Phytophthora ramorum data from OR Forests and Nurseries (OR and CA)

Source: R/poppr.R

This is the data set from <https://doi.org/10.5281/zenodo.13007>. It has been converted to the genclone object as of poppr version 2.0. It contains 729 samples of the Sudden Oak Death pathogen *Phytophthora ramorum* genotyped over five microsatellite loci (Kamvar et. al., 2015). 513 samples were collected from forests in Curry County, OR from 2001 to mid-2014 (labeled by watershed region). The other 216 samples represents genotypes collected from Nurseries in OR and CA from Goss et. al. (2009).

data(Pram)

Format

a [genclone-class] object with 3 hierarchical levels called "SOURCE", "YEAR", and, "STATE". The other slot contains a named vector of repeat lengths called "REPLEN", a matrix of xy coordinates for the forest samples called "xy", and a palette to color the ~SOURCE/STATE stratification called "comparePal".

References

Kamvar, Z. N., Larsen, M. M., Kanaskie, A. M., Hansen, E. M., & Grünwald, N. J. (2015). Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests. Phytopathology 105:982-989. doi: 10.1094/PHYTO-12-14-0350-FI

Zhian N. Kamvar, Meg M. Larsen, Alan M. Kanaskie, Everett M. Hansen, & Niklaus J. Grünwald. 2014. Sudden_Oak_Death_in_Oregon_Forests: Spatial and temporal population dynamics of the sudden oak death epidemic in Oregon Forests. ZENODO, doi: 10.5281/zenodo.13007

Goss, E. M., Larsen, M., Chastagner, G. A., Givens, D. R., and Grünwald, N. J. 2009. Population genetic analysis infers migration pathways of *Phytophthora ramorum* in US nurseries. PLoS Pathog. 5:e1000583. doi: 10.1371/journal.ppat.1000583

Examples

data(Pram)

# Repeat lengths (previously processed via fix_replen)
other(Pram)$REPLEN
#>  PrMS6A1  Pr9C3A1 PrMS39A1 PrMS45A1 PrMS43A1 
#>  3.00000  2.00000  4.00001  4.00000  4.00000 

# Color palette for source by state. Useful for minimum spanning networks
other(Pram)$comparePal
#>    Nursery_CA    Nursery_OR    JHallCr_OR NFChetHigh_OR      Coast_OR 
#>     "#000000"     "#808080"     "#A6CEE3"     "#99CD91"     "#B89B74" 
#>   HunterCr_OR   Winchuck_OR ChetcoMain_OR  PistolRSF_OR 
#>     "#F06C45"     "#ED8F47"     "#825D99"     "#B15928"