chamae3 {aster}R Documentation

Life History Data on Chamaecrista fasciculata

Description

Data on life history traits for the partridge pea Chamaecrista fasciculata

Usage

data(chamae3)

Format

A data frame with records for 2239 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.

fit

Zero-or-one-valued. Indicates “fitness” nodes of the graph.

SIRE

Categorical. Sire.

DAM

Categorical. Dam.

SITE

Categorical. Experiment site.

POP

Categorical. Population of sire and dam.

ROW

Numerical. Row. Position in site.

BLK

Categorical. Block within site.

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

fecund

Fecundity. Bernoulli, One if any fruit, zero if no fruit.

fruit

Integer. Number of fruits observed.

Source

Julie Etterson https://sites.google.com/d.umn.edu/dr-julie-r-etterson/home

References

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

Etterson, J. R. (2004). Evolutionary potential of Chamaecrista fasciculata in relation to climate change. II. Genetic architecture of three populations reciprocally planted along an environmental gradient in the great plains. Evolution, 58, 1459–1471. doi: 10.1111/j.0014-3820.2004.tb01727.x.

These data were 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. doi: 10.1214/13-AOAS653.

Examples

data(chamae3)
### wide version
## Not run: 
### CRAN policy says examples must take < 5 sec.  This doesn't.
foo <- chamae3
### delete fit because it makes no sense in wide version
foo$fit <- NULL
chamae3w <- reshape(foo, direction = "wide", timevar = "varb",
    v.names = "resp", varying = list(levels(chamae3$varb)))

## End(Not run)

[Package aster version 1.1-2 Index]