spaMM (version 1.7.2)

arabidopsis: Arabidopsis genetic and climatic data

Description

For 948 accessions from European Arabidopsis thaliana populations, this data set merges the genotypic information at four single nucleotide polmorphisms (SNP) putatively involved in adaptation to climate (Fournier-Level et al, 2011, Table 1), with 13 climatic variables from Hancock et al. (2011).

Usage

data(arabidopsis)

source

The data were retrieved from http://bergelson.uchicago.edu/regmap-data/climate-genome-scan on 22 February 2013 (they may no longer be available from there).

Details

The response is binary so HLmethod="PQL/L" seems warranted (see Rousset and Ferdy, 2014).

References

Fournier-Level A, Korte A., Cooper M. D., Nordborg M., Schmitt J., Wilczek AM (2011). A map of local adaptation in Arabidopsis thaliana. Science 334: 86-89. Hancock, A. M., Brachi, B., Faure, N., Horton, M. W., Jarymowycz, L. B., Sperone, F. G., Toomajian, C., Roux, F., and Bergelson, J. 2011. Adaptation to climate across the Arabidopsis thaliana genome, Science 334: 83-86. Rousset F., Ferdy, J.-B. (2014) Testing environmental and genetic effects in the presence of spatial autocorrelation. Ecography, 37: 781-790. http://dx.doi.org/10.1111/ecog.00566

Examples

data(arabidopsis)
if (spaMM.getOption("example_maxtime")>3) {
  HLCor(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
            ranPars=list(rho=0.129,lambda=4.28,nu=0.291),
            family=binomial(),HLmethod="PQL/L",data=arabidopsis)
}
## the above ranPars are deduced from an hour(s?)-long analysis:
verylong <- corrHLfit(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
              family=binomial(),HLmethod="PQL/L",data=arabidopsis)
summary(verylong)