STEPCAM-package: ABC-SMC Inference of STEPCAM

Description

ABC-SMC inference of the relative contribution of dispersal assembly, filtering and limiting similarity through the use of stepwise commmunity assembly. Updates Version 1.2 - STEPCAM can now be found on GitHub: https://github.com/thijsjanzen/STEPCAM - Merged STEPCAM code with the supplementary code of Hauffe et al. 2016 - Added two vignettes - Added a large number of code tests Version 1.1.2 - updated the prior - now all three processes have a mean prior value of 1/3, and a log-normal kind shape in [0,1] Version 1.1.1 - fixed a bug in the ABC-SMC code leading to the error "Error in if (fit < threshold) : missing value where TRUE/FALSE needed" Version 1.1 - calculation of the diversity indices is plit up into two parts: calculating the ordination axes, and the actual calculation of the indices - this allows for a speed up of the code by moving the calculation of the ordination axes outside the SMC algorithm. Many thanks to Torsten Hauffe for this improvement! - Corrected scaling of the dbFD function - it now always treats abundances as presence/absence data, much thanks to Torsten Hauffe for pointing this out! - updated references

Arguments

Details

Package:

STEPCAM

Type:

Package

Version:

1.2

Date:

2016-09-20

License:

GPL 2.0

The function STEPCAM_ABC performs an ABC-SMC analysis of the STEPCAM model on user provided data, the functions plotSMC, plotSTEPCAM and TernPlot provide functions to plot the output generated by the ABC-SMC analysis.

References

Fons van der Plas, Thijs Janzen, Alejandro Ordonez, Wimke Fokkema, Josephine Reinders, Rampal S. Etienne, and Han Olff 2015. A new modeling approach estimates the relative importance of different community assembly processes. Ecology 96:1502-1515.

Hauffe, Torsten, Christian Albrecht, and Thomas Wilke. Assembly processes of gastropod community change with horizontal and vertical zonation in ancient Lake Ohrid: a metacommunity speciation perspective. Biogeosciences 13.10 (2016): 2901-2911.