Package: EstimateBreed 1.0.0

Willyan Junior Adorian Bandeira

EstimateBreed: Estimation of Environmental Variables and Genetic Parameters

Performs analyzes and estimates of environmental covariates and genetic parameters related to selection strategies and development of superior genotypes. It has two main functionalities, the first being about prediction models of covariates and environmental processes, while the second deals with the estimation of genetic parameters and selection strategies. Designed for researchers and professionals in genetics and environmental sciences, the package combines statistical methods for modeling and data analysis. This includes the plastochron estimate proposed by Porta et al. (2024) <doi:10.1590/1807-1929/agriambi.v28n10e278299>, Stress indices for genotype selection referenced by Ghazvini et al. (2024) <doi:10.1007/s10343-024-00981-1>, the Environmental Stress Index described by Tazzo et al. (2024) <https://revistas.ufg.br/vet/article/view/77035>, industrial quality indices of wheat genotypes (Szareski et al., 2019), <doi:10.4238/gmr18223>, Ear Indexes estimation (Rigotti et al., 2024), <doi:10.13083/reveng.v32i1.17394>, Selection index for protein and grain yield (de Pelegrin et al., 2017), <doi:10.4236/ajps.2017.813224>, Estimation of the ISGR - Genetic Selection Index for Resilience for environmental resilience (Bandeira et al., 2024) <https://www.cropj.com/Carvalho_18_12_2024_825_830.pdf>, estimation of Leaf Area Index (Meira et al., 2015) <https://www.fag.edu.br/upload/revista/cultivando_o_saber/55d1ef202e494.pdf>, Restriction of control variability (Carvalho et al., 2023) <doi:10.4025/actasciagron.v45i1.56156>, Risk of Disease Occurrence in Soybeans described by Engers et al. (2024) <doi:10.1007/s40858-024-00649-1> and estimation of genetic parameters for selection based on balanced experiments (Yadav et al., 2024) <doi:10.1155/2024/9946332>.

Authors:Willyan Junior Adorian Bandeira [aut, cre], Ivan Ricardo Carvalho [aut, ctb], Murilo Vieira Loro [aut, ctb], Leonardo Cesar Pradebon [aut, ctb], Jose Antonio Gonzalez da Silva [aut, ctb]

EstimateBreed_1.0.0.tar.gz
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EstimateBreed.pdf |EstimateBreed.html
EstimateBreed/json (API)
NEWS

# Install 'EstimateBreed' in R:
install.packages('EstimateBreed', repos = c('https://willyanjnr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/willyanjnr/estimatebreed/issues

Datasets:
  • aveia - Dataset: Oat data
  • clima - Data: Climate Data Set for Predictions
  • coefend - Data: Data: Endogamy Coefficient Data Set
  • desvamb - Data: Data set for calculating the environmental deviation
  • genot - Data: GxE Interaction
  • genot2 - Data Set for obtaining genetic parameters.
  • leafarea - Data Set for Leaf Area Index
  • lin - Data: Wheat Data Set with Protein and Grain Yield
  • maize - Data: Maize Dataset
  • pheno - Soybean Plastochron Estimation Data Set
  • ptn - Data: Wheat Dataset 1
  • ptnrg - Data: Wheat Dataset 2
  • termaldata - Data Set with air temperature and incident radiation.
  • trigo - Data: Wheat Dataset 3
  • vig - Data Set for Seed Vigor Extraction

On CRAN:

Conda:

5.00 score 1 stars 26 exports 109 dependencies

Last updated 12 days agofrom:44417b7cef. Checks:9 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 23 2025
R-4.5-winOKMar 23 2025
R-4.5-macOKMar 23 2025
R-4.5-linuxOKMar 23 2025
R-4.4-winOKMar 23 2025
R-4.4-macOKMar 23 2025
R-4.4-linuxOKMar 23 2025
R-4.3-winOKMar 23 2025
R-4.3-macOKMar 23 2025

Exports:atsumCOIdefault_segdesv_climdidintgenparhethwindviabis_ptnergis_qindustrialisgritulailinearestoptempplastptermalrend_indrestrriskSGstindtameftdeltatransg

Dependencies:abindaskpassbackportsbase64encbitbit64bootbroomcarcarDataclicliprcolorspacecowplotcpp11crayoncrulcurlDerivdigestdoBydplyrextrafontextrafontdbfansifarverfastmapfontBitstreamVerafontLiberationfontquiverFormulagdtoolsgenericsggplot2ggrepelgluegridExtragtablehmshrbrthemeshtmltoolshttpcodehttrisobandjsonlitelabelinglatticelifecyclelme4lmtestlubridatemagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkmimeminqaminquemodelrmunsellnasapowernlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigprettyunitsprogresspurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRdpackreadrreformulasrlangRttf2pt1scalessommerSparseMstringistringrsurvivalsyssystemfontstibbletidyrtidyselecttimechangetriebeardtzdburltoolsutf8vctrsviridisviridisLitevroomwithrzoo

EnvironmentalAnalysis

Rendered fromEnvironmentalAnalysis.Rmdusingknitr::rmarkdownon Mar 23 2025.

Last update: 2025-03-14
Started: 2025-02-25

Selection Analysis

Rendered fromSelectionAnalysis.Rmdusingknitr::rmarkdownon Mar 23 2025.

Last update: 2025-03-20
Started: 2025-02-25

Readme and manuals

Help Manual

Help pageTopics
Accumulated Thermal Sumatsum
Dataset: Oat dataaveia
Data: Climate Data Set for Predictionsclima
Data: Data: Endogamy Coefficient Data Setcoefend
Inbreeding coefficientCOI
Standard Segregationdefault_seg
Auxiliary function for calculating ISGRdesv_clim
Data: Data set for calculating the environmental deviationdesvamb
Allelic and genotype-environment interactionsdidint
Data: GxE Interactiongenot
Data Set for obtaining genetic parameters.genot2
Genetic parameters for selectiongenpar
Heterosis and Heterobeltiosishet
Hectolitre weight of cerealshw
Ear Indexesindviab
Selection index for protein and grain yieldis_ptnerg
Industrial quality of wheatis_qindustrial
ISGR - Genetic Selection Index for Resilienceisgr
Environmental Stress Indexitu
Leaf Area Index (LAI)lai
Data Set for Leaf Area Indexleafarea
Data: Wheat Data Set with Protein and Grain Yieldlin
Estimates using polynomial equations.linearest
Data: Maize Datasetmaize
Plotting the optimum and cardinal temperatures for cropsoptemp
Soybean Plastochron Estimation Data Setpheno
Soybean plastochron estimationplast
Photothermal Indexptermal
Data: Wheat Dataset 1ptn
Data: Wheat Dataset 2ptnrg
Peeling Index and Industrial Yieldrend_ind
Restriction of control variabilityrestr
Risk of Disease Occurrence in Soybeansrisk
General Selection Gain FunctionSG
Stress indices for genotype selectionstind
Effective Population Sizetamef
Optimum conditions for pesticide applicationtdelta
Data Set with air temperature and incident radiation.termaldata
Selection Differential (Mean and Deviations)transg
Data: Wheat Dataset 3trigo
Data Set for Seed Vigor Extractionvig