biplots
Usage
# Default S3 method
biplots(
model,
burnin = 0.3,
thin = 0.2,
pb = 0.05,
plot_stable = TRUE,
plot_unstable = TRUE,
ncolors = 5
)Arguments
- model
Output from `bayes_ammi()`. This should contain the results of the Bayesian AMMI model, including all sampled iterations.
- burnin
Numeric. Percentage of iterations to discard as burn-in to avoid the effects of random initializations during sampling. For example, `burnin = 0.1` removes the first 10% of iterations.
- thin
Numeric. Proportion of sampled iterations to retain for analysis. For example, `thin = 0.2` keeps 20% of the iterations, selecting 1 out of every 5 iterations.
- pb
Numeric. Significance levels for the contours in the plot. Smaller values of `pb` result in wider contours, while higher values create smaller, more specific contours.
- plot_stable
Logical. If `TRUE`, stable instances are highlighted in the output plot.
- plot_unstable
Logical. If `TRUE`, unstable instances are highlighted in the output plot.
- ncolors
Integer. Specifies the number of distinct colors to use in the plot. Adjust this to control the visual differentiation of elements in the plot.
Value
A list with the following components:
- plot
A plot displaying the contours and final biplot values.
- contour_data
A `data.frame` containing the data used to create the contours.
- biplot_data
A `data.frame` containing the data used to recreate the final biplot values.
References
Crossa, J., Perez-Elizalde, S., Jarquin, D., Cotes, J.M., Viele, K., Liu, G., and Cornelius, P.L. (2011) Bayesian Estimation of the Additive Main Effects and Multiplicative Interaction Model Crop Science, 51, 1458–1469. (doi: 10.2135/cropsci2010.06.0343)
Author
Julian Garcia Abadillo Velasco (garciaabadillo.j@ufl.edu)
Diego Jarquin (diego.jarquin@gmail.com)
Examples
# \dontrun{
data(Maiz)
fm1 <-
bayes_ammi(
.data = Maiz,
.y = y,
.gen = entry,
.env = site,
.rep = rep,
.nIter = 200
)
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#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
#> Warning: number of rows of result is not a multiple of vector length (arg 2)
library(ggplot2)
output_05 <- biplots(model = fm1, plot_stable = TRUE, plot_unstable = TRUE, pb = 0.05)
output_05
#> $contorns
#> # A tibble: 9,605 × 9
#> level x y prob n_val byplot ID stable name
#> <dbl> <dbl> <dbl> <chr> <int> <chr> <int> <lgl> <int>
#> 1 0.269 -0.617 0.207 5% 1 Environment 1 TRUE 1
#> 2 0.269 -0.620 0.219 5% 2 Environment 1 TRUE 1
#> 3 0.269 -0.623 0.235 5% 3 Environment 1 TRUE 1
#> 4 0.269 -0.625 0.250 5% 4 Environment 1 TRUE 1
#> 5 0.269 -0.627 0.266 5% 5 Environment 1 TRUE 1
#> 6 0.269 -0.628 0.282 5% 6 Environment 1 TRUE 1
#> 7 0.269 -0.629 0.297 5% 7 Environment 1 TRUE 1
#> 8 0.269 -0.628 0.313 5% 8 Environment 1 TRUE 1
#> 9 0.269 -0.627 0.328 5% 9 Environment 1 TRUE 1
#> 10 0.269 -0.625 0.344 5% 10 Environment 1 TRUE 1
#> # ℹ 9,595 more rows
#>
#> $biplot_data
#> # A tibble: 29 × 6
#> # Groups: byplot [2]
#> byplot ID x y stable name
#> <chr> <int> <dbl> <dbl> <lgl> <int>
#> 1 Environment 1 0.0247 0.0543 TRUE 1
#> 2 Environment 2 0.0134 -0.0241 TRUE 2
#> 3 Environment 3 0.0959 -0.0871 TRUE 3
#> 4 Environment 4 -0.0779 -0.0310 TRUE 4
#> 5 Environment 5 -0.197 -0.0969 TRUE 5
#> 6 Environment 6 -0.0144 0.0157 TRUE 6
#> 7 Environment 7 -0.0578 0.0648 TRUE 7
#> 8 Environment 8 -0.0196 -0.0332 TRUE 8
#> 9 Environment 9 -0.0427 -0.0715 TRUE 9
#> 10 Environment 10 0.00518 -0.0940 TRUE 10
#> # ℹ 19 more rows
#>
#> $biplot
#>
output_95 <- biplots(model = fm1, plot_stable = TRUE, plot_unstable = TRUE, pb = 0.95)
output_95
#> $contorns
#> # A tibble: 1,391 × 9
#> level x y prob n_val byplot ID stable name
#> <dbl> <dbl> <dbl> <chr> <int> <chr> <int> <lgl> <int>
#> 1 1.59 -0.277 0.198 95% 1 Environment 1 FALSE 1
#> 2 1.59 -0.277 0.204 95% 2 Environment 1 FALSE 1
#> 3 1.59 -0.277 0.204 95% 3 Environment 1 FALSE 1
#> 4 1.59 -0.271 0.219 95% 4 Environment 1 FALSE 1
#> 5 1.59 -0.259 0.232 95% 5 Environment 1 FALSE 1
#> 6 1.59 -0.254 0.235 95% 6 Environment 1 FALSE 1
#> 7 1.59 -0.241 0.240 95% 7 Environment 1 FALSE 1
#> 8 1.59 -0.223 0.241 95% 8 Environment 1 FALSE 1
#> 9 1.59 -0.206 0.239 95% 9 Environment 1 FALSE 1
#> 10 1.59 -0.191 0.235 95% 10 Environment 1 FALSE 1
#> # ℹ 1,381 more rows
#>
#> $biplot_data
#> # A tibble: 29 × 6
#> # Groups: byplot [2]
#> byplot ID x y stable name
#> <chr> <int> <dbl> <dbl> <lgl> <int>
#> 1 Environment 1 -0.206 0.180 FALSE 1
#> 2 Environment 2 0.0351 0.303 FALSE 2
#> 3 Environment 3 0.383 -0.252 FALSE 3
#> 4 Environment 4 -0.232 0.261 FALSE 4
#> 5 Environment 5 -0.368 -0.253 FALSE 5
#> 6 Environment 6 -0.180 -0.343 FALSE 6
#> 7 Environment 7 -0.0961 0.151 FALSE 7
#> 8 Environment 8 -0.407 0.279 FALSE 8
#> 9 Environment 9 0.0253 0.0315 TRUE 9
#> 10 Environment 10 -0.0986 -0.336 FALSE 10
#> # ℹ 19 more rows
#>
#> $biplot
#>
# }