echin2: Life History Data on Echinacea angustifolia
In aster: Aster Models

echin2

R Documentation

Life History Data on Echinacea angustifolia

Description

Data on life history traits for the narrow-leaved purple coneflower Echinacea angustifolia

Usage

data(echin2)

Format

A data frame with records for 557 plants observed over five years. 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.
flat: Categorical. Position in growth chamber.
row: Categorical. Row in the field.
posi: Numerical. Position within row in the field.
crosstype: Categorical. See details.
yearcross: Categorical. Year in which cross was done.

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

lds1: Survival for the first month in the growth chamber.
lds2: Ditto for 2nd month in the growth chamber.
lds3: Ditto for 3rd month in the growth chamber.
ld01: Survival for first year in the field.
ld02: Ditto for 2nd year in the field.
ld03: Ditto for 3rd year in the field.
ld04: Ditto for 4th year in the field.
ld05: Ditto for 5th year in the field.
roct2003: Rosette count, measure of size and vigor, recorded for 3rd year in the field.
roct2004: Ditto for 4th year in the field.
roct2005: Ditto for 5th year in the field.

These data are complicated by the experiment being done in two parts. Plants start their life indoors in a growth chamber. The predictor variable flat only makes sense during this time in which three response variables lds1, lds2, and lds3 are observed. After three months in the growth chamber, the plants (if they survived, i. e., if lds3 == 1) were planted in an experimental field plot outdoors. The variables row and posi only make sense during this time in which all of the rest of the response variables are observed. Because of certain predictor variables only making sense with respect to certain components of the response vector, the R formula mini-language is unable to cope, and model matrices must be constructed "by hand".

Echinacea angustifolia is native to North American tallgrass prairie, which was once extensive but now exists only in isolated remnants. To evaluate the effects of different mating regimes on the fitness of resulting progeny, crosses were conducted to produce progeny of (a) mates from different remnants, (b) mates chosen at random from the same remnant, and (c) mates known to share maternal parent. These three categories are the three levels of crosstype.

Source

Stuart Wagenius, https://www.chicagobotanic.org/research/staff/wagenius

References

These data are analyzed in the following.

Shaw, R. G., Geyer, C. J., Wagenius, S., Hangelbroek, H. H., and Etterson, J. R. (2008) Unifying life history analyses for inference of fitness and population growth. American Naturalist, 172, E35-E47. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1086/588063")}.