Software

R packages :

  • TAMPO

Tampo is an R package that facilitates analyzing microchemical profiles (both mono- and multielemental composition) from fish otoliths using a recursive partitioning approach (zoning algorithm) that can accommodate some form of user-specified constraints. It also allows extracting environmental histories from otolith based on typical elemental/isotopic sequences generated using methods such as LA-ICPMS. Microchemical analysis is widely used in fisheries management and fisheries biology to identify stocks and characterize fish movements but the provided functions may be considered from the more general perspective of the chronological clustering of multivariate time series using piecewise constant regressions.

https://www6.bordeaux-aquitaine.inrae.fr/st_pee/UMR-Ecobiop/Outils/TAMPO/TAMPO

  • VarEFF

This R package estimates the effective population sizes from actual (present – sampling date) to ancestral time with a coalescent approach. This program uses microsatellites data.

https://forge-dga.jouy.inra.fr/projects/package-vareff-variation-of-effective-population-size/

Demogenetic Modelling :

  • IBASAM

Demogenetic Individual Based Modelling of Atlantic salmon populations dynamics under exploitation and climate change.

http://ibasam.github.io/IBASAM/

 

  • RUNAWAY

Demogenetic Individual Based Modelling to simulate evolution of traits and genetic architecture under sexual selection.

Executable Java version here: Runaway

Installation guide here.