Net reproductive rate (Ro)

Created: 2012-11-02 15:58:58 Last updated: 2014-07-25 08:59:08

Download Workflow

This workflow calculates the net reproductive rate (Ro) that is mean number of offspring by which a newborn individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next (Caswell, 2001)

===============================================================

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, 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

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/3291/download?version=2
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

Name	Description
stage_matrix_file	The stage matrix without the stage names (as you see in the example). It should be provied as a txt-file. Example from: J. Gerard B. Oostermeijer; 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.
stages	Stage input port: Here come the names of the stages or categories of the input matrix. It is very important that the stages names are not longer than 8 characters. The name of the stages must be added one by one. The respective name stages must be filled one by one. First press add value, fill a stage name (not longer than 8 characters) and press enter, then press add value and fill once again the next stage name, repeat the action until you have fill all the stages names. In the following example, the matrix has 5 stages or categories: S J V G D S 0.0000 0.0000 0.0000 7.6660 0.0000 J 0.0579 0.0100 0.0000 8.5238 0.0000 V 0.4637 0.8300 0.9009 0.2857 0.8604 G 0.0000 0.0400 0.0090 0.6190 0.1162 D 0.0000 0.0300 0.0180 0.0000 0.0232 The stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D
rows_fecundity	To perform the Net reproductive rate (Ro), the row(s) in which the recruitment values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. The Journal of Ecology): Selected lines are S and J (seedlings and juveniles, these stages receive recruits each year from the stage G): therefore, the numbers 1 and 2 are used to identify these rows (S and J). S J V G D S 0.0000 0.0000 0.0000 7.6660 0.0000 J 0.0579 0.0100 0.0000 8.5238 0.0000 V 0.4637 0.8300 0.9009 0.2857 0.8604 G 0.0000 0.0400 0.0090 0.6190 0.1162 D 0.0000 0.0300 0.0180 0.0000 0.0232
columns_fecundity	To perform the net reproductive rate (Ro), the column(s) in which the fecundity values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. The Journal of Ecology): The selected column is G (reproductive individuals): therefore number 4 will be used to identify the fecundity column (G). S J V G D S 0.0000 0.0000 0.0000 7.6660 0.0000 J 0.0579 0.0100 0.0000 8.5238 0.0000 V 0.4637 0.8300 0.9009 0.2857 0.8604 G 0.0000 0.0400 0.0090 0.6190 0.1162 D 0.0000 0.0300 0.0180 0.0000 0.0232

Processors (2)

Name	Type	Description
Net_reproductive_rat	workflow
StageMatrix_ReadFromFile	rshell	Script stageData <- read.table(stageMatrixFile) stageMatrix <- as.matrix(stageData) dimnames(stageMatrix) <- list(stages,stages) R Server localhost:6311

Beanshells (0)

Outputs (1)

Name	Description
netReproductiveRate	The net reproductive rate (Ro) is mean number of offspring by which a newborn individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next (Caswell, 2001)

Datalinks (6)

Source	Sink
columns_fecundity	Net_reproductive_rat:columns_fecundity
rows_fecundity	Net_reproductive_rat:rows_fecundity
StageMatrix_ReadFromFile:stageMatrix	Net_reproductive_rat:stage_matrix
stages	StageMatrix_ReadFromFile:stages
stage_matrix_file	StageMatrix_ReadFromFile:stageMatrixFile
Net_reproductive_rat:netReproductiveRate	netReproductiveRate

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Maria Paula Balcazar-Vargas

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (3)

(People/Groups)

Information Attributions (3)

(Workflows/Files)

Information Tags (6)

Uploader tags

Log in to add Tags

Information Shared with Groups (3)

Information Featured In Packs (1)

Net reproductive rate (Ro) pack

Log in to add to one of your Packs

Information Attributed By (4)

(Workflows/Files)

Net reproductive rate (Ro) documentation
Item doesn't exist anymore
Matrix Population Model construction and analysis v20
Matrix Population Model analysis v12

Information Favourited By (0)

No one

Information Statistics

2184 viewings

1225 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Net reproductive rate (Ro)

Created by Maria Paula Balcazar-Vargas on Friday 02 November 2012 15:58:58 (UTC)
Net reproductive rate (Ro)

Created by Maria Paula Balcazar-Vargas on Friday 25 July 2014 08:59:08 (UTC)

Revision comment:

Changes:
Inputs by default: [S,J,V,G,D] and [1,2]
Chage Springer for localhost