Applied Probability. Chapman and Hall, 1989).
Data from the article Experimental quantification of vaccine induced reduction in virus transmission, M.C.M. De Jong and T.G. Kinman, Vaccine, 12:761–766, 1994 and the data used in the LadyBug article are given as example.

Population Size and Sample Size Calculations

Maple and R-code accompanying the paper "Bayesian Estimation of the Size of a Population". A population of unknown size N is labeled using the serial numbers {1,2,...,N}. A random sample (X_1,...,X_n) of size n<N is observed without replacement. The task is to make Bayesian inference on the population size N.

binomSamSize -- An R package available from CRAN for computing confidence intervals and sample size determination for a binomial proportion under simple random sampling and grouped/pooled sampling. Useful when e.g. determining the prevalence of disease in an animal population or when trying to substantiate freedom from disease. A similar package for this task is the binGroup package from Frank Schaarschmidt.

Stochastic Petri Nets

Stochastic Petri Nets (SPNs) in R. The petRi (v1.0) package is a small R-package to read Petri Nets specified by CPN Tools and enhance them to SPNs. Supported features are: simulation (the token game), estimation of stationary distribution, analysis of mean number of tokens, distribution of firing transition, etc. Two examples from systems biology are given.

[petRi_1.0.tar.gz] [petRi_1.0.zip]

Computer Assisted Learning

Student programmer on the LDIP (digital photogrammetry) and LDIPInter (Image processing & digital photogrammetry) projects.

Miscellaneous

Emacs mode, and code for Dynamic Generalized Linear Models in Ox.