Pack: Matrix Population Model construction pack

Description:

This is a .txt file of four years 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 Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v19 (http://www.myexperiment.org/workflows/3684.html)

The input data has to have the format of a table containing the demographic data on a series of individuals in two years. 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 can be chosen by the user, but they have to be specified with a string (limit to characters) . The stages names cannot be longer than 8 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new in the second year census to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present.

This file allow users to run population modelling workflow.

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.

Description:

This workflow create a stage matrix model based on two years census data of tagged or mapped individuals of an animal or plant population. Each annual census describes for each individual its life stage, reproductive output (estimated number offprings) and whether or not it is a new recruit. The workflow converts this data into a stage matrix model from 1 year to 2 that contains transitions probabilities from each stage to the next.

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 based on Package ‘popbio’ in R.

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 is a .txt file of one year 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 Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population (http://www.myexperiment.org/workflows/3276.html) or Matrix Population Model construction and analysis v19 (http://www.myexperiment.org/workflows/3684.html)

The input data (a .txt-file) has to have the format of a table containing the demographic data on a series of individuals in two years. 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 can be chosen by the user, but they have to be specified with a string (limit to characters) . The stages names cannot be longer than 8 characters. For all individuals, the number of offspring is specified in a chosen way (in the example, 'repstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) had flowers. Individuals without offspring have to be indicated by filling in '0' in this column, which cannot have empty cells. The column 'recruitment' specifies those individuals that are new in the second year census to the population by means of a code. In the example, 'RS' is a new seedling, and 'RJ' a new juvenile plant. As can be seen in the example, no code is needed in this column for individuals that were already present.

If you use the file please quote as:<o:p></o:p>

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.

Description:

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

The Creation of a stage matrix model Workflow provides an environment to construct a stage matrix model. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population. The resulting is a stage matrix model.