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)