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Description
Hello I am trying to calculate iHS for a model i have built using Coala. I have added sumstat_ihh to my model and set calc_ihs =TRUE. It returns two data frames when simulated but no values for iHS just NA. Plus it discards all focal markers less than 0.05 which i would like to be set to 0.0, but can't find how to do so. I have copied my R script here, please tell me where i am going wrong.
Thanks!
modeliHS <- coal_model(
sample_size = 500,
loci_number = 5000,
loci_length = 1000,
ploidy = 1)
modeliHS <-
modeliHS + feat_mutation(
rate = 0.5,
model = "IFS",
base_frequencies = NA,
tstv_ratio = NA,
gtr_rates = NA,
fixed_number = FALSE,
locus_group = "all"
) + feat_recombination(0.4) + (sumstat_ihh(
name = "ihh",
population = "all",
max_snps = Inf,
calc_ihs = TRUE,
))
statsiHS <- simulate(modeliHS)
print(statsiHS$ihh)