Pack: Integral Projection Models pack

Description:

This is a .csv file of one year demographic data of the species: Cryptantha flava, collected and published by Roberto Salguero-Gómez (University of Queensland).

This file allow users to run Integral Projection Model workflow. http://www.myexperiment.org/workflows/3687.html

Each row represents one observation of an organism in the population at one census time t with the following column names:

• size: size of individuals in census time t

• sizeNext: size of individuals in census time t +1

• surv: survival of individuals from census time t to t +1 (contains: 0 for death or 1 for survival)

• fec0, ...: as many columns as desired relating size to sexual reproduction. For example, this might be:

• { fec0: probability of reproduction (output: 0 for no reproductive or 1 for reproductive)

• { fec1: number of reproductive structures (output: 1, 2, 3, ...) when individual is reproductive, that is, when fec0 = 1

• { fec2: number of propagules (output: 1, 2, 3, ...) per reproductive structure (e.g. seeds per flower in reproductive plant individual) 

• { ...

• stage: stage of individuals in census time t, used to distinguish discrete and continuous stages, etc. This workflow only analyse population with continuous stages. For rows in the table where size is not an NA, then this must be the word “continuous”. Where size is NA, stage will be NA as well.

• stageNext: stage of individuals in census time t +1, in the simples case, “continuous” or dead"(which is redundant with “0” in the surv column.

• offspringNext: if the size contained in sizeNext corresponds to the size of an offspring, this column will contain either the value “sexual” or “clonal” (depending on whether sexual or clonal reproduction is being considered) In this workflow only the sexual reproduction is considered. If this column exists, rows that take these two values will be excluded from the growth analyses

If you use the file please quote as:

Salguero-Gómez R, Siewert W, Casper BB & Tielbörger K. 2012. A demographic approach to study effects of climate change in desert plants. Philosophical Transactions of the Royal Society, series B 367, 3100-3114.

Description:

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.

The Integral Projection Model Workflow provides an environment for create an integral projection model and to calculate its population growth, structure, sensitivities and elasticities analyses, age-specific metrics, etc.

Create an IPM with no density dependence and perform several analyses on it.

Analyses:

• Lambda (λ).

• Sensitivity analysis.

• Elasticity analysis.

• Parameters elasticity and sensitivity of Lambda

• Parameters elasticity and sensitivity of Ro

• Parameters elasticity and sensitivity of Life Expectancy

• Survivorship

• Mean Life expectancy

• Passage Time

Description:

This workflow constructs and analyses an IPM with only continuous stages and without ramet production based on the IPMpack (R).

Information about the Input file:

The data must be organized in a table (in .csv format), where each row represents one observation of an organism in the population at one census time t with the following column names:

size: size of individuals in census time t sizeNext: size of individuals in census time t +1 surv: survival of individuals from census time t to t +1 (contains: 0 for death or 1 for survival) fec0, ...: as many columns as desired relating size to sexual reproduction. For example, this might be:

{ fec0: probability of reproduction (output: 0 for no reproductive or 1 for reproductive) { fec1: number of reproductive structures (output: 1, 2, 3, ...) when individual is reproductive, that is, when fec0 = 1 { fec2: number of propagules (output: 1, 2, 3, ...) per reproductive structure (e.g. seeds per flower in reproductive plant individual) { ... stage: stage of individuals in census time t, used to distinguish discrete and continuous stages, etc. This workflow only analyse population with continuous stages. For rows in the table where size is not an NA, then this must be the word “continuous”. Where size is NA, stage will be NA as well. stageNext: stage of individuals in census time t +1, in the simples case, “continuous” or dead"(which is redundant with “0” in the surv column. offspringNext: if the size contained in sizeNext corresponds to the size of an offspring, this column will contain either the value “sexual” or “clonal” (depending on whether sexual or clonal reproduction is being considered) In this workflow only the sexual reproduction is considered. If this column exists, rows that take these two values will be excluded from the growth analyses