oats: Life History Data on Avena barbata
In aster: Aster Models

oats	R Documentation

Life History Data on Avena barbata

Description

Data on life history traits for the invasive California wild oat Avena barbata

Usage

data(oats)

Format

A data frame with records for 821 plants. Data are already in “long” format; no need to reshape.

resp: Response vector.
varb: Categorical. Gives node of graphical model corresponding to each component of resp. See details below.
root: All ones. Root variables for graphical model.
id: Categorical. Indicates individual plants.
Plant.id: Categorical. Another indicator of individual plants.
Env: Categorical. Environment in which plant was grown, a combination of experimental site and year.
Gen: Categorical. Ecotype of plant: mesic (M) or xeric (X).
Fam: Categorical. Accession, nested within ecotype.
Site: Categorical. Experiment site. Two sites in these data.
Year: Categorical. Year in which data were collected. Four years in these data.
fit: Indicator (zero or one). Shorthand for as.numeric(oats$varb == "Spike"). So-called because the components of outcome indicated are the best surrogate of Darwinian fitness in these data.

Details

The levels of varb indicate nodes of the graphical model to which the corresponding elements of the response vector resp belong. This is the typical “long” format produced by the R reshape function. For each individual, there are several response variables. All response variables are combined in one vector resp. The variable varb indicates which “original” variable the number was for. The variable id indicates which individual the number was for. The levels of varb, which are the names of the “original” variables are

Surv: Indicator (zero or one). Bernoulli, One if individual survived to produce flowers.
Spike: Integer. Zero-truncated Poisson, number of spikelets (compound floral structures) observed.

Graphical model is

1 \longrightarrow \mbox{Surv} \longrightarrow \mbox{Spike}

Source

Robert Latta https://www.dal.ca/faculty/science/biology/faculty-staff/our-faculty/robert-latta.html

References

These data are a subset of data previously analyzed using non-aster methods in the following.

Latta, R. G. (2009). Testing for local adaptation in Avena barbata, a classic example of ecotypic divergence. Molecular Ecology, 18, 3781–3791. \Sexpr[results=rd]{tools:::Rd_expr_doi("https://doi.org/10.1111/j.1365-294X.2009.04302.x")}.

These data are reanalyzed by aster methods in the following.

Geyer, C. J., Ridley, C. E., Latta, R. G., Etterson, J. R., and Shaw, R. G. (2013) Local Adaptation and Genetic Effects on Fitness: Calculations for Exponential Family Models with Random Effects. Annals of Applied Statistics, 7, 1778–1795. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1214/13-AOAS653")}.