Generation time (T)
Created: 2012-11-02 15:04:47
Last updated: 2014-07-25 08:40:21
The time T required for the population to increase by a factor of Ro (net reproductive rate)
e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055
The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so.
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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
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Authors (1)
| Maria Paula Balcázar-Vargas, Jonathan Giddy and G. Oostermeijer
|
Titles (1)
Descriptions (1)
| The time T required for the population to increase by a factor of Ro (net reproductive rate)
e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055
The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so.
=========================================================
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 |
Dependencies (0)
Inputs (4)
| Name |
Description |
| stage_matrix_file |
A stage matrix
In this import port a stage-matrix should be add. The input data (a .txt-file) has to be a point delimited (see example).
In the pop-up ‘run workflow’ window, click-on ‘set a location’ and seach in your computer the txt-file of your matrix.
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 generation time (T), the row(s) 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 generation time (T), 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 |
| Generation_time_analysis |
rshell |
Scriptlibrary(popbio)
result <- generation.time(mat, r=rows, c=columns)
R Serverlocalhost:6311 |
| read_matrix |
rshell |
Scriptframe <- read.table(filename)
mat <- as.matrix(frame)
dimnames(mat) <- list(stages,stages)
R Serverlocalhost:6311 |
Outputs (1)
| Name |
Description |
| generation_time |
Generation time (T):
The time T required for the population to increase by a factor of Ro (net reproductive rate)
e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055
The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants and took approximately 8.05 years to do so.
|
Datalinks (6)
| Source |
Sink |
| read_matrix:mat |
Generation_time_analysis:mat |
| Columns_fecundity |
Generation_time_analysis:columns |
| Rows_fecundity |
Generation_time_analysis:rows |
| stages |
read_matrix:stages |
| stage_matrix_file |
read_matrix:filename |
| Generation_time_analysis:result |
generation_time |
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