Software

The Health Systems Research and Dynamical Modelling Unit and the Biostatistics Unit are developing an open-source platform, called OpenMalaria for comparing, fitting, and evaluating different models of Plasmodium falciparum malaria and for making quantitative predictions of effects of different interventions singly or combined. This work address the malaria control needs for planning using epidemiological models that provide realistic quantitative predictions of likely outcomes of a wide range of control and elimination strategies

 

In collaboration with the Liverpool School of Tropical Medicine (LSTM), a computer programme, called MalHaploFreq for estimating malaria haplotype frequencies from blood samples was developed (Hastings and Smith, Malaria J 2008). The programme may be freely downloaded and should enhance the use of frequency data to inform antimalarial drug policy choice.

Parasite epidemiology applications

 
Maximum likelihood estimation of allele frequencies for malaria parasites
Fortran source code, windows and compiled version (zip file)

 

Latent class model for non-parametric resolution of a two component mixture, with one component sampled directly.
Winbugs code (zip-file)
Documentation (pdf-format)
 
Two-state Hidden Markov Model with covariates
Winbugs code (zip-file)
Documentation (pdf-format)
 
Regression model with Poisson errors in both x and y.
Winbugs code (zip-file)
Documentation (pdf-format)

 

Amalid is a software for the statistical analysis of longitudinal genotyping data on Plasmodium falciparum infections. It implements several published analyses of panel datasets. The program estimates force of infection, duration of infection (modeled by parametric survival distributions), and detectability (probability of detecting a malaria infection) from data containing information on presence/absence of certain parasite genotypes in blood samples.