Pack: Calculate and Plot abundance over the years pack

Description:

This workflow calculates and plots the abundance per stage per year.

This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.

This workflow was created using and based on Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ==================================================================================

Literature

Caswell, H. 2001. Matrix population models: Construction, analysis and interpretation, 2nd Edition. Sinauer Associates, Sunderland, Massachusetts.

Oostermeijer J.G.B., M.L. Brugman; E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Variation in the Demography of Gentiana pneumonanthe, a Rare Perennial Herb. The Journal of Ecology, Vol. 84(2): 153-166.

Stubben, C & B. Milligan. 2007. Estimating and Analysing Demographic Models Using the popbio Package in R. Journal of Statistical Software 22 (11): 1-23

Stubben, C., B. Milligan, P. Nantel. 2011. Package ‘popbio’. Construction and analysis of matrix population models. Version 2.3.1

Description:

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.

This workflow calculate and plot the survival based on two or more years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population.

Description:

This is a .txt file of demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).

This file allow users to run the workflow Calculate and Plot abundance over the years (http://www.myexperiment.org/packs/664.html)

This table containing the demographic data on a series of individuals during 7 years, from 1987 to 1993 (6 periods: 1987-1988, 1988-1989 etc. until 1992-1993). Each individual has a table row for each year and is identified by a number (plant column in example). For the year specified in the column 'year', each individual has a certain life stage ('stage'). The stage codes must be a string (limit to 8 characters) . When an individual died after a year the stage will x .

If you use the file please quote as:

Oostermeijer, J.G.B. M.L. Brugman, E.R. de Boer; H.C.M. Den Nijs. 1996. Temporal and Spatial Variation in the Demography of Gentiana pneumonanthe, a Rare Perennial Herb. The Journal of Ecology, 84: 153-166.