TiagoOlivoto
commented
4 years ago Dear @adelinalarsen thank you for your report. metan was not accepting special characters in genotype or environment labels. This bug was already fixed in the development version of metan. Just install metan from github again.
devtools::install_github("TiagoOlivoto/metan")
For future issues, I'd suggest using the package reprex to report a reproducible example. Please, take a look in the example with your data.
library(metan)
#> Registered S3 method overwritten by 'GGally':
#> method from
#> +.gg ggplot2
#> []=====================================================[]
#> [] Multi-Environment Trial Analysis (metan) v1.4.0.9000[]
#> [] Author: Tiago Olivoto []
#> [] Type citation('metan') to know how to cite metan []
#> [] Type vignette('metan_start') for a short tutorial []
#> [] Visit http://bit.ly/2TIq6JE for a complete tutorial []
#> []=====================================================[]
library(readxl)
df <- read_excel("D:/Desktop/metan_docs/metan_errors/metan.xlsx")
model <-
waasb(df,
env = ENV,
gen = GEN,
rep = REP,
resp = GY)
#> Method: REML/BLUP
#> Random effects: GEN, GEN:ENV
#> Fixed effects: ENV, REP(ENV)
#> Denominador DF: Satterthwaite's method
#> ---------------------------------------------------------------------------
#> P-values for Likelihood Ratio Test of the analyzed traits
#> ---------------------------------------------------------------------------
#> model GY
#> COMPLETE NA
#> GEN 0.12115
#> GEN:ENV 0.00368
#> ---------------------------------------------------------------------------
#> All variables with significant (p < 0.05) genotype-vs-environment interaction
get_model_data(model, "vcomp")
#> Class of the model: waasb
#> Variable extracted: vcomp
#> # A tibble: 3 x 2
#> Group GY
#> <chr> <dbl>
#> 1 GEN 10185.
#> 2 GEN:ENV 39944.
#> 3 Residual 216753.
get_model_data(model, "ranef")$GEN
#> Class of the model: waasb
#> Variable extracted: ranef
#> GEN GY
#> 1 BICAR -48.3766075
#> 2 BIQUI 126.8142707
#> 3 BZAF 65.7360536
#> 4 CBW#10211 0.1770672
#> 5 CBW#10242 -37.0717310
#> 6 CBW#10416 -5.4692823
#> 7 CBW#10802 -101.8097707Created on 2020-04-08 by the reprex package (v0.3.0)
I'm planning a new stable release on CRAN within the next couple of days. Since this bug was already fixed in the development version I'm closing this issue now. Best regards
adelinalarsen
have you an issue?
Hello Tiago, I think your package "metan" is really good!!!. I am doing the short tutorial (https://tiagoolivoto.github.io/metan/) with my own data (csv file called "metan", I attach the file). Nevertheless, I have an issue in the BLUP model: model2 <- waasb(data_ge, env = ENV, gen = GEN, rep = REP, resp = everything()) R gives me this:
Convergence information
Number of iterations: 144 Final RMSE: 9.961795e-11 Number of axis: 1 Convergence: TRUE
Error in s$u[, 1:minimo] : subscript out of bounds In addition: Warning messages: 1: Expected 2 pieces. Additional pieces discarded in 48 rows [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, ...]. 2: Data imputation used to fill the GxE matrix
Could you help me?. Thank you in advance, Adelina.