diff --git a/vignettes/tutorial.Rmd b/vignettes/tutorial.Rmd index c26dee6f7f87c9b52eb63439e258f59c6c61f978..16c05f1beccc7203c0b5c6c9cfea62df33600def 100644 --- a/vignettes/tutorial.Rmd +++ b/vignettes/tutorial.Rmd @@ -115,7 +115,7 @@ By using the estimated intercept obtained from the previous analysis of publicly ```{r design_init, warning = FALSE, message = FALSE} ## -- init a design input_var_list <- init_variable(name = "environment", mu = -0.10047682, sd = sqrt(0.3198276), level = 4) %>% - init_variable(name = "genotype", mu = -0.01375802, sd = sqrt(0.6892266), level = N_GENOTYPES) %>% + init_variable(name = "genotype", mu = -0.01375802, sd = sqrt(0.6892266), level = 2) %>% add_interaction(between_var = c("environment", "genotype"), mu = 0.08256185, sd = sqrt(0.3123347)) %>% set_correlation(between_var = c("environment", "genotype"), corr = 0.7344005) %>% set_correlation(between_var = c("environment", "environment:genotype"), corr = -0.9213156) %>% @@ -231,10 +231,10 @@ resSimu$performances$byparams ``` -## Preparing and optimizing a futur experimental design +## Optimizing an analysis -Let's consider a scenario where a team is strategizing a new experiment encompassing 100 genotypes and 4 environments. To enhance the precision of their analysis, the team is conducting a power analysis through HTRfit. For this purpose, they are utilizing the experimental design template, `input_var_list`, which draws insights from the publicly available [SRP217588](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135473) dataset. They are adjusting the design levels to align with the specifics of their upcoming study involving 200 genotypes and 4 environments. +Let's consider a scenario where a team is strategizing a new experiment encompassing 100 genotypes and 4 environments. To enhance the precision of their analysis, the team is conducting a power analysis through HTRfit. For this purpose, they are utilizing the experimental design template, `input_var_list`, which draws insights from the publicly available [SRP217588](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE135473) dataset. They are adjusting the design levels to align with the specifics of their upcoming study involving 100 genotypes and 4 environments. #### Simulation @@ -243,7 +243,7 @@ Let's consider a scenario where a team is strategizing a new experiment encompas ```{r design_init_200, warning = FALSE, message = FALSE} ## -- init a design input_var_list <- init_variable(name = "environment", mu = -0.10047682, sd = sqrt(0.3198276), level = 4) %>% - init_variable(name = "genotype", mu = -0.01375802, sd = sqrt(0.6892266), level = N_GENOTYPES) %>% + init_variable(name = "genotype", mu = -0.01375802, sd = sqrt(0.6892266), level = 100) %>% add_interaction(between_var = c("environment", "genotype"), mu = 0.08256185, sd = sqrt(0.3123347)) %>% set_correlation(between_var = c("environment", "genotype"), corr = 0.7344005) %>% set_correlation(between_var = c("environment", "environment:genotype"), corr = -0.9213156) %>%