Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population
Created: 2012-11-01 12:59:45
Last updated: 2014-07-25 07:35:24
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
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Authors (1)
| Maria Paula Balcázar-Vargas, Jonathan Giddy and G. Oostermeijer |
Titles (1)
| Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population |
Descriptions (1)
| 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 |
Dependencies (0)
Inputs (1)
| Name |
Description |
| census_data_file |
The input data file must have the format of a table containing the demographic data on a series of individuals over several 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 cannot be longer than 8 characters.
For all individuals, the number of offspring is specified in a chosen way (in the example, 'reprstr' gives the number of flowers/fruits for each plant. In the example, it can be seen that only generative adults (stage=G) have flowers. Individuals without offspring must be indicated by filling in '0' in this column (i.e. the 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.
|
Processors (9)
| Name |
Type |
Description |
| GetStages |
workflow |
|
| stage |
stringconstant |
Valuestage |
| GetInitialYear |
workflow |
|
| year |
stringconstant |
Valueyear |
| StageMatrix_FromCens |
workflow |
|
| CensusData_ReadFromFile |
rshell |
Scriptcensus_data <- read.table(census_data_file, header=TRUE, fill=TRUE)
R Serverlocalhost:6311 |
| display |
rshell |
Scriptoptions(digits=16);sink(output)
print(input)
sink()
R Serverlocalhost:6311 |
| display_trans |
rshell |
Scriptoptions(digits=16);sink(output)
print(input)
sink() R Serverlocalhost:6311 |
| display_csv |
rshell |
Scriptwrite.csv(input, file=output) R Serverlocalhost:6311 |
Outputs (3)
| Name |
Description |
| MatrixOut |
It is the stage matrix in plane text.
|
| trans |
This table shows the input data in a different format (that can be easily checked):
Each row has one unique individual, with column plant giving its unique ID number
The other columns show:
year: the first census year;
stage: the stage in the first year,
repstr: the number of offspring (reproductive structures) in the first year
recruitment: column containing the indicators for new individuals in the population (remains empty here)
year2: the second census year;
fate: the stage in the second year,
repstr2: the number of offspring (reproductive structures) in the second year
recruitment2: column containing the indicators for new individuals in the population in year 2 (remains empty here)
|
| MatrixCSV |
It is the stage matrix in CSV format.
|
Datalinks (15)
| Source |
Sink |
| stage:value |
GetStages:stageColumnHeader |
| CensusData_ReadFromFile:census_data |
GetStages:census_data |
| year:value |
GetInitialYear:yearColumnName |
| CensusData_ReadFromFile:census_data |
GetInitialYear:census_data |
| GetStages:matrixStages |
StageMatrix_FromCens:stages |
| GetInitialYear:initialYears |
StageMatrix_FromCens:initialYear |
| GetStages:recruitedStages |
StageMatrix_FromCens:recruitedStages |
| CensusData_ReadFromFile:census_data |
StageMatrix_FromCens:census_data |
| census_data_file |
CensusData_ReadFromFile:census_data_file |
| StageMatrix_FromCens:stage_matrix |
display:input |
| StageMatrix_FromCens:trans |
display_trans:input |
| StageMatrix_FromCens:stage_matrix |
display_csv:input |
| display:output |
MatrixOut |
| display_trans:output |
trans |
| display_csv:output |
MatrixCSV |
Coordinations (1)
| Controller |
Target |
| GetStages |
GetInitialYear |
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