Table 2.
Selected list of free software packages that can be used in wildlife network epidemiology.
| Category name | Type | Programming skills required? | Comments | Ref./Download location |
|---|---|---|---|---|
| Capture-mark-recapture | ||||
|
| ||||
| M-Surge | Application | No | Windows platform | [75]/http://www.cefe.cnrs.fr/BIOM/logiciels.htm |
| MARK | Application | No | Windows platform | [76]/http://warnercnr.colostate.edu/~gwhite/mark/mark.htm |
|
| ||||
| Network simulation/analysis | ||||
|
| ||||
| Pajek | Application | No | Analysis of large networks | [77]/http://vlado.fmf.uni-lj.si/pub/networks/pajek/ |
| igraph | R Package | Basic | Used for all network visualizations in this article | [78]/http://www.r-project.org/ |
| sna | R package | Basic | Other related R packages available on http://statnet.org/ | [79]/http://www.r-project.org/ |
| network | R Package | Basic | Other related R packages available on http://statnet.org/ | [80]/http://www.r-project.org/ |
| ClustRNet | Python package | Basic | Simulates network with variable clustering degree | [81]/http://sbansal.com/ClustRNet/ |
| NetLogo | Interpreted language | Basic | Cross-platform | [82]/http://ccl.northwestern.edu/netlogo/ |
|
| ||||
| Epidemiological modelling | ||||
|
| ||||
| EpiFire (GUI) | Application | No | Cross-platform | unpublished/http://sourceforge.net/projects/epifire/ |
| NetLogo | Interpreted language | Basic | Cross-platform | [82]/http://ccl.northwestern.edu/netlogo/ |
| R | Interpreted language | Basic | Cross-platform | [83]/http://www.r-project.org/ |
| Python | Interpreted language | Basic | Cross-platform | http://www.python.org/ |
| EpiFire (API) | C++ library | Yes (C/C++) | Includes network simulation capabilities | unpublished/http://sourceforge.net/projects/epifire/ |