#Filzbach
Fit complex models to heterogeneous data: Bayesian and likelihood analysis made easy
Filzbach is a flexible, fast, robust, parameter estimation engine that allows you to parameterize arbitrary, non-linear models, of the kind that are necessary in biological sciences, against multiple, heterogeneous data sets. Filzbach allows for Bayesian parameter estimation, maximum likelihood analysis, priors, latents, hierarchies, error propagation and model selection, from just a few lines of code.
Home web site: http://research.microsoft.com/filzbach
#Build Filzbach library
##Windows
To build static library filzbach.lib in "Debug" configuration from command prompt:
cd filzbach
msbuild
To build a dynamically linked library filzbach.dll in "Release" configuration:
cd filzbach
msbuild /p:Configuration=Release_DLL
To build either a static or a dynamic library with support for OpenMP set the CL environment variable which affects Visual C++ compiler options, e.g.
set CL=/openmp
cd filzbach
msbuild /p:Configuration=Release_DLL
##Unix
Build a library libfilzbach.a from a shell prompt:
cd filzbach
make
#Run examples
The repository contains several sample programs that illustrate how to apply Filzbach to different kinds of models.
| Id | Name | Desciption |
|---|---|---|
| 1 | normal | How to learn parameters of a normal distribution |
| 2 | normal_priors | How to set up priors |
| 3 | mixednormal | Learn the location and width of several peaks |
| 4 | poisson | Learn parameters of a Poisson distribution |
| 5 | poisson_multispp | Learn parameters of several Poisson distributions at once with hierarchical modelling |
| 7 | lr | Linear regression |
| 8 | logistic_regression | Logistic regression |
| 9 | stepfunction | Step function |
| 11 | plantgrowth | Infer parameters of a simple plant growth model from observations |
| 12 | seedrain | Seed |
| 13 | SDM | Species distribution modelling |
| 16 | ProteinInteraction | Simple model of a protein interaction network |
| 17 | TreeMort | A model of tree mortality |
On Windows, the easiest is to start Microsoft Visual Studio, open filzbach.sln, uncomment one of the lines in examples/examples.h header file and run the examples project.
You can also compile and run from command prompt. You then first set set up the CL environment variable with an example Id. E.g., to run species distribution modelling sample (Id=13) do the following:
set CL=/DMODEL#13
msbuild /t:Clean
msbuild
Debug\examples
On Unix systems from the examples directory use make to build an individual example using its name or build all the examples with one command:
cd examples
make examples