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EstimateBreed

Lifecycle: experimental

EstimateBreed is an R package designed to perform analyses and estimate environmental covariates and genetic parameters related to selection strategies and the development of superior genotypes. The package offers two main functionalities:

Prediction models for environmental covariates and processes.
Estimation of genetic parameters and selection strategies for developing superior genotypes.

Installation

You can install the development version of EstimateBreed from GitHub with:

if (!requireNamespace("pak", quietly = TRUE)) {
  install.packages("pak")
}
pak::pak("willyanjnr/EstimateBreed")

Genotype selection

Obtain the genetic selection index for resilience (ISGR) for selecting genotypes for environmental stressors, as described by Bandeira et al. (2024).

library(EstimateBreed)

#Obtain environmental deviations
data("desvamb")
DPclim <- with(desvamb,desv_clim(ENV,TMED,PREC))
DPclim
# A tibble: 3 × 5
#  ENV   STMED TMEDR SPREC PRECIR
#  <chr> <dbl> <dbl> <dbl>  <dbl>
# 1 E1     2.65  24.8  5.46   339.
# 2 E2     3.65  23.8  5.27   344.
# 3 E3     2.81  24.5  5.47   362.

#Get the ISGR
data("genot")
isgr_index <- with(genot, isgr(GEN,ENV,NG,MG,CICLO))
isgr_index
#    Gen Env      ISGR
# 26 L454  E1  6.489941
# 22 L455  E1  7.084315
# 19 L541  E1  7.653157
# 18 L367  E1  7.862185
# 16 L380  E1  8.329434
# 12 L393  E1  9.638909
# 10 L439  E1 10.552056
# 28 L298  E3 12.209433
# 30 L358  E2 23.347984
# 29 L346  E2 23.793351
# 27 L195  E2 24.719927
# 25 L179  E2 25.747317
# 24 L359  E2 26.300686
# 23 L345  E2 26.886419
# 1  L445  E1 27.255375
# 21 L185  E2 28.211433
# 20 L310  E2 28.942165
# 17 L178  E2 31.418785
# 15 L261  E2 33.424611
# 14 L269  E2 34.605133
# 13 L209  E2 35.959423
# 11 L263  E2 39.127798
# 9  L201  E2 43.145922
# 8  L299  E2 45.686042
# 7  L152  E2 48.926278
# 6   L26  E2 52.988109
# 5  L166  E2 57.596139
# 4  L155  E2 64.251152
# 3  L277  E2 74.756384
# 2  L162  E2 86.543916

Selection of transgressive genotypes with the selection differential (mean and standard deviations).

library(EstimateBreed)

Gen <- paste0("G", 1:20)
Var <- round(rnorm(20, mean = 3.5, sd = 0.8), 2)
Control <- rep(3.8, 20)

data <- data.frame(Gen,Var,Control)

with(data,transg(Gen,Var,Control))

Returns the general parameters and the genotypes selected for each treshold. Also plot a representative graph of the selected genotypes based on the mean and standard deviations.

---------------------------------------------------------------------
Selection of Transgressive Genotypes - Selection Differential (SD)
---------------------------------------------------------------------
Parameters:
---------------------------------------------------------------------
Overall Mean         : 3.566
Control Mean         : 3.800
Standard Deviation   : 0.603
Mean + 1SD           : 4.169
Mean + 2SD           : 4.771
Mean + 3SD           : 5.374

---------------------------------------------------------------------
Genotypes above each threshold:
---------------------------------------------------------------------
Genotypes above Control Mean : G4, G7, G8, G9, G12, G14,
  G20 
Genotype above Overall Mean : G4, G7, G8, G9, G12, G14,
  G16, G18, G20 
Genotypes above Mean + 1SD : G7, G9, G20 
Genotypes above Mean + 2SD : G7 
Genotypes above Mean + 3SD     : None
---------------------------------------------------------------------

Estimation of environmental variables and processes

Predict ∆T to determine the ideal times to apply agricultural pesticides.

library(EstimateBreed)

# Forecasting application conditions
tdelta(-53.696944444444,-28.063888888889,type=1,days=10)

# Retrospective analysis of application conditions
tdelta(-53.6969,-28.0638,type=2,days=10,dates=c("2023-01-01","2023-05-01"))

Estimation of soybean plastochron using average air temperature and number of nodes

library(EstimateBreed)
data("pheno")

with(pheno, plast(GEN,TMED,EST,NN,habit="ind",plot=TRUE))

Documentation

Complete documentation can be found when using the package within R.

Citing

When citing this package, please use,

library(EstimateBreed)
citation("EstimateBreed")

To cite package ‘EstimateBreed’ in publications use:

  Willyan Jr. A. Bandeira, Ivan R. Carvalho, Murilo V. Loro, Leonardo
  C. Pradebon, José A. G. da Silva (2025). _EstimateBreed: Estimation
  of Environmental Variables and Genetic Parameters_. R package
  version 0.1.0, <https://github.com/willyanjnr/EstimateBreed>.

A BibTeX entry for LaTeX users is

  @Manual{,
    title = {EstimateBreed: Estimation of Environmental Variables and Genetic Parameters},
    author = {{Willyan Jr. A. Bandeira} and {Ivan R. Carvalho} and {Murilo V. Loro} and {Leonardo C. Pradebon} and {José A. G. da Silva}},
    year = {2025},
    note = {R package version 0.1.0},
    url = {https://github.com/willyanjnr/EstimateBreed},
  }

Getting Help

If you find any errors, please make a report with the commands used so that we can repeat, check and adjust the functions! Send it to github or send an email to bandeira.wjab@gmail.com.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.