MCMC
The twalk: A self-adjusting multi-scale MCMC algorithm, more information in the link.
Radiocarbon Dating:
BACON : The gamma autoregressive software for age-depth modeling (Maarten Blaauw’s page).
Create a Directed Acyclyc Graph (DAG) in Latex:
After loosing my time with other general software for ploting combinatorial graphs (eg. graphviz) it is better to fiddle with Tikz, it is not difficult. Here are two examples: DAG_complete.tex DAG_marg.tex .
Random sign model and the Pump Failure data, R program: PumpFailure.R data file: DatosBomba.txt
Multiproc.py, a tutorial for multiprocessing in Python (3.x): https://www.cimat.mx/~jac/software/Multiproc.py
fcmp, a Python module extension to compare two floats:
To compare two floating precision numbers ("reals", 3.4, 5.89e+03, etc.) you need an epsilon or radius within which the numbers are judge equal. There is no alternative. In base 10, 1.0/3.0 is not 0.33333 nor 0.333333333333 etc. A nine digit precision (default) will call the former less than 1/3 and the latter equal to 1/3. However, the radius is only relative, floating, as the precision in these numbers.
Floats are basically written inside computers (and python) as m * (2 ** e) . A mantissa, m, and an exponent, e. The exponents are first compared and if equal, then the mantisas are compared up to the precision required.
Please download the module extension (is in fact a simple C wraper using swig, for a function taken from the gsl library) and follow the instructions within: fcmp
Epidemic Outbreak detection:
A Python-Scipy implementation of Yury E. Garcia, J. Andres Christen and Marcos A. Capistran (2015), "A Bayesian Outbreak Detection Method for Influenza-Like Illness", Journal of Biomedicine and Biothechnology (revision): BayesFactor.py
Clinical Trials
tr: A software written in R for a dyniamic illustration and
ADeBay with the full implementation (written in Python) for the trial design in
Christen, J.A., P. Müller, K. Wathen and J. Wolf (2003) (see Main papers).
Unpack the zip file (in windows by double clicking on it) and read the README file. This project was in part supported by NSF award 203207.
Biodiversity
Cactus: Análisis de curvas de acumulación de especies, solo disponible para sistemas UNIX (Linux, Mac, etc.). Ponga
$ gunzip Cactus.tar.gz
$ tar xvf Cactus.tar
$ cd Cactus
Y siga las instrucciones en LEEME ($ more LEEME).
BioP: User friendly software for biodiversity studies. BioP: spicies distributions and biogeography.
Other Radiocarbon Dating
BCal: A user friendly web based software for Bayesian radiocarbon calibration.
http://bcal.shef.ac.uk/
Bwigg: A user friendly, Internet based, software for Bayesian radiocarbon wiggle matching. Sorry, not available for the moment, send me an email if you need to use it.
Bpeat: A user friendly, C++, R interphased software for the analysis of radiocarbon dated peat cores. Currently the Beta distribution has been tested for Linux and compiled for Mac OS. The cc and g++ compilers need to be available. Download, unpack and install with:
% tar xvf Bpeat-beta-1.0.tar
% cd Bpeat-beta-1.0
% ./Install
http://www.cimat.mx/~jac/software/Bpeat-beta-1.0.tar
Clustering, Bioinformatics
BClass: Bayesian self-organizing maps for classification of heterogeneous biological databases.
Unzip and untar the file and read the README file for a demo. For details see paper in main papers section.