Calculate and Plot abundance over the years

Created: 2014-08-28 12:59:34

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This workflow calculates and plots the abundance per stage per year.

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 & Milligan 2007; Stubben, Milligan & Nantel 2011). ==================================================================================

Literature

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

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.

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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Option 1:

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Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (3)

Name	Description
census_data_file	The input data file must have the format of a table (a .csv-file) 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 have to be specified with a string and cannot be longer than 8 characters. When an individual died after a year or later the stage will be: dead. First, click in Set file location, a window dialog appears and the user selects the file (e.g. Data_Gentiana.csv) and then clicks the Open button. Then the link to the file will appear on the Taverna window.
graph_title	Main title of the plots. As example, it can be the name of the species or the name of the place where the research has been conducted.
last_year	this value is used to calculate and plot the abundances of the submitted data. For example, data from 1987 to 1993 (Data_Gentiana.csv). If the year 1993 is submitted, the abundances will be calculated and graphed from 1987-1993.

Processors (4)

Name	Type	Description
graph	rshell	Script library(popbio) sv_excld<-sv[sv$stage %in% stages,] number_individuals<-table(as.vector(sv_excld$stage), sv_excld$year) temp <- NULL for (stage in stages) { temp <- rbind(temp, number_individuals[stage,]) } rownames(temp) <- stages number_individuals<-temp png(number_individuals_graph) par(xpd=T, mar=c(4,4,4,8)) stage.vector.plot(number_individuals, prop=FALSE, col= rainbow(length(stages)), legend.coords=FALSE, main=graph_title) last_year<- last_year+1 max_Ind<- max(number_individuals) legend(last_year, max_Ind+10, rownames(number_individuals), cex=0.8, lty=1, col= rainbow(length(stages))) dev.off() png(proportion_individuals_graph) par(xpd=T, mar=c(4,4,4,8)) stage.vector.plot(number_individuals, prop=TRUE, ylim=c(0,1), col= rainbow(length(stages)), legend.coords=FALSE, main=graph_title) legend(last_year, 1.05, rownames(number_individuals), cex=0.8, lty=1, col= rainbow(length(stages))) dev.off() R Server localhost:6311
OutputFundamentalMatrix_3	workflow
CategoriseStages_Interaction	interaction	With this dialogue automatically appears the names of the stages or categories of the census data file. When the dialogue appears, the stages are in disorder, so the user drags and organizes the stages according to the order in the life cycle. Then, the author chooses if the stage belongs to the recruited, reproductive category or it should be excluded. Recruited means that new individuals can be recruited to this (these) stage(s). Reproductive stages are those that reproduce (produce offspring) (in this example the stage G). In the census data file Dt1.txt, x is use to denote when a plant has died in the second year, so the user must selected in the excluded column. Then the user clicks in confirm and you will read stages submitted. In the following example, the life cycle of Gentiana pneumonanthe has 5 stages or categories: 1) Seedlings S 2) Juveniles J 3) Vegetative V 4) Reproductive individuals G 5) Dormant plants D Interaction Page http://biovel.googlecode.com/svn/tags/mpm-20130805/select_stages.html
table	rshell	Script library(popbio) sv<-read.table(census_data_file, sep=";", header=TRUE) number_individuals<-table(sv$stage, sv$year) stages<-rownames(number_individuals) R Server localhost:6311

Beanshells (0)

Outputs (3)

Name	Description
number_individuals_per_stage_per_year_graph	Graph showing the abundance per stage per year.
proportion_individuals_per_stage_per_year_graph	Graph showing the proportion of individuals per stage per year.
number_individuals_per_stage_per_year	A table with numerical results of abundance per stage per year (.csv or txt files).

Datalinks (11)

Source	Sink
table:number_individuals	graph:number_individuals
CategoriseStages_Interaction:sortedStages	graph:stages
last_year	graph:last_year
table:sv	graph:sv
graph_title	graph:graph_title
graph:number_individuals	OutputFundamentalMatrix_3:input
table:stages	CategoriseStages_Interaction:unsortedStages
census_data_file	table:census_data_file
graph:number_individuals_graph	number_individuals_per_stage_per_year_graph
graph:proportion_individuals_graph	proportion_individuals_per_stage_per_year_graph
OutputFundamentalMatrix_3:output	number_individuals_per_stage_per_year