spaMM: arabidopsis – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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 polymorphisms (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")

Format

The data frame includes 948 observations on the following variables:

pos1046738, pos5510910, pos6235221, pos8132698: Genotypes at four SNP loci
LAT: latitude
LONG: longitude
seasonal, tempWarmest, tempColdest, preciWettest, preciDriest, preciCV, PAR_SPRING,
growingL, conseqCold, conseqFrFree, RelHumidSp, dayLSp, aridity: Thirteen climatic variables. See Hancock et al. (2011) for details about these variables.

Details

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

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).

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. doi: 10.1111/ecog.00566

Examples

data("arabidopsis")
if (spaMM.getOption("example_maxtime")>2.5) {
  fitme(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
        fixed=list(rho=0.119278,nu=0.236990,lambda=8.599),
        family=binomial(),method="PQL/L",data=arabidopsis)
}
## The above 'fixed' values are deduced from the following fit:
if (spaMM.getOption("example_maxtime")>46) {
  SNPfit <- fitme(cbind(pos1046738,1-pos1046738)~seasonal+Matern(1|LAT+LONG),
              verbose=c(TRACE=TRUE), 
              family=binomial(),method="PQL/L",data=arabidopsis)
  summary(SNPfit) # p_v=-125.0392
}

spaMM

Mixed-Effect Models, with or without Spatial Random Effects

v3.10.0

CeCILL-2

Authors

François Rousset [aut, cre, cph] (<https://orcid.org/0000-0003-4670-0371>), Jean-Baptiste Ferdy [aut, cph], Alexandre Courtiol [aut] (<https://orcid.org/0000-0003-0637-2959>), GSL authors [ctb] (src/gsl_bessel.*)

Initial release

2022-02-06