InnoVaR

InnoVar is an R-package for simulating Multi Environmental Trials in a modular manner. The package allows for simulation of continous correlated and categorial associated variables considering different continuous and categorical marginal distributions.

Details are described in the package vignette

Installation

You can install the development version from GitHub with:

#install.packages("devtools")
#devtools::install_github("danilosarti/InnoVaR")

You can then load the package with:

library(InnoVaR)

MET simulations

You can simulate a MET obtaining a dataset like the one below. Details can be found in the vignette with the package flow in the Articles section.

head(final_soil_gen[c(1:3),c(1,5,100,102,103)])
#>     siteid trait_4 trait_99   genotype_id       DranaigeClass
#> 1 siteid_1       0        2 genotype_id_1 Imperfectly drained
#> 2 siteid_1       2        2 genotype_id_2 Imperfectly drained
#> 3 siteid_1       0        0 genotype_id_3 Imperfectly drained

Simulating phenomics

You can generate phenomic responses using different methods like Lasso, AMMI models and Gilberg (2019)

library(dplyr)
dat <- final_soil_gen %>%
  dplyr::mutate_if(is.character, as.factor)

library(InnoVaR)
target <- sim_target(
   X_gene = dat %>% dplyr::select(`trait_1`:`trait_100`),
   X_env = dat %>% dplyr::select(`DranaigeClass`:`yes_no_sample`),
   method = "lasso", pars = list(lambda = 0.5, sigma = 2,k=3),
   marginal_mean = 5.3, marginal_sd = 1.5
 )
head(target$target)
#> [1] 3.692807 4.573174 6.584955 4.172323 4.879207 6.431688