Age specific analysis

Created: 2012-11-02 14:28:56 Last updated: 2014-07-24 12:24:05

Download Workflow

The age specific analysis workflow gives the basic information on age-specific survival, this includes the mean, variance and coefficient of variation (cv) of the time spent in each stage class and the mean and variance of the time to death.

Fundamental matrix (N): is the mean of the time spent in each stage class.

Variance (var): is the variance in the amount of time spent in each stage class.

Coefficient of variation (cv): is the coefficient of variation of the time spent in each class (sd/mean- the ratio of the standard deviation to the mean).

Meaneta: is the mean of time to death, of life expectancy of each stage.

Vareta: is the variance of time to death.

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

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

============================================================ For further details see:

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

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://myexperiment.org/workflows/3286/download?version=3
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (4)

Name	Description
stage_matrix_file	Stage Matrix in a .txt file format. Click in Set file location, a window dialog appears and the user selects the file and then clicks the Open button. Then the link to the file will appear on the Taverna window. 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	Here come the names of the stages or categories of the input matrix. No longer than 8 characters. 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 e.g. the stages of this matrix are called: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D The name of stages or categories must be added one by one. First press add value, fill the name of the stage no longer than 8 characters and press enter; then press add value and fill once again the next name of the stage; repeat the action until you have fill all the names of all stages.
rows_fecundity	The row(s) in which the recruitment values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. Journal of Ecology): Selected rows 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. The numbers of the stages that receive recruits each year from the stage G must be added one by one (in the case that there are more than one recruit stage row). First press add value, fill the number of the row and press enter, then press add value and fill once again the next recruit stage row, repeat the action until you have fill all the numbers of all recruits rows. 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	The column(s) in which the fecundity values are found, should be selected. In the example of the Gentiana species (Oostermeijer et al. 1996. Journal of Ecology): The selected column is G (reproductive individuals), the number 4 will be used to identify the fecundity column (G). The numbers of the reproductive columns must be added one by one (in the case that there is more than one reproductive column. In this example there is only one). First press add value, fill the number of the column and press enter, then press add value and fill once again the next reproductive column, repeat the action until you have fill all the numbers of all reproductive columns. 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
Age_specific_survival_analysis	rshell	Script library(popbio) frame<-read.table(filename) matrix1 = as.matrix(frame) dimnames(matrix1) <- list(stages,stages) a<-fundamental.matrix(matrix1, r=rows, c=columns) R Server localhost:6311
display	rshell	Script options(digits=16);sink(output) print(input) sink() R Server localhost:6311

Beanshells (0)

Outputs (1)

Name	Description
Age_specific_survival	The age specific survival workflow gives the basic information on the mean, variance and coefficient of variation (cv) of the time spent in each stage class and the mean and variance of the time to death. Fundamental matrix (N): is the mean of the time spent in each stage class. e.g.:For our Gentiana example means a J plants will spends, on average, about 1 year as a Juvenile, 12 as vegetative plant, less than a year a reproductive and dormant plant. Variance (var): is the variance in the amount of time spent in each stage class. Coefficient of variation (cv): is the coefficient of variation of the time spent in each class (sd/mean- the ratio of the standart deviation to the mean). Meaneta: is the mean of time to death, of life expectancy of each stage. e.g.:The mean age at death is the life expectancy; the life expectancty of a new individual seedling is 8 years. Vareta: is the variance of time to death.

Datalinks (6)

Source	Sink
stage_matrix_file	Age_specific_survival_analysis:filename
stages	Age_specific_survival_analysis:stages
columns_fecundity	Age_specific_survival_analysis:columns
rows_fecundity	Age_specific_survival_analysis:rows
Age_specific_survival_analysis:a	display:input
display:output	Age_specific_survival

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 3 (latest) (of 3)

Information Credits (3)

(People/Groups)

Information Attributions (3)

(Workflows/Files)

Information Tags (8)

Uploader tags

Log in to add Tags

Information Shared with Groups (3)

Information Featured In Packs (1)

Age specific survival analysis pack

Log in to add to one of your Packs

Information Attributed By (5)

(Workflows/Files)

Age-specific survival documentation
Item doesn't exist anymore
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

2631 viewings

1966 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Age-specific survival analysis.

Created by Maria Paula Balcazar-Vargas on Friday 02 November 2012 14:28:56 (UTC)
Age specific analysis

Created by Maria Paula Balcazar-Vargas on Wednesday 02 July 2014 11:53:12 (UTC)

Revision comment:

This workflows runs R software in your onw computer.
Age specific analysis

Created by Maria Paula Balcazar-Vargas on Thursday 24 July 2014 12:24:05 (UTC)

Revision comment:

Changes:
* print values 16 digits
* Liberation sink memory
* Input values by default: stages ("[S,J,V,G,D]") and en rows_fecundity ("[1,2]")