R alphasimr

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August undefined, 2024

Webb20 okt. 2024 · These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Webblibrary(AlphaSimR) # Step 1 ---- # Load in founder haplotypes. # This requires a genetic map and phased genotypes # Load the genetic map in the below format # Format: Marker name, Chromosome, Position (in Morgans) # Modeling 10 chromosomes with 10 loci each # Loci are equally space along 1 Morgan chromosomes

Simulate genetic values based on an unstructured model for GxE ...

Webb9 feb. 2024 · AlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR … Webb15 dec. 2024 · ../check/ 14-Dec-2024 02:22 - stats/ 14-Dec-2024 02:33 - A3_1.0.0.zip 14-Dec-2024 02:22 90392 AATtools_0.0.1.zip 14-Dec-2024 02:22 227904 ABACUS_1.0.0.zip 14-Dec-2024 02:22 134212 ABC.RAP_0.9.0.zip 14-Dec-2024 02:22 4808804 ABCanalysis_1.2.1.zip 14-Dec ... the largest frog in the world

SIMplyBee:

WebbmakeCross {AlphaSimR} R Documentation: Make designed crosses Description. Makes crosses within a population using a user supplied crossing plan. Usage makeCross(pop, crossPlan, nProgeny = 1, simParam = NULL) Arguments. pop: an … WebbBy default, 'AlphaSimR' does not support complex models for GxE interaction. However, its functionality to simulate correlated genetic values can be utilised for this purpose by providing the required variance structures. compsym_asr_input is a wrapper function to construct the variance structures required to simulate GxE interaction in 'AlphaSimR' … WebbSimParam {AlphaSimR} R Documentation: Simulation parameters Description. Container for global simulation parameters. Saving this object as SP will allow it to be accessed by function defaults. Public fields. nThreads. number of threads used on platforms with OpenMP support. snpChips. the largest game size

selIndex: Selection index in AlphaSimR: Breeding Program …

R: Simulation parameters

Webb9 feb. 2024 · Data were simulated using the AlphaSimR package (Gaynor et al., 2024) in R. The genome consisted of three chromosomes each 1 CM in length with 11,100 evenly … Webb11 aug. 2024 · 25 This paper introduces AlphaSimR, an R package for stochastic simulations of 26 plant and animal breeding programs. Stochastic simulation is a powerful tool for design 27 and optimization of breeding programs, because it provides a fast, inexpensive method 28 for testing alternative breeding program designs. the largest gold nugget ever foundWebbAlphaSimR/R/AlphaSimR.R Go to file Cannot retrieve contributors at this time 30 lines (29 sloc) 1.57 KB Raw Blame #' @useDynLib AlphaSimR, .registration = TRUE #' @import Rcpp #' @importFrom methods new validObject is .hasSlot #' @importFrom methods show classLabel #' @importFrom stats aggregate rnorm qnorm var the largest genus in phoridae is

"Webb31 mars 2024 · AlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine … " - R alphasimr

R alphasimr

Using R: Animal model with simulated data R-bloggers

WebbSets phenotypes for all traits by adding random error from a multivariate normal distribution. WebbTraits in AlphaSimR Chris Gaynor 2024-03-27 This vignette describes AlphaSimR’s biological model for traits. The biological model is responsible for

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WebbAlphaSimR users do not directly observe nor set the value of the environmental covariate. Instead, they indirectly set its value by providing a randomly sampled p-value for each environment. Users should note that p-values follow a uniform distribution over the range of zero to one, so it is recommended that users randomly generate p-values using R’s … WebbDetails on how ‘AlphaSimR’ simulates additive and non-additive biological effects can be found in the “Traits in AlphaSimR” vignette. It should be noted, however, that a simple additive genetic model will be sufficient to answer most experimental questions and may be preferred to more complex models, especially if data to tune the simulation model is …

WebbBy default, 'AlphaSimR' does not support complex models for GxE interaction. However, its functionality to simulate correlated genetic values can be utilised for this purpose by providing the required variance structures. unstr_asr_input is a wrapper function to construct the variance structures required to simulate GxE interaction in 'AlphaSimR' … Webb15 mars 2024 · AlphaSimR is a package for performing stochastic simulations of plant and animal breeding programs. It is the successor to the AlphaSim software for breeding …

WebbDetails on how ‘AlphaSimR’ simulates additive and non-additive biological effects can be found in the “Traits in AlphaSimR” vignette. It should be noted, however, that a simple additive genetic model will be sufficient to answer most experimental questions and may be preferred to more complex models, especially if data to tune the simulation model is … Webb31 mars 2024 · AlphaSimR-package: AlphaSimR: Breeding Program Simulations; attrition: Lose individuals at random; bv: Breeding value; calcGCA: Calculate GCA; cChr: Combine …

Webb12 apr. 2024 · AlphaSimR is a GitLab repositorium with R code addressing multiple simulation questions for designing breeding programs. This includes proper program …

WebbFieldSimR is an R package to enable simulation of plot data in field trials for multiple traits across multiple environments. ... provides wrapper functions to simulate genetic values for multiple traits across multiple environments using the R package AlphaSimR. Installation. FieldSimR is available on CRAN. To install use: install.packages ... thylacine discovered aliveWebb20 okt. 2024 · AlphaSimR: Breeding Program Simulations. The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) … thylacine dernier albumAlphaSimR: Breeding Program Simulations. The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) ]. Used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. the largest gemstone in the worldWebbMethods (by generic) [: Extract Pop by index or id c(Pop): Combine multiple Pops show(Pop): Show population summary Slots id. an individual's identifier. iid. an individual's internal identifier. mother. the identifier of the individual's mother thylacine diagnosticsWebbAlphaSimR is a highly flexible software package able to simulate a wide range of plant and animal breeding programs for diploid and autopolyploid species. AlphaSimR is ideal for testing the overall strategy and detailed design of breeding programs. thylacine dc comicsWebb31 mars 2024 · AlphaSimR: Breeding Program Simulations. The successor to the 'AlphaSim' software for breeding program simulation [Faux et al. (2016) … thylacine distance thylacine design and project management