Package: FieldSimR 1.4.0

Christian Werner

FieldSimR: Simulation of Plot Errors and Phenotypes in Plant Breeding Field Trials

Simulates plot data in multi-environment field trials with one or more traits. Its core function generates plot errors that capture spatial trend, random error (noise), and extraneous variation, which are combined at a user-defined ratio. Phenotypes can be generated by combining the plot errors with simulated genetic values that capture genotype-by-environment (GxE) interaction using wrapper functions for the R package `AlphaSimR`.

Authors:Christian Werner [aut, cre], Daniel Tolhurst [aut], Jon Bancic [ctb]

FieldSimR_1.4.0.tar.gz
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FieldSimR.pdf |FieldSimR.html✨
FieldSimR/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/crwerner/fieldsimr/issues

Datasets:

On CRAN:

7.13 score 8 stars 62 scripts 309 downloads 21 exports 34 dependencies

Last updated 6 days agofrom:a19b87a3a7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:compsym_asr_inputcompsym_asr_outputfield_trial_errorgroup_cor_matmake_phenotypesmeasure_variancesmulti_asr_inputmulti_asr_outputplot_effectsplot_histplot_matrixqq_plotrand_cor_matrand_diag_matsample_metsample_variogramskew_diag_matstruc_cor_mattheoretical_variogramunstr_asr_inputunstr_asr_output

Dependencies:cliclustercolorspacedeldirfansifarverggplot2gluegtableinterpisobandlabelinglatticelifecyclemagrittrMASSMatrixmbendmgcvmunsellnlmepillarpkgconfigR6RColorBrewerRcppRcppEigenrlangscalestibbleutf8vctrsviridisLitewithr

Simulation of genetic values based on a compound symmetry model for genotype-by-environment (GxE) interaction

Rendered fromcompound_symmetry_GxE_demo.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-04-03
Started: 2023-03-31

Simulation of genetic values based on an unstructured model for genotype-by-environment (GxE) interaction

Rendered fromunstructured_GxE_demo.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-04-03
Started: 2023-03-31

Simulation of plot errors and phenotypes in a plant breeding field trial

Rendered fromspatial_variation_demo.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-03-16
Started: 2024-03-04

Readme and manuals

Help Manual

Help pageTopics
Simulate genetic values based on a compound symmetry model for GxE interaction - `AlphaSimR` input parameterscompsym_asr_input
Simulate genetic values based on a compound symmetry model for GxE interaction - Simulation with `AlphaSimR`compsym_asr_output
Plot errors - Example data frameerror_df_bivar
Simulate plot errors in plant breeding field trialsfield_trial_error
Simulate a reduced rank correlation matrix with multiple groupsgroup_cor_mat
Genetic values - Example data framegv_df_unstr
Generate phenotypes - Combine genetic values and plot errorsmake_phenotypes
Measure variances from a covariance matrixmeasure_variances
Simulate genetic values based on a multiplicative model for GxE interaction - `AlphaSimR` input parametersmulti_asr_input
Simulate genetic values based on a multiplicative model for GxE interaction - Simulation with `AlphaSimR`multi_asr_output
Graphics for plot effectsplot_effects
Histogram of valuesplot_hist
Graphics for matricesplot_matrix
Q-Q plotqq_plot
Simulate a random correlation matrixrand_cor_mat
Simulate a random diagonal variance matrixrand_diag_mat
Sample environments from a target populationsample_met
Sample variogramsample_variogram
Simulate a skewed diagonal variance matrixskew_diag_mat
Simulate a structured correlation matrix with reduced rankstruc_cor_mat
Theoretical variogramtheoretical_variogram
Simulate genetic values based on an unstructured model for GxE interaction - `AlphaSimR` input parametersunstr_asr_input
Simulate genetic values based on an unstructured model for GxE interaction - Simulation with `AlphaSimR`unstr_asr_output