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thierrygosselin / grur

grur: an R package tailored for RADseq data imputations
https://thierrygosselin.github.io/grur/
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rf_pred not working #10

Open thierrygosselin opened 5 years ago

thierrygosselin commented 5 years ago

Bug to fix: rf_pred option

btmartin721 commented 4 years ago

Hello. I am having this same issue. I have tried imputation = "rf" and "rf_pred". I ran my dataset through filter_rad first, and am trying to load the *.rad file when calling grur_imputations.

Here is the command I used:

library("grur")

imp <- grur_imputations(
      data = "./filterRAD.rad",
      strata = "./popmap.txt,
      output = c("vcf", 
                        "structure",
                        "genepop", 
                        "genlight",
                        "genind"),
  imputation.method = "rf_pred",
  parallel.core = 1,
  hierarchical.levels = "strata",
  filename = "rf",
  verbose = FALSE,
  num.tree = 5000,
  pmm = 2
)

Here's the standard out: 

Imputation method: rf_pred
Hierarchical levels: strata

Seed: 342336

Number of populations: 10
Number of individuals: 251
Number of markers: 1
Error: object 'GT' not found

Has this bug been fixed? I have the most recent version of grur.